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

description: Library name: Sample 117


title: Sacid, lib553, pHunk_85C, NaBH4HydBiotin, 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 169

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_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

molecule: total RNA

organism: Sulfolobus acidocaldarius

source_name: Bacterial culture

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).

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).

tag: tissue

value: Bacterial culture

tag: strain

tag: genotype

value: WT

tag: treatment

tag: batch


title: Tacid, lib553, pH1, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 80

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, NaHCO3+Heat, SSIII, 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_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: Paeru, lib553, OD2_30C, Bisulfite, TGIRT, rep2

description: Library name: Sample 116

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: Sacid, lib553, pH5_75C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 168


title: Sacid, lib553, pH5_75C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 167


title: Tacid, lib553, pH2, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 81


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

description: Library name: Sample 3

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

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: Sacid, lib553, pH3p5_75C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 166


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

description: Library name: Sample 115


title: Tacid, lib553, pH3, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 78


title: Tacid, lib553, pH1, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 79


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

description: Library name: Sample 62


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

description: Library name: Sample 68


title: Tacid, lib553, pH3, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 84


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

description: Library name: Sample 114


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

description: Library name: Sample 61


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

description: Library name: Sample 113


title: Paeru, lib553, 42C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 112


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

description: Library name: Sample 59


title: Tacid, lib553, pH2, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 75


title: Sacid, lib553, pH3_55C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 163


title: Tacid, lib553, pH1, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 74


title: Tacid, lib553, pH2, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 76


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

description: Library name: Sample 60


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

description: Library name: Sample 63


title: Sacid, lib553, pH3_55C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 164


title: Paeru, lib553, 42C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 111


title: Sacid, lib553, pH2p5_75C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 162


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

description: Library name: Sample 110


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

description: Library name: Sample 57


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

description: Library name: Sample 109


title: Sacid, lib553, pH2p5_75C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 161


title: Tacid, lib553, pH1, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 73


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

description: Library name: Sample 72


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

description: Library name: Sample 58


title: Sacid, lib553, pH3p5_75C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 165


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

description: Library name: Sample 56


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

description: Library name: Sample 160


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

description: Library name: Sample 108


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

description: Library name: Sample 55


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

description: Library name: Sample 71


title: Sacid, lib553, pH5_75C, Mock, TGIRT, rep2

description: Library name: Sample 158


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

description: Library name: Sample 107


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

description: Library name: Sample 70


title: Tacid, lib553, pH3, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 77


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

description: Library name: Sample 54


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

description: Library name: Sample 69


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

description: Library name: Sample 106


title: Sacid, lib553, pH5_75C, Mock, TGIRT, rep1

description: Library name: Sample 157


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

description: Library name: Sample 52


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

description: Library name: Sample 105


title: Paeru, lib553, 42C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 104


title: Sacid, lib553, pH3p5_75C, Mock, TGIRT, rep2

description: Library name: Sample 156


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

description: Library name: Sample 68


title: Sacid, lib553, pHunk_85C, Mock, TGIRT, rep1

description: Library name: Sample 159


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

description: Library name: Sample 51


title: Paeru, lib553, 42C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 103


title: Sacid, lib553, pH3p5_75C, Mock, TGIRT, rep1

description: Library name: Sample 155


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

description: Library name: Sample 50


title: Sacid, lib553, pH3_55C, Mock, TGIRT, rep1

description: Library name: Sample 153


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

description: Library name: Sample 65


title: Sacid, lib553, pH3_55C, Mock, TGIRT, rep2

description: Library name: Sample 154


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

description: Library name: Sample 102


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

description: Library name: Sample 66


title: Sacid, lib553, pH2p5_75C, Mock, TGIRT, rep2

description: Library name: Sample 152


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

description: Library name: Sample 101


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

description: Library name: Sample 64


title: Sacid, lib553, pH2p5_75C, Mock, TGIRT, rep1

description: Library name: Sample 151


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

description: Library name: Sample 100


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

description: Library name: Sample 63


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

description: Library name: Sample 47


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

description: Library name: Sample 53


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

description: Library name: Sample 46


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

description: Library name: Sample 98


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

description: Library name: Sample 67


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

description: Library name: Sample 150


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

description: Library name: Sample 62


title: Sacid, lib553, pHunk_85C, Bisulfite, TGIRT, rep1

description: Library name: Sample 149


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

description: Library name: Sample 97


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

description: Library name: Sample 61


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

description: Library name: Sample 45


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

description: Library name: Sample 44


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

description: Library name: Sample 96


title: Sacid, lib553, pH5_75C, Bisulfite, TGIRT, rep2

description: Library name: Sample 148


title: Tacid, lib553, pH3, NaCNBH3, TGIRT, rep2

description: Library name: Sample 60


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

description: Library name: Sample 49


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

description: Library name: Sample 48


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

description: Library name: Sample 43


title: Sacid, lib553, pH5_75C, Bisulfite, TGIRT, rep1

description: Library name: Sample 147


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

description: Library name: Sample 95


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

description: Library name: Sample 94


title: Tacid, lib553, pH2, NaCNBH3, TGIRT, rep2

description: Library name: Sample 58


title: Sacid, lib553, pH3p5_75C, Bisulfite, TGIRT, rep1

description: Library name: Sample 145


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

description: Library name: Sample 42


title: Sacid, lib553, pH3p5_75C, Bisulfite, TGIRT, rep2

description: Library name: Sample 146


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

description: Library name: Sample 41


title: Tacid, lib553, pH2, NaCNBH3, TGIRT, rep1

description: Library name: Sample 57


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

description: Library name: Sample 93


title: Sacid, lib553, pH3_55C, Bisulfite, TGIRT, rep2

description: Library name: Sample 144


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

description: Library name: Sample 99


title: Tacid, lib553, pH1, NaCNBH3, TGIRT, rep2

description: Library name: Sample 56


title: Tacid, lib553, pH1, NaCNBH3, TGIRT, rep1

description: Library name: Sample 55


title: Sacid, lib553, pH3_55C, Bisulfite, TGIRT, rep1

description: Library name: Sample 143


title: Tacid, lib553, pH3, NaCNBH3, TGIRT, rep1

description: Library name: Sample 59


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

description: Library name: Sample 92


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

description: Library name: Sample 91


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

description: Library name: Sample 38


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

description: Library name: Sample 40


title: Tacid, lib553, pH3, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 54


title: Sacid, lib553, pH2p5_75C, Bisulfite, TGIRT, rep2

description: Library name: Sample 142


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

description: Library name: Sample 37


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

description: Library name: Sample 89


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

description: Library name: Sample 36


title: Sacid, lib553, pHunk_85C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 139


title: Sacid, lib553, pHunk_85C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 140


title: Tacid, lib553, pH2, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 51


title: Sacid, lib553, pH5_75C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 138


title: Tacid, lib553, pH3, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 53


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

description: Library name: Sample 88


title: Tacid, lib553, pH2, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 52


title: Sacid, lib553, pH5_75C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 137


title: Tacid, lib553, pH1, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 50


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

description: Library name: Sample 35


title: Tacid, lib553, pH1, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 49


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

description: Library name: Sample 39


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

description: Library name: Sample 86


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

description: Library name: Sample 33


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

description: Library name: Sample 90


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

description: Library name: Sample 34


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

description: Library name: Sample 84


title: Sacid, lib553, pH3p5_75C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 135


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

description: Library name: Sample 32


title: Sacid, lib553, pH2p5_75C, Bisulfite, TGIRT, rep1

description: Library name: Sample 141


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

description: Library name: Sample 48


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

description: Library name: Sample 87


title: Sacid, lib553, pH3p5_75C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 136


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

description: Library name: Sample 83


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

description: Library name: Sample 31


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

description: Library name: Sample 46


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

description: Library name: Sample 82


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

description: Library name: Sample 30


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

description: Library name: Sample 45


title: Sacid, lib553, pH3_55C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 134


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

description: Library name: Sample 29


title: Sacid, lib553, pH2p5_75C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 132


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

description: Library name: Sample 28


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

description: Library name: Sample 44


title: Sacid, lib553, pH3_55C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 133


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

description: Library name: Sample 43


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

description: Library name: Sample 81


title: Sacid, lib553, pH2p5_75C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 131


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

description: Library name: Sample 85


title: Paeru, lib553, 42C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 80


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

description: Library name: Sample 27


title: Sacid, lib553, pHunk_85C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 130


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

description: Library name: Sample 47


title: Paeru, lib553, 42C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 79


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

description: Library name: Sample 26


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

description: Library name: Sample 78


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

description: Library name: Sample 77


title: Sacid, lib553, pHunk_85C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 129


title: Sacid, lib553, pH5_75C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 128


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

description: Library name: Sample 25


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

description: Library name: Sample 41


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

description: Library name: Sample 42


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

description: Library name: Sample 39


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

description: Library name: Sample 75


title: Sente, lib553, OD2_37C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 23


title: Sacid, lib553, pH5_75C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 127


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

description: Library name: Sample 76


title: Sacid, lib553, pH3p5_75C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 126


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

description: Library name: Sample 38


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

description: Library name: Sample 22


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

description: Library name: Sample 37


title: Sacid, lib553, pH3p5_75C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 125


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

description: Library name: Sample 73


title: Tacid, lib553, pH3, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 36


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

description: Library name: Sample 20


title: Sacid, lib553, pH3_55C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 124


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

description: Library name: Sample 74


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

description: Library name: Sample 21


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

description: Library name: Sample 35


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

description: Library name: Sample 24


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

description: Library name: Sample 72


title: Paeru, lib553, 42C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 71


title: Sacid, lib553, pH2p5_75C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 122


title: Sacid, lib553, pH2p5_75C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 121


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

description: Library name: Sample 18


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

description: Library name: Sample 34


title: Sacid, lib553, pH3_55C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 123


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

description: Library name: Sample 40


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

description: Library name: Sample 19


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

description: Library name: Sample 17


title: Paeru, lib553, 42C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 70


title: Tacid, lib553, pH2, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 33


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

description: Library name: Sample 69


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

description: Library name: Sample 16


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

description: Library name: Sample 120


title: Sacid, lib553, pHunk_85C, CMC, TGIRT, rep1

description: Library name: Sample 119


title: Tacid, lib553, pH1, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 32


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

description: Library name: Sample 68


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

description: Library name: Sample 15


title: Tacid, lib553, pH1, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 31


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

description: Library name: Sample 67


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

description: Library name: Sample 14


title: Tacid, lib553, pH3, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 30


title: Sacid, lib553, pH5_75C, CMC, TGIRT, rep2

description: Library name: Sample 118


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

description: Library name: Sample 66


title: Sacid, lib553, pH5_75C, CMC, TGIRT, rep1

description: Library name: Sample 117


title: Tacid, lib553, pH3, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 29


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

description: Library name: Sample 13


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

description: Library name: Sample 64


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

description: Library name: Sample 12


title: Tacid, lib553, pH2, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 27


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

description: Library name: Sample 65


title: Tacid, lib553, pH2, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 28


title: Sacid, lib553, pH3p5_75C, CMC, TGIRT, rep2

description: Library name: Sample 116


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

description: Library name: Sample 11


title: Sacid, lib553, pH3p5_75C, CMC, TGIRT, rep1

description: Library name: Sample 115


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

description: Library name: Sample 10


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

description: Library name: Sample 62


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

description: Library name: Sample 63


title: Sacid, lib553, pH3_55C, CMC, TGIRT, rep1

description: Library name: Sample 113


title: Tacid, lib553, pH1, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 26


title: Sacid, lib553, pH3_55C, CMC, TGIRT, rep2

description: Library name: Sample 114


title: Tacid, lib553, pH3, CMC, SSIII, rep2

description: Library name: Sample 24


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

description: Library name: Sample 9


title: Tacid, lib553, pH1, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 25


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

description: Library name: Sample 8


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

description: Library name: Sample 61


title: Tacid, lib553, pH3, CMC, SSIII, rep1

description: Library name: Sample 23


title: Sacid, lib553, pH2p5_75C, CMC, TGIRT, rep1

description: Library name: Sample 111


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

description: Library name: Sample 110


title: Tacid, lib553, pH2, CMC, SSIII, rep2

description: Library name: Sample 22


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

description: Library name: Sample 6


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

description: Library name: Sample 59


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

description: Library name: Sample 58


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

description: Library name: Sample 7


title: Sacid, lib553, pHunk_85C, AlkBmix, TGIRT, rep1

description: Library name: Sample 109


title: Tacid, lib553, pH1, CMC, SSIII, rep2

description: Library name: Sample 20


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

description: Library name: Sample 56


title: Sacid, lib553, pH5_75C, AlkBmix, TGIRT, rep2

description: Library name: Sample 108


title: Sacid, lib553, pH5_75C, AlkBmix, TGIRT, rep1

description: Library name: Sample 107


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

description: Library name: Sample 4


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

description: Library name: Sample 5


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

description: Library name: Sample 3


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

description: Library name: Sample 2


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

description: Library name: Sample 55


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

description: Library name: Sample 54


title: Tacid, lib553, pH3, NaCNBH3, SSIII, rep1

description: Library name: Sample 17


title: Tacid, lib553, pH1, CMC, SSIII, rep1

description: Library name: Sample 19


title: Sacid, lib553, pH3p5_75C, AlkBmix, TGIRT, rep2

description: Library name: Sample 106


title: Sacid, lib553, pH2p5_75C, CMC, TGIRT, rep2

description: Library name: Sample 112


title: Sacid, lib553, pH3p5_75C, AlkBmix, TGIRT, rep1

description: Library name: Sample 105


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

description: Library name: Sample 60


title: Sacid, lib553, pH3_55C, AlkBmix, TGIRT, rep2

description: Library name: Sample 104


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

description: Library name: Sample 51


title: Tacid, lib553, pH2, NaCNBH3, SSIII, rep1

description: Library name: Sample 15


title: d7 callus from Neurectomy

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

country: USA

institute: Johns Hopkins University

description:
Library name: Neurectomy  1w CD45+ cell depletion
nx 1w CD45+ cell depletion

library_source: transcriptomic single cell

data_processing:
Data were processed using the 10x Genomics Cell Ranger pipeline at default settings to generate FASTAQ files
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Callus

growth_protocol: Callus Mice were kept under a 12-h light/dark cycle with food and water provided ad libitum. All procedures involving mice were approved by the Institutional Animal Care and Use Committee of The Johns Hopkins University under Protocol MO22M368.

extract_protocol:
Callus: Mice forelimbs were harvested 14 days after loading (n=3 for each group). Callus tissue was dissected and marrow cells were flushed out with PBS through the opening on both ends of callus. After cutting into small pieces, fracture tissues were digested with 1mg/ml Collagenase 1/Collagenase 2 (Sigma-Aldrich) and 2mg/ml dispase II (Roche). As soon as the cells were dissociated, cell suspension was centrifuged at 100g for 10 mins at 4°C. The cell pellet was resuspended and incubated in ACK lysing buffer (Quality biological, Cat #:118156101) for 10 minutes to remove red blood cells. Next, after centrifugation, cells were resuspended with PBS and filtered using 40μm cell strainer (Corning). In select experiments for CD45+ cell depletion, cells were processed using MojoSort™ Mouse CD45 Nanobeads (BioLegend) according to the manufacturer's protocol. Briefly, cells were resuspended in ice-cold MojoSort™ Buffer, filtered through a 70 μm cell strainer, and adjusted to 1 × 10⁸ cells/ml. Aliquots of 100 μl cell suspension (1 × 10⁷ cells) were incubated with 10 μl CD45 nanobeads on ice for 15 min. After washing with MojoSort™ Buffer, cells were subjected to two consecutive magnetic separations (5 min each) to ensure complete CD45+ cell depletion.  The dissociated cells were centrifuged again and the supernatant was removed until 100ul remained.
for all samples, 10x Genomics Chromium standard protocol

treatment_protocol: Callus: For Neurectomy group, ulnar nerve transection was performed at 17 weeks old, 1 week prior to stress fracture. Sham surgerey was performed for Sham group, in which the nerve was exposed, but not excised.

value: Callus

tag: cell line

value: primary

tag: cell type

value: bone cell

value: Ulnar nerve transection surgery performed at 17 weeks old, stress fracture at 18 weeks old


title: d7 callus from Sham

description:
Library name: Sham  1w CD45+ cell depletion
sham 1w CD45+ cell depletion

value: Sham surgery performed at 17 weeks old, stress fracture at 18 weeks old


title: Tacid, lib553, pH2, CMC, SSIII, rep1

description: Library name: Sample 21


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

description: Library name: Sample 57


title: Sacid, lib553, pH3_55C, AlkBmix, TGIRT, rep1

description: Library name: Sample 103


title: Sacid, lib553, pH2p5_75C, AlkBmix, TGIRT, rep2

description: Library name: Sample 102


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

description: Library name: Sample 50


title: Tacid, lib553, pH1, NaCNBH3, SSIII, rep2

description: Library name: Sample 14


title: Sacid, lib553, pH2p5_75C, AlkBmix, TGIRT, rep1

description: Library name: Sample 101


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

description: Library name: Sample 1


title: FFC-shRNA 31 Liver SCRAMBLE

city: Rochester

first: Harmeet

last: Malhi

state: Mn

address: 200 1st SW

department: GI/Hep research

institute: Mayo Clinic

description:
Library name: ASM_56
ASM_56

data_processing:
Libraries were sequenced at greater than 100 million read pairs per sample following Illumina’s standard protocol for the NovaSeq 6000. The NovaSeq SP flow cell was sequenced as 100 X 2 paired end reads using the NovaSeq SP Reagent Kit v1.5 and NovaSeq Control Software v1.8.0. Base-calling was performing using Illumina’s RTA version 3.4.4.
Assembly: mm10 using MAP-Rseq v.3.1.4 on RHEL8.
Supplementary files format and content: Scramble controls compared to shAAV8 knockdown mice, expressed in Log2Fold

source_name: Liver

extract_protocol:
Livers lysed in Trizol and RNA isolated using Zymo Direct-zol Miniprep kit
DNAse I treatment and clean up with RNACleanXP beads.  Illumina Stranded Total RNA Prep with RiboZero Plus libraries were prepared with 100ng of total RNA.  Concentration and size distribution was deteremined on Agilent TapeStation's D1000 ScreenTape and Qubit fluorometry.

value: Liver

value: control

value: FFC Diet


title: FFC-shRNA 30 Liver SCRAMBLE

description:
Library name: ASM_55
ASM_55


title: Tacid, lib553, pH1, NaCNBH3, SSIII, rep1

description: Library name: Sample 13


title: Sacid, lib553, pHunk_85C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 100


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

description: Library name: Sample 49


title: Tacid, lib553, pH3, NaCNBH3, SSIII, rep2

description: Library name: Sample 18


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

description: Library name: Sample 53


title: Paeru, lib553, 42C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 48


title: Paeru, lib553, 42C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 47


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

description: Library name: Sample 11


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

description: Library name: Sample 12


title: Sacid, lib553, pHunk_85C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 99


title: Sacid, lib553, pH5_75C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 98


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

description: Library name: Sample 52


title: FFC-shRNA 2600 Liver S100a11

description:
Library name: ASM_53
ASM_53

value: knockdown (KO)


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

description: Library name: Sample 10


title: Tacid, lib553, pH2, NaCNBH3, SSIII, rep2

description: Library name: Sample 16


title: FFC-shRNA 3 Liver S100a11

description:
Library name: ASM_52
ASM_52


title: FFC-shRNA 2 Liver S100a11

description:
Library name: ASM_51
ASM_51


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

description: Library name: Sample 9


title: Sacid, lib553, pH3p5_75C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 96


title: Sacid, lib553, pH5_75C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 97


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

description: Library name: Sample 45


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

description: Library name: Sample 46


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

description: Library name: Sample 8


title: FFC-shRNA 28 Liver SCRAMBLE

description:
Library name: ASM_54
ASM_54


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

description: Library name: Sample 44


title: M2_1ug_Pam3

city: Irvine

first: Jonathan

middle: Van

last: Duong

state: CA

address: 843 Health Sciences Rd

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
Library name: Sample 14
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.

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: Sacid, lib553, pH3p5_75C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 95


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

description: Library name: Sample 43


title: M2_Saline

description:
Library name: Sample 15
PE150, mRNA:stranded

value: Saline


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

description: Library name: Sample 7


title: M2_10ug_Pam3

description:
Library name: Sample 13
PE150, mRNA:stranded


title: Sacid, lib553, pH3_55C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 94


title: Sacid, lib553, pH3_55C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 93


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

description: Library name: Sample 6


title: Paeru, lib553, OD2_25C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 42


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

description: Library name: Sample 4


title: Sacid, lib553, pH2p5_75C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 92


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

description: Library name: Sample 41


title: M1_Saline

description:
Library name: Sample 12
PE150, mRNA:stranded


title: Paeru, lib553, 42C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 40


title: M1_1ug_Pam3

description:
Library name: Sample 11
PE150, mRNA:stranded


title: Sacid, lib553, pH2p5_75C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 91


title: M1_10ug_Pam3

description:
Library name: Sample 10
PE150, mRNA:stranded


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

description: Library name: Sample 3


title: Sacid, lib553, pHunk_85C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 90


title: Paeru, lib553, 42C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 39


title: Paeru, lib553, OD2_37C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 38


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

description: Library name: Sample 2


title: Sacid, lib553, pHunk_85C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 89


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

description: Library name: Sample 1


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

description: Library name: Sample 5


title: Paeru, lib553, OD2_37C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 37


title: Sacid, lib553, pH5_75C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 88


title: F3_10ug_Pam3

description:
Library name: Sample 7
PE150, mRNA:stranded


title: F2_Saline

description:
Library name: Sample 6
PE150, mRNA:stranded


title: Paeru, lib553, OD2_30C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 35


title: Sacid, lib553, pH5_75C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 87


title: F3_1ug_Pam3

description:
Library name: Sample 8
PE150, mRNA:stranded


title: Phalo, lib697, 30C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 127

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_001687585.2
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Planococcus halocryophilus

growth_protocol: Was cultured in duplicate under 4 conditions at 10°C, 15°C, 20°C, and 25°C in Trypticase Soy Broth (TSB; Difco, BD Diagnostics, Franklin Lakes, NJ, USA) where cells were passaged daily for one week at the given temperature prior to growth to mid-log phase (OD 0.4-0.6) and pelleting

extract_protocol:
Total RNA was extracted using Trizol and a column based purification according to manufacturer's instructions (Direct-zol RNA Miniprep, Zymo Research)
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: Phalo, lib697, 25C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 126


title: Phalo, lib697, 30C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 128


title: Sacid, lib553, pH3p5_75C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 86


title: F2_1ug_Pam3

description:
Library name: Sample 5
PE150, mRNA:stranded


title: Sacid, lib553, pH3p5_75C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 85


title: F2_10ug_Pam3

description:
Library name: Sample 4
PE150, mRNA:stranded


title: Paeru, lib553, OD2_25C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 33


title: F3_Saline

description:
Library name: Sample 9
PE150, mRNA:stranded


title: Paeru, lib553, OD2_25C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 34


title: Phalo, lib697, 15C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 124


title: Paeru, lib553, 42C, CMC, SSIII, rep2

description: Library name: Sample 32


title: F1_Saline

description:
Library name: Sample 3
PE150, mRNA:stranded


title: Sacid, lib553, pH3_55C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 83


title: Sacid, lib553, pH3_55C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 84


title: Phalo, lib697, 15C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 123


title: Sacid, lib553, pH2p5_75C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 82


title: Phalo, lib697, 10C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 122


title: Paeru, lib553, OD2_30C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 36


title: Phalo, lib697, 10C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 121


title: Paeru, lib553, OD2_37C, CMC, SSIII, rep2

description: Library name: Sample 30


title: Sacid, lib553, pHunk_85C, Mock, SSIII, rep2

description: Library name: Sample 80


title: Sacid, lib553, pH2p5_75C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 81


title: Paeru, lib553, OD2_37C, CMC, SSIII, rep1

description: Library name: Sample 29


title: F1_10ug_Pam3

description:
Library name: Sample 1
PE150, mRNA:stranded


title: Phalo, lib697, 30C, Mock, TGIRT, rep1

description: Library name: Sample 119


title: Sacid, lib553, pH5_75C, Mock, SSIII, rep2

description: Library name: Sample 78


title: Sacid, lib553, pHunk_85C, Mock, SSIII, rep1

description: Library name: Sample 79


title: Phalo, lib697, 25C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 125


title: Paeru, lib553, OD2_30C, CMC, SSIII, rep1

description: Library name: Sample 27


title: Phalo, lib697, 25C, Mock, TGIRT, rep2

description: Library name: Sample 118


title: Paeru, lib553, OD2_30C, CMC, SSIII, rep2

description: Library name: Sample 28


title: Sacid, lib553, pH5_75C, Mock, SSIII, rep1

description: Library name: Sample 77


title: Paeru, lib553, OD2_25C, CMC, SSIII, rep1

description: Library name: Sample 25


title: Sacid, lib553, pH3p5_75C, Mock, SSIII, rep2

description: Library name: Sample 76


title: Phalo, lib697, 25C, Mock, TGIRT, rep1

description: Library name: Sample 117


title: Paeru, lib553, 42C, CMC, SSIII, rep1

description: Library name: Sample 31


title: Paeru, lib553, OD2_25C, CMC, SSIII, rep2

description: Library name: Sample 26


title: Paeru, lib553, 42C, NaCNBH3, SSIII, rep1

description: Library name: Sample 23


title: Phalo, lib697, 15C, Mock, TGIRT, rep2

description: Library name: Sample 116


title: Phalo, lib697, 30C, Mock, TGIRT, rep2

description: Library name: Sample 120


title: Paeru, lib553, 42C, NaCNBH3, SSIII, rep2

description: Library name: Sample 24


title: F1_1ug_Pam3

description:
Library name: Sample 2
PE150, mRNA:stranded


title: Sacid, lib553, pH3p5_75C, Mock, SSIII, rep1

description: Library name: Sample 75


title: Phalo, lib697, 15C, Mock, TGIRT, rep1

description: Library name: Sample 115


title: Sacid, lib553, pH3_55C, Mock, SSIII, rep2

description: Library name: Sample 74


title: Phalo, lib697, 10C, Mock, TGIRT, rep2

description: Library name: Sample 114


title: Sacid, lib553, pH3_55C, Mock, SSIII, rep1

description: Library name: Sample 73


title: Sacid, lib553, pH2p5_75C, Mock, SSIII, rep2

description: Library name: Sample 72


title: Phalo, lib697, 30C, Bisulfite, TGIRT, rep2

description: Library name: Sample 112


title: Paeru, lib553, OD2_30C, NaCNBH3, SSIII, rep2

description: Library name: Sample 20


title: Sacid, lib553, pH2p5_75C, Mock, SSIII, rep1

description: Library name: Sample 71


title: Phalo, lib697, 10C, Mock, TGIRT, rep1

description: Library name: Sample 113


title: Paeru, lib553, OD2_37C, NaCNBH3, SSIII, rep1

description: Library name: Sample 21


title: Paeru, lib553, OD2_30C, NaCNBH3, SSIII, rep1

description: Library name: Sample 19


title: Phalo, lib697, 30C, Bisulfite, TGIRT, rep1

description: Library name: Sample 111


title: Phalo, lib697, 25C, Bisulfite, TGIRT, rep2

description: Library name: Sample 110


title: Sacid, lib553, pHunk_85C, Bisulfite, SSIII, rep1

description: Library name: Sample 69


title: Phalo, lib697, 25C, Bisulfite, TGIRT, rep1

description: Library name: Sample 109


title: Paeru, lib553, OD2_25C, NaCNBH3, SSIII, rep2

description: Library name: Sample 18


title: Sacid, lib553, pHunk_85C, Bisulfite, SSIII, rep2

description: Library name: Sample 70


title: Sacid, lib553, pH5_75C, Bisulfite, SSIII, rep2

description: Library name: Sample 68


title: Phalo, lib697, 15C, Bisulfite, TGIRT, rep2

description: Library name: Sample 108


title: Paeru, lib553, OD2_25C, NaCNBH3, SSIII, rep1

description: Library name: Sample 17


title: Phalo, lib697, 15C, Bisulfite, TGIRT, rep1

description: Library name: Sample 107


title: Paeru, lib553, OD2_37C, NaCNBH3, SSIII, rep2

description: Library name: Sample 22


title: Western diet week 16, replicate 1

city: New York

first: Lauren

middle: E

last: Fries

state: NY

department: Medicine

institute: Columbia University

description:
Library name: W16R1
10X Chromium

data_processing:
Fastq files were process with Cell Ranger 5.0.1 from 10X genomics to generate count matrices of unique molecular identifiers (UMIs) and reads were mapped to the GRCh38 human reference genome and the transcript annotated by GENCODE v32 from 10X prebuilt reference package.
To obtain the .rds filtered files we performed filtering on each sample with Seurat v5.1.0, excluding cells with < 100 features, UMI count < 500, number of genes < 200, log10GenesperUMI < 0.8, mitochondrial ratio >0.1, any genes expressed in 10 or fewer cells or with zero counts from further analyses. We integrated the data using SCTransform and performed integration with Harmony v1.2.1. We then formed clusters using the top 21 principal components for the shared nearest neighbor (SNN) analysis and a resolution of 0.4.  To identify cell types we found conserved marker genes for the clusters with the “FindConservedMarkers” function along with utilizing previously established cell type markers from the literature. We identified six broad cell types, including B cells, T cells, fibroblasts, smooth muscle cells, macrophages, and endothelial cells. We merged all separate clusters into these six broad groups.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Aortic adventitia

extract_protocol:
Mice were deeply sedated with isoflurane and euthanized by cervical dislocation. 3 mice were pooled per sample, 2 samples were collected per time point, resulting in a total of 18 male mice used. The mice were immediately perfused with ice-cold DPBS. The aorta was sharply dissected from the ascending aorta to the bifurcation at the common iliac artery. The aorta was digested in 1 mg/mL of Collagenase A (Roche, 11088793001) in F12:DMEM (Cytiva, SH30023.01) containing 0.2% BSA (Sigma-Aldrich, A9647) at 37℃ to allow for the removal of the adventitia. After 5 minutes, the aorta was moved into DPBS, and the outer adventitia was peeled off. The adventitia layer from 3 mice was pooled and subsequently digested in a cocktail containing 2mg/mL of Collagenase A, 0.05 mg/mL of Elastase (Worthington, LS006365), and 60U/mL of DNase (Worthington Biochemical, LS006331) in F12:DMEM containing 0.2% BSA for 30 minutes at 37℃. The cells were subsequently passed through a 70uM cell strainer and spun down at 300 x g for 5 minutes. The cells were resuspended in F12: DMEM containing 0.2% BSA and 1mg/ml DNase stained with 1:10,000 DAPI and 1:1000 Draq5 (BioLegend, 424101), and live cells were sorted.
Samples were prepared using 10x Genomics Chromium Cell 3’ Reagent Kits according to the manufacturer’s instructions. 5000 cells were inputted with the goal of 100M reads per sample.

treatment_protocol: At 8-10 weeks of age, mice were initiated on a western diet (WD) (Research Diets, D12079Bi) for 0, 9, or 16 weeks.

tag: sample id

tag: altid

tag: mouse strain

value: Aortic adventitia

tag: weeks western_diet

tag: age

tag: replicateid

tag: Sex

value: male

tag: sequencing batch


title: Western diet week 9, replicate 2

description:
Library name: W9R2
10X Chromium


title: Sacid, lib553, pH5_75C, Bisulfite, SSIII, rep1

description: Library name: Sample 67

value: Bacterial culture


title: Sacid, lib553, pH3p5_75C, Bisulfite, SSIII, rep2

description: Library name: Sample 66

value: WT


title: Western diet week 9, replicate 1

description:
Library name: W9R1
10X Chromium


title: Phalo, lib697, 10C, Bisulfite, TGIRT, rep2

description: Library name: Sample 106


title: Sacid, lib553, pH3p5_75C, Bisulfite, SSIII, rep1

description: Library name: Sample 65


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

description: Library name: Sample 14


title: Phalo, lib697, 10C, Bisulfite, TGIRT, rep1

description: Library name: Sample 105


title: Western diet week 0, replicate 2

description:
Library name: W0R2
10X Chromium


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

description: Library name: Sample 13


title: Phalo, lib697, 30C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 104


title: Sacid, lib553, pH3_55C, Bisulfite, SSIII, rep2

description: Library name: Sample 64


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

description: Library name: Sample 12


title: Western diet week 0, replicate 1

description:
Library name: W0R1
10X Chromium


title: Western diet week 16, replicate 2

description:
Library name: W16R2
10X Chromium


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

description: Library name: Sample 11


title: SI, Cystine rep2, scRNAseq

city: CAMBRIDGE

first: Qiming

last: Zhang

state: MA

address: 88 Ames Street

institute: Koch institute

data_processing:
The Cell Ranger toolkit (version 3.1.0) provided by 10x Genomics was applied to aggregate raw data, filter low-quality reads, align reads to mouse reference genome (GRCm39), assign cell barcodes, and generate the unique molecular identifier (UMI) matrix. An R-based toolkit, Seurat (version 4.0.1), was used for analyzing the scRNA-seq data.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small intestine

extract_protocol:
Based on FACS analysis, single CD45+ cells from intra-crypts of mice fed with control and high-cysteine diets were sorted into 1.5 ml low-binding tubes with 500 ul FACS buffer. Single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and Library Kits (10x Genomics, Pleasanton) as per the manufacturer’s protocol. The loading cell number is 18,000 for each sample The cells were then partitioned into Gel Beads in Emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification. Amplified cDNA was then used for 5’ gene expression library construction
Amplified cDNA was fragmented and end-repaired, double-sided size-selected, PCR-amplified with sample indexing primers, and double-sided size-selected

value: Small intestine

value: Immune cell

value: Male

value: Control


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

description: Library name: Sample 16


title: Sacid, lib553, pH3_55C, Bisulfite, SSIII, rep1

description: Library name: Sample 63


title: Sacid, lib553, pH2p5_75C, Bisulfite, SSIII, rep1

description: Library name: Sample 61


title: SI, Cystine rep1, scRNAseq


title: Phalo, lib697, 25C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 101


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

description: Library name: Sample 15


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

description: Library name: Sample 10


title: SI, Control rep2, scRNAseq


title: Phalo, lib697, 15C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 100


title: SI, Control rep1, scRNAseq


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

description: Library name: Sample 9


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

description: Library name: Sample 8


title: Sacid, lib553, pHunk_85C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 60


title: Sacid, lib553, pHunk_85C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 59


title: Phalo, lib697, 15C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 99


title: R26CreERki_ki_Recql4flfl_sgKlhdc3_r4_E03

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

data_processing:
Reads were trimmed to 28bp (_1 only).
Reads were demultiplexed into individual FASTQ files per sample using BRB-seqTools (version 1.6.1, https://github.com/DeplanckeLab/BRB-seqTools).
Reads were aligned to the mouse reference genome mm10 (GRCm38) using STAR (version 2.7.10b) and counts generated (--quantMode GeneCounts).
Counts were analysed in degust (https://degust.erc.monash.edu/). Genes were filtered to keep at least 5 reads, and cpm > 1 in at least 3 samples.
Differential expression was cacluated using edgeR-quasi-likelihood.
Assembly: mm10
Supplementary files format and content: Annotated raw counts file file, csv.

source_name: cell line

growth_protocol: Immortalised myeloid cell lines (HoxB8) selected in GM-CSF were maintained in IMDM with 10% fetal bovine serum (FBS), antibiotics and glutamine. Cells were cultured with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit by Qiagen and was quantified using Nanodrop. 500 ng of total RNA was used for the construction of the sequencing library.
The library was prepared using Alithea Genomics BRB-Seq (MERCURIUS™ BRB-seq Library preparation kits for Illumina®) in a 96 well plate format) following the manufacturer's protocol. Quality was pre-checked using RNA ScreenTape Assay (TapeStation) and Qubit.

value: cell line

value: Myeloid cells (GMCSF)

value: R26CreER ki/ki Recql4 fl/fl sgKlhdc3

tag: barcode


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

description: Library name: Sample 7


title: Sacid, lib553, pH5_75C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 58


title: Phalo, lib697, 10C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 98


title: Phalo, lib697, 30C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 103


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

description: Library name: Sample 6


title: Phalo, lib697, 10C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 97


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

description: Library name: Sample 5


title: Phalo, lib697, 25C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 102


title: Sacid, lib553, pH2p5_75C, Bisulfite, SSIII, rep2

description: Library name: Sample 62


title: Sacid, lib553, pH3p5_75C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 56


title: R26CreERki_ki_Recql4flfl_sgKlhdc3_r1_B03


title: Phalo, lib697, 30C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 96


title: Phalo, lib697, 30C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 95


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

description: Library name: Sample 3


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

description: Library name: Sample 4


title: R26CreERki_plus_Recql4wt_sgKlhdc3_r3_H02

value: R26CreER ki/+ Recql4+/+ sgKlhdc3


title: Sacid, lib553, pH3p5_75C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 55


title: R26CreERki_plus_Recql4wt_sgKlhdc3_r4_A03


title: Phalo, lib697, 25C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 93


title: R26CreERki_plus_Recql4wt_sgKlhdc3_r2_G02


title: Phalo, lib697, 25C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 94


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

description: Library name: Sample 2


title: Sacid, lib553, pH3_55C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 53


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

description: Library name: Sample 1


title: Sacid, lib553, pH5_75C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 57


title: Sacid, lib553, pH2p5_75C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 52


title: R26CreERki_ki_Recql4flfl_sgKlhdc3_r3_D03


title: R26CreERki_ki_Recql4flfl_sgKlhdc3_r2_C03


title: Phalo, lib697, 15C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 92


title: SITW007B_2

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-Disome-Seq

organism: Homo sapiens

source_name: HeLa

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

value: HeLa

tag: condition

value: naive


title: Sacid, lib553, pH2p5_75C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 51

tag: tissue


title: Phalo, lib697, 15C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 91

tag: strain


title: SITW007B_1


title: Phalo, lib697, 10C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 90

tag: genotype


title: R26CreERki_plus_Recql4wt_r3_D02

value: R26CreER ki/+ Recql4+/+


title: R26CreERki_plus_Recql4wt_r4_E02


title: SITW012B_2

tag: treatment


title: Sacid, lib553, pH3_55C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 54

tag: batch


title: Sacid, lib553, pHunk_85C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 50


title: Sacid, lib553, pHunk_85C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 49


title: SITW012B_1

tag: cell line


title: Sacid, lib553, pH5_75C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 48


title: Phalo, lib697, 10C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 89


title: R26CreERki_plus_Recql4wt_r1_B02

tag: cell type


title: R26CreERki_plus_Recql4wt_r2_C02


title: SITW010A_4

description: MitoIP-Thor-Ribo-Seq

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


title: Sacid, lib553, pH5_75C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 47


title: R26CreERki_plus_Recql4wt_sgKlhdc3_r1_F02


title: Recql4ko_Klhdc3ko_r3_A02

growth_protocol: Immortalised E12.5 mouse embryonic fibroblasts (MEFs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), antibiotic and glutamine with 5% CO2 at 37°C.

value: Recql4 Klhdc3

value: Fibroblast

tag: genotype recql4

tag: genotype klhdc3

value: Recql4-/- Klhdc3-/-


title: Sacid, lib553, pH3p5_75C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 46


title: Phalo, lib697, 30C, CMC, TGIRT, rep1

description: Library name: Sample 87


title: SITW010A_3

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 25C, CMC, TGIRT, rep2

description: Library name: Sample 86


title: Recql4ko_Klhdc3ko_r2_H01


title: SITW010A_2

description: MitoIP-Thor-Ribo-Seq


title: Sacid, lib553, pH3p5_75C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 45


title: Recql4ko_Klhdc3ko_r1_G01


title: SITW010A_1

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 25C, CMC, TGIRT, rep1

description: Library name: Sample 85


title: Phalo, lib697, 15C, CMC, TGIRT, rep2

description: Library name: Sample 84


title: Klhdc3ko_r3_F01


title: Klhdc3ko_r2_E01


title: Phalo, lib697, 15C, CMC, TGIRT, rep1

description: Library name: Sample 83


title: SITW009B_4

description: MitoIP-Thor-Ribo-Seq

source_name: Myobrast

value: Myobrast


title: SITW009B_3

description: MitoIP-Thor-Ribo-Seq


title: Sacid, lib553, pH2p5_75C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 42

value: Bacterial culture


title: Sacid, lib553, pH3_55C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 43

value: WT


title: Phalo, lib697, 30C, CMC, TGIRT, rep2

description: Library name: Sample 88


title: Phalo, lib697, 10C, CMC, TGIRT, rep2

description: Library name: Sample 82


title: Klhdc3ko_r1_D01


title: SITW009B_2

description: MitoIP-Thor-Ribo-Seq


title: Sacid, lib553, pH2p5_75C, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 41


title: Phalo, lib697, 10C, CMC, TGIRT, rep1

description: Library name: Sample 81


title: WT_r3_C01


title: SITW009B_1

description: MitoIP-Thor-Ribo-Seq


title: Sacid, lib553, pHunk_85C, CMC, SSIII, rep2

description: Library name: Sample 40


title: SIMM076_10

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 30C, AlkBmix, TGIRT, rep2

description: Library name: Sample 80


title: Sacid, lib553, pHunk_85C, CMC, SSIII, rep1

description: Library name: Sample 39


title: WT_r2_B01


title: WT_r1_A01


title: Phalo, lib697, 25C, AlkBmix, TGIRT, rep2

description: Library name: Sample 78


title: SIMM076_8

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 30C, AlkBmix, TGIRT, rep1

description: Library name: Sample 79


title: SIMM076_9

description: MitoIP-Thor-Ribo-Seq


title: Sacid, lib553, pH3_55C, NaHCO3+NaCNBH3, SSIII, rep2

description: Library name: Sample 44


title: Sacid, lib553, pH5_75C, CMC, SSIII, rep2

description: Library name: Sample 38


title: SITW019_2

description:
L108
Ribo-Calibration Ribo-Seq

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 trimming 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 mouse nuclear genomes (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.
Library strategy: Ribo-Seq

extract_protocol:
Ribo-Calibration: 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-Calibration: The spike-in mixture of Rluc-disome and Fluc-trisome were added to the lysate. For Ribo-Seq, RNase treatment, ribosome pelleting, Ribo-FilterOut, size selection, ligation of linker with the antisense sequence of T7 promoter, rRNA depletion, in vitro transcription, ligation of second linker, reverse transcription, and PCR amplification. For RNA-Seq, the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).


title: Sacid, lib553, pH5_75C, CMC, SSIII, rep1

description: Library name: Sample 37


title: Phalo, lib697, 25C, AlkBmix, TGIRT, rep1

description: Library name: Sample 77


title: SITW019_1

description:
L107
Ribo-Calibration Ribo-Seq


title: SIMM076_7

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 15C, AlkBmix, TGIRT, rep2

description: Library name: Sample 76


title: Sacid, lib553, pH3p5_75C, CMC, SSIII, rep2

description: Library name: Sample 36


title: Sacid, lib553, pH3p5_75C, CMC, SSIII, rep1

description: Library name: Sample 35


title: SIMM076_6

description: MitoIP-Thor-Ribo-Seq


title: C7-T1 DRGs d1 1st library

description:
MXu111122_1       LO15  1st library
1st library prep

data_processing:
Data were processed using the 10x Genomics Cell Ranger pipeline at default settings.
Seurat v4.4.0 was used for further analysis.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: DRG

growth_protocol:
DRG: Mice were kept under a 12-h light/dark cycle with food and water provided ad libitum. All procedures involving mice were approved by the Institutional Animal Care and Use Committee of The Johns Hopkins University under Protocol MO22M368.
Callus Mice were kept under a 12-h light/dark cycle with food and water provided ad libitum. All procedures involving mice were approved by the Institutional Animal Care and Use Committee of The Johns Hopkins University under Protocol MO22M368.

extract_protocol:
DRG: Retrogradely labeled whole DRGs at C7-T1 from injected side were harvested from 4 time points (uninjured, 1-, 14- and 56-days post-fracture). The dissection and dissociation were conducted using previously published protocol [9], with minor modifications. Briefly, 18 DRGs from 6 mice were collected into ice-cold PBS. The DRGs then were digested with 1.8ml digestion solution with Papain (25U/ml, Worthington, Cat #:LS003126), Collagenase A (20mg/ml, Sigma-Aldrich, Cat #:10103586001), Dispase II (20mg/ml, Roche, Cat #:61926600) and BSA (0.5%, Sigma-Aldrich, Cat #:A7979) at 37 °C. 30ul of Collagenase A/Dispase II (20mg/ml) was added depending on the dissociation progress. Once DRGs were dissociated, the cell suspension was filtered using a 40μm cell strainer (Corning), diluted with 3ml aCSF (Tocris Bioscience) and centrifuged at 100g for 10 mins at 4°C. After removing the supernatant, the pellet was resuspended in 0.5ml aCSF and 0.5 ml complete Neurobasal medium. The cell suspension was then carefully layered on top of an Optiprep gradient (90ul Optiprep density solution (Sigma-Aldrich) + 455ul aCSF + 455ul complete Neurobasal). The gradient was centrifuged at 100g at 4°C for 20 mins. After centrifuging, the supernatant was removed until 100ul remained.
Callus: Mice forelimbs were harvested 14 days after loading (n=3 for each group). Callus tissue was dissected and marrow cells were flushed out with PBS through the opening on both ends of callus. After cutting into small pieces, fracture tissues were digested with 1mg/ml Collagenase 1/Collagenase 2 (Sigma-Aldrich) and 2mg/ml dispase II (Roche). As soon as the cells were dissociated, cell suspension was centrifuged at 100g for 10 mins at 4°C. The cell pellet was resuspended and incubated in ACK lysing buffer (Quality biological, Cat #:118156101) for 10 minutes to remove red blood cells. Next, after centrifugation, cells were resuspended with PBS and filtered using 40μm cell strainer (Corning). The dissociated cells were centrifuged again and the supernatant was removed until 100ul remained.
for all samples, 10x Genomics Chromium standard protocol

treatment_protocol:
DRG: For all DRG samples, C57BL/6 mice were used. For uninjured sample, AAV.PHP.S retrograde virus was injected into ulna midshaft periosteum at 14 weeks old and mice were sacrificed at 18 weeks old for extraction of DRG cells for scRNA-seq. For all injured samples, C57BL/6 mice were injected with AAV.PHP.S at 14 weeks old, stress fracture was induced at 18 weeks old, mice then were sacrificed at 1, 14, 56 days after fracture for extraction of DRG cells for scRNA-seq.
Callus: For Neurectomy group, ulnar nerve transection was performed at 17 weeks old, 1 week prior to stress fracture. Sham surgerey was performed for Sham group, in which the nerve was exposed, but not excised. To inhibit TrkA catalytic activity, TrkAWT and TrkAF592A animals were used. 1NMPP1 (Aurora Analytics LLC) was administered to inhibit TrkA catalytic activity according to previously established protocol in TrkAF592A animals.  1NMPP1 has previously been shown to have no effect on fracture healing in TrkAWT mice. Briefly, 1NMPP1 was injected intraperitoneally 48 hr and 2 hr before loading using a 5nM solution, then maintained on drinking water at 40μM concentration until sacrifice.

value: DRG

value: primary

value: AAV.PHP.S injection at 14wks, stress fracture at 18wks, sample collection at d1 after stress fracture


title: Sacid, lib553, pH3_55C, CMC, SSIII, rep2

description: Library name: Sample 34


title: SIMM076_5

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 10C, AlkBmix, TGIRT, rep2

description: Library name: Sample 74


title: d14 callus from Sham

description:
MXu070822 LO11  Sham  1st library
1st library prep

value: Callus

value: Sham surgery performed at 17 weeks old, stress fracture at 18 weeks old


title: SIMM076_4

description: MitoIP-Thor-Ribo-Seq


title: Sacid, lib553, pH3_55C, CMC, SSIII, rep1

description: Library name: Sample 33


title: d14 callus from Neurectomy

description:
MXu070822 LO11  Neurectomy  1st library
1st library prep

value: Ulnar nerve transection surgery performed at 17 weeks old, stress fracture at 18 weeks old


title: Sacid, lib553, pH2p5_75C, CMC, SSIII, rep2

description: Library name: Sample 32


title: SIMM076_3

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 10C, AlkBmix, TGIRT, rep1

description: Library name: Sample 73


title: d14 callus from TrkA WT

description:
MXu082922 LO13  WT  1st library
1st library prep

value: 1NMPP1 was injected intraperitoneally 48 hours and 2 hours before stress fracture at 18 weeks old using a 5-nM solution, then maintained on drinking water at 40μM concentration for 14 days


title: SIMM076_2

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 30C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 72


title: Sacid, lib553, pH2p5_75C, CMC, SSIII, rep1

description: Library name: Sample 31


title: d14 callus from TrkA homo

description:
MXu082922 LO13 homo  1st library
1st library prep

value: 1NMPP1 was injected intraperitoneally 48 hours and 2 hours before loading at 18 weeks old using a 5-nM solution, then maintained on drinking water at 40μM concentration for 14 days


title: Sacid, lib553, pHunk_85C, NaCNBH3, SSIII, rep2

description: Library name: Sample 30


title: Phalo, lib697, 25C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 70


title: SIMM076_1

description: MitoIP-Thor-Ribo-Seq


title: C7-T1 DRGs uninj

description:
MXu090622 LO13  1st library
1st library prep

value: AAV.PHP.S injection at 14wks,sample collection 4 wks after


title: Phalo, lib697, 30C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 71


title: Sacid, lib553, pHunk_85C, NaCNBH3, SSIII, rep1

description: Library name: Sample 29


title: Phalo, lib697, 25C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 69


title: SITW008D_4

description: MitoIP-Thor-Ribo-Seq

value: MTU1 KO


title: C7-T1 DRGs d14 2nd library

description:
MXu100622_2 LO14  2nd library
2nd library prep

value: AAV.PHP.S injection at 14wks, stress fracture at 18wks, sample collection at d14 after stress fracture


title: Sacid, lib553, pH5_75C, NaCNBH3, SSIII, rep2

description: Library name: Sample 28


title: Phalo, lib697, 15C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 68


title: C7-T1 DRGs d14 1st library

description:
MXu100622_1 LO14  1st library
1st library prep


title: SITW008D_3

description: MitoIP-Thor-Ribo-Seq


title: SITW008D_2

description: MitoIP-Thor-Ribo-Seq

value: naive


title: Phalo, lib697, 15C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 67


title: Sacid, lib553, pH5_75C, NaCNBH3, SSIII, rep1

description: Library name: Sample 27


title: SITW008D_1

description: MitoIP-Thor-Ribo-Seq


title: C7-T1 DRGs d56 2nd library

description:
MXu111722_2 LO15  2nd library
2nd library prep

value: AAV.PHP.S injection at 14wks, stress fracture at 18wks, sample collection at d56 after stress fracture


title: Sacid, lib553, pH3p5_75C, NaCNBH3, SSIII, rep2

description: Library name: Sample 26


title: Phalo, lib697, 10C, NaCNBH3, TGIRT, rep2

description: Library name: Sample 66


title: SITW008A_6

description: Ribo-Seq

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: Ribo-Seq

value: NSUN3 KO#2


title: C7-T1 DRGs d56 1st library

description:
MXu111722_1 LO15  1st library
1st library prep


title: HsSc, lib553, control, NaBH4HydBiotin, TGIRT, rep2

description:
Library name: Sample 34
RNA extracts from H. sapiens and S.cerevisiae were pooled together

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, GCF_000146045.2
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism:
Saccharomyces cerevisiae
Homo sapiens

source_name: cell culture

growth_protocol: Yeast - SK1 WT 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. Human - HEK 293T cells were 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. The cells were transfected with pmax-GFP plasmid (Lonza).

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

value: cell culture

value: HEK 293T

value: Human embryonic kidney cells

value: control


title: Phalo, lib697, 30C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 64

value: Bacterial culture

value: WT


title: Sacid, lib553, pH3_55C, NaCNBH3, SSIII, rep2

description: Library name: Sample 24

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


title: HsSc, lib553, control, NaBH4HydBiotin, TGIRT, rep1

description:
Library name: Sample 33
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Sacid, lib553, pH3p5_75C, NaCNBH3, SSIII, rep1

description: Library name: Sample 25


title: Phalo, lib697, 30C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 63


title: C7-T1 DRGs d1 2nd library

description:
MXu111122_2       LO15  2nd library
2nd library prep

value: DRG

value: primary

value: AAV.PHP.S injection at 14wks, stress fracture at 18wks, sample collection at d1 after stress fracture


title: SITW008A_3

description: Ribo-Seq

value: ALKBH1 KO#1


title: Phalo, lib697, 25C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 62


title: SITW008A_2

description: Ribo-Seq


title: HsSc, lib553, control, Mock, TGIRT, rep1

description:
Library name: Sample 31
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Sacid, lib553, pH3_55C, NaCNBH3, SSIII, rep1

description: Library name: Sample 23


title: Sacid, lib553, pH2p5_75C, NaCNBH3, SSIII, rep1

description: Library name: Sample 21


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

description: Library name: Sample 20


title: HsSc, lib553, control, Bisulfite, TGIRT, rep2

description:
Library name: Sample 30
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Phalo, lib697, 25C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 61


title: Phalo, lib697, 15C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 60


title: Sacid, lib553, pHunk_85C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 19


title: Phalo, lib697, 10C, NaCNBH3, TGIRT, rep1

description: Library name: Sample 65


title: Phalo, lib697, 15C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 59


title: HsSc, lib553, control, NaHCO3+Heat, TGIRT, rep2

description:
Library name: Sample 28
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Phalo, lib697, 15C, AlkBmix, TGIRT, rep1

description: Library name: Sample 75


title: SITW008A_4

description: Ribo-Seq

value: ALKBH1 KO#2


title: SITW008A_5

description: Ribo-Seq

value: NSUN3 KO#1


title: Sacid, lib553, pH5_75C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 18


title: HsSc, lib553, control, Mock, TGIRT, rep2

description:
Library name: Sample 32
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SITW008_5

description: RNA-Seq

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.

value: chloramphenicol


title: Phalo, lib697, 10C, MocklowdNTPs, SSIII, rep2

description: Library name: Sample 58


title: HsSc, lib553, control, NaHCO3+Heat, TGIRT, rep1

description:
Library name: Sample 27
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Sacid, lib553, pH5_75C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 17


title: Sacid, lib553, pH2p5_75C, NaCNBH3, SSIII, rep2

description: Library name: Sample 22


title: HsSc, lib553, control, NaHCO3+NaCNBH3, TGIRT, rep2

description:
Library name: Sample 26
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Phalo, lib697, 30C, Mock, SSIII, rep2

description: Library name: Sample 56


title: SITW008A_1

description: Ribo-Seq


title: HsSc, lib553, control, NaHCO3+NaCNBH3, TGIRT, rep1

description:
Library name: Sample 25
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Sacid, lib553, pH3p5_75C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 16


title: SITW008_6

description: RNA-Seq


title: SITW008_2

description: RNA-Seq


title: Phalo, lib697, 30C, Mock, SSIII, rep1

description: Library name: Sample 55


title: HsSc, lib553, control, Bisulfite, TGIRT, rep1

description:
Library name: Sample 29
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Sacid, lib553, pH3p5_75C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 15


title: HsSc, lib553, control, CMC, TGIRT, rep2

description:
Library name: Sample 24
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Sacid, lib553, pH3_55C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 14


title: SITW008_1

description: RNA-Seq


title: HsSc, lib553, control, CMC, TGIRT, rep1

description:
Library name: Sample 23
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Phalo, lib697, 25C, Mock, SSIII, rep2

description: Library name: Sample 54


title: Sacid, lib553, pH3_55C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 13


title: SIMM057_6

description: MitoIP-Thor-Disome-Seq


title: Phalo, lib697, 25C, Mock, SSIII, rep1

description: Library name: Sample 53


title: HsSc, lib553, control, AlkBmix, TGIRT, rep2

description:
Library name: Sample 22
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SITW008_4

description: RNA-Seq


title: Phalo, lib697, 10C, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 57


title: SIMM057_5

description: MitoIP-Thor-Disome-Seq


title: Phalo, lib697, 15C, Mock, SSIII, rep2

description: Library name: Sample 52


title: HsSc, lib553, control, AlkBmix, TGIRT, rep1

description:
Library name: Sample 21
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Sacid, lib553, pH2p5_75C, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 11


title: SITW008_3

description: RNA-Seq


title: HsSc, lib553, control, NaCNBH3, TGIRT, rep2

description:
Library name: Sample 20
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM057_4

description: MitoIP-Thor-Disome-Seq


title: Sacid, lib553, pHunk_85C, Mock, RTHIV, rep2

description: Library name: Sample 10


title: Phalo, lib697, 10C, Mock, SSIII, rep2

description: Library name: Sample 50


title: Phalo, lib697, 15C, Mock, SSIII, rep1

description: Library name: Sample 51


title: HsSc, lib553, control, NaCNBH3, TGIRT, rep1

description:
Library name: Sample 19
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM057_3

description: MitoIP-Thor-Disome-Seq


title: SIMM057_1

description: MitoIP-Thor-Disome-Seq


title: SIMM057_2

description: MitoIP-Thor-Disome-Seq


title: Phalo, lib697, 10C, Mock, SSIII, rep1

description: Library name: Sample 49


title: Sacid, lib553, pH5_75C, Mock, RTHIV, rep2

description: Library name: Sample 8


title: Sacid, lib553, pH2p5_75C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 12


title: Sacid, lib553, pHunk_85C, Mock, RTHIV, rep1

description: Library name: Sample 9


title: HsSc, lib553, control, MocklowdNTPs, SSIII, rep1

description:
Library name: Sample 17
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: HsSc, lib553, control, MocklowdNTPs, SSIII, rep2

description:
Library name: Sample 18
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM063_4

description: MitoIP-Thor-Ribo-Seq

value: OSGEPL1 KO


title: Sacid, lib553, pH5_75C, Mock, RTHIV, rep1

description: Library name: Sample 7


title: HsSc, lib553, control, Mock, SSIII, rep2

description:
Library name: Sample 16
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM063_3

description: MitoIP-Thor-Ribo-Seq


title: Sacid, lib553, pH3p5_75C, Mock, RTHIV, rep2

description: Library name: Sample 6


title: Phalo, lib697, 25C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 46


title: HsSc, lib553, control, Mock, SSIII, rep1

description:
Library name: Sample 15
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM063_2

description: MitoIP-Thor-Ribo-Seq

value: naive


title: Phalo, lib697, 25C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 45


title: Sacid, lib553, pH3p5_75C, Mock, RTHIV, rep1

description: Library name: Sample 5


title: Sacid, lib553, pH3_55C, Mock, RTHIV, rep2

description: Library name: Sample 4


title: HsSc, lib553, control, Bisulfite, SSIII, rep2

description:
Library name: Sample 14
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM060_6

description: MitoIP-Thor-Ribo-Seq

value: QTRT2 KO


title: Sacid, lib553, pH3_55C, Mock, RTHIV, rep1

description: Library name: Sample 3


title: HsSc, lib553, control, NaHCO3+Heat, SSIII, rep2

description:
Library name: Sample 12
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM060_5

description: MitoIP-Thor-Ribo-Seq


title: Phalo, lib697, 15C, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 43


title: Phalo, lib697, 30C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 48


title: Phalo, lib697, 15C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 44


title: Sacid, lib553, pH2p5_75C, Mock, RTHIV, rep2

description: Library name: Sample 2


title: Phalo, lib697, 10C, NaHCO3+Heat, SSIII, rep2

description: Library name: Sample 42


title: SIMM060_4

description: MitoIP-Thor-Ribo-Seq

value: QTRT1 KO