title: Verdin-AC-12-S12

city: Los Angeles

first: Ivan

middle: Alexander

last: Salladay-Perez

state: CA

address: 615 Charles E Young Dr S

department: Department of Microbiology Immunology and Molecular Genetics

institute: University of California, Los Angeles

description: Library name: sample12

data_processing:
Roughly 100 M high quality reads were sequenced per sample using a Novaseq x Plus (Illumina). Raw data in FASTAq format was filtered for adapter sequences or low-quality sequences using SOAPnuke. Reads were aligned to the mm10 reference genome using STAR.
Assembly: Aligned reads were processed using TopHat and a counts matrix was generated using FeatureCounts.
Supplementary files format and content: Raw reads were processed using the latest version of base R commands as of May 2025 (4.5.0)

source_name: BMDM

growth_protocol: BMDMs used in experiments were derived from bone marrow extracted from the femurs of euthanized mice (6-12 weeks old male C57BL/6J) by mortar and pestle. Femurs were placed in the mortar and were washed with 70% ethanol to sterilize followed by two washes with complete RPMI (cRPMI; standard RPMI (Corning) supplemented with 10% fetal calf serum, penicillin-streptomycin solution (Corning), 1mM sodium pyruvate solution (Corning), 2 mM L-Glutamine solution (Corning), 10nM HEPES buffer (Corning), and 50μM 2-mercaptoethanol). After washing, 10 ml of cRPMI was added to the mortar and the femur bones were gently crushed. The resulting media was collected and filtered through a 70μm filter and placed in a conical tube. The filtered supernatant was centrifuged at 100 g (150 RCF) for 5 minutes. Cells were resuspended, counted and plated at a density of 3E6 cells/10 cm dish in 10 ml of macrophage growth media (cRPMI containing 25% M-CSF containing L929 conditioned media (made in house)). Cells were left to grow for 7 days to differentiate and were supplemented with 5 ml of macrophage growth media on day 5. On day 7, BMDMs (yielding 10-12x106 cells/10cm dish) were lifted off the plate using cold PBS containing 5mM EDTA. BMDMs were counted and replated in macrophage growth media overnight prior to experiments

extract_protocol:
Mouse BMDM cell-culture experiments, RNA was isolated using RNA STAT 60 (Amsbio) as per the manufacturer’s protocol. ~ 2000 ng of RNA was converted to complementary DNA using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Mouse BMDM were lysed with RNA STAT 60 (Amsbio) and ~50 ng per uL of RNA was submitted to the UCLA’s Technology Center for Genomics & Bioinformatics (TCGB) core for library preparation and 2x100 paired-end sequencing.

treatment_protocol: On the day of experiments, macrophage growth media was replaced with cRPMI 6 hours prior to stimulation to remove M-CSF. M2 polarization was performed by stimulating macrophages with 10 ng/ml recombinant mouse IL-4 (Peprotech). For M1 polarization macrophages were stimulated with 100 ng/ml LPS (LPS EK-Ultrapure, Invivogen). To induce senescence, day 7 BMDMs were either irradiated (10 Gy) or treated with doxorubicin (Fisher) for 24 hours at 250 nM in 60% cRPMI: 40 MGM. DNA damaged cells were left in culture for 10 days and media components were replaced every 2-3 days. As a negative control, a mock irradiated or drug treated condition was cultured in parallel and required passing every 2-3 days. All senescent macrophage experiments were performed 10-13 days post DNA damage.

value: BMDM

value: Primary

value: Macrophage

value: Sen(Dox)


title: Verdin-AC-11-S11

status: Public on Feb 11 2026

type: SRA

country: USA

description: Library name: sample11

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: strain

tag: treatment

tag: batch


title: Drosophila melanogaster, male, head, 18C DD, day5, hour08, rep1

city: College Station

first: Wanhe

last: Li

state: Texas

address: 424 Nagle St

department: Biology

institute: Texas A&M University

description: Library name: T18.DD.d5h08.r1

data_processing:
Raw sequencing reads were filtered and trimmed using fastp (v0.23.2) with default parameters. Clean reads were then aligned to the Drosophila melanogaster reference genome using HISAT2 (v2.2.1). Gene-level read counts were calculated using featureCounts from the Subread package (v2.0.8).
Assembly: FlyBase r6.55
Supplementary files format and content: Tab-delimited text file. Rows represent genes (FlyBase gene IDs), columns represent individual samples. Values represent raw read counts generated by featureCounts.

molecule: total RNA

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Total RNA was purified using the RNeasy Mini Kit (Qiagen), and genomic DNA was removed with RNase-free DNase (Qiagen).
The cDNA library construction, including poly-A mRNA isolation, fragmentation, reverse transcription, and PCR amplification, was performed by Novogene Corporation Inc. using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

value: head

value: 18C DD

tag: time

value: day5, hour08

tag: Sex

value: male


title: Drosophila melanogaster, male, head, 18C DD, day5, hour04, rep2

description: Library name: T18.DD.d5h04.r2

value: day5, hour04


title: PETER001_HEPG2_6H_X1_B46:C06

type: RNA

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir

scan_protocol: Following treatment and lysis, gene expression was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.

label: biotin

organism: Homo sapiens

source_name: HEPG2 treated with Abacavir|Dolutegravir 0.5|0.1 uM for 6.0 h

label_protocol: biotin labeling. Processing was done by th Broad Institute as previously described (10.1016/j.cell.2017.10.049)

growth_protocol:
HepG2 cells (5000 cells/well; ATCC, HB-8065) were cultured in Eagle's Minimum Essential Medium (EMEM; ATCC, cat. no.  30-2003), supplemented with 10% FBS and 1% P/S  at 37°C, 5% CO2.
HK-2 cells (5000 cells/well; ATCC, cat. no. CRL-2190) were cultured in Keratinocyte Serum Free Medium (K-SFM), Kit (Gibco, cat. no. 17005-042)  at 37°C, 5% CO2.
THP-1 cells (10,000 cells/well; ATCC, cat. no. TIB-202) were cultured in RPMI-40 medium (Gibco, cat. no. 11875-093) supplemented with 10% fetal bovine serum (FBS, Gibco, cat. no. 10438026) and 1% penicillin/streptomycin (P/S, Corning, cat. no. 30-002) at 37°C, 5% CO2. Macrophage differentiation was induced in vitro with phorbol-12-myristate-13-acetate (PMA, 50 ng/mL; Sigma) for 72 hours at 37°C in 5% CO2

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.

treatment_protocol: After 24 hours of culture for HepG2 and HK-2 cells, and 72 hours for THP-1 macrophages, the cells were placed in their respected culture media supplemented with 2% FBS for 16 hours. Subsequently, they were treated for 6 or 24 hours with either vehicle (DMSO) or with ART medications at a concentration of 0.1, or 0.5 µM.

value: Abacavir|Dolutegravir 0.5|0.1 uM

tag: duration

tag: plate

tag: well


title: Drosophila melanogaster, male, head, 18C DD, day5, hour04, rep1

description: Library name: T18.DD.d5h04.r1


title: Sham 5

city: Zhengzhou

first: Shuai

last: Cheng

address: No.1, East Jian She Road

country: China

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: Sample 5
Column name in raw_counts.txt: Sham 5

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 0.1%, afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2 was applied to align the clean reads to the gene set. Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

source_name: infrarenal abdominal aorta

growth_protocol: All animals were housed under specific pathogen-free conditions with controlled temperature, 12-h light/dark cycles, and stable humidity.

extract_protocol:
Total RNA was extracted from tissues using RNeasy Micro Kit（QIAGEN，Germany）according to manual instruction. Subsequently, total RNA was qualified and quantified using an Agilent 2100 Bioanalyzer (Agilent, CA, USA).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) according to manual instruction.

treatment_protocol: Male 8-week-old C57BL/6J mice (GemPharmatech) fed a normal diet were treated as described below: The AAA model was established as previously described. Briefly, under 1% isoflurane anesthesia, midline laparotomy was performed to expose the abdominal aorta. A gelatin sponge saturated with 5 μL porcine pancreatic elastase was applied topically to the aortic surface for 5 min. The site was then rinsed thoroughly with sterile saline and the abdominal wall was closed in layers. Conversely, sham controls were treated with heat-inactivated elastase (100°C, 30 min). All mice were maintained under SPF conditions postoperatively, with AAA-induced mice receiving 0.2% β-aminopropionitrile in their drinking water.

value: infrarenal abdominal aorta

value: Male

tag: genotype

value: WT

value: Periadventitial application of heat-inactivated elastase


title: F11537438

type: protein

city: Silver Spring

first: Paula

middle: L

last: Hyland

state: MD

address: 10903 New Hampshire Avenue

department: CDER

institute: FDA

description: 55 ul of plasma was used for the  proteomic assay

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing: https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

source_name: EDTA Plasma

extract_protocol: EDTA plasma from whole blood

tag: participant id

tag: time point (days)

value: Day 1

value: EDTA Plasma

tag: delivery

value: SC

tag: treatment group (dose)

value: Mepolizumab [Mep] (24 mg)

tag: bmi (kg/m2)

tag: age

value: M

tag: race

value: White


title: PETER001_HEPG2_6H_X1_B46:C04

tag: cell line


title: Sham 3

description:
Library name: Sample 3
Column name in raw_counts.txt: Sham 3

tag: tissue

tag: strain


title: Sham 4

description:
Library name: Sample 4
Column name in raw_counts.txt: Sham 4

tag: treatment


title: Verdin-AC-10-S10

description: Library name: sample10

value: BMDM

value: Primary

tag: cell type

value: Macrophage

value: Sen(Dox)

tag: batch


title: Drosophila melanogaster, male, head, 18C DD, day5, hour00, rep2

description: Library name: T18.DD.d5h00.r2

value: head

value: 18C DD

tag: time

value: day5, hour00

tag: Sex

value: male


title: PETER001_HEPG2_6H_X1_B46:C05

value: Abacavir|Dolutegravir 0.5|0.1 uM

tag: duration

tag: plate

tag: well


title: Verdin-AC-08-S8

description: Library name: sample8

value: Sen(IR)


title: Drosophila melanogaster, male, head, 18C DD, day5, hour00, rep1

description: Library name: T18.DD.d5h00.r1


title: PETER001_HEPG2_6H_X1_B46:C03

description: L1000 inferred profile; pert_id: DMSO

source_name: HEPG2 treated with DMSO 0.5 uM for 6.0 h

value: DMSO 0.5 uM


title: Verdin-AC-07-S7

description: Library name: sample7


title: Verdin-AC-09-S9

description: Library name: sample9


title: PETER001_HEPG2_6H_X1_B46:C02

description: L1000 inferred profile; pert_id: DMSO


title: Sham 2

description:
Library name: Sample 2
Column name in raw_counts.txt: Sham 2

value: infrarenal abdominal aorta

value: Male

tag: genotype

value: WT

value: Periadventitial application of heat-inactivated elastase


title: Verdin-AC-06-S6

description: Library name: sample6


title: Sham 1

description:
Library name: Sample 1
Column name in raw_counts.txt: Sham 1


title: PETER001_HEPG2_6H_X1_B46:C01

description: L1000 inferred profile; pert_id: DMSO


title: SNU449_siSF3B6_3, Day2

city: Yangsan

first: young-In

last: Hwang

address: 49, Busandaehak-ro, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do, Republic of Korea

department: Department of Anbatomy

country: South Korea

institute: Pusan National University

description:
Library name: Sample 3
Sequenced using MGI DNBSEQ-T7 instrument

data_processing:
The trimmed reads were mapped to human reference (hg38) using STAR aligner (ver. 2.7.3)
The raw TPM values were calculated by RSEM (ver. 1.3.3)
Differentially expressed genes were identified by calculating normalized count with DESeq2
Assembly: hg38
Supplementary files format and content: The csv files contain normalized counts of transcripts. This values were calculated by DESeq2 to identify DEGs
Supplementary files format and content: TPM values were calcuated by RSEM and stored in tsv files

source_name: Liver

extract_protocol:
Cells were kept observing after siRNA transfection to check for the cell status, and 48 hours later, cells were harvested using Rneasy mini kit (Qiagen). 3ug of total RNA was used for the construction of the seuencing libraries.
RNA libraries were prepared for RNA sequencing based on the manusfactor's instructions. The adapter contamination were trimmed by Cutadapt and the trimmed read were further processed by Trimomatic to filter out low quality reads.

treatment_protocol: Cells were seeded onto 6 well plate and 24 hours later, they were transfected using 100nM (pre-optimized concentration) of siRNAs

value: Liver

value: Hepatocellular carcinoma liver cells

value: siRNA transfection


title: BKO 5

city: Wuhan

first: Jie

last: Jiang

address: 13 Hangkong Road, Qiaokou District

department: insititue of pathology

institute: Institute of pathology, Tongji Hospital，Tongji Medical College, Huazhong University of Science and Technology

description:
Library name: Sample10
Column name in raw_processed data file.xlsx: BKO 5-FPKM

data_processing:
Perform image recognition on sequencing results to remove contamination and adapter sequences. Conduct analysis and statistics on data output, including sequencing read yield, Q20 content, Q30 content, clean ratio, etc.
Align the sequencing reads to the reference genome using the STAR alignment software.
Perform quantification of the reference gene set using HTSeq to derive the corresponding FPKM values.
Assembly: mm39
Supplementary files format and content: .xlsx files include FPKM values for each Sample.

source_name: Brain cortex

growth_protocol: All experimental procedures involving mouse were hosted under specific-pathogen-free conditions at 22 ± 2ºC with a humidity of 40 ± 5% in single ventilated cages in a 12h/12h day/night cycle and fed with unlimited access to food and water.

extract_protocol:
RNA was extracted by Trizol and the total RNA was used for the contruction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA library preparation kit following manufacture's protocols.

treatment_protocol: no treatment for mice

value: Brain cortex

value: Mic19 knockout


title: Verdin-AC-05-S5

description: Library name: sample5

value: BMDM

value: Primary

value: Macrophage


title: BKO 3

description:
Library name: Sample8
Column name in raw_processed data file.xlsx: BKO 3-FPKM


title: BKO 4

description:
Library name: Sample9
Column name in raw_processed data file.xlsx: BKO 4-FPKM


title: PETER001_HEPG2_6H_X1_B46:B21

description: L1000 inferred profile; pert_id: Water

source_name: HEPG2 treated with Water 0.01 uM for 6.0 h

value: Water 0.01 uM


title: Drosophila melanogaster, male, head, 18C DD, day4, hour16, rep2

description: Library name: T18.DD.d4h16.r2

value: head

value: 18C DD

value: day4, hour16

value: male


title: PETER001_HEPG2_6H_X1_B46:B20

description: L1000 inferred profile; pert_id: Water


title: Verdin-AC-04-S4

description: Library name: sample4

value: Passage Control


title: Drosophila melanogaster, male, head, 18C DD, day4, hour20, rep2

description: Library name: T18.DD.d4h20.r2

value: day4, hour20


title: PETER001_HEPG2_6H_X1_B46:B19

description: L1000 inferred profile; pert_id: Water


title: BKO 2

description:
Library name: Sample7
Column name in raw_processed data file.xlsx: BKO 2-FPKM


title: Drosophila melanogaster, male, head, 18C DD, day4, hour16, rep1

description: Library name: T18.DD.d4h16.r1


title: Drosophila melanogaster, male, head, 18C DD, day4, hour12, rep1

description: Library name: T18.DD.d4h12.r1

value: day4, hour12


title: Drosophila melanogaster, male, head, 18C DD, day4, hour12, rep2

description: Library name: T18.DD.d4h12.r2


title: BKO 1

description:
Library name: Sample6
Column name in raw_processed data file.xlsx: BKO 1-FPKM


title: Verdin-AC-02-S2

description: Library name: sample2


title: Verdin-AC-01-S1

description: Library name: sample1


title: Drosophila melanogaster, male, head, 18C DD, day4, hour20, rep1

description: Library name: T18.DD.d4h20.r1


title: Verdin-AC-03-S3

description: Library name: sample3


title: Drosophila melanogaster, male, head, 18C DD, day4, hour08, rep2

description: Library name: T18.DD.d4h08.r2

value: day4, hour08


title: Sen_TREM2KO_12

description:
Library name: sample12
S-25-0850-12_S149_L006

source_name: Bone-marrow derived

value: Bone-marrow derived

value: Trem2 -/-

value: Irradiation


title: PETER001_HEPG2_6H_X1_B46:B16

description: L1000 inferred profile; pert_id: Dolutegravir

source_name: HEPG2 treated with Dolutegravir 0.1 uM for 6.0 h

value: Dolutegravir 0.1 uM


title: ctrl 5

description:
Library name: Sample5
Column name in raw_processed data file.xlsx: ctrl 5-FPKM

value: Brain cortex

value: Mic19 WT


title: ctrl 4

description:
Library name: Sample4
Column name in raw_processed data file.xlsx: ctrl 4-FPKM


title: Sen_TREM2KO_10

description:
Library name: sample10
S-25-0850-10_S147_L006

value: Primary


title: Sen_WT_9

description:
Library name: sample9
S-25-0850-09_S146_L006

value: Macrophage

value: Trem2 +/+


title: Sen_TREM2KO_11

description:
Library name: sample11
S-25-0850-11_S148_L006


title: ctrl 3

description:
Library name: Sample3
Column name in raw_processed data file.xlsx: ctrl 3-FPKM


title: Sen_WT_8

description:
Library name: sample8
S-25-0850-08_S145_L006


title: PETER001_HEPG2_6H_X1_B46:B12

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine

source_name: HEPG2 treated with Cobicistat|Emtricitabine 0.1|0.1 uM for 6.0 h

value: Cobicistat|Emtricitabine 0.1|0.1 uM


title: hic spermatocytes, pachytene, Senp3-SKO, rep2

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

description: Library name: hic Senp3-SKO early2mid  pachytene spermatocytes rep2

library_source: genomic

data_processing:
Illumina Casava1.8 software was used for basecalling.
Hi-C reads were processed using HiCPro v2.11.1 and replicates of same group were pooled together
Cmpartment and TAD analysis were done with  cooltools (v0.3.2) (Venev et al., 2020)
Hi-C data was visulalized with Juicebox (v1.11.08) (Durand et al., 2016)
Assembly: mm9
Supplementary files format and content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size

molecule: genomic DNA

source_name: testis

extract_protocol:
Spermatocytes were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Formaldehyde was then quenched with glycine for 10 min at RT.
sisHi-C libraries were produced as previously described (Du et al., 2017). Crosslinked spermatocytes were washed with 1 × PBS and lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min, the chromatin was solubilized with 0.5% SDS at 62 °C for 5 min. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP (Invitrogen, #19518018), the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, #65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Kapa HiFi PCR mix (Roche, #KK2602), and the products were purified and size-selected with AMPure XP beads (Beckman Coulter, #A63881).

value: spermatocytes


title: Sen_WT_7

description:
Library name: sample7
S-25-0850-07_S144_L006


title: PETER001_HEPG2_6H_X1_B46:B15

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir

source_name: HEPG2 treated with Cobicistat|Elvitegravir 0.1|0.1 uM for 6.0 h

value: Cobicistat|Elvitegravir 0.1|0.1 uM


title: ctrl 2

description:
Library name: Sample2
Column name in raw_processed data file.xlsx: ctrl 2-FPKM


title: PETER001_HEPG2_6H_X1_B46:B14


title: Drosophila melanogaster, male, head, 18C DD, day4, hour08, rep1

description: Library name: T18.DD.d4h08.r1

value: head

value: 18C DD

value: male


title: Control_TREM2KO_6

description:
Library name: sample6
S-25-0850-06_S143_L006

value: Control


title: PETER001_HEPG2_6H_X1_B46:B18


title: PETER001_HEPG2_6H_X1_B46:B10


title: Drosophila melanogaster, male, head, 18C DD, day4, hour04, rep1

description: Library name: T18.DD.d4h04.r1

value: day4, hour04


title: hic spermatocytes, pachytene, WT, rep2

description: Library name: hic WT early2mid pachytene spermatocytes rep2

value: WT


title: Drosophila melanogaster, male, head, 18C DD, day4, hour04, rep2

description: Library name: T18.DD.d4h04.r2


title: PETER001_HEPG2_6H_X1_B46:B13


title: Drosophila melanogaster, male, head, 18C DD, day4, hour00, rep2

description: Library name: T18.DD.d4h00.r2

value: day4, hour00


title: ctrl 1

description:
Library name: Sample1
Column name in raw_processed data file.xlsx: ctrl 1-FPKM


title: PETER001_HEPG2_6H_X1_B46:B09

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM for 6.0 h


title: Drosophila melanogaster, male, head, 18C DD, day4, hour00, rep1

description: Library name: T18.DD.d4h00.r1


title: hic spermatocytes, pachytene, Senp3-SKO, rep1

description: Library name: hic Senp3-SKO early2mid pachytene spermatocytes rep1


title: hic spermatocytes, pachytene, WT, rep1

description: Library name: hic WT early2mid pachytene spermatocytes rep1


title: Calu3, biological replicate 1, CD, 24 h

city: Vancouver

first: Diana

last: Bautista-Sánchez

state: British Columbia

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

description:
Library name: CD24HN11_S45
Column name in counts.final.txt: CD24HN11_S45

data_processing:
Sequence adaptor trimming was performed using Cutadapt v2.3
Reads were aligned to the human reference genome (Homo_sapiens.GRCh38.Ensembl87) using STAR (v2.6.1a)
Read counts was done  using FeatureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: Calu-3 cells (HTB-55) were obtained from American Type Culture Collection (ATCC) and maintained in Eagle's Minimum Essential medium (EMEM) with 10% fetal bovine serum (FBS) at 37C and 5% CO2.

extract_protocol:
At each collection time point, cells were treated with trypsin 0.25%, centrifuged (300g 5 min), and stored in RNAlater buffer. After the three biological replicates were collected, the total number of samples was randomly divided into groups for RNA extraction to avoid the batch effect. Before the lysis step, RNAlater buffer was removed by centrifuging samples at 5000g 15 min. Samples were lysed with RLT buffer and homogenized through QIA shredder columns (cat#79656). RNA extraction was performed with RNeasy Protect Kit (cat #74624) while incubating with RNase-free DNase I (cat #79254) treatment to eliminate DNA contamination. Samples were stored at -80°C until quantification and quality assessment using the NanoDrop One and Agilent 2100 Bioanalyzer, respectively. Subsequently, 80% of the samples tested were found to have a concentration higher than 100 ng/µL, and all of them had an RNA Integrity Number (RIN) between 8.8 and 10.
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq mRNA Stranded kit following manufacturer's protocol.

treatment_protocol: Calu-3 cells were seeded on six-well-plates 24 h before the compound treatment. A 3 h pretreatment was performed with 250 nM compounds with CA, CD, 100 nM BafA1, and 0.1% DMSO. Compounds were removed, and samples were incubated with fresh media until sample collection at the designated time points (3, 6, 12, and 24 h post-treatment).

value: CD


title: PETER001_HEPG2_6H_X1_B46:B17

description: L1000 inferred profile; pert_id: Dolutegravir

value: Dolutegravir 0.1 uM


title: Calu3, biological replicate 3, DMSO, 24 h

description:
Library name: DMSO24HN31_S49
Column name in counts.final.txt: DMSO24HN31_S49

value: DMSO


title: Calu3, biological replicate 1, DMSO, 24 h

description:
Library name: DMSO24HN11_S48
Column name in counts.final.txt: DMSO24HN11_S48


title: Control_WT_1

description:
Library name: sample1
S-25-0850-01_S138_L006

value: Bone-marrow derived


title: Calu3, biological replicate 2, CA, 24 h

description:
Library name: CA24HN21_S44
Column name in counts.final.txt: CA24HN21_S44

value: CA


title: hic spermatocytes, zygotene, WT, rep2

description: Library name: hic WT zygotene spermatocytes  rep2


title: PETER001_HEPG2_6H_X1_B46:B11

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine


title: Control_TREM2KO_5

description:
Library name: sample5
S-25-0850-05_S142_L006

value: Primary

value: Macrophage

value: Trem2 -/-


title: Control_WT_3

description:
Library name: sample3
S-25-0850-03_S140_L006

value: Trem2 +/+


title: hic spermatocytes, zygotene, Senp3-SKO, rep2

description: Library name: hic Senp3-SKO zygotene spermatocytes  rep2

value: spermatocytes


title: hic spermatocytes, zygotene, Senp3-SKO, rep1

description: Library name: hic Senp3-SKO zygotene spermatocytes  rep1


title: Calu3, biological replicate 2, BAFA, 24 h

description:
Library name: BAFA24HN22_S47
Column name in counts.final.txt: BAFA24HN22_S47

value: BAFA


title: PETER001_HEPG2_6H_X1_B46:B04

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM for 6.0 h


title: Control_TREM2KO_4

description:
Library name: sample4
S-25-0850-04_S141_L006


title: PETER001_HEPG2_6H_X1_B46:B08

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

value: Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM


title: MSenIR_19

description: Library name: sample19

value: Wildtype

value: IR


title: spermatocytes, pachytene, AZD6738, rep2

description: Library name: rna AZD6738 early2mid pachytene spermatocytes rep2

data_processing:
Illumina Casava1.8 software was used for basecalling.
All reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then mapped to mm9 genome by HISAT2 (v.2.2.0) (Kim et al., 2019) under the parameters –dta --no-softclip.
The gene expression level was calculated by StringTie (v.2.1.1) (Pertea et al., 2015) using the refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: spermatocytes

extract_protocol:
Spermatocytes were lysed in lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor). The polyadenylated mRNAs were captured by the oligodT primers,
mRNAs were subjected to the Smart-seq2 protocol as described previously (Picelli et al., 2014).


title: PETER001_HEPG2_6H_X1_B46:B06

value: Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM


title: Control_WT_2

description:
Library name: sample2
S-25-0850-02_S139_L006

value: Control


title: spermatocytes, pachytene, DMSO, rep2

description: Library name: rna DMSO early2mid pachytene spermatocytes rep2

value: WT


title: MSenIR_18

description: Library name: sample18


title: hic spermatocytes, zygotene, WT, rep1

description: Library name: hic WT zygotene spermatocytes  rep1


title: spermatocytes, pachytene, DMSO, rep1

description: Library name: rna DMSO early2mid pachytene spermatocytes rep1


title: PETER001_HEPG2_6H_X1_B46:B07


title: PETER001_HEPG2_6H_X1_B46:A19

description: L1000 inferred profile; pert_id: Ritonavir

source_name: HEPG2 treated with Ritonavir 0.5 uM for 6.0 h

value: Ritonavir 0.5 uM


title: PC_16

description: Library name: sample16

value: PC


title: Calu3, biological replicate 1, CD, 12 h

description:
Library name: CD12HN11_S39
Column name in counts.final.txt: CD12HN11_S39

value: CD


title: Calu3, biological replicate 2, BAFA, 12 h

description:
Library name: BAFA12HN21_S41
Column name in counts.final.txt: BAFA12HN21_S41


title: spermatocytes, pachytene, Npm1-CKI, rep3

description: Library name: rna Npm1-CKI early2mid pachytene spermatocytes rep3


title: PETER001_HEPG2_6H_X1_B46:B05


title: Calu3, biological replicate 3, DMSO, 12 h

description:
Library name: DMSO12HN31_S43
Column name in counts.final.txt: DMSO12HN31_S43

value: DMSO


title: MSenIR_20

description: Library name: sample20

value: Bone-marrow derived


title: PETER001_HEPG2_6H_X1_B46:A17

description: L1000 inferred profile; pert_id: Abacavir

source_name: HEPG2 treated with Abacavir 0.5 uM for 6.0 h

value: Abacavir 0.5 uM


title: Calu3, biological replicate 3, DMSO, 6 h

description:
Library name: DMSO6HN31_S37
Column name in counts.final.txt: DMSO6HN31_S37


title: Calu3, biological replicate 1, DMSO, 12 h

description:
Library name: DMSO12HN11_S42
Column name in counts.final.txt: DMSO12HN11_S42


title: spermatocytes, pachytene, AZD6738, rep1

description: Library name: rna AZD6738 early2mid pachytene spermatocytes rep1


title: PETER001_HEPG2_6H_X1_B46:A21


title: PETER001_HEPG2_6H_X1_B46:A20


title: spermatocytes, pachytene, Npm1-CKI, rep1

description: Library name: rna Npm1-CKI early2mid pachytene spermatocytes rep1


title: Calu3, biological replicate 3, CD, 12 h

description:
Library name: CD12HN31_S40
Column name in counts.final.txt: CD12HN31_S40


title: PC_13

description: Library name: sample13

value: Primary

value: Macrophage


title: spermatocytes, pachytene, Npm1-control2, rep2

description: Library name: rna Npm1-control2 early2mid pachytene spermatocytes rep2

value: NPM1 flox/+;Stra8-cre


title: Calu3, biological replicate 1, DMSO, 6 h

description:
Library name: DMSO6HN11_S36
Column name in counts.final.txt: DMSO6HN11_S36


title: MSenIR_17

description: Library name: sample17


title: Calu3, biological replicate 3, CD, 6 h

description:
Library name: CD6HN31_S34
Column name in counts.final.txt: CD6HN31_S34


title: M2_11

description: Library name: sample11


title: PC_15

description: Library name: sample15


title: PETER001_HEPG2_6H_X1_B46:A16


title: Calu3, biological replicate 2, CA, 12 h

description:
Library name: CA12HN21_S38
Column name in counts.final.txt: CA12HN21_S38

value: CA


title: M2_12

description: Library name: sample12


title: PC_14

description: Library name: sample14


title: spermatocytes, pachytene, Npm1-control2, rep1

description: Library name: rna Npm1-control2 early2mid pachytene spermatocytes rep1

value: spermatocytes


title: PETER001_HEPG2_6H_X1_B46:A12

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM for 6.0 h


title: spermatocytes, pachytene, Npm1-SKO, rep3

description: Library name: rna Npm1-SKO early2mid pachytene spermatocytes rep3


title: PETER001_HEPG2_6H_X1_B46:A15

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 6.0 h


title: Calu3, biological replicate 2, BAFA, 6 h

description:
Library name: BAFA6HN21_S35
Column name in counts.final.txt: BAFA6HN21_S35

value: BAFA


title: PETER001_HEPG2_6H_X1_B46:A14

value: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: spermatocytes, pachytene, Npm1-SKO, rep2

description: Library name: rna Npm1-SKO early2mid pachytene spermatocytes rep2


title: spermatocytes, pachytene, Npm1-CKI, rep2

description: Library name: rna Npm1-CKI early2mid pachytene spermatocytes rep2


title: PETER001_HEPG2_6H_X1_B46:A13


title: spermatocytes, pachytene, Npm1-control2, rep3

description: Library name: rna Npm1-control2 early2mid pachytene spermatocytes rep3


title: M1_8

description: Library name: sample8

value: Wildtype

value: LPS


title: PETER001_HEPG2_6H_X1_B46:A11

value: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM


title: spermatocytes, pachytene, Npm1-SKO, rep1

description: Library name: rna Npm1-SKO early2mid pachytene spermatocytes rep1


title: Calu3, biological replicate 1, DMSO, 3 h

description:
Library name: DMSO3HN11_S30
Column name in counts.final.txt: DMSO3HN11_S30

value: WT


title: PETER001_HEPG2_6H_X1_B46:A10


title: Calu3, biological replicate 1, CD, 6 h

description:
Library name: CD6HN11_S33
Column name in counts.final.txt: CD6HN11_S33


title: M2_10

description: Library name: sample10


title: PETER001_HEPG2_6H_X1_B46:A08

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM for 6.0 h


title: Calu3, biological replicate 2, CA, 6 h

description:
Library name: CA6HN22_S32
Column name in counts.final.txt: CA6HN22_S32


title: M1_6

description: Library name: sample6


title: M2_9

description: Library name: sample9


title: spermatocytes, pachytene, Npm1-control, rep2

description: Library name: rna Npm1-control early2mid pachytene spermatocytes rep2

value: Npm1 flox/+


title: M1_5

description: Library name: sample5


title: Calu3, biological replicate 3, DMSO, 3 h

description:
Library name: DMSO3HN31_S31
Column name in counts.final.txt: DMSO3HN31_S31


title: PETER001_HEPG2_6H_X1_B46:A09

value: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM


title: spermatocytes, pachytene, Npm1-control, rep3

description: Library name: rna Npm1-control early2mid pachytene spermatocytes rep3


title: spermatocytes, pachytene, Senp3-SKO, rep3

description: Library name: rna Senp3-SKO early2mid pachytene spermatocytes rep3


title: PETER001_HEPG2_6H_X1_B46:A06

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir|Emtricitabine

source_name: HEPG2 treated with Abacavir|Dolutegravir|Emtricitabine 0.5|0.1|0.1 uM for 6.0 h


title: Calu3, biological replicate 1, CD, 3 h

description:
Library name: CD3HN11_S27
Column name in counts.final.txt: CD3HN11_S27

value: CD


title: PETER001_HEPG2_6H_X1_B46:A07


title: Calu3, biological replicate 3, CD, 3 h

description:
Library name: CD3HN32_S28
Column name in counts.final.txt: CD3HN32_S28


title: spermatocytes, pachytene, Npm1-control, rep1

description: Library name: rna Npm1-control early2mid pachytene spermatocytes rep1


title: M1_7

description: Library name: sample7


title: PETER001_HEPG2_6H_X1_B46:A18

description: L1000 inferred profile; pert_id: Abacavir


title: PETER001_HEPG2_6H_X1_B46:A04


title: M0_4

description: Library name: sample4

value: NT


title: Calu3, biological replicate 2, CA, 3 h

description:
Library name: CA3HN21_S26
Column name in counts.final.txt: CA3HN21_S26


title: PETER001_HEPG2_6H_X1_B46:A05


title: spermatocytes, pachytene, Senp3-SKO, rep2

description: Library name: rna Senp3-SKO early2mid pachytene spermatocytes rep2


title: Calu3, biological replicate 2, BAFA, 3 h

description:
Library name: BAFA3HN21_S29
Column name in counts.final.txt: BAFA3HN21_S29


title: PETER001_HEPG2_24H_X1_B46:H19

description: L1000 inferred profile; pert_id: DMSO

source_name: HEPG2 treated with DMSO 0.5 uM for 24.0 h

value: DMSO 0.5 uM


title: Calu3, biological replicate 3, CA, 24 h

description:
Library name: CA24HN31_S21
Column name in counts.final.txt: CA24HN31_S21


title: PETER001_HEPG2_24H_X1_B46:H18

description: L1000 inferred profile; pert_id: Darunavir

source_name: HEPG2 treated with Darunavir 0.1 uM for 24.0 h

value: Darunavir 0.1 uM


title: RNA_BE3_rep3

city: Potsdam

first: Yang

last: Gao

state: Brandenburg

address: Am Mühlenberg 1

department: Organelle Biology, Biotechnology and Molecular Ecophysiology

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description: Library name: mpg_L31055-1_PoolE-006-RNA-BE3-3_S36_R1_001.fastq.gz

data_processing:
Sequencing reads were adapter-trimmed and filtered for size between 18 and 60 nt using Cutadapt. The 8-nt UMI sequence in the RNA adapter was extracted, and reads were deduplicated after mapping using umi_tools. Mapping was performed using STAR with the Arabidopsis TAIR 10 genome as reference and the following parameters: --outFilterMismatchNoverLmax 0.1 --alignIntronMin 500 --alignIntronMax 1200 --outSAMmultNmax 1.
Assembly: Arabidopsis TAIR 10
Supplementary files format and content: RIP-seq samples: xlsx file including total reads from each sample and MKIP1-specific immunoprecipitated RNA fragments analyzed by DiffSegR
Supplementary files format and content: RNA-seq samples: xlsx file including total reads from each sample

organism: Arabidopsis thaliana

source_name: 10-day-old seedlings

growth_protocol: Arabidopsis thaliana seedlings were surface sterilized using chlorine gas and sown on 0.8% (w/v) agar plates at pH 5.7 containing one half-strength Murashige and Skoog (MS) medium with vitamins (Duchefa Biochemie) and 15 mg/L Basta and stratified at 4°C in the dark for three days. Plates were transferred to controlled growth chambers with 12-h light and 12-h dark cycles. Seedlings were collected after 10 days incubation in the light chamber.

extract_protocol:
Soluble cell components were extracted by homogenizing 10 g of seedlings per replicate in a pre-cooled blender using 30 ml of ice-cold extraction buffer (50 mM Tris–HCl, pH 8.0, 150 mM NaCl, 1 mM DTT, 1% (v/v) Triton X-100, 1 mM EDTA, 4 mM MgCl2, 1x protease inhibitor cocktail [cOmplete EDTA-free, Roche], 40 U/ml RNase inhibitor [RiboLock RNase Inhibitor, Thermo Fisher Scientific]). The homogenates were filtered through two layers of Miracloth (Milipore) and cleared by two sequential centrifugation rounds at 4,000 g for 10 minutes at 4 °C. Per replicate, 20 ml of the supernatant were incubated with 150 µl pre-equilibrated magnetic agarose anti-YFP/GFP beads (GFP-Trap, ChromoTek) for two hours at 4 °C with rotation, washed three times with ice-cold wash buffer 1 (same as extraction buffer, but replacing Triton X-100 with 0.5 % [v/v] NP-40), followed by three washes with ice-cold wash buffer 2 (50 mM Tris–HCl, pH 8.0, 150 mM NaCl). In the last wash, 10% (v/v) of the resuspended beads were collected in a separate tube and used for immunoblot analysis, while the residual beads were transferred to a new microcentrifuge tube and were processed for RNA extraction. For RNA extraction, 500 µl of input soluble extract or immunoprecipitation-processed beads were brought to a total volume of 1 ml with DEPC-treated water, mixed with 1 ml phenol:chloroform:isoamyl alcohol (Roth Lot X985.1) and subjected to phenol-chloroform RNA extraction. Two µg input RNA was treated with TURBO DNase (Thermo Fisher Scientific) in a 50 µl reaction according to the manufacturer’s instructions. From this, 600 ng purified RNA was subjected to rRNA depletion treatment. The RNA was eluted in 18 µl of RNase-free water and supplemented with 2 µl RNA fragmentation buffer (400mM Tris-acetate pH 8.3, 1 M potassium acetate, 300mM magnesium acetate), followed by incubation at 94 °C for 5 minutes. Both pellet and input RNA were treated with T4 polynucleotide kinase (PNK; Thermo Fisher Scientific).
Library preparation for RNA sequencing was performed using the NEXTflex small RNA-seq kit v3 (Perkin Elmer, cat# NOVA-5132-06) according to the manufacturer’s instructions. The resulting cDNA was amplified with a barcode incorporated in the primer and purified according to the instructions of the NEXTflex kit.

value: 10-day-old seedlings

value: Input of coIP


title: kdm5b Cardiac specific KO mouse heart P1 sample 1

city: Houston

first: Riham

middle: Raafat Elgharib

last: Abouleisa

address: 6519 Fannin Street

department: surgery

institute: Baylor College of Medicine

description:
Library name: cKo_1
column  E in gene_fpkm.xls: cKo_1

data_processing:
Following end-repair and adapter ligation, libraries were PCR-amplified for nine cycles. Library quality was assessed using a Bioanalyzer High-Sensitivity DNA chip (Agilent), and concentrations were determined by qPCR (KAPA). Sequencing was performed on an Illumina NovaSeq platform using a 50-cycle single-read format. RNA-seq data processing followed a previously described pipeline. Briefly, adapter sequences and low-quality bases were removed using Fastq-mcf (http://code.google.com/p/ea-utils), and read quality was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the GRCh38 (human) or mm10 (mouse) reference genomes using TopHat v2.0.13. Gene expression levels were quantified using Subread featureCounts based on Ensembl annotations. Differential gene expression was analyzed using edgeR. Genes were filtered to include only those with at least two samples having counts per million (CPM) between 0.5 and 5000; genes with CPM < 0.5 were considered undetectable, and genes with CPM > 5000 (typically mitochondrial) were excluded to prevent skewed normalization. Remaining genes were normalized using the calcNormFactor function in edgeR, and P-values for differential expression were computed based on the negative binomial distribution model.
Assembly: GRCm39

source_name: heart

growth_protocol: P1 mice heartsisolated from control ff mice or kdm5bcko, snap frozen the RNA exrtractio

extract_protocol:
RNA was extracted following the miRNeasy micro kit protocol (Qiagen Cat# 217084).
the Ovation Ultralow V2 Kit (NuGEN)

treatment_protocol: ff mice hearts versus cko mice heats at P1

value: heart

value: kdm5b Cko


title: Calu3, biological replicate 2, CD, 24 h

description:
Library name: CD24HN21_S22
Column name in counts.final.txt: CD24HN21_S22


title: Calu3, biological replicate 1, CA, 24 h

description:
Library name: CA24HN11_S20
Column name in counts.final.txt: CA24HN11_S20

value: CA


title: spermatocytes, pachytene, Senp3-control, rep2

description: Library name: rna Senp3-control early2mid pachytene spermatocytes rep2

value: spermatocytes


title: Calu3, biological replicate 2, DMSO, 24 h

description:
Library name: DMSO24HN21_S25
Column name in counts.final.txt: DMSO24HN21_S25

value: DMSO


title: Flox mouse heart P1 sample 3

description:
Library name: f_3
column  D in gene_fpkm.xls: f_3

value: FF


title: Calu3, biological replicate 3, BAFA, 24 h

description:
Library name: BAFA24HN31_S24
Column name in counts.final.txt: BAFA24HN31_S24

value: BAFA


title: spermatocytes, pachytene, Senp3-SKO, rep1

description: Library name: rna Senp3-SKO early2mid pachytene spermatocytes rep1


title: RNA_BE3_rep2

description: Library name: mpg_L31055-1_PoolE-005-RNA-BE3-2_S35_R1_001.fastq.gz


title: PETER001_HEPG2_24H_X1_B46:H17


title: Calu3, biological replicate 3, CD, 24 h

description:
Library name: CD24HN31_S46
Column name in counts.final.txt: CD24HN31_S46


title: Calu3, biological replicate 2, DMSO, 12 h

description:
Library name: DMSO12HN21_S19
Column name in counts.final.txt: DMSO12HN21_S19


title: RNA_BE3_rep1

description: Library name: mpg_L31055-1_PoolE-004-RNA-BE3-1_S34_R1_001.fastq.gz


title: M0_1

description: Library name: sample1

source_name: Bone-marrow derived

value: Bone-marrow derived

value: Primary

value: Macrophage

value: Wildtype


title: spermatocytes, pachytene, Senp3-control, rep3

description: Library name: rna Senp3-control early2mid pachytene spermatocytes rep3

value: WT


title: PETER001_HEPG2_24H_X1_B46:H15

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir

source_name: HEPG2 treated with Emtricitabine|Ritonavir 0.1|0.5 uM for 24.0 h

value: Emtricitabine|Ritonavir 0.1|0.5 uM


title: RNA_MKIP1_rep2

description: Library name: mpg_L31055-1_PoolE-002-RNA-BE1-2_S32_R1_001.fastq.gz


title: PETER001_HEPG2_24H_X1_B46:H21

description: L1000 inferred profile; pert_id: DMSO

value: DMSO 0.5 uM


title: scRNA of spleen MASH-Phe-free treatment

city: Indianapolis

first: Yamei

last: Chen

state: Indiana

address: 975 W. Walnut St., IB552

institute: Indiana University

description: Library name: scRNA_spleen_MASH_Phe_free

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq data were processed using the 10x Genomics Cell Ranger pipeline (v9.0.1) to generate gene expression matrices. Downstream analyses were conducted in Seurat (v5.3.0) in R. Cells with fewer than 200 expressed genes and more than 10% mitochondrial gene content were removed. A total of 50,127 spots passed quality control and were included in further analysis.
Assembly: refdata-gex-GRCm39-2024-A/mm39 (GRCm39)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features.tsv.gz: list of gene IDs

source_name: Spleen

extract_protocol:
Cells were resuspended in PBS with 0.04% BSA at a concentration of 700-1200 cells/µl and more than 85% viability.
The single cell capture and library construction were performed by following the Chromium Next GEM Single cell 5ʹ Reagent Kits v2 protocol (CG000331). The single cells were loaded onto Chromium Next GEM Chip K with partitioning oil and barcoded singe cell gel beads. The barcoded and full-length cDNA is produced after incubation of the gel beads-in-emulsion (GEMs) and amplified via PCR for library construction. The library preparation is performed by following the protocol of Chromium Next GEM Single Cell 5ʹ GEM, Library & Gel Bead Kit v2 (PN-1000267). The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The qualified libraries were sequenced using the paired-end sequencing on an Illumina Novaseq System (Illumina, Inc., USA).

value: Spleen


title: Calu3, biological replicate 2, CD, 12 h

description:
Library name: CD12HN21_S16
Column name in counts.final.txt: CD12HN21_S16

value: CD


title: RNA_MKIP1_rep1

description: Library name: mpg_L31055-1_PoolE-001-RNA-BE1-1_S31_R1_001.fastq.gz

value: 10-day-old seedlings

value: Input of coIP


title: kdm5b Cardiac specific KO mouse heart P1 sample 2

description:
Library name: cKo_2
column  F in gene_fpkm.xls: cKo_2

value: heart

value: kdm5b Cko


title: M0_2

description: Library name: sample2

value: NT


title: PETER001_HEPG2_24H_X1_B46:H20

description: L1000 inferred profile; pert_id: DMSO


title: PETER001_HEPG2_24H_X1_B46:H13


title: PETER001_HEPG2_24H_X1_B46:H14


title: scRNA of spleen Chow treatment

description: Library name: scRNA_spleen_Chow


title: spermatocytes, pachytene, Senp3-control, rep1

description: Library name: rna Senp3-control early2mid pachytene spermatocytes rep1

value: spermatocytes


title: kdm5b Cardiac specific KO mouse heart P1 sample 3

description:
Library name: cKo_3
column  G in gene_fpkm.xls: cKo_3


title: PETER001_HEPG2_24H_X1_B46:H11

description: L1000 inferred profile; pert_id: Darunavir|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 24.0 h


title: Pellet_BE3_rep2

description: Library name: mpg_L31054-1_PoolD-005-Pellet-BE3-2_S29_R1_001.fastq.gz

value: CoIP


title: Calu3, biological replicate 1, BAFA, 24 h

description:
Library name: BAFA24HN11_S23
Column name in counts.final.txt: BAFA24HN11_S23

value: BAFA


title: Calu3, biological replicate 2, DMSO, 6 h

description:
Library name: DMSO6HN21_S13
Column name in counts.final.txt: DMSO6HN21_S13

value: DMSO


title: PETER001_HEPG2_24H_X1_B46:H16

description: L1000 inferred profile; pert_id: Darunavir

value: Darunavir 0.1 uM


title: Calu3, biological replicate 3, BAFA, 12 h

description:
Library name: BAFA12HN31_S18
Column name in counts.final.txt: BAFA12HN31_S18


title: M0_3

description: Library name: sample3

value: Bone-marrow derived

value: Primary

value: Macrophage


title: Flox mouse heart P1 sample 2

description:
Library name: f_2
column  C in gene_fpkm.xls: f_2

value: FF


title: Pellet_MKIP1_rep2

description: Library name: mpg_L31054-1_PoolD-002-Pellet-BE1-2_S26_R1_001.fastq.gz


title: biological replicate 3: 105 D9K1 (L001)

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description:
Library name: QVKSV006AP (L001)
Pilot1CountsWolbachia.txt

data_processing:
All read mappings were performed independently against the reference strain of Wolbachia pipientis wAlbB (RefSeq ID: NZ_CP031221.1) and the reference strain of Aedes albopictus (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_006496715.1/).
The resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.4 (Liao et al., 2014) based on the annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript).
A quality check for rRNA was performed with a self-written script based on the absolute counts of annotated rRNAs
All read mappings were performed independently against the reference strain of Wolbachia pipientis wAlbB (RefSeq ID: NZ_CP031221.1) and the reference strain of Aedes albopictus (RefSeq ID: NC_006817.1).
Assembly: NZ_CP031221.1
Supplementary files format and content: Pilot1: a tab-delimited count table from the feature counts step against Wolbachia
Supplementary files format and content: Pilot2: two tab-delimited count table from the feature counts step, one against Wolbachia and one against Aedes albopictus.

organism: Aedes albopictus

source_name: whole cell

growth_protocol: Wolbachia-infected C6/36 cells were incubated in plug-sealed 75 cm2 culture flasks (Greiner, Kremsmünster, Austria) at 26 °C in 15 ml Leibovitz’s L15 medium (Thermo Fisher Scientific, Waltham, Massachusetts, USA) supplemented with 20% heat-inactivated FCS (PAN-Biotech, Aidenbach, Germany), 1% MEM nonessential amino acids (Thermo Fisher Scientific), 2% tryptose phosphate broth (Sigma-Aldrich, St. Louis, Missouri, USA)  and 1% penicillin/streptomycin (Thermo Fisher Scientific). They were passaged every 7 days, with 3 ml of the passage added to a new flask with 12 ml fresh medium. Medium exchange (10 ml) was performed 3 days after passaging. For the assay with custom-designed riboPOOLs, 2 ml per sample were harvested from cell culture flasks.

extract_protocol:
Total RNA was extracted from wAlbB-infected C6/36 cells using the miRNeasy Mini Kit (Qiagen, Hilden, Germany), with protocol adaptations. Samples were incubated at 37 °C in a heating block until completely thawed, ensuring that all salts were fully dissolved. After an additional 5 min incubation at room temperature, samples were mixed with 100 µl 1-Bromo-3-chloro-2-propanol (BCP, Tokyo Chemical Industry, Tokyo, Japan). The sample-BCP mixture was vigorously shaken for 15 seconds, followed by a 2–3 min incubation at room temperature. Phase separation was achieved through a 15 min centrifugation at 12,000 g, 4 °C. The upper aqueous phase, containing the nucleic acids, was retained, with 350 µl applied to the Qiagen column. The extract was also subject to DNase I treatment to eliminate contaminating DNA.
Pilot 1: Three samples were subjected to rRNA depletion using Illumina TruSeq Stranded Total RNA with Ribo-Zero Plus rRNA Depletion according to the manufacturer’s instructions, using the maximum input of 5 µg RNA. Pilot 2: Four libraries corresponding to two technical replicates.

value: whole cell

value: Aedes albopictus C6/36 insect cells infected with Wolbachia

value: insect cell


title: Calu3, biological replicate 1, BAFA, 6 h

description:
Library name: BAFA6HN11_S11
Column name in counts.final.txt: BAFA6HN11_S11

value: WT


title: RNA_MKIP1_rep3

description: Library name: mpg_L31055-1_PoolE-003-RNA-BE1-3_S33_R1_001.fastq.gz

value: 10-day-old seedlings

value: Input of coIP


title: Calu3, biological replicate 1, BAFA, 12 h

description:
Library name: BAFA12HN11_S17
Column name in counts.final.txt: BAFA12HN11_S17


title: PETER001_HEPG2_24H_X1_B46:H08

description: L1000 inferred profile; pert_id: Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 24.0 h


title: Calu3, biological replicate 3, CA, 12 h

description:
Library name: CA12HN31_S15
Column name in counts.final.txt: CA12HN31_S15

value: CA


title: scRNA of spleen MASH treatment

description: Library name: scRNA_spleen_MASH

value: Spleen


title: Pellet_BE3_rep3

description: Library name: mpg_L31054-1_PoolD-006-Pellet-BE3-3_S30_R1_001.fastq.gz


title: Calu3, biological replicate 1, CA, 12 h

description:
Library name: CA12HN11_S14
Column name in counts.final.txt: CA12HN11_S14


title: Flox mouse heart P1 sample 1

description:
Library name: f_1
column  B in gene_fpkm.xls: f_1

value: heart


title: Calu3, biological replicate 1, CA, 6 h

description:
Library name: CA6HN11_S8
Column name in counts.final.txt: CA6HN11_S8


title: Ctrl 4-r/-mRNA, Replicate 2

description:
Library name: Q4WOL024AR
total RNA --> rRNA depletion with riboPOOLs + eukaryotic mRNA depletion

data_processing:
All read mappings were performed independently against the reference strain of Wolbachia pipientis wAlbB (RefSeq ID: NZ_CP031221.1) and the reference strain of Aedes albopictus (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_006496715.1/).
The resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.4 (Liao et al., 2014) based on the annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript).
A quality check for rRNA was performed with a self-written script based on the absolute counts of annotated rRNAs
All read mappings were performed independently against the reference strain of Wolbachia pipientis wAlbB (RefSeq ID: NZ_CP031221.1) and the reference strain of Aedes albopictus (RefSeq ID: NC_006817.1).
Assembly: NC_006817.1
Supplementary files format and content: a tab-delimited count table from the feature counts step

extract_protocol:
Total RNA was extracted from wAlbB-infected C6/36 cells using the miRNeasy Mini Kit (Qiagen, Hilden, Germany), with protocol adaptations. Samples were incubated at 37 °C in a heating block until completely thawed, ensuring that all salts were fully dissolved. After an additional 5 min incubation at room temperature, samples were mixed with 100 µl 1-Bromo-3-chloro-2-propanol (BCP, Tokyo Chemical Industry, Tokyo, Japan). The sample-BCP mixture was vigorously shaken for 15 seconds, followed by a 2–3 min incubation at room temperature. Phase separation was achieved through a 15 min centrifugation at 12,000 g, 4 °C. The upper aqueous phase, containing the nucleic acids, was retained, with 350 µl applied to the Qiagen column. The extract was also subject to DNase I treatment to eliminate contaminating DNA.
Two samples were subjected to rRNA depletion using riboPOOLs (siTOOLs Biotech, Planegg, Germany) according to the manufacturer’s instructions, using the maximum input of 5 µg RNA. Three riboPOOLs were employed: Aedes albopictus (dp-K012-47) and custom-designed riboPOOLs for Wolbachia and Aedes albopictus. The sequences of the riboPOOLs are proprietary knowledge of siTOOLs Biotech.

value: Aedes albopictus cell line C6/36


title: PETER001_HEPG2_24H_X1_B46:H12

description: L1000 inferred profile; pert_id: Darunavir|Tenofovir Disoproxil Fumarate

value: Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: biological replicate 3: 105 D9K1 (L002)

description:
Library name: QVKSV006AP (L002)
Pilot1CountsWolbachia.txt


title: Calu3, biological replicate 3, BAFA, 3 h

description:
Library name: BAFA3HN32_S5
Column name in counts.final.txt: BAFA3HN32_S5

value: BAFA


title: PETER001_HEPG2_24H_X1_B46:H10


title: Pellet_BE3_rep1

description: Library name: mpg_L31054-1_PoolD-004-Pellet-BE3-1_S28_R1_001.fastq.gz

value: CoIP


title: PETER001_HEPG2_24H_X1_B46:H09

value: Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: C43

city: BeiJing

first: Xi

last: Han

address: 5 Yiheyuan Road, Haidian District, Beijing, China   Postal Code: 100871

institute: Peking University

description: Library name: sample15

data_processing:
RSEM employs an expectation-maximization algorithm to establish a maximum likelihood abundance estimation model that comprehensively accounts for paired-end reads, read lengths, fragment length distributions, and quality scores to distinguish transcript isoforms originating from the same gene.
Assembly: GCF_000021485.1
Supplementary files format and content: FPKM values for each sample

organism: Acidithiobacillus ferrooxidans

source_name: biofilm

extract_protocol:
Total RNA was extracted from samples using the Trizol method, followed by quality control (QC) analysis using the Thermo NanoDrop One and Agilent 4200 TapeStation system.
Ribosomal RNA depletion was performed using the Epicentre Ribo-Zero rRNA Removal Kit, and subsequent library preparation was conducted with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: biofilm

value: A.ferrooxidans growing on pyrite surface

value: strain with AFE_1379 gene


title: biological replicate 2: 107 D6K1 (L002)

description:
Library name: QVKSV005AH (L002)
Pilot1CountsWolbachia.txt

value: whole cell


title: PETER001_HEPG2_24H_X1_B46:H01

description: L1000 inferred profile; pert_id: Water

source_name: HEPG2 treated with Water 0.01 uM for 24.0 h

value: Water 0.01 uM


title: 23047FL-37-01-27, snRNA-seq

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

description:
Library name: 23047FL-37-01-27
10x Genomics

data_processing:
Reads were aligned to the rat mRatBN7 reference genome with introns from UCSC [33270111] using the 10x Genomics CellRanger analytical pipeline[28091601]. CellRanger was used to perform dataset aggregation to normalize for total numbers of confidently mapped reads using the “count” function to generate raw gene-cell expression matrices. CellBender[37550580] was used to infer and remove ambient RNA contamination.
Assembly: mRatBN7
Supplementary files format and content: h5

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: brain

growth_protocol: Timed pregnant Sprague Dawley rats from Charles River Laboratories (Wilmington, MA, USA) were housed in a controlled temperature room under a 14/10-hour light/dark cycle with food and water ad libitum.

extract_protocol:
Brains were placed on ice and lysis buffer (Tris-HCl (pH 7.4) 10mM, NaCl 10 mM, 3mM MgCl2, Nonidet P40 Substitute ( MilliporeSigma Cat. 74385) 0.1%, in nuclease-free Water) was added for 15 minutes. Using a 2ml pipette, the tissue was gently transferred to a 50ml falcon tube adding 5ml of Hibernate E/B27/GlutaMAX (HEB) medium Gibco Cat.  A12476-01. Tissue was triturated with a pasteur pipette, homogenates were strained with 30 μm MACS SmartStrainer to remove large debris. Homogenates were centrifuged at 500 rcf for 5 min at 4°C, supernatant was removed and 10 ml of nuclei washing solution and resuspension buffer (BSA 1%, 0.2X (using 40X MilliporeSigma Cat. 3335399001), prepared in 1X PBS) was added. Lysis efficiency and viability were assessed by staining cells with trypan blue and counted using the Countess II FL Automated Cell Counter/ microscopy.
Isolated nuclei were processed by UTHealth Cancer Genomics Core at The University of Texas Health Science Center at Houston (CPRIT RPND240610). Single nuclei capture and library construction were performed by following the Chromium GEM-X Single Cell 3ʹ Reagent Kits v4 protocol (CG000731). Briefly, cells were resuspended in PBS with 0.04% BSA and RNase inhibitor at a concentration of 700-1200 cells/µl. The single nuclei were loaded onto Chromium GEM-X 3’ Chip (PN-1000690) with partitioning oil and barcoded single-cell gel beads. The barcoded and full-length cDNA was produced after incubation of gel beads-in-emulsion (GEMs) and amplified via PCR for library construction. The library preparation was performed by following the protocol of Chromium GEM-X Single Cell 3ʹ Kit v4 (PN-1000691). The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The qualified libraries were sent for the paired-end sequencing on an Illumina Novaseq System (Illumina, Inc., USA).

treatment_protocol: Rat pups were separated by sex and postanal day PND2 and PND5 groups for intraventricular injection. For injections, the scalp was prepped with betadine and a 30G needle was placed directly through the scalp with the following coordinates: for PND2, 3.8 mm from lambda, lateral 0.7 mm, 2 mm deep, and for PND5, 4.6 mm from lambda, lateral 1.1 mm, and 3.3 mm deep, measured through transillumination of the cranial sutures. 30μl of lysed blood from a female donor was injected into the right ventricle at a flow rate of 0.5 μl/sec. 30μl of sterile artificial CSF (Biotechne Tocris Cat. 3525)  was used as a control. The needle was left in place for 1 min after the injection to prevent retrograde flow out of the syringe tract. After the injections, the animals were immediately returned to their home cage and dam for recovery. 24h after IVH, animals were euthanized by rapid decapitation and meningeal tissue was removed. Whole brains were placed into 2 ml Eppendorf tubes in liquid nitrogen for fast freezing.

value: brain

value: Sprague Dawley

value: Wildtype

value: Control


title: Calu3, biological replicate 3, BAFA, 6 h

description:
Library name: BAFA6HN31_S12
Column name in counts.final.txt: BAFA6HN31_S12

value: WT


title: Pellet_MKIP1_rep3

description: Library name: mpg_L31054-1_PoolD-003-Pellet-BE1-3_S27_R1_001.fastq.gz

value: 10-day-old seedlings


title: Calu3, biological replicate 2, CD, 6 h

description:
Library name: CD6HN21_S10
Column name in counts.final.txt: CD6HN21_S10

value: CD


title: biological replicate 1: 107 D61 (L002)

description:
Library name: QVKSV004A9 (L002)
Pilot1CountsWolbachia.txt

value: Aedes albopictus C6/36 insect cells infected with Wolbachia

value: insect cell


title: biological replicate 2: 107 D6K1 (L001)

description:
Library name: QVKSV005AH (L001)
Pilot1CountsWolbachia.txt


title: Pellet_MKIP1_rep1

description: Library name: mpg_L31054-1_PoolD-001-Pellet-BE1-1_S25_R1_001.fastq.gz


title: PETER001_HEPG2_24H_X1_B46:H06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine

source_name: HEPG2 treated with Darunavir|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Darunavir|Emtricitabine 0.1|0.1 uM


title: C42

description: Library name: sample14


title: PETER001_HEPG2_24H_X1_B46:G21

description: L1000 inferred profile; pert_id: DMSO

value: DMSO 0.5 uM


title: Calu3, biological replicate 3, CA, 6 h

description:
Library name: CA6HN31_S9
Column name in counts.final.txt: CA6HN31_S9

value: CA


title: 23047FL-37-01-30, snRNA-seq

description:
Library name: 23047FL-37-01-30
10x Genomics

value: IVH


title: PETER001_HEPG2_24H_X1_B46:H05


title: PETER001_HEPG2_24H_X1_B46:H04


title: biological replicate 1: 107 D61 (L001)

description:
Library name: QVKSV004A9 (L001)
Pilot1CountsWolbachia.txt


title: 23047FL-37-01-29, snRNA-seq

description:
Library name: 23047FL-37-01-29
10x Genomics


title: 23047FL-37-01-25, snRNA-seq

description:
Library name: 23047FL-37-01-25
10x Genomics


title: Calu3, biological replicate 2, CD, 3 h

description:
Library name: CD3HN21_S3
Column name in counts.final.txt: CD3HN21_S3


title: Calu3, biological replicate 3, CA, 3 h

description:
Library name: CA3HN31_S2
Column name in counts.final.txt: CA3HN31_S2


title: 23047FL-37-01-24, snRNA-seq

description:
Library name: 23047FL-37-01-24
10x Genomics


title: 23047FL-37-01-23, snRNA-seq

description:
Library name: 23047FL-37-01-23
10x Genomics


title: PETER001_HEPG2_24H_X1_B46:G18

description: L1000 inferred profile; pert_id: Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Tenofovir Alafenamide Fumarate 0.5 uM for 24.0 h

value: Tenofovir Alafenamide Fumarate 0.5 uM


title: Calu3, biological replicate 2, DMSO, 3 h

description:
Library name: DMSO3HN21_S6
Column name in counts.final.txt: DMSO3HN21_S6

value: DMSO


title: 23047FL-37-01-28, snRNA-seq

description:
Library name: 23047FL-37-01-28
10x Genomics


title: C32

description: Library name: sample11

value: biofilm

value: A.ferrooxidans growing on pyrite surface

value: strain with AFE_0053 gene


title: Ctrl 3-r/-mRNA, Replicate 1

description:
Library name: Q4WOL023AJ
total RNA --> rRNA depletion with riboPOOLs + eukaryotic mRNA depletion

value: whole cell

value: Aedes albopictus cell line C6/36


title: C31

description: Library name: sample10


title: PETER001_HEPG2_24H_X1_B46:H02

description: L1000 inferred profile; pert_id: Water

value: Water 0.01 uM


title: C23

description: Library name: sample9

value: strain with AFE_1373 gene


title: Calu3, biological replicate 1, BAFA, 3 h

description:
Library name: BAFA3HN11_S4
Column name in counts.final.txt: BAFA3HN11_S4

value: WT

value: BAFA


title: PETER001_HEPG2_24H_X1_B46:G16


title: C41

description: Library name: sample13

value: strain with AFE_1379 gene


title: PETER001_HEPG2_24H_X1_B46:G20

description: L1000 inferred profile; pert_id: DMSO


title: 23047FL-37-01-20, snRNA-seq

description:
Library name: 23047FL-37-01-20
10x Genomics

value: brain

value: Sprague Dawley

value: Wildtype

value: Control


title: PETER001_HEPG2_24H_X1_B46:G14

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM for 24.0 h


title: 23047FL-37-01-26, snRNA-seq

description:
Library name: 23047FL-37-01-26
10x Genomics


title: PETER001_HEPG2_24H_X1_B46:G19

description: L1000 inferred profile; pert_id: DMSO

value: DMSO 0.5 uM


title: C33

description: Library name: sample12


title: 23047FL-37-01-19, snRNA-seq

description:
Library name: 23047FL-37-01-19
10x Genomics

value: IVH


title: C13

description: Library name: sample6

value: strain with yedQ gene


title: Subject5_exp1_vehicle

city: Dallas

first: Jonathan

last: Rios

state: TX

address: 2222 Welborn Street

institute: Scottish Rite for Children

description:
Library name: Subject5_exp1_vehicle
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt

data_processing:
Sequence reads were mapped to the human reference genome (hg38) using STAR (v2.7.8). Alignments were filtered to remove duplicates, singleton reads, and unaligned reads. Gene expression was quantified using the Ensembl database (release 109). Expression levels of protein-coding transcripts were normalized using the Median Ratio method for DESeq2 analysis. Processed files with FPKM normalization are also included.
Assembly: hg38
Supplementary files format and content: Gene expression matrix normalized by Median Ratio method for DESeq2 analysis
Supplementary files format and content: Gene expression matrix normalized by FPKM

source_name: lesion

growth_protocol: MEM-alpha with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was extracted using the Rneasy Plus minikit (Qiagen)
Transcriptome sequencing libraries were prepared using the TruSeq Stranded Total RNA LT sample preparation kit to deplete of ribosomal RNA prior to cDNA synthesis. After, indexed adaptors are ligated to cDNA fragments and purified using AMPureXP beads (Beckman Coulter Life Sciences, USA). Sequencing libraries are normalized prior to sequencing using the 150bp paired-end protocol on an Illumina NextSeq2000 instrument.

treatment_protocol: vehicle (DMSO), capmatinib (10uM, Catalog# S2788, Selleck Chemicals, USA), selumetinib (5uM, Catalog# S1008, Selleck Chemicals, USA), mirdametinib (100nM, Catalog# S1036, Selleck Chemicals, USA)

value: lesion

tag: individual

value: primary cell

value: vehicle


title: 23047FL-37-01-18, snRNA-seq

description:
Library name: 23047FL-37-01-18
10x Genomics


title: Subject5_exp2_mirdametinib

description:
Library name: Subject5_exp2_mirdametinib
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt

value: mirdametinib


title: Calu3, biological replicate 1, CA, 3 h

description:
Library name: CA3HN11_S1
Column name in counts.final.txt: CA3HN11_S1

value: CA


title: PETER001_HEPG2_24H_X1_B46:G17

value: Tenofovir Alafenamide Fumarate 0.5 uM


title: 23047FL-37-01-22, snRNA-seq

description:
Library name: 23047FL-37-01-22
10x Genomics


title: PETER001_HEPG2_24H_X1_B46:G12

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 24.0 h


title: 23047FL-37-01-21, snRNA-seq

description:
Library name: 23047FL-37-01-21
10x Genomics


title: 23047FL-37-01-16, snRNA-seq

description:
Library name: 23047FL-37-01-16
10x Genomics


title: Subject5_exp2_vehicle

description:
Library name: Subject5_exp2_vehicle
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt


title: C22

description: Library name: sample8

value: biofilm

value: A.ferrooxidans growing on pyrite surface

value: strain with AFE_1373 gene


title: S3

description: Library name: sample3

value: strain control


title: PETER001_HEPG2_24H_X1_B46:G15

value: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM


title: 23047FL-37-01-15, snRNA-seq

description:
Library name: 23047FL-37-01-15
10x Genomics

value: brain

value: Sprague Dawley


title: C21

description: Library name: sample7


title: PETER001_HEPG2_24H_X1_B46:G09

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 24.0 h


title: S2

description: Library name: sample2


title: Subject5_exp1_selumetinib

description:
Library name: Subject5_exp1_selumetinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt

value: selumetinib


title: Subject4_exp1_selumetinib

description:
Library name: Subject4_exp1_selumetinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt


title: Subject5_exp1_capmatinib

description:
Library name: Subject5_exp1_capmatinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt

value: capmatinib


title: Subject4_exp1_capmatinib

description:
Library name: Subject4_exp1_capmatinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt


title: Subject4_exp2_mirdametinib

description:
Library name: Subject4_exp2_mirdametinib
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt


title: 23047FL-37-01-14, snRNA-seq

description:
Library name: 23047FL-37-01-14
10x Genomics

value: Wildtype

value: Control


title: C12

description: Library name: sample5

value: strain with yedQ gene


title: 23047FL-37-01-13, snRNA-seq

description:
Library name: 23047FL-37-01-13
10x Genomics


title: Subject4_exp1_vehicle

description:
Library name: Subject4_exp1_vehicle
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt

value: lesion

value: primary cell


title: PETER001_HEPG2_24H_X1_B46:G07

value: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: 23047FL-37-01-17, snRNA-seq

description:
Library name: 23047FL-37-01-17
10x Genomics

value: IVH


title: Subject4_exp2_vehicle

description:
Library name: Subject4_exp2_vehicle
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt

value: vehicle


title: PETER001_HEPG2_24H_X1_B46:G10

value: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: PETER001_HEPG2_24H_X1_B46:G11


title: PETER001_HEPG2_24H_X1_B46:G05

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir

source_name: HEPG2 treated with Darunavir|Emtricitabine|Ritonavir 0.1|0.1|0.5 uM for 24.0 h


title: S1

description: Library name: sample1

value: biofilm

value: A.ferrooxidans growing on pyrite surface


title: C11

description: Library name: sample4


title: 23047FL-37-01-12, snRNA-seq

description:
Library name: 23047FL-37-01-12
10x Genomics


title: PETER001_HEPG2_24H_X1_B46:G03

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: Δlsr2ΔlsrL mutant cells, replicate 3 input

city: Ann Arbor

first: Vivian

last: Ramirez

state: MI

address: 1150 W. Medical Center Dr

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

description:
Library name: Δlsr2ΔlsrL rep 3, input
Mean enrichment scores across replicates included in *_mean.bedgraph files

data_processing:
Read pre-processing: Raw NGS reads were processed using a combination of read quality filtering, adapter trimming, alignment and mapping, and protein occupancy using the IPOD-HR pipeline (version 2.8.1) via a singularity container (accessible at https://github.com/freddolino-lab/ipod). Briefly, sequencing adapters were removed using Cutadapt (version 4.0), poor quality reads were trimmed with Trimmomatic (version 0.39) using the parameters “TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10”.
Alignment and protein occupancy calling: Remaining reads were aligned to the S. venezuelae NRRL B-65442 NZ_CP018074.1 reference genome using bowtie2 [53](version 2.4.4) with “very sensitive, end to end” presets and dovetail alignments allowed. Only concordant pairs were used for downstream quantitation. The surviving processed reads were assessed using FASTQC [54] for sequence content, quality, and duplication and bowtie2 outputs. The quality of alignments were evaluated using bowtie2 output metrics, including the overall alignment rates. Read densities were quantile normalized, and the log ratios of IPOD-HR and RNApol ChIP-seq were calculated at a 5 bp resolution relative to the corresponding input sample. To isolate occupancy scores attributable to DNA-binding proteins distinct from RNApol, the IPOD-HR pipeline subtracts RNApol ChIP-seq normalized robust z-scores (RNApol ChIP-seq vs. input) from the IPOD normalized robust z-scores. The resulting bedgraph files, containing enrichment scores for RNApol ChIP-seq and IPOD-HR, were used for downstream analyses.
Assembly: GCF_001886595.1
Supplementary files format and content: bedgraph

organism: Streptomyces venezuelae

source_name: S. venezuelae NRRL B-65442

growth_protocol: The S. venezuelae NRRL B-65442 strain served as the WT and base strain for all experiments conducted in this study. Spores of each strain (WT, Δlsr2, ΔlsrL, and Δlsr2ΔlsrL) were inoculated in 20 mL of MYM liquid medium and grown overnight with shaking at 30°C. Subsequently, each strain was subcultured into six independent flasks containing 100 mL of liquid MYM to a final OD600 of 0.1 and grown with shaking at 30°C. After 16 h, three 15 mL aliquots were removed from each culture, centrifuged at 7,500 rpm at 4°C for 5 minutes, and the supernatant discarded. . One of the six replicates served as the test sample for determining optimal DNase treatment conditions for the IPOD-HR and RNApol ChIP-seq experiments. For the remaining five replicates, the three replicates that yielded a complete set of the highest quality DNA for IPOD-HR and RNApol ChIP-seq were sent for next-generation sequencing (described below). This approach ensured that data was collected from the same replicates across each experiment.

extract_protocol:
Lysis of S. venezuelae cell pellets: Each of the washed cell pellets from above were resuspended in 1.5 mL lysis buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 14 mg/ml lysozyme, 0.8% Triton X-100, 1× protease inhibitor) and incubated at 37°C for 30 min. The samples were incubated on ice for 2 min, then sonicated for six cycles of 15 s continuous sonication followed by 45 s on ice (output 40%, 4). Cell debris was removed by centrifugation for 20 min at 13,000 rpm at 4°C and the supernatant was transferred to a 15 mL Falcon tube (~1.8 mL).  Determination of optimal DNase treatment conditions: One of the six replicates was used to determine the appropriate conditions for DNase treatment that would yield DNA fragments between 100-200 bp, as we found that required treatment was different for each sample. To determine the appropriate time for DNase treatment, 200 µL of 10× Turbo DNase Buffer, 10 µL Turbo DNase, and RNase A to a final concentration of 15 µg/mL were added to this sample, and incubated for 90 min at 37°C. Every 10 min during the 90-min time course, a 50 µL aliquot was collected from each sample, mixed with 10 µL of 0.5 M EDTA (pH 8), and incubated on ice to inhibit further DNase digestion. Once all aliquots had been collected, they were subjected to phenol-chloroform extraction, and 5-10 µL of the upper phase was run on a 2% agarose gel. The time that yielded the most DNA between 100-200 bp was used to digest the remaining five replicates.  DNase treatment: The remaining five replicates were DNase-treated using the experimentally determined optimal conditions. After DNase digestion, 500 µL of 0.5 M EDTA (pH 8.0) was added to quench the reaction. The samples were clarified by centrifuging at 7,500 rpm for 10 min at 4°C. A 50 µL aliquot (IPOD input DNA) was removed and diluted 1:9 in elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS) and kept on ice until the reverse crosslinking step. A 100 µL aliquot of the clarified lysate was phenol-chloroform extracted and 5 µL of the upper (DNA) phase was run on a 2% agarose gel to confirm that the DNase treatment was successful and had yielded DNA with a maxima centered between 100-200 bp.  RNA polymerase chromatin immunoprecipitation: Protein A-Sepharose beads were prepared in 1.5 mL tubes by resuspending 125 mg of the beads in 1.2 mL of Buffer A (0.02 M NaH2PO4, 150 mM NaCl, pH 8.0) and incubating at room temperature for 30 min. The beads were then aliquoted into separate 1.5 mL tubes for each sample (100 µL slurry per sample). The beads were equilibrated by removing the storage buffer and adding 1 mL of IP buffer with BSA (100 mM Tris pH 8.0, 300 mM NaCl, 2% Triton X-100, 0.1 mg/mL Bovine Serum Albumin). Beads were centrifuged at 3,000 rpm for 1 min at 4°C and allowed to settle on ice for 2 min. This wash step was repeated a second time, and the beads were resuspended in 100 µL IP buffer with BSA. To pre-clear the lysate, the remaining clarified lysate from after DNase treatment (~1 mL) was added to the equilibrated beads and incubated with gentle shaking at 4°C for 2 h. The beads were pelleted as above, the supernatant (pre-cleared lysate) was transferred to a clean tube, and 10 µL of anti-RNA polymerase antibody (developed in mouse) was added to each sample. The samples were incubated overnight with gentle shaking at 4°C. After removing the lysate, the beads were washed three times with 1 mL of Buffer A and stored at 4°C. The next day, the beads were equilibrated as before in IP buffer with BSA. The antibody-lysate mixture was added to the beads and incubated with gentle shaking at 4°C for 4 h. The beads were centrifuged as above and most of the supernatant discarded by removing with a pipette. The beads were washed at room temperature with 1 mL of each of the following solutions in order: ·       Wash buffer A (100 mM Tris, pH 8.0; 250 mM LiCl; 2% Triton X-100; 1 mM EDTA) ·       Wash buffer B (100 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 0.1% sodium deoxycholate; 1 mM EDTA) ·       Wash buffer C (10 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 1 mM EDTA) ·       IP buffer with EDTA (100 mM Tris, pH 8.0; 300 mM NaCl; 2% Triton X-100; 1 mM EDTA) ·       TE buffer (10 mM Tris, pH 8.0; 1 mM EDTA) After washing, the beads were resuspended in 500 µL elution buffer and protein-DNA crosslinking was reversed by incubating the samples at 65°C overnight. Samples were treated with RNase A and proteinase K, and the DNA precipitated.
All purified DNA samples were run on an Agilent TapeStation to assess DNA quality prior to library preparation. Libraries were prepared for Illumina sequencing using the NEBNext Ultra II DNA kit (New England Biolabs). The samples were pooled into libraries and sequenced on an Illumina NextSeq 2000, in a P3, 2x50bp configuration at the McMaster Genomics Facility.

treatment_protocol: To the remaining 50 mL of culture, rifampicin was added to a final concentration of 500 mg/mL and the cultures were incubated with shaking at room temperature for 10 min (rifampicin was used to trap RNA polymerase at the promoter and prevent further transcription initiation). Formaldehyde was then added to a final concentration of 1% (v/v) to induce protein and DNA crosslinking, and the cultures were incubated for an additional 30 min at room temperature. Next, glycine was added to a final concentration of 125 mM to quench the crosslinking, after which the cultures were incubated for another 5 min. The cultures were then centrifuged in 50 mL Falcon tubes at 7,500 rpm at 4°C for 5 min, after which the supernatant was discarded. The resulting cell pellets were washed three times with phosphate-buffered saline (PBS), by resuspending the pellets in 20-40 mL cold PBS and centrifuging as above.

value: S. venezuelae NRRL B-65442

tag: developmental stage

value: Pre-sporulation phase

tag: media

value: MYM liquid media

value: rifampicin

tag: chip antibody


title: 23047FL-37-01-10, snRNA-seq

description:
Library name: 23047FL-37-01-10
10x Genomics

value: brain

value: Sprague Dawley


title: Subject3_exp2_vehicle

description:
Library name: Subject3_exp2_vehicle
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt


title: 23047FL-37-01-11, snRNA-seq

description:
Library name: 23047FL-37-01-11
10x Genomics

value: Wildtype


title: Δlsr2ΔlsrL mutant cells, replicate 3 (ChIP)

description:
Library name: Δlsr2ΔlsrL rep 3, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: anti-RNA polymerase antibody


title: 23047FL-37-01-09, snRNA-seq

description:
Library name: 23047FL-37-01-09
10x Genomics


title: Subject3_exp1_vehicle

description:
Library name: Subject3_exp1_vehicle
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt


title: Δlsr2ΔlsrL mutant cells, replicate 2 input

description:
Library name: Δlsr2ΔlsrL rep 2, input
Mean enrichment scores across replicates included in *_mean.bedgraph files


title: PETER001_HEPG2_24H_X1_B46:G02

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.

value: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: Subject3_exp2_mirdametinib

description:
Library name: Subject3_exp2_mirdametinib
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt

value: lesion

value: mirdametinib


title: Δlsr2ΔlsrL mutant cells, replicate 2 (ChIP)

description:
Library name: Δlsr2ΔlsrL rep 2, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files


title: PETER001_HEPG2_24H_X1_B46:G04


title: Δlsr2ΔlsrL mutant cells, replicate 1 (ChIP)

description:
Library name: Δlsr2ΔlsrL rep 1, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files


title: 23047FL-37-01-08, snRNA-seq

description:
Library name: 23047FL-37-01-08
10x Genomics


title: Subject3_exp1_selumetinib

description:
Library name: Subject3_exp1_selumetinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt

value: primary cell

value: selumetinib


title: Δlsr2ΔlsrL mutant cells, replicate 1 input

description:
Library name: Δlsr2ΔlsrL rep 1, input
Mean enrichment scores across replicates included in *_mean.bedgraph files


title: PETER001_HEPG2_24H_X1_B46:F21

description: L1000 inferred profile; pert_id: Wortmannin

source_name: HEPG2 treated with Wortmannin 5 uM for 24.0 h

value: Wortmannin 5 uM


title: PETER001_HEPG2_24H_X1_B46:G13

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate

value: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM


title: Subject2_exp2_mirdametinib

description:
Library name: Subject2_exp2_mirdametinib
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt


title: PETER001_HEPG2_24H_X1_B46:G01

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate


title: 23047FL-37-01-07, snRNA-seq

description:
Library name: 23047FL-37-01-07
10x Genomics

value: IVH


title: 23047FL-37-01-06, snRNA-seq

description:
Library name: 23047FL-37-01-06
10x Genomics


title: ΔlsrL mutant cells, replicate 2 input

description:
Library name: ΔlsrL rep 2, input
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: dlsrL


title: Subject3_exp1_capmatinib

description:
Library name: Subject3_exp1_capmatinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt

value: capmatinib


title: ΔlsrL mutant cells, replicate 2 (ChIP)

description:
Library name: ΔlsrL rep 2, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: S. venezuelae NRRL B-65442

value: Pre-sporulation phase


title: Subject2_exp1_selumetinib

description:
Library name: Subject2_exp1_selumetinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt


title: 23047FL-37-01-05, snRNA-seq

description:
Library name: 23047FL-37-01-05
10x Genomics

value: Control


title: PETER001_HEPG2_24H_X1_B46:F18

description: L1000 inferred profile; pert_id: Bictegravir

source_name: HEPG2 treated with Bictegravir 0.5 uM for 24.0 h

value: Bictegravir 0.5 uM


title: Subject2_exp1_capmatinib

description:
Library name: Subject2_exp1_capmatinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt


title: 23047FL-37-01-04, snRNA-seq

description:
Library name: 23047FL-37-01-04
10x Genomics

value: brain

value: Sprague Dawley


title: ΔlsrL mutant cells, replicate 1 input

description:
Library name: ΔlsrL rep 1, input
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: MYM liquid media

value: rifampicin


title: PETER001_HEPG2_24H_X1_B46:F17


title: 23047FL-37-01-03, snRNA-seq

description:
Library name: 23047FL-37-01-03
10x Genomics

value: Wildtype


title: ΔlsrL mutant cells, replicate 1 (ChIP)

description:
Library name: ΔlsrL rep 1, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: anti-RNA polymerase antibody


title: Subject2_exp1_vehicle

description:
Library name: Subject2_exp1_vehicle
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt

value: lesion

value: primary cell

value: vehicle


title: PETER001_HEPG2_24H_X1_B46:F19

description: L1000 inferred profile; pert_id: Wortmannin

value: Wortmannin 5 uM


title: Subject1_exp2_mirdametinib

description:
Library name: Subject1_exp2_mirdametinib
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt

value: mirdametinib


title: Δlsr2 mutant cells, replicate 3 input

description:
Library name: Δlsr2 rep 3, input
Mean enrichment scores across replicates included in *_mean.bedgraph files


title: PETER001_HEPG2_24H_X1_B46:F20


title: PETER001_HEPG2_24H_X1_B46:F16


title: Δlsr2 mutant cells, replicate 3 (ChIP)

description:
Library name: Δlsr2 rep 3, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files


title: Subject1_exp1_capmatinib

description:
Library name: Subject1_exp1_capmatinib
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt


title: PETER001_HEPG2_24H_X1_B46:F15

description: L1000 inferred profile; pert_id: Elvitegravir

source_name: HEPG2 treated with Elvitegravir 0.1 uM for 24.0 h

value: Elvitegravir 0.1 uM


title: 23047FL-37-01-02, snRNA-seq

description:
Library name: 23047FL-37-01-02
10x Genomics

value: IVH


title: PETER001_HEPG2_24H_X1_B46:F14


title: Subject1_exp2_vehicle

description:
Library name: Subject1_exp2_vehicle
OFD_vehicle_mirdametinib_DESeq2_normalization.txt
OFD_vehicle_mirdametinib_FPKM_normalization.txt


title: 23047FL-37-01-01, snRNA-seq

description:
Library name: 23047FL-37-01-01
10x Genomics


title: PETER001_HEPG2_24H_X1_B46:F13


title: Δlsr2 mutant cells, replicate 2 (ChIP)

description:
Library name: Δlsr2 rep 2, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: S. venezuelae NRRL B-65442


title: Subject1_exp1_vehicle

description:
Library name: Subject1_exp1_vehicle
OFD_vehicle_capmatinib_selumetinib_DESeq2_normalization.txt
OFD_vehicle_capmatinib_selumetinib_FPKM_normalization.txt


title: Δlsr2 mutant cells, replicate 2 input

description:
Library name: Δlsr2 rep 2, input
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: Pre-sporulation phase


title: 23047FL-35-06-01, snRNA-seq

description:
Library name: 23047FL-35-06-01
10x Genomics

value: Control


title: PETER001_HEPG2_24H_X1_B46:F12

description: L1000 inferred profile; pert_id: Elvitegravir|Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h


title: HeLa, 1 ng/ml TcdB2 24 h, antibody CTCF (CUT&RUN), rep 2

city: Oklahoma City

first: Jason

last: Larabee

state: OK

address: 940 Stanton L. Young Blvd, BMSB 1035

department: Microbiology and Immunology

institute: The University of Oklahoma Health Science Center

description: Library name: T5

data_processing:
The FASTQ files were trimmed with Trim Galore and aligned to the human hg38 canonical genome using bowtie2 (v2.5.3) with the very sensitive end-to-end (--very-sensitive) parameter.  Resulting BAM files were converted to bigWig files and normalized to counts per million (CPM) using bamCoverage.
Assembly: Human GRCh38 genome
Supplementary files format and content: BigWig files
Library strategy: CUT&Run

source_name: HeLa

growth_protocol: HeLa cell cultures

extract_protocol:
DNA sites binding for CTCF were isolated using CUT&RUN reagents obtained from Cell Signaling Technology (product # 86652).  Antibodies used for this assay include a rabbit monoclonal antibody against CTCF (Cell Signaling Technology; product # 3418); a rabbit monoclonal antibody against H3K4me3 (Cell Signaling Technology; product # 9751); and a rabbit monoclonal isotype control (Cell Signaling Technology; product # 66362).
Sequencing libraries were constructed using XGen DNA Library Prep EZ Kit (IDT), and each library was indexed in order to multiplex for sequencing.

treatment_protocol: Treated with 1 ng/ml TcdB2 for 24 h.

value: HeLa


title: Δlsr2 mutant cells, replicate 1 input

description:
Library name: Δlsr2 rep 1, input
Mean enrichment scores across replicates included in *_mean.bedgraph files


title: 23047FL-35-05-01, snRNA-seq

description:
Library name: 23047FL-35-05-01
10x Genomics

value: brain


title: PETER001_HEPG2_24H_X1_B46:F11

value: Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: ALL, no protein, replicate 1

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

description:
Library name: ALL_NP_rep1
These samples were sequenced twice (once on NovaSeq X Plus and again on NovaSeq 6000 as read depth was too low). The data files include both sequencing runs merged

library_source: other

data_processing:
Sequence reads were fist trimmed to 40 nucleotides in length (total fragment length)
Cutadapt was used to ensure the reverse primer occured at the 3' end (this is to filter out any sequences where the sequencing adapter bound in the randomised region rather than at the 3' end as intended)
Sequence reads were filtered for a phred score of 30 or above with cutadapt
Sequence reads were trimmed to 14 nucleotides in length (possible randomised region) with cutadapt
cutadapt was used to remove contaminating sequences from FLANK and ALL libraries (they contained high counts of sequences matching the CORE library so these were all removed to prevent skewing of the data).
DESeq2 v1.50.0 was used to determine enrichment or depletion of DNA sequences in the mutant library upon protein binding. Prior to DESeq2 analysis, samples were filtered to remove sequences with less than five occurrences in the unbound library to avoid inaccurate log fold change (LFC) calculations due to low sequence counts.
Supplementary files format and content: *_counts.txt fragment counts (tab delimited text format)
Supplementary files format and content: *_deseq2.csv log fold change statistics between the bound library and the unbound source library for each DNA fragment

molecule: other

organism: synthetic construct

source_name: Artificial

extract_protocol:
DNA was purified from the electrophoresis gel using electroelution and isopropanol purification
Approximately 1 ng of extracted DNA was used in a low cycle number (12-14) PCR reaction (NEBNext Hi Fidelity 2X Mastermix) with Illumina sequencing adapters. Size selection was then performed using 2.5X AMPure XP beads (Beckman Coulter). The quality of samples was measured using the Agilent BioAnalyzer and concentration was measured using the HS dsDNA Qubit assay (Thermo Fisher Scientific).

treatment_protocol: EMSA-seq was performed either without NKX2.1 protein (control for sequence bias), or with DNA:protein ratios of 1:0.1 or 1:0.2

value: Binding reactions were performed in a tube - no cells used


title: HeLa, 1 ng/ml TcdB2 24 h, antibody CTCF (CUT&RUN), rep 1

description: Library name: T4


title: Wildtype cells, replicate 3 input

description:
Library name: WT rep 3, input
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: WT

value: MYM liquid media

value: rifampicin


title: PETER001_HEPG2_24H_X1_B46:F10

city: New York

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place, Box 1603

institute: Icahn School of Medicine at Mount Sinai


title: Δlsr2 mutant cells, replicate 1 (ChIP)

description:
Library name: Δlsr2 rep 1, ChIP
Mean enrichment scores across replicates included in *_mean.bedgraph files

value: anti-RNA polymerase antibody


title: ALL, no protein, replicate 2

description:
Library name: ALL_NP_rep2
These samples were sequenced twice (once on NovaSeq X Plus and again on NovaSeq 6000 as read depth was too low). The data files include both sequencing runs merged


title: HeLa, 1 ng/ml TcdB2 24 h, antibody H3K4me3 (CUT&RUN), rep 2

description: Library name: T3


title: HeLa, 1 ng/ml TcdB2 24 h, antibody H3K4me3 (CUT&RUN), rep 1

description: Library name: T2


title: PETER001_HEPG2_24H_X1_B46:F09

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir

source_name: HEPG2 treated with Darunavir|Ritonavir 0.1|0.5 uM for 24.0 h

value: Darunavir|Ritonavir 0.1|0.5 uM


title: PETER001_HEPG2_24H_X1_B46:F08


title: HeLa, untreated, antibody CTCF (CUT&RUN), rep 2

description: Library name: C5