title: 25314_P4_Saline

description:
Library name: Sample 18
PE150, mRNA:stranded


title: Hsapi, lib697, control, NaHCO3+NaCNBH3, TGIRT, rep1

status: Public on Oct 22 2025

type: SRA

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 30

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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).

tag: tissue

value: cell culture

tag: cell line

value: HEK 293T

tag: cell type

value: Human embryonic kidney cells

tag: genotype

value: WT

tag: treatment

value: control

tag: batch


title: Tkoda, lib524, 75deg, NaHCO3+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_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

source_name: Bacterial culture

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).

value: Bacterial culture

tag: strain

value: KOD1 substrain TS559


title: Tkoda, lib524, 75deg, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 108


title: 25314_P4_1ug_LPS

city: Irvine

first: Jonathan

middle: Van

last: Duong

state: CA

address: 843 Health Sciences Rd

department: Microbiology & Molecular Genetics

country: USA

institute: University of California, Irvine

description:
Library name: Sample 17
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: Hsapi, lib697, control, AlkBmix, TGIRT, rep1

description: Library name: Sample 28


title: Tkoda, lib524, 85deg, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 109


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

description: Library name: Sample 36

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: 25314_P4_10ug_Pam3

description:
Library name: Sample 16
PE150, mRNA:stranded


title: Hsapi, lib697, control, NaCNBH3, TGIRT, rep1

description: Library name: Sample 27


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

description: Library name: Sample 33


title: Tkoda, lib524, 65deg, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 106


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

description: Library name: Sample 30


title: Tkoda, lib524, 85deg, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 110


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

description: Library name: Sample 29


title: Pabys, lib524, 100deg, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 74


title: Hsapi, lib697, control, Mock, SSIII, rep1

description: Library name: Sample 25


title: SITW016_10

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

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

organism: Mus musculus

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).

tag: condition

value: naive


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

description: Library name: Sample 28


title: 25314_P47_10ug_Pam3

description:
Library name: Sample 19
PE150, mRNA:stranded


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

description: Library name: Sample 32


title: Hsapi, lib697, control, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 26


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

description: Library name: Sample 27


title: Pabys, lib524, 100deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 26


title: Hsapi, lib697, control, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 23


title: Tkoda, lib524, 85deg, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 102


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

description: Library name: Sample 25


title: SITW016_7


title: Tkoda, lib524, 85deg, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 101


title: SITW016_6


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

description: Library name: Sample 22


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

description: Library name: Sample 24


title: Hsapi, lib697, control, NaCNBH3, SSIII, rep1

description: Library name: Sample 21


title: Tkoda, lib524, 75deg, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 100


title: SITW016_5


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

description: Library name: Sample 23


title: Tkoda, lib524, 75deg, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 99


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

description: Library name: Sample 20


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

description: Library name: Sample 22


title: SITW016_9


title: SITW016_4


title: Hsapi, lib697, control, Mock, RTHIV, rep1

description: Library name: Sample 19


title: Tkoda, lib524, 95deg, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 103


title: Tkoda, lib524, 95deg, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 104


title: Hsapi, lib524, control, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 18


title: Tkoda, lib524, 65deg, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 98


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

description: Library name: Sample 21


title: SITW016_2


title: Tkoda, lib524, 65deg, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 97


title: SITW016_8


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

description: Library name: Sample 96


title: Hsapi, lib524, control, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 17


title: SITW016_1


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

description: Library name: Sample 20


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

description: Library name: Sample 19


title: Hsapi, lib524, control, Mock, TGIRT, rep1

description: Library name: Sample 16


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

description: Library name: Sample 95


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

description: Library name: Sample 18


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

description: Library name: Sample 24


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

description: Library name: Sample 94


title: Hsapi, lib524, control, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 14


title: Sente, lib553, OD2_37C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 204

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_000210855.2
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Salmonella enterica

growth_protocol: Grown in duplicate for three temperatures, 25°C, 30°C and 37°C. Indicated cells were grown in over-night cultures at indicated temperatures in LB media at 220 rpm. Cultures were inoculated 1:100 and grown at indicated temperatures in LB media at 220 rpm. At indicated OD600, cells were harvested and RNA was extracted with the hot phenol method followed by RNA precipitation with ethanol/acetate.

extract_protocol:
5 ml cells (at OD 2) were mixed with 0.2 volume stop solution (5% (v/v) phenol for RNA extraction, pH 4.5 (Roth), 95% (v/v) ethanol) and flash frozen in liquid nitrogen. Samples were thawed on ice, and cells pelleted at 4,000 g for 20 min at 4 °C. The supernatant was carefully removed, and the cells were resuspended in 0.8 ml Tris/EDTA (pH 8.0) with 0.5 mg/ml lysozyme (Roth) and incubated on ice for 10 min. 1% SDS was added to the sample. One volume phenol for RNA extraction (pH 4.5, Roth) was added to the samples for organic phase extraction, vortexted rigorously, and heated up to 64 °C for 7 min with shaking. Samples were cooled down to room temperature, the phases were separated by centrifugation at 13,000 g for 10 min and the upper aqueous fraction was collected in a new tube. One volume chloroform was added and samples were shaked for 5 min, the phases were separated by centrifugation at 13,000 g for 10 min and the upper aqueous fraction was collected in a new tube. The extraction with chloroform was repeated once more for Pseudomonas. The RNA in the sample was precipitated by addition of three volumes ethanol and 0.03 volume 3 M NaOAc pH 6.5, and storage over-night at -20 °C. The precipitated RNA was pelleted at 13,000 g for 10 min, the supernatant was removed, and the RNA was dried
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: Sente, lib553, OD2_37C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 203


title: SITW016_3


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

description: Library name: Sample 93


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

description: Library name: Sample 16


title: Hsapi, lib524, control, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 13


title: Tkoda, lib524, 65deg, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 105


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

description: Library name: Sample 92


title: Sente, lib553, OD2_30C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 201


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

description: Library name: Sample 15


title: Hsapi, lib524, control, CMC, TGIRT, rep1

description: Library name: Sample 12


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

description: Library name: Sample 91


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

description: Library name: Sample 14


title: Sente, lib553, OD2_25C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 200


title: Hsapi, lib524, control, AlkBmix, TGIRT, rep1

description: Library name: Sample 11


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

description: Library name: Sample 90


title: Hsapi, lib524, control, NaCNBH3, TGIRT, rep1

description: Library name: Sample 10


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

description: Library name: Sample 13


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

description: Library name: Sample 89


title: Sente, lib553, OD1_37C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 198


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

description: Library name: Sample 12


title: Hsapi, lib524, control, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 9


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

description: Library name: Sample 17


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

description: Library name: Sample 88


title: Sente, lib553, OD1_37C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 197


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

description: Library name: Sample 11


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

description: Library name: Sample 10


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

description: Library name: Sample 87


title: Hsapi, lib524, control, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 8


title: Hsapi, lib524, control, Bisulfite, TGIRT, rep1

description: Library name: Sample 15


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

description: Library name: Sample 86


title: Sente, lib553, OD1_30C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 195


title: Sente, lib553, OD2_30C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 202


title: Hsapi, lib524, control, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 6


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

description: Library name: Sample 85


title: Sente, lib553, OD1_30C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 196


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

description: Library name: Sample 84


title: Sente, lib553, OD2_25C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 199


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

description: Library name: Sample 7


title: Hsapi, lib524, control, CMC, SSIII, rep1

description: Library name: Sample 4


title: Sente, lib553, OD1_25C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 193


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

description: Library name: Sample 8


title: Sente, lib553, OD1_25C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 194


title: Sente, lib553, OD2_37C, Mock, TGIRT, rep2

description: Library name: Sample 192


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

description: Library name: Sample 6


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

description: Library name: Sample 83


title: Hsapi, lib524, control, NaCNBH3, SSIII, rep1

description: Library name: Sample 3


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

description: Library name: Sample 82


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

description: Library name: Sample 5


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

description: Library name: Sample 81


title: Hsapi, lib524, control, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 2


title: Hsapi, lib524, control, Mock, SSIII, rep1

description: Library name: Sample 7


title: Sente, lib553, OD2_37C, Mock, TGIRT, rep1

description: Library name: Sample 191


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

description: Library name: Sample 4


title: Sente, lib553, OD2_30C, Mock, TGIRT, rep2

description: Library name: Sample 190


title: Hsapi, lib524, control, Mock, RTHIV, rep1

description: Library name: Sample 1


title: Sente, lib553, OD2_30C, Mock, TGIRT, rep1

description: Library name: Sample 189


title: Hsapi, lib524, control, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 5


title: Sente, lib553, OD2_25C, Mock, TGIRT, rep2

description: Library name: Sample 188


title: A549 cells, CRISPRi_PRR11+SKA2 promoter-sgRNA#1

city: Chongqing

first: youquan

last: bu

address: Medical College Road No.1

country: China

institute: Chongqing Medical University

data_processing:
data filtering steps
read alignment bowtie2 version 2.3.5.1
Expression statistics RSEM v1.3.3
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: txt

molecule: polyA RNA

growth_protocol: A549 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol (invitrogen). 1ug of total RNA was used for the construction of sequencing libraries.
library construction were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA).

value: Human Non-Small Cell Lung Cancer Cells

value: Inhibition of PRR11/SKA2 promoter activity


title: Tkoda, lib524, 95deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 80


title: Tkoda, lib524, 95deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 79


title: A549 cells, CRISPRi_Mock sgRNA

value: Control


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

description: Library name: Sample 3


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

description: Library name: Sample 2


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

description: Library name: Sample 1


title: SITW022_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-Disome-Seq

value: mtIF3 KO


title: Cther, lib697, 60C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 64

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_000184925.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Acetivibrio thermocellus

growth_protocol: Was grown in anaerobic culturing, and duplicates under 50°C and 60°C

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).


title: Tkoda, lib524, 85deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 78


title: Sente, lib553, OD2_25C, Mock, TGIRT, rep1

description: Library name: Sample 187


title: Tkoda, lib524, 85deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 77


title: Tkoda, lib524, 75deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 76


title: SITW022_2


title: Sente, lib553, OD1_37C, Mock, TGIRT, rep1

description: Library name: Sample 185


title: Sente, lib553, OD1_37C, Mock, TGIRT, rep2

description: Library name: Sample 186


title: Tkoda, lib524, 75deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 75


title: Sente, lib553, OD1_30C, Mock, TGIRT, rep2

description: Library name: Sample 184


title: SITW022_3


title: Cther, lib697, 50C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 62


title: SITW022_1


title: Tkoda, lib524, 65deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 74


title: Sente, lib553, OD1_30C, Mock, TGIRT, rep1

description: Library name: Sample 183


title: Cther, lib697, 50C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 61


title: Sente, lib553, OD1_25C, Mock, TGIRT, rep2

description: Library name: Sample 182


title: NDMM6, OL

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: NDMM6, OL

library_source: transcriptomic single cell

data_processing:
cellranger count
SCANPY_SCVI
Assembly: refdata-cellranger-GRCh38-3.0.
Supplementary files format and content: AnnData object ( .h5ad format)

source_name: Left sacral

extract_protocol:
BM from healthy donors, and BM or FL samples from patients with MM, were freshly collected using either standard blind (for healthy volunteers) or CT guided biopsy (for patients). Ficoll paque was used to exclude red blood cells (RBCs). To keep neutrophils in the leukocytes, everything above the RBCs including Ficoll itself were collected. CD11b+CD3-CD56-CD138- myeloid cells were freshly isolated using a SONY flow sorter. Selected cells were immediately used for scRNA-seq.
Single cell GEX libraries are generated using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the 10X Genomics platform.  Cell suspensions are first assessed with ViaStain AOPI using a Cellometer K2 automated cell counter (Nexcelom), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells are loaded into the Chromium X Controller (10X Genomics) where they are partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription is performed and the resulting cDNA is amplified.  The full-length amplified cDNA is used to generate gene expression libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  The resulting libraries are evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies), and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina (Roche).

value: Left sacral

value: Lymphocytes

value: Myeloid cells


title: Cther, lib697, 60C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 63


title: NDMM6, BM

description: NDMM6, BM

source_name: Bone Marrow

value: Bone Marrow


title: Tkoda, lib524, 65deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 73


title: Cther, lib697, 60C, Mock, TGIRT, rep1

description: Library name: Sample 59


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

description: Library name: Sample 72


title: Sente, lib553, OD1_25C, Mock, TGIRT, rep1

description: Library name: Sample 181


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

description: Library name: Sample 71


title: NDMM2, OL

description: NDMM2, OL

source_name: Left humerus

value: Left humerus


title: Cther, lib697, 50C, Mock, TGIRT, rep2

description: Library name: Sample 58

value: WT


title: NDMM2, BM

description: NDMM2, BM


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

description: Library name: Sample 70


title: Sente, lib553, OD2_37C, Bisulfite, TGIRT, rep2

description: Library name: Sample 180


title: Sente, lib553, OD2_37C, Bisulfite, TGIRT, rep1

description: Library name: Sample 179


title: NDMM5, OL

description: NDMM5, OL

source_name: Left scapula

value: Left scapula


title: Cther, lib697, 50C, Mock, TGIRT, rep1

description: Library name: Sample 57

value: Bacterial culture


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

description: Library name: Sample 69

value: KOD1 substrain TS559


title: Sente, lib553, OD2_30C, Bisulfite, TGIRT, rep2

description: Library name: Sample 178


title: Cther, lib697, 60C, Bisulfite, TGIRT, rep2

description: Library name: Sample 56


title: Sente, lib553, OD2_30C, Bisulfite, TGIRT, rep1

description: Library name: Sample 177


title: Cther, lib697, 60C, Bisulfite, TGIRT, rep1

description: Library name: Sample 55


title: NDMM5, BM

description: NDMM5, BM


title: RRMM1, OL

description: RRMM1, OL

source_name: Lumbar bone

value: Lumbar bone


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

description: Library name: Sample 67


title: Sente, lib553, OD2_25C, Bisulfite, TGIRT, rep2

description: Library name: Sample 176


title: Cther, lib697, 60C, Mock, TGIRT, rep2

description: Library name: Sample 60


title: Cther, lib697, 50C, Bisulfite, TGIRT, rep2

description: Library name: Sample 54


title: Cther, lib697, 50C, Bisulfite, TGIRT, rep1

description: Library name: Sample 53


title: RRMM1, BM

description: RRMM1, BM


title: Cther, lib697, 60C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 52


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

description: Library name: Sample 66


title: Sente, lib553, OD2_25C, Bisulfite, TGIRT, rep1

description: Library name: Sample 175


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

description: Library name: Sample 65


title: Sente, lib553, OD1_37C, Bisulfite, TGIRT, rep2

description: Library name: Sample 174


title: NDMM4, OL

description: NDMM4, OL

source_name: Right Illiac lesion

value: Right Illiac lesion


title: Tkoda, lib524, 95deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 64


title: NDMM4, BM

description: NDMM4, BM


title: Sente, lib553, OD1_30C, Bisulfite, TGIRT, rep2

description: Library name: Sample 172


title: NDMM3, BM

description: NDMM3, BM


title: Cther, lib697, 50C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 50


title: Cther, lib697, 60C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 51


title: Cther, lib697, 50C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 49


title: Sente, lib553, OD1_37C, Bisulfite, TGIRT, rep1

description: Library name: Sample 173


title: Tkoda, lib524, 95deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 63


title: RRMM6, OL

description: RRMM6, OL


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

description: Library name: Sample 68


title: Sente, lib553, OD1_25C, Bisulfite, TGIRT, rep2

description: Library name: Sample 170


title: Cther, lib697, 60C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 48


title: RRMM6, BM

description: RRMM6, BM


title: Sente, lib553, OD1_25C, Bisulfite, TGIRT, rep1

description: Library name: Sample 169


title: Tkoda, lib524, 85deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 61


title: RRMM2, BM

description: RRMM2, BM


title: RRMM3, OL

description: RRMM3, OL

source_name: Ninth thoracic vertebra (T9)

value: Ninth thoracic vertebra (T9)


title: Tkoda, lib524, 65deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 58


title: Sente, lib553, OD2_37C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 167


title: Cther, lib697, 50C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 45


title: Sente, lib553, OD2_37C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 168


title: Tkoda, lib524, 75deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 60


title: Tkoda, lib524, 75deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 59


title: RRMM3, BM

description: RRMM3, BM


title: NDMM3, OL

description: NDMM3, OL

source_name: Lung

value: Lung


title: Tkoda, lib524, 85deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 62


title: Sente, lib553, OD1_30C, Bisulfite, TGIRT, rep1

description: Library name: Sample 171


title: Sente, lib553, OD2_30C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 166


title: Cther, lib697, 50C, CMC, TGIRT, rep2

description: Library name: Sample 42


title: NDMM1, OL

description: NDMM1, OL

source_name: Right hip lesion

value: Right hip lesion


title: Cther, lib697, 60C, CMC, TGIRT, rep1

description: Library name: Sample 43


title: Cther, lib697, 60C, CMC, TGIRT, rep2

description: Library name: Sample 44


title: Sente, lib553, OD2_25C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 163


title: Sente, lib553, OD2_30C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 165


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

description: Library name: Sample 54


title: Sente, lib553, OD2_25C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 164


title: RRMM5, OL

description: RRMM5, OL

source_name: Right acetabulum

value: Right acetabulum


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

description: Library name: Sample 56


title: Tkoda, lib524, 65deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 57


title: Cther, lib697, 50C, CMC, TGIRT, rep1

description: Library name: Sample 41


title: RRMM4, OL

description: RRMM4, OL

source_name: Lumber bone # 3

value: Lumber bone # 3


title: Cther, lib697, 60C, AlkBmix, TGIRT, rep1

description: Library name: Sample 39


title: RRMM4, BM

description: RRMM4, BM


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

description: Library name: Sample 52


title: RRMM5, BM

description: RRMM5, BM


title: Cther, lib697, 60C, AlkBmix, TGIRT, rep2

description: Library name: Sample 40


title: Sente, lib553, OD1_37C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 161


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

description: Library name: Sample 51


title: Sente, lib553, OD1_37C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 162


title: Cther, lib697, 50C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 46


title: Cther, lib697, 60C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 47


title: NDMM1, BM

description: NDMM1, BM


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

description: Library name: Sample 55


title: Sente, lib553, OD1_30C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 160


title: RRMM7, BM

description: RRMM7, BM


title: Cther, lib697, 50C, AlkBmix, TGIRT, rep2

description: Library name: Sample 38


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

description: Library name: Sample 50


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

description: Library name: Sample 49


title: Cther, lib697, 50C, AlkBmix, TGIRT, rep1

description: Library name: Sample 37


title: Sente, lib553, OD1_25C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 158


title: RRMM7, OL

description: RRMM7, OL

source_name: Lumber bone # 4

value: Lumber bone # 4


title: Sente, lib553, OD1_30C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 159


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

description: Library name: Sample 53


title: HC3, BM

description: Healthy control 3


title: Sente, lib553, OD1_25C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 157


title: Cther, lib697, 60C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 36


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

description: Library name: Sample 47


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

description: Library name: Sample 48


title: HC1, BM

description: Healthy control 1


title: Cther, lib697, 60C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 35


title: Sente, lib553, OD2_37C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 155


title: Tkoda, lib524, 85deg, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 46


title: Cther, lib697, 50C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 34


title: Tkoda, lib524, 85deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 45


title: Sente, lib553, OD2_30C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 154


title: Sente, lib553, OD2_37C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 156


title: Cther, lib697, 50C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 33


title: HC2, BM

description: Healthy control 2


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

description: Library name: Sample 9


title: Cther, lib697, 60C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 32


title: centipede, antennae, replicate-2

city: Harbin

first: Wenqi

last: Dong

state: Heilongjiang

address: 26 Hexing Road, Wenzheng Street

institute: Northeast Forestry University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using 10× Genomics CellRanger pipeline (version 7.0.1).
Assembly: centipede genome v1.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Scolopendra mutilans

source_name: antennae

extract_protocol:
Frozen tissues were dounce homogenized on ice in 3 mL lysis buffer with 10 strokes of the loose pestle, followed by 5 strokes with the tight pestle. The samples were lysed in 5 mL lysis buffer for 5 minutes, followed by the addition of 5 ml wash buffer. Cell lysates were passed through a 30-μm cell strainer and centrifuged at 500×g for 5 minutes at 4℃. The resulting pellets were resuspended in 5–10 ml wash buffer. After three washes, the nuclei were resuspended in 1 ml wash buffer and mixed with 25% OptiPrep. This mixture was layered on a 29% OptiPrep cushion and centrifuged at 10,000×g for 30 minutes at 4 ℃. The nuclei pellet was then carefully resuspended in wash buffer. Nuclei were counted using a LUNA cell counter with AO/PI fluorescent staining and observed under a microscope to assess their integrity. Finally, the nuclei were resuspended in nuclei resuspension buffer at a concentration of ~1×10^6/mL.
RNA from the barcoded cells was subsequently reverse-transcribed, and sequencing libraries were constructed with reagents from a Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics) according to the manufacturer’s instructions.

value: antennae

tag: Sex

value: female


title: centipede, antennae, replicate-3


title: Tkoda, lib524, 75deg, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 44


title: Sente, lib553, OD2_30C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 153


title: Cther, lib697, 60C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 31


title: Scere, lib726, KO.95C.tkMET.95C, Bisulfite, TGIRT, rep1

description: Library name: Sample 14

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_000146045.2, GCF_008245085.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism:
Pyrococcus furiosus
Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: P. furiosus strain VC1 ΔRsmB was cultivated anaerobically in ½ SME medium as described in (Blöchl, E. et al., 1997). The medium contained 0.1 % (w/v) starch, 0.1 % (w/v) yeast extract (YE) and 0.1 % (w/v) peptone, the pH value was set to 7.0 and the gas phase consisted of N2 (200 kPa). The cells were grown in 95°C to the late exponential growth phase and harvested by centrifugation at 10,000 x g. Yeast - S. cerevisiae BY4741 cells derived from the S288C lab strain were grown at 30°C overnight in YPD 2% medium, diluted in fresh YPD and grown to log phase. The cells were spun down in a chilled centrifuge and flash frozen in liquid nitrogen.

extract_protocol:
P. furiosus - Cell pellets were washed with 1x PBS and centrifuged 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. Yeast RNA was extracted using the MasterPure Yeast RNA purification kit (Biosearch Technologies), by the manufacturer’s instructions.
The samples were cleaned on a Zymo Research RNA Clean & Concentrator-5 kit (Zymo research). 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: Cell culture

value: WT; (delta)RsmB


title: Tkoda, lib524, 65deg, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 42


title: centipede, antennae, replicate-1


title: Sente, lib553, OD2_25C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 152


title: Cther, lib697, 50C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 30


title: Tkoda, lib524, 75deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 43


title: Scere, lib726, KO.95C.tkMET.85C, Bisulfite, TGIRT, rep1

description: Library name: Sample 13


title: Cther, lib697, 50C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 29


title: Tkoda, lib524, 95deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 40


title: Sente, lib553, OD1_37C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 149


title: Scere, lib726, KO.95C.tkMET.75C, Bisulfite, TGIRT, rep1

description: Library name: Sample 12


title: Tkoda, lib524, 95deg, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 39


title: Cther, lib697, 60C, Mock, SSIII, rep1

description: Library name: Sample 27


title: Tkoda, lib524, 65deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 41


title: Cther, lib697, 60C, Mock, SSIII, rep2

description: Library name: Sample 28


title: Sente, lib553, OD1_30C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 148


title: Tkoda, lib524, 85deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 38


title: Scere, lib726, KO.95C.tkMET.37C, Bisulfite, TGIRT, rep1

description: Library name: Sample 9


title: Scere, lib726, KO.95C.tkMET.105C, Bisulfite, TGIRT, rep1

description: Library name: Sample 8


title: Cther, lib697, 50C, Mock, SSIII, rep1

description: Library name: Sample 25


title: Cther, lib697, 50C, Mock, SSIII, rep2

description: Library name: Sample 26


title: Tkoda, lib524, 85deg, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 37


title: Sente, lib553, OD1_30C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 147


title: Cther, lib697, 60C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 24


title: Sente, lib553, OD1_25C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 146


title: Sente, lib553, OD2_25C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 151


title: Scere, lib726, KO.95C.pfuMET.95C, Bisulfite, TGIRT, rep1

description: Library name: Sample 7

value: Pfu-RsmB


title: Scere, lib726, KO.95C.pfuMET.85C, Bisulfite, TGIRT, rep1

description: Library name: Sample 6


title: Tkoda, lib524, 75deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 36

value: WT


title: Sente, lib553, OD1_37C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 150


title: Cther, lib697, 60C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 23


title: Sente, lib553, OD1_25C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 145


title: Scere, lib726, KO.95C.tkMET.55C, Bisulfite, TGIRT, rep1

description: Library name: Sample 10


title: Tkoda, lib524, 75deg, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 35


title: Cther, lib697, 50C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 22


title: Sente, lib553, OD2_37C, CMC, TGIRT, rep2

description: Library name: Sample 144


title: Cther, lib697, 50C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 21


title: Tkoda, lib524, 65deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 34


title: Scere, lib726, KO.95C.pfuMET.55C, Bisulfite, TGIRT, rep1

description: Library name: Sample 4


title: Tkoda, lib524, 65deg, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 33


title: Sente, lib553, OD2_37C, CMC, TGIRT, rep1

description: Library name: Sample 143


title: Scere, lib726, KO.95C.pfuMET.37C, Bisulfite, TGIRT, rep1

description: Library name: Sample 3


title: Cther, lib697, 60C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 20


title: Cther, lib697, 60C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 19


title: Scere, lib726, KO.95C.pfuMET.105C, Bisulfite, TGIRT, rep1

description: Library name: Sample 2


title: Sente, lib553, OD2_25C, CMC, TGIRT, rep2

description: Library name: Sample 140


title: Cther, lib697, 50C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 18


title: Sente, lib553, OD2_30C, CMC, TGIRT, rep1

description: Library name: Sample 141


title: Scere, lib726, KO.95C.noEnzyme.4C, Bisulfite, TGIRT, rep1

description: Library name: Sample 1

value: No enzyme


title: Tkoda, lib524, 95deg, CMC, SSIII, rep1

description: Library name: Sample 31

value: Bacterial culture


title: Sente, lib553, OD2_25C, CMC, TGIRT, rep1

description: Library name: Sample 139


title: Tkoda, lib524, 85deg, CMC, SSIII, rep2

description: Library name: Sample 30

value: KOD1 substrain TS559


title: Cther, lib697, 50C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 17


title: Cther, lib697, 60C, CMC, SSIII, rep2

description: Library name: Sample 16


title: Cther, lib697, 60C, CMC, SSIII, rep1

description: Library name: Sample 15


title: Scere, lib726, KO.95C.pfuMET.75C, Bisulfite, TGIRT, rep1

description: Library name: Sample 5


title: Sente, lib553, OD2_30C, CMC, TGIRT, rep2

description: Library name: Sample 142


title: Sente, lib553, OD1_37C, CMC, TGIRT, rep1

description: Library name: Sample 137


title: Pfuri, lib524, 95deg, CMC, TGIRT, rep1

description: Library name: Sample 71

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_008245085.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Pyrococcus furiosus

growth_protocol: Cultivated anaerobically in ½ SME medium as described in (Blöchl et al. 1997). If not otherwise stated, the medium contained 0.1 % (w/v) starch, 0.1 % (w/v) yeast extract (YE) and 0.1 % (w/v) peptone, the pH value was set to 7.0 and the gas phase consisted of N2 (200 kPa). The standard temperature for cultivation was 85 °C. For RNA preparation cells were grown in duplicates at 78 °C, 95 °C and 102 °C to the late exponential growth phase and harvested by centrifugation at 10,000 x g


title: Pfuri, lib524, 95deg, CMC, TGIRT, rep2

description: Library name: Sample 72


title: Tkoda, lib524, 95deg, CMC, SSIII, rep2

description: Library name: Sample 32


title: Sente, lib553, OD1_30C, CMC, TGIRT, rep2

description: Library name: Sample 136


title: Pfuri, lib524, 78deg, CMC, TGIRT, rep2

description: Library name: Sample 70


title: Cther, lib697, 50C, CMC, SSIII, rep2

description: Library name: Sample 14


title: Sente, lib553, OD1_30C, CMC, TGIRT, rep1

description: Library name: Sample 135


title: Tkoda, lib524, 75deg, CMC, SSIII, rep1

description: Library name: Sample 27


title: Pfuri, lib524, 78deg, CMC, TGIRT, rep1

description: Library name: Sample 69


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

description: Library name: Sample 68


title: Cther, lib697, 50C, CMC, SSIII, rep1

description: Library name: Sample 13


title: Sente, lib553, OD1_25C, CMC, TGIRT, rep2

description: Library name: Sample 134


title: Cther, lib697, 60C, NaCNBH3, SSIII, rep2

description: Library name: Sample 12


title: Tkoda, lib524, 85deg, CMC, SSIII, rep1

description: Library name: Sample 29


title: Sente, lib553, OD1_25C, CMC, TGIRT, rep1

description: Library name: Sample 133


title: Cther, lib697, 60C, NaCNBH3, SSIII, rep1

description: Library name: Sample 11


title: Tkoda, lib524, 95deg, NaCNBH3, SSIII, rep2

description: Library name: Sample 24


title: Tkoda, lib524, 95deg, NaCNBH3, SSIII, rep1

description: Library name: Sample 23


title: Pfuri, lib524, 95deg, AlkBmix, TGIRT, rep2

description: Library name: Sample 66


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

description: Library name: Sample 67


title: Tkoda, lib524, 65deg, CMC, SSIII, rep1

description: Library name: Sample 25


title: Sente, lib553, OD1_37C, CMC, TGIRT, rep2

description: Library name: Sample 138


title: Sente, lib553, OD2_37C, AlkBmix, TGIRT, rep2

description: Library name: Sample 132


title: Tkoda, lib524, 75deg, CMC, SSIII, rep2

description: Library name: Sample 28


title: Tkoda, lib524, 85deg, NaCNBH3, SSIII, rep2

description: Library name: Sample 22


title: Cther, lib697, 50C, NaCNBH3, SSIII, rep2

description: Library name: Sample 10


title: Pfuri, lib524, 95deg, AlkBmix, TGIRT, rep1

description: Library name: Sample 65


title: Sente, lib553, OD2_37C, AlkBmix, TGIRT, rep1

description: Library name: Sample 131


title: Cther, lib697, 50C, NaCNBH3, SSIII, rep1

description: Library name: Sample 9


title: Tkoda, lib524, 65deg, CMC, SSIII, rep2

description: Library name: Sample 26


title: Pfuri, lib524, 78deg, AlkBmix, TGIRT, rep2

description: Library name: Sample 64


title: Sente, lib553, OD2_30C, AlkBmix, TGIRT, rep2

description: Library name: Sample 130


title: Pfuri, lib524, 78deg, AlkBmix, TGIRT, rep1

description: Library name: Sample 63


title: Sente, lib553, OD2_30C, AlkBmix, TGIRT, rep1

description: Library name: Sample 129


title: Tkoda, lib524, 75deg, NaCNBH3, SSIII, rep2

description: Library name: Sample 20


title: Tkoda, lib524, 85deg, NaCNBH3, SSIII, rep1

description: Library name: Sample 21


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

description: Library name: Sample 62


title: Sente, lib553, OD2_25C, AlkBmix, TGIRT, rep2

description: Library name: Sample 128


title: Cther, lib697, 50C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 6


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

description: Library name: Sample 61


title: Cther, lib697, 50C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 5


title: Tkoda, lib524, 65deg, NaCNBH3, SSIII, rep2

description: Library name: Sample 18


title: Sente, lib553, OD1_37C, AlkBmix, TGIRT, rep2

description: Library name: Sample 126


title: Tkoda, lib524, 65deg, NaCNBH3, SSIII, rep1

description: Library name: Sample 17


title: Pfuri, lib524, 95deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 59


title: Cther, lib697, 60C, Mock, RTHIV, rep2

description: Library name: Sample 4


title: Sente, lib553, OD2_25C, AlkBmix, TGIRT, rep1

description: Library name: Sample 127


title: Sente, lib553, OD1_37C, AlkBmix, TGIRT, rep1

description: Library name: Sample 125


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

description: Library name: Sample 16


title: Cther, lib697, 60C, Mock, RTHIV, rep1

description: Library name: Sample 3


title: Pfuri, lib524, 78deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 58


title: Cther, lib697, 60C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 8


title: Sente, lib553, OD1_30C, AlkBmix, TGIRT, rep2

description: Library name: Sample 124


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

description: Library name: Sample 15


title: Cther, lib697, 50C, Mock, RTHIV, rep2

description: Library name: Sample 2


title: Cther, lib697, 60C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 7


title: Pfuri, lib524, 78deg, NaCNBH3, TGIRT, rep1

description: Library name: Sample 57


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

description: Library name: Sample 14


title: Sente, lib553, OD1_25C, AlkBmix, TGIRT, rep2

description: Library name: Sample 122


title: Tkoda, lib524, 75deg, NaCNBH3, SSIII, rep1

description: Library name: Sample 19


title: Cther, lib697, 50C, Mock, RTHIV, rep1

description: Library name: Sample 1


title: Sente, lib553, OD1_30C, AlkBmix, TGIRT, rep1

description: Library name: Sample 123


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

description: Library name: Sample 55


title: Pfuri, lib524, 95deg, NaCNBH3, TGIRT, rep2

description: Library name: Sample 60


title: HMSC.plate3

city: Jerusalem

first: Avishai

last: Wizel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

institute: The Hebrew University of Jerusalem

description: Library name: HMSC.P3

data_processing:
scRNA-seq data were aligned to GRCh38 with STAR42 and counted with featureCounts.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HPV-associated multiphenotypic sinonasal carcinoma

extract_protocol:
Samples were minced and dissociated with a Human Tumor Dissociation Kit (Miltenyi Biotec) according to manufacturer guidelines. Single cell suspensions were filtered, and cells were resuspended in PBS with 1% bovine serum albumin (BSA; Sigma-Aldrich). Trypan blue (ThermoFisher Scientific) was used to confirm cell viability of > 90% in all samples. Cells were stained with CD45-vioblue (Miltenyi Biotec), as well as 1 μM calcein AM (ThermoFisher Scientific), and 0.22 μM TO-PRO-3 iodide (ThermoFisher Scientific) for viability prior to sorting. Fluorescence-activated cell sorting (FACS) was performed on FACSAria Fusion Special Order System (BD Biosciences) using 488 nm (calcein AM, 530/30 filter), 640 nm (TO-PRO-3, 670/14 filter), and 405 nm (Vioblue, 450/50 filter) lasers. We captured singlet viable cells using standard forward scatter height versus area criteria, as well as calceinhigh and TO-PROlow gates. Subsquently, CD45- cells were captured to enrich for cancer cells and deplete immune cells. Individual cells were sorted into TCL- buffer (QIAGEN) with 1% β-mercaptoethanol in 96-well plates. Plates were snap frozen and stored at -80oC before cDNA synthesis and library construction.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol, with the following modifications: Agencourt RNAClean XP beads (Beckman Coulter) was used to purify RNA prior to reverse transcription with Superscript II (ThermoFisher Scientific) or Maxima (ThermoFisher Scientific) reverse transcriptase. Whole transcriptome amplification was performed using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems).

tag: site

value: Nasal cavity and paranasal sinuses

tag: histology

value: Salivary type carcinoma resembling solid-type adenoid cystic carcinoma

tag: ihc profile

value: Positive for p16, p63 (multifocal), MYB (multifocal). PCR positive for HPV33.

tag: perineural invasion

value: Present

tag: lymphovascular invasion


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

description: Library name: Sample 13

source_name: Bacterial culture


title: HMSC.plate2

description: Library name: HMSC.plate2

value: HPV-associated multiphenotypic sinonasal carcinoma


title: Sente, lib553, OD2_37C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 120


title: Sente, lib553, OD1_25C, AlkBmix, TGIRT, rep1

description: Library name: Sample 121


title: Pfuri, lib524, 95deg, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 53


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

description: Library name: Sample 11


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

description: Library name: Sample 10


title: CD3e-CD28

city: Shen Zhen

first: Rui

last: Li

state: NY

address: SZ

institute: BME

description: Library name: Sample 5

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and low-quality nucleotides using Trimmomatic v0.36. The trimmed reads were aligned to the Homo sapiens GRCh38 reference genome (ENSEMBL release) using the STAR aligner v2.5.2b, a splice-aware aligner that detects splice junctions and incorporates them to improve full-length read alignment. BAM files were generated during this alignment step. Unique gene hit counts were calculated using featureCounts from the Subread package v1.5.2, summarizing reads based on the gene_id annotation feature. Only uniquely mapped reads falling within annotated exon regions were counted. For strand-specific libraries, reads were counted according to their strand orientation. To estimate the expression levels of alternatively spliced transcripts, splice variant hit counts were extracted from genome-aligned RNA-seq reads. Differential splicing analysis was performed using DEXSeq, comparing exon and junction read counts between groups when multiple samples were available. For groups with only a single sample, exon-level hit count tables were generated and provided.
Assembly: Homo sapiens reference genome GRCh38, ENSEMBL release
Supplementary files format and content: Gene-level count matrix (.txt format): Rows represent genes; columns represent sample identifiers; entries are raw counts of uniquely mapped exon reads.

source_name: peripheral blood

growth_protocol: All CAR T Cells were cultured in ImmunoCult-XF T Cell Expansion Medium (Cat#10981, StemCell Technologies) supplemented with IL-2 (200 IU/mL, Cat#200-02, Peprotech) in a 37 °C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from CAR T cell samples using a Qiagen AllPrep Mini Kit, incorporating an on-column DNaseI treatment step per the manufacturer's guidelines. The isolated RNAs were eluted in nuclease-free water, subjected to validation for quality and quantity via UV spectrophotometry, and stored at −80 °C. The total RNA samples underwent Bioanalyzer quality control analysis using Agilent's Bioanalyzer technology.
Total RNA samples were processed by first performing ribosomal RNA (rRNA) depletion to remove abundant rRNA species and enrich for non-ribosomal transcripts. The depleted RNA was fragmented and primed with random hexamers for first-strand cDNA synthesis, followed by second-strand synthesis to generate double-stranded cDNA. End repair, 5′ phosphorylation, and 3′ adenylation were performed to prepare cDNA fragments for adapter ligation. Sequencing adapters were ligated to both ends of the cDNA fragments, and the resulting libraries were amplified by PCR. Final libraries were quantified and validated for size distribution and integrity. Libraries were sequenced on an Illumina HiSeq platform with paired-end 150 bp reads (2×150 bp).

value: peripheral blood

value: CAR T cells

value: Activated by CD3e and CD28


title: CD19

description: Library name: Sample 4

value: Activated by CD19 only


title: Pfuri, lib524, 95deg, Bisulfite+MgCl2+Heat, SSIII, rep2

description: Library name: Sample 54


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

description: Library name: Sample 9


title: Sente, lib553, OD2_30C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 117


title: Pfuri, lib524, 78deg, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 51


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

description: Library name: Sample 56


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

description: Library name: Sample 50


title: ICAM1-CD19

description: Library name: Sample 3

value: Activated by ICAM1 and CD19


title: Sente, lib553, OD2_30C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 118


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

description: Library name: Sample 8


title: ICAM1_R1_001.fastq

description: Library name: Sample 2

value: Activated by ICAM1 only


title: Pfuri, lib524, 78deg, Bisulfite+MgCl2+Heat, SSIII, rep2

description: Library name: Sample 52


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

description: Library name: Sample 49


title: BLANK_1_2

description: Library name: Sample 1

value: No treatment


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

description: Library name: Sample 12


title: Sente, lib553, OD2_25C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 116


title: Sente, lib553, OD1_37C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 114


title: PEO1-2

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

description: PEO1 parental

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC hg19 with default parameters.
Reads that aligned to the human genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Assembly: hg19
Supplementary files format and content: raw counts in tab-delimited text file

source_name: Ovary

growth_protocol: PEO1 and ABTR clones were grown in DMEM with 10% heat-inactivated Fetal Bovine Serum (FBS), 100 𝜇M nonessential amino acids, 10 𝜇g/mL insulin, 100 units/mL penicillin G, 100 𝜇g/mL streptomycin, and 2 mM glutamine

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: ABTR clones were treated continuously with 40 𝜇M veliparib for 6 months and removed from drug 4-5 days before RNA collection

value: Ovary

value: epithelial

value: Parental


title: Sente, lib553, OD2_37C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 119

value: Bacterial culture

value: WT


title: Pfuri, lib524, 95deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 47


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

description: Library name: Sample 7

value: KOD1 substrain TS559


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

description: Library name: Sample 5


title: Pfuri, lib524, 95deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 48


title: Sente, lib553, OD1_37C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 113


title: Complicated malaria (cerebral malaria) vs Uncomplicated malaria

type: genomic

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: The labeled DNA samples were hybridized on a Genotypic designed P. vivax 2x400K CGH microarray (AMADID: 25335). 5 micrograms of cy3 and cy5 labeled samples were hybridized.  Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 40 hours. The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22)

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C

data_processing: Raw data was analyzed using Agilent Genomic Workbench Software 7.0.

molecule: genomic DNA

organism: Plasmodium vivax

source_name: P. vivax patient material

label_protocol: The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 2 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 and Cy5 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.

extract_protocol: Total DNA was isolated from samples using manufacture’s protocol (TRI- Reagent, Sigma Aldrich, and USA).

tag: P. vivax patient isolate showing Uncomplicated disease

value: P. vivax patient isolates showing Complicated disease


title: ABTr4-2

description: ABTR clone #3

value: Veliparib resistant

value: Clones were treated continuously with 40 𝜇M veliparib for 6 months and removed from drug 4-5 days before RNA collection


title: Sente, lib553, OD1_30C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 112


title: Pfuri, lib524, 78deg, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 45


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

description: Library name: Sample 3


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

description: Library name: Sample 6


title: PEO1-1

description: PEO1 parental


title: Sente, lib553, OD2_25C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 115


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

description: Library name: Sample 2


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

description: Library name: Sample 44


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

description: Library name: Sample 1


title: Pfuri, lib524, 78deg, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 46


title: Sente, lib553, OD1_25C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 110


title: Sente, lib553, OD1_30C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 111


title: ABTr4-1

description: ABTR clone #3


title: MR_100-50_3

city: Viçosa

first: Maria Malane

middle: M

last: Muniz

state: MG

address: Av Peter Henry Rolfs S

department: Animal Science

country: Brazil

institute: University Federal of Vicosa

description:
Library name: Sample 3
Column C in FPKM_counts_all_samples.txt: Sample_3

data_processing:
reads trimming was performed using Trimmomatic, including the following parameters: removing adapter sequences, leading low-quality or N bases with a quality score below 20, trailing low-quality or N bases with a quality score below 15, and scanning the reads with a 4-base wide sliding window to cut when the average quality per base dropped below 15.
HISAT2 (v.2.0.5)
trimmed reads were aligned to Capra hircus. ARS1.112 using the HISAT2 (v.2.0.5) software with the parameters “-dta” for the de novo discovery of splice sites and “-known-splicesite-infile” provided with a list of known splice sites to facilitate aligning reads with small anchors, small-anchor-fraction 0.08, -min-isoform-fraction 0.20, -max-intron-length 300000, -overlap-radius 25, -max-bundle-frags 2000000, -trim-3-avgcov-thresh 0.05, -junc-alpha 0.001, and pre-mrna-fraction 0.15
Assembly: Capra hircus. ARS1.112
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: txt file includes FPKM values for each Sample

organism: Capra hircus

source_name: Longissimus thoracis muscle

extract_protocol:
Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (Qiagen Inc., Germantown, MD, USA) following the manufacturer’s recommendation
RNA-Seq libraries were prepared, and sequencing was performed using the Illumina HiSeq 4000 platform, generating 150 bp paired-end reads with an average of approximately 23 million raw reads per sample

value: Longissimus thoracis muscle

value: Maintenance-Restriction (MR) :fed 100% of maintenance requirements from days 8–84, followed by 50% from day 85 to parturition.


title: ABTr3-2

description: ABTR clone #2


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

description: Library name: Sample 43


title: Pfuri, lib524, 95deg, Mock, SSIII, rep2

description: Library name: Sample 42


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

description: Library name: Sample 4

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


title: ABTr3-1

description: ABTR clone #2


title: Sente, lib553, OD1_25C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 109


title: MR_100-50_1

description:
Library name: Sample 1
Column B in FPKM_counts_all_samples.txt: Sample_1


title: Sente, lib553, OD2_37C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 108


title: RM_50-100_15

description:
Library name: Sample 15
Column O in FPKM_counts_all_samples.txt: Sample_15

value: Restriction-Maintenance (RM) :fed 50% of maintenance requirements from days 8–84 of gestation, followed by 100% from day 85 to parturition.


title: ABTr2-2

description: ABTR clone #1


title: Pfuri, lib524, 95deg, Mock, SSIII, rep1

description: Library name: Sample 41


title: ABTr2-1

description: ABTR clone #1


title: Sente, lib553, OD2_37C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 107


title: RM_50-100_14

description:
Library name: Sample 14
Column N in FPKM_counts_all_samples.txt: Sample_14


title: Pfuri, lib524, 78deg, Mock, SSIII, rep2

description: Library name: Sample 40


title: ABTr1-2

description: ABTR clone #4


title: Sente, lib553, OD2_30C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 106


title: RM_50-100_13

description:
Library name: Sample 13
Column M in FPKM_counts_all_samples.txt: Sample_13


title: Pfuri, lib524, 78deg, Mock, SSIII, rep1

description: Library name: Sample 39


title: ABTr1-1

description: ABTR clone #4


title: Sente, lib553, OD2_30C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 105


title: Sente, lib553, OD2_25C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 104


title: S93 (53B_39b)

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
Library name: S93
S93

library_source: genomic

data_processing:
Sequencing was carried out on the Illumina MiSeq platform using the MiSeq Reagent Kit v2 (500 cycles; 2 × 250 bp paired-end reads).
Base calls were processed using bcl2fastq v2.2
Paired-end raw reads wre processed using a custom QIIME2 pipeline. Briefly, sequences were trimmed with cutadapt algorithm, paired ends were merged with vsearch algoritm, filtered using qfilter algorithm, and chimera-checked. Greengenes2 2022.10 database was used to construct the reference sequence file, on which the Naïve Bayes classifier was trained and then used to perform taxonomic assignment to the species level using representative sequences from each operational taxonomic unit (OTU).
Assembly: Greengenes2 2022.10 database
Supplementary files format and content: We provide comma-separated value files with counts of bacterial operational taxonomic units (OTUs) at different phylogenetic levels, from phylum to species level, for each sample. Samples are in rows, and OTU names are in columns. The first column in each csv file contains the sample ID.
Library strategy: 16S rRNA-seq

source_name: fecal samples

growth_protocol: Fecal samples were collected in sterile biopure tubes, directly from the rectum of the mouse

extract_protocol:
We extracted total bacterial DNA with QiaAMP Fast DNA stool Mini kit (Qiagen # 51604) according to the manufacturer’s instructions. In the final step DNA was eluted in 80ul AE elution buffer.
Amplicons targeting the V4 region of the bacterial 16S rRNA gene were generated using KOD One PCR Master Mix (Sigma-Aldrich) and universal primers 515F and 806R. The forward primer sequence was 5′-AATGATACGGCGACCACCGAGATCTACAC-TATGGTAATT-GT-GTGCCAGCMGCCGCGGTAA-3′, and the reverse primer was 5′-CAAGCAGAAGACGGCATACGAGAT-NNNNNNNNNNNN-AGTCAGTCAG-CC-GGACTACHVGGGTWTCTAAT-3′. These primers included the Illumina adapter sequences, a 12-bp Golay barcode (represented by ‘N’s) exclusive to the 3′ primer, pad, linker, and the locus-specific primer. PCR reactions were performed in duplicate and pooled. Amplicons were quantified using the Qubit dsDNA HS Assay Kit (Invitrogen) and pooled at equimolar concentrations. The final pooled library was purified using the GeneJET PCR Purification Kit (Thermo Scientific).

treatment_protocol: Chemotherapy cycle consisted of one intraperitoneal (i.p.) injection of oxaliplatin (3.5mg/kg, #2623, Tocris), followed 1 hour later by i.p. injection of 5-fluorouracil (5-FU, 50mg/kg, # F6627, SigmaAldrich) and a single dose of 5-FU (50mg/kg) the next day. Control mice received PBS or water treatment in the same treatment regimen as chemotherapy treated mice.

value: fecal samples

tag: timepoint

value: d5 post treatment

value: control


title: RM_50-100_6

description:
Library name: Sample 6
Column J in raw_counts_all_samples.txt: Sample_6


title: S94 (53B_40b)

description:
Library name: S94
S94


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

description: Library name: Sample 37


title: Pfuri, lib524, 95deg, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 36


title: RM_50-100_9

description:
Library name: Sample 9
Column K in FPKM_counts_all_samples.txt: Sample_9


title: S92 (53B_38b)

description:
Library name: S92
S92


title: Sente, lib553, OD1_37C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 101


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

description: Library name: Sample 38


title: Pfuri, lib524, 95deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 35


title: Sente, lib553, OD2_25C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 103


title: Sente, lib553, OD1_37C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 102


title: MR_100-50_20

description:
Library name: Sample 20
Column I in FPKM_counts_all_samples.txt: Sample_20


title: RM_50-100_12

description:
Library name: Sample 12
Column L in FPKM_counts_all_samples.txt: Sample_12


title: S89 (53B_35b)

description:
Library name: S89
S89

value: FO


title: S91 (53B_37b)

description:
Library name: S91
S91


title: MR_100-50_19

description:
Library name: Sample 19
Column H in FPKM_counts_all_samples.txt: Sample_19


title: Pfuri, lib524, 78deg, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 34


title: S90 (53B_36b)

description:
Library name: S90
S90


title: Sente, lib553, OD1_30C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 100


title: MR_100-50_17

description:
Library name: Sample 17
Column G in FPKM_counts_all_samples.txt: Sample_17


title: Sente, lib553, OD1_30C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 99


title: MR_100-50_7

description:
Library name: Sample 7
Column F in FPKM_counts_all_samples.txt: Sample_7


title: Pfuri, lib524, 78deg, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 33


title: S88 (53B_34b)

description:
Library name: S88
S88


title: Sente, lib553, OD1_25C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 98


title: MR_100-50_5

description:
Library name: Sample 5
Column E in FPKM_counts_all_samples.txt: Sample_5


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

description: Library name: Sample 32


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

description: Library name: Sample 31


title: S87 (53B_33b)

description:
Library name: S87
S87


title: Sente, lib553, OD1_25C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 97


title: Pfuri, lib524, 95deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 30


title: S86 (53B_32b)

description:
Library name: S86
S86


title: MR_100-50_4

description:
Library name: Sample 4
Column D in FPKM_counts_all_samples.txt: Sample_4


title: B16-OVA cells, KO.11_3

city: chongqing

first: Xue

last: Zhang

address: 2 Chongwen Road, Nanan District, Chongqing

institute: Chongqing University of Posts and Telecommunications

description:
Library name: B16OVA_KO.11_3
Column name in raw_counts_All_Samples.txt: B16OVA_KO.11_3

data_processing:
The raw sequencing data was qualitatively controlled with Fastp, which removed joints and filtered low-quality data to obtain relatively accurate and effective data.
HISAT2 was used to compare the valid data of the sample to the reference genome for statistical Mapping information.
According to the comparison results, the number of reads covered by each gene can be counted according to the location information of genes on the reference genome. Use Subread's featureCounts to calculate the amount of all genes expressed in each sample.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: B16-OVA cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and Penicillin-streptomycin(P/S) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA extraction from cells was used TRIzol™ (Invitrogen™ 15596026) and Direct-zol™ RNA Miniprep(zymo R2050). 0.2ug of total RNA was used for the construction of  sequencing libraries.
Based on the structural characteristics of polyA tail in most mRNA of eukaryotes, the mRNA with polyA tail was enriched by Oligo(dT) magnetic beads. Then, according to the process of library building kit, the first strand of cDNA was synthesized using fragmented mRNA as template and random oligonucleotides as primer, then the RNA strand was degraded by RNaseH, and the second strand of cDNA was synthesized using dNTPs as raw material under the DNA polymerase I system. After the purified double-stranded cDNA was end-repaired, A tail was added and a sequencing joint was connected, cDNA of about 150-200bp was screened, PCR amplification was performed and PCR products were purified again, and finally a library was obtained.

value: Murine Melanoma Cells

value: PUM1 knockput


title: Sente, lib553, OD2_37C, Mock, SSIII, rep2

description: Library name: Sample 96


title: Pfuri, lib524, 95deg, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 29


title: Sente, lib553, OD2_37C, Mock, SSIII, rep1

description: Library name: Sample 95


title: S85 (53B_31b)

description:
Library name: S85
S85


title: Pfuri, lib524, 78deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 28


title: Sente, lib553, OD2_30C, Mock, SSIII, rep2

description: Library name: Sample 94


title: B16-OVA cells, KO.11_2

description:
Library name: B16OVA_KO.11_2
Column name in raw_counts_All_Samples.txt: B16OVA_KO.11_2


title: S114 (56A_50b)

description:
Library name: S114
S114


title: Pfuri, lib524, 78deg, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 27


title: Sente, lib553, OD2_30C, Mock, SSIII, rep1

description: Library name: Sample 93


title: B16-OVA cells, KO.11_1

description:
Library name: B16OVA_KO.11_1
Column name in raw_counts_All_Samples.txt: B16OVA_KO.11_1


title: B16-OVA cells, KO.3_3

description:
Library name: B16OVA_KO.3_3
Column name in raw_counts_All_Samples.txt: B16OVA_KO.3_3


title: S113 (56A_49b)

description:
Library name: S113
S113


title: Sente, lib553, OD2_25C, Mock, SSIII, rep2

description: Library name: Sample 92


title: B16-OVA cells, KO.3_2

description:
Library name: B16OVA_KO.3_2
Column name in raw_counts_All_Samples.txt: B16OVA_KO.3_2


title: Sente, lib553, OD2_25C, Mock, SSIII, rep1

description: Library name: Sample 91


title: Pfuri, lib524, 102deg, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 25


title: S111 (56A_47b)

description:
Library name: S111
S111


title: Pfuri, lib524, 95deg, CMC, SSIII, rep2

description: Library name: Sample 24


title: S110 (56A_46b)

description:
Library name: S110
S110


title: Sente, lib553, OD1_37C, Mock, SSIII, rep2

description: Library name: Sample 90


title: B16-OVA cells, KO.3_1

description:
Library name: B16OVA_KO.3_1
Column name in raw_counts_All_Samples.txt: B16OVA_KO.3_1


title: B16-OVA cells, WT_3

description:
Library name: B16OVA_WT_3
Column name in raw_counts_All_Samples.txt: B16OVA_WT_3


title: Pfuri, lib524, 95deg, CMC, SSIII, rep1

description: Library name: Sample 23


title: Pfuri, lib524, 78deg, CMC, SSIII, rep2

description: Library name: Sample 22


title: S109 (56A_45b)

description:
Library name: S109
S109


title: Sente, lib553, OD1_37C, Mock, SSIII, rep1

description: Library name: Sample 89


title: Pfuri, lib524, 78deg, CMC, SSIII, rep1

description: Library name: Sample 21


title: B16-OVA cells, WT_1

description:
Library name: B16OVA_WT_1
Column name in raw_counts_All_Samples.txt: B16OVA_WT_1


title: Sente, lib553, OD1_30C, Mock, SSIII, rep2

description: Library name: Sample 88


title: S108 (56A_44b)

description:
Library name: S108
S108


title: B16-OVA cells, WT_2

description:
Library name: B16OVA_WT_2
Column name in raw_counts_All_Samples.txt: B16OVA_WT_2


title: S107 (56A_43b)

description:
Library name: S107
S107


title: Pfuri, lib524, 102deg, CMC, SSIII, rep2

description: Library name: Sample 20


title: Tacid, lib553, pH3, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 102

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_000195915.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Thermoplasma acidophilum

growth_protocol: was cultivated aerobically at 55°C in Darland medium (Darland et al. 1970). The medium contained 1 % (w/v) glucose and 0.1 % (w/v) yeast extract (YE) and the pH was adjusted using H2SO4. For RNA preparation cells were grown in duplicates at pH 1.0, pH 2.0 and pH 3.0 to the late exponential growth phase and harvested by centrifugation at 10,000 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: Sente, lib553, OD1_30C, Mock, SSIII, rep1

description: Library name: Sample 87

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_000210855.2
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position


title: Sente, lib553, OD1_25C, Mock, SSIII, rep2

description: Library name: Sample 86


title: Pfuri, lib524, 102deg, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 26


title: Sente, lib553, OD1_25C, Mock, SSIII, rep1

description: Library name: Sample 85


title: S112 (56A_48b)

description:
Library name: S112
S112


title: S105 (56A_41b)

description:
Library name: S105
S105


title: Sente, lib553, OD2_37C, Bisulfite, SSIII, rep2

description: Library name: Sample 84


title: Pfuri, lib524, 95deg, NaCNBH3, SSIII, rep2

description: Library name: Sample 18


title: Paeru, lib553, 42C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 136

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_000006765.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Pseudomonas aeruginosa

growth_protocol: Grown in duplicate at  25°C, 30°C, 37°C and 42°C. Cells were grown in over-night cultures at indicated temperatures in LB media at 220 rpm. Cultures were inoculated 1:100 and grown at indicated temperatures in LB media at 220 rpm. At indicated OD600, cells were harvested and RNA was extracted with the hot phenol method followed by RNA precipitation with ethanol/acetate


title: Pfuri, lib524, 95deg, NaCNBH3, SSIII, rep1

description: Library name: Sample 17


title: Pfuri, lib524, 78deg, NaCNBH3, SSIII, rep2

description: Library name: Sample 16


title: Tacid, lib553, pH1, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 98


title: Paeru, lib553, 42C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 135


title: Paeru, lib553, OD2_37C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 134


title: Sente, lib553, OD2_30C, Bisulfite, SSIII, rep2

description: Library name: Sample 82


title: Paeru, lib553, OD2_37C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 133


title: Pfuri, lib524, 102deg, NaCNBH3, SSIII, rep2

description: Library name: Sample 14


title: Tacid, lib553, pH1, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 97


title: Tacid, lib553, pH3, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 101


title: Pfuri, lib524, 102deg, NaCNBH3, SSIII, rep1

description: Library name: Sample 13


title: Tacid, lib553, pH3, Mock, TGIRT, rep1

description: Library name: Sample 95


title: Sente, lib553, OD2_30C, Bisulfite, SSIII, rep1

description: Library name: Sample 81


title: Sente, lib553, OD2_25C, Bisulfite, SSIII, rep2

description: Library name: Sample 80


title: Pfuri, lib524, 78deg, NaCNBH3, SSIII, rep1

description: Library name: Sample 15


title: S106 (56A_42b)

description:
Library name: S106
S106


title: Sente, lib553, OD2_25C, Bisulfite, SSIII, rep1

description: Library name: Sample 79


title: Pfuri, lib524, 102deg, CMC, SSIII, rep1

description: Library name: Sample 19


title: Paeru, lib553, OD2_30C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 132


title: Tacid, lib553, pH2, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 100


title: Pfuri, lib524, 95deg, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 12


title: Paeru, lib553, OD2_30C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 131


title: Tacid, lib553, pH2, Mock, TGIRT, rep2

description: Library name: Sample 94


title: Sente, lib553, OD1_37C, Bisulfite, SSIII, rep2

description: Library name: Sample 78


title: Tacid, lib553, pH2, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 99


title: Pfuri, lib524, 95deg, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 11


title: Tacid, lib553, pH2, Mock, TGIRT, rep1

description: Library name: Sample 93


title: Sente, lib553, OD2_37C, Bisulfite, SSIII, rep1

description: Library name: Sample 83


title: Sente, lib553, OD1_37C, Bisulfite, SSIII, rep1

description: Library name: Sample 77


title: Tacid, lib553, pH1, Mock, TGIRT, rep2

description: Library name: Sample 92


title: Pfuri, lib524, 78deg, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 10


title: Paeru, lib553, OD2_25C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 129


title: Tacid, lib553, pH3, Mock, TGIRT, rep2

description: Library name: Sample 96


title: Paeru, lib553, 42C, Mock, TGIRT, rep2

description: Library name: Sample 128


title: Sente, lib553, OD1_30C, Bisulfite, SSIII, rep2

description: Library name: Sample 76


title: Tacid, lib553, pH1, Mock, TGIRT, rep1

description: Library name: Sample 91


title: Pfuri, lib524, 78deg, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 9


title: Paeru, lib553, 42C, Mock, TGIRT, rep1

description: Library name: Sample 127


title: Sente, lib553, OD1_30C, Bisulfite, SSIII, rep1

description: Library name: Sample 75


title: Paeru, lib553, OD2_37C, Mock, TGIRT, rep1

description: Library name: Sample 125


title: Pfuri, lib524, 102deg, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 8


title: Paeru, lib553, OD2_37C, Mock, TGIRT, rep2

description: Library name: Sample 126


title: Sente, lib553, OD1_25C, Bisulfite, SSIII, rep2

description: Library name: Sample 74


title: Tacid, lib553, pH3, Bisulfite, TGIRT, rep2

description: Library name: Sample 90


title: Sente, lib553, OD1_25C, Bisulfite, SSIII, rep1

description: Library name: Sample 73


title: Tacid, lib553, pH2, Bisulfite, TGIRT, rep2

description: Library name: Sample 88


title: Tacid, lib553, pH3, Bisulfite, TGIRT, rep1

description: Library name: Sample 89


title: Paeru, lib553, OD2_30C, Mock, TGIRT, rep2

description: Library name: Sample 124


title: Pfuri, lib524, 95deg, Mock, RTHIV, rep2

description: Library name: Sample 6


title: Sente, lib553, OD2_37C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 72


title: Paeru, lib553, OD2_25C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 130


title: Pfuri, lib524, 102deg, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 7


title: Pfuri, lib524, 95deg, Mock, RTHIV, rep1

description: Library name: Sample 5


title: Sente, lib553, OD2_37C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 71


title: Tacid, lib553, pH2, Bisulfite, TGIRT, rep1

description: Library name: Sample 87


title: Paeru, lib553, OD2_30C, Mock, TGIRT, rep1

description: Library name: Sample 123


title: Pfuri, lib524, 78deg, Mock, RTHIV, rep2

description: Library name: Sample 4


title: Sente, lib553, OD2_30C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 70


title: Tacid, lib553, pH1, Bisulfite, TGIRT, rep2

description: Library name: Sample 86


title: Paeru, lib553, OD2_25C, Mock, TGIRT, rep2

description: Library name: Sample 122


title: Tacid, lib553, pH1, Bisulfite, TGIRT, rep1

description: Library name: Sample 85


title: Sente, lib553, OD2_30C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 69


title: Paeru, lib553, OD2_25C, Mock, TGIRT, rep1

description: Library name: Sample 121


title: Pfuri, lib524, 102deg, Mock, RTHIV, rep2

description: Library name: Sample 2


title: Paeru, lib553, 42C, Bisulfite, TGIRT, rep2

description: Library name: Sample 120


title: Pfuri, lib524, 102deg, Mock, RTHIV, rep1

description: Library name: Sample 1


title: Paeru, lib553, OD2_37C, Bisulfite, TGIRT, rep2

description: Library name: Sample 118


title: Tacid, lib553, pH3, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 83


title: Sente, lib553, OD1_37C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 66


title: Sente, lib553, OD2_25C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 67


title: Paeru, lib553, 42C, Bisulfite, TGIRT, rep1

description: Library name: Sample 119


title: Tacid, lib553, pH2, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 82


title: Sacid, lib553, pHunk_85C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 170

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_000012285.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Sulfolobus acidocaldarius

growth_protocol: Were grown in duplicates in Brock medium adjusted to pH 2, 3 (optimum) and 5, all at 75°C, as well as at low temperature (55°C) and high temperature (85°C) in Brock medium adjusted to pH 3 (optimum). Cells were kept in log phase by serial dilutions for several generations and harvested in log phase (OD600nm= ~0.5).


title: Sente, lib553, OD1_37C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 65