title: nsRBNS_RNA_input

status: Public on Jan 31 2025

type: SRA

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

country: USA

institute: UNC Chapel Hill

description: Input control for UNK nsRBNS

library_source: transcriptomic

data_processing:
Reads were trimmed to library sequencing size (20 nt for RBNS, 33 nt for posRBNS and compPosRBNS, 100 nt for nsRBNS)
For non-nsRBNS: Duplicate reads were collapsed
Counts were generated as dictated per experiment: RBNS (6mers), posRBNS and compPosRBNS (3mers, positionally), nsRBNS (STAR mapping against .fa)
For non-nsRBNS: Counts were normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: hg38
Supplementary files format and content: RBNS: 6mer enrichments
Supplementary files format and content: posRBNS & compPosRBNS: 3mer enrichments, positionally
Supplementary files format and content: nsRBNS: sequence enrichments

molecule: total RNA

organism:
Homo sapiens
Mus musculus

source_name: RBNS

extract_protocol:
Bound RNA was eluted from streptavidin magnetic beads in 0.1% SDS with 0.3 mg/mL proteinase K. RNA was concentrated via phenol-chloroform extraction.
RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified.

tag: tissue

value: RBNS


title: UNK ZnF1-3 nsRBNS, 500, rep2

description: Counts were normalized for library size prior to enrichment against nsRBNS_RNA_input


title: UNK ZnF4-6 nsRBNS, 500


title: HCC with  dICB + Dexa 200mg (3)

type: RNA

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the purified target/probe complexes are eluted out the beads and immobilized on the cartridge for data collection.

data_processing: Raw code counts

organism: Mus musculus

source_name: Hepatocellular carcinoma

extract_protocol: Total RNA was extracted from the formalin-fixed paraffin-embedded (FFPE) specimens of primary tumors by using Qiagen’s miRNeasy FFPE Kit (Qiagen, Valencia, CA, USA).

tag: group

value: anti-PD-1 + anti-CTLA4 + Dexa (200mg)


title: HCC with  dICB + Dexa 200mg (2)


title: HCC with  dICB + Dexa 10mg (3)

value: anti-PD-1 + anti-CTLA4 + Dexa (10mg)


title: HCC with  dICB + Dexa 200mg (1)


title: HCC with  dICB + Dexa 10mg (1)


title: HCC with  dICB + Dexa 10mg (2)


title: HCC with  dICB (2)

value: anti-PD-1 + anti-CTLA4


title: HCC with  dICB (3)


title: HCC with  isotype (3)

value: Isotype


title: CAFs cells, exo3

city: Guangzhou

first: Zexiong

last: Cheng

address: No.601, West Huangpu Avenue

country: China

institute: Jinan University

description: Library name: Sample 5

data_processing:
R Studio software (v.4.2.1, R Studio, Inc. Boston, USA)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each  Sample

organism: Homo sapiens

source_name: human CRC tissues

growth_protocol: CAFs were  cultured in DMEM/F-12 with 10% FBS and 1 × penicillin/streptomycin.HCT116 were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and maintained in a humidified tissue culture incubator at 37 ℃ and 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, 15596026) was used for the construction of sequencing libraries.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

treatment_protocol: Exosomes isolated from HCT116 cells were added to CAFs for 24 h with three replicates.

value: human CRC tissues

tag: cell line

value: CAFs

tag: cell type

value: colorectal cancer cells

tag: genotype

value: WT

tag: treatment

value: input exo


title: HCC with  dICB (1)


title: CAFs cells, exo1

description: Library name: Sample 3


title: CAFs cells, exo2

description: Library name: Sample 4


title: WT female injected with WT(star) serum #4

city: New York

first: Matthew

last: Smith-Raska

state: NY

address: 1300 York Ave.

department: Pediatrics

institute: Weill Cornell Medicine

description: Library name: Sample 8

data_processing:
The quality of sequenced reads was assessed with FastQC (v0.12.1)
Sequenced reads were aligned using STAR (v2.7.11b)
Gene expression estimates were obtained with featureCounts (Subread v2.0.3)
Assembly: GRCm38
Supplementary files format and content: read counts per gene

source_name: Liver

extract_protocol:
RNA was isolated using the Qiagen RNeasy Lipid Tissue RNA Kit
Libraries were prepared with Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: Liver

value: Hepatocyte

value: Wild Type


title: CAFs cells, wt1

description: Library name: Sample 1

value: control


title: WT female injected with WT(star) serum #3

description: Library name: Sample 7


title: WT female injected with WT(star) serum #2

description: Library name: Sample 6


title: WT female injected with WT(star) serum #1

description: Library name: Sample 5


title: WT female injected with WT serum #4

description: Library name: Sample 12


title: HCC with  isotype (1)


title: UNK ZnF1-3 nsRBNS, 500, rep1


title: WT female injected with WT serum #3

description: Library name: Sample 11


title: WT female injected with WT serum #2

description: Library name: Sample 10


title: Electronic Cigarette Processing Group

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description:
Library name: E-cigs
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation w ere madeusing the Cell Ranger softw are v2.1.1
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aorta

growth_protocol: All mice were maintained under standard conditions (20‐24°C, 40%‐60% humidity, 12/12‐hour light/dark cycle).

extract_protocol:
The whole aorta samples collected from mice after exposure.
scRNA-seq libraries were constructed using the 10x Genomics Single Cell Gene Expression Solution v3.1. All the procedures were performed according to the standard manufacturer’s protocol (CG000315 Rev E). Briefly, beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 3’end with UMI and cell label, indicating its cell of origin. Then cDNA along with cell barcodes were PCR-amplified.The constructed libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 4150 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). Then the libraries were sequenced on NovaSeq 6000 (Illumina) with a sequencing depth of at least 20,000 reads per cell with a pair-end 150 bp (PE150) reading strategy.

treatment_protocol: All animal studies were approved by the Capital Medical University (ethical review number: AEEI-2021-024). C57BL/6J male mice aged 8 weeks inhaled filtered air (as control) or e-cig (RELX, containing glycerin, propylene glycol, spices, and 3% nicotine) 1 h per day in the exposure chamber for consecutive 90 days.

value: Aorta


title: VML +Vehicle

city: Ann Arbor

first: Susan

middle: V

last: Brooks

state: Michigan

address: 109 Zina Pitcher Pl

department: Molecular and Integrative Physiology

institute: University of Michigan

description:
Library name: Sample 2
10X Genomics

data_processing:
The `count` command from CellRanger v8.0.0 (10X Genomics) was used with the `--include-introns` argument set to `true`, aligning reads to the GRCm39 genome build.
Assembly: GRCm39
Supplementary files format and content: Filtered features, barcodes, count matrices (h5 format)

source_name: Skeletal muscle

extract_protocol:
Bilateral 3mm biopsy punch defects were administered to the quadriceps muscles of (12-16-week-old) C57BL/6 mice. Mice were treated with AICAR and vehicle loaded synthetic protein nano particles (SPNPs) at the site of injury on days 1, 4, and 7 days post injury. At 8 days post injury, mice were humanely euthanized, quadriceps extracted and pooled according to treatment. After tissues were manually homogenized with scissors, they were digested into single cell suspensions for 1h at 37°C using 2 mg/ml collagenase II and 2.5 U/ml dispase II. The enzymatic reaction was stopped using 10% heat inactivated FBS with 5 mM EDTA and passed through a 70 mm strainer. Samples were centrifuged for 10 min at 300g, and resuspended in red blood cell lysis buffer for 2 min at room temperature. After washing, suspension was stained with DAPI and sorted by FACs to remove debris and dead cells (DAPI positive). Sorted cells were then labeled with 10x genomics cell multiplexing oligos (one per treatment) and then analyzed by single cell RNA sequencing.
Library preparation and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan. Cells were loaded into the 10X Genomics chromium single cell controller for each sample and captured into nanoliter-scale gel bead-in-emulsions. cDNAs were prepared using the single cell protocol as per manufacturer’s instructions.

value: Skeletal muscle

value: Mononucleated single cells

value: C57BL/6J (WT)

value: Control


title: WT female injected with WT serum #1

description: Library name: Sample 9


title: VML +AICAR

description:
Library name: Sample 1
10X Genomics

value: AICAR


title: Control group

description:
Library name: Con
10x Genomics


title: Normal diet +20% mannose, biol rep 3

city: NEW YORK

first: Charles

last: DeRossi

address: 1 Gustave L. Levy Place, Box, Annenberg 14-12

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: ND1_Man20_3
NDM20_13_Aligned.sortedByCoord.out.bam

data_processing:
fastq files were aligned to mouse reference genome (GRCm39.108) using STAR RNA-seq aligner (version 2.7.5b),
Read counts were extracted from .BAM files using featureCounts (version 2.0.6)
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

growth_protocol: Eight-week-old male C57BL/6J mice (Jackson Laboratory, Bar Harbor, ME) were housed 3-5 per cage and kept with a 12-hr dark/light cycle.

extract_protocol:
Total RNA was isolated and purified from homogenized mouse liver tissue in TRIzol reagent (ThermoFisher) following supplied protocol.  Isolated RNA samples were further purified using RNeasy mini kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Control mice received normal chow diet (LabDiet, Rodent diet 20, #5053) with drinking water ad libitum. MASH mice were placed on FAT-MASH regimen of 21.1% fat, 41% sucrose, and 1.25% cholesterol in chow (Teklad diets, 120528) with sugar water of 23.1 g/L d-fructose and 18.9 g/L d-glucose, and 0.2mL/g of body weight CCl4 intraperitoneal (IP) injections 1x/week. Mannose 5% or 20% (w/v) was supplemented in drinking water and supplied ad libitum for full 12 weeks (prevention groups), or final 6 weeks (therapy groups).

tag: diet regimen

value: Normal diet

tag: mannose supplements

tag: mannose duration

value: 12 weeks

value: Normal Diet +20% mannose

tag: batch


title: Normal diet +20% mannose, biol rep 2

description:
Library name: ND1_Man20_2
NDM20_12_Aligned.sortedByCoord.out.bam


title: Normal diet +5% mannose, biol rep 2

description:
Library name: ND1_Man5_2
NDM5_13_Aligned.sortedByCoord.out.bam

value: Normal Diet +5% mannose


title: Normal diet +5% mannose, biol rep 1

description:
Library name: ND1_Man5_1
NDM5_11_Aligned.sortedByCoord.out.bam


title: Normal diet +20% mannose, biol rep 1

description:
Library name: ND1_Man20_1
NDM20_11_Aligned.sortedByCoord.out.bam


title: CAFs cells, wt2

description: Library name: Sample 2

value: human CRC tissues

value: CAFs

value: colorectal cancer cells


title: Normal diet, biol rep 5

description:
Library name: ND1_5
ND_13_Aligned.sortedByCoord.out.bam

value: Liver

value: Normal Diet


title: Meningioma 466

type: genomic

city: Boston

first: Scott

middle: Thomas

last: Ryall

state: Massachusetts

address: 75 Francis Street

institute: Brigham and Women's Hospital

description: Hybridized to Agilent aCGH

hyb_protocol: As per manufacturer (Agilent)

scan_protocol: Scanned on an Agilent G2565AA scanner using Feature Extraction Software

data_processing:
As per manufacturer (Agilent)
[processed data definition] Normalized log10 ratio (Cy5/Cy3) (tumor/normal), i.e., the LogRatio column of the Agilent Feature Extraction files

molecule: genomic DNA

source_name: Brain Tumor  Tissue

label_protocol: As per manufacturer (Agilent)

growth_protocol: Not applicable

extract_protocol: DNA was extracted using the QIAamp DNA FFPE Tissue Kit and stored at 4˚C

treatment_protocol: Not applicable

value: Brain tumor

tag: Sex

value: F

tag: age

source_name: Normal Brain Tissue

value: Normal Brain


title: FAT-MASH diet +20% mannose therapy, biol rep 3

description:
Library name: MASH_Man20r_3_3
NASH3_M20rev_3_Aligned.sortedByCoord.out.bam

value: FAT-MASH regimen

value: 6 weeks

value: FAT-MASH Diet +20% mannose (Therapy)


title: HCC with  isotype (2)

value: Isotype


title: Normal diet, biol rep 4

description:
Library name: ND1_4
ND_11_Aligned.sortedByCoord.out.bam


title: Meningioma 467

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 465

description: Hybridized to Agilent aCGH


title: Meningioma 464

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +20% mannose therapy, biol rep 1

description:
Library name: MASH_Man20r_3_1
NASH3_M20rev_1_Aligned.sortedByCoord.out.bam


title: FAT-MASH diet +20% mannose therapy, biol rep 2

description:
Library name: MASH_Man20r_3_2
NASH3_M20rev_2_Aligned.sortedByCoord.out.bam


title: Meningioma 462

description: Hybridized to Agilent aCGH


title: Meningioma 463

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +5% mannose therapy, biol rep 2

description:
Library name: MASH_Man5r_3_2
NASH3_M5rev_2_Aligned.sortedByCoord.out.bam

value: FAT-MASH Diet +5% mannose (therapy)


title: FAT-MASH diet +5% mannose therapy, biol rep 1

description:
Library name: MASH_Man5r_3_1
NASH3_M5rev_1_Aligned.sortedByCoord.out.bam


title: Meningioma 460

description: Hybridized to Agilent aCGH


title: Meningioma 459

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +20% mannose, biol rep 3

description:
Library name: MASH_Man20_3_3
NASH3_M20_3_Aligned.sortedByCoord.out.bam

value: 12 weeks

value: FAT-MASH Diet +20% mannose


title: FAT-MASH diet +5% mannose therapy, biol rep 3

description:
Library name: MASH_Man5r_3_3
NASH3_M5rev_3_Aligned.sortedByCoord.out.bam


title: Meningioma 461

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +20% mannose, biol rep 1

description:
Library name: MASH_Man20_3_1
NASH3_M20_1_Aligned.sortedByCoord.out.bam


title: Meningioma 457

description: Hybridized to Agilent aCGH


title: Meningioma 458

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +20% mannose, biol rep 2

description:
Library name: MASH_Man20_3_2
NASH3_M20_2_Aligned.sortedByCoord.out.bam


title: Meningioma 456

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +5% mannose, biol rep 3

description:
Library name: MASH_Man5_3_3
NASH3_M5_3_Aligned.sortedByCoord.out.bam

value: FAT-MASH Diet +5% mannose


title: Meningioma 455

description: Hybridized to Agilent aCGH


title: Meningioma 454

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +5% mannose, biol rep 1

description:
Library name: MASH_Man5_3_1
NASH3_M5_1_Aligned.sortedByCoord.out.bam


title: FAT-MASH diet, biol rep 3

description:
Library name: MASH3_3
NASH3_3_Aligned.sortedByCoord.out.bam

value: FAT-MASH Diet


title: Meningioma 453

description: Hybridized to Agilent aCGH


title: FAT-MASH diet +5% mannose, biol rep 2

description:
Library name: MASH_Man5_3_2
NASH3_M5_2_Aligned.sortedByCoord.out.bam


title: Meningioma 451

description: Hybridized to Agilent aCGH


title: FAT-MASH diet, biol rep 1

description:
Library name: MASH3_1
NASH3_1_Aligned.sortedByCoord.out.bam


title: Meningioma 452

description: Hybridized to Agilent aCGH


title: Normal diet, biol rep 3

description:
Library name: ND3_3
ND3_3_Aligned.sortedByCoord.out.bam

value: Normal diet


title: Meningioma 450

description: Hybridized to Agilent aCGH


title: Meningioma 449

description: Hybridized to Agilent aCGH


title: FAT-MASH diet, biol rep 2

description:
Library name: MASH3_2
NASH3_2_Aligned.sortedByCoord.out.bam


title: Normal diet, biol rep 1

description:
Library name: ND3_1
ND3_1_Aligned.sortedByCoord.out.bam


title: Meningioma 447

description: Hybridized to Agilent aCGH


title: Normal diet, biol rep 2

description:
Library name: ND3_2
ND3_2_Aligned.sortedByCoord.out.bam


title: Meningioma 446

description: Hybridized to Agilent aCGH


title: Meningioma 448

description: Hybridized to Agilent aCGH


title: Dock7 motor neuron KO, 4m male, 4

city: Birmingham

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

institute: University of Alabama at Birmingham

description: Library name: vKO_4

data_processing:
Basecalls were performed using bcl2fastq
Raw sequence FASTQ files were trimmed with Trim Galore version 0.6.10 using parameters --paired --trim-n --nextseq 20
Trimmed sequence FASTQ files were aligned with STAR version 2.7.11a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from STAR aligned BAMs with HTSeq-count version 2.0.2 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm39 Release M32
Supplementary files format and content: tab-delimited text file containing Ensembl IDs with raw transcript abundances for each sample

source_name: Tibialis Anterior Muscle

growth_protocol: Standard mouse husbandry protocol, basic diet

extract_protocol:
Trizol isolation with Zymo purification
mRNA enrichment, Covaris RNA fragmentation, Library prep and QC, (all services provided by Novogene)

value: Tibialis Anterior Muscle

value: TA muscle

value: Dock7 fl/fl; vChAT-Cre

value: 4 months

value: male


title: Meningioma 443

description: Hybridized to Agilent aCGH

value: Brain tumor

value: F

value: Normal Brain


title: Dock7 motor neuron KO, 4m male, 1

description: Library name: vKO_1


title: Meningioma 445

description: Hybridized to Agilent aCGH


title: Dock7 muscle KO, 4m male, 3

description: Library name: mKO_3

value: Dock7 fl/fl; HSA-Cre


title: Dock7 muscle KO, 4m male, 4

description: Library name: mKO_4


title: Dock7 motor neuron KO, 4m male, 2

description: Library name: vKO_2


title: Meningioma 442

description: Hybridized to Agilent aCGH


title: Meningioma 444

description: Hybridized to Agilent aCGH


title: Meningioma 441

description: Hybridized to Agilent aCGH


title: Dock7 muscle KO, 4m male, 2

description: Library name: mKO_2


title: Meningioma 440

description: Hybridized to Agilent aCGH


title: Dock7 muscle KO, 4m male, 1

description: Library name: mKO_1


title: Dock7 null, 2m male, 4

description: Library name: gKO_4

value: Dock7 fl/fl; Sox2-Cre

value: 2 months


title: Meningioma 439

description: Hybridized to Agilent aCGH


title: Dock7 null, 2m male, 5

description: Library name: gKO_5


title: Meningioma 438

description: Hybridized to Agilent aCGH


title: Dock7 null, 2m female, 3

description: Library name: gKO_3

value: female


title: Meningioma 437

description: Hybridized to Agilent aCGH


title: Dock7 null, 2m female, 2

description: Library name: gKO_2


title: Meningioma 436

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 434

description: Hybridized to Agilent aCGH


title: Meningioma 435

description: Hybridized to Agilent aCGH


title: Dock7 control, 4m male, 5

description: Library name: flox_5

value: Dock7 fl/fl


title: Dock7 control, 4m male, 4

description: Library name: flox_4


title: Meningioma 433

description: Hybridized to Agilent aCGH


title: Meningioma 432

description: Hybridized to Agilent aCGH


title: Dock7 control, 4m male, 1

description: Library name: flox_1


title: Meningioma 430

description: Hybridized to Agilent aCGH


title: DMH3

city: Hangzhou, Zhejiang

first: xuefeng

last: Qu

address: Tianmushan Road 182th,

institute: Hangzhou Medical College

description: Library name: DMH3

data_processing:
llumina Casava1.7 software used for basecalling
Fastp used for filter out low-quality bases and remove adapters at the same time.
HISAT2 used for mapped to GRCm38 genome.
DESeq2 software for differential expression analysis of RNA sequencing data.
Assembly: GRCm38

source_name: liver tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was hanvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard lllumina protocols

value: liver tissue


title: Meningioma 431

description: Hybridized to Agilent aCGH


title: DMH2

description: Library name: DMH2


title: Meningioma 428

description: Hybridized to Agilent aCGH


title: Meningioma 429

description: Hybridized to Agilent aCGH


title: DMH1

description: Library name: DMH1


title: Meningioma 425

description: Hybridized to Agilent aCGH


title: Meningioma 427

description: Hybridized to Agilent aCGH


title: DM3

description: Library name: DM3


title: Meningioma 426

description: Hybridized to Agilent aCGH


title: Meningioma 424

description: Hybridized to Agilent aCGH


title: DM2

description: Library name: DM2


title: Dock7 motor neuron KO, 4m male, 3

description: Library name: vKO_3


title: Meningioma 423

description: Hybridized to Agilent aCGH


title: CTL4

description: Library name: CTL4


title: Meningioma 422

description: Hybridized to Agilent aCGH


title: DM1

description: Library name: DM1


title: Meningioma 421

description: Hybridized to Agilent aCGH


title: CTL3

description: Library name: CTL3


title: Meningioma 420

description: Hybridized to Agilent aCGH


title: CTL1

description: Library name: CTL1


title: CTL2

description: Library name: CTL2


title: Meningioma 419

description: Hybridized to Agilent aCGH


title: DM4

description: Library name: DM4


title: DMH4

description: Library name: DMH4


title: Meningioma 417

description: Hybridized to Agilent aCGH


title: Meningioma 418

description: Hybridized to Agilent aCGH


title: Retinoic acid-induced N2a cells , RSL3-3

city: jining

first: gao

last: xu

state: Shandong

address: 89 Guhuai Road

institute: Affiliated Hospital of Jining Medical University

description: Library name: RSL3-3

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with Hisat2 software.
The transcript abundances for each sample was estimated with StringTie (1.3.3).
Raw reads were normalized by calculated FPKM value using Ballgown (2.10.0).
Assembly: GRCm38
Supplementary files format and content: The csv format file contains theFPKM value of gene in every sample

source_name: N2a cells

growth_protocol: The cells were maintained in high glucose-DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin (100 units/mL)/streptomycin (100 μg/mL) at 37°C in a humidified 5% CO2-containing atmosphere.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). rRNA were removed using NEBNext® Poly(A) mRNA Magnetic Isolation Module. RNA libraries were constructed using KAPA Stranded RNA-Seq Library Prep Kit and following standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification.

treatment_protocol: N2a cells were cultured in six-well plates for 24 hours. DMEM+2% FBS and 10 μM retinoic acid induced differentiation. The culture medium was changed every day for 96 hours. Retinoic acid-treated, and control cells were imaged every day. Cells with axon length at least twice the diameter of the cell body were considered differentiated cells. Moreover, 5 μM RSL3  was used for 24 hours to establish ferroptosis in the RA-induced neuronal cells, and the same DMSO concentration was maintained in control cells.

value: N2a cells

value: Neuron


title: Retinoic acid-induced N2a cells , RSL3-2

description: Library name: RSL3-2


title: Meningioma 416

description: Hybridized to Agilent aCGH


title: Retinoic acid-induced N2a cells , RSL3-1

description: Library name: RSL3-1


title: Retinoic acid-induced N2a cells , DMSO-3

description: Library name: DMSO-3

value: DMSO


title: Meningioma 415

description: Hybridized to Agilent aCGH


title: Meningioma 413

description: Hybridized to Agilent aCGH


title: Retinoic acid-induced N2a cells , DMSO-2

description: Library name: DMSO-2


title: Retinoic acid-induced N2a cells , DMSO-1

description: Library name: DMSO-1


title: Meningioma 412

description: Hybridized to Agilent aCGH


title: Meningioma 414

description: Hybridized to Agilent aCGH


title: Co-cultured Tcell-Res_ctrl-3

city: Dallas

first: Maria

middle: A

last: Freitas-Cortez

state: Texas

address: 6000 Harry Hines Blvd

institute: UT Southwestern

description:
Library name: Tcell-NT-cell-3
ATAC-seq analysis of T cells co-cultured PD-1-resistant lung adenocarcinoma (control, replicate 3)

library_source: genomic

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore! (version 0.6.5) and cutadapt (version 2.8).
The reads were then mapped to the mouse genome (mm10) using Bowtie (version 1.1.2) with the following parameters: "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. After the removal of fragments from chrM, for each fragment, the 5’ end was offset by +4 bp and the 3’ end was offset by -5 bp to adjust both ends to represent the center of a transposon binding event.
For each sample, peaks were identified using MACS2 (version 2.2.7.1) without using any control. Each binding event (i.e., the 5’ or 3’ end of a fragment) was smoothed by 73 bp (i.e., extended 36 bp upstream and 36 bp downstream from the event center). MACS2 was configured to call peaks from the pile-up of smoothed binding events, and a q-value cutoff of  0.05 was applied.
The peaks that overlapped with ENCODE blacklisted regions were removed.
Assembly: mm10
Supplementary files format and content: PeakID: ID of the peak Chr: chromosome Start: start position (0-based) End: end position (1-based) Summit: summit of the peak Pvalue: -10*log10(pvalue) of the peak Qvalue: -10*log10(qvalue) of the peak Pileup: height of pileup of fragments over peak summit Fold: fold change to background

source_name: spleen

growth_protocol: Viable cells were quantified with a hemocytometer with a 0.4% Trypan blue solution, and subsequently diluted to a density of 300,000 cells per well in 6-well plates. Res-ctrl or Res-shFabp7 cells were seeded in the upper inserts (24.5-mm Transwell with 0.4-µm pore polycarbonate membrane inserts, Fisher Scientific), whereas CD8+ T cells were placed in the lower chamber of the transwell system. CD8+ T cells were isolated from splenocytes before seeding by using the Dynabeads Untouched Mouse CD8 Cells Kit (Thermo Fisher Scientific–Life Technologies, Catalog #11417D). The cells were then activated with Ultra-LEAF Purified anti-mouse CD3ε Antibody (5 μg/mL) (Biolegend, Catalog # 100301) and LEAF purified anti-mouse CD28 antibody (1 μg/mL) (Biolegend, Catalog # 102101). Cells were cultured in complete medium (RPMI-1640 supplemented with 100 units/mL penicillin, 100 μg/mL streptomycin, and 10% heat-inactivated fetal bovine serum), and incubated at 37°C in a 5% CO2 for 24 or 48 hours.

extract_protocol:
Genomic DNA was isolated using Dneasy (Qiagen) protocol. DNA was further used for the constructions of sequencing libraries
ATAC-Seq libraries were prepared from T cells cocultured with Res-ctrl or Res-shFabp7 for 48 hours at the MD Anderson Epigenomics Profiling Core Facility. The ATAC-Seq libraries were sequenced by using a 2´76 base paired-end protocol on an Illumina NovaSeq 6000 instrument at the MD Anderson Advanced Technology Genomics Core. In total, six ATAC-Seq libraries (three biological replicates per condition) were sequenced, generating 35-75 million pairs of reads per sample. Each pair of reads represents a DNA fragment from the library

value: spleen

value: T cells


title: Meningioma 410

description: Hybridized to Agilent aCGH


title: Meningioma 411

description: Hybridized to Agilent aCGH


title: Co-cultured Tcell-Res_shFabp7-2

description:
Library name: Tcell-Fab1-2
ATAC-seq analysis of T cells co-cultured PD-1-resistant lung adenocarcinoma with shFabp7 knockdown (replicate 2)


title: Co-cultured Tcell-Res_ctrl-1

description:
Library name: Tcell-NT-cell-1
ATAC-seq analysis of T cells co-cultured PD-1-resistant lung adenocarcinoma (control, replicate 1)


title: Co-cultured Tcell-Res_shFabp7-3

description:
Library name: Tcell-Fab1-3
ATAC-seq analysis of T cells co-cultured PD-1-resistant lung adenocarcinoma with shFabp7 knockdown (replicate 3)


title: Meningioma 408

description: Hybridized to Agilent aCGH


title: Meningioma 409

description: Hybridized to Agilent aCGH


title: Res_Ctrl-Input

description:
Library name: NTCtrl-Input
ChIP-seq input for PD-1-resistant lung adenocarcinoma cells (control)

data_processing:
The reads were mapped to the mouse genome (mm10) using Bowtie (version 1.1.2) with the following parameters: "-v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple reads mapped to the same genomic position was retained for further analysis.
For each ChIP-Seq sample, peaks were identified using MACS (version 1.4.2) by comparing against the corresponding input sample. A window size of 500 bp was used, and a p-value cutoff of 1e-5 was applied.
The peaks that overlapped with ENCODE blacklisted regions were removed.
Assembly: mm10
Supplementary files format and content: PeakID: ID of the peak Chr: chromosome Start: start position (0-based) End: end position (1-based) Summit: summit of the peak PVALUE: -10*log10(pvalue) of the peak NumTags: number tags in the peak Fold: fold change to input

source_name: Lung adenocarcinoma

growth_protocol: Cells were cultured in complete medium (RPMI-1640 supplemented with 100 units/mL penicillin, 100 μg/mL streptomycin, and 10% heat-inactivated fetal bovine serum) and incubated at 37°C in 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and sonicated for futher processing.
Samples from Sen, Res, Res-ctrl and Res-shFabp7 cells were processed for H3K27ac and H3K9ac ChIP and ChIP-Seq libraries were prepared at the MD Anderson Epigenomics Profiling Core Facility. The ChIP-Seq libraries, along with the corresponding input libraries, were sequenced by using a 50-base single-read protocol on an Illumina NovaSeq 6000 instrument at the MD Anderson Advanced Technology Genomics Core. In total, 24 ChIP-Seq libraries (three biological replicates per histone mark and condition), as well as the corresponding input libraries, were sequenced, generating 53-158 million reads per sample.

value: Lung adenocarcinoma

value: Resistant

value: Control

tag: chip antibody


title: Meningioma 406

description: Hybridized to Agilent aCGH

value: Brain tumor

value: F


title: Res_Ctrl_2-H3K9ac

description:
Library name: NTCtrl_2-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells (control)


title: Res_Ctrl_3-H3K27ac

description:
Library name: NTCtrl_3-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells (control)


title: Meningioma 403

description: Hybridized to Agilent aCGH

value: Normal Brain


title: Res_Ctrl_2-H3K27ac

description:
Library name: NTCtrl_2-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells (control)


title: Res_Ctrl_1-H3K9ac

description:
Library name: NTCtrl_1-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells (control)


title: Meningioma 407

description: Hybridized to Agilent aCGH


title: Meningioma 404

description: Hybridized to Agilent aCGH


title: Meningioma 402

description: Hybridized to Agilent aCGH


title: Co-cultured Tcell-Res_ctrl-2

description:
Library name: Tcell-NT-cell-2
ATAC-seq analysis of T cells co-cultured PD-1-resistant lung adenocarcinoma (control, replicate 2)


title: Res_Ctrl_1-H3K27ac

description:
Library name: NTCtrl_1-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells (control)


title: Meningioma 401

description: Hybridized to Agilent aCGH


title: Meningioma 400

description: Hybridized to Agilent aCGH


title: Res_shFabp7-Input

description:
Library name: Feb_1-Input
ChIP-seq input for PD-1-resistant lung adenocarcinoma cells with shFabp7 knockdown

value: shFabp7 knockdown


title: Res_shFabp7_3-H3K9ac

description:
Library name: Feb_1_3-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells with shFabp7 knockdown


title: Meningioma 398

description: Hybridized to Agilent aCGH


title: Res_shFabp7_3-H3K27ac

description:
Library name: Feb_1_3-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells with shFabp7 knockdown


title: Dock7 control, 4m male, 3

description: Library name: flox_3

value: Tibialis Anterior Muscle

value: TA muscle

value: 4 months

value: male


title: Meningioma 397

description: Hybridized to Agilent aCGH


title: Res_shFabp7_2-H3K9ac

description:
Library name: Feb_1_2-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells with shFabp7 knockdown


title: Meningioma 396

description: Hybridized to Agilent aCGH


title: Co-cultured Tcell-Res_shFabp7-1

description:
Library name: Tcell-Fab1-1
ATAC-seq analysis of T cells co-cultured PD-1-resistant lung adenocarcinoma with shFabp7 knockdown (replicate 1)


title: Meningioma 395

description: Hybridized to Agilent aCGH


title: Meningioma 394

description: Hybridized to Agilent aCGH


title: Res_shFabp7_2-H3K27ac

description:
Library name: Feb_1_2-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells with shFabp7 knockdown


title: Meningioma 405

description: Hybridized to Agilent aCGH


title: Res_shFabp7_1-H3K9ac

description:
Library name: Feb_1_1-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells with shFabp7 knockdown


title: Res_shFabp7_1-H3K27ac

description:
Library name: Feb_1_1-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells with shFabp7 knockdown


title: Meningioma 393

description: Hybridized to Agilent aCGH

value: M


title: Res_Ctrl_3-H3K9ac

description:
Library name: NTCtrl_3-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells (control)


title: Res-Input

description:
Library name: 344_SQR-Input
ChIP-seq input for PD-1-resistant lung adenocarcinoma cells

value: Wild-type


title: Meningioma 392

description: Hybridized to Agilent aCGH


title: Res_3-H3K9ac

description:
Library name: 344_SQR_3-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells treated with PD-1 inhibitors


title: Res_3-H3K27ac

description:
Library name: 344_SQR_3-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells treated with PD-1 inhibitors


title: Meningioma 391

description: Hybridized to Agilent aCGH


title: Meningioma 389

description: Hybridized to Agilent aCGH


title: Res_2-H3K9ac

description:
Library name: 344_SQR_2-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells treated with PD-1 inhibitors


title: Meningioma 399

description: Hybridized to Agilent aCGH


title: Meningioma 390

description: Hybridized to Agilent aCGH


title: Res_2-H3K27ac

description:
Library name: 344_SQR_2-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells treated with PD-1 inhibitors


title: Meningioma 388

description: Hybridized to Agilent aCGH


title: Res_1-H3K9ac

description:
Library name: 344_SQR_1-H3K9ac
ChIP-seq for H3K9ac in PD-1-resistant lung adenocarcinoma cells treated with PD-1 inhibitors


title: Meningioma 387

description: Hybridized to Agilent aCGH


title: Meningioma 385

description: Hybridized to Agilent aCGH


title: Meningioma 386

description: Hybridized to Agilent aCGH


title: Meningioma 383

description: Hybridized to Agilent aCGH


title: Sen_3-H3K9ac

description:
Library name: 344_SQP_3-H3K9ac
ChIP-seq for H3K9ac in PD-1-sensitive lung adenocarcinoma cells

value: Sensitive


title: Meningioma 384

description: Hybridized to Agilent aCGH


title: Sen-Input

description:
Library name: 344_SQP-Input
ChIP-seq input for PD-1-sensitive lung adenocarcinoma cells


title: Sen_1-H3K9ac

description:
Library name: 344_SQP_1-H3K9ac
ChIP-seq for H3K9ac in PD-1-sensitive lung adenocarcinoma cells


title: Sen_2-H3K9ac

description:
Library name: 344_SQP_2-H3K9ac
ChIP-seq for H3K9ac in PD-1-sensitive lung adenocarcinoma cells


title: Meningioma 382

description: Hybridized to Agilent aCGH


title: Sen_3-H3K27ac

description:
Library name: 344_SQP_3-H3K27ac
ChIP-seq for H3K27ac in PD-1-sensitive lung adenocarcinoma cells


title: Meningioma 381

description: Hybridized to Agilent aCGH


title: Meningioma 380

description: Hybridized to Agilent aCGH


title: Sen_2-H3K27ac

description:
Library name: 344_SQP_2-H3K27ac
ChIP-seq for H3K27ac in PD-1-sensitive lung adenocarcinoma cells


title: T cell: Res_shFabp7_3- 48H

city: Houston

first: Qi

last: Wang

state: TX

address: 7007 Bertner Ave

institute: UT MD Anderson Cancer Center

description:
Library name: Sample_21-T21
T cells co-cultured with Res_shFabp7, 48 hours, replicate 3

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to GRCm39 genome using tophat v2.0.13
Assembly: GRCm39
Supplementary files format and content: RNA-seq/miRNAseq reads count were calculated using HTSeq 0.6.1p1

extract_protocol:
Total RNA was isolated from cells  with Triazol (Life Technologies) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared at the Advanced Technology Genomics Core at MD Anderson Cancer Center.

value: T cell

value: shFabp7 48H


title: Meningioma 379

description: Hybridized to Agilent aCGH


title: T cell: Res_shFabp7_2- 48H

description:
Library name: Sample_20-T20
T cells co-cultured with Res_shFabp7, 48 hours, replicate 2

value: spleen


title: T cell: Res_shFabp7_1- 48H

description:
Library name: Sample_19-T19
T cells co-cultured with Res_shFabp7, 48 hours, replicate 1


title: Meningioma 376

description: Hybridized to Agilent aCGH


title: Meningioma 378

description: Hybridized to Agilent aCGH


title: Res_1-H3K27ac

description:
Library name: 344_SQR_1-H3K27ac
ChIP-seq for H3K27ac in PD-1-resistant lung adenocarcinoma cells treated with PD-1 inhibitors

value: Lung adenocarcinoma


title: T cell: Res_ctrl_3 - 48H

description:
Library name: Sample_18-T18
T cells co-cultured with Res_ctrl, 48 hours, replicate 3

value: Control 48H


title: Meningioma 375

description: Hybridized to Agilent aCGH


title: Meningioma 374

description: Hybridized to Agilent aCGH


title: T cell: Res_ctrl_1 - 48H

description:
Library name: Sample_16-T16
T cells co-cultured with Res_ctrl, 48 hours, replicate 1


title: Meningioma 373

description: Hybridized to Agilent aCGH


title: T cell: Res_shFabp7_2- 24H

description:
Library name: Sample_5-T5
T cells co-cultured with Res_shFabp7, 24 hours, replicate 2

value: shFabp7 24H


title: Meningioma 372

description: Hybridized to Agilent aCGH

value: Brain tumor


title: Meningioma 371

description: Hybridized to Agilent aCGH

value: F


title: T cell: Res_ctrl_2 - 48H

description:
Library name: Sample_17-T17
T cells co-cultured with Res_ctrl, 48 hours, replicate 2


title: Sen_1-H3K27ac

description:
Library name: 344_SQP_1-H3K27ac
ChIP-seq for H3K27ac in PD-1-sensitive lung adenocarcinoma cells


title: Meningioma 370

description: Hybridized to Agilent aCGH

value: Normal Brain


title: T cell: Res_ctrl_3 - 24H

description:
Library name: Sample_3-T3
T cells co-cultured with Res_ctrl, 24 hours, replicate 3

value: Control 24H


title: T cell: Res_ctrl_2 - 24H

description:
Library name: Sample_2-T2
T cells co-cultured with Res_ctrl, 24 hours, replicate 2


title: Meningioma 369

description: Hybridized to Agilent aCGH


title: Meningioma 368

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Saline, 969

city: Columbia

first: Jacob

middle: Jeffrey

last: Russell

state: MO

address: 1401 Ashland Rd, Apartment E

department: Biomedical Sciences

institute: University of Missouri

description: Library name: 969

data_processing:
A cDNA library constructed by technology from the pooled RNA from left ventricle samples of Mus Musculus was sequenced run with Illumina Novaseq TM 6000 sequence platform. Using the Illuminapaired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-endreads. Reads obtained from the sequencing machines includes raw reads containing adapters or lowqualitybaseswhich will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
Assembly: The trimmed sequences were aligned to the Mus_musculus_ensembl_v80_reference with gene track mus_musculis_ensembl_v86_Genes and mRNA track Mus_musculus_ensembl_v86_mRNA. Samples were aligned to the reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of thereads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch whenmappingthe reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparingthe previously unmapped reads against the database of putative junctions. The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomesfrom all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expressionlevels of all transcripts and perform expression abundance for mRNAs by calculating FPKM(fragment per kilobaseof transcript per million mapped reads) value.
Supplementary files format and content: Text file containing the FPKM for each gene for every sample

molecule: polyA RNA

source_name: Heart

extract_protocol:
Qiagen RNEasy Lipid Tissue Mini Kit (Cat # 74804)
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Heart

value: Left Ventricle

value: Female

value: Saline


title: T cell: Res_shFabp7_1- 24H

description:
Library name: Sample_4-T4
T cells co-cultured with Res_shFabp7, 24 hours, replicate 1


title: Heart, Female, WT, Saline, 968

description: Library name: 968


title: Meningioma 377

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 365

description: Hybridized to Agilent aCGH


title: Meningioma 364

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Ang II, 848

description: Library name: 848

value: Ang II


title: Heart, Male, Tg, Ang II, 847

description: Library name: 847

value: Male


title: T cell: Res_shFabp7_3- 24H

description:
Library name: Sample_6-T6
T cells co-cultured with Res_shFabp7, 24 hours, replicate 3

value: T cell


title: Meningioma 362

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Saline, 846

description: Library name: 846


title: Meningioma 360

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Ang II, 783

description: Library name: 783


title: Heart, Female, WT, Ang II, 779

description: Library name: 779


title: Meningioma 359

description: Hybridized to Agilent aCGH


title: Meningioma 358

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Ang II, 778

description: Library name: 778


title: Meningioma 357

description: Hybridized to Agilent aCGH


title: Meningioma 356

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Saline, 774

description: Library name: 774


title: Heart, Male, WT, Saline, 776

description: Library name: 776


title: T cell: Res_ctrl_1 - 24H

description:
Library name: Sample_1-T1
T cells co-cultured with Res_ctrl, 24 hours, replicate 1


title: Meningioma 366

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Ang II, 722

description: Library name: 722


title: Meningioma 367

description: Hybridized to Agilent aCGH


title: Meningioma 355

description: Hybridized to Agilent aCGH


title: Meningioma 354

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Ang II, 721

description: Library name: 721


title: Meningioma 353

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Saline, 719

description: Library name: 719


title: Meningioma 363

description: Hybridized to Agilent aCGH


title: Meningioma 352

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Saline, 718

description: Library name: 718


title: Heart, Male, Tg, Saline, 965

description: Library name: 965


title: Meningioma 351

description: Hybridized to Agilent aCGH


title: Meningioma 361

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Ang II, 717

description: Library name: 717


title: Meningioma 350

description: Hybridized to Agilent aCGH


title: Meningioma 349

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Saline, 716

description: Library name: 716


title: Meningioma 348

description: Hybridized to Agilent aCGH


title: Heart, Male, Tg, Ang II, 715

description: Library name: 715


title: Heart, Male, Tg, Ang II, 530

description: Library name: 530


title: Meningioma 345

description: Hybridized to Agilent aCGH


title: Meningioma 344

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Saline, 488

description: Library name: 488


title: Meningioma 343

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Ang II, 720

description: Library name: 720


title: Heart, Female, Tg, Ang II, 489

description: Library name: 489


title: Heart, Male, Tg, Saline, 487

description: Library name: 487


title: Meningioma 342

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Ang II, 331

description: Library name: 331


title: Heart, Female, Tg, Saline, 333

description: Library name: 333


title: Meningioma 340

description: Hybridized to Agilent aCGH


title: Meningioma 341

description: Hybridized to Agilent aCGH


title: Meningioma 339

description: Hybridized to Agilent aCGH


title: Meningioma 338

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Ang II, 328

description: Library name: 328


title: Heart, Male, Tg, Saline, 327

description: Library name: 327


title: Heart, Male, WT, Ang II, 329

description: Library name: 329


title: Heart, Male, Tg, Ang II, 326

description: Library name: 326


title: Meningioma 336

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Ang II, 299

description: Library name: 299


title: Meningioma 335

description: Hybridized to Agilent aCGH


title: Heart, Male, Tg, Ang II, 297

description: Library name: 297


title: Meningioma 347

description: Hybridized to Agilent aCGH


title: Heart, Male, Tg, Saline, 528

description: Library name: 528


title: Heart, Male, WT, Ang II, 296

description: Library name: 296


title: Meningioma 346

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Saline, 332

description: Library name: 332


title: Heart, Female, WT, Saline, 239

description: Library name: 239


title: Meningioma 332

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Saline, 237

description: Library name: 237


title: Meningioma 331

description: Hybridized to Agilent aCGH


title: Meningioma 330

description: Hybridized to Agilent aCGH


title: Heart, Male, Tg, Ang II, 295

description: Library name: 295


title: Meningioma 329

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Ang II, 238

description: Library name: 238


title: Meningioma 337

description: Hybridized to Agilent aCGH


title: Meningioma 325

description: Hybridized to Agilent aCGH


title: Meningioma 327

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Ang II, 234

description: Library name: 234


title: Meningioma 328

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Saline, 162

description: Library name: 162


title: Heart, Male, WT, Saline, 232

description: Library name: 232


title: Heart, Female, WT, Ang II, 165

description: Library name: 165


title: Meningioma 326

description: Hybridized to Agilent aCGH


title: Meningioma 334

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Ang II, 163

description: Library name: 163


title: Meningioma 324

description: Hybridized to Agilent aCGH


title: Meningioma 323

description: Hybridized to Agilent aCGH


title: Meningioma 333

description: Hybridized to Agilent aCGH


title: Meningioma 321

description: Hybridized to Agilent aCGH


title: Meningioma 322

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Ang II, 159

description: Library name: 159


title: Heart, Male, Tg, Saline, 158

description: Library name: 158


title: Meningioma 320

description: Hybridized to Agilent aCGH


title: Heart, Male, WT, Saline, 157

description: Library name: 157


title: Meningioma 319

description: Hybridized to Agilent aCGH


title: Heart, Female, Tg, Ang II, 154

description: Library name: 154


title: Heart, Female, Tg, Saline, 153

description: Library name: 153


title: Meningioma 318

description: Hybridized to Agilent aCGH


title: Meningioma 317

description: Hybridized to Agilent aCGH


title: Meningioma 316

description: Hybridized to Agilent aCGH


title: Meningioma 315

description: Hybridized to Agilent aCGH


title: Meningioma 313

description: Hybridized to Agilent aCGH


title: D84

city: Nashville

first: Mark

last: de Caestecker

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

description:
Library name: D84
10X Genomics

data_processing:
Data was demultiplexed, barcoded and gene counted using the Cell Ranger software (Cell Ranger v7.1)
Assembly: mm10
Supplementary files format and content: rds files and comma-separated value files

source_name: kidney papilla

extract_protocol:
Samples were dissociated into single cells using the 10x Genomics Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit #1000414, according to the manufacturer's instructions. For this, frozen samples were placed on a chilled glass petri dish on ice macerated in fixation buffer contraining formaldehyde using a razor blade before transfering into a 2ml low protein binding centrifuge tube, titurated using a wide bore 1ml pipette, and fixed for 20 hrs at 16-24C. The fixation buffer was then quenched and the tissue pellet dissociated using dissociation solution containing 0.2mg/ml Liberase LT for 20 minutes at 37C, titurated vigorously using a 1ml pipette before straining, and storing in quenching buffer. Cell concentration and dispension was then determined using the Countess III FL Automated Cell Counter (VANTAGE core) and propidium iodide staining solution, Invitrogen #P3566.
Dissociated cells from each of the pooled samples were individually hybridized with bar coded genome-wide probe sets from 10X Genomics Flex kits according to the manufacturer’s instructions. After probe hybridization and construction of libraries, samples were sequenced using an Illumina Novoseq 6000 PE150 sequencer, and bar codes deconvoluted to provide individual sample datasets.

value: kidney papilla

value: kidney cell

value: BALB/c

value: 84 days after R-UUO

value: RUUO


title: HiChIP-CTCF_WT

city: Hershey

first: Suming

last: Huang

state: PA

address: 500 University Dr.

institute: Penn State College of Medicine

description: Library name: HiChIP-CTCF_WT

data_processing:
*library strategy: CTCF-HiChIP-seq
Raw sequencing reads were cleaned to remove adaptor sequence with cutadapt (Martin 2011) ver.1.18 and trimmed the end of enzymatic sequences with homerTools (homerTools trim -3 GATC -mis 0 -matchStart 20 -min 20) from Homer (Heinz, Benner et al. 2010) ver.4.10 (Heinz et al. 2010). Trimmed reads were aligned to mouse reference genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) ver.2.5.2 with parameters “--local --very-sensitive -p 20 -n 1”. Aligned sam files were used to make a tag directory by makeTagDirectory package from Homer (Heinz, Benner et al. 2010) with “-tbp 1” parameter to remove PCR duplicates. After filtering uninformative reads using makeTagDirectory package with different parameters “-genome mm10 -removePEbg -restrictionSite GATC -both -removeSelfLigation -removeSpikes 10000 5”, the filtered tag directory file was converted to .hic files using tagDir2hicFile.pl.
Assembly: mm10
Supplementary files format and content: .hic file output from tagDir2hicFile.pl (Homer)

growth_protocol: 961C were maintained in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin (Gough, Lee et al. 2014).

extract_protocol:
20M cells were cross-linked in 2% formaldehyde (BP531, Fisher Bioregents) at room temperature for 10 min and quenched by 125 mM glycine solution.
CTCF-HiChIP assay was performed according to the protocol from Nature Methods (Mumbach et al., 2016).


title: D28

description:
Library name: D28
10X Genomics

value: 28 days after R-UUO


title: Meningioma 311

description: Hybridized to Agilent aCGH

value: Brain tumor


title: control

description:
Library name: control
10X Genomics

value: healthy controls

value: control


title: L5_WT_LIB041648_22C7J2LT4

city: St. Louis

first: Mati

middle: Tesfaye

last: Nemera

state: Missouri

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St. Louis School of Medicine

description:
L5_WT_KO_deep_INTACT_mCA_mm9_backgroundSub.bw
L5_WT_KO_deep_INTACT_mCG_mm9_backgroundSub.bw

data_processing:
Reads were mapped to the mm9 genome using bowtie2 alignment and then deduplicated.
BS-seeker2 was used to call reads for methylation.
The methylation level for an element was assessed by dividing the total number of reads mapping to Cs that supported mC by the total coverage in that region, using bedtools map -o sum. The bisulfite nonconversion rate, estimated by Lambda DNA, was subtracted from this value to get a final corrected methylation level.
Assembly: mm9
Supplementary files format and content: bigWig, tsv

source_name: Cortex

extract_protocol:
DNA was extracted using the AllPrep DNA/RNA kit from Qiagen.
DNA was fragmented for 45 seconds using the Covaris E220 sonicator (10% Duty Factory, 175 Peak Incidence Power, 200 cycles per burst, milliTUBE 200µL AFA Fiber). The DNA was purified using 0.7 volumes of SPRISelect Beads (Beckman Coulter Life Sciences). To enable estimation of bisulfite non-conversion rates, a small amount of unmethylated lambda DNA was spiked in. The EZ DNA Methylation-Direct Kit (Zymo Research Corporation, D5020) was used to bisulfite convert DNA. Libraries were generated using the xGen™ Methyl-Seq Lib Prep Kit (IDT, 10009860) with combinatorial dual indexes as instructed.10-15 cycles of final amplification were used. Libraries were pooled and sequenced at the Genome Technology Access Center at the Washington University McDonnell Genome Institute on the NovaSeq 6000 2x150.

value: Cortex

tag: strain

value: WT


title: Heart, Male, Tg, Saline, 160

description: Library name: 160

value: Heart

value: Left Ventricle


title: Meningioma 309

description: Hybridized to Agilent aCGH

value: F

value: Normal Brain


title: Meningioma 310

description: Hybridized to Agilent aCGH


title: Heart, Female, WT, Ang II, 161

description: Library name: 161

value: Female

value: Ang II


title: L5_WT_LIB041645_22C7J2LT4

value: Male


title: L5_KO_LIB041647_22C7J2LT4

value: Mecp2 KO


title: Meningioma 308

description: Hybridized to Agilent aCGH


title: L5_KO_LIB041646_22C7J2LT4


title: Meningioma 306

description: Hybridized to Agilent aCGH


title: Meningioma 307

description: Hybridized to Agilent aCGH


title: L4_WT_LIB042981_227WGJLT4

description:
L4_WT_KO_deep_INTACT_mCA_mm9_backgroundSub.bw
L4_WT_KO_deep_INTACT_mCG_mm9_backgroundSub.bw


title: L4_WT_LIB041634_227WGJLT4


title: HiChIP-CTCF_KO

description: Library name: HiChIP-CTCF_KO

value: NUP98-PHF23 with HoxBlinc KO


title: L4_KO_LIB041633_227WGJLT4


title: L4_KO_LIB042982_227WGJLT4


title: Meningioma 304

description: Hybridized to Agilent aCGH


title: Meningioma 314

description: Hybridized to Agilent aCGH


title: Meningioma 303

description: Hybridized to Agilent aCGH


title: SST_WT_LIB045574_22CGWFLT4

description:
SST_WT_KO_deep_INTACT_mCA_mm9_backgroundSub.bw
SST_WT_KO_deep_INTACT_mCG_mm9_backgroundSub.bw

value: SST


title: Meningioma 312

description: Hybridized to Agilent aCGH


title: SST_WT_LIB042979_227WGJLT4


title: SST_KO_LIB045575_22CGWFLT4


title: Meningioma 302

description: Hybridized to Agilent aCGH

value: M


title: SST_WT_LIB042980_227WGJLT4


title: Meningioma 301

description: Hybridized to Agilent aCGH


title: Meningioma 300

description: Hybridized to Agilent aCGH


title: Meningioma 297

description: Hybridized to Agilent aCGH


title: Meningioma 296

description: Hybridized to Agilent aCGH


title: PV_WT_LIB041644_22C7J2LT4

description:
PV_WT_KO_deep_INTACT_mCA_mm9_backgroundSub.bw
PV_WT_KO_deep_INTACT_mCG_mm9_backgroundSub.bw

value: PV


title: Meningioma 298

description: Hybridized to Agilent aCGH

value: Brain tumor


title: PV_WT_LIB041642_22C7J2LT4


title: PV_KO_LIB041643_22C7J2LT4


title: Meningioma 299

description: Hybridized to Agilent aCGH


title: SST_KO_LIB042978_227WGJLT4


title: Meningioma 295

description: Hybridized to Agilent aCGH


title: PV_KO_LIB041641_22C7J2LT4


title: STR_KO_Gabel_1_506-2_STR_D701_D501ATTACTCGAT_AGGCTATA

source_name: Striatum

value: Striatum


title: Meningioma 294

description: Hybridized to Agilent aCGH


title: STR_KO_Gabel_16_598-2_STR_D702_D502_TCCGGAGAAT_GCCTCTAT


title: Meningioma 293

description: Hybridized to Agilent aCGH


title: STR_WT_Gabel_2_506-3_STR_D702_D502TCCGGAGAAT_GCCTCTAT


title: Meningioma 305

description: Hybridized to Agilent aCGH


title: Meningioma 292

description: Hybridized to Agilent aCGH


title: Meningioma 291

description: Hybridized to Agilent aCGH


title: Meningioma 290

description: Hybridized to Agilent aCGH


title: HYPO_KO_Gabel_18_598-2_HYPO_D704_D504_GAGATTCCAT_TCAGAGCC

source_name: Hypothalamus

value: Hypothalamus


title: HYPO_KO_Gabel_3_506-2_HYPO_D703_D503CGCTCATTAT_AGGATAGG


title: STR_WT_Gabel_15_598-1_STR_D701_D501_ATTACTCGAT_AGGCTATA


title: Meningioma 289

description: Hybridized to Agilent aCGH


title: HYPO_WT_Gabel_4_506-3_HYPO_D704_D504GAGATTCCAT_TCAGAGCC


title: Meningioma 288

description: Hybridized to Agilent aCGH


title: HYPO_WT_Gabel_17_598-1_HYPO_D703_D503_CGCTCATTAT_AGGATAGG


title: Meningioma 287

description: Hybridized to Agilent aCGH


title: CB_KO_Gabel_5_506-2_CB_D705_D505ATTCAGAAAT_CTTCGCCT

source_name: Cerebellum

value: Cerebellum


title: Meningioma 286

description: Hybridized to Agilent aCGH


title: CB_KO_Gabel_20_598-2_CB_D706_D506_GAATTCGTAT_TAAGATTA


title: Meningioma 285

description: Hybridized to Agilent aCGH


title: CB_WT_Gabel_6_506-3_CB_D706_D506GAATTCGTAT_TAAGATTA

value: WT


title: Meningioma 283

description: Hybridized to Agilent aCGH


title: Meningioma 284

description: Hybridized to Agilent aCGH


title: Kidney, GLY, rep1

city: Wuhan

first: Chen

last: Duan

address: Donghu Road 169

institute: Zhongnan hospital of Wuhan University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: kidney

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: kidney

value: 6 to 8 weeks

value: GLY


title: CB_WT_Gabel_19_598-1_CB_D705_D505_ATTCAGAAAT_CTTCGCCT


title: Meningioma 282

description: Hybridized to Agilent aCGH

value: F

value: Normal Brain


title: RNA_A1929_HoxBlinc_KO3

data_processing:
Adaptor sequences were trimed by cutadaptSequenced reads were trimmed and quality filtered using cutadapt (Martin 2011) version 1.18 and aligned to human (hg19) or mouse genome (mm10) using HISAT2 (Kim, Paggi et al. 2019) version 2.2.1. The read counts were calculated by featureCounts (Liao, Smyth et al. 2014) ver.2.0.3. Normalized counts, fold change and p-value between cell condition were generated by DEseq2 (Love, Huber et al. 2014) ver.1.40.2.
Assembly: mm10 or hg19
Supplementary files format and content: Tabular file of raw counts (output from featureCounts) and/or .bigwig file

growth_protocol: BaF3 cells were cultured in in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin. 961C were maintained in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin (Gough, Lee et al. 2014). A1929 cells were maintained RPMI supplemented with 10% FBS, 50uM 2-ME and 10ng/ml mouse recombinant IL-7(Yin, Chung et al. 2018). Patient samples were maintained in StemSpan™ SFEM II supplemented with StemSpan™ CD34+ Expansion Supplement (10X) and 10ng/ml of Human Recombinant GM-CSF, ACF.

extract_protocol:
RNA is extracted using Quick-RNA miniprep kit (ZYMO research) according to manufacturer’s protocol.
1ug of RNA which have high RIN value (more than 8) were used as input for RNA-seq library preparation. We used NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) for enrichment mRNA and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) for library preparation according to manufacturer’s protocol.


title: Kidney, NC, rep1

value: NC


title: Meningioma 279

description: Hybridized to Agilent aCGH


title: Meningioma 280

description: Hybridized to Agilent aCGH


title: Meningioma 278

description: Hybridized to Agilent aCGH


title: RNA_A1929_HoxBlinc_KO2


title: RNA_A1929_HoxBlinc_KO1


title: Meningioma 281

description: Hybridized to Agilent aCGH


title: RNA_A1929_WT2


title: Meningioma 277

description: Hybridized to Agilent aCGH


title: Meningioma 275

description: Hybridized to Agilent aCGH


title: Meningioma 274

description: Hybridized to Agilent aCGH


title: RNA_A1929_WT1


title: RNA_961C_HoxBlinc_KO3


title: RNA_961C_HoxBlinc_KO4


title: Meningioma 276

description: Hybridized to Agilent aCGH


title: RNA_961C_HoxBlinc_KO2


title: Meningioma 273

description: Hybridized to Agilent aCGH


title: Meningioma 272

description: Hybridized to Agilent aCGH


title: RNA_961C-3


title: RNA_961C_HoxBlinc_KO1


title: RNA_961C-2


title: Meningioma 271

description: Hybridized to Agilent aCGH


title: Meningioma 270

description: Hybridized to Agilent aCGH


title: RNA_961C-1


title: Meningioma 268

description: Hybridized to Agilent aCGH


title: RNA_BaF3-2

value: pro-B cell


title: RNA_BaF3-1


title: Meningioma 269

description: Hybridized to Agilent aCGH


title: ChIRP_961C_HoxBlinc

data_processing:
Raw sequencing reads were cleaned to remove adaptor sequence with cutadapt (Martin 2011) ver.1.18. Trimmed reads were aligned to mouse reference genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) ver.2.5.2 with parameters “--local --very-sensitive -p 20 -n 1”. Alignment sam files were converted to bam file using samtools (Li et al., 2009). Bam files were sorted and filtered to keep only unique reads using sambamba (Tarasov, Vilella et al. 2015) ver.0.6.9. Peak calling was performed using MACS2 (Zhang, Liu et al. 2008) ver.2.2.6.
Assembly: mm10
Supplementary files format and content: .bigwig file and/or narrowPeak file from MACS2 callpeak
Library strategy: ChIRP-seq

growth_protocol: BaF3 cells were cultured in in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin. 961C were maintained in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin (Gough, Lee et al. 2014).

extract_protocol:
The cells were cross-linked in PBS with 1% formaldehyde for 10min at room temperature with rotating and quenched by 125mM glycine for 5min. After washing cell pellet by ice-chilled PBS, the pellet was lysed in 1ml of lysis buffer (50 mM Tris-HCl pH 7.0, 10 mM EDTA, 1% SDS, add PMSF, PIC and Superase-in in fresh) per 100mg of cell pellet. Chromatin was fragmented by sonication with Bioruptor UCD200 (Diagenode) and cleared by centrifuge (16100G, 15min, 4C). Cleared chromatin was diluted in 2X volume of freshly-made hybridization buffer (750 mM NaCl, 1% SDS, 50 mM Tris-HCl pH 7.0, 1 mM EDTA, 15% formamide, DTT, PMSF, P.I, and Superase-in) and hybridized with 100pmol of biotinylated DNA probes targeting HoxBlinc or LacZ at 37C overnight. DNA/RNA hybrids were precipitated using 100μL of Streptavidin-magnetic C1 beads (Invitrogen) and washed 5 times with washing buffer (2x SSC, 0.5% SDS). DNA was isolated using ZYMO ChIP DNA concentrator kit (D4014).
ChIRP-seq library was prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).


title: Meningioma 267

description: Hybridized to Agilent aCGH


title: ChIRP_961C_HoxBlinc_KO_HoxBlinc


title: ChIRP_961C_LaCZ


title: Meningioma 265

description: Hybridized to Agilent aCGH


title: ChIRP_BaF3_HoxBlinc


title: ChIRP_961C_HoxBlinc_KO_LaCZ


title: Meningioma 264

description: Hybridized to Agilent aCGH


title: Meningioma 262

description: Hybridized to Agilent aCGH


title: Meningioma 263

description: Hybridized to Agilent aCGH


title: CnR_961C_IgG_2

description: pair with HoxBlinc KO

data_processing:
Raw sequencing reads were cleaned to remove adaptor sequence with cutadapt (Martin 2011) ver.1.18. Trimmed reads were aligned to mouse reference genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) ver.2.5.2 with parameters “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”. Alignment sam files were filtered with picard MarkDuplicates and converted to bam file using samtools (Li et al., 2009). Bam files were converted to .bigwig file using deepTools bamCoverage.
Assembly: mm10
Supplementary files format and content: .bigwig file
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN assay were performed with CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, Cat#14-1048)
ChIP-seq library was prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).


title: ChIRP_BaF3_LaCZ


title: Meningioma 260

description: Hybridized to Agilent aCGH


title: CnR_961C_HoxBlinc_KO_IgG


title: Meningioma 261

description: Hybridized to Agilent aCGH


title: Meningioma 259

description: Hybridized to Agilent aCGH


title: CnR_961C_IgG

description: pair with BaF3


title: Meningioma 257

description: Hybridized to Agilent aCGH


title: CnR_BaF3_IgG


title: Meningioma 256

description: Hybridized to Agilent aCGH


title: Meningioma 258

description: Hybridized to Agilent aCGH


title: CnR_961C_H3K4me3_2

description: pair with HoxBlinc KO


title: CnR_961C_HoxBlinc_KO_H3K4me3


title: Meningioma 255

description: Hybridized to Agilent aCGH


title: Meningioma 266

description: Hybridized to Agilent aCGH


title: CnR_961C_H3K4me3

description: pair with BaF3


title: Meningioma 254

description: Hybridized to Agilent aCGH


title: Meningioma 253

description: Hybridized to Agilent aCGH


title: scRNA_HoxBlincTg_LK

description: 10X Genomics

data_processing:
Pooled samples were demultiplexed with cellranger mkfastq program (10x genomics), and demultiplexed FASTQ files were then performed the alignment with reference mm10 genome, filtering, barcode counting, and unique molecular identifier (UMI) counting with cellranger count under the default parameters (10x genomics). QC filtering was performed, and low complexity cell barcodes with number of genes detected were filtered out using the following parameters: percentage of reads mapping to the mitochondrial chromosome< 10%; UMI counts per cell > 500; and number of detected genes per cell (normalized counts >= 1) > 250.
Assembly: mm10
Supplementary files format and content: Barcodes.tsv, genes.tsv.gz, matrix.mtx

source_name: Bone marrow cell

extract_protocol:
Total bone marrow cells were isolate from WT and HoxBlinc-Tg mice, and sorted with Lin-, and Kit+ markers. Sorted LK cells were immediately processed for single cell RNA-seq.
Single cells were generated using Chromium Controller (10x Genomics), and scRNA-seq libraries were constructed using chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to the manufacturer’s recommendations.

value: Bone marrow cell

value: Lin- Kit+

value: HoxBlinc transgenic


title: CnR_BaF3_H3K4me3


title: scRNA_WT_LK

description: 10X Genomics


title: Meningioma 251

description: Hybridized to Agilent aCGH


title: Meningioma 250

description: Hybridized to Agilent aCGH


title: Meningioma 248

description: Hybridized to Agilent aCGH


title: HiC_WT

data_processing:
Raw sequencing reads were cleaned to remove adaptor sequence with cutadapt (Martin 2011) ver.1.18 and trimmed the end of enzymatic sequences with homerTools (homerTools trim -3 GATC -mis 0 -matchStart 20 -min 20) from Homer (Heinz, Benner et al. 2010) ver.4.10 (Heinz et al. 2010). Trimmed reads were aligned to mouse reference genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) ver.2.5.2 with parameters “--local --very-sensitive -p 20 -n 1”. Aligned sam files were used to make a tag directory by makeTagDirectory package from Homer (Heinz, Benner et al. 2010) with “-tbp 1” parameter to remove PCR duplicates. After filtering uninformative reads using makeTagDirectory package with different parameters “-genome mm10 -removePEbg -restrictionSite GATC -both -removeSelfLigation -removeSpikes 10000 5”, the filtered tag directory file was converted to .hic files using tagDir2hicFile.pl.
Assembly: mm10
Supplementary files format and content: .hic file output from tagDir2hicFile.pl (Homer)

source_name: Bone marrow cells

growth_protocol: BaF3 cells were cultured in in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin. 961C were maintained in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin (Gough, Lee et al. 2014). Total Bone marrow cells were isolated form HoxBlinc transgenic mice and parental mice control.

extract_protocol:
10M cells were cross-linked in 1 % formaldehyde (BP531, Fisher Bioregents) at room temperature for 10 min and quenched by 125 mM glycine solution. To estimate input number of crosslinked cells, DNA extraction was performed from 1M crosslinked cells and determined concentration by Qubit. 2M crosslinked cells were equivalent to 3ug of DNA and used as input.
Hi-C assay was performed with Arima-HiC+ Kit (A410030, Arima Genomics) according with manufacture protocol.

value: Bone marrow cells

value: Parental mice


title: HiC_961C_HoxBlinc_KO

value: NUP98-PHF23 with HoxBlinc KO


title: Meningioma 249

description: Hybridized to Agilent aCGH

data_processing:
As per manufacturer (Agilent)
[processed data definition] Normalized log10 ratio (Cy5/Cy3) (tumor/normal), i.e., the LogRatio column of the Agilent Feature Extraction files

extract_protocol: DNA was extracted using the QIAamp DNA FFPE Tissue Kit and stored at 4˚C

value: Brain tumor


title: HiC_HoxBlincTg_BALL

value: B-ALL

value: HoxBling transgenic mice


title: Meningioma 247

description: Hybridized to Agilent aCGH

value: M


title: HiC_961C


title: Meningioma 246

description: Hybridized to Agilent aCGH


title: ChIP_961C_IgG

description: Normal Rabbit IgG antibody, Cell Signaling Technology, Cat# 2729

data_processing:
Raw sequencing reads were cleaned to remove adaptor sequence with cutadapt (Martin 2011) ver.1.18. Trimmed reads were aligned to mouse reference genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) ver.2.5.2 with parameters “--local --very-sensitive -p 20 -n 1”. Alignment sam files were converted to bam file using samtools (Li et al., 2009). Bam files were sorted and filtered to keep only unique reads using sambamba (Tarasov, Vilella et al. 2015) ver.0.6.9. Filtered bam files were converted to .bigwig using deepTools bamCoverage.
Assembly: mm10
Supplementary files format and content: .bigwig file

extract_protocol:
10M cells were collected by centrifugation and then washed by 1×PBS. Washed cells were cross-linked by 1% formaldehyde and quenched by 125mM glycine. Crosslinked cell pellet was resuspended by ChIP lysis buffer and subjected to chromatin shearing using Bioruptor (Diagenode) with 30s on and 30s off condition. Sonicated chromatin was incubated with anti-CTCF, anti-V5, anti-H3K4me3 or anti-MLL1 antibody at 4C overnight. Prewashed Dynabeads™ Protein A or G beads (Invitrogen) were added to antibody-bounded chromatin and incubated for 4h at 4C. Antibody/Protein beads bounded chromatin were washed 5 times and reverse-crosslinked. ChIP DNA Clean & Concentrator™ (ZYMO research) was used for DNA purification.
ChIP-seq library was prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).


title: HiC_BaF3


title: ChIP_961C_HoxBlinc_KO_IgG


title: Meningioma 245

description: Hybridized to Agilent aCGH


title: Meningioma 244

description: Hybridized to Agilent aCGH


title: Meningioma 241

description: Hybridized to Agilent aCGH


title: ChIP_961C_HoxBlinc_KO_MLL1

description: Anti-MLL1 antibody, rabbit polyclonal, Bethyl Laboratories, Cat#A300-086A


title: Meningioma 243

description: Hybridized to Agilent aCGH


title: ChIP_961C_HoxBlinc_KO_NUP98-PHF23-V5

description: Anti-V5 tag antibody, mouse monoclonal, Invitrogen, Cat#R960-25


title: Meningioma 252

description: Hybridized to Agilent aCGH


title: Meningioma 240

description: Hybridized to Agilent aCGH


title: ChIP_961C_HoxBlinc_KO_CTCF

description: Anti-CTCF antibody, rabbit polyclonal, Cell Signaling Technology, Cat# 2899


title: Meningioma 239

description: Hybridized to Agilent aCGH


title: Meningioma 238

description: Hybridized to Agilent aCGH


title: ATAC_WT2

data_processing:
Sequenced reads were trimmed and quality filtered using cutadapt (Martin 2011) version 1.18 and aligned to human (hg19) or mouse genome (mm10) using Bowtie2 (Langmead and Salzberg 2012) ver.2.5.2 with options (--very-sensitive -X 1000 –dovetail). Reads with low mapping quality (mapQ<30), reads that are not properly paired and mitochondrial reads were removed using bamtools (Barnett, Garrison et al. 2011) ver.2.5.1. PCR duplicates were removed using Picard MarkDuplicates ver.2.26.10. Filtered alignment BAM files were converted to BED files. Peak calling was performed using MACS2 (Zhang, Liu et al. 2008) ver.2.2.6 with parameters (--qvalue '0.05' --keep-dup 'all' --d-min 20 --buffer-size 100000 --bdg -f BED --nomodel --extsize '200' --shift '-100'). Treatment bedgraph is converted to bigWig file using bedGraphToBigWig for visualization. ATAC-seq tracks were viewed using the Integrated Genomic Viewer (Thorvaldsdottir, Robinson et al. 2013) ver.2.8.13. Differential ATAC peaks were indentified using DiffBind(Ross-Innes, Stark et al. 2012) ver.2.10.0 and followed ChIPseeker (Yu, Wang et al. 2015) ver.1.28.3 for annotation.
Assembly: mm10 or hg19
Supplementary files format and content: Bed file of narrowPeak (output from MACS2 callpeak) and/or bigwig file

extract_protocol:
Cell pellets were then resuspended in 50ul cold lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40. Lysed nuclei were spun down immediately at 500g for 10min at 4°C, and cell pellets were resuspended and treated with a transposase reaction mixture containing 2.5ul Tn5 transposase at 37°C for 45 min. The fragmented DNA was purified using the MinElute Kit (QIAGEN).
ATAC-seq assay was performed using the Nextera DNA library preparation kit (Illumina).


title: ChIP_961C_CTCF


title: ATAC_WT1


title: Meningioma 236

description: Hybridized to Agilent aCGH


title: Meningioma 237

description: Hybridized to Agilent aCGH


title: ATAC_HoxBlincTg_BALL2


title: Meningioma 235

description: Hybridized to Agilent aCGH


title: ATAC_HoxBlincTg_BALL1


title: Meningioma 234

description: Hybridized to Agilent aCGH


title: ATAC_961C_HoxBlinc_KO2


title: ATAC_961C_HoxBlinc_KO1


title: Meningioma 231

description: Hybridized to Agilent aCGH


title: ATAC_961C-2


title: Meningioma 233

description: Hybridized to Agilent aCGH


title: Meningioma 242

description: Hybridized to Agilent aCGH


title: ATAC_961C-1


title: ChIP_961C_MLL1


title: Meningioma 230

description: Hybridized to Agilent aCGH


title: ATAC_BaF3-2


title: ChIP_961C_NUP98-PHF23-V5


title: Meningioma 228

description: Hybridized to Agilent aCGH


title: Meningioma 229

description: Hybridized to Agilent aCGH


title: ATAC_BaF3-1


title: Meningioma 227

description: Hybridized to Agilent aCGH


title: B6-URB

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

data_processing:
Raw reads were quality-controlled with FastQC 0.11.9. Trimming was performed with Trim Galore 0.6.10 and adapter sequences were removed using Cutadapt 4.2. Gene expression was quantified using Kallisto 0.46.1 based on Mus musculus reference genome GRCm38 genes.
Assembly: GRCm38
Supplementary files format and content: Matrix of Estimated counts

source_name: Small intestine (Duodenum)

growth_protocol: Organoids were cultured in advanced DMEM containing  HEPES, GlutaMAX,  mM n‑Acetylcysteine , penicillin and streptomycin,  recombinant mouse Noggin and R-spondin1 conditioned media  B27 supplements,  human epidermal growth factor and Y-27632 dihydrochloride

extract_protocol:
Organoids were collected by centrifugation and RNA was extracted using Trizol
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare mRNA sequencing libraries, according to manufacturer’s instruction. Briefly, 400 ng of total RNA were purified using the NEBNext poly(A) mRNA Magnetic Isolation module (New Englands Biolabs Inc., Ipswich, MA, USA) and used as a template for cDNA synthesis by reverse transcriptase with random primers. The specificity of the strand was obtained by replacing the dTTP with the dUTP. This cDNA was subsequently converted to double-stranded DNA and end-repaired. Ligation of adaptors was followed by a purification step with AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA), by an excision of the strands containing the dUTPs and finally, by a PCR enrichment step of 10 cycles to incorporate specific indexed adapters for the multiplexing. The quality of final amplified libraries was examined with a DNA screentape D1000 on a TapeStation 2200 and the quantification was done on the QuBit 3.0 fluorometer (ThermoFisher Scientific, Canada). Subsequently, mRNA-seq librairies with unique dual index were pooled together in equimolar ratio and sequenced for paired-end 100 pb sequencing on an Illumina NovaSeq 6000 at the Next-Generation Sequencing Platform, Genomics Center, CHU de Québec-Université Laval Research Center, Québec City, Canada.
The mean coverage/sample was 20M paired-end reads.

treatment_protocol: 24h incubation with the inflammatory cocktail (20 mM LPS, 100 nM TNFα, IL-1 β and IFN) or with 10 µM URB597 or 10 µM JZL184

value: Small intestine (Duodenum)

value: Culture B6

value: Intestinal epithelial cell (organoids)


title: B6-JZL


title: Meningioma 226

description: Hybridized to Agilent aCGH

source_name: Brain Tumor  Tissue


title: Meningioma 225

description: Hybridized to Agilent aCGH

value: F

source_name: Normal Brain Tissue


title: B6-Inflam+URB

value: Inflammatory cocktail + URB597


title: Meningioma 224

description: Hybridized to Agilent aCGH

value: Normal Brain


title: B6-Inflam+JZL+URB

value: Inflammatory cocktail + JZL184 + URB597


title: Meningioma 223

description: Hybridized to Agilent aCGH


title: B6-Inflam+JZL

value: Inflammatory cocktail + JZL184


title: Meningioma 222

description: Hybridized to Agilent aCGH


title: B6-Inflam

value: Inflammatory cocktail


title: B5-URB

value: Culture B5


title: Meningioma 221

description: Hybridized to Agilent aCGH


title: Meningioma 232

description: Hybridized to Agilent aCGH


title: B5-Inflam+JZL+URB


title: Meningioma 217

description: Hybridized to Agilent aCGH


title: B5-JZL


title: B5-Inflam+URB


title: Meningioma 219

description: Hybridized to Agilent aCGH


title: B5-Inflam+JZL


title: Meningioma 216

description: Hybridized to Agilent aCGH


title: B5-Inflam


title: B5-Ctrl

value: Culture B2

value: Control


title: Meningioma 214

description: Hybridized to Agilent aCGH


title: Meningioma 213

description: Hybridized to Agilent aCGH


title: B2-JZL


title: B2-URB


title: Meningioma 212

description: Hybridized to Agilent aCGH


title: Meningioma 215

description: Hybridized to Agilent aCGH


title: B2-Inflam+JZL+URB


title: B2-Inflam+URB


title: B2-Inflam+JZL


title: Meningioma 220

description: Hybridized to Agilent aCGH


title: Meningioma 210

description: Hybridized to Agilent aCGH


title: B2-Inflam


title: Meningioma 209

description: Hybridized to Agilent aCGH


title: Meningioma 208

description: Hybridized to Agilent aCGH


title: Meningioma 207

description: Hybridized to Agilent aCGH


title: Meningioma 218

description: Hybridized to Agilent aCGH


title: 10x snRNAseq, Gene Expression, CTLvsCKO

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
10x Genomics
filtered_feature_bc_matrix.CTLxCKO.tar.gz

data_processing:
10x Genomics Cellranger v7.0.0 was used to process fastq files and generate matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.1 in R v4.1.3/ Rstudio.
Assembly: mm10
Supplementary files format and content: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz, PBSvsINF
Supplementary files format and content: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz, CTLvsCKO

molecule: nuclear RNA

source_name: small intestine

growth_protocol: All mice were housed in specific-pathogen-free conditions at 22-24℃ with humidity of 40%–70% and a light/dark cycle of 12 hours, and were used and maintained in accordance with the Institutional Animal Care and Use Committee Guidelines of Westlake University

extract_protocol:
Flow-sorted GFP+ nuclei were processed through the GemCode Single Cell Platform
10x genomics scRNA-seq

treatment_protocol: 500 purified N. brasiliensis in 250 μl PBS were injected subcutaneously

value: small intestine

value: 8 weeks

value: male

value: Enteric neurons

value: Baf53-cre Sun1-GFP and Baf53-cre Il13ra1 flox Sun1-GFP

value: s.c 500 L3 N.brasiliensis infection


title: Meningioma 206

description: Hybridized to Agilent aCGH

value: Brain tumor

value: M


title: Meningioma 204

description: Hybridized to Agilent aCGH

value: F


title: 10x snRNAseq, HTO Hashtags, CTLvsCKO

library_source: other

molecule: other


title: 10x snRNAseq, Gene Expression, PBSvsINF

description:
10x Genomics
filtered_feature_bc_matrix.PBSxINF.tar.gz

value: Baf53-cre Sun1-GFP

value: s.c 500 L3 N.brasiliensis infection or PBS


title: Meningioma 203

description: Hybridized to Agilent aCGH

value: Normal Brain


title: Meningioma 205

description: Hybridized to Agilent aCGH


title: Meningioma 202

description: Hybridized to Agilent aCGH


title: Control_Islet_Progenitor_ND-2

first: Guoqiang

last: Gu

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
FACS-sorted cells
7127-GG-31

data_processing:
Sequencing reads were trimmed to remove adapter sequences using Cutadapt (v2.10).
Trimmed reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.8a)
Gencode vM24 gene annotations were provided to STAR to improve the accuracy of mapping.
featureCounts (v2.0.2) was used to count the number of reads mapped to each gene.
For further anaylsis, the 'countToFPKM' package was used to convert the feature counts of paired-end RNA-Seq into FPKM normalised values by library size and feature effective length.
Assembly: GRCm38.p6
Supplementary files format and content: 7127_RNAseq_mouse.count copy.xlsx (Processed data, counts of identfied features after alignments)
Supplementary files format and content: 7127_RNAseq_mouse.fpkm_original copy.xlsx (Processed data, feature levels after normalization against feature size and total counts per sample)
Supplementary files format and content: rna_stats_export_7127-GG.csv (Raw statistics from Illumina)

source_name: endocrine islet progenitors

growth_protocol: Mice were housed in AAALAC-Accredited facilitty, following protocols approved by Vanderbilt IACUC.

extract_protocol:
Pancreata were manually dissected in RPMI 1066 media with 10% FBS + antibiotics. They were then Dissociated using 0.25% trypsin at 37 degree (~ 5minutes). Cells were washed 2X with RPMI+FBS media and sent for FACS sorting. Cells were spundown, dissolved in Trizol, and used in a DNA-free RNA-isolation kit (Zymo R2050) for RNA purification.
Total RNA preps will subject to standard Sample Quality Control analysis by using fluorometry Qubit or Picogreen and integrity by BioAnalyzer or TapeStation.  Only those with a RIN>7.5 were used for down-stream studies. For each sample, 50 ng of RNA were used for linrary preparation using the Illumina Ribo-Zero Plus rRNA Depletion kit. The procedure followed that specified by manufacturer, which include the depletion of rRNAs, cDNA reverse transcription, strand specific labeling/amplification. Library Quality Control analysis will be performed by using Qubit and BioAnalyzer to determine the concentration and size bp. Only those with significan DNA fragments between 150-1000 bp were sequenced. Each library that passes the final QC undergoes qPCR using the KAPA library quantification kit and QuantStudio. qPCR allows highly accurate quantification of library molecules that can seed clusters and balance target sample representation during pooling. Multiplexed samples are pooled in equimolar or user-defined ratios to achieve the multiplexing level requested by the user using Illumina MiSeq platform.

treatment_protocol: Females were fed with ND, HFD, and lPD before crossing, with females continue with specified diet.

value: endocrine islet progenitors

value: pancreatic cells

value: ND

value: pooled male and female


title: Meningioma 211

description: Hybridized to Agilent aCGH


title: Control_Islet_Progenitor_ND-1

description:
FACS-sorted cells. Mixed genotype (not used for down-stream analysis)
7127-GG-29


title: Meningioma 199

description: Hybridized to Agilent aCGH


title: Meningioma 201

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_ND-3

description:
FACS-sorted cells
7127-GG-26


title: Meningioma 198

description: Hybridized to Agilent aCGH


title: Meningioma 197

description: Hybridized to Agilent aCGH


title: B2-Ctrl

value: Small intestine (Duodenum)

value: Culture B2

value: Intestinal epithelial cell (organoids)

value: Control


title: Meningioma 196

description: Hybridized to Agilent aCGH


title: Control-Neuron-1

description:
FACS-sorted cells
7127-GG-24

source_name: Neural progenitors

value: Neural progenitors


title: B6-Ctrl

value: Culture B6


title: Meningioma 192

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_LPD-4

description:
FACS-sorted cells
7127-GG-21

value: LPD


title: Control_Islet_Progenitor_ LPD-4

description:
FACS-sorted cells
7127-GG-22


title: Meningioma 195

description: Hybridized to Agilent aCGH

value: Brain tumor


title: Control_Islet_Progenitor_ND-3

description:
FACS-sorted cells
7127-GG-32


title: Meningioma 194

description: Hybridized to Agilent aCGH

value: M


title: Control_Islet_Progenitor_ LPD-3

description:
FACS-sorted cells
7127-GG-17


title: Meningioma 190

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_LPD-3

description:
FACS-sorted cells
7127-GG-20


title: 10x snRNAseq, HTO Hashtags, PBSvsINF

value: small intestine

value: 8 weeks

value: male

value: Enteric neurons


title: Mutant_Islet_Progenitor_LPD-2

description:
FACS-sorted cells
7127-GG-19

value: endocrine islet progenitors


title: Meningioma 193

description: Hybridized to Agilent aCGH

value: Normal Brain


title: Control_Islet_Progenitor_ HFD-3

description:
FACS-sorted cells
7127-GG-15

value: pancreatic cells

value: HFD


title: Meningioma 191

description: Hybridized to Agilent aCGH

value: F


title: Mutant_Islet_Progenitor_LPD-1

description:
FACS-sorted cells
7127-GG-18

value: pooled male and female


title: Mutant_Islet_Progenitor_HFD-3

description:
FACS-sorted cells
7127-GG-16


title: Meningioma 186

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_HFD-2

description:
FACS-sorted cells
7127-GG-14


title: Meningioma 188

description: Hybridized to Agilent aCGH


title: Meningioma 189

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_HFD-1

description:
FACS-sorted cells
7127-GG-13


title: Meningioma 200

description: Hybridized to Agilent aCGH


title: Meningioma 185

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_ND-4

description:
FACS-sorted cells
7127-GG-28

value: ND


title: Control_Islet_Progenitor_ HFD-2

description:
FACS-sorted cells
7127-GG-12


title: Meningioma 184

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_ND-2

description:
FACS-sorted cells
7127-GG-25


title: Mutant-Neuron-1

description:
FACS-sorted cells
7127-GG-23


title: Control_Islet_Progenitor_ HFD-1

description:
FACS-sorted cells
7127-GG-11


title: Meningioma 181

description: Hybridized to Agilent aCGH


title: Meningioma 187

description: Hybridized to Agilent aCGH


title: Meningioma 183

description: Hybridized to Agilent aCGH


title: Control_Islet_Progenitor_ND-4

description:
FACS-sorted cells
7127-GG-8


title: Meningioma 182

description: Hybridized to Agilent aCGH


title: Meningioma 180

description: Hybridized to Agilent aCGH


title: Meningioma 177

description: Hybridized to Agilent aCGH


title: Mutant_Islet_Progenitor_ND-1

description:
FACS-sorted cells
7127-GG-10


title: Meningioma 179

description: Hybridized to Agilent aCGH


title: Meningioma 176

description: Hybridized to Agilent aCGH


title: Meningioma 174

description: Hybridized to Agilent aCGH


title: Meningioma 178

description: Hybridized to Agilent aCGH


title: VORG4N4_S60

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

data_processing:
RNA-Seq data preprocessing: RNA-Seq data as FastQ files were processed with the nf-core/rna-seq pipeline (v: 3.12.0). Briefly raw data files (FastQ) quality was assessed with FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/], low quality bases and adapter sequences were removed with Trim Galore [https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/], in the final step data was aligned with Salmon to produce a matrix file with genes as rows and samples as columns.
Assembly: GRCm38
Supplementary files format and content: tab-delimited quant file includes raw counts and tpm for each Sample

source_name: tumor mouse cutaneous melanocytes cells treated with VORINOSTAT

extract_protocol:
RNA was extracted from tumor cell pellets and cell lines using an RNeasy Plus mini kit (Qiagen, Hilden, Germany). RNA quality was assessed with Nanodrop and BioAnalyzer tools (Agilent, St. Clara, CA).
Universal Plus Total RNA-Seq with NuQuant kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand). RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA).

treatment_protocol: in vivo treatment with Vorinostat

value: skin tumor

value: vorinostat


title: CTRG1N6_S57

source_name: tumor mouse cutaneous melanocytes cells


title: Meningioma 172

description: Hybridized to Agilent aCGH