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

description: Library name: Sample 1


title: Phalo, lib697, 30C, NaHCO3+Heat, SSIII, 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 47

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_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

molecule: total RNA

organism: Planococcus halocryophilus

source_name: Bacterial culture

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).

tag: tissue

value: Bacterial culture

tag: strain

tag: genotype

value: WT

tag: treatment

tag: batch


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

description:
Library name: Sample 11
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

tag: cell line

value: HEK 293T

tag: cell type

value: Human embryonic kidney cells

value: control


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

description: Library name: Sample 41


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

description:
Library name: Sample 13
RNA extracts from H. sapiens and S.cerevisiae were pooled together


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

description:
Library name: Sample 10
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Pfuri, lib721, 95C.WT, Bisulfite, TGIRT, rep3

description: Library name: Sample 6

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_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

extract_protocol:
Cell pellets were washed with 1x PBS and centrifuged at 2500 rpm for 3 minutes. The pellet was then resuspended in 1000 µl TRI Reagent, incubated at room temperature for 10 minutes, followed by centrifugation at 16,000 x g for 2 minutes.
Bisulfite-treatment – Bisulfite conversion was carried out using the EZ RNA methylation kit (Zymo research, R5001), according to the manufacturer’s instructions, except for the conversion step that was carried out by more stringent conditions (3 cycles of (1) 70 °C, 10 min. (2) 64 °C, 45 min), and the desulphonation step that was carried out in higher temperature (37 °C, 30 min).


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

description: Library name: Sample 40


title: SIMM060_2

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

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

organism: Homo sapiens

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

tag: condition

value: naive


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

description:
Library name: Sample 9
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: Pfuri, lib721, 95C.WT, Bisulfite, TGIRT, rep2

description: Library name: Sample 5


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

description: Library name: Sample 39


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

description:
Library name: Sample 8
RNA extracts from H. sapiens and S.cerevisiae were pooled together


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

description: Library name: Sample 38


title: Pfuri, lib721, 95C.WT, Bisulfite, TGIRT, rep1

description: Library name: Sample 4


title: SIMM060_1

description: MitoIP-Thor-Ribo-Seq


title: SIMM063_1

description: MitoIP-Thor-Ribo-Seq


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

description:
Library name: Sample 7
RNA extracts from H. sapiens and S.cerevisiae were pooled together


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

description: Library name: Sample 37


title: Pfuri, lib721, 95C.KO, Bisulfite, TGIRT, rep3

description: Library name: Sample 3

value: (delta)RsmB


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

description:
Library name: Sample 6
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM056_5

description: MitoIP-Thor-Ribo-Seq

value: GTPBP3 KO


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

description: Library name: Sample 36


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

description:
Library name: Sample 5
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM060_3

description: MitoIP-Thor-Ribo-Seq

value: QTRT1 KO


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

description: Library name: Sample 35


title: Pfuri, lib721, 95C.KO, Bisulfite, TGIRT, rep1

description: Library name: Sample 1


title: SIMM056_2

description: MitoIP-Thor-Ribo-Seq


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

description: Library name: Sample 108

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: HsSc, lib553, control, NaBH4HydBiotin, RTHIV, rep1

description:
Library name: Sample 3
RNA extracts from H. sapiens and S.cerevisiae were pooled together


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

description:
Library name: Sample 4
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM049_6

description: MitoIP-Thor-Ribo-Seq

value: NSUN3 KO#2


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

description: Library name: Sample 34


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

description: Library name: Sample 107


title: SIMM056_6

description: MitoIP-Thor-Ribo-Seq


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

description: Library name: Sample 32


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

description: Library name: Sample 106


title: SIMM049_5

description: MitoIP-Thor-Ribo-Seq

value: NSUN3 KO#1


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

description: Library name: Sample 33


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

description:
Library name: Sample 1
RNA extracts from H. sapiens and S.cerevisiae were pooled together


title: SIMM049_4

description: MitoIP-Thor-Ribo-Seq

value: ALKBH1 KO#2


title: Pfuri, lib721, 95C.KO, Bisulfite, TGIRT, rep2

description: Library name: Sample 2


title: SIMM056_1

description: MitoIP-Thor-Ribo-Seq


title: SIMM049_3

description: MitoIP-Thor-Ribo-Seq

value: ALKBH1 KO#1


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

description: Library name: Sample 31


title: A549 cells, CRISPRd_miR454-#1

city: Chongqing

first: youquan

last: bu

address: Medical College Road No.1

country: China

institute: Chongqing Medical University

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

molecule: polyA RNA

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

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

value: Human Non-Small Cell Lung Cancer Cells

value: Knockout miR454


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

description: Library name: Sample 105


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

description: Library name: Sample 30


title: A549 cells, CRISPRd_Control

value: Control


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

description: Library name: Sample 104

value: Bacterial culture


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

description: Library name: Sample 29

value: WT


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

description: Library name: Sample 103


title: SIMM049_2

description: MitoIP-Thor-Ribo-Seq


title: A549 cells, CRISPRd_miR301a-#2

value: Knockout miR301a


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

description: Library name: Sample 102


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

description: Library name: Sample 28


title: A549 cells, LV-3+4

value: Combined overexpression of miR301a and miR454


title: Small intestine, Lgr5-high, Cystine, rep7

city: CAMBRIDGE

first: Qiming

last: Zhang

state: MA

address: 88 Ames Street

country: USA

institute: Koch institute

data_processing:
The reads were used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 and gene level summaries were prepared using tximport version 1.16.1
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file includes raw counts for each sample

organism: Mus musculus

source_name: Small intestine

extract_protocol:
RNA was extracted from organoids using TRIzol and Ambion PureLink RNA Mini Kit (Thermo Fisher Scientific, 12-183-018 A) according to the manufacturer’s instructions
NEBNext Ultra II Directional RNA preparation with poly(A) selection is used to selectively capture mRNA from total RNA and barcoded libraries were generated

value: Small intestine

value: Cystine diet


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

description: Library name: Sample 101


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

description:
Library name: Sample 2
RNA extracts from H. sapiens and S.cerevisiae were pooled together

value: cell culture

value: HEK 293T

value: Human embryonic kidney cells

value: control


title: A549 cells, LV-miR454

value: Overexpression of miR454


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

description: Library name: Sample 100


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

description: Library name: Sample 26


title: Small intestine, Lgr5-high, Cystine, rep5


title: A549 cells, LV-miR301a

value: Overexpression of miR301a


title: A549 cells, LV-vector-34


title: Small intestine, Lgr5-high, Cystine, rep4


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

description: Library name: Sample 99


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

description: Library name: Sample 98


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

description: Library name: Sample 24


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

description: Library name: Sample 25


title: A549 cells, LV-P+S

value: Combined overexpression of PRR11 and SKA2


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

description: Library name: Sample 97


title: Small intestine, Lgr5-high, Cystine, rep3


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

description: Library name: Sample 96


title: A549 cells, LV-SKA2

value: Overexpression of SKA2


title: Small intestine, Lgr5-high, Cystine, rep2


title: A549 cells, LV-PRR11

value: Human Non-Small Cell Lung Cancer Cells

value: Overexpression of PRR11


title: SIMM049_1

description: MitoIP-Thor-Ribo-Seq

value: naive


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

description: Library name: Sample 22

value: Bacterial culture


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

description: Library name: Sample 21

value: WT


title: A549 cells, LV-vector-PS

value: Control


title: Small intestine, Lgr5-high, Cystine, rep6


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

description: Library name: Sample 94


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

description: Library name: Sample 18

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_000005845.2
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Escherichia coli

source_name: bacterial culture

growth_protocol: Grown in LB medium to mid-log phase (OD600  ~0.35) at  37°C

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

value: bacterial culture

value: K-12 substrain MG1655


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

description: Library name: Sample 20


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

description: Library name: Sample 27


title: Small intestine, Lgr5-high, CD, rep7

value: Small intestine

value: Control diet


title: Small intestine, Lgr5-high, CD, rep6


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

description: Library name: Sample 19


title: Small intestine, Lgr5-high, CD, rep5


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

description: Library name: Sample 17


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

description: Library name: Sample 93


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

description: Library name: Sample 18


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

description: Library name: Sample 92


title: Small intestine, Lgr5-high, Cystine, rep1

value: Cystine diet


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

description: Library name: Sample 95


title: Small intestine, Lgr5-high, CD, rep4


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

description: Library name: Sample 23


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

description: Library name: Sample 16


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

description: Library name: Sample 17


title: Small intestine, Lgr5-high, CD, rep3


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

description: Library name: Sample 15


title: Small intestine, Lgr5-high, CD, rep2


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

description: Library name: Sample 15


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

description: Library name: Sample 14


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

description: Library name: Sample 90


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

description: Library name: Sample 16


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

description: Library name: Sample 12


title: Small intestine, Lgr5-high, CD, rep1


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

description: Library name: Sample 91


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

description: Library name: Sample 13


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

description: Library name: Sample 89


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

description: Library name: Sample 87


title: Small intestine, Lgr5-low, Cystine, rep7


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

description: Library name: Sample 11


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

description: Library name: Sample 88


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

description: Library name: Sample 86


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

description: Library name: Sample 10


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

description: Library name: Sample 85


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

description: Library name: Sample 84


title: Small intestine, Lgr5-low, Cystine, rep5


title: Small intestine, Lgr5-low, Cystine, rep3


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

description: Library name: Sample 9


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

description: Library name: Sample 11


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

description: Library name: Sample 7


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

description: Library name: Sample 12


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

description: Library name: Sample 10


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

description: Library name: Sample 83


title: Phalo, lib697, 25C, NaBH4HydBiotin, RTHIV, rep2

description: Library name: Sample 14


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

description: Library name: Sample 9


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

description: Library name: Sample 8


title: Small intestine, Lgr5-low, Cystine, rep2


title: Small intestine, Lgr5-low, Cystine, rep1


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

description: Library name: Sample 6


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

description: Library name: Sample 7


title: Small intestine, Lgr5-low, Cystine, rep4


title: Small intestine, Lgr5-low, Cystine, rep6


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

description: Library name: Sample 13


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

description: Library name: Sample 82


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

description: Library name: Sample 5


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

description: Library name: Sample 81


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

description: Library name: Sample 80


title: Small intestine, Lgr5-low, CD, rep7


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

description: Library name: Sample 6


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

description: Library name: Sample 4


title: Small intestine, Lgr5-low, CD, rep6


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

description: Library name: Sample 8


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

description: Library name: Sample 79


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

description: Library name: Sample 5


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

description: Library name: Sample 3


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

description: Library name: Sample 77


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

description: Library name: Sample 1


title: Small intestine, Lgr5-low, CD, rep4


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

description: Library name: Sample 4


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

description: Library name: Sample 2


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

description: Library name: Sample 78


title: Small intestine, Lgr5-low, CD, rep5


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

description: Library name: Sample 2


title: Small intestine, Lgr5-low, CD, rep3


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

description: Library name: Sample 3


title: SIMM069_4

description: MitoIP-Thor-Ribo-Seq

source_name: Heart

value: Heart

value: NSUN3 KO


title: SITW051_2

description: Library name: L112

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

organism: Mus

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

value: naïve

value: chloramphenicol


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

description: Library name: Sample 1


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

description: Library name: Sample 75


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

description: Library name: Sample 74


title: Prx1 Cre; Ai9/+; Piezo1 fl/fl mice

city: ShangHai

first: Lijun

last: Wang

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description: BD Rhapsody system

library_source: transcriptomic single cell

data_processing: scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp[44] with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. UMI-tools was applied for Single Cell Transcriptome Analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to human genome (Ensemble version 100) utilizing STAR[45] mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample. Cells contained over 200 expressed genes and mitochondria UMI rate below 40% passed the cell quality filtering and mitochondria genes were removed in the expression table.  Seurat package (version:4.0.3, https://satijalab.org/seurat/) was used for cell normalization. The fastMNN function from R package scran (v3.6.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1. To identify the cell type detailed, the clusters of same cell type were selected for re-tSNE analysis, graph-based clustering and marker analysis. Pseudotime trajectories were constructed using the R package Monocle 2 [46]. We selected the certain genes in cell clusters 0, 1, 2, 3, and 4. Subsequently, the expression profile was reduced to two dimensions using the DDRTree algorithm and the cells were sorted using the certain genes to obtain a trajectory map.

source_name: periosteum

extract_protocol:
Periosteal cells were extracted from femurs and tibias of Prx1 Cre; Ai9/+ and Prx1 Cre; Ai9/+; Piezo1 fl/fl mice at 8 week.  The femurs and tibias were capped by 5-10% Low Melting Point Agarose and then digested for 3 times (10 min, 45 min,45 min) with digestion buffer (1mg/ml collagenase, 2mg/ml dispase II and 1U/ml Dnase I in αMEM). The digested cells of the last two times were collected for sorting.
The red blood cells were removed by RBC lysis buffer for 5 min (Beyotime, C3702). Then the Prx1 positive cells were sorted by BD FACS Aria Fusion. After thawing and resuscitation, the dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further captured using BD Rhapsody system.
BD Rhapsody system was used to capture the transcriptomic information of the 2 samples-derived single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. Cell-lysis buffer was added so that poly-adenylated RNA molecules hybridized to the beads. Beads were collected into a single tube for reverse transcription. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell label indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification workflow. In brief, second strand cDNA was synthesized, followed by ligation of the WTA adaptor for universal amplification. Eighteen cycles of PCR were used to amplify the adaptor-ligated cDNA products. Sequencing libraries were prepared using random priming PCR of the whole-transcriptome amplification products to enrich the 3′ end of the transcripts linked with the cell label and UMI. Sequencing libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). The library for each sample was sequenced by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: periosteum

value: Prx1 Cre; Ai9/+; Piezo1 fl/fl mice


title: SIMM069_3

description: MitoIP-Thor-Ribo-Seq


title: SIMM069_2

description: MitoIP-Thor-Ribo-Seq


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

description: Library name: Sample 73


title: MCF-7/ADR cells

status: Public on Oct 21 2025

city: Guangzhou

first: Shaohua

last: Qu

state: Guangdong

address: No. 613, Huangpu West Avenue, Tianhe District, Guangzhou, Guangdong, P.R. China

institute: Department of Breast Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China

description: Library name: Sample 2

data_processing:
Raw image files were converted to sequencing reads (FASTQ format) by base calling. Per-base sequencing quality scores (Qphred) were calculated using the standard Phred algorithm, where `Qphred = -10log10(e)` and `e` is the estimated probability of a base call being incorrect.
Raw data quality was assessed using FastQC. Adapters and low-quality sequences were filtered out using the fastp software to generate high-quality clean data. Quality metrics for both raw and clean data were summarized.
Transcript and gene-level expression abundance was estimated from the clean data using RSEM(RNA-Seq by Expectation-Maximization).
Assembly: GRCh38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: MCF-7 cells

growth_protocol: Both of the MCF-7 and MCF-7/ADR cells were grown in DMEM (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) and antibiotics (100 U/ml penicillin and 100 mg/ml streptomycin) (Gibco, USA) at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen)
Sequencing libraries were prepared from rRNA-depleted RNA using the VAHTS Universal V8 RNA-seq Kit for Illumina (Vazyme, NR611)per manufacturer instructions. RNA was fragmented (~300 bp) and reverse transcribed into cDNA. During second-strand synthesis, dTTP was replaced with dUTP to enable strand-specificity. Following adapter ligation, the **dUTP-marked second strand was digested with USER enzyme, preserving only the first strand. Libraries were then PCR-amplified, indexed, and purified.Final libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform for PE150 sequencing.

treatment_protocol: The ADM-resistant cell line, MCF-7/ADR cells have long been cultured in our laboratory and were treated with a low concentration ofADM (1μM) every 4 weeks to maintain cell resistance

value: MCF-7 cells

value: Breast cancer epithelial cells


title: Prx1 Cre; Ai9/+  mice

description: BD Rhapsody system

treatment_protocol: Periosteal cells were extracted from femurs and tibias of Prx1 Cre; Ai9/+ and Prx1 Cre; Ai9/+; Piezo1 fl/fl mice at 8 week.

value: Prx1 Cre; Ai9/+  mice


title: SITW051_1

description: Library name: L111


title: SIMM069_1

description: MitoIP-Thor-Ribo-Seq

value: naive


title: MCF-7 cells

description: Library name: Sample 1


title: Small intestine, Lgr5-low, CD, rep1


title: 3X-58_POST

city: Ann Arbor

first: Jeffrey

last: Horowitz

state: MI

address: 830 N University Ave

department: School of Kinesiology

institute: University of Michigan

description: Library name: Sample 90

data_processing:
Genes with low counts were filtered prior to differential expression analysis. Specifically, genes were retained if they had a count ≥10 in at least 15 samples (smallest group size), reducing the total number of genes from ~63,000 to 17,466. Differential expression was then performed using DESeq2 with the design: ~ group + group:ID.n + group:condition, which accounts for within-subject pairing across pre/post samples within each exercise group.
Assembly: GENCODE v44
Supplementary files format and content: csv file inlcudes raw counts for each Sample

source_name: abdominal subcutaneous adipose tissue

extract_protocol:
RNA was extracted by using a Qiagen Mini RNA extraction kit (74004, Qiagen)
Total RNAs were polyA enriched, and directional RNA-seq libraries were prepared using the NEBNext Ultra II RNA library prep Kit.The paired-end RNA-seq reads were mapped to human transcripts annotated in GENCODE v44 using Bowtie. Gene level read counts were estimated using rSeq.

value: abdominal subcutaneous adipose tissue

value: adipose tissue

value: wild type

value: Exercise(high, moderate, or low intensity)

tag: time

value: 1.5 h post-exercise


title: 3X-58_PRE

description: Library name: Sample 89

value: Pre-exercise


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

description: Library name: Sample 76

value: Bacterial culture

value: WT


title: 3X-57_POST

description: Library name: Sample 88


title: Small intestine, Lgr5-low, CD, rep2

value: Small intestine

value: Control diet


title: 3X-57_PRE

description: Library name: Sample 87


title: 3X-54_POST

description: Library name: Sample 82


title: 3X-55_PRE

description: Library name: Sample 83


title: 3X-56_POST

description: Library name: Sample 86


title: 3X-56_PRE

description: Library name: Sample 85


title: 3X-53_PRE

description: Library name: Sample 79


title: 3X-53_POST

description: Library name: Sample 80


title: 3X-55_POST

description: Library name: Sample 84


title: 3X-52_POST

description: Library name: Sample 78


title: 3X-54_PRE

description: Library name: Sample 81


title: 3X-52_PRE

description: Library name: Sample 77


title: 3X-51_POST

description: Library name: Sample 76


title: 3X-51_PRE

description: Library name: Sample 75


title: 3X-50_POST

description: Library name: Sample 74


title: 3X-49_PRE

description: Library name: Sample 71


title: 3X-50_PRE

description: Library name: Sample 73


title: 3X-48_POST

description: Library name: Sample 70


title: 3X-49_POST

description: Library name: Sample 72


title: 3X-47_POST

description: Library name: Sample 68


title: 3X-48_PRE

description: Library name: Sample 69


title: 3X-47_PRE

description: Library name: Sample 67


title: 3X-44_POST

description: Library name: Sample 64


title: 3X-46_POST

description: Library name: Sample 66


title: 3X-46_PRE

description: Library name: Sample 65


title: 3X-44_PRE

description: Library name: Sample 63


title: 3X-43_POST

description: Library name: Sample 62


title: 3X-42_POST

description: Library name: Sample 60


title: 3X-43_PRE

description: Library name: Sample 61


title: 3X-41_POST

description: Library name: Sample 58


title: 3X-39_POST

description: Library name: Sample 56


title: 3X-42_PRE

description: Library name: Sample 59


title: 3X-35_POST

description: Library name: Sample 48


title: 3X-38_PRE

description: Library name: Sample 53


title: 3X-38_POST

description: Library name: Sample 54


title: 3X-39_PRE

description: Library name: Sample 55


title: 3X-37_POST

description: Library name: Sample 52


title: 3X-37_PRE

description: Library name: Sample 51


title: 3X-36_POST

description: Library name: Sample 50


title: 3X-35_PRE

description: Library name: Sample 47


title: 3X-32_PRE

description: Library name: Sample 45


title: 3X-30_PRE

description: Library name: Sample 43


title: 3X-36_PRE

description: Library name: Sample 49


title: 3X-30_POST

description: Library name: Sample 44


title: 3X-32_POST

description: Library name: Sample 46


title: 3X-29_POST

description: Library name: Sample 42


title: 3X-28_POST

description: Library name: Sample 40


title: 3X-29_PRE

description: Library name: Sample 41


title: 3X-26_POST

description: Library name: Sample 38


title: 3X-26_PRE

description: Library name: Sample 37


title: 3X-25_PRE

description: Library name: Sample 35


title: 3X-24_POST

description: Library name: Sample 34


title: 3X-41_PRE

description: Library name: Sample 57


title: 3X-25_POST

description: Library name: Sample 36


title: 3X-24_PRE

description: Library name: Sample 33


title: 3X-22_POST

description: Library name: Sample 30


title: 3X-23_PRE

description: Library name: Sample 31


title: 3X-22_PRE

description: Library name: Sample 29


title: 3X-20_POST

description: Library name: Sample 28


title: 3X-20_PRE

description: Library name: Sample 27


title: 3X-19_PRE

description: Library name: Sample 25


title: 3X-18_PRE

description: Library name: Sample 23


title: 3X-17_POST

description: Library name: Sample 22


title: 3X-17_PRE

description: Library name: Sample 21


title: 3X-28_PRE

description: Library name: Sample 39


title: 3X-14_PRE

description: Library name: Sample 17


title: 3X-12_POST

description: Library name: Sample 16


title: 3X-11_PRE

description: Library name: Sample 13


title: 3X-10_PRE

description: Library name: Sample 11


title: 3X-10_POST

description: Library name: Sample 12


title: 3X-23_POST

description: Library name: Sample 32


title: 3X-09_POST

description: Library name: Sample 10


title: 3X-07_PRE

description: Library name: Sample 7


title: 3X-09_PRE

description: Library name: Sample 9


title: 3X-07_POST

description: Library name: Sample 8


title: 3X-04_POST

description: Library name: Sample 4


title: 3X-04_PRE

description: Library name: Sample 3


title: 3X-05_POST

description: Library name: Sample 6


title: 3X-05_PRE

description: Library name: Sample 5


title: 3X-01_PRE

description: Library name: Sample 1


title: 3X-15_PRE

description: Library name: Sample 19


title: HeLa, mutFTO, 0 Dt, rep1

city: Beijing

first: Jun

last: Liu

address: Haidian District

department: School of Life Sciences

institute: Peking University

description:
Library name: HeLa_mutFTO_0_Dt_rep1
HeLa_mutFTO_0_Dt_rep1

library_source: genomic

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.7), then trimmed reads mapping to ribosomal RNAs were removed by Bowtie2 (v2.2.5).
The remaining reads were aligned to the human genome (hg38) using HISAT2 (v2.2.1) with ‘--rna-strandness RF’ parameters.
Gene expression was analyzed using featureCounts (v2.0.1) with the annotation file (hg38) from UCSC table browser (https://genome.ucsc.edu/). Differential gene expression analysis was performed by DESeq2 (v1.42.0) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample
Library strategy: CRISPR screen

molecule: genomic DNA

source_name: cell line

extract_protocol:
Cells were harvested and total RNA was extracted using TRIZOL reagent (Invitrogen) following the manufacturer’s protocols. To isolate mRNA from total RNA, the Dynabeads® mRNA Purification Kit (Invitrogen) was used following the manufacturer’s protocols. The RNA concentration was determined using Nanodrop (Invitrogen) by measuring the UV absorbance at 260 nm.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) following manufacturer's protocols.

value: cell line

value: HeLa

value: human cervical cancer (CC) cell line

value: sgRNA transfection


title: 3X-01_POST

description: Library name: Sample 2


title: 3X-15_POST

description: Library name: Sample 20


title: HeLa, mutFTO, 14 Dt, rep1

description:
Library name: HeLa_mutFTO_14_Dt_rep1
HeLa_mutFTO_14_Dt_rep1


title: 3X-14_POST

description: Library name: Sample 18


title: 3X-19_POST

description: Library name: Sample 26


title: HeLa, wtFTO, 14 Dt, rep2

description:
Library name: HeLa_wtFTO_14_Dt_rep2
HeLa_wtFTO_14_Dt_rep2


title: 3X-18_POST

description: Library name: Sample 24


title: 3X-11_POST

description: Library name: Sample 14


title: HeLa, wtFTO, 14 Dt, rep1

description:
Library name: HeLa_wtFTO_14_Dt_rep1
HeLa_wtFTO_14_Dt_rep1


title: HeLa, wtFTO, 0 Dt, rep1

description:
Library name: HeLa_wtFTO_0_Dt_rep1
HeLa_wtFTO_0_Dt_rep1


title: 3X-12_PRE

description: Library name: Sample 15


title: HCT116, mutFTO, 14 Dt, rep1

description:
Library name: HCT116_mutFTO_14_Dt_rep1
HCT116_mutFTO_14_Dt_rep1

value: human colorectal cancer (CRC) cell line


title: HeLa, wtFTO, 0 Dt, rep2

description:
Library name: HeLa_wtFTO_0_Dt_rep2
HeLa_wtFTO_0_Dt_rep2


title: HCT116, wtFTO, 14 Dt, rep2

description:
Library name: HCT116_wtFTO_14_Dt_rep2
HCT116_wtFTO_14_Dt_rep2


title: HCT116, wtFTO, 14 Dt, rep1

description:
Library name: HCT116_wtFTO_14_Dt_rep1
HCT116_wtFTO_14_Dt_rep1


title: HCT116, wtFTO, 0 Dt, rep2

description:
Library name: HCT116_wtFTO_0_Dt_rep2
HCT116_wtFTO_0_Dt_rep2


title: HepG2, mutFTO, 14 Dt, rep1

description:
Library name: HepG2_mutFTO_14_Dt_rep1
HepG2_mutFTO_14_Dt_rep1

value: human hepatocellular carcinoma (HCC) cell line


title: HepG2, wtFTO, 14 Dt, rep2

description:
Library name: HepG2_wtFTO_14_Dt_rep2
HepG2_wtFTO_14_Dt_rep2


title: HepG2, mutFTO, 0 Dt, rep1

description:
Library name: HepG2_mutFTO_0_Dt_rep1
HepG2_mutFTO_0_Dt_rep1


title: HepG2, wtFTO, 0 Dt, rep2

description:
Library name: HepG2_wtFTO_0_Dt_rep2
HepG2_wtFTO_0_Dt_rep2


title: HepG2, wtFTO, 14 Dt, rep1

description:
Library name: HepG2_wtFTO_14_Dt_rep1
HepG2_wtFTO_14_Dt_rep1


title: HepG2, wtFTO, 0 Dt, rep1

description:
Library name: HepG2_wtFTO_0_Dt_rep1
HepG2_wtFTO_0_Dt_rep1


title: SMMC-7721, wtFTO, 14 Dt, rep2

description:
Library name: SMMC7721_wtFTO_14_Dt_rep2
SMMC7721_wtFTO_14_Dt_rep2


title: SMMC-7721, mutFTO, 0 Dt, rep1

description:
Library name: SMMC7721_mutFTO_0_Dt_rep1
SMMC7721_mutFTO_0_Dt_rep1


title: SMMC-7721, mutFTO, 14 Dt, rep1

description:
Library name: SMMC7721_mutFTO_14_Dt_rep1
SMMC7721_mutFTO_14_Dt_rep1


title: SMMC-7721, wtFTO, 14 Dt, rep1

description:
Library name: SMMC7721_wtFTO_14_Dt_rep1
SMMC7721_wtFTO_14_Dt_rep1


title: SMMC-7721, wtFTO, 0 Dt, rep2

description:
Library name: SMMC7721_wtFTO_0_Dt_rep2
SMMC7721_wtFTO_0_Dt_rep2


title: SMMC-7721, wtFTO, 0 Dt, rep1

description:
Library name: SMMC7721_wtFTO_0_Dt_rep1
SMMC7721_wtFTO_0_Dt_rep1


title: HCT116, wtFTO, 0 Dt, rep1

description:
Library name: HCT116_wtFTO_0_Dt_rep1
HCT116_wtFTO_0_Dt_rep1


title: Jurkat_Jur_Uninfected_CRISPRi_HIVTargeting_rep_2

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: 295 Congress Ave

institute: Yale University

description:
Library name: Jur_Hi_2
Column name: Jur_Hi_2

data_processing:
Adaptor sequences were removed with Cutadapt (Martin 2011) (v4)
Mapped reads to our reference genome with bowtie2 (v2.5) with set parameters “--very-sensitive  -k 20”(Langmead and Salzberg 2012)
We called ATAC peaks with Genrich (https://github.com/jsh58/Genrich) arguments “-j -y -r -e chrM -v” as in (Collora and Ho 2023) after Samtools (Li et al. 2009)(v1.17) was used to sort and index the mapped reads. Peaks were merged across all samples via Bedtools (Quinlan and Hall 2010)(v2.30.0).
Duplicate reads were identified with Piccard’s (v3.0.0; https://broadinstitute.github.io/picard/; Broad Institute) markduplicates function.
For each set of samples to be directly compared (that is, the gene-activating or gene-inhibiting samples for a given integration site), Samtools was used to down-sample reads without replacement to the lowest molecular complexity among the compared samples. The Piccard-identified duplicate reads were then removed.
We quantified reads in peaks with Bedtools multicov and generated coverage data in a Bigwig file at 10 nt resolution with the Deeptools (v3.5) bamCoverage function (Ramirez et al. 2014), normalizing to CPM (generating processed data .bw files). Tracks for plotting were also obtained with the ATACorrect function from TOBIAS. "Peaks" were added corresponding to 5kb on each side of the HIV integration sites to quantify HIV impact on accessibility.
Normalization of peak counts was performed by NormOffsets function from csaw, specifically between samples being compared at the time of differential expression analysis, so we provide the original counts of reads mapping to peaks that would be used in each comparison (followed by edgeR for differential accessibility analysis).
Assembly: Custom (To generate a reference genome for HIV-1 and the human genome, the HIV-1-d6-GFP sequence was added as a “25th chromosome” to the hg38 reference genome accessed from NCBI. Here, HIV chromosome is labeled as "25".)
Supplementary files format and content: csv file provides peaks and associated read counts for all samples.
Supplementary files format and content: bigwig file for each sample provides CPM-normalized coverage as assessed by Deeptools (v3.5) bamCoverage.

source_name: Jurkat

growth_protocol: Cell lines were cultured in RPMI 1640 (Thermo Fisher Scientific 11875093) supplemented with 10% heat-inactivated fetal bovine serum (Thermo Fisher Scientific 10438026). Two antibiotics were added to select for each of gRNA and dCas9 fusion protein transduction.

extract_protocol:
Approximately 200,000 cells from each Jurkat T cell clone underwent Ficoll density  gradient centrifugation for dead cell removal (Ficoll-Paque PLUS Medium, VWR #95038-168). Approximately 50,000 cells per aliquot (3 replicates per Jurkat T cell clone) were used for ATAC-seq and 50,000 cells per aliquot for RNA-seq. For ATAC-seq, aliquots 50,000 cells were resuspended in 50 µL ATAC-lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% digitonin) on ice for 3 min. We then diluted the mixture with 1mL ATAC-wash (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Cells were washed and pelleted then transposed for 30 min at 37˚C (1× TD buffer with 33% PBS, 0.1% Tween-20, 0.01% digitonin, 2.5 µL TDE1). After transposition, DNA was isolated using Qiagen MinElute PCR cleanup kit, #28004.
Library prep was performed using NEBNext Ultra II Q5 master mix (NEB #M0544X) and Nextera indexed according to NEBNext Ultra II (NEB #E7645) instructions. Following baseline amplification, typically 8 cycles, SYBR qPCR was used to determine total cycle numbers needed. Typically, a total of 12 additional PCR cycles of library amplification were added, depending on qPCR results. After validating library size on an Agilent TapeStation, 150-bp paired-end sequencing was performed by NovaSeq 6000 at Yale Center for Genome Sequencing.

treatment_protocol: For CRISPRa, gRNAs were clone into lentiSAMv216 (containing blasticidin selection marker, Addgene #75112)(Joung et al. 2017), which contains dCas9-VP64 and MS2 binding loop in the sgRNA backbone to recruit activation domains p65 and HSF1 (encoded on the Lenti-MPHv2 vector). This synergistic activation mediator (SAM) complex increases dCas9-VP64 mediated gRNA-specific activation. For CRISPRi, gRNAs were cloned into pCRISPRia-v2 (containing puromycin selection marker, Addgene #84832)(Horlbeck et al. 2016). Two days after transduction, cells underwent antibiotic selection for at least 1 week with 100 μg/mL hygromycin and 8 μg/mL blasticidin was used for CRISPRa and gRNA-transduced Jurkat T cell clones and 8 μg/mL blasticidin and 1.5 μg/mL puromycin for CRISPRi and gRNA transduced Jurkat T cell clones.

value: Jurkat


title: Jurkat_Jur_Uninfected_CRISPRi_nontargeting_rep_1

description:
Library name: Jur_Ni_1
Column name: Jur_Ni_1


title: Jurkat_Jur_Uninfected_CRISPRi_HIVTargeting_rep_3

description:
Library name: Jur_Hi_3
Column name: Jur_Hi_3


title: Jurkat_Jur_Uninfected_CRISPRa_HIVTargeting_rep_3

description:
Library name: Jur_Ha_3
Column name: Jur_Ha_3


title: Jurkat_Jur_Uninfected_CRISPRa_nontargeting_rep_3

description:
Library name: Jur_Na_3
Column name: Jur_Na_3


title: Jurkat_Jur_Uninfected_CRISPRa_nontargeting_rep_1

description:
Library name: Jur_Na_1
Column name: Jur_Na_1


title: Jurkat_Jur_Uninfected_CRISPRi_HIVTargeting_rep_1

description:
Library name: Jur_Hi_1
Column name: Jur_Hi_1


title: Jurkat_Jur_Uninfected_CRISPRi_nontargeting_rep_3

description:
Library name: Jur_Ni_3
Column name: Jur_Ni_3


title: Jurkat_Jur_Uninfected_CRISPRa_nontargeting_rep_2

description:
Library name: Jur_Na_2
Column name: Jur_Na_2


title: Jurkat_Jur_Uninfected_CRISPRa_HIVTargeting_rep_1

description:
Library name: Jur_Ha_1
Column name: Jur_Ha_1


title: Jurkat_Jur_Uninfected_CRISPRi_nontargeting_rep_2

description:
Library name: Jur_Ni_2
Column name: Jur_Ni_2


title: Jurkat_1D7_SPECC1_CRISPRa_geneTargeting_rep_3

description:
Library name: 1D7_ga_3
Column name: 1D7_ga_3


title: HCT116, mutFTO, 0 Dt, rep1

description:
Library name: HCT116_mutFTO_0_Dt_rep1
HCT116_mutFTO_0_Dt_rep1


title: Jurkat_1D7_SPECC1_CRISPRa_nontargeting_rep_2

description:
Library name: 22ATAC66
Column name: 22ATAC66


title: Jurkat_1D7_SPECC1_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1D7_Ha_3
Column name: 1D7_Ha_3


title: Jurkat_1D7_SPECC1_CRISPRa_nontargeting_rep_3

description:
Library name: 22ATAC67
Column name: 22ATAC67


title: Jurkat_1D7_SPECC1_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1D7_Ha_2
Column name: 1D7_Ha_2


title: Jurkat_1D7_SPECC1_CRISPRa_geneTargeting_rep_2

description:
Library name: 1D7_ga_2
Column name: 1D7_ga_2


title: Jurkat_1D7_SPECC1_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1D7_Ha_1
Column name: 1D7_Ha_1


title: Jurkat_1D7_SPECC1_CRISPRa_nontargeting_rep_1

description:
Library name: 22ATAC65
Column name: 22ATAC65


title: Jurkat_1D7_SPECC1_CRISPRa_geneTargeting_rep_1

description:
Library name: 1D7_ga_1
Column name: 1D7_ga_1


title: Jurkat_1D9_Intergenic_CRISPRi_HIVTargeting_rep_3

description:
Library name: 1D9_Hi_3
Column name: 1D9_Hi_3


title: Jurkat_1D9_Intergenic_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1D9_Ha_3
Column name: 1D9_Ha_3


title: Jurkat_1D9_Intergenic_CRISPRa_nontargeting_rep_3

description:
Library name: 1D9_Na_3
Column name: 1D9_Na_3


title: Jurkat_1D9_Intergenic_CRISPRi_nontargeting_rep_3

description:
Library name: 1D9_Ni_3
Column name: 1D9_Ni_3


title: Jurkat_1D9_Intergenic_CRISPRi_HIVTargeting_rep_2

description:
Library name: 1D9_Hi_2
Column name: 1D9_Hi_2


title: Jurkat_Jur_Uninfected_CRISPRa_HIVTargeting_rep_2

description:
Library name: Jur_Ha_2
Column name: Jur_Ha_2


title: Jurkat_1D9_Intergenic_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1D9_Ha_2
Column name: 1D9_Ha_2


title: Jurkat_1D9_Intergenic_CRISPRi_nontargeting_rep_2

description:
Library name: 1D9_Ni_2
Column name: 1D9_Ni_2


title: Jurkat_5F9_INPPL1_CRISPRi_HIVTargeting_rep_2

description:
Library name: 22ATAC38
Column name: 22ATAC38


title: Jurkat_1D9_Intergenic_CRISPRa_nontargeting_rep_2

description:
Library name: 1D9_Na_2
Column name: 1D9_Na_2


title: Jurkat_5F9_INPPL1_CRISPRi_HIVTargeting_rep_3

description:
Library name: 22ATAC39
Column name: 22ATAC39


title: Jurkat_1D9_Intergenic_CRISPRi_nontargeting_rep_1

description:
Library name: 1D9_Ni_1
Column name: 1D9_Ni_1


title: Jurkat_1D9_Intergenic_CRISPRa_nontargeting_rep_1

description:
Library name: 1D9_Na_1
Column name: 1D9_Na_1


title: Jurkat_5F9_INPPL1_CRISPRa_HIVTargeting_rep_3

description:
Library name: 5F9_Ha_3
Column name: 5F9_Ha_3


title: Jurkat_5F9_INPPL1_CRISPRi_geneTargeting_rep_3

description:
Library name: 5F9_gi_3
Column name: 5F9_gi_3


title: Jurkat_5F9_INPPL1_CRISPRi_nontargeting_rep_3

description:
Library name: 22ATAC42
Column name: 22ATAC42


title: Jurkat_1D9_Intergenic_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1D9_Ha_1
Column name: 1D9_Ha_1


title: Jurkat_5F9_INPPL1_CRISPRa_HIVTargeting_rep_2

description:
Library name: 5F9_Ha_2
Column name: 5F9_Ha_2


title: Jurkat_5F9_INPPL1_CRISPRi_nontargeting_rep_2

description:
Library name: 22ATAC41
Column name: 22ATAC41


title: Jurkat_5F9_INPPL1_CRISPRa_nontargeting_rep_2

description:
Library name: 22ATAC72
Column name: 22ATAC72


title: Jurkat_1D9_Intergenic_CRISPRi_HIVTargeting_rep_1

description:
Library name: 1D9_Hi_1
Column name: 1D9_Hi_1


title: Jurkat_5F9_INPPL1_CRISPRi_geneTargeting_rep_2

description:
Library name: 5F9_gi_2
Column name: 5F9_gi_2


title: Jurkat_5F9_INPPL1_CRISPRa_nontargeting_rep_1

description:
Library name: 22ATAC71
Column name: 22ATAC71


title: Jurkat_5F9_INPPL1_CRISPRi_HIVTargeting_rep_1

description:
Library name: 22ATAC37
Column name: 22ATAC37


title: Jurkat_5F9_INPPL1_CRISPRi_nontargeting_rep_1

description:
Library name: 22ATAC40
Column name: 22ATAC40


title: Jurkat_5F9_INPPL1_CRISPRi_geneTargeting_rep_1

description:
Library name: 5F9_gi_1
Column name: 5F9_gi_1


title: Jurkat_5F9_INPPL1_CRISPRa_geneTargeting_rep_1

description:
Library name: 5F9_ga_1
Column name: 5F9_ga_1


title: Jurkat_2F5_KLF12_CRISPRi_HIVTargeting_rep_3

description:
Library name: 2F5_Hi_3
Column name: 2F5_Hi_3


title: Jurkat_2F5_KLF12_CRISPRa_nontargeting_rep_3

description:
Library name: 2F5_Na_3
Column name: 2F5_Na_3


title: Jurkat_2F5_KLF12_CRISPRa_geneTargeting_rep_3

description:
Library name: 2F5_ga_3
Column name: 2F5_ga_3


title: Jurkat_2F5_KLF12_CRISPRi_geneTargeting_rep_3

description:
Library name: 2F5_gi_3
Column name: 2F5_gi_3


title: Jurkat_2F5_KLF12_CRISPRi_nontargeting_rep_3

description:
Library name: 2F5_Ni_3
Column name: 2F5_Ni_3


title: Jurkat_2F5_KLF12_CRISPRi_HIVTargeting_rep_2

description:
Library name: 2F5_Hi_2
Column name: 2F5_Hi_2


title: Jurkat_5F9_INPPL1_CRISPRa_nontargeting_rep_3

description:
Library name: 22ATAC73
Column name: 22ATAC73


title: Jurkat_5F9_INPPL1_CRISPRa_geneTargeting_rep_3

description:
Library name: 5F9_ga_3
Column name: 5F9_ga_3


title: Jurkat_2F5_KLF12_CRISPRa_HIVTargeting_rep_2

description:
Library name: 2F5_Ha_2
Column name: 2F5_Ha_2


title: Jurkat_5F9_INPPL1_CRISPRa_geneTargeting_rep_2

description:
Library name: 5F9_ga_2
Column name: 5F9_ga_2


title: Jurkat_2F5_KLF12_CRISPRi_nontargeting_rep_2

description:
Library name: 2F5_Ni_2
Column name: 2F5_Ni_2


title: Jurkat_2F5_KLF12_CRISPRi_geneTargeting_rep_2

description:
Library name: 2F5_gi_2
Column name: 2F5_gi_2


title: Jurkat_2F5_KLF12_CRISPRa_HIVTargeting_rep_1

description:
Library name: 2F5_Ha_1
Column name: 2F5_Ha_1


title: Jurkat_2F5_KLF12_CRISPRa_geneTargeting_rep_2

description:
Library name: 2F5_ga_2
Column name: 2F5_ga_2


title: Jurkat_2F5_KLF12_CRISPRa_nontargeting_rep_2

description:
Library name: 2F5_Na_2
Column name: 2F5_Na_2


title: Jurkat_2F5_KLF12_CRISPRi_HIVTargeting_rep_1

description:
Library name: 2F5_Hi_1
Column name: 2F5_Hi_1


title: Jurkat_1G2_RAP1B_CRISPRi_geneTargeting_rep_3

description:
Library name: 1G2_gi_3
Column name: 1G2_gi_3


title: Jurkat_2F5_KLF12_CRISPRa_HIVTargeting_rep_3

description:
Library name: 2F5_Ha_3
Column name: 2F5_Ha_3


title: Jurkat_1G2_RAP1B_CRISPRa_nontargeting_rep_3

description:
Library name: 22ATAC55
Column name: 22ATAC55


title: Jurkat_1G2_RAP1B_CRISPRi_nontargeting_rep_2

description:
Library name: 22ATAC29
Column name: 22ATAC29


title: Jurkat_1G2_RAP1B_CRISPRi_HIVTargeting_rep_3

description:
Library name: 22ATAC27
Column name: 22ATAC27


title: Jurkat_1G2_RAP1B_CRISPRa_geneTargeting_rep_3

description:
Library name: 1G2_ga_3
Column name: 1G2_ga_3


title: Jurkat_1G2_RAP1B_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1G2_Ha_3
Column name: 1G2_Ha_3


title: Jurkat_1G2_RAP1B_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1G2_Ha_2
Column name: 1G2_Ha_2


title: Jurkat_1G2_RAP1B_CRISPRi_nontargeting_rep_3

description:
Library name: 22ATAC30
Column name: 22ATAC30


title: Jurkat_1G2_RAP1B_CRISPRi_geneTargeting_rep_2

description:
Library name: 1G2_gi_2
Column name: 1G2_gi_2


title: Jurkat_1G2_RAP1B_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1G2_Ha_1
Column name: 1G2_Ha_1


title: Jurkat_1G2_RAP1B_CRISPRi_HIVTargeting_rep_1

description:
Library name: 22ATAC25
Column name: 22ATAC25


title: Jurkat_1G2_RAP1B_CRISPRa_nontargeting_rep_1

description:
Library name: 22ATAC53
Column name: 22ATAC53


title: Jurkat_5F9_INPPL1_CRISPRa_HIVTargeting_rep_1

description:
Library name: 5F9_Ha_1
Column name: 5F9_Ha_1


title: Jurkat_1G2_RAP1B_CRISPRa_geneTargeting_rep_1

description:
Library name: 1G2_ga_1
Column name: 1G2_ga_1


title: Jurkat_1G2_RAP1B_CRISPRi_HIVTargeting_rep_2

description:
Library name: 22ATAC26
Column name: 22ATAC26


title: Jurkat_1G2_RAP1B_CRISPRa_geneTargeting_rep_2

description:
Library name: 1G2_ga_2
Column name: 1G2_ga_2


title: Jurkat_8B10_NFX1_CRISPRi_geneTargeting_rep_3

description:
Library name: NFX_gi_3
Column name: NFX_gi_3


title: Jurkat_1G2_RAP1B_CRISPRi_geneTargeting_rep_1

description:
Library name: 1G2_gi_1
Column name: 1G2_gi_1


title: Jurkat_8B10_NFX1_CRISPRi_geneTargeting_rep_2

description:
Library name: NFX_gi_2
Column name: NFX_gi_2


title: Jurkat_8B10_VAV1_CRISPRi_nontargeting_rep_3

description:
Library name: 22ATAC36
Column name: 22ATAC36


title: Jurkat_8B10_NFX1_CRISPRi_geneTargeting_rep_1

description:
Library name: NFX_gi_1
Column name: NFX_gi_1


title: Jurkat_8B10_VAV1_CRISPRa_HIVTargeting_rep_3

description:
Library name: VAV_Ha_3
Column name: VAV_Ha_3


title: Jurkat_8B10_VAV1_CRISPRa_nontargeting_rep_3

description:
Library name: 22ATAC61
Column name: 22ATAC61


title: Jurkat_1G2_RAP1B_CRISPRa_nontargeting_rep_2

description:
Library name: 22ATAC54
Column name: 22ATAC54


title: Jurkat_8B10_VAV1_CRISPRi_geneTargeting_rep_3

description:
Library name: VAV_gi_3
Column name: VAV_gi_3


title: Jurkat_8B10_VAV1_CRISPRi_HIVTargeting_rep_3

description:
Library name: 22ATAC33
Column name: 22ATAC33


title: Jurkat_8B10_VAV1_CRISPRa_geneTargeting_rep_2

description:
Library name: VAV_ga_2
Column name: VAV_ga_2


title: Jurkat_8B10_VAV1_CRISPRi_HIVTargeting_rep_1

description:
Library name: 22ATAC31
Column name: 22ATAC31


title: Jurkat_8B10_VAV1_CRISPRi_nontargeting_rep_2

description:
Library name: 22ATAC35
Column name: 22ATAC35


title: Jurkat_8B10_VAV1_CRISPRa_nontargeting_rep_2

description:
Library name: 22ATAC60
Column name: 22ATAC60


title: Jurkat_8B10_VAV1_CRISPRi_HIVTargeting_rep_2

description:
Library name: 22ATAC32
Column name: 22ATAC32


title: Jurkat_8B10_VAV1_CRISPRa_nontargeting_rep_1

description:
Library name: 22ATAC59
Column name: 22ATAC59


title: Jurkat_8B10_VAV1_CRISPRa_HIVTargeting_rep_1

description:
Library name: VAV_Ha_1
Column name: VAV_Ha_1


title: Jurkat_8B10_VAV1_CRISPRa_HIVTargeting_rep_2

description:
Library name: VAV_Ha_2
Column name: VAV_Ha_2


title: Jurkat_8B10_VAV1_CRISPRa_geneTargeting_rep_3

description:
Library name: VAV_ga_3
Column name: VAV_ga_3


title: Jurkat_1A8_EEF2K_CRISPRi_nontargeting_rep_3

description:
Library name: 1A8_Ni_3
Column name: 1A8_Ni_3


title: Jurkat_1A8_EEF2K_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1A8_Ha_3
Column name: 1A8_Ha_3


title: Jurkat_1A8_EEF2K_CRISPRa_nontargeting_rep_3

description:
Library name: 1A8_Na_3
Column name: 1A8_Na_3


title: Jurkat_1A8_EEF2K_CRISPRi_geneTargeting_rep_3

description:
Library name: 1A8_gi_3
Column name: 1A8_gi_3


title: Jurkat_1A8_EEF2K_CRISPRi_HIVTargeting_rep_2

description:
Library name: 1A8_Hi_2
Column name: 1A8_Hi_2


title: Jurkat_1A8_EEF2K_CRISPRa_nontargeting_rep_2

description:
Library name: 1A8_Na_2
Column name: 1A8_Na_2


title: Jurkat_1A8_EEF2K_CRISPRi_nontargeting_rep_2

description:
Library name: 1A8_Ni_2
Column name: 1A8_Ni_2


title: Jurkat_1A8_EEF2K_CRISPRi_geneTargeting_rep_2

description:
Library name: 1A8_gi_2
Column name: 1A8_gi_2


title: Jurkat_1A8_EEF2K_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1A8_Ha_2
Column name: 1A8_Ha_2


title: Jurkat_1A8_EEF2K_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1A8_Ha_1
Column name: 1A8_Ha_1


title: Jurkat_1A8_EEF2K_CRISPRi_HIVTargeting_rep_3

description:
Library name: 1A8_Hi_3
Column name: 1A8_Hi_3


title: Jurkat_1A8_EEF2K_CRISPRi_nontargeting_rep_1

description:
Library name: 1A8_Ni_1
Column name: 1A8_Ni_1


title: Jurkat_1A8_EEF2K_CRISPRi_geneTargeting_rep_1

description:
Library name: 1A8_gi_1
Column name: 1A8_gi_1


title: Jurkat_8B10_VAV1_CRISPRi_nontargeting_rep_1

description:
Library name: 22ATAC34
Column name: 22ATAC34


title: Jurkat_1A8_EEF2K_CRISPRi_HIVTargeting_rep_1

description:
Library name: 1A8_Hi_1
Column name: 1A8_Hi_1


title: Jurkat_1A8_EEF2K_CRISPRa_nontargeting_rep_1

description:
Library name: 1A8_Na_1
Column name: 1A8_Na_1


title: Jurkat_1A8_EEF2K_CRISPRa_geneTargeting_rep_2

description:
Library name: 1A8_ga_2
Column name: 1A8_ga_2


title: Jurkat_8B10_VAV1_CRISPRi_geneTargeting_rep_2

description:
Library name: VAV_gi_2
Column name: VAV_gi_2


title: Jurkat_Jur_Uninfected_CRISPRa_nontargeting_rep_2

description:
Library name: Jur_Na_2
Column name: Jur_Na_2

data_processing:
Adaptor sequences were removed with Cutadapt (Martin 2011) (v4).
Mapping was done with the STAR aligner (v2.7.10b) on settings “--chimSegmentMin 20 —chimOutType WithinBAM” to identify splicing between HIV-1 and the human genome (Dobin et al. 2013).
Reads mapping to each gene were quantified with featureCounts, with TPM normalization calculated only between compared samples being done at time of differential expression analysis.
Assembly: Custom (To generate a reference genome for HIV-1 and the human genome, the HIV-1-d6-GFP sequence was added as a “25th chromosome” to the hg38 reference genome accessed from NCBI. We used the Gencode V44 basic gene annotations and added the HIV-1 annotations, and added annotations on each side of HIV integration sites. Here, HIV chromosome is labeled as "HIV")
Supplementary files format and content: csv file provides read counts from each annotated gene for all samples.

extract_protocol:
Approximately 200,000 cells from each Jurkat T cell clone underwent Ficoll density  gradient centrifugation for dead cell removal (Ficoll-Paque PLUS Medium, VWR #95038-168). Approximately 50,000 cells per aliquot (3 replicates per Jurkat T cell clone) were used for ATAC-seq and 50,000 cells per aliquot for RNA-seq. Triplicates of 50,000 cells were resuspended in TRIzol-reagent (Thermo Fisher Scientific, #15596026) for RNA extraction (Direct-zol-96 RNA, Zymo Research #R2056).
To identify sense versus anti-sense host gene and HIV-1 RNA transcription, we used NEBNext Ultra II Orientational RNA Library Prep Kit for Illumina for RNA-sequencing (NEB #E7760) for library prep with NEBNext rRNA Depletion Kit v2 (NEB #E7400). cDNA libraries were sequenced on NovaSeq 6000.


title: Jurkat_Jur_Uninfected_CRISPRi_HIVTargeting_rep_2

description:
Library name: Jur_Hi_2
Column name: Jur_Hi_2


title: Jurkat_1A8_EEF2K_CRISPRa_geneTargeting_rep_1

description:
Library name: 1A8_ga_1
Column name: 1A8_ga_1


title: Jurkat_Jur_Uninfected_CRISPRa_HIVTargeting_rep_2

description:
Library name: Jur_Ha_2
Column name: Jur_Ha_2


title: Jurkat_Jur_Uninfected_CRISPRi_nontargeting_rep_3

description:
Library name: Jur_Ni_3
Column name: Jur_Ni_3


title: Jurkat_Jur_Uninfected_CRISPRi_nontargeting_rep_2

description:
Library name: Jur_Ni_2
Column name: Jur_Ni_2


title: Jurkat_Jur_Uninfected_CRISPRa_HIVTargeting_rep_3

description:
Library name: Jur_Ha_3
Column name: Jur_Ha_3


title: Jurkat_Jur_Uninfected_CRISPRi_HIVTargeting_rep_1

description:
Library name: Jur_Hi_1
Column name: Jur_Hi_1


title: Jurkat_Jur_Uninfected_CRISPRa_HIVTargeting_rep_1

description:
Library name: Jur_Ha_1
Column name: Jur_Ha_1


title: Jurkat_Jur_Uninfected_CRISPRa_nontargeting_rep_3

description:
Library name: Jur_Na_3
Column name: Jur_Na_3


title: Jurkat_Jur_Uninfected_CRISPRa_nontargeting_rep_1

description:
Library name: Jur_Na_1
Column name: Jur_Na_1


title: Jurkat_1A8_EEF2K_CRISPRa_geneTargeting_rep_3

description:
Library name: 1A8_ga_3
Column name: 1A8_ga_3


title: Jurkat_Jur_Uninfected_CRISPRi_nontargeting_rep_1

description:
Library name: Jur_Ni_1
Column name: Jur_Ni_1


title: Jurkat_1D7_SPECC1_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1D7_Ha_3
Column name: 1D7_Ha_3


title: Jurkat_1D7_SPECC1_CRISPRa_geneTargeting_rep_3

description:
Library name: 1D7_ga_3
Column name: 1D7_ga_3


title: Jurkat_1D7_SPECC1_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1D7_Ha_1
Column name: 1D7_Ha_1


title: Jurkat_1D7_SPECC1_CRISPRa_nontargeting_rep_3

description:
Library name: 1D7_Na_3
Column name: 1D7_Na_3


title: Jurkat_1D7_SPECC1_CRISPRa_nontargeting_rep_1

description:
Library name: 1D7_Na_1
Column name: 1D7_Na_1


title: Jurkat_1D7_SPECC1_CRISPRa_geneTargeting_rep_1

description:
Library name: 1D7_ga_1
Column name: 1D7_ga_1


title: Jurkat_1D9_Intergenic_CRISPRi_HIVTargeting_rep_3

description:
Library name: 1D9_Hi_3
Column name: 1D9_Hi_3


title: Jurkat_Jur_Uninfected_CRISPRi_HIVTargeting_rep_3

description:
Library name: Jur_Hi_3
Column name: Jur_Hi_3


title: Jurkat_1D7_SPECC1_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1D7_Ha_2
Column name: 1D7_Ha_2


title: Jurkat_1D7_SPECC1_CRISPRa_nontargeting_rep_2

description:
Library name: 1D7_Na_2
Column name: 1D7_Na_2


title: Jurkat_1D9_Intergenic_CRISPRa_nontargeting_rep_3

description:
Library name: 1D9_Na_3
Column name: 1D9_Na_3


title: Jurkat_1D9_Intergenic_CRISPRi_HIVTargeting_rep_2

description:
Library name: 1D9_Hi_2
Column name: 1D9_Hi_2


title: Jurkat_1D9_Intergenic_CRISPRa_nontargeting_rep_2

description:
Library name: 1D9_Na_2
Column name: 1D9_Na_2


title: Jurkat_1D9_Intergenic_CRISPRi_nontargeting_rep_3

description:
Library name: 1D9_Ni_3
Column name: 1D9_Ni_3


title: Jurkat_1D9_Intergenic_CRISPRi_nontargeting_rep_2

description:
Library name: 1D9_Ni_2
Column name: 1D9_Ni_2


title: Jurkat_1D9_Intergenic_CRISPRi_HIVTargeting_rep_1

description:
Library name: 1D9_Hi_1
Column name: 1D9_Hi_1


title: Jurkat_1D9_Intergenic_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1D9_Ha_1
Column name: 1D9_Ha_1


title: Jurkat_1D9_Intergenic_CRISPRa_nontargeting_rep_1

description:
Library name: 1D9_Na_1
Column name: 1D9_Na_1


title: Jurkat_5F9_INPPL1_CRISPRi_HIVTargeting_rep_3

description:
Library name: 5F9_Hi_3
Column name: 5F9_Hi_3


title: Jurkat_5F9_INPPL1_CRISPRa_HIVTargeting_rep_3

description:
Library name: 5F9_Ha_3
Column name: 5F9_Ha_3


title: Jurkat_5F9_INPPL1_CRISPRi_geneTargeting_rep_3

description:
Library name: 5F9_gi_3
Column name: 5F9_gi_3


title: Jurkat_5F9_INPPL1_CRISPRi_nontargeting_rep_3

description:
Library name: 5F9_Ni_3
Column name: 5F9_Ni_3


title: Jurkat_5F9_INPPL1_CRISPRa_geneTargeting_rep_3

description:
Library name: 5F9_ga_3
Column name: 5F9_ga_3


title: Jurkat_5F9_INPPL1_CRISPRi_HIVTargeting_rep_2

description:
Library name: 5F9_Hi_2
Column name: 5F9_Hi_2


title: Jurkat_1D9_Intergenic_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1D9_Ha_2
Column name: 1D9_Ha_2


title: Jurkat_5F9_INPPL1_CRISPRa_HIVTargeting_rep_2

description:
Library name: 5F9_Ha_2
Column name: 5F9_Ha_2


title: Jurkat_5F9_INPPL1_CRISPRi_nontargeting_rep_2

description:
Library name: 5F9_Ni_2
Column name: 5F9_Ni_2


title: Jurkat_5F9_INPPL1_CRISPRa_nontargeting_rep_2

description:
Library name: 5F9_Na_2
Column name: 5F9_Na_2


title: Jurkat_5F9_INPPL1_CRISPRa_HIVTargeting_rep_1

description:
Library name: 5F9_Ha_1
Column name: 5F9_Ha_1


title: Jurkat_1D9_Intergenic_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1D9_Ha_3
Column name: 1D9_Ha_3


title: Jurkat_5F9_INPPL1_CRISPRa_nontargeting_rep_1

description:
Library name: 5F9_Na_1
Column name: 5F9_Na_1


title: Jurkat_5F9_INPPL1_CRISPRi_nontargeting_rep_1

description:
Library name: 5F9_Ni_1
Column name: 5F9_Ni_1


title: Jurkat_2F5_KLF12_CRISPRi_HIVTargeting_rep_3

description:
Library name: 2F5_Hi_3
Column name: 2F5_Hi_3


title: Jurkat_5F9_INPPL1_CRISPRi_geneTargeting_rep_1

description:
Library name: 5F9_gi_1
Column name: 5F9_gi_1


title: Jurkat_2F5_KLF12_CRISPRa_nontargeting_rep_3

description:
Library name: 2F5_Na_3
Column name: 2F5_Na_3


title: Jurkat_1D9_Intergenic_CRISPRi_nontargeting_rep_1

description:
Library name: 1D9_Ni_1
Column name: 1D9_Ni_1


title: Jurkat_2F5_KLF12_CRISPRa_HIVTargeting_rep_3

description:
Library name: 2F5_Ha_3
Column name: 2F5_Ha_3


title: Jurkat_2F5_KLF12_CRISPRi_geneTargeting_rep_3

description:
Library name: 2F5_gi_3
Column name: 2F5_gi_3


title: Jurkat_2F5_KLF12_CRISPRi_nontargeting_rep_3

description:
Library name: 2F5_Ni_3
Column name: 2F5_Ni_3


title: Jurkat_5F9_INPPL1_CRISPRa_nontargeting_rep_3

description:
Library name: 5F9_Na_3
Column name: 5F9_Na_3


title: Jurkat_2F5_KLF12_CRISPRi_geneTargeting_rep_2

description:
Library name: 2F5_gi_2
Column name: 2F5_gi_2


title: Jurkat_2F5_KLF12_CRISPRa_nontargeting_rep_2

description:
Library name: 2F5_Na_2
Column name: 2F5_Na_2


title: Jurkat_2F5_KLF12_CRISPRi_HIVTargeting_rep_2

description:
Library name: 2F5_Hi_2
Column name: 2F5_Hi_2


title: Jurkat_2F5_KLF12_CRISPRa_geneTargeting_rep_2

description:
Library name: 2F5_ga_2
Column name: 2F5_ga_2


title: Jurkat_2F5_KLF12_CRISPRa_geneTargeting_rep_3

description:
Library name: 2F5_ga_3
Column name: 2F5_ga_3


title: Jurkat_2F5_KLF12_CRISPRa_HIVTargeting_rep_1

description:
Library name: 2F5_Ha_1
Column name: 2F5_Ha_1


title: Jurkat_2F5_KLF12_CRISPRa_HIVTargeting_rep_2

description:
Library name: 2F5_Ha_2
Column name: 2F5_Ha_2


title: Jurkat_2F5_KLF12_CRISPRi_geneTargeting_rep_1

description:
Library name: 2F5_gi_1
Column name: 2F5_gi_1


title: Jurkat_2F5_KLF12_CRISPRi_nontargeting_rep_2

description:
Library name: 2F5_Ni_2
Column name: 2F5_Ni_2


title: Jurkat_2F5_KLF12_CRISPRi_HIVTargeting_rep_1

description:
Library name: 2F5_Hi_1
Column name: 2F5_Hi_1


title: Jurkat_2F5_KLF12_CRISPRa_nontargeting_rep_1

description:
Library name: 2F5_Na_1
Column name: 2F5_Na_1


title: Jurkat_1G2_RAP1B_CRISPRi_HIVTargeting_rep_3

description:
Library name: 1G2_Hi_3
Column name: 1G2_Hi_3


title: Jurkat_2F5_KLF12_CRISPRi_nontargeting_rep_1

description:
Library name: 2F5_Ni_1
Column name: 2F5_Ni_1


title: Jurkat_5F9_INPPL1_CRISPRa_geneTargeting_rep_2

description:
Library name: 5F9_ga_2
Column name: 5F9_ga_2


title: Jurkat_5F9_INPPL1_CRISPRi_geneTargeting_rep_2

description:
Library name: 5F9_gi_2
Column name: 5F9_gi_2


title: Jurkat_1G2_RAP1B_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1G2_Ha_3
Column name: 1G2_Ha_3


title: Jurkat_1G2_RAP1B_CRISPRa_nontargeting_rep_3

description:
Library name: 1G2_Na_3
Column name: 1G2_Na_3


title: Jurkat_1G2_RAP1B_CRISPRi_HIVTargeting_rep_2

description:
Library name: 1G2_Hi_2
Column name: 1G2_Hi_2


title: Jurkat_1G2_RAP1B_CRISPRi_geneTargeting_rep_3

description:
Library name: 1G2_gi_3
Column name: 1G2_gi_3


title: Jurkat_1G2_RAP1B_CRISPRa_geneTargeting_rep_3

description:
Library name: 1G2_ga_3
Column name: 1G2_ga_3


title: Jurkat_1G2_RAP1B_CRISPRi_nontargeting_rep_2

description:
Library name: 1G2_Ni_2
Column name: 1G2_Ni_2


title: Jurkat_1G2_RAP1B_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1G2_Ha_2
Column name: 1G2_Ha_2


title: Jurkat_1G2_RAP1B_CRISPRi_geneTargeting_rep_2

description:
Library name: 1G2_gi_2
Column name: 1G2_gi_2


title: Jurkat_1G2_RAP1B_CRISPRa_geneTargeting_rep_2

description:
Library name: 1G2_ga_2
Column name: 1G2_ga_2


title: Jurkat_1G2_RAP1B_CRISPRa_nontargeting_rep_2

description:
Library name: 1G2_Na_2
Column name: 1G2_Na_2


title: Jurkat_2F5_KLF12_CRISPRa_geneTargeting_rep_1

description:
Library name: 2F5_ga_1
Column name: 2F5_ga_1


title: Jurkat_1G2_RAP1B_CRISPRi_HIVTargeting_rep_1

description:
Library name: 1G2_Hi_1
Column name: 1G2_Hi_1


title: Jurkat_1G2_RAP1B_CRISPRi_nontargeting_rep_1

description:
Library name: 1G2_Ni_1
Column name: 1G2_Ni_1


title: Jurkat_1G2_RAP1B_CRISPRa_geneTargeting_rep_1

description:
Library name: 1G2_ga_1
Column name: 1G2_ga_1


title: Jurkat_1G2_RAP1B_CRISPRa_nontargeting_rep_1

description:
Library name: 1G2_Na_1
Column name: 1G2_Na_1


title: Jurkat_1G2_RAP1B_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1G2_Ha_1
Column name: 1G2_Ha_1


title: Jurkat_8B10_NFX1_CRISPRi_geneTargeting_rep_1

description:
Library name: 8B10_NFX1_gi_1
Column name: NFX_gi_1


title: Jurkat_8B10_VAV1_CRISPRi_nontargeting_rep_3

description:
Library name: 8B10_Ni_3
Column name: VAV_Ni_3


title: Jurkat_1G2_RAP1B_CRISPRi_geneTargeting_rep_1

description:
Library name: 1G2_gi_1
Column name: 1G2_gi_1


title: Jurkat_8B10_NFX1_CRISPRi_geneTargeting_rep_3

description:
Library name: 8B10_NFX1_gi_3
Column name: NFX_gi_3


title: Jurkat_8B10_NFX1_CRISPRi_geneTargeting_rep_2

description:
Library name: 8B10_NFX1_gi_2
Column name: NFX_gi_2


title: Jurkat_8B10_VAV1_CRISPRa_HIVTargeting_rep_3

description:
Library name: 8B10_Ha_3
Column name: 8B1_Ha_3


title: Jurkat_8B10_VAV1_CRISPRa_geneTargeting_rep_3

description:
Library name: 8B10_ga_3
Column name: VAV_ga_3


title: Jurkat_8B10_VAV1_CRISPRi_HIVTargeting_rep_2

description:
Library name: 8B10_Hi_2
Column name: 8B1_Hi_2


title: Jurkat_8B10_VAV1_CRISPRa_nontargeting_rep_3

description:
Library name: 8B10_Na_3
Column name: VAV_Na_3


title: Jurkat_8B10_VAV1_CRISPRa_HIVTargeting_rep_2

description:
Library name: 8B10_Ha_2
Column name: 8B1_Ha_2


title: Jurkat_8B10_VAV1_CRISPRi_nontargeting_rep_2

description:
Library name: 8B10_Ni_2
Column name: VAV_Ni_2


title: Jurkat_8B10_VAV1_CRISPRi_geneTargeting_rep_3

description:
Library name: 8B10_gi_3
Column name: VAV_gi_3


title: Jurkat_8B10_VAV1_CRISPRa_nontargeting_rep_2

description:
Library name: 8B10_Na_2
Column name: VAV_Na_2


title: Jurkat_8B10_VAV1_CRISPRa_geneTargeting_rep_2

description:
Library name: 8B10_ga_2
Column name: VAV_ga_2


title: Jurkat_8B10_VAV1_CRISPRi_HIVTargeting_rep_1

description:
Library name: 8B10_Hi_1
Column name: 8B1_Hi_1


title: Jurkat_1G2_RAP1B_CRISPRi_nontargeting_rep_3

description:
Library name: 1G2_Ni_3
Column name: 1G2_Ni_3


title: Jurkat_8B10_VAV1_CRISPRa_HIVTargeting_rep_1

description:
Library name: 8B10_Ha_1
Column name: 8B1_Ha_1


title: Jurkat_8B10_VAV1_CRISPRi_nontargeting_rep_1

description:
Library name: 8B10_Ni_1
Column name: VAV_Ni_1


title: Jurkat_8B10_VAV1_CRISPRi_geneTargeting_rep_2

description:
Library name: 8B10_gi_2
Column name: VAV_gi_2


title: Jurkat_8B10_VAV1_CRISPRa_nontargeting_rep_1

description:
Library name: 8B10_Na_1
Column name: VAV_Na_1


title: Jurkat_8B10_VAV1_CRISPRi_geneTargeting_rep_1

description:
Library name: 8B10_gi_1
Column name: VAV_gi_1


title: Jurkat_1A8_EEF2K_CRISPRa_HIVTargeting_rep_3

description:
Library name: 1A8_Ha_3
Column name: 1A8_Ha_3


title: Jurkat_8B10_VAV1_CRISPRi_HIVTargeting_rep_3

description:
Library name: 8B10_Hi_3
Column name: 8B1_Hi_3


title: Jurkat_1A8_EEF2K_CRISPRa_nontargeting_rep_3

description:
Library name: 1A8_Na_3
Column name: 1A8_Na_3


title: Jurkat_1A8_EEF2K_CRISPRi_geneTargeting_rep_3

description:
Library name: 1A8_gi_3
Column name: 1A8_gi_3


title: Jurkat_1A8_EEF2K_CRISPRa_geneTargeting_rep_3

description:
Library name: 1A8_ga_3
Column name: 1A8_ga_3


title: Jurkat_1A8_EEF2K_CRISPRa_HIVTargeting_rep_2

description:
Library name: 1A8_Ha_2
Column name: 1A8_Ha_2


title: Jurkat_8B10_VAV1_CRISPRa_geneTargeting_rep_1

description:
Library name: 8B10_ga_1
Column name: VAV_ga_1


title: Jurkat_1A8_EEF2K_CRISPRa_nontargeting_rep_2

description:
Library name: 1A8_Na_2
Column name: 1A8_Na_2


title: Jurkat_1A8_EEF2K_CRISPRi_nontargeting_rep_2

description:
Library name: 1A8_Ni_2
Column name: 1A8_Ni_2


title: Jurkat_1A8_EEF2K_CRISPRi_nontargeting_rep_3

description:
Library name: 1A8_Ni_3
Column name: 1A8_Ni_3


title: Jurkat_1A8_EEF2K_CRISPRi_geneTargeting_rep_2

description:
Library name: 1A8_gi_2
Column name: 1A8_gi_2


title: Jurkat_1A8_EEF2K_CRISPRi_HIVTargeting_rep_2

description:
Library name: 1A8_Hi_2
Column name: 1A8_Hi_2


title: Jurkat_1A8_EEF2K_CRISPRa_geneTargeting_rep_2

description:
Library name: 1A8_ga_2
Column name: 1A8_ga_2


title: Jurkat_1A8_EEF2K_CRISPRi_HIVTargeting_rep_3

description:
Library name: 1A8_Hi_3
Column name: 1A8_Hi_3


title: Jurkat_1A8_EEF2K_CRISPRi_HIVTargeting_rep_1

description:
Library name: 1A8_Hi_1
Column name: 1A8_Hi_1


title: Jurkat_1A8_EEF2K_CRISPRa_HIVTargeting_rep_1

description:
Library name: 1A8_Ha_1
Column name: 1A8_Ha_1


title: Jurkat_1A8_EEF2K_CRISPRa_nontargeting_rep_1

description:
Library name: 1A8_Na_1
Column name: 1A8_Na_1


title: Jurkat_1A8_EEF2K_CRISPRa_geneTargeting_rep_1

description:
Library name: 1A8_ga_1
Column name: 1A8_ga_1


title: Jurkat_1A8_EEF2K_CRISPRi_nontargeting_rep_1

description:
Library name: 1A8_Ni_1
Column name: 1A8_Ni_1


title: HeLa, sgZNF646_rep2

description:
Library name: HeLa_totalRNA_sgZNF646_rep2
HeLa_sgZNF646_rep2

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.7), then trimmed reads mapping to ribosomal RNAs were removed by Bowtie2 (v2.2.5).
The remaining reads were aligned to the human genome (hg38) using HISAT2 (v2.2.1) with ‘--rna-strandness RF’ parameters.
Gene expression was analyzed using featureCounts (v2.0.1) with the annotation file (hg38) from UCSC table browser (https://genome.ucsc.edu/). Differential gene expression analysis was performed by DESeq2 (v1.42.0) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene counts for each Sample

source_name: HeLa


title: HeLa, sgZNF646_rep1

description:
Library name: HeLa_totalRNA_sgZNF646_rep1
HeLa_sgZNF646_rep1


title: HeLa, sgZFP41_rep1

description:
Library name: HeLa_totalRNA_sgZFP41_rep1
HeLa_sgZFP41_rep1


title: HeLa, sgSTARD9_rep1

description:
Library name: HeLa_totalRNA_sgSTARD9_rep1
HeLa_sgSTARD9_rep1


title: HeLa, sgZFP41_rep2

description:
Library name: HeLa_totalRNA_sgZFP41_rep2
HeLa_sgZFP41_rep2


title: HeLa, sgPCNX3_rep2

description:
Library name: HeLa_totalRNA_sgPCNX3_rep2
HeLa_sgPCNX3_rep2


title: HeLa, sgSTARD9_rep2

description:
Library name: HeLa_totalRNA_sgSTARD9_rep2
HeLa_sgSTARD9_rep2


title: HeLa, sgFOSL2_rep2

description:
Library name: HeLa_totalRNA_sgFOSL2_rep2
HeLa_sgFOSL2_rep2


title: HeLa, sgPCNX3_rep1

description:
Library name: HeLa_totalRNA_sgPCNX3_rep1
HeLa_sgPCNX3_rep1


title: HeLa, sgKCTD1_rep1

description:
Library name: HeLa_totalRNA_sgKCTD1_rep1
HeLa_sgKCTD1_rep1


title: Jurkat_1G2_RAP1B_CRISPRi_nontargeting_rep_1

description:
Library name: 22ATAC28
Column name: 22ATAC28


title: HeLa, sgCTRL_rep2

description:
Library name: HeLa_totalRNA_sgCTRL_rep2
HeLa_sgCTRL_rep2


title: HeLa, sgFOSL2_rep1

description:
Library name: HeLa_totalRNA_sgFOSL2_rep1
HeLa_sgFOSL2_rep1


title: HeLa, sgEP300_rep1

description:
Library name: HeLa_totalRNA_sgEP300_rep1
HeLa_sgEP300_rep1


title: HeLa, sgCTRL_rep1

description:
Library name: HeLa_totalRNA_sgCTRL_rep1
HeLa_sgCTRL_rep1


title: HCT116, sgZNF646_rep2

description:
Library name: HCT116_totalRNA_sgZNF646_rep2
HCT116_sgZNF646_rep2


title: HeLa, sgC15orf39_rep2

description:
Library name: HeLa_totalRNA_sgC15orf39_rep2
HeLa_sgC15orf39_rep2


title: HCT116, sgZFP41_rep1

description:
Library name: HCT116_totalRNA_sgZFP41_rep1
HCT116_sgZFP41_rep1


title: HCT116, sgZNF646_rep1

description:
Library name: HCT116_totalRNA_sgZNF646_rep1
HCT116_sgZNF646_rep1


title: HCT116, sgSTARD9_rep2

description:
Library name: HCT116_totalRNA_sgSTARD9_rep2
HCT116_sgSTARD9_rep2


title: Jurkat_1A8_EEF2K_CRISPRi_geneTargeting_rep_1

description:
Library name: 1A8_gi_1
Column name: 1A8_gi_1


title: HeLa, sgC15orf39_rep1

description:
Library name: HeLa_totalRNA_sgC15orf39_rep1
HeLa_sgC15orf39_rep1


title: HeLa, sgEP300_rep2

description:
Library name: HeLa_totalRNA_sgEP300_rep2
HeLa_sgEP300_rep2


title: HCT116, sgSTARD9_rep1

description:
Library name: HCT116_totalRNA_sgSTARD9_rep1
HCT116_sgSTARD9_rep1


title: HCT116, sgKCTD1_rep1

description:
Library name: HCT116_totalRNA_sgKCTD1_rep1
HCT116_sgKCTD1_rep1


title: HCT116, sgKCTD1_rep2

description:
Library name: HCT116_totalRNA_sgKCTD1_rep2
HCT116_sgKCTD1_rep2


title: HCT116, sgPCNX3_rep2

description:
Library name: HCT116_totalRNA_sgPCNX3_rep2
HCT116_sgPCNX3_rep2


title: HCT116, sgPCNX3_rep1

description:
Library name: HCT116_totalRNA_sgPCNX3_rep1
HCT116_sgPCNX3_rep1


title: HCT116, sgFOSL2_rep2

description:
Library name: HCT116_totalRNA_sgFOSL2_rep2
HCT116_sgFOSL2_rep2


title: HeLa, sgKCTD1_rep2

description:
Library name: HeLa_totalRNA_sgKCTD1_rep2
HeLa_sgKCTD1_rep2


title: HCT116, sgEP300_rep2

description:
Library name: HCT116_totalRNA_sgEP300_rep2
HCT116_sgEP300_rep2


title: HCT116, sgC15orf39_rep2

description:
Library name: HCT116_totalRNA_sgC15orf39_rep2
HCT116_sgC15orf39_rep2


title: HCT116, sgC15orf39_rep1

description:
Library name: HCT116_totalRNA_sgC15orf39_rep1
HCT116_sgC15orf39_rep1


title: HCT116, sgCTRL_rep1

description:
Library name: HCT116_totalRNA_sgCTRL_rep1
HCT116_sgCTRL_rep1


title: HCT116, sgZFP41_rep2

description:
Library name: HCT116_totalRNA_sgZFP41_rep2
HCT116_sgZFP41_rep2


title: HCT116, sgEP300_rep1

description:
Library name: HCT116_totalRNA_sgEP300_rep1
HCT116_sgEP300_rep1


title: HepG2, sgZNF646_rep2

description:
Library name: HepG2_totalRNA_sgZNF646_rep2
HepG2_sgZNF646_rep2


title: HepG2, sgSTARD9_rep1

description:
Library name: HepG2_totalRNA_sgSTARD9_rep1
HepG2_sgSTARD9_rep1


title: HepG2, sgZFP41_rep2

description:
Library name: HepG2_totalRNA_sgZFP41_rep2
HepG2_sgZFP41_rep2


title: HepG2, sgPCNX3_rep2

description:
Library name: HepG2_totalRNA_sgPCNX3_rep2
HepG2_sgPCNX3_rep2


title: HepG2, sgFOSL2_rep1

description:
Library name: HepG2_totalRNA_sgFOSL2_rep1
HepG2_sgFOSL2_rep1


title: HepG2, sgC15orf39_rep2

description:
Library name: HepG2_totalRNA_sgC15orf39_rep2
HepG2_sgC15orf39_rep2


title: HepG2, sgKCTD1_rep2

description:
Library name: HepG2_totalRNA_sgKCTD1_rep2
HepG2_sgKCTD1_rep2


title: HepG2, sgEP300_rep1

description:
Library name: HepG2_totalRNA_sgEP300_rep1
HepG2_sgEP300_rep1


title: HCT116, sgCTRL_rep2

description:
Library name: HCT116_totalRNA_sgCTRL_rep2
HCT116_sgCTRL_rep2


title: HepG2, sgZFP41_rep1

description:
Library name: HepG2_totalRNA_sgZFP41_rep1
HepG2_sgZFP41_rep1


title: HepG2, sgEP300_rep2

description:
Library name: HepG2_totalRNA_sgEP300_rep2
HepG2_sgEP300_rep2


title: HepG2, sgCTRL_rep2

description:
Library name: HepG2_totalRNA_sgCTRL_rep2
HepG2_sgCTRL_rep2


title: HepG2, sgKCTD1_rep1

description:
Library name: HepG2_totalRNA_sgKCTD1_rep1
HepG2_sgKCTD1_rep1


title: HepG2, sgCTRL_rep1

description:
Library name: HepG2_totalRNA_sgCTRL_rep1
HepG2_sgCTRL_rep1


title: SMMC-7721, sgZNF646_rep1

description:
Library name: SMMC7721_totalRNA_sgZNF646_rep1
SMMC7721_sgZNF646_rep1


title: HCT116, sgFOSL2_rep1

description:
Library name: HCT116_totalRNA_sgFOSL2_rep1
HCT116_sgFOSL2_rep1


title: HepG2, sgC15orf39_rep1

description:
Library name: HepG2_totalRNA_sgC15orf39_rep1
HepG2_sgC15orf39_rep1


title: SMMC-7721, sgZNF646_rep2

description:
Library name: SMMC7721_totalRNA_sgZNF646_rep2
SMMC7721_sgZNF646_rep2


title: SMMC-7721, sgZFP41_rep2

description:
Library name: SMMC7721_totalRNA_sgZFP41_rep2
SMMC7721_sgZFP41_rep2


title: SMMC-7721, sgSTARD9_rep2

description:
Library name: SMMC7721_totalRNA_sgSTARD9_rep2
SMMC7721_sgSTARD9_rep2


title: HepG2, sgZNF646_rep1

description:
Library name: HepG2_totalRNA_sgZNF646_rep1
HepG2_sgZNF646_rep1


title: SMMC-7721, sgZFP41_rep1

description:
Library name: SMMC7721_totalRNA_sgZFP41_rep1
SMMC7721_sgZFP41_rep1


title: SMMC-7721, sgPCNX3_rep2

description:
Library name: SMMC7721_totalRNA_sgPCNX3_rep2
SMMC7721_sgPCNX3_rep2


title: SMMC-7721, sgKCTD1_rep2

description:
Library name: SMMC7721_totalRNA_sgKCTD1_rep2
SMMC7721_sgKCTD1_rep2


title: SMMC-7721, sgSTARD9_rep1

description:
Library name: SMMC7721_totalRNA_sgSTARD9_rep1
SMMC7721_sgSTARD9_rep1


title: HepG2, sgPCNX3_rep1

description:
Library name: HepG2_totalRNA_sgPCNX3_rep1
HepG2_sgPCNX3_rep1


title: HepG2, sgFOSL2_rep2

description:
Library name: HepG2_totalRNA_sgFOSL2_rep2
HepG2_sgFOSL2_rep2


title: HepG2, sgSTARD9_rep2

description:
Library name: HepG2_totalRNA_sgSTARD9_rep2
HepG2_sgSTARD9_rep2


title: SMMC-7721, sgFOSL2_rep1

description:
Library name: SMMC7721_totalRNA_sgFOSL2_rep1
SMMC7721_sgFOSL2_rep1


title: SMMC-7721, sgEP300_rep1

description:
Library name: SMMC7721_totalRNA_sgEP300_rep1
SMMC7721_sgEP300_rep1


title: SMMC-7721, sgC15orf39_rep2

description:
Library name: SMMC7721_totalRNA_sgC15orf39_rep2
SMMC7721_sgC15orf39_rep2


title: SMMC-7721, sgCTRL_rep1

description:
Library name: SMMC7721_totalRNA_sgCTRL_rep1
SMMC7721_sgCTRL_rep1


title: SMMC-7721, sgPCNX3_rep1

description:
Library name: SMMC7721_totalRNA_sgPCNX3_rep1
SMMC7721_sgPCNX3_rep1


title: HeLa, caRNA, MeRIP, rep2

description:
Library name: HeLa_caRNA_MeRIP_rep2
HeLa_caRNA_MERIP_rep2

library_source: other

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.7), then trimmed reads mapping to ribosomal RNAs were removed by Bowtie2 (v2.2.5).
The remaining reads were aligned to the human genome (hg38) using HISAT2 (v2.2.1) with ‘--rna-strandness RF’ parameters.
Strand-specific reads were separated using samtools view (v1.18) with flags 99,147,83,163. m6A peak calling was performed using macs2 (v2.2.7.1) with ‘--keep-dup 5 -q 0.01 --nomodel’ parameters.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)

molecule: other

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of SMMC-7721, HepG2, HCT116 and HeLa cells. To isolate mRNA from total RNA, the Dynabeads® mRNA Purification Kit (Invitrogen) was used following the manufacturer’s protocols. Non-ribosome RNA was enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg polyA or non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 following manufacturer's protocols.

tag: m6a antibody


title: HeLa, caRNA, MeRIP, rep1

description:
Library name: HeLa_caRNA_MeRIP_rep1
HeLa_caRNA_MERIP_rep1

value: EpiMark N6-Methyladenosine Enrichment Kit


title: SMMC-7721, sgFOSL2_rep2

description:
Library name: SMMC7721_totalRNA_sgFOSL2_rep2
SMMC7721_sgFOSL2_rep2


title: HeLa, caRNA, Input, rep2

description:
Library name: HeLa_caRNA_Input_rep2
HeLa_caRNA_Input_rep2


title: SMMC-7721, sgKCTD1_rep1

description:
Library name: SMMC7721_totalRNA_sgKCTD1_rep1
SMMC7721_sgKCTD1_rep1


title: SMMC-7721, sgEP300_rep2

description:
Library name: SMMC7721_totalRNA_sgEP300_rep2
SMMC7721_sgEP300_rep2


title: HeLa, totalRNA, Input, rep2

description:
Library name: HeLa_totalRNA_Input_rep2
HeLa_totalRNA_Input_rep2


title: SMMC-7721, sgC15orf39_rep1

description:
Library name: SMMC7721_totalRNA_sgC15orf39_rep1
SMMC7721_sgC15orf39_rep1


title: HeLa, totalRNA, Input, rep1

description:
Library name: HeLa_totalRNA_Input_rep1
HeLa_totalRNA_Input_rep1


title: HCT116, caRNA, MeRIP, rep1

description:
Library name: HCT116_caRNA_MeRIP_rep1
HCT116_caRNA_MERIP_rep1


title: HeLa, totalRNA, MeRIP, rep1

description:
Library name: HeLa_totalRNA_MeRIP_rep1
HeLa_totalRNA_MERIP_rep1


title: HeLa, caRNA, Input, rep1

description:
Library name: HeLa_caRNA_Input_rep1
HeLa_caRNA_Input_rep1


title: HCT116, totalRNA, MeRIP, rep2

description:
Library name: HCT116_totalRNA_MeRIP_rep2
HCT116_totalRNA_MERIP_rep2


title: HCT116, totalRNA, MeRIP, rep1

description:
Library name: HCT116_totalRNA_MeRIP_rep1
HCT116_totalRNA_MERIP_rep1


title: HepG2, caRNA, MeRIP, rep2

description:
Library name: HepG2_caRNA_MeRIP_rep2
HepG2_caRNA_MERIP_rep2


title: SMMC-7721, sgCTRL_rep2

description:
Library name: SMMC7721_totalRNA_sgCTRL_rep2
SMMC7721_sgCTRL_rep2


title: HepG2, caRNA, MeRIP, rep1

description:
Library name: HepG2_caRNA_MeRIP_rep1
HepG2_caRNA_MERIP_rep1


title: HCT116, totalRNA, Input, rep1

description:
Library name: HCT116_totalRNA_Input_rep1
HCT116_totalRNA_Input_rep1


title: HepG2, caRNA, Input, rep1

description:
Library name: HepG2_caRNA_Input_rep1
HepG2_caRNA_Input_rep1


title: HepG2, caRNA, Input, rep2

description:
Library name: HepG2_caRNA_Input_rep2
HepG2_caRNA_Input_rep2


title: HCT116, caRNA, Input, rep2

description:
Library name: HCT116_caRNA_Input_rep2
HCT116_caRNA_Input_rep2


title: HepG2, totalRNA, MeRIP, rep1

description:
Library name: HepG2_totalRNA_MeRIP_rep1
HepG2_totalRNA_MERIP_rep1


title: HCT116, totalRNA, Input, rep2

description:
Library name: HCT116_totalRNA_Input_rep2
HCT116_totalRNA_Input_rep2


title: HepG2, totalRNA, Input, rep2

description:
Library name: HepG2_totalRNA_Input_rep2
HepG2_totalRNA_Input_rep2


title: HeLa, GLORI, sgCTRL

description:
Library name: HeLa_GLORI_sgCTRL
HeLa_sgCTRL

data_processing:
Reads were firstly trimmed by Trim Galore (v0.6.7)96 to remove adapters and low-quality bases with command as follows: "trim_galore -q 20 --stringency 1 -e 0.3 --length 35".
Seqkit (v.2.8.2) was then used to deduplicate PCR based on the 10-base-pair UMI at the 5′ end of reads R2 with parameters as follows: "seqkit rmdup -s".
Finally, FASTX-Toolkit (v.0.0.14) was used to remove UMI in the deduplication reads with parameters as follows: "fastx_trimmer -f 15".
For the downstream analysis we used GLORI-tools (https://github.com/liucongcas/GLORI-tools) with default parameters.
Assembly: hg38
Supplementary files format and content: csv files include m6A site ratio for each Sample

extract_protocol:
Cells were harvested and total RNA was extracted using TRIZOL reagent (Invitrogen) following the manufacturer’s protocols. To isolate mRNA from total RNA, the Dynabeads® mRNA Purification Kit (Invitrogen) was used following the manufacturer’s protocols. The RNA concentration was determined using Nanodrop (Invitrogen) by measuring the UV absorbance at 260 nm.
Library preparation was then performed using SMARTer Stranded Total RNA-Seq kits v3 Pico Input mammalian (Takara, 634487)


title: HCT116, GLORI, sgTAF7

description:
Library name: HCT116_GLORI_sgTAF7
HCT116_sgTAF7


title: HeLa, GLORI, sgTAF7

description:
Library name: HeLa_GLORI_sgTAF7
HeLa_sgTAF7


title: HepG2, totalRNA, Input, rep1

description:
Library name: HepG2_totalRNA_Input_rep1
HepG2_totalRNA_Input_rep1