title: RA-57 GBM PDX59 RNA-seq Ciclopirox

description: Library name: RA-57

value: Ciclopirox


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_16_61bp

status: Public on Mar 06 2025

type: SRA

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Road, Weill Hall 301

department: Biomedical Engineering

country: USA

institute: Cornell University

library_source: transcriptomic

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, sequencing data from the Illumina NextSeq 500 and Novaseq 6000 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR29 (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts30 (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts30 (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap31 (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 3, if a sample had less than 75000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 3 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: comma seprated values .csv file contain gene counts for each sample in this study

molecule: total RNA

organism: Homo sapiens

source_name: urine from the AKI cohort

extract_protocol:
Before cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from the plasma supernatant (250-1500 μl) using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Urine samples were thawed at room temperature and centrifuged at 16,000 x g for 10 minutes at 4 °C. cfRNA was extracted from (450-2000 μl) supernatant using QIAamp Circulating Nucleic Acid Kit -Purification of Circulating microRNA in serum/plasma/urine protocol (Qiagen, product #55114).  Extracted RNA was DNase treated with 14 μl of 10 μl DNase Turbo Buffer (Invitrogen, AM2238), 3 μl DNase Turbo (Invitrogen, AM2238), and 1 μl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 10 μl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

tag: tissue

value: Urine, extracted cell-free RNA

tag: cell type

tag: treatment

value: Immune checkpoint inhibitor therapy

tag: time

tag: diagnosis

value: Acute Kidney Injury


title: RA-56 GBM PDX59 RNA-seq A485

city: Cincinnati

first: Matthew

last: Garrett

state: Ohio

address: 5061 myerdale drive

institute: Kettering Health

description: Library name: RA-56

data_processing:
Quality control check performed with FastQC v0.11.7
Adapter sequences and quality trimming with Trim Galore! v0.6.6
Trimmed reads aligned to GRCh38/hg38 using bowtie2 v2.5.1 with 'verysensitive' setting
Mitochondrial and duplicate reads removed using samtools v.1.17
Peak calling performed using MACS2 v2.2.9
Assembly: GRCh38/hg38
Supplementary files format and content: "Normalized Gene Expression after Drug Treatment.csv" Comma separated values; Log2-transformed, library size normalized expression data using rlog() function from DESeq2 v1.26.0
Supplementary files format and content: "RNA_SEQ_countMatrix.csv" Raw read counts per gene generated by featureCounts v1.6.2 using NCBI RefSeq annotations

source_name: Brain tumor

growth_protocol: Initial cell numbers were plated to maximize the number of viable cells at the target time point without over-growth. Additional drug and growth factor were added on a weekly basis.

extract_protocol:
50,000 cells were spun down at 500 x g for 5 minutes at 4°C, resuspended in ATAC-resuspension buffer (0.1% NP40, 0.1% tween-20, 0.01% digitonin), incubated on ice for 3 minutes and washed. Nuclei were pelleted at 500 x g at 4C for 10 minutes.
ATAC-seq libraries were created using 50,000 cells, cells were resuspended in ATAC-resuspension buffer, transposed using Illumina Nextera Tn5 Transposase, DNA purified with Qiagen MinElute PCR Purification Kit and amplified for 12 cycles.

treatment_protocol: Cells were treated at 500nM (in some cases reduced to 250nM to obtain enough viable material) for 7 days.

value: Brain tumor

tag: cell line

value: Glioblastoma

tag: alive (c/ml)

tag: acutal cell_count

tag: %alive

tag: batch


title: Lung, XY10.M

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

country: Canada

institute: McGill University

data_processing:
Data preprocessing and alignment was performed using the GenPipes RNA-seq pipeline
Reads were trimmed and filtered for quality, then aligned to the mouse reference genome (GRCm38) using STAR
Alignment bam files were used to generate bedGraph files with genomeCoverageBed and bedGraph files were converted to bigwig files with bedGraphToBigWig
Assembly: mm10
Supplementary files format and content: Bigwig

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was extracted from mouse organs using Trizol Reagent (Thermo Fisher Scientific, MA, US) and purified using the RNeasy MinElute Cleanup Kit (Qiagen, NL).
Library preparation and RNA-sequencing (RNA-seq) were performed at the McGill University and Genome Quebec Innovation Centre for the liver, and at the McGill Genome Centre for the brain, lung, and heart tissues.

value: Lung

tag: strain

tag: sex chromosome complement

value: XY

tag: gonadal sex

value: Male

tag: age

value: 8 weeks

tag: library type

value: rRNA depleted


title: RA-54 GBM PDX59 RNA-seq PF06726304

description: Library name: RA-54


title: Lung, XX14.F

value: XX

value: Female


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_15_61bp


title: RA-55 GBM PDX59 RNA-seq Decitabine

description: Library name: RA-55

value: Decitabine


title: RA-53 GBM PDX59 RNA-seq Control

description: Library name: RA-53

value: Control


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_14_61bp


title: Lung, XX13.F


title: RA-52 GBM PDX43 RNA-seq Hesperadin

description: Library name: RA-52

value: Hesperadin


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_13_61bp


title: Lung, XX8.F


title: RA-51 GBM PDX43 RNA-seq Alexidine

description: Library name: RA-51

value: Alexidine


title: RA-49 GBM PDX43 RNA-seq Rucaporib

description: Library name: RA-49

value: Rucaporib


title: Lung, XX17.F

value: XPaf


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_11_61bp

value: Urine, extracted cell-free RNA

value: Immune checkpoint inhibitor therapy


title: RA-60 GBM PDX59 RNA-seq SirReal2

description: Library name: RA-60

value: Brain tumor


title: RA-46 GBM PDX43 RNA-seq CPI203

description: Library name: RA-46

value: Glioblastoma


title: RA-48 GBM PDX43 RNA-seq Gavinostat

description: Library name: RA-48

value: Gavinostat


title: RA-59 GBM PDX59 RNA-seq CPI203

description: Library name: RA-59


title: Lung, XX16.F

value: Lung


title: RA-47 GBM PDX43 RNA-seq SirReal2

description: Library name: RA-47


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_10_61bp

value: Acute Kidney Injury


title: RA-45 GBM PDX43 RNA-seq ML228

description: Library name: RA-45


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_9_61bp


title: RA-43 GBM PDX43 RNA-seq A485

description: Library name: RA-43


title: Lung, XX11.F

value: 8 weeks


title: RA-44 GBM PDX43 RNA-seq Ciclopirox

description: Library name: RA-44

value: Ciclopirox


title: RA-41 GBM PDX43 RNA-seq PF06726304

description: Library name: RA-41


title: Lung, XO6.F

value: XO

value: rRNA depleted


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_7_61bp


title: RA-42 GBM PDX43 RNA-seq Decitabine

description: Library name: RA-42

value: Decitabine


title: RA-39 GBM PDX22 RNA-seq Hesperadin

description: Library name: RA-39


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_6_61bp


title: Lung, XO4.F

value: Female


title: RA-50 GBM PDX43 RNA-seq GSK591

description: Library name: RA-50


title: RA-40 GBM PDX43 RNA-seq Control

description: Library name: RA-40

value: Control


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_4_61bp


title: Lung, XO2.F


title: RA-38 GBM PDX22 RNA-seq Alexidine

description: Library name: RA-38

value: Alexidine


title: RA-37 GBM PDX22 RNA-seq GSK591

description: Library name: RA-37


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_3_61bp


title: RA-36 GBM PDX22 RNA-seq Rucaporib

description: Library name: RA-36

value: Rucaporib


title: Heart, XY5.F

source_name: Heart

value: Heart

value: XY


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_2_61bp

value: Urine, extracted cell-free RNA

value: Immune checkpoint inhibitor therapy


title: RA-34 GBM PDX22 RNA-seq SirReal2

description: Library name: RA-34

value: Brain tumor

value: Glioblastoma


title: Heart, XY4.F


title: RA-33 GBM PDX22 RNA-seq CPI203

description: Library name: RA-33

value: Lost pellet


title: RA-32 GBM PDX22 RNA-seq ML228

description: Library name: RA-32


title: Heart, XY3.F


title: Urine cell-free RNA, RNA seq gene counts for sample: aki_cfrna_1_61bp

value: Acute Kidney Injury


title: RA-29 GBM PDX22 RNA-seq Decitabine

description: Library name: RA-29


title: RA-30 GBM PDX22 RNA-seq A485

description: Library name: RA-30


title: RA-28 GBM PDX22 RNA-seq PF06726304

description: Library name: RA-28


title: OciLy1_NFR_CRISPRi_t14_rep3

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

library_source: genomic

data_processing:
(Tiling screens only): sgRNA sequence reads were trimmed to 21 bp with CutAdapt
(Tiling screens only): bowtie -v0 was used to align trimeed reads to a custom index of all designed sgRNAs for calculation of read counts for each replicate / time point. sgRNAs with specificity score >50, 10 of fewer "G" bases, or fewer than 50 reads in any T0 replicate were excluded.
(Tiling screens only): CRISPRi scores were calculated as mean log2-fold depletion from t) to Tend across replicates, normalized to the median CRISPRi score of non-targeting negative control sgRNAs.
(Tiling screens only): Mean CRISPRi scores were calculated for a sliding window of 20 consecutive sgRNAs and values plotted as bedgraphs over the corresponding regions.
(NFR screens only): Fastq files were trimmed with cutAdapt to keep only 20mer sgRNA sequences (“cutadapt -a GTTTAAGAGCTATGCTGGAAACAGCATAG”).
(NFR screens only): MAGeCK 0.9.5.4 was used to generate count tables for all designed sgRNAs in each time point and replicate (“mageck count”, default parameters).
(NFR screens only): Separate MAGeCK RRA (“mageck test”) analyses were then run for all gene promoter-targeting sgRNAs (grouped by gene) and for all NFR-targeting sgRNAs (grouped by NFR) with non-targeting sgRNAs used for normalization in both analyses (“--norm-method control”).
Assembly: hg19
Supplementary files format and content: Normalized sgRNA counts for each screen (tiling screens only)
Supplementary files format and content: Count tables for each replicate / sgRNA (NFR screens only)
Supplementary files format and content: Bedgraph of sgRNA log2-fold-change (20-sgRNA sliding window) versus median of non-targeting controls (tiling screens only)
Supplementary files format and content: Bedgraph of individual sgRNA log2-fold-change versus median of non-targeting controls (NFR screens only)
Library strategy: PCR-amplified sgRNA sequences

molecule: genomic DNA

growth_protocol:
All cell lines were cultured in RPMI 1640 + Glutamax supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1 mM sodium pyruvate, and 55 micromolar 2-mercaptoethanol.
Dox-inducible KRAB-dCas9 expressing cell lines were transduced with sgRNA library lentivirus at an MOI of 0.4 for an estimated overall coverage of 500x transduced cells per sgRNA per replicate. Transduced cells were selected in 1ug/mL puromycin for 72 hours. For dox-inducible cell lines, cell numbers sufficient for 500x coverage per sgRNA were harvested post selection (T0), while the transduced parental cells were harvested for DB. Doxycycline was then added at 100-500 ng/mL (optimized for individual cell lines) to induce KRAB-dCas9 expression, and replicates were passaged in the presence of doxycycline for 14 population doublings, maintaining at least 500x coverage at each passage prior to final harvest (T14). For the DB screen conducted in a cell line with non-inducible dCas9-KRAB (UCOE-SFFV-KRAB-dCas9-T2A-mCherry), the same protocol was followed except that equal numbers of the parental cell line were transduced in parallel and harvested as "T0" replicates following selection, while the KRAB-dCas9+ population was maintained for an additional 14 doublings prior to harvest.

extract_protocol:
Genomic DNA was harvested from transduced cell pellets  with Qiagen QIAmp DNA blood Maxi or Midi kits
PCR (ExTaq, Takara) with barcoded illumina adaptors was used to amplify sgRNA sequences from genomic DNA corresponding to 500 cell equivalents per library sgRNA, aliquoted into 50 uL PCR reactions (6ug DNA per reaction). All reactions from each replicate were pooled, and 100 ul was gel-purified with E-gel size-select II.

value: Diffuse large B-cell lymphoma cell line


title: Heart, XY1.F

value: 8 weeks


title: Heart, XY14.M

value: Male


title: RA-27 GBM PDX22 RNA-seq Control

description: Library name: RA-27


title: OciLy1_NFR_CRISPRi_t14_rep2


title: RA-26 GBM HK281 RNA-seq Hesperadin

description: Library name: RA-26

value: Hesperadin


title: RA-24 GBM HK281 RNA-seq GSK591

description: Library name: RA-24


title: OciLy1_NFR_CRISPRi_t14_rep1


title: Heart, XY11.M

value: rRNA depleted


title: RA-23 GBM HK281 RNA-seq Rucaporib

description: Library name: RA-23


title: RA-35 GBM PDX22 RNA-seq Gavinostat

description: Library name: RA-35

value: Gavinostat


title: RA-22 GBM HK281 RNA-seq Gavinostat

description: Library name: RA-22


title: OciLy1_NFR_CRISPRi_t0_rep3


title: Heart, XX8.F

value: XX

value: Female


title: OciLy1_NFR_CRISPRi_t0_rep2


title: RA-21 GBM HK281 RNA-seq SirReal2

description: Library name: RA-21


title: RA-19 GBM HK281 RNA-seq ML228

description: Library name: RA-19


title: Heart, XX7.F


title: RA-20 GBM HK281 RNA-seq CPI203

description: Library name: RA-20


title: RA-18 GBM HK281 RNA-seq Ciclopirox

description: Library name: RA-18

value: Ciclopirox


title: RA-31 GBM PDX22 RNA-seq Ciclopirox

description: Library name: RA-31


title: RA-17 GBM HK281 RNA-seq A485

description: Library name: RA-17


title: RA-25 GBM HK281 RNA-seq Alexidine

description: Library name: RA-25

value: Alexidine


title: OciLy1_NFR_CRISPRi_t0_rep1


title: DB_NFR_CRISPRi_t14_rep4

source_name: DB

value: DB


title: Heart, XX17.F

value: Heart

value: XPaf


title: Heart, XX12.F


title: DB_NFR_CRISPRi_t14_rep3


title: RA-16 GBM HK281 RNA-seq Decitabine

description: Library name: RA-16

value: Brain tumor

value: Decitabine


title: RA-14 GBM HK281 RNA-seq Control

description: Library name: RA-14

value: Glioblastoma

value: Control


title: Heart, XY12.M

value: XY


title: Heart, XX11.F

value: 8 weeks


title: DB_NFR_CRISPRi_t14_rep1

value: Diffuse large B-cell lymphoma cell line


title: DB_NFR_CRISPRi_t14_rep2


title: RA-13 GBM G83 RNA-seq Hesperadin

description: Library name: RA-13

value: Hesperadin


title: RA-10 GBM G83 RNA-seq Rucaporib

description: Library name: RA-10

value: Rucaporib


title: RA-12 GBM G83 RNA-seq Alexidine

description: Library name: RA-12


title: Heart, XX10.F

value: rRNA depleted


title: RA-11 GBM G83 RNA-seq GSK591

description: Library name: RA-11


title: DB_NFR_CRISPRi_t0_rep4


title: RA-9 GBM G83 RNA-seq Gavinostat

description: Library name: RA-9

value: Gavinostat


title: Heart, XO6.F

value: XO

value: Female


title: RA-8 GBM G83 RNA-seq SirReal2

description: Library name: RA-8


title: RA-7 GBM G83 RNA-seq CPI203

description: Library name: RA-7


title: RA-6 GBM G83 RNA-seq ML228

description: Library name: RA-6


title: Heart, XO7.F


title: RA-5 GBM G83 RNA-seq Ciclopirox

description: Library name: RA-5

value: Ciclopirox


title: RA-4 GBM G83 RNA-seq A485

description: Library name: RA-4


title: Heart, XO4.F


title: RA-3 GBM G83 RNA-seq Decitabine

description: Library name: RA-3


title: Brain, XY7.F

source_name: Brain

value: Brain


title: RA-15 GBM HK281 RNA-seq PF06726304

description: Library name: RA-15


title: DB_NFR_CRISPRi_t0_rep2

value: DB


title: DB_NFR_CRISPRi_t0_rep1


title: RA-2 GBM G83 RNA-seq PF06726304

description: Library name: RA-2


title: RA-1 GBM G83 RNA-seq Control

description: Library name: RA-1


title: Brain, XY6.F


title: RA-156 GBM 385 ATAC-seq Hesperadin

description: Library name: RA-156

data_processing:
Quality control check performed with FastQC v0.11.7
Adapter sequences and quality trimming with Trim Galore! v0.6.6
Trimmed reads aligned to GRCh38/hg38 using bowtie2 v2.5.1 with 'verysensitive' setting
Mitochondrial and duplicate reads removed using samtools v.1.17
Peak calling performed using MACS2 v2.2.9
Assembly: GRCh38/hg38
Supplementary files format and content: peaks_survival_genes_correlation.csv; Comma separated values (.csv); Peak coordinates, peak importance score, survival correlation, nearby genes with their correlation scores and genomic distances to the peak


title: Brain, XY5.F


title: WSUDLCL2_NFR_CRISPRi_t14_rep2


title: RA-154 GBM 385 ATAC-seq GSK591

description: Library name: RA-154


title: WSUDLCL2_NFR_CRISPRi_t14_rep1


title: RA-153 GBM 385 ATAC-seq Rucaporib

description: Library name: RA-153


title: Brain, XY4.F


title: RA-152 GBM 385 ATAC-seq Gavinostat

description: Library name: RA-152


title: RA-151 GBM 385 ATAC-seq SirReal2

description: Library name: RA-151


title: Brain, XY2.F


title: DB_NFR_CRISPRi_t0_rep3


title: WSUDLCL2_NFR_CRISPRi_t0_rep3


title: Brain, XY30.M

value: Male


title: RA-149 GBM 385 ATAC-seq ML228

description: Library name: RA-149

value: Brain tumor


title: RA-148 GBM 385 ATAC-seq Ciclopirox

description: Library name: RA-148


title: WSUDLCL2_NFR_CRISPRi_t0_rep1


title: RA-146 GBM 385 ATAC-seq Decitabine

description: Library name: RA-146

value: Decitabine


title: RA-147 GBM 385 ATAC-seq A485

description: Library name: RA-147

value: Glioblastoma


title: Brain, XY15.M


title: RA-144 GBM 385 ATAC-seq Control

description: Library name: RA-144

value: Control


title: RA-145 GBM 385 ATAC-seq PF06726304

description: Library name: RA-145


title: SUDHL4_NFR_CRISPRi_t14_rep3


title: WSUDLCL2_NFR_CRISPRi_t14_rep3


title: Brain, XY14.M

value: XY


title: SUDHL4_NFR_CRISPRi_t14_rep2


title: RA-155 GBM 385 ATAC-seq Alexidine

description: Library name: RA-155

value: Alexidine


title: Brain, XY13.M

value: 8 weeks


title: Brain, XX15.F

value: XX


title: RA-142 GBM 357 ATAC-seq Alexidine

description: Library name: RA-142


title: RA-141 GBM 357 ATAC-seq GSK591

description: Library name: RA-141


title: SUDHL4_NFR_CRISPRi_t14_rep1

value: Diffuse large B-cell lymphoma cell line


title: RA-139 GBM 357 ATAC-seq Gavinostat

description: Library name: RA-139


title: Brain, XX14.F

value: rRNA depleted


title: SUDHL4_NFR_CRISPRi_t0_rep3


title: RA-138 GBM 357 ATAC-seq SirReal2

description: Library name: RA-138


title: WSUDLCL2_NFR_CRISPRi_t0_rep2


title: Brain, XX13.F


title: RA-137 GBM 357 ATAC-seq CPI203

description: Library name: RA-137


title: SUDHL4_NFR_CRISPRi_t0_rep2


title: RA-136 GBM 357 ATAC-seq ML228

description: Library name: RA-136


title: RA-135 GBM 357 ATAC-seq Ciclopirox

description: Library name: RA-135


title: RA-134 GBM 357 ATAC-seq A485

description: Library name: RA-134


title: SUDHL4_NFR_CRISPRi_t0_rep1


title: RA-143 GBM 357 ATAC-seq Hesperadin

description: Library name: RA-143

value: Hesperadin


title: Brain, XX16.F

value: XPaf


title: Karpas422_NFR_CRISPRi_t14_rep4


title: RA-131 GBM 357 ATAC-seq Control

description: Library name: RA-131


title: RA-132 GBM 357 ATAC-seq PF06726304

description: Library name: RA-132


title: Karpas422_NFR_CRISPRi_t14_rep3


title: Brain, XX12.F

value: Female


title: RA-129 GBM MGG-119 ATAC-seq Alexidine

description: Library name: RA-129


title: Brain, XX10.F


title: RA-140 GBM 357 ATAC-seq Rucaporib

description: Library name: RA-140

value: Rucaporib


title: Karpas422_NFR_CRISPRi_t14_rep2


title: RA-128 GBM MGG-119 ATAC-seq GSK591

description: Library name: RA-128


title: RA-127 GBM MGG-119 ATAC-seq Rucaporib

description: Library name: RA-127


title: Brain, XO6.F

value: Brain

value: XO


title: RA-126 GBM MGG-119 ATAC-seq Gavinostat

description: Library name: RA-126

value: Gavinostat


title: Brain, XO5.F


title: RA-125 GBM MGG-119 ATAC-seq SirReal2

description: Library name: RA-125

value: Brain tumor


title: RA-124 GBM MGG-119 ATAC-seq CPI203

description: Library name: RA-124


title: RA-150 GBM 385 ATAC-seq CPI203

description: Library name: RA-150


title: Brain, XO4.F


title: RA-123 GBM MGG-119 ATAC-seq ML228

description: Library name: RA-123


title: Brain, XX8.F


title: Karpas422_NFR_CRISPRi_t0_rep3


title: Karpas422_NFR_CRISPRi_t0_rep4


title: RA-133 GBM 357 ATAC-seq Decitabine

description: Library name: RA-133

value: Decitabine


title: RA-121 GBM MGG-119 ATAC-seq A485

description: Library name: RA-121

value: Glioblastoma


title: RA-120 GBM MGG-119 ATAC-seq Decitabine

description: Library name: RA-120


title: RA-130 GBM MGG-119 ATAC-seq Hesperadin

description: Library name: RA-130


title: [spatial transcriptomics] HO-day 7

city: Hefei

first: Chen

last: Kan

state: Anhui

address: 81 Meishan road

department: Pathophysiology

country: China

institute: Anhui Medical University

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Raw data were processed using 10X Genomics Space Ranger pipeline to generate FASTQ files
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: spatial transcriptomics

source_name: Tibial muscle

extract_protocol:
Uninjured and injured tibial muscles at 1, 3 and 7 dpi from Nse-Bmp4 mice (3 tibial muscles were mixed for one group) were harvested
We used the Cell Ranger software pipeline (10× Genomics, version 5.0.0) 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.

value: Tibial muscle

value: 6-8 week old

tag: genotype


title: RA-119 GBM MGG-119 ATAC-seq PF06726304

description: Library name: RA-119


title: Karpas422_NFR_CRISPRi_t0_rep2


title: [spatial transcriptomics] HO-day 3


title: Karpas422_NFR_CRISPRi_t0_rep1


title: RA-122 GBM MGG-119 ATAC-seq Ciclopirox

description: Library name: RA-122

value: Ciclopirox


title: RA-117 GBM 252 ATAC-seq Hesperadin

description: Library name: RA-117


title: [spatial transcriptomics] HO-day 1


title: Karpas422_NFR_CRISPRi_t14_rep1


title: [spatial transcriptomics] HO-day 0


title: SUDHL5_NFR_CRISPRi_t14_rep3


title: RA-116 GBM 252 ATAC-seq Alexidine

description: Library name: RA-116

value: Alexidine


title: RA-114 GBM 252 ATAC-seq Rucaporib

description: Library name: RA-114


title: RA-118 GBM MGG-119 ATAC-seq Control

description: Library name: RA-118

value: Control


title: HO-day 7

description: 10X genomics

library_source: transcriptomic single cell

data_processing:
Using the R package Seurat (version 3.1.1), we processed the unique molecular identifier (UMI) count matrix. To remove low-quality cells and likely multiplet captures, we filtered out cells with UMI/gene count values that were more than 2 standard deviations from the mean, assuming a Gaussian distribution of each cells' UMI/gene numbers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Uninjured and injured tibial muscles at 1, 3 and 7 dpi from Nse-Bmp4 mice (3 tibial muscles were mixed for one group) were harvested  via collagenase digestion
We used the Cell Ranger software pipeline (10× Genomics, version 5.0.0) 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.


title: RA-113 GBM 252 ATAC-seq Gavinostat

description: Library name: RA-113


title: RA-111 GBM 252 ATAC-seq CPI203

description: Library name: RA-111


title: SUDHL5_NFR_CRISPRi_t0_rep3

value: Diffuse large B-cell lymphoma cell line


title: HO-day 3

description: 10X genomics


title: RA-110 GBM 252 ATAC-seq ML228

description: Library name: RA-110


title: RA-109 GBM 252 ATAC-seq Ciclopirox

description: Library name: RA-109


title: HO-day 1

description: 10X genomics


title: SUDHL5_NFR_CRISPRi_t0_rep2


title: RA-108 GBM 252 ATAC-seq A485

description: Library name: RA-108


title: HO-day 0

description: 10X genomics


title: RA-107 GBM 252 ATAC-seq Decitabine

description: Library name: RA-107


title: SUDHL5_NFR_CRISPRi_t0_rep1


title: RA-106 GBM 252 ATAC-seq PF06726304

description: Library name: RA-106


title: RA-105 GBM 252 ATAC-seq Control

description: Library name: RA-105


title: JeKo1_NFR_CRISPRi_t14_rep4

value: Mantle cell lymphoma cell line


title: ATAC-seq cortex TBI 2h rep3

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

description: Treatment:TBI;Degradation time:2h

data_processing:
ATAC-seq paired-end reads were trimmed for Illumina adapter sequences with parameters set at -q 25 --phred33 --length 35 -e 0.1 --stringency 4 –paired.
These trimmed sequences were then mapped to the mm10 reference genome using bowtie2.
The alignment results were sorted using samtools.
Duplicate reads were discarded using sambamba with parameters set at markdup -r. Mitochondrial DNA was removed with the parameter set at grep -v chrM.
Bed files were obtained using bedtools bamtobed.Bigwig files were abtained using bedGraphToBigWig tool provided by UCSC Genome Browser. Peaks were identified using macs2 with parameters set at callpeak -g mm --nomodel -shift -100 -extsize 200.
Assembly: mm10
Supplementary files format and content: The BigWig file format provides a compact and efficient way to store large-scale genomic data and enables easy visualization and analysis of genomic datasets in genome browsers

source_name: cortex

extract_protocol:
The mice were anesthetized and underwent transcardial perfusion with 10ml of isotonic saline. The ipsilateral cortex surrounding the injury site was swiftly dissected and preserved in pre-cooled DMEM supplemented with 10% FBS.
The nuclei were counted using acridine orange/propidium iodide (AO/PI) staining (at a 1:1 ratio of AO/PI to sample) and an automated cell counter hemocytometer (Countstar Rigel S5). Then, 50,000 nuclei were transferred into a 1.5 ml LoBind tube containing 1000 ul of ATAC-RSB-Tween Buffer. The nuclei were centrifuged for 10 minutes at 500 RCF at 4°C in a fixed-angle centrifuge. The supernatant was discarded from the centrifuged product, and the nuclei were resuspended in 35 ul of ddH2O and transferred into an EP tube. The ATAC-seq library preparation was performed using the TruePrep DNA Library Prep Kit V2 for Illumina TD501. A volume of 15 ul Tn5 reaction mix (10 ul of 5×TTBL and 5 ul of TTE Mix V50) was added according to the kit instructions and mixed well. The mixture was then incubated at 37°C for 30 minutes. The resulting product was purified using a MinElute column (MinElute PCR Purification Kit, Qiagen). The PCR reaction system was set up with the purified fragmented DNA (24 ul), 5×TAB (10 ul), PPM (5 ul), N5** (5 ul), N7** (5 ul), and TAE (1 ul). PCR amplification was performed following the recommended protocol in the manual. The number of cycles was determined based on the pre-experiment qPCR to be 12 cycles, calculated as the cycle number at which the curve reaches the plateau phase in qPCR plus 5. The DNA product was then purified again using a MinElute column (MinElute PCR Purification Kit, Qiagen). The DNA was sorted using VAHTS DNA Clean Beads (N411 Vazyme) according to the 0.55×/1.0× scheme. Fragmentation analysis of the DNA was performed using a Cartridge Kit (Bioptic). Finally, the libraries were sequenced using Illumina NovaSeq 6000 sequencing.

treatment_protocol: Mice were subjected to a controlled cortical impact (CCI) procedure with craniotomy as previously described . Briefly, mice were anesthetized using isoflurane (4% for induction and 1.5% for maintenance). The mouse's head was fixed on the frame of a stereotactic apparatus, hair from the head was removed, and the area was disinfected with iodophor. Following disinfection, subsequent surgical procedures were performed using sterilized instruments. A midline incision was made along the sagittal suture to expose the skull plate. Connective tissue on the surface of the skull was removed with a cotton swab. Then, a circular craniotomy with a diameter of 4.5mm was performed above the left parietal-temporal cortex using an electric drill. After exposure of the dura mater, a flat-tipped impactor with a diameter of 3mm was adjusted to the center of the craniotomy, ensuring it did not come into contact with the skull. The impact parameters for CCI were set to an impact speed of 5.0m/s, an impact depth of 2.0mm, and a dwell time of 100ms. Following hemostasis with a cotton swab, a plastic film with a diameter of 5.5mm was used to cover the bone window. The skin was sutured and disinfected with iodophor. The mice were then returned to their cages to recover from anesthesia. The entire operation took between 15 and 30 minutes for each mouse. Mice with dural lacerations were excluded from the study. The mice were randomly divided into four groups: Sham_0H, Sham_2H, TBI_0H, and TBI_2H, with three mice in each group. Sham mice did not undergo impact, but all other procedures were the same as those for the TBI mice. Tissue collection was performed 2 hours post-mortem for the Sham_2H and TBI_2H groups, while for the Sham_0H and TBI_0H groups, tissue collection was done immediately after euthanasia.

value: cortex

value: WT

value: TBI 2h


title: RA-115 GBM 252 ATAC-seq GSK591

description: Library name: RA-115


title: RA-104 GBM BT142 ATAC-seq Hesperadin

description: Library name: RA-104

value: Hesperadin


title: ATAC-seq cortex TBI 2h rep2

description: Treatment:TBI;Degradation time:2h


title: SUDHL5_NFR_CRISPRi_t14_rep2


title: RA-103 GBM BT142 ATAC-seq Alexidine

description: Library name: RA-103


title: JeKo1_NFR_CRISPRi_t14_rep3


title: RA-101 GBM BT142 ATAC-seq Rucaporib

description: Library name: RA-101

value: Rucaporib


title: RA-100 GBM BT142 ATAC-seq Gavinostat

description: Library name: RA-100


title: JeKo1_NFR_CRISPRi_t14_rep2


title: RA-102 GBM BT142 ATAC-seq GSK591

description: Library name: RA-102


title: ATAC-seq cortex TBI 2h rep1

description: Treatment:TBI;Degradation time:2h


title: SUDHL5_NFR_CRISPRi_t14_rep1


title: RA-112 GBM 252 ATAC-seq SirReal2

description: Library name: RA-112


title: RA-99 GBM BT142 ATAC-seq SirReal2

description: Library name: RA-99


title: ATAC-seq cortex TBI 0h rep3

description: Treatment:TBI;Degradation time:0h

value: TBI 0h


title: ATAC-seq cortex TBI 0h rep2

description: Treatment:TBI;Degradation time:0h


title: JeKo1_NFR_CRISPRi_t14_rep1


title: RA-97 GBM BT142 ATAC-seq ML228

description: Library name: RA-97


title: JeKo1_NFR_CRISPRi_t0_rep4


title: RA-96 GBM BT142 ATAC-seq Ciclopirox

description: Library name: RA-96


title: ATAC-seq cortex TBI 0h rep1

description: Treatment:TBI;Degradation time:0h


title: RA-95 GBM BT142 ATAC-seq A485

description: Library name: RA-95


title: JeKo1_NFR_CRISPRi_t0_rep3


title: ATAC-seq cortex Sham 2h rep3

description: Treatment:Sham;Degradation time:2h

value: Sham 2h


title: RA-92 GBM BT142 ATAC-seq Control

description: Library name: RA-92

value: Brain tumor


title: RA-94 GBM BT142 ATAC-seq Decitabine

description: Library name: RA-94

value: Decitabine


title: RA-93 GBM BT142 ATAC-seq PF06726304

description: Library name: RA-93

value: Glioblastoma


title: ATAC-seq cortex Sham 2h rep2

description: Treatment:Sham;Degradation time:2h


title: JeKo1_NFR_CRISPRi_t0_rep2


title: RA-91 GBM TS1156 ATAC-seq Hesperadin

description: Library name: RA-91


title: JeKo1_NFR_CRISPRi_t0_rep1


title: RA-90 GBM TS1156 ATAC-seq Alexidine

description: Library name: RA-90


title: ATAC-seq cortex Sham 2h rep1

description: Treatment:Sham;Degradation time:2h


title: RA-89 GBM TS1156 ATAC-seq GSK591

description: Library name: RA-89


title: SP49_NFR_CRISPRi_t14_rep4


title: SP49_NFR_CRISPRi_t14_rep3


title: ATAC-seq cortex Sham 0h rep3

description: Treatment:Sham;Degradation time:0h

value: Sham 0h


title: RA-88 GBM TS1156 ATAC-seq Rucaporib

description: Library name: RA-88


title: RA-86 GBM TS1156 ATAC-seq SirReal2

description: Library name: RA-86


title: ATAC-seq cortex Sham 0h rep2

description: Treatment:Sham;Degradation time:0h


title: RA-85 GBM TS1156 ATAC-seq CPI203

description: Library name: RA-85


title: SP49_NFR_CRISPRi_t14_rep2


title: RA-84 GBM TS1156 ATAC-seq ML228

description: Library name: RA-84


title: RA-98 GBM BT142 ATAC-seq CPI203

description: Library name: RA-98


title: RA-83 GBM TS1156 ATAC-seq Ciclopirox

description: Library name: RA-83


title: SP49_NFR_CRISPRi_t14_rep1


title: RA-82 GBM TS1156 ATAC-seq A485

description: Library name: RA-82


title: RA-81 GBM TS1156 ATAC-seq Decitabine

description: Library name: RA-81


title: Transplantation microglia, fluorescence-activated cell sorting, rep3

city: 厦门

first: 大典

last: 陈

address: 福建省厦门市翔安区翔安南路4221号

institute: 厦门大学

data_processing:
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
Used HISAT to align the clean reads to the reference genome.
Used Bowtie2 to align the clean reads to the reference genes.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include counts and RPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was purified from the isolated microglia using TRIzol reagent (Thermo Fisher Scientiﬁc, 15596018).
RNAwas used to produce thecDNAlibrary withSmart-Seq protocol. 1 ng of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Mice were fed with PLX3397 (Selleck, S7818, 600 mg/kg formulated in standard chow) to deplete microglia through three consecutive cycles, then discontinued from PLX3377 feed and transplanted microglia.

value: brain

value: microglia

value: fluorescence-activated cell sorting


title: Transplantation microglia, fluorescence-activated cell sorting, rep2

address: 福建省厦门市翔安区翔安南路4221号


title: RA-78 GBM TS600 ATAC-seq Hesperadin

description: Library name: RA-78


title: RA-79 GBM TS1156 ATAC-seq Control

description: Library name: RA-79

value: Control


title: SP49_NFR_CRISPRi_t0_rep3


title: RA-80 GBM TS1156 ATAC-seq PF06726304

description: Library name: RA-80


title: SP49_NFR_CRISPRi_t0_rep2


title: RA-76 GBM TS600 ATAC-seq GSK591

description: Library name: RA-76


title: SP49_NFR_CRISPRi_t0_rep1


title: RA-75 GBM TS600 ATAC-seq Rucaporib

description: Library name: RA-75


title: Transplantation microglia, fluorescence-activated cell sorting, rep1

address: 福建省厦门市翔安区翔安南路4221号


title: RA-87 GBM TS1156 ATAC-seq Gavinostat

description: Library name: RA-87

value: Gavinostat


title: RA-74 GBM TS600 ATAC-seq Gavinostat

description: Library name: RA-74


title: Resident microglia, fluorescence-activated cell sorting, rep3

address: 福建省厦门市翔安区翔安南路4221号


title: Resident microglia, fluorescence-activated cell sorting, rep4

address: 福建省厦门市翔安区翔安南路4221号


title: RA-71 GBM TS600 ATAC-seq ML228

description: Library name: RA-71


title: FHRCC85, adjacent normal kidney tissue

type: genomic

city: Sichuan

first: Hao

last: Zeng

address: Department of Urology, Third Inpatient Building, West China Hospital, Sichuan University, Chengdu,

institute: West China Hospital, Sichuan University

hyb_protocol: Bisulphite converted DNA was amplfied, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
Raw EPIC array data were processed using the ChAMP R/Bioconductor package with default settings.
processed data value: Average Beta

label: Cy3 and Cy5

source_name: kidney

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (gDNA) was treated with bisulfite using the EpiTect Fast Bisulfite Conversion Kits (59802, Qiagen). All samples were processed in the same batch.

value: kidney


title: FHRCC85, primary tumor


title: Transplantation microglia, fluorescence-activated cell sorting, rep4

address: 福建省厦门市翔安区翔安南路4221号


title: Resident microglia, fluorescence-activated cell sorting, rep2

address: 福建省厦门市翔安区翔安南路4221号


title: RA-72 GBM TS600 ATAC-seq CPI203

description: Library name: RA-72


title: FHRCC57, primary tumor


title: RA-69 GBM TS600 ATAC-seq A485

description: Library name: RA-69


title: RA-68 GBM TS600 ATAC-seq Decitabine

description: Library name: RA-68


title: ATAC-seq cortex Sham 0h rep1

description: Treatment:Sham;Degradation time:0h

value: cortex


title: Resident microglia, fluorescence-activated cell sorting, rep1

address: 福建省厦门市翔安区翔安南路4221号


title: SP49_NFR_CRISPRi_t0_rep4

value: Mantle cell lymphoma cell line


title: RA-77 GBM TS600 ATAC-seq Alexidine

description: Library name: RA-77

value: Alexidine


title: FHRCC79, adjacent normal kidney tissue


title: RA-67 GBM TS600 ATAC-seq PF06726304

description: Library name: RA-67


title: RA-65 GBM PDX59 ATAC-seq Hesperadin

description: Library name: RA-65

value: Hesperadin


title: RA-66 GBM TS600 ATAC-seq Control

description: Library name: RA-66


title: Primary microglial, cell culture, rep2

address: 福建省厦门市翔安区翔安南路4221号

value: cell culture


title: RA-64 GBM PDX59 ATAC-seq Alexidine

description: Library name: RA-64


title: RA-73 GBM TS600 ATAC-seq SirReal2

description: Library name: RA-73


title: RA-63 GBM PDX59 ATAC-seq GSK591

description: Library name: RA-63


title: FHRCC75, adjacent normal kidney tissue


title: RA-62 GBM PDX59 ATAC-seq Rucaporib

description: Library name: RA-62

value: Rucaporib


title: FHRCC75, primary tumor


title: Primary microglial, cell culture, rep1

address: 福建省厦门市翔安区翔安南路4221号


title: RA-59 GBM PDX59 ATAC-seq CPI203

description: Library name: RA-59


title: RA-70 GBM TS600 ATAC-seq Ciclopirox

description: Library name: RA-70

value: Ciclopirox


title: RA-60 GBM PDX59 ATAC-seq SirReal2

description: Library name: RA-60

value: Brain tumor


title: Healthy control 7

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

description:
Library name: H8
healthy TMJ

data_processing:
RNA-seq data analysis was performed using the Ion Torrent Software Suite version 5.4. The Torrent Mapping Alignment Program (TMAP) was used to align the raw sequencing reads generated by the Ion Torrent sequencing data against the reference sequence derived from the hg19 (GRCh37) assembly. The raw read counts of the targeted genes were normalized using the Fragments Per Kilobase Million (FPKM) normalization method. Principal component analysis (PCA) was performed using the indicated samples with R statistical software. Differentially expressed gene (DEG) analysis was performed using the DESeq2 R/Bioconductor package with raw read counts from the RNA sequencing data to identify the differentially expressed genes (DEGs) in each comparison of cell lines with CARD11 transfected against cell lines with empty vector transfected as well as of the patients with low (CARD11-) and high (CARD11+) CARD11 expressions
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Saliva

extract_protocol:
Total RNAs were extracted fromsaliva samples using the RNeasy kit (Qiagen, Hilden, Germany) using 700 μL saliva from each sample. The extracted RNA was then quantified using a NanoDrop spectrophotometer (ThermoFisher Scientific, USA) . All the extracted RNA was stored at -80 ºC.
Genomic DNA removal from RNA samples was ensured by treating the RNA with Turbo DNase (ThermoFisher Scientific, USA). Next, whole transcriptome sequencing was performed using targeted RNA-Seq with Ion AmpliSeq whole transcriptome human gene expression kit (ThermoFisher Scientific, USA). Briefly, cDNA was synthesized using a SuperScript VILO cDNA Synthesis kit (ThermoFisher Scientific, USA) and amplified using Ion AmpliSeq human gene expression core panel primers. The amplified products were subjected to enzymatic shearing to get amplicons of ~200 bp, then ligated with the adapter and the unique barcodes. Next, the constructed library was purified using Agencourt AMPure XP Beads (Beckman Coulter, USA), quantified using an Ion Library TaqMan™ quantitation kit (Applied Biosystems, USA), further diluted to 100 pM, and pooled equally with 16 individual samples. The diluted library was amplified and enriched in Ion Chef System (ThermoFisher Scientific) according to the manufacturer’s instructions. Ion 540 Chip was used to sequence the prepared template libraries using an Ion S5 XL Semiconductor sequencer (ThermoFisher Scientific).

value: Saliva


title: RA-61 GBM PDX59 ATAC-seq Gavinostat

description: Library name: RA-61

value: Glioblastoma


title: FHRCC81, primary tumor


title: Healthy control 6

description:
Library name: H7
healthy TMJ


title: FHRCC78, adjacent normal kidney tissue


title: RA-58 GBM PDX59 ATAC-seq ML228

description: Library name: RA-58


title: RA-57 GBM PDX59 ATAC-seq Ciclopirox

description: Library name: RA-57


title: RA-56 GBM PDX59 ATAC-seq A485

description: Library name: RA-56


title: FHRCC78, primary tumor


title: Healthy control 5

description:
Library name: H6
healthy TMJ


title: RA-55 GBM PDX59 ATAC-seq Decitabine

description: Library name: RA-55

value: Decitabine


title: FHRCC79, primary tumor


title: RA-52 GBM PDX43 ATAC-seq Hesperadin

description: Library name: RA-52


title: Healthy control 4

description:
Library name: H5
healthy TMJ


title: Healthy control 3

description:
Library name: H4
healthy TMJ


title: RA-54 GBM PDX59 ATAC-seq PF06726304

description: Library name: RA-54


title: FHRCC72, primary tumor


title: RA-51 GBM PDX43 ATAC-seq Alexidine

description: Library name: RA-51


title: RA-53 GBM PDX59 ATAC-seq Control

description: Library name: RA-53


title: Healthy control 2

description:
Library name: H2
healthy TMJ


title: RA-49 GBM PDX43 ATAC-seq Rucaporib

description: Library name: RA-49


title: RA-50 GBM PDX43 ATAC-seq GSK591

description: Library name: RA-50


title: Primary microglial, cell culture, rep3

address: 福建省厦门市翔安区翔安南路4221号

value: brain


title: FHRCC74, primary tumor


title: RA-47 GBM PDX43 ATAC-seq SirReal2

description: Library name: RA-47


title: Healthy control 1

description:
Library name: H1
healthy TMJ


title: RA-45 GBM PDX43 ATAC-seq ML228

description: Library name: RA-45


title: TMJOA7

description:
Library name: D4
TMJOA patient moderate  stage


title: RA-46 GBM PDX43 ATAC-seq CPI203

description: Library name: RA-46


title: RA-48 GBM PDX43 ATAC-seq Gavinostat

description: Library name: RA-48


title: TMJOA6

description:
Library name: D3
TMJOA patient moderate  stage


title: RA-44 GBM PDX43 ATAC-seq Ciclopirox

description: Library name: RA-44


title: RA-42 GBM PDX43 ATAC-seq Decitabine

description: Library name: RA-42


title: RA-43 GBM PDX43 ATAC-seq A485

description: Library name: RA-43


title: FHRCC77, adjacent normal kidney tissue


title: FHRCC77, primary tumor


title: RA-41 GBM PDX43 ATAC-seq PF06726304

description: Library name: RA-41


title: TMJOA5

description:
Library name: D2
TMJOA patient moderate  stage


title: RA-40 GBM PDX43 ATAC-seq Control

description: Library name: RA-40


title: FHRCC72, adjacent normal kidney tissue


title: RA-39 GBM PDX22 ATAC-seq Hesperadin

description: Library name: RA-39


title: FHRCC70, primary tumor


title: RA-38 GBM PDX22 ATAC-seq Alexidine

description: Library name: RA-38


title: TMJOA3

description:
Library name: DL3
TMJOA patient advance stage


title: TMJOA4

description:
Library name: D1
TMJOA patient moderate  stage


title: FHRCC71, primary tumor


title: RA-36 GBM PDX22 ATAC-seq Rucaporib

description: Library name: RA-36


title: FHRCC56, adjacent normal kidney tissue


title: FHRCC70, adjacent normal kidney tissue


title: RA-37 GBM PDX22 ATAC-seq GSK591

description: Library name: RA-37


title: TMJOA2

description:
Library name: DL2
TMJOA patient advance stage


title: FHRCC74, adjacent normal kidney tissue


title: RA-35 GBM PDX22 ATAC-seq Gavinostat

description: Library name: RA-35


title: RA-33 GBM PDX22 ATAC-seq CPI203

description: Library name: RA-33

value: Lost pellet


title: TMJOA1

description:
Library name: DL1
TMJOA patient advance stage


title: FHRCC52, adjacent normal kidney tissue


title: RA-34 GBM PDX22 ATAC-seq SirReal2

description: Library name: RA-34


title: FHRCC66, primary tumor


title: RA-32 GBM PDX22 ATAC-seq ML228

description: Library name: RA-32


title: Carcinoma_In_Situ_8

description:
Library name: CIS8
Carcinoma_In_Situ_Processed_Data.txt

source_name: Carcinoma In Situ

extract_protocol:
Three sequential sections, each 3µm thick, from formalin-fixed paraffin-embedded (FFPE) tissue biopsies from the cases mentioned in Table 4 were subjected to RNA extraction using the Recover All kit according to the manufacturer’s instructions (ThermoFisher Scientific, USA). Genomic DNA was removed from all RNA samples by treating the extracted RNA with the TURBO DNAase-free™ Kit (Invitrogen, Carlsbad, CA, USA).
A total of 100 ng of extracted and Turbo DNase treated RNAs, was utilized for whole transcriptome sequencing from 29 endoscopic biopsy samples. This was accomplished utilizing a targeted AmpliSeqTranscriptome Panel, meticulously designed to target over 21,000 human RNA transcripts through a high-throughput multiplexed approach on the Ion S5 XL Semiconductor Sequencer (Thermo Fisher Scientific, USA) equipped with the Ion 540 Chip (Life Technologies, Carlsbad, CA, USA). In summary, the total RNA underwent processing using the SuperScript VILO cDNA synthesis kit (Invitrogen; 11754050), followed by amplification of the resulting DNA using the lon AmeliSeq™ Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific; A26325) for library preparation. Subsequently, the libraries underwent purification using Agencourt AM-Rute XP Beads (Beckman Coulter, Indianapolis, IN, USA) and quantification employing the lon Library TaqMan™ Quantitation Kit (Applied Biosystems, Waltham, MA, USA). The libraries were diluted to -100 pM and pooled by combining equal volumes of each barcoded library. The resulting template libraries were then sequenced on the Ion S5 XL Semiconductor sequencer using the Ion 540 Chip (Life Technologies Corporation, Carlsbad, CA) prepared on fully automated Ion Chef System (Thermo Fisher Scientific).

value: Carcinoma In Situ

tag: tissue type

value: High Dysplesia Carcinoma In Situ


title: FHRCC67, primary tumor

tag: tissue


title: RA-30 GBM PDX22 ATAC-seq A485

description: Library name: RA-30

tag: cell type


title: Carcinoma_In_Situ_7

description:
Library name: CIS7
Carcinoma_In_Situ_Processed_Data.txt


title: FHRCC65, primary tumor


title: RA-29 GBM PDX22 ATAC-seq Decitabine

description: Library name: RA-29

tag: treatment


title: RA-28 GBM PDX22 ATAC-seq PF06726304

description: Library name: RA-28


title: RA-31 GBM PDX22 ATAC-seq Ciclopirox

description: Library name: RA-31


title: RA-27 GBM PDX22 ATAC-seq Control

description: Library name: RA-27

value: Control


title: Carcinoma_In_Situ_6

description:
Library name: CIS6
Carcinoma_In_Situ_Processed_Data.txt


title: Carcinoma_In_Situ_5

description:
Library name: CIS5
Carcinoma_In_Situ_Processed_Data.txt


title: FHRCC65, adjacent normal kidney tissue

value: kidney


title: Carcinoma_In_Situ_4

description:
Library name: CIS4
Carcinoma_In_Situ_Processed_Data.txt


title: RA-26 GBM HK281 ATAC-seq Hesperadin

description: Library name: RA-26


title: hSC40 cells, Combo, replicate 3

city: Singapore

first: Xing Yi

last: Woo

address: 30 Biopolis Street #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute, A*STAR

description: Library name: h40_c_COM

data_processing:
Whole transcriptome sequencing of cell lines was performed on the Illumina NovaSeq platform (Novogene, Singapore) using the standard Illumina RNA-seq protocol. Cutadapt (3.4) was used to perform quality and adapter trimming. STAR (2.7.10a) was used as the aligner, and RSEM (1.3.1) was used as the quantification tool to generate the count matrix.
R (4.3.1) was used for downstream post processing analyses. For differential expression gene analysis and batch correction, edgeR (4.0.9) was used. Genes with <10 counts were discarded before scaling factors to convert raw library sizes to a normalized effective library sizes was carried out. Subsequent analyses were done using PCAtools (2.14.0), clusterProfiler (4.10.1), fgsea (1.28.0) and msigdbr (7.5.1). Heatmaps were visualized using pheatmap (1.0.12).
Assembly: GRCh38
Supplementary files format and content: All files are in a tsv format.

extract_protocol:
RNA was extracted and purified with RNeasy Mini kit (Qiagen). At least 0.5𝑢g of total RNA was used for the construction of sequencing library.
Extracted RNA was converted into RNA sequencing library using the NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB) using manufacturer’s instructions.

value: dedifferentiated liposarcoma

value: AZD5153 + Pazopanib


title: RA-25 GBM HK281 ATAC-seq Alexidine

description: Library name: RA-25

value: Alexidine


title: Carcinoma_In_Situ_3

description:
Library name: CIS3
Carcinoma_In_Situ_Processed_Data.txt


title: FHRCC64, primary tumor


title: RA-24 GBM HK281 ATAC-seq GSK591

description: Library name: RA-24


title: Carcinoma_In_Situ_2

description:
Library name: CIS2
Carcinoma_In_Situ_Processed_Data.txt


title: hSC40 cells, Combo, replicate 1

description: Library name: h40_a_COM


title: FHRCC64, adjacent normal kidney tissue


title: RA-23 GBM HK281 ATAC-seq Rucaporib

description: Library name: RA-23


title: Carcinoma_In_Situ_1

description:
Library name: CIS1
Carcinoma_In_Situ_Processed_Data.txt


title: FHRCC60, primary tumor


title: hSC40 cells, Pazopanib, replicate 3

description: Library name: h40_c_PAZ

value: Pazopanib


title: hSC40 cells, Pazopanib, replicate 2

description: Library name: h40_b_PAZ


title: Adenocarcinoma_11

description:
Library name: CA11
Carcinoma_Processed_Data.txt

source_name: Carcinoma

value: Carcinoma

value: Adenocarcinoma


title: Adenocarcinoma_10

description:
Library name: CA10
Carcinoma_Processed_Data.txt


title: RA-21 GBM HK281 ATAC-seq SirReal2

description: Library name: RA-21


title: hSC40 cells, Pazopanib, replicate 1

description: Library name: h40_a_PAZ


title: RA-20 GBM HK281 ATAC-seq CPI203

description: Library name: RA-20


title: THP1-LPS

type: RNA

city: Innsbruck

first: Pablo

last: Monfort-Lanzas

address: Innrain 80-82

department: Medical Biochemistry

country: Austria

institute: Medical University Innsbruck

description: Gene expression data from EtOH (solvent control)-treated THP1 cells.

hyb_protocol: Hybridization solution was prepared as per Affymetrix’s GeneChip Expression Analysis Technical Manual. The final concentration of cRNA was 60 ng/µl. Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), controlled by Affymetrix’s software GeneChip Operating System (GCOS) v1.4.

data_processing: RMA using R 4.2.0 with the affy 1.74.0 package.

label: biotin

source_name: THP1 cells treated with EtOH (solvent control)

label_protocol: cDNA synthesis and in vitro-transcription were performed using Ambion’s Message Amp II 96 Kit (Cat. No. 1819) according to the manufacturer’s instructions, starting with 1 µg of total RNA.

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FCS and 2 mM L-glutamine. THP1-Blue cells additionally contained 200 µg/ml zeocin.

extract_protocol: Cells were harvested by centrifugation and total RNA was extracted using the Qiagen RNeasy Mini Kit with a DNase digest step. RNA quality was assessed by 18S/28S ribosomal RNA band intensities on an agarose gel.

treatment_protocol: THP-1 cells were treated with LPS [1 µg/ml] plus BB3 extract (25 µg/ml and 50 µg/ml) or vehicle control plus LPS for 24 hours.

value: EtOH


title: Adenocarcinoma_9

description:
Library name: CA9
Carcinoma_Processed_Data.txt


title: FHRCC59, primary tumor


title: FHRCC60, adjacent normal kidney tissue


title: hSC40 cells, AZD5153, replicate 3

description: Library name: h40_c_AZD


title: FHRCC59, adjacent normal kidney tissue


title: FHRCC43, adjacent normal kidney tissue


title: RA-19 GBM HK281 ATAC-seq ML228

description: Library name: RA-19

value: Brain tumor


title: Adenocarcinoma_8

description:
Library name: CA8
Carcinoma_Processed_Data.txt


title: THP1-LPS-HEP

description: Gene expression data from triphala-treated THP1 cells.

source_name: THP1 cells treated with triphala

value: Triphala


title: hSC40 cells, Combo, replicate 2

description: Library name: h40_b_COM


title: FHRCC58, adjacent normal kidney tissue


title: hSC40 cells, AZD5153, replicate 2

description: Library name: h40_b_AZD


title: FHRCC58, primary tumor


title: Adenocarcinoma_7

description:
Library name: CA7
Carcinoma_Processed_Data.txt


title: hSC40 cells, AZD5153, replicate 1

description: Library name: h40_a_AZD


title: RA-18 GBM HK281 ATAC-seq Ciclopirox

description: Library name: RA-18

value: Glioblastoma

value: Ciclopirox


title: RA-22 GBM HK281 ATAC-seq Gavinostat

description: Library name: RA-22

value: Gavinostat


title: Adenocarcinoma_6

description:
Library name: CA6
Carcinoma_Processed_Data.txt


title: RA-17 GBM HK281 ATAC-seq A485

description: Library name: RA-17


title: FHRCC57, adjacent normal kidney tissue


title: RA-16 GBM HK281 ATAC-seq Decitabine

description: Library name: RA-16

value: Decitabine


title: hSC40 cells, untreated, replicate 3

description: Library name: h40_c_NT

value: Untreated


title: Adenocarcinoma_5

description:
Library name: CA5
Carcinoma_Processed_Data.txt


title: hSC40 cells, untreated, replicate 2

description: Library name: h40_b_NT


title: FHRCC44, primary tumor


title: Adenocarcinoma_4

description:
Library name: CA4
Carcinoma_Processed_Data.txt


title: RA-15 GBM HK281 ATAC-seq PF06726304

description: Library name: RA-15


title: FHRCC56, primary tumor


title: Adenocarcinoma_3

description:
Library name: CA3
Carcinoma_Processed_Data.txt


title: hSC40 cells, untreated, replicate 1

description: Library name: h40_a_NT


title: RA-14 GBM HK281 ATAC-seq Control

description: Library name: RA-14


title: LPS141 cells, Combo, replicate 3

description: Library name: L141_c_COM


title: Adenocarcinoma_2

description:
Library name: CA2
Carcinoma_Processed_Data.txt


title: RA-13 GBM G83 ATAC-seq Hesperadin

description: Library name: RA-13

value: Hesperadin


title: LPS141 cells, Combo, replicate 2

description: Library name: L141_b_COM


title: Adenocarcinoma_1

description:
Library name: CA1
Carcinoma_Processed_Data.txt


title: RA-12 GBM G83 ATAC-seq Alexidine

description: Library name: RA-12


title: FHRCC52, primary tumor


title: LPS141 cells, Combo, replicate 1

description: Library name: L141_a_COM


title: Tubular_Adenoma_10

description:
Library name: AD10
Adenoma_Processed_Data.txt

source_name: Adenoma

value: Adenoma

value: Tubular adenomas


title: FHRCC46, primary tumor

value: kidney


title: LPS141 cells, Pazopanib, replicate 3

description: Library name: L141_c_PAZ

value: dedifferentiated liposarcoma


title: RA-10 GBM G83 ATAC-seq Rucaporib

description: Library name: RA-10

value: Rucaporib


title: RA-11 GBM G83 ATAC-seq GSK591

description: Library name: RA-11


title: LPS141 cells, Pazopanib, replicate 2

description: Library name: L141_b_PAZ

value: Pazopanib


title: Tubular_Adenoma_9

description:
Library name: AD9
Adenoma_Processed_Data.txt


title: FHRCC48, primary tumor


title: FHRCC46, adjacent normal kidney tissue


title: LPS141 cells, Pazopanib, replicate 1

description: Library name: L141_a_PAZ


title: Tubular_Adenoma_8

description:
Library name: AD8
Adenoma_Processed_Data.txt


title: RA-9 GBM G83 ATAC-seq Gavinostat

description: Library name: RA-9


title: RA-8 GBM G83 ATAC-seq SirReal2

description: Library name: RA-8


title: LPS141 cells, AZD5153, replicate 3

description: Library name: L141_c_AZD


title: FHRCC38, primary tumor


title: RA-7 GBM G83 ATAC-seq CPI203

description: Library name: RA-7


title: FHRCC53, adjacent normal kidney tissue


title: LPS141 cells, AZD5153, replicate 2

description: Library name: L141_b_AZD


title: RA-6 GBM G83 ATAC-seq ML228

description: Library name: RA-6


title: FHRCC40, primary tumor


title: Tubular_Adenoma_5

description:
Library name: AD5
Adenoma_Processed_Data.txt


title: LPS141 cells, AZD5153, replicate 1

description: Library name: L141_a_AZD


title: FHRCC39, primary tumor


title: RA-5 GBM G83 ATAC-seq Ciclopirox

description: Library name: RA-5


title: LPS141 cells, untreated, replicate 3

description: Library name: L141_c_NT


title: Tubular_Adenoma_4

description:
Library name: AD4
Adenoma_Processed_Data.txt


title: FHRCC53, primary tumor


title: RA-4 GBM G83 ATAC-seq A485

description: Library name: RA-4


title: LPS141 cells, untreated, replicate 2

description: Library name: L141_b_NT


title: Tubular_Adenoma_3

description:
Library name: AD3
Adenoma_Processed_Data.txt


title: Tubular_Adenoma_7

description:
Library name: AD7
Adenoma_Processed_Data.txt


title: RA-2 GBM G83 ATAC-seq PF06726304

description: Library name: RA-2


title: Tubular_Adenoma_1

description:
Library name: AD1
Adenoma_Processed_Data.txt


title: Karpas422_tiling_CRISPRi_t14_rep3

value: Diffuse large B-cell lymphoma cell line


title: RA-3 GBM G83 ATAC-seq Decitabine

description: Library name: RA-3


title: FHRCC36, primary tumor


title: LPS141 cells, untreated, replicate 1

description: Library name: L141_a_NT


title: FHRCC29, primary tumor


title: Tubular_Adenoma_6

description:
Library name: AD6
Adenoma_Processed_Data.txt


title: Karpas422_tiling_CRISPRi_t14_rep2


title: RA-1 GBM G83 ATAC-seq Control

description: Library name: RA-1

value: Control


title: E11.5 neural tube/somites

first: Teodorus Theo

last: Susanto

address: 60 Biopolis St

institute: Genome Institute of Singapore

data_processing:
HiFi reads generated by Genome Sequencing Service Center at Stanford University
minimap2, 2.24-r1122, -ax splice:hq -uf GRCm39.genome.mmi somite_neural-tube.hifi_reads.demux.5p--3p.flnc.fastq
samtools, 1.16.1, sort -o somite_neural-tube.bam
isoquant, 3.1.2, --reference GRCm39.genome.fa --genedb gencode.vM32.chr_patch_hapl_scaff.annotation.gtf --complete_genedb --bam somite_neural-tube.bam --data_type pacbio_ccs --output /out
Assembly: GRCm39
Supplementary files format and content: .tsv file that contains tpm quantification of discovered isoforms as part of transcript discovery outpout from isoquant

molecule: polyA RNA

source_name: neural tube/somites

growth_protocol: To generate E11.5 embryos, a male was housed with one or two females and the females monitored for vaginal plug formation.  On the day a plug was observed, the female was considered to be pregnant at E0.5. Embryos were harvested from the pregnant female at E11.5 and the limb buds and neural tube/somites dissected in filming media

extract_protocol:
Tissue was then rapidly ground by hand for 30 seconds on ice with a disposable RNAse free microcentrifuge pestle. Immediately after, 1 mL of  TRIzol reagent was added. The sample was lysed and mixed by vigorously inverting the tube several times, and then had the total RNA extracted following the manufacturer’s protocol, using a cleanup column instead of ethanol precipitation. Subsequently, the RNA were treated with TurboDNAse at 37 °C for 30 minutes and cleaned up using a column.
PolyA-selected Iso-seq library was made using SMRTbell 3.0 kit, following PacBio's protocol.

treatment_protocol: No treatment was performed

value: neural tube/somites

value: FVB/NJ


title: FHRCC37, primary tumor


title: Forelimb, D23, H3K4me3, biol rep 2, ChIP

city: Seville

first: Ismael

last: Sospedra-Arrufat

address: Carretera de Utrera km1, UPO

country: Spain

institute: CABD

description: ChIPmentation

data_processing:
Basecalling was performed using FastQC 0.11.9
Pig ChIP-seq libraries were sequenced 50-bp paired-end, except for H3K4me1. This last, together with mouse libraries were sequenced 100-bp paired-end reads, and subsequently cropped to 50-bp from 3' end with Trimmomatic 0.39.
Paired-end reads were aligned to GRCm38/mm10 mouse assembly or susScrofa11.1/susScr11 pig assembly using Bowtie2 2.3.5.
SAM to BAM conversions were performed using Samtools 1.9 with read deduplication using the ‘rmdup’ command.
BAM to BigWig conversions were performed using bamCoverage tool from Deeptools 3.5 toolkit, with the normalization option set for ‘RPKM’ (Reads Per Kilobase per Million mapped reads).
Peakcalling was performed using the IDR framework (idr 0.1 version) on BED files from biological replicate pairs, with a global IDR <0.01 cut-off, and ‘broad’ peaks parameters.
Assembly: Mouse GRCm38/mm10 or pig SusScrofa11.1/susScr11
Supplementary files format and content: BigWig, BED.

organism: Sus scrofa

source_name: Forelimb

growth_protocol: Wild-type mouse and pig embryos were generated by natural matting and collected on desired gestational day.

extract_protocol:
Nuclei homogenization was performed mechanically and chromatin crosslinking at 1% formaldehyde for 5 min at RT. Chromatin was sonicated (300-500 bp DNA smear) using a Covaris M220 sonicator.
ChIP-seq libraries were generated using NEBNext High-Fidelity 2x PCR Master Mix (NEB). The optimum number for enrichment cycles for each library was determined empirically by qPCR, using the same kit, and 1 μL of each ChIP per 10 μL reaction. DNA concentration was quantified by Qbit (Invitrogen).

value: Forelimb

value: wild-type

tag: Stage

tag: chip antibody

value: anti-H3K4me3 (Abcam ab8580)

tag: replicate


title: Karpas422_tiling_CRISPRi_t14_rep1

tag: cell line


title: Forelimb, D23, H3K4me3, biol rep 1, ChIP

description: ChIPmentation


title: TSC2null_RMC6272_Total_rep2

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

description: total mRNA

data_processing:
BBmap (v. 36.59)(parameters: k = 13, ktrim=n, useshortkmers=t, mink = 5, qtrim=t, trimq = 10, minlength = 25) was used to trim reads for adapter sequences and low-quality base calls. The resulting reads were aligned to the human reference genome (build hg38) using HISAT2 (v.2.0.4). The aligned reads were summarized using the "featureCounts" function of the RSubread (v.2.6.4) R/Bioconductor package and the reads were assigned using the GCF_000001405.40_GRCh38.p14 GTF annotation containing only protein coding genes from the RefSeq database (parameters:ignoreDup=FALSE, useMetaFeatures=TRUE, countMultiMappingReads=FALSE).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw gene counts for every gene and every sample.

source_name: iPSC derived NPC

growth_protocol: To achieve TSC2 patient-derived neural progenitor cells (NPCs), including TSC2-null (-/-) and CRISPR-corrected TSC2-WT (+/+), along with culture conditions we followed the same cloning and transfection strategy as we previously reported for TSC1 corrected-WT iPSCs described in Martin P, Wagh V, Reis SA, Erdin S, Beauchamp RL, Shaikh G, et al. TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling. Mol Autism. 2020;11:2.

extract_protocol:
Fractions corresponding to mRNA associated with more than two ribosomes were pooled and the RNA extracted using TRIzol (ThermoFisher) according to the manufacturer’s protocol. 10% of the lysate was removed from the extract prior to loading on the sucrose gradient, extracted using TRIzol, and denoted as total RNA.
Illumina v2.5 Kit

treatment_protocol: TSC2 NPC lines were treated for 2h with 10 nM RMC-6272, 50 nM EFT-508 or DMSO as a vehicle control followed by cell lysis

tag: Sex

value: female

value: iPSC derived NPC


title: TSC2null_RMC6272_Total_rep1

description: total mRNA


title: Karpas422_tiling_CRISPRi_t0_rep3


title: FHRCC33, primary tumor


title: FHRCC30, primary tumor


title: FHRCC42, primary tumor


title: Karpas422_tiling_CRISPRi_t0_rep2


title: Forelimb, D23, H3K4me1, biol rep 2, ChIP

description: ChIPmentation

value: anti-H3K4me1 (Abcam ab8895)


title: Tubular_Adenoma_2

description:
Library name: AD2
Adenoma_Processed_Data.txt


title: TSC2null_RMC6272_Poly_rep1

description: polysome associated mRNA

data_processing:
BBmap (v. 36.59)(parameters: k = 13, ktrim=n, useshortkmers=t, mink = 5, qtrim=t, trimq = 10, minlength = 25) was used to trim reads for adapter sequences and low-quality base calls. The resulting reads were aligned to the human reference genome (build hg38) using HISAT2 (v.2.0.4). The aligned reads were summarized using the "featureCounts" function of the RSubread (v.2.6.4) R/Bioconductor package and the reads were assigned using the GCF_000001405.40_GRCh38.p14 GTF annotation containing only protein coding genes from the RefSeq database (parameters:ignoreDup=FALSE, useMetaFeatures=TRUE, countMultiMappingReads=FALSE).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw gene counts for every gene and every sample.
Library strategy: Polysome-seq


title: Forelimb, D23, H3K4me1, biol rep 1, ChIP

description: ChIPmentation


title: FHRCC35, primary tumor


title: FHRCC32, primary tumor


title: FHRCC26, adjacent normal kidney tissue


title: FHRCC26, primary tumor


title: Karpas422_tiling_CRISPRi_t0_rep1


title: TSC2null_eFT508_Total_rep2

description: total mRNA


title: Forelimb, D23, H3K27ac, biol rep 2, ChIP

description: ChIPmentation

value: anti-H3K27ac (Abcam, ab4729)


title: SP49_tiling_CRISPRi_t14_rep2

value: Mantle cell lymphoma cell line


title: Forelimb, D23, H3K27ac, biol rep 1, ChIP

description: ChIPmentation


title: TSC2null_eFT508_Total_rep1

description: total mRNA


title: FHRCC28, adjacent normal kidney tissue


title: SP49_tiling_CRISPRi_t14_rep1


title: SP49_tiling_CRISPRi_t0_rep2


title: Midgut, adult, on-Tc, rep3

city: Kerrville

first: Mackenzie

last: Tietjen

state: TX

address: 2700 Fredericksburg Rd

department: Knipling-Bushland US Livestock Insects Research Laboratory

institute: USDA-ARS

description: Library name: ATT3_2_S14_R1_001

data_processing:
Reads were trimmed using Trimmomatic and aligned to the genome using STAR aligner. Counts were obtained using featureCounts and differential expression analysis was completed using DESeq2
Assembly: GCA_004302925.2
Supplementary files format and content: raw read counts of all samples for all genes tested in txt file

organism: Cochliomyia hominivorax

source_name: midgut

extract_protocol:
RNA was isolated from guts using Zymo Directzol (ZR2070, Research Co.)
cDNA libraries were synthesized using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7775)

value: midgut


title: TSC2null_eFT508_Poly_rep3

description: polysome associated mRNA


title: Midgut, adult, on-Tc, rep2

description: Library name: ATT2_1_S9_R1_001


title: TSC2null_RMC6272_Poly_rep2

description: polysome associated mRNA


title: FHRCC28, primary tumor

value: kidney


title: FHRCC27, primary tumor


title: TSC2null_eFT508_Poly_rep2

description: polysome associated mRNA


title: SP49_tiling_CRISPRi_t0_rep1


title: Midgut, adult, on-Tc, rep1

description: Library name: ATT1_2_S1_R1_001


title: TSC2null_eFT508_Poly_rep1

description: polysome associated mRNA


title: FHRCC27, adjacent normal kidney tissue


title: Granta519_tiling_CRISPRi_t14_rep1


title: TSC2null_eFT508_Total_rep3

description: total mRNA


title: Midgut, adult, control, rep2

description: Library name: ATN2_1_S11_R1_001


title: TSC2null_DMSO_Total_rep3

description: total mRNA

value: DMSO


title: Granta519_tiling_CRISPRi_t0_rep2


title: FHRCC12, primary tumor


title: TSC2null_DMSO_Total_rep2

description: total mRNA


title: Midgut, adult, control, rep1

description: Library name: ATN1_2_S10_R1_001


title: Granta519_tiling_CRISPRi_t0_rep1


title: TSC2null_DMSO_Total_rep1

description: total mRNA


title: Midgut, adult, post-Tc, rep3

description: Library name: AT03_1_S19_R1_001


title: FHRCC23, adjacent normal kidney tissue


title: Midgut, adult, post-Tc, rep2

description: Library name: AT02_2_S18_R1_001


title: Brown adipose tissue, cotadutide, mouse5

city: Gaithersburg

first: Rhianna

last: Laker

address: One Medimmune Way

department: eCVRM

institute: AstraZeneca

description: Library name: Cota 5 BAT D7

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software
Adaptor sequences were removed using Trimmomatic v.0.36
Short sequencing reads were mapped to the mouse genome (mm10) using STAR v.2.5.2b
Read counts were calculated using featureCounts from Subread v.1.5.2
Assembly: mm10
Supplementary files format and content: Tab delimited text file for each sample contains raw counts

source_name: Brown adipose tissue

growth_protocol: Male DIO C57Bl/6J at 14 weeks of age and acclimated for 3 weeks. Mice were weighed and maintained on 60% high fat diet until around ~50 g/mouse. Mice were single housed with ad libitum access to high fat food and water (automated watering system). Mice were not housed at thermoneutrality.

extract_protocol:
RNA was isolated from 30 mg of BAT. Samples were homogenized in 800 ul Trizol, incubated for 5 min and fat layer removed. An additional 200 ul of trizol was added to the homogenate followed by 200 ul 1-bromo-3-chloropropane (BCP). Samples were mixed, incubated at RT for 10 min and centrifuged at 12,000xg for 14 min at 4C. The aqueous phase was transferred to a new tube and 600 ul of 70% ethanol added. Samples were then transferred to an RNeasy Mini spin column, centrifuged at 10,000xg for 15s followed by 700 ul Buffer RW1 and centrifuged. Eighty ul of DNase was added to the column and incubated at RT for 15 min followed by 500ul RPE and centrifuged. RPE wash was performed a second time and the spin column was placed in a new tube. 30 ul of water was applied to the column and centrifuged at 10,000xg for 1 min to elute RNA
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples received were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: On the starting day of the study (Day 0), animals were injected daily SC with vehicle or Cotadutide  for 28 days.

value: Brown adipose tissue

tag: model

value: Diet-induced obese

value: Cotadutide


title: Brown adipose tissue, cotadutide, mouse4

description: Library name: Cota 4 BAT D6


title: TSC2null_DMSO_Poly_rep3

description: polysome associated mRNA


title: TSC2null_DMSO_Poly_rep1

description: polysome associated mRNA


title: FHRCC21, adjacent normal kidney tissue


title: Granta519_tiling_CRISPRi_t14_rep2


title: Brown adipose tissue, cotadutide, mouse2

description: Library name: Cota 2 BAT D4


title: Midgut, adult, post-Tc, rep1

description: Library name: AT01_2_S15_R1_001


title: FHRCC21, primary tumor


title: Midgut, adult, control, rep3

description: Library name: ATN3_2_S17_R1_001


title: Brown adipose tissue, cotadutide, mouse3

description: Library name: Cota 3 BAT D5


title: FHRCC12, adjacent normal kidney tissue


title: Midgut, larva, on-Tc, rep3

description: Library name: TT3_2_S12_R1_001


title: Midgut, larva, on-Tc, rep2

description: Library name: TT2_1_S3_R1_001


title: WT_RMC6272_Total_rep2

description: total mRNA

value: TSC2-Corrected WT


title: FHRCC22, adjacent normal kidney tissue


title: Brown adipose tissue, vehicle, mouse4

description: Library name: Vehicle 4 BAT C8

value: Vehicle


title: FHRCC22, primary tumor


title: TSC2null_DMSO_Poly_rep2

description: polysome associated mRNA


title: WT_RMC6272_Total_rep1

description: total mRNA


title: FHRCC20, primary tumor


title: Brown adipose tissue, cotadutide, mouse1

description: Library name: Cota 1 BAT D1


title: WT_RMC6272_Poly_rep2

description: polysome associated mRNA


title: Midgut, larva, control, rep2

description: Library name: TN2_1_S16_R1_001


title: FHRCC16, adjacent normal kidney tissue


title: Midgut, larva, control, rep3

description: Library name: TN3_1_S20_R1_001


title: Brown adipose tissue, vehicle, mouse3

description: Library name: Vehicle 3 BAT C5


title: Midgut, larva, control, rep1

description: Library name: TN1_1_S4_R1_001


title: WT_eFT508_Total_rep3

description: total mRNA


title: WT_RMC6272_Poly_rep1

description: polysome associated mRNA


title: FHRCC23, primary tumor


title: FHRCC16, primary tumor


title: FHRCC15, adjacent normal kidney tissue


title: WT_eFT508_Total_rep2

description: total mRNA


title: Midgut, larva, post-Tc, rep2

description: Library name: T02_1_S6_R1_001


title: Brown adipose tissue, vehicle, mouse1

description: Library name: Vehicle 1 BAT C2


title: Midgut, larva, post-Tc, rep3

description: Library name: T03_2_S13_R1_001


title: FGF_Neurog2_4 [RNA-Seq]

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

address: Großhaderner Straße 9

department: Department of Cell Biology and Anatomy III

country: Germany

institute: Biomedical Center (BMC),LMU - Munich

data_processing:
We checked the quality of the raw FASTQ reads using FastQC.
Mapping the raw paired-end FASTQ files to the mouse reference genome (mm10) using the STAR RNA-seq aligner (version 2.7.2b)
Quantifying the aligned reads in the BAM files by HTSeq-count (version 0.9.1) based on the annotation file GENCODE Release M25 (GRCm38.p6)
Importing the gene-level count matrix into the R/Bioconductor package DESeq2 (version 1.36.0) for normalization and differential expression with FC > 2 and adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: Excel tables (.xlsx) containing rlog normalized gene counts for each sample

source_name: Cortex (Grey matter)

growth_protocol: Following decapitation of postnatal (P5-P6) wild-type C57BL/6J mice, the skin and the skull were removed, and the brain was extracted avoiding any tissue damage and placed into the 10 mM HEPES solution for dissection. After separating the two hemispheres, the meninges were removed and a piece of cerebral cortex was dissected using fine forceps and collected in a tube with astrocyte medium (Fetal calf serum-FCS (10% (v/v); Horse serum-HS (5% (v/v)); glucose (3,5 mM); B27 supplement; Penicillin/Streptomycin (final dilution 1:100) in DMEM/F12+GlutaMAX). Tissue was mechanical dissociated with a 5 ml pipette and placed into uncoated plastic flasks for cell expansion in astrocyte medium supplemented with two growth factors EGF (10 ng/ml) +FGF (10 ng/ml) or with the FGF (10 ng/ml) only as specified for each experiment. After 4-5 days, the medium was exchanged and supplied with the fresh growth factors. After 10 days of culturing, cultured cells were rinsed with DPBS and contaminating oligodendrocyte precursor cells were removed by brusquely shaking the culture flasks several times. Astroglial cells were then detached from the flask by trypsinization and seeded onto poly-D-lysine (PDL)-coated glass coverslips at a density of 8x104 cells per well in a 24-well plate with astrocyte medium.

extract_protocol:
Astrocytes were collected by trypsinization 48 h after retroviral transduction, washed, resuspended in DPBS and analysed using a FACS Aria II instrument (BD Biosciences) in the FACSFlowTM medium. Debris and aggregated cells were gated out by forward-scatter area (FSC-A) and side-scatter area (SSC-A). Forward scatter area (FSC-A) vs. forward scatter width (FSC-W) was used to discriminate doublets from single cells. To set the gates for the sorting, untransduced astrocytes were recorded. Sorted cells were collected in the DPBS, counted and divided into two batches: 50000 cells were immediately processed for the ATAC-seq and the remainder of the cells were collected for the RNA-seq library preparation.
Sorted cells were resuspended in 100 μl of extraction buffer from PicoPureTM RNA isolation kit (Thermo Fischer Scientific) and the RNA was extracted according to the manufacturer’s protocol. The Agilent 2100 Bioanalyzer was used to assess RNA quality and concentration. For the RNA-seq library preparation, only high-quality RNA with the RIN value >8 was used. cDNA was synthesized from 10 ng of total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), according to the manufacturer's instructions. The total number of amplification cycles was determined by RT-qPCR side reaction according to manufacturer’s instruction. PCR-amplified cDNA was purified by immobilization on AMPure XP beads. Prior to generating the final library for the sequencing, the Covaris AFA system was used to perform the cDNA shearing in Covaris microtubes (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm), resulting in 200-500 bp long cDNA fragments that were subsequently purified by ethanol precipitation. The quality and concentration of the sheared cDNA were assessed on Agilent 2100 Bioanalyzer before proceeding to library preparation using MicroPlex Library Preparation kit v2 (Diagenode) following user manual. Final libraries were evaluated using an Agilent 2100 Bioanalyzer and the concentration was measured with Qubit Fluorometer (Thermo Fischer Scientific). The uniquely barcoded libraries were multiplexed onto one lane and 100-bp paired-end deep sequencing was carried out at the HiSeq 4000 (Illumina) generating ~20 million reads per sample.

treatment_protocol: For the RNA-seq experiments, the cells were kept in the astrocyte medium and collected 48 h after viral transduction (Control, Hmgb2, Neurog2, or  Neurog2+Hmgb2 transcription factor). Astrocytes were detached from the flask by trypsinization, prepared for the FACS and sorted for the following RNA-seq experiments according to the fluorophore expression.

value: Cortex (Grey matter)

value: Primary culture

value: Astrocytes

value: Wildtype

value: Neurog2 overexpression/bFGF


title: WT_eFT508_Total_rep1

description: total mRNA

value: female

value: iPSC derived NPC


title: FHRCC15, primary tumor


title: FHRCC13, primary tumor


title: Midgut, larva, on-Tc, rep1

description: Library name: LTT1_2_S2_R1_001


title: WT_eFT508_Poly_rep3

description: polysome associated mRNA


title: FGF_Neurog2_3 [RNA-Seq]


title: Midgut, larva, post-Tc, rep1

description: Library name: T01_2_S5_R1_001


title: FHRCC10, adjacent normal kidney tissue


title: WT_eFT508_Poly_rep2

description: polysome associated mRNA


title: DNAse3

city: New Ypok

first: Mengying

last: Hu

state: New York

address: 413 E 69th St, New York, NY 10021

institute: Weill Cornell Medical College

description: Library name: Sample-12

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (version 2.0.11) (http://ccb.jhu.edu/software/tophat/index.shtml), and transcriptome reconstruction was performed by Cufflinks (version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/). The abundance of transcripts was measured with Cufflinks in fragments per kilobase of exon model per million mapped reads (FPKM).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Lymph nodes

growth_protocol: DCs were FACS sorted from cervical lymph nodes without further culturing

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen, 74134) following the manufacturer’s instructions.
Illumina stranded total RNA preparation with Ribo-Zero Plus was conducted

treatment_protocol: Naïve C57BL/6 mice received i.v. injections retro-orbitally of PBS, 50 µg of NTEVs or 25 µg of ATEVs (containing 10 µg of EV-DNA), or 25 µg of Baseline-ZERO DNase-pretreated ATEVs every other day for in total 3 doses. Subsequently, cervical lymph nodes were subjected to FACS sorting of CD45+CD11b-CD11c+ dendritic cells (DCs) for RNAseq profiling

value: Lymph nodes

value: CD45+CD11b-CD11c+ DCs

value: WT

value: DNAse+ATEVs


title: FGF_Neurog2_1 [RNA-Seq]


title: WT_eFT508_Poly_rep1

description: polysome associated mRNA


title: FHRCC10, primary tumor

value: kidney


title: Brown adipose tissue, vehicle, mouse2

description: Library name: Vehicle 2 BAT C3

value: Brown adipose tissue


title: DNAse2

description: Library name: Sample-11


title: FHRCC09, adjacent normal kidney tissue


title: FGF_Neurog2_Hmgb2_3 [RNA-Seq]

value: Neurog2+Hmgb2 overexpression/bFGF


title: WT_DMSO_Total_rep3

description: total mRNA

value: DMSO


title: NTEV3

description: Library name: Sample-9

value: NTEVs


title: FGF_Neurog2_Hmgb2_2 [RNA-Seq]


title: WT_DMSO_Total_rep2

description: total mRNA

value: TSC2-Corrected WT


title: DNAse1

description: Library name: Sample-10


title: FHRCC08, adjacent normal kidney tissue


title: FGF_Neurog2_Hmgb2_1 [RNA-Seq]

value: Cortex (Grey matter)


title: WT_DMSO_Total_rep1

description: total mRNA


title: FHRCC08, primary tumor


title: FGF_Hmgb2_4 [RNA-Seq]

value: Primary culture

value: Hmgb2 overexpression/bFGF


title: NTEV1

description: Library name: Sample-7


title: FHRCC07, adjacent normal kidney tissue


title: FGF_Hmgb2_3 [RNA-Seq]

value: Astrocytes

value: Wildtype


title: WT_DMSO_Poly_rep2

description: polysome associated mRNA

value: female


title: FGF_Neurog2_2 [RNA-Seq]

value: Neurog2 overexpression/bFGF


title: ATEV3

description: Library name: Sample-6

value: Lymph nodes

value: ATEVs


title: FGF_Hmgb2_2 [RNA-Seq]


title: FGF_Hmgb2_1 [RNA-Seq]


title: FHRCC06, primary tumor


title: C42B_RNA_0.5kPa_rep3

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: C4-2B cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 U/µl penicillin and 100 µg/ml streptomycin. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: C4-2B cells were grown in Nunc Cell Culture dishes or Matrigen Softwell Petrisoft hydrogel dishes before start of nuclei extraction.

tag: disease

value: prostate cancer

value: LNCaP-derived C4-2

tag: stiffness

value: 0.5 kPa


title: ATEV2

description: Library name: Sample-5

tag: strain

value: CD45+CD11b-CD11c+ DCs

value: WT


title: FHRCC09, primary tumor

value: kidney


title: ATEV1

description: Library name: Sample-4


title: C42B_RNA_0.5kPa_rep2


title: FGF_Control_3 [RNA-Seq]

value: Control/bFGF


title: FHRCC04, adjacent normal kidney tissue


title: PBS3

description: Library name: Sample-3

value: PBS


title: C42B_RNA_0.5kPa_rep1


title: PBS2

description: Library name: Sample-2


title: NTEV2

description: Library name: Sample-8

value: NTEVs


title: WT_DMSO_Poly_rep3

description: polysome associated mRNA

value: iPSC derived NPC

value: TSC2-Corrected WT

value: DMSO


title: FHRCC04, primary tumor


title: FGF_Control_1 [RNA-Seq]

value: Cortex (Grey matter)

value: Primary culture

value: Astrocytes

value: Wildtype


title: C42B_RNA_50kPa_rep3

value: 50 kPa


title: FHRCC03, primary tumor


title: EGF_FGF_Hmgb2_4 [RNA-Seq]

value: Hmgb2 overexpression/EGF+bFGF


title: PBS1

description: Library name: Sample-1

value: Lymph nodes


title: FHRCC07, primary tumor


title: C42B_RNA_50kPa_rep2

value: prostate cancer

value: LNCaP-derived C4-2


title: WT_DMSO_Poly_rep1

description: polysome associated mRNA

value: female


title: FHRCC02, adjacent normal kidney tissue

value: kidney


title: CD8 T, Biotin-, rep3

city: Beijing

first: Xinyuan

last: Fan

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: College of Chemistry and Molecular Engineering

institute: Peking university

description:
Library name: CD8+Biotin-_3
Column name in CD8_raw_counts.csv: CD8+Biotin-_3

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information and corresponding sequencing quality information.
Trim_galore (0.6.7) was used to trim adapter sequences from the sequencing data, and the trimmed sequences were aligned to the GRCm39 reference genome using STAR (2.7.10a).
The aligned sequences were sorted using picard (1.14) and counted using featureCounts (2.0.1), generating a gene expression matrix.
Assembly: GRCm39
Supplementary files format and content: a csv file including raw counts for each sample

source_name: TILs

extract_protocol:
The sorted cells were lysed in 50-100 μL TRIzon reagent (CWBIO, CW0580S) by pipetting or vortexing. To the lysate, 20 μL of CHCl3 was added, mixed thoroughly, and the mixture was centrifuged at 12,000 rpm, 4 °C for 15 minutes to transfer the upper clear aqueous phase to a new RNase-free tube. Total RNA was extracted using RNA clean & concentrator kits (Zymo, R1015).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. After library quality control, quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Biotin+ and Biotin- CD8 T cells from murine MC38-hPD-L1 tumor were collected by FACS.

value: TILs

value: CD8+ T cells from MC38-hPD-L1 tumor

tag: biotin status

value: Biotin-


title: C42B_RNA_50kPa_rep1


title: EGF_FGF_Hmgb2_3 [RNA-Seq]


title: CD8 T, Biotin-, rep2

description:
Library name: CD8+Biotin-_2
Column name in CD8_raw_counts.csv: CD8+Biotin-_2


title: FHRCC05, primary tumor


title: EGF_FGF_Hmgb2_2 [RNA-Seq]


title: C42B_RNA_plastic_rep3

value: plastic


title: CD8 T, Biotin-, rep1

description:
Library name: CD8+Biotin-_1
Column name in CD8_raw_counts.csv: CD8+Biotin-_1


title: FHRCC01, primary tumor


title: FGF_Control_2 [RNA-Seq]

value: Control/bFGF


title: EGF_FGF_Hmgb2_1 [RNA-Seq]


title: FHRCC02, primary tumor


title: CD8 T, Biotin+, rep3

description:
Library name: CD8+Biotin+_3
Column name in CD8_raw_counts.csv: CD8+Biotin+_3

value: Biotin+


title: C42B_RNA_plastic_rep2


title: EGF_FGF_Neurog2_Hmgb2_3 [RNA-Seq]

value: Cortex (Grey matter)

value: Neurog2+Hmgb2 overexpression/EGF+bFGF


title: C42B_RNA_plastic_rep1


title: FHRCC25, primary tumor


title: EGF_FGF_Neurog2_Hmgb2_2 [RNA-Seq]

value: Primary culture

value: Astrocytes


title: C42B_ATAC_0.5kPa_rep2

data_processing:
Basecalls performed using CASAVA.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >6-fold over local background.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with Illumina Nextera DNA Library Prep kit (#FC-121-1030) according to instructions.

value: 0.5 kPa


title: FHRCC19, primary tumor


title: EGF_FGF_Neurog2_Hmgb2_1 [RNA-Seq]

value: Wildtype


title: CD8 T, Biotin+, rep1

description:
Library name: CD8+Biotin+_1
Column name in CD8_raw_counts.csv: CD8+Biotin+_1


title: EGF_FGF_Neurog2_3 [RNA-Seq]

value: Neurog2 overexpression/EGF+bFGF


title: MDA-MB-231 cells transduced with eSNAI1-g2 (Replicate #3)

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNAseq reads were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 (https://zenodo.org/record/5109461#.Ya2yLFPMJhE) developed at the LUMC.
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), alignment, read quantification, and optionally transcript assembly.
FastQC (v0.11.9) was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with the default settings.
RNAseq reads’ alignment was performed using STAR (v2.7.5a) on human reference genome GRCh38.
The gene read quantification was performed using HTSeq-count (v0.12.4) with the Ensembl gene annotation version 111.
Assembly: GRCh38
Supplementary files format and content: raw read count in TSV format

growth_protocol: MDA-MB-231 cells were purchased from American Type Culture Collection (ATCC) and cultured in Dulbecco’s modified Eagle medium (DMEM; Thermo Fisher Scientific; 41965062) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific; 16000044) and 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific; 15140163).

extract_protocol:
RNA was extracted by a NucleoSpin RNA kit (Macherey Nagel; Cat. Nr.: 740955) according to the manufacturer's instructions.
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI) in China using the DNBSEQ platform.

treatment_protocol: Cells were transduced with lentiviral expressing constructs overnight. After two days culture, 1 ng/mL puromycin was added to the medium for selecting stable cells. After another 3 days culture, cells were ready for RNA isolation.

value: human breast cancer cell line

value: Transduced with expressing construct for eSNAI1 gRNA-2


title: C42B_ATAC_0.5kPa_rep1

value: prostate cancer

value: LNCaP-derived C4-2


title: MDA-MB-231 cells transduced with eSNAI1-g2 (Replicate #2)


title: C42B_ATAC_50kPa_rep2

value: 50 kPa


title: EGF_FGF_Neurog2_2 [RNA-Seq]


title: C42B_ATAC_50kPa_rep1


title: MDA-MB-231 cells transduced with eSNAI1-g2 (Replicate #1)


title: MDA-MB-231 cells transduced with eSNAI1-g1 (Replicate #3)

value: Transduced with expressing construct for eSNAI1 gRNA-1


title: C42B_ATAC_plastic_rep2


title: EGF_FGF_Neurog2_1 [RNA-Seq]


title: MDA-MB-231 cells transduced with eSNAI1-g1 (Replicate #2)


title: EGF_FGF_Control_5 [RNA-Seq]

value: Control/EGF+bFGF


title: EGF_FGF_Control_4 [RNA-Seq]


title: C42B_ATAC_plastic_rep1

value: plastic


title: CD8 T, Biotin+, rep2

description:
Library name: CD8+Biotin+_2
Column name in CD8_raw_counts.csv: CD8+Biotin+_2

value: TILs

value: CD8+ T cells from MC38-hPD-L1 tumor


title: MDA-MB-231 cells transduced with eSNAI1-g1 (Replicate #1)


title: AGRR_021_DLBCL_HiC

city: Ann Arbor

first: Russell

last: Ryan

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

institute: University of Michigan Medical School

description: Genome-wide chromatin contact matrix

data_processing:
Hi-C sequencing reads were processed with the Arima-SV pipeline (A101060, version v01, 02/2022)
HiCUP was used for read alignment followed by hic_breakfinder for identification of structural variants
Juicer was used for generation of the hg38 genome-wide contact matrix file (.hic).
Assembly: hg38
Supplementary files format and content: .hic genome-wide contact matrix

source_name: Lymphoma biopsy

extract_protocol:
Five-micron sections (n=5-10) were cut from clinically-obtained formalin-fixed paraffin-embedded lymphoma tissue biopsies. Sections were macrodissected if needed to retain only areas with high lymphoma cellularity.
Tissue was sent to Arima Genomics and processed for Hi-C library construction with the Arima-HiC+ FFPE service as described by the manufacturer. Libraries were sequenced on an Illumina Nextseq and analyzed with the Arima-SV pipeline for hg38 contact matrix generation and structural variant detection.

value: Lymphoma biopsy

value: Diffuse large B-cell lymphoma


title: AGRR_020_DLBCL_HiC

description: Genome-wide chromatin contact matrix


title: EGF_FGF_Control_3 [RNA-Seq]

value: Cortex (Grey matter)

value: Primary culture


title: MDA-MB-231 cells transduced with gEV (Replicate #3)

value: Transduced with expressing construct for a gRNA


title: EGF_FGF_Control_2 [RNA-Seq]

value: Astrocytes

value: Wildtype


title: AGRR_003_DLBCL_HiC

description: Genome-wide chromatin contact matrix


title: MDA-MB-231 cells transduced with gEV (Replicate #1)

value: human breast cancer cell line


title: MDA-MB-231 cells transduced with gEV (Replicate #2)


title: EGF_FGF_Control_1 [RNA-Seq]


title: AGRR_002_DLBCL_HiC

description: Genome-wide chromatin contact matrix


title: Visceral_ASC_obese_differentiated_Ecs_rep3

city: Barcelona

first: Gemma

last: Arderiu

address: Avda. S. Antoni M. Claret 167

department: Cardiovascular area

institute: Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau IIB-Sant Pau

description: miRNA expression data from ASCs differentiated into Ecs

hyb_protocol: Biotin-labeled RNA was hybridized to affymetrix miRNA 4.0 GeneChips for 16 hours (48ºC, 60 rpm) using a GeneChip 645 hybridization oven and washed and stained on the GeneChip Fluidics Station 450 using protocol FS450_0002.

scan_protocol: Scanning of microarrays was performed using the Affymetrix GeneChip 3000 7G scanner. AGGC software was used for scanner images adquisition.

data_processing: Raw data was normalized in Transcriptome Analysis Console (TAC 4.0.2.15) software using RMA-DABG algorithm and CHP files were generated.

source_name: Adipose-derived stem cell

label_protocol: 500 ng of RNA was labeled using Applied Biosystems FlashTag Biotin HSR RNA labeling kit according to manufacturer's instructions.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM)-Low Glucose (Thermo Fisher Scientific) supplemented with 10% FBS, 100 U/ml penicillin and 0.1 mg/ml streptomycin (Invitrogen) in a humidified environment at 37°C with 5% CO2 and were used between passages 2 and 4.

extract_protocol: miRNA was isolated using a mirVana™ miRNA Isolation Kit with phenol (Life Technologies Corporation) according to the manufacturer's instructions.

treatment_protocol: To induce ASCs differentiation into ECs, ASCs were cultured in DMEM-Low Glucose supplemented with 10 ng/ml bFGF (233-FB, R&D Systems). Cells were supplied with fresh medium every 3 days and cultured for a total of 9 days

value: Visceral adipose tissue

tag: categorization

value: obese

tag: state

value: differenciated

tag: gender

value: female


title: Visceral_ASC_obese_differentiated_Ecs_rep2

value: male


title: Visceral_ASC_obese_basal_rep4

description: miRNA expression data from ASCs

value: basal


title: Visceral_ASC_obese_differentiated_Ecs_rep4