title: ΔlaeA-5mC-1

city: Tianjin

first: Jingen

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
FastQC (fastqc_v0.11.5) was used to perform basic statistics on the quality of the raw reads.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to M. thermophila genome (-X 700 --dovetail).
Bismark(bismark_methylation_extractor) (--multicore 4 --paired-end --no_overlap -ignore 5 --ignore_r2 5) was used to extract methylation levels of C and the results were transformed into bigWig format for visualization using IGV browser.
Differentially methylated regions (DMRs) were identified using the DSS software (DSS_2.12.0 smoothing.span=200，delta=0，p.threshold=1e-05，minlen=50，minCG=3，dis.merge=100，pct.sig=0.5).
Assembly: Myceliophthora thermophila ATCC 42464 (https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html).
Supplementary files format and content: *_5mC_level-1.txt: Tab-delimited text files include 5mC levels identified in strains.
Supplementary files format and content: DMR_results.txt: Tab-delimited text file includes differential methylation region (DMR).

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Myceliophthora thermophila

growth_protocol: Myceliophthora thermophila strains WT and ΔlaeA exposed to glucose for 24 h.

extract_protocol:
Genomic DNA extracted from harvested mycelium.
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Mycelium

value: laeA knockdown

tag: condition

value: Glucose

tag: time


title: TAM-C13

status: Public on Apr 12 2023

type: SRA

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

library_source: transcriptomic

data_processing:
Sequencing was carried out on Paired End 100b reads of Illumina NovaSeq.Image analysis and base calling is performed using Illumina Real Time Analysis (3.4.4) with default parameters.  Fastq were generated with bcl2fastq (2.17).
The reads were first trimmed for adapters and low-quality ends by the TrimGalore! Algorithm (-- t, -q, -e, -- length 20) available on the Galaxy web server (https://usegalaxy.org/). Reads were then aligned onto the mouse genome (mm10) by bowtie2 (-- fr, --no-mixed, --no-discordant, -- sensitive)
.bam files containing aligned reads were further processed by the featureCounts tool (-B, -C, -O) (Lio et al., 2013) to evaluate gene expression levels using the mus_musculus. GRCm38.98 Ensembl version of genes’ annotations was used.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files that includes  the number of reads aligned on Ensembl GRCm38.98 annotated genes.

molecule: total RNA

organism: Mus musculus

source_name: carotid artery

extract_protocol:
RNA was isolated from carotid arteries through the phenol-chloroform method using TRIzol (Ambion) reagent. The resulting RNA quality was determined using a Fragment Analyzer Instrument and all samples had RNA integrity numbers above 7.4.
RNA sequencing libraries were prepared according to Illumina's protocols using the Illumina Illumina TruSeq Stranded mRNA kit (ref #20020595). Eleven cycles of PCR were applied to amplify the libraries. Library quality was assessed using a Fragment Analyzer Instrument and libraries were quantified by QPCR using the kit KAPA KK4824, on the QuantStudio 6 of Thermo Fisher Scientific. Sequencing was performed in paired-end (2x150 pb) on an Illumina NovaSeq sequencer at the Integragen company platform

tag: strain

tag: treatment

value: Tamoxifen

tag: tissue

value: carotid artery

tag: age

value: 9 weeks


title: ΔlaeA-5mC-2

last: Li

country: China

library_source: genomic

molecule: genomic DNA

tag: genotype


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01F]

city: Seattle

first: Xiaoyi

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

data_processing:
For the sci-RNA-seq3 transcriptome libraries, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. Reads were filtered based on RT and ligation index, by allowing <2 hamming distance from reference. Filtered reads were trimmed with TrimGalore (v0.6.6) with parameters: -a AAAAAAAA --three_prime_clip_R1 1. Reads were then aligned to the GRCh38 reference genome using STAR (v2.7.6a). PCR duplicates were collapsed using the RT index, ligation index, UMI sequence and end coordinate of reads. Reads were further demultiplexed based on the combination of the RT, ligation and PCR index and split into files for individual cells. To generate gene expression count matrices, reads were assigned to the exonic and intronic region of closest genes with HTseq (v.2.0.2). Reads with ambiguous assignments were discarded. Cells were further filtered based on total UMI (> 100) and mitochondrial reads percentage (<10%). Cells with the number of features detected between 10% and 90% percentile of all cells were kept and considered high-quality cells. The single cell analysis was performed using the Seurat (v4.0.0) package in R.
For capture libraries of the synHEK3 and shRNA constructs, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. A custom script was used to further demultiplex and filter the synHEK3 and shRNA libraries based on the combination of RT, ligation and PCR index (cell ID), by allowing <2 hamming distance from reference. For the synHEK3 library, reporter barcodes (<2 hamming distance to the reference barcode set), prime editing outcomes and read UMIs were extracted. For the shRNA library, shRNA sequences (<2 hamming distance to the reference barcode set) and read UMIs were extracted. UMIs <3 hamming distance were collapsed.   A series of pre-processing steps were applied to the data. 1) We matched cell IDs between the sci-RNA-seq3 transcriptome libraries and the capture libraries, and only kept high-quality cells (number of features between 10% and 90% percentile). 2) For the shRNA library, cells with <3 or >200 UMIs or >20 shRNA were removed. 3) For the synHEK3 library, cells with <4 UMIs were first removed. We counted UMIs for synHEK3 reporters belonging to the two clones and calculated a clone UMI/total UMI ratio. If the ratio was >80% for a specific clone, the cell is assigned to the corresponding clone. Cells with extremely high UMIs (cutoff between 100 and 250 UMIs, depending on library complexity and sequencing depth of the plate) were also removed for downstream analysis. 4) For a cell-synHEK3 barcode combination, if multiple insertion sequences were observed, sequences <3 hamming distance were collapsed. Cell-synHEK3 barcode pairs having conflicting editing outcomes were discarded. 5) A cell-synHEK3 barcode-editing outcome-shRNA matrix was generated for a common set of cells identified by the shRNA and synHEK3 libraries.
Assembly: GRCh38
Supplementary files format and content: cell_synHEK3_shRNA.csv.gz contains a cell-synHEK3-shRNA capture matrix

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL).

extract_protocol: We performed a modified version of sci-RNA-seq3 (Martin et al., 2022). In brief, K562 cells were lysed with 5 mL of a hypotonic, PBS-based lysis buffer containing DEPC. The resulting nuclei were fixed with 4 volume of ice-cold methanol. After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton buffer (SPBST), the nuclei were treated with T7 polymerase in an NTP mix buffer at 37oC for 30 min. Then nuclei were washed, sonicated briefly and counted. The nuclei were distributed to a 96-well plate for reverse transcription, with a cocktail of three indexed primers: oligo-dT, HEK3 and CS1 -- specific for the cellular transcriptome, and RNAs produced from the synHEK3 reporter and the shRNA constructs, respectively. After reverse transcription, nuclei were pooled, washed in SPBST and redistributed to 4 fresh plates for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to 4 final plates at two different concentrations (1300 cell per well for 2 plates and 2500 cell per well for 2 plates) for second strand synthesis and extraction. Nuclear lysates were split in half, with one half undergoing normal sci-RNA-seq3 transcriptome library preparation (tagmentation and PCR to add the third index) and the other half subjected to indexed enrichment PCR for both the synHEK3 and shRNA constructs. Products were pooled by PCR plate, size-selected and sequenced on an Illumina Nextseq 2000 or Nextseq 550.

treatment_protocol: Two monoclonal K562 PE2-Puro lines (clone 3 and clone 5) containing multiple randomly integrated chromatin sensors for prime editing (synHEK3) were transduced with Lenti-rtTA-P2A-Blast viruses and selected in 10 ug/mL Blasticidin for 7 days. Monoclonal lines were derived and further transduced with a DNA damage response gene-focused lentiviral shRNA library containing 304 hairpins targeting 76 genes. Cells were transdcued at either low MOI (<1) or high MOI (~10) and selected in 800 ug/mL Geneticin for 7 days. For preparing sci-RNA-seq3 libraries, at the RT step, the low MOI cells are placed in the first 6 columns of the 96-well plate, while the high MOI cells were placed in the 7-12 columns of the 96-well palte. Low MOI and High MOI transduced cells can be distiguished by RT indices.

tag: cell line

tag: cell type

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: TAM-C12


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01E]

description: sci-RNA-seq3 library


title: AML patient (AML2), methylation table, onset phase

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

country: Italy

institute: Università degli Studi di Firenze

data_processing:
DNA from each of three pairs of matched AMLs was sequenced on the GridION X5 instrument with a  run-time of 48h by using five or six individual R9.4 flow
The reads generated by each run were base-called using Guppy v2.0.2
The reads generated by each run were base-called using Guppy v2.0.2
The and quality assessment was performed with NanoR and PyPore
High-quality pass reads were then aligned against the human reference genome (hg19) with minimap2
Assembly: hg19
Supplementary files format and content: Processed data files contain genomic coordinates (Chr, start, end), CpG found in the segment, methyalted CpG found in the segment

source_name: bone marrow

extract_protocol:
Genomic DNA was extracted from cryopreserved bone marrow (BM) mononuclear cells using QIAGEN’s AllPrep DNA/RNA kit.
Genomic DNA by ligation SQK-LSK109 (Oxford Nanopore Technologies, ONT)

tag: phase

value: onset

tag: disease state

value: AML

value: bone marrow


title: TAM-C11


title: AML patient (AML2), methylation table, relapse phase

value: relapse


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01D]

description: sci-RNA-seq3 library


title: WT-5mC-1

value: WT


title: WT-5mC-2


title: E2-C29

value: Estradiol


title: ΔlaeA_H3K9me3_Input-2

data_processing:
Raw data filtration: Low quality bases were trimmed by using Trimmomatic(version: 0.36).
Sequence alignment: Clean reads were mapped to Myceliophthora thermophila genome using Bowtie2 (version:2.3.4.3) with default parameters. The alignment file(SAM) was transformed to BAM file and was filtered by the following criteria: (1) only keep unique aligned reads; (2) remove reads with low MAPQ(<30).
Peak calling: The MACS2 (version: 2.1.2) was used to identify transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity.
Peak annotation: The peaks were annotated by ChIPseeker (version: 2.16.0), an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes. Comparison of ChIP peak profiles and annotation are also supported.
Assembly: Myceliophthora thermophila ATCC 42464 (https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: *.tdf files generated from .bam file of Bowtie2 (version:2.3.4.3).
Supplementary files format and content: *_peaks.txt files generated from MACS2 (version: 2.1.2).

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: M. thermophila strains WT and ΔlaeA were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 24h.

extract_protocol:
Lysates were clarified from sonicated mycelia and histone-DNA complexes were isolated with H3K9me3 antibody.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by E-GENE Corporation (Shenzhen, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: <delta>laeA

tag: chip antibody


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01C]

description: sci-RNA-seq3 library


title: E2-C27


title: AML patient (UD5), methylation table, onset phase


title: Glucose, T=60 (pH 8.0), rep 2 [S26]

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description:
GluT60-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

data_processing:
Mapping of fastq files to generate SAM files was carried out with the Bowtie2 software (Langmead & Salzberg, 2012) in local / sensitive mode against the GCA_000027005.1 assembly (98.4–99.2% mapped reads). The SeqMonk software v1.48.0 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was employed to analyze the SAM files. Mapped reads were counted using the RNA-Seq pipeline on mRNA features and differentially expressed genes with respect to time zero were identified using the built-in DESeq2 R package
Assembly: GCA_000027005.1
Supplementary files format and content: file "Annotated Probe Report for All Probes_RPKM.xlsx", excel file with "Reads Per Kilobase Million" data for each sample.
Supplementary files format and content: file "supplemental Table 2.xlsx", excel file conaining the diferentially expressed genes for each condition as defined by the DESeq2 R package (fold-change log2 >1 or <-1 and p-value < 0.01) plus functional annotations

organism: Komagataella phaffii

source_name: whole cell

growth_protocol: K. phaffii X-33 was grown at 28 °C in YP medium (10 g/L yeast extract, 20 g/L peptone) supplemented with a 20 g/L of glycerol (YPGly) or glucose (YPD).

extract_protocol:
Total RNA was extracted with the Ribo Pure™-Yeast kit (Ambion) following the manufacturer’s instructions. The quality was assessed by capillary electrophoresis in a Bioanalyzer equipment and RNA amounts quantified by measuring the A260 in a Nanodrop ND-1000 Spectrophotometer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP (non-directional library). The library was checked by Qubit™ assay (Thermofisher) and real-time PCR for quantification and size distribution monitored with a Bioanalyzer.

treatment_protocol: For the analysis of the transcriptional response of K. phaffii to alkalinization of the medium cells were grown overnight on YPD or YPGly medium, and then cultures were diluted in 200 ml of fresh medium at OD600=0.2 and grown until the OD600 of the cultures reached around 0.6. Then two 100 ml-aliquots were centrifuged (5 min at 1000xg). One aliquot was resuspended in the same volume of either fresh YPD or YPGly medium plus 50 mM TAPS pH 5.5 (control cells) or in YPD or YPGly supplemented with 50 mM TAPS adjusted to pH 8.0 or 8.2 (stressed cells). Samples (15 ml) were taken immediately after resuspension in medium at pH 5.5 (time=0) and, for each stressed culture, after 15, 30 and 60 min. In all cases samples were placed on ice and immediately centrifuged at 4 °C.

value: whole cell

value: wild type

tag: growth condition

value: Glucose, T=60 (pH 8.0)


title: WT, dam 2

type: RNA

city: London

first: Stephen

middle: J

last: Renaud

state: Ontario

address: 1151 Richmond St, MSB428

country: Canada

institute: University of Western Ontario

description: Gene expression data from placentas isolated from dams fed a normal diet

hyb_protocol: Samples were hybridized to the Clariom S GeneChip microarray (ThermoFisher) as per directions from the GeneChip WT Plus Reagent kit (ThermoFisher). Overnight hybridization to the Clariom S GeneChip took place at 45C for ~16 h.

scan_protocol: After washing and staining as per directions for the GeneChip WT Plus Reagent kit (ThermoFisher), images were captured using the GeneChip Scanner 3000 and raw data converted to .CEL files using the Affymetrx GCOS software (ThermoFisher).

data_processing: The CEL file was uploaded to Transcriptome Analysis Console Sotware 4.0 (ThermoFisher) to analyze expression patterns of genes, pathways, and network interactions.

label: biotin

organism: Rattus

source_name: Gestational day 9.5 Imp. Site from WT

label_protocol: Sense strand cDNA was generated, fragmented, and labelled using the GeneChip WT Plus Reagent kit (ThermoFisher) as per directions.

growth_protocol: Dams were aged 6-8 weeks before mating with a WT male. Implantation sites were isolated on gestaional day 9.5

extract_protocol: Frozen placental tissue was homogenized in TRIzol, the aqueous phase removed following mixing in chloroform, mixed with 70% ethanol, and then placed onto an Rneasy column (Qiagen). Following on-column Dnase I digestion, RNA was purified. RNA from two placentas per dam was pooled.

treatment_protocol: Implantation sites were isolated on gestational day 9.5, frozen in liquid nitrogen, and maintained at -80C until RNA extraction.

value: Placenta

tag: developmental stage

value: Gestational day 9.5


title: WT, dam 1


title: IL15Δ/Δ, dam 1

description: Gene expression data from placentas isolated from dams fed an iron-deficient diet

source_name: Gestational day 9.5 Imp. Site from Null


title: Glucose, T=60 (pH 8.0), rep 1 [S22]

description:
GluT60-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01B]

description: sci-RNA-seq3 library


title: ΔlaeA_H3K9me3_Input-1

value: Mycelium

value: Glucose


title: Glucose, T=30 (pH 8.0), rep 2 [S25]

description:
GluT30-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: Glucose, T=30 (pH 8.0)


title: E2-C26

value: carotid artery

value: 9 weeks


title: ΔlaeA_H3K9me3_ChIP-2

value: H3K9me3 (abcam, #ab8902)


title: ΔlaeA_H3K9me3_ChIP-1


title: TAM-C32

value: Tamoxifen


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-01A]

description: sci-RNA-seq3 library

value: lymphoblast

value: lentiviral transduction of a DDR-focused shRNA library


title: E2-C9


title: E2-C8


title: WT_H3K9me3_Input-2

value: WT


title: WT, dam 3


title: E2-C6

value: Estradiol


title: WT_H3K9me3_Input-1


title: WT_H3K9me3_ChIP-2

value: H3K9me3 (abcam, #ab8898)


title: SEM::EGR3 biol rep 2

city: Frankfurt am Main

first: Marius

last: Külp

address: Theodor-Stern-Kai 7

department: Department of Medicine II, Hematology/Oncology

country: Germany

institute: Goethe University Hospital Frankfurt

data_processing:
Illumina bcl2fastq software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Assembly: GRCh38
Supplementary files format and content: Matrix table as tab-delimited text file with raw and normalized gene counts for every gene and every sample
Library strategy: MACE-seq

source_name: proB cells

growth_protocol: SEM cells were maintained in RPMI 1640 (RPMI-HA, Capricorn Scientific) supplemented with 10% FBS (FBS-11A, Capricorn Scientific), 2 mM L-glutamine (STA-B, Capricorn Scientific), 100 U/ml penicillin and 100 μg/ml streptomycin (PS-B, Capricorn Scientific). Cells were kept at 37°C in 5% CO2 and a relative humidity of 95%.

extract_protocol:
RNA of 1x10^7 SEM cells was extracted using the RNeasy Mini Kit (Qiagen, Cat. No. / ID: 74104) according to the manufacturer's protocol
MACE-libraries were prepared at GenXPro GmbH using the Massive Analysis of cDNA   Ends (MACE) Library Preparation Kit (v2.0) from GenXPro GmbH.

treatment_protocol: Induction of transgene expression through Doxycycline treatment 1 µg/mL 48 h prior to RNA extraction

value: proB cells

value: SEM

value: B cell precursor leukemia

value: EGR3-overexpressing vector transfected

value: Induction of transgene expression through Doxycycline treatment 1 µg/mL 48 h prior to RNA prep


title: OVX-C24

value: Placebo


title: SEM::EGR3 biol rep 3


title: OVX-C25


title: SEM::mock biol rep 3

value: empty vector transfected


title: WT_H3K9me3_ChIP-1

value: Mycelium

value: Glucose


title: Glucose, T=15 (pH 8.0), rep 2 [S24]

description:
GluT15-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: whole cell

value: wild type

value: Glucose, T=15 (pH 8.0)


title: Glucose, T=0 (pH 5.5), rep 2 [S23]

description:
GluT0-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: Glucose, T=0 (pH 5.5)


title: Glucose, T=30 (pH 8.0), rep 1 [S21]

description:
GluT30-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: Glucose, T=30 (pH 8.0)


title: SEM::mock biol rep 2


title: OVX-C5

value: carotid artery

value: 9 weeks


title: SEM::mock biol rep 1


title: glycerol, T=60 (pH 8.2), rep 2 [S18]

description:
GlyT60-pH8.2 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: glycerol, T=60 (pH 8.2)


title: OVX-C4


title: glycerol, T=60 (pH 8.2), rep 1 [S14]

description:
GlyT60-pH8.2 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: Glucose, T=0 (pH 5.5), rep 1 [S19]

description:
GluT0-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: OVX-C3


title: n245.5 (bio rep 5)

city: Beijing

first: Daoxin

last: Xie

address: School of Life Sciences, Room 407, Renhuan Building, Tsinghua University

institute: Tsinghua University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
The quality-checked clean reads were mapped to TAIR10 reference genome using HISAT2 (v2.1.0)
The read count for each gene was determined by HTSeq (v0.6.0)
Read counts were normalized and differently expressed genes were identified using DESeq2 (v1.36.0)
Assembly: TAIR10
Supplementary files format and content: Excel file includes read counts and FPKM values for each sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were surface-sterilized for 12 minutes using bleach buffer (20% [v/v] bleach, 0.1% [v/v] triton-100), washed 5 times with sterile water, and chilled at 4℃ for 3 days. After plating on MS medium (Murashige and Skoog medium, Sigma-Aldrich), seeds were germinated in a growth room at 22℃ with a 16 h/8 h light/dark (long day, LD) photoperiod.

extract_protocol:
RNA was extrated with Transzol (TransGen Biotech, ET101-01)
mRNA was enriched using Oligo d(T) beads and fragmentated. cDNAs were synthesized using random hexamers as primer. The resulting cDNAs were purified using AMPure XP beads, followed by adaptor ligation and PCR amplication, to give the cDNA libraries.

treatment_protocol: Seedlings were sprayed with conidiospores of Botrytis cinerea or PDB medium for 24 hours.

value: seedlings

value: Seedlings sprayed with spores of Botrytis cinerea


title: Glucose, T=15 (pH 8.0), rep 1 [S20]

description:
GluT15-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: CV 025_Control PU

city: Cleveland

first: Christine

last: McDonald

state: Ohio

address: 9500 Euclid Avenue

department: Inflammation & Immunity

institute: Cleveland Clinic

description: FFPE extracted total RNA hybridized with Nanostring Human Autoimmune Profiling Panel and spike in Coronavirus Panel Plus probe sets

hyb_protocol: One-hundred nanograms of RNA was hybridized with the NanoString Human Autoimmune Profiling Panel and spike in Coronavirus Panel Plus probe sets (NanoString Technologies).

scan_protocol: Transcriptional analysis of immune related genes and SARS-CoV-2 genes in tissue biopsies was conducted using the NanoString nCounter Pro Analysis System (NanoString Technologies).

data_processing: Raw data was initially processed using the nSolver Analysis Software (V.4.0). Quality control and normalization was performed using the 6 positive control, 8 negative control, and 20 housekeeping probes. Samples flagged for failing quality control were removed. Remaining data was assessed for cell type scoring using nSolver Advanced Analysis (V.2.0) and exported for subsequent analysis in R software.

source_name: skin HASPI biopsy tissue

extract_protocol: Total RNA was extracted from 10um thick sections from formalin-fixed paraffin-embedded tissue using the Qiagen RNeasy FFPE kit with deparaffinization solution.

tag: ulcer histopathology

value: pressure ulcer

tag: covid-19 status

value: negative

tag: Sex

value: female


title: n245.4 (bio rep 4)


title: SEM::EGR3 biol rep 1

value: proB cells

value: SEM

value: B cell precursor leukemia

value: EGR3-overexpressing vector transfected

value: Induction of transgene expression through Doxycycline treatment 1 µg/mL 48 h prior to RNA prep


title: OVX-C2

value: Placebo


title: CV 024_Control PU


title: n245.3 (bio rep 3)


title: glycerol, T=30 (pH 8.2), rep 1 [S13]

description:
GlyT30-pH8.2 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: whole cell

value: wild type

value: glycerol, T=30 (pH 8.2)


title: n245.2 (bio rep 2)


title: n245.1 (bio rep 1)


title: glycerol, T=15 (pH 8.2), rep 1 [S12]

description:
GlyT15-pH8.2 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: glycerol, T=15 (pH 8.2)


title: C245.5 (bio rep 5)


title: glycerol, T=30 (pH 8.2), rep 2 [S17]

description:
GlyT30-pH8.2 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: glycerol, T=0 (pH 5.5), rep 1 [S11]

description:
GlyT0-pH8.2 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: glycerol, T=0 (pH 5.5)


title: CV 002_COVID19+ TV

value: thrombotic vasculopathy

value: positive


title: CV 023_Control PU

value: male


title: glycerol, T=60 (pH 8.0), rep 2 [a8]

description:
GlyT60-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: glycerol, T=60 (pH 8.0)


title: C245.4 (bio rep 4)

value: seedlings

value: Seedlings sprayed with spores of Botrytis cinerea


title: C245.3 (bio rep 3)


title: CV 021_Control PU

value: pressure ulcer

value: negative


title: glycerol, T=60 (pH 8.0), rep 1 [a4]

description:
GlyT60-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: C245.2 (bio rep 2)


title: CV 020_Control PU


title: glycerol, T=15 (pH 8.2), rep 2 [S16]

description:
GlyT15-pH8.2 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: CV 017_Control PU


title: glycerol, T=30 (pH 8.0), rep 2 [a7]

description:
GlyT30-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: glycerol, T=30 (pH 8.0)


title: CV 022_Control PU


title: nlp6nlp7_35min_repeat_3

city: Taipei

first: Yi-Fang

last: Tsay

address: 128 Academia Rd, Sec. 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: gene expression after 25mM nitrate induction for 35min

hyb_protocol: Samples were hybridized to an Affymetrix ATH1 GeneChip according to a standard Affymetrix protocol (Affymetrix Inc.) and scanned at the Academia sinica Affymetrix Gene Expression Service Lab Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with Microarray software (GeneSpring GX - Agilent Genomics). The average signal of all chips was scaled to 500 so that all chips had equivalent signal intensities.

source_name: nlp6nlp7 nitrate 35min

label_protocol: Total cDNAs were labeled and hybridized to an Affymetrix ATH1 GeneChip according to a standard Affymetrix protocol (Affymetrix Inc.)

growth_protocol: seeds were surface-sterilized for 2 min in 70% (v/v) ethanol and sterilized for 13 min in 20% bleach with 0.5% SDS solution. Seeds were then cold-treated at 4 °C in water for 3 days before being sown in a magenta box containing 57 ml medium. The medium (described in Chiu et al. 2004) containing 12.5 mM (NH4)2 succinate at pH6.5 was filter-sterilized. Seedlings were incubated at 25 °C under continuous light (80-95 μmol photons.m-2s-1) with shaking (70 rpm). After 8 days, plants were transferred to fresh medium for pH pretreatment containing 12.5 mM (NH4)2 succinate at pH 5.5, first for 16 h and then for a further 3 h.

extract_protocol: Total RNA was extracted using TRIzol® reagent (Thermo Fisher Scientific Inc.)

treatment_protocol: plants were treated with  25 mM KNO3 at pH 5.5 and the roots were harvested at time 0 (before induction) and after 35 minutes of nitrate treantment. Each experiment comprised three biological repeats, with ~200 seedlings grown in three boxes for each repeat.

value: roots


title: glycerol, T=0 (pH 5.5), rep 2 [S15]

description:
GlyT0-pH8.2 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: C245.1 (bio rep 1)


title: CV 001_COVID19+ TV


title: CV 016_Control PU

value: female


title: glycerol, T=30 (pH 8.0), rep 1 [a3]

description:
GlyT30-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: nlp6nlp7_35min_repeat_2


title: n24P.5 (bio rep 5)

value: Seedlings sprayed with PDB medium as control


title: nlp6nlp7_35min_repeat_1


title: glycerol, T=15 (pH 8.0), rep 4 [a6]

description:
GlyT15-pH8 rep4
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: whole cell

value: glycerol, T=15 (pH 8.0)


title: n24P.4 (bio rep 4)


title: glycerol, T=15 (pH 8.0), rep 3 [a2]

description:
GlyT15-pH8 rep3
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx

value: wild type


title: CV 015_COVID19+ PU


title: CV 018_Control PU


title: nlp7_35min_repeat_2

source_name: nlp7 nitrate 35min


title: CV 014_COVID19+ PU


title: n24P.3 (bio rep 3)


title: nlp7_35min_repeat_1


title: CV 013_COVID19+ PU


title: nlp6_35min_repeat_2

source_name: nlp6 nitrate 35min


title: glycerol, T=15 (pH 8.0), rep 2 [a10]

description:
GlyT15-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: nlp7_35min_repeat_3


title: nlp6_35min_repeat_1


title: Col-0_35min_repeat_3

source_name: Col-0 nitrate 35min


title: CV 008_COVID19+ TV


title: n24P.1 (bio rep 1)


title: n24P.2 (bio rep 2)


title: glycerol, T=15 (pH 8.0), rep 1 [a9]

description:
GlyT15-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: C24P.5 (bio rep 5)


title: glycerol, T=0 (pH 5.5), rep 2 [a5]

description:
GlyT0-pH8 rep2
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: glycerol, T=0 (pH 5.5), rep 1 [a1]

description:
GlyT0-pH8 rep1
Annotated Probe Report for All Probes_RPKM.xlsx
supplemental Table 2.xlsx


title: CV 007_COVID19+ TV

description: FFPE extracted total RNA hybridized with Nanostring Human Autoimmune Profiling Panel and spike in Coronavirus Panel Plus probe sets


title: CV 006_COVID19+ TV


title: nlp6_35min_repeat_3


title: C24P.4 (bio rep 4)


title: C24P.3 (bio rep 3)


title: CV 005_COVID19+ TV


title: Day7KO1

city: Wuhan

first: Lai

last: fengling

address: Wuhan University, Wuchang District, Hubei Province

institute: Wuhan university

description: FPKM-Day 7.txt

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads.
Clean reads were aligned to a reference genome sequence using HISAT
Clean reads were compared to reference gene sequences using Bowtie2
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Testis

growth_protocol: adult tissue

extract_protocol:
Total RNA was extracted from Sertoli cell of mouse testis 7 days after birth or adult testis using the TRIzol Reagent (15596-026, Thermo Fisher), according to manufacture’s instructions.
The extracted RNA samples were enriched with eukaryotic mRNA using magnetic beads with Oligo (dT), followed by terminal repair, poly (A) addition, sequencing junction, and PCR amplification.

treatment_protocol: untreatment

value: Testis

value: Sertoli

value: RNF20 conditional knockout


title: Day7KO2

description: FPKM-Day 7.txt


title: CV 019_Control PU


title: Day7WT2

description: FPKM-Day 7.txt

value: WT


title: C24P.2 (bio rep 2)


title: Col-0_35min_repeat_2


title: Col-0_35min_repeat_1


title: CV 012_COVID19+ PU

value: positive


title: C24P.1 (bio rep 1)


title: Day7WT1

description: FPKM-Day 7.txt


title: nlp6nlp7_0min_repeat_3

description: gene expression before nitrate induction (in ammonium for 9 days)

source_name: nlp6nlp7 0min in ammonium


title: nlp6nlp7_0min_repeat_2


title: nlp7_0min_repeat_3

source_name: nlp7 0min in ammonium


title: ADKO-3

description: FPKM-Adult.txt

value: tissue


title: nlp7_0min_repeat_2


title: nlp6nlp7_0min_repeat_1


title: primary astrocytes,Control-IgG 3,24h

city: Guang Zhou

first: Wei

last: Jiang

state: Guang dong

address: Tianhe street NO.600

institute: The Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Primary astrocytes isolated from adult mice were treated with hsCtrl-IgG or hsAQP4-IgG, and then astrocyte-conditioned medium (ACM) was collected. High-throughput RNA sequencing (RNA-seq) was performed by using the Illumina NovaSeq 6000 system. (Illumina, San Diego, CA) at CapitalBio Corporation (Beijing, China). The raw sequencing data were aligned to the mouse preference genome (GRCm38, mm10).
Assembly: GRCm38, mm10
Supplementary files format and content: all genes expression.xlsx

source_name: primary astrocytes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: primary astrocytes

value: astrocytes cells

value: Control-IgG


title: CV 010_COVID19+ TV

value: thrombotic vasculopathy


title: primary astrocytes,Control-IgG 2,24h


title: ADKO-2

description: FPKM-Adult.txt


title: CV 009_COVID19+ TV

value: male


title: MOUSE 04, Serum-PI

type: protein

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

institute: GSK Vaccines

description: FS00007304 Area1-MOUSE 04

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit). The array was then incubated 1h a room temperature (RT) with animal sera diluted 1:1000 for anti-mouse IgG-specific analysis. After two washing with 0.1% Tween in PBS buffer (TPBS), arrays were incubated with an AlexaFluor 647-conjugated IgG anti-mouse (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before and washed once in PBS, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a Powerscanner (Tecan Trading ) and the 16-bit images were generated with Powerscanner software at 10 µm per pixel resolution.

data_processing:
Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data  was performed using in-house developed R scripts. For each protein the fluorescence intensity data of the replicates was subtracted by local background values surrounding each spot and averaged, hence resulting in a single data point per sample named Mean Fluorescence Intensity (MFI).
Mean fluorescence intensity (MFI)

label: AlexaFluor 647-conjugated anti-mouse IgG secondary antibody

molecule: protein

source_name: Serum-PI

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol: Mouse pool sera

value: blood

value: PI (pre-immune treatment)


title: primary astrocytes,Control-IgG 1,24h


title: nlp7_0min_repeat_1

value: roots


title: ADKO-1

description: FPKM-Adult.txt


title: MOUSE 03, Serum-rMenB

description: FS00007302 Area1-MOUSE 03

source_name: Serum-rMenB

value: female

value: rMenB


title: primary astrocytes,AQP4-IgG 3,24h


title: nlp6_0min_repeat_3

source_name: nlp6 0min in ammonium


title: nlp6_0min_repeat_2


title: CV 011_COVID19+ PU

value: pressure ulcer


title: ADWT-2

description: FPKM-Adult.txt

value: Testis


title: primary astrocytes,AQP4-IgG 1,24h


title: nlp6_0min_repeat_1


title: ADWT-1

description: FPKM-Adult.txt


title: RNA-seq, D6, DKI, rep3

status: Public on Apr 11 2023

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: First column: entrez ID; second column: gene symbol; columns thereafter: RPKMs for each sample

source_name: liver

extract_protocol:
Total RNA was extracted using the Zymo RNA miniprep kit (Zymo Research).
500 ng RNA was used for RNA-Seq library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were recovered and purified with Zymoclean Gel DNA Recovery Kit (ThermoFisher). After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq2000 system.

value: DKI

value: GM-CSF

value: liver

value: Ly6C+ CCR2+ monocytes


title: RNA-seq, D6, WT, rep3

value: WT


title: RNA-seq, D6, DKI, rep2


title: RNA-seq, D6, WT, rep2


title: RNA-seq, D6, DKI, rep1


title: RNA-seq, D3, DKI, rep3


title: RNA-seq, D3, DKI, rep2


title: RNA-seq, D3, DKI, rep1


title: Col-0_0min_repeat_3

source_name: Col-0 0min in ammonium


title: Col-0_0min_repeat_2


title: RNA-seq, D6, WT, rep1


title: RNA-seq, D3, WT, rep2


title: RNA-seq, D3, WT, rep3


title: RNA-seq, D3, WT, rep1


title: RNA-seq, D0, DKI, rep3

value: untreated


title: Col-0_0min_repeat_1


title: RNA-seq, D0, DKI, rep2


title: MOUSE 02, Serum-4CMenB

description: FS00007303 Area2-MOUSE 02


title: primary astrocytes,AQP4-IgG 2,24h

value: primary astrocytes

value: astrocytes cells


title: RNA-seq, D0, WT, rep2


title: RNA-seq, D0, WT, rep3


title: MOUSE 01, Serum-OMV

description: FS00007534 Area2-MOUSE 01

source_name: Serum-OMV

value: OMV


title: RNA-seq, D0, DKI, rep1


title: ADWT-3

description: FPKM-Adult.txt

value: tissue


title: RNA-seq, D0, WT, rep1


title: MDA-MB-231 NRP-1 KO cells  (Replica #1)

city: Muscat

first: Noura

middle: Salim

last: Al-Zeheimi

address: Muscat

department: Department of Biology

country: Oman

institute: Sultan Qaboos University

data_processing:
The quality of sequencing was verified using the phred score Q30 of Raw and Trimmed data. Trimmed reads are mapped to reference genome with HISAT2 version 2.1.0, Bowtie2 2.3.4.1.
StringTie
The expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million). DEG (Differentially Expressed Genes) analysis was performed on a comparison pair (NRP-1 Knockout_vs_Control) using DESeq2.
The statistical method used was calculated based on fold change, nbinomWaldTest using DESeq2, and Hierarchical Clustering. Using each sample’s normalized value, the high expression similarities were grouped together. The significant results are selected on conditions of absolute value of fold change |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: GRCh38/ hg38
Supplementary files format and content: fold-change, read count, FPKM, TPM for all samples

source_name: Female, adherent Adenocarcinoma

growth_protocol: MDA-MB-231 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted for library preparation using mRNA with poly-A tail and non-coding RNAs
The RNA was fragmented for short read sequencing which was then reverse transcribed to cDNA that was ligated with adaptors at both ends. The DNA fragments were amplified using PCR, and the fragments with insert sizes between 200-400 bp were selected for paired-end sequencing, both ends of the cDNA are sequenced by the read length full method

value: Breast; Mammary gland

value: breast adenocarcinoma cell line

value: NRP-1 KO


title: MDA-MB-231 NRP-1 KO cells (Replica #2)


title: MDA-MB-231 cells parental cells  (Replica #1)


title: MDA-MB-231 cells parental cells (Replica #2)


title: day0, scATACseq

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
6477-RMM-002_1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.2 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/overview/welcome)
Assembly: hg38
Supplementary files format and content: cellranger-arc filtered feature matrix for scRNA and scATACseq

growth_protocol: NPCs were differentiated according to the Bardy, et al. BrainPhys protocol (doi: 10.1073/pnas.1504393112)

extract_protocol:
Nuclei from cultured neurons were isolated as detailed in 10x Genomics demonstrated protocol CG000375 Rev A with modifications. Cells were washed with cold 1X DPBS then 500 uL of NP-40 Lysis Buffer was added and cells were gently scraped off the dish while on ice, transferred to a 1.5 mL tube, and incubated 5 min on ice. Cells were centrifuged at 500 x g for 5 min at 4C and 500 uL 1X PBS + 1% BSA + DAPI + 0.5U/uL Protector RNAse Inhibitor (Roche) was added. Cells were spun again, gently resuspended 5X in 0.1X Lysis Buffer, and incubated 2 min on ice. After incubation, 1 mL of wash buffer was added and cells were immediately spun at 500 x g for 5 min at 4C. Nuclei were resuspended in <100 uL of Diluted Nuclei Buffer and counted using Countess FL II aiming for ~3,000 - 5,000 nuclei/uL.
Transposition, barcoding, and library preparation were performed according to the 10x Genomics Chromium Next GEM Single Cell Multiome protocol CG000338 Rev E.


title: SampleDT19_day22

description: column name: SampleDT19_day22

data_processing:
UMIs extracted with UMI-tools extract with the regex extraction method.
Reads were trimmed with bbduk and aligned to hg38 with STAR using the Lexogen recommended parameters.
Bams were deduplicated by UMI and mapping coordinate using UMI-tools dedup.
Counts were generated with htseq-count using the intersection-nonempty method. The count matrix was normalized to counts per million (CPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: NPCs were maintained in 2:1 DMEM:Ham's F12 supplemented with hFGF, hEGF, and heparin. NPCs were differentiated following the BrainPhys protocol from Bardy, et al. (doi:10.1073/pnas.1504393112)

extract_protocol:
RNA isolation was performed using the Norgen Total RNA isolation and RNase-Free DNase I kits (Norgen 17250 and 25720, respectively) and quantified using the Qubit RNA HS Assay Kit (Thermo Q32855).
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and UMI Second Strand Synthesis Module for QuantSeq FWD (Illumina, Read 1) from Lexogen (015.96 and 081.96, respectively). Libraries were quantified using the Qubit DNA HS Assay Kit (Thermo Q32854) and visualized with the BioAnalyzer High Sensitivity DNA Analysis kit (Agilent 5067-4626) and 2100 BioAnalyzer Instrument (Agilent).

value: Neurons


title: SampleDT15_day19

description: column name: SampleDT15_day19


title: day7, scRNAseq

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
6477-RMM-0001_2

library_source: transcriptomic single cell


title: day14, scRNAseq

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
6477-RMM-0001_3


title: SampleDT20_day22

description: column name: SampleDT20_day22


title: SampleDT13_day16

description: column name: SampleDT13_day16


title: SampleDT12_day13

description: column name: SampleDT12_day13


title: day7, scATACseq

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
6477-RMM-002_2


title: SampleDT11_day13

description: column name: SampleDT11_day13


title: day0, scRNAseq

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
6477-RMM-0001_1


title: SampleDT7_day9

description: column name: SampleDT7_day9


title: SampleDT10_day11

description: column name: SampleDT10_day11


title: SampleDT9_day11

description: column name: SampleDT9_day11


title: SampleDT6_day3

description: column name: SampleDT6_day3


title: day14, scATACseq

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
6477-RMM-002_3


title: SampleDT8_day9

description: column name: SampleDT8_day9


title: SampleDT4_day1

description: column name: SampleDT4_day1


title: SampleDT5_day3

description: column name: SampleDT5_day3


title: SampleDT3_day1

description: column name: SampleDT3_day1


title: SampleDT1_day0

description: column name: SampleDT1_day0


title: SampleDT2_day0

description: column name: SampleDT2_day0


title: SampleDT14_day16

description: column name: SampleDT14_day16


title: SCT_undiff_rep2 [Capture-C]

description:
column name: SCT_undiff_rep2
capC-MAP_counts.csv

data_processing:
library strategy: Capture-C
HiC and Capture-C data were analyzed using the Juicer Tools pipeline
HiC and Capture-C: Libraries from each replicate were first run individually. Restriction site positions were generated with generate_site_positions.py with Arima specified as the enzyme.
HiC and Capture-C:Reads were aligned to hg38 for HiC, but only to chr17 of hg38 for capture-C.
HiC and Capture-C:For both HiC and capture-C, all 3 replicates were merged to create a combined hic file with mega.sh.
HiC and Capture-C:Loops were called on the Knight-Ruiz normalized combined hic files using HiCCUPs at a resolution of 5 kb. Window width and peak width were set to 20 and 10 respectively. Loops with a FDR < 0.2 were determined to be significant.
Capture-C: For Neuron and NPC capture-C, samples were processed using the capC-MAP pipeline with the MAPT promoter set as the target and the restriction enzyme set as DpnII.
Capture-C: Contact counts were taken from capC-MAP output at a step size of 500bp and window size of 1kb.
Assembly: hg38
Supplementary files format and content: HiC and Capture-C:HiCCUPS loop calls
Supplementary files format and content: HiC and Capture-C:hic file
Supplementary files format and content: Capture-C: capC-MAP counts table for each sample

source_name: SCT

growth_protocol:
HiC and Capture-C: Cells were maintained according to FujiFilm Cellular Dynamics recommendations
Capture-C: NPCs were maintained in 2:1 DMEM:Ham's F12 supplemented with hFGF, hEGF, and heparin. NPCs were differentiated following the BrainPhys protocol from Bardy, et al. (doi:10.1073/pnas.1504393112)

extract_protocol:
HiC and Capture-C: Cells were fixed with 2% formaldehyde for 10 min at RT. Cells were lysed and homogenized before chromatin was digested with Arima enzyme cocktail.
Capture-C: Cells were fixed with 2% formaldehyde for 10 min at RT. Cells were lysed and homogenized before chromatin was digested with DpnII.
HiC and Capture-C: HiC was performed in iCell GlutaNeurons, and Capture-C was performed in iCell GlutaNeurons and GABANeurons. All experiments were performed in triplicate with independent cell grow-ups of approximately 15 million cells for biological replication. For HiC, we followed manufacturer recommendations from the Arima HiC kit- User Guide for Mammalian cell lines (A510008, V.Oct.2019) using the Arima HiC Library Prep using Swift Biosciences Accel-NGS 2S plus DNA library kit (A510008, V. Nov2018). iCell GlutaNeuron and GABANeuron Capture-C was performed following the HiC protocols, with the addition of the Agilent Technology SureSelect XT HS/SureSelect XT Low input target enrichment with pre-capture pooling protocol. 102 SureSelect DNA probes spanning a 2kb region (chr17:45892780-45893184 and chr17:45893527-45895196; hg38) were ordered from AgilentTechnologies. The region between the two probes could not be synthesized because of low sequence complexity.
Capture-C: Capture-C was performed in NPCs, Day 14 BrainPhys differentiated neurons. All experiments were performed in triplicate with independent cell grow-ups of approximately 15 million cells for biological replication. NPC and Day 14 BrainPhys differentiated neuron Capture-C was performed following the NG Capture-C Protocol (v2.4).46 For this experiment, enrichment for MAPT promoter contacts was performed by double capture using two biotinylated oligonucleotides targeting chr17:45892836–45892923 and chr17:45895092–45895179 (both hg38)

value: SCT

value: NPCs


title: BC1_diff_rep1 [Capture-C]

description:
column name: BC1_diff_rep1
capC-MAP_counts.csv


title: SampleDT16_day19

description: column name: SampleDT16_day19


title: SCT_diff_rep1 [Capture-C]

description:
column name: SCT_diff_rep1
capC-MAP_counts.csv


title: BC1_undiff_rep1 [Capture-C]

description:
column name: BC1_undiff_rep1
capC-MAP_counts.csv


title: SCT_undiff_rep1 [Capture-C]

description:
column name: SCT_undiff_rep1
capC-MAP_counts.csv


title: BC1_diff_rep3 [Capture-C]

description:
column name: BC1_diff_rep3
capC-MAP_counts.csv


title: Gluta_HiC_rep1

description:
Gluta_HiC_merged_loops.bedpe
Gluta_HiC_inter_30.hic

data_processing:
HiC and Capture-C data were analyzed using the Juicer Tools pipeline
HiC and Capture-C: Libraries from each replicate were first run individually. Restriction site positions were generated with generate_site_positions.py with Arima specified as the enzyme.
HiC and Capture-C:Reads were aligned to hg38 for HiC, but only to chr17 of hg38 for capture-C.
HiC and Capture-C:For both HiC and capture-C, all 3 replicates were merged to create a combined hic file with mega.sh.
HiC and Capture-C:Loops were called on the Knight-Ruiz normalized combined hic files using HiCCUPs at a resolution of 5 kb. Window width and peak width were set to 20 and 10 respectively. Loops with a FDR < 0.2 were determined to be significant.
Capture-C: For Neuron and NPC capture-C, samples were processed using the capC-MAP pipeline with the MAPT promoter set as the target and the restriction enzyme set as DpnII.
Capture-C: Contact counts were taken from capC-MAP output at a step size of 500bp and window size of 1kb.
Assembly: hg38
Supplementary files format and content: HiC and Capture-C:HiCCUPS loop calls
Supplementary files format and content: HiC and Capture-C:hic file
Supplementary files format and content: Capture-C: capC-MAP counts table for each sample

source_name: iCell Gluta

value: iCell Gluta

value: Gluta Neurons


title: GABA_CapC_rep2

source_name: iCell GABA

value: iCell GABA

value: GABA Neurons


title: Gluta_HiC_rep2


title: BC1_undiff_rep3 [Capture-C]

description:
column name: BC1_undiff_rep3
capC-MAP_counts.csv


title: BC1_undiff_rep2 [Capture-C]

description:
column name: BC1_undiff_rep2
capC-MAP_counts.csv


title: SCT_undiff_rep3 [Capture-C]

description:
column name: SCT_undiff_rep3
capC-MAP_counts.csv


title: SCT_diff_rep3 [Capture-C]

description:
column name: SCT_diff_rep3
capC-MAP_counts.csv


title: Gluta_CapC_rep2


title: SCT_diff_rep2 [Capture-C]

description:
column name: SCT_diff_rep2
capC-MAP_counts.csv


title: Gluta_CapC_rep1


title: Gluta_HiC_rep3


title: Input-KOLF2.1J_Neuron_Rep1

data_processing:
Each sample has a fastq for sonicated input control. Remove optical duplicates with clumpify and remove adapter reads with Cutadapt (v1.16)
Experiments were analyzed with ENCODE chip-seq-pipeline2. Pipeline was run with default settings
Peaks were called using IDR overlapping method with a threshold of 0.05
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor Pico.
Libraries were prepared by blunting and ligating ChIP DNA fragments to sequencing adapters for amplification with barcoded primers (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 15 cycles; 5 min at 72°C). Libraries were quantified with Qubit dsDNA HS Assay kit and visualized with Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical DNF-473) and Fragment Analyzer 5200 (Agilent).


title: H3K27ac-KOLF2.1J_Neuron_Rep2

description:
H3K27ac.pooled.fc.signal.bw
H3K27ac.optimal_peak.regionPeak.gz

value: H3K27ac (ActiveMotif, Cat:39133)


title: Input-KOLF2.1J_Neuron_Rep2


title: Gluta_CapC_rep3


title: KOLF2.1J_NGN2_rep1 [ATAC-seq]

description:
KOLF2.1J_NGN2_rep.pooled.pval.signal.bigwig
KOLF2.1J_NGN2_idr.optimal_peak.narrowPeak.gz

data_processing:
Reads were processed using the standard ENCODE ATAC-seq pipeline (v1.7.0).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: ATAC-seq was performed in the KOLF2.1J-hNGN2 cell line after 14 days of neuronal differentiation with three biological replicates per cell line.

extract_protocol:
We harvested 100,000 cells by mechanical dissociation and washed with 50 μL cold 1X PBS and centrifuged at 300xg for 5 minutes. The cell pellet was then resuspended in 50 μL cold Lysis Buffer (10 mM Tris-HCl at pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, and nuclease-free H2O) and incubated on ice for 3 minutes. After incubation, 1 mL of Wash Buffer (10 mM Tris-HCl at pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and nuclease-free H2O) was added, samples were inverted gently to mix, and centrifuged at 500xg for 10 minutes at 4°C. The supernatant was discarded and the remaining nuclei were resuspended in 50 μL Transposition Mix (2X TD Buffer, TDE1, and nuclease-free H2O) and incubated at 37°C on shaker at 1000 rpm for 30 minutes. Samples were immediately purified using the Qiagen MinElute Reaction Cleanup kit and eluted in a final volume of 11 μL. Recovered DNA was then used to generate sequencing libraries using primers from the Nextera XT Index Kit (15055293) and Q5 Hot Start Master Mix and amplified (30 sec at 98°C; [10 sec at 98°C, 30 sec at 63°C, and 72°C for 1 min] x10 cycles).
Libraries were quantified with Qubit dsDNA HS Assay kit and visualized with BioAnalyzer High Sensitivity DNA Analysis kit (Agilent 5067-4626) and 2100 BioAnalyzer Instrument (Agilent).


title: CTCF-KOLF2.1J_Neuron_Rep2

description:
CTCF.pooled.fc.signal.bw
CTCF.idr.optimal_peak.regionPeak.gz

value: CTCF (ActiveMotif, Cat:61311)


title: BC1_diff_rep2 [Capture-C]

description:
column name: BC1_diff_rep2
capC-MAP_counts.csv


title: H3K27ac-KOLF2.1J_Neuron_Rep1


title: GABA_CapC_rep1


title: KOLF2.1J_NGN2_rep2 [ATAC-seq]


title: KOLF2.1J_NGN2_rep2

description:
column name: KOLF2.1J_NGN2_rep2
7184.RMM.0001_18

source_name: KOLF2.1J NGN2

growth_protocol: For iCell Glutas, cells were maintained according to FujiFilm Cellular Dynamics recommendations. For XCL4 and BC1, NPCs were maintained in 2:1 DMEM:Ham's F12 supplemented with hFGF, hEGF, and heparin. NPCs were differentiated following the BrainPhys protocol from Bardy, et al. (doi:10.1073/pnas.1504393112)

value: KOLF2.1J NGN2


title: CTCF-KOLF2.1J_Neuron_Rep1


title: KOLF2.1J_NGN2_rep3

description:
column name: KOLF2.1J_NGN2_rep3
7184.RMM.0001_19


title: KOLF2.1J_NGN2_rep1

description:
column name: KOLF2.1J_NGN2_rep1
7184.RMM.0001_17


title: CRISPRi_target_chr17-45849095_rep4

description:
column name: CRISPRi_target_chr17-45849095_rep4
7136.NC.0008_96


title: GABA_CapC_rep3


title: KOLF2.1J_NGN2_rep3 [ATAC-seq]


title: CRISPRi_target_chr17-45849095_rep3

description:
column name: CRISPRi_target_chr17-45849095_rep3
7136.NC.0008_95


title: CRISPRi_target_chr17-45432051_rep4

description:
column name: CRISPRi_target_chr17-45432051_rep4
7136.NC.0008_94


title: CRISPRi_target_chr17-45429323_rep4

description:
column name: CRISPRi_target_chr17-45429323_rep4
7136.NC.0008_92


title: CRISPRi_target_chr17-45429323_rep3

description:
column name: CRISPRi_target_chr17-45429323_rep3
7136.NC.0008_91


title: CRISPRi_target_chr17-45956825_rep5

description:
column name: CRISPRi_target_chr17-45956825_rep5
7136.NC.0008_89


title: CRISPRi_target_chr17-45870936_rep5

description:
column name: CRISPRi_target_chr17-45870936_rep5
7136.NC.0008_86


title: CRISPRi_target_chr17-45941019_rep5

description:
column name: CRISPRi_target_chr17-45941019_rep5
7136.NC.0008_84


title: CRISPRi_target_chr17-45940494_rep5

description:
column name: CRISPRi_target_chr17-45940494_rep5
7136.NC.0008_83


title: CRISPRi_target_chr17-45946984_rep2

description:
column name: CRISPRi_target_chr17-45946984_rep2
7136.NC.0008_85


title: CRISPRi_target_chr17-46291354_rep6

description:
column name: CRISPRi_target_chr17-46291354_rep6
7136.NC.0008_80


title: CRISPRi_target_chr17-45894300_rep5

description:
column name: CRISPRi_target_chr17-45894300_rep5
7136.NC.0008_87


title: CRISPRi_target_chr17-45321056_rep6

description:
column name: CRISPRi_target_chr17-45321056_rep6
7136.NC.0008_81


title: CRISPRi_target_chr17-45949229_rep6

description:
column name: CRISPRi_target_chr17-45949229_rep6
7136.NC.0008_79


title: CRISPRi_target_chr17-45870177_rep5

description:
column name: CRISPRi_target_chr17-45870177_rep5
7136.NC.0008_88


title: CRISPRi_target_chr17-45942497_rep8

description:
column name: CRISPRi_target_chr17-45942497_rep8
7136.NC.0008_78


title: CRISPRi_target_chr17-45787210_rep9

description:
column name: CRISPRi_target_chr17-45787210_rep9
7136.NC.0008_75


title: CRISPRi_target_chr17-45309544_rep8

description:
column name: CRISPRi_target_chr17-45309544_rep8
7136.NC.0008_73


title: CRISPRi_target_chr17-45326805_rep7

description:
column name: CRISPRi_target_chr17-45326805_rep7
7136.NC.0008_74


title: CRISPRi_target_chr17-45309544_rep7

description:
column name: CRISPRi_target_chr17-45309544_rep7
7136.NC.0008_72


title: CRISPRi_target_chr17-44987687_rep9

description:
column name: CRISPRi_target_chr17-44987687_rep9
7136.NC.0008_71


title: CRISPRi_target_chr17-45219542_rep7

description:
column name: CRISPRi_target_chr17-45219542_rep7
7136.NC.0008_69


title: CRISPRi_target_chr17-44987687_rep8

description:
column name: CRISPRi_target_chr17-44987687_rep8
7136.NC.0008_70


title: CRISPRi_target_chr17-45241662_rep4

description:
column name: CRISPRi_target_chr17-45241662_rep4
7136.NC.0008_66


title: CRISPRi_target_chr17-46026698_rep5

description:
column name: CRISPRi_target_chr17-46026698_rep5
7136.NC.0008_67


title: CRISPRi_target_chr17-45223036_rep4

description:
column name: CRISPRi_target_chr17-45223036_rep4
7136.NC.0008_65


title: CRISPRi_target_chr17-45956825_rep4

description:
column name: CRISPRi_target_chr17-45956825_rep4
7136.NC.0008_64


title: CRISPRi_target_chr17-46193355_rep4

description:
column name: CRISPRi_target_chr17-46193355_rep4
7136.NC.0008_68


title: CRISPRi_target_chr17-45223036_rep5

description:
column name: CRISPRi_target_chr17-45223036_rep5
7136.NC.0008_90


title: CRISPRi_target_chr17-45813425_rep7

description:
column name: CRISPRi_target_chr17-45813425_rep7
7136.NC.0008_76


title: CRISPRi_target_chr17-45870177_rep4

description:
column name: CRISPRi_target_chr17-45870177_rep4
7136.NC.0008_63


title: CRISPRi_target_chr17-45326805_rep8

description:
column name: CRISPRi_target_chr17-45326805_rep8
7136.NC.0008_82


title: CRISPRi_target_chr17-45940494_rep4

description:
column name: CRISPRi_target_chr17-45940494_rep4
7136.NC.0008_59


title: CRISPRi_target_chr17-45894300_rep4

description:
column name: CRISPRi_target_chr17-45894300_rep4
7136.NC.0008_62


title: CRISPRi_target_chr17-45432051_rep3

description:
column name: CRISPRi_target_chr17-45432051_rep3
7136.NC.0008_93


title: CRISPRi_target_chr17-45870936_rep4

description:
column name: CRISPRi_target_chr17-45870936_rep4
7136.NC.0008_61


title: CRISPRi_target_chr17-46291354_rep5

description:
column name: CRISPRi_target_chr17-46291354_rep5
7136.NC.0008_58


title: CRISPRi_target_chr17-45309260_rep9

description:
column name: CRISPRi_target_chr17-45309260_rep9
7136.NC.0008_54


title: iCellGluta_rep2

description:
column name: iCellGluta_rep2
7136.NC.0008_52

source_name: iCellGluta

value: iCellGluta


title: iCellGluta_rep3

description:
column name: iCellGluta_rep3
7136.NC.0008_53


title: CRISPRi_target_chr17-45942497_rep7

description:
column name: CRISPRi_target_chr17-45942497_rep7
7136.NC.0008_57


title: CRISPRi_target_chr17-45787210_rep8

description:
column name: CRISPRi_target_chr17-45787210_rep8
7136.NC.0008_56


title: CRISPRi_target_chr17-45873822_rep5

description:
column name: CRISPRi_target_chr17-45873822_rep5
7136.NC.0008_55


title: CRISPRi_target_chr17-45147554_rep1

description:
column name: CRISPRi_target_chr17-45147554_rep1
7136.NC.0008_50


title: CRISPRi_target_chr17-46827080_rep1

description:
column name: CRISPRi_target_chr17-46827080_rep1
7136.NC.0008_49


title: iCellGluta_rep1

description:
column name: iCellGluta_rep1
7136.NC.0008_51


title: CRISPRi_target_chr17-45261951_rep3

description:
column name: CRISPRi_target_chr17-45261951_rep3
7136.NC.0008_47


title: CRISPRi_target_chr17-45132706_rep1

description:
column name: CRISPRi_target_chr17-45132706_rep1
7136.NC.0008_46


title: CRISPRi_target_chr17-45111031_rep3

description:
column name: CRISPRi_target_chr17-45111031_rep3
7136.NC.0008_45


title: CRISPRi_target_chr17-45784528_rep8

description:
column name: CRISPRi_target_chr17-45784528_rep8
7136.NC.0008_44


title: CRISPRi_target_chr17-45984001_rep1

description:
column name: CRISPRi_target_chr17-45984001_rep1
7136.NC.0008_48


title: CRISPRi_target_chr17-45247571_rep1

description:
column name: CRISPRi_target_chr17-45247571_rep1
7136.NC.0008_43


title: CRISPRi_target_chr17-45640752_rep1

description:
column name: CRISPRi_target_chr17-45640752_rep1
7136.NC.0008_42


title: CRISPRi_target_chr17-45813425_rep8

description:
column name: CRISPRi_target_chr17-45813425_rep8
7136.NC.0008_77


title: CRISPRi_target_chr17-46841711_rep1

description:
column name: CRISPRi_target_chr17-46841711_rep1
7136.NC.0008_41


title: CRISPRi_target_chr17-45941019_rep4

description:
column name: CRISPRi_target_chr17-45941019_rep4
7136.NC.0008_60


title: CRISPRi_target_chr17-45971758_rep3

description:
column name: CRISPRi_target_chr17-45971758_rep3
7136.NC.0008_38


title: CRISPRi_target_chr17-46778061_rep1

description:
column name: CRISPRi_target_chr17-46778061_rep1
7136.NC.0008_40


title: CRISPRi_target_chr17-45852751_rep1

description:
column name: CRISPRi_target_chr17-45852751_rep1
7136.NC.0008_37


title: CRISPRi_target_chr17-45432088_rep3

description:
column name: CRISPRi_target_chr17-45432088_rep3
7136.NC.0008_35


title: CRISPRi_target_chr17-45849135_rep1

description:
column name: CRISPRi_target_chr17-45849135_rep1
7136.NC.0008_36


title: CRISPRi_target_chr17-45371250_rep1

description:
column name: CRISPRi_target_chr17-45371250_rep1
7136.NC.0008_32


title: CRISPRi_target_chr17-45302897_rep1

description:
column name: CRISPRi_target_chr17-45302897_rep1
7136.NC.0008_30


title: CRISPRi_target_chr17-45307692_rep1

description:
column name: CRISPRi_target_chr17-45307692_rep1
7136.NC.0008_31


title: CRISPRi_target_chr17-45293628_rep1

description:
column name: CRISPRi_target_chr17-45293628_rep1
7136.NC.0008_29


title: CRISPRi_target_chr17-45291439_rep1

description:
column name: CRISPRi_target_chr17-45291439_rep1
7136.NC.0008_28


title: CRISPRi_target_chr17-45093169_rep1

description:
column name: CRISPRi_target_chr17-45093169_rep1
7136.NC.0008_26


title: CRISPRi_target_chr17-45021085_rep1

description:
column name: CRISPRi_target_chr17-45021085_rep1
7136.NC.0008_25


title: CRISPRi_target_chr17-45894000_rep16

description:
column name: CRISPRi_target_chr17-45894000_rep16
7136.NC.0008_21


title: CRISPRi_target_chr17-44960270_rep1

description:
column name: CRISPRi_target_chr17-44960270_rep1
7136.NC.0008_23


title: CRISPRi_target_chr17-45429139_rep1

description:
column name: CRISPRi_target_chr17-45429139_rep1
7136.NC.0008_34


title: CRISPRi_target_chr17-45228413_rep1

description:
column name: CRISPRi_target_chr17-45228413_rep1
7136.NC.0008_27


title: CRISPRi_target_chr17-46026698_rep4

description:
column name: CRISPRi_target_chr17-46026698_rep4
7136.NC.0008_20


title: CRISPRi_target_chr17-44970338_rep1

description:
column name: CRISPRi_target_chr17-44970338_rep1
7136.NC.0008_24


title: CRISPRi_target_chr17-45906479_rep7

description:
column name: CRISPRi_target_chr17-45906479_rep7
7136.NC.0008_19


title: CRISPRi_target_chr17-45977315_rep3

description:
column name: CRISPRi_target_chr17-45977315_rep3
7136.NC.0008_18


title: CRISPRi_target_chr17-45956833_rep4

description:
column name: CRISPRi_target_chr17-45956833_rep4
7136.NC.0008_16


title: CRISPRi_target_chr17-45942416_rep4

description:
column name: CRISPRi_target_chr17-45942416_rep4
7136.NC.0008_15


title: CRISPRi_target_chr17-45906479_rep6

description:
column name: CRISPRi_target_chr17-45906479_rep6
7136.NC.0008_14


title: CRISPRi_target_chr17-45288879_rep1

description:
column name: CRISPRi_target_chr17-45288879_rep1
7136.NC.0008_39


title: CRISPRi_target-Safe Harbor_rep12

description:
column name: CRISPRi_target-Safe Harbor_rep12
7136.NC.0008_13


title: CRISPRi_target_chr17-45965782_rep3

description:
column name: CRISPRi_target_chr17-45965782_rep3
7136.NC.0008_17


title: CRISPRi_target_chr17-45661411_rep4

description:
column name: CRISPRi_target_chr17-45661411_rep4
7136.NC.0008_11


title: CRISPRi_target_chr17-45385639_rep1

description:
column name: CRISPRi_target_chr17-45385639_rep1
7136.NC.0008_33


title: CRISPRi_target_chr17-45613065_rep4

description:
column name: CRISPRi_target_chr17-45613065_rep4
7136.NC.0008_10


title: CRISPRi_target_chr17-46884208_rep3

description:
column name: CRISPRi_target_chr17-46884208_rep3
7136.NC.0008_8


title: CRISPRi_target_chr17-45315000_rep3

description:
column name: CRISPRi_target_chr17-45315000_rep3
7136.NC.0008_9


title: CRISPRi_target_chr17-45771150_rep3

description:
column name: CRISPRi_target_chr17-45771150_rep3
7136.NC.0008_7


title: CRISPRi_target_chr17-45190950_rep3

description:
column name: CRISPRi_target_chr17-45190950_rep3
7136.NC.0008_6


title: CRISPRi_target_chr17-44901094_rep3

description:
column name: CRISPRi_target_chr17-44901094_rep3
7136.NC.0008_22


title: CRISPRi_target_chr17-44979760_rep4

description:
column name: CRISPRi_target_chr17-44979760_rep4
7136.NC.0008_5


title: CRISPRi_target_chr17-45771150_rep2

description:
column name: CRISPRi_target_chr17-45771150_rep2
7136.NC.0008_1


title: CRISPRi_target_chr17-45043372_rep3

description:
column name: CRISPRi_target_chr17-45043372_rep3
7136.NC.0007_93


title: CRISPRi_target_chr17-44979760_rep3

description:
column name: CRISPRi_target_chr17-44979760_rep3
7136.NC.0007_94


title: CRISPRi_target_chr17-45043372_rep4

description:
column name: CRISPRi_target_chr17-45043372_rep4
7136.NC.0008_4


title: CRISPRi_target_chr17-45190950_rep2

description:
column name: CRISPRi_target_chr17-45190950_rep2
7136.NC.0007_91


title: CRISPRi_target_chr17-44979760_rep2

description:
column name: CRISPRi_target_chr17-44979760_rep2
7136.NC.0007_90


title: CRISPRi_target_chr17-44976410_rep3

description:
column name: CRISPRi_target_chr17-44976410_rep3
7136.NC.0007_92


title: CRISPRi_target_chr17-46884208_rep1

description:
column name: CRISPRi_target_chr17-46884208_rep1
7136.NC.0007_87


title: CRISPRi_target-Safe Harbor_rep11

description:
column name: CRISPRi_target-Safe Harbor_rep11
7136.NC.0007_84


title: CRISPRi_target_chr17-45190950_rep1

description:
column name: CRISPRi_target_chr17-45190950_rep1
7136.NC.0007_85


title: CRISPRi_target_chr17-45043372_rep2

description:
column name: CRISPRi_target_chr17-45043372_rep2
7136.NC.0007_89


title: CRISPRi_target_chr17-45867320_rep4

description:
column name: CRISPRi_target_chr17-45867320_rep4
7136.NC.0008_12


title: CRISPRi_target_chr17-45771150_rep1

description:
column name: CRISPRi_target_chr17-45771150_rep1
7136.NC.0007_86


title: CRISPRi_target_chr17-44979760_rep1

description:
column name: CRISPRi_target_chr17-44979760_rep1
7136.NC.0007_83


title: CRISPRi_target_chr17-44976410_rep2

description:
column name: CRISPRi_target_chr17-44976410_rep2
7136.NC.0007_88


title: CRISPRi_target_chr17-46014089_rep2

description:
column name: CRISPRi_target_chr17-46014089_rep2
7136.NC.0007_79


title: CRISPRi_target_chr17-45043372_rep1

description:
column name: CRISPRi_target_chr17-45043372_rep1
7136.NC.0007_82


title: CRISPRi_target_chr17-44976410_rep1

description:
column name: CRISPRi_target_chr17-44976410_rep1
7136.NC.0007_81


title: CRISPRi_target_chr17-45861418_rep4

description:
column name: CRISPRi_target_chr17-45861418_rep4
7136.NC.0007_78


title: CRISPRi_target_chr17-46015344_rep3

description:
column name: CRISPRi_target_chr17-46015344_rep3
7136.NC.0007_77


title: CRISPRi_target_chr17-45956833_rep3

description:
column name: CRISPRi_target_chr17-45956833_rep3
7136.NC.0007_76


title: CRISPRi_target_chr17-45433464_rep3

description:
column name: CRISPRi_target_chr17-45433464_rep3
7136.NC.0007_73


title: CRISPRi_target_chr17-45661411_rep3

description:
column name: CRISPRi_target_chr17-45661411_rep3
7136.NC.0007_75


title: CRISPRi_target_chr17-45613065_rep3

description:
column name: CRISPRi_target_chr17-45613065_rep3
7136.NC.0007_74


title: CRISPRi_target_chr17-46884208_rep2

description:
column name: CRISPRi_target_chr17-46884208_rep2
7136.NC.0008_2


title: CRISPRi_target_chr17-46267785_rep4

description:
column name: CRISPRi_target_chr17-46267785_rep4
7136.NC.0007_72


title: CRISPRi_target_chr17-45965782_rep2

description:
column name: CRISPRi_target_chr17-45965782_rep2
7136.NC.0007_71


title: CRISPRi_target_chr17-44976410_rep4

description:
column name: CRISPRi_target_chr17-44976410_rep4
7136.NC.0008_3


title: CRISPRi_target_chr17-45867320_rep3

description:
column name: CRISPRi_target_chr17-45867320_rep3
7136.NC.0007_70


title: CRISPRi_target_chr17-45906479_rep4

description:
column name: CRISPRi_target_chr17-45906479_rep4
7136.NC.0007_67


title: CRISPRi_target_chr17-45956833_rep2

description:
column name: CRISPRi_target_chr17-45956833_rep2
7136.NC.0007_65


title: CRISPRi_target_chr17-45942416_rep3

description:
column name: CRISPRi_target_chr17-45942416_rep3
7136.NC.0007_68


title: CRISPRi_target-Safe Harbor_rep10

description:
column name: CRISPRi_target-Safe Harbor_rep10
7136.NC.0007_64


title: CRISPRi_target_chr17-46015344_rep2

description:
column name: CRISPRi_target_chr17-46015344_rep2
7136.NC.0007_66


title: CRISPRi_target_chr17-45894000_rep15

description:
column name: CRISPRi_target_chr17-45894000_rep15
7136.NC.0007_61


title: CRISPRi_target_chr17-45661411_rep2

description:
column name: CRISPRi_target_chr17-45661411_rep2
7136.NC.0007_62


title: CRISPRi_target_chr17-45613065_rep2

description:
column name: CRISPRi_target_chr17-45613065_rep2
7136.NC.0007_60


title: CRISPRi_target_chr17-45906479_rep5

description:
column name: CRISPRi_target_chr17-45906479_rep5
7136.NC.0007_80


title: CRISPRi_target_chr17-45906479_rep3

description:
column name: CRISPRi_target_chr17-45906479_rep3
7136.NC.0007_57


title: CRISPRi_target_chr17-45433464_rep2

description:
column name: CRISPRi_target_chr17-45433464_rep2
7136.NC.0007_59


title: CRISPRi_target_chr17-46014089_rep1

description:
column name: CRISPRi_target_chr17-46014089_rep1
7136.NC.0007_56


title: CRISPRi_target_chr17-45861418_rep3

description:
column name: CRISPRi_target_chr17-45861418_rep3
7136.NC.0007_55


title: CRISPRi_target_chr17-45867320_rep2

description:
column name: CRISPRi_target_chr17-45867320_rep2
7136.NC.0007_58


title: CRISPRi_target_chr17-45956833_rep1

description:
column name: CRISPRi_target_chr17-45956833_rep1
7136.NC.0007_53


title: CRISPRi_target_chr17-45613065_rep1

description:
column name: CRISPRi_target_chr17-45613065_rep1
7136.NC.0007_51


title: CRISPRi_target_chr17-46267785_rep3

description:
column name: CRISPRi_target_chr17-46267785_rep3
7136.NC.0007_49


title: CRISPRi_target_chr17-45433464_rep1

description:
column name: CRISPRi_target_chr17-45433464_rep1
7136.NC.0007_50


title: CRISPRi_target_chr17-45867320_rep1

description:
column name: CRISPRi_target_chr17-45867320_rep1
7136.NC.0007_47


title: CRISPRi_target_chr17-46004171_rep5

description:
column name: CRISPRi_target_chr17-46004171_rep5
7136.NC.0007_45


title: CRISPRi_target_chr17-44901094_rep2

description:
column name: CRISPRi_target_chr17-44901094_rep2
7136.NC.0007_46


title: CRISPRi_target_chr17-45111031_rep2

description:
column name: CRISPRi_target_chr17-45111031_rep2
7136.NC.0007_43


title: CRISPRi_target_chr17-45840618_rep5

description:
column name: CRISPRi_target_chr17-45840618_rep5
7136.NC.0007_63


title: CRISPRi_target_chr17-45948622_rep4

description:
column name: CRISPRi_target_chr17-45948622_rep4
7136.NC.0007_69


title: CRISPRi_target_chr17-45977315_rep2

description:
column name: CRISPRi_target_chr17-45977315_rep2
7136.NC.0007_42


title: CRISPRi_target_chr17-44947795_rep2

description:
column name: CRISPRi_target_chr17-44947795_rep2
7136.NC.0007_41


title: CRISPRi_target_chr17-45965782_rep1

description:
column name: CRISPRi_target_chr17-45965782_rep1
7136.NC.0007_48


title: CRISPRi_target_chr17-45661411_rep1

description:
column name: CRISPRi_target_chr17-45661411_rep1
7136.NC.0007_52


title: CRISPRi_target_chr17-46832437_rep2

description:
column name: CRISPRi_target_chr17-46832437_rep2
7136.NC.0007_39


title: CRISPRi_target_chr17-45971758_rep2

description:
column name: CRISPRi_target_chr17-45971758_rep2
7136.NC.0007_37


title: CRISPRi_target_chr17-45261951_rep1

description:
column name: CRISPRi_target_chr17-45261951_rep1
7136.NC.0007_33


title: CRISPRi_target_chr17-46764999_rep2

description:
column name: CRISPRi_target_chr17-46764999_rep2
7136.NC.0007_38


title: CRISPRi_target_chr17-46015344_rep1

description:
column name: CRISPRi_target_chr17-46015344_rep1
7136.NC.0007_54


title: CRISPRi_target_chr17-46764999_rep1

description:
column name: CRISPRi_target_chr17-46764999_rep1
7136.NC.0007_27


title: CRISPRi_target_chr17-44947795_rep1

description:
column name: CRISPRi_target_chr17-44947795_rep1
7136.NC.0007_30


title: CRISPRi_target_chr17-45942416_rep1

description:
column name: CRISPRi_target_chr17-45942416_rep1
7136.NC.0007_29


title: CRISPRi_target_chr17-45111031_rep1

description:
column name: CRISPRi_target_chr17-45111031_rep1
7136.NC.0007_32


title: CRISPRi_target_chr17-46832437_rep1

description:
column name: CRISPRi_target_chr17-46832437_rep1
7136.NC.0007_28


title: CRISPRi_target_chr17-45971758_rep1

description:
column name: CRISPRi_target_chr17-45971758_rep1
7136.NC.0007_26


title: CRISPRi_target_chr17-45977315_rep1

description:
column name: CRISPRi_target_chr17-45977315_rep1
7136.NC.0007_31


title: CRISPRi_target_chr17-45948622_rep3

description:
column name: CRISPRi_target_chr17-45948622_rep3
7136.NC.0007_24


title: CRISPRi_target_chr17-45906479_rep2

description:
column name: CRISPRi_target_chr17-45906479_rep2
7136.NC.0007_23


title: CRISPRi_target_chr17-45907842_rep7

description:
column name: CRISPRi_target_chr17-45907842_rep7
7136.NC.0007_22


title: CRISPRi_target_chr17-45261951_rep2

description:
column name: CRISPRi_target_chr17-45261951_rep2
7136.NC.0007_44


title: CRISPRi_target_chr17-45903110_rep5

description:
column name: CRISPRi_target_chr17-45903110_rep5
7136.NC.0007_21


title: CRISPRi_target_chr17-45942416_rep2

description:
column name: CRISPRi_target_chr17-45942416_rep2
7136.NC.0007_40


title: CRISPRi_target-Safe Harbor_rep9

description:
column name: CRISPRi_target-Safe Harbor_rep9
7136.NC.0007_19


title: CRISPRi_target_chr17-45219542_rep6

description:
column name: CRISPRi_target_chr17-45219542_rep6
7136.NC.0007_14


title: CRISPRi_target_chr17-46264873_rep8

description:
column name: CRISPRi_target_chr17-46264873_rep8
7136.NC.0007_16


title: CRISPRi_target_chr17-45432088_rep2

description:
column name: CRISPRi_target_chr17-45432088_rep2
7136.NC.0007_36


title: CRISPRi_target_chr17-46004171_rep4

description:
column name: CRISPRi_target_chr17-46004171_rep4
7136.NC.0007_34


title: CRISPRi_target_chr17-45583947_rep5

description:
column name: CRISPRi_target_chr17-45583947_rep5
7136.NC.0007_17


title: CRISPRi_target_chr17-44901094_rep1

description:
column name: CRISPRi_target_chr17-44901094_rep1
7136.NC.0007_35


title: CRISPRi_target_chr17-45784528_rep7

description:
column name: CRISPRi_target_chr17-45784528_rep7
7136.NC.0007_18


title: CRISPRi_target_chr17-46264873_rep7

description:
column name: CRISPRi_target_chr17-46264873_rep7
7136.NC.0007_15


title: CRISPRi_target_chr17-46026698_rep3

description:
column name: CRISPRi_target_chr17-46026698_rep3
7136.NC.0007_11


title: CRISPRi_target_chr17-46026698_rep2

description:
column name: CRISPRi_target_chr17-46026698_rep2
7136.NC.0007_10


title: CRISPRi_target_chr17-46193355_rep3

description:
column name: CRISPRi_target_chr17-46193355_rep3
7136.NC.0007_13


title: CRISPRi_target_chr17-45315000_rep2

description:
column name: CRISPRi_target_chr17-45315000_rep2
7136.NC.0007_8


title: CRISPRi_target_chr17-45894000_rep14

description:
column name: CRISPRi_target_chr17-45894000_rep14
7136.NC.0007_9


title: CRISPRi_target_chr17-46193355_rep2

description:
column name: CRISPRi_target_chr17-46193355_rep2
7136.NC.0007_12


title: CRISPRi_target_chr17-45241662_rep2

description:
column name: CRISPRi_target_chr17-45241662_rep2
7136.NC.0007_4


title: CRISPRi_target_chr17-45223036_rep3

description:
column name: CRISPRi_target_chr17-45223036_rep3
7136.NC.0007_3


title: CRISPRi_target_chr17-45315000_rep1

description:
column name: CRISPRi_target_chr17-45315000_rep1
7136.NC.0007_7


title: CRISPRi_target-Safe Harbor_rep8

description:
column name: CRISPRi_target-Safe Harbor_rep8
7136.NC.0007_2


title: CRISPRi_target_chr17-45241662_rep3

description:
column name: CRISPRi_target_chr17-45241662_rep3
7136.NC.0007_5


title: CRISPRi_target_chr17-46004171_rep3

description:
column name: CRISPRi_target_chr17-46004171_rep3
7136.NC.0007_1


title: CRISPRi_target_chr17-45873822_rep4

description:
column name: CRISPRi_target_chr17-45873822_rep4
7136.NC.0007_20


title: CRISPRi_target_chr17-45852747_rep1

description:
column name: CRISPRi_target_chr17-45852747_rep1
7136.NC.0005_96


title: CRISPRi_target_chr17-45432088_rep1

description:
column name: CRISPRi_target_chr17-45432088_rep1
7136.NC.0007_25


title: CRISPRi_target_chr17-45849095_rep2

description:
column name: CRISPRi_target_chr17-45849095_rep2
7136.NC.0005_94


title: CRISPRi_target_chr17-45849095_rep1

description:
column name: CRISPRi_target_chr17-45849095_rep1
7136.NC.0005_93


title: CRISPRi_target_chr17-45432051_rep2

description:
column name: CRISPRi_target_chr17-45432051_rep2
7136.NC.0005_92


title: CRISPRi_target_chr17-45894000_rep13

description:
column name: CRISPRi_target_chr17-45894000_rep13
7136.NC.0005_95


title: CRISPRi_target_chr17-45432051_rep1

description:
column name: CRISPRi_target_chr17-45432051_rep1
7136.NC.0005_91


title: CRISPRi_target_chr17-45429323_rep2

description:
column name: CRISPRi_target_chr17-45429323_rep2
7136.NC.0005_90


title: CRISPRi_target_chr17-46264953_rep3

description:
column name: CRISPRi_target_chr17-46264953_rep3
7136.NC.0005_87


title: CRISPRi_target_chr17-46291354_rep4

description:
column name: CRISPRi_target_chr17-46291354_rep4
7136.NC.0005_86


title: CRISPRi_target_chr17-46004145_rep6

description:
column name: CRISPRi_target_chr17-46004145_rep6
7136.NC.0005_85


title: CRISPRi_target_chr17-45321056_rep5

description:
column name: CRISPRi_target_chr17-45321056_rep5
7136.NC.0005_88


title: CRISPRi_target-Safe Harbor_rep7

description:
column name: CRISPRi_target-Safe Harbor_rep7
7136.NC.0005_84


title: CRISPRi_target_chr17-45429323_rep1

description:
column name: CRISPRi_target_chr17-45429323_rep1
7136.NC.0005_89


title: CRISPRi_target_chr17-46004145_rep5

description:
column name: CRISPRi_target_chr17-46004145_rep5
7136.NC.0005_83


title: CRISPRi_target_chr17-45949229_rep5

description:
column name: CRISPRi_target_chr17-45949229_rep5
7136.NC.0005_81


title: CRISPRi_target_chr17-45813425_rep6

description:
column name: CRISPRi_target_chr17-45813425_rep6
7136.NC.0005_79


title: CRISPRi_target_chr17-45894500_rep2

description:
column name: CRISPRi_target_chr17-45894500_rep2
7136.NC.0005_82


title: CRISPRi_target_chr17-45894000_rep12

description:
column name: CRISPRi_target_chr17-45894000_rep12
7136.NC.0005_78


title: CRISPRi_target_chr17-45813425_rep5

description:
column name: CRISPRi_target_chr17-45813425_rep5
7136.NC.0005_77


title: CRISPRi_target_chr17-45787210_rep7

description:
column name: CRISPRi_target_chr17-45787210_rep7
7136.NC.0005_76


title: CRISPRi_target_chr17-45906479_rep1

description:
column name: CRISPRi_target_chr17-45906479_rep1
7136.NC.0007_6


title: CRISPRi_target_chr17-45309544_rep6

description:
column name: CRISPRi_target_chr17-45309544_rep6
7136.NC.0005_74


title: CRISPRi_target_chr17-45309544_rep5

description:
column name: CRISPRi_target_chr17-45309544_rep5
7136.NC.0005_73


title: CRISPRi_target-Safe Harbor_rep6

description:
column name: CRISPRi_target-Safe Harbor_rep6
7136.NC.0005_72


title: CRISPRi_target_chr17-44987687_rep6

description:
column name: CRISPRi_target_chr17-44987687_rep6
7136.NC.0005_70


title: CRISPRi_target_chr17-44988418_rep12

description:
column name: CRISPRi_target_chr17-44988418_rep12
7136.NC.0005_69


title: CRISPRi_target_chr17-45326805_rep6

description:
column name: CRISPRi_target_chr17-45326805_rep6
7136.NC.0005_75


title: CRISPRi_target_chr17-45956825_rep3

description:
column name: CRISPRi_target_chr17-45956825_rep3
7136.NC.0005_66


title: CRISPRi_target_chr17-45894000_rep11

description:
column name: CRISPRi_target_chr17-45894000_rep11
7136.NC.0005_64


title: CRISPRi_target_chr17-45956825_rep2

description:
column name: CRISPRi_target_chr17-45956825_rep2
7136.NC.0005_65


title: CRISPRi_target_chr17-45223036_rep2

description:
column name: CRISPRi_target_chr17-45223036_rep2
7136.NC.0005_67


title: CRISPRi_target_chr17-45870177_rep3

description:
column name: CRISPRi_target_chr17-45870177_rep3
7136.NC.0005_63


title: CRISPRi_target_chr17-44987687_rep7

description:
column name: CRISPRi_target_chr17-44987687_rep7
7136.NC.0005_71


title: CRISPRi_target_chr17-45870177_rep2

description:
column name: CRISPRi_target_chr17-45870177_rep2
7136.NC.0005_62


title: CRISPRi_target_chr17-45894300_rep2

description:
column name: CRISPRi_target_chr17-45894300_rep2
7136.NC.0005_60


title: CRISPRi_target_chr17-44988418_rep11

description:
column name: CRISPRi_target_chr17-44988418_rep11
7136.NC.0005_68


title: CRISPRi_target_chr17-45870936_rep3

description:
column name: CRISPRi_target_chr17-45870936_rep3
7136.NC.0005_59


title: CRISPRi_target_chr17-45942497_rep6

description:
column name: CRISPRi_target_chr17-45942497_rep6
7136.NC.0005_80


title: CRISPRi_target_chr17-45894000_rep10

description:
column name: CRISPRi_target_chr17-45894000_rep10
7136.NC.0005_57


title: CRISPRi_target_chr17-45894300_rep3

description:
column name: CRISPRi_target_chr17-45894300_rep3
7136.NC.0005_61


title: CRISPRi_target_chr17-45870936_rep2

description:
column name: CRISPRi_target_chr17-45870936_rep2
7136.NC.0005_58


title: CRISPRi_target_chr17-45946984_rep1

description:
column name: CRISPRi_target_chr17-45946984_rep1
7136.NC.0005_56


title: CRISPRi_target_chr17-45941019_rep3

description:
column name: CRISPRi_target_chr17-45941019_rep3
7136.NC.0005_55


title: CRISPRi_target_chr17-45940494_rep2

description:
column name: CRISPRi_target_chr17-45940494_rep2
7136.NC.0005_51


title: CRISPRi_target-Safe Harbor_rep5

description:
column name: CRISPRi_target-Safe Harbor_rep5
7136.NC.0005_54


title: CRISPRi_target_chr17-45326805_rep5

description:
column name: CRISPRi_target_chr17-45326805_rep5
7136.NC.0005_47


title: CRISPRi_target_chr17-46264953_rep2

description:
column name: CRISPRi_target_chr17-46264953_rep2
7136.NC.0005_50


title: CRISPRi_target_chr17-45321056_rep4

description:
column name: CRISPRi_target_chr17-45321056_rep4
7136.NC.0005_46


title: CRISPRi_target_chr17-46291354_rep2

description:
column name: CRISPRi_target_chr17-46291354_rep2
7136.NC.0005_44


title: CRISPRi_target-Safe Harbor_rep4

description:
column name: CRISPRi_target-Safe Harbor_rep4
7136.NC.0005_42


title: U251MG_WWOX_3

city: Lodz

first: Żaneta

last: Kałuzińska-Kołat

address: Zeligowskiego St. 7/9

department: Deparment of Molecular Carcinogenesis

country: Poland

institute: Medical University of Lodz

description:
U251MG cells treated with GIPZ™ lentiviral system during stable transduction to represent WWOX overexpression.
Brain

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) v2.4.11.
Reads alignment and mapping to human reference genome (hg38) was performed with the use of STAR (Spliced Transcripts Alignment to a Reference).
Counting tags at each side was performed using SAMtools in R (Rsamtools v2.2.3). Tags were clustered using CAGEr 2.4.0.
Counts Per Million (CPM) were retrieved using limma-voom v3.42.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files include CPM values for each sample.

growth_protocol: T98G cells were grown according to the manufacturer’s protocol in Minimum Essential Media (MEM; Thermo Fisher Scientific, Naarden, The Netherlands) supplemented with 1% non-essential amino acids (NEAA; Gibco, Ghent, Belgium), DBTRG-05MG in RPMI 1640 supplemented with 1 mM sodium pyruvate (Gibco, Ghent, Belgium), whereas U251MG and U87MG in Eagle’s Minimum Essential Media (EMEM) supplemented with 1% NEAA and 1 mM sodium pyruvate. For all cell lines, the media were also complemented with 1% L-glutamine (Thermo Fisher Scientific, Naarden, The Netherlands), 10% heat-inactivated fetal bovine serum (FBS; Thermo Fisher Scientific, Naarden, The Netherlands), and 1% Antibiotic-Antimycotic (100 units/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of Fungizone; Thermo Fisher Scientific, Naarden, The Netherlands). All cell lines were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA was harvested using Extracol reagent, according to manufacturer protocol (EURX, Gdansk, Poland). Quality of total RNA was assessed by Agilent 2100 Bioanalyzer to confirm that RNA Integrity Number is over 8.0.
RNA libraries were prepared for sequencing using CAGE library preparation Kit (K.K. DNAFORM, Kanagawa, Japan).

treatment_protocol: The GIPZ™ lentiviral system (pLenti-GIII-CMV-GFP-2A-Puro) was chosen to overexpress WWOX, with Puro-Blank Lentivirus as control (Applied Biological Materials Inc., Richmond, BC, Canada). The cells were transduced in starvation medium with 8 µg/mL polybrene as the vehicle (Merck Life Sciences Sigma Aldrich, Darmstadt, Germany) and lentiviral particles at multiplicity of infection (MOI) = 1.5. After 24 h of incubation, the viral medium was changed to a complete medium. Antibiotic-based clone selection was performed using 1 µg/mL puromycin (Merck Life Sciences Sigma Aldrich, Darmstadt, Germany) after 72 h.

value: Cancer cells of glioblastoma

value: WWOX overexpression


title: U251MG_WWOX_1


title: U251MG_WWOX_2


title: U251MG_vec_2

description:
U251MG cells treated with Puro-Blank Lentivirus during stable transduction to serve as control variant.
Brain

value: Control


title: U251MG_vec_3


title: U251MG_vec_1


title: CRISPRi_target_chr17-46004145_rep3

description:
column name: CRISPRi_target_chr17-46004145_rep3
7136.NC.0005_43


title: CRISPRi_target_chr17-46004145_rep2

description:
column name: CRISPRi_target_chr17-46004145_rep2
7136.NC.0005_41


title: U87MG_WWOX_3

description:
U87MG cells treated with GIPZ™ lentiviral system during stable transduction to represent WWOX overexpression.
Brain


title: CRISPRi_target_chr17-45949229_rep4

description:
column name: CRISPRi_target_chr17-45949229_rep4
7136.NC.0005_39


title: CRISPRi_target_chr17-45941019_rep2

description:
column name: CRISPRi_target_chr17-45941019_rep2
7136.NC.0005_53


title: CRISPRi_target_chr17-45894000_rep9

description:
column name: CRISPRi_target_chr17-45894000_rep9
7136.NC.0005_40


title: U87MG_WWOX_2


title: CRISPRi_target_chr17-45813425_rep4

description:
column name: CRISPRi_target_chr17-45813425_rep4
7136.NC.0005_37


title: U87MG_vec_3

description:
U87MG cells treated with Puro-Blank Lentivirus during stable transduction to serve as control variant.
Brain


title: CRISPRi_target_chr17-45942497_rep5

description:
column name: CRISPRi_target_chr17-45942497_rep5
7136.NC.0005_38


title: CRISPRi_target_chr17-46291354_rep3

description:
column name: CRISPRi_target_chr17-46291354_rep3
7136.NC.0005_49


title: CRISPRi_target_chr17-46004145_rep4

description:
column name: CRISPRi_target_chr17-46004145_rep4
7136.NC.0005_48


title: U87MG_WWOX_1


title: CRISPRi_target_chr17-45894000_rep8

description:
column name: CRISPRi_target_chr17-45894000_rep8
7136.NC.0005_36


title: U87MG_vec_1


title: U87MG_vec_2


title: T98G_WWOX_3

description:
T98G cells treated with GIPZ™ lentiviral system during stable transduction to represent WWOX overexpression.
Brain


title: CRISPRi_target_chr17-45787210_rep6

description:
column name: CRISPRi_target_chr17-45787210_rep6
7136.NC.0005_34


title: CRISPRi_target_chr17-45813425_rep3

description:
column name: CRISPRi_target_chr17-45813425_rep3
7136.NC.0005_35


title: CRISPRi_target_chr17-45940494_rep3

description:
column name: CRISPRi_target_chr17-45940494_rep3
7136.NC.0005_52


title: CRISPRi_target_chr17-46264953_rep1

description:
column name: CRISPRi_target_chr17-46264953_rep1
7136.NC.0005_45


title: T98G_WWOX_2


title: CRISPRi_target_chr17-45326805_rep4

description:
column name: CRISPRi_target_chr17-45326805_rep4
7136.NC.0005_33


title: CRISPRi_target_chr17-45309544_rep3

description:
column name: CRISPRi_target_chr17-45309544_rep3
7136.NC.0005_31


title: T98G_WWOX_1


title: T98G_vec_2

description:
T98G cells treated with Puro-Blank Lentivirus during stable transduction to serve as control variant.
Brain


title: T98G_vec_3


title: CRISPRi_target_chr17-44987687_rep5

description:
column name: CRISPRi_target_chr17-44987687_rep5
7136.NC.0005_29


title: CRISPRi_target-Safe Harbor_rep3

description:
column name: CRISPRi_target-Safe Harbor_rep3
7136.NC.0005_30


title: T98G_vec_1


title: DBTRG-05MG_WWOX_3

description:
DBTRG-05MG cells treated with GIPZ™ lentiviral system during stable transduction to represent WWOX overexpression.
Brain


title: DBTRG-05MG_WWOX_2


title: DBTRG-05MG_WWOX_1


title: DBTRG-05MG_vec_3

description:
DBTRG-05MG cells treated with Puro-Blank Lentivirus during stable transduction to serve as control variant.
Brain


title: CRISPRi_target_chr17-44987687_rep4

description:
column name: CRISPRi_target_chr17-44987687_rep4
7136.NC.0005_28


title: DBTRG-05MG_vec_2


title: CRISPRi_target_chr17-45219542_rep5

description:
column name: CRISPRi_target_chr17-45219542_rep5
7136.NC.0005_25


title: CRISPRi_target_chr17-44988418_rep10

description:
column name: CRISPRi_target_chr17-44988418_rep10
7136.NC.0005_27


title: CRISPRi_target_chr17-46193355_rep1

description:
column name: CRISPRi_target_chr17-46193355_rep1
7136.NC.0005_24


title: DBTRG-05MG_vec_1


title: CRISPRi_target_chr17-46026698_rep1

description:
column name: CRISPRi_target_chr17-46026698_rep1
7136.NC.0005_23


title: CRISPRi_target_chr17-44988418_rep9

description:
column name: CRISPRi_target_chr17-44988418_rep9
7136.NC.0005_26


title: Cpa3Cre/+ day16 AS-935865-LR-66850

city: Heidelberg

first: Robin

last: Thiele

address: Im Neuenheimer Feld 280

department: Immunology

institute: German Cancer Research Center

data_processing:
reads were aligned via STAR aligner (default settings, v.2.5.2b)
and counted via FeatureCount (default settings, stranded library, subread/1.5.1)
Assembly: mm10 (Mus_musculus_GRCm38_102)
Supplementary files format and content: text delimeted file includes raw counts for each sample

source_name: stomach

extract_protocol:
Total RNA was extracted from whole stomach (fat removed) according to the instructions of the PureLink RNA Mini kit (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded RNA Kit (Illumina) following manufacturer's protocols.

value: stomach

value: male

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 26, 28, 30, 32, 34 and 37

tag: ova(ag) delivery

value: oral gavage


title: CRISPRi_target_chr17-45241662_rep1

description:
column name: CRISPRi_target_chr17-45241662_rep1
7136.NC.0005_22

value: Neurons


title: Cpa3Cre/+ day16 AS-935817-LR-66850

tag: time


title: CRISPRi_target-Safe Harbor_rep2

description:
column name: CRISPRi_target-Safe Harbor_rep2
7136.NC.0005_20


title: CRISPRi_target_chr17-45223036_rep1

description:
column name: CRISPRi_target_chr17-45223036_rep1
7136.NC.0005_21


title: Cpa3Cre/+ day11 AS-935859-LR-66850

value: female

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 25, 27, 29 and 32


title: Cpa3Cre/+ day16 AS-935847-LR-66850


title: CRISPRi_target_chr17-45956825_rep1

description:
column name: CRISPRi_target_chr17-45956825_rep1
7136.NC.0005_19


title: CRISPRi_target_chr17-45309544_rep4

description:
column name: CRISPRi_target_chr17-45309544_rep4
7136.NC.0005_32


title: CRISPRi_target_chr17-45870177_rep1

description:
column name: CRISPRi_target_chr17-45870177_rep1
7136.NC.0005_18


title: Cpa3Cre/+ day11 AS-935843-LR-66850


title: CRISPRi_target_chr17-45894300_rep1

description:
column name: CRISPRi_target_chr17-45894300_rep1
7136.NC.0005_17


title: CRISPRi_target_chr17-45870936_rep1

description:
column name: CRISPRi_target_chr17-45870936_rep1
7136.NC.0005_15


title: CRISPRi_target_chr17-45894000_rep7

description:
column name: CRISPRi_target_chr17-45894000_rep7
7136.NC.0005_16


title: Cpa3Cre/+ day 7 AS-935805-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 25 and 28

value: day 7


title: Cpa3Cre/+ day 7 AS-935777-LR-66850


title: Cpa3Cre/+ day 7 AS-935829-LR-66850


title: CRISPRi_target_chr17-45941019_rep1

description:
column name: CRISPRi_target_chr17-45941019_rep1
7136.NC.0005_13


title: Cpa3Cre/+ day16 AS-935845-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-37

value: 2-bottle test


title: CRISPRi_target_chr17-46291354_rep1

description:
column name: CRISPRi_target_chr17-46291354_rep1
7136.NC.0005_11


title: Cpa3Cre/+ day16 AS-935791-LR-66850


title: Cpa3Cre/+ day16 AS-935833-LR-66850


title: CRISPRi_target-Safe Harbor_rep1

description:
column name: CRISPRi_target-Safe Harbor_rep1
7136.NC.0005_10


title: Cpa3Cre/+ day11 AS-935841-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-32


title: CRISPRi_target_chr17-46004145_rep1

description:
column name: CRISPRi_target_chr17-46004145_rep1
7136.NC.0005_9


title: CRISPRi_target_chr17-45977337_rep3

description:
column name: CRISPRi_target_chr17-45977337_rep3
7136.NC.0005_8


title: CRISPRi_target_chr17-45942497_rep4

description:
column name: CRISPRi_target_chr17-45942497_rep4
7136.NC.0005_7


title: CRISPRi_target_chr17-45940494_rep1

description:
column name: CRISPRi_target_chr17-45940494_rep1
7136.NC.0005_12


title: CRISPRi_target_chr17-45787210_rep5

description:
column name: CRISPRi_target_chr17-45787210_rep5
7136.NC.0005_6


title: Cpa3Cre/+ day 7 AS-935803-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-28


title: Cpa3Cre/+ day11 AS-935783-LR-66850


title: Cpa3Cre/+ day 7 AS-935827-LR-66850


title: Cpa3Cre/+ day11 AS-935811-LR-66850