title: HeLa, control ProteinG IP, replicate 2

city: Warsaw

first: Damian

last: Graczyk

address: ul. Pawinskiego 5a

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

data_processing:
enDR3-DRIPc, S9.6 DRIPc, enDR3-ChIP, raw sequencing reads were mapped to human genome reference assembly GRh38/hg38 using bowtie2 (version 2.3.5.1) in the paired-end and local mode. The maximal distance between reads of 700 bp was allowed. Only reads with mapping quality equal to or greater than 30 were retained. Duplicate reads were removed. Reads filtering was performed using samtools (version 1.12). bigWig signal files (counts per million normalised) were generated using deeptools (version 3.5.1).
Peaks were called using MACS2 (PMID: 18798982). For stranded data, peaks were called on each strand separately and then merged into one file preserving the strand information. The visual inspection of our and previous data in the genome browser indicated that R-loop peaks are broad. The peaks were, therefore, called in the broad mode. In contrast, enDR3-ChIP-seq data visualisation showed that the peaks are narrow, thus, the peak calling was performed in the narrow mode. Where possible, replicate samples were used, and, as a background reference, an Input sample.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak (DRIPc-seq), narrowPeak (ChIP-seq; except for Input sample)
Library strategy: DRIPc-seq

source_name: Cervical cancer

growth_protocol: Cells were cultured in HyClone DMEM with high glucose, 4 mM L-glutamine, and sodium pyruvate (Cytiva) supplemented with 10% FBS (Gibco) at 37°C in an atmosphere of 5% CO2

extract_protocol:
DRIPc-seq procedure was based on previously published protocols (PMID: 32544226, PMID: 31053798) with some modifications. 1.25 x 106 HeLa cells were seeded onto 60 mm plates. After 24 hours, the culture medium was removed, and cells were washed once with cold PBS and twice with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Cell lysis was performed directly on the plate by adding 0.5 mL of lysis buffer (TE supplemented with 0.625 % SDS and 0.0625 mg/mL Proteinase K), and the suspension was immediately transferred to a fresh 2 mL tube and incubated for 4.5 hours at 37°C with gentle mixing every 15 minutes. Afterward, genomic DNA was purified by phenol: chloroform: isoamyl alcohol (25:24:1) extraction and ethanol precipitation. Precipitated DNA was washed with 70% ethanol, air-dried, and resuspended in 30 uL of TE buffer. Next, pure gDNA was sheared by sonication using Bioruptor Plus with a water cooling system (Diagenode) as follows: 3 µg of gDNA diluted to 200 µL in TE was placed in 1.5 mL DNA LoBind Tubes (Eppendorf) and subjected to 30 cycles of sonication 30 s ON, 90 s OFF at a "Low" mode. The length of fragments after sonication was evaluated by running DNA samples before and after shearing on a 1.5 % agarose gel in 1X TAE (40mM Tris pH 8.0, 20 mM acetic acid, 2 mM EDTA) at 70-80 V. Afterward, 4 µg of fragmented gDNA was mixed with 10 µg of  enDR3-3xFLAG or S9.6 antibody, diluted to 1 mL final volume with binding buffer (20 mM Hepes pH 7.4, 150 mM NaCl, 0.05 % Triton X-100), and incubated overnight with gentle rotation in a refrigeration cabinet. The next day, input fractions containing  enDR3-3xFLAG or S9.6 were added to 50 µL of M2 anti FLAG Magnetic Beads (Sigma) or Protein G Dynabeads (Thermo), respectively, and incubated for 2 hours. Additionally, negative controls were prepared by incubating 4 µg of sonicated gDNA with beads without the bait. Following the incubation, the unbound fraction was removed, and beads were washed three times with 500 µL of binding buffer for 5 min with gentle rotation in a refrigeration cabinet. Elution was performed by adding 125 µL of the elution buffer (50 mM Tris pH 8, 1mM EDTA, 0.5% SDS, 0.64 mg/mL Proteinase K) for 45 min at 55°C. Two replicates of each sample were pooled and purified using a DNA clean and concentrator kit (Zymo Research) according to the manufacturer's protocol. After elution with 30 µL of the elution buffer (Zymo Research), half of the eluate was treated with 2 µL of DNAse I (1 U/µL) in 1X DNase I digestion buffer (Thermo Fisher Scientific) for one hour at 37°C. For DNaseI inactivation, 1 µl of 0.5 M EDTA was added for 10 min at 65°C. RNA was purified using the RNA clean and concentrator kit (Zymo Research). ChIP-seq: HeLa Flp-In and derivative cell lines stably expressing enDR3-mEGFP and nb-enDR3-mEGFP were seeded on 100 mm dishes and treated with tetracycline at 25 ng/mL or 38 ng/mL, respectively. After 24 hours, cells were detached with trypsin and counted using hemocytometer. Then, 1.2 x 107 cells were pelleted by centrifugation for 4 min at 300 x g. The culture medium was removed, and cells were washed twice with 5 mL of PBS. Following 4 min centrifugation at 300 x g, cell pellets were suspended in 0.8 mL of cell lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.1% IGEPAL CA-630) supplemented with protease inhibitors cocktail, 1 mM PMSF, and 40 U/mL RiboLock (RL) RNase Inhibitor (Thermo Fisher Scientific), and incubated on ice for 15 min with gentle inverting every 3 min. Then samples were centrifuged at 700 x g for 5min at 4°C. Supernatants were removed and cell nuclei were lysed with 1.1 mL of nuclei lysis solution (20 mM Hepes pH 7.4, 1 mM EDTA, 100 mM NaCl, 5 % glycerol, 0.5 % Triton X-100, 0.1% SDS) supplemented with protease inhibitors cocktail, 1 mM PMSF, and40 U/mL RL. Nuclei lysates were transferred into milliTUBE AFA Fiber (Covaris) and sonicated using S220 Focused-ultrasonicator (Covaris) for 8 min at a Peak Power of 150 Watt, 10% Duty Factor and 200 cycles per burst. Chromatin shearing efficiency was examined by running 800 ng of DNA per well on 1.5 % agarose gel in 1X TAE at 70-80 V. Sonicated samples were transferred from milliTubes to 1.5 mL DNA LoBind tubes (Eppendorf) and centrifuged for 10 min at 20 000 x g at 4°C. Supernatants (hereafter inputs) were transferred to fresh LoBind tubes, and protein concentration was estimated by the Bradford method. For NGS and qPCR analyses, 65 µL (7.5 %) of the input fraction was collected, and 40 µL (4.5%) for the western blot analysis. For immunoprecipitation, 1 mg of input was added to 60 µL GFP-trap magnetic beads (homemade) and incubated with gentle rotation overnight at 4°C. The beads were captured using a magnetic stand, washed three times with 500 µL of low salt washing buffer I (20 mM Tris pH 8, 2 mM EDTA, 150 mM NaCl, 0.5% Triton X-100, 0.1% SDS) supplemented with 1X protease inhibitors cocktail. Next, beads were washed three times with 500uL of high salt washing buffer II (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 0.5% Triton X-100, 0.1% SDS) with 1X protease inhibitors cocktail, and once with 500uL of washing buffer III (10 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% Sodium deoxycholate) without inhibitors. Afterward, beads were washed twice with 500 µL of TE buffer (10 mM Tris pH 8, 1 mM EDTA), and 85 µl of the elution buffer (50 mM Tris pH 8, 50 mM NaHCO3, 1% SDS) was added and incubated for 15 min at 65°C with shaking (the 30s ON, 700 rpm/ 2 min OFF). Eluate (E1) was collected and transferred into a fresh 1.5 mL DNA LoBind tube. The elution step was repeated by adding 85 µl of fresh elution buffer, and the second eluate (E2) was pooled with E1. 20 µL of IPed fraction was collected for western blot analysis. Simultaneously, 85 µL elution buffer was added to the 65 µL of the input fractions and incubated for 15 min at 65°C with shaking (30s ON, 700rpm/2 min OFF). Next, 300 mM sodium chloride and 1 µl of RNase A (10 mg/mL) were added to each input and IPed sample and incubated for 45 min at 37°C in ThermoMixer (the 30s ON, 700 rpm/2 min OFF). Then the Proteinase K at a final concentration of 0.4 mg/ml was added, and the reaction was incubated at 55°C for one hour in ThermoMixer (the 30s ON, 1200 rpm/2 min OFF). DNA was purified using Zymo ChIP DNA clean & concentrator (Zymo Research) according to the manufacturer's protocol. The quality of the ChIP procedure was verified by qPCR.
For DRIPc-seq, purified RNA was used for stranded NGS library preparation using KAPA RNA HyperPrep Kit (Kapa Biosystems) according to the manufacturer's protocol. For ChIP-seq, purified DNA was used directly for NGS library preparation using KAPA RNA HyperPrep Kit (Kapa Biosystems) according to the manufacturer's protocol starting with the second DNA strand synthesis.
DRIPc-seq, ChIP-seq

treatment_protocol: No treatment

value: Cervical cancer

value: HeLa Flp-In T-Rex

value: Epithelial cells

tag: antibody

value: ProteinG


title: HeLa, enDR3-mEGFP, DNA after IP

status: Public on Aug 12 2025

type: SRA

country: Poland

library_source: genomic

data_processing:
enDR3-DRIPc, S9.6 DRIPc, enDR3-ChIP, raw sequencing reads were mapped to human genome reference assembly GRh38/hg38 using bowtie2 (version 2.3.5.1) in the paired-end and local mode. The maximal distance between reads of 700 bp was allowed. Only reads with mapping quality equal to or greater than 30 were retained. Duplicate reads were removed. Reads filtering was performed using samtools (version 1.12). bigWig signal files (counts per million normalised) were generated using deeptools (version 3.5.1).
Peaks were called using MACS2 (PMID: 18798982). For stranded data, peaks were called on each strand separately and then merged into one file preserving the strand information. The visual inspection of our and previous data in the genome browser indicated that R-loop peaks are broad. The peaks were, therefore, called in the broad mode. In contrast, enDR3-ChIP-seq data visualisation showed that the peaks are narrow, thus, the peak calling was performed in the narrow mode. Where possible, replicate samples were used, and, as a background reference, an Input sample.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak (DRIPc-seq), narrowPeak (ChIP-seq; except for Input sample)

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: enDR3-mEGFP-expressing cells

value: GFP-trap magnetic beads


title: HeLa, enDR3-FLAG IP, replicate 2

library_source: transcriptomic

molecule: total RNA

value: WT

value: FLAG


title: HeLa, control FLAG IP, replicate 1


title: HeLa, nb-enDR3-mEGFP, DNA after IP

value: Non-binding enDR3-mEGFP mutant-expressing cells


title: HeLa, Input DNA


title: HeLa, S9.6 IP, replicate 2


title: D105T77

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Assembly: hg38
Supplementary files format and content: Count matrix (raw counts) was obtained using DESeq2.

source_name: human monocytes

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample.

treatment_protocol: Human CD14+ monocytes were cultured in presence of an AhR inhibitor (SR1) or agonist (FICZ) for 6h.

value: human monocytes

tag: donor

tag: sample type

value: culture 6h

tag: treatment


title: D105T75

value: FICZ


title: HeLa, control FLAG IP, replicate 2


title: D105T73

value: medium


title: HeLa, enDR3-FLAG IP, replicate 1


title: D105T65


title: D105T63


title: CG_32_INPUT_R1

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description: ChIP-seq input of CG-dTAG-HA protein of hiPSC-derived long-term line CG_E5_HEM32/1

data_processing:
Raw sequence data were processed using the nf-core/chipseq pipeline v1.2.2.
Downstream analysis, quality control and motif enrichmenet analysis was performed in R mainly using motifmatchr v1.20.0 and with the aid of multiple, additional tools. For details, processing, please refer to the methods of the associated manuscript.
Supplementary files format and content: BED file of the set of consensus peaks defined by merging overlapping peaks detected in at least two HA replicates.
Assembly: GRCh38 human genome reference

source_name: Blood

growth_protocol: hiPSC line (Gibco A18945) was used  and routinely cultured under hypoxic conditions (37 °C, 3% O2, 5% CO2) on plates coated with hESC-qualified Matrigel (Corning) in TeSR E8 or mTeSR-Plus medium (STEMCELL Technologies). Cells were passaged every 3–4 days mostly at a split ratio of 1:6 using StemPro Accutase (Thermo Fisher Scientific), and medium was exchanged every 1-2 days

extract_protocol:
For differentiation, 2000 hiPSCs were seeded as clumps per well of a Matrigel-coated 12-well plate and 3 days later normoxic cell culture with STEMdiff hematopoietic differentiation basal medium with supplement A (containing BMP4, FGF2, VEGFA) for the first day with 3 µM CHIR99021 glycogen synthase kinase 3 inhibitor (Sigma-Aldrich) and another 2 days without. Next, cells were cultured for 9-10 days in differentiation medium with supplement B (containing BMP4, FGF2, VEGFA, SCF, FLT3L, TPO) with half media changes every 2–3 days. For CG protein degradation dTAG-13 compound (100 nM final; kindly provided by Nathanael Gray, Dana-Farber Cancer Institute, Boston, MA, USA; CG-negative isogenic control) was added from differentiation day 2 onwards.
Approx. 10^7 CG-expressing long-term or M-07e cells were fixed for 10 min at RT with 1% methanol-free formaldehyde in DPBS, and chromatin was prepared with the truChIP chromatin shearing kit according to NEXSON protocol 66 by ultrasonication for 20 min at 75 W peak incidence power, 10% duty factor, 200 cycles per burst and 7°C (Covaris M220). Immunoprecipation was performed with chromatin of 3-4 * 106 cells, 3 µg HA, CBFA2T3, or control normal mouse immunoglobulin G, and Protein G dynabeads (Invitrogen).
Libraries were prepared from input and immunoprecipitated DNA using the NEBnext Ultra II kit (New England Biolabs, E7645L) and sequenced on an Illumina NovaSeq (either 2x150 cycles in paired-end [CG_22_HA_IP_R1.1, CG_22_INPUT_R1.1, sub_M07E_CBFA2T3_IP, sub_M07E_INPUT] or 1x100 cycles in single-end [all other samples] setup) by the Vienna BioCenter Core Facilities (VBCF).

treatment_protocol: Parental hiPSCs (WT genotype) were genetically engineered by in trans paired nicking to carry CBFA2T3::GLIS2 (CG genotype) in one endogenous CBFA2T3 allele.

value: Blood

value: hiPSC (Gibco A18945)

value: hematopoietic

value: CG


title: D105T61


title: D105T41


title: D105T51


title: D105T53


title: D105T39


title: D105T49


title: D105T37


title: D105T29


title: D105T27


title: D105T25


title: HeLa, S9.6 IP, replicate 1

value: Cervical cancer


title: HeLa, control ProteinG IP, replicate 1

value: HeLa Flp-In T-Rex


title: D105T17


title: D105T15


title: S. aureus ParB_FLAG

city: Oeiras

first: Adrian

last: Izquierdo Martinez

state: Lisboa

address: Avenida da República

country: Portugal

institute: ITQB NOVA

description: Library name: ParB_FLAG

data_processing:
The CLC workbench (Qiagen) software was used to align the ChIP-seq reads to the reference genome (NCBI Reference Sequence GCF_002085525.1) and to export the sequence coverage data to a tabular .txt file for plotting.
Assembly: GCF_002085525.1
Supplementary files format and content: .txt, curves of coverage

organism: Staphylococcus aureus

growth_protocol: S. aureus strains were grown in TSB at 37°C with agitation overnight. The next day the cultures were diluted 1:200 in 50mL of TSB and incubated at 37°C with agitation until they reached the mid-exponential phase (OD600 0.6-0.8)

extract_protocol:
Formaldehyde (Sigma) was added to the cultures to a final concentration of 1% (v/v) and the mixture was incubated at room-temperature with shaking for 30 min. Afterwards, glycine was added to a final concentration of 125mM and further incubated at room-temperature with shaking for 10 min. Samples were resuspended in 300µl IP buffer (50mM Tris/HCl pH 7.5, 5mM EDTA, 150mM NaCl, 25mM sucrose, 1µg mL-1 lysostaphin, Sigma, 0.3 µg mL-1 RNase A, Sigma, and 1 tablet of cOmplete protease inhibitor cocktail, EDTA free, Roche, per 10mL of buffer) and incubated at 37°C for 1h with shaking. Afterwards the samples were cooled on ice, TritonX-100 was added to a final concentration of 1% (v/v) and they were vortexed. Samples were then sonicated using a Bioruptor Plus bath sonicator at 4°C using 50 cycles of alternating 30s on and 90s off in the high-power mode followed by centrifugation at 20000xg for 10min at 4°C.
Libraries were constructed using the NuGEN Ovation ultra low library preparation kit following the manufacturers instructions.

tag: chip antibody

value: anti-Flag M2 (SIGMA)


title: D105T13


title: P43_BrM_ROI_6_Protein

city: Houston

first: Nadim

last: Ajami

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: MD Anderson Cancer Center

description: Library name: DSP-1001660022407-Y-H02

library_source: other

data_processing:
Raw FASTQ files were processed with GeoMx NGS Pipeline v3.1.1.6.
RNA analysis was restricted to WTA probes and five 16S probes (Microbial16S_01, _03, _04, _07, _08). For RNA, probes failing manufacturer QC were excluded, LOQ set to two SD above background mean, and ROIs with <10% gene detection or genes detected in <10% of ROIs were removed.
For protein, only ROIs passing RNA QC were analyzed; targets with SNR > 2 in ≥10% of ROIs were retained.
RNA WTA counts were background-subtracted, Q3-normalized, thresholded at <1 to max < 1
16S counts were background-subtracted, then background-normalized using negative control probes.
Protein counts were normalized to IgG controls.
Both raw and normalized counts are provided. Raw counts include all ROIs (including those failing QC). Normalized counts include only QC-passed ROIs used in analysis.
Assembly: Assembly: hg38
Supplementary files format and content: Tab-delimited (.txt) files with rows = targets and columns = samples. RNA raw counts include WTA + pan-bacterial 16S probes.
Supplementary files format and content: Normalized counts are in separate files for WTA and 16S. Protein data provided separately (raw and IgG-normalized). RNA and protein data generated from the same ROIs; normalized datasets restricted to ROIs passing RNA QC.

molecule: protein

source_name: Brain metastasis (BrM)

extract_protocol:
ROIs (300 µm) from high- and low-TIL tumor regions (92 glioma, 90 brain metastases) were UV-cleaved after staining with Alexa Fluor 488–SYTO 13 (nuclei) and Alexa Fluor 594–anti-CD3 (TILs). Released RNA and protein oligos from the same ROIs were collected from FFPE tissue and used for library preparation.
RNA libraries: GeoMx Whole Transcriptome Atlas (~18,000 genes) + custom pan-microbial probe panel (incuding exploratory probes not tested in this study). Protein libraries: Immuno-Oncology Protein Atlas (>570 targets). Indexed per manufacturer’s Spatial Proteogenomic Library Prep Protocol.
Libraries were pooled at a 2:1 (RNA:protein) molar ratio and sequenced on Illumina NovaSeq 6000 S2 (paired-end, 2 × 27 bp, i5/i7 dual indexing).

value: Brain metastasis (BrM)

tag: patient

tag: primary tumor

value: Esophageal Cancer

tag: idh mutation

tag: recurrence


title: P43_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-H01


title: P49_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-H10

value: Renal Cell Carcinoma


title: P49_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-H09


title: P44_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-H06

value: Vascular Tumor


title: P43_BrM_ROI_7_Protein

description: Library name: DSP-1001660022407-Y-H03


title: P47_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-H11

value: Ovarian Cancer


title: P43_BrM_ROI_8_Protein

description: Library name: DSP-1001660022407-Y-H04


title: P44_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-H07


title: P47_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-H12


title: P45_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-H08

value: Thyroid Cancer


title: P44_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-H05


title: P41_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-G11

value: Liver Cancer


title: P41_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-G10


title: P39_BrM_ROI_8_Protein

description: Library name: DSP-1001660022407-Y-G06

value: Colorectal Cancer


title: P39_BrM_ROI_9_Protein

description: Library name: DSP-1001660022407-Y-G07


title: P40_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-G08

value: Neuroendocrine


title: P41_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-G12


title: P39_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-G03


title: P50_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-F12

value: Melanoma


title: P50_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-G01


title: P39_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-G04


title: P40_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-G09


title: P49_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-F09


title: P48_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-F08

value: Lymphoma


title: P49_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-F10


title: Squamous_6

type: genomic

city: Brisbane

first: Yufan

last: Feng

state: QLD

address: Building 71/918 RBWH Herston

department: UQ Centre for Clinical Research

country: Australia

institute: The University of Queensland

hyb_protocol: Hybridization was performed using the Illumina Infinium HD Methylation Assay protocol.

data_processing: Data were processed using the R package ChAMP v3.18.

label: other

source_name: FFPE

label_protocol: DNA was bisulfite converted with EZ-96 DNA Methylation kit (Zymo research).

extract_protocol: Tumor regions were annotated with a consultant pathologist (AS) enriching for a single phenotype where possible, with minimal tumor-infiltrating lymphocytes (TILs) to reduce normal contamination. Samples were sectioned (10 μm, 15 sections/sample), needle-dissected and DNA extracted (QIAamp DNA FFPE Tissue Kit, QIAGEN). Quality and quantity assessment of the samples was performed by QuantiFluor.

value: FFPE

value: breast tumor

tag: group

value: Squamous


title: P47_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-F06


title: P46_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-F02

value: Adenocarcinoma


title: P47_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-F05


title: Squamous_2

scan_protocol: Hybridization was performed using the Illumina Infinium HD Methylation Assay protocol.


title: Squamous_4


title: P46_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-F03


title: P46_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-E11


title: NST_2

value: NST


title: NST_5


title: P47_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-F07


title: P49_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-F11


title: Spindle_3

value: Spindle


title: P39_BrM_ROI_7_Protein

description: Library name: DSP-1001660022407-Y-G05

value: Brain metastasis (BrM)


title: Spindle_2


title: P42_BrM_ROI_7_Protein

description: Library name: DSP-1001660022407-Y-E09


title: P42_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-E07


title: P42_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-E08


title: P46_AjN_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-F01

source_name: Adjacent normal to brain metastasis

value: Adjacent normal to brain metastasis


title: Squamous_5


title: P45_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-E06


title: P42_BrM_ROI_8_Protein

description: Library name: DSP-1001660022407-Y-E10


title: NST_3


title: Chondroid_3

value: Chondroid


title: Chondroid_2


title: Spindle_1


title: Squamous_1


title: Squamous_3


title: P47_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-F04


title: P43_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-E01

value: Esophageal Cancer


title: P45_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-E05


title: Spindle_4


title: P44_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-E03

value: Vascular Tumor


title: P43_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-D12


title: P43_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-D10


title: P44_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-E04


title: P43_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-D11


title: NST_1


title: P42_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-D07


title: NST_4


title: Chondroid_1


title: P42_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-D06


title: P42_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-D08


title: P41_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-D05


title: P44_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-E02


title: P41_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-D03


title: P37_BrM_ROI_7_Protein

description: Library name: DSP-1001660022407-Y-D01

value: Leiomyosarcoma


title: P37_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-C12


title: P39_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-C11


title: P41_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-D04

value: Liver Cancer


title: P37_BrM_ROI_8_Protein

description: Library name: DSP-1001660022407-Y-D02


title: P39_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-C09

value: Colorectal Cancer


title: P39_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-C08


title: P37_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-C05


title: P37_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-C04


title: P38_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-C07

value: Angiosarcoma


title: P37_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-C03


title: P37_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-C01


title: P37_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-C02


title: P35_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-B06

value: Ovarian Cancer


title: P35_BrM_ROI_7_Protein

description: Library name: DSP-1001660022407-Y-B10


title: P35_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-B07


title: P35_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-B04


title: P33_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-B03

value: Glomangiosarcoma


title: P42_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-D09

value: Melanoma


title: P35_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-B09


title: P35_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-B08


title: P35_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-B05


title: P33_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-A11


title: P32_BrM_ROI_7_Protein

description: Library name: DSP-1001660022407-Y-B02

value: Unknown Origin


title: P33_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-A09


title: P32_BrM_ROI_6_Protein

description: Library name: DSP-1001660022407-Y-B01


title: P32_BrM_ROI_5_Protein

description: Library name: DSP-1001660022407-Y-A12


title: P33_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-A10


title: P32_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-A04


title: P32_BrM_ROI_4_Protein

description: Library name: DSP-1001660022407-Y-A07


title: P38_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-C06


title: P33_BrM_ROI_1_Protein

description: Library name: DSP-1001660022407-Y-A08


title: No_template_control_BrM_Protein

description: Library name: DSP-1001660022407-Y-A01

source_name: No template control

value: No template control


title: P30_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-H11

source_name: Glioma

value: Glioma

value: WT

value: Primary


title: P29_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-H10

value: Mut


title: P30_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-H12


title: P28_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-H08

source_name: Adjacent normal to Glioma

value: Adjacent normal to Glioma

value: Recurrent


title: P28_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-H05


title: P27_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-H04


title: P26_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-H03


title: P26_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-H02


title: P39_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-C10

value: Brain metastasis (BrM)


title: P23_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-G06


title: P23_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-G05


title: P25_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-G11


title: P23_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-G04


title: P25_AjN_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-G12


title: P24_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-G07


title: P24_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-G09


title: P26_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-H01


title: P32_BrM_ROI_3_Protein

description: Library name: DSP-1001660022407-Y-A06


title: P22_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-G03


title: P32_BrM_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-A05


title: P24_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-G08


title: P20_AjN_ROI_5_Protein

description: Library name: DSP-1001660022652-Z-F08


title: P22_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-G02


title: P28_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-H07


title: P20_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-F06


title: P29_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-H09


title: P22_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-G01


title: P19_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-F03


title: P21_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-F10


title: P21_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-F09


title: P18_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-E12


title: P21_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-F12


title: P20_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-F07


title: P17_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-E09


title: P15_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-E04


title: P15_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-E03


title: P17_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-E08


title: P20_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-F05


title: P21_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-F11


title: P15_AjN_ROI_5_Protein

description: Library name: DSP-1001660022652-Z-E05


title: P20_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-F04


title: P16_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-E07


title: P16_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-E06


title: P18_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-E10


title: P19_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-F01


title: P13_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-D09


title: P12_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-D07


title: P13_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-D10


title: P12_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-D05


title: P14_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-D11


title: P15_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-E02


title: P11_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-D04


title: P15_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-E01


title: P19_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-F02


title: P18_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-E11


title: P13_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-D08


title: P12_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-D06


title: P11_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-D03


title: P11_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-D01


title: P10_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-C12

value: Unknown


title: P10_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-C11


title: P9_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-C10


title: P9_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-C09


title: P9_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-C08


title: P11_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-D02


title: P8_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-C06


title: P7_AjN_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-C03


title: P8_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-C07


title: P14_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-D12


title: P7_AjN_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-C02


title: P8_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-C05


title: P28_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-H06


title: P7_AjN_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-C01


title: P6_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-B10


title: P6_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-B09


title: P7_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-B12


title: P46_Tumor_border_ROI_2_Protein

description: Library name: DSP-1001660022407-Y-E12

source_name: Brain metastasis border

value: Brain metastasis border

value: Adenocarcinoma


title: P6_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-B07


title: P6_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-B08


title: P5_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-B06


title: P5_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-B04


title: P4_Glioma_ROI_4_Protein

description: Library name: DSP-1001660022652-Z-B02


title: P5_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-B05


title: P4_Glioma_ROI_5_Protein

description: Library name: DSP-1001660022652-Z-B03


title: P25_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-G10


title: P4_Glioma_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-B01


title: P2_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-A07


title: P1_AjN_ROI_3_Protein

description: Library name: DSP-1001660022652-Z-A06


title: P8_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-C04


title: P3_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-A10


title: P2_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-A08


title: P3_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-A09


title: P1_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-A05


title: P1_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-A04


title: P47_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-H12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: No_template_control_Glioma_Protein

description: Library name: DSP-1001660022652-Z-A01


title: P47_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-H11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P45_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-H08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Thyroid Cancer


title: P49_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-H10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Renal Cell Carcinoma


title: P49_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-H09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_8_RNA

description:
Library name: DSP-1001660022407-A-H04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Esophageal Cancer


title: P44_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-H07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Vascular Tumor


title: P44_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-H06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_7_RNA

description:
Library name: DSP-1001660022407-A-H03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P44_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-H05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-H01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-H02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P41_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-G12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Liver Cancer


title: P40_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-G09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Neuroendocrine


title: P4_Glioma_ROI_2_Protein

description: Library name: DSP-1001660022652-Z-A12


title: P41_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-G10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P4_Glioma_ROI_1_Protein

description: Library name: DSP-1001660022652-Z-A11


title: P41_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-G11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P39_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-G03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Colorectal Cancer


title: P39_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-G04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P39_BrM_ROI_9_RNA

description:
Library name: DSP-1001660022407-A-G07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P50_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-F12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Melanoma


title: P40_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-G08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P49_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-F11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P39_BrM_ROI_7_RNA

description:
Library name: DSP-1001660022407-A-G05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P49_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-F09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P50_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-G01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P48_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-F08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Lymphoma


title: P47_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-F06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Ovarian Cancer


title: P46_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-F03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P46_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-F02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P46_AjN_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-F01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Adjacent normal to brain metastasis


title: P46_Tumor_border_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-E12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P46_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-E11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-E08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-E07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P39_BrM_ROI_8_RNA

description:
Library name: DSP-1001660022407-A-G06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P45_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-E05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P45_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-E06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P44_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-E03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P44_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-E04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P44_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-E02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-E01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-D12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-D10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P49_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-F10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P47_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-F07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P43_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-D11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-D08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P47_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-F05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-D06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P47_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-F04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P41_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-D04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-D09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_8_RNA

description:
Library name: DSP-1001660022407-A-E10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P37_BrM_ROI_8_RNA

description:
Library name: DSP-1001660022407-A-D02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Leiomyosarcoma


title: P37_BrM_ROI_7_RNA

description:
Library name: DSP-1001660022407-A-D01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_7_RNA

description:
Library name: DSP-1001660022407-A-E09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P41_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-D03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P37_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-C12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P39_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-C11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P38_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-C07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Angiosarcoma


title: P39_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-C08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Brain metastasis (BrM)


title: P38_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-C06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P37_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-C04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P42_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-D07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P41_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-D05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P37_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-C01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P37_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-C02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P35_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-B07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P37_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-C03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P35_BrM_ROI_7_RNA

description:
Library name: DSP-1001660022407-A-B10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P35_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-B06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P35_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-B09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P35_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-B08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P32_BrM_ROI_7_RNA

description:
Library name: DSP-1001660022407-A-B02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Unknown Origin


title: P35_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-B05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P35_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-B04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P32_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-A12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P32_BrM_ROI_6_RNA

description:
Library name: DSP-1001660022407-A-B01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P33_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-A11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Glomangiosarcoma


title: P39_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-C10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P33_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-A10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P33_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-A09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P32_BrM_ROI_3_RNA

description:
Library name: DSP-1001660022407-A-A06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P33_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-A08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P32_BrM_ROI_4_RNA

description:
Library name: DSP-1001660022407-A-A07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P39_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-C09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P37_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-C05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P32_BrM_ROI_1_RNA

description:
Library name: DSP-1001660022407-A-A04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P30_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-H12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Glioma

value: WT

value: Primary


title: P28_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-H08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Adjacent normal to Glioma

value: Mut

value: Recurrent


title: P29_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-H09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P29_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-H10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P30_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-H11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P28_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-H06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P28_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-H05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P28_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-H07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P27_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-H04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P26_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-H03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P33_BrM_ROI_5_RNA

description:
Library name: DSP-1001660022407-A-B03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P24_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-G08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P25_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-G11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P25_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-G10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P26_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-H01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P24_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-G07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P23_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-G05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P23_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-G06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P22_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-G02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P22_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-G01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P24_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-G09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P23_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-G04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P21_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-F11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P21_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-F10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P21_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-F12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P25_AjN_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-G12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P32_BrM_ROI_2_RNA

description:
Library name: DSP-1001660022407-A-A05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P22_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-G03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P21_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-F09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: No_template_control_BrM_RNA

description:
Library name: DSP-1001660022407-A-A01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: No template control


title: P20_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-F06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P26_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-H02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P20_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-F07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P20_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-F05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P20_AjN_ROI_5_RNA

description:
Library name: DSP-1001660022652-D-F08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P20_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-F04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P19_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-F03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P19_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-F02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P18_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-E12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P19_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-F01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P18_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-E11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P17_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-E09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P16_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-E07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P17_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-E08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P18_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-E10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P15_AjN_ROI_5_RNA

description:
Library name: DSP-1001660022652-D-E05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P15_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-E04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P15_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-E03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P15_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-E02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P13_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-D10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P14_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-D11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P13_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-D08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P13_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-D09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P12_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-D07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P15_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-E01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P12_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-D06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P12_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-D05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P11_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-D04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P11_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-D02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P11_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-D03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: ARPE-19 cells, LV1

city: Guangzhou

first: Junbiao

last: Zhang

state: Guangdong

address: No. 183, Zhongshan Avenue West

department: Ophthalmology

country: China

institute: The Third Affiliated Hospital of Southern Medical University

description:
Library name: SAMPLES 4
PDZK1 overexpression lentivirus,37.5mM High glucose,48h

data_processing:
RNA was extracted using the Trizol method，500ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit  following manufacturer's protocols.
Homo_sapiens GRCh38.112
Raw data were processed using fastp v0.20.1 for adapter trimming and removal of low-quality sequences.
CleanData were aligned to Homo sapiens GRCh38.112,using HISAT2 (version 2.2.1)
Assembly: Homo_sapiens GRCh38.112
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

growth_protocol: ARPE-19l cells were maintained in DMEM supplemented with 10%fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

treatment_protocol: Cells are maintained in DMEM with 10 % fetal bovine serum and 1 % penicillin–streptomycin at 37 °C in a humidified 5 % CO₂ incubator. At approximately 50 % confluence, cultures are transduced with PDZK1-overexpressing or control lentivirus (Tsingke) at MOI 10. After 48 h of transduction, 4 μg/ml puromycin is added for stable selection. Control and PDZK1-overexpressing cells are then exposed to 37.5 mM d-glucose for 48 h, after which total RNA is extracted for downstream analysis.

value: Retinal pigment epithelial cell line

value: PDZK1 overexpression lentivirus


title: ARPE-19 cells, LV2

description:
Library name: SAMPLES 5
PDZK1 overexpression lentivirus,37.5mM High glucose,48h

extract_protocol:
RNA was extracted using the Trizol method，500ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit  following manufacturer's protocols.


title: ARPE-19 cells, HG3

description:
Library name: SAMPLES 3
control lentivirus,37.5mM High glucose,48h

value: control lentivirus


title: ARPE-19 cells, LV3

description:
Library name: SAMPLES 6
PDZK1 overexpression lentivirus,37.5mM High glucose,48h


title: ARPE-19 cells, HG2

description:
Library name: SAMPLES 2
control lentivirus,37.5mM High glucose,48h


title: P11_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-D01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: ARPE-19 cells, HG1

description:
Library name: SAMPLES 1
control lentivirus,37.5mM High glucose,48h


title: P10_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-C11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Unknown


title: P9_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-C10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P9_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-C09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P9_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-C08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: NCRM5_PT4_R3 (RNA-seq)

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

description:
Library name: NCRM5_PT4_R3
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt

data_processing:
RNA-seq data from the human and chimpanzee diploids, autotetraploids, and allotetraploids was analyzed as previously described (Song et al., 2021). Briefly, sequencing reads were trimmed for adapter sequences and assessed for sequencing quality using trimgalore v0.6.6 with cutadapt v2.5 (Martin, 2011) and fastqc v0.11.5 (Andrews et al., 2010). Reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to a composite human-chimpanzee genome (hg38 and panTro6). The number of uniquely-mapped reads (MAPQ=255) that overlap each gene was counted using featureCounts from the subread v2.0.0 package (Liao et al., 2014).
For CRISPR inhibition experiments, UMIs were extracted using umi_tools v1.1.2 (Smith et al., 2017) and adapter sequences were trimmed using cutadapt v2.5 (Martin, 2011). Sequencing quality was assessed with fastqc v0.11.5 (Andrews et al., 2010). Reads that map to rDNA (https://www.ncbi.nlm.nih.gov/nuccore/U13369.1) were removed, and remaining reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to either the hg38 or panTro6 genome, as appropriate. Reads were then de-duplicated based on UMIs using umi_tools, and the number of reads that overlap each gene was counted using featureCounts from the subread v2.0.0 package with default parameters (Liao et al., 2014).
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: gene count files

growth_protocol:
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into neural progenitor cells (NPCs) using the StemDiff SMADi Neural Induction Kit (STEMCELL Technologies, cat #08582) as per the manufacturer’s instructions. On D7, cells were split using Accutase (Millipore, cat #SCR005) and infected with lentivirus (if applicable). Cells were harvested at D14 for sequencing.
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into patterned induced neurons (piNs) via induction of doxycycline-inducible NGN2 and as described in Nehme et al., 2018. Cells were harvested on D28

extract_protocol:
NPCs at D14 or piNs at D28 were collected in Trizol and RNA was extracted with the Direct-Zol Miniprep Kit (Zymo Research, cat #R2052) or the Direct-Zol Microprep Kit (Zymo Research, cat #R2062). Cells infected with lentivirus were collected by FACS prior to RNA extraction.
RNA sequencing libraries were made with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara Bio) or with the WatchMaker RNA Library Prep Kit with Polaris Depletion (WatchMaker Genomics) and the Twist UMI Adapter System - TruSeq Comp, 96 Samples Plate A (Twist Biosciences, cat #105041).

treatment_protocol: If applicable, cells were infected with lentivirus.

value: patterned induced neurons

value: Y

tag: ploidy

tag: grna

tag: grna target

tag: batch


title: NCRM5_PT3_R3 (RNA-seq)

description:
Library name: NCRM5_PT3_R3
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P16_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-E06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

tag: tissue


title: NCRM5_NT3181_R3 (RNA-seq)

description:
Library name: NCRM5_NT3181_R3
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt

tag: cell line

value: NTC


title: H2C_PT3_R3 (RNA-seq)

description:
Library name: NCRM5_PT3_R2
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt

tag: cell type


title: NCRM5_NTGN2_R3 (RNA-seq)

description:
Library name: NCRM5_NTGN2_R3
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P8_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-C06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P8_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-C05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: H2C_PT4_R3 (RNA-seq)

description:
Library name: NCRM5_PT4_R2
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P14_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-D12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P7_AjN_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-C03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P8_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-C07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: NCRM5_NT1872_R3 (RNA-seq)

description:
Library name: NCRM5_NT1872_R3
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P8_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-C04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: H2C_NT3181_R3 (RNA-seq)

description:
Library name: NCRM5_NT3181_R2
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P7_AjN_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-C02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: H2C_NTGN2_R3 (RNA-seq)

description:
Library name: NCRM5_NTGN2_R2
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: H2C_NT1872_R3 (RNA-seq)

description:
Library name: NCRM5_NT1872_R2
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P10_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-C12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P7_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-B12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P7_AjN_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-C01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: NCRM5_PT4_R2 (RNA-seq)

description:
Library name: NCRM5_PT4_R1
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5_PT2_R3 (RNA-seq)

description:
Library name: NCRM5_PT2_R3
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5_PT3_R2 (RNA-seq)

description:
Library name: NCRM5_PT3_R1
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P6_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-B10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: NCRM5_PT2_R2 (RNA-seq)

description:
Library name: NCRM5_PT2_R1
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P6_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-B09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: NCRM5_NT1872_R2 (RNA-seq)

description:
Library name: NCRM5_NT1872_R1
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: NCRM5_NT3181_R2 (RNA-seq)

description:
Library name: NCRM5_NT3181_R1
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P5_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-B06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P5_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-B05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_H2C_MT2 (RNA-seq)

description:
Library name: CRTF_E3_H2C_MT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt

value: neural progenitor cells

value: MAZ


title: P6_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-B08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P4_Glioma_ROI_5_RNA

description:
Library name: DSP-1001660022652-D-B03
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: NCRM5_NTGN2_R2 (RNA-seq)

description:
Library name: NCRM5_NTGN2_R1
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P6_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-B07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P5_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-B04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P4_Glioma_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-B01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_H2C_MT4 (RNA-seq)

description:
Library name: CRTF_E3_H2C_MT4
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E3_H2C_MT1 (RNA-seq)

description:
Library name: CRTF_E3_H2C_MT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: P4_Glioma_ROI_4_RNA

description:
Library name: DSP-1001660022652-D-B02
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P4_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-A12
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_H2C_FT3 (RNA-seq)

description:
Library name: CRTF_E3_H2C_FT3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E3_H2C_FT2 (RNA-seq)

description:
Library name: CRTF_E3_H2C_FT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E3_H2C_FT1 (RNA-seq)

description:
Library name: CRTF_E3_H2C_FT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: P4_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-A11
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_H2C_GN5 (RNA-seq)

description:
Library name: CRTF_E3_H2C_GN5
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E3_H2C_GN3 (RNA-seq)

description:
Library name: CRTF_E3_H2C_GN3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: P3_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-A09
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: P3_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-A10
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_H2C_GN2 (RNA-seq)

description:
Library name: CRTF_E3_H2C_GN2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: P2_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-A07
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_NCRM5_MT4 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_MT4
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E3_NCRM5_MT2 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_MT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: P1_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-A05
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_NCRM5_FT3 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_FT3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: H2C_PT2_R3 (RNA-seq)

description:
Library name: NCRM5_PT2_R2
The raw data are being made available for controlled access in dbGaP.
POU3F2_CRISPRi_human-NPC_gene_counts.txt


title: P1_Glioma_ROI_1_RNA

description:
Library name: DSP-1001660022652-D-A04
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_NCRM5_FT2 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_FT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E3_NCRM5_GN3 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_GN3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: No_template_control_Glioma_RNA

description:
Library name: DSP-1001660022652-D-A01
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.


title: CRTF_E3_NCRM5_GN5 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_GN5
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E3_NCRM5_GN2 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_GN2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_H2C_MT4 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_MT4
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_H2C_MT2 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_MT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: siSNRPA,ChIP

city: Shanghai

first: Yifan

last: Guo

address: Dongan Road No.150

institute: Fudan university, Shanghai, China

description: Library name: siSNRPA,ChIP

data_processing:
Uniquely mapped reads to GRCh38 were aligned using bowtie2 and peaks were identified using MACS2 with the default parameters
Assembly: GRCh38.p13
Supplementary files format and content: bigwig

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed with a ChIP assay kit (Bes5001, Bersinbio) according to the manufacturer’s protocol11. Cells were fixed in 1% formaldehyde and terminated by glycine solution, and then they were lysed in ChIP lysis buffer.
ChIP DNA library was established with Hieff NGS® Ultima Pro DNA Library Prep Kit (Cat#12197, Yeasen).


title: siZFPM2AS1,Input

description: Library name: siZFPM2AS1,Input


title: siZFPM2AS1,ChIP

description: Library name: siZFPM2AS1,ChIP


title: siSNRPA,Input

description: Library name: siSNRPA,Input


title: 293T_Control,ChIP

description: Library name: 293T_Control,ChIP


title: 293T_Control,Input

description: Library name: 293T_Control,Input


title: U251-D28WO, biol rep 3

city: Santa Monica

first: Santosh

last: Kesari

state: California

address: 2200 Santa Monica Blvd

department: Translational Neuro-oncology

institute: Saint John Cancer Institute

description:
Library name: U251_R15
Untreated, collected at Day 28 (withdrawn after 14 days)
TPM_U251.csv

data_processing:
Quality control was performed using FastQC, and adapter trimming was conducted with Trim Galore.
Reads were aligned to the GRCh38 human genome using STAR aligner.
Gene counts were generated using featureCounts.
Differential expression analysis was conducted using edgeR. Genes with FDR < 0.05 were considered significant.
Pathway and Gene Ontology enrichment analyses were performed using PANTHER.
Assembly: GRCh38 (Ensembl release 108)
Supplementary files format and content: TPM_*.csv

growth_protocol: U87-MG and U251-MG glioblastoma cell lines were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO₂.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA integrity was verified using an Agilent Bioanalyzer 2100 (RIN > 8).
RNA libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 to generate 150 bp paired-end reads.

treatment_protocol: Cells were treated with 1 μg/mL human IFN-γ (Life Technologies) for up to 28 days. Treatment was either continued or withdrawn after Day 14.

value: Human Glioblastoma Cells

tag: genotype

tag: time

value: Day 28 (withdrawn after 14 days)


title: P2_Glioma_ROI_2_RNA

description:
Library name: DSP-1001660022652-D-A08
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Glioma

value: WT


title: U251-D28WO, biol rep 2

description:
Library name: U251_R14
Untreated, collected at Day 28 (withdrawn after 14 days)
TPM_U251.csv


title: CRTF_E2F_H2C_FT3 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_FT3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_H2C_MT1 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_MT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: P1_AjN_ROI_3_RNA

description:
Library name: DSP-1001660022652-D-A06
Contains WTA probes and custom 16S probes; only a subset of the latter was analyzed.

value: Adjacent normal to Glioma


title: U251-D28WO, biol rep 1

description:
Library name: U251_R13
Untreated, collected at Day 28 (withdrawn after 14 days)
TPM_U251.csv


title: CRTF_E2F_H2C_FT2 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_FT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D28W, biol rep 3

description:
Library name: U251_R12
Treated with IFN-γ 1µL/mL for Day 28 (continued treatment)
TPM_U251.csv

value: IFN-γ 1µL/mL

value: Day 28 (continued treatment)


title: CRTF_E3_NCRM5_MT1 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_MT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_H2C_FT1 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_FT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_H2C_GN5 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_GN5
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_H2C_GN2 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_GN2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_H2C_GN3 (RNA-seq)

description:
Library name: CRTF_E2F_H2C_GN3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D14, biol rep 3

description:
Library name: U251_R9
Treated with IFN-γ 1µL/mL for Day 14
TPM_U251.csv

value: Day 14


title: CRTF_E2F_NCRM5_MT4 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_MT4
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D28W, biol rep 1

description:
Library name: U251_R10
Treated with IFN-γ 1µL/mL for Day 28 (continued treatment)
TPM_U251.csv


title: CRTF_E2F_NCRM5_MT2 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_MT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D14, biol rep 2

description:
Library name: U251_R8
Treated with IFN-γ 1µL/mL for Day 14
TPM_U251.csv


title: CRTF_E3_NCRM5_FT1 (RNA-seq)

description:
Library name: CRTF_E3_NCRM5_FT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D14, biol rep 1

description:
Library name: U251_R7
Treated with IFN-γ 1µL/mL for Day 14
TPM_U251.csv


title: CRTF_E2F_NCRM5_MT1 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_MT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D3, biol rep 3

description:
Library name: U251_R6
Treated with IFN-γ 1µL/mL for Day 3
TPM_U251.csv

value: Day 3


title: CRTF_E2F_NCRM5_FT2 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_FT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_NCRM5_FT1 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_FT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D3, biol rep 2

description:
Library name: U251_R5
Treated with IFN-γ 1µL/mL for Day 3
TPM_U251.csv


title: U251-Control, biol rep 3

description:
Library name: U251_R3
Untreated, collected at Day 3
TPM_U251.csv


title: U251-D3, biol rep 1

description:
Library name: U251_R4
Treated with IFN-γ 1µL/mL for Day 3
TPM_U251.csv


title: CRTF_E2F_NCRM5_GN5 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_GN5
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-Control, biol rep 2

description:
Library name: U251_R2
Untreated, collected at Day 3
TPM_U251.csv


title: U87-D28WO, biol rep 3

description:
Library name: U87_R15
Untreated, collected at Day 28 (withdrawn after 14 days)
TPM_U87.csv


title: U251-Control, biol rep 1

description:
Library name: U251_R1
Untreated, collected at Day 3
TPM_U251.csv


title: CRTF_E2F_NCRM5_GN3 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_GN3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E2F_NCRM5_GN2 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_GN2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-D28WO, biol rep 2

description:
Library name: U87_R14
Untreated, collected at Day 28 (withdrawn after 14 days)
TPM_U87.csv


title: U87-D28WO, biol rep 1

description:
Library name: U87_R13
Untreated, collected at Day 28 (withdrawn after 14 days)
TPM_U87.csv


title: CRTF_E1_H2C_MT1 (RNA-seq)

description:
Library name: CRTF_E1_H2C_MT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E1_H2C_MT4 (RNA-seq)

description:
Library name: CRTF_E1_H2C_MT4
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U251-D28W, biol rep 2

description:
Library name: U251_R11
Treated with IFN-γ 1µL/mL for Day 28 (continued treatment)
TPM_U251.csv


title: CRTF_E1_H2C_FT3 (RNA-seq)

description:
Library name: CRTF_E1_H2C_FT3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E1_H2C_MT2 (RNA-seq)

description:
Library name: CRTF_E1_H2C_MT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-D28W, biol rep 2

description:
Library name: U87_R11
Treated with IFN-γ 1µL/mL for Day 28 (continued treatment)
TPM_U87.csv


title: CRTF_E1_H2C_FT1 (RNA-seq)

description:
Library name: CRTF_E1_H2C_FT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-D14, biol rep 3

description:
Library name: U87_R9
Treated with IFN-γ 1µL/mL for Day 14
TPM_U87.csv


title: U87-D14, biol rep 2

description:
Library name: U87_R8
Treated with IFN-γ 1µL/mL for Day 14
TPM_U87.csv


title: CRTF_E1_H2C_GN5 (RNA-seq)

description:
Library name: CRTF_E1_H2C_GN5
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E1_H2C_FT2 (RNA-seq)

description:
Library name: CRTF_E1_H2C_FT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-D28W, biol rep 1

description:
Library name: U87_R10
Treated with IFN-γ 1µL/mL for Day 28 (continued treatment)
TPM_U87.csv


title: CRTF_E1_H2C_GN3 (RNA-seq)

description:
Library name: CRTF_E1_H2C_GN3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-D14, biol rep 1

description:
Library name: U87_R7
Treated with IFN-γ 1µL/mL for Day 14
TPM_U87.csv


title: CRTF_E2F_NCRM5_FT3 (RNA-seq)

description:
Library name: CRTF_E2F_NCRM5_FT3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E1_NCRM5_MT4 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_MT4
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-D3, biol rep 3

description:
Library name: U87_R6
Treated with IFN-γ 1µL/mL for Day 3
TPM_U87.csv


title: U87-D3, biol rep 1

description:
Library name: U87_R4
Treated with IFN-γ 1µL/mL for Day 3
TPM_U87.csv


title: CRTF_E1_NCRM5_MT2 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_MT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-Control, biol rep 3

description:
Library name: U87_R3
Untreated, collected at Day 3
TPM_U87.csv


title: U87-D28W, biol rep 3

description:
Library name: U87_R12
Treated with IFN-γ 1µL/mL for Day 28 (continued treatment)
TPM_U87.csv


title: U87-Control, biol rep 2

description:
Library name: U87_R2
Untreated, collected at Day 3
TPM_U87.csv


title: CRTF_E1_NCRM5_FT2 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_FT2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: CRTF_E1_NCRM5_FT1 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_FT1
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: U87-Control, biol rep 1

description:
Library name: U87_R1
Untreated, collected at Day 3
TPM_U87.csv


title: CRTF_E1_NCRM5_FT3 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_FT3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt


title: 083992_Mock-R3_S12_R1_filtered

city: Lafayette

first: Austin

last: Tedman

state: IN

address: 716 Brown St Apt 4

department: Chemistry

institute: Purdue University

description: Library name: Mock R3

data_processing:
Used STAR Alignment v 2.7.11b
Sequence reads were filtered for low quality and trimmed based on adaptor sequences
Trimmed sequences were mapped to GRCH39.p14 using STAR Alignment benchwork
Assembly: GRCH39.p14
Supplementary files format and content: csv files with RPKM values for each sample

source_name: HEK 293T

growth_protocol: HEK 293T cells were maintained in DMEM supplemented with 10% Fetabl Bovine Serum and 90 units/mL of Penicillin-Streptomycin incubated at 37 C with 5% CO2

extract_protocol:
Total RNA was extracted using Aurum Total RNA Mini Kit (Centrifugation Protocol) with about 3.2 ug of RNA used for sequncing libraries
Library Construction RNA polyA+

value: HEK 293T

value: Embryonic Kidney Cells

value: Mock


title: 083991_GPCR-Library-R3_S11_R1_filtered

description: Library name: GPCR Library R3

value: GPCR


title: 083988_Mock-R2_S8_R1_filtered

description: Library name: Mock R2


title: CRTF_E1_NCRM5_GN5 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_GN5
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt

value: Y


title: CRTF_E1_NCRM5_GN3 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_GN3
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt

value: NTC


title: CRTF_E1_NCRM5_GN2 (RNA-seq)

description:
Library name: CRTF_E1_NCRM5_GN2
The raw data are being made available for controlled access in dbGaP.
FOSL2_MAZ_CRISPRi_human-NPC_gene_counts.txt

value: neural progenitor cells


title: 083987_GPCR-Library-R2_S7_R1_filtered

description: Library name: GPCR Library R2


title: 083984_Mock-R1_S4_R1_filtered

description: Library name: Mock R1