title: RNA-seq of mouse cardiac tissue: AAV9_Irx3_MI_1

description:
Library name: AAV9_Irx3_MI_1
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.


title: ss3_23_056s_C02_accepted_hits_sorted_deduplicated.bam

status: Public on Feb 16 2026

type: SRA

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

description:
Library name: Single cell sample 32
Smart-seq3

library_source: transcriptomic single cell

data_processing:
Samples were de-multiplexed yielding single-cell fastq files that were quality-trimmed using Trim Galore and UMI were extracted using the UMI-tools package.
Reads were then mapped to the danio rerio reference genome GRCz11 using STAR and duplicates were removed using UMI-tools dedup based on identified UMI’s
Per cell and gene raw-count expression matrices were prepared using the featureCounts package
Counts data was processed and analyzed using Seurat and pagoda2 packages in R-software
Assembly: GRCz11
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: polyA RNA

organism: Danio rerio

source_name: meninges

extract_protocol:
3 brains per group were dissected and put in a buffer containing 0.5% Trypsin, 1mM EDTA, and 10U DNaseI (Promega) for 10 min at 30°C and shaken at 600rpm every 3 minutes until the BLECs were detached from the brain. Brains were removed, and the cells were centrifuged at 2000 rpm for 5 min. The pellet was washed and resuspended in PBS containing 3 % FCS and then filtered through a 40 µm nylon cell strainer. Cells were FACS-sorted into 384-well plates containing lysis buffer.
RNA libraries were prepared using the Smart-Seq3 protocol at SICOF Huddinge, Sweden.

tag: tissue

value: meninges

tag: cell type

value: Neuronal/Glia

tag: group

value: control

tag: batch


title: hapo_newborn_cordblood_B0129

type: genomic

city: Chicago

first: Jami

middle: L

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

country: USA

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

tag: Sex

value: Female

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: P3504_1169

city: Stockholm

first: Andreas

last: Liontos

state: Stockholm

address: Svante Arrheniusväg 20C

department: Molecular Biosciences-The Wenner Gren Institute

institute: Stockholm University

description:
single cell library
Smart-Seq2

data_processing:
Sequencing was done with Illumina 2500 HiSeq Rapid mode using paired-end (2x125 bp) and single-end (1x50 bp). For downstream analysis, we used the one strand sequencing out of paired-end libraries and trimmed the reads to 50 bp
High quality transcriptomic libraries were obtained after filtering, for doublet cells included in our experiment as sequencing controls, for cells obtaining less than 40% uniquely mapped reads, for cells that had number of detected genes outside mean ± 2s.d range and for cells whose GFP  expression ratio was lower than the GFP ration determined in embryonic epithelial cells.
The following single cells were removed as known doublets in our analysis: "P7657_1067", "P7657_1189", "P2661_1003", "P4730_1029". The following single cells were removed because they had <40% uniquely mapped reads: "P2272_1042", "P2661_1042", "P3504_1071", "P3504_1082", "P4730_1040", "P7657_1022", "P7657_1024", "P7657_1025", "P7657_1032", "P7657_1070".
Assembly: Custom Mus Musculus (GRCm38) reference genome that contained GFP sequence and Ai14 cassette (RFP and WPRE sequences). The reference genome was created with the 10x Genomics "cell ranger mkref" and the mapping of the reads was done with the "cellranger count" function, using default settings.
Supplementary files format and content: raw count matrix and metadata files for the 464/478 single cells remaining after removal of doublet cells (4 cells removed) and removal of cells that failed uniquely map read filtering (10 cells removed) step.

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
For full-length (Smart-Seq2) library preparation (Picelli et al., 2014), the left lungs were used for enzymatic digestion and right lungs were treated as described above for histological analysis. Briefly, we cut the lungs in small pieces using a razor blade and digested with elastase (Worthington, LS002292) and DNase I 0.5 mg/ml (Sigma-Aldrich, DN25) in HBSS (Gibco, 14175), at 37oC for 1 hour with rotation. Equal volume of HBSS++ [HBSS (Gibco, 14175), supplemented with 2% 0.2µm filtered FCS (Gibco, 10500), 0.1 M HEPES (Sigma-Aldrich, H0887), antibiotics (Gibco, 15240096) and EGTA 2 mM] was added and the suspension was mixed gently. Then cells were centrifuged at 800g for 10 minutes at 4oC. Supernatant was removed with a serological pipette and cells were resuspended in HBSS++. Viability was tested using trypan blue (Sigma-Aldrich, T8154) (1:1 dilution) and presence of fluorescence positive cells was evaluated using a normal fluorescence microscope. Just before sorting, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) in order to remove cell aggregates. For E16.5 lungs, after digestion, centrifuge and cell resuspension in HBSS++, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) and counted. We resuspented the cells in the proper amount of HBSS++ in order to obtain 20x106 cells/ml cell concentration. 100 µl of cell suspension were stained with 0.5 µl of anti-EpCam-PE antibody (Biolegend, 118205) and 0.5 µl anti-CD45-APC antibody (Biolegend, 103112). Replicates of the above reactions were set in separate tubes; in order to prevent the formation of cell aggregates, which is typical when we centrifuge large amount of epithelial cells.
For cell-sorting, we used a BD FACSARIA III cell-sorter, using 100 µm nozzle, applying single-cell sorting purity setting. For E16.5 lungs, EpCampos CD45neg cells were sorted. Cells from all other stages were isolated according to GFP expression.
Cell sorting and single-cell library preparation were done according to Smart Seq2 protocol (Picelli et al., 2013; Picelli et al., 2014) with some modifications. Cells were sorted in 96-well plates (Piko PCR Plates 24-well, Thermo Scientific, SPL0240 and Plate Frame for 24-well PikoPCR Plates, Thermo Scientific, SFR0241).  Each well contained Triton-X100 (0.2%) (Sigma-Aldrich, T9284-100ML), ERCC RNA Spike-In Mix (1:400.000) (Life-Technologies, 4456740), Oligo-dT30 VN (1,25uM) AAGCAGTGGTATCAACGCAGAGTAC (30 x T) VN, dNTPs (2.5mM/each) (Thermo Scientific-Fermentas, R0192) and Rnase Inhibitor (1U/ul) (Clontech, 2313A) in 4 µl final volume. After sorting, strips were covered with Axygen PCR-tube caps (VWR, PCR-02-FCP-C), centrifuged and placed on dry ice until storage at -80oC for further use. For cell culture cells were sorted into HBSS++ buffer and kept on ice until they were placed in culture.
Smart Seq2 protocol is optimal for cell lines and/or large human cells (Picelli et al., 2014). Mouse primary pulmonary cells are smaller and they contain smaller amount of RNA, as a result high amount of primer concatamers were formed during cDNA library preparation, compromising its efficiency. Our optimized protocol contains 50% less Oligo-dT30 VN and cDNA synthesis was divided into two steps, the first was without TSO LNA and the second contained 1µM TSO LNA and additional 40 U of SuperScript II RT (Thermo-Fisher Scientific, 18064071). Reaction lasted 30 minutes at 42oC. Then enzyme was deactivated at 70oC for 15 minutes. For Pre-Amplification PCR, we used the KAPA HiFi Hotstart ReadyMix (2x) (KAPA Biosystems, KK2602) and the ISPCR-primer AAGCAGTGGTATCAACGCAGAGT. PCR included 21 cycles and the total volume increased to 50ul in order to reduce the concentration of the unused Oligo-dT30 VN and TSO-LNA primers.
Tagmentation and indexed library amplification were done with Nextera® XT DNA Library Preparation Kit (Illumina, FC-131-1096) and Nextera® XT Index Kit (96 indexes, 384 samples), (Illumina, FC-131-1002) according to the manufacturer protocol (with 2.5 x volume reduction in all reactions). The quantity of the used library for tagmentation was 50 pg of the 500-9000 bp fraction of the library, as indicated by its Bioanalyzer profile.

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_MI_4

city: Changchun

first: BIng

last: Li

address: 130021, No. 1, Xinmin Street, Chaoyang District, Changchun, Jilin Province

country: China

institute: First Hospital of Jilin University

description:
Library name: AAV9_Ctrl_MI_4
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

library_source: transcriptomic

data_processing:
Raw sequencing data were processed using fastp to remove adaptor sequences and low-quality reads, generating clean reads; Q20, Q30, and GC content of clean reads were calculated.
Clean reads were aligned to the mouse reference genome (GRCm39/mm39), and gene expression levels were quantified.
Assembly: GRCm39/mm39 for mouse cardiac tissues.
Supplementary files format and content: GEO_gene_count.xls.csv

source_name: Left ventricle

growth_protocol: C57BL/6J mice were raised under specific pathogen-free (SPF) conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent and treated with DNase I to remove genomic DNA.
mRNA was enriched from total RNA using Oligo(dT) magnetic beads, randomly fragmented, and reverse-transcribed into double-stranded cDNA. The cDNA was then subjected to end repair, A-tailing, adaptor ligation, and PCR amplification. Qualified libraries (verified by Qubit quantification and Agilent fragment analysis) were sequenced on an Illumina platform (conducted by Novogene, Beijing, China).

treatment_protocol: Mice were injected with AAV9 control or AAV9-Irx3 vector via tail vein, followed by sham or MI surgery.

tag: tissue

value: Left ventricle

tag: cell type

value: Cardiomyocytes

value: Wild type

tag: treatment

value: Myocardial infarction (MI) surgery + AAV9 control vector


title: ss3_23_056s_C01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 31
Smart-seq3

value: meninges

tag: group

tag: batch


title: hapo_newborn_cordblood_B0128

tag: Sex

tag: developmental stage


title: P3504_1168

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: individual

tag: sorting date


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_MI_3

description:
Library name: AAV9_Ctrl_MI_3
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.


title: ss3_23_056s_B24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 30
Smart-seq3

value: Network


title: hapo_newborn_cordblood_E0949


title: P3504_1167

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_MI_2

description:
Library name: AAV9_Ctrl_MI_2
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.


title: ss3_23_056s_B23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 29
Smart-seq3

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_B0116

value: Female

value: cord clood


title: P3504_1166

description:
single cell library
Smart-Seq2

tag: lane

tag: plate well

tag: internal number

tag: n primer


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_MI_1

description:
Library name: AAV9_Ctrl_MI_1
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

tag: tissue

tag: cell type

tag: treatment


title: ss3_23_056s_B20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 28
Smart-seq3

value: Immune

tag: group

tag: batch


title: hapo_newborn_cordblood_B0114

tag: Sex

tag: developmental stage

value: newborn

value: whole blood cells


title: P3504_1165

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: genotype

tag: individual

tag: s primer


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_Sham_4

description:
Library name: AAV9_Ctrl_Sham_4
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

value: Sham surgery + AAV9 control vector


title: ss3_23_056s_D06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 49
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0111


title: P3504_1164

description:
single cell library
Smart-Seq2

value: WT

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

value: single-end 50bp


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_Sham_3

description:
Library name: AAV9_Ctrl_Sham_3
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

value: Left ventricle

value: Cardiomyocytes

value: Wild type


title: ss3_23_056s_B18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 26
Smart-seq3

value: meninges

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_B0110

value: Female

value: cord clood


title: P3504_1163

description:
single cell library
Smart-Seq2

tag: type of_sequencing

tag: lane

tag: plate well

tag: internal number


title: RNA-seq of mouse cardiac tissue: AAV9_Ctrl_Sham_2

description:
Library name: AAV9_Ctrl_Sham_2
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

tag: tissue

tag: cell type

tag: treatment


title: ss3_23_056s_B17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 25
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_B0105

tag: Sex

tag: developmental stage

value: newborn

value: whole blood cells


title: P3504_1162

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: individual

tag: n primer


title: E. coli, ΔqueF, 37°C, rep2

city: Berlin

first: Yu

last: Sun

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

description: Library name: E. coli_ΔqueF_37_rep2

library_source: other

data_processing:
Read alignment was carried out using Bowtie2 with parameters -N 1 -L 6 to allow up to one mismatch per 6 nt seed. To assess reverse transcription-derived misincorporation patterns, the misincorporation rate at each nucleotide position was quantified using CoverageAnalyzer.
Assembly: Reference curation: The reference for S. pombe tRNATyr contains sequences of all unique mature tRNATyr and intron-containing tRNATyr  from GtRNAdb, and both 5’ and 3’ primer sequences were added. For E. coli, sequences of all unique tRNAs were from GtRNAdb, and primer sequences were added.
Supplementary files format and content: The processed data includes the following information: position, refbase, coverage, mm_ratio, a_mism, g_mism, t_mism, c_mism, and arrest_rate.

molecule: other

organism: Escherichia coli

source_name: strain:BW25113 queFDEL

growth_protocol: The S. pombe strains were grown in YES medium with or without 0.1 μM of queuine at 30°C and 140 rpm. The E. coli strains were grown in M9 medium at 37°C or 42°C and 180 rpm.

extract_protocol:
Extraction of small RNAs from cells: Small RNAs were extracted according to the manufacturer’s protocol (PureLink™ miRNA Isolation Kit (Invitrogen)) with some adjustments. Briefly, cells were suspended in 1 ml Trizol (Ambion). The samples were vortexed for 2 min after adding 0.2 ml chloroform and glass beads, and then were centrifuged at 16 000 rcf, 4°C for 15 min. After adding 215 µl ethanol to the upper phase, the samples were transferred to a spin cartridge and centrifuged at 12 000 rcf for 1 min. 700 µl of ethanol was added to the flow-through, and the samples were transferred to a new spin cartridge followed by centrifugation at 12 000 rcf for 1 min. After washing the cartridge with wash buffer, small RNAs were eluted with 50 µl of DEPC-treated water.
For ms2i6A modification detection, in brief, 500 ng of deacylated small RNAs were hybridized with 1 μl of 10 μM tRNATyr stem-loop primer using the following thermocycling program: 95°C for 2 min, 65°C for 30 s, followed by a gradual ramp to 4°C at 5°C per 30 s. After incubation on ice for 1 min, reverse transcription was performed in 20 μl reactions containing 100 μM dA/C/GTP, 12.5 μM dTTP, 100 nM RT-KTq I614Y enzyme, and RT buffer [50 mM Tris-HCl (pH 9.2), 16 mM (NH₄)₂SO₄, 2.5 mM MgCl₂, 0.1% Tween-20], and incubation at 55°C for 1 hour. Following reverse transcription, 5 μl of cDNA was used for PCR amplification in a 50 μl reaction containing 0.5 µM forward and reverse primers, 250 μM dNTPs, 2 mM MgCl2, 1 x Taq buffer with KCl, and 1.25 U Taq polymerase (Thermo Fisher). The thermal cycling conditions were: 96°C for 3 min; 40 cycles of 96°C for 30 s, 50°C for 45 s, and 72°C for 45 s; followed by a final extension at 72°C for 5 min. 3′-end primers included sample-specific barcodes for multiplexing. PCR products were resolved on a 2% agarose gel and purified using the QIAquick Gel Extraction Kit (Qiagen). The purified PCR products were pooled and submitted for Next-generation sequencing. For i6A modification detection, deacylated small RNAs were further treated with 0.5 M I2 for 20 min on ice. Following iodine treatment, saturated Na2S2O3 was added to the reaction mixture until the solution became colorless. Subsequently, saturated Na2CO3 was added dropwise until effervescence ceased. Upon completion of the reaction, small RNAs were purified using the RNA Clean & Concentrator Kit (ZYMO Research) according to the manufacturer’s instructions. Iodine-treated samples were then used for sequencing library preparation following the same protocol as described above for ms2i6A detection.

value: strain:BW25113 queFDEL

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), lambda-, DeltaqueF721::kan, rph-1, Delta(rhaD-rhaB)568, hsdR514

value: grown in M9 medium  at 37°C


title: ss3_23_056s_B16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 24
Smart-seq3

value: Fibroblast


title: hapo_newborn_cordblood_B0104

value: Male


title: P3504_1161

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: s primer


title: SH77_129X1_16week_ath

city: Los Angeles

first: Ivan

middle: Alexander

last: Salladay-Perez

state: CA

address: 615 Charles E Young Dr S

department: Department of Microbiology Immunology and Molecular Genetics

institute: University of California, Los Angeles

description: Library name: SH77

data_processing:
Roughly 100 M high quality reads were sequenced per sample using a Novaseq x Plus (Illumina). Raw data in FASTAq format was filtered for adapter sequences or low-quality sequences using SOAPnuke. Reads were aligned to the mm10 reference genome using STAR.
Aligned reads were processed using TopHat and a counts matrix was generated using FeatureCounts.
Raw reads were processed using the latest version of base R commands as of May 2025 (4.5.0)
Assembly: mm10
Supplementary files format and content: raw reads

source_name: Liver

extract_protocol:
RNA was isolated using RNA STAT 60 (Amsbio) as per the manufacturer’s protocol. ~ 2000 ng of RNA was converted to complementary DNA using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
RNA was submitted to UCLA’s Technology Center for Genomics & Bioinformatics (TCGB) core for library preparation and 2x100 paired-end sequencing.

value: Liver


title: ss3_23_056s_B14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 23
Smart-seq3

value: meninges

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_B0101

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Female

value: cord clood

value: newborn


title: P3504_1160

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: plate well


title: SH76_129X1_16week_ath

description: Library name: SH76

tag: tissue

tag: treatment


title: ss3_23_056s_B13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 22
Smart-seq3

tag: cell type

tag: group

tag: batch


title: hapo_newborn_cordblood_B0100

tag: Sex

tag: developmental stage

value: whole blood cells


title: ss3_23_056s_H10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 112
Smart-seq3


title: SH75_129X1_16week_ath

description: Library name: SH75

tag: genotype


title: ss3_23_056s_B12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 21
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0099


title: P3504_1157

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: internal number

tag: n primer


title: SH74_129X1_16week_ath

description: Library name: SH74


title: ss3_23_056s_B11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 20
Smart-seq3


title: hapo_newborn_cordblood_B0097


title: P3504_1156

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: s primer


title: SH73_129X1_16week_chow

description: Library name: SH73


title: ss3_23_056s_B10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 19
Smart-seq3


title: E. coli, 75%wt+25%ΔmiaA, 42°C, rep1

description: Library name: E. coli_75pwt_42_rep1

source_name: strain:BW25113, BW25113 miaADEL

value: strain:BW25113, BW25113 miaADEL

value: grown in M9 medium  at 42°C


title: P3504_1155

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: plate well


title: SH72_129X1_16week_chow

description: Library name: SH72

tag: tissue

tag: treatment


title: ss3_23_056s_B09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 18
Smart-seq3

tag: cell type

tag: group

tag: batch


title: hapo_newborn_cordblood_B0091

tag: Sex

tag: developmental stage


title: P3504_1154

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

value: WT

tag: individual

tag: internal number


title: SH71_129X1_16week_chow

description: Library name: SH71


title: ss3_23_056s_B07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 17
Smart-seq3


title: hapo_newborn_cordblood_B0087


title: P3504_1153

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: n primer


title: SH70_129X1_16week_chow

description: Library name: SH70


title: hapo_newborn_cordblood_B0153

value: Male


title: hapo_newborn_cordblood_B0085


title: P3504_1152

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: s primer


title: SH69_129X1_12week_ath

description: Library name: SH69

tag: tissue

value: Liver

tag: treatment


title: ss3_23_056s_B05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 15
Smart-seq3

value: meninges

tag: cell type

value: Neuronal/Glia

tag: group

tag: batch


title: hapo_newborn_cordblood_B0080

tag: Sex

value: Female

tag: developmental stage


title: E. coli, 50%wt+50%ΔmiaA, 42°C, rep2

description: Library name: E. coli_50pwt_42_rep2


title: P3504_1151

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: individual

tag: plate well


title: SH68_129X1_12week_ath

description: Library name: SH68


title: ss3_23_056s_B04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 14
Smart-seq3

value: control


title: hapo_newborn_cordblood_B0073

value: cord clood

value: newborn


title: P3504_1150

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: internal number


title: SH67_129X1_12week_ath

description: Library name: SH67


title: ss3_23_056s_B03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 13
Smart-seq3


title: hapo_newborn_cordblood_B0066

value: whole blood cells


title: P3504_1149

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: n primer


title: SH66_129X1_12week_ath

description: Library name: SH66

tag: tissue

tag: treatment


title: hapo_newborn_cordblood_B0062

tag: cell type


title: P3504_1148

description:
single cell library
Smart-Seq2

tag: s primer


title: SH65_129X1_8week_ath

description: Library name: SH65

tag: batch


title: ss3_23_056s_B01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 11
Smart-seq3

tag: group


title: hapo_newborn_cordblood_B0057

tag: Sex

tag: developmental stage


title: hapo_newborn_cordblood_D0302


title: SH64_129X1_8week_ath

description: Library name: SH64

tag: genotype


title: ss3_23_056s_A20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 10
Smart-seq3

value: Immune


title: hapo_newborn_cordblood_B0052


title: P3504_1145

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date

tag: plate well


title: SH63_129X1_8week_ath

description: Library name: SH63


title: ss3_23_056s_A17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 9
Smart-seq3


title: hapo_newborn_cordblood_B0047


title: P4730_1033

description:
single cell library
Smart-Seq2

tag: isolation criteria

value: EpCam^pos CD45^neg

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: internal number


title: P3504_1144

description:
single cell library
Smart-Seq2

tag: tissue

value: lung epithelial secretory cells

tag: type of_sequencing

tag: lane

tag: n primer


title: SH62_129X1_8week_ath

description: Library name: SH62

tag: treatment

tag: batch


title: ss3_23_056s_A16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 8
Smart-seq3

tag: cell type

tag: group


title: hapo_newborn_cordblood_B0046

tag: Sex

tag: developmental stage


title: P3504_1143

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

value: WT

tag: individual

tag: s primer


title: SH61_129X1_4week_ath

description: Library name: SH61


title: hapo_newborn_cordblood_B0026


title: P3504_1142

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: plate well


title: SH60_129X1_4week_ath

description: Library name: SH60

tag: tissue


title: ss3_23_056s_A10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 6
Smart-seq3


title: hapo_newborn_cordblood_B0024


title: P3504_1141

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane

tag: internal number


title: SH59_129X1_4week_ath

description: Library name: SH59

tag: treatment

tag: batch


title: hapo_newborn_cordblood_G0458

tag: Sex

value: Male

tag: cell type


title: hapo_newborn_cordblood_B0017

tag: developmental stage


title: P3504_1140

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

value: single-end 50bp

tag: n primer


title: SH58_129X1_4week_ath

description: Library name: SH58

value: Liver


title: ss3_23_056s_A04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 4
Smart-seq3

value: meninges

tag: group


title: hapo_newborn_cordblood_B0016

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: P3504_1139

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

tag: s primer


title: SH57_129X1_2week_ath

description: Library name: SH57

tag: tissue


title: ss3_23_056s_A03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 3
Smart-seq3

value: Neuronal/Glia


title: hapo_newborn_cordblood_B0005


title: P3504_1138

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well


title: hapo_newborn_cordblood_B0239

value: Female


title: ss3_23_056s_A02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 2
Smart-seq3

value: control

tag: batch


title: hapo_newborn_cordblood_B0004

tag: Sex

value: cord clood


title: P3504_1137

description:
single cell library
Smart-Seq2

tag: cell type

tag: lane

tag: internal number


title: SH55_129X1_2week_ath

description: Library name: SH55

tag: genotype

tag: treatment


title: ss3_23_056s_A01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 1
Smart-seq3

tag: group


title: hapo_newborn_cordblood_B0001

tag: developmental stage

value: newborn


title: P3504_1136

description:
single cell library
Smart-Seq2

value: lung

tag: strain

tag: individual

tag: sorting date

tag: n primer


title: SH54_129X1_2week_ath

description: Library name: SH54

tag: tissue


title: 1 µM sodium arsenite + 30 µg/L uranyl nitrate, bio rep 4

city: Flagstaff

first: Phillip

middle: Hua

last: Kalaniopio

state: Arizona

address: 617 S Beaver St.

department: Department of Biological Sciences

institute: Northern Arizona University

description:
Library name: DrAsU_4
Column name in fpkm.txt: DrAsU_4

data_processing:
Qualified libraries were sequenced on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads, resulting in an average of 58.9 million read pairs.Raw reads were filtered to remove adapter sequences, reads with >10% unknown bases (N), or >50% low-quality bases (Q-score < 20). Mapped reads corresponded to approximately 75% exonic, 20% intergenic, and 5% intronic DNA, +/- 3%. Clean reads were used for downstream analysis. Raw sequencing reads were filtered to remove adapters, low-quality reads (more than 50% of bases with Phred quality scores below 20), and reads containing more than 10% undetermined bases (N). Clean reads were retained for downstream analysis.
Filtered reads were aligned to the Danio rerio reference genome using HISAT2 (v2.1.0) with default parameters. Gene-level quantification was performed using HTSeq (v0.6.1) in union mode, and expression levels were normalized and reported as fragments per kilobase of transcript per million mapped reads (FPKM). Differential expression analysis was performed using DESeq2 (v1.10.1) for comparisons with biological replicates, applying a significance threshold of adjusted p-value < 0.05. Gene Ontology (GO) enrichment analysis was conducted using GOseq and topGO, while pathway enrichment was performed using KOBAS (v3.0) against the KEGG database.
Assembly: GRCz11
Supplementary files format and content: .txt file with gene expression quantification table, calculation of all genes' FPKM

source_name: whole larvae

growth_protocol: Adult wildtype AB strain zebrafish were maintained in Tecniplast ZebTec Active BlueTM systems, housed in a temperature-controlled room with a 14/10-hour light-dark cycle. System water was continuously monitored while recirculated to control water temperature (28.5 °C ± 0.5), pH (7.5 ± 0.25), and conductivity (700 ± 100 µSiemens). Fish were fed twice daily with Skretting Gemma® 75, 150, or 500, depending on size. Embryos were obtained by spawning adult zebrafish (>6 mpf) in breeding tanks with perforated inserts that allow embryos to pass through but not adults. Embryos were collected from these breeder tanks and rinsed with fresh 0.3x Danieau’s solution (DanS), then moved to 15 cm petri dishes and maintained in an incubator set to 28.5 °C with a 14/10-hour light/dark cycle.

extract_protocol:
Total RNA was extracted from pooled zebrafish larvae (n = 10 per biological replicate per treatment) using TRIzol reagent (CAT# 15596018; Thermo Fisher Scientific), following the manufacturer's protocol. RNA concentration and purity were assessed using a Nanodrop Lite (CAT# ND-LITE; Thermo Fisher Scientific) spectrophotometer (A260/280 ratio between 1.8 and 2.2, A260/230 ≥ 1.8), and RNA integrity was qualitatively evaluated by 1% agarose gel electrophoresis. Qualified RNA samples were shipped on dry ice to Novogene Co., Ltd. (Beijing, China) for library construction, sequencing, and differential gene expression with functional analyses.
At Novogene, RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Samples met the following quality criteria: A260/280 ratio between 1.8 and 2.2, A260/230 ≥ 1.8, RNA Integrity Number (RIN) ≥ 5.8, smooth baseline, and total RNA yield ≥400 ng. Polyadenylated mRNA was enriched from total RNA using oligo(dT) magnetic beads and fragmented using a proprietary fragmentation buffer. First-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase, followed by second-strand synthesis using dNTPs, RNase H, and E. coli DNA polymerase I. The resulting double-stranded cDNA underwent end repair, A-tailing, ligation with Illumina-compatible adapters, size selection, and PCR amplification. Libraries were validated on an Agilent Bioanalyzer, quantified using a Qubit 2.0 fluorometer (Life Technologies), and further assessed by qPCR to ensure a minimum library activity of >2 nM.

treatment_protocol: At 4 hours post fertilization (hpf), larvae were moved into separate petri dishes containing treatment solutions of 1 or 10 µM sodium arsenite, 30 or 300 µg/L uranyl nitrate, or 1 µM sodium arsenite and 30 µg/L uranyl nitrate in combination, all in 0.3X DanS. Fish were maintained in these dishes with twice daily media changes until 5 dpf.

tag: background

value: wildtype

value: AB strain

value: whole larvae

tag: # fish

tag: bio replicate


title: hapo_newborn_cordblood_A2349

value: whole blood cells


title: hapo_newborn_cordblood_B0212


title: hapo_newborn_cordblood_B0124


title: SH53_129X1_0week_chow

description: Library name: SH53

tag: batch


title: P3504_1170

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well

tag: s primer


title: 1 µM sodium arsenite + 30 µg/L uranyl nitrate, bio rep 3

description:
Library name: DrAsU_3
Column name in fpkm.txt: DrAsU_3

tag: genotype

tag: cell type

tag: treatment


title: hapo_newborn_cordblood_A2348

tag: Sex

tag: developmental stage


title: P3504_1134

description:
single cell library
Smart-Seq2

tag: strain

value: WT

tag: individual

tag: sorting date

value: GFP^pos

tag: lane

tag: internal number

tag: n primer


title: SH52_129X1_0week_chow

description: Library name: SH52

tag: tissue

tag: batch


title: 1 µM sodium arsenite + 30 µg/L uranyl nitrate, bio rep 2

description:
Library name: DrAsU_2
Column name in fpkm.txt: DrAsU_2

tag: background

tag: # fish

tag: bio replicate


title: ss3_23_056s_B19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 27
Smart-seq3

value: Immune

tag: group


title: hapo_newborn_cordblood_A2347


title: P3504_1133

description:
single cell library
Smart-Seq2

tag: genotype

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: plate well

tag: s primer


title: hapo_newborn_cordblood_B0094

tag: Sex

value: Male

tag: developmental stage

tag: cell type


title: 1 µM sodium arsenite + 30 µg/L uranyl nitrate, bio rep 1

description:
Library name: DrAsU_1
Column name in fpkm.txt: DrAsU_1

tag: treatment


title: P3504_1135

description:
single cell library
Smart-Seq2

tag: tissue

tag: strain

tag: individual

tag: sorting date

tag: lane

tag: internal number

tag: n primer


title: SH51_129X1_0week_chow

description: Library name: SH51

value: Liver

tag: genotype

tag: batch


title: hapo_newborn_cordblood_A2346


title: ss3_23_056s_A05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 5
Smart-seq3

value: meninges

value: BLEC

tag: group


title: P3504_1132

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: SH50_129X1_0week_chow

description: Library name: SH50


title: hapo_newborn_cordblood_A2338

tag: Sex

value: Female

value: cord clood

tag: developmental stage


title: P3504_1131

description:
single cell library
Smart-Seq2

value: lung

tag: cell type

tag: plate well

tag: s primer


title: 300 µg/L uranyl nitrate, bio rep 4

description:
Library name: DrUH_4
Column name in fpkm.txt: DrUH_4

tag: background

value: wildtype

tag: treatment

value: 300 µg/L uranyl nitrate

tag: # fish

tag: bio replicate


title: SH49_BXD19_16week_ath

description: Library name: SH49

tag: tissue


title: hapo_newborn_cordblood_A2329

value: newborn


title: 300 µg/L uranyl nitrate, bio rep 3

description:
Library name: DrUH_3
Column name in fpkm.txt: DrUH_3

tag: genotype

value: AB strain

value: whole larvae


title: P3504_1130

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: individual

tag: sorting date

tag: lane

tag: internal number

tag: n primer


title: SH48_BXD19_16week_ath

description: Library name: SH48

tag: batch


title: 300 µg/L uranyl nitrate, bio rep 2

description:
Library name: DrUH_2
Column name in fpkm.txt: DrUH_2


title: hapo_newborn_cordblood_A2309

tag: Sex

tag: developmental stage

value: whole blood cells


title: P3504_1129

description:
single cell library
Smart-Seq2

tag: cell type

value: WT

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well


title: hapo_newborn_cordblood_A2296

value: Male

tag: tissue


title: SH47_BXD19_16week_ath

description: Library name: SH47

value: Liver

tag: genotype

tag: treatment


title: 300 µg/L uranyl nitrate, bio rep 1

description:
Library name: DrUH_1
Column name in fpkm.txt: DrUH_1

tag: background

tag: # fish

tag: bio replicate


title: P3504_1128

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date

value: single-end 50bp

tag: lane

tag: internal number

tag: s primer


title: SH46_BXD19_16week_ath

description: Library name: SH46

tag: batch


title: 30 µg/L uranyl nitrate, bio rep 4

description:
Library name: DrUL_4
Column name in fpkm.txt: DrUL_4

tag: cell type

value: 30 µg/L uranyl nitrate


title: hapo_newborn_cordblood_A2288

tag: Sex

value: Female

tag: developmental stage


title: SH45_BXD19_16week_chow

description: Library name: SH45


title: 30 µg/L uranyl nitrate, bio rep 3

description:
Library name: DrUL_3
Column name in fpkm.txt: DrUL_3


title: P3504_1127

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well

tag: n primer


title: hapo_newborn_cordblood_A2284

tag: tissue

value: cord clood


title: P3504_1126

description:
single cell library
Smart-Seq2

value: lung

tag: strain

tag: genotype


title: SH44_BXD19_16week_chow

description: Library name: SH44

tag: treatment


title: 30 µg/L uranyl nitrate, bio rep 2

description:
Library name: DrUL_2
Column name in fpkm.txt: DrUL_2

tag: background

value: wildtype

tag: # fish

tag: bio replicate


title: hapo_newborn_cordblood_A2282

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: P3504_1125

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: lane

tag: internal number

tag: s primer


title: 30 µg/L uranyl nitrate, bio rep 1

description:
Library name: DrUL_1
Column name in fpkm.txt: DrUL_1

tag: cell type


title: SH43_BXD19_16week_chow

description: Library name: SH43

tag: batch


title: hapo_newborn_cordblood_A2263

tag: Sex

tag: developmental stage


title: P3504_1124

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well

tag: n primer


title: SH42_BXD19_16week_chow

description: Library name: SH42

tag: tissue

tag: genotype

tag: treatment


title: 10 µM sodium arsenite, bio rep 4

description:
Library name: DrAsH_4
Column name in fpkm.txt: DrAsH_4

tag: background

value: 10 µM sodium arsenite

tag: # fish

tag: bio replicate


title: hapo_newborn_cordblood_A2261

value: newborn


title: SH41_BXD19_12week_ath

description: Library name: SH41


title: P3504_1123

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date

tag: lane

tag: internal number

tag: s primer


title: 10 µM sodium arsenite, bio rep 3

description:
Library name: DrAsH_3
Column name in fpkm.txt: DrAsH_3

value: AB strain

tag: cell type


title: hapo_newborn_cordblood_A2257

tag: Sex

tag: developmental stage


title: P3504_1122

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well


title: SH40_BXD19_12week_ath

description: Library name: SH40

tag: tissue

tag: genotype

tag: treatment

tag: batch


title: 10 µM sodium arsenite, bio rep 2

description:
Library name: DrAsH_2
Column name in fpkm.txt: DrAsH_2

tag: background

value: whole larvae

tag: # fish

tag: bio replicate


title: hapo_newborn_cordblood_A2256


title: P3504_1117

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

tag: lane

tag: internal number

tag: n primer


title: 10 µM sodium arsenite, bio rep 1

description:
Library name: DrAsH_1
Column name in fpkm.txt: DrAsH_1

tag: cell type


title: hapo_newborn_cordblood_A2254

tag: Sex

tag: developmental stage


title: ss3_23_056s_B02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 12
Smart-seq3

value: meninges

value: Neuronal/Glia

tag: group

value: control


title: ss3_23_056s_B06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 16
Smart-seq3

tag: tissue


title: ss3_23_056s_A12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 7
Smart-seq3

value: BLEC


title: SH56_129X1_2week_ath

description: Library name: SH56

tag: genotype


title: ss3_23_056s_C19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 38
Smart-seq3

value: Fibroblast


title: P7657_1022

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well

tag: s primer


title: RNA-seq of mouse cardiac tissue: AAV9_Irx3_MI_4

description:
Library name: AAV9_Irx3_MI_4
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

value: Left ventricle

value: Cardiomyocytes

value: Wild type

tag: treatment

value: Myocardial infarction (MI) surgery + AAV9-Irx3 overexpression vector

tag: batch


title: P3504_1146

description:
single cell library
Smart-Seq2

value: lung

tag: strain

tag: individual

tag: sorting date

value: single-end 50bp

tag: lane


title: SH39_BXD19_12week_ath

description: Library name: SH39

value: Liver


title: hapo_newborn_cordblood_B0598

tag: Sex

value: Female

value: cord clood

value: newborn

tag: cell type

value: whole blood cells


title: P3504_1158

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: developmental stage

tag: internal number

tag: n primer


title: hapo_newborn_cordblood_B0318

value: Male

tag: tissue


title: ss3_23_056s_D22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 60
Smart-seq3

value: meninges

tag: group

value: control


title: SH38_BXD19_12week_ath

description: Library name: SH38

tag: genotype


title: 1 µM sodium arsenite, bio rep 4

description:
Library name: DrAsL_4
Column name in fpkm.txt: DrAsL_4

tag: background

value: wildtype

value: AB strain

value: whole larvae

value: 1 µM sodium arsenite

tag: # fish

tag: bio replicate


title: P3504_1116

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well

tag: s primer


title: hapo_newborn_cordblood_A2251

tag: Sex


title: hapo_newborn_cordblood_A2240

tag: cell type


title: P3504_1115

description:
single cell library
Smart-Seq2

value: lung

tag: strain

tag: developmental stage

tag: individual

tag: sorting date

value: single-end 50bp

tag: lane


title: P3504_1113

description:
single cell library
Smart-Seq2

tag: tissue

tag: genotype

tag: internal number

tag: n primer


title: 1 µM sodium arsenite, bio rep 2

description:
Library name: DrAsL_2
Column name in fpkm.txt: DrAsL_2

tag: background

tag: treatment

tag: # fish

tag: bio replicate


title: hapo_newborn_cordblood_A2237

value: Female


title: P3504_1112

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: plate well


title: SH35_BXD19_8week_ath

description: Library name: SH35

value: Liver

tag: batch


title: 1 µM sodium arsenite, bio rep 3

description:
Library name: DrAsL_3
Column name in fpkm.txt: DrAsL_3

tag: cell type


title: hapo_newborn_cordblood_A2248

tag: Sex

value: cord clood

tag: developmental stage

value: newborn


title: P3504_1114

description:
single cell library
Smart-Seq2

tag: tissue

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

tag: lane

tag: s primer


title: SH36_BXD19_8week_ath

description: Library name: SH36

tag: genotype

tag: treatment


title: hapo_newborn_cordblood_A2235

value: Male

value: whole blood cells


title: 1 µM sodium arsenite, bio rep 1

description:
Library name: DrAsL_1
Column name in fpkm.txt: DrAsL_1

tag: background

tag: # fish

tag: bio replicate


title: SH33_BXD19_4week_ath

description: Library name: SH33


title: SH37_BXD19_8week_ath

description: Library name: SH37


title: SH34_BXD19_8week_ath

description: Library name: SH34


title: vehicle control, bio rep 3

description:
Library name: DrVeh_3
Column name in fpkm.txt: DrVeh_3

value: vehicle


title: vehicle control, bio rep 4

description:
Library name: DrVeh_4
Column name in fpkm.txt: DrVeh_4

value: wildtype


title: P3504_1110

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number

tag: n primer


title: SH32_BXD19_4week_ath

description: Library name: SH32

tag: tissue

tag: batch


title: hapo_newborn_cordblood_A2232

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

tag: developmental stage

tag: cell type


title: P3504_1109

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date

tag: lane

tag: plate well

tag: s primer


title: SH31_BXD19_4week_ath

description: Library name: SH31

tag: genotype

tag: treatment


title: vehicle control, bio rep 1

description:
Library name: DrVeh_1
Column name in fpkm.txt: DrVeh_1

tag: background

value: AB strain

tag: # fish

tag: bio replicate


title: P3504_1111

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number

tag: n primer


title: SH30_BXD19_4week_ath

description: Library name: SH30

tag: tissue

tag: batch


title: sp4-adult, wt, rep6

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

description: Library name: Sample 50

data_processing:
Paired-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.

source_name: single adult brain

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: single adult brain

tag: age

value: 3-4 months

tag: Sex

value: female

tag: clutch

value: clutch 1


title: P3504_1107

description:
single cell library
Smart-Seq2

tag: strain

tag: cell type

value: lung epithelial secretory cells

value: WT

tag: developmental stage

tag: individual

tag: sorting date

value: GFP^pos

tag: lane

tag: plate well

tag: s primer


title: SH29_BXD19_2week_ath

description: Library name: SH29

tag: genotype

tag: treatment


title: sp4-adult, het, rep6

description: Library name: Sample 49

value: sp4 heterozygous mutant

value: clutch 3


title: hapo_newborn_cordblood_A2214

value: Female

value: cord clood


title: hapo_newborn_cordblood_A2234

value: newborn


title: P3504_1106

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: internal number


title: hapo_newborn_cordblood_A2212

tag: Sex

tag: tissue

value: whole blood cells


title: vehicle control, bio rep 2

description:
Library name: DrVeh_2
Column name in fpkm.txt: DrVeh_2

tag: background

value: wildtype

value: AB strain

value: whole larvae

value: vehicle

tag: # fish

tag: bio replicate


title: hapo_newborn_cordblood_A2224

tag: developmental stage

tag: cell type


title: SH28_BXD19_2week_ath

description: Library name: SH28

value: Liver

tag: batch


title: SH27_BXD19_2week_ath

description: Library name: SH27


title: P3504_1104

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

tag: individual

tag: sorting date

tag: lane

tag: plate well

tag: n primer


title: P3504_1108

description:
single cell library
Smart-Seq2

tag: genotype

value: WT

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: s primer


title: hapo_newborn_cordblood_A2218

tag: Sex

value: Male

tag: tissue


title: hapo_newborn_cordblood_A2191


title: sp4-adult, hom, rep4

description: Library name: Sample 45

value: single adult brain

value: sp4 homozygous mutant

tag: age

value: 3-4 months

value: female

tag: clutch


title: sp4-adult, hom, rep5

description: Library name: Sample 48

value: clutch 3


title: P3504_1105

description:
single cell library
Smart-Seq2

value: lung

tag: cell type

tag: developmental stage

value: GFP^pos

tag: type of_sequencing

tag: internal number


title: hapo_newborn_cordblood_A2206

value: cord clood

value: newborn


title: sp4-adult, wt, rep5

description: Library name: Sample 47

value: wildtype


title: P3504_1102

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

value: single-end 50bp


title: SH26_BXD19_2week_ath

description: Library name: SH26

tag: treatment

tag: batch


title: sp4-adult, het, rep5

description: Library name: Sample 46

tag: genotype

value: sp4 heterozygous mutant

value: male


title: hapo_newborn_cordblood_A2197

value: whole blood cells


title: P3504_1103

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane

tag: plate well

tag: n primer


title: sp4-adult, het, rep4

description: Library name: Sample 43

tag: tissue

value: single adult brain

tag: age

tag: Sex


title: SH25_BXD19_0week_chow

description: Library name: SH25

value: Liver


title: SH24_BXD19_0week_chow

description: Library name: SH24


title: hapo_newborn_cordblood_A2180

value: Male

tag: developmental stage

tag: cell type


title: sp4-adult, wt, rep4

description: Library name: Sample 44

value: 3-4 months

value: female

tag: clutch


title: hapo_newborn_cordblood_A2186

value: Female


title: P3504_1101

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: GFP^pos

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number

tag: s primer


title: P3504_1100

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: sorting date


title: SH23_BXD19_0week_chow

description: Library name: SH23

tag: treatment

tag: batch


title: sp4-adult, hom, rep3

description: Library name: Sample 42

value: sp4 homozygous mutant

value: clutch 2


title: SH21_C57BL6J_16week_chow

description: Library name: SH21


title: sp4-adult, wt, rep3

description: Library name: Sample 41

value: wildtype


title: SH20_C57BL6J_16week_chow

description: Library name: SH20


title: P3504_1099

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: lane

tag: plate well

tag: n primer


title: SH22_BXD19_0week_chow

description: Library name: SH22

tag: tissue


title: hapo_newborn_cordblood_A2164

tag: Sex

value: cord clood

tag: developmental stage

value: newborn

tag: cell type


title: hapo_newborn_cordblood_A2153

value: whole blood cells


title: P3504_1098

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

value: WT

tag: cdna library_preparation_date

tag: type of_sequencing


title: hapo_newborn_cordblood_A2151


title: SH19_C57BL6J_16week_chow

description: Library name: SH19

value: Liver

tag: genotype


title: P3504_1097

description:
single cell library
Smart-Seq2

tag: individual

tag: internal number

tag: s primer


title: P3504_1096

description:
single cell library
Smart-Seq2

tag: sorting date


title: sp4-adult, het, rep3

description: Library name: Sample 40

value: single adult brain

value: sp4 heterozygous mutant

tag: age

value: male

tag: clutch


title: hapo_newborn_cordblood_A2154

value: Female


title: SH18_C57BL6J_16week_ath

description: Library name: SH18

tag: treatment

tag: batch


title: P3504_1095

description:
single cell library
Smart-Seq2

value: lung

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane

tag: plate well

tag: n primer


title: sp4-adult, het, rep2

description: Library name: Sample 37

tag: tissue

value: 3-4 months

tag: Sex

value: clutch 1


title: hapo_newborn_cordblood_A2142

value: Male

tag: developmental stage

tag: cell type


title: sp4-adult, hom, rep2

description: Library name: Sample 39

tag: genotype

value: sp4 homozygous mutant


title: sp4-adult, wt, rep2

description: Library name: Sample 38

value: wildtype


title: hapo_newborn_cordblood_A2145


title: SH17_C57BL6J_16week_ath

description: Library name: SH17


title: sp4-adult, hom, rep1

description: Library name: Sample 36

value: female


title: P3504_1094

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

value: GFP^pos

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: internal number


title: SH16_C57BL6J_16week_ath

description: Library name: SH16

tag: treatment


title: hapo_newborn_cordblood_A2132

value: cord clood

value: newborn

value: whole blood cells


title: P3504_1093

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: sorting date

tag: s primer


title: sp4-adult, wt, rep1

description: Library name: Sample 35

value: single adult brain

tag: age

tag: clutch


title: hapo_newborn_cordblood_A2129


title: P3504_1092

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane

tag: plate well


title: SH15_C57BL6J_12week_ath

description: Library name: SH15

tag: tissue

value: Liver

tag: batch


title: SH14_C57BL6J_12week_ath

description: Library name: SH14

tag: genotype


title: sp4-adult, het, rep1

description: Library name: Sample 34

value: sp4 heterozygous mutant

tag: Sex


title: hapo_newborn_cordblood_A2123

value: Female

tag: developmental stage

tag: cell type


title: SH13_C57BL6J_12week_ath

description: Library name: SH13


title: atp1a3a-v139m-adult, wt, rep7

description: Library name: Sample 33

value: 3-4 months

value: single clutch


title: P3504_1091

description:
single cell library
Smart-Seq2

value: lung

tag: strain

tag: individual

tag: cdna library_preparation_date

tag: type of_sequencing

tag: n primer


title: hapo_newborn_cordblood_A2121

value: Male


title: hapo_newborn_cordblood_A2116


title: P3504_1089

description:
single cell library
Smart-Seq2

tag: sorting date

tag: internal number

tag: s primer


title: P3504_1090

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no


title: atp1a3a-v139m-adult, hom, rep5

description: Library name: Sample 32

value: atp1a3a-v139m homozygous mutant

tag: age

value: male

tag: clutch


title: SH12_C57BL6J_8week_ath

description: Library name: SH12

tag: tissue

tag: treatment

tag: batch


title: hapo_newborn_cordblood_A2112

tag: Sex

tag: developmental stage


title: P3504_1088

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cell type

tag: genotype

value: GFP^pos

tag: lane

tag: plate well


title: SH11_C57BL6J_8week_ath

description: Library name: SH11


title: SH10_C57BL6J_8week_ath

description: Library name: SH10


title: atp1a3a-v139m-adult, het, rep6

description: Library name: Sample 31

value: atp1a3a-v139m heterozygous mutant


title: P3504_1087

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: n primer


title: hapo_newborn_cordblood_A2110

value: cord clood

value: newborn

value: whole blood cells


title: atp1a3a-v139m-adult, wt, rep6

description: Library name: Sample 30

value: single adult brain

value: wildtype

tag: age

value: female


title: SH9_C57BL6J_4week_ath

description: Library name: SH9

value: Liver


title: hapo_newborn_cordblood_A2109

value: Female


title: SH8_C57BL6J_4week_ath

description: Library name: SH8


title: atp1a3a-v139m-adult, hom, rep4

description: Library name: Sample 29

value: 3-4 months

tag: clutch

value: single clutch


title: P3504_1086

description:
single cell library
Smart-Seq2

tag: tissue

value: lung

value: lung epithelial secretory cells

value: WT

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: internal number

tag: s primer


title: hapo_newborn_cordblood_A2106

tag: Sex

value: Male

tag: developmental stage


title: hapo_newborn_cordblood_A2105

tag: cell type


title: P3504_1084

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

value: GFP^pos

tag: lane


title: SH7_C57BL6J_4week_ath

description: Library name: SH7

tag: treatment

tag: batch


title: atp1a3a-v139m-adult, het, rep5

description: Library name: Sample 28

value: atp1a3a-v139m heterozygous mutant

value: male


title: P3504_1085

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: plate well


title: atp1a3a-v139m-adult, wt, rep5

description: Library name: Sample 27

tag: tissue

tag: age

tag: clutch


title: hapo_newborn_cordblood_A2087

value: cord clood

value: newborn

value: whole blood cells


title: SH6_C57BL6J_2week_ath

description: Library name: SH6


title: atp1a3a-v139m-adult, wt, rep4

description: Library name: Sample 26

value: single adult brain

value: wildtype


title: SH5_C57BL6J_2week_ath

description: Library name: SH5

value: Liver


title: atp1a3a-v139m-adult, het, rep4

description: Library name: Sample 25

value: 3-4 months


title: hapo_newborn_cordblood_A2084

value: Female


title: P3504_1082

description:
single cell library
Smart-Seq2

value: lung

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: internal number

tag: n primer

tag: s primer


title: P3504_1083

description:
single cell library
Smart-Seq2

tag: strain

tag: cell type

value: lung epithelial secretory cells

tag: genotype

tag: developmental stage


title: SH4_C57BL6J_2week_ath

description: Library name: SH4

tag: treatment

tag: batch


title: SH3_C57BL6J_0week_chow

description: Library name: SH3


title: atp1a3a-v139m-adult, hom, rep3

description: Library name: Sample 23

value: atp1a3a-v139m homozygous mutant

tag: Sex

value: female

value: single clutch


title: hapo_newborn_cordblood_A2069

value: Male


title: atp1a3a-v139m-adult, wt, rep3

description: Library name: Sample 24


title: hapo_newborn_cordblood_A2062


title: P3504_1081

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: WT

tag: individual

tag: sorting date

value: GFP^pos

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: ss3_23_056s_F23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 92
Smart-seq3

tag: tissue

value: meninges

value: Neuronal/Glia

tag: group

value: control


title: SH2_C57BL6J_0week_chow

description: Library name: SH2


title: atp1a3a-v139m-adult, het, rep3

description: Library name: Sample 22

value: single adult brain

value: atp1a3a-v139m heterozygous mutant

tag: age

tag: clutch


title: P3504_1079

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: P3504_1080

description:
single cell library
Smart-Seq2

tag: strain

tag: cell type

tag: genotype

tag: developmental stage


title: SH1_C57BL6J_0week_chow

description: Library name: SH1

value: Liver

tag: treatment

tag: batch


title: hapo_newborn_cordblood_A2051

tag: Sex

value: Female

value: cord clood

value: newborn

value: whole blood cells


title: P3504_1078

description:
single cell library
Smart-Seq2

tag: tissue

value: lung

value: lung epithelial secretory cells

tag: individual

tag: sorting date

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_A2053


title: atp1a3a-v139m-adult, wt, rep2

description: Library name: Sample 21

value: wildtype

tag: age

value: 3-4 months

value: male

tag: clutch

value: single clutch


title: hapo_newborn_cordblood_A2039


title: atp1a3a-v139m-adult, hom, rep2

description: Library name: Sample 20

value: atp1a3a-v139m homozygous mutant


title: P3504_1077

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: WT

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: plate well

tag: internal number

tag: n primer


title: Astrocyte-TurboID pulldown miRNA-seq replicate 3

city: Atlanta

first: Christina

last: Ramelow

address: 615 Michael St RM 375

institute: Emory University

description:
Library name: Sample 60
mnt.novaoutput2.BI.RUO_bioinfo.smallRNA.21047.134.bowtie2map.21047FL.134.01.27_S6_L007.mm10.sort.bam
Aldh1l1_miRNA-seq_counts.txt

data_processing:
Global sequencing of 40 million paired-end reads per sample was completed using the Illumina-based platform at Admera Health. FASTQ files were evaluated for quality using FastQC and then mapped to the mouse genome, GRCm38 (mm10), or GRCh38, human genome (hg38), using the Spliced Transcripts Alignment to a Reference (STAR) (for mRNA-seq) or Bowtie 2 (for smRNA-seq) aligners with the paired-end option. The featureCounts package was used to generate a raw counts data matrix from mapped reads. Lowly abundant transcripts across all samples (average count value ≤ 10) were filtered out. After generating the filtered, raw counts data matrices, we used DESeq2 to normalize the matrices and perform differential gene ex-pression-based statistics.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file that includes raw counts for each sample.

source_name: cortex

growth_protocol: Mouse microglia BV2 cells were cultured in 0.2 µm vacuum filter sterilized Dulbecco’s Modified Eagle Medium (DMEM) supplemented with high glucose and L-glutamine containing 1% penicillin-streptomycin, and 10% fetal bovine serum. BV2 cells were incubated in 100 mm cell culture dish at 37°C and 5% CO2 until reaching 80-90% confluency. Cells were treated with 100 ng/mL of LPS for 48 h and 200 µM of biotin for 24 h during the second day of LPS treatment. Human embryonic kidney 293 cells (HEK293) were cultured in DMEM containing 1% penicillin-streptomycin and 10% fetal bovine serum. HEK293 cells were incubated in 6-well cul-ture dishes in the same condition as the BV2 cells described above. At 30% confluency, HEK293 cells were infected with 3 µL of the two LVs generated (TurboID-NES, viral titer: 3.9x108 IU/mL or TurboID-noNES, viral titer: 1.7x109 IU/mL). LV-containing media was removed after 3 days, and successful infection was determined by cellular GFP signal using the ECHO Revolve fluores-cence microscope (Echo, USA) prior to lysis. HEK293 cells were grown to 80-90% confluency cells before biotin treatment (200 µM for 24 h). The 48 h LPS and 24 h biotin treatment paradigms were used to model similar treatment and labeling kinetics for in vivo SPARO studies.

extract_protocol:
After protein enrichment using streptavidin and A/B beads, RNA was extracted from the beads and bulk/g;obal cell or bulk cortical lysates using a miRNeasy Mini Kit (Qiagen Inc., 217004) following the manufacturer’s instructions. 1-3 ug of total RNA was used to generate cDNA libraries.
The SMART-Seq® v4 PLUS Kit (Takara Bio) was used following the manufacturer’s protocol. For small RNA-sequencing library preparation, a QIAseq miRNA NGS kit (Qiagen, 331565) was used.

treatment_protocol: BV2 cells were treated with 100 ng/mL of lipopolysaccharide (LPS) for 48 h and 200 mM of biotin for 24 h during the second day of LPS treatment. All mice were given tamoxifen (75 mg/kg) intraperitoneally (i.p.) for 5 days at 6 weeks of age and allowed 3 weeks of Cre recombination. After Cre recombination, TurboID mice were given water supplemented with biotin (37.5 mg/L) for 2 weeks until euthanasia at 3-4 months of age. RiboTag mice were euthanized at 2.5 months of age. For astrocyte-TurboID LPS studies, systemic LPS at 0.75mg/kg/dose x 5 days was given via i.p. injection during the first week of biotin water supplementation. Mice from each cohort were anesthetized using ketamine/xylazine (ketamine 87.5 mg/kg, xylazine 12.5 mg/kg) followed by transcardial perfusion with ice-cold PBS.

value: cortex

tag: cell line

tag: cell type

value: mature astrocyte

tag: genotype


title: Astrocyte-TurboID pulldown miRNA-seq replicate 2

description:
Library name: Sample 59
mnt.novaoutput2.BI.RUO_bioinfo.smallRNA.21047.134.bowtie2map.21047FL.134.01.26_S5_L007.mm10.sort.bam
Aldh1l1_miRNA-seq_counts.txt

tag: Sex

tag: batch


title: atp1a3a-v139m-adult, wt, rep1

description: Library name: Sample 18

tag: tissue

value: single adult brain

value: female


title: hapo_newborn_cordblood_A2009

value: Male

value: cord clood

tag: developmental stage


title: atp1a3a-v139m-adult, het, rep2

description: Library name: Sample 19

value: atp1a3a-v139m heterozygous mutant


title: hapo_newborn_cordblood_A2007

value: Female

value: newborn

value: whole blood cells


title: Astrocyte-TurboID pulldown miRNA-seq replicate 1

description:
Library name: Sample 58
mnt.novaoutput2.BI.RUO_bioinfo.smallRNA.21047.134.bowtie2map.21047FL.134.01.25_S4_L007.mm10.sort.bam
Aldh1l1_miRNA-seq_counts.txt


title: hapo_newborn_cordblood_A1991


title: Astrocyte-TurboID bulk miRNA-seq replicate 3

description:
Library name: Sample 57
mnt.novaoutput2.BI.RUO_bioinfo.smallRNA.21047.134.bowtie2map.21047FL.134.01.24_S3_L007.mm10.sort.bam
Aldh1l1_miRNA-seq_counts.txt


title: atp1a3a-v139m-adult, hom, rep1

description: Library name: Sample 17

value: 3-4 months


title: P3504_1075

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: lung epithelial secretory cells

tag: individual

tag: sorting date

tag: cdna library_preparation_date

value: single-end 50bp

tag: s primer


title: P3504_1074

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: type of_sequencing

tag: lane


title: Astrocyte-TurboID bulk miRNA-seq replicate 1

description:
Library name: Sample 55
mnt.novaoutput2.BI.RUO_bioinfo.smallRNA.21047.134.bowtie2map.21047FL.134.01.22_S1_L007.mm10.sort.bam
Aldh1l1_miRNA-seq_counts.txt

value: male


title: Astrocyte-TurboID bulk miRNA-seq replicate 2

description:
Library name: Sample 56
mnt.novaoutput2.BI.RUO_bioinfo.smallRNA.21047.134.bowtie2map.21047FL.134.01.23_S2_L007.mm10.sort.bam
Aldh1l1_miRNA-seq_counts.txt


title: hapo_newborn_cordblood_A1980


title: Zfp750 fl/fl Lrig1CreER TdTomatoe 3 - Day50

city: San Diego

first: George

last: Sen

state: California

address: 9452 Medical Ctr Dr, La Jolla, CA

department: Department of Dermatology

institute: University of California San Diego

description: Library name: Sample 6

data_processing:
NovaSeq X plus PE100 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
Assembly: BAM files were imported into the RNA-seq pipeline of Partek FLow, version 9.0.20.0202 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 93 2020-02-03). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Zfp750 fl/fl Lrig1CreER+ tdTomatoe+ mouse skin

growth_protocol: Skin cells from control and Zfp750 knockout mice expressing tdTomato were sorted

extract_protocol:
PureLinkTMRNA mini kit (Thermo Fisher Scientific; 12183025) was used to extract RNA from sorted cells.
NEBNext Ultra II RNA Library Prep Kit  (Illumina) then multiplexed

treatment_protocol: 4-hydroxytamoxifen (4-OHT) from day 4 to 7 day old pups or day 5 to 8 day old pups

value: ZNF750 fl/fl Rosa26 -/-  Lrig1-CreERT2 +/-

tag: treatment


title: P3504_1076

description:
single cell library
Smart-Seq2

value: WT

value: GFP^pos

tag: ercc spike-in_lot_no

tag: plate well

tag: internal number

tag: n primer


title: atp1a3a-v139m-adult, het, rep1

description: Library name: Sample 16

value: single adult brain

tag: genotype

tag: age

tag: Sex

tag: clutch

value: single clutch


title: hapo_newborn_cordblood_A1953

tag: tissue

tag: developmental stage

tag: cell type


title: atp1a3a-v139m-6dpf, hom, rep5

description: Library name: Sample 14

source_name: 6 dpf head with eyes, 3-5 heads combined

value: atp1a3a-v139m homozygous mutant

value: 6 days


title: P3504_1073

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date

tag: cdna library_preparation_date


title: P3504_1071

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: type of_sequencing

tag: lane

tag: s primer


title: atp1a3a-v139m-6dpf, wt, rep5

description: Library name: Sample 15

value: 6 dpf head with eyes, 3-5 heads combined

value: wildtype


title: atp1a3a-v139m-6dpf, het, rep5

description: Library name: Sample 13

value: atp1a3a-v139m heterozygous mutant


title: P3504_1072

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: plate well

tag: internal number


title: hapo_newborn_cordblood_A1972

value: Female

value: cord clood

value: newborn

value: whole blood cells


title: Zfp750 fl/fl Lrig1CreER TdTomatoe 2 - Day50

description: Library name: Sample 5

value: Zfp750 fl/fl Lrig1CreER+ tdTomatoe+ mouse skin

tag: genotype

tag: treatment

value: 4-hydroxytamoxifen (4-OHT) from day 4 to 7 day old pups or day 5 to 8 day old pups


title: hapo_newborn_cordblood_A1947

tag: Sex

value: Male


title: CTL2-Day50

description: Library name: Sample 2

source_name: Control Mouse skin

tag: tissue

value: Control Mouse skin

value: ZNF750 wt/wt Rosa26 +/- Lrig1-CreERT2 +/-


title: hapo_newborn_cordblood_A1952

tag: developmental stage


title: P3504_1070

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cell type

value: lung epithelial secretory cells

value: WT

value: GFP^pos

value: single-end 50bp

tag: n primer


title: hapo_newborn_cordblood_A1948


title: Zfp750 fl/fl Lrig1CreER TdTomatoe 1 - Day50

description: Library name: Sample 4

value: ZNF750 fl/fl Rosa26 -/-  Lrig1-CreER +/-


title: CTL1-Day50

description: Library name: Sample 1

value: ZNF750 wt/fl Rosa26 -/- Lrig1-CreERT2 +/-


title: hapo_newborn_cordblood_A1949


title: atp1a3a-v139m-6dpf, wt, rep4

description: Library name: Sample 12

value: 6 dpf head with eyes, 3-5 heads combined

value: wildtype

tag: age

value: 6 days

tag: clutch

value: single clutch


title: P3504_1069

description:
single cell library
Smart-Seq2

tag: strain

tag: individual

tag: sorting date

tag: cdna library_preparation_date


title: CTL3-Day50

description: Library name: Sample 3

value: ZNF750 wt/fl Rosa26 -/- Lrig1-CreER +/-


title: atp1a3a-v139m-6dpf, hom, rep4

description: Library name: Sample 11

value: atp1a3a-v139m homozygous mutant


title: atp1a3a-v139m-6dpf, hom, rep3

description: Library name: Sample 8


title: Zfp750 fl/fl Lrig1CreER TdTomatoe-3 Day36

description: Library name: Sample 6

value: Zfp750 fl/fl Lrig1CreER+ tdTomatoe+ mouse skin

value: ZNF750 fl/fl Rosa26 -/-  Lrig1-CreERT2 +/-

value: 4-hydroxytamoxifen (4-OHT) from day 4 to 7 day old pups or day 5 to 8 day old pups


title: P3504_1065

description:
single cell library
Smart-Seq2

value: lung

tag: isolation criteria

tag: type of_sequencing

tag: lane

tag: s primer


title: P3504_1067

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: ercc spike-in_lot_no

tag: plate well

tag: internal number


title: P3504_1068

description:
single cell library
Smart-Seq2

tag: tissue

value: lung epithelial secretory cells

tag: developmental stage


title: atp1a3a-v139m-6dpf, het, rep4

description: Library name: Sample 10

value: atp1a3a-v139m heterozygous mutant


title: atp1a3a-v139m-6dpf, wt, rep3

description: Library name: Sample 9


title: P3504_1064

description:
single cell library
Smart-Seq2

tag: cell type

value: WT

value: GFP^pos

tag: n primer


title: hapo_newborn_cordblood_A1922

tag: Sex

value: Female

value: cord clood

value: newborn

value: whole blood cells


title: P3504_1066

description:
single cell library
Smart-Seq2

tag: strain

value: single-end 50bp


title: Zfp750 fl/fl Lrig1CreER TdTomatoe-4 Day36

description: Library name: Sample 7

value: ZNF750 fl/fl Rosa26 +/-  Lrig1-CreERT2 +/-

tag: treatment


title: Zfp750 fl/fl Lrig1CreER TdTomatoe 1-Day36

description: Library name: Sample 4

value: ZNF750 fl/fl Rosa26+/-  Lrig1-CreER +/-


title: hapo_newborn_cordblood_A1944

value: Male


title: P3504_1062

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date


title: atp1a3a-v139m-6dpf, hom, rep2

description: Library name: Sample 5

value: 6 dpf head with eyes, 3-5 heads combined

value: atp1a3a-v139m homozygous mutant

tag: age

value: 6 days

tag: clutch

value: single clutch


title: P3504_1061

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: CTL3-Day36

description: Library name: Sample 3

value: Control Mouse skin

tag: genotype

value: ZNF750 wt/wt Rosa26 +/- Lrig1-CreER +/-

value: 4-hydroxytamoxifen (4-OHT) from day 4 to 7 day old pups or day 5 to 8 day old pups


title: hapo_newborn_cordblood_A1943


title: atp1a3a-v139m-6dpf, het, rep2

description: Library name: Sample 4

value: atp1a3a-v139m heterozygous mutant


title: hapo_newborn_cordblood_A1928

value: Female

value: cord clood


title: atp1a3a-v139m-6dpf, het, rep3

description: Library name: Sample 7


title: hapo_newborn_cordblood_A1913

value: newborn

value: whole blood cells


title: hapo_newborn_cordblood_A1903


title: P3504_1059

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

value: GFP^pos

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: plate well

tag: internal number

tag: s primer


title: atp1a3a-v139m-6dpf, hom, rep1

description: Library name: Sample 2

tag: tissue

value: 6 dpf head with eyes, 3-5 heads combined

value: atp1a3a-v139m homozygous mutant


title: hapo_newborn_cordblood_A1924

tag: Sex

tag: developmental stage

tag: cell type


title: CTL.1-Day36

description: Library name: Sample 1

value: ZNF750 wt/fl Rosa26 +/- Lrig1-CreERT2 +/-

tag: treatment


title: atp1a3a-v139m-6dpf, het, rep1

description: Library name: Sample 1

value: 6 days

value: single clutch


title: hapo_newborn_cordblood_A1902


title: P3504_1058

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

tag: n primer


title: Zfp750 fl/fl Lrig1CreER TdTomatoe -2 Day36

description: Library name: Sample 5

value: Zfp750 fl/fl Lrig1CreER+ tdTomatoe+ mouse skin

value: ZNF750 fl/fl Rosa26 +/-  Lrig1-CreERT2 +/-

value: 4-hydroxytamoxifen (4-OHT) from day 4 to 7 day old pups or day 5 to 8 day old pups


title: atp1a3a-v139m-6dpf, wt, rep2

description: Library name: Sample 6

value: wildtype

tag: age

tag: clutch


title: ss3_23_056s_P20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 243
Smart-seq3

value: meninges

value: Immune

tag: group

value: control

tag: batch


title: P3504_1063

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_A1901

tag: Sex

value: Female

tag: tissue

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: HFD_fed_CDI_Female_6dpi-4

city: Ann Arbot

first: Raymond

last: Yung

state: Michigan

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Library name: 13375-NN-171

data_processing:
The reads were trimmed using Cutadapt v4.8. Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a  and assigned count estimates to genes with RSEM v1.3.3.
Assembly: GRCm38
Supplementary files format and content: counts

source_name: Cecum

growth_protocol: Young 4-6 weeks old male and female C57BL/6J mice housed at the University of Michigan were used in this study. Mice were either fed with high-fat diet (HFD) (42% Kcal from fat, Inotiv; TD.88137) or normal diet (ND) (13% Kcal from fat, LabDiet; 5L0D) for 12 weeks

extract_protocol:
Cecal samples were processed for RNA isolation using Direct-zol™ RNA Miniprep (Zymo Research). RNA samples were then submitted to University of Michigan Advanced Genomics Core for quality check, library preparation, sequencing and generating count files
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan

treatment_protocol: Sixteen-eighteen weeks old mice were intraperitoneally (i.p.) injected with clindamycin (10mg/kg) (Sigma). After 24 hours, mice were inoculated with 103 VPI 10643 via oral gavage, while mock mice were given distilled water at the same time

value: Cecum

tag: diet

value: HFD

tag: treatment

value: CDI

tag: days post_infection

tag: strain


title: CTL2-Day36

description: Library name: Sample 2

value: Control Mouse skin

value: ZNF750 wt/fl Rosa26 +/- Lrig1-CreERT2 +/-


title: HFD_fed_CDI_Female_6dpi-3

description: Library name: 13375-NN-170


title: hapo_newborn_cordblood_A1915

tag: cell type


title: HFD_fed_CDI_Female_6dpi-2

description: Library name: 13375-NN-169


title: hapo_newborn_cordblood_A1888

value: Male


title: P3504_1060

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

value: GFP^pos

value: single-end 50bp

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: 28hpf_sox17E_RNA_rep2

city: Coventry

first: Andrew

last: Nelson

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: Library name: 28hpf_sox17E_RNA_rep2

data_processing:
RNA-seq: Reads were mapped onto zebrafish genome, danRer11 using STAR (Dobin et al. 2013). HTSeq was used to count aligned reads per gene (Anders et al. 2015). The raw count matrix was imported into iDEP (Ge et al. 2018), and differentially expressed genes (DEGs) identified using default parameters.
Assembly: danRer11
Supplementary files format and content: RNA-seq processed data are differentially expressed genes between the sox17E and sox17N population called by iDEP using default parameters.

source_name: endoderm-enriched

growth_protocol: Embyos were maintained in E3 embryo medium at 28.5 degrees celcius

extract_protocol:
Cell populations were isolated according to fluorescence profiles using a BD FACSAria Fusion flow cytometer.  For RNA-seq cells were pelleted and total RNA extracted using QIAGEN Rneasy Mini kits.
RNA-seq libraries were produced from 10 ng total RNA each using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina according to the manufacturer’s instructions and were sequenced using Novaseq 6000-S4-type flow cell.

value: endoderm-enriched

tag: cell line

value: AB

tag: genotype

value: FACS isolated


title: P3504_1055

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: HFD_fed_CDI_Female_6dpi-5

description: Library name: 13375-NN-172

tag: tissue

tag: diet

tag: Sex

value: Female

tag: treatment


title: HFD_fed_CDI_Female_6dpi-1

description: Library name: 13375-NN-168

tag: days post_infection

tag: strain


title: P3504_1056

description:
single cell library
Smart-Seq2

tag: cell type

tag: developmental stage

tag: individual

tag: sorting date

tag: plate well


title: P7657_1150

description:
single cell library
Smart-Seq2

tag: genotype

tag: internal number

tag: n primer

tag: s primer


title: 48hpf_sox17N_ATAC_rep2

description: Library name: 48hpf_sox17N_ATAC_rep2

library_source: genomic

data_processing:
ATAC-seq: Reads were trimmed from the 3’ end to a uniform 75 bp using seqtk so that mapping of reads was not impacted by sequencing read length. Adapter sequences were trimmed using Trimmomatic version 0.39 (Bolger et al. 2014). Data quality control and confirmation of adapter removal was performed using FastQC (Andrews 2010). Reads were aligned to the genome reference consortium zebrafish build 11 (GRCz11v97) using Bowtie2 (Langmead and Salzberg 2012) using “Very sensitive” and 2 kb maximum fragment length for paired-end alignments. Samtools (Li et al. 2009) was also used to filter out reads that mapped to the mitochondrial genome, duplicated reads and low-quality reads with a MAPQ score < 22.
Assembly: danRer11
Supplementary files format and content: ATAC-seq processed data are CPM normalised bigWig files of ATAC-seq profiles with biological replicates merged, produced using deepTools bamCoverage.

source_name: sox17-negative lineages

extract_protocol:
Cell populations were isolated according to fluorescence profiles using a BD FACSAria Fusion flow cytometer.  ATAC-seq libraries were produced according to "Corces MR, Trevino AE, Hamilton EG, et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 14: 959".
ATAC-seq libraries were produced according to "Corces MR, Trevino AE, Hamilton EG, et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 14: 959".

value: sox17-negative lineages

tag: cell line


title: P3504_1057

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: ND_fed_CDI_Female_3dpi-4

description: Library name: 13375-NN-166

tag: tissue

value: Cecum

tag: diet

value: ND

tag: Sex

tag: treatment

tag: days post_infection


title: hapo_newborn_cordblood_A1871

value: cord clood

tag: developmental stage

value: newborn

tag: cell type

value: whole blood cells


title: 48hpf_sox17M_ATAC_rep2

description: Library name: 48hpf_sox17M_ATAC_rep2

source_name: hematovascular

value: hematovascular

tag: genotype


title: hapo_newborn_cordblood_A1872

value: Male


title: 28hpf_sox17N_RNA_rep2

description: Library name: 28hpf_sox17N_RNA_rep2


title: P3504_1052

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

tag: plate well

tag: internal number


title: P3504_1053

description:
single cell library
Smart-Seq2

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: n primer

tag: s primer


title: 48hpf_sox17E_ATAC_rep2

description: Library name: 48hpf_sox17E_ATAC_rep2

tag: tissue

value: endoderm-enriched

tag: cell line

value: AB


title: ND_fed_CDI_Female_3dpi-2

description: Library name: 13375-NN-164

tag: diet

tag: Sex

value: CDI


title: hapo_newborn_cordblood_A1895


title: 28hpf_sox17N_RNA_rep1

description: Library name: 28hpf_sox17N_RNA_rep1

tag: treatment

value: FACS isolated


title: P3504_1183

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: developmental stage

value: EpCam^pos CD45^neg

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: atp1a3a-v139m-6dpf, wt, rep1

description: Library name: Sample 3

value: 6 dpf head with eyes, 3-5 heads combined

tag: genotype

value: wildtype

tag: age

value: 6 days

tag: clutch

value: single clutch


title: hapo_newborn_cordblood_A1847

value: cord clood

value: newborn

tag: cell type

value: whole blood cells


title: 28hpf_sox17E_RNA_rep1

description: Library name: 28hpf_sox17E_RNA_rep1


title: hapo_newborn_cordblood_A1843

value: Female


title: P3504_1047

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: plate well

tag: internal number


title: 28hpf_sox17N_ATAC_rep2

description: Library name: 28hpf_sox17N_ATAC_rep2

tag: tissue

value: sox17-negative lineages

tag: cell line

value: AB


title: hapo_newborn_cordblood_A1832

tag: Sex

value: Male


title: hapo_newborn_cordblood_A1875

tag: developmental stage


title: 48hpf_sox17E_ATAC_rep1

description: Library name: 48hpf_sox17E_ATAC_rep1

value: endoderm-enriched

tag: treatment

value: FACS isolated


title: HFD_fed_Mock_Female_3dpi-2

description: Library name: 13375-NN-160

value: Cecum

tag: diet

value: HFD

value: Mock

tag: days post_infection


title: hapo_newborn_cordblood_A1815


title: P3504_1034

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: n primer

tag: s primer


title: P3504_1054

description:
single cell library
Smart-Seq2

tag: strain

tag: cell type

tag: individual

tag: sorting date

tag: isolation criteria


title: ND_fed_CDI_Female_3dpi-5

description: Library name: 13375-NN-167

tag: tissue

value: ND

tag: Sex

value: CDI


title: 28hpf_sox17E_ATAC_rep2

description: Library name: 28hpf_sox17E_ATAC_rep2

tag: cell line

tag: treatment


title: ND_fed_Mock_Female_3dpi-4

description: Library name: 13375-NN-158

tag: diet

value: Female

tag: days post_infection


title: hapo_newborn_cordblood_A1803

value: cord clood

tag: developmental stage

value: newborn

value: whole blood cells


title: ND_fed_CDI_Female_3dpi-3

description: Library name: 13375-NN-165


title: hapo_newborn_cordblood_A1870


title: P3504_1050

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: plate well

tag: internal number


title: F3

city: Champaign

first: QIQI

last: XIE

state: IL

address: 2753-11 Hunters Pond Run, Champaign, IL 61820

institute: University of Illinois Urbana-Champaign

description: Library name: Sample 6

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer ’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq Xten platform and paired-end reads were generated.
Raw reads were filtered to remove low-quality reads and adaptors. Clean reads were mapped to the reference genome (Rattus norvegicus) using standard alignment software STAR.
Gene expression levels were quantified and calculated using featureCounts. Differential expression analysis was performed comparing the TBHP group and the TBHP+FGF21 group. Differentially expressed genes (DEGs) were identified based on the threshold of |logFC| > 1 and P < 0.05.
Assembly: http://ftp.ensembl.org/pub/release-105/fasta/rattus_norvegicus/
Supplementary files format and content: The file format is CSV. The content is a gene count matrix. The first column contains gene symbols. Columns F1, F2, and F3 represent TBHP plus FGF21 samples. Columns T1, T2, and T3 represent TBHP samples. Values represent raw read counts.

organism: Rattus norvegicus

source_name: Nucleus pulposus

growth_protocol: Nucleus pulposus cells (NPCs) were isolated from the caudal vertebrae of male Sprague-Dawley rats (120–150 g). The NP tissues were digested with 0.1 mg/mL collagenase II (Proteintech, China) for 20 minutes. Cells were cultured in DMEM/F12 medium supplemented with 15% fetal bovine serum (FBS) and 1% antibiotics at 37°C in a 5% CO2 atmosphere.

extract_protocol:
RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR  UltraTM  Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. 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. 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 of preferentially 240 bp in 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, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The cells were divided into two groups to investigate the effect of FGF21 on senescence. The model group was treated with tert-butyl hydroperoxide (TBHP) to induce oxidative stress and senescence. The treatment group was co-treated with TBHP and recombinant rat FGF21. Total RNA was extracted after the treatment period.

value: Nucleus pulposus

value: Primary Nucleus Pulposus Cells

value: Nucleus Pulposus Cells

value: Wild type Sprague-Dawley (SD) rat

value: treated with tert-butyl hydroperoxide (TBHP) and recombinant FGF23


title: 48hpf_sox17N_ATAC_rep1

description: Library name: 48hpf_sox17N_ATAC_rep1

value: sox17-negative lineages

value: AB

value: FACS isolated


title: hapo_newborn_cordblood_A1857

source_name: newborn cordblood


title: ND_fed_CDI_Female_3dpi-1

description: Library name: 13375-NN-163

value: Cecum

value: ND

tag: strain