title: DMSO-H3K9me3-ChIP-seq-rep1

description:
DMSO-H3K9me3-ChIP-seq-rep1.bw
DMSO-H3K9me3-ChIP-seq-merge.bw

value: embryonic stem cells


title: ActA_BADC_120h_rep2

status: Public on Mar 07 2026

type: SRA

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description: Library name: ActA_BADC_120h_rep2

library_source: transcriptomic

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025.
Adapter sequences were trimmed from reads using cutadapt version 1.16 (-a ‘GATCGGAAGAGCACACGTCTGAACTCCAGTCAC’ -A ‘GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT’). Trimmed reads were aligned on mm10 with STAR version 2.7.7a69 with ENCODE options using a custom gtf based on Ensembl version 102 (https://doi.org/10.5281/zenodo.7510406). Only uniquely mapped reads (tag NH:i:1) were kept using bamFilter version 2.4.171 and Cufflinks  version 2.2.1 was run with default parameters to get FPKM values
Assembly: mm10
Supplementary files format and content: counts.txt.gz: raw counts from STAR
Supplementary files format and content: FPKM.txt.gz: FPKM from cufflinks identical ensembl Ids have been summed to have a single line per ID.

molecule: polyA RNA

organism: Mus musculus

source_name: Activin A gastruloids

growth_protocol: mES cells were maintained in a humidified incubator (5% CO2, 37°C), and passaged every 3 days into 2i LIF DMEM medium composed of DMEM supplemented with 10% mES certified FBS, 100ng ml-1 of mouse LIF, 3μM of GSK-3 inhibitor (CHIR99021) and 1μM of MEK1/2 inhibitor (PD0325901).

extract_protocol:
mES cells and endoderm differentiated mES cells were collected in RLT plus buffer (Qiagen) and stored at −80°C until RNA extraction. RNeasy Plus Micro kit (Qiagen) with on-column DNase digestion was used for RNA extraction.
RNA-seq library preparation with Poly-A selection was performed with 1μg of purified RNA using the TruSeq Stranded mRNA kit from Illumina. Library quality was assessed with a fragment analyzer before sequencing.

treatment_protocol: For  in vitro endoderm differentiation, round 50’000 cells of control and Hox-/- mES cells were seeded in a 6-wells plate in differentiation medium (DM) composed of DMEM/F12 with 0.2% FBS medium and 1x B27. After 24h, medium was replaced with DM supplemented with 100ng ml-1 of recombinant Activin A and 3μM of GSK-3 inhibitor (CHIR99021). The same treatment was repeated at 72h, before cells collection at 120h.

tag: tissue

value: Activin A gastruloids

tag: cell type

value: Mixed cells

tag: genotype

value: Hox-/-

tag: treatment


title: Control Larval Midgut, Day 4, rep 4

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

country: Germany

institute: University of Cologne

description: Library name: mex_attP40_D4_rep4

data_processing:
The quality of the raw sequencing reads was checked using FastQC (v0.11.7) [1] and MultiQC (v.1.12) [2], and sequencing adaptor were trimmed using Trimmomatic (v0.39) [3]. No issues were detected.                         [1] http://www.bioinformatics.babraham.ac.uk/projects/fastqc, [2] https://doi.org/10.1093/bioinformatics/btw354 [3] https://github.com/usadellab/Trimmomatic
List of adapters is as follows: Read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; AGATCGGAAGAGCACACGTCTGAAC; TGGAATTCTCGGGTGCCAAGG; AGATCGGAAGAGCACACGTCT; CTGTCTCTTATACACATCT; AGATGTGTATAAGAGACAG Read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; AGATCGGAAGAGCGTCGTGTAGGGA; TGGAATTCTCGGGTGCCAAGG; AGATCGGAAGAGCACACGTCT; CTGTCTCTTATACACATCT; AGATGTGTATAAGAGACAG"
Reads were aligned to the Drosophila melanogaster reference genome BDGP6.54.114 with STAR (v2.7.10b) [4], A raw count matrix for all sample was then generated from STAR “ReadsPerGene.out.tab” outputs as described here: https://ucdavis-bioinformatics-training.github.io/2019_March_UCSF_mRNAseq_Workshop/data_reduction/counts.html [4] https://doi.org/10.1093/bioinformatics/bts635
Data were further analysed using R (v4.5.1). Filtering was performed for low-count genes (>1 read in all samples), retaining 9536 genes out of 24254. DESeq2 package (v1.49.3) [5] was used to carry out differential expression analysis. [5] https://doi.org/10.1186/s13059-014-0550-8
Assembly: D. melanogaster annotated transcripts (BDGP6.54.114)
Supplementary files format and content: The Excel file contains three spreadsheets. The "RAW" spreadsheet contains the read counts for each transcript in each sample, after alignment with STAR. The “CPM” spreadsheet contains Counts Per Million (CPM) read counts for each transcript in each sample. The “DEG” spreadsheet contains the log2 fold change (log2FC) and the adjusted p-value (padj) for each transcript following a comparison of two conditions using DESeq2, and after filtering out transcripts with low-counts, as described above. The following pairwise comparisons were made: - controls D4 vs controls D3 (attP40_D4_vs_attP40_D3) - Hnf4 RNAi D4 vs Hnf4 RNAi D3 (Hnf4i_D4_vs_Hnf4i_D3) - HNF4 RNAi D3 vs controls D3 (Hnf4i_D3_vs_attP40_D3) - Hnf4 RNAi D4 vs controls D4 (Hnf4i_D4_vs_attP40_D4). The Flybase ID and symbol are provided for each transcript.

organism: Drosophila melanogaster

source_name: Midgut

growth_protocol: The embryos were collected after an overnight egg-laying period and transferred in batches of 40 to polystyrene vials containing a yeast-only diet. These vials were then kept at 25°C under a 12-hour light/dark cycle. Larvae were collected on days three and four after egg laying for midgut dissection.

extract_protocol:
Total RNA was extracted using the Promega Reliaprep RNA Tissue Miniprep System
Libraries were prepared by the Cologne Center for Genomics using the Illumina Stranded Truseq RNA sample Preparation Kit

treatment_protocol: Hnf4 was silenced in ECs by driving the expression of a UAS-Hnf4 RNAi transgene wiht the EC-specific mex-GAL4 driver.

value: Midgut

tag: Stage

value: mex-GAL4 / attP40

value: Yeast only diet


title: Hnf4 RNAi Larval midgut, Day 3, rep 4

description: Library name: mex_Hnf4i_D3_rep4

value: mex-GAL4 / UAS-Hnf4 RNAi


title: Inhibitor-H3K9me3-ChIP-seq-rep1

city: Guangzhou

first: Dai

last: ranran

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou, Guangdong Province

country: China

institute: Sun Yat-Sen University

description:
Inhibitor-H3K9me3-ChIP-seq-rep1.bw
Inhibitor-H3K9me3-ChIP-seq-merge.bw

library_source: genomic

data_processing:
ChIP-seq data process pipline. High-confidence reads of ChIP-seq data obtained by using fastp (v0.20.0) with default parameters, were mapped to mouse genome mm9 by using Bowtie2 (v2.5.1)2 with parameters ‘--sensitive –p 24’, and PCR duplicated fragments were filtered by Picard (v2.22.8) (http://broadinstitute.github.io/picard). Then, the unmapped, multi-mapped reads were filtered, and the reads mapping to chrM were removed. Unique reads were filtered by MAPQ > 30. We used deepTools (v3.5.0) bamCoverage to generate bigWig file with CPM normalization. SAM files were converted to BAM format for peak calling using SAMtools (v1.9). Peaks were identified by MACS2 (v2.2.4) callpeak pipeline.
RNA-seq data process pipline. Clean data were obtained by using trim_galore (v0.6.7) to remove reads containing adapter, reads containing ploy-N, and low quality reads from raw data. Clean reads with high quality were aligned to mm9 reference genome using STAR (v2.7.9a) with default parameters. The uniquely mapped reads were counted with HTSeq-count (v2.0.3). Raw counts were used as input to DESeq2 (v1.30.0) to generate differentially expressed genes as well as normalized count tables. Significantly differential expressed genes (DEGs) were identified when the adjusted p-value < 0.05 and the log2-fold change > 1.0.
Assembly: mm9
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.

molecule: genomic DNA

source_name: Non-tissue samples

growth_protocol: The mouse ESC line R1 was cultured on gelatin-coated dishes with ESC medium. The ESC medium composition included DMEM (Hyclone, #SH30022.01), 15% (v/v) fetal bovine serum (FBS, Lonsera, #S712-012S), 0.1 mM β-mercaptoethanol (Sigma, #M6250), 2 mM L-glutamine (Thermo Fisher, #35050061), 0.1 mM nonessential amino acids (Thermo Fisher, #11140050), 1% (v/v) nucleoside mix, and LIF.

extract_protocol:
For RNA-seq: Total RNA was extracted from cell pellets using RNAzol reagent. For ChIP-seq: 1% formaldehyde in PBS was used to crosslink the cells. Antibody enrich DNA fragments overnight from Sonicated lysates.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols.

value: Non-tissue samples

tag: cell line

value: ESC

tag: chip antibody


title: Control Larval Midgut, Day 4, rep 3

description: Library name: mex_attP40_D4_rep3


title: DMSO-H3K9me3-ChIP-seq-rep2

description:
DMSO-H3K9me3-ChIP-seq-rep2.bw
DMSO-H3K9me3-ChIP-seq-merge.bw

value: DMSO


title: ActA_BADC_120h_rep1

description: Library name: ActA_BADC_120h_rep1


title: Control Larval Midgut, Day 4, rep 2

description: Library name: mex_attP40_D4_rep2


title: GEX_ANRF24

city: Rochester

first: Hu

last: Zeng

state: MN

address: 209 Third Ave SW

department: Rheumatology

country: USA

institute: Mayo Clinic

description: Library name: Sample 8

library_source: transcriptomic single cell

data_processing:
Cell type annotation was conducted using the Azimuth package with the Human PBMC reference dataset.
To refine cell type classifications, we manually reviewed cluster-specific gene markers identified by Immunopipe and further annotated subpopulations of CD8 T cells. Gene set enrichment analysis was performed using the clusterProfiler package in R.
Additionally, ANOVA test was applied to compare gene expression scores across patient groups for selected genes involved in the CD8 T cell cytotoxicity pathway.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: Blood samples were collected into sodium heparin tubes, and plasma was collected after centrifuging at 4 °C, 1300 rpm for 10 mins.

extract_protocol:
Specifically, 13 mL Ficoll-Paque™ PLUS density gradient media (GE Healthcare, Cat# 17-1440-02) were added to the bottom of 30 mL diluted peripheral blood, and centrifuged at 4 °C, 400 g for 25 min with the acceleration and deceleration at lower speed. The PBMC layer was collected and washed with wash buffer (1×PBS + 10 mM HEPES + 0.1% BSA + 2 mM EDTA), and PBMCs were aliquoted and cryopreserved in a liquid nitrogen tank.
FASTQ files generated from the Gene Expression and Feature Barcode libraries were processed using the 10x Genomics Cell Ranger multi pipeline to create expression matrices for downstream analysis.
Integrated single-cell analysis of gene expression and T cell receptor data was performed using the Immunopipe package.

treatment_protocol: Peripheral blood mononuclear cells were isolated from the peripheral blood using Ficoll-Paque gradient centrifugation.

value: PBMC

tag: sample group

value: healthy control (HC)


title: Hnf4 RNAi Larval midgut, Day 3, rep 3

description: Library name: mex_Hnf4i_D3_rep3


title: Control Larval Midgut, Day 4, rep 1

description: Library name: mex_attP40_D4_rep1


title: Inhibitor-Buffer-ChIP-seq-rep2


title: GEX_ANRF-16

description: Library name: Sample 6

value: rheumatoid arthritis control (RAC)


title: GEX_H013

description: Library name: Sample 9


title: Hnf4 RNAi Larval midgut, Day 3, rep 2

description: Library name: mex_Hnf4i_D3_rep2


title: ActA_BADC_96h_rep1

description: Library name: ActA_BADC_96h_rep1


title: ActA_BADC_96h_rep2

description: Library name: ActA_BADC_96h_rep2


title: Inhibitor-ConA-ChIP-seq-rep2

description: Inhibitor-ConA-ChIP-seq-merge.bw

value: ConA-biotin


title: Hnf4 RNAi Larval midgut, Day 3, rep 1

description: Library name: mex_Hnf4i_D3_rep1


title: GEX_ANRF-08

description: Library name: Sample 5


title: DMSO-Buffer-ChIP-seq-rep2


title: ActA_wt_120h_rep1

description: Library name: ActA_wt_120h_rep1

value: wt


title: Control Larval Midgut, Day 3, rep 4

description: Library name: mex_attP40_D3_rep4


title: ActA_wt_120h_rep2

description: Library name: ActA_wt_120h_rep2


title: Control Larval Midgut, Day 3, rep 3

description: Library name: mex_attP40_D3_rep3


title: ActA_wt_96h_rep2

description: Library name: ActA_wt_96h_rep2


title: Inhibitor-Buffer-ChIP-seq-rep1


title: GEX_ANRF05

description: Library name: Sample 3


title: Inhibitor-ConA-ChIP-seq-rep1

description: Inhibitor-ConA-ChIP-seq-merge.bw


title: GEX_ANRF-06

description: Library name: Sample 4


title: ActA_wt_96h_rep1

description: Library name: ActA_wt_96h_rep1


title: Control Larval Midgut, Day 3, rep 2

description: Library name: mex_attP40_D3_rep2


title: DMSO-ConA-ChIP-seq-rep2

description: DMSO-ConA-ChIP-seq-merge.bw


title: GEX_ANRF-04

description: Library name: Sample 2


title: DMSO-Buffer-ChIP-seq-rep1


title: Larval Midgut, Day 4, rep 5

description: Library name: w1118 D4 biol rep 5

data_processing:
The RNA-seq dataset was processed on the CHEOPS HPC cluster at the University of Cologne using the nf-core [1] RNA-seq pipeline (v3.7) [2] within a Singularity environment [3] and managed by Nextflow (v21.10.6) [4]. [1] https://doi.org/10.1038/s41587-020-0439-x [2] https://doi.org/10.1371/journal.pone.0177459 [3] https://nf-co.re/rnaseq [4] https://doi.org/10.1038/nbt.3820
Quality control, including adapter trimming and sequence filtering, was performed with Trim Galore (v0.6.7) [5], ensuring high-quality reads. Read quality was assessed via MultiQC (v1.11) [6], aggregating FastQC [7], Picard [8], and Preseq [9] reports. No issues were detected. [5] https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ [6] https://doi.org/10.1093/bioinformatics/btw354 [7] http://www.bioinformatics.babraham.ac.uk/projects/fastqc [8] https://broadinstitute.github.io/picard/ [9] https://doi.org/10.1038/nmeth.2375
List of adapters is as follows
Read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; AGATCGGAAGAGCACACGTCTGAAC; TGGAATTCTCGGGTGCCAAGG; AGATCGGAAGAGCACACGTCT; CTGTCTCTTATACACATCT; AGATGTGTATAAGAGACAG
Read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; AGATCGGAAGAGCGTCGTGTAGGGA; TGGAATTCTCGGGTGCCAAGG; AGATCGGAAGAGCACACGTCT; CTGTCTCTTATACACATCT; AGATGTGTATAAGAGACAG
Reads were aligned to the Drosophila melanogaster reference genome BDGP6.32 with STAR (v2.7.10a) [https://doi.org/10.1093/bioinformatics/bts635], and gene quantification was done using Salmon (v1.5.2) [https://doi.org/10.1038/nmeth.4197].
CPM counts were further analysed using the iDEP interface (v0.96) [12]. Filtering of lowly expressed genes was performed by selecting genes with min. 0.5 CPM in at least 1 library, representing 9787 genes out of 12133. Log2FC and adjusted p-values were calculated for all filtered genes using DESeq2 with a FDR of 0.1 [12] https://doi.org/10.1186/s12859-018-2486-6
Assembly: D. melanogaster annotated transcripts (BDGP6.32)
Supplementary files format and content: The excel file contains two spreadsheets. The “CPM” spreadsheet contains Counts Per Million (CPM) read counts for each transcript in each sample. The “DEG” spreadsheet contains log2 fold change (logFC) and adjusted p-value after comparison between D2 and D3, D2 and D4, and D3 and D4. For each transcript, the Flybase ID and symbol are given.

growth_protocol: w1118 embryos were collected after overnight egg laying and transferred in batches of 40 to polystyrene vials containing a yeast-only diet. Larvae were maintained at 25°C with a 12h light/dark cycle and collected on days two, three and four for midgut dissection.

extract_protocol:
Total RNA was extracted using the Promega Reliaprep RNA Tissue Miniprep System (#Z6112)
Libraries were prepared using the Illumina Stranded Truseq RNA sample Preparation Kit

tag: age

value: 4 days after egg laying

tag: Sex

value: not determined


title: wt_120h_rep2

description: Library name: wt_120h_rep2

source_name: Chiron gastruloids

value: Chiron gastruloids


title: GEX_ANRF-22

description: Library name: Sample 7


title: Buffer-ChIP-seq-rep2

value: embryonic stem cells

value: WT


title: 19739X3 MDA-MB-468 cells 3D Multiplex

city: Salt Lake City

first: David

last: Freeman

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description: 10X Genomics

data_processing:
The fastq files were aligned to the refdata-gex-GRCh38-2020-A human reference from 10X genomics using cellranger multi version 7.0.0 with Gene Expression and Multiplexing Capture types.
Assembly: hg38
Supplementary files format and content: Per sample filtered feature barcode matrix in h5 format

extract_protocol:
Single-cell suspension of MDA-MB-468 organoids were generated by sequetional dissociation with dispase and trypsin and resuspended in phosphate buffer saline + 0.04% BSA. Cells were filtered through a 40micron filter and counted on a Countess 2 (Invitrogen, Carlsbad, CA)
Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000268) was used to barcode individual cells with 16nt 10x Barcode, to tag cell specific transcript molecules with 12 nt Unique Molecular Identifier (UMI) and to capture poly (A) mRNA with 30 nt ploy(dT) sequence according to the manufacturer's instructions. 15k cells were targeted for sequencing.

value: Human breast cancer cell line

value: s14-con and s14-A4

tag: library type

value: HTO


title: wt_120h_rep1

description: Library name: wt_120h_rep1

value: Mixed cells


title: Buffer-ChIP-seq-rep1

value: Non-tissue samples


title: Control Larval Midgut, Day 3, rep 1

description: Library name: mex_attP40_D3_rep1

value: Midgut

value: mex-GAL4 / attP40

value: Yeast only diet


title: ConA-ChIP-seq-rep2

description:
chr1-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr2-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr3-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr4-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr5-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr6-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr7-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr8-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr9-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr10-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr11-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr12-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr13-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr14-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr15-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr16-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr17-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr18-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chr19-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw
chrX-ChIP-seq_ConA_Buffer-log2ratio_bigwigCompare.bw

value: ESC


title: DMSO-ConA-ChIP-seq-rep1

description: DMSO-ConA-ChIP-seq-merge.bw

value: DMSO


title: Larval Midgut, Day 4, rep 3

description: Library name: w1118 D4 biol rep 3


title: Larval Midgut, Day 4, rep 2

description: Library name: w1118 D4 biol rep 2


title: 19738X3 MDA-MB-468 cells 3D GEX

description: 10X Genomics

value: multiplexed sampe:s14-con and s14-A4

value: GEX


title: wt_96h_rep2

description: Library name: wt_96h_rep2

value: wt


title: ChIPmentation of PBX1 on Hox-/- gastruloids at 120h

description: Library name: PBX1_BADC

data_processing:
For data analysis, adapter sequences and bad quality bases were trimmed from reads using cutadapt version 1.16 (-a 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' -a 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' for ChIPmentation --quality-cutoff=30). Trimmed reads were mapped on mm10 genome using bowtie2 version 2.3.4.1. Only alignments with proper pairs and mapping quality above 30 were kept using samtools 1.8. Peaks and coverage were obtained with macs2 version 2.1.1.20160309 (--format BAMPE --gsize 1870000000 --call-summits --bdg). Motif analysis of PBX1 ChIPmentation peaks was performed with HOMER version 4.10. ChIPmentation quantifications and heatmaps were performed with deeptools version 3.0.0.
Assembly: mm10
Supplementary files format and content: narrowPeak from macs2
Supplementary files format and content: bigwig macs2 coverage

source_name: Gastruloids

growth_protocol: For gastruloid differentiation, 300 mES cells were resuspended in 40μl of prewarmed N2B27 medium (50% DMEM/F12 and 50% Neurobasal supplemented with 0.5x N2 and 0.5x B27), and seeded into each well of a low-attachment, rounded-bottom 96-well plate. After 48h, 150µl of N2B27 medium supplemented with 3μM of GSK-3 inhibitor was added to each well. Medium was then replaced every 24h.

extract_protocol:
Collected gastruloid were pooled in a 15ml falcon tube, washed with PBS and resuspended in 1ml PBS containing 1% formaldehyde for fixation during 10 min at RT. The crosslink reaction was stopped by adding a glycine solution to a final concentration of 0.125M. Fixed gastruloids were pelleted and stored at -80°C until further use.
Samples were resuspended in a sonication buffer (Tris HCl pH=8.0 50mM; EDTA 10mM; SDS 0.25% and protease inhibitors) and sonicated in a Covaris S220 device for 14 min (duty cycle 2%, peak incident power 105W) to obtain an average chromatin fragment size of 300-500 bp. A dilution buffer (HEPES pH=7.3 20mM; EDTA 1mM; NP40 0.1%; NaCl 150mM and protease inhibitors) was added to the sonicated chromatin and incubated with the antibody-bead complex (Pierce Protein A/G Magnetic Beads, Thermo Scientific with 5µg anti-PBX1 (4342S, Cell Signaling)) overnight at 4°C. Sequential washes were then performed twice with RIPA buffer (Tris HCl pH=8.0 10mM; EDTA 1mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 140mM and protease inhibitors), RIPA High salt buffer (Tris HCl pH=8.0 10mM; EDTA 1mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 500mM and protease inhibitors), LiCl buffer (Tris HCl pH=8.0 10mM; EDTA 1mM; LiCl 250mM; Sodium Deoxycholate 0.5%; NP40 0.5% and protease inhibitors) and Tris HCl buffer (pH=8.0 10mM and protease inhibitors). DNA fragments bound to the antibody-bead complex were tegmented using the Nextera Tegmentation kit. Beads were resuspended in the tegmentation buffer and incubated at 37° for 2min with 1µl of the Tn5 transposase. Fragment were then eluted and purified as described previously, and amplified using Nextera primers. Final DNA libraries were purified and size selected using AMPure XP magnetic beads (Beckman Coulter), and a fragment analysis was performed before sequencing on a DNBSEQ-G40 sequencer as paired-end, 100bp reads.

value: Gastruloids

value: Hox-/-


title: Larval Midgut, Day 4, rep 1

description: Library name: w1118 D4 biol rep 1

value: 4 days after egg laying

value: not determined


title: Larval Midgut, Day 3, rep 5

description: Library name: w1118 D3 biol rep 5

value: 3 days after egg laying


title: brain, 44 dpf, rep2

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

description: Library name: Sample 9

data_processing:
The RRBS sequenced reads were aligned using BSMAP v2.90
Assembly: ASM1334776v1
Supplementary files format and content: txt files include methylation level at each citosine performed using the methratio.py script from BSMAP software.

organism: Scophthalmus maximus

source_name: brain

extract_protocol:
DNA was extracted and purified using the QIAGEN Genomic DNA kit (Qiagen, Germany), in accordance with the manufacturer's instructions.
The Diagenode Premium RRBS kit (Diagenode Inc., USA) was used in accordance with the manufacturer's instructions. The DNA from all samples was subjected to bisulfite conversion by MspI enzyme digestion, resulting in a total of 100 ng of DNA targeted for CCGG sites. The resulting DNA fragments were purified using AMPure XP Beads (Beckman-Coulter, USA), and their concentration was determined using a Qubit High Sensitivity assay (ThermoFisher Scientific, USA).

value: brain


title: brain, 44 dpf, rep4

description: Library name: Sample 11


title: brain, 44 dpf, rep3

description: Library name: Sample 10


title: Larval Midgut, Day 4, rep 4

description: Library name: w1118 D4 biol rep 4


title: GEX_ANRF03

description: Library name: Sample 1

value: PBMC

value: immune-related adverse event (irAE)


title: ConA-ChIP-seq-rep1

value: Non-tissue samples

value: embryonic stem cells

value: WT

value: ConA-biotin


title: Untreated Rep 3

data_processing:
Data was processed using the cloud-based alignment tool, Elysium. Source code can be found at https://github.com/maayanlab/elysium
Assembly: mm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

extract_protocol:
RNA was isolated from 3T3 cells using the RNAeasy kit from Qiagen (#74104) with on column Dnase digestion according to the manufacturer's instructions.
NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation

value: Mouse fibroblast cell line

value: Untreated


title: brain, 44 dpf, rep1

description: Library name: Sample 8


title: brain, 21 dpf, rep4

description: Library name: Sample 7


title: Untreated Rep 2


title: ChIPmentation of PBX1 on wt gastruloids at 120h

description: Library name: PBX1_wt


title: P. maniculatus nubiterrae replicate 5

city: Cambridge, MA

first: KT

last: Tyssowski

state: Massachusetts

address: 16 Divinity Ave

institute: Harvard University

description:
Library name: NB6
Parse Evercode WT Mega kit

data_processing:
Data were demultiplexed using python-based pipelines from Parse and aligned to the P. maniculatus bairdii genome. To avoid confounds from mapping to the genome of one of the subspecies, before alignment, genomes were “personalized” to each subspecies, using a method similar to the generation of the P. polionotus genome (see Bendesky et al., PMID 28424518). Briefly, we aligned our data to the P. maniculatus bairdii genome using STAR aligner. Then we performed variant calling for the individuals we sequenced for each subspecies using GATK. We then incorporated variants back into the final genomes to which we mapped reads. We did the final alignment using STAR aligner as a part of the Parse pipeline. Cells that passed a UMI threshold determined automatically by the Parse preprocessing script were carried on to the next steps.
Data were analyzed as a cell x gene count matrix in Seurat version 4.3.0 Data were normalized with the SCTransform method and integrated across samples and subspecies using harmony. Data were then clustered using the default Seurat settings with the FindClusters and FindNeighbors functions. Data were then mapped to the BICNN mouse motor cortex dataset using Azimuth to identify cell types. Clusters with low prediction scores for the mapping (median prediction score < 0.75 out of 1.0) were further assessed by finding marker genes. If clusters showed markers of multiple larger cell types (e.g., neurons and oligodendrocytes) or if they appeared to be non-cortical cell types (e.g., from dissection error), they were removed from the dataset. After removing this contaminating signal, this alignment resulted in 96% of cells with a prediction score greater than 0.75 when mapping to gene classes. The remaining clusters were then re-normalized, re-integrated, and re-clustered.
Assembly: HU_Pman_2.1.3 (Peromyscus maniculatus bairdii)
Supplementary files format and content: RDS file with Seurat object. Genes x cells matrix with metadata labeling sample and cell type information

organism: Peromyscus maniculatus nubiterrae

source_name: frontal cortex

extract_protocol:
The anterior half of the cortex was extracted from both hemispheres for each animal (this includes all of sensorimotor cortex, as well as other areas) and flash-frozen in liquid nitrogen. Samples were stored at -70°C until further processing. Nuclei were extracted as described in Matson et al. (PMID 30371670) except that the high sucrose buffer had 1.2M sucrose. Nuclei were fixed using the Parse Evercode Fixation kit, according to the instructions of the manufacturer. Fixed nuclei were stored at -80C for up to 3 months.
Library construction was performed using the Parse Evercode WT Mega kit according to the instructions of the manufacturer. Samples from other projects were included in the run. The data here is de-multiplexed by sample, so as to include only the data for this project.

value: frontal cortex

value: 3-6 months

value: female


title: wt_96h_rep1

description: Library name: wt_96h_rep1

value: Chiron gastruloids

value: Mixed cells

value: wt


title: Larval Midgut, Day 3, rep 4

description: Library name: w1118 D3 biol rep 4

value: Midgut

value: not determined

value: Yeast only diet


title: Untreated Rep 1


title: Larval Midgut, Day 3, rep 3

description: Library name: w1118 D3 biol rep 3

value: 3 days after egg laying


title: P. maniculatus nubiterrae replicate 4

description:
Library name: NB5
Parse Evercode WT Mega kit

value: male


title: brain, 21 dpf, rep3

description: Library name: Sample 6

value: brain


title: P. maniculatus nubiterrae replicate 3

description:
Library name: NB4
Parse Evercode WT Mega kit


title: shCr Rep 3

value: EVs from CRIPTO knockdownl MDA-MB-468 cells


title: Larval Midgut, Day 3, rep 2

description: Library name: w1118 D3 biol rep 2


title: P. maniculatus nubiterrae replicate 2

description:
Library name: NB3
Parse Evercode WT Mega kit


title: brain, 21 dpf, rep2

description: Library name: Sample 5


title: shCr Rep 1


title: brain, 21 dpf, rep1

description: Library name: Sample 4


title: Larval Midgut, Day 2, rep 5

description: Library name: w1118 D2 biol rep 5

value: 2 days after egg laying


title: Larval Midgut, Day 3, rep 1

description: Library name: w1118 D3 biol rep 1


title: shCon Rep 3

value: EVs from control MDA-MB-468 cells


title: brain, 13 dpf, rep2

description: Library name: Sample 2


title: Larval Midgut, Day 2, rep 4

description: Library name: w1118 D2 biol rep 4


title: shCon Rep 2

value: Mouse fibroblast cell line


title: brain, 13 dpf, rep1

description: Library name: Sample 1


title: sgLkb1 sgLifr

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

description: Library name: G3

data_processing:
Gene expression together with Hashtag oligo (HTO) libraries were processed using Cell Ranger (v5.0.0) in multi mode. Cell containing droplets were selected using the default filtering from Cell Ranger. UMI count matrices from each modality were imported into the same Seurat object as separate assays. Viable cells were filtered based on having more than 200 genes detected and less than 10% of total UMIs stemming from mitochondrial transcripts. HTO counts were normalized using centered log ratio transformation before hashed samples were demultiplexing using the Seurat::HTODemux function. RNA counts were normalized using Seurat::SCTransform function with regressions of cell cycle score, ribosomal and mitochondrial percentages. Cells from multiple conditions were combined using Seurat standard scRNSeq integration workflow with 3000 anchor genes. A shared nearest neighbor graph was then built based on the first 40 principal components (PCs) followed by identification of cell clusters using Leiden algorithm and Seurat::FindClusters function at multiple resolutions in order to identify potential rare cell types. Cell types were annotated based on canonical cell type markers and differential expressed genes of each cluster identified using Seurat::FindAllMarkers function with a logistic regression model. Clusters expressing markers of the same cell type were merged into a single cluster. Cells were then projected on to a uniform manifold using the top 40 PCs for visualization. Protein counts were normalized using centered log ratio transformation. Multimodal integration was performed using the weighted nearest neighbor (WNN) method in Seurat.
Assembly: GRCm38
Supplementary files format and content: Seurat object
Library strategy: CITE-seq

source_name: Lung

growth_protocol: 2 mice per tumor genotype

extract_protocol:
Mouse lung tissue was digested with Collagenase/DNAse in RPMI +10% FBS at 37 degrees for 35 minutes. Samples were washed and underwent RBC lysis. Samples were washed again and resuspended in FACS buffer, then stained for CD45 prior to sorting.
5' scRNA-seq Gene Expression library + HTO/ADT library + TCR library

treatment_protocol: No treatment

value: Lung

value: Lkb1 mutant + Lifr KO


title: sgLkb1 + Isotype Control

description: Library name: G3

treatment_protocol: Isotype Control or Anti-LIF Antibody

value: KP GEMM

value: Isotype Control


title: Larval Midgut, Day 2, rep 3

description: Library name: w1118 D2 biol rep 3


title: amniotic fluid P8308-750knsp

type: genomic

city: Fuzhou

first: Xiaoqing

last: Wu

address: 18 daoshan road, Gulou district

institute: Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University

description: Hybridized to 750K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (ChAS 4.0). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: amniotic fluid P8308

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from uncultured amniotic fluid, fetal cord blood using a QIAGEN kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: amniotic fluid

tag: ultrasound abnormality

value: Increased nuchal translucency (12w); unilateral ventriculomegaly, short humerus and short femurs (23w)

tag: other clinical indications


title: Larval Midgut, Day 2, rep 2

description: Library name: w1118 D2 biol rep 2


title: amniotic fluid P506-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P506

value: Increased NT (13w)


title: Larval Midgut, Day 2, rep 1

description: Library name: w1118 D2 biol rep 1

value: Midgut


title: CrOE Rep 3

value: EVs from CRIPTO overexpressing MDA-MB-468 cells


title: sgLkb1 sgNeo (NT control)

description: Library name: G1

value: Lkb1 mutuant


title: sgLkb1 sgLif

description: Library name: G2

value: Lkb1 mutant + Lif KO


title: CrOE Rep 2


title: shCr Rep 2


title: brain, 13 dpf, rep3

description: Library name: Sample 3


title: sgLkb1 + Anti-LIF Antibody

description: Library name: G4

value: Anti-LIF


title: cord blood E2301_750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2301

value: cord blood

value: FGR


title: P. maniculatus nubiterrae replicate 1

description:
Library name: NB2
Parse Evercode WT Mega kit

value: frontal cortex

value: 3-6 months

value: male


title: MCAO mice, JU, rep3 [JU6]

city: Beijing

first: danli

last: hao

address: 16 Baixincang, Dongzhimennei

institute: China Academy of Chinese Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to GRCm38 using HISAT2.
FPKM  of each gene was calculated using Cufflinks   , and the read counts of each gene were obtained by HTSeqcount.
Differential expression analysis was performed using the DESeq (2012) R package.
q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly  differential expression.
Supplementary files format and content: mm10
Supplementary files format and content: FPKM, counts values for each Sample

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following   the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,   CA, USA) according to the manufacturer’s instructions.

value: brain

value: JU

tag: strain background

value: Kunming


title: shCon Rep 1

value: Mouse fibroblast cell line

value: EVs from control MDA-MB-468 cells


title: CrOE Rep 1


title: mettl8KO_hic

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
For ATAC-seq:Bowtie2 with ‘-very-sensitive’ option was used to map the high-quality reads to mm10 version of mice genome. The uniquely properly paired mapped reads were extracted for downstream analysis. MACS2 with the ‘-nomodel’ and ‘-extsize 147′ was used to call ATAC peaks. DESeq2 was used to identify significantly differential (FDR <=0.05) ATAC peaks between different conditions.
For cuttag:Cutadapt was used to remove low quality bases and adaptors. Clean reads were mapped to mm10 genome by using bowtie2. MACS2 was used to call cut&tag peaks with default settings. Bam2wig.py script was used to generate bigwig tracks for visualization in IGV5.
For HiC: HiC-Pro was used to perform reads alignment, quality control, and pairing reads. The h5 file was generated by using HiC-Pro. DeepLoops was applied to predict loops.
Assembly: mm10
Supplementary files format and content: bigwig and normalized coverage signal
Supplementary files format and content: h5 format contain hic information

source_name: spleen

extract_protocol:
For ATAC-seq, the extracted nuclei were re-suspended fragmented buffer including 1.5 μL transposome (novoprotein N248), and incubated at 37 oC for 30 min. For CUT&Tag, cells were sorted enriched by ConA-magnetic beads, and then incubated overnight with antibody. The next day, beads were washed and incubated with anti-rabbit secondary antibody. Then the beads were washed and incubated with proteinA/G-Tnp transposome in Chitag. Next, cells were resuspended in 100 μL Tagmentation buffer (10 mM MgCl in Chitag Buffer) and incubated at 37 °C for 1 hr. The tagmentation was terminated by adding 1 μL of 10% SDS at 55 °C for 10 min. For HiC, the sorted cells were crosslinked with 1% formaldehyde and lysed in 1 ml lysis buffer. The resulting chromatin was then digested with NUB I (NEB) restriction enzymes at at 37 °C overnight. The DNA ends were blunted and labelled with biotin by Klenow DNA polymerase, followed by ligation using T4 DNA ligase (NEB). After reverse crosslinking, DNA was fragmented by sonication.
For ATAC-seq, the products were purified with tagment DNA extract beads (novoprotein N245), and then amplified by PCR for 14 cycles with NovoNGS index kit for illumine (N239). For CUT&Tag, the DNA fragments added 1 μL spike in (Vazyme) and were extracted by DNA extract beads, then amplified by PCR for 12 cycles with TruePrep index kit for illumine. For HiC, the DNA fragments were then end-repaired and the biotinylated DNA fragments were captured using Dynabeads MyOne Streptavidin C1 beads (Invitrogen, Termo Fisher Scientifc). The DNA on beads was ligated to the Truseq adaptors and amplifed with PCR for library construction.

value: spleen

value: Mettl8 KO

value: TFH cells


title: sgLkb1 (Lkb1 Mutant KP Tumor) - GEX

description: Library name: sgLkb1

data_processing:
Gene expression together with Hashtag oligo (HTO) libraries were processed using Cell Ranger (v5.0.0) in multi mode. Cell containing droplets were selected using the default filtering from Cell Ranger. UMI count matrices were imported into the same Seurat object as separate assays. Viable cells were filtered based on having more than 200 genes detected and less than 15% of total UMIs stemming from mitochondrial transcripts. HTO counts were normalized using centered log ratio transformation before hashed samples were demultiplexing using the Seurat::HTODemux function. RNA counts were normalized using Seurat::SCTransform function with regressions of cell cycle score, ribosomal and mitochondrial percentages. Cells from multiple conditions were combined using Seurat standard scRNSeq integration workflow with 3000 anchor genes. A shared nearest neighbor graph was then built based on the first 40 principal components (PCs) followed by identification of cell clusters using Leiden algorithm and Seurat::FindClusters function at multiple resolutions in order to identify potential rare cell types. Cell types were annotated based on canonical cell type markers and differential expressed genes of each cluster identified using Seurat::FindAllMarkers function with a logistic regression model. Clusters expressing markers of the same cell type were merged into a single cluster. Cells were then projected on to a uniform manifold using the top 40 PCs for visualization.
Assembly: GRCm38
Supplementary files format and content: Seurat object

extract_protocol:
Mouse lung tissue was digested with Collagenase/DNAse in RPMI +10% FBS at 37 degrees for 35 minutes. Samples were washed and underwent RBC lysis. Samples were washed again and resuspended in FACS buffer, then stained for CD45 prior to sorting.
3' scRNA-seq 10x library +  HTO library

value: Lung

value: Lkb1 Mutant

value: gex


title: MCAO mice, JU, rep1 [JU3]


title: amniotic fluid Z18-7501knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid Z18

value: amniotic fluid

value: Ventricular septum defect; aberrant right subclavian artery; tricuspid regurgitation; polyhydramnios; single umbilical artery; pericardial effusion; ventriculomegaly


title: cord blood E2213-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2213

value: cord blood

value: Normal


title: mettl8KO1_H3K27ac

value: Abcam, ab4729


title: sgLkb1 (Lkb1 Mutant KP Tumor) - HTO

description: Library name: sgLkb1_HTO

library_source: other

molecule: protein

value: hto


title: MCAO mice, UA, rep3 [UA5]

value: brain

value: UA


title: amniotic fluid G8565-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid G8565

value: Ventricular septum defect, aortic vacular dysplasia; polyhydramnios; single umbilical artery


title: sgNeo (Lkb1 WT KP Tumor) - GEX

description: Library name: WT

value: Lkb1 Wildtype


title: mettl8KO2_H3K27ac


title: MCAO mice, JA, rep3 [JA4]

value: JA

value: Kunming


title: amniotic fluid R7819-7501knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R7819


title: amniotic fluid R8402-7501knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R8402

value: Left choroid plexus cyst, left accessory renal artery

value: Positive NIPT results


title: MCAO mice, JA, rep2 [JA2]


title: sgNeo (Lkb1 WT KP Tumor) - HTO

description: Library name: WT_HTO

value: Lung


title: Ctrl1_H3K27ac

value: spleen

value: control

value: TFH cells


title: Ctrl2_H3K27ac


title: Normal Lung - GEX

description: Library name: Healthy

value: Non-transduced GEMM

value: gex


title: Arabidopsis, 2-week-old, Col-0 rep3

city: Anseong

first: Eojin

last: Cho

address: Seodong-daero, Daedeok-myeon

department: Plant Science and Technology

country: South Korea

institute: College of Biotechnology, Chung-Ang University

description: Library name: Sample 9

data_processing:
Raw FASTQ reads were trimmed and quality-filtered
Alignment to A. thaliana TAIR10 genome was performed using Tophat2
Assembly: A. thaliana TAIR10 reference genome
Supplementary files format and content: Genome-wide RNA-seq read coverage tracks generated from paired-end BAM files using RPKM normalization (bin size = 10 bp).

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were sterilized with 1.5% bleach solution and stratified for 3 days at 4 ℃, then germinated and grown under long day condition (16-h light/8-h dark) at 22 ˚C.

extract_protocol:
RNA was harvedsted using RNeasy Plant mini kit (QIAGEN, USA) according to the manufacturer's instructions.
RNA libraries for RNA-seq werer prepared using TruSeq Stranded mRNA Library prep Kit following manufacturer's protocols.

treatment_protocol: Seedling were 2-weed old

value: seedlings

value: WT


title: MCAO mice, UA, rep1 [UA2]


title: amniotic fluid R7737-7501knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R7737

value: amniotic fluid

value: VSD


title: MCAO mice, JU, rep2 [JU5]

value: brain

value: JU


title: Ctrl_hic


title: MCAO mice, UA, rep2 [UA4]

value: UA


title: mettl8KO2_Tcf1

data_processing:
For ATAC-seq:Bowtie2 with ‘-very-sensitive’ option was used to map the high-quality reads to mm10 version of mice genome. The uniquely properly paired mapped reads were extracted for downstream analysis. MACS2 with the ‘-nomodel’ and ‘-extsize 147′ was used to call ATAC peaks. DESeq2 was used to identify significantly differential (FDR <=0.05) ATAC peaks between different conditions.
For cuttag:Cutadapt was used to remove low quality bases and adaptors. Clean reads were mapped to mm10 genome by using bowtie2. MACS2 was used to call cut&tag peaks with default settings. Bam2wig.py script was used to generate bigwig tracks for visualization in IGV5.
For HiC: HiC-Pro was used to perform reads alignment, quality control, and pairing reads. The h5 file was generated by using HiC-Pro. DeepLoops was applied to predict loops.
Assembly: mm10
Supplementary files format and content: bigwig and normalized coverage signal
Supplementary files format and content: h5 format contain hic information
Library strategy: CUT&Tag

value: Mettl8 KO

value: CST, Clone C63D9


title: Arabidopsis, 2-week-old, Col-0 rep1

description: Library name: Sample 7


title: amniotic fluid R6826-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R6826

value: Endocardial cushion defects; aberrant right subclavian artery; talipes


title: MCAO mice, vehicle, rep3 [M6]

value: Vehicle

value: Kunming


title: amniotic fluid R6987-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R6987

value: Normal

value: High-risk result from serological screening


title: MCAO mice, JA, rep1 [JA1]

value: JA


title: Arabidopsis, 2-week-old, Col-0 rep2

description: Library name: Sample 8


title: mettl8KO1_Tcf1

value: spleen

value: TFH cells


title: Normal Lung - HTO

description: Library name: Healthy_HTO

value: Lung

value: Non-transduced GEMM

value: hto


title: Arabidopsis, 2-week-old, bpc1 bpc2 double mutant rep3

description: Library name: Sample 6

value: seedlings

value: BPC1, BPC2 knockout


title: amniotic fluid R1417-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R1417

value: amniotic fluid

value: Positive NIPT results


title: amniotic fluid R3732-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R3732

value: Right choroid plexus cyst


title: Arabidopsis, 2-week-old, bpc1 bpc2 double mutant rep2

description: Library name: Sample 5


title: MCAO mice, vehicle, rep2 [M3]

source_name: brain

value: brain


title: MCAO mice, sham, rep3 [CK3]

value: Sham


title: mettl8KO2_ATAC

value: Mettl8 KO


title: amniotic fluid R787-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid E2275

value: Left duplex kidney, left hydronephrosis with ureterectasis,pericardial effusion, single umbilical artery


title: Arabidopsis, 2-week-old, bpc1 bpc2 double mutant rep1

description: Library name: Sample 4


title: mettl8KO1_ATAC


title: MCAO mice, vehicle, rep1 [M1]

value: Vehicle

value: Kunming


title: MDA MB 468, METTL3 Heterozygous Knockout, rep2

status: Public on Mar 06 2026

city: Aarhus C

first: Samir

last: Watson

state: Midtjylland

address: Universitetsbyen 83

department: Institute of Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description:
Direct RNA seq
WT_v_HKO_DRS.3_nanocompore_results.tsv.tar.gz
m6Anet.HKO.data.site_proba.csv
xpore_WT.v.HKO.majority_direction_kmer_diffmod.table.tar.gz

data_processing:
Basecalling was carried out using Guppy v4.0.11  (rna_r9.4.1_70bps_hac.cfg). With the following options --fast5_out --calib_detect--enable_trimming true --reverse_sequence --kit SQK-RNA002 --flowcell FLO-MIN106 -x cuda:all:100% -r
reads were indexed with nanopolish and reads aligned to the Gencode v33 transcriptome using the -x map-ont preset. Mapped reads were then filtered using samtools view using the -F 2324 flagstat and a minimum map quality of 10. Following this the reads were polished using nanopolish eventalign using the --scale-events and --signal-index, and--print-read-names options. Reads were mapped using minimap2 with the following options minimap2 -ax map-ont -L
Differential m6A mapping using Nanocompore v1.04 using the following parameters, logit =TRUE, min_coverage =30, bed_fn, comparison_methods= [“GMM”, “KS”, “MW”, “TT”], sequence_context=2, sequence_context_weights= ”harmonic”.
m6A mapping also carried out using m6Anet v2.0.2. data was first preprocessed using the m6anet dataprep module after which m6anet inference was ran with the number of iterations set to 1000.
Differential m6A mapping using xPore v2.0 was run with the following configuration criteria, readcount_min=15, readcount_max=1000, prefiltering method= t-test, prefiltering threshold=0.1, max_iters=500 and stopping criteria=0.00001
Assembly: hg38
Supplementary files format and content: nanocompore processed data: tab delimited. Contains p values from different comparison methods, single position context and a sequence context of 2.
Supplementary files format and content: m6Anet processed data (Both for WT and HKO): Comma delimited. Contains p values generated by m6Anet for each position on each transcript. As well as predicted modification ratios.
Supplementary files format and content: xpore processed data: Tab delimited.Output from xpore analysis pipeline. Contains xpore calculated differential modifcation rate, z score and significance from z test of siginificant differentially modified sites.

source_name: MDA MB 468

growth_protocol: All cells were grown in DMEM, 25mM Glucose supplemented with 10% FBS and 1%Pen/Strep

extract_protocol:
RNA was extracted using trizol followed by polyA purification
500ng of polyA purified RNA was used to construct Direct RNA seq libraries using the ONT SQK-RNA002 kit and sequenced on a R9.4.1 flowcell in a minion sequencing device.
Direct RNA Sequencing

value: MDA MB 468

value: breast adenocarcinoma

value: METTL3 Heterozygous knockout


title: amniotic fluid P9608-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P9608

value: Aortic valve malformation, brachiocephalic trunk and left common carotid artery open into the aortic arch


title: MCAO mice, sham, rep1 [CK1]


title: amniotic fluid R827-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R827

value: Increased prenasal thickness (22w); cleft palate, increased prenasal thickness, increased nuchal fold thickness (24w)


title: Ctrl2_ATAC

source_name: spleen

value: spleen

value: control

value: TFH cells


title: MCAO mice, sham, rep2 [CK2]


title: Ctrl1_ATAC


title: cord blood E3167-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E3167

value: cord blood

value: Normal


title: Arabidopsis, 2-week-old, bpc1 single mutant rep3

description: Library name: Sample 3

value: seedlings

value: BPC1 knockout


title: MDA MB 468, METTL3 Heterozygous Knockout, rep3


title: MDA MB 468, WT, rep3

description:
Direct RNA seq
WT_v_HKO_DRS.3_nanocompore_results.tsv.tar.gz
m6Anet.wt.data.site_proba.csv
xpore_WT.v.HKO.majority_direction_kmer_diffmod.table.tar.gz

value: WT


title: Ctrl2_Tcf1

value: CST, Clone C63D9


title: MDA MB 468, WT, rep2


title: Arabidopsis, 2-week-old, bpc1 single mutant rep1

description: Library name: Sample 1


title: MDA MB 468, METTL3 Heterozygous Knockout, rep1


title: IRE1-KO-IRE1-mNeonGreen + Tm + DOX (Rep2)

city: Redwood City

first: Altos Labs

last: Bioinformatics Hub

state: CA

address: 2600 Island Dr.

department: Institute of Technology

institute: Altos Labs

description:
Library name: Sample 35
MAT-LIBR-18540_AS_35_S35

data_processing:
Raw sequencing data were demultiplexed using bclconvert. RNA-seq FASTQ files were trimmed, aligned to the human reference genome (GRCh38, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0). Gene-level length-scaled counts were used for all downstream analyses.
Assembly: GRCh38 v108
Supplementary files format and content: salmon.merged.gene_counts_length_scaled.tsv contains gene-level length-scaled estimated counts from Salmon across all samples.
Supplementary files format and content: quant.sf files for each sample contain Salmon transcript-level quantification results.

source_name: Bone

growth_protocol: U-2 OS (ATCC HTB-96) cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1X GlutaMax (Gibco). All cell lines used in the study tested negative for Mycoplasma contamination when assayed with the Universal Mycoplasma Detection Kit.

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Miniprep Plus kit (Zymo Research) according to the manufacturer’s protocols. The yield and the integrity of RNA were determined by the spectrophotometer NanoDrop 2000.
Libraries were prepared according to the Watchmaker mRNA Library Prep Kits (Watchmaker Genomics 7BK0001-096) protocol, using 200 ng of RNA input, and sequenced on a NextSeq 2000 using XLEAP-SBS chemistry.

value: Bone

value: Female

value: U-2 OS IRE1-KO IRE1-mNeonGreen

value: Osteosarcoma

tag: induction

value: Doxycycline

value: Tunicamycin


title: IRE1-KO-IRE1-mNeonGreen + Tm + DOX (Rep3)

description:
Library name: Sample 36
MAT-LIBR-18541_AS_36_S36


title: IRE1-KO-IRE1-mNeonGreen + Tm + DOX (Rep1)

description:
Library name: Sample 34
MAT-LIBR-18539_AS_34_S34


title: IRE1-KO-IRE1-mNeonGreen + RocA + DOX (Rep2)

description:
Library name: Sample 32
MAT-LIBR-18537_AS_32_S32

value: Rocaglamide


title: MDA MB 468, WT, rep1

value: MDA MB 468

value: breast adenocarcinoma


title: IRE1-KO-IRE1-mNeonGreen + RocA + DOX (Rep3)

description:
Library name: Sample 33
MAT-LIBR-18538_AS_33_S33


title: IRE1-KO-IRE1-mNeonGreen + DMSO + DOX (Rep3)

description:
Library name: Sample 30
MAT-LIBR-18535_AS_30_S30

value: DMSO


title: IRE1-KO-IRE1-mNeonGreen + RocA + DOX (Rep1)

description:
Library name: Sample 31
MAT-LIBR-18536_AS_31_S31


title: IRE1-KO-IRE1-mNeonGreen + DMSO + DOX (Rep1)

description:
Library name: Sample 28
MAT-LIBR-18533_AS_28_S28


title: IRE1-KO-IRE1-mNeonGreen + Tm - NO DOX ADDED (Rep1)

description:
Library name: Sample 25
MAT-LIBR-18530_AS_25_S25


title: IRE1-KO-IRE1-mNeonGreen + Tm - NO DOX ADDED (Rep2)

description:
Library name: Sample 26
MAT-LIBR-18531_AS_26_S26


title: IRE1-KO-IRE1-mNeonGreen + Tm - NO DOX ADDED (Rep3)

description:
Library name: Sample 27
MAT-LIBR-18532_AS_27_S27


title: IRE1-KO-IRE1-mNeonGreen + DMSO - NO DOX ADDED (Rep1)

description:
Library name: Sample 19
MAT-LIBR-18524_AS_19_S19


title: IRE1-KO-IRE1-mNeonGreen + DMSO - NO DOX ADDED (Rep3)

description:
Library name: Sample 21
MAT-LIBR-18526_AS_21_S21


title: IRE1-KO-IRE1-mNeonGreen + RocA - NO DOX ADDED (Rep1)

description:
Library name: Sample 22
MAT-LIBR-18527_AS_22_S22


title: IRE1-KO + RocA (Rep3)

description:
Library name: Sample 15
MAT-LIBR-18520_AS_15_S15

value: U-2 OS IRE1-KO


title: IRE1-KO + RocA (Rep2)

description:
Library name: Sample 14
MAT-LIBR-18519_AS_14_S14


title: IRE1-KO + DMSO (Rep3)

description:
Library name: Sample 12
MAT-LIBR-18517_AS_12_S12


title: IRE1-KO + RocA (Rep1)

description:
Library name: Sample 13
MAT-LIBR-18518_AS_13_S13


title: WT + Tm (Rep3)

description:
Library name: Sample 9
MAT-LIBR-18514_AS_9_S9

value: U-2 OS


title: IRE1-KO + DMSO (Rep2)

description:
Library name: Sample 11
MAT-LIBR-18516_AS_11_S11


title: IRE1-KO + Tm (Rep2)

description:
Library name: Sample 17
MAT-LIBR-18522_AS_17_S17


title: IRE1-KO + Tm (Rep1)

description:
Library name: Sample 16
MAT-LIBR-18521_AS_16_S16


title: WT + RocA (Rep3)

description:
Library name: Sample 6
MAT-LIBR-18511_AS_6_S6


title: IRE1-KO-IRE1-mNeonGreen + DMSO + DOX (Rep2)

description:
Library name: Sample 29
MAT-LIBR-18534_AS_29_S29


title: WT + RocA (Rep1)

description:
Library name: Sample 4
MAT-LIBR-18509_AS_4_S4


title: WT + Tm (Rep2)

description:
Library name: Sample 8
MAT-LIBR-18513_AS_8_S8


title: WT + Tm (Rep1)

description:
Library name: Sample 7
MAT-LIBR-18512_AS_7_S7


title: WT + RocA (Rep2)

description:
Library name: Sample 5
MAT-LIBR-18510_AS_5_S5


title: IRE1-KO-IRE1-mNeonGreen + RocA - NO DOX ADDED (Rep3)

description:
Library name: Sample 24
MAT-LIBR-18529_AS_24_S24


title: WT + DMSO (Rep3)

description:
Library name: Sample 3
MAT-LIBR-18508_AS_3_S3


title: WT + DMSO (Rep1)

description:
Library name: Sample 1
MAT-LIBR-18506_AS_1_S1


title: IRE1-KO + Tm (Rep3)

description:
Library name: Sample 18
MAT-LIBR-18523_AS_18_S18


title: IRE1-KO-IRE1-mNeonGreen + RocA - NO DOX ADDED (Rep2)

description:
Library name: Sample 23
MAT-LIBR-18528_AS_23_S23


title: IRE1-KO-IRE1-mNeonGreen + DMSO - NO DOX ADDED (Rep2)

description:
Library name: Sample 20
MAT-LIBR-18525_AS_20_S20


title: snRNA-seq from adrenal gland (ENCLB499QNZ)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 2
technical replicate number: 6
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB499QNZ

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6CASTF1/J female postnatal (14 days) adrenal gland tissue nuclear fraction

value: adrenal gland

value: tissue

tag: description

value: B6/Cast F1 adrenal P14 female 2

tag: biosample encode accession

value: female

tag: dev stage

value: postnatal

value: 14 day

tag: lab

value: Ali Mortazavi, UCI

tag: subcellular fraction term name

value: nucleus

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS608STD at ENCODE; https://www.encodeproject.org/ENCBS608STD/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: WT + DMSO (Rep2)

description:
Library name: Sample 2
MAT-LIBR-18507_AS_2_S2

tag: tissue

value: Bone

value: Female

tag: cell line

tag: cell type

value: Osteosarcoma

tag: treatment


title: snRNA-seq from adrenal gland (ENCLB602JIF)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB602JIF

tag: Sex

tag: age


title: snRNA-seq from adrenal gland (ENCLB981UAK)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB981UAK


title: snRNA-seq from adrenal gland (ENCLB905XCB)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB905XCB

value: B6/Cast F1 adrenal P14 female 1

value: ENCBS829KDQ at ENCODE; https://www.encodeproject.org/ENCBS829KDQ/


title: snRNA-seq from adrenal gland (ENCLB298FCI)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB298FCI


title: snRNA-seq from adrenal gland (ENCLB354MNN)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB354MNN


title: snRNA-seq from adrenal gland (ENCLB284ONO)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB284ONO


title: snRNA-seq from adrenal gland (ENCLB779JXT)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 1
technical replicate number: 6
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB779JXT


title: snRNA-seq from layer of hippocampus (ENCLB506MGR)

description:
https://www.encodeproject.org/experiments/ENCSR983TAK/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P25 male normal 2k
experiment encode accession: ENCSR983TAK
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB506MGR
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J male postnatal (25 days) layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: B6/Cast F1 hippocampus P25 male 1

value: male

value: 25 day

value: ENCBS747PJX at ENCODE; https://www.encodeproject.org/ENCBS747PJX/


title: snRNA-seq from layer of hippocampus (ENCLB481LCB)

description:
https://www.encodeproject.org/experiments/ENCSR983TAK/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P25 male normal 2k
experiment encode accession: ENCSR983TAK
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB481LCB
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 hippocampus P25 male 2

value: postnatal

value: ENCBS929ZLW at ENCODE; https://www.encodeproject.org/ENCBS929ZLW/


title: snRNA-seq from layer of hippocampus (ENCLB463YUO)

description:
https://www.encodeproject.org/experiments/ENCSR979MRY/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P10 male ont_match 2k
experiment encode accession: ENCSR979MRY
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB463YUO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J male postnatal (10 days) layer of hippocampus tissue nuclear fraction

value: B6/Cast F1 hippocampus P10 male 1

value: 10 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS749DZM at ENCODE; https://www.encodeproject.org/ENCBS749DZM/


title: snRNA-seq from adrenal gland (ENCLB882RXT)

description:
https://www.encodeproject.org/experiments/ENCSR982GYD/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P18-20mo male normal 2k
experiment encode accession: ENCSR982GYD
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB882RXT
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J male adult (18-20 months) adrenal gland tissue nuclear fraction

value: adrenal gland

value: B6/Cast F1 adrenal P18-20mo male 2

value: adult

value: 18-20 month

value: ENCBS997ZIT at ENCODE; https://www.encodeproject.org/ENCBS997ZIT/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from adrenal gland (ENCLB164PSU)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB164PSU

value: B6/Cast F1 adrenal P14 female 2

value: female

value: 14 day

value: ENCBS608STD at ENCODE; https://www.encodeproject.org/ENCBS608STD/


title: snRNA-seq from heart (ENCLB363WWI)

description:
https://www.encodeproject.org/experiments/ENCSR975YAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P10 male normal 2k
experiment encode accession: ENCSR975YAQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB363WWI
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J male postnatal (10 days) heart tissue nuclear fraction

value: heart

value: tissue

value: B6/Cast F1 heart P10 male 1

value: male

value: postnatal

value: ENCBS052PTJ at ENCODE; https://www.encodeproject.org/ENCBS052PTJ/


title: snRNA-seq from layer of hippocampus (ENCLB259RAA)

description:
https://www.encodeproject.org/experiments/ENCSR979MRY/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P10 male ont_match 2k
experiment encode accession: ENCSR979MRY
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB259RAA
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: B6/Cast F1 hippocampus P10 male 2

value: 10 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS578PCE at ENCODE; https://www.encodeproject.org/ENCBS578PCE/


title: snRNA-seq from heart (ENCLB134RGQ)

description:
https://www.encodeproject.org/experiments/ENCSR975YAQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P10 male normal 2k
experiment encode accession: ENCSR975YAQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB134RGQ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 heart P10 male 2

value: ENCBS491RGY at ENCODE; https://www.encodeproject.org/ENCBS491RGY/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from adrenal gland (ENCLB836SOT)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB836SOT

value: adrenal gland

value: B6/Cast F1 adrenal P14 female 2

value: female

value: 14 day

value: ENCBS608STD at ENCODE; https://www.encodeproject.org/ENCBS608STD/


title: snRNA-seq from adrenal gland (ENCLB970APW)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB970APW

value: tissue

value: B6/Cast F1 adrenal P14 female 1

value: postnatal

value: ENCBS829KDQ at ENCODE; https://www.encodeproject.org/ENCBS829KDQ/


title: snRNA-seq from layer of hippocampus (ENCLB144UXB)

description:
https://www.encodeproject.org/experiments/ENCSR973WCI/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P14 female ont_match 2k
experiment encode accession: ENCSR973WCI
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB144UXB
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J female postnatal (14 days) layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: B6/Cast F1 hippocampus P14 female 2

value: ENCBS300KQE at ENCODE; https://www.encodeproject.org/ENCBS300KQE/


title: Ctrl1_Tcf1

value: spleen

tag: genotype

value: control

value: TFH cells

tag: chip antibody

value: CST, Clone C63D9


title: snRNA-seq from adrenal gland (ENCLB400DOF)

description:
https://www.encodeproject.org/experiments/ENCSR998YMP/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read B6/Cast F1 adrenal P14 female normal 12k
experiment encode accession: ENCSR998YMP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB400DOF

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from gastrocnemius (ENCLB390UOV)

description:
https://www.encodeproject.org/experiments/ENCSR974ODT/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P18-20mo female normal 1k
experiment encode accession: ENCSR974ODT
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB390UOV
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J female adult (18-20 months) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P18-20mo female 2

value: female

value: adult

value: 18-20 month

value: ENCBS743KNR at ENCODE; https://www.encodeproject.org/ENCBS743KNR/


title: snRNA-seq from gastrocnemius (ENCLB246EKZ)

description:
https://www.encodeproject.org/experiments/ENCSR974ODT/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P18-20mo female normal 1k
experiment encode accession: ENCSR974ODT
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB246EKZ
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 gastrocnemius P18-20mo female 1

value: ENCBS613QQM at ENCODE; https://www.encodeproject.org/ENCBS613QQM/


title: snRNA-seq from layer of hippocampus (ENCLB970EMO)

description:
https://www.encodeproject.org/experiments/ENCSR973WCI/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P14 female ont_match 2k
experiment encode accession: ENCSR973WCI
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB970EMO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: B6/Cast F1 hippocampus P14 female 1

value: postnatal

value: 14 day

value: ENCBS454DBZ at ENCODE; https://www.encodeproject.org/ENCBS454DBZ/


title: snRNA-seq from layer of hippocampus (ENCLB949MPH)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB949MPH

source_name: Mus musculus strain B6CASTF1/J female postnatal (36 days) layer of hippocampus tissue nuclear fraction

value: B6/Cast F1 hippocampus P36 female 2

value: 36 day

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS317KAV at ENCODE; https://www.encodeproject.org/ENCBS317KAV/


title: snRNA-seq from layer of hippocampus (ENCLB581NMZ)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB581NMZ

value: female

value: The Jackson Laboratory

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from layer of hippocampus (ENCLB849IUX)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB849IUX

value: B6/Cast F1 hippocampus P36 female 1

value: ENCBS462MCF at ENCODE; https://www.encodeproject.org/ENCBS462MCF/


title: snRNA-seq from layer of hippocampus (ENCLB668NNX)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB668NNX

value: tissue


title: snRNA-seq from layer of hippocampus (ENCLB106EUK)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB106EUK


title: snRNA-seq from gastrocnemius (ENCLB702IUX)

description:
https://www.encodeproject.org/experiments/ENCSR966QJD/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 15k
experiment encode accession: ENCSR966QJD
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB702IUX

source_name: Mus musculus strain B6CASTF1/J female postnatal (36 days) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P36 female 1

value: ENCBS865MRB at ENCODE; https://www.encodeproject.org/ENCBS865MRB/


title: snRNA-seq from gastrocnemius (ENCLB007ICU)

description:
https://www.encodeproject.org/experiments/ENCSR966QJD/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 15k
experiment encode accession: ENCSR966QJD
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB007ICU

value: B6/Cast F1 gastrocnemius P36 female 2

value: postnatal

value: ENCBS888VUS at ENCODE; https://www.encodeproject.org/ENCBS888VUS/


title: snRNA-seq from layer of hippocampus (ENCLB685EVN)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB685EVN

value: layer of hippocampus


title: snRNA-seq from gastrocnemius (ENCLB103KCU)

description:
https://www.encodeproject.org/experiments/ENCSR966QJD/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 15k
experiment encode accession: ENCSR966QJD
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB103KCU

value: 36 day


title: snRNA-seq from gastrocnemius (ENCLB568YQY)

description:
https://www.encodeproject.org/experiments/ENCSR966QJD/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 15k
experiment encode accession: ENCSR966QJD
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB568YQY

value: Ali Mortazavi, UCI


title: snRNA-seq from layer of hippocampus (ENCLB006MIO)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB006MIO

value: nucleus


title: snRNA-seq from gastrocnemius (ENCLB676XJX)

description:
https://www.encodeproject.org/experiments/ENCSR961HBK/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 1k
experiment encode accession: ENCSR961HBK
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB676XJX
nucleic acid starting quantity: 21
nucleic acid starting quantity units: cells


title: snRNA-seq from layer of hippocampus (ENCLB410KOF)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB410KOF


title: snRNA-seq from left cerebral cortex (ENCLB440WWI)

description:
https://www.encodeproject.org/experiments/ENCSR964OQW/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P25 female normal 2k
experiment encode accession: ENCSR964OQW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB440WWI
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J female postnatal (25 days) left cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: B6/Cast F1 cortex P25 female 1

value: 25 day

value: ENCBS920SFB at ENCODE; https://www.encodeproject.org/ENCBS920SFB/


title: snRNA-seq from layer of hippocampus (ENCLB685RWW)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB685RWW

value: B6/Cast F1 hippocampus P36 female 2

value: female

value: The Jackson Laboratory

value: ENCBS317KAV at ENCODE; https://www.encodeproject.org/ENCBS317KAV/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from gastrocnemius (ENCLB533ZGL)

description:
https://www.encodeproject.org/experiments/ENCSR961HBK/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P36 female normal 1k
experiment encode accession: ENCSR961HBK
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB533ZGL
nucleic acid starting quantity: 21
nucleic acid starting quantity units: cells

value: gastrocnemius

value: tissue


title: snRNA-seq from layer of hippocampus (ENCLB722QCL)

description:
https://www.encodeproject.org/experiments/ENCSR967YET/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 hippocampus P36 female normal 12k
experiment encode accession: ENCSR967YET
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB722QCL

value: B6/Cast F1 hippocampus P36 female 1

value: postnatal

value: ENCBS462MCF at ENCODE; https://www.encodeproject.org/ENCBS462MCF/


title: snRNA-seq from layer of hippocampus (ENCLB983GFA)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 1
technical replicate number: 6
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB983GFA

source_name: Mus musculus strain 5xFAD/CAST female adult (8 months) layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: 5xFAD/Cast F1 hippocampus P8mo female 1

value: adult

value: 8 month

value: ENCBS024SIK at ENCODE; https://www.encodeproject.org/ENCBS024SIK/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: snRNA-seq from adrenal gland (ENCLB260YXF)

description:
https://www.encodeproject.org/experiments/ENCSR950SIX/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P2mo female normal 2k
experiment encode accession: ENCSR950SIX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB260YXF
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) adrenal gland tissue nuclear fraction

value: adrenal gland

value: B6/Cast F1 adrenal P2mo female 2

value: 2 month

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS266BTE at ENCODE; https://www.encodeproject.org/ENCBS266BTE/


title: snRNA-seq from left cerebral cortex (ENCLB156QHU)

description:
https://www.encodeproject.org/experiments/ENCSR964OQW/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P25 female normal 2k
experiment encode accession: ENCSR964OQW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB156QHU
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: left cerebral cortex

value: B6/Cast F1 cortex P25 female 2

value: female

value: 25 day

value: The Jackson Laboratory

value: ENCBS038OUJ at ENCODE; https://www.encodeproject.org/ENCBS038OUJ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snRNA-seq from layer of hippocampus (ENCLB930DSB)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB930DSB

value: layer of hippocampus

value: tissue

value: 5xFAD/Cast F1 hippocampus P8mo female 1

value: adult


title: snRNA-seq from layer of hippocampus (ENCLB569WKO)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB569WKO

value: 8 month

value: ENCBS024SIK at ENCODE; https://www.encodeproject.org/ENCBS024SIK/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: snRNA-seq from adrenal gland (ENCLB755SWT)

description:
https://www.encodeproject.org/experiments/ENCSR950SIX/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P2mo female normal 2k
experiment encode accession: ENCSR950SIX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB755SWT
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: B6/Cast F1 adrenal P2mo female 1

value: 2 month

value: Ali Mortazavi, UCI

value: ENCBS194GJK at ENCODE; https://www.encodeproject.org/ENCBS194GJK/


title: snRNA-seq from layer of hippocampus (ENCLB823CQQ)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB823CQQ

value: 5xFAD/Cast F1 hippocampus P8mo female 2

value: female

value: nucleus

value: ENCBS850WBJ at ENCODE; https://www.encodeproject.org/ENCBS850WBJ/


title: snRNA-seq from layer of hippocampus (ENCLB491UKP)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB491UKP

value: The Jackson Laboratory


title: snRNA-seq from layer of hippocampus (ENCLB179IST)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB179IST

value: layer of hippocampus


title: snRNA-seq from layer of hippocampus (ENCLB759XXA)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB759XXA

value: tissue


title: snRNA-seq from layer of hippocampus (ENCLB546OWV)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB546OWV

value: 5xFAD/Cast F1 hippocampus P8mo female 1


title: IRE1-KO + DMSO (Rep1)

description:
Library name: Sample 10
MAT-LIBR-18515_AS_10_S10

value: Bone

value: Female

value: U-2 OS IRE1-KO

value: Osteosarcoma

value: DMSO


title: snRNA-seq from adrenal gland (ENCLB174YPQ)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 2
technical replicate number: 6
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB174YPQ

source_name: Mus musculus strain 5xFAD/CAST male adult (8 months) adrenal gland tissue nuclear fraction

value: adrenal gland

value: 5xFAD/Cast F1 adrenal P8mo male 2

value: male

value: adult

value: 8 month

value: ENCBS818LDL at ENCODE; https://www.encodeproject.org/ENCBS818LDL/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: snRNA-seq from adrenal gland (ENCLB805ZPV)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB805ZPV

value: Ali Mortazavi, UCI

value: nucleus


title: snRNA-seq from layer of hippocampus (ENCLB136ANA)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB136ANA

value: layer of hippocampus

value: female

value: The Jackson Laboratory

value: ENCBS024SIK at ENCODE; https://www.encodeproject.org/ENCBS024SIK/


title: snRNA-seq from layer of hippocampus (ENCLB520ZCC)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB520ZCC

value: tissue

value: 5xFAD/Cast F1 hippocampus P8mo female 2

value: ENCBS850WBJ at ENCODE; https://www.encodeproject.org/ENCBS850WBJ/


title: snRNA-seq from adrenal gland (ENCLB668YGF)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB668YGF


title: snRNA-seq from layer of hippocampus (ENCLB764EAJ)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 2
technical replicate number: 6
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB764EAJ


title: snRNA-seq from adrenal gland (ENCLB318KTQ)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB318KTQ


title: snRNA-seq from adrenal gland (ENCLB055MEO)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB055MEO

value: 5xFAD/Cast F1 adrenal P8mo male 1

value: ENCBS807DYE at ENCODE; https://www.encodeproject.org/ENCBS807DYE/


title: snRNA-seq from layer of hippocampus (ENCLB954IWI)

description:
https://www.encodeproject.org/experiments/ENCSR944KUB/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read 5xFAD/Cast F1 hippocampus P8mo female 8mo 12k
experiment encode accession: ENCSR944KUB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB954IWI


title: snRNA-seq from adrenal gland (ENCLB358MQM)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB358MQM

value: adrenal gland

value: 5xFAD/Cast F1 adrenal P8mo male 2


title: snRNA-seq from adrenal gland (ENCLB645KPT)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 1
technical replicate number: 6
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB645KPT

value: male

value: adult


title: snRNA-seq from adrenal gland (ENCLB416OOA)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB416OOA

value: 8 month


title: snRNA-seq from adrenal gland (ENCLB996GNY)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB996GNY

value: ENCBS818LDL at ENCODE; https://www.encodeproject.org/ENCBS818LDL/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: snRNA-seq from adrenal gland (ENCLB737CIY)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB737CIY

value: Ali Mortazavi, UCI

value: nucleus


title: snRNA-seq from adrenal gland (ENCLB721WTE)

description:
https://www.encodeproject.org/experiments/ENCSR943REW/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read 5xFAD/Cast F1 adrenal P8mo male 8mo 12k
experiment encode accession: ENCSR943REW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB721WTE


title: snRNA-seq from layer of hippocampus (ENCLB572DYH)

description:
https://www.encodeproject.org/experiments/ENCSR940VCU/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 hippocampus P36 male normal 12k
experiment encode accession: ENCSR940VCU
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB572DYH

source_name: Mus musculus strain B6CASTF1/J male postnatal (36 days) layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: B6/Cast F1 hippocampus P36 male 2

value: postnatal

value: 36 day

value: ENCBS373BVD at ENCODE; https://www.encodeproject.org/ENCBS373BVD/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/