title: PETER001_HK2_24H_X1_B46:B13


title: HEK293 cells treated with 12micromolar of  ncpCUL1-ASO-R2

status: Public on Feb 11 2026

type: SRA

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 John Sharp Pkwy MREB 2

country: USA

institute: Texas A&M University

description: Library name: H_CU_M2

library_source: transcriptomic

data_processing:
Reads were aligned to the hg38 genome using STAR
Gene-level quantification was performed using RefSeq annotations
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: K562 cells were treted  in 1% FBS with IMDM contaning media, KMS34 cells were treated in 7.5% FBS  in RPMI, 10% FBS in DMEM High Glucose.

extract_protocol:
RNA was extracted using Trizol method
Non-Directional, Poly-A Selection

treatment_protocol: Cells were treated with scaramble(12micromolar) or ncpCUL1-ASO (12micromolar) for 44hr.

tag: cell line

tag: cell type

value: human embryonic kidney

tag: genotype

value: Wild Type

tag: treatment

value: 12uM of ncpCUL1-ASO for 44h


title: PETER001_HK2_24H_X1_B46:B12

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: Cobicistat|Emtricitabine

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

source_name: HK2 treated with Cobicistat|Emtricitabine 0.1|0.1 uM for 24.0 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: Cobicistat|Emtricitabine 0.1|0.1 uM

tag: duration

tag: plate

tag: well


title: HEK 293 cells treated with 12micromolar of scarmble-ASO-R3

description: Library name: H_S_C3

value: 12uM of Scramble-ASO for44h


title: HEK293 cells treated with 12micromolar of  ncpCUL1-ASO-R1

description: Library name: H_CU_M1


title: HEK 293 cells treated with 12micromolar of scarmble-ASO-R2

description: Library name: H_S_C2


title: F12383447

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 28

tag: tissue

value: EDTA Plasma

tag: delivery

value: SC

tag: treatment group (dose)

value: Mepolizumab (24 mg)

tag: bmi (kg/m2)

tag: age

tag: Sex

value: M

tag: race

value: White


title: F12383427

scan_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/).

value: Day 21


title: F12296550

label_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/).

value: Day 7


title: F12296829

value: Day 14


title: HEK 293 cells treated with 12micromolar of scarmble-ASO-R1

description: Library name: H_S_C1


title: PETER001_HK2_24H_X1_B46:B11


title: KMS34 cells treated with 12micromolar of  ncpCUL1-ASO-R3

description: Library name: K34_CU_M3

value: Multiple myeloma


title: KMS34 cells treated with 12micromolar of  ncpCUL1-ASO-R2

description: Library name: K34_CU_M2


title: PETER001_HK2_24H_X1_B46:B10


title: KMS34 cells treated with 12micromolar of  ncpCUL1-ASO-R1

description: Library name: K34_CU_M1


title: F12296422

value: Day 3


title: KMS34 cells treated with 12micromolar of scarmble-ASO-R3

description: Library name: K34_S_C3


title: F12296312

value: Day 2


title: KMS34 cells treated with 12micromolar of scarmble-ASO-R2

description: Library name: K34_S_C2


title: KMS34 cells treated with 12micromolar of scarmble-ASO-R1

description: Library name: K34_S_C1


title: PETER001_HK2_24H_X1_B46:B09

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

source_name: HK2 treated with Cobicistat|Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.1|0.5 uM for 24.0 h


title: K562 cells treated with 12micromolar of  ncpCUL1-ASO-R3

description: Library name: K5_CU_M3

value: lymphoblast cells dervied from chronic myelogenous leukemia patient


title: PETER001_HK2_24H_X1_B46:B08

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


title: F12383276

value: Day 123


title: PETER001_HK2_24H_X1_B46:B07


title: K562 cells treated with 12micromolar of  ncpCUL1-ASO-R2

description: Library name: K5_CU_M2

value: Wild Type

value: 12uM of ncpCUL1-ASO for 44h


title: PETER001_HK2_24H_X1_B46:B06

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

source_name: HK2 treated with Darunavir|Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.1|0.5|0.1 uM for 24.0 h


title: K562 cells treated with 12micromolar of scarmble-ASO-R3

description: Library name: K5_S_C3

value: 12uM of Scramble-ASO for44h


title: K562 cells treated with 12micromolar of scarmble-ASO-R2

description: Library name: K5_S_C2


title: K562 cells treated with 12micromolar of  ncpCUL1-ASO-R1

description: Library name: K5_CU_M1


title: F12383236

value: Day 63

value: EDTA Plasma


title: PETER001_HK2_24H_X1_B46:B04

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


title: PETER001_HK2_24H_X1_B46:B05


title: H1299_41nc_3

city: Ann Arbor

first: Alyssa

last: Winkler

state: MI

address: 1150 W Medical Ctr Dr

department: Pathology

institute: University of Michigan Medical School

description: Library name: Sample 9

data_processing:
fastq files trimmed for adapter content and poly A/G/T tails using trimGalore
reads were aligned to Hg38 genome using bowtie2 and gene expression using RSEM
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Differentially expressed genes (1.5-fold and <5% false discovery rate) were identified by the edgeR R package
log2CPM exported from edgeR package for pathway analysis using cpm() function
Supplementary files format and content: tab-delimited text files include counts per million (CPM) values for each Sample

source_name: NCI-H1299 cells

growth_protocol: 1x104 NCI-H1299 cells/well were plated in T25 tissue culture-treated flasks and placed in a 5% CO2 37 °C incubator for 7 days with media change and expansion to 10mL at day 3

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
DNA libraries were prepared using the IDT xGen Broad-Range RNA Library Prep Kit according to the manufacturer’s instructions using IDT UDI indices.

treatment_protocol: Treated with either DMSO, 1.5µM DLG-41, 1.5µM DLG-41nc (0.25% DMSO final)

value: wild-type

value: 1.5µM DLG-41nc, 7 days


title: F12383251

value: Day 93

value: SC

value: M

value: White


title: H1299_41nc_2

description: Library name: Sample 8


title: H1299_41nc_1

description: Library name: Sample 7


title: H1299_41_3

description: Library name: Sample 6

value: 1.5µM DLG-41, 7 days


title: F12383044

value: Day 28


title: F12295873

value: Day 1

value: Mepolizumab (24 mg)


title: F12383206

value: Day 49


title: PETER001_HK2_24H_X1_B46:A21

description: L1000 inferred profile; pert_id: Ritonavir

source_name: HK2 treated with Ritonavir 0.5 uM for 24.0 h

value: Ritonavir 0.5 uM


title: H1299_41_2

description: Library name: Sample 5


title: H1299_41_1

description: Library name: Sample 4


title: H1299_DMSO_rep3

description: Library name: Sample 3

value: untreated


title: PETER001_HK2_24H_X1_B46:A20


title: F12383024

value: Day 21


title: H1299_DMSO_rep2

description: Library name: Sample 2


title: F12295543

value: Day 14


title: PETER001_HK2_24H_X1_B46:A19


title: PETER001_HK2_24H_X1_B46:A18

description: L1000 inferred profile; pert_id: Abacavir

source_name: HK2 treated with Abacavir 0.5 uM for 24.0 h

value: Abacavir 0.5 uM


title: Stage 4 Non-Carrier 2

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

description: Library name: X35

data_processing:
CLC Genomic Workbench version 24.0
Assembly: hg38 (Refseq)
Supplementary files format and content: Geneexpression Track for each sample als xlsx file

source_name: Differentiating cells

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini
Performed by QIAGEN

value: Differentiating cells

value: induced pluripotent stem cells

value: non carrier

value: Differentiation towards pancreatic endocrine progenitors


title: Stage 4 Non-Carrier 3

description: Library name: X36


title: F12295264

value: Day 7

value: EDTA Plasma

value: SC


title: H1299_DMSO_rep1

description: Library name: Sample 1

value: wild-type


title: PETER001_HK2_24H_X1_B46:A17


title: Stage 4 Non-Carrier 1

description: Library name: X34


title: K562 cells treated with 12micromolar of scarmble-ASO-R1

description: Library name: K5_S_C1

value: lymphoblast cells dervied from chronic myelogenous leukemia patient

value: Wild Type

value: 12uM of Scramble-ASO for44h


title: F12295026

value: Day 2

value: M

value: White


title: Stage 4 HNF1A-MODY 2

description: Library name: X38


title: F12295136

value: Day 3


title: PETER001_HK2_24H_X1_B46:A16


title: sc-RNAseq-CAR-T_TAIII

city: Hefei

first: Mingqi

last: Hou

country: China

institute: USTC

description:
Library name: Sample17
NRCA_TALL

library_source: transcriptomic single cell

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: peripheral blood

extract_protocol:
Bulk-seq: RNA was extracted by trizol method (Invitrogen, USA), RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries. sc-RNA-seq: The cell suspension was loaded into Chromium microfluidic chips with 3’ v2 chemistry and barcoded with a 10× Chromium Controller. RNA from the barcoded cells was subsequently reverse-transcribed and constructed sequencing libraries.
Bulk-seq:Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. sc-RNA-seq:Sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions.

value: peripheral blood

value: T cell

value: TAIII


title: CAR-T_TAIII_3

description:
Library name: Sample15
TAIII_3


title: Stage 4 HNF1A-MODY 1

description: Library name: X37

value: Differentiating cells

value: induced pluripotent stem cells


title: Stage 4 HNF1A-MODY 3

description: Library name: X39

value: Differentiation towards pancreatic endocrine progenitors


title: F12294587

value: Day 1


title: F12386097

value: Day 123

value: EDTA Plasma

value: Mepolizumab (24 mg)

value: F


title: CAR-T_TAIII_1

description:
Library name: Sample13
TAIII_1


title: PETER001_HK2_24H_X1_B46:A15

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

source_name: HK2 treated with Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: sc-RNAseq-CAR-T_NECA

description:
Library name: Sample16
NECA

value: NECA


title: CAR-T_TAIII_2

description:
Library name: Sample14
TAIII_2


title: PETER001_HK2_24H_X1_B46:A12

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

source_name: HK2 treated with Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM for 24.0 h


title: CAR-T_NECA_2

description:
Library name: Sample11
NECA_2


title: CAR-T_NECA_1

description:
Library name: Sample10
NECA_1


title: CAR-T_DMSO_3

description:
Library name: Sample9
DMSO_3

value: DMSO


title: PETER001_HK2_24H_X1_B46:A14

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


title: F12386027

value: Day 49

value: SC


title: F12386072

value: Day 93

value: White


title: Human CTE Brain (Superior Frontal Cortex) patient6 replicate 2

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

description:
Library name: CTE_brain_6912_REP2
Column name in raw featureCounts_count_matrix.txt: CTE_brain_6912_REP2

data_processing:
The reads were aligned with STAR (version 2.5.2b), and genes annotated in Gencode v40 were quantified with featureCounts from Subread (v2.0.3).
Assembly: hg38
Supplementary files format and content: Tab-separated file with raw read counts per gene

source_name: Brain

extract_protocol:
Total RNA was isolated using the Zymo Miniprep Plus Kit (Cat# R1057). A total of 250 ng RNA was used for library preparation.
RNA-seq libraries were prepared using the NEB rRNA Depletion Kit and the NEBNext Ultra II Library Prep Kit according to the manufacturer’s instructions. Samples were sequenced on an Illumina NovaSeq 6000 platform with 2 × 100 bp paired-end reads.

value: Brain


title: PETER001_HK2_24H_X1_B46:A13


title: CAR-T_NECA_3

description:
Library name: Sample12
NECA_3

value: peripheral blood

value: T cell


title: PETER001_HK2_24H_X1_B46:A11

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


title: PETER001_HK2_24H_X1_B46:A10


title: F12386057

value: Day 63


title: PETER001_HK2_24H_X1_B46:A09

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

source_name: HK2 treated with Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM for 24.0 h


title: Human CTE Brain (Superior Frontal Cortex) patient5 replicate 2

description:
Library name: CTE_brain_7126_REP2
Column name in raw featureCounts_count_matrix.txt: CTE_brain_7126_REP2


title: Human CTE Brain (Superior Frontal Cortex) patient6 replicate 1

description:
Library name: CTE_brain_6912_REP1
Column name in raw featureCounts_count_matrix.txt: CTE_brain_6912_REP1


title: F12385865

value: Day 28


title: PETER001_HK2_24H_X1_B46:A08

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


title: F12307117

value: Day 14

value: EDTA Plasma


title: Human CTE Brain (Superior Frontal Cortex) patient5 replicate 1

description:
Library name: CTE_brain_7126_REP1
Column name in raw featureCounts_count_matrix.txt: CTE_brain_7126_REP1


title: CAR-T_DMSO_2

description:
Library name: Sample8
DMSO_2


title: Stage 3 Day 2 Non-Carrier 3

description: Library name: X48

treatment_protocol: For some of the conditions SANT1, which is included in the standart protocol, was not given to the cells on the first day of stage 3, for a duration of 24 hours.

value: Differentiating cells

value: induced pluripotent stem cells

value: non carrier

value: Differentiation towards pancreatic endocrine progenitors


title: PETER001_HK2_24H_X1_B46:A07


title: CAR-T_DMSO_1

description:
Library name: Sample7
DMSO_1

value: DMSO


title: Stage 3 Day 2 Non-Carrier 2

description: Library name: X47


title: F12385845

value: Day 21

value: SC

value: Mepolizumab (24 mg)

value: F


title: Stage 3 Day 2 Non-Carrier 1

description: Library name: X46


title: PETER001_HK2_24H_X1_B46:A06

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

source_name: HK2 treated with Abacavir|Dolutegravir|Emtricitabine 0.5|0.1|0.1 uM for 24.0 h


title: F12306838

value: Day 7

value: White


title: F12306600

value: Day 2


title: Stage 3 Day 1 Non-Carrier minus SANT1 3

description: Library name: X45

value: Differentiation towards pancreatic endocrine progenitors Minus SANT3


title: Human CTE Brain (Superior Frontal Cortex) patient3 replicate 2

description:
Library name: CTE_brain_6489_REP2
Column name in raw featureCounts_count_matrix.txt: CTE_brain_6489_REP2

value: Brain


title: F12306161

value: Day 1


title: Human CTE Brain (Superior Frontal Cortex) patient4 replicate 2

description:
Library name: CTE_brain_7932_REP2
Column name in raw featureCounts_count_matrix.txt: CTE_brain_7932_REP2


title: PETER001_HK2_24H_X1_B46:A04


title: Stage 3 Day 1 Non-Carrier minus SANT1 2

description: Library name: X44

value: Differentiation towards pancreatic endocrine progenitors Minus SANT2


title: Human CTE Brain (Superior Frontal Cortex) patient4 replicate 1

description:
Library name: CTE_brain_7932_REP1
Column name in raw featureCounts_count_matrix.txt: CTE_brain_7932_REP1


title: F12382873

value: Day 123

value: EDTA Plasma

value: IV

value: Reslizumab (0.8 mg/kg)

value: M


title: PETER001_HK2_24H_X1_B46:A05


title: PETER001_HEPG2_6H_X1_B46:H21

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: F12306710

value: Day 3


title: Human CTE Brain (Superior Frontal Cortex) patient3 replicate 1

description:
Library name: CTE_brain_6489_REP1
Column name in raw featureCounts_count_matrix.txt: CTE_brain_6489_REP1


title: Human CTE Brain (Superior Frontal Cortex) patient2 replicate 1

description:
Library name: CTE_brain_6666_REP1
Column name in raw featureCounts_count_matrix.txt: CTE_brain_6666_REP1


title: Stage 2 Day 2 Non-Carrier 2

description: Library name: X32

value: Differentiating cells

value: induced pluripotent stem cells

value: non carrier

value: Differentiation towards pancreatic endocrine progenitors


title: F12382848

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

value: Day 93

value: White


title: Human CTE Brain (Superior Frontal Cortex) patient1 replicate 2

description:
Library name: CTE_brain_7610_REP2
Column name in raw featureCounts_count_matrix.txt: CTE_brain_7610_REP2


title: Stage 3 Day 1 Non-Carrier minus SANT1 1

description: Library name: X43

value: Differentiation towards pancreatic endocrine progenitors Minus SANT1


title: PETER001_HEPG2_6H_X1_B46:H18

description: L1000 inferred profile; pert_id: Darunavir

source_name: HEPG2 treated with Darunavir 0.1 uM for 6.0 h

value: Darunavir 0.1 uM


title: F12382833

value: Day 63


title: Human CTE Brain (Superior Frontal Cortex) patient2 replicate 2

description:
Library name: CTE_brain_6666_REP2
Column name in raw featureCounts_count_matrix.txt: CTE_brain_6666_REP2

value: Brain


title: Stage 2 Day 2 Non-Carrier 3

description: Library name: X33


title: Human CTE Brain (Superior Frontal Cortex) patient1 replicate 1

description:
Library name: CTE_brain_7610_REP1
Column name in raw featureCounts_count_matrix.txt: CTE_brain_7610_REP1


title: Stage 3 Day 2 HNF1A-MODY 3

description: Library name: X30


title: PETER001_HEPG2_6H_X1_B46:H20

description: L1000 inferred profile; pert_id: DMSO


title: F12382641

value: Day 28


title: PETER001_HEPG2_6H_X1_B46:H17


title: PETER001_HEPG2_6H_X1_B46:H19

description: L1000 inferred profile; pert_id: DMSO


title: Stage 3 Day 2 HNF1A-MODY 2

description: Library name: X29


title: PETER001_HEPG2_6H_X1_B46:H16


title: Stage 2 Day 2 Non-Carrier 1

description: Library name: X31


title: Human Control Brain (Superior Frontal Cortex) donor6 replicate 2

description:
Library name: Control_brain_6904_REP2
Column name in raw featureCounts_count_matrix.txt: Control_brain_6904_REP2


title: Human Control Brain (Superior Frontal Cortex) donor6 replicate 1

description:
Library name: Control_brain_6904_REP1
Column name in raw featureCounts_count_matrix.txt: Control_brain_6904_REP1


title: F12382803

value: Day 49

value: EDTA Plasma


title: F12382621

value: Day 21

value: IV

value: Reslizumab (0.8 mg/kg)


title: Human Control Brain (Superior Frontal Cortex) donor5 replicate 2

description:
Library name: Control_brain_6047_REP2
Column name in raw featureCounts_count_matrix.txt: Control_brain_6047_REP2


title: PETER001_HEPG2_6H_X1_B46:H13

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir

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

value: Emtricitabine|Ritonavir 0.1|0.5 uM


title: Stage 3 Day 1 HNF1A-MODY minus SANT1 3

description: Library name: X27

value: Differentiating cells

value: Differentiation towards pancreatic endocrine progenitors Minus SANT3


title: Human Control Brain (Superior Frontal Cortex) donor5 replicate 1

description:
Library name: Control_brain_6047_REP1
Column name in raw featureCounts_count_matrix.txt: Control_brain_6047_REP1


title: F12293978

value: Day 7

value: M


title: F12294257

value: Day 14


title: Stage 3 Day 2 HNF1A-MODY 1

description: Library name: X28

value: induced pluripotent stem cells

value: Differentiation towards pancreatic endocrine progenitors


title: PETER001_HEPG2_6H_X1_B46:H12

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 6.0 h


title: Stage 3 Day 1 HNF1A-MODY minus SANT1 1

description: Library name: X25

value: Differentiation towards pancreatic endocrine progenitors Minus SANT1


title: F12293740

source_name: EDTA Plasma

value: Day 2

value: White


title: PETER001_HEPG2_6H_X1_B46:H14


title: F12293301

value: Day 1


title: Human Control Brain (Superior Frontal Cortex) donor4 replicate 1

description:
Library name: Control_brain_9316_REP1
Column name in raw featureCounts_count_matrix.txt: Control_brain_9316_REP1

value: Brain


title: Stage 3 Day 1 HNF1A-MODY minus SANT1 2

description: Library name: X26

value: Differentiation towards pancreatic endocrine progenitors Minus SANT2


title: Stage 2 Day 2 HNF1A-MODY 2

description: Library name: X20


title: Human Control Brain (Superior Frontal Cortex) donor3 replicate 2

description:
Library name: Control_brain_9552_REP2
Column name in raw featureCounts_count_matrix.txt: Control_brain_9552_REP2


title: F12293850

value: Day 3

value: EDTA Plasma


title: PETER001_HEPG2_6H_X1_B46:H11

value: Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: Human Control Brain (Superior Frontal Cortex) donor4 replicate 2

description:
Library name: Control_brain_9316_REP2
Column name in raw featureCounts_count_matrix.txt: Control_brain_9316_REP2


title: Stage 2 Day 2 HNF1A-MODY 1

description: Library name: X19


title: Human Control Brain (Superior Frontal Cortex) donor3 replicate 1

description:
Library name: Control_brain_9552_REP1
Column name in raw featureCounts_count_matrix.txt: Control_brain_9552_REP1


title: PETER001_HEPG2_6H_X1_B46:H09

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 6.0 h


title: Stage 2 Day 2 HNF1A-MODY 3

description: Library name: X21


title: F12386500

value: Day 123

value: SC

value: F


title: PETER001_HEPG2_6H_X1_B46:H10


title: PETER001_HEPG2_6H_X1_B46:H08

value: Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: Human Control Brain (Superior Frontal Cortex) donor2 replicate 2

description:
Library name: Control_brain_7160_REP2
Column name in raw featureCounts_count_matrix.txt: Control_brain_7160_REP2


title: F12386460

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

value: Day 63


title: PETER001_HEPG2_6H_X1_B46:H07


title: F12386430

value: Day 49


title: Human Control Brain (Superior Frontal Cortex) donor2 replicate 1

description:
Library name: Control_brain_7160_REP1
Column name in raw featureCounts_count_matrix.txt: Control_brain_7160_REP1


title: Human Control Brain (Superior Frontal Cortex) donor1 replicate 2

description:
Library name: Control_brain_8592_REP2
Column name in raw featureCounts_count_matrix.txt: Control_brain_8593_REP2


title: CORE, 1:0.1, replicate 2

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Library name: CORE_0.1_rep2
CORE_0.1_deseq2.csv

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: F12386268

value: Day 28


title: PETER001_HEPG2_6H_X1_B46:H06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine

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

value: Darunavir|Emtricitabine 0.1|0.1 uM


title: Human Control Brain (Superior Frontal Cortex) donor1 replicate 1

description:
Library name: Control_brain_8592_REP1
Column name in raw featureCounts_count_matrix.txt: Control_brain_8592_REP1


title: CORE, no protein, replicate 2

description: Library name: CORE_NP_rep2


title: PETER001_HEPG2_6H_X1_B46:H05


title: CORE, 1:0.1, replicate 1

description:
Library name: CORE_0.1_rep1
CORE_0.1_deseq2.csv


title: PETER001_HEPG2_6H_X1_B46:H04


title: CORE, no protein, replicate 1

description: Library name: CORE_NP_rep1


title: PETER001_HEPG2_6H_X1_B46:H01

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: K562 + S-Exo

city: Guangzhou

first: Fei

last: Li

state: Guangdong

address: 135 Xingang West Road, Haizhu District

institute: Sun Yat-sen University

description: Library name: K562SE

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: human NCBI genome build 36
Supplementary files format and content: Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

source_name: Peripheral blood

growth_protocol: CML cells were treated with or without Exo and cultured in 10%FBS RPMI medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: CML cells were treated with or without Exo for 48h

value: Peripheral blood

value: Chronic myeloid leukemia cells

value: S-Exo treatment


title: F12309689

value: Day 14

value: White


title: K562 + R-Exo

description: Library name: K562RE

value: R-Exo treatment


title: F12386248

value: Day 21

value: EDTA Plasma


title: PETER001_HEPG2_6H_X1_B46:G21

description: L1000 inferred profile; pert_id: DMSO

value: DMSO 0.5 uM


title: K562 IMR

description: Library name: K562R

value: IM-resistant

value: NC


title: leaf_wild type_3

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No 2

institute: Chinese Academy of Science

description:
Library name: Sample 18
J_3
leaf_3_all.result.txt
leaf_4_all.result.txt
clean data of leaf_wild type_3

data_processing:
Remove adapters and low-quality reads with FASTP (v.0.19.7).
Build an index and align the clean data to the reference genome Wm82.a4.v1 using HISAT2 (v.2.1.0).
FeatureCounts (v.2.0.0) was used to quantify the reads that mapped to the reference genome.
Differentially expressed genes were identified using the R package edgeR (v.3.12).
Assembly: Glycine max Wm82.a4.v1
Supplementary files format and content: txt files, FPKM and fold change

organism: Glycine max

source_name: leaf

growth_protocol: Soybean plants were grown in pots in green house, with a photoperiod of 16 h light/8 h dark. Room temperature is kept at about 30°C at daytime and about 22°C at night.

extract_protocol:
RNA was extracted using TRNzol Universal RNA reagent (Tiangen company).
RNA sequencing was prepared using SMARTER mRNA-seq Library Prep Kit following its protocol.

treatment_protocol: The plants were normally watered everyday.

value: leaf

value: leaf cell

value: WT


title: K562 NC

description: Library name: K562


title: PETER001_HEPG2_6H_X1_B46:G20

description: L1000 inferred profile; pert_id: DMSO


title: leaf_wild type_1

description:
Library name: Sample 16
J_1
leaf_3_all.result.txt
leaf_4_all.result.txt
clean data of leaf_wild type_1


title: leaf_wild type_2

description:
Library name: Sample 17
J_2
leaf_3_all.result.txt
leaf_4_all.result.txt
clean data of leaf_wild type_2


title: F12386475

value: Day 93

value: SC

value: F


title: F12309172

value: Day 2


title: CORE, 1:0.2, replicate 2

description:
Library name: CORE_0.2_rep2
CORE_0.2_deseq2.csv

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


title: HiC of LMNAC KO, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: HIC.KO.2

library_source: genomic

data_processing:
HiC data were preprocessed using HiC-Pro v2.10.0 pipeline with default settings using the human genome at various resolutions.
Assembly: hg19
Supplementary files format and content: Hic-Pro output containing all valid alignment pairs

molecule: genomic DNA

extract_protocol:
5x10^6 WT and KO cells were collected for in-situ Hi-C. Libraries of total ligation products were produced using Ultralow Library Systems V2 (Tecan Genomics, 0344NB-32) as per the manufacturer's protocol
Libraries were sequenced using the Illumina HiSeq 2500 sequencing platform with paired-end 75 bp read length

tag: lmnac genotype

value: KO

tag: replicate


title: F12309282

value: Day 3


title: leaf_overexpression of GmMYB331_4_3

description:
Library name: Sample 15
4_3
leaf_4_all.result.txt
clean data of leaf_over expression of GmMYB331_4_3

tag: cell type

value: transgenic


title: PETER001_HEPG2_6H_X1_B46:G19

description: L1000 inferred profile; pert_id: DMSO

tag: cell line


title: F12308733

value: Day 1

value: White


title: HiC of LMNAC KO, replicate 1

description: Library name: HIC.KO.1


title: PETER001_HEPG2_6H_X1_B46:G17

description: L1000 inferred profile; pert_id: Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Tenofovir Alafenamide Fumarate 0.5 uM for 6.0 h

tag: treatment

value: Tenofovir Alafenamide Fumarate 0.5 uM


title: HiC of LMNAC WT, replicate 2

description: Library name: HIC.WT.2


title: leaf_overexpression of GmMYB331_4_2

description:
Library name: Sample 14
4_2
leaf_4_all.result.txt
clean data of leaf_over expression of GmMYB331_4_2

tag: genotype


title: F12309410

value: Day 7

value: EDTA Plasma


title: F12385694

value: Day 123

value: IV


title: PETER001_HEPG2_6H_X1_B46:G18

tag: duration

tag: plate


title: leaf_overexpression of GmMYB331_4_1

description:
Library name: Sample 13
4_1
leaf_4_all.result.txt
clean data of leaf_over expression of GmMYB331_4_1

value: leaf

value: leaf cell


title: PETER001_HEPG2_6H_X1_B46:G16

tag: well


title: HiC of LMNAC WT, replicate 1

description: Library name: HIC.WT.1

value: WT


title: F12385669-1

tag: participant id

tag: time point (days)

value: Day 93


title: PETER001_HEPG2_6H_X1_B46:G15

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 6.0 h


title: F12385669

tag: tissue

tag: delivery

value: F


title: H3K9me2 CHIP for LMNAC KO, replicate 2

description: Library name: H3K9me2.KO.2

data_processing:
Reads were mapped against the human genome assembly using BWA and MACS2 was used for peak calling using input samples as controls
Assembly: hg19
Supplementary files format and content: MACS2 output .bed files

extract_protocol:
DNA was purified using Wizard SV Gel and PCR Clean-up Kit (Promega, A9285).
Libraries for sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7103) and sequenced on the Illumina HiSeq 2500

tag: chip antibody

value: H3K9me2 Abcam, ab1220

tag: experiment


title: F12385654

value: Day 63

tag: treatment group (dose)

tag: bmi (kg/m2)

tag: age

tag: Sex


title: PETER001_HEPG2_6H_X1_B46:G14

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


title: leaf_overexpression of GmMYB331_3_1

description:
Library name: Sample 10
3_1
leaf_3_all.result.txt
clean data of leaf_over expression of GmMYB331_3_1

tag: cell type


title: H3K9me2 CHIP for LMNAC KO, replicate 1

description: Library name: H3K9me2.KO.1

tag: cell line

tag: lmnac genotype

value: KO


title: leaf_overexpression of GmMYB331_3_2

description:
Library name: Sample 11
3_2
leaf_3_all.result.txt
clean data of leaf_over expression of GmMYB331_3_2

tag: genotype

value: transgenic


title: seed_wild type_3

description:
Library name: Sample 9
J_3
seed_3_all.result.txt
seed_4_all.result.txt
clean data of seed_wild type_3

source_name: seed

value: seed

value: seed cell


title: H3K9me2 CHIP for LMNAC WT, replicate 2

description: Library name: H3K9me2.WT.2


title: F12385462

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

value: Day 28

tag: race

value: White


title: F12385624

value: Day 49

value: EDTA Plasma


title: PETER001_HEPG2_6H_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 6.0 h

tag: treatment

tag: duration

tag: plate


title: PETER001_HEPG2_6H_X1_B46:G13

tag: well


title: seed_wild type_2

description:
Library name: Sample 8
J_2
seed_3_all.result.txt
seed_4_all.result.txt
clean data of seed_wild type_2

tag: tissue


title: PETER001_HEPG2_6H_X1_B46:G11

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


title: H3K9me2 CHIP for LMNAC WT, replicate 1

description: Library name: H3K9me2.WT.1


title: LMNAC KO input for H3K9me2, replicate 2

description: Library name: inpH.KO.2

value: input


title: LMNAC KO input for H3K9me2, replicate 1

description: Library name: inpH.KO.1


title: seed_overexpression of GmMYB331_4_3

description:
Library name: Sample 6
4_3
seed_4_all.result.txt
clean data of seed_over expression of GmMYB331_4_3


title: F12304266

tag: participant id

tag: time point (days)

value: Day 7

tag: delivery

value: IV


title: F12385442

value: Day 21

tag: treatment group (dose)


title: seed_wild type_1

description:
Library name: Sample 7
J_1
seed_3_all.result.txt
seed_4_all.result.txt
clean data of seed_wild type_1

value: WT


title: PETER001_HEPG2_6H_X1_B46:G10


title: F12304545

value: Day 14

tag: bmi (kg/m2)

value: F


title: PETER001_HEPG2_6H_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 6.0 h


title: PETER001_HEPG2_6H_X1_B46:G08

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


title: LMNAC WT input for H3K9me2, replicate 1

description: Library name: inpH.WT.1

tag: chip antibody

tag: experiment


title: F12304138

value: Day 3

tag: age

tag: Sex


title: LMNAC WT input for H3K9me2, replicate 2

description: Library name: inpH.WT.2

tag: cell line

tag: lmnac genotype


title: seed_overexpression of GmMYB331_4_1

description:
Library name: Sample 4
4_1
seed_4_all.result.txt
clean data of seed_over expression of GmMYB331_4_1

tag: cell type

tag: genotype

value: transgenic


title: PETER001_HEPG2_6H_X1_B46:G07

tag: treatment

tag: duration


title: F12304028

value: Day 2

tag: race


title: CTCF CHIP for LMNAC KO, replicate 2

description: Library name: CTCF.KO.2

value: KO

value: CTCF Abcam, ab128873


title: seed_overexpression of GmMYB331_3_3

description:
Library name: Sample 3
3_3
seed_3_all.result.txt
clean data of seed_over expression of GmMYB331_3_3

tag: tissue

value: seed

value: seed cell


title: PETER001_HEPG2_6H_X1_B46:G06

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 6.0 h

tag: plate

tag: well


title: seed_overexpression of GmMYB331_3_2

description:
Library name: Sample 2
3_2
seed_3_all.result.txt
clean data of seed_over expression of GmMYB331_3_2


title: PETER001_HEPG2_6H_X1_B46:G04


title: CTCF CHIP for LMNAC KO, replicate 1

description: Library name: CTCF.KO.1


title: CTCF CHIP for LMNAC WT, replicate 2

description: Library name: CTCF.WT.2


title: leaf_overexpression of GmMYB331_3_3

description:
Library name: Sample 12
3_3
leaf_3_all.result.txt
clean data of leaf_over expression of GmMYB331_3_3

value: leaf

value: leaf cell


title: F12384888

tag: participant id

tag: time point (days)

value: Day 123

value: EDTA Plasma

tag: delivery

value: SC

value: Mepolizumab (24 mg)

value: M

value: Black or African America


title: PETER001_HEPG2_6H_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 6.0 h


title: seed_overexpression of GmMYB331_3_1

description:
Library name: Sample 1
3_1
seed_3_all.result.txt
clean data of seed_over expression of GmMYB331_3_1


title: F12303589

value: Day 1

value: IV

tag: treatment group (dose)

tag: bmi (kg/m2)

value: F

value: White


title: Drosophila melanogaster, male, head, 29C DD, day5, hour20, rep2

city: College Station

first: Wanhe

address: 424 Nagle St

department: Biology

description: Library name: T29.DD.d5h20.r2

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.

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: 29C DD

tag: time

value: day5, hour20

tag: strain

value: male


title: CTCF CHIP for LMNAC WT, replicate 1

description: Library name: CTCF.WT.1

tag: cell line

value: WT

tag: chip antibody

value: CTCF Abcam, ab128873

tag: experiment


title: LMNAC KO input for CTCF, replicate 2

description: Library name: inpC.KO.2

tag: lmnac genotype

value: KO

value: input


title: F12384863

value: Day 93

value: EDTA Plasma

tag: age

tag: Sex


title: PETER001_HEPG2_6H_X1_B46:G02

tag: treatment

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

tag: duration


title: Drosophila melanogaster, male, head, 29C DD, day5, hour20, rep1

description: Library name: T29.DD.d5h20.r1

tag: tissue


title: F12384818

value: Day 49

value: SC

value: Mepolizumab (24 mg)

value: M

tag: race


title: Liver - control - infected - rep6

status: Public on Feb 16 2026

city: Frederiksberg

first: Björn

last: Klabunde

address: Dyrlægevej 68

country: Denmark

institute: Copenhagen University

description: Library name: L_855

data_processing:
The annotated gene information of porcine genome was obtained from Ensembl (release 99). The script htseq-count was used to generate a gene-count matrix, followed by analyses of DEGs using DESeq2.
Assembly: Sscrofa11.1
Supplementary files format and content: "Processed data Ketone experiment.xlsx", containing NCBI gene ID, sample ID (see Metadata file) and gene information. Results are depicted as read counts

organism: Sus scrofa

source_name: Liver

extract_protocol:
shock-frozen hepatic tissue was homogenized using gentleMACS™ Tubes (Miltenyi) and extracted using the QIAGEN Rneasy kit
RNA-Seq libraries were constructed using 1000 ng of RNA and the VAHTS mRNA-Seq V3 Library Prep Kit for Illumina (Vazyme). The libraries were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads. Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Bioinformatics).

value: Liver


title: Drosophila melanogaster, male, head, 29C DD, day5, hour16, rep2

description: Library name: T29.DD.d5h16.r2

value: day5, hour16


title: PETER001_HEPG2_6H_X1_B46:G01

tag: plate

tag: well


title: seed_overexpression of GmMYB331_4_2

description:
Library name: Sample 5
4_2
seed_4_all.result.txt
clean data of seed_over expression of GmMYB331_4_2

value: seed

tag: cell type

value: seed cell

tag: genotype

value: transgenic


title: LMNAC KO input for CTCF, replicate 1

description: Library name: inpC.KO.1


title: PETER001_HEPG2_6H_X1_B46:F21

description: L1000 inferred profile; pert_id: Wortmannin

source_name: HEPG2 treated with Wortmannin 5 uM for 6.0 h

value: Wortmannin 5 uM


title: Drosophila melanogaster, male, head, 29C DD, day5, hour16, rep1

description: Library name: T29.DD.d5h16.r1

value: head

value: 29C DD

value: male


title: LMNAC WT input for CTCF, replicate 2

description: Library name: inpC.WT.2

value: WT

value: input


title: F12384848

source_name: EDTA Plasma

tag: participant id

tag: time point (days)

value: Day 63

value: EDTA Plasma

tag: delivery

tag: treatment group (dose)

tag: bmi (kg/m2)

value: Black or African America


title: PETER001_HEPG2_6H_X1_B46:F18

description: L1000 inferred profile; pert_id: Bictegravir

source_name: HEPG2 treated with Bictegravir 0.5 uM for 6.0 h

tag: cell line

value: Bictegravir 0.5 uM


title: RP-1390_PDO-25321_SM-LLY79

city: Boston

first: Wenya Linda

last: Bi

state: MA

address: 60 Fenwood Road

department: Neurosurgery

institute: Mass General Brigham

description: Library name: Sample 47

data_processing:
The transcriptome product combines poly(A)-selection of mRNA transcripts with a strand-specific cDNA library preparation, with a mean insert size of 550bp. Libraries were sequenced on the HiSeq 2500 platform to a minimum depth of 50-75 million STAR-aligned reads. ERCC RNA controls are included for all samples, allowing additional control of variability between samples.
Assembly: hg19 (GRCh37)
Supplementary files format and content: Tab-delimited text file including raw counts for each individual.

molecule: polyA RNA

source_name: Human meningioma

growth_protocol: Cells were derived from 47 human meningioma samples.

extract_protocol:
Rneasy Mini Kit (Qiagen)
RNA libraries for RNA-seq were repared using the Smart-seq RNA Library Prep Kit from Illumina following manufacturer's protocols

value: Human meningioma

value: female

tag: who grade


title: LMNAC WT input for CTCF, replicate 1

description: Library name: inpC.WT.1

tag: lmnac genotype

tag: chip antibody

tag: experiment


title: Drosophila melanogaster, male, head, 29C DD, day5, hour12, rep2

description: Library name: T29.DD.d5h12.r2

tag: treatment

tag: time

value: day5, hour12

tag: strain

tag: Sex


title: F12300687

value: Day 14

tag: tissue

value: SC

value: Mepolizumab (24 mg)

tag: age

value: M

tag: race


title: F12384656

tag: participant id

value: Day 28


title: F12384636

tag: time point (days)

value: Day 21


title: RP-1390_PDO-25321_SM-LLY78

description: Library name: Sample 46


title: Drosophila melanogaster, male, head, 29C DD, day5, hour08, rep2

description: Library name: T29.DD.d5h08.r2

value: head

value: 29C DD

value: day5, hour08


title: RP-1390_PDO-25321_SM-LLY77

description: Library name: Sample 45

value: male


title: PETER001_HEPG2_6H_X1_B46:F17

tag: duration

tag: plate

tag: well


title: PETER001_HEPG2_6H_X1_B46:F20

tag: cell line

value: Wortmannin 5 uM


title: PETER001_HEPG2_6H_X1_B46:F16


title: F12300280

value: Day 3

value: EDTA Plasma

tag: delivery

tag: treatment group (dose)

tag: bmi (kg/m2)


title: F12300408

value: Day 7

value: Black or African America


title: F12300170

value: Day 2


title: Drosophila melanogaster, male, head, 29C DD, day5, hour12, rep1

description: Library name: T29.DD.d5h12.r1

value: day5, hour12


title: RP-1390_PDO-25321_SM-LLY76

description: Library name: Sample 44

value: Human meningioma

tag: who grade


title: PETER001_HEPG2_6H_X1_B46:F15

description: L1000 inferred profile; pert_id: Elvitegravir

source_name: HEPG2 treated with Elvitegravir 0.1 uM for 6.0 h

tag: treatment

value: Elvitegravir 0.1 uM


title: F12299731

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

value: Day 1

value: SC

value: Mepolizumab (24 mg)


title: PETER001_HEPG2_6H_X1_B46:F14


title: Drosophila melanogaster, male, head, 29C DD, day5, hour08, rep1

description: Library name: T29.DD.d5h08.r1

tag: time


title: Drosophila melanogaster, male, head, 29C DD, day5, hour04, rep2

description: Library name: T29.DD.d5h04.r2

value: day5, hour04

tag: strain


title: RP-1390_PDO-25321_SM-LLY74

description: Library name: Sample 42

tag: Sex


title: Drosophila melanogaster, male, head, 29C DD, day5, hour04, rep1

description: Library name: T29.DD.d5h04.r1

tag: tissue

value: head


title: RP-1390_PDO-25321_SM-LLY75

description: Library name: Sample 43

tag: age

value: female


title: PETER001_HEPG2_6H_X1_B46:F13


title: F12384082

value: Day 123

value: IV

value: M

tag: race


title: F12384057

tag: participant id

value: Day 93


title: Drosophila melanogaster, male, head, 29C DD, day5, hour00, rep2

description: Library name: T29.DD.d5h00.r2

value: 29C DD

value: day5, hour00

value: male


title: RP-1390_PDO-25321_SM-LLY73

description: Library name: Sample 41


title: PETER001_HEPG2_6H_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 6.0 h


title: RP-1390_PDO-25321_SM-LLY71

description: Library name: Sample 40


title: Drosophila melanogaster, male, head, 29C DD, day5, hour00, rep1

description: Library name: T29.DD.d5h00.r1


title: PETER001_HEPG2_6H_X1_B46:F11

value: Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: Drosophila melanogaster, male, head, 29C DD, day4, hour20, rep2

description: Library name: T29.DD.d4h20.r2

value: day4, hour20


title: F12384012

tag: time point (days)

value: Day 49

value: EDTA Plasma

value: Black or African America


title: Drosophila melanogaster, male, head, 29C DD, day4, hour20, rep1

description: Library name: T29.DD.d4h20.r1


title: F12383850

value: Day 28


title: RP-1390_PDO-25321_SM-LLY7X

description: Library name: Sample 39

value: Human meningioma


title: PETER001_HEPG2_6H_X1_B46:F10

tag: duration


title: F12384042

value: Day 63


title: RP-1390_PDO-25321_SM-LLY7W

description: Library name: Sample 38


title: F12383830

value: Day 21


title: PETER001_HEPG2_6H_X1_B46:F09

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir

source_name: HEPG2 treated with Darunavir|Ritonavir 0.1|0.5 uM for 6.0 h

value: Darunavir|Ritonavir 0.1|0.5 uM

tag: plate


title: Drosophila melanogaster, male, head, 29C DD, day4, hour16, rep2

description: Library name: T29.DD.d4h16.r2

value: head

value: day4, hour16


title: PETER001_HEPG2_6H_X1_B46:F08

tag: well


title: Drosophila melanogaster, male, head, 29C DD, day4, hour16, rep1

description: Library name: T29.DD.d4h16.r1


title: PETER001_HEPG2_6H_X1_B46:F07

tag: cell line


title: F12298115

value: Day 14

tag: delivery

value: IV

value: M


title: Drosophila melanogaster, male, head, 29C DD, day4, hour12, rep1

description: Library name: T29.DD.d4h12.r1

value: 29C DD

value: day4, hour12


title: Drosophila melanogaster, male, head, 29C DD, day4, hour12, rep2

description: Library name: T29.DD.d4h12.r2

value: male


title: PETER001_HEPG2_6H_X1_B46:F06

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

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


title: RP-1390_PDO-25321_SM-LLY7T

description: Library name: Sample 35


title: RP-1390_PDO-25321_SM-LLY7V

description: Library name: Sample 37

value: female


title: Drosophila melanogaster, male, head, 29C DD, day4, hour08, rep2

description: Library name: T29.DD.d4h08.r2

value: day4, hour08


title: F12297836

value: Day 7

value: EDTA Plasma

tag: treatment group (dose)


title: F12297708

value: Day 3

tag: bmi (kg/m2)

value: Black or African America


title: PETER001_HEPG2_6H_X1_B46:F04

value: Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: PETER001_HEPG2_6H_X1_B46:F03

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

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


title: RP-1390_PDO-25321_SM-LLY7R

description: Library name: Sample 33

value: Human meningioma

tag: who grade


title: RP-1390_PDO-25321_SM-LLY7P

description: Library name: Sample 32


title: F12297598

value: Day 2


title: Drosophila melanogaster, male, head, 29C DD, day4, hour04, rep2

description: Library name: T29.DD.d4h04.r2

value: head

tag: treatment

value: day4, hour04


title: RP-1390_PDO-25321_SM-LLY7S

description: Library name: Sample 34


title: F12297159

value: Day 1


title: F12347577

value: Day 93

value: IV


title: F12347602

value: Day 123

value: M


title: Drosophila melanogaster, male, head, 29C DD, day4, hour04, rep1

description: Library name: T29.DD.d4h04.r1

value: 29C DD

tag: time

value: male


title: PETER001_HEPG2_6H_X1_B46:F02

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


title: PETER001_HEPG2_6H_X1_B46:F01


title: RP-1390_PDO-25321_SM-LLY7M

description: Library name: Sample 29


title: PETER001_HEPG2_6H_X1_B46:F05


title: Drosophila melanogaster, male, head, 29C DD, day4, hour00, rep1

description: Library name: T29.DD.d4h00.r1

value: day4, hour00

tag: strain


title: PETER001_HEPG2_6H_X1_B46:E21

description: L1000 inferred profile; pert_id: Rapamycin

source_name: HEPG2 treated with Rapamycin 5 uM for 6.0 h

value: Rapamycin 5 uM


title: PETER001_HEPG2_6H_X1_B46:E20


title: RP-1390_PDO-25321_SM-LLY7O

description: Library name: Sample 31

tag: Sex


title: RP-1390_PDO-25321_SM-LLY7L

description: Library name: Sample 28

tag: tissue

value: female


title: Drosophila melanogaster, male, head, 25C LD, day5, hour20, rep2

description: Library name: T25.LD.d5h20.r2

value: 25C LD

value: day5, hour20


title: F12347370

value: Day 28

value: EDTA Plasma

tag: age

value: Black or African America


title: RP-1390_PDO-25321_SM-LLY7K

description: Library name: Sample 27

value: Human meningioma


title: RP-1390_PDO-25321_SM-LLY7U

description: Library name: Sample 36


title: RP-1390_PDO-25321_SM-LLY7J

description: Library name: Sample 26


title: PETER001_HEPG2_6H_X1_B46:E19


title: PETER001_HEPG2_6H_X1_B46:E18

description: L1000 inferred profile; pert_id: Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Tenofovir Disoproxil Fumarate 0.1 uM for 6.0 h

value: Tenofovir Disoproxil Fumarate 0.1 uM


title: F12347350

value: Day 21

tag: race


title: RP-1390_PDO-25321_SM-LLY7N

description: Library name: Sample 30


title: F12347562

tag: participant id

value: Day 63

value: IV


title: Drosophila melanogaster, male, head, 25C LD, day5, hour16, rep2

description: Library name: T25.LD.d5h16.r2

value: head

value: day5, hour16


title: F12125699

tag: time point (days)

value: Day 14

value: M


title: Drosophila melanogaster, male, head, 29C DD, day4, hour00, rep2

description: Library name: T29.DD.d4h00.r2

value: 29C DD

value: day4, hour00

value: male


title: F12125292

value: Day 3


title: RP-1390_PDO-25321_SM-LLY7I

description: Library name: Sample 25

value: female


title: F12125420

value: Day 7


title: Drosophila melanogaster, male, head, 25C LD, day5, hour16, rep1

description: Library name: T25.LD.d5h16.r1

value: 25C LD


title: PETER001_HEPG2_6H_X1_B46:E16

tag: duration


title: Drosophila melanogaster, male, head, 25C LD, day5, hour12, rep2

description: Library name: T25.LD.d5h12.r2

value: day5, hour12


title: RP-1390_PDO-25321_SM-LLY7F

description: Library name: Sample 23

value: Human meningioma


title: RP-1390_PDO-25321_SM-LLY7G

description: Library name: Sample 24


title: Drosophila melanogaster, male, head, 29C DD, day4, hour08, rep1

description: Library name: T29.DD.d4h08.r1

value: day4, hour08


title: PETER001_HEPG2_6H_X1_B46:E17

value: Tenofovir Disoproxil Fumarate 0.1 uM

tag: plate


title: RP-1390_PDO-25321_SM-LLY7E

description: Library name: Sample 22


title: Drosophila melanogaster, male, head, 25C LD, day5, hour08, rep2

description: Library name: T25.LD.d5h08.r2

value: day5, hour08


title: PETER001_HEPG2_6H_X1_B46:E14

description: L1000 inferred profile; pert_id: Cobicistat

source_name: HEPG2 treated with Cobicistat 0.1 uM for 6.0 h

value: Cobicistat 0.1 uM

tag: well


title: F12124743

value: Day 1

value: EDTA Plasma

value: IV

value: Black or African America


title: Drosophila melanogaster, male, head, 25C LD, day5, hour12, rep1

description: Library name: T25.LD.d5h12.r1

value: head


title: RP-1390_PDO-25321_SM-LLY7D

description: Library name: Sample 21


title: PETER001_HEPG2_6H_X1_B46:E13

tag: cell line


title: F12349617

value: Day 123

tag: delivery

value: SC

value: Mepolizumab (24 mg)

value: F

value: White


title: F12125182

value: Day 2

tag: treatment group (dose)

value: M


title: Drosophila melanogaster, male, head, 25C LD, day5, hour08, rep1

description: Library name: T25.LD.d5h08.r1

value: 25C LD

value: male


title: RP-1390_PDO-25321_SM-LLY7C

description: Library name: Sample 20

value: Human meningioma

value: female


title: F12349592

value: Day 93

tag: bmi (kg/m2)


title: Drosophila melanogaster, male, head, 25C LD, day5, hour04, rep2

description: Library name: T25.LD.d5h04.r2

value: day5, hour04


title: PETER001_HEPG2_6H_X1_B46:E11

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

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


title: F12349577

value: Day 63

value: EDTA Plasma


title: PETER001_HEPG2_6H_X1_B46:E12

value: Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM


title: Drosophila melanogaster, male, head, 25C LD, day5, hour04, rep1

description: Library name: T25.LD.d5h04.r1

value: head


title: RP-1390_PDO-25321_SM-LLY7B

description: Library name: Sample 19

tag: who grade


title: RP-1390_PDO-25321_SM-LLY7A

description: Library name: Sample 18


title: PETER001_HEPG2_6H_X1_B46:E10

tag: treatment


title: Drosophila melanogaster, male, head, 25C LD, day5, hour00, rep2

description: Library name: T25.LD.d5h00.r2

tag: time

value: day5, hour00


title: PETER001_HEPG2_6H_X1_B46:E15

value: Cobicistat 0.1 uM


title: RP-1390_PDO-25321_SM-LLY6Z

description: Library name: Sample 17


title: Drosophila melanogaster, male, head, 25C LD, day5, hour00, rep1

description: Library name: T25.LD.d5h00.r1

tag: strain


title: F12349385

value: Day 28

value: SC

value: Mepolizumab (24 mg)

tag: Sex


title: PETER001_HEPG2_6H_X1_B46:E07

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine

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

value: Bictegravir|Emtricitabine 0.5|0.1 uM


title: F12138559

value: Day 14

tag: tissue

value: F

value: White


title: RP-1390_PDO-25321_SM-LLY6X

description: Library name: Sample 15

value: Human meningioma

tag: age

value: male


title: RP-1390_PDO-25321_SM-LLY6Y

description: Library name: Sample 16


title: Drosophila melanogaster, male, head, 25C LD, day5, hour20, rep1

description: Library name: T25.LD.d5h20.r1

value: 25C LD

value: day5, hour20


title: RP-1390_PDO-25321_SM-LLY6W

description: Library name: Sample 14

value: female


title: PETER001_HEPG2_6H_X1_B46:E06

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

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


title: F12349365

value: Day 21

value: EDTA Plasma

tag: race


title: Drosophila melanogaster, male, head, 25C LD, day4, hour16, rep2

description: Library name: T25.LD.d4h16.r2

source_name: head

value: head

value: day4, hour16


title: F12349547

tag: participant id

value: Day 49


title: PETER001_HEPG2_6H_X1_B46:E09


title: PETER001_HEPG2_6H_X1_B46:E08


title: Drosophila melanogaster, male, head, 25C LD, day4, hour20, rep2

description: Library name: T25.LD.d4h20.r2

value: day4, hour20


title: PETER001_HEPG2_6H_X1_B46:E05

value: Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: RP-1390_PDO-25321_SM-LLY6V

description: Library name: Sample 13


title: Drosophila melanogaster, male, head, 25C LD, day4, hour20, rep1

description: Library name: T25.LD.d4h20.r1


title: RP-1390_PDO-25321_SM-LLY6U

description: Library name: Sample 12


title: Drosophila melanogaster, male, head, 25C LD, day4, hour12, rep2

description: Library name: T25.LD.d4h12.r2

value: day4, hour12


title: PETER001_HEPG2_6H_X1_B46:E04


title: PETER001_HEPG2_6H_X1_B46:E03

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine

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


title: F12138280

tag: time point (days)

value: Day 7

value: SC

value: Mepolizumab (24 mg)


title: F12137603

value: Day 1

value: F

value: White


title: Drosophila melanogaster, male, head, 25C LD, day4, hour16, rep1

description: Library name: T25.LD.d4h16.r1

value: 25C LD

value: male


title: Drosophila melanogaster, male, head, 25C LD, day4, hour12, rep1

description: Library name: T25.LD.d4h12.r1


title: Drosophila melanogaster, male, head, 25C LD, day4, hour08, rep2

description: Library name: T25.LD.d4h08.r2

value: day4, hour08


title: RP-1390_PDO-25321_SM-LLY6S

description: Library name: Sample 10

value: Human meningioma


title: F12138042

value: Day 2

value: EDTA Plasma


title: PETER001_HEPG2_6H_X1_B46:D21

description: L1000 inferred profile; pert_id: Vorinostat

source_name: HEPG2 treated with Vorinostat 5 uM for 6.0 h

value: Vorinostat 5 uM

tag: duration


title: PETER001_HEPG2_6H_X1_B46:E01

tag: plate


title: RP-1390_PDO-25321_SM-LLY6Q

description: Library name: Sample 8

value: female


title: F12138152

source_name: EDTA Plasma

value: Day 3


title: Drosophila melanogaster, male, head, 25C LD, day4, hour08, rep1

description: Library name: T25.LD.d4h08.r1

value: head


title: F12348408

value: Day 123

value: IV

value: Reslizumab (0.8 mg/kg)

value: Black or African America


title: PETER001_HEPG2_6H_X1_B46:E02

tag: well


title: RP-1390_PDO-25321_SM-LLY6T

description: Library name: Sample 11


title: RP-1390_PDO-25321_SM-LLY6P

description: Library name: Sample 7


title: F12348383

value: Day 93


title: PETER001_HEPG2_6H_X1_B46:D20

tag: cell line


title: F12348338

value: Day 49

tag: delivery

value: F


title: Drosophila melanogaster, male, head, 25C LD, day4, hour04, rep2

description: Library name: T25.LD.d4h04.r2

value: 25C LD

value: day4, hour04


title: F12348176

value: Day 28

tag: treatment group (dose)


title: F12348368

value: Day 63

tag: bmi (kg/m2)


title: RP-1390_PDO-25321_SM-LLY6R

description: Library name: Sample 9

value: Human meningioma

tag: who grade


title: PETER001_HEPG2_6H_X1_B46:D19

tag: treatment


title: Drosophila melanogaster, male, head, 25C LD, day4, hour04, rep1

description: Library name: T25.LD.d4h04.r1

tag: time

value: male


title: RP-1390_PDO-25321_SM-LLY6O

description: Library name: Sample 6


title: RP-1390_6601538_0

description: Library name: Sample 4


title: PETER001_HEPG2_6H_X1_B46:D18

description: L1000 inferred profile; pert_id: Efavirenz

source_name: HEPG2 treated with Efavirenz 0.5 uM for 6.0 h

value: Efavirenz 0.5 uM


title: PETER001_HEPG2_6H_X1_B46:D17


title: Drosophila melanogaster, male, head, 25C LD, day4, hour00, rep2

description: Library name: T25.LD.d4h00.r2

value: day4, hour00

tag: strain


title: Drosophila melanogaster, male, head, 25C DD, day5, hour20, rep1

description: Library name: T25.DD.d5h20.r1

value: 25C DD

value: day5, hour20

tag: Sex


title: RP-1390_3_8847018E7

description: Library name: Sample 3

source_name: Human meningioma

tag: tissue

value: female


title: Drosophila melanogaster, male, head, 25C DD, day5, hour20, rep2

description: Library name: T25.DD.d5h20.r2

value: head


title: RP-1390_PDO-25321_SM-LLY6N

description: Library name: Sample 5

tag: age


title: PETER001_HEPG2_6H_X1_B46:D15

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

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


title: RP-1390_3_8701736E7

description: Library name: Sample 2


title: F12131722

value: Day 3

value: EDTA Plasma

value: IV

value: Reslizumab (0.8 mg/kg)

tag: race


title: F12348156

tag: participant id

value: Day 21

value: F

value: Black or African America


title: Drosophila melanogaster, male, head, 25C DD, day5, hour16, rep2

description: Library name: T25.DD.d5h16.r2

value: day5, hour16


title: F12131173

tag: time point (days)

value: Day 1


title: F12132129

value: Day 14


title: F12131612

value: Day 2


title: PETER001_HEPG2_6H_X1_B46:D14

value: Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM

tag: duration


title: Drosophila melanogaster, male, head, 25C DD, day5, hour16, rep1

description: Library name: T25.DD.d5h16.r1

value: male


title: F12131850

value: Day 7


title: C4-2B  cell with RP-6306 treatment-1

city: Jinan

first: Lin

last: Gao

address: No.44, Wenhua Xi Road

institute: shandong university

description:
Library name: RP-6306-1
Column name in raw_counts_All Samples.txt: RP-6306-1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

extract_protocol:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C4-2B  cells treated with DMSO or RP-6306.

tag: cell type

value: prostate cancer cell

tag: genotype

value: WT

tag: batch


title: PETER001_HEPG2_6H_X1_B46:D13

tag: cell line

tag: plate

tag: well


title: RP-1390_3_0289979E7

description: Library name: Sample 1

value: Human meningioma

value: female

tag: who grade


title: PETER001_HEPG2_6H_X1_B46:D16

tag: treatment

value: Efavirenz 0.5 uM


title: Drosophila melanogaster, male, head, 25C LD, day4, hour00, rep1

description: Library name: T25.LD.d4h00.r1

value: head

value: 25C LD

tag: time

value: day4, hour00


title: F11731208

value: Day 49

value: EDTA Plasma

tag: delivery

value: IV

tag: treatment group (dose)

value: Reslizumab (0.8 mg/kg)

tag: bmi (kg/m2)

value: M

value: White


title: Drosophila melanogaster, male, head, 25C DD, day5, hour08, rep1

description: Library name: T25.DD.d5h08.r1

tag: tissue

value: 25C DD

value: day5, hour08

tag: strain

tag: Sex


title: C4-2B cell with DMSO treatment -3

description:
Library name: DMSO-3
Column name in raw_counts_All Samples.txt: DMSO-3

value: DMSO


title: F11731278

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

tag: participant id

tag: time point (days)

value: Day 123

tag: age

tag: race


title: C4-2B cell with DMSO treatment -2

description:
Library name: DMSO-2
Column name in raw_counts_All Samples.txt: DMSO-2

tag: cell type

value: prostate cancer cell

tag: genotype

value: WT

tag: batch


title: PETER001_HEPG2_6H_X1_B46:D10

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

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

tag: cell line

tag: duration

tag: plate

tag: well


title: F11731238

value: Day 63

tag: delivery


title: Drosophila melanogaster, male, head, 25C DD, day5, hour12, rep2

description: Library name: T25.DD.d5h12.r2

tag: treatment

tag: time

value: day5, hour12

value: male


title: Drosophila melanogaster, male, head, 25C DD, day5, hour12, rep1

description: Library name: T25.DD.d5h12.r1

tag: tissue

value: head


title: C4-2B  cell with RP-6306 treatment-2

description:
Library name: RP-6306-2
Column name in raw_counts_All Samples.txt: RP-6306-2


title: PETER001_HEPG2_6H_X1_B46:D11

value: Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: F11731253

value: Day 93

tag: treatment group (dose)

tag: bmi (kg/m2)


title: PETER001_HEPG2_6H_X1_B46:D09

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

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


title: C4-2B cell with DMSO treatment-1

description:
Library name: DMSO-1
Column name in raw_counts_All Samples.txt: DMSO-1


title: Drosophila melanogaster, male, head, 25C DD, day5, hour08, rep2

description: Library name: T25.DD.d5h08.r2

tag: strain

tag: Sex


title: Drosophila melanogaster, male, head, 25C DD, day5, hour04, rep2

description: Library name: T25.DD.d5h04.r2

value: day5, hour04


title: F11731026

tag: participant id

tag: time point (days)

value: Day 21

value: EDTA Plasma

value: IV

tag: age


title: Drosophila melanogaster, male, head, 25C DD, day5, hour04, rep1

description: Library name: T25.DD.d5h04.r1


title: F11731046

value: Day 28

value: Reslizumab (0.8 mg/kg)

value: M

tag: race

value: White


title: PETER001_HEPG2_6H_X1_B46:D08

value: Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: F11539938

value: Day 14


title: C4-2B  cell with RP-6306 treatment-3

description:
Library name: RP-6306-3
Column name in raw_counts_All Samples.txt: RP-6306-3

tag: cell type

value: prostate cancer cell

tag: genotype

value: WT

tag: batch


title: PETER001_HEPG2_6H_X1_B46:D06

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine

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

tag: cell line

value: Efavirenz|Emtricitabine 0.5|0.1 uM

tag: duration

tag: plate


title: Drosophila melanogaster, male, head, 25C DD, day5, hour00, rep1

description: Library name: T25.DD.d5h00.r1

tag: treatment

value: 25C DD

value: day5, hour00

value: male


title: PETER001_HEPG2_6H_X1_B46:D12

value: Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM

tag: well


title: PE2_gfp3

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

data_processing:
saples were mapped with STAR split read alligner
mapped reads were processed, QC and filtered by custom scripts empling elements of SAMtools, bedtools, Bwtool, RSeQC packages
Differential expression analysis was performed using the DESeq2 bioconductor package
genomic structural variants were called using SVDetect
mait-pair reads preprocessed using Nxtrim
Genome_build: human samples were mapped to the GRCh38 reference geneome murine samples were mapped to the GRCm38 reference geneome

source_name: Human Multiple Myeloma PE2 cell line with a lentivirilly introduced mEGPF protein replicat_3

growth_protocol: The Human Multiple Myeloma PE2 cell line was kindly provided by Prof. Michael Kuehl from the Center for Cancer Research, National Cancer Institute. Cells were cultured in RPMI 1640 ATCC’s modified medium supplemented with 4% FBS, penicillin/streptomycin  and 2 ng/ml of recombinant human IL6 at density between 0.5-1 x 106 cells/ml.

extract_protocol: RNA was isolated using TRIreagent DNA was extracted

value: Human myeloma cell line

tag: dis3 genotype/expressed variant


title: PETER001_HEPG2_6H_X1_B46:D07


title: Drosophila melanogaster, male, head, 25C DD, day5, hour00, rep2

description: Library name: T25.DD.d5h00.r2

tag: tissue

value: head

tag: time


title: F11539445

value: Day 2

value: EDTA Plasma

tag: delivery

tag: treatment group (dose)

tag: bmi (kg/m2)


title: PE2_gfp2

source_name: Human Multiple Myeloma PE2 cell line with a lentivirilly introduced mEGPF protein replicat_2


title: PETER001_HEPG2_6H_X1_B46:D03


title: PE2_gfp1

source_name: Human Multiple Myeloma PE2 cell line with a lentivirilly introduced mEGPF protein replicat_1


title: F11539673

tag: participant id

tag: time point (days)

value: Day 7

value: IV

tag: Sex


title: PE2_dis_wt1

source_name: Human Multiple Myeloma PE2 cell line with a lentivirilly reintroduced WT DIS3 protein replicat_1

tag: cell type

value: DIS3 A507P/A507P with lentiviral reconstitution of DIS3 WT expression


title: PETER001_HEPG2_6H_X1_B46:D02


title: PETER001_HEPG2_6H_X1_B46:D05


title: F11730875

value: Day 123

value: SC

value: Mepolizumab (24 mg)

tag: age

value: M

tag: race

value: White


title: Small intestine tissue from mice treated with Am80-LNP (biological replicate 3)

first: Li

last: Jingjiao

address: Zhongguancun North First Street 2

institute: Institute of Chemistry, Chinese Academy of Sciences

description:
Library name: Am80_3_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/14 mice

data_processing:
Raw sequencing reads were filtered using SOAPnuke (v2.2.1) to remove adaptor-contaminated reads, reads with more than 5% unknown bases, and low-quality reads.
Clean reads were aligned to the mouse reference genome using HISAT2 (v2.2.1).
Gene expression levels were quantified by aligning clean reads to the reference gene set using Bowtie2 (v2.4.5) and estimating transcript abundance with RSEM (v1.3.1).
Assembly: Mus musculus reference genome (mm10)
Supplementary files format and content: Processed data consist of a gene-level expression matrix. Expression values are reported as raw counts and FPKM and TPM.

organism: Mus musculus

source_name: small intestine

growth_protocol: Wild-type C57BL/6 mice were maintained under standard laboratory conditions according to institutional animal care guidelines.

extract_protocol:
Total RNA was extracted from small intestinal tissue using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality and quantity were assessed using  Agilent 2100 Bioanalyzer.
mRNA libraries were prepared using the BGI Optimal Dual-Module mRNA Library Preparation Kit. Poly(A)+ mRNA was enriched using oligo(dT) magnetic beads, fragmented, and reverse transcribed into cDNA. Double-stranded cDNA was end-repaired, A-tailed, adapter-ligated, PCR-amplified, circularized, and converted into DNA nanoballs for sequencing.

treatment_protocol: Mice were immunized with PBS, SM102-LNP, or Am80-LNP at day 0 and day 21, and small intestinal tissues were collected at day 14 after booster immunization.

value: small intestine

tag: strain

tag: genotype

value: wild-type

tag: batch


title: Small intestine tissue from mice treated with Am80-LNP (biological replicate 2)

description:
Library name: Am80_2_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/13 mice

tag: treatment


title: PETER001_HEPG2_6H_X1_B46:D04

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.

tag: cell line

value: Efavirenz|Emtricitabine 0.5|0.1 uM

tag: duration

tag: plate

tag: well


title: Drosophila melanogaster, male, head, 25C DD, day4, hour12, rep2

description: Library name: T25.DD.d4h12.r2

tag: tissue

value: 25C DD

tag: time

value: day4, hour12

value: male


title: PE2_dis_wt2

source_name: Human Multiple Myeloma PE2 cell line with a lentivirilly reintroduced WT DIS3 protein replicat_2

value: Human myeloma cell line

tag: dis3 genotype/expressed variant


title: PETER001_HEPG2_6H_X1_B46:D01


title: Drosophila melanogaster, male, head, 25C DD, day4, hour20, rep1

description: Library name: T25.DD.d4h20.r1

value: head

value: day4, hour20


title: F11539553

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.

extract_protocol: EDTA plasma from whole blood

tag: participant id

value: Day 3

value: EDTA Plasma

tag: delivery

tag: treatment group (dose)

value: Reslizumab (0.8 mg/kg)

tag: bmi (kg/m2)


title: F11539008

tag: time point (days)

value: Day 1

value: IV

value: Reslizumab [Res](0.8 mg/kg)

tag: age

tag: Sex


title: Drosophila melanogaster, male, head, 25C DD, day4, hour20, rep2

description: Library name: T25.DD.d4h20.r2

tag: strain


title: PETER001_HEPG2_6H_X1_B46:C21

description: L1000 inferred profile; pert_id: Genistein

source_name: HEPG2 treated with Genistein 5 uM for 6.0 h

value: Genistein 5 uM


title: Drosophila melanogaster, male, head, 25C DD, day4, hour16, rep2

description: Library name: T25.DD.d4h16.r2

source_name: head

value: day4, hour16


title: Small intestine tissue from mice treated with Am80-LNP (biological replicate 1)

description:
Library name: Am80_1_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/12 mice

value: small intestine

tag: genotype

tag: batch


title: Drosophila melanogaster, male, head, 25C DD, day4, hour16, rep1

description: Library name: T25.DD.d4h16.r1

tag: treatment


title: Small intestine tissue from mice treated with SM102-LNP (biological replicate 3)

description:
Library name: SM102_3_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/11 mice

value: wild-type


title: Drosophila melanogaster, male, head, 25C DD, day4, hour08, rep1

description: Library name: T25.DD.d4h08.r1

value: day4, hour08


title: Small intestine tissue from mice treated with SM102-LNP (biological replicate 2)

description:
Library name: SM102_2_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/10 mice


title: PETER001_HEPG2_6H_X1_B46:C19

tag: cell line

tag: duration


title: PETER001_HEPG2_6H_X1_B46:C18

description: L1000 inferred profile; pert_id: Emtricitabine

source_name: HEPG2 treated with Emtricitabine 0.1 uM for 6.0 h

value: Emtricitabine 0.1 uM

tag: plate

tag: well


title: F11730805

value: Day 49

tag: tissue

value: SC

value: Mepolizumab (24 mg)

value: M

tag: race

value: White


title: F11730835

tag: participant id

value: Day 63


title: PETER001_HEPG2_6H_X1_B46:C20


title: F11538368

value: Day 14

value: EDTA Plasma

tag: delivery


title: F11730643

value: Day 28

tag: treatment group (dose)


title: Small intestine tissue from mice treated with PBS (biological replicate 3)

description:
Library name: PBS_3_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/8 mice

value: PBS


title: Drosophila melanogaster, male, head, 25C DD, day4, hour08, rep2

description: Library name: T25.DD.d4h08.r2

value: head

value: 25C DD

tag: time

value: male


title: Drosophila melanogaster, male, head, 25C DD, day4, hour12, rep1

description: Library name: T25.DD.d4h12.r1

value: day4, hour12


title: Drosophila melanogaster, male, head, 25C DD, day4, hour04, rep2

description: Library name: T25.DD.d4h04.r2

value: day4, hour04


title: Small intestine tissue from mice treated with SM102-LNP (biological replicate 1)

description:
Library name: SM102_1_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/9 mice

value: small intestine

value: wild-type


title: PETER001_HEPG2_6H_X1_B46:C17

value: Emtricitabine 0.1 uM


title: PETER001_HEPG2_6H_X1_B46:C16


title: F11537983

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

tag: time point (days)

value: Day 3

value: SC

tag: bmi (kg/m2)


title: Small intestine tissue from mice treated with PBS (biological replicate 2)

description:
Library name: PBS_2_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/7 mice


title: Drosophila melanogaster, male, head, 25C DD, day4, hour04, rep1

description: Library name: T25.DD.d4h04.r1

tag: Sex


title: Drosophila melanogaster, male, head, 25C DD, day4, hour00, rep2

description: Library name: T25.DD.d4h00.r2

value: day4, hour00

tag: strain


title: F11730623

value: Day 21

value: Mepolizumab (24 mg)

tag: age

value: M

value: White


title: Small intestine tissue from mice treated with PBS (biological replicate 1)

description:
Library name: PBS_1_SI
Bulk RNA-seq of small intestine tissue from immunized C57BL/6 mice

tag: genotype

tag: batch


title: PETER001_HEPG2_6H_X1_B46:C15

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine

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

tag: cell line

tag: treatment

value: Elvitegravir|Emtricitabine 0.1|0.1 uM


title: F11537875

source_name: EDTA Plasma

value: Day 2

value: EDTA Plasma


title: Drosophila melanogaster, male, head, 25C DD, day4, hour00, rep1

description: Library name: T25.DD.d4h00.r1

value: head

value: 25C DD


title: PETER001_HEPG2_6H_X1_B46:C14

tag: duration

tag: plate


status: Public on Feb 14 2026

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description: Library name: ZAP1_aS74_aT55_aN110_aQ61_aD16_aE14_aF67_3

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: cell type

value: yeast cells

value: MATa his3D0 leu2D0 met15D0 ura3D0 ZAP1::ZAP1(S74 T55 N110 Q61 D16 E14 F67) SV40 NLS Mnase

value: budding yeast culture at OD=4


title: AAA 5

city: Zhengzhou

first: Shuai

last: Cheng

address: No.1, East Jian She Road

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: Sample 12
Column name in raw_counts.txt: AAA 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.

tag: tissue

value: infrarenal abdominal aorta

value: Male

value: WT

value: Periadventitial incubation with porcine pancreatic elastase combined with 0.2% β-aminopropionitrile administration


title: AAA 6

description:
Library name: Sample 13
Column name in raw_counts.txt: AAA 6


title: SNU449_siSCR_2, 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 5
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: Control

value: siRNA transfection


title: PETER001_HEPG2_6H_X1_B46:C12

city: New York

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place, Box 1603

institute: Icahn School of Medicine at Mount Sinai

description: L1000 inferred profile; pert_id: Abacavir|Emtricitabine

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

value: Abacavir|Emtricitabine 0.5|0.1 uM

tag: well


title: AAA 4

description:
Library name: Sample 11
Column name in raw_counts.txt: AAA 4


title: Drosophila melanogaster, male, head, 18C DD, day5, hour20, rep1

institute: Texas A&M University

description: Library name: T18.DD.d5h20.r1

value: 18C DD

value: day5, hour20

value: male


title: F11538103

city: Silver Spring

first: Paula

last: Hyland

address: 10903 New Hampshire Avenue

institute: FDA

tag: participant id

value: Day 7

value: EDTA Plasma

tag: delivery

value: SC

value: Mepolizumab (24 mg)

value: M

tag: race

value: White


title: SNU449_siSCR_3, Day2

description:
Library name: Sample 6
Sequenced using MGI DNBSEQ-T7 instrument


title: Drosophila melanogaster, male, head, 18C DD, day5, hour16, rep2

description: Library name: T18.DD.d5h16.r2

value: head

tag: time

value: day5, hour16


title: PETER001_HEPG2_6H_X1_B46:C13

value: Elvitegravir|Emtricitabine 0.1|0.1 uM


title: PETER001_HEPG2_6H_X1_B46:C11


title: SNU449_siSCR_1, Day2

description:
Library name: Sample 4
Sequenced using MGI DNBSEQ-T7 instrument

value: Liver


title: AAA 3

description:
Library name: Sample 10
Column name in raw_counts.txt: AAA 3

value: infrarenal abdominal aorta

value: Male

value: WT

value: Periadventitial incubation with porcine pancreatic elastase combined with 0.2% β-aminopropionitrile administration


title: Drosophila melanogaster, male, head, 18C DD, day5, hour20, rep2

description: Library name: T18.DD.d5h20.r2

value: 18C DD


title: Drosophila melanogaster, male, head, 18C DD, day5, hour16, rep1

description: Library name: T18.DD.d5h16.r1


title: Drosophila melanogaster, male, head, 18C DD, day5, hour12, rep2

description: Library name: T18.DD.d5h12.r2

value: day5, hour12


title: AAA 2

description:
Library name: Sample 9
Column name in raw_counts.txt: AAA 2


title: PETER001_HEPG2_6H_X1_B46:C10

value: Abacavir|Emtricitabine 0.5|0.1 uM


title: AAA 1

description:
Library name: Sample 8
Column name in raw_counts.txt: AAA 1


title: Drosophila melanogaster, male, head, 18C DD, day5, hour12, rep1

description: Library name: T18.DD.d5h12.r1

value: male


title: SNU449_siSF3B6_2, Day2

description:
Library name: Sample 2
Sequenced using MGI DNBSEQ-T7 instrument

value: Hepatocellular carcinoma liver cells

value: siRNA transfection


title: PETER001_HEPG2_6H_X1_B46:C09

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine

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

value: Dolutegravir|Emtricitabine 0.1|0.1 uM


title: PETER001_HEPG2_6H_X1_B46:C08


title: SNU449_siSF3B6_1, Day2

description:
Library name: Sample 1
Sequenced using MGI DNBSEQ-T7 instrument


title: Sham 7

description:
Library name: Sample 7
Column name in raw_counts.txt: Sham 7

value: Periadventitial application of heat-inactivated elastase


title: Sham 6

description:
Library name: Sample 6
Column name in raw_counts.txt: Sham 6


title: Drosophila melanogaster, male, head, 18C DD, day5, hour08, rep2

description: Library name: T18.DD.d5h08.r2

value: day5, hour08


title: PETER001_HEPG2_6H_X1_B46:C07