title: Single Cell ATAC-seq of Gallus gallus embryonic tissue

city: Plön

first: Stella

last: Kyomen

address: August-Thienemann-Strasse 2

country: Germany

institute: Max Planck Institute for Evolutionary Biology

description: Library name: kyomen_HH22_scATAC

library_source: genomic single cell

data_processing:
Raw sequencing reads were processed using the Cell Ranger ATAC pipeline (v2.1.0). Base calls were demultiplexed with the “cellranger-atac mkfastq” function. For chicken, a custom reference genome was created using “cellranger-atac mkref” based on the galGal6 assembly (GenBank assembly GCA_000002315.5).
Assembly: galGal6
Supplementary files format and content: Tab-separated file containing fragments of chicken scATAC-seq data.

organism: Gallus gallus

source_name: Facial prominences

extract_protocol:
Frontonasal prominences were carefully dissected from freshly collected chicken HH22 embryos using sharp forceps. For both single-cell technologies, facial prominences from at least 30 embryos were pooled. The following procedure was applied to both species independently. Dissected facial tissues were placed into 1.5ml Eppendorf tubes containing ice-cold PBS. The samples were centrifuged at 500g for 5 minutes at +4°C. After carefully removing the PBS, 1 ml of pre-warmed Trypsin solution (0.05% Trypsin/0.02% EDTA, Pan Biotech, P10-0235SP) was added to each tube and incubated in a thermomixer at 37°C for 15 minutes with gentle agitation. To ensure thorough mixing, the samples were gently vortexed for 30 seconds every 5 minutes during the incubation period. Following incubation, tissue dissociation was carried out by carefully pipetting the samples up and down for 15 seconds. Once the cell suspension appeared homogeneous, 200µl of pre-warmed FBS was added to the samples to quench the enzymatic reaction. After another round of centrifugation at 500g for 5 minutes at +4°C, the supernatant was carefully removed without disrupting the pellet. The cells were then resuspended in 1ml of cold PBS and 2.5µl of RNAse inhibitor (Thermo Fisher Scientific, N8080119) and spun down at 500g for 5 minutes at +4°C. The washing step was repeated three more times to remove any excess trypsin and cell debris. The resulting suspension was subsequently filtered through a 35µm cell strainer (Falcon™, 352235). Assessment of cell viability and concentration was performed by adding 1:1 proportion of 0.4% Trypan blue dye (Gibco™, 15250061) to an aliquot of the cell suspension. Cells were loaded in C-Chip haemocytometer slides (NanoEnTek, DHC-N01) and assessed using a stereomicroscope. When the cell viability was at least 95%, the cell suspension was diluted in nuclease-free water to contain 1.2k cells/µl, ensuring optimal conditions for downstream processes and aligned with the experimental requirements outlined by 10x Genomics protocol, targeting 10,000 cells. For scATAC-seq, the nuclei isolation protocol was executed following the guidelines of 10x Genomics. After dissociation, cells were centrifuged for 5 min 500g at 4+C. The supernatant was removed and the cell pellet was incubated in 100µl of cold Lysis Buffer (Tris-HCL 10mM, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, BSA 1%) for 5 minutes on ice. After incubation, 500µl of Wash Buffer (Tris-HCL 10mM, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, BSA 1%) was added. The samples were then centrifuged at 500g for 5 minutes at +4°C, and the resulting nuclei pellet was resuspended in Diluted Nuclei Buffer (10x Genomics Nuclei Buffer; 2000153). Nuclei concentration and viability were assessed using the same procedures as for the scRNA-seq. The nuclei concentration was appropriately adjusted to achieve the desired input for tagmentation.
The scATAC-seq libraries were generated in accordance with the recommended protocol provided by 10x Genomics (Chromium Single Cell ATAC). In summary, 5µl of resuspended nuclei dilution was combined with 10µl of Transposition Mix to yield a final volume of 15µl. These samples were then subjected to an incubation step in a thermal cycler at 37°C for 30 minutes. GEM generation was performed using the Chromium Next GEM Chip H, following the protocol of the manufacturer. After the incubation, 40µl of eluted DNA was retrieved using the magnetic separator. An additional cleanup step was conducted using reagent SPRIselect (Beckman Coulter SPRIselect Reagent Kit B23318). For library preparation, each sample was supplemented with 57.5µl of Sample Index PCR Mix along with 2.5µl of individual Single Index N Set A (3000427). These samples were then incubated following the 10x Genomics protocol for a specified number of cycles that match the targeted nuclei recovery. Subsequent to amplification, fragment size selection was carried out until a recovered sample volume of 20µl was obtained. DNA was quantified using Invitrogen™ Qubit™ dsDNA assay-kit and a Qubit™ fluorometer (Thermo Fisher Scientific, 10616763). The resulting libraries were stored at -20°C until sequencing. Libraries were sequenced with paired-end 50 bp reads, targeting 50k reads per nucleus on the Illumina NovaSeq 6000 S1.

value: Facial prominences

value: WT

tag: time

value: HH22 embryonic stage


title: Melanoma, A-F05

status: Public on Mar 24 2026

type: SRA

city: ANN ARBOR

first: Ziyin

last: Huang

state: MI

address: 3003 S. STATE STREET

country: USA

institute: University of Michigan

description: Library name: DSP-1001250002572-A-F05

library_source: transcriptomic

data_processing:
The GeoMx DSP Analysis Pipeline version 2.3.3.10 performed trimming, alignment, and deduplication of UV-cleaved probe barcodes
Assembly: GRCh38
Supplementary files format and content: csv files include TPM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Melanoma

extract_protocol:
The TMA underwent staining for CD20 (B cells), CD3 (T cells), and DNA to guide region of interest (ROI) selection. ROIs were drawn to maximize tumor content within each tissue spot on the TMA. Full ROIs were profiled without the use of segmentation to avoid inadequate cell counts.
DSP-derived oligos were dried down and rehydrated in 10 µL nuclease-free water. Libraries were prepared and pooled according to the NanoString GeoMx DSP protocol for Human Whole Transcriptome Atlas (WTA) RNA samples. Final pooled libraries were assessed for quality and quantity using the Agilent TapeStation D1000 assay and Qubit prior to sequencing.

tag: aoi

tag: tissue

value: Melanoma

tag: patient

tag: has replicate_(1=yes,_0=no)

tag: replicate (1=yes,_0=no)

tag: included in_analysis_(1=yes,0=no)

tag: lymph node_status_(1=yes,_0=no)

tag: distant metastasis_(1=yes,_0=no)

tag: acral melanoma_(1=yes,_0=no)

tag: vital status

tag: overall survival(years)


title: S2W-CCL4-PBS-HSC-3

city: Shanghai

first: Tao

last: Le

address: LANXI ROAD 164

country: China

institute: Shanghai University of traditional Chinese Medicine

description: Library name: SAMPLES3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence / low - quality sequence using CLC genomic benchwork ( parameter - Quality limit :0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork ( parameters - mismath cost :2 insertion cost :3 deletion cost :3 length fraction :0.8 similarity fraction :0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: hg38
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

organism: Mus musculus

source_name: primary hepatic stellate cells

growth_protocol: BucheKI/KI-Hep mice were housed in a room at 25℃ with a 12-hour lingh/dark cycle and understricted access to chow food and water

extract_protocol:
RNA was harvested using Rneasy mini plus kit ( Qiagen ).1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell type

value: primary hepatic stellate cells

tag: genotype

value: BucheKI/KI-Hep

tag: treatment

value: CCL4 treatment

tag: sample group


title: Melanoma, A-F06

description: Library name: DSP-1001250002572-A-F06


title: Single Cell RNA-seq of Gallus gallus embryonic tissue

description: Library name: kyomen_HH22_scRNA

library_source: transcriptomic single cell

data_processing:
The 10x Genomics Cell Ranger (7.1.0) pipeline was used to process the chicken RNA-seq data. First, a custom chicken reference was constructed based on the galGal6 assembly (GenBank assembly GCA_000002315.5) using “cellranger mkref”. The reads were then aligned to this reference and quantified with “cellranger count”. After alignment, quality check and downstream analyses were performed in Seurat (4.3.0). Low-quality cells containing extensive mitochondrial counts, low gene counts and doublets were filtered out. Data was then normalized and regressed out for cell cycle heterogeneity. After scaling, linear dimensional reduction with Principal Component Analysis (PCA) was performed on variable genes. Cells were then subject to unbiased clustering under resolution 0.8. For 2D visualization of clusters, Uniform Manifold Approximation and Projection (UMAP) was applied to principal component embeddings. Cell clusters were then annotated based on the output of the function FindAllMarkers (Wilcoxon rank-sum test, min.pct = 0.25, log-change threshold = 0.25) alongside manual inspection of expression profiles of known cell-specific markers.
Assembly: galGal6
Supplementary files format and content: Tab-separated files containing barcodes, features and matrix of chicken scRNA-seq

extract_protocol:
Frontonasal prominences were carefully dissected from freshly collected chicken HH22 embryos using sharp forceps. For both single-cell technologies, facial prominences from at least 30 embryos were pooled. The following procedure was applied to both species independently. Dissected facial tissues were placed into 1.5ml Eppendorf tubes containing ice-cold PBS. The samples were centrifuged at 500g for 5 minutes at +4°C. After carefully removing the PBS, 1 ml of pre-warmed Trypsin solution (0.05% Trypsin/0.02% EDTA, Pan Biotech, P10-0235SP) was added to each tube and incubated in a thermomixer at 37°C for 15 minutes with gentle agitation. To ensure thorough mixing, the samples were gently vortexed for 30 seconds every 5 minutes during the incubation period. Following incubation, tissue dissociation was carried out by carefully pipetting the samples up and down for 15 seconds. Once the cell suspension appeared homogeneous, 200µl of pre-warmed FBS was added to the samples to quench the enzymatic reaction. After another round of centrifugation at 500g for 5 minutes at +4°C, the supernatant was carefully removed without disrupting the pellet. The cells were then resuspended in 1ml of cold PBS and 2.5µl of RNAse inhibitor (Thermo Fisher Scientific, N8080119) and spun down at 500g for 5 minutes at +4°C. The washing step was repeated three more times to remove any excess trypsin and cell debris. The resulting suspension was subsequently filtered through a 35µm cell strainer (Falcon™, 352235). Assessment of cell viability and concentration was performed by adding 1:1 proportion of 0.4% Trypan blue dye (Gibco™, 15250061) to an aliquot of the cell suspension. Cells were loaded in C-Chip haemocytometer slides (NanoEnTek, DHC-N01) and assessed using a stereomicroscope. When the cell viability was at least 95%, the cell suspension was diluted in nuclease-free water to contain 1.2k cells/µl, ensuring optimal conditions for downstream processes and aligned with the experimental requirements outlined by 10x Genomics protocol, targeting 10,000 cells.
The scRNA-seq library was generated following the 10x Genomics protocol designed for the Chromium Next GEM Single Cell 3 Reagent Kits v3. Briefly, the Chromium Next GEM Chip G was loaded with a mixture of the final cell suspension and Master Mix (RT Reagent B 2000165, Template Switch Oligo 3000228, Reducing Agent B 2000087, and RT Enzyme C 2000085/2000102). The remaining rows were allocated for Single Cell 3 v3.1 Gel Beads (2000164) and partitioning oil, with one row left unfilled. Any unused wells were filled with a 50% glycerol solution, in line with the 10x Genomics protocol. The droplet formation was visually assessed according to the manufacturer's protocol. Upon the conclusion of the run, the GEMs were recovered from the chip and placed into a PCR tube on ice. The GEMs were subsequently incubated in a thermal cycler lasting 55 minutes (53C for 45 seconds, followed by 85C for 5 seconds). The GEMs cleanup procedure was performed according to the manufacturer's instructions similarly to what was previously described for scATAC-seq. Post-cleanup, and a recovered sample volume of 35l was combined with the cDNA Amplification Reaction Mix. An additional round of incubation was conducted, as following the settings described in the cDNA Amplification process outlined in the manufacturer s 10x Genomics protocol, for a total of 13 cycles. Finally, the sample underwent cleanup using SPRIselect (Beckman Coulter SPRIselect Reagent Kit, B23318), after which the quantification of cDNA was assessed using Invitrogen Qubit dsDNA assay-kits and a Qubit fluorometer (Thermo Fisher Scientific, 10616763).


title: S2W-DOX2

description: Library name: SAMPLES5

source_name: liver

value: liver

value: DDC treatment


title: S2W-CCL4-PBS-HSC-1

description: Library name: SAMPLES1


title: Melanoma, A-F03

description: Library name: DSP-1001250002572-A-F03


title: Melanoma, A-F04

description: Library name: DSP-1001250002572-A-F04


title: S2W-DOX3

description: Library name: SAMPLES6


title: P5

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on HTA 2.0 Array(human, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: OSCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Normal clinical colon mucosa tissue samples from different colorectal cancer patients were collected immediately after surgical resection prior to any other therapeutic intervention

extract_protocol: Total RNA was extracted from tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) and purified with a RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: All tissue samples were stored at -80 °C.

tag: gender

value: female

value: oral squamous cell carcinoma


title: transposon mutant library pool grown on solid LB plate after 100000 time dilution

city: GRONINGEN

first: Biwen

last: Wang

state: Groningen

address: Zernikeplein 11

department: Research Centre Biobased Economy

country: Netherlands

institute: Hanze University of Applied Sciences

description:
Library name: Solid-Tn-5.fastq
transposon inserted DNA

library_source: genomic

data_processing:
Raw data were preliminary analyzed on the web-based platform Galaxy
Trimmomatic was applied to remove adaptors and filter bad reads
Cutadapt was used to remove the transposon inverted repeat (IR) sequence ACAGGTTGGATGATAAGT from 3’ end, reads didn’t consist the IR sequence were discarded and only reads of 13-18 bp size were kept.
Bowtie2 was used to aligned trimed reads to reference genome fasta (NC_000964.3), and resulted in a set of alignments in SAM format
We used the in-house python package map_functions to extract the mapping information from the SAM files based on the “TA” dinucleotides locations, the reads maps in known genetic features based on BSU loci were counted and reads mapped in inter-locus were stripped. Furthermore, reads/insertions located within the 10% of the 5’ and 3’ extremity of each genetic feature were removed for not fully disrupting the gene function by end insertions.
Assembly: NC_000964.3
Supplementary files format and content: excel files include transposon inserted reads for each gene feature for each sample

molecule: genomic DNA

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: For the first Tn-seq experiment in liquid medium, 1 ml aliquot of the transposon library was quickly thawed and diluted to an OD600 of 0.2 using prewarmed LB. Cells were allowed to recuperate for 1 h at 37°C with vigorous shaking (210 rpm). Then, the culture was further diluted in 100 ml prewarmed LB to an OD600 of 0.00625 (Time point 1), and the culture was grown for approximately 8 doubling periods, reaching an OD600 of 1.6 (Time point 2). Cells were sampled for genomic DNA extraction. For the second Tn-seq experiment on solid medium, an aliquot of the transposon library was thawed, and 200 μl was plated on LB agar supplemented with spectinomycin (10 cm x10 cm plates). The rest of the library was subjected to a 10-fold series of dilutions in LB medium, before plating. Tn 100, 10-1 and 10-2 dilutions grew confluent, whereas the 10-5 dilution formed discrete colonies on the plates. Around 250,000 single colonies from plates of 10^-5 dilution were scraped and pooled together for genomic DNA extraction. Cells from plates without dilution (1x) and of 10^-1 and 10^-2 dilution were also scraped separately for the same subsequent operation.

extract_protocol:
DNA of Tn-mutant pool was extracted using phenol/chloroform/isoamyl alcohol mixture (PCI, 25:24:1) method, precipitated by sodium acetate and ethanol, and washed twice with 70 % ice-cold ethanol.
The purified genomic DNA from Tn library was subjected to MmeI digestion for 2.5 h at 37 °C, then subjected to calf intestinal phosphatase for 1 h at 37 °C. DNA was cleaned up with phenol/chloroform/isoamyl alcohol mixture (PCI, 25:24:1) method, and then ligated with customized illumina R1 adapter. The adapter-ligated DNA junctions were purified using AMPure XP beads. Purified adapter-ligated DNA was used as template for PCR amplification of Illumina sequencing libraries using a universal primer and a specific barcode primer. PCR products were separated on an 8 % non-Urea PAGE gel, and DNA bands of approximately 165 bp were excised. The library DNA was extracted from gel slices and Tn-seq libraries were sequenced using an Illumina NextSeq 550 System with NextSeq 500/550 High Output v2.5 kit (1x 75-bp read length).

value: Bacteria

value: Single Colonies


title: S2W-CCL4-PBS-HSC-2

description: Library name: SAMPLES2


title: Melanoma, A-F02

description: Library name: DSP-1001250002572-A-F02


title: Week 8 and Week 16 hearts

city: Rochester

first: Baul

last: Yoon

state: MN

address: ST4-16 150 3rd St SW

institute: Mayo Clinic

description:
Library name: Week 8 and Week 16 hearts
10x Genomics

data_processing:
As each sublibrary was sequenced across two lanes (L1 and L2) of a 10B flowcell, the corresponding raw sequencing files were merged and converted to paired-end FASTQ files. For each sublibrary, paired-end FASTQ files were aligned to the killifish reference genome using Parse BioSciences split-pipe. After alignment, outputs from all sublibraries were merged using Parse BioSciences split-pipe.
Assembly: Nothobranchius furzeri GRZ-RIMD1 (GCA_043380555.1)
Supplementary files format and content: Tab-separated values files, matrix files, R data serialization file

organism: Nothobranchius furzeri

source_name: Heart

extract_protocol:
Week 8 and Week 16 Killifish hearts were removed from the body and dissected further to remove atrium and outflow tract while leaving ventricle. Dissected ventricles were quickly transferred to a RNAse-free tube containing tissue dissociation solution (1mL HBSS + 7.5 mg Collagenase/Dispase + 7.5 mg Collagenase type II). Within the tube, dissected ventricles were minced with a plastic pestle for 2 minutes. The tubes were then placed on a rotator at room temperature for 45 minutes and centrifuged at 1,000 rpm for 5 minutes. The supernatant was removed, and the pellet was washed with 400 uL HBSS/10% FBS followed by centrifugation at 1,000 rpm for 2 minutes. The supernatant was removed again, and the pellet was mixed with 400 uL HBSS/10% FBS. Cells were filtered through a 70 μm sterile cell strainer to enrich the population of rarely detected cell types, such as immune cells and epicardium, and about 250 μL of the filtrate was collected in an Eppendorf Protein LoBind tube to assess cell number, morphology, and viability
Cell fixation was completed following the Parse Biosciences Evercode cell fixation kit v3 kit protocol. scRNA-seq library preparation was performed using the Parse Biosciences Evercode Whole Transcriptome (WT) kit. Briefly, fixed single cells were loaded across three rounds of combinatorial barcoding processes to generate eight sublibraries. cDNA synthesis, fragmentation, and end repair, Illumina Truseq adapter ligation, and i5/i7 unique dual indexing were conducted for all sublibraries.

value: Heart


title: S2W-PBS3

description: Library name: SAMPLES3


title: Melanoma, A-F01

description: Library name: DSP-1001250002572-A-F01


title: S2W-PBS2

description: Library name: SAMPLES2


title: transposon mutant library pool grown on solid LB plate after 100 time dilution

description:
Library name: Solid-Tn-2.fastq
transposon inserted DNA

value: Bacterial Lawn


title: transposon mutant library pool grown on solid LB plate after 10 time dilution

description:
Library name: Solid-Tn-1.fastq
transposon inserted DNA


title: S2W-PBS1

description: Library name: SAMPLES1


title: Melanoma, A-E12

description: Library name: DSP-1001250002572-A-E12


title: S2W-DOX1

description: Library name: SAMPLES4


title: transposon mutant library pool grown on solid LB plate without dilution

description:
Library name: Solid-Tn-0.fastq
transposon inserted DNA


title: TNF_ROSI_Biol rep 3

city: Baton Rouge

first: Jacqueline

last: Stephens

state: LA

address: 6400 Perkins Road

institute: Louisiana State University

description: Library name: JS-Sample31

data_processing:
reads trimmed with cutadapt v.4.9; (cutadapt -m 20 -O 20 -a "polyA=AAAAAAAAAAAAAAAAAAAA" -a "QUALITY=GGGGGGGGGGGGGGGGGGGG" -n 1 {input} | cutadapt -m 20 -O 3 --nextseq-trim=10 -a "r1adapter=AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=3;max_error_rate=0.100000" - | cutadapt -m 20 -O 3 -a "r1polyA=AAAAAAAAAAAAAAAAAA" - | cutadapt -m 20 -O 20 -g "r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=20" --discard-trimmed -o {output} - )  2> {log}
reads aligned with STAR v.2.7.11b; params: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
features counted with htseq v.2.0.5
genes annotated with biomaRt v.2.60.1, R v4.4.1
differential expression was analyzed using the limma-voom pipeline (limma v3.60.6) in R v4.4.1.
Assembly: GRCm39 release 112
Supplementary files format and content: tab-delimited txt

growth_protocol: 3T3-L1 preadipocytes were cultured in DMEM supplemented with 10% calf serum until they reached confluence. Differentiation was then induced using DMEM containing 10% fetal bovine serum (FBS) and a standard cocktail of insulin, dexamethasone, and IBMX. After 48 hours, the medium was replaced with DMEM containing 10% FBS and 0.25× insulin to support further differentiation.

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (Qiagen) and assessed for quality using an Agilent Bioanalyzer.
RNA libraries for RNA-seq were prepared using Quant-Seq  3' mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Fully differentiated 3T3-L1 adipocytes were treated with DMSO vehicle, SCO, Cap 7, or rosiglitazone (ROSI), with or without TNF-alpha, for 24 hours prior to RNA extraction.

tag: cell line

value: adipocyte


title: transposon mutant library pool grown in liquid LB at T2 replicate 2

description:
Library name: liquid-T2b.fastqsanger
transposon inserted DNA

value: Stationaryl growth


title: TNF_ROSI_Biol rep 4

description: Library name: JS-Sample32


title: TNF_SCO_Biol rep 3

description: Library name: JS-Sample23


title: TNF_CAP7_Biol rep 3

description: Library name: JS-Sample27


title: transposon mutant library pool grown in liquid LB at T1 replicate 1

description:
Library name: liquid-T1a.fastqsanger
transposon inserted DNA

value: Exponential growth


title: TNF_CAP7_Biol rep 4

description: Library name: JS-Sample28


title: TNF_ROSI_Biol rep 1

description: Library name: JS-Sample29


title: Melanoma, A-E10

description: Library name: DSP-1001250002572-A-E10

tag: aoi


title: TNF_ROSI_Biol rep 2

description: Library name: JS-Sample30


title: TNF_CAP7_Biol rep 2

description: Library name: JS-Sample26


title: TNF_DMSO_Biol rep 3

description: Library name: JS-Sample19


title: TNF_DMSO_Biol rep 4

description: Library name: JS-Sample20


title: TNF_SCO_Biol rep 4

description: Library name: JS-Sample24


title: transposon mutant library pool grown in liquid LB at T1 replicate 2

description:
Library name: liquid-T1b.fastqsanger
transposon inserted DNA


title: Melanoma, A-E08

description: Library name: DSP-1001250002572-A-E08

tag: tissue


title: transposon mutant library pool grown in liquid LB at T2 replicate 1

description:
Library name: liquid-T2a.fastqsanger
transposon inserted DNA


title: TNF_CAP7_Biol rep 1

description: Library name: JS-Sample25


title: TNF_SCO_Biol rep 2

description: Library name: JS-Sample22


title: Melanoma, A-E09

description: Library name: DSP-1001250002572-A-E09

tag: patient


title: Melanoma, A-E05

description: Library name: DSP-1001250002572-A-E05

tag: has replicate_(1=yes,_0=no)


title: TNF_SCO_Biol rep 1

description: Library name: JS-Sample21


title: Melanoma, A-E11

description: Library name: DSP-1001250002572-A-E11

tag: replicate (1=yes,_0=no)


title: Melanoma, A-E04

description: Library name: DSP-1001250002572-A-E04

tag: included in_analysis_(1=yes,0=no)


title: Leg, TRAP, 2d_rep3

city: Cambridge

first: Alex

last: Whitworth

address: Hills road

department: MRC MBU

country: United Kingdom

institute: University of Cambridge

description:
Library name: Leg_TRAP4
column name in L3_raw_counts_all_samples.txt: Leg_TRAP4

data_processing:
Trim Galore was used for adapter removal and quality trimming
HISAT2 (v2.2.1) for alignment to the Drosophila melanogaster genome (BDGP6, Ensembl v95)
BAM files were sorted and indexed using SAMtools (v1.12)
Assembly: BDGP6 (Ensembl v95)
Supplementary files format and content: tab delimited text file containing raw counts for each sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Adult axonal sections

growth_protocol: L3 larvae or two day-old flies were used for the study.

extract_protocol:
Lysates were incubated with anti-Flag antibody–conjugated beads to immunoprecipitate Flag-GFP-tagged ribosomes. RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research). RNA integrity (RIN ≥ 8) was verified using an Agilent TapeStation.
SMART-Seq HT v4 (Takara), Illumina Nextera XT library

value: Adult axonal sections

value: 2 day old flies

tag: batch


title: Melanoma, A-E07

description: Library name: DSP-1001250002572-A-E07

value: Melanoma

tag: lymph node_status_(1=yes,_0=no)

tag: distant metastasis_(1=yes,_0=no)


title: Leg, CNT, 2d_rep2

description:
Library name: Leg_CNT2
column name in L3_raw_counts_all_samples.txt: Leg_CNT2


title: TNF_DMSO_Biol rep 1

description: Library name: JS-Sample17


title: Leg, TRAP, 2d_rep2

description:
Library name: Leg_TRAP3
column name in L3_raw_counts_all_samples.txt: Leg_TRAP3


title: basal_ROSI_Biol rep 4

description: Library name: JS-Sample16


title: Melanoma, A-E06

description: Library name: DSP-1001250002572-A-E06

tag: acral melanoma_(1=yes,_0=no)

tag: vital status


title: basal_ROSI_Biol rep 3

description: Library name: JS-Sample15

tag: cell type


title: TNF_DMSO_Biol rep 2

description: Library name: JS-Sample18


title: Leg, CNT, 2d_rep1

description:
Library name: Leg_CNT1
column name in Legs_raw_counts_all_samples.txt: Leg_CNT1

tag: genotype


title: basal_ROSI_Biol rep 1

description: Library name: JS-Sample13

tag: treatment


title: basal_CAP7_Biol rep 3

description: Library name: JS-Sample11


title: basal_CAP7_Biol rep 4

description: Library name: JS-Sample12


title: Melanoma, A-E02

description: Library name: DSP-1001250002572-A-E02

tag: overall survival(years)


title: basal_ROSI_Biol rep 2

description: Library name: JS-Sample14


title: Melanoma, A-E03

description: Library name: DSP-1001250002572-A-E03


title: L3, TRAP_rep3

description:
Library name: L3_TRAP4
column name in L3_raw_counts_all_samples.txt: L3_TRAP4

source_name: Larval axonal sections

value: Larval axonal sections

value: larval stage - L3


title: basal_CAP7_Biol rep 2

description: Library name: JS-Sample10


title: Melanoma, A-D12

description: Library name: DSP-1001250002572-A-D12


title: L3, TRAP_rep1

description:
Library name: L3_TRAP1
column name in L3_raw_counts_all_samples.txt: L3_TRAP1


title: Melanoma, A-E01

description: Library name: DSP-1001250002572-A-E01


title: Melanoma, A-D11

description: Library name: DSP-1001250002572-A-D11


title: basal_SCO_Biol rep 4

description: Library name: JS-Sample08


title: basal_CAP7_Biol rep 1

description: Library name: JS-Sample09


title: Melanoma, A-D10

description: Library name: DSP-1001250002572-A-D10


title: basal_SCO_Biol rep 1

description: Library name: JS-Sample05


title: Melanoma, A-D09

description: Library name: DSP-1001250002572-A-D09


title: basal_DMSO_Biol rep 4

description: Library name: JS-Sample04


title: basal_SCO_Biol rep 3

description: Library name: JS-Sample07


title: Melanoma, A-D08

description: Library name: DSP-1001250002572-A-D08


title: basal_DMSO_Biol rep 3

description: Library name: JS-Sample03


title: basal_DMSO_Biol rep 2

description: Library name: JS-Sample02


title: L3, TRAP_rep2

description:
Library name: L3_TRAP3
column name in L3_raw_counts_all_samples.txt: L3_TRAP3


title: basal_DMSO_Biol rep 1

description: Library name: JS-Sample01


title: basal_SCO_Biol rep 2

description: Library name: JS-Sample06


title: head, TRAP, 2d_rep3

description:
Library name: TRAP 2d_57
column name in heads_raw_counts_all_samples.txt: TRAP 2d_57

source_name: Heads

value: Heads


title: L3, CNT_rep2

description:
Library name: L3_Cnt3
column name in L3_raw_counts_all_samples.txt: L3_Cnt3


title: fetal liver, E14.5, BulkRNA-seq, CD127posRunx3negRORgtneg_gtposRunx3neg_4

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description:
SMART-Seq HT PLUS
neg_4

data_processing:
Raw RNA-seq reads were trimmed and filtered for quality control using fastp. The clean reads were mapped to the GRCm39 reference genome using HISAT2 and then read counts for each sample were obtained using featureCounts.
Assembly: GRCm39
Supplementary files format and content: normalized_counts txt files

source_name: fetal liver

growth_protocol: RPMI supplemented with 10%FBS, IL-7(20ng/ml), SCF(20ng/ml), MEN-NEAA and sodium pyruvate with 5%CO2 at 37℃.

extract_protocol:
Runx3-negative CLPs fractions and RORγt-mid fractions were each cultured on TSt4/DLL4 for 10-12 days. After collection by pipetting, the RORγt-positive cells with or without Runx3 expression were re-sorted respectively.
Bulk RNA-seq was performed on 50-200 sorted cells using the SMART-Seq HT PLUS Kit following the manufacturer's instructions (Takara Bio).

value: fetal liver

value: CD45+ CD3- CD19- RORgt+ Runx3-

tag: strain

value: Runx3-tdTomato; RORgt-EGFP

tag: age

value: embryonic day 14.5


title: fetal liver, E14.5, BulkRNA-seq, CD127posRunx3negRORgtneg_gtposRunx3neg_3

description:
SMART-Seq HT PLUS
neg_3


title: Melanoma, A-D07

description: Library name: DSP-1001250002572-A-D07

tag: aoi


title: head, TRAP, 2d_rep2

description:
Library name: TRAP 2d_26
column name in heads_raw_counts_all_samples.txt: TRAP 2d_26

tag: tissue


title: Leg, TRAP, 2d_rep1

description:
Library name: Leg_TRAP2
column name in L3_raw_counts_all_samples.txt: Leg_TRAP2


title: L3, CNT_rep1

description:
Library name: L3_Cnt2
column name in L3_raw_counts_all_samples.txt: L3_Cnt2


title: fetal liver, E14.5, BulkRNA-seq, CD127posRunx3negRORgtneg_gtposRunx3neg_1

description:
SMART-Seq HT PLUS
neg_1


title: L3, CNT_rep3

description:
Library name: L3_Cnt4
column name in L3_raw_counts_all_samples.txt: L3_Cnt4


title: Melanoma, A-D06

description: Library name: DSP-1001250002572-A-D06

tag: patient


title: Melanoma, A-D05

description: Library name: DSP-1001250002572-A-D05

tag: has replicate_(1=yes,_0=no)


title: head, TRAP, 2d_rep1

description:
Library name: TRAP 2d_18
column name in heads_raw_counts_all_samples.txt: TRAP 2d_18


title: Cortex, snap-frozen, sample 2

city: Kunshan

first: Dominika

last: Wilczok

address: No 8 Duke Avenue

department: Division of Natural and Applied Sciences

institute: Duke Kunshan University

description:
Library name: CS2
cleaned_rna_seq_CORTEX (1).xlsx

data_processing:
Sequencing was performed on the DNBSEQ platform.
Raw reads were filtered using SOAPnuke v2.3 with parameters: -l 20 -q 0.4 -n 0.01.
FASTQ files contain filtered clean reads.  Processed files contain genes that have at least one non zero read for any of the samples.
Filtering steps included: removal of reads containing adaptor contamination, removal of reads with >1% ambiguous bases (N), and removal of low-quality reads in which bases with quality score ≤20 accounted for >40% of the read.
Clean reads were aligned using HISAT2 v2.0.4 (--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF). Gene expression quantification and downstream analyses were performed on aligned reads. Sequencing saturation analysis was performed using a Perl script.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: readcounts

source_name: Cerebral Cortex

extract_protocol:
Following group-appropriate treatment, each sample was homogenized in TRIzol (Thermo Fisher Scientific) according to the manufacturer’s instructions using a hand-held tissue homogenizer (Qiagen). Samples were subsequently shipped to the Beijing Genomics Institute (BGI) on dry ice for RNA extraction and RNA-seq.
RNA libraries were prepared using the DNBSEQ Eukaryotic Stranded Transcriptome library preparation workflow. mRNA was enriched using oligo dT beads to capture poly(A)+ RNA. The enriched RNA was fragmented, and first-strand cDNA was synthesized using random N6 primers, followed by second-strand cDNA synthesis with dUTP replacing dTTP. The cDNA then underwent end repair, 3′ adenylation, and adaptor ligation. Before PCR amplification, the dUTP-marked strand was selectively degraded by Uracil-DNA-Glycosylase (UDG), and the remaining strand was amplified to generate a strand-specific cDNA library. The PCR products were heat denatured, circularized by splint oligo and DNA ligase, converted to DNA nanoballs, and sequenced on the DNBSEQ platform

treatment_protocol: For vitrification groups: The vitrification stock solution (total weight of 100 wt%) was prepared by combining ethylene glycol (28 wt%) and dimethyl sulfoxide (DMSO) (22.3 wt%) as permeating cryoprotectants, sucrose (17.1 g) as a non-permeating osmotic agent, and phosphate-buffered saline (32.6 wt%) as the buffered aqueous carrier.  As an initial pre-equilibration step, tissues were incubated in 100 μL of 25% vitrification solution for 5 minutes, after which the solution was aspirated and replaced with 100 μL of 50% vitrification solution.  This process was repeated with 75% and subsequently 100% vitrification solutions, with a 5-minute incubation at each step. After exposure to the 100% vitrification solution, samples containing both the tissue and the 100% vitrification solution were immersed in liquid nitrogen for 5 minutes and stored −80 °C for 4 days. Subsequently, a rewarming stock solution (total weight of 100g) was prepared by combining 28 g ethylene glycol, 22.3 g DMSO, 34.2 g sucrose, and 15.5 g PBS.  Upon removal from liquid nitrogen, the tubes with vitrified hippocampal and cortical samples were immediately rewarmed by gentle agitation in a 37 °C water bath until the vitrifying solution returned to the liquid phase. The 100% vitrification solution was then removed by pipette aspiration and replaced with 100 μL of 75% rewarming solution. Cryoprotectant unloading was performed stepwise in descending concentration order (75%, 50%, and 25%), with samples incubated for 5 minutes at each step. Following incubation in the 25% rewarming solution, tissues were submerged in 100 μL PBS for 5 minutes.

value: Cerebral Cortex

value: Snap-freezing (direct immersion in liquid nitrogen)


title: fetal liver, E14.5, BulkRNA-seq, RORgtmid_gtpos_Runx3pos_1

description:
SMART-Seq HT PLUS
mid_1

value: CD45+ CD3- CD19- RORgt+ Runx3+


title: fetal liver, E14.5, BulkRNA-seq, RORgtmid_gtpos_Runx3pos_4

description:
SMART-Seq HT PLUS
mid_4


title: Cortex, snap-frozen, sample 3

description:
Library name: CS3
cleaned_rna_seq_CORTEX (1).xlsx


title: Melanoma, A-D03

description: Library name: DSP-1001250002572-A-D03

tag: replicate (1=yes,_0=no)


title: Melanoma, A-D04

description: Library name: DSP-1001250002572-A-D04

tag: included in_analysis_(1=yes,0=no)


title: Cortex, snap-frozen, sample 1

description:
Library name: CS1
cleaned_rna_seq_CORTEX (1).xlsx


title: fetal liver, E14.5, BulkRNA-seq, RORgtmid_gtpos_Runx3pos_3

description:
SMART-Seq HT PLUS
mid_3


title: head, CNT, 2d_rep3

description:
Library name: control 2d_62
column name in heads_raw_counts_all_samples.txt: control 2d_62

tag: batch


title: fetal fetus, E14.5, BulkRNA-seq, RORgt_LTi_3

description:
SMART-Seq HT PLUS
LTi._3

source_name: fetal fetus

extract_protocol:
E14.5 fetal livers were separated under a microscope, and single-cell suspension was generated by pipetting with a 1000-micropipette. The cell suspension  was then filtered through a 100 μm strainer and resuspended in FACS buffer (2% FBS/0.05% NaN3/1% PBS).
Bulk RNA-seq was performed on 50-200 sorted cells using the SMART-Seq HT PLUS Kit following the manufacturer's instructions (Takara Bio).

value: fetal fetus

value: Lin-c-kit+GFPhigh

value: RORgt-EGFP


title: Cortex, vitrified, sample 1

description:
Library name: CV1
cleaned_rna_seq_CORTEX (1).xlsx

value: Vitrification with step loading of cryoprotective agents


title: fetal liver, E14.5, BulkRNA-seq, CD127posRunx3negRORgtneg_gtposRunx3neg_2

description:
SMART-Seq HT PLUS
neg_2


title: Whole Exome Sequencing (WES)-p53null GPx4 KO mammary tumors Sample B6

city: San Francisco

first: Hugo

middle: A

last: Gonzalez

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

description:
Library name: Sample_B6
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

data_processing:
Paired-end sequencing reads (FASTQ format) were aligned to the Mus musculus reference genome (GRCm39, Ensembl release) using bwa-mem2 (version 2.2.1). The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools (version 1.19.2). Duplicate reads were identified and marked using the MarkDuplicates tool from the Genome Analysis Toolkit (GATK; version 4.4.0.0). Base quality score recalibration (BQSR) was performed with GATK, with recalibration tables generated using BaseRecalibrator and known variant sites from the Mouse Genomes Project (mgp_REL2021), followed by application of the recalibration using ApplyBQSR with default parameters. A Panel of Normals (PoN) was constructed from two normal samples (wild-type Balb/c tail tissue) processed with GATK Mutect2 in tumor-only mode. Variant calls from the normal samples were jointly processed using GenomicsDBImport and combined with CreateSomaticPanelOfNormals to generate the final PoN. Somatic variant calling was then performed using Mutect2, incorporating the PoN to filter recurrent technical artifacts and germline variants. Variant calls were further refined using GATK FilterMutectCalls to retain high-confidence somatic variants. Functional annotation of variants was carried out using SnpEff (version 5.3a).
Assembly: Mus musculus reference genome (GRCm39) Ensembl release
Supplementary files format and content: VCF including the variants from GATK annotated using snpEff and ,txt file with variant per gene exported from snpEff.

source_name: mammary tumor/end-point

extract_protocol:
Tumor tissues were mechanically digested in DNA lysis buffer (4 M guanidine thiocynate, 100 mM Tris/HCl pH 7.4, 30 mM EDTA pH 8.0, 1% Triton X-100, 100 mM b-mercaptoethanol). Lysates were incubated with acid-washed diatomaceous earth to enhance nucleic acid binding, followed by silica column-based purification (Promega). Column-bound DNA was purified through sequential washes with guanidine- and ethanol-based DNA wash buffers. RNA was isolated from the DNA flowthrough by sodium acetate-phenol:chloroform extraction. The aqueous phase was incubated with acid-washed diatomaceous earth and ethanol to promote RNA binding to the column, followed by purification through guanidine- and ethanol-based RNA wash buffers. DNA was used in WES, and RNA was used in RNA-Seq and RT-qPCR analyses.
WES was performed by Novogene (https://www.novogene.com/us-en/). DNA libraries were prepared using SureSelectXT Mouse Exon Kit (Agilent Technologies) and sequenced on the Illumina NovaSeq 6000 or NovaSeq X Plus platform with paired-end 150 bp reads (PE150), with an effective sequencing depth above 50x (6 Gb / sample).

treatment_protocol: Orthotopic animal models. High concentration rat tail Col1 (Corning, Cat #354249) was incubated with 0.1% acetic acid (non-crosslinked; soft) or 0.1% acetic acid with 500 mM L-ribose (Chem Impex, Cat #28127) (crosslinked; stiff) for 10-14 days. The Col1 mixtures were then combined with BM extract (R&D Systems, Cat #3532-005-02) at a final concentration of 20%. Col1/BM hydrogels were injected into a cleared fourth mammary pat pad of 3- to 4-week-old mice prior to implantation of a mammary fragment isolated from an 8- to 10-week-old syngeneic p53null mouse. For LysM-Cre GPX4 mice, a p53null mammary fragment was implanted into the mammary fat pad as described. Mice were euthanized at a tumor end-point of a maximum tumor diameter of 2 cm for tissue analysis.

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null

value: LysM-Cre GPX4 knockout (KO)


title: Melanoma, A-D01

description: Library name: DSP-1001250002572-A-D01

value: Melanoma

tag: lymph node_status_(1=yes,_0=no)


title: Melanoma, A-D02

description: Library name: DSP-1001250002572-A-D02

tag: distant metastasis_(1=yes,_0=no)


title: Cortex, fresh control, sample 3

description:
Library name: CF3
cleaned_rna_seq_CORTEX (1).xlsx

value: Fresh control (no treatment)


title: Cortex, vitrified, sample 3

description:
Library name: CV3
cleaned_rna_seq_CORTEX (1).xlsx


title: Melanoma, A-C12

description: Library name: DSP-1001250002572-A-C12

tag: acral melanoma_(1=yes,_0=no)


title: Cortex, vitrified, sample 2

description:
Library name: CV2
cleaned_rna_seq_CORTEX (1).xlsx


title: head, CNT, 2d_rep1

description:
Library name: control 2d_22
column name in heads_raw_counts_all_samples.txt: control 2d_22

value: Heads

value: 2 day old flies


title: fetal fetus, E14.5, BulkRNA-seq, RORgt_LTi_1

description:
SMART-Seq HT PLUS
LTi._1


title: Whole Exome Sequencing (WES)-p53null GPx4 KO mammary tumors Sample B5

description:
Library name: Sample_B5
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene


title: Melanoma, A-C11

description: Library name: DSP-1001250002572-A-C11

tag: vital status


title: fetal fetus, E14.5, BulkRNA-seq, RORgt_LTi_2

description:
SMART-Seq HT PLUS
LTi._2

tag: cell type


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_3

description:
SMART-Seq HT PLUS
ChiLP.RORgt.high_3

value: fetal liver

tag: genotype


title: Cortex, fresh control, sample 1

description:
Library name: CF1
cleaned_rna_seq_CORTEX (1).xlsx

tag: treatment


title: Melanoma, A-C10

description: Library name: DSP-1001250002572-A-C10

tag: overall survival(years)


title: head, CNT, 2d_rep2

description:
Library name: control 2d_30
column name in heads_raw_counts_all_samples.txt: control 2d_30


title: Cortex, fresh control, sample 2

description:
Library name: CF2
cleaned_rna_seq_CORTEX (1).xlsx


title: Whole Exome Sequencing (WES)-p53null GPx4 WT mammary tumors Sample B2

description:
Library name: Sample_B2
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

value: LysM-Cre GPX4 wild-type (WT)


title: Hippocampus, snap-frozen, sample 3

description:
Library name: HS3
official_hippocampus_readcounts.xlsx

source_name: Hippocampus

value: Hippocampus


title: Whole Exome Sequencing (WES)-p53null GPx4 KO mammary tumors Sample B4

description:
Library name: Sample_B4
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene


title: Melanoma, A-C09

description: Library name: DSP-1001250002572-A-C09


title: Hippocampus, snap-frozen, sample 2

description:
Library name: HS2
official_hippocampus_readcounts.xlsx

value: Snap-freezing (direct immersion in liquid nitrogen)


title: Hippocampus, snap-frozen, sample 1

description:
Library name: HS1
official_hippocampus_readcounts.xlsx


title: fetal liver, E14.5, BulkRNA-seq, RORgt_middle_2

description:
SMART-Seq HT PLUS
ChiLP.RORgt.mid_2

tag: strain

value: embryonic day 14.5


title: Melanoma, A-C08

description: Library name: DSP-1001250002572-A-C08


title: fetal liver, E14.5, BulkRNA-seq, RORgt_middle_3

description:
SMART-Seq HT PLUS
ChiLP.RORgt.mid_3

tag: age


title: Whole Exome Sequencing (WES) tail Sample C2

description:
Library name: Sample_C2
Fastq.gz files of WES

source_name: tail

value: tail

value: Tail

value: Balb/c wild type


title: Hippocampus, vitrified, sample 3

description:
Library name: HV3
official_hippocampus_readcounts.xlsx

value: Vitrification with step loading of cryoprotective agents


title: Whole Exome Sequencing (WES)-p53null GPx4 WT mammary tumors Sample B3

description:
Library name: Sample_B3
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

value: mammary tumor/end-point


title: Whole Exome Sequencing (WES) tail Sample C1

description:
Library name: Sample_C1
Fastq.gz files of WES


title: Melanoma, A-C07

description: Library name: DSP-1001250002572-A-C07

tag: aoi


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_1

description:
SMART-Seq HT PLUS
ChiLP.RORgt.high_1

tag: tissue

value: RORgt-EGFP


title: Whole Exome Sequencing (WES)-p53null GPx4 WT mammary tumors Sample B1

description:
Library name: Sample_B1
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

value: Mammary Breast Tumor

value: Balb/c mammary p53null


title: fetal liver, E14.5, BulkRNA-seq, RORgt_middle_1

description:
SMART-Seq HT PLUS
ChiLP.RORgt.mid_1


title: Melanoma, A-C06

description: Library name: DSP-1001250002572-A-C06

value: Melanoma

tag: patient


title: WTG 3

city: Qingdao

first: Panpan

last: Zhang

address: No. 72, Coastal Road, Aoshanwei Sub-district, Jimo District, Qingdao City, Shandong Province

institute: ShanDong University

description: Library name: sample18

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: strain

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon resources for 24h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: strain

value: 114-2(wild type)

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: Hippocampus, vitrified, sample 2

description:
Library name: HV2
official_hippocampus_readcounts.xlsx


title: WTG 1

description: Library name: sample16


title: Melanoma, A-C05

description: Library name: DSP-1001250002572-A-C05

tag: has replicate_(1=yes,_0=no)


title: fetal liver, E14.5, BulkRNA-seq, RORgtKO_RORgt_middle_1

description:
SMART-Seq HT PLUS
ChiLP.RORgtKO_1

value: fetal liver

value: RORgtKO; RORgt-EGFP


title: WTG 2

description: Library name: sample17


title: fetal liver, E14.5, BulkRNA-seq, RORgtKO_RORgt_middle_3

description:
SMART-Seq HT PLUS
ChiLP.RORgtKO_3


title: Hippocampus, vitrified, sample 1

description:
Library name: HV1
official_hippocampus_readcounts.xlsx

value: Hippocampus


title: fetal liver, E14.5, BulkRNA-seq, RORgtKO_RORgt_middle_2

description:
SMART-Seq HT PLUS
ChiLP.RORgtKO_2


title: Melanoma, A-C04

description: Library name: DSP-1001250002572-A-C04

tag: replicate (1=yes,_0=no)


title: Melanoma, A-C03

description: Library name: DSP-1001250002572-A-C03

tag: included in_analysis_(1=yes,0=no)


title: Hippocampus, fresh control, sample 3

description:
Library name: HF3
official_hippocampus_readcounts.xlsx

value: Fresh control (no treatment)


title: Hippocampus, fresh control, sample 1

description:
Library name: HF1
official_hippocampus_readcounts.xlsx


title: WTCW 3

description: Library name: sample15

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: Melanoma, A-B12

description: Library name: DSP-1001250002572-A-B12


title: Melanoma, A-C01

description: Library name: DSP-1001250002572-A-C01


title: Hippocampus, fresh control, sample 2

description:
Library name: HF2
official_hippocampus_readcounts.xlsx


title: fetal liver, E14.5, BulkRNA-seq, RORgt_neg_3

description:
SMART-Seq HT PLUS
ChiLP.RORgt.neg.CD127pos.Runx3.neg_3

value: embryonic day 14.5


title: WTCW 2

description: Library name: sample14


title: Microglia, LACTB ED, mice 3

city: Houston

first: Ruben

last: Gomez-Gutierrez

state: TX

address: 1881 East Road

department: Therapeutics Discovery Division

institute: The University of Texas MD Anderson Cancer Center

description: Library name: LB_MG_E3

data_processing:
Mapping sequence reads to the reference genome: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Extracting gene hit counts: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Differential gene expression analysis: After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: GRCm38
Supplementary files format and content: Excel file (.xlsx) containing normalized gene hit counts of all samples used in the differential gene expression analysis.

source_name: Brain

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit (Invitrogen, 12183025) following manufacturer’s instructions. RNA quantity was assessed using NanoDrop 8000 (Thermo Fisher Scientific). The RNA sample received by GENEWIZ (South Plainfield, NJ, USA) was quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA).
Sample processing, library preparations, and sequencing reactions were conducted at GENEWIZ(South Plainfield, NJ, USA) as follows: RNA-seq libraries were prepared by using the The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations.Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3' ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq X instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

value: Brain

value: Isolated Microglia

value: ED


title: Melanoma, A-C02

description: Library name: DSP-1001250002572-A-C02

source_name: Melanoma


title: fetal liver, E14.5, BulkRNA-seq, RORgt_neg_2

description:
SMART-Seq HT PLUS
ChiLP.RORgt.neg.CD127pos.Runx3.neg_2


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_2

description:
SMART-Seq HT PLUS
ChiLP.RORgt.high_2


title: fetal liver, E14.5, BulkRNA-seq, RORgt_neg_1

description:
SMART-Seq HT PLUS
ChiLP.RORgt.neg.CD127pos.Runx3.neg_1


title: Melanoma, A-B10

description: Library name: DSP-1001250002572-A-B10


title: fetal liver, E14.5, scRNA-seq, RORgt_high

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
E14.5 fetal livers were separated under a microscope, and single-cell suspension was generated by pipetting with a 1000-micropipette. The cell suspension was then filtered through a 100 μm strainer and resuspended in FACS buffer (2% FBS/0.05% NaN3/1% PBS).
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification.  Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).


title: WTCW 1

description: Library name: sample13


title: WTN 2

description: Library name: sample11

value: Modified Mendal’s medium with 2% N-GlcNAc as carbon resource


title: Dvib1N3

description: Library name: sample9

value: vib1 deletion strain


title: WTN 3

description: Library name: sample12


title: Microglia, LACTB WT, mice 3

description: Library name: LB_MG_D3

value: WT


title: Melanoma, A-B09

description: Library name: DSP-1001250002572-A-B09


title: Microglia, LACTB ED, mice 2

description: Library name: LB_MG_E2


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127neg_MHC2pos_1

description: Active Motif

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality control using Cutadapt with the adapter sequence "CTGTCTCTTATACACATCT". The trimmed reads were then aligned to the mouse genome (mm10) using Bowtie2 v2.2.5 with the parameter -X 2000. Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were filtered out using Samtools. Only concordantly mapped reads were used for further analysis. Peaks were called using Genrich with the following parameters: -j (ATAC-seq mode), -q 0.01 (FDR threshold), -y (exclude mitochondrial reads), and -e chrM (exclude mitochondrial chromosome).
Assembly: mm10
Supplementary files format and content: Tdf files

extract_protocol:
The LTi progenitor cells were collected from E14.5 fetal liver, and E17.5 DP thymocytes were collected from E17.5 thymus. Th17 and γΔ17 cells were collected from the small intestine of 8-10 week-old mice. The E14.5 fetal liver and E17.5 thymus were separated under a microscope, and single-cell suspension was generated by pipetting with a 1000-micropipette. The cell suspension  was then filtered through a 100 μm strainer and resuspended in FACS buffer (2% FBS/0.05% NaN3/1% PBS). The collected adult intestines were cut into  1 cm pieces and washed with PBS. After opening the intestines along the longitudinal axis, they were treated with 30mM EDTA-containing PBS at room temperature for 15 minutes to remove the epithelium. The tissues were then digested by incubating at 37°C in DMEM containing 1 mg/mL Collagenase D and 0.33 mg/mL DNase I. Dissociated cells were collected every 30 min and strained with a 100 μm strainer, and then lymphocytes were further enriched on a 40%/80% Percoll gradient.  After staining by antibodies,  cell sorting were performed with  MA900 (Sony Imaging Products & Solutions).
100-200 cells were used for ATAC-seq following the manufacturer's instructions (Active Motif, #53150).

value: RORgt-EGFP


title: Microglia, LACTB WT, mice 1

description: Library name: LB_MG_D1


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127pos_MHC2pos_3

description: Active Motif


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127pos_MHC2pos_2

description: Active Motif


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127neg_MHC2pos_3

description: Active Motif


title: Dvib1N2

description: Library name: sample8


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127neg_MHC2pos_2

description: Active Motif


title: GFP_pos_SIX2_plasmid_rep2

city: Hong Kong

first: Dawon

last: Choi

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: Library name: Sample 11

data_processing:
The Fastq files were mapped to the mouse reference genome GRCm38 using STAR (v2.7.11a).
Quantification was conducted with RSEM (v1.3.3) based on the Gencode vM25 annotation.
Quality control was carried out using FastQC (v0.12.1) and aggregated with multiQC (v1.19).
Raw gene counts were normalized and analyzed for differential expression using DESeq2 (v1.42.0).
Assembly: GRCm38
Supplementary files format and content: csv file containing gene normalized counts

source_name: Muscle stem cells

growth_protocol: MuSCs isolated by flow cytometry were plated at 20,000 cells (proliferation assay), 40,000 cells (differentiation assay) per 1cm2 and 1,000 cells (clonal expansion) per 10cm2 on detachable 8 well-PCA treated m-slides (Sarstedt) pre-coated with Matrigel (Corning, 354248) for 30 min at 37°C and cultured in DMEM (Gibco, 41966029) with 20% FCS (Eurobio, CVFSVF00-01), 1% Pen/Step (Gibco, 15070063), and 4 ng/mL basic FGF (bFGF) (Peprotech, 450-33).

extract_protocol:
A minimum of 50,000 cells, cultured in high serum-containing medium and at low density, were collected per sample for RNA extraction (Quick-RNA, Zymogen, ZR1050) following the manufacturer’s protocol. Reverse transcription was performed using the SuperScript III Reverse Transcriptase (Invitrogen, 18080-093) following the manufacturer’s guidelines.
cDNA was generated following the SMART-Seq2 protocol. The RNA-Seq libraries were fragmented using Tn5 transposases with adaptors and amplified using PCR.

treatment_protocol: PAX3⁺(GFP⁺) and PAX3⁻(GFP⁻) MuSCs were isolated by FACS and cultured in growth medium. To overexpress Six2, PAX3-pos (GFP-pos) and PAX3-neg (GFP-neg) MuSCs were transfected with 2 µg of pCR3-Six2 plasmid containing the mouse Six2 cDNA, or control, empty pCR3 plasmid (Clontech). Lipofectamine LTX with PLUS reagent (Thermo Fisher Scientific, 15338100) was used according to the manufacturer’s protocol. Transfection efficiency was verified by RT-qPCR for Six2 mRNA.

value: Muscle stem cells

value: Plasmid transfection


title: Melanoma, A-B11

description: Library name: DSP-1001250002572-A-B11

extract_protocol:
The TMA underwent staining for CD20 (B cells), CD3 (T cells), and DNA to guide region of interest (ROI) selection. ROIs were drawn to maximize tumor content within each tissue spot on the TMA. Full ROIs were profiled without the use of segmentation to avoid inadequate cell counts.
DSP-derived oligos were dried down and rehydrated in 10 µL nuclease-free water. Libraries were prepared and pooled according to the NanoString GeoMx DSP protocol for Human Whole Transcriptome Atlas (WTA) RNA samples. Final pooled libraries were assessed for quality and quantity using the Agilent TapeStation D1000 assay and Qubit prior to sequencing.

value: Melanoma


title: GFP_pos_SIX2_plasmid_rep1

description: Library name: Sample 10


title: Dvib1G2

description: Library name: sample5

value: strain

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127pos_MHC2neg_2

description: Active Motif

value: fetal liver


title: GFP_pos_CTR_plasmid_rep3

description: Library name: Sample 9


title: Melanoma, A-B03

description: Library name: DSP-1001250002572-A-B03


title: Melanoma, A-B08

description: Library name: DSP-1001250002572-A-B08


title: small intestine, 8w, ATAC-seq, NKp46neg_RORgt_high_1

description: Active Motif

source_name: small intestine

value: small intestine

value: CD3- NKp46- RORgt+


title: Dvib1CW3

description: Library name: sample3

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: Microglia, LACTB WT, mice 2

description: Library name: LB_MG_D2


title: Melanoma, A-B06

description: Library name: DSP-1001250002572-A-B06


title: WTN 1

description: Library name: sample10

value: 114-2(wild type)


title: Melanoma, A-B07

description: Library name: DSP-1001250002572-A-B07


title: Dvib1CW2

description: Library name: sample2


title: Melanoma, A-B05

description: Library name: DSP-1001250002572-A-B05


title: GFP_pos_SIX2_plasmid_rep3

description: Library name: Sample 12


title: Microglia, LACTB ED, mice 1

description: Library name: LB_MG_E1

value: Brain


title: Dvib1CW1

description: Library name: sample1


title: GFP_pos_CTR_plasmid_rep1

description: Library name: Sample 7


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127pos_MHC2pos_1

description: Active Motif

value: embryonic day 14.5


title: Dvib1N1

description: Library name: sample7


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127pos_MHC2neg_3

description: Active Motif


title: Melanoma, A-A12

description: Library name: DSP-1001250002572-A-A12


title: fetal liver, E14.5, ATAC-seq, CD127pos_Runx3pos_2

description: Active Motif


title: Melanoma, A-B04

description: Library name: DSP-1001250002572-A-B04


title: Melanoma, A-A11

description: Library name: DSP-1001250002572-A-A11


title: GFP_neg_SIX2_plasmid_rep3

description: Library name: Sample 6


title: fetal liver, E14.5, ATAC-seq, CD127pos_Runx3pos_1

description: Active Motif


title: 5P0_rep_4

city: Kunming

first: Qiu

last: Zhao

state: Yunnan

address: Chenggong

department: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan

institute: Yunnan University

description: Library name: 5P0_rep_4

data_processing:
RNA was converted into Illumina-compatible libraries via poly(A) selection, fragmentation, cDNA synthesis (random hexamers), end repair/adapter ligation, and size selection (300–400 bp, AMPure XP beads), followed by PCR amplification.
Clean reads were aligned to the C. elegans genome (WBcel235) using HISAT2, retaining only uniquely mapped, properly paired reads (MAPQ≥10). Gene-level counts were generated with HTSeq, quantifying exonic reads while excluding multi-mapping and low-quality alignments.
Assembly: WBcel235
Supplementary files format and content: FPKMs_all_samples.txt
Supplementary files format and content: column 1 = WormBase Gene_ID, columns 2-9 = FPKM values for 8 experimental samples

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Synchronized L1 larvae cultured on NGM/OP50 at 20°C for 60 h to adult day1(1P0).Synchronized L1 larvae cultured on NGM/OP50 at 20°C for 180 h to adult day5(5P0).

extract_protocol:
Total RNA was extracted from synchronized C. elegans using TRIzol reagent (Invitrogen，USA) following the manufacturer's protocol.
PolyA-selected mRNA was used for library preparation with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7530). mRNA was fragmented, reverse-transcribed, and converted to double-stranded cDNA. After end repair, A-tailing, and adapter ligation (NEB Next Multiplex Oligos), libraries were size-selected (250–300 bp) using AMPure XP beads and PCR-amplified

treatment_protocol: One-day-old (1P0 group) or five-day-old (5P0 group) hermaphrodites.

value: whole organism

value: wild-type (N2)

value: adult day5

tag: batch


title: GFP_neg_SIX2_plasmid_rep2

description: Library name: Sample 5


title: Dvib1G3

description: Library name: sample6

value: vib1 deletion strain


title: 5P0_rep_2

description: Library name: 5P0_rep_2


title: Melanoma, A-A09

description: Library name: DSP-1001250002572-A-A09

data_processing:
The GeoMx DSP Analysis Pipeline version 2.3.3.10 performed trimming, alignment, and deduplication of UV-cleaved probe barcodes
Assembly: GRCh38
Supplementary files format and content: csv files include TPM for each sample

tag: lymph node_status_(1=yes,_0=no)


title: Dvib1G1

description: Library name: sample4


title: 5P0_rep_1

description: Library name: 5P0_rep_1


title: Melanoma, A-A08

description: Library name: DSP-1001250002572-A-A08

tag: distant metastasis_(1=yes,_0=no)


title: Melanoma, A-B01

description: Library name: DSP-1001250002572-A-B01

tag: acral melanoma_(1=yes,_0=no)


title: small intestine, 8w, ATAC-seq, NKp46pos_RORgt_high_1

description: Active Motif

value: CD3- NKp46+ RORgt+

value: RORgt-EGFP


title: Melanoma, A-B02

description: Library name: DSP-1001250002572-A-B02

tag: vital status


title: 1P0_rep_4

description: Library name: 1P0_rep_4

value: adult day1


title: 5P0_rep_3

description: Library name: 5P0_rep_3


title: GFP_pos_CTR_plasmid_rep2

description: Library name: Sample 8

tag: cell type

value: Muscle stem cells

value: Plasmid transfection


title: fetal liver, E14.5, ATAC-seq, CD127pos_Runx3pos_3

description: Active Motif

tag: genotype


title: GFP_neg_CTR_plasmid_rep3

description: Library name: Sample 3

tag: treatment


title: fetal liver, E14.5, ATAC-seq, CD127pos_Runx3neg_2

description: Active Motif


title: GFP_neg_SIX2_plasmid_rep1

description: Library name: Sample 4


title: Melanoma, A-A10

description: Library name: DSP-1001250002572-A-A10

value: Melanoma

tag: overall survival(years)


title: CS20_E1S7, run5

status: Public on Mar 26 2026

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description:
Library name: V2.5R2305180073
single nucleus RNA sequencing

data_processing:
Gene count matrices were generated from FASTQ files by an in-house pipeline (BGI-Research, China).
The downstream analyses were performed using Scanpy package (V1.8.2).
Briefly, in the quality control step, cells with less than 1k genes, less than 2k counts, more than 10% mitochondrial genes, or more than 90 quantiles of total counts per library were filtered out from raw counts by scanpy.pp.filter_cells.
Genes that were captured in less than 3 cells were filtered out as well by scanpy.pp.filter_genes.
Assembly: GRCh38.p12
Supplementary files format and content: h5ad: raw counts, normalized counts and cell type annotation

source_name: embryo

extract_protocol:
Fresh frozen tissue were OCT embedded, and sagittal sections next to Stereo-seq section in five embryos (CS19E1, CS19E2, CS20E1, CS20E2 and CS23E1) were obtained for snRNA-seq.
Single-nucleus sequencing libraries were prepared with DNBelab C4 kits.

value: embryo

tag: developmental stage

tag: Sex

value: Female


title: GFP_neg_CTR_plasmid_rep2

description: Library name: Sample 2


title: fetal liver, E14.5, ATAC-seq, RORgt_high_CD127pos_MHC2neg_1

description: Active Motif

value: fetal liver

tag: strain

tag: age


title: fetal liver, E14.5, ATAC-seq, CD127pos_Runx3neg_3

description: Active Motif

tag: tissue


title: Medicago roots infected with M. hapla strain VW9 bio rep 2

city: Raleigh

first: Dahlia

middle: M

last: Nielsen

state: NC

address: Campus Box 7566

department: Biological Sciences

institute: North Carolina State University

description: Library name: medicago_VW9_2

data_processing:
RNA-Sequencing reads were aligned to the appropriate genome using HISAT2 version 2-2.2.1 (Kim, Langmead, and Salzberg 2015; Pertea et al. 2016; Kim et al. 2019) with default settings.
Gene expression counts were generated from aligned sequence reads using HTSeq version 2.0.2 (Anders, Pyl, and Huber 2015; Putri et al. 2022).
Counts were normalized using edgeR (Robinson, McCarthy, and Smyth 2010; Y. Chen et al. 2025).
Assembly: Medicago truncatula Mt4.0v1 (Tang et al. 2014; Young et al. 2011; Goodstein et al. 2012).
Assembly: Glycine max Wm82.a4.v1 (Valliyodan et al. 2019; Schmutz et al. 2010; Goodstein et al. 2012).
Supplementary files format and content: medicago_raw_counts.dat is a matrix-formatted ascii text file containing the medicago raw counts derived from HTSeq-Count.
Supplementary files format and content: medicago_norm_counts.dat is a matrix-formatted ascii text file containing the medicago adjusted counts derived from edgeR.
Supplementary files format and content: soybean_raw_counts.dat is a matrix-formatted ascii text file containing the soybean raw counts derived from HTSeq-Count.
Supplementary files format and content: soybean_norm_counts.dat is a matrix-formatted ascii text file containing the soybean adjusted counts derived from edgeR.

organism:
Medicago truncatula
Meloidogyne hapla

source_name: root gall

growth_protocol: Plants were grown in a growth chamber for 16 hr under 200-300 µmol/m-2s-1 of light at 22° C and 60% humidity, and for 8 hr at 18° in the dark.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Valencia, CA). One sample (soybean-VW9 bio rep 7) did not produce sufficient RNA.
Libraries were prepared using a TruSeq RNA library prep kit.

treatment_protocol: After four weeks, plants were inoculated with 2,500 freshly hatched J2 per pot. At three weeks post inoculation, resected sections of plant root (galls or root knots) harboring feeding nematodes were collected for RNA-Seq.

value: root gall

tag: variety

value: Jemalong A17


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_middle_3

description: Active Motif

value: RORgtKO; RORgt-EGFP


title: Melanoma, A-A05

description: Library name: DSP-1001250002572-A-A05

tag: aoi

tag: patient

tag: has replicate_(1=yes,_0=no)

tag: replicate (1=yes,_0=no)


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_middle_4

description: Active Motif

value: embryonic day 14.5


title: fetal liver, E14.5, ATAC-seq, CD127pos_Runx3neg_1

description: Active Motif


title: Melanoma, A-A02

description: Library name: DSP-1001250002572-A-A02

tag: included in_analysis_(1=yes,0=no)

tag: lymph node_status_(1=yes,_0=no)

tag: distant metastasis_(1=yes,_0=no)


title: GFP_neg_CTR_plasmid_rep1

description: Library name: Sample 1

tag: cell type


title: Medicago roots infected with M. hapla strain VW9 bio rep 4

description: Library name: medicago_VW9_4


title: ZNF_ChIP_ZNF281_OE_1

city: Edmonton

first: Maria Areli

last: Lorenzana Carillo

state: Alberta

country: Canada

institute: University of Alberta

description: Library name: CM_10

data_processing:
Raw sequencing reads were quality-checked, trimmed, and aligned to mm10 (mouse) or hg38 (human) reference genomes using STAR (RNA-seq) or Bowtie2 (ChIP-seq). Gene counts were generated using HTSeq-count, followed by TMM normalization and differential expression analysis using limma–voom. ChIP-seq peaks were identified using MACS2 and annotated using BEDtools. Analyses were performed using the Galaxy platform.
Assembly: mm10 (Mus musculus) and hg38 (Homo sapiens)
Supplementary files format and content: Processed RNA-seq data include raw gene count matrices generated using HTSeq-count and normalized expression values (log2 CPM) for A549 human cells and mouse cardiomyocytes analyzed as separate experimental systems. Differential expression results are also provided. ChIP-seq data include peak files in BED format and peak annotation files mapping peaks to the nearest transcription start site.

source_name: Cardiomyocyte

growth_protocol: A549 human lung carcinoma cells were maintained under standard culture conditions. Primary mouse cardiomyocytes were isolated and cultured as described in the Methods section.

extract_protocol:
Total RNA was isolated using QIAzol reagent according to the manufacturer’s instructions.
RNA-seq libraries were prepared using standard library preparation protocols. ChIP-seq libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations.

treatment_protocol: A549 cells were genetically modified to generate ZNF281 knockout (KO) cells alongside parental controls. Mouse cardiomyocytes were genetically modified to induce ZNF281 overexpression (OE) and compared with control cells.

tag: cell line

value: Cardiomyocyte

value: ZNF281 OE


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_middle_1

description: Active Motif

tag: genotype


title: Melanoma, A-A06

city: ANN ARBOR

first: Ziyin

last: Huang

institute: University of Michigan

description: Library name: DSP-1001250002572-A-A06

tag: acral melanoma_(1=yes,_0=no)

tag: vital status

tag: overall survival(years)


title: Melanoma, A-A07

description: Library name: DSP-1001250002572-A-A07


title: Medicago roots infected with M. hapla strain VW9 bio rep 1

description: Library name: medicago_VW9_1


title: Medicago roots infected with M. hapla strain LM bio rep 3

description: Library name: medicago_LM_3


title: Melanoma, A-A03

description: Library name: DSP-1001250002572-A-A03


title: 1P0_rep_1

description: Library name: 1P0_rep_1

value: whole organism

value: wild-type (N2)

tag: treatment

tag: batch


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_middle_5

description: Active Motif

tag: tissue

tag: strain

tag: age


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_neg_6

description: Active Motif


title: Medicago roots infected with M. hapla strain LM bio rep 2

description: Library name: medicago_LM_2

tag: variety


title: 1P0_rep_2

description: Library name: 1P0_rep_2


title: transplanted hBOs at 150dpt after Target neuromuduation

city: Tianjin

first: Xiaohong

last: Li

address: 92 Weijin Road

institute: Tianjin University

description:
Library name: Sample2
10× Genomics

data_processing:
Raw sequencing data were processed using the CellRanger software suite (v7.0) and aligned to the GRCh38-GRCm39 dual genome. FastQC (v0.11.2) for Data filtering. DoubletFinder (v2.0.3) for Dual-species alignment. The human transcript ratio (h-ratio) was calculated for each cell barcode; cells with h-ratio > 0.8 were classified as human, < 0.2 as mouse, and intermediate values as unknown. Downstream analysis was performed in Seurat (v4.1.1) using human-derived cells filtered for nUMI > 500, nGenes > 500, and mitochondrial percentage < 25%.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files

molecule: nuclear RNA

source_name: brain

extract_protocol:
Single-nuclei suspensions were prepared from snap-frozen hBOs grafts collected at 150 dpt. Grafts were retrieved from liquid nitrogen, placed on dry ice, and further finely dissected using a stereomicroscope. Grafts were then disrupted using a detergent-mechanical cell lysis method. Crude nuclei were filtered through a 40 μm strainer, centrifuged, and purified via sucrose density gradient centrifugation. Purified nuclei were resuspended in 0.04% BSA/PBS containing an RNase inhibitor.
Approximately 18,000 nuclei per sample were loaded onto the Chromium Single Cell 3' Chip (10× Genomics, USA), and libraries were constructed using the v3 reagent kit. Pooled libraries were sequenced on an Illumina NovaSeq S4 platform (Admera Health, USA).

value: brain

value: Human embryonic stem cells (hESCs)

value: WT

value: Target neuromodulation


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_middle_2

description: Active Motif


title: 1P0_rep_3

description: Library name: 1P0_rep_3

value: adult day1


title: Medicago roots infected with M. hapla strain VW9 bio rep 3

description: Library name: medicago_VW9_3


title: Melanoma, A-A01

address: 3003 S. STATE STREET

description: Library name: DSP-1001250002572-A-A01

tag: aoi

value: Melanoma

tag: patient

tag: has replicate_(1=yes,_0=no)


title: ZNF_ChIP_ZNF281_OE_2

description: Library name: CM_11


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_middle_6

description: Active Motif


title: Melanoma, A-A04

description: Library name: DSP-1001250002572-A-A04

tag: replicate (1=yes,_0=no)

tag: included in_analysis_(1=yes,0=no)

tag: lymph node_status_(1=yes,_0=no)


title: Medicago roots infected with M. hapla strain LM bio rep 4

description: Library name: medicago_LM_4


title: NOZ-R rep3

city: Chongqing

first: Yunping

last: Hu

address: No.30 Gaotanyan Main Street

institute: The First Affiliated Hospital, Third Military Medical University (Army Medical University)

description:
Library name: sample6
Column name in counts_table.txt & FPKM_table.txt:NOZ_R3

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.
Assembly: GRCh38
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

source_name: NOZ-R

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

tag: cell line

value: NOZ-R

tag: cell type

value: gemcitabine resistant gallbladder cancer cells


title: Medicago roots infected with M. hapla strain LM bio rep 1

description: Library name: medicago_LM_1


title: ZNF_ChIP_Control_1

description: Library name: CM_7

value: Control


title: ZNF_ChIP_ZNF281_OE_3

description: Library name: CM_12


title: Escherichia coli MG1655, wild-type with pTOPO_CMY145, biol rep3

city: RENNES

first: Charlotte

last: Michaux

address: 2 avenue du Pr Leon Bernard

department: Inserm

country: France

institute: University of Rennes

description:
Library name: Sample 12
CMY145_biol3 sheet in TPM_counts_allsamples.xlsx

data_processing:
The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq X plus instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.3.1 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
CLC software (Qiagen) version 24 was used to process and analyze the data.
Raw data were paired, trimmed, and mapped against the reference genome of Escherichia coli K12 MG1655 (accession number NC_000913.3)
Differential expression analysis (DE) and volcano plots were generated using CLC, with a choosen cutoff of log2 fold change and FDR < 0.05 to narrow down the deregulated transcripts.
Unsupervised heatmaps were generated using the mean of Transcript Per Million (TPM) in log10 of each condition and plotted using R package ggplot2
Assembly: Trimmed data were mapped  against the reference genome of Escherichia coli K12 MG1655 (accession number NC_000913.3)
Supplementary files format and content: csv file include TPM and total count values for each sample
Supplementary files format and content: In addition, protein (GI) and gene names have been included

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria

growth_protocol: Escherichia coli strains  were grown overnight in LB in three biological replicates. Bacteria were then diluted in MOPS (1:100) and grow aerobically until OD600 of 0.6.

extract_protocol:
RNA extraction was performed using the zymo kit for quick RNA extraction. DNase treatment was carried out using the Turbo DNase kit from Invitrogen. After quality checking with a TapeStation (Agilent), RNA samples were sent to Genewiz.
rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria). RNA sequencing library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).

treatment_protocol: Bacteria were centrifuged and the pellets froze at -80°C.

value: bacteria

tag: genotype

value: wild-type

value: 8th of September 2024


title: ZNF_ChIP_Control_3

description: Library name: CM_9


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_neg_2

description: Active Motif

source_name: fetal liver

value: fetal liver

value: RORgtKO; RORgt-EGFP

value: embryonic day 14.5


title: Escherichia coli MG1655, wild-type with pTOPO_CMY145, biol rep2

description:
Library name: Sample 11
CMY145_biol2 sheet in TPM_counts_allsamples.xlsx


title: NOZ-R rep1

description:
Library name: sample4
Column name in counts_table.txt & FPKM_table.txt:NOZ_R1


title: ZNF_ChIP_Control_2

description: Library name: CM_8

value: Cardiomyocyte


title: transplanted hBOs at 150dpt after Non-Target neuromuduation

description:
Library name: Sample1
10× Genomics

value: Non-Target neuromodulation


title: NOZ rep3

description:
Library name: sample3
Column name in counts_table.txt & FPKM_table.txt:NOZ3

source_name: NOZ

value: NOZ

value: gallbladder cancer cells


title: NOZ rep2

description:
Library name: sample2
Column name in counts_table.txt & FPKM_table.txt:NOZ2


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_neg_5

description: Active Motif


title: Escherichia coli MG1655, wild-type with pTOPO_CMY42, biol rep2

description:
Library name: Sample 8
CMY42_biol2 sheet in TPM_counts_allsamples.xlsx


title: Escherichia coli MG1655, wild-type with pTOPO_CMY42, biol rep3

description:
Library name: Sample 9
CMY42_biol3 sheet in TPM_counts_allsamples.xlsx


title: RNA_Control_1

description: Library name: CM_1


title: RNA_ZNF281_OE_3

description: Library name: CM_6

value: ZNF281 OE


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_neg_4

description: Active Motif


title: fetal liver, E14.5, ATAC-seq, RORgt_LTi_1

description: Active Motif

source_name: fetal fetus

value: fetal fetus

value: Lin-c-kit+GFPhigh

value: RORgt-EGFP


title: RNA_ZNF281_OE_2

description: Library name: CM_5


title: RNA_ZNF281_OE_1

description: Library name: CM_4


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_neg_3

description: Active Motif


title: Escherichia coli MG1655, wild-type with pTOPO_CMY42, biol rep1

description:
Library name: Sample 7
CMY42_biol1 sheet in TPM_counts_allsamples.xlsx


title: RNA_Control_2

description: Library name: CM_2


title: NOZ-R rep2

description:
Library name: sample5
Column name in counts_table.txt & FPKM_table.txt:NOZ_R2

value: NOZ-R


title: Escherichia coli MG1655, wild-type with pTOPO_CMY145, biol rep1

description:
Library name: Sample 10
CMY145_biol1 sheet in TPM_counts_allsamples.xlsx


title: fetal liver, E14.5, ATAC-seq, RORgtKO_RORgt_neg_1

description: Active Motif


title: BHPrS1DGAT1_2

city: Shreveport

first: Omar

last: E. Franco

address: 1501 Kings Hwy

department: Biochemistry and Molecular Biology

institute: LSU Health Shreveport

description: Library name: Sample 4

data_processing:
Sequencing was performed with 2 x 150 bp reads on a NovaSeq 6000 PE150, followed by bioinformatics analysis.
Read mapping was conducted using STAR v2.6.1d (RRID:SCR_004463), differential gene expression analysis was performed with DESeq2 v1.26.0 (RRID:SCR_000154), and significantly differentially expressed genes between groups with sufficient power were identified based on an adjusted p-value ≤ 0.05
Assembly: GRCh38 (hg38)
Supplementary files format and content: Raw counts all data.csv

source_name: Prostate

extract_protocol:
Total RNA was extracted from cells BHPrS1 and DGAT1 overexpressing BHPrS1 using an RNeasy Mini Kit (74106, Qiagen, Hilden, Germany).
For RNA-seq studies, total RNA was cleaned with the RNeasy Plus Mini Kit (Qiagen 74134) and shipped to Novogene (Sacramento, CA) for poly A selection and library preparation with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs E7770)

value: Prostate

value: Fibroblast

value: DGAT1 overexpressing


title: fetal liver, E14.5, ATAC-seq, RORgt_high_1

description: Active Motif


title: BHPrS1DGAT1_1

description: Library name: Sample 3


title: fetal liver, E14.5, ATAC-seq, RORgt_LTi_2

description: Active Motif


title: NOZ rep1

description:
Library name: sample1
Column name in counts_table.txt & FPKM_table.txt:NOZ1


title: KPCY tumor, ATEV2

city: Columbus

first: Mengying

state: Ohio

address: 496 W 12th Ave

department: Pharmaceutics and Pharmacology

institute: The Ohio State University

description: Library name: ATEV2

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (version 2.0.11) (http://ccb.jhu.edu/software/tophat/index.shtml), and transcriptome reconstruction was performed by Cufflinks (version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/). The abundance of transcripts was measured with Cufflinks in fragments per kilobase of exon model per million mapped reads (FPKM).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: subcutaneous tumor

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen, 74134) following the manufacturer’s instructions.
TruSeq stranded mRNA library was prepared according to manufacturer's instructions

treatment_protocol: 5 × 10^5 of KPCY (6419c5) cells in 50 µL of Corning Matrigel matrix were subcutaneously injected into the right flank of 8-week-old female C57BL/6 mice. 4 days after tumor inoculation, mice were randomized blindly into different treatment groups, and the investigator was blinded to the group allocation during the animal experiments. Each mice received one intratumoral injection of PBS or 25 µg of ATEVs (containing 10 µg of EVDNA) in the volume of 30 µL every 3 days for in total 6 doses. Mice were euthanized 9 days after the final treatment. Tumors were harvested for flow cytometry analysis and bulk RNAseq.

value: subcutaneous tumor

value: KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre; Rosa26YFP/YFP

value: ATEV


title: RNA_Control_3

description: Library name: CM_3

value: Control


title: Escherichia coli MG1655, wild-type with pTOPO_CMY2, biol rep1

description:
Library name: Sample 4
CMY2_biol1 sheet in TPM_counts_allsamples.xlsx

value: bacteria

value: wild-type

value: 8th of September 2024


title: fetal liver, E14.5, ATAC-seq, RORgt_middle_2

description: Active Motif

value: fetal liver

value: embryonic day 14.5


title: KPCY tumor, ATEV1

description: Library name: ATEV1


title: fetal liver, E14.5, ATAC-seq, RORgt_high_2

description: Active Motif


title: Escherichia coli MG1655, wild-type with pTOPO, biol rep3

description:
Library name: Sample 3
pTOPO_biol3 sheet in TPM_counts_allsamples.xlsx


title: KPCY tumor, PBS2

description: Library name: PBS2

value: PBS


title: Escherichia coli MG1655, wild-type with pTOPO_CMY2, biol rep3

description:
Library name: Sample 6
CMY2_biol3 sheet in TPM_counts_allsamples.xlsx


title: KPCY tumor, ATEV3

description: Library name: ATEV3


title: Escherichia coli MG1655, wild-type with pTOPO, biol rep2

description:
Library name: Sample 2
pTOPO_biol2 sheet in TPM_counts_allsamples.xlsxx


title: BHPrS1EV_2

description: Library name: Sample 2

value: WT


title: Escherichia coli MG1655, wild-type with pTOPO_CMY2, biol rep2

description:
Library name: Sample 5
CMY2_biol2 sheet in TPM_counts_allsamples.xlsx


title: BHPrS1EV_1

description: Library name: Sample 1


title: Escherichia coli MG1655, wild-type with pTOPO, biol rep1

description:
Library name: Sample 1
pTOPO_biol1 sheet in TPM_counts_allsamples.xlsx


title: fetal liver, E14.5, ATAC-seq, RORgt_middle_1

description: Active Motif


title: KPCY tumor, PBS3

description: Library name: PBS3


title: small intestine, 10w, ATAC-seq, gdT17

description: Active Motif

value: small intestine


title: siRbFox2_Rep2

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

description: Library name: siRbm9_2

data_processing:
Starting from raw PacBio HiFi reads, lima was used to remove cDNA primers.
Subsequently, the "pbmm2" algorithm in Isoseq 4.3.0 was used to align the resulting BAM file to the Rattus Norvegicus genome (rn7.2).
Isoquant v3.5.0 was used to quantify the aligned BAMs at the gene and transcript level (Rattus_norvegicus.mRatBN7.2.112.chr.gtf)
Assembly: rn7.2
Supplementary files format and content: gene/transcript Ensembl ID with associated counts.

organism: Rattus norvegicus

growth_protocol: A7R5 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 5% fetal bovine serum and 1% penicillin–streptomycin and maintained at 37°C with 5% CO2.

extract_protocol:
Novogene’s RNA detection for RNA samples primarily includes four methods: 1.Agarose gel electrophoresis to analyze the degree of RNA degradation and to check for contamination. 2.Nanodrop to assess the purity of RNA (OD260/280 ratio). 3.Qubit for precise quantification of RNA concentration. 4.Agilent 2100 for accurate assessment of RNA integrity.
The Iso-Seq Express 2.0 kit was used to synthesize cDNA using QC-passed RNA. This was followed by library construction using the Kinnex Full-Length RNA Kit.

treatment_protocol: A7R5 cells were treated with either siRNA targeting RbFox2 and RhoBTB1 mRNA or negative control pool of 4 siRNAs .


title: thymus, E17.5, ATAC-seq, thymocyte

city: Fukuoka

first: Shinichiro

institute: Kyushu University

description: Active Motif

source_name: thymus

value: thymus

value: Lin- CD4+ CD8+

value: RORgt-EGFP

value: embryonic day 17.5


title: fetal liver, E14.5, ATAC-seq, RORgt_neg_1

description: Active Motif


title: isolated living cells from young mouse brai after Pacitaxel treatment_5

city: Oklahoma City

first: Roland

last: Patai

state: Oklahoma

address: 975 NE 10th street

department: Department of Neurosurgery

institute: University of Oklahoma Health Campus

description:
Library name: PTX5
10X Genomics Chromium Single Cell 3′ Gene Expression v2

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger software count pipeline v.6.0.0.
Assembly: gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mice were euthanized and transcardially perfused with PBS, after which brains were rapidly harvested, rinsed in ice-cold PBS, and minced into small fragments. Tissue was enzymatically digested using collagenase, hyaluronidase, and elastase at 37 °C, then filtered through a 100 μm cell strainer to obtain a single-cell suspension. Cells were washed, centrifuged, and enriched for cerebrovascular and neurovascular unit cells using an iodixanol (OptiPrep) density gradient. The enriched cell fraction was collected and resuspended in PBS containing 0.4% BSA for downstream processing.
Single-cell suspensions were loaded onto the 10x Genomics Chromium Single Cell 3′ platform for droplet-based capture. Libraries were generated using the Chromium Single Cell 3′ v2 kit following the manufacturer’s protocol, pooled based on molar concentration, and sequenced on an Illumina NovaSeq 6000 system. Raw sequencing data were processed using the Cell Ranger pipeline for read alignment, barcode processing, and gene expression quantification

treatment_protocol: Mice used for single-cell RNA sequencing were transgenic p16-3MR males treated with paclitaxel (PTX; 5 mg/kg/day, intraperitoneally) administered in two cycles of 5 consecutive days with a 7-day interval between cycles. Control animals received vehicle (DMSO + saline). Following treatment and recovery, animals were maintained for up to 6 months post-chemotherapy before brain collection. Whole brains were harvested after perfusion and processed for single-cell dissociation and downstream transcriptomic analysis.

value: brain

value: multiple

value: wild-type  p16- 3MR mouse

tag: Sex

value: male

value: 9-10 months

value: Pacitaxel