title: SMARTER_308

tag: tissue

value: FFPEs from DLBCL

tag: treatment


title: Hek293T,EGFP-2,Day 4

status: Public on Sep 06 2025

type: SRA

city: Hangzhou

first: Wei

last: Xie

address: No. 866 Yuhangtang Road, West Lake District

country: China

institute: Zhejiang University

description:
Library name: sample 17
control
total-2_count.txt
EGFP-2-3

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed usingCLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: embryonic kidney

growth_protocol: HEK293t cells were maintained in DMEM suppiemented with 10% fetal bovine serum (FBS) and antibiodics in humidied atmosphere with 5% CO2 at 37℃.

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

treatment_protocol: The recombinant pLVX-EF1α-HA-NSP14-IRES-EGFP-Puro plasmid was transiently transfected into HEK293t mammalian cells when the cell density reached 60%.

value: embryonic kidney

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: genotype

value: WT

value: TRANSFECTION


title: Whole blood, KY-TBCO-10_B1

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

description:
PCM047
batch2_fc_counts.txt

data_processing:
Forward and reverse reads were then aligned to the reference genome index using the Rsubread align function.
Gene counts were quantified using the BAM files generated from this step, featureCounts (v2.0.3).
Assembly: GRCh38 DNA primary assembly
Supplementary files format and content: .txt formatted gene count matrix

molecule: polyA RNA

source_name: Whole blood

extract_protocol:
RNA was extracted from thawed Tempus tubes using PerfectPure™ Blood RNA Kit (5 PRIME) or Norgen Preserved Blood RNA kits (for Tempus Tubes), including DNAse treatment.
1000 ng of the isolated total RNA was globin reduced, where indicated, using the Human Globinclear Kit and 200 ng of RNA was used to make cDNA libraries for sequencing using the MGIeasy RNA Library Prep with PE100 chemistry.

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Female

tag: hiv status

value: HIV-

tag: tb history

value: No

tag: disease status

value: Active TB

tag: symtoms at_tb_diagnosis

value: Symptomatic

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

tag: petct definition

value: No PETCT

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status

value: Not globin depleted


title: EMT6_Control_2

city: Xiamen

last: Su

state: Fujian

address: No. 4221 Xiang'an South Road

institute: Xiamen university

description: Library name: EMT6_WT_2

data_processing:
Reads cleaning: pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N:0.1)
Alignment: clean reads were processed to pseudo-align to mouse transcriptome GRCm38 using Hisat2 (v2.2.1)
Quantification: transcriptional level expression was aggregated to gene level expression using HTSeq (v0.6.1)
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 1.5 and adjusted p-value < 0.05
Assembly: mm 10
Supplementary files format and content: CSV files include FPKM values for samples

organism: Mus musculus

growth_protocol: 4T1 and EMT6 cell culture in DMEM supplentment with 10%FBS and 0.1%PS at 37°C in a humidified incubator (95% air, 5% CO2)

extract_protocol:
Total RNA were extract using HiPure Unviersal RNA Mini Kit (Magen, R4130)
The cDNA libraries were constructed using VAHTS mRNA Capture Beads (N401, Vazyme)+VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina（NR605, Vazyme）following the guidelines of the manufacturers

tag: cell line

tag: genotype

tag: batch


title: SMARTER_225

type: RNA

city: Hannover

first: Robin

last: Kosch

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

hyb_protocol: Total RNA was hybridized to the codesets at 65°C overnight.

scan_protocol: standard protocol

data_processing: For processing of the reaction on nCounter PrepStation “high sensitivity” setting was used and gene expression data was then obtained on the nCounter™ Digital Analyzer at the “max resolution” setting (1155 FOV).

label: not provided

source_name: FFPEs from DLBCL

label_protocol: 200 ng RNA were used for digital GEP using the NanoString nCounter technology (NanoString Technologies, Seattle, WA).

extract_protocol: Nucleic acids were extracted with Qiagen AllPrep DNA/RNA FFPE Kit (Qiagen, Hil-den, Germany).

tag: tissue

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: SMARTER


title: CL316-2

city: Guangzhou

first: Yao

last: Lei

address: 107 Yan Jiang West Road

department: Department of Cardiology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Library name: sample2
CL316-2_tpm

data_processing:
Reads were filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: mm10
Supplementary files format and content: TPM

source_name: Aorta

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.

value: Aorta

value: ApoE-/-

value: Ang II-infused mice treated with CL316,243


title: SMARTER_278

value: FFPEs from DLBCL


title: Hek293T,EGFP-2,Day 3

description:
Library name: sample 16
control
total-2_count.txt
EGFP-2-2

value: embryonic kidney

tag: cell type

value: human embryonic kidney cells

value: WT


title: Whole blood, KY-0090-01_PETCT2

description:
PCM046
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Male

tag: hiv status

tag: tb history

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

value: Other cold lung lesion

value: Yes

value: No change


title: SMARTER_221


title: EMT6_KO_3

description: Library name: EMT6_KO_3

tag: cell line

tag: genotype

value: KO

tag: batch


title: EMT6_Control_1

description: Library name: EMT6_WT_1


title: Hek293T,NSP14,20uM C10,Day 3

description:
Library name: sample 14
treatment
total-1_count.txt
Drug2-20uM-2

tag: tissue

tag: treatment

value: TRANSFECTION


title: Whole blood, KY-0088-01_PETCT2

description:
PCM045
batch2_fc_counts.txt

tag: participant id

value: HIV-

value: No

value: Positive

value: Normal lung

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status

value: Not globin depleted


title: SMARTER_217

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: SMARTER


title: 4T1_KO_3

description: Library name: 4T1_KO_3


title: SMARTER_215


title: Whole blood, KY-0085-02_PETCT2

description:
PCM044
batch2_fc_counts.txt

tag: pet/ct visit

tag: initial age

tag: Sex

value: Female

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Negative

tag: qft-plus

tag: petct definition

value: Worsening


title: Whole blood, KY-0085-02_PETCT1

description:
PCM043
batch2_fc_counts.txt

tag: tissue

value: Whole blood

tag: participant id

value: no TB

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion


title: SMARTER_209

tag: treatment

tag: cohort


title: Whole blood, KY-0084-05_PETCT2

description:
PCM042
batch2_fc_counts.txt

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: Yes

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Hek293T,NSP14,20uM C10,Day 2

description:
Library name: sample 13
treatment
total-1_count.txt
Drug2-20uM-1

tag: tissue

value: embryonic kidney

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: genotype

value: WT


title: Hek293T,NSP14,10uM C10,Day 3

description:
Library name: sample 12
treatment
total-1_count.txt
Drug2-10uM-2

value: TRANSFECTION


title: 4T1_KO_2

description: Library name: 4T1_KO_2

value: KO

tag: batch


title: 4T1_KO_1

description: Library name: 4T1_KO_1


title: SMARTER_188


title: SMARTER_203


title: 4T1_Control_3

description: Library name: 4T1_WT_3


title: Whole blood, KY-0084-03_PETCT1

description:
PCM041
batch2_fc_counts.txt

tag: participant id

value: Male

value: HIV-

tag: tb history

value: No

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung


title: Hek293T,NSP14,20uM C7,Day 3

description:
Library name: sample 10
treatment
total-1_count.txt
Dr-1-20uM-2

tag: tissue

tag: treatment


title: Whole blood, KY-0084-03_PETCT2

description:
PCM040
batch2_fc_counts.txt

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: Subclinical TB

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status

value: Not globin depleted


title: Hek293T,NSP14,10uM C10,Day 2

description:
Library name: sample 11
treatment
total-1_count.txt
Drug2-10uM-1

tag: cell line

tag: cell type

tag: genotype


title: 4T1_Control_2

description: Library name: 4T1_WT_2

tag: batch


title: SMARTER_184

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: SMARTER


title: SMARTER_172


title: Hek293T,EGFP-2,Day 2

description:
Library name: sample 15
control
total-2_count.txt
EGFP-2-1


title: Whole blood, KY-0084-01_PETCT2

description:
PCM039
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

value: Mixed


title: 4T1 cells, sgZfp296-1-rep2

city: Beijing

first: Deng

last: Pan

address: Tsinghua University Medical Science Building

department: School of Basic Medical Sciences

institute: Tsinghua University

description: Library name: Sample16

data_processing:
Raw RNA-Seq reads were quality-checked using Fastp to remove low-quality bases and adapter contamination.
RNA-seq reads were aligned to either the mm9 or GRCh38 genome using HISAT2 (version 2.2.1) with default parameters, and unmapped reads were removed.
Gene-level counts were calculated using featureCounts (version 2.0.6) based on uniquely mapped reads
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Breast

extract_protocol:
Total mRNA from A549, MDA-MB-453, and 4T1 cells was extracted using TRIzol (Invitrogen, Cat# 15596026)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer's protocol.

tag: tissue

value: Breast

tag: cell line

value: breast cancer

value: Zfp296 knockdown


title: 4T1_Control_1

description: Library name: 4T1_WT_1

tag: genotype

value: WT


title: Whole blood, KY-0081-07_PETCT2

description:
PCM038
batch2_fc_counts.txt

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: Yes

value: DN/A detected not treated

value: no TB

value: Subclinical TB-inactive

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

value: Minimal worsening

tag: globin status


title: Hek293T,NSP14,20uM C7,Day 2

description:
Library name: sample 9
treatment
total-1_count.txt
Dr-1-20uM-1

value: embryonic kidney

tag: cell type

value: human embryonic kidney cells

tag: treatment

value: TRANSFECTION


title: Whole blood, KY-0081-07_PETCT1

description:
PCM037
batch2_fc_counts.txt

tag: participant id

value: Male

value: HIV-

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

tag: petct definition

tag: subclinical tb

value: No

tag: subclinical tb-inactive

value: Not globin depleted


title: SMARTER_170

tag: tissue

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: SMARTER


title: 4T1 cells, sgZfp296-1-rep1

description: Library name: Sample15

value: Breast

tag: cell line

value: breast cancer

tag: genotype

value: Zfp296 knockdown


title: Hek293T,NSP14,10uM C7,Day 3

description:
Library name: sample 8
treatment
total-1_count.txt
Dr1-10uM-2

value: WT


title: Hek293T,NSP14,10uM C7,Day 2

description:
Library name: sample 7
treatment
total-1_count.txt
Dr1-10uM-1


title: SMARTER_154


title: SMARTER_151


title: 4T1 cells, sgNTC-rep2

description: Library name: Sample14


title: Hek293T,NSP14,DMSO,Day 3

description:
Library name: sample 6
treatment
total-1_count.txt
NSP-DMSO-2


title: 4T1 cells, sgNTC-rep1

description: Library name: Sample13


title: BAL, KY-0081-07_BAL1

description:
PCM036
batch2_fc_counts.txt

source_name: BAL

value: BAL

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: Yes

value: DN/A detected not treated

value: no TB

value: No PETCT

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status

value: Globin Depleted


title: Hek293T,NSP14,DMSO,Day 2

description:
Library name: sample 5
treatment
total-1_count.txt
NSP-DMSO-1

value: embryonic kidney

tag: cell type

value: human embryonic kidney cells

tag: treatment

value: TRANSFECTION


title: Whole blood, KY-0078-02_PETCT2

description:
PCM032
batch2_fc_counts.txt

tag: tissue

value: Whole blood

tag: participant id

value: Female

value: HIV-

tag: tb history

value: No

tag: disease status

value: NTM

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

tag: petct definition

value: Other cold lung lesion

tag: subclinical tb

tag: subclinical tb-inactive

value: No change

value: Not globin depleted


title: SMARTER_148

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: SMARTER


title: Whole blood, KY-0078-02_PETCT1

description:
PCM031
batch2_fc_counts.txt

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: no TB

tag: other hot_lung

tag: other cold_lung

value: Yes

tag: no lesion

tag: hot lymph_nodes

tag: hot lung


title: Hek293T,NSP14,Day 2

description:
Library name: sample 3
treatment
total-1_count.txt
NSP14-1

tag: tissue

value: embryonic kidney

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: Hek293T,NSP14,Day 3

description:
Library name: sample 4
treatment
total-1_count.txt
NSP14-2

value: human embryonic kidney cells

value: TRANSFECTION


title: SMARTER_140


title: Germination phase replicate 5

city: Vancouver

first: Elitza

last: Tocheva

state: BC

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

description:
Library name: Sample 19
Column ET15 in the raw counts table "counts_unnormalized.csv"

data_processing:
Adaptors were trimmed using Cutadapt v2.3.
Reads were aligned to the Acetonema longum APO-1 DSM 6540 genome (GCA_000219125.2) using STAR v2.7.10b.
Gene counts were obtained with FeatureCounts v2.0.1.
Assembly: Acetonema longum DSM 6540
Assembly: ASM21912v1
Supplementary files format and content: Raw counts provided in the table "counts_unnormalized.csv".

organism: Acetonema longum

source_name: Germinating spores

growth_protocol: Cells or pure spores were inoculated into 4×YACO broth supplemented with 1.5 g/L yeast extract and incubated at 28-30 °C at an atmosphere of 5% H2, 10% CO2 and 85% N2. Exponential and stationary phase cells were harvested as 3-day-old and 5-day-old subcultures, respectively. Pure spores were inoculated into broth, subjected to heat shock at 60 °C for 15 min, then incubated as described above for 16 hours prior to harvesting. Sporulation stage was confirmed by observing cell morphology under a light microscope.

extract_protocol:
Total RNA was isolated with the RNeasy Mini kit (QIAGEN) with enzymatic lysis and on-column DNase digestion. RNA was eluted in ~25 µl nuclease-free H2O and 1 µl SUPERaseIn (Invitrogen), and stored at -80 °C.
Altogether, total RNA isolates were processed and sequenced in two separate batches (2021 and 2023). Sample quality was assessed with Bioanalyzer on RNA 6000 Nano chip (Agilent Technologies), and library concentrations were measured with a Qubit Quant-iT kit (Fisher Scientific). For samples from the 2021 batch, after rRNA depletion with the Ribo-Zero kit for bacteria (Illumina), clean-up was performed with Agencourt AMPure RNAClean XP (Agencourt Bioscience), and the cDNA libraries were prepared using the KAPA RNA HyperPrep kit (Roche). For samples from the 2023 batch, NEBNext rRNA Depletion Bacteria (New England BioLabs) and NEBNext Ultra II Directional RNA Library Prep (New England BioLabs) kits were used.

treatment_protocol: Pellets were harvested under anoxic conditions and resuspended in RNAprotect Bacteria reagent (QIAGEN).

tag: strain

value: Germinating spores

tag: growth stage

value: Germinating

tag: time point

value: 16 hours post-inoculation

tag: batch


title: Germination phase replicate 4

description:
Library name: Sample 18
Column ET14 in the raw counts table "counts_unnormalized.csv"


title: Whole blood, KY-0077-02_PETCT2

description:
PCM030
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

value: Female

value: HIV-

tag: tb history

value: No

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: SMARTER_133

tag: tissue

tag: treatment

tag: cohort


title: Germination phase replicate 3

description:
Library name: Sample 17
Column ET13 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

tag: time point

tag: genotype

tag: batch


title: Hek293T,EGFP,Day 3

description:
Library name: sample 2
control
total-1_count.txt
EGFP-2

tag: cell line


title: SMARTER_126


title: Whole blood, KY-0075-02_PETCT2

description:
PCM029
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

value: Other hot lung lesion

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

value: Mixed

value: Not globin depleted


title: Germination phase replicate 2

description:
Library name: Sample 16
Column ET12 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

tag: time point

tag: genotype

tag: batch


title: Hek293T,EGFP,Day 2

description:
Library name: sample 1
control
total-1_count.txt
EGFP-1

tag: tissue

tag: cell line

tag: treatment


title: Whole blood, KY-0074-04_PETCT2

description:
PCM028
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Male

tag: hiv status

tag: tb history

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

value: Negative

tag: qft-plus

tag: petct definition

value: Subclinical TB-inactive

tag: subclinical tb

tag: subclinical tb-inactive

tag: combined par_+_ln_vs_change_summary

value: Improvement

tag: globin status


title: Germination phase replicate 1

description:
Library name: Sample 15
Column ET11 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

tag: time point

tag: genotype

value: WT

tag: batch


title: SMARTER_227

tag: tissue

value: FFPEs from DLBCL

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: SMARTER


title: SKM-1 cells, DMSO 3

city: Shenzhen

first: Fuxiang

last: Zheng

address: Fuhua 1 Road

department: Department of Clinical Laboratory

institute: The fourth Clinical Medical College of Guangzhou University of Chinese Medicine

data_processing:
(1)Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence; (2) paired-end clean reads were aligned to the reference genome using hisat2 (v2.0.5)；(3)featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: SKM-1 cell

growth_protocol: SKM-1 cells were maintained in 1640 media supplemented with 10% fetal bobine serum and in humidified at mospher with 5% C02 at 37 ℃.

extract_protocol:
RNA were harvested  with Trizol regent. 1.3μg of total RNA were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SKM-1 cells were treated with celastrol for 48 hours.

tag: cell line

value: SKM-1 cell

value: cancer cell

value: DMSO

tag: time

value: 48 hours


title: SMARTER_270


title: Stationary phase replicate 6

description:
Library name: Sample 14
Column ET19 in the raw counts table "counts_unnormalized.csv"

source_name: Vegetative cells

value: Vegetative cells

value: Stationary

value: 5 day subculture


title: Whole blood, KY-0073-02_PETCT2

description:
PCM027
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: HIV-

tag: tb history

value: No

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

value: Positive

value: Normal lung

tag: other hot_lung

tag: other cold_lung

tag: no lesion

value: Yes

tag: hot lymph_nodes

tag: hot lung

value: No change

value: Not globin depleted


title: SMARTER_258

tag: tissue

value: FFPEs from DLBCL

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort


title: Whole blood, KY-0073-02_PETCT1

description:
PCM026
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

value: Male

value: no TB

value: Negative

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: SKM-1 cells, DMSO 1

tag: cell line

value: SKM-1 cell

tag: cell type

value: cancer cell

value: DMSO

tag: time

value: 48 hours


title: SKM-1 cells, DMSO 2


title: Whole blood, KY-0069-02_PETCT2

description:
PCM024
batch2_fc_counts.txt

value: Whole blood

tag: Sex

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: other hot_lung

tag: other cold_lung

tag: no lesion


title: SMARTER_229

tag: tissue

tag: treatment

tag: cohort

value: SMARTER


title: Exponential phase replicate 7

description:
Library name: Sample 7
Column ET17 in the raw counts table "counts_unnormalized.csv"

tag: strain

value: Vegetative cells

tag: growth stage

value: Exponential

tag: time point

value: 3 day subculture

tag: genotype

value: WT

tag: batch


title: SKM-1 cells, Celastrol 3

tag: cell line

tag: cell type

value: Celastrol

tag: time


title: SMARTER_181


title: Whole blood, KY-0069-02_PETCT1

description:
PCM023
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: HIV-

tag: tb history

value: No

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

value: Positive

tag: petct definition

value: Normal lung

tag: subclinical tb

tag: subclinical tb-inactive

value: Yes

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

value: No change

tag: globin status

value: Not globin depleted


title: Exponential phase replicate 6

description:
Library name: Sample 6
Column ET16 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

tag: time point

tag: genotype

tag: batch


title: SKM-1 cells, Celastrol 1

tag: cell line

value: SKM-1 cell

value: cancer cell

tag: treatment

tag: time


title: Whole blood, KY-TBCO-06_W24

description:
PCM022
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Female

tag: hiv status

tag: tb history

tag: disease status

value: Active TB

tag: symtoms at_tb_diagnosis

value: Symptomatic

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

value: No PETCT

tag: other hot_lung

tag: other cold_lung

tag: no lesion


title: SKM-1 cells, Celastrol 2

tag: cell line

tag: cell type

tag: treatment

value: 48 hours


title: Stationary phase replicate 4

description:
Library name: Sample 12
Column ET05 in the raw counts table "counts_unnormalized.csv"

tag: strain

value: Vegetative cells

tag: growth stage

value: Stationary

tag: time point

value: 5 day subculture

tag: genotype

tag: batch


title: Whole blood, KY-TBCO-06_B1

description:
PCM021
batch2_fc_counts.txt

tag: tissue

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: HIV-

tag: tb history

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: RICOVER-noRTh_1501

value: FFPEs from DLBCL

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: RICOVER-noRTh


title: Whole blood, KY-0067-02_PETCT2

description:
PCM020
batch2_fc_counts.txt

value: No

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

value: Subclinical TB-inactive

value: Yes

tag: other hot_lung

tag: other cold_lung

tag: no lesion

value: No change


title: RICOVER-noRTh_1491

tag: tissue


title: Whole blood, KY-0067-02_PETCT1

description:
PCM019
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Female

tag: hiv status

tag: tb history

tag: petct definition

tag: subclinical tb

value: Not globin depleted


title: Stationary phase replicate 2

description:
Library name: Sample 9
Column ET02 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

tag: time point

tag: genotype

value: WT

tag: batch


title: Stationary phase replicate 1

description:
Library name: Sample 8
Column ET01 in the raw counts table "counts_unnormalized.csv"

value: Vegetative cells


title: Stationary phase replicate 5

description:
Library name: Sample 13
Column ET18 in the raw counts table "counts_unnormalized.csv"

value: Stationary


title: RICOVER-noRTh_1483

tag: treatment

tag: cohort


title: RICOVER-noRTh_1469

tag: tissue


title: Whole blood, KY-0066-01_PETCT2

description:
PCM018
batch2_fc_counts.txt

tag: participant id

value: Male

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Negative

tag: qft-plus

value: Other cold lung lesion

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Whole blood, KY-0066-01_PETCT1

description:
PCM017
batch2_fc_counts.txt

value: Whole blood

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: HIV-

tag: tb history

tag: petct definition

tag: subclinical tb


title: Exponential phase replicate 4

description:
Library name: Sample 4
Column ET09 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

value: Exponential

tag: time point

value: 3 day subculture

tag: genotype

tag: batch


title: RICOVER-noRTh_1445

tag: tissue

value: FFPEs from DLBCL

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: RICOVER-noRTh


title: Whole blood, KY-0064-02_PETCT2

description:
PCM016
batch2_fc_counts.txt

tag: participant id

value: No

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

value: Normal lung

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

value: Yes

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Exponential phase replicate 3

description:
Library name: Sample 3
Column ET08 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

tag: time point

tag: genotype

value: WT

tag: batch


title: Stationary phase replicate 3

description:
Library name: Sample 11
Column ET04 in the raw counts table "counts_unnormalized.csv"

value: Vegetative cells

value: 5 day subculture


title: Whole blood, KY-0064-02_PETCT1

description:
PCM015
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Male

tag: hiv status

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: petct definition

tag: subclinical tb

value: No change

value: Not globin depleted


title: RICOVER-noRTh_1499

tag: treatment

tag: cohort


title: RICOVER-noRTh_1470


title: Whole blood, KY-0060-03_PETCT2

description:
PCM014
batch2_fc_counts.txt

value: Whole blood

tag: qft-gold

value: Positive

tag: qft-plus

tag: subclinical tb-inactive

tag: other hot_lung

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Exponential phase replicate 2

description:
Library name: Sample 2
Column ET07 in the raw counts table "counts_unnormalized.csv"

tag: strain

tag: cell type

tag: growth stage

value: Exponential

tag: time point

tag: genotype

tag: batch


title: RICOVER-noRTh_1457

tag: tissue

tag: treatment

tag: cohort


title: DLD1_TREATED_rep1

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

description: Gene expression of DLD1 cell line after treatment with digested red grape anthocyanins at IC50 concentration

hyb_protocol: The probes were hybridized for 17 h at 65oC on Agilent SurePrint G3 Human GE v3 8x60k arrays

scan_protocol: The slides were scanned with Agilent G2505C Microarray Scanner at 5 µm resolution

data_processing: Microarray images were processed with Agilent Feature Extraction software v. 11.5.1.1.

source_name: imortalized cell line

label_protocol: Microarray probes labeled with Cy3 were synthesized from 100 ng of total RNA with Low Input Quick Amp Labeling Kit and checked for quality and quantity with NanoDrop ND-1000 (Thermo Fischer Scientific)

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin and 1% glutamine.

extract_protocol: Total RNA was extracted using the phenol-chloroform method following cell lysis with TriReagent solution

treatment_protocol: Cells were treated with the IC50 concentration of the digested red grape anthocyanin extract for 24h before RNA extraction

tag: cell line

value: treated


title: DLD1_TREATED_rep4


title: RICOVER-noRTh_1365

value: FFPEs from DLBCL


title: Exponential phase replicate 1

description:
Library name: Sample 1
Column ET06 in the raw counts table "counts_unnormalized.csv"

value: 3 day subculture


title: DLD1_TREATED_rep2


title: DLD1_TREATED_rep3


title: Exponential phase replicate 5

description:
Library name: Sample 5
Column ET10 in the raw counts table "counts_unnormalized.csv"


title: Q4D046

city: London,

first: Khaleda Afrin

last: Bari

state: ON

address: 1151 Richmond St

department: Anatomy and Cell Biology

institute: Western University

description: Library name: Sample 6

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to S. cerevisiae whole genome using STAR v2.5.4b
Raw counts for each sample were obtained using featureCounts v1.6.0
Differentially expressed genes were determined using DESeq2 v1.26.0
Assembly: Saccharomyces cerevisiae S288C reference genome (assembly R64-2-1)
Supplementary files format and content: Raw gene counts table for every gene and every sample
Supplementary files format and content: Normalized counts text files for each gene for each sample

organism: Saccharomyces cerevisiae

source_name: Mutant

growth_protocol: Strains were grown to mid-log phase in synthetic complete media and then washed with galactose 3 times. After washing with galactose strains were cultured in galactose medium

extract_protocol:
RNA was extracted using the MasterPure Yeast RNA purification kit (Lucigen) according to the manufacturer’s instructions.
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)

value: yeast cell

value: Mutant

value: MATa ade2-1 can1-100 trp1-1 leu2-3 his3-11 ura3-1

value: disease associated


title: Whole blood, KY-0056-03_PETCT1

description:
PCM012
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

value: HIV-

tag: tb history

value: No

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

value: Normal lung

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Yes


title: Li+ Input, rep 3

city: Perth

first: Nicole

last: Smith

state: WA

address: 35 Stirling Hwy

institute: The University of Western Australia

description:
Library name: P9-L-Inp
Input RNA, 150 mM Li+

data_processing:
Quality checks of the raw fastq files were performed using MultiQC
Raw RIP-seq reads were mapped to the human reference genome GrCh38 using STAR version 2.7.6a. Parameters: --readFilesCommand zcat \ --outFilterType BySJout \ --outSAMunmapped Within \ --outSAMtype BAM SortedByCoordinate \ --outSAMattrIHstart 0 \ --outFilterIntronMotifs RemoveNoncanonical \ --quantMode TranscriptomeSAM \ --outWigType bedGraph \ --outWigStrand Stranded \
Abundance estimates were computed with HTSeq version 2.0.2. Parameters: -f bam -r pos -s reverse
Genes with low expression (<10 counts across all samples) were removed and the filtered set of genes was used for differential gene expression analysis using EBSeq.
Assembly: hg38
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample
Supplementary files format and content: HTSeq counts for every gene in the sample

growth_protocol: SH-SY5Y cells were cultured in DMEM/F-12 (1:1) media supplemented with 10% foetal bovine serum under standard culture conditions (37 °C, 5% CO2)

extract_protocol:
Total RNA was purified using the Qiagen RNeasy Mini Kit with RNase-free DNase set. RNA secondary structures were annealed in RIP buffer containing 150 mM of K+ or Li+, and annealed RNA was bound to recombinant C-terminal FUS protein. FUS-bound RNA was immunoprecipitated and pulled-down RNA purified with neutral phenol-chloroform. Input samples were subject to all steps as FUS-RNA samples except for immunoprecipitation and subsequent washes.
cDNA libraries were prepared using the NEBNext Ultra II Directional Library Prep Kit for Illumina with the NEBNext rRNA Depletion Kit and Unique Dual Index Primer Pair Multiplex Oligos as per manufacterer's protocols.

tag: cell type

value: Neuroblastoma


title: DLD1_CTR_rep4

description: Gene expression of DLD1 cell line

tag: cell line

tag: treatment

value: untreated


title: DLD1_CTR_rep2

description: Gene expression of DLD1 cell line


title: DLD1_CTR_rep3

description: Gene expression of DLD1 cell line


title: RICOVER-noRTh_1392

tag: tissue

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort

value: RICOVER-noRTh


title: Whole blood, KY-0056-03_PETCT2

description:
PCM013
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Male

value: Positive

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

value: No change

tag: globin status

value: Not globin depleted


title: DENSER_41

value: FFPEs from DLBCL

value: DENSER


title: Li+ Input, rep 2

description:
Library name: P6-L-Inp
Input RNA, 150 mM Li+


title: Q3D046

description: Library name: Sample 5

value: yeast cell

value: Mutant

tag: strain

tag: genotype

value: MATa ade2-1 can1-100 trp1-1 leu2-3 his3-11 ura3-1

value: disease associated

tag: batch


title: Whole blood, KY-0053-04_PETCT2

description:
PCM011
batch2_fc_counts.txt

value: Female

tag: hiv status

value: HIV-

tag: tb history

value: No

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

value: Other cold lung lesion

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung


title: MInT_D-58-14

tag: tissue

tag: treatment

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort


title: Q1D046

description: Library name: Sample 4

tag: cell type

tag: cell line

tag: strain


title: Li+ Input, rep 1

description:
Library name: P5-L-Inp
Input RNA, 150 mM Li+

value: Neuroblastoma


title: Whole blood, KY-0051-08_PETCT2

description:
PCM010
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

tag: other cold_lung

value: Yes

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: K+ Input, rep 3

description:
Library name: P9-K-Inp
Input RNA, 150 mM K+


title: DENSER_1

tag: tissue


title: Q4D025

description: Library name: Sample 3

source_name: WT

value: WT

tag: genotype

tag: treatment

value: non-disease associated

tag: batch


title: Whole blood, KY-0048-02_PETCT2

description:
PCM009
batch2_fc_counts.txt

tag: tb history

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

tag: petct definition

value: Normal lung

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: No change

value: Not globin depleted


title: DLD1_CTR_rep1

description: Gene expression of DLD1 cell line

tag: cell line

value: untreated


title: Mixed SARS-COV-2 Passage3

description:
Library name: sample 9
sample

data_processing:
Perform statistical analysis on hifi reads data.
Split CCS reads according to barcode by using lima software (version 1.9.0).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

organism: Chlorocebus sabaeus

source_name: kidney

extract_protocol:
RNA was further purifified using the RNA simple Total RNA Extraction Kit (Tiangen, DP419).
cDNA was prepared using a transcription kit (TransGen Biotech). For PCR amplifification of the NSP14 coding region the following primers were used: NSP14-forward (5’-GAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGG-3’) and NSP14-reverse (5’-CTGAAGTCTTGTAAAAGTGTTCCAGAGG-3’).

value: kidney

value: Vero E6

tag: cell type

value: epithelial cell

value: Mixed Severe acute respiratory syndrome coronavirus 2


title: Q2D025

description: Library name: Sample 2

value: yeast cell

tag: strain

value: MATa ade2-1 can1-100 trp1-1 leu2-3 his3-11 ura3-1


title: K+ Input, rep 2

description:
Library name: P6-K-Inp
Input RNA, 150 mM K+


title: Mixed SARS-COV-2 Passage2

description:
Library name: sample 8
sample

tag: tissue


title: RICOVER-60_685

value: FFPEs from DLBCL

value: CHO(E)P-like treatment with rituximab dosed at 375 mg/m²

tag: cohort


title: Q1D025

description: Library name: Sample 1

tag: genotype

tag: treatment


title: Whole blood, KY-0048-02_PETCT1

description:
PCM008
batch2_fc_counts.txt

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Female

tag: hiv status

value: HIV-

tag: tb history

value: No

value: no TB

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: Whole blood, KY-0022-02_PETCT2

description:
PCM007
batch2_fc_counts.txt

value: Male

tag: disease status

value: NTM

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

tag: petct definition

value: Other cold lung lesion

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Yes


title: K+ Input, rep 1

description:
Library name: P5-K-Inp
Input RNA, 150 mM K+

tag: cell line

tag: cell type

value: Neuroblastoma


title: Mixed SARS-COV-2 Passage1

description:
Library name: sample 7
sample

tag: tissue

value: kidney

value: Vero E6

value: epithelial cell

tag: treatment


title: Whole blood, KY-0022-02_PETCT1

description:
PCM006
batch2_fc_counts.txt

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

tag: tb history

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

value: No change

value: Not globin depleted


title: V290A NSP14 SARS-COV-2 Passage3

description:
Library name: sample 6
sample

value: V290A NSP14 Severe acute respiratory syndrome coronavirus 2


title: Li+ FUS-bound RNA, rep 3

description:
Library name: P9-L-FR
FUS-bound RNA, 150 mM Li+


title: Li+ FUS-bound RNA, rep 2

description:
Library name: P6-L-FR
FUS-bound RNA, 150 mM Li+


title: pH3

description: Library name: Sample 6

source_name: yeast cell

growth_protocol: Strains were grown to mid-log phase in synthetic complete media

treatment_protocol: Strains were grown to mid-log phase in synthetic complete buffer adjustedmedia

value: yeast cell

tag: strain

tag: genotype

value: MATa ade2-1 can1-100 trp1-1 leu2-3 his3-11 ura3-1

value: buffer treated

tag: batch


title: pH2

description: Library name: Sample 5


title: Whole blood, KY-0016-02_PETCT2

description:
PCM005
batch2_fc_counts.txt

value: Whole blood

value: Female

value: HIV-

value: No

tag: disease status

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status


title: pH1

description: Library name: Sample 4

tag: cell type

tag: treatment


title: Whole blood, KY-0007-04_PETCT2

description:
PCM004
batch2_fc_counts.txt

tag: tissue

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

tag: hiv status

tag: tb history

value: no TB

value: Positive

value: Subclinical TB-inactive

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes

value: Minimal improvement


title: Li+ FUS-bound RNA, rep 1

description:
Library name: P5-L-FR
FUS-bound RNA, 150 mM Li+

tag: cell line

value: Neuroblastoma


title: Wild-type SARS-COV-2 Passage3

description:
Library name: sample 3
control

value: kidney

value: Vero E6

value: Wild-type Severe acute respiratory syndrome coronavirus 2


title: K+ FUS-bound RNA, rep 3

description:
Library name: P9-K-FR
FUS-bound RNA, 150 mM K+


title: V290A NSP14 SARS-COV-2 Passage1

description:
Library name: sample 4
sample

value: epithelial cell


title: CTL2

description: Library name: Sample 1

tag: strain

tag: genotype

value: WT

tag: batch


title: K+ FUS-bound RNA, rep 2

description:
Library name: P6-K-FR
FUS-bound RNA, 150 mM K+


title: Whole blood, KY-TBCO-05_W24

description:
PCM002
batch2_fc_counts.txt

tag: disease status

value: Active TB

tag: symtoms at_tb_diagnosis

value: Symptomatic

tag: months to_diagnosis_from_baseline

tag: qft-gold

tag: qft-plus

tag: petct definition

value: No PETCT

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

tag: hot lung

tag: combined par_+_ln_vs_change_summary

tag: globin status

value: Not globin depleted


title: Whole blood, KY-TBCO-05_B1

description:
PCM001
batch2_fc_counts.txt

tag: tissue

value: Whole blood

tag: participant id

tag: pet/ct visit

tag: initial age

tag: Sex

value: Female

tag: hiv status

tag: tb history

tag: other cold_lung

tag: no lesion

tag: hot lymph_nodes


title: K+ FUS-bound RNA, rep 1

description:
Library name: P5-K-FR
FUS-bound RNA, 150 mM K+

tag: cell line

tag: cell type


title: CTL5

description: Library name: Sample 2

value: yeast cell

tag: strain

tag: genotype

value: MATa ade2-1 can1-100 trp1-1 leu2-3 his3-11 ura3-1

tag: treatment

tag: batch


title: Wild-type SARS-COV-2 Passage1

description:
Library name: sample 1
control


title: CT9-7_piece_1

status: Public on Sep 05 2025

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

country: USA

institute: Washington University in St. Louis

description: Library name: CT9-7-1

data_processing:
nf-callingcards
Reads are prepared by extracting barcodes (UMItools) and trimming adapters (Trimmomatic)
If not already done, genome is prepared (Samtools faidx and aligner indicies)
Reads were aligned (bwamem2)
Alignment QC metrics were extracted (samtools) and reads were mapped to identify Calling Cards insertions (custom scripts).
Peak calling and significance statistics were determined (pycallingcards)
Assembly: mm10
Supplementary files format and content: Analyzed Calling Cards data is outputted as qBED (formerly CCF) files. Each row is a discrete SRT insertion and has six columns: CHROM,START,END,VALUE,STRAND,ANNOTATION. The VALUE represents the number of sequencing reads associated with that insertion. The ANNOTATION column stores sample-specific information such as i5/i7/SRT barcode.

source_name: cortex

extract_protocol:
Tissue was homogenized in Trizol. RNA was extracted using commercial kits according to the manufacturer’s instructions (Zymo RNA Clean & Concentrator-5 Kit and QIAGEN RNEasy Plus Mini Kit).
First strand cDNA synthesis was performed by reverse transcribing polyA mRNAs using an oligo(dT) primer that also adds on a common primer sequence. RNA/DNA duplexes were removed by RNase H treatment. TdTomato self-reporting transcripts (SRTs) were amplified by PCR. PCR products were tagmented and indexed using the Illumina Nextera XT library preparation kit.

value: cortex

tag: seizure score


title: CT7-4_piece_1

description: Library name: CT7-4-1

tag: tissue


title: CT9-4_piece_1

description: Library name: CT9-4-1


title: CT8-1_piece_1

description: Library name: CT8-1-1


title: CT9-5_piece_1

description: Library name: CT9-5-1


title: V290A NSP14 SARS-COV-2 Passage2

description:
Library name: sample 5
sample

value: V290A NSP14 Severe acute respiratory syndrome coronavirus 2


title: CT5-5_piece_1

description: Library name: CT5-5-1


title: CT5-2_piece_1

description: Library name: CT5-2-1


title: CT4-2_piece_1

description: Library name: CT4-2-1


title: CT1-5_piece_1

description: Library name: CT1-5-1


title: CT3-2_piece_1

description: Library name: CT3-2-1


title: CT3-1_piece_1

description: Library name: CT3-1-1


title: CTL8

description: Library name: Sample 3


title: CT6-5_piece_1

description: Library name: CT6-5-1


title: CT4-3_piece_1

description: Library name: CT4-3-1


title: Whole blood, KY-0007-03_PETCT2

description:
PCM003
batch2_fc_counts.txt

tag: participant id

value: Male

value: HIV-

value: No

tag: disease status

value: no TB

tag: symtoms at_tb_diagnosis

tag: months to_diagnosis_from_baseline

tag: qft-gold

value: Positive

tag: qft-plus

tag: petct definition

value: Other cold lung lesion

tag: subclinical tb

tag: subclinical tb-inactive

tag: other hot_lung

value: Yes

tag: hot lung

tag: combined par_+_ln_vs_change_summary

value: No change

tag: globin status


title: CT2-2_piece_1

description: Library name: CT2-2-1

tag: genotype


title: Wild-type SARS-COV-2 Passage2

description:
Library name: sample 2
control

value: kidney

tag: cell line

value: Vero E6

tag: cell type

value: epithelial cell

tag: treatment

value: Wild-type Severe acute respiratory syndrome coronavirus 2


title: CT9-7_piece_5

description: Library name: CT9-7-5

tag: tissue

tag: seizure score


title: CT9-7_piece_4

description: Library name: CT9-7-4


title: CT9-5_piece_6

description: Library name: CT9-5-6


title: CT9-5_piece_4

description: Library name: CT9-5-4


title: CT9-5_piece_3

description: Library name: CT9-5-3


title: CT9-4_piece_4

description: Library name: CT9-4-4


title: CT8-1_piece_3

description: Library name: CT8-1-3


title: CT8-1_piece_2

description: Library name: CT8-1-2


title: CT9-4_piece_5

description: Library name: CT9-4-5


title: CT6-5_piece_4

description: Library name: CT6-5-4


title: CT7-4_piece_2

description: Library name: CT7-4-2


title: CT6-5_piece_3

description: Library name: CT6-5-3


title: CT6-5_piece_2

description: Library name: CT6-5-2


title: CT1-3_piece_1

description: Library name: CT1-3-1


title: CT5-5_piece_2

description: Library name: CT5-5-2


title: CT5-2_piece_3

description: Library name: CT5-2-3


title: CT5-2_piece_2

description: Library name: CT5-2-2


title: CT4-3_piece_3

description: Library name: CT4-3-3


title: CT5-1_piece_3

description: Library name: CT5-1-3


title: CT9-7_piece_6

description: Library name: CT9-7-6


title: CT4-3_piece_2

description: Library name: CT4-3-2


title: CT4-2_piece_3

description: Library name: CT4-2-3


title: CT4-2_piece_2

description: Library name: CT4-2-2


title: CT3-1_piece_3

description: Library name: CT3-1-3


title: CT3-2_piece_2

description: Library name: CT3-2-2


title: CT3-2_piece_3

description: Library name: CT3-2-3


title: CT2-2_piece_3

description: Library name: CT2-2-3


title: CT9-5_piece_5

description: Library name: CT9-5-5


title: CT2-2_piece_2

description: Library name: CT2-2-2


title: CT16-7_piece_6

description: Library name: CT16-7-6


title: CT16-7_piece_5

description: Library name: CT16-7-5


title: CT16-7_piece_1

description: Library name: CT16-7-1


title: CT16-7_piece_4

description: Library name: CT16-7-4


title: CT16-7_piece_2

description: Library name: CT16-7-2


title: CT16-7_piece_3

description: Library name: CT16-7-3


title: CT16-6_piece_6

description: Library name: CT16-6-6


title: CT5-5_piece_3

description: Library name: CT5-5-3


title: CT16-6_piece_5

description: Library name: CT16-6-5


title: CT16-6_piece_4

description: Library name: CT16-6-4


title: CT16-6_piece_3

description: Library name: CT16-6-3


title: CT16-6_piece_1

description: Library name: CT16-6-1


title: CT15-7_piece_2

description: Library name: CT15-7-2


title: CT15-7_piece_1

description: Library name: CT15-7-1


title: CT14-5_piece_6

description: Library name: CT14-5-6


title: CT3-1_piece_2

description: Library name: CT3-1-2


title: CT14-5_piece_1

description: Library name: CT14-5-1


title: CT15-7_piece_6

description: Library name: CT15-7-6


title: CT14-5_piece_5

description: Library name: CT14-5-5


title: CT11-5_piece_5

description: Library name: CT11-5-5


title: CT15-7_piece_4

description: Library name: CT15-7-4


title: CT11-5_piece_2

description: Library name: CT11-5-2


title: CT11-5_piece_6

description: Library name: CT11-5-6


title: CT14-5_piece_4

description: Library name: CT14-5-4


title: CT11-5_piece_1

description: Library name: CT11-5-1


title: CT11-5_piece_3

description: Library name: CT11-5-3


title: CT14-5_piece_2

description: Library name: CT14-5-2


title: CT11-1_piece_2

description: Library name: CT11-1-2


title: CT11-1_piece_1

description: Library name: CT11-1-1


title: CT1-5_piece_3

description: Library name: CT1-5-3


title: CT16-6_piece_2

description: Library name: CT16-6-2


title: CT11-1_piece_3

description: Library name: CT11-1-3


title: CT11-1_piece_5

description: Library name: CT11-1-5


title: CT11-1_piece_4

description: Library name: CT11-1-4


title: LA83_16_KTC

city: Stanford

first: Yuning

last: Tang

state: CA

address: 279 Campus Drive, Beckman Center

institute: Stanford University

description: Library name: LA83_16

library_source: genomic

data_processing:
Custom Tuba-seqUltra library construction protocol. For detailed methodology, please refer to the "Quantification and statistical analysis" section in the Methods of the manuscript "Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1
Assembly: sgRNA library sequence
Supplementary files format and content: .csv

molecule: genomic DNA

source_name: Lung

extract_protocol:
The tissues were homogenized in 20 ml lysis buffer (100mM NaCl, 20mM Tris, 10mM EDTA, 0.5% SDS) with 200 μl of 20 mg/ml Proteinase K (Life Technologies, AM2544). Homogenized tissues were incubated at 55°C overnight.  Genomic DNA was extracted with phenol-chloroform (ThermoFisher Scientific, 15593049) or the Qiagen Puregene Kit (Qiagen, 158063) and precipitated with ethanol. Plasmid DNA extraction was performed following QIAGEN Plasmid Plus Midi Kit instructions
Custom Tuba-seqUltra library construction protocol. For detailed methodology, please refer to the "Tuba-seqUltra library preparation" section in the Methods of the manuscript "Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1

value: Lung

value: Total lung

value: KTC


title: LA83_18_KTC

description: Library name: LA83_18


title: LA83_17_KTC

description: Library name: LA83_17


title: LA83_15_KTC

description: Library name: LA83_15


title: LA83_14_KTC

description: Library name: LA83_14


title: CT1-3_piece_2

description: Library name: CT1-3-2

value: cortex


title: CT1-5_piece_2

description: Library name: CT1-5-2


title: LA83_12_KT

description: Library name: LA83_12

value: KT


title: LA83_13_KTC

description: Library name: LA83_13


title: LA83_07_KTC;Kat7f/f

description: Library name: LA83_07


title: LA83_04_KTC;Kat7f/f

description: Library name: LA83_04


title: LA83_05_KTC;Kat7f/f

description: Library name: LA83_05


title: LA83_11_KT

description: Library name: LA83_11


title: LA83_09_KT

description: Library name: LA83_09


title: LA83_02_KTC;Kat7f/f

description: Library name: LA83_02


title: LA83_10_KT

description: Library name: LA83_10


title: LA83_01_KTC;Kat7f/f

description: Library name: LA83_01


title: LA83_06_KTC;Kat7f/f

description: Library name: LA83_06


title: LA79_38_KTC

description: Library name: LA79_38


title: LA83_03_KTC;Kat7f/f

description: Library name: LA83_03


title: LA79_37_KTC

description: Library name: LA79_37


title: LA79_32_KTC

description: Library name: LA79_32


title: LA79_31_KTC

description: Library name: LA79_31


title: LA79_28_KTC

description: Library name: LA79_28


title: LA79_30_KTC

description: Library name: LA79_30


title: LA83_08_KT

description: Library name: LA83_08


title: LA79_26_KTC

description: Library name: LA79_26


title: LA79_25_KTC

description: Library name: LA79_25


title: LA79_24_KTC

description: Library name: LA79_24


title: LA79_22_KTC

description: Library name: LA79_22


title: LA79_21_KTC

description: Library name: LA79_21


title: LA79_23_KTC

description: Library name: LA79_23


title: LA79_20_KTC

description: Library name: LA79_20


title: LA79_19_KTC

description: Library name: LA79_19


title: LA79_14_KT

description: Library name: LA79_14


title: LA79_13_KT

description: Library name: LA79_13


title: LA79_12_KT

description: Library name: LA79_12


title: LA79_18_KTC

description: Library name: LA79_18


title: LA79_34_KTC

description: Library name: LA79_34


title: LA79_36_KTC

description: Library name: LA79_36


title: LA79_15_KT

description: Library name: LA79_15


title: LA79_11_KT

description: Library name: LA79_11


title: LA79_35_KTC

description: Library name: LA79_35


title: LA79_33_KTC

description: Library name: LA79_33


title: LA79_27_KTC

description: Library name: LA79_27


title: LA79_29_KTC

description: Library name: LA79_29


title: LA79_10_KC;Kat7f/f

description: Library name: LA79_10


title: LA79_16_KTC

description: Library name: LA79_16


title: LA79_07_KC;Kat7f/f

description: Library name: LA79_07


title: LA79_17_KTC

description: Library name: LA79_17


title: LA79_05_KT/+C;Kat7f/f

description: Library name: LA79_05


title: LA79_09_KC;Kat7f/f

description: Library name: LA79_09


title: LA79_04_KTC;Kat7f/f

description: Library name: LA79_04


title: LA79_03_KTC;Kat7f/f

description: Library name: LA79_03


title: LA79_06_KC;Kat7f/f

description: Library name: LA79_06


title: LA79_02_KTC;Kat7f/f

description: Library name: LA79_02


title: LA79_01_KTC;Kat7f/f

description: Library name: LA79_01


title: KP787_H3K14ac_WM3835_rep2

description: Library name: CR11_6

data_processing:
CUT&RUN data were processed following the pipeline described by the Henikoff laboratory (Zheng et al., 2020; Protocol.io). Paired-end sequencing reads were first trimmed and quality-filtered using Trimmomatic (version 0.39). Trimmed reads were then aligned to the mouse reference genome (mm10) and the E. coli spike-in genome (U00096.3) using Bowtie2 (version 2.2.0). Scaling factors for read-depth normalization were calculated as the inverse of the alignment rate of sequencing reads to the E. coli spike-in genome (scaling factor = 1 / spike-in alignment rate).  Peak calling was performed on the normalized bedgraph files using SEACR (version 1.3; Meers et al., 2019), with IgG samples serving as controls. Consensus peaks for each target antibody were determined separately for each cell line using Bedtools -intersect function (version 2.27.1). Peak annotation was performed on these consensus peaks using the annotatePeak function from the ChIPseeker R package (version 1.4.0) with the mouse genome annotation database. Analysis of overlapping genomic regions between different antibody targets was performed separately for each cell line using the findOverlaps function from the GenomicRanges R package (version 1.5.6). For visualization, normalized and smoothed coverage tracks were generated using the bamCoverage tool from the deepTools suite (version 3.3.0). Coverage values were scaled using the sample-specific normalization factors derived from the E. coli spike-in normalization described above. Heatmaps of CUT&RUN signal enrichment around transcription start sites (TSS) were generated using the EnrichedHeatmap R package (version 1.3.4). Peak tracks were visualized using IGV (version 2.14).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

extract_protocol:
DNA extraction follows Epicypher CUTANA™ ChIC/CUT&RUN Kit instructions
CUT&RUN library preparation follows Epicypher CUTANA™ CUT&RUN Library Prep Kit instructions

value: Lung Adenocarcinoma

tag: antibody

value: H3K14ac (Abcam ab52946)


title: KP787_H3K27me3_WM3835

description: Library name: CR11_2


title: KP787_H3K4me3_WM3835_rep2

description: Library name: CR11_4

value: H3K4me3 (Epicypher:13-0060)


title: KP787_H3K14ac_WM3835_rep1

description: Library name: CR11_5


title: KP787_H3K4me3_DMSO_rep2

description: Library name: CR10_4

value: DMSO


title: KP787_H3K4me3_WM3835_rep1

description: Library name: CR11_3


title: KP787_H3K4me3_DMSO_rep1

description: Library name: CR10_3


title: _802T4_KMT2A_rep2

description: Library name: CR9_4

value: KMT2A (Epicypher:13-2004)


title: LA79_08_KC;Kat7f/f

description: Library name: LA79_08


title: _802T4_KMT2A_rep1

description: Library name: CR9_3


title: KP787_H3K14ac_DMSO_rep2

description: Library name: CR10_6


title: KP787_H3K27me3_DMSO

description: Library name: CR10_2


title: _802T4_H3K4me3_rep3

description: Library name: CR9_2


title: _802T4_CTCF

description: Library name: CR7_2

value: CTCF (Epicypher:13-2014)


title: _802T4_KAT7_rep1

description: Library name: CR7_7


title: _802T4_IgG_rep2

description: Library name: CR9_1

value: IgG (Epicypher:13-0042)


title: _802T4_H3K14ac_rep2

description: Library name: CR7_6


title: _802T4_KAT7_rep2

description: Library name: CR7_8


title: KPTC_H3K4me3_rep3

description: Library name: CR8_4

value: KPTC


title: _802T4_H3K4me3_rep1

description: Library name: CR7_3


title: KP787_IgG

description: Library name: CR11_1


title: KPTC_IgG_rep2

description: Library name: CR8_1


title: _802T4_H3K14ac_rep1

description: Library name: CR7_5


title: KPTC_KAT7_rep2

description: Library name: CR6_8


title: KPTC_H3K4me3_rep2

description: Library name: CR8_3


title: KPTC_KMT2A_rep2

description: Library name: CR6_6


title: KP787_H3K14ac_DMSO_rep1

description: Library name: CR10_5


title: KPTC_H3K14ac_rep2

description: Library name: CR6_4


title: KPTC_H3K4me3_rep1

description: Library name: CR6_2


title: KPTC_KMT2A_rep1

description: Library name: CR6_5


title: KPTC_IgG_rep1

description: Library name: CR6_1


title: KPTC_H3K14ac_rep1

description: Library name: CR6_3


title: Kat7-proficient tdTomato+ AT2 cells mouse 3

description: Library name: THC3

data_processing:
Paired-end FASTQ files were aligned to the mouse reference genome using STAR (version 2.7.0). The mm10 genome was indexed with STAR. Gene-level quantification was performed using featureCounts from the Subread package (version 2.0.6). Differential gene expression analysis was conducted using DESeq2 (version 1.4.4).
Assembly: mm10
Supplementary files format and content: tab-delimited file including raw counts from featureCounts for each sample

extract_protocol:
FACS isolated tdTomato+ cells are pelleted and RNA is extracted using Norgen Biotek Single Cell RNA Purification Kit
RNA-seq library prepared by Novogene

treatment_protocol: Intrathecal injection

value: AT2 cells

value: R26LSL-tdTomato; H11LSL-Cas9

value: SPC-Cre adenovirus


title: Kat7-proficient tdTomato+ AT2 cells mouse 1

description: Library name: THC1


title: _802T4_H3K4me3_rep2

description: Library name: CR7_4


title: _802T4_IgG_rep1

description: Library name: CR7_1


title: Kat7-deficient tdTomato+ AT2 cells mouse 3

description: Library name: Kat7f_3

value: R26LSL-tdTomato; H11LSL-Cas9; Kat7f/f


title: Kat7-deficient tdTomato+ AT2 cells mouse 2

description: Library name: Kat7f_2

value: Lung


title: Kat7-deficient tdTomato+ AT2 cells mouse 1

description: Library name: Kat7f_1


title: KP787 cell WM3835 treatment replicate 1

description:
Library name: KP787_3_WM1
column name in raw counts KP787_3_WM1_Aligned.sortedByCoord.out.bam

extract_protocol:
Total RNA is extracted using Norgen Biotek Single Cell RNA Purification Kit
RNA-seq library prepared by Novogene

value: Lung adenocarcinoma


title: KP787 cell DMSO treatment replicate 1

description:
Library name: KP787_3_DMSO_1
column name in raw counts KP787_3_D1_Aligned.sortedByCoord.out.bam


title: KP787 cell DMSO treatment replicate 2

description:
Library name: KP787_3_DMSO_3
column name in raw counts KP787_3_D3_Aligned.sortedByCoord.out.bam


title: KPTC_CTCF

description: Library name: CR8_2


title: N1019R

city: Ann Arbor

first: Christina

middle: Vadala

last: Angeles

state: MI

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

description:
Library name: N1019
1 ACPP tumor

data_processing:
Fastq, raw reads, files were processed through fastp software. Reads were aligned to the reference genome (GRCm39) using Hisat2 v2.05. featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Assembly: GRCm39
Supplementary files format and content: raw and filtered/combined count matricies

source_name: ACPP tumor

extract_protocol:
ACPP tumors and normal fat were stored in liquid nitrogen or RNAlater stablization solution until extraction. 30 mg of frozen tissue was dissociated using the BeadBug Homogenizer (Southern Labware, D1030). RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen #80204). RNA concentrations were determined using the NanoDrop 2000 (Thermo Fisher Scientific). Messenger RNA was purified from total RNA using poly-T-oligo-attached magnetic beads.
Library construction was performed and completed by Novogene or the UM Advanced Genomics Core

value: ACPP tumor

tag: condition

value: DDLPS

value: Trp53f/fPtenf/f C57BL/6J


title: N1062R

description:
Library name: N1062
1 ACPP tumor


title: Kat7-proficient tdTomato+ AT2 cells mouse 2

description: Library name: THC2


title: T cell 0.5 μM MRTX1719_3

city: Houston

first: Shuyue

last: Wang

address: 1901 East Rd

institute: MD Anderson

description:
Tcell_MRTX1719_05uM_3
Tcell_raw_counts.txt
Tcell_normalized_counts.txt

data_processing:
FASTQ files were mapped to the mouse reference genome(GRCm39) using TOPHAT (v2.0.10) and BOWTIE (v2.1.0). Differenal analysis were performed using DESeq_1.18.0.
Assembly: mm39
Supplementary files format and content: tab delimited text files includes raw counts for each sample
Supplementary files format and content: tab delimited text files includes DeSeq normalized counts for each sample

source_name: cell type

growth_protocol: Tumor cell lines were maintained in RPMI1640 with 10% heat inactive FBS and 50mg/ml normocin. T cells were maintained in MEM with 10% heat inactive FBS, IL-2 (Final 500 IU/ml), and beta mercaptoethenol (55mM).

extract_protocol:
Tumor and T cells were directly lysed using Trizol (Life Technologies, 15596018). RNA for cell lines was isolated using a Direct-Zol RNA miniprep plus kit (R2072, Zymo Research).
NEBNext® Ultral II Directional RNA Library Prep with PolyA selection. NovaSeq X plus was used for sequencing.

treatment_protocol: Tumor cells and T cells were seeded in flask and treated by PRMT5is for 5 and 3 days, respectively.

value: cell type

value: T cell

value: WT


title: T cell 0.5 μM GSK3326595_3

description:
Tcell_GSK3326595_05uM_3
Tcell_raw_counts.txt
Tcell_normalized_counts.txt


title: T cell 0.5 μM MRTX1719_1

description:
Tcell_MRTX1719_05uM_1
Tcell_raw_counts.txt
Tcell_normalized_counts.txt


title: set3_12_6_2023

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

institute: NYU Langone

description:
Library name: set3
set3_12_6_2023

library_source: transcriptomic single cell

data_processing:
Illumina base call (bcl) files for the samples were converted to fastq files and aligned to the mm10 pre-mRNA assembly using CellRanger v7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files (barcodes and features), and matrix files

source_name: aortic plaque

growth_protocol: Baseline mice were put on high-fat high-cholesterol diet for 20 weeks. aIgG-treated mice were put on high-fat high-cholesterol diet for 23 weeks where the last 3 received apoB ASO and aIgG treatment every 3 days. aCD42-treated mice were put on high-fat high-cholesterol diet for 23 weeks where the last 3 received apoB ASO and aCD42 treatment every 3 days.

extract_protocol:
Aortic arches were isolated from all groups after saline perfusion via cardiac puncture. Minced tissue was suspended in digestion buffer containing liberase (273582, Roche, Switzerland), Hyaluronidase (3506, Sigma Aldrich, MO) and DNase I (DN25, Sigma Aldrich, MO) in 1% BSA- Hank’s Balanced Salt Solution and 1mM EDTA. Tissue was incubated at 37oC for 15 minutes using C-tubes, placed in genlteMACS dissociator (Miltenyi Biotech, Germany), as previously described (30). The digested tissue was filtered with a 100μm cell strainer, washed with 1X cold PBS and centrifuged at 350g for 5 minutes at 4oC. Aortic arch cells were resuspended in eBioscience™ Fixable Viability Dye eFluor™ 660 (65-0864-14, ThermoFisher, MA) for dead cell staining, and in PE/Cyanine7 anti-mouse CD45 Antibody (103113, Biolegend, CA). Alive CD45+ cells were sorted in fluorescent-activated cell sorter (FACS) SY3200 highly automated parallel sorting (HAPS) (100μm) cytometer, for downstream single cell RNA sequencing.
Isolated cells were loaded into single-cell gel beads and barcoded with a unique molecular identifier using the Single cell 3’ reagent kit (10X Genomics, 3' CellPlex Kit Set A and Cell Multiplexing Oligos; CMO). For set 2, CMO308 is a baseline sample; CMO309 is regression control; CMO310 and CMO11 are regression depleted. For set 3, CMO304 is a baseline sample; CMO305 and CMO307 are regression depleted; CMO306 is regression control.

value: aortic plaque

value: leukocytes

value: multiplexed baseline, regression control and regression platelet depletion

tag: batch


title: N1006R

description:
Library name: N1006
1 ACPP tumor

value: WDLPS


title: KPTC_KAT7_rep1

description: Library name: CR6_7

value: KPTC

value: Lung Adenocarcinoma


title: N1010R

description:
Library name: N1010
1 ACPP tumor


title: T cell DMSO_3

description:
Tcell_DMSO_3
Tcell_raw_counts.txt
Tcell_normalized_counts.txt

value: DMSO


title: set1_Control_regression

description:
Library name: set1
set1_Control_regression

value: multiplexed, 4 control regression samples (aIgG treated)


title: T cell 0.5 μM MRTX1719_2

description:
Tcell_MRTX1719_05uM_2
Tcell_raw_counts.txt
Tcell_normalized_counts.txt


title: T cell 0.5 μM GSK3326595_2

description:
Tcell_GSK3326595_05uM_2
Tcell_raw_counts.txt
Tcell_normalized_counts.txt


title: T cell DMSO_1

description:
Tcell_DMSO_1
Tcell_raw_counts.txt
Tcell_normalized_counts.txt


title: T cell 0.5 μM GSK3326595_1

description:
Tcell_GSK3326595_05uM_1
Tcell_raw_counts.txt
Tcell_normalized_counts.txt


title: MC38/gp100 Mtap KO 0.5 μM GSK3326595_1

description:
MC38gp100_MtapKO_GSK3326595_05uM_1
MC38_raw_counts.txt
MC38_normalized_counts.txt

source_name: cell line

value: cell line

value: colon adenocarcinoma cells

value: Mtap knockout


title: MC38/gp100 0.5 μM MRTX1719_3

description:
MC38gp100_n_MRTX1719_05uM_3
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: set2_12_7_2023

description:
Library name: set2
set2_12_7_2023


title: MC38/gp100 Mtap KO 0.5 μM GSK3326595_2

description:
MC38gp100_MtapKO_GSK3326595_05uM_2
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: T cell DMSO_2

description:
Tcell_DMSO_2
Tcell_raw_counts.txt
Tcell_normalized_counts.txt


title: MC38/gp100 Mtap KO DMSO_3

description:
MC38gp100_MtapKO_DMSO_3
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 0.5 μM GSK3326595_3

description:
MC38gp100_n_GSK3326595_05uM_3
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 Mtap KO 0.5 μM MRTX1719_3

description:
MC38gp100_MtapKO_MRTX1719_05uM_3
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 Mtap KO 0.5 μM MRTX1719_2

description:
MC38gp100_MtapKO_MRTX1719_05uM_2
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 0.5 μM GSK3326595_1

description:
MC38gp100_n_GSK3326595_05uM_1
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 0.5 μM GSK3326595_2

description:
MC38gp100_n_GSK3326595_05uM_2
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 Mtap KO 0.5 μM GSK3326595_3

description:
MC38gp100_MtapKO_GSK3326595_05uM_3
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: KP787 cell WM3835 treatment replicate 2

description:
Library name: KP787_3_WM3
column name in raw counts KP787_3_WM3_Aligned.sortedByCoord.out.bam

value: Lung adenocarcinoma


title: MC38/gp100 Mtap KO 0.5 μM MRTX1719_1

description:
MC38gp100_MtapKO_MRTX1719_05uM_1
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 Mtap KO DMSO_1

description:
MC38gp100_MtapKO_DMSO_1
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 0.5 μM MRTX1719_1

description:
MC38gp100_n_MRTX1719_05uM_1
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 DMSO_3

description:
MC38gp100_n_DMSO_3
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 Mtap KO DMSO_2

description:
MC38gp100_MtapKO_DMSO_2
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 DMSO_1

description:
MC38gp100_n_DMSO_1
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: MC38/gp100 DMSO_2

description:
MC38gp100_n_DMSO_2
MC38_raw_counts.txt
MC38_normalized_counts.txt


title: SAH81 DNA from patient after aSAH with symptomatic cerebral vasospasm

type: genomic

city: Szczecin

first: Tomasz

last: Klepinowski

state: West Pomerania

address: Ul. Unii Lubelskiej 1

department: Department of Neurosurgery

country: Poland

institute: Pomeranian Medical University Hospital No.1

description: DNA extracted from Patients with symptomatic cerebral vasospasm

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC v2.0 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data were processed in R, normalized using SeSAME with settings recommended for EPICv2.0 array (QCDPB).

label: Cy5 and Cy3

source_name: Peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.

value: Peripheral blood

tag: Sex

value: Female

tag: age


title: SAH75 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH78 DNA from patient after aSAH with symptomatic cerebral vasospasm

value: Male


title: SAH74 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH72 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH63 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH71 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH70 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH62 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH65 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH55 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH57 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH52 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH36 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH37 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH34 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH31 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH29 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH42 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH33 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH35 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH41 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH44 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH27 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH43 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH24 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH5 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH23 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH3 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH1 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH80 DNA from patient after aSAH without cerebral vasospasm

description: DNA extracted from patient after aSAH without cerebral vasospasm


title: SAH66 DNA from patient after aSAH without cerebral vasospasm


title: SAH68 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH61 DNA from patient after aSAH without cerebral vasospasm


title: SAH76 DNA from patient after aSAH without cerebral vasospasm


title: SAH79 DNA from patient after aSAH without cerebral vasospasm


title: SAH73 DNA from patient after aSAH without cerebral vasospasm


title: SAH64 DNA from patient after aSAH without cerebral vasospasm


title: SAH59 DNA from patient after aSAH without cerebral vasospasm


title: SAH58 DNA from patient after aSAH without cerebral vasospasm


title: SAH10 DNA from patient after aSAH with symptomatic cerebral vasospasm


title: SAH54 DNA from patient after aSAH without cerebral vasospasm


title: SAH28 DNA from patient after aSAH without cerebral vasospasm


title: SAH56 DNA from patient after aSAH without cerebral vasospasm


title: SAH38 DNA from patient after aSAH without cerebral vasospasm


title: SAH30 DNA from patient after aSAH without cerebral vasospasm


title: SAH48 DNA from patient after aSAH without cerebral vasospasm


title: SAH45 DNA from patient after aSAH without cerebral vasospasm


title: SAH26 DNA from patient after aSAH without cerebral vasospasm


title: SAH49 DNA from patient after aSAH without cerebral vasospasm


title: SAH25 DNA from patient after aSAH without cerebral vasospasm


title: SAH77 DNA from patient after aSAH without cerebral vasospasm


title: SAH15 DNA from patient after aSAH without cerebral vasospasm


title: SAH12 DNA from patient after aSAH without cerebral vasospasm


title: SAH17 DNA from patient after aSAH without cerebral vasospasm


title: SAH60 DNA from patient after aSAH without cerebral vasospasm


title: SAH9 DNA from patient after aSAH without cerebral vasospasm


title: SAH4 DNA from patient after aSAH without cerebral vasospasm


title: SAH2 DNA from patient after aSAH without cerebral vasospasm


title: SAH6 DNA from patient after aSAH without cerebral vasospasm


title: SAH8 DNA from patient after aSAH without cerebral vasospasm


title: HMC_unenrichment2

first: yuanfang

last: Liu

state: Guangdong

address: Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-sen University (Shenzhen)

description: Library name: Sample8

data_processing:
Remove the low-quality sequences and adapters (trim-galore (v.0.6.10))
Align with the reference genome (HISAT2 (v.2.2.1))
File format conversion and sorting after align (samtools (v.1.21))
Remove PCR duplication (picard (v.3.3.0))
peak-calling (Macs2 (v.2.2.9.1))
Assembly: GCA_000001405.28
Supplementary files format and content: The .bw format includes quantified data used to draw conclusions for this study.

organism: mixed organisms

source_name: lambda phage with 5hmC

extract_protocol:
30 μg genomic DNA extracted from NCM460 or HCT116 cell lines was fragmented to about 250 bp by sonication, and then mixed with 100 mM of Azide-PEG3-Amino (2 μL) and 25 mM of K2IrBr6 (2 μL) in NaPi buffer (100 mM, pH 8.0) in a 50 μL reaction system for 30 min at 37 °C. The reaction was terminated by adding 300 μL of ice-ethanol, and then purified using MolPure®PCR Purification Kit (Yesean) to obtain the azide-modified cytogenomic DNA. Next, the obtained azide-modified cell genomic DNA was mixed with 0.01 mg of DBCO-IgG in a 100 μL reaction system at 37 ℃ for 2 h. After the reaction was completed, the IgG-coupled DNA product to be enriched was purified by magnetic bead purification and further enriched using protein G magnetic beads (New England Biolabs). In the enrichment process, 10 μL of magnetic beads were washed three times with 500 μL of binding buffer (0.1 M sodium phosphate buffer, pH 8.0). Then 1 μg of fragmented λDNA genome was added and pre-incubated for 1 h. Later, the DNA to be enriched was added to the magnetic beads and incubated at 37 ℃ for 30 min. After that, the beads were washed three times with 500 μL of binding buffer. Next, 50 μL of enzyme-free water was added to the beads for resuspension, and 1 μL of Proteinase K (40 mg/mL) was added and incubated at 55 oC for 1 h. The supernatant was aspirated and purified by the MolPure®PCR Purification Kit.
The enriched nucleic acid product was subjected to end repair, adding A-tails, adapter ligation and PCR library amplification in accordance with conventional methods, and then the prepared cell genome libraries were used for subsequent sequencing analysis.

value: lambda phage with 5hmC


title: HMC_unenrichment1

description: Library name: Sample7

value: WT


title: 8OG_enrichment2

description: Library name: Sample2

source_name: lambda phage with 80G

value: lambda phage with 80G


title: 8OG_unenrichment1

description: Library name: Sample3


title: HMC_enrichment2

description: Library name: Sample6


title: HMC_enrichment1

description: Library name: Sample5


title: 8OG_enrichment1

description: Library name: Sample1


title: HUVEC_cocul 3

city: Montpellier

first: Donovan

last: PINEAU

address: 141 Rue de la Cardonille

country: France

institute: IGF

description: Library name: HUVEC_cocul3

data_processing:
BGI took care of the quality control of the samples, the construction of the mRNA library, the sequencing of the mRNAs making at least more than 30 million read lengths with 150 paired-end base pairs facilitating the alignment and therefore the reliability of the analysis as well as the verification and analysis steps of the data generated. Data filtering was done by SOAPnuke (R. Li et al., 2008) to (1) remove the readings from the sequencing adapters used; (2) remove low-quality readings with a baseline ratio ≤ 15 if the reading is greater than 20% of the reading phase; (3) remove reads where the number of unknown databases detected is greater than 5%. Then, the "clean" readings were stored in the standard FASTQ format. These reads were mapped to the reference genome using HISAT (D. Kim et al., 2015). To detect gene fusions and differentially expressed genes, Ericscript (0.5.5-5) (Benelli et al., 2012) and rMATS (v4.1.1) (Shen et al., 2014) were used, respectively. The Bowtie2 software (Langmead & Salzberg, 2012) was used to align the "clean" readings with the gene set. Gene expression levels were calculated by RSEM (v1.2.28) (B. Li & Dewey, 2011) to obtain quantification in read count, fragment per kilobase per million (FPKM) and number of transcripts per kilobase million (TPM). An analysis of differentially expressed genes (DEG) is also possible with DESeq2 (Love et al., 2014) or DEGseg (L. Wang et al., 2010) or PossionDis (Audic & Claverie, 1997) with the Q-value ≤ 0.05. The bioinformatics analyses were performed on the BGI, Dr. Tom software platform to visualize the data and extract gene expression in TPM.
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: One tab-delimited text file includes TPM for all samples

growth_protocol: Gb7 were infected with YFP lentivirus (PO Guichet et al, 2015; Augustus et al, 2021)and  HUVEC cells (Human Umbilical Vein Endothelial Cell, Promocell) were infected with a mCherry lentivirus (#VB010000-9485zvg, Vector Builder) and selected by FACS. 1 day prior to the co-cultures. 3,4.105 HUVEC cells were seeded on 0,2% gelatin coated plates (#G2500, Sigma) in Endothelial Cell Basal Medium (#C-22111, Promocell) supplemented with recombinant human EGF (5 ng/ml), recombinant human basic Fibroblast growth factor (10 ng/ml), recombinant human Insulin-like Growth Factor (Long R3 IGF) (20 ng/ml), recombinant human Vascular Endothelial Growth Factor 165 (0,5 ng/ml), Ascorbic Acid (1 µg/ml), Heparin (22.5 µg/ml) and Hydrocortisone (0.2 µg/ml) and fetal calf serum (0.02 ml/ml). 3,0.105 glioma cells were added on top of HUVEC so that co-cultures experiments were performed at a ratio of 1:1,3 (HUVEC: glioma cells LGG275) for 48 hours before FACS isolation of transduced cells YFP+ and mCherry+ cells and subsequent RNA extractions.

extract_protocol:
RNAs were immediately extracted using the Arcturus Picopure RNA kit (Thermo Fisher) and shipped to BGI platform for RNA sequencing.
BGI Genomics-BGISEQ (Poland) to perform sequencing via their DNBSEQTM platform for DNBSEQ stranded mRNA library [DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing]

value: HUVEC cells with diffuse IDH wildtype glioblastoma stem cell line

value: YFP+mCherry


title: HUVEC_cocul 1

description: Library name: HUVEC_cocul1


title: Neuron Cells

city: Tsukuba

first: Haruki

last: Odaka

state: Ibaraki

address: Tsukuba Central 6, 1-1-1 Higashi

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Library name: Neuron.1

data_processing:
Processing of sc-RNAseq data was performed by Subio Platform (version 1.24.5849, Subio inc.) which uses fastp (version 0.22.0) for quality control of FASTQ and HISAT2 (version 2.2.0) for mapping to the human reference genome (GRCh38), and StringTie (version 2.1.1) for calculation of the raw count data.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: 201B7 hiPSCs were cultured in 2 mL of mTeSR Plus (VERITAS ) on 6 well plate coated with Matrigel (Corning international ).

extract_protocol:
Single-cell cDNA library was prepared using GenNextⓇRamDA-seqTM Single Cell Kit (Toyobo Co., LTD. Tokyo, Japan) followed by manufacturer’s protocol.
cDNA library from each single cell was prepared using GenNextⓇRamDA-seqTM Single Cell Kit (Toyobo Co., LTD. Tokyo, Japan) followed by manufacturer’s protocol.

treatment_protocol: Differentiation into NPCs was performed using STEMdiff SMADi Neural Induction Kit according to the manufacturer’s protocol (VERITAS). NPCs were expanded until P4 in STEMdiff SMADi medium. For differentiation into neurons, the NPCs were detached and dissociated into a single cell with Accutase (Innovative Cell Technologie) and seeded on polyethyleneimine (0.07%, Sigma-Aldrich) and laminin (3.3 μg/ml, FUJIFILM Wako)-coated plates. Cells were cultured with neurobasal medium (Thermo Fisher) supplemented with 2% B27 supplement  (Thermo Fisher), 1% GlutaMax (Thermo Fisher), and 5 μM DAPT (Sigma-Aldrich) for 1 week. At day 7, the medium was changed to neurobasal plus medium (Thermo Fisher) supplemented with 2% B27 plus supplement  (Thermo Fisher) and 1% GlutaMax. Half of the medium was changed twice a week until days 21.

value: iPSC-derived Neuron


title: HUVEC_cocul 2

description: Library name: HUVEC_cocul2


title: Gb7_cocul2

description: Library name: Gb7_cocul2

value: diffuse IDH wildtype glioblastoma stem cell line with HUVEC


title: Gb7_cocul3

description: Library name: Gb7_cocul3


title: HUVEC_alone 3

description: Library name: HUVEC_alone3

source_name: HUVEC

value: HUVEC

value: endothelial cells alone

value: mCherry


title: Gb7_alone3

description: Library name: Gb7_alone3

value: diffuse IDH wildtype glioblastoma stem cell line

value: YFP


title: HUVEC_alone 1

description: Library name: HUVEC_alone1


title: HUVEC_alone 2

description: Library name: HUVEC_alone2


title: HCMEC_cocul3

description: Library name: HCMEC_cocul3

growth_protocol: LGG275 were infected with GFP lentivirus (#VB200526-1117awv, Vector Builder) and  hCMEC/D3 cells (Human Umbilical Vein Endothelial Cell, Promocell) were infected with a mCherry lentivirus (#VB010000-9485zvg, Vector Builder) and selected by FACS. 1 day prior to the co-cultures, 3,4.105 HCMEC cells were seeded on 0,2% gelatin coated plates (#G2500, Sigma) in Endothelial Cell Basal Medium (#C-22111, Promocell) supplemented with recombinant human EGF (5 ng/ml), recombinant human basic Fibroblast growth factor (10 ng/ml), recombinant human Insulin-like Growth Factor (Long R3 IGF) (20 ng/ml), recombinant human Vascular Endothelial Growth Factor 165 (0,5 ng/ml), Ascorbic Acid (1 µg/ml), Heparin (22.5 µg/ml) and Hydrocortisone (0.2 µg/ml) and fetal calf serum (0.02 ml/ml). 3,0.105 glioma cells were added on top of HCMEC so that co-cultures experiments were performed at a ratio of 1:1,3 (HCMEC: glioma cells LGG275) for 48 hours before FACS isolation of transduced cells GFP+ and mCherry+ cells and subsequent RNA extractions.

value: diffuse IDH-mutant low-grade astrocytoma cell line-HCMEC

value: GFP+mCherry


title: Gb7_alone2

description: Library name: Gb7_alone2


title: Gb7_cocul1

description: Library name: Gb7_cocul1


title: HCMEC_cocul1

description: Library name: HCMEC_cocul1


title: HCMEC_alone1

description: Library name: HCMEC_alone1

source_name: HCMEC

value: HCMEC

value: endothelial cells


title: Gb7_alone1

description: Library name: Gb7_alone1


title: 275_cocul2

description: Library name: 275_cocul2


title: 8OG_unenrichment2

description: Library name: Sample4


title: HCMEC_cocul2

description: Library name: HCMEC_cocul2


title: 275_cocul3

description: Library name: 275_cocul3


title: 275_cocul1

description: Library name: 275_cocul1


title: HCMEC_alone2

description: Library name: HCMEC_alone2


title: HUVEC_cocul2

description: Library name: HUVEC_cocul2

data_processing:
BGI took care of the quality control of the samples, the construction of the mRNA library, the sequencing of the mRNAs making at least more than 30 million read lengths with 150 paired-end base pairs facilitating the alignment and therefore the reliability of the analysis as well as the verification and analysis steps of the data generated. Data filtering was done by SOAPnuke (R. Li et al., 2008) to (1) remove the readings from the sequencing adapters used; (2) remove low-quality readings with a baseline ratio ≤ 15 if the reading is greater than 20% of the reading phase; (3) remove reads where the number of unknown databases detected is greater than 5%. Then, the "clean" readings were stored in the standard FASTQ format. These reads were mapped to the reference genome using HISAT (D. Kim et al., 2015). To detect gene fusions and differentially expressed genes, Ericscript (0.5.5-5) (Benelli et al., 2012) and rMATS (v4.1.1) (Shen et al., 2014) were used, respectively. The Bowtie2 software (Langmead & Salzberg, 2012) was used to align the "clean" readings with the gene set. Gene expression levels were calculated by RSEM (v1.2.28) (B. Li & Dewey, 2011) to obtain quantification in read count, fragment per kilobase per million (FPKM) and number of transcripts per kilobase million (TPM). An analysis of differentially expressed genes (DEG) is also possible with DESeq2 (Love et al., 2014) or DEGseg (L. Wang et al., 2010) or PossionDis (Audic & Claverie, 1997) with the Q-value ≤ 0.05. The bioinformatics analyses were performed on the BGI, Dr. Tom software platform to visualize the data and extract gene expression in TPM.
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: One tab-delimited text file includes TPM for all sample

growth_protocol: LGG275 were infected with GFP lentivirus (#VB200526-1117awv, Vector Builder) and  HUVEC cells (Human Umbilical Vein Endothelial Cell, Promocell) were infected with a mCherry lentivirus (#VB010000-9485zvg, Vector Builder) and selected by FACS. 1 day prior to the co-cultures, 3,4.105 HUVEC cells were seeded on 0,2% gelatin coated plates (#G2500, Sigma) in Endothelial Cell Basal Medium (#C-22111, Promocell) supplemented with recombinant human EGF (5 ng/ml), recombinant human basic Fibroblast growth factor (10 ng/ml), recombinant human Insulin-like Growth Factor (Long R3 IGF) (20 ng/ml), recombinant human Vascular Endothelial Growth Factor 165 (0,5 ng/ml), Ascorbic Acid (1 µg/ml), Heparin (22.5 µg/ml) and Hydrocortisone (0.2 µg/ml) and fetal calf serum (0.02 ml/ml). 3,0.105 glioma cells were added on top of HUVEC so that co-cultures experiments were performed at a ratio of 1:1,3 (HUVEC: glioma cells LGG275) for 48 hours before FACS isolation of transduced cells GFP+ and mCherry+ cells and subsequent RNA extractions.

value: diffuse IDH-mutant low-grade astrocytoma cell line-HUVEC


title: 275_alone2

description: Library name: 275_alone2

value: diffuse IDH-mutant low-grade astrocytoma cell line

value: GFP


title: HCMEC_alone3

description: Library name: HCMEC_alone3


title: HUVEC_alone3

description: Library name: HUVEC_alone3


title: HUVEC_cocul1

description: Library name: HUVEC_cocul1


title: HUVEC_cocul3

description: Library name: HUVEC_cocul3


title: 275_alone3

description: Library name: 275_alone3


title: HUVEC_alone2

description: Library name: HUVEC_alone2


title: HUVEC_alone1

description: Library name: HUVEC_alone1


title: 275_cocul 3

description: Library name: 275_cocul3


title: 275_cocul 1

description: Library name: 275_cocul1


title: 275_cocul 2

description: Library name: 275_cocul2


title: 275_alone 1

description: Library name: 275_alone1


title: 275_alone 3

description: Library name: 275_alone3


title: 275_alone 2

description: Library name: 275_alone2