title: HMC-AGEs, rep 1, RNA-seq

value: kidney

value: 100 ug/ml advanced glycation end products


title: Jlat5A8 vRNA IBET Rep2

status: Public on Aug 15 2023

type: SRA

city: Seattle

first: Terry

last: Hafer

email: tjhafe@gmail.com, thafer@fredhutch.org

state: Washington

address: 1100 Fairview Ave N

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

library_source: other

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v3.9.25 software followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v2.20.
FASTX barcode splitter was used to separate reads by barcode matching.
Alignment to reference and guide-level quantification was performed using Liu lab's MAGeCK software.
Liu lab's CRISPR analysis tool, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK), was used to perform differential guide analysis between various groups of interest. PMID: 25476604.
Assembly: HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
Supplementary files format and content: Tab delimited file with read counts for each guide sequence across all samples
Library strategy: CRISPR screen

molecule: other

organism: Homo sapiens

source_name: Jurkat (J-Lat 5A8)

growth_protocol: J-Lat cells were cultured in RPMI 1640 media (ThermoFisher, 11875093) supplemented with Pen/Strep, 10% Fetal Bovine Serum (FBS), and 10 mM HEPES (ThermoFisher, 15630080). Cells were maintained at 37ºC with 5% CO2. 24 hours after viral transduction, cells were subjected to puromycin treatment (Sigma, P8833) at a final concentration of 0.4 ug/mL to select for cells that received the vector. Latency reversal agent drug treatments were performed 11 days after viral transduction, and cell and viral pellets were isolated 12 days after viral transduction.

extract_protocol:
To isolate Genomic DNA  for the screen, cells were spun down for each treatment for 5 minutes at 1,000 xg at room temperature, washed in 1x PBS, spun down again, and cell pellets frozen at -80ºC until ready for extraction. Genomic DNA (gDNA) was isolated from each treatment using the QIAamp DNA Blood Midi Kit (Qiagen #51183). Viral RNA (vRNA) was extrated from supernatant of pelleted cells by concentrating over a 20% sucrose solution (70,000 xg for 1 hour at 4C), and then isolating vRNA from pellets using the QIAamp Viral RNA Mini Kit (Qiagen, #52904).
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

treatment_protocol: 11 days after transduction, cells were treated with either DMSO, AZD5582 (25 nM, MedChemExpress, HY-12600), I-BET151 (10 uM, SelleckChem, S2780), or combination AZD5582 (1 nM) and I-BET151 (2.5 uM) for 24 hours.

tag: cell line

value: Jurkat (J-Lat 5A8)

tag: cell type

value: T Lymphocyte

tag: treatment


title: MCF7 cells, shHot_-E2_FOXA1_ChIP-seq

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

library_source: genomic

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
The raw reads (single-end, 100 bp) were aligned to human reference genome hg19 using bowtie (v1.1.0) allowing up to one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs.  Peak calling was performed using MACS (v1.4.2) with the default cutoff of P ≤ 1 × 10-8. Clonal reads were automatically removed by MACS.

molecule: genomic DNA

growth_protocol: MCF7 cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 1% antibiotics.

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were performed with following modifications to previously described high-throughput ChIP protocol (Blecher-Gonen et al, 2013). Briefly, cells were crosslinked in 1% formaldehyde for 10 min, followed by incubation with glycine to stop crosslinking. Cells were collected and washed with ice cold PBS, incubated with cell lysis buffer (5mM PIPES pH 8.0, 85 mM KCl and 0.5% NP40) with protease inhibitor cocktail (Roche) to isolate nuclei. The nuclei were lysed for 30 min on ice using nuclei lysis buffer (12 mM Tris-HCl pH 8.0, 6 mM EDTA pH 8.0, 0.5% SDS) supplemented with protease inhibitor cocktail. Lysate were fragmented with a Bioruptor (Diagenode) to obtain DNA fragments ranging 200-600 bp. The supernatant was incubated with respective antibodies conjugated with Dynabeads Protein G (Invitrogen) in dilution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 0.1% Na-DOC, 1% Triton X-100) overnight at 4°C. The immunocomplexes were collected using Dynamag, washed twice with low-salt buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-DOC) and high-salt buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-DOC) and then once with LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% Na-Deoxycholate), and reverse crosslinked overnight followed by DNA extraction.
ChIP–seq libraries were prepared using NEBNext Ultra II DNA library prep kit.

treatment_protocol: For hormone (estrogen) depletion, cells were changed to charcoal-stripped hormone-free medium (Gibco, Grand Island, NY) supplemented with 10% charcoal dextran-treated fetal bovine serum (Thermal Scientific Hyclone, Logan, UT) for 72 hours. Estrogen induction was performed using 10 nM of 17β-estradiol (Sigma, St. Louis, MO) for the indicated times. Ethanol was used as a vehicle control.

value: Breast Adenocarcinoma cell line MCF7

value: shHOTAIRM1, - estrogen

tag: chip antibody

value: FOXA1 (ab5089 from Abcam)


title: Jlat106 vRNA COMBO Rep2

source_name: Jurkat (J-Lat 10.6)

value: Jurkat (J-Lat 10.6)

value: AZD5582 and I-BET151


title: MCF7 cells, shHot_+E2_ERalpha_ChIP-seq

value: shHOTAIRM1, + estrogen

value: ERalpha (SC-8002 from Santa Cruz Biotech)


title: Jlat106 vRNA IBET Rep2


title: MCF7 cells, shHot_-E2_ERalpha_ChIP-seq


title: HRPC-AGEs, rep 1, RNA-seq

city: nanjing

first: XU

last: Ying

state: jiangsu

address: xuanwu district

country: China

institute: Nanjing university

library_source: transcriptomic

data_processing:
scRNA-seq samples: the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
RNA-seq samples: CLC Genomics Workbench v 11.0.1, sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05), trimmed sequence reads were mapped to  hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8), read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files for scRNA-seq samples.
Supplementary files format and content: Tab-delimited text files include RPKM values for RNA-seq samples.

molecule: total RNA

source_name: retina

growth_protocol: HMC and HRPC were  maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
21 weeks old wide type (wt) and leptin receptor-deficient (db/db) in C57BLKs/J background mice were sacrificed. Kidneys were perfused with PBS, followed by dynabead perfusion. Minced kidneys were digested with 1 mg/ml collagenase II , 1 mg/ml Protease E  plus 50 units/ml DNase I  at 37 °C for 5 min. Separated glomeruli were washed three times, then placed in 2 ml digestion buffer and incubated for an additional 30 minutes at 37℃ with rotating. Globes were removed and dissected in PBS on ice. Retina tissues were dissociated with dissociation system containing 2 mg/ml collagenase  II  and 200 units/ml DNase I at 37℃ for 30 minutes on a rotator. The retinal cells were then sorted by magnetic bead separation using PE anti-mouse CD140b antibody and PE-anti PECAM1 antibody.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HMC and HRPC was induced by treatment of 100 µg/ml AGEs for 6 hours while 100 µg/ml BSA as control.

tag: tissue

value: retina

value: retinal pericyte


title: MCF7 cells, shCtrl_+E2_Input_ChIP-seq

value: control vector, + estrogen


title: MCF7 cells, shCtrl_-E2_Input_ChIP-seq

value: control vector, - estrogen


title: Jlat106 vRNA DMSO Rep2

value: DMSO


title: MCF7 cells, shCtrl_+E2_FOXA1_ChIP-seq


title: MCF7 cells, shHot_+E2_FOXA1_ChIP-seq


title: Jlat5A8 vRNA COMBO Rep1


title: MCF7 cells, shCtrl_-E2_FOXA1_ChIP-seq


title: Jlat5A8 vRNA IBET Rep1


title: Jlat5A8 vRNA AZD Rep1


title: Jlat5A8 vRNA DMSO Rep1


title: MCF7 cells, shCtrl_-E2_ERalpha_ChIP-seq


title: MCF7 cells, shCtrl_+E2_ERalpha_ChIP-seq


title: MCF7 cells, siHOTAIRM1_rep3 RNA-seq

description: AllGene_FPKM_siHOTAIRM1_vs_siControl.tsv

value: HOTAIRM1 knockdown


title: Jlat106 vRNA COMBO Rep1


title: MCF7 cells, siHOTAIRM1_rep1 RNA-seq


title: MCF7 cells, siControl_rep3 RNA-seq

value: control vector


title: MCF7 cells, siControl_rep2 RNA-seq


title: MCF7 cells, siHOTAIRM1_rep2 RNA-seq


title: Jlat106 vRNA DMSO Rep1


title: Jlat106 vRNA AZD Rep1


title: Jlat106 vRNA AZD Rep2


title: Jlat5A8 gDNA AZD Rep1


title: MCF7 cells, siControl_rep1 RNA-seq


title: Jlat106 gDNA DMSO Rep1


title: AK4M_wildtype

city: London

first: Michael

middle: A

last: Skinner

address: St Mary's Campus, Norfolk Place

department: Faculty of Medicine, Section of Virology

country: United Kingdom

institute: Imperial College London

data_processing:
Illumina data were processed using RTA with default filter and quality settings then the reads were demultiplexed (allowing no mismatches in the index sequence) with CASAVA
Paired Fastq files were imported into CLC bio’s Genomics Workbench (CLC bio, Qiagen Bioinformatics, Aarhus, Denmark), quality-controlled and thereafter processed using that package (version 20.0.4)
After quality control, the reads were subjected to quality trimming then mapped and aligned against ENSEMBL galGal5-annotated genes (GRCg6a;  15-12-2020) for quantitative analysis of expression using CLC's  RNA-Seq Analysis tool.
RPKM expression levels, Fold change and False Discovery Rates (FDR) were calculated using CLC's Test Differential Expression tool
Genome_build: release 102
Supplementary_files_format_and_content: TAB-delimited text files, prepared with CLC bio GWB, showing gene expression analysis for each sample  (not filtered for NaN, INF, -INF)

organism: Gallus gallus

source_name: PGC

growth_protocol: As chicken PGCs do not support IAV replication, CRISPR/Cas9-edited PGC lines were also differentaited into fibroblast-like cells, which are permissive for IAV replication

extract_protocol:
Total RNA was extracted and processed from wild-type and genome-edited PGCs, as well as derived fibroblast-like cell lines, using the RNeasy kit (Qiagen) according to manufacturers' instructions.
RNA libraries were prepared sequenced using the Illumina HiSeq2000 system at the Beijing Genomics Institute (BGI Hong Kong) using standard Illumina protocols.Poly (A) mRNA was purified from total RNA using magnetic beads with oligo (dT) (New England BioLabs, UK). The mRNA was then broken into short fragments using divalent cations at an elevated temperature. Using these cleaved RNA fragments as templates, random hexamer primers (Ivitrogen, Carlsbad, CA) was used for first-strand cDNA synthesis, followed by second-strand cDNA synthesis using DNA polymerase I (New England BioLabs, UK) and RNase H (Invitrogen).

treatment_protocol: To simultaneously introduce the N129I and D130N substitutions in exon 4, chicken primordial germ cells (PGCs) were transfected with PX459 CRISPR/Cas9 vector and short single stranded oligonucleotide (ssODN) repair template using Lipofectamine 2000 transfection reagent (Thermo Fisher Scientific). To generate ANP32A-knockout cells (‘Delta_ANP32A’), chicken PGCs were transfected with PX459 CRISPR/Cas9 only to introduce INDEL mutations in exon 1 using Lipofectamine 2000 transfection reagent. Subsequently, the PGCs were incubated for 24 hrs and treated with 0.6 µg/ml puromycin for 48 hrs  to enrich for transfected cells. Puromycin-selected PGCs were expanded in culture for two weeks to eliminate transient CRISPR expression and then used to isolate single cells for the generation of clonal PGC populations. To generate PGC fibroblast-like cells, PGCs were cultured in high calcium medium containing 1.8 mM CaCl2 in fibronectin-coated wells for 48 hrs. Subsequently, PGCs were resuspended in PGC fibroblast medium which was refreshed every 48 hours, while maintaining the cells in the fibronectin-coated wells. Adherent fibroblast-like cells are observable within 72 hours of resuspending PGCs in PGC fibroblast medium and reached 85-90% confluency within two weeks.

tag: strain

value: Hy-Line layer

value: PGC

tag: line

tag: genotype


title: AK4M_del33


title: AK4M_AKO


title: Con_NOX_6_18_liver_1

city: Jinan

first: Jin-Peng

last: Sun

address: 44 West Wenhua Road

institute: Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in_houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy_N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired_end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0_p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Liver

extract_protocol:
The isolated WAT or Liver are quickly put into liquid nitrogen and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from macrophages of WAT or Liver according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA_seq libraries were prepared using the KAPA Stranded RNA_Seq Library Preparation Kit.

value: Liver


title: CKO_vehicle_liver_2


title: CKO_vehicle_liver_1


title: CKO_NOX_6_18_liver_1


title: Con_NOX_6_18_liver_2


title: FR7M_wildtype


title: Con_vehicle_liver_2


title: Jlat106 vRNA IBET Rep1

value: T Lymphocyte


title: Con_vehicle_liver_1


title: FR5M_wildtype


title: CKO_NOX_6_18_WAT_2

source_name: WAT

value: WAT


title: FR6F_N129I_CL10


title: FR6F_wildtype


title: CKO_NOX_6_18_WAT_1


title: Jlat106 gDNA AZD Rep1


title: FR5M_N129I_7


title: Jlat5A8 gDNA DMSO Rep1

value: Jurkat (J-Lat 5A8)


title: CKO_Vehicle_WAT_1


title: FR5M_N129I_2


title: CKO_NOX_6_18_liver_2


title: Con_NOX_6_18_WAT_2


title: FR5M_N129I_3


title: Con_NOX_6_18_WAT_1


title: FR5M_N129I_1


title: Con_vehicle_WAT_2


title: FR5M_AKO_7_wildtype


title: Con_vehicle_WAT_1


title: FR5M_AKO_6


title: FR5M_AKO_5


title: FR5M_AKO_3


title: FR5M_AKO_13


title: HFD_2

address: 44 Wenhua Xi Rd

source_name: macrophage of islet

extract_protocol:
The isolated islet are quickly put into liquid nitrogen and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from macrophages of isletr according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA_seq libraries were prepared using the KAPA Stranded RNA_Seq Library Preparation Kit.

value: macrophage of islet

value: WT


title: HFD_1


title: NCD_2


title: NCD_1


title: FR4M_wildtype


title: FR3F_wildtype_Fb

source_name: Fib

value: Differentiated Fibroblast


title: CKO_Vehicle_WAT_2


title: Abca4KO biological rep 2

city: San Francisco

first: Li Xuan

last: Tan

address: 10 Koret Way

department: Ophthalmology

institute: UCSF

data_processing:
Paired-end clean reads were aligned to the reference genome using STAR software.
Parameter: mismatch = 2
Quantification was performed using HTSeq.
Parameter: -m union
Assembly: mm10
Supplementary files format and content: tab-delimited text includes raw counts for each sample

source_name: retinal pigment epithelium

growth_protocol: Wild-type (Jackson Labs; 129S1/SvlmJ) and Abca4−/− mice (Jackson Labs Abca4tm1Ght/J), both on Rpe65 Leu450 background were raised under 12-h cyclic light with standard diet.

extract_protocol:
RNA was harvested using RNAqueousTM-Micro Total RNA Isolation Kit (Thermo Fisher). A total of 1 µg RNA per sample was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's recommendations.

value: retinal pigment epithelium


title: Abca4KO biological rep 3


title: FR3F_N129I_40_Fb


title: FR3F_N129I_3_Fb


title: WT biological rep 3


title: FR3F_N129I_3


title: 16h after light onset_biol rep 3

growth_protocol: Wild-type (Jackson Labs; 129S1/SvlmJ) mice on Rpe65 Leu450 background were raised under 12-h cyclic light with standard diet.


title: FR3F_N129I_40


title: WT biological rep 1


title: Abca4KO biological rep 1


title: FR3F_N129I_2


title: WT biological rep 2


title: FR3F_N129I_2_Fb


title: 16h after light onset_biol rep 2


title: 15h after light onset_biol rep 3


title: FR3F_N129I_11


title: FR3F_AKO_6_wildtype


title: 15h after light onset_biol rep 2


title: FR3F_AKO_14_Fb


title: 15h after light onset_biol rep 1


title: 9h after light onset_biol rep 3


title: FR3F_AKO_14


title: 9h after light onset_biol rep 2


title: FR3F_AKO_12


title: FR3F_wildtype


title: 9h after light onset_biol rep 1


title: AK4M_AKO_Fb


title: 6h after light onset_biol rep 3


title: 5h after light onset_biol rep 3


title: 6h after light onset_biol rep 1


title: 5h after light onset_biol rep 2


title: Stage E6.0 embryo 2 section 4 region Epi2

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

description:
E6.0_2.txt
E6.0_2_4Epi2

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit.

treatment_protocol: Sample from each location was laser-microdissected and collected for single-cell based RNA sequencing. For the single cells isolated from known positions, embryos were dissected from the decidua in 10% FBS-DMEM medium, and cells were isolated from a specific position of the embryo by mouth pipetting guided by microscopy, then subject to Smart-seq2.

tag: developmental stage

value: embryo


title: 6h after light onset_biol rep 2


title: 5h after light onset_biol rep 1


title: 3h after light onset_biol rep 3


title: Stage E6.0 embryo 2 section 2 region Epi2

description:
E6.0_2.txt
E6.0_2_2Epi2


title: Stage E6.0 embryo 2 section 5 region Epi2

description:
E6.0_2.txt
E6.0_2_5Epi2


title: Stage E6.0 embryo 2 section 3 region Epi2

description:
E6.0_2.txt
E6.0_2_3Epi2


title: 16h after light onset_biol rep 1


title: Stage E6.0 embryo 2 section 4 region Epi1

description:
E6.0_2.txt
E6.0_2_4Epi1


title: Stage E6.0 embryo 2 section 2 region Epi1

description:
E6.0_2.txt
E6.0_2_2Epi1


title: Stage E6.0 embryo 2 section 1

description:
E6.0_2.txt
E6.0_2_1


title: 3h after light onset_biol rep 2


title: Stage E6.0 embryo 2 section 3 region Epi1

description:
E6.0_2.txt
E6.0_2_3Epi1


title: Stage E6.0 embryo 2 section 5 region Epi1

description:
E6.0_2.txt
E6.0_2_5Epi1


title: 1h after light onset_biol rep 3


title: Stage E6.0 embryo 1 section 5 region Epi1

description:
E6.0_1.txt
E6.0_1_5Epi1


title: 3h after light onset_biol rep 1


title: 1h after light onset_biol rep 1


title: Stage E6.0 embryo 1 section 4 region VE

description:
E6.0_1.txt
E6.0_1_4VE


title: 0h after light onset_biol rep 3


title: Stage E6.0 embryo 1 section 5 region VE

description:
E6.0_1.txt
E6.0_1_5VE


title: Stage E6.0 embryo 1 section 5 region Epi2

description:
E6.0_1.txt
E6.0_1_5Epi2


title: Stage E6.0 embryo 1 section 4 region Epi2

description:
E6.0_1.txt
E6.0_1_4Epi2


title: 0h after light onset_biol rep 2


title: Stage E6.0 embryo 1 section 4 region Epi1

description:
E6.0_1.txt
E6.0_1_4Epi1


title: Stage E6.0 embryo 1 section 3 region VE

description:
E6.0_1.txt
E6.0_1_3VE


title: Stage E6.0 embryo 1 section 3 region Epi2

description:
E6.0_1.txt
E6.0_1_3Epi2


title: Stage E6.0 embryo 1 section 2 region VE

description:
E6.0_1.txt
E6.0_1_2VE


title: Tumor infiltrated dendritic cell,MAVS KO,day10,rep2

city: shanghai

first: Lingling

last: Wu

address: 227 Chongqing South Road, Huangpu District, Shanghai

institute: Shanghai Jiaotong University

data_processing:
Samples with RIN>9 were selected for sequencing library construction using SMART-Seq® v4 PLUS Kit (Takara).
The final library was sequenced using an Illumina Novaseq 6000 sequencer.
Using HISAT2 RNA-sequencing alignment software, the raw reads were aligned to the mouse reference genome
The mapping rate was 96%, on average, across all the samples in the dataset. The alignment files (bam files) were processed to generate read counts for every gene using HISAT and HTSeq.
The read counts were normalized using the R package DESeq2 and then were centered and scaled for each gene, generating z-scores. P values obtained from multiple tests were adjusted using the Benjamini-Hochberg correction.
Assembly: mm10
Supplementary files format and content: csv file includes read counts for each sample

source_name: tumor

extract_protocol:
Total RNA from each sample was extracted using Trizol Reagent (ThermoFisher Scientific) following standard protocols. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: tumor

value: tumor infiltrated dendritic cells

value: MAVS knockout


title: Tumor infiltrated dendritic cell,MAVS KO,day10,rep3


title: Tumor infiltrated dendritic cell,WT,day10,rep2


title: Stage E6.0 embryo 1 section 2 region Epi2

description:
E6.0_1.txt
E6.0_1_2Epi2


title: Tumor infiltrated dendritic cell,WT,day10,rep3


title: Tumor infiltrated dendritic cell,MAVS KO,day10,rep1


title: Stage E6.0 embryo 1 section 2 region Epi1

description:
E6.0_1.txt
E6.0_1_2Epi1


title: 1h after light onset_biol rep 2


title: Stage E6.0 embryo 1 section 1 region VE

description:
E6.0_1.txt
E6.0_1_1VE


title: Stage E6.0 embryo 1 section 1 region AP

description:
E6.0_1.txt
E6.0_1_1AP


title: Tumor infiltrated dendritic cell,WT,day10,rep1


title: Stage E5.5 embryo 2 section 3 region Epi2

description:
E5.5_2.txt
E5.5_2_3Epi2


title: Stage E5.5 embryo 2 section 3 region Epi1

description:
E5.5_2.txt
E5.5_2_3Epi1


title: Stage E5.5 embryo 2 section 2 region Epi2

description:
E5.5_2.txt
E5.5_2_2Epi2


title: FR3F_N129I_11_Fb


title: featureCounts_t24_tbGFPpos_Rep1

city: Munich

first: Maria Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Galaxy
After contol with FastQC, Fastq files were mapped to mm10 using HiSAT2 for paired library
Read count were assessed using FeatureCounts using UCSC KnownGene as annotation file.
Differential expression between conditions were performed using DESeq2 with a pre-filter value of 10 and a ratio estimation size factor for all transcripts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FeatureCounts for each sample and DESeq2 of 5 comparisons.

source_name: mES cells, tbGFPpos, t24

growth_protocol: mES cells were cultured on gelatin-coated plates in DMEM with Glutamax (Gibco), supplemented with 15% ES-certified FCS (Gibco), 2X LIF, 0.05mM 2-betamercaptoethanol (Gibco), 0.1mM non-essential amino acids (Gibco) and 100 units/mL penicilin-streptomycin. For expansion, medium was supplemented with 3µM CHIR99021 and 1µM PD0325901

extract_protocol:
50 000 mES cells were FACS-sorted as tbGFP-positive or negative. Total RNA was extracted using PicoPure RNA Isolation Kit (ThermoFisher Scientific). RNA samples were treated with turbo DNAse (Life Technologies).
120ng of RNA was used and library prepared with TruSeq Stranded Gold Total RNA Library Prep Human/Mouse/Rat (Illumina)

treatment_protocol:
Cells are passaged and plated without the 2 kinase inhibitors.
Cells were collected after 48 hours of culture after 0, 6 or 24 hours of sorbitol treatment.

value: mESC

value: Sorbitol treatment

tag: time

value: 24 hours

tag: group

value: tbGFPpos


title: featureCounts_t24_tbGFPneg_Rep2

source_name: mES cells, tbGFPneg, t24

value: tbGFPneg


title: Stage E5.5 embryo 2 section 2 region Epi1

description:
E5.5_2.txt
E5.5_2_2Epi1


title: featureCounts_t24_tbGFPneg_Rep1


title: featureCounts_t6_tbGFPpos_Rep1

source_name: mES cells, tbGFPpos, t6

value: 6 hours


title: featureCounts_t6_tbGFPpos_Rep2


title: 0h after light onset_biol rep 1


title: Stage E5.5 embryo 1 section 1

description:
E5.5_2.txt
E5.5_2_1


title: featureCounts_t6_tbGFPneg_Rep2

source_name: mES cells, tbGFPneg, t6


title: Stage E6.0 embryo 1 section 3 region Epi1

description:
E6.0_1.txt
E6.0_1_3Epi1


title: featureCounts_t6_tbGFPneg_Rep1


title: Stage E5.5 embryo 1 section 3 region Epi2

description:
E5.5_1.txt
E5.5_1_3Epi2


title: featureCounts_t0_tbGFPpos_Rep2

source_name: mES cells, tbGFPpos, t0

value: 0 hour


title: Stage E5.5 embryo 1 section 3 region Epi1

description:
E5.5_1.txt
E5.5_1_3Epi1


title: Stage E5.5 embryo 1 section 2 region VE

description:
E5.5_1.txt
E5.5_1_2VE


title: Stage E5.5 embryo 1 section 2 region Epi2

description:
E5.5_1.txt
E5.5_1_2Epi2


title: featureCounts_t0_tbGFPpos_Rep1


title: featureCounts_t0_tbGFPneg_Rep2

source_name: mES cells, tbGFPneg, t0


title: Stage E5.5 embryo 1 section 2 region Epi1

description:
E5.5_1.txt
E5.5_1_2Epi1


title: featureCounts_t24_tbGFPpos_Rep2


title: featureCounts_t0_tbGFPneg_Rep1


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-MHCII- cells, Day 7 post-STIA, ADT

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

description:
ADT 10x Genomics
C57Bl/6  MHCII- (Day 7 STIA) CITE-seq B

data_processing:
CITE-seq libraries were processed using cellranger pipeline v6 and reference genome mm10 3.0.0.  ADT reads were assigned to proteins using the included ADT_reference.csv.  Processed files include Unique Molecular Identifier (UMI) counts per genes and ADT counts per protein.
ATAC-seq libraries were processed using the cellranger atac pipeline v.1.1.0 and refdata-cellranger-atac-mm10-1.2.0.  Processed files include fragment counts per peak.
Assembly: mm10
Supplementary files format and content: Matrix files with all data (raw)
Supplementary files format and content: Matrix files after filtering for cells (filtered)
Library strategy: ADT-seq

molecule: protein

source_name: Ankle Joint Synovium

extract_protocol:
Synovial tissue was processed into a single-cell suspension and live cells were sorted as indicated for each population
Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) libraries were prepared using 10x Chromium Single Cell 3’ Solution v3. Cellular mRNA and antibody-derived tag (ADT) oligos were indexed with a shared cellular barcode.
single-cell Assay for Transposase Accessible Chromatin (scATAC-seq) libraries were prepared using the 10x Chromium Single Cell ATAC kit

treatment_protocol: To induce serum transfer arthritis (STIA), 85μL/20g K/BxN serum was given intravenously (I.V) to each mouse.  STIA mice were euthanized at peak inflammation (ie. Day 7 post treatment)

value: Ankle Joint Synovium

value: serum-transfer-induced arthritis (STIA)


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-MHCII- cells, Day 7 post-STIA, scRNA

description:
3' 10x Genomics
C57Bl/6  MHCII- (Day 7 STIA) CITE-seq A

library_source: transcriptomic single cell

data_processing:
CITE-seq libraries were processed using cellranger pipeline v6 and reference genome mm10 3.0.0.  ADT reads were assigned to proteins using the included ADT_reference.csv.  Processed files include Unique Molecular Identifier (UMI) counts per genes and ADT counts per protein.
ATAC-seq libraries were processed using the cellranger atac pipeline v.1.1.0 and refdata-cellranger-atac-mm10-1.2.0.  Processed files include fragment counts per peak.
Assembly: mm10
Supplementary files format and content: Matrix files with all data (raw)
Supplementary files format and content: Matrix files after filtering for cells (filtered)


title: OT-I cells from E.G7 tumors, Bcl6pos_rep2

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Low quality reads and adaptor sequences were removed by Trim galore0.6.6
The clean reads were aligned to mm10 by Hisat2 with default parameter and uniquely mapping reads were summarized by featureCounts
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05 using DEseq2
Assembly: mm10
Supplementary files format and content: FPKMs

source_name: E.G7-infiltrating OT-I cells

growth_protocol: Co-transferred control, Prdm1-overexpressing OT-I cells, Bcl6-overexpressing OT-I cells were FACS-sorted from E.G7 tumors on about day 8 post transfer for RNA-seq.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: No

value: E.G7-infiltrating OT-I cells


title: Stage E5.5 embryo 1 section 1 region VE

description:
E5.5_1.txt
E5.5_1_1VE


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64+ cells, scRNA

description:
3' 10x Genomics
C57BL/6 CD64+ CITE-seq A


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-MHCII+ cells, scRNA

description:
3' 10x Genomics
C57Bl/6 MHCII+ CITE-seq A


title: Stage E5.5 embryo 1 section 1 region AP

description:
E5.5_1.txt
E5.5_1_1AP


title: OT-I cells from E.G7 tumors, Bcl6neg_rep2

value: Control (Bcl6neg)


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-MHCII- cells, scRNA

description:
3' 10x Genomics
C57Bl/6 MHCII- CITE-seq A


title: EC-bmpr2-/-_reoxy, replicate 3, scRNAseq

city: Stanford

first: Sarasa

last: Isobe

address: 269 Campus Drive, CCSR 1220

department: Pediatrics, Cardiology

institute: Stanford University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made by using the Cell Ranger software v6.0.0. followed by mapping with mm10 reference genome and added sequences of tdTomato. Cells expressing tdTomato (>0) were retained.
Assembly: mm10/ added sequences of tdTomato
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Mice lungs were digested with  0.4 mg/ml Liberase and 10 mg/ml elastase. Each sample was dissociated using the gentle MACS Dissociator system following the manufacturer’s protocol qnd incubate 37°C for 30 min. The cell suspension was placed on ice, neutralized with cold PBS with 5% BSA, and filtered through a 70 μm cell strainer. The cell suspension was depleted of CD45-positive cells and enriched for EC using CD31 microbeads according to the manufacturer’s instructions, and collected in cold PBS with 2% BSA.  Stanford Genome Sequencing Service Center for 10X chromium single-cell RNA-seq paired end library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10X Genomics).

treatment_protocol: Mice injected with tamoxifen for 8days and were exposed to 10% hypoxia for 3 weeks followed by room air for 4 weeks.

value: Endothelial cells

value: lung

value: Cdh5CreER/Rosa tdTomato/ Bmpr4fl/fl


title: Stage E5.5 embryo 1 section 3 region VE

description:
E5.5_1.txt
E5.5_1_3VE

value: embryo


title: EC-bmpr2-/-_reoxy, replicate 1, scRNAseq

description: 10x Genomics

value: Cdh5CreER/Rosa tdTomato/ Bmpr2fl/fl


title: OT-I cells from E.G7 tumors, Bcl6neg_rep1


title: Control_reoxy, replicate 4, scRNAseq

description: 10x Genomics

value: Cdh5CreER/Rosa tdTomato


title: OT-I cells from E.G7 tumors, Prdm1pos_rep2


title: Control_reoxy, replicate 3, scRNAseq

description: 10x Genomics


title: Stage E7.5 posterior cell 3

description:
Single_cell_E7.5_P.txt
E7.5_P3


title: Stage E7.5 posterior cell 4

description:
Single_cell_E7.5_P.txt
E7.5_P4


title: Control, mouse pulmonary EC, reoxygenation, rep4

data_processing:
Basecalls were performed using Bcl2fastq.
The FASTQ reads were QC-checked using FastQC v0.11.9 and underwent quality and adapter trimming using Trim Galore v0.6.6.
The resulting FASTQ reads were analyzed using the nf-core/rnaseq pipeline v3.3 and aligned to the mouse reference genome mm10 using STAR v2.6.1d.
The aligned transcripts were quantitated by RSEM v1.3.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files, gene counts for each sample

source_name: lung endothelial cells

extract_protocol:
RNA was harvested using Quick-RNA MiniPrep Kit (Zymo Research #R1055).
The RNA was enriched for poly-A templates and libraries were prepared with CORALL mRNA-seq library prep kits (Lexogen, #162-96) following manufacturer's protocols.

treatment_protocol: Lung endothelial cells were isolated from single cell suspension of lungs from transgenic mice following reoxygenation and depleted of CD45 positive cells and then enriched CD31 positive cells using magnetic beads.

value: lung endothelial cells

value: Control mouse

value: reoxygenation


title: Stage E7.5 posterior cell 2

description:
Single_cell_E7.5_P.txt
E7.5_P2


title: OT-I cells from E.G7 tumors, Prdm1neg_rep2

value: Control (Prdm1neg)


title: Stage E7.5 posterior cell 15

description:
Single_cell_E7.5_P.txt
E7.5_P15


title: OT-I cells from E.G7 tumors, Prdm1pos_rep1


title: Control, mouse pulmonary EC, reoxygenation, rep3


title: Control, mouse pulmonary EC, reoxygenation, rep2


title: Control_reoxy, replicate 1, scRNAseq

description: 10x Genomics


title: Control_reoxy, replicate 2, scRNAseq

description: 10x Genomics


title: OT-I cells from E.G7 tumors, Prdm1neg_rep1


title: OT-I cells from E.G7 tumors, Bcl6pos_rep1


title: Stage E7.5 posterior cell 12

description:
Single_cell_E7.5_P.txt
E7.5_P12


title: Stage E7.5 posterior cell 1

description:
Single_cell_E7.5_P.txt
E7.5_P1


title: EC-Bmpr2-/-, mouse pulmonary EC, reoxygenation, rep5

value: EC-Bmpr2-/- mouse


title: EC-bmpr2-/-_reoxy, replicate 2, scRNAseq

description: 10x Genomics

value: Cdh5CreER/Rosa tdTomato/ Bmpr3fl/fl


title: Stage E7.25 posterior cell 9

description:
Single_cell_E7.25_P.txt
E7.25_P9


title: Tet1_KO_BCSP_round_2

first: Nidhi

last: Bhutani

address: 240 Pasteur drive

department: Orthopaedic Surgery

institute: Stanford School of Medicine

description: 150 bp PE

data_processing:
Cleaned reads were mapped to the mm10 reference genome using the RNA STAR aligner
featureCounts was used to determine read abundance and generate FPKM count files for genes
DEseq2 was then used with default parameters to identify differentially expressed genes
Assembly: mm10
Supplementary files format and content: WT_KO_BCP_SCC_counts_v2.txt contains count matrix for samples

source_name: Femur

extract_protocol: RNA was extracted from FACS sorted SSCs and BCSPs from WT and Tet1 KO mice

value: Femur

value: Bone cartilage stromal progenitors

value: Tet1 KO

value: neonate (day 3-5)


title: Tet1_KO_BCSP_round_1

description: 150 bp PE


title: EC-Bmpr2-/-, mouse pulmonary EC, reoxygenation, rep2


title: Stage E7.25 posterior cell 8

description:
Single_cell_E7.25_P.txt
E7.25_P8


title: EC-Bmpr2-/-, mouse pulmonary EC, reoxygenation, rep1


title: Tet1_KO_SSC_round_2

description: 150 bp PE

value: Skeletal Stem cells


title: EC-Atm-/-,  mouse pulmonary EC, reoxygenation, rep5

value: EC-Atm-/- mouse


title: Stage E7.25 posterior cell 7

description:
Single_cell_E7.25_P.txt
E7.25_P7


title: EC-Atm-/-,  mouse pulmonary EC, reoxygenation, rep3


title: Tet1_KO_SSC_round_1

description: 150 bp PE


title: EC-Atm-/-,  mouse pulmonary EC, reoxygenation, rep4


title: Stage E7.25 posterior cell 6

description:
Single_cell_E7.25_P.txt
E7.25_P6


title: EC-Atm-/-,  mouse pulmonary EC, reoxygenation, rep2


title: siRNA-microinjected embryo, Replicate 2, region R

description:
MicroInject_siRNA_Rep_2-R
genes_fpkm.csv

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Assembly: mm10
Supplementary files format and content: Csv file includes FPKM values for each embryo

value: Mouse embryonic cells

tag: Stage

value: siRNA-microinjected embryo

tag: location

value: region R


title: Control, mouse pulmonary EC, reoxygenation, rep1


title: EC-Atm-/-,  mouse pulmonary EC, reoxygenation, rep1


title: siRNA-microinjected embryo, Replicate 2, region MR

description:
MicroInject_siRNA_Rep_2-MR
genes_fpkm.csv

value: region MR


title: Stage E7.25 posterior cell 24

description:
Single_cell_E7.25_P.txt
E7.25_P24

value: embryo


title: siRNA-microinjected embryo, Replicate 2, region P

description:
MicroInject_siRNA_Rep_2-P
genes_fpkm.csv

value: region P


title: siRNA-microinjected embryo, Replicate 2, region ML

description:
MicroInject_siRNA_Rep_2-ML
genes_fpkm.csv

value: region ML


title: EC-Bmpr2-/-, mouse pulmonary EC, reoxygenation, rep4

value: lung endothelial cells

value: reoxygenation


title: Wildtype_SSC_round_2

description: 150 bp PE

value: WT


title: EC-Bmpr2-/-, mouse pulmonary EC, reoxygenation, rep3

value: EC-Bmpr2-/- mouse


title: siRNA-microinjected embryo, Replicate 2, region L

description:
MicroInject_siRNA_Rep_2-L
genes_fpkm.csv

value: region L


title: Wildtype_BCSP_round_1

description: 150 bp PE

value: Femur

value: Bone cartilage stromal progenitors


title: Wildtype_SSC_round_1

description: 150 bp PE

value: neonate (day 3-5)


title: Stage E7.25 posterior cell 23

description:
Single_cell_E7.25_P.txt
E7.25_P23


title: siRNA-microinjected embryo, Replicate 2, region A

description:
MicroInject_siRNA_Rep_2-A
genes_fpkm.csv

value: region A


title: LFA-/- Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-Ly6c- cells, scRNA-seq

description: 3' 10x Genomics

data_processing:
Libraries were processed using cellranger pipeline v3.1.0 and reference genome mm10 3.0.0.  Processed files include Unique Molecular Identifier (UMI) counts per gene.
Assembly: mm10
Supplementary files format and content: Matrix files with all data (raw)
Supplementary files format and content: Matrix files after filtering for cells (filtered)

molecule: polyA RNA

extract_protocol:
Synovial tissue was processed into a single-cell suspension and live CD45+CD11b+Ly6g-SiglecF-Cd64-Ly6c- cells were sorted
scRNA-seq libraries were prepared using 10x Chromium Single Cell 3’ Solution v3

value: Ankle Joint Synovium

value: LFA-/-


title: Stage E7.25 posterior cell 22

description:
Single_cell_E7.25_P.txt
E7.25_P22


title: Stage E7.25 posterior cell 21

description:
Single_cell_E7.25_P.txt
E7.25_P21


title: siRNA-microinjected embryo, Replicate 1, region ML

description:
MicroInject_siRNA_Rep_1-ML
genes_fpkm.csv

value: Mouse embryonic cells

value: siRNA-microinjected embryo


title: siRNA-microinjected embryo, Replicate 1, region P

description:
MicroInject_siRNA_Rep_1-P
genes_fpkm.csv


title: siRNA-microinjected embryo, Replicate 1, region R

description:
MicroInject_siRNA_Rep_1-R
genes_fpkm.csv

value: region R


title: siRNA-microinjected embryo, Replicate 1, region MR

description:
MicroInject_siRNA_Rep_1-MR
genes_fpkm.csv

value: region MR


title: CCR2-/- Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-Ly6c- cells, scRNA-seq

description: 3' 10x Genomics


title: siRNA-microinjected embryo, Replicate 1, region L

description:
MicroInject_siRNA_Rep_1-L
genes_fpkm.csv


title: Wildtype_BCSP_round_2

description: 150 bp PE


title: Stage E7.25 posterior cell 5

description:
Single_cell_E7.25_P.txt
E7.25_P5

value: embryo


title: Stage E7.25 posterior cell 20

description:
Single_cell_E7.25_P.txt
E7.25_P20


title: NR4A1-/- Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-Ly6c- cells, scRNA-seq

description: 3' 10x Genomics


title: Stage E7.25 posterior cell 19

description:
Single_cell_E7.25_P.txt
E7.25_P19


title: siRNA-microinjected embryo, Replicate 1, region A

description:
MicroInject_siRNA_Rep_1-A
genes_fpkm.csv


title: Ctrl embryo, Replicate 2, region R

description:
MicroInject_Ctrl_Rep_2-R
genes_fpkm.csv

value: Ctrl embryo


title: Ctrl embryo, Replicate 2, region P

description:
MicroInject_Ctrl_Rep_2-P
genes_fpkm.csv

value: region P


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-Ly6c- cells, scRNA-seq

description: 3' 10x Genomics


title: Stage E7.25 posterior cell 18

description:
Single_cell_E7.25_P.txt
E7.25_P18


title: Ctrl embryo, Replicate 2, region MR

description:
MicroInject_Ctrl_Rep_2-MR
genes_fpkm.csv


title: Ctrl embryo, Replicate 2, region ML

description:
MicroInject_Ctrl_Rep_2-ML
genes_fpkm.csv

value: region ML


title: Ctrl embryo, Replicate 2, region L

description:
MicroInject_Ctrl_Rep_2-L
genes_fpkm.csv


title: si-NC-2 [small RNA]

city: Nanning

first: dandan

last: zhong

state: Guangxi

address: state Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University

institute: Guangxi university

data_processing:
Illumina HiSeqTM 4000 used for basecalling.
reads were further filtered by fastp), the parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
reads alignment tool Bowtie2  was used for mapping reads to  mm10 whole genome
Transcripts abundances were quantified by software StringTie in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per millio n mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: mm10
Supplementary files format and content: All miRNAs expression
Supplementary files format and content: Differently expressed miRNAs

source_name: GC-1spg cell line

growth_protocol: The cells are GC-1spg cells, 10% FBS in DMEM medium, cultured in an incubator with 5% carbon dioxide and 37% constant temperature.

extract_protocol:
Cells were lysed and extracted using TRIzol™  reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: METTL3 (siRNA: GCTACCGTATGGGACATTA) and control NC (siRNA: GCTACCGTATGGGACATTA) siRNA (Ribo, Guangzhou, China) were transfected when the cell density reached 60%, and cell samples were collected 48 hours later for subsequent experiments.

value: GC-1spg cell line

value: control NC (siRNA:GCTACCGTATGGGACATTA) siRNA

value: untreated


title: si-NC-3 [small RNA]


title: Ctrl embryo, Replicate 2, region A

description:
MicroInject_Ctrl_Rep_2-A
genes_fpkm.csv


title: Stage E7.25 posterior cell 17

description:
Single_cell_E7.25_P.txt
E7.25_P17


title: Stage E7.25 posterior cell 16

description:
Single_cell_E7.25_P.txt
E7.25_P16


title: Ctrl embryo, Replicate 1, region R

description:
MicroInject_Ctrl_Rep_1-R
genes_fpkm.csv


title: si-NC-1 [small RNA]


title: Ctrl embryo, Replicate 1, region P

description:
MicroInject_Ctrl_Rep_1-P
genes_fpkm.csv


title: Stage E7.25 posterior cell 14

description:
Single_cell_E7.25_P.txt
E7.25_P14


title: Ctrl embryo, Replicate 1, region MR

description:
MicroInject_Ctrl_Rep_1-MR
genes_fpkm.csv


title: si-METTL3-3 [small RNA]

value: METTL3 (siRNA:GCTACCGTATGGGACATTA)

value: treated with knock down METTL3


title: Ctrl embryo, Replicate 1, region ML

description:
MicroInject_Ctrl_Rep_1-ML
genes_fpkm.csv


title: Stage E7.25 posterior cell 11

description:
Single_cell_E7.25_P.txt
E7.25_P11


title: Ctrl embryo, Replicate 1, region L

description:
MicroInject_Ctrl_Rep_1-L
genes_fpkm.csv

value: region L


title: si-METTL3-2 [small RNA]


title: Stage E7.25 posterior cell 13

description:
Single_cell_E7.25_P.txt
E7.25_P13


title: Stage E7.25 posterior cell 10

description:
Single_cell_E7.25_P.txt
E7.25_P10


title: si-METTL3-1 [small RNA]


title: Pancreatic islet, STIM1KO, 3

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Data analysis was performed using Partek flow software. The raw sequencing files were aligned to mouse genome (mm10) using STAR aligner v 2.6.1.
Annotation database - RefSeq transcripts 93
DESeq2 was used for identifying differentially expressed mRNAs (Fold change >=1.5 andp-value < 0.05).
Assembly: mm10
Supplementary files format and content: .xlsx file format was used for processed files - raw counts and log cpm counts

source_name: Pancreatic islet

growth_protocol: Mice were caged in Max 75 plastic cages with 75 square inch floor space (Alternative Design, AR, USA), which were sterilized by autoclaving as full sets (wire bar, bottom and filter top) or bundles (stacks of bottoms). Cages were enriched with bedding (¼” Teklad 7097 Corncob) and tissue paper (Kleenex). Mice were kept in standard environmental temperature conditions (22 ± 2 °C) monitored remotely. A 12:12 hr light:dark cycle was maintained from 7AM-7PM. Relative humidity was maintained between 30-70%. Mice were housed in individually ventilated cage system (Alternative Design, AR, USA), with daily checks for function/errors and monthly pre-filter changes. Mice were fed ad libitum to autoclaved standard rodent chow or high-fat diet and standard city water reverse osmosis filtered, provided by an auto-water lixit. We obtained pancreatic beta cells specific knockout of STIM1 by crossing STIM1 fl/fl line and INS1-Cre line. The mice were fed with HFD (60 kcal%), initiated at 8wk of age (Research Diets). Isolated mouse islets were islets were hand-picked and allowed to recover overnight in Dulbecco’s modified essential medium (DMEM) medium containing 5.5mM glucose, 10% fetal bovine serum (FBS), 100U/ml penicillin, and 100μg/ml streptomycin.

extract_protocol:
Picked islets were homogenized by lysis with Qiazol® by pipetting. Homogenized samples were incubated for 5 min at 15 to 30°C. Then, 0.2mL chloroform per 1mL of Qiazol® was added and shaken vigorously by hand for 15 seconds and incubated at 15 to 30°C for 2-3 min. Samples were centrifuged at 12,000 x g for 15 minutes at 4°C. Following centrifugation, the colorless, clear upper aqueous phase was isolated and added onto a QIAGEN RNeasy Micro Kit Columns. RNA was isolated as per manufacturer's protocols. total mRNA was treated with TurboDNase as per manufacturer's protocol.
cDNA library preparation includes mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. The pooled libraries were then denatured, and neutralized, before loading to NovaSeq 6000 sequencer at 300pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 30M reads per library was generated.

value: Pancreatic islet

value: [beta] cell STIM1-Knock out (STIM1fl/fl, Cre+)

value: High-fat diet (ResearchDiets D12492) 8wk

tag: Sex

value: Female

tag: age

tag: nomenclature for_stim1_fl/fl

tag: stock number_on_jackson_laboratory


title: Pancreatic islet, STIM1KO, 4


title: Stage E7.0 posterior cell 9

description:
Single_cell_E7.0_P.txt
E7.0_2P9


title: TIM3_rep1

data_processing:
Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 2fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (or read count) for each sample

source_name: CD8+ TILs

growth_protocol: Bcl6-RFP mice were inoculated with E.G7 tumors (s.c.)

treatment_protocol: Tumor-infiltrating CD8+ T cells were isolated from E.G7 tumors on day 21 post tumor inoculation, then were FACS sorted for RNA-seq

value: E.G7 tumor

value: tumor

value: TIM-3+ CD8+ TILs


title: Pancreatic islet, STIM1KO, 1


title: Pancreatic islet, Control, 1

value: Control (STIM1fl/fl, Cre-)


title: Pancreatic islet, Control, 2


title: Pancreatic islet, Control, 5


title: Pancreatic islet, Control, 4


title: Pancreatic islet, Control, 3


title: Stage E7.0 posterior cell 7

description:
Single_cell_E7.0_P.txt
E7.0_2P7

value: embryo


title: Stage E7.0 posterior cell 8

description:
Single_cell_E7.0_P.txt
E7.0_2P8


title: DN_rep1

value: DN


title: DN_rep2


title: FMT-aged

city: Hangzhou

first: Xiangjun

last: Zeng

address: Zhejiang univerisity

institute: Zhejiang univerisity

description: 10x Genomics

data_processing:
Cellranger  count  takes  FASTQ  files  performs  alignment,  filtering,  Barcode  counting,  and UMI counting. It uses the Chromium  cellular  Barcodes to generate feature  Barcode  matrices  by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Whole bone marrow cells, immature hematopoietic cells (Lin-) and hematopoietic progenitor cells (Lin- cKit+) were collected by flow cytometric sorting and admixed at a 1:1:4 ratio.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3  (10x  Genomics)  ,  according  to  the  manufacturer’s  instructions.

value: bone marrow

tag: cell line

value: bone marrow cell

value: Aged mice tranplanted with aged gut microbiota


title: Bcl6_rep2

tag: cell type


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8R2

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8R2

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Text file includes FPKM values for each embryo

source_name: Mouse embryonic cells


title: FMT-young

description: 10x Genomics

tag: treatment

value: Aged mice tranplanted with young gut microbiota


title: Stage E7.0 posterior cell 5

description:
Single_cell_E7.0_P.txt
E7.0_2P5


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8R1

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8R1


title: Ctrl embryo, Replicate 1, region A

description:
MicroInject_Ctrl_Rep_1-A
genes_fpkm.csv

value: Mouse embryonic cells

value: Ctrl embryo

value: region A


title: Stage E7.0 posterior cell 4

description:
Single_cell_E7.0_P.txt
E7.0_2P4


title: si-METTL3-3

data_processing:
Illumina HiSeqTM 4000 used for basecalling.
reads were further filtered by fastp), the parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
reads alignment tool Bowtie2  was used for mapping reads to  mm9 whole genome
Transcripts abundances were quantified by software StringTie in a reference-based approach. For   each transcription region, a FPKM (fragment per kilobase of transcript per millio n mapped   reads) value was calculated to quantify its expression abundance and variations, using   RSEM software.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: GC-1spg cells

value: treated with knock down METTL3


title: Bcl6_rep1


title: Pancreatic islet, STIM1KO, 2

value: Pancreatic islet

value: [beta] cell STIM1-Knock out (STIM1fl/fl, Cre+)


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8MPL

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8MPL


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8P

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8P


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8MPR

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8MPR


title: TIM3_rep2


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8MAR

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8MAR


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8MAL

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8MAL


title: si-METTL3-2


title: Stage E7.0 posterior cell 6

description:
Single_cell_E7.0_P.txt
E7.0_2P6

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8L2

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8L2


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8L1

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8L1


title: si-METTL3-1


title: Stage E7.0 posterior cell 35

description:
Single_cell_E7.0_P.txt
E7.0_2P35


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8EP

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8EP


title: Stage E7.0 posterior cell 34

description:
Single_cell_E7.0_P.txt
E7.0_2P34


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8EA

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8EA


title: si-NC-2

value: untreated


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4R1

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4R1


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 8A

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_8A


title: si-NC-1


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4P

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4P


title: Stage E7.0 posterior cell 32

description:
Single_cell_E7.0_P.txt
E7.0_2P32


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4MPR

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4MPR


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4MPL

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4MPL


title: Stage E7.0 posterior cell 37

description:
Single_cell_E7.0_P.txt
E7.0_2P37


title: Stage E7.0 posterior cell 30

description:
Single_cell_E7.0_P.txt
E7.0_2P30


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4MAR

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4MAR


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4MAL

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4MAL


title: Stage E7.0 posterior cell 31

description:
Single_cell_E7.0_P.txt
E7.0_2P31


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4L2

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4L2


title: Stage E7.0 posterior cell 36

description:
Single_cell_E7.0_P.txt
E7.0_2P36


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4L1

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4L1


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4EP

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4EP


title: si-NC-3


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4R2

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4R2


title: Stage E7.0 posterior cell 33

description:
Single_cell_E7.0_P.txt
E7.0_2P33


title: Stage E7.0 posterior cell 3

description:
Single_cell_E7.0_P.txt
E7.0_2P3


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4EA

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4EA


title: Ventral hippocampus, LPS-MET treated, female 1

city: Pittsburgh

first: Micah

middle: Aaron

last: Shelton

state: Pennsylvania

address: 2602 PITCAIRN RD

department: Psychiatry

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench v.23.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic workbench (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to mRatBN7.2 using CLC Genomics workbench (parameters-mismatch cost: 2 insertion cost: 3 deletion cost:3 length fraction: 0.8 similarity fraction 0.8)
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

organism: Rattus norvegicus

source_name: Ventral Hippocampus

extract_protocol:
RNA was isolated and extracted using RNeasy Plus Micro kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared and sequenced at Azenta Life Sciences using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Ventral Hippocampus

value: Female

value: LPS-MET


title: Ventral hippocampus, LPS-MET treated, female 3


title: Stage E7.0 posterior cell 29

description:
Single_cell_E7.0_P.txt
E7.0_2P29


title: Ventral hippocampus, MET treated, female 3

value: MET


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8R2

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8R2

value: embryo


title: Ventral hippocampus, MET treated, female 2


title: Stage E7.0 posterior cell 28

description:
Single_cell_E7.0_P.txt
E7.0_2P28


title: Pkd1l1 mutant stage E7.5 embryo 2 section region 4A

description:
Pkd1l1_mutant_2_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_2_4A


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8R1

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8R1


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8P

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8P


title: Ventral hippocampus, LPS-MET treated, female 2


title: Stage E7.0 posterior cell 27

description:
Single_cell_E7.0_P.txt
E7.0_2P27


title: Ventral hippocampus, LPS treated, female 3

value: LPS


title: Ventral hippocampus, LPS treated, female 2


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8MPR

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8MPR


title: Stage E7.0 posterior cell 25

description:
Single_cell_E7.0_P.txt
E7.0_2P25


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8MAR

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8MAR


title: Stage E7.0 posterior cell 26

description:
Single_cell_E7.0_P.txt
E7.0_2P26


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8MAL

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8MAL


title: Ventral hippocampus, LPS treated, female 1


title: Ventral hippocampus, saline treated, female 3

value: Saline


title: Stage E7.0 posterior cell 23

description:
Single_cell_E7.0_P.txt
E7.0_2P23


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8A

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8A


title: Ventral hippocampus, saline treated, female 2


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8L2

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8L2


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4R1

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4R1


title: Ventral hippocampus, LPS-MET treated, male 3

value: Male


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8L1

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8L1


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4MAR

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4MAR


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4MPR

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4MPR


title: Stage E7.0 posterior cell 24

description:
Single_cell_E7.0_P.txt
E7.0_2P24


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8EA

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8EA


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8EP

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8EP


title: Stage E7.0 posterior cell 21

description:
Single_cell_E7.0_P.txt
E7.0_2P21


title: Ventral hippocampus, saline treated, female 1


title: Ventral hippocampus, LPS-MET treated, male 2


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 8MPL

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_8MPL


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4MPL

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4MPL


title: Stage E7.0 posterior cell 20

description:
Single_cell_E7.0_P.txt
E7.0_2P20


title: Stage E7.0 posterior cell 2

description:
Single_cell_E7.0_P.txt
E7.0_2P2


title: Stage E7.0 posterior cell 19

description:
Single_cell_E7.0_P.txt
E7.0_2P19


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4MAL

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4MAL


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4EP

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4EP


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4R2

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4R2


title: Ventral hippocampus, LPS-MET treated, male 1


title: Ventral hippocampus, MET treated, male 2


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4L1

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4L1


title: Stage E7.0 posterior cell 22

description:
Single_cell_E7.0_P.txt
E7.0_2P22


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4L2

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4L2


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4P

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4P


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4EA

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4EA


title: Stage E7.0 posterior cell 18

description:
Single_cell_E7.0_P.txt
E7.0_2P18


title: Ventral hippocampus, MET treated, male 1


title: Stage E7.25 cell 9

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_9


title: Pkd1l1 mutant stage E7.5 embryo 1 section region 4A

description:
Pkd1l1_mutant_1_FPKM_Filter_Log2.txt
Pkd1l1_mutant_E7.5_1_4A


title: Stage E7.0 posterior cell 17

description:
Single_cell_E7.0_P.txt
E7.0_2P17


title: Stage E7.25 cell 7

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_7


title: Ventral hippocampus, LPS treated, male 3


title: Stage E7.25 cell 6

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_6


title: Stage E7.25 cell 5

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_5


title: Ventral hippocampus, LPS treated, male 2


title: Stage E7.0 posterior cell 15

description:
Single_cell_E7.0_P.txt
E7.0_2P15


title: Stage E7.0 posterior cell 16

description:
Single_cell_E7.0_P.txt
E7.0_2P16


title: Stage E7.25 cell 3

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_3


title: Ventral hippocampus, LPS treated, male 1


title: Stage E7.0 posterior cell 14

description:
Single_cell_E7.0_P.txt
E7.0_2P14


title: Stage E7.0 posterior cell 13

description:
Single_cell_E7.0_P.txt
E7.0_2P13


title: Ventral hippocampus, saline treated, male 3


title: Stage E7.25 cell 2

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_2


title: Stage E7.25 cell 23

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_23


title: Ventral hippocampus, MET treated, male 3


title: Stage E7.25 cell 22

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_22


title: Ventral hippocampus, saline treated, male 2


title: Stage E7.0 posterior cell 12

description:
Single_cell_E7.0_P.txt
E7.0_2P12


title: Stage E7.25 cell 21

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_21


title: Ventral hippocampus, saline treated, male 1


title: Stage E7.25 cell 8

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_8


title: Stage E7.25 cell 20

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_20


title: Stage E7.0 posterior cell 11

description:
Single_cell_E7.0_P.txt
E7.0_2P11


title: Stage E7.25 cell 19

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_19


title: Stage E7.0 posterior cell 10

description:
Single_cell_E7.0_P.txt
E7.0_2P10


title: Stage E7.25 cell 4

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_4


title: liver MDA rep5

city: Bunkyo

first: Tadahaya

last: Mizuno

state: Tokyo

address: 7-3-1, Hongo, Pharmaceutical Sciences, Sogo-kenkyuto 8th floor, Dotai

department: Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Quality control of all reads was performed using PINSEQ++ (version 1.2.4) with the indicated parameters (trim_left = 5, trim_tail_right = 5, trim_qual_right = 30, ns_max_n = 20, min_len = 30) (https://peerj.com/preprints/27553/)
The expression of transcripts was quantified using Salmon (version 1.6.0) with the indicated parameters (validationMappings, gcBias, seqBias) and a decoy-aware index created using Salmon and Rattus_norvegicus.Rnor_6.0.cdna.all was obtained from EMBL-EBI (https://www.ebi.ac.uk/)
Transcripts per kilobase million data were obtained using tximport, which is implemented in the software package Bioconductor with R (version 4.1.3)
Assembly: mRatBN7.2
Supplementary files format and content: Files with gene raw counts and transcripts per millions (TPM)

source_name: liver

extract_protocol:
Rats were euthanized and the liver was harvested after compound administration. Briefly, the superior vena cava was clipped using a clamp, and the liver perfusion was performed through an inferior vena cava using a plastic cannula-type puncture needle (SR-OT1832C, 18G 32 mm) (Terumo corporation, Tokyo, Japan) and 5 mM HEPES (345-06681, Fujifilm Wako Pure Chemical Corporation) /5 mM EDTA (6381-92-6, Dojindo Laboratories, Kumamoto, Japan) Hanks' balanced salt solution (17461-05, Nacalai Tesque, Kyoto, Japan). Finally, a part of the liver’s largest lobe was subjected to RNA isolation. Total RNA was prepared using ISOGEN II (311-07361, Nippon Gene Co., Tokyo, Japan) and purified using an RNeasy Plus Mini Kit (74136, Qiagen, Limburg, Netherland) with gDNA elimination using an RNase-Free DNase set (79254, Qiagen) according to the manufacturer’s protocols.
Total RNA was used to prepare RNA-Seq libraries with a NEBNext Ultra ll Directional RNA Library Prep Kit for Illumina.

treatment_protocol: To induce liver injury, acetaminophen (H0190, Tokyo Chemical Industry Co., Tokyo, Japan) or 4,4′-methylene dianiline (M0220, Tokyo Chemical Industry Co.) was administered at 3 g/kg or 300 mg/kg, respectively by gavage. As a vehicle control group, 0.5 (w/v)% methylcellulose 400 solution (133-17815, Fujifilm Wako Pure Chemical Corporation, Osaka, Japan) was given at 10 µL/g. The Rats that were subjected to RNA sequencing had fasted between 21:00 and 9:00, which was the administration time.

value: Sprague-Dawley

value: male

value: liver

value: WT

value: 4,4'-methylene dianiline (MDA)

tag: route

value: gavage

value: 24 hr

tag: concentration

value: 300 mg/kg


title: Stage E7.25 cell 24

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_24

tag: strain

value: Mouse embryonic cells


title: Stage E7.25 cell 18

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_18


title: Stage E7.0 posterior cell 1

description:
Single_cell_E7.0_P.txt
E7.0_2P1

tag: tissue


title: liver MDA rep3

tag: genotype


title: Stage E7.25 cell 17

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_17

tag: developmental stage


title: liver MDA rep4

tag: time


title: Stage E7.25 cell 1

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_1


title: Stage E6.5 posterior cell 9

description:
Single_cell_E6.5_P.txt
E6.5_P9


title: Stage E7.25 cell 15

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_15


title: Stage E7.25 cell 16

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_16


title: Stage E7.25 cell 13

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_13


title: Stage E7.25 cell 12

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_12


title: Stage E7.25 cell 14

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_14


title: liver MDA rep2


title: liver MDA rep1


title: Stage E7.25 cell 10

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_10


title: Stage E6.5 posterior cell 8

description:
Single_cell_E6.5_P.txt
E6.5_P8


title: liver APAP rep5

value: acetaminophen (APAP)

value: 3 g/kg


title: Stage E6.5 posterior cell 7

description:
Single_cell_E6.5_P.txt
E6.5_P7


title: Stage E7.25 cell 11

description:
Genes_FPKM_E7.25_SCs_Log2.txt
E7.25_cell_11


title: Stage E6.75 cell 8

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_8


title: Stage E6.75 cell 9

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_9


title: liver APAP rep4


title: Stage E6.5 posterior cell 5

description:
Single_cell_E6.5_P.txt
E6.5_P5


title: Stage E6.5 posterior cell 6

description:
Single_cell_E6.5_P.txt
E6.5_P6


title: liver APAP rep3


title: Stage E6.75 cell 7

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_7


title: Stage E6.75 cell 6

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_6


title: Stage E6.75 cell 5

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_5


title: Stage E6.75 cell 4

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_4


title: Stage E6.5 posterior cell 4

description:
Single_cell_E6.5_P.txt
E6.5_P4


title: liver APAP rep2


title: Stage E6.75 cell 3

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_3


title: liver APAP rep1


title: Stage E6.5 posterior cell 3

description:
Single_cell_E6.5_P.txt
E6.5_P3


title: Stage E6.5 posterior cell 19

description:
Single_cell_E6.5_P.txt
E6.5_P19


title: Stage E6.75 cell 31

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_31


title: Stage E6.5 posterior cell 2

description:
Single_cell_E6.5_P.txt
E6.5_P2


title: liver Ctrl rep5

value: 0.5 % methylcellulose


title: Stage E6.75 cell 2

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_2


title: Stage E6.5 posterior cell 18

description:
Single_cell_E6.5_P.txt
E6.5_P18


title: liver Ctrl rep4


title: Stage E6.75 cell 28

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_28


title: liver Ctrl rep3


title: Stage E6.75 cell 25

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_25


title: Stage E6.75 cell 27

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_27


title: liver Ctrl rep2


title: Stage E6.5 posterior cell 17

description:
Single_cell_E6.5_P.txt
E6.5_P17


title: Stage E6.75 cell 23

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_23


title: Stage E6.75 cell 26

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_26


title: Stage E6.75 cell 22

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_22


title: liver Ctrl rep1


title: Stage E6.75 cell 21

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_21


title: Stage E6.5 posterior cell 16

description:
Single_cell_E6.5_P.txt
E6.5_P16


title: spleen rep5

source_name: spleen

extract_protocol:
An untreated rat was euthanized, and the spleen was collected. Single-cell suspensions from the spleen were obtained by gently forcing the tissues through a 70 µm nylon mesh grid in RPMI-1640 (06261-65, Nacalai Tesque). After washing with the wash buffer, 15 mL of ACK buffer was added into the sample, and then incubated in a 37 °C water bath for 6 min to eliminate the splenic erythrocytes. The sample was washed with the wash buffer three times. Total RNA was prepared using ISOGEN II (311-07361, Nippon Gene Co., Tokyo, Japan) and purified using an RNeasy Plus Mini Kit (74136, Qiagen, Limburg, Netherland) with gDNA elimination using an RNase-Free DNase set (79254, Qiagen) according to the manufacturer’s protocols.
Total RNA was used to prepare RNA-Seq libraries with a NEBNext Ultra ll Directional RNA Library Prep Kit for Illumina.

treatment_protocol: no treatment

value: spleen


title: Stage E6.5 posterior cell 15

description:
Single_cell_E6.5_P.txt
E6.5_P15

value: embryo


title: Stage E6.75 cell 29

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_29


title: Stage E6.75 cell 24

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_24


title: Stage E6.75 cell 30

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_30


title: spleen rep4


title: Stage E6.75 cell 19

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_19


title: Stage E6.75 cell 20

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_20


title: Stage E6.75 cell 18

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_18


title: spleen rep3


title: Stage E6.75 cell 32

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_32


title: Stage E6.75 cell 1

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_1


title: Stage E6.75 cell 16

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_16


title: Stage E6.5 posterior cell 12

description:
Single_cell_E6.5_P.txt
E6.5_P12


title: spleen rep2


title: Stage E6.75 cell 15

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_15


title: spleen rep1


title: Stage E6.75 cell 17

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_17


title: Stage E6.75 cell 13

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_13


title: Stage E6.75 cell 14

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_14


title: Stage E6.5 posterior cell 10

description:
Single_cell_E6.5_P.txt
E6.5_P10


title: whole blood cells rep5

source_name: blood

extract_protocol:
An untreated was placed under anesthesia, and blood was collected from the heart by cardiopuncture. The blood was washed once with wash buffer once. After removing the supernatant, 15 mL of ACK buffer was added to the sample and then incubated in a 37 °C water bath for 6 min to eliminate erythrocytes. After incubation, 25 mL of the wash buffer was added to the sample, which was then centrifuged at 400 g at 4 °C for 5 min. The incubation and wash operations were repeated twice. After the last wash, the sample was washed with the wash buffer three times. Total RNA was prepared using ISOGEN II (311-07361, Nippon Gene Co., Tokyo, Japan) and purified using an RNeasy Plus Mini Kit (74136, Qiagen, Limburg, Netherland) with gDNA elimination using an RNase-Free DNase set (79254, Qiagen) according to the manufacturer’s protocols.
Total RNA was used to prepare RNA-Seq libraries with a NEBNext Ultra ll Directional RNA Library Prep Kit for Illumina.

value: blood


title: Stage E6.75 cell 12

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_12


title: Stage E6.5 posterior cell 11

description:
Single_cell_E6.5_P.txt
E6.5_P11


title: Stage E6.75 cell 11

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_11


title: Stage E6.5 posterior cell 14

description:
Single_cell_E6.5_P.txt
E6.5_P14


title: Stage E6.75 cell 10

description:
Genes_FPKM_E6.75_SCs_Log2.txt
E6.75_cell_10


title: Stage E6.5 posterior cell 1

description:
Single_cell_E6.5_P.txt
E6.5_P1


title: whole blood cells rep4


title: Dnah11 mutant stage E7.5 embryo 2 section region 8R2

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8R2


title: Dnah11 mutant stage E7.5 embryo 2 section region 8MPL

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8MPL


title: Dnah11 mutant stage E7.5 embryo 2 section region 8R1

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8R1


title: Dnah11 mutant stage E7.5 embryo 2 section region 8MAR

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8MAR


title: Dnah11 mutant stage E7.5 embryo 2 section region 8MAL

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8MAL


title: Dnah11 mutant stage E7.5 embryo 2 section region 8L2

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8L2


title: whole blood cells rep3


title: Monocytes rep6

extract_protocol:
Cell sorting was performed with a FACSAria III (BD Biosciences, NJ, USA). monocytes (CD45+/CD11b+/CD3-/CD45RA-/CD161-/SSC-low) and neutrophils (CD45+/CD11b+/CD3-/CD45RA-/CD161-/CD43int/SSC-high) were obtained from the rat blood. Cells were suspended in wash buffer containing 5% 7-AAD solution (559925, BD Pharmgen) 5 min before analysis to exclude dead cells. The sorted cells were at once pooled in RPMI-1640 containing 10% fetal bovine serum. After centrifugation at 400 g at 4 °C for 5 min, total RNA was prepared using ISOGEN II (311-07361, Nippon Gene Co., Tokyo, Japan) and purified using an RNeasy Plus Mini Kit (74136, Qiagen, Limburg, Netherland) with gDNA elimination using an RNase-Free DNase set (79254, Qiagen) according to the manufacturer’s protocols.
Total RNA was used to prepare RNA-Seq libraries with a NEBNext Ultra ll Directional RNA Library Prep Kit for Illumina.


title: Stage E6.5 posterior cell 13

description:
Single_cell_E6.5_P.txt
E6.5_P13

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit.


title: Dnah11 mutant stage E7.5 embryo 2 section region 8L1

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8L1


title: Dnah11 mutant stage E7.5 embryo 2 section region 8EP

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8EP


title: Dnah11 mutant stage E7.5 embryo 2 section region 8P

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8P


title: Monocytes rep5


title: Stage E7.5 embryo 3 section 9 region R2

description:
E7.5_3.txt
E7.5_3_9R2


title: Stage E7.5 embryo 3 section 9 region P

description:
E7.5_3.txt
E7.5_3_9P


title: Monocytes rep4


title: Dnah11 mutant stage E7.5 embryo 2 section region 8MPR

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8MPR


title: Dnah11 mutant stage E7.5 embryo 2 section region 4R1

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4R1


title: whole blood cells rep2


title: Stage E7.5 embryo 3 section 9 region L1

description:
E7.5_3.txt
E7.5_3_9L1


title: whole blood cells rep1


title: Stage E7.5 embryo 3 section 9 region R1

description:
E7.5_3.txt
E7.5_3_9R1


title: Dnah11 mutant stage E7.5 embryo 2 section region 4P

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4P


title: Dnah11 mutant stage E7.5 embryo 2 section region 8EA

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8EA


title: Stage E7.5 embryo 3 section 9 region EP

description:
E7.5_3.txt
E7.5_3_9EP


title: Dnah11 mutant stage E7.5 embryo 2 section region 8A

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_8A


title: Stage E7.5 embryo 3 section 9 region MP

description:
E7.5_3.txt
E7.5_3_9MP


title: Stage E7.5 embryo 3 section 9 region L2

description:
E7.5_3.txt
E7.5_3_9L2


title: Dnah11 mutant stage E7.5 embryo 2 section region 4MPR

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4MPR


title: Dnah11 mutant stage E7.5 embryo 2 section region 4R2

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4R2


title: Dnah11 mutant stage E7.5 embryo 2 section region 4MAR

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4MAR


title: Dnah11 mutant stage E7.5 embryo 2 section region 4MAL

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4MAL


title: Monocytes rep3


title: Monocytes rep2


title: Stage E7.5 embryo 3 section 9 region A

description:
E7.5_3.txt
E7.5_3_9A


title: Stage E7.5 embryo 3 section 9 region EA

description:
E7.5_3.txt
E7.5_3_9EA


title: Stage E7.5 embryo 3 section 9 region MA

description:
E7.5_3.txt
E7.5_3_9MA


title: Neutrophils rep6


title: Dnah11 mutant stage E7.5 embryo 2 section region 4MPL

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4MPL


title: Monocytes rep1


title: Stage E7.5 embryo 3 section 8 region MP

description:
E7.5_3.txt
E7.5_3_8MP


title: Dnah11 mutant stage E7.5 embryo 2 section region 4L1

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4L1


title: Stage E7.5 embryo 3 section 8 region P

description:
E7.5_3.txt
E7.5_3_8P


title: Dnah11 mutant stage E7.5 embryo 2 section region 4A

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4A


title: Neutrophils rep4


title: Dnah11 mutant stage E7.5 embryo 1 section region 8R2

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8R2


title: Dnah11 mutant stage E7.5 embryo 1 section region 8R1

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8R1


title: Stage E7.5 embryo 3 section 8 region MA

description:
E7.5_3.txt
E7.5_3_8MA


title: Neutrophils rep3


title: Dnah11 mutant stage E7.5 embryo 1 section region 8P

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8P


title: Neutrophils rep2


title: Dnah11 mutant stage E7.5 embryo 1 section region 8MPR

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8MPR


title: Stage E7.5 embryo 3 section 8 region EP

description:
E7.5_3.txt
E7.5_3_8EP


title: Dnah11 mutant stage E7.5 embryo 1 section region 8MPL

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8MPL


title: Dnah11 mutant stage E7.5 embryo 1 section region 8MAR

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8MAR


title: Dnah11 mutant stage E7.5 embryo 2 section region 4L2

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4L2


title: Neutrophils rep1


title: Stage E7.5 embryo 3 section 8 region EA

description:
E7.5_3.txt
E7.5_3_8EA


title: Neutrophils rep5


title: Stage E7.5 embryo 3 section 7 region P

description:
E7.5_3.txt
E7.5_3_7P


title: Dnah11 mutant stage E7.5 embryo 1 section region 8MAL

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8MAL


title: Dnah11 mutant stage E7.5 embryo 1 section region 8L2

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8L2


title: Dnah11 mutant stage E7.5 embryo 2 section region 4EP

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4EP


title: Stage E7.5 embryo 3 section 7 region MP

description:
E7.5_3.txt
E7.5_3_7MP


title: Dnah11 mutant stage E7.5 embryo 1 section region 8L1

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8L1


title: Dnah11 mutant stage E7.5 embryo 1 section region 8EP

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8EP


title: Dnah11 mutant stage E7.5 embryo 1 section region 8EA

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8EA


title: CD8 T cells rep6

extract_protocol:
Cell sorting was performed with a FACSAria III (BD Biosciences, NJ, USA). CD4 T cells (CD45+/CD11b-/CD3+/CD4+), CD8 T cells (CD45+/CD11b-/CD3+/CD8a+), NK cells (CD45+/CD11b-/CD3-/CD161+), and B cells (CD45+/CD11b-/CD3-/CD45RA+) were obtained from the rat spleen. Cells were suspended in wash buffer containing 5% 7-AAD solution (559925, BD Pharmgen) 5 min before analysis to exclude dead cells. The sorted cells were at once pooled in RPMI-1640 containing 10% fetal bovine serum. After centrifugation at 400 g at 4 °C for 5 min, total RNA was prepared using ISOGEN II (311-07361, Nippon Gene Co., Tokyo, Japan) and purified using an RNeasy Plus Mini Kit (74136, Qiagen, Limburg, Netherland) with gDNA elimination using an RNase-Free DNase set (79254, Qiagen) according to the manufacturer’s protocols.
Total RNA was used to prepare RNA-Seq libraries with a NEBNext Ultra ll Directional RNA Library Prep Kit for Illumina.


title: CD8 T cells rep5


title: Dnah11 mutant stage E7.5 embryo 1 section region 8A

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_8A


title: CD8 T cells rep4


title: Dnah11 mutant stage E7.5 embryo 1 section region 4R2

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4R2


title: Dnah11 mutant stage E7.5 embryo 2 section region 4EA

description:
Dnah11_mutant_2_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_2_4EA


title: Stage E7.5 embryo 3 section 7 region MA

description:
E7.5_3.txt
E7.5_3_7MA


title: Dnah11 mutant stage E7.5 embryo 1 section region 4R1

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4R1


title: Dnah11 mutant stage E7.5 embryo 1 section region 4MPR

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4MPR


title: Stage E7.5 embryo 3 section 7 region EA

description:
E7.5_3.txt
E7.5_3_7EA


title: Dnah11 mutant stage E7.5 embryo 1 section region 4P

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4P


title: CD8 T cells rep3


title: CD8 T cells rep2


title: Stage E7.5 embryo 3 section 6 region R2

description:
E7.5_3.txt
E7.5_3_6R2


title: Dnah11 mutant stage E7.5 embryo 1 section region 4MPL

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4MPL


title: Stage E7.5 embryo 3 section 6 region R1

description:
E7.5_3.txt
E7.5_3_6R1


title: Dnah11 mutant stage E7.5 embryo 1 section region 4MAR

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4MAR


title: CD8 T cells rep1


title: Dnah11 mutant stage E7.5 embryo 1 section region 4MAL

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4MAL


title: Dnah11 mutant stage E7.5 embryo 1 section region 4L2

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4L2


title: CD4 T cells rep6


title: Dnah11 mutant stage E7.5 embryo 1 section region 4L1

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4L1


title: Dnah11 mutant stage E7.5 embryo 1 section region 4EP

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4EP


title: Stage E7.5 embryo 3 section 6 region MP

description:
E7.5_3.txt
E7.5_3_6MP


title: Dnah11 mutant stage E7.5 embryo 1 section region 4A

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4A


title: Dnah11 mutant stage E7.5 embryo 1 section region 4EA

description:
Dnah11_mutant_1_FPKM_Filter_Log2.txt
Dnah11_mutant_E7.5_1_4EA


title: CD4 T cells rep5


title: CD4 T cells rep4


title: Dand5 mutant stage E7.5 embryo 2 section 8 region R2

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8R2


title: Stage E7.5 embryo 3 section 6 region MA

description:
E7.5_3.txt
E7.5_3_6MA


title: Dand5 mutant stage E7.5 embryo 2 section 8 region P

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8P


title: Stage E7.5 embryo 3 section 7 region EP

description:
E7.5_3.txt
E7.5_3_7EP


title: Dand5 mutant stage E7.5 embryo 2 section 8 region R1

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8R1


title: Dand5 mutant stage E7.5 embryo 2 section 8 region MPR

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8MPR


title: CD4 T cells rep2


title: Dand5 mutant stage E7.5 embryo 2 section 8 region MPL

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8MPL


title: Stage E7.5 embryo 3 section 6 region L2

description:
E7.5_3.txt
E7.5_3_6L2


title: CD4 T cells rep1


title: Dand5 mutant stage E7.5 embryo 2 section 8 region L2

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8L2


title: Stage E7.5 embryo 3 section 6 region EP

description:
E7.5_3.txt
E7.5_3_6EP


title: Dand5 mutant stage E7.5 embryo 2 section 8 region MAR

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8MAR


title: Dand5 mutant stage E7.5 embryo 2 section 8 region L1

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8L1


title: NK cells rep6


title: Stage E7.5 embryo 3 section 6 region P

description:
E7.5_3.txt
E7.5_3_6P


title: Dand5 mutant stage E7.5 embryo 2 section 8 region MAL

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8MAL


title: Dand5 mutant stage E7.5 embryo 2 section 8 region EP

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8EP


title: NK cells rep5


title: Stage E7.5 embryo 3 section 6 region EA

description:
E7.5_3.txt
E7.5_3_6EA


title: Stage E7.5 embryo 3 section 6 region A

description:
E7.5_3.txt
E7.5_3_6A


title: CD4 T cells rep3


title: Dand5 mutant stage E7.5 embryo 2 section 8 region EA

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8EA


title: Dand5 mutant stage E7.5 embryo 2 section 8 region A

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_8A


title: Stage E7.5 embryo 3 section 5 region P

description:
E7.5_3.txt
E7.5_3_5P


title: NK cells rep3


title: NK cells rep2


title: Dand5 mutant stage E7.5 embryo 2 section 4 region R1

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4R1


title: Dand5 mutant stage E7.5 embryo 2 section 4 region P

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4P


title: Stage E7.5 embryo 3 section 5 region MP

description:
E7.5_3.txt
E7.5_3_5MP


title: Dand5 mutant stage E7.5 embryo 2 section 4 region MPL

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4MPL


title: Dand5 mutant stage E7.5 embryo 2 section 4 region MPR

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4MPR


title: Stage E7.5 embryo 3 section 6 region L1

description:
E7.5_3.txt
E7.5_3_6L1


title: Dand5 mutant stage E7.5 embryo 2 section 4 region MAR

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4MAR


title: Stage E7.5 embryo 3 section 5 region MA

description:
E7.5_3.txt
E7.5_3_5MA


title: Dand5 mutant stage E7.5 embryo 2 section 4 region L2

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4L2


title: NK cells rep1


title: Dand5 mutant stage E7.5 embryo 2 section 4 region L1

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4L1


title: Dand5 mutant stage E7.5 embryo 2 section 4 region MAL

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4MAL


title: Stage E7.5 embryo 3 section 5 region EP

description:
E7.5_3.txt
E7.5_3_5EP


title: B cells rep6


title: NK cells rep4


title: B cells rep5


title: Dand5 mutant stage E7.5 embryo 2 section 4 region R2

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4R2


title: Dand5 mutant stage E7.5 embryo 2 section 4 region EP

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4EP


title: Stage E7.5 embryo 3 section 4 region P

description:
E7.5_3.txt
E7.5_3_4P


title: Dand5 mutant stage E7.5 embryo 2 section 4 region EA

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4EA


title: B cells rep4


title: Dand5 mutant stage E7.5 embryo 2 section 4 region A

description:
Dand5_mutant_2_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_2_4A


title: Stage E7.5 embryo 3 section 4 region MP

description:
E7.5_3.txt
E7.5_3_4MP


title: Stage E7.5 embryo 3 section 5 region EA

description:
E7.5_3.txt
E7.5_3_5EA


title: B cells rep3


title: Dand5 mutant stage E7.5 embryo 1 section 8 region R1

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8R1


title: Dand5 mutant stage E7.5 embryo 1 section 8 region P

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8P


title: Dand5 mutant stage E7.5 embryo 1 section 8 region R2

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8R2


title: Stage E7.5 embryo 3 section 4 region MA

description:
E7.5_3.txt
E7.5_3_4MA


title: Dand5 mutant stage E7.5 embryo 1 section 8 region MAR

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8MAR


title: Dand5 mutant stage E7.5 embryo 1 section 8 region MPL

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8MPL


title: Stage E7.5 embryo 3 section 4 region EP

description:
E7.5_3.txt
E7.5_3_4EP


title: B cells rep1


title: B cells rep2


title: Stage E7.5 embryo 3 section 4 region EA

description:
E7.5_3.txt
E7.5_3_4EA


title: Dand5 mutant stage E7.5 embryo 1 section 8 region MPR

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8MPR


title: Dand5 mutant stage E7.5 embryo 1 section 8 region EP

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8EP


title: Dand5 mutant stage E7.5 embryo 1 section 8 region MAL

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8MAL


title: Dand5 mutant stage E7.5 embryo 1 section 8 region EA

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8EA