title: Wnt3a-treated WT AMs

city: Rochester

first: Bibo

last: Zhu

state: MN

address: 200 1st ST SW

department: Pulmonary and Critical Care Medicine

institute: Mayo Clinic

description: single cell RNA library

data_processing:
Paired-end sequencing was performed using an Illumina HiSeq 2500 in rapid-run mode.
CellRanger software package (10x Genomics) were used to align and quantify sequencing data from 10x Genomics.
All scRNA-seq analyses were performed in R using the package Seurat (version 3.0; Butler, 2018)
To analyze the cell cycle signature from the dataset, we used Seurat to calculate a cell cycle score for each cell based on expression across a list of reported core gene set including 43 G1/S and 54 G2/M markers. Scaled residual expression obtained from Seurat modeling the relationship between gene expression and the cell cycle scores, that was used for dimensionality reduction and clustering.
UMAP dimensional reduction was performed to visualize data in 2D space. DEGs between clusters were determined using a Wilcoxon rank sum test.
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: Bronchoalveolar lavage

growth_protocol: AMs were obtained from bronchoalveolar lavage of mice and purified by adherence for 2 h in complete medium (RPMI-1640, 10% FBS, 1% Pen/Strep/glutamate) at 37 ̊C and 5% CO2. The non-adherent cells were washed off with warm PBS. The remaining adherent cells were cultured in complete medium supplemented with 10 ng/ml recombinant murine granulocyte macrophage CSF (GM-CSF).

extract_protocol:
Wnt3a-treated AMs or control AMs were loaded on the Chromium Controller (10x Genomics).
Single-cell libraries were prepared using the Chromium Single Cell 3’ Reagent kit (10x Genomics)

treatment_protocol: AMs were pre-treated with Wnt3a (100 ng/ml) or vehicle in complete medium without GM-CSF for overnight. Subsequently, cells were washed with warm PBS and treated with the same amount of Wnt3a or vehicle in complete medium with 10 ng/ml GM-CSF for another overnight. Then, the cells were havested for scRNA-seq.

value: Lung

value: Alveolar macrophages


title: Day7.6.pTEICM_12

status: Public on May 05 2021

type: SRA

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

library_source: transcriptomic

data_processing:
Trim-Galore
STAR
FeatureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts_raw.txt: Raw counts text file.

molecule: total RNA

organism: Homo sapiens

source_name: Blastocyst

growth_protocol: Frozen human blastocysts (E5 or E6) were thawed and cultured in N2B27 medium under mineral oil. The majority of embryos were cultured for 24 hours for development to late blastocysts (E6 or E7). Human naïve pluripotent stem cells (HNES1-GATA3:mKO2) [Ge Guo et al., 2021] or niPSC [Bredenkamp Nicholas et al.,2019] were cultured in PXGL on MEF. Dissociated human naïve pluripotent stem cells were cultured in a low attachment 96-well plate in N2B27 supplemented with 1.5uMPD03 and 1uMA83 and 10uM Y-27632 for 44h. The formed aggregates were transferred in N2B27 supplemented with 0.5uM A83. After 18h, they were transferred to N2B27 to form blastocyst-like structure.

extract_protocol:
Dissociated single cells were transferred immediately into Smart-Seq2 single-cell lysis buffer and immediately frozen.
The Smart-Seq2 library was prepared as described in Picelli S et al. 2014.

treatment_protocol: The zona pellucida was removed using acid Tyrode’s solution. Human embryos and human blastocyst model were moved to filtered M2 drop and cut mTE manually using glass pipettes. mTE and the other part containing ICM and pTE were transferred to a drop of Accutase or TrypLE respectively using glass capillary or Pasteur pipette and incubated for 7-10 min at 37 oC or room temperature. Then mTE and ICM with pTE were transferred to a drop of filtered M2 respectively and dissociated by repetitive pipetting using a finely drawn Pasteur pipette or glass capillary of which diameter is just larger than a cell.

tag: tissue

value: Blastocyst

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: Embryonic day 7


title: Day7.6.pTEICM_11


title: Control WT Ams

country: USA

description: single cell RNA library

organism: Mus musculus

tag: cell type

tag: treatment

value: Medium

tag: strain


title: C57BL6_Diet 6 (CA)_Liver 4

city: Sydney

first: Saeed

last: Esmaili

state: NSW

address: 176 Hawkesbury Rd, Westmead

department: Storr Liver Centre

country: Australia

institute: Westmead Institute for Medical Research

description: Diet 2m Raw Read Counts.xlsx

data_processing:
base calling software, versions, parameters.....
Data filtering steps?..............
Read alignment and junction finding was accomplished using STAR 2.6.1c using the ‘quantmode GeneCounts’ option and an Ensemble mm10 annotation in GTF format.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files files include raw read counts for each Sample.

source_name: Liver

extract_protocol:
Liver were harvested, a small portion rapidly snap frozen in liquid nitrogen and stored at -80 ºC. Total liver RNA was extracted using RNAeasy (Qiagen). RNA purity and integrity were confirmed using an Agilent Bioanalyzer.
Libraries were prepared from 100 ng total RNA (TruSeq Stranded Total RNA kit, Illumina) and singled-ended sequencing performed on the Illumina HiSeq 2500 using bar-coded multiplexing and a 50 bp read length

treatment_protocol: Mice fed different diets for 8 weeks starting at 8-10 weeks of age.

value: Liver

tag: diet

value: cholic acid

tag: genotype/variation

value: wild type


title: Day7.4.pTEICM_13


title: con_2

city: Hangzhou

first: Huajun

last: Zhao

address: 548 Binwen Road

country: China

institute: Zhejiang Chinese Medical University

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):  Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Supplementary_files_format_and_content: readcount of different miRNA readcount in each sample replicate

extract_protocol:
RNA was extracted with Trizol reagent. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: cell line

value: triple negative breast cancer cell

value: non-transfected


title: Caco-2.Gal-9-Treated.Xenograft.tissue3

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: microRNA

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: The human colon cancer cell lines CACO-2, CW-2, COLO-320, LoVo, and the colorectal cancer cell line WiDr were obtained from the Japanese Cancer Research Resources Bank (Tokyo, Japan). All the cell lines were certified by STRA and mycoplasma testing has been done for cell lines used in our experiments. The cells were cultured in RPMI-1640 (Gibco Invitrogen, Carlsbad, CA, USA) supplemented with 10% heat-inactivated FBS, and penicillin-streptomycin (100 μg/ml; Invitrogen) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: After incubation for 24 h, cells were treated with 0.01, 0.03, 0.1, and 0.3 μM of Gal-9 added to the culture medium and subsequently cultured for an additional 48 h.

tag: sample type

value: Colon cancer cell xenograft tumor

value: 90ug of galectin-9


title: Caco-2.Control.Xenograft.tissue3

description: microRNA

value: control


title: C57BL6_Diet 6 (CA)_Liver 3

description: Diet 2m Raw Read Counts.xlsx


title: Caco-2.Control.Xenograft.tissue4

description: microRNA


title: Day7.6.pTEICM_9


title: con_1


title: Day7.6.mTE_1

value: mural


title: Day7.6.pTEICM_8

value: Epiblast


title: C57BL6_Diet 6 (CA)_Liver 1

description: Diet 2m Raw Read Counts.xlsx


title: Caco-2.Control.Xenograft.tissue2

description: microRNA


title: C57BL6_Diet 5 (Chol2%_CA)_Liver 4

description: Diet 2m Raw Read Counts.xlsx

value: 2% cholestrol_cholic acid


title: Day7.6.pTEICM_6


title: Caco-2.Gal-9-Treated.Xenograft.tissue1

description: microRNA


title: OEyDOX_S9 - over expression of RNF4 with dox_1 ( plasmid is activated)

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

data_processing:
Quality control for total RNA was performed using TapeStation (Agilent). The RINe value of all samples was above 9, indicates that all samples have a good quality.
50 bp single-end reads were aligned to  Human reference genome and annotation file (Homo_sapiens.GRCh38 downloaded from ENSEMBL) using TopHat (v2.0.13) allowing 2 mismatches per read with options -very-sensitive and –GTF.
The number of reads per gene was counted using Htseq (0.6.0).
The number of reads per sample and the number of aligned reads suggest that reads' quality and number are good and that data analysis using all 9 samples can proceed.
Samples' clustering and differential expressed genes (DEGs) were calculated using Deseq2 package (version 1.10.1).
Genome_build: Homo_sapiens.GRCh38

source_name: Melanoma cell line

growth_protocol: Cells were cultured in DMEM High glucose, 100U/ml Penicilin, 0.1mg/ml streptomycin

extract_protocol:
RNA was extracted with Rneasy Mini Kit (Qiagene)
9  RNAseq libraries were produced using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, cat no. E7420) according to manufacture protocol and starting with 800 ng of total RNA. mRNA pull-up was performed using the Magnetic Isolation Module (NEB, cat no. E7490). libraries were mixed into a single tube at an equal molar concentration. The RNAseq data was generated on two lanes of HiSeq2500, 50SR.

treatment_protocol: doxycycline was added in drinking water 3 days after cell injection. Tumors were measured every 3 days , till extraction of tumors after 30 days.

tag: mutation

value: BRAF mutation


title: OEyDOX_S3 - over expression of RNF4 with dox_2 ( plasmid is activated)


title: OEmDOX_S6 - over expression of RNF4 ring mutant with dox_2 ( plasmid is expressed but the RNF4 is not active )


title: C57BL6_Diet 5 (Chol2%_CA)_Liver 3

description: Diet 2m Raw Read Counts.xlsx


title: OEmDOX_S1 -  over expression of RNF4 ring mutant with dox_1 ( plasmid is expressed but the RNF4 is not active )


title: OEnDOX_S10 - over expression of RNF4 w/o dox_2 ( plasmid not activated)


title: Caco2.Gal-9-Treated.Xenograft.tissue8

description: microRNA

value: 30 ug galectin-9


title: Caco-2.Control.Xenograft.tissue1

description: microRNA


title: C57BL6_Diet 6 (CA)_Liver 2

description: Diet 2m Raw Read Counts.xlsx


title: C57BL6_Diet 5 (Chol2%_CA)_Liver 2

description: Diet 2m Raw Read Counts.xlsx


title: Day7.6.pTEICM_4

value: Blastocyst

value: Trophectoderm


title: OEmDOX_S7 - over expression of RNF4 ring mutant with dox_1 ( plasmid is expressed but the RNF4 is not active )


title: Day7.6.pTEICM_2

value: Primitive Endoderm

value: polar

value: Embryonic day 7


title: C57BL6_Diet 5 (Chol2%_CA)_Liver 1

description: Diet 2m Raw Read Counts.xlsx

value: Liver


title: OEyDOX_S13 - over expression of RNF4 with dox_1 ( plasmid is activated)


title: Caco2.Control.Xenograft.tissue8

description: microRNA


title: Day7.6.pTEICM_1


title: OEnDOX_S8 - over expression of RNF4 w/o dox_1 ( plasmid not activated)


title: C57BL6_Diet 4 (HS_Chol2%_CA)_Liver 3

description: Diet 2m Raw Read Counts.xlsx

value: High sucrose_2% cholestrol_cholic acid

value: wild type


title: Day7.4.pTEICM_11


title: Caco2.Control.Xenograft.tissue7

description: microRNA


title: Caco2.Gal-9-Treated.Xenograft.tissue7

description: microRNA


title: C57BL6_Diet 4 (HS_Chol2%_CA)_Liver 1

description: Diet 2m Raw Read Counts.xlsx


title: Day7.4.pTEICM_10


title: primary cortical neurons, IgG  - rep3

city: Marburg

first: Sharof

last: Khudayberdiev

department: Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg

country: Germany

institute: Philipps-University of Marburg,

data_processing:
Sequenced reads were filtered according to quality, trimmed for adaptor sequence, collapsed based on UMI and barcodes using FASTX-Toolkit.
Clean reads were mapped to rn6 whole genome using STAR RNA-aligner software with default parameters. Only unique reads that mapped with NH:1: up to 10 mismatches and single best position were used for subsequent analysis.
Unique reads that map to a best single genomic position were used as an input for the peak-caller software Piranha (http://smithlabresearch.org/software/piranha/) and analysed with default parameters either with -bin_size=1 or -bin_size=20.
Genome_build: rn6
Supplementary_files_format_and_content: bed files include genomic location, number of unique reads per peak and FDR value

molecule: cytoplasmic RNA

organism: Rattus norvegicus

source_name: primary cortical neurons

growth_protocol: Rat primary cortical neurons were grown on 10 cm plates at a density of 10 million cells/plate

extract_protocol:
Cell pellet was resuspended in lysis buffer (10 mM Tris-HCl (pH=7.5), 100 mM NaCl, 0.25 % Igepal CA630, 1 mM EDTA, 1x Complete™ Protease Inhibitor Cocktail), incubated on ice for 10 min and homogenized with 20 stokes in a teflon-coated Dounce-Potter.
iCLIP libraries were constructed based on Sutandy et al.,  2016

treatment_protocol: Cells were subjected to UV-C irradiation (300 mJ/cm2)

value: Sprague-Dawley

value: brain

value: primary cortical neurons

tag: age

value: day in vitro 6

tag: iclip antibody

value: mAb IgG1 Isotype (#5415, Cell signaling)

tag: barcode

value: NNNAGTCNN


title: primary cortical neurons, SYNCRIP - rep3

value: anti-hnRNPQ antibody (clone 18E4, Sigma)

value: NNNTGGCNN


title: C57BL6_Diet 3 (HS_Chol2%)_Liver 4

description: Diet 2m Raw Read Counts.xlsx

value: High sucrose_2% cholestrol


title: Day7.6.pTEICM_7

value: Blastocyst


title: primary cortical neurons, IgG - rep2

value: NNNGGCGNN


title: Caco2.Control.Xenograft.tissue6

description: microRNA

value: Colon cancer cell xenograft tumor

value: control


title: Day7.6.pTEICM_5

value: Trophectoderm

value: polar

value: Embryonic day 7


title: C57BL6_Diet 3 (HS_Chol2%)_Liver 3

description: Diet 2m Raw Read Counts.xlsx

value: Liver

value: wild type


title: Caco-2.Gal-9-Treated.Xenograft.tissue2

description: microRNA

value: 90ug of galectin-9


title: Day7.4.pTEICM_7


title: Caco2.Gal-9-Treated.Xenograft.tissue5

description: microRNA

value: 30 ug galectin-9


title: Caco2.Control.Xenograft.tissue5

description: microRNA


title: Day7.4.pTEICM_6


title: C57BL6_Diet 3 (HS_Chol2%)_Liver 2

description: Diet 2m Raw Read Counts.xlsx


title: primary cortical neurons, IgG  - rep1

value: Sprague-Dawley

value: brain

value: primary cortical neurons

value: day in vitro 6

value: NNNTTGTNN


title: C57BL6_Diet 4 (HS_Chol2%_CA)_Liver 2

description: Diet 2m Raw Read Counts.xlsx

value: High sucrose_2% cholestrol_cholic acid


title: Caco2.Gal-9-Treated.Xenograft.tissue4

description: microRNA


title: C57BL6_Diet 3 (HS_Chol2%)_Liver 1

description: Diet 2m Raw Read Counts.xlsx

value: High sucrose_2% cholestrol


title: Caco2.Gal-9-Treated.Xenograft.tissue6

description: microRNA


title: OEnDOX_S5- over expression of RNF4 w/o dox_1 ( plasmid not activated)

value: BRAF mutation


title: Day7.4.pTEICM_5

value: Blastocyst


title: primary cortical neurons, SYNCRIP - rep1

value: anti-hnRNPQ antibody (clone 18E4, Sigma)

value: NNNGGTTNN


title: Day7.4.pTEICM_4

value: Trophectoderm

value: polar


title: C57BL6_Diet 2 (HS)_Liver 4

description: Diet 2m Raw Read Counts.xlsx

value: Liver

value: High sucrose


title: Day6.5.mTE_10

value: mural

value: Embryonic day 6


title: C57BL6_Diet 2 (HS)_Liver 5

description: Diet 2m Raw Read Counts.xlsx

value: wild type


title: C57BL6_Diet 2 (HS)_Liver 3

description: Diet 2m Raw Read Counts.xlsx


title: heifer 2660 [liver]

city: Meath

first: Clare

last: Mckenna

address: Dunsaney

department: Animal Bioscience

country: Ireland

institute: Teagasc

description: High feed efficienct

data_processing:
FASTQC software (v0.11.5) was used to check the quality of the raw sequencing reads.
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.5.1).
HTSeq (v0.6.1p2) software was used to calculate the number of sequenced fragments overlapping all protein-coding genes from the ENSEMBLv88 annotation of the bovine genome. The number of counts of reads mapping to each annotated gene from HTSeq was than collated into a single file and used for subsequent differential gene expression.
The R (v3.4) Bioconductor package, EdgeR (v3.5), which uses a negative binomial distribution model to account for both biological and technical variability, was applied to identify statistically significant differentially expressed genes. The analysis was undertaken using moderated tagwise dispersion
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt files
Supplementary_files_format_and_content: First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene

organism: Bos taurus

source_name: liver

growth_protocol: The animals used in this study were derived from a purebred herd of Simmental cattle originally established to examine various aspects of the biological control of the RFI trait and which has been well characterised to date in the published literature [13-19]. In order to generate animals for the current study, the 20 highest (inefficient) and 20 lowest (efficient) ranking cows on RFI were subjected to a multiple ovulation and embryo recovery programme and breeding using artificial insemination to bulls with high and low economic breeding values for RFI, respectively. Resultant embryos were transferred to crossbred beef heifer recipients. Pregnant heifers were managed under standard protocols and following calving were allowed to suckle their calves for a period of up to 7 days. In order to standardise rearing, calves were then abruptly weaned and were subsequently reared on an electronic calf feeder. Briefly calves were offered milk replacer (MR) (Blossom Easymix; Volac, Co. Cavan, Ireland) and concentrate in pelleted form using an electronic feeding system (Vario; Foster-Tecknik, Engen, Germany), which recorded all feed-related events including intake of both MR and concentrate, drinking speed, as well as number of rewarded (when calves receive milk) and unrewarded (no milk dispensed) visits to the machine. Calves were subsequently weaned at 10 weeks of age and were offered concentrate and hay on a 50:50 dry matter basis until turnout to pasture at approximately six months of age.  At approximately 15 months of age all cattle were housed within pens of between 5-7 animals/pen in a slatted floor shed. Cattle were fed once daily (0800 h) and were offered  ad libitum concentrate (860 g/kg rolled barley, 60 g/kg soya bean meal, 60 g/kg molasses and 20 g/kg minerals/vitamins) and 3kg grass silage to retain ruminal function. The animals had an acclimatisation period of 14 d to the ad libitum regime and test facilities before the experimental recoding period commenced. Feed intake was recorded daily and body weight (BW) was recorded twice weekly. The recording period lasted 70d. Concentrates and silage offered were sampled three times weekly and samples were stored at -20°C pending laboratory analysis. Samples of concentrates and silage were subsequently pooled on a weekly basis for dry matter (DM) determination. Concentrate samples were dried in an oven with forced-air circulation at 98°C for 16 h for DM determination and forage samples dried at 40° for 48 h.

extract_protocol:
Total RNA was isolated from 50mg of biopsy samples using QIAzol (Qiagen, UK). Tissue samples were homogenised in 1mL of QIAzol reagent using a rotor-strator tissue lyser (Qiagen, UK) and chloroform (Sigma-Aldrich Ireland, Dublin, Ireland). RNA was subsequently precipitated and purified using the RNeasy plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA. The quantity of the RNA isolated was determined by measuring the absorbance at 260nm using a Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA). RNA quality was assessed on the Agilent Bioanalyser 2100 using the RNA 6000 Nano Lab Chip kit (Agilent Technologies Ireland Ltd., Dublin, Ireland). RNA quality was also verified by ensuring all RNA samples had an absorbance (A260/280) of between 1.8 to 2.0 and RIN (RNA integrity number) values of between 8 and 10 were deemed high quality. Any samples that had a (A260/280) absorbance of less than 1.8 were cleaned using Zymo Research RNA clean & concentrator kit (Cambridge Biosciences, UK).  High quality RNA samples were selected for cDNA synthesis.
cDNA libraries were prepared from high quality RNA following the manufacturer’s instructions using the Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA, USA). For each sample, 1 μg of RNA was used for cDNA library preparation. Briefly, mRNA was purified from total RNA and subsequently fragmented. First strand cDNA was synthesised using Superscript II Reverse Transcriptase (Applied Biosystems Ltd., Life Technologies) followed by second strand synthesis using components of the Illumina TruSeq RNA sample prep kit. Adaptors were ligated to the cDNA which was subsequently enriched by 15 cycles of PCR. Libraries were validated on the Agilent Bioanalyser 2100 using the DNA 1000 Nano Lab Chip kit. cDNA concentration was assessed using Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and samples with >25ng/μl were deemed suitable for further analysis. Following quality control procedures, individual RNAseq libraries were pooled based on their respective sample-specific 6bp adaptors and sequenced at 100bp/sequence single-end read using and Illumina HiSeq 2500 sequencer.

treatment_protocol: Average daily live weight gain (ADG) during the RFI measurement period for each animal was computed as the coefficient of the linear regression of BW (kg) on time (d) by using the GLM procedure of SAS 9.1 (SAS Inst. INC., Cary, NC). Mid-test metabolic BW (MBW) was represented as BW0.75 35 d before the end of the test which was estimated from the intercept and slope of the regression line. Residual feed intake was calculated for each animal as the difference between actual DMI (Dry matter intake) and expected DMI. Expected DMI was computed for each animal using a multiple regression model, regressing DMI on MBW, ADG and mean lumbar BF change. Animals were ranked within gender and following a power analysis (www.biomath.info/power/ttest.htm) the most extreme animals for high RFI (n=5) and low RFI (n=5) were selected for further analysis.

tag: group

value: Low RFI

value: liver

tag: Sex

value: Female


title: heifer 2632 [liver]

description: High feed efficienct


title: Caco2.Control.Xenograft.tissue3

description: microRNA

value: Colon cancer cell xenograft tumor

value: control


title: Day6.5.mTE_9


title: Caco2.Gal-9-Treated.Xenograft.tissue3

description: microRNA

value: 30 ug galectin-9


title: primary cortical neurons, SYNCRIP  - rep2

value: Sprague-Dawley

value: brain

value: primary cortical neurons

value: day in vitro 6

value: NNNCAATNN


title: heifer L16 [liver]

description: High feed efficienct


title: Caco2.Gal-9-Treated.Xenograft.tissue2

description: microRNA


title: heifer L59 [liver]

description: High feed efficienct


title: Caco2.Control.Xenograft.tissue2

description: microRNA


title: Day6.5.mTE_7

value: Blastocyst

value: Trophectoderm


title: C57BL6_Diet 2 (HS)_Liver 1

description: Diet 2m Raw Read Counts.xlsx

value: Liver

value: Normal chow


title: Caco2.Control.Xenograft.tissue4

description: microRNA


title: C57BL6_Diet 1 (NC)_Liver 4

description: Diet 2m Raw Read Counts.xlsx


title: Day6.5.mTE_6

value: mural

value: Embryonic day 6


title: Caco2.Gal-9-Treated.Xenograft.tissue1

description: microRNA


title: C57BL6_Diet 1 (NC)_Liver 3

description: Diet 2m Raw Read Counts.xlsx

value: wild type


title: Day6.5.mTE_4


title: heifer L60 [liver]

description: Low feed efficient

value: High RFI

value: liver


title: heifer L58 [liver]

description: High feed efficienct

value: Low RFI

value: Female


title: Day7.4.pTEICM_8

value: polar

value: Embryonic day 7


title: heifer 2728 [liver]

description: Low feed efficient


title: Caco2.Control.Xenograft.tissue1

description: microRNA

value: Colon cancer cell xenograft tumor

value: control


title: Day7.4.pTEICM_3


title: C57BL6_Diet 2 (HS)_Liver 2

description: Diet 2m Raw Read Counts.xlsx

value: High sucrose


title: Day6.5.mTE_8


title: heifer 2705 [liver]

description: Low feed efficient


title: C57BL6_Diet 1 (NC)_Liver 1

description: Diet 2m Raw Read Counts.xlsx


title: Day7.4.pTEICM_2


title: Day7.3.mTE_8


title: Caco2.Control.24h.3

description: microRNA

value: Colon cancer cell line


title: P15,B_RafVE

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR and gene abundance estimation using featurecounts
Differential gene expression computed using DESeq2
Genome_build: GRCh38

source_name: myeloid cells

growth_protocol: For macrophage differentiation, human monocytes isolated from PBMCs were cultured at 37°C for 7 days in complete RPMI 1640 medium supplemented with 20 ng/mL mouse Macrophage Colony Stimulating Factor (M-CSF; Miltenyi Biotec).

extract_protocol:
Total RNA was isolated using ReliaPrepTM RNA Miniprep Systems (Promega Corporation), according to the manufacturer’s instructions.
300 ng of total RNA were used for library preparation with TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina) and sequenced on an NextSeq 500 (Illumina)

treatment_protocol: Purified monocytes were transduced by adding noninfectious virus-like particles carrying Vpx (Vpx-VLPs) together with lentiviral constructs encoding for either BRAF-WT or BRAF-V600E.

value: Monocyte-derived macrophages

tag: donor

value: Healthy Donor #15

value: Infected with lentiviral construct encoding for BRAF-V600E


title: heifer 2704 [liver]

description: Low feed efficient

tag: tissue


title: P15,B_RafWT

value: Infected with lentiviral construct encoding for BRAF-WT


title: Day6.5.pTEICM_31

value: Blastocyst

tag: lineage

value: Unknown


title: Caco2.Gal.Treated.24h.2

description: microRNA


title: Caco2.Control.24h.2

description: microRNA


title: heifer 2670 [liver]

description: Low feed efficient


title: heifer M70 [muscle]

description: High feed efficienct

source_name: muscle

value: muscle


title: Day6.5.pTEICM_30

value: Trophectoderm

tag: time point

value: Embryonic day 6


title: P15,Untransduced

tag: cell type

value: Untransduced


title: Caco2.Gal.Treated.24h.3

description: microRNA

tag: treatment


title: Day6.5.pTEICM_29

value: Primitive Endoderm


title: C57BL6_Diet 1 (NC)_Liver 2

description: Diet 2m Raw Read Counts.xlsx

tag: strain

value: Liver

value: Normal chow

value: wild type


title: P14,B_RafVE

value: Healthy Donor #14


title: P14,B_RafWT


title: Caco2.Control.24h.1

description: microRNA

value: control


title: Caco2.Gal.Treated.24h.1

description: microRNA

value: Colon cancer cell line


title: Day6.5.pTEICM_28

value: polar


title: heifer 2724 [muscle]

description: High feed efficienct

value: Low RFI

value: Female


title: Caco2.Control.12h.3

description: microRNA


title: Caco2.Gal.Treated.12h.3

description: microRNA


title: P14,Untransduced

value: Monocyte-derived macrophages


title: Day6.5.pTEICM_27

value: Blastocyst

value: Epiblast


title: heifer M62 [muscle]

description: High feed efficienct

value: muscle


title: heifer 2690 [muscle]

description: High feed efficienct


title: Day6.5.pTEICM_26


title: Caco2.Gal.Treated.12h.2

description: microRNA


title: heifer 2632 [muscle]

description: High feed efficienct


title: P13,B_RafWT

value: Healthy Donor #13

value: Infected with lentiviral construct encoding for BRAF-WT


title: Day6.5.pTEICM_25

value: Trophectoderm

value: Embryonic day 6


title: Caco2.Control.12h.2

description: microRNA


title: heifer M73 [muscle]

description: Low feed efficient

value: High RFI


title: P13,Untransduced

value: Untransduced


title: heifer M69 [muscle]

description: Low feed efficient


title: PBMC_Patient #2

source_name: PBMC

growth_protocol: PBMC were isolated from whole blood of ECD patients

extract_protocol:
Total RNA from ECD biopsy and PBMCs was isolated using AllPrep DNA/RNA FFPE kit (Qiagen) and ReliaPrepTM RNA Miniprep Systems (Promega Corporation) respectively, according to the manufacturer’s instructions.
300 ng of total RNA were used for library preparation with TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina) and sequenced on an NextSeq 500 (Illumina)

tag: tissue/cell type

value: Peripheral Blood Mononuclear cells

value: ECD Patient #2


title: Caco2.Gal.Treated.12h.1

description: microRNA


title: Day7.3.mTE_4

value: mural

value: Embryonic day 7


title: Day6.5.pTEICM_24

value: Primitive Endoderm

value: polar


title: heifer 2704 [muscle]

description: Low feed efficient

value: Female


title: Day7.3.mTE_3


title: PBMC_Patient #1

value: ECD Patient #1


title: PBMC_Patient #3

value: ECD Patient #3


title: heifer 2628 [muscle]

description: Low feed efficient


title: heifer 2647 [muscle]

description: Low feed efficient


title: bull 2723 [liver]

description: High feed efficienct

value: Low RFI

value: liver

value: Male


title: ECD biopsy_Patient #3

source_name: ECD biopsy

value: ECD biopsy


title: Day7.3.mTE_2

value: Blastocyst

value: Trophectoderm


title: Day7.3.mTE_1


title: P13,B_RafVE

value: Monocyte-derived macrophages

value: Healthy Donor #13

value: Infected with lentiviral construct encoding for BRAF-V600E


title: CW2.Gal.Treated.12h.3

description: microRNA

value: Colon cancer cell line


title: CW2.Control.12h.3

description: microRNA

value: control


title: CW2.Gal.Treated.12h.2

description: microRNA


title: ECD biopsy_Patient #2

value: ECD Patient #2


title: bull 2713 [liver]

description: High feed efficienct


title: Day7.3.pTEICM_26

value: Embryonic day 7


title: CW2.Control.12h.2

description: microRNA


title: ECD biopsy_Patient #1


title: CW2.Gal.Treated.12h.1

description: microRNA


title: Caco2.Control.12h.1

description: microRNA


title: Day7.3.pTEICM_25

value: polar


title: bull 2712 [liver]

description: High feed efficienct


title: Day7.3.pTEICM_24


title: bull 2669 [liver]

description: High feed efficienct


title: bull 2659 [liver]

description: High feed efficienct


title: Day7.3.pTEICM_23


title: CW2.Control.12h.1

description: microRNA


title: Breast cancer patient T185

type: genomic

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

description: Hybridized to SNP 6.0

hyb_protocol: Affymetrix standard protocol

scan_protocol: Arrays were placed into the autoloader of an Affymetrix 3000 7G scanner and scanned. Single chip QC was performed in Genotyping Console 3.0.2 software (Affymetrix) to calculate the Contrast QC score along with the Dynamic Model (DM) Algorithm on the 3022 QC SNPs.

data_processing: The raw CEL files were imported into the Partek Genomic Suite software using its default settings to generate the corresponding copy number values. The reference baseline for generating the copy number values was distributed by the Partek software, and copy number analysis was performed accordingly. Data matrix contains CN = copy number value.

label: Biotin

molecule: genomic DNA

source_name: Breast cancer patient T185

label_protocol: Affymetrix standard protocol

extract_protocol: QIAamp DNA Mini Kit (Qiagen Inc., Valencia, CA, USA)

tag: disease

value: Breast cancer

value: tumor

tag: gender

value: Female

tag: grade

tag: er

tag: pr


title: Breast cancer patient T186

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T186

tag: age


title: Breast cancer patient T184

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T184


title: bull 68 [liver]

description: Low feed efficient

value: High RFI


title: ATAC-seq, cell line MUN14, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: ATAC-seq, cell line MUN14, replicate 2

library_source: genomic

data_processing:
ATAC-seq data was aligned using bowtie against hg19 version of the human genome and HOMER version 4.8.3 was used to call peaks
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq signal in bigwig track format

source_name: neuroinvasive EBV+ B cell lymphoma cell line subpopulation MUN14

extract_protocol:
DNA was purified using a MinElute PCR purification kit (Qiagen) and eluted in 10 l Elution Buffer for library amplification.  PCR amplification of tagmented DNA was done using the NEBNext HiFi PCR mastermix (New England Bioloabs) with a universal forward and sample-specific reverse oligo for sample barcoding using the following PCR conditions: initial incubations of 72C for 5 min and 98C for 30 s, followed by 5 cycles of 98C for 10 s, 63C for 30 s, and 72C for 1 min. Additional number of cycles was determined for each sample through a “side” qPCR reaction using an aliquot of the PCR as template to determine the number of cycles needed to reach 1/3 of the max fluorescence. Total cycle numbers ranged from 8 to 9 cycles. PCR products were run on a 1% agarose gel, regions from ~50 bp to ~1 kb were excised, and DNA was extracted using a gel extraction kit (Qiagen).
PCR amplification of tagmented DNA was done using the NEBNext HiFi PCR mastermix (New England Bioloabs) with a universal forward and sample-specific reverse oligo for sample barcoding

tag: cell line

tag: replicate


title: ATAC-seq, cell line MUN14, replicate 3

description: ATAC-seq, cell line MUN14, replicate 3


title: ATAC-seq, cell line MUN14, replicate 1

description: ATAC-seq, cell line MUN14, replicate 1


title: Day6.5.pTEICM_23

value: Unknown

value: Embryonic day 6


title: bull 64 [liver]

description: Low feed efficient

tag: group

value: liver

tag: Sex

value: Male


title: ATAC-seq, cell line M14, replicate 3

description: ATAC-seq, cell line M14, replicate 3

source_name: parental EBV+ B cell lymphoma cell line M14


title: bull 2641 [liver]

description: Low feed efficient

tag: tissue


title: Breast cancer patient T182

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T182


title: ATAC-seq, cell line M14, replicate 2

description: ATAC-seq, cell line M14, replicate 2


title: bull 2703 [liver]

description: Low feed efficient


title: Breast cancer patient T181

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T181


title: Day6.5.pTEICM_21

value: Blastocyst

tag: lineage

value: Epiblast


title: ATAC-seq, cell line M14, replicate 1

description: ATAC-seq, cell line M14, replicate 1


title: Day6.5.pTEICM_20

tag: time point


title: Breast cancer patient T179

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T179


description:
MUN14.b.6
RNAseq, cell line MUN14,  harvested from mouse kidney, replicate 6

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using a QiaShredder followed by RNA isolation with the RNeasy kit (Qiagen)
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

tag: celline

tag: condition

value: mouse


title: bull M74 [muscle]

description: High feed efficienct

value: Low RFI

value: muscle


title: Breast cancer patient T178

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T178


title: Breast cancer patient T177

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T177


description:
MUN14.b.5
RNAseq, cell line MUN14,  harvested from mouse kidney, replicate 5


title: bull 2712 [muscle]

description: High feed efficienct


title: Breast cancer patient T183

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T183


description:
MUN14.b.3
RNAseq, cell line MUN14,  harvested from mouse kidney, replicate 3


title: Breast cancer patient T176

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T176


description:
MUN14.b.2
RNAseq, cell line MUN14,  harvested from mouse kidney, replicate 2


title: bull M6 [muscle]

description: High feed efficienct


title: bull M67 [muscle]

description: High feed efficienct


title: Breast cancer patient T174

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T174


title: Breast cancer patient T175

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T175


title: Day6.5.pTEICM_18

source_name: Blastocyst

value: Trophectoderm


title: bull 2723 [muscle]

description: High feed efficienct

source_name: muscle


title: Day7.3.pTEICM_21


title: Breast cancer patient T172

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T172


description:
MUN14.tc
RNAseq, cell line MUN14, tissue culture, replicate 1

value: tissue culture


title: bull M12 [muscle]

description: Low feed efficient


title: bull 2701 [liver]

description: Low feed efficient

source_name: liver


title: Day6.5.pTEICM_17


title: Breast cancer patient T171

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T171


title: Day6.5.pTEICM_16

value: Primitive Endoderm


description:
MUN14.b.4
RNAseq, cell line MUN14,  harvested from mouse kidney, replicate 4


title: bull M65 [muscle]

description: Low feed efficient


description:
M14.k.6
RNAseq, cell line M14,  harvested from mouse kidney, replicate 6


title: Day6.5.pTEICM_22

value: polar


title: Breast cancer patient T170

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T170

value: Breast cancer


title: Day7.3.pTEICM_19

value: Embryonic day 7


title: Day7.3.pTEICM_18


description:
M14.k.5
RNAseq, cell line M14,  harvested from mouse kidney, replicate 5


title: Breast cancer patient T169

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T169

value: tumor

value: Female


description:
MUN14.b.1
RNAseq, cell line MUN14,  harvested from mouse kidney, replicate 1

source_name: neuroinvasive EBV+ B cell lymphoma cell line subpopulation MUN14


title: bull 2666 [muscle]

description: Low feed efficient

value: High RFI


title: bull M57 [muscle]

description: Low feed efficient


title: bull 2641 [muscle]

description: Low feed efficient


title: Breast cancer patient T168

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T168


description:
M14.k.4
RNAseq, cell line M14,  harvested from mouse kidney, replicate 4

source_name: parental EBV+ B cell lymphoma cell line M14


title: Day7.3.pTEICM_16


title: Day6.5.pTEICM_19

value: Embryonic day 6


description:
M14.k.3
RNAseq, cell line M14,  harvested from mouse kidney, replicate 3


description:
M14.k.2
RNAseq, cell line M14,  harvested from mouse kidney, replicate 2


title: MD17 at 2 DPA epidermal cell replicate 2

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Collected cells by using LCM

data_processing:
Raw RNA-seq reads were mapped onto the Gossypium hirsutum (ZJU v2.0) and Gossypium barbadense (ZJU v1.0) by Tophat 2.1.1.
Uniquely mapped reads were extracted by using Samtools 1.5.
FPKM is analyzed by using Cufflinks 2.2.1.
Genome_build: ZJU
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

organism: Gossypium hirsutum

source_name: MD17 at 2 DPA epidermal cell collected by using LCM

growth_protocol: All plants were grown under a natural sunlight in greenhouse at The University of Texas at Austin

extract_protocol:
LCM epidermal and fiber tissues were subject to total RNA extraction by RNA Aqueous Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, Massachusetts)
NEB Next Ultra RNA Library Prep Kit (New England Biolabs, Ipswich, Massachusetts)

tag: genotype

value: fiberless mutant MD17

value: epidermal cells

tag: Stage

value: 2 DPA


title: Breast cancer patient T167

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T167

tag: disease


title: Breast cancer patient T166

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T166

tag: gender


title: Day7.3.pTEICM_15

value: Blastocyst


title: Breast cancer patient T165

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T165

tag: grade


description:
M14.k.1
RNAseq, cell line M14,  harvested from mouse kidney, replicate 1

value: mouse


title: MD17 at 0 DPA epidermal cell replicate 2

description: Collected cells by using LCM

source_name: MD17 at 0 DPA epidermal cell collected by using LCM

value: 0 DPA


title: Day7.3.pTEICM_20


description:
M14.tc
RNAseq, cell line M14, tissue culture, replicate 1


title: Day6.5.pTEICM_15


title: Day6.5.pTEICM_14


title: MD17 at 0 DPA epidermal cell replicate 1

description: Collected cells by using LCM


title: Breast cancer patient T164

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T164

tag: er


title: Day7.3.pTEICM_17


title: Breast cancer patient T163

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T163

tag: pr


title: TM1 at 2 DPA fiber cell replicate 2

description: Collected cells by using LCM

source_name: TM1 at 2 DPA fiber cell collected by using LCM

value: wildtype

value: fiber cells


title: Day6.5.pTEICM_12

source_name: Blastocyst


title: Day6.5.pTEICM_11

value: Trophectoderm


title: Breast cancer patient T162

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T162

tag: age


title: 11531_7F8T2

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: RNA-Seq of high-grade serous ovarian tumour

data_processing:
Fastq files from multiple lanes were concatenated and trimmed for adapter sequences and quality by Trim Galore.
Sequencing reads were mapped to the UCSC hg19 human genome assembly using STAR (v2.4.2a).
Read counts were obtained using subread FeatureCounts (v1.4.5-p1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing gene features and the count matrix

source_name: High-grade serous ovarian carcinoma

extract_protocol:
Frozen tumor samples were embedded in OCT (NEG-50, Richard-Allan Scientific) and 10 μm sections were taken using MB DynaSharp microtome blades (ThermoFisher Scientific) in a CryoStar cryostat microtome (ThermoFisher Scientific). The first tissue section was mounted onto regular glass slides (SuperFrost Plus, VWR International) for hematoxylin (Hematoxylin solution, Gill No. 3, Sigma) and eosin (Eosin Y solution, Sigma) staining (H&E), according to manufacturer's instructions, followed by six to ten sequential tissue sections onto polyethylenenaphthalate membrane (PEN) glass slides (MembraneSlide 1.0 PEN, Zeiss) which were immediately stained on ice (2 min in 70% ethanol, 2 min in 1% Cresyl violet (Sigma-Aldrich) in 50% ethanol, followed by rinse in 100% ethanol) then stored at−80 °C. Nuclease-free technique was used throughout the procedure. After each H&E slide was reviewed by a gynaecological oncology pathologist to confirm the presence of cancer cells and delineate their location, a PALM Laser Microdissection System (Zeiss) was used to catapult individual tumor islets into a 200 μl opaque AdhesiveCap (Zeiss). Images of target area in 5× and 10× magnification as well as of caps with captured material were obtained for documentation. For the “pre-chemo” samples and the “post-chemo” sites where there was evidence of poor response, scrolls were also collected to be used for bulk RNA-seq. Both Laser Capture Microdissected tumor islets and bulk scrolls were immediately processed for RNA extraction using the RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher Scientific) and the RNeasy Mini (Qiagen) respectively. Both extraction procedures were performed according to the manufacturer’s instructions, including DNase digestion, after which RNA integrity was evaluated using the 2200 TapeStation (Agilent).
The SMARTer Stranded Total RNA-Seq kit v2 - Pico Input (Takara) was used to prepare sequencing libraries from LCM material, the KAPA mRNA HyperPrep Kits (Roche) for the bulk scrolls.  All libraries were assessed with TapeStation (Agilent) and then quantified by Qubit (ThermoFisher Scientific). Multiplexed library pools were quantified with the KAPA Library Quantification Kit (Roche) and sequenced using 75bp PE reads on the NextSeq500 platform (Illumina).

value: high-grade serous ovarian tumour

tag: patient

value: POST

value: LCM


title: MD17 at 2 DPA epidermal cell replicate 1

description: Collected cells by using LCM


title: Breast cancer patient T161

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T161

value: Breast cancer


title: 11531_7F8T1


title: TM1 at 2 DPA epidermal cell replicate 1

description: Collected cells by using LCM

source_name: TM1 at 2 DPA epidermal cell collected by using LCM


title: Breast cancer patient T159

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T159

value: tumor


title: Day7.3.pTEICM_14

value: polar

value: Embryonic day 7


title: TM1 at 2 DPA epidermal cell replicate 2

description: Collected cells by using LCM


title: Breast cancer patient T160

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T160

value: Female


title: Day7.3.pTEICM_13


title: 11152_OM3

value: PRE


title: 11152_OM2T2


title: Breast cancer patient T158

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T158


title: 11152_OM2T1


title: TM1 at 0 DPA epidermal cell replicate 1

description: Collected cells by using LCM

source_name: TM1 at 0 DPA epidermal cell collected by using LCM

value: epidermal cells


title: 11152_K24


title: Day7.3.pTEICM_12


title: Day7.3.pTEICM_11


title: Breast cancer patient T157

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T157


title: TM1 at 2 DPA fiber cell replicate 1

description: Collected cells by using LCM

value: 2 DPA


title: Day6.5.pTEICM_9

value: Blastocyst

value: Embryonic day 6


title: Day7.3.pTEICM_10

value: Epiblast


title: 11531_7F8T3


title: Breast cancer patient T156

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T156


title: 19LHet3_KO3 (Knock-out)

city: Charlottesville

first: Anupreet

last: Kour

state: Virginia

address: 415 Lane road

department: CVRC

institute: University of Virginia

data_processing:
Raw data was aligned to reference transcriptome using Kallisto. Significantly differentially expressed genes were obtained using DESeq package in R.
Genome_build: Mus_musculus.GRCm38 (Ensembl)
Supplementary_files_format_and_content: The format is tsv and content is read counts and TPM values per transcript

source_name: peripheral blood

extract_protocol:
Total RNA was extracted form sorted neutrophils from peripheral blood
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dox administration (15 µg/g single injection)

tag: cell type

value: neutrophils

tag: strain

value: Trp53- heterozygous


title: 20RLHet4_KO4 (Knock-out)


title: Day7.3.pTEICM_9

value: Trophectoderm


title: 14RHet2_KO2 (Knock-out)


title: Breast cancer patient T155

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T155


title: TM1 at 0 DPA epidermal cell replicate 2

description: Collected cells by using LCM

value: wildtype

value: 0 DPA


title: Day7.3.pTEICM_8


title: 13NHet1_KO1 (Knock-out)


title: 1039_2C4

value: high-grade serous ovarian tumour

value: SECTIONS


title: Day6.5.pTEICM_7


title: 18R_WT4 (wild-type)

value: WT


title: 17N_WT3 (wild-type)


title: Day6.5.pTEICM_6

value: polar


title: 1038_2C1_T2

value: POST

value: LCM


title: Breast cancer patient T153

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T153

value: Breast cancer

value: tumor

value: Female


title: Breast cancer patient T154

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T154


title: 11152_G25

value: PRE


title: Breast cancer patient T148

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T148


title: Breast cancer patient T149

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T149


title: 1038_2C1_T1


title: Hif1a-cKO-Wnt3a-2

data_processing:
Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie (v2.3.4). Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
Differential expression for each gene between various groups was identified by Cuffdiff. For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark and C5 databases of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Genome_build: mm10
Supplementary_files_format_and_content: csv file include FPKM values for each Sample.

source_name: Bronchoalveolar lavage

extract_protocol:
Total RNA from in vitro cultured AMs was extracted using RNeasy Plus Mini Kit, and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: AMs were pre-treated with Wnt3a (100 ng/ml) or vehicle in complete medium without GM-CSF for overnight. Subsequently, cells were washed with warm PBS and treated with the same amount of Wnt3a or vehicle in complete medium with 10 ng/ml GM-CSF for another overnight. Then, the cells were havested for RNA-seq.

value: Hif1a ko

tag: treatment

value: lung

value: Alveolar macrophages


title: 4N_WT1 (wild-type)

value: neutrophils


title: Breast cancer patient T150

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T150

tag: tissue


title: 11152_C21

source_name: High-grade serous ovarian carcinoma


title: Day6.5.pTEICM_5

source_name: Blastocyst

value: Blastocyst

tag: lineage

value: Epiblast

value: Embryonic day 6


title: Day6.5.pTEICM_4

tag: time point


title: 1036_2A1_B2

value: high-grade serous ovarian tumour


title: 1038_2C1


title: Day6.5.pTEICM_3


title: Day6.5.pTEICM_1

value: Trophectoderm


title: Day6.4.mTE_6

value: mural


title: Breast cancer patient T147

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T147


title: Ctnnb1-cKO-Wnt3a-2

value: Ctnnb1 ko


title: 1036_2A1_A2

value: SECTIONS


title: 1039_2C6

value: POST

value: LCM


title: Breast cancer patient T145

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T145

value: Breast cancer

value: tumor


title: Ctnnb1-cKO-Wnt3a-1


title: Day7.3.pTEICM_6

value: Primitive Endoderm

value: polar

value: Embryonic day 7


title: Breast cancer patient T152

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T152

value: Female


title: 1036_2A1_A1

value: PRE


title: 1038_2B4


title: Day7.3.pTEICM_5

value: Blastocyst


title: WT-Wnt3a-2

value: WT

value: lung

value: Alveolar macrophages


title: Breast cancer patient T144

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T144


title: WT-Wnt3a-1


title: Breast cancer patient T143

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T143


title: 1036_1I4

value: high-grade serous ovarian tumour


title: 1036_2A1_B1


title: Breast cancer patient T142

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T142


title: 1028_3E3T3


title: WT-Ctrl-2

value: Medium


title: Day7.3.pTEICM_2

value: Epiblast


title: Breast cancer patient T146

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T146


title: Day7.3.pTEICM_3


title: WT-Ctrl-1


title: 1028_3E3T2


title: Day7.3.pTEICM_1


title: 1028_3E3T1


title: Breast cancer patient T141

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T141


title: 15L_WT2 (wild-type)

source_name: peripheral blood

value: neutrophils


title: Breast cancer patient T139

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T139


title: 1028_3E3ori

value: POST


title: Hif1a-cKO-Wnt3a-1

value: Hif1a ko


title: Day7.2.mTE_11

value: Trophectoderm

value: mural


title: Day6.4.mTE_5

value: Embryonic day 6


title: Breast cancer patient T55

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T55

value: Breast cancer

value: tumor


title: 1028_3C5

value: SECTIONS


title: 1036_1I8T1

value: LCM


title: Day7.3.pTEICM_4

value: Blastocyst

value: polar

value: Embryonic day 7


title: Day6.4.mTE_4


title: Breast cancer patient T138

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T138

value: Female


title: Breast cancer patient T54

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T54


title: 1027_GO7A1

value: high-grade serous ovarian tumour


title: Breast cancer patient T8

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T8


title: Day6.4.pTEICM_37


title: Breast cancer patient T53

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T53


title: Day7.2.mTE_9


title: 1027_7A2_T1

source_name: High-grade serous ovarian carcinoma


title: 1022_3C8


title: Breast cancer patient T49

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T49


title: Day7.2.mTE_7

source_name: Blastocyst


title: 1027_7A1_T1


title: 1022_3C7_T3


title: Day7.2.mTE_8


title: Breast cancer patient T52

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T52


title: Breast cancer patient T48

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T48


title: Day7.2.mTE_5


title: Breast cancer patient T46

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T46


title: 1022_3C7_T1


title: Day7.2.mTE_6


title: Day7.2.mTE_4


title: Breast cancer patient T45

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T45


title: Breast cancer patient T43

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T43


title: 1022_3C7


title: 1022_3C6


title: Breast cancer patient T42

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T42


title: 1022_3A4

value: PRE


title: Day6.4.pTEICM_28


title: 1022_3A1


title: Day6.4.pTEICM_27


title: Breast cancer patient T36

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T36


title: Breast cancer patient T37

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T37


title: 1019_RPPpost_T4


title: Breast cancer patient T33

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T33


title: Day7.2.mTE_1


title: Breast cancer patient T31

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T31


title: 1022_3C7_T2


title: Day7.3.pTEICM_22

value: Epiblast


title: 1019_RPPpost_T2


title: Day7.2.pTEICM_35


title: Day7.2.pTEICM_36


title: Day7.2.pTEICM_37

value: Primitive Endoderm


title: 1019_RPPpost_T3

value: POST


title: Breast cancer patient T136

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T136


title: 3-79 at 2 DPA fiber cell replicate 2

description: Collected cells by using LCM

organism: Gossypium barbadense

source_name: 3-79 at 2 DPA fiber cell collected by using LCM

value: wildtype

value: fiber cells

value: 2 DPA


title: Day7.2.mTE_3

value: Trophectoderm

value: mural


title: 1019_RPPpost_T1


title: Breast cancer patient T134

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T134

value: Breast cancer

value: tumor


title: 3-79 at 2 DPA fiber cell replicate 1

description: Collected cells by using LCM


title: Breast cancer patient T123

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T123


title: 1019_LPPpreT4

source_name: High-grade serous ovarian carcinoma

value: LCM


title: Day7.2.mTE_2

value: Blastocyst


title: Breast cancer patient T122

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T122


title: Day7.2.pTEICM_34

source_name: Blastocyst

value: polar


title: Day7.2.pTEICM_33

value: Embryonic day 7


title: 1016_1G8T4


title: 1016_1G8T2


title: Breast cancer patient T116

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T116

value: Female


title: Breast cancer patient T115

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T115


title: Day6.4.pTEICM_26

value: Embryonic day 6


title: Day6.4.pTEICM_25


title: Breast cancer patient T114

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T114


title: Day6.4.pTEICM_21


title: 3-79 at 2 DPA epidermal cell replicate 1

description: Collected cells by using LCM

source_name: 3-79 at 2 DPA epidermal cell collected by using LCM

value: epidermal cells


title: 3-79 at 2 DPA epidermal cell replicate 2

description: Collected cells by using LCM


title: Day6.4.pTEICM_19


title: SMC12

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava 1.8 software used for basecalling.
Adapter sequences and low quality reads were trimmed uisng Trim Galore.
Reads were then aligned to human genome UCSC build hg38 using bowtie2.
Low-quality alignments and PCR duplicates were removed using samtools and Picard MarkDuplicates.
Gene expression was counted using htseq-count.
Genome_build: Human (hg38)
Supplementary_files_format_and_content: tab-delimited text files include gene expression count values for each Sample

source_name: pulmonary artery

extract_protocol:
Total RNA was extracted and purified from cells using the Quick-RNA MiniPrep Kit (Zymo Research). The quantity and quality of RNA was determined using a spectrophotometer (BioTek Synergy H1 Hybrid Reader).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary pulmonary artery smooth muscle cell

tag: ID


title: 1015_1F7

value: high-grade serous ovarian tumour

value: SECTIONS


title: 1015_1F6

value: POST


title: 1015_1F5_T3


title: SMC11

value: vehicle


title: 1019_LPPpreT5

value: PRE


title: 3-79 at 0 DPA epidermal cell replicate 2

description: Collected cells by using LCM

source_name: 3-79 at 0 DPA epidermal cell collected by using LCM

value: wildtype

value: 0 DPA


title: Breast cancer patient T107

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T107

value: Breast cancer


title: 1015_1F5_T2


title: SMC10


title: SMC9


title: Breast cancer patient T105

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T105

value: tumor


title: 1015_1F5


title: Day6.4.pTEICM_18

extract_protocol:
Dissociated single cells were transferred immediately into Smart-Seq2 single-cell lysis buffer and immediately frozen.
The Smart-Seq2 library was prepared as described in Picelli S et al. 2014.

value: Trophectoderm


title: Breast cancer patient T106

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T106


title: 1015_1F4


title: SMC8


title: Breast cancer patient T103

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T103


title: Day6.4.pTEICM_17

value: Blastocyst


title: 1011_1D7T3

value: LCM


title: Breast cancer patient T110

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T110


title: Day6.4.pTEICM_11

value: Epiblast

value: polar


title: Breast cancer patient T102

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T102

value: Female


title: Day7.2.pTEICM_26

value: Embryonic day 7


title: Day6.4.pTEICM_16

value: Embryonic day 6


title: 1011_1D5

value: high-grade serous ovarian tumour


title: 3-79 at 0 DPA epidermal cell replicate 1

description: Collected cells by using LCM

value: epidermal cells


title: SMC6

value: primary pulmonary artery smooth muscle cell


title: 1008_GO5A2

value: POST


title: Day7.2.pTEICM_23


title: Breast cancer patient T96

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T96


title: 1008_GO5A1

value: SECTIONS


title: Day7.2.pTEICM_24


title: SMC5

value: vehicle


title: Day6.4.pTEICM_10

value: Primitive Endoderm


title: SMC3


title: Day6.4.pTEICM_9


title: Breast cancer patient T91

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T91

value: Breast cancer


title: Day6.4.pTEICM_8


title: SMC4


title: SMC2


title: 1008_1D1

source_name: High-grade serous ovarian carcinoma

value: PRE


title: 1006_PEL_N


title: Breast cancer patient T88

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T88

value: tumor


title: 1006_OMR1


title: Day6.4.pTEICM_7

source_name: Blastocyst

value: Blastocyst

value: Trophectoderm


title: SMC7


title: SMC1


title: Breast cancer patient T87

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T87


title: Breast cancer patient T98

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T98


title: Breast cancer patient T86

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T86


title: Day6.4.pTEICM_6


title: PAEC12

value: primary pulmonary artery endothelial cell


title: 1006_NP


title: Breast cancer patient T94

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T94


title: Breast cancer patient T84

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T84


title: Day6.4.pTEICM_5

value: polar


title: PAEC11

source_name: pulmonary artery


title: 1006_1B9


title: PAEC10


title: Day6.4.pTEICM_4


title: 1006_1B8


title: Breast cancer patient T26

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T26

value: Female


title: Day6.4.pTEICM_3

value: Epiblast


title: PAEC9


title: Breast cancer patient T79

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T79


title: 1004_GO4F4

value: LCM


title: Breast cancer patient T77

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T77


title: Day6.4.pTEICM_2

value: Embryonic day 6


title: PAEC8


title: 1002_GO4H8T4

value: high-grade serous ovarian tumour


title: Day6.4.pTEICM_1


title: 1004_1A7


title: PAEC7


title: Breast cancer patient T75

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T75


title: Day6.3.pTEICM_11


title: PAEC6


title: Breast cancer patient T71

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T71


title: Breast cancer patient T69

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T69


title: 1002_GO4H8T2


title: Day6.3.pTEICM_9


title: PAEC5


title: 1002_GO4H8T3


title: Day7.1.pTEICM_9

value: Embryonic day 7


title: 1002_GO4H8T1

value: POST


title: PAEC4


title: Breast cancer patient T68

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T68


title: PAEC3


title: Day6.3.pTEICM_8


title: Breast cancer patient T66

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T66


title: 1002_GO4H7

source_name: High-grade serous ovarian carcinoma

value: SECTIONS


title: Day6.3.pTEICM_7


title: Breast cancer patient T65

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T65


title: 1002_GO4H3T3


title: 1002_GO4H3T2


title: Breast cancer patient T63

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T63


title: PAEC1

value: vehicle


title: PAEC2


title: 1002_GO4H3T1


title: Day6.3.pTEICM_5

source_name: Blastocyst


title: Breast cancer patient T62

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T62


title: Day6.3.pTEICM_4


title: 1002_GO4H1T4


title: Breast cancer patient T61

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T61


title: IEC11

source_name: skin-fibroblast derived iPSC

value: iPSC-derived endothelial cell


title: 1002_GO4H1T3


title: Day6.3.pTEICM_2


title: IEC10


title: Day6.3.pTEICM_1


title: 1002_GO4H1T2


title: Breast cancer patient T59

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T59

value: Breast cancer


title: IEC9


title: 1002_GO4H1T1


title: Breast cancer patient T60

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T60


title: Day7.1.pTEICM_8


title: 1002_GO4G8


title: Day7.1.pTEICM_4


title: Breast cancer patient T111

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T111


title: Day6.3.pTEICM_6


title: 1002_3F5

value: PRE


title: Day7.1.pTEICM_3


title: IEC12


title: IEC8


title: Breast cancer patient T108

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T108

value: tumor


title: IEC6


title: IEC7


title: IEC5


title: Breast cancer patient T109

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T109


title: ccRCC2, Left clear cell renal cell carcinoma Homogenate

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V3.1
R1 end, at the beginning of 16bp is CellBarcode sequence, then 10bp is UMI sequence, R2 end, we can truncate 151bp to 98bp
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat R package
Genome_build: GRCh38 for human data
Supplementary_files_format_and_content: CellRanger output files  (the barcode, gene, expression matrix file of each sample)

source_name: clear cell renal cell carcinoma

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v3 user guide   to perform single cell suspension which were prepared before. Briefly, the  single-cell samples were passed through a 40μm cells strainer and counted using  a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to  recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the  oils onto the 10x Genomics single-cell-A chip and run this machine. After  droplet generation, samples were transferred onto a PCR tube and reverse  transcription was performed using T100 Thermal Cycler (BIO-RAD). After the  reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics  followed by a Silane DynaBead clean-up as outlined in the user guide. Purified  cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect  beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to  determine cDNA concentration.
10X Genomics Single Cell 3' v3 Reagent Kit


title: HEK293T_B2_posctrl_polyA

city: Rehovot

first: Anna

last: Uzonyi

address: 234 Herzl street

department: Department of Molecular Genetics

institute: Weizmann Institute of Science

description: poly-A RNA

data_processing:
Fastq files of amplicon libraries were processed and analysed using a custom R script. During the filtering process, reads that don’t start or end at the proper position, don’t contain one of the planned barcodes or have non-A or G nucleotides at A positions were removed. Single-reads were assembled by truncating and matching read 1 and 2. Based on the barcodes, information about the variable strand was matched to each read. Editing percentage was determined as G/(A+G) at a given position. For the positive and negative control constructs sequenced as total, poly-A selected RNA, A to G mismatch rate was quantified with Jacusa (Piechotta et al., 2017).
Supplementary_files_format_and_content: Compressed folder containing csv and txt files. 24 file contains average editing at every position and single construct for the first arm samples (1-24). 2 files contain mismatch quantification of B2 and mNG positive control construct. 2 files contain merged, filtered reads of the variable strand libraries.

source_name: human cell line

growth_protocol: HEK293T, MCF7, A549 and NIH3T3 cells were cultured in DMEM (Gibco) supplemented with 10% FBS and 1% Penicillin and Streptomycin.

extract_protocol:
RNA was extracted with NucleoZOL (Macherey-Nagel)
RNA was poly-A selected with oligo dT-beads (Dynabeads® mRNA DIRECT™ Kit life tech). For the control constructs, poly-A selected libraries were prepared. Poly-A RNA from oligo-pool transfected cells was reverse transcribed to obtain the constant or variable fragments of the constructs with the matching 8 nt barcode. PCR amplicons of these fragments were generated.

treatment_protocol: 2 million cells were seeded on a 10 cm plate 24 hours prior to transfection. 5 µg DNA was transfected with PolyJet reagent (SignaGen Laboratories). Cells were harvested 24 hours after transfection. For the IFN-stimulated samples, HEK293T cells were seeded on a 10 cm plate and transfected with the plasmid construct as before. At the same time, 650 U/ml IFN-α (pbl assay science) was added. For the Adar knockdown samples, HEK293T cells were subjected to two rounds of Adar siRNA (Ambion #4427038) treatment using the Lipofectamine RNAiMAX (Thermo Fisher Scientific) reagent, and 15 pmol siRNA in a 6-well format, with 24 h interval. Cells were reseeded on 10 cm plates and transfected with the plasmid as before.

tag: cell line

value: no treatment

tag: condition


title: HEK293T_mNG_posctrl_polyA

description: poly-A RNA

value: mNG


title: Breast cancer patient T104

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T104


title: IEC3


title: Breast cancer patient T101

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T101


title: Jurkat_Mnase-seq

city: Dallas

last: D'Orso

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

description: +single copy HIV

data_processing:
Illumina bcl2fastq (v 2.19.0) software used for basecalling
Sequenced reads were trimmed for adaptor sequence with trim galore, and aligned to GRCh38 using BWA sampe
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using SAMtools v1.3 and Sambamba v0.6.6.
bedtools v2.26.0 bamtobed converted the bed file to tagalign
Peaks were called with iNPS v1.2.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file from iNPS output

source_name: Jurkat J-Lat 10.6 Cell Line (https://www.aidsreagent.org/reagentdetail.cfm?t=cell_lines&id=437)

growth_protocol: Cells were cultured in RPMI 1640 media supplemented with 10% Fetal Bovine Serum (FBS) and 1X Penicillin/Streptomycin at 37°C with 5% CO2 at an optimal density of 0.5-1 million cells per mL. Cells were passaged every two days at a 1/3 dilution.

extract_protocol:
Cell suspensions were transferred to 50 mL conical tubes and pelleted at 420g for 10 min. Cells were then resuspended in PBS at a density of 1x106 cells/mL for crosslinking with 0.5% methanol-free formaldehyde (ThermoFisher) at room temperature with rotation for 10 min. The reaction was then quenched with 150 mM glycine (PBS buffer pH 7.5) for 10 min at room temperature. Cells were then pelleted by centrifuging at 420g for 10 min at 4°C and then washed twice with 20 mL cold PBS each time. Nuclei were collected by lysing the cells in Farnham’s lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40 freshly supplemented with 1mM PMSF and EDTA-free Protease inhibitor cocktail), washed once with cold MNase buffer (20 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 2 mM CaCl2) and then resuspended in MNase buffer at a concentration of 10x106 cells/mL before digestion. Micrococcal nuclease (New England BioLabs, M0247S) digestion was performed using 1100 U enzyme/106 cells at 37C for 10 min to achieve roughly 80% mono-nucleosome – 20% di-nucleosome populations. The reaction was interrupted with Stop buffer (20 mM EDTA pH 8.0, 20 mM EGTA pH 8.0, 0.4% SDS) and then centrifuged at 21,000g for 5 min at 4C. The supernatants were saved and the small white pellet discarded. Samples (100 μl) were mixed with 1 volume of 2X Proteinase K buffer (4 mM EDTA pH 8.0, 40 mM Tris-HCl pH 6.8, 1M NaCl and 1 mg/mL Proteinase K) for reverse crosslinking at 65°C for 16 hrs. After reverse crosslinking the samples were first extracted with 1 volume of phenol-chloroform-isoamylic alcohol (25:24:1 ratio) with centrifugation at 21,000g for 5 min at 4°C and later with 1 volume of chloroform-isoamylic alcohol (24:1 ratio). The aqueous phase was transferred to a 1.5 mL epitube and precipitated with 2.5 volumes of 100% cold Ethanol and 1/10 volume of 3M NaOAc with centrifugation at 21,000g for 15 min at 4°C. Samples were finally washed with 75% Ethanol, air dried for ~5 min and resuspended in 20 μl of water. DNA concentration was measured by Qubit/Nanodrop.
About 3 μg of DNA were loaded onto a 1.5% DNA agarose gel to verify the expected nucleosomal size distribution (80% mono- and 20% di-nucleosome). The mono-nucleosome band (~150 bp size) was excised and gel cleaned up using DNA Clean & Concentrator kit (Zymo Research) following the manufacturer’s instructions. DNA was eluted with 20 μl water (25 ng/μl final concentration). Replicate DNA samples were analyzed on high sensitivity DNA tape on Agilent 2200 TapeStation and used for library preparation. Library was prepared with ~375 ng of mono-nucleosomal DNA using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8502) according to the manufacturer’s instructions. For the PCR amplification step, we inputted ~7.5 ng and performed 9 cycles of amplification, obtaining 700 ng (~35 ng/μl). The quality control of the MNase-seq library was done on Agilent 2200 Tapestation. A single peak with average size of 306 bp (including ligated adapters) was observed. The MNase-seq DNA library was diluted to 4.2 nM for sequencing on an Illumina NextSeq 500 instrument.

tag: passages

value: Under 15

value: Parental

value: Jurkat derivative J-Lat 10.6 T cell line


title: IEC2


title: IEC1


title: Breast cancer patient T58

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T58

tag: disease

value: Female


title: Breast cancer patient T99

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T99

tag: gender


title: Breast cancer patient T90

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T90

tag: grade


title: Breast cancer patient T100

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T100

tag: er


title: Vector#3

city: Qingdao

first: Yu

last: Cao

address: 308 Ningxia Road

institute: Qingdao University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38.91 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include normalized Conut values and raw fragment counts for each Sample

growth_protocol: The conditionally immortalized BxPC-3 cells was cultured under growth permissive conditions at 37 °C in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: BxPC-3 cells overexpress LECT2 and its control Vector.

value: Vector


title: LECT2#3


title: LECT2#1


title: LECT2#2


title: Vector#2


title: Breast cancer patient T81

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T81

tag: pr


title: neuroblastoma cell line TDP-43 knockdown rep2

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description:
SH-SY5Y KO2
4901-WD-4
messenger RNA
raw_counts.csv

data_processing:
FASTQC
STAR align
featureCount
edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.csv: Raw counts in comma-separated text file.

source_name: neuroblastoma cell line

growth_protocol: Cells maintained in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated with TRIzol, and rRNA depleted.
Collibri Stranded RNA library prep kit (Thermo).

treatment_protocol: TDP-43 knockdown by CRISPR.

value: Neuroblastoma cell line

tag: genotype/variation

value: TDP-43 knockdown


title: Breast cancer patient T64

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T64

tag: age


title: Breast cancer patient T76

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T76


title: Breast cancer patient T23

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T23


title: Breast cancer patient T22

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T22


title: neuroblastoma cell line rep2

description:
SH-SY5Y WT2
4901-WD-2
messenger RNA
raw_counts.csv

tag: cell type

value: Wild type


title: neuroblastoma cell line TDP-43 knockdown rep1

description:
SH-SY5Y KO1
4901-WD-3
messenger RNA
raw_counts.csv


title: neuroblastoma cell line rep1

description:
SH-SY5Y WT1
4901-WD-1
messenger RNA
raw_counts.csv


title: Breast cancer patient T21

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T21


title: ccRCC1, Right clear cell renal cell carcinoma Homogenate


title: IEC4

source_name: skin-fibroblast derived iPSC


title: Breast cancer patient T5

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T5


title: MCF7_B2_variable_rep1

description: RNA amplicon

source_name: human cell line


title: MCF7_B2_variable_rep2

description: RNA amplicon


title: Breast cancer patient T18

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T18


title: Breast cancer patient T19

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T19


title: HEK293T_IFN_B2_variable_rep1

description: RNA amplicon

value: IFN-a


title: Breast cancer patient T16

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T16


title: Breast cancer patient T15

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T15


title: Breast cancer patient T14

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T14


title: HEK293T_B2_variable_rep2

description: RNA amplicon


title: Vector#1


title: Breast cancer patient T10

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T10


title: Breast cancer patient T11

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T11


title: Breast cancer patient T9

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T9


title: Breast cancer patient T3

description: Hybridized to SNP 6.0

source_name: Breast cancer patient T3


title: A549_mNG_rep2

description: RNA amplicon


title: MCF7_mNG_rep2

description: RNA amplicon


title: A549_B2_rep2

description: RNA amplicon


title: A549_B2_rep1

description: RNA amplicon


title: L3_R9D11_10Xv2

first: Sylvia

middle: N

last: Michki

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Alignment (STAR-solo)
Cell filtering (scanpy, min_genes=200, max_genes=4100)
Gene filtering (scanpy, min_cells=2)
Normalization (scanpy, ln(1+UMI))
Batch correction (harmony-pytorch v0.1.4)
Genome_build: BDGP6.94
Supplementary_files_format_and_content: hdf5 file, containing an anndata object (readable by scanpy) that has the filtered, normalized, log-transformed data matrix inside, along with other related cell-type clustering and projection parameters/values.

organism: Drosophila melanogaster

source_name: developing central nervous system

growth_protocol: Growth at 27C

extract_protocol:
10X chromium v2 chemistry
Illumina nextera xt library preparation

treatment_protocol: Dissection in Rinaldini’s soln., dissociation at 37C for 1hr in 2mg/mL papain and 2mg/mL collagenase (I), mechanical trituration, FACS sorting into Schneider’s + 10% FBS

tag: strain

tag: developmental stage

value: 3rd instar larva

value: brain

value: type-II lineage derived cells and optic lobe cells from the developing 3rd instar larval brain


title: MCF7_mNG_rep1

description: RNA amplicon

tag: treatment


title: MCF7_B2_rep2

description: RNA amplicon


title: MCF7_B2_rep1

description: RNA amplicon


title: HEK293T_siAdar_mNG_rep1

description: RNA amplicon

value: siAdar


title: HEK293T_siAdar_mNG_rep2

description: RNA amplicon


title: control replicate 3

city: Chongqing

first: Yuxi

last: Dai

address: Daxuecheng west street, Huxi town, Shapingba

institute: Chongqing university

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: Ensemble genome（WBcel235）
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Synchronized L1 worms were cultured on an NGM plate seeded with L4440 (control, HT115) and let-607 RNAi (HT115) bacteria.

extract_protocol:
Synchronized L4 worms were harvested , frozen on ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Growing the worms cultured at 20°C.

tag: e. coli b strain for diet


title: let-607 RNAi replicate 1

value: let-607 RNAi


title: let-607 RNAi replicate 2


title: HEK293T_B2_variable_rep1

description: RNA amplicon


title: HEK293T_IFN_B2_variable_rep2

description: RNA amplicon


title: control replicate 1


title: A549_mNG_rep1

description: RNA amplicon


title: N2_Nof_3

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Sequences were mapped to W275 C elegans genome
The htseq-count were further analyesd for the differentially expressed features from count tables using DESeq2
Genome_build: Genome_build: Caenorhabditis elegans genome WS275
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample

source_name: C elegans whole animal

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to L4 larval stage at 20oC

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Residual genomic DNA was removed using TURBO DNase (Life Technologies, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were washed off the plates with M9 and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

value: Wild type (N2)

tag: tissue

value: whole animal

tag: genotype


title: let-607 RNAi replicate 3


title: HEK293T_siAdar_B2_rep2

description: RNA amplicon

tag: cell line


title: N2_Nof_2


title: HEK293T_IFN_mNG_rep1

description: RNA amplicon

tag: condition

value: mNG


title: N2_Nof_1


title: HEK293T_IFN_B2_rep2

description: RNA amplicon


title: HEK293T_IFN_B2_rep1

description: RNA amplicon


title: U30_No_3


title: U30_No_2


title: HEK293T_mNG_rep2

description: RNA amplicon

value: no treatment


title: HEK293T_mNG_rep1

description: RNA amplicon


title: control replicate 2


title: FaDu_JQ1

city: Richmond

first: Jiong

last: Li

address: 800 E Leigh Street, suite 212

institute: VCU

data_processing:
RNAs were single-end sequenced on Illumina HiSeq 3000 machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Head and neck squamous cell carcinoma cells

growth_protocol: 10% FBS in DMEM

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen, cat#74104).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)

treatment_protocol: SCC1, SCC22B and FaDu cells were treated with 500nM JQ1 or with control for 24 hours.

value: FaDu cells


title: HEK293T_B2_rep1

description: RNA amplicon


title: HEK293T_siAdar_B2_rep1

description: RNA amplicon


title: SCC22B_JQ1

value: SCC22B cells


title: Young sedentary adult, Y4

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

institute: University of Colorado Boulder

data_processing:
QC and adapters trimmed using fastp.
Reads aligned and counted using STAR.
Repetitive element transcripts counted using TEtranscripts.
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene and repetitive element counts for each sample.

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
Total RNA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit with Ribo-Zero Depletion.

tag: Sex

value: Male

tag: exercise status

value: sedentary

value: Peripheral blood mononuclear cells


title: Young sedentary adult, Y5


title: HEK293T_IFN_mNG_rep2

description: RNA amplicon


title: SCC22B_con


title: Young sedentary adult, Y3

value: Female


title: Young sedentary adult, Y1


title: H3K27Ac JQ1 treatment

description: H3K27Ac JQ1 treatment

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.2.0.
The unique mapped reads was used for peak calling by MACS2 with default setting
Supplementary_files_format_and_content: bedGraph files and big wig files

extract_protocol:
ChIP was performed uing EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Sigma, Cat#17-10086). 10–50 ng of ChIP DNA for each sample was sonicated and used for the ligation of barcoded Kapa adapters.
Sequencing libraries were generated using a KAPA Hyper DNA Kit (KAPA Biosystems, Cat# KK8503)

treatment_protocol: SCC1 cells were treated with 500nM JQ1 or with control for 24 hours.

tag: agent

tag: chip antibody

value: H3K27Ac rabbit antibody (Abacm, cat#ab4729)


title: SCC1_JQ1

value: SCC1 cells


title: Young sedentary adult, Y2


title: D6_3: Organoid Bulk RNA-seq Day 6 - replicate 3

city: Davis

first: Stefan

last: Siebert

address: One Shields Avenue

institute: University of California, Davis

description: iPSC derivatives isolated from organoid at day 6 of  differentiation

data_processing:
Raw reads were trimmed for adapters and low-quality bases using Cutadapt 1.18 (-j 8 -b file:adapters.fa -B file:adapters.fa --trim-n -m 20 -o trimmed_R1.fq -p trimmed_R2.fq input_R1.fq input_R2.fq) prior to alignment to the reference genome (Human genome – hg38, annotation Gencode_v24) using STAR 2.6.1. Gene expression quantification analysis was performed using RSEM 1.2.31.
genome build: hg38
processed data files format and content: tab-delimited text file of RSEM gene level raw expression estimates

source_name: NL5-GFP derived organoid at day 6 of differentiation

extract_protocol:
RNeasy Mini Kit (QIAGEN)
TruSeq Stranded Total RNA

value: GFP+ cells isolated from organoid at day 6 of the differentiation


title: D13_2: Organoid Bulk RNA-seq Day 13 - replicate 2

description: iPSC derivatives isolated from organoid at day 13 of  differentiation

source_name: NL5-GFP derived organoid at day 13 of differentiation

value: GFP+ cells isolated from organoid at day 13 of the differentiation


title: D13_3: Organoid Bulk RNA-seq Day 13 - replicate 3


title: D6_2: Organoid Bulk RNA-seq Day 6 - replicate 2


title: D13_1: Organoid Bulk RNA-seq Day 13 - replicate 1


title: H3K27Ac contol

description: H3K27Ac contol

value: contol


title: D6_1: Organoid Bulk RNA-seq Day 6 - replicate 1


title: p65 JQ1 treatment

description: p65 JQ1 treatment

value: p65 rabbit antibody (Santa Cruz, cat#SC-372)


title: Older habitually exercising adult, T4

value: habitually exercising


title: U30_No_1


title: HEK293T_B2_rep2

description: RNA amplicon

source_name: human cell line


title: Older habitually exercising adult, T3


title: sc_d6_d13: Organoid single-cell RNA-seq, Day 6 and Day13

description: iPSC derivatives isolated from organoids at day 6 and day 13 of differentiation

data_processing:
Raw sequencing data were converted to fastq format using cellranger mkfastq (10x Genomics, v.3.1.0). scRNA-seq reads were aligned to the GRCh38 human reference genome and gene expression counts and feature barcode counts were determined using cellranger count (10x Genomics, v.3.1.0).
genome build: hg38
processed data files format and content: umi_mtx - tab-delimited text file of UMI counts, columns are cells, and rows are genes; hto_mtx.txt - tab-delimited text file of HTO counts, columns are cells, and rows are HTOs.

source_name: NL5-GFP derived organoid at day 6 and day 13 of the differentiation

extract_protocol: Chromium Single Cell 3' Reagent Kit (v3 Chemistry)

value: GFP+ cells isolated from organoid at day 6 and day 13 of differentiation


title: FaDu_con


title: Older habitually exercising adult, T2


title: p65 control

description: p65 control

value: control


title: Nl5_2: Organoid Bulk RNA-seq Day 0 - replicate 2

description: human iPSC

source_name: GFP-labeled human iPSC (NL5-GFP)

value: human iPSC


title: Nl5_1: Organoid Bulk RNA-seq Day 0 - replicate 1

description: human iPSC


title: SCC1_con


title: BRD4 JQ1 treatment

description: BRD4 JQ1 treatment

value: BRD4 rabbit antibody (Abacm, cat#ab128874)


title: BRD4 control

description: BRD4 control


title: Older sedentary adult, O5


title: Plagl1+/-pat retina #2

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

data_processing:
Basecalling and demultiplexing: CASAVA1.9
Initial quality controls: FastQC
Adapter trimming: TrimGalore! v.0.6.4
Mapping: bowtie v.2.3.5.1 with –very-sensitive option
SAM to BAM conversion, sorting and indexing: samtools v.0.1.19
Removal of mitochondrial reads using samtools idxstats
Creation of normalized coverage file in bigwig format using Deeptools 3.3.0 bamCoverage with RPGC normalization
Peak calling was done using MACS v.2.2.7.1 with -f BAMPE and –broad options specified
Differentially accessible peaks were called with DiffBind v.3.013 with TMM normalization and library sizes determined based in background method
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig, broadPeak

source_name: Plagl1+/-pat retina

extract_protocol: Active Motif ATAC-seq kit was used for libraries construction

value: Post-natal stage (P)7

value: retina


title: Plagl1+/-pat retina #3


title: MED1 JQ1 treatment

description: MED1 JQ1 treatment

value: MED1 rabbit antibody (Bethyl, cat#A300-793A)


title: Plagl1+/-pat retina #1


title: Older sedentary adult, O4

value: sedentary