title: Lung 2.3Gy Animal 17R

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Porcine (v2) Gene Expression Microarrays 4x44K Design ID 026440 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

label: Alexa 555

organism: Sus scrofa

source_name: Lung 2.3Gy

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA).  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: Samples were bathed in liquid nitrogen and pulverized into a fine powder using a mortar and pestle. Approximately 100 μg of powdered sample was lysed with 700 μl of Qiazol lysis buffer (Cat # 79306, Qiagen) and homogenized by passing the sample through a Qiashredder spin column (Cat # 79654, Qiagen). RNA extraction was performed using standard miRNeasy mini kits (Cat # 217004, Qiagen) according to the manufacturer’s protocol. Quality and quantity of the RNA samples were assessed using a Denovix DS-11 nanodrop spectrophotometer (Denovix, DE, US) and an Agilent Bioanalyzer using RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male Gottingen minipigs (Sus scrofa domesticus), aged five-six months, were used for this study. Animals were unilaterally sequentially exposed to total midline body doses of 1.7, 1.9, 2.1 or 2.3 Gy (n=6/dose) of TBI at dose rate of 0.5-0.6Gy/minute using a Cobalt-60 source in the AFRRI Cobalt facility. Animals were anesthetized with an IM injection of TelazolVR (100 mg/mL, 2 mg/kg) and Xylazine (50 mg/mL, 1 mg/kg) before placing in a sling for the duration of irradiation. The two sources were raised sequentially with a lateral geometry of exposure. The unilateral sequential exposure is derived from the set-up of the AFRRI Cobalt-60 Radiation Facility which contains two sets of Cobalt-60 rods that are lifted sequentially to generate a field. Dose rates were determined using an alanine/ESR (electron spin resonance) dosimetry system (American Society for Testing and Material Standard E 1607) contained in water-filled cylindrical pig phantoms. AFRRI’s dose calibration curves are based on alanine dosimeters irradiated at either the National Institute of Standards and Technology (Gaithersburg, MD) or the National Physical Laboratory (Teddington, England). This provides direct traceability of AFRRI’s doses to the national radiation standards. Dose rates in phantoms were converted to the dose rate for the animals by accounting for the decay of the 60Co source, the small difference in mass energy-absorption coefficients for water and soft tissue, and size of the animal. The radiation field was uniform within ±2%. Additionally, real time dosimetry of the output dose was measured using an ion chamber system. The doses chosen were previously estimated to correspond to LD10/45 (1.7 Gy), LD25/45 (1.9 Gy), LD50/45 (2.1 Gy) and LD75/45 (2.3 Gy). With a limited number of animals per dose group (n=6), the observed LD values (LD100/45, LD50/45, LD33/45 and LD0/45 respectively for 2.3 Gy, 2.1 Gy, 1.9 Gy and 1.7 Gy) in our study were close to the predicted survival values. Three sham-irradiated animals served as controls (total 27 animals). The animals were followed up for 45 days. During the 45-day study period, pigs were assessed at least twice daily for signs of pre-established criteria that necessitated unscheduled euthanasia. Prior to euthanasia, anesthesia was induced with 5-2% isoflurane and animals received an IM injection of Xylazine and Telazol (as described above). Euthasol® (sodium pentobarbital) was injected IV for euthanasia. Unscheduled euthanasia was necessitated if one absolute criteria (non-responsiveness, dyspnea, loss of ≥20% body weight, hypothermia) or four non-absolute criteria (hyperthermia, anorexia, anemia, vomiting/diarrhea, lethargy, seizures/vestibular signs, prolonged hemorrhage) were observed. Organ samples were collected at the time of necropsy within one hour of euthanasia (scheduled or unscheduled). Samples meant for RNA extraction were transferred to dry ice and later stored at -80°C until further processing. Samples meant for histopathological assessment were dropped into 10 % zinc buffered formalin.

tag: breed

value: Gottingen minipigs

value: Lung

tag: gender

value: male

tag: dose

tag: batch

tag: survived upto 45 days

value: No


title: Lung Sham Animal CA

status: Public on Apr 27 2021

type: RNA

country: USA

molecule: total RNA

source_name: Lung Sham Batch 1

tag: tissue

value: sham


title: Lung 2.3Gy Animal 16R


title: Lung Sham Animal CB


title: Lung Sham Animal CC


title: Lung Sham 1053493 Batch 2

source_name: Lung Sham Batch 2


title: Lung Sham 1053990 Batch 2


title: Lung Sham 1053256 Batch 2


title: Lung 2.3Gy Animal 14R


title: Lung 2.3Gy Animal 18R


title: Lung 2.3Gy Animal 15R


title: Lung 2.1Gy Animal 11R-2

source_name: Lung 2.1Gy


title: Lung 1.9Gy 5507295 Batch 2

source_name: Lung 1.9Gy Batch2

value: Yes


title: Lung 2.3Gy Animal 13R


title: Lung 2.1Gy Animal 8R


title: Lung 1.7Gy Animal 4R

source_name: Lung 1.7Gy


title: Lung 2.1Gy Animal 12R


title: Lung 2.1Gy Animal 9R


title: Lung 2.1Gy Animal 10R-2


title: Lung 1.9Gy 5503532 Batch 2


title: Lung 1.9Gy 5489734 Batch 2


title: Lung 1.7Gy Animal 5R


title: Lung 1.9Gy 5490775 Batch 2


title: Lung 1.7Gy Animal 2R


title: Lung 2.1Gy Animal 7R


title: Lung 1.9Gy 5507384 Batch 2


title: Lung 1.9Gy 5493112 Batch 2


title: Lung 1.7Gy Animal 6R-2


title: Lung 1.7Gy Animal 3R


title: Lung 1.7Gy Animal 1R-2


title: Liver Sham Animal CC

source_name: Liver Sham Batch 1

value: Liver


title: Liver Sham Animal CA


title: Liver Sham 1053493 Batch 2

source_name: Liver Sham Batch 2


title: Liver Sham Animal CB


title: Liver 2.1Gy Animal 11

source_name: Liver 2.1Gy


title: Liver 2.3Gy Animal 17

source_name: Liver 2.3Gy


title: Liver Sham 1053990 Batch 2


title: Liver 2.1Gy Animal 10


title: Liver 2.3Gy Animal 18


title: Liver 2.3Gy Animal 14


title: Liver 2.1Gy Animal 12


title: Liver 2.3Gy Animal 16


title: Liver 2.1Gy Animal 8


title: Liver 1.7Gy Animal 3

source_name: Liver 1.7Gy


title: Liver Sham 1053256 Batch 2


title: Liver 2.3Gy Animal 15


title: Liver 1.9Gy 5489734 Batch 2

source_name: Liver 1.9Gy Batch2


title: Liver 2.1Gy Animal 7


title: Liver 2.3Gy Animal 13


title: Liver 1.7Gy Animal 6


title: Liver 1.7Gy Animal 4


title: Liver 1.7Gy Animal 5


title: Liver 1.9Gy 5507384 Batch 2


title: Liver 1.9Gy 5493112 Batch 2


title: Liver 1.9Gy 5503532 Batch 2


title: Liver 1.9Gy 5490775 Batch 2


title: Heart Sham Animal CC

source_name: Heart Sham Batch 1

value: heart


title: Heart 2.3Gy Animal 16

source_name: Heart 2.3Gy


title: Heart 2.3Gy Animal 17


title: Heart Sham 1053493 Batch 2

source_name: Heart Sham Batch 2


title: Liver 1.7Gy Animal 1


title: Heart 2.3Gy Animal 13R


title: Heart Sham 1053990 Batch 2


title: Heart 1.9Gy 5503532 Batch 2

source_name: Heart 1.9Gy Batch2


title: Heart 2.1Gy Animal 7

source_name: Heart 2.1Gy


title: Heart 2.3Gy Animal 15


title: Heart 2.3Gy Animal 18


title: Heart 1.9Gy 5493112 Batch 2


title: Heart 2.1Gy Animal 9


title: Heart 2.1Gy Animal 8


title: Heart Sham Animal CA


title: Heart 1.9Gy 5507384 Batch 2


title: Heart 2.1Gy Animal 12


title: Heart 1.9Gy 5490775 Batch 2


title: Heart Sham 1053256 Batch 2


title: Heart 2.3Gy Animal 14R


title: Heart 1.9Gy 5507295 Batch 2


title: Heart Sham Animal CB


title: Heart 2.1Gy Animal 11


title: Liver 1.9Gy 5507295 Batch 2


title: Liver 2.1Gy Animal 9


title: Heart 1.9Gy 5489734 Batch 2


title: Liver 1.7Gy Animal 2


title: Heart 2.1Gy Animal 10


title: 48 h tala

type: SRA

city: Heidelberg

first: Stefan

last: Gröschel

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ German Cancer Research Center

description: 100bp PE

library_source: transcriptomic

data_processing:
Fastq files are aligned to the hg38 human genome using the STAR 2-pass alignment (version 2.7.3a).
Duplicate reads are marked with Picard MarkDuplicate (v. 2.21.2).
Features are counted using the featureCount function from the Rsubread package (v. 2.0.1).
TPM values are computed using a custom R script.
The pipeline is implemented as a Snakemake workflow.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_featureCounts.tsv: Tab-separated counts and tpm.

organism: Homo sapiens

source_name: myeloid leukemia

growth_protocol: MUTZ-3 cells were grown in MEMalpha with 20% FBS, 20% conditioned medium from 5637 cells, 10 ng/ml GM-CSF and 1x Pen/Strep.

extract_protocol:
RNA was extracted with the Qiagen RNeasy Plus Mini Kit.
Library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol:
PARP inhibition: 10 µM olaparib, 1 µM talazoparib or the DMSO vehicle control was added to the cell culture medium and the cells were harvested after the indicated time points.
EVI1 Knockdown: MUTZ-3 were lentivirally transduced with the pLKO.1 vector coding for either a commercial non-targeting control (SHC002) or shRNAs directed against EVI1 (TRCN0000002532, TRCN0000002531). Cells were selected with puromycin and harvested at the indicated time points.

tag: cell line

tag: treatment

value: 1 uM talazoparib

tag: time point


title: Day 3 NTC

description: 100bp PE

value: non-targeting shRNA

value: day 3


title: Day 6 shEVI1-2531

description: 100bp PE

value: EVI1 shRNA #2531

value: day 6


title: Day 3 shEVI1-2532

description: 100bp PE

value: EVI1 shRNA #2532


title: Day 6 shEVI1-2532

description: 100bp PE


title: 12 h tala

description: 100bp PE


title: Day 3 shEVI1-2531

description: 100bp PE


title: pDC_rep2

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

data_processing:
Adapters were trimmed using CUTADAPT and the reads were aligned using the STAR aligner.
Read Duplicates were marked using PICARD MARKDUPLICATES.
The BAM file was sorted using SAMBAMBA.
Read Summarization was performed using FeatureCounts.
Genome_build: GRCh37
Supplementary_files_format_and_content: DC_all.txt: Gene expression processed for all samples as log2(RPKM+1).

source_name: PBMC

growth_protocol: Ex vivo PBMC isolation and cryopreservation.

extract_protocol:
RNA extraction was done with the Promega Maxwell RSC instrument using the Maxwell RSC simply RNA cell extraction kit (Promega AS 1390).
Clontech SMART-seq v4 protocol.

treatment_protocol: Thawing of PBMC of all donors, resting over night in RPIMI/10% FBS at 37°C, 5% CO2.

tag: donor

tag: diagnosis

value: Healthy

value: pDC


title: Day 6 NTC

description: 100bp PE


title: 24 h tala

description: 100bp PE


title: 24 h ola

description: 100bp PE

value: 10 uM olaparib


title: 12 h ola

description: 100bp PE


title: Heart 1.7Gy Animal 6

source_name: Heart 1.7Gy

value: Gottingen minipigs


title: 12 h DMSO

description: 100bp PE

value: DMSO


title: CD14_rep3

value: HDBNR


title: 0 h untreated

description: 100bp PE

value: untreated

value: 0 h


title: Heart 1.7Gy Animal 5

value: male

value: Yes


title: Heart 1.7Gy Animal 3

value: heart


title: 48 h ola

description: 100bp PE


title: mDC_rep2

value: mDC


title: mDC_rep3


title: Heart 1.7Gy Animal 2


title: pDC_rep3


title: pDC_rep1


title: mDC_rep1


title: Heart 1.7Gy Animal 1


title: CD14_rep2


title: 48 h DMSO

description: 100bp PE


title: Heart 1.7Gy Animal 4


title: 24 h DMSO

description: 100bp PE


title: CD14_rep1


title: Donor q TLR4 KO PBS rep 1

city: Boston

first: Marco

last: Jost

state: MA

address: 77 Ave Louis Pasteur, NRB848

institute: Harvard Medical School

data_processing:
Sequencing reads were aligned to GRCh38 with Gencode annotations version 34 using STAR version 2.6.0. The first base was trimmed (--clipNbases 1)
Quantification of gene counts (exon features) was carried out with featureCounts, version 1.6.2, using only uniquely mapped reads to the reverse strand.
Genome_build: hg38, features from Gencode release 34
Supplementary_files_format_and_content: txt file with raw gene counts for every gene in a given sample
Supplementary_files_format_and_content: txt matrix with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Dendritic cells

growth_protocol: Human monocytes from 2 independent donors were isolated from commercially sourced, fresh peripheral blood mononuclear cells by negative magnetic selection (StemCell human monocyte enrichment kit). Monocytes were differentiated into dendritic cells in RPMI + 10% FBS + 1% Pen/Strep/Gln in the presence of 50 ng/mL recombinant GM-CSF and 20 ng/mL recombinant IL-4 for 7 days. Dendritic cells were electroporated with Cas9 ribonucleoprotein complexes with sgRNAs targeting the indicated genes and cultured for 5 additional days.

extract_protocol:
Total RNA was extrated by adding a 3x volume of TRIzol™ LS reagent (Ambion) or TRI Reagent® (Zymo Research) to the cells. The suspension was mixed by pipetting to lyse the cells, followed by RNA isolation using the Direct-zol™ RNA Miniprep kit (Zymo Research) including an on-column DNase I digestion step.
RNA-seq libraries were prepared from purified RNA using the Stranded mRNA Prep Ligation kit (Illumina) in 96-well format, following the manufacturer’s instructions. Input RNA amounts were held constant for all samples for a given donor, between 250 and 400 ng per reaction. Final libraries were validated and quantified using the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA kit (Agilent). Paired-end 150 sequencing was performed on two lanes of a HiSeq 4000 (Illumina).

treatment_protocol: Dendritic cells were harvested using CellStripper. 100,000 to 250,000 cells were dispensed into wells of a 24-well plate in a volume of 250 uL. Cells were allowed to rest at 37 C, 5% CO2 for 2-3 h. The indicated molecules or PBS were added to the wells to the indicated final concentration to start the treatments. Cells were harvested 2 h post-treatment.

tag: individual

value: donor q

tag: cell type

value: monocyte-derived dendritic cells

tag: genotype

value: knockout of TLR4

value: PBS (control) for 2 h


title: Donor q TLR4 KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor2_TLR4_30_ng_mL_dCPS_5P_LOS_rep1_S33

value: 30 ng/mL B. theta delta CPS 5P LPS for 2 h


title: Donor q TLR4 KO B. theta dCPS LPS rep 2

description: PBMC36_edit_donor2_TLR4_30_ng_mL_dCPS_5P_LOS_rep2_S36


title: Donor q RPE65 (neutral control) KO PBS rep 1

value: knockout of RPE65 (neutral control)


title: Donor q RPE65 (neutral control) KO B. theta dCPS LPS rep 2

description: PBMC36_edit_donor2_RPE65_30_ng_mL_dCPS_5P_LOS_rep2_S54


title: Donor q RPE65 (neutral control) KO PBS rep 2


title: Donor q TLR4 KO E. coli LPS rep 1

description: PBMC36_edit_donor2_TLR4_10_ng_mL_O55_LPS_rep1_S32

value: 10 ng/mL E. coli O55 LPS for 2 h


title: Donor q TLR4 KO PBS rep 2


title: Donor q RPE65 (neutral control) KO E. coli LPS rep 2

description: PBMC36_edit_donor2_RPE65_10_ng_mL_O55_LPS_rep2_S53


title: Donor q LY96 KO PBS rep 2

value: knockout of LY96


title: Donor q RPE65 (neutral control) KO E. coli LPS rep 1

description: PBMC36_edit_donor2_RPE65_10_ng_mL_O55_LPS_rep1_S50


title: Donor q LY96 KO B. theta dCPS LPS rep 2

description: PBMC36_edit_donor2_LY96_30_ng_mL_dCPS_5P_LOS_rep2_S48


title: Donor q CD14 KO PBS rep 2

value: knockout of CD14


title: Donor q LY96 KO PBS rep 1


title: Donor q LY96 KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor2_LY96_30_ng_mL_dCPS_5P_LOS_rep1_S45


title: Donor q RPE65 (neutral control) KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor2_RPE65_30_ng_mL_dCPS_5P_LOS_rep1_S51


title: Donor q CD14 KO PBS rep 1


title: Donor q TLR4 KO E. coli LPS rep 2

description: PBMC36_edit_donor2_TLR4_10_ng_mL_O55_LPS_rep2_S35


title: Donor q LY96 KO E. coli LPS rep 2

description: PBMC36_edit_donor2_LY96_10_ng_mL_O55_LPS_rep2_S47


title: Donor q CD14 KO B. theta dCPS LPS rep 2

description: PBMC36_edit_donor2_CD14_30_ng_mL_dCPS_5P_LOS_rep2_S42


title: Donor p TLR4 KO PBS rep 2

value: donor p


title: Donor q CD14 KO E. coli LPS rep 2

description: PBMC36_edit_donor2_CD14_10_ng_mL_O55_LPS_rep2_S41


title: Donor q CD14 KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor2_CD14_30_ng_mL_dCPS_5P_LOS_rep1_S39


title: Donor q CD14 KO E. coli LPS rep 1

description: PBMC36_edit_donor2_CD14_10_ng_mL_O55_LPS_rep1_S38


title: Donor p TLR4 KO E. coli LPS rep 2

description: PBMC36_edit_donor1_TLR4_3_ng_mL_O55_LPS_rep2_S12

value: 3 ng/mL E. coli O55 LPS for 2 h


title: Donor p TLR4 KO PBS rep 1


title: Donor p TLR4 KO E. coli LPS rep 1

description: PBMC36_edit_donor1_TLR4_3_ng_mL_O55_LPS_rep1_S9


title: Donor p RPE65 (neutral control) KO PBS rep 1


title: Donor p TLR4 KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor1_TLR4_100_ng_mL_dCPS_5P_LOS_rep1_S10

value: 100 ng/mL B. theta delta CPS LPS for 2 h


title: Donor p TLR4 KO B. theta dCPS LPS rep 2

description: PBMC36_edit_donor1_TLR4_100_ng_mL_dCPS_5P_LOS_rep2_S13


title: Donor p RPE65 (neutral control) KO E. coli LPS rep 1

description: PBMC36_edit_donor1_RPE65_3_ng_mL_O55_LPS_rep1_S27


title: Donor p RPE65 (neutral control) KO E. coli LPS rep 2

description: PBMC36_edit_donor1_RPE65_3_ng_mL_O55_LPS_rep2_S30


title: Donor p LY96 KO PBS rep 2


title: Donor p LY96 KO PBS rep 1


title: Donor p LY96 KO E. coli LPS rep 2

description: PBMC36_edit_donor1_LY96_3_ng_mL_O55_LPS_rep2_S24


title: Donor p RPE65 (neutral control) KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor1_RPE65_100_ng_mL_dCPS_5P_LOS_rep1_S28


title: Donor p LY96 KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor1_LY96_100_ng_mL_dCPS_5P_LOS_rep1_S22


title: Donor q LY96 KO E. coli LPS rep 1

description: PBMC36_edit_donor2_LY96_10_ng_mL_O55_LPS_rep1_S44


title: Donor p CD14 KO PBS rep 2


title: Donor p CD14 KO E. coli LPS rep 2

description: PBMC36_edit_donor1_CD14_3_ng_mL_O55_LPS_rep2_S18


title: Donor p CD14 KO E. coli LPS rep 1

description: PBMC36_edit_donor1_CD14_3_ng_mL_O55_LPS_rep1_S15


title: Donor p CD14 KO B. theta dCPS LPS rep 1

description: PBMC36_edit_donor1_CD14_100_ng_mL_dCPS_5P_LOS_rep1_S16


title: Donor p CD14 KO B. theta dCPS LPS rep 2

description: PBMC36_edit_donor1_CD14_100_ng_mL_dCPS_5P_LOS_rep2_S19


title: Donor s B. theta dCPS 4PP LPS rep2

growth_protocol: Human monocytes from 2 independent donors were isolated from commercially sourced, fresh peripheral blood mononuclear cells by negative magnetic selection (StemCell human monocyte enrichment kit). Monocytes were differentiated into dendritic cells in RPMI + 10% FBS + 1% Pen/Strep/Gln in the presence of 50 ng/mL recombinant GM-CSF and 20 ng/mL recombinant IL-4 for 7 days.

extract_protocol:
Total RNA was extrated by adding a 3x volume of TRIzol™ LS reagent (Ambion) or TRI Reagent® (Zymo Research) to the cells. The suspension was mixed by pipetting to lyse the cells, followed by RNA isolation using the Direct-zol™ RNA Miniprep kit (Zymo Research) including an on-column DNase I digestion step.
RNA-seq libraries were prepared from purified RNA using the Stranded mRNA Prep Ligation kit (Illumina) in 96-well format, following the manufacturer’s instructions. Input RNA amounts were held constant for all samples for a given donor, between 300 and 600 ng per reaction. Final libraries were validated and quantified using the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA kit (Agilent). Paired-end 100 sequencing was performed on a HiSeq 4000 (Illumina).

treatment_protocol: Dendritic cells were harvested using CellStripper. 200,000 to 250,000 cells were dispensed into wells of a 24-well plate at a density of 1,000,000 cells per mL. Cells were allowed to rest at 37 C, 5% CO2 for 2-4 h. The indicated molecules or PBS were added to the wells to the indicated final concentration to start the treatments. Cells were harvested 2 h post-treatment.

value: 100 ng/mL B. theta deltaCPS 4PP LPS for 2 h


title: Donor s B. theta dCPS 4PP LPS rep1


title: Donor s B. theta dCPS 4PP LPS rep3


title: Donor s B. theta dCPS LPS rep1

value: 100 ng/mL B. theta deltaCPS LPS for 2 h


title: Donor s Pam3CSK4 rep2

value: 100 ng/mL Pam3CSK4 for 2 h


title: Donor s Pam3CSK4 rep3


title: Donor s Pam3CSK4 rep1


title: Donor s E. coli LPS rep3


title: Donor p RPE65 (neutral control) KO PBS rep 2


title: Donor s B. theta dCPS LPS rep2


title: Donor p LY96 KO B. theta dCPS LPS rep 2

description: PBMC36_edit_donor1_LY96_100_ng_mL_dCPS_5P_LOS_rep2_S25


title: Donor p LY96 KO E. coli LPS rep 1

description: PBMC36_edit_donor1_LY96_3_ng_mL_O55_LPS_rep1_S21


title: Donor s E. coli LPS rep1


title: Donor s PBS rep3


title: Donor s E. coli LPS rep2


title: Donor p CD14 KO PBS rep 1


title: Donor s PBS rep2


title: Donor r B. theta dCPS 4PP LPS rep3


title: Donor r B. theta dCPS 4PP LPS rep1


title: Donor r B. theta dCPS 4PP LPS rep2


title: Donor r Pam3CSK4 rep1


title: Donor r Pam3CSK4 rep2


title: Donor s PBS rep1


title: Donor r B. theta dCPS LPS rep2


title: Donor s B. theta dCPS LPS rep3


title: Donor r E. coli LPS rep3


title: Donor r B. theta dCPS LPS rep3


title: Donor r B. theta dCPS LPS rep1


title: Donor r PBS rep3


title: Donor r PBS rep1


title: Donor r E. coli LPS rep1


title: MDA-MB-231_EtOH_24h_RNAiMAX_Rep4

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

description: rawcounts.csv

data_processing:
Aligned with HiSat2
Establish count matrix with Htseq-Count
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containg matrix of read counts for individual genes. Genes are stored by Entrez Gene ID.

source_name: Breast Epithelial Cell Line

growth_protocol: Cells were grown in phenol red free DMEM +10% Charcoal Stripped FBS

extract_protocol:
RNA was extracted by  RNeasy mini kit
TruSeq RNA Library Prep Kit

treatment_protocol: Cells were treateded with SMARTpool siRNA targeting the gene of interest as per the manufactures protocol. After 24 hours cells were stimulated with Oestrogen or EtOH. Cells were then harvested at specified time point after stimulation.

tag: condition

value: RNAiMAX

value: EtOH

tag: time point of treatment

tag: passage

tag: replicate


title: MDA-MB-231_EtOH_24h_siZMIZ1_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siZMIZ1_Rep4

description: rawcounts.csv

value: Oestrogen


title: MDA-MB-231_Oestrogen_24h_RNAiMAX_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_24h_siZMIZ1_Rep4

description: rawcounts.csv


title: Donor r Pam3CSK4 rep3

value: monocyte-derived dendritic cells


title: MDA-MB-231_EtOH_24h_siCTRL_Rep4

description: rawcounts.csv

value: siCTRL


title: T47D_EtOH_24h_siZMIZ1_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_24h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siZMIZ1_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_24h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_EtOH_24h_siCTRL_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_EtOH_24h_RNAiMAX_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siCTRL_Rep4

description: rawcounts.csv


title: MCF7_EtOH_24h_siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siZMIZ1_Rep4

description: rawcounts.csv


title: Donor r E. coli LPS rep2


title: MCF7_EtOH_24h_RNAiMAX_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_RNAiMAX_Rep4

description: rawcounts.csv


title: Donor r PBS rep2

value: PBS (control) for 2 h


title: MCF7_EtOH_24h_siZMIZ1_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_24h_RNAiMAX_Rep4

description: rawcounts.csv


title: T47D_EtOH_12h_siZMIZ1_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_12h_siZMIZ1_Rep4

description: rawcounts.csv


title: T47D_EtOH_12h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_12h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_12h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_EtOH_12h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siZMIZ1_Rep4

description: rawcounts.csv


title: MCF7_EtOH_12h_siZMIZ1_Rep4

description: rawcounts.csv


title: MCF7_EtOH_12h_siCTRL_Rep4

description: rawcounts.csv


title: MCF7_EtOH_12h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_12h_RNAiMAX_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siZMIZ1_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siZMIZ1_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_RNAiMAX_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_RNAiMAX_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_6h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_EtOH_6h_siZMIZ1_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_6h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siZMIZ1_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_6h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_EtOH_6h_siCTRL_Rep4

description: rawcounts.csv


title: T47D_EtOH_6h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_EtOH_6h_RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_EtOH_6h_siZMIZ1_Rep4

description: rawcounts.csv


title: T47D_EtOH_6h_siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _siZMIZ1_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _siZMIZ1_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _RNAiMAX_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _RNAiMAX_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _siCTRL_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_3h _siZMIZ1_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_3h _siCTRL_Rep4

description: rawcounts.csv


title: T47D_EtOH_3h _siCTRL_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_6h_siZMIZ1_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_3h _RNAiMAX_Rep4

description: rawcounts.csv


title: MCF7_Oestrogen_3h _siZMIZ1_Rep4

description: rawcounts.csv


title: MCF7_EtOH_3h _siZMIZ1_Rep4

description: rawcounts.csv


title: MCF7_EtOH_3h _siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_3h _RNAiMAX_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_24h_siCTRL_Rep3

description: rawcounts.csv


title: T47D_EtOH_24h_siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_siCTRL_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_RNAiMAX_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_24h_siZMIZ1_Rep3

description: rawcounts.csv


title: T47D_EtOH_3h _siZMIZ1_Rep4

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siZMIZ1_Rep3

description: rawcounts.csv


title: T47D_EtOH_3h _RNAiMAX_Rep4

description: rawcounts.csv


title: T47D_EtOH_24h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_EtOH_3h _RNAiMAX_Rep4

description: rawcounts.csv


title: T47D_Oestrogen_24h_RNAiMAX_Rep3

description: rawcounts.csv


title: MCF7_EtOH_24h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siZMIZ1_Rep3

description: rawcounts.csv


title: T47D_EtOH_24h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siZMIZ1_Rep4

description: rawcounts.csv


title: MCF7_EtOH_24h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_3h _siCTRL_Rep4

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_EtOH_24h_siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siCTRL_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_RNAiMAX_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_24h_RNAiMAX_Rep3

description: rawcounts.csv


title: T47D_EtOH_12h_siZMIZ1_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_12h_siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siCTRL_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_12h_siCTRL_Rep3

description: rawcounts.csv


title: T47D_EtOH_12h_RNAiMAX_Rep3

description: rawcounts.csv


title: T47D_EtOH_12h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_EtOH_12h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_EtOH_12h_siZMIZ1_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_12h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_12h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_RNAiMAX_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_6h_siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_RNAiMAX_Rep3

description: rawcounts.csv


title: T47D_EtOH_6h_siCTRL_Rep3

description: rawcounts.csv


title: T47D_EtOH_6h_siZMIZ1_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_6h_RNAiMAX_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_EtOH_6h_siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_EtOH_6h_siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_6h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_EtOH_12h_RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _siCTRL_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_6h_siCTRL_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siCTRL_Rep3

description: rawcounts.csv


title: T47D_EtOH_3h _siCTRL_Rep3

description: rawcounts.csv


title: T47D_EtOH_3h _siZMIZ1_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _RNAiMAX_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_3h _siZMIZ1_Rep3

description: rawcounts.csv


title: T47D_EtOH_3h _RNAiMAX_Rep3

description: rawcounts.csv


title: MCF7_EtOH_3h _siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_3h _siZMIZ1_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_3h _siCTRL_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_3h _RNAiMAX_Rep3

description: rawcounts.csv


title: MCF7_EtOH_3h _siCTRL_Rep3

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_24h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_RNAiMAX_Rep2

description: rawcounts.csv


title: MCF7_EtOH_3h _RNAiMAX_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_3h _RNAiMAX_Rep3

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_siCTRL_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_24h_siCTRL_Rep2

description: rawcounts.csv


title: T47D_EtOH_24h_siCTRL_Rep2

description: rawcounts.csv


title: T47D_EtOH_24h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _siCTRL_Rep3

description: rawcounts.csv


title: T47D_Oestrogen_24h_RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_3h _siCTRL_Rep3

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_EtOH_24h_RNAiMAX_Rep2

description: rawcounts.csv


title: MCF7_EtOH_24h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siZMIZ1_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_EtOH_24h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_EtOH_24h_RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siCTRL_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siZMIZ1_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_24h_RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_12h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_EtOH_12h_siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_EtOH_12h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_EtOH_12h_siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_12h_RNAiMAX_Rep2

description: rawcounts.csv


title: MCF7_EtOH_12h_siCTRL_Rep2

description: rawcounts.csv


title: T47D_EtOH_12h_RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_12h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siZMIZ1_Rep2

description: rawcounts.csv


title: MCF7_EtOH_12h_RNAiMAX_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_12h_RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siCTRL_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siCTRL_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siCTRL_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_6h_siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_EtOH_6h_siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_EtOH_6h_siCTRL_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_6h_RNAiMAX_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_EtOH_6h_siCTRL_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_6h_RNAiMAX_Rep2

description: rawcounts.csv


title: MCF7_EtOH_6h_RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_EtOH_3h _siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h _siCTRL_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _siCTRL_Rep2

description: rawcounts.csv


title: T47D_EtOH_3h _RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h _RNAiMAX_Rep2

description: rawcounts.csv


title: MCF7_EtOH_3h _siZMIZ1_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_3h _siZMIZ1_Rep2

description: rawcounts.csv


title: MCF7_EtOH_3h _siCTRL_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_3h _siCTRL_Rep2

description: rawcounts.csv


title: MCF7_Oestrogen_3h _RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_EtOH_3h _siCTRL_Rep2

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_3h _RNAiMAX_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_siCTRL_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_3h _siCTRL_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_6h_siCTRL_Rep2

description: rawcounts.csv


title: T47D_EtOH_6h_RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_24h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_EtOH_6h_siZMIZ1_Rep2

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_EtOH_3h _RNAiMAX_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_24h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_EtOH_24h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_24h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_24h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_EtOH_24h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_24h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_EtOH_24h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_EtOH_24h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_24h_RNAiMAX_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_12h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_EtOH_24h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_12h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_24h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_EtOH_12h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_12h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_EtOH_12h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_3h _siZMIZ1_Rep2

description: rawcounts.csv


title: T47D_Oestrogen_12h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_EtOH_12h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_EtOH_12h_siZMIZ1_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_12h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_12h_siCTRL_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_12h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_EtOH_24h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_EtOH_12h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_EtOH_6h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_6h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_EtOH_6h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_EtOH_6h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_6h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_6h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siCTRL_Rep1

description: rawcounts.csv


title: MCF7_EtOH_6h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_6h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_EtOH_6h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_6h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_6h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_EtOH_12h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_3h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h_RNAiMAX_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_RNAiMAX_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h_RNAiMAX_Rep1

description: rawcounts.csv


title: MDA-MB-231_Oestrogen_3h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_EtOH_6h_siCTRL_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_6h_siZMIZ1_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_3h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_EtOH_3h_siZMIZ1_Rep1

description: rawcounts.csv


title: MDA-MB-231_EtOH_3h_siCTRL_Rep1

description: rawcounts.csv


title: T47D_Oestrogen_3h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_3h_siZMIZ1_Rep1

description: rawcounts.csv


title: T47D_EtOH_3h_RNAiMAX_Rep1

description: rawcounts.csv


title: T47D_EtOH_3h_siCTRL_Rep1

description: rawcounts.csv


title: MCF7_EtOH_3h_siZMIZ1_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_3h_RNAiMAX_Rep1

description: rawcounts.csv


title: MCF7_Oestrogen_3h_siCTRL_Rep1

description: rawcounts.csv


title: MCF7_EtOH_3h_siCTRL_Rep1

description: rawcounts.csv


title: OS1

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

data_processing:
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore.
Trimmed reads were aligned to the human genome (v.38) using HISAT2.
Count matrix for lncRNAs and snoRNAs was created using Kallisto.
LncRNA and snoRNA expression was compared between bone cancer and publically available controls (GSE55282) using the DESeq2 package available in R.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include read counts.

source_name: bone cancer tissue

growth_protocol: Tumour tissue resected by surgery.

extract_protocol:
RNA extracted from primary tumours using standard methods.
SENSE mRNA library prep kit (Lexogen).
Illumina 150 bp paired end.

tag: disease status

value: osteosarcoma

value: bone cancer


title: OS2


title: FL-ApoE4_rep3

city: Boise

first: James

middle: David

last: Beck

state: ID

address: 1910 University Drive

institute: Boise State University

data_processing:
Quality Assessment: FASTQC, v0.11.8
Compile Reference Index: Hisat2, v2.2.1, using hisat2-build, built using GRCm39.fna.gz from NCBI
Alignment: Hisat2, v2.2.1
Count Reads: HTSeq v,0.13.5, using htseq-count, set --type=gene, --idattr=Name --stranded=no and used GRCm39_genomic.gff from NCBI
Process Counts for Input: Custom code using AWK and grep to assure only 2 columns remained in count results and remove rows starting with "__"
Differential Expression Analysis: DESeq2 v1.30.1, set Conditions for 6 samples as (Control, Control, Control, FL_E4, FL_E4, FL_E4,) and design=~condition
Process Expression Results: Custom code using AWK and sed to limit results with p-values < 0.05, magnitude of 2 or greater fold change, translate log2 to negative fold change.
Genome_build: GRCm39.fna.gz
Supplementary_files_format_and_content: normalized_*_all.txt: Differential Expression Data
Supplementary_files_format_and_content: normalized_sigs_*.txt: Differential Expression Data - p <0.05
Supplementary_files_format_and_content: normalized_sigs_*_gt2.txt: Differential Expression Data - p <0.05, >=|2|
Supplementary_files_format_and_content: normalized_sigs_pos_gt2_negfold.txt: Differential Expression Data - p <0.05, >=|2|, convert to negative fold

organism: Mus musculus

source_name: Microglia cells_FL-ApoE4

growth_protocol: BV2, murine microglial cells, were maintained at 37°C and 6% CO2 in a humidified incubator.  Cells were maintained in RPMI 1640 Media (Hyclone) supplemented with 10% standard fetal bovine serum (Hyclone), 10% Cellgro MEM Nonessential Amino Acid (Corning) and 10% Penicillin streptomycin (Hyclone).

extract_protocol:
Total RNA was extracted from cells with the Direct-zol RNA MicroPrep Kit (Zymo Research Corp., CA, USA) according to manufacturer’s instructions.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Treatment of BV2 cells was undertaken by incubation with the human FL-ApoE protein (Prosci Inc., Poway, CA) at a concentration of 25 µg/ml for 5 hours to assess changes in mRNA expression.

tag: strain background

value: Treated (FL-ApoE4)

value: Microglia cells


title: ControlA_rep2

source_name: Microglia cells_ControlA

value: Untreated (Control for FL-ApoE4)


title: FL-ApoE4_rep1


title: FL-ApoE4_rep2


title: E14.5_cKO_rep1

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

description:
scRNA-seq data from isolated male germ cells of Rb1 cKO mice
KO1

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline and aligned to the mouse mm10 transcriptome.
A total of 6 transcriptomes (n=3 for control and n=3 for cKO) were merged and analyzed in R using the Seurat package (v 3.0).
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Gene-Cell Matrix filled with Raw Read/Expression Values
Supplementary_files_format_and_content: Processed data in the form of a gene-cell matrix of trascript reads.
Supplementary_files_format_and_content: Library and clustering information for each cell reported in the associated publication.

source_name: mouse testicular germ cells

extract_protocol:
Single-cell suspensions of E14.5 control or cKO testes were prepared. Germ cells were isolated using FACS with an SH800 machine (Sony Biotechnology) gating for tdTomato+ cells. Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v2 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).

tag: strain

value: Mixed C57/B6 and 129

value: testicular germ cells

tag: Sex

value: male

tag: developmental age

value: Rb1 cKO


title: E14.5_Con_rep3

description:
scRNA-seq data from isolated male germ cells of control mice
CON3

value: wildtype


title: E14.5_cKO_rep2

description:
scRNA-seq data from isolated male germ cells of Rb1 cKO mice
KO2


title: E14.5_cKO_rep3

description:
scRNA-seq data from isolated male germ cells of Rb1 cKO mice
KO3


title: E14.5_Con_rep2

description:
scRNA-seq data from isolated male germ cells of control mice
CON2


title: ControlA_rep1

tag: cell line


title: E14.5_Con_rep1

description:
scRNA-seq data from isolated male germ cells of control mice
CON1


title: ES

value: Ewing sarcoma

tag: tissue


title: scRNAseq_olig2_eGFP_36hpf [reanalysis]

city: Aurora

first: Kathryn

middle: Fay

last: Scott

state: Colorado

department: Pediatrics, Section of Developmental Biology

institute: University of Colorado Anschutz Medical Campus

description:
GSM4718657
appel.int.metadata.csv.gz
appel.int.RDS.gz

data_processing:
Generated cell feature counts for each single cell RNAseq library using cellranger count --transcriptome=GRCz11
Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X, CreateSeuratObject functions (3 separate Seurat objects)
filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature_RNA <50000 (24 hpf and 48 hpf samples) or <30000 (36 hpf)
Processed and filtered Seurat objects using Seurat NormalizeData, FindVariableFeatures(selection.method = 'vst', nfeatures = 2000), ScaleData (vars.to.regress=c('nCount_RNA','percent.mito','CC.difference'), RunPCA(npcs=100), RunUMAP(dims = 1:40), FindNeighbors(reduction - 'pca', dims = 1:40), FindClusters(resolution= 0.9 (48 hpf); 1 (36 hpf); 1.2 (24 hpf) ,dims = 1:40) and RunUMAP(dims=1:40)
Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 and 36 hpf datasets
Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchors(dims 1:40) and IntergrateData(dims = 1:40) Seurat functions
Processed and filtered intergrated Seurat object using Seurat NormalizeData, FindVariableFeatures(selection.method = 'vst', nfeatures = 2000), ScaleData (vars.to.regress=c('nCount_RNA','percent.mito','CC.difference'), RunPCA(npcs=100), RunUMAP(dims = 1:40), FindNeighbors(reduction = 'pca', dims = 1:40), FindClusters(resolution=  1.2 ,dims = 1:40) and RunUMAP(dims=1:40)
Genome_build: GRCz11
Supplementary_files_format_and_content: gzipped rds file of intergrated Seurat object
Supplementary_files_format_and_content: gzipped csv file of metadata for cells

organism: Danio rerio

source_name: spinal cord cells

growth_protocol: Embryos were raised at 28.5°C in E3 media (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4 at pH 7.4, with sodium bicarbonate), sorted for good health and staged accordingly to developmental morphological features and hours post-fertilization

extract_protocol:
24, 36, and 48 hpf Tg(olig2:EGFP) euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre-chilled Ca free Ringers solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES, pH 7.0) on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution (10 mg/ml BI protease, 125 U/ml DNase, 2.5 mM EDTA, 1X PBS) was added  to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution (30% FBS, 0.8 mM CaCl2, 1X PBS) was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice, 1 ml of chilled suspension media (1% FBS, 0.8 mM CaCl2, 50 U/ml Penicillin, 0.05 mg/ml Streptomycin) was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed, and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU-SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS.
The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell 3' Reagent Kit part no. PN-1000075.  Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.

treatment_protocol: No treatment was applied to the samples.

tag: developmental stage

value: 36 hours post fertilization

value: Tg(olig2:EGFP) ZFIN ID:ZDB-ALT-041129-8


title: scRNAseq_olig2_eGFP_24hpf [reanalysis]

description:
GSM4718656
appel.int.metadata.csv.gz
appel.int.RDS.gz

value: 24 hours post fertilization


title: MCF7_EtOH_3h_RNAiMAX_Rep1

description: rawcounts.csv

value: RNAiMAX

tag: treatment

value: EtOH


title: STS

value: soft tissue sarcoma


title: scRNAseq_olig2_eGFP_48hpf [reanalysis]

description:
GSM4718658
appel.int.metadata.csv.gz
appel.int.RDS.gz

value: 48 hours post fertilization


title: H28 parental cell

city: Sendai

first: Takeo

last: Tatsuta

state: Miyagi

address: 4-4-1 Komatsushima, Aoba-ku,

department: Institute of Molecular Biomembrane and Glycobiology

country: Japan

institute: Tohoku Medical and Pharmaceutical University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: H28, parental cell line

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (RPMI-FBS), penicillin-G (100 U/mL), and streptomycin (100 g/mL), and maintained in a 5% CO2 incubator at 37 ˚C under humidified conditions.

extract_protocol: The total RNA was isolated from each cell lines using TRI Reagent and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions. RNA samples were quantified by an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality was confirmed with a 2200 TapeStation (Agilent technologies, Santa Clara, CA).

tag: phenotype

value: cSBL-sensitive

value: lung; derived from metastatic


title: H28-cSR-B1

source_name: H28 cells,  clone of cSBL-resistant

value: cSBL-resistant


title: Embryo GED rep3

city: Shanghai

first: Zejun

last: Hu

address: Yangpu District Songhu Road No. 2005

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ZS97RS3
Supplementary_files_format_and_content: gene.tpm.matrix.annot

organism: Oryza sativa

source_name: Rice grain

extract_protocol:
Embryos were removed, flash frozen on dry ice, 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

value: NIL-D

value: Embryo

tag: age

value: post flowering day 15

value: CMP-/-


title: Embryo GED rep2


title: Embryo WT rep3

value: NIL-X

value: wild type


title: Embryo GED rep1


title: ControlA_rep3

value: Untreated (Control for FL-ApoE4)

tag: cell type

value: Microglia cells


title: Whole Cord WT rep2

city: La Jolla

first: Samuel

middle: L

last: Pfaff

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Raw sequencing data was demultiplexed using bcl2fastq v2.18.0.12. Sequencing and demultiplexing of two biological replicates into FASTQ format files were performed by the UCSD sequencing core.
Reads from the two samples were aligned and quantified separately for gene expression using Cellranger (10x genomics) and then combined into a single expression matrix using Cellranger’s ‘aggr’ program. We used the estimated cell count from Cellranger for downstream analysis. This experiment did not require additional QC steps to further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: UMI expression matrix and cell annotation matrix

source_name: Whole cord

extract_protocol:
The entire developing spinal cord was dissected from one Hb9:GFP embryo from one litter and another Hb9:GFP embryo from another litter in HBSS with HEPES (note: cells were not sorted for GFP). Cell dissociation was conducted using Papain following the manufacturer’s instruction (Worthington Biochemical). Specifically, spinal cords were placed in 750 uL papain solution in 37C water bath for 20 minutes, gently triturated, incubated again for additional 25 minutes, fully triturated, and quenched with 250 uL ovomucoid solution. Dissociated cells were then spun down at 150 rcf for 5 minutes. The cell pellet was resuspended in 5% FCS in DMEM/F12 with HEPES without phenol red, and the cells were passed through a cell strainer. Via FACS (FACSDIVA, BD), 20,000 cells were collected (not gated for GFP) into 500 uL of 5% FCS with DMEM/F12 with HEPES without phenol red. Sorted cells were spun down at 300 rcf for 2 minutes, and 370uL were removed to leave remaining 130 uL. The cells were resuspended in this remaining media. 32.5uL of the resuspended cells (~5,000 cells) were loaded into 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics). 14 cycles were used for cDNA amplification, and 10 cycles were used for library amplification. The resulting sequencing library was sequenced with Paired End reads, with a Read 1 of 26 basepairs and a Read 2 of 98 basepairs, on an Illumina HiSeq 4000 at the UCSD IGM Genomics Center.
Chromium Single Cell 3’ v2

value: embryonic day 12.5

value: whole spinal cord

tag: genotype


title: Lumbar neurons 1

data_processing:
Raw sequencing data was demultiplexed using bcl2fastq v2.18.0.12. Sequencing and demultiplexing of two biological replicates into FASTQ format files were performed by the UCSD sequencing core.
Alignment and quantification of 10x single-cell data was performed with Kallisto + BUS
Downstream analysis was performed in R
Genome_build: mm10
Supplementary_files_format_and_content: UMI expression matrix and cell annotation matrix

source_name: Lumbar spinal cord

extract_protocol:
Lumbar segments were dissected from Vglut2; tdTomato (2 female and 1 male) and Vgat; tdTomato (2 female and 1 male) in aCSF. Cell dissociation was conducted using Papain following the manufacturer’s instruction (Worthington Biochemical) with 5% Trehalose, 50uM APV, and 800uM KA added during the dissociation process (41). Via FACS (FACSDIVA, BD), 30,000 Vglut2; tdTomato cells and 30,000 Vgat;tdTomato cells were sequentially collected into 500ul of FACS buffer (DMEM w/o Phenol Red; 1mM EDTA; 25mM Hepes pH7.0; 5% FBS). Cell suspension was centrifuged at 300 rcf for 2 minutes, and supernatant was removed leaving 60 ul of FACS buffer and cell pellet. The cells were resuspended, and 33.4 ul of the resuspended cells (~30,000 cells) were loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics). 9 cycles were used for cDNA amplification, and 12 cycles were used for library amplification. The resulting sequencing library was sequenced with Paired End reads, with a Read 1 of 26 basepairs and a Read 2 of 98 basepairs, on an Illumina HiSeq 4000 and demultiplexed using bcl2fastq v2.18.0.12 at the UCSD IGM Genomics Center.
Chromium Single Cell 3’ v2

value: lumbar spinal cord

value: post natal day 0


title: Embryo WT rep1


title: Embryo WT rep2


title: Sample1031.Beluga.205128010039_R04C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

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

department: Human Genetics

institute: University of California, Los Angeles

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

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: Delphinapterus leucas

source_name: Blood

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: canbeusedforagingstudies

value: yes

value: Male

value: Blood


title: Sample911.Rough-toothed dolphin.205128010041_R04C02

description: genomic DNA methylation from tissue=Blood species=Rough-toothed dolphin

organism: Steno bredanensis


title: Sample932.Bottlenose dolphin.205128010032_R01C02

description: genomic DNA methylation from tissue=Skin species=Bottlenose dolphin

organism: Tursiops truncatus

source_name: Skin

value: Female

value: Skin


title: Sample904.Rough-toothed dolphin.205128010041_R03C01

description: genomic DNA methylation from tissue=Skin species=Rough-toothed dolphin


title: Sample903.Rough-toothed dolphin.205128010041_R02C01


title: Sample1056.Bottlenose dolphin.205128010020_R05C02

description: genomic DNA methylation from tissue=Blood species=Bottlenose dolphin


title: Sample910.Rough-toothed dolphin.205128010041_R03C02


title: Sample1034.Beluga.205128010025_R01C01

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


title: Sample899.Rough-toothed dolphin.205128010038_R04C02


title: Sample1035.Beluga.205128010025_R02C01


title: H28-cSR-A1

value: cSBL-resistant

value: lung; derived from metastatic


title: Sample898.Rough-toothed dolphin.205128010038_R03C02


title: Sample900.Rough-toothed dolphin.205128010038_R05C02


title: Sample934.Bottlenose dolphin.205128010032_R03C02


title: Whole Cord WT rep1


title: Sample913.Bottlenose dolphin.205128010041_R06C02


title: Sample892.Bottlenose dolphin.205128010038_R03C01


title: Sample891.Common dolphin.205128010038_R02C01

description: genomic DNA methylation from tissue=Skin species=Common dolphin

organism: Delphinus delphis


title: Sample912.Bottlenose dolphin.205128010041_R05C02


title: Sample1033.Beluga.205128010039_R06C02


title: Sample933.Bottlenose dolphin.205128010032_R02C02


title: Sample1036.Beluga.205128010025_R03C01


title: Sample905.Rough-toothed dolphin.205128010041_R04C01


title: Sample902.Rough-toothed dolphin.205128010041_R01C01


title: Sample901.Rough-toothed dolphin.205128010038_R06C02


title: Sample897.Rough-toothed dolphin.205128010038_R02C02


title: Sample883.Bottlenose dolphin.205128010026_R06C01


title: Sample906.Rough-toothed dolphin.205128010041_R05C01


title: Sample893.Bottlenose dolphin.205128010038_R04C01


title: Sample887.Bottlenose dolphin.205128010026_R04C02


title: Sample882.Bottlenose dolphin.205128010026_R05C01


title: Sample1032.Beluga.205128010039_R05C02


title: Sample896.Bottlenose dolphin.205128010038_R01C02


title: Sample881.Bottlenose dolphin.205128010026_R04C01


title: Sample879.Bottlenose dolphin.205128010026_R02C01


title: Sample877.Bottlenose dolphin.205128010001_R06C02


title: Sample876.Bottlenose dolphin.205128010001_R05C02


title: Sample874.Common dolphin.205128010001_R03C02


title: Sample889.Commerson's dolphin.205128010026_R06C02

description: genomic DNA methylation from tissue=Skin species=Commerson's dolphin

organism: Cephalorhynchus commersonii


title: Sample888.Bottlenose dolphin.205128010026_R05C02


title: Sample884.Bottlenose dolphin.205128010026_R01C02


title: Sample878.Bottlenose dolphin.205128010026_R01C01


title: Sample880.Bottlenose dolphin.205128010026_R03C01


title: Sample872.Bottlenose dolphin.205128010001_R01C02


title: Sample886.Bottlenose dolphin.205128010026_R03C02


title: Sample871.Bottlenose dolphin.205128010001_R06C01


title: Sample875.Bottlenose dolphin.205128010001_R04C02


title: Sample890.Commerson's dolphin.205128010038_R01C01


title: Sample873.Bottlenose dolphin.205128010001_R02C02


title: Sample869.Bottlenose dolphin.205128010001_R04C01


title: Sample864.Commerson's dolphin.205128010037_R05C02


title: Sample870.Bottlenose dolphin.205128010001_R05C01


title: Sample866.Bottlenose dolphin.205128010001_R01C01


title: Sample867.Bottlenose dolphin.205128010001_R02C01


title: Sample860.Bottlenose dolphin.205128010037_R01C02


title: Sample868.Bottlenose dolphin.205128010001_R03C01


title: Sample859.Bottlenose dolphin.205128010037_R06C01


title: Sample854.Bottlenose dolphin.205128010037_R01C01


title: Sample865.Commerson's dolphin.205128010037_R06C02


title: Sample858.Bottlenose dolphin.205128010037_R05C01


title: Sample856.Bottlenose dolphin.205128010037_R03C01


title: Sample861.Bottlenose dolphin.205128010037_R02C02


title: Sample863.Bottlenose dolphin.205128010037_R04C02


title: Sample862.Bottlenose dolphin.205128010037_R03C02


title: Sample849.Bottlenose dolphin.205128010030_R02C02


title: Sample855.Bottlenose dolphin.205128010037_R02C01


title: Sample857.Bottlenose dolphin.205128010037_R04C01


title: Sample852.Bottlenose dolphin.205128010030_R05C02


title: Sample845.Bottlenose dolphin.205128010030_R04C01


title: Sample848.Bottlenose dolphin.205128010030_R01C02


title: Sample853.Bottlenose dolphin.205128010030_R06C02


title: Sample846.Bottlenose dolphin.205128010030_R05C01


title: Sample851.Bottlenose dolphin.205128010030_R04C02


title: Sample850.Bottlenose dolphin.205128010030_R03C02


title: Sample847.Bottlenose dolphin.205128010030_R06C01


title: Sample842.Bottlenose dolphin.205128010030_R01C01


title: Sample844.Bottlenose dolphin.205128010030_R03C01


title: Sample834.Bottlenose dolphin.205128010023_R05C01


title: Sample839.Bottlenose dolphin.205128010023_R04C02


title: Sample826.Bottlenose dolphin.205128010024_R03C02


title: Sample828.Bottlenose dolphin.205128010024_R05C02


title: Sample843.Bottlenose dolphin.205128010030_R02C01


title: Sample841.Bottlenose dolphin.205128010023_R06C02


title: Sample840.Bottlenose dolphin.205128010023_R05C02


title: Sample837.Bottlenose dolphin.205128010023_R02C02


title: Sample832.Bottlenose dolphin.205128010023_R03C01


title: Sample833.Bottlenose dolphin.205128010023_R04C01


title: Sample835.Bottlenose dolphin.205128010023_R06C01


title: Sample836.Bottlenose dolphin.205128010023_R01C02


title: Sample829.Bottlenose dolphin.205128010024_R06C02


title: Sample830.Bottlenose dolphin.205128010023_R01C01


title: Sample838.Bottlenose dolphin.205128010023_R03C02


title: Sample825.Bottlenose dolphin.205128010024_R02C02


title: Sample823.Bottlenose dolphin.205128010024_R06C01


title: Sample824.Bottlenose dolphin.205128010024_R01C02


title: Sample820.Beluga whale.205128010024_R03C01

description: genomic DNA methylation from tissue=Skin species=Beluga whale


title: Sample827.Bottlenose dolphin.205128010024_R04C02


title: Sample821.Short-finned pilot whale.205128010024_R04C01

description: genomic DNA methylation from tissue=Skin species=Short-finned pilot whale

organism: Globicephala macrorhynchus


title: Sample822.Killer whale.205128010024_R05C01

description: genomic DNA methylation from tissue=Skin species=Killer whale

organism: Orcinus orca


title: Sample819.Short-finned pilot whale.205128010024_R02C01


title: Sample818.Short-finned pilot whale.205128010024_R01C01


title: Sample810.Beluga whale.204529320053_R05C02

description: genomic DNA methylation from tissue=Blood species=Beluga whale


title: Sample812.Beluga whale.204529320113_R01C01


title: Sample811.Beluga whale.204529320053_R06C02


title: Sample814.Beluga whale.204529320113_R03C01


title: Sample808.Pacific white-sided dolphin.204529320053_R03C02

description: genomic DNA methylation from tissue=Blood species=Pacific white-sided dolphin

organism: Sagmatias obliquidens


title: Sample806.Pacific white-sided dolphin.204529320053_R01C02


title: Sample805.Pacific white-sided dolphin.204529320053_R06C01


title: Sample813.Beluga whale.204529320113_R02C01


title: Sample809.Beluga whale.204529320053_R04C02


title: Sample816.Harbor porpoise.204529320113_R05C01

description: genomic DNA methylation from tissue=Blood species=Harbor porpoise

organism: Phocoena phocoena


title: Sample807.Pacific white-sided dolphin.204529320053_R02C02


title: Sample815.Beluga whale.204529320113_R04C01


title: Sample802.Killer whale.204529320053_R03C01

description: genomic DNA methylation from tissue=Blood species=Killer whale


title: Sample801.Killer whale.204529320053_R02C01


title: Sample803.Killer whale.204529320053_R04C01


title: Sample795.Killer whale.204529320105_R02C02


title: Sample791.Killer whale.204529320105_R04C01


title: Sample804.Killer whale.204529320053_R05C01


title: Sample790.Killer whale.204529320105_R03C01


title: Sample722.Killer whale.204529320031_R01C02


title: Sample793.Killer whale.204529320105_R06C01


title: Sample794.Killer whale.204529320105_R01C02


title: Sample720.Killer whale.204529320031_R05C01


title: Sample719.Killer whale.204529320031_R04C01


title: Sample800.Killer whale.204529320053_R01C01


title: Sample789.Killer whale.204529320105_R02C01


title: Sample721.Killer whale.204529320031_R06C01


title: Sample717.Killer whale.204529320031_R02C01


title: Sample792.Killer whale.204529320105_R05C01


title: Sample714.Short-finned pilot whale.204529320054_R05C02


title: Sample703.Beluga whale.204529320048_R06C02


title: Sample716.Killer whale.204529320031_R01C01


title: Sample713.Short-finned pilot whale.204529320054_R04C02


title: Sample704.Beluga whale.204529320054_R01C01


title: Sample701.Beluga whale.204529320048_R04C02


title: Sample706.Beluga whale.204529320054_R03C01


title: Sample707.Beluga whale.204529320054_R04C01


title: Sample699.Pacific white-sided dolphin.204529320048_R02C02

description: genomic DNA methylation from tissue=Skin species=Pacific white-sided dolphin


title: Sample698.Pacific white-sided dolphin.204529320048_R01C02


title: Sample705.Beluga whale.204529320054_R02C01


title: Sample708.Harbor porpoise.204529320054_R05C01

description: genomic DNA methylation from tissue=Skin species=Harbor porpoise


title: Sample695.Killer whale.204529320048_R04C01


title: Sample700.Pacific white-sided dolphin.204529320048_R03C02


title: Sample718.Killer whale.204529320031_R03C01


title: Sample697.Pacific white-sided dolphin.204529320048_R06C01


title: Sample694.Killer whale.204529320048_R03C01


title: Sample702.Beluga whale.204529320048_R05C02


title: Sample696.Killer whale.204529320048_R05C01


title: Sample715.Short-finned pilot whale.204529320054_R06C02


title: Sample693.Killer whale.204529320048_R02C01


title: Sample673.Bottlenose dolphin.204529320059_R06C01


title: Sample676.Bottlenose dolphin.204529320059_R03C02


title: Sample675.Bottlenose dolphin.204529320059_R02C02


title: Sample831.Bottlenose dolphin.205128010023_R02C01


title: Sample677.Bottlenose dolphin.204529320059_R04C02


title: Sample634.Beluga whale.204551090023_R03C01


title: Sample669.Bottlenose dolphin.204529320059_R02C01


title: Sample632.Beluga whale.204551090023_R01C01


title: Sample662.Bottlenose dolphin.204529320051_R01C02


title: Sample656.Bottlenose dolphin.204529320051_R01C01


title: Sample663.Bottlenose dolphin.204529320051_R02C02


title: Sample657.Bottlenose dolphin.204529320051_R02C01


title: Sample631.Beluga whale.204551090057_R06C02


title: Sample629.Beluga whale.204551090057_R04C02


title: Sample630.Beluga whale.204551090057_R05C02


title: Sample623.Bottlenose dolphin.204551090057_R04C01


title: Sample633.Beluga whale.204551090023_R02C01


title: Sample624.Bottlenose dolphin.204551090057_R05C01


title: Sample604.Beluga whale.204551090022_R03C02


title: Sample601.Beluga whale.204551090022_R06C01


title: Sample606.Beluga whale.204551090022_R05C02


title: Sample599.Beluga whale.204551090022_R04C01


title: Sample605.Beluga whale.204551090022_R04C02


title: Sample600.Beluga whale.204551090022_R05C01


title: Sample598.Beluga whale.204551090022_R03C01


title: Sample596.Beluga whale.204551090022_R01C01


title: Sample602.Beluga whale.204551090022_R01C02


title: Sample595.Beluga whale.204529320109_R06C02


title: Sample597.Beluga whale.204551090022_R02C01


title: Sample594.Beluga whale.204529320109_R05C02


title: Sample591.Beluga whale.204529320109_R02C02


title: Sample593.Beluga whale.204529320109_R04C02


title: Sample590.Pacific white-sided dolphin.204529320109_R01C02


title: Sample578.Beluga whale.204529320102_R01C02


title: Sample587.Pacific white-sided dolphin.204529320109_R04C01


title: Sample585.Pacific white-sided dolphin.204529320109_R02C01


title: Sample583.Pacific white-sided dolphin.204529320102_R06C02


title: Sample584.Pacific white-sided dolphin.204529320109_R01C01


title: Sample588.Pacific white-sided dolphin.204529320109_R05C01


title: Sample586.Pacific white-sided dolphin.204529320109_R03C01


title: Sample575.Beluga whale.204529320102_R04C01


title: Sample589.Pacific white-sided dolphin.204529320109_R06C01


title: Sample577.Beluga whale.204529320102_R06C01


title: Sample573.Beluga whale.204529320102_R02C01


title: Sample592.Beluga whale.204529320109_R03C02


title: Sample574.Beluga whale.204529320102_R03C01


title: Sample571.Beluga whale.204529320121_R06C02


title: Sample572.Beluga whale.204529320102_R01C01


title: Sample570.Beluga whale.204529320121_R05C02


title: Sample565.Killer whale.204529320121_R06C01


title: Sample603.Beluga whale.204551090022_R02C02


title: Sample556.Killer whale.204529320099_R03C02


title: Sample569.Beluga whale.204529320121_R04C02


title: Sample560.Bottlenose dolphin.204529320121_R01C01


title: Sample566.Killer whale.204529320121_R01C02


title: Sample558.Killer whale.204529320099_R05C02


title: Sample561.Killer whale.204529320121_R02C01


title: Sample563.Killer whale.204529320121_R04C01


title: Sample576.Beluga whale.204529320102_R05C01


title: Sample559.Bottlenose dolphin.204529320099_R06C02


title: Sample564.Killer whale.204529320121_R05C01


title: Sample554.Killer whale.204529320099_R01C02


title: Sample551.Killer whale.204529320099_R04C01


title: Sample546.Killer whale.204529320096_R05C02


title: Sample538.Killer whale.204529320096_R03C01


title: Sample544.Killer whale.204529320096_R03C02


title: Sample548.Pacific white-sided dolphin.204529320099_R01C01


title: Sample547.Pacific white-sided dolphin.204529320096_R06C02


title: Sample542.Killer whale.204529320096_R01C02


title: Sample545.Killer whale.204529320096_R04C02


title: Sample549.Pacific white-sided dolphin.204529320099_R02C01


title: Sample557.Killer whale.204529320099_R04C02


title: Sample541.Killer whale.204529320096_R06C01


title: Sample550.Pacific white-sided dolphin.204529320099_R03C01


title: Sample543.Killer whale.204529320096_R02C02


title: Sample540.Killer whale.204529320096_R05C01


title: Sample535.Beluga whale.204529320092_R06C02


title: Sample537.Killer whale.204529320096_R02C01


title: Sample532.Beluga whale.204529320092_R03C02


title: Sample527.Killer whale.204529320092_R04C01


title: Sample530.Killer whale.204529320092_R01C02


title: Sample536.Beluga whale.204529320096_R01C01


title: Sample529.Killer whale.204529320092_R06C01


title: Sample525.Killer whale.204529320092_R02C01


title: Sample533.Beluga whale.204529320092_R04C02


title: Sample528.Killer whale.204529320092_R05C01


title: Sample531.Beluga whale.204529320092_R02C02


title: Sample518.Pacific white-sided dolphin.204529320101_R01C02


title: Sample524.Killer whale.204529320092_R01C01


title: Sample534.Beluga whale.204529320092_R05C02


title: Sample521.Killer whale.204529320101_R04C02


title: Sample516.Killer whale.204529320101_R05C01


title: Sample523.Killer whale.204529320101_R06C02


title: Sample522.Killer whale.204529320101_R05C02


title: Sample511.Killer whale.204529320086_R06C02


title: Sample519.Pacific white-sided dolphin.204529320101_R02C02


title: Sample515.Killer whale.204529320101_R04C01


title: Sample512.Killer whale.204529320101_R01C01


title: Sample520.Pacific white-sided dolphin.204529320101_R03C02


title: Sample517.Pacific white-sided dolphin.204529320101_R06C01


title: Sample513.Killer whale.204529320101_R02C01


title: Sample514.Killer whale.204529320101_R03C01


title: Sample509.Killer whale.204529320086_R04C02


title: Sample510.Killer whale.204529320086_R05C02


title: Sample508.Killer whale.204529320086_R03C02


title: Sample507.Killer whale.204529320086_R02C02


title: Sample506.Beluga whale.204529320086_R01C02


title: Sample503.Beluga whale.204529320086_R04C01


title: Sample500.Beluga whale.204529320086_R01C01


title: Sample505.Beluga whale.204529320086_R06C01


title: Sample501.Beluga whale.204529320086_R02C01


title: Sample498.Killer whale.203877620024_R01C02


title: Sample497.Killer whale.203877620024_R06C01


title: Sample445.Pacific white-sided dolphin.203877620079_R02C01


title: Sample447.Bottlenose dolphin.203877620079_R04C01


title: Sample443.Pacific white-sided dolphin.203877620032_R06C02


title: Sample446.Pacific white-sided dolphin.203877620079_R03C01


title: Sample468.Bottlenose dolphin.203877620091_R01C01


title: Sample466.Bottlenose dolphin.203877620076_R05C02


title: Sample469.Bottlenose dolphin.203877620091_R02C01


title: Sample444.Pacific white-sided dolphin.203877620079_R01C01


title: Sample499.Killer whale.203877620024_R02C02


title: Sample442.Pacific white-sided dolphin.203877620032_R05C02


title: Sample439.Bottlenose dolphin.203877620032_R02C02


title: Sample440.Bottlenose dolphin.203877620032_R03C02


title: Sample433.Bottlenose dolphin.203877620032_R02C01


title: Sample434.Bottlenose dolphin.203877620032_R03C01


title: Sample438.Common dolphin.203877620032_R01C02

description: genomic DNA methylation from tissue=Blood species=Common dolphin


title: Sample430.Bottlenose dolphin.203877620043_R05C02


title: Sample437.Common dolphin.203877620032_R06C01


title: Sample424.Bottlenose dolphin.203877620043_R05C01


title: Sample428.Bottlenose dolphin.203877620043_R03C02


title: Sample420.Bottlenose dolphin.203877620043_R01C01


title: Sample429.Bottlenose dolphin.203877620043_R04C02


title: Sample376.Bottlenose dolphin.203867110005_R05C01


title: Sample555.Killer whale.204529320099_R02C02


title: Sample419.Bottlenose dolphin.203877620080_R06C02


title: Sample412.Bottlenose dolphin.203877620080_R05C01


title: Sample389.Bottlenose dolphin.203877620002_R06C01


title: Sample441.Bottlenose dolphin.203877620032_R04C02


title: Sample386.Bottlenose dolphin.203877620002_R03C01


title: Sample407.Bottlenose dolphin.203877620072_R06C02


title: Sample539.Killer whale.204529320096_R04C01


title: Sample380.Bottlenose dolphin.203867110005_R03C02


title: Sample354.Beluga whale.203867110006_R01C02


title: Sample360.Bottlenose dolphin.203877620001_R01C01


title: Sample375.Bottlenose dolphin.203867110005_R04C01


title: Sample358.Beluga whale.203867110006_R05C02


title: Sample340.Bottlenose dolphin.203877620071_R05C01


title: Sample355.Beluga whale.203867110006_R02C02


title: Sample339.Bottlenose dolphin.203877620071_R04C01


title: Sample353.Bottlenose dolphin.203867110006_R06C01


title: Sample357.Beluga whale.203867110006_R04C02


title: Sample363.Bottlenose dolphin.203877620001_R04C01


title: Sample359.Short-finned pilot whale.203867110006_R06C02


title: Sample331.Bottlenose dolphin.203877620075_R02C02


title: Sample332.Bottlenose dolphin.203877620075_R03C02


title: Sample364.Bottlenose dolphin.203877620001_R05C01


title: Sample366.Common dolphin.203877620001_R01C02


title: Sample338.Bottlenose dolphin.203877620071_R03C01


title: Sample365.Bottlenose dolphin.203877620001_R06C01


title: Sample325.Bottlenose dolphin.203877620075_R02C01


title: Sample356.Beluga whale.203867110006_R03C02


title: Sample362.Common dolphin.203877620001_R03C01


title: Sample324.Bottlenose dolphin.203877620075_R01C01


title: Sample337.Bottlenose dolphin.203877620071_R02C01


title: Cov2-M3_m_IP

last: Li

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

data_processing:
Basecalls performed using FastQC v0.11.8
RNA-seq reads and MeRIP reads were aligned to the SARS-CoV-2 (NC_045512.2) genome or hg38 genome assembly using STAR or Bowtie2 aligner
Data were filtered using cutadapt: Phred quality score > 30 and remove adapters
peaks were called by MACS2 using the following configuration:  p-value< 0.05, call-summit, keep-dup 1 --nomodel --extsize 200 or keep-dup all --nomodel --extsize 200 for SARS-CoV-2 alignment; p<1e-5, -keep-dup auto --extsize 200 nomodel for human alignment
Raw read gene counts are generated using htseq-count; normalized read gene counts are generated by DESeq2.
Genome_build: SARS-CoV-2 (NC_045512.2), GRCh38, ChlSab1.1
Supplementary_files_format_and_content: xlsx: contains normailzed gene expression by DESeq2; bigBed: contains peaks detecting by MACS2 (1: keep-dup 1; all: keep-dup all)

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: SARS-CoV-2 viral infected METTL3 KD (M3) Caco-2 cells

growth_protocol: The human colorectal adenocarcinoma Caco-2 cells were purchased from ATCC. Caco-2 cells were cultured in high-glucose MEM (Thermo Fisher Scientific) supplemented with 20% fetal bovine serum (FBS; Gibco), MEM NEAA (Thermo Fisher Scientific) and 50 U/ml penicillin-streptomycin (Gibco) in a humidified 5% CO2 atmosphere.  For SARS-CoV-2 live cell infection, SARS-CoV-2 isolate USA-WA1/2020 was obtained from BEI Resources. SARS-CoV-2 virus was propagated, and infectious units were quantified by plaque assay using Vero E6 cells.

extract_protocol:
Cellular mRNA from infected METTL3 KD (M3) Caco-2 cells were extracted and purified for IP of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).

treatment_protocol: Infected with SARS-CoV-2

value: Human colorectal adenocarcinoma Caco-2 cells

value: METTL3 KD

tag: infection

value: SARS-CoV-2 virus

tag: passages

tag: viral strain

value: Betacoronavirus

tag: merip antibody

value: anti-m6A polyclonal antibody (ab151230, abcam)


title: Epidermal keratinocytes_in vitro_M7

city: Niigata

first: Kenji

last: Izumi

state: Niigata

address: 2-5274, Gakkocho-dori, Chuo-ku

department: Dentistry

institute: Niigata University

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (SST-RMA) were used Affymetrix® Expression Console™ Software.

label: biotin

organism: Macaca fuscata

source_name: Japanese macaque

growth_protocol: Keratinocytes were cultured in a serum-free condition.

extract_protocol: We used RNeasy mini kit (QIAGEN).

value: Epidermal keratinocytes

tag: assay

value: in vitro


title: Oral (mucosa) keratinocytes_in vitro_M6

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

value: Oral (mucosa) keratinocytes


title: Cov2-Ctrl_m_IP

source_name: SARS-CoV-2 viral infected control (Ctrl) Caco-2 cells

extract_protocol:
Cellular mRNA from infected control (Ctrl) Caco-2 cells were extracted and purified for IP of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).

value: control (Ctrl)


title: Cov2-M3_m_Input

extract_protocol:
Cellular mRNA from infected METTL3 KD (M3) Caco-2 cells were extracted and purified for input of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).


title: Cov2-Ctrl_m_Input

extract_protocol:
Cellular mRNA from infected control (Ctrl) Caco-2 cells were extracted and purified for input of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).


title: Vermillion keratinocytes_in vitro_M5

value: Vermillion keratinocytes


title: Sample526.Killer whale.204529320092_R03C01

value: yes

tag: Sex


title: Cov2-M3_IP

extract_protocol:
RNA from infected METTL3 KD (M3) Caco-2 cells were extracted and purified for IP of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).


title: Oral mucosa epithelium_in vivo_M2

value: Oral mucosa epithelium

value: in vivo


title: Epidermis (skin epithelium)_in vivo_M4

value: Epidermis (skin epithelium)


title: Sample320.Bottlenose dolphin.203531420021_R03C02

value: Male

value: Skin


title: cov2-shM3-3

extract_protocol:
Total RNA from infected METTL3 KD (M3) cells were extracted and purified
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).


title: Vermillion epithelium_in vivo_M1

value: Vermillion epithelium


title: Cov2-Ctrl_IP

extract_protocol:
RNA from infected control (Ctrl) Caco-2 cells were extracted and purified for IP of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).

value: Human colorectal adenocarcinoma Caco-2 cells


title: Cov2-M3_Input

extract_protocol:
RNA from infected METTL3 KD (M3) Caco-2 cells were extracted and purified for input of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).

value: METTL3 KD


title: Cov2-Ctrl_Input

extract_protocol:
RNA from infected control (Ctrl) Caco-2 cells were extracted and purified for input of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).

value: SARS-CoV-2 virus


title: Sample318.Beluga whale.203531420021_R01C02

value: Female


title: Sample322.Beluga whale.203531420021_R05C02


title: Sample317.Beluga whale.203531420021_R06C01


title: cov2-shM3-2

value: Betacoronavirus


title: Sample319.Beluga whale.203531420021_R02C02


title: cov2-shNTC-3

source_name: SARS-CoV-2 viral infected control (shNTC) Caco-2 cells

extract_protocol:
Total RNA from infected control (shNTC) cells were extracted and purified
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).

value: control (shNTC)


title: cov2-shNTC-2


title: Sample315.Beluga whale.203531420021_R04C01


title: Sample309.Killer whale.203531420079_R04C02


title: Sample310.Killer whale.203531420079_R05C02


title: Sample314.Beluga whale.203531420021_R03C01


title: cov2-shNTC-1


title: Sample312.Killer whale.203531420021_R01C01


title: Sample308.Bottlenose dolphin.203531420079_R03C02


title: Sample307.Killer whale.203531420079_R02C02


title: Sample305.Killer whale.203531420079_R06C01


title: MT2_2 snATAC-seq

city: Irvine

first: Elisabeth

last: Rebboah

address: 2300E Biological Sciences 3

department: Developmental and Cell Biology

institute: University of California, Irvine

description: Tn5 tagmented C2C12 myotube nuclei from unfiltered myotubes were collected for snATAC-seq (technical rep 2). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.

library_source: genomic

data_processing:
Use Docker container to run FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and generate HTML report for each fastq file in input directory. docker run --rm -v $1:/data/ bioraddbg/atac-seq-fastqc:v1.0.0  -i /data/ -o /data/fastqc_results --name fastqc. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run BAP (https://github.com/caleblareau/bap) and debarcode fastq files. Barcodes are parsed from read 1 and appended to read name for valid barcodes only. docker run --rm -v $1:/data/ bioraddbg/atac-seq-debarcode-dbg:v1.0.0  -i /data/  -o /data/debarcoded_reads  --name debarcode. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run BWA (http://bio-bwa.sourceforge.net) to align to mm10. docker run --rm -v $1:/data/ -v /path/to/mm10/bwa/:/genome/ bioraddbg/atac-seq-bwa:v1.0.0 -i /data/debarcoded_reads/ -o /data/alignments/ -r /genome/ --name align. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run QC on aligned file with Picard (https://broadinstitute.github.io/picard/) CollectAlignmentSummaryMetrics and writes a text file with alignment summary metrics. docker run --rm -v $1:/data/ -v /path/to/mm10/:/genome/ bioraddbg/atac-seq-alignment-qc:v1.0.0  -i /data/alignments/  -r /genome/mm10.fa -o /data/alignment_qc --name alignment_qc. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to filter beads (barcodes) from cell-free nanodroplets, and identify beads that ended up in the same nanodroplet with a nucleus using Jaccard indexing. docker run --rm -v $1:/data/ bioraddbg/atac-seq-filter-beads:v1.0.0 -i /data/alignments/  -o /data/bead_filtration/  -r mm10  --name bead_filtration --cpus="10". (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to merge beads that ended up in the same nanodroplet with a nucleus using BAP (https://github.com/caleblareau/bap) . docker run --rm -v $1:/data/ bioraddbg/atac-seq-deconvolute:v1.0.0 -i /data/alignments/ -f /data/bead_filtration/ -r mm10  -o /data/deconvoluted_data --name deconv_${2}. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to filter out cells with low read depth using a UMI- (unique molecular identifier) based "knee call". Outputs bam file and cell list included in this submission. docker run --rm -v $1:/data/  bioraddbg/atac-seq-cell-filter:v1.0.0 -i /data/deconvoluted_data/  -o /data/cells_filtered/ -r mm10  --name cell_filtration. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run MACS2 (https://github.com/taoliu/MACS). Outputs peaks included in this submission. docker run --rm -v $1:/data/ bioraddbg/atac-seq-macs2:v1.0.0  -i /data/deconvoluted_data/ -r mm10  -o /data/peaks  --name peak_calling. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to run QC on deconvoluted alignment data, generating a FRIP score, insert size metrics histogram, and TSS score. In v.1.0.1, docker tool is fixed to run chromVar and generate peaks-by-cells counts matrix; v. 1.0.0 crashed at this step, hence our custom code. docker run --rm -v $1:/data/  bioraddbg/atac-seq-qc:v1.0.0  -r mm10 -d /data/deconvoluted_data/ -p /data/peaks  -o /data/atac_qc --name atac_qc. (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Use Docker container to generate an HTML and PDF report of all the outputs using MultiQC (https://multiqc.info). (Protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_7191.pdf)
Merge peaks across all samples (https://github.com/fairliereese/lab_pipelines/tree/master/sc_atac_pipeline). For example, python merge_peaks.py -p peakfiles.csv --o merged_peaks
Use custom script to generate CSV file of peaks-by-cells matrix using merged peaks, cell list, and alignments (https://github.com/fairliereese/lab_pipelines/tree/master/sc_atac_pipeline). For example, python gen_count_matrix.py -p merged_peaks.bed  -b  MB1/MB1.bam  -bc MB1/MB1.aboveKneeBarcodes.csv -e MB1 --o MB1/ --full_csv
Genome_build: mm10
Supplementary_files_format_and_content: Peak calls from MACS2.
Supplementary_files_format_and_content: CSV file of cell IDs passing UMI cutoff.
Supplementary_files_format_and_content: Peaks-by-cells matrix generated using custom code (https://github.com/fairliereese/lab_pipelines/tree/master/sc_atac_pipeline) and provided processed files: peaks, barcodes, and aligned reads.

growth_protocol: C2C12 cells  (ATCC, CRL-1772) were cultured on 10 cm plates  in 10 mL myoblast growth media: high-glucose DMEM with L-glutamine and without sodium pyruvate, supplemented with 20% fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin. Cells were maintained at 20-50% confluency at 37C with 5% CO2 and passaged at 1:3 or 1:4 every 2 to 3 days.

extract_protocol:
Cells were rinsed with 1X PBS and incubated with 2 mL TrypLE-Express for 5 minutes at 37C, which was then neutralized with 8 mL myoblast growth media. Nuclei were prepared following Bio-Rad's SureCell WTA 3' Nuclei Isolation protocol (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/surecell/surecell-wta3-nuclei-demonstrated-protocol-1000000044178-00.pdf). Myotubes were both filtered (3 samples) and not filtered (2 samples) through a 40uM strainer before nuclei isolation but data were very similar between the two different nuclei preps. Tagmented DNA was barcoded and amplified in nanodroplets, then extracted following Bio Rad's SureCell ATAC-seq library kit (cat. #17004620; protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf).
Bio-Rad's SureCell ATAC-seq library kit (cat. #17004620; protocol document: https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf)

treatment_protocol: To differentiate myoblasts to myotubes, cells at 90-100% confluency were rinsed with 1X PBS and myoblast growth media was replaced with 10 mL differentiation media: high-glucose DMEM with L-glutamine and without sodium pyruvate, supplemented with 2% donor horse serum, 100 units/mL penicillin, 100 ug/mL streptomycin, and freshly-added 1uM insulin. Differentiation media was replaced every 24 hours for 3 days. ENCODE protocol: https://www.encodeproject.org/documents/b42974fd-1490-4d51-bdcf-7db97a3e8fe0/@@download/attachment/C2C12_Wold_protocol.pdf

value: myotube

tag: treatment protocol

value: Differentiation of C2C12, ENCODE (https://www.encodeproject.org/documents/b42974fd-1490-4d51-bdcf-7db97a3e8fe0/@@download/attachment/C2C12_Wold_protocol.pdf)

tag: library prep protocol

value: snATAC-seq protocol; SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620).


title: Sample304.Killer whale.203531420079_R05C01

tag: tissue


title: MT1_2 snATAC-seq

description: Tn5 tagmented C2C12 myotube nuclei from unfiltered myotubes were collected for snATAC-seq (technical rep 1). Library preparation was performed following manufacturer’s instructions for the SureCell ATAC-seq Library Preparation Kit (Bio-Rad, cat. #17004620, https://www.bio-rad.com/webroot/web/pdf/lsr/literature/10000106678.pdf) for the target output of 5,000 cells per well, one well per sample. Nuclei and barcoded beads are streamed together in the microfluidics device to produce nanodroplets where the first amplification reaction takes place. Droplets are then broken and barcoded, tagmented DNA is purified for sequencing.

tag: cell line


title: cov2-shM3-1