title: Hvolc, lib553, pH1p4_42C, AlkBmix, TGIRT, rep1

description: Library name: Sample 101


title: WT_2year_1

status: Public on Oct 22 2025

type: SRA

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

country: USA

institute: Cornell University

library_source: transcriptomic

data_processing:
The sequencing reads were aligned to the mouse genome (mm10). RNA-sequencing reads were mapped to genome release using STAR (v2.5.3a)
Transcript quantification was performed using Salmon (v0.6.0)
Normalization, sex and batch corrections and differential expression analysis were performed using DESeq2. The Benjamini-Hochberg method was used for multiple testing corrections.
Assembly: mm10
Supplementary files format and content: Normalized counts files are comma separated value matrices containing DESeq2 normalized counts for each of the samples.

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Illumina TruSeq polyA + Sample Prep Kit
Total RNA was isolated from mouse liver tissues using the Total RNA Purification Kit (Norgen Biotek). RNA was quantified with the Nanodrop 2000 (ThermoFisher), and RNA integrity was assessed by the Agilent 4200 Tapestation (Agilent Technologies).
Batch_A: Libraries were prepared using Illumina TruSeq polyA + Sample Prep Kit and sequenced on the NextSeq2000 platform at the UNC High Throughput Sequencing Core Facility. Batch_B: Libraries were prepared using NEBNext Ultra II Directional Library Prep Kit and sequenced on the NextSeq2000 (Illumina) at the Biotechnology Research Center at the Cornell University.

tag: batch

tag: genotype

value: WT

tag: age

tag: Sex

value: Female

tag: tissue

value: liver


title: WT_2year_2


title: Hvolc, lib553, pH4_42C, NaCNBH3, TGIRT, rep1

city: Rehovot

first: Miguel

middle: A.

last: Garcia-Campos

state: Center District

address: Herzl 234, Meyer Bldg., Room 1410

department: Molecular Genetics

country: Israel

institute: Weizmann Insitute of Science

description: Library name: Sample 99

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_000025685.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

molecule: total RNA

organism: Haloferax volcanii

source_name: Bacterial culture

growth_protocol: Were grown in duplicates in YPC medium containing  1.4M, 2.4M (optimum) and 4M salt at 42°C (optimum), as well as at low temperature (30°C) and high temperature (50°C) in YPC containing  2.4M salt

extract_protocol:
The aqueous phase was collected after centrifugation and mixed with an equal volume of ethanol. RNA was processed with the NEB Monarch Total RNA Miniprep Kit. DNase digestion to eliminate genomic DNA.
Remaining primers left in the reaction were digested by addition of 3 μL ExoSAP-IT (Applied Biosystems, 78205) to the 20 μL reverse transcription reaction, and incubation at 37°C for 12 min. RNA was degraded by adding 2.5 μL of NaOH 1M and 1 μL of 0.5M EDTA, and incubation at 70°C for 12 min. The base was neutralized with the addition of 1M HCl, cDNA was cleaned using MyOne silane beads. An adapter was added to the 3’ end of the cDNA by ligating 50 pmoles 5iLL-22 DNA adapter using T4 RNA Ligase 1, High concentration (NEB, M0437M), DMSO 4%, ATP 1mM and PEG8000 25% at 23°C for 3 h. After clean-up with MyOne silane beads, we amplified the cDNA library for 12 cycles using Illumina Library PCR primers F and R and KAPA HiFi HotStart ReadyMix (Roche, KK2601). Amplified libraries were cleaned with Kapa pure beads (Roche, KK8002), quantified using Qubit (Life Technologies) and the distribution of library size was determined using TapeStation (Agilent Technologies).

value: Bacterial culture

tag: strain

tag: treatment


title: WT_2year_5

extract_protocol:
NEBNext Ultra II Directional Library Prep Kit
Total RNA was isolated from mouse liver tissues using the Total RNA Purification Kit (Norgen Biotek). RNA was quantified with the Nanodrop 2000 (ThermoFisher), and RNA integrity was assessed by the Agilent 4200 Tapestation (Agilent Technologies).
Batch_A: Libraries were prepared using Illumina TruSeq polyA + Sample Prep Kit and sequenced on the NextSeq2000 platform at the UNC High Throughput Sequencing Core Facility. Batch_B: Libraries were prepared using NEBNext Ultra II Directional Library Prep Kit and sequenced on the NextSeq2000 (Illumina) at the Biotechnology Research Center at the Cornell University.

value: Male


title: WTsh_3

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

description: Library name: sample 9

data_processing:
transcriptome mapping and counts of reads by gene locus are done with Tophat2/HTSeqcount; exact multihits are removed and count only consistent PE reads (in PE case).
Assembly: transcriptome of annotation Ath_versionTAIR10-Mitocorrected_FuncDescription-040321
Supplementary files format and content: tab delimited text file with raw count by gene. Column content: GeneID,RawCount no_stranded,RawCount forward,RawCount reverse

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Hygrometry : 60% Temperature : 22°C Light : 80 microE

extract_protocol:
total RNA, quantity=100mg
rna_selection:selection polyA, single, stranded:yes, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx

treatment_protocol:
Amino acid_treatment-compound based treatment-compound addition-amino-acids 100 mg/lquantity 100  In vitro culture on solid media for 10 days containing amino-acids (100 mg/l).
Control_treatment-compound based treatment-compound addition-mock
Humic substance_treatment-compound based treatment-compound addition-humic substance 50 mg/lquantity 50  In vitro culture on solid media for 10 days containing humic substance (50 mg/l).

value: wild type (wild type)

value: seedling

tag: developmental stage

value: Humic substance_treatment


title: WTsh_1

description: Library name: sample 7


title: Hvolc, lib553, pH4_42C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 100


title: Hvolc, lib553, pH2p4_50C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 97


title: WTsh_2

description: Library name: sample 8


title: Hvolc, lib553, pH2p4_42C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 96


title: Hvolc, lib553, pH2p4_50C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 98


title: WTcontrol_3

description: Library name: sample 6


title: WTcontrol_2

description: Library name: sample 5


title: TG_2mon_1

value: TG


title: WTcontrol_1

description: Library name: sample 4


title: WTaa_2

description: Library name: sample 2

value: Amino acid_treatment


title: Hvolc, lib553, pH1p4_42C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 92


title: Hvolc, lib553, pH2p4_30C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 93


title: WTaa_3

description: Library name: sample 3


title: Hvolc, lib553, pH2p4_42C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 95


title: Hvolc, lib553, pH2p4_30C, AlkBmix, TGIRT, rep2

description: Library name: Sample 104


title: Healthy control rep9

type: genomic

city: Valencia

first: Estefanía

last: Tarazón

address: Avenida Fernando Abril Martorell 106

country: Spain

institute: Instituto de investigación Sanitaria La Fe

description:
DNA from healthy control 200
CNT.200._s2

hyb_protocol: Bisulfite conversion of 600 ng of genomic DNA was performed using the EZ-96 DNA Methylation Kit (Zymo Research Corp., Irvine, CA, USA) according to the manufacturer’s instructions. Approximately 200 ng of bisulfite-converted DNA was then hybridized onto the Infinium MethylationEPIC BeadChip. Briefly, the workflow included whole-genome amplification, enzymatic endpoint fragmentation, precipitation, and resuspension. The resuspended samples were hybridized onto the BeadChip for 16 hours at 48 °C, followed by washing. Single-nucleotide extension with labelled dideoxynucleotides was performed, followed by multiple rounds of staining using a combination of labelled antibodies against biotin and 2,4-dinitrophenol.

scan_protocol: Arrays were imaged using BearArray Reader (HiScan) and standard recommended Illumina scanner settings.

data_processing:
For the methylation analysis, differentially methylated CpG positions (DMPs) were identified and mapped to their genomic locations using coordinate data from the Illumina Database (Infinium MethylationEPIC v1.0 B5 Manifest File, March 13, 2020). For the analysis, a linear model was used, incorporating sex as a covariate. CpG sites with a high sex-dependency effect were excluded, and the beta values of the remaining sites were adjusted to discriminate between patients and controls, regardless of sex. To increase statistical power, the t-statistics were moderated using an empirical Bayesian approach.
DNA methylation levels are expressed as beta values (β) ranging from 0 to 1

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Heart

label_protocol: Standard Illumina protocol

extract_protocol: Twenty milligrams of frozen LV tissue (iDCM: n = 6; CNT: n = 9) were homogenized in a buffer containing 10 mM EDTA, 200 mM NaCl and 10 mM Tris–HCl (pH 7.4), along with 10% SDS, and proteinase K (20 mg/mL). The mixture was incubated overnight at 37 ºC with continuous stirring. The homogenates were then heated at 75 °C for 15 minutes and treated with RNase A (10 mg/mL) for 1.5 hours at 37 °C. DNA was extracted using a modified phenol–chloroform protocol, as previously described[Gil-Cayuela C et al. Int J Cardiol 2017]. The extraction products were quantified using the Quant-iT PicoGreen dsDNA Assay (Life Technologies, Carlsbad, CA, USA), and DNA purity was assessed using a NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) by measuring the 260/280 and 260/230 ratios. DNA integrity was evaluated by electrophoresis on a 1.3% agarose gel.

value: Heart

value: female

tag: disease state

value: Healthy control


title: WTaa_1

description: Library name: sample 1


title: Hvolc, lib553, pH2p4_50C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 89


title: Hvolc, lib553, pH2p4_42C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 87


title: Dilated cardiomyopathy patient5

description:
DNA from dilated cardiomyopathy patient 105
DIL.105._s2

value: male

value: Dilated cardiomyopathy patient


title: Dilated cardiomyopathy patient6

description:
DNA from dilated cardiomyopathy patient 106
DIL.106._s2


title: Healthy control rep4 b

description:
DNA from healthy control 67
CNT.67.Avg


title: Healthy control rep3 b

description:
DNA from healthy control 66
CNT.66.Avg


title: Hvolc, lib553, pH2p4_42C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 88


title: Hvolc, lib553, pH2p4_30C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 86


title: Hvolc, lib553, pH2p4_50C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 90


title: Dilated cardiomyopathy patient4

description:
DNA from dilated cardiomyopathy patient 28
DIL.28._s2


title: Hvolc, lib553, pH2p4_30C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 85


title: Dilated cardiomyopathy patient2

description:
DNA from dilated cardiomyopathy patient 20
DIL.20._s2


title: Hvolc, lib553, pH4_42C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 84


title: Dilated cardiomyopathy patient3

description:
DNA from dilated cardiomyopathy patient 24
DIL.24._s2


title: Hvolc, lib553, pH4_42C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 83


title: Hvolc, lib553, pH2p4_30C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 94


title: Dilated cardiomyopathy patient1

description:
DNA from dilated cardiomyopathy patient 8
DIL.8._s2


title: Hvolc, lib553, pH1p4_42C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 82


title: Healthy control rep7

description:
DNA from healthy control 181
CNT.181._s1


title: Healthy control rep8

description:
DNA from healthy control 182
CNT.182._s1


title: Hvolc, lib553, pH4_42C, Mock, SSIII, rep2

description: Library name: Sample 80


title: Hvolc, lib553, pH1p4_42C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 81


title: Hvolc, lib553, pH4_42C, Mock, SSIII, rep1

description: Library name: Sample 79


title: Healthy control rep6

description:
DNA from healthy control 180
CNT.180._s1


title: Healthy control rep5

description:
DNA from healthy control 115
CNT.115._s1


title: Hvolc, lib553, pH2p4_50C, Mock, SSIII, rep1

description: Library name: Sample 77


title: Healthy control rep4 a

description:
DNA from healthy control 67
CNT.67.Avg


title: Hvolc, lib553, pH2p4_42C, Mock, SSIII, rep2

description: Library name: Sample 76


title: Healthy control rep3 a

description:
DNA from healthy control 66
CNT.66.Avg


title: Healthy control rep1

description:
DNA from healthy control 3
CNT.3._s1


title: Hvolc, lib553, pH2p4_42C, Mock, SSIII, rep1

description: Library name: Sample 75


title: Hvolc, lib553, pH2p4_30C, Mock, SSIII, rep1

description: Library name: Sample 73


title: Hvolc, lib553, pH2p4_30C, Mock, SSIII, rep2

description: Library name: Sample 74


title: Hvolc, lib553, pH1p4_42C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 91


title: Hvolc, lib553, pH1p4_42C, Mock, SSIII, rep2

description: Library name: Sample 72


title: Hvolc, lib553, pH1p4_42C, Mock, SSIII, rep1

description: Library name: Sample 71


title: Donor 3, NS-Y, rep2

city: Bilthoven

first: Amadeo

last: Muñoz

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

description: Library name: 106062-001-022

data_processing:
The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (STAR2 v2.7.10) with default settings.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v2.0.2
Assembly: GRCh38.p13 - Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: The counts were saved to count files, which serve as input for downstream RNA-Seq differential expression analysis

source_name: Primary nasal epithelial cells

growth_protocol: Primary human nasal epithelial cells (HNEC) from healthy donors (EP51AB, Epithelix, Switzerland) were expanded in complete PneumaCult Ex Plus medium (Stemcell Technologies, #05040, Canada) until the cells reached log phase. Cells were then harvested using trypsin (Lonza, CC-5012), which was inactivated using trypsin neutralizing solution (Lonza, CC-5002). Passage 1 cells were frozen in 78% Ham’s nutrient mix F12 (Merck/Sigma, 51651C) with 10% FCS, 2% 1.5M Hepes [pH 7.2], and 10% DMSO, and stored at -135°C until further use.  Stored cells were thawed in Complete PneumaCult Ex Plus medium in a T75 culture flask and expanded until log phase was reached, replacing the medium every 1-2 days. The cells were harvested using trypsin as described above and seeded at a density of 8x104 cells/well on the apical side of transwell inserts with a PET membrane with pore size 0.4 μm and diameter 6.5mm (Corning, #CLS3470, New York, USA) in 100 μL PneumaCult Ex Plus medium. In addition, 650 μL culture medium was added to the basolateral compartment. After 48-72 hours, confluent monolayers were airlifted by aspirating the media from both compartments and adding 500 μL complete PneumaCult ALI medium (Stemcell Technologies, #05001) supplemented with 100 units/mL Penicillin and 0.1 mg/mL Streptomycin (Pen/Strep, Sigma, P4333-100mL), 0.48 μg/mL Hydrocortisone (Stemcell Technologies, #07926) and 4 μg/mL Heparin solution (Stemcell Technologies, #07980), to the basolateral compartment only. Medium was replaced every 2-3 days (500 μL/well for 2 days, 650 μL/well for 3 days of culture). From week 2 post airlift, the apical side of the cells was washed 1-2 times per week using 200 μL PBS (Gibco, #20012-068) to remove excess mucus. Cells were kept in a humidified incubator at 37ᵒC and 5% CO2.

extract_protocol:
120uL sample in lysis buffer was added to 50uL AMPure XP Reagent (Beckman Coulter, A63881) in a 96-well PCR plate and incubated for 20 minutes to allow RNA binding to the beads. The beads were pulled down using a DynaMag™-96 Side Skirted Magnet (Invitrogen, 12027) and washed 3x using 70% EtOH (100% EtOH (VWR, 20.816) mixed with ultrapure water). RNA was eluted by resuspending the beads in nuclease free water (Ambion, AM9937) and samples were stored at -80ᵒC until further use.
Sequence reads were trimmed to remove possible adapter sequences and filtered on low-quality bases using fastp v0.23.2. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters). To remove noise introduced by sequencing errors, the reads were filtered based on the base quality score. Reads of which more than 40% of the bases had an average phred score below Q15 or which had more than 5 unknown bases (N) were removed. If the resulting reads were shorter than 15 bp, they were removed altogether (both pairs in paired-end reads). For each sample, the trimmed reads were mapped to the human GRCh38.p13 (Homo_sapiens.GRCh38.dna.primary_assembly.fa).

treatment_protocol: Well-differentiated HNEC were used for infection between 5-7 weeks post airlifting. Three days before infection, the basal cell culture medium was replaced with complete PneumaCult ALI medium without heparin and hydrocortisone (ALI infection medium). Directly before infection, cells were washed apically using 200μL/well HBSS (Gibco, #14025092) for 10 min at 37ᵒC, and the basal medium was replaced with 500 µL infection medium/well. Sucrose-purified virus was diluted to 5x10^5 TCID50/mL in HBSS. Cells were infected in duplo with wild-type, NS1Y125A or NS1L1232/133A or mock-infected, apically using 200 μL inoculum, corresponding to 1x10^5 TCID50 per well, and incubated at 37ᵒC and 5% CO2 for 1 h, after which the inoculum was aspirated. Cells were immediately washed thrice with 200 μL HBSS. At 20 hpi, whole cell lysates were obtained by adding 90 μL MagNA pure External Lysis Buffer to each transwell, which was incubated at RT for 10 min. Samples were resuspended in 60uL HBSS and stored at -80ᵒC until further analysis.

tag: cell type

value: Primary nasal epithelial cells

value: RSV-X NS1Y125A (Y125A point mutation in the NS1 protein)


title: Donor 3, NS-Y, rep1

description: Library name: 106062-001-021


title: Donor 3, NS-LL, rep2

description: Library name: 106062-001-024

value: RSV-X NS1L132A/L133A (L132A/L133A point mutations in the NS1 protein)


title: Donor 3, NS-LL, rep1

description: Library name: 106062-001-023


title: Hvolc, lib553, pH4_42C, Bisulfite, SSIII, rep1

description: Library name: Sample 69

value: WT


title: Hvolc, lib553, pH2p4_50C, Bisulfite, SSIII, rep2

description: Library name: Sample 68


title: Healthy control rep2

description:
DNA from healthy control 38
CNT.38._s1


title: Hvolc, lib553, pH2p4_42C, Bisulfite, SSIII, rep2

description: Library name: Sample 66


title: Hvolc, lib553, pH2p4_50C, Mock, SSIII, rep2

description: Library name: Sample 78


title: Donor 3, mock, rep 2

description: Library name: 106062-001-018

value: Mock


title: Hvolc, lib553, pH2p4_42C, Bisulfite, SSIII, rep1

description: Library name: Sample 65

value: Bacterial culture


title: Donor 3, wt, rep 1

description: Library name: 106062-001-019

value: Wild type


title: Donor 3, mock, rep 1

description: Library name: 106062-001-017


title: Hvolc, lib553, pH2p4_50C, Bisulfite, SSIII, rep1

description: Library name: Sample 67


title: Donor 3, wt, rep 2

description: Library name: 106062-001-020


title: Hvolc, lib553, pH2p4_30C, Bisulfite, SSIII, rep2

description: Library name: Sample 64


title: Donor 2, NS-LL, rep1

description: Library name: 106062-001-015


title: Hvolc, lib553, pH2p4_30C, Bisulfite, SSIII, rep1

description: Library name: Sample 63


title: Donor 2, NS-Y, rep2

description: Library name: 106062-001-014


title: Hvolc, lib553, pH1p4_42C, Bisulfite, SSIII, rep2

description: Library name: Sample 62


title: Donor 2, NS-Y, rep1

description: Library name: 106062-001-013


title: Hvolc, lib553, pH1p4_42C, Bisulfite, SSIII, rep1

description: Library name: Sample 61


title: Hvolc, lib553, pH4_42C, Bisulfite, SSIII, rep2

description: Library name: Sample 70


title: Donor 2, NS-LL, rep2

description: Library name: 106062-001-016


title: Donor 2, wt, rep 2

description: Library name: 106062-001-012


title: Donor 2, wt, rep 1

description: Library name: 106062-001-011


title: Hvolc, lib553, pH4_42C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 59


title: Donor 2, mock, rep 2

description: Library name: 106062-001-010


title: Hvolc, lib553, pH4_42C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 60


title: Hvolc, lib553, pH2p4_50C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 58


title: Hvolc, lib553, pH2p4_42C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 56


title: Hvolc, lib553, pH2p4_50C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 57


title: Donor 2, mock, rep 1

description: Library name: 106062-001-009


title: Hvolc, lib553, pH2p4_30C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 54


title: Donor 1, NS-LL, rep1

description: Library name: 106062-001-007


title: Hvolc, lib553, pH1p4_42C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 52


title: Donor 1, NS-LL, rep2

description: Library name: 106062-001-008


title: Donor 1, NS-Y, rep1

description: Library name: 106062-001-005


title: Donor 1, wt, rep 2

description: Library name: 106062-001-004


title: Donor 1, mock, rep 2

description: Library name: 106062-001-002


title: Hvolc, lib553, pH1p4_42C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 51


title: Hvolc, lib553, pH2p4_42C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 55


title: Hvolc, lib553, pH2p4_30C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 53


title: Hvolc, lib553, pH4_42C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 50


title: Donor 1, NS-Y, rep2

description: Library name: 106062-001-006


title: Donor 1, wt, rep 1

description: Library name: 106062-001-003


title: Donor 1, mock, rep 1

description: Library name: 106062-001-001


title: Hvolc, lib553, pH4_42C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 49


title: Hvolc, lib553, pH2p4_50C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 48


title: NXG2_NL, NXG patient 2 non-lesional skin

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

country: Germany

institute: University of Cologne

description: Library name: Sample 7

data_processing:
we used our in‐house pipeline of CCG for RNA‐Seq analysis which is based on the nextflow DSL (version 20.01.0 build 5264)
We performed adaptertrimming of the fastq files with the help of trimmomatic (v0.38) and removed sequences of <18 nt in length. Using the default setting of the STAR aligner (v2.6.1a), we mapped these files against the hg38 human reference genome and the gene assembly v101. For the DEGs analysis, we used DeSeq2 (v1.20.0) with a Padj. cutoff value of 0.05.
Assembly: GRCh38
Supplementary files format and content: Excel file containing raw counts and FPKM values

source_name: Skin

growth_protocol: We generated primary fibroblasts from skin biopsies from the patients and control individual. Cells were grown with DMEM Medium supplemented with fetal bovine serum, L-glutamine and antibiotics (Penicillin/Streptomycin)

extract_protocol:
RNA from homogenized tissue was isolated using the RNeasy Fibrous Tissue Kit (Qiagen, 74704) according to the manufacturer´s protocol
We prepared RNA-seq libraries using the Illumina® Stranded mRNA Sample Preparation Kit with 500 ng of total RNA input per sample

treatment_protocol: No treatment

value: Skin

tag: cell line

value: Fibroblasts

value: Primary fibroblasts

value: Patient

value: No treatment


title: NXG2_L, NXG patient 2 lesional skin

description: Library name: Sample 6


title: NXG1_pTx, NXG patient 1 lesional skin post treatment

description: Library name: Sample 5


title: NXG1_NL, NXG patient 1 non-lesional skin

description: Library name: Sample 4


title: Hvolc, lib553, pH2p4_50C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 47


title: Hvolc, lib553, pH2p4_42C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 46


title: NXG1_L, NXG patient 1 lesional skin

description: Library name: Sample 3


title: HS_2, Healthy skin control 2

description: Library name: Sample 2


title: HS_1, Healthy skin control 1

description: Library name: Sample 1


title: Hvolc, lib553, pH2p4_30C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 43


title: iPSC-derived cerebral organoids, WT, day 79

city: Zurich

first: Ruxandra

last: Bachmann-Gagescu

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Library name: D141122_WT_D79

library_source: transcriptomic single cell

data_processing:
Data processing was performed using Cell Ranger v.7.1.0
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited files with cell barcodes and features. Matrix files with raw counts.

source_name: hiPSC-derived cerbral organoid

growth_protocol: Cerebral organoid differentiation protocol adapted from Lancaster et al 2018.

extract_protocol:
Three whole cerebal organoids were pooled washed three times in HBSS per sample. Dissociation was performed using the gentleMACS™ Dissociator with the Neural Tissue Dissociation Kit in C tubes. The enzyme mix was stopped by adding 5 mL of HBSS + 5% FBS after dissociation and in between rotation steps. Cell suspension was passed through a 40 μM cell strainer and FACS tube strainer. Lastly, ultra-slow centrifugation at 90 g for 10 min was performed.
Library was constructed according to the 10X Genomics protocol.

value: hiPSC-derived cerbral organoid

value: ISFi001-A cl.5

value: hiPSC

tag: time

value: Day 79 of differentiation

value: Control


title: iPSC-derived cerebral organoids, WT, day 72

description: Library name: D211122_WT_D72

value: Day 72 of differentiation


title: Hvolc, lib553, pH1p4_42C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 41


title: Hvolc, lib553, pH2p4_50C, CMC, SSIII, rep1

description: Library name: Sample 37


title: Hvolc, lib553, pH2p4_42C, CMC, SSIII, rep2

description: Library name: Sample 36


title: Hvolc, lib553, pH4_42C, CMC, SSIII, rep2

description: Library name: Sample 40


title: SUP-B15 leukemia cells, ATAC Rep3

city: Morgantown

first: Halima Akhter

last: Akhter

state: West Virginia

address: 1 Medical Center Dr, Morgantown, WV 26506

department: Immunology, and Cell Biology

institute: West Virginia University

description:
Library name: SUPB15_Parental_ATAC_3
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq

library_source: genomic single cell

data_processing:
Raw FASTQ data processed via Cell Ranger ARC pipeline (version 2.0.1) generating count matrices and fragment files.
Gene expression matrices extracted via Seurat (v5.1.0), normalized with log2 CPM, retaining genes detected in ≥200 cells.
Assembly: hg38
Supplementary files format and content: Cell Ranger ARC outputs: reh_barcodes.tsv.gz, reh_features.tsv.gz, reh_matrix.mtx.gz, reh_atac_fragments.tsv.gz, reh_atac_peaks.bed
Supplementary files format and content: Cell Ranger ARC outputs: sup_barcodes.tsv.gz, sup_features.tsv.gz, sup_matrix.mtx.gz, sup_atac_fragments.tsv.gz, sup_atac_peaks.bed

growth_protocol: REH (ATCC #CRL-8286) and SUP-B15 (ATCC #CRL-1929) cultured as previously described (Rellick et al., 2021; Sci Rep 2021;11:15840).

extract_protocol:
We followed 10X Nuclei Isolation protocol for Single Cell Multiome ATAC + Gene Expression Sequencing protocol (CG000365)
Single-cell multiome libraries were prepared per manufacturer's instructions (10X Genomics, 1000283; CG000338 Rev E)

value: B-cell leukemia

tag: library type

value: scATAC


title: SUP-B15 leukemia cells, ATAC Rep2

description:
Library name: SUPB15_Parental_ATAC_2
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq


title: Hvolc, lib553, pH2p4_42C, CMC, SSIII, rep1

description: Library name: Sample 35

value: WT


title: SUP-B15 leukemia cells, ATAC Rep1

description:
Library name: SUPB15_Parental_ATAC_1
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq


title: Hvolc, lib553, pH2p4_30C, CMC, SSIII, rep2

description: Library name: Sample 34


title: Hvolc, lib553, pH2p4_30C, CMC, SSIII, rep1

description: Library name: Sample 33


title: SUP-B15 leukemia cells, GEX

description:
Library name: SUPB15_Parental_GEX
GEX (3' mRNA): R1 contains cell barcode & UMI; R2 contains RNA transcript sequence

value: scRNA


title: Hvolc, lib553, pH2p4_42C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 45

value: Bacterial culture


title: Hvolc, lib553, pH1p4_42C, CMC, SSIII, rep2

description: Library name: Sample 32


title: REH leukemia cells, ATAC Rep4

description:
Library name: REH_Parental_ATAC_4
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq

source_name: REH

value: REH


title: Hvolc, lib553, pH1p4_42C, CMC, SSIII, rep1

description: Library name: Sample 31


title: REH leukemia cells, ATAC Rep3

description:
Library name: REH_Parental_ATAC_3
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq


title: Hvolc, lib553, pH2p4_30C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 44


title: Hvolc, lib553, pH1p4_42C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 42


title: Hvolc, lib553, pH4_42C, NaCNBH3, SSIII, rep2

description: Library name: Sample 30


title: Hvolc, lib553, pH4_42C, NaCNBH3, SSIII, rep1

description: Library name: Sample 29


title: REH leukemia cells, ATAC Rep1

description:
Library name: REH_Parental_ATAC_1
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq


title: SUP-B15 leukemia cells, ATAC Rep4

description:
Library name: SUPB15_Parental_ATAC_4
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq


title: Hvolc, lib553, pH2p4_50C, NaCNBH3, SSIII, rep2

description: Library name: Sample 28


title: iPSC-derived cerebral organoids, CEP290 CRISPR gene edited, clone 2, day 79

description: Library name: D141122_34_D79

value: CEP290 CRISPR-gene editing


title: REH leukemia cells, GEX

description:
Library name: REH_Parental_GEX
GEX (3' mRNA): R1 contains cell barcode & UMI; R2 contains RNA transcript sequence


title: Thy1-KO, TCP substrate, 72hr culture, rep2

city: Charlottesville

first: Andrew

last: Miller

state: Virginia

address: 415 Lane Rd.

department: Biomedical Engineering

institute: University of Virginia

description: Library name: T-T-72_2

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequences and QC metrics assessed using TrimGalore! And FastQC packages, respectively. Reads with Phred quality scores < 20 were excluded from downstream analysis.
Trimmed reads that passed QC were aligned to the GRCh38/hg38 genome using Bowtie2. Paired-end alignments with a maximum fragment length of <500bp were passed forward. Default parameters were used for all remaining alignment options.
Peaks were called on aligned data using MACS2 with significance cut-off q-value <= 0.05.
To generate ATAC-seq coverage plots, regions stratifying 100bp upstram and downstream of peak summits identified using MACS2 were generated for all samples. Biological replicates were merged into a singular bam file using samtools. The resulting bam file(s) was then converted to bigWig file format using the bedtools and kent-tools packages.
Assembly: hg38
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of each condition.

source_name: immortalized human lung fibroblasts

growth_protocol: WT and Thy-1 KO immortalized human lung fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1mM sodium pyruvate, and antibiotics at 37C and 5% CO2.

extract_protocol:
Cells were trypsinized, collected in a 1.5mL DNA Lobind (Eppendorf) tube, and washed with ice cold ATAC-seq resuspension buffer (ATAC-RSB). After washing cells were lysed with ATAC-RSB containing .005% digitonin, .05% NP-40, and .05% Tween-20. Transposition was performed using TDE1 Tn5 tranposase (Nextera) in TD buffer (Nextera) for 45 minutes on a thermoshaker set to 37C with 1000 RPM mixing. The resulting DNA products were purified using a Qiagen MinElute purification kit.
Samples were double-barcoded using Nextera i7 and i5 indexes (Illumina), amplified on a thermocycler, size selected to exclude fragments >600 bp using the SPRIselect system (Beckman-Coulter) and pooled to a final concentration of 20nM. Proper fragment size distribution was validated prior to sequencing via TapeStation (Agilent) as preliminary quality control (QC) to confirm DNA fragment sizes followed the anticipated pattern of nucleosomal periodicity.

treatment_protocol: WT and Thy-1 KO fibroblasts were seeded on 4kPa polyacrylamide hydrogels (Matrigen), 25kPa polyacrylamide hydrogels (Matrigen), or tissue culture plastic (TCP) pre-coated with 10μg/mL full length human fibronectin.

value: immortalized human lung fibroblasts

value: fibroblast

value: TCP substrate


title: Thy1-KO, TCP substrate, 72hr culture, rep1

description: Library name: T-T-72_1


title: Hvolc, lib553, pH2p4_30C, NaCNBH3, SSIII, rep2

description: Library name: Sample 24


title: Hvolc, lib553, pH2p4_50C, CMC, SSIII, rep2

description: Library name: Sample 38


title: Thy1-KO, TCP substrate, 72hr culture, rep4

description: Library name: T-T-72_4


title: Hvolc, lib553, pH2p4_30C, NaCNBH3, SSIII, rep1

description: Library name: Sample 23


title: Hvolc, lib553, pH2p4_42C, NaCNBH3, SSIII, rep1

description: Library name: Sample 25


title: Hvolc, lib553, pH2p4_50C, NaCNBH3, SSIII, rep1

description: Library name: Sample 27


title: Thy1-KO, TCP substrate, 24hr culture, rep3

description: Library name: T-T-24_3


title: Thy1-KO, TCP substrate, 24hr culture, rep4

description: Library name: T-T-24_4


title: Hvolc, lib553, pH2p4_42C, NaCNBH3, SSIII, rep2

description: Library name: Sample 26


title: Thy1-KO, TCP substrate, 24hr culture, rep2

description: Library name: T-T-24_2


title: Thy1-KO, TCP substrate, 24hr culture, rep1

description: Library name: T-T-24_1


title: Hvolc, lib553, pH1p4_42C, NaCNBH3, SSIII, rep1

description: Library name: Sample 21


title: Hvolc, lib553, pH4_42C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 20


title: Thy1-KO, 25kPa substrate, 72hr culture, rep4

description: Library name: T-25-72_4

value: 25kPa substrate


title: Hvolc, lib553, pH4_42C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 19


title: Thy1-KO, TCP substrate, 72hr culture, rep3

description: Library name: T-T-72_3


title: Hvolc, lib553, pH1p4_42C, NaCNBH3, SSIII, rep2

description: Library name: Sample 22


title: Thy1-KO, 25kPa substrate, 72hr culture, rep3

description: Library name: T-25-72_3


title: Hvolc, lib553, pH2p4_50C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 18


title: Thy1-KO, 25kPa substrate, 72hr culture, rep2

description: Library name: T-25-72_2


title: Hvolc, lib553, pH2p4_50C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 17


title: Thy1-KO, 25kPa substrate, 72hr culture, rep1

description: Library name: T-25-72_1


title: Hvolc, lib553, pH2p4_42C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 16


title: Thy1-KO, 25kPa substrate, 24hr culture, rep4

description: Library name: T-25-24_4


title: Hvolc, lib553, pH2p4_42C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 15


title: Thy1-KO, 25kPa substrate, 24hr culture, rep3

description: Library name: T-25-24_3


title: Hvolc, lib553, pH2p4_30C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 14


title: Thy1-KO, 25kPa substrate, 24hr culture, rep1

description: Library name: T-25-24_1


title: Hvolc, lib553, pH2p4_30C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 13


title: Hvolc, lib553, pH1p4_42C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 12


title: Hvolc, lib553, pH1p4_42C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 11


title: Thy1-KO, 4kPa substrate, 72hr culture, rep4

description: Library name: T-4-72_4

value: 4kPa substrate


title: Thy1-KO, 4kPa substrate, 72hr culture, rep3

description: Library name: T-4-72_3


title: Hvolc, lib553, pH4_42C, Mock, RTHIV, rep2

description: Library name: Sample 10


title: Thy1-KO, 4kPa substrate, 72hr culture, rep2

description: Library name: T-4-72_2


title: Hvolc, lib553, pH4_42C, Mock, RTHIV, rep1

description: Library name: Sample 9


title: Hvolc, lib553, pH2p4_50C, Mock, RTHIV, rep2

description: Library name: Sample 8


title: Thy1-KO, 4kPa substrate, 24hr culture, rep3

description: Library name: T-4-24_3


title: Thy1-KO, 4kPa substrate, 24hr culture, rep2

description: Library name: T-4-24_2


title: Hvolc, lib553, pH2p4_50C, Mock, RTHIV, rep1

description: Library name: Sample 7


title: Thy1-KO, 4kPa substrate, 24hr culture, rep4

description: Library name: T-4-24_4


title: Hvolc, lib553, pH2p4_42C, Mock, RTHIV, rep2

description: Library name: Sample 6


title: Hvolc, lib553, pH2p4_42C, Mock, RTHIV, rep1

description: Library name: Sample 5


title: Thy1-KO, 4kPa substrate, 24hr culture, rep1

description: Library name: T-4-24_1


title: Hvolc, lib553, pH2p4_30C, Mock, RTHIV, rep2

description: Library name: Sample 4


title: Hvolc, lib553, pH2p4_30C, Mock, RTHIV, rep1

description: Library name: Sample 3


title: Hvolc, lib553, pH1p4_42C, Mock, RTHIV, rep2

description: Library name: Sample 2


title: Thy1-KO, Suspension/0hr, rep4

description: Library name: T-0_4

value: Suspension


title: Thy1-KO, Suspension/0hr, rep3

description: Library name: T-0_3


title: Thy1-KO, Suspension/0hr, rep2

description: Library name: T-0_2


title: Thy1-KO, 25kPa substrate, 24hr culture, rep2

description: Library name: T-25-24_2


title: Hvolc, lib553, pH1p4_42C, Mock, RTHIV, rep1

description: Library name: Sample 1


title: WT, TCP substrate, 72hr culture, rep4

description: Library name: W-T-72_4


title: Thy1-KO, Suspension/0hr, rep1

description: Library name: T-0_1


title: WT, TCP substrate, 72hr culture, rep3

description: Library name: W-T-72_3


title: SITW034C_3

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: Library name: L115

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Assembly: Read quantitation using custom scripts
Supplementary files format and content: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpcount text files contain three columns:  1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts. Fpframing text files contain nine columns:  1. the length of ribosome footprint; 2. the fraction of ribosome footprint; 3~5. the number of ribosome footprint at each frames;  6~8,the fraction of ribosome footprint at each frames; 9. the relative entropy of ribosome footprint.
Library strategy: MitoIP-Thor-Ribo-Seq

extract_protocol:
MitoIP-Thor-Ribo-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. RNA-Seq: Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
MitoIP-Thor-Ribo-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input (TaKaRa).

tag: condition

value: naïve


title: WT, TCP substrate, 72hr culture, rep2

description: Library name: W-T-72_2


title: Tkoda, lib745, WT, Bisulfite.Treat, WT3

description: Library name: Sample 6

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_000009965.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Thermococcus kodakarensis

growth_protocol: T.  kodakarensis cells were grown anaerobically at 85°C in artificial sea-water with yeast, tryptone, pyruvate (ASW-YTP) and supplemented with sulfur and agmatine. Cultures were grown to mid exponential growth phase (OD600  ~0.4-0.5) and harvested by centrifugation at 12,000 x g.

extract_protocol:
T. kodakarensis cell pellets were resuspended in 1000µl TRI reagent (Sigma aldrich), RNA extraction was carried out from 500µl. 200 µl of chloroform was added to the pellets in the TRI-reagent, followed by vigorous invert mixing and allowing the tube to rest at RT for 5 mins to allow the phases to separate. The supernatant was transferred to a new eppendorf tube. To the supernatant, an equal volume of 95-100% ethanol  was added and mixed gently at least a few times with micropipette tips. This mixture was then introduced into Zymo spin columns from RNA Clean & Concentrator kit-5 (Zymo Research) and subsequent steps were conducted as per the manufacturer’s instructions.
In vitro methylation of 2ug of total RNA isolated from TkNat10 wt and ΔTkNat10 was conducted at at 85°C  for 30mins in buffer containing 50mM Tris-HCL(pH=7), 300mM NaCl, 5mM MgCl2, 1mM SAM , 10ug of purified Pfu RsmB in a total reaction volume of 50ul. RNA post in vitro methylation treatment was purified employing Zymo RNA clean and concentrator kit-5 (Zymo Research) as per manufacturer’s instructions. Library preparation was carried out without the fragmentation step and subjected to bisulfite and Mock treatments. Bisulfite-treatment – Bisulfite conversion was carried out using the EZ RNA methylation kit (Zymo research, R5001), according to the manufacturer’s instructions, except for the conversion step that was carried out by more stringent conditions (3 cycles of (1) 70 °C, 10 min. (2) 64 °C, 45 min), and the desulphonation step that was carried out in higher temperature (37 °C, 30 min).

value: KOD1 substrain TS559


title: Tkoda, lib745, WT, Bisulfite.Treat, WT2

description: Library name: Sample 5


title: Thy1-KO, 4kPa substrate, 72hr culture, rep1

description: Library name: T-4-72_1


title: Hvolc, lib553, pH4_42C, CMC, SSIII, rep1

description: Library name: Sample 39


title: SITW034C_4

description: Library name: L116


title: WT, TCP substrate, 24hr culture, rep3

description: Library name: W-T-24_3


title: WT, TCP substrate, 24hr culture, rep4

description: Library name: W-T-24_4


title: WT, TCP substrate, 24hr culture, rep2

description: Library name: W-T-24_2


title: SITW034C_1

description: Library name: L113


title: SITW034C_2

description: Library name: L114


title: WT, TCP substrate, 24hr culture, rep1

description: Library name: W-T-24_1


title: Tkoda, lib745, KO, Bisulfite.Treat, KO2

description: Library name: Sample 2

value: KO


title: Tkoda, lib745, WT, Bisulfite.Treat, WT1

description: Library name: Sample 4


title: WT, 25kPa substrate, 72hr culture, rep3

description: Library name: W-25-72_3


title: Tkoda, lib745, KO, Bisulfite.Treat, KO1

description: Library name: Sample 1


title: SITW017_4

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpcount text files contain three columns:  1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts. Fpframing text files contain nine columns:  1. the length of mitoribosome footprint; 2. the fraction of mitoribosome footprint; 3~5. the number of mitoribosome footprint at each frames;  6~8,the fraction of mitoribosome footprint at each frames; 9. the relative entropy of mitoribosome footprint.
Library strategy: MitoIP-Thor-Ribo-Seq

extract_protocol:
MitoIP-Ribo-Seq, MitoIP-Thor-Ribo-Seq, and MitoIP-Thor-Disome-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. For the mitoribosome run-off assay, HEK293 cells were pre-treated with 100 µg/ml retapamulin for 30, 60, 90, 120 s, or 30 min and then incubated with 100 µg/ml chloramphenicol and 100 µg/ml cycloheximide to arrest translation elongation. Subsequently, cell lysis and mitochondrial purification were performed as described above, adding 100 µg/ml retapamulin to all the solutions. For the mouse cardiac muscle, the frozen tissues were pulverized with 600 µl of liquid nitrogen-frozen hypotonic buffer using the Multi-beads Shocker at 3000 rpm for 30 sec for 2 cycles (Yasui Kikai). The lysate was clarified by an EASYstrainer (Greiner Bio-One), and mitochondria isolation was conducted as described above. Ribo-Seq and RNA-Seq: Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
Ribo-seq and MitoIP-Ribo-Seq: RNase treatment, ribosome pelleting, Ribo-FilterOut, size selection, preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, and PCR amplification. MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

value: naive


title: SITW017_3


title: WT, 25kPa substrate, 72hr culture, rep2

description: Library name: W-25-72_2


title: WT, 25kPa substrate, 72hr culture, rep1

description: Library name: W-25-72_1


title: WT, TCP substrate, 72hr culture, rep1

description: Library name: W-T-72_1


title: WT, 25kPa substrate, 24hr culture, rep3

description: Library name: W-25-24_3


title: WT, 25kPa substrate, 72hr culture, rep4

description: Library name: W-25-72_4


title: WT, 25kPa substrate, 24hr culture, rep4

description: Library name: W-25-24_4


title: WT, 25kPa substrate, 24hr culture, rep1

description: Library name: W-25-24_1


title: SITW017_1


title: Tkoda, lib747, Tko35.95deg, Treat, _a_

description: Library name: Sample 34

growth_protocol: T.  kodakarensis cells were grown anaerobically at 65°, 75°, 85°, or 95°C in artificial sea-water with yeast, tryptone, pyruvate (ASW-YTP) and supplemented with sulfur and agmatine. Tko105 mutant strain and Tko35 mutant strain cells were grown at 75°C and 95°C. Cultures were grown to mid exponential growth phase (OD600  ~0.4-0.5) and harvested by centrifugation at 12,000 x g.

extract_protocol:
T. kodakarensis cell pellets were resuspended in 1000µl TRI reagent (Sigma aldrich), RNA extraction was carried out from 500µl. 200 µl of chloroform was added to the pellets in the TRI-reagent, followed by vigorous invert mixing and allowing the tube to rest at RT for 5 mins to allow the phases to separate. The supernatant was transferred to a new eppendorf tube. To the supernatant, an equal volume of 95-100% ethanol  was added and mixed gently at least a few times with micropipette tips. This mixture was then introduced into Zymo spin columns from RNA Clean & Concentrator kit-5 (Zymo Research) and subsequent steps were conducted as per the manufacturer’s instructions.
200 ng per sample were used as the starting amounts for the BID-seq library. RNA fragmentation was conducted using Zinc RNA Fragmentation kit (Invitrogen), according to the manufacturer’s protocol, followed by a cleanup with Dynabeads MyOne Silane (Invitrogen). Each sample was subjected to DNase and dephosphorylation treatment by incubation with T4 PNK (NEB T4 Polynucleotide Kinase), TURBO DNase (Invitrogen), and FastAP (Thermo Scientific Thermosensitive Alkaline Phosphatase) for 30 minutes at 37°C. The incubation was carried out in a 1: 1: 2 ratio of T4 PNK buffer, FastAP buffer, and H2O, followed by a cleanup using silane beads. Next, the samples were adapter ligated employing 30 pmoles of a general barcoded RNA adapter (Supplementary Table S4). Ligations were conducted using 36 U of T4 RNA ligase 1 (High Concentration, NEB) for 1.5 hours at room temperature (23°C) for each sample. After the 3′ ligation of barcoded RNA adapters, the samples were pooled in groups of eight and cleaned using silane beads. RNA from each pool was eluted in 11 µl of nuclease free water. BID-seq treatment was adapted from Qing Dai et al. (2022) with minor modifications. An aliquot of 2.5 µl from each pool was reserved for 'Input' library construction, while 7.5 µl was designated as the 'Treated' sample for BID-seq bisulfite treatment. This 7.5 µl of RNA was combined with 45 µl of freshly prepared BID-seq BS reagent (consisting of 2.4 M Na2SO3 and 0.36 M NaHSO3, made by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl of RNase-free water) and incubated at 70 °C for 3 hours. Following incubation, 75 µl of RNase-free H2O, 270 µl of RNA binding buffer (RNA Clean and Concentrator), and 400 µl of ethanol were added to the reaction mixture, which was then thoroughly mixed and loaded onto an RNA Clean and Concentrator-5 column. After centrifugation, the column was washed with 200 µl of RNA wash buffer (RNA Clean and Concentrator). Next, 200 µl of RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 hour. Finally, the column was spun and washed twice with 700 µl of RNA wash buffer, and RNA was eluted with 11.5 µl of RNase-free water. The reserved 'Input' sample was diluted to 11.5 µl with RNase-free water. Reverse transcription and post treatment steps: Both ‘Input’ and ‘Treated’ samples were mixed with 1µl of 10µM RT primer (5′- AGACGTGTGCTCTTCCG -3′) , incubated at 65 °C for 2 min and moved immediately onto ice. To this we added 4 µl 5× SSIV Buffer, 1 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl murine RNase Inhibitor (NEB) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 hour.


title: Tkoda, lib745, KO, Bisulfite.Treat, KO3

description: Library name: Sample 3


title: SITW017_2


title: WT, 4kPa substrate, 72hr culture, rep3

description: Library name: W-4-72_3


title: WT, 4kPa substrate, 72hr culture, rep1

description: Library name: W-4-72_1


title: Pabys, lib524, 80deg, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 107

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_036323395.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Pyrodictium abyssi

growth_protocol: Cultivated anaerobically in ½ SME medium. The medium contained 0.1 % (w/v) thiosulfate and 0.05 % (w/v) yeast extract (YE), the pH value was set to 5.5 to 6.0 and the gas phase consisted of H2/CO2 (300 kPa; 80:20, v/v). For RNA preparation cells were grown in duplicates at 80 °C, 100 °C and 102 °C to the late exponential growth phase and harvested by centrifugation at 10,000 x g

extract_protocol:
Cell pellets were washed with 1x PBS and centrifuged again at 2500 rpm for 3 minutes. The pellet was then resuspended in 1000 µl TRI Reagent, incubated at room temperature for 10 minutes, followed by centrifugation at 16,000 x g for 2 minutes
Remaining primers left in the reaction were digested by addition of 3 μL ExoSAP-IT (Applied Biosystems, 78205) to the 20 μL reverse transcription reaction, and incubation at 37°C for 12 min. RNA was degraded by adding 2.5 μL of NaOH 1M and 1 μL of 0.5M EDTA, and incubation at 70°C for 12 min. The base was neutralized with the addition of 1M HCl, cDNA was cleaned using MyOne silane beads. An adapter was added to the 3’ end of the cDNA by ligating 50 pmoles 5iLL-22 DNA adapter using T4 RNA Ligase 1, High concentration (NEB, M0437M), DMSO 4%, ATP 1mM and PEG8000 25% at 23°C for 3 h. After clean-up with MyOne silane beads, we amplified the cDNA library for 12 cycles using Illumina Library PCR primers F and R and KAPA HiFi HotStart ReadyMix (Roche, KK2601). Amplified libraries were cleaned with Kapa pure beads (Roche, KK8002), quantified using Qubit (Life Technologies) and the distribution of library size was determined using TapeStation (Agilent Technologies).


title: Pabys, lib524, 80deg, Bisulfite+MgCl2+Heat, TGIRT, rep2

description: Library name: Sample 108


title: WT, 4kPa substrate, 24hr culture, rep4

description: Library name: W-4-24_4


title: Pabys, lib524, 102deg, Bisulfite+MgCl2+Heat, TGIRT, rep2

description: Library name: Sample 106


title: WT, 4kPa substrate, 24hr culture, rep3

description: Library name: W-4-24_3


title: Tkoda, lib747, Tko35.75deg, Treat, _a_

description: Library name: Sample 31


title: Tkoda, lib747, Tko35.95deg, Treat, _c_

description: Library name: Sample 36


title: WT, 4kPa substrate, 72hr culture, rep4

description: Library name: W-4-72_4


title: Tkoda, lib747, Tko35.75deg, Treat, _c_

description: Library name: Sample 33


title: Tkoda, lib747, Tko35.75deg, Treat, _b_

description: Library name: Sample 32


title: Tkoda, lib747, wt.95deg, Treat, _c_

description: Library name: Sample 30


title: WT, 25kPa substrate, 24hr culture, rep2

description: Library name: W-25-24_2


title: WT, 4kPa substrate, 24hr culture, rep2

description: Library name: W-4-24_2


title: WT, Suspension/0hr, rep4

description: Library name: W-0_4


title: Tkoda, lib747, Tko35.95deg, Treat, _b_

description: Library name: Sample 35


title: Pabys, lib524, 100deg, Bisulfite+MgCl2+Heat, TGIRT, rep2

description: Library name: Sample 104


title: Tkoda, lib747, wt.95deg, Input, _c_

description: Library name: Sample 29


title: WT, Suspension/0hr, rep2

description: Library name: W-0_2


title: WT, Suspension/0hr, rep1

description: Library name: W-0_1


title: Tkoda, lib747, wt.95deg, Treat, _b_

description: Library name: Sample 28


title: WT, 4kPa substrate, 72hr culture, rep2

description: Library name: W-4-72_2


title: Thy1-KO, TCP substrate, 72hr culture, rep4

description: Library name: T-T-72_4

data_processing:
Sequence reads were trimmed for adaptor sequences and QC metrics assessed using TrimGalore! And FastQC packages, respectively. Reads with Phred quality scores < 20 were excluded from downstream analysis.
Reads were aligned to the GRCh38/hg38 genome assembly using HISAT2 with default parameters.
Tables of raw RNA counts for each gene within each sample were quantified using the Stringtie and Ballgown packages.
Assembly: hg38
Supplementary files format and content: Table of raw counts for each gene within each sample in CSV file format.
Supplementary files format and content: Table of DESeq2-normalized counts for each sample in CSV file format.

extract_protocol:
Cells were lysed using TriZol (Thermo Fischer) and RNA isolated with Qiagen's RNeasy Micro Prep kit. RNA isolates with masses >= 0.5μg and RNA integrity number (RIN) scores >= 9.0 were used to create sequencing libraries.
RNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.


title: Pabys, lib524, 80deg, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 102


title: Thy1-KO, TCP substrate, 72hr culture, rep3

description: Library name: T-T-72_3


title: Tkoda, lib747, wt.95deg, Input, _b_

description: Library name: Sample 27


title: Thy1-KO, TCP substrate, 72hr culture, rep2

description: Library name: T-T-72_2


title: Pabys, lib524, 80deg, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 101


title: Thy1-KO, TCP substrate, 72hr culture, rep1

description: Library name: T-T-72_1


title: Pabys, lib524, 102deg, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 105


title: Tkoda, lib747, wt.95deg, Treat, _a_

description: Library name: Sample 26


title: Pabys, lib524, 102deg, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 100


title: WT, 4kPa substrate, 24hr culture, rep1

description: Library name: W-4-24_1


title: Thy1-KO, TCP substrate, 24hr culture, rep3

description: Library name: T-T-24_3


title: Tkoda, lib747, wt.95deg, Input, _a_

description: Library name: Sample 25


title: nkx25, 14-somite stage, slide2

type: RNA

city: Boston

first: Yunxia

last: Wang

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Panel of 133 genes was measured by MERFISH

scan_protocol: MERFISH was performed using the commercialized MERSCOPE platform (Vizgen, MA, US) according to the manufacturer’s instructions for formalin-fixed paraffin-embedded (FFPE) tissues. Briefly, autofluorescence was quenched from sections with MERSCOPE Photobleacher for three hours. Quenched sections were stained with anti-ß-catenin and anti-ZsYellow antibodies using the Vizgen Staining Kit and counterstained with DAPI. After 48 hours of probe incubation at 37℃, the sections were covered with glass plate coating gel for tissue clearing following the manufacturer’s guidelines for non-resistant samples. Imaging was performed on the MERSCOPE Platform using a 140-gene imaging kit.

data_processing: Two slides containing 10 sections each were processed using the MERSCOPE™ Image Processing Software, which generated a list of all detected transcripts (CSV format), raw images (TIFF format), and image metadata (CSV format) for four staining channels, including DAPI, Poly T, anti-ß-catenin, and anti-ZsYellow.  Cell segmentation was performed as follows: DAPI was used to identify cell nuclei, ß-catenin to delineate cell boundaries and shapes, and ZsYellow to identify the nkx2.5 lineage in the ALPM. Based on the raw images and metadata from these three staining channels, cell boundaries were defined using the Cellpose algorithm (version 1.0.2) within the Vizgen Post-processing Tool vpt (version 1.3.0). Next, these defined boundaries were used to group transcripts into cells using vpt. Subsequently, cell metadata, including location, size, and shape, were calculated, and cell signals, such as the brightness of each mosaic TIFF image within each cell, were summarized. Finally, we used vpt to adjust the cell boundaries in the Vizgen MERSCOPE™ Visualizer. After cell segmentation, we obtained a list of files including the cells-by-genes file (CSV format), cell metadata file (CSV format), and sum signal file (CSV format). ZsYellow+ cells were selected through UMAP clustering based on these files by some steps. Next, cell types were annotated using marker genes with the Python package Decoupler (version 1.6.0).  Single-cell RNA-seq data provided cell type-specific markers. To assign cell type labels to single-cell clusters, we identified communities of cells with similar transcriptional profiles and checked for the expression of cell type-specific markers. Functional enrichment scores, measuring the overrepresentation of gene sets at the top or bottom of a ranked list, were inferred using the Over Representation Analysis (ORA) method within Decoupler. The built-in function rank_sources_groups in Decoupler were used to identify the top predicted cell types per cluster. This process enabled the annotation of single-cell clusters with specific cell types.

organism: Danio rerio

source_name: 14-ss Tg(nkx2.5:ZsYellow) embryos

extract_protocol: For the 133 probe panel, we selected the top 7-15 most specifically expressed genes identified for each cell cluster in our scRNA-seq samples (n=94 genes), 35 genes from a previously published scRNA-seq of gata5:GFP+ cells from 8-ss zebrafish embryos, 4 genes cherry-picked from the literature, and ZsYellow.  Probes were designed with the Vizgen Gene Panel Portal (https://portal.vizgen.com) and manufactured by Vizgen.

treatment_protocol: 14-ss Tg(nkx2.5:ZsYellow) embryos were fixed overnight with 4% paraformaldehyde (PFA) at 4°C and rinsed the following day in PBSTw (0.1% Tween-20 in PBS). Embryos were dehydrated in a graduated PBSTw:methanol series and stored in 100% methanol at -20°C. Embryos were cleared in Butyl alcohol (1-Butanol) for 10 min and embedded in paraffin wax.  10 μm transverse embryonic sections were cut, floated in a nuclease-free water bath, mounted onto MERSCOPE Slides, and incubated for 4 hours at RT prior to storing at -20°C.

value: embryo

tag: Stage

value: nkx2.5:ZsYellow cells


title: WT, Suspension/0hr, rep3

description: Library name: W-0_3

value: WT


title: nkx25, 14-somite stage, slide1


title: Tkoda, lib747, wt.85deg, Treat, _c_

description: Library name: Sample 24


title: Thy1-KO, TCP substrate, 24hr culture, rep1

description: Library name: T-T-24_1


title: Pabys, lib524, 100deg, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 98


title: Pabys, lib524, 100deg, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 103


title: Pabys, lib524, 102deg, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 99


title: Thy1-KO, TCP substrate, 24hr culture, rep2

description: Library name: T-T-24_2


title: Tkoda, lib747, wt.85deg, Input, _c_

description: Library name: Sample 23


title: Thy1-KO, 25kPa substrate, 72hr culture, rep4

description: Library name: T-25-72_4


title: Pabys, lib524, 100deg, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 97


title: Tkoda, lib747, wt.85deg, Treat, _b_

description: Library name: Sample 22


title: activated_50_3 (11a)

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

description:
Library name: activated_50_3
activated_50_3

data_processing:
Fastq generation was done using Base2Fastq v.1.7
Sequencing reads were pre-processed and aligned to the mouse genome using the RNA-seq method of the bcbio-nextgen pipeline v. 1.2.4.
The reads were first trimmed for quality and adapter using Atropos (v. 1.1.28). Trimmed reads were aligned to the Mus musculus genome (mm10) using hisat2 (v. 2.2.1). Numbers of reads were summarized at the gene level per sample using featureCounts v. 2.0.1 and Ensembl release 94 genome annotation. Raw counts were imported into R (v. 4.3.0) and downstream differential gene expression analysis was performed using DESeq2 (v. 1.40.2).
Assembly: mm10, GRCm38.p6, Ensembl release 94
Supplementary files format and content: The supplementary csv file contains the raw counts per sample (in columns) per gene (in rows), as summarized by featureCounts. The first column of the csv file contains the Ensembl gene identifier, while the last column of the csv file contains the gene symbol. The sample names in the csv file include the treatment applied to samples (activated = vehicle; activated_10 = 10uM IPA; activated_50 = 50uM IPA)

source_name: bone marrow

growth_protocol: BM cells were isolated and incubated in RPMI medium supplemented with 1% P/S, 10% FBS and GM-CSF  and Il-6, media was changed at d3, and cells were harvested at day 5.

extract_protocol:
RNA was isolated using Qiagen mini kit (RNAsy Qiagen mini kit; #74134)
Illumina Stranded mRNA Prep using a unique dual indexing strategy,  following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer).

treatment_protocol: Cells were incubated with 0.1 DMSO (vehicle) or 10µM or 50µM IPA and were resplenished at day 3 when media was changed.

value: bone marrow

value: bone marrow cells

value: 50µM IPA


title: Thy1-KO, 25kPa substrate, 72hr culture, rep3

description: Library name: T-25-72_3


title: Tkoda, lib747, wt.85deg, Input, _b_

description: Library name: Sample 21

value: Bacterial culture


title: Thy1-KO, TCP substrate, 24hr culture, rep4

description: Library name: T-T-24_4

value: immortalized human lung fibroblasts


title: activated_50_2 (10a)

description:
Library name: activated_50_2
activated_50_2


title: Tkoda, lib747, wt.85deg, Treat, _a_

description: Library name: Sample 20


title: Pabys, lib524, 80deg, Mock, TGIRT, rep1

description: Library name: Sample 95


title: Thy1-KO, 25kPa substrate, 72hr culture, rep2

description: Library name: T-25-72_2

value: fibroblast


title: Thy1-KO, 25kPa substrate, 72hr culture, rep1

description: Library name: T-25-72_1


title: activated_50_1 (9a)

description:
Library name: activated_50_1
activated_50_1


title: Tkoda, lib747, wt.85deg, Input, _a_

description: Library name: Sample 19


title: activated_10_4 (8a)

description:
Library name: activated_10_4
activated_10_4

data_processing:
Fastq generation was done using Base2Fastq v.1.7
Sequencing reads were pre-processed and aligned to the mouse genome using the RNA-seq method of the bcbio-nextgen pipeline v. 1.2.4.
The reads were first trimmed for quality and adapter using Atropos (v. 1.1.28). Trimmed reads were aligned to the Mus musculus genome (mm10) using hisat2 (v. 2.2.1). Numbers of reads were summarized at the gene level per sample using featureCounts v. 2.0.1 and Ensembl release 94 genome annotation. Raw counts were imported into R (v. 4.3.0) and downstream differential gene expression analysis was performed using DESeq2 (v. 1.40.2).
Assembly: mm10, GRCm38.p6, Ensembl release 94
Supplementary files format and content: The supplementary csv file contains the raw counts per sample (in columns) per gene (in rows), as summarized by featureCounts. The first column of the csv file contains the Ensembl gene identifier, while the last column of the csv file contains the gene symbol. The sample names in the csv file include the treatment applied to samples (activated = vehicle; activated_10 = 10uM IPA)

value: 10µM IPA


title: Pabys, lib524, 102deg, Mock, TGIRT, rep2

description: Library name: Sample 94


title: Pabys, lib524, 102deg, Mock, TGIRT, rep1

description: Library name: Sample 93


title: Thy1-KO, 25kPa substrate, 24hr culture, rep4

description: Library name: T-25-24_4

value: 25kPa substrate


title: iPSC-derived cerebral organoids, CEP290 CRISPR gene edited, clone 1, day 79

description: Library name: D141122_21_D79

value: hiPSC-derived cerbral organoid

value: hiPSC

value: Day 79 of differentiation

value: CEP290 CRISPR-gene editing


title: activated_10_2 (6a)

description:
Library name: activated_10_2
activated_10_2


title: activated_50_4 (12a)

description:
Library name: activated_50_4
activated_50_4


title: Tkoda, lib747, wt.75deg, Treat, _c_

description: Library name: Sample 18

value: KOD1 substrain TS559


title: Thy1-KO, 25kPa substrate, 24hr culture, rep2

description: Library name: T-25-24_2


title: Thy1-KO, 25kPa substrate, 24hr culture, rep3

description: Library name: T-25-24_3


title: activated_10_2 (7a)

description:
Library name: activated_10_3
activated_10_3


title: Pabys, lib524, 100deg, Mock, TGIRT, rep1

description: Library name: Sample 91


title: Pabys, lib524, 80deg, Mock, TGIRT, rep2

description: Library name: Sample 96


title: Tkoda, lib747, wt.75deg, Input, _c_

description: Library name: Sample 17


title: Tkoda, lib747, wt.75deg, Treat, _b_

description: Library name: Sample 16


title: activated_10_1 (5a)

description:
Library name: activated_10_1
activated_10_1


title: Pabys, lib524, 80deg, Bisulfite, TGIRT, rep2

description: Library name: Sample 90


title: Tkoda, lib747, wt.75deg, Input, _b_

description: Library name: Sample 15


title: activated_4 (4a)

description:
Library name: activated_4
activated_4

value: vehicle (0.1DMSO)


title: Pabys, lib524, 80deg, Bisulfite, TGIRT, rep1

description: Library name: Sample 89


title: Tkoda, lib747, wt.75deg, Treat, _a_

description: Library name: Sample 14


title: Pabys, lib524, 102deg, Bisulfite, TGIRT, rep2

description: Library name: Sample 88


title: activated_3 (3a)

description:
Library name: activated_3
activated_3


title: Thy1-KO, 4kPa substrate, 72hr culture, rep3

description: Library name: T-4-72_3

value: 4kPa substrate


title: Pabys, lib524, 100deg, Mock, TGIRT, rep2

description: Library name: Sample 92


title: Tkoda, lib747, wt.75deg, Input, _a_

description: Library name: Sample 13


title: activated_2 (2a)

description:
Library name: activated_2
activated_2


title: Pabys, lib524, 102deg, Bisulfite, TGIRT, rep1

description: Library name: Sample 87


title: Thy1-KO, 4kPa substrate, 72hr culture, rep2

description: Library name: T-4-72_2


title: Tkoda, lib747, wt.65deg, Treat, _c_

description: Library name: Sample 12


title: activated_1 (1a)

description:
Library name: activated_1
activated_1


title: REH leukemia cells, ATAC Rep2

description:
Library name: REH_Parental_ATAC_2
ATAC-seq: I1=index; R1=cell barcode/UMI; R2=ATAC seq; R3=ATAC seq

value: REH

value: B-cell leukemia

value: scATAC


title: Thy1-KO, 4kPa substrate, 72hr culture, rep1

description: Library name: T-4-72_1


title: Thy1-KO, 4kPa substrate, 24hr culture, rep4

description: Library name: T-4-24_4


title: Thy1-KO, 4kPa substrate, 24hr culture, rep3

description: Library name: T-4-24_3


title: Tkoda, lib747, wt.65deg, Input, _c_

description: Library name: Sample 11

value: WT


title: vector control, skin, 7 day, rep 5

city: Washington DC

first: Leon

last: Grayfer

address: 800 22nd ST NW

department: Biological Sciences

institute: George Washington University

description: Library name: 7V8

data_processing:
Reads aligned with minimap2 (v2.29) with “-ax sr” and samtools (v1.16.1) to produce a .bam file for each paired-end read set. An expression matrix was produced from all samples using featureCounts (v2.1.1) with parameters “--countReadPairs -B -t exon -g gene_id” using the GCF_017654675.1 genomic.gtf annotated from NCBI.
Assembly: GCF_017654675.1 (Xenopus_laevis_v10.1)
Supplementary files format and content: Raw read counts protein coding genes
Supplementary files format and content: Matrix for all samples

organism: Xenopus laevis

source_name: skin

extract_protocol:
Trizol extraction
Library prep was completed by Azenta using NEBNext Ultra II RNA Library Preparation kit according to the manufacturer's instructions; The Qiagen FastSelect kit was used for the rRNA depletion.

value: skin

value: subcutaneous empty vector injection


title: vector control, skin, 7 day, rep 6

description: Library name: 7V9


title: Pabys, lib524, 100deg, Bisulfite, TGIRT, rep1

description: Library name: Sample 85

value: Bacterial culture


title: Thy1-KO, 25kPa substrate, 24hr culture, rep1

description: Library name: T-25-24_1

value: immortalized human lung fibroblasts

value: fibroblast


title: Tkoda, lib747, wt.65deg, Input, _b_

description: Library name: Sample 9


title: Thy1-KO, 4kPa substrate, 72hr culture, rep4

description: Library name: T-4-72_4


title: vector control, skin, 7 day, rep 4

description: Library name: 7V6


title: Tkoda, lib747, wt.65deg, Treat, _b_

description: Library name: Sample 10


title: Pabys, lib524, 100deg, Bisulfite, TGIRT, rep2

description: Library name: Sample 86


title: Thy1-KO, 4kPa substrate, 24hr culture, rep2

description: Library name: T-4-24_2


title: Pabys, lib524, 80deg, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 83


title: Pabys, lib524, 80deg, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 84


title: Pabys, lib524, 102deg, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 82


title: vector control, skin, 7 day, rep 3

description: Library name: 7V5


title: Thy1-KO, 4kPa substrate, 24hr culture, rep1

description: Library name: T-4-24_1


title: vector control, skin, 7 day, rep 2

description: Library name: 7V3


title: Thy1-KO, Suspension/0hr, rep4

description: Library name: T-0_4

value: Suspension


title: vector control, skin, 7 day, rep 1

description: Library name: 7V1


title: Pabys, lib524, 100deg, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 80


title: Thy1-KO, Suspension/0hr, rep3

description: Library name: T-0_3


title: Pabys, lib524, 102deg, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 81


title: Tkoda, lib747, Tko105.95deg, Treat, _b_

description: Library name: Sample 5


title: il34, skin, 7 day, rep 6

description: Library name: 7I8

value: subcutaneous il34 injection


title: Tkoda, lib747, Tko105.95deg, Treat, _a_

description: Library name: Sample 4


title: Thy1-KO, Suspension/0hr, rep2

description: Library name: T-0_2


title: Pabys, lib524, 80deg, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 78


title: Tkoda, lib747, Tko105.75deg, Treat, _c_

description: Library name: Sample 3


title: il34, skin, 7 day, rep 5

description: Library name: 7I5


title: WT, TCP substrate, 72hr culture, rep4

description: Library name: W-T-72_4

value: TCP substrate


title: Tkoda, lib747, Tko105.75deg, Treat, _b_

description: Library name: Sample 2


title: il34, skin, 7 day, rep 3

description: Library name: 7I3


title: il34, skin, 7 day, rep 4

description: Library name: 7I4


title: WT, TCP substrate, 72hr culture, rep3

description: Library name: W-T-72_3


title: Pabys, lib524, 80deg, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 77


title: il34, skin, 7 day, rep 2

description: Library name: 7I2


title: Tkoda, lib747, Tko105.75deg, Treat, _a_

description: Library name: Sample 1


title: Pabys, lib524, 102deg, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 76


title: Thy1-KO, Suspension/0hr, rep1

description: Library name: T-0_1


title: Pabys, lib524, 102deg, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 75


title: WT, TCP substrate, 72hr culture, rep2

description: Library name: W-T-72_2


title: Tkoda, lib747, wt.65deg, Input, _a_

description: Library name: Sample 7


title: Tkoda, lib522, 95deg.Treated, NaCNBH3.Treat.Treat, rep1

description: Library name: Sample 7

source_name: Cell culture

growth_protocol: T.  kodakarensis cells were grown anaerobically at 37°, 55°, 65°, 75°, 85°, or 95°C in artificial sea-water with yeast, tryptone, pyruvate (ASW-YTP) and supplemented with sulfur and agmatine. Cultures were grown to mid exponential growth phase (OD600  ~0.4-0.5) and harvested by centrifugation at 12,000 x g.

extract_protocol:
T. kodakarensis cell pellets were resuspended in TRIzol reagent (Thermofisher Scientific, cat# 15596018) and stored at -20°C, followed by RNA extraction according to the manufacturer’s protocol.
For each reaction, RNA was treated as in (Thalalla Gamage et al., 2021). Briefly, RNA was incubated with either NaCNBH3 (100 mM in H2O + 100 mM HCl) or untreated ‘mock’ control (H2O + 100 mM HCl) in a final reaction volume of 100 ul. Samples were incubated for 20 min at 20 °C. Reactions were stopped by neutralization of pH by the addition of 30 μl 1 M Tris pH 8.0. Reactions were adjusted to 200 μl with H2O, precipitated with ethanol, and desalted with 70% ice-cold ethanol. Strand-specific ac4C-seq libraries were generated on the basis of previously described protocols (SHishkin et al., 2015). In brief, RNA was first subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3′ ligation of an RNA adaptor using T4 ligase (NEB). Ligated RNA was reverse transcribed using TGIRT-III (InGex), and the cDNA was subjected to a 3′ ligation with a second adaptor using T4 ligase. The single-stranded cDNA product was then amplified for 9–12 cycles in a PCR reaction.

value: Cell culture


title: il34, skin, 7 day, rep 1

description: Library name: 7I1


title: Tkoda, lib522, 85deg.Treated, NaCNBH3.Treat.Treat, rep1

description: Library name: Sample 6


title: Pabys, lib524, 100deg, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 79


title: csf1, skin, 7 day, rep 6

description: Library name: 7C9

value: subcutaneous csf1 injection


title: WT, TCP substrate, 24hr culture, rep4

description: Library name: W-T-24_4


title: Pabys, lib524, 100deg, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 73


title: Tkoda, lib522, 75deg.Treated, NaCNBH3.Treat.Treat, rep1

description: Library name: Sample 5

value: KOD1 substrain TS559


title: WT, TCP substrate, 24hr culture, rep3

description: Library name: W-T-24_3


title: csf1, skin, 7 day, rep 5

description: Library name: 7C8


title: Pabys, lib524, 80deg, CMC, TGIRT, rep2

description: Library name: Sample 72


title: Tkoda, lib747, Tko105.95deg, Treat, _c_

description: Library name: Sample 6


title: Tkoda, lib522, 65deg.Treated, NaCNBH3.Treat.Treat, rep1

description: Library name: Sample 4


title: Tkoda, lib522, 65deg.Control, NaCNBH3.Treat, rep1

description: Library name: Sample 3


title: Pabys, lib524, 102deg, CMC, TGIRT, rep2

description: Library name: Sample 70


title: Pabys, lib524, 80deg, CMC, TGIRT, rep1

description: Library name: Sample 71


title: WT, TCP substrate, 24hr culture, rep2

description: Library name: W-T-24_2


title: csf1, skin, 7 day, rep 3

description: Library name: 7C2


title: csf1, skin, 7 day, rep 2

description: Library name: 7C10


title: Pabys, lib524, 102deg, CMC, TGIRT, rep1

description: Library name: Sample 69


title: Tkoda, lib522, 37deg.Treated, NaCNBH3.Treat.Treat, rep1

description: Library name: Sample 1


title: WT, 25kPa substrate, 72hr culture, rep3

description: Library name: W-25-72_3

value: 25kPa substrate


title: WT, TCP substrate, 24hr culture, rep1

description: Library name: W-T-24_1


title: Tkoda, lib522, 55deg.Treated, NaCNBH3.Treat.Treat, rep1

description: Library name: Sample 2


title: csf1, skin, 7 day, rep 4

description: Library name: 7C4


title: WT, 25kPa substrate, 72hr culture, rep4

description: Library name: W-25-72_4


title: csf1, skin, 7 day, rep 1

description: Library name: 7C1


title: WT, TCP substrate, 72hr culture, rep1

description: Library name: W-T-72_1


title: Tkoda, lib524, 95deg, Bisulfite+MgCl2+Heat, TGIRT, rep2

description: Library name: Sample 144

growth_protocol: Grown anaerobically at 65°, 75°, 85°, or 95°C in artificial sea-water with yeast, tryptone, pyruvate (ASW-YTP) and supplemented with sulfur and agmatine. Cultures were grown to mid exponential growth phase (OD600  ~0.4-0.5) in duplicate and harvested by centrifugation at 12,000 x g

extract_protocol:
Cell pellets were resuspended directly in 1000 µl TRI Reagent and incubated at room temperature for 5 minutes. A volume of 200 µl chloroform was added to the solution, vigorously shaken for 15 seconds, and incubated at room temperature for 3 minutes. The mixture was then centrifuged at 12,000 x g for 15 minutes at 4°C. The aqueous phase was collected after centrifugation and mixed with an equal volume of ethanol. RNA was processed with the NEB Monarch Total RNA Miniprep Kit. DNase digestion to eliminate genomic DNA.
Remaining primers left in the reaction were digested by addition of 3 μL ExoSAP-IT (Applied Biosystems, 78205) to the 20 μL reverse transcription reaction, and incubation at 37°C for 12 min. RNA was degraded by adding 2.5 μL of NaOH 1M and 1 μL of 0.5M EDTA, and incubation at 70°C for 12 min. The base was neutralized with the addition of 1M HCl, cDNA was cleaned using MyOne silane beads. An adapter was added to the 3’ end of the cDNA by ligating 50 pmoles 5iLL-22 DNA adapter using T4 RNA Ligase 1, High concentration (NEB, M0437M), DMSO 4%, ATP 1mM and PEG8000 25% at 23°C for 3 h. After clean-up with MyOne silane beads, we amplified the cDNA library for 12 cycles using Illumina Library PCR primers F and R and KAPA HiFi HotStart ReadyMix (Roche, KK2601). Amplified libraries were cleaned with Kapa pure beads (Roche, KK8002), quantified using Qubit (Life Technologies) and the distribution of library size was determined using TapeStation (Agilent Technologies).


title: Pabys, lib524, 100deg, CMC, TGIRT, rep2

description: Library name: Sample 68


title: vector control, skin, 14 day, rep 6

description: Library name: 14V9


title: WT, 25kPa substrate, 72hr culture, rep2

description: Library name: W-25-72_2


title: Pabys, lib524, 100deg, CMC, TGIRT, rep1

description: Library name: Sample 67


title: Tkoda, lib524, 95deg, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 143


title: vector control, skin, 14 day, rep 5

description: Library name: 14V8


title: WT, 25kPa substrate, 72hr culture, rep1

description: Library name: W-25-72_1


title: vector control, skin, 14 day, rep 4

description: Library name: 14V7


title: Tkoda, lib524, 85deg, Bisulfite+MgCl2+Heat, TGIRT, rep2

description: Library name: Sample 142


title: Pabys, lib524, 80deg, AlkBmix, TGIRT, rep1

description: Library name: Sample 65


title: Tkoda, lib524, 75deg, Bisulfite+MgCl2+Heat, TGIRT, rep2

description: Library name: Sample 140


title: Pabys, lib524, 102deg, AlkBmix, TGIRT, rep2

description: Library name: Sample 64


title: WT, 25kPa substrate, 24hr culture, rep4

description: Library name: W-25-24_4


title: Tkoda, lib524, 85deg, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 141


title: WT, 25kPa substrate, 24hr culture, rep3

description: Library name: W-25-24_3


title: Pabys, lib524, 100deg, AlkBmix, TGIRT, rep2

description: Library name: Sample 62


title: vector control, skin, 14 day, rep 1

description: Library name: 14V2


title: WT, 25kPa substrate, 24hr culture, rep1

description: Library name: W-25-24_1


title: vector control, skin, 14 day, rep 2

description: Library name: 14V4


title: Tkoda, lib524, 65deg, Bisulfite+MgCl2+Heat, TGIRT, rep2

description: Library name: Sample 138


title: Pabys, lib524, 100deg, AlkBmix, TGIRT, rep1

description: Library name: Sample 61


title: il34, skin, 14 day, rep 5

description: Library name: 14I5


title: WT, 4kPa substrate, 72hr culture, rep4

description: Library name: W-4-72_4

value: 4kPa substrate


title: WT, 4kPa substrate, 72hr culture, rep3

description: Library name: W-4-72_3


title: Tkoda, lib524, 95deg, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 136


title: WT, 25kPa substrate, 24hr culture, rep2

description: Library name: W-25-24_2


title: il34, skin, 14 day, rep 6

description: Library name: 14I7


title: Pabys, lib524, 80deg, AlkBmix, TGIRT, rep2

description: Library name: Sample 66


title: il34, skin, 14 day, rep 4

description: Library name: 14I3


title: Tkoda, lib524, 65deg, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 137


title: WT, 4kPa substrate, 72hr culture, rep2

description: Library name: W-4-72_2


title: Tkoda, lib524, 95deg, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 135


title: il34, skin, 14 day, rep 3

description: Library name: 14I2


title: Pabys, lib524, 80deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 59


title: vector control, skin, 14 day, rep 3

description: Library name: 14V6


title: Pabys, lib524, 102deg, AlkBmix, TGIRT, rep1

description: Library name: Sample 63


title: Pabys, lib524, 102deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 58


title: Tkoda, lib524, 75deg, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 139


title: Pabys, lib524, 102deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 57


title: Tkoda, lib747, wt.65deg, Treat, _a_

description: Library name: Sample 8


title: WT, 4kPa substrate, 24hr culture, rep4

description: Library name: W-4-24_4


title: il34, skin, 14 day, rep 1

description: Library name: 14I1


title: Pabys, lib524, 100deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 56


title: Pabys, lib524, 80deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 60


title: WT, 4kPa substrate, 24hr culture, rep3

description: Library name: W-4-24_3


title: Tkoda, lib524, 75deg, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 132


title: csf1, skin, 14 day, rep 6

description: Library name: 14C9


title: Tkoda, lib524, 85deg, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 133


title: WT, 4kPa substrate, 72hr culture, rep1

description: Library name: W-4-72_1


title: Pabys, lib524, 100deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 55


title: csf1, skin, 14 day, rep 5

description: Library name: 14C8


title: Pabys, lib524, 80deg, Bisulfite+MgCl2+Heat, SSIII, rep2

description: Library name: Sample 54


title: Tkoda, lib524, 75deg, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 131


title: WT, 4kPa substrate, 24hr culture, rep2

description: Library name: W-4-24_2


title: WT, 4kPa substrate, 24hr culture, rep1

description: Library name: W-4-24_1


title: Tkoda, lib524, 65deg, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 130


title: csf1, skin, 14 day, rep 4

description: Library name: 14C7


title: WT, Suspension/0hr, rep4

description: Library name: W-0_4


title: Tkoda, lib524, 65deg, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 129


title: Pabys, lib524, 80deg, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 53


title: csf1, skin, 14 day, rep 3

description: Library name: 14C6


title: Pabys, lib524, 102deg, Bisulfite+MgCl2+Heat, SSIII, rep2

description: Library name: Sample 52


title: Tkoda, lib524, 85deg, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 134


title: il34, skin, 14 day, rep 2

description: Library name: 14I10


title: WT, Suspension/0hr, rep3

description: Library name: W-0_3


title: Tkoda, lib524, 95deg, Mock, TGIRT, rep2

description: Library name: Sample 128


title: csf1, skin, 14 day, rep 2

description: Library name: 14C5


title: WT, Suspension/0hr, rep2

description: Library name: W-0_2


title: Pabys, lib524, 102deg, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 51


title: Tkoda, lib524, 95deg, Mock, TGIRT, rep1

description: Library name: Sample 127


title: csf1, skin, 14 day, rep 1

description: Library name: 14C3


title: Pabys, lib524, 100deg, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 49


title: WT, Suspension/0hr, rep1

description: Library name: W-0_1


city: Hangzhou

first: Shengjie

last: Hao

address: 1 Xihu Avenue

country: China

institute: Zhejiang University

description:
Library name: KO_PM3
HCECs, PAI-2 KO, with PM2.5 exposure for 3 hours 3

data_processing:
Reads containing ploy-N and low-quality reads were removed from raw data to get clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

source_name: cornea

extract_protocol:
The total RNA of cells or tissues was extracted by FlaPure Animal Tissue Total RNA Extraction Kit (Genesand, RE705). Spectrophotometers (NanoDrop 2000c, Thermo Scientific) were used to detect the quality and concentration of RNA samples.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Beverly, MA, USA) was applied to prepare sequencing cDNA libraries.

value: cornea

value: HCECs PCS-700-010

value: epitehlial cells


title: 25558_1ug_Pam3

city: Irvine

first: Jonathan

middle: Van

last: Duong

state: CA

address: 843 Health Sciences Rd

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
Library name: Sample 35
PE150, mRNA:stranded

data_processing:
CLC Genomics Workbench v24.0
Assembly: GCF_004664715.2 for P. leucopus LL stock and GCF_000001635.27_GRCm39 for M. musculus C57Bl/6.
Supplementary files format and content: Excel spreadsheet with raw TPM and gene length values for each sample.

organism: Peromyscus leucopus

source_name: Skin of ear

growth_protocol: Roswell Park Memorial Institute (RPMI) 1640 medium: 10% heat-inactivated fetal bovine serum (FBS), 2 mM glutamine, 100 µM asparagine, 1% penicillin-streptomycin solution (500 U/ml-500 µl/ml). Incubation in humidified incubator at 37C with 5% CO2.

extract_protocol:
RNA was extracted using the Quick-RNA Miniprep Plus Kit (Zymo) and cells were lysed while adherent in the 6-well plate.
Illumina TruSeq Stranded mRNA

treatment_protocol: TLR agonist was added to medium at 1 or 10 µg/ml for and incubated  humidified incubator at 37C with 5% CO2 for 4 hours.

value: Skin of ear

value: Primary

value: Fibroblasts


title: Tkoda, lib524, 85deg, Mock, TGIRT, rep1

description: Library name: Sample 125

value: Bacterial culture

value: WT


title: Pabys, lib524, 100deg, Bisulfite+MgCl2+Heat, SSIII, rep2

description: Library name: Sample 50


title: 25558_Saline

description:
Library name: Sample 36
PE150, mRNA:stranded

value: Saline


description:
Library name: KO_PM2
HCECs, PAI-2 KO, with PM2.5 exposure for 3 hours 2


title: Tkoda, lib524, 85deg, Mock, TGIRT, rep2

description: Library name: Sample 126


title: Tkoda, lib524, 75deg, Mock, TGIRT, rep2

description: Library name: Sample 124


title: Pabys, lib524, 80deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 48


description:
Library name: KO_PM1
HCECs, PAI-2 KO, with PM2.5 exposure for 3 hours 1


title: 25558_10ug_Pam3

description:
Library name: Sample 34
PE150, mRNA:stranded


title: Pabys, lib524, 80deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 47


title: Tkoda, lib524, 75deg, Mock, TGIRT, rep1

description: Library name: Sample 123


title: 25510_Saline

description:
Library name: Sample 33
PE150, mRNA:stranded


title: Tkoda, lib524, 65deg, Mock, TGIRT, rep2

description: Library name: Sample 122


title: 25510_1ug_Pam3

description:
Library name: Sample 32
PE150, mRNA:stranded


title: HCECs, PAI-2 KO, without treatment3

description:
Library name: KO3
HCECs, PAI-2 KO, without treatment3


title: Pabys, lib524, 102deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 45


title: Tkoda, lib524, 65deg, Mock, TGIRT, rep1

description: Library name: Sample 121


title: HCECs, PAI-2 KO, without treatment2

description:
Library name: KO2
HCECs, PAI-2 KO, without treatment2


title: 25510_10ug_Pam3

description:
Library name: Sample 31
PE150, mRNA:stranded


title: Pabys, lib524, 100deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 44


title: HCECs, PAI-2 KO, without treatment1

description:
Library name: KO1
HCECs, PAI-2 KO, without treatment1


title: 25459_Saline

description:
Library name: Sample 30
PE150, mRNA:stranded


title: Pabys, lib524, 100deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 43


description:
Library name: NC_PM3
HCECs, negative control, with PM2.5 exposure for 3 hours 3


title: 25459_1ug_Pam3

description:
Library name: Sample 29
PE150, mRNA:stranded


title: Tkoda, lib524, 95deg, Bisulfite, TGIRT, rep1

description: Library name: Sample 119


title: Pabys, lib524, 80deg, Mock, SSIII, rep2

description: Library name: Sample 42


description:
Library name: NC_PM2
HCECs, negative control, with PM2.5 exposure for 3 hours 2


title: 25459_10ug_Pam3

description:
Library name: Sample 28
PE150, mRNA:stranded


title: Tkoda, lib524, 85deg, Bisulfite, TGIRT, rep1

description: Library name: Sample 117


title: 25418_Saline

description:
Library name: Sample 27
PE150, mRNA:stranded


title: Pabys, lib524, 80deg, Mock, SSIII, rep1

description: Library name: Sample 41


title: Tkoda, lib524, 85deg, Bisulfite, TGIRT, rep2

description: Library name: Sample 118


description:
Library name: NC_PM1
HCECs, negative control, with PM2.5 exposure for 3 hours 1


title: Tkoda, lib524, 75deg, Bisulfite, TGIRT, rep2

description: Library name: Sample 116


title: 25418_1ug_Pam3

description:
Library name: Sample 26
PE150, mRNA:stranded


title: Pabys, lib524, 102deg, Mock, SSIII, rep2

description: Library name: Sample 40


title: Pabys, lib524, 102deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 46


description:
Library name: NC2
HCECs, negative control, without treatment2


title: 25418_10ug_Pam3

description:
Library name: Sample 25
PE150, mRNA:stranded


title: Pabys, lib524, 102deg, Mock, SSIII, rep1

description: Library name: Sample 39


title: Tkoda, lib524, 75deg, Bisulfite, TGIRT, rep1

description: Library name: Sample 115


title: Pabys, lib524, 100deg, Mock, SSIII, rep2

description: Library name: Sample 38


title: Tkoda, lib524, 95deg, Bisulfite, TGIRT, rep2

description: Library name: Sample 120


description:
Library name: NC1
HCECs, negative control, without treatment1


title: Tkoda, lib524, 65deg, Bisulfite, TGIRT, rep2

description: Library name: Sample 114


title: Pabys, lib524, 100deg, Mock, SSIII, rep1

description: Library name: Sample 37


title: 25417_Saline

description:
Library name: Sample 24
PE150, mRNA:stranded


title: Hsapi, lib697, control, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 34

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_000001405.40
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

source_name: cell culture

growth_protocol: Grown in a humidified incubator at 37°C and 5% CO2 to 80% confluency, in DMEM media containing grown 10% FBS and 1% pen-strep solution

extract_protocol:
Purified using NucleoZOL (Macherey-Nagel) by the manufacturer's instructions
Remaining primers left in the reaction were digested by addition of 3 μL ExoSAP-IT (Applied Biosystems, 78205) to the 20 μL reverse transcription reaction, and incubation at 37°C for 12 min. RNA was degraded by adding 2.5 μL of NaOH 1M and 1 μL of 0.5M EDTA, and incubation at 70°C for 12 min. The base was neutralized with the addition of 1M HCl, cDNA was cleaned using MyOne silane beads. An adapter was added to the 3’ end of the cDNA by ligating 50 pmoles 5iLL-22 DNA adapter using T4 RNA Ligase 1, High concentration (NEB, M0437M), DMSO 4%, ATP 1mM and PEG8000 25% at 23°C for 3 h. After clean-up with MyOne silane beads, we amplified the cDNA library for 12 cycles using Illumina Library PCR primers F and R and KAPA HiFi HotStart ReadyMix (Roche, KK2601). Amplified libraries were cleaned with Kapa pure beads (Roche, KK8002), quantified using Qubit (Life Technologies) and the distribution of library size was determined using TapeStation (Agilent Technologies).

value: cell culture

value: HEK 293T

value: Human embryonic kidney cells

value: control


title: Tkoda, lib524, 65deg, Bisulfite, TGIRT, rep1

description: Library name: Sample 113


title: 25417_1ug_Pam3

description:
Library name: Sample 23
PE150, mRNA:stranded


description:
Library name: NC3
HCECs, negative control, without treatment3


title: Tkoda, lib524, 95deg, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 112


title: 25417_10ug_Pam3

description:
Library name: Sample 22
PE150, mRNA:stranded


title: Pabys, lib524, 80deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 35


title: Pabys, lib524, 102deg, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 34


title: Hsapi, lib697, control, Bisulfite, TGIRT, rep1

description: Library name: Sample 32


title: Hsapi, lib697, control, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 31


title: Tkoda, lib524, 95deg, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 111


title: 25314_P47_1ug_LPS

description:
Library name: Sample 20
PE150, mRNA:stranded


title: Pabys, lib524, 102deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 33


title: 25314_P47_Saline

description:
Library name: Sample 21
PE150, mRNA:stranded


title: Hsapi, lib697, control, CMC, TGIRT, rep1

description: Library name: Sample 29


title: Pabys, lib524, 100deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 31