title: shnat10-2

first: Ji

last: Wu

address: No.800, Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: shnat10-2-L

data_processing:
Cutadapt used for triming reads. It can bin reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
normalization and differential expression analysis with DESeq2 to calculate fold-changes and p-values between sample groups.
Assembly: MM10
Supplementary files format and content: Tab-delimited text files include the number of reads, relative RPKM values, and P-values for control and experimental group Sample.

source_name: Ovary

extract_protocol:
Total RNA was extracted from shnc and shnat10 FGSCs using Trizol reagent (Life Technologies, CA). Next, 1000 ng of the digested RNA was used for the VAHTSTM mRNA-seqv2 Library Prep kit for Illumina1, and sequencing libraries were created according to the manufacturer's protocol.
The extracted further treated with DNase to remove genomic DNA contamination. Isolation of mRNA was performed using the Oligotex mRNA Mini Kit (Qiagen GmbH, Hilden, Germany) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.

value: Ovary

value: FGSCs

value: germ stem cells

tag: genotype

value: shnat10 group


title: P6201_dpa002

status: Public on Jun 18 2026

type: SRA

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

country: USA

institute: UCLA

description: Library name: P6201

library_source: genomic

data_processing:
Illumina adapter sequences were trimmed off from the raw reads using Cutadapt and only reads with minimum 30bp were kept for downstream analysis.  Trimmed reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function.  CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 20 -min-sample 1.0.
Assembly: GRCh38
Supplementary files format and content: tab-separated file of methylation levels per CpG locus (row) for all samples (column)

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Genomic DNA was extracted from PBMCs using phenol-chloroform method.
500ng genomic DNA was sheared and subject to end-repair, A-tailing and ligated with methylated adaptors.  Purified libraries were hybridized to biotinylated probes and subjected for bisulfite conversion (Zymo Cat# D5030).  Captured DNA was PCR amplified with KAPA HiFi HotStart Uracil+ (Cat# KK2801) into a final TBS-seq library.  Library quality was evaluated using TapeStation with the high-sensitivity D1000 tape (Agilent Cat# 5067- 5584).

tag: tissue

value: Blood

tag: cell type

value: PBMC

tag: Sex

value: Male

tag: age

tag: trajectory group

tag: days post_admission


title: shnat10-1

city: Shanghai

country: China

description: Library name: shnat10-1-L

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line


title: P6501_dpa005

description: Library name: P6501

value: Female


title: P6104_dpa024

description: Library name: P6104


title: shnc-2

description: Library name: shnc-2-L

value: shnc group


title: shnc-1

description: Library name: shnc-1-L


title: P6103_dpa024

description: Library name: P6103


title: P6204_dpa212

description: Library name: P6204


title: P6102_dpa003

description: Library name: P6102


title: GBM154 p300

city: Austin

first: Gaspar

last: Kitange

address: 16th Avenue NE

institute: University of Minnesota

data_processing:
Data were analyzed by the HiChIP pipeline (PMID: 25128017)
Reads were mapped to the hg19 reference genome using BWA v0.7.10).Pairs with at least one of the ends being Uniquely mapped were extracted.
Duplicates were removed using Picard (https://broadinstitute.github.io/picard/).
Peaks were identified using MACS v2.0.10.
Reads-per-million signal tracks (tdf files) were generated using Bedtools "genomeCoverageBed" command and igvtools "toTDF" command with 200bp window size and a step size of 20bp.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited encodePeak files include peaks; tdf files include count-per-million signals.

source_name: glioblastoma cells

growth_protocol: Flank PDX tumors were harvested and minced to form a tumor mash, which was then suspended in Dulbecco’s Modified Eagles Media (DMEM) supplemented with 10%FBS/1% penicillin-streptomycin antibiotics (complete DMEM) and plated in culture flasks following by incubation in a humidified incubator at 37°C and 5% CO2 conditions.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared from 10 ng of ChIP and input DNAs with the Ovation Ultralow DR Multiplex system (NuGEN, San Carlos, CA). The ChIP-seq libraries were sequenced to 51 base pairs from both ends using the Illumina HiSeq 2000 (Illumina) at Mayo Clinic Medical Genome Core.

treatment_protocol: Gene silencing by shRNA

tag: cell line/genotype

value: Primary culture

tag: source type

value: Patient derived Xenograft

tag: chip antibody

value: p300 Active Motif (mouse)


title: P6003_dpa191

description: Library name: P6003


title: P6101_dpa003

description: Library name: P6101


title: GBM154 Input


title: P6002_dpa023

description: Library name: P6002


title: GBM44 p300


title: T24 cells, siNC-3

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

description:
Library name: sample3
Column name in All.fpkm_anno.txt: NC-3

data_processing:
Raw sequencing reads were quality-filtered using Cutadapt (version 2.6). Cleaned reads were aligned to the Homo sapiens reference genome (GRCh38, NCBI) with subsequent quantification of exonic reads mapped to annotated genes using Hisat2(v2.2.1).
Assembly: GRCh38
Supplementary files format and content: .txt file includes raw counts and FPKM values for each Sample

growth_protocol: T24 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods. A total of 2 μg of high-quality RNA was used for the construction of sequencing libraries.
VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech, cat. NO NR60502) following the manufacturer’s instruction

value: bladder cancer cell

value: WT

tag: treatment

tag: batch


title: P6001_dpa002

description: Library name: P6001


title: GBM44 RBBP4

value: RBBP4 Epigentek (rabbit)


title: P5902_dpa195

description: Library name: P5902


title: P7501_dpa003

description: Library name: P7501


title: P7402_dpa023

description: Library name: P7402


title: GBM44 Input


title: P7401_dpa004

description: Library name: P7401


title: P7301_dpa002

description: Library name: P7301


title: P5901_dpa002

description: Library name: P5901


title: P5802_dpa369

description: Library name: P5802


title: GBM43shp300 H3K27Ac


title: GBM43shp300 input


title: GBM43shp300 H3K9Ac


title: P5801_dpa001

description: Library name: P5801


title: P5703_dpa109

description: Library name: P5703


title: GBM43shRBBP4 H3K27Ac


title: P5702_dpa016

description: Library name: P5702


title: GBM43shRBBP4 H3K9Ac


title: P5701_dpa002

description: Library name: P5701


title: P5603_dpa155

description: Library name: P5603


title: GBM43shRBBP4 input


title: GBM43shNT H3K27Ac


title: P5602_dpa010

description: Library name: P5602


title: GBM43shNT H3K9Ac


title: GBM43shNT input


title: P5601_dpa003

description: Library name: P5601


title: RNA sequencing of sample B3

city: Hefei

first: Mingzhao

last: Zhang

state: Anhui

address: Jixi Rd

institute: The First Affiliated Hospital of Anhui Medical University

description: Library name: B3

data_processing:
Raw reads were quality filtered and aligned to the mouse reference genome (GRCm39, Release 109) using HISAT2.
Gene expression levels were normalized as FPKM values.
Differential expression analysis was performed using DESeq2 based on raw read counts.
Assembly: Mus musculus GRCm39 release-109
Supplementary files format and content: featureCounts_merged_count.annot.tsv
Supplementary files format and content: DESeq2_norm_counts.tsv
Supplementary files format and content: fpkm_merged_count.annot.tsv
Supplementary files format and content: B-vs-A_diffexp.DEG.xls

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's instructions.
Poly(A)+ RNA was enriched from total RNA and used for cDNA library construction according to the TruSeq RNA Sample Preparation Guide. Libraries were quality assessed using a Qubit 2.0 Fluorometer and an Agilent 2100 Bioanalyzer and sequenced on the Illumina HiSeq platform in paired-end mode.

value: macrophage

value: hypoxia-preconditioned tendon stem cell-derived EVs


title: P6801_dpa002

description: Library name: P6801


title: P5503_dpa390

description: Library name: P5503


title: P5502_dpa048

description: Library name: P5502


title: RNA sequencing of sample B2

description: Library name: B2


title: P5501_dpa002

description: Library name: P5501


title: RNA sequencing of sample B1

description: Library name: B1


title: P5403_dpa093

description: Library name: P5403


title: RNA sequencing of sample A3

description: Library name: A3

value: normoxic-preconditioned tendon stem cell-derived EVs


title: RNA sequencing of sample A2

description: Library name: A2


title: P5402_dpa044

description: Library name: P5402


title: RNA sequencing of sample A1

description: Library name: A1


title: P5401_dpa002

description: Library name: P5401


title: EDL, high fat diet (HFD)-fed mouse with imeglimin administration (HFD-Ime) rep5

city: Tokyo

first: Motoharu

last: Awazawa

state: - Select State/Region -

address: 1-21-1, Toyama, Shinjuku-ku

country: Japan

institute: Research Institutte, National Center for Global Health and Medicine (NCGM)

description: Library name: EDL_89

data_processing:
Quality check for sequence reads were performed using FastQC version 0.11.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic version 0.38 with LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36 as command option
Trimmed sequence reads were mapped using HISAT2 version 2.1.0
Raw read counts were determined using featureCounts version 1.6.3
TPM was calculated based on raw read counts
Assembly: mm10(Mouse)
Supplementary files format and content: tab-delimited text file includes TPM for each sample

source_name: extensor digitorum longus muscle

extract_protocol:
Total RNA was isolated from the EDL using TRIZOL reagent (Invitrogen), followed by column purification with FavorPrep Tissue Total RNA Mini Kit (FAVORGEN).
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module for PolyA selection and NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina for strand specific library follwing manufacturer's protocols.

value: extensor digitorum longus muscle

tag: strain

value: male


title: P5301_dpa002

description: Library name: P5301


title: VCaP_DMSO_BRD4

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

description: Library name: SI_41275

data_processing:
ChIP-seq reads were trimmed using Trimmomatic (v0.39, settings TruSeq3-PE-2.fa:2:30:10, minlen 50). Alignment was then performed separately to both the human genome (hg38) and the drosophila genome (dm6) using BWA (v0.7.17 “bwa mem”, options -5S -T0, version 0.7.17-r1198-dirty). Low-quality and duplicate reads were filtered with SAMtools and Picard, respectively. Normalization ratios were calculated based on the lowest amount of uniquely aligned reads per ChIP target to each genome as reccomended in ActiveMotifs protocols. Reads were then downsampled per the normalization ratios. P300 Samples did not have this normalization step. Then peak calling was performed with MACS2 using narrow or broad settings depending on the target, and blacklisted genomic regions were removed using BEDTools with the ENCODE exclusion list. MACS was run with a bam vcap IgG control. Processed data were converted to BigWig format using UCSC wigToBigWig for visualization. Read density heatmaps and average enrichment profiles were generated using deepTools. For histone marks, signals were plotted within ±2.5 kb of the reference point, and for other transcriptome factors within ±1 kb. The parameters --skipZeros, --averageType mean, and --plotType se were applied. ENCODE blacklist regions (ENCFF356LFX) were excluded from analysis.
Assembly: hg38
Supplementary files format and content: .bed: peak locations from macs bed calling with blacklist removed; .bw: signal files

source_name: VCaP

growth_protocol: VCaP cells were maintained in DMEM GlutaMAX supplemented with 10% FBS (Thermo Fisher Scientific).

extract_protocol:
In brief, cells were crosslinked in 1% formaldehyde, quenched with glycine, and lysed for chromatin extraction. Chromatin was sheared to 200–600 bp fragments using a Bioruptor (Diagenode) and subjected to immunoprecipitation with antibodies against transcription factors (AR, FOXA1, p300, ERG and BRD4) or histone marks (H3K27ac, H2BK20ac, and RNA Pol II) using the iDeal ChIP-seq Kit (Diagenode). Drosophila spike-in chromatin (Active Motif, 53083) and spike-in antibody (Active Motif, 61686) were added during the overnight incubation. After reverse crosslinking and DNA purification, sequencing libraries were prepared and sequenced on an Illumina HiSeq 2500 platform.
ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: The cells were treated with 100 nM DALTAC-1 or p300i+ARi for 1 and 3 hours

value: VCaP

value: prostate cancer

value: DMSO


title: P5202_dpa009

description: Library name: P5202

value: Blood

value: PBMC


title: EDL, high fat diet (HFD)-fed mouse with imeglimin administration (HFD-Ime) rep4

description: Library name: EDL_88


title: P5201_dpa006

description: Library name: P5201

value: Female


title: EDL, high fat diet (HFD)-fed mouse with imeglimin administration (HFD-Ime) rep3

description: Library name: EDL_87


title: EDL, high fat diet (HFD)-fed mouse with imeglimin administration (HFD-Ime) rep2

description: Library name: EDL_86


title: P5103_dpa008

description: Library name: P5103

value: Male


title: P5102_dpa008

description: Library name: P5102


title: P5101_dpa008

description: Library name: P5101


title: EDL, high fat diet (HFD)-fed mouse with imeglimin administration (HFD-Ime) rep1

description: Library name: EDL_85


title: EDL, high fat diet (HFD)-fed mouse (HFD) rep5

description: Library name: EDL_79


title: P5002_dpa032

description: Library name: P5002


title: EDL, high fat diet (HFD)-fed mouse (HFD) rep4

description: Library name: EDL_78


title: P5001_dpa007

description: Library name: P5001


title: EDL, high fat diet (HFD)-fed mouse (HFD) rep3

description: Library name: EDL_77


title: P4903_dpa141

description: Library name: P4903


title: EDL, high fat diet (HFD)-fed mouse (HFD) rep2

description: Library name: EDL_76


title: P4902_dpa008

description: Library name: P4902


title: EDL, high fat diet (HFD)-fed mouse (HFD) rep1

description: Library name: EDL_75


title: P4901_dpa002

description: Library name: P4901


title: VCaP_100nM_DALTAC_1_12hr_Rep2

description: Library name: SI_40723

data_processing:
Alignment was  performed using kalliso (v0.46.1) quant to human (hg38/GRCh38) reference (Homo_sapiens.GRCh38.96.gtf gene reference). Read counts were adjusted for normalization then filtered in R via package EdgeR. Package Limma-Voom (vlimma_3.53.10) was involved for differential expression analysis. GSEA analysis and corresponding heatmaps and figures were created using R package fgsea (vfgsea_1.24.0), ComplexHeatmap and ggplot2.
Assembly: hg38
Supplementary files format and content: Counts Matrix

extract_protocol:
Total RNA was extracted from cells using QIAzol Lysis Reagent (QIAGEN). Initially, 1x10^6 cells were lysed with 700 µL of QIAzol. The lysates were incubated at room temperature for 5 minutes to dissociate nucleoproteins, then mixed with 140 µL chloroform and centrifuged at 12,000 g for 15 minutes at 4°C to achieve phase separation. The aqueous phase was then mixed with 1.5x volume of ethanol and applied to a RNeasy Mini spin column (QIAGEN) for RNA purification, following the miRNeasy Mini Kit protocol. The RNA was then eluted in RNase-free water, and its concentration and purity assessed using a NanoDrop spectrophotometer.
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. PolyA+ RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2 × 100 nucleotide read length) with sequence coverage to 15–20M paired reads.

treatment_protocol: The cells were treated with 100 nM DALTAC-1 or p300i+ARi for 4, 12 and 24 hours


title: P4802_dpa014

description: Library name: P4802


title: EDL, normal chow diet (NCD)-fed lean control mouse (NCD) rep4

description: Library name: EDL_68


title: EDL, normal chow diet (NCD)-fed lean control mouse (NCD) rep5

description: Library name: EDL_69


title: P4801_dpa002

description: Library name: P4801


title: EDL, normal chow diet (NCD)-fed lean control mouse (NCD) rep3

description: Library name: EDL_67


title: P4702_dpa198

description: Library name: P4702


title: EDL, normal chow diet (NCD)-fed lean control mouse (NCD) rep2

description: Library name: EDL_66


title: P4701_dpa001

description: Library name: P4701


title: EDL, normal chow diet (NCD)-fed lean control mouse (NCD) rep1

description: Library name: EDL_65


title: P4603_dpa081

description: Library name: P4603


title: mice, heart, male, hom, rep6

city: Turku

first: Pekka

last: Taimen

address: Kiinanmyllynkatu 10D

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description: Library name: Lmna S143P/S143P M 58

data_processing:
quality control and preprocessing, trimming minimum 35bp length
alignment with GRCm38.94 mouse reference genome
data filtered with, normalized
Assembly: alignment with GRCm38.94 mouse reference genome
Supplementary files format and content: LMNA-raw_countdata_final_Males.txt

source_name: moce heart tissue

extract_protocol:
mRNA isolation from tissue extracted from left ventricle of mouse heart
Ilumina TruSeq stranded RNA-seq libraries

value: moce heart tissue

value: homozygous, male


title: P4602_dpa016

description: Library name: P4602


title: mice, heart, male, hom, rep5

description: Library name: Lmna S143P/S143P M 56

source_name: mice heart tissue

value: mice heart tissue


title: P4601_dpa005

description: Library name: P4601


title: mice, heart, male, hom, rep4

description: Library name: Lmna S143P/S143P M 55


title: P4503_dpa370

description: Library name: P4503


title: mice, heart, male, hom, rep3

description: Library name: Lmna S143P/S143P M 54


title: P4502_dpa005

description: Library name: P4502


title: mice, heart, male, hom, rep2

description: Library name: Lmna S143P/S143P M 53


title: P4501_dpa001

description: Library name: P4501


title: mice, heart, male, hom, rep1

description: Library name: Lmna S143P/S143P M 52


title: mice, heart, male, hez, rep6

description: Library name: Lmna WT/S143P M 51

value: heterozygous, male


title: P4403_dpa442

description: Library name: P4403


title: P4402_dpa017

description: Library name: P4402


title: mice, heart, male, hez, rep5

description: Library name: Lmna WT/S143P M 48


title: P4401_dpa006

description: Library name: P4401


title: P4302_dpa009

description: Library name: P4302


title: mice, heart, male, hez, rep3

description: Library name: Lmna WT/S143P M 45


title: mice, heart, male, hez, rep4

description: Library name: Lmna WT/S143P M 46


title: P4301_dpa002

description: Library name: P4301


title: mice, heart, male, hez, rep2

description: Library name: Lmna WT/S143P M 44


title: P4203_dpa187

description: Library name: P4203


title: P4202_dpa007

description: Library name: P4202


title: HeLa PR-3

city: Guangzhou

first: Li

last: Yuan

address: 58, Zhongshan 2nd road

institute: sun yat-sen university

description: Library name: Sample 3

data_processing:
The libraries were quality controlled with Agilent 2200 and sequenced by  Illumina NovaSeq 6000 on a 150 bp paired-end run.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to genome using the Hisat2.
HTseq was used to get gene expression.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HeLa cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qjagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

value: HeLa cells

value: cervical cancer cells

value: parental conteraparts


title: mice, heart, male, hez, rep1

description: Library name: Lmna WT/S143P M 43


title: mice, heart, male, wt, rep6

description: Library name: Lmna WT/WT M 40

value: wild-type, male


title: P4201_dpa001

description: Library name: P4201


title: mice, heart, male, wt, rep5

description: Library name: Lmna WT/WT M 39


title: mice, heart, male, wt, rep4

description: Library name: Lmna WT/WT M 38


title: P4102_dpa015

description: Library name: P4102


title: P4103_dpa114

description: Library name: P4103


title: mice, heart, male, wt, rep3

description: Library name: Lmna WT/WT M 36


title: P4101_dpa005

description: Library name: P4101


title: mice, heart, male, wt, rep2

description: Library name: Lmna WT/WT M 35


title: P4003_dpa193

description: Library name: P4003


title: KMR46, STING1 KO, Dox 3

city: Hershey

first: Yoshinori

last: Takahashi

state: PA

address: 500 University DR., Rm C7814B

department: Pediatrics

institute: Penn State College of Medicine

description: Library name: F3

data_processing:
Raw FASTQ reads were processed with FASTQ software to remove adapter sequences, reads containing poly-N, and low-quality reads.
The trimmed FASTQ files were aligned to the Mus musculus reference genome (mm10) using HISAT2 (v2.0.5), and gene-level read counts were obtained with featureCounts (v1.5.0-p3).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing raw read counts.

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% v/v FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA samples were extracted using RNeasy Plus Mini Kit (Qiagen).
cDNA libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Cells were treated with 1 µg/mL Dox for 10 h.

value: STING1 KO

value: Dox (DN-VPS4)


title: P4002_dpa010

description: Library name: P4002


title: P4001_dpa003

description: Library name: P4001


title: mice, heart, male, wt, rep1

description: Library name: Lmna WT/WT M 31


title: KMR46, STING1 KO, Dox 2

description: Library name: F2


title: KMR46, STING1 KO, Dox 1

description: Library name: F1


title: P3903_dpa093

description: Library name: P3903


title: KMR46, IRF3 KO, Dox 3

description: Library name: E3

value: IRF3 KO


title: P3902_dpa004

description: Library name: P3902


title: P3901_dpa002

description: Library name: P3901


title: KMR46, IRF3 KO, Dox 2

description: Library name: E2


title: P3801_dpa009

description: Library name: P3801


title: KMR46, IRF3 KO, Dox 1

description: Library name: E1


title: P3702_dpa023

description: Library name: P3702


title: P3701_dpa006

description: Library name: P3701


title: KMR46, WT, Dox 3

description: Library name: D3

value: WT


title: KMR46, WT, Dox 2

description: Library name: D2


title: P3601_dpa002

description: Library name: P3601


title: P3602_dpa103

description: Library name: P3602


title: KMR46, STING1 KO, DMSO 3

description: Library name: C3


title: KMR46, WT, Dox 1

description: Library name: D1


title: P3503_dpa110

description: Library name: P3503


title: GBM154 RBBP4

value: Primary culture

value: Patient derived Xenograft

value: RBBP4 Epigentek (rabbit)


title: KMR46, STING1 KO, DMSO 2

description: Library name: C2


title: KMR46, STING1 KO, DMSO 1

description: Library name: C1


title: P3501_dpa002

description: Library name: P3501

value: Blood

value: PBMC


title: P3502_dpa008

description: Library name: P3502

value: Male


title: KMR46, IRF3 KO, DMSO 3

description: Library name: B3


title: P3402_dpa374

description: Library name: P3402

value: Female


title: KMR46, IRF3 KO, DMSO 2

description: Library name: B2


title: P3401_dpa001

description: Library name: P3401


title: KMR46, IRF3 KO, DMSO 1

description: Library name: B1


title: P3302_dpa348

description: Library name: P3302


title: P3301_dpa007

description: Library name: P3301


title: KMR46, WT, DMSO 2

description: Library name: A2


title: TPC-1-Len replicate 3

first: jun

middle: Yun

last: Wang

address: Fudan University Shanghai Cancer Center, 270 Dong'an Road, Xuhui District, Shanghai, China

department: Head and Neck Surgery

institute: Fudan University Shanghai Cancer Center

description: Library name: tpc_lenv_res3

data_processing:
aw sequencing reads were filtered to remove low-quality reads and adapter sequences.
Assembly: GRCh38
Supplementary files format and content: A tab-delimited text file containing a matrix of raw, un-normalized integer counts. Rows correspond to genes, identified by gene symbols, and columns correspond to the samples listed above.

source_name: thyroid epithelial

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10 % fetal bovine serum and 1 % penicillin-streptomycin at 37 °C with 5 % CO₂.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Thermo Fisher, 15596026) following the manufacturer’s instructions. RNA integrity (RIN ≥ 8) was confirmed with Agilent 2100 Bioanalyzer.
Poly(A)-selected stranded mRNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) according to the vendor’s protocol.

treatment_protocol: Lenvatinib-resistant sub-line (TPC-1-Len) was generated by continuous exposure to 6 µM lenvatinib for >3 months; parental TPC-1 cells were maintained drug-free. No drug was present during RNA harvest.

value: thyroid epithelial

value: papillary thyroid carcinoma cell line


title: P3202_dpa024

description: Library name: P3202


title: KMR46, WT, DMSO 3

description: Library name: A3


title: KMR46, WT, DMSO 1

description: Library name: A1


title: P3102_dpa015

description: Library name: P3102


title: KMR46, GFP, Dox 3

description: Library name: R3

value: Dox (GFP)


title: P3201_dpa002

description: Library name: P3201


title: KMR46, GFP, Dox 2

description: Library name: R2


title: P3101_dpa002

description: Library name: P3101


title: KMR46, GFP, Dox 1

description: Library name: R1


title: P3002_dpa269

description: Library name: P3002


title: KMR46, GFP-DN-VPS4A, Dox 3

description: Library name: P3


title: KMR46, GFP-DN-VPS4A, Dox 2

description: Library name: P2


title: P2802_dpa305

description: Library name: P2802


title: P3001_dpa002

description: Library name: P3001


title: KMR46, GFP-DN-VPS4A, Dox 1

description: Library name: P1


title: KMR19, GFP, Dox 3

description: Library name: L3


title: P2801_dpa001

description: Library name: P2801


title: KMR19, GFP, Dox 2

description: Library name: L2


title: P2901_dpa002

description: Library name: P2901


title: P2701_dpa008

description: Library name: P2701


title: KMR19, GFP, Dox 1

description: Library name: L1


title: P2602_dpa007

description: Library name: P2602


title: KMR19, GFP-DN-VPS4A, Dox 3

description: Library name: J3

value: Dox (GFP-DN-VPS4)


title: P2601_dpa001

description: Library name: P2601


title: KMR19, GFP-DN-VPS4A, Dox 2

description: Library name: J2


title: P2504_dpa187

description: Library name: P2504


title: P2503_dpa041

description: Library name: P2503


title: Ethanol + LPS Mouse Liver Resident Immune Cells Sample 3

city: Rochester

first: Vijay

middle: H

last: Shah

state: MN

address: 200 First Street SW, Guggenheim Building 10th Floor

institute: Mayo Clinic

description:
Library name: EL3
10X Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v6.1) was used for alignment and gene counting (32).
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5

molecule: cytoplasmic RNA

source_name: Liver Resident Immune Cells

extract_protocol:
Liver and peripheral blood were harvested at sacrifice. For single-cell RNA sequencing (scRNA-seq), liver perfusion was performed via the portal vein using established protocols. Hepatic mononuclear cells were isolated by Percoll gradient centrifugation and enriched for CD45⁺ immune cells using magnetic-activated cell sorting (MACS; Miltenyi Biotec, Cat#130-052-301). LSEC enrichment was performed on CD45- fraction with CD146+ MACS beads (Miltenyi Biotec, Cat#130-092-007). CD45+ immune cells and LSECs were sorted by flow cytometry cell sorting for CD45+ or CD146+ cells (BD Biosciences FACS Aria III cell sorter). Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll gradient centrifugation from heparinized blood, then sorted for CD45+ cells on the same cell sorter. For intrahepatic cytometry experiments, liver perfusion, Percoll gradient centrifugation, and MACS beads enrichment steps are as described above. Enriched CD45+ cells were then processed for flow cytometry staining as described below.
90,000 CD45⁺ immune cells and 10,000 sorted liver sinusoidal endothelial cells (LSECs) were combined and processed using the 10x Genomics Chromium platform following manufacturer’s protocols. Single-cell suspensions were subjected to library preparation and sequencing at the Mayo Clinic Genomic Core.

treatment_protocol: Wild-type C57BL/6 mice (10 weeks old; Charles River Laboratories) were acclimated for 5 days to a Lieber-DeCarli liquid diet. Mice were then fed either 5% (v/v) ethanol diet (Bio-Serv, Cat#F1258) or isocaloric pair-fed control diet (Bio-Serv, Cat#F1259). On day 11, mice received a single oral gavage of ethanol (5 g/kg; ethanol group) or maltose dextran (control group). Alcohol-fed mice also received intraperitoneal injection of LPS (InvivoGen, Cat#tlrl-pb5lps, 4mg/kg) and pair-fed mice received equal volume of PBS 8 hours post gavage. Animals were sacrificed 8 hours after the final intervention.

value: Liver Resident Immune Cells

value: primary

value: CD45+ liver resident

value: ETOH + LPS


title: KMR19, GFP-DN-VPS4A, Dox 1

description: Library name: J1


title: Ethanol + LPS Mouse Liver Resident Immune Cells Sample 2

description:
Library name: EL2
10X Genomics


title: Ethanol + LPS Mouse Liver Resident Immune Cells Sample 1

description:
Library name: EL1
10X Genomics


title: P2402_dpa302

description: Library name: P2402


title: Ethanol + LPS Mouse PBMC Sample 3

description:
Library name: EB3
10X Genomics

source_name: PBMC


title: P2502_dpa041

description: Library name: P2502


title: P2501_dpa005

description: Library name: P2501


title: P2401_dpa008

description: Library name: P2401


title: Ethanol + LPS Mouse PBMC Sample 2

description:
Library name: EB2
10X Genomics


title: P2302_dpa013

description: Library name: P2302


title: Ethanol + LPS Mouse PBMC Sample 1

description:
Library name: EB1
10X Genomics


title: P2301_dpa005

description: Library name: P2301


title: P2203_dpa202

description: Library name: P2203


title: Control Mouse Liver Resident Immune Cells Sample 3

description:
Library name: CL3
10X Genomics

value: pair fed control


title: Control Mouse Liver Resident Immune Cells Sample 2

description:
Library name: CL2
10X Genomics


title: P2202_dpa025

description: Library name: P2202


title: P2201_dpa002

description: Library name: P2201


title: Control Mouse Liver Resident Immune Cells Sample 1

description:
Library name: CL1
10X Genomics


title: Control Mouse PBMC Sample 3

description:
Library name: CB3
10X Genomics


title: Control Mouse PBMC Sample 2

description:
Library name: CB2
10X Genomics


title: P2102_dpa009

description: Library name: P2102


title: P2101_dpa002

description: Library name: P2101


title: Control Mouse PBMC Sample 1

description:
Library name: CB1
10X Genomics


title: N/P(14)_Abemaciclib_24h_rep2

type: RNA

city: Taipei

first: Tsung-Han

last: Hsieh

address: XinYi dist.,WuXing Street, No.250.

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx OneArray Plus Hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The scanned images were analyzed with Agilent G2505C Microarray Scanner and processing by GenePix software GenePix Pro 4.1.1.44 to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: The resulting GPR files were loaded into Rosetta Resolver® System (Rosetta Biosoftware) for data processing and analysis. Differentially expressed genes were identified using standard selection criteria of log2 |Fold change| ≥ 1 and P values < 0.05, as previously described [29]. Gene ontology analysis, Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA) were employed to interpret gene functions and networks [27].

source_name: N/P(14) cells

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: N/P(14)  cells were cultured in RPMI 1640 growth median at 37 °C with 5% CO2, supplemented with 10% FBS and 1X antibiotic-antimycotic (Thermo Fisher Scientific; Waltham, MA, USA).

extract_protocol: Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific). RNA quality was assessed by the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA, USA).

treatment_protocol: N/P(14) cells were treated with Abemaciclib (0.625 M) for 24 h, and total RNA was isolated for microarray analysis.

value: Abemaciclib


title: P2002_dpa018

description: Library name: P2002


title: CBP/p300-alphaDKO

first: Shushu

address: 197 Ruijin Road Ⅱ

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 2
10x Genomics

data_processing:
The scRNAseq data were subsequently processed using Cell Ranger v. 5.0.1 (10× Genomics) to make fastq files for each sample. Cell Ranger Count aligned reads to the mm10 reference genome via STAR. Cell filtration was performed with Seurat v4.0.0, removing low quality sequencing data (parameters: nFeature > 200, nUMI > 1000, log10GenesPerUMI > 0.7, mt < 30%, percent of rbc < 0.05) and potential doublets were removed by DoubleFinder69. Count matrices were normalized and scaled using the NormalizeData function with standard parameters. Dimensionality reduction was performed via principal-component analysis (PCA) to enable cell clustering. Cell clustering was done using the FindClusters method with variable-feature 2000 and resolution 0.4. Uniform manifold approximation and projection (u-MAP) was performed.
Assembly: Mouse mm10
Supplementary files format and content: Hierarchical data format for large datasets.

source_name: Islets

extract_protocol:
For the single-cell RNA-seq, islets were pooled from three Gcg-Cre;ROSAflox/+ mice and three CBP/p300αDKO;ROSAflox/+ mice at 4 weeks of age. Each group contained 300-400 islets, which were digested with 0.25% Trypsin-EDTA (Sigma-Aldrich) for 5 min at 37 ℃. Digestion was terminated with an equal volume of ice-cold RPMI-1640 containing 10% FBS and the sample was centrifuged at 500 g for 3 min. The suspension was then sieved and the pellet was resuspended in ice cold PBS containing 0.2% BSA. Cell viability and number were assessed by Trypan blue staining and the Eve automatic cell counter respectively.
Approximately 10,000 - 15,000 cells for each sample were loaded into the 10× Chromium Chip B according to the 10× Genomics Single Cell 30 Reagent Kit v3 GEM protocol.

value: Islets

value: 4 weeks-old

value: male


title: N/P(14)_CTRL_24h_rep2


title: HUVEC, 24h, Rep1

city: Tallahassee

first: Ayush

last: Singh

state: Florida

address: 319 Stadium Dr,

department: Department of Biological Science

institute: Flordia State University

description: Library name: 24h_huvec_MOA_rep1

data_processing:
Sequence reads (FASTQ format) were trimmed for adapters using Cutadapt with default parameters. For the MOA control, SeqPurge was used with default parameters.
Trimmed paired-end reads were merged using FLASh with the parameters -t 40 --cap-mismatch-quals -M 100 -d -q
Merged reads were aligned to the human reference genome (hg38) using the bwa-mem2 mem function with the parameters -M -t 40. Alignment files (SAM) were converted to BAM format using SAMtools, and filtering was applied to retain reads with a mapping quality score (MAPQ) of 20 or greater. PCR duplicates were removed.
BAM files were converted to BED files using bamToBed in Bedtools.
Fragment center tracks ("frenters") were created by shortening mapped reads to their central 20 bp using a custom awk command. Bedgraphs were generated using genomeCoverageBed in Bedtools with a counts-per-million (CPM) scaling factor for sequencing depth normalization.
BigWig files for UCSC Genome Browser visualization were produced using bedGraphToBigWig.
Peak calling was performed using MACS3. Fragment center BED files for each biological replicate pair per treatment were used as input to the callpeak function. The Irreproducibility Discovery Rate (IDR) framework was applied to identify consistent peaks between biological replicates, which were designated as within-sample peaks. To minimize artifacts, within-sample peaks were filtered using intersect in Bedtools. ENCODE blacklist  regions and MOA control regions (chromatin-free total DNA light digests with MNase) were used as exclusion criteria. For MOA control, peak calling was performed using only MACS3 callpeak.
Differential peak calling was performed using bdgdiff in MACS3, comparing each hypoxia time point (1h, 3h, 24h) to the normoxic sample. The optimal likelihood ratio (LHR) cutoff was determined using the elbow method to maximize sensitivity while minimizing noise.
Assembly: hg38
Supplementary files format and content: The narrowPeak file includes genomic peak data with associated scores and significance metrics for each region.
Supplementary files format and content: The BigWig file includes continuous data, such as the MOA-seq signal intensity, across a genomic region.
Supplementary files format and content: The differential peak BED file stores genomic regions with varying enrichment between hypoxia and normoxic conditions, categorizing peaks as gained, lost, or shared. Each entry represents a genomic region, with the last column containing the log10 likelihood ratio, quantifying the likelihood that the observed signal originates from one condition over the other. Regions enriched in hypoxia compared to normoxic are classified as gained peaks, while those enriched in normoxic conditions are lost peaks. Shared peaks represent regions with similar enrichment in both conditions, where the difference is not statistically significant.

source_name: endothelium of the umbilical vein

extract_protocol:
HUVEC cells were cultured to 90–95% confluency and subjected to induced hypoxia (2% O₂) for 1, 3, or 24 hours. MOA-seq was performed on formaldehyde-fixed cells collected at each time point. Fixed cells were dispersed using a hand mixer and a 5/8-gauge needle, followed by nuclei isolation using Nucleus Isolation Buffer (NIB) containing 0.3 M sucrose, 2 mM MgOAc, 2.1% Triton X-100, 10 mM HEPES (pH 7.4), and 1 mM CaCl₂. Nuclei purity and density were assessed by fluorescence microscopy after staining with Vectashield DAPI mounting medium. For MOA control libraries, A549 human DNA (ATCC, CCL-185) was used. Cells were cultured in F12K media supplemented with fetal bovine serum, 1% L-glutamine, and 1% penicillin-streptomycin. DNA was isolated using the TRIzol Reagent protocol (cat no. 15596026). Qualitative and quantitative checks were performed on the samples received. Initially, 1 µL of DNA was run on a 1% agarose 1X TBE gel, confirming the presence of high molecular weight total naked DNA. DNA concentration was further assessed using a NanoDrop UV spectrophotometer.
MNase digestion was performed on isolated nuclei using serial dilutions of MNase enzymes (ranging from 1280 U/mL to 0 U/mL) at 37ºC for 15 minutes. Reactions were stopped with 0.5 M EGTA-NaOH (pH 8.0). DNA was decrosslinked overnight at 65°C in the presence of SDS, NaCl, Proteinase K, and ddH₂O. Following decrosslinking, DNA was purified via sequential phase extraction using Tris-saturated phenol, phenol:chloroform, and chloroform. Purified DNA was precipitated with sodium acetate, linear polyacrylamide (LPA), and ethanol, washed with 70% ethanol, and resuspended in TE buffer containing RNase A. After RNase treatment, DNA was re-precipitated, washed, and air-dried before final resuspension in TE buffer. DNA quality was assessed by spectrophotometry, and digestion patterns were visualized using gel electrophoresis on a 1% agarose, 1X TBE gel. DNA was further quality-controlled using an Agilent 2100 Bioanalyzer, Q-PCR, and a Qubit 2.0 Fluorometer. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep kits (Cat. E7103S). Indexed libraries were size-selected to enrich for sub-nucleosomal (<150 bp) genomic insert sequences and submitted for paired-end 150 bp reads on the Illumina HiSeq or NovaSeq (FSU College of Medicine, Translational Science Lab). Two biological replicates were analyzed per condition. For MOA control libraries, DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7103). After adapter ligation, samples were flash frozen, and library-specific index sequences (dual indices method) were added by the NGS Library Facility, Department of Biological Science, FSU.

value: endothelium of the umbilical vein

value: HUVEC

value: endothelial cell


title: N/P(14)_Abemaciclib_24h_rep1


title: P2001_dpa003

description: Library name: P2001

value: Blood

value: PBMC

value: Male


title: HUVEC, 3h, Rep2

description: Library name: 03h_huvec_MOA_rep2


title: WT

description:
Library name: Sample 1
10x Genomics

value: WT


title: P1903_dpa275

description: Library name: P1903

value: Female


title: N/P(14)_CTRL_24h_rep1


title: mice infected with ΔvgrG2-3

city: Hangzhou

first: xu

last: wenzeng

address: Department of Respiratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310016, China.

institute: Zhejiang University

description:
Library name: Sample9
10x Genomics

data_processing:
Downstream analysis was performed in R (v4.3.1) using the Seurat package (v5.2). Cells were filtered based on the following quality-control thresholds: number of detected genes (nFeature_RNA) between 200 and 6000, mitochondrial gene percentage < 20%, and hemoglobin gene percentage < 5%. Data were normalized using the SCTransform method, and integration of all samples was performed to correct for batch effects. Principal component analysis (PCA) was conducted on the top 3000 variable genes, followed by uniform manifold approximation and projection (UMAP) for two-dimensional visualization. Cell type annotation was performed manually based on the expression of canonical marker genes. Differential gene expression between experimental groups was identified DESeq2; genes with adjusted P < 0.05 and |log₂(fold change)| > 0.5 were considered significant. Functional enrichment analysis of GO terms and KEGG pathways was performed using the clusterProfiler package60. Custom gene sets relevant to inflammation and M2 polarization were compiled from KEGG and GO Term gene sets as described. The activity of these gene sets in individual cells was scored using the AddModuleScore function in Seurat. Cell–cell communication networks were inferred using CellChat (v2.2.0) with the default mouse ligand–receptor interaction database. Signaling pathways showing differential interaction strength or number of links between groups were identified and visualized. For trajectory analysis, neutrophil and macrophage subsets were subsetted from the integrated object and analyzed using monocle3 (v1.3.4). Cells were ordered along pseudotime after dimensionality reduction (UMAP) and graph-based trajectory construction, and genes significantly associated with pseudotime progression were identified using the graph_test function.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Table-seprated values files and matrix files

source_name: Lung

extract_protocol:
At 24 hours post-infection, lungs were harvested, minced, and subjected to dissociation into single-cell suspensions using a gentle tissue dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions. Cell viability was assessed by trypan blue exclusion and exceeded 85% in all samples.
Single-cell libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) and sequenced on an Illumina NovaSeq 6000 platform by Beijing Novogene Co., Ltd. Raw sequencing data were processed with Cell Ranger (v7.1.0) using the mouse reference genome (mm10) for alignment and gene counting.

value: Lung


title: HUVEC, 3h, Rep1

description: Library name: 03h_huvec_MOA_rep1


title: HUVEC, 1h, Rep2

description: Library name: 01h_huvec_MOA_rep2


title: HUVEC, 1h, Rep1

description: Library name: 01h_huvec_MOA_rep1


title: P1902_dpa010

description: Library name: P1902


title: mice infected with ΔvgrG2-2

description:
Library name: Sample8
10x Genomics


title: P1901_dpa002

description: Library name: P1901


title: HUVEC, 0h, Rep1

description: Library name: 00h_huvec_MOA_rep1


title: HUVEC, 0h, Rep2

description: Library name: 00h_huvec_MOA_rep2


title: P1802_dpa024

description: Library name: P1802


title: HUVEC, 24h, Rep2

description: Library name: 24h_huvec_MOA_rep2


title: Amygdala, cKO 6

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Library name: AMY_F_KO_6

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with homo sapiens  genome GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCm38
Supplementary files format and content: counts

source_name: Amygdala, Brain (BLA)

growth_protocol: Adult male and female Aldh1l1-CreERT2 x Arl13b f/f mice were housed under standard conditions (12-hour light/dark cycle, 22°C, 50% humidity) and provided standard chow and water ad libitum. The mice received tamoxifen (200 ug per mouse per day) from P7 to P9. Four weeks later, mice were deeply anesthetized with isoflurane, then decapitated and the amygdala was quickly microdissected.

extract_protocol:
RNA from thedissected tissue was extracted using an RNA extraction kit (Qiagen, 74034).
Library constructed with TruSeq library prep RNA kit from Illumina

treatment_protocol: The mice did not receive any treatment.

value: Amygdala, Brain (BLA)

value: female

value: Aldh1l1-CreERT2 x Arl13b f/f

value: Tmx


title: mice infected with ΔvgrG2-1

description:
Library name: Sample7
10x Genomics


title: Amygdala, cKO 5

description: Library name: AMY_F_KO_5


title: mice infected with AB5075 WT-3

description:
Library name: Sample6
10x Genomics


title: Amygdala, cKO 4

description: Library name: AMY_F_KO_4


title: P1801_dpa003

description: Library name: P1801

data_processing:
Illumina adapter sequences were trimmed off from the raw reads using Cutadapt and only reads with minimum 30bp were kept for downstream analysis.  Trimmed reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function.  CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 20 -min-sample 1.0.
Assembly: GRCh38
Supplementary files format and content: tab-separated file of methylation levels per CpG locus (row) for all samples (column)

extract_protocol:
Genomic DNA was extracted from PBMCs using phenol-chloroform method.
500ng genomic DNA was sheared and subject to end-repair, A-tailing and ligated with methylated adaptors.  Purified libraries were hybridized to biotinylated probes and subjected for bisulfite conversion (Zymo Cat# D5030).  Captured DNA was PCR amplified with KAPA HiFi HotStart Uracil+ (Cat# KK2801) into a final TBS-seq library.  Library quality was evaluated using TapeStation with the high-sensitivity D1000 tape (Agilent Cat# 5067- 5584).


title: Amygdala, cKO 3

description: Library name: AMY_M_KO_3


title: mice infected with AB5075 WT-2

description:
Library name: Sample5
10x Genomics


title: P1702_dpa016

description: Library name: P1702


title: Amygdala, cKO 1

description: Library name: AMY_M_KO_1


title: mice infected with AB5075 WT-1

description:
Library name: Sample4
10x Genomics


title: Amygdala, Ctrl 6

description: Library name: AMY_F_CTRL_6


title: P1701_dpa005

description: Library name: P1701


title: Amygdala, Ctrl 5

description: Library name: AMY_F_CTRL_5


title: Amygdala, cKO 2

description: Library name: AMY_M_KO_2


title: Amygdala, Ctrl 4

description: Library name: AMY_F_CTRL_4


title: mice infected with PBS-3

description:
Library name: Sample3
10x Genomics


title: P1604_dpa345

description: Library name: P1604


title: Amygdala, Ctrl 3

description: Library name: AMY_M_CTRL_3


title: mice infected with PBS-2

description:
Library name: Sample2
10x Genomics


title: Amygdala, Ctrl 2

description: Library name: AMY_M_CTRL_2


title: P1603_dpa010

description: Library name: P1603


title: Amygdala, Ctrl 1

description: Library name: AMY_M_CTRL_1


title: Ctrl 4

description: Library name: Ctrl_4_S4

growth_protocol: Adult male and female Arl13b f/f mice were housed under standard conditions (12-hour light/dark cycle, 22°C, 50% humidity) and provided standard chow and water ad libitum. Homozygous Arl13b f/f mice received intracranial micro-injections in the BLA of AAVs carrying either GfaABC1D-tdT or GfaABC1D-Cre. Two months later, mice were deeply anesthetized with isoflurane, then decapitated and the amygdala was quickly microdissected.

extract_protocol:
The cells were separated and astrocytes were isolated using ACSA-2 beads in a MACS protocol.RNA from the isolated astrocytes was extracted using an RNA extraction kit (Qiagen, 74034).
Library constructed with SMARTSeq library prep RNA kit from Illumina

value: Arl13b f/f

value: astrocyte-tdT


title: P1602_dpa002

description: Library name: P1602


title: Ctrl 3

description: Library name: Ctrl_3_S3


title: P7 SVZ multiomic data, snRNA-seq

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: Library name: P7 SVZ RNA

data_processing:
Raw data was processed through Cell Ranger ARC v2. Reads were aligned to the wild-type mouse genome (mm10).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and HDF5 files

molecule: nuclear RNA

source_name: Dorsal and lateral ventricular-subventricular zone

extract_protocol:
For single-cell isolation of the embryonic (E14, E17) cortex, the meninges were removed and tissue immediately dorsal to the lateral ventricles—including the cortical layers and the V-SVZ—was collected. For single-cell isolation of the postnatal (P1, P2, P6, P7) V-SVZ, the cortex was removed to expose the lateral ventricles, and the dorsolateral V-SVZ was microdissected out and collected. During dissections, collected tissue was placed in either DMEM (Gibco) or Hibernate A without calcium (BrainBits) supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane) and left on ice until subsequent processing steps. For some datasets (E17 cortex multiomic, P2 V-SVZ n2 multiomic, P7 V-SVZ multiomic), tissue collection was immediately followed by an enzymatic digestion step. Samples were incubated in 20 units/mL Papain with 1 mM L-cysteine, 0.5 mM EDTA, and 0.005% DNase I (Worthington) dissolved in Hibernate A medium without calcium (BrainBits) and DRAQ5 (Abcam) diluted 1:3000 for 30 minutes at 37°C to simultaneously enzymatically digest the tissue and label nuclei. Following enzyme treatment, cells were spun down at 300 g for 5 minutes and resuspended in media, either DMEM (Gibco) or Hibernate A medium without calcium, supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane). Following enzymatic digestion or immediately following collection, tissue was triturated using blunt needles with sequentially decreasing diameters (McMaster-Carr). Cells were then spun down at 300 g for 5 minutes and resuspended in 0.25% BSA (Jackson) in HBSS, after which the cell suspension was filtered through a 40 µm cell strainer and incubated in 1:1000 propidium iodide (PI) (Abcam) to label dead/damaged cells. Samples were then FACS sorted using a MoFlo Cell Sorter (Beckman Coulter) or Aria Fusion A (Becton Dickinson) to enrich for viable (PI-negative, DRAQ5-positive) cells, which were collected in media, either DMEM or Hibernate A without calcium, supplemented with 2% B27 and 500 µM L-glutamine.
Libraries were constructed according to the manufacturer's instructions (Single Cell Multiome ATAC + Gene Expression v1, 10x Genomics).

value: Postnatal day 7

value: Early postnatal ventricular-subventricular zone cell types


title: Ctrl 1

description: Library name: Ctrl_1_S1


title: P1601_dpa002

first: Fei-Man

address: 610 Charles E Young Dr S

institute: UCLA

description: Library name: P1601


title: mice infected with PBS-1

description:
Library name: Sample1
10x Genomics


title: Ctrl 2

description: Library name: Ctrl_2_S2


title: P7 SVZ multiomic data, snATAC-seq

description: Library name: P7 SVZ ATAC

library_source: genomic single cell

value: Dorsal and lateral ventricular-subventricular zone


title: cKO 4

description: Library name: cKO_4_S8

value: astrocyte-Cre


title: P1503_dpa222

description: Library name: P1503


title: cKO 3

description: Library name: cKO_3_S7


title: P2 SVZ n1 multiomic data, snRNA-seq

description: Library name: P2 SVZ n1 RNA

value: Postnatal day 2


title: cKO 2

description: Library name: cKO_2_S6


title: P1502_dpa029

description: Library name: P1502

value: Blood


title: P2 SVZ n1 multiomic data, snATAC-seq

description: Library name: P2 SVZ n1 ATAC


title: cKO 1

description: Library name: cKO_1_S5


title: H3K27ac.PBS-WT.362

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: Library name: K27-362

data_processing:
Alignment: chIP-seq tags generated with the NextSeq 550 platform were demultiplexed with the bcl2fastq utility and aligned to the mouse reference genome (assembly GRCm38/mm10) using Bowtie2 v2.3.4.1 with parameters --local -X 1000).
PCR deduplication: aligned tags were filtered for poor alignments using samtools v1.1 view -bS -q 5, sorted by tag ID using samtools sort -n and PCR-deduplicated using PICARD MarkDuplicates v 2.21.3-SNAPSHOT with parameters REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname.
Differential peaks: statistical significance of differential H3K27ac enrichments was assessed by using RGT-THOR v0.13.2 with default parameters. After BAM files were sorted by chromosome position using samtools sort and indexed using samtools index, two samples of WT PBS (K27-362 and K27-363) were compared to three samples of ACSS2 KO Tau (K27-321, K27-322, K27-323) with per-replicate input adjustment. Differential enrichments reported by THOR were filtered for p-values < 1E-20.
Track creation: UCSC Genome Browser track views were created for ChIP-seq data by first pooling replicates across the four study groups and generating coverage maps using deepTools bamCompare v3.4.3 with parameter --operation subtract to adjust for the input signal and default parameters otherwise.
Assembly: GRCm38
Supplementary files format and content: BigWig files are input-subtracted H3K27ac chIP-seq tracks for four study groups, pooling over biological replicates.

source_name: dorsal hippocampus

growth_protocol: To prevent genetic drift, Acss2KO and corresponding WT controls were generated through homozygous crosses of F1 progeny from heterozygote breeding cages. Mice were housed on a 12/12h light/dark cycle (7 am to 7 pm), with food and water provided ad libitum.

extract_protocol:
~20 mg dorsal hippocampus from each mouse was minced on ice and crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min. Nuclei were prepared by Dounce homogenization of crosslinked tissue in nuclei isolation buffer (50 mM Tris-HCl at pH 7.5, 25 mM KCl, 5 mM MgCl2, 0.25 M sucrose) with freshly added protease inhibitors and sodium butyrate. Nuclei were lysed in nuclei lysis buffer (10 mM Tris-HCl at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) with freshly added protease inhibitors and sodium butyrate and chromatin was sheared using a Covaris S220 sonicator to ~250 bp size. Equal aliquots of sonicated chromatin were used per immunoprecipitation reaction with 4 ul H3K27ac antibody (Abcam, cat #4729; lot # GR323132-1) preconjugated to Protein G Dynabeads (Life Technologies). 10% of the chromatin was saved as Input. ChIP reactions were incubated overnight at 4°C with rotation and washed three times in wash buffer. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked and purified together with Input DNA.
10 ng DNA (either ChIP or Input) was used to construct sequencing libraries using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and paired-end sequenced (42 bp) on the NextSeq 550 platform (Illumina) in accordance with the manufacturer’s protocol.

treatment_protocol: Tau protein was purified in the following way: 6–14 g of frontal cortical gray matter from AD patients was homogenized using a Dounce homogenizer in nine volumes (v/w) of high-salt buffer (10 mM Tris-HCl, pH 7.4, 0.8 M NaCl, 1 mM EDTA, and 2 mM dithiothreitol [DTT], with protease inhibitor cocktail, phosphatase inhibitor, and PMSF) with 0.1% sarkosyl and 10% sucrose added and centrifuged at 10,000 g for 10 min at 4°C. Pellets were reextracted once or twice using the same buffer conditions as the starting materials, and the supernatants from all two to three initial extractions were filtered and pooled. Additional sarkosyl was added to the pooled low-speed supernatant to reach 1%. After 1h nutation at room temperature, samples were centrifuged again at 300,000 g for 60 min at 4°C. The resulting sarkosyl-insoluble pellets, which contain pathological Tau, were washed once in PBS and then resuspended in PBS (∼100 μl/g gray matter) by passing through 27-G 0.5-in needles. The resuspended pellets were further purified by a brief sonication (20 pulses at ∼0.5 s/pulse) using a hand-held probe (QSonica) followed by centrifugation at 100,000 g for 30 min at 4°C, whereby the majority of protein contaminants were partitioned into the supernatant, with 60–70% of tau remaining in the pellet fraction. The pellets were resuspended in PBS at one fifth to one half of the precentrifugation volume, sonicated with 20–60 short pulses (∼0.5 s/pulse), and spun at 10,000 g for 30 min at 4°C to remove large debris. The final supernatants were used in the study and referred to as AD Tau.  6 months old male WT and ACSS2 KO mice were anaesthetized with isoflurane gas (1–5% to maintain surgical plane) and placed in a sterile field within a stereotaxic device. Artificial tears were applied to eyes to ensure sufficient lubrication. Animals received an injection of bupivacaine (2.5 mg kg−1) for local anaesthesia before the skin was disinfected with betadine solution and the skull exposed with a short incision using sterile surgical equipment. A small hole (about 0.5 mm) was drilled in the skull over the target area using a stereotax and a stereotactic drill. A micro-syringe filled with AD Tau lysate was inserted into the right dorsal hippocampus and slowly removed following injection of 1 ug Tau (AP, − 2.5 mm; DV, − 1.4 mm; ML, + 2 mm from bregma). All animals received a single dose of subcutaneous meloxicam (5 mg/kg) as analgesia at induction and one dose per day for two days postoperatively as needed. To allow sufficient time for the development of AD-like pathology, mice underwent behavioral or molecular characterization 6 months post-injection.

value: dorsal hippocampus

tag: antibody

value: PBS

value: male


title: H3K27ac.PBS-WT.363

description: Library name: K27-363

value: WT


title: H3K27ac.PBS-KO.354

description: Library name: K27-354


title: P2 Emx1 n2 scRNA-seq

description: Library name: P2 Emx1 n2

data_processing:
Raw data was processed through Cell Ranger v4. For the E18 cortex sample, reads were aligned to the wild-type mouse genome (mm10). For the P2 Emx1 lineage-traced dataset, reads were aligned to a custom reference gnome containing the Eyfp open reading frame concatenated to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files.

molecule: polyA RNA

source_name: Brain (dorsal and lateral ventricular-subventricular zone)

extract_protocol:
For single-cell isolation of the E18 cortex, thick coronal sections rostral to the hippocampus were generated and tissue dorsal to the lateral ventricles, including the ventricular-subventricular zone (V-SVZ), was dissected out. For single-cell isolation of the P2 V-SVZ, the cortex was removed to expose the lateral ventricles, and the dorsolateral V-SVZ was microdissected out and collected. During dissections, collected tissue was placed in either DMEM (Gibco) or Hibernate A without calcium (BrainBits) supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane) and left on ice until subsequent processing steps. Tissue collection was immediately followed by an enzymatic digestion step. Samples were incubated in 20 units/mL Papain with 1 mM L-cysteine, 0.5 mM EDTA, and 0.005% DNase I (Worthington) dissolved in Hibernate A medium without calcium (BrainBits) and DRAQ5 (Abcam) diluted 1:3000 for 30 minutes at 37°C to simultaneously enzymatically digest the tissue and label nuclei. Following enzyme treatment, cells were spun down at 300 g for 5 minutes and resuspended in media, either DMEM (Gibco) or Hibernate A medium without calcium, supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane). Following enzymatic digestion or immediately following collection, tissue was triturated using blunt needles with sequentially decreasing diameters (McMaster-Carr). Cells were then spun down at 300 g for 5 minutes and resuspended in 0.25% BSA (Jackson) in HBSS, after which the cell suspension was filtered through a 40 µm cell strainer and incubated in 1:1000 propidium iodide (PI) (Abcam) to label dead/damaged cells. Samples were then FACS sorted using a MoFlo Cell Sorter (Beckman Coulter) or Aria Fusion A (Becton Dickinson) to enrich for viable (PI-negative, DRAQ5-positive) cells, which were collected in media, either DMEM or Hibernate A without calcium, supplemented with 2% B27 and 500 µM L-glutamine.
Libraries were constructed according to the manufacturer's instructions (Single Cell 3' v2, 10x Genomics).


title: P1401_dpa002

last: Hsu

description: Library name: P1401

source_name: Blood

value: PBMC

value: Male


title: H3K27ac.PBS-KO.353

description: Library name: K27-353


title: liver,Lyve1-Cre;Hegfl/fl,knockout4,postnatal day 42 (P42)

city: Tianjin

first: Min

last: Zheng

state: Tianjin

address: Xinxing Street

department: School of Basic Medical Sciences

institute: Tianjin Medical University

description:
Library name: aKO4
Column name in FPKMs_all_Samples.txt: aKO4

data_processing:
All clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach
Differential expression analysis was performed using the DESeq2
In addition, gene ontology (GO) functional enrichment analysis was performed using the clusterProfiler to identify which DEGs were significantly enriched in GO terms and metabolic pathway enrichment with Bonferroni-corrected P value≤0.05 compared with all expressed genes as background.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fpkms for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: liver

growth_protocol: P3/P42 mice were randomly divided into a control group and a treatment group

extract_protocol:
Total RNA was extracted from tissue or cell homogenates using Trizol reagent (Invitrogen)
Paired-end RNA-seq sequencing library was sequenced with the standard Illumina protocols

treatment_protocol: Endothelial cells were isolated from the liver of P3 mice by enzymatic digestion and magnetic-activated cell sorting (MACS)

value: liver


title: H3K27ac.Tau-WT.335

description: Library name: K27-335

value: Tau


title: P1303_dpa201

city: Los Angeles

description: Library name: P1303

value: Female


title: H3K27ac.Tau-WT.334

description: Library name: K27-334


title: H3K27ac.Tau-WT.333

description: Library name: K27-333


title: liver,Lyve1-Cre;Hegfl/fl,knockout2,postnatal day 42 (P42)

description:
Library name: aKO2
Column name in FPKMs_all_Samples.txt: aKO2


title: P1302_dpa005

description: Library name: P1302


title: H3K27ac.Tau-KO.323

description: Library name: K27-323


title: H3K27ac.Tau-KO.322

description: Library name: K27-322


title: liver,Lyve1-Cre;Hegfl/fl,knockout1,postnatal day 42 (P42)

description:
Library name: aKO1
Column name in FPKMs_all_Samples.txt: aKO1


title: P1301_dpa002

description: Library name: P1301


title: P1501_dpa006

description: Library name: P1501


title: H3K27ac.Tau-KO.321

description: Library name: K27-321


title: liver,Hegfl/fl,Control4,postnatal day 42 (P42)

description:
Library name: aCO4
Column name in FPKMs_all_Samples.txt: aCO4

value: Hegfl/fl


title: Input.PBS-WT.363

description: Library name: Inp-363


title: P1203_dpa200

description: Library name: P1203


title: liver,Hegfl/fl,Control2,postnatal day 42 (P42)

description:
Library name: aCO2
Column name in FPKMs_all_Samples.txt: aCO2


title: Input.PBS-WT.362

description: Library name: Inp-362


title: Input.PBS-KO.353

description: Library name: Inp-353


title: Input.PBS-KO.354

description: Library name: Inp-354


title: P1202_dpa001

description: Library name: P1202


title: Input.Tau-WT.335

description: Library name: Inp-335


title: liver,Hegfl/fl,Control1,postnatal day 42 (P42)

description:
Library name: aCO1
Column name in FPKMs_all_Samples.txt: aCO1


title: Input.Tau-WT.334

description: Library name: Inp-334


title: liver,Lyve1-Cre;Hegfl/fl,knockout4,postnatal day 3 (P3)

description:
Library name: KO6
Column name in FPKMs_all_Samples.txt: ko6


title: P1201_dpa001

description: Library name: P1201


title: Input.Tau-WT.333

description: Library name: Inp-333


title: P1102_dpa009

description: Library name: P1102


title: Input.Tau-KO.323

description: Library name: Inp-323


title: liver,Lyve1-Cre;Hegfl/fl,knockout3,postnatal day 3 (P3)

description:
Library name: KO5
Column name in FPKMs_all_Samples.txt: ko5


title: Input.Tau-KO.322

description: Library name: Inp-322


title: P1101_dpa002

description: Library name: P1101


title: Amygdala SAL IP Replicate 4

description:
Library name: AMY_SAL_IP_4
Amygdala SAL IP Replicate 4

growth_protocol: Adult male and female Aldh1l1-Cre/ERT2 x Ribotag mice were housed under standard conditions (12-hour light/dark cycle, 22°C, 50% humidity) and provided standard chow and water ad libitum. Hemizygous transgenic-homozygous knock-in mice were injected with 75 mg/kg tamoxifen (Sigma-Aldrich, T5648) dissolved in corn oil once per day for 5 consecutive days at 6-8 weeks of age and used 2-3 weeks after tamoxifen injections for astrocyte RNAseq experiments. Mice were deeply anesthetized with isoflurane, then decapitated and the amygdala was quickly microdissected.

extract_protocol:
The tissue was homogenized in buffer as indicated in Bravo-Ferrer 2022 STAR Protocols. RNA was extracted from 10-20% of cleared lysate as input containing RNA from all cell types using RNA extraction kit (Qiagen, 74034). The remaining lysate was incubated with mouse anti-HA antibody (Biolegend, 901514) for 4 hr at 4 °C followed by addition of magnetic beads (Thermo Scientific, 88817) and overnight incubation at 4 °C. RNA was extracted from the immunoprecipitation (IP) samples containing astrocyte enriched RNA using RNA extraction kit (Qiagen, 74034).
TruSeq Stranded Total RNA with Ribozero Gold

treatment_protocol: The mice received saline or LPS (5 mg/kg) and were sacrified 24 h later.

value: Amygdala, Brain (BLA)

value: Aldh1l1-Cre/ERT2 x Ribotag

value: LPS


title: liver,Lyve1-Cre;Hegfl/fl,knockout2,postnatal day 3 (P3)

description:
Library name: KO4
Column name in FPKMs_all_Samples.txt: ko4


title: Input.Tau-KO.321

description: Library name: Inp-321


title: P1003_dpa374

description: Library name: P1003


title: Amygdala SAL IP Replicate 3

description:
Library name: AMY_SAL_IP_3
Amygdala SAL IP Replicate 3


title: Amygdala SAL IP Replicate 2

description:
Library name: AMY_SAL_IP_2
Amygdala SAL IP Replicate 2


title: liver,Lyve1-Cre;Hegfl/fl,knockout1,postnatal day 3 (P3)

description:
Library name: KO2
Column name in FPKMs_all_Samples.txt: ko2


title: P1002_dpa016

description: Library name: P1002


title: Amygdala SAL IP Replicate 1

description:
Library name: AMY_SAL_IP_1
Amygdala SAL IP Replicate 1


title: liver,Hegfl/fl,Control4,postnatal day 3 (P3)

description:
Library name: CO5
Column name in FPKMs_all_Samples.txt: co5


title: Amygdala SAL Input Replicate 4

description:
Library name: AMY_SAL_COM_4
Amygdala SAL Input Replicate 4


title: P1001_dpa006

description: Library name: P1001


title: Amygdala SAL Input Replicate 3

description:
Library name: AMY_SAL_COM_3
Amygdala SAL Input Replicate 3


title: liver,Hegfl/fl,Control3,postnatal day 3 (P3)

description:
Library name: CO4
Column name in FPKMs_all_Samples.txt: co4


title: Amygdala SAL Input Replicate 2

description:
Library name: AMY_SAL_COM_2
Amygdala SAL Input Replicate 2


title: Amygdala SAL Input Replicate 1

description:
Library name: AMY_SAL_COM_1
Amygdala SAL Input Replicate 1


title: P0902_dpa271

description: Library name: P0902


title: liver,Hegfl/fl,Control2,postnatal day 3 (P3)

description:
Library name: CO2
Column name in FPKMs_all_Samples.txt: co2


title: Amygdala LPS IP Replicate 4

description:
Library name: AMY_LPS_IP_4
Amygdala LPS IP Replicate 4

value: Saline


title: P0901_dpa008

description: Library name: P0901


title: liver,Lyve1-Cre;Hegfl/fl,knockout3,HFD4W

description:
Library name: 18663_S119
Column name in FPKMs_all_Samples.txt: S119

growth_protocol: 6x-week-old male mice were randomly divided into a control group and a treatment group

treatment_protocol: 6-week-old male mice were fed with a high-fat diet (HFD) for 4 weeks


title: Amygdala LPS IP Replicate 3

description:
Library name: AMY_LPS_IP_3
Amygdala LPS IP Replicate 3


title: Amygdala LPS IP Replicate 2

description:
Library name: AMY_LPS_IP_2
Amygdala LPS IP Replicate 2


title: MiaPaCa2_CCRX_ctrl_1

city: Göttingen

first: Nignjun

last: Duan

address: Robert-Koch-Straße 40

country: Germany

institute: Universitätsmedizin Göttingen

description: Library name: CCRX-8-1

data_processing:
Raw read quality was checked with FastQC, mapping to the reference gemone with STAR, and quantified with Stringtie.
Assembly: GCRH38
Supplementary files format and content: The processed file is a CSV file contains raw counts of each sample.

growth_protocol: To obtain mRNA for RNA sequencing, cells were seeded into 6-well plates in 2 mL of respective medium per well. The seeding number was adjusted to ensure that the cells reached a maximum of 60% confluency after 2 days of incubation at cell culture conditions.

extract_protocol:
The cells were lysed by adding 100 μL of RL Lysis Buffer from the innuPREP RNA Mini Kit 2.0 to each well. Cell lysates were processed by the manufacturer’s instructions from the kit mentioned above. RNA concentrations were measured using the DS-11+ Spectrophotometer (DeNovix). The samples were then stored at -80°C until further use.
RNA-seq library is constructed with a TruSeq RNA library preparation kit following relevant protocol.

value: pancreatic cancer cell line


title: P0803_dpa209

description: Library name: P0803


title: Amygdala LPS IP Replicate 1

description:
Library name: AMY_LPS_IP_1
Amygdala LPS IP Replicate 1


title: liver,Lyve1-Cre;Hegfl/fl,knockout2,HFD4W

description:
Library name: 18662_S118
Column name in FPKMs_all_Samples.txt: S118


title: P0802_dpa009

description: Library name: P0802


title: Amygdala LPS Input Replicate 4

description:
Library name: AMY_LPS_COM_4
Amygdala LPS Input Replicate 4


title: liver,Lyve1-Cre;Hegfl/fl,knockout1,HFD4W

description:
Library name: 18669_S117
Column name in FPKMs_all_Samples.txt: S117


title: Amygdala LPS Input Replicate 2

description:
Library name: AMY_LPS_COM_2
Amygdala LPS Input Replicate 2


title: Amygdala LPS Input Replicate 3

description:
Library name: AMY_LPS_COM_3
Amygdala LPS Input Replicate 3


title: P0801_dpa002

description: Library name: P0801


title: liver,Hegfl/fl,Control2,HFD4W

description:
Library name: 18659_S116
Column name in FPKMs_all_Samples.txt: S116


title: Amygdala US hM4Di IP Replicate 4

description:
Library name: AMY_US_Gi_IP_4
Amygdala US hM4Di IP Replicate 4

treatment_protocol: The mice were locally injected in the BLA with GfaABC1D-hM4Di and then underwent US or CRS and received 4 daily injections of DREADD agonist DCZ.

value: CRS + hM4Di


title: P0702_dpa219

description: Library name: P0702

value: Blood


title: Amygdala US hM4Di IP Replicate 3

description:
Library name: AMY_US_Gi_IP_3
Amygdala US hM4Di IP Replicate 3


title: P0701_dpa015

description: Library name: P0701


title: liver,Hegfl/fl,Control1,HFD4W

description:
Library name: 18668_S115
Column name in FPKMs_all_Samples.txt: S115


title: Amygdala US hM4Di IP Replicate 1

description:
Library name: AMY_US_Gi_IP_1
Amygdala US hM4Di IP Replicate 1


title: Amygdala US hM4Di IP Replicate 2

description:
Library name: AMY_US_Gi_IP_2
Amygdala US hM4Di IP Replicate 2


title: Amygdala US hM4Di Input Replicate 4

description:
Library name: AMY_US_Gi_COM_4
Amygdala US hM4Di Input Replicate 4


title: Batch1_KO_tumor

city: Duarte

first: Zhen

last: Chen

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description:
Library name: COHP_53334
Sequencing run was performed on the NovaSeq 6000 platform with S4 reagent kit v1.5 (200 cycles). Real-Time Analysis (RTA) v3.4.4 software was used for base calling and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

data_processing:
The demultiplexing, barcoding processing, gene counting and aggregation were made using CellRanger software 7.1.0.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Briefly, the tumor was dissected from the mammary fat pad of the mouse after 21 days. The tumor was then minced in a collagenase-hyaluronidase in 5% FBS/DMEM (High glucose) and incubated at 37 C for 30 min at 200 RPM. Cells were washed and resuspended in cold DBPS and the supernatant was discarded after spinning. A 0.25% trypsin, EDGA, polyvinyl alcohol solution in DPBS was added and incubated for 1 min at 37 C in water bath. Samples were neutralized with 2% FBS/DPBS and Dispase solution was added and incubated for 5 min at 37C. ACK lysis solution was used and pellets were kept in cold 2% FBS.PBS and stored. Cell viability was assessed prior to sequencing.
Library was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10X genomics) using the 10XGenomics Chromium Controller.

treatment_protocol: Tumor

value: Tumor

value: KO


title: Amygdala US hM4Di Input Replicate 3

description:
Library name: AMY_US_Gi_COM_3
Amygdala US hM4Di Input Replicate 3


title: P0604_dpa009

description: Library name: P0604


title: Batch1_WT_tumor

description:
Library name: COHP_53333
Sequencing run was performed on the NovaSeq 6000 platform with S4 reagent kit v1.5 (200 cycles). Real-Time Analysis (RTA) v3.4.4 software was used for base calling and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: Amygdala US hM4Di Input Replicate 2

description:
Library name: AMY_US_Gi_COM_2
Amygdala US hM4Di Input Replicate 2


title: Amygdala LPS Input Replicate 1

description:
Library name: AMY_LPS_COM_1
Amygdala LPS Input Replicate 1


title: P0603_dpa009

description: Library name: P0603


title: SCNT, ExE, rep2 (Input)

city: Shanghai

first: Shanshan

last: Yi

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: College of Life Science and Technology

institute: Tongji University

description:
Library name: SCNT_E75ExE_input_rep2
SCNT_E75ExE_input.bw

data_processing:
Adapters and low-quality sequences were trimmed using trim_galore (v 0.6.10) and then mapped to mm10 using Bowtie2 (v2.5.3) with parameters: --no-mixed --no-discordant --no-unal. Mapped reads with high confidence were further sorted, indexed and transferred to bam format by SAMtools (v1.18). Duplicates were removed using sambamba (v1.0.1). Additionally, histone modification signal levels were calculated with 50-bp window and normalized to uniquely mapped fragments using bamCompare from deeptools (v3.5.4).
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: Extraembryonic ectoderm (ExE)

extract_protocol:
The extraembryonic ectoderm (ExE) was precisely isolated using forceps under 40× magnification on a stereomicroscope. Isolated ExE fragments were incubated in pre-warmed Ca2+-free CZB medium at 37°C/5% CO₂ for 20 minutes , followed by gentle mechanical dissociation into single cells using a pipette with a diameter of 40–60 μm.
500 trophoblast cells were processed per immunoprecipitation reaction with two biological replicates. Prior to chromatin preparation, isolated cells were washed three times in ice-cold PBS containing 0.5% bovine serum albumin (BSA-PBS; Sigma-Aldrich) to minimize sample contamination. Chromatin immunoprecipitation was using 1 μg anti-H3K27me3 (Diagenode, pAb-069-050) antibodies per reaction. Sequencing libraries were constructed using the KAPA Hyper Prep Kit (Roche, KK8504) with PCR amplification, following the manufacturer’s instructions.

value: Extraembryonic ectoderm (ExE)

value: trophoblast

tag: origin

value: Somatic cell nuclear transfer

tag: developmental stage

value: embryonic day (E) 7.5

value: C57BL/6n x PWK/PhJ


title: Amygdala US hM4Di Input Replicate 1

description:
Library name: AMY_US_Gi_COM_1
Amygdala US hM4Di Input Replicate 1

tag: genotype


title: P0602_dpa007

description: Library name: P0602

tag: tissue

value: PBMC

value: Male


title: Amygdala CRS hM4Di IP Replicate 4

description:
Library name: AMY_CRS_Gi_IP_4
Amygdala CRS hM4Di IP Replicate 4

value: US + hM4Di


title: Amygdala CRS hM4Di IP Replicate 3

description:
Library name: AMY_CRS_Gi_IP_3
Amygdala CRS hM4Di IP Replicate 3

value: Amygdala, Brain (BLA)


title: SCNT, ExE, rep1 (Input)

description:
Library name: SCNT_E75ExE_input_rep1
SCNT_E75ExE_input.bw

tag: cell type


title: Amygdala CRS hM4Di IP Replicate 2

description:
Library name: AMY_CRS_Gi_IP_2
Amygdala CRS hM4Di IP Replicate 2

value: Aldh1l1-Cre/ERT2 x Ribotag


title: P0601_dpa007

description: Library name: P0601

tag: Sex


title: Amygdala CRS hM4Di IP Replicate 1

description:
Library name: AMY_CRS_Gi_IP_1
Amygdala CRS hM4Di IP Replicate 1


title: WT, ExE, rep2 (Input)

description:
Library name: WT_E75ExE_input_rep2
WT_E75ExE_input.bw

value: In vitro fertilized


title: Amygdala CRS hM4Di Input Replicate 4

description:
Library name: AMY_CRS_Gi_COM_4
Amygdala CRS hM4Di Input Replicate 4


title: P0502_dpa366

description: Library name: P0502

tag: age


title: Amygdala CRS hM4Di Input Replicate 3

description:
Library name: AMY_CRS_Gi_COM_3
Amygdala CRS hM4Di Input Replicate 3


title: WT, ExE, rep1 (Input)

description:
Library name: WT_E75ExE_input_rep1
WT_E75ExE_input.bw


title: Amygdala CRS hM4Di Input Replicate 2

description:
Library name: AMY_CRS_Gi_COM_2
Amygdala CRS hM4Di Input Replicate 2


title: Amygdala CRS hM4Di Input Replicate 1

description:
Library name: AMY_CRS_Gi_COM_1
Amygdala CRS hM4Di Input Replicate 1


title: P0501_dpa009

description: Library name: P0501

tag: trajectory group


title: SCNT, ExE, H3K27me3, rep2 (ChIP)

description:
Library name: SCNT_E75ExE_H3K27me3_rep2
SCNT_E75ExE_H3K27me3.bw

value: H3K27me3 (Diagenode, pAb-069-050)


title: P0402_dpa016

description: Library name: P0402

tag: days post_admission


title: Amygdala WAS IP Replicate 4

description:
Library name: AMY_WAS_IP_4
Amygdala WAS IP Replicate 4

treatment_protocol: Mice received control handling (US), chronic restraint stress (CRS) or water aversion stress (WAS) for two weeks.

tag: cell line

value: WAS


title: Amygdala WAS IP Replicate 3

description:
Library name: AMY_WAS_IP_3
Amygdala WAS IP Replicate 3


title: SCNT, ExE, H3K27me3, rep1 (ChIP)

description:
Library name: SCNT_E75ExE_H3K27me3_rep1
SCNT_E75ExE_H3K27me3.bw


title: P0401_dpa005

description: Library name: P0401


title: Amygdala WAS IP Replicate 1

description:
Library name: AMY_WAS_IP_1
Amygdala WAS IP Replicate 1


title: WT, ExE, H3K27me3, rep2 (ChIP)

description:
Library name: WT_E75ExE_H3K27me3_rep2
WT_E75ExE_H3K27me3.bw


title: Amygdala WAS IP Replicate 2

description:
Library name: AMY_WAS_IP_2
Amygdala WAS IP Replicate 2


title: Amygdala WAS Input Replicate 4

description:
Library name: AMY_WAS_COM_4
Amygdala WAS Input Replicate 4


title: P0302_dpa376

description: Library name: P0302

value: Female


title: Amygdala WAS Input Replicate 3

description:
Library name: AMY_WAS_COM_3
Amygdala WAS Input Replicate 3


title: WT, ExE, H3K27me3, rep1 (ChIP)

description:
Library name: WT_E75ExE_H3K27me3_rep1
WT_E75ExE_H3K27me3.bw


title: Amygdala WAS Input Replicate 1

description:
Library name: AMY_WAS_COM_1
Amygdala WAS Input Replicate 1

value: US


title: P0301_dpa030

description: Library name: P0301

value: Blood


title: Amygdala WAS Input Replicate 2

description:
Library name: AMY_WAS_COM_2
Amygdala WAS Input Replicate 2


title: P0202_dpa006

description: Library name: P0202


title: FGSCs_917KO-2

first: Ji

last: Wu

address: No.800, Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: 917KO-2

data_processing:
The raw sequencing data were processed by removing adapter sequences, reads containing excessive N bases, and low-quality reads to obtain high-quality clean data.
The filtered reads were then aligned against a ribosomal RNA database to eliminate rRNA-derived sequences. Candidate Ribosome-Protected Fragments (RPFs) were selected based on size (24-34 nt) and subsequently mapped to the reference genome for further analysis.
The translation profile was characterized using RiboCode to identify high-confidence open reading frames (ORFs), followed by differential expression analysis and functional enrichment analysis of the translated ORFs.
Assembly: MM10
Supplementary files format and content: Tab-delimited text files include the number of reads, relative RPKM values, and P-values for control and experimental group Sample.
Library strategy: Ribo-Seq

source_name: Ovary

extract_protocol:
The cells were treated with CHX (100 μg/mL; Sigma, USA) and washed with CHX (in PBS). Cells were scraped off and centrifuged to collect cell precipitates, stored at -80℃.
The ribo-seq library was constructed by digesting cell lysates with RNase I, followed by ribosome complex isolation through ultracentrifugation over a 1M sucrose cushion. RNA was extracted using the miRNeasy Micro Kit, and ~28 nt ribosome-protected fragments were purified by urea-PAGE. A small RNA library was prepared through adapter ligation, reverse transcription, and PCR amplification, with final size selection using SPRI beads. Library quality was verified by Bioanalyzer before equimolar pooling and sequencing on NovaSeq 6000.

value: Ovary

value: FGSCs

value: germ stem cells

value: shGm26917 group


title: Amygdala US IP Replicate 5

description:
Library name: AMY_US_IP_5
Amygdala US IP Replicate 5


title: Amygdala US IP Replicate 4

description:
Library name: AMY_US_IP_4
Amygdala US IP Replicate 4


title: Amygdala US IP Replicate 3

description:
Library name: AMY_US_IP_3
Amygdala US IP Replicate 3


title: P0201_dpa001

description: Library name: P0201


title: FGSCs_917NC-2

description: Library name: 917NC-2

value: shnc group


title: Amygdala US Input Replicate 4

description:
Library name: AMY_US_COM_5
Amygdala US Input Replicate 4


title: FGSCs_917KO-1

description: Library name: 917KO-1


title: Amygdala US Input Replicate 3

description:
Library name: AMY_US_COM_4
Amygdala US Input Replicate 3


title: P0101_dpa383

description: Library name: P0101


title: location 3 adult

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

data_processing:
The quality of raw sequences was checked using FastQC.
Adaptor trimming was performed using cutadapt. The fastp tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides).
The reads from the chicken samples were mapped to the  reference genome AaegL5  using the STAR aligner.
Differential gene expression analysis was performed using edgeR
Assembly: AaegL5
Supplementary files format and content: Read counts of genes and splice junctions in tab separated text filles for each  sample seprately.

organism: Aedes aegypti

source_name: whole body

extract_protocol:
Total RNA was isolated from the  samples  using AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID:80204) following the manufacturers’ instructions.
Each library was sequenced to 20 million paired end reads of 150 bases using a NovaSeq 6000 sequencer.

value: whole body

value: Adult

tag: collection site

value: C


title: Amygdala US Input Replicate 2

description:
Library name: AMY_US_COM_3
Amygdala US Input Replicate 2


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 5.

first: Guangxing

last: Lu

address: 上海市淞沪路2005号

institute: Fudan University

description: Library name: Enza5

data_processing:
The raw data were aligned using HISAT2 and quantified by Stringtie.
Differentially expressed genes were determined by DESeq2.
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for each sample
Supplementary files format and content: comma-separated values file includes normalized counts (using DESeq2) for each sample

source_name: Alpha TC1 cells

growth_protocol: The αTC1 cells were grown in low-glucose (1 g/L) DMEM medium with10% FBS, 50 U/mL penicilin, and 50 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted from cells using RNAiso Plus reagent (Takara).
The RNA with poly-A in eukaryotic total RNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN). Then, using the captured RNA as the starting sample, TIANSeq Fast RNA Library Kit (Illumina) was used to construct the transcriptome sequencing libraries.

treatment_protocol: The αTC1 cells were treated with 10 μM enzalutamide for 48 hrs.

value: Alpha TC1 cells

value: Enzalutamide, 10 μM, 48 hrs


title: FGSCs_917NC-1

description: Library name: 917NC-1


title: location 3 larvae

value: Larva


title: RPE-1 TKO gene knockout of HDAC7, replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

description: Library name: R036_TKO.HDAC7.G213_r2

data_processing:
Base-calling Q-scores were obtained with RTA 3.4.4. Demultiplexing of raw sequencing data was performed using Illumina’s bclfastq.
Alternative splicing analysis was performed as follows: RNA-Seq data were processed using the vast-tools pipeline, version 2.5.1 https://github.com/vastgroup/vast-tools (Braunschweig et al., 2014; Irimia et al., 2014; Tapial et al., 2017). From primary output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW/VLOW for cassette exon [CE], microexon [MIC], and alternative 5' or 3' splice site [Alt5/3] events or coverage less than 10 reads for intron retention [IR] events; score 4 other than OK/B1/B2/Bl/Bn for CE and MIC events and score 5 of less than 0.05 for IR events). If more than one replicate was present, the point estimate from vast-tools diff was used and if the coverage/balance filtering step failed for an event in more than half of the replicates, its value was set to NA. Differential AS was assessed through the vast-tools diff module available with the main pipeline. Changes were considered significant if they were greater than 10 dPSI/dPIR and the expected minimum change was different from zero at p > 0.95 according to vast-tools’ diff module.
Gene expression changes were analyzed by pseudo-aligning pre-trimmed reads to GENCODE v43 transcripts using Salmon v1.10 (Patro et al., 2017) and aggregated per gene using the R package tximport (Soneson et al., 2015). Differential expression was then assessed using the classic mode (exactTest) edgeR (McCarthy et al., 2012), and genes with an FDR < 0.05 and a greater than 2-fold change were considered differential. For each comparison, only genes expressed at a minimum of 5 RPKM in one or both conditions were considered.
RNAseq.HAP1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Assembly: GENCODE v43
Supplementary files format and content: RNAseq.RPE1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Supplementary files format and content: RNAseq.RPE1_altSplicing.tab.gz is a tab-delimited file and contains mean percent-spliced-in values per treatment and significance calls for the difference vs intergenic hgRNA control.
Supplementary files format and content: Expression_RPE1.tab.gz is a tab-delimited file and contains RPKM, log2 fold-change and p-values per treatment vs intergenic hgRNA control.

source_name: RPE-1 retinal pigment epithelium

growth_protocol: hTERT-RPE-1 cells were maintained under standard sterile cell culture conditions in Dulbecco's Modified Eagle Medium (DMEM; Sigma-Aldrich, #D5796) supplemented with 10% heat-inactivated FBS, penicillin/streptomycin, and sodium pyruvate (Gibco, #11360070) at 37°C in a humidified incubator containing 5% CO2 and at subconfluent densities (50-70%).

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen #74106). Briefly, cells were washed in PBS twice and lysed directly in the vessel using RLT buffer supplemented with reducing agent β-Mercaptoethanol (Milipore #444203-250ML). All RNA samples were DNase-treated using RNase-Free DNase Set (Qiagen #79256) according to the manufacturer's protocol.
Biological duplicates were processed for RNA-Seq. Stranded/directional total RNA-Seq (ribo-depletion) libraries were prepared as follows. RNA concentration was measured using Qubit RNA BR (cat # Q10211, Thermo Fisher Scientific Inc., Waltham, USA) and RNA quality was assessed from 1 ng input on the Bioanalyzer RNA 6000 Pico kit (cat # 5067-1513, Agilent Technologies Inc., Santa Clara, USA). RIN score ranged from 8.4- 9.8 ; with a median RIN score of 9.6. For library preparation, 300 ng of DNase-treated RNA per sample was first subjected to rRNA depletion (H/M/R) and then processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat #E7760L; New England Biolabs; protocol 6.0_7/24), with 7.5 minutes of fragmentation at 94 °C and 12 cycles of amplification. To assess final library quality, 1 μl of the library was analyzed on the Agilent Bioanalyzer dsDNA High Sensitivity chip (cat # 5067-4626, Agilent Technologies Inc., Santa Clara, USA). The libraries were quantified using the Qubit 1X dsDNA HS (cat # Q33231, Thermo Fisher Scientific Inc., Waltham, USA) and were pooled at equimolar ratios after adjusting for fragment size. The final pool, with an average library size of ~395 bp was run on the Bioanalyzer and quantified using NEBNext Library Quant Kit for Illumina (cat # E7630L, New England Biolabs, Ipswich, USA).

treatment_protocol: Cells were transduced at an estimated MOI < 1 with lentivirus encoding the indicated hgRNAs from pLCHKO-EGFP-P2A-Puro vector. Cells were selected for the integration of the CHyMErA cassette by puromycin (Gibco A11138-03) at 20 µg/ml for 72 hours. At T0, puromycin was removed from the medium and cells were grown for 4 days prior to harvesting RNA at 50-70% confluency.

value: RPE-1 retinal pigment epithelium

value: Deletion of HDAC7 with hybrid guide RNA comprising exonic TKOv3 Cas9 guide GAAGTCTGGGATGAGAACAC and intergenic Cas12a guide GAAGTCTGGGATGAGAACAC.


title: RPE-1 TKO gene knockout of HDAC7, replicate 1

description: Library name: R035_TKO.HDAC7.G213_r1


title: location 2 adult


title: Amygdala US Input Replicate 1

description:
Library name: AMY_US_COM_1
Amygdala US Input Replicate 1

value: Amygdala, Brain (BLA)

value: Aldh1l1-Cre/ERT2 x Ribotag


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 4.

description: Library name: Enza4


title: Amygdala CRS IP Replicate 4

description:
Library name: AMY_CRS_IP_4
Amygdala CRS IP Replicate 4

value: CRS


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 3.

description: Library name: Enza3


title: Amygdala CRS IP Replicate 3

description:
Library name: AMY_CRS_IP_3
Amygdala CRS IP Replicate 3


title: location 2 larvae


title: RPE-1 TKO gene knockout of FNBP4, replicate 2

description: Library name: R034_TKO.FNBP4.G216_r2

value: Deletion of FNBP4 with hybrid guide RNA comprising exonic TKOv3 Cas9 guide GAAGTCTGGGATGAGAACAC and intergenic Cas12a guide AGCTGGGAAAGGTGGGTGCTGAT.


title: RPE-1 TKO gene knockout of FNBP4, replicate 1

description: Library name: R033_TKO.FNBP4.G216_r1


title: location 1 adult


title: Amygdala CRS IP Replicate 2

description:
Library name: AMY_CRS_IP_2
Amygdala CRS IP Replicate 2


title: RPE-1 TKO gene knockout of DDX17, replicate 2

description: Library name: R032_TKO.DDX17.G223_r2

value: Deletion of DDX17 with hybrid guide RNA comprising exonic TKOv3 Cas9 guide TAGGTGGTCGTTCTCGTTAC and intergenic Cas12a guide GTTATCTACCATTCTTCACACAT.


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 2.

description: Library name: Enza2


title: location 1 larvae


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 1.

description: Library name: Enza1


title: RPE-1 TKO gene knockout of DDX17, replicate 1

description: Library name: R031_TKO.DDX17.G223_r1