title: HOM-C3 day 6 ac-IP

city: Shanghai

first: Domgmin

last: Yin

state: Shanghai

address: No.3663, Zhongshan North Road

institute: Shanghai Key Laboratory of Brain Functional Genomics

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30 and FastQC. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes
Assembly: mm10
Supplementary files format and content: The excle contains the identified ac4C modification site information

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent
Total RNA was subjected to immunoprecipitation with the GenSeq® ac4C RIP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions.
acRIP-Seq

value: Hippocampus


title: HOM-C3 day 6 Input

status: Public on Mar 24 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype


title: HOM-L3 day 6 Input


title: HOM-L2 day 6 ac-IP


title: Neurospora crassa, TERB, rep1

city: Beijing

first: pengju

last: YU

address: No.1 Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Basecalling was performed using a software developed for DNBSEQ-T7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al.,  Genome Research, 1997.
Assembly: GCA_000182925.2
Supplementary files format and content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Sterol biosynthesis inhibitors, including ketoconazole (Sigma), terbinafine (J&K), and amorolfine (J&K), were added, with final concentrations of 1.5, 2.5 and 0.375 μg/mL, respectively.

value: mycelia

value: WT

tag: treatment

value: Terbinafine


title: HOM-L2 day 6 Input


title: C. capitata, mock dose, 24 hpi, rep 2

city: Hilo

first: Kelsey

last: Coffman

state: HI

address: 64 Nowelo St

department: Tropical Pest Genetics and Molecular Biology Research Unit

country: USA

institute: USDA-ARS

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_24_3

data_processing:
Raw read pairs were quality filtered using Trimmomatic v0.38 with default settings, which resulted in > 99.99% read pairs retained for each sample.
Virus differential gene expression analysis was conducted on the 54 virus-infected samples by first mapping quality-filtered reads onto the DlEPV reference genome using HISAT2 v2.2.1.
StringTie v2.1.1 was used on each sample with the ‘-eB’ flag to quantify the expression for each DlEPV gene, measured in reads per kilobase per million sequenced reads (RPKMS).
Ballgown v2.26.0 was then used to perform differential expression testing of viral genes among the different fly species for each nonzero time point and dosage combination by using default settings, except the ‘libadjust’ option was set to “FALSE”
Quality-filtered read pairs from each sample were then mapped to its respective fly reference genome using HISAT2.
Fly transcript abundances were estimated with StringTie ‘-eB’ and measured in fragments per kilobase per million mapped reads (FPKM).
Assembly: Diachasmimorpha longicaudata entomopoxvirus (GenBank accession KR095315)
Assembly: Bactrocera dorsalis (Refseq accession GCF_000789215.1)
Assembly: Ceratitis capitata (Refseq accession GCF_000347755.3)
Assembly: Zeugodacus cucurbitae (Refseq accession GCF_000806345.1)
Supplementary files format and content: DlEPV_all_sample_log2_rpkms.csv: comma-delimited text file contains log2-transformed RPKMS values for each gene (rows) in each of the 81 samples (columns)
Supplementary files format and content: Bdor_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each B. dorsalis gene (rows) in each of the 27 B. dorsalis tissue samples (columns)
Supplementary files format and content: Ccap_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each C. capitata gene (rows) in each of the 27 C. capitata tissue samples (columns)
Supplementary files format and content: Zcur_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each Z. cucurbitae gene (rows) in each of the 27 Z. cucurbitae tissue samples (columns)

molecule: polyA RNA

organism: Ceratitis capitata

source_name: whole body fly tissue

extract_protocol:
Each fly was collected in 300 µL TRIsure (Bioline), a guanidine thiocyanate and phenol mixture, and immediately bead homogenized prior to storage at -80℃ . Total RNA was isolated from homogenized samples using the Zymo Direct-zol-96 RNA Purification Kit performed on a KingFisher Flex instrument, which included a mid-protocol DNase I (6U/µL, 5µL) treatment, as well as a secondary Zymo DNase I treatment following RNA isolation. Final RNA was eluted in 20 µL nuclease-free water. RNA quality was assessed using a 4200 TapeStation System with RNA ScreenTape (Agilent), and 3 of the 6 replicates with highest quality for each treatment were selected to constitute the final 81 samples submitted for sequencing.
Messenger RNA library was formed by polyA capture (or rRNA removal) and reverse transcription of cDNA, performed by Novogene Corporation Inc.

value: whole body fly tissue

tag: developmental stage

value: third-instar larva

tag: time

value: 24 h post injection

value: mock-saline dose


title: Neurospora crassa NcSR mutant, Control, rep3

value: ncSR knockout

value: No treatment


title: Neurospora crassa, Control, rep2


title: C. capitata, mock dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_24_4


title: Neurospora crassa, TERB, rep2


title: Neurospora crassa NcSR mutant, Control, rep2


title: HOM-C2 day 6 ac-IP


title: Neurospora crassa, Control, rep1


title: C. capitata, mock dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_24_1


title: 3DCC_2_Day_35

city: Brisbane

first: Hazel

last: Quek

state: QLD

address: Bancroft, 300 Herston Road

department: Mental Health & Neuroscience Department

country: Australia

institute: QIMR Berghofer Medical Research

library_source: transcriptomic single cell

data_processing:
scRNAseq data were analyzed using the Seurat package (version 4.3.1) in R (version 4.2.3).
Raw sequencing reads were processed and aligned to the reference genome (GRCh38-2020-A) using CellRanger (version 7.1.0).
The resulting count matrix was imported into R using the Seurat function Read10X().
Cells with more than 2.5% mitochondrial genes were filtered out as well as genes expressed in fewer than three cells or with low expression levels were removed
Data normalisation was performed using the Seurat function NormalizeData(), and data scaling was performed using the Seurat function ScaleData().
Assembly: GRCh38-2020-A
Supplementary files format and content: barcodes.tsv, features.tsv and matrix.mtx files for each sample
Supplementary files format and content: combined barcodes, features and matrix .h5 files for each sample

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells (PBMCs)

growth_protocol: MDMi were cultured for 14 days (2D) or 35 days (3D) under a culture medium containing IL-34 and GM-CSF. 3D co-cultured with ReNcells VM was maintained in DMEM/F12 GlutaMAX medium with 2% (v/v) B27 supplement, 20 μg/ml epithelial growth factor (EGF), 20 μg/ml fibroblast growth factor 2 (FGF-2)

extract_protocol:
Fixed samples for scRNAseq were processed using the Chromium Next GEM single cell fixed RNA kit (10X Genomics, #PN-1000414 and #PN-1000474) following the standard manufacturer’s instructions.
GEM generation and barcoding, and library construction were performed according to the 10X Genomics Chromium User Guide.

value: Male

value: Day 35


title: C. capitata, mock dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_12_4

value: 12 h post injection


title: 3DMDMi_2_Day_35

value: Peripheral blood mononuclear cells (PBMCs)


title: HOM-C2 day 6 Input


title: 3DCC_1_Day_35


title: HOM-L3 day 6 ac-IP


title: C. capitata, mock dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_12_3


title: 3DMDMi_1_Day_35


title: HOM-L1 day 6 ac-IP


title: C. capitata, mock dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_12_1


title: HOM-L1 day 6 Input


title: 2DMDMi_1_Day_14

value: Day 14


title: Neurospora crassa, Control, rep3


title: monocyte_2_Day_1

value: Day 1


title: 2DMDMi_2_Day_14


title: RNA-seq 48h washout Beko cells_2

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Quality control of FASTQ files was done using the seeFastq command within systemPipeR.
The fastq files were aligned using HISAT v.2.2.1.
Count tables were generated from BAM files using the summarizeOverlaps function.
Normalization of read counts and the detection of differential expression was done using DESeq2 v.1.24.0 with default parameters.
Assembly: mm9
Supplementary files format and content: Raw read counts per gene stored as tab-separated format.

source_name: Beko

growth_protocol: Mouse pre-T (Beko) cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin.

extract_protocol:
Rneasy Mini Kit (Qiagen #74104) using the QIAshredder (Qiagen #79654) and  RNase-free DNase (Qiagen #79254).
Lybrary-prep kit: Illumina TruSeq® Stranded Total RNA LT - Ribo-Zero Gold (RS-122-2301/2).

treatment_protocol: Mouse pre-T (Beko) cells were treated for 48 hours with 10 mg/ml DAPT (GSI) or with DMSO as control. After washing out the inhibitor, cells were placed back in culture for 24 hours.

tag: cell line

value: Beko

tag: cell type

value: Progenitor T-cell

value: Beko cells were treated for 48 hours with 10 mg/ml DAPT (GSI) and, after washing out the inhibitor, placed back in culture for 24 hours.


title: C. capitata, mock dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_0_3

value: 0 h post injection


title: RNA-seq 48h washout Beko cells_1


title: HOM-C1 day 6 Input

value: Hippocampus


title: monocyte_1_Day_1


title: RNA-seq 48h Beko cells_2

value: Beko cells were treated for 48 hours with 10 mg/ml DAPT (GSI).


title: GSI_RBPJ_Rep3

library_source: genomic

data_processing:
Aligment was performed using HISAT v.2.2.1.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 and followed by MSPC to combine peak sets.
Assembly: mm9
Supplementary files format and content: Peaks as bed files and normalized coverage tracks as bigWig files.

molecule: genomic DNA

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907).
Lybrary-prep kit for ChIP-Seq: Diagenode MicropPlex Library Preparation kit v2 (C05010012)

treatment_protocol: Mouse pre-T (Beko) cells were treated for 24 hours with 10 mg/ml DAPT (GSI) or with DMSO as control.

value: Beko cells were treated for 24 hours with 10 mg/ml DAPT (GSI).

tag: chip antibody

value: Cell Signaling, #5313


title: HOM-C1 day 6 ac-IP


title: RNA-seq 48h Beko cells_1


title: C. capitata, mock dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_0_4

value: whole body fly tissue

value: third-instar larva

value: mock-saline dose


title: GSI_RBPJ_Rep4


title: GSI_RBPJ_Rep2


title: SYN-L day 20 Input


title: C. capitata, mock dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_mk_0_1


title: C. capitata, 0.1x dose, 24 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_24_3

value: 24 h post injection

value: 0.1x viral dose


title: C. capitata, 0.1x dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_24_1


title: GSI_Input_RBPJ_Rep2


title: GSI_RBPJ_Rep1


title: SYN-C day 20 Input


title: GSI_Input_RBPJ_Rep1


title: GSI_Input_H3K4me_Rep2


title: SYN-C day 20 ac-IP


title: C. capitata, 0.1x dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_12_3

value: 12 h post injection


title: GSI_Input_H3K4me_Rep1


title: C. capitata, 0.1x dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_12_2


title: GSI_H3K4me3_Rep2

value: Diagenode pAb-003-050


title: SYN-L day 6 ac-IP


title: SYN-L day 20 ac-IP


title: GSI_H3K4me3_Rep1


title: C. capitata, 0.1x dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_24_5


title: C. capitata, 0.1x dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_12_1


title: SYN-L day 6 Input


title: GSI_H3K4me1_Rep2

value: abcam ab8895


title: GSI_H3K4me1_Rep1


title: SYN-C day 6 ac-IP


title: C. capitata, 0.1x dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_0_6


title: SYN-C day 6 Input


title: DMSO_Input_RBPJ

value: Beko cells were treated for 24 hours with DMSO.


title: DMSO_RBPJ_Rep4

value: Beko


title: DMSO_Input_H3K4me_Rep2

value: Progenitor T-cell


title: C. capitata, 0.1x dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_0_3


title: C. capitata, 0.1x dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_lo_0_1


title: SYN-L day 1 Input


title: SYN-L day 1 ac-IP


title: DMSO_Input_H3K4me_Rep1


title: intestine_CRxCR_F1_5, mRNA-seq

first: Natalie

middle: Alyce

last: Trigg

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Transcriptomic analysis was performed in the R statistical computing environment version 4.2 and RStudio version 2022.02.1 using a pipeline adopted from an open-source toolkit for RNA sequencing analysis (Berry et al. 2021).
Assembly: GRCm39cDNA
Supplementary files format and content: xlsx spreadsheet with one tab per tissue type/comparison

source_name: Small intestine

extract_protocol:
1 cm of distal ileum was snap frozen and stored at −80°C until further processing. Tissue was homogenized in tubes with metal beads using TRIzol extraction
Illumina Stranded mRNA Prep, Ligation kit

value: Small intestine

tag: generation

value: WT

tag: environment


title: intestine_CRxCR_F1_3, mRNA-seq


title: C. capitata, 1x dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_24_4

value: 1x viral dose


title: SYN-C day 1 ac-IP

value: Hippocampus


title: intestine_CRxCR_F1_2, mRNA-seq


title: DMSO_H3K4me3_Rep2


title: intestine_CRxCR_F1_1, mRNA-seq


title: C. capitata, 1x dose, 24 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_24_2


title: DMSO_H3K4me3_Rep1


title: SYN-C day 1 Input


title: intestine_GFxCR_F1_3, mRNA-seq


title: DMSO_H3K4me1_Rep2


title: DMSO_H3K4me1_Rep1


title: DMSO_RBPJ_Rep3


title: C. capitata, 1x dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_12_4


title: skin_GFxCR_F2_5, mRNA-seq

source_name: Skin

extract_protocol:
To isolate RNA from skin, frozen tissue was transferred to TissueTube TT05M XT tissue bags (Covaris, 520140) and pulverized using a Covaris automated dry pulverizer (Covaris CP02) by submerging the tissue bag in liquid nitrogen for 10 seconds and immediately transferring for pulverization. Pulverized tissue was then transferred to 1 mL of TRIzol (ThermoFisher 15596026) and RNA extracted according to the TRIzol manufacturer’s protocols.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit

value: Skin


title: skin_GFxCR_F2_6, mRNA-seq


title: intestine_GFxCR_F1_2, mRNA-seq


title: skin_GFxCR_F2_4, mRNA-seq


title: C. capitata, 1x dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_12_1


title: ATAC_GSI_Rep3

data_processing:
Aligment was performed using HISAT v.2.2.1.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using MACS2.
Assembly: mm9
Supplementary files format and content: Peaks as bed files and normalized coverage tracks as bigWig files.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907). ATAC-Seq was performed using a kit (Active Motif 53150).
ATAC-Seq was performed using a kit (Active Motif 53150).

value: Beko cells were treated for 24 hours with 10 mg/ml DAPT (GSI).


title: skin_GFxCR_F2_3, mRNA-seq


title: ATAC_GSI_Rep2


title: SG_F1_GF_3, mRNA-seq

source_name: Sebaceous gland

extract_protocol:
Laser capture microdissection (LMD7000) from FFPE tissue; Qiagen All Prep DNA/RNA FFPE Kit
Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit

value: Sebaceous gland

value: GF


title: C. capitata, 1x dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_0_2

value: whole body fly tissue

value: third-instar larva

value: 0 h post injection


title: C. capitata, 1x dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_0_3


title: ATAC_GSI_Rep1


title: SG_F1_GF_1, mRNA-seq


title: skin_GFxCR_F2_1, mRNA-seq


title: SG_F1_GF_2, mRNA-seq


title: C. capitata, 1x dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_24_1

value: 24 h post injection


title: C. capitata, 1x dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_0_1


title: ATAC_DMSO_Rep3


title: SG_F1_CR_2, mRNA-seq

value: CR


title: human AML CD34+ cells 24

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PB

growth_protocol: Human AML CD34+cells were maintained in StemSpan Serum-Free Expansion Media (SFEM, Stem cell Technologies, Cat# 02691) supplemented with granulocyte-macrophage colony-stimulating factor (GM-CSF) 200pg/mL, leukemia inhibitory factor (LIF) 50pg/mL, granulocyte colony-stimulating factor (G-CSF) 1ng/mL, stem cell factor (SCF) 200pg/mL, macrophage-inflammatory protein-1α (MIP-1α) 200pg/mL, and interleukin-6 (IL-6) 1ng/mL (Peprotech Inc.).

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA)
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems) according to the manufacturer's protocol.
RNA-seq libraries were sequencing on Illumina NovaSeq6000 with the sequencing length of 2x101bp. RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.

treatment_protocol: AML CD34+ blasts from R/R AML patients (n=6) were treated with vehicle, ADV (5 μΜ), VEN (100 nΜ), or ADV+VEN for 24 hours.

value: PB

tag: disease

value: R/R AML

value: AML primary cells

value: ADV+VEN


title: SG_F1_CR_1, mRNA-seq


title: skin_GFxGF_F2_3, mRNA-seq


title: skin_GFxGF_F2_2, mRNA-seq


title: intestine_GFxCR_F1_1, mRNA-seq

value: Small intestine


title: human AML CD34+ cells 23

value: VEN


title: C. capitata, 1x dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Ccap_all_gene_fpkm.csv
Ccap_hi_12_2

value: 12 h post injection

value: 1x viral dose


title: skin_GFxGF_F2_1, mRNA-seq

value: Skin

value: WT


title: SG_F0_GF_3, mRNA-seq

value: Sebaceous gland


title: ATAC_DMSO_Rep2

value: Beko

value: Progenitor T-cell

value: Beko cells were treated for 24 hours with DMSO.


title: human AML CD34+ cells 22

value: ADV


title: SG_F0_GF_2, mRNA-seq

value: GF


title: skin_CRxCR_F2_5, mRNA-seq


title: skin_GFxCR_F2_2, mRNA-seq


title: human AML CD34+ cells 21

value: vehicle


title: human AML CD34+ cells 20

value: PB


title: SG_F0_GF_1, mRNA-seq


title: skin_CRxCR_F2_4, mRNA-seq


title: SG_F0_CR_3, mRNA-seq

value: CR


title: human AML CD34+ cells 19

value: R/R AML

value: AML primary cells


title: skin_CRxCR_F2_3, mRNA-seq


title: SG_F0_CR_2, mRNA-seq


title: skin_CRxCR_F2_2, mRNA-seq


title: human AML CD34+ cells 18


title: ATAC_DMSO_Rep1


title: skin_CRxCR_F2_1, mRNA-seq


title: human AML CD34+ cells 17


title: skin_GFmxCRf_F1_3, mRNA-seq


title: Col×C24-clf_replicate3

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

data_processing:
Fastp was used to filter low-quality reads from raw RNA-seq data.
We used STAR to map the filtered reads to TAIR10 genome reference.
The mapped file was filtered by Samtools to retain the unique mapping reads.
The differential expression genes between every two samples were analyzed using Cuffdiff.
Assembly: Tair10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Total RNA was extracted using the Trizol(Invitrogen, CA, USA). RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel.
Poly-A RNASeq library preparation and high-throughput sequencing were performed by Wuhan Frasergen Bioinformatics Co. Ltd and we used the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) to generate sequencing libraries, following the manufacturer’s recommendations.
Libraries were sequenced based on Novaseq 6000 guidelines (Illumina). Three biological replicates were performed for RNA-seq.

value: seedlings

value: hybrid


title: skin_GFmxCRf_F1_2, mRNA-seq


title: Donor 2, CD28-Low, Resting

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens Street

institute: Gladstone-UCSF Institute of Genomic Immunology

description: sgRNA library sequencing

library_source: other

data_processing:
sgRNA libraries were generated and sequenced as for the CRISPRi screens.
Sequencing data were analyzed in MAGeCK (v0.5.8) using the `count` and `test` commands.
Assembly: hg38
Supplementary files format and content: Results from Mageck `test` quantifying ("fdr," "lfc") whether each transcriptional regulator ("id") serves as a positive or negative regulator ("hit_value") for each target ("screen")
Library strategy: sgRNA Amplicon

molecule: other

source_name: Conventional T cells

growth_protocol: Complete RPMI [cRPMI: RPMI (Sigma #R0883), 10% FCS (R&D Systems lot #M19187), 100U/mL Pen-Strep, 2mM L-Glutamine, 10mM HEPES, 1X MEM Non-essential Amino Acids, 1mM Sodium Pyruvate, and 50U/mL IL-2 (Amerisource Bergen #10101641)]. Cells were activated with Immunocult Human CD3/CD28/CD2 T Cell Activator (STEMCELL #10970) at 6.25uL per 1e6 cells.

extract_protocol:
Sorted samples were pelleted and resuspended in 400uL ChIP Lysis Buffer (1% SDS, 50mM Tris, pH 8, 10mM EDTA) per 5e6 cells. Each 400uL reaction received 16µl NaCl (5M) and was incubated at 66°C overnight. Subsequently, each reaction received 8µl RNAse A (Fisher Scientific #EN0531) and was incubated at 37°C 1h. Then, 8µl Proteinase K (Fisher Scientific #25530049) was added and the samples incubated at 55°C 1h. One phase lock tube (Quantabio, #2302820) per sample was spun at 20,000g 1 minute and received 400µl Phenol:Chloroform:Isoamyl Alcohol (25:24:1). 400µl sample was added to each phase lock tube, shaken vigorously, and centrifuged at 20,000g 25°C 5 minutes. Aqueous phases were transferred to low-binding tubes (Eppendorf, #022431021) and received 40µl of Sodium Acetate (Fisher Scientific #46-033-CI), 1µl GlycoBlue (Invitrogen, #AM9515), and 600µl isopropanol. Samples were vortexed and frozen at -80°C ≥30 minutes. Frozen samples were centrifuged 20,000g 4°C 30 minutes, pellets washed with fresh 70% ethanol, and allowed to air dry for 15 minutes. Genomic DNA pellets were resuspended in Zymo DNA elution buffer (Zymo, #D3004-4-10) and reconstituted at 65°C for 1 hour, or until dissolution.
Sequencing libraries were generated using 3.75ug genomic DNA per 50uL PCR reaction with 0.25uM CM_oligo_4 and 0.25uM unique p7 reverse primer as in CM_oligo_5 (see Supplementary Information). PCR reactions were run with the following parameters: 95°C 1’, [95°C 30”, 60°C 30”, 72°C 30”] x 28, 72°C 10’, 4°C hold. Amplicons were purified with DNA Clean & Concentrator-25 kits (Zymo Research #D4033)100. One sample (Donor 2 Tconv cells, ICOS screen) was re-indexed before sequencing. Pooled libraries were sequenced with a custom sequencing primer CM_oligo_6 on an Illumina NextSeq500 instrument.

treatment_protocol: Cells were harvested at rest or restimulated for the indicated length of time with 1uL/mL Cell Activation Cocktail without Brefeldin A (Biolegend #423302).

value: Conventional T cells

value: Resting


title: Donor 2, ICOS-High, 24 hour Restimulation

description: sgRNA library sequencing

value: Restimulated, 24h


title: Donor 2, ICOS-Low, 24 hour Restimulation

description: sgRNA library sequencing


title: Donor 2, CD28-High, Resting

description: sgRNA library sequencing


title: Donor 1, ICOS-Low, 24 hour Restimulation

description: sgRNA library sequencing


title: Col×C24-clf_replicate2


title: human AML CD34+ cells 16

value: ADV+VEN


title: Donor 1, CD28-Low, Resting

description: sgRNA library sequencing


title: Donor 1, CD28-High, Resting

description: sgRNA library sequencing


title: human AML CD34+ cells 15

value: VEN


title: Donor 1, ICOS-High, 24 hour Restimulation

description: sgRNA library sequencing


title: human AML CD34+ cells 13


title: Donor 2 Tconv, 24 hour Restimulation, ICOS-High

description: sgRNA library sequencing

data_processing:
Raw Illumina sequencing data were demultiplexed and fastqs generated using bcl2fastq (v2.20.0).
Short guide RNA abundances were quantified using MAGeCK (v0.5.9.4) with a reference file listing sgRNA sequences, a sgRNA ID, and the 5’ genomic position of the sgRNA (hg38).
Unnormalized sgRNA count files for each sample were loaded into R (v4.1.2), and statistical testing of sgRNA effects across donors was performed with DESeq2 (v1.34.0).
Assembly: hg38
Supplementary files format and content: .rds file containing differential sgRNA abundance in High vs Low populations across all samples as quantified by DESeq2
Library strategy: sgRNA Amplicon

growth_protocol: All cells were cultured in Complete X-VIVO [cX-VIVO: Lonza Bioscience #04-418Q, 5% FCS (R&D Systems, lot #M19187), 55uM 2-mercaptoethanol, and 4mM N-Acetyl L-Cysteine]. Regulatory and Conventional T cells were activated by CTS Dynabeads Treg Xpander (Thermo Fisher #46000D) or CTS Dynabeads CD3/CD28 (Thermo Fisher #40203D), respectively, with 1:1 cell:bead ratio at 1e6 cells/mL in cX-VIVO supplemented with recombinant human IL-2. Primary human Tconv cells were activated and maintained in 300U/mL rhIL-2. Treg cells were activated in 300U/mL rhIL-2 and subsequently maintained in 200U/ml rhIL-2.


title: skin_GFxGF_F1_2, mRNA-seq

value: Skin

value: WT


title: skin_GFmxCRf_F1_1, mRNA-seq


title: Donor 2 Tconv, 6 hour Restimulation, CTLA4-Low

description: sgRNA library sequencing

value: Restimulated, 6h


title: Donor 2 Tconv, 24 hour Restimulation, ICOS-Low

description: sgRNA library sequencing


title: Col×C24-clf_replicate1


title: human AML CD34+ cells 14

value: ADV


title: Donor 2 Tconv, 6 hour Restimulation, CTLA4-High

description: sgRNA library sequencing


title: C24×Col-clf_replicate3


title: SG_F0_CR_1, mRNA-seq

value: Sebaceous gland


title: human AML CD34+ cells 11


title: C24×Col-clf_replicate2


title: skin_CRxCR_F1_5, mRNA-seq


title: human AML CD34+ cells 10


title: skin_CRxCR_F1_4, mRNA-seq


title: human AML CD34+ cells 9

value: vehicle


title: C24×Col-clf_replicate1


title: C24-clf_replicate2


title: skin_CRxCR_F1_3, mRNA-seq


title: C24-clf_replicate3


title: skin_GFxGF_F1_1, mRNA-seq


title: Donor 2 Tconv, Resting, CD28-Low

description: sgRNA library sequencing


title: Col-clf_replicate3

value: Col


title: human AML CD34+ cells 8

value: PB


title: C24-clf_replicate1


title: skin_GFxGF_F1_3, mRNA-seq


title: Donor 2 Tconv, Resting, CD28-High

description: sgRNA library sequencing


title: Donor 1 Tconv, 24 hour Restimulation, ICOS-Low

description: sgRNA library sequencing


title: human AML CD34+ cells 12

value: R/R AML


title: Donor 1 Tconv, 24 hour Restimulation, ICOS-High

description: sgRNA library sequencing


title: human AML CD34+ cells 6

value: AML primary cells


title: skin_CRxCR_F1_1, mRNA-seq


title: Donor 1 Tconv, 6 hour Restimulation, CTLA4-Low

description: sgRNA library sequencing


title: Col-clf_replicate2

value: seedlings


title: human AML CD34+ cells 7


title: Col-clf_replicate1


title: Donor 1 Tconv, 6 hour Restimulation, CTLA4-High

description: sgRNA library sequencing


title: human AML CD34+ cells 5


title: 8W_chip_R2

city: London

first: Roberta

last: Migale

state: UK

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Reads were processed using the publicly available nf-core [109] chipseq pipeline v1.2.2 against the mouse genome assembly GRCm38 (--narrow_peak, --single_end, --deseq2_vst, min_reps_consensus 2, --macs_fdr 0.05), applying the Encode GRCm38 blacklist definitions to filter out problematic regions.  A peak was only considered to be genuine if present in both biological replicates for each treatment group.
A consensus peak set was then constructed by combining the peak calls from the individual treatment groups into a set of non-overlapping intervals. Consensus peaks were annotated using the Bioconductor package ChIPpeakAnno’s annotatePeakInBatch function against the protein-coding gene component of Ensembl release 81. Gene
Assembly: mm10
Supplementary files format and content: bigWig

source_name: ovary

extract_protocol:
Ovaries from E14.5, 1W and 8-weeks old C57BL/6 mice were dissected in PBS, snap-frozen, and stored at −80 °C. Chromatin was prepared using a modified version of the Active Motif High Sensitivity Chromatin Prep Kit protocol. ChIP-SICAP experiments were performed in parallel using 2 biological replicates for each timepoint. After overnight immunoprecipitation at 4ºC with a FOXL2-specific antibody, immune-protein complexes were captured on protein G Dynabeads. ChIP-SICAP protocol was followed for labelling of DNA following immunoprecipitation. Protease-resistant streptavidin beads carrying DNA samples were processed for DNA purification. SDS buffer and proteinase K (20mg/ml) were added to resuspend the beads followed by incubation for 30 minutes at 55°C. The beads were then heated at 80°C for two hours to reverse the cross-linking. A magnetic rack was used to separate the beads from the DNA, now in the supernatant. Supernatant was collected and 50 µL of Ampure beads used to purify the DNA.
NEB Ultra II DNA kit
Purified input (no SICAP) and ChIP-SICAP DNA samples were used to generate libraries. NEB Ultra II DNA kit was used. Samples were sequenced on the NovaSeq 6000 system. Paired-end sequencing was performed (30 million reads).

value: ovary

value: primary ovarian cells

value: wildtype


title: 8W_input_R2


title: human AML CD34+ cells 4


title: 8W_chip_R1


title: Donor 1 Tconv, Resting, CD28-Low

description: sgRNA library sequencing

value: Conventional T cells

value: Resting


title: Col×C24_replicate3

value: hybrid


title: Donor 1 Tconv, Resting, CD28-High

description: sgRNA library sequencing


title: Col×C24_replicate1


title: human AML CD34+ cells 2


title: skin_CRxCR_F1_2, mRNA-seq

value: Skin


title: Col×C24_replicate2


title: C24×Col_replicate3


title: 8W_input_R1


title: human AML CD34+ cells 1


title: Donor 2 Treg, 24 hour Restimulation, CD28-High

description: sgRNA library sequencing

source_name: Regulatory T cells

value: Regulatory T cells

value: Restimulated, 24h


title: C24×Col_replicate2


title: 1W_input_R2


title: Donor 1 Treg, 24 hour Restimulation, CD28-High

description: sgRNA library sequencing


title: C24×Col_replicate1


title: Donor 1 Treg, 24 hour Restimulation, ICOS-Low

description: sgRNA library sequencing


title: C24_replicate3


title: 1W_chip_R1


title: G6/7R_M452L, donor 2

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequenced reads were trimmed with low-quality bases using fastp. Read lengths less than 15 nucleotides or a PHRED Quality Score of less than 15 were removed.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.1.0).
Read counts for each gene were calculated using featureCounts of the Subread package (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: Calculated raw read counts for individual genes are shown in a tab-delimited text file.

source_name: CD8+ T cells

growth_protocol: Human T cells were stimulated by K562 cells that express anti-CD3 mAb (clone OKT3)-derived scFV linked to the transmembrane and cytoplasmic domain of CD8a, and CD80 (K562-OKT3/CD80) (day 0). The stimulated T cells were transduced with anti-CD19 CAR (FMC63-28z), FMC63-28z and G6/7R, or FMC63-28z and G6/7R-M452L on day 2. The CAR-T cells were expanded in vitro with RPMI media supplemented with 10% FBS and 100 IU/ml human recombinant IL-2.

extract_protocol:
CD8+ CAR-T cell populaiton was isolated by an MA900 Cell Sorter (SONY). Total RNA was isolated from the purified CD8+ T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina according to standard Illumina protocols.

treatment_protocol: Control, G6/7R, or G6/7R-M452L-expressing CAR-T cells were stimulated by NALM-6 cells on day 9. The CAR-T cells were expanded in cytokine-free media for 7 days.

value: CD8+ T cells

value: CAR and G67R-M452L


title: 1W_input_R1


title: G6/7R_M452L, donor 1


title: Donor 2 Treg, Resting, CD28-High

description: sgRNA library sequencing


title: C24_replicate2


title: human AML CD34+ cells 3

value: VEN


title: G6/7R, donor 3

value: CAR and G67R


title: E14_5_input_R2


title: Donor 2 Treg, 24 hour Restimulation, ICOS-Low

description: sgRNA library sequencing


title: E14_5_chip_R2


title: C24_replicate1


title: G6/7R, donor 2


title: 1W_chip_R2


title: E14_5_chip_R1


title: G6/7R, donor 1


title: Donor 1 Treg, Resting, CD28-High

description: sgRNA library sequencing


title: Col_replicate2

value: Col


title: E14_5_input_R1


title: Donor 2 Treg, 6 hour Restimulation, CTLA4-Low

description: sgRNA library sequencing

value: Restimulated, 6h


title: G6/7R_M452L, donor 3


title: Control, donor 3

value: CAR


title: 8W_rna_R3

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.3 with the STAR /RSEM option against mouse genome assembly GRCm38 and Ensembl release 81 transcript annotations.  Other options were left as default.
Gene-level RSEM abundance estimates were imported into R using the Bioconductor package tximport’s tximport function for further analysis using DESeq2
Normalisation factors were calculated per gene using the default DESeq2 function, correcting for library size and feature length.
Variance-stabilised abundance estimates were calculated using the VST function. PCA analysis was performed on the variance stabilised values using all available genes.
Assembly: mm10
Supplementary files format and content: bigWig, counts normalised.csv

extract_protocol:
A total of 50000 GFP positive cells were sorted, and RNA was extracted using the RNeasy Plus Micro Kit (cat. no. 74034) by Qiagen.
RNA quality was assessed by Bioanalyzer and samples with a RIN value>8 were processed for library preparation. A total of 10ng of RNA was used to prepare libraries using the NEBNext® Low Input RNA Library Prep Kit (E6420L) following the manufacturer's instructions.

value: primary granulosa cells


title: Control, donor 2


title: Donor 2 Treg, 6 hour Restimulation, CTLA4-High

description: sgRNA library sequencing


title: Donor 2 Treg, Resting, CTLA4-Low

description: sgRNA library sequencing


title: PR2

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: H1650 cells were treated with PR (200ug/ml) for 24 hours.

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to the Human reference genome GRCh38 via the STAR aligner (v2.7.9a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with gene annotation GRCh38.104.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

source_name: Lung

growth_protocol: H1650 was purchased from ATCC. The cells were cultured in RPMI containing 10% FBS, penicillin (100 U/mL), and streptomycin (100 ug/mL) and maintained at 37 C in a humidified incubator with 5% CO2and 95% air.

extract_protocol:
Total RNA (1 µg) was processed to prepare an mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1,000,006,386; MGI Tech Co., Ltd., China) according to the manufacturer's instruction.
The library was quantified using the QauntiFluor® ssDNA System (E3190; Promega Corporation, WI, USA). Sequencing of the prepared DNA nanoballs was performed using the MGISeq platform (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: H1650 cells treated with PR (200ug/ml), erlotinib(2uM) or gefitinib(2uM), and their combinations.

value: Lung

value: tumor cells

value: Wildtype

value: PR (200ug/ml)


title: PR3


title: Donor 2 Treg, Resting, CTLA4-High

description: sgRNA library sequencing

value: Resting


title: Parse, H2, replicate8, scRNA-seq

city: Singapore

first: Enrico

last: Petretto

address: 8 College Rd

country: Singapore

institute: Duke-NUS Medical School

data_processing:
For 10x data, read mapping and gene expression quantification were done using CellRanger (v7.1.0) using default parameters except for --include-introns=true. For Parse data, sample demultiplexing, read mapping and gene expression quantification were done using split-pipe (v1.0.4p) with the following parameters: --mode all --chemistry v2 --kit WT --kit_score_skip --no_allwell.
Assembly: GRCh38
Supplementary files format and content: 10x: Tab-separated values files, matrix files. Parse: comma-separated values files, matrix files.

source_name: PBMC

extract_protocol:
Frozen vials of PBMCs were rapidly thawed in a 37°C water bath until pea-sized frozen cryopreserved cells remained. Thawed PBMCs were quenched by adding 12 mL 37°C pre-warmed 10% human serum media (Human Serum, Sigma Aldrich, # H4522; RPMI 1640 Medium, Gibco, # 11875-093; Penicillin-Streptomycin-Glutamine, Gibco, # 10378-016) and were centrifuged at 500 x g for 5 min at room temperature. The cell pellet was resuspended in 0.5 mL of pre-warmed human serum media and rested in the 37°C, 5% CO2 incubator for 30 mins. After resting, cell solutions were passed through a 40 𝞵m Falcon cell strainer (Thermo Fisher, # 08-771-1), and then centrifuged. Single live PBMCs were selected using fluorescence-activated cell sorting (FACS) with gating based on forward scatter (FSC), side scatter (SSC), and DAPI dye (Thermo Fisher, #D1306). The purified PBMCs were then resuspended with 1 mL 1X PBS containing 1% bovine serum albumin (BSA, Sigma Aldrich, # B2518).
For the 10x Genomics platform, the cell count for each sample was determined using the TC20™ Automated Cell Counter (Sigma Aldrich). Approximately 16,000 cells per sample were used for library construction, utilizing the Chromium Next GEM Automated Single Cell 3ʹ Reagent Kits (10x Genomics). For the Parse Biosciences platform, the cells were prepared using the Fixation Kit (Parse Biosciences) according to the manufacturer's protocol. After fixation, the cell count was determined using the TC20™ Automated Cell Counter (Sigma Aldrich), resulting in an average of approximately 35,500 cells per donor. These cells were subjected to the Single Cell Whole Transcriptome Kit v2 (Parse Biosciences) for library construction.

value: PBMC

tag: disease state

value: Healthy

tag: subject

value: Donor H2


title: Donor 2 Treg, Resting, CD28-Low

description: sgRNA library sequencing

value: Regulatory T cells


title: Col_replicate3

value: seedlings


title: Col_replicate1


title: 1W_rna_R4

value: ovary


title: Donor 1 Treg, Resting, CD28-Low

description: sgRNA library sequencing


title: Gefitinib+PR3

description: H1650 cells were  treated with PR (200ug/ml) and Gefitinib (2uM) for 24 hours.

value: PR (200ug/ml) and Gefitinib (2uM)


title: Parse, H1, replicate8, scRNA-seq

value: Donor H1


title: 1W_rna_R3


title: Donor 1 Treg, 6 hour Restimulation, CTLA4-High

description: sgRNA library sequencing


title: Donor 1 Treg, 6 hour Restimulation, CTLA4-Low

description: sgRNA library sequencing


title: Parse, H2, replicate7, scRNA-seq


title: Gefitinib+PR2


title: Donor 1 Treg, Resting, CTLA4-Low

description: sgRNA library sequencing


title: 1W_rna_R2


title: Parse, H1, replicate7, scRNA-seq


title: Donor 1 Treg, Resting, CTLA4-High

description: sgRNA library sequencing


title: Gefitinib+PR1


title: 8W_rna_R2


title: Gefitinib3

description: H1650 cells were treated with Gefitinib (2uM) for 24 hours.

value: Gefitinib (2uM)


title: Parse, H2, replicate6, scRNA-seq


title: E14_5_rna_R2


title: E14_5_rna_R3


title: 8W_rna_R1


title: Parse, H1, replicate6, scRNA-seq


title: PR1


title: E14_5_rna_R1


title: Gefitinib2


title: Control, donor 1

value: CD8+ T cells


title: Gefitinib1


title: Parse, H1, replicate5, scRNA-seq


title: Erlotinib+PR3

description: H1650 cells were  treated with PR (200ug/ml) and Erlotinib (2uM) for 24 hours.

value: PR (200ug/ml) and Erlotinib (2uM)


title: ATAC-seq_Donor A, AAVS1 KO

description: Concatenated NextSeq500 and NovaSeq X sequencing

data_processing:
Raw sequencing reads were trimmed with cutadapt (v2.10) to a minimum read length of 20bp.
Reads were aligned to the GRCh38 reference genome using bowtie2 (v2.4.1).
Low-quality reads were filtered using SAMtools (v1.10), reads mapping within ENCODE blacklist regions were removed using bedtools intersect (v2.29.2), and read duplicates were removed using picard (v2.23.3).
Peaks were called using MACS2 (v2.2.7.1) before merging biological replicate samples into a consensus peak file.
A count matrix was generated by quantifying the number of Tn5 insertion sites overlapping each consensus peak using the summarizeOverlaps function (GenomicAlignments, v1.24.0).
The estimateSizeFactorsForMatrix function (DESeq2, v1.34.0) was used to estimate size factors for determination of normalized coverage based on Tn5 insertion sites.
Replicate samples were merged into consensus bigwig files for plotting.
Assembly: hg38
Supplementary files format and content: Normalized coverage across 2q33.2 TAD region for merged biological replicates

growth_protocol: All cells were cultured in Complete X-VIVO [cX-VIVO: Lonza Bioscience #04-418Q, 5% FCS (R&D Systems, lot #M19187), 55uM 2-mercaptoethanol, and 4mM N-Acetyl L-Cysteine]. Regulatory T cells were activated by CTS Dynabeads Treg Xpander (Thermo Fisher #46000D) with 1:1 cell:bead ratio at 1e6 cells/mL in cX-VIVO supplemented with 300U/mL rhIL-2. Tregs were subsequently maintained in 200U/ml rhIL-2.

extract_protocol:
Nine days after the initial isolation and stimulation, 15000 resting Treg cells per sample were resuspended in ATAC Lysis Buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL).
Nuclei subjected to tagmentation using Nextera DNA Library Preparation Kit (Illumina). Tagmentation DNA was purified with the MinElute PCR Purification Kit (Qiagen #28004) and amplified with Phusion High-Fidelity PCR Master Mix (NEB #F531L) using 16 PCR cycles. Amplified libraries were re-purified.

value: AAVS1 KO


title: ATAC-seq_Donor B, AAVS1 KO


title: ATAC-seq_Donor A, FOXP3 KO

value: FOXP3 KO


title: 8W_atac_R2

data_processing:
Reads were processed using the publicly available nf-core [109] atacseq pipeline v1.2.1 against the mouse genome assembly GRCm38 (--deseq2_vst --min_reps_consensus), applying the Encode GRCm38 blacklist definitions to filter out problematic regions.
A peak was only considered to be genuine if present in at least 2 biological replicates for each treatment group.
A consensus peak set was then constructed by combining the peak calls from the individual treatment groups into a set of non-overlapping intervals.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
A total of 100000 GFP positive cells isolated by FACS from gonads at E14.5, 1W and 8W (three biological replicates per timepoint) were used for ATAC-Seq library preparation using Active Motif ATAC-Seq Kit (cat. number 53150).
Libraries were prepared using the  KAPA Real-Time Library Amplification Kit following the recommendations of the ATAC-Seq kit by Active Motif
Tagmented DNA was purified using DNA purification columns and library amplification was performed using Illumina’s Nextera adapters. A unique combination of i7/i5 primers was used to allow for multiplexing and sequencing on the same flow cell. PCR amplification included 5 minutes incubation at 72°C, followed by 30 sec of DNA denaturation at 98°C and 10 cycles of: 98°C for 10 sec, 63°C for 30 sec and 72°C for 1 minute. PCR products were cleaned up using SPRI beads and size distribution of PCR amplified libraries was assessed on Tapestation.

value: 8 weeks

value: primary granulosa cells


title: 8W_atac_R1


title: Erlotinib+PR2

value: Lung

value: tumor cells

value: Wildtype


title: Donor B, NTC CRISPRi

data_processing:
4C sequencing reads were processed and aligned to hg38 using pipe4C processing pipeline103, normalizing to one million reads and using a default window size of 21.
The resulting wig files were imported in R and smoothed using spline models (smoothing parameter 0.75).
Assembly: hg38
Supplementary files format and content: Normalized read coverage in wig and rds formats
Library strategy: 4C-Seq

growth_protocol: All cells were cultured in Complete X-VIVO [cX-VIVO: Lonza Bioscience #04-418Q, 5% FCS (R&D Systems, lot #M19187), 55uM 2-mercaptoethanol, and 4mM N-Acetyl L-Cysteine]. Conventional T cells were activated by CTS Dynabeads CD3/CD28 (Thermo Fisher #40203D) with 1:1 cell:bead ratio at 1e6 cells/mL in cX-VIVO supplemented with 300U/mL rhIL-2.

extract_protocol:
Cell pellets were thawed, fixed with 1% PFA, and re-pelleted. Cell pellets were resuspended with 500ul 4C lysis buffer (50mM Tris-HCl pH 7.5, 150mM NaCl, 5mM EDTA, 0.5% NP-40 (IGEPAL CA-630), 1% Triton-X100, and 1X protease inhibitors (ThermoFisher #1862209)). Pellets were pipetted vigorously and lysed on ice for 10 minutes. Pellets were centrifuged 750g, 5 minutes, 4°C and washed twice with cold PBS. Nuclear pellets were resuspended in H2O and 1X rCutSmart buffer (NEB #R3104T).
0.25% SDS and 2.5% Triton-X100 were added for denaturation at 37°C for one hour on a thermomixer set to 900 rpm. Genomic DNA was digested with 400UI-600UI HindIII-HF (NEB #R3104T) overnight before heat inactivation. Digested genomic DNA was ligated by T4 DNA ligase system (NEB #M0202T) at 25°C 4 hours. The mixture was digested by proteinase K (ThermoFisher #EO0491) and RNase (Roche #11119915001) and purified by phenol-chloroform. DNA pellets were resuspended in TE buffer and subjected to DpnII secondary digestion overnight (200UI, NEB #R0543T) before heat inactivation. DNA was again ligated using the T4 DNA ligase system (NEB #M0202T) at 25°C 4 hours and then pelleted with 60mM sodium acetate, 3ug/ml glycogen, and 70% Ethanol. Two probe sets spanning the entire Stim-Responsive CiRE were tested, but only the probe covering the latter half of the enhancer region (which aligns with maximum CRISPRi responsiveness) yielded sufficiently diverse libraries and is included here. PCR was performed on 200ng DNA with CM_oligo_8 and CM_oligo_9 using Platinum™ SuperFi™ DNA Polymerase system (ThermoFisher #12351010) with the program [98°C 10”, 52°C 10”, 72°C 1’] x 30 cycles. Final amplified libraries were purified with SPRI clean-up, quantified, and sequenced.

treatment_protocol: Cells were restimulated for 6 hours with 1uL/mL Cell Activation Cocktail without Brefeldin A (Biolegend #423302) before being snap frozen

value: Conventional T cells


title: Erlotinib+PR1


title: 1W_atac_R4

value: 1 week


title: Parse, H2, replicate5, scRNA-seq

value: PBMC

value: Healthy

value: Donor H2


title: Parse, H1, replicate4, scRNA-seq


title: Donor B, CTCF-2 CRISPRi


title: Parse, H2, replicate4, scRNA-seq


title: ATAC-seq_Donor B, FOXP3 KO

value: Regulatory T cells


title: 1W_atac_R3

value: ovary


title: Erlotinib3

description: H1650 cells were treated with Erlotinib (2uM) for 24 hours.

value: Erlotinib (2uM)


title: Parse, H1, replicate3, scRNA-seq

value: Donor H1


title: Erlotinib2


title: 1W_atac_R2


title: Donor A, NTC CRISPRi


title: Parse, H2, replicate3, scRNA-seq


title: 8W_atac_R3


title: Donor A, CTCF-2 CRISPRi


title: Erlotinib1


title: Parse, H2, replicate2, scRNA-seq


title: Parse, H1, replicate2, scRNA-seq


title: E14_5_atac_R3


title: Control3

description: H1650 cells were treated with DMSO for 24 hours.

value: DMSO


title: Apicidin_RBPJ_Rep2

data_processing:
Aligment was performed using HISAT v.2.2.1.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Assembly: mm9
Supplementary files format and content: Normalized coverage tracks as bigWig files.

value: Beko

value: Progenitor T-cell

value: 24 hours with 001ug/ml Apicidin

value: RBPJSUH Cell Signaling #5313


title: E14_5_atac_R2

value: primary granulosa cells


title: Apicidin_RBPJ_Rep1


title: Parse, H2, replicate1, scRNA-seq


title: Apicidin_Input_RBPJ


title: Parse, H1, replicate1, scRNA-seq


title: Beko_24h_DMSO_Input_batch3

value: 24 hours with DMSO


title: Control1

value: Lung

value: tumor cells

value: Wildtype


title: 10x, H2, scRNA-seq

value: PBMC


title: Z. cucurbitae, mock dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_24_5

data_processing:
Raw read pairs were quality filtered using Trimmomatic v0.38 with default settings, which resulted in > 99.99% read pairs retained for each sample.
Virus differential gene expression analysis was conducted on the 54 virus-infected samples by first mapping quality-filtered reads onto the DlEPV reference genome using HISAT2 v2.2.1.
StringTie v2.1.1 was used on each sample with the ‘-eB’ flag to quantify the expression for each DlEPV gene, measured in reads per kilobase per million sequenced reads (RPKMS).
Ballgown v2.26.0 was then used to perform differential expression testing of viral genes among the different fly species for each nonzero time point and dosage combination by using default settings, except the ‘libadjust’ option was set to “FALSE”
Quality-filtered read pairs from each sample were then mapped to its respective fly reference genome using HISAT2.
Fly transcript abundances were estimated with StringTie ‘-eB’ and measured in fragments per kilobase per million mapped reads (FPKM).
Assembly: Diachasmimorpha longicaudata entomopoxvirus (GenBank accession KR095315)
Assembly: Bactrocera dorsalis (Refseq accession GCF_000789215.1)
Assembly: Ceratitis capitata (Refseq accession GCF_000347755.3)
Assembly: Zeugodacus cucurbitae (Refseq accession GCF_000806345.1)
Supplementary files format and content: DlEPV_all_sample_log2_rpkms.csv: comma-delimited text file contains log2-transformed RPKMS values for each gene (rows) in each of the 81 samples (columns)
Supplementary files format and content: Bdor_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each B. dorsalis gene (rows) in each of the 27 B. dorsalis tissue samples (columns)
Supplementary files format and content: Ccap_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each C. capitata gene (rows) in each of the 27 C. capitata tissue samples (columns)
Supplementary files format and content: Zcur_all_gene_fpkm.csv: comma-delimited text file contains FPKM values for each Z. cucurbitae gene (rows) in each of the 27 Z. cucurbitae tissue samples (columns)

organism: Zeugodacus cucurbitae

extract_protocol:
Each fly was collected in 300 µL TRIsure (Bioline), a guanidine thiocyanate and phenol mixture, and immediately bead homogenized prior to storage at -80℃ . Total RNA was isolated from homogenized samples using the Zymo Direct-zol-96 RNA Purification Kit performed on a KingFisher Flex instrument, which included a mid-protocol DNase I (6U/µL, 5µL) treatment, as well as a secondary Zymo DNase I treatment following RNA isolation. Final RNA was eluted in 20 µL nuclease-free water. RNA quality was assessed using a 4200 TapeStation System with RNA ScreenTape (Agilent), and 3 of the 6 replicates with highest quality for each treatment were selected to constitute the final 81 samples submitted for sequencing.
Messenger RNA library was formed by polyA capture (or rRNA removal) and reverse transcription of cDNA, performed by Novogene Corporation Inc.

value: whole body fly tissue

value: third-instar larva

value: 24 h post injection

value: mock-saline dose


title: 10x, H1, scRNA-seq

value: Healthy


title: Beko_24h_DMSO_Input_batch2_Rep1

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907).
Lybrary-prep kit for ChIP-Seq: Diagenode MicropPlex Library Preparation kit v2 (C05010012)


title: Z. cucurbitae, mock dose, 24 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_24_2


title: Beko_24h_DMSO_Input_batch2_Rep2


title: Z. cucurbitae, mock dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_24_1


title: Z. cucurbitae, mock dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_12_6

value: 12 h post injection


title: 293T_Suntag_NOguide_rep2

city: Haining

first: Yixin

last: Guo

address: 718 East Haizhou Rd.

institute: Zhejiang University

data_processing:
Quality control was performed by FastQC v0.11.8. The quality is good and reads were aligned to human reference genome GRCh38.97 using STAR v2.7.0e. We kept the reads with maximal 5000 mulitple mapping sites(–outFilterMultimapNmax 1000) and the only best hit(–outSAMmultNmax 1). FeatureCounts v2.0.0 was used to quantify TE expression. Multiple mapped reads were also included(-p -M) when TE quantification.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: HEK 293T

extract_protocol: Total RNA was extracted using TRIzol, and cDNA was synthesized with M-MuLV Reverse Transcriptase and DNA Polymerase I. Post-PCR, cDNA (370-420bp) was selected with AMPure XP beads and subjected to paired-end sequencing on an Illumina NovaSeq 6000 sequencer

value: HEK 293T

value: human embryonic kidney cells

value: WT

value: Transfected with dCas9-VP64 and rtTA


title: Beko_24h_DMSO_Input_batch1_Rep1

value: Beko

value: Progenitor T-cell


title: Beko_24h_GSI_Input_batch3

value: 24 hours with 10 mg/ml DAPT (GSI)


title: 293T_Suntag_NOguide_rep1


title: Z. cucurbitae, mock dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_12_4


title: Z. cucurbitae, mock dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_12_1


title: 293T_Suntag_SVAD_rep3

value: CRISPRa

value: Transfected with dCas9-VP64, rtTA and SVAD sgRNA


title: Beko_24h_GSI_Input_batch2_Rep2


title: E14_5_atac_R1

value: ovary

value: primary granulosa cells


title: Z. cucurbitae, mock dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_0_5

value: whole body fly tissue

value: 0 h post injection


title: Beko_24h_GSI_Input_batch2_Rep1


title: Plagl1 KO replicate 2

city: Toronto

first: yacine

last: touahri

address: 2075 Bayview Ave

country: Canada

institute: Sunnybrook Research Institute

description: 10x Genomics

data_processing:
software_version: "Cell Ranger 4", "format_version": 2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
retinas were dissected in cold PBS(311-010-CL, Wisent), enucleated and cutinto 2mm pieces. Retinal tissues were dissociated intosingle cell suspensionsusingaPapain dissociation system (LK003150, WorthingtonBiochemical Corp) according to the manufacturer’s instructions andthenresuspended in PBSwith 0.04% BSA. Dead cells were eliminated using a Dead Cell Removal Kit (130-090-101,Miltenyi Biotec) with MS columns and a gentleMACS™ Octo Dissociator according to themanufacturer’s instructions. Cell number and viability were determined usingaCountess®II FLAutomated CellCounter (ThermoFisherScientific). Cells were diluted in 1X PBS with 0.04%bovine serum albumin (BSA)to 1X 10^6 cells/ml and cellular concentration and viability wereaccessed again, withonly samples with 90% viability and higherused.
Live cells were processedusing theChromium Next GEMSingleCell 5’ReagentKit v2 (10X genomics, Cat # 1000263).For each reaction, 16500 cells were loaded onto GEM Chip K for an expected recovery of10,000 cells. Gel Beads-in-emulsion were generated using the Chromium Controller followed bycDNA generation and amplification (13 cycles) as per manufacturer’s instructions. For eachsample, 50ng of cDNA was used for library generation

value: Retina

tag: age

value: Plagl1 KO


title: 293T_Suntag_SVAD_rep1


title: Beko_24h_GSI_Input_batch1_Rep2


title: wild type replicate2

description: 10x Genomics

value: Wild type


title: 293T_Suntag_SVAD_rep2


title: Tt_3

city: Tainan City

first: Wei-Chen

last: Lin

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

data_processing:
The obtained raw paired-end reads were filtered by Trimmomatic to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The clean read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by 2021_Q2 the HISAT2 software
Read count extraction and normalization were performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Direct-zolTM RNA MiniPrep (AYMO RESEAECH). 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: lung carcinoma mucoepidermoid epithelial cell

value: cocultured with Trichomonas tenax


title: Z. cucurbitae, mock dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_0_3

value: third-instar larva

value: mock-saline dose


title: Z. cucurbitae, mock dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_mk_0_4


title: 293T_Suntag_NOguide_rep3

value: HEK 293T

value: human embryonic kidney cells

value: WT

value: Transfected with dCas9-VP64 and rtTA


title: wild type replicate 1

description: 10x Genomics


title: Tt_2


title: Z. cucurbitae, 0.1x dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_24_4

value: 24 h post injection

value: 0.1x viral dose


title: Beko_24h_GSI_H3K27me3_batch1_Rep2

value: Beko

value: Progenitor T-cell

value: 24 hours with 10 mg/ml DAPT (GSI)

value: H3K27me3 (Active Motif 39155)


title: Beko_24h_DMSO_Input_batch1_Rep2

value: 24 hours with DMSO


title: Tt_1


title: Z. cucurbitae, 0.1x dose, 24 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_24_3

value: whole body fly tissue


title: Control2

value: Lung

value: tumor cells

value: Wildtype

value: DMSO


title: Mouse intestinal crypt epithelial cells from adult male C57BL/6J (8 weeks old), untreated snRNA-seq (multiome)

city: New York City

first: Alessandro

last: Vasciaveo

state: NY

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

institute: Columbia University

description:
TE013
snRNA + ATAC fragments (multiome)

data_processing:
Sequencing was performed in a NovaSeq 6000 sequencer (Illumina)
10x genomics' cellranger software v3 was used to process the data
Assembly: mm10
Supplementary files format and content: HDF5 file format for read counts, atac_fragments.tsv.gz for fragment counts

source_name: intestinal crypt

extract_protocol:
Library preparation and sequencing were performed by the JP Sulzberger Columbia Genome Centre (Single cell analysis core), using standard methodologies. For scRNA-seq crypt epithelial cells were sorted to exclude dead cells and contaminating villi (Alive/Epcam+/B6A6-). Immediately after sorting, cells were counted using an automated cell counter (ThermoFisher Countess II FL) to check viability and processed for library preparation (10x chromium). For single cell Multiome, immediately after sorting, isolated cells (>100’000) were processed to extract nuclei following manufacturer recommendation (protocol CG000365, Rev B). Isolated nuclei were counted and quality control using an automated cell counter (ThermoFisher Countess II FL) and immediately processed for library preparation.
single-cell RNA-seq and snRNA-Seq+snATAC-Seq (multiome)

value: intestinal crypt

value: epithelial cells

value: untreated

tag: strain

value: 8 weeks

tag: Sex

value: male


title: mock3

value: lung carcinoma mucoepidermoid epithelial cell

value: WT


title: Z. cucurbitae, 0.1x dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_24_2

source_name: whole body fly tissue

value: third-instar larva

value: 24 h post injection

value: 0.1x viral dose


title: Mouse intestinal crypt epithelial cells from adult male C57BL/6J (8 weeks old), untreated, snATAC-seq (multiome)

description:
TE013
snRNA + ATAC fragments (multiome)

library_source: genomic single cell


title: Plagl1 KO replicate 1

description: 10x Genomics

value: Retina

value: Plagl1 KO


title: Mouse intestinal crypt epithelial cells from adult male Lgr5-DTR-eGFP (8 weeks old), DT treated, scRNA-seq

treatment_protocol: To induce selective Lgr5-expressing cells’ ablation mice where treated with Diphteria Toxin (50ug/Kg) as previously described (Tian, Nature 2011)

value: DT-ablation


title: Z. cucurbitae, 0.1x dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_12_5

value: whole body fly tissue

value: 12 h post injection


title: mock2


title: Mouse intestinal crypt epithelial cells from adult male Lgr5-DTR-eGFP (8 weeks old), untreated, scRNA-seq


title: Beko_24h_GSI_H3K9ac_batch2_Rep2

value: Beko

value: Progenitor T-cell

value: 24 hours with 10 mg/ml DAPT (GSI)

value: H3K9ac (abcam ab4441)


title: Beko_24h_GSI_H3K27me2_batch1_Rep2

value: H3K27me2 (Diagenode pAb-046-050)


title: mock1

value: untreated


title: Z. cucurbitae, 0.1x dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_12_3


title: Tt_treated3

value: lung carcinoma epithelail cell

value: cocultured with Trichomonas tenax at MOI1


title: Beko_24h_GSI_H3K27me1_batch1_Rep2

value: H3K27me1 (Diagenode pAb-045-050)


title: Z. cucurbitae, 0.1x dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_12_2

value: third-instar larva


title: Beko_24h_GSI_Input_batch1_Rep1


title: Mouse intestinal crypt epithelial cells from adult male C57BL/6J (8 weeks old), 60 hours post IR-damage, scRNA-seq

treatment_protocol: For irradiation studies mice received a single dose of 12Gy whole body irradiation using Mark I Cesium-137 based gamma-ray irradiator. To induce selective Lgr5-expressing cells’ ablation mice where treated with Diphteria Toxin (50ug/Kg) as previously described (Tian, Nature 2011)

value: intestinal crypt

value: epithelial cells

value: IR-damage

value: 8 weeks

value: male


title: Mouse intestinal crypt epithelial cells from adult male C57BL/6J (8 weeks old), untreated, scRNA-seq


title: Beko_24h_GSI_H3K36me3_batch2_Rep2

value: H3K36me3 (Cell Signaling #4909S)


title: Z. cucurbitae, 0.1x dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_0_3

value: whole body fly tissue

value: 0 h post injection

value: 0.1x viral dose


title: Beko_24h_GSI_H3K9me3_batch1_Rep2

value: Beko

value: Progenitor T-cell

value: 24 hours with 10 mg/ml DAPT (GSI)

value: H3K9me3 (Diagenode C15410193)


title: Tt_treated2

value: lung carcinoma epithelail cell

value: WT


title: Tt_treated1

value: cocultured with Trichomonas tenax at MOI1


title: Z. cucurbitae, 0.1x dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_0_2

value: third-instar larva


title: Lats-Plp Tumor 2 Grade II

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to mouse (GRCm38, mm10) or human (GRCh38, hg38) genome assembly (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotations (vM22 for GRCm38,  v31 for GRCh38)
Supplementary_files_format_and_content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: Tumor tissue

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Miniprep kit (Zymo), quantified by Qubit 3.0 Fluorometer, and quality checked by 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent).
Libraries were prepared from 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina 20020599)
Libraries were sequenced on Illumina NovaSeq 6000, obtaining 100 million 100-bp paired-end reads.

tag: mouse line

value: Lats-Plp

tag: diagnosis

value: GEM PNST/Grade II


title: Lats-Plp Tumor 3 Grade II


title: Beko_24h_GSI_H3K36me2_batch2_Rep2

source_name: Beko


title: mock_3

tag: genotype

value: untreated


title: Beko_24h_GSI_H3K18ac_batch2_Rep2

tag: treatment

value: H3K18ac (Cell Signaling #9675S)


title: Z. cucurbitae, 0.1x dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_lo_0_1

tag: tissue

tag: developmental stage


title: mock_2

tag: cell line


title: Beko_24h_GSI_H3K9me2_batch1_Rep2

tag: cell type

value: H3K9me2 (Active Motif 39753)


title: Z. cucurbitae, 1x dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_24_5

tag: time

value: 24 h post injection

value: 1x viral dose


title: Lats-Nes Tumor 7 Grade III

value: Lats-Nes

value: GEM PNST/Grade III


title: Beko_24h_GSI_H3K9me1_batch3_Rep2

value: Beko

tag: chip antibody

value: H3K9me1 (Cell Signaling 14186)


title: Z. cucurbitae, 1x dose, 24 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_24_4

value: whole body fly tissue


title: mock_1


title: Lats-Nes Tumor 6 Grade III


title: Beko_24h_GSI_H3K36me1_batch2_Rep2

value: Progenitor T-cell

value: 24 hours with 10 mg/ml DAPT (GSI)

value: H3K36me1 (Cell Signaling #14111)


title: G6/7R, IL6+, donor 3

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequenced reads were trimmed with low-quality bases using fastp. Read lengths less than 20 nucleotides or a PHRED Quality Score of less than 15 were removed.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.1.0).
Read counts for each gene were calculated using HTSeq (version 0.11.2).
Assembly: GRCh38
Supplementary files format and content: Calculated raw read counts for individual genes are shown in a tab-delimited text file.

growth_protocol: Human T cells were stimulated by K562 cells that express anti-CD3 mAb (clone OKT3)-derived scFV linked to the transmembrane and cytoplasmic domain of CD8a, and CD80 (K562-OKT3/CD80) (day 0). The stimulated T cells were transduced with FMC63-28z and G6/7R, or FMC63-28z alone on day 2. The CAR-T cells were expanded in vitro with RPMI media supplemented with 10% FBS and 100 IU/ml human recombinant IL-2.

extract_protocol:
CD8+ CAR-T cell populaiton was isolated by FACSAria III (BD Biosciences). Total RNA was isolated from the purified CD8+ T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the TruSeq Standard mRNA Library Prep kit according to standard Illumina protocols

treatment_protocol: Control or G6/7R-expressing CAR-T cells were incubated overnight in cytokine-free media. On the next day, the CAR-T cells were left untreated or treated with recombinant human IL-6 (50 ng/ml).

tag: transduced with

value: FMC63-28z and G6/7R

value: CD8+ T cells

tag: donor


title: Lats-Nes Tumor 5 Grade III


title: Beko_24h_DMSO_H3K27me3_batch1_Rep2

value: 24 hours with DMSO

value: H3K27me3 (Active Motif 39155)


title: Z. cucurbitae, 1x dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_12_6

value: third-instar larva

value: 12 h post injection


title: Lats-Nes Tumor 4 Grade UD

value: GEM PNST/UD (grade undetermined)


title: G6/7R, IL6-, donor 3


title: G6/7R, IL6+, donor 2


title: Beko_24h_DMSO_H3K27me2_batch1_Rep2

value: H3K27me2 (Diagenode pAb-046-050)


title: Z. cucurbitae, 1x dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_12_5

value: 1x viral dose


title: Lats-Nes Tumor 3 Grade III

value: Lats-Nes


title: Z. cucurbitae, 1x dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_12_4


title: Lats-Nes Tumor 2 Grade UD


title: G6/7R, IL6-, donor 2


title: G6/7R, IL6+, donor 1


title: Beko_24h_DMSO_H3K18ac_batch2_Rep2

value: H3K18ac (Cell Signaling #9675S)


title: Lats-Plp Tumor 1 Grade II

value: Lats-Plp

value: GEM PNST/Grade II


title: Z. cucurbitae, 1x dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_0_4

value: whole body fly tissue

value: 0 h post injection


title: Beko_24h_DMSO_H3K27me1_batch1_Rep2

value: Beko

value: Progenitor T-cell

value: H3K27me1 (Diagenode pAb-045-050)


title: Beko_24h_DMSO_H3K9ac_batch2_Rep2

value: H3K9ac (abcam ab4441)


title: G6/7R, IL6-, donor 1

value: FMC63-28z and G6/7R

value: CD8+ T cells


title: Lats-Nes Tumor 1 Grade UD


title: Beko_24h_DMSO_H3K36me3_batch2_Rep2

value: 24 hours with DMSO

value: H3K36me3 (Cell Signaling #4909S)


title: NPcis Tumor 3 Grade III

value: NPcis

value: GEM PNST/Grade III


title: Z. cucurbitae, 1x dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_0_3

value: third-instar larva

value: 1x viral dose


title: Control, IL6+, donor 3

value: FMC63-28z alone


title: Z. cucurbitae, 1x dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_24_2

value: 24 h post injection


title: Z. cucurbitae, 1x dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Zcur_all_gene_fpkm.csv
Zcur_hi_0_1


title: B. dorsalis, mock dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_24_6

organism: Bactrocera dorsalis

value: mock-saline dose


title: Control, IL6-, donor 3


title: Control, IL6+, donor 2


title: Control, IL6-, donor 2


title: B. dorsalis, mock dose, 24 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_24_5

value: whole body fly tissue


title: Beko_24h_DMSO_H3K36me2_batch2_Rep2


title: NP-Plp Tumor 9 Grade UD

value: NP-Plp

value: GEM PNST/UD (grade undetermined)


title: NPcis Tumor 1 Grade III


title: Beko_24h_DMSO_H3K9me2_batch1_Rep2

value: Beko

value: Progenitor T-cell

value: H3K9me2 (Active Motif 39753)


title: B. dorsalis, mock dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_24_3


title: B. dorsalis, mock dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_12_6

value: 12 h post injection


title: NP-Plp Tumor 8 Grade III


title: Control, IL6+, donor 1

value: CD8+ T cells


title: NP-Plp Tumor 7 Grade UD


title: Beko_24h_DMSO_H3K9me1_batch3_Rep2

value: 24 hours with DMSO

value: H3K9me1 (Cell Signaling 14186)


title: B. dorsalis, mock dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_12_3


title: Beko_24h_DMSO_H3K36me1_batch2_Rep2

value: H3K36me1 (Cell Signaling #14111)


title: Control, IL6-, donor 1


title: NP-Plp Tumor 6 Grade III

value: GEM PNST/Grade III


title: Beko_24h_GSI_H3K27me3_batch1_Rep1

value: 24 hours with 10 mg/ml DAPT (GSI)

value: H3K27me3 (Active Motif 39155)


title: NPcis Tumor 2 Grade III

value: NPcis


title: Beko_24h_DMSO_H3K9me3_batch1_Rep2

value: H3K9me3 (Diagenode C15410193)


title: NP-Plp Tumor 5 Grade III


title: B. dorsalis, mock dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_12_2

value: third-instar larva

value: mock-saline dose


title: MPNST 8

value: MPNST


title: B. dorsalis, mock dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_0_6

value: whole body fly tissue

value: 0 h post injection


title: Beko_24h_GSI_H3K27me2_batch1_Rep1

value: Beko

value: Progenitor T-cell

value: H3K27me2 (Diagenode pAb-046-050)


title: NP-Plp Tumor 4 Grade III

value: NP-Plp


title: Beko_24h_GSI_H3K27me1_batch1_Rep1

value: H3K27me1 (Diagenode pAb-045-050)


title: B. dorsalis, mock dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_0_3


title: NF 8

value: NF


title: NP-Plp Tumor 3 Grade UD

value: GEM PNST/UD (grade undetermined)


title: Beko_24h_GSI_H3K18ac_batch2_Rep1

value: H3K18ac (Cell Signaling #9675S)


title: NF 6


title: B. dorsalis, mock dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_mk_0_2


title: B. dorsalis, 0.1x dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_24_4

value: 24 h post injection

value: 0.1x viral dose


title: Beko_24h_GSI_H3K9ac_batch2_Rep1

value: 24 hours with 10 mg/ml DAPT (GSI)

value: H3K9ac (abcam ab4441)


title: T30-4_3dpi-RNA-seq_rep2

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Phytophthora infestans whole genome using hisat2 v2.1.0 with default parameters
FPKM were calculated using stringtie v1.3.3b with default parameters
Assembly: Phytophthora infestans
Supplementary files format and content: Excel file with gene expression matrix

organism: Phytophthora infestans

source_name: 3dpi Pinfestans infected potato leaves

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: 3 dpi


title: B. dorsalis, 0.1x dose, 24 hpi, rep 2

first: Kelsey

last: Coffman

address: 64 Nowelo St

institute: USDA-ARS

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_24_3

value: third-instar larva


title: Beko_24h_GSI_H3K9me3_batch1_Rep1

value: H3K9me3 (Diagenode C15410193)


title: MPNST 9

value: MPNST


title: NF 5


title: NP-Plp Tumor 1 Grade UD


title: NF 4


title: Beko_24h_GSI_H3K36me3_batch2_Rep1

value: H3K36me3 (Cell Signaling #4909S)


title: B. dorsalis, 0.1x dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_24_1

value: whole body fly tissue


title: PNF 5

value: PNF


title: T30-4_2dpi-RNA-seq_rep2

source_name: 2dpi Pinfestans infected potato leaves

value: 2 dpi


title: B. dorsalis, 0.1x dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_12_6

value: 12 h post injection


title: T30-4_3dpi-RNA-seq_rep1


title: PNF 4


title: T30-4_2dpi-RNA-seq_rep1


title: Beko_24h_GSI_H3K36me2_batch2_Rep1

value: Beko

value: Progenitor T-cell


title: NF 7

value: NF


title: NF 3


title: T30-4_MY-ChIP-seq_input_rep2

data_processing:
Clean reads were aligned to Phytophthora infestans whole genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Assembly: Phytophthora infestans
Supplementary files format and content: Bigwig files, scores represent enriched value(log2(fold-change))

source_name: mycelium

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

value: mycelium

tag: antibody


title: B. dorsalis, 0.1x dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_12_4


title: NP-Plp Tumor 2 Grade UD

value: NP-Plp

value: GEM PNST/UD (grade undetermined)


title: Beko_24h_GSI_H3K36me1_batch2_Rep1

value: 24 hours with 10 mg/ml DAPT (GSI)

value: H3K36me1 (Cell Signaling #14111)


title: Beko_24h_GSI_H3K9me1_batch3_Rep1

value: H3K9me1 (Cell Signaling 14186)


title: T30-4_MY-ChIP-seq_input_rep1


title: PNF 2


title: Beko_24h_GSI_H3K9me2_batch1_Rep1

value: H3K9me2 (Active Motif 39753)


title: Beko_24h_DMSO_H3K27me2_batch1_Rep1

value: 24 hours with DMSO

value: H3K27me2 (Diagenode pAb-046-050)


title: Beko_24h_DMSO_H3K27me3_batch1_Rep1

value: H3K27me3 (Active Motif 39155)


title: MPNST 7

value: MPNST


title: Beko_24h_DMSO_H3K27me1_batch1_Rep1

value: H3K27me1 (Diagenode pAb-045-050)


title: B. dorsalis, 0.1x dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_0_6

value: whole body fly tissue

value: third-instar larva

value: 0 h post injection

value: 0.1x viral dose


title: B. dorsalis, 0.1x dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_0_4


title: T30-4_MY-ChIP-seq_H3K36me3_rep2


title: NF 2

value: NF


title: B. dorsalis, 0.1x dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_0_1


title: T30-4_MY-ChIP-seq_H3K36me3_rep1

value: mycelium


title: T30-4_MY-ChIP-seq_H3K27me3_rep2


title: NF 1


title: B. dorsalis, 1x dose, 24 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_24_4

value: 24 h post injection

value: 1x viral dose


title: T30-4_MY-ChIP-seq_H3K27me3_rep1


title: B. dorsalis, 0.1x dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_lo_12_1

value: 12 h post injection


title: Beko_24h_DMSO_H3K9ac_batch2_Rep1

value: Beko

value: Progenitor T-cell

value: H3K9ac (abcam ab4441)


title: Beko_24h_DMSO_H3K18ac_batch2_Rep1

value: 24 hours with DMSO

value: H3K18ac (Cell Signaling #9675S)


title: B. dorsalis, 1x dose, 24 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_24_2


title: PNF 1

value: PNF


title: Beko_24h_DMSO_H3K9me3_batch1_Rep1

value: H3K9me3 (Diagenode C15410193)


title: PNF 3


title: MPNST 6

value: MPNST


title: T30-4_MY-ChIP-seq_H3K9me3_rep2


title: Beko_24h_DMSO_H3K36me3_batch2_Rep1

value: H3K36me3 (Cell Signaling #4909S)


title: T30-4_MY-ChIP-seq_H3K9me3_rep1


title: B. dorsalis, 1x dose, 12 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_12_3

value: whole body fly tissue

value: third-instar larva


title: MPNST 5


title: T30-4_MY-ChIP-seq_H3K4me3_rep2


title: Beko_24h_DMSO_H3K9me2_batch1_Rep1

value: H3K9me2 (Active Motif 39753)


title: MPNST 4


title: T30-4_MY-ChIP-seq_H3K4me3_rep1


title: B. dorsalis, 1x dose, 12 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_12_2


title: B. dorsalis, 1x dose, 24 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_24_3


title: T30-4_MY-ATAC-seq_rep2

data_processing:
Clean reads were aligned to Phytophthora infestans whole genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Assembly: Phytophthora infestans
Supplementary files format and content: Bigwig files, scores represent enriched value(log2(RPKM)）

extract_protocol:
The protoplast of P. infestans T30-4 mycelium stage sample were sent to BGI
Libraries were prepared for sequencing using standard Illumina protocols


title: Beko_24h_DMSO_H3K9me1_batch3_Rep1

value: H3K9me1 (Cell Signaling 14186)


title: MPNST 3


title: B. dorsalis, 1x dose, 12 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_12_1


title: B. dorsalis, 1x dose, 0 hpi, rep 3

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_0_6

value: 0 h post injection


title: MPNST 2


title: T30-4_MY-ATAC-seq_rep1


title: MPNST 1


title: Beko_24h_DMSO_H3K36me1_batch2_Rep1

value: H3K36me1 (Cell Signaling #14111)


title: B. dorsalis, 1x dose, 0 hpi, rep 1

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_0_3

value: 1x viral dose


title: B. dorsalis, 1x dose, 0 hpi, rep 2

description:
DlEPV_all_sample_log2_rpkms.csv
Bdor_all_gene_fpkm.csv
Bdor_hi_0_4


title: Zn3: Mus musculus

status: Public on Mar 23 2024

first: Shuang

last: Li

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).  5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Mouse Mononuclear Macrophages Cells

value: Zn


title: Zn2: Mus musculus


title: Zn1: Mus musculus


title: Beko_24h_DMSO_H3K36me2_batch2_Rep1

first: Tobias

last: Friedrich

address: 421 Curie Boulevard

institute: University of Pennsylvania

value: Beko

value: Progenitor T-cell


title: test 3

type: RNA

description: circRNA RNAs expression after incomplete ultrasound-guided RFA treatment

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays v2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: The samples preparation were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Total RNA from each sample was quantified using the NanoDrop ND-1000.

value: liver


title: control 4

description: circRNA RNAs expression after no treatment


title: C2: Mus musculus

value: control


title: control 2


title: control 1


title: test 2


title: T-9_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
library strategy: Smart-seq120
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

source_name: Oocyte

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 268 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: Tcf3/12 KO

value: oocyte


title: control 3


title: test 4


title: T-8_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq116
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 264 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-95_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq119
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 267 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-93_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq118
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 266 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-7_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq115
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 263 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: test 1


title: T-79_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq114
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 262 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).