title: MDR CIBIN:UMF:15:99 UCI-05 rep3

city: Monterrey

first: Katia

last: Penuelas-Urquides

state: Nuevo León

address: Calle 2 de abril 501, Col. Independencia

department: Molecular Biology Dept.

country: Mexico

institute: Instituto Mexicano del Seguro Social

description: Gene expression data of MDR-MTB clone treated with compund 1

hyb_protocol: The labeled cDNA product was heated to 95°C and hybridized to the Affymetrix GeneChip TB-All Antisense microarrays for 17 h at 45°C.

scan_protocol: Fluorescent signal was measured and the Affymetrix GeneChip Expression Console was used to obtain the intensity signal and quality control data of the scanned arrays.

data_processing: Microarray data was pre-processed using the MAS5 algorithm. Raw intensity values were background-corrected, log2-transformed, and then quantile-normalized. A linear model using the limma package was fit to the normalized data to identify differential expression

organism: Mycobacterium tuberculosis H37Rv

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 3 treated with UCI-05

label_protocol: The cDNA was fragmented with DNaseI and labeled at the 3' termini using 60U of Terminal Deoxynucleotidyl Transferase and 7.5 mM biotinylated GeneChip DNA Labeling Reagent.GeneChip DNA Labeling Reagent

growth_protocol: 1.0 mL of McF 1 inoculum was growth in 10 mL Middlebrook 7H9 medium supplemented with 10% OADC and incubated at 37 °C in 5% CO2 atmosphere with constant shaking (at 300 rpm) until mycobacteria reached growth log phase

extract_protocol: Total RNA was extracted using TRIzol reagent and the Fast Prep instrument.

treatment_protocol: Each clone culture was treated with compound 1, 2  (at a final concentration equivalent to their respective MICs) or 0.1% DMSO (as control) and incubated under the same conditions for additional 4 h.

tag: drug resistance

value: MDR

tag: replicate

value: MDR biological rep 3 treated with UCI-05


title: MLL-AF9_3

status: Public on Nov 01 2021

type: SRA

city: Rotterdam

first: Stefan

middle: J.

last: Erkeland

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Department of Immunology

country: Netherlands

institute: Erasmus University Medical Center

description:
RNA-seq of MLL-AF9-transformed WT HSPC-enriched bone marrow cells
MLL_AF9_WT_NEO3
The file str-ReadCount.tab includes samples from GSE160405.

library_source: transcriptomic

data_processing:
After sequencing and demultiplexing, the quality of the reads was determined with fastQC(v 0.11.8).
Fastq files were mapped to the reference GRCm38 using STAR (v.2.5.3e).
The annotation was done with FeatureCounts (v1.6.0) using genecodevM15.annotation.gtf as a reference.
The quality of the data was assessed with MultiQC.
Noise reduction was applied to the count data by removing the rows with read counts lower than 10.
Next, rlog transformation was used for visualization and comparison purposes which include correlation and clustering analysis generating the heatmaps and PCA plots.
For differential expression analysis, DESeq2(v1.22.2) was used.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimeted text file containing raw RNA counts per gene

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow cells

growth_protocol: HSPCs were isolated from femur and tibiae from WT or Mir139KO C57BL/6 mice (8 – 20 wks) using the BD Mouse Hematopoietic Progenitor (Stem) Cell  Enrichment Set (cat 558451, Becton Dickinson). Cells were immediately resuspended in TRIzol or HPSCs were expanded in StemPro-34 SFM (Thermo Fisher Scientific, 10639011) supplemented with Interleukin (IL)-3 (1:1000 supernatant), IL-6 (10 ng/mL; SRP3330 Sigma Aldrich), Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) (10 ng/mL; CYT-222, Prospec Ltd) and Stem Cell Factor (SCF) (20 ng/mL; 5223SF, Cell Signaling Technology) and Penicillin-Streptomycin (P/S) (100U/mL; 15140163, Thermo Fisher Scientific) overnight, followed by retroviral transduction with pMSCV-MLL-AF9-neo or pMSCV-MLL-AF9-puro (Wong et al., 2007) with RetroNectin (T100A, Takara) according to manufacturer’s  protocol. Transduced cells were selected on Neomycin (800µg/mL; 10131035, Thermo Fisher Scientific) or Puromycin. After at least two re-platings in MethoCult (M3231, Stem Cell Technologies), MLL-AF9 cells were resuspended in TRIzol.

extract_protocol:
Total RNA was isolated with TRIzol, according to the manufacturer’s protocol. The quality of the was analyzed with the Bioanalyzer RNA 6000 Nano Kit (5067-1511, Agilent).
Libraries were generated with 500ng of RNA using the KAPA RNA HyperPrep Kit with RiboErase (KK8560, Roche) according to manufacturer’s protocol. Quality control of the libraries was performed with the Bioanalyzer High Sensitivity DNA kit (5067-4626, Agilent Technologies). Library quantity was determined with NEBNext Library Quant Kit (E6730, New England Biolabs). Libraries were run on the NovaSeq (Illumina).

treatment_protocol: WT HSPCs were cultured overnight, followed by retroviral transduction with pMSCV-MLL-AF9-neo or pMSCV-MLL-AF9-puro (Wong et al., 2007) with RetroNectin (T100A, Takara) according to manufacturer’s  protocol. Transduced cells were selected on Neomycin (800µg/mL; 10131035, Thermo Fisher Scientific) or Puromycin. After at least two re-platings in MethoCult (M3231, Stem Cell Technologies), MLL-AF9 cells were resuspended in TRIzol.

tag: background strain

tag: tissue

value: MLL-AF9-transformed HSPC-enriched bonemarrow cells

tag: genotype

value: WT

tag: retroviral transduction


title: HSPCKO_2

description:
RNA-seq of Mir139KO HSPC-enriched bone marrow cells
HSPCKO1764405
The file str-ReadCount.tab includes samples from GSE160405.

value: HSPC-enriched bone marrow cells


title: MDR CIBIN:UMF:15:99 UCI-14 rep3

type: RNA

description: Gene expression data of MDR-MTB clone treated with compund 2

label: Biotin

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 3 treated with UCI-14

value: MDR biological rep 3 treated with UCI-14


title: C43_F

city: Vancouver

first: Alexandre

middle: A

last: Lussier

state: British Columbia

department: Department of Medical Genetics

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
Fastq files were aligned to the rat genome (Rn6, July 2014) using the Burrows-Wheeler Transform (BWA) tool to obtain .bam files (Li and Durbin, 2009).
Bam files were filtered using samtools to remove duplicate reads, unpaired reads, and reads with a minimum quality score below 10.
Following alignment and filtering, each the two runs for each sample were merged using samtools to obtain a single .bam file for each sample (Li et al., 2009).
Model-based analysis of ChIP-seq (MACS2; version 2.1.0.20140616) was used to identify enriched regions of DNA methylation across the genome (Zhang et al., 2008). The peak calling to identify peak regions (DNA methylation windows) was performed using the ‘callpeaks’ function on paired end bam files with no control input and the following options: –f BAMPE –m 5 50 –bw 300 –g 2.9e9 –q 0.05. Each sample was modeled individually, generating 60 total peaksets. These were imported into R using the DiffBind package (Stark and Brown, 2011). As all samples had slightly different predicted peaks, peaksets were combined into common regions using the dba.count function in DiffBind, which removed peaks found in less than 3 samples across the entire dataset and provided the total number of reads within each peak/sample. This created a final dataset of 469,162 peaks and 48 samples from the developmental profile of the hypothalamus, and a final dataset of 350,960 peaks and 24 samples in the P22 hypothalamus and WBC (tissue-concordant) peakset.
Genome_build: rn6
Supplementary_files_format_and_content: MACS2.1.4 peak file, one/animal/sex/group

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Prefrontal cortex, postnatal day 22, Control

growth_protocol: Details of the procedures for breeding and handling have been published previously (Bodnar et al., 2016). Briefly, outbred male and female Sprague-Dawley rats were obtained Charles River Laboratories (St. Constant, Quebec, Canada). Following a one-week habituation period, nulliparous females (n=39) were pair-housed with a male and vaginal lavage samples were collected daily for estrous cycle staging and to check for the presence of sperm, indicating gestation day (GD) 1. Pregnant dams were singly housed and assigned to one of three prenatal treatment groups: Prenatal alcohol exposure (PAE) - ad libitum access to liquid ethanol diet, 36% ethanol-derived calories, 6.37% v/v, n =13; Pair-fed (PF) - liquid-control diet, maltose-dextrin isocalorically substituted for ethanol, in the amount consumed by an PAE partner, g/kg body weight/GD, n =14; or Control (C) - pelleted version of the liquid control diet, ad libitum, n =12. All animals had ad libitum access to water. Experimental diets (Weinberg/Keiver Liquid Ethanol Diet #710324, Weinberg/Keiver Liquid Control Diet #710109, and Pelleted Control Diet #102698, Dyets Inc., Bethlehem, PA) were fed from gestation days 1-21, and then replaced with laboratory chow.

extract_protocol:
For each sample, 500 ng of DNA were diluted in a total volume of 60µL of EB buffer (Qiagen, Hilden, Germany). DNA was then transferred to a 96-well plate and sheared for 1 hour using the Covaris Focused-ultrasonicator. DNA was purified using Ampure XP in 20% polyethylene glycol (PEG) beads to obtain fragments sized from 200-500 basepairs (Beckman-Coulter, Brea, USA). Library preparation was performed on the Bravo Automated Liquid Handling Platform (Agilent, Santa Clara, USA) using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina, San Diego, USA). Following end-repair and A-tailing, adapters were ligated overnight at room temperature. PCR-free library preparation allowed for the conservation of methylated cytosines for subsequent methylated DNA immunoprecipitation. Finally, DNA was resuspended in 35µL of EB buffer (Qiagen, Hilden, Germany). DNA was quality controlled using Qubit Fluorometric Quantitation and the DNA 1000 Bioanalyzer 2100 kit (Agilent, Santa Clara, USA) to verify concentration and fragment size (250-550bp).
methylated DNA immunoprecipitation (meDIP): For each sample, 400ng of the sequencing library were diluted in a total volume of 50µL of IP Buffer (10mM sodium phosphate buffer, pH7.0, 140mM NaCl, 0.05% triton). DNA was denatured by incubation at 95˚C for 10 minutes, followed by the addition of 48µL ice-cold IP buffer and incubation on ice for 10 minutes. 2µL of anti-5-methylcytosine antibody (Eurogenetec, Liège, Belgium), diluted to 1/50 in IP buffer (1µL of antibody per 1µg of DNA ratio), was added to each sample. Immunoprecipitation reactions were incubated for 16 hours at 4˚C with overhead rotation. Following two 5 minute washes with 150uL of 0.1% BSA/PBS, 50µL of Dynabeads Protein G were incubated with 5µL of secondary antibody (rabbit anti-mouse IgG; Jackson Immunoresearch, West Grove, USA) in 45uL ice-cold IP buffer for 15 minutes at room temperature with overhead rotation. Beads were washed twice with IP buffer to remove unbound secondary antibody and resuspended in 50µL IP buffer. The antibody-bound beads were added to the immunoprecipitation reactions and incubated for 2 hours at 4˚C with overhead rotation. Beads were then washed 6 times with 150µL of ice-cold IP buffer and resuspended in 98.97µL of Proteinase K digestion buffer (TE with 0.5% SDS). Following the addition of 1.25µL Proteinase K (20mg/mL; Qiagen, Hilden, Germany), samples were incubated in a thermomixer for 2 hours at 55˚C with a rotation speed of 1250rpm. The reaction was then allowed to cool at room temperature for 15 minutes. Supernatant was collected and bead cleanup was performed using equal volume SeraMag beads with 30% PEG. DNA was resuspended in 35µL of EB buffer (Qiagen, Hilden, Germany). Two parallel rounds of the following PCR amplification cycle conditions were performed on each sample in order to reduce PCR amplification bias. The reaction mixes were as follows: 15µL DNA, 27µL H2O, 12µL 5X HF buffer, 1.5µL DMSO, 1.0µL paired-end primer (Illumina), 0.5µL Phusion High-Fidelity DNA polymerase (New England Biolabs), 2µL indexing primer (Illumina – specific to each sample). The amplification cycle was as follows: 98˚C for 1 minute, 12X (98˚C for 15 seconds, 65˚C for 30 seconds, 72˚C for 30 seconds), 72˚C for 5 minutes. Reactions from the same sample were pooled and bead cleanup was performed using SeraMag beads in 20% PEG (102µL of beads per 120µL of reaction). DNA was resuspended in a final volume of 35µL of EB buffer.
Indexed meDIP libraries were pooled as part of a larger set of 60 samples, which were combined into 5 pools of 12 samples each. Samples were distributed evenly by sex, prenatal treatment, and tissue type. Next-generation sequencing was performed on the pools by the Genome Sciences Centre in Vancouver, BC, Canada. Each sample pool was run on one HiSeq lanes, which produced approximately 600,000,000 paired-end reads of 125 bases per lane.

treatment_protocol: Total RNA and DNA were simultaneously extracted from the prefrontal cortex on postnatal day 22 (n=5/group/sex; Qiagen AllPrep DNA/RNA Mini kit, Hilden, Germany). Frozen tissue was thawed on ice, quickly weighed and placed in lysis buffer for 5 minutes. Homogenization was performed by 5 strokes of an 18G needle, 10 strokes of a 20G needle, and 10 strokes of a 23G needle. The resulting homogenate was centrifuged at 21,000g for 3 minutes and the supernatant was collected for DNA and RNA extraction. White blood cells were thawed on ice and then centrifuged at 10,000g for 10 minutes. RNAlater was carefully removed without disturbing the cell pellet and cells were resuspended in lysis buffer. The cells were then frozen at -80˚C to disrupt cell membranes and then thawed on ice. The resulting homogenate was then used for DNA and RNA extraction. DNA concentration was assessed using Qubit Fluorometric Quantitation (Life Technologies, Carlsbad, USA).

value: Control

tag: dam (i.e., litter)

tag: age

value: postnatal day 22

value: Prefrontal cortex

tag: strain

value: Sprague-Dawley

tag: Sex

value: Female

value: CCGCAA


title: high LCFA + GW0742 rep 2

city: New York

first: Nadeera

middle: M

last: Wickramasinghe

state: NY

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Sample 62

data_processing:
FASTQ files were aligned with kallisto to a reference transcriptome model generated from the human genome hg38 using default parameters. Transcript-level counts were added to generate a collapsed gene-level count matrix. DESeq2 was used to normalize read counts and determine differentially expressed genes with p<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing gene-level counts for each RNA-Seq sample.

organism: Homo sapiens

source_name: cardiomyocyte

growth_protocol: Standard EB-differentiation protocols were used to generate PSC-derived cardiomyocytes, which were either cultured as Ebs, dissociated and plated as monolayers or dissociated and constructed into EHTs. A subset of cells were also subjected to lactate selection.

extract_protocol:
PSC-derived cardiomyocytes were dissociated using Collagenase Type II and FACS-isolated through SIRPA+ CD90- gating.
RNA libraries were prepared for sequencing using RiboZero Gold library prep and standard Illumina protocols

treatment_protocol: PSC-derived cardiomyocytes were treated with either GW0742 (5µM), WY14643(5µM), Rosiglitazone (5µM), GSK0660 (2.5µM) or AICAR (2.5µM), and with or without LCFAs (12.5µM; palmitic acid, oleic acid, linoleic acid).

tag: cell type

value: PSC-derived cardiomyocyte

tag: treatment

value: high LCFA + GW0742

tag: treatment duration

value: 28 days

tag: cell line


title: MDR CIBIN:UMF:15:99 UCI-14 rep2

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 2 treated with UCI-14

value: MDR biological rep 2 treated with UCI-14


title: HSPCKO_3

description:
RNA-seq of Mir139KO HSPC-enriched bone marrow cells
HSPCKO1797801
The file str-ReadCount.tab includes samples from GSE160405.


title: HSPCKO_4

description:
RNA-seq of Mir139KO HSPC-enriched bone marrow cells
HSPCKO1797802
The file str-ReadCount.tab includes samples from GSE160405.


title: HSPCKO_1

description:
RNA-seq of Mir139KO HSPC-enriched bone marrow cells
HSPCKO1764404
The file str-ReadCount.tab includes samples from GSE160405.


title: C44_F

value: AACCCC


title: HSPCWT_4

description:
RNA-seq of WT HSPC-enriched bone marrow cells
HSPCWT1925901
The file str-ReadCount.tab includes samples from GSE160405.


title: MDR CIBIN:UMF:15:99 control rep3

description: Gene expression data of MDR-MTB clone treated with vehicule as assay control

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 3 control

value: MDR

value: MDR biological control rep 3


title: high LCFA + GW0742 rep 1

description: Sample 61


title: MDR CIBIN:UMF:15:99 UCI-05 rep2

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 2 treated with UCI-05

value: MDR biological rep 2 treated with UCI-05


title: Slow_3

city: Chongqing

first: chuanchuan

last: lin

state: China

address: Shayang Road, Shapingba distract,

country: China

institute: Chongqing University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: 10% FBS, 1% penicillin/streptomycin, low glucose DMEM

extract_protocol:
About 10e6 MSCs were isolated from different group and the mRNA library constructed using QIAseq FX Single Cell RNA Library Kit (QIAGEN) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cell culture matrix with different stress relaxation

value: Mesenchymal stem cells (MSCs)

tag: cell states

value: slow stress relaxation

tag: intervention

value: Slow


title: C41_F

value: Control

value: GTAGAG


title: HSPCWT_3

description:
RNA-seq of WT HSPC-enriched bone marrow cells
HSPCWT1764303
The file str-ReadCount.tab includes samples from GSE160405.

value: HSPC-enriched bone marrow cells

value: WT


title: MDR CIBIN:UMF:15:99 control rep2

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 2 control

value: MDR biological control rep 2


title: high LCFA rep 3

description: Sample 60

value: high LCFA


title: MDR CIBIN:UMF:15:99 UCI-14 rep1

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 1 treated with UCI-14

value: MDR biological rep 1 treated with UCI-14


title: HSPCWT_2

description:
RNA-seq of WT HSPC-enriched bone marrow cells
HSPCWT1707403
The file str-ReadCount.tab includes samples from GSE160405.


title: LCFA + GW0742 7d-phased rep 3

description: Sample 57

value: PSC-derived cardiomyocyte

value: LCFA + GW0742 7d-phased


title: Medium_3

value: medium stress relaxation

value: Medium


title: high LCFA rep 1

description: Sample 58

value: 28 days


title: HSPCWT_1

description:
RNA-seq of WT HSPC-enriched bone marrow cells
HSPCWT1707401
The file str-ReadCount.tab includes samples from GSE160405.


title: high LCFA rep 2

description: Sample 59


title: Slow_2


title: GW0742 7d-phased rep 3

description: Sample 54

value: GW0742 7d-phased


title: Medium_1


title: Medium_2


title: Pansensitive H37Rv UCI-14 rep3

description: Gene expression data of sensitive MTB clone treated with compund 2

source_name: RNA from M. tuberculosis, H37Rv clone 3 treated with UCI-14

value: Sensitive

value: Sensitive biological rep 3 treated with UCI-14


title: LCFA + GW0742 7d-phased rep 2

description: Sample 56


title: MDR CIBIN:UMF:15:99 UCI-05 rep1

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 1 treated with UCI-05

value: MDR

value: MDR biological rep 1 treated with UCI-05


title: MDR CIBIN:UMF:15:99 control rep1

source_name: RNA from M. tuberculosis, CIBIN:UMF:15:99 clone 1 control

value: MDR biological control rep 1


title: Fast_3

value: Mesenchymal stem cells (MSCs)

value: fast stress relaxation

value: Fast


title: LCFA + GW0742 7d-phased rep 1

description: Sample 55


title: Pansensitive H37Rv UCI-05 rep3

description: Gene expression data of sensitive MTB clone treated with compund 1

source_name: RNA from M. tuberculosis, H37Rv clone 3 treated with UCI-05

value: Sensitive biological rep 3 treated with UCI-05


title: Fast_2


title: Slow_1

value: slow stress relaxation

value: Slow


title: S394_22_GFA_FAD_522_Hip

first: Daniel

last: Erny

address: Breisacher Str. 64

department: Neuropathology

country: Germany

institute: University hospital Freiburg

data_processing:
Fastq files were aligned to the Gencode 25 / GRCh38 genome annotation using STAR aligner version 2.5.2b with options STAR --runThreadN 10 --genomeDir /xxx/Annotations/Gencode_v25/STAR_50bp --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn .R1, .R2 --readFilesCommand zcat --outFileNamePrefix yyy --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --quantMode GeneCounts
Gene counts were generated using featureCounts v1.5.1 with command: featureCounts -a /xxx/Annotations/Gencode_v25/gencode.v25.annotation.gtf -G /xxx/Annotations/GRCh38/GRCh38.primary_assembly.genome.fa -o counts.tsv -p -F GTF -g gene_name -t exon -T 10 --largestOverlap
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Hippocampus

growth_protocol: Mice were housed under SPF or germ-free condiotions. Animals were 6-16 weeks old.

extract_protocol:
Adult microglia were harvested using density gradient separation. CD11b+CD45lo microglial cell populations were FACS-sorted and collected directly in cell lysis buffer.
The sequencing run was performed on a HiSeq 1000 instrument and TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq files by the CASAVA1.8.2 software.

treatment_protocol: One group of GF mice was treated with acetate for 4 weeks prior to analysis. One group of GF WT and 5xFAD mice was treated with acetate for 8 weeks prior to analysis.

value: microglia

value: Hippocampus

value: 16 weeks

tag: strain background

tag: microbiota

value: GF (+Acetate)


title: GW0742 7d-phased rep 1

description: Sample 52

value: PSC-derived cardiomyocyte

value: 28 days


title: GW0742 7d-phased rep 2

description: Sample 53

value: GW0742 7d-phased


title: Fast_1


title: Pansensitive H37Rv UCI-14 rep2

source_name: RNA from M. tuberculosis, H37Rv clone 2 treated with UCI-14

tag: drug resistance

value: Sensitive

tag: replicate

value: Sensitive biological rep 2 treated with UCI-14


title: Hep3b cells-WIPI2 knockdown-rp3

city: Nanjing

first: Xianwen

last: Yuan

state: Jiangsu

address: 321 Zhongshan Road

department: Department of Hepatobiliary Surgery

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

description:
E1268-3
Gene expression data from Hep3b cells transfected with si-RNA targeting WIPI2.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip PrimeView human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2013, Affymetrix).

growth_protocol: The Hep3b cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL of penicillin and 100 µg/mL of streptomycin (complete medium) at 37˚C in a humidified atmosphere containing 5% CO2.

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

treatment_protocol: Total RNA of Hep3b cells transfected with si-RNA targeting WIPI2 (si-WIPI2) and non-silencing sequence (si-NC) after 48h were extracted by Trizol solution.

value: Liver cancer cell line

tag: sirna


title: Pansensitive H37Rv UCI-05 rep2

source_name: RNA from M. tuberculosis, H37Rv clone 2 treated with UCI-05

value: Sensitive biological rep 2 treated with UCI-05


title: Pansensitive H37Rv control rep3

description: Gene expression data of sensitive MTB clone treated with vehicule as assay control

source_name: RNA from M. tuberculosis, H37Rv clone 3 control

value: Sensitive biological control rep 3


title: LCFA + GW0742 7d rep 3

description: Sample 51

value: LCFA + GW0742 7d

value: 7 days


title: Pansensitive H37Rv UCI-14 rep1

source_name: RNA from M. tuberculosis, H37Rv clone 1 treated with UCI-14

value: Sensitive biological rep 1 treated with UCI-14


title: S394_19_GFA_FAD_519_Hip

tag: tissue

tag: genotype


title: FACS sorted NC cells 30 hpf

city: Irvine

first: Thomas

middle: F

last: Schilling

state: CA

address: 4462 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California Irvine

description:
aggregated.arch.counts.matrix.csv
Sample 6

data_processing:
FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger.
Further processing was performed using Seurat v3 in R
Low quality cells and doublets were excluded based on thresholds for number of genes detected (>1500; <4000)
Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected (<4%)
Genome_build: GRCz11
Supplementary_files_format_and_content: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds.  In aggregated.arch.counts.matrix.csv, barcode.1 corresponds to "Sample 1", barcode.2 corresponds to "Sample 2", and so on.

organism: Danio rerio

source_name: FACS sorted sox10:nEOS cells

extract_protocol:
Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II.
Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7, which used chemistry v3

value: 30 hpf

value: NC cell


title: Hep3b cells-WIPI2 knockdown-rp2

description:
E1268-2
Gene expression data from Hep3b cells transfected with si-RNA targeting WIPI2.


title: S394_21_GFA_FAD_521_Hip

value: microglia


title: Pansensitive H37Rv control rep2

source_name: RNA from M. tuberculosis, H37Rv clone 2 control

value: Sensitive biological control rep 2


title: S394_20_GFA_FAD_520_Hip

value: Hippocampus

value: 16 weeks


title: FACS sorted NC cells 18 hpf second data set

value: 18 hpf


title: LCFA 7d rep 3

description: Sample 48

source_name: cardiomyocyte

value: PSC-derived cardiomyocyte

value: LCFA 7d


title: LCFA + GW0742 7d rep 1

description: Sample 49


title: S394_18_GFA_WT_525_Hip

value: WT

value: GF (+Acetate)


title: LCFA 7d rep 2

description: Sample 47


title: Hep3b cells- Negative control-rp1

description:
E1267-1
Gene expression data from Hep3b cells transfected with negative control sequence.

value: Liver cancer cell line

value: si-NC


title: Hep3b cells-WIPI2 knockdown-rp1

description:
E1268-1
Gene expression data from Hep3b cells transfected with si-RNA targeting WIPI2.


title: S394_17_GFA_WT_524_Hip


title: LCFA + GW0742 7d rep 2

description: Sample 50


title: FACS sorted NC cells 20 hpf

description:
aggregated.arch.counts.matrix.csv
Sample 4

value: 20 hpf


title: LCFA 7d rep 1

description: Sample 46


title: Pansensitive H37Rv control rep1

source_name: RNA from M. tuberculosis, H37Rv clone 1 control

value: Sensitive

value: Sensitive biological control rep 1


title: S394_16_GFA_WT_523_Hip


title: GW0742 7d rep 3

description: Sample 45

value: 7 days


title: GW0742 7d rep 2

description: Sample 44


title: FACS sorted NC cells 18 hpf

description:
aggregated.arch.counts.matrix.csv
Sample 3


title: S394_15_GFA_WT_518_Hip


title: Mouse ES cells replicate 3; Capture-C, interacting promoters viewpoints

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_int_ES3

data_processing:
Library strategy: Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2 -v 3) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: E14 embryonic stem cells

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, as described in Davies et al, Nature Methods, 2016.

treatment_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).

value: E14 embryonic stem cell line

tag: viewpoint analyzed


title: Mouse ES cells replicate 2; Capture-C, interacting promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_int_ES2


title: Hep3b cells- Negative control-rp2

description:
E1267-2
Gene expression data from Hep3b cells transfected with negative control sequence.


title: Pansensitive H37Rv UCI-05 rep1

source_name: RNA from M. tuberculosis, H37Rv clone 1 treated with UCI-05

value: Sensitive biological rep 1 treated with UCI-05


title: Mouse ES cells replicate 1; Capture-C, interacting promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_int_ES1


title: FACS sorted NC cells 14 hpf

description:
aggregated.arch.counts.matrix.csv
Sample 2

tag: age

value: 14 hpf

value: NC cell


title: GW0742 7d rep 1

description: Sample 43


title: Control 7d rep 3

description: Sample 42

value: Control 7d


title: SKP1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

description: Gene expression data from human skin-derived precursors

hyb_protocol: According to manufacturer's protocol (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Expression values were quantile normalized using Dchip (https://sites.google.com/site/dchipsoft/)

source_name: Foreskin dermis

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was extracted and quality assessed with Trizol (Invitrogen) and an Agilent BioAnalyzer.

tag: gender

value: male

value: foreskin dermis, skin-derived precursors (SKP)

value: skin-derived precursors from human foreskin


title: S394_12_GF_FAD_526_Hip

value: microglia

value: Hippocampus

value: 16 weeks

value: GF


title: FACS sorted NC cells 24 hpf

description:
aggregated.arch.counts.matrix.csv
Sample 5

value: 24 hpf


title: S394_13_GF_FAD_527_Hip


title: S394_14_GF_FAD_531_Hip


title: Hep3b cells- Negative control-rp3

description:
E1267-3
Gene expression data from Hep3b cells transfected with negative control sequence.

value: Liver cancer cell line

value: si-NC


title: Mouse erythroid cells biological replicate 3; Capture-C, interacting promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_int_C57-3

source_name: Primary erythroid cells

tag: strain

value: Ter-119+ cells isolated from phenylhydrazine treated spleen


title: Control 7d rep 2

description: Sample 41

tag: cell type

value: PSC-derived cardiomyocyte

value: 7 days


title: Mouse erythroid cells biological replicate 2; Capture-C, interacting promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_int_C57-2


title: S394_11_GF_WT_532_Hip

value: WT


title: Mouse erythroid cells biological replicate 1; Capture-C, interacting promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_int_C57-1


title: Control 7d rep 1

description: Sample 40

tag: treatment


title: S394_10_GF_WT_530_Hip


title: FACS sorted NC cells 12 hpf

description:
aggregated.arch.counts.matrix.csv
Sample 1

value: 12 hpf


title: S394_09_GF_WT_529_Hip


title: GW0742 3d rep 2

description: Sample 38

tag: treatment duration

value: 3 days


title: GW0742 3d rep 1

description: Sample 37

tag: cell line


title: GW0742 2d rep 3

description: Sample 36

value: 2 days


title: GW0742 2d rep 1

description: Sample 34


title: GW0742 2d rep 2

description: Sample 35


title: S394_05_SPF_FAD_2140_Hip

value: SPF


title: S394_06_SPF_FAD_2142_Hip


title: S394_04_SPF4_WT_Hip


title: wild type, replicate 4

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description: Gene expression data from bone marrow cells, wild type

hyb_protocol: Hybridization was performed according to standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G Plus Affymetrix scanner

data_processing: The data were normalized and background corrected using the RMA function in R/Bioconductor

label: biotin

source_name: bone marrow, wild-type

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies)

tag: background

value: Bone marrow

tag: condition

value: wild type


title: GW0742 3d rep 3

description: Sample 39


title: wild type, replicate 3


title: GW0742 1d rep 3

description: Sample 33

value: 1 day


title: wild type, replicate 2


title: S394_08_SPF_FAD_2153_Hip

value: microglia

value: Hippocampus

tag: strain background


title: S394_07_SPF_FAD_2152_Hip

value: 16 weeks

tag: microbiota


title: GW0742 1d rep 2

description: Sample 32


title: S394_03_SPF3_WT_Hip


title: LKO (L4-249)

city: Fukuoka

first: Shigeki

last: Furuya

address: 6-10-1, Hakozaki, Higashi-ku

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (Whole Mouse Genome Microarray 4x44K v2 ; Agilent Technologies) according to the manufacturer's instructions.

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

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

source_name: liver

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

growth_protocol: Mice were maintained in a 12-h light/dark cycle with unlimited access to water and laboratory chow containing 20% casein.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Livers of LKO and littermate Floxed mice (male, 30 weeks old, n = 6, each genotype) were disected after deep anesthesia.

value: liver

tag: genotype/variation

value: knockout


title: LKO (L5-258)


title: S394_02_SPF2_WT_Hip


title: wild type, replicate 1


title: GW0742 1d rep 1

description: Sample 31


title: LKO (L3-238)


title: LKO (L6-266)


title: LKO (L1-231)


title: GSK0660 rep 3

description: Sample 30

value: 28 days


title: mutant, replicate 3

description: Gene expression data from bone marrow cells, transgenic Plgf

source_name: bone marrow, mutant

value: transgenic Plgf


title: LKO (L2-234)


title: Floxed (F6-265)

value: control


title: mutant, replicate 1


title: S394_34_GFA_WT_525_Ctx

source_name: cortex

value: cortex

value: GF (+Acetate)


title: mutant, replicate 4


title: S394_33_GFA_WT_524_Ctx

value: WT


title: Floxed (F5-257)


title: mutant, replicate 2


title: Resorted CD244+HSC from 7-days culture #4

city: Kumamoto

first: Kenichi

last: Miharada

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

description: Gene expression data from CD244+ CD48- c-Kit+ Sca-I+ Lineage- cells re-sorted after 7 days culture

hyb_protocol: 3.7 µg of fragmented and labeled ds cDNA were hybridized to Affymetrix Mouse Genome 430 PM Array Plates using an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v4.3.3

scan_protocol: The fluorescent signals were measured with an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v4.3.3

data_processing: Gene level summarized probe set signals in log2 scale were calculated from Affymetrix CEL files by using the RMA algorithm as implemented in the Affymetrix GeneChip Expression Console v1.4 Software

source_name: Resorted CD244+CD48-KSL cells from in vitro culture

label_protocol: 300 pg of total RNA was used for reverse transcription to synthesize single-stranded (ss) cDNA with a T7 promoter sequence at the 5' end. Next a 3’ adaptor was added and the ss cDNA was converted to double-stranded cDNA, which acted as a template for a pre- in vitro transcription (IVT) amplification by a 12 cycle PCR. Afterwards antisense RNA (complimentary RNA or cRNA) was synthesized and linearly amplified by an in vitro transcription (IVT) of the double-stranded cDNA template. 20 µg of cRNA was purified and reverse transcribed into double-stranded (ds) cDNA, whereat unnatural dUTP residues were incorporated at a fixed ratio relative to dTTP. Purified ds cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin (Affymetrix GeneChip Pico Reagent Kit User Guide)

growth_protocol: CD244-CD48-KSL cells were sorted from bone marrow of 10 weeks old mice. A part of the cells were then cultured in Stemspan SFEM medium (STEMCELL Technologies) supplemented with 100 ng/ml of murine stem cell factor (mSCF) and 100 ng/ml of human thrombopoietin (hTPO)  for 7 days.

extract_protocol: Total RNA was isolated from the sorted cells using RNeasy® Micro Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: After 7-days culture, CD244- or CD244+ fractions of CD48-KSL cells were re-sorted. Other cohorts of mice were injected with PBS or phenylhydrazine, or phlebotomized, and 24 hours later CD150+CD48-KSL cells were sorted.

tag: group

value: Resorted CD244+HSC

value: Resorted CD244+CD48-KSL cells

value: male

value: 10 weeks


title: Floxed (F4-250)


title: Resorted CD244+HSC from 7-days culture #3


title: GSK0660 rep 2

description: Sample 29

value: PSC-derived cardiomyocyte


title: Floxed (F3-239)


title: LCFA + Rosiglitazone rep 3

description: Sample 27

value: LCFA + Rosiglitazone


title: Resorted CD244-HSC from 7-days culture #4

description: Gene expression data from CD244- CD48- c-Kit+ Sca-I+ Lineage- cells re-sorted after 7 days culture

source_name: Resorted CD244-CD48-KSL cells from in vitro culture

value: Resorted CD244-HSC

value: Resorted CD244-CD48-KSL cells


title: S394_01_SPF1_WT_Hip

source_name: Hippocampus

value: microglia

value: Hippocampus

value: 16 weeks

value: SPF


title: Resorted CD244+HSC from 7-days culture #1


title: LCFA + Rosiglitazone rep 2

description: Sample 26

value: 28 days


title: S394_31_GFA_WT_518_Ctx


title: DCIScom_pCDHHotair1

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

description: DCIS.COM cells transduced with HOTAIR vector

data_processing:
The short-sequenced reads were mapped to the human reference genome (hg19) by the splice junction aligner Rsubread package.
We employed several R/Bioconductor packages to accurately calculate the gene expression abundance at the whole-genome level using the aligned records (BAM files) and to identify differentially expressed genes between cells stably transduced with HOTAIR and empty vector. Briefly, the number of reads mapped to each gene based on the UCSC.hg19.KnownGene database were counted, reported and annotated using the featureCounts and org.Hs.eg.db packages.
To identify differentially expressed genes (log2 fold change [FC] > ±1.5, False Discovery Rate [FDR] <0.05) between the empty vector and HOTAIR overexpressing counterparts, we utilized the edgeR Bioconductor package.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: The processed data file contains the normalized log2 based count per million values.

source_name: MCF10 DCIS.COM cell line

growth_protocol: MCF10A cell line was obtained from the American Type Culture Collection (#CRL-10318; ATCC, VA, USA) and validated by DNA fingerprinting. MCF10A cells were cultured in Dulbecco’s Modified Eagle Medium F-12 (DMEM/F-12, Sigma-Aldrich) supplemented with 5% horse serum, 20 ng/mL epidermal growth factor (Sigma-Aldrich), 100 µg/mL hydrocortisone (Sigma-Aldrich), 10 µg/mL insulin (Sigma-Aldrich), 100 ng/mL cholera toxin (Sigma-Aldrich) and 100 U/ml penicillin - 100 μg/ml streptomycin (Sigma-Aldrich). MCF10 DCIS.COM (hereafter DCIS.COM) cells were a kind gift from Dr. Daniel Medina [30] and were maintained in DMEM/F-12 supplemented with 5% horse serum. Cell lines were maintained to 37°C with 5% CO2.

extract_protocol:
MCF10A and DCIS.COM stably transduced cells were used for RNA isolation from subconfluent plates using the RNeasy kit (Qiagen, CA, USA). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
RNA-seq library construction was perfomed using the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) according to the manufacturer's protocol.
We performed 76 nt paired-end sequencing using an Illumina HiSeq2000 platform and ~20 million reads per sample were obtained.

treatment_protocol: Normal breast epithelial cell lines MCF10A and DCIS (ductal carcinoma in situ) cell line DCIS.COM were stably transduced with pCDH-HOTAIR or pCDH-empty vector (as control)  and selected with 10µg/ml puromycin.

value: MCF10 DCIS.COM

value: ductal carcinoma in situ

value: HOTAIR vector


title: DCIScom_pCDHHotair2


title: Resorted CD244-HSC from 7-days culture #3


title: LCFA + Rosiglitazone rep 1

description: Sample 25


title: DCIScom_pCDHempty2

description: DCIS.COM cells transduced with empty vector

value: empty vector


title: Floxed (F1-232)

value: liver

value: control


title: GSK0660 rep 1

description: Sample 28


title: Floxed (F2-233)


title: S394_29_GF_WT_530_Ctx

value: cortex

value: WT

value: GF


title: Rosiglitazone rep 3

description: Sample 24

value: PSC-derived cardiomyocyte

value: Rosiglitazone


title: DCIScom_pCDHempty1


title: Resorted CD244-HSC from 7-days culture #1

value: Resorted CD244-HSC

value: Resorted CD244-CD48-KSL cells

value: male

value: 10 weeks


title: Resorted CD244-HSC from 7-days culture #2


title: S394_28_GF_WT_529_Ctx

value: microglia

value: 16 weeks


title: S394_32_GFA_WT_523_Ctx

value: GF (+Acetate)


title: MCF10A_pCDHHotair2

description: MCF10A cells transduced with HOTAIR vector

source_name: MCF10A cell line

value: normal breast epithelial


title: S394_27_GF_WT_528_Ctx


title: Rosiglitazone rep 1

description: Sample 22

value: 28 days


title: S394_26_SPF4_WT_Ctx

value: SPF


title: Freshly isolated HSC #4

description: Gene expression data from CD244- CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse

source_name: CD244-CD48-KSL cells from bone marrow of 10 weeks old mouse

value: Freshly isolated HSC

value: CD244-CD48-KSL cells


title: Freshly isolated HSC #3


title: S394_30_GF_WT_532_Ctx

value: cortex


title: LCFA + WY14643 rep 3

description: Sample 21

value: LCFA + WY14643


title: MCF10A_pCDHHotair1

value: HOTAIR vector


title: S394_25_SPF3_WT_Ctx

value: WT


title: MCF10A_pCDHempty2

description: MCF10A cells transduced with empty vector

value: empty vector


title: LCFA + WY14643 rep 2

description: Sample 20

value: PSC-derived cardiomyocyte


title: MCF10A_pCDHempty1


title: S394_24_SPF2_WT_Ctx


title: Freshly isolated HSC #2


title: HSC from phlebotomized mouse #4

description: Gene expression data from CD150+ CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse, 24 hours after phlebotomy

source_name: CD150+CD48-KSL cells from bone marrow of 10 weeks old mouse

value: phlebotomized mouse

value: CD150+CD48-KSL cells


title: S394_23_SPF1_WT_Ctx


title: Rosiglitazone rep 2

description: Sample 23

source_name: cardiomyocyte

value: Rosiglitazone


title: WY14643 rep 3

description: Sample 18


title: Freshly isolated HSC #1

value: male

value: 10 weeks


title: LCFA + WY14643 rep 1

description: Sample 19


title: GF_8w_F_5

source_name: whole brain

value: microglia

value: whole brain

value: 6-12 weeks

value: GF


title: RNA seq sample 22_PVpleurodont_mesenchyme_Sca1

city: University of Helsinki

first: Nicolas

last: Di-Poi

address: Viikinkaari 1

department: Institute of Biotechnology, Helsinki Institute of Life Sciences

country: Finland

institute: University of Helsinki

data_processing:
Quality trimming and adapter sequence removal of reads were done using the Trimmomatic tool, and the SortMeRNA pipeline was used for ribosomal RNA (rRNA) filtering.
Sequence alignment to the Pogona vitticeps genome and generation of count data using the STAR software
Filtering and TMM normalization of count data
Genome_build: Pogona vitticeps genome
Supplementary_files_format_and_content: Excel file including mean normalized count CPM values

organism: Pogona vitticeps

extract_protocol:
Laser capture microdissection of epithelial and mesenchymal tissues using a Zeiss PALM Microbeam device equipped with a Zeiss AxioCam IC camera and PALM Robo software
Libraries were produced using the Nugen Ovation SoLo kit

value: Mesenchyme from dental tissues

value: Hatchling

value: Scaleless


title: RNA seq sample 24_PVpleurodont_mesenchyme_Sca3


title: WY14643 rep 2

description: Sample 17

value: 28 days


title: WY14643 rep 1

description: Sample 16


title: RNA seq sample 21_PVpleurodont_epithelium_Sca3

value: Epithelium from dental tissues


title: GF_8w_F_4

value: WT


title: Resorted CD244+HSC from 7-days culture #2

value: Resorted CD244+HSC

value: Resorted CD244+CD48-KSL cells


title: LCFA + GW0742 rep 4

description: Sample 15

value: PSC-derived cardiomyocyte

value: LCFA + GW0742


title: GF_8w_F_3


title: RNA seq sample 20_PVpleurodont_epithelium_Sca2


title: LCFA + GW0742 rep 3

description: Sample 14


title: RNA seq sample 19_PVpleurodont_epithelium_Sca1


title: RNA seq sample 23_PVpleurodont_mesenchyme_Sca2


title: LCFA + GW0742 rep 2

description: Sample 13


title: RNA seq sample 18_PVacrodont_mesenchyme_Sca3


title: SPF_8w_F_4

value: SPF


title: HSC from phlebotomized mouse #2

value: phlebotomized mouse

value: CD150+CD48-KSL cells

value: male


title: HSC from phlebotomized mouse #3

value: 10 weeks


title: HSC from phenylhydrazine injected mouse #4

description: Gene expression data from CD150+ CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse, 24 hours after 60 mg/kg phenylhydrazine injection

value: phenylhydrazine injected mouse


title: RNA seq sample 17_PVacrodont_mesenchyme_Sca2


title: LCFA + GW0742 rep 1

description: Sample 12


title: HSC from phenylhydrazine injected mouse #3


title: HSC from phenylhydrazine injected mouse #2


title: HSC from phlebotomized mouse #1


title: RNA seq sample 16_PVacrodont_mesenchyme_Sca1


title: LCFA rep 4

description: Sample 11

value: LCFA


title: HSC from phenylhydrazine injected mouse #1


title: GF_8w_F_2

value: microglia

value: whole brain

value: 6-12 weeks

value: GF


title: HSC from steady state mouse #3

description: Gene expression data from CD150+ CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse, 24 hours after PBS injection

value: steady state mouse


title: SPF_8w_F_3

value: WT


title: GF_8w_F_1


title: RNA seq sample 14_PVacrodont_epithelium_Sca2

value: Epithelium from dental tissues

value: Hatchling

value: Scaleless


title: SPF_8w_F_1


title: LCFA rep 3

description: Sample 10

value: PSC-derived cardiomyocyte

value: 28 days


title: ChIP-seq_Sld2_IP_D_strain-40

city: Cambridge

first: Fiona

last: Jenkinson

address: Tennis court road

department: Biochemistry

institute: University of Cambridge

data_processing:
Sequence reads were mapped using Bowtie2 (version 2.2.6).
Repli-Seq - Unique reads mapping to a single genomic location were summed in 1 kb bins, using Samtools (version 1.7.2) and Bedtools (version 2.26.0).
ChIP-Seq - IP samples and correspoding input BAM files were compared using bamCompare (version 3.0.2). To  compare the BAM files, the genome is partitioned into bins of equal size, then  the number of reads found in each bin is counted per file, and finally the log2 ratio is reported. The IP and input are normalised for sequencing depth.
Genome_build: sacCer3
Supplementary_files_format_and_content: Repli-Seq - csv files containing number of unique reads in 1 kb bins normalised to G1 controls.
Supplementary_files_format_and_content: ChIP-Seq - bigWig files containing containing the bin location and the log2 ratio of the IP over input (normalised to sequencing depth)

organism: Saccharomyces cerevisiae

source_name: S-phase yeast cells - 40 min after G1 release

growth_protocol: Mid log phase yeast culture grown in standard media (YPAD ) in synchronous progression from G1 phase

extract_protocol:
For Repli-seq, DNA was purified by phenol chloroform extraction. For CHIP DNA was extracted using beadbeating, IP, SDS elution and purified with CHIP clean concentrator kit (Zymo).
Library preparation was carried out according to Illumina TruSeq Nano instructions for Repli-seq. For CHIP-seq: Sequencing libraries were prepared according to instructions of Illumina Truseq-Nano except: size selection was adjusted for 200bp fragments; adaptors were used at 1:100 dilution and 14-16 cycles of amplification were performed.

treatment_protocol: Yeast culture at 1x10^7 cells/ml were arrested and maintained in G1 with 5ug/ml alpha factor, upon arrest of >90% of cells 1mM IAA was added with a 30 minute temperature shift to 37 degrees C to induce degradation of cdc55-aid and pph3-aid, cells were then washed and released synchronously into fresh YPAD medium containing 1mM IAA. 5ml samples were taken and mixed with Sodium Azide/EDTA for Repli-seq. 200ml samples were taken for CHIP-seq, fixing with 1% formaldehyde for 25mins (Mcm) or 1.5mM EGS for 10mins followed by 1% Formaldehyde for 10 mins (Sld2). Crosslinking was quenched in 125mM Glycine.

value: swe1delta pph3-AID cdc55-AID sld3-r-13myc

value: MATa swe1delta::TRP1 cse4delta::NatMX leu2::CSE4-HA6::LEU2 CDC55-AID::KanMx PPH3-AID::HphMx his3::PGPD1-osTir1::HIS3 sld3-R(2A)-13myc::KanMx Sld2-6HA::URA3

tag: antibody


title: LCFA rep 1

description: Sample 8


title: RNA seq sample 13_PVacrodont_epithelium_Sca1

tag: tissue


title: HSC from steady state mouse #2

value: CD150+CD48-KSL cells

value: male


title: LCFA rep 2

description: Sample 9


title: Young HSC cultured with TCDCA #4

description: Gene expression data from re-sorted CD48- c-Kit+ Sca-I+ Lineage- cells after 14-days culture with TCDCA

hyb_protocol: 3.0 µg of fragmented and labeled ds cDNA were hybridized to Affymetrix Mouse Genome 430 PM Array Plates using an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v4.2

scan_protocol: The fluorescent signals were measured with an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v4.2

source_name: Resorted CD48-KSL cells from in vitro culture with TCDCA

label_protocol: Between 1 and 3 ng of total RNA were reverse transcribed into double-stranded cDNA in a two-step process, introducing a SPIA tag sequence. Bead purified cDNA was amplified by a SPIA amplification reaction followed by an additional bead purification. 3,0 µg of SPIA cDNA was fragmented and terminally biotin-labeled (Nugen Ovation Pico WTA System V2 User Guide and Nugen Encore Biotin Labeling Module User Guide)

growth_protocol: CD48-KSL cells were sorted from bone marrow of 10 weeks old or 18 months old C57BL/6 SJL mice. A part of young HSCs were then cultured in Stemspan SFEM medium (STEMCELL Technologies) supplemented with 100 ng/ml of murine stem cell factor (mSCF) and 100 ng/ml of human thrombopoietin (hTPO) with or without 100 μM of tauroursodeoxycholic acid (TUDCA) or 100 μM of tauroursodeoxycholic acid (TUDCA).

treatment_protocol: After 14-days culture, CD48-KSL fraction was re-sorted.

value: Resorted CD48-KSL cells

value: cultured with TCDCA

value: 10 weeks


title: ChIP-seq_Sld2_IP_D_strain-25

source_name: S-phase yeast cells - 25 min after G1 release

tag: genotype


title: ChIP-seq_Sld2_IP_D_strain-G1

source_name: Synchronised G1 phase yeast cells


title: HSC from steady state mouse #1


title: RNA seq sample 12_PVpleurodont_mesenchyme_WT3

value: Mesenchyme from dental tissues

value: Wild-type


title: HSC from steady state mouse #4


title: GW0742 rep 3

description: Sample 6


title: RNA seq sample 15_PVacrodont_epithelium_Sca3


title: GW0742 rep 4

description: Sample 7


title: ChIP-seq_Sld2_input_D_strain-25


title: RNA seq sample 11_PVpleurodont_mesenchyme_WT2


title: GW0742 rep 2

description: Sample 5


title: RNA seq sample 10_PVpleurodont_mesenchyme_WT1


title: GW0742 rep 1

description: Sample 4


title: ChIP-seq_Sld2_IP_A_strain-40

value: swe1delta cdc55-AID sld3-13myc

value: MATa swe1delta::TRP1 cse4delta::NatMX leu2::CSE4-HA6::LEU2 CDC55-AID::KanMx  his3::PGPD1-osTir1::HIS3 sld3-13myc::KanMx Sld2-6HA::URA3


title: Young HSC cultured with TCDCA #2


title: Young HSC cultured with TUDCA #5

description: Gene expression data from re-sorted CD48- c-Kit+ Sca-I+ Lineage- cells after 14-days culture with TUDCA

source_name: Resorted CD48-KSL cells from in vitro culture with TUDCA

value: cultured with TUDCA


title: RNA seq sample 9_PVpleurodont_epithelium_WT3

value: Epithelium from dental tissues


title: Control rep 3

description: Sample 3

value: Control


title: ChIP-seq_Sld2_input_D_strain-G1


title: Young HSC cultured with TCDCA #1


title: RNA seq sample 8_PVpleurodont_epithelium_WT2

value: Hatchling


title: ChIP-seq_Sld2_input_D_strain-40


title: Control rep 2

description: Sample 2

value: PSC-derived cardiomyocyte


title: RNA seq sample 7_PVpleurodont_epithelium_WT1


title: Control rep 1

description: Sample 1

value: 28 days


title: Young HSC cultured with TUDCA #4


title: RNA seq sample 6_PVacrodont_mesenchyme_WT3


title: ChIP-seq_Sld2_IP_A_strain-G1


title: ChIP-seq_Sld2_input_A_strain-40


title: Young HSC cultured with TCDCA #3


title: Young HSC cultured with TUDCA #3


title: RNA seq sample 5_PVacrodont_mesenchyme_WT2


title: ChIP-seq_Sld2_input_A_strain-25


title: RNA seq sample 4_PVacrodont_mesenchyme_WT1


title: ChIP-seq_Sld2_input_A_strain-G1


title: ChIP-seq_Sld2_IP_A_strain-25


title: THP-1 Cells nLDL-treated 3

city: Nashville

first: Ryan

last: Allen

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
Trimmed to remove adapter sequences with Cutadaptv1.16
Aligned to hg19 using STAR v2.5.3a, with GENCODE humanv19 gene annotations
Quality control on raw and adaptor-trimmed reads performed using FastQC
featureCounts v1.15.2 used to count the number of mapped reads to each gene
Genome_build: hg19
Supplementary_files_format_and_content: count file contains raw counts /gene

source_name: PMA-stimulated THP-1 cells

growth_protocol: Cells were differentiated in the presence of PMA (5 ng/mL) for 48h, washed twice with PBS to remove non-adherent cells and given fresh media without PMA for 24h prior to treatment.

extract_protocol:
Media was removed and total RNA was isolated using a commerically available kit (Norgen).
Libraries were constructed using the Ovation Human FFPE RNA-Seq Multipleex System (NuGen).

treatment_protocol: Differentiated cells were given fresh media (RPMI1640 +10% serum + antibiotics) spiked with or without 0.5 mg/mL native LDL for 24h.

value: THP-1 macrophage

value: nLDL (Case)


title: RNA seq sample 3_PVacrodont_epithelium_WT3


title: THP-1 Cells untreated 3


title: Young HSC cultured with TUDCA #2


title: RNA seq sample 2_PVacrodont_epithelium_WT2


title: RNA seq sample 1_PVacrodont_epithelium_WT1


title: THP-1 Cells untreated 2


title: THP-1 Cells nLDL-treated 1


title: Tumor_PBS

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

description: Control

data_processing:
processed with 10X standardard cellranger (3.1.0) pipeline reference (cellranger-mm10-3.0.0) using STAR aligner (version 2.6)
Genome_build: cellranger-mm10-3.0.0
Supplementary_files_format_and_content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: tumor

extract_protocol:
Cells were prepared according to 10x Genomics® Single Cell Protocols Cell Preparation Guide, followed by MACS Dead Cell Removal Kit 130-090-101 and RBC removal
Single-cell transcritpome caputred by 10X 3' Reagent Kiits (v3)
After running on 10X Chromium Single Cell Controller, gel beads-in-emulsion (GEMs) were generated. The barcoded and full-length cDNAs were produced after incubation of the GEMs and amplified via PCR.
Library was qualified by Agilent Bioanalyzer 2100 and quantified by real-time PCR on QuantStudio3. Sequenced was done with Illumina NextSeq 550 System using High Output Kit v2.5 (50,000 reads per cell).

value: Balb/c

tag: organ

value: subcutaneous CT26 tumor

tag: cells

value: Cancer and Stromal/vascular


title: Young HSC cultured #5

description: Gene expression data from re-sorted CD48- c-Kit+ Sca-I+ Lineage- cells after 14-days culture

source_name: Resorted CD48-KSL cells from in vitro culture

value: Resorted CD48-KSL cells

value: cultured

tag: gender

value: male

tag: age


title: THP-1 Cells untreated 1

tag: cell type


title: LTC_127_rep2

city: Boston

first: Soo Mi

last: Lee

state: MA

address: 3 BLACKFAN CIRCLE, CLS 417

department: Pathology

institute: BIDMC/Harvard Medical School

description: processed data file: comparison_2.xlsx

data_processing:
Single-end reads were mapped to the human genome (Ensembl GRCh37) using Bowtie2 v2.2.9. The abundance of gene expression was estimated using RSEM v1.3.0 and the differential expression analysis was performed using edgeR v3.12.1.
Paired-end reads were mapped to the human genome (Ensembl GRCh38) using HISAT2 v2. The abundance of gene expression was estimated using StringTie v1.3.4 and edgeR v3.30.3, and the differential expression analysis was performed using edgeR v3.30.3.
Genome_build: GRCh37;GRCh38
Supplementary_files_format_and_content: excel,expression profiles

source_name: LTC cells transfected with miR-127 mimic

growth_protocol: LTC and TIVE cell lines were cultured in Medium 199 (Sigma-Aldrich) supplemented with 15% FBS, 200 mM L-glutamine (Gibco), 1% penicillin-streptomycin (Gibco) and 30 mg endothelial cell growth supplement from bovine neural tissue (ECGS) (Sigma-Aldrich).

extract_protocol:
Total RNA was extracted using mirVana miRNA isolation Kit following the manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.
RNA libraries were prepared according to the Illumina's TruSeq stranded mRNA sample preparation protocol or Illumina's TruSeq small RNA sample preparation protocol (Illumina, San Diego, CA, USA).

tag: tissue source

value: Human umbilical cord

tag: cell type source

value: Human umbilical vein endothelial cells

value: Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC)

tag: treatment

value: Transfected with 30 nM miR-127 mimic for 3 days

tag: library construction method

value: Illumina TruSeq stranded mRNA sample preparation

tag: reference assembly


title: Motor neurons - Unaffected parent clone 3 - tRNA

city: Cleveland

first: Ashleigh

last: Schaffer

state: OH

address: 2109 Adelbert Road

department: Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics

institute: Case Western Reserve University

description: Mature d28 motor neurons differentiated from Unaffected parent, iPSC clone 3

data_processing:
Reads were first processed to remove 5′ adapter sequences using cutadapt --cut 2 then cutadapt -g TCCAACTGGATACTGGN -e 0.2 followed by cutadapt –a CCAGTATCCAGTTGGAATT -e 0.2 to remove 3′ CCA and adapter sequences.
Custom human or mouse tRNA references were generated by collapsing identical tRNA sequences from gtRNAdb Release 18 hg38 or mm10 high-confidence mature tRNA fasta files. Mapping of human or mouse reads with the corresponding reference was done with bowtie2 using the parameters: --quiet --min-score G,1,8 --local -D 20 -R 3 -N 1 -L 10 -i S,1,0.5.
Isodecoder-level read count tables for further analyses were produced by counting reads with MAPQ > 10 over reference tRNAs using the Rsubread package’s featureCounts function in R.
Anticodon-level read count tables were then created by summing reads from all isodecoders with the same anticodon.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited count files using custom gtRNAdb release 18 hg38 annotations, per isodecoder or aggregated per anticodon
Supplementary_files_format_and_content: Comma separated value matrix of tRNA isodecoder counts by sample

source_name: iPSC-derived motor neurons

growth_protocol: Primary fibroblast cell lines were established from skin biopsies of affected children and an unaffected parent according to standard methods. Reprogramming of patient fibroblasts into induced pluripotent stem cells (iPSCs) was performed using the Epi5 Episomal iPSC Reprogramming Kit (ThermoFisher) with the following modifications. Electroporated fibroblasts were plated on Matrigel membrane matrix (Fisher). Reprogramming vectors were prepared in house and the medium was changed to StemFlex (ThermoFisher) at day 15. iPSC clones were selected for expansion and plated on vitronectin-coated plates. Motor neurons were differentiated from patient-derived iPSCs using a previously published protocol (Markmiller et a., Cell, 2018)

extract_protocol:
TRIzol
3-5 ug of isolated total RNA were used to construct tRNA-Seq libraries as described in Pinkard et al., Nature Communications, 2020

tag: pch10 disease status

value: Unaffected


title: Motor neurons - Unaffected parent clone 2 - tRNA

description: Mature d28 motor neurons differentiated from Unaffected parent, iPSC clone 2


title: Tumor_FusOn


title: LTC_127_rep1

description: processed data file: comparison_2.xlsx


title: THP-1 Cells nLDL-treated 2


title: Motor neurons - Affected child clone 2 - tRNA

description: Mature d28 motor neurons differentiated from Affected patient, iPSC clone 2

value: Affected


title: Young HSC cultured with TUDCA #1

value: cultured with TUDCA

tag: strain

value: 10 weeks


title: LTC_NC_rep2

description: processed data file: comparison_2.xlsx

source_name: LTC cells transfected with negative control (NC) mimic

value: Transfected with 30 nM NC mimic for 3 days


title: Young HSC cultured #4


title: Young HSC cultured #3


title: Motor neurons - Affected child clone 1 - tRNA

description: Mature d28 motor neurons differentiated from Affected patient, iPSC clone 1


title: #1649_MRS

city: Kunitachi

first: Eiji

last: Ishikawa

state: Tokyo

address: Izumi 5-11

institute: Yakult Central Institute

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Custom Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1200_Jun14) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bifidobacterium bifidum

source_name: #1649 cultured in MRS medium

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp WT Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: WT and three non-adahesive mutants (#1476, #1543, and #1649) growing exponentially in MRS or m-ILS medium were sampled at 3 hours after 5%(v/v) inoculation.

extract_protocol: A volume  of bacterial culture in exponential growth phase was mixed with twice the volume of RNA Protect Bacteria Reagent (Qiagen) and centrifuged (20,000 g, 5 min, 4°C). The bacterial pellet was suspended in 1.0 mL of Tris–EDTA buffer (Tris, 50 mM Tris,; 10 mM EDTA, 10 mM; (pH 8.0), that contained 10% (w/v) of sucrose.; thereafter, Llysozyme (50 mg/mL , 50 μL;) (Sigma-Aldrich) was added to break the cell walls.  Tand the suspension was incubated for 10 min at 37°C. The enzyme-treated suspensionsand were centrifuged (20,000 g, 5 min, 4°C). RNA was extracted from the precipitated spheroplasts with RiboPure-Bacteria (Thermo Fisher Scientific).

treatment_protocol: not applicable

tag: genotype/variation

value: non-adahesive mutant

tag: adherence

value: negative

tag: culture medium

value: MRS medium

tag: growth phase

value: exponential growth phase


title: #1649_m-ILS

source_name: #1649 cultured in m-ILS medium

value: m-ILS medium


title: Young HSC cultured #2

value: Resorted CD48-KSL cells

tag: group

value: cultured


title: Young HSC cultured #1

value: male


title: Old HSC #5

description: Gene expression data from CD48- c-Kit+ Sca-I+ Lineage- cells of 10 months old male mouse

source_name: CD48-KSL cells from bone marrow of 18 months old mice

value: CD48-KSL cells

value: old HSC

value: 18 months


title: LTC_NC_rep1

description: processed data file: comparison_2.xlsx

value: Human umbilical cord

value: Human umbilical vein endothelial cells

value: Kaposi's sarcoma-associated herpesvirus (KSHV)-infected human endothelial cells (LTC)

value: Illumina TruSeq stranded mRNA sample preparation


title: #1543_MRS

source_name: #1543 cultured in MRS medium


title: sponge-1

city: Shanghai

first: Sun

last: Hai-Xiang

address: 180 Fenglin Road Shanghai China

institute: Zhongshan Hospital

description: all.rpkm.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HCC cell line

growth_protocol: The cell lines were treated with DMEM with 10% FBS

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The tissues were lysate in Trizol directly and do total RNA extraction

tag: tissue

value: HCC

value: knockdown


title: NL_2

city: San Francisco

first: Tien

last: Peng

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

description: Adult human lung cells

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1.1 using default parameteres.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: Fresh sorted human lung epithelial and mesenchymal cells

extract_protocol:
Human lung fragments were digested with a cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) . The cell suspension then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 °C and washed with FACS buffer. The following antibodies were used at 1:200 for staining: anti-CD45, anti-CD11b, anti-CD31, and anti-Epcam. DRAQ7 was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DRAQ7 fluorescence. Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument, using Single cell 3' v2 chemistry kit.

tag: developmental stage

value: adult

value: lung


title: NL_3

description: Adult human lung cells


title: Old HSC #4

tag: gender


title: 238-3

description: all.rpkm.txt

value: control


title: sponge-2

description: all.rpkm.txt


title: sponge-3

description: all.rpkm.txt


title: NL_1

description: Adult human lung cells


title: 30th Day_scRNA-seq

city: shanghai

first: Renkai

last: Wang

address: 168 Changhai Road,

institute: changhai hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
MT% < 40%;
Cell Gene Number < 5000;
Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV file contain counts for each sample

source_name: fracture tissues

growth_protocol: No growth are needed

extract_protocol:
To obtain bone and bone marrow cells for scRNA-seq.Bone fracture tissues (including bones and bone marrow 0.5cm from the fracture end) were dissected from mice and placed in DMEM/F12(Gibco), and cut bone fracture tissues into small fragments and digested them with 0.1mg/ml collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube, and erythrocytes lysed in ACK-lysis buffer.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

treatment_protocol: Obtained the bone marrow and bone tissue of the patient through the ethics committee review, and extracting bone fracture end tissue at different time ( 0day,30 days),and extracting single cells by digestion

value: bone fracture tissues (bone and bone marrow)

tag: time

value: 30 days


title: 238-2

description: all.rpkm.txt


title: Old HSC #3

tag: cell type

tag: age


title: #1476_MRS

source_name: #1476 cultured in MRS medium

value: non-adahesive mutant

value: negative

value: MRS medium

value: exponential growth phase


title: 238-1

description: all.rpkm.txt


title: Old HSC #2

value: CD48-KSL cells

value: old HSC

value: male


title: #1476_m-ILS

source_name: #1476 cultured in m-ILS medium

value: m-ILS medium


title: #1543_m-ILS

source_name: #1543 cultured in m-ILS medium


title: control group_scRNA-seq

value: 0 day (control group)


title: WT Ly6Chi macrophage with IL-21 stimulation rep2

status: Public on Oct 31 2021

city: Chiba City

first: Akihiko

last: Kubota

state: Chiba

address: 1-8-1 Inohana

department: Department of Cardiovascular Medicine

institute: Graduate School of Medicine, Chiba University

data_processing:
Quality-controlled reads were mapped on mouse mm10 reference genome and UMI counts were measured using Strand NGS.
Expression data were normalized and differentially expressed genes were identified with Wald test for heart samples and likelihood ratio test for macrophages using DESeq2 package of R project (version 3.6.2).
Genome_build: mm10
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample

source_name: Ly6Chi macrophage

extract_protocol:
RNA was extracted using a ReliaPrep RNA Cell Miniprep System. 2.5 ng of total RNA was used for the construction of sequencing libraries. RNA-seq libraries were prepared using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina and UMI Second Strand Synthesis Module for QuantSeq FWD. Sequencing was performed on an Illumina NexSeq500 in a 75-base single-end mode.
RNA-seq libraries were prepared using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina and UMI Second Strand Synthesis Module for QuantSeq FWD.

treatment_protocol: We sorted Ly6Chi macrophages and Ly6Clo macrophages from the infarcted hearts of WT mice and il21 receptor deficient mice (il21r-/-) at 3 days after MI. Sorted Ly6Chi and Ly6Clo macrophages were stimulated with or without IL-21 (100ng/mL) in RPMI 1640 medium supplemented with 10% FCS, 50 µM 2-Mercaptoethanol, and 100 U/ml Penicillin-Streptomycin (Cellgro) for 24 hours.

value: harvested from infarcted heart tissue

value: Ly6Chi macrophage

value: post natal 8 week

tag: disease state

value: 3 days after myocardial infarction

tag: genotype

value: wild type

value: with IL-21 stimulation


title: WT Ly6Clo macrophage with IL-21 stimulation rep2

source_name: Ly6Clo macrophage

value: Ly6Clo macrophage

tag: treatment


title: WT Ly6Clo macrophage without IL-21 stimulation rep2

value: without IL-21 stimulation


title: Young HSC Fresh #5

description: Gene expression data from CD48- c-Kit+ Sca-I+ Lineage- cells of 10 weeks old male mouse

source_name: CD48-KSL cells from bone marrow of 10 weeks old mice

value: 10 weeks


title: WT_m-ILS

source_name: Wild Type cultured in m-ILS medium

value: positive


title: WT_MRS

source_name: Wild Type cultured in MRS medium

value: MRS medium


title: Young HSC Fresh #3

value: Young HSC Fresh


title: Old HSC #1

value: CD48-KSL cells

value: 18 months


title: Young HSC Fresh #1

value: male


title: Young HSC Fresh #4


title: WT Ly6Clo macrophage without IL-21 stimulation rep1


title: WT Ly6Clo macrophage with IL-21 stimulation rep1


title: WT Ly6Chi macrophage with IL-21 stimulation rep1


title: Young HSC Fresh #2


title: OFT tissue-WT

status: Public on Oct 30 2021

first: Yufei

last: Wu

address: Siping Campus,1239 Siping Road, Yangpu District, Shangha.

institute: School of Medicine, Tongji University

description: One RNA sample was obtained from ten wt embryos.

data_processing:
The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PITM Ion SphereTM Particles (Life Technologies) according to Ion PITM Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PITM Ion SphereTM Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies). A total of 12.9 and 12.8 million raw reads were obtained from two libraries.
The raw reads were cleaned by removing adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads, and the clean reads aligned to the rat genome (Rnor 6.0) using the MapSplice program (v2.1.8).
We applied the EBseq algorithm to identify differentially expressed genes, based on a false discovery rate (FDR) and the following criteria: i) FC>1.5 or <0.67; ii) FDR<0.05.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The Microsoft Excel Binary File with  raw gene counts for every gene and two samples
Supplementary_files_format_and_content: The Microsoft Excel Binary File with FPKM values  for every gene and two samples

source_name: cardiac outflow tract

extract_protocol:
Total RNA was extracted from cardiac OFT samples of SNX17-knockout and wild-type embryos using Trizol reagent (Invitrogen) separately. RNA quality was checked on the Agilent 2200 system (Agilent technologies, Santa Clara, CA, USA), then RNA with a RNA integrity number (RIN) > 7.8 used to construct cDNA libraries .
RNA libraries were prepared for sequencing using the Ion Total RNA-Seq Kit v2.0 (Life Technologies, 4475936) according to the manufacturer’s instructions.

value: Sprague-Dawley (SD) rats

value: Cardiac outflow tract (OFT)


title: STN_RNASeq

status: Public on Oct 29 2021

city: Ste-Anne-de-Bellevue

first: Martina

last: Stromvik

state: Quebec

address: 21,111 Lakeshore Rd

department: Department of Plant Science

institute: McGill University

data_processing:
Raw reads were trimmed and cleaned using trimmomatic with the following parameters: TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50
RNA-Seq reads were aligned to the potato DM v4.04 genome using STAR aligner.
Regions with read depth less than 10 were removed. Bases with quality less than 20 were removed.
Variant calling was performed with Freebayes.
The RNA-Seq data were de novo assembles using Trans-ABySS software.
Genome_build: DM v4.04
Supplementary_files_format_and_content: gene-level expression, Cufflinks output
Supplementary_files_format_and_content: transcript-level expression, Cufflinks output

organism: Solanum stenotomum subsp. stenotomum

source_name: Young Leaf

growth_protocol: In vitro plants.

extract_protocol:
Leaves from young plants were collected, put on dry ice, and RNA was harvested using TIANGEN RNAprep Pure Plant Kit(Polysaccharides& Polyphenolies-rich). The RNA extraction was performed by Novogene.
RNA libraries were prepared by Novogene for sequencing standard Illumina protocols.

treatment_protocol: No special treatment. The leaves of young plant material were used for the extraction of RNA.

tag: potato landraces

value: STN


title: OFT tissue-KO

description: One RNA sample was obtained from ten HO embryos


title: TBR_RNASeq

description: subsp. suberosum

organism: Solanum tuberosum

value: TBR


title: WT Ly6Chi macrophage without IL-21 stimulation rep1

value: harvested from infarcted heart tissue

value: Ly6Chi macrophage

value: post natal 8 week


title: ADG1_RNASeq

description: subsp. andigena

organism: Solanum tuberosum subsp. andigenum


title: BE2C_ATRA_12d_RARA_MWZ5969 [Lab: Look]

status: Public on Oct 25 2021

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Neuroblastoma

growth_protocol: Cells were grown in 6-well plates in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 12 days.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.

tag: chip antibody

value: RARa

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: antibody lot

tag: drug

value: ATRA

tag: treatment protocol

value: 5 uM ATRA, 12 days


title: ADG2_RNASeq

description: subsp. andigena


title: WT Ly6Chi macrophage without IL-21 stimulation rep2

tag: strain

value: 3 days after myocardial infarction

value: wild type

value: without IL-21 stimulation


title: BE2C_ATRA_12d_Input_MWZ5969 [Lab: Look]


title: AA1_dmc1_SSDS [re-analysis]

status: Public on Oct 26 2021

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description:
GSM1447325
AA1_dmc1_SSDS

data_processing:
Basecalling was performed using Illumina HCS 1.5.15.1
The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome (https://github.com/kevbrick/SSDSpipeline.git). Uniquely mapping fragments unambiguously derived from ssDNA (ssDNA type 1) and having both reads with a mapping quality score ≥ 30 were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS]  -g mm --bw 1000 --keep-dup all --slocal 5000. (https://github.com/kevbrick/callHotspotsSSDS.git) and using the matching input dlibrary as a control. DSB hotspots within regions previously blacklisted were removed and hotspot strength was calculated as described previously (Brick & Pratto et al., Meth. Enzym. 2019).
BIGWIG files were generated from ssDNA type1 data using the deeptools3.0.1 bamCoverage function and the following arguments: --binSize 150 --normalizeUsing RPKM --ignoreDuplicates
Genome_build: hg38
Supplementary_files_format_and_content: BIGWIG: Genomic coverage
Supplementary_files_format_and_content: BAM: Processed ssDNA aligned to reference genome
Supplementary_files_format_and_content: BAI: Index files for BAMs
Supplementary_files_format_and_content: BEDGRAPH: DMC1-SSDS peaks with associated strength
Supplementary_files_format_and_content: HOTSPOTS TABLE: SSDS peaks in each individual
Supplementary_files_format_and_content: HAPLOTYPES TABLE: PRDM9 genotyping information for all individuals

source_name: Human testes

extract_protocol:
Samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Sequencing libraries were prepared following the method described in (Khil et al., 2012).

tag: population

tag: Sex

value: Male

tag: sequencing technique

value: ChIP-Single Stranded DNA Sequencing (SSDS)

tag: antibody

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)


title: BE2C Ctrl RARA [Lab: Look]

growth_protocol: Cells were grown in T-75 flasks in RPMI media containing 10% FBS and 1% pen-strep. Cells were treated with DMSO or ATRA (5uM) for 12 days.

tag: cell type

tag: tissue

value: Brain

value: DMSO


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 35 [ALL35]

city: Salt Lake City

first: James

last: Gagnon

state: UT

address: 1390 Presidents Circle, Crocker Science Center Receiving

institute: University of Utah

data_processing:
library strategy: Amplicon-seq
Following the GESTALT pipeline (Mckenna Science 2016), low quality bases were removed with Trimmomatic
Paired reads were merged using FLASH
Merged reads were aligned to unedited barcode sequence using NEEDLEALL with gap open penalty 10 and gap extension penalty 0.5
Reads were required to have >85% matching bases, and match at least 90 bases of the reference
Target sites were deemed edited if there was an insertion or deletion event present within 3 bases of the predicted cut site (4 nucleotides 5' of the SpyCas9 PAM, 3 nucleotides 5' of SauCas9 PAM, 21 nucleotides 3' of LbaCas12a PAM), or if a deletion spanned the site entirely.
An edited barcode was then defined as the complete list of insertion and deletion events (i.e. ‘editing events’) within the consensus sequence
Genome_build: N/A
Supplementary_files_format_and_content: event - string of insertion and deletions within a barcode; array - index of barcode after sorting for descending abundance; count - number of reads mapped to a given barcode; proportion - proportion of total reads mapped to a given barcode within a sample

source_name: whole embryo

growth_protocol: Embryos were grown at 28.5C for 2 days

extract_protocol:
Genomic DNA was prepared using HoTSHOT lysis
Libraries were prepared using two rounds of PCR to add Illumina adapters and 8 bp dual indexes for multiplexing.

treatment_protocol: SpyCas9 editing was induced by heat shock at 37C for 30 minutes

tag: developmental stage

value: 2 dpf embryo

tag: strain background

value: TU wild type

tag: sample group

value: LbaCas12a, SauCas9, SpyCas9 edited


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 33 [ALL33]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 30 [ALL30]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 28 [ALL28]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 32 [ALL32]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 29 [ALL29]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 26 [ALL26]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 25 [ALL25]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 21 [ALL21]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 24 [ALL24]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 20 [ALL20]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 19 [ALL19]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 18 [ALL18]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 16 [ALL16]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 15 [ALL15]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 17 [ALL17]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 13 [ALL13]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 12 [ALL12]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 8 [ALL8]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 10 [ALL10]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 11 [ALL11]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 6 [ALL6]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 14 [ALL14]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 5 [ALL5]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 4 [ALL4]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 9 [ALL9]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 3 [ALL3]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 31 [ALL31]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 1 [ALL1]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 22 [ALL22]


title: SpyCas9 edited embryo 5 [Spy5]

value: SpyCas9 edited


title: SpyCas9 edited embryo 7 [Spy7]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 23 [ALL23]


title: SpyCas9 edited embryo 6 [Spy6]


title: SpyCas9 edited embryo 4 [Spy4]


title: SpyCas9 edited embryo 3 [Spy3]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 7 [ALL7]


title: SpyCas9 edited embryo 2 [Spy2]


title: SauCas9 edited embryo 8 [Sau8]

value: SauCas9 edited


title: SpyCas9 edited embryo 1 [Spy1]


title: SauCas9 edited embryo 5 [Sau5]


title: SauCas9 edited embryo 6 [Sau6]


title: SauCas9 edited embryo 7 [Sau7]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 2 [ALL2]


title: SauCas9 edited embryo 4 [Sau4]


title: SauCas9 edited embryo 3 [Sau3]


title: LbaCas12a edited embryo 7 [Lba7]

value: LbaCas12a edited


title: LbaCas12a edited embryo 8 [Lba8]


title: LbaCas12a edited embryo 6 [Lba6]


title: LbaCas12a edited embryo 3 [Lba3]


title: LbaCas12a edited embryo 5 [Lba5]


title: LbaCas12a edited embryo 2 [Lba2]


title: SauCas9 edited embryo 1 [Sau1]


title: LbaCas12a edited embryo 1 [Lba1]


title: SauCas9 edited embryo 2 [Sau2]


title: Unedited embryo 13 [Control13]

value: Unedited


title: LbaCas12a edited embryo 4 [Lba4]


title: Unedited embryo 12 [Control12]


title: Unedited embryo 11 [Control11]


title: Unedited embryo 10 [Control10]


title: Unedited embryo 9 [Control9]


title: Unedited embryo 8 [Control8]


title: Unedited embryo 5 [Control5]


title: Unedited embryo 6 [Control6]


title: Unedited embryo 4 [Control4]


title: Unedited embryo 3 [Control3]


title: Unedited embryo 2 [Control2]


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 27 [ALL27]


title: Unedited embryo 14 [Control14]


title: E2.75_embryo_male_matdel7_RNA

status: Public on Oct 24 2021

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate2_Collected_20190603_C2_RNA

data_processing:
as described in Wanigasuriya, Gouil et al. 2020 (https://doi.org/10.7554/eLife.55529)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: gene counts matrices. RRBS/WGBS: bismark coverage reports of mC and C counts (total and by allele)

source_name: E2.75 embryo

tag: mating

value: B6 SMCH/MMTV-Cre ♀ (FL/FL, +/+) X Cast ♂

value: male

tag: age

value: embryo

tag: genotype

value: matdel


title: E2.75_embryo_male_matdel2_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate1_Collected_20190513_E2_RNA

extract_protocol: as described in Wanigasuriya, Gouil et al. 2020 (https://doi.org/10.7554/eLife.55529)

value: B6 SMCH/MMTV-Cre ♀ (DEL/FL, T/+) X Cast ♂


title: E2.75_embryo_male_matdel4_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate1_Collected_20190513_H2_RNA


title: E2.75_embryo_male_wt5_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Control_Plate2_Collected_20190603_G2_RNA

value: wt


title: E2.75_embryo_male_wt4_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Control_Plate2_Collected_20190603_E2_RNA


title: E2.75_embryo_male_wt2_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Control_Plate1_Collected_20190513_D1_RNA


title: E2.75_embryo_male_matdel5_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate2_Collected_20190603_A2_RNA


title: RNASeq_H1_WT replicate 2

status: Public on Oct 22 2021

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Analysis of RNA-seq data was carried out in User-friendly Transcriptome Analysis Pipeline UTAP 27. In short, reads were trimmed using ‘cutadapt’ function.
Reads were then mapped to the mouse genome mm10 using STAR method. Followed by quantification with RefSeq annotated genes. Counting was performed using HTSeq.
Normalization of the counts was done using DESeq2. Raw P-values were adjusted for multiple testing using Benjamini and Hochberg.
Genome_build: mm10
Supplementary_files_format_and_content: csv matrix file containing raw + normalized counts per gene, and KO/WT FoldChange and p-value

source_name: mouse embryonic stem cells

growth_protocol: Cells were grown in 2i/LIF for 3-4 passages.

extract_protocol:
Total RNA was extracted from cells using Trizol (Ambion Life Technologies) and chloroform, followed by washes with isopropanol and 70% ethanol. 1 mg of extracted RNA was used as an input for mRNA isolation using PolyA beads.
For H1-TKO RNA-seq: Libraries preparation was carried out using Lexogen's SENSETM mRNA-Seq Kit V2 according to manufacturer’s instruction.
For Ubc9-depletion RNA-seq: Libraries preparation was carried out using ScriptSeq v2 RNA-seq library preparation kit according to manufacturer’s instruction.

treatment_protocol: For Ubc9 depletion, DOX was added for 72 hours.

tag: cell line

value: taken from PMID 16377562

value: mouse embryonic stem cells


title: E2.75_embryo_male_matdel8_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate2_Collected_20190603_H1_RNA


title: E2.75_embryo_male_matdel1_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate1_Collected_20190513_C2_RNA


title: RNASeq_H1_WT replicate 1


title: E2.75_embryo_male_matdel6_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate2_Collected_20190603_C1_RNA


title: RNASeq_H1-TKO replicate 1


title: E2.75_embryo_male_matdel3_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Test_Plate1_Collected_20190513_G2_RNA


title: E2.75_embryo_male_wt3_RNA

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Control_Plate1_Collected_20190513_F1_RNA


title: RNASeq_H1-TKO replicate 2


title: RNASeq_Ubc9-WT_replicate2


title: Unedited embryo 7 [Control7]


title: Unedited embryo 1 [Control1]


title: RNASeq_Ubc9-depleted_replicate2


title: RNASeq_Ubc9-depleted_replicate1