title: fibroblasts, OE-miR203a-3p M3

city: Guangzhou

first: Julin

last: Xie

state: State...

address: Zhongshan 2nd Road, Yuexiu District, Guangzhou city, Guangdong Province, China

country: China

institute: First Affiliated Hospital of Sun Yat-sen University

data_processing:
tab-delimited text file includes raw counts for each Sample
tab-delimited text files include FKPM values for each Sample

source_name: hypertrophic scar

growth_protocol: Fibroblasts were maintained in DMEM supplemented with 10% fatal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

treatment_protocol: Fibroblasts were infected with miR-203a-3p overexpression or control lentivirus

value: hypertrophic scar

value: fibroblasts

value: hypertrophic scar fibroblasts

value: miR-203a-3p overexpression

value: lentivirus infection


title: NRAS-/- CCl4  N32

status: Public on Jul 15 2023

type: RNA

city: Madrid

first: Francisco

middle: Javier

last: Cubero

address: c/Doctor Severo Ochoa, 9

department: Department of Immunology, Ophthalmology & ENT

country: Spain

institute: Complutense University School of Medicine

description: Gene expression data from livers of NRAS-/- mouse underwent CCl4

hyb_protocol: The labeled and fragmented ss cDNA was spiked with cDNA hybridization controls. The spiked cDNA samples were hybridized in a GeneChip Hybridization Oven at 45°C for 16 h with rotation (60 rpm). After hybridization, microarrays were stained in two binding cycles using anti-Biotin antibodies and a Streptavidin-phycoerythrin conjugate

scan_protocol: Subsequently, the microarrays were washed with increasing stringency and conserved in holding buffer using the Affymetrix GeneChip® 3000 7 G Fluidics Station in combination with the Affymetrix GeneChip® Command Console (AGCC) software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: NRAS-/- mouse CCl4

label_protocol: 200 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. The quality of second cycle cDNA and fragmented single-stranded (ss) cDNA were analyzed on the 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Wildtype or NRAS-/- male mouse was included at the age of 8-10 weeks, then they were randomly assigned in to one of the eight groups.

extract_protocol: The RNA was isolated by using the Trizol total RNA extraction method according to the manufacturer's instructions including on-column DNase digestion. Total RNA was eluted in 30 µl RNase-free water. RNA concentration and purity were measuered on the NanoDrop One spectral photometer (peqlab) and on the 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 Nano LabChip Kit (Agilent Technologies).

treatment_protocol: In BDL experiment, wildtype and NRAS-/- mice received either sham operation or bile duct ligation operation, the operated mice were sacrified on day 28 after operations. In CCl4 treatment experimetnt,  wildtype and NRAS-/- mice received either corn oil or CCl4 injection twice a week, the mice were sacrified after 4 weeks treatments.

tag: tissue

value: liver

tag: genotype

value: NRAS-/-

tag: treatment


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep12

type: SRA

city: Munich

first: Louis

last: Kuemmerle

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Centre Munich

description:
P5F9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F9

library_source: transcriptomic

data_processing:
BCL files were demultiplexed with the bcl2fastq software from Illumina. After quality control with FastQC, reads were aligned using rnaSTAR65 to the GRCm38 (mm10) genome with ERCC synthetic RNA added. Read counts were collected using the parameter “quantMode GeneCounts” of rnaSTAR and using the unstranded values.
Data points with less than 6000 genes or a mitochondrial fraction above 0.0015 were filtered out.
Assembly: mm10
Supplementary files format and content: hf5 files with raw counts and meta data of all samples (5xFAD_adata_raw.h5ad) and after QC (5xFAD_adata.h5ad)

molecule: polyA RNA

source_name: Skull, bone marrow

extract_protocol:
The bones were dissected from the body and the muscles and connective tissue were meticulously cleared off. The bone marrow inside was flushed out to the collection tube with the help of a syringe and further dissection of the bone was performed by fine pincers. The remaining bone was cut in to small pieces and added to the cell mix. This mixture was shortly vortexed with 37C warmed DMEM with 10% heat inactivated FBS and filtered with 70 μm. Staining for sorting was performed for 15 min using 7AAD (Thermo Fisher, A1310, 25 ug/ml) and the antibodies against CD45 (eFluor 450,30-F11, eBioscience,Cat.:48-0451-82, 1:200) and CD11b (PE/Cy7,M1/70, eBioscience, Cat:25-0112-82,1:200). Cells were then washed with PBS (Sigma, D8537). Viable (7AAD negative) immune cells (CD45 and CD11b positive cells) were sorted by flow cytometry (SH800; Sony) into the 96-well plates by groups of 50 cells per well. The 96-well plates were filled with 4 µl lysis buffer containing 0.05% Triton X-100 (Sigma), ERCC (External RNA Controls Consortium) RNA spike-in Mix (Ambion,Life Technologies) (1:24000000 dilution), 2.5 µM oligo-dT, 2.5 mM dNTP and 2 U/µl of recombinant RNase inhibitor (Clontech). The plate was spun down and frozen at -80 C.
cDNA libraries were generated using an improved version of the Smart-seq2 protocol. The plates with the sorted pools were first thawed and then incubated for 3 min at 72°C and immediately placed on ice. To perform reverse transcription (RT), we added to each well a mix of 0.59 μl H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μl Recombinant RNase Inhibitor (Clontech), 2 μl Betaine (5 M Sigma), 0.5 μl DTT (100 mM), 0.06 μl MgCl2 (1 M Sigma), and 0.1 μl Template-switching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next, RT reaction mixes were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; finally ending with 70°C for 5 min for enzyme inactivation. Pre-amplification of cDNA was performed by adding 12.5 μl KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μl H2O, 0.25 μl ISPCR primers (10 μM, 5′ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μl Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 20 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure bead (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Library was assessed by Bioanalyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and also fluorometrically using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies) to measure the concentrations. Samples were normalized to 160 pg/µL. Sequencing libraries were constructed by using an in-house produced Tn5 transposase101. Libraries were barcoded with the Illumina Nextera XT (FC-131-1096, Illumina) and pooled, then went through three rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library.

value: Skull, bone marrow

tag: cell type

value: Cd45+/Cd11b+ cells

value: 5xFAD (B6SJL)

tag: disease state

value: AD


title: fibroblasts, OE-miR203a-3p M2

organism: Homo sapiens

tag: cell line


title: NRAS-/- corn oil  N27

description: Gene expression data from livers of NRAS-/- mouse underwent corn oil

source_name: NRAS-/- mouse corn oil

value: corn oil


title: wildtype CCl4  N26

description: Gene expression data from livers of wildtype mouse underwent CCl4

source_name: Wildtype mouse CCl4

value: wildtype


title: NRAS-/- corn oil  N29


title: mouse, bulk, Pelvis, MCAo, donorM5

description:
X23L000462
bulk_rna_raw_counts.tsv

data_processing:
For count matrix generation reads were aligned to the GRCm39 genome with Salmon using the nf-core/rnaseq pipeline (v. 3.9)
Assembly: GRCm39
Supplementary files format and content: The raw count matrix with sample ids and gene ids/symbols is given as a tab-delimited text file

source_name: Pelvis, bone marrow

extract_protocol:
The bones were dissected from the body and the muscles and connective tissue were meticulously cleared off. The bone marrow inside was flushed out to the collection tube with the help of a syringe and further dissection of the bone was performed by fine pincers. The remaining bone was cut in to small pieces and added to the cell mix. This mixture was shortly vortexed with 37C warmed DMEM with 10% heat inactivated FBS and filtered with 70 μm. The sample was placed in 5 ml of trypsin enzyme with 0.05% concentration and incubated in a pre-heated 37 °C water bath for 2 minutes. Following this, the reaction was stopped with 10 ml of 37°C pre-warmed DMEM with 10% heat inactivated FBS, the cells were dissociated by gentle trituration with a 1000μl and 200μl pipette and filtered through 70 μm Falcon™ Cell Strainers. Samples were centrifuged at 4 °C, with 1000 rpm, for 5 minutes.The supernatant of all samples was then discarded and remaining precipitate was put into small 1.5 ml Eppendorf tubes after resuspension with DMEM.
Illumina ligation stranded mRNA prep kit

value: Pelvis, bone marrow

value: MCAo

tag: strain


title: mouse, bulk, Pelvis, MCAo, donorM6

description:
X23L000463
bulk_rna_raw_counts.tsv


title: fibroblasts, OE-miR203a-3p M1


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep11

description:
P5F8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F8


title: mouse, bulk, Pelvis, MCAo, donorM4

description:
X23L000461
bulk_rna_raw_counts.tsv


title: fibroblasts, OE-Control B3

value: WT


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep10

description:
P5F7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F7


title: mouse, bulk, Pelvis, MCAo, donorM3

description:
X23L000460
bulk_rna_raw_counts.tsv


title: fibroblasts, OE-Control B2


title: mouse, bulk, Pelvis, MCAo, donorM2

description:
X23L000459
bulk_rna_raw_counts.tsv


title: wildtype CCl4  N24


title: wildtype corn oil  N21

description: Gene expression data from livers of wildtype mouse underwent corn oil

source_name: Wildtype mouse corn oil


title: wildtype corn oil  N22


title: mouse, bulk, Pelvis, MCAo, donorM1

description:
X23L000458
bulk_rna_raw_counts.tsv


title: wildtype corn oil  N23


title: para-carcinoma tissue15

city: Wuhan

first: Yiqi

last: Wang

address: Shizishan Street

institute: Huazhong Agricultural University, China

data_processing:
Quality control with data trimming, fastp version 0.21.0, default parameters
Use bowtie to hg38 and miRBase index construction for alignment , default parameters
Use samtools to transfer sam to sorted bam, Version: 1.3.1, default parameters
Use featureCounts to bam counts statistiction, Version2.0.1, default parameters
R library DESeq2 to obtain differential expression genes, R 4.1.2, pvalue<0.05, |log2FC|>1
Assembly: hg38
Supplementary files format and content: fastq

source_name: para-carcinoma tissue

extract_protocol:
25 pairs of cancer and peritumoral tissues, and the other 13 cancer tissues alone were pathologically confirmed before being frozeninliquidnitrogenand preserved at -80 ºC. Total RNA degradation and contamination of the frozen samples were monitored on 1% agarose gels.
The library was constructed using a Small RNA Sample Pre Kit. Using the special structure of the 3 'and 5' ends of Small RNA (complete phosphate group at the 5 'end and hydroxyl group at the 3' end), taking total RNA as the starting sample, the two ends of Small RNA were directly added to the splice. The cDNA is then synthesized by reverse transcription. After PCR amplification, the target DNA fragments were separated by PAGE gel electrophoresis, and the cDNA library was recovered by cutting the glue
Qubit2.0 was used for preliminary quantification, the library was diluted to 1ng/ul, and then Agilent 2100 was used to detect the insert size of the library. After the insert size met the expectation, Q-PCR method was used to accurately quantify the effective concentration of the library

value: para-carcinoma tissue


title: mouse, bulk, Vertebra, MCAo, donorM6

description:
X23L000457
bulk_rna_raw_counts.tsv

source_name: Vertebra, bone marrow

value: Vertebra, bone marrow


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep6

description:
P5F3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F3


title: para-carcinoma tissue14


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep9

description:
P5F6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F6


title: NRAS-/- BDL N12

description: Gene expression data from livers of NRAS-/- mouse underwent BDL

source_name: NRAS-/- mouse BDL

value: underwent BDL


title: para-carcinoma tissue13


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep5

description:
P5F2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F2


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep4

description:
P5F12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F12


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep8

description:
P5F5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F5


title: mouse, bulk, Vertebra, MCAo, donorM2

description:
X23L000455
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep7

description:
P5F4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F4


title: NRAS-/- BDL N10


title: NRAS-/- BDL N11


title: NRAS-/- sham operation N09

description: Gene expression data from livers of NRAS-/- mouse underwent sham operation

source_name: NRAS-/- mouse sham operation

value: underwent sham operation


title: para-carcinoma tissue12


title: mouse, bulk, Femur, MCAo, donorM1

description:
X23L000464
bulk_rna_raw_counts.tsv

source_name: Femur, bone marrow

value: Femur, bone marrow


title: mouse, bulk, Vertebra, MCAo, donorM1

description:
X23L000454
bulk_rna_raw_counts.tsv


title: wildtype BDL N06

description: Gene expression data from livers of wildtype mouse underwent BDL

source_name: Wildtype mouse BDL


title: para-carcinoma tissue11


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep3

description:
P5F11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F11


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep2

description:
P5F10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F10


title: mouse, bulk, Vertebra, MCAo, donorM4

description:
X23L000456
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor379, rep1

description:
P5F1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5F1


title: NRAS-/- sham operation N08


title: para-carcinoma tissue9


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep11

description:
P5E9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E9


title: NRAS-/- sham operation N07


title: mouse, bulk, Humerus, MCAo, donorM5

description:
X23L000452
bulk_rna_raw_counts.tsv

source_name: Humerus, bone marrow

value: Humerus, bone marrow


title: mouse, bulk, Humerus, MCAo, donorM4

description:
X23L000451
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue8


title: mouse, bulk, Humerus, MCAo, donorM3

description:
X23L000450
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep10

description:
P5E8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E8


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep9

description:
P5E7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E7


title: mouse, bulk, Humerus, MCAo, donorM2

description:
X23L000449
bulk_rna_raw_counts.tsv


title: mouse, bulk, Humerus, MCAo, donorM1

description:
X23L000448
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue10


title: Tree shrew2

city: Kunming

first: Xiao-Lin

last: Zhuang

address: Longxin Road

institute: ology, Kunming Institute of Zoology, Chinese Academy of Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We used fastp software to perform basic statistics on the quality of the raw reads, ensuring the raw reads of Read1 and Read2 were adequate for subsequent analyses.
The raw data were analyzed by cellranger 3.1.0. In brief, the cellranger mkfastq transformed raw base call (BCL) files generated by Illumina sequencers into FASTQ files and decoded the multiplexed samples. Cellranger count took FASTQ files from cellranger mkfastq and performed sequencing alignment, filtering, barcode counting and UMI counting using the default parameters. The reference genome and annotation files of the tree shrew were downloaded from the Tree Shrew Database (TS_2.0 long-read assembly, http://www.treeshrewdb.org/). The standard output files generated by cellranger count served as input data for further analyses with Seurat v3.
Assembly: TS_2.0 long-read assembly (From: http://www.treeshrewdb.org/)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Tupaia belangeri

source_name: whole brain

extract_protocol:
The entire brains of the tree shrew embryos were immediately transferred to ice-cold DMEM solution with 10% FBS (DMEM/FBS) after dissection. Centrifugation of the samples was performed at 4°C. After transferring the whole brains of tree shrew embryos to ice-cold DMEM solution with 10% FBS (DMEM/FBS), the dura mater and blood vessels were removed from the brains. Brain tissues were dissociated using a modified protocol from the Worthington Papain Dissociation System. In brief, the dissected brains were cut into small pieces of less than 1mm3. The small pieces were then digested with 1mg/ml papain and 0.4% DNaseI at 37°C for 30min, shaking once every 5 minutes. After 40 minutes, the digestion process was blocked with DMEM/FBS. Cell suspensions were filtered through a 100 µm cell strainer and pelleted in a benchtop centrifuge at 200×g for 5 minutes. Pellets were re-suspended in DMEM and strained through a 40 µm filter.    To remove cell debris, 2ml cell suspension were layered onto a gradient composed of 1ml layers of 11%, 20% and 35% Optiprep1.32 pH 7.4 in DMEM and centrifuged for 5 min at 430×g with no brake. The bottom 1ml of the gradient was collected and mixed with 1ml DMEM. The cells were then pelleted at 550×g for 5min before being re-suspended in 100-200 µl DMEM with 0.2% BSA.
The input cells were loaded onto the channel of Single Cell B Chip (v3 chemistry, PN-1000153). The 10x library was constructed using 10x Chromium Controller and Chromium Single Cell 3’ Reagent Kits (v3 chemistry CG000183) following the detailed protocol of the manufacturer. In brief, single-cell suspensions in each channel of the chip were loaded on a Chromium Controller (10x Genomics, Pleasanton, CA) to generate single-cell GEMs (gel beads in the emulsion). The 10x libraries of each channel were then prepared using the Chromium Single Cell 3’Gel Bead and Library Kit v3 (PN-1000153, 1000075, 120262; 10x Genomics).

value: whole brain


title: wildtype CCl4  N25

description: Gene expression data from livers of wildtype mouse underwent CCl4

value: liver


title: para-carcinoma tissue6


title: C57BL/6J, Aged mouse3, RPE/choroid, 20-24 months, total RNA

city: Johnson City

first: Mark

middle: Ellsworth

last: Kleinman

state: Tennessee

address: Quillen College of Medicine

department: Department of Surgery

country: USA

institute: East Tennessee State University

data_processing:
Paired-end 100-bp reads were trimmed and filtered using BBDuk (https://github.com/BioInfoTools/BBMap/blob/master/sh/bbduk.sh) and read pairs were mapped to Ensembl GRCm38 transcripts annotation (release 82), using STAR
Transcripts per million (TPM) values were quantified using Sailfish version 0.9.0 with the default parameters using paired-end mode and transformed into normalized counts using the total count method.
Assembly: GRCm38
Supplementary files format and content: Excel file includes TPM values tabulated for all the samples
Supplementary files format and content: Excel file includes DESeq2 results for all the samples

source_name: RPE/choroid

growth_protocol: The mice were purchased from the Jackson Laboratory and housed under standard conditions (23±1°C, 40%–50% humidity, and ad libitum access to food and water).

extract_protocol:
All mice were humanely euthanized by administering CO2 gas followed by cervical dislocation. The eyes were immediately enucleated to collect the neural retina and RPE/choroid tissues. The isolated eyes were placed in the cold petri dish under a surgical microscope. With careful precision, the anterior parts, including the cornea, lens, and iris, as well as connective tissues, muscles, and optic nerve, were excised. Radial cuts were made symmetrically in a four-leaf pattern, allowing for the careful removal of the neural retina from the mouse eyecup. The pigmented RPE/choroid layer was gently scraped from the sclera. RPE/choroid and neural retina tissues were immediately transferred to TRIzol reagent (Invitrogen 15596026, Carlsbad, CA). Subsequently, RNA purification and on-column genomic DNA digestion were conducted using the Pure Link RNA Micro Kit (Invitrogen 12183016, Carlsbad, CA).
Ribosomal RNAs were removed with the Ribozero Gold Human/Mouse from Illumina. No PolyA selection was performed. RNA libraries were constructed using TruSeq Stranded Total RNA Sample Prep kit (Illumina, CA) as per manufacturer's instructions.

value: RPE/choroid

tag: time

value: 22-24 months

tag: Sex

value: Male


title: para-carcinoma tissue5


title: mouse, bulk, Scapula, MCAo, donorM6

description:
X23L000447
bulk_rna_raw_counts.tsv

source_name: Scapula, bone marrow

value: Scapula, bone marrow


title: wildtype BDL N05


title: C57BL/6J, Aged mouse2, RPE/choroid, 20-24 months, total RNA


title: wildtype sham operation N02

description: Gene expression data from livers of wildtype mouse underwent sham operation

source_name: Wildtype mouse sham operation


title: para-carcinoma tissue3


title: C57BL/6J, Aged mouse1, RPE/choroid, 20-24 months, total RNA


title: wildtype BDL N04


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep6

description:
P5E4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E4

value: Skull, bone marrow

value: Cd45+/Cd11b+ cells

value: 5xFAD (B6SJL)

value: AD


title: mouse, bulk, Scapula, MCAo, donorM5

description:
X23L000446
bulk_rna_raw_counts.tsv

value: wildtype

value: MCAo


title: wildtype sham operation N01


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep8

description:
P5E6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E6


title: Tree shrew1

description: 10x Genomics


title: mouse, bulk, Scapula, MCAo, donorM4

description:
X23L000445
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue2

value: para-carcinoma tissue


title: mouse, bulk, Scapula, MCAo, donorM3

description:
X23L000444
bulk_rna_raw_counts.tsv


title: wildtype sham operation N03


title: C57BL/6J, Young mouse2, RPE/choroid, 1-2 months, total RNA

value: 1-2 months


title: para-carcinoma tissue1


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep4

description:
P5E2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E2


title: para-carcinoma tissue7


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep3

description:
P5E11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E11


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep7

description:
P5E5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E5


title: fibroblasts, OE-Control B1

source_name: hypertrophic scar

value: hypertrophic scar

value: fibroblasts

value: hypertrophic scar fibroblasts

value: WT

value: lentivirus infection


title: C57BL/6J, Young mouse1, RPE/choroid, 1-2 months, total RNA

value: RPE/choroid


title: mouse, bulk, Scapula, MCAo, donorM2

description:
X23L000443
bulk_rna_raw_counts.tsv


title: C57BL/6J, Aged mouse3, RPE/choroid, 20-24 months

extract_protocol:
All mice were humanely euthanized by administering CO2 gas followed by cervical dislocation. The eyes were immediately enucleated to collect the neural retina and RPE/choroid tissues. The isolated eyes were placed in the cold petri dish under a surgical microscope. With careful precision, the anterior parts, including the cornea, lens, and iris, as well as connective tissues, muscles, and optic nerve, were excised. Radial cuts were made symmetrically in a four-leaf pattern, allowing for the careful removal of the neural retina from the mouse eyecup. The pigmented RPE/choroid layer was gently scraped from the sclera. RPE/choroid and neural retina tissues were immediately transferred to TRIzol reagent (Invitrogen 15596026, Carlsbad, CA). Subsequently, RNA purification and on-column genomic DNA digestion were conducted using the Pure Link RNA Micro Kit (Invitrogen 12183016, Carlsbad, CA).
Ribosomal RNAs were removed with the Ribozero Gold Human/Mouse from Illumina. RNA libraries were constructed using TruSeq Stranded Total RNA Sample Prep kit (Illumina, CA) as per manufacturer's instructions.

value: 22-24 months


title: mouse, bulk, Scapula, MCAo, donorM1

description:
X23L000442
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep2

description:
P5E10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E10

source_name: Skull, bone marrow


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep5

description:
P5E3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E3


title: normal tissue9

source_name: normal tissue

value: normal tissue


title: C57BL/6J, Aged mouse2, RPE/choroid, 20-24 months

value: Male


title: C57BL/6J, Young mouse3, RPE/choroid, 1-2 months, total RNA


title: C57BL/6J, Aged mouse1, RPE/choroid, 20-24 months


title: para-carcinoma tissue4


title: normal tissue7


title: normal tissue8


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep10

description:
P5D8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D8

value: Femur, bone marrow

value: healthy


title: mouse, bulk, Calvaria, MCAo, donorM5

description:
X23L000440
bulk_rna_raw_counts.tsv

source_name: Calvaria, bone marrow

value: Calvaria, bone marrow


title: C57BL/6J, Young mouse3, RPE/choroid, 1-2 months


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor438, rep1

description:
P5E1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5E1

value: Skull, bone marrow

value: Cd45+/Cd11b+ cells

value: 5xFAD (B6SJL)

value: AD


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep11

description:
P5D9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D9

value: wildtype


title: normal tissue6


title: mouse, bulk, Calvaria, MCAo, donorM4

description:
X23L000439
bulk_rna_raw_counts.tsv

value: MCAo


title: C57BL/6J, Young mouse2, RPE/choroid, 1-2 months

value: 1-2 months


title: mouse, bulk, Calvaria, MCAo, donorM3

description:
X23L000438
bulk_rna_raw_counts.tsv


title: mouse, bulk, Humerus, MCAo, donorM6

description:
X23L000453
bulk_rna_raw_counts.tsv

value: Humerus, bone marrow


title: normal tissue10


title: C57BL/6J, Young mouse1, RPE/choroid, 1-2 months


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep9

description:
P5D6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D6


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep7

description:
P5D7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D7


title: mouse, bulk, Calvaria, MCAo, donorM2

description:
X23L000437
bulk_rna_raw_counts.tsv


title: mouse, bulk, Calvaria, MCAo, donorM1

description:
X23L000436
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep8

description:
P5D5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D5


title: mouse, bulk, Calvaria, MCAo, donorM6

description:
X23L000441
bulk_rna_raw_counts.tsv


title: normal tissue3


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep7

description:
P5D4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D4


title: Case 24 Recurrence

city: Hamburg

first: Lea

last: Altendorf

address: Martinistraße 52

institute: Universitätsklinikum Hamburg-Eppendorf

description:
Processed_RNA_sequencing_count_data.txt
VST_normalized_RNA_sequencing_count_data.txt
DESeq2_featureCounts_of_RNA_sequencing_data.txt
Log2_of_DESeq2_featureCounts_of_RNA_sequencing_data.txt

data_processing:
usegalaxy, R Studio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (reads with quality < 20 were trimmed)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner (length of genome sequence around annotated junction = 100, using basic 2 pass-mapping,excluding alignements with indels or soft clippings, MAPQ value for unique mapper filter = 60, number of genome bins for coordinate-sorting = 50 and maximum number of loci anchor allowed to map to = 50)
Read count extraction and normalization using featureCount and VST normalized files from DESeq2 were used for downstream analysis
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count data, processed count data, DESeq2 featureCounts, VST-normalized count data, Log2 of DESeq2 featureCounts

source_name: tumor tissue

extract_protocol:
RNA was extracted and purified from FFPE and KRYO tissue using “Maxwell® RSC RNA FFPE Kit” (Promega). Depletion of ribosomal RNA was performed using the “RiboCop rRNA Depletion Kit” (Lexogen).
The “CORALL Total RNA-Seq Library Prep Kit” (Lexogen) was used for the generation of an RNA sequencing library. Concentration measurement was performed with the “Qubit 2.0 Fluorometer” (Thermo Fisher Scientific) and the distribution of the final libraries fragment lengths was determined using the “DNA High Sensitivity Chip” on an “Agilent 2100 Bioanalyzer” (Agilent Technologies). The concentration was adjusted to 2nM in order to pool them at equimolar concentrations. Sequencing of the library pool was done on a “NextSeq500” (Illumina) with 1x75bp, with 24.5 to 35.1 million reads per sample.

value: tumor tissue

tag: genotype (smarcb1_germline_mutation)

value: SMARCA4 germline


title: normal tissue2


title: Case 24 Primary


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep6

description:
P5D3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D3


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep5

description:
P5D2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D2


title: Case 22 Recurrence


title: normal tissue5


title: mouse, bulk, Femur, Sham, donorS4

description:
X23L000434
bulk_rna_raw_counts.tsv

value: Sham


title: mouse, bulk, Femur, Sham, donorS3

description:
X23L000433
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue38

source_name: bladder carcinoma tissue

value: bladder carcinoma tissue


title: Case 21 Recurrence


title: normal tissue1

value: normal tissue


title: bladder carcinoma tissue37


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep3

description:
P5D11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D11


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep4

description:
P5D12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D12


title: mouse, bulk, Femur, Sham, donorS1

description:
X23L000431
bulk_rna_raw_counts.tsv


title: mouse, bulk, Femur, Sham, donorS2

description:
X23L000432
bulk_rna_raw_counts.tsv


title: Case 22 Primary


title: normal tissue4


title: mouse, bulk, Pelvis, Sham, donorS5

description:
X23L000430
bulk_rna_raw_counts.tsv

source_name: Pelvis, bone marrow

value: Pelvis, bone marrow


title: Case 20 Recurrence


title: Case 21 Primary


title: bladder carcinoma tissue35


title: bladder carcinoma tissue36


title: mouse, bulk, Femur, Sham, donorS5

description:
X23L000435
bulk_rna_raw_counts.tsv

value: Femur, bone marrow


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep2

description:
P5D10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D10

value: healthy


title: mouse, bulk, Cd11b+, Femur, WT, donor373, rep1

description:
P5D1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5D1


title: Case 20 Primary


title: mouse, bulk, Pelvis, Sham, donorS4

description:
X23L000429
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue34


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep12

description:
P5C9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C9


title: Case 19 Recurrence


title: mouse, bulk, Pelvis, Sham, donorS3

description:
X23L000428
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep11

description:
P5C8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C8


title: mouse, bulk, Pelvis, Sham, donorS2

description:
X23L000427
bulk_rna_raw_counts.tsv


title: Case 19 Primary


title: bladder carcinoma tissue33


title: Case 16 Recurrence

value: wild type


title: bladder carcinoma tissue32


title: mouse, bulk, Pelvis, Sham, donorS1

description:
X23L000426
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep10

description:
P5C7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C7


title: bladder carcinoma tissue30


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep9

description:
P5C6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C6


title: Case 16 Primary


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep8

description:
P5C5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C5


title: mouse, bulk, Vertebra, Sham, donorS6

description:
X23L000425
bulk_rna_raw_counts.tsv

source_name: Vertebra, bone marrow

value: Vertebra, bone marrow


title: bladder carcinoma tissue31


title: mouse, bulk, Vertebra, Sham, donorS4

description:
X23L000424
bulk_rna_raw_counts.tsv


title: Case 15 Recurrence


title: mouse, bulk, Vertebra, Sham, donorS3

description:
X23L000423
bulk_rna_raw_counts.tsv


title: Case 15 Primary


title: bladder carcinoma tissue28


title: Case 11 Recurrence


title: bladder carcinoma tissue27


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep7

description:
P5C4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C4

value: Cd45+/Cd11b+ cells


title: mouse, bulk, Vertebra, Sham, donorS2

description:
X23L000422
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep6

description:
P5C3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C3


title: mouse, bulk, Vertebra, Sham, donorS1

description:
X23L000421
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep5

description:
P5C2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C2


title: Case 11 Primary


title: mouse, bulk, Humerus, Sham, donorS6

description:
X23L000420
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue26


title: Case 10 Primary


title: Case 10 Recurrence


title: bladder carcinoma tissue29


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep4

description:
P5C12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C12


title: Case 8 Recurrence


title: bladder carcinoma tissue24


title: bladder carcinoma tissue23


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep1

description:
P5C1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C1


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep2

description:
P5C10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C10


title: Case 8 Primary

description:
Processed_RNA_sequencing_count_data.txt
VST_normalized_RNA_sequencing_count_data.txt
DESeq2_featureCounts_of_RNA_sequencing_data.txt
Log2_of_DESeq2_featureCounts_of_RNA_sequencing_data.txt


title: mouse, bulk, Humerus, Sham, donorS4

description:
X23L000418
bulk_rna_raw_counts.tsv


title: mouse, bulk, Humerus, Sham, donorS5

description:
X23L000419
bulk_rna_raw_counts.tsv


title: mouse, bulk, Humerus, Sham, donorS3

description:
X23L000417
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue25


title: bladder carcinoma tissue22


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep12

description:
P5B9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B9

value: 5xFAD (B6SJL)


title: Case 7 Recurrence #1


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep11

description:
P5B8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B8

value: AD


title: bladder carcinoma tissue20


title: Case 7 Primary #1


title: bladder carcinoma tissue21


title: mouse, bulk, Humerus, Sham, donorS1

description:
X23L000415
bulk_rna_raw_counts.tsv

value: wildtype


title: mouse, bulk, Humerus, Sham, donorS2

description:
X23L000416
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep10

description:
P5B7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B7


title: mouse, bulk, Scapula, Sham, donorS6

description:
X23L000414
bulk_rna_raw_counts.tsv

value: Scapula, bone marrow


title: Case 6 Recurrence #2


title: mouse, bulk, Cd11b+, Femur, WT, donor294, rep3

description:
P5C11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5C11


title: bladder carcinoma tissue19


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep9

description:
P5B6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B6


title: Case 6 Primary


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep8

description:
P5B5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B5


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep7

description:
P5B4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B4


title: mouse, bulk, Scapula, Sham, donorS3

description:
X23L000411
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep6

description:
P5B3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B3


title: mouse, bulk, Scapula, Sham, donorS4

description:
X23L000412
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue17


title: bladder carcinoma tissue18


title: Case 3 Primary


title: iTAZ 3

city: Göttingen

first: André

last: Fischer

state: Niedersachsen

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)

data_processing:
Illumina’s bcl2fastq (v2.20.0) was used for base calling, adaptor trimming and demultiplexing to generate FASTQ files.
Quality control of raw sequencing data was performed using FastQC (v 0.11.9)
Reads were  mapped to the genome using STAR (v2.7.3a), with a maximum number of two mismatches allowed per pair, and other default parameters.
The number of aligned reads overlapping with exons for each gene was counted with the featureCounts program from the Subread package (v2.0.0) .
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: iPS- cardiomyocytes

growth_protocol: Control and patient-specific iPS-CM: Ethics, the study was approved by the Ethics Committee of the University Medical Center Göttingen (approval number: 10/9/15) and carried out in accordance with the approved guidelines. Written informed consent was obtained from all participants before participation in the study.    Generation and cardiac differentiation of iPSC lines: Human iPSC lines from a healthy donor and from a Barth syndrome patient with a pathological missense variant in TAZ were used in this study. Wild type iPSC line UMGi014-C clone 14 (isWT1.14) was generated from dermal fibroblasts using the integration-free Sendai virus and described previously46. The iPSC line UMGi054-A clone 3 (iTAZ10.3) from a Barth syndrome patient carrying a heterozygous variant c.590G>T/p.Gly197Val in the TAZ gene was generated from dermal fibroblasts using the STEMCCA lentivirus system and described previously11,13. Human iPSC lines were differentiated into ventricular cardiomyocytes via WNT signaling modulation and subsequent metabolic selection and cultured for at least 30 days, as previously described47. Human iPSCs and derived cardiomyocytes were cultured in feeder-free and serum-free culture conditions in a humidified incubator at 37°C and 5% CO2. Starvation conditions were simulated using Substrate limited media II (HBSS supplemented with 1mM glutamine).

extract_protocol:
1. Cells were plated in a 6 well plate (300000 cells per well), washed with PBS and 500 uL of TRIZOL was added before storing them at -20.   2. Frozen cells containing TRIZOL are moved to a 1.5 mL tube and incubated at 24oC for 5 minutes (no shaking).  3. Add 100 ul of chloroform and vortex the samples for 15 seconds vigorously.  4. Incubate samples for 3 minutes in a thermal heater at 24oC.   5. Centrifuge for 15 minutes at 12000g at 4oC.  6. Remove the upper phase very carefully into an Eppendorf and throw away the rest (do not touch the middle phase. You can leave a little bit behind.)  7. To this upper phase add 250 ul of isopropanol.  8. Shake the samples gently and incubate for 10 minutes at 24oC.  9. Centrifuge the samples for 10 minutes at 12000g at 4oC.  10. Decant the supernatant  11. Add 500 mL of 75% Ethanol to each sample and mix the samples briefly.   12. Centrifuge for 5 minutes at 7500g at 40C.  13. Decant the supernatant using a pipette since it is loose.   14. Keep the samples in a thermal heater at 24oC for 10 to 15 minutes until the pellet is dry. (Pellet will become translucent from white).  15. Resuspend pellet in DNase, RNase free water 25 ul (10-50 ul).  16. Incubate for 10 minutes at 60oC in thermal heater.   17. Measure concentration immediately or store at -80C until usage.
cDNA libraries were prepared with 500 ng of total RNA using the TrueSeq® Library preparation kit (Illumina, USA).

value: iPS- cardiomyocytes


title: mouse, bulk, Scapula, Sham, donorS1

description:
X23L000409
bulk_rna_raw_counts.tsv


title: iTAZ 2


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep5

description:
P5B2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B2


title: bladder carcinoma tissue15


title: Case 3 Recurrence


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep4

description:
P5B12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B12


title: bladder carcinoma tissue13


title: bladder carcinoma tissue14


title: iTAZ 1


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep3

description:
P5B11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B11


title: mouse, bulk, Calvaria, Sham, donorS5

description:
X23L000407
bulk_rna_raw_counts.tsv

value: Calvaria, bone marrow


title: Control 3

value: WT


title: mouse, bulk, Scapula, Sham, donorS5

description:
X23L000413
bulk_rna_raw_counts.tsv


title: Syngeneic_mouse_lung, 2hrs_post_reperfusion, Vehicle_donor, scRNAseq

city: Saint Louis

first: Daniel

last: Kreisel

state: Missouri

address: 660 S Euclid Ave

department: Surgery

institute: Washington University

description: 10x Genomics

data_processing:
Analysis was performed using the R Seurat v4.0.0 package. The following quality control steps were performed to filter the count matrices: 1) Cells expressing fewer than 500 genes were removed; 2) cells expressing over 6,000 genes were discarded as these could be potential multiplet events where more than a single cell was encapsulated within the same barcoded GEM; 3) cells with >5% mitochondrial content were filtered out as these were deemed to be of low-quality. Normalization and variance-stabilization of raw counts was performed using  SCTransform, and cell cycle scores were computed and regressed out in combination with percentage mitochondrial reads. The normalized R object was then used for subsequent clustering and differential expression testing. Briefly, clusters were annotated into major cell populations, each major cell type was subsetted, and renormalized, PCA, Uniform Manifold Approximation and Projection (UMAP) embedding, clustering, and DE analysis performed. Clusters which resembled low-quality cells or doublets were removed from subsequent analysis. We then computed the principal components and used these to integrate all samples with harmony. Informed by the ElbowPlot, we used 50 components to construct the UMAP embedding, find nearest neighbors, and clustered the data at multiple resolutions. We then used the FindAllMarkers function in Seurat to perform differential expression testing and annotated clusters into distinct cell types based on canonical gene markers. We identified a single population that represented a stromal contaminant consistent with vascular endothelium, which was excluded from further analysis. To identify genetic changes induced by treatment, major cell populations were subsetted, renormalized, reclustered, recomputed the UMAP, and differential gene expression analyzed. All differential gene expression used to identify cell types was performed using the normalized assay with the FindAllMarkers function and the Wilcoxon rank sum test with a min.pct = 0.1 and logfc.threshold = 0.25. Differential gene expression of violin plots for individual genes between treatment groups was performed using pairwise comparisons using Wilcox test through the ggpubr package. For pathway analysis, differentially down-regulated genes in RvD1-treated compared to vehicle-treated lungs were used if P < 0.05 and Log2FC > 0.58 and analyzed by MSigDB Hallmark 2020 Pathway analysis (https://maayanlab.cloud/Enrichr).
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: B6 left lung 2 hours after syngeneic transplantation

extract_protocol:
Two hours after lung transplantation, left lung grafts from two mice were collected and pooled for submission of each sample. Lung tissue was digested and single cell suspensions were prepared as previously described [PMID 28615357].
Single-cell suspensions were submitted to the Genome Technology Access Center core facility (Washington University in St. Louis) for single-cell GEM construction and cDNA synthesis and library construction. Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit (10X Genomics, v3) following the manufacterer's protocol. The libraries were sequenced on NovaSeq S4 (Illumina) targeting 50,000 reads per cell and 500 million read pairs per library.

treatment_protocol: Recipient mice were treated with intravenous Resolvin D1 (200 ng per mouse in 200 uL 1% ethanol) or vehicle immediately prior to transplantation. Left lung grafts were stored in low-potassium dextran glucose solution for 60 minutes at 4 degrees Celsius with an additional 45 minutes at 28 degrees Celcius priuor to orthotopic vascularized transplantation into syngeneic recipients.

value: CD45+ donor leukocytes

value: vehicle


title: bladder carcinoma tissue12

value: bladder carcinoma tissue


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep2

description:
P5B10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B10

source_name: Femur, bone marrow


title: mouse, bulk, Calvaria, Sham, donorS4

description:
X23L000406
bulk_rna_raw_counts.tsv

value: Sham


title: bladder carcinoma tissue16


title: mouse, bulk, Scapula, Sham, donorS2

description:
X23L000410
bulk_rna_raw_counts.tsv


title: Control 2


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor379, rep1

description:
P5B1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5B1


title: Control 1


title: mouse, bulk, Calvaria, Sham, donorS3

description:
X23L000405
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue10


title: bladder carcinoma tissue11


title: mouse, bulk, Calvaria, Sham, donorS6

description:
X23L000408
bulk_rna_raw_counts.tsv


title: mouse, bulk, Calvaria, Sham, donorS2

description:
X23L000404
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue9


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep10

description:
P5A8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A8


title: bladder carcinoma tissue8


title: mouse, bulk, Calvaria, Sham, donorS1

description:
X23L000403
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep9

description:
P5A7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A7


title: mouse, bulk, Femur, Naive, donorN6

description:
X23L000402
bulk_rna_raw_counts.tsv

value: Naive


title: bladder carcinoma tissue7


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep8

description:
P5A6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A6

value: Femur, bone marrow


title: mouse, bulk, Femur, Naive, donorN5

description:
X23L000401
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue6


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep7

description:
P5A5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A5


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep6

description:
P5A4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A4


title: bladder carcinoma tissue5


title: mouse, bulk, Femur, Naive, donorN1

description:
X23L000399
bulk_rna_raw_counts.tsv


title: Ovarian follicle with control (FSH-) [6_NT_S16_L003]

city: Aurora

first: T. Rajendra

last: Kumar

state: CO

department: Obstetrics & Gynecology

institute: University of Colorado Anschutz Medical Campus

data_processing:
bcl2fastq2 software (Illumina, version 2.20.0)
Sequencing quality control was performed using FastQC tool developed by Babraham Institute
The reads were aligned to the mouse genome, Mus Musculus (mm10), using the STAR aligner
The read-count for each gene was obtained using the -quantMode TranscriptomeSAM GeneCounts command from STAR 2.7 aligner
The ReadsPerGene.out/tab and Aligned.toTanscriptome.out.bam files generated were used for further downstream analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Ovarian follicle

growth_protocol: Follicles were grown in growth media containing α-MEM-Glutamax, 3 mg/ml bovine serum albumin, 1 mg/ml fetuin,  0.1% insulin-transferrin-selenium at 37C under humidified conditions with 5% CO2.

extract_protocol:
RNA was isolated using RNAeasy Mini colums (Qiagen). 50 ng of total RNA was used for constuction of sequencing libraries for each sample.
RNA libraries for RNA-seq were prepared using the NuGEN Universal Plus mRNA-seq library kit from TECAN following the manufacturer’s recommended procedure

treatment_protocol: Follicles were treated with no (control), 1 ng/ml , or 10ng/ml of FSH21 or FSH24 for 24 hrs

value: Ovarian follicle

value: control (FSH-)


title: Ovarian follicle treated with 1ng/ml FSH24 [6_24-1_S18_L004]

value: 1ng/ml FSH24


title: Ovarian follicle treated with 1ng/ml FSH24 [6_24-1_S18_L003]


title: Ovarian follicle with control (FSH-) [6_NT_S16_L002]


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep11

description:
P5A9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A9

value: Cd45+/Cd11b+ cells


title: bladder carcinoma tissue4


title: mouse, bulk, Pelvis, Naive, donorN5

description:
X23L000398
bulk_rna_raw_counts.tsv

value: Pelvis, bone marrow


title: Ovarian follicle with control (FSH-) [6_NT_S16_L004]


title: Ovarian follicle with control (FSH-) [6_NT_S16_L001]


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep4

description:
P5A2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A2

value: 5xFAD (B6SJL)

value: AD


title: bladder carcinoma tissue3


title: Ovarian follicle treated with 1ng/ml FSH24 [6_24-1_S18_L002]


title: Ovarian follicle treated with 1ng/ml FSH24 [6_24-1_S18_L001]


title: mouse, bulk, Pelvis, Naive, donorN4

description:
X23L000397
bulk_rna_raw_counts.tsv

value: wildtype


title: bladder carcinoma tissue2


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep6

description:
P5A12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A12

value: Skull, bone marrow

value: healthy


title: mouse, bulk, Pelvis, Naive, donorN3

description:
X23L000396
bulk_rna_raw_counts.tsv


title: bladder carcinoma tissue1


title: Ovarian follicle treated with 1ng/ml FSH21 [6_21-1_S17_L004]

value: 1ng/ml FSH21


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep3

description:
P5A11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A11


title: Ovarian follicle treated with 1ng/ml FSH21 [6_21-1_S17_L003]


title: mouse, bulk, Femur, Naive, donorN2

description:
X23L000400
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep2

description:
P5A10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A10


title: mouse, bulk, Pelvis, Naive, donorN1

description:
X23L000394
bulk_rna_raw_counts.tsv


title: Ovarian follicle treated with 1ng/ml FSH21 [6_21-1_S17_L002]


title: para-carcinoma tissue9

data_processing:
Quality control with data trimming, fastp version 0.21.0, default parameters
Use hisat2 to align reads to hg38 genome, HISAT2 version 2.1.0, default parameters
Use samtools to transfer sam to sorted bam, Version: 1.3.1, default parameters
mRNA and lncRNA used htcount to bam counts statistiction, Public License v3, htseq-count with default parameters ; circRNA applied CLEAR and CIRI2 pipeline analysing.
R library DESeq2 to obtain differential expression genes, R 4.1.2, pvalue<0.05, |log2FC|>1
Assembly: hg38
Supplementary files format and content: fastq

source_name: para-carcinoma tissue

extract_protocol:
25 pairs of cancer and peritumoral tissues, and the other 13 cancer tissues alone were pathologically confirmed before being frozeninliquidnitrogenand preserved at -80 ºC. Total RNA degradation and contamination of the frozen samples were monitored on 1% agarose gels.
RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). And, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following the manufacturer’s recommendations. The first-strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H– ). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina, and index (X) primer. PCR products were purified and harvested.

value: para-carcinoma tissue


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep5

description:
P5A3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A3


title: para-carcinoma tissue8


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor438, rep1

description:
P5A1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5A1


title: mouse, bulk, Vertebra, Naive, donorN3

description:
X23L000391
bulk_rna_raw_counts.tsv

value: Vertebra, bone marrow


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep5

description:
P4G7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P4G7


title: para-carcinoma tissue7


title: Ovarian follicle treated with 1ng/ml FSH21 [6_21-1_S17_L001]


title: Ovarian follicle with control (FSH-) [5_NT_S13_L004]


title: Ovarian follicle with control (FSH-) [5_NT_S13_L003]


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep3

description:
P4F10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P4F10


title: mouse, bulk, Vertebra, Naive, donorN1

description:
X23L000389
bulk_rna_raw_counts.tsv


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep4

description:
P4F12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P4F12


title: para-carcinoma tissue6


title: mouse, bulk, Vertebra, Naive, donorN2

description:
X23L000390
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue5


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep2

description:
P4C11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P4C11


title: mouse, bulk, Humerus, Naive, donorN5

description:
X23L000388
bulk_rna_raw_counts.tsv

source_name: Humerus, bone marrow

value: Humerus, bone marrow


title: mouse, bulk, Pelvis, Naive, donorN2

description:
X23L000395
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue3


title: Ovarian follicle with control (FSH-) [5_NT_S13_L001]


title: mouse, bulk, Humerus, Naive, donorN4

description:
X23L000387
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue4


title: Ovarian follicle treated with 1ng/ml FSH24 [5_24-1_S15_L004]


title: Ovarian follicle with control (FSH-) [5_NT_S13_L002]


title: mouse, bulk, Humerus, Naive, donorN3

description:
X23L000386
bulk_rna_raw_counts.tsv


title: scRNAseq, mouse, Brain, Naive, rep1

data_processing:
The 10X Genomics core computational software Cellranger v.3.0.2 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment. (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
For QC, filtering, normalization, and doublet exclusion the scanpy python package v.1.6.1, anndata v0.7.5 and scrublet v.0.2.3 were used.
Genome_build: mm10
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format (sc_adata_oct22m.h5ad, sc_adata_march22h.h5ad) as generated and used in the code at https://github.com/erturklab/skull_immune. The files contain the raw, preprocessed, normalized and annotated count data of all single cell experiments.
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.

source_name: Brain

extract_protocol:
The bones were dissected from the body and the muscles and connective tissue were meticulously cleared off. The bone marrow inside was flushed out to the collection tube with the help of a syringe and further dissection of the bone was performed by fine pincers. The remaining bone was cut in to small  pieces and added to the cell mix. This mixture was shortly vortexed with 37C warmed DMEM with 10% heat inactivated FBS and filtered with 70 μm. The brain was isolated from the calvaria and the rest of the body, then, the cortex was separated and the leptomeninges was removed from the surface, the final sample consisted of the injured region. The sample was placed in 5 ml of trypsin enzyme with 0.05% concentration and incubated in a pre-heated 37 °C water bath for 2 minutes.Following this, the reaction was stopped with 10 ml of 37°C pre-warmed DMEM with 10% heat inactivated FBS, the cells were dissociated by gentle trituration with a 1000μl and 200μl pipette and filtered through 70 μm Falcon™ Cell Strainers. For meningeal cell isolation; after the brain was removed, the meningeal dura layer that was attached to the calvaria bone, was plucked carefully using fine tipped dissection pincers under a dissection microscope. Leptomeninges was not isolated and therefore is not included in this study. The dissected meninges was placed in 37°C pre-warmed DMEM with 10% heat inactivated FBS solution, shredded with a fine scalpel, gently titrating with a 200μl pipette and filtered through a 70 μm Falcon™ Cell Strainers.Samples were centrifuged at 4 °C, with 1000 rpm, for 5 minutes.The supernatant of all samples was then discarded and remaining precipitate was put into small 1.5 ml Eppendorf tubes after resuspension with DMEM.
10x single-cell protocol

value: Brain


title: mouse, bulk, Vertebra, Naive, donorN4

description:
X23L000392
bulk_rna_raw_counts.tsv

value: Naive


title: para-carcinoma tissue15


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep1

description:
P4B11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P4B11


title: Ovarian follicle treated with 1ng/ml FSH24 [5_24-1_S15_L003]


title: mouse, bulk, Humerus, Naive, donorN2

description:
X23L000385
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue2


title: scRNAseq, mouse, Scapula, Naive, rep1

source_name: Scapula

value: Scapula, bone marrow


title: mouse, bulk, Humerus, Naive, donorN1

description:
X23L000384
bulk_rna_raw_counts.tsv


title: Ovarian follicle treated with 1ng/ml FSH24 [5_24-1_S15_L002]

value: Ovarian follicle


title: para-carcinoma tissue14


title: scRNAseq, mouse, Humerus, Naive, rep1

source_name: Humerus


title: mouse, bulk, Scapula, Naive, donorN5

description:
X23L000383
bulk_rna_raw_counts.tsv

source_name: Scapula, bone marrow


title: scRNAseq, mouse, Vertebra, Naive, rep1

source_name: Vertebra


title: mouse, bulk, Scapula, Naive, donorN4

description:
X23L000382
bulk_rna_raw_counts.tsv


title: Ovarian follicle treated with 1ng/ml FSH21 [5_21-1_S14_L004]


title: scRNAseq, mouse, Femur, Naive, rep1

source_name: Femur

value: Femur, bone marrow


title: Ovarian follicle treated with 1ng/ml FSH21 [5_21-1_S14_L002]


title: para-carcinoma tissue11


title: mouse, bulk, Scapula, Naive, donorN3

description:
X23L000381
bulk_rna_raw_counts.tsv


title: para-carcinoma tissue12


title: Ovarian follicle treated with 1ng/ml FSH21 [5_21-1_S14_L003]


title: mouse, bulk, Scapula, Naive, donorN2

description:
X23L000380
bulk_rna_raw_counts.tsv


title: Ovarian follicle treated with 1ng/ml FSH21 [5_21-1_S14_L001]


title: scRNAseq, mouse, Pelvis, Naive, rep1

source_name: Pelvis


title: para-carcinoma tissue1


title: scRNAseq, mouse, Calvaria, Naive, rep1

source_name: Calvaria

value: Calvaria, bone marrow


title: mouse, bulk, Scapula, Naive, donorN1

description:
X23L000379
bulk_rna_raw_counts.tsv


title: scRNAseq, mouse, Brain, MCAo, rep2

value: MCAo


title: Ovarian follicle with control (FSH-) [4_NT9_S10_L004]

value: control (FSH-)


title: mouse, bulk, Calvaria, Naive, donorN5

description:
X23L000378
bulk_rna_raw_counts.tsv

source_name: Calvaria, bone marrow


title: normal tissue9

source_name: normal tissue

value: normal tissue


title: Ovarian follicle with control (FSH-) [4_NT9_S10_L003]


title: normal tissue8


title: Ovarian follicle treated with 1ng/ml FSH24 [5_24-1_S15_L001]

value: 1ng/ml FSH24


title: scRNAseq, mouse, Scapula, MCAo, rep2

value: wildtype


title: para-carcinoma tissue13


title: mouse, bulk, Calvaria, Naive, donorN4

description:
X23L000377
bulk_rna_raw_counts.tsv


title: scRNAseq, mouse, Meninges, Naive, rep1

source_name: Meninges

value: Meninges


title: para-carcinoma tissue10


title: Ovarian follicle with control (FSH-) [4_NT9_S10_L002]


title: Ovarian follicle with control (FSH-) [4_NT9_S10_L001]


title: normal tissue6


title: normal tissue7


title: scRNAseq, mouse, Humerus, MCAo, rep2


title: scRNAseq, mouse, Vertebra, MCAo, rep2


title: normal tissue5


title: Ovarian follicle treated with 10ng/ml FSH24 [4_24-10_S12_L004]

value: 10ng/ml FSH24


title: mouse, bulk, Calvaria, Naive, donorN1

description:
X23L000374
bulk_rna_raw_counts.tsv

value: Naïve


title: scRNAseq, mouse, Meninges, MCAo, rep2


title: Ovarian follicle treated with 10ng/ml FSH24 [4_24-10_S12_L003]


title: normal tissue4


title: scRNAseq, mouse, Femur, MCAo, rep2


title: normal tissue3


title: Ovarian follicle treated with 10ng/ml FSH24 [4_24-10_S12_L002]


title: Ovarian follicle treated with 10ng/ml FSH24 [4_24-10_S12_L001]


title: A2783

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

data_processing:
Cell Ranger pipeline v6.1
Seurat package (version 4.1.0)
DoubletFinder package (version 2.0)
Assembly: mm10
Supplementary files format and content: The processed data file is a big matrix of SCT normalized gene expression features for high-quality cells. Each row is a gene and each column represents a barcode (cell). All samples are combined in one matrix.

source_name: brain

extract_protocol:
Mice were perfused with cold PBS, and half of each brain tissue, excluding olfactory and cerebellum, were immediately dissected and dissociated using Neural Tissue Dissociation Kit (P) (Miltenyi). Myelin was removed after tissue dissociation using Myelin Removal Beads II (Miltenyi). Dead Cell Removal Kit (Miltenyi, USA) was applied to dead cells and debris.
Libraries were prepared using the Chromium Next GEM Single Cell 3’ Kit v3.1 and Chip G Single Cell Kit (10x Genomics, USA) according to manufacturer’s protocol.

value: brain

value: APP/PS +

value: S. aureus


title: A2806


title: normal tissue2


title: A2780


title: Ovarian follicle treated with 10ng/ml FSH21 [4_21-10_S11_L004]

value: 10ng/ml FSH21


title: scRNAseq, mouse, Calvaria, MCAo, rep2


title: normal tissue10


title: A2814

value: PBS


title: mouse, bulk, Calvaria, Naive, donorN3

description:
X23L000376
bulk_rna_raw_counts.tsv

value: Naive


title: scRNAseq, mouse, Brain, Sham, rep1

value: Brain

value: Sham


title: Ovarian follicle treated with 10ng/ml FSH21 [4_21-10_S11_L003]

value: Ovarian follicle


title: mouse, bulk, Calvaria, Naive, donorN2

description:
X23L000375
bulk_rna_raw_counts.tsv

value: Calvaria, bone marrow


title: scRNAseq, mouse, Scapula, Sham, rep1

value: Scapula, bone marrow


title: A2804


title: bladder carcinoma tissue9

source_name: bladder carcinoma tissue

value: bladder carcinoma tissue


title: Ovarian follicle treated with 10ng/ml FSH21 [4_21-10_S11_L002]


title: normal tissue1

value: normal tissue


title: A2779


title: scRNAseq, mouse, Humerus, Sham, rep1

value: Humerus, bone marrow

value: wildtype


title: bladder carcinoma tissue8


title: scRNAseq, mouse, Vertebra, Sham, rep1

value: Vertebra, bone marrow


title: scRNAseq, mouse, Pelvis, MCAo, rep2

value: Pelvis, bone marrow

value: MCAo


title: Ovarian follicle with control (FSH-) [3_NT_S7_L004]

value: control (FSH-)


title: Ovarian follicle with control (FSH-) [3_NT_S7_L003]


title: A2597

data_processing:
FASTQ TO BAM
FEATURECOUNTS
EDGER
Assembly: mm10
Supplementary files format and content: Statistical analysis was carried out using Rsubread(Liao et al., 2019) (v1.34.2), DEseq2(Love et al., 2014) (1.24.0), and EdgeR(Robinson et al., 2010) (v3.26.5), in R environment (v3.6.0). The processed data file is an excel sheet contains the logCPM of each sample as well as the comparison between groups. All samples are merged into one table and colored according to treatment group and sex.

source_name: brain, cortex

extract_protocol:
mRNA were isolated from the mouse brain cortex using Rneasy mini kit (Qiagen), and RNA quality was assessed using 2100 Bioanalyzer (Agilent).
After RNA isolation, concentration was measured with a Qubit 3.0 Fluorometer (Thermofisher) before quality assessment with the 2100 Bioanalyzer instrument (Agilent Technologies). Sequencing libraries were generated using mRNA Library Prep Reagent set (Illumina) as previously described.

value: brain, cortex

value: APP/PS +

value: S. aureus


title: Ovarian follicle with control (FSH-) [3_NT_S7_L002]

source_name: Ovarian follicle


title: bladder carcinoma tissue7


title: Ovarian follicle with control (FSH-) [3_NT_S7_L001]


title: A2587


title: scRNAseq, mouse, Calvaria, Sham, rep1


title: scRNAseq, mouse, Pelvis, Sham, rep1


title: bladder carcinoma tissue5


title: Ovarian follicle treated with 10ng/ml FSH24 [3_24-10_S9_L004]

value: 10ng/ml FSH24


title: Ovarian follicle treated with 10ng/ml FSH21 [4_21-10_S11_L001]

value: 10ng/ml FSH21


title: scRNAseq, mouse, Femur, Sham, rep1

value: Femur, bone marrow

value: Sham


title: bladder carcinoma tissue6


title: bladder carcinoma tissue37


title: Ovarian follicle treated with 10ng/ml FSH24 [3_24-10_S9_L003]

value: Ovarian follicle


title: A2776

value: brain

value: PBS


title: scRNAseq, mouse, Scapula, MCAo, rep1

value: Scapula, bone marrow


title: bladder carcinoma tissue4

value: bladder carcinoma tissue


title: A2585


title: Ovarian follicle treated with 10ng/ml FSH24 [3_24-10_S9_L002]


title: bladder carcinoma tissue38


title: scRNAseq, mouse, Meninges, Sham, rep1

value: Meninges

value: wildtype


title: A2584


title: A2595


title: bladder carcinoma tissue36


title: Ovarian follicle treated with 10ng/ml FSH24 [3_24-10_S9_L001]


title: scRNAseq, mouse, Humerus, MCAo, rep1

value: Humerus, bone marrow


title: bladder carcinoma tissue35


title: scRNAseq, mouse, Vertebra, MCAo, rep1

value: Vertebra, bone marrow

value: MCAo


title: A2588

value: brain, cortex


title: A2581

value: APP/PS +


title: scRNAseq, mouse, Femur, MCAo, rep1


title: A2568

value: S. aureus


title: A2578


title: scRNAseq, mouse, Brain, MCAo, rep1

value: Brain


title: bladder carcinoma tissue33


title: scRNAseq, mouse, Calvaria, MCAo, rep1

value: Calvaria, bone marrow


title: Ovarian follicle treated with 10ng/ml FSH21 [3_21-10_S8_L001]

value: 10ng/ml FSH21


title: A2586


title: Ovarian follicle treated with 10ng/ml FSH21 [3_21-10_S8_L004]


title: A2582


title: Ovarian follicle with control (FSH-) [2_NT_S4_L004]

value: control (FSH-)


title: scRNAseq, mouse, Pelvis, MCAo, rep1

value: Pelvis, bone marrow


title: scRNAseq, mouse, Meninges, MCAo, rep1


title: bladder carcinoma tissue31


title: bladder carcinoma tissue30


title: Ovarian follicle treated with 10ng/ml FSH21 [3_21-10_S8_L002]

value: Ovarian follicle


title: bladder carcinoma tissue34


title: bladder carcinoma tissue3


title: Ovarian follicle with control (FSH-) [2_NT_S4_L002]


title: bladder carcinoma tissue29


title: A2564


title: Ovarian follicle treated with 10ng/ml FSH21 [3_21-10_S8_L003]


title: Ovarian follicle with control (FSH-) [2_NT_S4_L003]


title: H3

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Assembly: ensembl_danio_rerio_grcz11_gca_000002035_4
Supplementary files format and content: Low vs. control excel files containing read count, fpkm, log2 fold change, p-value
Supplementary files format and content: High versus control excel files containing read count, fpkm, log2 fold change, p-value

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library"
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencing was performed by Novogene.

value: larvae

value: HighDose broflanilide


title: H2


title: bladder carcinoma tissue32

value: bladder carcinoma tissue


title: H1


title: A2583


title: bladder carcinoma tissue28


title: Ovarian follicle with control (FSH-) [2_NT_S4_L001]


title: A2561


title: Ovarian follicle treated with 10ng/ml FSH24 [2_24-10_S6_L004]

value: 10ng/ml FSH24


title: A2552


title: L1

value: Low dose broflanilide


title: Ovarian follicle treated with 10ng/ml FSH24 [2_24-10_S6_L003]


title: L4


title: bladder carcinoma tissue27


title: A2548


title: bladder carcinoma tissue26


title: A2545

value: PBS


title: L2


title: A2547


title: Ovarian follicle treated with 10ng/ml FSH24 [2_24-10_S6_L002]


title: A2591


title: A2544


title: L3


title: C4

value: Control


title: Ovarian follicle treated with 10ng/ml FSH21 [2_21-10_S5_L004]


title: bladder carcinoma tissue24


title: bladder carcinoma tissue25


title: bladder carcinoma tissue23


title: Ovarian follicle treated with 10ng/ml FSH21 [2_21-10_S5_L003]


title: Ovarian follicle treated with 10ng/ml FSH24 [2_24-10_S6_L001]


title: C3


title: bladder carcinoma tissue22


title: A2540


title: A2556


title: C5


title: Ovarian follicle treated with 10ng/ml FSH21 [2_21-10_S5_L002]


title: bladder carcinoma tissue21


title: C2


title: A2324


title: Ovarian follicle treated with 10ng/ml FSH21 [2_21-10_S5_L001]


title: Ovarian follicle with control (FSH-) [1_NT_S1_L004]


title: C1


title: bladder carcinoma tissue20


title: bladder carcinoma tissue2


title: A2309


title: Ovarian follicle with control (FSH-) [1_NT_S1_L002]


title: bladder carcinoma tissue18


title: bladder carcinoma tissue19


title: bladder carcinoma tissue16


title: A2303


title: A2294


title: Ovarian follicle with control (FSH-) [1_NT_S1_L001]


title: bladder carcinoma tissue17


title: A2305


title: A2285


title: Ovarian follicle treated with 1ng/ml FSH24 [1_24-1_S3_L004]

value: 1ng/ml FSH24


title: Ovarian follicle treated with 1ng/ml FSH24 [1_24-1_S3_L003]


title: bladder carcinoma tissue15


title: A2284

value: brain, cortex


title: Ovarian follicle treated with 1ng/ml FSH24 [1_24-1_S3_L002]


title: Ovarian follicle with control (FSH-) [1_NT_S1_L003]


title: bladder carcinoma tissue14


title: A2278

value: APP/PS +


title: Ovarian follicle treated with 1ng/ml FSH24 [1_24-1_S3_L001]


title: bladder carcinoma tissue13


title: IVO MII-2

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

data_processing:
Raw reads of the RNA-seq data were trimmed using fastp with default parameters.
Quality control was performed using the trimmed reads with fastqc.
The remaining clean reads was aligned to the reference genome using bowtie2.
Then, the resulted SAM files were converted to BAM files and indexed using samtools.
The raw counts of each sample were obtained using featureCounts with default parameters.
Assembly: macFas5
Supplementary files format and content: A txt file containing the counts of the total raw counts of each sample

organism: Macaca fascicularis

source_name: oocyte, stripped, rep2

extract_protocol:
The oocytes were lysed in 72℃ and then put back on ice. Then the samples were spined down and reverse transcribed to cDNA based on polyA tail. Switch the template at 5’ end of the RNA and amplify the full-length cDNA by PCR. Quality control of the amplification products were performed using Agilent 2100 bioanalyzer instrument.  The library was constructed following the Tagmentation-based library construction protocol. The double stranded PCR products were purified using the Agencourt AMPure XP-Medium kit and quantified by Agilent 2100 bioanalyzer. Next, the DNA were heat denatured and circularized by the split oligo sequence. The qualified single strand circle DNA were formatted as the final library. Finally, the library was amplified to make DNA nanoballs (DNB) which were loaded into the patterned nanoarray and the reads of paired-end 100 bases were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS).
The library construction method and sequencing process are carried out according to the following steps:   1. Take appropriate amount of total RNA samples, and add oligo-dT reverse transcription primer and denature the total RNA sample by heat;  2. Add the reverse mix reagent, and reverse transcribed to first-strand cDNA by SMART amplification technology;  3. Synthesize the second-strand cDNA，and use magnetic beads to purify the cDNA, and validate the cDNA;  4. The qualified double stranded cDNA，were used to construct the library with transposase;  5. The library was qualified by the Agilent Technologies 2100 bioanalyzer;  6. The library was circularized;  7. Sequencing: The library was amplified to make DNA nanoball (DNB) and sequenced on DNBSEQ platform.
DNBSEQ Low Input Single Cell Smart-Seq Eukaryotic mRNA library

value: oocyte

value: in vivo matured MII

value: wild type

value: non-treatment


title: IVO MII-1

source_name: oocyte, stripped, rep1


title: A2262


title: Ovarian follicle treated with 1ng/ml FSH21 [1_21-1_S2_L004]

value: 1ng/ml FSH21


title: IVM MII-2

value: in vitro matured MII


title: Ovarian follicle treated with 1ng/ml FSH21 [1_21-1_S2_L003]

value: Ovarian follicle


title: A2261


title: bladder carcinoma tissue12


title: bladder carcinoma tissue11


title: IVM MII-1


title: A2299


title: FB-area_Fiboblasts_patient1

city: Kashihara

first: Toshihiro

last: Ito

state: Nara

address: 840 Shijo-cho

country: Japan

institute: Nara Medical University

description:
Sample1F
Gene expression in fibroblasts from fibrotic area in patient 1.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software Ver.11.5.1.1 (Sample 1N,1F,2N,2F) and Ver. 12.1.1.1 (Sample 3N, 3F) (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Fibroblasts from fibrotic area in patient 1

label_protocol: For cRNA amplification and labeling, Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) were used following the manufacturer’s instructions.

growth_protocol: Human lung samples were collected from lung cancer patients with IPF who underwent curative surgical resection. Non-fibrotic and fibrotic areas without lung cancer in resected lung samples, which were determined under thin-section computed tomography, were minced into 0.5 mm2 pieces with a razor blade and the dispersed tissue pieces in DMEM with 15% heat-inactivated fetal bovine serum  and antibiotics (penicillin, streptomycin, and amphotericin B) at 37°C in a 10% CO2 incubator. Adherent cells were serially passaged a total of five times to yield pure populations of lung fibroblasts.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) in accordance with the manufacturers’ instructions. RNA was quantified using a NanoDrop One spectrophotometer (Thermo Fisher Scientific) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fibroblasts were cultured in in DMEM with 15% heat-inactivated FBS and antibiotics (penicillin, streptomycin, and amphotericin B).

tag: diagnosis

value: Idiopathic pulmonary fibrosis (IPF)

value: Lung fibroblasts from fibrotic area


title: A2258


title: FB-area_Fiboblasts_patient3

description:
Sample3F
Gene expression in fibroblasts from fibrotic area in patient 3.

source_name: Fibroblasts from fibrotic area in patient 3


title: FB-area_Fiboblasts_patient2

description:
Sample2F
Gene expression in fibroblasts from fibrotic area in patient 2.

source_name: Fibroblasts from fibrotic area in patient 2


title: Non-FB-area_Fiboblasts_patient3

description:
Sample3N
Gene expression in fibroblasts from non-fibrotic area in patient 3.

source_name: Fibroblasts from non-fibrotic area in patient 3

value: Lung fibroblasts from non-fibrotic area


title: Ovarian follicle treated with 1ng/ml FSH21 [1_21-1_S2_L002]


title: A2257


title: bladder carcinoma tissue10

value: bladder carcinoma tissue


title: Non-FB-area_Fiboblasts_patient2

description:
Sample2N
Gene expression in fibroblasts from non-fibrotic area in patient 2.

source_name: Fibroblasts from non-fibrotic area in patient 2


title: Non-FB-area_Fiboblasts_patient1

description:
Sample1N
Gene expression in fibroblasts from non-fibrotic area in patient 1.

source_name: Fibroblasts from non-fibrotic area in patient 1


title: bladder carcinoma tissue1


title: A2254


title: GV-1

value: GV


title: GV-2


title: Ovarian follicle treated with 1ng/ml FSH21 [1_21-1_S2_L001]


title: ntESC, CASP, female, line4

status: Public on Jul 14 2023

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

description: TruSeq standed mRNA

data_processing:
Low quality reads and adapters were removed with fastp (0.22.0).
Retained reads were aligned to the reference mouse genome (GRCm38) using HISAT2 (2.2.1).
Read count data was obtained with StringTie (2.1.7).
The count data was normalized to CPM values with EdgeR.
Assembly: GRCm38
Supplementary files format and content: Counts_Data, Normalized_Data

organism: Mus musculus castaneus

growth_protocol: NtESCs were established and maintained by 2i/LIF method on feeder. Cells were cultured at 37C at 5% CO2

extract_protocol: Total RNA was extracted by RNeasy Mini Kit. The library was prepared with TruSeq standed mRNA Library Prep Kit.

value: CASP

value: ntESC

value: SCNT

value: female


title: ntESC, CASP, female, line6

description: TruSeq standed mRNA


title: ntESC, CAST, female, line2

description: TruSeq standed mRNA

value: CAST


title: Fibro, CAST

description: TruSeq standed mRNA

value: Fibro

value: WT


title: ntESC, CASP, male, line3

description: TruSeq standed mRNA

value: male


title: ntESC, CAST, male, line2

description: TruSeq standed mRNA


title: ntESC, CAST, female, line1

description: TruSeq standed mRNA


title: ntESC, CASP, male, line5

description: TruSeq standed mRNA


title: ntESC, CAST, male, line8

description: TruSeq standed mRNA


title: dsHR96-LBD-1 on tomato rep 3

city: Gent

first: Marilou

last: Vandenhole

address: Coupure links 653

department: Department of Plants and Crops

country: Belgium

institute: UGent

data_processing:
Reads were aligned to the genome with STAR (version 2.7.3a)
BAM files were sorted with samtools (version 1.9).
Raw read counts were obtained with htseq-count (version 2.0.1) using the Tetranychus_urticae_2022_12 genome annotation.
Assembly: Bulk segregant analysis scaffolded Tetranychus urticae reference genome reported by Wybouw et al. 2019 (GENETICS; 211: 1409–1427: doi: 10.1534/genetics.118.301803).
Supplementary files format and content: Processed data files consist of raw read counts per sample (from htseq-count output).

organism: Tetranychus urticae

source_name: whole organism

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using IlluminaTruseq stranded mRNA library prep (carried out at Fasteris, Switzerland)

value: whole organism

value: Near isogenic line B-NIL-HS1(RR)

value: Grown on tomato (Solanum lycopersicum) as host plant, injection with dsHR96-LBD-1


title: dsGFP on bean rep 4

value: Grown on bean (Phaseolus vulgaris) as host plant, injection with dsGFP


title: dsGFP on bean rep 1


title: dsHR96-LBD-1 on tomato rep 2


title: dsGFP on tomato rep 1

value: Grown on tomato (Solanum lycopersicum) as host plant, injection with dsGFP


title: dsHR96-LBD-1 on bean rep 5

value: Grown on bean (Phaseolus vulgaris) as host plant, injection with dsHR96-LBD-1


title: dsHR96-LBD-1 on bean rep 4


title: dsHR96-LBD-1 on tomato rep 1


title: dsGFP on bean rep 3


title: dsGFP on tomato rep 4


title: dsGFP on tomato rep 2


title: dsGFP on bean rep 2


title: dsGFP on tomato rep 3


title: dsHR96-LBD-1 on bean rep 2


title: dsHR96-LBD-1 on bean rep 3


title: dsGFP on bean rep 5


title: B-NIL-HS1(F1)-5

value: F1 of cross between near isogenic lines B-NIL-HS1(RR) and B-NIL-HS1(SS)

value: Grown on bean (Phaseolus vulgaris) as host plant


title: dsHR96-LBD-1 on tomato rep 4


title: dsHR96-LBD-1 on bean rep 1


title: B-NIL-HS1(F1)-4


title: B-NIL-HS1(F1)-3


title: B-NIL-HS1(F1)-2


title: A-NIL-HS1(F1)-3

value: F1 of cross between near isogenic lines A-NIL-HS1(RR) and A-NIL-HS1(SS)


title: A-NIL-HS1(F1)-2


title: A-NIL-HS1(F1)-1


title: A-NIL-HS1(F1)-4


title: A-NIL-HS1(F1)-5


title: B-NIL-HS1(SS)-5

value: Near isogenic line B-NIL-HS1(SS)


title: B-NIL-HS1(SS)-4


title: B-NIL-HS1(SS)-3


title: B-NIL-HS1(SS)-2


title: B-NIL-HS1(RR)-1


title: B-NIL-HS1(RR)-2


title: B-NIL-HS1(RR)-3


title: B-NIL-HS1(SS)-1


title: B-NIL-HS1(RR)-5


title: A-NIL-HS1(RR)-3

value: Near isogenic line A-NIL-HS1(RR)


title: A-NIL-HS1(RR)-5


title: A-NIL-HS1(SS)-1

value: Near isogenic line A-NIL-HS1(SS)


title: A-NIL-HS1(RR)-2


title: A-NIL-HS1(SS)-2


title: A-NIL-HS1(RR)-4


title: F3 sample 456

value: F3 eQTL population sample 456


title: F3 sample 457

value: F3 eQTL population sample 457


title: A-NIL-HS1(RR)-1


title: A-NIL-HS1(SS)-5


title: B-NIL-HS1(F1)-1


title: F3 sample 450

value: F3 eQTL population sample 450


title: F3 sample 452

value: F3 eQTL population sample 452


title: A-NIL-HS1(SS)-3


title: A-NIL-HS1(SS)-4


title: B-NIL-HS1(RR)-4


title: F3 sample 455

value: F3 eQTL population sample 455


title: F3 sample 449

value: whole organism

value: F3 eQTL population sample 449


title: F3 sample 453

value: F3 eQTL population sample 453


title: F3 sample 448

value: F3 eQTL population sample 448


title: F3 sample 454

value: F3 eQTL population sample 454


title: F3 sample 447

value: F3 eQTL population sample 447


title: F3 sample 445

value: F3 eQTL population sample 445


title: F3 sample 446

value: F3 eQTL population sample 446

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 444

value: F3 eQTL population sample 444


title: F3 sample 441

value: F3 eQTL population sample 441


title: F3 sample 443

value: F3 eQTL population sample 443


title: F3 sample 442

value: F3 eQTL population sample 442


title: F3 sample 458

value: F3 eQTL population sample 458


title: F3 sample 451

value: F3 eQTL population sample 451


title: F3 sample 439

value: F3 eQTL population sample 439


title: F3 sample 440

value: F3 eQTL population sample 440


title: F3 sample 434

value: whole organism

value: F3 eQTL population sample 434


title: F3 sample 428

value: F3 eQTL population sample 428


title: F3 sample 426

value: F3 eQTL population sample 426


title: F3 sample 430

value: F3 eQTL population sample 430


title: F3 sample 437

value: F3 eQTL population sample 437


title: F3 sample 431

value: F3 eQTL population sample 431


title: F3 sample 432

value: F3 eQTL population sample 432


title: F3 sample 438

value: F3 eQTL population sample 438

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 429

value: F3 eQTL population sample 429


title: F3 sample 433

value: F3 eQTL population sample 433


title: F3 sample 427

value: F3 eQTL population sample 427


title: F3 sample 435

value: F3 eQTL population sample 435


title: F3 sample 423

value: F3 eQTL population sample 423


title: F3 sample 436

value: F3 eQTL population sample 436


title: F3 sample 420

value: F3 eQTL population sample 420


title: F3 sample 425

value: whole organism

value: F3 eQTL population sample 425


title: F3 sample 422

value: F3 eQTL population sample 422


title: F3 sample 424

value: F3 eQTL population sample 424


title: F3 sample 421

value: F3 eQTL population sample 421


title: F3 sample 419

value: F3 eQTL population sample 419


title: F3 sample 415

value: F3 eQTL population sample 415


title: F3 sample 411

value: F3 eQTL population sample 411


title: F3 sample 407

value: F3 eQTL population sample 407


title: F3 sample 418

value: F3 eQTL population sample 418

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 416

value: F3 eQTL population sample 416


title: F3 sample 414

value: F3 eQTL population sample 414


title: F3 sample 413

value: F3 eQTL population sample 413


title: F3 sample 417

value: F3 eQTL population sample 417


title: F3 sample 412

value: F3 eQTL population sample 412


title: F3 sample 409

value: F3 eQTL population sample 409


title: F3 sample 408

value: whole organism

value: F3 eQTL population sample 408


title: F3 sample 406

value: F3 eQTL population sample 406


title: F3 sample 399

value: F3 eQTL population sample 399


title: F3 sample 410

value: F3 eQTL population sample 410


title: F3 sample 396

value: F3 eQTL population sample 396


title: F3 sample 405

value: F3 eQTL population sample 405


title: F3 sample 389

value: F3 eQTL population sample 389


title: F3 sample 404

value: F3 eQTL population sample 404


title: F3 sample 401

value: F3 eQTL population sample 401


title: F3 sample 400

value: F3 eQTL population sample 400

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 386

value: F3 eQTL population sample 386


title: F3 sample 398

value: F3 eQTL population sample 398


title: F3 sample 402

value: F3 eQTL population sample 402


title: F3 sample 397

value: F3 eQTL population sample 397


title: F3 sample 403

value: F3 eQTL population sample 403


title: F3 sample 395

value: whole organism

value: F3 eQTL population sample 395


title: F3 sample 394

value: F3 eQTL population sample 394


title: F3 sample 383

value: F3 eQTL population sample 383


title: F3 sample 382

value: F3 eQTL population sample 382


title: F3 sample 384

value: F3 eQTL population sample 384


title: F3 sample 393

value: F3 eQTL population sample 393


title: F3 sample 392

value: F3 eQTL population sample 392


title: F3 sample 388

value: F3 eQTL population sample 388


title: F3 sample 390

value: F3 eQTL population sample 390


title: F3 sample 376

value: F3 eQTL population sample 376


title: F3 sample 375

value: F3 eQTL population sample 375

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 374

value: F3 eQTL population sample 374


title: F3 sample 377

value: F3 eQTL population sample 377


title: F3 sample 391

value: F3 eQTL population sample 391


title: F3 sample 381

value: F3 eQTL population sample 381


title: F3 sample 371

value: whole organism

value: F3 eQTL population sample 371


title: F3 sample 373

value: F3 eQTL population sample 373


title: F3 sample 366

value: F3 eQTL population sample 366


title: F3 sample 372

value: F3 eQTL population sample 372


title: F3 sample 363

value: F3 eQTL population sample 363


title: F3 sample 368

value: F3 eQTL population sample 368


title: F3 sample 367

value: F3 eQTL population sample 367


title: F3 sample 369

value: F3 eQTL population sample 369


title: F3 sample 370

value: F3 eQTL population sample 370


title: F3 sample 361

value: F3 eQTL population sample 361


title: F3 sample 387

value: F3 eQTL population sample 387


title: F3 sample 360

value: F3 eQTL population sample 360

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 364

value: F3 eQTL population sample 364


title: F3 sample 385

value: F3 eQTL population sample 385


title: F3 sample 358

value: F3 eQTL population sample 358


title: F3 sample 362

value: whole organism

value: F3 eQTL population sample 362


title: F3 sample 355

value: F3 eQTL population sample 355


title: F3 sample 365

value: F3 eQTL population sample 365


title: F3 sample 356

value: F3 eQTL population sample 356


title: F3 sample 357

value: F3 eQTL population sample 357


title: F3 sample 354

value: F3 eQTL population sample 354


title: F3 sample 352

value: F3 eQTL population sample 352


title: F3 sample 353

value: F3 eQTL population sample 353


title: F3 sample 379

value: F3 eQTL population sample 379


title: F3 sample 380

value: F3 eQTL population sample 380


title: F3 sample 349

value: F3 eQTL population sample 349


title: F3 sample 359

value: F3 eQTL population sample 359


title: F3 sample 346

value: F3 eQTL population sample 346

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 348

value: F3 eQTL population sample 348


title: F3 sample 344

value: F3 eQTL population sample 344


title: F3 sample 351

value: whole organism

value: F3 eQTL population sample 351


title: F3 sample 342

value: F3 eQTL population sample 342


title: F3 sample 340

value: F3 eQTL population sample 340


title: F3 sample 339

value: F3 eQTL population sample 339


title: F3 sample 335

value: F3 eQTL population sample 335


title: F3 sample 337

value: F3 eQTL population sample 337


title: F3 sample 338

value: F3 eQTL population sample 338


title: F3 sample 334

value: F3 eQTL population sample 334


title: F3 sample 350

value: F3 eQTL population sample 350


title: F3 sample 332

value: F3 eQTL population sample 332


title: F3 sample 331

value: F3 eQTL population sample 331


title: F3 sample 327

value: F3 eQTL population sample 327


title: F3 sample 325

value: F3 eQTL population sample 325


title: F3 sample 326

value: F3 eQTL population sample 326

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 328

value: F3 eQTL population sample 328


title: F3 sample 323

value: whole organism

value: F3 eQTL population sample 323


title: F3 sample 347

value: F3 eQTL population sample 347


title: F3 sample 330

value: F3 eQTL population sample 330


title: F3 sample 345

value: F3 eQTL population sample 345


title: F3 sample 324

value: F3 eQTL population sample 324


title: F3 sample 343

value: F3 eQTL population sample 343


title: F3 sample 321

value: F3 eQTL population sample 321


title: F3 sample 378

value: F3 eQTL population sample 378


title: F3 sample 320

value: F3 eQTL population sample 320


title: F3 sample 319

value: F3 eQTL population sample 319


title: F3 sample 336

value: F3 eQTL population sample 336


title: F3 sample 322

value: F3 eQTL population sample 322


title: F3 sample 341

value: F3 eQTL population sample 341


title: F3 sample 318

value: F3 eQTL population sample 318


title: F3 sample 312

value: F3 eQTL population sample 312

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 314

value: whole organism

value: F3 eQTL population sample 314


title: F3 sample 313

value: F3 eQTL population sample 313


title: F3 sample 333

value: F3 eQTL population sample 333


title: F3 sample 311

value: F3 eQTL population sample 311


title: F3 sample 329

value: F3 eQTL population sample 329


title: F3 sample 310

value: F3 eQTL population sample 310


title: F3 sample 309

value: F3 eQTL population sample 309


title: F3 sample 307

value: F3 eQTL population sample 307


title: F3 sample 308

value: F3 eQTL population sample 308


title: F3 sample 305

value: F3 eQTL population sample 305


title: F3 sample 304

value: F3 eQTL population sample 304


title: F3 sample 301

value: F3 eQTL population sample 301


title: F3 sample 302

value: F3 eQTL population sample 302


title: F3 sample 300

value: F3 eQTL population sample 300


title: F3 sample 297

value: F3 eQTL population sample 297


title: F3 sample 317

value: F3 eQTL population sample 317

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 315

value: whole organism

value: F3 eQTL population sample 315


title: F3 sample 298

value: F3 eQTL population sample 298


title: F3 sample 299

value: F3 eQTL population sample 299


title: F3 sample 316

value: F3 eQTL population sample 316


title: F3 sample 294

value: F3 eQTL population sample 294


title: F3 sample 296

value: F3 eQTL population sample 296


title: F3 sample 291

value: F3 eQTL population sample 291


title: F3 sample 293

value: F3 eQTL population sample 293


title: F3 sample 292

value: F3 eQTL population sample 292


title: F3 sample 289

value: F3 eQTL population sample 289


title: F3 sample 285

value: F3 eQTL population sample 285


title: F3 sample 286

value: F3 eQTL population sample 286


title: F3 sample 288

value: F3 eQTL population sample 288


title: F3 sample 283

value: F3 eQTL population sample 283


title: F3 sample 284

value: F3 eQTL population sample 284


title: F3 sample 306

value: F3 eQTL population sample 306

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 282

value: whole organism

value: F3 eQTL population sample 282


title: F3 sample 303

value: F3 eQTL population sample 303


title: F3 sample 281

value: F3 eQTL population sample 281


title: F3 sample 280

value: F3 eQTL population sample 280


title: F3 sample 279

value: F3 eQTL population sample 279


title: F3 sample 276

value: F3 eQTL population sample 276


title: F3 sample 295

value: F3 eQTL population sample 295


title: F3 sample 278

value: F3 eQTL population sample 278


title: F3 sample 274

value: F3 eQTL population sample 274


title: F3 sample 273

value: F3 eQTL population sample 273


title: F3 sample 272

value: F3 eQTL population sample 272


title: F3 sample 270

value: F3 eQTL population sample 270


title: F3 sample 269

value: F3 eQTL population sample 269


title: F3 sample 268

value: F3 eQTL population sample 268


title: F3 sample 271

value: F3 eQTL population sample 271


title: F3 sample 267

value: F3 eQTL population sample 267

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 265

value: whole organism

value: F3 eQTL population sample 265


title: F3 sample 266

value: F3 eQTL population sample 266


title: F3 sample 287

value: F3 eQTL population sample 287


title: F3 sample 290

value: F3 eQTL population sample 290


title: F3 sample 264

value: F3 eQTL population sample 264


title: F3 sample 263

value: F3 eQTL population sample 263


title: F3 sample 262

value: F3 eQTL population sample 262


title: F3 sample 257

value: F3 eQTL population sample 257


title: F3 sample 261

value: F3 eQTL population sample 261


title: F3 sample 258

value: F3 eQTL population sample 258


title: F3 sample 260

value: F3 eQTL population sample 260


title: F3 sample 259

value: F3 eQTL population sample 259


title: F3 sample 256

value: F3 eQTL population sample 256


title: F3 sample 255

value: F3 eQTL population sample 255


title: F3 sample 277

value: F3 eQTL population sample 277


title: F3 sample 254

value: F3 eQTL population sample 254

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 253

value: whole organism

value: F3 eQTL population sample 253


title: F3 sample 252

value: F3 eQTL population sample 252


title: F3 sample 251

value: F3 eQTL population sample 251


title: F3 sample 250

value: F3 eQTL population sample 250


title: F3 sample 248

value: F3 eQTL population sample 248


title: F3 sample 249

value: F3 eQTL population sample 249


title: F3 sample 245

value: F3 eQTL population sample 245


title: F3 sample 244

value: F3 eQTL population sample 244


title: F3 sample 247

value: F3 eQTL population sample 247


title: F3 sample 246

value: F3 eQTL population sample 246


title: F3 sample 243

value: F3 eQTL population sample 243


title: F3 sample 242

value: F3 eQTL population sample 242


title: F3 sample 240

value: F3 eQTL population sample 240


title: F3 sample 241

value: F3 eQTL population sample 241


title: F3 sample 237

value: F3 eQTL population sample 237