title: Input_Ascl1_QA_D2_rep2

description: Library name: 22_Input_QA_D2_rep2_S1

data_processing:
Index creation: human hg19 genome assemblies were used for bowtie2 index with bowtie2-build -f.
Alignment: FASTQs were aligned to the hg19 with bowtie2 v2.3.4.1 -p 16 --local -X 1000.
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3
PCR duplicates removal were performed using PICARD: picard.jar MarkDuplicates REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname
Track creation: bigWig files of ChIP and Input samples were created using deeptools 3.5.1: bamCoverage --normalizeUsing RPGC --extendReads
Input Subtracted tracks: Input subtracted ChIP-seq bigWig files were created using deeptools 3.5.1: bigwigCompare --operation subtract
Peak calling: narrow peaks were called using macs2 2.2.7.1 callpeak -f BAMPE -g hs --qvalue 0.01 --keep-dup all
The macs2 narrow peaks for each sample and PCR duplicates removed bam files were used in Differential Peak analysis using R/4.3 DiffBind package.
Assembly: GRCh37/hg19
Supplementary files format and content: BigWig files ending in *.bw were input subtrated as indicated above.
Supplementary files format and content: The table DiffBind_consensus_peaks.Named.bed is the conensus peak sets generated by the DiffBind differential peak analysis.

extract_protocol:
The crosslinked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM DTT, and 1x complete protease inhibitors cocktail) and lysis buffer 2 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1x complete protease inhibitors cocktail) for 5 minutes each at 4 °C. The nuclei were then washed once in the lysis buffers 3 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x complete protease inhibitors cocktail) on ice, followed by centrifugation at 1350g for 5 minutes. The nuclei pellets were sonicated in lysis buffer 3 with Covaris (Incident peak power: 140; Duty Cycle: 5; Burst/Cycle: 200) for 10 minutes at 4 °C. The sonicated chromatin was collected and supplemented with 1% Triton before centrifuging at 20,000g for 20 minutes. The soluble chromatin were collected, and 20 μl chromatin was de-crosslinked in 200 μl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65 °C over night and the rest was aliquoted, snap frozen in liquid nitrogen and stored in -80 °C freezer. The de-crosslinked chromatin was treated with proteinase K and RNase, followed by ethanol precipitation and DNA was resuspended in nuclease-free H2O. For V5-Ascl1 ChIP-seq, 50 μg of chromatin was combined with 40 μl pre-wahed Protein G Dynabeads and 4 μg of V5 (Thermo Fisher, R960-25) on a rotating wheel at 4 °C overnight. The chromatin-antibody-dynabead slurry was then washed 5 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x complete protease inhibitors cocktail) and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The chromatin was eluted in the elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 1% SDS) and de-crosslinked at 65 °C overnight, followed by proteinase and RNase treatment and ethanol precipitation. The DNA concentration was quantified with Qubit HS DNA kit and stored in -20 °C.
ChIP-seq DNA libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645), following the manufacturer’s instructions. Briefly, 10 ng of Input DNA and all ChIP DNA were used for library construction and amplified with 10 and 13 PCR cycles respectively for Input and ChIP samples. The PCR products were purified with Ampure XP beads and the distribution of the library DNA were analyzed using High Sensitivity D1000 DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

treatment_protocol: For ChIP-seq experiments, cells were plated at 2 million cells per 15cm dish, and induced with 0.5 μg/mL dox for 48 hrs before being fixed with 1% Formaldehyde for 10 minutes at room temperature (RT), followed by quenching with 0.125 M glycine for 5 minutes at RT. Cells were then washed with ice-cold DPBS for 3 times, and incubated with swelling buffer (25 mM HEPES, pH 7.9, 1.5 mM MgCl, 10 mM KCl, 0.1 % NP-40 and 1x Proteinase inhibitor cocktail) at 4 °C for 10 minutes, before being scraped and collected by centrifugation at 3000 g for 5 minutes at 4 degree. The cell pellets were snap frozen in liquid nitrogen, and stored in -80 degree for storage.

value: hBJ fibroblast

value: human fribroblast

value: Doxycycline day2

tag: antibody

tag: replicate

tag: matching input


title: 2DM3F203LU_S27

status: Public on Jun 01 2026

type: SRA

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

country: USA

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 2DM3F203LU_S27_R1_001

library_source: transcriptomic

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq mouse S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Mouse S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

tag: tissue

value: Lung

tag: cell line

value: B6D2F1/Crl (BDF-1)

tag: Sex

value: female

tag: age

value: 9 weeks

tag: treatment

tag: concentration (ppm)

tag: animal id

tag: sample status

value: Used in Analysis

tag: qc issue


title: ARPE-19 – QMR+Secretome Rescue 24h (biol rep 1) [TRR-B1]

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

country: Italy

institute: University of Messina

description:
Library name: ARPE19_RESSEC_24h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch1.

data_processing:
Raw reads were quality-checked with FastQC (v0.11.9) and trimmed for adapter sequences and low-quality bases using Trimmomatic (v0.39; ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
High-quality reads were aligned to the Homo sapiens reference genome (GRCh38/hg38, Ensembl release 109) using STAR (v2.7.10a) with chimeric alignment enabled (--chimSegmentMin 10 --chimOutType Junctions SeparateSAMold) for back-splice junction detection.
Circular RNA candidates were identified from chimeric alignments using CIRI2 (v2.0.6) and/or find_circ (v1.2). Back-splice junctions supported by ≥2 reads were retained. Candidates were classified into confidence tiers (Tier 1–3) based on read support, annotation overlap, and cross-batch reproducibility.
Linear gene expression quantification was performed using featureCounts (Subread v2.0.3) on STAR-aligned BAM files against Ensembl GRCh38 release 109 GTF annotation.
Differential expression analysis of linear transcripts was carried out using DESeq2 (v1.38.0) in R (v4.2.2). Circular RNA differential expression was assessed using a negative binomial model on back-splice read counts, correcting for sequencing depth. Adjusted p-value threshold: FDR < 0.05; |log2FC| > 1.
Pathway and gene ontology (GO) enrichment analyses were performed using clusterProfiler (v4.6.0) and ReactomePA (v1.42.0) in R. circRNA–miRNA–mRNA interaction networks were constructed using miRanda and TargetScan predictions.
Assembly: Homo sapiens GRCh38 (hg38), Ensembl release 109
Supplementary files format and content: chimeric_events_tier3_all_samples.csv: rows = circular RNA loci (chr:start:end:strand); columns = samples; values = back-splice junction read counts (BSJ). Includes annotation columns: gene name, circBase ID (if available), confidence tier, genomic coordinates (GRCh38).
Supplementary files format and content: linear_counts_matrix.csv: rows = genes (Gene_name, Gene_ID); columns = 74 GEO library names; values = featureCounts-derived gene-level abundance values after downstream processing (non-integer values).

organism: Homo sapiens

growth_protocol: ARPE-19 human retinal pigment epithelial cells (ATCC CRL-2302) were maintained in DMEM/F-12 (1:1) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere of 5% CO2. Cells were seeded at 2×10⁵ cells/well in 6-well plates and allowed to reach 70–80% confluency before treatment.

extract_protocol:
Cells were lysed directly in culture wells using TRIzol Reagent (Thermo Fisher Scientific). Total RNA was extracted according to the manufacturer's protocol, including chloroform phase separation and isopropanol precipitation. RNA pellets were washed with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer and NanoDrop 2000 spectrophotometer; samples with RNA Integrity Number (RIN) ≥ 7 were used for library preparation.
RNA-seq libraries were constructed from total RNA using a ribosomal RNA depletion strategy (Ribo-Zero Plus, Illumina) to preserve both polyadenylated and non-polyadenylated transcripts, including circular RNAs. Depleted RNA was fragmented, reverse-transcribed to cDNA, end-repaired, A-tailed, ligated to indexed adapters, and PCR-amplified following the manufacturer's protocol. Library quality was verified on an Agilent Bioanalyzer High Sensitivity DNA chip; libraries were pooled equimolarly and sequenced on an Illumina NovaSeq platform with paired-end 150 bp reads.

treatment_protocol: Oxidative stress was induced by exposing ARPE-19 cells to H2O2 (400 µM, 1 h), followed by replacement with fresh medium. QMR (Quantum Molecular Resonance) electromagnetic stimulation was delivered using a dedicated device (Tecar Winback; 4 MHz carrier, 3-min sessions) immediately after H2O2 washout. Secretome (conditioned medium) was obtained from MSC cultures and applied at 30% v/v. For combined rescue (QMR + Secretome), both treatments were applied simultaneously. Cells were harvested at 8 h, 24 h, and 72 h after the oxidative challenge. Control cells received no H2O2 and no therapeutic treatment.

tag: cell type

value: Retinal Pigment Epithelium

value: no oxidative stress; QMR electromagnetic stimulation + Secretome (conditioned medium)


title: 2DM2F103LI_S36

description: Library name: 2DM2F103LI_S36_R1_001

source_name: Liver Left Lobe

value: Liver Left Lobe


title: 3374_20

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

description: Library name: L1

data_processing:
All bioinformatic analyses were performed using RNAlysis. For sRNA-seq data, sRNA reads were aligned to PRJNA13758 ce11 genome assembly using ShortStack111 and aligned anti-sense reads were quantified using FeatureCounts. We included all reads with > 5 RPM without imposing any constraint on the length and 5′ nucleotide. For mRNA, we pseudo-aligned reads using Kallisto. We then performed differential expression analysis using DESeq2.
Assembly: PRJNA13758 ce11
Supplementary files format and content: mRNA_kallisto_output.xlsx

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: C. elegans strains were maintained on standard Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 20 degree, unless stated otherwise

extract_protocol:
Total RNA was isolated from day 1 adults (~72 hours following L1 synchronization) using standard phenol-chloroform method with TRIzolTM (Invitrogen). RNA quality was accessed using Agilent 4150 BioAnalyzer instrument and High Sensitivity RNA ScreenTapes.
To sequence the mRNA, RNA libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® coupled with NEBNext® Poly(A) mRNA Magnetic Isolation Module. The cDNA libraries were pooled and paired-end sequencing was performed on the Nextseq 2000 platform.  For sRNA sequencing, we treated the RNA samples with RNA 5′ Polyphosphatase (epicentre) and the libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) or TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. RNA ranging from ~140 to 160 nt was size-selected by gel extraction using 4% agarose E-Gel (Life Technologies). The pooled samples were the sequenced using the Illumina HiSeq 2500 instrument.

treatment_protocol: For experiment at 25 degree, worms were move from 20 to 25 degree at L4 stage

value: Whole worm

tag: genotype


title: ARPE-19 – QMR Rescue + Oxidative Stress 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RES_8h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=8h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation


title: 2DM2F103KI_S31

description: Library name: 2DM2F103KI_S31_R1_001

source_name: Kidney

value: Kidney


title: C24_H3K4me1_rep2

city: Beijing

first: xinjian

last: he

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

description: Library name: Sample 2

library_source: genomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C for 12 d.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: Arabidopsis seedlings

tag: chip antibody

value: Abcam, ab8895


title: mbd715mbd709_RNAseq_rep3

description: Library name: Sample 18

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using STAR.  The clean reads were aligned to the Oryza sativa genome (IRGSP-1.0) using HISAT2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10; IRGSP-1.0
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Oryza sativa

source_name: Oryza sativa leaves

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, under a 8 h light/16 h dark photoperiod at 22°C.Oryza sativa were grown in the controlled growth chamber at 28°C, under LD conditions (14-h light/10-h dark) with 70% relative humidity.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings or 50-day-old Oryza sativa leaves with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000 platform, paired-end 150bp).

value: Oryza sativa leaves

tag: time


title: ARPE-19 – QMR Rescue 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RES_8h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=8h; OX=No; Rep1; sequencing batch=TRR_Batch1.

value: no oxidative stress; QMR electromagnetic stimulation


title: Male, KO, rep4

status: Public on Jun 02 2026

city: Edmonton

first: Richard

last: Lehner

state: Alberta

address: 315 Heritage Medical Research Centre, 11207 - 87 Ave

department: Pediatrics

country: Canada

institute: University of Alberta

description: Library name: M_KO_4

data_processing:
STAR (version 2.5.2b) was used to align RNA-Seq data to the genome reference; RSEM (version 1.3.0) was used to quantify gene and isoform expression; Ensembl 100 gene annotation GTF was used to build the RSEM reference and to add gene and transcript specific information to the output files.
Differential expression (DE) analysis was performed using R (version 4.4.1) and DESeq2 package (version 1.46.0) with raw counts (gene-level abundances) as input data.
Assembly: mm10
Supplementary files format and content: Raw_counts_matrix.txt is a tab-delimited text file contains unnormalized gene-level read counts for all samples, rows = genes, columns = samples. Sample IDs match the library name field in the metadata.
Supplementary files format and content: TPM_matrix.txt is a tab-delimited text file contains TPM-normalized values for all samples, rows = genes, columns = samples. Sample IDs match the library name field in the metadata.
Supplementary files format and content: DESeq2 differential expression results are provided in three files: DESeq2_male_KO_vs_WT.txt, DESeq2_female_KO_vs_WT.txt, and DESeq2_female_vs_male_WT.txt, each containing Gene_Symbol, baseMean, log2FoldChange, lfcSE, stat, p-value, and adjusted p-value (padj). All files are tab-delimited text.

source_name: Liver

growth_protocol: 10-week old AADAC KO and WT mice were fed with western-type diet for one week, livers were harvested at fed state.

extract_protocol:
Total RNA was extracted using Trizol, and cleaned up with a RNeasy Mini Kit (Qiagen). Messenger RNA was purified from 700ng-1000ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
First-strand cDNA was synthesized from heat-denatured purified mRNA using a Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher) and random hexamer primers, followed by PCR Clean DX (Aline Biosciences) bead purification on a Microlab NIMBUS robot (Hamilton Robotics). The second strand cDNA was synthesized following the NEBNext Ultra Directional Second Strand cDNA Synthesis protocol (NEB) with dUTP incorporation. cDNA fragmented to 250-300bp using Covaris LE220, followed by end-repair, A-tailing, and Illumina adapter ligation. Products digested with USER enzyme and immediately amplified with 10 cycles of indexed PCR using NEBNext Ultra II Q5 polymerase (NEB) and Illumina’s dual index primer set. Final libraries purified, size-selected with PCR Clean DX beads, and QC performed using Agilent DNA 1000 and Qubit quantification before pooling for paired-end 150 bp sequencing.

treatment_protocol: Livers were harvested and snap frozen

value: Liver

value: Male

value: AADAC KO

value: One week western-type diet, fed state


title: XIAPΔRING

type: RNA

city: Rio de Janeiro

first: Gabriela

last: Nestal de Moraes

state: Rio de Janeiro

address: venida Carlos Chagas Filho, 373, Sala H2-003,  Cidade Universitária

department: Instituto de Bioquímoca Médica Leopoldo de Meis

country: Brazil

institute: Universidade Federal do Rio de Janeiro

description: RMA expression value derived from TAC software

hyb_protocol: The biotinylated cRNA was subsequently hybridized to a Clariom S Array human (Thermo Scientific, USA).

scan_protocol: The GeneChip arrays were washed and stained according to the manufacturer’s protocols and scanned using a GeneChip® Scanner 3000 (Affymetrix, USA)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) software (Affymetrix, USA).

label: biotin

source_name: Breast cancer cells transfected with vector encoding XIAPΔRING

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix, USA) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix, USA).

extract_protocol:
The MCF-7 breast cancer cells were transfeted  with plasmid vectors: pEBB (empty vector), pEBB-HA-XIAPwild type (cytoplasmic XIAP expression), pEBB-HA-XIAPH467A (lack of ubiquitin ligase activity; cytoplasmic XIAP expression), pEBB-HA-XIAPΔRING (deletion of the RING domain; nuclear and cytoplasmic XIAP expression) and XIAPNLS (insertion of a nuclear localization signal; nuclear and cytoplasmic XIAP expression) using the Lipofectamine 2000 reagent.
After 24h of transfection, the total RNA from all conditions cells used in this study was obtained using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions.

tag: cell

value: MCF-7 cells


title: XIAPNLS

source_name: Breast cancer cells transfected with vector encoding XIAPNLS


title: mbd715mbd709_RNAseq_rep2

description: Library name: Sample 17


title: XIAPH467A

source_name: Breast cancer cells transfected with vector encoding XIAPH467A


title: 2DM2F103HE_S31

description: Library name: 2DM2F103HE_S31_R1_001

source_name: Heart

value: Heart

value: B6D2F1/Crl (BDF-1)

value: female

value: 9 weeks


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RES_72h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: Retinal Pigment Epithelium


title: XIAPwild type

source_name: Breast cancer cells transfected with vector encoding XIAPwild type


title: mbd715mbd709_RNAseq_rep1

description: Library name: Sample 16


title: pEBB

source_name: Breast cancer cells transfected with empy vector


title: hd18_RNAseq_rep3

description: Library name: Sample 15


title: 2DM2F102OV_S112

description: Library name: 2DM2F102OV_S112_R1_001

source_name: Ovary

value: Ovary

value: Used in Analysis


title: ARPE-19 – QMR Rescue 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RES_72h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch1.


title: hd18_RNAseq_rep2

description: Library name: Sample 14


title: 2DM2F102LU_S30

description: Library name: 2DM2F102LU_S30_R1_001

value: Lung


title: 2DM3F203KI_S22

description: Library name: 2DM3F203KI_S22_R1_001

value: Kidney


title: hd18_RNAseq_rep1

description: Library name: Sample 13


title: ARPE-19 – QMR Rescue + Oxidative Stress 24h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RES_24h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation


title: ARPE-19 – QMR Rescue + Oxidative Stress 24h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_RES_24h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: Nip_RNAseq_rep3

description: Library name: Sample 12

value: Oryza sativa leaves

value: Nipponbare


title: 2DM2F102LI_S30

description: Library name: 2DM2F102LI_S30_R1_001

value: Liver Left Lobe

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: Nip_RNAseq_rep2

description: Library name: Sample 11


title: Nip_RNAseq_rep1

description: Library name: Sample 10


title: ARPE-19 – QMR Rescue 24h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RES_24h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch1.

value: no oxidative stress; QMR electromagnetic stimulation


title: 2DM2F102KI_S25

description: Library name: 2DM2F102KI_S25_R1_001


title: pho23Δ, Rpd3-HA, -glucose, rep2, ChIP

city: Dallas

first: Saikat

last: Bhattacharya

state: Texas

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: Library name: delPho23_Rpd3_-D_rep2

data_processing:
Sequencing adapters from the raw reads in FASTQ format were removed using Trim Galore using default settings.
For spike-in normalization, reads were first mapped to the Drosophila melanogaster genome (dm6) using Bowtie2, and unmapped reads were then aligned to the Saccharomyces cerevisiae genome (sacCer3).
The unmapped reads were removed using the tool Split BAM by reads mapping status.
Counts per million (CPM) normalized bigWig tracks were generated using bamCompare while extending reads to the given average fragment size.
Peaks were called using MACS2 callpeak by normalizing against the pooled input and without building the shifting model.
Assembly: sacCer3
Supplementary files format and content: bigwig (except for Input samples)

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Strains of interest were grown in SD medium overnight. Cells from overnight cultures were inoculated into fresh SD to 0.2 optical density (OD)/mL and grown at least two generations to log phase (OD600 ~1). To perform glucose starvation, the media was quickly replaced by spinning down the cells, washing the pellets with pre-warmed S media, and then resuspending cells in the same volume of warmed S media. Samples were collected after 30 mins. All centrifugations were performed at 3000 rpm, 2 min at room temperature.

extract_protocol:
Cell pellets were washed twice with a buffer containing 100 mM NaCl,10 mM Tris-HCl pH 8.0, 1 mM PMSF, and 1 mM benzamide-HCl, and snap-frozen in liquid nitrogen. Frozen pellets were lysed in 0.45 mL ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS,1 mM PMSF, 10 mM leupeptin, 5 mM pepstatin A, and Roche protease inhibitor cocktail) and lysed by bead-beating. Lysates were split into 100ul aliquots for shearing for 40 minutes at default settings- Pulse (N) 50, pulse rate frequency (kHz) 1, burst rate (Hz) 20- using the PIXUL (Active Motif). The lysates were then combined and cleared by two consecutive spins at 15,000 rpm for 10 min. For HA ChIP, the lysate was incubated overnight with 10 µg of antibody. For spike-in normalization, the spike-in chromatin and antibody were added to the reaction as per the manufacturer’s recommendation (Active Motif). 25 µl magnetic beads were added and incubated for an additional 1.5 h. Beads were then washed twice with ChIP lysis buffer, once with deoxycholate buffer (10 mM Tris-HCl, 0.25 M LiCl, 0.5% deoxycholate, 1 mM EDTA), and once with TE buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA). Elution was performed using TES buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS). Reverse crosslinking was performed at 65°C. An equal volume of TE containing 1.25 mg/mL proteinase K and 0.4 mg/mL RNase A was then added and incubated for 2 h at 37°C. DNA was then purified using the QIAGEN PCR purification kit.
Library was prepared and sequenced by Novogene.

tag: strain

value: Yeast

value: pho23 -

value: HA


title: ARPE-19 – Control + Oxidative Stress 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_CTRL_8h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=8h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: H2O2 400 µM (oxidative stress); untreated


title: pho23Δ, Rpd3-HA, -glucose, rep1, ChIP

description: Library name: delPho23_Rpd3_-D_rep1


title: col-3

city: hangzhou

first: xiaoxiao

last: Li

address: #866 Yuhangtang Rd.

institute: zhejiang university

description: Library name: col-rep3

data_processing:
Reads were mapped to the Arabidopsis thaliana (TAIR10) genome using Hisat2 (version 2.1.0) with default settings.
Transcripts assembled from three independent biological replicates were included in the analysis, compared using DESeq2 (version 1.30.1) with default settings.
The R package DESeq2 (version 1.30.1) in v4.0.3 was employed to identify differentially expressed genes with at least a 1.5-fold change
Assembly: TAIR10
Supplementary files format and content: text files include genecounts for each files

source_name: leaves

growth_protocol: The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 10 d. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).

extract_protocol:
Total RNA was extracted from 10-d-old seedlings using TRIzol reagent (Invitrogen, USA) and reverse-transcribed into cDNAs using commercial kits (TOYOBO, FSQ-301) following the manufacturer's instruction. Real-time PCR was performed using SYBR Green qPCR Master Mix (TRANS, AQ601) on the C1000 Touch™ Thermal Cycler (YEASEN). The constitutively reference genes were used as the endogenous control to normalize the amount of cDNA templates.
RNA sequencing was carried out using the Illumina NovaSeq 6000 with Hiseq-PE150 strategy, conducted by Novogene Corporation (Beijing, China).

value: leaves

value: Columbia

value: WT

value: mock


title: eaf3Δ, Rpd3-HA, -glucose, rep2, ChIP

description: Library name: delEaf3_Rpd3_-D_rep2

value: eaf3 -


title: 2DM2F102HE_S25

description: Library name: 2DM2F102HE_S25_R1_001

value: Heart

value: B6D2F1/Crl (BDF-1)

value: female

value: 9 weeks

value: Used in Analysis


title: ARPE-19 – Control 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_CTRL_8h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=8h; OX=No; Rep1; sequencing batch=TRR_Batch1.

value: Retinal Pigment Epithelium

value: no oxidative stress; untreated


title: Wild Type, Pho23-HA, -glucose, rep2, ChIP

description: Library name: WT_Pho23_-D_rep2

value: Wild type


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_CTRL_72h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.


title: 2DM2F101OV_S110

description: Library name: 2DM2F101OV_S110_R1_001

value: Ovary


title: 2DM3F202OV_S98

description: Library name: 2DM3F202OV_S98_R1_001


title: eaf3Δ, Rpd3-HA, -glucose, rep1, ChIP

description: Library name: delEaf3_Rpd3_-D_rep1

value: Yeast


title: 2DM2F101LU_S28

description: Library name: 2DM2F101LU_S28_R1_001

value: Lung


title: Wild Type, Eaf3-HA, -glucose, rep2, ChIP

description: Library name: WT_Eaf3_-D_rep2

value: HA


title: Wild Type, Pho23-HA, -glucose, rep1, ChIP

description: Library name: WT_Pho23_-D_rep1


title: ARPE-19 – Control 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_CTRL_72h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch1.


title: Wild Type, Rpd3-HA, -glucose, rep2, ChIP

description: Library name: WT_Rpd3_-D_rep2


title: ARPE-19 – Control + Oxidative Stress 24h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_CTRL_24h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: H2O2 400 µM (oxidative stress); untreated


title: Wild Type, Rpd3-HA, -glucose, rep1, ChIP

description: Library name: WT_Rpd3_-D_rep1


title: ARPE-19 – Control 24h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_CTRL_24h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch1.


title: pho23Δ_1, -glucose, Input

description: Library name: Input_3_-D

value: pho23 -


title: 2DM2F101HE_S23

description: Library name: 2DM2F101HE_S23_R1_001


title: AD-iPSC derived MSC3

first: liquan

last: wang

address: Peking Union Medical College Hospital

institute: 北京协和医院

description:
Library name: AD-iMSC_Rep3
B3

data_processing:
Raw reads in FASTQ format were processed using Trimmomatic (v0.39) to remove adapters and low-quality bases.
Quality control of clean reads was performed using FastQC (v0.11.9).
Assembly: GRCh38 (hg38).
Supplementary files format and content: gene.count.matrix.annotation.xlsx

source_name: adipose tissue

growth_protocol: ADSCs: Subcutaneous adipose samples were enzymatically dissociated using 1 mg/mL type I collagenase. Cells were maintained in DMEM supplemented with 10% FBS and 50 U/ml penicillin/streptomycin at 37 °C and 5% CO2.AD-iMSCs: iPSCs were differentiated into MSCs using a two-dimensional culture system with MSC differentiation media (DMEM/F-12 with 20% KOSR and 10 µM SB431542) for 10 days.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA quality was quantified using a NanoDrop ND-2000 spectrophotometer and evaluated by a 5300 Bioanalyzer.
Libraries were prepared using the Illumina Stranded mRNA Prep kit (or similar). Poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

treatment_protocol: None. Cells were harvested at a stable passage (passage 3-5) for RNA extraction.

value: adipose tissue

value: AD-iMSC

value: iPSC-derived mesenchymal stromal cells

value: wild type


title: Wild Type, -glucose, Input

description: Library name: Input_1_-D


title: pho23Δ, Rpd3-HA, glucose, rep2, ChIP

description: Library name: delPho23_Rpd3_D_rep2


title: 2DM1F9OV_S108

description: Library name: 2DM1F9OV_S108_R1_001

value: B6D2F1/Crl (BDF-1)


title: pho23Δ, Rpd3-HA, glucose, rep1, ChIP

description: Library name: delPho23_Rpd3_D_rep1


title: eaf3Δ, Rpd3-HA, glucose, rep2, ChIP

description: Library name: delEaf3_Rpd3_D_rep2

value: eaf3 -


title: AD-iPSC derived MSC1

description:
Library name: AD-iMSC_Rep1
B1


title: eaf3Δ, Rpd3-HA, glucose, rep1, ChIP

description: Library name: delEaf3_Rpd3_D_rep1


title: Wild Type, Pho23-HA, glucose, rep1, ChIP

description: Library name: WT_Pho23_D_rep1


title: Adipose-derived MSC3

description:
Library name: ADSC_Rep3
A3

value: adipose-derived stem cells


title: Wild Type, Pho23-HA, glucose, rep2, ChIP

description: Library name: WT_Pho23_D_rep2


title: 2DM1F9LI_S26

description: Library name: 2DM1F9LI_S26_R1_001

value: Liver Left Lobe

value: female

value: 9 weeks

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: Wild Type, Eaf3-HA, glucose, rep2, ChIP

description: Library name: WT_Eaf3_D_rep2

value: Yeast

value: Wild type


title: Adipose-derived MSC2

description:
Library name: ADSC_Rep2
A2


title: Wild Type, Eaf3-HA, glucose, rep1, ChIP

description: Library name: WT_Eaf3_D_rep1

value: HA


title: Wild Type, Rpd3-HA, glucose, rep2, ChIP

description: Library name: WT_Rpd3_D_rep2


title: Wild Type, Rpd3-HA, glucose, rep1, ChIP

description: Library name: WT_Rpd3_D_rep1


title: pho23Δ_2, glucose, Input

description: Library name: Input_4_D


title: J9

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: J9

library_source: transcriptomic single cell

data_processing:
CellRanger was used to map the reads (paired end) to the reference genome to generate the bam files.
Raw base call (BCL) files from the NovaSeq 6000 were converted and demultiplexed to sample-level FASTQ files using Illumina BCL Convert (or bcl2fastq2) with an Illumina SampleSheet specifying unique dual indexes. Default quality and index mismatch filters were applied, and per-lane FASTQs were concatenated by sample to produce a single FASTQ set per library for downstream single-cell RNA-seq analysis.
Assembly: hg38
Supplementary files format and content: cellranger output format

source_name: human skin

extract_protocol:
Skin samples are incubated with dispase overnight, followed by tissue dissociation using collagenase and trypsin-EDTA. The epidermis and dermis are minced, incubated with enzymes, and then processed through mesh filtration and centrifugation. After cell counting, the epidermal and dermal cells are recombined in a desired ratio for library preparation.
https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: human skin

value: a pool of single cells

tag: disease

value: Nonles AD


title: 2DM1F8LU_S37

description: Library name: 2DM1F8LU_S37_R1_001

source_name: Lung

value: Lung

value: Used in Analysis


title: eaf3Δ, glucose, Input

description: Library name: Input_2_D


title: J8

description: Library name: J8

value: Les AD


title: 2DM1F8LI_S37

description: Library name: 2DM1F8LI_S37_R1_001

source_name: Liver Left Lobe

value: B6D2F1/Crl (BDF-1)


title: Wild Type, glucose, Input

description: Library name: Input_1_D


title: J7

description: Library name: J7


title: Endothelial cells of Foxq1flox/flox brain,E12.5

city: Chongqing

first: Yulin

last: Yan

address: No. 83 Shabei Street

institute: Bioengineering College of Chongqing University

description: Library name: Sample1

data_processing:
scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp (v0.24.0) with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data. To quantify the gene expression of the single-cell data, we used STARsolo (version 2.7.11b) along with mouse genome mm10 (Ensemble annotation version 100). We applied the down sample analysis among samples sequenced according to the mapped barcoded reads per cell of each sample and finally achieved the aggregated matrix.
Assembly: mm10
Supplementary files format and content: Feature-barcode matrix in MEX format (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz)

source_name: brain

extract_protocol:
The single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co., Ltd. The tissues were removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with RPMI-1640 culture solution, minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 2mg/mL Collagenase IV, 1mg/mL Dispase II, DNase I 100U/mL for 90 min at 37°C. The digestion solution was changed every 30 minutes during digestion: RPMI-1640 culture solution containing 10% FBS was added to the samples, mix well. Then, the digestion solution was added to the precipitate obtained via low-speed centrifugation for further digestion, until no obvious cell clumps were detected in quality inspection. After washing, the cell pellets were re-suspended in RPMI-1640 containing 10% FBS. CD31 microbeads were used to sort target cells. Single cells were then stained for viability assessment.
The NovelCyto Single-Cell Analysis System (NovelBio Co., Ltd, China) was utilized to collect transcriptome data. First, a single-cell suspension was randomly distributed across more than 100,000 microwells using a limited dilution method. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. Cell-lysis buffer was added so that poly-adenylated RNA molecules hybridized to the beads. Beads were collected into a single tube for reverse transcription. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell label indicating its cell of origin. Whole transcriptome libraries were prepared using the NovelCyto single-cell whole-transcriptome amplification (WTA) workflow. In brief, second strand cDNA was synthesized, followed by ligation of the WTA adaptor for universal amplification. Eighteen cycles of PCR were used to amplify the adaptor-ligated cDNA products. Sequencing libraries were prepared using random priming PCR of the whole-transcriptome amplification products to enrich the 3′ end of the transcripts linked with the cell label and UMI. Sequencing libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). All libraries were sequenced using a DNBSEQ-T7 Sequencer (MGI, Shenzhen, China) in a 150 bp paired-end run

value: brain

value: Endothelial cells

tag: developmental stage


title: Endothelial cells of Foxq1iECKO brain,E12.5

description: Library name: Sample2

tag: tissue


title: 2DM1F8KI_S32

description: Library name: 2DM1F8KI_S32_R1_001

source_name: Kidney

value: Kidney

tag: cell line


title: 061522ICN_anterior

city: New Haven

first: Qian

last: Xu

state: Connecticut

address: 100 College

institute: Yale university

description:
Library name: sample2
10x genomics

data_processing:
Raw sequencing data were aligned to the mm10-2020-A mouse genome reference using the Cell Ranger software v.7.1.0 (10X Genomics). Cells were filtered using the following quality control thresholds: number of detected genes per cell > 2,500 and < 20,000; and percentage of mitochondria genes < 10%. To select neuronal populations, cells with Plp1 expression ³1 and Fabp7 ³1 were excluded, and those expressing Phox2b >0 and Snap25 >0 were retained. A total of 2,870 high-quality ICNs passed filtering (1,111 from mixed ganglia, 933 from anterior ganglia, and 826 from posterior ganglia). Filtered datasets were integrated and analyzed using the Seurat R package v.4.4.2. Dimensionality reduction was performed using the top 50 principal components, and UMAP was used for visualization. ICN cell types were annotated based on unsupervised clustering. DEGs between ICN subtypes were identified using the Seurat’s built-in likelihood-ratio test based on the bimod distribution.
Assembly: mouse mm10-2020
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart atria anterior section

extract_protocol:
ICNs were acutely isolated using a modified protocol for peripheral neurons. Briefly, hearts were harvested from 10 age- and sex-matched Baf53bGFP mice into ice-cold Leibovitz's L-15 Medium (GibcoTM). ICN-containing regions were identified and dissected under a Leica M205FCA Fluorescence Stereo Microscope. Tissues were trimmed into 1-3 mm2 pieces and incubated with 0.25% trypsin-EDTA (GibcoTM) at 37 ˚C for 25 minutes. After washing in L-15 medium supplemented with 10% fatal bovine serum (FBS), tissues were digested with 1 mg/mL Collagenase A (Sigma) and 3 mg/mL of Dispase II (Sigma) in 1 x Hank’s Balanced Salt Solution (HBSS, Stemcell Technologies) at 37°C for 40 minutes. Dissociated tissues were triturated using a series of three fire-polished Pasteur pipettes of decreasing opening size, then filtered through a 40 mm cell strainer (Corning). Cells were centrifuged at 200 x g for 10 minutes at 4°C and resuspended in 1x HBSS containing 0.04% BSA. For regional transcriptomic analysis, anterior and posterior ganglia were dissected and processed separately. For mixed ganglia samples, tissues were pooled. Fluorescently labelled cells were sorted using a BD FACS Aria cell sorter into ice-cold 1x HBSS with 0.04% BSA at the Yale Flow Cytometry Facility.
Approximately 5,000-10,000 sorted cells were loaded per channel on the 10x Genomics Chromium microfluidic device to target a recovery of 3,000-6,000 cells per sample. Single-cell cDNA libraries were prepared using the Chromium Single Cell 3’ V3 reagent kit at the Yale Center for Genomic Analysis (YCGA) and sequenced on an Illumina NovaSeq S4 sequencer at 150-300 million reads to achieve a target depth of 30,000-50,000 reads per cell.

value: Heart atria anterior section

value: neuron

value: 3 months

tag: Sex

value: female and male


title: 2DM1F8HE_S32

description: Library name: 2DM1F8HE_S32_R1_001

value: Heart

value: female

tag: age

value: 9 weeks


title: 021320ICN

description:
Library name: sample1
10x genomics

source_name: Heart atria

value: Heart atria

value: 2 months


title: J4

description: Library name: J4

value: human skin

value: a pool of single cells


title: Ctrl_LNA_2

city: St. Louis

first: Dylan

last: Galloway

state: MO

address: 4370 Duncan Ave

department: Neurology

institute: Washington University in St. Louis

description: Library name: Scram_Ctrl_2

data_processing:
Reads aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1
Quantification via featureCounts
Assembly: GRCm38
Supplementary files format and content: Tab-delimited file with counts, CPM, and TPM

growth_protocol: Mice were housed on a standard 12hr light/dark cycle. Motor neurons were generated from mESCs using a standard -2/+4 protocol with retinoic acid and SAG. Motor neurons were cultured in growth factor supplemented neuronal media.

extract_protocol:
Norgen Total RNA Plus
KAPA RiboErase

treatment_protocol: Mice were divided by genotype, cells were transfected with Lipofectamine 2000 and 10nM of miR-146a LNA or control LNA (Qiagen) for 72hrs.

value: RW.4 mESC

value: Motor Neuron

value: Wild-type

tag: treatment

value: Control LNA


title: 2DM1F7OV_S96

description: Library name: 2DM1F7OV_S96_R1_001

value: Ovary

value: B6D2F1/Crl (BDF-1)

tag: concentration (ppm)

value: Used in Analysis


title: J2

description: Library name: J2

value: Nonles AD


title: 2DM1F7LU_S14

description: Library name: 2DM1F7LU_S14_R1_001

value: Lung

tag: animal id


title: Ctrl_LNA_1

description: Library name: Scram_Ctrl_1


title: miR-146a_LNA_3

description: Library name: LNA_146a_3

value: miR-146a LNA


title: J22

description: Library name: J22

value: Control


title: 2DM1F7LI_S14

description: Library name: 2DM1F7LI_S14_R1_001

value: Liver Left Lobe

value: female

tag: sample status


title: miR-146a_LNA_1

description: Library name: LNA_146a_1


title: 9454_LS

description: Library name: 9454_LS

source_name: Spinal Cord

value: Spinal Cord

value: miR-146a KO


title: 2DM1F7KI_S9

description: Library name: 2DM1F7KI_S9_R1_001

value: Kidney

value: 9 weeks

tag: qc issue


title: 8210_LS

description: Library name: 8210_LS

tag: cell type


title: 2DM1F7HE_S9

description: Library name: 2DM1F7HE_S9_R1_001

value: Heart


title: 8175_LS

description: Library name: 8175_LS

tag: genotype


title: J17

description: Library name: J17

value: human skin

value: a pool of single cells


title: 7707_LS

description: Library name: 7707_LS


title: 2DM1F6OV_S114

description: Library name: 2DM1F6OV_S114_R1_001


title: J14

description: Library name: J14


title: 7149_LS

description: Library name: 7149_LS


title: 1764_LS

description: Library name: 1764_LS


title: J13

description: Library name: J13

value: Les AD


title: 1585_LS

description: Library name: 1585_LS

value: miR-146a WT


title: 2DM1F6LI_S32

description: Library name: 2DM1F6LI_S32_R1_001

value: B6D2F1/Crl (BDF-1)


title: 8003_LS

description: Library name: 8003_LS


title: 1524_LS

description: Library name: 1524_LS


title: J12

description: Library name: J12


title: 1522_LS

description: Library name: 1522_LS


title: 2DM1F6KI_S27

description: Library name: 2DM1F6KI_S27_R1_001

value: Not Used in Analysis

value: Potential Tissue Contamination


title: H3

description: Library name: H3


title: 475_LS

description: Library name: 475_LS


title: CXCR5-negative_Treg, WT, rep1, CUT&Run

city: Pohang-si

first: Dahun

last: Um

address: 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673

department: Life science

country: South Korea

institute: Pohang University of Science and Technology(POSTECH)

description: Library name: CXCR5-negative_Treg_CEBPa

data_processing:
Low-quality bases and adapter sequences were trimmed using Trim Galore(v0.6.10). Trimmed reads were aligned to the GENCODE vM25 reference genome using Bowtie2(v2.5.4). PCR duplicates were removed using sambamba markdup(v1.0.1). BigWig files were generated based on properly aligned fragments and normalized to 1,000,000 reads using bedtools(v2.29.1) and bedGraphToBigWig.
Assembly: mm10 (GENCODE vM25)
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: Spleen

growth_protocol: All mice were bred onto the C57BL/6 background and maintained in specific pathogen-free conditions at Pohang University of Science and Technology (POSTECH) Biotech Center, Republic of Korea. Mice were housed under a 12-h light/dark cycle and food and water were available ad libitum. Both sexes of mice, aged between 8–10 weeks were used.

extract_protocol:
CUT&RUNs were performed following the EpiCypher protocol with minor modification. From ~300,000 sorted T cells, nuclei were isolated using nuclear extraction buffer (20 mM HEPES-KOH [pH 7.9], 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine, and protease inhibitors (GenDEPOT, Altair, Texas, USA; P3100-010)) in ice for 10 minutes. The pelleted nuclei were resuspended in CUT&RUN wash buffer (20 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 0.01 % Digitonin (Merck Millipore, Burlington, Massachusetts, USA; 300410-250MGCN), 0.5 mM spermidine, and protease inhibitors). Nuclei were bound to CUTANA concanavalin A-conjugated paramagnetic beads (EpiCypher, Durham, North Carolina, USA; 21-1401) that had been washed with bead activation buffer (20 mM HEPES-KOH [pH 7.9], 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) at room temperature for 10 minutes. The ConA-bead-bound nuclei were then incubated at 4 ℃ on a nutator overnight in CUT&RUN antibody buffer (CUT&RUN wash buffer supplemented with 2 mM EDTA [pH 8.0]) and antibodies anti-CEBPa (Cell Signaling Technologies, Danvers, Massachusetts, USA; #8178), IgG antibody (EpiCypher, 13-0042). The Con-A-bead-bound nuclei were washed and resuspended in CUT&RUN wash buffer. The Con-A-bead bound nuclei were treated with 20X pAG-MNase (EpiCypher, 15-1116) and incubated at 4 ℃ on a nutator for 1 hour. The Con-A-bead bound nuclei were washed and resuspended in CUT&RUN Triton-wash buffer, followed by the addition of 100 mM CaCl2 (final concentration 2 mM), and incubated at 4 ℃ on a nutator for 2 hours. 2X STOP buffer (340 mM NaCl, 20 mM EDTA [pH 8.0], 4 mM EGTA [pH 8.0], and 0.2 μg/μl RNase A (Thermo Fisher Scientific, Waltham, Massachusetts, USA; EN0531)) was added to stop chromatin digestion and incubated at 37 ℃ for 20 minutes. The Con-A-bead bound nuclei were captured using a magnet, and supernatants were collected. The fragmented DNA was treated 1.6 U proteinase K (NEB, P8107S) containing 0.1 % SDS at 65 ℃ for 1 hour. The DNA was purified using phenol:chloroform:isoamyl alcohol (Thermo Fisher Scientific, 15593) followed by ethanol precipitation. The DNA was resuspended in 1X TE (10 mM Tris-HCl [pH 8.0] and 1 mM EDTA [pH 8.0]) buffer.
CUT&RUN library construction was performed using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L) following the manufacturer’s instructions with minor modifications. Briefly, the end-prepped DNAs were ligated with adaptors. The adaptor-ligated DNAs were digested with USER enzyme and size selected using 0.6X and 1.4X SPRIselect beads (Beckman Coulter, Brea, California, USA; B23317). Size-selected adaptor-ligated DNAs were amplified by 14 ~ 15 cycles of PCR. The amplified CUT&RUN library was size-selected using 1.4X SPRIselect beads and proceeded to sequencing. CUT&RUN library samples were sequenced on Illumina NovaSeq-X (Illumina) with 100bp paired-end reads.

treatment_protocol: Intraperitoneal injection of OVA (100ug) mixed with Alum at a 1:1 ratio

value: Spleen

value: CXCR5- Treg cells

value: Wild-type (WT)

value: OVA/Alum immunization

value: pooled male and female

value: 8-10 weeks

tag: cell source

value: Ex Vivo Sorted spleen cells


title: Tfr, WT, rep1, CUT&Run

description: Library name: Tfr_CEBPa

value: Tfr cells


title: 7877-JF-4

description: Library name: 7877-JF-4


title: 2DM1F5OV_S113

description: Library name: 2DM1F5OV_S113_R1_001

value: Ovary

value: female

value: 9 weeks

value: Used in Analysis


title: 7877-JF-2

description: Library name: 7877-JF-2

value: human skin

value: a pool of single cells

value: Nonles AD


title: Chow NoImm Tm 6

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: H6

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mouse genome (GRCm39)
DEG determined using DESeq2
Assembly: GRCm39
Supplementary files format and content: excel file with count data and gene symbol for each sample

source_name: Caecum

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen) following instructions provided by the manufacturer
standard Illumina

value: Caecum


title: Chow NoImm Tm 5

description: Library name: H5


title: 6.32 Geriatric day 4

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

description:
Library name: Geriatric_D4_6.32
6-32_S41

data_processing:
150 bp paired-end reads were aligned using Hisat2 version 2.1.0 using the Sigmodon hispidus complete DNA reference assembly
Mapped reads are quantified using featureCounts software and the Sigmodon hispidus annotation in gtf format.
The resulting count matrix was annotated with Sigmodon hispidus gene IDs, associated Ensembl gene IDs, and mouse gene orthologs
Assembly: Sigmodon hispidus complete DNA (https://denovo.cnag.cat/cottonrat_data)
Supplementary files format and content: format: Tab separated txt file
Supplementary files format and content: content: Sigmodon hispidus gene IDs, associated Ensembl gene IDs, and mouse (Mus musculus) gene orthologs, raw counts for each sample (quantified by featurecounts)

organism: Sigmodon hispidus

growth_protocol: Inbred cotton rats (Sigmodon hispidus) were purchased from Inotiv (formerly Envigo; West Lafayette, IN). All cotton rats were maintained in NexGen Rat 900 polysulfone microisolator cages (Allentown Inc., Allentown, NJ) in a barrier facility with 12:12 hour light cycles, 22 ± 2 °C, and 20-70% relative humidity. Age ranges were 1-4 months for adult animals and >8 months for geriatric animals.

extract_protocol:
RNA was extracted and isolated with RNeasy Plus Mini extraction kits (QIAGEN) following manufacturer instructions, with a final elution volume of 30 µL. RNA concentrations, 260/280 ratios, and 260/230 ratios were measured using a NanoDrop One spectrophotometer (Thermo Fisher), ensuring a minimum concentration of 100 ng/µL and 260/280 ratios between 1.8 and 2.2 for all extracted RNA samples.
The RNA Integrity Number (RIN) for DNase-treated total RNA were assessed using Agilent BioAnalyzer RNA Nano Kit (Agilent Technologies, Inc., Santa Clara, CA) and the RNA amount was assayed with the Invitrogen Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA). Samples with RIN > 7 were used in mRNA-seq library generation using the QIAseq FastSelect RNA Lib Core Kit (QIAGEN) and the QIAseq Stranded mRNA Enrichment Kit (QIAGEN). Briefly, 100 ng DNase-treated total RNA was used as input for library generation. RNA fragmentation was set for 3 minutes at 94C. 17 PCR cycles were used in final library generation. Library quantification and characterization were assessed with Agilent BioAnalyzer HS DNA Kit and the Invitrogen Qubit DNA HS Assay Kit. Libraries were pooled together with other index – compatible RNA-seq libraries for sequencing on Illumina NovaSeq X Plus 10B (Illumina Technology, Portland, OR) flow cell lane to a minimum depth of 15 - 20 million clusters per sample.

treatment_protocol: At indicated end-points, cotton rats were euthanized by CO2-induced asphyxiation followed by exsanguination. The left lung lobe was collected and placed in 2 mL RNAprotect (QIAGEN, Hilden, Germany) at room temperature. Homogenization of lung was performed the same day as collection, following transportation at room temperature in RNAprotect (QIAGEN). 25-30 µg of each lung sample was removed by sterile dissection and placed in 2 mL Precellys® bead tubes (Bertin Technologies, France) with 600 µL Buffer RLT Plus (QIAGEN) and 6 µL β-mercaptoethanol. Samples were homogenized at room temperature with a Precellys® 24 tissue homogenizer (Bertin) at 6000 RPM, 3 cycles for 30 seconds each with 10-second breaks. The homogenate was passed through QIAshredder tubes (QIAGEN).

value: Lung

value: RSV intranasal 4 days prior to lung collection


title: 2DM1F5LU_S31

description: Library name: 2DM1F5LU_S31_R1_001

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq mouse S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Mouse S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: B6D2F1/Crl (BDF-1)


title: Chow NoImm Tm 4

description: Library name: H4


title: Chow Imm Tm 6

description: Library name: G6


title: 7877-JF-1

description: Library name: 7877-JF-1

value: Les AD


title: 2DM1F5LI_S31

description: Library name: 2DM1F5LI_S31_R1_001

value: Liver Left Lobe


title: Chow Imm Tm 5

description: Library name: G5


title: 1518_LS

description: Library name: 1518_LS

value: Spinal Cord

value: miR-146a WT


title: Chow Imm Tm 4

description: Library name: G4


title: 7824-JF-3

description: Library name: 7824-JF-3

value: Control


title: 2DM1F5KI_S26

description: Library name: 2DM1F5KI_S26_R1_001

value: Kidney

value: Not Used in Analysis

value: Outlier based on PCA/correlation


title: Chow Imm Control 4

description: Library name: F4


title: 2DM1F6HE_S27

description: Library name: 2DM1F6HE_S27_R1_001

source_name: Heart

value: Heart

value: female

value: 9 weeks


title: 7824-JF-1

description: Library name: 7824-JF-1

value: human skin

value: a pool of single cells


title: Chow Imm Control 3

description: Library name: F3

value: Caecum


title: 2DM1F5HE_S26

description: Library name: 2DM1F5HE_S26_R1_001

value: Used in Analysis


title: Chow NoImm Control 4

description: Library name: E4


title: 7781-JF-2

description: Library name: 7781-JF-2

value: Nonles AD


title: Chow NoImm Control 3

description: Library name: E3


title: SSD NoImm Tm 6

description: Library name: D6


title: 2DM1F4OV_S103

description: Library name: 2DM1F4OV_S103_R1_001

value: Ovary

value: B6D2F1/Crl (BDF-1)


title: 7781-JF-1

description: Library name: 7781-JF-1

value: Les AD


title: 2DM2F101LI_S28

description: Library name: 2DM2F101LI_S28_R1_001

value: Liver Left Lobe

value: SEQ DEPTH < 300000


title: Wild Type, Eaf3-HA, -glucose, rep1, ChIP

description: Library name: WT_Eaf3_-D_rep1

value: Yeast

value: Wild type

tag: chip antibody

value: HA


title: pho23Δ_2, -glucose, Input

description: Library name: Input_4_-D

value: pho23 -


title: eaf3Δ, -glucose, Input

description: Library name: Input_2_-D

value: eaf3 -


title: SSD NoImm Tm 5

description: Library name: D5


title: 2DM2F101KI_S23

description: Library name: 2DM2F101KI_S23_R1_001

value: Kidney

value: female


title: 2DM1F9LU_S26

description: Library name: 2DM1F9LU_S26_R1_001

value: Lung

value: 9 weeks


title: AD-iPSC derived MSC2

description:
Library name: AD-iMSC_Rep2
B2

value: adipose tissue

value: AD-iMSC

value: iPSC-derived mesenchymal stromal cells

value: wild type


title: 2DM1F4LU_S21

description: Library name: 2DM1F4LU_S21_R1_001

value: B6D2F1/Crl (BDF-1)

value: Used in Analysis


title: SSD NoImm Tm 4

description: Library name: D4

value: Caecum


title: SSD Imm Tm 6

description: Library name: C6


title: 2DM1F4LI_S21

description: Library name: 2DM1F4LI_S21_R1_001

value: Liver Left Lobe


title: 7744-JF-2

description: Library name: 7744-JF-2

value: human skin

value: a pool of single cells

value: Nonles AD


title: SSD Imm Tm 5

description: Library name: C5


title: 7744-JF-1

description: Library name: 7744-JF-1

value: Les AD


title: 2DM1F9HE_S21

description: Library name: 2DM1F9HE_S21_R1_001

value: Heart


title: Adipose-derived MSC1

description:
Library name: ADSC_Rep1
A1

value: adipose-derived stem cells


title: SSD Imm Tm 4

description: Library name: C4


title: 2DM1F4KI_S16

description: Library name: 2DM1F4KI_S16_R1_001

value: Kidney

value: female

value: Not Used in Analysis

value: Potential Tissue Contamination


title: SSD Imm Control 4

description: Library name: B4


title: 2DM1F9KI_S21

description: Library name: 2DM1F9KI_S21_R1_001

value: 9 weeks


title: 2DM1F8OV_S119

description: Library name: 2DM1F8OV_S119_R1_001

value: Ovary


title: SSD Imm Control 3

description: Library name: B3


title: 2DM1F4HE_S16

description: Library name: 2DM1F4HE_S16_R1_001


title: 7726-JF-1

description: Library name: 7726-JF-1

value: Control


title: pho23Δ_1, glucose, Input

description: Library name: Input_3_D

value: Yeast

value: pho23 -


title: SSD NoImm Control 4

description: Library name: A4

value: Caecum


title: 7687-JF-2

description: Library name: 7687-JF-2


title: SSD NoImm Control 3

description: Library name: A3


title: Chow NoImm Tm 3

description: Library name: H3


title: 2DM1F3OV_S101

description: Library name: 2DM1F3OV_S101_R1_001

value: B6D2F1/Crl (BDF-1)

value: Used in Analysis


title: 7687-JF-1

description: Library name: 7687-JF-1

value: human skin

value: a pool of single cells


title: Chow NoImm Tm 2

description: Library name: H2


title: Chow NoImm Tm 1

description: Library name: H1


title: 2DM1F3LU_S19

description: Library name: 2DM1F3LU_S19_R1_001

value: Lung


title: Chow Imm Tm 3

description: Library name: G3


title: Chow Imm Tm 2

description: Library name: G2


title: 7681-JF-1

description: Library name: 7681-JF-1


title: 2DM1F3LI_S19

description: Library name: 2DM1F3LI_S19_R1_001

value: Liver Left Lobe


title: 7649-JF-3

description: Library name: 7649-JF-3

value: Les AD


title: Chow Imm Control 2

description: Library name: F2


title: 2DM1F3KI_S14

description: Library name: 2DM1F3KI_S14_R1_001

value: Kidney


title: 7649-JF-1

description: Library name: 7649-JF-1


title: Chow Imm Control 1

description: Library name: F1


title: Chow NoImm Control 2

description: Library name: E2


title: 2DM1F3HE_S14

description: Library name: 2DM1F3HE_S14_R1_001

value: Heart

value: female


title: 7640-JF-1

description: Library name: 7640-JF-1


title: 2DM1F2OV_S85

description: Library name: 2DM1F2OV_S85_R1_001


title: SSD NoImm Tm 3

description: Library name: D3


title: Chow NoImm Control 1

description: Library name: E1


title: SSD NoImm Tm 2

description: Library name: D2


title: 7608-JF-3

description: Library name: 7608-JF-3


title: 2DM1F2LU_S3

description: Library name: 2DM1F2LU_S3_R1_001


title: SSD NoImm Tm 1

description: Library name: D1


title: SSD Imm Tm 3

description: Library name: C3


title: SSD Imm Tm 2

description: Library name: C2


title: 7563-JF-1

description: Library name: 7563-JF-1


title: SSD Imm Tm 1

description: Library name: C1


title: 2DM1F2KI_S35

description: Library name: 2DM1F2KI_S35_R1_001


title: 7527-JF-4

description: Library name: 7527-JF-4


title: SSD Imm Control 1

description: Library name: B1


title: 2DM1F2HE_S35

description: Library name: 2DM1F2HE_S35_R1_001


title: 7527-JF-2

description: Library name: 7527-JF-2

value: Nonles AD


title: Meninges_P1_biol rep 3

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description:
Library name: sample 18
Column name in tpm_all_Samples.csv: Meninges_P1_3_tpm

data_processing:
Libraries were sequenced on an Illumina NovaSeq X apparatus at the NHLBI Genomics Facility at NIH. Reads of library were collected, converted by bcl2fastq (version 2) into fastq files and further analyzed for gene expression using Kallisto v0.51.1  (https://github.com/pachterlab/kallisto/releases)  given as TPM (transcripts per million read counts) according to the quantification of the reads on GRCm38/mm10 index.
Assembly: mm10
Supplementary files format and content: csv file include tpm values for each sample

source_name: meninges

extract_protocol:
RNA from different samples was purified using an RNeasy plus mini or macro kit (Qiagen #74134 or #74034)
150 - 300 ng RNA per sample were used to construct libraries with a SMARTer total RNA sample prep kit (Takara #634875) following manufacture's protocol.

treatment_protocol: Meninges and choroid plexus tissues were micro-dissected from embryos and neonatal mice at the ages indicated, then immediately frozen on dry-ice in readiness for RNA extraction.

value: meninges

tag: time

value: postnatal day 1

value: wt


title: 7527-JF-1

description: Library name: 7527-JF-1


title: 2DM1F1LU_S11

first: Scott

last: Auerbach

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 2DM1F1LU_S11_R1_001

value: 9 weeks


title: Meninges_P1_biol rep 1

description:
Library name: sample 16
Column name in tpm_all_Samples.csv: Meninges_P1_1_tpm


title: 7515-JF-1

description: Library name: 7515-JF-1

value: Control


title: Meninges_E17_biol rep 5

description:
Library name: sample 15
Column name in tpm_all_Samples.csv: Meninges_E17_5_tpm

value: embryonic day 17.5


title: 2DM1F1LI_S11

description: Library name: 2DM1F1LI_S11_R1_001

value: B6D2F1/Crl (BDF-1)


title: Meninges_E17_biol rep 4

description:
Library name: sample 14
Column name in tpm_all_Samples.csv: Meninges_E17_4_tpm


title: Meninges_E17_biol rep 3

description:
Library name: sample 13
Column name in tpm_all_Samples.csv: Meninges_E17_3_tpm


title: 7471-JF-1

description: Library name: 7471-JF-1


title: Meninges_E17_biol rep 2

description:
Library name: sample 12
Column name in tpm_all_Samples.csv: Meninges_E17_2_tpm


title: 2DM1F1HE_S6

description: Library name: 2DM1F1HE_S6_R1_001

value: Used in Analysis


title: Meninges_E14_biol rep 2

description:
Library name: sample 9
Column name in tpm_all_Samples.csv: Meninges_E14_2_tpm

value: embryonic day 14.5


title: 2DM1F10OV_S102

description: Library name: 2DM1F10OV_S102_R1_001

value: Ovary


title: Meninges_E14_biol rep 1

description:
Library name: sample 8
Column name in tpm_all_Samples.csv: Meninges_E14_1_tpm


title: 7461-JF-4

description: Library name: 7461-JF-4

value: human skin

value: a pool of single cells


title: 2DM1F10LU_S20

description: Library name: 2DM1F10LU_S20_R1_001

value: Lung


title: ChoroidP_E17_biol rep 3

description:
Library name: sample 6
Column name in tpm_all_Samples.csv: ChoroidP_E17_4_tpm

source_name: choroid plexus

value: choroid plexus


title: ChoroidP_E17_biol rep 2

description:
Library name: sample 5
Column name in tpm_all_Samples.csv: ChoroidP_E17_3_tpm


title: 7461-JF-2

description: Library name: 7461-JF-2


title: 2DM1F10LI_S20

description: Library name: 2DM1F10LI_S20_R1_001

value: Liver Left Lobe


title: ChoroidP_E17_biol rep 1

description:
Library name: sample 4
Column name in tpm_all_Samples.csv: ChoroidP_E17_2_tpm


title: 7461-JF-1

description: Library name: 7461-JF-1

value: Les AD


title: ChoroidP_E14_biol rep 3

description:
Library name: sample 3
Column name in tpm_all_Samples.csv: ChoroidP_E14_3_tpm


title: 2DM1F10KI_S15

description: Library name: 2DM1F10KI_S15_R1_001

value: Kidney

value: female


title: ChoroidP_E14_biol rep 1

description:
Library name: sample 1
Column name in tpm_all_Samples.csv: ChoroidP_E14_1_tpm


title: 7450-JF-4

description: Library name: 7450-JF-4


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_24h_D4_rep2

first: Kai

last: Ge

address: 50 South Dr Rm 4154

description: Library name: Sample 58

library_source: other

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER (v2) with following configuration: For ChIP-seq of HIRA and SPT6, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-10 were used. For S5P-Pol II, S2P-Pol II, and CDK9, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-3 were used. For H3K27ac, a window size of 200 bp, gap size of 200 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all ChIP-Seq data.
Paired-end reads of RNA-seq were aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Assembly: mm9
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

molecule: other

growth_protocol: Mouse 3T3-L1 white preadipocytes were maintained in growth (DMEM +10%BS) medium

extract_protocol:
Total RNA was subjected to rRNA depletion using theNEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads (NEB, E7405L) before using Click-iT™ Nascent RNA Capture Kit (C10365) to capture nascent RNA.
Isolated nascent RNAs were reverse-transcribed into cDNA using  SuperScript™ VILO™ cDNA Synthesis Kit (Thermo, 11754050) and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

treatment_protocol: For the adipogenesis assay, cells were plated in growth medium (DMEM plus 10% BS) 4 days before the induction and were induced with 10 μg/mL insulin, 0.5 mM IBMX and 1 μM DEX in FBS medium (DMEM plus 10% FBS) for 2 days. After 2 days of induction, the culture medium was changed to DMEM supplemented with FBS and insulin only.

value: Differentiating preadipocytes

value: HIRA depleted

value: adipogenic differentiation

value: day 4


title: 7450-JF-2

description: Library name: 7450-JF-2

value: Nonles AD


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_24h_D4

description: Library name: Sample 57


title: CCI/R2A_CFF_5

city: Washington

first: John

middle: R

last: Bethea

state: DC

address: 2300 I Street NW

institute: The George Washington University

description:
Library name: HC-275
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-275_Raw.Read.Count

data_processing:
Raw fastq read quality was assessed using fastqC v0.11.8.
Adapter and low-quality reads were trimmed using fastq-mcf v1.05 and cutadapt v2.5.
Contaminant reads, including mitochondrial, ribosomal RNA, transfer RNA, and adapter sequences, were removed using Bowtie2 v2.5.1.
Paired-end reads were aligned to the mouse reference genome using STAR v2.7.3a with a two-pass mapping strategy.
Raw gene counts were generated using HTSeq v0.11.2; normalized counts and differential expression were generated using DESeq2, and FPKM values were generated using Cufflinks v2.2.1.
Assembly: GRCm38/mm10, Ensembl release 92; genome-build accession NCBI:GCA_000001635.8
Supplementary files format and content: csv files include FPKM values for each sample

source_name: Brain - Hippocampus

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s instructions. RNA integrity was confirmed using an Agilent Bioanalyzer 2100; samples with RIN ≥ 7.0 were used.
RNA library for RNA-seq were prepared using Illumina TruSeq stranded mRNA kit following manufacturer's protocol

treatment_protocol: A TNFR2 agonist (10 mg/kg, i.p.), composed of a covalently stabilized TNFR2-selective single-chain TNF trimer fused to an effector-deficient Fc domain, was diluted in sterile PBS (Thermo Fisher J67670.K2) and administered on post-injury days (dpi) 7, 10, and 13 to half of the animal group. As control group, animals were treated with sterile PBS.

value: Brain - Hippocampus

value: Nex-CreERT2:TNFR2 F/F (CFF)

value: CCI + TNFR2 Agonist


title: 7450-JF-1

description: Library name: 7450-JF-1


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_rep2

description: Library name: Sample 56


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4

description: Library name: Sample 55


title: CCI/R2A_CFF_4

description:
Library name: HC-274
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-274_Raw.Read.Count


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_3h_D4_rep2

description: Library name: Sample 54


title: 2DM1F10HE_S15

city: Durham

description: Library name: 2DM1F10HE_S15_R1_001

value: Heart

value: B6D2F1/Crl (BDF-1)

value: 9 weeks

value: Used in Analysis


title: 7318-JF-2

description: Library name: 7318-JF-2

value: human skin

value: a pool of single cells


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_3h_D4

description: Library name: Sample 53


title: CCI/R2A_CFF_3

description:
Library name: HC-269
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-269_Raw.Read.Count


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D4_rep2

description: Library name: Sample 52

value: wild type


title: 7303-JF-2

description: Library name: 7303-JF-2


title: EU-RNA_3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D4

description: Library name: Sample 51


title: CCI/R2A_CFF_2

description:
Library name: HC-268
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-268_Raw.Read.Count


title: Chow Imm Tm 1

description: Library name: G1

value: Caecum


title: 3T3-L1_D4_rep2

description: Library name: Sample 50


title: 7303-JF-1

description: Library name: 7303-JF-1

value: Les AD


title: 3T3-L1_D4_rep1

description: Library name: Sample 49

value: Differentiating preadipocytes


title: 2DM1F2LI_S3

description: Library name: 2DM1F2LI_S3_R1_001

value: Liver Left Lobe

value: female


title: CCI/R2A_CFF_1

description:
Library name: HC-267
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-267_Raw.Read.Count


title: 7608-JF-1

description: Library name: 7608-JF-1


title: 7275-JF-1

description: Library name: 7275-JF-1

value: Control


title: 3T3-L1_D0_rep2

description: Library name: Sample 48

value: Preadipocyte

value: adipogenic differentiation

value: day 0


title: 3T3-L1_D0_rep1

description: Library name: Sample 47


title: SSD Imm Control 2

description: Library name: B2


title: SSD NoImm Control 2

description: Library name: A2


title: SSD NoImm Control 1

description: Library name: A1


title: 2DM1F1OV_S93

description: Library name: 2DM1F1OV_S93_R1_001

source_name: Ovary

value: Ovary


title: CCI/R2A_FF_5

description:
Library name: HC-262
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-262_Raw.Read.Count

value: Brain - Hippocampus

value: TNFR2 F/F (FF)

value: CCI + TNFR2 Agonist


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 8

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description: Library name: 23248XR-02-158

data_processing:
Raw paired-end sequence data in Fastq format was initially trimmed using the Flexbar package with the adapters of read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and read 2: GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT. Trimmed reads were aligned to mm10 genome reference by STAR, version 2.7.10b  to generate the bam files. The featureCounts package with multimapping reads as counted was employed to count the reads inside the bam files that were aligned to the 6 categories/classes of small RNAs: circRNA, miRNA, piRNA, snoRNA, snRNA, and tRNA. The annotations of snoRNA and snRNA are extracted from the Gencode mm10 GTF file. The miRNA sequences and annotations are based on the miRBase database. The genomic tRNA database is the source of the tRNA information. The piRNABank is the sources of the empirically known sequences and other related information on piRNAs. The circRNA sequences and annotations are from the circAtlas 3.0 database.
Deseq2 was used for normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: Raw_Counts_SmallRNA_CircRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_CircRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_miRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_miRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_piRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_piRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_snoRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_snoRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_snRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_snRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_tRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_tRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers)

source_name: Hippocampus

extract_protocol:
RNA was isolated from samples using Qiazol phase separation followed by cleanup with RNeasy 96 Kit per manufacturer’s instruction. Isolated RNA sample quality was assessed by both RNA Tapestation assay and High Sensitivity RNA Tapestation assay (Agilent Technologies Inc., California, USA and quantified by Infinite F Nano+ 200 Pro Tecan® (Tecan, Switzerland).
Library construction was prepared using NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) following the manufacturer's protocol (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 250bp with an insert size of about 100bp. Illumina® 6-nt single-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus (Illumina, California, USA) with a read length configuration of 150 PE for 20M PE reads per sample (10M in each direction).

value: Hippocampus

value: Tau-Wildtype Control


title: Meninges_P1_biol rep 2

description:
Library name: sample 17
Column name in tpm_all_Samples.csv: Meninges_P1_2_tpm

value: meninges

value: postnatal day 1

value: wt


title: 7208-JF-1

description: Library name: 7208-JF-1

value: human skin

value: a pool of single cells


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biolrep 7

description: Library name: 23248XR-02-157

value: Tau-MeCP2 Over-expression


title: CCI/R2A_FF_4

description:
Library name: HC-261
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-261_Raw.Read.Count


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 7

description: Library name: 23248XR-02-156


title: 7180-JF-1

description: Library name: 7180-JF-1


title: 7503-JF-1

description: Library name: 7503-JF-1


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 6

description: Library name: 23248XR-02-155


title: 2DM1F1KI_S6

description: Library name: 2DM1F1KI_S6_R1_001

value: Kidney

value: B6D2F1/Crl (BDF-1)

value: female

value: 9 weeks

value: Not Used in Analysis

value: Potential Tissue Contamination


title: CCI/R2A_FF_3

description:
Library name: HC-260
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-260_Raw.Read.Count

value: Brain - Hippocampus


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 5

description: Library name: 23248XR-02-154


title: 7169-JF-1

description: Library name: 7169-JF-1

value: Les AD


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 4

description: Library name: 23248XR-02-153


title: CCI/R2A_FF_2

description:
Library name: HC-259
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-259_Raw.Read.Count

value: TNFR2 F/F (FF)

value: CCI + TNFR2 Agonist


title: 7161-JF-2

description: Library name: 7161-JF-2

value: Nonles AD


title: Meninges_E14_biol rep 3

description:
Library name: sample 10
Column name in tpm_all_Samples.csv: Meninges_E14_3_tpm

value: meninges

value: embryonic day 14.5


title: Meninges_E17_biol rep 1

description:
Library name: sample 11
Column name in tpm_all_Samples.csv: Meninges_E17_1_tpm

value: embryonic day 17.5

value: wt


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biolrep 5

description: Library name: 23248XR-02-151

value: Hippocampus


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biolrep 6

description: Library name: 23248XR-02-152

value: Tau-MeCP2 Over-expression


title: CCI/R2A_FF_1

description:
Library name: HC-247
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-247_Raw.Read.Count


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biolrep 4

description: Library name: 23248XR-02-150


title: 7461-JF-5

description: Library name: 7461-JF-5

value: human skin

value: a pool of single cells


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biolrep 3

description: Library name: 23248XR-02-149


title: 7161-JF-1

description: Library name: 7161-JF-1


title: CCI/P_CFF_4

description:
Library name: HC-252
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-252_Raw.Read.Count

value: Nex-CreERT2:TNFR2 F/F (CFF)

value: CCI + PBS


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 3

description: Library name: 23248XR-02-148

value: Tau-Wildtype Control


title: 7148-JF-1

description: Library name: 7148-JF-1


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biolrep 2

description: Library name: 23248XR-02-147


title: CCI/P_CFF_3

description:
Library name: HC-251
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-251_Raw.Read.Count


title: 7117-JF-2

description: Library name: 7117-JF-2


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 1

description: Library name: 23248XR-02-145


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biolrep 1

description: Library name: 23248XR-02-144


title: CCI/P_CFF_2

description:
Library name: HC-189
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-189_Raw.Read.Count


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 12

description: Library name: 23248XR-02-143

value: MeCP2:-/Y rtt271a

value: injected rtt271 3e11


title: 7117-JF-1

description: Library name: 7117-JF-1

value: Les AD


title: CCI/P_CFF_1

description:
Library name: HC-187
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-187_Raw.Read.Count

value: Brain - Hippocampus


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 11

description: Library name: 23248XR-02-142


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 10

description: Library name: 23248XR-02-141


title: CCI/P_FF_4

description:
Library name: HC-246
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-246_Raw.Read.Count

value: TNFR2 F/F (FF)


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 9

description: Library name: 23248XR-02-140


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 8

description: Library name: 23248XR-02-139


title: CCI/P_FF_3

description:
Library name: HC-245
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-245_Raw.Read.Count


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 7

description: Library name: 23248XR-02-138


title: 7115-JF-1

description: Library name: 7115-JF-1


title: 7087-JF-1

description: Library name: 7087-JF-1


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 5

description: Library name: 23248XR-02-136


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 4

description: Library name: 23248XR-02-135


title: CCI/P_FF_1

description:
Library name: HC-196
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-196_Raw.Read.Count


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 3

description: Library name: 23248XR-02-134


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 2

description: Library name: 23248XR-02-133


title: Naïve_CFF_4

description:
Library name: HC-185
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-185_Raw.Read.Count

value: Naïve


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 1

description: Library name: 23248XR-02-132


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 13

description: Library name: 23248XR-02-131

value: injected rtt271 1e11


title: 7063-JF-1

description: Library name: 7063-JF-1


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 12

description: Library name: 23248XR-02-130


title: 7063-JF-2

description: Library name: 7063-JF-2

value: Nonles AD


title: Naïve_CFF_3

description:
Library name: HC-184
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-184_Raw.Read.Count


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 11

description: Library name: 23248XR-02-129


title: Naïve_CFF_2

description:
Library name: HC-183
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-183_Raw.Read.Count


title: 7027-JF-1

description: Library name: 7027-JF-1

value: Control


title: Naïve_CFF_1

description:
Library name: HC-179
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-179_Raw.Read.Count


title: Hippocmapus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 8

description: Library name: 23248XR-02-126


title: 7012-JF-2

description: Library name: 7012-JF-2


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 7

description: Library name: 23248XR-02-125


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 9

description: Library name: 23248XR-02-127


title: Naïve_FF_4

description:
Library name: HC-TNFR2
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-TNFR2_Raw.Read.Count


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 6

description: Library name: 23248XR-02-124


title: 7012-JF-1

description: Library name: 7012-JF-1


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 5

description: Library name: 23248XR-02-123


title: Naïve_FF_3

description:
Library name: HC-191
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-191_Raw.Read.Count


title: 7003-JF-1

description: Library name: 7003-JF-1


title: Hippocmapus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 3

description: Library name: 23248XR-02-121


title: Naïve_FF_2

description:
Library name: HC-190
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-190_Raw.Read.Count


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 1

description: Library name: 23248XR-02-119


title: 6967-JF-2

description: Library name: 6967-JF-2


title: Naïve_FF_1

description:
Library name: HC-186
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-186_Raw.Read.Count


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 20

description: Library name: 23248XR-02-117

value: injected pbs controls


title: 6967-JF-1

description: Library name: 6967-JF-1