title: Sample 3_2007

description: Library name: Sample 3

data_processing:
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline, which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads
The annotation was performed using the annotatePeak function in the default mode of the R ChIPseeker (version 1.38.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file compressed in .gz format includes information about all methylated positions on both strands, as well as columns for differential analysis and methylation annotations.
Library strategy: EM-seq

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction
Enzymatic methyl-seq (EM-seq): DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines.

value: Controls


title: CC5325, Chlamydomonas reinhardtii, DEA treatment, repeat 2

status: Public on Sep 05 2025

type: SRA

city: Shanghai

first: Fanchen

last: Wang

state: Shanghai

address: 1239 Siping Road

country: China

institute: Tongji University

description: Library name: CC5325_DEA2

library_source: genomic

data_processing:
The sequencing data derived from WGBS were trimmed and filtered using Trimmomatic[1] (v0.39), followed by using FastQC (v0.12.1). Clean reads were aligned to the reference sequence (C.reinhardtii CC_4532_707_v6.0) by used of Bismark (v0.24.2). Deduplication and methylation extraction were performed by used of deduplicate_bismark and bismark_methylation_extractor (both sub-tools in Bismark).
By taking the average of the values for each site, we merged the data from 2 experimental replicates to obtain the processed data.
Assembly: C.reinhardtii CC_4532_707_v6.0 (JGI)
Supplementary files format and content: bed files: tab-delimited text files include 5mC or 5gmC sites information and modification level for each Sample.

molecule: genomic DNA

organism: Chlamydomonas reinhardtii

growth_protocol: The C. reinhardtii strains (CC125 and CC5325) were cultured mixotrophically in TAP medium on a rotary shaker at 25 °C, with a light intensity of 20 μmol photons m-2∙s-1.

extract_protocol:
Total DNA was isolated using the CTAB method.
The treated DNA was then for sequencing library preparation, following the manufacturer’s protocol (Vazyme). Briefly, DNA libraries were generated by 3' adapter ligation, extension, 5' adapter ligation and library amplification.

tag: cell line

tag: genotype

value: WT


title: PA01, wildtype, no treatment, replicate 2

city: Birmingham

first: Jessica

last: Scoffield

state: Alabama

address: 1720 2nd Ave S

department: Microbiology

country: USA

institute: The University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
Reads were mapped to the P. aeruginosa reference genome GCF_000006765.1 using RNA STAR
Determination of read counts and normalization were performed using featureCounts
Assembly: GCF_000006765.1
Supplementary files format and content: tabular file with counts for each sample

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: P. aeruginosa cultures were grown in 2mL of SCFM2 +/- tobramycin at 37oC shaking and 250 rpm.

extract_protocol:
Pellets were resuspended in Trizol and cells were lysed using a BeadBlaster24, pelleting debris after bead beating. RNA was extracted from the lysate using the Zymo Research Direct-zol RNA MiniPrep kit using spin columns and DNAse digestion.
Performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices.

treatment_protocol: Culture tubes receiving treatment were prepared with 5 μg/mL tobramycin prior to inoculation with P. aeruginosa.

tag: strain

tag: cell type

value: bacterial cells

value: wildtype

tag: treatment


title: AM_RNA_328 rep2

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
RNA-seq data from liver samples of E11.5, E15.5, P1, P10, P30, and Adult stage mapped to a mouse genome mm39 using STAR aligner (Dobin et al., 2013). Count read tables were generated by the same program. Differential expression analysis was performed by the DEseq2 package (Love et al., 2014) in R version 4.2. (R-Core-Team, 2021). Differentially expressed genes were defined as having a fold-change bigger or equal to 1.5, an adjusted P-value smaller or equal to 0.01, and a minimum mean read count across the experiment samples of 50 reads.
Assembly: mm39
Supplementary files format and content: RNA-seq: comma separated file with raw counts
Supplementary files format and content: scRNA-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated Perturb-seq gRNA library count file

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

growth_protocol: 8-week-old and P30 liver: C57BL/6 mice were euthanized by the cervical dislocation and 24-gauge intravenous catheter (BD) was inserted into the portal vein. The inferior vena cava was cut for the drainage of the circulation solutions. EGTA solution (Calcium-free Earle's balanced salt solution (EBSS; Thermo) supplemented with 0.5mM ethylene glycol-bis (β-aminoethyl ether) N, N, N',N'-tetra-acetic acid (EGTA) (Sigma)) was circulated by the peristaltic pump at 37 °C at a rate of 3.3ml/min for 8 minutes. Followingly, the Liberase solution (40μg/ml Liberase (MERCK) in the Ca/Mg-plus EBSS buffer (Thermo)) was circulated at 37 °C at a rate of 3.3ml/min for 9 minutes. The liver cells were released from the liver capsule in the cold PBS (-)() and harvested into the 50ml conical tube. The supernatant was discarded after the centrifuge (180G, 2 min, 22 °C) then the cell pellets were resuspended in 2ml of 0.25% Trypsin/EDTA (Thermo) and incubated in the water bath at 37 °C for 5 minutes. The reaction was stopped by giving the 3ml of wash buffer KnockOut DMEM containing 10%FCS and 0.05mg/ml DNaseI (Merck)), then cells were dissociated by gently pipetting with 5ml pipet. Cell suspension was filtrated through the 70μm strainer (MERCK). Cell suspension was transferred into the 15ml conical tube and centrifuged at 50G for 2 minutes at 4 °C, then the supernatant was discarded to remove the debris. The pellet was resuspended into the 5ml of wash buffer and centrifuged at 50G for 2 minutes at 4 °C and this step was repeated again, resulting in a total 3 times of washing. The cell pellet after 3rd time centrifuge was resuspended in 5ml of wash buffer and 10μl of the cell suspension was used for the cell counting. 10 million of cells were separated in the new tube and used for the following step. Cells were centrifuged at 180G 2 minutes at 4 °C and performed blocking by the normal mouse serum (Thermo) 5 minutes on ice. Then the cells were resupended in the 500ul of antibody solution (Ceacam1-APC:1/500, F4/80-Alexa488: 1/500) diluted in the FACS buffer and incubated on ice for 10 minutes. The cells were washed twice with FACS buffer and resuspended in the 0.5μlg/ml PI (Propidium Iodide, Biolegend) containing FACS buffer.  P10 neonatal liver: Mice were anesthetized and a 23-G butterfly needle was inserted into the left ventricle of the heart for the perfusion of the enzyme solution77. For the drainage, an incision was made on the right atrial appendage with scissors. Perfusion of the enzyme solution was done using the same solutions as an adult with a modified flow rate (EGTA solution: 3.3ml/min, 7 minutes, Liberase solution: 3.3ml/min 7 minutes).  P1 liver: Pups were euthanized by decapitation and the isolated liver tissue was gently minced into small pieces by forceps. The minced liver tissue was harvested and resuspended in 1ml of enzyme solution (KnockOut DMEM containing 2mg/ml Collagenase XI (MERCK), 2.55mg/ml DispaseII (Thermo), 0.05mg/ml DNaseI, 1mM CaCl2) in the 15ml conical tube. The tissue was incubated at 37°C for 10 minutes, then stopped reaction by adding 4ml PBS (-). After centrifuge (180G, 1 minutes, at 4°C), the cell pellet was resuspended into 2ml PBS (-) and centrifuged again (180G, 1 minutes, at 4°C). The cell pellet was resuspended into 1ml of 0.25% trypsin/EDTA solution and incubated at 37°C for 5 minutes. The reaction was stopped by adding 1ml of cold wash buffer and cell clumps are dissociated by pipetting with P1000 pipet. The cell suspension was centrifuged (50G, 2 min, 4°C) and resuspended in 1ml of cold wash buffer and pipetted to obtain single cell suspension. Cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 min, 4°C) to remove the debris. The resultant cell pellet was further resuspended into the red blood cell lysis buffer (Thermo) and incubated at room temperature for 5 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Ceacam1-APC:1/500.   E15.5 liver dissociation: Embryonic liver was isolated and minced into pieces by forceps. 2 liver tissues were harvested into the 15ml conical tube and resuspended into the 500μl of 0.25% trypsin/EDTA solution. The tissues were incubated at 37°C for 9 minutes. The reaction was stopped by adding a 1ml of wash buffer and gently pipetted with a P1000 pipet. The cell suspension was centrifuged (50G, 2 minutes, 4°C), then resuspended in 1ml of stop solution and pipetted with P1000 pipet to dissociate into single cell suspension. The cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 minutes, 4°C). The resultant cell pellet was further resuspended into the red blood cell lysis buffer and incubated at room temperature for 3 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Pdgfra-APC:1/500.   E11.5 liver dissociation: Embryonic liver was isolated and 3 to 4 liver tissues were harvested into the 15ml conical tube and resuspended into the 400μl of 0.25% trypsin/EDTA solution. The tissues were incubated at 37°C for 7 minutes. The reaction was stopped by adding a 0.8ml of wash buffer and gently pipetted with a P1000 pipet. The cell suspension was centrifuged (180G, 2 minutes, 4°C), then resuspended in 1ml of stop solution and pipetted with P1000 pipet to dissociate into single cell suspension. The cell suspension was filtrated through the 70μm cell strainer and centrifuged (180G, 2 minutes, 4°C). The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Pdgfra-APC:1/500.

extract_protocol:
Harvested cells were homogenized, and total RNA was isolated using a RNeasy Plus Micro Kit (Qiagen).
The RNA-sequencing library was prepared using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA BIOSYSTEMS) and sequenced on an Illumina HiSeq 4000 sequencer as 75-bp paired-end reads

tag: tissue

value: Liver

tag: strain background

value: Hepatocyte

tag: time


title: E15.5 liver 10x Genomics

library_source: transcriptomic single cell

data_processing:
The single-cell RNA-seq datasets were processed with 10x Genomics' Cell Ranger pipeline version 7.0.0 (Zheng et al., 2017) and mapped to a mouse genome mm39
Assembly: mm39
Supplementary files format and content: RNA-seq: comma separated file with raw counts
Supplementary files format and content: scRNA-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated files and matrix
Supplementary files format and content: Perturb-seq: TAB separated Perturb-seq gRNA library count file

growth_protocol: "8-week-old : C57BL/6 mice were euthanized by the cervical dislocation and 24-gauge intravenous catheter (BD) was inserted into the portal vein. The inferior vena cava was cut for the drainage of the circulation solutions. EGTA solution (Calcium-free Earle's balanced salt solution (EBSS; Thermo) supplemented with 0.5mM ethylene glycol-bis (β-aminoethyl ether) N, N, N',N'-tetra-acetic acid (EGTA) (Sigma)) was circulated by the peristaltic pump at 37 °C at a rate of 3.3ml/min for 8 minutes. Followingly, the Liberase solution (40μg/ml Liberase (MERCK) in the Ca/Mg-plus EBSS buffer (Thermo)) was circulated at 37 °C at a rate of 3.3ml/min for 9 minutes.The liver cells were released from the liver capsule in the cold PBS (-)() and harvested into the 50ml conical tube. The supernatant was discarded after the centrifuge (180G, 2 min, 22 °C) then the cell pellets were resuspended in 2ml of 0.25% Trypsin/EDTA (Thermo) and incubated in the water bath at 37 °C for 5 minutes. The reaction was stopped by giving the 3ml of wash buffer KnockOut DMEM containing 10%FCS and 0.05mg/ml DNaseI (Merck)), then cells were dissociated by gently pipetting with 5ml pipet. Cell suspension was filtrated through the 70μm strainer (MERCK). Cell suspension was transferred into the 15ml conical tube and centrifuged at 50G for 2 minutes at 4 °C, then the supernatant was discarded to remove the debris. The pellet was resuspended into the 5ml of wash buffer and centrifuged at 50G for 2 minutes at 4 °C and this step was repeated again, resulting in a total 3 times of washing. The cell pellet after 3rd time centrifuge was resuspended in 5ml of wash buffer and 10μl of the cell suspension was used for the cell counting. 10 million of cells were separated in the new tube and used for the following step. Cells were centrifuged at 180G 2 minutes at 4 °C and performed blocking by the normal mouse serum (Thermo) 5 minutes on ice. Then the cells were resupended in the 500ul of antibody solution (Ceacam1-APC:1/500, F4/80-Alexa488: 1/500) diluted in the FACS buffer and incubated on ice for 10 minutes. The cells were washed twice with FACS buffer and resuspended in the 0.5μlg/ml PI (Propidium Iodide, Biolegend) containing FACS buffer.  P10 neonatal liver: Mice were anesthetized and a 23-G butterfly needle was inserted into the left ventricle of the heart for the perfusion of the enzyme solution77. For the drainage, an incision was made on the right atrial appendage with scissors. Perfusion of the enzyme solution was done using the same solutions as an adult with a modified flow rate (EGTA solution: 3.3ml/min, 7 minutes, Liberase solution: 3.3ml/min 7 minutes).  P1 liver: Pups were euthanized by decapitation and the isolated liver tissue was gently minced into small pieces by forceps. The minced liver tissue was harvested and resuspended in 1ml of enzyme solution (KnockOut DMEM containing 2mg/ml Collagenase XI (MERCK), 2.55mg/ml DispaseII (Thermo), 0.05mg/ml DNaseI, 1mM CaCl2) in the 15ml conical tube. The tissue was incubated at 37°C for 10 minutes, then stopped reaction by adding 4ml PBS (-). After centrifuge (180G, 1 minutes, at 4°C), the cell pellet was resuspended into 2ml PBS (-) and centrifuged again (180G, 1 minutes, at 4°C). The cell pellet was resuspended into 1ml of 0.25% trypsin/EDTA solution and incubated at 37°C for 5 minutes. The reaction was stopped by adding 1ml of cold wash buffer and cell clumps are dissociated by pipetting with P1000 pipet. The cell suspension was centrifuged (50G, 2 min, 4°C) and resuspended in 1ml of cold wash buffer and pipetted to obtain single cell suspension. Cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 min, 4°C) to remove the debris. The resultant cell pellet was further resuspended into the red blood cell lysis buffer (Thermo) and incubated at room temperature for 5 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Ceacam1-APC:1/500.   E15.5 liver dissociation: Embryonic liver was isolated and minced into pieces by forceps. 2 liver tissues were harvested into the 15ml conical tube and resuspended into the 500μl of 0.25% trypsin/EDTA solution. The tissues were incubated at 37°C for 9 minutes. The reaction was stopped by adding a 1ml of wash buffer and gently pipetted with a P1000 pipet. The cell suspension was centrifuged (50G, 2 minutes, 4°C), then resuspended in 1ml of stop solution and pipetted with P1000 pipet to dissociate into single cell suspension. The cell suspension was filtrated through the 70μm cell strainer and centrifuged (50G, 2 minutes, 4°C). The resultant cell pellet was further resuspended into the red blood cell lysis buffer and incubated at room temperature for 3 minutes. The cell suspension was centrifuged (180G, 2 minutes, 4°C) to remove the supernatant and resuspended in 1ml of wash buffer, then filtrated through the 70μm cell strainer. The obtained single-cell suspension was applied for the antibody staining procedures as described above. For this stage, following antibodies were used; Dlk1-PE:1/100, Pdgfra-APC:1/500.

extract_protocol:
A single cell suspension was loaded into the 10X Chromium device and libraries were prepared using the 10X Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121), following manufacturer’s instructions.
A single cell suspension of individual cell lines was loaded into the 10X Chromium device and libraries were prepared using the 10X Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121), following manufacturer’s instructions.


title: CC5325, Chlamydomonas reinhardtii, DEA treatment, repeat 1

description: Library name: CC5325_DEA1


title: AM_RNA_327 rep1


title: resected tumor samples from 15 mg dose cohort_5-Rep3

city: Cincinnati

first: Pankaj

middle: B.

last: Desai

state: OH

address: 231 Albert Sabin Way, Medical Science Building Suite 3303 (Desai Lab)

department: Pharmaceutical Sceinces

institute: University Of Cincinnati

description: Library name: PD15-8343A

data_processing:
The quality control of raw and aligned reads was performed using FastQC software
Differentially expressed genes were identified by fitting generalized linear model based on negative-binomial distribution of read counts as implemented in the edgeR Bioconductor package and FDR-adjusting p values.
Assembly: Sequence reads were aligned to the human reference genome (hg38) using the STAR aligner and the reads aligned to each known gene were counted based on the latest GENCODE definitions of gene features.
Supplementary files format and content: .xls files contain differential expression results comparing treated and control samples. Columns include name, gene ID, log2 fold change, adjusted p-value etc.
Supplementary files format and content: fastq.gz contain raw counts for each sample (R1 and R2)

organism: Homo sapiens

source_name: resected tumor sample from 15 mg cohort - Replicate 3

extract_protocol:
The tumor tissue samples were stored in RNAlater™-ICE before being extracted with the mirVana miRNA Isolation Kit with total RNA extraction protocol to extract the total RNA.
The mRNA libraries were prepared, indexed, and pooled to obtain 50 to 100 million reads per sample. Library sequencing for 50 bp reads was performed using the Illumina HiSeq system.

value: Letrozole (15 mg)


title: CC125, Chlamydomonas reinhardtii, TET and bisulfite treatment, repeat 2

description: Library name: CC125_TET-BS2


title: WT_scRNA

city: Hangzhou

first: Yu

last: Qian

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

institute: Zhejiang University

description:
Library name: WT_scRNA
MGI single-cell RNA-seq

data_processing:
Raw data were processed with DNBC4tools (v2.1.0) and downstream analysis using the Seura R package (v5.0). Cells with fewer than 200 or more than 6000 expressed genes, or with >15% mitochondrial gene content, were excluded. Doublets were removed using DoubletFinder (v2.0.4). Batch correction was performed with Harmony, followed by clustering, dimensionality reduction (PCA, UMAP), and differential expression analysis.
Assembly: GRCm39 (Mus musculus)
Supplementary files format and content: Processed data are provided in MTX format, including gene expression count matrix, gene annotation, and cell barcodes.

source_name: colon

growth_protocol: Eight-week-old mice were maintained under standard specific pathogen-free (SPF) conditions with free access to food and water.

extract_protocol:
Colonic tissues were dissected from AOM/DSS-treated Alkbh8 knockout and control mice. Epithelial and stromal cells were dissociated using enzymatic digestion (collagenase and DNase treatment), followed by filtration to obtain single-cell suspensions.
scRNA-seq libraries were prepared using the DNBelab C Series High-throughput Single-Cell RNA Library Preparation Set (940-001818-00, MGI) following the manufacturer’s instructions.

treatment_protocol: Male Alkbh8CTL and Alkbh8cKO littermates at 8 weeks of age received a single intraperitoneal injection of azoxymethane (AOM, Sigma) at a dose of 10 mg/kg body weight. Beginning one week later, animals were exposed to three cycles of dextran sulfate sodium (DSS, MP Biomedicals) treatment, each cycle consisting of 7 consecutive days of 2.5% (w/v) DSS in drinking water followed by a 14-day recovery period on regular water. At week 12, mice were euthanized, and colons were harvested for assessment of tumor incidence, number, and size.

value: colon

value: epithelial and stromal cells

value: Alkbh8 F/F

value: AOM/DSS


title: A8_KO_scRNA

description:
Library name: A8_KO_scRNA
MGI single-cell RNA-seq

value: Alkbh8 cKO


title: resected tumor samples from 15 mg dose cohort_5-Rep2

description: Library name: PD14-8343A

source_name: resected tumor sample from 15 mg cohort - Replicate 2


title: CC125, Chlamydomonas reinhardtii, TET and bisulfite treatment, repeat 1

description: Library name: CC125_TET-BS1


title: AM-RNA-309 rep3


title: AM-RNA-308 rep2


title: resected tumor samples from 15 mg dose cohort_5-Rep1

description: Library name: PD13-8343A

source_name: resected tumor sample from 15 mg cohort - Replicate 1


title: AK5PX

city: Liaoning

first: Rui

last: Ma

address: No. 9, West Section of Lushun South Road, Dalian City, Liaoning Province

institute: Dalian Medical University

description: Library name: Sample10

data_processing:
Library quantification was initially performed using Qubit 3.0, followed by dilution to 1 ng/μL. The insert size of the library was then validated using the Agilent 2100 Bioanalyzer. Upon confirmation of expected insert size, Q-PCR was conducted with the Bio-RAD CFX 96 system and Bio-RAD iQ SYBR® Green Supermix to determine the effective library concentration (>10 nM), ensuring library quality. Qualified libraries were subjected to sequencing on the Illumina platform with a PE150 strategy.
Assembly: GRCm39
Supplementary files format and content: fpkm.anno.txt

source_name: Inguinal white adipose tissue

growth_protocol: Flox and Ad-GHRKO mice were housed in an IVC system with 12-hour light/12-hour dark cycles and provided ad libitum access to regular chow and water, until they reached 20 months of age.

extract_protocol:
RNA was harvested using Agilent 2100 RNA Nano 6000 Assay Kit. 1.3 ug of total RNA was usedfor the construction of sequencing libraries.
Polyadenylated (polyA+) mRNAs from eukaryotic samples were enriched using oligo(dT) magnetic beads. Purified mRNA was fragmented by incubation with Fragmentation Buffer. First-strand cDNA synthesis was then performed using fragmented RNA as template with random hexamer priming. Second-strand cDNA synthesis was subsequently carried out using Second Strand Marking Buffer and Second Strand/End Repair Enzyme Mix. The resulting double-stranded cDNA underwent end repair, 3′-end adenylation, and adapter ligation. Size-selected fragments were purified using magnetic beads, followed by PCR amplification to complete library preparation.

treatment_protocol: Subcutaneous adipose tissue was harvested from 20-month-old Flox and Ad-GHRKO mice during necropsy.

value: Inguinal white adipose tissue

value: GHR Knockdown


title: Old baseline, replicate 1

city: Bethesda

first: Olivier

last: Duverger

state: MD

address: 30 Convent Drive - Bldg 30 - Room 202

institute: National Institute of Dental and Craniofacial Research

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a custom GRCm38.vM11 mouse genome that was modified to include common mouse transgenes, ERCCs and SIRVs using STAR v2.5.2a in single-pass mode with the --quantMode GeneCounts parameter.
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a GRCm38.vM11 genome annotation GTF which included common mouse transgenes, ERCCs and SIRVs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCm38.vM11
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: Composite tissue (bone, bone marrow, and intercoastal muscle) from old skeletally mature mice collected after rib resection

extract_protocol:
Composite tissue (bone and intercostal muscle) was dissected from the rib cage at different stages of rib regeneration (baseline, D0, D2, D5, D14) and snap frozen. Frozen tissue was ground using a mortar and pestle kept in liquid nitrogen. Powdered frozen tissue was immediately transferred to a clear tube and total RNA was extracted using TriPure Isolation Reagent (Sigma-Aldrich) followed by PureLink™ RNA Mini Kit (Thermo Fisher Scientific).
Library preparation was performed according to the manufacturer’s instructions for the Illumina TruSeq stranded library kit. The libraries were then pooled and sequenced on separate runs on a NovaSeq 6000 sequencer (Illumina) on 150bp paired-end mode.

tag: age

value: > 10 months

value: not applicable

value: Wild Type


title: CC5325KO, Chlamydomonas reinhardtii, TET and bisulfite treatment, repeat 2

description: Library name: CC5325KO_TET-BS2

value: Dnmt1 KO


title: AK4PX

description: Library name: Sample9


title: resected tumor samples from 12.5 mg dose cohort_4-Rep3

description: Library name: PD12B-8343A_L1

source_name: resected tumor sample from 12.5 mg cohort - Replicate 3

value: Letrozole (12.5 mg)


title: CC5325KO, Chlamydomonas reinhardtii, TET and bisulfite treatment, repeat 1

description: Library name: CC5325KO_TET-BS1


title: AM-RNA-307 rep3


title: AK3PX

description: Library name: Sample8


title: resected tumor samples from 15 mg dose cohort_5-Rep5

description: Library name: PD17-8343A

source_name: resected tumor sample from 15 mg cohort - Replicate 5


title: resected tumor samples from 12.5 mg dose cohort_4-Rep2

description: Library name: PD11B-8343A_L1

source_name: resected tumor sample from 12.5 mg cohort - Replicate 2


title: AM-RNA-306 rep2


title: P1 liver 10x Genomics


title: CC5325, Chlamydomonas reinhardtii, TET and bisulfite treatment, repeat 2

description: Library name: CC5325_TET-BS2

value: WT


title: AM-RNA-305 rep3


title: AK2PX

description: Library name: Sample7


title: resected tumor samples from 12.5 mg dose cohort_4-Rep1

description: Library name: PD10-8343A

source_name: resected tumor sample from 12.5 mg cohort - Replicate 1


title: CC5325, Chlamydomonas reinhardtii, TET and bisulfite treatment, repeat 1

description: Library name: CC5325_TET-BS1


title: resected tumor samples from 15 mg dose cohort_5-Rep4

description: Library name: PD16-8343A

source_name: resected tumor sample from 15 mg cohort - Replicate 4


title: CC125, Chlamydomonas reinhardtii, bisulfite treatment, repeat 2

description: Library name: CC125_BS2


title: AM-RNA-303 rep3


title: resected tumor samples from 10 mg dose cohort_3-Rep3

description: Library name: PD9-8343A

source_name: resected tumor sample from 10 mg cohort - Replicate 3

value: Letrozole (10 mg)


title: resected tumor samples from 10 mg dose cohort_3-Rep2

description: Library name: PD8-8343A

source_name: resected tumor sample from 10 mg cohort - Replicate 2


title: CC125, Chlamydomonas reinhardtii, bisulfite treatment, repeat 1

description: Library name: CC125_BS1


title: AL5PX

description: Library name: Sample5

value: Flox


title: AM-RNA-302 rep3

value: Liver

value: Hepatocyte


title: AL4PX

description: Library name: Sample4


title: CC5325KO, Chlamydomonas reinhardtii, bisulfite treatment, repeat 2

description: Library name: CC5325KO_BS2


title: AL3PX

description: Library name: Sample3


title: AM-RNA-301 rep1


title: resected tumor samples from 10 mg dose cohort_3-Rep1

description: Library name: PD7-8343A

source_name: resected tumor sample from 10 mg cohort - Replicate 1


title: CC5325KO, Chlamydomonas reinhardtii, bisulfite treatment, repeat 1

description: Library name: CC5325KO_BS1


title: AM-RNA-300 rep1


title: AL2PX

description: Library name: Sample2


title: resected tumor samples from 5 mg dose cohort_2-Rep3

description: Library name: PD6-8343A

source_name: resected tumor sample from 5 mg cohort - Replicate 3

value: Letrozole (5 mg)


title: CC5325, Chlamydomonas reinhardtii, bisulfite treatment, repeat 2

description: Library name: CC5325_BS2


title: AL1PX

description: Library name: Sample1


title: resected tumor samples from 5 mg dose cohort_2-Rep2

description: Library name: PD5-8343A

source_name: resected tumor sample from 5 mg cohort - Replicate 2


title: AK1PX

description: Library name: Sample6


title: AM-RNA-304 rep2

source_name: Liver


title: CC5325, Chlamydomonas reinhardtii, bisulfite treatment, repeat 1

description: Library name: CC5325_BS1


title: resected tumor samples from 5 mg dose cohort_2-Rep1

description: Library name: PD4-8343A

source_name: resected tumor sample from 5 mg cohort - Replicate 1


title: resected tumor samples from 2.5 mg dose cohort_1-Rep3

description: Library name: PD3-8343A

source_name: resected tumor sample from 2.5 mg cohort - Replicate 3

value: Letrozole (2.5 mg)


title: OSK Mouse control

type: RNA

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

hyb_protocol: Tissue sections (5 μm) were mounted on Xenium slides. Samples were processed according to the manufacturer’s demonstrated protocol for the 10x Genomics Xenium In Situ Analyzer using the Mouse Whole Transcriptome Panel. Hybridization of target transcripts to barcoded oligonucleotide probes was performed on the Xenium Analyzer.

scan_protocol: Samples were run on Xenium Analyzer.

data_processing: To improve the accuracy of cell segmentation in Xenium spatial transcriptomics data, we re-segmented the retinal tissue using high-resolution fluorescent imaging. Tissue sections were imaged with the DAPI channel on a ZEISS Apotome 3 fluorescence microscope (Carl Zeiss Microscopy) using a 20X objective. Z-stack images were acquired across the full thickness of the section with a z-step size of 2.0 µm. A 2D maximum intensity projection was generated from each z-stack using ZEISS Zen software (Carl Zeiss Microscopy), producing high-resolution DAPI images that captured nuclear architecture throughout the tissue.  The 2D projection DAPI images were aligned to the original Xenium DAPI images using the image registration function in Xenium Explorer 2.0 (10x Genomics), generating alignment matrices. Alignment accuracy was verified visually by comparing prominent anatomical landmarks and nuclear contours. Custom Python code was used to apply these alignment matrices to transform the projection images (10.5281/zenodo.15777981).  The aligned images were imported into QuPath 0.5.0 for layer-specific segmentation. Using the cell detection classifier tool, we trained custom classifiers to segment nuclei within the outer nuclear layer (ONL), inner nuclear layer (INL), and ganglion cell layer (GCL) 132. Due to the distinct compactness of nuclei in the ONL, segmentation for this layer was performed separately using manual selection to ensure accurate annotation.

label: Xenium probe panel (10x Genomics)

source_name: Mouse retina, OSK section processed on Xenium Analyzer

label_protocol: Xenium Mouse Whole Transcriptome Panel probes (10x Genomics) were hybridized in situ to target RNA molecules. Each probe contained a unique barcode sequence to enable transcript identification during sequencing-free imaging on the Xenium Analyzer.

growth_protocol: Mice used in these experiments were maintained in accordance with guidelines established by the National Institutes of Health and approved by the Institutional Animal Care and Use Committee (IACUC) at Johns Hopkins School of Medicine (Protocol#MO22022). Mice were housed in a climate controlled facility on a 14/10h light/dark cycle. C57BL/6J mice were used for all experiment and were obtained from Jackson Labs (strain #:000664). GlastCreER;Sun1-GFP mice were obtained from Dr. Jeremy Nathants (cite) and crossed onto B6;129S4-Gt(ROSA)26Sortm1(rtTA*M2)JaeCol1a1tm7(tetO-Pou5f1,-Klf4,-Sox2,-mCherry)Hoch/J mice from Jackson Labs (strain #: 034917). These mice were back crossed onto C57BL/6J mice to remove the rtTA gene, and subsequently crossed onto B6.Cg-Gt(ROSA)26Sortm1(rtTA,EGFP)Nagy/J from Jackson Labs (strain #: 005670), to generate a tamoxifen and doxycycline inducible line, which we refer to as GlastCreER;OSK. Tamoxifen was administered intraperitoneally once per day for 5 consecutive days (1.5mg/dose). Mice were then put on Doxycycline Diet (6kmg/kg) from Teklad Global Rodent Diets (TD.01533) for 4 weeks.

extract_protocol: Mouse eyes were enucleated and dissected in ice cold PBS. Eyes were hemisected and lenses removed. Eyes were then embedded in chilled OCT and flash frozen on pre-cooled isopentane and dry ice. Two 14 micron slices were collected from each retina, one peripherally and one centrally, onto a Xenium Prime 5K Mouse Pan Tissue & Pathways Panel slide. Retinas from 1 male and 1 female mouse were collected for each age. Xenium slides were processed at the Single Cell Transcriptomics Core at Johns Hopkins University.

treatment_protocol: Retinal tissue from one eye of 2 male and 2 female mice were pooled for each age timepoint and flash frozen on dry ice and stored at -80°C. For all aged mouse multiome libraries, nuclei were extracted per 10X Genomics Protocol CG000366 Rev C protocol from fresh frozen tissue. Nuclei were resuspended in 1 U/µl RNase inhibitor (Promega, N2615) and Diluted Nuclei Buffer (10X Genomics, 2000207). RNA and ATAC libraries were prepared according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG0000338 Rev F). Libraries were sequenced via Illumina NovaSeq or NovaseqX Pus targeting 30,000 reads per cell for 10-15000 cells at the Single Cell and transcriptomics sequencing core (STAC) at Johns Hopkins University.

value: Retina

tag: sample

value: OSK control


title: OSK Mouse diet

value: OSK overexpression


title: AM-RNA-297 rep1


title: resected tumor samples from 2.5 mg dose cohort_1-Rep2

description: Library name: PD2B-8343A_L1

source_name: resected tumor sample from 2.5 mg cohort - Replicate 2


title: AM-RNA-298 rep2


title: half, 24-hour post-fertilization, rep2

city: Chiba

first: Koki

last: Tsuyuzaki

address: 1-8-1, Inohana, Chuo-ku, Chiba-shi

country: Japan

institute: Chiba University

description: Library name: 24h-half-2

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling, through integrated primary analysis software called RTA (Real Time Analysis). The BCL/cBCL (base call) binary files are converted into FASTQ files using bcl2fastq, which is an Illumina provided package.
Assembly: The reference genome file (HpulGenome_v1_scaffold.fa) and the annotation file (HpulGenome_v1.gff3) of H. pulcherrimus were retrieved from HpBase (https://cell-innovation.nig.ac.jp/Hpul/).
Supplementary files format and content: Reference genome and annotation files for H. pulcherrimus were retrieved from Hpbase. Trimmomatic (v0.39) was used to trim Illumina adapter sequences from FASTQ files. STAR aligner (v2.7.10a) indexed and mapped trimmed FASTQ files to the reference genome. FeatureCounts (v2.0.1) quantified gene expression levels. FastQC (v0.11.9) and MultiQC (v1.12) checked read quality. R (v4.4.2) with ggplot2 (v3.5.1) generated correlation heatmaps and PCA plots. edgeR (v4.4.1) and DESeq2 (v1.46.0) detected DEGs, visualized with ggplot2. Analyses were performed using Snakemake (v6.5.3) with Docker containers and Singularity (v3.5.3) for reproducibility.
Supplementary files format and content: featureCounts

organism: Hemicentrotus pulcherrimus

source_name: half

extract_protocol:
Embryos/larvae were collected and washed twice in ice-cold Ca2+-free seawater. Total RNA was extracted with RNeasy plus mini kit (Qiagen) by following the instruction.
Library was performed according to the manufacter’s instructions (SMARTer Standard RNA-seq Kit).

value: half

value: bisected


title: Aging Mouse 112wk

source_name: Mouse retina, aging section processed on Xenium Analyzer

value: Aging 112wk


title: resected tumor samples from 2.5 mg dose cohort_1-Rep1

description: Library name: PD1-8343A

source_name: resected tumor sample from 2.5 mg cohort - Replicate 1


title: Aging Mouse 55wk

value: Aging 55wk


title: half, 24-hour post-fertilization, rep1

description: Library name: 24h-half-1


title: Aging Mouse 12wk

value: Aging 12wk


title: control, 24-hour post-fertilization, rep3

description: Library name: 24h-cont-3

source_name: whole

value: whole


title: AM-RNA-299 rep1


title: Aging Mouse 5wk

value: Aging 5wk


title: control, 24-hour post-fertilization, rep2

description: Library name: 24h-cont-2


title: D3

city: Urumqi

first: Xuwen

last: Mao

address: CollNo.567, Shangde North Road, Shuimogou District

institute: Xinjiang medical university

description:
Library name: sample12
Column name in gene_count.txt: D3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file included raw counts for each Sample
Supplementary files format and content: csv file included FPKM values for each Sample

source_name: Colon

growth_protocol: Sixty 5-week-old male C57BL/6J mice used in this work, the housing conditions were maintained with a 12 h light/12 h dark cycle, at a temperature of 21±2°C, and a humidity of 40-45%.

extract_protocol:
Following euthanasia, the colon was excised and washed with PBS containing 1 mM Phenylmethanesulfonyl fluoride (PMSF) and 0.2 mM sodium orthovanadate. Measurements of colon length and weight were taken, and sections of the colon were sampled for RNA extraction.
An mRNA sequencing library was prepared from 5 μg of total RNA, and its concentration was quantified using the Qubit fluorometric quantitation method. Sequencing was performed on the HiSeq X10 system

treatment_protocol: Acute colitis was induced in C57BL/6J mice using DSS. We randomly divided the mice into these groups: Control, Model, Dexamethasone (DXM, 4 mg·kg-1), and Rhy low (Rhy-L, 2 mg·kg-1), medium (Rhy-M, 4 mg·kg-1), and high dose (Rhy-H, 8 mg·kg-1) groups.

value: Colon

tag: Sex

value: male

value: WT

value: DXM+DSS


title: D2

description:
Library name: sample11
Column name in gene_count.txt: D2


title: half, 24-hour post-fertilization, rep3

description: Library name: 24h-half-3


title: 9395-AS-9

city: Ann Arbor

first: Christina

middle: Vadala

last: Angeles

state: MI

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

description:
Library name: N1692
1 ACPP tumor

data_processing:
Fastq, raw reads, files were processed through fastp software. Reads were aligned to the reference genome (GRCm39) using Hisat2 v2.05. featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Assembly: GRCm39
Supplementary files format and content: raw and filtered/combined count matricies

source_name: ACPP tumor

extract_protocol:
ACPP tumors and normal fat were stored in liquid nitrogen or RNAlater stablization solution until extraction. 30 mg of frozen tissue was dissociated using the BeadBug Homogenizer (Southern Labware, D1030). RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen #80204). RNA concentrations were determined using the NanoDrop 2000 (Thermo Fisher Scientific). Messenger RNA was purified from total RNA using poly-T-oligo-attached magnetic beads.
Library construction was performed and completed by Novogene or the UM Advanced Genomics Core

value: ACPP tumor

tag: condition

value: DDLPS

value: Trp53f/fPtenf/f C57BL/6J


title: D1

description:
Library name: sample10
Column name in gene_count.txt: D1


title: C3

description:
Library name: sample9
Column name in gene_count.txt: C3

value: Rhy+DSS


title: AM-RNA-296 rep2

value: Liver

value: Hepatocyte


title: half, 18-hour post-fertilization, rep3

description: Library name: 18h-half-3

value: half


title: control, 24-hour post-fertilization, rep1

description: Library name: 24h-cont-1


title: half, 18-hour post-fertilization, rep2

description: Library name: 18h-half-2

value: bisected


title: C2

description:
Library name: sample8
Column name in gene_count.txt: C2


title: 9395-AS-6

description:
Library name: N1722
1 ACPP tumor

value: WDLPS


title: 9395-AS-4

description:
Library name: N1760
1 Normal Fat Pad (uninjected)

source_name: Normal Fat Pad (uninjected)

value: Normal Fat Pad (uninjected)

value: Normal Fat


title: 9395-AS-5

description:
Library name: N1285
1 ACPP tumor


title: AM-RNA-295 rep1


title: hMSC-2D_sub2

city: Hong Kong

first: Pui

last: Chan

state: Hong Kong

address: Room 711, Haking Wong Building, The University of Hong Kong, Pokfulam Road

department: Department of Mechanical Engineering

institute: The University of Hong Kong

description: Gene expression data from tranmigration of cells between 3DM gp and 2D gp in 2 subjects

hyb_protocol: The GeneChips were finally washed and stained by the GeneChip Fluidics Station 450 and then

scan_protocol: The GeneChips were scanned with the GeneChip Scanner 3000 7G.

data_processing: Raw data was processed and analyzed by GeneSpring GX version 14.9 (Agilent) for normalization, filtering and then statistical data analysis. Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure and probesets between 20th-100th percentiles of the intensity value were included for subsequent statistical analysis by moderated t-test with P value asymptotic computation and Benjamin Hochberg FDR multiple testing correction under a P value cut-off of 0.05. Significant DEGs with fold change ≥2 in 3DM vs 2D vs 3DM groups were selected for gene ontology (GO) analysis. The GO terms or pathways with P value ≤ 0.05 were selected.

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 2D and 3D collagen-encapsulated MSCs cultivated in DMEM-LG full medium up to 9 days with a change of medium every 3days.

extract_protocol: Total RNAs were extracted from cell suspension from 2D and 3DM groups by the RNeasy Mini Kit (Qiagen) followed by QC checking using Agilent 2100 bioanalyzer.

treatment_protocol: hMSCs (1e5 cell/ml) encapsulated in 3D collagen in  a culture dish with medium for 3days at 37C and 5%CO2, followed by replating in other culture dish for cultivation and transmigration out from 3D collagen barrier into the dish for up to extra 6 days in compared to those groups from 2D monolayer MSCs

tag: individual

value: subject 2

value: MSC


title: half, 18-hour post-fertilization, rep1

description: Library name: 18h-half-1


title: hMSC-2D_sub1

value: subject 1


title: Follicular B cells from Dot1l conditional knockout mice, BCR-seq, rep 3

city: Clayton

first: Kim

middle: L

last: Good-Jacobson

state: Vitoria

address: 19 Innovation Walk

department: Biochemistry & Molecular Biology

country: Australia

institute: Monash University

description:
Library name: Follicular B cell DOT1L KO Biological Replicate 3
250bp Pair-End V2 500 cycle

data_processing:
Raw data files were loaded onto VDJserver paired and filtered using pRESTO. Files were aligned to the genome using IgBlast which was then followed by repertoire analysis by RepCalc. Relative gene distribution and clonal information could be visualised on VDJserver.
Assembly: mm10 (GRCm38)
Supplementary files format and content: "VDJserver_RepCalc_Output.csv" contains the absolute read counts and relative frequency of gene usage for each VH gene family for each biological replicate.
Library strategy: BCR-Seq

source_name: Spleen

extract_protocol:
DNA was extracted using the Machery Nagel Nucleospin DNA extraction kit according to manufacturer’s instructions. V(D)J genes were amplified using the KAPA HiFi HotStart ReadyMix PCR kit (KAPA, Roche). Amplicons were purified using the Agencourt AMPure XP beads (Beckman Coulter), and second-round PCRs were performed to add Illumina NexteraXT adaptors to the IgH library. 10ng of each amplicon pool was amplified with Illumina Nextera XT adaptors to add both indexes and P5/P7 sequences for 8 cycles of PCR. Sequencing was performed using Illumina MiSeq V2 chemistry and 251base PE reads.
ChIP-processed and input control samples were processed using the MGI Easy DNA FS Library preparation kit V1 (MGI Tech) and sequenced using a MGISEQ-2000RS High-Throughput Sequencing Set (PE100).

treatment_protocol: Follicular B-cells (CD19+CD21intCD23+) were sort-purified from Mb1Cre/+ and Dot1lf/fMb1Cre/+ mice.

value: Spleen

value: Follicular B cells

tag: amplification primers


title: hMSC-3DM_sub2


title: Follicular B cells from Dot1l conditional knockout mice, BCR-seq, rep 2

description:
Library name: Follicular B cell DOT1L KO Biological Replicate 2
250bp Pair-End V2 500 cycle


title: Follicular B cells from Dot1l conditional knockout mice, BCR-seq, rep 1

description:
Library name: Follicular B cell DOT1L KO Biological Replicate 1
250bp Pair-End V2 500 cycle


title: C1

description:
Library name: sample7
Column name in gene_count.txt: C1

value: Colon

value: male

value: WT


title: B3

description:
Library name: sample6
Column name in gene_count.txt: B3

value: DSS


title: 9395-AS-3

description:
Library name: N1759
1 Normal Fat Pad (uninjected)

value: Trp53f/fPtenf/f C57BL/6J


title: Follicular B cells from Cre control mice, BCR-seq, rep 3

description:
Library name: Follicular B cell Control Biological Replicate 3
250bp Pair-End V2 500 cycle


title: control, 18-hour post-fertilization, rep3

description: Library name: 18h-cont-3

value: whole


title: Follicular B cells from Cre control mice, BCR-seq, rep 2

description:
Library name: Follicular B cell Control Biological Replicate 2
250bp Pair-End V2 500 cycle


title: 9395-AS-24

description:
Library name: N1319
1 ACPP tumor

value: ACPP tumor

value: DDLPS


title: control, 18-hour post-fertilization, rep1

description: Library name: 18h-cont-1


title: 9395-AS-23

description:
Library name: N1307
1 ACPP tumor


title: B1

description:
Library name: sample4
Column name in gene_count.txt: B1


title: Follicular B cells from Cre control mice, BCR-seq, rep 1

description:
Library name: Follicular B cell Control Biological Replicate 1
250bp Pair-End V2 500 cycle


title: 9395-AS-22

description:
Library name: N1345
1 ACPP tumor


title: FACS sorted Venus+ EECs and Venus- non EECs from tHIOs, plate IGB-AA-s029

city: ILLKIRCH

first: Adèle

last: DE ARCANGELIS

address: 1 rue Laurent Fries

department: Development & Stem Cells

country: France

institute: IGBMC, CNRS UMR 7104, Inserm U 1258

description:
Library name: tHIO_IGB-AA-s029
SORT-seq
tHIOs.h5ad
tHIOs_ec.h5ad
human_pre-processed.h5ad
integration_human_thios_scVI.h5ad

data_processing:
Demultiplexing, alignment and quantification were performed by Single Cell Discoveries (Utrecht, The Netherlands, https://www.scdiscoveries.com), using scRNAseq analysis  based on Seurat v3.1. For all the additional analyses we carried out, we used the transcript count matrix and the python-based Scanpy API (Wolf et al., 2018).
Assembly: For mouse samples: mm10
Assembly: For HIO and tHIO samples: GRCh38
Supplementary files format and content: Annotated data matrix (adata) objects saved in h5ad-file format are provided. The file contains the preprocessed, normalized and annotated count data of all experiments. Mouse data : adata_e15.h5ad;  adata_e18.h5ad;  adata_P12.h5ad -> adata for each individual stage (E15.5; E18.5; P12 respectively);  adata_3stages.h5ad -> adata including the integration of all 3 stages; adata_3stages_pt.h5ad -> adata including pseudotime analysis of all 3 stages. HIOs data : HIOs.h5ad -> adata for HIOs tHIOs data : tHIOs.h5ad -> adata including all tHIO intestinal epithelial cells (Venus+ EECs and Venus- non EECs) ; tHIOs_ec.h5ad -> adata including only Venus+ EECs ; human_pre-processed.h5ad -> adata including data on human EECs from the study of  Elmentaite et al., 2021; integration_human_thios_scVI.h5ad -> adata integrating the human EECs data from the study of Elmentaite et al, 2021 and the Venus+ EECs data from tHIOs.

source_name: tHIO, hiPSC differentiated into proximal small intestine

growth_protocol: Mouse study: Heterozygous Neurog3eYFP/+ mice were collected at embryonic day E15.5 (n=18 embryos from 3 litters) and E18.5 (n=27 embryos from 3 litters), and 12 days after birth (P12) (n=7 pups from 1 litter). Single cells were isolated from the whole small intestine either directly for stages E15.5 and E18.5, or by first separating the epithelial cells  from the rest of the intestine tissue at P12 (Piccand et al., 2019). Human study: HIOs derived from NEUROG3-HA-P2A-Venus hiPSCs were generated using STEMdiff™ Intestinal Organoid Kit (STEMCELL™ Technologies), according to manufacturer’s protocol with some modifications. Spheroids were collected 2-3 days after exposure to MHG (mid-/hindgut) medium, and embedded in Matrigel domes (growth factor reduced-phenol red free Matrigel; Corning) to allow their 3D growth, in presence of STEMdiff™ Intestinal Organoid Growth Medium (OGM). Organoids were split every 10-14 days and embedded in new Matrigel domes. Medium was changed every 3-4 days. HIOs were maintained in 3D culture for 31-42 days. For the HIOs that were subsequently transplanted (tHIOs) into immunocompromised NSG mice, the OGM medium was replaced by a medium containing only EGF (Advanced DMEM/F-12, HEPES 10 mM, GlutaMAX 2 mM, penicillin/streptomycin 100 U/mL, supplement B27 1X, supplement N2 1X (all from Gibco™), human recombinant EGF 50 ng/mL (PeproTech®) in order to promote the development of mesenchyme-rich HIOs, essential to ensure good engraftment and growth of the transplant (Múnera et al., 2017; Watson et al., 2014).

extract_protocol:
Isolation of mouse EECs: Mouse intestinal samples were digested into single cells for 30 to 40 min at 37°C in TrypLETM Express with vigorous up and downs shakings each 5 min. The cells were centrifuged twice at 900rpm, 5min, 4°C in Advanced DMEM, HEPES 10mM, fetal calf serum (FCS) 10%. For the P12 small intestine, an additional filtering step, onto a 70µm cell strainer, was performed before centrifugation. Cells were resuspended in Advanced DMEM F12, HEPES 10mM, FCS 5%, Y-27632 10µM, filtered through a 50µm cell strainer and sorted with a FACS Aria Fusion II (BD) in SORT-seq 384-well cell-capture plates (Single Cell Discoveries). Plates were sealed, centrifuged 2min at 1500g, 4°C, and snap-frozen and stored at -80°C until sequencing. Dissociation of HIOs and tHIOs into single cells and isolation of EECs for single-cell RNA sequencing: Around 40 HIOs (from a single differentiation) were dissociated to single cells as previously described with some modifications (Grün et al., 2015). Briefly, after medium removal, rinsing of each well with PBS1X, and Matrigel disruption, HIOs were dissociated in TrypLE™ Express (1X) (Gibco™) at 37 °C for 20 min, assisted by a mechanical dissociation (up and down with a p1000 pipette). The dissociation was stopped in a basal medium containing Advanced DMEM/F-12, HEPES 10 mM, fetal calf serum 10%, and Y27632 10µM (STEMCELL™ Technologies). After 3 washes, the cells were resuspended in the FACS medium (basal medium containing only 5% of fetal calf serum), strained through a 50 μm cell strainer, and stained with DAPI (to exclude dead cells) before being sorted by flow cytometry (FACSAria Fusion, BD) based on Venus fluorescence levels. Individual cells were sorted directly in pre-filled 384-well cell capture plates (one cell/well) containing the reagents to perform single-cell RNA-sequencing (scRNA-Seq) according to the SORT-Seq technology (Muraro et al. 2016)(Single Cell Discoveries, Utrecht, The Netherlands). tHIOs were dissociated to single cells as described by Yu et al., (2021) with modifications. Briefly, a total of 8 individual tHIOs were harvested 15 weeks post-transplantation. Samples were first minced into small pieces using a scalpel in ice-cold 1X HBSS, then enzymatically digested in the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) at 10°C, following the manufacturer’s instructions. After complete dissociation, the cells were filtered through a 70µm cell strainer, centrifuged (500g, 5 min, 10°C) and the pellet was resuspended in the basal medium. The cell suspensions (from 1 to 3 tHIOs, depending on their size) were then labeled using an anti-EpCAM antibody to collect only epithelial cells (APC anti-human CD326 (EpCAM) antibody, BioLegend) and DAPI (to exclude dead cells). Cells were filtered through a 50 μm cell strainer before being sorted by FACS (FACSAria Fusion, BD) directly into the 384-well plates for SORT-Seq analysis (Single Cell Discoveries, Utrecht, The Netherlands), as described above. Both DAPI-; EpCAM+; Venus+ or Venus- cells were harvested. Reads were mapped to the human GRCh38 genome assembly.
Single cells were sequenced with the SORT-seq method (Muraro et al., 2016), a partially robotized version of the CEL-seq2 protocol (Hashimshony et al., 2016). Library preparation and single-cell RNA sequencing were performed by Single Cell Discoveries (Utrecht, The Netherlands, https://www.scdiscoveries.com). Briefly, single cells were sorted by FACS into each well of a cell-capture 384-well plate, containing well-specific barcoded primers. Each primer contains a cell-specific barcode and a unique molecular identifier (UMI). The protocol involves the following steps: 1) lysis of cells by heat (65°C, 5min) and hybridization of primers to the poly-A tail of mRNAs. 2) Reverse transcription & second-strand synthesis (Invitrogen). 3) Pooling of all the wells. 4) In vitro transcription (IVT) (Ambion) to generate many copies of RNA via linear amplification.5) Fragmentation & reverse transcription: the amplified RNA (aRNA) is fragmented into segments of approximately 300-400 base pairs and reverse transcribed. 6) Amplification of the cDNA by PCR and addition of sequencing adapters (10-12 cycles with Illumina TruSeq primers). The resulting cDNA libraries were paired-end sequenced at a depth of 150.000 reads/cell on an Illumina NextSeq 500.

treatment_protocol: In vivo transplantation of HIOs into the renal subcapsular space of NSG immunocompromised mice. Transplantations of HIOs under the kidney capsule were carried out as described by Watson and collaborators (Watson et al. 2014) with some modifications. Prior to transplantation, HIOs were maintained in culture for 40-42 days. Transplants (tHIOs) were harvested 15 weeks post-transplantation and immediately processed to obtain single cells.

value: NEUROG3-HA-P2A-Venus hiPSCs

value: EECs, other intestinal epithelial cells

value: NEUROG3 Venus/+

value: tHIO analyzed 15 weeks after transplantation


title: A3

description:
Library name: sample3
Column name in gene_count.txt: A3

value: control


title: hMSC-3DM_sub1

value: MSC


title: FACS sorted Venus+ EECs from tHIOs, plate IGB-AA-s028

description:
Library name: tHIO_IGB-AA-s028
SORT-seq
tHIOs.h5ad
tHIOs_ec.h5ad
human_pre-processed.h5ad
integration_human_thios_scVI.h5ad

value: tHIO, hiPSC differentiated into proximal small intestine

value: EECs


title: 9395-AS-2

description:
Library name: N1314
1 ACPP tumor


title: half, 14-hour post-fertilization, rep1

description: Library name: 14h-half-1

value: half

value: bisected


title: control, 18-hour post-fertilization, rep2

description: Library name: 18h-cont-2


title: 9395-AS-19

description:
Library name: N1369
1 ACPP tumor


title: FACS sorted Venus+ EECs from tHIOs, plate IGB-AA-s026

description:
Library name: tHIO_IGB-AA-s026
SORT-seq
tHIOs.h5ad
tHIOs_ec.h5ad
human_pre-processed.h5ad
integration_human_thios_scVI.h5ad


title: KO_MPP3

city: Nanjing

first: Lei

last: Cao

address: 101 Longmian Avenue

institute: Nanjing Medical University

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

source_name: primary astrocyte

growth_protocol: The neonatalmidbrain (P0–3) was trypsinized and dissociated. Tissue was centrifugedfor 5 min at 1000 rpm centrifugation, triturated, and resuspended inDulbecco’s modified Eagle’s medium/Ham’s F12 medium containing 10% fetal bovine serum, GIBCO, Gaithersburg, MD, USA). Cells were plated ontopoly-D-lysine-coated T-75flasks at 50,000 cells/cm2to generate mixed glialcultures. Confluent mixed glial cultures were shaken at 220 rpm for 6 h at37 °C  to remove unwanted cell types (microglia, oligodendrocytes,neurons, andfibroblasts). The purity of astrocytes was >95% as determinedwith GFAP immunocytochemistry.

extract_protocol:
Total RNA was extracted from primary astrocyte with TRIzol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Astrocytes were treated with MPP+(500μM, Sigma, St. Louis, MO,USA) for 24 h.

value: primary astrocyte

value: MPP+

value: Day 14


title: A1

description:
Library name: sample1
Column name in gene_count.txt: A1

value: Colon

value: male

value: WT


title: FACS sorted Venus+ EECs from tHIOs, plate IGB-AA-s027

description:
Library name: tHIO_IGB-AA-s027
SORT-seq
tHIOs.h5ad
tHIOs_ec.h5ad
human_pre-processed.h5ad
integration_human_thios_scVI.h5ad


title: 9395-AS-18

description:
Library name: N1656
1 Normal Fat Pad (uninjected)

value: Normal Fat Pad (uninjected)

value: Normal Fat

value: Trp53f/fPtenf/f C57BL/6J


title: control, 14-hour post-fertilization, rep2

description: Library name: 14h-cont-2

value: whole


title: KO_MPP2


title: FACS sorted Venus+ EECs from HIOs, plate IGB-AA-s008

description:
Library name: HIO_IGB-AA-s008
SORT-seq
HIOs.h5ad

source_name: HIO, hiPSC differentiated into proximal small intestine

value: NEUROG3-HA-P2A-Venus hiPSCs

value: NEUROG3 Venus/+

value: HIOs cultured for 31 days in matrigel


title: control, 14-hour post-fertilization, rep1

description: Library name: 14h-cont-1


title: KO_MPP1


title: control, 14-hour post-fertilization, rep3

description: Library name: 14h-cont-3


title: half, 14-hour post-fertilization, rep3

description: Library name: 14h-half-3


title: 9395-AS-1

description:
Library name: N1108
1 ACPP tumor

value: ACPP tumor

value: DDLPS


title: FACS sorted Venus+ EECs from HIOs, plate IGB-AA-s007

description:
Library name: HIO_IGB-AA-s007
SORT-seq
HIOs.h5ad

value: HIO, hiPSC differentiated into proximal small intestine

value: EECs


title: half, 14-hour post-fertilization, rep2

description: Library name: 14h-half-2

value: half

value: bisected


title: KO_CON3

value: primary astrocyte

value: PBS

value: Day 14


title: D25_Young_Dura_EAE

city: Toronto

first: Michelle

last: Zuo

state: ON

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

description: Library name: D25_Young_Dura_EAE

data_processing:
Alignment and preprocessing was done using CellRanger Count pipeline from 10X Genomics (v.7.2.0)
Assembly: Mouse mm10
Supplementary files format and content: Matrix files

source_name: Dura

extract_protocol:
The skin overlying the skull was removed and mice were decapitated to separate the skull from the spinal column. The skull cap was then carefully separated from the brain by making incisions from the occipital to the frontal bone to the using fine surgical scissors. The skull cap was placed in a petri dish with 1 mL of PBS. Briefly, the dura mater was scored off the skull cap using forceps to release attachment points between the dura and the skull cap. The dura 1mL of digestion buffer [RPMI 1640 (Sigma-Aldrich) supplemented with 2% fetal bovine serum (Gibco), 1 mM Hepes (Corning), 1× penicillin/streptomycin (Gibco), and 1× GlutaMAX (Gibco)].  Digestion enzymes DNase I (dura: 0.5 mg/mL, LM: 60 μg/mL, Sigma-Aldrich) and collagenase P (1 mg/ml, Roche) were added. Tubes were mixed by gentle vortex and digestion allowed to proceed for 15 min at 37°C with gentle agitation. The digestion was stopped with 1 mL of PBS and samples were filtered through 35-μm mesh strainer caps into 5-ml FACS tubes prior to downstream applications.
Library prep was performed according to manufacturer's instructions (10X Genomics 3' Next-GEM chemistry)

treatment_protocol: EAE was induced in SJL/J mice using adoptive transfer of PLP-primed T cells

value: Dura

value: stromal & immune cells

value: SJL/J

value: Post-AcuteEAE

tag: batch


title: half, 11-hour post-fertilization, rep3

description: Library name: 11h-half-3


title: 9395-AS-21

description:
Library name: N1489
1 Normal Fat Pad (uninjected)

value: Normal Fat Pad (uninjected)

value: Normal Fat

value: Trp53f/fPtenf/f C57BL/6J


title: D25_Old_Dura_EAE

description: Library name: D25_Old_Dura_EAE


title: 14-E

city: Tampa

first: Kieran

last: Smalley

state: Fl

address: 12902 USF Magnolia Drive,

institute: Moffitt cancer Center

description:
Library name: sample_9
10X genomics

data_processing:
Approximately 25,000 to 50,000 mean sequencing reads per cell were generated on the Illumina NextSeq 500 instrument using v2.5 flow cells.
Demultiplexing, barcode processing, alignment and gene counting were performed using the 10X Genomics CellRanger software (SCIGA, RRID:SCR_021002).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

growth_protocol: Collect CSF into an additive-free, preservative-free blue-top tube or Falcon 15 mL conical tube (or equivalent). Immediately after CSF is obtained, put the tubes on ice.Spin CSF down at 200 x g for 5 minutes.Decant off CSF and aliquot into cryopreservation vials (1mL per tube), pre-labeled with patient identifier and date.Freeze CSF aliquots at -20C.Resuspend cell pellet at the bottom of the CSF spin-down tube in 1mL of freezing media (10% dimethyl sulfoxide in fetal bovine serum).

extract_protocol:
Samples were enriched for live cells using FACS sorting prior to quantification and loading.  A single-cell suspension from each sample was quantified and analyzed for viability using the Nexcelom Cellometer K2 and then loaded onto the 10X Genomics Chromium Single Cell Controller for scRNA-seq library preparation (10X Genomics, Pleasanton, CA)
The cDNA was amplified and purified, and cDNA libraries were then prepared in bulk reactions using the 10X Chromium Single Cell 3’ Library Prep Kit.

value: Tumor

value: Breast Cancer w/ LMD

value: ER/PR+, Her2-


title: KO_CON2


title: 14-I

description:
Library name: sample_8
10X genomics


title: half, 11-hour post-fertilization, rep1

description: Library name: 11h-half-1


title: KO_CON1


title: 10-E

description:
Library name: sample_7
10X genomics

value: Triple Negative


title: control, 11-hour post-fertilization, rep3

description: Library name: 11h-cont-3

value: whole


title: D11_Young_Dura_EAE

description: Library name: D11_Young_Dura_EAE

value: AcuteEAE


title: control, 11-hour post-fertilization, rep2

description: Library name: 11h-cont-2


title: WT_MPP2

value: WT

value: MPP+


title: Dura_Young_Naive

description: Library name: Dura_Young_Naive

value: Naïve


title: 7-I

description:
Library name: sample_5
10X genomics


title: WT_MPP1

value: primary astrocyte

value: Day 14


title: control, 11-hour post-fertilization, rep1

description: Library name: 11h-cont-1


title: Dura_Old_Naive

description: Library name: Dura_Old_Naive

value: Dura

value: stromal & immune cells


title: 5-E

description:
Library name: sample_4
10X genomics


title: control, 2-cell stage, rep3

description: Library name: 2cell-cont-3


title: Dura_Young_EAE

description: Library name: Dura_Young_EAE

value: SJL/J


title: 5-I

description:
Library name: sample_3
10X genomics


title: WT_CON3

value: PBS


title: control, 2-cell stage, rep2

description: Library name: 2cell-cont-2


title: half, 11-hour post-fertilization, rep2

description: Library name: 11h-half-2

value: half

value: bisected


title: Dura_Old_EAE

description: Library name: Dura_Old_EAE


title: WT_CON2


title: 4-E

description:
Library name: sample_2
10X genomics

value: Tumor


title: control, 2-cell stage, rep1

description: Library name: 2cell-cont-1


title: D11_Old_Dura_EAE

description: Library name: D11_Old_Dura_EAE


title: Young_Naive

description: Library name: Young_Naive


title: WT_CON1


title: 7-E

description:
Library name: sample_6
10X genomics

value: Breast Cancer w/ LMD


title: WT_MPP3


title: Young_EAE

description: Library name: Young_EAE


title: KMS11 cells, STK17B overexpression REP2

city: Durham

first: Mikhail

last: Nikiforov

state: NC

address: 210 Research Drive, GSRB II Rm. 4020

institute: Duke University

description: Library name: Sample12

data_processing:
The sequencing data, also known as raw reads or raw data, were subjected to quality control (QC) to determine whether the sequencing data were suitable for subsequent analysis. After QC, the clean reads were aligned to the reference sequences. After alignment, the alignment results were subjected to a second QC to evaluate the alignment quality, including alignment rate and distribution of reads on the reference sequences. After that, gene quantification analysis, various analyses based on gene expression levels (such as principal component analysis, correlation analysis, differential gene screening, etc.) were performed. Differential expressed genes between samples were further analyzed for gene ontology (GO) functional enrichment, pathway enrichment, clustering, protein- protein interaction networks, and transcription factors. The complete analysis pipeline is illustrated below:
The raw data obtained from sequencing were filtered using SOAPnuke.
The filtered data, referred to as clean data, were subsequently analyzed, visualized, and mined using Online Multi-Omics Data Mining System.
HISAT [2] (Hierarchical Indexing for Spliced Alignment of Transcripts) is a software used for aligning RNA-seq reads to a reference genome.
Clean data was aligned to the reference gene set using Bowtie2 (v2.3.4.3) [3]. Gene expression quantification was performed using RSEM (v1.3.1) [4] software, and gene expression clustering heatmaps across different samples were generated using pheatmap (v1.0.8) [5]. DESeq2 (v1.4.5) [6] (or DEGseq [7] or PoissonDis [8]) was employed for differential gene detection, with criteria set as Q value ≤ 0.05 or FDR ≤ 0.001. Gene fusion detection was performed using Ericscript (v0.5.5) [10], and alternative splicing and differential alternative splicing were detected using rMATS (V3.2.5)
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: txt file including TPM values

source_name: multiple myeloma

extract_protocol:
RNA was extracted using RNeasy Mini Kit. DNBSEQ-mRNA-Seq-oligo dT(also called polyA selection), stranded.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double- stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

value: multiple myeloma

value: STK17B overexpression

value: no treatment


title: 4-I

description:
Library name: sample_1
10X genomics

value: ER/PR+, Her2-


title: PDAC mouse Kras G12D sample 4956

status: Public on Sep 04 2025

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

description:
Library name: G12D_4956
10x Genomics

data_processing:
raw sequencing reads are processed by Cell Ranger pipeline version 7.1.0 using assembly mm10 (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz)
Assembly: mm10
Supplementary files format and content: processed data are from cellranger output filtered matrix folder with three gz compressed files of barcodes, features, and matrix mtx

source_name: pancreas

extract_protocol:
The dissected tumor tissues were resuspended in digestion buffer (RPMI with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 C for 30 min. Cells were washed and re-suspended in PBS.
single cell suspension was loaded on a Chromium controller to obtain single cell GEMS (Gel Beads-In-Emulsions) for the reaction. The library was prepared with Chromium Next GEM single cell 3’ kit V2 (10X Genomics) and sequenced on Illumina Novaseq 6000

value: pancreas

value: Kras G12D


title: PDAC mouse Kras G12D sample 57614

description:
Library name: G12D_57614
10x Genomics


title: PDAC mouse Kras G12C sample 9726

description:
Library name: G12C_9726
10x Genomics

value: Kras G12C


title: PDAC mouse Kras G12C sample 6304

description:
Library name: G12C_6304
10x Genomics


title: CC5325KO, Chlamydomonas reinhardtii, repeat 1

city: Shanghai

first: Fanchen

last: Wang

address: 1239 Siping Road

institute: Tongji University

description: Library name: CC5325KO-1

data_processing:
The sequencing data derived RNA-seq were trimmed and filtered using Trimmomatic[1] (v0.39), followed by using FastQC (v0.12.1). Clean reads were aligned to the reference sequence (C.reinhardtii CC_4532_707_v6.0) by used of Hisat2 (v2.2.1). Transcript assembling and expression quantification were performed by used of StringTie (v2.2.3).
Assembly: C.reinhardtii CC_4532_707_v6.0 (JGI)
Supplementary files format and content: gtf files: tab-delimited text files include gene imformation and FPKM values for each Sample.

extract_protocol:
Total RNA was extracted using Trizol (Sangon) according to the manufacturer's instructions. rRNA was depleted from total RNA using the Ribo-off rRNA Depletion Kit (Vazyme).
RNA library construction was then performed using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme), following the manufacturer's instructions. The libraries were assessed using the Agilent 2100 Bioanalyzer and sequenced on the Illumina platform using 150 bp paired-end sequencing.

value: Dnmt1 KO


title: PDAC mouse Kras G12C sample 7825

description:
Library name: G12C_7825
10x Genomics


title: sham group, replicate 2

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

description: Library name: Sample_X_J2

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were processed using fastp version 0.20.0. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference  N. coloratarep genome using hisat2(v2.1.0) with parameters -p 8 --fr --dta-cufflinks
FPKM value of each gene was calculated using cufflinks(v2.2.1) with parameters --no-update-check -u -p 8 --library-type fr-firststrand, and the read counts of each gene were obtained by htseq-count(version 0.7.2) with parameters -i gene_id -f bam -s reverse -r name.
DEGs were identified using the Deseq library . P value < 0.05 and absolute value of foldchange >=2 was set as the threshold for significantly differential expression.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Left Ventricle

extract_protocol:
The total RNA was extracted by trizol method from heart tissues of each sample using the three biological repeats.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

treatment_protocol: Fresh Left Ventricle tissue samples were immediately frozen in liquid nitrogen and stored at -80 °C.

value: Left Ventricle

value: Subcutaneous injection of normal saline


title: heart failure group, replicate 2

description: Library name: Sample_X_M2

value: Subcutaneous injection of ISO


title: heart failure group, replicate 3

description: Library name: Sample_X_M3


title: sham group, replicate 3

description: Library name: Sample_X_J3


title: heart failure group, replicate 1

description: Library name: Sample_X_M1


title: sham group, replicate 1

description: Library name: Sample_X_J1


title: B16F10 cell, Ozonated olive oil, 6h_3

city: Sapporo-shi

first: Seong-jin

last: An

state: Hokkaido

address: Kita 12 nishi 6, kita-ku

department: Graduate School of Pharmaceutical Sciences

institute: Hokkaido university

description: Library name: B16F10_OZO_6h_3

data_processing:
RNA-seq reads were preprocessed with bcl2fastq and FastQC software (v. 0.11.7) and aligned to mm10 reference genome with HISAT2 (v. 2.1.0)
StringTie algorithm (v.1.3.4d) was then used with default parameter settings to assemble RNA-Seq alignments into annotated transcripts to estimate their expression using the UCSC annotated human genome (mm10) assembly files.
Transcript expression was normalized using the transcripts per million (TPM) algorithms.  For differential expression analysis, we used featurecounts (v2.1.1+galaxy0) and limma-voom (v3.58.1+galaxy0).
For analysis and interpretation, we used SAMtools (v.1.9), BEDTools (v.2.27.1), Seqkit (version 0.13.2), RSeQC (v.3.0.1), and Ngsplot (v.2.6.3).
Assembly: mm10
Supplementary files format and content: Text files include TPM values for each Sample

source_name: Skin

growth_protocol: B16F10 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Sigma-aldrich) contained 10% fetal bovine serum (FBS; cosmobio) at 37℃ in humidified 5% CO2/95% air atmosphere.

extract_protocol:
Total mRNA was extracted by using Tri reagent (Trizol; Sigma-aldrich) according to manufacturer's protocol
RNA libraries for RNA-seq were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer's manual. After which library quality was further assessed using the TapeStation 4200 with High sensitivity D1000 Screen Tape (Agilent Technologies).

treatment_protocol: Cells were cultured in presence of 0.01% ozonated olive oil or olive oil for 6h.

value: Skin

value: Melanoma

value: WT

value: ozonated olive oil-treated for 6h


title: B16F10 cell, Olive oil, 6h_3

description: Library name: B16F10_OLO_6h_3

value: olive oil-treated for 6h


title: B16F10 cell, Ozonated olive oil, 6h_2

description: Library name: B16F10_OZO_6h_2


title: B16F10 cell, Olive oil, 6h_2

description: Library name: B16F10_OLO_6h_2


title: B16F10 cell, Ozonated olive oil, 6h_1

description: Library name: B16F10_OZO_6h_1


title: B16F10 cell, Olive oil, 6h_1

description: Library name: B16F10_OLO_6h_1


title: P60, Mouse Brain, Rostral migratory stream

city: Storrs

first: Daria

last: Yeroshenko

state: Connecticut

address: 75 North Eagleville Road

department: PNB

institute: University of Connecticut

description:
Library name: P60
10x Genomics

data_processing:
Sequencing data was processed using Cell Ranger (v9.0.1). FASTQ files were generated with the cellranger mkfastq command and aligned to the mouse reference genome (mm10) using cellranger count.
Assembly: Mouse mm10
Supplementary files format and content: Matrix, barcodes and features for each age

source_name: Brain

extract_protocol:
For the P6 and P12 ages, mice (2 males and 2 females for each timepoint) were anesthetized with isoflurane and then perfused intracardially with 0.9% saline. Brains were removed and the RMS was carefully micro-dissected from the rest of the brain. The RMS is a relatively narrow pathway; therefore, our data likely includes some cell types from regions immediately adjacent to the RMS. RMS tissue was dissociated according to the 10X Genomics Chromium sample preparation protocol. Tissue was cut into smaller pieces and placed into 2mL papain solution (BrainBits PAPHE, NC0435282). Tissue was incubated at 37oC for 20 minutes, the papain solution was removed and 2mL of Hibernate E medium (BrainBits HE500, NC9063748) was added to the samples and the sample was triturated with a fire-polished 9-inch Pasteur pipette. The sample was then set aside for 1 minute to allow for the tissue debris to settle. Cells in the supernatant were removed and passed through a 70µm mesh filter (Electron Microscopy Sciences, 6475200) two times. Cells were centrifuged for 2 minutes at 200rcf., the supernatant discarded, the cells resuspended in 1mL of NbActiv1 medium (BrainBits NB1100, NC1482275) and passed through a 70µm mesh filter one final time before being placed on ice. Cells were stained with DAPI (1µg/mL) for 5 minutes and live (DAPI-negative) singlets were sorted using Aurora Cell Sorter (Cytek) with a 100µm nozzle at low pressure. Sorted live cells were collected into NbActiv1 medium (BrainBits NB1100, NC1482275). For our P60 sample, the same harvesting and microdissection procedures were followed. However, tissue dissociation was performed using the Singulator 200 (S2 Genomics) following the manufacturer's protocol (Cell Isolation from Fresh Tissue for Single Cell Sequencing Applications, S2 Genomics). Cell viability and concentration were assessed using a Bio-Rad TC20 Automated Cell Counter and loaded onto 10X Genomics Chromium System. Libraries were generated with the 10X Chromium Single Cell 3′ v2 reagent kit according to the manufacturer’s instructions and sequenced on an Illumina NextSeq 550.
Prepared cells were processed for single cell transcriptome analysis using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, Pleasanton, CA, USA).  Cells were diluted to the appropriate concentration per manufacturer recommendations prior to ensure proper loading.  GEM reverse transcription, cDNA amplification and library generation followed manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).  Briefly, cells are captured in emulsion and reverse transcription is performed while simultaneously barcoding individual cells.  After RT, cDNA is released from the GEMs and amplified.  cDNA is used as an input for library preparation where its first fragmented, size selected and then ligated with Illumina P5 and P7 adapter ends, using unique dual index barcodes for each sample.

value: Brain

tag: region

value: Rostral migratory stream


title: P6, Mouse Brain, Rostral migratory stream

description:
Library name: P6
10x Genomics


title: 12-week TH WT, Bulk RNA-seq Sample 5

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

description: Library name: akap11_12w_TH_WT_5

data_processing:
Reads were aligned to mm10 and gene and isoform level expression leves were estimated using Salmon
Assembly: mm10
Supplementary files format and content: CSV file contains Salmon's counts estimation for all genes and all samples

source_name: Thalamus

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Akap11 mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

value: Thalamus


title: 12-week TH WT, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_TH_WT_4


title: 4-week SSC Akap11 +/-, Bulk RNA-seq Sample 22

description: Library name: akap11_4w_SSC_HT_22

source_name: Somatosensory Cortex

value: Somatosensory Cortex


title: P12, Mouse Brain, Rostral migratory stream

description:
Library name: P12
10x Genomics


title: 12-week TH WT, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_TH_WT_2


title: 12-week TH WT, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_TH_WT_1


title: 12-week TH WT, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_TH_WT_3


title: 12-week TH Akap11 -/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_TH_KO_4


title: 12-week TH Akap11 -/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_TH_KO_3


title: 12-week TH Akap11 -/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_TH_KO_5


title: 12-week TH Akap11 -/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_TH_KO_2


title: 12-week TH Akap11 -/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_TH_KO_1


title: 12-week TH Akap11 +/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_TH_HT_5


title: 12-week TH Akap11 +/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_TH_HT_1


title: 12-week STR Akap11 -/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_STR_KO_3

source_name: Striatum

value: Striatum


title: 12-week STR WT, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_STR_WT_5


title: 12-week TH Akap11 +/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_TH_HT_3


title: 12-week STR WT, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_STR_WT_2


title: 12-week TH Akap11 +/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_TH_HT_4


title: 12-week STR WT, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_STR_WT_3


title: 12-week TH Akap11 +/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_TH_HT_2


title: 12-week STR WT, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_STR_WT_4


title: 12-week STR Akap11 -/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_STR_KO_5


title: 4-week TH WT, Bulk RNA-seq Sample 92

description: Library name: akap11_4w_TH_WT_92


title: 12-week SSC Akap11 -/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_SSC_KO_4


title: 12-week STR Akap11 -/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_STR_KO_1


title: 12-week STR Akap11 -/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_STR_KO_2


title: 12-week STR Akap11 +/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_STR_HT_3


title: 12-week STR Akap11 +/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_STR_HT_4


title: 12-week SSC WT, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_SSC_WT_5


title: 12-week STR Akap11 +/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_STR_HT_5


title: 12-week STR Akap11 +/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_STR_HT_2


title: 12-week SSC Akap11 -/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_SSC_KO_3


title: 12-week SSC WT, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_SSC_WT_2


title: 12-week SSC Akap11 -/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_SSC_KO_5


title: 12-week SSC WT, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_SSC_WT_1


title: 12-week STR Akap11 -/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_STR_KO_4


title: 12-week SSC WT, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_SSC_WT_3


title: 12-week STR WT, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_STR_WT_1


title: A2

description:
Library name: sample2
Column name in gene_count.txt: A2

source_name: Colon

value: Colon

value: male

value: control


title: 12-week SSC Akap11 +/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_SSC_HT_3


title: 12-week SSC Akap11 -/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_SSC_KO_1


title: 12-week SSC Akap11 +/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_SSC_HT_2


title: 12-week SSC Akap11 +/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_SSC_HT_4


title: 12-week SN WT, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_SN_WT_2

source_name: Substantia Nigra

value: Substantia Nigra


title: 12-week SN Akap11 -/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_SN_KO_3


title: 12-week SSC Akap11 +/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_SSC_HT_1


title: 12-week SN WT, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_SN_WT_4


title: 12-week SN Akap11 -/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_SN_KO_1


title: 12-week SN Akap11 -/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_SN_KO_2


title: 12-week SN Akap11 -/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_SN_KO_4


title: 12-week SN WT, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_SN_WT_5


title: 12-week STR Akap11 +/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_STR_HT_1


title: 12-week SN Akap11 +/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_SN_HT_4


title: 12-week SN Akap11 -/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_SN_KO_5


title: 12-week SSC WT, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_SSC_WT_4


title: 12-week SN Akap11 +/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_SN_HT_5


title: 12-week SN WT, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_SN_WT_3


title: 12-week SN Akap11 +/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_SN_HT_3


title: 12-week PFC WT, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_PFC_WT_5

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: 12-week SN Akap11 +/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_SN_HT_2


title: 12-week PFC WT, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_PFC_WT_4


title: 12-week PFC WT, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_PFC_WT_3


title: 12-week SSC Akap11 -/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_SSC_KO_2


title: 12-week SSC Akap11 +/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_SSC_HT_5


title: 12-week PFC WT, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_PFC_WT_2


title: 12-week PFC WT, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_PFC_WT_1


title: 12-week PFC Akap11 -/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_PFC_KO_5


title: 12-week PFC Akap11 -/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_PFC_KO_4


title: 12-week PFC Akap11 -/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_PFC_KO_1


title: 12-week PFC Akap11 +/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_PFC_HT_4


title: 12-week PFC Akap11 -/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_PFC_KO_2


title: 12-week PFC Akap11 +/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_PFC_HT_5


title: 12-week SN WT, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_SN_WT_1


title: 12-week PFC Akap11 -/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_PFC_KO_3


title: 12-week HP WT, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_HP_WT_4

source_name: Hippocampus

value: Hippocampus


title: 12-week HP WT, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_HP_WT_3


title: 12-week SN Akap11 +/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_SN_HT_1


title: 12-week HP WT, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_HP_WT_2


title: 12-week PFC Akap11 +/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_PFC_HT_2


title: 12-week HP Akap11 -/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_HP_KO_3


title: 12-week HP Akap11 -/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_HP_KO_4


title: 12-week PFC Akap11 +/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_PFC_HT_3


title: 12-week HP Akap11 -/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_HP_KO_1


title: 12-week PFC Akap11 +/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_PFC_HT_1


title: 12-week HP Akap11 -/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_HP_KO_2


title: 12-week HP Akap11 +/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_HP_HT_5


title: 12-week HP WT, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_HP_WT_1


title: 12-week HP Akap11 +/-, Bulk RNA-seq Sample 4

description: Library name: akap11_12w_HP_HT_4


title: 12-week HP Akap11 -/-, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_HP_KO_5


title: 12-week HP Akap11 +/-, Bulk RNA-seq Sample 1

description: Library name: akap11_12w_HP_HT_1


title: 12-week HP Akap11 +/-, Bulk RNA-seq Sample 2

description: Library name: akap11_12w_HP_HT_2


title: 4-week SSC Akap11 +/-, Bulk RNA-seq Sample 162

description: Library name: akap11_4w_SSC_HT_162


title: 4-week SN WT, Bulk RNA-seq Sample 92

description: Library name: akap11_4w_SN_WT_92


title: 4-week SN Akap11 -/-, Bulk RNA-seq Sample 163

description: Library name: akap11_4w_SN_KO_163


title: 4-week SN Akap11 -/-, Bulk RNA-seq Sample 161

description: Library name: akap11_4w_SN_KO_161


title: 12-week HP WT, Bulk RNA-seq Sample 5

description: Library name: akap11_12w_HP_WT_5


title: 4-week SN Akap11 -/-, Bulk RNA-seq Sample 44

description: Library name: akap11_4w_SN_KO_44


title: 4-week SN Akap11 -/-, Bulk RNA-seq Sample 932

description: Library name: akap11_4w_SN_KO_932


title: 4-week STR Akap11 -/-, Bulk RNA-seq Sample 163

description: Library name: akap11_4w_STR_KO_163


title: 4-week STR Akap11 -/-, Bulk RNA-seq Sample 161

description: Library name: akap11_4w_STR_KO_161


title: 4-week STR Akap11 -/-, Bulk RNA-seq Sample 932

description: Library name: akap11_4w_STR_KO_932


title: 4-week SN Akap11 -/-, Bulk RNA-seq Sample 91

description: Library name: akap11_4w_SN_KO_91


title: B2

description:
Library name: sample5
Column name in gene_count.txt: B2

value: DSS


title: 4-week STR Akap11 -/-, Bulk RNA-seq Sample 12

description: Library name: akap11_4w_STR_KO_12


title: 4-week SN Akap11 +/-, Bulk RNA-seq Sample 931

description: Library name: akap11_4w_SN_HT_931


title: 4-week STR Akap11 -/-, Bulk RNA-seq Sample 51

description: Library name: akap11_4w_STR_KO_51


title: 4-week STR Akap11 +/-, Bulk RNA-seq Sample 11

description: Library name: akap11_4w_STR_HT_11


title: 4-week SN Akap11 +/-, Bulk RNA-seq Sample 22

description: Library name: akap11_4w_SN_HT_22


title: 4-week HP WT, Bulk RNA-seq Sample 42

description: Library name: akap11_4w_HP_WT_42


title: 4-week SN Akap11 +/-, Bulk RNA-seq Sample 62

description: Library name: akap11_4w_SN_HT_62


title: 4-week SN Akap11 +/-, Bulk RNA-seq Sample 941

description: Library name: akap11_4w_SN_HT_941


title: 4-week STR Akap11 +/-, Bulk RNA-seq Sample 93

description: Library name: akap11_4w_STR_HT_93


title: 4-week SN Akap11 +/-, Bulk RNA-seq Sample 93

description: Library name: akap11_4w_SN_HT_93


title: 4-week STR Akap11 +/-, Bulk RNA-seq Sample 162

description: Library name: akap11_4w_STR_HT_162


title: 12-week HP Akap11 +/-, Bulk RNA-seq Sample 3

description: Library name: akap11_12w_HP_HT_3


title: 4-week STR Akap11 +/-, Bulk RNA-seq Sample 22

description: Library name: akap11_4w_STR_HT_22


title: 4-week STR Akap11 +/-, Bulk RNA-seq Sample 931

description: Library name: akap11_4w_STR_HT_931


title: 4-week SN Akap11 +/-, Bulk RNA-seq Sample 11

description: Library name: akap11_4w_SN_HT_11


title: 4-week TH WT, Bulk RNA-seq Sample 42

description: Library name: akap11_4w_TH_WT_42


title: 4-week PFC Akap11 +/-, Bulk RNA-seq Sample 53

description: Library name: akap11_4w_PFC_HT_53


title: 4-week SN WT, Bulk RNA-seq Sample 142

description: Library name: akap11_4w_SN_WT_142


title: 4-week SN WT, Bulk RNA-seq Sample 42

description: Library name: akap11_4w_SN_WT_42


title: 4-week SN WT, Bulk RNA-seq Sample 23

description: Library name: akap11_4w_SN_WT_23


title: 4-week SN WT, Bulk RNA-seq Sample 914

description: Library name: akap11_4w_SN_WT_914


title: 4-week SN WT, Bulk RNA-seq Sample 913

description: Library name: akap11_4w_SN_WT_913


title: 4-week STR WT, Bulk RNA-seq Sample 142

description: Library name: akap11_4w_STR_WT_142


title: 4-week SSC WT, Bulk RNA-seq Sample 142

description: Library name: akap11_4w_SSC_WT_142


title: 4-week STR WT, Bulk RNA-seq Sample 913

description: Library name: akap11_4w_STR_WT_913


title: 4-week SSC Akap11 -/-, Bulk RNA-seq Sample 163

description: Library name: akap11_4w_SSC_KO_163


title: 4-week STR WT, Bulk RNA-seq Sample 92

description: Library name: akap11_4w_STR_WT_92


title: 4-week SSC Akap11 +/-, Bulk RNA-seq Sample 93

description: Library name: akap11_4w_SSC_HT_93


title: 4-week STR WT, Bulk RNA-seq Sample 914

description: Library name: akap11_4w_STR_WT_914


title: 4-week HP Akap11 +/-, Bulk RNA-seq Sample 53

description: Library name: akap11_4w_HP_HT_53


title: 4-week HP Akap11 -/-, Bulk RNA-seq Sample 163

description: Library name: akap11_4w_HP_KO_163


title: 4-week TH Akap11 +/-, Bulk RNA-seq Sample 93

description: Library name: akap11_4w_TH_HT_93


title: 4-week HP Akap11 +/-, Bulk RNA-seq Sample 162

description: Library name: akap11_4w_HP_HT_162


title: 4-week HP WT, Bulk RNA-seq Sample 142

description: Library name: akap11_4w_HP_WT_142


title: 4-week HP Akap11 -/-, Bulk RNA-seq Sample 161

description: Library name: akap11_4w_HP_KO_161


title: 4-week TH Akap11 -/-, Bulk RNA-seq Sample 161

description: Library name: akap11_4w_TH_KO_161


title: 4-week PFC Akap11 +/-, Bulk RNA-seq Sample 93

description: Library name: akap11_4w_PFC_HT_93


title: 4-week TH Akap11 +/-, Bulk RNA-seq Sample 162

description: Library name: akap11_4w_TH_HT_162


title: 4-week SSC WT, Bulk RNA-seq Sample 92

description: Library name: akap11_4w_SSC_WT_92


title: 4-week TH WT, Bulk RNA-seq Sample 142

description: Library name: akap11_4w_TH_WT_142


title: 4-week PFC Akap11 +/-, Bulk RNA-seq Sample 162

description: Library name: akap11_4w_PFC_HT_162


title: 4-week TH Akap11 -/-, Bulk RNA-seq Sample 163

description: Library name: akap11_4w_TH_KO_163