title: ND3_LD rep1

city: Southampton

first: Rosanna

last: Smith

address: Centre for Cancer Immunology, University Hospital Southampton (MP 127), Tremona Road

institute: University of Southampton

description: Primary human monocytes - Donor 3

data_processing:
Unmapped bam files were converted to separate read1 and read2 fastqs using samtools fastq v1.3.1.
Reads were aligned to the human genome (GRCh38) using Hisat2 (v2.1.0) and the non-default parameter --no-spliced-alignment
Peaks were called for each sample separately using macs2 (v2.2.1) callpeak  function with non-default parameters --nomodel --shift -100 --extsize 200 -B --broad.
Genome_build: GRCh38 (primary assembly).
Supplementary_files_format_and_content: ENCODE broadPeak (BED 6+3) file for each sample

source_name: Primary human monocytes

growth_protocol: PBMCs were sourced from 3 healthy adult human donors. Primary human monocytes were isolated using the Pan Monocyte Isolation Kit, human (Miltenyi Biotech) from 1x10^8 PBMCs per isolation, according to the manufacturer’s protocol. These monocytes were then cultured at low density (LD) defined as 1 x 10^6 cells/mL or at high density (HD) defined as 1 x10^7 cells/mL, in serum free complete CTL-Test Medium ((Europe GmbH, Bonn, Germany), supplemented with glutamine (2 mM), pyruvate (1 mM), penicillin (100 IU/mL), and streptomycin (100 IU/mL)), at 37°C in 5% CO2. 1.5 mL of cells at the aforementioned concentrations were cultured in flat bottomed 24-well plates (Corning Centristar) for 24 hours.

extract_protocol:
50,000 monocytes per sample were harvested 24 hours post-culture. Cells were centrifuged at 300 xg for 5 minutes at 4°C and each sample resuspended in a transposase reaction mix (12.5 μL 2x TD buffer, 2 μL TDE1 (Illumina)), 10.25 μL nuclease-free water and 0.25 μl 1% digitonin (Sigma-Aldrich) and incubated for 30 minutes at 37°C. 1 μL of eluted DNA from each sample was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles for library amplification.
Each sample library was amplified for the number of cycles corresponding to the test qPCR Cq value, using custom Nextera primers (Buenrostro et al., Nat Methods 10, 1213–1218, 2013). Library amplification was followed by Solid Phase Reversible Immobilization (SPRI, Beckman Coulter) size selection to exclude fragments >1,200 bp. Single-end, 50bp sequencing was carried out on an Illumina HiSeq 3000/4000 instrument  by the Biomedical Sequencing Facility at CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences.

tag: donor

tag: initial culture density

value: 1x10^6 cells/mL (LD)


title: MIHCF 13

status: Public on Apr 13 2022

type: SRA

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

library_source: genomic

data_processing:
Library strategy: 16S rDNA
Illumina HiSeq software used for basecalling.
Take the method of removing low quality by window, the specific operation is as follows: set a window of 25 bp, if the average quality value of the window is less than 20, the back-end bases will be truncated from the window; the read length after truncation is lower than the original read length For 75%, remove the entire sequence.
Remove linker contamination of reads (default adapter sequence and read sequence have an overlap of 15 bp, set to 15 bp, and allow the number of mismatches to be 3);
Remove reads containing N;Remove low-complexity reads (default reads with continuous base length ≥10 are low-complexity reads) finally, get the Cleandata
Splice the reads into tags through the overlap relationship between the reads; cluster the tags into OTUs and compare them with the database, and annotate species; based on the OTU and annotation results, perform sample species complexity analysis, analysis of species differences between groups, and association analysis. Model prediction, etc.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

molecule: genomic DNA

organism: Mus musculus

source_name: small intestinal

extract_protocol:
small intestinal were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

tag: strain

value: ICR

tag: tissue

value: small intestinal

tag: age

value: 10 weeks

tag: treatment

value: High fat diet +control-FMT


title: MIHCF 11


title: ND3_LD rep2

middle: C G

state: Hampshire

department: Cancer Sciences Unit, Faculty of Medicine

country: United Kingdom

description: Primary human monocytes - Donor 3

organism: Homo sapiens


title: ND3_HD rep2

description: Primary human monocytes - Donor 3

value: 1x10^7 cells/mL (HD)


title: XH33 15DPA Fiber rep2

city: Beijing

address: China Agricultural University Yuanmingyuan West Road 2#,Haidian District Beijing

institute: China Agricultural University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to 3-79 whole genome using HISAT v2.0.4 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: assembly 3-79

molecule: total RNA

organism: Gossypium barbadense

source_name: fiber

extract_protocol:
Total RNA was extracted from the fibers of the boll samples with an EASYspin RNA Plant Mini Kit (Cat # RN0902, Aidlab Biotechnologies., Ltd).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fiber

tag: developmental stage


title: MIHCF 7


title: MIHCF 6


title: XH33 15DPA Fiber rep3


title: MIHCF 3


title: XH33 5DPA Fiber rep1


title: XH33 10DPA Fiber rep1


title: XH33 5DPA Fiber rep2


title: ND3_HD rep1

description: Primary human monocytes - Donor 3


title: Sample62.Yellow-bellied marmot.203531420042_R02C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Blood species=Yellow-bellied marmot

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Marmota flaviventris

source_name: Blood

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

value: Blood


title: ND2_HD rep2

description: Primary human monocytes - Donor 2


title: XH33 5DPA Fiber rep3


title: MIHAF 23

value: High fat diet +AOS10mg/kg-FMT


title: Sample63.Yellow-bellied marmot.203531420042_R03C01


title: Sample66.Yellow-bellied marmot.203531420042_R06C01


title: XH33 0DPA Fiber rep3


title: MIHCF 5


title: Sample65.Yellow-bellied marmot.203531420042_R05C01


title: ND2_LD rep2

description: Primary human monocytes - Donor 2


title: Sample64.Yellow-bellied marmot.203531420042_R04C01


title: Sample61.Yellow-bellied marmot.203531420042_R01C01


title: ND2_LD rep1

description: Primary human monocytes - Donor 2


title: XH33 10DPA Fiber rep2


title: ND1_LD rep2

description: Primary human monocytes - Donor 1


title: Sample55.Yellow-bellied marmot.203531420010_R01C02


title: Sample58.Yellow-bellied marmot.203531420010_R04C02


title: Sample59.Yellow-bellied marmot.203531420010_R05C02


title: Sample56.Yellow-bellied marmot.203531420010_R02C02


title: MIHCF 1


title: ND2_HD rep1

description: Primary human monocytes - Donor 2


title: XH33 0DPA Fiber rep2


title: Sample57.Yellow-bellied marmot.203531420010_R03C02


title: Sample60.Yellow-bellied marmot.203531420010_R06C02


title: MIHAF 20


title: XH58 25DPA Fiber rep3


title: ND1_HD rep2

description: Primary human monocytes - Donor 1


title: MIHAF 18


title: XH33 0DPA Fiber rep1


title: MIHAF 17


title: XH58 20DPA Fiber rep3


title: ND1_HD rep1

description: Primary human monocytes - Donor 1


title: Sample53.Yellow-bellied marmot.203531420010_R05C01


title: XH58 25DPA Fiber rep1


title: XH58 20DPA Fiber rep1


title: MIHAF 14


title: MIHAF 15


title: Sample51.Yellow-bellied marmot.203531420010_R03C01


title: Sample54.Yellow-bellied marmot.203531420010_R06C01


title: Sample52.Yellow-bellied marmot.203531420010_R04C01


title: H_24_hrs_UNTREATED

data_processing:
Unmapped bam files were converted to separate read1 and read2 fastqs using samtools fastq v1.9.
Adapter sequencers were trimmed from sequencing reads using cutadapt v2.4.
Reads were aligned to the human genome (GRCh38) using Hisat2 (v2.1.0) and the non-default parameter --no-spliced-alignment.
Peaks were called for each sample separately using macs2 (v2.2.6) callpeak  function with non-default parameters --nomodel --call-summits.
Genome_build: GRCh38 (primary assembly)
Supplementary_files_format_and_content: ENCODE narrowPeak (BED 6+4) file for each sample

source_name: Primary human monocytes - Donor H, 24hr, untreated

growth_protocol: Anonymized leukocyte cones were sourced from healthy adult donors attending blood donation clinics at the National Blood Service (Southampton, UK). Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation (Lymphoprep, Axis-Shield). Primary human monocytes were isolated from PBMCs using the Pan Monocyte Isolation Kit, human, (Miltenyi Biotech) from 1x108 PBMCs per isolation, according to the manufacturer’s protocol and cultured at low density (1 x 106/mL in a 24-well plate) in complete CTL medium at 37°C and 5% CO2.

extract_protocol:
50,000 monocytes per sample were harvested immediately (0hr) or 2, 10, 24 hours post-culture. Cells were centrifuged at 300 xg for 5 minutes at 4°C and each sample resuspended in a transposase reaction mix (12.5 μL 2x TD buffer, 2 μL TDE1 (Illumina)), 10.25 μL nuclease-free water and 0.25 μl 1% digitonin (Sigma-Aldrich) and incubated for 30 minutes at 37°C. 1 μL of eluted DNA from each sample was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles for library amplification.
Each sample library was amplified for the number of cycles corresponding to the test qPCR Cq value, using custom Nextera primers (Buenrostro et al., Nat Methods 10, 1213–1218, 2013). Library amplification was followed by Solid Phase Reversible Immobilization (SPRI, Beckman Coulter) size selection to exclude fragments >1,200 bp. Paired-end, 75bp sequencing was carried out on an Illumina HiSeq 3000/4000 instrument  by the Biomedical Sequencing Facility at CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences.

treatment_protocol: Samples were either cultured in the absence (untreated (U)) or presence (treated (T)) of 20μM Dimethyloxalylglycine (DMOG, EMD Millipore).

value: H

tag: timepoint

value: Untreated

tag: cell type

value: Primary human monocytes


title: Sample49.Yellow-bellied marmot.203531420010_R01C01


title: Sample50.Yellow-bellied marmot.203531420010_R02C01


title: Sample48.Yellow-bellied marmot.203531420052_R06C02


title: MIHAF 2


title: H_10_hrs_TREATED

source_name: Primary human monocytes - Donor H, 10hr, DMOG treated

value: DMOG


title: ND1_LD rep1

description: Primary human monocytes - Donor 1


title: MIHAF 5


title: XH58 20DPA Fiber rep2


title: H_24_hrs_TREATED

source_name: Primary human monocytes - Donor H, 24hr, DMOG treated


title: MIHAF 4


title: MIHA10 12

value: High fat diet +AOS10mg/kg


title: XH58 15DPA Fiber rep1


title: H_2_hrs_UNTREATED

source_name: Primary human monocytes - Donor H, 2hr, untreated


title: H_2_hrs_TREATED

source_name: Primary human monocytes - Donor H, 2hr, DMOG treated


title: H_10_hrs_UNTREATED

source_name: Primary human monocytes - Donor H, 10hr, untreated


title: H_0_hrs

source_name: Primary human monocytes - Donor H, 0hr, untreated


title: XH58 15DPA Fiber rep3


title: MIHA10 9


title: XH58 25DPA Fiber rep2


title: XH58 15DPA Fiber rep2


title: MIHAF 3


title: XH58 5DPA Fiber rep3


title: Sample44.Yellow-bellied marmot.203531420052_R02C02


title: XH58 10DPA Fiber rep3


title: Sample47.Yellow-bellied marmot.203531420052_R05C02


title: Sample45.Yellow-bellied marmot.203531420052_R03C02


title: MIHA10 5


title: MIHA10 11


title: Sample41.Yellow-bellied marmot.203531420052_R05C01


title: Sample42.Yellow-bellied marmot.203531420052_R06C01


title: Sample46.Yellow-bellied marmot.203531420052_R04C02


title: MIHA10 10


title: XH58 10DPA Fiber rep2


title: G_24_hrs_UNTREATED

source_name: Primary human monocytes - Donor G, 24hr, untreated

value: G


title: Sample43.Yellow-bellied marmot.203531420052_R01C02


title: XH58 5DPA Fiber rep2


title: G_24_hrs_TREATED

source_name: Primary human monocytes - Donor G, 24hr, DMOG treated


title: XH58 10DPA Fiber rep1


title: G_10_hrs_UNTREATED

source_name: Primary human monocytes - Donor G, 10hr, untreated


title: G_10_hrs_TREATED

source_name: Primary human monocytes - Donor G, 10hr, DMOG treated


title: MIHA10 6


title: G_2_hrs_UNTREATED

source_name: Primary human monocytes - Donor G, 2hr, untreated


title: XH58 5DPA Fiber rep1


title: MIHA10 4


title: MIHA10 3


title: XH58 0DPA Fiber rep3


title: G_2_hrs_TREATED

source_name: Primary human monocytes - Donor G, 2hr, DMOG treated


title: MIHA10 2


title: MIHA10 1


title: Sample38.Yellow-bellied marmot.203531420052_R02C01


title: Sample40.Yellow-bellied marmot.203531420052_R04C01


title: Sample39.Yellow-bellied marmot.203531420052_R03C01


title: F_24_hrs_TREATED

source_name: Primary human monocytes - Donor F, 24hr, DMOG treated

value: F


title: Sample37.Yellow-bellied marmot.203531420052_R01C01


title: G_0_hrs

source_name: Primary human monocytes - Donor G, 0hr, untreated


title: MIHFD 19

source_name: small intestinal

value: High fat diet


title: XH58 0DPA Fiber rep2

source_name: fiber


title: MIHFD 20


title: Sample35.Yellow-bellied marmot.203531420092_R05C02

source_name: Blood


title: F_24_hrs_UNTREATED

source_name: Primary human monocytes - Donor F, 24hr, untreated


title: XH37 25DPA Fiber rep3


title: F_10_hrs_UNTREATED

source_name: Primary human monocytes - Donor F, 10hr, untreated


title: F_10_hrs_TREATED

source_name: Primary human monocytes - Donor F, 10hr, DMOG treated


title: MIHFD 18


title: XH37 25DPA Fiber rep2


title: Sample33.Yellow-bellied marmot.203531420092_R03C02


title: MIHFD 11


title: XH37 25DPA Fiber rep1


title: Sample36.Yellow-bellied marmot.203531420092_R06C02


title: XH37 20DPA Fiber rep2


title: Sample34.Yellow-bellied marmot.203531420092_R04C02


title: F_2_hrs_UNTREATED

source_name: Primary human monocytes - Donor F, 2hr, untreated


title: XH37 20DPA Fiber rep3


title: MIHFD 10


title: XH58 0DPA Fiber rep1


title: XH37 20DPA Fiber rep1


title: F_0_hrs

source_name: Primary human monocytes - Donor F, 0hr, untreated


title: XH37 15DPA Fiber rep3


title: E_24_hrs_TREATED

source_name: Primary human monocytes - Donor E, 24hr, DMOG treated

value: E


title: E_24_hrs_UNTREATED

source_name: Primary human monocytes - Donor E, 24hr, untreated


title: MIHFD 17

value: ICR


title: E_10_hrs_UNTREATED

source_name: Primary human monocytes - Donor E, 10hr, untreated


title: MIHFD 5

value: small intestinal


title: Sample30.Yellow-bellied marmot.203531420092_R06C01


title: XH37 15DPA Fiber rep1


title: MIHFD 1

value: 10 weeks


title: E_10_hrs_TREATED

source_name: Primary human monocytes - Donor E, 10hr, DMOG treated


title: Sample32.Yellow-bellied marmot.203531420092_R02C02


title: F_2_hrs_TREATED

source_name: Primary human monocytes - Donor F, 2hr, DMOG treated


title: XH37 10DPA Fiber rep3


title: MIcon 12

value: control


title: E_2_hrs_UNTREATED

source_name: Primary human monocytes - Donor E, 2hr, untreated


title: MIHFD 8


title: XH37 10DPA Fiber rep2


title: Sample31.Yellow-bellied marmot.203531420092_R01C02


title: E_2_hrs_TREATED

source_name: Primary human monocytes - Donor E, 2hr, DMOG treated


title: Sample29.Yellow-bellied marmot.203531420092_R05C01


title: Sample26.Yellow-bellied marmot.203531420092_R02C01


title: Sample27.Yellow-bellied marmot.203531420092_R03C01


title: MIHFD 7


title: XH37 15DPA Fiber rep2


title: XH37 10DPA Fiber rep1


title: MIcon 10


title: Sample25.Yellow-bellied marmot.203531420092_R01C01


title: XH37 5DPA Fiber rep3


title: Sample24.Yellow-bellied marmot.203531420077_R06C02


title: Sample28.Yellow-bellied marmot.203531420092_R04C01


title: MIcon 9


title: D_24_hrs_UNTREATED

source_name: Primary human monocytes - Donor D, 24hr, untreated

value: D


title: Sample23.Yellow-bellied marmot.203531420077_R05C02


title: XH37 5DPA Fiber rep2

value: fiber


title: MIcon 8


title: D_24_hrs_TREATED

source_name: Primary human monocytes - Donor D, 24hr, DMOG treated


title: MIcon 11

source_name: small intestinal


title: D_10_hrs_UNTREATED

source_name: Primary human monocytes - Donor D, 10hr, untreated


title: XH37 5DPA Fiber rep1

source_name: fiber


title: Sample22.Yellow-bellied marmot.203531420077_R04C02

source_name: Blood

value: Blood


title: XH37 0DPA Fiber rep3


title: D_10_hrs_TREATED

source_name: Primary human monocytes - Donor D, 10hr, DMOG treated


title: MIcon 5


title: XH37 0DPA Fiber rep2


title: XH37 0DPA Fiber rep1


title: MIcon 3


title: Sample21.Yellow-bellied marmot.203531420077_R03C02


title: Sample20.Yellow-bellied marmot.203531420077_R02C02


title: Sample18.Yellow-bellied marmot.203531420077_R06C01


title: Sample17.Yellow-bellied marmot.203531420077_R05C01


title: MIcon 4


title: D_2_hrs_TREATED

source_name: Primary human monocytes - Donor D, 2hr, DMOG treated


title: MIcon 2


title: Sample19.Yellow-bellied marmot.203531420077_R01C02


title: D_0_hrs

source_name: Primary human monocytes - Donor D, 0hr, untreated


title: MIcon 1


title: E_0_hrs

source_name: Primary human monocytes - Donor E, 0hr, untreated


title: MIA10 8


title: C_10_hrs_UNTREATED

source_name: Primary human monocytes - Donor C, 10hr, untreated

value: C


title: Sample14.Yellow-bellied marmot.203531420077_R02C01


title: D_2_hrs_UNTREATED

source_name: Primary human monocytes - Donor D, 2hr, untreated


title: Sample16.Yellow-bellied marmot.203531420077_R04C01


title: MIA10 10


title: MIA10 6


title: C_24_hrs_TREATED

source_name: Primary human monocytes - Donor C, 24hr, DMOG treated


title: MIA10 7


title: C_10_hrs_TREATED

source_name: Primary human monocytes - Donor C, 10hr, DMOG treated


title: MIA10 4


title: C_24_hrs_UNTREATED

source_name: Primary human monocytes - Donor C, 24hr, untreated


title: MIA10 3

value: AOS 10mg/kg


title: C_2_hrs_UNTREATED

source_name: Primary human monocytes - Donor C, 2hr, untreated

value: Untreated


title: B_24_hrs_UNTREATED

source_name: Primary human monocytes - Donor B, 24hr, untreated

value: B

value: Primary human monocytes


title: MIA10 2


title: Sample12.Yellow-bellied marmot.203531420048_R06C02


title: Sample15.Yellow-bellied marmot.203531420077_R03C01


title: MIA10 5


title: Sample13.Yellow-bellied marmot.203531420077_R01C01


title: Sample11.Yellow-bellied marmot.203531420048_R05C02


title: Sample9.Yellow-bellied marmot.203531420048_R03C02


title: C_2_hrs_TREATED

source_name: Primary human monocytes - Donor C, 2hr, DMOG treated

value: DMOG


title: Sample6.Yellow-bellied marmot.203531420048_R06C01


title: B_10_hrs_TREATED

source_name: Primary human monocytes - Donor B, 10hr, DMOG treated


title: Sample10.Yellow-bellied marmot.203531420048_R04C02


title: C_0_hrs

source_name: Primary human monocytes - Donor C, 0hr, untreated


title: B_10_hrs_UNTREATED

source_name: Primary human monocytes - Donor B, 10hr, untreated


title: B_24_hrs_TREATED

source_name: Primary human monocytes - Donor B, 24hr, DMOG treated


title: miRNA Mature_1

city: Shenzhen

first: Saineng

last: Hu

address: Lianhua Road Futian District

department: Biomedical Research Institute

institute: Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center

description:
miRNA.expression.xls
GHR191286_order_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: Bone marow B cells

extract_protocol:
Total RNA was purified from sorted populations of cells by using Trizol Reagent kit and Spin Column & Collection Tube.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

tag: development stage

value: Mature B cells

tag: genotype

value: wild type


title: MIA10 1

source_name: small intestinal


title: Sample8.Yellow-bellied marmot.203531420048_R02C02

source_name: Blood


title: Sample7.Yellow-bellied marmot.203531420048_R01C02


title: B_2_hrs_UNTREATED

source_name: Primary human monocytes - Donor B, 2hr, untreated


title: miRNA Pre_1

description:
miRNA.expression.xls
GHR191286_order_1

value: Pre-B cells


title: Sample5.Yellow-bellied marmot.203531420048_R05C01


title: Sample4.Yellow-bellied marmot.203531420048_R04C01


title: B_0_hrs

source_name: Primary human monocytes - Donor B, 0hr, untreated


title: B_2_hrs_TREATED

source_name: Primary human monocytes - Donor B, 2hr, DMOG treated


title: Sample3.Yellow-bellied marmot.203531420048_R03C01


title: RNA-seq data of Pig replicate 3

status: Public on Apr 12 2022

city: Chengdu

first: Mengnan

last: He

address: Huimin road 211#

institute: Sichuan Agriculture University

description:
pig_quant_TPM-1.txt
rRNA-remove
PE125
Specific

data_processing:
RNA sequencing reads were aligned to reference genomes applying the STAR (2.6.0c) (Dobin, A. et al.).
Transcript quantification was conducted with kallisto (0.44.0) (Bray, N. L. et al.)
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

organism: Sus scrofa

source_name: RongChang Pig Embryo  Fibroblasts

growth_protocol: Most of the fibroblasts were grown in Dulbecco's Modified Eagle Medium (DMEM, 11995-065, Gibco) containing 10% Fetal Bovine Serum (FBS, 10099-141, Gibco) and 1× penicillin/streptomycin (P/S, 15140-122, Gibco), incubated at 37 °C in 5% CO2.

extract_protocol:
total RNA  of each cell sample was extracted by using the Trizol  (Invitrogen).
We used an rRNA depletion protocol (Epicentre Ribo-zero™ rRNA Removal Kit, Epicentre, USA) or  mRNA capture protocol (Oligo (dT) magnetic beads, Promega, USA) coupled with the strand specific or non-specific RNA-seq library protocol  for each sample.

value: Fibroblasts

tag: tissue source

value: Embyo


title: RNA-seq data of Pig replicate 4

source_name: RongChang Pig Embryo Fibroblasts


title: RNA-seq data of Pig replicate 1

source_name: Large White Pig Ear Skin Fibroblasts

value: Ear Skin

value: 12 days


title: RNA-seq data of Pig replicate 2


title: RNA-seq data of Zbrafish replicate 1

description:
zebrafish_quant_TPM.txt
rRNA-remove
PE150
Specific

organism: Danio rerio

source_name: Zebrafish Fibroblasts

value: Caudal fin

value: adult


title: Sample2.Yellow-bellied marmot.203531420048_R02C01

value: Blood


title: Hi-C data of Zbrafish replicate 1

data_processing:
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Hiclib.
TADs were identified using DomainCaller
Compartment A/B identification at 20-Kb was performed by using A-B index value which represented the comparative likelihood of a sequence interacting with A or B (100-Kb) as described previously (Rowley, M. J. et al. ). Bins at 20-Kb with positive values (more association with A at 100-Kb) were called as A compartments, while 20-Kb bins with negative values (more association with B at 100-Kb) were called as B compartments. These positive or negative values were termed as A-B index values.
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

extract_protocol:
Briefly, about 20 to 25 million cells were crosslinked with 2% formaldehyde for 10 min at room temperature (20–25 °C), then used glycine to quench the formaldehyde in a final concentration of 0.25 M at room temperature for 5 min, and subsequently on ice for 15 min.
Dilution Hi-C was performed as a previous study (Lieberman-Aiden, E. et al. ). Nuclei were permeabilized by a Dounce homogenizer in the presence of cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, and 1× protease inhibitor solution). DNA was digested with 400 units of HindⅢ, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume (8 mL). After reversal of cross-links, ligated DNA was puriﬁed and prepped for Illumina sequencing.


title: Smartseq2_AXL-E3_endo_Danio

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
AXL-E3_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv

data_processing:
ScRNA-seq alignment process was completed by STAR_2.6.0a
DESeq2 standard workflow
Genome_build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human
Supplementary_files_format_and_content: csv files with raw counts and FPKM

molecule: polyA RNA

source_name: endothelial cells

extract_protocol:
1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope, the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes, and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. After digestion, a single-cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope, a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells, zebrafish were injected with GBM-U251-mCherry cells, and allowed to form widespread, tumor invasion for 3-5 days. At that point, the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope, the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes, and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. After digestion, a single-cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously, GBM-U251-mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform and modified SMART-seq2 protocol based on published previously (Fuchou Tang, 2010).

tag: cell tye

value: endothelial cells


title: Smartseq2_AXL-E1_endo_Danio

description:
AXL-E1_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: Smartseq2_AXL-E2_endo_Danio

description:
AXL-E2_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: miRNA Immature_1

description:
miRNA.expression.xls
GHR191286_order_1

value: Immature B cells


title: Smartseq2_AXL-D3_endo_Danio

description:
AXL-D3_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: Smartseq2_AXL-C3_endo_Danio

description:
AXL-C3_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: Smartseq2_AXL-C1_endo_Danio

description:
AXL-C1_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: MIA10 9

value: ICR

value: small intestinal

value: 10 weeks


title: Smartseq2_AXL-C2_endo_Danio

description:
AXL-C2_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: Smartseq2_AXL-A2_endo_Danio

description:
AXL-A2_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: Smartseq2_AXL-B1_endo_Danio

description:
AXL-B1_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: Smartseq2_AXL-A1_endo_Danio

description:
AXL-A1_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: RNA-seq data of Rhesus replicate 1

description:
monkey_quant_TPM.txt
ployA
PE125
Specific

organism: Macaca mulatta

source_name: Rhesus Lung Fibroblasts

value: Lung

value: Fetus


title: Smartseq2_AXL-A3_endo_Danio

description:
AXL-A3_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv


title: Hi-C data of Rhesus replicate 1


title: miRNA Pro_1

description:
miRNA.expression.xls
GHR191286_order_1

value: Bone marrow

value: Pro-B cells


title: D2.8, Syngas, rep3

city: Tartu

first: Kaspar

last: Valgepea

state: Tartu

address: Nooruse 1, room 520

department: Institute of Technology

country: Estonia

institute: University of Tartu

description:
Syngas chemostat at 2.8 day-1_replicate 3
Compiled_RPKM_Syngas.txt

data_processing:
The quality of NextSeq raw reads was verified using MultiQC (Ewels et al., 2016) and adapter sequences were trimmed using the Cutadapt package (version 2.10; Martin 2011)
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum DSM 10061 (NC_022592.1) using the Rsubread package (version 2.4.2; Liao et al., 2019).
Four .bam files per sample were merged using the Samtools (version 1.10; Li et al., 2009)
Genomic features were assigned using the featureCounts functions within Rsubread
Raw library sizes were normalized and transcript abundances in reads per kilobase of transcript per million mapped reads (RPKM) were estimated from feature counts and gene lengths using edgeR (version 3.32.1; Robison et al., 2010).
Genome_build: NC_022592.1
Supplementary_files_format_and_content: RPKM value tab-delimited text files

organism: Clostridium autoethanogenum

source_name: bacteria cell

growth_protocol: Clostridium autoethanogenum was grown on syngas or CO in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate ~1, 2.0 , and 2.8 day-1

extract_protocol:
Frozen pellets were thawed and total RNA was extracted using cellular lysis in RNase-free acid-washed glass beads (Merck) and RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research). Next, ribosomal RNA was removed using the Ribo-Zero rRNA removal kit (Illumina).
mRNA libraries were prepared using standard TruSeq library preparation protocols (Illumina).

treatment_protocol: Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.

tag: physiological state

value: Syngas chemostat

tag: time

value: 2.8 day


title: D2.8, Syngas, rep2

description:
Syngas chemostat at 2.8 day-1_replicate 2
Compiled_RPKM_Syngas.txt


title: D2.8, Syngas, rep1

description:
Syngas chemostat at 2.8 day-1_replicate 1
Compiled_RPKM_Syngas.txt


title: D2, Syngas, rep3

description:
Syngas chemostat at 2 day-1_replicate 3
Compiled_RPKM_Syngas.txt

value: 2 day


title: D2, Syngas, rep2

description:
Syngas chemostat at 2 day-1_replicate 2
Compiled_RPKM_Syngas.txt


title: D1, Syngas, rep4

description:
Syngas chemostat at 1 day-1_replicate 4
Compiled_RPKM_Syngas.txt

value: 1 day


title: D1, Syngas, rep2

description:
Syngas chemostat at 1 day-1_replicate 2
Compiled_RPKM_Syngas.txt


title: D2, Syngas, rep1

description:
Syngas chemostat at 2 day-1_replicate 1
Compiled_RPKM_Syngas.txt


title: Sample1.Yellow-bellied marmot.203531420048_R01C01

description: genomic DNA methylation from tissue=Blood species=Yellow-bellied marmot


title: D1, Syngas, rep1

description:
Syngas chemostat at 1 day-1_replicate 1
Compiled_RPKM_Syngas.txt


title: Sample16.Fibroblast.205814880128_R05C01

description: genomic DNA methylation from tissue=Fibroblast species=Human

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol

data_processing: Noob normalization as implemented in the minfi R package M. Aryee et al 2014. PMID: 24478339

source_name: Fibroblast

tag: Sex

value: Male

value: Fibroblast

tag: condition

value: Healthy


title: D2.8, CO, rep3

description:
CO chemostat at 2.8 day-1_replicate 3
Compiled_RPKM_CO.txt

value: CO chemostat


title: D2.8, CO, rep2

description:
CO chemostat at 2.8 day-1_replicate 2
Compiled_RPKM_CO.txt


title: Smartseq2_AXL-B2_endo_Danio

description:
AXL-B2_HHVK7CCXY_L3
processed data file:
Zebrafish_scRNA_smartseq2_12_samples_FPKM.csv
Zebrafish_scRNA_smartseq2_12_samples_count.csv

value: endothelial cells


title: Sample12.Fibroblast.205814880084_R07C01

value: Werner syndrome


title: D2, CO, rep1

description:
CO chemostat at 2 day-1_replicate 1
Compiled_RPKM_CO.txt


title: D2, CO, rep2

description:
CO chemostat at 2 day-1_replicate 2
Compiled_RPKM_CO.txt


title: Sample13.Fibroblast.205814880128_R02C01


title: D2.8, CO, rep1

description:
CO chemostat at 2.8 day-1_replicate 1
Compiled_RPKM_CO.txt


title: Sample11.Fibroblast.205814880084_R06C01

value: Scrambled AntiSense Oligonucleotides


title: Sample15.Fibroblast.205814880128_R04C01


title: Sample10.Fibroblast.205814880084_R05C01


title: D1, CO, rep2

description:
CO chemostat at 1 day-1_replicate 2
Compiled_RPKM_CO.txt


title: FLV_086

city: Singapore

first: Christine

last: Cheung

address: Nanyang Dr

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
All analyses were performed on Partek Flow software, version 7.0 (St. Louis, MO, USA).
Reads were aligned to the human reference genome GRCh37 using STAR version 2.6.1d.
Transcript abundances were quantified with the Partek E/M algorithm based on Ensembl Transcripts Release 83, subsequently normalized by CPM (counts per million) method.
Differentially expressed genes in the transcriptome data were identified using the gene specific analysis (GSA) method for p-values and Benjamini-Hochberg method for FDR.
Genes were called differentially expressed if p-value < 0.05, FDR < 0.05, and fold change ≥ 2 or ≤ -2.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every technical replicate.

source_name: Blood outgrowth endothelial cell

growth_protocol: BOECs were derived from blood samples and maintained in EGM-2 + 10% FBS.

extract_protocol:
Total RNA was isolated from the BOECs as per manufacturer’s instructions (RNeasy Micro Kit, Qiagen).
PolyA library preparation and 150 base-pair paired end sequencing was performed by Novogene sequencing facility (Singapore) using an Illumina HiSeq sequencer. The average sequencing depth was 50 million reads.

tag: cell

value: Endothelial cell

tag: disease state

value: heathly


title: D1, CO, rep4

description:
CO chemostat at 1 day-1_replicate 4
Compiled_RPKM_CO.txt

tag: strain


title: Sample7.Fibroblast.205814880084_R02C01


title: Sample14.Fibroblast.205814880128_R03C01


title: FLV_095


title: D1, CO, rep3

description:
CO chemostat at 1 day-1_replicate 3
Compiled_RPKM_CO.txt


title: D1, CO, rep1

description:
CO chemostat at 1 day-1_replicate 1
Compiled_RPKM_CO.txt


title: FLAPD_190

value: NAFLD


title: FLAPD_177


title: Sample9.Fibroblast.205814880084_R04C01


title: IF-V3

city: London

first: Elisabeth

last: Serger

state: London

address: Du Cane Road

department: Brain Sciences

institute: Imperial College London

data_processing:
Primers were trimmed off demultiplexed R1 sequence reads using cutadapt v1.18.
Reads were processed via the DADA2 pipeline using the following parameters for filtering and trimming: truncLen=125, maxN=0, maxEE=2, truncQ=2, rm.phix=TRUE, compress=TRUE, verbose = TRUE, multithread=FALSE.
Errors were estimated, samples variants were inferred and chimeras were removed from the data to yield an amplicon sequence variant (ASV) table and taxonomy was assigned using the SILVA reference database (v132).
Data was further processed in phyloseq (v1.26.1) for alpha and beta diversity as well as relative abundance investigations. Data was not normalised for alpha diversity (results are identical to using rarefied data) but was normalised by log transformation with a pseudo-count of +1 for beta diversity. Alpha diversity was calculated as Shannon index and visualised as a box plot. Beta diversity was calculated by Bray-Curtis dissimilarity and visualised in a PCoA plot. Statistical significance of beta diversity was calculated by PERMANOVA and variance calculated by betadisper function in the vegan package (v2.5-5). Data was agglomerated by taxa level and plotted as relative abundance bar charts.
Differential abundance was estimated using DESeq2 package (v1.22.2). Output tables are ASVs that attain statistically significant differences between groups that were compared. Alpha was set at p = 0.05. P adjustment method = Benjamini-Hochberg FDR.
Supplementary_files_format_and_content: DESeq2 output

source_name: IF-V_microbial genomic DNA from cecum content

extract_protocol:
Cecum content was collected from mice and immediately frozen in liquid nitrogen. Samples were stored at -80 °C. Faecal DNA was extracted using Fast DNA spin kit (MP Biomedicals).
Libraries were prepared using the 16S Metagenomic Sequencing Library Preparation protocol for the Illumina MiSeq System. In brief, PCR primers (16S Amplicon PCR Forward Primer = 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG; 16S Amplicon PCR Reverse Primer = 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC) directed at the V3/V4 region of bacterial rRNA genes were used to generate libraries and libraries were validated by the Agilent 2100 Bioanalyzer. Sequencing was performed with 250 bp paired-end reads on Illumina Miseq2500

treatment_protocol: Mice (6-8 weeks) underwent following procedures: a) 10 days of ad libitum food supply b) 10 days of intermittent fasting c) 10 days of ad libitum food co-treated with vancomycin in the drinking water (50mg/kg/day; 214.27 mg/l) d) 10 days of intermittent fasting food cotreated with vancomycin in the drinking water

value: 6-8 weeks old

value: 10 days of intermittent fasting food cotreated with vancomycin in the drinking water (IF-V)

tag: tissue/molecule


title: IF-V6

tag: age

value: microbial genomic DNA from cecum content


title: D1, Syngas, rep3

description:
Syngas chemostat at 1 day-1_replicate 3
Compiled_RPKM_Syngas.txt

value: Syngas chemostat


title: IF-V4

tag: treatment


title: IF-V7


title: IF-V5


title: IF-V8


title: AL-V8

source_name: AL-V_microbial genomic DNA from cecum content

value: 10 days of ad libitum food co-treated with vancomycin in the drinking water (AL-V)


title: IF-V2


title: AL-V7


title: Sample4.Fibroblast.205814880083_R04C01

value: Hutchinson-Gilford progeria syndrome


title: IF-V1


title: AL-V5


title: AL-V6


title: Sample6.Fibroblast.205814880083_R06C01


title: AL-V3


title: AL-V1


title: Sample8.Fibroblast.205814880084_R03C01


title: AL-V2


title: AL-V4


title: IF7

source_name: IF_microbial genomic DNA from cecum content

value: 10 days of intermittent fasting (IF)


title: Sample3.Fibroblast.205814880083_R03C01

value: Male


title: IF8


title: IF2


title: D2, CO, rep3

description:
CO chemostat at 2 day-1_replicate 3
Compiled_RPKM_CO.txt

value: 2 day


title: IF5


title: IF4


title: AL3

source_name: AL_microbial genomic DNA from cecum content

value: 10 days of ad libitum food supply (AL)


title: AL6


title: Sample5.Fibroblast.205814880083_R05C01

value: Fibroblast


title: IF1


title: B16F1_pPOLII_DMSO

city: La Jolla

first: Jelena

last: Ostojic

address: 10010 N Torrey Pines Road

department: PBL-M

institute: Salk Institute for Biological Studies

data_processing:
High-throughput sequencing was performed on the HiSeq 2500 system (Illumina) at a run configuration of single read 50 bases.
Image analysis and base calling were done with Illumina CASAVA-1.8.2.on HiSeq 2500 system and sequenced reads were quality-tested using FASTQC.
FASTQ files were aligned to the mouse mm10 genome builds using STAR.
Tag directories of uniquely mapped reads were generated with HOMER and Peaks.txt were called and annotated using HOMER (findPeaks.txt in “factor” mode for CREB, CRTC2, CRTC3, POLII and MITF and in “histone” mode for H3AcK27; annotatePeaks.txt.pl, default parameters)
Overlapping Peaks.txt were visualized by generating BigWig files with HOMER (makeMultiWigHub.pl, default parameters) and uploading the hubs in the UCSC Genome Browser (http://genome.ucsc.edu).
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files for each sample.
Supplementary_files_format_and_content: Annotated peak text files for each IP sample.

source_name: B16F1 mouse melanoma cell line

growth_protocol: Cells were grown to 80% confluency in 150mm dishes (one per IP).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated through IP with indicated antibodies.
Libraries were prepared with NebNext® ChIP seq reagents for Illumina (E6240 and E7335, New England Biolabs), following the manufacturer’s protocol.

treatment_protocol: Cells were treated with DMSO or 5µM FSK for 30min, fixed in 1% formaldehyde for 10min and quenched with 125mM glycine for 5min.

value: DMSO (vehicle), 1h

tag: chip antibody

value: RNA polymerase II (CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095))


title: IF6


title: AL5


title: B16F1_pPOLII_FSK

value: Forskolin, 1h


title: Sample2.Fibroblast.205814880083_R02C01

value: Scrambled AntiSense Oligonucleotides


title: AL7


title: B16F1_Input DNA_DMSO


title: B16F1_Input DNA_FSK


title: B16F1_MITF_DMSO

value: MITF (ChIP grade ab12039, Abcam)


title: B16F1_H3acK27_DMSO

value: H3AcK27 (ab4729, Abcam)


title: AL2

value: 6-8 weeks old


title: AL1


title: B16F1_CRTC3_FSK


title: FLV_113

value: Endothelial cell

value: heathly


title: B16F1_H3acK27_FSK


title: B16F1_MITF_FSK


title: Sample1.Fibroblast.205814880083_R01C01


title: B16F1_CRTC3_DMSO


title: AL8

value: microbial genomic DNA from cecum content


title: B16F1_CRTC3KO_RESCUE_FSK

data_processing:
High-throughput sequencing was performed on the HiSeq 2500 system (Illumina) at a run configuration of single read 50 bases.
Image analysis and base calling were done with Illumina CASAVA-1.8.2.on HiSeq 2500 system and sequenced reads were quality-tested using FASTQC.
FASTQ files were aligned to the mouse mm10 genome builds using STAR.
Raw counts and differential expression analyses were preformed using HOMER (analyzeRepeats.pl with options –raw -count exons -condenseGenes; getDiffExpression.pl using DESeq2)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw exon counts for every gene and every sample.

growth_protocol: Cells were grown to 70% confluency on 10cm dishes.

extract_protocol:
Cels were collected in Trizol reagent for Trizol-chloroform RNA extraction. RNA extracts were further purified and DNAse treated by using RNAeasy Qiagen columns (DNAse 79254, Qiagen). 1µg RNA was used for further analysis.
TruSeq stranded mRNA Sample Preparation Kit v2 (RS-122-2001) was used according to Illumina protocols.

treatment_protocol: Cells were treated with DMSO or 1µM FSK for 1h.

value: CRTC3 re-expression in CRTC3-/-


title: B16F1_CRTC3KO2_FSK

value: CRTC3 -/-


title: B16F1_CRTC3KO1_DMSO


title: B16F1_CTRL2_DMSO

value: Wild-type


title: B16F1_CRTC3KO1_FSK


title: B16F1_CRTC3KO2_DMSO


title: IF3

value: 10 days of intermittent fasting (IF)


title: B16F1_CRTC3KO_RESCUE_DMSO


title: B16F1_CTRL2_FSK


title: B16F1_CTRL1_FSK


title: B16F1_CTRL1_DMSO


title: Whole skin_CRTC3KO2

source_name: Whole skin

extract_protocol:
Skin samples were weighted, frozen in liquid nitrogen and equal amounts of frozen tissue were ground with mortar and pestle before extracting RNAs in TRIzol-chloroform. RNA extracts were further purified and DNAse treated by using RNAeasy Qiagen columns (DNAse 79254, Qiagen). 1µg RNA was used for further analysis.
TruSeq stranded mRNA Sample Preparation Kit v2 (RS-122-2001) was used according to Illumina protocols.

value: Post natal day 2


title: Whole skin_WT1


title: Whole skin_WT3


title: Whole skin_CRTC3KO4


title: Whole skin_CRTC3KO1


title: B16F1_CREB_FSK

value: CREB (244, in-house)


title: Allergic patients 3 - day3 - diluent

city: Linköping

first: Sandra

last: Lilja

address: Sandbäcksgatan 7

department: BKV

country: Sweden

institute: Linköping University

data_processing:
Processed of scRNA-seq data into digital gene expression matrices following James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com) using bcl2fastq conversion and Picard software. The indexed reference for alignment of the reads was generated from GRCh38 (April 2017, Ensembl) using STAR software.
Quality control, where cells with less than 10,000 reads, 400 transcripts, or 200 genes, or more than 20% mitochondrial genes were sorted out.
Noise reduction by k-nearest neighbor smoothing (k = ~0.1% the total number of cells) was applied.
Cell type identification using Reference Component Analysis. The references were produced based on bulk data, from HG_U133A/GNF1H gene atlas and PMID: 31358043.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with denoised transcript counts of each gene (rows) within each cell (columns).

source_name: PBMC

extract_protocol:
The bam files were extracted following all the steps of James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com), using bcl2fastq conversion and Picard software.
Libraries were prepared from GRCh38 (April 2017, Ensembl) using STAR software.

treatment_protocol: PBMCs were challenged with allergen (10 µg/mL birch pollen extract) or diluent, and incubated for different time points in RPMI 1640 supplemented with 10% fetal bovine serum. Samples were obtained at 0 hours (before stimulation), 12 hours, 1 day, 2 days, 3 days, 5 days, and 7 days, for scRNA-seq using the Seq-Well method.

value: diluent challenged

tag: timepoint

tag: disease

value: seasonal allergic rhinitis (SAR)

value: PBMC


title: Allergic patients 3 - day2 - diluent

tag: cell type


title: Allergic patients 3 - day5 - allergen challenged

value: allergen challenged


title: Allergic patients 3 - day5 - diluent


title: Whole skin_CRTC3KO3

tag: genotype


title: B16F1_CREB_DMSO

value: DMSO (vehicle), 1h


title: Allergic patients 3 - day1 - diluent


title: Whole skin_WT4


title: Whole skin_WT2


title: Allergic patients 3 - day1 - allergen challenged


title: Allergic patients 3 - day3 - allergen challenged


title: Allergic patients 3 - day7 - diluent


title: Allergic patients 2 - day3 - diluent


title: Allergic patients 2 - day2 - allergen challenged


title: Allergic patients 2 - day2 - diluent


title: Allergic patients 2 - day5 - diluent


title: Allergic patients 2 - day1 - diluent


title: Allergic patients 2 - day1 - allergen challenged


title: Allergic patients 2 - 12h - diluent


title: Allergic patients 3 - day2 - allergen challenged


title: Allergic patients 3 - day7 - allergen challenged


title: Allergic patients 2 - 12h - allergen challenged


title: Allergic patients 1 - day7 - allergen challenged


title: Allergic patients 1 - day7 - diluent


title: Allergic patients 2 - day7 - allergen challenged


title: Allergic patients 1 - day5 - allergen challenged


title: Allergic patients 1 - day3 - diluent


title: Allergic patients 3 - 12h - diluent


title: Allergic patients 2 - day5 - allergen challenged


title: Allergic patients 1 - day3 - allergen challenged


title: Allergic patients 3 - 12h - allergen challenged


title: Allergic patients 1 - day5 - diluent


title: Allergic patients 3 - 0h

value: control


title: Allergic patients 2 - 0h


title: Healthy control 8 - day2 - diluent

value: Healthy


title: Allergic patients 1 - 12h - allergen challenged


title: Allergic patients 1 - day2 - diluent


title: Allergic patients 2 - day3 - allergen challenged


title: Allergic patients 2 - day7 - diluent


title: Healthy control 8 - day1 - allergen challenged


title: AL4

value: 6-8 weeks old

value: 10 days of ad libitum food supply (AL)


title: Healthy control 7 - day1 - allergen challenged


title: Healthy control 7 - day1 - diluent


title: Allergic patients 1 - day1 - diluent


title: Healthy control 5 - day5 - diluent


title: Healthy control 7 - 0h


title: Healthy control 7 - 12h - allergen challenged


title: Allergic patients 1 - day2 - allergen challenged


title: Healthy control 5 - day3 - diluent


title: Healthy control 8 - 0h


title: Healthy control 2 - day7 - diluent


title: Allergic patients 1 - 12h - diluent


title: Healthy control 7 - day2 - allergen challenged


title: Healthy control 2 - day7 - allergen challenged


title: Allergic patients 1 - day1 - allergen challenged


title: Healthy control 8 - 12h - diluent


title: Healthy control 7 - 12h - diluent


title: Healthy control 5 - day5 - allergen challenged


title: Allergic patients 1 - 0h


title: Healthy control 8 - day2 - allergen challenged


title: Healthy control 2 - day5 - allergen challenged


title: Healthy control 8 - day1 - diluent


title: Healthy control 8 - 12h - allergen challenged


title: Healthy control 5 - day3 - allergen challenged


title: Healthy control 2 - day3 - diluent


title: Healthy control 2 - day2 - diluent


title: Healthy control 2 - day3 - allergen challenged


title: Healthy control 2 - day5 - diluent


title: RNA-seq data of Dog replicate 2

description:
dog_quant_TPM.txt
ployA
PE125
Specific

organism: Canis lupus familiaris

source_name: Beagle Ear Skin Fibroblasts

value: Fibroblasts

tag: tissue source

value: Ear Skin

value: 3 months


title: Healthy control 2 - 0h


title: RNA-seq data of Dog replicate 1

description:
dog_quant_TPM.txt
ployA
PE125
Specific

source_name: Dog Tumor Fibroblasts

value: unknown

value: 8 years


title: Healthy control 2 - day2 - allergen challenged


title: RNA-seq data of Dog replicate 3

description:
dog_quant_TPM.txt
ployA
PE125
Specific


title: Hi-C data of Dog replicate 2


title: RNA-seq data of Human replicate 3

source_name: Human Lung Fibroblasts

value: Lung

value: Embyo


title: RNA-seq data of Human replicate 2


title: Hi-C data of Human replicate 3


title: Hi-C data of Human replicate 2


title: RNA-seq data of Human replicate 1

source_name: Human Skin Fibroblasts

value: Skin


title: Smartseq2_AXL-axl22_GBM-U251_Homo

description:
AXL-axl22_TKR180500272-23
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv

source_name: GBM-U251 cell lines

tag: cell line

value: GBM-U251-mCherry cells

tag: cell tye

value: GBM cells implanted in zebrafish brain


title: Smartseq2_AXL-axl20_GBM-U251_Homo

description:
AXL-axl20_TKR180500272-21
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl21_GBM-U251_Homo

description:
AXL-axl21_TKR180500272-22
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl18_GBM-U251_Homo

description:
AXL-axl18_TKR180500272-19
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl12_GBM-U251_Homo

description:
AXL-axl12_TKR180500272-12
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl16_GBM-U251_Homo

description:
AXL-axl16_TKR180500272-16
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl15_GBM-U251_Homo

description:
AXL-axl15_TKR180500272-15
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl13_GBM-U251_Homo

description:
AXL-axl13_TKR180500272-13
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl17_GBM-U251_Homo

description:
AXL-axl17_TKR180500272-18
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl10_GBM-U251_Homo

description:
AXL-axl10_TKR180500272-10
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Hi-C data of Dog replicate 3


title: Hi-C data of Dog replicate 1


title: Smartseq2_AXL-axl8_GBM-U251_Homo

description:
AXL-axl8_TKR180500272-8
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl6_GBM-U251_Homo

description:
AXL-axl6_TKR180500272-6
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl7_GBM-U251_Homo

description:
AXL-axl7_TKR180500272-7
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl4_GBM-U251_Homo

description:
AXL-axl4_TKR180500272-4
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl5_GBM-U251_Homo

description:
AXL-axl5_TKR180500272-5
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl2_GBM-U251_Homo

description:
AXL-axl2_TKR180500272-2
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl3_GBM-U251_Homo

description:
AXL-axl3_TKR180500272-3
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl1_GBM-U251_Homo

description:
AXL-axl1_TKR180500272-1
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl19_GBM-U251_Homo

description:
AXL-axl19_TKR180500272-20
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Smartseq2_AXL-axl14_GBM-U251_Homo

description:
AXL-axl14_TKR180500272-14
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Hi-C data of Human replicate 1


title: Smartseq2_AXL-axl11_GBM-U251_Homo

description:
AXL-axl11_TKR180500272-11
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Pax7 lineage - E16.5b1_95

city: Hong Kong

first: Angela

last: Wu

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description:
ss2_filtered_count.csv
E16.5_b1_9

data_processing:
Smart-seq2 samples basecalling were performed using bcl2fastq2; 10x samples were performed using bcl2fastq.
Smart-seq2 samples were quantified using kallisto 0.44.0, summarized using tximport in R; 10x samples were aligned using STAR and matrices were generated with cellranger count
Both datasets were loaded in R environment as Seurat object and filtered for poor quality reads.
Genome_build: mm10
Supplementary_files_format_and_content: csv containing raw counts

source_name: Mouse embryonic cells

extract_protocol:
YFP+ signals reporting Pax7-lineage cells were FACS sorted. Additional sorting with antibody labeling were done for bulk samples regarding surface marker studies.
Sequencing libraries for single-cell samples were constructed using Smart-seq2 protocol or 10x protocol. Smart-seq2 was also applied to bulk samples.

treatment_protocol: The progeny Pax7-expressing cells during early developmental stage were traced by injecting a single dose of TMX (75 µg/g body weight) intraperitoneally into the pregnant mice at E9.5 to initiate Cre-Lox recombination in Pax7-expressing cells. Embryos were harvested later at E12.5, E14.5, and E16.5.

tag: tissue

value: embryonic cells

tag: method

tag: sequencng type

value: Single-cell

tag: time point

tag: plate batch

value: Plate 11

tag: sequence batch

value: Batch 6

tag: medium

tag: marker


title: Pax7 lineage - E16.5b1_94

description:
ss2_filtered_count.csv
E16.5_b1_9


title: Pax7 lineage - E16.5b2_1

description:
ss2_filtered_count.csv
E16.5_b2_9

value: Plate 12


title: Pax7 lineage - E16.5b1_91

description:
ss2_filtered_count.csv
E16.5_b1_9


title: Smartseq2_AXL-axl9_GBM-U251_Homo

description:
AXL-axl9_TKR180500272-9
processed data file:
human_scRNA_smartseq2_22_samples_FPKM.csv
human_scRNA_smartseq2_22_samples_raw.csv


title: Pax7 lineage - E16.5b1_92

description:
ss2_filtered_count.csv
E16.5_b1_9


title: Pax7 lineage - E16.5b1_90

description:
ss2_filtered_count.csv
E16.5_b1_9


title: Pax7 lineage - E16.5b1_88

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_96

description:
ss2_filtered_count.csv
E16.5_b1_9


title: Pax7 lineage - E16.5b1_84

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_82

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_78

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_85

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_77

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_75

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b2_2

description:
ss2_filtered_count.csv
E16.5_b2_9


title: Pax7 lineage - E16.5b1_83

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_93

description:
ss2_filtered_count.csv
E16.5_b1_9


title: Pax7 lineage - E16.5b1_80

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_79

description:
ss2_filtered_count.csv
E16.5_b1_7


title: FLAPD_049

tag: cell

value: Endothelial cell

tag: disease state

value: NAFLD


title: Pax7 lineage - E16.5b1_74

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_71

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_69

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_73

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_87

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_68

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_70

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_67

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b2_3

description:
ss2_filtered_count.csv
E16.5_b2_9


title: Pax7 lineage - E16.5b1_72

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_89

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_86

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_66

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_63

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_62

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_76

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_60

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_65

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_64

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_61

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E16.5b1_81

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_54

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_53

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_57

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_51

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_59

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_55

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_56

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_52

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_47

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_50

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_48

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_46

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_49

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_45

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_43

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_40

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_37

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_41

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_38

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_42

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_58

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_39

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_44

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_31

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_32

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_35

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_34

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_30

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_28

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_27

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_36

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_29

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_23

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_25

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_22

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_17

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_20

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_16

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_26

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_15

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_21

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_13

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_12

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_10

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_9

description:
ss2_filtered_count.csv
E16.5_b1_9


title: Pax7 lineage - E16.5b1_4

description:
ss2_filtered_count.csv
E16.5_b1_4


title: Pax7 lineage - E16.5b1_33

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E16.5b1_11

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_18

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_24

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E16.5b1_2

description:
ss2_filtered_count.csv
E16.5_b1_2


title: Pax7 lineage - E12.5b6_93

description:
ss2_filtered_count.csv
E12.5_b6_3

value: Plate 10

value: Batch 5


title: Pax7 lineage - E16.5b1_7

description:
ss2_filtered_count.csv
E16.5_b1_7


title: Pax7 lineage - E16.5b1_8

description:
ss2_filtered_count.csv
E16.5_b1_8


title: Pax7 lineage - E16.5b1_3

description:
ss2_filtered_count.csv
E16.5_b1_3


title: Pax7 lineage - E12.5b6_95

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E16.5b1_19

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E12.5b6_91

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E16.5b1_5

description:
ss2_filtered_count.csv
E16.5_b1_5


title: Pax7 lineage - E16.5b1_14

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E12.5b6_90

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_94

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_92

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_89

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_82

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_96

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_81

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_86

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_85

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_87

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_83

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_77

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E16.5b1_1

description:
ss2_filtered_count.csv
E16.5_b1_1


title: Pax7 lineage - E16.5b1_6

description:
ss2_filtered_count.csv
E16.5_b1_6


title: Pax7 lineage - E12.5b6_80

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_75

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_76

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_79

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_72

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_66

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_65

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_74

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_67

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_70

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_64

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_68

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_78

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_71

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_61

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_88

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_69

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_63

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_62

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_73

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_84

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_58

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_56

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_59

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_57

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_60

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_55

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_51

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_49

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_54

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_50

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_52

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_53

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_47

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_46

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_43

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_44

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_36

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_41

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_39

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_48

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_40

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_37

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_38

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_34

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_33

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_42

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_30

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_28

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_27

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_26

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_35

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_32

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_24

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_45

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_31

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_25

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_20

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_16

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_22

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_13

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_21

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_12

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_17

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_18

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_23

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_10

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b6_6

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b6_29

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_14

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_1

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b5_95

description:
ss2_filtered_count.csv
E12.5_b5_2

value: Plate 9


title: Pax7 lineage - E12.5b6_19

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b6_11

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b5_93

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b6_8

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b5_92

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_96

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_94

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b6_15

description:
ss2_filtered_count.csv
E12.5_b6_3


title: Pax7 lineage - E12.5b5_90

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b6_7

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b6_5

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b5_87

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b6_4

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b6_2

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b6_3

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b6_9

description:
ss2_filtered_count.csv
E12.5_b6_2


title: Pax7 lineage - E12.5b5_86

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_91

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_77

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_80

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_79

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_78

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_89

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_75

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_83

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_88

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_82

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_74

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_71

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_84

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_69

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_67

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_66

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_76

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_73

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_70

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_65

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_62

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_85

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_63

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_68

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_81

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_64

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_61

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_59

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_58

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_60

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_56

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_57

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_72

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_51

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_52

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_54

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_53

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_49

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_46

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_55

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_50

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_47

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_45

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_42

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_43

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_37

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_48

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_35

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_44

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_40

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_39

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_41

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_36

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_38

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_33

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_32

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_34

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_31

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_30

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_24

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_28

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_26

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_29

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_27

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_23

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_25

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_21

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_19

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_16

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_18

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_17

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_13

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_7

description:
ss2_filtered_count.csv
E12.5_b5_1


title: Pax7 lineage - E12.5b5_10

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_14

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_20

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_11

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_6

description:
ss2_filtered_count.csv
E12.5_b5_1


title: Pax7 lineage - E12.5b5_9

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_8

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_22

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_1

description:
ss2_filtered_count.csv
E12.5_b5_1


title: Pax7 lineage - E12.5b5_3

description:
ss2_filtered_count.csv
E12.5_b5_1


title: Pax7 lineage - E12.5b4_95

description:
ss2_filtered_count.csv
E12.5_b4_1

value: Plate 8


title: Pax7 lineage - E12.5b4_89

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b5_12

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b5_4

description:
ss2_filtered_count.csv
E12.5_b5_1


title: Pax7 lineage - E12.5b5_5

description:
ss2_filtered_count.csv
E12.5_b5_1


title: Pax7 lineage - E12.5b4_88

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_87

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b5_2

description:
ss2_filtered_count.csv
E12.5_b5_1


title: Pax7 lineage - E12.5b4_90

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_86

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_92

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_96

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b5_15

description:
ss2_filtered_count.csv
E12.5_b5_2


title: Pax7 lineage - E12.5b4_93

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_82

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_83

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_79

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_78

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_84

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_81

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_85

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_76

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_94

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_74

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_71

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_72

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_66

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_91

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_70

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_73

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_69

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_80

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_64

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_65

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_75

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_59

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_57

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_61

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_56

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_63

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_77

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_58

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_55

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_53

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_51

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_52

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_47

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_49

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_46

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_44

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_41

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_50

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_68

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_48

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_60

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_67

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_39

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_40

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_45

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_54

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_38

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_62

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_36

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_33

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_37

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_32

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_35

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_31

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_42

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_43

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_30

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_28

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_26

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_34

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_20

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_21

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_24

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_25

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_19

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_22

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_13

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_17

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_18

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_11

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_15

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_14

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_9

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_12

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_7

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_8

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_10

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_16

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_29

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_5

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_4

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_6

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_27

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b4_23

description:
ss2_filtered_count.csv
E12.5_b4_1


title: Pax7 lineage - E12.5b3_96

description:
ss2_filtered_count.csv
E12.5_b3_9

value: Plate 7


title: Pax7 lineage - E12.5b4_1

description:
ss2_filtered_count.csv
E12.5_b4_9


title: Pax7 lineage - E12.5b4_2

description:
ss2_filtered_count.csv
E12.5_b4_9


title: Pax7 lineage - E12.5b4_3

description:
ss2_filtered_count.csv
E12.5_b4_9


title: Pax7 lineage - E12.5b3_95

description:
ss2_filtered_count.csv
E12.5_b3_9


title: Pax7 lineage - E12.5b3_86

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_89

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_90

description:
ss2_filtered_count.csv
E12.5_b3_9


title: Pax7 lineage - E12.5b3_94

description:
ss2_filtered_count.csv
E12.5_b3_9


title: Pax7 lineage - E12.5b3_93

description:
ss2_filtered_count.csv
E12.5_b3_9


title: Pax7 lineage - E12.5b3_92

description:
ss2_filtered_count.csv
E12.5_b3_9


title: Pax7 lineage - E12.5b3_77

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_80

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_88

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_91

description:
ss2_filtered_count.csv
E12.5_b3_9


title: Pax7 lineage - E12.5b3_82

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_74

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_78

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_73

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_84

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_81

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_75

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_85

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_83

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_72

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_79

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_71

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_76

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_70

description:
ss2_filtered_count.csv
E12.5_b3_7


title: Pax7 lineage - E12.5b3_69

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_66

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_87

description:
ss2_filtered_count.csv
E12.5_b3_8


title: Pax7 lineage - E12.5b3_68

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_67

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_64

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_63

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_61

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_54

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_58

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_57

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_55

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_56

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_53

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_51

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_50

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_46

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_48

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_42

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_65

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_52

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b3_44

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_41

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_47

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_49

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_43

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b3_39

description:
ss2_filtered_count.csv
E12.5_b3_3


title: Pax7 lineage - E12.5b3_38

description:
ss2_filtered_count.csv
E12.5_b3_3


title: Pax7 lineage - E12.5b7_94

description:
ss2_filtered_count.csv
E12.5_b7_3


title: Pax7 lineage - E12.5b3_36

description:
ss2_filtered_count.csv
E12.5_b3_3


title: Pax7 lineage - E12.5b3_59

description:
ss2_filtered_count.csv
E12.5_b3_5


title: Pax7 lineage - E12.5b7_82

description:
ss2_filtered_count.csv
E12.5_b7_3


title: Pax7 lineage - E12.5b7_84

description:
ss2_filtered_count.csv
E12.5_b7_3


title: Pax7 lineage - E12.5b3_62

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_33

description:
ss2_filtered_count.csv
E12.5_b3_3


title: Pax7 lineage - E12.5b3_60

description:
ss2_filtered_count.csv
E12.5_b3_6


title: Pax7 lineage - E12.5b3_45

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b7_79

description:
ss2_filtered_count.csv
E12.5_b7_2


title: Pax7 lineage - E12.5b3_31

description:
ss2_filtered_count.csv
E12.5_b3_3


title: Pax7 lineage - E12.5b7_81

description:
ss2_filtered_count.csv
E12.5_b7_3


title: Pax7 lineage - E12.5b3_30

description:
ss2_filtered_count.csv
E12.5_b3_3


title: Pax7 lineage - E12.5b3_40

description:
ss2_filtered_count.csv
E12.5_b3_4


title: Pax7 lineage - E12.5b7_67

description:
ss2_filtered_count.csv
E12.5_b7_2


title: Pax7 lineage - E12.5b3_20

description:
ss2_filtered_count.csv
E12.5_b3_2


title: Pax7 lineage - E12.5b7_62

description:
ss2_filtered_count.csv
E12.5_b7_2


title: Pax7 lineage - E12.5b3_21

description:
ss2_filtered_count.csv
E12.5_b3_2


title: Pax7 lineage - E12.5b7_56

description:
ss2_filtered_count.csv
E12.5_b7_2


title: Pax7 lineage - E12.5b3_22

description:
ss2_filtered_count.csv
E12.5_b3_2


title: Pax7 lineage - E12.5b7_53

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E12.5b7_51

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E12.5b3_16

description:
ss2_filtered_count.csv
E12.5_b3_1


title: Pax7 lineage - E12.5b7_55

description:
ss2_filtered_count.csv
E12.5_b7_2


title: Pax7 lineage - E12.5b3_15

description:
ss2_filtered_count.csv
E12.5_b3_1


title: Pax7 lineage - E12.5b3_24

description:
ss2_filtered_count.csv
E12.5_b3_2


title: Pax7 lineage - E12.5b3_18

description:
ss2_filtered_count.csv
E12.5_b3_1


title: Pax7 lineage - E12.5b7_47

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E12.5b7_43

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E12.5b7_44

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E12.5b7_33

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E12.5b7_29

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E12.5b7_21

description:
ss2_filtered_count.csv
E12.5_b7_7


title: Pax7 lineage - E12.5b7_27

description:
ss2_filtered_count.csv
E12.5_b7_9


title: Pax7 lineage - E12.5b7_20

description:
ss2_filtered_count.csv
E12.5_b7_6


title: Pax7 lineage - E12.5b7_19

description:
ss2_filtered_count.csv
E12.5_b7_5


title: Pax7 lineage - E12.5b7_64

description:
ss2_filtered_count.csv
E12.5_b7_2


title: Pax7 lineage - E12.5b7_15

description:
ss2_filtered_count.csv
E12.5_b7_2


title: Pax7 lineage - E12.5b7_16

description:
ss2_filtered_count.csv
E12.5_b7_3


title: Pax7 lineage - E12.5b7_17

description:
ss2_filtered_count.csv
E12.5_b7_4


title: Pax7 lineage - E14.5b4_64

description:
ss2_filtered_count.csv
E14.5_b4_1

value: Plate 6

value: Batch 4


title: Pax7 lineage - E12.5b7_3

description:
ss2_filtered_count.csv
E12.5_b7_1


title: Pax7 lineage - E14.5b4_62

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E12.5b7_26

description:
ss2_filtered_count.csv
E12.5_b7_8