title: Cumulus, rep2

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

description: Library name: C2

data_processing:
Sequence reads were trimmed for adaptor sequence using fastp.
Trimmed sequence reads were mapped to the mouse genome build mm39 using STAR.
Read count extraction and normalization were performed using featureCounts and R, respectively.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include raw read counts for genes in each sample.

source_name: Somatic cells

growth_protocol: (C57BL/6N × DBA2)F1 (BDF1) (Japan SLC, Shizuoka, Japan) female mice at 8–12 weeks of age were superovulated by injecting 7.5 IU equine chorionic gonadotropin (eCG) (PMS 1000, Nippon Zenyaku Kogyo Co., Ltd., Fukushima, Japan), followed 46–52 h later by injection of 7.5 IU human chorionic gonadotropin (hCG) (GONATROPIN, ASKA Pharmaceutical Co., Ltd., Tokyo, Japan). Female mice were euthanized by cervical dislocation 16 h after the hCG injection, and cumulus–oocyte complexes were collected from the ampullae of excised oviducts and placed in 80 μL droplets of human tubal fluid medium (Quinn et al., 1985). Spermatozoa were collected from the cauda epididymis of adult C57BL/6N male mice (Japan SLC) and preincubated for at least 50 min in a 200 μL droplet of human tubal fluid. After preincubation, 1–2 μL of the sperm suspension was added to the drops of oocyte culture. At 3 h post-insemination (hpi), morphologically normal fertilized embryos were collected and cultured in CZB (Chatot et al., 1990). All incubations were performed at 37°C under 5% CO2 in air. Nuclear transfer was performed following a previous report (Ogura, 2017). Cumulus cells used as nuclear donors were collected from BDF1 female mice. Recipient oocytes were collected from BDF1 female mice following superovulation as above and placed in CZB droplets containing 0.1% bovine testicular hyaluronidase (385931, Merck, Darmstadt, Germany) to remove cumulus cells. The cumulus-free oocytes were enucleated in Hepes-buffered CZB containing 7.5 μg/mL cytochalasin B (250233, Merck) using a Piezo-driven micromanipulator (PMM-150FU, Prime Tech, Ibaraki, Japan). After being cultured in fresh CZB for 1 h, the enucleated oocytes were injected with cumulus cell nuclei in Hepes-buffered CZB at room temperature. After 1 h of culture, the injected oocytes were activated by Ca2+-free CZB containing 3 mM strontium chloride and 5 μg/mL cytochalasin B for 1 h. Continuously, the reconstructed oocytes were cultured in CZB containing 5 μg/mL cytochalasin B for 5 h. After washing, embryos were cultured in CZB at 37 °C under 5% CO2 in air. Cumulus cells were collected from BDF1 oocytes after 0.1% bovine testicular hyaluronidase treatment.

extract_protocol:
Two-cell and four-cell stage embryos derived from IVF and SCNT were collected at 24 and 48 hpi or hpa, washed twice in 0.05% BSA in PBS, and flash-frozen in liquid nitrogen. Ten embryos were pooled as a single sample. After thawing, polyadenylated RNAs were reverse transcribed and amplified, using SMART-Seq HT kits (R400748, Takara Bio, Shiga, Japan).
Library preparation and sequencing were performed using a SMART-Seq HT kits (R400748, Takara Bio, Shiga, Japan).

value: Somatic cells

value: Wildtype

value: Donor


title: CAR-iMac-3

status: Public on Sep 01 2025

type: SRA

city: Guangzhou

first: Baoqiang

last: Kang

address: Kaiyuan Avenue 190

country: China

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

description: Library name: Sample3

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Assembly: GRCh38/hg38
Supplementary files format and content: count

molecule: total RNA

organism: Homo sapiens

source_name: cord blood

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: cord blood

tag: cell line

tag: cell type

value: induced pluripotent stem cell derived macrophage

tag: genotype

value: CAR knock in

tag: treatment

value: macrophage differentiation


title: NTVE lysate-3_ISBM-064

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description:
Library name: 24L006462
Stable NTVE line

data_processing:
Deduplication via czid-dedup (paired-end mode)
featurecounts_harmonized.csv: Paired-end reads were aligned to the combined human-murine index via STAR  (star --readFilesCommand zcat --genomeDir {COMBINED_INDEX_STAR} --readFilesIn {R1} {R2} --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix {OUTPUT_NAME} --quantMode GeneCounts TranscriptomeSAM))
featurecounts_harmonized.csv: Gene level feature counting via featurecounts (featureCounts -a {COMBINED_INDEX_GTF} -o {OUTPUT_FILE}  -g gene_id -t exon -s 2 -p)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: featurecounts_harmonized.csv: comma seperated plaintext file containing the raw counts mapping to features and metadata for all samples
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

molecule: polyA RNA

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

value: immortalised cell line

value: NTVE Gag:PABP(ZF:Hibit); Pgk-TetON3g (ISBM-064)

tag: rna origin

value: Cell Lysate

tag: spike-in

value: doxycycline 500ng/ul


title: Cumulus, rep1

description: Library name: C1

organism: Mus musculus


title: Control plants 1

city: Cambridge

first: Ignacy

last: Bonter

address: Downing site

country: United Kingdom

institute: University of cambridge

data_processing:
Galaxy
Assembly: Tak 6.1
Supplementary files format and content: Count tables in .tabular files

organism: Marchantia polymorpha

source_name: thallus

growth_protocol: 21 celcius on either half gamborg plates or half gamborg + 2.5uM Sodium Arsenite

extract_protocol:
RNA easy plant kit from Qiagen
Novogene

value: thallus

value: Half B5


title: NTVE lysate-6_ISBM-064

description:
Library name: 24L006465
Stable NTVE line


title: Control plants 2


title: NTVE lysate-1_ISBM-064

description:
Library name: 24L006460
Stable NTVE line


title: CAR-iMac-2

description: Library name: Sample2


title: myc_3

city: Beijing

first: Jialong

last: Zhang

address: Malianwa Street

institute: China Agricultural University

data_processing:
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Assembly: SL 3.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome
Supplementary files format and content: text files include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: fruits

extract_protocol: Total RNA was extracted from above tomato fruits by TRIzol reagent and three biological replicates were taken

value: slmyc2 mutant

value: fruits


title: Arsenic treated plants 3

value: As(III)


title: CAR-iMac-1

description: Library name: Sample1


title: Day8 TS-EVT RNA

city: Pittsburgh

first: Leah

last: Cabo

state: PA

address: 4249 Fifth Avenue

country: USA

institute: University of pittsburgh

data_processing:
Resulting fastq files were processed with 10X Genomics cellranger  and aggregated using aggr
Assembly: Homo sapiens hg38
Supplementary files format and content: processed data files contain aggr and cellranger outputs
Library strategy: single nuclei multiome ATAC _ Gene Expression

source_name: trophoblast stem cells

growth_protocol: Human trophoblast stem cells were maintained as published in Okae et. al 2018 Cell Stem Cell. TS-CTB were plated at 70,000 cells per well of a 6 well plate and grown for 24-48 hours in TS-CTB media before treatment. TS-EVT were differentiated for 4 (intermediate) or 8 (terminal) days according to published protocols.

extract_protocol:
Adherent cells from CTB and EVT samples were trypsinized for 12 minutes with 1:1 TrypLE and PBS. Nonadherent 3D STB were collected from wells. Trypsinized cells were collected by pipetting and centrifuged for 250 x g for 5 minutes. Nuclear extraction was performed according to 10x Genomics Chromium Single Cell Nuclei Isolation protocols. Nuclei viability was tested prior to use in library preparation
Library construction was performed according to 10X Genomics Chromium single nuclei multiome ATAC _ Gene Expression protocols

treatment_protocol: After 24-48 hours of growth, TS-CTB were switched to 2 mL TS-basal medium + Y27632 and either mock-infected or infected with T. gondii. T. gondii parasites were cultured in HFFs (human foreskin fibroblasts), syringe lysed, filtered with 5.0 um syringe filter to remove host cell debris, centrifuged at 800 x g for 10 minutes, pellet was resuspended in new TS-basal + Y27632 media, and parasites were counted via hemocytometer. Tg-infected TS-CTB were infected with a 3:1 ratio of parasites (70,000 TS-CTB plated, 210,000 parasites used for infection) in 200 uL media per well. Remaining parasite suspension was filtered through 0.2 um syringe filter to remove all parasites. The same volume (200 uL) of filtered parasite suspension was used to mock-infected TS-CTB. TS-EVT were differentiated according to published protocols

value: trophoblast stem cells

value: EVT

value: terminally differentiated


title: myc_1


title: myc_2


title: Day4 TS-EVT RNA

value: intermediately differentiated


title: Arsenic treated plants 2


title: WT3

value: wild type (Ailsa Craig)


title: Arsenic treated plants 1


title: T47D siNR2C2, rep 3

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

description:
Library name: T47D siNR2C2 3
Column name in deseq2_results_STAR_T47D_annotated.csv: siNR2C2_Rep3; Column name in T47D_counts_allsamples.csv: siNR2C2_Rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality sequence using fastp (0.24.0). (Default parameters)
Sequences were then mapped to Homo sapiens GRCh38 using STAR 2.7.11b. (parameters: outFilterMultimapNmax 20, outFilterMismatchNoverLmax 0.6, outFilterType BySJout)
Feature counts were generated setting Quantmode to gene counts in STAR 2.7.11b
Feature count normalization and diffrential gene expression analysis was performed using DEseq2 3.21.
Assembly: Genome used: Homo sapiens GRCh38; Annotations used: ENSEMBL
Supplementary files format and content: csv files include output from DEseq2 3.21 and normalized counts per sample (dese2_results file)
Supplementary files format and content: csv file includes raw counts for each sample (counts file)

growth_protocol: MCF7 and T47D cell lines were maintained in DMEM (Gibco 11995065) + 15% FBS (J.C. Gonzalez Inc. HFB001) + 1% penicillin/streptomycin (Corning MT30002CI)

extract_protocol:
RNA was extracted using Zymo Research Quick-RNA Miniprep kit, following manfacturers intructions.
RNA-seq libraries were constructed by PROMIC using Illumina Stranded mRNA prep kit using 1ug of RNA and sequenced using Illumina NextSeq 550.

treatment_protocol: MCF7 and T47D cells were either treated with 30pmol siRNA targeting NR2C2 or Scramble (control) for 72 hours.

value: breast ductal carcinoma

value: siRNA


title: T47D, siNR2C2, rep 2

description:
Library name: T47D siNR2C2 2
Column name in deseq2_results_STAR_T47D_annotated.csv: siNR2C2_Rep2; Column name in T47D_counts_allsamples.csv: siNR2C2_Rep2


title: mock-infected TS-CTB RNA

value: CTB

value: mock-infected


title: Tg-infected TS-CTB RNA

value: Tg-infected


title: WT2


title: Wildtype, DRG, Injured (Input) 3

city: Daegu

first: Eunsu

last: Jang

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

country: South Korea

institute: DGIST

description: Library name: wild-type_Input_dx3

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts

source_name: Dorsal root ganglion(DRG)

extract_protocol:
For CSDE1-IP sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-CSDE1 antibody, and the RNA from the immunoprecipitated product was extracted using RNeasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB112.24))

value: Dorsal root ganglion(DRG)

value: Wildtype

value: Injury


title: NTVE lysate-2_ISBM-064

description:
Library name: 24L006461
Stable NTVE line

value: immortalised cell line

value: NTVE Gag:PABP(ZF:Hibit); Pgk-TetON3g (ISBM-064)

value: Cell Lysate

value: doxycycline 500ng/ul


title: T47D, siNR2C2, rep 1

description:
Library name: T47D siNR2C2 1
Column name in deseq2_results_STAR_T47D_annotated.csv: siNR2C2_Rep1; Column name in T47D_counts_allsamples.csv: siNR2C2_Rep1


title: T47D, control, rep 3

description:
Library name: T47D siScramble 3
Column name in deseq2_results_STAR_T47D_annotated.csv: control_Rep3; Column name in T47D_counts_allsamples.csv: control_Rep3

value: siScramble


title: WT1

value: fruits


title: H2AZ + rapamycin

city: Boston

first: Zlata

last: Gvozdenov

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

description: H2AZ anchor away

data_processing:
RNA-Seq reads were trimmed using trimmomatic (Bolger et al., 2014) with TRAILING:20 MINLEN:40.
Reads were aligned to the reference genome sacCer3 (UCSC, April 2011) using STAR (Dobin 2013).
Differential expressed genes were computed using GFold (V1.1.0) (Feng et al. 2012); files with extensions *.read_cnt and *.diff. correspond to differential gene expression analysis.
Metagene profiles were generated using Galaxy deepTools (http://deeptools.ie-freiburg.mpg.de/).
Cryptic transcription regions were identified with Interval_identifier.py. cct12_over_cct_rep12.bed indicates regions with differential transcription upon CCT inactivation. cct_over_cct12_rep12.bed is a vise versa run (transcripts that got lost upon CCT inactivation). Only regions that intersect between HiSeq2000 and HiSeq4000 runs (i.e., are detectable in both replicates) were considered.
The aligned reads were visually displayed with IGV (2.3.25 and 2.3.94).
Assembly: sacCer3
Supplementary files format and content: Interval_identifier.py-generated tab-separated files contain information about the chromosome, coordinate start, coordinate end, transcript fold change (WT wrt. cct1-2 or vice versa), directionality.

organism: Saccharomyces cerevisiae

growth_protocol: WT and cct1-2 strains were grown in YPD to log phase at 30°C and shifted to 37°C for 4 h. VDY1874 H2A.Z-FRB::KAN was grown in YPD at 30°C.

extract_protocol:
Total RNA was extracted with RiboPure Yeast kit (Ambion).
The RNA-Seq libraries were prepared with Illumina’s TruSeq Stranded mRNA Sample Prep kit.

treatment_protocol: VDY1874 with H2A.Z-FRB::KAN: cells were divided into two flasks – rapamycin was added at 1 µg/ml final concentration to first half (treated sample) and the same amount of ethanol without rapamycin was added to the second half of the culture (control).

tag: strain

value: VDY1874 H2A.Z-FRB::KAN

value: 4 h rapamycin at 1 ug/ml


title: Wildtype, DRG, Injured (Input) 2

description: Library name: wild-type_Input_dx2


title: Wildtype, DRG, Injured (Input) 1

description: Library name: wild-type_Input_dx1


title: HUVEC+DPSC+CM  fibrin tissue day 10 sample1

city: Toronto

first: Shira

last: Landau

state: ON

address: 170 College St.,, MB317

country: Canada

institute: University of Toronto

library_source: transcriptomic single cell

data_processing:
Samples were mapped individually then aggregated with cellranger (v7.2.0).
Assembly: A human reference refdata-gex-GRCh38-2020-A downloaded from the 10x website was used.
Supplementary files format and content: tab seperetad values files and matrix files

source_name: HUVEC+DPSC+cardiomyocytes

extract_protocol:
10x sample preparation of macrophages suspension: 1 mL of cold lysis buffer comprising 0.32M Sucrose, 5mM CaCl2, 3mM Mg(Ac)2, 20mM Tris-HCl pH 7.5, 0.10% Triton X-100, 0.1mM EDTA pH 8.0, DEPC Water, 40U/mL RNase Inhibitor (Millipore Sigma, cat. No. 3335402001) was added to the frozen cell pellet for 5-minute lysis. The pellet was dissociated by pipette mixing. After the 5-minute lysis, nuclei were pelleted by spinning at 4C for 10 minutes at 800 x g. The supernatant was removed, and the nuclei pellet was resuspended with 2 mL wash buffer comprising 1x PBS, 1% BSA, and 0.1U/uL RNase Inhibitor. Centrifugation and resuspension with wash buffer was repeated for a total of 2 washes. After the second wash, the nuclei suspension was filtered using a 40um Flowmi cell strainer (Millipore Sigma, cat. no. BAH136800040). The purified nuclei suspension was centrifuged at 4C for 10 min at 800 rcf and the nuclei pellet was resuspended in wash buffer for a final nuclei concentration of 1000 nuclei/uL. Nuclei counting was done using AOPI (Revvity, cat. no. CS2-0106-25ML) on a haemocytometer (Thermo Fisher, cat. no. 22-600-100). Following counting, the appropriate volume for each sample was calculated for a target capture of 10,000 cells and loaded onto 10x single cell G chip.  After droplet generation, samples were transferred to a pre-chilled strip tube (USA Scientific, US14024700), and incubated in a Bio-Rad thermos cycler. Sample cDNA was recovered using Recovery Agent provided by 10x and subsequently cleaned up using a Silane DynaBead (Thermo Fisher) mix as outlined by the user guide 3’ Reagent Kits v3.1 . Purified cDNA was amplified for 11 cycles before being cleaned up using SPRIselect beads (Beckman Coulter). Samples were run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration.
10x sample preparation of tissue samples:  Nuclei were isolated using 10x Genomics’ Chromium Nuclei Isolation Kit (10x Genomics, cat. no. 1000493). The frozen tissue was transferred to a 2mL tissue grinder (Millipore Sigma, cat. no D8938). 500ul of Lysis buffer comprised of Lysis Reagent (10x Genomics, cat. no. 2000558), Reducing Agent B (10x Genomics, cat. no. 2000087), and Surfactant A (10x Genomics, cat. no. 2000559) was added to the frozen tissue on ice. The tissue was homogenized using 5 strokes with the loose pestle (pestle A) and 5 strokes with the tight pestle (pestle B). The sample was incubated on ice for a 10-minute lysis. At the end of the lysis incubation, the lysate was transferred to the Nuclei Isolation Column (10x Genomics, cat. no. 2000562) and spun at 16,000 rcf for 20 seconds at 4C. The supernatant was removed and the nuclei pellet was resuspended in Debris Removal Buffer comprised of Debris Removal Reagent (10x Genomics, cat. no. 2000560) and Reducing Agent B. The sample was spun at 700 rcf for 10 minutes at 4C. The supernatant was removed the purified nuclei pellet was washed twice with Wash Buffer comprised of 1x PBS, 10% BSA and RNase Inhibitor (Millipore Sigma, cat. No. 3335402001). The purified nuclei suspension was centrifuged at 4C for 5 min at 500 rcf and the nuclei pellet was resuspended in wash buffer for a final nuclei concentration of 1000 nuclei/uL. Nuclei counting was done using AOPI (Revvity, cat. no. CS2-0106-25ML) on a haemocytometer (Thermo Fisher, cat. no. 22-600-100). Following counting, the appropriate volume for each sample was calculated for a target capture of 10,000 cells and loaded onto 10x single cell G chip.  After droplet generation, samples were transferred to a pre-chilled strip tube (USA Scientific, US14024700), and incubated in a Bio-Rad thermos cycler. Sample cDNA was recovered using Recovery Agent provided by 10x and subsequently cleaned up using a Silane DynaBead (Thermo Fisher) mix as outlined by the user guide 3’ Reagent Kits v3.1 . Purified cDNA was amplified for 11 cycles before being cleaned up using SPRIselect beads (Beckman Coulter). Samples were run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3’ Reagent Kits v3.1 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.
cDNA libraries were prepared as outlined by the Single Cell 3’ Reagent Kits v3.1 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.
Sequencing – The molarity of each library was calculated based on library size as measured bioanalyzer (Agilent Technologies) and qPCR amplification data (Roche, cat. no. 07960140001). Gene Expression libraries were sequenced on Illumina’s NovaSeqX with the following run parameters: read 1 – 28 cycles, read 2 – 90 cycles, index 1 – 10 cycles and index 2 – 10 cycles.

value: HUVEC+DPSC+cardiomyocytes


title: HUVEC+DPSC+CM+MAC  fibrin tissue day 10 sample4

source_name: HUVEC+DPSC+cardiomyocytes+macrophages

value: HUVEC+DPSC+cardiomyocytes+macrophages


title: T47D, control, rep 2

description:
Library name: T47D siScramble 2
Column name in deseq2_results_STAR_T47D_annotated.csv: control_Rep2; Column name in T47D_counts_allsamples.csv: control_Rep2

value: breast ductal carcinoma

value: siRNA


title: macrophages in suspension

source_name: macrophages

value: macrophages


title: T47D, control, rep 1

description:
Library name: T47D siScramble 1
Column name in deseq2_results_STAR_T47D_annotated.csv: control_Rep1; Column name in T47D_counts_allsamples.csv: control_Rep1


title: Wildtype, DRG, Uninjured (Input) 2

description: Library name: wild-type_Input_du2

value: Uninjury


title: Wildtype, DRG, Uninjured (Input) 3

description: Library name: wild-type_Input_du3

value: Dorsal root ganglion(DRG)


title: MCF7, siNR2C2, rep 3

description:
Library name: MCF7 siNR2C2 3
Column name in deseq2_results_STAR_MCF7_annotated.csv: siNR2C2_Rep3: Column name in MCF7_counts_allsamples.csv: siNR2C2_Rep3

value: breast adenocarcinoma


title: H2AZ – rapamycin

description: H2AZ anchor away (final processed file is derived from rapamycin plus and minus samples)

value: 4 h ethanol control


title: WT RNA-Seq, HiSeq 4000

description: Rep 2 (final processed files are derived from WT and cct1-2 data)

value: JFY143 (CCT WT W303, matA)

value: 4 h at 37C


title: MZtulp3, 2dpf, biol rep 2

city: Freiburg

first: Ralf

last: Mertes

address: Breisacher Str.  153

institute: University Medical Center Freiburg

description: Library name: Sample 4

data_processing:
processing of raw RNA-seq files with the nf-core/rnaseq workflow (v3.18.0) including pre-processing with TrimGalore!, 2-pass alignment using the STAR aligner and quantification with RSEM
nomalization and differential expression analysis with the R/Bioconductor package DESeq2
Assembly: GRCz10
Supplementary files format and content: csv file with counts and statistics for each Sample

organism: Danio rerio

source_name: whole organism

extract_protocol:
extraction of total RNA using RNeasy Mini Kit (Qiagen)
mRNA library preparation (poly A enrichment)

value: whole organism


title: MZtulp3, 2dpf, biol rep 1

description: Library name: Sample 3


title: MCF7, siNR2C2, rep 2

description:
Library name: MCF7 siNR2C2 2
Column name in deseq2_results_STAR_MCF7_annotated.csv: siNR2C2_Rep2: Column name in MCF7_counts_allsamples.csv: siNR2C2_Rep2


title: thalamus,WT,thalamus_8

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

institute: University of Edinburgh

description: 10x Genomics

data_processing:
Fastq files were renamed in order to match the illumina naming convention, downsampled to 3M reads per sample and cropped with trimmomatic.
The alignment to the reference genome, demultiplexing, barcoded processing, gene counting and cell calling were made using the Cell Ranger software ( v7.00).
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix_sample.h5 contain the output from cellranger.

source_name: thalamus

extract_protocol:
Mice were culled via cervical dislocation and brains were dissected, with the olfactory bulbs and cerebellum being removed.The desired area of the brain were collected in ice-cold HBSS (w/o Ca2+ and Mg2+; 14175-053; Gibco) with 5% trehalose (T0167; Sigma Aldrich) and 30 µM actinomycin D (A1410; Sigma Aldrich) and were finely minced using a 22A scalpel. Brains were digested using the Adult Brain Dissociation Kit (130-107-677; Miltenyi Biotec), with the following modifications: (i) tissues were dissociated as described in the “manual dissociation” section of the Neural Tissue Dissociation Kit protocol (130-092-628; Miltenyi Biotec), (ii) enzymatic digestions were performed at 35°C, (iii) half the concentration of enzyme P was used, (iv) actinomycin D was used to limit dissociation-induced transcriptional changes,  (v) 5% trehalose was added in all buffers to increase cellular viability, (vi) cell clusters were removed by filtration through prewetted 70 μm (352350; Falcon) and 40 μm (352340; Falcon) cell strainers, (vii) erythrocyte and myelin debris removal steps were omitted during dissociation steps, and (viii) all centrifugations were performed at 200 g at 4°C. After dissociation, cells were collected in PBS with 0.2% BSA before being sorted on a Sony SH800 cell sorter. Gates were chosen based on forward and side scatter to exclude myelin debris, erythrocytes, and doublets. Non-viable cells were excluded based on Draq7 and/or DAPI staining (Draq7high and/or DAPIhigh cells were classified as non-viable).
single cells were processed through the Chromium Single Cell Platform using the Chromium Next GEM Single Cell 3’ GEM Library and Gel Bead Kit (v3.1 chemistry, PN-1000121, 10x genomics) and the Chromium Next GEM Chip G kit (PN-1000120) and processed following manufacturer’s instructions.

value: thalamus

value: WT

value: 1y 5m 7d

value: M

tag: sample


title: tent-5_male_2

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

description: Nanopore Direct RNA Sequencing of C. elegans tent-5(tm3504) mutant males in young adult stage, biological replicate 2

data_processing:
Sequencing was performed with the MinION device, followed by basecalling with Guppy 6.0.0 (ONT), mapping to WBCel235 reference (MiniMap v2.17 (25) with options -k 14 -ax map-ont –secondary = no), and processing with samtools v1.9. Lengths of poly(A) tails were estimated with Nanopolish (v0.13.2). Differential expression analysis was performed using DESeq2 v1.28 Bioconductor package.
Assembly: WBcel235
Supplementary files format and content: Excel file with differential expression and differential polyadenylation analyses.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: All strains were cultured at 20°C on nematode growth medium (NGM) plates seeded with E. coli HB101 as a food source.

extract_protocol:
Wild-type or tent-5(tm3504) young adult males were hand-picked from the male-enriched plates and transferred to an Eppendorf tube containing 10 μl of 50 mM NaCl. The worm pellet was then resuspended in 200 μl of TRI Reagent (Sigma-Aldrich), vortexed for 15 min at room temperature, and stored at -80°C before RNA isolation. TRIzol samples from three different pickings were combined just before RNA isolation, resulting in approximately 300 male worms per sample. The wild-type hermaphrodite population was age-synchronized by bleaching gravid adults and seeding isolated embryos on plates. Worms were grown until they reached the young adult stage, then collected and washed three times using 50 mM NaCl. The worm pellet was resuspended in 1 ml of TRI Reagent (Sigma-Aldrich), vortexed for 15 min at room temperature, and stored at -80°C. RNA was isolated from TRIzol according to the manufacturer’s instructions. The samples were additionally purified with KAPA Pure magnetic beads (RNA to beads ratio: 1:3 v/v), and RNA quality was assessed using the Agilent TapeStation system.
Sequencing libraries were prepared using the DRS Kit (Oxford Nanopore Technologies, SQK- RNA002) according to the manufacturer’s protocol. In each library, mRNA isolated from male or hermaphrodite worms (0,5 - 1,5 μg depending on the amount of isolated RNA) was mixed with 2 ng of in vitro transcribed poly(A) standards.

value: whole worm

value: tent-5(tm3504) mutant

value: tent-5(tm3504) I (NBRP)

tag: Sex

value: male

tag: developmental stage

value: young adult

value: grown at 20C on NGM plates seeded with E. coli HB101


title: control, 2dpf, biol rep 2

description: Library name: Sample 2


title: tent-5_male_1

description: Nanopore Direct RNA Sequencing of C. elegans tent-5(tm3504) mutant males in young adult stage, biological replicate 1


title: MCF7, siNR2C2, rep 1

description:
Library name: MCF7 siNR2C2 1
Column name in deseq2_results_STAR_MCF7_annotated.csv: siNR2C2_Rep1: Column name in MCf7_counts_allsamples.csv: siNR2C2_Rep1

value: siRNA


title: thalamus,KO,thalamus_7

description: 10x Genomics

value: KO


title: control, 2dpf, biol rep 1

description: Library name: Sample 1


title: MCF7, control, rep 3

description:
Library name: MCF7 siScramble 3
Column name in deseq2_results_STAR_MCF7_annotated.csv: control_Rep3: Column name in MCF7_counts_allsamples.csv: control_Rep3

value: breast adenocarcinoma

value: siScramble


title: WT_male_2

description: Nanopore Direct RNA Sequencing of C. elegans wild-type males in young adult stage, biological replicate 2

value: wild type

value: N2 Bristol (CGC)


title: thalamus,WT,thalamus_6

description: 10x Genomics

value: F


title: regeneration, 10dpa

city: Shanghai

first: yue

last: chen

state: Shanghai

address: 320 Yue-Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Single cell RNA-seq data were aligned to the same S. mediterranea transcriptome smed_20140614 using Cell Ranger (v7.0.0) as described (Zeng et al., 2018). Filtered UMI counts were further preprocessed using Seurat (v4.1.0) (Stuart et al., 2019). Scanorama was used to correct the potential batch effects in time-series scRNA-seq data. The corrected expression value was used for PCA in Seurat, and the first 30 PCs were used as input in clustering and UMAP visualization.
Assembly: Schmidtea mediterranea transcriptome is available from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72389
Supplementary files format and content: scRNA_filtered_feature_bc_matrix.zip

organism: Schmidtea mediterranea

source_name: neck

growth_protocol: Asexual S. mediterranea (strain CIW4) anamials were maintained at 20 °C as previously described (Newmark and Sanchez Alvarado, 2000). For all experiments, animals were starved for at least 7 days.

extract_protocol:
For regenerated fragments, planarians were chopped and dissociated in CMFB (CMF+1% FBS) on a cold plate (4 °C). After dissociation, cells were pelleted by centrifugation (290g for 5 min at 4 °C). Before loading onto the flow cytometry sorter, cells were strained through a 40um strainer and stained with DAPI (1:1000; Beyotime) and DRAQ5 (1:1000; BioStatus). Afterward, the collected live cells were washed and suspended with CMFB buffer.
Around 20,000 cells were loaded into 10x Genomics' Chromium platform for making single-cell libraries. The deep sequencing of samples (2-4 million reads per cell) was performed using the Novaseq-150PE sequencer.

value: neck

tag: time point

value: regeneration, 10dpa

value: asexual strain CIW4

value: amputation


title: regeneration, 5dpa

value: regeneration, 5dpa


title: WT_herm_2b

description: Nanopore Direct RNA Sequencing of C. elegans wild-type hermaphrodites in young adult stage, biological replicate 2, technical replicate 2

value: whole worm

value: hermaphrodite


title: MCF7, control, rep 1

description:
Library name: MCF7 siScramble 1
Column name in deseq2_results_STAR_MCF7_annotated.csv: control_Rep1; Column name in MCF7_counts_allsamples.csv: control_Rep1


title: WT_male_1

description: Nanopore Direct RNA Sequencing of C. elegans wild-type males in young adult stage, biological replicate 1

value: male


title: Wildtype, DRG, Uninjured (Input) 1

description: Library name: wild-type_Input_du1

value: Dorsal root ganglion(DRG)

value: Wildtype

value: Uninjury


title: cct1-2 RNA-Seq, HiSeq 4000

value: JFY148 (cct1-2 ts mutant)

value: 4 h at 37C


title: TGF3 [ATAC-seq]

city: NEW HAVEN

first: Rongmo

state: CT

address: 300 George street

institute: Yale

description: Library name: TGF3

data_processing:
Fastqc was used to check the quality of the data and identify the adapters. Trimmomatic was used to cut the adapters. The trimmed data then was aligned to human reference genome, hg38. Quality control of mapped data, including sort the data, make duplicate reads, and removing ENCODE blacklist were performed using the samtools and bedtools. MACS2 was used to call the peaks. Mapped data was converted to bigwig files using deepTools,
Assembly: human genome (Hg38)
Supplementary files format and content: Mapped data was converted to bigwig files using deepTools, and can be visualized by Integrative Genomics Viewer

source_name: aorta

growth_protocol: Primary Human Aortic smooth muscle cells (HASMCs) from two donors were purchased from Promocell (C-12533) and Lonza (CC-2571) respectively. The HASMCs were cultured in Smooth Muscle Cell Growth Medium-2 (SmGM-2, CC-3181, Lonza), supplemented with BulletKit (CC-4149, Lonza), 100 µg/mL penicillin and 100 µg/mL streptomycin. Cell culture dishes were maintained in a humidified 37 °C incubator with 5% CO2.

extract_protocol:
100,000 treated HASMCs were trypsinized and cryopreserved in 90% fetal bovine serum + 10% dimethyl sulfoxide, for further processing.
Novaseq sequencings with 25 million reads per sample were performed to detect the whole transcriptome. RNA-seq data was aligned to the reference human genome (Hg19) using STAR aligner on PartekFlow platform

treatment_protocol: For TGFβ treatments, 10 ng/ml TGFβ2 or PBS were added into the complete SmGM-2 growth media for 7 days with media changes every other day. For PDK4 knockdown, 20 nM siPDK4 were transfected at day 0 and day 4.

value: aorta

value: primary cells

value: aortic smooth muscle cells

value: WT

value: 10 ng/mL TGFb2


title: WT_herm_2a

description: Nanopore Direct RNA Sequencing of C. elegans wild-type hermaphrodites in young adult stage, biological replicate 2, technical replicate 1

value: wild type

value: N2 Bristol (CGC)

value: young adult

value: grown at 20C on NGM plates seeded with E. coli HB101


title: regeneration, 3dpa

value: neck

value: regeneration, 3dpa

value: asexual strain CIW4

value: amputation


title: TGF2 [ATAC-seq]

description: Library name: TGF2


title: thalamus,KO,thalamus_3

description: 10x Genomics

value: thalamus

value: KO

value: 1y 6m 7d

value: M


title: thalamus,WT,thalamus_2

description: 10x Genomics

value: F


title: WT_herm_1b

description: Nanopore Direct RNA Sequencing of C. elegans wild-type hermaphrodites in young adult stage, biological replicate 1, technical replicate 2

value: whole worm

value: hermaphrodite


title: regeneration, 12hpa

value: regeneration, 12hpa


title: regeneration, 1.5dpa

value: regeneration, 1.5pa


title: TGF1 [ATAC-seq]

description: Library name: TGF1

value: aorta

value: primary cells

value: aortic smooth muscle cells

value: WT

value: 10 ng/mL TGFb2


title: thalamus,WT,thalamus_1

description: 10x Genomics


title: regeneration, 0hpa

value: neck

value: regeneration, 0hpa

value: wild type


title: xol-1 sex-1, L3, rep4

city: Ann Arbor

first: Gyorgyi

last: Csankovszki

state: MI

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

description: xol-1 sex-1 L3

data_processing:
The reads were trimmed using CutAdapt v2.3. FastQC v0.11.8 was used to ensure the quality of data. Reads were mapped to the reference genome WBcel235 and read counts were generated using Salmon v1.9.0. Differential gene expression analysis was performed using DESeq2 v1.42.0. Downstream analyses were performed using R scripts and packages. WT and xol-1(ne4472) samples used for normalization of early embryo and L1 larval xol-1(ne4472) sex-1(gk829) samples are available using the GEO accession GSE262626.
Assembly: WS235
Supplementary files format and content: tab-delimited text files with FPKM values

growth_protocol: Embryo samples: synchronized young adult worms were bleached to isolate early embryos. L1 larval samples: Worms were synchronized by bleaching young adult worms to isolate embryos that were allowed to hatch overnight in M9. Newly hatched L1 larval worms were plated and grown for 3h on HGM plates with NA22. L3 larval samples: Worms were synchronized by bleaching young adult worms to isolate embryos that were allowed to hatch overnight in M9. Newly hatched L1 larvae were plated and grown for 24h on HGM plates with NA22.

extract_protocol:
Samples were resuspended in TRIzol. RNA was extracted and purified using the Qiagen RNeasy kit with on-column DNAse digestion.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L), and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6448S) were used for library prep. The mRNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3' ends of the cDNA were then adenylated and adapters were ligated. The products were purified and enriched by PCR to create the final cDNA library.

treatment_protocol: Worms grown under standard conditions

value: xol-1 sex-1


title: siPDK4-2 [ATAC-seq]

description: Library name: siPDK4-2

value: 20nM siPDK4


title: 95

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

data_processing:
Trimming was performed using fastp
Alignment to the zebrafish genome (GRCz11, Ensembl release 109) was performed using STAR
Aligned reads which contained the same unique molecular identifier (UMI) were deduplicated using umi_tools dedup function
Number of reads per gene with a minimum mapping quality of 10 was calculated using featurecounts
Assembly: GRCz11, Ensembl release 109
Supplementary files format and content: The output of featurecounts is found in the RNA-seqCounts.csv file, with the sample title as the column names and the first row as the ensembl gene id

source_name: whole brain

extract_protocol:
Adult fish were euthanised by sudden immersion in an ice water slurry for at least ~30 seconds before decapitation. The whole head was submerged in RNAlater solution for 24 hours at 4°C and stored at -80°C. The brain was dissected from the RNALater preserved head. Then total RNA was extracted from the brain using Qiagen RNeasy columns.
RNA samples were QC’d by PE Labchip for quality and Qubit for quantity. Libraries were generated according to the Nugen Universal Plus mRNA-seq (Part No. 0508) protocol M01442 v2 and included 13 cycles of amplification. Cluster generation was performed using llumina to MGI Library Conversion (MGIEasy Universal Library Conversion Kit, Part No. MGI1000004155. protocol M01442 v2 and included 13 cycles of amplification.

treatment_protocol: zebrafish were subjected to an intraperitoneal injection of either 10 µg of ferric citrate (Sigma Cat F3388) in 0.85% saline, or 0.85% saline vehicle control. They were then allowed to recover for 7 days isolated from other fish before brains were extracted for RNA-seq

value: whole brain

tag: hometank

value: male

value: hom

value: 10 ug Fe-citrate


title: siPDK4-3 [ATAC-seq]

description: Library name: siPDK4-3


title: H26/0.9 M NaCl/ 68h Repl 2

city: Frankfurt am Main

first: Andreas

last: Borst

address: Max-von-Laue-Str. 9

institute: Goethe-Universität Frankfurt

data_processing:
All downstream analysis of the RNA-Seq results were done using the galaxy platform (https://usegalaxy.eu/).
The “FastQC” tool (version 0.11.9) was used for quality control, while the “RNA STAR” tool (2.7.8a) was applied for mapping to the Haloferax volcanii reference genome and soft-clipping of non-matching sequences. Standard parameters were applied, except for the following: “Maximum ratio of mismatches to mapped length”, which was set to 0.04; “Minimum alignment score, normalized to read length” and “Minimum number of matched bases, normalized to read length”, which were set to 0.66, respectively. Afterwards, the tool “htseq-count” (version 0.9.1) was used for counting all mapped reads of annotated genes. An up-to-date annotation file (September 2023) was thankfully provided by Friedhelm Pfeiffer of the the Max Planck Institute of Biochemistry in Martinsried (Munich, Germany). Finally, differential expression was calculated with the “DESeq2” tool (2.11.40.8) and the data exported for further procession using Microsoft Excel. Significance was obtained by filtering for results with adjusted value of p < 0.05 and at least a 2-fold up- or downregulation. For visualization, the “bamCoverage” tool (version 3.5.1.0.0) was used to create normalized bigwig files.
Assembly: published Haloferax volcanii DS2 genome (Hartman, Amber L et al. “The complete genome sequence of Haloferax volcanii DS2, a model archaeon.” PloS one vol. 5,3 e9605. 19 Mar. 2010, doi:10.1371/journal.pone.0009605)
Supplementary files format and content: normalized perstrand genomic coveragecoverage in bigwig files

organism: Haloferax volcanii

growth_protocol: H. volcanii H26 cultures were grown in glucose medium with either 2.1 M or 0.9 M NaCl

extract_protocol:
total RNA was isolated using phenol/chloroform extraction. Afterwards, the RNA was DNase-I (Thermo Fisher Scientific) digested and again purified with phenol/chloroform extraction. The RNA was shipped to StarSEQ GmbH (Mainz, Germany), where after another quality check the rRNA depletion (NEBNext rRNA depletion Kit) and Sequencing was done (Illumina Next Seq 500; 25 mio PE reads with 2x 150 nt).
NEBNext Ultra II directional, dual index library

treatment_protocol: H. volcanii cultures were grown in 45 ml glucose medium with either 2.1 M or 0.9 M NaCl. 10 ml of cell culture was harvested after 26h while 5ml was taken after 68h by centrifugation.

value: strain DS2

value: WT (deltapyrE2)

value: 0.9 M Nacl


title: xol-1 sex-1, L3, rep3

description: xol-1 sex-1 L3


title: MCF7, control, rep 2

description:
Library name: MCF7 siScramble 2
Column name in deseq2_results_STAR_MCF7_annotated.csv: control_Rep2: Column name in MCF7_counts_allsamples.csv: control_Rep2

value: breast adenocarcinoma

value: siScramble

value: siRNA


title: thalamus,KO,thalamus_5

description: 10x Genomics

value: thalamus

value: KO

value: F


title: thalamus,KO,thalamus_4

description: 10x Genomics

value: 1y 6m 7d

value: M


title: H26/0.9 M NaCl/ 68h Repl 1


title: 89

value: het

value: 0.85% saline


title: xol-1 sex-1, L3, rep2

description: xol-1 sex-1 L3

value: xol-1 sex-1


title: 82

value: whole brain

value: male


title: Scr3 [ATAC-seq]

description: Library name: Scr3

value: aorta

value: primary cells

value: aortic smooth muscle cells

value: WT

value: Scr


title: xol-1 sex-1, L3, rep1

description: xol-1 sex-1 L3


title: siPDK4-1 [ATAC-seq]

description: Library name: siPDK4-1

value: 20nM siPDK4


title: H26/0.9 M NaCl/ 26h Repl 1

value: strain DS2

value: WT (deltapyrE2)

value: 0.9 M Nacl


title: H26/0.9 M NaCl/ 26h Repl 2


title: H26/2.1 M NaCl/ 26h Repl 2

value: 2.1 M Nacl


title: Scr2 [ATAC-seq]

description: Library name: Scr2


title: 79

value: hom

value: 10 ug Fe-citrate


title: xol-1, L3, rep3

description: xol-1 L3


title: WT_herm_1a

description: Nanopore Direct RNA Sequencing of C. elegans wild-type hermaphrodites in young adult stage, biological replicate 1, technical replicate 1

value: whole worm

value: wild type

value: N2 Bristol (CGC)

value: hermaphrodite

value: young adult

value: grown at 20C on NGM plates seeded with E. coli HB101


title: Scr1 [ATAC-seq]

description: Library name: Scr1

value: aorta

value: primary cells


title: H26/2.1 M NaCl/ 26h Repl 1


title: xol-1, L3, rep4

description: xol-1 L3


title: 67

value: whole brain

value: male

value: het

value: 0.85% saline


title: Inflamed_small_intestine_Patient2

type: RNA

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

institute: University of Ulsan College of Medicine

hyb_protocol: The Xenium custom probes were treated on the section slide for hybridization at 50℃ overnight. After slide washing,  ligation was performed at 37°C for 30 minutes. Amplification was immediately processed on the thermal cycler (C1000 96-well, Bio-Rad).  After slide washing, autofluorescence quenching and nuclei staining were performed on the sectioned slide. Subsequently, the sectioned slide was loaded onto the Xenium analyzer (XOA v1.7.6, 10x Genomics) to begin fluorescence signal detection.

scan_protocol: Xenium In Situ Analyzer

data_processing: Raw data were preprocessed with XeniumRanger v1.7.1 (10x Genomics)

label: Xenium Human Probe Set

source_name: 10 µm section Inflamed small intestine

label_protocol: Xenium Human Probe Set

extract_protocol: The OCT embedded frozen tissue blocks were carefully sectioned as 10μm thickness at –18°C cryostat. The sections were mounted onto a Xenium slide. Fixation and Permeabilization followed the manufacturer’s instructions(CG000581, 10x Genomics).

tag: disease state

value: Crohn's disease


title: siACSS2-2 [RNA-seq]

description:
Library name: siACSS2-2
ACSS2-2_002_191_S28

data_processing:
PartekFlow platform
Strict paired-end compatibility was applied for gene expression quantification. Read counts were normalized using the trimmed mean of M-values method.
Assembly: human genome (Hg19)
Supplementary files format and content: normalized Counts per millions generated from raw fastqz files

extract_protocol:
Extraction of total RNA was performed using the RNeasy Mini Kit (14734, Qiagen), according to the manufacturer’s instructions.
Novaseq sequencings with 25 million reads per sample were performed to detect the whole transcriptome. RNA-seq data was aligned to the reference human genome (Hg19) using STAR aligner on PartekFlow platform

treatment_protocol: For RNAi knockdown treatments, 20 nM of PDK4 or ACSS2 siRNA were transfected with RNAimax on day 0 and day 4. RNAs were extracted on day 7.

value: aortic smooth muscle cells

value: WT

value: 20 nM siACSS2


title: xol-1, L3, rep2

description: xol-1 L3


title: 66

value: hom


title: xol-1, L3, rep1

description: xol-1 L3


title: Inflamed_small_intestine_Patient1


title: 65

value: female


title: WT, L3, rep4

description: WT L3


title: siACSS2-1 [RNA-seq]

description:
Library name: siACSS2-1
ACSS2-1_014_179_S27


title: Patient no. 80

first: Katharina

last: Imkeller

address: Heinrich-Hoffmann-Str. 7

institute: University Hospital Frankfurt

description: Xenium In Situ Analyzer

hyb_protocol: Probe hybridisation was performed overnight using a custom pre-designed panel targeting 468 genes, in accordance with the 10x Genomics Xenium platform protocol.

scan_protocol: Data acquisition was performed on the Xenium Analyzer (10x Genomics; instrument software v3.0.2.0, analysis version Xenium-3.0.0.15), generating transcript-by-cell and transcript-by-location matrices. Cell segmentation was performed using the Xenium multimodal cell segmentation kit. Post-acquisition H&E staining was performed for quality control. The transcripts.parquet file from Xenium output were filtered to contain the TLS regions analysed in the study. These cell ids of the TLS regions were manually selected after inspecting the TLS regions on the Xenium Explorere.

data_processing:
Transcript matrices were imported into R using "readXenium" function from the Voyager package. Cells with zero transcripts or nuclear area >400 were excluded. Samples with uniformly low normalised counts were removed. Data were combined into a SpatialFeatureExperiemnt object. TLS regions were identified using Xenium Explorer, and clustering (Leiden) and marker gene analysis were performed for subtype classification. T cell subclustering was performed using a subset of T cell-related genes. Cell-cell communication analysis was performed with CellPhoneDB and visualised using ktplots.
The data contains parquet files of  transcripts, cells, cell_boundaries and nucleus_boundaries along with cell_feature_matrix folder for the transcripts located in the TLS regions, morphology image and the annotations of cell in the TLS regions for each sample.

source_name: TLS+ Glioma

label_protocol: Transcript targets were labelled via enzymatic rolling circle amplificaiton of gene-specific barcodes following probe hybridisation and ligation, as part of the Xenium platform workflow.

extract_protocol: FFPE tissue sections (5 μm) were deparaffinised and decrosslinked according to the manufacturer's protocol prior to probe hybridisation for in situ transcriptomic profiling.

value: TLS+ Glioma


title: WT, L3, rep3

description: WT L3


title: 64

value: 10 ug Fe-citrate


title: 63


title: Patient no. 511

description: Xenium In Situ Analyzer


title: siPDK4-3 [RNA-seq]

description:
Library name: siPDK4-3
siPDK4-3_026_167_S26

value: 20 nM siPDK4


title: 77


title: WT, L3, rep2

description: WT L3


title: siPDK4-2 [RNA-seq]

description:
Library name: siPDK4-2
siPDK4-2_038_155_S25


title: 57


title: siACSS2-3 [RNA-seq]

description:
Library name: siACSS2-3
ACSS2-3_085_108_S29


title: WT, L3, rep1

description: WT L3


title: siPDK4-1 [RNA-seq]

description:
Library name: siPDK4-1
siPDK4-1_050_143_S24


title: Patient no. 565

description: Xenium In Situ Analyzer


title: xol-1 sex-1, L1, rep4

description: xol-1 sex-1 L1, control samples under GSE262626

value: xol-1 sex-1


title: Patient no. 484

description: Xenium In Situ Analyzer


title: Scr3 [RNA-seq]

description:
Library name: Scr3
Scr3_062_131_S23

value: PBS


title: 55


title: Patient no. 548

description: Xenium In Situ Analyzer


title: xol-1 sex-1, L1, rep3


title: 54


title: 52


title: xol-1 sex-1, L1, rep2


title: Scr1 [RNA-seq]

description:
Library name: Scr1
Scr1_086_107_S21

value: aorta


title: Patient no. 567

description: Xenium In Situ Analyzer


title: SLE Patient – Mon 18

city: Heraklion

first: George

last: Bertsias

address: Andrea Kalokerinou 13

department: Medical School

country: Greece

institute: University of Crete

description: SLE Patient – Mon 18

data_processing:
Raw fastQ files were pre-processed by assessing quality control (QC) with FASTQC. Low-quality 3’ read ends (minimum two-colour chemistry score of 20), N tails, and adapter remains were trimmed/clipped using cutadapt, allowing reads of at least 25 nucleotide length. Filtered reads were then mapped against the UCSC hg19 human reference transcriptome using STAR aligner by setting the “-- outFilterMultimapNmax” parameter to 5. Μapped reads were filtered in order to discard chimeric alignments, alignments with more than 2 mismatches, and keep only uniquely aligned reads (MAPQ = 255).
Counting on Ensembl genes and statistical analysis (differential expression analysis) was performed with metaseqR using DESeq2 for normalization and differential testing, and applying default settings for each assay (exon count summarization for RNA-seq and 3’ UTR summarization for Quant-seq). For paired-samples comparisons, ‘donor id’ was included in the DESeq2 model.
Assembly: hg19
Supplementary files format and content: count_matrix_SLEpatients_wholeblood20.txt: contains raw counts for each individual.
Supplementary files format and content: normalized_counts_silencing.txt: contains normalized gene expression counts for each donor across different conditions, using deseq2 normalization.
Supplementary files format and content: normalized_counts_SLEvsHealthy_monocytes.txt: includes normalized counts using deseq2 package.
Supplementary files format and content: metaseqr_all_out_untr_female_vs_untr_male.txt: includes normalized read counts for all analyzed genes for female and male SLE patients, extracting from metaseq.

source_name: peripheral blood

growth_protocol: RPMI-1640, GlutaMAX Supplement (Gibco) including 10% heat-inactivated FBS (Gibco), 100 IU/mL penicillin and 100 μg/mL streptomycin (Gibco)

extract_protocol:
RNA was isolated using the NucleoSpin RNA extraction kit (Macherey-Nagel). RNA was quantitated with the Nanodrop photometric method and quality control was performed with the Agilent Bioanalyzer RNA nano kit.
RNA libraries for RNA-seq were prepared with Illumina TruSeq RNA library prep kit following manufacturer 's protocol.

treatment_protocol: Cultured monocytes were stimulated with 10 ng/ml human macrophage colony-stimulating factor (M-CSF; Peprotech), 10ng/ml recombinant human TNF (Peprotech), 100 IU/ml IFN-α (PBL Science) overnight at 37oC/5% CO2, followed by 10ng/ml LPS (Sigma) challenge for 1-4 hours

value: peripheral blood

value: monocytes

value: untreated

value: SLE


title: Patient no. 157

description: Xenium In Situ Analyzer


title: Patient no. 496

description: Xenium In Situ Analyzer


title: 51

value: whole brain

value: male

value: het


title: xol-1 sex-1, L1, rep1


title: xol-1 sex-1, early embryo, rep3

description: xol-1 sex-1 early embryo, control samples under GSE262626

value: early embryo


title: SLE Patient – Mon 17

description: SLE Patient – Mon 17


title: 48


title: SLE Patient – Mon 16

description: SLE Patient – Mon 16


title: Scr2 [RNA-seq]

description:
Library name: Scr2
Scr2_074_119_S22

value: primary cells

value: aortic smooth muscle cells

value: WT


title: xol-1 sex-1, early embryo, rep1


title: SLE Patient – Mon 15

description: SLE Patient – Mon 15

value: female


title: SLE Patient – Mon 14

description: SLE Patient – Mon 14


title: 43

value: hom

value: 0.85% saline


title: Patient no. 569

description: Xenium In Situ Analyzer

value: TLS+ Glioma


title: Patient no. 210

description: Xenium In Situ Analyzer


title: 41


title: patient 9, AXLN2 LEC, non-metastatic

city: Turku

first: Akira

last: Takeda

state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
The demultiplexing, read alignment and quality control were carried out using the 10X Genomics Cell Ranger package (ver 3.0.1 or 3.1.0).
Assembly: hg19
Supplementary files format and content: Tab-separated values and matrix files

source_name: Non-metastatic lymph node

extract_protocol:
Axillary lymph nodes (AXLNs) were collected from breast cancer patients undergoing mastectomy and AXLN removal. LNs were cut into small pieces, and digested with RPMI containing 0.2 mg/ml collagenase P, 0.8 mg/ml dispase, and 0.1 mg/ml DNase. To confirm the presence of cancer cells in the LNs, a portion of single-cell suspension was stained with AF488-anti-pancytokeratin antibody. Pan-cytokeratin-positive or -negative LNs were considered as metastatic or distant LN, respectively. CD45+ cells were depleted using Human CD45 depletion kit, and the single-cell suspension was incubated with PE-anti-PDPN, AF488-anti-CD45, and APC-anti-CD31. Live CD45- PDPN+ CD31+ LECs were sorted and processed following 10X Genomics guidelines.
scRNA-seq libraries were prepared to according to the manufacturer’s instructions using Chromium Single Cell 3’ Library and Gel Bead Kit v2 and v3 (10x Genomics, 120237) along with Chromium Single Cell A Chip Kit.

value: Non-metastatic lymph node

value: CD31+ PDPN+ cells


title: SLE Patient – Mon 13

description: SLE Patient – Mon 13

value: peripheral blood


title: 53


title: 47

value: 10 ug Fe-citrate


title: SCNT, 4-cell, rep3

city: Tsukuba

first: Inoue

last: Kimiko

address: 3-1-1 Koyadai

institute: RIKEN

description: Library name: SCNT_4C_3

data_processing:
Sequence reads were trimmed for adaptor sequence using fastp.
Trimmed sequence reads were mapped to the mouse genome build mm39 using STAR.
Read count extraction and normalization were performed using featureCounts and R, respectively.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include raw read counts for genes in each sample.

source_name: Embryo

extract_protocol:
Two-cell and four-cell stage embryos derived from IVF and SCNT were collected at 24 and 48 hpi or hpa, washed twice in 0.05% BSA in PBS, and flash-frozen in liquid nitrogen. Ten embryos were pooled as a single sample. After thawing, polyadenylated RNAs were reverse transcribed and amplified, using SMART-Seq HT kits (R400748, Takara Bio, Shiga, Japan).
Library preparation and sequencing were performed using a SMART-Seq HT kits (R400748, Takara Bio, Shiga, Japan).

value: Embryo

value: Wildtype

value: SCNT


title: Patient no. 377

description: Xenium In Situ Analyzer


title: 40

value: whole brain

value: male


title: 39

value: het


title: patient 8, AXLN2 LEC, non-metastatic


title: SLE Patient – Mon 12

description: SLE Patient – Mon 12

value: monocytes

value: untreated

value: SLE


title: Patient no. 351

description: Xenium In Situ Analyzer


title: SLE Patient – Mon 11

description: SLE Patient – Mon 11

value: female


title: patient 8, AXLN1 LEC, metastatic

source_name: Metastatic lymph node

value: Metastatic lymph node


title: SCNT, 4-cell, rep1

description: Library name: SCNT_4C_1


title: patient 9, AXLN1 LEC, metastatic


title: 34

value: hom

value: 0.85% saline


title: xol-1 sex-1, early embryo, rep2

value: early embryo

value: xol-1 sex-1


title: SLE Patient – Mon 10

description: SLE Patient – Mon 10

value: peripheral blood


title: patient 7, AXLN2 LEC, non-metastatic

value: Non-metastatic lymph node

value: CD31+ PDPN+ cells


title: SCNT, 2-cell, rep3

description: Library name: SCNT_2C_3

value: Embryo

value: Wildtype


title: 33

value: whole brain


title: SLE Patient – Mon 9

description: SLE Patient – Mon 9

value: male


title: SCNT, 2-cell, rep2

description: Library name: SCNT_2C_2

value: SCNT


title: SCNT, 2-cell, rep1

description: Library name: SCNT_2C_1


title: SLE Patient – Mon 7

description: SLE Patient – Mon 7

value: monocytes


title: IVF, 4-cell, rep3

description: Library name: IVF_4C_3

value: IVF


title: SCNT, 4-cell, rep2

description: Library name: SCNT_4C_2


title: patient 6, AXLN3 LEC, non-metastatic


title: 32

value: het

value: 10 ug Fe-citrate


title: SLE Patient – Mon 6

description: SLE Patient – Mon 6

value: untreated

value: SLE


title: patient 6, AXLN2 LEC, metastatic

value: Metastatic lymph node


title: IVF, 4-cell, rep2

description: Library name: IVF_4C_2


title: 27

value: female

value: hom

value: 0.85% saline


title: patient 7, AXLN1 LEC, metastatic


title: SLE Patient – Mon 8

description: SLE Patient – Mon 8

value: peripheral blood


title: SLE Patient – Mon 5

description: SLE Patient – Mon 5


title: 26


title: patient 6, AXLN1 LEC, metastatic

value: CD31+ PDPN+ cells


title: patient 5, AXLN4 LEC, metastatic


title: 25


title: IVF, 4-cell, rep1

description: Library name: IVF_4C_1

value: Embryo


title: SLE Patient – Mon 4

description: SLE Patient – Mon 4


title: patient 5, AXLN3 LEC, non-metastatic

value: Non-metastatic lymph node


title: IVF, 2-cell, rep3

description: Library name: IVF_2C_3

value: Wildtype


title: 23

value: whole brain

value: male


title: patient 5, AXLN2 LEC, non-metastatic


title: SLE Patient – Mon 3

description: SLE Patient – Mon 3

value: monocytes


title: IVF, 2-cell, rep2

description: Library name: IVF_2C_2

value: IVF


title: SLE Patient – Mon 2

description: SLE Patient – Mon 2


title: patient 5, AXLN1 LEC, metastatic


title: IVF, 2-cell, rep1

description: Library name: IVF_2C_1


title: 31

value: het


title: SLE Patient – Mon 1

description: SLE Patient – Mon 1


title: 15

value: 10 ug Fe-citrate


title: patient 4, AXLN1 LEC, metastatic


title: 17


title: NTVE-3_ISBM-061_NIH/3T3_spike-in

city: Munich

first: Gil

last: Westmeyer

address: Arcisstrasse 21

institute: Technical University Munich

description:
Library name: 24L010906
Stable NTVE line

data_processing:
Deduplication via czid-dedup (paired-end mode)
featurecounts_harmonized.csv: Paired-end reads were aligned to the combined human-murine index via STAR  (star --readFilesCommand zcat --genomeDir {COMBINED_INDEX_STAR} --readFilesIn {R1} {R2} --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix {OUTPUT_NAME} --quantMode GeneCounts TranscriptomeSAM))
featurecounts_harmonized.csv: Gene level feature counting via featurecounts (featureCounts -a {COMBINED_INDEX_GTF} -o {OUTPUT_FILE}  -g gene_id -t exon -s 2 -p)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: featurecounts_harmonized.csv: comma seperated plaintext file containing the raw counts mapping to features and metadata for all samples
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

value: immortalised cell line

value: Gag:PABP(ZF:Hibit)PABP; Pgk-TetON3g  (ISBM-061)

value: Supernatant

value: 1pg mGL mRNA

value: doxycycline 500ng/ul


title: patient 3, AXLN1 LEC, metastatic

value: Metastatic lymph node


title: ERL, Treated with Erlotinib  10µM - Replicate 2

city: Melbourne

first: Goknur

last: Giner

state: VIC

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
SgRNA counts were obtained via these steps: The human GeCKO v2.1 sgRNA library was obtained in TSV format and loaded into R using read.delim(). The sgRNA sequences were extracted and converted into a DNAStringSet object from the Biostrings package. Each sgRNA sequence was labeled using its unique identifier (UID) for tracking purposes during the alignment process. FASTQ files containing the sequencing data were aligned to the indexed GeCKO library using the align() function in Rsubread. For each FASTQ file, the aligned reads were output to BAM format. To ensure specificity, only uniquely mapped reads were retained (unique = TRUE), and alignments were constrained to allow no mismatches (maxMismatches = 0) and no indels (indels = 0). After alignment, the BAM files were read using the readGAlignments() function from the GenomicAlignments package. Only reads with a width of 20 nucleotides, corresponding to the length of the sgRNA sequences, were retained for counting. The counts were stored in a data frame and combined across all samples to generate a count matrix.
Assembly: Human GeCKOv2A & 2B CRISPR knockout pooled library
Supplementary files format and content: Tab-separated file containing raw sequence sgRNA counts for all samples together with Entrez Geneid.

source_name: ERL

extract_protocol:
All breast cancer cell lines were obtained from the American Type Culture Collection (ATCC). The 4T1.2 cell line was kindly provided by Dr Norman Pouliot, Olivia Newton-John Cancer Research Institute, Australia. All breast cancer cell lines were cultured in DMEM media supplemented with 10% fetal bovine serum (FBS) and 100 nM Sodium Selenite. All cell lines were tested for Mycoplasma infection and authenticated using short tandem repeat (STR) profiling by scientific services at QIMR Berghofer Medical Research Institute. Auranofin was purchased from Cayman Chemicals (Cat #: 15316). Erlotinib (Cat #: S7786) and Osimertinib (Cat #: S7297) were purchased from Selleck Chemicals.  TRi-1 was purchased from MedChem Express (Cat #: HY-125006.
We used the Human GeCKOv2A & 2B CRISPR knockout pooled library to identify genes responsible for erlotinib resistance in TNBC cells. The library was a gift from Feng Zhang (Addgene # 1000000049)
We established a stable Cas9-expressing MDA-MB-231 cell line by lentiviral transduction of Cas9 coding sequence. We then transduced Cas9-expressing MDA-MB-231 cells with GeCKO v2A and B library which contains 123,411 unique sgRNA sequences targeting 19,052 human genes and 1864 miRNAs (6 sgRNAs per gene, 4 sgRNAs per miRNA, and 1000 non-targeting control sgRNAs) at an MOI 0.3 to ensure each cell represents one sgRNA. The transduced cells were then selected with 1 µg/mL of puromycin for 7 days to generate a mutant cell line. The mutant cells were then treated with vehicle (DMSO) and Erlotinib (10 µM) for 7 days, respectively. After 7 days of treatment, the residual cells were collected, and genomic DNA was isolated from each treatment group. The sgRNA sequences were amplified using 9 different sets of primers listed in supplementary Table S2. The amplified sgRNA sequences were subjected to parallel amplicon sequencing at Ramaciotti Centre for Genomics to identify sgRNAs lost in Erlotinib-treated cells.

value: ERL

value: Treated with Erlotinib  10µM


title: NTVE lysate-3_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010903
Stable NTVE line

value: Lysate


title: patient 3, AXLN2 LEC, non-metastatic

value: Non-metastatic lymph node

value: CD31+ PDPN+ cells


title: patient 4, AXLN2 LEC, non-metastatic


title: ERL, Treated with Erlotinib  10µM - Replicate 1


title: ERL, Treated with Erlotinib  10µM - Replicate 3


title: 21

value: whole brain

value: hom


title: ERL, DMSO - Replicate 2

value: DMSO


title: NTVE-2_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010905
Stable NTVE line


title: 20

value: female

value: 0.85% saline


title: NTVE lysate-1_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010901
Stable NTVE line


title: patient 2, AXLN1 LEC, metastatic


title: 12

value: male

value: het


title: NTVE lysate-2_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010902
Stable NTVE line

value: immortalised cell line

value: Gag:PABP(ZF:Hibit)PABP; Pgk-TetON3g  (ISBM-061)


title: 22

value: 10 ug Fe-citrate


title: Purified Neuro2a (ISBM-095) NTVE from co-culture with HEK293T (ISBM-083) via HA-pull-down_spike-in_3

description:
Library name: 24L010909
HA Purified sample of  co-cultivation of two stable NTVE lines

value: NTVE Gag:PABP(ZF:Hibit):P2A:dVSVG:HA; CAG-TetON3g (ISBM-095)

value: Supernatant

value: 1pg mGL mRNA

value: doxycycline 500ng/ul


title: ERL, DMSO - Replicate 3

value: ERL


title: 14


title: ERL, DMSO - Replicate 1


title: patient 1, AXLN4 LEC, metastatic

value: Metastatic lymph node


title: patient 1, AXLN3 LEC, metastatic

value: CD31+ PDPN+ cells


title: 5

value: whole brain


title: NTVE-1_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010904
Stable NTVE line


title: 3


title: CTRL, brain organoid, day56 [scRNA-seq]

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road 268

institute: zhejiang university

description: 10x Genomics

data_processing:
Initial processing was done using Cell Ranger(3.0.2)
data analysis including standardization, cell subpopulation, difference of gene expression, and marker gene screening were achieved by Seurat software
Assembly: Genome_build: GRCh38
Supplementary files format and content: h5 exported by cellranger

source_name: neuron

extract_protocol:
Three sets of human D56 forebrain organoids derived from three sets of CTRL and WS iPSCs were dissociated with 3 mL Tryp-LE (Sigma-Aldrich) and for 15 minutes at 37°C, followed by 2 washes with 3% FBS in DPBS and gentle titration using a P1000 pipette. A single-cell suspension was subsequently collected into 2 mL microtubes with a cell density of 1000 cells/μL. Then the suspensions were added to a 10X Genomics GemCode Single-cell instrument to generates a single-cell Gel Bead-In-EMlusion
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs 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 apropiated sized 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.

tag: tissue/cell type

value: brain organoids

value: neuron

value: wt


title: 2

value: female

value: hom

value: 0.85% saline


title: Purified Neuro2a (ISBM-095) NTVE from co-culture with HEK293T (ISBM-083) via HA-pull-down_spike-in_2

description:
Library name: 24L010908
HA Purified sample of  co-cultivation of two stable NTVE lines

value: immortalised cell line


title: patient 1, AXLN1 LEC, metastatic


title: DN0_4106

status: Public on Aug 31 2025

city: jerusalem

first: hermona

last: soreq

state: -- Select --

address: The Edmond J. Safra Campus, Givat Ram

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Base calling, QC and fastq file generation by the illumina Basespace platform
counts were normalized using RLE
Alignment to mirBase v.21 using miRExpress 2
Normalization and Differential expression using Deseq2
Genome_build: mirBase v.21
Supplementary_files_format_and_content: One .txt file per sample with aligned miR counts

source_name: Human blood leukocytes

extract_protocol:
[sample collection and cell extraction] Blood was withdrawn between 8 and 9 AM after over-night fasting after excluding current infection and heavy physical activity, heavy meal, and alcohol consumption on the previous day. 3 x 9.5 ml blood was collected in EDTA monovettes (not containing heparin) for white blood cell isolation. Tubes were gently mixed by manually inverting ten times each. For plasma collection 2 x 8 ml were used; for white blood cell isolation 3 x 1.5 ml were further processed. Buffer EL (7.5 ml, Qiagen, cat#: 79217) was added and samples were incubated on ice for 25 min. At 7 and 15 min the samples were mixed and then centrifuged (400 g, 10 min, 4°C). The supernatant was discarded and the cell pellet was re-suspended in 3 ml of Buffer EL before centrifuged again (400 g, 10 min, 4°C). The supernatant was again discarded and the cell pellet re-suspended in 1.5 ml of RNA protect cell reagent (Qiagen, cat#: 76526). Samples were then stored at -80°C before further processing.
Total RNA was extracted using the MiRNeasy miRNA isolation kit (Quiagen). All samples were kept on ice, tubes were centrifuged at 5000rcf to precipitate the cells, and overlaying RNA later solution was removed. Cells were disrupted with a plastic pestle and homogenized in 500µl (700µl for mouse tissues) Trizol lysis buffer. Following incubation for 5 min in room temperature 100 µl (accounting for 1:5 of the total volume) of chloroform was added to each sample. Samples were shortly vortexed and incubated for 2-3 min at room temperature, and were centrifuged at 4°C for 15 min at 12000rcf. The supernatant was mixed with absolute ethanol (1.25 times the supernatant volume) and the mixture was washed using the provided washing solutions and filter sets. Samples were eluted in 15µl (14µl for mouse tissues) RNAse free DDW. RNA quality and quantity was measured using a Nanodrop 2000 (PeqLab/Thermo Scientific). A total of 100µg per sample was run on an agarose gel for quality control. And RNA integrity was further tested using the 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano LabChip Kits (Agilent Technologies) and achieved an average RIN value of 7.5.
An even amount of 150ng RNA per sample was used for small-RNA library construction using the New England BioLabs NEB-next multiplex small-RNA library construction kit. The library was size selected based on DNA 1000 LabChip kits by 2100 Bioanalyzer (Agilent Technologies) results to 146bp long transcripts which include the barcodes, adaptors and ca. 20bp long miRNAs. This ensures that sequenced transcripts are in the maximum length of 30 bp only. Libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen)
Sequencing was run in the The NextSeq Series desktop sequencing system of the Illumina platform. The number of Pass Filter reads per sample was at the range of (13-14*10^6 reads). Read counts and quality for each sample were evaluated with the BaseSpace Sequencing QC report tool.

tag: individual

value: patient no. 4106

value: Adult greater than or equal to 18 years old

tag: gender

value: pooled male and female

value: Diabetes polyneuropathy without pain

value: leukocytes


title: DN0_4116

value: patient no. 4116


title: DN0_4110

value: patient no. 4110


title: DN0_4112

value: patient no. 4112


title: DN1_4115

value: patient no. 4115

value: Diabetes polyneuropathy with pain


title: DN1_4100

value: patient no. 4100


title: DN1_4098

value: patient no. 4098


title: NL0_4096

value: patient no. 4096

value: nerve lesion without pain


title: DN1_4102

value: patient no. 4102


title: DN0_4105

value: patient no. 4105


title: DN0_4114

value: patient no. 4114


title: DN0_4101

value: patient no. 4101


title: DN1_4094

value: patient no. 4094

value: Adult greater than or equal to 18 years old


title: DN1_4099

value: patient no. 4099

value: pooled male and female


title: DN0_4093

value: patient no. 4093

value: Diabetes polyneuropathy without pain

value: leukocytes


title: DN1_4092

value: patient no. 4092


title: DN1_4117

value: patient no. 4117

value: Diabetes polyneuropathy with pain


title: DN1_4108

value: patient no. 4108


title: DN0_4095

value: patient no. 4095


title: NL1_4091

value: patient no. 4091

value: nerve lesion with pain


title: NL1_4090

value: patient no. 4090


title: WS, brain organoid, day56 [scRNA-seq]

description: 10x Genomics

value: brain organoids

value: neuron

value: ws


title: patient 1, AXLN2 LEC, metastatic

tag: tissue

value: Metastatic lymph node

value: CD31+ PDPN+ cells


title: Purified Neuro2a (ISBM-095) NTVE from co-culture with HEK293T (ISBM-083) via HA-pull-down_spike-in_1

description:
Library name: 24L010907
HA Purified sample of  co-cultivation of two stable NTVE lines

tag: cell line

value: immortalised cell line

value: NTVE Gag:PABP(ZF:Hibit):P2A:dVSVG:HA; CAG-TetON3g (ISBM-095)

value: Supernatant

value: 1pg mGL mRNA

value: doxycycline 500ng/ul


title: DN0_4109

value: patient no. 4109

value: Adult greater than or equal to 18 years old

value: pooled male and female

value: Diabetes polyneuropathy without pain

tag: cell type

value: leukocytes


title: DN1_4111

value: patient no. 4111

value: Diabetes polyneuropathy with pain


title: DN0_4088

value: patient no. 4088


title: DN0_4087

value: patient no. 4087


title: DN1_4089

value: patient no. 4089


title: DN1_4086

value: patient no. 4086


title: DN1_4085

value: patient no. 4085


title: NL1_4084

value: patient no. 4084

value: nerve lesion with pain


title: DN1_4082

value: patient no. 4082


title: C_4081

value: patient no. 4081

value: Healthy controls


title: DN0_4080

value: patient no. 4080


title: DN1_4083

value: patient no. 4083

value: Adult greater than or equal to 18 years old


title: NL1_4079

value: patient no. 4079

value: pooled male and female


title: C_4078

value: patient no. 4078

value: leukocytes


title: C_4075

value: patient no. 4075


title: DN1_4066

value: patient no. 4066

value: Diabetes polyneuropathy with pain


title: DN0_4071

value: patient no. 4071

value: Diabetes polyneuropathy without pain


title: DN1_4072

value: patient no. 4072


title: DN1_4069

value: patient no. 4069


title: NL1_4070

value: patient no. 4070

value: nerve lesion with pain


title: DN1_4073

value: patient no. 4073


title: C_4076

value: patient no. 4076

value: Healthy controls


title: DN1_4065

value: patient no. 4065

value: Adult greater than or equal to 18 years old


title: DN0_4068

value: patient no. 4068

value: pooled male and female


title: DN1_4067

value: patient no. 4067

value: leukocytes


title: C_4063

value: patient no. 4063


title: C_4064

value: patient no. 4064


title: DN1_4062

value: patient no. 4062

value: Diabetes polyneuropathy with pain


title: DN1_4059

value: patient no. 4059


title: DN1_4057

value: patient no. 4057


title: DN1_4060

value: patient no. 4060


title: DN1_4058

value: patient no. 4058


title: DN1_4061

value: patient no. 4061


title: DN1_4056

value: patient no. 4056


title: C_4077

value: patient no. 4077

value: Healthy controls


title: C_4074

value: patient no. 4074

value: Adult greater than or equal to 18 years old


title: DN0_4055

value: patient no. 4055

value: pooled male and female

value: Diabetes polyneuropathy without pain


title: DN1_4052

value: patient no. 4052

value: leukocytes


title: C_4051

value: patient no. 4051


title: DN1_4050

value: patient no. 4050

value: Diabetes polyneuropathy with pain


title: DN0_4049

value: patient no. 4049


title: DN1_4046

value: patient no. 4046


title: DN0_4045

value: patient no. 4045


title: DN1_4044

value: patient no. 4044


title: DN1_4041

value: patient no. 4041


title: DN1_4039

value: patient no. 4039


title: NL1_4038

value: patient no. 4038

value: nerve lesion with pain


title: DN0_4047

value: patient no. 4047

value: Adult greater than or equal to 18 years old


title: DN1_4040

value: patient no. 4040

value: pooled male and female


title: DN1_4037

value: patient no. 4037


title: DN1_4036

value: patient no. 4036

value: leukocytes


title: DN1_4032

value: patient no. 4032


title: DN1_4034

value: patient no. 4034

value: Diabetes polyneuropathy with pain


title: DN1_4035

value: patient no. 4035


title: C_4029

value: patient no. 4029

value: Healthy controls


title: DN1_4028

value: patient no. 4028


title: DN1_4031

value: patient no. 4031


title: DN0_4027

value: patient no. 4027

value: Diabetes polyneuropathy without pain


title: DN1_4026

value: patient no. 4026


title: DN1_4053

value: patient no. 4053

value: Adult greater than or equal to 18 years old


title: DN1_4054

value: patient no. 4054

value: pooled male and female


title: DN0_4025

value: patient no. 4025


title: DN0_4024

value: patient no. 4024

value: leukocytes


title: NL0_4023

value: patient no. 4023

value: nerve lesion without pain


title: DN1_4048

value: patient no. 4048

value: Diabetes polyneuropathy with pain


title: DN0_4043

value: patient no. 4043


title: DN0_4042

value: patient no. 4042


title: DN1_4021

value: patient no. 4021


title: DN1_4020

value: patient no. 4020


title: C_4019

value: patient no. 4019

value: Healthy controls


title: DN0_4033

value: patient no. 4033

value: Diabetes polyneuropathy without pain


title: DN1_4016

value: patient no. 4016

value: Adult greater than or equal to 18 years old


title: C_4013

value: patient no. 4013

value: pooled male and female


title: DN1_4017

value: patient no. 4017

value: leukocytes


title: DN1_4011

value: patient no. 4011


title: DN1_4018

value: patient no. 4018


title: C_4022

value: patient no. 4022


title: C_4007

value: patient no. 4007


title: C_4006

value: patient no. 4006


title: DN0_4008

value: patient no. 4008


title: C_4012

value: patient no. 4012


title: C_4005

value: patient no. 4005


title: DN1_4015

value: patient no. 4015

value: Diabetes polyneuropathy with pain


title: C_4030

value: patient no. 4030

value: Healthy controls


title: C_4002

value: patient no. 4002

value: Adult greater than or equal to 18 years old


title: C_4010

value: patient no. 4010

value: pooled male and female


title: C_4003

value: patient no. 4003

value: leukocytes


title: C_4009

value: patient no. 4009


title: C_4001

value: patient no. 4001


title: noCRPS_3067

value: patient no. 3067

value: Heathy healing fracture patients


title: DN1_4004

value: patient no. 4004


title: noCRPS_3062

value: patient no. 3062


title: noCRPS_3065

value: patient no. 3065


title: CRPS_3064

value: patient no. 3064

value: CRPS patient


title: CRPS_3063

value: patient no. 3063


title: C_3066

value: patient no. 3066

value: Healthy controls


title: noCRPS_3061

value: patient no. 3061

value: Adult greater than or equal to 18 years old


title: CRPS_3058

value: patient no. 3058

value: pooled male and female


title: noCRPS_3060

value: patient no. 3060

value: leukocytes


title: noCRPS_3059

value: patient no. 3059


title: noCRPS_3057

value: patient no. 3057


title: C_3055

value: patient no. 3055


title: CRPS_3054

value: patient no. 3054


title: noCRPS_3052

value: patient no. 3052

value: Heathy healing fracture patients


title: C_3051

value: patient no. 3051


title: C_3050

value: patient no. 3050


title: NL0_3048

value: patient no. 3048

value: nerve lesion without pain


title: CRPS_3046

value: patient no. 3046

value: CRPS patient


title: NL1_3047

value: patient no. 3047

value: Adult greater than or equal to 18 years old

value: nerve lesion with pain


title: CRPS_3045

value: patient no. 3045

value: pooled male and female


title: CRPS_3044

value: patient no. 3044

value: leukocytes


title: CRPS_3042

value: patient no. 3042


title: CRPS_3041

value: patient no. 3041


title: CRPS_3043

value: patient no. 3043


title: CRPS_3037

value: patient no. 3037


title: CRPS_3036

value: patient no. 3036


title: CRPS_3040

value: patient no. 3040


title: CRPS_3039

value: patient no. 3039


title: NL1_3034

value: patient no. 3034


title: CRPS_3035

value: patient no. 3035


title: CRPS_3032

value: patient no. 3032

value: CRPS patient


title: NL1_3025

value: patient no. 3025

value: Adult greater than or equal to 18 years old


title: CRPS_3026

value: patient no. 3026


title: CRPS_3033

value: patient no. 3033

value: pooled male and female


title: CRPS_3031

value: patient no. 3031

value: leukocytes


title: CRPS_3027

value: patient no. 3027


title: CRPS_3024

value: patient no. 3024


title: CRPS_3023

value: patient no. 3023


title: CRPS_3053

value: patient no. 3053


title: CRPS_3022

value: patient no. 3022


title: CRPS_3019

value: patient no. 3019


title: CRPS_3020

value: patient no. 3020


title: CRPS_3017

value: patient no. 3017


title: CRPS_3016

value: patient no. 3016


title: DN1_3013

value: patient no. 3013

value: Diabetes polyneuropathy with pain


title: noCRPS_3010

value: patient no. 3010

value: Adult greater than or equal to 18 years old

value: Heathy healing fracture patients


title: CRPS_3012

value: patient no. 3012

value: pooled male and female

value: CRPS patient


title: CRPS_3005

value: patient no. 3005

value: leukocytes


title: CRPS_3006

value: patient no. 3006


title: CRPS_3003

value: patient no. 3003


title: C_2032

value: patient no. 2032

value: Healthy controls


title: CRPS_3002

value: patient no. 3002


title: noCRPS_2031

value: patient no. 2031


title: noCRPS_2030

value: patient no. 2030


title: noCRPS_2026

value: patient no. 2026


title: C_2027

value: patient no. 2027


title: C_2028

value: patient no. 2028


title: C_2025

value: patient no. 2025

value: Adult greater than or equal to 18 years old


title: C_2023

value: patient no. 2023


title: C_2029

value: patient no. 2029

value: pooled male and female


title: C_2024

value: patient no. 2024


title: CRPS_3018

value: patient no. 3018

value: CRPS patient

value: leukocytes


title: C_2021

value: patient no. 2021


title: CRPS_3015

value: patient no. 3015


title: C_2022

value: patient no. 2022

value: Healthy controls


title: CRPS_2019

value: patient no. 2019


title: noCRPS_2020

value: patient no. 2020

value: Heathy healing fracture patients


title: noCRPS_2018

value: patient no. 2018


title: noCRPS_2017

value: patient no. 2017


title: CRPS_3008

value: patient no. 3008

value: Adult greater than or equal to 18 years old


title: noCRPS_2013

value: patient no. 2013


title: CRPS_3004

value: patient no. 3004

value: pooled male and female


title: CRPS_2014

value: patient no. 2014


title: CRPS_2012

value: patient no. 2012

value: CRPS patient


title: NL1_3009

value: patient no. 3009

value: nerve lesion with pain

value: leukocytes


title: noCRPS_2011

value: patient no. 2011


title: noCRPS_2009

value: patient no. 2009


title: noCRPS_2008

value: patient no. 2008


title: noCRPS_2007

value: patient no. 2007

value: Heathy healing fracture patients


title: noCRPS_2006

value: patient no. 2006


title: noCRPS_2010

value: patient no. 2010


title: CRPS_2005

value: patient no. 2005

value: Adult greater than or equal to 18 years old


title: noCRPS_2004

value: patient no. 2004


title: CRPS_2001

value: patient no. 2001

value: pooled male and female


title: CRPS_2003

value: patient no. 2003


title: NL1_1034

value: patient no. 1034


title: NL0_1036

value: patient no. 1036

value: nerve lesion without pain


title: C_1035

value: patient no. 1035

value: Healthy controls

value: leukocytes


title: CRPS_2002

value: patient no. 2002

value: CRPS patient


title: NL1_1033

value: patient no. 1033

value: nerve lesion with pain


title: noCRPS_2015

value: patient no. 2015

value: Heathy healing fracture patients


title: C_1032

value: patient no. 1032

value: Adult greater than or equal to 18 years old


title: C_1031

value: patient no. 1031


title: CRPS_2016

value: patient no. 2016

value: pooled male and female


title: NL0_1027

value: patient no. 1027


title: NL0_1026

value: patient no. 1026


title: NL1_1029

value: patient no. 1029


title: NL0_1028

value: patient no. 1028

value: nerve lesion without pain


title: NL0_1025

value: patient no. 1025

value: leukocytes


title: NL1_1023

value: patient no. 1023


title: NL0_1024

value: patient no. 1024


title: NL0_1021

value: patient no. 1021


title: NL0_1022

value: patient no. 1022


title: NL0_1020

value: patient no. 1020


title: NL0_1019

value: patient no. 1019


title: C_1017

value: patient no. 1017

value: Adult greater than or equal to 18 years old

value: Healthy controls


title: C_1018

value: patient no. 1018

value: pooled male and female


title: NL0_1016

value: patient no. 1016


title: C_1015

value: patient no. 1015


title: DN0_1014

value: patient no. 1014

value: Diabetes polyneuropathy without pain


title: C_1013

value: patient no. 1013


title: NL0_1030

value: patient no. 1030

value: nerve lesion without pain

value: leukocytes


title: NL0_1009

value: patient no. 1009


title: NL0_1011

value: patient no. 1011


title: DN1_1008

value: patient no. 1008

value: Diabetes polyneuropathy with pain


title: DN1_1005

value: patient no. 1005


title: CRPS_1004

value: patient no. 1004

value: Adult greater than or equal to 18 years old

value: CRPS patient


title: DN0_1010

value: patient no. 1010

value: pooled male and female


title: NL1_1007

value: patient no. 1007

value: nerve lesion with pain


title: DN1_1001

value: patient no. 1001


title: E9_floxsham

source_name: Dorsal root ganglia

extract_protocol:
[sample collection and cell extraction] Dorsal Root Ganglia (DRG) containing the cell bodies of primary sensory afferents were harvested in cold Dulbecco's Modified Eagle Medium (DMEM, Gibco) and subsequently transferred to cold Phosphate Buffered Saline (PBS, Gibco). PBS was carefully discarded and samples were snap-frozen in liquid nitrogen. All samples were kept at -80°C until use. Only ipsilateral to the injury DRGs of the spinal level lumbar 3-5 were taken since neurons of these ganglia give rise to the sciatic nerve in mice.
Total RNA was extracted using the MiRNeasy miRNA isolation kit (Quiagen). All samples were kept on ice, tubes were centrifuged at 5000rcf to precipitate the cells, and overlaying RNA later solution was removed. Cells were disrupted with a plastic pestle and homogenized in 500µl (700µl for mouse tissues) Trizol lysis buffer. Following incubation for 5 min in room temperature 100 µl (accounting for 1:5 of the total volume) of chloroform was added to each sample. Samples were shortly vortexed and incubated for 2-3 min at room temperature, and were centrifuged at 4°C for 15 min at 12000rcf. The supernatant was mixed with absolute ethanol (1.25 times the supernatant volume) and the mixture was washed using the provided washing solutions and filter sets. Samples were eluted in 15µl (14µl for mouse tissues) RNAse free DDW. RNA quality and quantity was measured using a Nanodrop 2000 (PeqLab/Thermo Scientific). A total of 100µg per sample was run on an agarose gel for quality control. And RNA integrity was further tested using the 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano LabChip Kits (Agilent Technologies) and achieved an average RIN value of 7.5.
An even amount of 150ng RNA per sample was used for small-RNA library construction using the New England BioLabs NEB-next multiplex small-RNA library construction kit. The library was size selected based on DNA 1000 LabChip kits by 2100 Bioanalyzer (Agilent Technologies) results to 146bp long transcripts which include the barcodes, adaptors and ca. 20bp long miRNAs. This ensures that sequenced transcripts are in the maximum length of 30 bp only. Libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen)
Sequencing was run in the The NextSeq Series desktop sequencing system of the Illumina platform. The number of Pass Filter reads per sample was at the range of (13-14*10^6 reads). Read counts and quality for each sample were evaluated with the BaseSpace Sequencing QC report tool.

tag: genotype

value: gp130 Floxed

value: sham

value: Dorsal root ganglia


title: Primary white adipose SVF cells (P0)

city: Madison

first: Andrea

last: Galmozzi

state: WI

address: 6151 WIMR, 1111 Highland Av, WIMR I, room 6151

institute: UW Madison SMPH

description:
Library name: 0WAT
10x Genomics Chromium Single Cell 3ʹ v3.1

data_processing:
Cell Ranger 7.0.1 from 10X Cloud analysis was utilized for demultiplexing, alignment, filtering, barcode counting, UMI counting, and gene expression estimation, using default parameters.
Assembly: mouse mm10 2020-A genome.
Supplementary files format and content: tab-separated values files, matrix files

source_name: Primary

growth_protocol: Primary WAT and BAT progenitors were isolated as previously described(Galmozzi et al., 2021). Briefly, subcutaneous white and interscapular brown depots were dissected from male and female C57/BL6 P0 mice into 250 μL ice-cold PBS and 200 μL 2X isolation buffer (123 mM NaCl, 5 mM KCl, 1.3 mM CaCl2, 5 mM glucose, 100 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), penicillin-streptomycin, and 4% fatty acid-free bovine serum albumin). Tissues were minced using small scissors, then 50 μL of 15 mg/mL collagenase type I was added and incubated at 37°C on a shaker for 35 (WAT) and 50 (BAT) minutes, respectively. After digestion, samples were filtered through a 100 μm cell strainer into 10 mL isolation medium (Dulbecco’s modified Eagle medium (DMEM) + 20% fetal bovine serum (FBS), 10 mM HEPES, 1% penicillin-streptomycin) into a 10 cm dish and incubated at 37°C, 5% CO2 for 1.5 hours, followed by three washes with serum-free DMEM to remove blood cells and tissue debris. After washing, 10 mL of isolation medium was added, and cells were incubated overnight. The following day, cells were washed again with serum-free DMEM and maintained in isolation media, which was thereafter refreshed every 2 days.

extract_protocol:
After reaching confluency (in 4 days), cells were washed with PBS and lifted with Trypsin-EDTA for 3 minutes. WAT and BAT progenitor suspensions were then washed in isolation media, counted and live cells processed for single-cell sequencing
Single-cell RNA sequencing was conducted by the University of Wisconsin-Madison Biotechnology Center’s Gene Expression Center Core Facility using the 10x Genomics Chromium Single Cell 3ʹ v3.1 platform. Single-cell suspensions were loaded onto the Chromium Next GEM Chip, where cells were partitioned into Gel Bead-In-EMulsions (GEMs) for reverse transcription (RT). Post GEM-RT, cDNA was recovered and purified using DynaBeads MyOne Silane beads (Lot# 160221), followed by amplification through 12 cycles of PCR. The amplified cDNA underwent cleanup with SPRIselect beads (0.6X, Lot# 18198500) and quality was checked using an Agilent HS DNA chip. For library construction, cDNA was fragmented, end-repaired, and A-tailed, with double-sided size selection using SPRIselect beads (0.6x and 0.8x, Lot# 18198500). Adapter ligation was performed, followed by post-ligation cleanup with SPRIselect beads (0.8x). Index PCR was carried out with 7 cycles using the Chromium Dual Index TT Set A (Lot# 160185). The final library was cleaned using SPRIselect beads (0.6x and 0.8x), recovering 35 μL in EB buffer. Library concentration was determined using a Qubit Fluorometer with Qubit dsDNA HS reagents. Final quality control was performed using an Agilent TapeStation with D1000 ScreenTape. Sequencing was initially conducted on a MiSeq Nano, followed by final sequencing on an SP flow cell.

value: White adipose

value: Adipose precursor cells

tag: age


title: Primary brown adipose SVF cells (P0)

description:
Library name: 0BAT
10x Genomics Chromium Single Cell 3ʹ v3.1

value: Brown adipose


title: E7_floxsham

tag: treatment


title: DN0_1002

value: patient no. 1002

value: Diabetes polyneuropathy without pain

value: leukocytes


title: E2_floxno

value: no


title: E8_floxsham


title: E3_floxno


title: E15_floxsni

value: sni


title: E1_floxno


title: E14_floxsni


title: E13_floxsni


title: medullary thymic epithelial cell, Aebp2-flox, replicate 2, cut-tag_H3K27me3

status: Public on Aug 30 2025

city: Hangzhou

first: Yiyan

last: Zheng

address: Zhiqiang Road 428

institute: Westlake Laboratory of Life Sciences and Biomedicine

description: Library name: WT2 mTEC_cuttag_H3K27me3

library_source: other

data_processing:
For bulkRNAseq, raw reads were mapped to the Mus musculus (mm10) reference genome using HISAT2. HISAT was run in a 2-pass approach with options “--score-min L,0.0,-0.2” and known splice sites for the first pass, and novel splice sites detected across all samples for the second pass. Gene-level count data was obtained using featureCounts program (http://bioinf.wehi.edu.au/featureCounts/). For scRNAseq and scATACseq, barcode processing and mapping to the mouse genome was performed with Cell Ranger v3.0. For Cut&tag, all peak calling was performed with MACS2 (v 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Assembly: Mouse mm10
Supplementary files format and content: Excel file, matrix files and bigwig files
Library strategy: CUT&Tag

molecule: other

source_name: thymus

extract_protocol:
Thymi were isolated and cleaned to get rid of the residual fat and connective tissue, followed by a serial steps of enzymatic digestion with 0.15% mg/ml Liberase TM in RPMI 1640 at 37 °C. For adult thymi, CD45- cells were enriched with anti-CD45 beads and MACS LS columns (Miltenyi) followed by FACS sorting to harvest living CD45-Ter119-EpCAM+ thymic epithelial cells. The enriched total TECs or mTEChi (UEA1+MHCIIhi) were subjected to scRNA-seq, scATAC-seq, Cut&Tag, bulk RNA-seq.
Liraries for scRNAseq, scATACseq, Cut&tag, and bulkRNAseq were prepared following the manufactures' instructions described in the paper's method section.

value: thymus

value: thymic epithelial cell

value: medullary thymic epithelial cell

value: wild type


title: medullary thymic epithelial cell, Aebp2-ko, replicate 2, cut-tag_H3K27me3

description: Library name: KO2 mTEC_cuttag_H3K27me3

value: knockout