title: Neuro2a Passage 6 Experimental 3

first: Ashutosh

last: Dharap

address: 4001 E Fletcher Ave

department: Molecular Medicine

institute: University of South Florida

description:
P6Exp3.FPKM
Passage6_GeneFPKMs

data_processing:
Quality Read Filtering: Low-quality reads (i.e., adaptor contamination, undetermined bases, etc.) were filtered using the Cutadapt tool.
Genome Alignment: Reads were aligned to the mouse reference genome using the HISAT2 package.
Transcriptome Construction: Transcript assembly was performed by StringTie followed by transcriptome reconstruction using the gffcompare tool.
FPKM Calculations: Expression level quantifications (FPKM) were calculated using StringTie and ballgown.
Differential Expression Analysis: Differential expression analysis, including calculations of Benjamini-Hochberg FDR corrected p-values (q-val), was performed using DESeq2 and edgeR packages.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and associated Ensembl IDs for each sample at each timepoint

growth_protocol: Cells were cultured with Dulbecco's Modified Eagle Medium (DMEM; Catalog Number SH30243.02 Fisher Scientific USA) supplemented with 10% Fetal Bovine Serum (FBS; Catalog Number S1620, Biowest USA) and 1% antibiotic-antimycotic (Catalog Number 30-004-CI Fisher Scientific USA) at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the MagMax mirVana Total RNA Isolation Kit (Catalog Number A27828, Thermo Fisher Scientific, USA). Samples were processed using an acid phenol-chloroform extraction protocol and the RNA was eluted in molecular-grade water. The RNA was treated with DNase I (15 min at 25°C) and purified using the RNA Clean & Concentrator-5 kit (Catalog Number R1014, Zymo Research, USA), as per the manufacturer’s instructions. Purified RNA was eluted in molecular-grade water and the purity and concentration of the samples were evaluated on a NanoDrop 1000 instrument.
Library preparation and subsequent sequencing was performed by LC Sciences (Houston, TX, USA). The total RNA quantity and purity were analyzed on a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). High-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.  mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations at elevated temperatures (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) at 94°C 5-7min). The cleaved RNA fragments were then reverse-transcribed to create the cDNA using the SuperScriptTM II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesize U-labeled second-stranded DNAs using E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95°C for 3 min; 8 cycles of denaturation at 98°C for 15 sec, annealing at 60°C for 15 sec, and extension at 72°C for 30 sec; and then final extension at 72°C for 5 min

treatment_protocol: Experimental N2a cells were dissociated using 0.25% trypsin and aliquoted at a concentration of 1 million cells per vial in 10% DMSO (Catalog Number D2438, Fisher Scientific) in 1 mL cryovials and placed inside a dewar flask containing two liters of liquid nitrogen. The container was stored at 4°C for a standardized duration of 34 h (10 h for LN2 to evaporate and 24 h for the temperature to stabilize to 4°C). Following this, the vials were removed from the container and stored at -80°C for 72 h. After 72 h, the cells from each cryovial were quickly thawed at 37°C and the contents were added to 15 mL of DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic. Cells were centrifuged at 300 RCF for 5 min, resuspended in fresh complete DMEM, seeded in T-25 flasks, and maintained under standard conditions. Control N2a cells were stored and plated using the same protocol described above but did not undergo the thawing and re-freezing condition and were instead maintained in normal cryostorage for the entire duration prior to plating.

tag: group

value: experimental

value: passage 6


title: W.10.F.3.Li.1

status: Public on Oct 24 2024

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

country: USA

institute: University of New Mexico

description:
RNA extracted from 10 week old WKY female liver replicate 3
Rat liver

data_processing: Initial quality control included melt-curve analysis and removal of samples and genes with >60% failed reactions. Genes with >60% working reactions were used to generate a median expression level across all samples. Raw Ct values were normalized against this median expression level to obtain DCt values. DCt values were generated for each gene according to the following equation: DCt_gene = Ct_gene - (median sample Ct). The median across all samples within a gene was then used to calculate -DDCt from DCt values by use of the following equation: -DDCt_gene = -(DCt_gene - DCt_median_across_samples).

label: Evagreen

molecule: total RNA

organism: Rattus norvegicus

label_protocol: The reverse transcriptase reaction was performed using SuperScript VILO Master Mix (Thermo Fisher Scientific, Waltham, MA). cDNA samples were processed for 12 cycles of specific target amplification of 96 genes using TaqMan PreAmp Master Mix as per the manufacturer’s protocol (Applied Biosystems, Foster City, CA, USA) followed by real-time PCR using Evagreen intercalated dye-based approach to detect the PCR-amplified product. Intron-spanning PCR primers were designed for every assay using Primer3 and BLAST. Real-time PCR reactions were performed using 96x96 BioMark Dynamic Arrays (Fluidigm, South San Francisco, CA, USA) of 150 samples and 96 genes enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions. Each run consisted of 30 amplification cycles (15 s at 95C, 5 s at 70C, 60 s at 60C). Two 96x96 BioMark Arrays were used to measure gene expression across all the 150 samples before QC. The same serial dilution sample set was included in each chip to verify reproducibility and test for technical variability. This 6-point dilution series also serves to detect any over-amplification that may lead to a bias in the data. Samples from each animal were run across the two chips to obtain data on 96 genes per sample. Each set of chip runs contained overlapping assays that served as technical replicates to evaluate chip-to-chip variability.

extract_protocol: Direct-Zol miniprep kit from Zymo Research

tag: Sex

value: Female

tag: strain

value: Wistar-Kyoto rat (WKY)

tag: age

value: 10 weeks

tag: organ

value: Liver


title: Neuro2a Passage 6 Experimental 2

type: SRA

city: Tampa

state: FL

description:
P6Exp2.FPKM
Passage6_GeneFPKMs

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: cell line

tag: treatment


title: W.10.F.2.Li.1

description:
RNA extracted from 10 week old WKY female liver replicate 2
Rat liver


title: BL-106a_VDJ

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

description:
10x Genomics
tumor_vdj.tsv.gz
barcodes.tsv.gz

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8. The files for each sample can be analyzed and de-multiplexed directly using the 10X Genomics CellRanger software.
Gene expression and VDJ data were mapped to the human genome (GRCh38) and processed together using the 10X Genomics CellRanger v6.0.0 multi pipeline.
Assembly: grch38
Supplementary files format and content: Gene expression consists of UMI counts for cells/genes. Barcodes.tsv is a summary that contains cell ids, from which sample they originated, and whether they are classified as “tumor” or “not tumor”. tumor_vdj.tsv contains VDJ information for the tumor cells.

organism: Homo sapiens

source_name: Ascites

extract_protocol:
Burkitt lymphoma diagnostic specimens, including pleural or abdominal effusions and nodal tumor masses, were collected at diagnosis and frozen as viable single cell suspensions. Upon thawing, cell suspensions were subject to Ficoll density centrifugation to remove dead cells and diluted at the concentration of 1,000 cells/ul.
Single cells were captured and analyzed in a Chromium Controller (10x Genomics) using the Chromium Next GEM Single Cell 5’ kit v2 and the Chromium Next GEM Single Cell V(D)J Enrichemtn Human B cell Kit following manufacturer's instructions (10x Genomics).

tag: tissue

value: Ascites

tag: cell type

value: Burkitt lymphoma


title: Neuro2a Passage 6 Experimental 1

description:
P6Exp1.FPKM
Passage6_GeneFPKMs


title: Zfp36l1 fl/fl Zfp36l2 fl/fl, replicate 1

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

description: TrAEL-seq adaptor 1

library_source: genomic

data_processing:
Sequencing data was processed with a custom script (TrAELseq_preprocessing_UMIplusBarcode.py; https://github.com/s-andrews/TrAEL-seq/) to demultiplex based on the in-line sample barcodes (4bp) and transfer these, together with the first 8bp of each sequence (UMI, unique molecular identifier) to the readID of the FastQ file. In addition, up to and including 3 T bases were removed from the 5'-end following the UMI clipping. The read lengths in the submitted FastQ files thus vary by up to 3bp, and the end of the readID comprises: Illumina barcode (6N):Sample barcode (4N):UMI (8N)
The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified by correcting for total read counts per million reads mapped.
Assembly: GRCm38
Supplementary files format and content: Worksheet contains TrAEL-seq read density, indicating where replications forks are located in replicating cells across the genome. These values for each biological replicate are running windows of 100,000 bp with step size of 10,000 bp using Read Count Quantification of All reads corrected for total read counts per million reads mapped.
Library strategy: TrAEL-seq

molecule: genomic DNA

source_name: Peripheral LN

growth_protocol: Naive B cells were isolated from the peripheral lymph nodes of mice using the B cell isolation kit (Miltenyi Biotec), and cultured in Dutch-modified RPMI-1640 media supplemented with 8% FBS, 1x GlutaMAX (Gibco), 50µM 2-mercaptoethanol, 100units/ml penicillin and 100μg/ml streptomycin (both ThermoFisher Scientific)

extract_protocol:
Half an agarose plug of 2x10^6 cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µlof indicated TrAEL-seq adaptor (eg. TrAEL-seq adaptor 1 [App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT)) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs with different TrAEL-seq adaptors were pooled into one eppendorf tube (as indicated in Sample description), equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. One third of this solution from ascynhronously dividing wild type cells were spiked into each pool (i.e. T0, T1 and T2 pools). DNA was then ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5 µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2 µl 10 mM dNTPs and 1 µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: For inducible germinal centre B cell culture (iGCB), 3T3 cells expressing mouse CD40L and human BAFF (40LB cells33) were irradiated (~120Gγ) and seeded at 100×10^3 cells per well in a 12-well plate. One day later (day 0), 40×10^3 naive B cells were added to 40LB cells in the presence of 2ng/ml mIL-4. On day 4, B cells were harvested and re-seeded on freshly irradiated 40LB cells in the presence of 5 ng/ml recombinant mouse IL-21 (PeproTech). Cells were harvested on day 7.

value: Peripheral LN

value: B cell

tag: genotype

value: Zfp36l1 fl/fl Zfp36l2 fl/fl

value: Induced germinal center B cell culture, day 7

value: Male

value: 15 weeks


title: BL-101_VDJ

source_name: Pleural Effusion

value: Pleural Effusion


title: W.10.F.1.Li.1

description:
RNA extracted from 10 week old WKY female liver replicate 1
Rat liver


title: S.10.F.3.Li.1

description:
RNA extracted from 10 week old SHR female liver replicate 3
Rat liver

value: Spontaneously Hypertensive rat (SHR)


title: BL-115_GEX

description:
10x Genomics
counts_tumor.tsv.gz
counts_not_tumor.tsv.gz
barcodes.tsv.gz

source_name: Tumor mass

value: Tumor mass


title: Mucoepidermoid Carcinomas sample 5

city: Beijing

first: Yan-ping

last: Zou

address: Haidian District

country: China

institute: Peking university

description: gene expression in mucoepidermoid carcinoma

hyb_protocol: 1 ug of Cy3-labelled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mucoepidermoid Carcinomas sample

label_protocol: Each RNA sample was amplified and transcribed into cyanine-3 (Cy3) labeled cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: Tissues were collected immediately upon lesion extraction and preserved in liquid nitrogen.

extract_protocol: Total RNA was isolated usingusing TRIzol reagent (Invitrogen). The quantity and quality of the extracted total RNA were assessed using a NanoDrop ND-1000 spectrophotometer, and RNA integrity was evaluated via standard denaturing agarose gel electrophoresis or an Agilent 2100 Bioanalyzer.

tag: differentiation

value: high to moderate differentiation

tag: gender

value: male

tag: lymphnode metastasis

value: Yes

tag: location

value: oropharynx


title: Neuro2a Passage 6 Control 3

description:
P6Ctrl3.FPKM
Passage6_GeneFPKMs

value: control

value: passage 6


title: Neuro2a Passage 6 Control 2

description:
P6Ctrl2.FPKM
Passage6_GeneFPKMs


title: BL-113_GEX


title: Mucoepidermoid Carcinomas sample 4

value: moderate differentiation

value: No

value: left palate


title: Mucoepidermoid Carcinomas sample 1

value: female

value: left parotid gland


title: S.10.F.2.Li.1

description:
RNA extracted from 10 week old SHR female liver replicate 2
Rat liver

value: Female

value: 10 weeks

value: Liver


title: S.10.F.1.Li.1

description:
RNA extracted from 10 week old SHR female liver replicate 1
Rat liver


title: Neuro2a Passage 6 Control 1

description:
P6Ctrl1.FPKM
Passage6_GeneFPKMs


title: BL-106b_VDJ

value: Ascites

value: Burkitt lymphoma


title: BL-112_GEX

value: Pleural Effusion


title: Mucoepidermoid Carcinomas sample 2


title: Normal adjacent salivary gland 5

description: gene expression in normal salivary gland

source_name: Normal adjacent salivary gland

value: high to moderate differentiation


title: Normal adjacent salivary gland 4

value: male


title: Normal adjacent salivary gland 3

value: Yes

value: right palate


title: W.8.F.3.Li.1

description:
RNA extracted from 8 week old WKY female liver replicate 3
Rat liver

value: Wistar-Kyoto rat (WKY)

value: 8 weeks


title: S.12.F.1.Li.1

description:
RNA extracted from 12 week old SHR female liver replicate 1
Rat liver

value: Spontaneously Hypertensive rat (SHR)

value: 12 weeks


title: BL-110-E_GEX


title: Neuro2a Passage 1 Experimental 4

description:
P1Exp4.FPKM
Passage1_GeneFPKMs

value: experimental

value: passage 1


title: Mucoepidermoid Carcinomas sample 3

value: moderate differentiation

value: female


title: W.8.F.2.Li.1

description:
RNA extracted from 8 week old WKY female liver replicate 2
Rat liver

value: Female


title: BL-109_GEX

value: Tumor mass


title: S.8.F.3.Li.1

description:
RNA extracted from 8 week old SHR female liver replicate 3
Rat liver

value: Liver


title: 3P-Seq in undifferentiated SH-SY5Y cells

city: Worcester

first: Sarah

middle: Marie

last: Davis

state: Massachusetts

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: University of Massachusetts Chan Medical School

data_processing:
Data were pre-processed using the fastx_toolkit/0.014 to trim the adapter sequences from the 3' ends of reads and convert the reads to the reverse complement.  Umitools was used to de-duplicate reads and remove UMIs prior to taking the reverse complement of the reads.
The reverse complement of the pre-processed data was aligned to the hg38 reference genome using STAR/2.7.6a
The resulting .bam file was filtered to include only APP, BACE1, MAPT or SNCA by location: chr21:25,878,550-26,173,128, chr11:117,283,686-117,318,256, chr17:45,892,382-46,030,334, and chr4:89,722,099-89,840,304, respectively
Sorted .bam files were supplied as input to generate raw per base count .wig files from gene of interest coordinates using IGVtools count (IGVTools/2.3.31).
Supplementary files format and content: .wig files for APP, BACE1, MAPT, and SNCA

growth_protocol: SH-SY5Y cells were maintained in DMEM/F-12, GlutaMAX supplemented with 9% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. 75 ug total RNA was used for input in library preparations
RNA libraries for 3P-seq were prepared as described in Jan et al., 2011 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057491/) with the following exceptions:
After elution of the mRNA 3′ ends from oligo-d(T) beads, a mixture of two pre-adenylated 3′ DNA adapters (AppNN NGT ANN NTA GNN NGA TCG TCG GAC TGT AGA ACT CTG AAC /3AmMO/, AppNN NAC TNN NGA TNN NGA TCG TCG GAC TGT AGA ACT CTG AAC /3AmMO/), adenylated as described in Hildebrand et al., 2022 (https://pubmed.ncbi.nlm.nih.gov/37059467/) were ligated to these eluted mRNAs using Rnl2KQ. The ligation products were gel purified and phosphorylated as described in Jan et al., 2011 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057491/)  and a 5′ RNA adapter (rCrCrU rUrGrG rCrArC rCrCrG rArGrA rArUrU rCrCrA rNrNrN rCrUrA rNrNrN rGrArC rNrNrN) was ligated to the 5′ RNA ends using Rnl1. This ligation product was then reverse transcribed using Superscript 2  with the primer sequence: GTT CAG AGT TCT ACA GTC CGA CGA TC. The RT product was then gel purified and the final libraries were amplified using AccuPrime pfx DNA polymerase and the following primers: Forward Primer: AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GA and Reverse Primer: CAA GCA GAA GAC GGC ATA CGA GAT CGT GAT GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA. The final amplified libraries were gel extracted, quantified, and sequenced on a NextSeq 550 (Illumina) for 79 cycles.

value: neuroblastoma


title: NK_untreated_4

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

data_processing:
Data were aligned using Tophat (v 2.0.11) (Kim, Pertea et al. 2013) and Cufflinks (v2.2.1) (Trapnell, C., et al. 2012) with default settings and with the Homo sapiens GRCh37 reference genome. On average 43.2 million reads were obtained for each sample and the average genome mapping rate was 96.6%.
Differential analysis from transcripts counts was performed using the edgeR R package (Lun et al. Methods in Molecular Biology 2016). Poorly expressed genes were filtered out by keeping genes with at least 0.5 count per million reads (cpm) in at least half samples. After normalization using trimmed mean of M-values (TMM) method, differential expressed genes were identified using the quasi-likelihood F method.
Genome_build: Homo sapiens GRCh37
Supplementary_files_format_and_content: Transcript reads were normalized using trimmed mean of M-values (TMM) method with the edgeR R package (Lun et al. Methods in Molecular Biology 2016) after poorly expressed genes were filtered out by keeping genes with at least 0.5 count per million reads (cpm) in at least half samples.

source_name: untreated NK cells

extract_protocol:
Total RNA were extracted using  the RNeasy Mini kit (Qiagen) following manufacturer's protocol. RNA quality was assessed using an Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA).
The library preparation was done using TruSeq Stranded mRNA Sample preparation kit (Illumina inc) with 250ng of total RNA. Enriched mRNA using oligodT beads were fragmented using enzymatic fragmentation and used for cDNA synthesis before double stranded cDNA were purified (AMPure XP, Beckman Coulter). The cDNA was end-repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The mRNA stranded libraries were pre-amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a BioAnalyzer 4200 tapeStation (Agilent Technologies). Single end sequencing was carried out on a NextSeq500 instrument (75 cycles) according to the manufacturer instructions (Illumina Inc.).

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated from fresh cytapheresis ring from healthy donors (EFS, Nantes). Human NK cells were isolated by negative selection with the Mylteni’s NK cells isolation kit (ref 130-092-657). NK cells were incubated overnight in complet RPMI medium supplemented with 10UI rhIL-2 and stimulated or not with 10ug/ml of anti-CD28H (clone 4/5) or the isotype control. Sixteen hours later, 2 millions of NK cells from each condition were washed in PBS and the dry pellet was frozen at -80°C.

value: Natural Killer (NK)

value: untreated

tag: patient id

tag: rin


title: NK_untreated_0


title: BL-107_GEX

value: Pleural Effusion

value: Burkitt lymphoma


title: Neuro2a Passage 1 Control 3

description:
P1Ctrl3.FPKM
Passage1_GeneFPKMs

value: control


title: Neuro2a Passage 1 Experimental 2

description:
P1Exp2.FPKM
Passage1_GeneFPKMs


title: Neuro2a Passage 1 Experimental 3

description:
P1Exp3.FPKM
Passage1_GeneFPKMs


title: W.8.F.1.Li.1

description:
RNA extracted from 8 week old WKY female liver replicate 1
Rat liver

value: Wistar-Kyoto rat (WKY)


title: Neuro2a Passage 1 Experimental 1

description:
P1Exp1.FPKM
Passage1_GeneFPKMs


title: BL-108_GEX

value: Ascites


title: NK_untreated_3


title: Neuro2a Passage 1 Control 2

description:
P1Ctrl2.FPKM
Passage1_GeneFPKMs


title: Normal adjacent salivary gland 1

value: Yes

value: left parotid gland


title: S.8.F.2.Li.1

description:
RNA extracted from 8 week old SHR female liver replicate 2
Rat liver

value: Spontaneously Hypertensive rat (SHR)

value: 8 weeks


title: BL-103b_GEX


title: S.8.F.1.Li.1

description:
RNA extracted from 8 week old SHR female liver replicate 1
Rat liver


title: BL-103a_GEX


title: NK_untreated_2


title: Normal adjacent salivary gland 2

value: moderate differentiation

value: left palate


title: BL-110_GEX


title: BL-102b_GEX


title: CRS/N, replicate 2

city: Suzhou

first: meng

last: shan

address: shizi street

institute: Soochow university

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (3.0.0) was used to perform alignment, filtering, barcode and unique molecular identifier (UMI) counting to generate feature-barcode-UMI matrices.
The cDNA insert was aligned to the GRCm38/mm10 reference genome.
Seurat (4.3.0) R tool kit was used to perform quality control and unsupervised clustering. Cells whose gene number was less than 1000 and mitochondrial gene ratio was more than 10 % were regarded as abnormal and filtered out.
In order to reduce batch effect of the samples, we performed data integration using the Harmony method.
The top 3,000 variable genes of scaled data were used for principal component analysis (PCA) to reduce dimensionality.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Bone marrow

extract_protocol:
C-kit+ and Mac1+ BM cells from WT/V, WT/N, CRL/V, CRL/N, CRS/V or CRS/N mice were flow-sorted and mixed in a 1:1 ratio. Cells were loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual gel-bead-in-emulsions (GEMs). Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1.

value: Bone marrow

value: primary cells

value: Mac1+ and c-kit+ cells with 1:1 ratio

value: CRS/N

value: 8-10 weeks


title: W.24.F.2.Kd.1

description:
RNA extracted from 24 week old WKY female kidney replicate 2
Rat kidney

value: Female

value: 24 weeks

value: Kidney


title: CRS/N, replicate 1

description: 10× Genomics


title: W.24.F.3.Kd.1

description:
RNA extracted from 24 week old WKY female kidney replicate 3
Rat kidney


title: NK_untreated_1

value: Natural Killer (NK)

value: untreated


title: NK_untreated_6


title: W.24.F.1.Kd.1

description:
RNA extracted from 24 week old WKY female kidney replicate 1
Rat kidney

value: Wistar-Kyoto rat (WKY)


title: S.24.F.3.Kd.1

description:
RNA extracted from 24 week old SHR female kidney replicate 3
Rat kidney


title: BL-106b_GEX

value: Ascites

value: Burkitt lymphoma


title: NK_anti_CD28H_2

source_name: NK cells with anti-CD28H

value: anti-CD28H antibody


title: BL-102a_GEX

value: Pleural Effusion


title: CRS/V, replicate 2

description: 10× Genomics

value: CRS/V


title: S.24.F.2.Kd.1

description:
RNA extracted from 24 week old SHR female kidney replicate 2
Rat kidney

value: Spontaneously Hypertensive rat (SHR)


title: NK_anti_CD28H_3


title: BL-106a_GEX

description:
10x Genomics
counts_tumor.tsv.gz
counts_not_tumor.tsv.gz
barcodes.tsv.gz


title: NK_anti_CD28H_1


title: CRL/N, replicate 1

description: 10× Genomics

value: Bone marrow

value: CRL/N


title: CRL/N, replicate 2

description: 10× Genomics

value: primary cells

value: Mac1+ and c-kit+ cells with 1:1 ratio


title: HepG2_Taze_2, RNA-seq

city: Cheongju-si

first: Jaehyun

last: Lee

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu

department: Biological Science and Biotechnology

country: South Korea

institute: Chungbuk National University

description:
HepG2_Ctrl_Taze.raw.txt
HepG2_Ctrl_Taze_tpm.txt

data_processing:
Sequenced reads were mapped to the reference human genome (hg38 assembly) using STAR aligner (v 2.7.1a) with default parameters
The expression levels of genes in each sample were normalized by means of transcript per million (TPM).
Differentially expressed genes (DEGs) were identified using edgeR with raw read counts.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes TPM values for each sample.

source_name: Liver

growth_protocol: HepG2 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cells using the Ribospin II kit (GeneAll). 1 μg of total RNA was used  for the construction of sequencing libraries.
RNA libraries for sequencing were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: HepG2 cells were stabilized for 24 h and 5 μM Tazemetostat (MCE) dissolved in DMSO was treated for 48 h.

value: Liver

value: Epithelial cell

value: WT

value: Tazemetostat treatment


title: NK_untreated_5

value: Natural Killer (NK)


title: BL-101_GEX


title: CRS/V, replicate 1

description: 10× Genomics

value: 8-10 weeks


title: S.24.F.1.Kd.1

description:
RNA extracted from 24 week old SHR female kidney replicate 1
Rat kidney

value: Female

value: 24 weeks

value: Kidney


title: Neuro2a Passage 1 Control 1

description:
P1Ctrl1.FPKM
Passage1_GeneFPKMs

value: control

value: passage 1


title: NK_anti_CD28H_4

value: anti-CD28H antibody


title: CRL/V, replicate 2

description: 10× Genomics

value: CRL/V


title: NK_anti_CD28H_6


title: HepG2_Taze_1, RNA-seq


title: W.16.F.2.Kd.1

description:
RNA extracted from 16 week old WKY female kidney replicate 2
Rat kidney

value: Wistar-Kyoto rat (WKY)

value: 16 weeks


title: W.16.F.1.Kd.1

description:
RNA extracted from 16 week old WKY female kidney replicate 1
Rat kidney


title: HepG2_Ctrl_2, RNA-seq

value: Untreated


title: NK_anti_CD28H_5


title: WT/N, replicate 2

description: 10× Genomics

value: Bone marrow

value: primary cells

value: Mac1+ and c-kit+ cells with 1:1 ratio

value: WT/N


title: S.16.F.3.Kd.1

description:
RNA extracted from 16 week old SHR female kidney replicate 3
Rat kidney

value: Spontaneously Hypertensive rat (SHR)


title: S.16.F.2.Kd.1

description:
RNA extracted from 16 week old SHR female kidney replicate 2
Rat kidney


title: CRL/V, replicate 1

description: 10× Genomics


title: WT/N, replicate 1

description: 10× Genomics


title: NK_ISO_6

source_name: NK cells with isotype

value: Natural Killer (NK)

value: isotype antibody


title: W.16.F.3.Kd.1

description:
RNA extracted from 16 week old WKY female kidney replicate 3
Rat kidney

value: Female


title: WT/V, replicate 1

description: 10× Genomics

value: WT/V

value: 8-10 weeks


title: W.12.F.3.Kd.1

description:
RNA extracted from 12 week old WKY female kidney replicate 3
Rat kidney

value: 12 weeks

value: Kidney


title: human brown adipocyte cell line, Mettl14 KO, biol rep 2

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

description:
hBAT_Deseq2.csv
Processed file's Sample column: CF15

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.2)
Trimmed sequence reads were mapped to mm10 using HISAT2 (2.2.1).
Read count extraction and differential expression levels of exons and genes were analyzed using RADAR (0.2.4) followed by DEseq2 (1.36.0).
For differential m6A regions of mRNA, RADAR software (0.2.4) was used as well.
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107)
Supplementary files format and content: DESeq2 results with normalized reads for each sample and m6A analysis results from RADAR

source_name: hBAT

growth_protocol:
All mice were fed with chow-diet for twenty-four weeks from four week of age. At the end of the experiment, mice were euthanized after overnight fasting, followed by serum and tissue sample collection.
hBAT cells were differentiated for 21 days, washed with PBS and cultured in 1% BSA containing high-glucose DMEM medium for 24 hours, and then collected cell pallet for RNA extraction.

extract_protocol:
Total RNA was then extracted from iBAT by TRIzol. 1 μg of mRNAs was isolated from total RNA using a Dynabeads mRNA DIRECT purification kit (Thermo Fisher). Then, mRNA was adjusted to about 10 ng μl−1 in 100 μl and fragmented using a Bioruptor ultrasonicator (Diagenode) with 30 s on/off for 30 cycles. m6A immunoprecipitation (m6A-IP) and library preparation were performed using the EpiMark N6-Methyladenosine enrichment kit (NEB).
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

value: Mettl 14 knockout

value: hBAT


title: human brown adipocyte cell line, Control, biol rep 3

description:
hBAT_Deseq2.csv
Processed file's Sample column: CF13

value: WT


title: human brown adipocyte cell line, Mettl14 KO, biol rep 1

description:
hBAT_Deseq2.csv
Processed file's Sample column: CF14


title: LysM-CRS, replicate 2

data_processing:
Cell Ranger (3.0.0) was used to perform alignment, filtering, barcode and unique molecular identifier (UMI) counting to generate feature-barcode-UMI matrices
The cDNA insert was aligned to the GRCm38/mm10 reference genome.
Seurat (4.3.0) R tool kit was used to perform quality control and unsupervised clustering. Cells whose gene number was less than 1000 and mitochondrial gene ratio was more than 10 % were regarded as abnormal and filtered out.
In order to reduce batch effect of the samples, we performed data integration using the Harmony method
The top 3,000 variable genes of scaled data were used for principal component analysis (PCA) to reduce dimensionality
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: bone marrow

extract_protocol:
C-kit+ and Mac1+ BM cells from WT, LysM-CRL or LysM-CRS mice were flow-sorted and mixed in a 1:1 ratio. Cells were loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual gel-bead-in-emulsions (GEMs). Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1.

value: bone marrow

value: LysM-Cre; CRS+/flox

value: 12-month old


title: NK_ISO_0


title: human brown adipocyte cell line, Control, biol rep 2

description:
hBAT_Deseq2.csv
Processed file's Sample column: CF12


title: W.12.F.2.Kd.1

description:
RNA extracted from 12 week old WKY female kidney replicate 2
Rat kidney

value: Wistar-Kyoto rat (WKY)


title: NK_ISO_2


title: NK_ISO_3


title: LysM-CRS, replicate 1

value: primary cells

value: Mac1+ and c-kit+ cells with 1:1 ratio


title: human brown adipocyte cell line, Control, biol rep 1

description:
hBAT_Deseq2.csv
Processed file's Sample column: CF11


title: NK_anti_CD28H_0

value: anti-CD28H antibody


title: LysM-CRL, replicate 2

value: LysM-Cre; CRL+/flox


title: HepG2_Ctrl_1, RNA-seq

value: Liver

value: Epithelial cell

value: Untreated


title: NK_ISO_5

value: Natural Killer (NK)

value: isotype antibody


title: NK_ISO_4


title: Human CD34+ cells (d0 fresh,d7  DMSO, d7 UM171)

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Single-cell RNAseq from each of these cultures was performed on a Chromium Single-Cell Controller (10X Genomics). Sequencing of the scRNAseq libraries was performed on an Illumina NovaSeq device. Cell hashing and superloading were used to multiplex the 3 samples (fresh, DMSO and UM171). A standard kallisto pipeline was used for read mapping (GRCh38 annotation) and hashtag mapping. Subsequent analyses were done in Seurat (v4) and included (i)Hashtag oligos demultiplex using HTODemux function (ii) exclusion of cells with less than 1,000 genes or unique molecular identifiers (UMI), (iii) exclusion of cells with more genes or UMIs than the respective means plus 2 standard deviations (likely representing multiplets), (iv) exclusion of cells with more than 6% mitochondrial gene.expression (representing apoptotic cells). Expression counts were log-normalized (scale factor 10,000) and scaled including regression on number of UMI\u2019s, cell cycle scores and mitochondrial gene content.
Assembly: GRCh38
Supplementary files format and content: metadata.csv: Cell barcodes with cluster identification (done by label transfer, predicted.id), conditions (d0 fresh,d7  DMSO, d7 UM171), cellcycle score, prediction score max and predicted.id.scores.
Supplementary files format and content: barcodes.tsv:  cell barcode (see meta data for assiging cell barcode to condition). Seurat object containing all cells analyzed in this manuscript were exported into 10X format (barcode.tsv, genes.tsv, matrix.mtx) using function write10xCounts() from library(DropletUtils).
Supplementary files format and content: genes.tsv:  gene names . Seurat object containing all cells analyzed in this manuscript were exported into 10X format (barcode.tsv, genes.tsv, matrix.mtx) using function write10xCounts() from library(DropletUtils).
Supplementary files format and content: matrix.mtx: matrix of RNA counts. Seurat object containing all cells analyzed in this manuscript were exported into 10X format (barcode.tsv, genes.tsv, matrix.mtx) using function write10xCounts() from library(DropletUtils).

source_name: Cord blood

growth_protocol: Human CD34+ cells were cultured in HSC expansion media consisting of StemSpan SFEM (StemCell Technologies) supplemented with human 100 ng/ml stem cell factor (SCF, Shenandoah Biotechnology), 100 ng/ml FMS-like trysine kinase 3 ligand (FLT3, Shenandoah Biotechnology), 50 ng/ml thrombopoietin (TPO, R&D Systems) and interleukin 6 (IL6, Shenandoah Biotechnology) for 7 days

extract_protocol:
Single cells were processed using the 10X Chromium controlller. 10X Chromium version 2 3' RNAseq
Chromium NextGEM Single Cell 3' v3.1

treatment_protocol: UM171 were used at 35nM

value: Cord blood

value: primary hematopoietic cell


title: S.12.F.3.Kd.1

description:
RNA extracted from 12 week old SHR female kidney replicate 3
Rat kidney

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 12 weeks

value: Kidney


title: WT/V, replicate 2

description: 10× Genomics

value: Bone marrow

value: WT/V

value: 8-10 weeks


title: S.12.F.2.Kd.2

description:
RNA extracted from 12 week old SHR female kidney replicate 2
Rat kidney


title: NK_ISO_1


title: S.16.F.1.Kd.1

description:
RNA extracted from 16 week old SHR female kidney replicate 1
Rat kidney

value: 16 weeks


title: ChIPseq_LaminB1_MAD_hMSC_R2

city: Guangzhou

first: Xinyi

last: Liu

state: Guangdong

address: No. 74, 2nd Zhongshan Road

institute: Sun Yat-Sen University

data_processing:
Trimming the adaptor sequence: Trim Galore (version 0.6.7, https://github.com/FelixKrueger/TrimGalore), removed the bases with quality below 20 and the adaptor sequences from the 3' end, and filtered the reads with length less than 50nt. Spetially for Hi-C data, bridge linkers of paired-end reads were trimmed with trimLinker program (part of ChIA-PET2, version 0.9.3, https://github.com/GuipengLi/ChIA-PET2, parameters: '-t 20 -m 1 -k 1').
Alignment: Reads were aligned to hg19. For RNA-seq data, STAR (PMID: 23104886) was used with default parameters. For ATAC-seq and ChIP-seq data, Bowtie2 was used with default parameters and reads with a mapq score less than 30 and PCR duplications were filtered out by using Samtools (PMID: 19505943) (version 1.9, http://samtools.sourceforge.net). After that, reads aligned to the regions in ENCODE blacklist (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/) were discarded through bedtools (PMID: 20110278) (version 2.29.1, https://bedtools.readthedocs.io/en/latest/). For Hi-C data, HiC-Pro (PMID: 26619908) was used (version 2.11.1, parameters: 'LIGATION_SITE = AGCT' which digested hg19 by AluI).
Quantification of gene expression: uniquely mapped reads of RNA-seq data were counted by HTSeq-count with default parameters (PMID: 25260700).
Peak calling: Peaks of ChIP-seq and ATAC-seq data were called with macs2 (PMID: 18798982) (version 2.1.2, parameters: '-g mm -q 0.05 -m 5 50' for ATAC-seq, H3K27ac and CTCF, '-g mm -q 0.05 -m 5 50 --broad' for H3K27me3, H3K9me3, Lamin A/C and Lamin B1) using Input as control.
LAD calling. The replicates of Lamin A/C and Lamin B1 ChIP and Input BAM files were combined and down-sampled to 16M read counts prior to LAD calling using Samtools (PMID: 19505943) (version 1.9, http://samtools.sourceforge.net). LADs were called using Enriched Domain Detector (PMID: 24782521) (EDD, version 1.1.19, http://github.com/CollasLab/edd, parameters: 'max_CI_value = 0.25, required_fraction_of_informative_bins = 0.80, p_hat_CI_method = agresti_coull, log_ratio_bin_size = 10').
Generation of bigwig or bedgraph files: Bam files from the alignment step were converted to bigwig files by deepTools (PMID: 24799436) (version 3.1.1, https://deeptools.readthedocs.io/en/develop/, parameters: 'bamCoverage -bs 10 --normalizeUsing RPKM -e 200 --centerReads'). The bigwig files containing the log ratio of Lamin ChIP-seq to Input were generated by Enriched Domain Detector with bin size of 10kb (PMID: 24782521) (EDD, version 1.1.19, http://github.com/CollasLab/edd, parameters: log_ratio_bin_size = 10').
Generation of hic files: For Hi-C data, valid pairs from the alignment step were converted to hic format by HiC-Pro (PMID: 26619908) (version 3.0.0, parameters: ' hicpro2juicebox.sh -g chrom_hg19.sizes -r hg19_AluI.bed').
Genome_build: hg19
Supplementary_files_format_and_content: *_raw_read_counts.txt: raw read counts of each genes from RNA-seq data for differential expression analysis;  *_peak.*Peak: peaks from ChIP-seq and ATAC-seq data  for viewing in a genome browser;  *.bw: bigWig files with bin size of 10bp normalized by RPKM from RNA-seq, ChIP-seq and ATAC-seq data for viewing in a genome browser;  *.bed: bed files containing genomic intervals of LADs from Lamin ChIP-seq data;  *.bedgraph: bedGraph files containing the log ratio of Lamin ChIP-seq to Input with bin size of 10kb for viewing in a genome browser;  *_allValidPairs: valid read pairs from Hi-C data for domain analysis or differential contact analysis;  *.hic: heatmap of chromatin contacts from Hi-C data for visualization in juicebox (PMID: 25497547) (version 1.11.08, https://www.aidenlab.org/juicebox). All text files were compressed by tar (version 1.30, https://ftp.gnu.org/gnu/tar/, parameters: '-czvf')

source_name: MAD-iPSCs derived human MSCs

growth_protocol: The dermal tissues were collected from a  5-year-old male MAD patient and a 26-year-old female normal people through skin biopsy upon the consent given by guardians and human tissue procurement under the guidance of ethical regulations in The Dongguan Women & Children Hospital. The dermal tissues were quickly sterilized with 75% ethanol for 1-2 min, washed with Phosphate buffered saline (PBS buffer pH .2) twice, excluded extra fat and fascia, and then cut into several 1mm2 pieces before seeding to T25 flask. Five milliliter of fibroblast culture medium containing DMEM/HG, 10% human umbilical cord blood serum (homemade), 1mM GlutaMax, and Penicillin/Streptomycin, was then added for culture and the expansion of spindle-like fibroblast cells was regularly monitored within every 24 hrs. Early passages of these cells were cryopreserved with medium plus 10% DMSO. After large-scale cryopreservation, commercial Fetal Bovine Serum (Hyclone) was used to replace hUCBS for the following experiments. All the cell cultures were maintained in a humid incubator at 37 °C and 5% CO2. All the cells were cultured at 37 °C in 5% CO2 and tested negative for mycoplasma infection based on PCR method by the Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine.

extract_protocol:
Lysis of 5 X 10 ^6 fixed cells was sonicated with Diagenode Bioruptor Pico (HKU, Imaging & Flow Cytometry Core facility) for 20 cycles to generate DNA fragments ranging from 200-1000 bp and discarded insoluble part after 15,000 RPM for 20min. The chromatin supernatants were treated as described in PMID: 17406303 and ChIP libraries were prepared by NEBNext® ΜltraTM DNA Library Prep Kit for Illumina® (NEB E7370). Information of antibodies used in ChIP: CTCF (Rb, Active motif 61311), H3K27ac (Rb, Active motif 39034), H3K27me3 (Rb, Abcam ab6002), H3K9me3 (Rb, Abcam ab176916), Lamin A/C (Ms, Active motif 39287) and Lamin B1 (Rb, CST 13435S).
ChIP

treatment_protocol: Generation of iPSC: The minicircle DNA mediated reprogramming was performed following previously described with modifications (PMID: 25628230). The minicircle vector MIP247 was a kind gift from Mark Kay & Joseph Wu (Addgene # 63726). Early passages of human primary fibroblasts (<passage 10) were cultured and 10^6 of cells were harvested and nucleofected with 15 μg plasmid using commercial kit (Lonza, VPD-1001) under program U-023 before seeding onto two wells of Geltrex coated 6-well plate for feeder-free or autogenous feeder cells with fibroblast culture medium. Half of the medium was replenished next day, and 2 mM Valproic Acid (VPA) and 50 μg/mL ascorbic acid were added. On day 3-14, the medium was switched to N2B27 medium containing 50 μg/mL L-ascorbic acid, 50 ng/ml bFGF. Pre-iPSC clones were observed on day 7 and became larger and maturation along with reprogramming process. The medium was replaced with Essential 8 medium for feeder free or knockout serum replacement medium for feeder culture after day 15. The iPSC clones became fully reprogramed for mechanical picking on day 25-30. At least six different clones of each sample were picked, expanded and cryopreserved.        Generation of hMSCs from iPSCs:  iPSCs is routinely cultured in mTeSR1 or Essential 8 media with splitting at 1:4-1:6 every 3 days. For neuralized ectoderm differentiation, 1 x 10^5 of signalized iPSCs were seeded on Matrigel coated 6-well plate with 10 μM Y27632. The medium was discarded, washed with DMEM: F12 twice and changed to neural ectoderm induction medium, consisting of 50% Neurobasal, 50% DMEM/F12 medium, 1% N2 and 2% B27 and 3-6 μM CHIR-99021 and 10 μM SB-431542. Replenish the medium daily for 5 days until the cells exhibited neural-like morphology, spread out and separated from each other. Signalized the cells and re-seeded them on Matrigel-coated plate with MSC cμlture medium, consisting of alpha-MEM basal medium, 10% FBS, 1X Glutamax solution, 5 ng/ml bFGF, 5 ng/ml EGF and 1% Penicillin-Streptomycin. After additional 5-7 days of induction, fibroblast-like morphology is observed. Split the cell at low ratio, such as 1:2-1:3 at early passages with TrypLE Express.

tag: isolate

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: Skin

value: MAD-iPSCs derived human MSCs

tag: passage

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Cell culture

tag: disease

tag: karyotype

tag: phenotype

value: Accelerated cellular senescence


title: WT, replicate 2

value: bone marrow

value: primary cells

value: Mac1+ and c-kit+ cells with 1:1 ratio

value: WT

tag: age

value: 12-month old


title: S.12.F.1.Kd.1

description:
RNA extracted from 12 week old SHR female kidney replicate 1
Rat kidney

tag: Sex

value: Female

tag: strain

value: Spontaneously Hypertensive rat (SHR)

value: 12 weeks

tag: organ

value: Kidney


title: ChIPseq_LaminB1_MAD_hMSC_R1

tag: tissue


title: WT, replicate 1

tag: cell line

tag: cell type

tag: genotype


title: W.10.F.2.Kd.1

description:
RNA extracted from 10 week old WKY female kidney replicate 2
Rat kidney

value: Wistar-Kyoto rat (WKY)

value: 10 weeks


title: W.12.F.1.Kd.1

description:
RNA extracted from 12 week old WKY female kidney replicate 1
Rat kidney


title: ChIPseq_LaminB1_WT_hMSC_R1

source_name: WT-iPSCs derived human MSCs

value: Normal people

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Non


title: homozygous male mouse, Mettl14 KO, m6A IP, biol rep 4

description:
iBAT_RADRA.csv
Processed file's Sample column: CF28IP

source_name: iBAT

value: Mettl 14 knockout

value: iBAT


title: Arabidopsis Sha grown in mediterranean climate mock treated replicate 2

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

institute: INRAE

description:
Mock treatment - Plants grown in mediterranean climate
Sha_cont_Cl3_2

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Reads QC was performed using spiked-PhiX in-lane controls yielding Q30 error rate <0.4% for all lanes
Basecalling was performed with the HiSeq Control Software 2.2.58, RTA 1.18.64.0 and CASAVA-1.8.2
Paired-end reads were trimmed and mapped to the TAIR10.0 reference genome using the RNA-seq analysis tool of the CLC Genomics Workbench 11.0.1 software (Qiagen). The following mapping parameters were used: mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.8, both strands mapping, and 10 hits maximum per read
Assembly: Arabidopsis thaliana TAIR10.0
Supplementary files format and content: tab-delimited text files include Expression values; Transcripts annotated; Detected transcripts; Exon length; Unique gene reads; Total gene reads; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads; Exons; RPKM; Chromosome; Chromosome region start; Chromosome region end per gene

organism: Arabidopsis thaliana

source_name: leaves of 5-week old plants

growth_protocol: Plants were grown in jiffy pots for 35 or 70 days in Percival E41-L3 and E41-L2PLT growth cabinets at day temperatures of 23°C (mediterranean), 20°C (temperate) or 10°C (continental), night temperatures of 7°C (mediterranean), 9°C (temperate) and 1°C (continental), with a 13 hour light period (temperate and mediterranean climate) or 14 hour light period (continental climate) at intensity of 120 μmol/m²/s.

extract_protocol:
The border (ring of ~5mm wide) of disease lesions were collected with a scalpel at 30 hours post inoculation (hpi) for temperate and mediterranean acclimation and 48 hpi for continental acclimation,  and frozen in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min). RNA was extracted using the RNAplus kit (Macherey Nagel) following the manufacturer’s instructions. A Turbo DNAse treatment (Ambion) was applied to remove genomic DNA. The quality and concentrations of RNAs preparations were assessed with an Agilent Bioanalyzer using the Agilent RNA 6000 Nano kit
HiSeq SBS Kit v4

treatment_protocol:
S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed on the adaxial surface of leaves on 5-week old plants. Inoculations were performed on detached leaves under constant 21°C temperature, constant light (120 μmol/m²/s) and 90% relative humidity.
Temperate acclimation consisted in growth for 35 days under cycles of 13 hours at 20°C (day) followed by 11 hours at 9°C (night); mediterranean acclimation consisted in growth for 35 days under cycles of 13 hours at 23°C (day) followed by 11 hours at 7°C (night); continental acclimation consisted in growth for 70 days under cycles of 14 hours at 10°C (day) followed by 10 hours at 1°C (night).

value: leaves of 5-week old plants

value: A. thaliana Sha

value: Sha

tag: treatment 1_(inoculation)

value: mock

tag: treatment 2_(acclimation)

value: mediterranean


title: Arabidopsis Sha grown in mediterranean climate mock treated replicate 3

description:
Mock treatment - Plants grown in mediterranean climate
Sha_cont_Cl3_3


title: Arabidopsis Sha grown in mediterranean climate mock treated replicate 1

description:
Mock treatment - Plants grown in mediterranean climate
Sha_cont_Cl3_1


title: ChIPseq_LaminB1_WT_hMSC_R2

value: Skin

value: Cell culture


title: Arabidopsis Sha grown in mediterranean climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in mediterranean climate
Sha_Fr_Cl3_3

value: A. thaliana Sha - Sclerotinia sclerotiorum 1980

value: inoculated


title: S.10.F.3.Kd.1

description:
RNA extracted from 10 week old SHR female kidney replicate 3
Rat kidney

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 10 weeks

value: Kidney


title: homozygous male mouse, Mettl14 KO, m6A IP, biol rep 1

description:
iBAT_RADRA.csv
Processed file's Sample column: CF25IP


title: ChIPseq_LaminAC_MAD_hMSC_R2

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Accelerated cellular senescence


title: Arabidopsis Sha grown in mediterranean climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in mediterranean climate
Sha_Fr_Cl3_1

value: leaves of 5-week old plants


title: ChIPseq_LaminAC_MAD_hMSC_R1


title: homozygous male mouse, Mettl14 KO, m6A IP, biol rep 2

description:
iBAT_RADRA.csv
Processed file's Sample column: CF26IP

value: Mettl 14 knockout

value: iBAT


title: LysM-CRL, replicate 1

value: bone marrow

value: primary cells

value: Mac1+ and c-kit+ cells with 1:1 ratio

value: LysM-Cre; CRL+/flox

value: 12-month old


title: Arabidopsis Sha grown in mediterranean climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in mediterranean climate
Sha_Fr_Cl3_2

value: A. thaliana Sha - Sclerotinia sclerotiorum 1980

value: Sha

value: inoculated

value: mediterranean


title: homozygous male mouse, Control, m6A IP, biol rep 4

description:
iBAT_RADRA.csv
Processed file's Sample column: CF24IP

value: WT


title: ChIPseq_LaminAC_WT_hMSC_R2

value: Normal people

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: Skin

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Cell culture

value: Non


title: S.10.F.2.Kd.1

description:
RNA extracted from 10 week old SHR female kidney replicate 2
Rat kidney

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 10 weeks

value: Kidney


title: W.10.F.3.Kd.1

description:
RNA extracted from 10 week old WKY female kidney replicate 3
Rat kidney

value: Wistar-Kyoto rat (WKY)


title: S.10.F.1.Kd.1

description:
RNA extracted from 10 week old SHR female kidney replicate 1
Rat kidney


title: ChIPseq_LaminAC_WT_hMSC_R1


title: homozygous male mouse, Mettl14 KO, m6A IP, biol rep 3

description:
iBAT_RADRA.csv
Processed file's Sample column: CF27IP

value: Mettl 14 knockout

value: iBAT


title: ChIPseq_H3K9me3_MAD_hMSC_R2

value: Progeria patient (homozygous LMNA p.R527C)

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Accelerated cellular senescence


title: W.8.F.3.Kd.1

description:
RNA extracted from 8 week old WKY female kidney replicate 3
Rat kidney

value: 8 weeks


title: W.8.F.2.Kd.1

description:
RNA extracted from 8 week old WKY female kidney replicate 2
Rat kidney


title: homozygous male mouse, Control, m6A IP, biol rep 2

description:
iBAT_RADRA.csv
Processed file's Sample column: CF22IP

value: WT


title: Arabidopsis Rld2 grown in mediterranean climate mock treated replicate 1

description:
Mock treatment - Plants grown in mediterranean climate
Rld2_cont_Cl3_1

value: leaves of 5-week old plants

value: A. thaliana Rld2

value: mock

value: mediterranean


title: W.8.F.1.Kd.1

description:
RNA extracted from 8 week old WKY female kidney replicate 1
Rat kidney

value: Female


title: Arabidopsis Rld2 grown in mediterranean climate mock treated replicate 2

description:
Mock treatment - Plants grown in mediterranean climate
Rld2_cont_Cl3_2


title: Arabidopsis Rld2 grown in mediterranean climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in mediterranean climate
Rld2_Fr_Cl3_3

value: A. thaliana Rld2 - Sclerotinia sclerotiorum 1980

value: inoculated


title: homozygous male mouse, Control, m6A IP, biol rep 1

description:
iBAT_RADRA.csv
Processed file's Sample column: CF21IP


title: W.10.F.1.Kd.1

description:
RNA extracted from 10 week old WKY female kidney replicate 1
Rat kidney

value: 10 weeks

value: Kidney


title: ChIPseq_H3K9me3_MAD_hMSC_R1

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: Skin

value: Cell culture


title: ChIPseq_H3K9me3_WT_hMSC_R2

value: Normal people

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Non


title: S.8.F.3.Kd.1

description:
RNA extracted from 8 week old SHR female kidney replicate 3
Rat kidney

value: Spontaneously Hypertensive rat (SHR)

value: 8 weeks


title: homozygous male mouse, Mettl14 KO, input, biol rep 3

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF27C

value: Mettl 14 knockout

value: iBAT


title: Arabidopsis Rld2 grown in mediterranean climate mock treated replicate 3

description:
Mock treatment - Plants grown in mediterranean climate
Rld2_cont_Cl3_3

value: leaves of 5-week old plants

value: A. thaliana Rld2

value: mock

value: mediterranean


title: ChIPseq_H3K9me3_WT_hMSC_R1


title: Arabidopsis Rld2 grown in mediterranean climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in mediterranean climate
Rld2_Fr_Cl3_1

value: A. thaliana Rld2 - Sclerotinia sclerotiorum 1980

value: inoculated


title: homozygous male mouse, Mettl14 KO, input, biol rep 2

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF26C


title: S.8.F.2.Kd.1

description:
RNA extracted from 8 week old SHR female kidney replicate 2
Rat kidney

value: Female

value: Kidney


title: homozygous male mouse, Mettl14 KO, input, biol rep 4

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF28C


title: ChIPseq_H3K27me3_MAD_hMSC_R2

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: Skin

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Cell culture

value: Accelerated cellular senescence


title: Arabidopsis Col-0 grown in mediterranean climate mock treated replicate 3

description:
Mock treatment - Plants grown in mediterranean climate
Col-0_cont_Cl3_3

value: A. thaliana Col-0


title: homozygous male mouse, Control, m6A IP, biol rep 3

description:
iBAT_RADRA.csv
Processed file's Sample column: CF23IP

value: WT

value: iBAT


title: Arabidopsis Col-0 grown in mediterranean climate mock treated replicate 2

description:
Mock treatment - Plants grown in mediterranean climate
Col-0_cont_Cl3_2

value: leaves of 5-week old plants


title: ChIPseq_H3K27me3_MAD_hMSC_R1


title: W.24.F.3.Ag.1

description:
RNA extracted from 24 week old WKY female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-WKY-24wk-Female-3

value: Wistar-Kyoto rat (WKY)

value: 24 weeks

value: Adrenal gland


title: homozygous male mouse, Mettl14 KO, input, biol rep 1

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF25C

value: Mettl 14 knockout


title: S.8.F.1.Kd.1

description:
RNA extracted from 8 week old SHR female kidney replicate 1
Rat kidney

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 8 weeks


title: homozygous male mouse, Control, input, biol rep 4

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF24C


title: ChIPseq_H3K27me3_WT_hMSC_R2

value: Normal people

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Non


title: homozygous male mouse, Control, input, biol rep 3

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF23C


title: Arabidopsis Col-0 grown in mediterranean climate mock treated replicate 1

description:
Mock treatment - Plants grown in mediterranean climate
Col-0_cont_Cl3_1

value: mock

value: mediterranean


title: Arabidopsis Rld2 grown in mediterranean climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in mediterranean climate
Rld2_Fr_Cl3_2

value: A. thaliana Rld2 - Sclerotinia sclerotiorum 1980

value: inoculated


title: ChIPseq_H3K27me3_WT_hMSC_R1

value: Skin

value: Cell culture


title: W.24.F.2.Ag.1

description:
RNA extracted from 24 week old WKY female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-WKY-24wk-Female-2

value: Wistar-Kyoto rat (WKY)

value: 24 weeks


title: homozygous male mouse, Control, input, biol rep 2

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF22C

value: WT

value: iBAT


title: W.24.F.1.Ag.1

description:
RNA extracted from 24 week old WKY female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-WKY-24wk-Female-1

value: Female

value: Adrenal gland


title: Arabidopsis Col-0 grown in mediterranean climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in mediterranean climate
Col-0_Fr_Cl3_3

value: leaves of 5-week old plants

value: A. thaliana Col-0 - Sclerotinia sclerotiorum 1980


title: ChIPseq_H3K27ac_MAD_hMSC_R2

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Accelerated cellular senescence


title: Arabidopsis Col-0 grown in mediterranean climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in mediterranean climate
Col-0_Fr_Cl3_2

value: mediterranean


title: S.24.F.3.Ag.1

description:
RNA extracted from 24 week old SHR female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-SHR-24wk-Female-3

value: Spontaneously Hypertensive rat (SHR)


title: ChIPseq_H3K27ac_MAD_hMSC_R1

value: Skin


title: S.24.F.2.Ag.1

description:
RNA extracted from 24 week old SHR female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-SHR-24wk-Female-2


title: Arabidopsis Col-0 grown in mediterranean climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in mediterranean climate
Col-0_Fr_Cl3_1

value: inoculated


title: ChIPseq_H3K27ac_WT_hMSC_R2

value: Normal people

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Cell culture

value: Non


title: homozygous male mouse, Control, input, biol rep 1

description:
iBAT_Deseq2.csv
Processed file's Sample column: CF21C

value: WT

value: iBAT


title: S.24.F.1.Ag.1

description:
RNA extracted from 24 week old SHR female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-SHR-24wk-Female-1

value: Female

value: 24 weeks

value: Adrenal gland


title: ChIPseq_H3K27ac_WT_hMSC_R1

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong


title: W.16.F.3.Ag.1

description:
RNA extracted from 16 week old WKY female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-WKY-16wk-Female-3

value: Wistar-Kyoto rat (WKY)

value: 16 weeks


title: HRCS96A Het+MYBPC3Δ25bp Hom_3

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

data_processing:
The raw data containing reads of low quality, connector contamination and excessively high leveles of unknown base N were removed before data analysis. The clean reads thus generated were aligned to the reference genome using HISAT, mapped to reference genes using Bowtie2. The mapped genes were  subjected to differential expression analysis using DEseq2. The nondiabetic samples were grouped as control-2 and the diabetic samples were  grouped as case-2 for the DESeq2 analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: The processed file is in Excel format and contains FPKM, TPM, read counts, log2fc, qvalue, p value for the respetive genes with their gene symbol, gene ID and other gene related informations.

source_name: Heart

growth_protocol: Transgenic mice and C57BL/WT mice were used for experiments in this work from 2 months of age. The animal facility had a controlled environment (20°C temperature, 60% humidity, and 12 hours of light/dark cycles), and mice were fed ad libitum with a standard diet.

extract_protocol:
Mice hearts were dissected at 6 months of age, followed by total RNA isolation using an RNA isolation kit (Qiagen, cat# 763134), according to the manufacturer’s instructions. Total RNA concentration and quality (A260/280 ratio ≥2.0) were evaluated using a Nanodrop spectrophotometer (ThermoFisher Scientific). The quality of total RNA was further measured using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
After Sample QC was by qubit and Agilent Bioanalyzer, a certain amount of RNA samples were denatured at suitable temperatures to open-up their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads followed by mRNA fragmentation and cDNA Synthesis. The double-stranded cDNA fragments were subjected to end-repair, the addition of a single ‘A’ nucleotide to the 3’ ends of the blunt fragments and ligated to adaptors before amplification.
After quality control of the prepared library, the amplified products were denatured to generate single stranded PCR products which was then circularized to replicate using rolling cycle amplification yielding a DNA nanoball (DNB) containing multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Heart

value: 6 Months


title: Arabidopsis Sha grown in continental climate mock treated replicate 2

description:
Mock treatment - Plants grown in continental climate
Sha_cont_Cl2_2

value: leaves of 5-week old plants

value: A. thaliana Sha

value: Sha

value: mock

value: continental


title: ChIPseq_CTCF_MAD_hMSC_R2

value: Progeria patient (homozygous LMNA p.R527C)

value: Skin

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Cell culture

value: Accelerated cellular senescence


title: HRCS96A Het+MYBPC3Δ25bp Hom_2

value: Female


title: Arabidopsis Sha grown in continental climate mock treated replicate 1

description:
Mock treatment - Plants grown in continental climate
Sha_cont_Cl2_1


title: W.16.F.2.Ag.1

description:
RNA extracted from 16 week old WKY female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-WKY-16wk-Female-2

value: Adrenal gland


title: W.16.F.1.Ag.1

description:
RNA extracted from 16 week old WKY female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-WKY-16wk-Female-1

value: Wistar-Kyoto rat (WKY)


title: ChIPseq_CTCF_MAD_hMSC_R1

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong


title: HRCS96A mutant heterozygous_3

value: Heart


title: HRCS96A mutant heterozygous_2

value: 6 Months


title: ChIPseq_CTCF_WT_hMSC_R2

value: Normal people

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Non


title: Arabidopsis Sha grown in continental climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in continental climate
Sha_Fr_Cl2_2

value: leaves of 5-week old plants

value: A. thaliana Sha - Sclerotinia sclerotiorum 1980

value: Sha

value: inoculated

value: continental


title: Arabidopsis Sha grown in continental climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in continental climate
Sha_Fr_Cl2_3


title: HRCS96A mutant heterozygous_1


title: ChIPseq_CTCF_WT_hMSC_R1

value: Skin

value: Cell culture


title: S.16.F.2.Ag.1

description:
RNA extracted from 16 week old SHR female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-SHR-16wk-Female-2

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 16 weeks


title: MYBPC3Δ25bp homozygous_3


title: Arabidopsis Sha grown in continental climate mock treated replicate 3

description:
Mock treatment - Plants grown in continental climate
Sha_cont_Cl2_3

value: A. thaliana Sha

value: mock


title: ChIPseq_Input_MAD_hMSC_R1

extract_protocol:
Lysis of 5 X 10 ^6 fixed cells was sonicated with Diagenode Bioruptor Pico (HKU, Imaging & Flow Cytometry Core facility) for 20 cycles to generate DNA fragments ranging from 200-1000 bp and discarded insoluble part after 15,000 RPM for 20min. Input material was reserved.
ChIP

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Accelerated cellular senescence


title: S.16.F.1.Ag.1

description:
RNA extracted from 16 week old SHR female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-SHR-16wk-Female-1

value: Adrenal gland


title: MYBPC3Δ25bp homozygous_2

value: Male

value: Heart

value: 6 Months


title: Arabidopsis Rld2 grown in continental climate mock treated replicate 2

description:
Mock treatment - Plants grown in continental climate
Rld2_cont_Cl2_2

value: leaves of 5-week old plants

value: A. thaliana Rld2

value: continental


title: W.12.F.3.Ag.1

description:
RNA extracted from 12 week old WKY female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-WKY-12wk-Female-3

value: Female

value: Wistar-Kyoto rat (WKY)

value: 12 weeks


title: ChIPseq_Input_WT_hMSC_R2

value: Normal people

value: Skin

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Cell culture

value: Non


title: W.12.F.2.Ag.1

description:
RNA extracted from 12 week old WKY female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-WKY-12wk-Female-2


title: HRCS96A Het+MYBPC3Δ25bp Hom_1


title: MYBPC3Δ25bp homozygous_1


title: ChIPseq_Input_WT_hMSC_R1

source_name: WT-iPSCs derived human MSCs

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong


title: Arabidopsis Rld2 grown in continental climate mock treated replicate 1

description:
Mock treatment - Plants grown in continental climate
Rld2_cont_Cl2_1

value: mock


title: Non transgenic_3


title: S.16.F.3.Ag.1

description:
RNA extracted from 16 week old SHR female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-SHR-16wk-Female-3

value: Spontaneously Hypertensive rat (SHR)

value: 16 weeks

value: Adrenal gland


title: W.12.F.1.Ag.1

description:
RNA extracted from 12 week old WKY female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-WKY-12wk-Female-1


title: Arabidopsis Sha grown in continental climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in continental climate
Sha_Fr_Cl2_1

source_name: leaves of 5-week old plants

value: leaves of 5-week old plants

value: A. thaliana Sha - Sclerotinia sclerotiorum 1980

value: Sha

value: inoculated


title: Non transgenic_2

value: Male

value: Heart

value: 6 Months


title: Arabidopsis Rld2 grown in continental climate mock treated replicate 3

description:
Mock treatment - Plants grown in continental climate
Rld2_cont_Cl2_3

value: A. thaliana Rld2

value: continental


title: Arabidopsis Rld2 grown in continental climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in continental climate
Rld2_Fr_Cl2_3

value: A. thaliana Rld2 - Sclerotinia sclerotiorum 1980


title: HiC_WT_hMSC_R2

extract_protocol:
BAT Hi-C was performed on 5 x 10^7 cells as described in PMID: 31442560.
BAT Hi-C same as Jie Huangang et al. Methods (2019)

value: Normal people

value: Skin

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Cell culture


title: ChIPseq_Input_MAD_hMSC_R2

source_name: MAD-iPSCs derived human MSCs

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Accelerated cellular senescence


title: HiC_MAD_hMSC_R1


title: HiC_MAD_hMSC_R2


title: KO_Polyribosome_rep3

first: Hao

last: Peng

address: Zhongshan 2nd Road, Guangzhou, 510080, China

department: Department of Breast Cancer

institute: Guangdong General Hospital

description: PolyA mRNA

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Fragments per kilo base per million mapped reads (FPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
Supplementary_files_format_and_content: The txt files of RNA-seq and Ribo-seq include the FPKM values for every gene.

source_name: Nasopharyngeal carcinoma 5-8F cells

growth_protocol: Human 5-8F cells were maintained in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: METTL5 was knocked out by sgRNA.

value: METTL5 knockout

value: Nasopharyngeal carcinoma 5-8F cells


title: S.12.F.2.Ag.2

description:
RNA extracted from 12 week old SHR female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-SHR-12wk-Female-2

extract_protocol: Direct-Zol miniprep kit from Zymo Research

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 12 weeks

value: Adrenal gland


title: S.12.F.1.Ag.1

description:
RNA extracted from 12 week old SHR female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-SHR-12wk-Female-1


title: KO_Polyribosome_rep2

description: PolyA mRNA


title: Arabidopsis Rld2 grown in continental climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in continental climate
Rld2_Fr_Cl2_2

value: leaves of 5-week old plants

value: A. thaliana Rld2 - Sclerotinia sclerotiorum 1980

value: inoculated

value: continental


title: HiC_WT_hMSC_R1

value: Normal people

value: Skin

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Non


title: S.12.F.3.Ag.1

description:
RNA extracted from 12 week old SHR female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-SHR-12wk-Female-3


title: ATACseq_MAD_hMSC_R2

extract_protocol:
Genome DNA of 5 x 10^4 cells was tagmentated by 2μl homemade assembled Tn5 at 37℃ for 30min and 200-1000bp fragments were selected by AMPure XP beads (Beckman Coulter).
Tn5

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Cell culture


title: W.10.F.3.Ag.1

description:
RNA extracted from 10 week old WKY female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-WKY-10wk-Female-3

value: Female

value: Wistar-Kyoto rat (WKY)

value: 10 weeks


title: Arabidopsis Col-0 grown in continental climate mock treated replicate 2

description:
Mock treatment - Plants grown in continental climate
Col-0_cont_Cl2_2

value: leaves of 5-week old plants

value: A. thaliana Col-0

value: mock


title: KO_Polyribosome_rep1

description: PolyA mRNA

value: METTL5 knockout

value: Nasopharyngeal carcinoma 5-8F cells


title: Arabidopsis Col-0 grown in continental climate mock treated replicate 1

description:
Mock treatment - Plants grown in continental climate
Col-0_cont_Cl2_1

value: continental


title: ATACseq_MAD_hMSC_R1

value: Skin

value: Accelerated cellular senescence


title: KO_Input_rep3

description: PolyA mRNA


title: Arabidopsis Col-0 grown in continental climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in continental climate
Col-0_Fr_Cl2_3

value: A. thaliana Col-0 - Sclerotinia sclerotiorum 1980

value: inoculated


title: W.10.F.1.Ag.1

description:
RNA extracted from 10 week old WKY female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-WKY-10wk-Female-1

value: Adrenal gland


title: ATACseq_WT_hMSC_R2

value: Normal people

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Non


title: Arabidopsis Rld2 grown in continental climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in continental climate
Rld2_Fr_Cl2_1

value: A. thaliana Rld2 - Sclerotinia sclerotiorum 1980


title: Non transgenic_1

source_name: Heart

value: Male

value: Heart

value: 6 Months


title: ATACseq_WT_hMSC_R1

value: Cell culture


title: Arabidopsis Col-0 grown in continental climate mock treated replicate 3

description:
Mock treatment - Plants grown in continental climate
Col-0_cont_Cl2_3

value: leaves of 5-week old plants

value: A. thaliana Col-0

value: mock


title: KO_Input_rep2

description: PolyA mRNA

value: METTL5 knockout

value: Nasopharyngeal carcinoma 5-8F cells


title: Arabidopsis Col-0 grown in continental climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in continental climate
Col-0_Fr_Cl2_2

value: A. thaliana Col-0 - Sclerotinia sclerotiorum 1980

value: inoculated

value: continental


title: S.10.F.2.Ag.1

description:
RNA extracted from 10 week old SHR female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-SHR-10wk-Female-2

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 10 weeks

value: Adrenal gland


title: KO_Input_rep1

description: PolyA mRNA


title: S.10.F.3.Ag.1

description:
RNA extracted from 10 week old SHR female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-SHR-10wk-Female-3


title: RNAseq_MAD_hMSC_R2

extract_protocol:
Total RNA of 5 x 10^6 cells was extracted from cell pellets using RNAzol reagent (MRC) and the library was prepared by VAHTSTM mRNA-seq V2 Library Prep Kit (Vazyme).
cDNA_oligo_dT

value: Progeria patient (homozygous LMNA p.R527C)

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: Skin

value: MAD-iPSCs derived human MSCs

value: Passage 9-13 MAD_iPSCs derived hMSCs

value: Accelerated cellular senescence


title: Arabidopsis Sha grown in temperate climate mock treated replicate 3

description:
Mock treatment - Plants grown in temperate climate
Sha_cont_Cl1_3

value: leaves of 5-week old plants

value: A. thaliana Sha

value: Sha

value: temperate


title: S.10.F.1.Ag.1

description:
RNA extracted from 10 week old SHR female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-SHR-10wk-Female-1


title: Vector_Polyribosome_rep3

description: PolyA mRNA

value: Wild type

value: Nasopharyngeal carcinoma 5-8F cells


title: RNAseq_MAD_hMSC_R1

value: Cell culture


title: RNAseq_WT_hMSC_R2

value: Normal people

value: WT-iPSCs derived human MSCs

value: Passage 9-13 of WT_iPSCs derived hMSCs

value: Non


title: Arabidopsis Sha grown in temperate climate mock treated replicate 2

description:
Mock treatment - Plants grown in temperate climate
Sha_cont_Cl1_2

value: mock


title: Vector_Polyribosome_rep2

description: PolyA mRNA


title: W.8.F.3.Ag.1

description:
RNA extracted from 8 week old WKY female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-WKY-8wk-Female-3

value: Female

value: Wistar-Kyoto rat (WKY)

value: 8 weeks

value: Adrenal gland


title: W.10.F.2.Ag.1

description:
RNA extracted from 10 week old WKY female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-WKY-10wk-Female-2

value: 10 weeks


title: RNAseq_WT_hMSC_R1

source_name: WT-iPSCs derived human MSCs

value: Wei Jin, Zhongjun Zhou's Lab in University of Hong Kong

value: Skin


title: Arabidopsis Sha grown in temperate climate mock treated replicate 1

description:
Mock treatment - Plants grown in temperate climate
Sha_cont_Cl1_1

value: leaves of 5-week old plants

value: A. thaliana Sha

value: Sha


title: Vector_Polyribosome_rep1

description: PolyA mRNA

value: Widl type

value: Nasopharyngeal carcinoma 5-8F cells


title: Vector_Input_rep3

description: PolyA mRNA

value: Wild type


title: W.8.F.2.Ag.1

description:
RNA extracted from 8 week old WKY female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-WKY-8wk-Female-2


title: W.8.F.1.Ag.1

description:
RNA extracted from 8 week old WKY female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-WKY-8wk-Female-1


title: HTEC cDNA sample 2-2

city: San Francisco

first: Min Cheol

last: Kim

state: CA

address: 505 Parnassus Ave

institute: University of California, San Francisco

description:
10X Genomics V2 3' kit
HTEC_counts.h5ad

data_processing:
CellRanger + scanpy
Assembly: GRCh38
Supplementary files format and content: h5ad file containing gene expression counts, cell barcodes, feature names, experimental covariates

source_name: HTEC

extract_protocol:
Human tracheal epithelial cells were harvested from deceased organ donors according to established protocols (PMID: 1616056). Frozen cell aliquots were reactivated and cultured in epithelial growth media (EGM) [3:1 (v/v) F-12 Nutrient Mixture (Gibco)–Dulbecco's modified Eagle's medium (Invitrogen), 5\% fetal bovine serum (Gibco), 0.4 ug/mL hydrocortisone (Sigma-Aldrich), 5 ug/mL insulin (Sigma-Aldrich), 8.4 ng/mL cholera toxin (Sigma-Aldrich), 10 ng/mL epidermal growth factor (Invitrogen), 24 ug/mL adenine (Sigma-Aldrich), and 10 uM Y-27632 (Enzo Life Sciences)] on 10 mm dishes coated with rat tail collagen (Sigma-Aldrich). EGM was changed three times a week until dishes were confluent, at which point the cells were passaged with 0.25\% trypsin for 30 minutes. For air liquid interface culture, expanded basal cells were plated at 50,000 cells per 6.5 mm transwell insert (Corning 3470) coated with human placental collagen (Sigma-Aldrich) and cultured with Pneumacult ALI (StemCell) for 21-28 days according to the manufacturer’s instructions.
Starting on day 27, interferon stimulation (IFN-beta: 10 ng/ml, IFN-alpha2: 10 ng/ml, IFN-gamma: 10 ng/ml, IFN-lambda2: 10 ng/ml) was added at hours 0, 24, 39, 42, and 45 prior to harvesting (For final timepoints 3, 6, 9, 24, and 48 hours). On the day of harvest, basal media was aspirated and both basal and apical chambers were rinsed twice with PBS. Following two washes, trypsin-EDTA (0.25% Fisher cat. 25200072) was added to both the basal and apical chambers (300 ul basal, 100 ul apical) and incubated for 30 minutes at 37degree C while pipette mixing every 10 minutes. Trypsinization was quenched with 300 ul of maintenance media and transferred to a 1.5ml eppendorf tube (eppendorf cat. 022431021) and centrifuged at 350xg for 5 minutes at 4degree C. Cells were resuspended in 94 ul of cell staining buffer (Biolegend cat. 420201) and blocked with 5 ul of TruStain FcX (Biolegend cat. 422302) for 10 minutes on ice. Blocked cells were stained with 1 ul of Biolegend Totalseq-B hashtags (Biolegend Totalseq-B hashtags 1-11) for 30 minutes on ice. Staining was quenched with 1 ml of cell staining buffer and spun at 300xg for 5 minutes at 4degree C prior to two more washes with 1 ml of cell staining buffer. Cells were resuspended in 100 ul of 0.05% BSA in PBS and counted via Countess II (Fisher cat. A27977). Counted cells were pooled equally into two pools and spun at 300xg for 5 minutes at 4degree C.

value: HTEC

tag: treatment

value: interferons

tag: library type

value: mRNA


title: Arabidopsis Sha grown in temperate climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in temperate climate
Sha_Fr_Cl1_3

source_name: leaves of 5-week old plants

value: A. thaliana Sha - Sclerotinia sclerotiorum 1980

value: inoculated

value: temperate


title: Vector_Input_rep2

description: PolyA mRNA

source_name: Nasopharyngeal carcinoma 5-8F cells


title: HTEC cDNA sample 2-1

description:
10X Genomics V2 3' kit
HTEC_counts.h5ad


title: Arabidopsis Sha grown in temperate climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in temperate climate
Sha_Fr_Cl1_2


title: Arabidopsis Col-0 grown in continental climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in continental climate
Col-0_Fr_Cl2_1

value: A. thaliana Col-0 - Sclerotinia sclerotiorum 1980

value: continental


title: S.8.F.3.Ag.1

description:
RNA extracted from 8 week old SHR female adrenal gland replicate 3
Rat adrenal gland

source_name: Adrenal gland-SHR-8wk-Female-3

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 8 weeks

value: Adrenal gland


title: Arabidopsis Sha grown in temperate climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in temperate climate
Sha_Fr_Cl1_1

value: leaves of 5-week old plants


title: S.8.F.2.Ag.1

description:
RNA extracted from 8 week old SHR female adrenal gland replicate 2
Rat adrenal gland

source_name: Adrenal gland-SHR-8wk-Female-2


title: S.8.F.1.Ag.1

description:
RNA extracted from 8 week old SHR female adrenal gland replicate 1
Rat adrenal gland

source_name: Adrenal gland-SHR-8wk-Female-1


title: Vector_Input_rep1

description: PolyA mRNA


title: HTEC cDNA sample 1-2

description:
10X Genomics V2 3' kit
HTEC_counts.h5ad


title: PM1_MLN_B_7 VDJ

first: Patrick

last: Wilson

address: 413 E 69th St

department: Drukier Institute

institute: Weill Cornell Medicine

description: 10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: GRCh38
Supplementary files format and content: Comma-separated files and fasta files
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format

source_name: Human Mediastinal LN 7

extract_protocol:
10x Genomics CG000424_C
10x Genomics CG000424_C

value: Human Mediastinal LN 7

value: B cell


title: Arabidopsis Rld2 grown in temperate climate mock treated replicate 3

description:
Mock treatment - Plants grown in temperate climate
Rld2_cont_Cl1_3

value: A. thaliana Rld2

value: mock


title: HTEC cDNA sample 1-1

description:
10X Genomics V2 3' kit
HTEC_counts.h5ad

value: HTEC


title: Arabidopsis Rld2 grown in temperate climate mock treated replicate 2

description:
Mock treatment - Plants grown in temperate climate
Rld2_cont_Cl1_2


title: HTEC HTO sample 2-2

description:
10X Genomics V2 3' kit
feature_reference.csv
HTEC_counts.h5ad

library_source: other

molecule: protein

value: interferons

value: HTO


title: PM1_MLN_B_7 RNA

description: 10x Genomics


title: PM1_MLN_B_4R VDJ

description: 10x Genomics

source_name: Human Mediastinal LN 4R

value: Human Mediastinal LN 4R


title: HTEC HTO sample 1-2


title: Arabidopsis Rld2 grown in temperate climate mock treated replicate 1

description:
Mock treatment - Plants grown in temperate climate
Rld2_cont_Cl1_1


title: PM1_MLN_B_4R RNA

description: 10x Genomics


title: LB, 10min, Rep3

city: Basel

first: Knut

last: Drescher

state: BS

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description: data for chromosome I and II

data_processing:
Sequencing of the cDNA libraries was performed by MPGC
cDNA reads were imported into CLC Genomics Workbench v11.0 and analyzed using mostly standard parameters.
The reads were checked for quality and mapped to the V. cholerae reference genomes: NCBI Acc.number: AE003852 and AE003853 using the default settings in CLC Genomics Workbench v11.0.
Reads mapping in CDS were counted, and read counts were normalized (TPM), and transformed (log2). Differential expression was tested using the built in tool with CLC Genomics Workbench v11.0. Genes with a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Assembly: AE003852, AE003853; Vibrio cholerae O1 biovar eltor str. N16961 chromosome I and II, complete genome
Supplementary files format and content: Read count table by TPM normalization

organism: Vibrio cholerae

source_name: Biofilm cells collected from microfluidics

growth_protocol: Bacterial cells in exponential phase (OD600=0.4) were inoculated in microfluidic flow chambers and supplied with LB or LB+peptidolgycan (300 µg/mL) for 10 min.

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods,2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.

treatment_protocol: Bacterial cells were collected from microfluidic flow chambers in a 1:1 mixture of PBS and RNAstop solution (a mixture of 95% (vol/vol) EtOH and 5% (vol/vol) phenol). After centrifugation and removal of the supernatant, the cells were resuspended in 50 μL of lysozyme buffer, which consisted of TE (10 mM Tris, adjusted to pH 8.0 with HCl), 1 mM EDTA, and 20 U μL-1 Ready-lyse lysozyme (Lucigen, R1804M) and immediately snap frozen in liquid nitrogen until further processing.

value: bacterial cell

tag: condition

value: Grown with LB for 10 min

tag: replicate

value: rep 3


title: Arabidopsis Rld2 grown in temperate climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in temperate climate
Rld2_Fr_Cl1_3

value: A. thaliana Rld2 - Sclerotinia sclerotiorum 1980

value: inoculated

value: temperate


title: PG, 10min, Rep3

description: data for chromosome I and II

value: Grown with LB+PG for 10 min


title: PM1_MLN_B_2L VDJ

description: 10x Genomics

source_name: Human Mediastinal LN 2L

value: Human Mediastinal LN 2L


title: Arabidopsis Rld2 grown in temperate climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in temperate climate
Rld2_Fr_Cl1_2

value: leaves of 5-week old plants


title: PG, 10min, Rep2

description: data for chromosome I and II

value: rep 2


title: Arabidopsis Rld2 grown in temperate climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in temperate climate
Rld2_Fr_Cl1_1


title: HTEC HTO sample 1-1