title: Hi-C, HEK293T cells, VPA-treated

data_processing:
Raw reads for VPA-treated and untreated samples were processed separately using Juicer pipeline (v1.9.9) to obtain contact matrices. Hg38 reference genome, or GRCh38 (GRCh38 Genome Reference Consortium Human Reference 38) from UCSC was used for the assembly (without alternative contigs). Singletons, low-quality, unmapped, dangling, self-circle paired-end reads, and PCR duplicates were removed during the data processing. Only Hi-C contacts with MAPQ< 30 were used for further analyses.
Assembly: hg38
Supplementary files format and content: .hic file contains Hi-C contact matrix

extract_protocol:
293T cells without (CTRL) and with 1mM VPA treatment for 1 day (VPA) were prepared and Hi-C was performed according to a protocol of EpiTect Hi-C Kit from Qiagen.
Hi-C libraries were prepared for both VPA-treated HEK293 cells and experimental control as described in EpiTect Hi-C Kit from Qiagen.

value: VPA-treated


title: Ch1-S3-0E-A4

status: Public on Feb 02 2026

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

country: USA

institute: University of New Mexico

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

data_processing: Target gene signals normalized to median expression of each sample across all genes followed by centering the delta CT values across all samples within a gene.

label: EvaGreen

molecule: total RNA

organism: Mus musculus

label_protocol: qPCR was performed using 96.96 BioMark™ Dynamic Arrays (Fluidigm®, South San Francisco, CA) enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions (Spurgeon et al. 2008). DNA intercalating dye based approach (EvaGreen ) was used for quantitative detection of qPCR products. Each qPCR experiment consisted of 30 amplification cycles (15s at 95°C, 5s at 70°C, 60s at 60°C). Ct values were calculated by the Real-Time PCR Analysis Software (Fluidigm).

growth_protocol: Fetal dorsal telencephalic ventricular neuroepithelium corresponding to the precursor projection neurons of the developing cerebral cortical plate were obtained by sterile microsurgical dissection from gestational day (GD) 12.5 C57/Bl6 mouse fetuses. This period corresponds to the late 1st trimester-equivalent period for cortical development in human pregnancy. Neuroepithelial cells collected from two entire litters at a time, were dispersed in a defined culture medium DMEM F12 (Invitrogen, #11039-047), 20 ng/ml Basic Fibroblast Growth Factor (bFGF, BD Biosciences, #354060), 20 ng/ml human recombinant Epidermal Growth factor (EGF, Invitrogen #47743-568), 0.15 ng/ml recombinant human Leukemia Inhibitory Factor (LIF, Alomone, #L-200), ITS (Insulin, Transferrin, Selenium) supplement (Invitrogen, #51500-056), 0.85 units/ml Heparin (Sigma-Aldrich, #H-4784), 20 nM progesterone (Sigma-Aldrich, #P7556) and cultured as non-adherent neurosphere aggregates. Independent replicates for the reported experiments were from neurospheres established from a total of six sets of neuroepithelium isolations, from 12 different pregnancies.

extract_protocol: Each neurosphere was imaged, prior to collection in 6ul of Cells Direct Lysis Buffer (Invitogen #117753-100) and stored at -80oC, prior to being processed for RT-qPCR using the Biomark HD system (protocol ADP 42), for mRNA expression across 96 genes. Single neurospheres were processed directly to reverse transcription and pre-amplification reaction (Fluidigm protocol ADP 42), without RNA extraction to minimize RNA loss.

treatment_protocol: Neurosphere cultures were randomly assigned to control and ethanol-exposed (120 mg/dl (26 mM), 320 mg/dl (70 mM) and 450mg/dl (100mM)) groups. The final ethanol concentration in the culture media was determined by gas chromatography (TRACE™ 1310, Thermo Fisher Scientific), from samples of the media collected at the beginning of the treatment at day 0, at day 3 for re-feeding and at day 5 before collection.

tag: strain

value: C57/Bl6 mouse

tag: tissue

value: dorsal telencephalon

tag: developmental stage

tag: culture group

value: Set-B

tag: ethanol (etoh) treatment

tag: neurosphere diameter (um)

tag: neurosphere size group

value: M


title: Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #1

type: SRA

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: KO-1

library_source: genomic

data_processing:
Data was processed following the recommendations of the ENCODE consortium (The ENCODE Consortium, n.d.): Reads were aligned to the mouse reference genome (version GRCm38) with BWA-backtrack. Post-alignment filtering was done with samtools and Picard tools  to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates. To identify regions of open chromatin, peak calling was performed with MACS2. The narrowPeak results of MACS2 were used after filtering for adjusted p-values smaller than 0.01.
Coverage files (bigWig) were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --blackListFileName mm10.blacklist --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40.
Assembly: mm10
Supplementary files format and content: BigWig files for each sample

molecule: genomic DNA

source_name: tdLN

growth_protocol: Naïve WT and KO TCRSMARTA transgenic CD4 T cells were transferred into cytoxan-treated B16-GP61 tumor-bearing mice

extract_protocol:
Cells were sorted and frozen in 10% DMSO/FCS. Frozen cells were thawed, washed in PBS, and lysed. Transposition was performed at 42°C for 45 min. DNA was purified with the MinElute PCR purification kit (Qiagen)
DNA was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5Å~ ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).

treatment_protocol: Tumor-bearing mice received congenically marked WT (Ly5.12) and KO (Ly5.1) TCRSMARTA

value: tdLN

tag: cell line

tag: cell type

value: CD4 T cells

tag: genotype

value: KO

tag: cd4 t cells

value: TCRSMARTA transgenic CD4 T cells


title: KP.2

city: Stony Brook

first: Harold

last: Bien

address: 100 Nicolls Road

institute: Stony Brook University

description: Library name: RZL3_2

library_source: transcriptomic

data_processing:
Sequence reads were quantified with GC bias trimming using Salmon
Trimmed sequence reads were mapped to the GrCM39/mm39 reference genome
Assembly: GrCM39/mm39
Supplementary files format and content: tab-delimited sf files including name, length, effective length, transcripts per million, and total number of reads

source_name: KP

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina with the Ploy(A) mRNA Magnetic Isolation Module

value: KP

value: lung adenocarcinoma

value: Kras G12D, Tp53 null

tag: batch


title: Ch1-S3-0E-A3

source_name: fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)


title: KPA.3

description: Library name: RZL3_6

source_name: KPA

value: KPA

value: PIK3CA knockout


title: KP.1

description: Library name: RZL3_1


title: Hi-C, HEK293T cells, untreated

city: Tokyo

first: Yutaka

last: Saito

department: Artificial Intelligence Research Center (AIRC)

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

organism: Homo sapiens

value: human embryonic kidney cells

value: WT

tag: treatment


title: NormalControl4

city: Kuala Lumpur

first: Siow-Wee

last: Chang

address: Faculty of Science

country: Malaysia

institute: Universiti Malaya

data_processing:
Sequence reads were trimmed for adaptor sequence of TGGAATTCTCGGGTGCCAAGG (3' adapter sequence) using Cutadapt.
Trimmed sequence reads were mapped to Ensembl 99 (H_sapiens) using Bowtie.
The matched reads were aligned to identify mature miRNAs in miRbase version 22.
Read counts were normalized using TMM in edgeR.
Assembly: Ensembl 99 (H_sapiens)
Supplementary files format and content: tab-delimited text files for the normalized expression file.

source_name: Blood

extract_protocol:
miRNA was harvested using GeneAll HybridRTM Blood RNA Kit. 5ug of total RNA was extracted.
miRNA library was constructed NEXTflex Illumina Small RNA Sequencing Kit v3 following manufacturer's protocol.

value: Blood

value: Plasma

tag: disease state

value: normal


title: Ch1-S3-0E-A2

value: C57/Bl6 mouse

value: dorsal telencephalon


title: Mnk3_Ctrl_RNA_Seq

city: Columbus

first: Ankita

last: Saini

state: Ohio

address: 460 W 12th Ave

department: Microbial Infection and Immunity

institute: The Ohio State University Wexner Medical Center

description:
Library name: Mnk3_Ctrl_RNA
Ribo-depletion

library_source: other

data_processing:
Aligned using STAR
Assembly: Reference build Ensembl_R76
Supplementary files format and content: Text file generated by Subread featureCounts containing counts of uniquely aligned unambigous reads per gene.

molecule: other

extract_protocol:
Total RNA was prepped using Qiagen kit followed by Ribo depletion
RNA-seq

treatment_protocol: Cells were either stimulated with 10ng/ml each of IL-1b+IL-23 or left untreated for ~16 hours

value: Control


title: CYP4

city: Wuhan

first: yunqing

last: sun

state: 洪山区

address: Luoyu Road 237#

country: China

institute: wuhan university

description: Library name: CYP4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: GCRm38
Supplementary files format and content: tab-delimited text files include raw read count
Supplementary files format and content: content

source_name: Spleen

extract_protocol:
Total RNA was extracted from pTh17 cells cultured for 2 days using the Direct-zol RNA Microprep Kit (ZYMO Research,R2061).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). 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. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Spleen

value: Primary cell

value: CYP1B1 knockout

value: pathogenic Th17 differentiation


title: NormalControl3


title: Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #2

description: Library name: KO-2

value: tdLN

value: CD4 T cells

value: KO

value: TCRSMARTA transgenic CD4 T cells


title: CYP3

description: Library name: CYP3


title: Mnk3_Stim_RNA_Seq

description:
Library name: Mnk3_Stim_RNA
Ribo-depletion

value: Stimulated with IL-1b+IL-23


title: Ch1-S3-0E-A10

value: Set-B

value: M


title: K27ac_Mnk3_Stim2

description: Library name: Mnk3_Stim_Chipseq_K27ac_replicate2

data_processing:
Sequencing data were mapped to mm9 using Bowtie2. BigWig files were created from BAM files using deepTools package.
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
Chip-seq was performed using antibody against H3K27ac (Abcam #ab4729). Preparation of samples for ChIP was carried out as described (Brind'Amour et al, 2015).
Chip-seq


title: NormalControl2

value: Blood


title: K27ac_Mnk3_Stim1

description: Library name: Mnk3_Stim_Chipseq_K27ac_replicate1


title: CYP1

description: Library name: CYP1


title: K27ac_Mnk3_Ctrl2

description: Library name: Mnk3_Ctrl_Chipseq_K27ac_replicate2

value: Control untreated


title: Ch1-S2-70E-A8

value: Set-A


title: Ch1-S3-0E-A11

value: C57/Bl6 mouse

value: L


title: WT4

description: Library name: WT4

value: WT


title: ADpatient7

value: Plasma

value: Alzheimer's Disease


title: NormalControl1

value: normal


title: ADpatient6


title: K27ac_Mnk3_Ctrl1

description: Library name: Mnk3_Ctrl_Chipseq_K27ac_replicate1


title: CYP2

description: Library name: CYP2

value: Spleen

value: Primary cell

value: CYP1B1 knockout

value: pathogenic Th17 differentiation


title: Mnk3_Stim_ATAC_rep2

description: Library name: ATAC_Mnk3_Stim2

extract_protocol:
Nuclei were isolated from freshly harvested cells. The nuclei were then subjected to transposition reactions for 30 minutes using Tagment DNA TDE1 Enzyme (Illumina, 20034197). Purified DNA was then amplified to generate libraries using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-2001).
Libraries generated using Nextera XT DNA Library Preparation Kit

value: Stim with IL-1b+IL-23


title: Ch1-S2-70E-A9

value: dorsal telencephalon


title: Ch1-S3-0E-A1

value: Set-B


title: WT3

description: Library name: WT3


title: Ch1-S2-70E-A7

value: M


title: ADpatient5

value: Blood


title: ADpatient4


title: WT1

description: Library name: WT1


title: Mnk3_Stim_ATAC_rep1

description: Library name: ATAC_Mnk3_Stim1


title: Ch1-S2-70E-A6


title: ADpatient3


title: Mnk3_Ctrl_ATAC_rep2

description: Library name: ATAC_Mnk3_Ctrl2

value: Control


title: Ch1-S2-70E-A5

value: Set-A

value: S


title: Ch1-S2-70E-A4

value: C57/Bl6 mouse


title: WT2

description: Library name: WT2

value: WT


title: ADpatient2

value: Plasma


title: Mnk3_Ctrl_ATAC_rep1

description: Library name: ATAC_Mnk3_Ctrl1


title: scMultiome_KO_GEX

first: Tong

last: Xiao

state: OH

address: 2255 Kenny Rd, Room 3130

institute: Pelotonia Institute for Immuno-oncology

description:
Library name: KO_RNA
3' mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read 2 contains transcript sequence

library_source: transcriptomic single cell

data_processing:
scRNA-seq/scATAC-seq data was generated using the 10x Cell Ranger ARC pipeline (v.2.0.2).
Assembly: mm10
Supplementary files format and content: CellRanger output files: Control_barcodes.tsv.gz, Control_features.tsv.gz, Control_matrix.mtx.gz, KO_barcodes.tsv.gz, KO_features.tsv.gz, KO_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Control_atac_fragments.tsv.gz, KO_atac_fragments.tsv.gz

molecule: polyA RNA

source_name: Spleens

extract_protocol:
CD44High GP33-41 tetramer+ CD8+ T cells were FACs-sorted from the spleens of control or ZFP148 KO mice 21 days-post LCMV C13 infection. After sorting, cells were washed with PBS containing 0.04% BSA, then approximately 10,000 nuclei of either control or ZFP148 KO sample were isolated and processed with the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kit following manufacture’s manual (10x genomics).
Two separate sets of libraries, Gene expression (GEX) and ATAC, were generated from each sample according to manufacturer’s instructions. Pre-sequencing quality control was performed using an Agilent Tapestation. GEX libraries and ATAC libraries were sequenced on an Illumina Novaseq X plus platform by Azenta Life Sciences.

value: Spleens

value: CD8+ T cells

value: E8i-cre+ Zfp148flox/flox

value: LCMV Cl13, day 21

tag: library type

value: mRNA


title: dom_embryo_female_litter#8_individual#E3

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

description: Library name: M8_E3

data_processing:
Quality control, trimming of raw sequencing reads, filtering and mapping were performed as described in Arévalo et al. (2021). To improve comparability, all samples (Dom, Spret, and hybrid) were mapped to a pseudo-hybrid genome, generated using the genome preparation tool of the program SNPsplit (Krueger and Andrews 2016). Briefly, SNPs from both Dom (WSB/EiJ) and Spret (SPRET/EiJ) relative to the mouse genome (GRCm38.89) available from the Ensembl FTP server (ftp://ftp.ensembl.org) were introduced into the mouse genome. SNPs between Dom and Spret were then N-masked to allow mapping of both Dom- and Spret-derived reads. We randomly downsampled all alignment files to the same number of reads (~40 million reads) using SAMtools 0.1.19 (Li et al. 2009). For analysis of allele specific expression (ASE) in hybrids we used SNPsplit to split the hybrid alignment files, separating reads originating from the Spret and Dom alleles. Reads that were unassignable (did not overlap SNPs between WSB/EiJ and SPRET/EiJ) or contained conflicting or non-informative (polymorphic) SNPs were removed. On average, 69% of mapped RNAseq reads were assignable, 26% unassignable and 5% conflicting.
Transcript quantification and annotation was done using StringTie 1.3.3 (Pertea et al. 2015). Mouse genome annotation information (GRCm38.89) was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org). We used the python script (preDE.py) included in the StringTie package to prepare gene-level count matrices for analysis of differential expression (DE; Table 1) and ASE in DESeq2 1.16.1 (Love et al. 2014). Pseudogenes were removed from the count matrices based on “biotype” annotation information extracted from Biomart (R-package biomaRt, Durinck et al. 2005). Low counts were removed by the independent filtering process implemented in DESeq2 (Bourgon et al. 2010). The adjusted p-value (Benjamini-Hochberg method) cutoff was set at ≤ 0.05. Following the recommendations of Love et al. (2014; see also Vallejos et al. 2016; Schurch et al. 2016), we chose an absolute log2 fold change (LFC) cutoff of ≥ 0.5 (1.41 times higher or lower expression) for standard DE analysis.
Assembly: GRCm38.89 (with N-masked SNPs between WSB/EiJ) and Spret (SPRET/EiJ))
Supplementary files format and content: tab delimited file including DEseq-normalized read counts for all samples

organism: Mus musculus domesticus

source_name: murine hypothalamus

extract_protocol:
Total RNA was extracted from hypothalamus tissue using the AllPrep RNA/DNA Mini Kit (Qiagen), and was stored at -80°C until sequencing.
Illumina library preparation was done at the sequencing facility (Novogene, Sacramento, CA) using the NEB Next Ultra RNA library prep kit for Illumina.  Individual libraries were sequenced on the Illumina HiSeq 4000 platform, producing >40 million, 150bp paired-end reads per sample.

treatment_protocol: Mice used in this study were maintained on a 12:12 light:dark cycle with lights on at 9:00 AM and were provided with 5001 Rodent Diet (LabDiet, Brentwood, MO, U.S.A.) and water ad lib. All animal procedures were approved by the Oklahoma State University IACUC under protocol #141-AS. M. m. domesticus (hereafter, Dom) was represented by the wild-derived inbred strain WSB/EiJ (Jackson Laboratory) and M. spretus (hereafter, Spret) was represented by the wild-derived inbred strain SFM/Pas (Montpellier Wild Mice Genetic Repository). We conducted three crosses, Dom x Dom, Dom x Spret, Spret x Spret (female listed first). For embryonic tissue collections we used timed mating to establish embryonic age ±24h as described previously (Arévalo and Campbell 2020; Arévalo et al. 2021). Pregnant females (n=5/cross) were euthanized by cervical dislocation between 10:00 and 11:00 AM on embryonic day 17-18 (e17.5).  Tissues (maternal brain, embryo heads, placentas) were collected into RNAlater (Thermo Fisher, USA), kept at 4°C overnight to allow RNAlater perfusion, and stored at -20°C until processing. Embryo sex was determined by PCR for the Y-linked gene, Zfy1, and the hypothalamus was dissected from 1 female and 1 male embryo per litter per genotype with the exception of one all-male hybrid litter (n=5 males/genotype, n=5 Dom females, n=5 Spret females, n=4 hybrid females).  Brains from juvenile and adult animals were collected into RNAlater at day 21 (average 21.3, SD 0.73, n=5/sex/genotype), and day 71 (average 70.9, SD 2.09, n=5/sex/genotype), respectively. The hypothalamus was dissected and stored at -20°C in RNAlater until processing. Adult animals were sexually naïve and singly housed for at least 24h prior to euthanasia.

value: murine hypothalamus

value: embryo

tag: Sex

value: female

value: M. m. domesticus


title: Ch1-S2-70E-A3

value: dorsal telencephalon

value: M


title: NIKhKO4

city: Nanjing

first: Wen

last: Zhang

address: No. 101 Longmian Avenue, Jiangning District, Nanjing, China

institute: Nanjing Medical University

description: Library name: SAMPLE9

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: raw counts and FPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: liver

value: NIKhKO

value: Lieber-DeCarli ethanol liquid diet containing 5% ethanol for 4 weeks


title: NIKhKO5

description: Library name: SAMPLE10


title: scMultiome_Control_GEX

description:
Library name: Control_RNA
3' mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read 2 contains transcript sequence

value: E8i-cre- Zfp148flox/flox


title: NIKhKO2

description: Library name: SAMPLE7


title: ADpatient1

value: Blood

value: Alzheimer's Disease


title: NIKhKO3

description: Library name: SAMPLE8


title: Ch1-S2-70E-A2

value: C57/Bl6 mouse

value: Set-A


title: Ch1-S2-70E-A11

value: S


title: CD8+ T cells, C57BL/6J mice, 24 hours-post activation in vitro, IgG

description: Library name: IgG

data_processing:
CUT&Tag sequencing data were processed using the nf-core/cutandrun pipeline (v3.0.0) [https://nf-co.re/cutandrun/3.2.2/], a community-curated Nextflow pipeline. Raw sequencing reads were first subjected to adapter trimming using fastp (v0.23.2), followed by alignment to the mouse reference genome (mm10) using Bowtie2 (v2.4.4). Aligned reads were filtered to remove low-quality mappings, PCR duplicates (using Picard MarkDuplicates v2.27.5), and mitochondrial reads. Peaks were called using SEACR (v1.3) in "relaxed" mode with appropriate IgG or input control normalization. Genome-wide signal tracks were generated using deepTools (v3.5.1) and IGV (v2.18.4)for visualization. Quality control metrics, including fragment size distribution, duplication rates, and library complexity, were assessed and summarized using MultiQC (v1.13). All steps were run with default settings unless otherwise specified.
Assembly: GRCm38
Supplementary files format and content: bigWig file for each sample
Library strategy: CUT&Tag

source_name: Splenic CD8+ T cells

growth_protocol: Naïve CD8+ T cells were isolated from the spleens of healthy mice and activated with 5 μg/ml plate-bound anti-CD3 and 2 μg/ml soluble anti-CD28 antibody for 24 hours in 24-well plate.

extract_protocol:
A total of 1 million cells were used for library construction of each target (ZFP148 or IgG control) using the CUT&Tag-seq following the stepwise protocol from Epicypher https://www.epicypher.com/resources/protocols/cutana-cut-and-tag-protocol/.
Libaries were constructed as part of the protocol from Epicypher https://www.epicypher.com/resources/protocols/cutana-cut-and-tag-protocol/. Libraries with equal molar ratio were pooled together.

value: Splenic CD8+ T cells

value: primary CD8+ T cells


title: NIKhKO1

description: Library name: SAMPLE6


title: scMultiome_Control_ATAC

description:
Library name: Control_ATAC
ATAC: read 1 contains cell barcode and UMI; read 2 and read 3 contain ATAC sequences

library_source: genomic single cell

value: Spleens

value: CD8+ T cells

value: LCMV Cl13, day 21

value: ATAC


title: Ch1-S2-70E-A10

value: dorsal telencephalon


title: CD8+ T cells, C57BL/6J mice, 24 hours-post activation in vitro, ZFP148

description: Library name: ZFP148

value: 5 μg/ml plate-bound anti-CD3 and 2 μg/ml soluble anti-CD28 antibody for 24 hours


title: scMultiome_KO_ATAC

description:
Library name: KO_ATAC
ATAC: read 1 contains cell barcode and UMI; read 2 and read 3 contain ATAC sequences

value: E8i-cre+ Zfp148flox/flox


title: Ch1-S2-70E-A1


title: NIKflox5

description: Library name: SAMPLE5

value: liver

value: NIKflox


title: Old tail epidermis, biol rep 5

city: Baltimore

first: Andrew

middle: Paul

last: Feinberg

state: Maryland

address: 855 N. Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

description: Library name: O-992

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Assembly: mm10
Supplementary files format and content: bigWig format.  Tracks include mean methylation level (MML) and normalized methylation entropy (NME).

source_name: Tail epidermis

extract_protocol:
Master Pure kit (LGC Biosearch Technologies)
Illumina TruSeq, NEBNext

treatment_protocol: Epidermis isolated from skin tail with dispase treatment, flash frozen and stored at -80 °C.

value: Tail epidermis

tag: age at_time_of_collection

value: 22 months


title: dom_embryo_male_litter#21_individual#E2

description: Library name: M21_E2

value: murine hypothalamus

value: embryo

value: male

value: M. m. domesticus


title: Old tail epidermis, biol rep 4

description: Library name: O-991

tag: strain


title: dom_embryo_male_litter#8_individual#E1

description: Library name: M8_E1

tag: tissue


title: dom_embryo_male_litter#18_individual#E4

description: Library name: M18_E4

tag: developmental stage


title: NIKflox4

description: Library name: SAMPLE4

value: Lieber-DeCarli ethanol liquid diet containing 5% ethanol for 4 weeks


title: Ch1-S2-25E-A8

value: C57/Bl6 mouse

tag: culture group

value: Set-A

value: M


title: dom_embryo_female_litter#21_individual#E4

description: Library name: M21_E4

value: female


title: Ch1-S2-25E-A9

tag: ethanol (etoh) treatment


title: dom_embryo_female_litter#18_individual#E3

description: Library name: M18_E3


title: Ch1-S2-25E-A7

tag: neurosphere diameter (um)


title: NIKflox2

description: Library name: SAMPLE2


title: NIKflox3

description: Library name: SAMPLE3


title: Old tail epidermis, biol rep 3

description: Library name: O-990


title: Old tail epidermis, biol rep 2

description: Library name: O-989


title: dom_embryo_male_litter#16_individual#E2

description: Library name: M16_E2


title: dom_embryo_female_litter#16_individual#E1

description: Library name: M16_E1


title: Ch1-S2-25E-A5

tag: neurosphere size group


title: Young tail epidermis, biol rep 5

description: Library name: Y-464

value: 3 months


title: Ch1-S2-25E-A6

value: dorsal telencephalon


title: Ch1-S2-25E-A4


title: dom_embryo_male_litter#15_individual#E2

description: Library name: M15_E2


title: Old tail epidermis, biol rep 1

description: Library name: O-005


title: NIKflox1

description: Library name: SAMPLE1


title: MDA-MB-231 treated with GDC-0941_2

city: Shaoxing

first: Xin

last: Xie

address: No. 508, Huancheng West Road, Shaoxing

department: School of life sceince

institute: Shaoxing Univeristy

description: mRNA sequencing

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the GRCh38.p13 version human reference genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Assembly: Human genome GRCh38.p13 version
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Breast cancer cell line

growth_protocol: MCF-7 and MDA-MB-231 cell lines were obtained from the Cell bank of Shanghai Academy of Sciences (Shanghai, China), and cultured in McCoy's 5A modified media (High glucose with L-glutamine) containing 10% fetal bovine serum, 100 U/ml of penicillin and 100 μg/ml of streptomycin in a conditions of a humidified incubator containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer protocol.
Total RNA was used for library construction using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Cells were cultured in 6 well-plates at 60% confluence and treatd with 1μM GDC-0941 for 24 hours. The control cells were terated with an equivalent % of DMSO.

value: Breast cancer

value: Cell line

tag: passages

value: 10 to 15 passages


title: dom_juvenile_male_litter#8_individual#2

description: Library name: J8_2

value: juvenile


title: MDA-MB-231 treated with GDC-0941_1

description: mRNA sequencing

tag: cell type


title: Young tail epidermis, biol rep 3

description: Library name: Y-461

value: Tail epidermis


title: Ch1-S2-25E-A3


title: MDA-MB-231 treated with GDC-0941_3

description: mRNA sequencing


title: dom_embryo_female_litter#15_individual#E1

description: Library name: M15_E1

tag: genotype


title: Young tail epidermis, biol rep 4

description: Library name: Y-463


title: Young tail epidermis, biol rep 2

description: Library name: Y-459


title: MDA-MB-231 treated with DMSO_3

description: mRNA sequencing


title: MDA-MB-231 treated with DMSO_2

description: mRNA sequencing


title: Young tail epidermis, biol rep 1

description: Library name: Y-458


title: Ch1-S2-25E-A11


title: Ch1-S2-25E-A2


title: MDA-MB-231 treated with DMSO_1

description: mRNA sequencing


title: dom_juvenile_female_litter#8_individual#1

description: Library name: J8_1


title: Ch1-S2-25E-A1

value: L


title: Ch1-S2-25E-A10

value: S


title: dom_juvenile_female_litter#7_individual#1

description: Library name: J7_1

value: murine hypothalamus


title: Old tail epidermis, INPUT, biol rep 3

description: Library name: O-3_epidermis_INPUT

data_processing:
Base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bowtie2
bamCoverage function from DeepTools
Assembly: mm10
Supplementary files format and content: bigWig files with RPKM normalized signal

extract_protocol:
ChIP-Seq, Zymo ChIP Clean and Concentrator kit
NEBNext Ultra II

tag: chip antibody

tag: age at_time_of_sample_collection

value: 22 months


title: dom_juvenile_male_litter#7_individual#2

description: Library name: J7_2

value: male

value: M. m. domesticus


title: dom_juvenile_female_litter#5_individual#2

description: Library name: J5_2


title: dom_juvenile_male_litter#5_individual#1

description: Library name: J5_1


title: Old tail epidermis, INPUT, biol rep 2

description: Library name: O-2_epidermis_INPUT

tag: batch


title: Old tail epidermis, INPUT, biol rep 1

description: Library name: O-1_epidermis_INPUT


title: MCF-7 treated with GDC-0941_2

description: mRNA sequencing


title: Ch1-S2-100E-A9

value: C57/Bl6 mouse


title: Ch1-S2-100E-A8

value: Set-A


title: dom_juvenile_female_litter#11_individual#2

description: Library name: J11_2


title: MCF-7 treated with DMSO_3

description: mRNA sequencing


title: MCF-7 treated with GDC-0941_3

description: mRNA sequencing


title: Young tail epidermis, INPUT, biol rep 3

description: Library name: Y-3_epidermis_INPUT


title: Young tail epidermis, INPUT, biol rep 2

description: Library name: Y-2_epidermis_INPUT


title: Ch1-S2-100E-A7


title: dom_juvenile_male_litter#11_individual#1

description: Library name: J11_1


title: dom_juvenile_female_litter#10_individual#2

description: Library name: J10_2


title: MCF-7 treated with GDC-0941_1

description: mRNA sequencing


title: MCF-7 treated with DMSO_2

description: mRNA sequencing


title: Old tail epidermis, H3K27me3, biol rep 3

description: Library name: O-3_epidermis_H3K27me3


title: G. biloba stage 3

city: Shanghai

first: Tao

last: Jin

address: Handan Rd. 220

institute: Fudan University

description:
Library name: GB_s3
Fresh frozen Spatial transcriptome sequencing

data_processing:
Sequences were aligned to corresponding genome to gene expression count using BSTMatrix's default settings
Raw sequencing data were processed using BSTMatrix to generate matrix files
Assembly: gigadb(GB)/ DRYAD(GM)/ NGBdb(PT, CP)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: he.tif: image of tissue
Library strategy: Spatial Transcriptomics

organism: Ginkgo biloba

source_name: ovules

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with BMK S1000 Gene Expression Slides

value: ovules


title: Old tail epidermis, H3K27me3, biol rep 2

description: Library name: O-2_epidermis_H3K27me3


title: Ch1-S2-100E-A6


title: Ch1-S2-100E-A5


title: dom_adult_female_litter#6_individual#1

description: Library name: A6_1

value: adult

value: female


title: dom_adult_male_litter#6_individual#2

description: Library name: A6_2


title: Ch1-S2-100E-A4

value: dorsal telencephalon


title: dom_juvenile_male_litter#10_individual#1

description: Library name: J10_1


title: MCF-7 treated with DMSO_1

description: mRNA sequencing

value: Breast cancer


title: Old tail epidermis, H3K27me3, biol rep 1

description: Library name: O-1_epidermis_H3K27me3


title: G. biloba stage 2

description:
Library name: GB_s2
Fresh frozen Spatial transcriptome sequencing


title: Ch1-S2-100E-A2


title: Young tail epidermis, INPUT, biol rep 1

description: Library name: Y-1_epidermis_INPUT

value: 3 months


title: dom_adult_male_litter#5_individual#2

description: Library name: A5_2


title: dom_adult_female_litter#5_individual#1

description: Library name: A5_1


title: Ch1-S2-100E-A3

value: M


title: Young tail epidermis, H3K27me3, biol rep 2

description: Library name: Y-2_epidermis_H3K27me3


title: Treated Tumor- HER2 DC1+aSEMA4D #3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: PanCancer IO360 Pathway

hyb_protocol: The CodeSet of each NanoString panel was hybridized to approximately 100 ng of RNA according to the manufacturer's protocol and the bound probes were immobilized to cartridge on the nCounter PrepStation following the vendor protocol.

scan_protocol: Each cartridge was scanned on the NanoString Digital Analyzer at 555 fields of view (FOV).

data_processing:
Gene expression data was analysed using nSolver™ Analysis Software version 4.0 from NanoString Technologies (NanoString Technologies, WA, USA).
Default parameters were used for QC. Normalizations were done by using selected housekeeping genes with low CV at different data ranges.
Selected house keeping genes are as follows: GPL30557 (Cog7,Oaz1,Sap130,Sdha,Ubb); GPL31165 (Alas1,Eef1g,Eif2b4,Nubp1,Oaz1,Polr1b);GPL32407 (Alas1,Eef1g,Gapdh,G6pdx,Oaz1,Ppia); GPL32728 (Abcf1,G6pdx,Eef1g,Polr1b,Hprt,Sdha).
Differential expression was analyzed using Limma package.

source_name: Soft Tissue

label_protocol: Not applicable

growth_protocol: TUBO tumor cell lines were cultured in standard complete media before injected into BALB/c mice

extract_protocol: Mice were euthanized at the same timepoint and the tumors were dissected. Tumor samples were flash frozen in liquid nitrogen, then stored at -80C before RNA sequencing

treatment_protocol: TUBO bearing mice were treated with a combination of spmaphorin4D blocking antibody and intratumoral dendritic cell therapy for 3 weeks before analysis

tag: gender

value: Female

value: BALB/c

tag: tissue type

value: Tumor


title: Young tail epidermis, H3K27me3, biol rep 1

description: Library name: Y-1_epidermis_H3K27me3

value: Tail epidermis


title: Treated Tumor- HER2 DC1+aSEMA4D #2

description: PanCancer IO360 Pathway


title: Leaves, GmNRPE1-RNAi-T-BS-Seq-r3

city: Riverside

first: Brandon

last: Le

state: CA

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

data_processing:
Raw 150-nt paired-end reads were subjected to quality control filter using FASTQC v0.11.5 (Robinson, McCarthy et al. 2010) and trimmed using Trim Galore v0.4.3 (Krueger 2015).
Remaining high quality trimmed reads were aligned to the soybean genome (Gmax_275_v2.0; Phytozome 10) using bismark v0.17.0 (Krueger and Andrews 2011).
Reads de-duplication and methylation calling were also processed using bismark v0.17.0.
Methylation level was calculated as [C/(C+T); number of C divided by the total number of C plus T at each position].
Genome_build: Soybean (Glycine max) genome; Gmax_275_v2.0 (Phytozome 10)
Supplementary_files_format_and_content: Tab-delimited perC text file containing counts and methylation level per cytosine with greater than one read. The column headers for each file are as follows: Chromosome,  position, strand, methylation level [C/(C+T)], total_C, total_T, sequence context

organism: Glycine max

source_name: Leaves, GmNRPE1-RNAi-T-BS-Seq

extract_protocol:
Mature leaf tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA was isolated using the DNAzol ES (MRC, DN128) following the manufacturer's protocol.
One microgram of genomic DNA with five nanograms of spiked unmethylated lambda DNA (Promega, D1521), was sonicated into 150-300bp fragments using a Covaris S220 Focused-ultrasonicator (Covaris) with the Target BP Peak at 200, in a 130 µl sample volume in a microTUBE AFA Fiber Snap-Cap tube. The sonicated DNA was end-repaired using the End-It DNA End-Repair Kit (Epicentre, ER0720) and purified with Agencourt AMPure XP beads (Beckman Coulter, A63881). The repaired DNA was subjected to 3’end adenylation using Klenow 3’-5’ exo- (NEB, M0212S) and ligated using T4 DNA ligase (NEB, M0202L) with methylated  adapters from the TruSeq DNA LT Sample Prep Kit (Illumina, FC121-4001).  The adapter-ligated DNA was bisulfite-treated using the MethylCode Bisulfite Conversion Kit (Thermo-Fisher, MECOV50) and libraries were made following the TruSeq DNA LT Sample Prep Kit protocol. The libraries were sequenced on an Illumina HiSeq X10 using PE150 mode at Berry Genomics.

tag: cultivar

value: Mustang

tag: RNAi

tag: transgene

value: T

tag: replicate

value: Leaves


title: Treated Tumor- HER2 DC1+aSEMA4D #1

description: PanCancer IO360 Pathway

tag: strain


title: Ch1-S2-100E-A1

data_processing: Target gene signals normalized to median expression of each sample across all genes followed by centering the delta CT values across all samples within a gene.

extract_protocol: Each neurosphere was imaged, prior to collection in 6ul of Cells Direct Lysis Buffer (Invitogen #117753-100) and stored at -80oC, prior to being processed for RT-qPCR using the Biomark HD system (protocol ADP 42), for mRNA expression across 96 genes. Single neurospheres were processed directly to reverse transcription and pre-amplification reaction (Fluidigm protocol ADP 42), without RNA extraction to minimize RNA loss.

tag: tissue

tag: developmental stage

tag: culture group


title: dom_adult_male_litter#18_individual#1

description: Library name: A18_1

value: murine hypothalamus

tag: Sex

value: male

value: M. m. domesticus


title: Treated Tumor- anti-Semaphorin4D #2

description: PanCancer IO360 Pathway


title: dom_adult_female_litter#17_individual#2

description: Library name: A17_2


title: Leaves, GmNRPE1-RNAi-T-BS-Seq-r1


title: Ch1-S2-0E-A9

value: C57/Bl6 mouse

value: Set-A

tag: ethanol (etoh) treatment

tag: neurosphere diameter (um)

tag: neurosphere size group


title: Ch1-S2-100E-A11


title: G. biloba stage 1

description:
Library name: GB_s1
Fresh frozen Spatial transcriptome sequencing

value: ovules


title: Leaves, GmNRPE1-RNAi-NT-BS-Seq-r3

source_name: Leaves, GmNRPE1-RNAi-NT-BS-Seq

value: NT


title: Treated Tumor- anti-Semaphorin4D #1

description: PanCancer IO360 Pathway


title: dom_adult_female_litter#18_individual#2

description: Library name: A18_2

value: adult

value: female

tag: genotype


title: dom_adult_male_litter#16_individual#2

description: Library name: A16_2


title: Ch1-S2-100E-A10

value: dorsal telencephalon

value: S


title: dom_adult_male_litter#17_individual#1

description: Library name: A17_1


title: Ch1-S2-0E-A7

value: L


title: Treated Tumor- HER2 DC1 Treatmen #1

description: PanCancer IO360 Pathway

value: Female

value: BALB/c

value: Tumor


title: Treated Tumor- HER2 DC1 Treatment #2

description: PanCancer IO360 Pathway


title: Leaves, GmNRP(D/E)2-RNAi-T-BS-Seq-r3

source_name: Leaves, GmNRP(D/E)2-RNAi-T-BS-Seq

value: Mustang

value: T


title: dom_adult_female_litter#16_individual#1

description: Library name: A16_1

value: murine hypothalamus


title: Ch1-S2-0E-A8


title: Treated Tumor- Untreated Control #1

description: PanCancer IO360 Pathway


title: Leaves, GmNRP(D/E)2-RNAi-NT-BS-Seq-r6

source_name: Leaves, GmNRP(D/E)2-RNAi-NT-BS-Seq

value: Leaves


title: Treated Tumor- Untreated Control #2

description: PanCancer IO360 Pathway


title: Leaves, GmNRPE1-RNAi-NT-BS-Seq-r1


title: Leaves, GmNRP(D/E)2-RNAi-NT-BS-Seq-r2


title: human PBMC a24-CMV exposed to mutated antigen

city: Kobe

first: Yoko

last: Nakai-Futatsugi

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

institute: RIKEN

description:
Library name: A24-3
10x Genomics

data_processing:
Data processing was performed using cellranger-7.1.0.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab separated values files and matrix files

source_name: PBMC

extract_protocol:
PBMC cultured for two weeks were havested and frozen at a concentration of 1x10^6/ml, then were thawed at a viability > 80% for library preparation.
For cDNA library construction, Chromium Next GEM Single Cell 3' GEM kit v3.1, Gel Bead kit v3.1, Chip G kit, Library constructuion kit, Dual Index TT set (10x Genomics) were used following manufacture's instructions. Quality controls of cDNA and Library were peformed using Agilent TapeStation. GEX-PCR cycles for cDNA and Library were 11 and 12, respectively.

treatment_protocol: Human PBMC were cultured with (A24-3) or without (A24-1) single amino acid mutated CMV-antigen (QYDPVSALF) for 24 hours before stimulation with the original CMV-antigen (QYDPVAALF).

tag: cell type

value: PBMC

tag: treatment

value: mutated CMV-antigen


title: Ch1-S2-0E-A5

source_name: fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

value: C57/Bl6 mouse

value: Set-A


title: human PBMC a24-CMV control

description:
Library name: A24-1
10x Genomics

value: control


title: Untreated Tumor- HER2 DC1+aSEMA4D #3

description: PanCancer IO360 Pathway

tag: gender


title: RNA-seq, HEK293T cells, VPA-treated, Rep2

data_processing:
Raw reads were filtered using SOAPnuke. The filtering includes removal of adaptor sequences, contamination and low-quality reads .
Filtered reads were aligned to Hg38 reference genome, or GRCh38 (GRCh38 Genome Reference Consortium Human Reference 38) from UCSC (without alternative contigs) using STAR aligner (version 2.7.10b) with the following parameters: --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM
Read counts for each gene were calculated using Htseq-count (version 2.0.1) with the following parameters: -f bam -s reverse -m union -t exon -i
Differential gene expression analysis was performed using DESeq2 R package  (log2(fold change)>1 or <-1 and FDR < 0.05).
Assembly: hg38
Supplementary files format and content: tab-delimited text files contain raw counts for each gene

extract_protocol:
Total RNA was extracted from control (CTRL) 293T cells that had not been treated with anything, or from cells treated with 1 mM VPA for 1 day (VPA) using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
RNA-seq library was constructed according to DNBSEQ Eukaryotic Strand-specific mRNA library protocol.

tag: cell line

value: human embryonic kidney cells

value: VPA-treated

value: valproic acid (VPA)


title: Leaves, GmNRPD1-RNAi-T-BS-Seq-r2

source_name: Leaves, GmNRPD1-RNAi-T-BS-Seq

tag: cultivar

value: Jack


title: Ch1-S2-0E-A4

value: dorsal telencephalon

value: L


title: Leaves, GmNRP(D/E)2-RNAi-T-BS-Seq-r2

tag: RNAi


title: Untreated Tumor- HER2 DC1+aSEMA4D #2

description: PanCancer IO360 Pathway

value: Female

value: BALB/c

tag: tissue type


title: RNA-seq, HEK293T cells, VPA-treated, Rep3


title: Ch1-S2-0E-A6


title: Ch1-S2-0E-A11


title: Ch1-S2-0E-A2


title: Ch1-S2-0E-A3


title: Leaves, GmNRPD1-RNAi-T-BS-Seq-r1

tag: transgene

tag: replicate


title: RNA-seq, HEK293T cells, VPA-treated, Rep1


title: Untreated Tumor- HER2 DC1+aSEMA4D #1

description: PanCancer IO360 Pathway

tag: strain

value: Tumor


title: Ch1-S2-0E-A10

tag: tissue

tag: developmental stage

value: M


title: Leaves, GmNRPD1-RNAi-NT-BS-Seq-r2

source_name: Leaves, GmNRPD1-RNAi-NT-BS-Seq

value: NT


title: Untreated Tumor- anti-Semaphorin4D #2

description: PanCancer IO360 Pathway


title: RNA-seq, HEK293T cells, untreated, Rep3

value: WT


title: Leaves, GmNRPD1-RNAi-NT-BS-Seq-r1

value: Leaves


title: Untreated Tumor- anti-Semaphorin4D #1

description: PanCancer IO360 Pathway


title: Liver RNA-seq HSC-PCK1-KO 4 (96)

city: Santiago de Compostela

first: Rubén

last: Nogueiras Pozo

state: A Coruña

address: Campus Vida Avenida Barcelona, s/n, CIMUS

department: Fisiology

institute: CIMUS - USC

description: Library name: CD_+_96

data_processing:
Raw reads were filtered using SOAPnuke software developed by BGI. The filtering steps included: (1) removing reads containing adaptor sequences (matches ≥ 25%, max 2 mismatches); (2) removing reads with N content > 1%; (3) removing reads containing polyX > 50bp ; and (4) removing low-quality reads where > 40% of bases had a quality score < 20. Reads shorter than 100bp were discarded.
Clean reads were aligned to the mouse reference genome (GRCm39). Differential gene expression analysis was performed using the EgoGenomics platform. Functional enrichment analysis was conducted using the clusterProfiler package (v4.10.1) in R (v4.3.2).
Assembly: GRCm39
Supplementary files format and content: Individual text files (.txt) containing raw read counts for each gene/transcript per sample, generated by the EgoGenomics platform.

source_name: Liver

growth_protocol: Mice were maintained on a Choline-Deficient High-Fat Diet (CDHFD) for 8 weeks prior to tissue collection.

extract_protocol:
Total RNA was extracted from liver tissue using the TRIzol–chloroform method following the manufacturer’s protocol. RNA quality and quantity were assessed using a NanoDrop spectrophotometer (selecting samples with A260/A280 ratios between 1.8 and 2.0). RNA integrity was subsequently confirmed (RIN ≥ 8) prior to library preparation.
Messenger RNA (mRNA) was enriched from total RNA using oligo(dT) beads. The enriched mRNA was fragmented into small pieces and reverse-transcribed into first-strand cDNA using random primers. Second-strand cDNA synthesis was performed using dUTP to achieve strand specificity. The cDNA fragments underwent end-repair, 3'-adenylation, and adaptor ligation. After PCR amplification and quality control , the library products were circularized to generate DNA Nanoballs (DNBs). Sequencing was performed on the DNBSEQ platform with a PE100 (paired-end 100bp) strategy.

treatment_protocol: Liver tissues were dissected from HSC-PCK1-KO (knockout) mice and control (wild-type) mice. Samples were snap-frozen in liquid nitrogen immediately after dissection and stored at –80°C until RNA extraction.

value: Liver

tag: Sex

value: male

tag: diet

value: CDHFD 8 weeks

tag: batch


title: spret_embryo_female_litter#7_individual#E3

description: Library name: M7_E3

organism: Mus spretus

value: murine hypothalamus

value: embryo

value: female

value: M. spretus


title: RNA-seq, HEK293T cells, untreated, Rep2

value: human embryonic kidney cells


title: Ch1-S2-0E-A1

first: Rajanikanth

last: Vadigepalli

institute: University of New Mexico

value: C57/Bl6 mouse

value: dorsal telencephalon

tag: culture group

value: Set-A

tag: ethanol (etoh) treatment

tag: neurosphere diameter (um)

tag: neurosphere size group


title: RNA-seq, HEK293T cells, untreated, Rep1

tag: cell type

tag: genotype

tag: treatment


title: Untreated Tumor- HER2 DC1 Treatment #2

description: PanCancer IO360 Pathway

tag: gender

value: Female

value: BALB/c


title: Liver RNA-seq HSC-PCK1-KO 3 (87)

description: Library name: CD_+_87


title: spret_embryo_male_litter#6_individual#E2

description: Library name: M6_E2


title: Liver RNA-seq HSC-PCK1-KO 2 (82)

description: Library name: CD_+_82


title: Liver RNA-seq HSC-PCK1-KO 1 (69)

description: Library name: CD_+_69


title: Untreated Tumor- Untreated Control #2

description: PanCancer IO360 Pathway

tag: tissue type

value: Tumor


title: Untreated Tumor- HER2 DC1 Treatmen #1

description: PanCancer IO360 Pathway


title: ORG-0128_R normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: RNA extracted from FFPE tissue sections of histologically normal breast lobules.

hyb_protocol: NanoString nCounter protocol

scan_protocol: Cartridges were scanned on the nCounter Digital Analyzer (555 fields of view).

data_processing: Raw RCC files were imported into NanoString nSolver. Counts were background-corrected using negative controls and normalized using standard positive-control and housekeeping normalization. Normalized linear counts for endogenous targets are provided as processed data; internal control probe counts are available in the RCC files.

label: NanoString bar coding

source_name: histologically normal breast lobules (FFPE)

label_protocol: Not applicable (nCounter uses reporter and capture probes; no separate labeling step).

growth_protocol: Benign breast tissue was obtained from reduction mammoplasty or contralateral prophylactic mastectomy specimens. Histologically normal lobules were identified on H&E-stained sections.

extract_protocol: From each FFPE block, three consecutive 10 µm sections were collected and RNA was isolated using the Qiagen RNeasy FFPE kit (cat. 73504) according to the manufacturer’s protocol. RNA quantity and quality were assessed; samples meeting QC thresholds were used for NanoString hybridization.

treatment_protocol: No treatment; ex vivo tissue.

tag: race

value: non-Hispanic White

tag: age

tag: bmi

tag: surgical procedure

value: reduction mammoplasty

tag: menopausal status

value: postmenopausal

tag: parity

value: Yes


title: Untreated Tumor- Untreated Control #1

description: PanCancer IO360 Pathway

tag: strain


title: spret_embryo_female_litter#14_individual#E4

description: Library name: M14_E4

source_name: murine hypothalamus

tag: tissue

tag: developmental stage

tag: Sex


title: Liver RNA-seq Control 3 (89)

description: Library name: CD_-_89

value: Liver

value: male

value: WT

tag: diet

tag: batch


title: ATAC_WT_2

city: Fuzhou

first: Sun

last: Minghui

address: Cangshan

institute: Fujian Agriculture and Forestry University

description: Library name: Sample 4

data_processing:
Data analysis was performed as previously described. Raw sequence reads were initially processed for quality control by FastQC (version: 0.11.5) and then the adapter sequences and poor quality reads were removed by Trim momatic (version 0.36). Subsequently, the remaining reads were mapped to the reference genome of A. flavus strain NRRL 3357 through hisat2 (version: 2.0.1-beta). Then, the pair-wise Spearman correlation between any pair of ATAC-seq samples was calculated. MACS2 (version 2.1.0) was used to call peaks, and motif was predicted by Homer Software (version 3). The standard condition for screening of differential peak is: an FDR value<0.05, and the Fold is >0.
Assembly: NRRL_3357
Supplementary files format and content: tab-delimited text files include Arp9_vs_WT. peak_annotation
Supplementary files format and content: tab-delimited text files include gene fpkm for each sample

organism: Aspergillus flavus

growth_protocol: ATAC-seq was performed according to the described protocol. WT and Δarp9 strains were inoculated in PDB at 29℃, 180 r/min, for 3 d, after which the hyphae were frozen with liquid nitrogen.

extract_protocol:
Samples were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and NP-40) for 10 min to prepare the nuclei. Then, the nuclei were incubated with the Tn5 transposome and tagmentation buffer at 37°C for 30 min (Vazyme Biotech).
The library was prepared by PCR, assessed with Bioanalyzer and Q-bit, and sequenced using an Illumina NovaSeq/DNBSEQ-T7 platform with 150-bp paired ends in Igenebook Biotechnology Co., Ltd. (Wuhan, China).

value: mycelium


title: ORG-0062 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

value: pre

value: yes


title: spret_embryo_male_litter#7_individual#E1

description: Library name: M7_E1

value: murine hypothalamus

value: embryo

value: M. spretus


title: spret_embryo_female_litter#6_individual#E3

description: Library name: M6_E3

value: female


title: spret_embryo_male_litter#14_individual#E3

description: Library name: M14_E3


title: Liver RNA-seq Control 4 (90)

description: Library name: CD_-_90

value: CDHFD 8 weeks


title: ORG-0022 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360


title: Liver RNA-seq Control 2 (86)

description: Library name: CD_-_86


title: ATAC_WT_1

description: Library name: Sample 3


title: Liver RNA-seq Control 1 (83)

description: Library name: CD_-_83


title: spret_embryo_female_litter#13_individual#E4

description: Library name: M13_E4


title: ATAC_Arp9_2

description: Library name: Sample 2

value: Arp9 gene knock-out strain


title: ORG-0059_L normal breast lobule RNA (non-Hispanic White); Breast Cancer 360


title: spret_embryo_male_litter#13_individual#E1

description: Library name: M13_E1


title: ORG-0090 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

value: prophylactic mastectomy


title: ATAC_Arp9_1

description: Library name: Sample 1


title: ORG-0016 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

value: non-Hispanic White


title: spret_embryo_male_litter#12_individual#E1

description: Library name: M12_E1


title: AOM_DSS_Tumors_Mouse

city: Vari

first: Vasiliki

last: Koliaraki

state: Attiki

address: 34 Fleming street

country: Greece

institute: BSRC "Alexander Fleming"

description:
Library name: AOM_DSS
10x Genomics

data_processing:
The initial processes including alignment, UMI counting, filtering of empty droplets and generation of sample-specific count matrices were performed by the 10X CellRanger 7.1.0 pipeline.
Seurat (v4) R package was used for the manipulation of the scRNA data including sample-specific quality control and downstream analysis. DoubletFinder was used to exclude potential doublets. Please refer to the corresponding manuscript for a detailed description of the QC metrics and thresholds.
The normalization of raw UMI counts was done by using NormalizeData() seurat function which normalizes each cell for it’s library size, then multiplies by the scale factor 10,000 and finally applies a log1p transformation
Assembly: mm10
Supplementary files format and content: Tab-seperated txt matrix of raw UMI counts for QC filtered cells
Supplementary files format and content: Tab-seperated txt matrix of seurat normalized UMI counts for QC filtered cells
Supplementary files format and content: Tab-seperated metadata txt file including celltype annotation before and after subclustering

source_name: Colon

growth_protocol: Cells were used fresh after FACS sorting

extract_protocol:
AOM/DSS tumors were dissected and washed with HBSS (Gibco) supplemented with antibiotic antimycotic solution (Gibco). The tumors were minced and digested in in 1000 U/mL Collagenase IV (Sigma-Aldrich, St. Louis, MO, USA), 1 mg/mL Dispase II (Roche, Basel, Switzerland), and 100 U/mL Dnase I (Sigma-Aldrich, St. Louis, MO, USA) in DMEM (BioSera, France) in three serial 20-min digestions. Cell suspensions were centrifuged and washed in FACS buffer (5% FBS (Biowest) in PBS). 1–2 million cells/100 μL were incubated with anti-CD45 and anti-CD326 antibodies for the exclusion of immune and remaining epithelial cells, respectively, and 1 μg/mL Propidium Iodide (PI) (Sigma) for dead cell exclusion. Cell sorting was performed using the FACSAria III cell sorter (BD) and the FACSDiva (BD) software.
For each sample, approximately 16,000 cells were loaded onto a 10X Genomics Chromium Controller using the Chromium Next GEM Single Cell 3' Kit v3.1 according to the manufacturer's protocol. Library preparation was performed following the 10X Genomics workflow, with quality control performed using an Agilent Bioanalyzer High Sensitivity DNA chip.

treatment_protocol: Colitis-associated cancer was induced using the azoxymethane (AOM)/dextran sodium sulfate (DSS) model. Briefly, mice were injected intraperitoneally with a single dose of AOM (10 mg/kg body weight; Sigma-Aldrich) on day 0. One week after AOM injection (day 7), mice were administered 2.5% DSS (molecular weight 36,000-50,000 Da; MP Biomedicals) in the drinking water for 5 consecutive days, followed by 16 days of regular drinking water. This DSS treatment cycle was repeated twice more for a total of three cycles. Mice were monitored daily for body weight, stool consistency, and rectal bleeding. Animals were sacrificed on day 60 after AOM injection by CO₂ inhalation followed by cervical dislocation. The entire colon was removed, flushed with ice-cold PBS, and opened longitudinally. The number, size, and location of visible tumors were recorded. The colon was then fixed in 4% PFA for 24 hours and processed for agarose embedding and vibratome sectioning.

value: Colon

tag: cell type

value: Sorted Epcam-,CD45- Stromal cells

tag: disease state

value: Colon adenocarcinomas

value: AOM DSS


title: Control_Colon_Mouse

description:
Library name: Cnt_colon
10x Genomics

data_processing:
The initial processes including alignment, UMI counting, filtering of empty droplets and generation of sample-specific count matrices were performed by the 10X CellRanger 7.1.0 pipeline.
Seurat (v4) R package was used for the manipulation of the scRNA data including sample-specific quality control and downstream analysis. DoubletFinder was used for doublet extraction.
The normalization of raw UMI counts was done by using NormalizeData() seurat function which normalizes each cell for cell library size, then multiplies by the scale factor 10,000 and finally applies a log1p transformation
Assembly: mm10
Supplementary files format and content: Tab-seperated txt matrix of raw UMI counts for QC filtered cells
Supplementary files format and content: Tab-seperated txt matrix of seurat normalized UMI counts for QC filtered cells
Supplementary files format and content: Tab-seperated metadata txt file including celltype annotation

extract_protocol:
The mouse colon or small intestine were dissected and washed with HBSS (Gibco) supplemented with antibiotic antimycotic solution (Gibco). Epithelial cells were removed by incubating the tissue with 5 mM EDTA and 1 mM DTT in HBSS for 25 minutes at 37°C. The tissues were digested in 300 U/mL Collagenase XI (Sigma-Aldrich) and 1 mg/mL Dispase II (Roche) in DMEM at 37°C for 60 min or 45 min, for the colon and small intestine, respectively. Cell suspensions were centrifuged and washed in FACS buffer (5% FBS (Biowest) in PBS). 1–2 million cells/100 μL were incubated with anti-CD45 and anti-CD326 antibodies for the exclusion of immune and remaining epithelial cells, respectively, and 1 μg/mL Propidium Iodide (PI) (Sigma) for dead cell exclusion. Cell sorting was performed using the FACSAria III cell sorter (BD) and the FACSDiva (BD) software.
For each sample, approximately 16,000 cells were loaded onto a 10X Genomics Chromium Controller using the Chromium Next GEM Single Cell 3' Kit v3.1 according to the manufacturer's protocol. Library preparation was performed following the 10X Genomics workflow, with quality control performed using an Agilent Bioanalyzer High Sensitivity DNA chip.

value: Healthy

tag: treatment

value: untreated


title: Foam Cell 4

city: St Louis

first: Junedh

last: Amrute

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: Library name: Foam_4

data_processing:
Can be found in Methods Amrute et al, 2025
Assembly: GRCh38
Supplementary files format and content: .rds

source_name: foam cell

extract_protocol:
THP-1 cells (#TIB-202, ATCC;) were cultivated in RPMI-1640 medium (#10-041-CV, Corning;) with 10% FBS. They were then treated with PMA (#5.00582.0001, Millipore Sigma) to reach 15 nM concentration and plated in a 12-well plate (#150628, Thermo Fisher Scientific) at a density of 5 x 105 cells per well. The plate was incubated for a duration of 3 days to promote differentiation. On the fourth day, the cells were gently washed with 1 mL of fresh medium to remove any residual PMA and other soluble factors. Following this, oxLDL (#L34357, Invitrogen) was introduced to each well to reach a final concentration of 50 µg mL-1, ensuring thorough mixing for uniform exposure. The cells were incubated for an additional four days to allow for foam cell formation. Upon completion of the incubation period, the medium was carefully aspirated from each well. The cells were detached by adding 200 µL of trypsin-EDTA (#25-053-CI, Corning) per well and incubating at 37°C for 5 min to facilitate cell detachment. To neutralize the trypsin activity, 1 mL of medium was added per well and the mixture was gently pipetted to ensure complete suspension of the cells. Finally, the cell solution was filtered through a 100 µm nylon cell strainer (#352360, Falcon) to remove any cell clumps, thereby obtaining a uniform single-cell suspension ready for further analysis.
Library preparation was conducted with Chromium GEM-X Single Cell 3' Reagent Kits v4 (10x Genomics). Libraries were sequenced on NovaSeq X Plus.

tag: cell line

value: foam cell


title: ORG-0159 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

value: Mastect/Prophy

value: premenopausal

value: Yes


title: spret_juvenile_female_litter#17_individual#1

description: Library name: J17_1

data_processing:
Quality control, trimming of raw sequencing reads, filtering and mapping were performed as described in Arévalo et al. (2021). To improve comparability, all samples (Dom, Spret, and hybrid) were mapped to a pseudo-hybrid genome, generated using the genome preparation tool of the program SNPsplit (Krueger and Andrews 2016). Briefly, SNPs from both Dom (WSB/EiJ) and Spret (SPRET/EiJ) relative to the mouse genome (GRCm38.89) available from the Ensembl FTP server (ftp://ftp.ensembl.org) were introduced into the mouse genome. SNPs between Dom and Spret were then N-masked to allow mapping of both Dom- and Spret-derived reads. We randomly downsampled all alignment files to the same number of reads (~40 million reads) using SAMtools 0.1.19 (Li et al. 2009). For analysis of allele specific expression (ASE) in hybrids we used SNPsplit to split the hybrid alignment files, separating reads originating from the Spret and Dom alleles. Reads that were unassignable (did not overlap SNPs between WSB/EiJ and SPRET/EiJ) or contained conflicting or non-informative (polymorphic) SNPs were removed. On average, 69% of mapped RNAseq reads were assignable, 26% unassignable and 5% conflicting.
Transcript quantification and annotation was done using StringTie 1.3.3 (Pertea et al. 2015). Mouse genome annotation information (GRCm38.89) was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org). We used the python script (preDE.py) included in the StringTie package to prepare gene-level count matrices for analysis of differential expression (DE; Table 1) and ASE in DESeq2 1.16.1 (Love et al. 2014). Pseudogenes were removed from the count matrices based on “biotype” annotation information extracted from Biomart (R-package biomaRt, Durinck et al. 2005). Low counts were removed by the independent filtering process implemented in DESeq2 (Bourgon et al. 2010). The adjusted p-value (Benjamini-Hochberg method) cutoff was set at ≤ 0.05. Following the recommendations of Love et al. (2014; see also Vallejos et al. 2016; Schurch et al. 2016), we chose an absolute log2 fold change (LFC) cutoff of ≥ 0.5 (1.41 times higher or lower expression) for standard DE analysis.
Assembly: GRCm38.89 (with N-masked SNPs between WSB/EiJ) and Spret (SPRET/EiJ))
Supplementary files format and content: tab delimited file including DEseq-normalized read counts for all samples

extract_protocol:
Total RNA was extracted from hypothalamus tissue using the AllPrep RNA/DNA Mini Kit (Qiagen), and was stored at -80°C until sequencing.
Illumina library preparation was done at the sequencing facility (Novogene, Sacramento, CA) using the NEB Next Ultra RNA library prep kit for Illumina.  Individual libraries were sequenced on the Illumina HiSeq 4000 platform, producing >40 million, 150bp paired-end reads per sample.

value: murine hypothalamus

value: juvenile

tag: genotype


title: Control_Small_Intestine_Mouse

description:
Library name: Cnt_si
10x Genomics

source_name: Small Intestine

value: Small Intestine


title: Foam Cell 3

description: Library name: Foam_3


title: spret_juvenile_male_litter#17_individual#2

description: Library name: J17_2

value: male

value: M. spretus


title: ORG-0130_R1 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

tag: race

value: prophylactic mastectomy


title: YSGnr.3

city: Houston

first: Nourhan

last: Abdelfattah

state: TX

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

description:
KY16-22-GT16-02753
AllP8_BulkRNAseq.log2CPM.csv

data_processing:
Bulk RNA-seq analysis was carried out using the in-house pipeline at The Jackson Laboratory. Trimmomatic was used to remove adapters and also leading and trailing low quality bases. Reads fewer than 36 bases long were discarded. Reads with more than 50% low-quality bases overall were filtered out, and the remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM . RSEM uses bowtie2 as an aligner to align the mapped reads against the mm10 reference genome. Data quality control was performed using Picard and bamtools  to obtain general alignment statistics from the BAM file. The read counts estimated for each gene by RSEM were given as input to the R package edgeR  for differential expression analysis.
Assembly: mm10
Supplementary files format and content: comma separated file containig the log2CPM values for all samples

source_name: MB

extract_protocol:
RNA was isolated  from tumor tissue using the standard Triazol protocol.
Whole RNA was sent to BGI for library prep and sequencing on the DNBseq platform

value: MB


title: ORG-0103 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

value: non-Hispanic White

tag: age


title: YSGnr.2

description:
KY16-21-GT16-02752
AllP8_BulkRNAseq.log2CPM.csv


title: spret_juvenile_female_litter#16_individual#2

description: Library name: J16_2

value: female


title: spret_embryo_female_litter#12_individual#E2

description: Library name: M12_E2

value: embryo


title: SMC, Foam Cell Media

description: Library name: SMC_FoamCell

source_name: smooth muscle cell

extract_protocol:
Human primary coronary artery smooth muscle cells (SMC) (Lot# 20TL266549, Cat# CC-2583, Lonza) were cultured in completed SmGM-2 growth medium (#CC-3182, Lonza). Foam cell conditioned medium was collected from cultures of THP-1-derived foam cells as previously described, with supernatant retrieval following centrifugation at 150 g for 5 minutes and filtration through a 0.22 μm membrane filter (#GSWP02500, Millipore). On day 0, the medium swap group was plated in 6-well plates (#140675, Thermo Fisher Scientific) at a density of 1 x 105 cells per well in SmGM basal medium containing 5% FBS (BM-FBS medium). On day 4 and day 8, the medium was replaced with fresh BM-FBS medium containing 50% foam cell conditioned medium. The control group was plated at the same density in completed SmGM-2 growth medium three days before harvest. On day 12, SMCs were detached by adding 1 mL of 0.05% trypsin-EDTA (#25300-054, Gibco) per well and incubating at 37°C for 3 minutes, then neutralized with 10 mL of BM-FBS medium. Viable cells were counted using trypan blue solution (#15250061, Gibco). The cell suspension was subsequently filtered through a 100 µm nylon cell strainer (#352360, Falcon) to remove clumps, resulting in a uniform single-cell suspension for further analysis.
Library preparation was conducted with Chromium GEM-X Single Cell 3' Reagent Kits v4 (10x Genomics). Libraries were sequenced on NovaSeq X Plus. The initial 10x scRNA-seq dataset was processed using the Cell Ranger pipeline (v.8.0.0). The workflow included demultiplexing the bcl files with cellranger mkfastq, followed by running cellranger count using the pre-built Cell Ranger reference GRCh38-2020-A from 10x Genomics.

value: smooth muscle cell


title: ORG-0100 normal breast lobule RNA (non-Hispanic White); Breast Cancer 360

tag: bmi

value: postmenopausal


title: Foam Cell 1

description: Library name: Foam_1


title: YSGnr.1

description:
KY16-20-GT16-02751
AllP8_BulkRNAseq.log2CPM.csv


title: ORG-0018 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360

value: non-Hispanic Black

tag: surgical procedure


title: Foam Cell 2

description: Library name: Foam_2

value: foam cell


title: YSGr.3

description:
KY16-18-GT16-02749
AllP8_BulkRNAseq.log2CPM.csv


title: spret_juvenile_male_litter#15_individual#2

description: Library name: J15_2


title: ORG-0147_R4 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360

tag: menopausal status


title: ORG-0064 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360

tag: parity


title: spret_juvenile_male_litter#14_individual#2

description: Library name: J14_2


title: spret_juvenile_male_litter#13_individual#2

description: Library name: J13_2


title: YSGr.1

description:
KY16-16-GT16-02747
AllP8_BulkRNAseq.log2CPM.csv


title: Anti-CD3/28 duoCAR-T cells cultured with 293T-gp120 (HIV-1 antigen), biological replicate 2

city: Bronx

first: Harris

last: Goldstein

address: 1300 Morris Park Avenue

department: Pediatrics

institute: Albert Einstein College of Medicine

description: Library name: E7

data_processing:
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file of raw gene counts per samples (column)

source_name: CD8+ HIV-specific duoCAR-T cell

growth_protocol: Cells were cultured in complete Iscove's Modified Dulbecco's Media (IMDM) supplemented with 10% FBS, 1X GlutaMAX (Gibco, Ref# 35050-061), 1X Penicillin Streptomycin Solution (Corning, Ref# 30-002-CI), and 100mM HEPES buffer.

extract_protocol:
RNA was isolated using the micro RNeasy Plus kit (Qiagen, Cat# 74034)
For the 16-hour timepoint experiment, Novogene's standard mRNA library preparation was used

treatment_protocol: CD8+ T cells were isolated from PBMCs by immunomagnetic sorting using anti-CD8 microbeads according to the manufacturer’s protocol (Miltenyi Biotec). Anti-HIV duoCAR-T cells were generated through lentiviral transduction following activation with 100nM of HCW9206 supplemented in IMDM media for 7-days. Alternatively, T-cells were activated with αCD3 (OKT3) and αCD28 (BioLegend) antibodies at 100 ng/mL and 2 μg/mL, respectively, in the presence of IL-2 (100U/mL; NCI-Frederick BRB Repository, NIH) for 3 days. DuoCAR-T cells were collected 5-days after lentiviral transduction and co-cultured with either 293T or 293T-gp120 cells at a 5:1 E:T ratio for 16-hours.

value: CD8+ HIV-specific duoCAR-T cell

value: Female

value: anti-CD3/28 + rhIL-2

tag: time

value: 16 hours


title: HCW9206 duoCAR-T cells cultured with 293T-gp120 (HIV-1 antigen), biological replicate 2

description: Library name: E8


title: SG.2

description:
KY16-14-GT16-02745
AllP8_BulkRNAseq.log2CPM.csv

tag: tissue


title: spret_juvenile_female_litter#12_individual#2

description: Library name: J12_2

value: murine hypothalamus

tag: developmental stage

value: juvenile


title: HCW9206 duoCAR-T cells cultured with 293T (no antigen), biological replicate 2

description: Library name: E6

tag: Sex


title: spret_juvenile_male_litter#12_individual#1

description: Library name: J12_1

value: male


title: ORG-0051 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360

value: premenopausal

value: Yes


title: spret_juvenile_female_litter#13_individual#1

description: Library name: J13_1

value: M. spretus


title: SG.3

description:
KY16-15-GT16-02746
AllP8_BulkRNAseq.log2CPM.csv

value: MB


title: Anti-CD3/28 duoCAR-T cells cultured with 293T (no antigen), biological replicate 2

description: Library name: E5


title: ORG-0146_R1 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360

value: reduction mammoplasty


title: spret_adult_male_litter#8_individual#2

description: Library name: A8_2

value: adult


title: HCW9206 duoCAR-T cells cultured with 293T (no antigen), biological replicate 1

description: Library name: E3

value: Male


title: SG.1

description:
KY16-13-GT16-02744
AllP8_BulkRNAseq.log2CPM.csv


title: SGf

data_processing:
Raw sequencing reads  were aligned to mm10 genome (mouse) using Cell Ranger
Assembly: mm10
Supplementary files format and content: Filtered Barcodes,features and matrix files /Output of Cell Ranger

extract_protocol:
Fresh tumor tissues were dissociated and captured using 10X Genomics Chromium system following the 10X Genomics 3' Transcriptomics kit V3
Following 10X Genomics 3' Transcriptomics kit V3, Sequenced at BGI using DNBseq.


title: ORG-0111 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360

value: postmenopausal


title: HCW9206 duoCAR-T cells cultured with 293T-gp120 (HIV-1 antigen), biological replicate 1

description: Library name: E4


title: Anti-CD3/28 duoCAR-T cells cultured with 293T-gp120 (HIV-1 antigen), biological replicate 1

description: Library name: E2


title: ORG-0093 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360

value: non-Hispanic Black

value: prophylactic mastectomy


title: ORG-0097 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360


title: spret_adult_female_litter#8_individual#1

description: Library name: A8_1

value: female


title: ORG-0095 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360


title: SGm


title: Anti-CD3/28 duoCAR-T cells cultured with 293T (no antigen), biological replicate 1

description: Library name: E1

value: CD8+ HIV-specific duoCAR-T cell


title: spret_adult_male_litter#7_individual#2

description: Library name: A7_2


title: cr-buds.sRNA.WT.AGO1_IP.replicate2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Library name: buds_wt_AGO1_rep2
Capsella rubella WT unopened buds, sRNAs were profiled from proteins obtained by AGO1 immunoprecipitation

data_processing:
Adapters were removed from the reads using Cutadapt, and the resulting 18–30 bp long reads were selected. Reads belonging to chloroplast, mitochondria, and structural noncoding RNAs (tRNAs, snRNAs, rRNAs, or snoRNAs) were removed using Bowtie (-v 1). The remaining reads were mapped to the eight chromosome scaffolds of the Capsella genome v.1.0 build.
Assembly: Capsella rubella v1.0  (also listed as 183) http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Supplementary files format and content: Unique small RNAs (between 18-25 nts) and their accumulation number (raw reads) are represented in a two column format file: <unique_smallRNA> <number_of_raw_reads>.<length_nts>

organism: Capsella rubella

source_name: buds

growth_protocol: Seeds were sterilized with 70% EtOH, rinsed with distilled water, and sown on half-strength Murashige and Skoog (MS) medium with 1% sucrose. Seeds were stratified for two days in the dark at 4°C and then transferred to a growth chamber with a long-day photoperiod (16h of light / 8h of dark, 22°C, 50% humidity) for two weeks. Seedlings were then transferred to soil and grown under long-day conditions in the phytotron under 16h of light at 21 °C and 8h of darkness at 18°C with a light intensity of 150 µE and 70% humidity.

extract_protocol:
Total RNA was extracted using mirVanaTM miRNA isolation Kit, small RNA was extracted by gel size selection of 10~40 nt
sRNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (E7300). Final libraries were purified from a size selection of bands of about 150bp on a 6% polyacrylamide gel. Two biological replicates were used for anther, pollen, and endosperm samples, three biological replicates were used for root samples

treatment_protocol: For endosperm and pollen, sample were collected from the scion of grafted plants as indicated genotypes.

value: buds


title: ORG-0163 normal breast lobule RNA (non-Hispanic Black); Breast Cancer 360


title: YSGm


title: Treated Tumor- HER2 DC1+aSEMA4D #3

description: Metabolic Pathways

source_name: Soft Tissue

extract_protocol: Mice were euthanized at the same timepoint and the tumors were dissected. Tumor samples were flash frozen in liquid nitrogen, then stored at -80C before RNA sequencing

tag: gender

value: Female

tag: strain

value: BALB/c

tag: tissue type

value: Tumor


title: cr-buds.sRNA.WT.AGO1_IP.replicate1

description:
Library name: buds_wt_AGO1_rep1
Capsella rubella WT unopened buds, sRNAs were profiled from proteins obtained by AGO1 immunoprecipitation

value: WT (Cr1Gr1)


title: spret_adult_female_litter#7_individual#1

first: Lena

last: Arévalo

institute: INIA-CSIC

description: Library name: A7_1

value: murine hypothalamus


title: spret_adult_male_litter#3_individual#2

description: Library name: A3_2

value: male


title: spret_adult_male_litter#4_individual#2

description: Library name: A4_2

value: M. spretus


title: spret_adult_female_litter#4_individual#1

description: Library name: A4_1


title: YSGf

value: MB


title: cr-pollen.sRNA.wt / nrpd1.replicate2

description:
Library name: pollen_wt_x_pol_rep2
Capsella rubella wt scion grafting to nrpd1 root: pollen of the grafting plants

source_name: pollen

value: pollen

value: wt(Cr1Gr1) / nrpd1(Cr1Gr1)

value: grafting (scion/root)


title: cr-buds.sRNA.nrpd1.AGO1_IP.replicate2

description:
Library name: buds_pol4_AGO1_rep2
Capsella rubella nrpd1 unopened buds, sRNAs were profiled from proteins obtained by AGO1 immunoprecipitation

value: nrpd1 (Cr1Gr1)


title: Treated Tumor- HER2 DC1+aSEMA4D #1

description: Metabolic Pathways


title: Treated Tumor- HER2 DC1+aSEMA4D #2

description: Metabolic Pathways


title: OPC_Demyelination-5

city: Edinburgh

first: Tim

last: Czopka

address: 49 Little France Crescent

department: Institute of Neuroscience and Cardiovascular Research

country: United Kingdom

institute: The University of Edinburgh

description: Library name: OPC_Demyelination-5_lib1

data_processing:
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 22.0.2 was used to demultiplex the raw sequencing reads according to the sample indices. The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings.
Assembly: Zebrafish genome GRCz11
Supplementary files format and content: Processed data files are .csv tables containing chromosome, region complement, expression value, TPM, RPKM, Exons, Gene ID, Gene Length, ensembl ID, Biotype, unique gene reads, total gene reads, annotated transcripts, uniquely identified transcripts, exon length, unique exon reads, total exon reads, ratio of unique to total, unique exon-exon reads, total exon-exon reads, unique exon reads, total exon reads, ratio of intron to total gene reads.

organism: Danio rerio

source_name: oligodendrocyte precursor cell

extract_protocol:
RNA was extracted using the RNeasy micro UCP kit (QIAGEN), as per kit instructions
The library preparation was done using the QIAseq UPX 3'™ Transcriptome Kit (QIAGEN). A total of 1ng or 4ng purified RNA was converted into cDNA NGS libraries.

tag: cell type

value: oligodendrocyte precursor cell

value: demyelination


title: cr-buds.sRNA.nrpd1.AGO1_IP.replicate1

description:
Library name: buds_pol4_AGO1_rep1
Capsella rubella nrpd1 unopened buds, sRNAs were profiled from proteins obtained by AGO1 immunoprecipitation


title: Treated Tumor- anti-Semaphorin4D #2

description: Metabolic Pathways

data_processing:
Gene expression data was analysed using nSolver™ Analysis Software version 4.0 from NanoString Technologies (NanoString Technologies, WA, USA).
Default parameters were used for QC. Normalizations were done by using selected housekeeping genes with low CV at different data ranges.
Selected house keeping genes are as follows: GPL30557 (Cog7,Oaz1,Sap130,Sdha,Ubb); GPL31165 (Alas1,Eef1g,Eif2b4,Nubp1,Oaz1,Polr1b);GPL32407 (Alas1,Eef1g,Gapdh,G6pdx,Oaz1,Ppia); GPL32728 (Abcf1,G6pdx,Eef1g,Polr1b,Hprt,Sdha).
Differential expression was analyzed using Limma package.


title: spret_adult_female_litter#2_individual#2

city: Madrid

address: Avda. Puerta de Hierro, 18

description: Library name: A2_2

value: adult

value: female


title: OPC_Demyelination-4

description: Library name: OPC_Demyelination-4_lib1

tag: treatment


title: Treated Tumor- anti-Semaphorin4D #1

description: Metabolic Pathways


title: OPC_Demyelination-1

description: Library name: OPC_Demyelination-1_lib1


title: OPC_Demyelination-2

description: Library name: OPC_Demyelination-2_lib1


title: Treated Tumor- HER2 DC1 Treatment #2

description: Metabolic Pathways


title: cr-root.sRNA.wt.replicate3

description:
Library name: root_wt_rep3
Capsella rubella wt root

source_name: root

value: root


title: spret_adult_female_litter#3_individual#1

description: Library name: A3_1


title: OPC_Demyelination-3

description: Library name: OPC_Demyelination-3_lib1


title: spret_adult_male_litter#2_individual#1

description: Library name: A2_1


title: cr-pollen.sRNA.wt / nrpd1.replicate1

description:
Library name: pollen_wt_x_pol_rep1
Capsella rubella wt scion grafting to nrpd1 root: pollen of the grafting plants


title: YSGr.2

description:
KY16-17-GT16-02748
AllP8_BulkRNAseq.log2CPM.csv


title: cr-root.sRNA.wt.replicate2

description:
Library name: root_wt_rep2
Capsella rubella wt root


title: OPC_Demyelination_ctrl-5

description: Library name: OPC_Demyelination_ctrl-5_lib1

value: demyelination control


title: hybrid_embryo_male_litter#9_individual#E3

description: Library name: M9_E3

organism: Mus musculus domesticus x Mus spretus

value: embryo

value: M. m. domesticus/M. spretus hybrid


title: Treated Tumor- Untreated Control #2

description: Metabolic Pathways

value: Female

value: BALB/c

value: Tumor


title: OPC_Demyelination_ctrl-4

description: Library name: OPC_Demyelination_ctrl-4_lib1


title: hybrid_embryo_female_litter#9_individual#E1

description: Library name: M9_E1

value: murine hypothalamus


title: OPC_Demyelination_ctrl-3

description: Library name: OPC_Demyelination_ctrl-3_lib1


title: cr-root.sRNA.nrpd1.replicate3

description:
Library name: root_pol4_rep3
Capsella rubella nrpd1 root


title: cr-root.sRNA.wt replicate1

description:
Library name: root_wt_rep1
Capsella rubella wt root


title: hybrid_embryo_male_litter#20_individual#E1

description: Library name: M20_E1

value: male


title: OPC_Demyelination_ctrl-1

description: Library name: OPC_Demyelination_ctrl-1_lib1


title: Treated Tumor- Untreated Control #1

description: Metabolic Pathways


title: Untreated Tumor- HER2 DC1+aSEMA4D #3

description: Metabolic Pathways


title: OPC_Demyelination_ctrl-2

description: Library name: OPC_Demyelination_ctrl-2_lib1


title: Treated Tumor- HER2 DC1 Treatmen #1

description: Metabolic Pathways


title: cr-root.sRNA.nrpd1.replicate1

description:
Library name: root_pol4_rep1
Capsella rubella nrpd1 root


title: hybrid_embryo_male_litter#19_individual#E1

description: Library name: M19_E1


title: cr-pollen.sRNA.wt / wt.replicate2

description:
Library name: pollen_wt_x_wt_rep2
Capsella rubella wt scion grafteing to wt root: pollen of the grafting plants

value: pollen

value: wt(Cr1Gr1) / wt(Cr1Gr1)


title: OPC_4AP-5

description: Library name: OPC_4AP-5_lib1


title: hybrid_embryo_female_litter#19_individual#E2

description: Library name: M19_E2


title: OPC_4AP-4

description: Library name: OPC_4AP-4_lib1


title: hybrid_embryo_male_litter#11_individual#E2

description: Library name: M11_E2


title: Untreated Tumor- HER2 DC1+aSEMA4D #2

description: Metabolic Pathways


title: cr-root.sRNA.nrpd1.replicate2

description:
Library name: root_pol4_rep2
Capsella rubella nrpd1 root


title: cr-pollen.sRNA.wt / wt.replicate1

description:
Library name: pollen_wt_x_wt_rep1
Capsella rubella wt scion grafteing to wt root: pollen of the grafting plants

value: grafting (scion/root)


title: Untreated Tumor- anti-Semaphorin4D #2

description: Metabolic Pathways


title: cr-pollen.sRNA.nrpd1 / wt.replicate2

description:
Library name: pollen_pol_x_wt_rep2
Capsella rubella nrpd1 scion grafteing to wt root: pollen of the grafting plants

value: nrpd1(Cr1Gr1) / wt(Cr1Gr1)


title: Untreated Tumor- anti-Semaphorin4D #1

description: Metabolic Pathways


title: hybrid_embryo_female_litter#10_individual#E2

description: Library name: M10_E2


title: OPC_4AP-3

description: Library name: OPC_4AP-3_lib1

value: oligodendrocyte precursor cell


title: OPC_4AP-2

description: Library name: OPC_4AP-2_lib1


title: cr-pollen.sRNA.nrpd1 / wt.replicate1

description:
Library name: pollen_pol_x_wt_rep1
Capsella rubella nrpd1 scion grafteing to wt root: pollen of the grafting plants


title: Untreated Tumor- HER2 DC1 Treatment #2

description: Metabolic Pathways


title: hybrid_embryo_female_litter#11_individual#E1

description: Library name: M11_E1


title: cr-pollen.sRNA.nrpd1 / nrpd1.replicate2

description:
Library name: pollen_pol_x_pol_rep2
Capsella rubella nrpd1 scion grafteing to nrpd1 root: pollen of the grafting plants

value: nrpd1(Cr1Gr1) / nrpd1(Cr1Gr1)


title: Untreated Tumor- HER2 DC1+aSEMA4D #1

description: Metabolic Pathways


title: OPC_4AP-1

description: Library name: OPC_4AP-1_lib1


title: hybrid_juvenile_male_litter#9_individual#1

description: Library name: J9_1

value: juvenile


title: hybrid_juvenile_female_litter#9_individual#2

description: Library name: J9_2

value: female


title: cr-endosperm.sRNA.wt / wt.replicate2

description:
Library name: endo_wt_x_wt_rep2
Capsella rubella wt scion grafteing to wt root: endosperm of the grafting plants

source_name: endosperm

value: endosperm


title: OPC_4AP_ctrl-5

description: Library name: OPC_4AP_ctrl-5_lib1

value: 4AP control


title: OPC_4AP_ctrl-4

description: Library name: OPC_4AP_ctrl-4_lib1


title: Untreated Tumor- HER2 DC1 Treatmen #1

description: Metabolic Pathways


title: hybrid_embryo_male_litter#10_individual#E1

description: Library name: M10_E1

value: embryo


title: cr-pollen.sRNA.nrpd1 / nrpd1.replicate1

description:
Library name: pollen_pol_x_pol_rep1
Capsella rubella nrpd1 scion grafteing to nrpd1 root: pollen of the grafting plants


title: Untreated Tumor- Untreated Control #2

description: Metabolic Pathways


title: cr-endosperm.sRNA.wt / wt.replicate1

description:
Library name: endo_wt_x_wt_rep1
Capsella rubella wt scion grafteing to wt root: endosperm of the grafting plants


title: hybrid_juvenile_female_litter#6_individual#2

description: Library name: J6_2

value: M. m. domesticus/M. spretus hybrid


title: Untreated Tumor- Untreated Control #1

description: Metabolic Pathways

value: Female


title: hybrid_juvenile_male_litter#6_individual#1

description: Library name: J6_1


title: OPC_4AP_ctrl-2

description: Library name: OPC_4AP_ctrl-2_lib1


title: scATAC enriched HSPCs from pooled spleen cells  of untreated controls replicate 2

city: Würzburg

first: Haisam

last: Alattar

state: Bayern

address: Versbacherstr. 7

department: Inistitute of Virology and Immunobiology

country: Germany

institute: Wuerzburg University

description:
Library name: SCC0212_Lutz_Multiome_ATAC_UB_2
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences I; read3 contains ATAC sequences; I index

data_processing:
Raw base call (BCL) files were demultiplexed and converted to FASTQ files using Cell Ranger ATAC mkfastq (10x Genomics). FASTQ files were aligned to the mm10 reference genome using Cell Ranger ATAC count (10x Genomics, v2.1.0) with default parameters. Sequencing reads were processed using Cell Ranger ATAC (v2.1.0) and aligned to the mouse reference genome (GRCm38). Downstream analysis was performed using Seurat and Signac, including quality filtering, peak calling, generation of a unified peak set, dimensionality reduction, clustering, and gene activity inference. This dataset was used to identify GM-CSF-induced changes in chromatin accessibility across hematopoietic progenitors and differentiated immune populations, including the expansion and epigenetic profiling of immunoregulatory B-1b plasma cells.
Assembly: mm10
Supplementary files format and content: CellRnager output files: fragments.tsv, filtered_peak_bc_matrix.h5, fragments.tsv.gz.tbi, peaks.bed

source_name: Spleen

growth_protocol: C57BL/6 and B6.luciferase, 8 weeks old, mice were bred and maintained under SPF conditions in the animal facilities of the Institute of Hygiene and Microbiology and the Institute of Virology and Immunobiology of the University of Würzburg.

extract_protocol:
On day 11, mice were euthanized. Spleens were harvested, and single-cell suspensions were prepared by passing the tissue through a 70 µm cell strainer followed by red blood cell (RBC) lysis. For each group (GM-CSF treated and untreated), cells from C57BL/6 WT and B6.luciferase mice were pooled at a 1:1 ratio. HSPCs were enriched from these pools by cell sorting (FACS Aria III, Becton Dickinson) for the Lin- (Ter119, B220, CD4, CD8, CD11b), and c-Kit+ phenotype.
The luciferase sequence flanked by the two primers, Luc 1A: 5' -TCAAAGAGGCGAACTGTGTGTG -3' and Luc 2B: 5' -GGTGTTGGAGCAAGATGGAT -3', was used as a genetic barcode to annotate cells to their respective animals and to bioinformatically analyze individual mice within each group separately. Single-cell ATAC-seq libraries were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kit v1.1(10x Genomics) according to the manufacturer’s protocol (CG000209, Rev D). Briefly, nuclei were isolated from freshly collected sorted HSPCs. The 10x Genomics Nuclei Isolation protocol (CG000124, Rev G) was used with minor modifications. Nuclei were counted and assessed for integrity using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Approximately 10,000 nuclei per sample were loaded onto a Chromium Next GEM Chip H for gel bead-in-emulsion (GEM) generation and barcoding on the Chromium Controller (10x Genomics).

treatment_protocol: In the first group, C57BL/6 and B6.luciferase mice were injected intraperitoneally daily with 1 µg of recombinant glycosylated GM-CSF for 10 days. The second group consisted of untreated mice serving as controls.

value: Spleen

value: Enriched HSPCs

value: WT & Luciferase

value: untreated


title: scATAC enriched HSPCs from pooled spleen cells  of GM-CSF treated mice replicate 1

description:
Library name: SCC0212_Lutz_Multiome_ATAC_GM_1
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences I; read3 contains ATAC sequences; I index

value: recombinant glycosylated GM-CSF


title: scATAC enriched HSPCs from pooled spleen cells  of GM-CSF treated mice replicate 2

description:
Library name: SCC0212_Lutz_Multiome_ATAC_GM_2
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences I; read3 contains ATAC sequences; I index


title: hybrid_juvenile_male_litter#4_individual#1

description: Library name: J4_1

value: murine hypothalamus

value: male


title: OPC_4AP_ctrl-3

description: Library name: OPC_4AP_ctrl-3_lib1


title: scATAC enriched HSPCs from pooled spleen cells  of untreated controls replicate 1

description:
Library name: SCC0212_Lutz_Multiome_ATAC_UB_1
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences I; read3 contains ATAC sequences; I index


title: hybrid_juvenile_female_litter#3_individual#2

description: Library name: J3_2


title: cr-endosperm.sRNA.nrpd1 / wt.replicate1

description:
Library name: endo_pol_x_wt_rep1
Capsella rubella nrpd1 scion grafteing to wt root: endosperm of the grafting plants

value: nrpd1(Cr1Gr1) / wt(Cr1Gr1)

value: grafting (scion/root)


title: hybrid_juvenile_male_litter#3_individual#1

description: Library name: J3_1