title: HL-60_EZH2_KD_shEZH2#2_replicate2


title: HL-60_non-targeting_control_Scr+ATRA_replicate2

status: Public on Mar 10 2023

type: RNA

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Staining, washing and scanning on the final day of this protocol was performed and the images were processed by the affymetrix software to produce .CEL files, which were then used for the bioinformatics analysis of the arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Partek software. Batch effect remove function in Partek was applied after GC-RMA quantile normalisation

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: ss-cDNA was digested and labelled according to manufacturers protocol (WT plus kit by Affymetrix).

growth_protocol: HL-60 cells were obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ) and maintained in them RPMI 1640 (Sigma) supplemented with 10% FBS (Gibco), 100 μml−1 penicillin and 100 μg ml−1 streptomycin. For EZH2 KD experiments, HL-60 cells were grown in puromycin (1.5 µM) for at least 3 days, then allowed to recover and expand for another few days before experiments were set up.

extract_protocol: Total RNA was isolated using the ZR RNA MiniPrep Kit (Zymo Research). The concentration and quality of the total RNA was assessed on an Agilent 2100 BioAnalyzer (Agilent Technologies). cDNA, cRNA and then single-stranded cDNA were made with a number of amplification and purification steps in between following standard Affymetrix protocol and using WT plus kit by Affymetrix

treatment_protocol: Cells were treated with 10µM GSK343 or 2.5µM HKMTI-1-005 (+/- 0.1µM AtRA) for 3 days.

tag: cell line

tag: cell type

value: Acute myeloid leukaemia

tag: treatment


title: COL_ABX_LD168_3

type: SRA

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

country: China

institute: Yangzhou University

library_source: transcriptomic

data_processing:
Briefly, the Fastp software (v0.23.1) was firstly used to perform quality control on the raw data and obtain clean data. Then, the HISAT2 software (v2.1.0) was used to align the obtained clean data referred to the latest reference genome in mouse (GRCm39). After that, the Samtools software (v.1.10) was used to sort and convert the SAM files to BAM format, and finally, the Stringtie software (v2.2.1) was used to assemble and quantify the transcripts and genes based on read counts.
Assembly: GRCm39
Supplementary files format and content: a excel file named "RNA_Seq_processed_data" of raw counts  for each sample

organism: Mus musculus

source_name: Colon epithelium

extract_protocol:
Total RNA  was extracted and purified using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for transcriptomic sequencing
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: strain

tag: tissue

value: Colon epithelium

tag: diets

value: antibiotics infusion


title: COL_ABX_LD168_2


title: HL-60_EZH2_KD_shEZH2#1_replicate2


title: Aged S1 B3

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

country: USA

institute: Washington University in Saint Louis

description: RNA was isolated from 5 mice

data_processing:
Demultiplexing with custom Python and perl script
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mm10
Supplementary files format and content: gzipped csv file with raw gene counts for all cells in each sample

source_name: Brain meninges

extract_protocol: Mice were given a lethal dose of anesthetics via i.p. Euthasol (10% v/v) and transcardial perfusion performed with 0.025% heparin in PBS. Mice were decapitated immediately posterior to the occipital bone, and overlying skin and muscle was removed from the skull. Meninges were peeled from the skull cap using fine forceps, and placed in ice-cold DMEM for the entirety of collection. Meninges were then digested for 15 minutes at 37 °C with constant agitation using 1 mL of pre-warmed digestion buffer (DMEM, with 2% FBS, 1 mg/mL collagenase VIII (Sigma Aldrich), and 0.5 mg/mL DNase I (Sigma Aldrich)), filtered through a 70 μm cell strainer, and neutralized with 1 mL of complete medium (DMEM with 10% FBS). An additional 2 mL of FACS buffer was added, samples were centrifuged at 400 × g for five minutes, and resuspended in FACS buffer and kept on ice. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice. Library preparation was performed with 2 μL of single cell lysates arrayed in 96-well PCR  plates.  ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods and scaled to a 5μL reaction volume. This method introduces a unique barcode upstream of the polyA tail using a modified oligo-dT primer. Briefly, 0.5μLof the Takara dilution buffer with 5% RNase inhibitor and 0.25μL of 25μM FACSseq barcode primer was added to the lysate and heated to 72 °C for 3 minutes. Then, 2.25 μL of the reverse transcription master mix was added to each well with 1 μL 5X first strand buffer, 0.125μL 100 mM DTT, 0.25 μL 20mM dNTPs, 0.25 μL, 50μM FACSseq TSO primer, 0.125 μLRNase inhibitor, and 0.5 μL SMARTscribe reverse transcriptase (Takara). The reaction was incubated at 42 °C for 90 minutes, 70 °C for 10minutes, then a 4 °C hold. All wells from the plate were then pooled and purified with Ampure XP beads (Beckman Coulter) with a 1X ratio. cDNA was eluted in 39μLwater. cDNA was amplified using 5 μL10X PCR buffer, 2 μL10mM dNTPs, 2 μL 12μM FACSseq206TSO PCR primer, 2 μL 50X Advantage 2 Polymerase (Takara). PCR conditions were 95 °C for 1 minute, 16 cycles of 95 °C for 15 seconds, 65 °C for 30 seconds, 68 °C for 6 minutes, 1 cycle of 72 °C for 10 minutes, followed by a 4 °C hold. cDNA was purified with 1.2XAmpure bead cleanup, measured with 209 Qubit  dsDNA  assay, and visualized on bioanalyzer. cDNA was fragmented using a Covaris E220 210 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 16 cycles using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NextSeq using paired end reads with 25 cycles for read 1, 7 cycles for the i7 index, and 100 cycles for the paired read. The sequencing run was performed with a custom sequencing primer for read 1 to read the 10bp barcode unique to each cell. The i7 index allows for multiple plates to be sequenced together. Read 2 contains the mRNA sequences. Two plates (S1 and S2) for each age time point were sequenced in separate sequencing runs.

value: Brain meninges

tag: age

value: 20-24 months

value: Lymphatic endothelial cells

tag: genotype

tag: gender

value: male


title: HL-60_ATRA_replicate3

value: ATRA


title: Aged S1 B2

description: RNA was isolated from 5 mice


title: HL-60_untreated_replicate3

value: untreated


title: COL_ABX_LD1212_2


title: COL_ABX_LD168_1


title: COL_ABX_LD1212_3


title: JEJ_CD_LD024_1

source_name: Jejunum epithelium

value: Jejunum epithelium

value: chow diet


title: HL-60_GSK343_replicate3


title: Aged S1 B1

description: RNA was isolated from 5 mice


title: COL_ABX_LD816_3


title: COL_ABX_LD816_2


title: HL-60_GSK343+ATRA_replicate3


title: COL_ABX_LD816_1


title: HL-60_HKMTI-1-005_replicate3


title: Aged S1 A12

description: RNA was isolated from 5 mice


title: COL_ABX_LD024_1


title: Aged S1 A11

description: RNA was isolated from 5 mice


title: COL_ABX_LD024_2


title: HL-60_HKMTI-1-005+ATRA_replicate3


title: COL_CD_LD240_3


title: Aged S1 A9

description: RNA was isolated from 5 mice


title: COL_CD_LD240_2


title: COL_CD_LD168_3


title: HL-60_GSK343+ATRA_replicate2


title: Aged S1 A8

description: RNA was isolated from 5 mice


title: COL_ABX_LD1212_1


title: HL-60_HKMTI-1-005+ATRA_replicate2


title: COL_CD_LD168_2


title: Aged S1 A10

description: RNA was isolated from 5 mice


title: HL-60_ATRA_replicate2


title: COL_CD_LD168_1


title: COL_CD_LD1212_3


title: Aged S1 A7

description: RNA was isolated from 5 mice


title: COL_ABX_LD024_3


title: COL_CD_LD1212_2


title: HL-60_GSK343_replicate2


title: COL_CD_LD1212_1


title: Aged S1 A6

description: RNA was isolated from 5 mice


title: HL-60_HKMTI-1-005_replicate2


title: Aged S1 A5

description: RNA was isolated from 5 mice


title: COL_CD_LD816_3


title: COL_CD_LD240_1


title: HL-60_HKMTI-1-005+ATRA_replicate1


title: HL-60_untreated_replicate2


title: COL_CD_LD816_1


title: COL_CD_LD024_3


title: HL-60_GSK343+ATRA_replicate1


title: Aged S1 A2

description: RNA was isolated from 5 mice


title: COL_CD_LD024_1


title: Aged S1 A1

description: RNA was isolated from 5 mice


title: HL-60_EZH2_KD_shEZH2#2+ATRA_replicate2


title: ILE_CD_LD240_2

source_name: Ileum epithelium

value: Ileum epithelium


title: ILE_CD_LD240_1


title: COL_CD_LD816_2


title: ILE_CD_LD168_3


title: ILE_CD_LD1212_3


title: HL-60_HKMTI-1-005_replicate1


title: ILE_CD_LD168_2


title: ILE_CD_LD168_1


title: Vehicle Sample 2

description: RNA isolated from in vitro cell cultures

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Assembly: mm10
Supplementary files format and content: gzipped CSV table of gene counts

extract_protocol: C57BL/6 mouse primary lymphatic endothelial cells were purchased from Cell Biologics. Cells were maintained in T25 tissue culture flasks with gelatin-based coating solution (Cell Biologics) and Complete Human Endothelial Cell Medium (Cell Biologics). Cells were passaged with Trypsin/EDTA 0.25% Solution (Cell Biolgics) and plated at 15,000 cells/cm2 surface area in coated 6 well plates or 6 well chamber slides. Cells were grown ~72-96 hours until a confluent monolayer was formed. At completion, RNA was extracted using the RNAqueous™-Micro Total RNA Isolation Kit and DNAase performed using the Invitrogen Ambion TURBO DNA free Kit. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Lympathic endothelial cells

value: sterile PBS


title: HL-60_untreated_replicate1


title: Vehicle Sample 3


title: HL-60_ATRA_replicate1


title: COL_CD_LD024_2


title: ILE_CD_LD816_3


title: ILE_CD_LD240_3


title: ILE_CD_LD1212_2


title: Aged S1 A4

description: RNA was isolated from 5 mice


title: Vehicle Sample 1


title: ILE_CD_LD816_1


title: ILE_CD_LD024_3


title: IFN Sample 2

value: mouse IFNy (5 ng/mL; R&D Systems)


title: IFN Sample 3


title: ptid3-paxgene-Post.infection-118DaysAfterHiv

city: Seattle

first: Romel

middle: D

last: Mackelprang

state: WA

address: 1959 NE Pacific Street  Box 356460

institute: University of Washington

description:
PAXgene Sample
Array_5727946085_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with the limma package in R

source_name: Paxgene from PTID3 at 118 days after HIV-1 infection

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment. Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system. With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: Gene expression microarrays were undertaken using whole blood samples.

tag: individual

value: PTID 3

tag: group

tag: time

value: 118 days after infection

tag: infection

value: whole blood


title: ptid3-paxgene-Post.infection-17DaysAfterHiv

description:
PAXgene Sample
Array_5727946085_H

source_name: Paxgene from PTID3 at 17 days after HIV-1 infection

value: 17 days after infection


title: ptid2-paxgene-Post.infection-218DaysAfterHiv

description:
PAXgene Sample
Array_5727946085_J

source_name: Paxgene from PTID2 at 218 days after HIV-1 infection

value: PTID 2

value: 218.5 days after infection


title: HL-60_GSK343_replicate1

value: Acute myeloid leukaemia


title: ILE_CD_LD024_2


title: ILE_CD_LD024_1


title: iWAT_CD_LD168_3

source_name: Inguinal white adipose tissue

value: Inguinal white adipose tissue


title: iWAT_CD_LD240_2


title: ILE_CD_LD816_2


title: IFN Sample 1

value: Brain meninges

value: male


title: Heart_old_GEX

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
GEX library
Heart_Aging.Robj

library_source: transcriptomic single cell

data_processing:
The sequencing data was processed using CellRanger software (version 3.1.0).
Assembly: mm10 for GEX and GRCm38 for V(D)J
Supplementary files format and content: tsv; gene barcode matrices and feature barcode matrix
Supplementary files format and content: csv; clonotypes and contigs

molecule: polyA RNA

source_name: Heart

extract_protocol:
Heart and medistinal lymph nodes were collected from mice from the different age groups and all tissues were kept in HBSS/BSA 0.5% at 4°C until processing. Heart samples were digested in collagenase II 1000U/mL and dispase II 1.2U/ml for 45 minutes, at 37ºC. After digestion, both tissues were grinded through a 30um mesh and seeded in a plate for FACS staining. Each condition was stained with a different Hashtag TotalSeq-C antibodies to enable multiplexing. Gating strategy is defined in the supplemental methods. After sorting, cells were combined at different ratios for single cell RNA sequencing application.
Cells were loaded in the 10X Genomics Chromium with the aim of recovering 8,000 cells. Libraries were generated with the Chromium Next GEM Single Cell 3’ Reagents Kit v3 Chemistry according to manufacturer ´s instructions.

value: Heart

value: Lymphocyte

tag: cell subtype

value: non-cardiomyocytes

value: Aging

value: 18 months


title: iWAT_CD_LD168_1

value: chow diet


title: iWAT_CD_LD240_3


title: Aged S1 A3

description: RNA was isolated from 5 mice

value: 20-24 months

value: Lymphatic endothelial cells


title: ptid5-paxgene-Post.infection-140DaysAfterHiv

description:
PAXgene Sample
Array_5727946085_C

source_name: Paxgene from PTID5 at 140 days after HIV-1 infection

value: PTID 5

value: 140.5 days after infection


title: iWAT_CD_LD1212_3


title: iWAT_CD_LD240_1


title: ptid3-paxgene-Post.infection-107DaysAfterHiv

description:
PAXgene Sample
Array_5727946085_A

source_name: Paxgene from PTID3 at 107 days after HIV-1 infection

value: PTID 3

value: 107 days after infection

value: whole blood


title: ptid12-paxgene-Post.infection-278DaysAfterHiv

description:
PAXgene Sample
Array_5727946085_E

source_name: Paxgene from PTID12 at 278 days after HIV-1 infection

value: PTID 12

value: 278 days after infection


title: iWAT_CD_LD168_2

value: Inguinal white adipose tissue


title: Tcells_LN_FB

description:
FB library (feature barcoding)
The file Supplemental table I.xlsx contains the age associated with each Hashtag
LN_T_cells_Aging_Productive_TCRs.Robj
LN_T_cells_Aging.Robj

source_name: MedLN

extract_protocol:
Heart and medistinal lymph nodes were collected from mice from the different age groups and all tissues were kept in HBSS/BSA 0.5% at 4°C until processing. Heart samples were digested in collagenase II 1000U/mL and dispase II 1.2U/ml for 45 minutes, at 37ºC. After digestion, both tissues were grinded through a 30um mesh and seeded in a plate for FACS staining. Each condition was stained with a different Hashtag TotalSeq-C antibodies to enable multiplexing. Gating strategy is defined in the supplemental methods. After sorting, cells were combined at different ratios for single cell RNA sequencing application.
Cells were loaded in the 10X Genomics Chromium with the aim of recovering 12,000 cells. Libraries were generated with the Chromium Next GEM Single Cell 5’ Reagents Kit v2 Chemistry according to manufacturer ´s instructions.

value: MedLN

value: CD4+ and CD8+ T-cells

value: multiplexed sample:2, 6, 12, 18 months


title: ptid8-paxgene-Post.infection-112DaysAfterHiv

description:
PAXgene Sample
Array_5727946076_L

source_name: Paxgene from PTID8 at 112 days after HIV-1 infection

value: PTID 8

value: 112 days after infection


title: iWAT_CD_LD1212_2


title: Tcells_LN_VDJ

description:
VDJ library
The file Supplemental table I.xlsx contains the age associated with each Hashtag
LN_T_cells_Aging_Productive_TCRs.Robj

data_processing:
The sequencing data was processed using CellRanger software (version 3.1.0).
Assembly: mm10 for GEX and GRCm38 for V(D)J
Supplementary files format and content: tsv; gene barcode matrices and feature barcode matrix
Supplementary files format and content: csv; clonotypes and contigs
Library strategy: VDJ-seq

value: Lymphocyte

value: Aging


title: iWAT_CD_LD1212_1

value: chow diet


title: Tcells_LN_GEX

description:
GEX library
The file Supplemental table I.xlsx contains the age associated with each Hashtag
LN_T_cells_Aging_Productive_TCRs.Robj
LN_T_cells_Aging.Robj


title: iWAT_CD_LD816_2


title: iWAT_CD_LD816_3


title: Heart_young_GEX

description:
GEX library
Heart_Aging.Robj

value: Heart

value: non-cardiomyocytes

value: 2 months


title: ptid1-paxgene-Pre.infection-124DaysBeforeHiv

description:
PAXgene Sample
Array_5727946076_K

source_name: Paxgene from PTID1 at 124 days before HIV-1 infection

value: PTID 1

value: -124 days after infection


title: iWAT_CD_LD816_1


title: sciPlex_4

city: New York

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

state: NY

department: Biomedical Engineering

institute: Columbia University

description: sci-Plex combinatorial chemical genomic profiling of A172, T98G and U87MG cells exposed to small molecules targeting diverse cellular pathways predicted to modulate an adaptive resistance program. Specifically, Alectinib, AZ628, AZD7762, BI-D1870, BM3-345541, DDR1-IN-1, Doxorubicin, GSK690693, Infigratinib, KU-5933, MK-2206, Nintedanib, Nutlin-3A, Palbociclib, PHA-767491, RIPA-56, Roscovitine, Salubrinal, Temozolomide, Temsirolimus, VE-821, Volasertib or dmso vehicle control in the absence or presence of trametinib co-exposure.

data_processing:
Expression matrices, cell annotations and gene annotations were generated according to the protocol described in our manuscript as well as in Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq).
Nuclear barcodes "hash" sequences were extracted from fastq files if the first 10 bp of read 2 match a hash from the appropriate hashSampleSheet.txt (2nd column) within a hamming distance of 2, the last column of the hashSampleSheet.txt file pertains to whether 1 or 2 hashes were used to identify a condition (only single hashes were used, associated metadata to deconvolve hash combinations can be found in the appropriate hashTable_metadata.txt file). Reads were then deduplicated by cell barcode and UMI to create a file of hash UMI counts (hashTable.out files) for each nuclear transcriptome in the  experiment. Tab-delimited columns of hashTable.out files correspond to a sample id, the cell barcode identified for that hash, a "_" delimited string with treatment metadata, an axis id for each hash (not used in these experiments), and umi counts for each hash. The first tab-delimited column of the appropriate hashSampleSheet.txt files contains metadata for the experiment divided by underscores. For sciPlexGxE_1, the first "_" delimited string corresponds to the hash plate used, and the second to the well within the hash plate, the third denotes the cell line, the fourth the CRISPR system (CRISPRi for gene knockdown and CRISPRa for overexpression), the fifth to the experiment (MMR or HPRT1 perturbation), the sixth to the dose of the drug and the seventh to the specific drug, and the last "_" string corresponds to the well format of multiwell plates. For sciPlexGxE_2, only the hash oligo was specified. Please refer to the separate hash metadata file (sciPlexGxE_2_hash_metadata.txt). For sciPlex_3, the first "_" delimited string corresponds to the hash plate used, the second to the well within the hash plate, the third denotes the cell line, the fourth to the specific drug, the fifth to the dose of the drug and the six and seventh to biological replicate. For sciPlex_4, the first "_" delimited string corresponds to the hash plate used, the second to the dose of drug, the third denotes the specific drug, the fourth the concentration of trametinib used for combinatorial exposure, and the fifth to the biological replicate. Note that the cell line was assigned based on the RT barcode during the first indexing step of combinatorial indexing RNA-seq.
Single-guide RNA (sgRNA) sequences were extracted from fastq files if a sequence contained a TGTGG at position 3-7 of read 2 and the 18 base pairs spanning position 24-42 of read 2 match a sgRNA from the appropriate gRNASampleSheet.txt (2nd column) within a hamming distance of 2, the last column of the gRNASampleSheet.txt file pertains to whether 1 or 2 sgRNAs were expected K562_hashTable_metadata.txt). Reads were then deduplicated by cell barcode and UMI to create a file of sgRNA read counts (gRNATable.out files). The first tab-delimited column of the appropriate gRNASampleSheet.txt file contains sgRNA metadata where the first “_” delimited string denotes the targeted gene, non-targeting control (NTC) or random control (radnom), and the second the sgRNA rank from Horlbeck et al. 2016 eLife 5:e19760. The second column refers to the 19 bp protospacer sequence in positions 24-42 of read 2. The full protospacer sequences can be found in the appropriate gRNA_whitelist.txt file.
Assembly: GRCh38
Supplementary files format and content: Expression matrices are output by our pipeline in matrix market exchange format and the cell and gene annotation files that accompany these files are in tsv file format.

source_name: A172, T98G and U87MG cells

growth_protocol: All cell lines were cultured in DMEM supplemented with 10% FBS and 1% penn-strep. For genetically pertrubed experiments, glioblastoma cells expressing either dCas9-KRAN or dCAS9-SunTag were transduced with a CROPseq lentiviral library targeting genes of interest or non-targeting control single-guide RNAs as described in our Methods section and McFaline-Figueroa et. al. 2019 Nature Genetics, 51, p. 1389-1398.

extract_protocol:
72 (sciPlexGxE_2,sciPlex_3,sciPlex_4) or 96 (sciPlexGxE_1) hours after drug exposure, cells were harvested following the sciPlexGxE or sci-Plex protocols as described in the methods section of our manuscript. Nuclei were isolated in-well and nuclei barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sci-RNA-seq library preparation.
Nucle were subjected tothree-level sci-RNA-seq following the protocols described in  Cao et al. 2019 Nature 566(7745) p. 496-502. For sciPlexGxE experiments, changes to protocol include the addition of a CROP-seq targeting RT primer and an enrichment PCR for the capture of sgRNA contaitnign puromycin mRNA transcripts delivered by lentiviral transdution of the CROP-seq system.

treatment_protocol: Cells were seeded at 10,000 (sciPlexGxE_1) or 25,000 (sciPlexGxE_2,sciPlex_3,sciPlex_4) cells per well in 96 well plates. 24 hours after seeding cells were exposed to increasing doeses of small molecules or dmso vehicle control.

value: A172, T98G and U87MG cells

value: Human glioblastoma brain cancer cells

value: Cells were treated with increasing doses of the small molecules Alectinib, AZ628, AZD7762, BI-D1870, BM3-345541, DDR1-IN-1, Doxorubicin, GSK690693, Infigratinib, KU-5933, MK-2206, Nintedanib, Nutlin-3A, Palbociclib, PHA-767491, RIPA-56, Roscovitine, Salubrinal, Temozolomide, Temsirolimus, VE-821, Volasertib or dmso vehicle control in the absence or presence of trametinib co-exposure.


title: iWAT_CD_LD024_3

value: Inguinal white adipose tissue


title: C3H10_Six1_rep1 [CUT&Tag]

city: Shanghai

first: Songyuan

last: Luo

address: 639 Zhi-Zao-Ju Road

institute: Shanghai Ninth People’s Hospital

library_source: genomic

data_processing:
library strategy: CUT&Tag
Raw data were trimmed from 3' end until the final base had a quality score > 30, using Trimgalore-0.4.5, discarding reads left with < 20 bp
Raw data were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS2 v2.2.7 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

growth_protocol: MEM-a, 10% fetal bovine serum, 1% penicillin/streptomycin, 1% Non-Essential Amino Acids, and 1% GlutaMAX™ Supplement. Cells were cultured at 37C at 5% CO2.

extract_protocol:
We digested adherent cultured cells with 0.25% trypsin, and 50 000 C3H10 cells per sample were used in two biological replicates.
Cleavage under targets and tagmentation (CUT and Tag) libraries were prepared by In-Situ ChIP Library Prep Kit (TD901, Vazyme, China).

value: mesenchymal stem cells

tag: chip antibody


title: ILE_CD_LD1212_1

value: Ileum epithelium


title: C3H10_Six1_rep2 [CUT&Tag]


title: ptid25-paxgene-Pre.infection-136DaysBeforeHiv

description:
PAXgene Sample
Array_5727946076_I

source_name: Paxgene from PTID25 at 136 days before HIV-1 infection

value: PTID 25

value: -136.5 days after infection

value: whole blood


title: ptid26-paxgene-Pre.infection-162DaysBeforeHiv

description:
PAXgene Sample
Array_5727946076_F

source_name: Paxgene from PTID26 at 162 days before HIV-1 infection

value: PTID 26

value: -162 days after infection


title: ptid10-paxgene-Pre.infection-32DaysBeforeHiv

description:
PAXgene Sample
Array_5727946076_J

source_name: Paxgene from PTID10 at 32 days before HIV-1 infection

value: PTID 10

value: -31.5 days after infection


title: iWAT_CD_LD024_2

value: chow diet


title: HYP_ABX_LD240_3

source_name: Hypothalamus

value: Hypothalamus

value: antibiotics infusion


title: sciPlex_3

description: sci-Plex chemical genomic profiling of GBM4, GBM8, GSC0131 and GSC0827 cells exposed to small molecules targeting the receptor tyrosine kinase pathway. Specifically, Lapatinib, Nintedanib, Trametinib, ZSTK474 or dmso vehicle control.

source_name: GBM4, GBM8, GSC0131 and GSC0827 cells

value: GBM4, GBM8, GSC0131 and GSC0827 cells

value: Cells were treated with increasing doses of the small molecules Lapatinib, Nintedanib, Trametinib, ZSTK474 or dmso vehicle control.


title: iWAT_CD_LD024_1


title: ptid9-paxgene-Pre.infection-46DaysBeforeHiv

description:
PAXgene Sample
Array_5727946076_G

source_name: Paxgene from PTID9 at 46 days before HIV-1 infection

value: PTID 9

value: -46.5 days after infection


title: E_6Mo2_2854

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

data_processing:
The sample primary processing was performed with miRMaster2 using standard parameters. As output, miRMaster generated a list with the expression of 80,668 RNAs from 10 RNA classes.
The data were normalized to expression in one million reads and further processed with R (R 4.0.4 GUI 1.74 Catalina build (7936)).
Assembly: mm10
Supplementary files format and content: sncRNA_quantification_raw.tsv: Tab-separated file of raw feature counts per sample.
Supplementary files format and content: sncRNA_quantification_rpm_norm.tsv: Tab-separated file of rpm-normalized feature counts per sample.

source_name: Blood

growth_protocol: The animals were housed in groups on wood chips as bedding in the conventional animal facility of the Institute for Clinical & Experimental Surgery (Saarland University, Homburg/Saar, Germany). They had free access to tap water and standard pellet food (Altromin, Lage, Germany) and were maintained under a controlled 12-h day/night cycle. This animal study was approved by the local State Office for Health and Consumer Protection and conducted in accordance with Directive 2010/63/EU and the NIH Guidelines for the Care and Use of Laboratory Animals (NIH Publication #85-23 Rev. 1985).

extract_protocol:
The mice were anesthetized by an intraperitoneal injection of ketamine (100 mg/kg bw; Ursotamin®; Serumwerke Bernburg, Bernburg, Germany) and xylazine (12 mg/kg bw; Rompun®; Bayer, Leverkusen, Germany). Subsequently, they were fixed on a heating pad in the supine position. After midline laparotomy, a maximal volume of blood (~700-1000 µL) was taken from the vena cava and transferred into plasma tubes (Sarstedt, Nümbrecht, Germany). The blood samples were then centrifuged at 20°C and 10.000 x g for 5 min to remove platelets, large vesicles, and cell debris; the resulting platelet-free plasma was stored at -80°C until further use. Two hundred microliters of mouse plasma was transferred to a 1 mL open-top thickwall polypropylene ultracentrifugation tube (Beckman-Coulter, USA) and diluted with 800 µL of phosphate-buffered saline to prevent the tube from collapsing in the ultracentrifuge vacuum. Samples were centrifuged for 2 h at 4°C at 100,000 x g using Type 50.4 Ti fixed-angle rotor (Beckmann-Coulter, USA). Supernatants were carefully removed, and the EV-containing pellets were resuspended in 20 µL of phosphate-buffered saline. Samples were stored at –80°C until further analyses. EV-enriched pellets further referred to as EV fractions and EV-depleted plasma referred to as the free circulating (fc) fraction were used for RNA isolation. All samples (blood from one animal corresponding to one sample) were treated separately, and no samples were pooled. EV- and fc- total RNAs were isolated semi-automated using the miRNeasy Micro kit (Qiagen, Hilden, Germany) and Qiacube isolation robot according to the manufacturer’s recommendations with the addition of 2 µL RNase-free glycogen (20 mg/mL, Invitrogen, Carlsbad, CA, USA) to facilitate RNA precipitation. For each sample, at least two replicated sequencing results were available (12- and 18-month replicates, all other time points in triplicate). The RNA concentrations of the EV- and fc-fractions were measured using a Qubit™ microRNA Assay Kit.
Isolated EV-RNA and fc-RNA samples were analyzed by Agilent small RNA chips, and 2 ng each (EV-RNA and fc RNA) was used for Illumina-compatible library preparation using the D-Plex Small RNA Kit (Diagenode, BE). The kits employ 3´-poly A tailing and template switch-based cDNA generation using unique molecular identifier (UMI)-tagged template switch oligos. After PCR amplification involving 13 cycles, libraries were purified from TBE-PAGEs. Illumina sequencing was carried out on a HiSeq2500 platform using the High Output mode for 96 cycles.

value: Blood

value: Wildtype

tag: replicate

tag: Sex

value: Female

tag: fraction

value: Plasma

tag: subfraction

value: EV-enriched

value: 6 months


title: E185_KO_1201_mb

data_processing:
The PE150 raw reads of RNA-Seq libraries were filtered by removing adaptor sequences, contamination and low-quality (phred quality < 20) reads. Reads quality was assessed using FastQC.
Sequenced reads were then mapped to the mm10 genome using STAR aligner version 2.7.3a. Reads were counted using htseq-count version 0.12.4 at the union mode.
Assembly: mm10
Supplementary files format and content: counts

source_name: skeletal and muscle tissue

growth_protocol: C3H10T1/2 mesenchymal cells were maintained in cultured in at 37◦C with 5% CO2, and were cultured in MEN-a containing 10% FBS (10099141C, Gibco™), 1% penicillin/streptomycin, 1% Non-Essential Amino Acids, and 1% GlutaMAX™ Supplement. E18.5 mouse embryonic mandibular tissue

extract_protocol:
RNA was extracted using a total RNA extraction kit (LS1040, Promega). 2 ug of total RNA was used for the construction of sequencing libraries.
The RNA sequencing library was prepared with NEBNext UltraTM RNA Library Prep Kit for Illumina and was sequenced on an Illumina novaseq6000.

value: E18.5 mouse embryonic mandibular tissue

value: skeletal and muscle tissue

tag: treatment

value: Surgical separation


title: E_6Mo1_2853

tag: strain


title: E_2Mo4_2852

tag: tissue

value: 2 months


title: E185_WT_1204_mb

value: WT


title: E_2Mo3_2851


title: JEJ_CD_LD816_1

source_name: Jejunum epithelium

value: Jejunum epithelium

tag: diets

value: chow diet


title: HYP_ABX_LD168_3

value: Hypothalamus

value: antibiotics infusion


title: ptid9-paxgene-Post.infection-144DaysAfterHiv

description:
PAXgene Sample
Array_5727946076_E

source_name: Paxgene from PTID9 at 144 days after HIV-1 infection

value: PTID 9

value: 144.5 days after infection

value: whole blood


title: E_2Mo1_2850

value: Blood

value: Wildtype

tag: age


title: E_18Mo4_2849

tag: genotype

value: Female

value: Plasma

value: 18 months


title: E185_WT_1703_mb

value: E18.5 mouse embryonic mandibular tissue


title: HYP_ABX_LD240_1


title: C3H10T1/2 cells, Six1kd_rep3

tag: cell line

tag: cell type

value: mesenchymal stem cells

value: Lentivirus infections


title: C3H10T1/2 cells, Six1kd_rep2


title: HYP_ABX_LD240_2


title: HYP_ABX_LD168_2


title: ptid4-paxgene-Pre.infection-310DaysBeforeHiv

description:
PAXgene Sample
Array_5727946076_D

source_name: Paxgene from PTID4 at 310 days before HIV-1 infection

tag: individual

value: PTID 4

tag: group

value: -309.5 days after infection


title: C3H10T1/2 cells, Six1kd_rep1


title: E_18Mo1_2848

value: EV-enriched


title: ptid4-paxgene-Post.infection-30DaysAfterHiv

description:
PAXgene Sample
Array_5727946066_K

source_name: Paxgene from PTID4 at 30 days after HIV-1 infection

tag: time

value: 29.5 days after infection

tag: infection


title: ptid1-paxgene-Pre.infection-314DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_L

source_name: Paxgene from PTID1 at 314 days before HIV-1 infection

value: PTID 1

value: -314 days after infection


title: C3H10T1/2 cells, Control_rep2

value: WT


title: HYP_ABX_LD1212_2

value: Hypothalamus

value: antibiotics infusion


title: S_8Mo4_2873

value: Blood

value: Free circulating

value: 8 months


title: HYP_ABX_LD1212_3


title: Annexin positive and PI negative sample rep5

city: Beijing

first: Zhenhua

last: Chen

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software)
Fastq reads were filtered using Trimmomatic to discard low-quality reads and trim poor-quality bases.The remaining clean reads were aligned to GRCm38 (mm10) genome. STAR with default parameter settings was used for alignment to generate  BAM files. Gene-counting tools, featureCounts were used to generate TPM(transcripts per million) gene counts per cell/sample.
Seurat R package (v4) was used for standard Single-cell RNA sequencing data analysis.
Assembly: mm10
Supplementary files format and content: Matrix table with  gene TPM for every gene and every sample; WT_all_cell_20220427.rds. rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with readRDS(“WT_all_cell_20220427.rds”). It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.

source_name: E11.5 Medial cortex

extract_protocol:
The medial cortex was dissociated at E11.5 for Single-cell RNA sequencing. And we using AnnexinV and PI co-staining protocol to sort AnnexinV positive, PI negative and AnnexinV, PI double negative cells for bulk RNA sequencing.
The Single-cell RNA sequencing libraries were prepared for sequencing following the manufacturer’s recommendations for the DNBelab C Series High-throughput Single-cell System (BGI-research). The bulk RNA sequencing libraries were applied to modify smart-seq2 protocols.

tag: sorted cells

value: Annexin positive and P1 negative

tag: development stage


title: Annexin positive and PI negative sample rep6


title: S_8Mo1_2871

value: Wildtype

tag: replicate

tag: Sex

value: Female

value: Plasma


title: ptid10-paxgene-Post.infection-420DaysAfterHiv

description:
PAXgene Sample
Array_5727946066_J

source_name: Paxgene from PTID10 at 420 days after HIV-1 infection

value: PTID 10

value: 419.5 days after infection

value: whole blood


title: ptid13-paxgene-Post.infection-502DaysAfterHiv

description:
PAXgene Sample
Array_5727946076_C

source_name: Paxgene from PTID13 at 502 days after HIV-1 infection

value: PTID 13

value: 502 days after infection


title: ptid8-paxgene-Pre.infection-74DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_I

source_name: Paxgene from PTID8 at 74 days before HIV-1 infection

value: PTID 8

value: -74 days after infection


title: HYP_ABX_LD1212_1


title: ptid10-paxgene-Post.infection-240DaysAfterHiv

description:
PAXgene Sample
Array_5727946066_H

source_name: Paxgene from PTID10 at 240 days after HIV-1 infection

value: 240.5 days after infection


title: S_8Mo3_2872

tag: fraction

tag: subfraction


title: C3H10T1/2 cells, Control_rep1

value: mesenchymal stem cells

value: WT

tag: treatment

value: Lentivirus infections


title: HYP_ABX_LD816_3

tag: strain

tag: tissue

value: Hypothalamus

value: antibiotics infusion


title: ptid23-paxgene-Pre.infection-226DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_F

source_name: Paxgene from PTID23 at 226 days before HIV-1 infection

value: PTID 23

value: -225.5 days after infection


title: HYP_ABX_LD168_1

tag: diets


title: ptid3-paxgene-Post.infection-173DaysAfterHiv

description:
PAXgene Sample
Array_5727946066_G

source_name: Paxgene from PTID3 at 173 days after HIV-1 infection

value: PTID 3

value: 173 days after infection


title: C3H10T1/2 cells, Control_rep3

tag: genotype


title: S_6Mo4_2870

value: Blood

value: Wildtype

value: Female

value: Plasma

value: Free circulating

tag: age

value: 6 months


title: E_12Mo2_2847

value: EV-enriched

value: 12 months


title: S_6Mo3_2869


title: ptid2-paxgene-Pre.infection-220DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_E

source_name: Paxgene from PTID2 at 220 days before HIV-1 infection

value: PTID 2

value: -220.5 days after infection

value: whole blood


title: Annexin and PI double negative sample rep6

value: Annexin and P1 double negative


title: HYP_ABX_LD816_2

source_name: Hypothalamus

value: Hypothalamus

value: antibiotics infusion


title: Annexin positive and PI negative sample rep4

value: Annexin positive and P1 negative


title: HYP_ABX_LD816_1


title: ptid9-paxgene-Pre.infection-232DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_D

source_name: Paxgene from PTID9 at 232 days before HIV-1 infection

value: PTID 9

value: -231.5 days after infection


title: HYP_ABX_LD024_3


title: Annexin and PI double negative sample rep5


title: HYP_ABX_LD024_2


title: S_6Mo1_2867

source_name: Blood

value: Blood


title: ptid24-paxgene-Pre.infection-182DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_B

source_name: Paxgene from PTID24 at 182 days before HIV-1 infection

value: PTID 24

value: -182 days after infection


title: Annexin positive and PI negative sample rep3


title: Annexin positive and PI negative sample rep2


title: HYP_CD_LD240_3

value: chow diet


title: S_2Mo3_4_2865

value: Wildtype

value: Female

value: Plasma

value: Free circulating

value: 2 months


title: ptid15-paxgene-Pre.infection-186DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_C

source_name: Paxgene from PTID15 at 186 days before HIV-1 infection

value: PTID 15

value: -185.5 days after infection


title: E_12Mo1_2846

value: EV-enriched

value: 12 months


title: HYP_CD_LD240_2

value: Hypothalamus


title: Annexin positive and PI negative sample rep1

value: Annexin positive and P1 negative


title: S_6Mo2_2868

value: 6 months


title: Annexin and PI double negative sample rep4

value: Annexin and P1 double negative


title: ptid17-paxgene-Pre.infection-227DaysBeforeHiv

description:
PAXgene Sample
Array_5727946066_A

source_name: Paxgene from PTID17 at 227 days before HIV-1 infection

value: PTID 17

value: -227 days after infection

value: whole blood


title: S_18Mo4_2863

value: Blood

value: 18 months


title: HYP_CD_LD240_1

value: chow diet


title: S_2Mo1_2864

value: Wildtype

value: Female

value: Plasma


title: ptid6-paxgene-Post.infection-241DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_L

source_name: Paxgene from PTID6 at 241 days after HIV-1 infection

value: PTID 6

value: 241 days after infection


title: Annexin and PI double negative sample rep3


title: ptid21-paxgene-Post.infection-42DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_J

source_name: Paxgene from PTID21 at 42 days after HIV-1 infection

value: PTID 21

value: 42 days after infection


title: S_18Mo1_2862

value: Free circulating


title: S_2Mo3_4_2866

value: 2 months


title: Annexin and PI double negative sample rep2


title: HYP_ABX_LD024_1

value: Hypothalamus

value: antibiotics infusion


title: S_12Mo2_2861

value: 12 months


title: HYP_CD_LD168_3


title: Naive.Single.Cells [10X]

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
The sample is aligned to GRCm38 transcriptome and quantified using Kallisto, Cellranger and RSEM
Assembly: GRCm38
Supplementary files format and content: gzipped abundance.tsv output from Kallisto, Cellranger and RSEM

source_name: EAE

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol and 10X Single Cell V3 as described (Trombetta et al 2014).

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: cell type

value: Whole Tissue

value: Wild Type

value: 12 weeks


title: ptid1-paxgene-Post.infection-407DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_G

source_name: Paxgene from PTID1 at 407 days after HIV-1 infection

tag: individual

value: PTID 1

value: 407 days after infection

value: whole blood


title: ptid5-paxgene-Post.infection-70DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_I

source_name: Paxgene from PTID5 at 70 days after HIV-1 infection

value: PTID 5

tag: group

value: 70.5 days after infection


title: Annexin and PI double negative sample rep1

source_name: E11.5 Medial cortex

value: Annexin and P1 double negative


title: E185_KO_1702_mb

source_name: skeletal and muscle tissue

value: E18.5 mouse embryonic mandibular tissue

value: skeletal and muscle tissue

value: Surgical separation


title: HYP_CD_LD168_2

value: chow diet


title: ptid1-paxgene-Post.infection-317DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_H

source_name: Paxgene from PTID1 at 317 days after HIV-1 infection

tag: time

value: 317 days after infection


title: HYP_CD_LD168_1

value: Hypothalamus


title: ptid3-paxgene-Pre.infection-163DaysBeforeHiv

description:
PAXgene Sample
Array_5727946064_K

source_name: Paxgene from PTID3 at 163 days before HIV-1 infection

value: PTID 3

value: -163 days after infection

tag: infection


title: EAE.Single.Cells [10X]

value: Female

value: Whole Tissue


title: S_12Mo1_2860

value: Blood

value: Wildtype

value: Plasma

value: Free circulating

value: 12 months


title: HYP_CD_LD1212_3


title: GFAP, EGFR-2, AS (4M67_TGCAGCTA_CTAGTCGA)

source_name: GFAP, EGFR-2, AS

value: Astrocytes

value: Egfr Knockout

value: 12 weeks


title: HYP_CD_LD1212_2


title: GFAP, EGFR-2, MG (4M67_TGCAGCTA_AGCTAGAA)

source_name: GFAP, EGFR-2, MG

value: Microglia


title: ptid3-paxgene-Post.infection-263DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_F

source_name: Paxgene from PTID3 at 263 days after HIV-1 infection

value: 263 days after infection

value: whole blood


title: E_8Mo3_2858

value: EV-enriched

value: 8 months


title: E_8Mo4_2859


title: E_6Mo4_2856

value: 6 months


title: GFAP, EGFR-3, AS (4M67_TCGACGTC_CTAGTCGA)

source_name: GFAP, EGFR-3, AS


title: E_8Mo1_2857

source_name: Blood


title: HYP_CD_LD816_3

source_name: Hypothalamus

value: Hypothalamus

value: chow diet


title: HYP_CD_LD816_2


title: ptid7-paxgene-Pre.infection-67DaysBeforeHiv

description:
PAXgene Sample
Array_5727946064_C

source_name: Paxgene from PTID7 at 67 days before HIV-1 infection

value: PTID 7

value: -67 days after infection


title: GFAP, EGFR-3, MG (4M67_TCGACGTC_AGCTAGAA)

source_name: GFAP, EGFR-3, MG

value: Female


title: ptid3-paxgene-Post.infection-382DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_E

source_name: Paxgene from PTID3 at 382 days after HIV-1 infection

value: PTID 3

value: 382 days after infection


title: ptid1-paxgene-Post.infection-47DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_D

source_name: Paxgene from PTID1 at 47 days after HIV-1 infection

value: PTID 1

value: 47 days after infection


title: NGT146F-gCDH1

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

country: Japan

institute: Kyushu University

data_processing:
Reads were mapped to the reference genome by HISAT2.
The resulting BAMs were input to featureCounts to generate the count table.
Genome_build: hg19
Supplementary_files_format_and_content: The tab-delimited text file contains read counts per genes.

source_name: Fundic gland

growth_protocol: hGOs were routinely generated from fragmented and digested normal gastric glands and were cultured in Matrigel with specific supplements. To manufacture genetic KO of CDH1, hGOs were transfected lentiviral vectors encoding Cas9 protein and the guideRNA sequence that was complematary to CDH1 gene. WT hGOs were transfected lentiviral vectors encoding Cas9 protein and guideRNA sequence that was not complemntary to any genes.

extract_protocol:
Total RNA was extracted from hGO cells using ISOGEN (Nippon Gene, Tokyo, Japan). NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing according to the manufacturer’s protocol.

value: Stomach - human Gastric Organoids

value: CDH1 KO


title: GFAP, Scramble-1, MG (4M67_TAGCGCTC_AGCTAGAA)

source_name: GFAP, Scramble-1, MG

value: Microglia

value: Wild Type

value: 12 weeks


title: HYP_CD_LD024_3


title: E_6Mo3_2855

value: Blood

value: Wildtype

value: Plasma

value: EV-enriched


title: NGT143F-gCDH1


title: ptid14-paxgene-Post.infection-48DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_A

source_name: Paxgene from PTID14 at 48 days after HIV-1 infection

value: PTID 14

value: 48.5 days after infection

value: whole blood


title: ptid15-paxgene-Post.infection-86DaysAfterHiv

description:
PAXgene Sample
Array_5727946064_B

source_name: Paxgene from PTID15 at 86 days after HIV-1 infection

value: PTID 15

value: 85.5 days after infection


title: HYP_CD_LD024_2

value: Hypothalamus

value: chow diet


title: HYP_CD_LD1212_1


title: CD11b, Areg-2, AS (4M67_TACGCTGC_CTAGTCGA)

source_name: CD11b, Areg-2, AS

value: Female

value: Astrocytes

value: Areg Knockout


title: ptid18-paxgene-Post.infection-408DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_J

source_name: Paxgene from PTID18 at 408 days after HIV-1 infection

value: PTID 18

value: 408 days after infection


title: NGT133F-gCDH1

value: Stomach - human Gastric Organoids

value: CDH1 KO


title: ptid2-paxgene-Post.infection-128DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_L

source_name: Paxgene from PTID2 at 128 days after HIV-1 infection

value: PTID 2

value: 128.5 days after infection


title: CD11b, Areg-2, MG (4M67_TACGCTGC_AGCTAGAA)

source_name: CD11b, Areg-2, MG

value: Microglia

value: 12 weeks


title: HYP_CD_LD024_1


title: HYP_CD_LD816_1


title: LIV_ABX_LD240_6

source_name: Liver

value: Liver

value: antibiotics infusion


title: GFAP, Scramble-1, AS (4M67_TAGCGCTC_CTAGTCGA)

source_name: GFAP, Scramble-1, AS

value: Wild Type


title: NGT133F-gEmpty

value: WT


title: ptid12-paxgene-Post.infection-453DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_I

source_name: Paxgene from PTID12 at 453 days after HIV-1 infection

value: PTID 12

value: 453 days after infection

value: whole blood


title: LIV_ABX_LD240_5


title: NGT146F-gEmpty


title: ptid8-paxgene-Post.infection-465DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_G

source_name: Paxgene from PTID8 at 465 days after HIV-1 infection

value: PTID 8

value: 465 days after infection


title: LIV_ABX_LD240_4


title: CD11b, Scramble-2, MG (4M67_GGAGCTAC_AGCTAGAA)

source_name: CD11b, Scramble-2, MG

value: Female


title: ptid16-paxgene-Post.infection-446DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_F

source_name: Paxgene from PTID16 at 446 days after HIV-1 infection

value: PTID 16

value: 446 days after infection


title: CD11b, Scramble-3, AS (4M67_GCGTAGTA_CTAGTCGA)

source_name: CD11b, Scramble-3, AS

value: Astrocytes


title: LIV_ABX_LD240_3


title: ptid11-paxgene-Post.infection-513DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_E

source_name: Paxgene from PTID11 at 513 days after HIV-1 infection

value: PTID 11

value: 513 days after infection


title: ptid11-paxgene-Post.infection-286DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_D

source_name: Paxgene from PTID11 at 286 days after HIV-1 infection

value: 286 days after infection


title: CD11b, Scramble-3, MG (4M67_GCGTAGTA_AGCTAGAA)

source_name: CD11b, Scramble-3, MG

value: Microglia

value: 12 weeks


title: LIV_ABX_LD240_1

value: Liver

value: antibiotics infusion


title: CD11b, Areg-1, MG (4M67_CGGAGCCT_AGCTAGAA)

source_name: CD11b, Areg-1, MG

value: Areg Knockout


title: CD11b, Scramble-2, AS (4M67_GGAGCTAC_CTAGTCGA)

source_name: CD11b, Scramble-2, AS

value: Wild Type


title: LIV_ABX_LD168_6


title: ptid14-paxgene-Pre.infection-184DaysBeforeHiv

description:
PAXgene Sample
Array_5727946076_B

source_name: Paxgene from PTID14 at 184 days before HIV-1 infection

value: PTID 14

value: -183.5 days after infection


title: LIV_ABX_LD168_5


title: ptid4-paxgene-Post.infection-204DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_B

source_name: Paxgene from PTID4 at 204 days after HIV-1 infection

value: PTID 4

value: 204.5 days after infection

value: whole blood


title: Normal [AN1]

city: Bengaluru

first: Kshitish

middle: K

last: Acharya

state: Karnataka

address: Electronic City Ph 1

country: India

institute: Institute of Bioinformatics and Applied Biotechnology

description:
AN1
Normal
mRNA

data_processing:
Quality check performed using FastQC, and sequence reads were trimmed for adaptor sequence/low-quality sequence using seqtk.
Read alignment and quantification performed using Kallisto (v0.43.0).
Assembly: GRCh38 (hg38)
Supplementary files format and content: *.tsv: Tab-delimited text files include TPM values for each Sample.

source_name: Testis

extract_protocol:
Testicular biopsy of azoospermic and varicocele donors collected in 'RNA later' & RNA isolated [RiboPure kit, Ambion-AM1924].
Library made with TruSeq RNA Library Prep Kit v2, & sequenced (PE70 or 100).

value: Testis

value: Male

tag: diagnosis

value: Normal

tag: biomaterial provider

value: Clontech cat. No.:636533; lot No:1105041


title: ptid22-paxgene-Post.infection-17DaysAfterHiv

description:
PAXgene Sample
Array_5727946076_H

source_name: Paxgene from PTID22 at 17 days after HIV-1 infection

value: PTID 22

value: 17 days after infection


title: Normal [CN1]

description:
CN1
Normal
mRNA

value: Clontech cat. No.:636533; lot No:LOT1105214A


title: ptid6-paxgene-Post.infection-150DaysAfterHiv

description:
PAXgene Sample
Array_5727049061_H

source_name: Paxgene from PTID6 at 150 days after HIV-1 infection

value: PTID 6

value: 150 days after infection


title: LIV_ABX_LD240_2

source_name: Liver

value: Liver

value: antibiotics infusion


title: L

city: Tokyo

first: Yasuhiro

last: Kato

state: Bunkyo Ku

address: Sendagi 1-1-5

department: Pulmonary Medicine and Oncology

institute: Nippon Medical School

description: gene expression on colorectal cancer cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on WT GeneAtlas Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChipScanner 3000 7G System.

data_processing: The data were analyzed with Genechip Expression Console Software ver.1.3.0 using Affymetrix default analysis settings and global scaling as normalization method. The scanned images were analyzed with Genechip Expression Console Software ver.1.3.0 using Affymetrix default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label: Biotin

source_name: L

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: KM12 and each resistance cell lines were cultured in RPMI-1640 (FUJIFILM, Osaka, Japan) containing 10% fetal bovine serum (FBS; Biowest, Nuaille, France) and 1% penicillin and streptomycin (FUJIFILM) at 37°C in a 5% CO2 incubator. Each resistance cell lines were incubated with 2 µM of each corresponding agent.

value: Colorectal cancer

tag: cell line

value: L


title: CD11b, Areg-1, AS (4M67_CGGAGCCT_CTAGTCGA)

source_name: CD11b, Areg-1, AS

tag: Sex

value: Female

value: Astrocytes

value: Areg Knockout

value: 12 weeks


title: KM12 parental cells.

source_name: KM12 parental cells.

value: KM12 parental cells.


title: ptid8-paxgene-Post.infection-105DaysAfterHiv

description:
PAXgene Sample
Array_5727049102_C

source_name: Paxgene from PTID8 at 105 days after HIV-1 infection

value: PTID 8

value: 105 days after infection

value: whole blood


title: KM12SR2


title: GFAP, EGFR-1, MG (4M67_CGATCAGT_AGCTAGAA)

source_name: GFAP, EGFR-1, MG

value: Microglia

value: Egfr Knockout


title: GFAP, Scramble-3, AS (4M67_CCTAAGAC_CTAGTCGA)

source_name: GFAP, Scramble-3, AS

value: Wild Type


title: ptid5-paxgene-Post.infection-382DaysAfterHiv

description:
PAXgene Sample
Array_5727049061_D

source_name: Paxgene from PTID5 at 382 days after HIV-1 infection

value: PTID 5

value: 382.5 days after infection


title: R

source_name: R

value: R


title: ptid13-paxgene-Post.infection-263DaysAfterHiv

description:
PAXgene Sample
Array_5727049061_A

source_name: Paxgene from PTID13 at 263 days after HIV-1 infection

value: PTID 13

value: 263 days after infection


title: LIV_ABX_LD168_3

value: Liver

value: antibiotics infusion


title: Varicocele [VA2]

description:
VA2
Disease
mRNA

value: Testis

value: Male

value: Varicocele


title: NGT143F-gEmpty

source_name: Fundic gland

value: Stomach - human Gastric Organoids

value: WT


title: Varicocele [VA1]

description:
VA1
Disease
mRNA


title: LIV_ABX_LD168_2


title: GFAP, EGFR-1, AS (4M67_CGATCAGT_CTAGTCGA)

source_name: GFAP, EGFR-1, AS

value: Female

value: Astrocytes

value: 12 weeks


title: LIV_ABX_LD168_4


title: CD11b, Areg-3, AS (4M67_ATGCGCAG_CTAGTCGA)

source_name: CD11b, Areg-3, AS

value: Areg Knockout


title: GFAP, Scramble-3, MG (4M67_CCTAAGAC_AGCTAGAA)

source_name: GFAP, Scramble-3, MG

value: Microglia

value: Wild Type


title: ptid6-paxgene-Post.infection-76DaysAfterHiv

description:
PAXgene Sample
Array_5727049050_I

source_name: Paxgene from PTID6 at 76 days after HIV-1 infection

value: PTID 6

value: 76 days after infection

value: whole blood


title: ptid14-paxgene-Post.infection-118DaysAfterHiv

description:
PAXgene Sample
Array_5727049050_J

source_name: Paxgene from PTID14 at 118 days after HIV-1 infection

value: PTID 14

value: 117.5 days after infection


title: CD11b, Areg-3, MG (4M67_ATGCGCAG_AGCTAGAA)

source_name: CD11b, Areg-3, MG


title: LIV_ABX_LD168_1

source_name: Liver

value: Liver

value: antibiotics infusion


title: LIV_ABX_LD1212_6


title: Obstructive azoospermia [OA1]

description:
OA1
Disease
mRNA

source_name: Testis

value: Testis

value: Male

value: Obstructive azoospermia


title: GFAP, Scramble-2, AS (4M67_ACTGAGCG_CTAGTCGA)

source_name: GFAP, Scramble-2, AS


title: Non-Obstructive Azoospermia [NOA8]

description:
NOA8
Disease
mRNA

value: Non-Obstructive Azoospermia


title: Non-Obstructive Azoospermia [NOA7]

description:
NOA7
Disease
mRNA


title: LIV_ABX_LD1212_4


title: Non-Obstructive Azoospermia [NOA6]

description:
NOA6
Disease
mRNA


title: GFAP, Scramble-2, MG (4M67_ACTGAGCG_AGCTAGAA)

source_name: GFAP, Scramble-2, MG

value: Female


title: LIV_ABX_LD1212_3


title: Obstructive azoospermia [OA2]

description:
OA2
Disease
mRNA


title: LIV_ABX_LD1212_1


title: ptid2-paxgene-Post.infection-308DaysAfterHiv

description:
PAXgene Sample
Array_5727049050_F

source_name: Paxgene from PTID2 at 308 days after HIV-1 infection

value: PTID 2

value: 308.5 days after infection


title: CD11b, Scramble-1, MG (4M67_ACTCGCTA_AGCTAGAA)

source_name: CD11b, Scramble-1, MG

value: 12 weeks


title: CD11b, Scramble-1, AS (4M67_ACTCGCTA_CTAGTCGA)

source_name: CD11b, Scramble-1, AS

value: Astrocytes


title: ST2, KO, Microglia (4OTR.ATCTCAGG_AGCTAGAA)

source_name: ST2, KO, Microglia

value: Microglia

value: ST2 Knockout


title: LIV_ABX_LD1212_5


title: ST2, KO, Microglia (4OTR.GCTCATGA_AGCTAGAA)


title: Non-Obstructive Azoospermia [NOA3]

description:
NOA3
Disease
mRNA


title: Non-Obstructive Azoospermia [NOA4]

description:
NOA4
Disease
mRNA


title: LIV_ABX_LD816_6


title: ST2, KO, Microglia (4OTR.GTAGAGGA_AGCTAGAA)


title: Non-Obstructive Azoospermia [NOA5]

description:
NOA5
Disease
mRNA


title: LIV_ABX_LD816_5


title: ST2, WT, Microglia (4OTR.AAGAGGCA_AGCTAGAA)

source_name: ST2, WT, Microglia

value: Wild Type


title: LIV_ABX_LD816_4


title: LIV_ABX_LD1212_2


title: LIV_ABX_LD816_3


title: ST2, WT, Microglia (4OTR.CGAGGCTG_AGCTAGAA)


title: LIV_ABX_LD816_2


title: ST2, KO, Astrocytes (4OTR.TAGGCATG_AGCTAGAA)

source_name: ST2, KO, Astrocytes


title: LIV_ABX_LD816_1


title: P3

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Adapters were removed using Trimmomatic-0.39
Reads were aligned to hg19 genome using STAR v2.7.2
Gene expression was quantified using Cuffnorm v2.2.1
The number of reads was summarized at the gene level using featureCounts v1.6.4
DESeq2 v1.24 was used to determine differential expression. Genes were considered to differentially expressed with a FDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Counts.txt is a tab-delimited file that includes read-counts for each sample. Fpkms.txt is a tab-delimited file includes the fpkm values for each sample

source_name: NHBE C16 P3

growth_protocol: NHBE C16 P4 cells were seeded on the apical side of transwell in airway epithelial cell (AEC) culture medium with supplement and 2% Pen/Strep and 1% AmphoterecinB. The same medium was also added on the bottom of the well (basal site). As soon cells were confluent medium form apical site was removed. On the basal site old AEC medium was replaced by Pneumacult-ALI differentiation medium with required supplement and 2% Pen/Strep and 1% AmphoterecinB. The cells were maintained for 28 days with a basal medium change every alternate day. The mucus removal by 1x DPBS washes from day 14 post-seeding, around once every four-day.

extract_protocol:
Cells were scraped out in 1xDPS from the transwell, spun 10000 rpm @4C to have cell pellet. The cell pellet was incubated with RLT + BME buffer for a minute, transfer into a Qiashredder, spun 15,000 rpm for 3 min @4C, collected the elusion and stored -80C. QIAGEN total DNA/RNA kit was used for RNA extraction including DNase treatment according to the protocol.
RNA-Seq libraries were prepared using the NEBNext Ultra II nondirectional Ribodepletion kit

treatment_protocol: RSV (A2 strain) wild-type virus prepared in Vero cells and sucrose purified. RSV infection (multiplicity of infection of 4) in the respiratory epithelium was done by incubating RSV in 1x DPBS on the apical side of the epithelium for two hours followed by 4x wash with 1xDPBS. RSV infected respiratory epithelium was kept for six days. The basal medium sample was collected up to six days post-infection and the collected amount was replaced by adding new Pneumacult-ALI medium with required supplements and 2% Pen/Strep and 1% AmphoterecinB.


title: P2

source_name: NHBE C16 P2


title: P1

source_name: NHBE C16 P1


title: P4

source_name: NHBE C16 P4


title: LIV_ABX_LD024_6


title: Mock-4

value: Mock


title: ST2, WT, Microglia (4OTR.CTCTCTAC_AGCTAGAA)


title: RSV-3

value: RSV


title: ST2, KO, Astrocytes (4OTR.GGACTCCT_AGCTAGAA)


title: LIV_ABX_LD024_4


title: RSV-2


title: LIV_ABX_LD024_3


title: LIV_ABX_LD024_5


title: ptid4-paxgene-Post.infection-110DaysAfterHiv

description:
PAXgene Sample
Array_5727049050_H

source_name: Paxgene from PTID4 at 110 days after HIV-1 infection

value: PTID 4

value: 110.5 days after infection

value: whole blood


title: Non-Obstructive Azoospermia [NOA1]

description:
NOA1
Disease
mRNA

value: Testis


title: RSV-1


title: Non-Obstructive Azoospermia [NOA2]

description:
NOA2
Disease
mRNA

value: Male


title: LIV_ABX_LD024_2

value: Liver

value: antibiotics infusion


title: ST2, WT, Astrocytes (4OTR.TAAGGCGA_AGCTAGAA)

source_name: ST2, WT, Astrocytes

value: Female


title: ST2, WT, Astrocytes (4OTR.AGGCAGAA_AGCTAGAA)


title: ST2, KO, Astrocytes (4OTR.TCCTGAGC_AGCTAGAA)


title: ST2, WT, Astrocytes (4OTR.CGTACTAG_AGCTAGAA)


title: Mock-3


title: IL33, KO, Microglia (4OTR.ATCTCAGG_CTAGTCGA)

source_name: IL33, KO, Microglia

value: IL33 Knockout


title: LIV_ABX_LD024_1

source_name: Liver


title: IL33, KO, Microglia (4OTR.GCTCATGA_CTAGTCGA)


title: ptid5-paxgene-Pre.infection-42DaysBeforeHiv

description:
PAXgene Sample
Array_5719680052_L

source_name: Paxgene from PTID5 at 42 days before HIV-1 infection

value: PTID 5

value: -41.5 days after infection


title: Mock-2


title: ptid19-paxgene-Post.infection-17DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_J

source_name: Paxgene from PTID19 at 17 days after HIV-1 infection

value: PTID 19

value: 17 days after infection


title: ptid15-paxgene-Post.infection-52DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_E

source_name: Paxgene from PTID15 at 52 days after HIV-1 infection

value: PTID 15

value: 52.5 days after infection


title: ptid6-paxgene-Post.infection-419DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_G

source_name: Paxgene from PTID6 at 419 days after HIV-1 infection

value: PTID 6

value: 419 days after infection


title: LIV_CD_LD240_6

value: chow diet


title: ptid5-paxgene-Post.infection-294DaysAfterHiv

description:
PAXgene Sample
Array_5727049050_C

source_name: Paxgene from PTID5 at 294 days after HIV-1 infection

value: 293.5 days after infection


title: IL33, KO, Microglia (4OTR.GTAGAGGA_CTAGTCGA)

value: Microglia

value: 12 weeks


title: ptid16-paxgene-Pre.infection-261DaysBeforeHiv

description:
PAXgene Sample
Array_5719680052_A

source_name: Paxgene from PTID16 at 261 days before HIV-1 infection

value: PTID 16

value: -261 days after infection

value: whole blood


title: ptid11-paxgene-Post.infection-17DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_K

source_name: Paxgene from PTID11 at 17 days after HIV-1 infection

value: PTID 11


title: ptid14-paxgene-Post.infection-34DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_D

source_name: Paxgene from PTID14 at 34 days after HIV-1 infection

value: PTID 14

value: 34.5 days after infection


title: ptid2-paxgene-Pre.infection-38DaysBeforeHiv

description:
PAXgene Sample
Array_5719680025_L

source_name: Paxgene from PTID2 at 38 days before HIV-1 infection

value: PTID 2

value: -38.5 days after infection


title: Mock-1

value: Mock


title: ptid9-paxgene-Post.infection-60DaysAfterHiv

description:
PAXgene Sample
Array_5727049050_D

source_name: Paxgene from PTID9 at 60 days after HIV-1 infection

value: PTID 9

value: 60.5 days after infection


title: ptid7-paxgene-Post.infection-501DaysAfterHiv

description:
PAXgene Sample
Array_5727049050_B

source_name: Paxgene from PTID7 at 501 days after HIV-1 infection

value: PTID 7

value: 501 days after infection


title: ptid7-paxgene-Post.infection-154DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_H

source_name: Paxgene from PTID7 at 154 days after HIV-1 infection

value: 154 days after infection


title: ptid2-paxgene-Post.infection-56DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_C

source_name: Paxgene from PTID2 at 56 days after HIV-1 infection

value: 56.5 days after infection


title: IL33, WT, Microglia (4OTR.AAGAGGCA_CTAGTCGA)

source_name: IL33, WT, Microglia

value: Female

value: Microglia

value: Wild Type


title: ptid2-paxgene-Post.infection-398DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_I

source_name: Paxgene from PTID2 at 398 days after HIV-1 infection

value: 398.5 days after infection


title: LIV_CD_LD240_5

value: Liver

value: chow diet


title: LIV_CD_LD240_4


title: ptid8-paxgene-Post.infection-285DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_I

source_name: Paxgene from PTID8 at 285 days after HIV-1 infection

value: PTID 8

value: 285 days after infection

value: whole blood


title: ptid4-paxgene-Post.infection-42DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_K

source_name: Paxgene from PTID4 at 42 days after HIV-1 infection

value: PTID 4

value: 42.5 days after infection


title: sciPlexGxE_1

description: sci-Plex-GxE combined chemical and genetic profiling of A172 dCas9-KRAB cells genetically perturbed for HPRT1 or mismtach repair genes exposed to 6-thioguanine and temozolomide, respectively, and A172 dCas9-SunTag cells genetically perturbed for HPRT1 exposed to 6-thioguanine.

source_name: A172 cells

value: A172 cells

value: Human glioblastoma brain cancer cells expressing dCas9-KRAB or dCas9-SunTag and further transduced to express single-guide RNAs against HPRT1, mismatch repair genes or non-targeting control single-guide RNAs.

value: Cells were treated with increasing doses of 6-thioguanine, Temozolomide or dmso vehicle control.


title: ptid5-paxgene-Post.infection-232DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_J

source_name: Paxgene from PTID5 at 232 days after HIV-1 infection

value: PTID 5

value: 231.5 days after infection


title: LIV_CD_LD240_3

source_name: Liver


title: IL33, WT, Microglia (4OTR.CTCTCTAC_CTAGTCGA)

value: 12 weeks


title: IL33, WT, Microglia (4OTR.CGAGGCTG_CTAGTCGA)

value: Female


title: ptid13-paxgene-Post.infection-131DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_B

source_name: Paxgene from PTID13 at 131 days after HIV-1 infection

value: PTID 13

value: 131 days after infection


title: ptid12-paxgene-Post.infection-17DaysAfterHiv

description:
PAXgene Sample
Array_5719680052_F

source_name: Paxgene from PTID12 at 17 days after HIV-1 infection

value: PTID 12

value: 17 days after infection


title: LIV_CD_LD240_2

value: Liver

value: chow diet


title: IL33, KO, Astrocytes (4OTR.TAGGCATG_CTAGTCGA)

source_name: IL33, KO, Astrocytes

value: Astrocytes

value: IL33 Knockout


title: LIV_CD_LD240_1


title: Sperm_ChIP_H3K27me3_DTT

first: Qiangzong

last: Yin

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

data_processing:
Paired-end reads were trimmed using Trim Galore (version 0.4.5), followed by reads alignment to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 700 no-mixed no-discordant.
PCR duplicates were removed using “MarkDuplicates” from Picard Tools (version 2.8.0) (https://broadinstitute.github.io/picard/). Only non-PCR duplicates and uniquely aligned reads (alignment records without “XS” tag) were used for downstream analyses.
The RPKM values for each 100-bp bin were calculated following the formula “read counts/((bin_length/1000) × (total_reads/106))
Peak calling for H3K4me3 and H3K27me3 datasets were done by MACS2 with parameters: --nolambda --nomodel, and --broad-cutoff 0.1 ---nolambda --nomodel, respectively.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Sperm

extract_protocol:
Sperm were first fixed with 1% formaldehyde in PBS for 10 min at room temperature, followed by quenching with Glycine. Next, sperm were pre-treated with 50 mM DTT and 1 mg/ml heparin at 37°C for 2 hr. Sperm were then quenched with NEM and washed with PBS twice.  After lysing sperm in complete buffer containing detergent, equal volume of 2x RIPA buffer was supplied to make a 1x RIPA condition. Chromatin shearing was performed using Covaris S220 platform with parameters: peak power 140 W, duty factor 5% and 200 Cycles/burst for a total of 30 min. Sonicated sperm chromatin were directly subjected to immunoprecipitation with corresponding antibodies
Library preparation was carried out using NEBNext Ultra II DNA Library Prep kit (NEB E7645)

value: DTT

value: Sperm

value: WT

tag: chip antibody

value: H3K27me3:Diagenode, C15410195


title: IL33, KO, Astrocytes (4OTR.GGACTCCT_CTAGTCGA)


title: Sperm_ChIP_H3K4me3_DTT

value: H3K4me3:Diagenode, C15410003


title: ptid10-paxgene-Post.infection-94DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_H

source_name: Paxgene from PTID10 at 94 days after HIV-1 infection

value: PTID 10

value: 93.5 days after infection

value: whole blood


title: IL33, KO, Astrocytes (4OTR.TCCTGAGC_CTAGTCGA)

value: Female

value: 12 weeks


title: ptid11-paxgene-Post.infection-121DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_G

source_name: Paxgene from PTID11 at 121 days after HIV-1 infection

value: PTID 11

value: 121 days after infection


title: Sperm_ChIP_H3K27me3_DNaseDTT

value: DNaseDTT


title: LIV_CD_LD168_6

data_processing:
Briefly, the Fastp software (v0.23.1) was firstly used to perform quality control on the raw data and obtain clean data. Then, the HISAT2 software (v2.1.0) was used to align the obtained clean data referred to the latest reference genome in mouse (GRCm39). After that, the Samtools software (v.1.10) was used to sort and convert the SAM files to BAM format, and finally, the Stringtie software (v2.2.1) was used to assemble and quantify the transcripts and genes based on read counts.
Assembly: GRCm39
Supplementary files format and content: a excel file named "RNA_Seq_processed_data" of raw counts  for each sample

extract_protocol:
Total RNA  was extracted and purified using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) for transcriptomic sequencing
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Liver


title: ptid7-paxgene-Post.infection-322DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_F

source_name: Paxgene from PTID7 at 322 days after HIV-1 infection

value: PTID 7

value: 322 days after infection


title: Sperm_ChIP_CTCF_DTT

value: CTCF:Millipore 07-792


title: IL33, WT, Astrocytes (4OTR.AGGCAGAA_CTAGTCGA)

source_name: IL33, WT, Astrocytes

value: Astrocytes

value: Wild Type


title: LIV_CD_LD168_5

value: chow diet


title: ptid1-paxgene-Post.infection-61DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_E

source_name: Paxgene from PTID1 at 61 days after HIV-1 infection

value: PTID 1

value: 61 days after infection


title: Sperm_ChIP_H3K4me3_DNaseDTT

value: Sperm

value: WT

value: H3K4me3:Diagenode, C15410003


title: Sperm_ChIP_CTCF_DNaseDTT


title: LIV_CD_LD168_4


title: IL33, WT, Astrocytes (4OTR.CGTACTAG_CTAGTCGA)

value: Female


title: LIV_CD_LD168_3


title: ptid13-paxgene-Post.infection-17DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_D

source_name: Paxgene from PTID13 at 17 days after HIV-1 infection

value: PTID 13

value: 17 days after infection

value: whole blood


title: ptid17-paxgene-Post.infection-477DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_B

source_name: Paxgene from PTID17 at 477 days after HIV-1 infection

value: PTID 17

value: 477 days after infection


title: LIV_CD_LD168_2

value: Liver


title: ptid6-paxgene-Pre.infection-45DaysBeforeHiv

description:
PAXgene Sample
Array_5719680025_C

source_name: Paxgene from PTID6 at 45 days before HIV-1 infection

value: PTID 6

value: -45 days after infection


title: Sperm_ATAC_DNaseβME

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_DNasebetaME.bw

data_processing:
Paired-end ATAC-seq reads were adapter-trimmed and aligned to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 2000 no-mixed no-discordant.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. MACS2 (Zhang et al. 2008) was used for peak calling with parameters: --nolambda --nomodel.
Reads with insert size larger than 150 bp were separated and used for nucleosome positioning analysis.
TSS enrichment analysis was done using Homer annotatePeaks (Heinz et al. 2010)
Assembly: mm10
Supplementary files format and content: bigWig

source_name: DNaseβME

extract_protocol:
About 100,000 sperm were on-ice lysed with hypotonic lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin) for 10 min.
Sperm were then resuspended in Tagmentation buffer (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF, 0.05% Digitonin) and tagmentation was conducted by adding Tn5 transposase (Diagenode, C01070012) at 1:20 and incubated at 37C for 30min. Reaction was stopped by SDS and proteinase K and incubated at 55°C  overnight. SDS was quenched by tween-20 and library amplification was done with 1x NEBNext High-Fidelity PCR Master Mix containing 0.5 mM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 3 min; and 14 cycles at 98°C for 15 s, 63°C for 30 s, and 72°C for 1 min.

value: DNaseβME


title: AC_O157_3

city: Changchun

first: Xue-song

last: Li

address: Xincheng Street No. 2888

institute: Jilin Agricultural University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementar /Trimmomatic).Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameters
Supplementary files format and content: tab-delimited text files include abundance values for each Sample

organism: Escherichia coli

source_name: bacterial culture

growth_protocol: E. coli O157 was cultured in Luria-Bertani (LB) liquid medium under aerobic condition at 37 ℃.

extract_protocol: Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed usingDNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0,>10μg) is used to construct sequencing

treatment_protocol: The strain E.coli O157 was cultured overnight and added 1% citric acid for 6 hours. After the citric acid was removed by centrifugation, the strain was suspended overnight.

value: bacterial culture

value: Continuous passage induction of citric acid


title: LIV_CD_LD168_1

value: chow diet


title: ptid7-paxgene-Post.infection-142DaysAfterHiv

description:
PAXgene Sample
Array_5706504045_K

data_processing: The data were normalized using quantile normalization with the limma package in R

source_name: Paxgene from PTID7 at 142 days after HIV-1 infection

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment. Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system. With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

value: PTID 7

value: 142 days after infection


title: AC_O157_2


title: Sperm_ATAC_DNaseTCEP

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_DNaseTCEP.bw

source_name: DNaseTCEP

value: DNaseTCEP

value: Sperm

value: WT


title: AC_O157_1


title: Sperm_ATAC_DNaseDTT_rep2

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_DNaseDTT.bw

source_name: DNaseDTT

value: DNaseDTT


title: LIV_CD_LD1212_5

source_name: Liver


title: Sperm_ATAC_Untreated_Prep3

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_Untreated_Prep3.bw

source_name: Untreated

value: Untreated


title: O157_3


title: LIV_CD_LD1212_4


title: Sperm_ATAC_DNaseDTT_rep1


title: Sperm_ATAC_DTT_rep2

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_DTT.bw

source_name: DTT

value: DTT


title: O157_2


title: Sperm_ATAC_Untreated_Prep2

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_Untreated_Prep2.bw


title: Δsir2, Charcoal, Rep3

city: Seville

first: Blanca

last: Navarrete

state: Seville

address: Ctra. de Utrera, Km 1

department: Genetic

country: Spain

institute: Pablo de Olavide University (UPO)

data_processing:
Sequence reads were trimmed removing adaptor sequences, contamination (reads in which unknown bases are more than 10%), and low-quality reads (the percentage of low quality bases is over 50%) from raw reads
Trimmed sequence reads were mapped to U. maydis genome using HISAT2 and reads from infected plant tissues were previously filtered against the annotated maize genome
Reads were counted for U. maydis using the HTseq tool in the Galaxy platform.
For expression analysis, only uniquely mapping exon read counts were considered. Pairwise comparisons were performed using the R package DESeq2 (Love et al., 2014)
Assembly: Ustilago maydis (p3_t237631_Ust_maydi_v2GB)
Supplementary files format and content: Raw Count data table contains the read counts from Htseq

organism: Mycosarcoma maydis

growth_protocol: For axenic growth, cells from exponential culture in YEPSL medium were collected. For filament-formation conditions, cells incubated in PD-Charcoal plates for 18 hours were harvested. Cells from infected leave were harvested by excising 2–3 cm segments from below the injection hole.

extract_protocol:
All the samples were ground into a powder using a mortar/pestle under liquid nitrogen. Total RNA was purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and the Direct-zol RNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA).
RNA libraries for RNA-seq were performed by BGI TECH SOLUTIONS (HONGKONG) CO., LIMITED

value: PD-Charcoal plates


title: ptid9-paxgene-Post.infection-46DaysAfterHiv

description:
PAXgene Sample
Array_5706504045_J

source_name: Paxgene from PTID9 at 46 days after HIV-1 infection

value: PTID 9

value: 46.5 days after infection

value: whole blood


title: LIV_CD_LD1212_3

value: Liver


title: IL33, WT, Astrocytes (4OTR.TAAGGCGA_CTAGTCGA)

value: Female

value: Astrocytes

value: Wild Type

value: 12 weeks


title: LIV_CD_LD1212_6

value: chow diet


title: Sperm_ATAC_DTT_rep1


title: O157_1

value: bacterial culture


title: Δsir2, Charcoal, Rep2


title: LIV_CD_LD1212_2


title: Sperm_ATAC_DNase_rep2

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_DNase.bw

source_name: DNase

value: DNase


title: Zbtb14_WGBS_clone3

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

data_processing:
RNA-seq data: Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.3.0) and visualized in IGV (Thorvaldsdottir et al., 2013) (v2.8.9).
CRISPR Screen : The sgRNA distribution and enrichment at different time points were analyzed with the MAGeCK workflow (Doench et al, 2016)
ChIP-seq data : FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters:ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) in --local mode. Following alignment, Picard (v2.23.4) CleanSam, SamFormatConverter, SortSam and Markduplicates were used to generate a duplicate-marked bam file. The resulting bam files were converted to bigwig using deeptools (v3.3.0) Bamcoverage and options –ignoreDuplicates –normalizeUsing CPM –minMappingQuality 10 –ignoreForNormalization chrX chrY chrM.
WGBS data : As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: mm10
Supplementary files format and content: All processed files are in bigWig format. RNA-seq: genomic coverage counts, WGBS: percent methylation over CpGs covered by at least 5 reads, ChIP-seq/CUT&RUN-seq: signal coverage

extract_protocol:
Genomic DNA was extracted from the cells with QIAmp DNA Mini kit (Qiagen), according to the manufacturer’s instructions.
The library preparation for WGBS was performed with the tPBAT protocol described previously (Miura 2012, Miura 2019; NAR). One hundred nanograms of genomic DNA spiked with 1% (w/w) of unmethylated lambda DNA (Promega, Madison, WI) was served for the library preparation. The sequencing was performed by Macrogen Japan Inc. (Tokyo, Japan) using the HiSeq X Ten system.

value: mouse embryonic stem cells

value: Zbtb14 KO


title: Δsir2, Charcoal, Rep1


title: Zbtb14_WGBS_clone2


title: LIV_CD_LD1212_1

first: Yongkang

last: Zhen

institute: Yangzhou University


title: Sperm_ATAC_DNase_rep1

value: Sperm

value: WT


title: LIV_CD_LD816_6


title: WT, Charcoal, Rep3


title: Zbtb14_WGBS_clone1


title: LIV_CD_LD816_4


title: Spop_WGBS_clone3

value: Spop KO


title: WT, Charcoal, Rep1

value: PD-Charcoal plates


title: Sperm_ATAC_Untreated_rep4

description:
Tn5 transposase (Diagenode, C01070012)
Sperm_ATAC_Untreated.bw

value: Untreated


title: Spop_WGBS_clone2


title: Sperm_ATAC_Untreated_rep2


title: LIV_CD_LD816_5


title: Sperm_ATAC_Untreated_rep3


title: Δsir2, Axenic, Rep2

value: Axenic growth


title: Spop_WGBS_clone1


title: LIV_CD_LD816_2


title: LIV_CD_LD816_3


title: Δsir2, Axenic, Rep1


title: Mcm3ap_WGBS_clone3

value: Mcm3ap KO


title: WT, Axenic, Rep2


title: Sperm_CUTandRUN_H3K4me3_Untreated

data_processing:
Paired-end reads were trimmed using Trim Galore (version 0.4.5), followed by reads alignment to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 700 no-mixed no-discordant.
PCR duplicates were removed using “MarkDuplicates” from Picard Tools (version 2.8.0) (https://broadinstitute.github.io/picard/). Only non-PCR duplicates and uniquely aligned reads (alignment records without “XS” tag) were used for downstream analyses.
The RPKM values for each 100-bp bin were calculated following the formula “read counts/((bin_length/1000) × (total_reads/106))
Peak calling for H3K4me3 and H3K27me3 datasets were done by MACS2 with parameters: --nolambda --nomodel, and --broad-cutoff 0.1 ---nolambda --nomodel, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Sperm

extract_protocol:
0.1% NP40, 0.1% Tween-20, and 0.05% digitonin was used in the antibody incubation buffer and wash buffer, and SPRI beads were used for DNA extraction after proteinase K treatment.
Library preparation was carried out using NEBNext Ultra II DNA Library Prep kit (NEB E7645)

tag: antibody

value: H3K4me3:Diagenode, C15410003


title: Sperm_CUTandRUN_H3K4me3_DTT

tag: treatment

value: DTT


title: WT, Charcoal, Rep2


title: Mcm3ap_WGBS_clone2


title: WT, Axenic, Rep1


title: LIV_CD_LD816_1

tag: strain

value: Liver


title: Mcm3ap_WGBS_clone1


title: LIV_CD_LD024_6

tag: tissue


title: Kdm5c_WGBS_clone3

value: Kdm5c KO


title: LIV_CD_LD024_4

tag: diets


title: Sperm_ATAC_Untreated_rep1

tag: genotype


title: LIV_CD_LD024_5


title: Sperm_CUTandRUN_H3K4me3_Dnase

value: Dnase


title: Sperm_CUTandRUN_H3K4me3_DNaseDTT

value: DNaseDTT


title: Sperm_CUTandRUN_H3K27me3_Untreated

value: H3K27me3:Diagenode, C15410195


title: ptid6-paxgene-Post.infection-314DaysAfterHiv

description:
PAXgene Sample
Array_5706504045_E

source_name: Paxgene from PTID6 at 314 days after HIV-1 infection

value: PTID 6

value: 314 days after infection

value: whole blood


title: ptid12-paxgene-Post.infection-121DaysAfterHiv

description:
PAXgene Sample
Array_5719680025_A

source_name: Paxgene from PTID12 at 121 days after HIV-1 infection

value: PTID 12

value: 121 days after infection


title: ptid20-paxgene-Post.infection-476DaysAfterHiv

description:
PAXgene Sample
Array_5706504045_I

source_name: Paxgene from PTID20 at 476 days after HIV-1 infection

value: PTID 20

value: 476 days after infection


title: LIV_CD_LD024_3

value: chow diet


title: Kdm5c_WGBS_clone1

value: mouse embryonic stem cells


title: ptid4-paxgene-Post.infection-384DaysAfterHiv

description:
PAXgene Sample
Array_5706504045_D

source_name: Paxgene from PTID4 at 384 days after HIV-1 infection

value: PTID 4

value: 383.5 days after infection


title: ptid1-paxgene-Post.infection-226DaysAfterHiv

description:
PAXgene Sample
Array_5706504045_C

source_name: Paxgene from PTID1 at 226 days after HIV-1 infection

value: PTID 1

value: 226 days after infection


title: HACAT_rep2

city: Barretos

first: Rhafaela

middle: Lima

last: Causin

state: SP

address: Antenor Duarte Villela, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

hyb_protocol: 3 µL of sample containing 100 ng of total RNA were used, a reporter and a capture probe were added and hybridized in the respective genes of interest, according to the manufacturer's instructions (NanoString Technologies).

scan_protocol: the cartridge containing immobilized and aligned reporter complexes were transferred to nCounter® Digital Analyzer (NanoString Technologies), with 280 fields of view. These results were tabulated in RCC (Reporter Code Count) format.

data_processing: Raw data were collected and pre-processed by nSolver™ Analysis Software v4.0 (NanoString Technologies), and further normalization and differential expression analysis were performed in the R statistical environment (R-project v3.6.3; The R Foundation, Viena, Austria). The data were normalized using the housekeeping method by the NanoStringNorm package (Bioconductor). Normalized data were log2-transformed and used as input for the differential expression analysis.

label: not provided

source_name: Immortalized human keratinocyte line - HaCaT

label_protocol: not provided

growth_protocol: HaCaT: were cultured in Dulbecco’s modified Eagle’s media (DMEM; Sigma) supplemented with 10% FBS (Thermo Fisher Scientific) at a humidified incubator with 5% CO2 at 37°C. HCB-514: were cultured in DMEM to one part Ham’s F12 media (F12; Sigma). The media was then supplemented with 1% P/S, 0.4 µg/mL hydrocortisone, 2.5 µg/mL insulin, 13 ng/mL liothyronine, 5 µg/mL transferrin, 2.5 µg/mL insulin and 0.1 µg/mL cholera enterotoxin and 5% FBS (all supplements were purchased from Sigma). Cells were maintained in a T25 flask at 37 °C, 5% CO2.

extract_protocol: Total RNA was extracted from cervical cancer cells using RecoverAll Total Nucleic Acid Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's instructions. After, the purity and concentration of total RNA were evaluated by NanoDrop Spectrophotometer v3.7 (Thermo Fisher Scientific, Waltham, MA, USA).

value: HaCaT

tag: origin

value: Derived from sampling site:Back; skin; epidermis. Cell type=Keratinocyte

value: Male

tag: age

value: 62 years


title: HACAT_rep3


title: Sperm_CUTandRUN_H3K27me3_DTT

value: DTT

tag: cell type

value: Sperm

value: WT

value: H3K27me3:Diagenode, C15410195


title: LIV_CD_LD024_2

city: Yangzhou

address: Yangzhou University

value: Liver


title: Sperm_CUTandRUN_H3K27me3_Dnase

value: DNase


title: HCB514_rep3

source_name: Cervical cancer cell line HCB-514

value: Endocervical adenocarcinoma; HPV-16 positive

value: Female

value: 30 years


title: HACAT_rep1


title: Serum_WGBS_rep1

value: mouse embryonic stem cells


title: 2i_WGBS_rep1


title: LIV_CD_LD024_1

value: chow diet


title: Sperm_CUTandRUN_H3K27me3_DNaseDTT

value: DNaseDTT


title: Kdm5c_WGBS_clone2

value: Kdm5c KO


title: HCB514_rep1


title: HCT-15-TP-2

status: Public on Mar 09 2023

first: Andrea

last: Califano

address: 1130 St. Nicholas Avenue

department: Department of Systems Biology

institute: Califano Laboratory of Systems Biology

data_processing:
Alignment of NGS with sgRNA guides was conducted using the “Biostrings” R-package (2.64.1). Essential genes for the DMSO vs T0 comparison were obtained from a generalized resource (MAGeCKFlute ), as well as a CRC-specific subset of DepMap, filtered to the 10% quantile of the gene effect. Differential expression analysis was conducted separately for each guide with the “DESeq2” R-package (1.36.0). P-values were integrated using Stouffer’s Method and corrected for multiple-testing by the Benjamini-Hochberg FDR approach.
Supplementary files format and content: Differential gene expression results of DEseq2 are provided in CSV format.
Library strategy: sgRNA-seq

growth_protocol: sgRNA containing lentiviruses were transduced into Cas9 expressing CRC cell lines (in 15cm plate-format) in quadruplicates (in presence of 8μg/ml polybrene), at an estimated MOI = 0.2   0.3. After 24h, the lentivirus containing media was removed, cells were washed with PBS, and puromycin-containing media (3μg/ml) was added to the cells for 48-96h until all control cells (not virus-infected) were dead. After this the cells were cultured for extra couple of days so that the plates reached approx. 80% confluency.

extract_protocol:
After the screen, the genomic DNA from the first and the last timepoints (DMSO & Drug perturbed) were extracted by using Blood and Cell culture DNA Maxi kits (Qiagen).
NGS library preparations were done the following way: Briefly, 40 μg of gDNA, theoretically corresponding to 6 million diploid cells, was used as PCR template in 4 parallel PCR1 reactions (10 μg template DNA each) using ExTaq DNA polymerase (Takara bio). After 18 cycles, the reactions were pooled. 2 μl of pooled PCR1 product was used as template for PCR2 which was run with qPCR with index primers and stopped before the amplification started to saturate. The resulting products of approx. 360 bp were gel purified (GeneJet), pooled together and Next generation sequenced.

treatment_protocol: At this point the cells were divided into 3 parts; 1/3 going into -80 °C as time point 1 to assess sgRNA representation baseline, 1/3 to continue to culture with DMSO and 1/3 to continue to culture with either with Linsitinib or Trametinib. Cells were always maintained at >1,500 cells per guide throughout the screens and finally harvested after 10 population doublings (the exact time (in days) for this varied for DMSO / Linsitinib / Trametinib with different cell lines) to assess gene essentiality.

value: colorectal adenocarcinoma

tag: crispr-ko

value: kinases, phosphatases, E3 ligases


title: HCT-15-TP-3

tag: time


title: HCT-15-TP-4


title: HCT-15-TRAMET-0-1-LAST-4

value: trametinib, 0.1 uM


title: HCT-15-TP-1


title: HCT-15-TRAMET-0-1-LAST-3


title: OE-MAGI2-AS3_rep1

city: Chongqing

first: Guo

last: Yang

address: 1 Youyi Road, Yuzhong District

department: Department of Urology

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions
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
HISAT2 (version 2.0.4) tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of  transcript per million fragments mapped.
Assembly: Homo_sapiens.GRCh38_release95.genome.fa
Supplementary files format and content: the processed data file contained the ID, symbol and all gene FPKM value. The formula is shown as follow: FPKM=cDNAFragmentsMappedFragments(Millions)∗TranscriptLength(kb)

source_name: cell

growth_protocol: 22RV1 cell lines were maintained in RPMI 1640 supplemented with 10% FBS. The cells were cultured in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).Purity, concentration and integrity of RNA sample were examined by NanoDrop, Qubit 2.0, Agilent 2100, etc. Only RNA with good quality could move on to following procedures.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were  added to attribute sequences to each sample.

treatment_protocol: Cells were plated in 100mM plates at a desired concentration and infected with overexpression plasimds targeting MAGI2-AS3 or a miR-106a-5p.Transfection efficiency was determined by qPCR.

value: cell

value: prostate cancer cell line

value: MAGI2-AS3 overexpression

value: Day 2


title: NC_rep2

value: NC


title: miR-106a-5p mimics_rep1

value: miR-106a-5p mimics


title: miR-106a-5p mimics_rep2


title: NC_rep1


title: OE-MAGI2-AS3_rep2


title: HCT-15-TRAMET-0-1-LAST-2


title: HCB514_rep2


title: HCT-15-LIN-4-LAST-4

value: linsitinib, 4 uM


title: HCT-15-LIN-4-LAST-3


title: HCT-15-LIN-4-LAST-2


title: HCT-15-LIN-1-LAST-4

value: linsitinib, 1 uM


title: HCT-15-LIN-1-LAST-2


title: HCT-15-TRAMET-0-7-LAST-2

value: trametinib, 0.7 uM


title: HCT-15-LIN-4-LAST-1


title: HCT-15-LIN-1-LAST-1


title: HCT-15-TRAMET-0-1-LAST-1


title: HCT-15-LIN-1-LAST-3


title: HCT-15-TRAMET-0-7-LAST-1


title: HCT-15-DMSO-LAST-4

value: DMSO (Control)


title: HCT-15-DMSO-LAST-3


title: HCT-15-TRAMET-0-7-LAST-4


title: HCT-15-DMSO-LAST-2