title: mouse brain, sham, rep3

city: Wuhan

first: Qiong

last: Yuan

address: Huangjiahu Road 2#

data_processing:
The expression level of lncRNA was estimated by reads per kilobase of transcript per million mapped reads. A log2 fold change >1 and q < 0.001 were used as thresholds for significantly altered lncRNAs.
Assembly: mm10
Supplementary files format and content: gene_exp-hxm.txt: Matrix table of all gene expression includes count and RPKM values for each Sample.
Supplementary files format and content: gene differential_expression.all.gene-hxm.txt: Gene expression differently for every gene and every Sample.

source_name: brain

growth_protocol: Adult male C57/BL6 mice, 22-25g, 8-9 weeks old, were purchased from the Experimental Animal Center of Hubei, China (license number: SCXK (Q) 2015-0018). The mice were housed under a standard environment of 24 ± 1 °C and 55% – 70% humidity, with a 12-hour light/dark cycle. Food and water were available ad libitum. Animals experimental procedures involving animals were approved by the Animal Protection and Utilization Committee of Wuhan University of Science and Technology.

extract_protocol:
The total RNA samples were treated with Trizol (Life Technologies, USA) in accordance with the kit’s instructions. The total RNA concentrations and quality were assessed by NanoDrop-1000 and Agilent 2200. Specifically, OD260/OD280 remained between 1.8 and 2.2, and 28S/18S > 1.5, RIN >8, while the concentrations of total RNA were to be over 400 ng/μl. EpicentreRibo-Zero rRNA Removal Kit (Illumina, USA) was used to eliminate all rRNAs from the total RNA.
Purified RNA fragments were subjected to the first strand and second-strand cDNA synthesis. Afterwards, adapter-ligated and enriched RNA-Seq libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). DNA was amplified. The library’s quality and concentration were validated by Agilent 2200 TapeStation (Agilent Technologies, USA). The obtained libraries were subjected to paired-end sequencing on an Illumina HiSeq2500 platform.

treatment_protocol:
The MCAO model was processed according to a previous study. In brief, the mice were anesthetized with 10% chloral hydrate (350 mg/kg IP) to the right carotid arteries, external carotid artery (ECA), and internal carotid artery (ICA) were exposed through a longitudinal median neck incision. A 6-0 monofilament nylon suture with a silicone-coated (Ethicon, England) was inserted into the ECA incision and advanced towards the middle cerebral artery (MCA) origin through the ICA to obstruct the MCA.
After 60 min of occlusion, the filament was withdrawn to allow blood reperfusion. Sham mice were subjected to the same operation, except the filament was not inserted. The surgery was done under a microscope and body temperature was maintained at 37 °C during surgery with a heating pad. High-throughput sequencing was performed at RiboBio (Guangzhou, China).

value: brain

tag: Sex

value: male

value: adult

value: sham


title: mouse brain, sham, rep2

status: Public on May 12 2023

type: SRA

country: China

institute: Wuhan University of Science and Technology

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: strain

tag: age

tag: treatment


title: mouse brain, ischemia 1h/reperfusion 6h, rep1

value: ischemia/reperfusion


title: mouse brain, ischemia 1h/reperfusion 6h, rep3


title: Liver_ECs_Control Biol rep 1

city: Madrid

first: Rui

last: Benedito

state: Madrid

address: C. de Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
For Experiment 1, 2 and 3: the number of reads per sample was between 12 and 42 million. Reads were processed with a pipeline that assessed read quality using FastQC and trimmed sequencing reads using cutadapt, eliminating Illumina and SMARTer adaptor remains and discarding reads < 30 bp. More than 93% of reads were kept for all samples. Resulting reads were mapped against the mouse transcriptomes GRCm38.76 (Experiments 1 and 3) and GRCm38.91 (Experiment 2), and gene expression levels were estimated with RSEM. The percentage of aligned reads was above 83% for most samples. Expression count matrices were then processed with an analysis pipeline that used Bioconductor package limma for normalization (using the TMM method) and differential expression testing, taking into account only those genes expressed with at least 1 count per million (CPM) in at least two samples (the number of samples for the condition with the least replicates), and using a random variable to define blocks of samples obtained from the same animal. Changes in gene expression were considered significant if associated with a Benjamini and Hochberg adjusted p-value < 0.05.
Assembly: GRCm38_76 and GRCm38_91
Supplementary files format and content: tab separated normalized counts matrix: NormCounts_GRCm38_76.txt, NormCounts_GRCm38_91.txt

source_name: Liver

extract_protocol:
For Experiment 1, 2 and 3, Heart, lungs, brain and/or liver were dissected, minced and digested with 2.5 mg/ml collagenase type I (Thermofisher), 2.5 mg/ml dispase II (Thermofisher), and 50 ng/ml DNAseI (Roche) at 37°C for 30 min to create a single-cell suspension. Cells were passed through a 70 µm filter to remove non-dissociated tissue. Erythroid cells were removed from cell suspensions by incubation with blood lysis buffer (0.15 M NH4Cl, 0.01M KHCO3, and 0.01 M EDTA in distilled water) for 10 min on ice. Cell suspensions were blocked in blocking buffer (DPBS containing no Ca2+ or Mg2+ and supplemented with 3% dialyzed FBS; Thermo Fisher). For EC analysis, cells were incubated at 4°C for 30 min with APC-conjugated rat anti-mouse CD31 (1:200, BD Bioscience, 551262). DAPI (5 mg/ml) was added to the cells immediately before FACS, which was performed with FACS Aria (BD Biosciences) or Synergy4L cell sorters. For the isolation of ECs from dissociated tissues, viable cells were selected by DAPI-negative fluorescence. All viable cells were interrogated by examining FSC and SSC to select for size and complexity, and by comparing FSC-H and FSC-W repeated with SSC-H and SSC-W to discern single cells. An additional channel lacking any fluorescent label was also acquired to detect and exclude autofluorescence. Cells were selected by their APC and/or endogenous MbTomato positive signal and were gated with a negative control sample. For bulk RNA-seq experiments, approximately 10000-20000 cells for each group of DAPI-negative APC-CD31+ ECs (for Dll4 loss of function, anti-Dll4 treatment and control samples), DAPI negative APC-CD31+/MbTomato+ ECs (for Rbpj loss of function and control) were sorted directly to RLT buffer (RNAeasy Micro kit - Qiagen). RNA was extracted with the RNAeasy Micro kit and stored at -80°C
For Experiment 1 samples, 1 ng of total RNA was used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara) following manufacturer´s instructions. Then, 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). For Experiment 2, between 400 and 3000 pg of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions For Experiment 3, libraries were generated using the Ovation® Single Cell RNA-Seq System  (NuGEN) following manufacturer´s instructions. All libraries were sequenced on a HiSeq2500 (Illumina)

treatment_protocol: For Experiment 1, 1 mg tamoxifen was injected on 3 consecutive days into Tg(Cdh5-CreERT2); Dll4flox/flox mice and control mice (Dll4flox/flox mice). Mice were processed following day 14 after the first tamoxifen injection For the Experiment 2, 2 mg tamoxifen was injected on 5 consecutive days into  Tg(Cdh5-CreERT2); Tg(iSuRe-Cre); Rbpjflox/flox  mice and control mice (Tg(Cdh5-CreERT2); Tg(iSuRe-Cre). Mice were processed following day 14 after the first tamoxifen injection. For the Experiment 3 in adult mice, 20 mg/kg of Dll4 blocking antibody was injected into C57BL6 mice and mouse IgG were used for control mice. 48 hours after injection mice were processed.

tag: cell type

value: Endothelial cells

value: Liver

tag: genotype

value: C57BL6 or C57BL6x129SV genetic backgrounds

value: 8-20 weeks old

tag: group


title: Liver_ECs_aDll4 Biol rep 2


title: mouse brain, ischemia 1h/reperfusion 6h, rep2


title: M1BP, RNAi, 25, Rep3

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped to the dm6 genome using subread-align (Subread package v2.0.3) on the command line using default parameters
Reads aligning to dm6 (release r6.19) exons were counted using featureCounts (Subread package v2.0.3) on the command line using default paramters
Differentially expressed genes were called using DESeq2 (version 1.3.0)
Assembly: dm6
Supplementary files format and content: Differentially expressed genes from DESeq2 analyses in tab-delimited text format

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: FACS-purified larval myoblasts from dissected wing discs (~25 000 cells) from M1BP RNAi (raised at 25oC)

extract_protocol:
For the wing, disc-associated myoblasts dissociation was performed according to a modified protocol (Khan et al., 2016). 0 h APF Mef2-GAL4, UAS-GFP::Gma/WT or UAS-M1BP RNAi #1 expressing larvae were washed in PBS, sterilised with 70% ethanol and dissected in Supplemented Schneider’s Medium (SSM) containing 10% Foetal bovine serum, 2% Penicillin/Streptomycin and 0.02 mg/mL Insulin. 30 to 35 wing discs were collected in ice-cold PBS and dissociated using preheated TrypLE 10x at 30°C for 45 min at 300rpm. The reaction was stopped by adding SSM and the cells were mechanically resuspended by gentle pipetting. Aggregates were removed by filtering cells in a cell strainer (30µm, Miltenyi) and cells were sorted using a FACS AriaII Machine (BD), according to cell viability, size and GFP intensity. Myoblasts were sorted directly in the kit-provided Lysis buffer supplemented with 2-Mercaptoethanol (#M6250, Sigma) and kept at -80°C until RNA extraction, which was preferentially performed the same day. RNA was isolated from the pure myoblast population of approximately 50 000 cells using RNA extraction Microkit (#74004, Qiagen).
Full length cDNA were generated from 2ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

tag: cells

value: Late larval (0h APF) myoblasts

value: 0h APF

tag: gal4 driver

value: M1BP RNAi


title: Ecoli rRNA ic Rep1 SS2 Modified

city: Houston

first: Anthony

middle: McDowell

last: Mustoe

state: TX

address: 1 Baylor Plaza

department: Biochemistry

country: USA

institute: Baylor College of Medicine

data_processing:
Fastq files were aligned and parsed using ShapeMapper2 (v.2.1.5; https://github.com/Weeks-UNC/shapemapper2) for files designated Orig or Shapemapper2.2 for files designated 22dev-DMS
Parsed mutation files were analyzed using RingMapper (v1)
Assembly: sequence files used for alignment are included as supplementary files
Supplementary files format and content: Processed data archives (.tar) include Shapemapper reactivity profiles (profile.txt), normalized DMS reactivites (.dms), and pairmap analysis files (pairmap.txt). A complete description of these files is provided in the ShapeMapper and RingMapper documentation

organism: Escherichia coli

source_name: liquid cell culture

growth_protocol: E. coli cells were grown in liquid LB media, while HEK293 cells were grown on 10 cm cell culture dishes in DMEM media.

extract_protocol:
Reverse-transcription was performed using specific primers, and DNA libraries were generated using a two-step PCR protocol.  Sample-specific modification and extraction details are provided in the SAMPLES section. All samples were DNase treated and purified using Qiagen RNeasy prior to reverse transcription.  Mutational profiling (MaP) reverse transcription (RT) was performed using an updated protocol that substantially improves yield and product length. In an 11 μL volume, RNA was mixed with 200 nM specific primer or 20 ng/μL random 9mer and 2 mM dNTPs and incubated at 65 °C for 10 min followed by 4 °C for 2 min. 8 uL 3x MaP buffer [1x MaP buffer consists of 6 mM MnCl2, 1 M betaine, 50 mM Tris (pH 8.0), 75 mM KCl, 10 mM DTT] was added and the combined solution incubated at 23 °C for 2 min. Finally, 1 μL SuperScript II Reverse Transcriptase (Invitrogen) was added and the RT reaction was performed according to the following temperature program: 25 °C for 10 min, 42 °C for 90 min, 10x[50 °C for 2 min, 42 °C for 2 min], 72 °C for 10 min. For the adenine riboswitch, ~1 pmol RNA was input into RT. For E. coli and human short RNAs, 0.5-2 μg total RNA was input into RT. For randomly primed E. coli RNA samples (16S and 23S rRNA), 1.5-3 μg total RNA was input into RT. RT products were then purified (Agencourt RNAclean XP beads, Beckman Coulter). Sequencing adaptors were added according to protocols listed in the SAMPLES section.
RNA was converted to cDNA using mutational profiling (MaP) reverse transcription, and libraries were prepared by 2-step PCR.

treatment_protocol:
Exponential E. coli cultures were treated for 20 minutes with rifampicin, pelleted, resuspended in 200 mM bicine (pH 8.0), 200 mM KOAc, 5 mM MgCl2, and modified with 700 mM DMS for 6 minutes at 37 °C. Total RNA was then extracted using Trizol.
RNA was folded at 30 C in 300 mM bicine (pH 8.0), 100 mM NaCl, 5 mM MgCl2 with variable adenine and modified with DMS (or ethanol) for 10 minutes, quenched with 20% 2-mercaptoethanol, and ethanol precipitated.

tag: substrain

tag: probing condition

value: in-cell

value: DMS


title: mouse brain, sham, rep1


title: Liver_ECs_aDll4 Biol rep 3


title: Liver_ECs_Control Biol rep 2


title: Ecoli rRNA ic Rep1 Mara Untreated

extract_protocol:
Reverse-transcription was performed using specific primers, and DNA libraries were generated using a two-step PCR protocol.  Sample-specific modification and extraction details are provided in the SAMPLES section. All samples were DNase treated and purified using Qiagen RNeasy prior to reverse transcription.  Mutational profiling (MaP) reverse transcription (RT) was performed using an updated protocol that substantially improves yield and product length. In a 5.8 μL volume, RNA was mixed with 200 nM specific primer or 20 ng/μL random 9mer and 2 mM dNTPs and incubated at 65 °C for 10 min followed by 4 °C for 2 min. 12.2 uL 3x MaP buffer [1x MaP buffer consists of 1 mM MnCl2, 50 mM Tris (pH 8.3), 200 mM KCl, 5 mM DTT, 20% glycerol] was added and the combined solution incubated at 23 °C for 2 min. Finally, 1 μL MarathonRT Reverse Transcriptase (Kerafast) was added and the RT reaction was performed according to the following temperature program: 42 °C for 3 h. For E. coli and human short RNAs, 0.5-2 μg total RNA was input into RT. For randomly primed E. coli RNA samples (16S and 23S rRNA), 1.5-3 μg total RNA was input into RT. RT products were then purified (Agencourt RNAclean XP beads, Beckman Coulter). Sequencing adaptors were added according to protocols listed in the SAMPLES section.
RNA was converted to cDNA using mutational profiling (MaP) reverse transcription, and libraries were prepared by 2-step PCR.

value: EtOH


title: amhc:EGFP+;myl7:dsRED-NLS+ nr2f1a mutant

city: Cincinnati

first: Joshua

last: Waxman

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology Division

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
RNA-seq reads in FASTQ format were subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments using FastQC v0.11.5 , Trim Galore! v0.4.2  and cutadapt v1.9.1.
The trimmed reads were aligned to the reference zebrafish genome version danRer10 with the program STAR v2.5.2.
Aligned reads were stripped of duplicate reads with the program picard v1.89.
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database.
Read counting was done with the program featureCounts v1.5.3 from the Rsubread package.
Raw counts were normalized as transcripts per million (TPM).
ATAC-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments using FastQC v0.11.5, Trim Galore! v0.4.2 and cutadapt v1.9.1
The trimmed reads were aligned to the reference zebrafish genome version danRer10 with the program STAR v2.5.2 with splice awareness turned off.
Aligned reads were stripped of duplicate reads with the program picard v1.89.
Peaks were called using the program MACS v2.1.2 using the broad peaks mode.
Peaks with q-value < 0.01 were selected for further analysis.
Common peaks among all samples were obtained by merging called peaks at 50% overlap using BEDtools v2.27.0.
The common peaks, originally in BED format were converted to a Gene Transfer Format (GTF) to enable fast counting of reads under the peaks with the program featureCounts v1.5.3 (Rsubread package).
BAM files are converted into wig format using bedtools v2.27.0.
The normalization is performed using a scaling factor proportional to the total number of per million mapped reads in the BAM file.
Wig files are converted to bigWig format using the tool wigToBigWig.
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: text file of matrix table with normalized transcripts per million read counts
Supplementary_files_format_and_content: text file of matrix table with raw read counts of ATAC peak coordinates
Supplementary_files_format_and_content: bigwig file of the ATAC-Seq data from wt and nr2f1a mutant samples

molecule: genomic DNA

organism: Danio rerio

source_name: amhc:EGFP+;myl7:dsRED-NLS cells

extract_protocol:
For amhc:EGFP+ and amhc:EGFP+/myl7:DsRED-NLS cells, they were flow sorted following digestion of whole embryos at 48 hours post-fertlization. For RNA, the RNA was harvested using TRIZOL and a PureLink RNA Micro Kit (Invitrogen). The libary was then amplified using a Single Cell Purification Kit (Norgen Biotek). For ATAC-seq, the harvested cells were processed for ATAC-seq with the Tn protein and libraries generated.
RNA and ATAC libraries were prepared for sequencing using standard protocols

value: AB/TU

value: sorted amhc:EGFP+;myl7:dsRED-NLS cells

value: 48 hours post-fertilization


title: Ecoli rRNA ic Rep1 Mara Modified


title: Liver_ECs_Control Biol rep2

value: Cdh5-CreERT2 iSuRe-Cre with C57BL6 or C57BL6x129SV genetic backgrounds


title: M1BP, RNAi, 25, Rep1


title: Liver_ECs_Control Biol rep1


title: Liver_ECs_Rbpjdeletion Biol rep3

value: Rbpj floxed/floxed Cdh5-CreERT2 iSuRe-Cre with C57BL6 or C57BL6x129SV genetic backgrounds


title: MV4-11 cells, Chidamide combined with Cytarabine group 2

city: chengdu

first: qing

last: li

state: Sichuan

address: No.37 Guoxue Lane, Wuhou District

department: Hematology

institute: West China Hospital of Sichuan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Reference genome
Supplementary files format and content: An excel file including the RPKM values for each sample

organism: Homo sapiens

growth_protocol: Mv4-11 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA was harvested using Trizol (Cwbio, Jiangsu, China). 1.0 ug of total RNA was used for the construction of sequencing libraries.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.

treatment_protocol: MV4-11 cells were treated with 1µM chidamide and 2µM cytarabine alone or in combination for 24 hours to explore the mechanism of their synergistic effect

tag: cell line

value: Mononuclear cells

value: WT

value: Chidamide combined with cytarabine group treated for 24 h


title: WT, 25, Rep3

source_name: FACS-purified larval myoblasts from dissected wing discs (~25 000 cells) from WT (raised at 25oC)


title: MV4-11 cells, Cytarabine group 3

value: Cytarabine treatment for 24 h


title: HEK293 RMRP ic Rep1 Mara Modified

source_name: adherent cell culture

treatment_protocol:
HEK293 cell cultures were supplemented with bicine buffer [200 mM bicine (pH 8.0), final concentration], and modified with 170 mM DMS for 6 minutes at 37 °C. Total RNA was then extracted using Trizol.
RNA was folded at 30 C in 300 mM bicine (pH 8.0), 100 mM NaCl, 5 mM MgCl2 with variable adenine and modified with DMS (or ethanol) for 10 minutes, quenched with 20% 2-mercaptoethanol, and ethanol precipitated.


title: Liver_ECs_Rbpjdeletion Biol rep2

value: Endothelial cells

value: Liver


title: MV4-11 cells, Chidamide combined with Cytarabine group 3


title: Liver_ECs_aDll4 Biol rep 1

value: C57BL6 or C57BL6x129SV genetic backgrounds

value: 8-20 weeks old


title: WT, 25, Rep2

value: Late larval (0h APF) myoblasts

value: 0h APF


title: Brain_ECs_Dll4deletion_Biol rep 3

source_name: Brain

value: Brain

value: Dll4 floxed/floxed Cdh5-CreERT2


title: MV4-11 cells, Cytarabine group 2


title: Mef2-GAL4 x M1BP RNAi 2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped to the dm6 genome using subread-align (Subread package) on the command line using default parameters
Reads aligning to dm6 (release r6.19) exons were counted using featureCounts (Subread package) on the command line using default paramters
Differentially expressed genes were called using DESeq2 (version 1.3.0)
Assembly: dm6
Supplementary files format and content: Differentially expressed genes from DESeq2 analyses in Microsoft Excel format

source_name: Mef2-GAL4 x M1BP RNAi

extract_protocol:
RNA isolation was performed on hand dissected indirect flight muscles from 30, 2-days old females. The tissue was collected in batches of 15 flies at a time to minimize the time between samples and TRIzol treatment and transferred to Eppendorf tubes, then centrifuged at 2000 g for 5 min at 4 ºC. The flight muscle pellet was resuspended in TRIzol reagent (Thermofisher cat #15596026), shock froze in liquid nitrogen and kept at -80 ºC. RNA was isolated directly from the TRIzol muscle samples using a tube-based purification kit from Zymo Research (Direct-zol RNA Microprep, Zymo Research, #R2060)
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: dorsolongitudinal flight muscle

value: adult 2-day

value: M1BP RNAi


title: WT, 25, Rep1


title: MV4-11 cells, Cytarabine group 1


title: Mef2-GAL4 x M1BP RNAi 3


title: M1BP, RNAi, 25, Rep2


title: MV4-11 cells, Chidamide group 3

value: Chidamide treatment for 24 h


title: MV4-11 cells, Chidamide combined with Cytarabine group 1


title: Brain_ECs_Control_Biol rep 2

value: Dll4 floxed/floxed


title: Brain_ECs_Dll4deletion_Biol rep 2


title: Heart_ECs_Control_Biol rep 3

source_name: Heart

value: Heart


title: MV4-11 cells, Chidamide group 2

value: Mononuclear cells

value: WT


title: Heart_ECs_Dll4deletion_Biol rep 3


title: Lung_ECs_Dll4deletion_Biol rep 1

source_name: Lung

value: Lung


title: Mef2-GAL4 x M1BP RNAi 1


title: Heart_ECs_Dll4deletion_Biol rep 2

value: Endothelial cells


title: Liver_ECs_Rbpjdeletion Biol rep1

value: Liver

value: Rbpj floxed/floxed Cdh5-CreERT2 iSuRe-Cre with C57BL6 or C57BL6x129SV genetic backgrounds


title: Mef2-GAL4 x w1888 3

source_name: Mef2-GAL4 x w1888


title: MV4-11 cells, Chidamide group 1


title: MV4-11 cells, Control group 3

value: Incubation for 24 h


title: Lung_ECs_Dll4deletion_Biol rep 2

value: C57BL6 or C57BL6x129SV genetic backgrounds

value: 8-20 weeks old


title: Mef2-GAL4 x w1888 2


title: Lung_ECs_Control_Biol rep 3


title: MV4-11 cells, Control group 2


title: Lung_ECs_Control_Biol rep 2


title: Heart_ECs_Control_Biol rep 2


title: Mef2-GAL4 x w1888 1


title: MV4-11 cells, Control group 1


title: Liver_ECs_Dll4deletion_Biol rep 1


title: M1BP RNAi, 64h APF, 3

source_name: indirect flight muscle dissected from 64-hour old Drosophila pupae

extract_protocol:
Mef2-GAL4/WT or UAS-M1BP RNAi expressing pupa were staged at 25°C and dissected in ice-cold PBS. The dissection was performed according to a published protocol (Weitkunat and Schnorrer, 2014). Hand-isolated IFM from 6 to 8 pupa were directly collected in the kit-provided Lysis buffer supplemented with 2-Mercaptoethanol (#M6250, Sigma), homogenised with a small pestle and RNA was extracted using RNA extraction Microkit (#74004, Qiagen).
P2637 : RNA-Seq libraries were generated according to manufacturer's instructions from 100 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dTTP in place of dUTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 13 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

tag: tag

value: 64h-old pupae


title: Liver_ECs_Dll4deletion_Biol rep 2

value: Dll4 floxed/floxed Cdh5-CreERT2


title: Brain_ECs_Dll4deletion_Biol rep 1

value: Brain


title: Liver_ECs_Control_Biol rep 1


title: M1BP RNAi, 64h APF, 2

value: dorsolongitudinal flight muscle


title: Brain_ECs_Control_Biol rep 1


title: Lung_ECs_Control_Biol rep 1


title: Liver_ECs_Control_Biol rep 2


title: Heart_ECs_Control_Biol rep 1


title: mouse uterus, BPAF, rep2

city: Taiyuan

first: Xiaoyun

last: Wu

state: Shanxi

address: Wucheng Road 92, Xiaodian District

institute: Shanxi University

data_processing:
The quality of the original sequencing data was evaluated and filtered with Seqtk (https://github.com/lh3/seqtk) to remove unqualified reads. To compare gene expression levels quantitatively, reads were transformed into Fragments Per Kilobase of exon model per Million mapped reads (FPKM) for standardization.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: uterus

growth_protocol: Female CD-1 (ICR) mice aged seven to eight weeks were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd. (Beijing, China). The animals were acclimatized for one week in a controlled environment (temperature: 22 ± 2°C, relative humidity: 40–60%), with light-dark cycles of 12 h. To limit the interference from background bisphenol, the mice were placed in standard cages containing corncob bedding and provided with estrogen-free food (Beijing Vital River Laboratory Animal Technology Co., Ltd.) and filtered water (water bottles with rubber plugs and metal sippers).

extract_protocol:
RNAiso Plus Total RNA extraction reagent (Cat 9109, TAKARA) was used to extract total RNA from uterus samples.1.3 ug of total RNA was used for the construction of sequencing libraries.
Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US) was used for quality inspection to evaluate thAgilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US) was used for quality inspection to evaluate the integrity of RNA. After passing the quality inspection, total RNA was purified using RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc.Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat 79254, QIAGEN, GmBH, Germany). According to the manufacturer's protocol (VAHTS Stranded mRNA-seq Library Prep Kit for Illumina, Illumina, USA), mRNA isolation, fragmentation, cDNA synthesis, end repair, 3′ adenylation, adapter ligation, and cDNA templates enrichment were carried out to complete library construction. The concentration of the library was detected by Qubit® 2.0 Fluorometer and Qubit™ dsDNA HS kit, and the library was inspected by Agilent 2100 Bioanalyzer.

treatment_protocol: BPB/BPAF (300 μg/kg body weight (bw)/day) or corn oil (control) were continuously given by gavage for 28 days.

value: uterus

value: CD-1 (ICR)

value: female

value: BPAF

tag: time

value: 28 days


title: WT, 64h APF, 3

value: WT


title: mouse uterus, BPAF, rep1


title: mouse uterus, BPAF, rep3


title: mouse uterus,BPB, rep3

value: BPB


title: mouse uterus,BPB, rep2


title: HHL-5 cells, ZBED3-OE, FFAs750μM, rep1

city: Wanzhou

first: he

middle: xiao

last: luo

state: Chongqing

address: No. 165 Xincheng Road

institute: Chongqing university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample,  please see the ExpressionProfile.txt for details.

growth_protocol: HHL-5 hepatocytes were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Retains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina Truseq RNA Sample Prep Kit (Cat#FC-111-1001) was used with 1ug of total RNA for the construction.
RNA libraries were prepared for sequencing using stantard Illumina protocols.

treatment_protocol: Cells were fed with DMEM supplemented with 10% FBS and 750uM FFAs for 24 hours.

value: human embryonic hepatocytes

value: ZBED3 overexpression


title: HHL-5 cells, Control, FFAs750μM, rep2


title: HHL-5 cells, Control, FFAs750μM, rep3


title: Heart_ECs_Dll4deletion_Biol rep 1

value: Endothelial cells

value: Heart


title: HHL-5 cells, ZBED3-OE, FFAs750μM, rep3


title: WT, 64h APF, 2


title: WT, 64h APF, 1


title: mouse uterus,BPB, rep1


title: mouse uterus, control, rep3

value: pure corn oil


title: HHL-5 cells, Control, FFAs750μM, rep1


title: HHL-5 cells, ZBED3-OE, FFAs750μM, rep2


title: mouse uterus, control, rep1


title: mouse uterus, control, rep2


title: M1BP RNAi, 48h APF, 3

source_name: indirect flight muscle dissected from 48h old Drosophila pupae

value: 48h-old pupae

value: M1BP RNAi


title: Lipo-246, 10uM Nutlin, 12.5nM Carfilzomib 28hr, Combo replicate 2

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (RPKM).

source_name: Lipo-246 liposarcoma cells

growth_protocol: 94T778 and Lipo-246 cells were cultured in DMEM/F12 supplemented with 10% Equa Fetal and 1x anti-anti and were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Qiagen RNeasy
Strand-specific poly(A)+-enriched mRNA library (Illumina TruSEQ mRNA)
RNA library sequencing

treatment_protocol: 94T778 and Lipo-246 cells were treated with vehicle (DMSO 0.05%) or 10 uM Nutlin3R and/or 12.5 nM Carfilzomib for 28 hr

value: liposarcoma cells

value: 28 hr 10µM Nutlin3R + 12.5nM Carfilzomib


title: M1BP RNAi, 64h APF, 1

value: dorsolongitudinal flight muscle

value: 64h-old pupae


title: M1BP RNAi, 48h APF, 2


title: WT, 48h APF, 3


title: Lipo-246, 10uM Nutlin, 12.5nM Carfilzomib 28hr, Combo replicate 1


title: Lipo-246, 12.5nM Carfilzomib 28hr, replicate 2

value: 28 hr 12.5nM Carfilzomib


title: WT, 48h APF, 1


title: Lipo-246, 10uM Nutlin 28hr, replicate 2

value: 28 hr 10µM Nutlin3R


title: Lipo-246, 10uM Nutlin 28hr, replicate 1


title: TIGER_HAP1_D14_R4

city: New York

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
Infected with pooled RfxCas13d gRNA library (lentivirus).
Pooled CRISPR screen
TIGER_Ontarget_counts.csv
TIGER_Titration_counts.csv

data_processing:
Illumina Casava software used for basecalling.
Reads were demultiplexed based on Illumina i7 barcodes present in PCR2 reverse primers using bcl2fastq and by their custom in-read 5' barcode using a custom python script correcting 5' barcodes with up to one mismatch to the expected barcode.
Reads were trimmed to the expected gRNA length by searching for known anchor sequences relative to the guide sequence. Reads were collapsed (FASTX-Toolkit) to count perfect duplicates followed by exact string-match intersection with the reference to retain only perfectly matching and unique alignments.
Assembly: Custom crRNA library
Supplementary files format and content: *.csv: Comma-separated text files contain raw guide RNA counts.

extract_protocol:
Genomic DNA was extracted from screen cells using the following protocol: Per 100 million cells, 12 mL of NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8) was used for cell lysis. Once cells were resuspended, 60 µL of 20 mg/ml Proteinase K (Qiagen) was added and the sample was incubated at 55°C overnight. The next day, 60 µL of 20 mg/ mL RNase A (Qiagen) was added, mixed, and samples were incubated at 37 C for 30 min. Then 4 mL of pre-chilled 7.5 M ammonium acetate was added, samples were vortexed and spun at 4,000 g for 10 min. The supernatant was placed in a new tube, mixed well with 12 mL isopropanol and spun at 4,000 g for 10 min. DNA pellets were washed with 12 mL of 70% ethanol, spun, dried and pellets were resuspended with 0.2x TE buffer (Sigma). In addition, we also generated linearized plasmid library input and diluted it down to mimic similar copy number conditions as the genomic DNA samples.
We used a two-step PCR protocol (PCR1 and PCR2) to amplify the guide RNA cassette for Illumina sequencing from genomic DNA (gDNA). For the PCR1 reaction, we used 960µg [Offtarget screen (1)] or 880µg [Tiger screens in HEK cells (2) and HAP1 cells (3)] gDNA for each sample. Per sample we performed 96 or 88 100µL PCR1 reactions with a 100µl reaction volume: 10µl 10x Taq buffer, 0.02U/µl Taq-B enzyme (Enzymatics #P7250L), 0.2mM dNTPs, 0.2µM forward and reverse primers and 100ng gDNA/µl; PCR1 thermocycling conditions were: 94°C/30s, 10x (screen 1) or 18x (screens 2 and 3) [94°C/10s, 55°C/30s, 68°C/45s], 68°C/3min. For each sample, all PCR1 products were pooled and thoroughly mixed before PCR2.
For each sample, we performed 24 (screen 1) or 6 (screen 2 and 3) PCR2 reactions with a 100µl reaction volume: 20µl 5x Q5 buffer (NEB), 0.01U/µl Q5 enzyme, 20µl PCR1-product, 0.2mM dNTPs, 0.4µM forward and reverse PCR2-primers in 100µl. PCR2 thermocycling conditions were: 98°C/30s, 18x (screen1) or 8x (screen 2 and 3) [98°C/10s, 63°C/30s, 72°C/45s], 72°C/5min.
For each sample, PCR2 products were pooled, followed by normalization (gel-based band densitometry quantification), before combining equal amounts of uniquely-barcoded samples. The pooled product was then purified using SPRI beads. First, we performed a 0.6x vol/vol SPRI to remove gDNA carryover, followed by addition of a 0.3x vol/vol SPRI (0.6 + 0.3 = 0.9x final) to the supernatant to purify the ~260bp PCR product. The final amplicons were sequenced on Illumina NextSeq 500 – II MidOutput 1x150 v2.5 (screen 1) and Illumina NextSeq 500 – II HighOutput 1x150 v2.5 (screen 2 and 3).

value: chronic myelogenous leukemia

value: HAP1 TetO-RfxCas13d cells

value: doxycycline 1ug/ml

tag: sample type

value: Fitness Screen Day 14


title: TIGER_HAP1_D14_R3


title: TIGER_HAP1_D7_R2

value: Fitness Screen Day 7


title: TIGER_HAP1_D0_R2

value: Input Day 0


title: TIGER_HAP1_D0_R4


title: TIGER_HAP1_D14_R2


title: TIGER_HAP1_D0_R3


title: Lipo-246, 12.5nM Carfilzomib 28hr, replicate 1


title: PB52-T48-Rep-2

city: Tampa

first: Caroline

last: Simmons

state: Florida

address: 3720 E Spectrum Blvd

institute: University of South Florida

data_processing:
RNAseq reads from each sample were aligned to the P. falciparum reference genome usinf HISAT2.
Mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using SAMtools and the abundances were estimated using Feature Counts
Assembly: P. falciparum reference genome (PlasmoDB version 47)
Supplementary files format and content: feature_counts_output_MRST.xlsx is the output of Feature counts and contains ID (GeneID), chromosome (Chr), and the counts (number of reads), for each mapped gene from each RNAseq sample.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

growth_protocol: Parasite cultures were maintained according to standard methods with gassing (5% O2 and 5% CO2, nitrogen balanced) and 5% hematocrit (O+ blood; Interstate Blood Bank) in RPMI 1640 medium (Invitrogen) supplemented with 0.5% Albumax II (Invitrogen), 0.25% sodium bicarbonate, and 0.01 mg/ml gentamicin, maintained at 37°C.

extract_protocol:
Parasites were separated from red blood cells via incubation with 0.015% saponin at room temperature for 5 min. Cultures were then pelleted and washed three times in cold PBS. Samples were stored at − 80 °C in 1 mL TRIzol reagent (Fisher Scientific, Hampton, NH) until extraction. At RNA extraction, 200 μl of chloroform was added and samples were vortexed vigorously for 15 seconds, followed by incubation at room temperature for up to 5 minutes. Samples were then spun down at 12000×g (10,800 rpm) at 4 °C for 10 minutes and the supernatant discarded. 1 mL of 75% ethanol was added to the pellet, and samples were spun down at 10000×g (9800 rpm) for 5 minutes. The resulting supernatant was discarded and the pellet briefly allowed to dry. The RNA pellet was then dissolved in 20–50 μl of DEPC-treated water while being incubated at 55 °C for 10–15 min.
0.5 μg–1.0 μg of RNA samples were prepped for sequencing using the Illumina TruSeq Stranded mRNA Kit as per kit protocol. Library quantification was measured by qPCR and TapeStation (Agilent Technologies). Sequencing was performed on an Illumina NextSeq V2.5 mid-output 300-cycle.

treatment_protocol: Cultures of wildtype NF54 and PB52 (MRST mutant)  were synchronized at ~2% ring stage with 10% sorbitol solution. After 48 hours of growth, cultures were again synchronized with 10% sorbitol. After 8hrs, cultures were synchronized for a third time with 10% sorbitol to yield highly synchronized cultures. 0hpi was determined (half schizonts and half ring cultures) and samples were collected for RNA extraction and sequencing at 6hpi, 12hpi, 24hpi, 36hpi, and 48hpi.

value: PB52 (MRST mutant)

value: piggyBac mutant

tag: disrupted gene id

tag: developmental stage

value: late schizont


title: TIGER_HAP1_D7_R4


title: TIGER_HAP1_D7_R1


title: TIGER_HAP1_D7_R3


title: HEK293 RMRP ic Rep2 TGIRT Untreated

extract_protocol:
Reverse-transcription was performed using specific primers, and DNA libraries were generated using a two-step PCR protocol.  Sample-specific modification and extraction details are provided in the SAMPLES section. All samples were DNase treated and purified using Qiagen RNeasy prior to reverse transcription.  Mutational profiling (MaP) reverse transcription (RT) was performed using an updated protocol that substantially improves yield and product length. In a 10 μL volume, RNA was mixed with 200 nM specific primer or 20 ng/μL random 9mer and 2 mM dNTPs and incubated at 65 °C for 10 min followed by 4 °C for 2 min. 8 uL of 5x MaP buffer [final concentration 50 mM Tris–HCl (pH 8.3), 75 mM KCl, and 3 mM MgCl2] was added and the combined solution incubated at 23 °C for 2 min. Finally, 1 μL TGIRT-III Reverse Transcriptase (InGex) was added and the RT reaction was performed according to the following temperature program: 60 °C for 2 h. For E. coli and human short RNAs, 0.5-2 μg total RNA was input into RT. For randomly primed E. coli RNA samples (16S and 23S rRNA), 1.5-3 μg total RNA was input into RT. RT products were then purified (Agencourt RNAclean XP beads, Beckman Coulter). Sequencing adaptors were added according to protocols listed in the SAMPLES section.
RNA was converted to cDNA using mutational profiling (MaP) reverse transcription, and libraries were prepared by 2-step PCR.

value: in-cell

value: EtOH


title: PB52-T48-Rep-1


title: TIGER_HAP1_D14_R1


title: TIGER_HAP1_D0_R1


title: Lipo-246, DMSO, replicate 2

value: liposarcoma cells


title: TIGER_Ontarget_HEK293FT_D7_R3

description:
Infected with pooled RfxCas13d gRNA library (lentivirus).
Pooled CRISPR screen
TIGER_Ontarget_counts.csv

value: human embryonic kidney cells

value: HEK293FT TetO-RfxCas13d cells


title: TIGER_Ontarget_HEK293FT_D14_R3


title: PB52-T36-Rep-2

value: late trophozoite


title: TIGER_Ontarget_HEK293FT_D0_R3


title: PB52-T36-Rep-1


title: Lipo-246, DMSO, replicate 1


title: 94T778, 10uM Nutlin, 12.5nM Carfilzomib 28hr, Combo replicate 2

source_name: 94T778 liposarcoma cells

value: 28 hr 10µM Nutlin3R + 12.5nM Carfilzomib


title: WT, 48h APF, 2

tag: tissue

value: dorsolongitudinal flight muscle

value: 48h-old pupae

value: WT


title: TIGER_Ontarget_HEK293FT_D14_R2

value: doxycycline 1ug/ml


title: PB52-T24-Rep-2

tag: strain

value: early trophozoite


title: TIGER_Ontarget_HEK293FT_D0_R2


title: 94T778, 10uM Nutlin, 12.5nM Carfilzomib 28hr, Combo replicate 1


title: 94T778, 12.5nM Carfilzomib 28hr, replicate 1

value: 28 hr 12.5nM Carfilzomib


title: PB52-T12-Rep-2

value: ring


title: TIGER_Ontarget_HEK293FT_D14_R1

value: Fitness Screen Day 14


title: 94T778, 10uM Nutlin 28hr, replicate 1

value: 28 hr 10µM Nutlin3R


title: TIGER_Ontarget_HEK293FT_D7_R1

value: Fitness Screen Day 7


title: PB52-T24-Rep-1

value: PB52 (MRST mutant)

value: piggyBac mutant


title: 94T778, 12.5nM Carfilzomib 28hr, replicate 2

value: liposarcoma cells


title: PB52-T6-Rep-1

value: early ring


title: PB52-T6-Rep-2


title: PB52-T12-Rep-1


title: TIGER_Ontarget_HEK293FT_D0_R1

value: human embryonic kidney cells

value: HEK293FT TetO-RfxCas13d cells

value: Input Day 0


title: Offtarget_HEK293FT_D30_R3

description:
Infected with pooled RfxCas13d gRNA library (lentivirus).
Pooled CRISPR screen
Offtarget_HEK293FT_counts.csv

value: Fitness Screen Day 30


title: 94T778, 10uM Nutlin 28hr, replicate 2


title: TIGER_Ontarget_HEK293FT_D7_R2


title: NF54-T48-Rep-1

value: wildtype

value: late schizont


title: NF54-T48-Rep-2


title: Offtarget_HEK293FT_D0_R2

value: doxycycline 1ug/ml


title: Offtarget_HEK293FT_D30_R2


title: Offtarget_HEK293FT_D15_R1

value: Fitness Screen Day 15


title: Offtarget_HEK293FT_D15_R2


title: Offtarget_HEK293FT_D30_R1


title: CT-FT282-IgG-03012021

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

institute: Cedars Sinai Medical Center

data_processing:
library strategy: CUT&TAG
Both Cut&Run and Cut&Tag  data were processed based on Zheng Y et al (2020). Protocol.io FASTQ was first trimmed using trimmomatic (v0.39) and aligned using bowtie2 (v2.3.4.3). Then, duplicate reads were removed using Picard (v2.20). Remaining reads were then converted to bed files using bedtools(v2.29) for peak calling. Peaks were called using SEACR (v1.3)  with pval for Cut and Run and control with IgG  control (bedgrah).
ATAC seq was processed thorugh atac/dnase piepline (https://github.com/kundajelab/atac_dnase_pipelines/commit/a648870bf353d61c971246f4735b0f708615d8f3)
Assembly: hg38

source_name: Cell Line

extract_protocol: NEBnext

value: Cell Line

tag: antibody

value: IgG (Abcam)


title: 94T778, DMSO, replicate 1

tag: treatment


title: Offtarget_HEK293FT_D0_R3

tag: cell type


title: Offtarget_HEK293FT_D15_R3

tag: genotype


title: 94T778, DMSO, replicate 2


title: Offtarget_HEK293FT_D0_R1


title: CT-FT246-IgG-03012021


title: CT-FT19170-IgG-042421

source_name: Primary Ex-vivo Culture

value: Primary Ex-vivo Culture


title: NF54-T36-Rep-2

value: late trophozoite


title: CT-FT19168-IgG-050521


title: NF54-T36-Rep-1


title: AT-FT282-2

data_processing:
Both Cut&Run and Cut&Tag  data were processed based on Zheng Y et al (2020). Protocol.io FASTQ was first trimmed using trimmomatic (v0.39) and aligned using bowtie2 (v2.3.4.3). Then, duplicate reads were removed using Picard (v2.20). Remaining reads were then converted to bed files using bedtools(v2.29) for peak calling. Peaks were called using SEACR (v1.3)  with pval for Cut and Run and control with IgG  control (bedgrah).
ATAC seq was processed thorugh atac/dnase piepline (https://github.com/kundajelab/atac_dnase_pipelines/commit/a648870bf353d61c971246f4735b0f708615d8f3)
Assembly: hg38

value: Fallopian Tube Secretory Epithelium


title: AT-FT282-1


title: AT-Kuramochi-yLab-2

value: KURAMOCHI

value: High-grade serous "ovary" cancer


title: NCI-H295R, NFATc4 KO 2

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build GENCODE Homo sapiens GRCh38 Release 37
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited .txt files include 5 columns, ensemble transcripts identifier, transcript length, effective transcript length, estimated counts and transcripts per million.

growth_protocol: The NCI-H295R human adrenocortical carcinoma cell line was maintained in DMEM-F12 (GIBCO) supplemented with 10% FCS (Amimed) and 1X insulin-transferrin-selenium (ITS) (GIBCO).

extract_protocol:
RNA was extracted using the Quiagen RNeasy Mini Kit following manufacturer’s protocol. Extracted RNA was prepared for sequencing using the Illumina Truseq mRNA Library assay following manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For active-NFATc4 overexpression experiments, NCI-H295R cells were transfected with pcDNA3.T7 (mock),  and pcNDA3.T7 delta-NFAT3 (active NFATc4) plasmids and seeded onto 12-well plates. Three days after transfection, RNA was extracted from the cells.

value: Adrenocortical carcinoma

value: NFATc4 knock-out


title: NCI-H295R, NFATc4 KO 1


title: AT-Kuramochi-yLab-1


title: NF54-T24-Rep-1

value: early trophozoite


title: NCI-H295R, NFATc4 KO 3


title: CT-FT282-H3K27ac-03012021

value: H3K27ac (Diagenode)


title: NCI-H295R, control overexpression 4

value: WT

value: Empty vector overexpression


title: CT-FT246-H3K27ac-030421


title: NCI-H295R, control overexpression 3


title: NF54-T12-Rep-2

value: wildtype

value: ring


title: NCI-H295R, control overexpression 2


title: CT-FT19168-H3K27ac-050521


title: CT-FT246-H3K27ac-03012021


title: CT-FT19170-H3K27ac-042421


title: KURAMOCHI_WT1_071621

data_processing:
library strategy: CUT&RUN
Both Cut&Run and Cut&Tag  data were processed based on Zheng Y et al (2020). Protocol.io FASTQ was first trimmed using trimmomatic (v0.39) and aligned using bowtie2 (v2.3.4.3). Then, duplicate reads were removed using Picard (v2.20). Remaining reads were then converted to bed files using bedtools(v2.29) for peak calling. Peaks were called using SEACR (v1.3)  with pval for Cut and Run and control with IgG  control (bedgrah).
ATAC seq was processed thorugh atac/dnase piepline (https://github.com/kundajelab/atac_dnase_pipelines/commit/a648870bf353d61c971246f4735b0f708615d8f3)
Assembly: hg38

value: WT1 (Santa Cruz)


title: NF54-T12-Rep-1


title: NF54-T6-Rep-2

value: early ring


title: KURAMOCHI_SOX17_052122

value: Cell Line

value: SOX17 (Abcam)


title: NCI-H295R, NFATc4 KO 5


title: NCI-H295R, control overexpression 1


title: KURAMOCHI_PAX8_071621

value: PAX8 (Novus)


title: KURAMOCHI_MECOM_071621

value: MECOM (Cell Signaling)


title: NF54-T6-Rep-1


title: NF54-T24-Rep-2


title: NCI-H295R, KO control 4


title: KURAMOCHI_H3K27me3_071621

value: H3K27me3 (Cell Signaling)


title: CT-FT282-H3K27ac-030421

value: Fallopian Tube Secretory Epithelium


title: KURAMOCHI_H3K27ac_071621

value: KURAMOCHI

value: High-grade serous "ovary" cancer


title: FT282_WT1_090221


title: NCI-H295R, KO control 2

value: Adrenocortical carcinoma


title: NCI-H295R, KO control 3


title: FT282_PAX8_090221


title: FT282_H3K27ac_090221


title: drvvA_AKI_3

city: Santa Cruz

first: Giordan

last: Kitts

state: CA

address: 1156 High St.

department: METX

institute: UCSC

description:
Vibrio cholerae O1 El Tor A1552
AKI_drvvA_3

data_processing:
QC performed on reads with FastQC. FastQC output deemed trimming not required.
Transcript abundance against the reference transcriptome was determined using Salmon v1.5.2
Transcript abundance from Salmon was then imported into DESeq2 (1.32.0) for differential expression and downstream analyses
Assembly: NC_002505 and NC_002506, (using updated transcriptome deposited on genoscope from: https://doi.org/10.1186/s12864-018-4716-8)
Supplementary files format and content: CSV, normalized counts

organism: Vibrio cholerae

growth_protocol: Vibrio cholerae A1552 strains were grown in AKI medium (0.5% NaCl, 0.3% NaHCO3, 0.4% yeast extract, 1.5% Bacto-Peptone) following virulence-inducing growth conditions: For the first 4 hours, cells were grown in 10mls culture in a culture tube, static, 37˚C. After 4hours static, the 10ml culture was transferred to a 125ml flask and grown at 37˚C and 250RPM for 1 hour. After 1 hour, samples were collected for RNA-sequencing

extract_protocol:
TRIzol-Chloroform total RNA extraction was performed as stated in manufacturers instructions (Invitrogen/Fisher). Samples were DNAase treated, and RiboZero Plus was used for rRNA depletion.
Illumina Stranded RNA library preparation (no modifcations from protocol)

value: NA (bacterial culture)

value: virulence-inducing conditions (AKI)


title: WT_AKI_3

description:
Vibrio cholerae O1 El Tor A1552
AKI_WT_3

value: WT


title: drvvA_AKI_1

description:
Vibrio cholerae O1 El Tor A1552
AKI_drvvA_1


title: drvvA_AKI_2

description:
Vibrio cholerae O1 El Tor A1552
AKI_drvvA_2


title: NCI-H295R, KO control 1


title: FT282_SOX17_031522


title: NCI-H295R, Constitutively active NFATc4 overexpression 3

value: Active-NFATc4 overexpression


title: WT_AKI_1

description:
Vibrio cholerae O1 El Tor A1552
AKI_WT_1


title: FT282_MECOM_092421


title: FT282_H3K27me3_090221


title: WT_AKI_2

description:
Vibrio cholerae O1 El Tor A1552
AKI_WT_2


title: hiPSC-CM TKI cardiotoxicity

city: Beijing

first: Huan

last: Wang

address: Peking University Health Science Center, No. 38 Xueyuan Road, Haidian District

department: Basic Medical Sciences

institute: Peking University

description: 3' digital gene expression based on Unique Molecular Identifier

library_source: transcriptomic single cell

data_processing:
umi_tools extract --bc-pattern=CCCCCCNNNNNNNNNN \  based on the supplementary file of treatment_barcodes.tsv
STAR --runThreadN 64 --genomeDir ../referenceGenomes/hg38_genomeIndex/star_index_hg38release98__74overhang/ --readFilesIn N701_S1.R2_2_extracted.fastq.gz --readFilesCommand zcat --outFilterMultimapNmax 1
Use samtools to sort bam files
Use featureCounts to calculate the number of reads
Assembly: hg38
Supplementary files format and content: counts.tsv contains three columns, first column is the ensembl ID of genes, second column are cell barcodes (in our experiment, it corresponds to barcodes for different drug treatments), third column is count.
Supplementary files format and content: In fda_metadata_clean.csv, 204 samples were prepared by Mirra (see "Originator“ column), 36 samples were prepared by Sharon. Only the 204 samples were used for the analysis in the publication. The Sharon sample were included as internal controls, and they were samples sequenced in GSE114686 (a previous pubication based on similar authors).

source_name: cardiac

growth_protocol: Cells were grown in growth media (Cor.4U Complete Culture Medium which contains 10% FBS and other essential nutrients, Catalog number Ax-M-HC250 from Ncardia) and treated in minimal media (BMCC Serum-Free Culture Medium, Catalog Number Ax-MBMCC250 from Ncardia, supplemented with 1% fetal bovine serum from Thermo Fisher Scientific) in a humidified incubator with 5% CO2 and 37°C.

extract_protocol:
Total RNA was isolated using MagMAX™-96 total RNA isolation kit.
RNA was transferred into 384-well plates and the subsequent library preparation was done according to this publication(https://pubmed.ncbi.nlm.nih.gov/30333485/) and using an automated liquid dispensing system. RNA was reverse transcribed using the Maxima H Minus Reverse Transcriptase (Thermo Fisher) and barcoded primers containing poly(T) sequence about 24 bases long, a random 10-nucleotide sequence as unique molecular identifiers, a random 6-nucleotide sequence as well barcodes and a sequence complimentary to pre-amplification primers. The other end of cDNA sequences were filled with a sequence complementary to pre-amplication primers through a template switching oligo and the same reverse transcriptase. The cDNAs of different drug treatments were pooled and amplified by PCR. In this experiment, the 10-nucleotide unique molecular identifiers were used to label different RNA species and the 6-nucleotide well barcodes were used to label the 129 TKI treatments, not single cells.

treatment_protocol: hiPSC-CMs were cultured in minimal media for 1.5 days prior to drug treatment and maintained in minimal media during drug treatment with media exchanged every other day. Drug stocks were usually prepared in DMSO at 10mM and stored at −20°C until use. Cells were treated wtih 8 tyrosine kinase inhibitors (Afatinib, Gefitinib, Crizotinib, Dasatinib, Nilotinib, Ponatinib, Sorafenib and Sunitinib) at five different conbinations of doses and treatment durations. Treatment doses range from 0~10µM. Treatment time ranges from 1 to 5 days.

value: cardiac

value: human induced pluripotent stem cell derived cardiomyocytes

tag: Sex

value: male

value: multiplexed sample:various tyrosine kinase inhibitors and doses


title: hPGCLCs, wild-type, rep 2

city: Philadelphia

first: Youngsun

last: Hwang

state: PA

address: 3800 Spruce Street Old Vet Quad 220E

institute: University of Pennsylvania

data_processing:
The quality of FASTQ files was checked by FastQC v0.11.2.
All samples were aligned to the human genome, build hg38, using the Rsubead aligner v1.24.1(Liao et al, 2019).
The number of fragments overlapping each Entrez gene were summarized using featureCounts (Liao et al, 2014) and Rsubread's inbuilt hg38 annotation.
Differentially expressed genes (DEG) were identified by using DESeq2 package with FDR ≤ 0.05 as a significance threshold.
Assembly: hg38
Supplementary files format and content: tab-delimited text matrix include logCPM values

growth_protocol: hiPSCs were cultured on plates coated with Recombinant laminin-511 E8 (iMatrix-511 Silk, Nacalai USA) and were maintained under a feeder-free condition in the StemFit® Basic04 medium (Ajinomoto) containing basic FGF (Peprotech) at 37ºC under an atmosphere of 5% CO2 in air.

extract_protocol:
Total RNA was extracted by using RNeasy Micro Kit.
Library was prepared with Takara SMART-Seq HT kit and adapters ligated with Nextera XT DNA Library Preparation Kit and Index Kit v2 according to manufacturers’ protocols.

treatment_protocol:
For the induction of iMeLCs, hiPSCs were plated at a density of 4-5×104 cells/cm2 onto a human fibronectin (Millipore)-coated 12-well plate in GK15 medium (GMEM [Life Technologies]) with 15% KSR, 0.1 mM NEAA, 2 mM L-glutamine, 1 mM sodium pyruvate and 0.1 mM 2-mercaptoethanol) containing 50 ng/ml of ACTA (R&D Systems), 3 uM CHIR99021 (Tocris Bioscience) and 10 uM of a ROCK inhibitor.
After 31 hrs, iMeLCs were harvested and dissociated into single cells with TrypLE Select. Cells were then plated into a low-cell-binding V-bottom 96-well plate (V-bottom plate, Thermo Fisher Scientific) at 3,500 cells per well for induction into hPGCLCs. Wells contained GK15 medium supplemented with 200 ng/ml BMP4 (R&D Systems, 314-BP-010), 100 ng/ml SCF (R&D Systems, 255-SC-010), 50 ng/mL EGF (R&D Systems, 236-EG), 10 ng/ml LIF (Millipore, #LIF1010) and 10 uM of Y-27632 (GK15+BSELY).

value: human primordial germ cell-like cells


title: hPGCLCs, TCL1A_KO, rep 1

value: TCL1A knockout


title: NCI-H295R, Constitutively active NFATc4 overexpression 1


title: 94T_Nutlin_2

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

extract_protocol:
Qiagen RNeasy
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: 94T778 and Lipo-246 cells were treated with vehicle (DMSO 0.05%), or 10 uM Nutlin3R for 16 hr

value: 16 hr 10µM Nutlin3R

tag: library type

value: strand-specific


title: hPGCLCs, wild-type, rep 1


title: iMeLCs, TCL1A_KO, rep 1

value: incipient mesoderm-like cells


title: 94T_Nutlin_1


title: iMeLCs, TCL1A_KO, rep 2


title: iMeLCs, wild-type, rep 2


title: Sample 8_highBCAA

city: Ann Arbor

first: Scott

last: Pletcher

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastP
Trimmed sequence reads were aligned to the Drosophila melanogaster transcriptome using STAR (parameters: -runThreadN -runMode genome Generate)
Read counts were calculated by couting all the reads that overlapped any exon for each gene using featureCounts.
Assembly: ftp.flybase.net/genomes/Drosophila_melanogaster/  version: r6.27
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using Trizol/Chloroform extraction of 10 pooled brains per sample.
RNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Kit for Illumina following manufacturer's protocols.

value: brain

value: Canton-S

value: high BCAA diet


title: iMeLCs, wild-type, rep 1


title: hiPSCs, wild-type, rep 2

value: human induced pluripotent stem cells


title: 94T_DMSO_1


title: hiPSCs, TCL1A_KO, rep 2


title: NCI-H295R, Constitutively active NFATc4 overexpression 2

value: Adrenocortical carcinoma


title: hiPSCs, wild-type, rep 1


title: Lipo246_Nutlin_2


title: sEV-NDB-20

city: Bedford Park

first: George

last: Mayne

state: SA

address: Room 3D213, Dept of Surgery, Flinders Medical Center

department: Surgery

country: Australia

institute: Flinders University of South Australia

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc., San Diego, CA, USA).
All primary analysis was carried out usingCLC Genomics Server 20.0.4. The workflow “QIAseq miRNA Quantification” of CLC Genomics Server with standard parameters was used to map the reads to miRBase version 22.
the reads were processed by (1) trimming of the common sequence, UMI and adapters, and (2) filtering of reads with length < 15nt or length > 55nt.
The reads were then deduplicated using their Unique Molecular Identifier (UMI). Reads were grouped into UMI groups when they (1) started at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) were from the same strand, and (3) had identical UMIs. Groups that contained only one read (singletons) were merged into non-singleton groups if the singleton’s UMI could be converted to a UMI of a non-singleton group by introducing a SNP (the biggest group was chosen).
All reads that didn’t map to miRBase with perfect matches were mapped to the human genome GRCh38 with ENSEMBL GRCh38 version 98 annotation.
For normalisation, the trimmed mean of M-values method based on log-fold and absolute gene-wise changes in expression levels between samples (TMM normalisation) was used. The resultant normalised levels were expressed in counts per million (CPM).
Assembly: human genome GRCh38 with ENSEMBL GRCh38 version 98 annotation
Supplementary files format and content: comma-delimited text file include CPM values for each Sample

source_name: peripheral serum small extracellular vesicles, from patients who had endoscopically visible Barrett’s oesophagus which was confirmed by histology to be negative for dysplasia

extract_protocol:
for small extracellular vesicle isolation, 1 mL aliquots of serum were retrieved from -80 degrees Celsius storage, quick thawed, and centrifuged at 16,000× g at 4 ◦C for 30 min to exclude larger microparticles. 250 μL supernatant from each sample was then processed with an ExoQuickTM kit (System Biosciences, Palo Alto, CA, United States; EXOQ20A-1) according to the manufacturer’s protocol. Samples were incubated with ExoQuickTM at 4 ◦C for 16 h. The pellet isolated from each sample was resuspended with 50 μL phosphate buffered saline (PBS). We refer to these as small EVs, as recommended in the Minimal Information for Studies of Extracellular Vesicles 2018 Guidelines
extraction of miRNA from small EVs was performed using the commercial miRNeasy Serum/Plasma kit (QIAGEN, #217184, Dusseldorf, Germany) according to the manufacturer’s protocol. Twenty-four μL of RNase-free ultrapure water was used for the final RNA elution step
the library preparation was done using the QIAseq miRNA Library Kit (Qiagen, Hilden, Germany). A total of 5 μL total RNA was converted into miRNA NGS libraries. Adapters containing unique molecular identifiers were ligated to the RNA. Then RNA was converted to cDNA, and the cDNA was amplified, with the addition of indices, using 22 cycles of PCR. The samples were then purified, and library preparation QC was performed. One of the HGD samples failed library QC and was not sequenced. The libraries were pooled in equimolar ratios based on the quality of the inserts and the concentration measurements. The library pools were quantified using qPCR


title: Sample 4_highBCAA


title: Sample 7_highBCAA


title: Lipo246_Nutlin_1


title: Sample 6_highBCAA


title: sEV-NDB-17

value: peripheral serum small extracellular vesicles, from patients who had endoscopically visible Barrett’s oesophagus which was confirmed by histology to be negative for dysplasia


title: sEV-NDB-18


title: 94T_DMSO_2


title: sEV-NDB-19


title: Lipo246_DMSO_2


title: hiPSCs, TCL1A_KO, rep 1


title: hPGCLCs, TCL1A_KO, rep 2


title: Sample 3_highBCAA


title: sEV-NDB-16


title: sEV-NDB-15


title: Sample 1_highBCAA


title: Lipo246_DMSO_1


title: sEV-NDB-13


title: sEV-NDB-14


title: Sample 8_lowBCAA

value: low BCAA diet


title: Sample 5_highBCAA


title: sEV-NDB-21


title: Sample 7_lowBCAA


title: Sample 2_highBCAA


title: sEV-NDB-12


title: Sample 5_lowBCAA


title: Sample 6_lowBCAA


title: Sample 4_lowBCAA


title: Sample 3_lowBCAA


title: Sample 2_lowBCAA


title: sEV-NDB-1


title: sEV-NDB-10


title: sEV-NDB-5


title: sEV-NDB-6


title: sEV-NDB-7


title: sEV-NDB-2


title: sEV-NDB-4


title: sEV-NDB-9


title: sEV-NDB-3


title: sEV-NDB-8


title: sEV-NDB-11


title: MDM cells of HC3 patient not stimulated

city: Paris

first: Jeremy

last: Manry

address: 24 boulevard du Montparnasse

institute: INSERM, Institut Imagine

data_processing:
The RNA-seq fastq files were first inspected with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure that the raw data were of high quality.
For each subject, the two fastq files generated were then mapped to the human reference genome (Ensembl GRCh37 release 75) with STAR v.2.7.3a in the two-pass mode
The mapping quality of each bam file was then evaluated with RSeQC
Reads were quantified to generate gene-level feature counts from the read mapping, with HTSeq-count v.0.11.2
Assembly: Ensembl GRCh37 release 75
Supplementary files format and content: Raw counts were obtained using HTSeq-count v.0.11.2

source_name: monocyte-derived macrophages

extract_protocol:
Total RNA was extracted from primary fibroblasts from patients or healthy controls with the the miRNeasy Mini Kit (Zimo), and treated with DNAse (Zymo) to remove residual genomic DNA. Quality controls were performed and all RNA samples were of good quality (RIN>8).
RNA-Seq libraries were prepared with the Illumina RiboZero TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the Illumina NextSeq platform in the 150-nt (for monocyte-derived and iPSC-derived macrophages) or 100-nt (for primary fibroblasts), paired-end configuration.

value: monocyte-derived macrophages

tag: disease state

value: healthy control

tag: stimulation

value: no treatment

tag: treatment dose

tag: stimulation duration


title: MDM cells of HC3 patient stimulated with IFNg for 2h

value: IFNg

value: 2 hours


title: MDM cells of HC2 patient stimulated with IFNg for 2h


title: MDM cells of HC1 patient stimulated with IFNg for 2h


title: MDM cells of HC2 patient stimulated with IFNg for 8h

value: 8 hours


title: Sample 8_controlDiet

value: reference diet


title: MDM cells of HC3 patient stimulated with IFNg for 8h


title: sEV-HGD-17

source_name: peripheral serum small extracellular vesicles, from patients with histological confirmation of high-grade dysplasia within the Barrett’s oesophagus segment

value: male


title: sEV-HGD-14

value: peripheral serum small extracellular vesicles, from patients with histological confirmation of high-grade dysplasia within the Barrett’s oesophagus segment


title: MDM cells of HC2 patient not stimulated


title: MDM cells of HC1 patient stimulated with IFNg for 8h


title: sEV-HGD-13


title: MDM cells of HC1 patient not stimulated


title: sEV-HGD-16


title: Sample 1_lowBCAA


title: sEV-HGD-15


title: Sample 7_controlDiet


title: sEV-HGD-12


title: sEV-HGD-10


title: sEV-HGD-11


title: MDM cells of P2 patient stimulated with IFNg for 2h

value: IRF1 patient


title: sEV-HGD-6


title: sEV-HGD-8


title: sEV-HGD-7


title: sEV-HGD-5


title: Sample 6_controlDiet

value: brain


title: sEV-HGD-3


title: sEV-HGD-4


title: iPSC cells of HC16 patient stimulated with IFNg for 8h

source_name: iPSC-derived macrophages

value: iPSC-derived macrophages


title: sEV-HGD-2


title: iPSC cells of HC16 patient stimulated with IFNg for 2h


title: Sample 3_controlDiet

value: Canton-S


title: Sample 5_controlDiet


title: Sample 4_controlDiet


title: iPSC cells of HC16 patient not stimulated


title: Offtarget_LinearPlasmid_Q5

description:
Pooled CRISPR screen
Offtarget_HEK293FT_counts.csv

library_source: other

molecule: other

organism: synthetic construct

value: Linearized plasmid library


title: Sample 2_controlDiet


title: sEV-HGD-9


title: Sample 1_controlDiet


title: Offtarget_LinearPlasmid_TaqB


title: MIFsnp_967

city: Cleveland

first: Vladimir

last: Makarov

address: 9500 Euclid Ave

institute: CLEVELAND CLINIC LERNER COM-CWRU

data_processing:
raw counts, tpm, fpkm
Supplementary files format and content: counts

source_name: CG

extract_protocol: none provided

value: CG

tag: cell line

value: Tumor

value: GBM

value: STUPP Protocol


title: sEV-HGD-1


title: sEV-CON2-13

source_name: peripheral serum small extracellular vesicles, from patients with  visibly normal oesophageal mucosa at endoscopy


title: MDM cells of P2 patient stimulated with IFNg for 8h

value: monocyte-derived macrophages


title: iPSC cells of HC11 patient stimulated with IFNg for 8h

value: healthy control


title: iPSC cells of HC11 patient stimulated with IFNg for 2h

value: IFNg


title: KO H3K27ac HiChIP

city: Houston

first: Jiexi

last: Li

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

data_processing:
HiChIP data were aligned to mm9 genomes using the HiC-Pro pipeline (version 2.11.1) with the default settings
Interaction loops were called with hichipper (version 0.7.7) (https://github.com/aryeelab/hichipper) and converted into .hic format files and loaded into juicer tools (version 1.13.02) (https://github.com/aidenlab/juicer/wiki/Download) for visualization.
Assembly: mm9
Supplementary files format and content: hic
Library strategy: HiChIP

source_name: KO

growth_protocol: Cells were cultured in DMEM with 10% tetracycline-free Fetal Bovine Serum (FBS), 1X penicillin/streptomycin (Invitrogen) and 1 µg/ml doxycycline.

extract_protocol:
The cells were fixed in 1% formaldehyde for 10 minutes at RT and quenched by glycine for 10 minutes. After washing with PBS, cells were resuspended in Hi-C lysis buffer and rotated at 4 ºC for 30 minutes. Nuclei were pelleted, washed with Hi-C Lysis Buffer and resuspended in 0.5% SDS, which was diluted and quenched by Triton X-100. NEB buffer 2 and Mbol restriction enzyme (New England Biolabs, Cat#R0147) were used to fragment the genome and the DNA fragments were labeled with biotin-dATP (Thermo Fisher Scientific). Proximal DNA fragments were then ligated using NEB T4 DNA ligase (New England Biolabs, Cat#M0202). The nuclear pellet was lysed in nuclear lysis buffer and chromatins were then sonicated using a Covaris E220 and clarified by centrifugation. Clarified samples were diluted in ChIP Dilution Buffer. Samples were precleared with Dynabeads Protein G (Invitrogen). H3K27ac antibody (Abcam, Cat#ab4729) was added at a concentration of 3.75 μg per 5x106 cells and incubated overnight at 4 ºC. Dynabeads Protein G beads were used to capture the antibody-protein-DNA complex. The captured samples were washed with low-salt wash buffer, high-salt wash buffer and LiCl wash buffer. The DNA was reverse crosslinked in DNA elution buffer and incubated with Proteinase K (Invitrogen). The DNA was purified using DNA Clean and Concentrator columns (Zymo Research) and eluted in water. After quantification using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), Streptavidin C-1 beads (Thermo Fisher Scientific) were added to samples to capture the biotin-labeled DNA.
After washing, DNA was mixed with Tn5 transposase (Illumina) for tagmentation for library preparation. DNA was amplified by Phusion HF (New England Biolabs), Nextera Ad1_noMx and Nextera Ad2.X (see reference for primer sequences). After removing the primers with Ampure XP beads (Beckman Coulter) cleanup, the Nextera_i7Short and Nextera_i5Short primers (see reference for primer sequences) were added to samples for additional PCR reactions. The DNA was size-selected using Ampure XP beads to capture fragments between 300bp and 700bp.

value: KO

value: mouse CRC cell line

tag: chip antibody

value: anti-H3K27ac (Abcam, Cat#ab4729)


title: MDM cells of P2 patient not stimulated

value: no treatment


title: L2-3 H3K27ac HiChIP


title: iPSC cells of HC11 patient not stimulated


title: sEV-CON2-10

value: peripheral serum small extracellular vesicles, from patients with  visibly normal oesophageal mucosa at endoscopy

value: male


title: sEV-CON2-11


title: iPSC cells of P1 patient stimulated with IFNg for 8h

value: IRF1 patient

value: 8 hours


title: MIFsnp_728


title: MIFsnp_698

source_name: GG

value: GG


title: iPSC cells of STAT1 patient not stimulated

value: iPSC-derived macrophages

value: STAT1 patient


title: MIFsnp_792

value: Tumor


title: iPSC cells of STAT1 patient stimulated with IFNg for 8h


title: iPSC cells of P1 patient not stimulated


title: iPSC cells of STAT1 patient stimulated with IFNg for 2h

value: 2 hours


title: iPSC cells of P1 patient stimulated with IFNg for 2h


title: sEV-CON2-9


title: sEV-CON2-8


title: sEV-CON2-7


title: CD8_CTL_48h_IgG

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
library quality were evaluated by FastQC
alignment were done with bowtie2 or STAR
CUT&Run peaks were called using MACS2 and IDR
RNAseq qunatification were done using featureCounts
heatmaps were generated by deeptools
Assembly: mm10
Supplementary files format and content: txt file containing peaks
Supplementary files format and content: txt file containing raw counts for RNAseq
Library strategy: CUT&RUN

source_name: CD8+ T cell, Vehicle, 48h, IgG

growth_protocol: OT-I mouse splenocytes were ACK-lysed and resuspended to 2 million splenocytes/mL in complete RPMI media supplemented with 10% FBS, pen/strep, HEPES, glutamine, and β-mercaptoethanol, or in complete RPMI without glutamine (No Q).

extract_protocol:
For CUT&RUN, genomic DNA was release by Mnase. For RNAseq, RNA was extracted use Quick-RNA™ Microprep Kit.
For CUT&RUN, libraries were preparaed by KAPA HpyerPrep Kit. For RNAseq, stranded library preparations were used

treatment_protocol: OT-I cells were activated with 100 IU/mL recombinant human IL-2 (rhIL-2, NCI) and 10ng/mL SIINFEKL peptide (Sigma-Aldrich S7951). CB-839 (MedChemExpress HY-12248) or equal volume DMSO vehicle and DON (Sigma-Aldrich D2131) or equal volume PBS vehicle were added to a final concentration of 1μM (14, 17, 19). 2-deoxyglucose (Cayman Chemical 14325) or equal volume water vehicle was added to a final concentration of 1mM.

value: OT-I

value: CD8+ T cell

value: Vehicle


title: MIFsnp_752

value: GBM

value: STUPP Protocol


title: CD8_DON_48h_IgG

source_name: CD8+ T cell, DON, 48h, IgG

value: DON


title: CD8_CB839_48h_IgG

source_name: CD8+ T cell, CB839, 48h, IgG


title: CD8_NoQ_48h_IgG

source_name: CD8+ T cell, Glutamine free, 48h, IgG

value: Glutamin Free


title: MIFsnp_3982


title: MIFsnp_3789

value: CG


title: sEV-CON2-5

value: peripheral serum small extracellular vesicles, from patients with  visibly normal oesophageal mucosa at endoscopy


title: sEV-CON2-6

value: male


title: fibroblast cells of C3 patient stimulated with IFNg for 8h

source_name: primary fibroblasts

value: primary fibroblasts

value: healthy control

value: IFNg


title: sEV-CON2-12


title: MIFsnp_832

value: GG


title: MIFsnp_4291


title: CD8_NoQ_48h_C

data_processing:
library quality were evaluated by FastQC
alignment were done with bowtie2 or STAR
CUT&Run peaks were called using MACS2 and IDR
RNAseq qunatification were done using featureCounts
heatmaps were generated by deeptools
Assembly: mm10
Supplementary files format and content: txt file containing peaks
Supplementary files format and content: txt file containing raw counts for RNAseq

source_name: CD8+ T cell, Glutamine free, 48h, RNAseq


title: CD8_NoQ_48h_D


title: sEV-CON2-4


title: CD8_NoQ_48h_B


title: sEV-CON2-3


title: CD8_NoQ_48h_A


title: sEV-CON2-2


title: CD8_DON_48h_D

source_name: CD8+ T cell, DON, 48h, RNAseq


title: sEV-CON2-1


title: fibroblast cells of C3 patient stimulated with IFNg for 2h


title: fibroblast cells of C3 patient stimulated with IFNa for 8h

value: IFNa

value: 8 hours


title: fibroblast cells of C3 patient stimulated with IFNg for 30min

value: 30 minutes


title: MIFsnp_3438

value: Tumor


title: MIFsnp_3655


title: fibroblast cells of C3 patient stimulated with IFNa for 30min


title: CD8_DON_48h_B

value: OT-I

value: CD8+ T cell


title: MIFsnp_3332

value: GBM


title: MIFsnp_3185

value: STUPP Protocol


title: CoTHP1_repIII

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

data_processing:
FastQC v0.11.7 was used to visualize the libraries quality before and after trimming.
Trimmomatic v0.36 was used to remove adapters and quality filtered setting the cutoff threshold for average base quality score at 15 over a window of 4 bases. Reads shorter than 36 bases post-trimming were excluded.
Filtered reads were mapped onto the human genome (hg38) using the STAR v2.5.2b.
Gene level read-counts were quantified using STAR’s –quantMode GeneCounts parameter.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.0 (upregulation) or <= -1.0 (downregulation) were called as differentially expressed.
Genome_build: Human genome (hg38).
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

organism:
Trichophyton rubrum
Homo sapiens

source_name: Co-culture, replicate III

growth_protocol: The Trichophyton rubrum strain CBS 118892 was cultured on Sabouraud dextrose agar for 15 days at 28ºC. Macrophages were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) at 37ºC in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA extraction of T. rubrum and THP-1 were performed using an Illustra RNAspin Mini RNA Isolation according to GE Healthcare guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Pre-cultured conidia and heat inactive of T. rubrum were added to THP-1 cell line and the co-culture was incubated for 24 h at 37ºC in a humidified atmosphere containing 5% CO2.

value: human THP-1 macrophages and T.rubrum (co-culture)


title: CD8_CB839_48h_D

source_name: CD8+ T cell, CB839, 48h, RNAseq


title: CD8_DON_48h_A

value: DON


title: CoTHP1_repII

source_name: Co-culture, replicate II


title: CD8_CB839_48h_C


title: MIFsnp_3184

value: CG


title: fibroblast cells of C2 patient stimulated with IFNg for 8h


title: CoTHP1_repI

source_name: Co-culture, replicate I


title: CD8_CB839_48h_B


title: MIFsnp_3688


title: CD8_DON_48h_C


title: MIFsnp_3454


title: fibroblast cells of C2 patient stimulated with IFNg for 2h

value: 2 hours


title: fibroblast cells of C3 patient stimulated with IFNa for 2h


title: CD8_CB839_48h_A


title: 137B

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

institute: University of the Basque Country (UPV/EHU)

description: Neutered

data_processing:
Sequence reads were trimmed and filtered with Trimmomatic [v0.39] to remove adaptor sequences , low quality reads and reads shorter than 16 nucleotides.
rRNA reads were removed with bbduk from bbtools [v39.90] and with the rRNA SILVA database (release 138.1).
The sRNAbench module from the sRNAtoolboxVM program was applied to align sequences to the reference genome, allowing a maximum of 20 multiple mappings per read, to profile the expression of  miRBase sheep miRNAs. In addition to sheep miRNAs from miRBase, sequences were screened for caprine and bovine miRNAs, with a priority of search ovine > caprine > bovine. The reads that were not assigned to any ruminant miRNA were used for novel miRNA characterization with srnabench following author recommendations.
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: miRNA_counts.txt: Tab-delimited text file matrix with the raw counts of sequencing reads for miRNAs. The miRNAs are identified with the miRBase ID and the samples are identified by the name of the title column of the SAMPLES section.
Supplementary_files_format_and_content: miRNA_info.xlsx: Excel file with the localization and sequence of the detected miRNAs (after filtering lowly expressed miRNAs).

organism: Ovis aries

source_name: Spleen

growth_protocol: The animals were kept under uniform housing conditions and nutritional regimens in Zaragoza (Spain). All experimental procedures were approved and licensed by the EthicalCommittee of the University of Zaragoza (ref: PI15/14). Requirements of the Spanish Policy for Animal Protection (RED53/2013) and the European Union Directive 2010/63 on protection of experimental animals were always fulfilled.

extract_protocol:
Samples from spleen were aseptically taken from each animal at necropsy and tissue sections were preserved in RNAlater solution (Ambion, Austin, TX, USA) at −80 ⁰C. Total RNA was isolated from spleen tissue using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and PureLink RNA Mini Kit (Invitrogen). 60 mg tissue samples were homogenized in 1 ml of TRIzol Reagent using Precellys®24 homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) combined with 1.4 and 2.8 mm ceramic beads mix lysing tubes (Bertin Technologies). RNA isolation was performed following manufacturer instructions and RNA was suspended in RNase free water and stored at −80 ⁰C. The TruSeq Small RNA library prep kit (Illumina, San Diego, CA, USA) was used for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The animals were treated with three different treatments: one group was inoculated with nine different commercial vaccines, other one was inoculated only with the adjuvant (aluminium hydroxide, AL(OH)3), giving an equivalent dose of aluminium, and other was treated with PBS. Established legal periods between vaccinations were always fulfilled. The vaccination schedule was between February of 2015 and June of 2106, giving a total of 19 doses and 81.5 mg Al3+ per animal during that period.

tag: group

value: Control

tag: breed

value: Rasa Aragonesa

value: spleen

value: Male

tag: age

value: 21 months


title: fibroblast cells of C2 patient stimulated with IFNg for 30min

value: primary fibroblasts

value: healthy control

value: IFNg


title: CD8_CTL_48h_C

source_name: CD8+ T cell, Vehicle, 48h, RNAseq

value: Vehicle


title: MIFsnp_2541

tag: tissue

value: GG

value: Tumor


title: MIFsnp_2519

value: GBM


title: 136B

description: Neutered


title: 133B

description: Neutered


title: 134B

description: Neutered


title: CD8_CTL_48h_D

value: OT-I

value: CD8+ T cell


title: fibroblast cells of C3 patient not stimulated

value: no treatment


title: MIFsnp_2509

value: STUPP Protocol


title: 127B

description: Neutered

value: Vaccine


title: MIFsnp_2455

source_name: CG

value: CG


title: fibroblast cells of C2 patient stimulated with IFNa for 30min

value: IFNa

value: 30 minutes


title: fibroblast cells of C2 patient not stimulated


title: 126B

description: Neutered

value: Rasa Aragonesa

value: spleen

value: Male


title: MIFsnp_2437


title: fibroblast cells of C1 patient stimulated with IFNg for 8h

value: primary fibroblasts

value: healthy control

value: 8 hours


title: CD8_NoQ_24h_D

source_name: CD8+ T cell, Glutamine free, 24h, RNAseq

value: Glutamin Free


title: 122B

description: Neutered

value: 21 months


title: MIFsnp_2793

value: Tumor

value: GBM


title: fibroblast cells of C2 patient stimulated with IFNa for 8h


title: MIFsnp_2388


title: CD8_NoQ_24h_C

value: OT-I

value: CD8+ T cell


title: 121B

description: Neutered


title: fibroblast cells of C2 patient stimulated with IFNa for 2h

value: 2 hours


title: fibroblast cells of C1 patient stimulated with IFNg for 30min

value: IFNg


title: CD8_CTL_48h_B

value: Vehicle


title: fibroblast cells of C1 patient stimulated with IFNg for 2h


title: 117B

description: Neutered

value: Adjuvant


title: CD8_NoQ_24h_B


title: fibroblast cells of C1 patient stimulated with IFNa for 8h

value: IFNa


title: MIFsnp_2943

value: GG

value: STUPP Protocol


title: MIFsnp_2025

value: CG


title: 115B

description: Neutered

value: Rasa Aragonesa

value: spleen

value: Male


title: CD8_CTL_48h_A


title: MIFsnp_1971


title: fibroblast cells of C1 patient stimulated with IFNa for 2h

value: primary fibroblasts

value: healthy control


title: 113B

description: Neutered

value: 21 months


title: CD8_DON_24h_B

source_name: CD8+ T cell, DON, 24h, RNAseq

value: DON


title: CD8_DON_24h_C

value: OT-I


title: 114B

description: Neutered


title: MIFsnp_1789

value: Tumor

value: GBM


title: MIFsnp_1956

source_name: GG


title: MIFsnp_2379


title: fibroblast cells of C1 patient not stimulated

value: no treatment


title: fibroblast cells of C1 patient stimulated with IFNa for 30min

value: 30 minutes


title: MIFsnp_1764


title: CD8_NoQ_24h_A

value: CD8+ T cell

value: Glutamin Free


title: fibroblast cells of STAT1 patient stimulated with IFNg for 8h

value: STAT1 patient

value: IFNg

value: 8 hours


title: CD8_CB839_24h_C

source_name: CD8+ T cell, CB839, 24h, RNAseq


title: CD8_DON_24h_A


title: CD8_DON_24h_D


title: CD8_CB839_24h_D


title: MIFsnp_1515

value: CG

value: STUPP Protocol


title: fibroblast cells of STAT1 patient stimulated with IFNg for 30min


title: GFP_vivo_IP

city: GuangZhou

first: Yan

state: GuangDong

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: School of Life Science

institute: Sun Yat-sen University

data_processing:
Quality of all reads was inspected using FastQC. Low-quality and adapter-containing reads were trimmed from raw data using Cutadapt. Then, the filtered reads were mapped to the reference human genome (hg19) using the bowtie2 aligner with default settings. The SAM files were subsequently converted to the BAM file format, sorted and indexed using SAMtools. Duplicate reads were removed using picard-tools.
Peaks were called using MACS (version 2.1.2) with default settings (-p 0.01). No-sgRNA (CRISPR alone) and GFP samples were used as negative control. Common peaks between the edited and control sample were removed by BEDtools intersect command. We then compared the results with ENCODE DAC Exclusion List Regions (ENCODE #: ENCSR636HFF) to filter out artifacts using BEDtools intersect command. The rest of peaks in edited sample were candidates of off-target sites.
CROss-seq sequencing data was analyzed using custom computational pipeline. The scoring program used for capturing off-target cleavage sites or editing sites have illustrated in paper.
Genome_build: hg19
Supplementary_files_format_and_content: XLS files include peaks for each sample, TDF files for loaded in IGV for visualization

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in Dulbecco's modified eagle medium supplemented 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Genomic DNA was freshly extracted using FastPure Cell/Tissue DNA Isolation MiniKit and stored in 25 mM K3BO3 buffer (pH 7.0) at -20 °C. Treated genomic DNA was  purified by DNeasy Blood & Tissue Kit and eluted by  25 mM K3BO3 buffer (pH 7.0).
For library preparation, fragmented DNA first be repaired and ligated to adapters, then, the IP sample was subjected to biotin enrichment using Dynabeads MyOne Streptavidin C1 (Thermo, 65001). All reactions were followed the protocol of VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) with some modifications. The biotin pull-down experiments were performed following the recommendations from the Dynabeads MyOne Streptavidin C1 (Thermo, 65001) with some modifications.
CROss-seq (biotin enriched ChIP-seq), Amplicon

treatment_protocol: CROss-seq in vivo: 6-well-plate HEK293T cells were transfected with px330, ABE8e, pCMV-BE4max, and pUC19-Cas9 sgRNA expression plasmids (3 μg/well) using PEI. To perform N3-kethoxal labeling, 24 hours after transfection, previous medium was removed and pre-warmed (37 ˚C) cell culture medium with 5mM N3-kethoxal was used to incubate cells for 45min at 37 ˚C. Genomic DNA was then extracted by FastPure Cell/Tissue DNA Isolation MiniKit and eluted by 25 mM K3BO3 solution (pH 7.0). CROss-seq in vitro: 8 μg Genomic DNA extracted from HEK293T cells was incubated with 300 nM recombinant proteins (SpCas9, ABE7.10, or BE3), 900 nM sgRNA, 0.05mM N3-kethoxal, and 80 μL 5 × CRB buffer (50 mM MgCl2, 750 mM KCl, 100 mM HEPES (pH=7.4), 500 mM Sodium cacodylate) in a 400 μL reaction mix for 2 h at 37 °C. Treated genomic DNA was then purified by DNeasy Blood & Tissue Kit and eluted by using 50 μL 25 mM K3BO3 (pH 7.0).

value: embryonic kidney cells

tag: tissue source

value: kidney

tag: sample type

value: IP

tag: guide rna

value: GFP

tag: vivo or vitro

value: in vivo

tag: editor


title: GFP_vivo_In

tag: cell type

value: input


title: fibroblast cells of STAT1 patient stimulated with IFNg for 2h

value: primary fibroblasts

value: 2 hours


title: Cas9_nogRNA_vivo_IP

value: no


title: CD8_CB839_24h_B

value: OT-I

tag: treatment


title: fibroblast cells of STAT1 patient stimulated with IFNa for 8h

tag: disease state

value: IFNa


title: MIFsnp_1226

value: GG

value: Tumor

value: GBM

tag: genotype


title: CD8_CB839_24h_A

value: CD8+ T cell


title: BE4max_nogRNA_vivo_IP


title: fibroblast cells of STAT1 patient stimulated with IFNa for 2h

value: STAT1 patient

tag: stimulation

tag: treatment dose


title: MIFsnp_1165

tag: cell line

value: STUPP Protocol


title: Cas9_HEK2_vivo_IP

value: embryonic kidney cells


title: CD8_CTL_24h_D

source_name: CD8+ T cell, Vehicle, 24h, RNAseq

value: Vehicle


title: BE4max_HEK2_vivo_IP

value: kidney

value: IP


title: fibroblast cells of STAT1 patient stimulated with IFNa for 30min

tag: stimulation duration

value: 30 minutes


title: 94T778, 72 hr 10 uM Nutlin3R, replicate 3

city: Aurora

first: Matthew

institute: University of Colorado Anschutz Medical Campus

description: sgRNA cassette amplicon

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Samples were demultiplexed using fastx_barcode_splitter from the fastx_toolkit (v0.0.13.2), allowing up to 2 mismatches.
FASTQC v0.11.2 was used to assess sequence data quality.
Sequences were trimmed using fastx_trimmer from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -f 27 -l 46. This keeps only the section of each read corresponding to the unique sgRNA sequences (positions 27-46 inclusive).
Bases with qual ≥10 were removed with fastx_quality_filter from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -q 10 -p 94.
Trimmed and filtered sequences were mapped with Bowtie2 v2.2.3 using the following options (--phred33 --end-to-end --very-sensitive).
Alignments were filtered to keep primary alignments with 0 mismatches using Samtools view.
Observed counts for each sgRNA were obtained using Samtools idxstats.
To avoid large differences in total sgRNA counts, samples with >20 million sgRNA-aligned reads were downsampled to 20 million reads.
Assembly: A reference index was generated for Bowtie2 using only the unique sgRNA sequences from the Human GeCKOv2 library annotation available from https://media.addgene.org/cms/filer_public/7d/87/7d87eaa7-e940-41bf-bf2f-47b43c7ab905/zhang_human_geckov2_grna_sequences.zip (PMID: 24336571; PMID: 25075903)
Supplementary files format and content: Tab delimited text files containing raw sgRNA counts for each sample

source_name: 94T778 liposarcoma cells

growth_protocol: 94T778 cells were cultured in DMEM/F12 supplemented with 10% Equa Fetal and 1x anti-anti and were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Genomic DNA was extracted using a DNeasy Blood and Tissue kit (Qiagen)
Custom

treatment_protocol:
Cells were treated with vehicle (DMSO 0.05%), or 10 uM Nutlin3R for 72 hr
94T778 cells were transduced with the GeCKOv2 A or B libraries and propogated for 10 days to clear sgRNAs targeting essential genes. The resulting cell populations were treated in triplicate with 0.05% DMSO (vehicle) or 10 uM Nutlin3R for 72 hr.

value: 94T778 liposarcoma cells

value: Well-differentiated

tag: gecko library

value: HGLibA+B

tag: culture condition

value: Nutlin3R 10 µM


title: CD8_CTL_24h_C

value: OT-I


title: ABE8e_nogRNA_vivo_IP

value: no

value: in vivo


title: 94T778, 72 hr 10 uM Nutlin3R, replicate 2

description: sgRNA cassette amplicon


title: fibroblast cells of STAT1 patient not stimulated

source_name: primary fibroblasts

value: primary fibroblasts

value: IRF9 patient

value: no treatment


title: MIFsnp_1315

value: GG

value: Tumor

value: GBM


title: CD8_CTL_24h_B

value: CD8+ T cell

value: Vehicle


title: 94T778, 72 hr 10 uM Nutlin3R, replicate 1

description: sgRNA cassette amplicon


title: ABE8e_HEK2_vivo_IP

value: embryonic kidney cells

value: kidney

value: IP


title: fibroblast cells of IRF9 patient stimulated with IFNg for 8h

value: IFNg

value: 8 hours


title: fibroblast cells of IRF9 patient stimulated with IFNg for 2h

value: 2 hours


title: PE2_nogRNA_vivo_IP


title: 94T778, 72 hr DMSO, replicate 3

description: sgRNA cassette amplicon

value: 94T778 liposarcoma cells

value: Well-differentiated

value: HGLibA+B


title: 94T778, 72 hr DMSO, replicate 2

description: sgRNA cassette amplicon


title: CD8_NoQ_4h_D

source_name: CD8+ T cell, Glutamine free, 4h, RNAseq

value: OT-I

value: Glutamin Free


title: 94T778, 72 hr DMSO, replicate 1

description: sgRNA cassette amplicon


title: fibroblast cells of IRF9 patient stimulated with IFNg for 30min

value: primary fibroblasts

value: IRF9 patient

value: 30 minutes


title: CD8_NoQ_4h_C


title: CD8_CTL_24h_A


title: PE2_GFP_vivo_IP

value: GFP

value: in vivo


title: CD8_NoQ_4h_B

value: CD8+ T cell


title: PE2_HEK3_vivo_IP

value: embryonic kidney cells


title: PE2_GFP_vivo_In

value: kidney

value: input