title: Pro03

extract_protocol:
Single cells were index sorted using a BD FACS Influx into 384-well hardshell plates (BioRad) that were pre-filled with 5 µL of light mineral oil (Sigma Aldrich) and 50 nL of lysis buffer [22 mM Tris-HCl pH 7.5, 16.5 mM MgCl2, 5.5 mM CaCl2, 165 mM NaCl, 1.1 % Triton X-100, 2.2 U/µL RNaseIN Plus (Promega), 0.11 mg/mL Cyclohexamide (Sigma Aldrich)]. After sorting, plates were spun down at 2000 ×g for 2 minutes and kept on wet ice until all plates were ready for further processing. No RNA purification was performed.
To generate ribosome-protected footprints, 50 nL of Micrococcal Nuclease (MNase, 10500 U/µL, New England Biolabs) was added to each well, and plates were incubated at 37 °C for 30 minutes. In order to stop digestion, 50 nL of stop mix [0.0186 U/µL Thermolabile Proteinase K (New England Biolabs), 62 mM EGTA (Sigma Aldrich), 16.5 mM EDTA (Ambion), and 697.5 mM guanidium thiocyanite (GuSCN, Sigma Aldrich)] was added to each well, and plates were incubated at 37 °C for 30 minutes then 55 °C for 10 minutes and held at 4 °C.
After ribosome footprint digestion, libraries were constructed using a one-pot small-RNA library preparation protocol that incorporated end repair, two RNA ligations, cDNA synthesis, and an indexing PCR. First, 50 nL of end-repair mix [4.1× of 10× T4 RNA Ligase Buffer (New England Biolabs), 16.4 mM MgCl2, 4.1 mM uridine triphosphate (New England Biolabs), 1.37 U/µL T4  Polynucleotide Kinase (New England Biolabs), and 0.82 U/µL RNaseIN Plus] was added to each well, and plates were incubated at 37 °C for 1 hour and held at 4 °C. Next, 264 nL of 3’ ligation brew [1× T4 RNA Ligase Buffer (New England Biolabs), 1 µM pre-adenylated 3’ adapter (OMV630 Integrated DNA Technologies), 35.5 % PEG-8000 (New England Biolabs), 0.1 % Tween-20 (Sigma Aldrich), 1 U/µL RNaseIN Plus, and 21.3 U/µL T4 RNA Ligase 2 Truncated KQ (New England Biolabs)] was added to each well and plates were incubated at 4 °C for 18 hours. The cDNA synthesis primer was then pre-annealed to the 3’ ligation products by adding 50 nL of the RT primer mix [5.2 µM RT primer (OMV572, Integrated DNA Technologies), 13.5 µM adenosine triphosphate (ATP, New England Biolabs), and 1 % Tween-20] to each well, heating to 65 °C for 1 minute, 37 °C for 2 minutes, 25 °C for 2 minutes, and holding at 4 °C. Five-prime adapters were then ligated by adding 156 nL of 5’ ligation brew [1× T4 RNA Ligase Buffer, 30.75 % PEG-8000, 0.1 % Tween-20, 0.5 µM 5’ adapter (OMV632, Integrated DNA Technologies), 1.25 U/µL T4 RNA Ligase 1 (Ambion)] and incubating at 37 °C for 2 hours and holding at 4 °C. Complementary DNA synthesis was then peformed by adding 771 nL of reverse transcription brew [1.88× 5× RT Buffer (ThermoFisher Scientific), 1.25 mM dNTPs (Promega), 0.1875 % Tween-20, 1.875 U/µL RNaseIN Plus, and 9.375 U/µL Maxima H Minus Reverse Transcriptase (ThermoFisher Scientific)] to each well, and heating at 50 °C for 1 hour, then 85 °C for 5 minutes and holding at 4 °C. Finally, single-cell libraries were indexed during PCR by first transferring 150 nL of 20 µM unique forward index primers (Integrated DNA Technologies) and 3.2 µL of PCR brew [1.5× Q5 Hot Start High-Fidelity 2× Master Mix (New England Biolabs), 0.15 % Tween-20, and 0.94 µM reverse index primer (Integrated DNA Technologies)] to each well. Plates were then incubated at 98 °C for 30 s followed by 10 cycles of 98 °C for 15 s, 65 °C 30 s, 72 °C for 30 s, and then a final incubation at 72 °C for 5 min and holding at 4 °C. Plates were then frozen at -20 °C until pooling.
After library construction the plates were pooled and purified. The contents of each plate were first collected in VBLOK200 reservoirs (Click Bio) by centrifuging at 2000 ×g for 2 min. The aqueous phase (~1.9 mL per plate) was separated from the light mineral oil by centrifugation, and concentrated to approximately 500 µL using n-butanol (Sigma Aldrich) and diethyl ether (Sigma Aldrich). Product was then cleaned up using AMPure XP beads (Beckman Coulter) that had been diluted 5× in bead binding buffer [20 % PEG-8000 (Sigma Aldrich) 2.5 M Sodium Chloride (Sigma Aldrich)]; diluted beads were added to the sample at a 2.1:1 ratio, and the final product was resuspended in 50 µL of low TE buffer [LoTET, 3 mM Tris-HCl pH 8.0 (Ambion), 0.2 mM EDTA pH 8.0 (Gibco), 0.1 % Tween-20]. Half of each of the cleaned-up library pools was then run on a 10 cm 7 % polyacrylamide gel at 200 V for ~6 h, and the ~10 base-pair region from 175-185, corresponding to an insert size of ~30-40 nt was excised. The band was then crushed and soaked overnight at 4 °C in elution buffer [5:1 LoTET:7.5 M ammonium acetate (Sigma Aldrich)]. Finally, eluate was precipitated in ethanol.
barcode: CTTGTA; 5' Adapter: rCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUr(N1:25252525)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1); 3' Adapter: /5rApp/TGGAATTCTCGGGTGCCAAGG/3ddC/


title: cHiC_LBinv

status: Public on Jun 30 2021

type: SRA

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: cHi-C, LB-inv

library_source: genomic

data_processing:
4C:  FASTQ reads were demultiplexed based on the presence of a 129 or cas SNP. For each of the two possible SNPs, we searched for the SNP and its flanking four nucleotides (text searches for 9-nucleotide sequences). For each SNP, R1 reads were allocated into new FASTQ files that were used for mapping using a 4C data processing pipeline (Krijger et al., 2020 and github.com/deLaatLab/pipe4C) with the following parameters:  normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed.
cHiC:  Raw sequence data for biological and technical replicates with the same genotype were combined and subsequently mapped and processed using HiC-Pro v.2.11.1 (Servant et al., 2015) with mm10 as a reference genome. SNPs for the 129S1_SvImJ and CAST_EiJ genomes were extracted from the Mouse Genomes Project (Keane et al., 2011) and N-masked in the reference genome. Reads in which both reads were assigned to the same allele or for which one read was assigned to one allele and for which the other was unassigned were used to generate Juicebox input files (Durand et al., 2016).
Sequenced reads were processed following the standard MC-4C protocol  and MC-4C pipeline v1.2 (Allahyar et al., 2018, https://github.com/deLaatLab/mc4c_py). Fragments were mapped to the reference genome using BWA-SW v0.7.17-r1188 (settings: -b 5 -q 2 -r 1 -z 5 -T 15) (Li and Durbin, 2010). Fragments with mapping quality (MQ) < 20 were considered unmapped. Mapped fragments were extended to the nearest DpnII or HindIII restriction site. Pairs of fragments mapping closer than 20 bp were fused and considered single fragments. PCR duplicates were removed under the premise that far-cis or -trans fragments can be directly used as unique molecular identifiers (Vermeulen et al., 2020). The region of interest (ROI) used in this study was chr1:12.840-13.185 Mb. Reads with fewer than two fragments within the ROI were discarded as uninformative for multi-way contact association analysis.
Genome_build: mm10
Supplementary_files_format_and_content: 4C:  interaction coverage file (wig files generated using pipe4C)
Supplementary_files_format_and_content: cHi-C: normalized Hi-C matrix per genotype per allele (hic files generated using Juicer)
Supplementary_files_format_and_content: MC-4C:Multi-contact interaction coverage file (hdf5 files generated using MC-4C pipeline v1.2)

molecule: genomic DNA

organism: Mus musculus

source_name: LBinv

growth_protocol: 129SvJ/castaneous female mouse embryonic stem cells (Jonkers et al., 2008; Splinter et al., 2011) were cultured at 37°C and 5% CO2 on gelatin-coated dishes in the following growth medium:  DMEM GlutaMAX (Gibco), 45% BRL-conditioned medium (11% FBS (Sigma), 1% P/S (Gibco), 1% NEAA (Gibco)), 7% FBS (Sigma), 1% P/S (Gibco), 1% NEAA (Gibco), 0.1 mM β-mercaptoethanol (Sigma-Aldrich), and 0.2% home-made LIF protein.  Medium was changed at least every other day and cells regularly tested negative for Mycoplasma infection.

extract_protocol:
4C:  4C template preparation was performed as described in (van de Werken et al., 2012), using DpnII and Csp6I as first and second cutters, respectively, with the following modifications:  omission of protease inhibitors in lysis buffer; omission of RNAse A at crosslinking removal; replacement of phenol-chloroform and ethanol purifications with magnetic bead purification (Macherey-Nagel NucleoMag PCR Beads), as described in (Krijger et al., 2020).
cHiC: Hi-C template preparation was performed as described in (Rao et al., 2014) with modifications as follows. Ten million cells per sample were harvested; two biological replicates were generated per genotype. Cells were fixed with 2% formaldehyde; fixation was quenched by glycine at final concentration of 0.2 M. Restriction enzyme XapI (ApoI, ThermoFisher ER1381) (Kolovos et al., 2018) was used for in situ digestion (400 U/10 million cells). Digested DNA ends were labeled with biotin-14–dATP (Life Technologies) in a Klenow end-filling reaction. End-repaired, ligated, and reverse-crosslinked DNA was subsequently purified using isopropanol and magnetic beads (Macherey-Nagel NucleoMag PCR Beads). Purified DNA was sheared to 300-500 bp with Covaris. After AMPure XP size selection, appropriately-sized ligation fragments marked by biotin were immobilized using MyOne Streptavidin C1 DynaBeads (Invitrogen) and ligated to SureSelectXT2 indexed adaptors. The non-amplified, immobilized and indexed Hi-C library was subsequently used as input for target-specific capture using RNA baits.
MC-4C:  MC-4C was performed generally as described in (Vermeulen et al., 2020), using DpnII and HindIII as first and second cutters, respectively.
4C:  The allele-specific 4C strategy is similar to that described as PE-4Cseq in (Holwerda et al., 2013). Briefly, 4C PCR primers were designed generally in keeping with considerations described in (van de Werken et al., 2012), with the following considerations:  primer binding sites must not contain any SNPs, and one of the primers must be positioned to allow reading of a SNP in the viewpoint fragment by Illumina sequencing, to facilitate splitting 4C reads by allele. If no SNP was present near the primary cut site, then a SNP following the “non-read” primer (P2) was used, in which case paired-end sequencing was required.
cHi-C:  We designed a custom biotinylated RNA bait library (Table S7) using Agilent SureDesign (https://earray.chem.agilent.com/suredesign/). Biotinylated 120-mer RNA baits were designed to target both ends of ApoI restriction fragments within the targeted region (mm10:chr1:10500000-15500000). 120-mers mapping more than once to the mm10 reference genome were excluded from the final library. The library included unrelated baits for a locus on Chromosome 18 (mm10:chr18:64200000-67200000).  Capture Hi-C of the targeted genomic sequences was carried out with SureSelectXT2 Target Enrichment System (Agilent G9621A) with the bait library according to manufacturer’s instructions (Agilent Technologies), with the modification of either single-round or double-round capture. For single-round capture, a pre-capture PCR amplification of the immobilized and indexed Hi-C template and a post-capture PCR amplification of the enriched library was carried out with 10 and 12 PCR amplification cycles, respectively. For double-round capture, a pre-capture PCR amplification of the Hi-C template and a post-capture PCR amplification of the single-round enriched library was carried out with 10 and 10 cycles, respectively. The total output of post-capture PCR amplification of the single-round enriched library was further captured the second time with the same bait library followed by final amplification with 12 cycles.
MC-4C:  To digest the Slco5a1 VP (5’Slc) and neighbor fragments with Cas9 in vitro, gRNAs CTATAGCGCCTTTCGATGG, TCTACACCGATTTACACCCT, and ACTAGTGCTAAGTAACCTCG were used. Primers for the final PCR step were designed to specifically amplify 129 template by forcing the 3’ end of each primer to terminate on a validated SNP and by introducing destabilizing mismatches near the 3’ end of each primer, according to guidelines for allele-specific PCR described in (Liu et al., 2012). 129 allele specific amplification was further optimized by performing annealing temperature gradient PCRs in parallel on 129/cas and cas/cas genomic DNA and selecting the optimal annealing temperature which did not produce any product from cas/cas template. For the 5’Slc VP MC-4C PCR, we used primers GGACAGCTCCAACCGAAGGCG and GAGTTGAACGCTTCGGCCTTC, where destabilizing mismatches are underlined; PCR conditions were: 98°C 20’’; 30 cycles of 98°C 10’’, 69°C 20’’, 72°C 90’’; 72°C 5’.  MC-4C libraries were size selected at 1.5–8 kb by Pippin HT and then prepared for sequencing using Oxford Nanopore Ligation Sequencing Kit LSK109.
OTHER:  4C, Hi-C, and MC-4C

tag: cell type

value: ESC

tag: strain

tag: genetic modification

value: LBinv


title: cHiC_WT

description: cHi-C, WT

source_name: WT

value: WT


title: cHiC_4C_4C_LBdel

description: cHi-C, LBdel

source_name: LBdel

value: LBdel


title: 4C_LBdel_mutC_1_129_VP_SE

description: 4C, LBdel-mutC, 129, VP 5'Slc

tag: viewpoint

tag: barcode

value: TCTTCGTCCATGGCTCTTAAA


title: 4C_LBdel_mutC_2_129_VP_SE

description: 4C, LBdel-mutC, 129, VP 5'Slc

value: CTACTTCGTCCATGGCTCTTAAA


title: 4C_LBinv_CAS_VP_Slc

description: 4C, LB-inv, CAS, VP 5'Slc


title: cHiC_4C_LBdel_RBtotdel

description: cHi-C, LBdel-RBtotdel


title: 4C_LBdel_CAS_VP_Slc

description: 4C, LBdel, CAS, VP 5'Slc

value: TGCTTCGTCCATGGCTCTTAAA


title: 4C_RBdel_129_VP_LB

description: 4C, RBdel, 129, VP LB

value: RBdel

value: TCATCTCTTTGGTGGATGATC


title: 4C_LBinv_CAS_VP_LB

description: 4C, LB-inv, CAS, VP LB

value: ACTCATCTCTTTGGTGGATGATC


title: NRF2 KO MR_7632

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

country: USA

institute: Pennington Biomedical Research Center

library_source: transcriptomic

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Mouse – GRCm38.84  mm10
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

molecule: total RNA

source_name: NRF2 KO MR_liver

growth_protocol: Mice began the experimental diets at 8 weeks of age and remained on these diets for 8 weeks total. Body weight, food and water intake, and NMR was taken weekly. Energy expenditure was mearused using Promethion on all mice in weeks 1 and 2 and 9. After two week of recovery, animals were sacrificed after a 4h fast using Co2 inhalation and decapitation.

extract_protocol:
Flash frozen liver was dissected and a small piece was placed in Trizol.  After homogenization, BCP was added, samples were vortexed vigorously, and then spun. The aqueous phase was combined with an equal volume of ethanol and the sample was processed through a Qiagen RNeasy column according to the manufacturer's instructions. mRNA was stored at -80°C and samples were diluted to 200ng/µl for RNAseq.
Quant-Seq  3' mRNA-Seq Library Prep Kit; indexed and pooled samples, 50bp forward read

treatment_protocol: The diets used consisted of standard diet containing elemental amino acids with a methionine concentration of either 0.86% methionine (Con) or 0.17% methionine (MR; Dyets). All mice were fed ad libitum

tag: genotype/variation

tag: Sex

value: Male

tag: age

value: 5 months

tag: diet

value: MR 0.17% methionine

tag: tissue

value: liver


title: NRF2 KO MR_7631


title: NRF2 KO MR_7629


title: NRF2 KO MR_7628


title: B2-zhi

city: Nanjing

first: Yong

last: Su

address: Weigang 1#

country: China

institute: Nanjing Agricultural University

description: Fat tissue treated with sodium butyrate

data_processing:
Using the Illumina paired-end RNA-seq approach
The clean reads were mapped to the reference pig genome (Sus scrofa 10.2) by the mapping tool TopHat (version: 2.0.9)
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: ftp://ftp.ensembl.org/pub/release-83/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa1 0.2.dna.toplevel.fa.gz
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Sus scrofa

source_name: Fat tissue

growth_protocol: This study was approved by the Nanjing Agricultural University Animal Care and Use Committee (Nanjing, Jiangsu province, China). All animal procedures were previously described by Chen et al. (15). In detail, 12 growing barrows (Duroc × Landrace × Large White) from the research pig farm  were used. Each barrow was placed in an individual pen and received a commercial diet (metabolizable energy = 14.20 MJ/kg; crude protein = 16.8%) and water ad libitum. A medical polyethylene cannula (Braintree Scientific Inc, Braintree, MA) was surgically installed into the internal jugular vein to enable the infusion of SB.

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA) following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Twelve crossbred barrows (Duroc × Landrace × Large White, 60 days of age) were fitted with a medical polyethylene cannula via internal jugular vein and were daily infused with 10 ml SB (200 mmol/l) or the same volume of physiological saline.The infusion from each pig was performed in 5 mins. After a 7-day experimental period, all pigs were weighed and euthanized after 12 h of fasting. The 10th-rib longissimus dorsi muscle and dorsal subcutaneous adipose tissue were collected and preserved in liquid nitrogen for further transcriptomic analysis.

tag: treatment

value: Fat tissue treated with sodium butyrate


title: 4C_LBdel_CAS_VP_RB

description: 4C, LBdel, CAS, VP RB

value: TGGTCAATCAGACCCAACTGAG


title: NRF2 KO MR_7627


title: NRF2 KO MR_7625


title: NRF2 KO CON_7623

source_name: NRF2 KO CON_liver

value: CON 0.86% methionine


title: Pro07

first: Michael

last: VanInsberghe

state: Utrecht

description:
processed data files: EE_metadata.csv.gz
processed data files: EE_RPFcounts.csv.gz
processed data files: EE_Pro_layout.csv.gz

data_processing:
See github repository https://github.com/mvanins/scRiboSeq_manuscript for code and detailed instructions.
Basecalls were performed on the Illumina NextSeq 500. Reads from each plate were demultiplexed using bcl2fastq (version 2.20.0.422) with --use-bases-mask Y*,I*,Y* --no-lane-splitting --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0. Read 1 contains the insert and Read 2 contains the cell barcode.
Next, the UMI was extracted from the first 10 bases of read 1 and concatenated to the start of the cell barcode. Adapter sequences were then trimmed from read 1 using cutadapt (version 2.7) with -m 15: -a TGGAATTCTCGGGT. Trimmed reads were aligned to the reference genome using STARSolo (version 2.7.3a_2020-05-22) with a 50-base overhang (--sjdbOverhang 50) with the following parameters: --seedSearchStartLmax 10 –alignIntronMax 1000000 --outFilterScoreMin 0 --outFilterMultimapNmax 1 --chimScoreSeparation 10 --chimScoreMin 20 --chimSegmentMin 15 --outFilterMismatchNmax 5. Aligned reads were deduplicated with UMI-tools (version 1.0.1) using --spliced-is-unique --per-cell --read-length --no-sort-output, and sorted using sambamba (version 0.7.1). Finally, aligned and deduplicated reads were parsed to extract the mapping coordinates and the reference sequence contexts around both the 5’ and 3’ ends of the reads.
Count tables report the number of unique RPFs aligning within any annotated coding sequence for each gene. Reads were only counted if they aligned to the correct strand, if the trimmed length was between 30 and 45 nt long, and if the trimmed length was equal to the mapped length. Additionally, for these counts, the coding sequence was expanded to include 25 nt upstream and downstream of the start and stop codons, respectively.
A random forest model was trained to predict the A-site location within an RPF read based on the footprint length and the sequence context around the 5’ and 3’ ends. The model was implemented in R (version 3.6.3) using ranger (version 0.12.1) with mlr (version 2.17.1) wrappers for training, tuning, assessment, and prediction. The model was trained on reads spanning a stop codon that satisfied the counting requirements listed above. The number of nucleotides between the 5’ end of these reads and the annotated stop codon was used for training.
hTERT-RPE1-FUCCI cells were only included in downstream analyses if they had more than 4500 unique reads aligning to protein-coding genes, and if more than 85% aligned to coding sequences.
Supplementary_files_format_and_content: Metadata file: Cell-level metadata for cells passing QC. Column Headers: CB: Cell barcode. treatment: Culture/starvation condition prior to sequencing. well: Well location in plate. plate: Plate name. cds: Number of unique reads aligning to coding sequences. utr5: Number of unique reads aligning to 5' UTRs. utr3: Number of unique reads aligning to 3' UTRs. cell_total: Total number of unique reads aligning to protein-coding genes. cds_frac: Fraction of unique total reads aligning to CDS.
Supplementary_files_format_and_content: Count file: Cell-level count tables denoting the number of unique reads aligned to CDS regions for each gene.
Supplementary_files_format_and_content: Plate layout file: Description of the plate layout. Column Headers: well: well location in plate. CB: cell barcode for this well. fraction: Cell fraction/population/treatment.
Genome_build: GRCm38.p6

source_name: Mouse enteroendocrine cells from the proximal section of the intestine.

extract_protocol:
Single cells were index sorted using a BD FACS Influx into 384-well hardshell plates (BioRad) that were pre-filled with 5 µL of light mineral oil (Sigma Aldrich) and 50 nL of lysis buffer [22 mM Tris-HCl pH 7.5, 16.5 mM MgCl2, 5.5 mM CaCl2, 165 mM NaCl, 1.1 % Triton X-100, 2.2 U/µL RNaseIN Plus (Promega), 0.11 mg/mL Cyclohexamide (Sigma Aldrich)]. After sorting, plates were spun down at 2000 ×g for 2 minutes and kept on wet ice until all plates were ready for further processing. No RNA purification was performed.
To generate ribosome-protected footprints, 50 nL of Micrococcal Nuclease (MNase, 10500 U/µL, New England Biolabs) was added to each well, and plates were incubated at 37 °C for 30 minutes. In order to stop digestion, 50 nL of stop mix [0.0186 U/µL Thermolabile Proteinase K (New England Biolabs), 62 mM EGTA (Sigma Aldrich), 16.5 mM EDTA (Ambion), and 697.5 mM guanidium thiocyanite (GuSCN, Sigma Aldrich)] was added to each well, and plates were incubated at 37 °C for 30 minutes then 55 °C for 10 minutes and held at 4 °C.
After ribosome footprint digestion, libraries were constructed using a one-pot small-RNA library preparation protocol that incorporated end repair, two RNA ligations, cDNA synthesis, and an indexing PCR. First, 50 nL of end-repair mix [4.1× of 10× T4 RNA Ligase Buffer (New England Biolabs), 16.4 mM MgCl2, 4.1 mM uridine triphosphate (New England Biolabs), 1.37 U/µL T4  Polynucleotide Kinase (New England Biolabs), and 0.82 U/µL RNaseIN Plus] was added to each well, and plates were incubated at 37 °C for 1 hour and held at 4 °C. Next, 264 nL of 3’ ligation brew [1× T4 RNA Ligase Buffer (New England Biolabs), 1 µM pre-adenylated 3’ adapter (OMV630 Integrated DNA Technologies), 35.5 % PEG-8000 (New England Biolabs), 0.1 % Tween-20 (Sigma Aldrich), 1 U/µL RNaseIN Plus, and 21.3 U/µL T4 RNA Ligase 2 Truncated KQ (New England Biolabs)] was added to each well and plates were incubated at 4 °C for 18 hours. The cDNA synthesis primer was then pre-annealed to the 3’ ligation products by adding 50 nL of the RT primer mix [5.2 µM RT primer (OMV572, Integrated DNA Technologies), 13.5 µM adenosine triphosphate (ATP, New England Biolabs), and 1 % Tween-20] to each well, heating to 65 °C for 1 minute, 37 °C for 2 minutes, 25 °C for 2 minutes, and holding at 4 °C. Five-prime adapters were then ligated by adding 156 nL of 5’ ligation brew [1× T4 RNA Ligase Buffer, 30.75 % PEG-8000, 0.1 % Tween-20, 0.5 µM 5’ adapter (OMV632, Integrated DNA Technologies), 1.25 U/µL T4 RNA Ligase 1 (Ambion)] and incubating at 37 °C for 2 hours and holding at 4 °C. Complementary DNA synthesis was then peformed by adding 771 nL of reverse transcription brew [1.88× 5× RT Buffer (ThermoFisher Scientific), 1.25 mM dNTPs (Promega), 0.1875 % Tween-20, 1.875 U/µL RNaseIN Plus, and 9.375 U/µL Maxima H Minus Reverse Transcriptase (ThermoFisher Scientific)] to each well, and heating at 50 °C for 1 hour, then 85 °C for 5 minutes and holding at 4 °C. Finally, single-cell libraries were indexed during PCR by first transferring 150 nL of 20 µM unique forward index primers (Integrated DNA Technologies) and 3.2 µL of PCR brew [1.5× Q5 Hot Start High-Fidelity 2× Master Mix (New England Biolabs), 0.15 % Tween-20, and 0.94 µM reverse index primer (Integrated DNA Technologies)] to each well. Plates were then incubated at 98 °C for 30 s followed by 10 cycles of 98 °C for 15 s, 65 °C 30 s, 72 °C for 30 s, and then a final incubation at 72 °C for 5 min and holding at 4 °C. Plates were then frozen at -20 °C until pooling.
After library construction the plates were pooled and purified. The contents of each plate were first collected in VBLOK200 reservoirs (Click Bio) by centrifuging at 2000 ×g for 2 min. The aqueous phase (~1.9 mL per plate) was separated from the light mineral oil by centrifugation, and concentrated to approximately 500 µL using n-butanol (Sigma Aldrich) and diethyl ether (Sigma Aldrich). Product was then cleaned up using AMPure XP beads (Beckman Coulter) that had been diluted 5× in bead binding buffer [20 % PEG-8000 (Sigma Aldrich) 2.5 M Sodium Chloride (Sigma Aldrich)]; diluted beads were added to the sample at a 2.1:1 ratio, and the final product was resuspended in 50 µL of low TE buffer [LoTET, 3 mM Tris-HCl pH 8.0 (Ambion), 0.2 mM EDTA pH 8.0 (Gibco), 0.1 % Tween-20]. Half of each of the cleaned-up library pools was then run on a 10 cm 7 % polyacrylamide gel at 200 V for ~6 h, and the ~10 base-pair region from 175-185, corresponding to an insert size of ~30-40 nt was excised. The band was then crushed and soaked overnight at 4 °C in elution buffer [5:1 LoTET:7.5 M ammonium acetate (Sigma Aldrich)]. Finally, eluate was precipitated in ethanol.
barcode: TGACCA; 5' Adapter: rCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUr(N1:25252525)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1)r(N1); 3' Adapter: /5rApp/TGGAATTCTCGGGTGCCAAGG/3ddC/

treatment_protocol: Mouse enteroendocrine cells were isolated from the intestines of Neurog3Chrono mice, closely following the methods outlined by Gehart et al. Cell 2019 doi:10.1016/j.cell.2018.12.029. Briefly, mouse small intestines were harvested, cleaned, flushed with PBS0, and separated into proximal, medial, and distal sections. Pieces were cut open and villi were scraped off with a glass cover slip and discarded. Tissue pieces were then washed in cold PBS0 before transferring to PBS0 with 2 mM EDTA (Gibco), incubated at 4 °C for 30 minutes on a roller, and then vigorously shaken. Detached crypts were pelleted, resuspended in warm TrypLE Select (Gibco), and mechanically disrupted by pipetting to generate single-cell suspensions. Single-cell suspensions were washed 2× in Advanced DMEM/F12 (Gibco), strained with a 20-µm mesh, and resuspended in Advanced DMEM/F12 containing 4 mM EDTA and 1 µg/mL DAPI for sorting. In sorting, doublets, debris, and dead cells were excluded by gating forward and side scatter in combination with the DAPI channel. The measurements of dTomato and mNeonGreen were used to select enteroendocrine cells expressing the Neurog3Chrono reporter and DAPI was used to exclude dead cells.

value: enteroendocrine

tag: tissue lineage

value: Enteroendocrine, intestinal epithelium

tag: genetic tag

tag: cell fraction

value: Proximal intestine


title: NRF2 KO CON_7622


title: NRF2 KO CON_7621


title: NRF2 KO CON_7620


title: NRF2 KO CON_7618


title: NRF2 WT MR_7616

source_name: NRF2 WT MR_liver


title: NRF2 KO CON_7617


title: NRF2 WT MR_7609


title: NRF2 WT MR_7611


title: NRF2 WT CON_7607

source_name: NRF2 WT CON_liver


title: NRF2 WT CON_7605


title: NRF2 WT CON_7604


title: NRF2 WT MR_7615


title: NRF2 WT CON_7603


title: NRF2 WT MR_7613


title: Stim_fibroblasts

city: Los angeles

first: Xue

last: Liu

state: CA

address: AHSP A9404, 127 S. San Vicente Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

data_processing:
We used Cell Ranger version 1.3.1 (10x Genomics) to process raw sequencing data and Cell Ranger R kit version 3.0.0 and Seurat suite version 3.0.0 for downstream analysis.
For clustering, principal-component analysis was performed for dimension reduction.
Top 10 principal components (PCs) were selected by using a permutationbased test implemented in Seurat and passed to t-SNE for clustering visualization. sSeq version 1.0.0 integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters. The Benjamini-Hochberg procedure was used for correcting errors of multiple testing.

source_name: mouse lung single cells

extract_protocol:
Murine lungs were dissociated and the entire cell suspension was then plated on appropriately sized tissue culture plasticware. Fibroblasts were cultured in advanced DMEM/F12 (#12634010, Thermo Fisher Scientific), with 10 % vol/vol FBS (HyClone) or to induce a lipofibroblast like phenotype with the addition of 1 % vol/vol ITS+3 liquid media supplement (#I2771, Merck Milipore, Burlington, MA, USA) to the culture media. Media was changed every other day and the cells sub cultured when 80 % confluent. Fibroblasts cultured to passage three (P3) were considered free of contaminating cells based on previous experience in the laboratory. At P3 the cultured fibroblasts were then stimulated with one or a combination (as indicated) of 10 μM rosiglitazone (#72622, Stem Cell Technologies, Cambridge, MA, USA), 1 μM SB4315442 (#1614, R&D Systems, Minneapolis, MO, USA), 4 μM, rhBMP4 (#314-BP, R&D Systems) for 14 days. Matched control cells isolated from the same lung were stimulated in an identical media, for an identical duration, with the appropriate vehicle.
Library preparation and sequencing were performed as our previously published papers. Sequencing libraries for cDNA from single cells were prepared as per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, CA, USA). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-reverse transcription (RT) was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). GEMs were collected and the cDNA was amplified and purified with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA, USA). Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Roche Holding AG, Basel, Switzerland). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA, USA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2) to obtain a sequencing depth of ~200K reads per cell.

tag: mouse lung cells

value: Cultured and stimulated WT lung fibroblasts

tag: assay

value: scRNA-sequencing


title: Aged mouse lung mesenchymal cells-1

source_name: aged mouse lung single cells

extract_protocol:
Isolated tissues were taken immediately to a sterile laminar flow tissue culture hood where they were, rinsed in fresh PBS and then minced finely using a scissors in a 100mm2 Petri dish. The minced lung tissue was then suspended in a digestion media containing 0.125% vol/vol Trypsin-EDTA (#25300056, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 1mg/ml Bovine Serum Albumin (#15260037, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 100 U/ml DNase 1 (#DN25, Sigma Aldrich, St. Louis, MO, USA), 1 mg/ml Collagenase IV (#LS004209, Worthington Biochemical, Lakewood, NJ, USA)  and transferred a tissue culture incubator at 37C for 30 minutes. At 10-minute intervals the lung digestion solution was titurated 10 times using a 10 ml glass pipette. Following the incubation period, the supernatant and remaining tissue was passed through a 100 m strainer into a 50ml tube. The strainer was washed with Dulbecco’s Modified Eagle Medium (#11995065, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) containing 10% vol/vol fetal bovine serum (#SH3062601, HyClone, GE Healthcare, Chicago, IL USA). The tube was then centrifuged at 1600 rpm for 10 minutes at 4C and the pellet resuspended in Hank’s Buffered Saline Solution (#14175095, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) containing 0.2 mM EGTA, 10mM HEPES (#15630106, Gibco, Thermo Fisher Scientific, Waltham, MO, USA), 2% vol/vol FBS and 1% vol/vol antibiotic-antimycotic (#15240062, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) referred to hereafter as HBSS+. Red blood cells were preferentially lysed by treating the isolated cells with 1X RBC lysis buffer (# 00-4333-57, eBiosceinces, Thermo Fisher Scientific, Waltham, MA, USA) for 45 seconds, followed by immediate dilution in 20 ml HBSS+. Cells were centrifuged again and resuspended in fresh HBSS+ prior to florescence-activated cell sorting (FACS). Mesenchymal cells were sorted by negative selection, EPCAM/CD31/CD45-.
mRNA from single cells sorted from lung into lysis plates was reverse transcribed to complementary DNA (cDNA) and amplified as previously described. Library preparation and sequencing were performed as described previously. Sequencing libraries for cDNA from single cells were prepared as per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, CA, USA). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-reverse transcription (RT) was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). GEMs were collected and the cDNA was amplified and purified with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA, USA). Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Roche Holding AG, Basel, Switzerland). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA, USA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2) to obtain a sequencing depth of ~200K reads per cell.

value: Sorted lung mesenchymal cells


title: Aged fibrotic mouse lung mesenchymal cells-2

source_name: aged fibrotic mouse lung single cells

value: Sorted fibrotic lung mesenchymal cells


title: E17.5 WT2 scRNA-seq

source_name: embryonic mouse lung single cells

extract_protocol:
Isolated tissues were taken immediately to a sterile laminar flow tissue culture hood where they were, rinsed in fresh PBS and then minced finely using a scissors in a 100mm2 Petri dish. The minced lung tissue was then suspended in a digestion media containing 0.125% vol/vol Trypsin-EDTA (#25300056, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 1mg/ml Bovine Serum Albumin (#15260037, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 100 U/ml DNase 1 (#DN25, Sigma Aldrich, St. Louis, MO, USA), 1 mg/ml Collagenase IV (#LS004209, Worthington Biochemical, Lakewood, NJ, USA)  and transferred a tissue culture incubator at 37C for 30 minutes. At 10-minute intervals the lung digestion solution was titurated 10 times using a 10 ml glass pipette. Following the incubation period, the supernatant and remaining tissue was passed through a 100 m strainer into a 50ml tube. The strainer was washed with Dulbecco’s Modified Eagle Medium (#11995065, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) containing 10% vol/vol fetal bovine serum (#SH3062601, HyClone, GE Healthcare, Chicago, IL USA). The tube was then centrifuged at 1600 rpm for 10 minutes at 4C and the pellet resuspended in Hank’s Buffered Saline Solution (#14175095, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) containing 0.2 mM EGTA, 10mM HEPES (#15630106, Gibco, Thermo Fisher Scientific, Waltham, MO, USA), 2% vol/vol FBS and 1% vol/vol antibiotic-antimycotic (#15240062, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) referred to hereafter as HBSS+. Red blood cells were preferentially lysed by treating the isolated cells with 1X RBC lysis buffer (# 00-4333-57, eBiosceinces, Thermo Fisher Scientific, Waltham, MA, USA) for 45 seconds, followed by immediate dilution in 20 ml HBSS+. Cells were centrifuged again and resuspended in fresh HBSS+ prior to florescence-activated cell sorting (FACS).
mRNA from single cells sorted from lung into lysis plates was reverse transcribed to complementary DNA (cDNA) and amplified as previously described. Library preparation and sequencing were performed as described previously. Sequencing libraries for cDNA from single cells were prepared as per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, CA, USA). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-reverse transcription (RT) was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). GEMs were collected and the cDNA was amplified and purified with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA, USA). Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Roche Holding AG, Basel, Switzerland). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA, USA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2) to obtain a sequencing depth of ~200K reads per cell.

value: E17.5 WT lung single cells


title: Aged fibrotic mouse lung mesenchymal cells-1


title: Aged mouse lung mesenchymal cells-3


title: Aged fibrotic mouse lung mesenchymal cells-3


title: Aged mouse lung mesenchymal cells-2


title: Ctl_fibroblasts

value: Cultured WT lung fibroblasts


title: E16.5 Tbx4-lineage+, αSMA+ scRNA-seq

value: E16.5 Tbx4-lineage+, αSMA+ fibroblasts


title: v_36_c_i

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
RNA derived from HIV viral particles extracted from concentrated virus-containing supernatant
input sample
Viral RNA

data_processing:
Cutadapters: cutadapt --minimum-length 25 -a AGATCGGAAGAGCACACGTCTGAAC
transcript quantification with salmon (0.8.2)  quant -l SR --gcBias  --numBootstraps 30
alignmnet with hisat2 (2.1.0)
sorting and indexig with samtools (1.6)
peak calling with MACS2 (2.1.2)
ummarize transcript to gene with the R package tximport (1.10.1), R version 3.5.1
Genome_build: merged: hg38,  NC_001802
Supplementary_files_format_and_content: NarrowPeak, list of called peaks
Supplementary_files_format_and_content: CSV, count matrix

organism: Human immunodeficiency virus

source_name: SupT1 culture supernatant (containing NL4-3-ΔEnv-GFP/VSV-G)

growth_protocol: SupT1 cells are human T cell lymphoblasts. They were cultured in R10 (RPMI 1640 with 1x glutamax (#61870-010, Invitrogen) containing 10% heat-inactivated FBS and 50 µg/ml Gentamicin) and split twice a week at 0.5x106 cells/ml to maintain a maximal concentration of 1x106 cells/ml.

extract_protocol:
Total RNA was extracted from concentrated or non-concentrated viral particles  using Trizol Reagent (#15596026 Invitrogen) according to suppliers’s instructions. Briefly, samples were thawed at room temperature and 200µl chloroform were added to the mixture. Samples were centrifuged for 30min at 10000g, at 4°C and the RNA–containing, aqueous (upper) phase was transferred to a fresh tube and subjected to precipitation with 0,5 ml of isopropanol for 1h at -80°C. Samples where then centrifuged for 10 min at 12000g, washed once in 1ml of 75% ethanol and resuspended in 50 μl H2O. PolyA viral RNA was then subjected to fragmentation using Ambion RNA Fragmentation Reagents (#AM8740, Life Technologies), in order to obtain fragments of 100-200nt. An aliquot of fragmented RNA (100 ng) was retained as an input control for RNA sequencing (v_36_c_i) while the rest was used for MeRIP-Seq (v_36_c_m6A) allowing m6A analysis
Libraries for sequencing (input RNA-Seq and MeRIP-Seq) were prepared using Illumina TruSeq Stranded mRNA kits (#20020594, Illumina), starting the protocol at the Elute-Prime-Fragment step, and with a protocol modification consisting in incubating the samples at 80 °C for 2 minutes to only prime but not further fragment the samples.

treatment_protocol: SupT1 cells (5×106 cells) were either mock-treated or infected with 5 µg p24 equivalent of HIV-GFP by spinoculation at 1500 g for 30 min at 20°C, in presence of 4 µg/ml polybrene (Sigma), in 400 µl final volume in 14 ml round bottom polypropylene tubes - a total of 50 tubes were used for mock condition and 50 tubes for infected condition to obtain a total of 250 million cells for each condition. At 12, 24 and 36h post-infection virus-containing supernatant was collected and either directly frozen at -80° for RNA extraction or previously concentrated by filtration on Centricon units (Centricon Plus-70/100K, Millipore).

value: CD4+ T cells (SupT1)

tag: viral strain

tag: time point


title: E17.5 WT3 scRNA-seq

tag: strain


title: E17.5 WT1 scRNA-seq


title: v_36_c_m6a

description:
m6A immunoprecipitated RNA derived from HIV viral particles extracted from concentrated virus-containing supernatant
m6A immunoprecipitated sample
Viral RNA

tag: cell type


title: NRF2 WT MR_7612

value: Male

value: 5 months


title: NRF2 WT CON_7608

value: liver


title: NRF2 WT CON_7602


title: v_12_c_bc

description:
Bisulfite converted RNA derived from HIV viral particles extracted from concentrated cellular supernatant collected 12h post-infection
Bisulfite converted sample
Viral RNA

data_processing:
Cutadapters: cutadapt --minimum-length 25 -a AGATCGGAAGAGCACACGTCTGAAC
Reverse complement reads: seqkit seq -r -p
Align using meRanGh: meRanGh align -o ${outdir} -f 12_LV_bc__L6_R1_001_z4n6O3Spnge2_trim_rev.fastq -t 24 -S ${outdir}/12_LV.sam -ud ${outdir}/un -un -MM -id /data/hg38_hiv/BSgenomeIDX -GTF /mnt/biodata/genomes/Hsapiens/hg38/rnaseq/ref-transcripts.gtf -bg -mbgc 10
Extract and assign multimapped LTR regions from multimap alignment file to beginning of HIV strand: sambamba merge ${f1/sorted/hivltr} $f1 <(samtools view -b ${f1/sorted/multimappers_sorted} integrated:8500-100000)
Call methylated bases: meRanCall -p 12 -o ${output} -bam ${input}    -f /data/hg38_hiv/hg38_hiv.fa      -rl 126     -sc 10     -ei 0.1     -cr 0.99     -bed63  -np  -gref
Genome_build: merged: hg38,  NC_001802
Supplementary_files_format_and_content: Text, methylated base calls with annotations

extract_protocol:
Total RNA was extracted from concentrated or non-concentrated viral particles  using Trizol Reagent (#15596026 Invitrogen) according to suppliers’s instructions. Briefly, samples were thawed at room temperature and 200µl chloroform were added to the mixture. Samples were centrifuged for 30min at 10000g, at 4°C and the RNA–containing, aqueous (upper) phase was transferred to a fresh tube and subjected to precipitation with 0,5 ml of isopropanol for 1h at -80°C. Samples where then centrifuged for 10 min at 12000g, washed once in 1ml of 75% ethanol and resuspended in 50 μl H2O. PolyA viral RNA was then subjected to fragmentation using Ambion RNA Fragmentation Reagents (#AM8740, Life Technologies), in order to obtain fragments of 100-200nt. Samples were then subjected to bisulfite conversion using the EZ RNA methylation Kit (#R5001, Zymo Research).
Libraries for sequencing were prepared using Illumina TruSeq Stranded mRNA kits (#20020594, Illumina), starting the protocol at the Elute-Prime-Fragment step, and with a protocol modification consisting in incubating the samples at 80 °C for 2 minutes to only prime but not further fragment the samples


title: v_36_c_bc

description:
Bisulfite converted RNA derived from HIV viral particles extracted from concentrated cellular supernatant collected 36h post-infection
Bisulfite converted sample
Viral RNA


title: v_24b_s_bc

description:
Bisulfite converted RNA derived from HIV viral particles extracted from non-concentrated cellular supernatant collected 24h post-infection
Bisulfite converted sample
Viral RNA


title: v_36b_s_bc

description:
Bisulfite converted RNA derived from HIV viral particles extracted from non-concentrated cellular supernatant collected 36h post-infection
Bisulfite converted sample
Viral RNA


title: v_24_c_bc

description:
Bisulfite converted RNA derived from HIV viral particles extracted from concentrated cellular supernatant collected 24h post-infection
Bisulfite converted sample
Viral RNA


title: v_24_s_bc


title: v_12_s_bc

description:
Bisulfite converted RNA derived from HIV viral particles extracted from non-concentrated cellular supernatant collected 12h post-infection
Bisulfite converted sample
Viral RNA


title: v_12b_s_bc


title: v_36_s_bc


title: 3W_LSK: BCR/ABL expressing LSK cells

type: RNA

city: Shanghai

first: Zhiwei

last: Chen

address: Room 807, Research and Education Plaza, 197 Ruijin 2nd Road, Luwan District, Shanghai, PRC

department: Shanghai Institute Of Hematology

institute: Shanghai Jiao Tong Universtiy School of Medicine

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in  hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization  section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: Hematopoietic stem-progenitor cells

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: Scl-BA mice were fed with doxycycline (Clontech) in the drinking water (20mg/L) for normal keeping.

extract_protocol: LSKs were sorted by BD FACSAria, total RNA was isolated from LSKs using the miRNeasy mini RNA isolation kit (Qiagen) according to the manual description.

treatment_protocol: Bone marrow LSKs were sorted at week 0 and week 3 after doxycycline withdrawal for RNA extraction.

value: Bone marrow

value: Hematopoietic stem-progenitor cells

tag: time

value: 3 weeks after BCR/ABL expression induced

tag: sorting antibody

value: Lineage Cell Depletion Kit (Miltenyi Biotec). Lineage-negative cells were then stained with Biotin Mouse Lineage Panel (BD Pharmingen), Streptavidin APC-Cy7 (BD Pharmingen), Sca1-PE (BD Pharmingen) and c-Kit-APC (Biolegend)


title: 0W_LSK: control

value: 0 week after BCR/ABL expression induced


title: PH_24hour_rep11

city: Heidelberg

first: Christian

middle: H.

last: Holland

address: Im Neuenheimer Feld 267

department: Institute for Computational Biomedicine

country: Germany

institute: Heidelberg University

hyb_protocol: Labeled and fragmented cRNA was hybridized to Mouse Genome 430 2.0 Affymetrix GeneChips for 16 h at 45 °C according to the manufacturer’s instructions. Microarrays were washed using an Affymetrix fluidics station 450 and stained initially with streptavidin-phycoerythrin. For each sample the signal was further enhanced by incubation with biotinylated goat anti-streptavidin followed by a second incubation with streptavidin-phycoerythrin and a second round of intensities were measured.

scan_protocol: not provided

data_processing: A probe-level model was fitted to the raw data to control the array quality based on the relative log expression values (RLE) and the normalized unscaled standard errors (NUSE) using the R/Bioconductor package oligo (version 1.52.0). Arrays that deviated more than 0.1 from 0 for RLE and from 1 for NUSE were discarded due to expected poor quality. Subsequently, the raw data was normalized with the RMA algorithm, also implemented within the oligo package.

label: biotin

source_name: liver

label_protocol: Affymetrix gene array analysis was performed using the Affymetrix GenChip® Mouse Genome 430 2.0 arrays (Santa Clara, CA, USA). Briefly, five µg RNA were transcribed into cDNA by oligo dT primers, and reverse transcribed to biotinylated cRNA with the Gene Chip IVTÒ Labeling kit (Affymetrix, High Wycombe, UK). Cleanup of the IVT product was done using CHROMA SPIN-100 columns (Clontech, USA). Spectrophotometric analysis was used for the quantification of cRNA with an acceptable A260/A280 ratio of 1.9 to 2.1. Afterward, the cRNA was fragmented using the standard protocol of Affymetrix.

extract_protocol: RNA was isolated using the TRIzol method. Briefly, 1 ml TRIzol was added to 5 x 106 cells followed by vortexing, a 5-min incubation at room temperature, and the addition of 200 μl chloroform. After mixing, further incubation at room temperature for 2–3 min and centrifugation (12,000 g) at 4 °C for 5 min, the clear supernatant was mixed with 500 μl isopropanol and incubated at room temperature for 10 min. After centrifugation (12,000 g) at 4 °C for 10 min, the supernatant was discarded and the pellet washed with 1 ml cold 75% ethanol followed by vortexing and centrifugation (7,500 g, 4 °C, 5 min). The pellet was dried and dissolved in RNase-free water.

value: male

value: Partial hepatectomy

tag: time after treatment


title: PH_control_rep4

tag: Sex

value: none (control)


title: PH_control_rep5


title: PH_24hour_rep8


title: PH_24hour_rep10


title: PH_6hour_rep4


title: PH_control_rep1


title: PH_24hour_rep7


title: PH_1hour_rep2


title: PH_24hour_rep9


title: PH_control_rep2


title: PH_1hour_rep1


title: PH_control_rep3


title: PH_24hour_rep5


title: PH_2week_rep1


title: PH_24hour_rep6


title: PH_6hour_rep2


title: PH_12hour_rep3


title: PH_4week_rep3


title: PH_12hour_rep1


title: PH_2week_rep2


title: PH_6hour_rep3


title: PH_1hour_rep3


title: PH_12hour_rep4


title: PH_6hour_rep1


title: PH_4week_rep4


title: PH_4week_rep2


title: PH_4week_rep1


title: PH_12hour_rep2


title: PH_4day_rep4


title: PH_4day_rep3


title: PH_3day_rep3


title: PH_4day_rep2


title: PH_3day_rep2


title: PH_3day_rep4


title: PH_4day_rep1


title: PH_48hour_rep3


title: PH_1week_rep2


title: PH_24hour_rep1


title: PH_1week_rep4


title: PH_1week_rep1


title: CCL4_ctrl_rep5

scan_protocol: Microarrays were scanned with an Affymetrix scanner controlled by Affymetrix Microarray Suite software (Campos et al., 2014; DOI: 10.1007/s00204-014-1240-8).

tag: time post treatment


title: PH_3month_rep1


title: PH_48hour_rep2


title: CCL4_ctrl_rep4


title: PH_3day_rep1


title: CCL4_ctrl_rep2


title: PH_48hour_rep4


title: PH_1week_rep3


title: PH_24hour_rep4


title: PH_3month_rep2


title: PH_3month_rep3


title: CCL4_ctrl_rep1


title: PH_24hour_rep2


title: PH_48hour_rep1


title: PH_24hour_rep3


title: CCL4_8d_rep4


title: CCL4_ctrl_rep3


title: CCL4_8d_rep5


title: CCL4_6d_rep3


title: CCL4_8d_rep2


title: CCL4_6d_rep4


title: CCL4_8d_rep1


title: CCL4_4d_rep3


title: CCL4_6d_rep1


title: CCL4_4d_rep5


title: CCL4_8d_rep3


title: CCL4_6d_rep2


title: CCL4_4d_rep4


title: CCL4_2d_rep1


title: CCL4_4d_rep1


title: CCL4_2d_rep2


title: CCL4_2d_rep4


title: CCL4_2d_rep5


title: CCL4_2d_rep3


title: CCL4_1d_rep3


title: CCL4_16d_rep3


title: CCL4_1d_rep2


title: CCL4_1d_rep5


title: CCL4_4d_rep2


title: CCL4_1d_rep4


title: CCL4_16d_rep4


title: CCL4_16d_rep2


title: CCL4_16d_rep5


title: CCL4_1d_rep1


title: CCL4_8h_rep5


title: CCL4_6d_rep5


title: CCL4_16d_rep6


title: CCL4_16d_rep1


title: CCL4_2h_rep2


title: CCL4_8h_rep3


title: CCL4_2h_rep5


title: CCL4_2h_rep4


title: CCL4_8h_rep2


title: APAP_control_rep5


title: APAP_control_rep4


title: CCL4_8h_rep4


title: APAP_8day_rep5

value: APAP


title: CCL4_8h_rep1


title: APAP_control_rep1


title: CCL4_2h_rep3


title: APAP_control_rep3


title: APAP_8day_rep1


title: APAP_control_rep2


title: APAP_8day_rep3


title: CCL4_2h_rep1


title: APAP_6hour_rep1


title: APAP_8day_rep2


title: APAP_6day_rep4


title: APAP_8day_rep4


title: APAP_6hour_rep4


title: APAP_6day_rep5


title: APAP_6hour_rep5


title: APAP_6day_rep3


title: APAP_4day_rep5


title: APAP_4day_rep4


title: APAP_6day_rep2


title: APAP_6day_rep1


title: APAP_6hour_rep2


title: APAP_4day_rep3


title: APAP_4day_rep2


title: APAP_4day_rep1


title: APAP_2day_rep4


title: APAP_2day_rep5


title: APAP_2day_rep2


title: APAP_2day_rep1


title: APAP_1day_rep2


title: APAP_1hour_rep1


title: APAP_1hour_rep3


title: APAP_12hour_rep4


title: APAP_1hour_rep4


title: APAP_1hour_rep5


title: APAP_1day_rep1


title: APAP_1hour_rep2


title: APAP_2day_rep3


title: lps_rep5

tag: age

value: 8-10 weeks


title: APAP_1day_rep5

tag: tissue


title: control_rep3


title: APAP_1day_rep4

tag: treatment


title: APAP_16day_rep5


title: APAP_12hour_rep2


title: APAP_12hour_rep5


title: APAP_16day_rep1


title: APAP_1day_rep3


title: APAP_12hour_rep3


title: APAP_16day_rep4


title: lps_rep4


title: APAP_16day_rep3


title: lps_rep1


title: control_rep2


title: APAP_12hour_rep1


title: APAP_16day_rep2


title: lps_rep3


title: lps_rep2


title: Lib3 mouse IgG ChIP-seq

first: Gang

last: Wei

state: Select a State or Province

address: No 2005, Songhu Rd, Yangpu District

institute: Fudan University

data_processing:
ChIP-seq and RNA-seq data were mapped to human genome using BWA.
Pro-seq data were mapped to human genome using Bowtie.
Bedgraph files of ChIP-seq data were generated using Homer.
For the calculation of percentage of CpG island-associated peaks, ChIP-seq peaks are called by ChIPseeqer (Giannopoulou and Elemento, 2011).
Average gene plots of Pro-seq data were generated using Homer.
Genome_build: hg19
Supplementary_files_format_and_content: peaks for ChIP-Seq, RPKM normalized data for RNA-Seq, peaks data for PRO-Seq

source_name: acute myeloid leukemia cells, iMA9

growth_protocol:
HEL, CCRF-CEM, THP1, MOLM-13, and iMA9 cells were grown in RPMI-1640 + 10% FBS.
SEM cells were grown in IMDM + 10% FBS.

extract_protocol:
ChIP experiments and RNA extraction were performed as previously described (Yu et al. Science 2015) .
Pro-seq experiments were performed as previouly described (Kwak et al. Science 2013)
ChIP-seq and RNA-seq libraries were constructed as previously described (Yu et al. Science 2015) .
Pro-seq libraries were constructed as previouly described (Kwak et al. Science 2013)

treatment_protocol: RNAi experiments were performed as previously described (Yu et al. Science 2015)

tag: sample type

value: Lib3 mouse IgG


title: C14

city: Pyeongchang-gun

first: Eun Seo

last: Kim

address: 25354 Pyeongchang-daero, Daehwa-myeon

department: Department of International Agricultural Technology

country: South Korea

institute: Seoul National University

description: Suppl Table_02_C14 OG-seq.txt

data_processing:
Image analysis and base calls were performed using the Illumina pipeline (v1.8) with default settings
Reads were aligned to the bovine reference genome (bosTau8) using the Isaac aligner (Illumina)
Duplicate reads were identified and removed as Picard (http://broadinstitute.github.io/picard)
In the reads mapped using MACS241, the enhanced peaks were called, and the peaks were annotated with ChIPseeker
8-OxoG loci that differ significantly from the input DNA (fold change > 2, q < 0.05) were selected for further analysis
Genome_build: bosTau8
Supplementary_files_format_and_content: Tab-delimited text files including 8-oxoG abundance (pileup), p-value, q-value, fold-enrichment, distance from transcription start site, and annotation information

organism: Bos taurus

source_name: C14 sperm DNA

growth_protocol: Sperm sample collection from fertile and infertile Korean native striped cattle at 6-year old

extract_protocol:
5 µg of the genomic DNA extracted from sperms were fragmented with an S2 ultrasonicator (Covaris, Woburn, MA, USA) in 10 mM Tris buffer (pH 8.0) to obtain approximately 150-bp fragments. After sonication, the fragmented DNA was concentrated to 20 µL in 100 mM NaPi buffer (pH 8.0) using QIAquick PCR purification kit (Qiagen). A 100 µL volume of 100 mM NaPi buffer with 20 mM amine-PEG2-biotin (Thermo Fisher Scientific) was added and the mixture was heated to 75 °C for 10 min. After thermal equilibration to room temperature, 5 mM K2IrBr6 (Sigma-Aldrich) was added for 8-oxoG biotinylation. The biotinylated DNA fragments were eluted with 125 µL Tris buffer using the QIAquick PCR purification kit and collected using Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific). Complementary DNA strands to those with bound biotinylated 8-oxoG were released by incubation in 150 mM NaOH at 20 °C for 30 min, and concentrated to 10 µL ddH2O using ssDNA/RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA).
The OG-seq library was constructed using the TruSeq Nano DNA kit (Illumina, San Diego, CA, USA)
ChIP-Seq using captured 8-oxoG containing DNA fragments

treatment_protocol: Fertile vs. infertile sperm

value: Sperm

tag: condition

value: Infertile


title: Lib1 MLL-AF9 ChIP-seq

tag: tag

value: FLAG

value: Lib1 MLL-AF9


title: C14-1

description: Suppl Table_02_C14 OG-seq.txt

source_name: C14 sperm input DNA


title: C13-1

description: Suppl Table_01_C13 OG-seq.txt

source_name: C13 sperm input DNA

value: Fertile


title: control_rep1

value: liver


title: embryo of 48 HAI seeds developed at 28oC, biological rep1

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

country: Canada

institute: University of Manitoba

description: Gene expression data from embryo of 48 HAI seeds developed at 28oC

hyb_protocol: Following fragmentation, labelled cRNA samples were hybridized for 16 hr at 45C on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix Scanner 3000.

data_processing: The data were analyzed with Robust Multi-array Average methodology (RMA).

organism: Triticum aestivum

source_name: Mature seeds developed at 28oC & imbibed for 48 h

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT Labelling Kit and the GeneChip Sample Cleanup Module

growth_protocol: Wheat plants were grown in a growth chamber at at 22/18°C (day/night) under a 16/8 h photoperiod until anthesis.

extract_protocol: Total RNA of the embryo tissue was extracted using a high quality RNA isolation protocol reported previously (Li and Trick 2005; Biotechniques 38:872-876)

treatment_protocol: After anthesis, a group of plants were grown at either 13°C or 28°C. Spikes were harvested at maturity.

value: seed

tag: genotype

value: AC Domain

value: mature


title: embryo of 48 HAI seeds developed at 28oC, biological rep2


title: embryo of 48 HAI seeds developed at 28oC, biological rep3


title: embryo of 48 HAI seeds developed at 13oC, biological rep1

description: Gene expression data from embryo of 48 HAI seeds developed at 13oC

source_name: Mature seeds developed at 13oC & imbibed for 48 h


title: embryo of 48 HAI seeds developed at 13oC, biological rep2


title: embryo of 48 HAI seeds developed at 13oC, biological rep3


title: C13

description: Suppl Table_01_C13 OG-seq.txt

source_name: C13 sperm DNA


title: 960wt 1d Sham

hyb_protocol: Labeled and fragmented cRNA was hybridized to Affymetrix GeneChips for 16 h at 45 °C according to the manufacturer’s instructions. Microarrays were washed using an Affymetrix fluidics station 450 and stained initially with streptavidin-phycoerythrin. For each sample the signal was further enhanced by incubation with biotinylated goat anti-streptavidin followed by a second incubation with streptavidin-phycoerythrin and a second round of intensities were measured.

scan_protocol: Microarrays were scanned with an Affymetrix scanner controlled by Affymetrix Microarray Suite software.

source_name: 1d Sham

value: Sham

value: Liver


title: 928wt 1d BDL

source_name: 1d BDL

value: male

value: BDL


title: 927wt 3d Sham

source_name: 3d Sham


title: 886wt 21d BDL

source_name: 21d BDL


title: Vascepa-HFD 3

city: Toronto

first: Dana

last: Al Rijjal

address: Department of Physiology, Medical Sciences Building, Room 3352, University of Toronto, 1 King's College Circle

institute: University of Toronto

description: Gene expression data from livers isolation from mice administered with Vascepa and fed high fat diet for 6 weeks

hyb_protocol: Hybridization was performed for 16hr at 45oC.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using Expression Console. RMA algorithm.

source_name: liver, 7 days Vascepa administration followed by 6 weeks high fat diet

label_protocol: Biotin Allonamid Triphosphate was used for labeling. GeneChips were washed and stained using Affymetrix Fluidics Station 450.

growth_protocol: 8 week old mice were acclimatized in standard 12 hour dark/light cycle for one week.

extract_protocol: RNA was extracted using the RNeasy Mini Plus kit (Qiagen) from liver samples.

treatment_protocol: Livers were isolated from mice that were treated with Vascepa for 7 days followed by high fat diet feeding for 6 weeks.

tag: gender


title: 911wt 3d BDL

source_name: 3d BDL


title: Control-HFD 1

description: Gene expression data from livers isolation from mice administered with vehical and fed high fat diet for 6 weeks

source_name: liver, 7 days vehicle administration followed by 6 weeks high fat diet

value: vehicle and fed high fat diet for 6 weeks


title: 853wt 21d BDL


title: 939wt 1d BDL


title: 806wt 21d BDL


title: Vascepa-HFD 1

value: Vascepa and fed high fat diet for 6 weeks


title: 931wt 1d Sham


title: 956wt 1d BDL


title: Control-HFD 2


title: Control-HFD 3


title: 940wt 1d BDL


title: 913wt 3d Sham


title: Vascepa-HFD 2


title: 945wt 1d BDL


title: 957wt 1d Sham


title: 750wt 7d BDL

source_name: 7d BDL


title: 714wt 7d BDL


title: 855wt 21d BDL


title: 776wt 3d BDL


title: 713wt 7d BDL


title: 740wt 3d BDL


title: 709wt 7d BDL


title: 697wt 7d Sham

source_name: 7d Sham


title: 778wt 3d BDL


title: 691wt 7d Sham


title: 744wt 7d BDL


title: 741wt 3d BDL


title: 690wt 7d Sham


title: App[NL-F/NL-F] mouse fed with control diet, biological rep3

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

description: 18 month-old male mouse

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into the Transcriptome Analysis Console (TAC) Software 4.0 and CHP files were generated.

source_name: hippocampus from App[NL-F/NL-F] mouse fed with control diet for 12 months

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 18 months of age.

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene) according to the manufacturers’ instructions.

treatment_protocol: Each mouse was anesthetized, transcardially perfused with saline, and hippocamppus was isolated quickly, preserved at –80°C until RNA preparation.

tag: diabetes status

value: non-diabetic

tag: diet

value: control

value: App knock-in

value: hippocampus

value: 18 months


title: wild-type mouse fed with high fat diet, biological rep3

description: 18 month-old male mouse

source_name: hippocampus from wild-type mouse fed with high fat diet for 12 months

value: diabetic

value: high fat diet

value: wild-type


title: wild-type mouse fed with control diet, biological rep2

description: 18 month-old male mouse

source_name: hippocampus from wild-type mouse fed with control diet for 12 months


title: App[NL-F/NL-F] mouse fed with high fat diet, biological rep2

description: 18 month-old male mouse

source_name: hippocampus from App[NL-F/NL-F] mouse fed with high fat diet for 12 months


title: WJ-MSC-Fenbendazole treat-RNA,rep2

hyb_protocol: Approximately 5.5 μg of labeled cDNA was hybridized to the Affymetrix GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) at 45 °C for 16 h.

scan_protocol: After hybridization, the arrays were scanned on a GCS3000 Scanner (Affymetrix) and data analyses were carried out with the GeneChip Command Console Software (Affymetrix).

data_processing: Expression data were normalized using the robust multi-array average (RMA) approach.

organism: Homo sapiens

source_name: hWJ-MSC, treated with Fenbendazole

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: For 2D culture, hWJ-MSCs were cultured in MEMα medium (Gibco, Grand Island, NY, USA) supplemented with 10% (v/v) FBS and 1% (v/v) antibiotic-antimycotic solution (2D medium) under 5% CO2 and 37°C conditions, and the medium was changed every 3 days. When the cells reached 80% confluence, cells were passaged using 0.25% (w/v) trypsin-EDTA (Gibco). For 3D culture of hWJ-MSCs, 3D medium was prepared by supplementing MEMα medium described above with 0.05% (v/v) Cellhesion VP (Nissan Chemical Industries, Ltd., Tokyo, Japan) according to the manufacturer’s instruction. Cells were seeded at a density of 1 × 106 cells/flask in 10 mL of 3D medium in a 125 mL non-adherent flask (Corning, Corning, NY, USA) and incubated on a rocker (LABOGENE, Seoul, Korea) at 9 rpm with mechanical dissociation daily up to 15 days under 5% CO2 and 37°C conditions. The medium was changed every 3 days. Nine days after 3D culture, primed hMSCs were retrieved by transferring the cell-Cellhesion VP aggregates to a tissue culture plate. The aggregates were spin-down at 1,500 rpm for 3 min and the supernatant was discarded. The aggregates were resuspended by pipetting in 5 mL of 2D medium, transferred to the 100 mm tissue culture plate (Corning), and subjected to cell retrieval from the aggregates. The retrieved cells were maintained in 2D culture condition until used.

extract_protocol: Total RNA from hWJ-MSCs was prepared using a RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. During RNA preparation, DNase (Qiagen) was applied to prevent the genomic DNA contamination.

treatment_protocol: For transcriptome analysis, RNA was prepared from 2D and 3D cultured hMSCs, DPBS-treated, 2D EV- or 3D EV-treated cells as well as Fenbendazole or Brompheniramine-treated cells. Treatment was performed for 6 hrs. All of the treatment was independently carried out in triplicate.

value: Wharton's Jelly Derived Mesenchymal Stem Cells (WJ-MSCs)

value: Fenbendazole


title: App[NL-F/NL-F] mouse fed with high fat diet, biological rep3

description: 18 month-old male mouse


title: wild-type mouse fed with high fat diet, biological rep2

description: 18 month-old male mouse


title: 678wt 7d Sham

tag: strain


title: wild-type mouse fed with control diet, biological rep1

description: 18 month-old male mouse


title: App[NL-F/NL-F] mouse fed with control diet, biological rep2

description: 18 month-old male mouse


title: App[NL-F/NL-F] mouse fed with high fat diet, biological rep1

description: 18 month-old male mouse


title: App[NL-F/NL-F] mouse fed with control diet, biological rep1

description: 18 month-old male mouse


title: WJ-MSC-Fenbendazole treat-RNA,rep1

tag: cell type


title: WJ-MSC-Fenbendazole treat-RNA,rep3


title: wild-type mouse fed with control diet, biological rep3

description: 18 month-old male mouse


title: WJ-MSC-3D exosome treat-RNA,rep1

source_name: hWJ-MSC, treated with 3D extracellular vesicles

value: 3D extracellular vesicles


title: WJ-MSC-BLANK control-RNA,rep1

source_name: hWJ-MSC, treated with DPBS

value: DPBS


title: 36_NI_m6A

description:
m6A immunoprecipitated RNA derived from mock-infected SupT1 cells collected 36h post-mock-infection
m6A immunoprecipitated sample
36_NI_peaks.narrowPeak
Cellular RNA

source_name: SupT1 cells

extract_protocol:
Total RNA was extracted from infected and non infected cells using Trizol Reagent (#15596026 Invitrogen) according to suppliers’s instructions. Briefly, samples were thawed at room temperature and 200µl chloroform were added to the mixture. Samples were centrifuged for 30min at 10000g, at 4°C and the RNA–containing, aqueous (upper) phase was transferred to a fresh tube and subjected to precipitation with 0,5 ml of isopropanol for 1h at -80°C. Samples where then centrifuged for 10 min at 12000g, washed once in 1ml of 75% ethanol and resuspended in 50 μl H2O. PolyA viral RNA was then subjected to fragmentation using Ambion RNA Fragmentation Reagents (#AM8740, Life Technologies), in order to obtain fragments of 100-200nt. Samples were then subjected to bisulfite conversion using the EZ RNA methylation Kit (#R5001, Zymo Research)
Libraries for sequencing (input RNA-Seq and MeRIP-Seq) were prepared using Illumina TruSeq Stranded mRNA kits (#20020594, Illumina), starting the protocol at the Elute-Prime-Fragment step, and with a protocol modification consisting in incubating the samples at 80 °C for 2 minutes to only prime but not further fragment the samples

treatment_protocol: SupT1 cells (5×106 cells) were either mock-treated or infected with 5 µg p24 equivalent of HIV-GFP by spinoculation at 1500 g for 30 min at 20°C, in presence of 4 µg/ml polybrene (Sigma), in 400 µl final volume in 14 ml round bottom polypropylene tubes - a total of 50 tubes were used for mock condition and 50 tubes for infected condition to obtain a total of 250 million cells for each condition. At 12,24 and 36h post infection cells were collected for RNA extraction and m6A immunoprecipitation.

value: CD4+ T cells (SupT1)

tag: time point


title: 36_LV_m6A

description:
m6A immunoprecipitated RNA derived from HIV- infected SupT1 cells collected 36h post-infection
m6A immunoprecipitated sample
36_LV_peaks.narrowPeak
Cellular RNA

tag: viral strain


title: 24_NI_m6A

description:
m6A immunoprecipitated RNA derived from mock-infected SupT1 cells collected 24h post-mock-infection
m6A immunoprecipitated sample
24_NI_peaks.narrowPeak
Cellular RNA


title: 24_LV_m6A

description:
m6A immunoprecipitated RNA derived from HIV- infected SupT1 cells collected 24h post-infection
m6A immunoprecipitated sample
24_LV_peaks.narrowPeak
Cellular RNA


title: WJ-MSC-2D exosome treat-RNA,rep2

source_name: hWJ-MSC, treated with 2D extracellular vesicles

value: 2D extracellular vesicles


title: 12_LV_m6A

description:
m6A immunoprecipitated RNA derived from HIV- infected SupT1 cells collected 12h post-infection
m6A immunoprecipitated sample
12_LV_peaks.narrowPeak
Cellular RNA


title: 12_NI_m6A

description:
m6A immunopreciptated RNA derived from mock-infected SupT1 cells collected 12h post-mock-infection
m6A immunoprecipitated sample
12_NI_peaks.narrowPeak
Cellular RNA


title: WJ-MSC-Brompheniramine treat-RNA,rep1

source_name: hWJ-MSC, treated with Brompheniramine

value: Brompheniramine


title: 36_LV_input

description:
RNA derived from HIV- infected SupT1 cells collected 36h post-infection
input sample
counts.genes.csv
Cellular RNA


title: wild-type mouse fed with high fat diet, biological rep1

description: 18 month-old male mouse

value: male


title: WJ-MSC-2D exosome treat-RNA,rep1


title: WJ-MSC-Brompheniramine treat-RNA,rep3


title: WJ-MSC-Brompheniramine treat-RNA,rep2


title: WJ-MSC-3D exosome treat-RNA,rep2


title: WJ-MSC-2D exosome treat-RNA,rep3


title: WJ-MSC-3D exosome treat-RNA,rep3


title: WJ-MSC-BLANK control-RNA,rep2


title: 36_NI_input

description:
RNA derived from mock-infected SupT1 cells collected 36h post-mock-infection
input sample
counts.genes.csv
Cellular RNA


title: WJ-MSC-2D EV treat-RNA


title: 24_LV_input

description:
RNA derived from HIV- infected SupT1 cells collected 24h post-infection
input sample
counts.genes.csv
Cellular RNA


title: 24_NI_input

description:
RNA derived from mock-infected SupT1 cells collected 24h post-mock-infection
input sample
counts.genes.csv
Cellular RNA


title: 12_LV_input

description:
RNA derived from HIV- infected SupT1 cells collected 12h post-infection
input sample
counts.genes.csv
Cellular RNA


title: WJ-MSC-BLANK control-RNA,rep3


title: WJ-MSC-BLANK control-RNA

source_name: hWJ-MSC, treated with XE buffer

value: XE buffer


title: WJ-MSC-2D-RNA

source_name: 2D cultured hWJ-MSC

value: 2D cultured


title: 36_LV_bc

description:
Bisulfite converted RNA derived from HIV- infected SupT1 cells collected 36h post-infection
Bisulfite converted sample
Cellular RNA

extract_protocol:
Total RNA was extracted from infected and non infected cells using Trizol Reagent (#15596026 Invitrogen) according to suppliers’s instructions. Briefly, samples were thawed at room temperature and 200µl chloroform were added to the mixture. Samples were centrifuged for 30min at 10000g, at 4°C and the RNA–containing, aqueous (upper) phase was transferred to a fresh tube and subjected to precipitation with 0,5 ml of isopropanol for 1h at -80°C. Samples where then centrifuged for 10 min at 12000g, washed once in 1ml of 75% ethanol and resuspended in 50 μl H2O. PolyA viral RNA was then subjected to fragmentation using Ambion RNA Fragmentation Reagents (#AM8740, Life Technologies), in order to obtain fragments of 100-200nt. Samples were then subjected to bisulfite conversion using the EZ RNA methylation Kit (#R5001, Zymo Research)
Libraries for sequencing were prepared using Illumina TruSeq Stranded mRNA kits (#20020594, Illumina), starting the protocol at the Elute-Prime-Fragment step, and with a protocol modification consisting in incubating the samples at 80 °C for 2 minutes to only prime but not further fragment the samples.

treatment_protocol: SupT1 cells (5×106 cells) were either mock-treated or infected with 5 µg p24 equivalent of HIV-GFP by spinoculation at 1500 g for 30 min at 20°C, in presence of 4 µg/ml polybrene (Sigma), in 400 µl final volume in 14 ml round bottom polypropylene tubes - a total of 50 tubes were used for mock condition and 50 tubes for infected condition to obtain a total of 250 million cells for each condition. At 12,24 and 36h post-infection cells were collected for RNA extraction and bisulfite conversion with the EZ RNA methylation Kit (#R5001, Zymo Research).


title: 12_NI_input

description:
RNA derived from mock-infected SupT1 cells collected 12h post-mock-infection
input sample
counts.genes.csv
Cellular RNA


title: 24_NI_bc

description:
Bisulfite converted RNA derived from mock-infected SupT1 cells collected 24h post-mock-infection
Bisulfite converted sample
Cellular RNA


title: 12_NI_bc

description:
Bisulfite converted RNA derived from mock-infected SupT1 cells collected at 12h post-mock-infection
Bisulfite converted sample
Cellular RNA


title: 24_LV_bc

description:
Bisulfite converted RNA derived from HIV- infected SupT1 cells collected 24h post-infection
Bisulfite converted sample
Cellular RNA


title: 36_NI_bc

description:
Bisulfite converted RNA derived from mock-infected SupT1 cells collected 36h post-mock-infection
Bisulfite converted sample
Cellular RNA


title: WJ-MSC-3D EV treat-RNA


title: sha_2 (Abl1 shRNA cells RNA-seq)

city: Maywood

first: Wei

last: Qiu

address: 2160 S 1st Ave

institute: Loyola University Chicago

data_processing:
The original reads were mapped to human genome (UCSC hg38) using HISAT2 (version 2.0.4), and then the number of reads unambiguously mapped to each RefSeq gene was counted using HTSeq (version 0.6.1). Genes with less than five reads per sample were removed. Then the count data was normalized by the samr.norm.data function in R package samr (version 2.0).
Genome_build: hg38
Supplementary_files_format_and_content: norm count data

source_name: Huh7 cells

growth_protocol: DMEM culture medium

extract_protocol:
RNA extration with Qiagen kit
250~300 bp insert cDNA library

tag: passage

value: One week after puromycin selection

tag: shRNA

value: ABL1 shRNA

tag: cell line


title: sha_3 (Abl1 shRNA cells RNA-seq)


title: WJ-MSC-3D-RNA

source_name: Retrieved 3D cultured hWJ-MSC

value: 3D cultured


title: sha_1 (Abl1 shRNA cells RNA-seq)


title: scr_3 (Scrambled cells RNA-seq)

value: scrambled shRNA


title: scr_1 (Scrambled cells RNA-seq)


title: scr_2 (Scrambled cells RNA-seq)


title: ProLib10 Pro-seq

source_name: HEL

value: ENL knockdown


title: ProLib11 Pro-seq

value: AFF4 knockdown


title: ProLib5 Pro-seq

value: DOT1L knockdown


title: ProLib4 Pro-seq

value: AF4 knockdown


title: RLib32 strand-specific mRNA-seq


title: RLib31 strand-specific mRNA-seq


title: RLib30 strand-specific mRNA-seq

value: Control


title: RLib29 strand-specific mRNA-seq


title: RLib28 strand-specific mRNA-seq


title: RLib27 strand-specific mRNA-seq


title: 12_LV_bc

description:
Bisulfite converted RNA derived from HIV- infected SupT1 cells collected at 12h post-infection
Bisulfite converted sample
Cellular RNA


title: RLib26 strand-specific mRNA-seq


title: RLib25 strand-specific mRNA-seq


title: RLib24 strand-specific mRNA-seq


title: RLib18 strand-specific mRNA-seq


title: RLib22 strand-specific mRNA-seq


title: RLib21 strand-specific mRNA-seq


title: RLib17 strand-specific mRNA-seq


title: RLib15 strand-specific mRNA-seq

value: AF9 knockdown


title: RLib14 strand-specific mRNA-seq


title: RLib13 strand-specific mRNA-seq


title: Lib248 Pol II (ser-5p) ChIP-seq

value: Lib248 Pol II (ser-5p)


title: Lib247 Pol II (ser-2p) ChIP-seq

value: Lib247 Pol II (ser-2p)


title: RLib23 strand-specific mRNA-seq


title: Lib231 Pol II (ser-2p) ChIP-seq

value: Lib231 Pol II (ser-2p)


title: ProLib12 Pro-seq


title: Lib249 Pol II (ser-5p) ChIP-seq

value: Lib249 Pol II (ser-5p)


title: ProLib3 Pro-seq


title: Lib246 Pol II (ser-2p) ChIP-seq

value: Lib246 Pol II (ser-2p)


title: Lib230 Pol II ChIP-seq

value: Lib230 Pol II


title: Lib228 Pol II ChIP-seq

value: Lib228 Pol II


title: Lib217 Pol II ChIP-seq

value: Lib217 Pol II


title: VcdP rep 3

city: Jena

first: Kavyaa

last: Venkat

address: Winzerlaer Straße 2

institute: Friedrich-Schiller-University Jena

description:
pVcdP-rep3_ACTGAT
pVcr082-pept III
∆vcdRP pBAD1K-VcdP
VcdRP_pulse_read_counts.xlsx

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, Munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v12.0.3.
Adaptor- and quality trimming was performed using the trim reads command with the following settings: sequence=NEB P7:AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, NEB P5:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; reads: all; when an adapter is found: trim 3'end; for reads without adapters: keep the read; scores=mismatch:2, gapcost:3, cutoff:10; cutoff at end: 4
The trimmed reads were checked for quality and mapped with CLC Genomics Workbench v12.0.3 to the V. cholerae reference genome (NCBI Acc.number: NC_002505.1, NC_002506.1) using the following settings: Mismatch cost=2, Insertion cost=3, Deletion cost=3, Length fraction=0.8, Similarity fraction=0.8, Global alignment=yes, Strand specific=reverse, Maximum number of hits for a read=5
Reads mapping to annotated genes were counted, and genes with a total count cutoff of >10 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 2.0 and a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: VcdRP_pulse_read_counts.xlsx: Read count table and edgeR (exact mode) analysis.

organism: Vibrio cholerae C6706

source_name: whole bacterial cells

growth_protocol: V. cholerae C6706 ∆vcdRP strains carrying pBAD1K-Ctrl, pBAD1K-VcdRP, pBAD1K-VcdR, or pBAD1K-VcdP were cultivated to early exponential phase (OD600=0.1) in 200 ml LB media containing 50 µg/ml kanamycin.

extract_protocol:
RNA was isolated using AGPC with EXTRAzol according to standard protocols. Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using the Ribo-Zero rRNA Removal kit (Epicentre) for gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760), according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: L-arabinose (0.2% final conc.) was added when cells reached early exponential phase (OD600=0.1). After 15 minutes of treatment, 4 OD600 units of cells were harvested in tubes containing 20% "stop-mix" (95% ethanol, 5% phenol) and snap-frozen in liquid nitrogen until further processing.

value: <delta>vcdRP pBAD1K-VcdP

tag: growth phase

value: exponential phase

value: 0.2% L-arabinose


title: VcdP rep 2

description:
pVcdP-rep2_GTGGCC
pVcr082-pept II
∆vcdRP pBAD1K-VcdP
VcdRP_pulse_read_counts.xlsx


title: VcdP rep 1

description:
pVcdP-rep1_ATGTCA
pVcr082-pept I
∆vcdRP pBAD1K-VcdP
VcdRP_pulse_read_counts.xlsx


title: 884wt 21d BDL

source_name: 21d BDL

tag: Sex

value: male

value: BDL

tag: time

tag: tissue

value: Liver


title: Lib216 Pol II ChIP-seq

tag: treatment

tag: sample type

value: Lib216 Pol II


title: VcdR rep 3

description:
pVcdR-rep3_GAGTGG
pVcr082-stop III
∆vcdRP pBAD1K-VcdR
VcdRP_pulse_read_counts.xlsx

tag: genotype

value: <delta>vcdRP pBAD1K-VcdR


title: VcdR rep 2

description:
pVcdR-rep2_GTGAAA
pVcr082-stop II
∆vcdRP pBAD1K-VcdR
VcdRP_pulse_read_counts.xlsx


title: VcdR rep 1

description:
pVcdR-rep1_AGTTCC
pVcr082-stop I
∆vcdRP pBAD1K-VcdR
VcdRP_pulse_read_counts.xlsx


title: RLib16 strand-specific mRNA-seq

value: AF9 knockdown


title: Lib214 MLL1-N ChIP-seq

value: Lib214 MLL1-N


title: VcdRP rep 3

description:
pVcdRP-rep3_CGTACG
pVcr082-full III
∆vcdRP pBAD1K-VcdRP
VcdRP_pulse_read_counts.xlsx

value: <delta>vcdRP pBAD1K-VcdRP


title: VcdRP rep 2

description:
pVcdRP-rep2_GTCCGC
pVcr082-full II
∆vcdRP pBAD1K-VcdRP
VcdRP_pulse_read_counts.xlsx


title: Ctrl rep 3

description:
pCtrl-rep3_ATTCCT
pCtrl III
∆vcdRP pBAD1K-Ctrl
VcdRP_pulse_read_counts.xlsx

value: <delta>vcdRP pBAD1K-Ctrl


title: Ctrl rep 1

description:
pCtrl-rep1_CCGTCC
pCtrl I
∆vcdRP pBAD1K-Ctrl
VcdRP_pulse_read_counts.xlsx


title: Lib202 Pol II (ser-2p) ChIP-seq

value: Control

value: Lib202 Pol II (ser-2p)


title: Ctrl rep 2

description:
pCtrl-rep2_GTTTCG
pCtrl II
∆vcdRP pBAD1K-Ctrl
VcdRP_pulse_read_counts.xlsx


title: Lib197 Input ChIP-seq

value: Lib197 Input


title: Lib196 MLL-N ChIP-seq

value: Lib196 MLL-N


title: Lib229 Pol II (ser-2p) ChIP-seq

value: Lib229 Pol II (ser-2p)


title: Sample39 [204027220054_R04C01]

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

description:
204027220054_R04C01_Grn.idat
204027220054_R04C01_Red.idat

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
the Nicks_raw_Signal.csv contains unmethylated and methylated signal intensities

label: hapten-labeled dideoxynucleotides

source_name: Human fetal brain

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: phenol-chloroform extraction

value: M

tag: age (post-conceptional weeks)

value: fetal brain


title: Sample40 [204027220054_R05C01]

description:
204027220054_R05C01_Grn.idat
204027220054_R05C01_Red.idat


title: Sample38 [204027220054_R03C01]

description:
204027220054_R03C01_Grn.idat
204027220054_R03C01_Red.idat

value: F


title: Sample35 [204027220050_R05C01]

description:
204027220050_R05C01_Grn.idat
204027220050_R05C01_Red.idat


title: Sample36 [204027220050_R08C01]

description:
204027220050_R08C01_Grn.idat
204027220050_R08C01_Red.idat


title: Lib185 Input ChIP-seq

source_name: CCRF-CEM

value: Lib185 Input


title: VcdRP rep 1

description:
pVcdRP-rep1_AGTCAA
pVcr082-full I
∆vcdRP pBAD1K-VcdRP
VcdRP_pulse_read_counts.xlsx

value: exponential phase

value: 0.2% L-arabinose


title: Lib203 Pol II (ser-2p) ChIP-seq

value: Lib203 Pol II (ser-2p)


title: Sample37 [204027220054_R01C01]

description:
204027220054_R01C01_Grn.idat
204027220054_R01C01_Red.idat


title: Lib121 AF4 ChIP-seq

value: Lib121 AF4


title: Sample31 [204027220043_R07C01]

description:
204027220043_R07C01_Grn.idat
204027220043_R07C01_Red.idat


title: Lib119 Pol II ChIP-seq

value: Lib119 Pol II


title: Sample32 [204027220043_R08C01]

description:
204027220043_R08C01_Grn.idat
204027220043_R08C01_Red.idat


title: Sample29 [204027220043_R05C01]

description:
204027220043_R05C01_Grn.idat
204027220043_R05C01_Red.idat


title: Lib115 Input ChIP-seq

value: Lib115 Input


title: Sample28 [204027220043_R04C01]

description:
204027220043_R04C01_Grn.idat
204027220043_R04C01_Red.idat


title: Lib91 AF4 ChIP-seq

value: Lib91 AF4


title: Sample27 [204027220043_R03C01]

description:
204027220043_R03C01_Grn.idat
204027220043_R03C01_Red.idat


title: Sample26 [204027220043_R02C01]

description:
204027220043_R02C01_Grn.idat
204027220043_R02C01_Red.idat


title: Sample23 [204026590099_R07C01]

description:
204026590099_R07C01_Grn.idat
204026590099_R07C01_Red.idat


title: Sample25 [204027220043_R01C01]

description:
204027220043_R01C01_Grn.idat
204027220043_R01C01_Red.idat


title: Sample24 [204026590099_R08C01]

description:
204026590099_R08C01_Grn.idat
204026590099_R08C01_Red.idat


title: Lib27 p300 ChIP-seq


title: Lib23 MLL-N ChIP-seq

value: Lib23 MLL-N


title: Sample21 [204026590099_R05C01]

description:
204026590099_R05C01_Grn.idat
204026590099_R05C01_Red.idat


title: Sample18 [204026590099_R02C01]

description:
204026590099_R02C01_Grn.idat
204026590099_R02C01_Red.idat


title: Sample22 [204026590099_R06C01]

description:
204026590099_R06C01_Grn.idat
204026590099_R06C01_Red.idat


title: Sample17 [204026590099_R01C01]

description:
204026590099_R01C01_Grn.idat
204026590099_R01C01_Red.idat


title: Sample34 [204027220050_R04C01]

description:
204027220050_R04C01_Grn.idat
204027220050_R04C01_Red.idat


title: Sample33 [204027220050_R01C01]

description:
204027220050_R01C01_Grn.idat
204027220050_R01C01_Red.idat


title: Sample16 [204026590072_R08C01]

description:
204026590072_R08C01_Grn.idat
204026590072_R08C01_Red.idat


title: Lib179 MLL-N ChIP-seq

value: Lib179 MLL-N


title: Sample19 [204026590099_R03C01]

description:
204026590099_R03C01_Grn.idat
204026590099_R03C01_Red.idat


title: Sample20 [204026590099_R04C01]

description:
204026590099_R04C01_Grn.idat
204026590099_R04C01_Red.idat


title: Sample30 [204027220043_R06C01]

description:
204027220043_R06C01_Grn.idat
204027220043_R06C01_Red.idat


title: Sample13 [204026590066_R06C01]

description:
204026590066_R06C01_Grn.idat
204026590066_R06C01_Red.idat


title: Sample12 [204001350069_R08C01]

description:
204001350069_R08C01_Grn.idat
204001350069_R08C01_Red.idat


title: Sample14 [204026590066_R07C01]

description:
204026590066_R07C01_Grn.idat
204026590066_R07C01_Red.idat


title: Sample11 [204001350069_R07C01]

description:
204001350069_R07C01_Grn.idat
204001350069_R07C01_Red.idat


title: Sample10 [204001350069_R06C01]

description:
204001350069_R06C01_Grn.idat
204001350069_R06C01_Red.idat


title: Sample7 [204001350068_R06C01]

description:
204001350068_R06C01_Grn.idat
204001350068_R06C01_Red.idat


title: Sample6 [204001350047_R08C01]

description:
204001350047_R08C01_Grn.idat
204001350047_R08C01_Red.idat


title: Sample5 [204001350047_R07C01]

description:
204001350047_R07C01_Grn.idat
204001350047_R07C01_Red.idat


title: Sample4 [204001350047_R06C01]

description:
204001350047_R06C01_Grn.idat
204001350047_R06C01_Red.idat


title: Sample3 [204001350046_R08C01]

description:
204001350046_R08C01_Grn.idat
204001350046_R08C01_Red.idat


title: Sample2 [204001350046_R07C01]

description:
204001350046_R07C01_Grn.idat
204001350046_R07C01_Red.idat


title: Sample1 [204001350046_R06C01]

description:
204001350046_R06C01_Grn.idat
204001350046_R06C01_Red.idat


title: SKNO1.GSK862

city: Collegeville

first: Shawn

last: Foley

state: PA

address: 1250 S. Collegeville Rd

department: Oncology

institute: GlaxoSmithKline

hyb_protocol: Hybridization was carried out by Q2 Solutions

scan_protocol: Scanning was carried out by Q2 Solutions

data_processing:
Arrays were swan normalized using minfi R package and normalized beta values reported for each sample.
Processed data file includes normalized beta values

label: Cy5 and Cy3

label_protocol: Labeling was carried out by Q2 Solutions

growth_protocol: Cell lines were obtained from the American Type Culture Collection, the Deutsche Sammlung von Mikroorganismen und Zellbulturen, or AddexBio and maintained in the recommended cell culture media at 37°C in 5%

extract_protocol: Genomic DNA was collected using Zymo Quick gDNA Miniprep and quantified on a nanodrop.

treatment_protocol: Cells were plated 24 hours before treatment with either DMSO or  1 µM GSK3484862 then grown for 96 hours before collection.


title: NOMO1.GSK862


title: SKNO1.DMSO

value: DMSO


title: NOMO1.DMSO


title: SHI1.GSK862


title: Sample9 [204001350068_R08C01]

description:
204001350068_R08C01_Grn.idat
204001350068_R08C01_Red.idat


title: Flight-SH-W6

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: F-SH-W6 CALLUS

hyb_protocol: cRNA was hybridized to a whole mouse genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner Agilent Technologies G2600D Images were quantified using Agilent Feature Extraction Software v.11.5.1.1 (Agilent Technologies, Inc.).

data_processing: Agilent Feature Extraction Software (v.12.0) was used for background subtraction and LOWESS normalization

source_name: Callus

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labeled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labeled cRNA was quantified using a NanoDrop ND-8000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: Invitrogen TRIzol RNA extraction methods and the miRNeasy mini kit total RNA purification procedures (QIAGEN Inc., Germantown, MD) were followed to extract the RNA.

tag: age

value: 9-week old

tag: gender

value: Male

tag: sample group

value: Flight

value: unoperated sham controls

value: Callus

source_name: Agilent's Universal Mouse Reference RNA composed of total RNA from 11 mouse cell lines

value: reference


title: Ground -SH-W4

description: G-SH-W4 CALLUS

tag: strain

value: Ground


title: SHI1.DMSO


title: Sample8 [204001350068_R07C01]

description:
204001350068_R07C01_Grn.idat
204001350068_R07C01_Red.idat

value: M

value: fetal brain


title: Ground -SH-W1

description: G-SH-W1 CALLUS


title: Ground -SAL-W3

description: G-SAL-W3 CALLUS

value: segmental bone defect (SBD) surgery


title: Flight-SH-W8

description: F-SH-W8 CALLUS


title: Flight-SH-W9

description: F-SH-W9 CALLUS


title: Ground -SH-W5

description: G-SH-W5 CALLUS


title: Flight-SAL-W1

description: F-SAL-W1 CALLUS


title: Flight-SAL-W5

description: F-SAL-W5 CALLUS


title: THP1.GSK862


title: Ground -SAL-W5

description: G-SAL-W5 CALLUS


title: THP1.DMSO


title: Flight-SH-W4

description: F-SH-W4 CALLUS


title: Flight-SAL-W3

description: F-SAL-W3 CALLUS


title: MOLM13.DMSO


title: GDM1.GSK862