title: CLPs, WT (PAJ011719-010)

description: WTvHet_genes.tpm.csv, WTvTAD_genes.tpm.csv

value: WT


title: TSC_Day35_TSC010Het_35_B

status: Public on Nov 22 2024

type: SRA

city: Atlanta

first: Zhexing

last: Wen

address: 100 Woodruff Circle

department: Department of Psychiatry and Behavioral Sciences

country: USA

institute: Emory University

library_source: transcriptomic

data_processing:
raw fastq files were trimmed by fastp (v0.23.0)
trimmed fastq files were mapped to hg38 genome using STAR (2.7.10b)
raw read counts were extracted by subread (v2.0.6)
Assembly: hg38
Supplementary files format and content: csv text file includes raw read counts for reac sample

molecule: polyA RNA

organism: Homo sapiens

source_name: cortical organoids

extract_protocol:
RNA was isolated using the Direct-zol™ RNA Miniprep Kit (Zymo, R2052). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq is a standard protocol widely utilized in our laboratory at Emory. RNA-seq libraries were generated using the NEB Next Ultra II Directional with Poly A Selection Kit. A qPCR-based KAPA library quantification kit was applied to accurately quantify library concentration.

tag: cell type

value: cortical organoids


title: H3K4me3 ChIP-seq mESC 24h recovery after TSA washout rep1

city: Montpellier

first: Marco

last: Di Stefano

address: 141 rue de la Cardonille

country: France

institute: Institut de Génétique Humaine - CNRS

library_source: genomic

data_processing:
Data were mapped using bowtie2 against mm10 and hg19 and duplicates reads were discarded. Unique mouse and human reads were discarded and a donwsampling factor for spike-in normalisation was calulated as in Fursova et al. (2019) and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the Method section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a spike-in normalised mouse bigwig file of the two merged replicates. Peak files correspond to high-confidence peaks present in both replicates.

molecule: genomic DNA

organism: Mus musculus

source_name: cell line

growth_protocol: ESC were grown in FBS+LIF media with standard conditions.

extract_protocol:
Chromatin was fixed with 1% formaldehyde for 10 min at RT. To each 12 million mouse cells 1 million HEK cells were added for spike-in calibration. Nuclei were isolated with three different lysis buffers as in Lee et al., 2006 and sonicated in the lysis buffer 3 until the chromatin was disrupted to the size between 200 and 500bp.  For detailed protocol see adjoning paper.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer's instructions.

treatment_protocol: DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery

tag: tissue

value: cell line

tag: cell line

value: mESC wt

tag: genotype

value: Wild type

tag: treatment

value: 24h recovery from TSA treatment


title: H3K4me3 ChIP-seq of mESC TSA-treated rep2

value: 100 ng/ml TSA


title: TSC_Day35_TSC010Het_35_A


title: At.SD.WT-8h,Dark Repeat2

type: RNA

city: MISSISSIPPI STATE

first: Lei

last: Wang

state: MS

address: 414 LEE BLVD 3677

department: Department of Biological Sciences

institute: Mississippi State University

description: Replicate2: WT material was harvested at 8h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).

hyb_protocol: Synthesis of labeled cRNAs, hybridization with Affymetrix Arabidopsis ATH1 arrays (22,810 Arabidopsis probe sets, Affymetrix, Santa Clara, CA),

scan_protocol: scanning of the probe arrays were performed at the Iowa State University Gene Chip Facility (Ames, IA). Hybridization intensities were collected by an Agilent GeneArray Scanner (Agilent Technologies, Palo Alto, CA).

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments.
Algorithm: ExpressionStat 5.0

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: The antisense-ACLA mutant and WT plants were arranged according to a Randomized Complete Block Design. The plants were planted in rows with seven rows in each flat; two plants of the same genotype/pot. Plants were grown under a SD photoperiod (8 h light/16 h dark) in a growth chamber as described. Eight randomly selected rows were harvested for each time point from different flats. Plant material was harvested at 11 time points in the diurnal cycle (0, 0.5,1, 4, 6, 8,12 h in the dark condition, and 0, 0.5, 1, 4 h in the light condition; Time 0 is the beginning of the light period); harvesting was conducted under a green safety light. Each sample consisted of rosette leaves (leaves 5 to 8, staged following Bowmann (1994); photosynthetically active (Stessman et al., 2002)) from sixteen six-week-old plants.

extract_protocol: Leaf samples were frozen in liquid N2 immediately after harvest and stored at -80‚°C for RNA extraction through the standard Trizol protocol.

treatment_protocol: Leaf samples were frozen in liquid N2 immediately after harvest and stored at -80‚°C for RNA extraction. The experiment was done twice and independent randomizations for plant growth and harvest were used for the two replicates.

value: WT (Col-0)

value: rosette leaves


title: CLPs, Notch1+/dTAD (PAJ011719-009)

city: Chicago

first: Kostandin

middle: V

last: Pajcini

state: IL

address: 909 S Wolcott Ave.

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Adaptor trimming performed with FASTQ Toolkit Version: 2.2.0 on BaseSpace (Illumina)
Alignment to mm10 performed using RNA-Seq Alignment Version: 2.0.0 on BaseSpace (Illumina)
Differential expression analysis performed using RNA-Seq Differential Expression Version: 1.0.1 on BaseSpace (Illumina)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Common Lymphoid Progenitor (CLP)

extract_protocol:
4-11x10^6 adult BM CLP cells from WT, Notch1+/-, or Notch1+/ΔTAD were sorted into RNA lysis buffer (Invitrogen) and stored at -80ºC until RNA extraction. Total RNA was extracted using PicoPure™ RNA Isolation Kit (ThemoFisher Scientific, USA) with inclusion of DNase treatment step.
RNA sequencing libraries for Illumina sequencing were prepared in one batch using strand-specific QuantSeq 3’ RNAseq kit (Lexogen, FWD, Cat. No. 015) along with negative and positive controls.

tag: strain

value: Common Lymphoid Progenitor (CLP)

tag: cell source

value: bone marrow

tag: developmental stage

value: Adult

tag: age

value: 6-12 weeks old

tag: sorting markers


title: H3K4me3 ChIP-seq of mESC TSA-treated rep1


title: At.SD.WT-12h,Dark Repeat1

description: Replicate1: WT material was harvested at 12h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).

label_protocol: Synthesis of labeled cRNAs, hybridization with Affymetrix Arabidopsis ATH1 arrays (22,810 Arabidopsis probe sets, Affymetrix, Santa Clara, CA),


title: TSC_Day35_TSC010Homo_35_B


title: CLPs, Notch1+/dTAD (PAJ011719-007)


title: CTRL_Day56_C1_2_56_B


title: CLPs, Notch1+/- (PAJ011719-006)


title: CLPs, WT (PAJ011719-011)


title: CLPs, Notch1+/- (PAJ011719-005)


title: H3K4me3 ChIP-seq of mESC DMSO control rep2


title: H3K4me1 ChIP-seq mESC 24h recovery after TSA washout rep2


title: TSC_Day35_TSC010_35_B


title: TSC_Day35_TSC010Homo_35_A


title: CLPs, Notch1+/- (PAJ011719-004)


title: TSC_Day35_TSC010_35_A


title: At.SD.WT-8h,Dark Repeat1

description: Replicate1: WT material was harvested at 8h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-12h,Dark Repeat2

description: Replicate2: WT material was harvested at 12h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: H3K4me1 ChIP-seq mESC 24h recovery after TSA washout rep1


title: TSC_Day35_TSC009Homo_35_B


title: At.SD.WT-4h,Light Repeat2

description: Replicate2: WT material was harvested at 4h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-6h,Dark Repeat2

description: Replicate2: WT material was harvested at 6h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: CLPs, WT (PAJ011719-002)


title: At.SD.WT-4h,Dark Repeat2

description: Replicate2: WT material was harvested at 4h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: CLPs, WT (PAJ011719-001)


title: At.SD.WT-4h,Light Repeat1

description: Replicate1: WT material was harvested at 4h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: H3K4me3 ChIP-seq of mESC DMSO control rep1


title: H3K4me1 ChIP-seq of mESC TSA-treated rep1


title: At.SD.WT-6h,Dark Repeat1

description: Replicate1: WT material was harvested at 6h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: TSC_Day35_TSC009Homo_35_A


title: H3K4me1 ChIP-seq of mESC TSA-treated rep2


title: TSC_Day35_TSC009_35_B


title: PoolD_REP1_FDU_END

city: New York

first: Mariano

last: Oppikofer

address: 450 East 29th Street

data_processing:
sequence fastQC, align to library sequences, sgRNA-level and gene-level counts matrix were generated; the count files were feed to MAGeCK (MLE or RRA) to calculate gene-level selection scores.
Assembly: GRCh38
Supplementary files format and content: sgRNA count matrix, gene matrix, MAGeCK-RRA or MLE output (indicating gene selection)
Library strategy: CRISPR-screening

extract_protocol:
gDNA from cell pellets was isolated using QIAGEN Gentra Puregene kit.
Genome-integrated sgRNA sequences were amplified by PCR using KOD Hot Start Polymerases. i5 and i7 multiplexing barcodes (Ilumina) were added in a second round of PCR and final gel-purified products were sequenced.

tag: time point

value: Day 14


title: H3K4me1 ChIP-seq of mESC DMSO control rep1


title: PoolD_REP2_DMSO_END


title: TSC_Day35_TSC007_35_B


title: TSC_Day35_TSC009_35_A


title: H3K4me1 ChIP-seq of mESC DMSO control rep2


title: PoolD_REP2_FDU_END


title: At.SD.WT-4h,Dark Repeat1

description: Replicate1: WT material was harvested at 4h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-1h,Light Repeat1

description: Replicate1: WT material was harvested at 1h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: CLPs, WT (PAJ011719-003)


title: ATAC-seq mESC 24h recovery after TSA washout replicate 2

data_processing:
Data were mapped using bowtie2 against mm10 and hg19 and duplicates reads were discarded. Unique mouse and human reads were discarded and a donwsampling factor for spike-in normalisation was calulated as in Fursova et al. (2019) and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the Method section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a spike-in normalised mouse bigwig file of the two merged replicates. Peak files correspond to individual replicates.

extract_protocol:
90.000 live mESCs and 10.000 like HEK cells were used for each condition accotding to Active Motif ATAC-seq kit manual.
Libraries were prepared according to Active Motif ATAC-seq kit manual.


title: At.SD.WT-1h,Dark Repeat1

description: Replicate1: WT material was harvested at 1h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: TSC_Day35_TSC007_35_A


title: PoolD_REP1_DMSO_END


title: At.SD.WT-1h,Light Repeat2

description: Replicate2: WT material was harvested at 1h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: TSC_Day35_TSC001_35_B


title: PoolD_REP2_T0

value: Day 0


title: TSC_Day35_TSC001_35_A


title: PoolD_REP1_T0


title: At.SD.WT-0.5h,Light Repeat1

description: Replicate1: WT material was harvested at 0.5h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: PoolC_REP2_FDU_END


title: PoolC_REP1_FDU_END


title: ATAC-seq mESC TSA-treated replicate 1


title: ATAC-seq mESC TSA-treated replicate 2


title: ATAC-seq mESC DMSO control replicate 1


title: CTRL_Day35_11C1_35_B


title: CTRL_Day35_PGP1_35_A


title: PoolC_REP2_DMSO_END


title: Micro-C of TSA-treated mouse ESCs following 24 hours of recovery (H-REC)

data_processing:
Hi-C data was processed using the HiC-Pro v3.1.0 pipeline (https://github.com/nservant/HiC-Pro). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode and non-informative reads were removed using the default options. See adjoning paper for the detailed pipeline.
Assembly: mm10
Supplementary files format and content: Each processed .mcool file represent pairwise information of the observed genome contacts (produced by the cooler package https://cooler.readthedocs.io/en/latest/index.html). Loop files represent coodrinates of focal contacts idenitied by mustache v1.0 (https://github.com/ay-lab/mustache) with default parameters on ICE-balanced .mcool maps at 1 kb and 4 kb resolutions. Redundant loops between different resolutions were filtered in 20 kb windows, and in case of overlap loop coordinates were retained at the finer resolution.
Library strategy: Micro-C

extract_protocol:
Cell lysis, MNase digestion, ligation, biotin labeling  and pulldown were preformed according to Dovetail Micro-C kit User Guide version 1.0.
Libraries were prepared as in the Dovetail Micro-C kit User Guide version 1.0, except that Dovetail reagents were replaced by reagents from the NEBNext Ultra II DNA Library Prep Kit for Illumina kit. For detailed protocol see adjoning paper.


title: ATAC-seq mESC 24h recovery after TSA washout replicate 1


title: CTRL_Day35_11C1_35_A


title: Micro-C of TSA-treated mouse ESCs following 24 hours of recovery (G-REC)


title: CTRL_Day35_C1_2_35_B


title: PoolC_REP1_DMSO_END


title: At.SD.WT-0h,Light Repeat2

description: Replicate2: WT material was harvested at 0h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-0.5h,Dark Repeat2

description: Replicate2: WT material was harvested at 0.5h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-0.5h,Dark Repeat1

description: Replicate1: WT material was harvested at 0.5h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-0.5h,Light Repeat2

description: Replicate2: WT material was harvested at 0.5h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: PoolC_REP2_T0


title: ATAC-seq mESC DMSO control replicate 2


title: Micro-C of TSA-treated mouse ESCs (I-TSA)


title: PoolC_REP1_T0


title: CTRL_Day35_C1_2_35_A


title: At.SD.WT-0h,Light Repeat1

description: Replicate1: WT material was harvested at 0h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: CTRL_Day35_PGP1_35_B


title: At.SD.WT-0h,Dark Repeat1

description: Replicate1: WT material was harvested at 0h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-1h,Dark Repeat2

description: Replicate2: WT material was harvested at 1h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.WT-0h,Dark Repeat2

description: Replicate2: WT material was harvested at 0h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: At.SD.ACLA1-4h,Dark Repeat2

description: Replicate2: antisense-ACLA material was harvested at 4h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).

value: antisense-ACLA mutant


title: Smh mutant, clutch 4

city: Trondheim

first: Nathalie

last: Jurisch-Yaksi

address: Erling Skjalgsons gate 1

country: Norway

institute: NTNU

data_processing:
The filtering of sequencing data was done using SOAPnuke, v1.5.2, using the parameters Parameters -l 15 -q 0.2 -n 0.05
The Hierarchical Indexing for Spliced Alignment of Transcripts software (HISAT2 v2.0.4 with parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF) was used for mapping RNA-seq reads
We used Bowtie2 (Version：v2.2.5, Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) to map the clean reads to the reference gene sequence (transcriptome), and then RSEM (Version：v1.2.8, Parameters：-p 8 --forward-prob 0 --paired-end) to calculate the gene expression level of each sample
The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized, and log transformed using the voom algorithm from the limma package of Bioconductor
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized_read_counts_smh.xlsx
Supplementary files format and content: excel file containing differential expression: smhMUT_vs_smhCTRL_mRNA_diff_expr_CPM1.xlsx

organism: Danio rerio

source_name: whole larvae

extract_protocol:
To isolate RNA for sequencing, 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples, 500μL trizol was added and the euthanized larvae were homogenized through a 27-gauge needle until the mixture looked uniform. After adding another 500μL trizol, the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform, and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. After centrifugation, the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column (Qiagen) and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme (Qiagen) in RDD buffer (10μL Dnase+ 70μL RDD buffer per tube) for 45 minutes at room temperature. After incubation, 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice, and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column, 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke, v1.5.2, using the parameters Parameters -l 15 -q 0.2 -n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software (HISAT2 v2.0.4 with parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF) was used for mapping RNA-seq reads. We used Bowtie2 (Version：v2.2.5, Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) to map the clean reads to the reference gene sequence (transcriptome), and then RSEM (Version：v1.2.8, Parameters：-p 8 --forward-prob 0 --paired-end) to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized, and log transformed using the voom algorithm from the limma package of Bioconductor (Law et al., 2014; Ritchie et al., 2015).
standard procedure performed by BGI

value: whole larvae

value: no treatment


title: PMBC16

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description:
mRNA
Expr_raw_count.txt

data_processing:
Aligned to genome using cell ranger 3.1.0.
Quality control using Seurat 3. Genes expressed in less than 3 cells were removed. Cells expressing less than 200 genes or more than 2500 genes were removed.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Expr_raw_count.txt: Tab-delimited text file format showing the raw count matrix with rows as genes and columns as cells.
Supplementary_files_format_and_content: cluster.lst.ann.txt: Tab-delimited text file format

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
PBMCs were isolated from EDTA anticoagulated venous blood of patients, using a Ficoll Paque Plus (Sigma Aldrich) solution according to standard density gradient centrifugation methods. Cells were harvested and counted via Automated cell counter (Invitrogen). The PBMCs were resuspended in 90% fetal bovine serum (FBS, HyClone), 10% DMSO freezing media and frozen using a Mr. Frosty Cryo Freezing Container (Thermo Fisher Scientific) in a 80C freezer for 24 h before being transferred to liquid nitrogen for long-term storage.
Frozen vials of PBMCs were rapidly thawed in a 37C water bath for 2 min, and the vials were removed when a tiny ice crystal was left. Thawed PBMCs were quenched with 4 mL 37C pre-warmed 1X phosphate-buffered saline (PBS, Thermo Fisher Scientific) and supplemented with 10% FBS. Cells were centrifuged at 500 x g for 10 min at room temperature each time. The supernatant was removed, and the cell pellet was resuspended in 3 mL 1X PBS containing 0.04% bovine serum albumin (BSA, Sangon Biotech), passed through a 40mm cell strainer (Falcon), and then centrifuged. Cells were resuspended with cell resuspension buffer at a viable cell concentration of 1,000 cells/ml. Single cells from PBMC were captured using the Chromium Single Cell 3’ Library & Gel Bead Kit, v3 (10x Genomics, Pleasanton, CA) and processed following exactly the supplier provided protocol. The resulting mRNA libraries were sequenced on NovaSeq 6000 (Illumina, San Diego, CA) platform with typical setup as a 26 cycles + 57 cycles non-symmetric run. Demultiplexing was done allowing 1 mismatch per barcode. Sequencing data were analyzed with the Cellranger v2.2.0 software (10x Genomics) applying default parameters.

tag: disease status

value: Dialysis

tag: transplant rejection risk score

value: High

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: PBMC22

description:
mRNA
Expr_raw_count.txt

value: Low


title: Micro-C of TSA-treated mouse ESCs (G-TSA)

value: cell line

value: mESC wt

value: Wild type


title: Micro-C of TSA-treated mouse ESCs (F-TSA)

value: 100 ng/ml TSA


title: PoolB_REP2_FDU_END

value: Day 15


title: Micro-C of TSA-treated mouse ESCs (E-TSA)


title: Micro-C of TSA-treated mouse ESCs (H-TSA)


title: PoolB_REP2_DMSO_END


title: PoolB_REP1_DMSO_END


title: Smh mutant, clutch 2


title: PoolB_REP2_T0


title: Micro-C of control mouse ESCs (I-DMSO)


title: Micro-C of control mouse ESCs (H-DMSO)


title: PoolB_REP1_T0


title: Smh mutant, clutch 1


title: At.SD.ACLA1-4h,Dark Repeat1

description: Replicate1: antisense-ACLA material was harvested at 4h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).

value: rosette leaves


title: Smh control, clutch 4

value: mixture wt and +/-


title: At.SD.ACLA1-1h,Light Repeat1

description: Replicate1: antisense-ACLA material was harvested at 1h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: Solanum lycopersicum, Experiment, Replicate 2

city: Shanghai

first: Yingji

last: Chen

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

country: China

institute: Fudan University

data_processing:
Raw RNA-seq reads were first assessed for quality using Trimmomatic version 0.32 (Bolger et al., 2014). Parameters for trimming and filtering were applied according to the software's standard settings to remove low-quality reads and adapter sequences.
The clean reads were aligned to the Arabidopsis thaliana TAlR10 genome using Hisat2 version 2.1.0 (Kim et al., 2019). Default parameters were used for alignment to ensure high accuracy in mapping the reads to the reference genome.
The number of fragments per kilobase of transcript per million mapped reads (FPKM) was calculated using StringTie version 1.3.3 (Pertea et al., 2015) to estimate transcript abundance.
Differentially expressed genes (DEGs) were identified using DESeq2 version 1.18.1. Criteria for significance included a fold change greater than 2 and an adjusted P-value of less than 0.05.
Assembly: S_lycopersicum_chromosomes.2.50.fa
Supplementary files format and content: txt file includes raw counts for each Sample

organism: Solanum lycopersicum

source_name: whole Individual plant

extract_protocol:
Total RNA was isolated from cell lysates using TRIzol reagent (Invitrogen). The concentration and purity of RNA were measured with a Nano-Drop ND-1000 spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA) and the Agilent 2100 Bioanalyzer system (Agilent BioTek; Winooski, VT, USA).
RNA with high quality was sent for library construction. The RNA-Seq library was further sequenced with Illumina Novaseq 6000 platform (Illumina) to generate 150 base pair (bp) reads. Quality control and raw sequencing data filtration were achieved with the Fastp v0.23.2 and sortmerna v4.3.4 software. The STAR v2.7.10 software was then applied to align clean reads to the human genome GRCh38.

value: whole Individual plant

tag: group

value: Experiment


title: Solanum lycopersicum, Experiment, Replicate 1


title: At.SD.ACLA1-1h,Light Repeat2

description: Replicate2: antisense-ACLA material was harvested at 1h in the light in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: Solanum lycopersicum, Experiment, Replicate 3


title: COL1A1_mini_L2, replicate 2, scRNAseq

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

description:
Parse Biosciences
COL1A1_mini_L2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the split-pipe software (1.0.3p) (ParseBiosciences-Pipeline.1.0.3p, https://support.parsebiosciences.com/hc/en-us)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Organoid

growth_protocol: HB cells were forming HO in Growth and Differentiation Medium (GDM)

extract_protocol:
Control, PDGFB- or TGFb1-induced microHOs (n>30 per group) from 4 batches were harvested on day 21, and single cell suspensions were prepared by protease digestion
The single cell suspensions were visually inspected under a microscope, cells were counted using a Scepter™ 2.0 Handheld Automated Cell Counter (EMD Millipore, Burlington, MA), and then resuspended in PBS with 0.01% BSA. scRNA-seq libraries were prepared by using the spit-pool based scRNA-seq method (Evercode™ WT Mini v2 from Parse biosciences) according to the manufacturer’s instructions. In brief, 1668 cells from each sample were loaded in one wells for the first round of sample barcoding, and the final pooled cells were divided into two equal libraries for sequencing.

treatment_protocol: HB cells on day 9 were used directly for scRNA preparation. 50 ng/ml of TGFB1 or 50 ng/ml of PDGFB was added to each group on day 13.

value: Organoid

value: HO on day 21


title: PoolB_REP1_FDU_END


title: At.SD.ACLA1-0.5h,Dark Repeat2

description: Replicate2: antisense-ACLA material was harvested at 0.5h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).

value: antisense-ACLA mutant


title: Micro-C of control mouse ESCs (G-DMSO)


title: Smh control, clutch 3

value: whole larvae

value: no treatment


title: At.SD.ACLA1-0.5h,Dark Repeat1

description: Replicate1: antisense-ACLA material was harvested at 0.5h in the dark in the diurnal cycle under a SD photoperiod (8 h light/16 h dark).


title: Micro-C of control mouse ESCs (MS-DMSO)


title: Solanum lycopersicum, Control, Replicate 3

value: hrcV

value: Control


title: Smh mutant, clutch 3


title: COL1A1_mini_L1, replicate 1, scRNAseq

description:
Parse Biosciences
COL1A1_mini_L1


title: Solanum lycopersicum, Control, Replicate 2


title: Smh control, clutch 1


title: Micro-C of control mouse ESCs (E-DMSO)


title: Solanum lycopersicum, Control, Replicate 1


title: L1, replicate 1, scRNAseq

description: Parse Biosciences

extract_protocol:
Control, PDGFB- or TGFb1-induced microHOs (n>30 per group) were harvested on day 21, and single cell suspensions were prepared by protease digestion
The single cell suspensions were visually inspected under a microscope, cells were counted using a Scepter™ 2.0 Handheld Automated Cell Counter (EMD Millipore, Burlington, MA), and then resuspended in PBS with 0.01% BSA. scRNA-seq libraries were prepared by using the spit-pool based scRNA-seq method (Evercode™ WT Mini v2 from Parse biosciences) according to the manufacturer’s instructions. In brief, 5000 cells from each group were split into 3 wells for the first round of sample barcoding, and the final pooled cells were divided into two equal libraries for sequencing.

value: Control HBs and Control, PDGFB, TGFb1 HOs

tag: time

value: HB on day 9, HO on day 21


title: Leaves, 12d post transition, ZT4, rep 2

status: Public on Nov 21 2024

city: York

first: Ethan

middle: James

last: Redmond

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: University of York

data_processing:
Before analysis of the raw sequencing data, FastQC v0.11.7(Andrews et al. 2012) was used to assess read quality.
Illumina adapters were trimmed using CutAdapt v3.4 (Martin 2011). (parameters: -a AGATCGGAAGAG -A AGATCGGAAGAG -j 0 -q 10,10 -m 30 -u 10 -U 10)
Reads were quantified using Salmon v1.6.0 (Patro et al. 2017) and the TAIR10 transcriptome (Berardini et al. 2015). (parameters: -l A  --validateMappings)
Assembly: TAIR10
Supplementary files format and content: Salmon quantification folder for each sample, included as a .tar file

source_name: 3rd and 4th rosette leaves

growth_protocol: The Arabidopsis thaliana ecotype Wassilewskija Ws-2 seeds were surface sterilized and then grown in MS-agar, 1% sucrose plates. The plates were cold stratified at 4C in the dark for 3 days. These plates were then transferred to short-day conditions (8h light; 16h dark) at 21C and left for 10 days. The seedlings were then transferred to soil and thinned to one seedling per pot 3 days later. 3rd and 4th true rosette leaves were tracked for each individual plant. 12 days after transferring to soil, the conditions were changed to long-day conditions (16h light; 8h dark) at 21C. The samples were collected over three separate days after the transition to long-day conditions. Specifically, these days were: day 2 (starting 24 hours after the start of the first long day), day 7 (starting 144 hours after the start of the first long day), and day 12 (starting 264 hours after the start of the first long day). On each day, samples were collected at the following timepoints, in terms of ZT (hours after dawn): 0, 1, 4, 8, 12, 16, 20.  5 biological replicates for each time point were taken - with each replicate consisting of the 3rd and 4th leaves of two separate plants. These were flash frozen in liquid nitrogen and then stored at -80C. For collections during dark conditions (i.e., ZT16 and ZT20), this work was carried out under green-filtered light.

extract_protocol:
Total RNA was isolated from these samples using the Qiagen RNeasy Plant Mini Kit (Cat no. 74904). Residual genomic DNA was removed using the Invitrogen Turbo DNA-free kit (Cat no. AM1907), according to the manufacturer’s protocol.
Libraries were prepared with the NEBNext Ultra II Directional Library Prep Kit for Illumina (Cat no. E7765), using the NEBNext poly(A) magnetic isolation module (Cat no. E7490). Quality control was performed with the Agilent 2100 Bioanalyzer instrument (Part no. G2939BA). Finally, a total of 70 libraries were pooled and sequenced, via Novagene, using one lane on an Illumina NovaSeq system.

value: 3rd and 4th rosette leaves

value: 12d post transition, ZT4, rep 2


title: Leaves, 12d post transition, ZT8, rep 1

value: 12d post transition, ZT8, rep 1


title: Leaves, 12d post transition, ZT8, rep 3

value: 12d post transition, ZT8, rep 3


title: Leaves, 12d post transition, ZT8, rep 2

value: 12d post transition, ZT8, rep 2


title: Leaves, 12d post transition, ZT4, rep 3

value: 12d post transition, ZT4, rep 3


title: Leaves, 12d post transition, ZT20, rep 3

value: 12d post transition, ZT20, rep 3


title: Leaves, 12d post transition, ZT4, rep 1

value: 12d post transition, ZT4, rep 1


title: Leaves, 12d post transition, ZT20, rep 2

value: 12d post transition, ZT20, rep 2


title: Leaves, 12d post transition, ZT16, rep 3

value: 12d post transition, ZT16, rep 3


title: Leaves, 12d post transition, ZT1, rep 1

value: 12d post transition, ZT1, rep 1


title: Leaves, 12d post transition, ZT20, rep 1

value: 12d post transition, ZT20, rep 1


title: Micro-C of control mouse ESCs (F-DMSO)

value: cell line

value: mESC wt

value: Wild type


title: Leaves, 12d post transition, ZT16, rep 1

value: 12d post transition, ZT16, rep 1


title: Leaves, 12d post transition, ZT16, rep 2

value: 12d post transition, ZT16, rep 2


title: Leaves, 12d post transition, ZT12, rep 3

value: 3rd and 4th rosette leaves

value: 12d post transition, ZT12, rep 3


title: L2, replicate 2, scRNAseq

description: Parse Biosciences

value: Organoid

value: Control HBs and Control, PDGFB, TGFb1 HOs

value: HB on day 9, HO on day 21


title: Leaves, 12d post transition, ZT12, rep 2

value: 12d post transition, ZT12, rep 2


title: Smh control, clutch 2

value: whole larvae

value: mixture wt and +/-

value: no treatment


title: Leaves, 12d post transition, ZT12, rep 1

value: 12d post transition, ZT12, rep 1


title: Leaves, 7d post transition, ZT8, rep 3

value: 7d post transition, ZT8, rep 3


title: Leaves, 12d post transition, ZT0, rep 3

value: 12d post transition, ZT0, rep 3


title: Leaves, 12d post transition, ZT0, rep 2

value: 12d post transition, ZT0, rep 2


title: Leaves, 12d post transition, ZT0, rep 1

value: 12d post transition, ZT0, rep 1


title: Leaves, 7d post transition, ZT8, rep 2

value: 7d post transition, ZT8, rep 2


title: Leaves, 7d post transition, ZT8, rep 1

value: 7d post transition, ZT8, rep 1


title: Leaves, 7d post transition, ZT4, rep 2

value: 7d post transition, ZT4, rep 2


title: Leaves, 7d post transition, ZT4, rep 3

value: 3rd and 4th rosette leaves

value: 7d post transition, ZT4, rep 3


title: Leaves, 7d post transition, ZT4, rep 1

value: 7d post transition, ZT4, rep 1


title: Leaves, 12d post transition, ZT1, rep 2

value: 12d post transition, ZT1, rep 2


title: Leaves, 12d post transition, ZT1, rep 3

value: 12d post transition, ZT1, rep 3


title: Leaves, 7d post transition, ZT16, rep 2

value: 7d post transition, ZT16, rep 2


title: Leaves, 7d post transition, ZT20, rep 3

value: 7d post transition, ZT20, rep 3


title: Leaves, 7d post transition, ZT20, rep 2

value: 7d post transition, ZT20, rep 2


title: Leaves, 7d post transition, ZT20, rep 1

value: 7d post transition, ZT20, rep 1


title: Leaves, 7d post transition, ZT16, rep 3

value: 7d post transition, ZT16, rep 3


title: Leaves, 7d post transition, ZT12, rep 2

value: 7d post transition, ZT12, rep 2


title: Leaves, 7d post transition, ZT16, rep 1

value: 7d post transition, ZT16, rep 1


title: Leaves, 7d post transition, ZT12, rep 3

value: 7d post transition, ZT12, rep 3


title: Leaves, 7d post transition, ZT0, rep 3

value: 7d post transition, ZT0, rep 3


title: Leaves, 7d post transition, ZT0, rep 2

value: 7d post transition, ZT0, rep 2


title: Leaves, 7d post transition, ZT12, rep 1

value: 7d post transition, ZT12, rep 1


title: Leaves, 7d post transition, ZT0, rep 1

value: 7d post transition, ZT0, rep 1


title: Leaves, 7d post transition, ZT1, rep 2

value: 3rd and 4th rosette leaves

value: 7d post transition, ZT1, rep 2


title: Leaves, 2d post transition, ZT8, rep 3

value: 2d post transition, ZT8, rep 3


title: Leaves, 2d post transition, ZT4, rep 3

value: 2d post transition, ZT4, rep 3


title: Leaves, 2d post transition, ZT8, rep 1

value: 2d post transition, ZT8, rep 1


title: Leaves, 2d post transition, ZT4, rep 2

value: 2d post transition, ZT4, rep 2


title: Leaves, 2d post transition, ZT20, rep 1

value: 2d post transition, ZT20, rep 1


title: Leaves, 2d post transition, ZT8, rep 2

value: 2d post transition, ZT8, rep 2


title: Leaves, 2d post transition, ZT20, rep 2

value: 2d post transition, ZT20, rep 2


title: Leaves, 2d post transition, ZT4, rep 1

value: 2d post transition, ZT4, rep 1


title: Leaves, 2d post transition, ZT1, rep 3

value: 2d post transition, ZT1, rep 3


title: Leaves, 2d post transition, ZT20, rep 3

value: 2d post transition, ZT20, rep 3


title: Leaves, 7d post transition, ZT1, rep 1

value: 7d post transition, ZT1, rep 1


title: Leaves, 2d post transition, ZT1, rep 1

value: 2d post transition, ZT1, rep 1


title: Leaves, 7d post transition, ZT1, rep 3

value: 7d post transition, ZT1, rep 3


title: Leaves, 2d post transition, ZT16, rep 3

value: 2d post transition, ZT16, rep 3


title: Leaves, 2d post transition, ZT16, rep 2

value: 2d post transition, ZT16, rep 2


title: Leaves, 2d post transition, ZT12, rep 3

value: 3rd and 4th rosette leaves

value: 2d post transition, ZT12, rep 3


title: Leaves, 2d post transition, ZT16, rep 1

value: 2d post transition, ZT16, rep 1


title: Leaves, 2d post transition, ZT12, rep 1

value: 2d post transition, ZT12, rep 1


title: Leaves, 2d post transition, ZT12, rep 2

value: 2d post transition, ZT12, rep 2


title: Leaves, 2d post transition, ZT0, rep 3

value: 2d post transition, ZT0, rep 3


title: Leaves, 2d post transition, ZT0, rep 1

value: 2d post transition, ZT0, rep 1


title: Pa01c-scram rep3

city: ST LOUIS

first: SAPANA

middle: PRAKASHRAO

last: BANSOD

state: MO

address: 4482 LINDELL BLVD, 608

department: INTERNAL MEDICINE

institute: WASHINGTON UNIVERSITY, ST LOUIS

description: Pa01c cells expressing empty vector replicate 3

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: Pancreatic cancer

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: expressing empty vector

tag: passages

value: <20 from being generated


title: Pa01c-shTRIM21#2 rep2

description: Pa01c cells espressing shTRIM21#2  replicate 2

value: expressing shTRIM21#2


title: Pa01c-shTRIM21#2 rep1

description: Pa01c cells espressing shTRIM21#2 replicate 1


title: Pa01c-scram rep2

description: Pa01c cells expressing empty vector replicate 2


title: MCF10A cells, Ctrl,#1

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

institute: Institut Curie

data_processing:
Raw counts were generated using Star gene quantification mode (--quantMode GeneCounts) on the Gencode v19 gene database.
Raw counts were normalized using  the TMM method using EdgeR (v3.38.2) and Limma's voom function (v3.52.2).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample
Supplementary files format and content: Tab-delimited text file containing TPM for each sample

growth_protocol: MCF10A cells were grown in DMEM-HG/F-12 supplemented with 5% horse serum, 20 ng/ml human epidermal growth factor, 0.5 mg/ml hydrocortisone, 100 ng/ ml cholera toxin, 10 µg/ ml insulin, and 1% penicillin–streptomycin

extract_protocol:
2x106 cells were harvested and RNA isolated using the NucleoSpin Triprep kit
Stranded mRNA prep Ligation-Illumina

treatment_protocol: del5 and delT MCF10A cells were obtained using CRISPR/Cas9- or TALEN gene editing , clones  from these and MCF10A parental controls were selected, confirmed by Sanger sequencing and expanded  prior to RNA extraction

value: non-malignant breast epithelial cell line

value: WT


title: Pa01c-shTRIM21#2 rep3

description: Pa01c cells espressing shTRIM21#2 replicate 3


title: Mitotic phase – MLN8237 - Replicate 1

city: Barcelona

first: Estefania

last: Mancini

state: Barcelona

address: C/ Dr. Aiguader, 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Centre for Genomic Regulation

data_processing:
Genome_build: Hg38
Gene count table was produced using STAR aligner with the option --quantMode GeneCounts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Alternative splicing analysis was carried out using vast-tools v2.2.0 pipeline
Supplementary_files_format_and_content: Matrix table with raw PSI value for every AS event  and every sample

source_name: Mitotic phase – MLN8237

growth_protocol: The HeLa cells were grown in Dulbecco's modified Eagle's medium (DMEM)- GlutaMAX ™ -I (Sigma-Aldrich) supplemented with 10% fetal bovine serum (GE Healthcare) and 1% penicillin-streptomycin (GE Healthcare).

extract_protocol:
Total RNA was isolated from two replicates of the synchronized HeLa cells using the RNeasy Plus Mini Kit (QIAGEN) as per the manufacturer’s protocol. While isolating total RNA for RNA-seq analysis, on-column digestion of DNA was additionally performed using RNase-Free DNase Set (QIAGEN) as a precautionary measure and later subjected to the mRNA-seq library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HeLa cells synchronisations were achieved by double thymidine arrest-release and were coupled to treatment with the Aurora-A inhibitor MLN8237 for 24 hours, i.e. a complete cell cycle. Synchronization of cells in mitosis was reached by further treating cells with nocodazole.

value: HeLa

tag: cell cycle phase

value: synchronized at Mitosis phase


title: Pa01c-scram rep1

description: Pa01c cells expressing empty vector replicate 1


title: Mitotic phase - DMSO - Replicate 1

source_name: Mitotic phase - DMSO

value: DMSO


title: G2 phase – MLN8237- Replicate 1

source_name: G2 phase – MLN8237

value: synchronized at G2 phase


title: Mitotic phase - DMSO - Replicate 2


title: G2 phase - DMSO - Replicate 2

source_name: G2 phase - DMSO


title: Mitotic phase – MLN8237 - Replicate 2


title: G1 phase -MLN8237 - Replicate 2

source_name: G1 phase -MLN8237

value: synchronized at G1 phase


title: G1 phase - DMSO - Replicate 2

source_name: G1 phase - DMSO


title: Leaves, 2d post transition, ZT1, rep 2

value: 3rd and 4th rosette leaves

value: 2d post transition, ZT1, rep 2


title: G2 phase - DMSO - Replicate 1


title: AS-779407-LR-60677

city: Heidelberg

first: Stephanie

last: Gehrs

address: Im Neuenheimer Feld

country: Germany

institute: DKFZ

data_processing:
scRNA-sew: Raw sequencing data were demultiplexed and FASTQ files were generated using bcl2fastq software (Illumina, v2.20.0.422). Using salmon, FASTQ files were mapped to the GRCm39 mouse reference genome and count matrices were constructed with the R package tximport.
Assembly: GRCm39
Supplementary files format and content: CSV files containing the count matrix (count_matrix.csv) and the Seurat object metadata (GEO_metadata.csv)

extract_protocol: Whole transcriptome scRNA-seq was performed following an adapted SMARTseq2.5 protocol.

value: Placenta

tag: cell type

value: Endothelial cells


title: AS-779405-LR-60677

tag: tissue


title: G1 phase - MLN8237 - Replicate 1

source_name: G1 phase - MLN8237

tag: cell line


title: Leaves, 2d post transition, ZT0, rep 2

tag: genotype

value: 2d post transition, ZT0, rep 2


title: G1 phase - DMSO - Replicate 1

tag: treatment


title: AS-779397-LR-60677


title: AS-779399-LR-60677


title: AS-779403-LR-60677


title: AS-779439-LR-60677


title: AS-779437-LR-60677


title: AS-779401-LR-60677


title: G2 phase -MLN8237  Replicate 2

source_name: G2 phase -MLN8237


title: AS-779435-LR-60677


title: AS-779427-LR-60677


title: AS-779433-LR-60677


title: AS-779419-LR-60677


title: AS-779417-LR-60677


title: AS-779431-LR-60677


title: AS-779395-LR-60677


title: AS-779429-LR-60677


title: AS-779415-LR-60677


title: AS-779425-LR-60677


title: AS-779413-LR-60677


title: AS-779411-LR-60677


title: AS-779357-LR-60677


title: AS-779423-LR-60677


title: AS-779393-LR-60677


title: AS-779359-LR-60677


title: AS-779355-LR-60677


title: AS-779349-LR-60677


title: AS-779421-LR-60677


title: AS-779351-LR-60677


title: AS-779361-LR-60677


title: AS-779353-LR-60677


title: AS-779387-LR-60677


title: AS-779385-LR-60677


title: AS-779383-LR-60677


title: AS-779389-LR-60677


title: AS-779391-LR-60677


title: AS-779381-LR-60677


title: AS-779379-LR-60677


title: AS-779371-LR-60677


title: AS-779375-LR-60677


title: AS-779367-LR-60677


title: AS-779373-LR-60677


title: AS-779369-LR-60677


title: AS-779365-LR-60677


title: AS-779345-LR-60677


title: AS-779363-LR-60677


title: AS-779309-LR-60677


title: AS-779305-LR-60677


title: AS-779307-LR-60677


title: AS-779311-LR-60677


title: AS-779303-LR-60677


title: AS-779313-LR-60677


title: AS-779343-LR-60677


title: AS-779331-LR-60677


title: AS-779301-LR-60677


title: AS-779335-LR-60677


title: AS-779327-LR-60677


title: AS-779339-LR-60677


title: AS-779347-LR-60677


title: AS-779341-LR-60677


title: AS-779377-LR-60677


title: AS-779333-LR-60677


title: AS-779329-LR-60677


title: AS-779323-LR-60677


title: AS-779321-LR-60677


title: AS-779317-LR-60677


title: AS-779319-LR-60677


title: AS-779297-LR-60677


title: AS-779315-LR-60677


title: AS-779263-LR-60677


title: AS-779257-LR-60677


title: AS-779337-LR-60677


title: AS-779261-LR-60677


title: AS-779299-LR-60677


title: AS-779265-LR-60677


title: AS-779295-LR-60677


title: AS-779293-LR-60677


title: AS-779253-LR-60677


title: AS-779325-LR-60677


title: AS-779291-LR-60677


title: AS-779287-LR-60677


title: AS-779251-LR-60677


title: AS-779289-LR-60677


title: AS-779285-LR-60677


title: AS-779283-LR-60677


title: AS-779271-LR-60677


title: AS-779277-LR-60677


title: AS-779279-LR-60677


title: AS-779275-LR-60677


title: AS-779273-LR-60677


title: AS-779269-LR-60677


title: AS-779267-LR-60677


title: AS-779255-LR-60677


title: AS-779215-LR-60677


title: AS-779249-LR-60677


title: AS-779259-LR-60677


title: AS-779209-LR-60677


title: AS-779247-LR-60677


title: AS-779241-LR-60677


title: AS-779245-LR-60677


title: AS-779207-LR-60677


title: AS-779203-LR-60677


title: AS-779239-LR-60677


title: AS-779213-LR-60677


title: AS-779211-LR-60677


title: AS-779281-LR-60677


title: AS-779205-LR-60677


title: AS-779243-LR-60677


title: Tape_stripped_skin_replicate_7

city: Boston

first: Manuel

last: Leyva-Castillo

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
Run metrics, read alignment and detection of on-target transcripts was done using Torrent Suite Software 5.12.1 according to standard analysis procedures
CHP files were generated using Ion AmpliSeq RNA plug-in
Assembly: mm9
Supplementary files format and content: CHP format. Processed data files (.chp) contain normalized counts (read per million) .

source_name: skin

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen) and RNA was retrotranscribed using SuperScript VILO cDNA Synthesis Kit (ThermoFisher Scientific)
cDNA libraries were prepare using Ion AmpliSeqTM Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit in the the Ion Chef System

treatment_protocol: Skin samples were stored in RNAlater and store at -80 C until RNA extraction

value: skin

tag: strain

value: Balb/c

value: Tape stripped


title: AS-779231-LR-60677


title: Tape_stripped_skin_replicate_6


title: AS-779237-LR-60677


title: AS-779217-LR-60677


title: AS-779235-LR-60677


title: Tape_stripped_skin_replicate_4


title: Tape_stripped_skin_replicate_3


title: AS-779225-LR-60677


title: Tape_stripped_skin_replicate_8


title: Tape_stripped_skin_replicate_2


title: AS-779233-LR-60677


title: AS-779223-LR-60677


title: Tape_stripped_skin_replicate_1


title: Untreated_skin_replicate_8

value: Untreated


title: AS-779229-LR-60677


title: AS-779221-LR-60677


title: Untreated_skin_replicate_6


title: AS-779167-LR-60677


title: AS-779169-LR-60677


title: Untreated_skin_replicate_3


title: Untreated_skin_replicate_7


title: AS-779201-LR-60677


title: Tape_stripped_skin_replicate_5


title: AS-779165-LR-60677


title: Untreated_skin_replicate_5


title: AS-779163-LR-60677


title: AS-779227-LR-60677


title: Untreated_skin_replicate_2


title: AS-779161-LR-60677


title: Untreated_skin_replicate_1


title: AS-779159-LR-60677


title: Bitten_jejunum_Day 10_biological replicate 3

source_name: jejunum

treatment_protocol: jejuna samples were stored in RNAlater and store at -80 C until RNA extraction

value: jejunum

value: Bitten


title: AS-779157-LR-60677

value: WT


title: Bitten_jejunum_Day 10_biological replicate 2


title: AS-779199-LR-60677


title: AS-779197-LR-60677


title: Bitten_jejunum_Day 10_biological replicate 4


title: Bitten_jejunum_Day 10_biological replicate 1


title: AS-779219-LR-60677


title: AS-779195-LR-60677


title: Unbitten_jejunum_biological replicate 4

value: unbitten


title: Untreated_skin_replicate_4


title: Unbitten_jejunum_biological replicate 3


title: AS-779193-LR-60677


title: AS-779191-LR-60677


title: Unbitten_jejunum_biological replicate 2


title: Bitten_skin_Day 10_biological replicate 4

value: Day 10


title: Bitten_skin_Day 10_biological replicate 3


title: AS-779189-LR-60677


title: AS-779187-LR-60677


title: AS-779155-LR-60677


title: Bitten_skin_Day 10_biological replicate 2


title: AS-779185-LR-60677


title: Bitten_skin_Day 10_biological replicate 1


title: AS-779183-LR-60677


title: Bitten_skin_Day 4_biological replicate 7

value: Day 4


title: AS-779179-LR-60677


title: AS-779181-LR-60677


title: Bitten_skin_Day 4_biological replicate 6


title: Bitten_skin_Day 4_biological replicate 5


title: AS-779175-LR-60677


title: AS-779177-LR-60677


title: Bitten_skin_Day 4_biological replicate 4


title: AS-779171-LR-60677


title: Bitten_skin_Day 4_biological replicate 3


title: Bitten_skin_Day 4_biological replicate 2


title: AS-779173-LR-60677


title: Bitten_skin_Day 4_biological replicate 1


title: AS-779121-LR-60677


title: AS-779119-LR-60677


title: Unbitten_skin_biological replicate 6


title: Unbitten_jejunum_biological replicate 1


title: AS-779117-LR-60677


title: Unbitten_skin_biological replicate 5


title: Unbitten_skin_biological replicate 4


title: Unbitten_skin_biological replicate 2


title: AS-779115-LR-60677


title: AS-779113-LR-60677


title: Unbitten_skin_biological replicate 1


title: Unbitten_skin_biological replicate 3


title: AS-779109-LR-60677


title: AS-779111-LR-60677


title: AS-779149-LR-60677


title: AS-779147-LR-60677


title: AS-779151-LR-60677


title: Group 1 ILCs

city: Zürich

first: Colin

last: Sparano

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

description: 10X Genomics

data_processing:
Analysis, including quality control (QC), processing, graph-based clustering, visualizations, and differential gene expression analyses of the scRNA-seq data were performed in R using the Seurat pipeline (version 4.0) (Hao et al. 2021). Potential low-quality cells with number of features below 500, above 5000 or with more than 5% mitochondrial genes were filtered out using the QC parameters of nFeature_RNA and percent.mt. Following QC, global count normalization was performed, followed by selection of variable features (n = 2000), linear transformation using ScaleData, and dimensionality reduction (PCA). Graph-based clustering and dimensionality reduction were performed using the first 12 principal components and a resolution value of 0.6. Cell type assignment and selection of group 1 ILCs were based on cluster-specific genes identified with the FindAllMarkers function (only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25).
Assembly: GRCm38.p6
Supplementary files format and content: CellRanger output and processed Seurat Objects

source_name: Salivary gland

extract_protocol:
Live CD45+ cells from SGs of male and female 3-weeks-old mice were sorted into PBS containing 0.05% BSA for the 10X Genomics protocol. Viability of the sorted cells was evaluated with trypan blue and was over 95% for all samples. Sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared following manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v7.0.1) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23). Starting from the filtered gene-cell count matrices produced by CellRranger's built-in cell calling algorithms, we proceeded with Seurat v4 workflow (Hao et al. 2021).
Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23). Starting from the filtered gene-cell count matrices produced by CellRranger's built-in cell calling algorithms, we proceeded with Seurat v4 workflow. Analysis, including quality control (QC), processing, graph-based clustering, visualizations, and differential gene expression analyses of the scRNA-seq data were performed in R using the Seurat pipeline (version 4.0).

value: Salivary gland

value: Group 1 Innate Lymphoid Cells

value: wild-type


title: AS-779153-LR-60677


title: Sheep I, Pre-term ctrl, I3

city: Durham

first: Nicholas

middle: G

last: O'Grady

state: NC

address: 2301 Erwin Rd

department: Department of Medicine, CRU

institute: Duke University

data_processing:
Paired end sequences were assessed for quality using SeqKit.  Adapter and poly G/X tails were removed using fastp.  Post processing quality assessment is then repeated on the paired-end reads using SeqKit.  Sequences were aligned to the ovis aries genome, version 107, using STAR.  Reference files are available from Ensembl (https://ftp.ensembl.org/pub/release-107/fasta/ovis_aries/).  Gene expression was quantified against the gene transfer format (GTF), v107 annotation file using STAR’s ‘--quantMode GeneCounts’ parameter.  The reference GTF annotation file is also available from Ensembl (https://ftp.ensembl.org/pub/release-107/gtf/ovis_aries/). Sample-level quantifications from the resulting 'ReadsPerGene.out.tab’ file, column 2 for inward unstranded (IU) reads, were combined across all samples to generate the gene count matrix.
Assembly: Sequences were aligned to the ovis aries genome, version 107.  Reference files are available from Ensembl (https://ftp.ensembl.org/pub/release-107/fasta/ovis_aries/).
Supplementary files format and content: Matrix of processed paired end rna-seq, using STAR aligner.

organism: Ovis aries

source_name: basal ganglia

extract_protocol:
Flash frozen tissue was procured from ovine brain at the time of necropsy and sent to GeneWiz for RNA extraction and RNA-sequencing.
Total RNA was extracted from frozen cell pellet and fresh frozen tissue samples using Qiagen RNAeasy Plus Universal mini kit following Manufacturer’s instructions (Qiagen, Hilden, Germany).
GeneWiz conducted RNA-seq library preparation as follows: A) mRNA enrichment, mRNA fragmentation, and random priming; B) first and second strand cDNA synthesis; C) end repair, 5’ phosphorylation, and dA-Tailing; D) adaptor ligation, PCR enrichment, and sequencing.

value: basal ganglia

tag: Sex

value: Male

tag: experimental group

value: Pre-term ctrl

tag: sheep

value: I


title: Sheep I, Pre-term ctrl, I4

source_name: cerebellum

value: cerebellum


title: Sheep I, Pre-term ctrl, I2

source_name: motor cortex

value: motor cortex


title: Unbitten_skin_biological replicate 7

value: skin


title: AS-779107-LR-60677

value: Placenta

tag: age

value: Endothelial cells


title: WGBS-WT-3

data_processing:
WGBS: Differentially methylated regions were identified using the Bioconductor package dmrseq (CpGs per region≥5; max. distance between CpGs: 1kb). Genomic feature annotation was done using the Bioconductor package annotatr.
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file containing the beta values for the WGBS; excel file containing the identified DMRs.

source_name: placenta

extract_protocol:
For WGBS, DNA was isolated using the QIAmp DNA Micro kit (Qiagen) according to manufacturer instructions.
For the WGBS library preparation, the Zymo-Seq WGBS library kit (Zymo Research) was used.

value: placenta

value: endothelial cell


title: AS-779145-LR-60677

value: WT


title: Sheep I, Pre-term ctrl, I1

source_name: hippocampus

value: hippocampus


title: WGBS-WT-2


title: Sheep H, Pre-term ctrl, H4

value: Female

value: H


title: AS-779139-LR-60677


title: AS-779141-LR-60677


title: AS-779137-LR-60677


title: WGBS-WT-1


title: Sheep H, Pre-term ctrl, H2


title: Sheep H, Pre-term ctrl, H3


title: AS-779131-LR-60677


title: WGBS-KO-2

value: DNMT3A KO


title: AS-779129-LR-60677


title: AS-779125-LR-60677


title: AS-779127-LR-60677


title: AS-779123-LR-60677


title: AS-779105-LR-60677


title: Sheep G, Late pre-term ctrl, G3

value: Late pre-term ctrl

value: G


title: AS-779073-LR-60677


title: AS-779143-LR-60677


title: AS-779071-LR-60677


title: AS-779135-LR-60677


title: Day 4 Post-Wounding Skin Male PTIX1+ 3

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description:
10X Genomics Chromium 5'
8w_Skin_D4_Male_Dox_3

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were made with Cell Ranger v7.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Dorsal skin, POD 4 Wounded

extract_protocol:
Tissues were harvested: 1) Unwounded samples consisted of two 6mm punch biopsies of the healthy dorsal skin. 2) Wounded skin samples were three 3.5mm punch biopsies of the entire parially-healed full-thickness dorsal skin wounds on POD4. 3) Buccal mucosa samples were collected from both side cheeks inside the mouth. All tissues were then digested using the Whole Skin Dissociation Kit (Miltenyi) according to manufacturer's instructions. Tissues were incubated in enzyme mixture for 2.5 hours at 37°C prior to dissociation on the gentleMACS Dissociator with the gentleMACS C-tubes (Miltenyi; 'h_skin_01' cycle one time). Cells were filtered through 70µm and 30µm Pre-Separation Filters (Miltenyi) prior to resuspension in KBM-Gold (Lonza) and counting for scRNA-seq library prep. Unwounded skin and buccal samples were all >90% viable; live cells were sorted from Day 4 Wound Skin samples by FACS prior to scRNA-seq library prep.
Up to 50,000 cells were prepared for scRNA-seq with Chromium Single Cell 5' (10X Genomics) according to manufacturer's protocol.

value: Dorsal skin, POD 4 Wounded

value: Mixed

value: Doxycycline


title: AS-779067-LR-60677


title: Sheep G, Late pre-term ctrl, G2

value: Male


title: AS-779069-LR-60677


title: AS-779065-LR-60677


title: WGBS-KO-3


title: AS-779133-LR-60677


title: Sheep H, Pre-term ctrl, H1

value: Pre-term ctrl


title: AS-779061-LR-60677


title: AS-779063-LR-60677


title: WGBS-KO-1


title: Day 4 Post-Wounding Skin Male PTIX1+ 1

description:
10X Genomics Chromium 5'
8w_Skin_D4_Male_Dox_1


title: AS-779103-LR-60677


title: Sheep G, Late pre-term ctrl, G4

value: cerebellum


title: Day 4 Post-Wounding Skin Male Control 2

description:
10X Genomics Chromium 5'
8w_Skin_D4_Male_Control_2

value: Control

value: Vehicle


title: Sheep G, Late pre-term ctrl, G1


title: AS-779101-LR-60677

value: Placenta

value: Endothelial cells


title: AS-779099-LR-60677

value: WT


title: Day 4 Post-Wounding Skin Female PITX1+ 4

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Dox_4


title: Sheep F, Late pre-term ctrl, F2

value: motor cortex

value: F


title: AS-779097-LR-60677


title: Day 4 Post-Wounding Skin Male Control 1

description:
10X Genomics Chromium 5'
8w_Skin_D4_Male_Control_1


title: Day 4 Post-Wounding Skin Female PITX1+ 3

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Dox_3


title: Sheep F, Late pre-term ctrl, F1

value: hippocampus


title: AS-779091-LR-60677


title: Sheep E, Experimental, E4

value: Female

value: Experimental

value: E


title: AS-779089-LR-60677


title: Day 4 Post-Wounding Skin Female PITX1+ 1

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Dox_1

value: Dorsal skin, POD 4 Wounded


title: AS-779087-LR-60677


title: AS-779093-LR-60677


title: Sheep E, Experimental, E3

value: basal ganglia


title: Sheep F, Late pre-term ctrl, F4

value: Late pre-term ctrl


title: AS-779085-LR-60677


title: Day 4 Post-Wounding Skin Female Control 4

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Control_4

value: Mixed


title: Sheep E, Experimental, E2


title: AS-779083-LR-60677


title: Sheep F, Late pre-term ctrl, F3

value: Male


title: AS-779081-LR-60677


title: AS-779079-LR-60677


title: AS-779095-LR-60677


title: Sheep E, Experimental, E1


title: AS-779059-LR-60677


title: AS-779075-LR-60677


title: AS-779077-LR-60677


title: Sheep D, Experimental, D3

value: D


title: AS-779025-LR-60677


title: Sheep D, Experimental, D4

value: cerebellum


title: Day 4 Post-Wounding Skin Female Control 2

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Control_2

value: Control

value: Vehicle


title: AS-779057-LR-60677

value: Placenta

value: Endothelial cells


title: Day 4 Post-Wounding Skin Female Control 3

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Control_3


title: Day 4 Post-Wounding Skin Female PITX1+ 2

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Dox_2

value: Doxycycline


title: Sheep D, Experimental, D2

value: motor cortex


title: AS-779023-LR-60677

value: WT


title: AS-779017-LR-60677


title: AS-779021-LR-60677


title: Day 0 Unwounded Skin Male PITX1+ 4

description:
10X Genomics Chromium 5'
8w_Skin_D0_Male_Dox_4

source_name: Dorsal skin, healthy

value: Dorsal skin, healthy


title: Sheep D, Experimental, D1

value: hippocampus

value: Female

value: Experimental


title: AS-779013-LR-60677


title: AS-779019-LR-60677


title: AS-779015-LR-60677


title: Sheep C, Experimental, C4

value: C


title: AS-779055-LR-60677


title: Day 0 Unwounded Skin Male PITX1+ 2

description:
10X Genomics Chromium 5'
8w_Skin_D0_Male_Dox_2


title: Day 0 Unwounded Skin Male Control 3

description:
10X Genomics Chromium 5'
8w_Skin_D0_Male_Control_3


title: AS-779051-LR-60677


title: Sheep C, Experimental, C2


title: Day 4 Post-Wounding Skin Female Control 1

description:
10X Genomics Chromium 5'
8w_Skin_D4_Female_Control_1

value: Dorsal skin, POD 4 Wounded


title: Day 0 Unwounded Skin Male PITX1+ 3

description:
10X Genomics Chromium 5'
8w_Skin_D0_Male_Dox_3

value: Mixed


title: Day 0 Unwounded Skin Male PITX1+ 1

description:
10X Genomics Chromium 5'
8w_Skin_D0_Male_Dox_1


title: AS-779047-LR-60677


title: Sheep C, Experimental, C3

value: basal ganglia

value: Male


title: Day 0 Unwounded Skin Male Control 1

description:
10X Genomics Chromium 5'
8w_Skin_D0_Male_Control_1


title: AS-779053-LR-60677


title: AS-779043-LR-60677


title: AS-779011-LR-60677


title: Sheep B, Experimental, B3

value: B


title: Day 0 Unwounded Skin Male Control 2

description:
10X Genomics Chromium 5'
8w_Skin_D0_Male_Control_2

value: Control


title: Sheep B, Experimental, B4

value: cerebellum


title: AS-779037-LR-60677

value: Placenta


title: AS-779039-LR-60677

value: Endothelial cells


title: AS-779041-LR-60677


title: Day 0 Unwounded Skin Female PITX1+ 3

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Dox_3

value: Doxycycline


title: AS-779035-LR-60677


title: Sheep B, Experimental, B1


title: Day 0 Unwounded Skin Female PITX1+ 2

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Dox_2


title: Sheep B, Experimental, B2

value: motor cortex


title: AS-779033-LR-60677

value: WT


title: AS-779031-LR-60677


title: Sheep C, Experimental, C1


title: Sheep A, Experimental, A4

value: A


title: AS-779029-LR-60677


title: Day 0 Unwounded Skin Female PITX1+ 1

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Dox_1

value: Dorsal skin, healthy


title: AS-779045-LR-60677


title: Day 0 Unwounded Skin Female PITX1+ 4

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Dox_4


title: AS-778977-LR-60677


title: Sheep A, Experimental, A2

value: Female


title: AS-779027-LR-60677


title: AS-778973-LR-60677


title: Sheep A, Experimental, A3

value: Experimental


title: AS-779009-LR-60677


title: Day 0 Unwounded Skin Female Control 5

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Control_5

value: Vehicle


title: Day 0 Unwounded Skin Female Control 4

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Control_4


title: AS-778971-LR-60677


title: Day 0 Unwounded Skin Female Control 3

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Control_3


title: AS-778967-LR-60677


title: AS-778965-LR-60677


title: AS-778969-LR-60677


title: Day 0 Unwounded Skin Female Control 1

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Control_1


title: AS-778975-LR-60677


title: AS-779007-LR-60677


title: mutant-3 -Fra2hep - 2 months [LB04012]

city: Vienna

first: Latifa

last: Bakiri

address: Lazarettgasse 14, BT25/2, 6th floor Lab 2

department: Laboratory Medicine

country: Austria

institute: Medical University of Vienna

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
Reads were converted from .bam to .fastq format using bedtools v2.27.1 (1) and compressed using gzip
Reads in fastq format were aligned to the mouse reference genome version GRCm38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Raw reads per gene were counted by STAR. Differential gene expression was calculated using DESeq2 version 1.22.2. TPM were generated by RSEM
Assembly: mm10 murine reference genome downloaded from Ensembl (2018-09-28, link last accessed 2023-02-10):
Supplementary files format and content: raw counts for each sample

source_name: liver

extract_protocol:
RNA was extracted using Trizol -Sample RNA Integrity Numbers were in the rangethe range 9-10 when assayed on an Agilent 2100 Bioanalyzer.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: liver

value: not applicable :primary material

value: mostly hepatocyte

value: mutant

value: male

tag: strain background

value: Dox OFF at 3 weeks during 9 months

tag: read counts>q30


title: Day 0 Unwounded Skin Female Control 2

description:
10X Genomics Chromium 5'
8w_Skin_D0_Female_Control_2

value: Mixed

value: Control


title: Sheep A, Experimental, A1

value: hippocampus


title: mutant-1 -Fra2hep - 2 months [LB04010]


title: AS-779001-LR-60677

value: Placenta

value: Endothelial cells


title: mutant-2 -Fra2hep - 2 months [LB04011]


title: Buccal Mucosa Unwounded Male Control 2

description:
10X Genomics Chromium 5'
8w_BM_Male_Control_2

source_name: Buccal mucosa

value: Buccal mucosa


title: Buccal Mucosa Unwounded Male Control 3

description:
10X Genomics Chromium 5'
8w_BM_Male_Control_3


title: AS-779005-LR-60677

value: WT


title: AS-778999-LR-60677


title: control-3 -Fra2hep - 2 months [LB04009]

value: control

value: Dox OFF at 3 weeks during 2 months


title: AS-779003-LR-60677


title: control-2 -Fra2hep - 2 months [LB04008]


title: AS-778997-LR-60677


title: AS-778995-LR-60677


title: Buccal Mucosa Unwounded Male Control 1

description:
10X Genomics Chromium 5'
8w_BM_Male_Control_1


title: control-1 -Fra2hep - 2 months [LB04007]


title: AS-778991-LR-60677


title: AS-778963-LR-60677


title: Buccal Mucosa Unwounded Female Control 3

description:
10X Genomics Chromium 5'
8w_BM_Female_Control_3


title: mutant-3 -Fra1hep - 2 months [LB04006]


title: AS-778993-LR-60677


title: AS-778985-LR-60677


title: AS-778983-LR-60677


title: Buccal Mucosa Unwounded Female Control 1

description:
10X Genomics Chromium 5'
8w_BM_Female_Control_1


title: Buccal Mucosa Unwounded Female Control 4

description:
10X Genomics Chromium 5'
8w_BM_Female_Control_4


title: AS-778981-LR-60677


title: control-3 -Fra1hep - 2 months [LB04003]


title: SY-Mg2800-5

first: Teresina

last: Laragione

state: NY

address: 1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data. At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on thecleandata with high quality
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%).
Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality
Assembly: mm10
Supplementary files format and content: The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

source_name: synovium

growth_protocol: Male C57BL/6 mice were purchased from Taconic (Rensselaer, NY). female NOD/ShiLtJ were purchased from Jackson Laboratories (Farmington, CT).  KBxN (KRN) TCR transgenic mice (gift from Dr. C. Benoist, Boston, MA) were bred and maintained at Mount Sinai. Mice were housed under specific pathogen-free conditions and all experiments conducted under a protocol approved by the Mount Sinai Institutional Animal Care and Use Committee.

extract_protocol:
Total RNAextracted by Qiagen RNAeasy kit, and quantified by Nanodrop. 400 ng per sample was sent to Novogene (Beijing, China) for sequencing and analyses
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional libraryor dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, amplification, and purificationFor the directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer forsize distribution detection. Quantified libraries will be pooled and sequenced on Illuminaplatforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’sinstructions. After cluster generation, the library preparations were sequenced on an Illuminaplatform and paired-end reads were generated

treatment_protocol: KRN TCR transgenic mice were crossed with NOD (KRNxNOD F1) and the arthritogenic serum was collected from 60-day old arthritic mice. Serum from different batches was pooled and administered to male C57BL/6 mice at 100 µL IP on days 0 and 2. Mice typically develop arthritis on day 3, and were followed for 15 days and scored three times a week

value: synovium

value: High Mg2800


title: AS-778987-LR-60677


title: Buccal Mucosa Unwounded Female Control 2

description:
10X Genomics Chromium 5'
8w_BM_Female_Control_2

value: Vehicle


title: control-2 -Fra1hep - 2 months [LB04002]

value: liver

value: not applicable :primary material


title: LMNSC02 neural stem cells-EV, replicate 2, bulk RNAseq

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

description: Illumina XLEAP-SBS chemistry

data_processing:
Bulk RNA sequencing (RNAseq) data for LMNSC01 and LMNSC02 EVs were analyzed using Illumina Partek™ Flow™ v12.1.0 bioinformatics software. Data were imported into Partek Flow, following processing according to the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero globin protocol. Pre-alignment quality control (QA/QC) assessed the quality of raw reads, which were then mapped to the Homo sapiens genome (hg38) using STAR v2.7.8a, followed by transcript quantification and annotation based on Ensemble release v102.
Data normalization and differential gene expression (DGE) analysis were performed using DESeq2, identifying significantly differentially expressed genes with |FC| > 1.5 and p-value < 0.05. This analysis facilitated the generation of hierarchical clustering heatmaps, gene set enrichment, and pathway analysis. Qiagen Ingenuity Pathway Analysis (IPA) was conducted to investigate interactions among DEGs and identify enriched canonical pathways, calculated against a background gene set relevant to this study.
Assembly: GRCh38
Supplementary files format and content: tab-delimited csv file include raw count matrix file

source_name: brain

growth_protocol: LMNSC01 and LMNSC02 cells were grown in T-175 flasks  in NeuroCultTM NS-A Basal Medium (Human), supplemented with NeuroCultTM NS-A Proliferation Supplement , bFGF at concentration 10ng/mL, EGF at concentration 10 ng/mL, and heparin under physiological hypoxia conditions at at 4% O2 and 37C.

extract_protocol:
Each EV sample was brought up to 500 µl with ultrapure, distilled, DNase-RNase free water prior to isolation. RNA was isolated from EVs using the plasma/serum circulating and exosomal RNA purification kit with DNase on-column treatment (Norgen Biotek, Cat# 51000). Ribogreen assay was utilized to determine RNA concentration (Invitrogen); High Sensitivity RNA Screentape was used to measure RNA quality (Agilent). Due to an excess amount of DNA found after genomic DNA tapestation, an off-column DNase treatment was completed with the RNA Clean & Concentrator™-5 (Zymo Research, Cat# R1015).
Sequencing libraries were generated from RNA using SMARTer Stranded Total RNA-Seq Kit v3-Pico Input Mammalian (Takara). Ribosomal RNA is depleted using Takara’s ribogone Technology and single stranded DNA is generated with their template switching mechanism without the need for adapter ligation. cDNA fragments are purified using AMPure XP beads and then amplified using PCR. Libraries are characterized using D1000 high sensitivity screen tapes (Agilent) and quantified using qRT-PCR (Roche, Cat# KK4824P). Equimolar pools were generated, quantified (Roche, Cat# KK4824P), and sequenced on the Novaseq6000.
Cells were immediately processed with the 10× Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) kit (10× Genomics, Pleasanton, CA). Samples were loaded, cDNA amplified, and library constructed following the manufacturer’s protocol. Library quality control was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flowcell for 28×10×10×90 cycles for estimated reads per cell. After demultiplexing, libraries were normalized based on their reads per cell. Rebalanced pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 101×11×11×101 cycles.

treatment_protocol: no treatment

value: brain

value: neural stem cells-EV

value: wild type

value: no treatment


title: AS-778979-LR-60677


title: LMNSC02 neural stem cells-EV, replicate 1, bulk RNAseq

description: Illumina XLEAP-SBS chemistry


title: SY-Mg2800-4


title: SY-Mg2800-3


title: SY-Mg2800-6


title: AS-778989-LR-60677


title: LMNSC01 neural stem cells-EV, replicate 2, bulk RNAseq

description: Illumina XLEAP-SBS chemistry


title: mutant-1 -Fra1hep - 2 months [LB04004]

value: mostly hepatocyte

value: mutant

value: male


title: mutant-2 -Fra1hep - 2 months [LB04005]


title: Mouse VDJ

first: Patrick

last: Wilson

address: 413 E 69th St

department: Drukier Institute

institute: Weill Cornell Medicine

description: 10X Genomics

library_source: other

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes
Library strategy: VDJ-seq

molecule: protein

source_name: spleen

extract_protocol: 10x Genomics CG000424_C

value: spleen

value: B cell


title: Mouse GEX

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes


title: LMNSC01 neural stem cells-EV, replicate 1, bulk RNAseq

description: Illumina XLEAP-SBS chemistry


title: AS-778927-LR-60677

value: Placenta

value: Endothelial cells

value: WT


title: control-1 -Fra1hep - 2 months [LB04001]

value: control

value: Dox OFF at 3 weeks during 2 months


title: SY-Mg2800-2

value: synovium

value: High Mg2800


title: SY-Mg2800-1


title: AS-778925-LR-60677


title: 12°C-NtCP29A-rep3

city: Berlin

first: Florian

last: Rösch

address: Unter den Linden 6

institute: Humboldt Universität zu Berlin

data_processing:
Data were processed using the nf-core rnaseq (https://github.com/nf-core/rnaseq/). Reads were only mapped to the tobacco chloroplast. Reads were counted using featureCounts (https://subread.sourceforge.net/featureCounts.html) in R with the parameter Min overlaping bases: 50. Transcripts with < 50 counts in at least one sample as well as rRNAs were removed from further analysis. Differentially expression analysis was done with DeSeq2 ( https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: Nicotiana tabacum plastid, complete genome- Included in the common tobacco reference assembly (Ntab-TN90); NCBI Reference Sequence: NC_001879.2
Supplementary files format and content: semicolon-delimited csv file

organism: Nicotiana tabacum

source_name: whole leaf

growth_protocol: The plants were grown at 24°C for 21 days. Afterwards, the plants for the cold-treated samples were grown at 12°C for an additional 7 days

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using Turbo DNase (Thermo Fisher Scientific)
rRNA depletion and library construction was done by Azenta/GENEWIZ

value: whole leaf

tag: cultivar

value: petit havanna

value: NtCP29A knockout


title: 12°C-NtCP29A-rep2


title: SY-Mg500-6

value: regular Mg500


title: AS-778961-LR-60677


title: AS-778923-LR-60677


title: AS-778929-LR-60677


title: SY-Mg500-5


title: 12°C-NtCP29A-rep1


title: Brain section (left parietal)

city: St. Petersburg

first: Oscar

middle: E

last: Ospina

state: FL

address: 600 5th Street South

department: Health Informatics

institute: Johns Hopkins All Children's Hospital

description: Fresh frozen Visium

data_processing:
Two illumina NextSeq 2000 runs were and accompanying tissue H&E images were processed using the Space Ranger mkfastq pipeline to generate demultiplexed .fastq files for each sample.
Sequences in the .fastq files were aligned to the GRCh38-2020-A human genome to generate gene expression counts using Space Ranger count. The .fastq files for the two runs of each sample were combined at this point, resulting in the gene expression count files (.h5 and MEX). The Space Ranger count pipeline also generated the spot X,Y coordinates (_tissue_positions_list.csv).
Assembly: GRCh38-2020-A
Supplementary files format and content: _raw_feature_bc_matrix.h5: Unfiltered gene expression in HDF5 format
Supplementary files format and content: _raw_barcodes.tsv.gz: Spot IDs (spatial barcodes) accompanying unfiltered MEX gene expression matrix
Supplementary files format and content: _raw_features.tsv.gz: Gene IDs accompanying unfiltered MEX gene expression matrix
Supplementary files format and content: _raw_matrix.mtx.gz: Unfiltered gene expresion matrix in Matrix Market Exchange (MEX) format
Supplementary files format and content: _filtered_feature_bc_matrix.h5: Gene expression in HDF5 format
Supplementary files format and content: _filtered_barcodes.tsv.gz: Spot IDs (spatial barcodes) accompanying MEX gene expression matrix
Supplementary files format and content: _filtered_features.tsv.gz: Gene IDs accompanying MEX gene expression matrix
Supplementary files format and content: _filtered_matrix.mtx.gz: Gene expresion matrix in Matrix Market Exchange (MEX) format
Supplementary files format and content: _tissue positions list.csv: X,Y spatial coordinates of the spots in the Visium array
Supplementary files format and content: _tissue_hires_image.png: High-resolution version of the H&E stained tissue image
Supplementary files format and content: _tissue_lowres_image.png: Low-resolution version of the H&E stained tissue image
Supplementary files format and content: _scalefactors_json.json: File containing pixel to spot scaling factors in json format
Library strategy: Spatial transcriptomics

source_name: Brain melanoma metastasis

extract_protocol:
Fresh frozen tissue prepared according the Visium Spatial Gene Expression User Guide using reagents from the Visium Spatial Gene Expression Kit.
Spatial transcriptome sequencing libraries were prepared with Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: Brain melanoma metastasis


title: 12°C-wt-rep3

value: wt


title: AS-778921-LR-60677


title: AS-778919-LR-60677


title: 12°C-wt-rep2


title: SY-Mg500-4

city: New York


title: SY-Mg500-3


title: AS-778917-LR-60677


title: 12°C-wt-rep1


title: sgNT-chase 12h_rep1_SLAM21

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Raw data from machine were de-multiplexed and converted to fastq files using bcl2fastq.
The SLAM-seq data was processed with the slam dunk pipeline (https://github.com/t-neumann/slamdunk 0.3.3.).
The reads were aligned to the human genome GRCh38.
Assembly: Human genome assembly GRCh38
Supplementary files format and content: Processed data is in an excel sheet showing the T>C conversion ratio of each transcript in each sample at each timepoint.

source_name: Human embryonic kidney

growth_protocol: HEK293T cells were cultured in Dulbeccoʹs Modified Eagleʹs Medium (DMEM) (Invitrogen) supplemented with 10% (v/v) fetal bovine serum (Sigma) and 1×Antibiotic-Antimycotic (Invitrogen).

extract_protocol:
Total RNA was isolated using TRIzol reagent(Thermofisher Scientific), accoding to the manufacturer’s instructions.
Total RNA was treated with IAA according to the SLAM-seq Kinetics Kit (Lexogen, 062.24) manufacturer’s instructions.  SLAM-seq libraries were constructed using the QuantSeq 3' mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt Set B1 (Lexogen, 192.24).
QuantSeq 3' mRNA-seq

treatment_protocol: Cells were transduced with lentiCRISPR_v2 expressing negative control guides (sgNT1 and sgNT2) or guides targeting CNOT3 (sgCNOT3-1 and sgCNOT3-2), selected in puromycin for four days, and seeded into 6-well plates coated with poly-D-lysine. 24 hours later, cells were incubated with 75 µM 4-SU for 24 hours, during which media was exchanged every 3 hours, to label newly synthesized RNA. Cells were then washed 2 times with PBS, and fresh medium containing 10 mM UTP was added to stop labelling. Cells were harvested at 0, 1, 2, 4, 8, 12 hours after UTP addition.

value: Human embryonic kidney


title: AS-778959-LR-60677


title: sgNT-chase 8h_rep2_SLAM18


title: Day 4 Post-Wounding Skin Male PTIX1+ 2

description:
10X Genomics Chromium 5'
8w_Skin_D4_Male_Dox_2

value: Dorsal skin, POD 4 Wounded

value: Mixed

value: Doxycycline


title: SY-Mg500-2


title: Brain section (left occipital)

description: Fresh frozen Visium


title: Down syndrome heart CDH1

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

country: Italy

institute: Unversity of Naples Federico II

description:
The heart tissue was explanted from a human fetus with chromosome 21 trisomy and atrio-ventricular septal defects at 22 week of gestation, following therapeutic abortion. The posterior half representing all the four heart chambers was dissected by a longitudinal cut. Total RNA was extracted and PolyA+ mRNA was obtained to prepare biotinilated target cRNA according to Affymetrix protocols (http://www.affymetrix.com/support/technical/manuals/expression_manual.affx). Target cRNA was hybridized to Affymetrix HG-U133A chip using an Affymetrix GeneChip Instrument System according to the procedures described at http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf.
Image data were analyzed using the Affymetrix  expression analysis software. The Affymetrix software Microarray Suite (MAS 5.0) assigned to each probe set of the chip an average difference value corresponding to the expression level of the gene it represents and an absolute call that indicates whether the transcript is present in the sample.  Data sets were scaled to a total targeted fluorescence of 100.
Keywords = Down syndrome
Keywords = heart gene expression profile

data_processing: Affymetrix CEL files were imported into GeneSping 7.2 software (Agilent Technologies Inc.) and normalized by MAS5 algorithm

source_name: Fetal heart at 22 week of gestation

label_protocol: In vitro transcription was performed to obtain biotin labeled cRNA according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

extract_protocol: Total RNA was extracted by Trizol

value: heart from fetus with Down syndrome and septal defects.

value: 22 gestation weeks


title: sgNT-chase 8h_rep1_SLAM17


title: 24°C-NtCP29A-rep3


title: SY-Mg500-1


title: 24°C-NtCP29A-rep2


title: sgNT-chase 4h_rep2_SLAM14


title: Brain section (right parietal)

description: Fresh frozen Visium


title: SP-Mg2800-7

value: spleen


title: 24°C-NtCP29A-rep1


title: AS-778955-LR-60677

value: Placenta

value: Endothelial cells

value: WT


title: SP-Mg2800-6

value: High Mg2800


title: sgNT-chase 12h_rep2_SLAM22

value: control


title: AS-778953-LR-60677


title: sgNT-chase 4h_rep1_SLAM13


title: 24°C-wt-rep3

value: whole leaf

value: petit havanna


title: SP-Mg2800-5


title: 24°C-wt-rep2


title: sgNT-chase 2h_rep1_SLAM9


title: AS-778951-LR-60677


title: AS-778915-LR-60677


title: 24°C-wt-rep1


title: SP-Mg2800-4


title: AS-778949-LR-60677


title: SP-Mg2800-3


title: sgNT-chase 1h_rep2_SLAM6


title: Synovium, Clodronate

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

description: 10x Genomic

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: ensembl_102
Supplementary files format and content: h5 file generated from Cellranger Count output

organism: Rattus norvegicus

source_name: Synovium

extract_protocol:
Synovial tissues were digested with Liberase. After lysing erythrocytes with ACK Lysing Buffer, the digested cells were cryopreserved in CELLBANKER 1plus (Zenoaq, Fukushima, Japan).
Library construction involved encapsulating single cells, reagents, and barcoded Gel Beads into nanoliter GEMs using GemCode Technology. Inside GEMs, mRNA underwent lysis and barcoded reverse transcription, followed by cDNA amplification, fragmentation, and adaptor ligation.

value: Synovium

value: Clodronate liposome injection


title: sgNT-chase 1h_rep1_SLAM5


title: SP-Mg2800-2


title: AS-778957-LR-60677


title: Synovium, Control

description: 10x Genomic

value: Control liposome injection


title: AS-778947-LR-60677


title: SP-Mg2800-1


title: sgNT-chase 0h_rep2_SLAM2

value: Human embryonic kidney


title: AS-778945-LR-60677


title: LMNSC02 human cell line, replicate 2,scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, libraries were normalized based on their reads per cell. Rebalanced pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 101×11×11×101 cycles.
scRNAseq data was analyzed by Illumina Partek™ Flow™ v12.1.0 bioinformatics software (https://www.partek.com/partek-flow/).  Using two replicates for each of LMNSC01 and LMNSC02 cell lines, data were imported into Partek Flow, data were processed based on Illumina Single Cell 3' v3 protocol with estimated 13,705 cells, followed by pre-alignment QA/QC to assess the overall quality of the cells then further filtered by three quality control filters: Mitochondrial reads (>5%), the count of read between 500 - 10,000. Features where the value was <=1.0 in at least 99.9% of the cells, were excluded. PCA was made with 100 principal components, and the variance was set as the features contribute. For the UMAP the local neighborhood size was set at 30, a minimal distance of 0.3, distance metric was set as Cosine, 0 iterations, random generator seed 42, the initialize output values Random, and the number of principal components was set as 20. Normalization with the setting of log2(cpm+1) followed by differential gene expression (DGE) analysis using ANOVA to generate the statistical significant differential genes filtered by |FC|>2 and FDR < 0.001 by comparing between LMNSC01 and LNDSC02 cell lines for downstream analysis of Hierarchical clustering heatmap,  gene set enrichment and Pathway analysis. Additionally, an Qiagen Ingenuity Pathway Analysis was done to explore the interactions between the DEGs based on enrichment score calculated relative to a set of background genes relevant for this experiment.
Assembly: GRCh38
Supplementary files format and content: tab-delimited csv file include raw count matrix file

growth_protocol: LMNSC01 and LMNSC02 cells were grown in T-75 flasks  in NeuroCultTM NS-A Basal Medium (Human) (Stem Cell Technologies, Cat# 05750), supplemented either with NeuroCultTM NS-A Proliferation Supplement (Human) (Stem Cell Technologies, Cat# 05751) or NeuroCultTM NS-A Differentiation Supplement (Human) (Stem Cell Technologies, Cat# 05752), basic Fibroblast Growth Factor (bFGF) at concentration 10ng/mL (Stem Cell Technologies, Cat# 78003), Epidermal Growth Factor (EGF) at concentration 10 ng/mL (Stem Cell Technologies, Cat# 78006), and heparin at 0.2x104% concentration (Stem Cell Technologies, Cat# 07980#) under physiological hypoxia conditions at at 4% O2 and 37C.

extract_protocol:
LMNSC01 and LMNSC02 cells were dissociated from T75 cell culture flasks and counted, and a targeted recovery of 15,000 cells was calculated for each sample by loading a concentration of approximately 15,000 cells.
The library constructed following the manufacturer’s protocol. Library quality control was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA)
Cells were immediately processed with the 10× Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) kit (10× Genomics, Pleasanton, CA). Samples were loaded, cDNA amplified, and library constructed following the manufacturer’s protocol. Library quality control was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flowcell for 28×10×10×90 cycles for estimated reads per cell. After demultiplexing, libraries were normalized based on their reads per cell. Rebalanced pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 101×11×11×101 cycles.

value: brain

value: neural stem cells

value: wild type

value: no treatment


title: sgNT-chase 2h_rep2_SLAM10


title: AS-779049-LR-60677

data_processing:
scRNA-sew: Raw sequencing data were demultiplexed and FASTQ files were generated using bcl2fastq software (Illumina, v2.20.0.422). Using salmon, FASTQ files were mapped to the GRCm39 mouse reference genome and count matrices were constructed with the R package tximport.
Assembly: GRCm39
Supplementary files format and content: CSV files containing the count matrix (count_matrix.csv) and the Seurat object metadata (GEO_metadata.csv)


title: sgNT-chase 0h_rep1_SLAM1


title: LMNSC02 human cell line, replicate 1,scRNAseq

description: 10x Genomics


title: SP-Mg500-7

value: regular Mg500


title: sgCNOT3-chase 12h_rep2_SLAM24


title: SP-Mg500-6

value: spleen


title: LMNSC01 human cell line, replicate 2,scRNAseq

description: 10x Genomics


title: AS-778941-LR-60677

value: Placenta


title: AS-778939-LR-60677

value: Endothelial cells


title: sgCNOT3-chase 12h_rep1_SLAM23


title: SP-Mg500-5


title: SP-Mgg500-3


title: AS-778943-LR-60677

value: WT


title: SP-Mg500-4


title: AS-778937-LR-60677


title: sgCNOT3-chase 8h_rep1_SLAM19


title: AS-778933-LR-60677