title: small_RNA_NT.BDC.4

city: Logan

first: Abby

middle: D

last: Benninghoff

state: UT

address: 4815 Old Main Hill

department: Animal, Dairy and Veterinary Sciences

institute: Utah State University

data_processing:
Sequence data were processed to remove low quality reads and any artificial reads introduced during library preparation (Perl script Trim Galore, Python script SortMeRNA).
Annotation and abundance analyses of sncRNAs was performed as described previously (Russell, et al. 2017  Reproduction 153: 305-318).  Briefly, data processing and bioinformatics analysis for other sncRNA were performed primarily with command line tools available at http://www.smallrnagroup.uni-mainz.de/software.html. First, data were filtered for sequence length between 17 and 32 nucleotides (nt), which includes the canonical size range for mature small RNAs (miRNA, tRFs, piRNA). A separate analysis was performed for sequences between 33-93 nt, which encompassed longer reads characteristic of snoRNA, tRNA and mitochondrial rRNA. This split analysis approach avoided possible skewing of the data when comparing between these diverse sncRNA classes.
Sequence annotation was performed with Unitas v1.6.1, which uses the latest available public small RNA databases to annotate input sequences.  Non-annotated sequences were then mapped to the bovine genome (BosTau8) with sRNAmapper to determine which non-annotated sequences were likely of biological, not technical, origin. The mapped sequence reads were redistributed across the genome based on number of mapping locations by using reallocate with the parameters ‘5000 1000 b 0’ (reallocate.pl).
Reallocated map files were then analyzed with ProTRAC v2.4.2, which identifies probable piRNAs through their genomic clustering based on size, sequence, and cluster characteristics (all options at default settings, including repeatmasker and geneset references).  Predicted piRNA clusters were compared among samples by using the Galaxy merge tool (usegalaxy.org) to first generate lists of predicted clusters by sample type followed by the join tool to identify overlapping genomic intervals among samples. Sequence logos representing nucleotide biases were generated with ggseqlogo.
Count tables of sncRNAs were generated from the output of Unitas.  Normalization and differential expression analysis was performed with the DESeq2 R package.  Potential outlier sample replicates were identified by using principal components analyses of the complete sncRNA profile prior to statistical analyses.
Genome_build: UMD3.1
Supplementary_files_format_and_content: txt file for normalized reads for annotated small non-coding RNAs organized by sample ID across columns and annotation in the first column

organism: Bos taurus

source_name: scNT Blastocyst-derived cells

growth_protocol:
Frozen/thawed cells were grown to 80-100% confluence then passaged, with cells from passages 4-5 used as nuclear donors. Three days prior to a cloning session, donor fibroblast cells were thawed and propagated, and incubated in DMEM medium (Hyclone) supplemented with 15% (v/v) FBS at 39 deg C with 5% CO2. Bovine fibroblasts at 80-90% confluence were serum-starved by replacing culture medium with DMEM containing 0.5% (v/v) FBS 24 hr prior to scNT.Oocytes were matured for 18-20 hr, then denuded using 100 microliters of 1% (v/v) hyaluronidase (MP Biomedical), incubated for 5 min at 38.5 deg C with 5% CO2, followed by gentle pipetting. The removed cumulus cells were centrifuged at 500xg for 5 min at room temperature, and the supernatant was removed. Cumulus cells were then cultured in SOFaa under oil for use in embryo culture. The denuded oocytes were then rinsed using PB1+, and oocytes with polar bodies were selected and separated. ScNT was performed according to established protocols [49-51]. Briefly, oocytes with polar bodies were incubated in 0.6 microgram/ml demecolcine for 30-40 min and a metaphase plate and a polar body were removed using a beveled pipette. Fibroblast cells were covered in 0.25% trypsin (Gibco, Carlsbad, CA) for 1 min, and then the trypsin was removed and fibroblasts were incubated for anther 6 min at 39 deg C with 5% CO2. Once fibroblast cells were detached, they were rinsed in warm medium and centrifuged at 150xg for 6 min. The supernatant was removed, and the cellular pellet was resuspended in 100 microliters Hepes SOF medium [47]. One fibroblast cell was injected into the perivitelline space of the recipient oocyte, and fused using one direct pulse of 1.2 kV/cm for 22 μs by an Electro Cell Manipulator 2001 (BTX, San Diego, CA) in 0.28 M sorbitol, 0.05% (w/v) BSA, 0.1 mM CaCl2, 0.5 mM MgCl2, and 0.5 mM Hepes. Following fusion, embryos were washed through Hepes SOF, and incubated in embryo culture medium for 1 hr. Activation was then performed, with successfully fused embryos cultured in 5 μM ionomycin for 5 min, followed by 4 hr of incubation in activation medium composed of SOFaa medium with 10 μg/ml cyclohexamide and 1 mM 6-dimethylamino¬pyridine at 38.5 deg C with 5% CO2. Following activation, embryos were cultured on a monolayer of bovine cumulus cells in 50 µl drops of SOFaa with 3% (v/v) FBS overlaid with mineral oil. The embryos were cultured at 38.5 deg C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture.
Provided above

extract_protocol:
RNA was isolated based on size using the RNA Clean & ConcentratorTM 5 kit (Zymo) from three pools each of oocytes, 2-cell stage embryos, 8-cell stage embryos, morula stage embryos, or blastocyst stage embryos according to the manufacturer’s protocol for purification of small RNA (<200 nt) and large RNA (>200 nt) as separate fractions.
Small RNA sequencing was performed on the Ion Proton Sequencer by using the Ion Total RNA-seq kit v2 (Thermo Fisher Scientific) according to manufacturer’s procedure for small RNA library preparation with no deviations from the specified protocol. By using an RNA isolation protocol that yielded a specific fraction of small RNA, an enrichment step was not needed.  Sample volumes were reduced to 3 l by vacuum centrifugation, and the entire sample was used to prepare the small RNA library for sequencing.  The cDNA sample was then processed on the Agilent Bioanalyzer (Agilent, Santa Clara, California) to ensure the presence of small RNA bound to a barcode (86 to 106 nt).

tag: developmental stage

value: Blastocyst-derived cells

tag: production method

value: somatic cell nuclear transfer

tag: molecule subtype

value: RNA < 200 nt in length


title: F KO midbrain PFF d90 SAM24378255

status: Public on Jun 18 2021

type: SRA

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

library_source: transcriptomic

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

organism: Mus musculus

source_name: RNA from brain region tissue

extract_protocol: Tissue was rapidly frozen and stored until a full collection was obtained. RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.

tag: tissue

value: brain

tag: Sex

value: F

tag: genotype

value: KO

tag: region

value: midbrain

tag: treatment

value: PFF

tag: days


title: ATAC_C57_BMDM_timecourse_24hIL4_rep2

city: La Jolla

first: Christopher

middle: K

last: Glass

address: 9500 Gilman Drive

department: CMM

institute: University of California, San Diego

library_source: genomic

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using Bowtie2 with default parameters (Langmead and Salzberg, 2012). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
The reproducible enriched regions (i.e. peaks) were identified by first using HOMER (Heinz et al., 2010) to call unfiltered 200-bp peaks (command “findPeaks -style factor -L 0 -C 0 -fdr 0.9 -size 200”) and then running IDR (Li et al., 2011) on replicates with default parameters.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

molecule: genomic DNA

growth_protocol: Bone marrow was isolated from mice and differentiated for 7 days using media containing M-CSF to bone marrow-derived macrophages (BMDMs) as described previously (Link et al., 2018).

extract_protocol:
Approximately 80k cells were lysed in 50 μL room temperature ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), 2.5 μL DNA Tagmentation Enzyme mix (Nextera DNA Library Preparation Kit, Illumina) was added. The mixture was incubated at 37°C for 30 minutes and subsequently purified using the ChIP DNA purification kit (Zymo Research) as described by the manufacturer.
DNA was amplified using the Nextera Primer Ad1 and a unique Ad2.n barcoding primers using NEBNext High-Fidelity 2X PCR MM for 8-14 cycles. PCR reactions were size selected using TBE gels for 175 – 350 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research). Samples were quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 75bp single-end sequenced on HiSeq 4000 or NextSeq 500 (Illumina).

treatment_protocol: Macrophages were left untreated or treated with 20 ng/mL mouse recombinant IL-4 (Peprotech) for 1, 6 or 24 hours

tag: strain

tag: cell type

value: BMDMs (bone marow-derived macrophages)


title: tonsil_surface_epithelium_subject2

type: RNA

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description:
tonsil surface epithelium from patient 2
S2

hyb_protocol: The biotin-labeled single-strand DNA was hybridized to Illumina HT-12 V4.0 expression beadchips following Illumina’s protocols but with the hybridization temperature at 48°C.

scan_protocol: Signal was detected with streptavidin-Cy3 and all signal intensity quantification was performed using an Illumina iScan high speed scanner, using the standard Illumina scanning protocol.

data_processing:
For each sample, a single intensity (expression) value for each Illumina probe on the array was obtained using
Illumina GenomeStudio software with standard settings and no background correction.
For the data matrices, the ID_REF is the Illumina Probe_ID, and the Detection Pval is as provided by the Illumina software.
Detection Pvalues < 0.01 were taken to indicate Present  (i.e., the corresponding expression level was considered to be above background).
Normalization of the expression values in each sample was done by scaling: for each sample all its expression values were
multiplied by the constant which made the median of the expression values for that sample equal to 256. The scaled values
were then log base 2 transformed. Two group comparisons of expression levels were done for each Illumina probe using the paired
t-test since samples from the 3 tonsil compartments were obtained from each of the 4 patients.
Note due to the processing of the RNA described above (Total RNA was first converted to 1st-strand cDNA using special primers), the
material hybridized to the Illumina HT-12 V4.0 expression beadchips only contained oligonucleotides corresponding to a subset of the
probes on this beadchip.  Hence the appropriate GEO platform is GPL13369 (which contains the proper subset of the
probes for the Illumina HT-12 V4.0 expression beadchip, whose GEO platform is GPL10558).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: tonsil surface epithelium

label_protocol:
Total RNA was first converted to 1st-strand cDNA using special primers and linear amplication was done following 2nd-strand cDNA synthesis,
as detailed in the manuscript. Amplified single strand DNA was then biotinylated using
the Encore (TM) BiotinIL Module following the manufacturer's instructions.

extract_protocol: Sample acquisition and RNA isolation from tonsil specimens were performed as described in the reference above.

tag: tonsil tissue compartment

value: PD-L1 negative squamous surface epithelium


title: RNAseq_DIDO3_WT_rep3

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10_3UTR_2kb.gtf
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cov, FPKM, and TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with TPM values for every transcript and every sample

source_name: mouse embryonic stem cell

growth_protocol: All mouse embryonic stem cells were cultured in KO-DMEM (Gibco, Invitrogen) supplemented with 20% fetal calf serum, GlutaMAX (Gibco, Invitrogen), non-essential amino acids, 2-mercaptoethanol, antibiotics and mouse leukemia inhibitory factor (LIF) (Millipore) on a layer of mitomycin C-treated mouse embryonic fibroblasts (MEF) or gelatinized tissue culture plates.

extract_protocol:
Total RNA was performed with a SPLIT RNA extraction kit (Lexogen, Austria) using the manufacturer´s protocol and approximately 2.5x10^6 cells. Triplicate RNA probes from wild-type mESC, DIDO3_exon16, and DIDO3_dCT+HADIDO3 were sent to Centro Nacional de Análisis Genómico (CNAG-CRG) in Barcelona, Spain.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell

tag: source

value: cell culture

value: wild type


title: ATAC_C57_BMDM_timecourse_24hIL4_rep1


title: ATAC_C57_BMDM_timecourse_basal_rep1


title: small_RNA_NT.Bl.3

source_name: scNT blastocyst stage embryos

value: Blastocyst stage


title: P184_08_P12

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: 3.8 µg of fragmented and labeled ss cDNA were hybridized to Affymetrix Porcine Gene 1.0 ST arrays for 16 h at 45° C in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software. Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.

label: Biotin

organism: Sus scrofa

source_name: liver

label_protocol: 200 ng of total RNA were used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: The animal experiment was approved by the local Animal Care and Use Com-mittee (Regierungspräsidium Giessen; permission no: GI 19/3 No. 30/2013). All experimental procedures described followed established guidelines for the care and handling of laboratory animals. For the experiment a total of 12, 5-weeks-old, male cross-bred piglets (Pietrain x (German Landrace x German Edelschwein)) were used, which were kept in pairs in flat-deck pens under controlled conditions (23 ± 2°C room temperature, 50-60 % relative humidity, light from 06.00 a.m. to 07.00 p.m.).

extract_protocol: Total RNA from liver aliquots (20 mg) was extracted using TRIzol reagent (Invi-trogen, Karlsruhe, Germany) according to the manufacturer’s protocol. RNA quantity and quality were determined spectrophotometrically and by electrophoresis. For microarray hybridization, RNA samples were processed at the Center of Excellence for Fluorescent Bioanalytics (Regensburg, Germany).

treatment_protocol: The piglets were randomly allocated to two groups (group CON, group PIV) of n = 6 piglets each, and fed identical nutrient-adequate diets according to a phase feeding system (phase I: until a body weight of 15 kg; phase II: until the end of the experiment) throughout the experimental period of 28 days. The diet in phase I consisted of (g/kg): wheat, 381.7; barley, 315; soybean meal (44% crude protein), 250; soybean oil, 15; min-eral and vitamin premix, 33.5; L-lysin, 2.6; DL-methionine, 1.0 and L-threonine, 1.2. The diet of phase II consisted of (g/kg): wheat, 401.9; barley, 302; soybean meal (44% crude protein), 240; soybean oil, 15; mineral and vitamin premix, 33.4; L-lysin, 1.5; DL-methionine, 0.5 and L-threonine, 0.7 and a mixture of organic acids (containing 45% formic acid, 7.7% lactic acid, 5% sodium acetate), 5. The carnitine concentration in the diets was below 10 mg/kg diet as analyzed by LC-MS/MS. In ad-dition, piglets were given orally either (per kg body weight (BW)): NaHCO3 (Sig-ma-Aldrich, Steinheim, Germany) solution (60 mg/100 mL) (group CON) or 30 mg so-dium pivalate (95% purity; Sigma-Aldrich, Steinheim, Germany) dissolved in NaHCO3 solution (group PIV) each day throughout the experimental period of 28 days. Water was constantly available ad libitum from nipple drinkers during both experiments. At the end of the experiment, the pigs were killed in the post-prandial period (2 h after their last meal) by electronarcosis followed by exsanguination. Blood was col-lected into heparinized polyethylene tubes (Sarstedt, Nümbrecht, Germany) and plasma obtained by centrifugation at 1100 x g for 10 min at 4°C and subsequently stored at -80°C. Aliquots from liver and selected muscles (longissimus dorsi, semitendi-nosus, superficial biceps femoris) were collected, snap-frozen in liquid nitrogen and stored at -80°C pending analysis.

tag: condition

value: Pivalate

tag: breed

value: German Landrace x German Edelschwein

tag: gender

value: male

value: liver


title: F KO midbrain mono d90 SAM24378235

value: mono


title: P184_12_P50


title: F WT brainstem mono d90 SAM24378269

value: WT

value: brainstem


title: P184_11_P31


title: tonsil_surface_epithelium_subject1

description:
tonsil surface epithelium from patient 1
S1


title: MeDIP_P10_rep3

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: MeDIP-seq

data_processing:
The MeDIP sequencing data were aligned to the mouse reference genome mm9 using segemehl (v0.2.0, default parameters) and the alignment was filtered to remove unusual insert sizes (>1kb) and multiple mappers.
Post-processing was done using the R package QSEA with the DKOL methylation rates as reference to obtain position-wise read counts.
Genome build: mm9
processed data files format and content: bigWig coverage files

source_name: J1 mESC

growth_protocol: mES cells were cultured in Knock Out DMEM media (Gibco) containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. For ES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CD1 mouse embryonic fibroblasts (MEFs) were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells per well of a six-well plate and were split every 3–4 days.

extract_protocol:
DNA was extracted from 500,000 - 1 million mES cells using phenol-chloroform-isoamyl alcohol (Thermo) extraction. 500ng of purified DNA was subjected to sonication on a Covaris S220 sonicator (10% duty cycle, Intensity 5, 200 cycles/burst, 6 one minute cycles).
After sonication fragmented DNA was end repaired and A-tailed using Ultra II End Repair/dA-Tailing Module (NEB) then adapters (Broad Institute, single index P7) were ligated using Blunt/TA Ligase Master Mix (NEB). Both protocols were carried out as recommended by the manufacturer. MagMeDIP kit (Diagenode) was used for precipitation and wash steps according to manufacturer’s recommendations. Libraries were PCR amplified with universal primers to add the P7/P5 graft sites using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) then size selected between 200-700bp on an E-Gel Agarose Gels 2% (Thermo). DNA was purified using MinElute Gel Extraction Kit (Qiagen). Purified DNA was quantified using Bioanalyzer HS DNA (Agilent) and qBit HS dsDNA (Thermo) kits then sequenced on a HiSeq 4000 system.

treatment_protocol: Passaged ten times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: mESC

value: Dnmt3a + Dnmt3b KO


title: RNAseq_DIDO3_WT_rep1


title: ATAC_C57_BMDM_timecourse_6hIL4_rep1

value: IL-4 6h


title: P184_05_K23

value: Control


title: MeDIP_P10_rep2

description: MeDIP-seq


title: ATAC_C57_BMDM_timecourse_1hIL4_rep2

value: IL-4 1h

value: BMDMs (bone marow-derived macrophages)


title: P184_10_P30


title: M KO midbrain mono d90 SAM24378238

value: brain

value: M

value: KO

value: midbrain


title: F WT midbrain PFF d60 SAM24378249

value: F

value: PFF


title: P184_09_P29

value: Pivalate

value: German Landrace x German Edelschwein

value: male


title: MeDIP_P10_rep1

description: MeDIP-seq


title: small_RNA_NT.BDC.3

value: Blastocyst-derived cells

value: somatic cell nuclear transfer

value: RNA < 200 nt in length


title: M WT striatum mono d90 SAM24378205

value: WT

value: striatum

value: mono


title: ATAC_C57_BMDM_timecourse_basal_rep2


title: M WT midbrain PFF d60 SAM24378254


title: small_RNA_NT.BDC.1


title: ATAC_C57_BMDM_timecourse_1hIL4_rep1

value: IL-4 1h


title: small_RNA_NT.Mo.3

source_name: scNT morula stage embryos

value: Morula stage


title: small_RNA_NT.Bl.4

value: Blastocyst stage


title: M WT brainstem PFF d60 SAM24378302

value: brain

value: M

value: brainstem


title: F WT midbrain PFF d60 SAM24378246

value: F

value: midbrain


title: MeDIP_P5_rep2

description: MeDIP-seq

treatment_protocol: Passaged five times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: mESC

value: Dnmt3a + Dnmt3b KO


title: small_RNA_NT.Bl.1


title: MeDIP_P1_rep3

description: MeDIP-seq

treatment_protocol: Passaged once after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid


title: P184_07_P10

value: Pivalate

value: German Landrace x German Edelschwein

value: male

value: liver


title: small_RNA_NT.Bl.2

value: somatic cell nuclear transfer

value: RNA < 200 nt in length


title: P184_06_K42

value: Control


title: P184_04_K22


title: P184_01_K1


title: P184_02_K3


title: RH6-3 skeletal muscle

city: Shijiazhuang

first: Linlin

last: Yang

state: Hebei

address: 348, Heping west road

country: China

institute: Hebei General Hospital

description:
mRNA, lncRNA
RH6-3M

data_processing:
fastp software was used for sequence filtering.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.91 whole genome using Hisat2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38.91
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: skeletal muscle

growth_protocol: 6 weeks old clean-grade C57BL/6J male mice weighing around 22g were purchased from Beijing Viton Lihua Experimental Center and sustained on a standard 12h light-dark cycles, with temperature (20-25℃) and humidity (40-60%). HFD mice were developed by feeding with a diet containing D12492J feed (20% protein, 20% carbohydrate, 60% fat) for 8 weeks.

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

treatment_protocol: Eight weeks after C57BL / 6J mice fed a high-fat diet (HFD), the degree of insulin resistance was assessed by intraperitoneal glucose tolerance test (IPGTT) and the insulin resistance model was successfully established. Mice were then treated with resveratrol and metformin for 6 weeks and skeletal muscle was collected.

value: skeletal muscle

value: HFD + reveratrol


title: F KO striatum mono d90 SAM24378198

value: KO

value: striatum

value: mono


title: small_RNA_NT.8c.2

source_name: scNT 8-cell stage embryos

value: 8-cell stage


title: F WT brainstem PFF d60 SAM24378281

value: brain

value: F

value: WT

value: brainstem

value: PFF


title: P184_03_K4

value: German Landrace x German Edelschwein


title: small_RNA_NT.8c.1


title: small_RNA_NT.Mo.2

value: Morula stage


title: MeDIP_P5_rep1

description: MeDIP-seq

value: mESC

value: Dnmt3a + Dnmt3b KO


title: RH3-3 skeletal muscle

description:
mRNA, lncRNA
RH3-3M

value: male


title: DKO0_Uhrf1_A10

description: WGBS

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the mm9 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads).
Genome build: mm9
processed data files format and content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

extract_protocol:
Purelink Genomic DNA mini kit (Invitrogen)
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

treatment_protocol: CRISPR Cas9 mediated knockout of Uhrf1, passaged seven times after Dnmt1 shRNA reversal with transiently transfected Cre recombinase plasmid

value: Dnmt3a + Dnmt3b + Uhrf1 KO


title: MH8-2 skeletal muscle

description:
mRNA, lncRNA
MH8-2M

value: skeletal muscle

value: HFD + metformin


title: DKO0_Uhrf1_C5

description: WGBS


title: MH4-3 skeletal muscle

description:
mRNA, lncRNA
MH4-3M


title: M KO brainstem mono d90 SAM24378276

value: M

value: KO


title: small_RNA_NT.8c.4

value: somatic cell nuclear transfer

value: RNA < 200 nt in length


title: F WT striatum PFF d60 SAM24378211

value: brain

value: striatum


title: MeDIP_P1_rep1

description: MeDIP-seq


title: RH1-4 skeletal muscle

description:
mRNA, lncRNA
RH1-4M

value: HFD + reveratrol


title: M KO brainstem PFF d60 SAM24378286

value: brainstem


title: MeDIP_P5_rep3

description: MeDIP-seq


title: small_RNA_NT.Mo.4


title: H7-5 skeletal muscle

description:
mRNA, lncRNA
H7-5M

value: HFD


title: small_RNA_NT.8c.3

value: 8-cell stage


title: M KO brainstem PFF d90 SAM24378297

value: PFF


title: MeDIP_P1_rep2

description: MeDIP-seq

value: mESC


title: RH1-2 skeletal muscle

description:
mRNA, lncRNA
RH1-2M


title: small_RNA_NT.2c.1

source_name: scNT 2-cell stage embryos

value: 2-cell stage


title: SCLC rep2

city: Aberdeen

first: Ryohei

last: Sekido

address: Foresterhill

department: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimgalore
Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters --outSAMtype BAM Unsorted --outSAMunmapped Within
Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates
Count files were created using htseq -count (v0.6.1) and modelled using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Testicular somatic cell-like cells derived from tc;Sf1ESCs

extract_protocol:
Cultured cells were harvested and total RNAs were extracted by using The ARCTURUS® PicoPure® RNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Testicular somatic cell-like cells


title: M KO midbrain PFF d90 SAM24378264

value: midbrain


title: M WT striatum PFF d90 SAM24378228

value: WT


title: small_RNA_NT.2c.4


title: F KO midbrain mono d90 SAM24378233

value: F

value: mono


title: todPGCLC rep2

source_name: ES cell-derived primordial germ cell-like cells isolated from a testicular organoid

value: Primordial germ cell-like cells


title: MH8-4 skeletal muscle

description:
mRNA, lncRNA
MH8-4M

value: skeletal muscle

value: HFD + metformin

value: male


title: F KO striatum PFF d60 SAM24378210

value: brain

value: KO

value: striatum


title: MH6-5 skeletal muscle

description:
mRNA, lncRNA
MH6-5M


title: tc;Sf1ESC rep1

source_name: A tcESC clone overexpressing mouse Sf1 transgene

value: ES cels


title: small_RNA_NT.2c.3

value: somatic cell nuclear transfer

value: RNA < 200 nt in length


title: todPGCLC rep1


title: small_RNA_IVF.BDC.2

source_name: IVF Blastocyst-derived cells

growth_protocol:
Following 22 to 24 hr of maturation, MII oocytes were fertilized using the laboratory’s standard in vitro fertilization protocol [46]. Briefly, one straw of cryopreserved bovine semen obtained from a Holstein bull (Hoffman AI, Logan, Utah) was removed from the liquid nitrogen tank and placed into a 35C water bath to thaw. Live sperm were isolated by centrifugation through a 45%/90% percoll gradient (MP Biomedical, Irvine, California), suspended (final concentration 1x106/ml) in Tyrode’s albumin lactate pyruvate containing 10 microgram/ml procine heparin and used to fertilize the oocytes. Twenty to 22 hr post-IVF, cumulus cells were removed by vortexing, and fertilized zygotes were washed in phosphate buffered saline with 0.32 mM sodium pyruvate, 5.55 mM glucose, and 3 mg/ml bovine serum albumin (PB1+). After washing, zygotes were cultured on a monolayer of bovine cumulus cells in 50 microliters of synthetic oviductal fluid (SOFaa) [47] with 3% FBS (Hyclone, lot number AC10240545) overlaid with mineral oil. The embryos were cultured at 38.5 deg C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture.
Provided above

value: Blastocyst-derived cells

value: In vitro fertilization


title: small_RNA_IVF.BDC.1


title: H7-4 skeletal muscle

description:
mRNA, lncRNA
H7-4M

value: HFD


title: small_RNA_NT.2c.2

value: 2-cell stage


title: M KO striatum mono d90 SAM24378208

value: M


title: small_RNA_IVF.BDC.3


title: small_RNA_IVF.Bl.4

source_name: IVF blastocyst stage embryos

value: Blastocyst stage


title: tc;Sf1ESC rep2

value: ES cells


title: F WT brainstem PFF d90 SAM24378295

value: F

value: WT

value: brainstem

value: PFF


title: H7-3 skeletal muscle

description:
mRNA, lncRNA
H7-3M

value: skeletal muscle

value: male


title: small_RNA_IVF.BDC.4


title: C1-4 skeletal muscle

description:
mRNA, lncRNA
C1-4M

value: normal diet


title: tcESC rep1

source_name: An ES cell line established from male tesco-cfp transgenic mouse embryos

value: XY;tesco-cfp


title: tcESC rep2


title: C1-5 skeletal muscle

description:
mRNA, lncRNA
C1-5M


title: F KO brainstem PFF d60 SAM24378283

value: brain

value: KO


title: M WT striatum PFF d60 SAM24378219

value: striatum


title: C2-2 skeletal muscle

description:
mRNA, lncRNA
C2-2M


title: H7-2 skeletal muscle

description:
mRNA, lncRNA
H7-2M


title: F KO striatum mono d90 SAM24378200

value: mono


title: small_RNA_IVF.Bl.3

value: In vitro fertilization

value: RNA < 200 nt in length


title: C1-1 skeletal muscle

description:
mRNA, lncRNA
C1-1M


title: vHIP POL M [27_32_vHIP]

city: Montreal

first: Mallar

last: Chakravarty

state: Quebec

address: 6875, boulevard LaSalle

country: Canada

institute: McGill

description: NS.1223.004.NEBNext_dual_i7_G1---NEBNext_dual_i5_G1.27_32_vHIP

data_processing:
Reads were filtered for a minimum Phred score of 30 and a minimum read length of 20 as well as trimmed off the first base pair from the 5’ end. Alignment was performed using the STAR aligner (Version 2.7.3a_2020-01-23) on the mouse genome build (mm10)/(GRCm38.p6)
Non-specific filtering removed genes with zero counts and lowly expressed genes that did not meet the requirement of a minimum of one count per million (cpm) in at least six samples. Only genes annotated as protein coding according to ensembl’s biomart Mus.musculus package (https://bioconductor.org/packages/release/data/annotation/html/Mus.musculus.html)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Matrix table with CPM of gene counts for every gene above 0 expression in at least one sample

source_name: vHIP POL M

extract_protocol:
RNA extraction was performed using ReliaPrep Tissue RNA Miniprep system (Promega).
The samples were randomized during library preparation and sequencing was performed on Illumina NovaSeq 6000 at the McGill University Génome Québec Innovation Centre. Sequencing was performed with Illumina NovaSeq 6000 for 72 samples, 3 regions in adolescent POL E or SAL E mice (PND 38; 6males/6females per group).

value: M

value: POL

value: ventral hippocampus


title: SCLC rep1

value: Testicular somatic cell-like cells


title: small_RNA_IVF.Bl.2

value: Blastocyst stage


title: F WT striatum PFF d90 SAM24378223

source_name: RNA from brain region tissue

value: F

value: WT


title: M WT midbrain PFF d90 SAM24378263

value: midbrain

value: PFF


title: small_RNA_IVF.Mo.4

source_name: IVF morula stage embryos

value: Morula stage


title: M WT midbrain PFF d60 SAM24378267


title: ACC POL M [27_32_ACC]

description: NS.1223.004.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.27_32_ACC

source_name: ACC POL M

value: anterior cingulate cortex


title: F WT brainstem PFF d60 SAM24378282

value: brain

value: brainstem


title: small_RNA_IVF.Mo.2


title: small_RNA_IVF.Mo.3


title: vHIP POL M [25_31_vHIP]

description: NS.1223.004.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.25_31_vHIP


title: small_RNA_IVF.Mo.1


title: ACC POL M [25_31_ACC]

description: NS.1223.004.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.25_31_ACC


title: vHIP POL F [24_32_vHIP]

description: NS.1223.004.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.24_32_vHIP

source_name: vHIP POL F


title: dHIP POL M [27_32_dHIP]

description: NS.1223.004.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.27_32_dHIP

source_name: dHIP POL M

value: dorsal hippocampus


title: small_RNA_IVF.8c.3

source_name: IVF 8-cell stage embryos

value: 8-cell stage


title: F WT brainstem PFF d60 SAM24378284


title: F KO brainstem PFF d90 SAM24378290

value: KO


title: small_RNA_IVF.8c.2

value: In vitro fertilization

value: RNA < 200 nt in length


title: dHIP POL F [24_32_dHIP]

description: NS.1223.004.NEBNext_dual_i7_B6---NEBNext_dual_i5_B6.24_32_dHIP

source_name: dHIP POL F

value: POL


title: small_RNA_IVF.8c.4


title: M WT brainstem mono d90 SAM24378274

value: M

value: mono


title: small_RNA_IVF.2c.4

source_name: IVF 2-cell stage embryos

value: 2-cell stage


title: dHIP POL M [25_31_dHIP]

description: NS.1223.004.NEBNext_dual_i7_F7---NEBNext_dual_i5_F7.25_31_dHIP


title: M WT brainstem mono d90 SAM24378277


title: ACC POL F [24_32_ACC]

description: NS.1223.004.NEBNext_dual_i7_A6---NEBNext_dual_i5_A6.24_32_ACC

source_name: ACC POL F

value: F


title: small_RNA_IVF.2c.3


title: M WT striatum mono d90 SAM24378207

value: WT

value: striatum


title: small_RNA_IVF.2c.2


title: 3R62PF Liver Donor

city: Bethesda

first: Ronald

middle: E

last: Engle

address: 50 South Drive 6345

department: NIAID

institute: NIH

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8 µg) of cRNA was hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using MAS 5.0 algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

source_name: Liver tissue

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

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

tag: age stage

value: Young (<40 years)

value: liver


title: R84PF Liver Donor


title: vHIP POL F [23_38_vHIP]

description: NS.1223.004.NEBNext_dual_i7_D4---NEBNext_dual_i5_D4.23_38_vHIP

value: ventral hippocampus


title: M KO midbrain PFF d60 SAM24378253

value: brain

value: midbrain

value: PFF


title: F WT striatum PFF d90 SAM24378225


title: small_RNA_IVF.2c.1

tag: developmental stage


title: M KO striatum mono d90 SAM24378206


title: 99PF Liver Donor

value: Old (>40 years)


title: vHIP POL M [21_38_vHIP]

description: NS.1223.004.NEBNext_dual_i7_F6---NEBNext_dual_i5_F6.21_38_vHIP


title: F WT midbrain PFF d90 SAM24378256


title: 116PF Liver Donor


title: 112PF Liver Donor


title: ACC POL F [23_38_ACC]

description: NS.1223.004.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.23_38_ACC

value: anterior cingulate cortex


title: M KO brainstem mono d90 SAM24378278

value: KO

value: brainstem


title: dHIP POL M [21_38_dHIP]

description: NS.1223.004.NEBNext_dual_i7_E6---NEBNext_dual_i5_E6.21_38_dHIP

value: POL

value: dorsal hippocampus


title: small_RNA_Oo.1

source_name: MII stage oocytes

growth_protocol:
The oocytes were cultured in TCM199 maturation medium containing Earle’s salts, L-glutamine, and sodium bicarbonate (Hyclone, Logan, Utah) supplemented with 10% (v/v) fetal bovine serum (FBS) (Hyclone, lot number AC10240545), 0.05 mg/ml bovine follicle stimulating hormone (Sioux Biochemicals, Sioux city, IA), 5 mg/ml bovine luteinizing hormone (Sioux Biochemical, Sioux Center, Iowa), 100 U/ml penicillin, and 100 mg/ml streptomycin.
Provided above

value: MII oocyte

tag: production method

value: RNA < 200 nt in length


title: 109PF Liver Donor


title: ACC POL M [21_38_ACC]

description: NS.1223.004.NEBNext_dual_i7_D6---NEBNext_dual_i5_D6.21_38_ACC

value: M


title: small_RNA_Oo.3

tag: molecule subtype


title: F KO striatum PFF d90 SAM24378220

tag: tissue

value: F


title: small_RNA_Oo.4


title: 101PF Liver Donor


title: small_RNA_Fb.4

source_name: Fibroblast cells

growth_protocol:
Primary bovine fibroblast cultures were established from ear biopsy tissues from a Brahma Spanish bull cross using well-established procedures (Kubota, et al. 2000. PNAS 97:990-995).
Provided above

value: fibroblast


title: M WT brainstem PFF d60 SAM24378287

tag: Sex

value: WT


title: small_RNA_Fb.3


title: F KO brainstem mono d90 SAM24378270

tag: genotype

value: mono


title: dHIP POL F [23_38_dHIP]

description: NS.1223.004.NEBNext_dual_i7_C4---NEBNext_dual_i5_C4.23_38_dHIP


title: R87PF Liver Donor

value: liver


title: vHIP POL M [19_26_vHIP]

description: NS.1223.004.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.19_26_vHIP

value: ventral hippocampus


title: 89PF Liver Donor


title: small_RNA_Fb.1


title: dHIP POL M [19_26_dHIP]

description: NS.1223.004.NEBNext_dual_i7_D5---NEBNext_dual_i5_D5.19_26_dHIP


title: F WT midbrain PFF d90 SAM24378258

value: brain

tag: region

value: midbrain


title: M KO midbrain PFF d90 SAM24378265

tag: treatment

value: PFF


title: vHIP POL F [17_32_vHIP]

description: NS.1223.004.NEBNext_dual_i7_B2---NEBNext_dual_i5_B2.17_32_vHIP


title: dHIP POL F [17_32_dHIP]

description: NS.1223.004.NEBNext_dual_i7_A2---NEBNext_dual_i5_A2.17_32_dHIP


title: H4_9406

city: New York

first: Alexander

last: Charney

state: New York

address: 1424 Madison Ave, 14-52

institute: Icahn Medical School at Mount Sinai

data_processing:
After sequencing,  base calls were converted into raw reads and filtered after quality assessment
The quality-filtered raw data was then converted into FASTQ files using bcl2fastq Conversion tool
RNA-seq reads were aligned to the GRCh38 primary assembly with Gencode release annotation by STAR (v2.7.3a)49 using per-sample 2-pass mapping (--twopassMode Basic) and chimeric alignment options (--chimOutType Junctions SeparateSAMold -chimSegmentMin 15 -chimJunctionOverhangMin 15)
RNA-seq QC metrics were calculated by fastqc (v0.11.8) and Picard Tools (v2.22.3)50
Quantification was done at the gene-level with STAR (--quantMode GeneCounts), at the transcript level with kallisto (v0.46.1), and with antisense specificity using featureCounts51 (Subread R package v1.6.3 and strandness option -s 2) for various counting criteria, including gene-level grouping (-t exon -g gene_id), gene-level grouping / primary alignments only / count all overlapped features (-t exon -g gene_id -primary -O), transcript-level grouping (-t exon -g transcript_id), and exon level / count all overlapped features (-t exon -f -O)
Quantification was done at the gene-level with STAR (--quantMode GeneCounts), at the transcript level with kallisto (v0.46.1), and with antisense specificity using featureCounts51 (Subread R package v1.6.3 and strandness option -s 2) for various counting criteria, including gene-level grouping (-t exon -g gene_id), gene-level grouping / primary alignments only / count all overlapped features (-t exon -g gene_id -primary -O), transcript-level grouping (-t exon -g transcript_id), and exon level / count all overlapped features (-t exon -f -O)
A customized version of MultiQC52 was used the compile and summarize the per-sample statistics from STAR, Picard Tools and featureCounts (i.e. gene-level counts, mtRNA counts, globinRNA counts, etc) into an interactive HTML report
For further steps please refer to the paper
Genome_build: GRCh38 primary assembly
Supplementary_files_format_and_content: Adjusted Count Matrix

source_name: Blood

extract_protocol:
Peripheral blood was collected in Tempus tubes then extracted using the MagMax protocol for Stabilized Blood Tubes RNA Isolation Kit
Total RNA was examined for quantity and quality using the Fragment Analyzer and Quant-It RNA systems. Whole-transcriptome library preparation using the TruSeq Stranded Total RNA Library Prep Gold

tag: subject id

tag: diagnosis

value: healthy

value: blood

tag: age range (years)

value: Female

tag: ethnicity

value: White

tag: comorbidities

tag: immnosuppressive

tag: timepoint (t0 =before treatment, t#>0= sample taken after treatment )


title: 93PF Liver Donor

value: Young (<40 years)


title: H4_9406.1

tag: gender


title: ACC POL M [19_26_ACC]

description: NS.1223.004.NEBNext_dual_i7_C5---NEBNext_dual_i5_C5.19_26_ACC

tag: strain

value: POL

value: anterior cingulate cortex


title: 84PF Liver Donor

tag: age stage


title: M WT midbrain mono d90 SAM24378240

value: M

tag: days


title: H3_3590


title: ACC POL F [17_32_ACC]

description: NS.1223.004.NEBNext_dual_i7_H1---NEBNext_dual_i5_H1.17_32_ACC

value: F


title: F KO midbrain PFF d90 SAM24378259

value: KO


title: M KO striatum PFF d90 SAM24378230

value: striatum


title: H3_3590.1


title: H2_4714

value: Male


title: vHIP POL F [16_38_vHIP]

description: NS.1223.004.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.16_38_vHIP


title: WT contra MB Null SAM24372699

value: WT

tag: side

value: contralateral

tag: aav

tag: samid


title: dHIP POL F [16_38_dHIP]

description: NS.1223.004.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.16_38_dHIP

tag: Sex

tag: tissue

value: dorsal hippocampus


title: 2R167PF Liver Donor

value: Old (>40 years)

value: liver


title: KO contra MB Null SAM24372703

value: brain

tag: genotype

value: gpnmb KO

tag: region

value: midbrain


title: 1R187PF Liver Donor


title: H1_1241

tag: subject id

tag: diagnosis

value: healthy

value: blood

value: Female

value: Asian


title: Young SIRT6KO mouse brain, 21 days old, biological replicate 1

city: Beer Sheva

first: Debra

last: Toiber

state: Israel

address: Ben Gurion Road #1, Building 40, room 205

country: Israel

institute: Ben Gurion University of the Negev

description: brain sample of 21-day-old SIRT6KO (-/-) mouse

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed using Affymetrix Power Tools, APT version 1.10.1, with the following parameters: #%affymetrix-algorithm-param-apt-opt-analysis-spec=rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true.target=0.doavg=false.subsetmd5=6939e6d4c979d793c87e21aab959a6b4,pm-only,med-polish.FixFeatureEffect=false.UseInputModel=false.FitFeatureResponse=true.expon=false.attenuate=true.l=0.005.h=-1,expr.genotype=false.strand=false.allele-a=false

source_name: young SIRT6KO

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol reagent RNA extraction followed by additional purification using RNeasy from Qiagen

tag: age

value: 21 days


title: KO ipsi STR Null SAM24372750

value: ipsilateral

value: whole stratum


title: Young SIRT6 heterozygous mouse brain, 21 days old, biological replicate 3

description: brain sample of 21-day-old heterozygous (+/-) mouse. In this animal model, SIRT6WT (+/+) and SIRT6het (+/-) present no phenotypical differences.

source_name: young het

value: het


title: H1_1241.1

tag: age range (years)

tag: ethnicity

tag: comorbidities


title: Old WT mouse brain, biological replicate 2

description: brain sample of 22-26-month-old WT (+/+) mouse

source_name: Old WT

value: 22-26 months


title: 185PF Liver Donor


title: 1R183PF Liver Donor


title: Young SIRT6KO mouse brain, 21 days old, biological replicate 3


title: 181PF Liver Donor


title: KO ipsi MB Null SAM24372731


title: M8_2423

value: MISC

tag: gender

value: Hispanic

tag: immnosuppressive

tag: timepoint (t0 =before treatment, t#>0= sample taken after treatment )


title: Young WT mouse brain, 21 days old, biological replicate 2

description: brain sample of 21-day-old WT (+/+) mouse

source_name: young WT

value: WT


title: vHIP SAL M [14_35_vHIP]

description: NS.1223.004.NEBNext_dual_i7_F3---NEBNext_dual_i5_F3.14_35_vHIP

source_name: vHIP SAL M

tag: strain

value: M

tag: treatment

value: SAL

value: ventral hippocampus


title: Young SIRT6KO mouse brain, 21 days old, biological replicate 2

value: brain


title: H2_4714.1

value: Male

value: White


title: WT ipsi STR aSyn SAM24372759

source_name: RNA from brain region tissue

tag: side

tag: aav


title: dHIP SAL M [14_35_dHIP]

description: NS.1223.004.NEBNext_dual_i7_E3---NEBNext_dual_i5_E3.14_35_dHIP

source_name: dHIP SAL M

tag: Sex

value: dorsal hippocampus


title: M6_6681

tag: tissue

value: blood

value: Appendicitis


title: ACC POL F [16_38_ACC]

description: NS.1223.004.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.16_38_ACC

value: F

value: POL

value: anterior cingulate cortex


title: WT ipsi MB aSyn SAM24372735

tag: genotype

value: ipsilateral

value: midbrain

tag: samid


title: WT ipsi MB Null SAM24372725

tag: region


title: R60PF2 Liver Donor

tag: age stage

value: Old (>40 years)

value: liver


title: WT contra MB Null SAM24372700

value: WT

value: contralateral


title: ACC SAL M [14_35_ACC]

description: NS.1223.004.NEBNext_dual_i7_D3---NEBNext_dual_i5_D3.14_35_ACC

source_name: ACC SAL M

value: M

value: SAL


title: dHIP SAL F [13_09_dHIP]

description: NS.1223.004.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.13_09_dHIP

source_name: dHIP SAL F


title: M7_8542

tag: subject id

tag: diagnosis

value: MISC

value: Female

value: Black

value: Major Depression Disorder, Post Tramatic Stress Disorder


title: Old WT mouse brain, biological replicate 3

tag: age

value: 22-26 months

value: brain


title: M5_1134

value: blood

tag: age range (years)

value: Male

tag: ethnicity

value: Hispanic

tag: comorbidities

value: Asthma


title: Old WT mouse brain, biological replicate 1


title: vHIP SAL F [13_09_vHIP]

description: NS.1223.004.NEBNext_dual_i7_H5---NEBNext_dual_i5_H5.13_09_vHIP

source_name: vHIP SAL F

value: F

value: ventral hippocampus


title: vHIP SAL M [11_09_vHIP]

description: NS.1223.004.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.11_09_vHIP


title: 174PF Liver Donor

value: Old (>40 years)

value: liver


title: ACC SAL F [13_09_ACC]

description: NS.1223.004.NEBNext_dual_i7_F5---NEBNext_dual_i5_F5.13_09_ACC

source_name: ACC SAL F

value: anterior cingulate cortex


title: 176PF Liver Donor


title: 178PF Liver Donor


title: Young WT mouse brain, 21 days old, biological replicate 1

value: 21 days

value: WT


title: dHIP SAL M [11_09_dHIP]

description: NS.1223.004.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.11_09_dHIP

value: M

value: SAL

value: dorsal hippocampus


title: KO contra MB Null SAM24372706

value: gpnmb KO

value: contralateral

value: midbrain


title: WT contra MB aSyn SAM24372709

value: brain


title: M2_3742

value: MISC

value: blood

tag: gender

value: Female

tag: immnosuppressive

tag: timepoint (t0 =before treatment, t#>0= sample taken after treatment )


title: M3_8776

value: Male

value: Black

value: Asthma


title: WT ipsi MB aSyn SAM24372734

tag: side

value: ipsilateral


title: R62PF Liver Donor

value: Young (<40 years)

value: liver


title: vHIP SAL F [10_35_vHIP]

description: NS.1223.004.NEBNext_dual_i7_A4---NEBNext_dual_i5_A4.10_35_vHIP

tag: strain

value: F

tag: treatment

value: ventral hippocampus


title: KO ipsi STR Null SAM24372754

tag: tissue

value: whole stratum

tag: aav


title: 169PF Liver Donor

value: Old (>40 years)


title: 1R128PF Liver Donor


title: ACC SAL M [11_09_ACC]

description: NS.1223.004.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.11_09_ACC

tag: Sex

value: M

value: SAL

value: anterior cingulate cortex


title: KO ipsi MB Null SAM24372728

value: brain

tag: genotype

value: gpnmb KO

tag: region

value: midbrain

tag: samid


title: M4_3253

tag: subject id

tag: diagnosis

value: MISC

value: blood

value: Female

value: Hispanic


title: M1_1054

tag: age range (years)

value: Male


title: C7_7534.1

value: covid

tag: ethnicity

value: Black

value: Inflammatory Bowel Disease

value: Infliximab


title: 143PF Liver Donor

tag: age stage

value: Young (<40 years)

value: liver


title: 141PF Liver Donor

value: Old (>40 years)


title: KO ipsi MB Null SAM24372729

value: ipsilateral


title: C7_7534

tag: gender

tag: comorbidities


title: 139PF Liver Donor


title: ACC SAL F [10_35_ACC]

description: NS.1223.004.NEBNext_dual_i7_G3---NEBNext_dual_i5_G3.10_35_ACC

value: F

value: SAL

value: anterior cingulate cortex


title: KO ipsi STR aSyn SAM24372765

value: brain

value: gpnmb KO

value: whole stratum


title: vHIP POL F [08_31_vHIP]

description: NS.1223.004.NEBNext_dual_i7_B5---NEBNext_dual_i5_B5.08_31_vHIP

source_name: vHIP POL F

value: POL

value: ventral hippocampus


title: C6_8972

value: blood

value: Male

value: White

value: Gastrochisis

tag: immnosuppressive

value: Tacrolimus

tag: timepoint (t0 =before treatment, t#>0= sample taken after treatment )


title: 137PF Liver Donor


title: WT ipsi STR aSyn SAM24372755

value: WT

tag: side


title: C5_1971

value: covid

value: Hispanic

value: B-cell Acute Lymphoblastic Leukemia

value: Chemotherapy


title: 1R126PF Liver Donor

value: Young (<40 years)

value: liver


title: dHIP POL F [08_31_dHIP]

description: NS.1223.004.NEBNext_dual_i7_A5---NEBNext_dual_i5_A5.08_31_dHIP

source_name: dHIP POL F

tag: strain

value: F

tag: treatment

value: dorsal hippocampus


title: WT ipsi STR Null SAM24372747

tag: tissue

value: brain

value: ipsilateral

value: whole stratum

tag: aav


title: C5_1971.1

value: blood


title: dHIP SAL F [10_35_dHIP]

description: NS.1223.004.NEBNext_dual_i7_H3---NEBNext_dual_i5_H3.10_35_dHIP

tag: Sex

value: SAL


title: ACC POL F [08_31_ACC]

description: NS.1223.004.NEBNext_dual_i7_H4---NEBNext_dual_i5_H4.08_31_ACC

source_name: ACC POL F

value: POL

value: anterior cingulate cortex


title: KO ipsi MB Null SAM24372730

tag: genotype

value: gpnmb KO

tag: region

value: midbrain


title: WT ipsi STR Null SAM24372743

value: WT

tag: samid


title: vHIP SAL F [08_09_vHIP]

description: NS.1223.004.NEBNext_dual_i7_H2---NEBNext_dual_i5_H2.08_09_vHIP

value: ventral hippocampus


title: dHIP SAL F [08_09_dHIP]

description: NS.1223.004.NEBNext_dual_i7_G2---NEBNext_dual_i5_G2.08_09_dHIP


title: 163PF Liver Donor

source_name: Liver tissue

value: Old (>40 years)


title: C5_2836

tag: subject id

tag: diagnosis

value: covid

value: Male

value: Hispanic

value: B-cell Acute Lymphoblastic Leukemia

value: Chemotherapy


title: 1R135PF Liver Donor

value: Young (<40 years)

value: liver


title: C4_3964

tag: age range (years)

value: Female

tag: ethnicity

value: Not Reported

value: Pineoblastoma


title: ACC SAL F [08_09_ACC]

description: NS.1223.004.NEBNext_dual_i7_F2---NEBNext_dual_i5_F2.08_09_ACC

value: F

value: SAL


title: C4_8386

value: blood

tag: gender


title: WT ipsi MB Null SAM24372724

value: brain

value: ipsilateral

value: midbrain


title: WT ipsi MB Null SAM24372720

value: WT


title: WT ipsi STR Null SAM24372745

value: whole stratum


title: C4_5194

value: covid

tag: comorbidities


title: 161PF Liver Donor

tag: age stage

value: Old (>40 years)


title: vHIP POL M [07_26_vHIP]

description: NS.1223.004.NEBNext_dual_i7_C3---NEBNext_dual_i5_C3.07_26_vHIP

source_name: vHIP POL M

value: M

value: POL

value: ventral hippocampus


title: 157PF Liver Donor

value: liver


title: dHIP POL M [07_26_dHIP]

description: NS.1223.004.NEBNext_dual_i7_B3---NEBNext_dual_i5_B3.07_26_dHIP

source_name: dHIP POL M

value: dorsal hippocampus


title: 155PF Liver Donor


title: C5_1268

source_name: Blood

value: Male

value: Hispanic

value: B-cell Acute Lymphoblastic Leukemia

tag: immnosuppressive

value: Chemotherapy

tag: timepoint (t0 =before treatment, t#>0= sample taken after treatment )


title: C4_5358

value: blood

value: Female

value: Not Reported

value: Pineoblastoma


title: 165PF Liver Donor


title: WT ipsi STR aSyn SAM24372756

value: brain

value: WT

tag: side

value: ipsilateral


title: ACC POL M [07_26_ACC]

description: NS.1223.004.NEBNext_dual_i7_A3---NEBNext_dual_i5_A3.07_26_ACC

source_name: ACC POL M

tag: strain

tag: treatment

value: anterior cingulate cortex


title: C4_3925

value: covid

tag: tissue


title: 153PF Liver Donor

value: Young (<40 years)


title: vHIP SAL M [07_09_vHIP]

description: NS.1223.004.NEBNext_dual_i7_D7---NEBNext_dual_i5_D7.07_09_vHIP

tag: Sex

value: M

value: SAL

value: ventral hippocampus


title: 151PF Liver Donor

value: Old (>40 years)

value: liver


title: C3_4525

value: Male

value: Hispanic

value: Autoimmune Anemia

value: Steroids


title: KO ipsi STR aSyn SAM24372762

tag: genotype

value: gpnmb KO

value: whole stratum

tag: aav


title: dHIP SAL M [07_09_dHIP]

description: NS.1223.004.NEBNext_dual_i7_C7---NEBNext_dual_i5_C7.07_09_dHIP

value: dorsal hippocampus


title: C3_3524

value: blood


title: WT contra MB aSyn SAM24372713

value: brain

value: WT

value: contralateral

tag: region

value: midbrain

tag: samid


title: 149PF Liver Donor


title: C3_3215

tag: subject id

tag: diagnosis

value: covid


title: ACC SAL M [07_09_ACC]

description: NS.1223.004.NEBNext_dual_i7_B7---NEBNext_dual_i5_B7.07_09_ACC

value: M

value: SAL

value: anterior cingulate cortex


title: KO ipsi STR aSyn SAM24372764

value: ipsilateral


title: KO contra MB aSyn SAM24372718


title: WT ipsi MB Null SAM24372723


title: 147PF Liver Donor

value: Old (>40 years)

value: liver


title: dHIP POL F [06_38_dHIP]

description: NS.1223.004.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.06_38_dHIP

value: F

value: POL


title: vHIP POL F [06_38_vHIP]

description: NS.1223.004.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.06_38_vHIP

value: ventral hippocampus


title: 132PF Liver Donor


title: C2_3057.1

tag: age range (years)

value: Male

tag: ethnicity

value: Hispanic

value: Asthma


title: C3_5793

value: blood

tag: gender

tag: comorbidities

value: Autoimmune Anemia

value: Steroids


title: 130PF Liver Donor

tag: age stage


title: ACC POL F [06_38_ACC]

description: NS.1223.004.NEBNext_dual_i7_C8---NEBNext_dual_i5_C8.06_38_ACC


title: KO ipsi STR Null SAM24372751

value: brain

value: gpnmb KO

value: whole stratum


title: vHIP SAL F [05_13_vHIP]

description: NS.1223.004.NEBNext_dual_i7_B8---NEBNext_dual_i5_B8.05_13_vHIP

value: SAL


title: WT ipsi STR aSyn SAM24372758

value: WT


title: C2_3057

value: covid

tag: immnosuppressive

tag: timepoint (t0 =before treatment, t#>0= sample taken after treatment )


title: C2_3597


title: 122PF Liver Donor

value: Young (<40 years)


title: dHIP SAL F [05_13_dHIP]

description: NS.1223.004.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.05_13_dHIP

tag: strain

value: dorsal hippocampus


title: KO contra MB Null SAM24372705

tag: side

value: contralateral

value: midbrain


title: 120PF Liver Donor

tag: tissue

value: liver


title: 8PF Liver Donor


title: C1_3748.1

value: Female

value: B-cell Acute Lymphoblastic Leukemia

value: Chemotherapy


title: C1_6250

value: blood

value: Hispanic


title: KO ipsi MB Null SAM24372726

value: ipsilateral


title: vHIP SAL M [04_09_vHIP]

description: NS.1223.004.NEBNext_dual_i7_G4---NEBNext_dual_i5_G4.04_09_vHIP

tag: Sex

value: M

tag: treatment

value: ventral hippocampus


title: 29PF Liver Donor


title: KO contra MB aSyn SAM24372719

value: brain

tag: genotype

value: gpnmb KO

tag: aav


title: WT ipsi STR Null SAM24372748

value: WT

tag: region

value: whole stratum

tag: samid


title: dHIP SAL M [04_09_dHIP]

description: NS.1223.004.NEBNext_dual_i7_F4---NEBNext_dual_i5_F4.04_09_dHIP

value: SAL


title: C1_9383

tag: subject id

tag: diagnosis

value: covid


title: WT contra MB Null SAM24372697

value: contralateral


title: 124PF Liver Donor

value: Old (>40 years)


title: 25PF Liver Donor

value: liver


title: WT ipsi MB aSyn SAM24372732

value: midbrain


title: 18PF Liver Donor


title: DLD1_mAID_POL2RA_Factory_async_aux_rep2

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

institute: University Medical Center Goettingen

description:
nascsent RNA
DLD1_async_factory_gene_irnaseq_GRCh38_qval0.05n.csv
DLD1_factory_async_irnaseq_gene_quant.txt
A006850074_126018_S20_L001_sorted.bam

data_processing:
alignment with STAR aligner
count quantification with iRNAseq tool
normalization with RUV-seq
differential gene expression analysis with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Raw read gene level quantification table for all the samples

source_name: colorectal adenocarcinoma cell lines

growth_protocol: mAID-POLR2A(RPB1)-mClover DLD-1 and TO2B-/-TOP2A- mAID HCT116 cells were passaged in RPMI-1640 medium supplemented with 10% FBS under 5% CO2.

extract_protocol:
Nascent RNA from ~10 million mAID-RPB1-mCLover DLD-1 or TO2B-/-  -TOP2A-mAID HCT116 cells was isolated according to “factory-seq” protocol. Briefly, cells were gently scraped and lysed in isotonic “physiological buffer” supplemented with 0.5% NP40 buffer. After assessing lysis and nuclei integrity on a hemocytometer microscopy, nuclei were treated with DNase I for 30 min at 33°C, washed, and nuclei were lysed in “native lysis buffer” and treated with caspase group III enzyme mix, pelleted by centrifugation, before the supernatant holding nascent RNA was collected in TRIzol and purified using the Direct-Zol RNA purification kit.
TruSeq RNA library kit (Illumina)

treatment_protocol: Inducible depletion of RPB1 or TOP2A initiated via treatment with doxycycline for 24 h to induce TIR1 expression, before addition of 500 µM indole-3-acetic acid solution (“auxin”) for  14 h (asynchronised) to induce RPB1 degradation. Asynchronous cells treated with auxin were harvested, where applicable resuspended in 1 µg/ml propidium iodide to counterstain DNA, and sorted to isolate G1 cells using a FACS Canto II flow cytometer.

tag: cell line

value: 14h treatment with Auxin

tag: agent


title: DLD1_mAID_POL2RA_Factory_async_aux_rep1

description:
nascsent RNA
DLD1_async_factory_gene_irnaseq_GRCh38_qval0.05n.csv
DLD1_factory_async_irnaseq_gene_quant.txt
A006850074_126016_S19_L001_sorted.bam


title: ACC SAL M [04_09_ACC]

description: NS.1223.004.NEBNext_dual_i7_E4---NEBNext_dual_i5_E4.04_09_ACC

value: anterior cingulate cortex


title: vHIP POL M [03_32_vHIP]

description: NS.1223.004.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.03_32_vHIP

value: POL


title: 16PF Liver Donor


title: ACC POL M [03_32_ACC]

description: NS.1223.004.NEBNext_dual_i7_G9---NEBNext_dual_i5_G9.03_32_ACC


title: ACC SAL F [05_13_ACC]

description: NS.1223.004.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.05_13_ACC

value: F


title: WT contra MB Null SAM24372702


title: WT ipsi STR aSyn SAM24372757

value: ipsilateral


title: DLD1_mAID_POL2RA_Factory_async_ctrl_rep1

description:
nascsent RNA
DLD1_async_factory_gene_irnaseq_GRCh38_qval0.05n.csv
DLD1_factory_async_irnaseq_gene_quant.txt
A006850074_126012_S17_L001_sorted.bam

value: untreated


title: 69PF Liver Donor


title: R60PF Liver Donor


title: C1_3748

value: blood

tag: age range (years)

tag: gender

value: Female

tag: ethnicity

value: Hispanic

tag: comorbidities

value: B-cell Acute Lymphoblastic Leukemia

value: Chemotherapy


title: WT ipsi STR Null SAM24372744

value: brain

value: WT

value: whole stratum


title: dHIP SAL M [03_15_dHIP]

description: NS.1223.004.NEBNext_dual_i7_E9---NEBNext_dual_i5_E9.03_15_dHIP

tag: strain

value: M

value: SAL

value: dorsal hippocampus


title: KO ipsi STR Null SAM24372753

value: gpnmb KO

tag: side


title: ChIP_GFP_Auxin

data_processing:
ENCODE ChIP-seq pipeline v 1.6.0, histone peak calling for GFP tagged Pol II
Genome_build: hg38
Supplementary_files_format_and_content: Input normalized ChIP signal bigwig files

growth_protocol: POLR2A-mAID-mClover DLD-1 were passaged in RPMI-1640 medium supplemented with 10% FBS under 5% CO2.

extract_protocol:
DLD-1 cells cultured to 80% confluence in 15-cm dishes were crosslinked in 1% PFA/PBS 10 min at room temperature. Cells were processed using the NEXSON ChIP protocol as previously described (Arrigoni et al, 2015). In brief, nuclei were isolated via sonication using a Bioruptor Pico (Diagenode; 9 cycles of 10 sec on and 30 sec off). Chromatin was then sheared in the recommended shearing buffer (27-30 cycles, 30 sec on and 30 sec off) to a range of 200-500 bp-long fragments, and immunoprecipitation was performed using 4 µg of the appropriate antibody
DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

treatment_protocol: Inducible depletion of RPB1 initiated via treatment with doxycycline for 24 h to induce TIR1 expression, before addition of 500 µM indole-3-acetic acid solution (“auxin”). For cell synchronization, G2/M arrest was achieved by addition of 10 µM RO-3306 inhibitor for 21 h. Following this incubation time, cells were washed with PBS, and auxin-supplemented medium was added for up to 6 h to allow cells to quantitatively enter G1. At this point, cells were harvested, where applicable resuspended in 1 µg/ml propidium iodide to counterstain DNA, and sorted using a FACS Canto II flow cytometer.

tag: cell cycle

value: synchronous G1 reenter sorted

value: 14h treatment with Auxin

tag: chip antibody

value: anti-GFP:ab290, Abcam


title: Input_GFP_Auxin


title: 20PF Liver Donor

tag: age stage

value: Young (<40 years)

tag: tissue

value: liver


title: KO ipsi MB aSyn SAM24372737

tag: genotype

value: ipsilateral

value: midbrain

tag: aav


title: ACC SAL M [03_15_ACC]

description: NS.1223.004.NEBNext_dual_i7_D9---NEBNext_dual_i5_D9.03_15_ACC

tag: Sex

tag: treatment

value: anterior cingulate cortex


title: dHIP POL M [03_32_dHIP]

description: NS.1223.004.NEBNext_dual_i7_H9---NEBNext_dual_i5_H9.03_32_dHIP

value: POL


title: WT ipsi MB aSyn SAM24372736

tag: region

tag: samid


title: ChIP_GFP_Control

tag: agent

value: untreated


title: KO contra MB aSyn SAM24372715

value: brain

value: contralateral


title: vHIP SAL M [03_13_vHIP]

description: NS.1223.004.NEBNext_dual_i7_E2---NEBNext_dual_i5_E2.03_13_vHIP

value: ventral hippocampus


title: Input_GFP_Control


title: DLD1_mAID_POL2RA_Factory_async_ctrl_rep2

description:
nascsent RNA
DLD1_async_factory_gene_irnaseq_GRCh38_qval0.05n.csv
DLD1_factory_async_irnaseq_gene_quant.txt
A006850074_126014_S18_L001_sorted.bam

tag: cell line


title: 56PF Liver Donor


title: 51PF Liver Donor

value: Old (>40 years)


title: KO contra MB aSyn SAM24372714


title: dHIP SAL M [03_13_dHIP]

description: NS.1223.004.NEBNext_dual_i7_D2---NEBNext_dual_i5_D2.03_13_dHIP

value: M

value: SAL


title: vHIP SAL M [03_15_vHIP]

description: NS.1223.004.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.03_15_vHIP


title: shTUBG U2OS NS IP PCNA (2)

city: Malmö

first: Maria

middle: Alvarado

last: Kristensson

address: 59 Jan Waldenströms street

country: Sweden

institute: Lund University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie 2, version 2.1.0. The option “-k 1” was chosen so that only uniquely mapped reads are allowed. The mapping results in SAM are converted to BAM and sorted by coordinates using samtools, version 1.7-13-g8dee2a2.
Peaks were identified using MACS2 (parameters: callpeak -B -g hs --nomodel --extsize 200 -q 0.05). BAM files of replicate samples were merged into one file before peak calling was performed. FDR cut-off of 0.05 was used to determining significant peaks.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were generated; Scores represent signal values

source_name: osteosarcoma

growth_protocol: U2OS osteosarcoma epitelial cells were grown in McCoy'5A medium supplemented with 5% fetal calf serum and 1% PEST.

extract_protocol:
Nuclei were lysed and  chromatin was micrococcal treated. The fragmented chromatin was pre-cleared  with Dynabeads. Gamma-tubulin-, PCNA-, Mcm5-, and FoxM1-DNA-complexes were isolated with the correspondant antibody and isolated with Dynabeads.
ChIP DNA using the Smarter ThruPLEX DNA-seq Kit (cat# R400676, Takara) with HT dual indexes (cat# R400660, Takara)

treatment_protocol: Cells were subjected to dubble thymidine syncronization and released for 3h, 7h, 9h prior to harvest. Alternatively, non-synchronous cells were harvested.

value: bone

tag: time point

value: Non-synchronous

tag: antibody

value: PCNA


title: shTUBG U2OS NS IP PCNA (1)


title: 60PF Liver Donor


title: KO ipsi STR Null SAM24372752

value: gpnmb KO

value: whole stratum


title: Ba1613

first: Tasos

last: Gogakos

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: size fractionated RNA (~60-100 nt)

data_processing:
Barcoded samples were demultiplexed by assigning 5 nt barcodes using cutadapt. Adapters and barcodes were removed (cutadapt) from fastq files. Fastq files were converted to fasta using perl scripts.
Fasta files were collapsed into a non-redundant fasta file in which the read count is contained within the read header and mapped against an experimentally validated tRNA reference database (Gogakos T., et al. 2017, Cell Reports)  http://gtrna.ucsc.edu. BWA was v0.5.9 used, with parameters aln -n 2 -t 16 -i 0 -d 0
Multi-mapping reads are first assigned to hits with the lowest number of errors, then the count is split equally between the number of locations mapped.
Genome_build: hg19
Supplementary_files_format_and_content: Tab seperated file. Columns represent transcript name, read counts and/or ratio of read counts.  All reads are split over the number of mapping positions

source_name: fibroblasts

growth_protocol: Fibroblasts were grown in DMEM complete medium supplemented with 10% (v/v) FCS, and collected at ~80% confluence, adding Trizol directly to the plates.

extract_protocol:
Total RNA for sequencing was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions
For hydro-tRNAseq: 4 μg of 60-100 nt-sized total RNA were hydrolyzed in a 15 μL buffer of 10 mM in a 15 µL buffer of 10 mM Na2CO3 and 10 mM NaHCO3 at pH 9.7 at 65 °C for 1 h. The partially hydrolyzed RNA was dephosphorylated with 10 U of calf intestinal phosphatase (NEB) in a 50 µL reaction of 100 mM NaCl, 50 mM Tris-HCl, pH 7.9 at 25 °C, 10 mM MgCl2, 1 mM DTT, 3 mM Na2CO3 and 3 mM NaHCO3, at 37 ºC for 1 h. The resulting RNA was re-phosphorylated with 10 U of T4 polynucleotide kinase (NEB) in a 20 µlL reaction of 70 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 5 mM DTT and 1 mM ATP, at 37 °C for 1 h. Fragments of 19-35 nt were converted into barcoded small RNA cDNA libraries. Samples Ba12, Ba13, Ba17, Ba19, Ba245 were part of a barcoded library in a single lane. 3' adapters used (frist 5 nts represent barcodes): Ba12  TCCTATCGTATGCCGTCTTCTGCTTG, Ba13, TCATCTCGTATGCCGTCTTCTGCTTG, Ba17  TCCACTCGTATGCCGTCTTCTGCTTG, Ba19, TCGATTCGTATGCCGTCTTCTGCTTG, Ba245 TCTAGTCGTATGCCGTCTTCTGCTTG, 5' adapter (common): AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC. Samples Ba1230, Ba14, Ba1597, Ba1613, Ba1614 were part of a second barcoded library in a single lane. 3' adapters used (first 5 nts represnt barocdes): Ba1230, TCTAGTCGTATGCCGTCTTCTGCTTG, Ba14  TCGATTCGTATGCCGTCTTCTGCTTG, Ba1597 TCCTATCGTATGCCGTCTTCTGCTTG, Ba1613  TCCACTCGTATGCCGTCTTCTGCTTG, Ba1614  TCATCTCGTATGCCGTCTTCTGCTTG, 5' adapter (common): AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC. Two size markers were used as controls: 19-nt marker: CGTACGCGGGTTTAAACGA; 35-nt marker: TCATCTTGGTCGTACGCGGAATAGTTTAAACTGT

tag: cell type

value: fibroblasts


title: Ba1614

description: size fractionated RNA (~60-100 nt)


title: 37PF Liver Donor

value: Young (<40 years)

value: liver


title: shTUBG U2OS NS IP TUBG (2)

value: gamma tubulin


title: shTUBG U2OS NS IP TUBG (1)


title: vHIP SAL F [01_09_vHIP]

description: NS.1223.004.NEBNext_dual_i7_C9---NEBNext_dual_i5_C9.01_09_vHIP

tag: strain

value: F


title: vHIP SAL F [01_15_vHIP]

description: NS.1223.004.NEBNext_dual_i7_A7---NEBNext_dual_i5_A7.01_15_vHIP


title: KO ipsi MB Null SAM24372727

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from brain region tissue

extract_protocol: Tissue was rapidly frozen and stored until a full collection was obtained. RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.

tag: side

value: ipsilateral

value: midbrain


title: Ba14

description: size fractionated RNA (~60-100 nt)


title: Ba1230

description: size fractionated RNA (~60-100 nt)


title: Ba1597

description: size fractionated RNA (~60-100 nt)


title: ACC SAL M [03_13_ACC]

description: NS.1223.004.NEBNext_dual_i7_C2---NEBNext_dual_i5_C2.03_13_ACC

value: anterior cingulate cortex


title: ACC SAL F [01_15_ACC]

description: NS.1223.004.NEBNext_dual_i7_G6---NEBNext_dual_i5_G6.01_15_ACC


title: shTUBG U2OS NS Input (2)


title: shTUBG U2OS 9h IP PCNA (2)


title: WT ipsi MB Null SAM24372722

value: brain

value: WT


title: dHIP SAL F [01_09_dHIP]

description: NS.1223.004.NEBNext_dual_i7_B9---NEBNext_dual_i5_B9.01_09_dHIP

value: dorsal hippocampus


title: 47PF Liver Donor

value: Old (>40 years)


title: Ba245

description: size fractionated RNA (~60-100 nt)


title: KO contra MB Null SAM24372707

value: contralateral


title: dHIP SAL F [01_15_dHIP]

description: NS.1223.004.NEBNext_dual_i7_H6---NEBNext_dual_i5_H6.01_15_dHIP

value: SAL


title: 66PF Liver Donor


title: WT contra MB Null SAM24372698


title: shTUBG U2OS NS Input (1)

value: bone

value: Non-synchronous


title: 39PF Liver Donor


title: shTUBG U2OS 9h IP PCNA (1)

value: PCNA


title: KO contra MB aSyn SAM24372716

value: gpnmb KO


title: KO contra MB Null SAM24372708


title: ACC SAL F [01_09_ACC]

description: NS.1223.004.NEBNext_dual_i7_A9---NEBNext_dual_i5_A9.01_09_ACC


title: Ba19

description: size fractionated RNA (~60-100 nt)

value: fibroblasts


title: shTUBG U2OS 9h IP TUBG (2)


title: Ba17

description: size fractionated RNA (~60-100 nt)


title: KO ipsi STR Null SAM24372749

value: whole stratum


title: KO ipsi STR aSyn SAM24372760


title: WT contra MB aSyn SAM24372712


title: Ba12

description: size fractionated RNA (~60-100 nt)


title: shTUBG U2OS 9h Input (2)


title: Ba13

description: size fractionated RNA (~60-100 nt)


title: PBT003 gliblastoma stem cells, PUS7 sgRNA 2

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description: Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing PUS7 sgRNA 2

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to hg19 using Tophat2 with default settings.
Gene expression level of Refseq coding genes were quantified using HTseq-count
RPKM value was calculated by dividing the read count by total aligned reads and gene length
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with RPKM values

growth_protocol: Cells were cultured in DMEM-F12 medium supplemented with B27 and growth factors EGF and FGF.

extract_protocol:
Total RNA was extracted by Trizol reagent (Ambion) according to the manufacturer's instructions.
Kapa mRNA stranded protocol
poly(A) RNA-seq

treatment_protocol: Cells were treated with lentivurs expressing constrol sgRNA or target (PUS7) sgRNA for 24 hours and were cultured for one week before RNA extraction.

value: PUS7 sgRNA 2


title: PBT003 gliblastoma stem cells, control sgRNA

description: Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing control sgRNA 1

value: control sgRNA


title: PBT003 gliblastoma stem cells, PUS7 sgRNA 1

description: Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing PUS7 sgRNA 1

value: PUS7 sgRNA 1


title: p5v : Ventral subiculum preconditioning

city: Campinas

first: Andre

last: Schwambach Vieira

state: SP

address: Rua Monteiro Lobato, 255 - Bloco J - 1 piso - Sala 3

country: Brazil

institute: State University of Campinas

data_processing:
Illumina HiSeq 4000
Reads were aligned to the Rattus norvegicus Ensembl Rnor 5.0 assemble genome using the STAR aligner tool (https://github.com/alexdobin/STAR).
The DESEq2 statistics package (http://www.bioconductor.org/ packages/release/bioc/html/DESeq2.html) was used to estimate gene expression and for statistical analysis.
Genome_build: Ensembl Rnor 5.0

organism: Rattus norvegicus

source_name: Ventral subiculum preconditioning

extract_protocol:
Frozen brains were processed in a cryostat to obtain hippocampus sections. Subsequently, the dorsal and ventral subiculum were laser-microdissected and collected. The RNA was isolated from microdissected samples using Trizol’s.
cDNA libraries were produced using the TruSeq Stranded mRNA LT library preparation kit according to manufacturer instructions

value: Wistar

value: Brain

tag: age

value: Wild-type

value: Ventral subiculum

value: preconditioning


title: shTUBG U2OS 9h IP TUBG (1)

value: gamma tubulin


title: p4v : Ventral subiculum preconditioning


title: shTUBG U2OS 9h Input (1)


title: p3v : Ventral subiculum preconditioning


title: liver, 293 ko (RNA-seq)

city: Chicago

first: Tatiana

middle: L.

last: Fonseca

state: IL

address: 5841 S. Maryland Ave. MC1027, room N246B

department: Medicine

institute: University of Chicago

description:
gene_list from GSA report.txt
Gene set enrichment report go_report.txt
Pathway enrichment report.txt
Summary of reads quantified to mm10 - GENCODE Genes - release M24.txt
gene_level_feature_distribution.txt

data_processing:
Libraries were pair-end sequenced with NovaSeqS4 (Illumina).  Base-calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
The FASTQ files were aligned to gencode.vM24 transcriptome with STAR using the Partek flow platform (Partek Inc.)
All pre- and post-alignment QA/QC was performed in Partek Flow (Partek Inc.)
Aligned reads were quantified to annotation model (Partek E/M) and normalized (absolute value).
Following the differential analysis (GSA), the biological significance of the changes was interpreted using gene set enrichment analysis (GSEA) and pathway enrichment analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include total counts, P-value, FDR, ratio, fold change, LSMean (KO) and LS (Cre) for the significant genes.

source_name: liver

extract_protocol:
livers were removed, flash frozen on liquid nitogen, and RNA was harvested using RNeasy Kit (Qiagen). RNA degradation was monitored using a BioAnalyzer (Agilent). Samples of total RNA with RIN >7.5 were sent to Genome Technology Access Center at Washington University in St. Louis for library preparation and sequence.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: developmental stage

value: adult


title: liver, 289 ko (RNA-seq)


title: liver, 517 ko (RNA-seq)


title: shTUBG U2OS 7h IP TUBG (1)

value: bone


title: shTUBG U2OS 7h IP TUBG (2)


title: shTUBG U2OS 7h Input (2)


title: shTUBG U2OS 7h IP PCNA (2)


title: shTUBG U2OS 7h IP PCNA (1)


title: p2v : Ventral subiculum preconditioning


title: shTUBG U2OS 3h IP PCNA (2)


title: shTUBG U2OS 7h Input (1)


title: p1v : Ventral subiculum preconditioning


title: liver, TF 23 - Cre 57 input  (ChIP-seq)

description:
control adult peaks
Diff ko vs con adult peaks

data_processing:
FASTQ files obtained from sequencing were aligned to the Mouse mm10 genome in Partek-flow platform using the BWA. The peaks were identified using MACS2 tool, broad region and p<0.05, compared with respective input samples and annotated using the gencodev.M24.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

extract_protocol:
Liver ChIP-seq for H3K9me3 was performed in P1, P5 and adult control and Alb-D2KO mice, using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads; Cell Signaling). Liver from pups and adult control and Alb-D2KO mice were snap frozen and stored at -80C. A pool of 3 livers was processed for P1 or P5; adult livers were processed individually. Chromatin lysates were prepared, pre-cleared with Protein G magnetic beads, and immunoprecipitated with antibodies against the H3K9me3 (Cell Signaling). Beads were extensively washed before reverse crosslinking. Chip-enriched DNA was submitted to the Genome facility at University of Chicago for library preparation and sequence using Illumina NovaSEQ6000.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: control

tag: chip antibody


title: liver, TF 24 - KO 56 input  (ChIP-seq)

description:
Alb-D2KO adult peaks
Diff ko vs con adult peaks

tag: tissue


title: liver, TF 16 - KO 56 (ChIP-seq)

tag: genotype

value: H3K9me3 (Cell Signaling)


title: p5d : Dorsal subiculum preconditioning

source_name: Dorsal subiculum preconditioning

value: Dorsal subiculum


title: shTUBG U2OS 3h IP PCNA (1)

value: PCNA


title: liver, TF 15 - Cre 57 (ChIP-seq)


title: p4d : Dorsal subiculum preconditioning


title: shTUBG U2OS 3h IP TUBG (2)


title: liver, TF 12 - P5 KO input  (ChIP-seq)

description:
Alb-D2KO P5 peaks
Diff Ko vs con P5 peaks

value: postnatal day 5


title: shTUBG U2OS 3h IP TUBG (1)


title: WT ipsi MB aSyn SAM24372733

city: South San Francisco

first: Brad

last: Friedman

address: 1 DNA Way

institute: Genentech, Inc.

value: brain

value: WT

value: ipsilateral

value: midbrain

tag: aav


title: WT ipsi MB Null SAM24372721


title: KO ipsi MB aSyn SAM24372738

value: gpnmb KO


title: KO ipsi MB aSyn SAM24372742


title: KO contra MB Null SAM24372704

value: contralateral


title: KO ipsi MB aSyn SAM24372739


title: KO ipsi MB aSyn SAM24372741


title: WT ipsi STR Null SAM24372746

value: whole stratum


title: KO ipsi STR aSyn SAM24372761


title: WT contra MB aSyn SAM24372710


title: WT contra MB aSyn SAM24372711


title: p3d : Dorsal subiculum preconditioning

value: Wistar

value: Brain

value: Wild-type

value: preconditioning


title: liver, 164 cre (RNA-seq)

value: liver

value: adult


title: liver, 294 cre (RNA-seq)

value: control


title: liver, 178 cre (RNA-seq)


title: WT contra MB Null SAM24372701


title: liver, TF 11 - P5 Cre input  (ChIP-seq)

description:
control P5 peaks
Diff Ko vs con P5 peaks


title: liver, 490 cre (RNA-seq)


title: liver, 207 cre (RNA-seq)


title: liver, 245 ko (RNA-seq)


title: p2d : Dorsal subiculum preconditioning

value: Dorsal subiculum


title: shTUBG U2OS 3h Input (2)

value: bone


title: liver, TF 8 - P1 KO input  (ChIP-seq)

description:
Alb-D2KO P1 peaks
Diff ko vs con P1 peaks

value: postnatal day 1


title: shTUBG U2OS 3h Input (1)


title: c5v : Ventral subiculum control

source_name: Ventral subiculum control

value: Ventral subiculum


title: p1d : Dorsal subiculum preconditioning


title: PBMCs of COVID patient 5.47

city: Oxford

first: Nicholas

last: Lim

state: Oxfordshire

address: 26 Bullingdon Road

department: Paediatrics

institute: University of Oxford

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: PBMCs

extract_protocol:
Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well S^3 method (Hughes et al., BioRxiv 2019)
Nextera XT DNA Library Prep Kit

tag: Sex

value: Female

tag: survival outcome

value: No

tag: disease


title: U2OS NS IP Mcm5 (2)

value: Non-synchronous


title: c2v: Ventral subiculum control

tag: treatment


title: U2OS NS IP FoxM1(2)


title: PBMCs of COVID patient 5.13


title: PBMCs of COVID patient 5.14


title: c4v : Ventral subiculum control


title: liver, TF 5 - P5 Cre  (ChIP-seq)

value: postnatal day 5

value: H3K9me3 (Cell Signaling)


title: c1v : Ventral subiculum control


title: U2OS NS IP Mcm5 (1)


title: c3v : Ventral subiculum control


title: U2OS NS IP PCNA (2)

value: PCNA


title: liver, TF 6 - P5 KO  (ChIP-seq)


title: U2OS NS IP FoxM1 (1)


title: PBMCs of COVID patient 5.21


title: c5d: Dorsal subiculum control

source_name: Dorsal subiculum control

value: Wistar


title: liver, TF 1 - P1 Cre  (ChIP-seq)

description:
control P1 peaks
Diff ko vs con P1 peaks


title: U2OS NS IP PCNA (1)


title: PBMCs of COVID patient 5.11


title: PBMCs of COVID patient 5.31

value: Male


title: liver, TF 2 - P1 KO  (ChIP-seq)


title: PBMCs of COVID patient 5.23


title: liver, TF 7 - P1 Cre input  (ChIP-seq)


title: U2OS NS IP TUBG (2)

value: gamma tubulin


title: c4d: Dorsal subiculum control

value: Brain

value: Wild-type


title: PBMCs of COVID patient 5.43

value: Yes


title: DKO0_Uhrf1_Input_rep2

description: ChIP-seq

data_processing:
The ChIPseq data as well as the control input sequencing were aligned to the mouse mm9 reference genome using BWA mem using the default parameter. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Genome build: mm9
processed data files format and content: bigWig coverage files

source_name: J1 mESC

extract_protocol:
5 (histone) or 25 (Trim28) million cells were crosslinked with 1% FA for 5 or 8 minutes respectively at RT. Glycine was added to a final concentration of 125mM and mixed for 5 minutes at RT. Crosslinked cells were washed with DPBS 2x then spun down 3min 15000g.  Cells were then incubated with 500µL cell lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40) for 10 minutes on ice then spun down for 3min at 2500g. Supernatant was removed and the cell pellet was resuspended in 500µL of nuclear lysis buffer (10 mM Tris–HCl, pH 7.5, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) then incubated for 10 minutes on ice. Volume was increased to 1mL using Nuclei Lysis Buffer then sonicated on a Covaris E220 Evolution sonicator (PIP = 140.0, Duty Factor = 5.0, Cycles/Burst = 200, 10minutes).
After sonication, chromatin was spun down at 15000g for 10 minutes to pellet insoluble material. Volume was increased to 1.5mL with Chip Dilution Buffer (0.01% SDS, 1.1% Triton X-100,1.2mM EDTA, 16.7mM Tris-HCl pH 8.1, 167mM NaCl) and 2ug of H3K4me3 antibody (Abcam: ab8580), H3K36me3 (Active Motif 61101), H3K9me3 (Abcam, ab8898), or Trim28(Abcam, ab22553) were added. Immunoprecipitation mixture was allowed to rotate overnight at 4°C. The next day, 40µLs of Protein A Dynabeads (Thermo, 10001D) were added to the IP mixture and allowed to rotate for 4 hours at 4°C. This was followed by two washes of each: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl  pH 8.1, 150mM NaCl); high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20mM Tris, pH 8.1, 500 mM NaCl); LiCl wash buffer (0.25M LCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1); and TE buffer pH 8.0 (10mM Tris-HCl, pH 8.0, 1mM EDTA pH 8.0). DNA was eluted twice using 50µLs of elution buffer (0.5 to 1% SDS and 0.1 M NaHCO3) at 65°C for 15 minutes. 16µL of reverse crosslinking salt mixture (250 mM Tris-HCl, pH 6.5, 62.5 mM EDTA pH 8.0, 1.25 M NaCl, 5mg/ml Proteinase K) was added and samples were allowed to incubate at 65°C overnight. For library preparation, DNA was purified using AMPure XP beads (Beckman-Coulter) and treated with DNase-free RNase (Roche) for 30 minutes at 37 °C. DNA libraries were then end repaired and A-tailed using Ultra II End Repair/dA-Tailing Module (NEB) and adapters (Broad Institute, single index P7) were ligated using Blunt/TA Ligase Master Mix (NEB). Next, libraries were PCR amplified using Pfu Ultra II Fusion High-fidelity DNA Polymerase (Agilent) then size selected on a gel for fragments between 200-1000bp

value: mESC

value: Dnmt3a + Dnmt3b KO


title: TKOL_Uhrf1_Input_rep2

description: ChIP-seq

value: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA


title: TKOL_Uhrf1_Input_rep1

description: ChIP-seq


title: PBMCs of COVID patient 5.10


title: c3d: Dorsal subiculum control

value: Dorsal subiculum

value: control


title: PBMCs of COVID patient 5.17


title: U2OS NS IP TUBG (1)

value: bone


title: DKO0_Uhrf1_Input_rep1

description: ChIP-seq


title: WT_Uhrf1_Input_rep2

description: ChIP-seq

source_name: V65 mESC

value: WT


title: PBMCs of COVID patient 5.18

value: No


title: PBMCs of COVID patient 5.44


title: PBMCs of flu patient 5.5

value: Female

value: flu


title: c2d: Dorsal subiculum control


title: NT.BDC.4

city: Logan

first: Abby

last: Benninghoff

address: 4815 Old Main Hill

institute: Utah State University

data_processing:
For the large RNAseq data, high quality sequencing data were confirmed with FastQC and visualized across samples with MultiQC.  A STAR index was generated for read alignment using B. taurus UMD3.1 using the parameter --sjdbOverhang 74. Reads were aligned with default parameters including --quantMode GeneCounts to generate feature count tables.
Count tables were imported to R where the DESeq2 R package was used to identify differentially expressed genes with a Benjamini–Hochberg false discovery rate (FDR) adjusted p-value < 0.05.
Genome_build: UMD3.1
Supplementary_files_format_and_content: txt file for normalized reads for annotated mRNA transcripts organized by sample ID across columns and Ensembl transcript ID in the first column

source_name: scNT Blastocyst-derived cells

growth_protocol: Frozen/thawed cells were grown to 80-100% confluence then passaged, with cells from passages 4-5 used as nuclear donors. Three days prior to a cloning session, donor fibroblast cells were thawed and propagated, and incubated in DMEM medium (Hyclone) supplemented with 15% (v/v) FBS at 39 deg C with 5% CO2. Bovine fibroblasts at 80-90% confluence were serum-starved by replacing culture medium with DMEM containing 0.5% (v/v) FBS 24 hr prior to scNT.Oocytes were matured for 18-20 hr, then denuded using 100 microliters of 1% (v/v) hyaluronidase (MP Biomedical), incubated for 5 min at 38.5 deg C with 5% CO2, followed by gentle pipetting. The removed cumulus cells were centrifuged at 500xg for 5 min at room temperature, and the supernatant was removed. Cumulus cells were then cultured in SOFaa under oil for use in embryo culture. The denuded oocytes were then rinsed using PB1+, and oocytes with polar bodies were selected and separated. ScNT was performed according to established protocols [49-51]. Briefly, oocytes with polar bodies were incubated in 0.6 microgram/ml demecolcine for 30-40 min and a metaphase plate and a polar body were removed using a beveled pipette. Fibroblast cells were covered in 0.25% trypsin (Gibco, Carlsbad, CA) for 1 min, and then the trypsin was removed and fibroblasts were incubated for anther 6 min at 39 deg C with 5% CO2. Once fibroblast cells were detached, they were rinsed in warm medium and centrifuged at 150xg for 6 min. The supernatant was removed, and the cellular pellet was resuspended in 100 microliters Hepes SOF medium [47]. One fibroblast cell was injected into the perivitelline space of the recipient oocyte, and fused using one direct pulse of 1.2 kV/cm for 22 μs by an Electro Cell Manipulator 2001 (BTX, San Diego, CA) in 0.28 M sorbitol, 0.05% (w/v) BSA, 0.1 mM CaCl2, 0.5 mM MgCl2, and 0.5 mM Hepes. Following fusion, embryos were washed through Hepes SOF, and incubated in embryo culture medium for 1 hr. Activation was then performed, with successfully fused embryos cultured in 5 μM ionomycin for 5 min, followed by 4 hr of incubation in activation medium composed of SOFaa medium with 10 μg/ml cyclohexamide and 1 mM 6-dimethylamino¬pyridine at 38.5 deg C with 5% CO2. Following activation, embryos were cultured on a monolayer of bovine cumulus cells in 50 µl drops of SOFaa with 3% (v/v) FBS overlaid with mineral oil. The embryos were cultured at 38.5 deg C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture.

extract_protocol:
RNA was isolated based on size using the RNA Clean & ConcentratorTM 5 kit (Zymo) from three pools each of oocytes, 2-cell stage embryos, 8-cell stage embryos, morula stage embryos, or blastocyst stage embryos according to the manufacturer’s protocol for purification of small RNA (<200 nt) and large RNA (>200 nt) as separate fractions.  The large RNA fraction was used to generate sequencing libraries using the Ovation SoLo RNA-Seq System (NuGen Technologies, San Carlos, California) as directed by the manufacturer’s protocol for total RNA input.
Briefly, first strand cDNA synthesis, cDNA processing, second strand synthesis, and end repair were conducted according to manufacturer’s protocols, and samples were then stored at -20°C overnight.  Then, adaptor ligation and purification were performed, followed by PCR amplification of the sequence libraries (optimized to 16 cycles per instructions) and bead purification (twice) of the resulting samples.  Library DNA concentrations were quantified using the Qubit dsDNA HS Assay (Thermo Fisher Scientific, Waltham, Massachusetts).  Because DNA concentrations were low, the PCR amplification step was repeated once more with an additional 19 cycles to improve yield.  Next, InDA-C treatment was conducted (Ovation SoLo RNA-Seq System kit), a third round of PCR was performed, and the resulting libraries were bead-purified according to the manufacturer’s protocol.

value: Blastocyst-derived cells

tag: production method

value: somatic cell nuclear transfer

tag: molecule subtype

value: total RNA > 200 nt in length


title: PBMCs of flu patient 6.13


title: c1d: Dorsal subiculum control

value: Wistar


title: U2OS 9h IP Mcm5 (1)

tag: cell line

tag: time point


title: U2OS 9h IP Mcm5 (2)

tag: antibody


title: WT_Uhrf1_Input_rep1

description: ChIP-seq

tag: cell type

tag: strain


title: PBMCs of flu patient 6.3


title: U2OS 9h IP FoxM1(2)


title: NT.BDC.3


title: U2OS 9h IP FoxM1 (1)


title: NT.BDC.2


title: PBMCs of flu patient 6.1


title: U2OS 9h IP PCNA (2)

value: PCNA


title: NT.BDC.1


title: NT.Bl.4

source_name: scNT blastocyst stage embryos

value: Blastocyst stage


title: PBMCs of flu patient 5.1

value: Yes


title: PBMCs of flu patient 6.18

value: Male


title: U2OS NS Input (2)

value: Non-synchronous


title: U2OS 9h IP PCNA (1)


title: NT.Bl.3


title: U2OS 9h IP TUBG (2)

value: gamma tubulin


title: U2OS NS Input (1)


title: PBMCs of flu patient 6.9


title: NT.Bl.2


title: U2OS 9h IP TUBG (1)


title: NT.Mo.4

source_name: scNT morula stage embryos

value: Morula stage


title: PBMCs of flu patient 6.14


title: NT.Mo.3


title: PBMCs of flu patient 6.10


title: PBMCs of flu patient 6.16


title: NT.Mo.2


title: NT.8c.4

source_name: scNT 8-cell stage embryos

value: 8-cell stage


title: U2OS 7h IP Mcm5 (2)

value: bone


title: U2OS 7h IP FoxM1(2)


title: PBMCs of flu patient 6.7


title: PBMCs of flu patient 6.12


title: U2OS 9h Input (1)


title: U2OS 7h IP Mcm5 (1)


title: CRISPRi_RBN_R2

city: Cambridge

first: Mario

last: Niepel

state: MA

address: 35 Cambridgepark Dr Suite 300

institute: Ribon Therapeutics, Inc.

data_processing:
Library strategy: CRISPR screen
Analysis of NGS data sets e.g. sgRNA abundance was achieved using Horizon’s data processing scripts, based on published analysis tool MAGeCK (PMID:25476604)
Dual screen analysis was achieved by normalizing average log-fold changes in guide abundance by the difference in population doubling for each screen track: Phenotype score = LFC (DMSO vs RBN)/ΔPD (DMSO vs RBN).
Genome_build: hg38
Supplementary_files_format_and_content: "CRISPRa_Raw_counts.txt" and "CRISPRi_Raw_counts.txt" contain the abundance of each sgRNA in each sample, "CRISPRa_REF_Library.txt" and "CRISPRi_REF_Library.txt" contain the sgRNA sequences and target genes for each sgRNA.

growth_protocol: For transduction by spinfection, cells were seeded in multiple 12-well plates (2x106 cells/well) in the presence of 8 μg/ml polybrene.  Horizon high complexity off-the-shelf library lentivirus was added to each well and cells centrifuged.  Appropriate section marker (e.g. Puromycin for CRISPRi, combination of Blasticidin/Puromycin or Zeocin for CRISPRa) was applied 48 hrs post transduction.

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Blood Maxi kit (Qiagen #51194). Samples were prepared and purified for amplicon sequencing using an Illumina NextSeq next generation sequencing platform.
Genomic DNA was extracted using the QIAamp DNA Blood Maxi kit (Qiagen #51194). Samples were prepared and purified for amplicon sequencing using an Illumina NextSeq next generation sequencing platform.

treatment_protocol: The screen cultures were maintained at >300-fold library coverage, or a minimum of 32 x 106 cells per replicate and were treated with RBN-2397 at each split. After the DMSO control treated populations had reached 12 doublings, all screen end pellets were collected.

tag: crispr library

value: CRISPRi

value: Compound (RBN012397, 2.5nM) treated sample


title: U2OS 7h IP FoxM1 (1)


title: NT.8c.2

tag: developmental stage


title: NT.8c.1


title: U2OS 7h IP PCNA (2)


title: U2OS 7h IP PCNA (1)


title: CRISPRi_RBN_R1


title: CRISPRi_LIB_R1

value: Library sample


title: CRISPRi_LIB_R2


title: U2OS 7h IP TUBG (2)


title: NT.Bl.1


title: CRISPRi_DMSO_R2

value: DMSO treated sample


title: U2OS 9h Input (2)


title: NT.2c.4

source_name: scNT 2-cell stage embryos

value: 2-cell stage


title: U2OS 7h IP TUBG (1)


title: CRISPRi_DMSO_R1


title: NT.2c.2

value: somatic cell nuclear transfer


title: NT.8c.3

value: total RNA > 200 nt in length