title: Zebrafish embryos, Strain: ABTU, Stage: 17-18 somite (Biol rep 3)


title: Drought1_47d_rep3

status: Public on Nov 30 2023

type: SRA

city: Tsukuba

first: FUMIYUKI

last: SOMA

state: Ibaraki

address: 2-1-2 Kan-non-dai

department: Institute of Crop Science

country: Japan

institute: National Agriculture and Food Research Organization

library_source: transcriptomic

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MSU7 gene models using the STAR aligner (Dobin et al., 2013)
Read counts were quantified using the featureCounts (Liao et al., 2014) with option” -S 2 -p -B -C -T”.
Supplementary files format and content: Tab-delimited text files include row counts for each Sample

molecule: total RNA

organism: Oryza sativa

growth_protocol: Rice plants were grown in a growth chamber under a 14 h light/10 h dark photoperiod, with 50% R.H. at daytime and 60% R.H. at nighttime. The temperature in the growth chamber varied from 25°C to 30℃ at daytime,

extract_protocol:
Total RNA was extracted using TRIzol RNA Isolation Reagents (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs)

treatment_protocol: The water level in each pot was maintained at 6 cm above the bottom of the pot under WW conditions. Drought stress was initiated at each indicated days after sowing by withdrawing water supply.

tag: tissue

tag: genotype

value: Nipponbare

tag: treatment


title: PSC4_cntrl_3

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

data_processing:
Estimated transcript counts were counted using Salmon (version 1.4.0)
DEA was performed in R using DESeq package (V2) with default parameters.
GSEA was performed using genes ranked by their p-values using the GSEA program (Broad Institute)
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw count data in tab-delimited text format.

organism: Mus musculus

source_name: PSC4 in control media #3

growth_protocol: PSCs were grown in Matrigel

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent and stored at -80C. The RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).
mRNA library preparations (Illumina) were performed using 30 µL of 10 ng/mL (300 ng) per sample

treatment_protocol: PSCs were treated with the conditiones detailed above for 4 days

tag: cell line

tag: cell type

value: Murine pancreatic stellate cells (PSCs)

value: WT

tag: agent

value: Control Media

value: Day 4

tag: strain

tag: passage


title: Zebrafish embryos, Strain: ABTU, Stage: 17-18 somite (Biol rep 1)

city: Hong Kong

first: Andrew

last: Miller

address: Division of LIFS, HKUST, Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
Performed adapter trimming with cutadapt v3.4 software with parameters: "--minimum-length=30 -a A\{100\} -A A\{100\} -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -g AGATGTGTATAAGAGACAG -G AGATGTGTATAAGAGACAG".
Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters "--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts".
Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0.
Assembly: danRer10 (Genome Reference Consortium Zebrafish Build 10)
Supplementary files format and content: all.tsv: Tab-delimited text file includes raw counts.
Supplementary files format and content: Treatment_1-vs-Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Embryos were collected from wild-type ABTU and mutant TPC2 fish line and kept at 28 °C.

extract_protocol:
RNA extraction was performed using RNAzol® according to the manufacturer’s instructions.
Samples were submitted to the Bioscience Central Research Facility for library construction.

value: Whole embryo

value: ABTU

tag: developmental stage

value: 17-18 somite stage


title: fat, Female, B6, Chow, Age 20 Week, Replicate 3

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

country: USA

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed using Trimmomatic version 0.39 in PE mode, to remove Illumina adapters, to remove the first 12 bases from the reads, to crop to a maximum of 37 bases in length, to remove low quality reads, and to filter any reads less than 25 bases in length. Parameters: ILLUMINACLIP TruSeq3-PE-2.fa:2:30:10 HEADCROP:12 CROP:37 SLIDINGWINDOW:4:15 MINLEN:25
Reads were aligned to the mouse genomeGRCm39 using HISAT2 version 2.2.1 with default parameters
Alignment files were sorted by name using samtools sort -n with samtools version
Mate coordinate and insert size fields were added to alignment files with samtools fixmate using samtools version
Alignment files were sorted by position using samtools sort with samtools version
Duplicate reads were removed using samtools markdup -r with samtools version
Gene level counts were generated using the makeTxDbFromGFF and exonsBy functions from the Bioconductor package GenomicFeatures, version and the summarizeOverlaps function from the Bioconductor package GenomicAlignments, version. The latter was run with parameters mode="IntersectionStrict", singleEnd=F, ignore.strand=T, fragments=F
Gene counts were normalized using the DESeq function, and FPKM values computed using the fpkm function from Bioconductor package DESeq2 version
Assembly: Genome GRCm39 Mus_musculus.GRCm39.dna.toplevel.fa from Ensembl. Gene annotations used in creating read counts are Ensembl Genes version 108, Mus_musculus.GRCm39.108.gtf
Supplementary files format and content: raw_counts.csv is a comma deliminted file containing the raw read counts from each sample
Supplementary files format and content: normalized_counts.csv is a comma delimited file containing the normalized counts (using the DESeq function from Bioconductor package DESeq2) from each sample
Supplementary files format and content: fpkm.csv is a comma delimited file containing the FPKM values (computed using the fpkm function from Bioconductor package DESeq2) for each sample

source_name: fat

extract_protocol:
Total RNA was isolated from the tissue using RNeasy Plus Universal Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
All RNA samples were assessed using the Bioanalyzer 2100 and quantified using the Thermo Fisher Qubit RNA assay. Each RNA sample with a RIN value above 8 and a quantity of 1000ng was utilized to generate a Poly(A)-based RNAseq library following the Illumina TruSeq stranded mRNA protocol. Briefly, the poly(A) RNAs were purified using oligo dT magnetic beads and were then fragmented with divalent cations, followed by reverse transcription into cDNA. The Illumina paired-end oligo adapters were ligated to the cDNA fragments, and the RNAseq libraries were amplified using PCR. The finished libraries were purified and analyzed on an Agilent Bioanalyzer 2100, revealing an average library size ranging from 285 to 300 base pairs. To determine the quantity of these libraries, they were further measured using the Thermo Fisher Qubit HS dsDNA assay.

treatment_protocol: At 4 weeks of age, male and female TALLYHO/Jng (TH) and C57BL/6J (B6) mice were weaned onto either standard chow or high fat diets and maintained on the respective diets. After 1 and 16 weeks of feeding (5 and 20 weeks of age), mice were euthanized by CO2 inhalation followed by cervical dislocation and exsanguination via cardiac puncture. Tissues including liver, gonadal fat, soleus muscle, and pancreas were then collected for RNA isolation.

value: fat

tag: Sex

value: F

tag: diet

value: Chow

tag: age


title: Drought1_47d_rep2


title: PSC4_TGFb_3

source_name: PSC4 in control media with 20 ng/mL TGFbeta #3

value: TGFbeta


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 5

source_name: Pancreas

value: Pancreas


title: Well-watered1_47d_rep3


title: Drought2_47d_rep2


title: PSC4_TGFb_2

source_name: PSC4 in control media with 20 ng/mL TGFbeta #2


title: liver, Female, B6, Chow, Age 20 Week, Replicate 4

source_name: liver

value: liver


title: PSC5_CM_T8_nera_1

source_name: PSC5 in tumor organoid conditioned media 300 nM Neratinib  #1

value: Conditioned Media ERBBi


title: Drought1_47d_rep1


title: PSC4_cntrl_1

source_name: PSC4 in control media #1


title: Well-watered1_47d_rep2


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 4


title: 351CTRL

city: Bern

first: Kerstin

last: Klein

state: Bern

address: Murtenstrasse 28

department: Department of Rheumatology and Immunology

country: Switzerland

institute: University Hospital Bern

data_processing:
quality control was conducted using FASTQC
reads were cleaned using Trimmomatic
Reads were mapped to the human reference genome (hg 19) using STAR
Counts per gene were assessed using Feature Counts
Assembly: hg19

organism: Homo sapiens

source_name: RA synovial tissue (wrist)

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit (Qiagen), including Dnase digest.
Librariesfor RNAseq were generated using the Illumina TruSeq Stranded total RNA Sample Preparation Kit.

value: RA synovial tissue (wrist)

value: synovial fibroblast

value: unstimulated


title: PSC5_CM_T6_nera_2

source_name: PSC5 in tumor organoid conditioned media 300 nM Neratinib #2

value: Murine pancreatic stellate cells (PSCs)


title: liver, Female, B6, Chow, Age 20 Week, Replicate 3


title: 351CTRL_TNF

value: TNF


title: 351BRD3_TNF


title: liver, Female, B6, Chow, Age 20 Week, Replicate 2


title: PSC4_CM_T8_nera_1

source_name: PSC4 in tumor organoid conditioned media 300 nM Neratinib #1

value: WT


title: 365BRD3_TNF


title: soleus, Female, B6, Chow, Age 20 Week, Replicate 2

source_name: soleus

value: soleus


title: Drought4_44d_rewater2_rep3

value: Nipponbare


title: PSC4_CM_T6_nera_2

source_name: PSC4 in tumor organoid conditioned media 300 nM Neratinib #2

value: Day 4


title: Well-watered1_47d_rep1


title: PSC4_cntrl_2

source_name: PSC4 in control media #2

value: Control Media


title: 351BRD3


title: fat, Female, B6, Chow, Age 20 Week, Replicate 2

value: fat


title: soleus, Female, B6, Chow, Age 20 Week, Replicate 1

value: F


title: 365CTRL_TNF


title: PSC5_CM_T8_1

source_name: PSC5 in tumor organoid conditioned media #1

value: Conditioned Media


title: Drought4_44d_rewater2_rep1


title: 365CTRL


title: PSC4_CM_T8_1

source_name: PSC4 in tumor organoid conditioned media #1


title: 481BRD3_TNF


title: PSC5_CM_T6_2

source_name: PSC5 in tumor organoid conditioned media #2


title: Drought4_44d_rewater2_rep2


title: fat, Female, B6, Chow, Age 20 Week, Replicate 1

value: Chow


title: PSC4_CM_T6_2

source_name: PSC4 in tumor organoid conditioned media #2


title: 481CTRL_TNF


title: 365BRD3


title: Drought3_44d_rewater2_rep1


title: 481BRD3


title: HTO library for GLI1KO_JAK2V617F

city: Rotterdam

first: Jessica

last: Pritchard

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

library_source: other

data_processing:
The Cell Ranger Software (version 4.0.0) was used for processing sequencing information.
Seurat (version 4.0.4) was used to integrate the singlecell RNA-seq data
Assembly: mm10 + GFP sequence
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Bone Marrow

growth_protocol: Recipient mice received 4-5x105 cells from 8-week-old WT or Gli1 knock out mice that had been harvested 48 hours prior to transplantation and transduced with JAK2V617F or control JAK2WT retrovirus and transplanted into 10.5 Gy-irradiated 8-10-week-old female B6.SJL recipients. Mice were randomly assigned to transplant groups. Mice were sacrificed at 112 days post-BM transplant.

extract_protocol: Single cell solutions were subject to 10x pipeline. All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression (Single Cell 3' v3.1) and additional hashtag libraries were generated alongside following the protocol described by Stoeckius et al, 2019 (https://doi.org/10.1186/s13059-018-1603-1)

treatment_protocol: Whole bone marrow from 3 mice per condition was incbuated with hashtagging antibodies prior to MACS-depletion for CD11b, GR1, TER119, B220, and CD3. Samples were poled per condition and subsequently two populations were FACS-sorted for viability, lineage negativity and +/- GFP.

value: Bone Marrow

tag: transduction

tag: library type

value: HTO


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 2

value: Pancreas


title: Drought3_44d_rewater2_rep2


title: liver, Female, B6, Chow, Age 20 Week, Replicate 1

value: liver


title: HTO library for GLI1KO_JAK2WT


title: Drought3_44d_rewater2_rep3


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 1


title: 481CTRL

value: RA synovial tissue (wrist)

value: synovial fibroblast


title: HTO library for WT_JAK2V617F


title: Well-watered2_44d_rewater2_rep3


title: Well-watered2_44d_rewater2_rep2


title: carnation petal, ethylene treatment, 24h, rep3, IP [IP-E24h-3]

city: Wu han

first: feng

last: shan

address: Shizishan Street

country: China

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.19.1.403 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, Timmomatic v0.36   discarding reads left with < 20 bp
Clean reads were mapped to the carnation genome by Bwa (version 0.7.15)
Trimmomatic (version 0.38) was used to filter out low-quality reads
MACS2 software (version 2.1.1.20160309) was used to call peaks by default parameters (bandwidth,300 bp; model fold, 5, 50;q value, 0.05)
Assembly: carnation genome
Supplementary files format and content: peaks

molecule: genomic DNA

organism: Dianthus caryophyllus

source_name: petal

extract_protocol:
petals were fixed with 1% formaldehyde for 30 minutes and sonicated into DNA fragments. 6% of the sonicated chromatin was saved as the input. The left samples were subsequently incubated with 2 µl of antibodies of anti-H3K4me3 (abcam ab8580) overnight at 4°C with gentle agitation.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX ChIP-Seq Library Prep Kit for Illumina Sequencing（NOVA-5143-02，Bioo Scientific） and sequenced on Illumina NovaSeq 6000 with PE 150 method.

value: petal

tag: chip antibody

value: ethylene for 24h


title: HTO library for WT_JAK2WT

value: WT


title: Well-watered2_44d_rewater2_rep1


title: carnation petal, ethylene treatment, 24h, rep2, IP [IP-E24h-2]


title: Drought2_44d_rewater2_rep3


title: carnation petal, ethylene treatment, 24h, rep1, IP [IP-E24h-1]


title: Drought2_44d_rewater2_rep2


title: Gli1KO_JAK2V617F

library_source: transcriptomic single cell

value: mRNA


title: carnation petal, ethylene treatment, 4h, rep2, IP [IP-E4h-2]

value: ethylene for 4h


title: Drought1_44d_rewater2_rep3

value: Nipponbare


title: WT_JAK2WT


title: GLI1KO_JAK2WT


title: Drought2_44d_rewater2_rep1


title: WT_JAK2V617F


title: carnation petal, ethylene treatment, 4h, rep1, IP [IP-E4h-1]


title: Pancreas, Female, B6, Chow, Age 20 Week, Replicate 3

source_name: Pancreas


title: Drought1_44d_rewater2_rep2


title: liver-Treatment-3

city: Chengdu

first: yuan

last: teng

address: huimin road 211

institute: Sichuan Agricultural University

data_processing:
Kallistov0.44.0
Use from the ensemble Mus_musculus.GRCm39.105.gtf and Mus_musculus.GRCm39.cdna.all.fa.gz. All. The fa. Gz file as reference genome, using R for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file including TPM value and counts value for each sample

growth_protocol: All apcmin/+ mouse were maintained on a 12-hour light cycle and were provided with water and standard rodent chow ad libitum

extract_protocol:
Colorectal RNA extraction with Trizol(Life Technologies, China,15596026). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit ( NEB, USA， 7530) following manufacturer's protocols.

treatment_protocol: The control group drank low-concentration Neu5Gc water (0.0127mg/ml), and the treatment group drank high-concentration Neu5Gc water (0.2535mg/ml) for 14 consecutive days.

value: Drink high concentration neu5gc


title: DICER-R1855A rescue replicate 1

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

data_processing:
The sequencing reads of mRNA were also adapter-trimmed by cutadapt (Martin 2011) (-a AGATCGGAAGAGCACACGTCT for Read 1 and -a GATCGTCGGACTGTAGAACTCTGAAC for Read 2).
Processed pair-end reads were then joined by using fastq-join (Aronesty 2013), and low-quality reads were then discarded by using fastq_quality_filter (-q 20 -p 90) (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13).
Reads are then mapped to human genome reference (GRCh38) using bowtie2 (bowtie2 --local --score-min L,-4,2 --ma 2 -k 5) (Langmead and Salzberg, 2012).
miRNA genomic coordination file was obtained from miRBase (Griffiths-Jones et al., 2006), and annotation of the mapped reads was done by using bedtools intersect (Quinlan A.R. and Hall I. M., 2010).
Assembly: home-made reference shRNA sequences
Supplementary files format and content: Bed files of control samples contain the raw read count of each shRNA in the control library.
Supplementary files format and content: Bed files of the single cleavage and double cleavage samples contains the assigned cleavage sites, cleavage accuracy, positional cleavage efficiency, global cleavage efficiency.

growth_protocol: The HCT116 DICER-KO cells were cultured in McCoyʼs 5A medium (Gibco, 16600082) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10270106) and 1% of  Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
The total RNAs were isolated from the cells by using TRIzol Reagent (Invitrogen, 15596018) following the manufacturer's mannual.
Transfected cells were harvested 48 h post-transfection and total RNA was extracted using Trizol (Ambion, #15596018). Small RNA fractions were obtained from 10 µg of total RNA by using 12% urea-gel and IPA precipitation. The small RNA sequencing libraries were constructed by using the TruSeq Small RNA Library Prep Kits (Illumina). The DNA libraries of small RNAs were sequenced by Illumina Nextseq 6000. The concentration and size distribution of the DNA libraries were examined by Qubit dsDNA HS Assay Kit (Invitrogen, #Q32854) and Fragment Analyzer system, respectively. Finally, the examined DNA libraries were subjected to the next-generation sequencing (NGS).

treatment_protocol: Cells were transfected with pXG-DICER-WT, pXG-DICER∆dsRBD, pXG-DICER-R1855A, pXG-DICER-E1859A using Lipofectamine 3000.

value: HCT116 DICER-KO

value: culture cells

value: pXG-DICER-R1855A plasmid rescue


title: DICER-deldsRBD rescue replicate 3

value: pXG-DICER-deldsRBD plasmid rescue


title: DICER-E1859A rescue replicate 3

value: pXG-DICER-E1859A plasmid rescue


title: DICER-E1859A rescue replicate 1


title: DICER-E1859A rescue replicate 2


title: liver-Treatment-2


title: DICER-R1855A rescue replicate 3


title: DICER-R1855A rescue replicate 2


title: carnation petal, full blooming, rep2, IP [IP-E0h-2]


title: DICER-deldsRBD rescue replicate 2


title: Drought1_44d_rewater2_rep1


title: carnation petal, full blooming, rep1, IP [IP-E0h-1]


title: liver-Treatment-1


title: DICER-deldsRBD rescue replicate 1


title: Well-watered1_44d_rewater2_rep3


title: carnation petal, ethylene treatment, 4h, rep3, IP [IP-E4h-3]


title: Well-watered1_44d_rewater2_rep2


title: liver-Control-3

value: Drink low concentrations of neu5gc


title: carnation petal, ethylene treatment, 24h, rep3, Input [In-E24h-3]


title: carnation petal, full blooming, rep3, IP [IP-E0h-3]


title: Well-watered1_44d_rewater2_rep1


title: DICER-WT rescue replicate 2

value: pXG-DICER WT plasmid rescue


title: liver-Control-1

value: liver


title: Drought4_44d_rewater1_rep3


title: DICER-WT rescue replicate 3


title: carnation petal, ethylene treatment, 24h, rep2, Input [In-E24h-2]


title: carnation petal, ethylene treatment, 24h, rep1, Input [In-E24h-1]


title: DICER-WT rescue replicate 1


title: carnation petal, ethylene treatment, 4h, rep3, Input [In-E4h-3]


title: Drought4_44d_rewater1_rep2


title: colorectal-Treatment-4

source_name: colorectum

value: colorectum


title: carnation petal, ethylene treatment, 4h, rep2, Input [In-E4h-2]


title: Drought3_44d_rewater1_rep3


title: carnation petal, ethylene treatment, 4h, rep1, Input [In-E4h-1]


title: Drought4_44d_rewater1_rep1


title: colorectal-Treatment-6


title: G4_IDH2-Wt

city: Stanford

first: Niklas

last: Landberg

state: CA

address: 265 Campus Dr Stanford

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

data_processing:
Reads were trimmed using skewer (v.0.2.2)
Reads were aligned to the GRCh38p.13 reference genome using STAR (v.2.7.10a) for first pass mapping with extraction of novel splice junctions and a second pass mapping after rebuilding the genome index.
RSEM was used for quantifying transcript abundances
Data normalization and visualization were done using DESeq2 (v1.38.3) and Qlucore
Assembly: GRCh38p.13
Supplementary files format and content: Processed data are shown as normalized RSEM transcript reads per million

molecule: polyA RNA

source_name: Human umbilical cord blood

extract_protocol:
>100 000 viable cells were FACS isolated directly into 300ul DNA/RNA Shield and flash frozen and submitted to Novogene
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Human umbilical cord blood

value: HSPCs donor G


title: colorectal-Treatment-3


title: G5_IDH2-R140Q


title: Drought3_44d_rewater1_rep2


title: colorectal-Treatment-2


title: carnation petal, full blooming, rep3, Input [In-E0h-3]

value: petal


title: G1_AAVS1


title: Well-watered2_44d_rewater1_rep3


title: Drought3_44d_rewater1_rep1


title: liver-Control-2

source_name: liver


title: F5_IDH2-R140Q

value: HSPCs donor F


title: colorectal-Control-4


title: colorectal-Treatment-1


title: G3_IDH1-R132H


title: refr_72_hpa_D

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Reads were filtered for low quality reads and adaptor sequences, using TrimmomaticPE (v. 0.36), while ribosomal RNA reads were filtered out using Sortmerna (v. 2.1b) (default parameters).
The cleaned reads were then aligned using STAR (v. 2.7.9a) to the Xenopus laevis genome version 10.1 and annotation version XENLA_10.1_GCF.
A count table was then generated using the python script htseq-count (v. 0.6.1p1) with the parameter “–m union”. The counts were normalized and analyzed using DESeq2 (v. 1.32.0)[84] under R (v. 4.1.0).
Outlier samples were assessed by analyzing the PCA of the 500 most variable genes.
Assembly: Xenopus laevis genome version 10.1
Supplementary files format and content: 02_bulk_data_non_normalized_refrac.xlsx: non-normalized count data from the refractory experiment
Supplementary files format and content: 02_bulk_data_non_normalized_regen.xlsx: non-normalized count data from the regeneration experiment
Supplementary files format and content: 02_bulk_data_normalized_refrac.xlsx: median of ratios normalized data for the refractory dataset using DESeq2. Outlier samples were removed.
Supplementary files format and content: 02_bulk_data_normalized_regen.xlsx: median of ratios normalized data for the regeneration dataset using DESeq2. Outlier samples were removed.

organism: Xenopus laevis

source_name: tail

growth_protocol: Xenopus laevis females were stimulated with 500 U of human chorionic gonadotropin (Sigma-Aldrich). Eggs were collected the following day and fertilized by testes suspension which were surgically obtained from the male. After the removal of jelly coats by the 2% cysteine treatment, embryos were incubated in 0.1x MBS until the experimental procedure. Embryonic stages were determined based on Nieuwkoop and Faber table. Embryos were immediately transferred to the 0.1x MMR solution with gentamycin. Solution was changed every day.

extract_protocol:
All samples were stored at -80°C. Total RNA was extracted from 20 embryos per sample at the regenerative stage. Total RNA was extracted using TriReagent extraction and LiCl precipitation (Sigma) according to the manufacturer’s instructions. The concentration of total RNA was determined using a spectrophotometer (Nanodrop 2000; ThermoFisher Scientific), and the quality of RNA was assessed using a Fragment Analyzer (Agilent, Standard Sensitivity RNA analysis kit, DNF-471).
100 ng of total RNA was used for library preparation using the Lexogen SENSE Total RNA-Seq Library Prep Kit.
Library quality was tested by capillary electrophoresis on Fragment Analyzer (Agilent, NGS High Sensitivity kit DNF-474). The libraries were pooled and sequenced using Illumina NextSeq 500, 2x76 bp.

treatment_protocol: Bulk RNA-Seq analysis was done to analyze the temporal changes in gene expression during the regeneration and refractory periods of 0, 0.5, 6 hpa and 3 dpa. The experiment was done in four biological repeats.

value: tail

tag: time

value: 72 hours post amputation

tag: condition

value: refractory

value: amputated


title: Well-watered2_44d_rewater1_rep1

tag: tissue

value: Nipponbare


title: colorectal-Treatment-5

value: Drink high concentration neu5gc


title: Well-watered2_44d_rewater1_rep2

tag: genotype


title: colorectal-Control-3

tag: treatment


title: refr_6_hpa_D

value: 6 hours post amputation


title: G2_IDH1-Wt


title: Drought2_44d_rewater1_rep3


title: carnation petal, full blooming, rep1, Input [In-E0h-1]


title: Drought2_44d_rewater1_rep2


title: colorectal-Control-2


title: refr_0_hpa_D

value: 0 minutes post amputation


title: refr_0.5_hpa_D

value: 0.5 hours post amputation


title: colorectal-Control-1

value: Drink low concentrations of neu5gc


title: F2_IDH1-Wt


title: Drought2_44d_rewater1_rep1


title: F1_AAVS1


title: refr_72_hpa_C


title: Drought1_44d_rewater1_rep3


title: E5_IDH2-R140Q

value: HSPCs donor E


title: refr_6_hpa_C


title: F4_IDH2-Wt


title: 18674X2 MIG-OCA-B

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 3.1.0 to create the I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-3.0.0 reference from 10x Genomics
Barcodes and UMIs were counted using cellranger count with expected-cells=6000
Assembly: mm10
Supplementary files format and content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: splenic T cells

extract_protocol:
CD4+ T cells were purified from female Ly5.1 SMARTA and Ly5.1/5.2 SMARTA mice, and separately transduced with pMIG-OCA-B or empty vector (EV). On the following day, transduced GFP+ cells were isolated by FACS and 20,000 of each combined 1:1, and injected intravenously into C57BL/6J male recipients. 24h later, each recipient mouse was injected intraperitoneally with 2x10E5 pfu LCMV-Arm. After eight days, splenic CD4+ T cells were purified using a Miltenyi CD4 T cell isolation kit. Cells were stained with PerCP-Cy5.5 Ly5.1 and AF700 Ly5.2 antibodies. GFP+Ly5.1+Ly5.2+ (EV) and GFP+ Ly5.1+ (OCA-B-expressing) cells were sorted by fluorescence-activated cell sorting (FACS) and deposited for single-cell RNA sequencing.
10X Genomics Single Cell 5' Gene Expression library prep

value: spleen

value: T cells

value: MIG-OCA-B


title: 18674X1 empty vector

value: empty vector


title: 18317X8 OE 5

data_processing:
Reads were aligned to the mouse mm10 genome (GRCm38, December 2011) plus splice junctions using novoalign
Tests for differential gene expression were performed with DESeq2, version 1.10.0
Assembly: mm10
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited file

source_name: OE

extract_protocol:
Total RNAs were purified from sorted CD4+GFP+Ly5.1+Ly5.2+ (EV) and GFP+Ly5.1+ (OCA-B-expressing) splenic cells with Rneasy Mini kit (Qiagen) following their standard protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GFP+Ly5.1+ (OCA-B-expressing) cells


title: E4_IDH2-Wt

value: Human umbilical cord blood


title: refr_0.5_hpa_C

value: tail


title: E3_IDH1-R132H


title: F3_IDH1-R132H

value: HSPCs donor F


title: Drought1_44d_rewater1_rep2


title: E2_IDH1-Wt


title: 18317X7 OE 4


title: refr_72_hpa_B

value: 72 hours post amputation

value: refractory


title: Well-watered1_44d_rewater1_rep3

value: Nipponbare


title: refr_0_hpa_C

value: amputated


title: 18317X6 OE 3


title: E1_AAVS1


title: Drought1_44d_rewater1_rep1


title: 18317X5 OE 2


title: Well-watered1_44d_rewater1_rep2


title: D5_IDH2-R140Q

value: HSPCs donor D


title: refr_6_hpa_B

value: 6 hours post amputation


title: Well-watered1_44d_rewater1_rep1


title: refr_0.5_hpa_B

value: 0.5 hours post amputation


title: D4_IDH2-Wt


title: D3_IDH1-R132H


title: refr_0_hpa_B

value: 0 minutes post amputation


title: 18317X3 EV 3

source_name: EV

value: CD4+GFP+Ly5.1+Ly5.2+ (EV) cells


title: refr_72_hpa_A


title: 18317X2 EV 2

value: spleen


title: Drought4_44d_rep2


title: D2_IDH1-Wt


title: 18317X1 EV 1


title: D1_AAVS1


title: Drought3_44d_rep3


title: Drought3_44d_rep2


title: Drought4_44d_rep1


title: L1EHA0400858--panc1_Med12_sg5_3

city: Shanghai

first: JIng

last: Xue

address: No.1630 dongfang road, pudong new district, Shanghai

institute: Renji Hospital, School of Medicine,Shanghai Jiaotong University

description:
human PDAC cell line_gene.TPM.matrix.annot.xls
human PDAC cell line_gene.count.matrix.annot.xls

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to hg38 with orientation mode using HISAT2  software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
differential expression analysis was performed using the DESeq2
Assembly: GRCh38
Supplementary files format and content: excel sheet includs tpm of each sample
Supplementary files format and content: excel sheet includs count of each sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA)

tag: cell line

value: Pancreatic tumor cell

value: Med12 Knockout


title: Leptomeninges, Young_2

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description:
RNA was isolated from the brains of 5 mice.
total mRNA
3' RNAseq

data_processing:
Illumina bcl2fastq software used for basecalling.
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as tar archives containing count, barcode, and gene matrices.
Assembly: mm10
Supplementary files format and content: Tar archives containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes (matrix.mtx, features.tsv, barcodes.tsv).

source_name: Leptomeninges

extract_protocol:
10x Genomics Chromium single-cell preparation.
NGS Illumina Next Seq.

value: Leptomeninges

tag: gender

value: male

value: 2-3 months


title: refr_6_hpa_A

value: tail


title: refr_0.5_hpa_A


title: Drought3_44d_rep1


title: Drought4_44d_rep3


title: L1EHA0400857--panc1_Med12_sg5_2

tag: cell type


title: Leptomeninges, Aged

value: 20 months


title: refr_0_hpa_A


title: ctrl_72_hpa_D

value: 72 hours post amputation

value: regeneration


title: Well-watered2_44d_rep3

value: Nipponbare


title: L1EHA0400856--panc1_Med12_sg5_1


title: Leptomeninges, EAE

value: MOG35-55 peptide


title: ctrl_6_hpa_D

value: amputated


title: Leptomeninges, Young_1


title: 18317X4 OE 1

value: GFP+Ly5.1+ (OCA-B-expressing) cells


title: Well-watered2_44d_rep2


title: Leptomeninges, Control

value: Control


title: Well-watered2_44d_rep1


title: L1EHA0400855--panc1_Med12_sg4_3


title: Unvaccinated, replicate 2 [unvax2]

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Pulmonary immune cells from unvaccinated mice, replicate 2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: rds

source_name: Lung

extract_protocol:
Bronchoalveolar lavage was performed by exposing the trachea of euthanized mice, puncturing the trachea with Vannas Micro Scissors (VWR) and injecting 1 mL PBS using a 20G-1” IV catheter (McKesson) connected to a 1 mL syringe. The PBS was flushed into the lung and then aspirated three times and the recovered fluid was placed in a 15mL tube on ice. The wash was repeated 3 additional times. Cells were filtered and spun down.
Libraries were prepared according to the manufacter’s instructions (single cell Gene Expression 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

treatment_protocol: BCG-Pasteur was cultured in Middlebrook 7H9 broth at 37°C to an OD of 0.1–0.3. Bacteria was diluted in PBS and 1e6 CFU in 200 ml was injected sub-cutaneously. For establishment of CoMtb, 1e4 CFU of Mtb (H37Rv) in logarithmic phase growth were injected intradermally in 10 μL PBS.

value: Lung

value: Multiple

value: unvaccinated


title: L1EHA0400854--panc1_Med12_sg4_2

value: Pancreatic tumor cell


title: ctrl_0_hpa_D

value: 0 minutes post amputation


title: L1EHA0400853--panc1_Med12_sg4_1

value: Med12 Knockout


title: Unvaccinated, replicate 1 [unvax1]

description: Pulmonary immune cells from unvaccinated mice, replicate 1


title: ctrl_72_hpa_C


title: L1EHA0400852--panc1_lacz_3

value: WT


title: ctrl_0.5_hpa_C

value: 0.5 hours post amputation


title: Drought2_44d_rep1


title: Drought2_44d_rep2


title: L1EHA0400850--panc1_lacz_1


title: L1EHA0400851--panc1_lacz_2


title: Drought2_44d_rep3


title: Drought1_44d_rep3


title: ctrl_0_hpa_C

value: tail


title: BCG vaccinated, replicate 1 [scBCG1]

description: Pulmonary immune cells from BCG-vaccinated mice, replicate 1

value: scBCG


title: CoMtb, replicate 1 [cotb1]

description: Pulmonary immune cells from mice with contained Mtb infection, replicate 1

value: CoMtb


title: L1EHA0400849--Mia_Med12_sg5_3


title: ctrl_72_hpa_B

value: 72 hours post amputation

value: regeneration


title: BCG vaccinated, replicate 2 [scBCG2]

description: Pulmonary immune cells from BCG-vaccinated mice, replicate 2


title: ctrl_0.5_hpa_D


title: Drought1_44d_rep1

value: Nipponbare


title: CoMtb, replicate 2 [cotb2]

description: Pulmonary immune cells from mice with contained Mtb infection, replicate 2


title: Well-watered1_44d_rep3


title: unvaccinated, unstimuluated, replicate 2 [unvax.none.2]

data_processing:
Stranded paired-end reads of length 151 bp were preprocessed: The first three nucleotides of R2  were removed as described in the SMARTer Stranded RNA-Seq Kit  User Manual and read ends consisting of 100 or more of the same nucleotide were removed.
The remaining read pairs were aligned to the mouse genome (mm10) + Mtb H37Rv genome using the gsnap aligner (v. 2018-07-04) allowing for novel splicing. (gsnap options: -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 )
Concordantly mapping read pairs (average 20-million / sample) that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Assembly: mm10 + Mtb H37Rv
Supplementary files format and content: rawCounts.tsv contains the raw counts for each sample generated by subRead, tab-separated

growth_protocol: Cells were plated at a density of 5e4 cells/well (96-well plate) in complete RPMI (RPMI plus FBS (10%, VWR), L-glutamine (2mM, Invitrogen), and Penicillin-Streptomycin (100 U/ml; Invitrogen) and allowed to adhere overnight in a 37°C humidified incubator (5% CO2). Media with antibiotics were washed out prior to infection with M. tuberculosis.

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
cDNA libraries were constructed and amplified using the SMARTer Stranded RNA-Seq Kit (Clontech) per the manufacturers instructions. Libraries were amplified and then sequenced on an Illumina NovaSeq 6000 (2 x 151, paired-end).

value: Alveolar macrophages

value: unvax

tag: stimulus


title: ctrl_6_hpa_B

value: 6 hours post amputation

value: amputated


title: unvaccinated, unstimuluated, replicate 3 [unvax.none.3]

value: Lung


title: ctrl_6_hpa_C


title: L1EHA0400848--Mia_Med12_sg5_2


title: L1EHA0400847--Mia_Med12_sg5_1


title: L1EHA0400846--Mia_Med12_sg4_3


title: unvaccinated, unstimuluated, replicate 1 [unvax.none.1]


title: Drought1_44d_rep2

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MSU7 gene models using the STAR aligner (Dobin et al., 2013)
Read counts were quantified using the featureCounts (Liao et al., 2014) with option” -S 2 -p -B -C -T”.
Supplementary files format and content: Tab-delimited text files include row counts for each Sample

extract_protocol:
Total RNA was extracted using TRIzol RNA Isolation Reagents (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs)


title: Drought4_41d_rep3


title: L1EHA0400844--Mia_Med12_sg4_1


title: L1EHA0400843--Mia_lacz_3


title: unvaccinated, PAM3CSK4 stimuluated, replicate 2 [unvax.pam.2]

value: pam


title: Well-watered1_44d_rep2


title: L1EHA0400845--Mia_Med12_sg4_2

value: Pancreatic tumor cell


title: unvaccinated, PAM3CSK4 stimuluated, replicate 3 [unvax.pam.3]


title: Drought4_41d_rep2


title: ctrl_72_hpa_A


title: unvaccinated, PAM3CSK4 stimuluated, replicate 1 [unvax.pam.1]


title: Drought4_41d_rep1


title: unvaccinated, lps stimuluated, replicate 3 [unvax.lps.3]

value: lps


title: ctrl_0_hpa_A

value: 0 minutes post amputation


title: ctrl_0.5_hpa_B


title: L1EHA0400842--Mia_lacz_2

value: WT


title: L1EHA0400841--Mia_lacz_1


title: Drought3_41d_rep3


title: unvaccinated, lps stimuluated, replicate 2 [unvax.lps.2]


title: unvaccinated, lps stimuluated, replicate 1 [unvax.lps.1]


title: 7-dpa-C_regeneration

data_processing:
Reads were filtered for low quality reads and adaptor sequences, using TrimmomaticPE (v. 0.36), while ribosomal RNA reads were filtered out using Sortmerna (v. 2.1b) (default parameters).
The cleaned reads were then aligned using STAR (v. 2.7.9a) to the Xenopus laevis genome version 10.1 and annotation version XENLA_10.1_GCF.
A count table was then generated using the python script htseq-count (v. 0.6.1p1) with the parameter “–m union”. The counts were normalized and analyzed using DESeq2 (v. 1.32.0)[84] under R (v. 4.1.0).
Outlier samples were assessed by analyzing the PCA of the 500 most variable genes.
Assembly: Xenopus laevis genome version 10.1
Supplementary files format and content: 01_bulk_data_non_normalized.xlsx: non-normalized count data
Supplementary files format and content: 01_bulk_data_normalized.xlsx: median of ratios normalized data using DESeq2. Outlier samples were removed.

treatment_protocol: Bulk RNA-Seq analysis was done to analyze the temporal changes in gene expression during the regeneration  periods of 0, 0.5, 1.5, 3, 6 hpa and 1, 3, 7 dpa. The experiment was done in biological triplicates.

value: 7 days post amputation


title: 7-dpa-B_regeneration

value: tail


title: ctrl_0_hpa_B


title: GD2.CAR(I)IL12 in vivo R3

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Alignment: STAR (v.2.7.6a)
Quantification: Salmon (v.1.4.0)
QA: FastQC (v0.11.9)
QA: Picard (v2.22.4) CollectRnaSeqMetrics
Assembly: Ensembl release 99, GRCh38
Supplementary files format and content: Salmon count data

source_name: Extracted from M musculus peripheral blood

growth_protocol: Buffy coats from healthy volunteer blood donors were purchased from the Gulf Coast Regional Blood Center (Houston, Texas, USA). Peripheral blood mononuclear cells (PBMCs) were isolated by Lymphoprep (Accurate Chemical and Scientific Corporation) density gradient centrifugation. NKTs were purified from PBMCs as previously described. NKTs were transduced in retronectin coated plates on day 5 and further expanded for 10 days in the presence of IL-2 and then used for functional assays.

extract_protocol:
Total RNA was extracted from NKTs using the Rneasy Plus Mini kit (Qiagen) per manufacturers instructions.
Messenger RNA libraries were prepared (TruSeq Stranded mRNA LibraryPrep, Illumina) and sequenced on the Illumina HiSeq4000 platform (UNC High-Throughput Sequencing Facility) using paired-end 100-bp reads, with 44 million reads on average (range, 1.5-149 million).

treatment_protocol: All retroviral vectors were generated using the SFG backbone. The sequence of the p40 and p35 subunits of IL-12 were obtained from the NCBI website (NM_002187.2 and NM_000882.2 respectively) and were linked together with a flexible linker described from Anderson R. et al. through overlapping PCR. The whole IL-12 cassette was cloned into the SFG retroviral vector containing the IRES and GFP or ∆NGFR. As control the vector SFG containing the IRES and GFP or ∆NGFR only was used. The GD2.CAR, CSPG4.CAR and CD19.CAR were previously described. IL-12 was then cloned in the CAR cassettes separated by the IRES element (GD2.CAR(I)IL12, CSPG4.CAR(I)IL12 and CD19.CAR(I)IL12). The sequence of CD62L (SELL) was obtained from NCBI (NM_000655) and made by gene synthesis (Genewiz, Azenta Life Sciences) and cloned in the SFG vector containing the IRES and the ∆NGFR as selection marker. The sequence of CD1d (CD1D) was obtained from NCBI (NM_001766.3) and made by gene synthesis (Genewiz, Azenta Life Sciences) and cloned in the SFG vector. To generate the membrane-bound IL-12 we added the CD8α stalk with the mutations C164S and C181S to prevent dimerization with the CAR. Retroviral supernatants were prepared by transient transfection of 293T cells.

value: Human NKT

value: GD2.CAR + IL12 transduced, injected into mice bearing CHLA-255 tumor


title: Well-watered1_44d_rep1


title: ctrl_0.5_hpa_A

value: 0.5 hours post amputation


title: unvaccinated, mtb stimuluated, replicate 2 [unvax.mtb.2]

value: mtb


title: 7-dpa-A_regeneration


title: Drought3_41d_rep1

value: Nipponbare


title: ctrl_6_hpa_A

value: regeneration


title: 3-dpa-B_regeneration

value: 3 days post amputation


title: IL12(I)GFP in vivo R3

value: Extracted from M musculus peripheral blood

value: IL12 + GFP transduced, injected into mice bearing CHLA-255 tumor


title: unvaccinated, mtb stimuluated, replicate 3 [unvax.mtb.3]

value: Lung

value: Alveolar macrophages

value: unvax


title: Well-watered2_41d_rep3


title: GD2.CAR(I)IL12 in vivo R2


title: IL12(I)GFP in vivo R2


title: GD2.CAR(I)IL12 in vivo R1


title: 3-dpa-A_regeneration

value: amputated


title: CoMtb, unstimuluated, replicate 2 [cotb.none.2]

description: CoMtb, unstimuluated, replicate 2

value: cotb


title: CoMtb, unstimuluated, replicate 3 [cotb.none.3]

description: CoMtb, unstimuluated, replicate 3


title: carnation petal, full blooming, rep2, Input [In-E0h-2]

value: petal


title: CoMtb, unstimuluated, replicate 1 [cotb.none.1]

description: CoMtb, unstimuluated, replicate 1


title: Drought2_41d_rep3


title: Drought3_41d_rep2


title: 1-dpa-B_regeneration

value: 1 day post amputation


title: BM, C12, UPN#1

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing analysis was carried out using 10X Genomics’ CellRanger software. Fastq files were generated using the CellRanger mkfastq pipeline.
Raw reads were mapped to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using the CellRanger count pipeline. The expression matrices from different samples were concatenated.
Assembly: hg38
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

extract_protocol:
FACS-purified live BM MNCs cells were sequenced at the Advanced Technology Genomics Core facility at MDACC. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific) and manual counting.
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented for library preparation. Pooled libraries were sequenced on a NovaSeq6000 SP 100-cycle flow cell (Illumina, San Diego, CA).

value: Bone Marrow

value: Bone Marrow Derived Mononuclear Cell

value: Venetoclax-based therapy


title: IL12(I)GFP in vivo R1

value: Human NKT


title: Drought2_41d_rep2

city: Tsukuba

first: FUMIYUKI

last: SOMA

address: 2-1-2 Kan-non-dai


title: unvaccinated, mtb stimuluated, replicate 1 [unvax.mtb.1]

value: mtb


title: Well-watered2_41d_rep2

value: Nipponbare


title: IL12(I)GFP in vivo R4


title: 3-dpa-C_regeneration

value: tail


title: Drought2_41d_rep1


title: 1-dpa-C_regeneration


title: BM, C8, UPN#1


title: CoMtb, PAM3CSK4 stimuluated, replicate 3 [cotb.pam.3]

value: pam


title: 1-dpa-A_regeneration


title: Drought1_41d_rep3


title: 6-hpa-C_regeneration

value: 6 hours post amputation


title: CoMtb, PAM3CSK4 stimuluated, replicate 2 [cotb.pam.2]


title: Drought1_41d_rep2


title: CoMtb, PAM3CSK4 stimuluated, replicate 1 [cotb.pam.1]


title: BM, C7, UPN#1


title: BM, C4, UPN#1, replicate 2


title: 6-hpa-B_regeneration


title: Well-watered2_41d_rep1


title: 6-hpa-A_regeneration


title: CoMtb, lps stimuluated, replicate 2 [cotb.lps.2]

description: CoMtb, lps stimuluated, replicate 2

value: lps


title: Drought1_41d_rep1


title: BM, C4, UPN#1, replicate 1


title: CoMtb, lps stimuluated, replicate 3 [cotb.lps.3]

description: CoMtb, lps stimuluated, replicate 3

value: Lung


title: 3-hpa-C_regeneration

value: 3 hours post amputation


title: Well-watered1_41d_rep3


title: BM, C2, UPN#1, replicate 2


title: 3-hpa-B_regeneration


title: Well-watered1_41d_rep1


title: CoMtb, mtb stimuluated, replicate 3 [cotb.mtb.3]

description: CoMtb, mtb stimuluated, replicate 3

value: Alveolar macrophages


title: Well-watered1_41d_rep2


title: CoMtb, lps stimuluated, replicate 1 [cotb.lps.1]

description: CoMtb, lps stimuluated, replicate 1


title: BM, C1, UPN#1, replicate 2


title: 3-hpa-A_regeneration

value: amputated


title: Drought4_38d_rep3


title: CoMtb, mtb stimuluated, replicate 2 [cotb.mtb.2]

description: CoMtb, mtb stimuluated, replicate 2

value: cotb


title: BM, C1, UPN#1, replicate 1


title: CoMtb, mtb stimuluated, replicate 1 [cotb.mtb.1]

description: CoMtb, mtb stimuluated, replicate 1


title: BM, C2, UPN#1, replicate 1


title: Drought4_38d_rep1


title: BM, C0, UPN#1, replicate 2


title: 60-mpa-C_regeneration

value: 60 minutes post amputation


title: BCG vaccinated, unstimuluated, replicate 2 [scBCG.none.2]

value: scBCG


title: 90-mpa-A_regeneration

value: 90 minutes post amputation


title: BM, C8, UPN#2

value: Bone Marrow

value: Bone Marrow Derived Mononuclear Cell


title: BM, C9, UPN#2

value: Venetoclax-based therapy


title: BCG vaccinated, PAM3CSK4 stimuluated, replicate 3 [scBCG.pam.3]


title: 60-mpa-A_regeneration


title: Drought3_38d_rep2


title: BCG vaccinated, PAM3CSK4 stimuluated, replicate 2 [scBCG.pam.2]


title: 30-mpa-C_regeneration

value: 30 minutes post amputation


title: 60-mpa-B_regeneration


title: Well-watered2_38d_rep3

value: Nipponbare


title: Drought3_38d_rep1


title: BCG vaccinated, PAM3CSK4 stimuluated, replicate 1 [scBCG.pam.1]


title: BM, C2, UPN#2


title: 90-mpa-C_regeneration

value: tail


title: BCG vaccinated, unstimuluated, replicate 3 [scBCG.none.3]


title: Well-watered2_38d_rep2


title: 90-mpa-B_regeneration


title: BM, C2, UPN#3


title: Drought3_38d_rep3


title: Drought4_38d_rep2


title: BM, C0, UPN#1, replicate 1


title: BCG vaccinated, lps stimuluated, replicate 3 [scBCG.lps.3]


title: 30-mpa-A_regeneration


title: Well-watered2_38d_rep1


title: BCG vaccinated, unstimuluated, replicate 1 [scBCG.none.1]


title: BM, C0, UPN#2


title: BM, C1, UPN#3


title: BCG vaccinated, lps stimuluated, replicate 2 [scBCG.lps.2]


title: 30-mpa-B_regeneration


title: BM, C0, UPN#3


title: BCG vaccinated, lps stimuluated, replicate 1 [scBCG.lps.1]


title: Drought2_38d_rep3


title: Drought2_38d_rep2


title: Plasma small RNA, sporadic woman (AAA4616179), breast cancer

city: L'Hospitalet del llobregat

first: Miquel Angel

last: Pujana

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals

department: ProCURE

country: Spain

institute: Catalan Institute of Oncology IDIBELL

data_processing:
Sequencing was done on Illumina’s NovaSeq 6000, using v1.5 SP 100 cycle reagents with XP workflow
Sequencing data were demultiplexed using Illumina’s bcl2fastq software to generate fastq files for each sample
Samples were analyzed using the exceRpt small RNA pipeline
Trimming of 4 bp from both the 5’ and 3’ end of the sequencing data
Assembly: hg38
Supplementary files format and content: tab-delimited raw counts per sample
Supplementary files format and content: tab-delimited CPM values per sample

molecule: other

source_name: Blood

growth_protocol: Blood samples were collected in EDTA or heparinized tubes

extract_protocol:
Plasma small RNAs were isolated using the Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen Biotek), washed and concentrated using the RNeasy MinElute Cleanup Kit (74204, QIAGEN)
Small RNA libraries were generated using NEXTflex Small RNA Library Prep Kit v3 following the manufacturer’s instructions

treatment_protocol: For plasma collected in heparinized tubes, the RNA samples were further purified using a heparinase-based protocol (Kondratov et al., Biomol. Detect. Quantif. 8, 9–14 (2016))

value: Blood

value: Plasma

value: Adult woman, 44 yr

value: XX

value: Plasma heparinase-treated


title: Plasma small RNA, sporadic woman (AAA3871759), cancer-free

value: Adult woman, 45 yr


title: BCG vaccinated, mtb stimuluated, replicate 3 [scBCG.mtb.3]

value: Lung

value: Alveolar macrophages

value: mtb


title: BCG vaccinated, mtb stimuluated, replicate 2 [scBCG.mtb.2]

value: scBCG


title: Plasma small RNA, sporadic woman (AAA6102584), cancer-free

value: Adult woman, 53 yr


title: 0-mpa-A_regeneration

value: 0 minutes post amputation

value: amputated


title: 0-mpa-C_regeneration


title: Drought2_38d_rep1

institute: National Agriculture and Food Research Organization


title: Drought1_38d_rep2


title: BCG vaccinated, mtb stimuluated, replicate 1 [scBCG.mtb.1]


title: MBP.R1

city: Wuhan

first: Faming

last: Zhao

state: Hubei

address: Hangkong road 13

department: Tongji Medical College

institute: Huazhong University of Science and Technology

description: CUT&Tag

data_processing:
For RNA-seq FASTQ files, the pseudocounts generated by Salmon are represented as normalized TPM (transcripts per million) counts and map to transcripts.
We conducted ATAC-seq downstream analysis with FASTQ files, following the ATAC-seq guideline tutorial (https://informatics.fas.harvard.edu/atac-seq-guidelines.html). Briefly, the overall quality of sequencing reads was evaluated using FastQC (v0.11.9). After quality control, we aligned them to the hg38 reference genome using the Bowtie2 (v2.4.5). PCR duplicates were removed by Sambamba (v1.0.0), and the BAM files were then indexed by Samtools (v1.7). ATAC peak calling was performed using Macs2 (v2.2.7.1). Visualization was conducted using Deeptools (v.3.5.1), IGV (v.2.9.4) and R package ChIPseeker (v.1.34.1). Differential binding analysis was performed using DiffBind (v.3.8.4).
Data analysis on CUT&Tag sequencing reads was performed following CUT&Tag data processing and analysis tutorial (https://yezhengstat.github.io/CUTTag_tutorial/).
Genome_build: hg38
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for each gene and each sample
Supplementary files format and content: MBP_HepG2_L02_TPM.data.xlsx

growth_protocol: HCC cells were cultured in regular growth medium (DMEM + 10% FBS + 1%P/S)

extract_protocol:
For Bulk RNA-seq, the TruSeq stranded RNA sample prep kit was used for library generation according to Illumina's protocol. For ATAC-seq, the cells were then harvested for ATAC-seq and carried out at Biomarker Technologies Corporation (Beijing, China). For CUT&Tag-seq, the cells were then harvested for CUT&Tag seq analysis using reagents from Vazyme (#TD904, China) according to the manufacturer's instructions.
For Bulk RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols. ATAC-seq was carried out at Biomarker Technologies Corporation (Beijing, China).  CUT&Tag-seq was performed by using reagents from Vazyme (#TD904, China) according to the manufacturer's instructions.
RNA-seq, ARAC-seq or CUT&Tag

treatment_protocol: MBP (5 nM) or Vehicle

value: human HCC cell line

value: MBP, P30


title: MBP.R2

description: CUT&Tag


title: Drought1_38d_rep1

value: Nipponbare


title: Plasma small RNA, sporadic woman (AAA4619553), breast cancer

value: Adult woman, 43 yr


title: Ctrl2.R1

description: CUT&Tag

value: Vehicle, P30


title: 0-mpa-B_regeneration

value: tail


title: sod1_aso3_10

city: St. Louis

first: Abhirami Kannan

last: Iyer

state: MISSOURI

address: 425 South euclid ave, BJC Institute of Health, Room 9202

department: Psychiatry

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions. KEGG and WikiPathways (species: Mus musculus, year queried: 2019) were used to derive functional annotations of the differentially expressed genes into pathways.
Genome_build: Mouse Ensembl GRCm38.76

source_name: primary mouse astrocytes

growth_protocol: Primary murine astrocytes used in this study were generated from the cortices of post-natal day 2 (P2) pups from SOD1*G93A mice as described before.

extract_protocol:
Primary mouse astrocytes were monitored for their viability post-nucleofection and were harvested 96 hours later. Total RNA extraction was performed using RNeasy Mini Kit (Qiagen, 74104).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: primary mouse astrocytes were harvested by trypsinization, and after determining cell counts, cells were centrifuged at 100xg for 10 minutes at room temperature. 1-2x106 cells were used for each nucleofection with a non-targeting negative control A (control ASO) or Atp1a2-specific ASOs using the P3 Primary Cell 4D-NucleofectorTM X Kit (Lonza, V4XP-3032) following the manufacturer’s protocol and CL-133 program optimized for primary mouse astrocytes in the 4D Nucleofector™ unit.

value: primary mouse astrocytes

tag: strain

value: B6SJL-Tg (SOD1*G93A)1Gur/J

value: Atp1a2 ASO3


title: Well-watered1_38d_rep3


title: IgG.R1

description: CUT&Tag


title: Plasma small RNA, sporadic woman (AAA1848147), cancer-free

value: Blood

value: Plasma

value: Adult woman, 54 yr

value: XX

value: Plasma heparinase-treated


title: Well-watered1_38d_rep2


title: Plasma small RNA, sporadic woman (AAA4274678), breast cancer

value: Adult woman, 55 yr


title: Plasma small RNA, sporadic woman (AAA3232188), breast cancer

value: Adult woman, 50 yr


title: Plasma small RNA, sporadic woman (AAA4831873), cancer-free

value: Adult woman, 49 yr


title: Drought1_38d_rep3


title: Ctrl1.R1

description: CUT&Tag

value: human HCC cell line


title: sod1_aso3_08


title: sod1_aso3_09


title: HepG2-MBP-2

description: ATAC-seq

value: MBP, P30


title: Well-watered1_38d_rep1

value: Nipponbare


title: sod1_aso3_02


title: Plasma small RNA, sporadic woman (AAA4017033), breast cancer

value: Adult woman, 62 yr


title: Drought4_35d_rep3


title: Drought4_35d_rep2


title: HepG2-MBP-1

description: ATAC-seq


title: Plasma small RNA, sporadic woman (AAA1603863), cancer-free

value: Adult woman, 63 yr


title: HepG2-Ctrl-2

description: ATAC-seq

value: Vehicle, P30


title: sod1_aso1_10

value: primary mouse astrocytes

value: Atp1a2 ASO1


title: sod1_aso3_05

value: B6SJL-Tg (SOD1*G93A)1Gur/J

value: Atp1a2 ASO3


title: sod1_aso1_09


title: Drought4_35d_rep1


title: Drought3_35d_rep3


title: Plasma small RNA, sporadic woman (AAA3244026), breast cancer

value: Blood

value: Plasma

value: Adult woman, 59 yr


title: Plasma small RNA, sporadic woman (AAA1868074), cancer-free

value: Adult woman, 58 yr

value: XX

value: Plasma heparinase-treated


title: L02_P30_MBP-1

description: RNA-seq

value: human liver cell line


title: Plasma small RNA, sporadic woman (AAA1866333), breast cancer

value: Adult woman, 51 yr


title: sod1_aso1_07


title: Drought3_35d_rep1


title: L02_P30_MBP-2

description: RNA-seq

value: MBP, P30


title: Drought3_35d_rep2

value: Nipponbare


title: sod1_aso1_08


title: HepG2-Ctrl-1

description: ATAC-seq

value: human HCC cell line


title: Plasma small RNA, sporadic woman (AAA3259949), cancer-free


title: L02_P30_ctrl-1

description: RNA-seq


title: Well-watered2_35d_rep3


title: sod1_aso1_01


title: Well-watered2_35d_rep2


title: sod1_ctrl_10

value: control ASO


title: Plasma small RNA, sporadic woman (AAA4270971), cancer-free

value: Adult woman, 57 yr


title: sod1_ctrl_09

value: primary mouse astrocytes


title: L02_P10_MBP-2

description: RNA-seq

value: MBP, P10


title: Well-watered2_35d_rep1


title: Plasma small RNA, woman BRCA2 mutation carrier (2010/10348), cancer-free

value: Adult woman, 67 yr

value: Plasma EDTA


title: L02_P10_MBP-1

description: RNA-seq


title: sod1_ctrl_08

value: B6SJL-Tg (SOD1*G93A)1Gur/J


title: Drought2_35d_rep3


title: sod1_ctrl_05


title: Plasma small RNA, woman BRCA1 mutation carrier (2009/8977), cancer-free

value: Blood

value: Plasma

value: Adult woman, 63 yr


title: L02_P10_ctrl-2

description: RNA-seq

value: Vehicle, P10


title: Plasma small RNA, sporadic woman (AAA1643538), breast cancer

value: XX

value: Plasma heparinase-treated


title: Drought2_35d_rep2


title: sod1_ctrl_02


title: Plasma small RNA, woman BRCA1 mutation carrier (2008/7521), cancer-free

value: Adult woman, 62 yr


title: L02_P10_ctrl-1

description: RNA-seq

value: human liver cell line


title: Drought2_35d_rep1

value: Nipponbare


title: Plasma small RNA, woman BRCA1 mutation carrier (2007/6321), cancer-free

value: Adult woman, 60 yr


title: Drought1_35d_rep3


title: DscamKO-5, RNASeq

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

institute: The National Institutes of Natural Sciences NINS

data_processing:
The RNA-seq libraries were each sequenced (151 cycles) using the Illumina NovaSeq platforms.
Raw sequence reads were aligned to the reference mouse genomes (GRCm38) by HISAT2.
Genome-wide expression levels were measured as a unit of transcripts per kilobase million (TPM) using StringTie and the numbers of reads were counted per gene per sample using htseq-count within HTSeq.
Differentially expressed genes (DEGs) were identified by DESeq2.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include TPM values

source_name: cerebellum

extract_protocol:
Total RNA was extracted from cerebellum tissues of 5 control and 5 KO mice at P21 using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively.
Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) and the KAPA HTP Library Preparation Kits (KAPA Biosystems) according to the manufacturer’s instructions. The RNA-seq libraries were each sequenced (151 cycles) using the Illumina NovaSeq platforms.

value: BALB/c

value: cerebellum

value: DscamKO


title: HepG2_P30_MBP-2

description: RNA-seq

value: human HCC cell line

value: MBP, P30


title: DscamKO-4, RNASeq


title: HepG2_P30_MBP-1

description: RNA-seq


title: Plasma small RNA, woman BRCA2 mutation carrier (2010/10056), cancer-free

value: Adult woman, 52 yr

value: Plasma EDTA


title: Drought1_35d_rep2


title: Plasma small RNA, woman BRCA2 mutation carrier (2009/9469), cancer-free

value: Blood

value: Adult woman, 49 yr


title: Plasma small RNA, woman BRCA1 mutation carrier (2008/8190), cancer-free

value: Plasma

value: Adult woman, 38 yr


title: L02_P30_ctrl-2

description: RNA-seq

value: Vehicle, P30


title: HepG2_P30_ctrl-1

description: RNA-seq


title: DscamKO-3, RNASeq


title: DscamKO-1, RNASeq


title: DscamKO-2, RNASeq


title: Well-watered1_35d_rep3


title: Plasma small RNA, woman BRCA1 mutation carrier (2010/09680), cancer-free

value: Adult woman, 35 yr

value: XX


title: Well-watered1_35d_rep2


title: Control-5, RNASeq

value: Control


title: Plasma small RNA, woman BRCA2 mutation carrier (2010/10666), cancer-free


title: HepG2_P10_MBP-1

description: RNA-seq

value: MBP, P10


title: Well-watered1_35d_rep1

value: Nipponbare


title: HepG2_P10_ctrl-2

description: RNA-seq

value: Vehicle, P10


title: Control-4, RNASeq

value: BALB/c

value: cerebellum


title: Plasma small RNA, woman BRCA1 mutation carrier (2006/5458), cancer-free

value: Adult woman, 34 yr


title: Drought4_32d_rep3


title: HepG2_P30_ctrl-2

description: RNA-seq

value: human HCC cell line


title: Control-3, RNASeq


title: HepG2_P10_ctrl-1

description: RNA-seq


title: Drought1_35d_rep1


title: AC16  treated 12h with 5µM of Digoxin-rep3

type: RNA

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 3.5microgrammes of ssDNA were hybridized for 16 hr at 45C on HuGene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on gene level with NetAffx Annotation Release 36.
HuGene2.0ST.mps
HuGene-2_0-st-v1.na36.hg19.probeset.csv
Log2 RMA

label: biotin

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: DMEM/F12 [D6434] + L-glutamine + P/S + 12,5% SVF

extract_protocol: Total RNA was extracted using Nucleospin RNA kit from Macherey Nagel according to the manufacturer's instructions.

treatment_protocol: 2h synchronization (100nM dexamethasone) then 5microM Digoxin during 0-6-12-18 or 24h. Vehicule = chloroform/ethanol


title: Plasma small RNA, woman BRCA2 mutation carrier (2009/9490), cancer-free

value: Adult woman, 33 yr


title: Drought4_32d_rep2


title: Control-2, RNASeq


title: HepG2_P10_MBP-2

description: RNA-seq


title: Plasma small RNA, woman BRCA2 mutation carrier (2008/7882), cancer-free

value: Adult woman, 32 yr

value: Plasma EDTA


title: Drought4_32d_rep1


title: Plasma small RNA, woman BRCA2 mutation carrier (2011/10994), breast cancer

value: Blood

value: Adult woman, 61 yr


title: Control-1, RNASeq


title: Suv39h1 knockdown under hypoxia rep3 [RNA]

city: Beijing

first: Wang

last: Li

address: 167 Beilishi Rd

department: State Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences

data_processing:
The script for RNAseq analysis can be found in github (https://github.com/zhaoshuoxp/Pipelines-Wrappers/blob/master/RNAseq.sh). Briefly, QC of sequencing data was performed using fastqc. Then STAR was used to map the reads to the reference genome (mm10).
FeatureCounts from the Subread package was then used to count the number of reads mapped, and DESeq2 was used to generate the list of differentially regulated genes based on the FDR <0.05 filtering.
Assembly: mm10
Supplementary files format and content: text, raw reads counts on each gene

source_name: Heart

growth_protocol: Neonatal cardiac ECs were used for validation of gene knockdown and overexpression prior to actual modification in adult cardiac ECs used in in vivo experiments. The hearts of neonatal mice were excised, washed with PBS, and cut into small pieces (approximately 1mm3). After centrifugation, the supernatant was discarded, and 1 ml of 2 mg/ml Collagenase II (Gibco, 17101015) and 20µg/ml DNase I (Thermo Fisher, EN0521) was added. Tissue was digested at 37 ° C for 30 min using magnetic stirring. After neutralization, the supernatant was discarded by centrifugation. Red blood cells were lysed, and cells were washed with FACS liquid. Then, cells were incubated with CD31 MicroBeads. The remaining steps were the same as in adult mouse EC purification. The hearts of 5 neonatal mice were placed in one well of a six-well plate, and the hearts of 3 neonatal mice were placed in one confocal dish.

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kits (Qiagen, #74034).
RNA was extracted from primary neonatal mice cardiac endothelial cells transfected with lentivirus by the GeneJET RNA Purification Kit (Thermo, K0732). Sequencing libraries were prepared using the TruSeq RNA Library Prep Kit V2(RS-122-2002, Illumina) according to manufacturer’s instructions. All libraries were sequenced on the NextSeq500 sequencer (FC-404-2005, Illumina) using the 35nt paired-end sequencing protocol.

treatment_protocol: shRNA sequences were designed as follows:  shsuv39h1: CGAGTCCGTATTGAATGCAAA. shRNA was cloned into the pLKO1 lentivirus-based vector;  The overexpression sequence was designed as follows.  F: TTAGAATTCGCCACCATGAAGACGAAGTCCACATGTGCTCAGA  R:GTAGGATCCTTAGGGGTCGGAGGTCAATCCCCCT.   cDNA was cloned into the pCDH lentivirus-based vector, and lentivirus was packaged according to manufacturer’s instructions. Adult and neonatal cardiac endothelial cells were transduced with corresponding lentiviruses at approximately 80% confluency. After 24 hours of infection, the adult endothelial normal medium was changed, the cells were digested with trypsin after another 72 hours. For injection into infarcted hearts, cell suspensions of 1×105 cells were prepared. For validation of gene knockdown and overexpression by qPCR, RNA was extracted at 48 h after transduction. Confocal dishes of neonatal ECs were used to demonstrate the effect of gene modulation on the level of H3K9me3.

value: Heart

value: endothelial

tag: protocol

value: Suv39h1 knockdown under hypoxia


title: old mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 3

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

address: 1170 Veterans blvd

institute: Calico

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_24m_3

data_processing:
PacBio SMRT LINK V11 software to generate circular consensus sequences (CCS), requiring a predicted accuracy ≥ Q20.
mm10 + Gencode vM25 primary assembly annotation
demultiplex.<sample_name>.bam is a file containing the CCS demultipled reads

source_name: spleen

extract_protocol:
Spleens were removed by dissection, transferred to a sterile petri dish containing PBS with 5% FBS, and minced using surgical blades. Spleen fragments were then ground through 100 μm and 40 μm cell strainers, pelleted, and resuspended in the ACK lysis buffer as described in the thymus tissue collection section. Cell density and viability were determined using Countness II Cell Counter. Subsequently, splenocytes were resuspended at 1 million cells per ml of 0.04% BSA/PBS. In order to sort out the splenocyte T-cell subsets for constructing 10× GEM single-cell libraries, splenocytes were resuspended at 1 million cells per ml of FACS buffer (PBS with 1% FBS and 5mM EDTA).splenocytes were pre-incubated with 1ug mouse Fc blocker (BD 553141) per 1 million cells/100ul FACS buffer for 5 minutes, and incubated with an anti-mouse CD3e (clone 17A2, eFlour450, 2 ug/ml) and an anti-mouse CD11b (M1/70, Alexa 488, 2 ug/ml) on ice for 40 minutes.after incubation, cells were washed and resuspended in the FACS buffer containing Sytox Blue Live/Dead dye for cell sorting using FACS BD Aria. Viable, single cells were gated, and the CD11b-/CD3e+ cells were collected for the generation of 10× GEM single-T-cell libraries
Biotinylated lockdown probes targeting all constant regions of the four TCR loci were added tp the 10× Chromium Next Gen Single-Cell 3’ V3 3′-barcoded scRNA-seq cDNA libraries using the xGen Hybridization and Wash kit with customized Discovery Pools from Integrated DNA Technologies, Inc (IDT, Coralville, Iowa).500 ng of amplified cDNA was mixed with the blocking probes and xGen human Cot DNA, and the mixtures were dried down in a SpeedVac system (ThermoFisher). The hybridization and washing steps were performed according to the protocol from IDT. The hybridization and post-capture amplification steps were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA). Fourteen cycles were used for post-capture PCR amplification, and the amplified cDNA was evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
Amplified cDNA at >200ng per sample was used to generate Pacific Biosciences (PB) SMRTcell libraries. Full-length PB sequencing was performed on the PB Sequel II platform at Histogenetics (Ossining, NY)

value: spleen

value: mostly spleen T cells

value: 24 months

tag: Sex

value: male

tag: colony/strain


title: Drought3_32d_rep3

value: Nipponbare


title: Suv39h1 knockdown under hypoxia rep2 [RNA]


title: Suv39h1 knockdown under hypoxia rep1 [RNA]


title: Plasma small RNA, woman BRCA2 mutation carrier (2011/11016), breast cancer

value: Plasma

tag: age

value: XX


title: Drought3_32d_rep2


title: old mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 4

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_24m_4


title: Plasma small RNA, woman BRCA1 mutation carrier (2011/10938), cancer-free


title: Plasma small RNA, woman BRCA1 mutation carrier (2009/9242), breast cancer


title: Drought3_32d_rep1


title: old mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 1

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_24m_1


title: old mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 2

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_24m_2


title: Well-watered2_32d_rep3


title: untreated Rep3 [RNA]

value: untreated


title: untreated Rep2 [RNA]


title: Plasma small RNA, woman BRCA1 mutation carrier (2008/7303), breast cancer


title: Plasma small RNA, woman BRCA2 mutation carrier (2009/8922), breast cancer

value: Adult woman, 49 yr


title: untreated Rep1 [RNA]


title: adult mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 4

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_2m_4

value: 2 months


title: adult mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 3

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_2m_3


title: Well-watered2_32d_rep2


title: Kdm4d overexpression under hypoxia rep3 [RNA]

value: Kdm4d overexpression under hypoxia


title: Plasma small RNA, woman BRCA1 mutation carrier (2009/9502), breast cancer

value: Adult woman, 38 yr

value: Plasma EDTA


title: Kdm4d overexpression under hypoxia rep2 [RNA]


title: adult mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 2

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_2m_2


title: Plasma small RNA, woman BRCA1 mutation carrier (2009/9027), breast cancer

value: Blood

value: Adult woman, 42 yr


title: Well-watered2_32d_rep1


title: Drought2_32d_rep1


title: Kdm4d overexpression under hypoxia rep1 [RNA]

value: Heart

value: endothelial


title: adult mouse anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 1

description:
mostly TCR RNA
10x Genomics
mouse_spleen.TCRs_2m_1

value: spleen


title: adult female naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 4

description:
10x Genomics
nmr.female.cervical.thymus_4

data_processing:
Cell Ranger mkfastq for demultiplexing
Cell Ranger count for generating gene-barcode-matrix
HetGla2.0 + GCF_000247695.1 and Heterocephalus_glaber_female 1.0 combined annotations
barcodes.tsv.gz is the gunzipped list of sequenced barcodes. genes.tsv.gz is the gunzipped list of sequenced genes. matrix.mtx.gz is the gunzipped compressed sparse gene-barcode-matrix

organism: Heterocephalus glaber

source_name: cervical thymus

extract_protocol:
Thoracic tissue was dissected using sterile surgical techniques and subsequently transferred to a petri dish containing PBS. Fat tissue surrounding the thymic parenchyma was carefully removed with microscissors and tissue forceps under a surgical microscope. Excess liquid/PBS was carefully removed with Kimwipes before weight measurement. For histological analysis, the tissues were fixed in 10% formalin and following standard tissue processing procedures. For the purpose of creating single-cell suspensions, thymic tissues were ground through 100 μm and 40 μm cell strainers (Falcon 352360 and 352340, Corning, NY) with a syringe plunger. Cells were subsequently pelleted (300g, 3 minutes, 4 ̊C), resuspended in 5 mL of ACK lysis buffer (Lonza BP10-548E, Basel, Switzerland) for 5 minutes at room temperature, and washed and resuspended with PBS with 0.04% BSA. Cell density and viability were determined using the Countness II Cell Counter (Thermofisher AMQAF1000). The cells were pelleted and resuspended at 1 million cells per ml of 0.04% BSA/PBS prior generating the 10× GEM single-cell libraries.
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and GEM single-cell libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 30 Gel Bead and Library 3’ V3 kit (10× Genomics, Pleasanton, CA). In brief, cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1×106 cells/mL (1,000 cells per μL). Cells were loaded in each channel with a target output of 10,000 cells per sample. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
paired-end ilimina next-seq

value: cervical thymus

value: all cells

value: 2 years

value: female


title: Drought1_32d_rep3

value: Nipponbare


title: Plasma small RNA, woman BRCA1 mutation carrier (2009/8881), breast cancer

value: Plasma

value: Adult woman, 34 yr

value: XX


title: Drought2_32d_rep2


title: adult female naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 4

description:
10x Genomics
nmr.female.thoracic.thymus_4

source_name: thoracic thymus

value: thoracic thymus


title: Hypoxia treated Rep3 [RNA]

value: Hypoxia treated


title: Drought1_32d_rep2


title: Hypoxia treated Rep2 [RNA]


title: adult male naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 4

description:
10x Genomics
nmr.male.cervical.thymus_4

value: male


title: Hypoxia treated Rep1 [RNA]


title: Plasma small RNA, woman BRCA2 mutation carrier (2007/6810), breast cancer

value: Adult woman, 33 yr

value: Plasma EDTA


title: adult male naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 4

description:
10x Genomics
nmr.male.thoracic.thymus_4


title: Drought1_32d_rep1


title: infection control rep3 [RNA]

value: infection control


title: Well-watered1_32d_rep3


title: E198K midbrain neuron sample 2

city: Sacramento

first: Julian

last: Halmai

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

data_processing:
star align 2.7a
edgeR
Assembly: hg38
Supplementary files format and content: .csv with raw reads per gene

source_name: midbrain neuron

growth_protocol: iPSCs were converted to a feeder-free culture system using StemFlex medium on matrigel, passaged and frozen using dispase. Undifferentiated human iPSCs were cultured in Corning Matrigel hESC Qualified Matrix with StemFlex medium kit. Cells were routinely cultured at 37C in a standard 5% CO2 incubator with every other day medium change.  hiPSCs were plated into Aggrewell 800 plates in embryoid body (EB) medium containing Knockout DMEM/F12, 15% Gibco™ KnockOut™ Serum Replacement, 100X MEM non-essential amino acids, 100X Glutamax Supplement, 0.55mM 2-Mercaptoethanol and Y-27632 RHO/ROCK pathway inhibitor. On day 2, EBs were plated in suspension in low-attachment plates in EB medium supplemented with Noggin  and SB43152 over 4 days with media change on day 4. On day 5, EBs were plated onto Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix and subsequently transitioned to neural stem cell medium containing Neurobasal Medium , GlutaMAX Supplement (100X), MEM Non-Essential Amino Acids Solution (100X), Penicillin-Streptomycin Solution, N2 Supplement and 10ug/mL Recombinant Human FGF basic/FGF2/bFGF,  over days 6 – 12. Rosettes were enzymatically lifted using Accutase and plated on poly-L-ornithine solution (PLO) and laminin from Engelbreth-Holm-Swarm murine sarcoma basement membrane coated plates supplemented with neural stem cell medium.  For assessments in midbrain iPSC-derived neurons, Isogenic and E198K NSCs were plated at a density of 50,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates in NSC media. 24-hours post-seeding media was changed to STEMdiff Midbrain Neuron Differentiation Kit supplemented with Human Recombinant Sonic hedgehog (Shh) C2411 to differentiate NSCs into midbrain NSCs. Once midbrain NSCs reached 80% confluency, cells were plated at 15,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates to allow for midbrain NSCs to mature into midbrain neurons in STEMdiff Midbrain Neuron Maturation Kit over 9 days.  iPSCs were converted to a feeder-free culture system using StemFlex medium on matrigel, passaged and frozen using dispase. Undifferentiated human iPSCs were cultured in Corning Matrigel hESC Qualified Matrix with StemFlex medium kit. Cells were routinely cultured at 37C in a standard 5% CO2 incubator with every other day medium change.  hiPSCs were plated into Aggrewell 800 plates in embryoid body (EB) medium containing Knockout DMEM/F12, 15% Gibco™ KnockOut™ Serum Replacement, 100X MEM non-essential amino acids, 100X Glutamax Supplement, 0.55mM 2-Mercaptoethanol and Y-27632 RHO/ROCK pathway inhibitor. On day 2, EBs were plated in suspension in low-attachment plates in EB medium supplemented with Noggin  and SB43152 over 4 days with media change on day 4. On day 5, EBs were plated onto Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix and subsequently transitioned to neural stem cell medium containing Neurobasal Medium , GlutaMAX Supplement (100X), MEM Non-Essential Amino Acids Solution (100X), Penicillin-Streptomycin Solution, N2 Supplement and 10ug/mL Recombinant Human FGF basic/FGF2/bFGF,  over days 6 – 12. Rosettes were enzymatically lifted using Accutase and plated on poly-L-ornithine solution (PLO) and laminin from Engelbreth-Holm-Swarm murine sarcoma basement membrane coated plates supplemented with neural stem cell medium.  For assessments in midbrain iPSC-derived neurons, Isogenic and E198K NSCs were plated at a density of 50,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates in NSC media. 24-hours post-seeding media was changed to STEMdiff Midbrain Neuron Differentiation Kit supplemented with Human Recombinant Sonic hedgehog (Shh) C2411 to differentiate NSCs into midbrain NSCs. Once midbrain NSCs reached 80% confluency, cells were plated at 15,000 cells/cm2 on poly-L-ornithine (PLO) and laminin coated plates to allow for midbrain NSCs to mature into midbrain neurons in STEMdiff Midbrain Neuron Maturation Kit over 9 days.

extract_protocol:
Cells were lysed using TriZol Reagent and RNA extractions were performed on with the Direct-zol RNA Miniprep kit (Zymo Research). 500ng total RNA was used to construct libraries according to Novogene sample submission guidelines.
Library construction was performed by Novogene.

treatment_protocol: An iPSC isogenic line was created with a sgRNA targeting the patient-specific E198K variant in PPP2R5D using CRISPR-mediated homology-directed repair, courtesy of Synthego.  Sanger sequencing of the E198K and isogenic iPSC lines was conducted to verify the patient variant and correction of the mutation.

value: midbrain neuron


title: adult female naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
nmr.female.cervical.thymus_3

value: MS 51


title: infection control rep1 [RNA]

value: Heart

value: endothelial


title: Well-watered1_32d_rep2


title: infection control rep2 [RNA]


title: adult female naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
nmr.female.thoracic.thymus_3

value: all cells


title: isogenic midbrain neuron sample 2

value: WT


title: adult male naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
nmr.male.cervical.thymus_3

value: cervical thymus

value: 2 years


title: Drought2_29d_rewater2_rep3

value: Nipponbare


title: isogenic midbrain neuron sample 1


title: Well-watered1_32d_rep1


title: Suv39h1KD2, input

data_processing:
Raw fastq files were evaluated with fastqc, and then low-quality bases and adaptor contamination were trimmed by cutadapt. Reads were mapped to mm10 using bwa. Duplicate reads were marked by Picard Markduplicate module and removed with unmapped reads by samtools. bedtools was used to generate BED file from filtered reads.
Bigwig files were generated with deeptools
Assembly: mm10
Supplementary files format and content: bigWig, quantitative ChIPseq signal

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature. Glycine was added to 75mM quenched formaldehyde, then incubated with RT for 5min and rinsed twice with PBS. Cells were added with 1ml PBS and collected into EP tubes with a scraper. The cells were rotated at 1400g at 4℃ for 5min. The supernatant was discarded and re-suspended with 1mL LB1(50mM HEPES pH= 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5%NP-40, 0.25% Triton X-100). The cells were incubated on a rotating wheel at 4°C for 10min. Cells were centrifuged at 1400g for 5min at 4 ° C, then resuspended with 1mL LB2 (10mM Tris-HCl pH=8.0, 200mM NaCl, 1mM EDTA, 0.5mm EGTA) and incubated on RT rotating wheels for 10min. Cells were centrifuged at 1400g for 5min at 4 ° C and resuspended in 1mL buffered 1mL LB3 (10mM Tris-HCl pH=8.0, 100mM NaCl, 0.5mM EDTA, 0,5mM EGTA, 0.1% Na-Deoxycholate, 0.5%N-lauroylsarcosine). Cells were placed on ice for 10min and then transferred to ultrasound tube. Ultrasonic processing was performed using Bioruptor :30 seconds on - 30 seconds off, 10 cycles, a total of 20 cycles at high power, resting on ice for 10min every 10 cycles. The sonicated chromatin was centrifuged at full speed for 10min at 4°C. To check ultrasonic efficiency, 10mL samples were back-cross-linked by the addition of 40mL ChIP elution buffer (10mM Tris pH8, 300mM NaCl, 5mM EDTA, 0.5% SDS). DNA was cultured at 65°C for 12h, and 1mL of RNase A (10mg/mL) was added to the sonicated DNA and incubated at 37°C for 1h. Finally, 5mL proteinase K (20mg/mL) was added and incubated for 2h at 55°C. DNA size distribution was examined on 1.5% agarose gel.  Take 10% supernatant as input, mix proteinG beads (Invitrogen, #1004D) in advance30ul, add 1ml block solution blocking solution (0.5%BSA, IgG-free, Protease-free, ImmumoReasearch #1001-000-062) into EP tube, then centrifuge vortex, place on magnetic magnetic frame, wait for 1min, wash three times. Add 5ug of antibody into beads, rotate at 4℃ for 8h, and resuspended with 50ul blocking solution. Add 50ul antibody /beads mixture into the cleavage product and rotate overnight at 4℃. Then Wash Buffer(50mM Hepes-KOH, pH 7.6, 500mM LiCl, 1mM EDTA, 1%NP-40, 0.7%Na-Deoxycholate) was washed and resuspended with Elution Buffer(50mM Tris-HCl, pH 8.0, 10mM EDTA, 1%SDS ), RNA and protein were digested, DNA was extracted, resuspended with 10ul water, quantitative concentration (≥0.2ng/ul), and 1ng was used on machine.
DNA integrity was determined via bioanalyzer (Agilent) using standard  Pico chip. The libraries of samples for unstranded sequencing were constrcuted by TruSeq RNA Library Prep Kit and sequenced on Illumina NextSeq 500.

value: Suv39h1 knockdown under hypoxia


title: Suv39h1KD1, input


title: Drought2_29d_rewater2_rep2


title: E198K midbrain neural stem cell sample 4

source_name: midbrain neural stem cell

value: midbrain neural stem cell


title: Plasma small RNA, woman BRCA1 mutation carrier (2006/5584), breast cancer

value: Blood

value: Plasma

value: XX


title: Drought2_29d_rewater2_rep1


title: E198K midbrain neural stem cell sample 3


title: Normoxia2, input

value: untreated


title: Drought2_32d_rep3


title: adult female naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
nmr.female.thoracic.thymus_2

value: thoracic thymus

value: female


title: E198K midbrain neural stem cell sample 2


title: adult male naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 3

description:
10x Genomics
nmr.male.thoracic.thymus_3

value: male


title: Drought1_29d_rewater2_rep3


title: Drought1_29d_rewater2_rep2


title: E198K midbrain neural stem cell sample 1


title: adult male naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
nmr.male.cervical.thymus_2


title: E198K midbrain neuron sample 1

value: midbrain neuron


title: adult male naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
nmr.male.thoracic.thymus_2


title: Drought1_29d_rewater2_rep1


title: Kdm4dOE2, input

value: Heart

value: Kdm4d overexpression under hypoxia


title: adult female naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
nmr.female.cervical.thymus_1

value: all cells

value: MS 86


title: isogenic midbrain neural stem cell sample 4

value: WT


title: Well-watered1_29d_rewater2_rep3


title: Hypoxia2, input

value: endothelial

value: Hypoxia treated


title: isogenic midbrain neural stem cell sample 2

source_name: neural stem cell

value: neural stem cell


title: Well-watered1_29d_rewater2_rep2

value: Nipponbare


title: isogenic midbrain neural stem cell sample 1

value: midbrain neural stem cell


title: Suv39h1 knockdown under hypoxia rep2

value: Suv39h1 knockdown under hypoxia

tag: antibody


title: Well-watered1_29d_rewater2_rep1


title: Suv39h1 knockdown under hypoxia rep1


title: Normoxia1, input


title: Kdm4dOE1, input


title: adult male naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 2

description:
10x Genomics
nmr.BM.M_2_2

source_name: bone marrow

extract_protocol:
Femurs and tibias of the euthanized animals were dissected using sterile surgical techniques and transferred to a petri dish containing the basal medium (Minimal Essential Medium supplemented with 10% FBS and 1X antibiotics antimycotic solution (Gibco)). The dorsal and distal ends of femurs and tibias were cut with scissors to reveal the bone marrow cavity, and the bone marrow cells were flushed out with the basal medium using needles/syringes. Cells were then passed through 100 μm and 40 μm cell strainers, washed, pelleted, and resuspended in 5 mL of ACK lysis buffer (Lonza BP10-548E, Basel, Switzerland) for 5 minutes at room temperature. After determining their density and viability, cells were resuspended at 1 million cells per ml of 0.04% BSA/PBS prior to generating the 10× GEM single-cell libraries.
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and GEM single-cell libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 30 Gel Bead and Library 3’ V3 kit (10× Genomics, Pleasanton, CA). In brief, cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1×106 cells/mL (1,000 cells per μL). Cells were loaded in each channel with a target output of 10,000 cells per sample. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
paired-end ilimina next-seq

value: bone marrow

value: 2 years

value: MS 90


title: E198K neural stem cell sample 2


title: isogenic midbrain neural stem cell sample 3


title: untreated Rep2

value: untreated


title: Hypoxia1, input


title: Drought2_29d_rewater1_rep3


title: E198K neural stem cell sample 1


title: Drought2_29d_rewater1_rep1


title: Drought2_29d_rewater1_rep2


title: isogenic neural stem cell sample 3


title: adult male naked mole-rat cervical thymus short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
nmr.male.cervical.thymus_1

value: cervical thymus

value: male


title: untreated Rep1

value: Heart


title: adult male naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 1

description:
10x Genomics
nmr.BM.M_1_1


title: Kdm4d overexpression under hypoxia rep2

value: Kdm4d overexpression under hypoxia


title: adult male naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
nmr.male.thoracic.thymus_1

value: thoracic thymus

value: all cells


title: adult female naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 2

description:
10x Genomics
nmr.BM.F_2_2

value: female


title: adult male naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 1

description:
10x Genomics
nmr.BM.M_2_1


title: isogenic neural stem cell sample 2

value: WT


title: isogenic neural stem cell sample 1

source_name: induced pluripotent stem cell

value: induced pluripotent stem cell


title: Hypoxia treated Rep2

value: endothelial

value: Hypoxia treated


title: Drought1_29d_rewater1_rep2

value: Nipponbare


title: Drought1_29d_rewater1_rep1


title: adult female naked mole-rat thoracic thymus short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
nmr.female.thoracic.thymus_1

value: MS 86


title: Hypoxia treated Rep1


title: Well-watered1_29d_rewater1_rep3


title: adult female naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 2 library 1

description:
10x Genomics
nmr.BM.F_2_1

value: bone marrow


title: Well-watered1_29d_rewater1_rep2


title: Drought1_29d_rewater1_rep3


title: adult female mouse thymus short-read 10x scRNA-seq, replicate 1

description:
10x Genomics
mouse.female.thymus_1

data_processing:
Cell Ranger mkfastq for demultiplexing
Cell Ranger count for generating gene-barcode-matrix
mm10 + Gencode vM25 primary assembly annotation
barcodes.tsv.gz is the gunzipped list of sequenced barcodes. genes.tsv.gz is the gunzipped list of sequenced genes. matrix.mtx.gz is the gunzipped compressed sparse gene-barcode-matrix

source_name: thymus

value: thymus

value: 2 months


title: Well-watered1_29d_rewater1_rep1


title: E198K induced pluirpotent stem cell sample 2


title: E198K neural stem cell sample 3

value: neural stem cell


title: adult female mouse thymus short-read 10x scRNA-seq, replicate 2

description:
10x Genomics
mouse.female.thymus_2


title: Kdm4d overexpression under hypoxia rep1


title: Plasma small RNA, woman BRCA2 mutation carrier (2010/09740), breast cancer

value: Blood

value: Plasma

value: Adult woman, 35 yr

value: XX

value: Plasma EDTA


title: adult male naked mole-rat bone-marrow cells short-read 10x scRNA-seq, replicate 1 library 2

description:
10x Genomics
nmr.BM.M_1_2

value: all cells

value: 2 years

value: male