title: PBMC cr biological rep1

status: Public on Nov 25 2021

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

description: Gene expression data from monkeys consuming a calorie restricted diet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells, Calorie Restricted diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

value: male

tag: diet

value: calorie restricted


title: PBMC cr biological rep7

type: RNA

country: USA

label: biotin

molecule: total RNA

tag: gender


title: PBMC control biological rep5

description: Gene expression data from monkeys consuming a control diet

source_name: Peripheral blood mononuclear cells, Control diet

value: control


title: PBMC cr biological rep4


title: PBMC cr biological rep6


title: yw control lavae after bacteria injection, biological replica1

city: Sendai

first: Naoyuki

last: Fuse

state: Miyagi

address: Aoba 6-3, Aramaki, Aoba-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Tohoku University

description: control fly with bacteria

hyb_protocol: Labeled cRNAs were hybridized on Affymetrix Drosophila Genome 2.0 arrays.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymeteix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: Biotin

organism: Drosophila melanogaster

source_name: larvae 4hours after injection of Staphylococcus saprophyticus

label_protocol: Biotinylated cRNA were prepared using an IVT Labeling Kit (Affymetrix).

growth_protocol: Larvae for each genotype were reared in standard cornmeal medium at 25C.

extract_protocol: Extraction of total RNA was performed using RNeasy kit (Qiagen).

treatment_protocol: 3rd inster larvae before or 4hours after injection of Staphylococcus saprophyticus were homogenized in the Trizol solution (Invitrogen).

tag: tissue

value: whole body

tag: genotype

value: yw

tag: age

value: 3rd inster larvae


title: PBMC cr biological rep3


title: PBMC cr biological rep2


title: PBMC cr biological rep5


title: gyc76c[KG03723] mutant larvae after bacteria injection, biological replica1

description: experimental fly with bacteria


title: PBMC control biological rep6


title: yw control lavae after bacteria injection, biological replica2

description: control fly with bacteria


title: PBMC control biological rep1


title: PBMC control biological rep7


title: gyc76c[KG03723] mutant adult flies injected with bacteria

description: experimental fly with bacteria

source_name: adult flies 12hours after injection of Staphylococcus saprophyticus

growth_protocol: Adult flies for each genotype were reared in standard cornmeal medium at 25C.

treatment_protocol: Adult flies 12hours after injection of PBS or Staphylococcus saprophyticus were homogenized in the Trizol solution (Invitrogen).

value: adult fly


title: gyc76c[KG03723] mutant larvae after bacteria injection, biological replica2

description: experimental fly with bacteria


title: gyc76c[revert] control adult flies injected with bacteria

description: control fly with bacteria


title: PBMC control biological rep2


title: gyc76c[KG03723] mutant larvae before injection, biological replica1

description: experimental fly without bacteria

source_name: larvae before injection


title: PBMC control biological rep4


title: spz[rm7] mutant adult flies injected with bacteria

description: experimental fly with bacteria


title: yw control lavae before injection, biological replica1

description: control fly without bacteria


title: Dif/Dl[J4] mutant larvae before injection

description: control fly without bacteria


title: Dif/Dl[J4] mutant larvae after bacteria injection

description: control fly with bacteria


title: spz[rm7] mutant adult flies injected with PBS

description: experimental fly without bacteria

source_name: adult flies 12hours after injection of PBS


title: PBMC control biological rep3


title: gyc76c[KG03723] mutant larvae before injection, biological replica2

description: experimental fly without bacteria


title: gyc76c[KG03723] mutant adult flies injected with PBS

description: experimental fly without bacteria


title: Tfpi KD [Sample-5M]

type: SRA

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

library_source: transcriptomic

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)
Supplementary_files_format_and_content: Tfpi_rat_TS_KD_processed_data.xlsx: Excel file includes RPKM values.

organism: Rattus norvegicus

source_name: Rat trophoblast stem cell

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility.

tag: cell type

value: trophoblast stem cells

tag: shRNA

value: Tfpi

tag: time point

value: differentiation day 8


title: Tfpi KD [Sample-6M]

description:
Sample-6M
Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age). Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.


title: Tfpi KD [Sample-4M]

description:
Sample-4M
Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age). Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.


title: Control [Sample-3M]

description:
Sample-3M
Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age). Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.


title: yw control lavae before injection, biological replica2

description: control fly without bacteria


title: Differentiated Rat trophoblast stem cell [Sample_D8-3]

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: rat reference genome (Ensembl Rnor_5.0.78)
Supplementary_files_format_and_content: Stem_vs_D8.xlsx: Excel file includes RPKM values.


title: Control [Sample-2M]

description:
Sample-2M
Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age). Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.


title: Rat trophoblast stem cell [Sample_C2Stem]


title: Differentiated Rat trophoblast stem cell [Sample_D8-2]


title: Rat trophoblast stem cell [Sample_C1Stem]


title: Differentiated Rat trophoblast stem cell [Sample_D8-1]


title: wsj_C3: rat helenalin rep3

city: Nanning

first: xing

last: lin

address: Shuangyong Road

country: China

institute: Guangxi medical university

data_processing:
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Genome_build: mm9

source_name: hepatitis stage liver

growth_protocol: model group and TA group were induced liver fibrosis  by CCl4,normal group were given same dose normal saline

extract_protocol:
Total RNA was extracted from liver tissues with Trizol reagent
NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）,AMPure XP system

treatment_protocol: helenalin group were treated with helenalin

tag: Sex

tag: strain

value: SD

value: liver

tag: condition

value: hepatitis stage


title: wsj_A2: rat wt rep2

source_name: normal control liver

value: normal control


title: wsj_A3: rat wt rep3


title: gyc76c[revert] control adult flies injected with PBS

description: control fly without bacteria


title: larvae overexpressing Gyc76C, biological replica 2

description: experimental larvae overexpressing Gyc76c in fat body

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

source_name: larvae over-exp Gyc76C

growth_protocol: Progenies from crossing between C564-Gal4 and UAS-GFP or UAS-Gyc76C were developed until 3rd inster larvae at 25C.

treatment_protocol: Larvae for each genotype were homogenized in the Trizol solution (Invitrogen).

value: C564-Gal4; UAS-Gyc76C


title: wsj_C1: rat helenalin rep1


title: larvae overexpressing GFP, biological replica 1

description: control larvae expressing GFP

source_name: larvae over-exp GFP

value: C564-Gal4; UAS-GFP


title: wsj_B3: rat model rep3


title: wsj_B2: rat model rep2


title: wsj_B1: rat model rep1


title: wsj_A1: rat wt rep1


title: Control [Sample-1M]

description:
Sample-1M
Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age). Mating was assessed by inspection of vaginal lavages. The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.


title: larvae overexpressing Gyc76C, biological replica 1


title: Sample117.Zebra.204551090061_R03C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

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

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Skin species=Zebra

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

molecule: genomic DNA

organism: Equus quagga burchellii

source_name: Skin

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: confidenceinageestimate

tag: canbeusedforagingstudies

value: yes

value: Male


title: Sample118.Zebra.204551090061_R04C02

value: Female


title: Sample116.Zebra.204551090061_R02C02


title: Sample112.Zebra.204551090061_R04C01


title: Sample113.Zebra.204551090061_R05C01


title: Sample114.Zebra.204551090061_R06C01


title: Sample115.Zebra.204551090061_R01C02


title: Rat trophoblast stem cell [Sample_C3Stem]


title: larvae overexpressing GFP, biological replica 2

description: control larvae expressing GFP


title: Sample103.Zebra.204551090030_R01C02


title: Sample97.Zebra.204551090030_R01C01


title: Sample101.Zebra.204551090030_R05C01


title: Sample102.Zebra.204551090030_R06C01


title: Sample100.Zebra.204551090030_R04C01


title: Sample111.Zebra.204551090061_R03C01


title: Sample104.Zebra.204551090030_R02C02


title: Sample99.Zebra.204551090030_R03C01


title: Sample107.Zebra.204551090030_R05C02


title: wsj_C2: rat helenalin rep2

value: male


title: Sample119.Zebra.204551090061_R05C02


title: Sample92.Zebra.203203210168_R02C02

description: genomic DNA methylation from tissue=Blood species=Zebra

source_name: Blood


title: Sample96.Zebra.203203210168_R06C02


title: Sample110.Zebra.204551090061_R02C01


title: Sample109.Zebra.204551090061_R01C01


title: Sample90.Zebra.203203210168_R06C01


title: Sample86.Zebra.203203210168_R02C01


title: Sample106.Zebra.204551090030_R04C02


title: Sample91.Zebra.203203210168_R01C02


title: Sample95.Zebra.203203210168_R05C02


title: Sample84.Zebra.203203210119_R06C02


title: Sample94.Zebra.203203210168_R04C02


title: Sample93.Zebra.203203210168_R03C02


title: Sample83.Zebra.203203210119_R05C02


title: Sample89.Zebra.203203210168_R05C01


title: Sample87.Zebra.203203210168_R03C01


title: Sample88.Zebra.203203210168_R04C01


title: Sample76.Zebra.203203210119_R04C01


title: Sample78.Zebra.203203210119_R06C01


title: Sample73.Zebra.203203210119_R01C01


title: Sample77.Zebra.203203210119_R05C01


title: Sample105.Zebra.204551090030_R03C02


title: Sample85.Zebra.203203210168_R01C01


title: Sample68.Zebra.203203210155_R02C02


title: Sample70.Zebra.203203210155_R04C02


title: Sample69.Zebra.203203210155_R03C02


title: Sample81.Zebra.203203210119_R03C02


title: Sample80.Zebra.203203210119_R02C02


title: Sample82.Zebra.203203210119_R04C02


title: Sample79.Zebra.203203210119_R01C02


title: Sample64.Zebra.203203210155_R04C01


title: Sample65.Zebra.203203210155_R05C01


title: Sample75.Zebra.203203210119_R03C01


title: Sample74.Zebra.203203210119_R02C01


title: Sample62.Zebra.203203210155_R02C01


title: Sample71.Zebra.203203210155_R05C02


title: Sample72.Zebra.203203210155_R06C02


title: Sample63.Zebra.203203210155_R03C01


title: Sample67.Zebra.203203210155_R01C02


title: Sample61.Zebra.203203210155_R01C01


title: Sample66.Zebra.203203210155_R06C01


title: Sample59.Zebra.203203210188_R05C02


title: Sample57.Zebra.203203210188_R03C02


title: Sample60.Zebra.203203210188_R06C02


title: Sample56.Zebra.203203210188_R02C02


title: Sample54.Zebra.203203210188_R06C01


title: Sample55.Zebra.203203210188_R01C02


title: Sample51.Zebra.203203210188_R03C01


title: Sample53.Zebra.203203210188_R05C01


title: Sample52.Zebra.203203210188_R04C01


title: Sample50.Zebra.203203210188_R02C01


title: Sample48.Zebra.203203210116_R06C02


title: Sample49.Zebra.203203210188_R01C01


title: Sample46.Zebra.203203210116_R04C02


title: Sample42.Zebra.203203210116_R06C01


title: Sample41.Zebra.203203210116_R05C01


title: Sample43.Zebra.203203210116_R01C02


title: Sample45.Zebra.203203210116_R03C02


title: Sample37.Zebra.203203210116_R01C01


title: Sample39.Zebra.203203210116_R03C01


title: Sample35.Zebra.203203210213_R05C02


title: Sample38.Zebra.203203210116_R02C01


title: Sample34.Zebra.203203210213_R04C02


title: Sample33.Zebra.203203210213_R03C02


title: Sample32.Zebra.203203210213_R02C02


title: Sample58.Zebra.203203210188_R04C02


title: Sample36.Zebra.203203210213_R06C02


title: Sample29.Zebra.203203210213_R05C01


title: Sample31.Zebra.203203210213_R01C02


title: Sample26.Zebra.203203210213_R02C01


title: Sample25.Zebra.203203210213_R01C01


title: Sample27.Zebra.203203210213_R03C01


title: Sample24.Zebra.203203210185_R06C02


title: Sample30.Zebra.203203210213_R06C01


title: Sample47.Zebra.203203210116_R05C02


title: Sample23.Zebra.203203210185_R05C02


title: Sample22.Zebra.203203210185_R04C02


title: Sample21.Zebra.203203210185_R03C02


title: Sample44.Zebra.203203210116_R02C02


title: Sample28.Zebra.203203210213_R04C01


title: Sample40.Zebra.203203210116_R04C01


title: Sample20.Zebra.203203210185_R02C02


title: Sample17.Zebra.203203210185_R05C01


title: Sample16.Zebra.203203210185_R04C01


title: Sample18.Zebra.203203210185_R06C01


title: Sample19.Zebra.203203210185_R01C02


title: Sample13.Zebra.203203210185_R01C01


title: Sample14.Zebra.203203210185_R02C01


title: Sample15.Zebra.203203210185_R03C01


title: Sample10.Zebra.203203210171_R04C02


title: Sample11.Zebra.203203210171_R05C02


title: Sample7.Zebra.203203210171_R01C02


title: Sample9.Zebra.203203210171_R03C02


title: Sample6.Zebra.203203210171_R06C01


title: Sample12.Zebra.203203210171_R06C02


title: Sample8.Zebra.203203210171_R02C02


title: Sample5.Zebra.203203210171_R05C01


title: Sample4.Zebra.203203210171_R04C01


title: Sample1.Zebra.203203210171_R01C01


title: Sample764.Grevy's zebra.204529320041_R01C01

description: genomic DNA methylation from tissue=Blood species=Grevy's zebra

organism: Equus grevyi

tag: basename


title: Sample2.Zebra.203203210171_R02C01


title: Sample3.Zebra.203203210171_R03C01


title: Sample763.Grevy's zebra.204529320032_R06C02


title: Sample759.Grevy's zebra.204529320032_R02C02


title: Sample744.Somali wild ass.204529320039_R05C01

description: genomic DNA methylation from tissue=Blood species=Somali wild ass

organism: Equus asinus somalicus


title: Sample769.Somali wild ass.204529320041_R06C01


title: Sample732.Somali wild ass.204529320115_R05C01


title: Sample645.Grevy's zebra.204529320038_R02C01


title: Sample758.Somali wild ass.204529320032_R01C02


title: Sample347.Somali wild ass.203877620071_R06C02


title: Sample346.Somali wild ass.203877620071_R05C02


title: Sample348.Somali wild ass.203867110006_R01C01


title: Sample762.Grevy's zebra.204529320032_R05C02


title: Sample328.Horse.203203210081_R04C01

description: genomic DNA methylation from tissue=Liver species=Horse

label: Cy3 and Cy5

organism: Equus caballus

source_name: Liver

value: Liver

tag: tissuedetailed


title: Sample336.Horse.203203210081_R06C02


title: Sample324.Horse.203203210175_R06C02


title: Sample327.Horse.203203210081_R03C01


title: Sample326.Horse.203203210081_R02C01


title: Sample335.Horse.203203210081_R05C02


title: Sample333.Horse.203203210081_R03C02


title: Sample317.Horse.203203210175_R05C01


title: Sample329.Horse.203203210081_R05C01


title: Sample334.Horse.203203210081_R04C02


title: Sample331.Horse.203203210081_R01C02


title: Sample321.Horse.203203210175_R03C02


title: Sample316.Horse.203203210175_R04C01


title: Sample320.Horse.203203210175_R02C02


title: Sample323.Horse.203203210175_R05C02


title: Sample322.Horse.203203210175_R04C02


title: Sample330.Horse.203203210081_R06C01


title: Sample318.Horse.203203210175_R06C01


title: Sample332.Horse.203203210081_R02C02


title: Sample311.Horse.203203210181_R05C02


title: Sample314.Horse.203203210175_R02C01


title: Sample312.Horse.203203210181_R06C02


title: Sample313.Horse.203203210175_R01C01


title: Sample308.Horse.203203210181_R02C02


title: Sample315.Horse.203203210175_R03C01


title: Sample98.Zebra.204551090030_R02C01


title: Sample309.Horse.203203210181_R03C02


title: Sample325.Horse.203203210081_R01C01


title: Sample310.Horse.203203210181_R04C02


title: Sample307.Horse.203203210181_R01C02


title: Sample319.Horse.203203210175_R01C02


title: Sample303.Horse.203203210181_R03C01


title: Sample306.Horse.203203210181_R06C01


title: Sample302.Horse.203203210181_R02C01


title: Sample305.Horse.203203210181_R05C01


title: Sample300.Horse.203203210120_R06C02


title: Sample293.Horse.203203210120_R05C01


title: Sample289.Horse.203203210120_R01C01

tag: thoroughbred mare identifier

value: Chatty Patty


title: Sample292.Horse.203203210120_R04C01


title: Sample287.Horse.203203210197_R05C02

description: genomic DNA methylation from tissue=Mammary species=Horse

source_name: Mammary

value: Mammary


title: Sample294.Horse.203203210120_R06C01


title: Sample291.Horse.203203210120_R03C01


title: Sample301.Horse.203203210181_R01C01


title: Sample295.Horse.203203210120_R01C02

value: Wild Guneva Star


title: Sample282.Horse.203203210197_R06C01

description: genomic DNA methylation from tissue=ParietalCortex species=Horse

source_name: ParietalCortex

value: ParietalCortex

value: Parietal Lobe


title: Sample284.Horse.203203210197_R02C02

description: genomic DNA methylation from tissue=Cecum species=Horse

source_name: Cecum

value: Cecum


title: Sample298.Horse.203203210120_R04C02


title: Sample296.Horse.203203210120_R02C02


title: Sample304.Horse.203203210181_R04C01


title: Sample279.Horse.203203210197_R03C01

description: genomic DNA methylation from tissue=Pituitary species=Horse

source_name: Pituitary

value: Pituitary


title: Sample286.Horse.203203210197_R04C02

description: genomic DNA methylation from tissue=Hypothalamus species=Horse

source_name: Hypothalamus

value: Hypothalamus


title: Sample285.Horse.203203210197_R03C02


title: Sample281.Horse.203203210197_R05C01


title: Sample277.Horse.203203210197_R01C01

description: genomic DNA methylation from tissue=Muscle species=Horse

source_name: Muscle

value: Muscle

value: Longissimus


title: Sample297.Horse.203203210120_R03C02


title: Sample276.Horse.203203210196_R06C02

description: genomic DNA methylation from tissue=Kidney species=Horse

source_name: Kidney

value: Kidney

value: Kidney Medulla


title: Sample275.Horse.203203210196_R05C02


title: Sample278.Horse.203203210197_R02C01


title: Sample280.Horse.203203210197_R04C01


title: Sample283.Horse.203203210197_R01C02


title: Sample265.Horse.203203210196_R01C01

description: genomic DNA methylation from tissue=Cortex species=Horse

source_name: Cortex

value: Cortex

value: Frontal Lobe


title: Sample299.Horse.203203210120_R05C02


title: Sample272.Horse.203203210196_R02C02

description: genomic DNA methylation from tissue=Cerebellum species=Horse

source_name: Cerebellum

value: Cerebellum

value: Cerebellum Vermis


title: Sample271.Horse.203203210196_R01C02


title: Sample266.Horse.203203210196_R02C01


title: Sample288.Horse.203203210197_R06C02


title: Sample270.Horse.203203210196_R06C01


title: Sample269.Horse.203203210196_R05C01


title: Sample274.Horse.203203210196_R04C02

description: genomic DNA methylation from tissue=Heart species=Horse

source_name: Heart

value: Heart

value: Heart Left Ventricle


title: Sample261.Horse.203203210184_R03C02

value: Chatty Patty


title: Sample263.Horse.203203210184_R05C02

description: genomic DNA methylation from tissue=Uterus species=Horse

source_name: Uterus

value: Uterus


title: Sample268.Horse.203203210196_R04C01

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

source_name: Fibroblast

value: Wild Guneva Star

value: Fibroblast

value: Fibroblasts


title: Sample257.Horse.203203210184_R05C01

value: Cerebellum Lateral Hemisphere


title: Sample262.Horse.203203210184_R04C02

value: Cecum


title: Sample273.Horse.203203210196_R03C02


title: Sample267.Horse.203203210196_R03C01


title: Sample258.Horse.203203210184_R06C01


title: Sample256.Horse.203203210184_R04C01

value: Muscle


title: Sample260.Horse.203203210184_R02C02

description: genomic DNA methylation from tissue=Sacrocaudalis species=Horse

source_name: Sacrocaudalis

value: Sacrocaudalis


title: Sample264.Horse.203203210184_R06C02


title: Sample259.Horse.203203210184_R01C02


title: Sample250.Horse.203203210177_R04C02

value: Mammary


title: Sample251.Horse.203203210177_R05C02

description: genomic DNA methylation from tissue=Lamina species=Horse

source_name: Lamina

value: Lamina


title: Sample254.Horse.203203210184_R02C01

value: Kidney

value: Kidney Medulla


title: Sample253.Horse.203203210184_R01C01


title: Sample249.Horse.203203210177_R03C02


title: Sample248.Horse.203203210177_R02C02

value: Liver


title: sirt3ko_cr biological replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

data_processing: The data were analyzed with Affymetrix Exression Console version 1.4 using RMA

organism: Mus musculus

source_name: Sirt3 knockout mouse, calorie restricted diet

tag: genotype/variation

value: Sirt3 knockout

value: male

value: calorie restricted


title: sirt3ko_cr biological replicate 2

tag: diet


title: sirt3ko_cr biological replicate 3

tag: gender


title: Sample255.Horse.203203210184_R03C01

value: Chatty Patty

tag: tissue

value: Longissimus


title: sirt3ko_cr biological replicate 4


title: Sample245.Horse.203203210177_R05C01

description: genomic DNA methylation from tissue=TemporalCortex species=Horse

source_name: TemporalCortex

value: TemporalCortex

value: Temporal Lobe


title: sirt3ko_control biological replicate 3

source_name: Sirt3 knockout mouse, control diet

value: control


title: sirt3ko_control biological replicate 2


title: sirt3ko_control biological replicate 4


title: Sample246.Horse.203203210177_R06C01

value: Wild Guneva Star


title: Sample252.Horse.203203210177_R06C02


title: Sample243.Horse.203203210177_R03C01

description: genomic DNA methylation from tissue=Tendon species=Horse

source_name: Tendon

value: Tendon

value: Superficial Digital Flexor Tendon


title: Sample244.Horse.203203210177_R04C01


title: HF-Sugar_M3

city: Seoul

first: Woo-Jeong

last: Shon

address: 103 Daehak-ro, Jongno-gu,

department: College of Medicine

country: South Korea

institute: Seoul National University

data_processing:
Sequenced reads were mapped to mm10 whole genome using Torrent Suite Software version 4.0.2.
After mapping and aligning, the resulting BAM files were imported into Partek® Genomics Suite software v6.3 (Partek Inc.) (http://www.partek.com/partekgs) and converted into gene transcript levels as reads per kilobase of exon per million mapped reads (RPKM) with the use of a mixed-model approach.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: Small intestine (ileum)

extract_protocol:
Ileum was removed and snap frozen in liquid nitrogen. Total RNA from each mouse ileum tissue was isolated individually using RNA queouse-4PCR Kit (Ambion). Quality and concentration of the extracted total RNA using Agilent 2100 Bioanalyzer (Agilent Technologies). Out of the samples with RNA integrity number (RIN) greater than 8, a total of 12 samples (3 samples per group) were randomly selected to be sequenced.
Libraries were prepared for sequencing using the Ion Total RNA-Seq Kit v2 protocol (Life Technologies) using an equal total RNA input of 5µg from every sample.

value: Small intestine (ileum)

value: 16 weeks (6 weeks + diet induction for 10 weeks)

value: High fat (60% Kcal from fat) diet + 23%(w/v) sugar drink


title: sirt3ko_control biological replicate 1


title: Sample247.Horse.203203210177_R01C02

description: genomic DNA methylation from tissue=Liver species=Horse

source_name: Liver


title: Sample240.Horse.203203210194_R06C02

value: Deep Digital Flexor Tendon


title: wildtype cr biological replicate 4

source_name: wildtype mouse, calorie restricted diet

value: wildtype


title: wildtype cr biological replicate 2


title: wildtype cr biological replicate 1


title: Sample242.Horse.203203210177_R02C01

description: genomic DNA methylation from tissue=Duodenum species=Horse

source_name: Duodenum

value: Duodenum


title: wildtype cr biological replicate 3


title: Sample238.Horse.203203210194_R04C02

description: genomic DNA methylation from tissue=Keratinocyte species=Horse

source_name: Keratinocyte

value: Keratinocyte

value: Keratinocytes


title: Sample239.Horse.203203210194_R05C02


title: PR8

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

data_processing:
The Cell Ranger software pipeline (version 5.0) provided by 10X Genomics was used to demultiplex celluar barcodes, map reads to the genome
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: Lung

extract_protocol:
Mock or IAV infected mice (250 PFUS) were euthanized at 7 days p.i. and whole lungs were perfused with cold PBS. Lungs were aseptically removed and placed in 1 mL complete media (10% FBS, 1% Pen/Strep in RPMI). A single-cell suspension was prepared as noted above. For CD45+ cell isolation, mock and IAV-infected lungs (n=5/group) were pooled, stained for CD45 (30-F11, BioLegend) for 1 h at RT, and sorted using the BD FACSAriaTM into 40% FBS/RPMI. After sorting, 2 x 106 cells were washed and resuspended in medium containing 10% DMSO, 20% FBS and RPMI. Cells were slowly frozen in Mr. Frosty and shipped to SingulOmics (NYC, NY).
RNA libraries were prepared with the Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: Lung

tag: genotype

value: wild type

tag: treatment

value: Influenza A Virus (IAV)


title: Mock infection, Lung

tag: age

value: mock


title: HF-Sugar_M2


title: wildtype control biological replicate 2

source_name: wildtype mouse, control diet

value: male


title: Sample236.Horse.203203210194_R02C02

value: Heart

value: Heart Right Ventricle


title: Sample233.Horse.203203210194_R05C01

description: genomic DNA methylation from tissue=Cartilage species=Horse

source_name: Cartilage

value: Chatty Patty

value: Cartilage


title: Sample232.Horse.203203210194_R04C01

description: genomic DNA methylation from tissue=Suspensory species=Horse

source_name: Suspensory

value: Wild Guneva Star

value: Suspensory


title: Sample234.Horse.203203210194_R06C01


title: Sample235.Horse.203203210194_R01C02

source_name: Heart


title: HF-Sugar_M1

value: Small intestine (ileum)

value: 16 weeks (6 weeks + diet induction for 10 weeks)

value: High fat (60% Kcal from fat) diet + 23%(w/v) sugar drink


title: wildtype control biological replicate 3

value: wildtype

value: control


title: Sample231.Horse.203203210194_R03C01


title: Sample237.Horse.203203210194_R03C02

value: Keratinocyte

value: Keratinocytes


title: Sample230.Horse.203203210194_R02C01

description: genomic DNA methylation from tissue=SpinalCord species=Horse

source_name: SpinalCord

value: SpinalCord

value: Spinal Cord T8


title: Sample229.Horse.203203210194_R01C01


title: HF_M2

value: High fat (60% Kcal from fat) diet + plain water


title: wildtype control biological replicate 1

value: male


title: NF-Sugar_M3

value: Normal fat diet + 23%(w/v) sugar drink


title: HF_M1


title: NF-Sugar_M2


title: NF-Sugar_M1


title: Sample227.Horse.203203210182_R05C02

description: genomic DNA methylation from tissue=AdrenalCortex species=Horse

source_name: AdrenalCortex

value: AdrenalCortex

value: Adrenal Cortex


title: Sample222.Horse.203203210182_R06C01

description: genomic DNA methylation from tissue=Skin species=Horse

source_name: Skin

value: Skin


title: Sample223.Horse.203203210182_R01C02

description: genomic DNA methylation from tissue=ParietalCortex species=Horse

source_name: ParietalCortex

value: Chatty Patty

value: ParietalCortex

value: Parietal Lobe


title: Sample226.Horse.203203210182_R04C02

value: Wild Guneva Star

value: Heart

value: Heart Left Atrium


title: HF_M3

value: Small intestine (ileum)

value: 16 weeks (6 weeks + diet induction for 10 weeks)


title: Sample221.Horse.203203210182_R05C01


title: Sample228.Horse.203203210182_R06C02


title: Sample218.Horse.203203210182_R02C01

description: genomic DNA methylation from tissue=OccipitalCortex species=Horse

source_name: OccipitalCortex

value: OccipitalCortex

value: Occipital Lobe


title: NF_M3

value: Normal fat diet + plain water


title: NF_M2


title: Sample225.Horse.203203210182_R03C02

description: genomic DNA methylation from tissue=Heart species=Horse


title: Sample219.Horse.203203210182_R03C01

description: genomic DNA methylation from tissue=MitralValve species=Horse

source_name: MitralValve

value: MitralValve

value: Mitral Valve


title: NF_M1


title: Sample220.Horse.203203210182_R04C01


title: Sample217.Horse.203203210182_R01C01


title: Amplicon_combo_ko_Donor3_gDNA9_KLF2

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

library_source: genomic

data_processing:
Adapter sequences were trimmed from fastq files using cutadapt version 2.8 using default settings keeping a minimum read length of 50 bp. Insertions and deletions at each CRISPR target site were then calculated using Crispresso2 version 2.0.42 (Clement et al. 2019) with the following options "--quantification_window_size 3" and "--ignore_substitutions".
Genome_build: hg38
Supplementary_files_format_and_content: Combo_KO_amplicons_modified.txt

organism: Homo sapiens

source_name: CD4+CD25- T cells

growth_protocol: Cells were grown in RPMI (Sigma, Cat # R0883) with 10% FCS (Sigma, Cat # F0926), with 100U/mL Pen-Strep (Gibco, Cat # 15140-122), 2mM L-Glutamine (Sigma, Cat # G7513), 10mM HEPES (Sigma, Cat # H0887), 1X MEM Non-essential Amino Acids (Gibco, Cat # 11140-050), 1mM Sodium Pyruvate (Gibco, Cat # 11360-070), and 50 U/mL IL-2 (Amerisource Bergen, Cat #10101641) at a concentration of 1E6 cells/mL.

extract_protocol:
On day 5 post-electroporation, genomic DNA was isolated from each sample using DNA QuickExtract (Lucigen, Cat #QE09050) according to the manufacturer’s protocol.
Primers were designed to flank each sgRNA genomic target site. Amplicons containing CRISPR edit sites were generated by adding 1.25 µL each of forward and reverse primer at 10nM to 5 µL of sample in QuickExtract, 12.5 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), and H2O to a total 25 µL reaction volume. The following PCR cycling conditions were used: 98°C for 3 minutes, 15 cycles of 94°C for 20 seconds followed by 65°C-57.5°C for 20 seconds (0.5°C incremental decreases per cycle), and 72°C for 1 minute, and a subsequent 20 cycles at 94°C for 20 seconds, 58°C for 20 seconds and 72°C for 1 minute, and a final 10 minute extension at 72°C. Samples were then diluted 1:200 and subsequently Illumina sequencing adapters and indices were added in a second PCR reaction. Indexing reactions included 1 µL of the diluted PCR1 sample, 2.5 µL of each the forward and reverse indexing primers at 10 µM each, 12.5 µL of NEB Q5 master mix, and H2O to a total 25 µL reaction volume. The following PCR cycling conditions were used: 98°C for 30 seconds, followed by 98°C for 10 seconds, 60°C for 30 seconds, and 72°C for 30 seconds for 12 cycles, and a final extension period at 72°C for 2 minutes. Samples were quantified in a 96-well plate reader using the Quant-IT DNA high sensitivity assay kit (Invitrogen, Cat #Q33232) according to the manufacturer’s protocol and pooled into 1 tube. Post pooling, samples were then SPRI purified, and quantified using an Agilent 4200 TapeStation. Samples were then sequenced on an Illumina NovaSeq with PE 300 reads.
Amplicon sequencing

treatment_protocol: GuideRNA/Cas9 ribonucleoprotein complexes were electroporated into CD4+CD25- T cells.

tag: cell type

value: CD4+CD25- T cells


title: Sample216.Horse.203203210193_R06C02

value: SpinalCord

value: Spinal Cord C1


title: Sample215.Horse.203203210193_R05C02


title: Sample214.Horse.203203210193_R04C02

description: genomic DNA methylation from tissue=Muscle species=Horse

source_name: Muscle

value: Muscle

value: Gluteal


title: Amplicon_combo_ko_Donor3_gDNA9_IRF4


title: Amplicon_combo_ko_Donor3_gDNA8_CBFB


title: Amplicon_combo_ko_Donor3_gDNA7_KLF2


title: Amplicon_combo_ko_Donor3_gDNA8_IRF4


title: Sample211.Horse.203203210193_R01C02

description: genomic DNA methylation from tissue=Spleen species=Horse

source_name: Spleen

value: Chatty Patty

value: Spleen


title: Sample212.Horse.203203210193_R02C02

value: Wild Guneva Star


title: Sample207.Horse.203203210193_R03C01

description: genomic DNA methylation from tissue=Larynx species=Horse

source_name: Larynx

value: Larynx


title: Sample213.Horse.203203210193_R03C02


title: Amplicon_combo_ko_Donor3_gDNA7_STAT5B


title: Amplicon_combo_ko_Donor3_gDNA6_CBFB


title: Sample209.Horse.203203210193_R05C01

value: Heart

value: Heart Right Atium


title: Sample208.Horse.203203210193_R04C01


title: Sample204.Horse.203203210045_R06C02

description: genomic DNA methylation from tissue=Ileum species=Horse

source_name: Ileum

value: Ileum


title: Sample199.Horse.203203210045_R01C02

description: genomic DNA methylation from tissue=Lung species=Horse

value: Lung


title: Sample201.Horse.203203210045_R03C02

description: genomic DNA methylation from tissue=Adipose species=Horse

source_name: Adipose

value: Adipose

value: Gluteal Adipose


title: Sample196.Horse.203203210045_R04C01

description: genomic DNA methylation from tissue=Kidney species=Horse

source_name: Kidney

value: Kidney

value: Kidney Cortex


title: Sample195.Horse.203203210045_R03C01


title: Sample202.Horse.203203210045_R04C02


title: Sample205.Horse.203203210193_R01C01

description: genomic DNA methylation from tissue=Jejunum species=Horse

source_name: Jejunum

value: Jejunum


title: Amplicon_combo_ko_Donor3_gDNA6_STAT5B

value: CD4+CD25- T cells


title: Sample203.Horse.203203210045_R05C02


title: Sample198.Horse.203203210045_R06C01

description: genomic DNA methylation from tissue=Pituitary species=Horse

source_name: Pituitary

value: Pituitary


title: Sample200.Horse.203203210045_R02C02

source_name: Lung


title: Amplicon_combo_ko_Donor3_gDNA5_STAT5B


title: Sample197.Horse.203203210045_R05C01


title: Sample210.Horse.203203210193_R06C01

source_name: Heart


title: Sample206.Horse.203203210193_R02C01


title: Amplicon_combo_ko_Donor3_gDNA4_KLF2


title: Amplicon_combo_ko_Donor3_gDNA4_JAK3


title: Amplicon_combo_ko_Donor3_gDNA5_IRF4


title: Amplicon_combo_ko_Donor3_gDNA3_JAK3


title: Amplicon_combo_ko_Donor3_gDNA3_CBFB


title: Sample192.Horse.203203210206_R06C02

description: genomic DNA methylation from tissue=Blood species=Horse

source_name: Blood

value: Blood

value: Blood -Buffy Coat


title: Sample188.Horse.203203210206_R02C02


title: Sample190.Horse.203203210206_R04C02


title: Amplicon_combo_ko_Donor3_gDNA2_IRF4


title: Amplicon_combo_ko_Donor3_gDNA2_JAK3


title: Sample189.Horse.203203210206_R03C02


title: Sample191.Horse.203203210206_R05C02


title: Sample194.Horse.203203210045_R02C01

description: genomic DNA methylation from tissue=Ovaries species=Horse

source_name: Ovaries

value: Ovaries

value: Ovary


title: Sample187.Horse.203203210206_R01C02


title: Amplicon_combo_ko_Donor3_gDNA1_STAT5B


title: Sample186.Horse.203203210206_R06C01


title: Sample193.Horse.203203210045_R01C01

value: Chatty Patty


title: Sample185.Horse.203203210206_R05C01


title: Sample241.Horse.203203210177_R01C01

description: genomic DNA methylation from tissue=Duodenum species=Horse

source_name: Duodenum

value: Duodenum


title: Sample184.Horse.203203210206_R04C01


title: Sample183.Horse.203203210206_R03C01


title: Amplicon_combo_ko_Donor3_gDNA20_AAVS1_8


title: Amplicon_combo_ko_Donor3_gDNA19_AAVS1_7


title: Sample177.Horse.203203210080_R03C02


title: Sample178.Horse.203203210080_R04C02


title: Sample179.Horse.203203210080_R05C02


title: Sample180.Horse.203203210080_R06C02


title: Sample182.Horse.203203210206_R02C01


title: Sample174.Horse.203203210080_R06C01


title: Amplicon_combo_ko_Donor3_gDNA18_AAVS1_4


title: Amplicon_combo_ko_Donor3_gDNA16_IL2RA


title: Amplicon_combo_ko_Donor3_gDNA17_AAVS1_3


title: Amplicon_combo_ko_Donor3_gDNA16_AAVS1_3


title: Amplicon_combo_ko_Donor3_gDNA1_JAK3


title: Sample173.Horse.203203210080_R05C01


title: Amplicon_combo_ko_Donor3_gDNA15_KLF2


title: Sample176.Horse.203203210080_R02C02


title: Sample181.Horse.203203210206_R01C01


title: Sample172.Horse.203203210080_R04C01


title: Sample171.Horse.203203210080_R03C01


title: kidney_cr_biologicalrep4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
program-name = Expression Console
program-id = 1.3.1.187

source_name: Kidney_Calorie Restricted diet

value: male

tag: diet group

value: Calorie Restricted diet

value: kidney


title: Sample170.Horse.203203210080_R02C01


title: Sample169.Horse.203203210080_R01C01


title: Sample224.Horse.203203210182_R02C02

source_name: ParietalCortex

value: Wild Guneva Star

value: ParietalCortex

value: Parietal Lobe


title: Amplicon_combo_ko_Donor3_gDNA14_AAVS1_3


title: Sample168.Horse.203203210150_R06C02


title: Amplicon_combo_ko_Donor3_gDNA15_AAVS1_3


title: kidney_cr_biologicalrep1


title: kidney_cr_biologicalrep2


title: kidney_cr_biologicalrep5


title: Sample167.Horse.203203210150_R05C02


title: kidney_control_biologicalrep4

source_name: Kidney_Control diet

value: control diet


title: kidney_control_biologicalrep2


title: kidney_control_biologicalrep5


title: N2/Ca, rep3

city: Marseille

first: Thomas

last: Vannier

address: Campus de Luminy, 163 Av. de Luminy

country: France

institute: Aix-Marseille University

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
The quality of the raw reads was assessed using FastQC v0.11.9 toolkit.
Adapters and low-quality reads were trimmed using Trimmomatic v0.39
The reads were aligned with HiSat2 v2.2.1 using default options.
Gene counts were then normalized and used for differential expression testing using DESeq2 v1.28.0
Genome_build: Saccharomyces cerevisiae S288C (assembly R64)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts value from DESeq2 of each Sample

organism: Saccharomyces cerevisiae

source_name: Total RNA

growth_protocol: Budding yeast cells (2 ODs) were harvested from log phase cultures growing in YPD (2% bacto-peptone, 1% yeast extract, 2% dextrose) at 25ºC.

extract_protocol:
RNA was extracted using a RNeasy Mini Kit (Qiagen) following manufacturer’s instructions.
P2598 : RNA-Seq libraries were generated according to manufacturer's instructions from 500 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dTTP in place of dUTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 10 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Cells were lysed mechanically using glass beads (425-600 μm, Sigma-Aldrich) in Precellys 24 Tissue Homogenizer. Samples were cleared on QIAshredder columns (Qiagen).

tag: ploidy

value: diploid


title: N2/Ca, rep2

tag: strain


title: Amplicon_combo_ko_Donor3_gDNA12_AAVS1_3

source_name: CD4+CD25- T cells


title: kidney_cr_biologicalrep3


title: Amplicon_combo_ko_Donor3_gDNA14_CBFB


title: N2/Ca, rep1


title: Sc/Sc, rep3

value: Sc/Sc


title: kidney_control_biologicalrep3


title: Sample175.Horse.203203210080_R01C02


title: Amplicon_combo_ko_Donor3_gDNA11_AAVS1_3

value: CD4+CD25- T cells


title: Sample164.Horse.203203210150_R02C02


title: Sample166.Horse.203203210150_R04C02


title: Sc/Sc, rep2


title: Amplicon_combo_ko_Donor3_gDNA13_IRF4


title: Amplicon_combo_ko_Donor3_gDNA10_KLF2


title: Amplicon_combo_ko_Donor3_gDNA13_AAVS1_3


title: Sc/Sc, rep1


title: Sample165.Horse.203203210150_R03C02


title: kidney_control_biologicalrep1


title: Amplicon_combo_ko_Donor3_gDNA12_STAT5B


title: Sample160.Horse.203203210150_R04C01


title: Sample158.Horse.203203210150_R02C01


title: Sample159.Horse.203203210150_R03C01


title: Sample157.Horse.203203210150_R01C01


title: Sample163.Horse.203203210150_R01C02


title: liver_krillpowder_rep7

description: Gene expression data from mice consuming diet containing krill powder

source_name: Liver, krill powder diet, replicate 7

growth_protocol: Male CBA/J mice were purchased from Jackson Laboratory at six weeks of age and were individually housed and fed 84 kcal/week of a diet based on the AIN93M formulation

treatment_protocol: Starting at two months of age, mice were maintained on the control diet or were fed a test diet containing a krill powder extract (Aker BioMarine ASA, Norway). The two diets had equal amounts of total protein and total lipid, although the amino acid and fatty acid compositions differed. All diets were formulated by Bio-Serv (Frenchtown NJ, USA)

value: CBA/J

value: krill powder

value: liver


title: Ca, rep1

value: Ca

value: haploid


title: Sample162.Horse.203203210150_R06C01

value: Blood

value: Blood -Buffy Coat


title: Amplicon_combo_ko_Donor2_gDNA9_KLF2


title: liver_krillpowder_rep6

source_name: Liver, krill powder diet, replicate 6

value: male


title: N2, rep3


title: liver_control_rep7

description: Gene expression data from mice consuming control diet

source_name: Liver, Control diet, replicate 7

value: control


title: liver_control_rep6

source_name: Liver, Control diet, replicate 6


title: liver_krillpowder_rep5

source_name: Liver, krill powder diet, replicate 5


title: Amplicon_combo_ko_Donor2_gDNA8_CBFB


title: Sample161.Horse.203203210150_R05C01


title: Amplicon_combo_ko_Donor3_gDNA11_JAK3


title: Sample155.Horse.203203210167_R05C02


title: liver_control_rep5

source_name: Liver, Control diet, replicate 5


title: Sample154.Horse.203203210167_R04C02


title: Amplicon_combo_ko_Donor2_gDNA7_STAT5B


title: Amplicon_combo_ko_Donor2_gDNA8_IRF4


title: Amplicon_combo_ko_Donor3_gDNA10_CBFB


title: liver_krillpowder_rep4

source_name: Liver, krill powder diet, replicate 4


title: Amplicon_combo_ko_Donor2_gDNA6_STAT5B


title: liver_krillpowder_rep3

source_name: Liver, krill powder diet, replicate 3


title: Sc[At], rep3

value: Sc[At]


title: liver_krillpowder_rep2

source_name: Liver, krill powder diet, replicate 2


title: Ca, rep3


title: Sample153.Horse.203203210167_R03C02

source_name: Blood


title: Amplicon_combo_ko_Donor2_gDNA6_CBFB


title: liver_control_rep3

source_name: Liver, Control diet, replicate 3


title: Ca, rep2


title: Amplicon_combo_ko_Donor2_gDNA9_IRF4


title: liver_krillpowder_rep1

source_name: Liver, krill powder diet, replicate 1


title: Sample151.Horse.203203210167_R01C02


title: Sample152.Horse.203203210167_R02C02


title: Sample149.Horse.203203210167_R05C01


title: Sample156.Horse.203203210167_R06C02


title: Sample150.Horse.203203210167_R06C01


title: Sc[Sp], rep3

value: Sc[Sp]


title: liver_control_rep1

source_name: Liver, Control diet, replicate 1


title: 16354.T1

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 Bd Laurier

institute: Université Laval

description:
16S rRNA
See "Protocol 3" in the protocol section
16S_v1_species_count.txt

data_processing:
MiSeq BaseCalling
Trimming using trimmomatic v0.37 (ILLUMINACLIP:2:30:1, TRAILING:30 and MINLEN:36)
Pair merging using pandaseq  v2.11
Qiime 1.9.2 pipeline (doi:10.1038/nmeth.f.303)
Tab-separated file, Species raw count table, 16S_v1_species_count.txt

source_name: stool

extract_protocol:
DNA was isolated from fecal samples using the DNeasy PowerSoil Kit (QIAGEN)
Protocols 1 and 3: 15ng of DNA was used for an initial PCR amplification step of 25 cycles with specific bacterial 16S rRNA (V3-341F and V4-785R) hypervariable region oligos using Q5 High-Fidelity DNA polymerase (New England Biolabs, Whitby, Ontario, Canada). After purification with AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA), a second PCR amplification step of 8 cycles was performed to incorporate specific index adaptors for multiplexing. This step was followed by a purification step using AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA). The quality of the final libraries was examined with a DNA screentape D1000 on a TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA) and the quantification was performed with Quant-it HS (ThermoFisher Scientific, Canada) on a Victor3 plate reader fluorometer (PerkinElmer, Waltham, MA, USA). Protocol 2: DNA was quantified using QuantiFluor dye (Promega). Sequencing libraries were prepared using the Nextera Sample Preparation Kit (Illumina, San Diego, CA, USA) with 50 ng of purified DNA. Dual indices were added during library preparation. Libraries were validated using Agilent Bioanalyzer 2100 high sensitivity DNA chips (Agilent Technologies, Santa Clara, CA, USA) and were re-quantified with QuBit (ThermoFisher Scientific).
Protocols 1 and 3: 16S rRNA gene V3-V4 region. Protocol 2: Whole-genome shotgun sequencing

treatment_protocol: Protocol 1: Mice were administered ampicillin (1 g/l) in their drinking water and neomycin (10 mg/ml), metronidazole (10 mg/ml) and vancomycin (5 mg/ml) via oral gavage twice daily for 1 week. Twenty-four hours following the last antibiotic administration, mice were transferred to new cages and deprived of chow. Mice were fasted for 2 hours prior to receiving 250 µl of Moviprep at 30-minute intervals for a total of 5 administrations. Mice were then fasted for 6 additional hours before oral administration of 200 µl of fecal solution (fresh fecal pellets homogenized in sterile PBS 1× at 70–120 mg/ml and passed through a 70-µm filter) prepared using fecal pellets from donor WT or sPLA2-IIATGN mice. The administration of fresh fecal solution was repeated on the two following days. Arthritis was induced two weeks later, and its severity was monitored daily for 9 days before mice were euthanized. Feces were collected on days 0, 15 and 21 for microbiota composition assessment. Protocol 2: Mice were housed in an SPF animal facility for 8 months before their fecal microbiota was sequenced. Protocol 3: Mice were housed for up to 14 months in an Elite SPF+ animal facility and their fecal microbiota was sequenced at approximately 14 weeks and 14 months of age.

value: WT

tag: timepoint

value: 14 weeks


title: Sc[Sp], rep2


title: N2, rep2


title: N2, rep1


title: liver_control_rep4

source_name: Liver, Control diet, replicate 4


title: Amplicon_combo_ko_Donor2_gDNA7_KLF2


title: 16595.T2

value: 13 months


title: Sc[Sp], rep1

source_name: Total RNA


title: Sc[At], rep2


title: Amplicon_combo_ko_Donor2_gDNA3_JAK3

source_name: CD4+CD25- T cells


title: Sc[Ca], rep3

value: Sc[Ca]


title: Sample145.Horse.203203210167_R01C01


title: Sc[At], rep1


title: liver_control_rep2

source_name: Liver, Control diet, replicate 2


title: 16354.T2

value: 13.3 months


title: Amplicon_combo_ko_Donor2_gDNA5_STAT5B

value: CD4+CD25- T cells


title: Sample148.Horse.203203210167_R04C01


title: 16595.T1

value: 12 weeks


title: Sample144.Horse.203203210132_R06C02


title: Amplicon_combo_ko_Donor2_gDNA2_JAK3


title: Amplicon_combo_ko_Donor2_gDNA5_IRF4


title: Sc[Ca], rep1


title: Amplicon_combo_ko_Donor2_gDNA4_KLF2


title: ScNI, rep3

value: ScNI


title: 16343.T1


title: 16348.T2


title: Sample147.Horse.203203210167_R03C01


title: Sample146.Horse.203203210167_R02C01


title: 16348.T1


title: Amplicon_combo_ko_Donor2_gDNA4_JAK3


title: 16347.T2


title: Sample141.Horse.203203210132_R03C02


title: Sc[Ca], rep2


title: Amplicon_combo_ko_Donor2_gDNA19_AAVS1_7


title: Sample140.Horse.203203210132_R02C02


title: siDis3l2-2cell-Rep1 [49]

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description: processed data file: siDis3l2-FPKM.txt

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the zygote sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

growth_protocol: The embyos are clutured in KSOM in vitro.

extract_protocol:
Embryos were collected from indicated genotypes (10 embryos per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

treatment_protocol: Samples were collected with 0.2% BSA in DPBS at indicated time directly without extra treatment.

tag: stain

tag: developmental stage

value: 2Cell embryo


title: Sample143.Horse.203203210132_R05C02


title: Sample136.Horse.203203210132_R04C01


title: 16347.T1


title: Amplicon_combo_ko_Donor2_gDNA18_AAVS1_4


title: Amplicon_combo_ko_Donor2_gDNA3_CBFB


title: 15951.T1

value: 13 weeks


title: Amplicon_combo_ko_Donor2_gDNA17_AAVS1_3


title: Control-2cell-Rep2 [5]

description: processed data file: siDis3l2-FPKM.txt

value: Control


title: 15950.T2

value: 13.1 months


title: 16343.T2.2

value: 13.8 months


title: Amplicon_combo_ko_Donor2_gDNA16_IL2RA


title: Sample142.Horse.203203210132_R04C02

value: Blood

value: Blood -Buffy Coat


title: Amplicon_combo_ko_Donor2_gDNA20_AAVS1_8


title: Amplicon_combo_ko_Donor2_gDNA2_IRF4


title: Control-2cell-Rep1 [4]

description: processed data file: siDis3l2-FPKM.txt


title: siPabpn1-8cell-Rep2 [PaKD-8C-2]

description: processed data file: Pabpn1.FPKM.normbyERCC.txt

value: 8Cell embryo


title: ScNI, rep1

value: haploid


title: Amplicon_combo_ko_Donor2_gDNA1_STAT5B


title: siDis3l2-2cell-Rep2 [50]

description: processed data file: siDis3l2-FPKM.txt


title: 15952.T2.2

value: WT

value: 13.6 months


title: 16268.T1

value: 13.5 weeks


title: Amplicon_combo_ko_Donor2_gDNA1_JAK3


title: Amplicon_combo_ko_Donor2_gDNA15_AAVS1_3


title: Sample139.Horse.203203210132_R01C02


title: Control-2cell-Rep3 [6]

description: processed data file: siDis3l2-FPKM.txt


title: 16268.T2.2

value: 14.2 months


title: 15952.T1


title: Sample138.Horse.203203210132_R06C01


title: Sample133.Horse.203203210132_R01C01


title: Sample132.Horse.203203210025_R06C02


title: 15951.T2.2


title: ScNI, rep2


title: Amplicon_combo_ko_Donor2_gDNA14_CBFB


title: 15947.T2


title: Amplicon_combo_ko_Donor2_gDNA16_AAVS1_3


title: Sample137.Horse.203203210132_R05C01


title: 15947.T1


title: siPabpn1-8cell-Rep1 [PaKD-8C-1]


title: Sample135.Horse.203203210132_R03C01


title: Amplicon_combo_ko_Donor2_gDNA15_KLF2


title: 15950.T1


title: siPabpn1-2cell-Rep1 [PaKD-2C-1]


title: 15281.T2.3

value: 13.9 months


title: WT-2cell-Rep2 [PaWT-2C-2]


title: WT-8cell-Rep2 [PaWT-8C-2]


title: Amplicon_combo_ko_Donor2_gDNA13_IRF4

value: CD4+CD25- T cells


title: 15284.T2.3


title: Sample134.Horse.203203210132_R02C01


title: siPabpn1-2cell-Rep2 [PaKD-2C-2]


title: 15284.T1

value: 12.5 weeks


title: 15032.T1


title: Amplicon_combo_ko_Donor2_gDNA12_AAVS1_3


title: WT-8cell-Rep1 [PaWT-8C-1]


title: 15031.T2

value: 13.2 months


title: Amplicon_combo_ko_Donor2_gDNA11_JAK3


title: Sample130.Horse.203203210025_R04C02


title: WT-2cell-Rep1 [PaWT-2C-1]

value: 2Cell embryo


title: Sample129.Horse.203203210025_R03C02


title: Sample131.Horse.203203210025_R05C02


title: Amplicon_combo_ko_Donor2_gDNA13_AAVS1_3


title: 15032.T2


title: Sample128.Horse.203203210025_R02C02


title: Sample125.Horse.203203210025_R05C01


title: Amplicon_combo_ko_Donor2_gDNA12_STAT5B


title: Amplicon_combo_ko_Donor2_gDNA14_AAVS1_3


title: Amplicon_combo_ko_Donor2_gDNA10_CBFB


title: Sample126.Horse.203203210025_R06C01


title: Sample122.Horse.203203210025_R02C01


title: WT-Zygote-Rep1 [WT-1C-1]

source_name: WT-Zygote

value: 1Cell embryo


title: Amplicon_combo_ko_Donor2_gDNA11_AAVS1_3


title: 15031.T1


title: Sample123.Horse.203203210025_R03C01


title: Amplicon_combo_ko_Donor1_gDNA9_IRF4


title: Amplicon_combo_ko_Donor1_gDNA8_IRF4


title: 26877-D29_S75

description:
16S rRNA
See "Protocol 1" in the protocol section
16S_v2_ASV.txt

data_processing:
MiSeq BasCalling
16S metagenome reads (ASV) were processed using the DADA2 pipeline (10.1038/nmeth.3869)
Tab-seprarated file, ASV raw count, ASV, 16S_v2_ASV.txt

tag: transplanted flora

value: Flora during arthritis (Day 29)


title: CD105+_rep4

city: Fukuoka

first: Taro

last: Tochigi

address: Maidashi

institute: Kyushu university

description: Gene expression of CD105+ generated from Len-treated MEPs

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw expression data was imported and normalized by using GeneSpring GX software (Agilent Technologies).

source_name: CD105+, generated from Len-treated MEPs, replicate 4

label_protocol: Cyanine 3 (Cy3)-labeled cRNA was synthesized with Low Input Quick Amp Labeling kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted by using Isogen2 (NIPPON GENE) according to the manufacturer's instructions.

treatment_protocol: Megakaryocyte/erythrocyte progenitors from healthy volunteers were incubated for 72 hours in IMDM supplemented with 10% fetal bovine serum in the presence of cytokine cocktail including SCF, IL-3, G-CSF, GM-CSF, EPO, TPO.10 µM lenalidomide was added into the media. All of the cultures were incubated at 39ºC in a humidified chamber under 10% CO2.


title: CD41+_rep3

description: Gene expression of CD41+ generated from Len-treated MEPs

source_name: CD41+, generated from Len-treated MEPs, replicate 3


title: Sample124.Horse.203203210025_R04C01

tag: tissuedetailed


title: WT-Zygote-Rep2 [WT-1C-2]


title: CD41+_rep4

source_name: CD41+, generated from Len-treated MEPs, replicate 4


title: Amplicon_combo_ko_Donor2_gDNA10_KLF2


title: 26878-D21_S45

value: Reconstituted flora (Day 21)


title: 26878-D0_S24

value: None yet

value: Initial flora (Day 0)


title: Amplicon_combo_ko_Donor1_gDNA9_KLF2


title: Sample119.Horse.203203210110_R05C02

value: Blood

value: Blood -Buffy Coat


title: Sample127.Horse.203203210025_R01C02


title: CD41+_rep2

source_name: CD41+, generated from Len-treated MEPs, replicate 2


title: 26834-D29_S60


title: 26878-D29_S65


title: 26877-D21_S55


title: Sample120.Horse.203203210110_R06C02


title: 26877-D0_S34


title: Amplicon_combo_ko_Donor1_gDNA8_CBFB


title: Amplicon_combo_ko_Donor1_gDNA6_STAT5B


title: ZXL-B1

description: rat DMDD liposome rep1

source_name: tumor

growth_protocol: model group and DMDD liposome group were induced breast cancer  by 4T1 cells

extract_protocol:
Total RNA was extracted from tumor with Trizol reagent
NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）,AMPure XP system

treatment_protocol: DMDD liposome were treated with DMDD liposome

tag: Sex

value: male

value: BALB/c


title: ZXL-B3

description: rat DMDD liposome rep3


title: ZXL-B2

description: rat DMDD liposome rep2


title: 26834-D21_S40

value: WT


title: CD105+_rep2

source_name: CD105+, generated from Len-treated MEPs, replicate 2


title: 26834-D0_S19


title: 15281.T1


title: Sample118.Horse.203203210110_R04C02


title: Amplicon_combo_ko_Donor1_gDNA7_KLF2


title: 26833-D29_S70


title: CD105+_rep1

source_name: CD105+, generated from Len-treated MEPs, replicate 1


title: Sample121.Horse.203203210025_R01C01

source_name: Blood


title: CD105+_rep3

source_name: CD105+, generated from Len-treated MEPs, replicate 3


title: Amplicon_combo_ko_Donor1_gDNA6_CBFB


title: Sample117.Horse.203203210110_R03C02


title: Sample116.Horse.203203210110_R02C02


title: Sample114.Horse.203203210110_R06C01


title: Sample115.Horse.203203210110_R01C02


title: Sample113.Horse.203203210110_R05C01


title: ZXL-A3

description: rat model rep3


title: CD41+_rep1

source_name: CD41+, generated from Len-treated MEPs, replicate 1


title: Amplicon_combo_ko_Donor1_gDNA5_STAT5B


title: Amplicon_combo_ko_Donor1_gDNA4_KLF2


title: Sample112.Horse.203203210110_R04C01


title: 26833-D21_S50


title: 26798-D21_S54


title: mice model rep3

description: mice model rep3

source_name: hepatofibrosis stage liver

growth_protocol: mice in model group  were  exposed to 20%CCl4 for 10 weeks to induce liver fibrosis, and normal group were given same dose normal saline

value: hepatofibrosis stage liver


title: Sample110.Horse.203203210110_R02C01


title: 26798-D29_S74

source_name: stool


title: 26798-D0_S33


title: Amplicon_combo_ko_Donor1_gDNA4_JAK3


title: mice model rep2

description: mice model rep2


title: Amplicon_combo_ko_Donor1_gDNA3_CBFB


title: ZXL-A1

description: rat model rep1


title: 26797-D21_S53


title: Amplicon_combo_ko_Donor1_gDNA2_JAK3


title: 26833-D0_S29


title: mice model rep1

description: mice model rep1


title: 26797-D29_S73


title: Amplicon_combo_ko_Donor1_gDNA3_JAK3


title: Sample107.Horse.203203210023_R05C02


title: Amplicon_combo_ko_Donor1_gDNA7_STAT5B


title: 26797-D0_S32


title: mice wt rep2

description: mice wt rep2

source_name: normal control liver

value: normal control liver


title: Amplicon_combo_ko_Donor1_gDNA2_IRF4


title: Sample108.Horse.203203210023_R06C02


title: mice wt rep1

description: mice wt rep1


title: 26792-D29_S59


title: Amplicon_combo_ko_Donor1_gDNA20_AAVS1_8


title: Sample105.Horse.203203210023_R03C02


title: mice wt rep3

description: mice wt rep3


title: Amplicon_combo_ko_Donor1_gDNA1_STAT5B


title: Sample106.Horse.203203210023_R04C02


title: Sample111.Horse.203203210110_R03C01


title: Amplicon_combo_ko_Donor1_gDNA1_JAK3


title: 26792-D0_S18


title: 26791-D29_S58


title: 3685-xx-8

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Reads were mapped to the human reference genome using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: Skin

extract_protocol:
Skin was flash frozzen in liquid nitrogen, and RNA was isolated using Quick-RNA miniprep kit (Zymo).
1ug of RNA was used for mRNA enrichement using NEBNext Poly(A) mRNA magentic isolation module. RNA-seq libraries were constructed using NEBNext Ultra II Directiona RNA Library Prep Kit for Illumina

value: Het


title: 3685-xx-9

value: KO


title: 3685-xx-6


title: Sample104.Horse.203203210023_R02C02


title: Amplicon_combo_ko_Donor1_gDNA19_AAVS1_7

source_name: CD4+CD25- T cells

value: CD4+CD25- T cells


title: 26791-D15_S35

value: Reconstituted flora (Day 15)


title: Amplicon_combo_ko_Donor1_gDNA18_AAVS1_4


title: 3685-xx-7


title: Amplicon_combo_ko_Donor1_gDNA17_AAVS1_3


title: 26791-D0_S17


title: 3685-xx-5


title: 26792-D15_S36


title: 3685-xx-4


title: 26791-92-D21_S39


title: Sample101.Horse.203203210023_R05C01


title: 26790-D29_S69


title: 3685-xx-48


title: Amplicon_combo_ko_Donor1_gDNA16_AAVS1_3


title: 3685-xx-47


title: Amplicon_combo_ko_Donor1_gDNA15_KLF2


title: 3685-xx-46


title: Amplicon_combo_ko_Donor1_gDNA15_AAVS1_3


title: 26790-D0_S28


title: Amplicon_combo_ko_Donor1_gDNA16_IL2RA


title: Sample103.Horse.203203210023_R01C02


title: 26789-D29_S64


title: Sample98.Horse.203203210023_R02C01


title: Sample97.Horse.203203210023_R01C01


title: Sample100.Horse.203203210023_R04C01


title: Amplicon_combo_ko_Donor1_gDNA14_CBFB


title: 26790-D21_S49


title: Sample96.Horse.203203210048_R06C02


title: 3685-xx-45


title: Sample99.Horse.203203210023_R03C01


title: 26789-D21_S44


title: 26789-D0_S23


title: Amplicon_combo_ko_Donor1_gDNA14_AAVS1_3


title: Sample95.Horse.203203210048_R05C02


title: 3685-xx-44


title: Amplicon_combo_ko_Donor1_gDNA13_IRF4


title: Sample93.Horse.203203210048_R03C02


title: 26787-D29_S68


title: 26787-D21_S48


title: Amplicon_combo_ko_Donor1_gDNA12_STAT5B


title: 3685-xx-41


title: Amplicon_combo_ko_Donor1_gDNA12_AAVS1_3


title: 3685-xx-40


title: 3685-xx-43


title: 3685-xx-3


title: Sample94.Horse.203203210048_R04C02


title: 26787-D0_S27


title: Sample91.Horse.203203210048_R01C02


title: 26786-D29_S67


title: Amplicon_combo_ko_Donor1_gDNA11_JAK3


title: Sample92.Horse.203203210048_R02C02


title: 3685-xx-39


title: Amplicon_combo_ko_Donor1_gDNA11_AAVS1_3


title: 26786-D21_S47


title: 3685-xx-38


title: 26786-D0_S26


title: Amplicon_combo_ko_Donor1_gDNA10_KLF2


title: 26785-D29_S66


title: 26785-D21_S46


title: 3685-xx-36


title: 3685-xx-37


title: CD37_enhancer_amplicon_CD37_low_Donor3

data_processing:
Adapter sequences were trimmed from fastq files using cutadapt version 2.8 using default settings keeping a minimum read length of 150 bp. Insertions and deletions at the CD37 enhancer CRISPR target site were then calculated using Crispresso2 version 2.2.6 with the following options "-q 30 " (Minimum average phred33 quality score to keep a read) and  "--min_bp_quality_or_N 20 " (bases with a phred33 quality score less than 20 will be set to N). Reads were assigned to the reference SNP or alternative bases if they perfectly matched those sequences within a 40bp window centered around the SNP. Insertions/deletions (indels) were quantified if they overlapped the predicted guide RNA cut site. Non indels substitutions or “N” bases were ignored.
Genome_build: hg38
Supplementary_files_format_and_content: CD37_enhancer_reads.txt

extract_protocol:
Five days after electroporation, cells were stained for CD37 (Miltenyi Biotec Cat# 130-123-268) 1:50. The cells were sorted into the 15% lowest and 15% highest expressing cells. Genomic DNA was isolated from each sample using DNA QuickExtract (Lucigen, Cat #QE09050) according to the manufacturer’s protocol.
Amplicons around the SNP were generated by adding 2.5 µL each of forward (cgacgctcttccgatctCAGAGGCCACTGGGTGTG) and reverse primer (cgtgtgctcttccgatctCAGCCTGTTCTGGACCAGG) at 10 uM to 20 µL of sample, 25 µL of NEB Ultra II Q5 master mix (NEB, Cat #M0544L). The following PCR cycling conditions were used: 98°C for 30 seconds, followed by 98°C for 10 seconds, 67°C for 30 seconds, and 72°C for 30 seconds for 35 cycles, and a final extension period at 72°C for 2 minutes. Samples were then diluted 1:200 and subsequently Illumina sequencing adapters and indices were added in a second PCR reaction. Indexing reactions included 1 µL of the diluted PCR1 sample, 2.5 µL of the forward and reverse indexing primers 10 µM each, 12.5 µL of NEB Ultra II master mix, and H2O to a total 25 µL reaction volume. The following PCR cycling conditions were used: 98°C for 30 seconds, followed by 98°C for 10 seconds, 65°C for 1:15 for 15 cycles, and a final extension period at 65°C for 5 minutes. Samples were cleaned up with a 1X SPRI reaction and sequenced on a NovaSeq with paired end 150bp reads.
Amplicon sequencing


title: Amplicon_combo_ko_Donor1_gDNA10_CBFB


title: 3685-xx-35


title: 26785-D0_S25


title: CD37_enhancer_amplicon_CD37_low_Donor2


title: Sample86.Horse.203203210048_R02C01


title: Sample89.Horse.203203210048_R05C01


title: 3685-xx-34


title: Sample87.Horse.203203210048_R03C01


title: CD37_enhancer_amplicon_CD37_low_Donor1


title: Sample90.Horse.203203210048_R06C01

tag: thoroughbred mare identifier

value: Chatty Patty


title: Sample88.Horse.203203210048_R04C01


title: 26784-D29_S57


title: 3685-xx-33


title: 26784-D21_S38


title: Sample102.Horse.203203210023_R06C01


title: Sample85.Horse.203203210048_R01C01


title: Sample84.Horse.203203210134_R06C02


title: Sample83.Horse.203203210134_R05C02


title: Amplicon_combo_ko_Donor1_gDNA5_IRF4


title: Sample82.Horse.203203210134_R04C02


title: CD37_enhancer_amplicon_CD37_high_Donor3


title: CD37_enhancer_amplicon_CD37_high_Donor2


title: 3685-xx-32


title: 26784-D0_S16


title: Sample81.Horse.203203210134_R03C02


title: 26783-D29_S56


title: 3685-xx-31


title: 3685-xx-30


title: CD37_enhancer_amplicon_AAVS1_low_Donor3


title: 3685-xx-2


title: 26783-D0_S15


title: 3685-xx-29


title: CD37_enhancer_amplicon_AAVS1_low_Donor2


title: Sample79.Horse.203203210134_R01C02


title: Sample109.Horse.203203210110_R01C01


title: CD37_enhancer_amplicon_AAVS1_low_Donor1


title: 26763-D29_S72


title: 3685-xx-28


title: 26783-D21_S37


title: Sample80.Horse.203203210134_R02C02


title: 26763-D21_S52


title: Sample78.Horse.203203210134_R06C01


title: CD37_enhancer_amplicon_AAVS1_high_Donor3


title: Sample75.Horse.203203210134_R03C01


title: CD37_enhancer_amplicon_AAVS1_high_Donor2


title: 3685-xx-27


title: 3685-xx-26


title: 26762-D29_S63


title: CD37_enhancer_amplicon_AAVS1_high_Donor1


title: Sample74.Horse.203203210134_R02C01


title: Sample72.Horse.203203210192_R06C02


title: Sample73.Horse.203203210134_R01C01


title: Sample76.Horse.203203210134_R04C01


title: Sample71.Horse.203203210192_R05C02


title: 26762-D21_S43


title: 26761-D21_S42


title: 3685-xx-22


title: 3685-xx-23


title: 3685-xx-25


title: 3685-xx-24


title: 26762-D0_S22


title: 26761-D0_S21


title: 3685-xx-20


title: 26761-D29_S62


title: p6 E6A-2

city: Shanghai

first: Gui

last: Qian

address: Dongan road

department: School of Basic Medical Sciences

institute: Fudan university

data_processing:
DESeq
Supplementary_files_format_and_content: processed data-WT_vs_p6E6A.DESeq.xlsx

source_name: macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy adult blood using Ficoll(AS1114546; Axis-shiel) according to the manufacturers’ instructions. PBMCs were cultured in RPMI-1640 supplemented with 10% FBS and 10 ng/ml rhGM-CSF (300-03; Peprotech) for 7 days to induce the differentiation of macrophages.

extract_protocol:
Supernatants were removed and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with medium or indicated viruses for 48h and cultured with RPMI-1640 supplemented with 2% FBS.

value: monocyte-derived macrophages

value: peripheral blood

tag: stimulator

value: HIV-1 p6 E6A pseudoviruses


title: p6 E6A-3


title: p6 E6A-1


title: 26707-D29_S61

value: Flora during arthritis (Day 29)


title: 3685-xx-1


title: 26707-D21_S41

value: Reconstituted flora (Day 21)


title: Sample69.Horse.203203210192_R03C02

value: Blood


title: Sample68.Horse.203203210192_R02C02

value: Blood -Buffy Coat


title: 3685-xx-21


title: Sample67.Horse.203203210192_R01C02


title: Sample66.Horse.203203210192_R06C01


title: Sample70.Horse.203203210192_R04C02


title: 3685-xx-19


title: Amplicon_combo_ko_Donor1_gDNA13_AAVS1_3


title: Sample65.Horse.203203210192_R05C01


title: monocyte-derived macrophage, WT-2

value: HIV-1 pseudoviruses


title: 3685-xx-18


title: ZXL-A2

description: rat model rep2

value: male

value: BALB/c


title: 26707-D0_S20

value: None yet

value: Initial flora (Day 0)


title: 26706-D29_S71

value: WT


title: Sample64.Horse.203203210192_R04C01


title: 3685-xx-42

value: Het


title: 3685-xx-16


title: 26706-D21_S51


title: monocyte-derived macrophage, WT-1


title: monocyte-derived macrophage, WT-3


title: 26706-D0_S30


title: X33

data_processing:
QuantSeq QC and llumina standard primers trimming
Reads were mapped to the human reference genome using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

extract_protocol:
RNA was isolated from 10mm sections from formalin-fized paraffin embedded blocks using the E.N.Z.A. FFPE RNA Kit.
Quant-Seq library preparation

tag: condition

value: PostTreatment


title: X34

value: Normal


title: 26577-Donor_S6

value: Day 0


title: X32


title: Sample62.Horse.203203210192_R02C01

tag: tissue


title: Sample61.Horse.203203210192_R01C01


title: Sample63.Horse.203203210192_R03C01


title: Sample60.Horse.203203210107_R06C02


title: 26576-Donor_S5

tag: genotype


title: Sample59.Horse.203203210107_R05C02


title: 26575-Donor_S4


title: X31


title: 3685-xx-15


title: 26701-Donor_S7


title: 3685-xx-17


title: 3685-xx-14


title: X9

value: Lesional


title: 3685-xx-11

value: KO


title: 3685-xx-10


title: X8


title: 3685-xx-13


title: 26573-Donor_S13


title: X7


title: JK-47-5022019_S38


title: JK-48-5022019_S39


title: Sample55.Horse.203203210107_R01C02


title: Sample54.Horse.203203210107_R06C01


title: X6

value: Non-lesional


title: Sample56.Horse.203203210107_R02C02


title: Sample53.Horse.203203210107_R05C01


title: 26574-Donor_S14


title: Sample57.Horse.203203210107_R03C02


title: X5


title: 26494-Donor_S11


title: 3685-xx-12


title: 26493-Donor_S10


title: 26496-Donor_S3


title: JK-44-5022019_S29

value: HET


title: 26492-Donor_S9


title: CD37_enhancer_amplicon_CD37_high_Donor1

value: CD4+CD25- T cells


title: X3


title: Sample51.Horse.203203210107_R03C01

value: Blood


title: Sample52.Horse.203203210107_R04C01

value: Blood -Buffy Coat


title: X30


title: 26491-Donor_S8


title: JK-46-5022019_S37


title: JK-42-5022019_S35


title: 26399-Donor_S2


title: JK-45-5022019_S36


title: X4


title: 26398-Donor_S1


title: JK-41-5022019_S31


title: Sample49.Horse.203203210107_R01C01


title: OSCC_16-P

city: Camperdown

first: Dario

last: Strbenac

state: NSW

address: City Road

department: School of Mathematics and Statistics

country: Australia

institute: University of Sydney

data_processing:
Base calling was performed by Illumina Real-Time Analysis version 3.4.4
The median insert size is 140 bases and read length of each read in a pair is 150 bases, so cutadapt version 2.4 was required to remove Illumina TruSeq adapters.
STAR version 2.7.2 aligned the trimmed reads to hg38 reference genome, supplemented with GENCODE Genes version 31 to aid in alignment across splice sites.
RSEM version 1.3.1 was used to disambiguate reads mapping to multiple genomic locations and estimate effective gene length in each sample, thus calculating the FPKM values.
Genome_build: hg38
Supplementary_files_format_and_content: unnormalisedGeneCounts.txt: The number of read pairs whose second read aligns to the same strand as the gene is annotated as being on.
Supplementary_files_format_and_content: genesFPKMs.txt: The read counts, adjusted for library size and gene length, as estimated by RSEM. The gene length could differ from one sample to another based on the exons actually transcribed in a sample.

source_name: Tongue

extract_protocol:
Nucleic acids were extracted fresh frozen OSCC tissue and matched normal (oral mucosa) using the Qiagen AllPrep Kit (Qiagen, Germantown, Maryland, USA) in accordance with the manufacturer’s instructions with purification of DNA and RNA from the same sample.
TruSeq Stranded Total RNA with Ribo-Zero Gold (Human, Mouse, Rat) ribosomal depletion

tag: patient diagnosis

value: HPV-negative Oral Squamous Cell Carcinoma

tag: patient id

value: fresh frozen OSCC

value: Primary Tumour

tag: gender

value: Male

tag: smoking

value: Yes


title: 26495-Donor_S12


title: Sample48.Horse.203203210216_R06C02


title: JK-43-5022019_S32


title: OSCC_16-N

value: oral mucosa

value: Adjacent Normal

tag: age


title: X2


title: JK-40-5022019_S28


title: JK-38-5022019_S27

value: WT


title: Sample46.Horse.203203210216_R04C02


title: Sample47.Horse.203203210216_R05C02


title: Sample50.Horse.203203210107_R02C01


title: OSCC_14-N

value: Female

value: No


title: X1

value: Normal


title: JK-36-5022019_S25

value: KO


title: Sample44.Horse.203203210216_R02C02


title: OSCC_14-P


title: OSCC_12-P


title: JK-34-5022019_S33


title: 26763-D0_S31

tag: strain

value: None yet

value: Initial flora (Day 0)


title: OSCC_12-N


title: JK-30-5022019_S30


title: OSCC_13-N


title: OSCC_11-P

source_name: Floor of mouth


title: JK-37-5022019_S26

value: HET


title: 43_S26


title: OSCC_11-N


title: OSCC_13-P


title: 40_S22


title: JK-35-5022019_S34


title: OSCC_10-N


title: 38_S21


title: 44_S23


title: OSCC_9-P


title: 37_S20


title: OSCC_9-N


title: Sample43.Horse.203203210216_R01C02

value: Blood


title: 36_S19


title: Sample41.Horse.203203210216_R05C01

value: Blood -Buffy Coat


title: Sample45.Horse.203203210216_R03C02


title: OSCC_8-P

value: HPV-negative Oral Squamous Cell Carcinoma


title: 41_S25


title: 35_S18


title: OSCC_8-N


title: Sample37.Horse.203203210216_R01C01


title: OSCC_10-P

value: fresh frozen OSCC


title: Sample38.Horse.203203210216_R02C01


title: Sample40.Horse.203203210216_R04C01


title: Sample34.Horse.203203210090_R04C02


title: Sample39.Horse.203203210216_R03C01


title: 30_S24


title: Sample35.Horse.203203210090_R05C02


title: Sample42.Horse.203203210216_R06C01


title: Sample33.Horse.203203210090_R03C02


title: Sample32.Horse.203203210090_R02C02


title: Sample36.Horse.203203210090_R06C02


title: OSCC_7-N

source_name: Palatal mucosa to maxilla


title: OSCC_7-P

description: HPV35 genomic integration detected by WGS

value: Oral Squamous Cell Carcinoma

value: Primary Tumour


title: Coronal brain section, Sham

city: Zürich

first: Raphael

middle: Matthias

last: Buzzi

address: Rämistrasse 100

department: Division of Internal Medicine

country: Switzerland

institute: Universitätsspital and University of Zurich

description: spatial transcriptome

data_processing:
The Space Ranger Software Suite (spaceranger-1.1.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing.
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library.
Genome_build: Ensembl GRCm38.p6 Release M23
Supplementary_files_format_and_content: sham_tissue_positions_list.csv (A text file containing the table with rows that correspond to spots and columns specifiying the barcode, the tissue state, the row and column coordinate in the array, and the row and column pixel coordinate in the histological image.)
Supplementary_files_format_and_content: sham_aligned_fiducials.jpg (Image with the overlay of the histological image and the fiducial spots found by the fiducial alignment algorithm.)
Supplementary_files_format_and_content: sham_detected_tissue_image.jpg (Image with the overlay of the histological image and all features, where the features under tissue found by the  alignment algorithm are highted in red.)
Supplementary_files_format_and_content: sham_scalefactors_json.json (Scale factors for the alignement of the feature spots and the image of the histological section calculagted by the alignment algorithm.)
Supplementary_files_format_and_content: sham_tissue_hires_image.png (Image of the H&E stained histological section (high resolution))
Supplementary_files_format_and_content: sham_tissue_lowres_image.png (Image of the H&E stained histological section (low resolution))
Supplementary_files_format_and_content: sham_matrix.mtx.gz (Count expression matrix)
Supplementary_files_format_and_content: sham_barcodes.tsv.gz (List of all unique 10 x barcode with sample origin)
Supplementary_files_format_and_content: sham_features.tsv.gz (Identifier and name of all features)
Supplementary_files_format_and_content: sham_filtered_feature_bc_matrix.h5 (Feature-barcode matrix filtered for barcodes from spots under tissue, where each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).)
Supplementary_files_format_and_content: sham_cloupe.cloupe (Proprietary file for visualization of the data in the Loupe browser from 10X genomics.)
Supplementary_files_format_and_content: sham_metrics_summary.csv (Table with the summary of the experiment)

source_name: coronal brain section

extract_protocol:
Mice were transcardially perfused with 50 mL ice cold PBS. Then the brain was extracted, immediately flash frozen in cold Tissue-Tek OCT Compound (Sakura Finetek, Netherlands) using liquid nitrogen cooled isopentane and stored at -80 °C until sectioning. Time of brain extraction until freezing was kept below one minute. Then, using a Leica CM3050 S Cryostat (Leica, Germany) 10 µm coronal cryosections were prepared and placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide (10X Genomics, Pleasanton, CA, USA) and processed according to the manufacturer’s instructions (User Guide CG000239, Rev A). In brief, sections were fixed with cold methanol (-20°C), stained with haematoxylin and eosin. Brightfield images of stained sections in the fiducial frames were obtained with an AxioObserver (Zeiss, Germany) prior to permeabilization. Stained tissue sections were permeabilized for 6 minutes, as experimentally determined using the Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics). After permeabilization the released mRNA bound to oligonucleotides on the capture areas, followed by reverse transcription, second strand synthesis, denaturation, cDNA amplification and SPRIselect cDNA cleanup.
The resulting barcoded cDNA was  and amplified for 15 cycles (as recommended by the 10x Genomics user guide based on the result of the RT-PCR). After amplification and clean up with SPRIselectc reagents, library was constructed as recommended by the 10x Genomics user guide. The quality and concentration of the cDNA were assessed using High-Sensitivity D5000 ScreenTape (Agilent) and then subjected to enzymatic fragmentation, end repair and A-tailing. Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). Then the  3ʹ Gene Expression libraries for each sample were pooled at an equimolar amount and sequenced using the Illumina NovaSeq 6000 system following the  recommendations of 10x Genomics.

treatment_protocol: Mice (C57BL/6J, male, 10-12 weeks) were anesthetized with isoflurane (4-5% for induction, 1-2% for maintenance; Baxter Healthcare Co. Deerfield, IL, USA) evaporated in 100% oxygen and placed in a motorized stereotaxic frame (Stoelting, Dublin, Ireland). Throughout the surgical procedure, body temperature was maintained constant. After a cranial midline skin incision, a small borehole was stereotactically localized and drilled, and a 33G needle was slowly advanced (0.1 mm/s) into the right striatum (bregma coordinates: 2 mm ML, 0.5 mm AP, 3.5 mm DV) followed by injection of 10 µl heme-albumin, heme-Hpx, or saline (sham) with an infusion rate of 1000 nL/min. The needle was left in place for 5 minutes, then removed slowly and the skin incision was closed with a suture. After the surgical procedure, the animals were placed in a heated wake-up box and monitored until they fully recovered and could be transferred back to their homecages.

value: male

value: 10-12 weeks

value: coronal brain section

tag: treatment

value: 10 µL saline (sham)


title: OSCC_6-P

value: Female


title: Sample29.Horse.203203210090_R05C01

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


title: Sample31.Horse.203203210090_R01C02


title: OSCC_5-P

value: Male

value: Yes


title: OSCC_5-N

value: oral mucosa

value: Adjacent Normal


title: Sample30.Horse.203203210090_R06C01


title: OSCC_4-P


title: OSCC_6-N

value: No


title: OSCC_3-P

source_name: Gingivolingual sulcus


title: Coronal brain section, Control

description: spatial transcriptome

data_processing:
The Space Ranger Software Suite (spaceranger-1.1.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing.
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library.
Genome_build: Ensembl GRCm38.p6 Release M23
Supplementary_files_format_and_content: control_tissue_positions_list.csv (A text file containing the table with rows that correspond to spots and columns specifiying the barcode, the tissue state, the row and column coordinate in the array, and the row and column pixel coordinate in the histological image.)
Supplementary_files_format_and_content: control_aligned_fiducials.jpg (Image with the overlay of the histological image and the fiducial spots found by the fiducial alignment algorithm.)
Supplementary_files_format_and_content: control_detected_tissue_image.jpg (Image with the overlay of the histological image and all features, where the features under tissue found by the  alignment algorithm are highted in red.)
Supplementary_files_format_and_content: control_scalefactors_json.json (Scale factors for the alignement of the feature spots and the image of the histological section calculagted by the alignment algorithm.)
Supplementary_files_format_and_content: control_tissue_hires_image.png (Image of the H&E stained histological section (high resolution))
Supplementary_files_format_and_content: control_tissue_lowres_image.png (Image of the H&E stained histological section (low resolution))
Supplementary_files_format_and_content: control_matrix.mtx.gz (Count expression matrix)
Supplementary_files_format_and_content: control_barcodes.tsv.gz (List of all unique 10 x barcode with sample origin)
Supplementary_files_format_and_content: control_features.tsv.gz (Identifier and name of all features)
Supplementary_files_format_and_content: control_filtered_feature_bc_matrix.h5 (Feature-barcode matrix filtered for barcodes from spots under tissue, where each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).)
Supplementary_files_format_and_content: control_cloupe.cloupe (Proprietary file for visualization of the data in the Loupe browser from 10X genomics.)
Supplementary_files_format_and_content: control_metrics_summary.csv (Table with the summary of the experiment)

value: control, no treatment (untouched brain)


title: 9464D-anlo3

city: tianjin

first: Yudong

last: Su

address: Huanhuxi Road

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Tumor

growth_protocol: 975A2 and 9464D cells were cultured in high-glucose DMEM (Gibco) containing 10% FBS (BI) and 100 IU ml−1 penicillin/streptomycin (Gibco). Both cell lines were grown in a humidified incubator at 37°C with 5% CO2 and were tested regularly for mycoplasma contamination.

extract_protocol:
Tumors were snap-frozen with liquid nitrogen immediately after resection and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Anlotinib (6mg/kg) was intragastrically administered to mice for 9 consecutive days.

tag: injected cell line

value: neuroblastoma tumor

value: 9 days after anlo treatment


title: OSCC_4-N

value: HPV-negative Oral Squamous Cell Carcinoma


title: OSCC_3-N


title: 9464D-anlo1


title: OSCC_2-P

value: fresh frozen OSCC


title: OSCC_2-N


title: 9464D-veh3

value: 9 days after vehicle treatment


title: 9464D-anlo2


title: Sample27.Horse.203203210090_R03C01

value: Blood

value: Blood -Buffy Coat


title: 9464D-veh2


title: Sample25.Horse.203203210090_R01C01


title: Sample22.Horse.203203210163_R04C02


title: Sample20.Horse.203203210163_R02C02


title: Sample19.Horse.203203210163_R01C02


title: Sample23.Horse.203203210163_R05C02


title: Sample24.Horse.203203210163_R06C02

value: Wild Guneva Star


title: Sample26.Horse.203203210090_R02C01


title: Sample28.Horse.203203210090_R04C01


title: 9464D-veh1


title: Sample_9020

description:
Whole Metagenome Shotgun
See "Protocol 2" in the protocol section
WGS_species_count.csv

data_processing:
HiSeq BaseCalling
Whole Metagenome Reads were trimmed with Trimmomatic v0.37 (ILLUMINACLIP:2:30:1, TRAILING:30 and MINLEN:36)
WMS Read were assembled using RayMeta v2.3.1 (kmer = 31)
Quantification of the contigs was performed using kallisto v0.43.0
Blastn v2.4.0 against nt was used to assign taxonomy to the contigs
CSV file, Species raw count table, WGS_species_count.csv

value: WT


title: Sample18.Horse.203203210163_R06C01


title: Sample21.Horse.203203210163_R03C02


title: OSCC_1-N


title: 975A2-anlo3


title: Sample_9019


title: 975A2-anlo2


title: Tfpi Knockdown 7

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: human reference genome (GRCh37)

source_name: human trophoblast stem cell

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

tag: cell type

value: human trophoblast stem cell

tag: shRNA

value: Tfpi shRNA


title: 975A2-anlo1


title: Sample_9017


title: Tfpi Knockdown 6


title: Sample17.Horse.203203210163_R05C01

extract_protocol: genomic DNA was extracted

tag: tissuedetailed


title: Sample_9018


title: 975A2-veh3


title: OSCC_1-P

value: Primary Tumour

value: Male


title: Sample_8896


title: Tfpi Knockdown 5


title: Sample15.Horse.203203210163_R03C01


title: Sample16.Horse.203203210163_R04C01


title: Sample_8889


title: Control 4

value: Scrambled


title: 975A2-veh2


title: 975A2-veh1


title: Sample14.Horse.203203210163_R02C01


title: Sample13.Horse.203203210163_R01C01


title: Control 3


title: Sample_8887


title: Control 2


title: Sample_8839


title: Sample_8840


title: Control 1


title: Sample12.Horse.203203210051_R06C02


title: Sample11.Horse.203203210051_R05C02


title: Sample_8836


title: Sample_8832