title: Input DMSO A

description: Library name: 1D

tag: replicate

value: A

tag: antibody

value: Input


title: Sample_13 [9769100151_R05C02]

status: Public on Jan 26 2026

type: genomic

city: Wantirna South

first: Rust

last: Turakulov

state: Victoria

address: u23 105 Mountain Hwy

department: Bioinformatics

country: Australia

institute: AGRF

description:
9769100151_R05C02
CLL

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: Blood

tag: group

value: Ref set

tag: material

value: Frozen

tag: age

tag: Sex

value: M

value: Sample 29

tag: mcf


title: Endocervical, SPD, noGV, replicate 1

type: SRA

city: Hanover

first: Olha

last: Kholod

state: NH

address: 15 Thayer Drive

country: USA

institute: Dartmouth College

description: Library name: ENDO_SPD-1_S10

library_source: transcriptomic

data_processing:
Transcript quantification from RNA-seq data was performed using Salmon and release 44 (GRCh38.p13) of the human genome. QC analyses were done with Fastqc for the raw fastq files. Several Bioconductor (v3.17) packages in R (v4.32) were used for subsequent steps. The transcriptome count data was annotated and summarized to the gene level with tximeta and further annotated with biomaRt.
Assembly: GRCh38.p13
Supplementary files format and content: combined count matrix and metadata file

molecule: total RNA

source_name: Endo

extract_protocol:
Cell culture media was collected for cell death assays, metabolomics analysis and Luminex and/or the cells were collected in Trizol for RNA extraction and RNA sequencing.
RNA-sequencing libraries were generated according to manufacturer’s instructions for the CORALL Total RNA-Seq Library Prep kit (Lexogen GmbH). Unique Dual Indexes Primer Pair Set were incorporated for multiplexed high-throughput sequencing.

tag: cell line

value: Endo

tag: cell type

value: Endocervical

tag: treatment

value: noGV


title: Ectocervical, SPM, noGV, replicate 1

description: Library name: ECTO_SPM-1_S3

source_name: Ecto

value: Ecto

value: Ectocervical


title: Ryp1 DMSO A

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description: Library name: 1A

library_source: genomic

data_processing:
Single or paired-end reads were aligned to the Histoplasma ohiense G217B genome (GCA_017607445.1) using BOWTIE2 version 2.4.2 with default parameters.  Peaks were called for each individual replicate with MACS2 version 2.2.7.1 with default parameters except that min-length was set to 100 for paired-end reads as recommended by Gaspar 2018.  Aggregate peaks were defined by taking the union of the coordinates of overlapping peaks among replicates for regions where peaks were called for at least two replicates. The aggregate peaks defined for 37 °C samples for a given TF were used for quantification of all samples for that TF.  Per peak signal was quantified by counting reads or read pairs in each aggregate peak, log2 transforming with pseudocount of 1 to handle missing data, and normalizing to the signal in the NPS1 negative control region. This negative control region was defined as the middle 500 bp of NPS1 (I7I48_05472, JAEVHH010000002: 444765..449764 (+)). Differential enrichment was then calculated as the difference of the means of the log2 signal over replicates from each condition. Peaks were assigned to individual genes if any part of the peak fell in the intergenic region between the stop codon of the upstream gene and before the start codon for that gene, limiting the intergenic size to a maximum of 10 kb as described in.
Assembly: GCA_017607445.1
Supplementary files format and content: Processed data file for each non-input sample is in MACS2 tab delimited text peaks format
Supplementary files format and content: Supplementary file Table_S8_S9.tar.gz is a tarball of two tab delimited text files, one for Ryp1 ChIP and one for Ryp2 ChIP.  Each file is Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format.  Each row represents a unique gene to peak association as given in the UNIQID column.  The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), HcG217B_acc (UCSF1 gene accessions [PMID:35089059]), and HcG217B (Gilmore et al transcript accessions [PMID: 26177267]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_ChIP (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  Following a GWEIGHT column, included for JavaTreeView compatibility, is ChIP enrichment for each sample followed by mean enrichment over all samples (A) and differential enrichment (DMSO/Ent50), with all enrichment values on a log2 scale.

organism: Histoplasma ohiense

source_name: fungal cell

growth_protocol: Cultures used for growth assays, RNA-seq and ChIP-seq studies were set up in triplicate biological replicates. When possible, inoculum from a single colony grown at 37 °C was used to start a liquid culture in HMM media. This liquid culture was passaged every 2-3 days in HMM media for a total of 2 passages before being used to inoculate a master culture in HMM + GlcNAc at an OD600 of 0.2 that was then aliquoted into replicates with equal volumes of each HDACi concentration being tested or DMSO. Cultures were incubated for 2 days at 37 °C and 5 % CO2 or at RT with shaking. Microscopy samples were harvested and fixed for 30 minutes with a solution of 4 % paraformaldehyde (PFA) every 24 hours for up to 3 days following incubation and stored long-term at 4 °C in PBS. Samples for genomic DNA isolation were harvested through centrifugation. Cell pellets used for isolating RNA, and protein samples were harvested through filtration using SFCA Membrane Nalgene Rapid-Flow Sterile Disposable Bottle Top Filters (Fisher 09-740-22G). 10-25 mL of culture was harvested from each flask and immediately flash frozen in liquid nitrogen before being stored at -80 °C.

extract_protocol:
Cultures processed for ChIP-seq were crosslinked with formaldehyde (Polysciences 18814-10) added to a final concentration of 1 % and kept under culture conditions (shaking at 37 °C with 5 % CO2 or ambient RT) for 20 minutes to allow fixing to take place. Crosslinking was quenched with glycine added to a final concentration of 125 mM for 5 minutes at RT. Fixed cells were pelleted at 3000 g for 10 minutes at 4 °C and washed twice with TBS (20 mM Tris-HCl (pH 7.5), 150 mM NaCl). Washed cells were harvested through filtration, aliquoted into pellets of equal mass (between 150-300 mg/tube) and flash frozen in liquid nitrogen as described above. Frozen pellets were resuspended in lysis buffer (50 mM Hepes/KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % sodium deoxycholate, protease/phosphatase inhibitors) at 4 °C before being bead beat with 500 µL of 0.5 mm zirconia beads in 5 x 1 minute cycles at RT with 2 minute rests on ice in between. The resulting lysate was then spun down at 8000 rpm for 10 minutes at 4 °C to isolate the insoluble chromatin fraction. This chromatin pellet was resuspended in 600-900 µL of lysis buffer and sonicated at 4 °C using the Diagenode Bioruptor® Pico for 30-35 cycles (30s on, 30s off). Sonicated samples were spun down for 5 min at 14,000 rpm at 4 °C to pellet cell debris and aliquots for input DNA were reserved at -20 °C in TE + 1 % SDS. Input samples were also used to assess shearing using a High Sensitivity DNA Bioanalyzer chip from Agilent. Equal lysate volumes were aliquoted for each IP to be performed and brought to a final volume of 500 µL with lysis buffer and 20 µg of each polyclonal ⍺-Ryp antibody (Ryp1: 3873, Ryp2: 387, and Ryp3: 356) or 3 µg of a ChIP-grade monoclonal ⍺-histone-acetyl antibody (H3K9Ac: ab177177 , H3K14Ac: ab52946, H4K16Ac: ab109463). Samples were incubated overnight with agitation at 4 °C before being incubated with 50 µL of a 50% slurry of Protein A Dynabeads (Life Technologies Corporation 10002D) pre-washed 2x with TBS and 3x lysis buffer for 2 hours at 4 °C with agitation.  Immunoprecipitated DNA was recovered through pulldown on Protein A beads using a magnetic rack. Pellets containing DNA-protein complexes were washed 2x in lysis buffer, 2x with high-salt (500 mM NaCl) lysis buffer, 2x with wash buffer (10 mM Tris/HCl (pH 8.0), 250 mM LiCl, 0.5 % NP-40, 0.5 % Na-deoxycholate, 1 mM EDTA) and 1x with TE before adding elution buffer (50 mM Tris/HCl (pH 8.0), 10 mM EDTA, 1 % SDS) and incubating at 65 °C for 10 minutes. DNA was eluted using a magnetic rack and the resulting beads were subjected to second round of resuspension and elution with 150 µl TE + 0.65 % SDS and pooled with the initial eluate to maximize total yield of DNA. IP and input samples were treated with 1 µL of Proteinase K (20 mg/mL Qiagen 19131) and incubated at 65 °C for approximately 16 hours. IP and Input DNA samples were then treated with 2 µg of RNase A (Qiagen) and incubated at 37 °C for 1 hour. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit (D5205) and eluted in 31 µL of ddH2O or TE.
Purified IP and input DNA were used for Illumina library preparation using the NEBNext Ultra II DNA Library Prep Kit (NEB E7103S) and Illumina dual-indexed primer pairs sourced from the UCSF CAT. The quality and size distribution of each library was assessed using the Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent Technologies 5067-4626) to ensure proper fragment size and the absence of contaminating adapters. Final library concentrations were measured using a Qubit HS dsDNA assay kit (Life Technologies Q33230) and used to pool equimolar amounts of each sample into final libraries for sequencing. Pooled libraries were used for single-end sequencing using one NovaSeq X 10B lane at the UCSF CAT.

tag: genotype

tag: additive

value: DMSO

value: fungal cell


title: Sample_21 [9769100165_R06C01]

description:
9769100165_R06C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Test set

value: Sample 27


title: MCL-135

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

data_processing:
Sample sequencing was performed on the Illumina NextSeq 500 to generate paired-end 50- nucleotide reads (discovery cohort) or Illumina HiSeq 2500 to generate paired-end 75-nucleotide reads (validation cohort).
Basespace (Illumina) was used for demultiplexing and FASTQ file generation.
A Nextflow v21.10.6 RNA-Seq pipeline aligned reads using hg38 and STAR v2.6.0c.
Counts were calculated using RSEM v1.3.1 using Ensembl v108 annotation. Quality metrics were calculated with STAR and RSeQC. RNA-seq processing pipeline software (https://github.com/compbiomed/RNA_Seq/blob/master/RNA_Seq.nf): nextflow v21.10.16, star v2.6.0c, rsem v1.3.1, FastQC v0.11.7, Picard tools v2.18.11, GATK v3.8-1, rseqc v3.0.0, multiqc v1.6, samtools v1.9.
Assembly: hg38
Supplementary files format and content: exp_count.txt: tab-delimited text file with raw expected counts for each sample

source_name: lung adenocarcinoma

extract_protocol:
Total RNA was extracted from FFPE tissue with the Qiagen AllPrep DNA/RNA Universal Kit.
Exome-targeted sequencing libraries were prepared with the Illumina TruSeq RNA Exome Library Prep Kit.

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: NST

tag: tnm 8th_edition_stage

tag: passed qc

value: FALSE

tag: mean tin

tag: site

value: LHMC

tag: sequence batch


title: MCL-092

tag: tissue

value: LMP

value: TRUE


title: MCL-113

value: BMC


title: TCGA-FA-A82F-01 [9828653029_R01C02]

description:
9828653029_R01C02
DLBCL_EN

source_name: Diffuse large B-cell lymphoma, IPTNA

value: Diffuse large B-cell lymphoma, IPTNA

value: Small intestine

tag: group

value: Ref set

tag: material

value: Frozen

tag: age

tag: Sex

value: F

value: TCGA


title: MCL-057


title: MCL-054


title: Sample_7 [9769100165_R04C01]

description:
9769100165_R04C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

tag: mcf


title: Ectocervical, NT, noGV, replicate 1

description: Library name: ECTO_NT-1_S1

tag: cell line

value: Ecto

tag: cell type

value: Ectocervical

tag: treatment

value: noGV


title: Sample_41 [9769100151_R05C01]

description:
9769100151_R05C01
CLL

value: Sample 28


title: Plasma EV miRNA from CC patient 2

city: Xining

first: Rui

last: yang

state: Qinghai

address: Affiliated Hospital of Qinghai University

country: China

description:
Library name: CC_P2
Plasma EV miRNA profiling

data_processing:
Raw reads were quality-checked using FastQC.
Adapter sequences were trimmed using Cutadapt.
Reads were aligned to the human reference genome (GRCh38) using Bowtie/STAR.
miRNA counts were quantified using miRDeep2 or featureCounts.
Differential expression analysis was performed using DESeq2 or edgeR.
GRCh38 (human)
Assembly: FASTA-formatted miRNA expression matrix; contains miRNA IDs as headers and expression counts per sample.
Supplementary files format and content: Optional: normalized count table in TXT/CSV format.

source_name: plasma

growth_protocol: N/A (Plasma samples; no cell growth)

extract_protocol:
Extracellular vesicles were isolated from plasma using differential ultracentrifugation, followed by RNA extraction using a miRNA-specific kit.
Small RNA libraries were prepared from EV RNA using Illumina TruSeq Small RNA Library Prep Kit according to manufacturer’s instructions.

treatment_protocol: N/A (No treatment applied; clinical plasma samples)

value: plasma

value: EV

tag: batch


title: Ryp3 DMSO A

description: Library name: 1C

tag: genotype

tag: additive

value: DMSO

tag: replicate

value: A

tag: antibody

value: fungal cell


title: Plasma EV miRNA from CC patient 3

institute: Affiliated Hospital of Qinghai University

description:
Library name: CC_P3
Plasma EV miRNA profiling


title: rpd3delta RT C

description: Library name: RT_rpd3_C

data_processing:
Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Histoplasma G217B transcriptome (S5 Data of Gilmore et al. 2015).  Relative abundances (reported as TPM values and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.2. Further analysis was restricted to transcripts with estimated counts ≥ 10 in at least nine samples.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.46.0.  Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 2x (absolute log2 fold change ≥ 1) for a given contrast.
Assembly: Version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PMID:26177267)
Supplementary files format and content: The results of the LIMMA analysis are in processed data file Table_S7.txt, an Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the ucsf_hc.01_1.G217B systematic gene name. The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), and HcG217B_acc (UCSF1 gene accessions [PMID:35089059]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_ChIP (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  The next 5 columns give LIMMA BH-adjusted p-values for differential expression in each of the 5 contrasts, and the corresponding LIMMA-fit log2 ratios are given in the final 5 columns.  The next 18 columns give KALLISTO estimated counts for each transcript in each sample. GWEIGHT is a place-holder column for JavaTreeView compatibility.  The estimated counts in this file are sufficient to recapitulate the LIMMA analysis.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from fungal cells as previously described [18-19] with Qiazol (Qiagen 79306). Frozen cell pellets were resuspended in equal volumes of Qiazol and subjugated to bead beating with 0.5 µM zirconia beads (Spectrum Chemical 140-19990-E1) and extraction using chloroform. The resulting aqueous phase was transferred to Epoch SpinTM RNA columns (Epoch Life Sciences 1940-250) to isolate RNA and subjected to sequential washes with 3 M NaOAc (pH = 5.5) and 10 mM TrisCl (pH = 7.5) in 80 % ethanol. The columns were then treated with Purelink DNAse (Invitrogen 12185010) and subjected to additional washes with 3 M NaOAc (pH = 5.5) and 10 mM TrisCl (pH = 7.5) in 80 % ethanol before being eluted with RNAse-free water. The organic phases of each sample were reserved at -20 °C for total protein extraction.  Equal amounts of total RNA (between 5-10 ng) across all samples were used for mRNA isolation. These samples were subjected to a second round of DNAse treatment (Turbo DNAse, Fisher Scientific AM1907) and their quality was assessed with an RNA 6000 Nano Bioanalyzer Kit (Agilent Technologies 5067-1511). Three rounds of poly-A selection using oligo-dT Dynabeads® (Invitrogen 61005) was used to purify mRNA, and mRNA enrichment was verified with an RNA 6000 Nano Bioanalyzer chip.
Poly-A-selected RNA was used to generate libraries with the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S). Each sample was dual indexed with unique primers (UCSF Center For Advanced Technology (CAT)) compatible for multiplexed sequencing. Library quality and size was assessed with the Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent Technologies 5067-4626) to ensure proper fragment size (~300-400 bp) and the absence of contaminating adapters. Final library concentrations were measured using a Qubit HS dsDNA assay kit (Life Technologies Q33230) and equal amounts were pooled into a final library for sequencing. Pooled libraries were used for single-end sequencing using one NovaSeq X lane at the UCSF CAT.

value: C

tag: temperature

value: RT


title: G217B RT C

description: Library name: RT_G217B_C


title: MCL-036

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: VI

tag: tnm 8th_edition_stage

tag: passed qc

value: FALSE

tag: mean tin

tag: site

value: BMC


title: hos2delta RT C

description: Library name: RT_hos2_C


title: rpd3delta RT B

description: Library name: RT_rpd3_B

value: B


title: Plasma EV miRNA from healthy control 3

description:
Library name: HC_C3
Plasma EV miRNA profiling

tag: tissue


title: MCL-029

value: NST

value: TRUE

tag: sequence batch


title: Plasma EV miRNA from CC patient 1

description:
Library name: CC_P1
Plasma EV miRNA profiling

tag: cell type


title: Sample_65 [9769100134_R02C01]

description:
9769100134_R02C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

tag: group

value: Test set

tag: material

value: Frozen

tag: age

tag: Sex

value: M

value: Sample 30

tag: mcf


title: Sample_77 [9769100151_R02C02]

description:
9769100151_R02C02
CLL

value: F


title: Plasma EV miRNA from healthy control 2

description:
Library name: HC_C2
Plasma EV miRNA profiling

value: plasma

value: EV

tag: batch


title: Sample_3 [9769100151_R03C02]

description:
9769100151_R03C02
CLL

value: Ref set


title: Sample_2 [9769100124_R03C02]

description:
9769100124_R03C02
CLL


title: IL17_PA_GW4064_3

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

description:
Library name: Sample 9
RNA-seq

data_processing:
RNA-seq raw files (fastq, PE150) were aligned to the GRCm38/hg38 version of the human reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCh38/hg38
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.

source_name: Skin

growth_protocol: Human epidermal keratinocytes (HaCaTs) (XL biotec, #300493) were cultured in Dulbecco's modified Eagle’s medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 100 U/mL penicillin‒streptomycin (Thermo Fisher Scientific) at 37°C in 5% CO2.

extract_protocol:
Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.
The RNA-seq library preparation was followed by the instructions of LC Bio Technology CO., Ltd.

treatment_protocol: After reaching 70% confluence, keratinocytes were treated with IL-17 (50 ng/mL) and palmitic acid  (PA, 100 μM) for 24 hours. GW4064 (10 μM) and GCDCA (bile acids, 100 μM) were added to the culture medium to activate FXR signaling.

value: Skin

tag: cell line

value: HaCaT

value: Keratinocytes

tag: genotype

value: Immortalized cell line

tag: treatment


title: G217B RT A

description: Library name: RT_G217B_A

tag: replicate

value: A

tag: temperature

value: RT

value: fungal cell


title: N-2

city: Shanghai

first: Tiansheng

last: Xu

state: Shanghai

address: Shanghai

institute: OE

description:
Library name: 4
commen method

data_processing:
Base calling and quality control. Raw reads were processed to remove adapter sequences and low-quality reads using  Cutadapt. Reads shorter than 15 nt and longer than 41 nt were discarded.
Clean reads were mapped to the reference genome and/or miRBase (v22) using Bowtie.
miRNA expression levels were quantified.
Read counts were normalized to TPM
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited text file of all samples' TPM

organism: Rattus norvegicus

source_name: serum

extract_protocol:
Total RNA was extracted from tissue samples using Trizol reagent (Invitrogen, USA) following the manufacturer's instructions. RNA purity and concentration were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer's protocol. Briefly, 1 µg of total RNA was used as input. 3' and 5' SR adaptors were ligated to the RNA, followed by reverse transcription and PCR amplification. The PCR products were size-selected using 6% polyacrylamide gel electrophoresis (PAGE) to isolate fragments of ~140-160 bp.

value: serum

value: Exercise


title: E-2

description:
Library name: 2
commen method

value: Sedentary


title: N-1

description:
Library name: 3
commen method


title: Sample_14 [9769100124_R02C01]

description:
9769100124_R02C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

value: Frozen


title: hos2delta RT B

description: Library name: RT_hos2_B

value: B


title: MCL-007

value: lung adenocarcinoma

tag: sample type

value: FFPE

tag: patient id

tag: cohort

value: discovery cohort

tag: novel grade

value: LMP

tag: tnm 8th_edition_stage

tag: passed qc

value: TRUE

value: LHMC


title: rpd3delta RT A

description: Library name: RT_rpd3_A

tag: cell type


title: Sample_1 [9769100124_R01C01]

description:
9769100124_R01C01
CLL

tag: tissue

tag: group

value: Ref set

tag: material

value: M


title: IL17_PA_GW4064_1

description:
Library name: Sample 7
RNA-seq

value: Skin

value: HaCaT

value: Keratinocytes

value: Immortalized cell line


title: hos2delta 37 C

description: Library name: 37_hos2_C

value: C

value: fungal cell


title: HLA-A2 "high" cells, sorted on HLA-A2 surface expression

city: Philadelphia

first: Nikolaos

last: Sgourakis

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Library name: tapasin-TM library sorted for the rescue of surface HLA-A2 expression in EBc-1 cells

data_processing:
Generate protein sequence using ./seqkit translate
Perform Read alignment to reference sequence and generate BAM file
Run GATK DSM analysis tool on local directory
Compute amino acid log2 enrichment/depletion ratios and sequence conservation scores
Assembly: Reference DNA sequence: atggccgtcatggcgccccgaaccctcgtcctgctactctcgggggccctggccctgacccagacctgggcgggctccgactacaaggacgatgatgacaagggaggatccggccctgccgtaatcgagtgttggtttgttgaagacgctagtggtaaagggctggctaaacggccaggcgcacttctgttgcggcaaggtccgggagaaccacctccacgacccgacttggaccctgaattgtacctctctgtacacgacccagctggagcactccaagctgctttccgacggtacccaagaggtgctccagcaccgcattgcgagatgagtcggttcgttcctttgcctgcgagtgcaaagtgggcatcaggtctgacaccagcacaaaactgtccacgagcgcttgatggagcgtggctgatggtttccataagctctccggtgctttcactgtcatcactgctcaggccacaacctgaaccccaacaagaacccgtactgataacaatggcgacggtagtccttacggtccttacgcatacaccagcacccagggtgcgattgggacaagacgcactcctcgaccttagctttgcgtacatgccaccaacctcagaggcggcttcctctcttgcaccaggaccaccaccgttcggccttgaatggagacgacagcacttggggaagggccatttgctgttggctgctaccccagggctgaacgggcagatgccggcagcacaagagggagccgtagcttttgctgcgtgggatgatgacgaaccatggggaccatggactggaaacgggactttctggctgccaacagtacagccctttcaagaaggaacgtatctggccaccatccatttgccttatctgcaaggccaggtcacacttgaactcgctgtctataaaccgcctaaggtgagtctcatgcccgcaactttggctagggcagcacctggcgaagctccacctgaattgctctgtttggtatcccatttctaccccagtggtggccttgaagtggaatgggaacttagaggaggaccaggtggtcgatctcagaaagctgaagggcagcgatggctctccgctctcaggcaccactcagacggatctgtatcactgtcagggcatttgcagccaccgccagttaccaccgagcagcatggagctcggtatgcgtgtcgcattcaccaccctagccttccggcgtcaggaagatcagcggaggtaacacttgaggtcgctgggttgtccggacccagcttggaggacagttctggagccggaagtgctatccccatcatgggtatcgttgctggcctggttgtccttgcagctgtagtcactggagctgcggtcgctgctgtgctgtggagaaagaagagctcagattga
Supplementary files format and content: Processed data file includes WT amino acid residue (column B) and residue number (Column A), subsitution (Column C), and frequency of each mutation in the naïve library (Column D). Log2 enrichment of each mutation in the sorted population relative to the naïve library is also listed (Column E).

source_name: Adrenal mass

growth_protocol: EBc-1 cells were cultured in Advanced RPMI Medium (Thermo Fisher) supplemented with 10% premium heat inactivated fetal bovine serum, 5% HEPES, 5% Glutamine, 5% Penicillin Streptavidin (Thermo Fisher). Cells were cultured at 37 °C and 5% CO2.

extract_protocol:
Sorted and naïve cell populations were harvested, genomic DNA was isolated (Monarch) and the tapasin gene was PCR amplified and isolated (Monarch).
The same library was used as in submission GSE159247

treatment_protocol: Cell transduced with the tapasin library were sorted using the transduction marker FLAG (DYKDDDDK). FLAG sorted cells were used as the naïve cell population. This population was then sorted to isolate cells with the highest surface HLA-A2 expression.

value: Adrenal mass

value: neuroblastoma

value: anti HLA-A2 antibody (BB7.2)


title: rpd3delta 37 C

description: Library name: 37_rpd3_C


title: Sample_3 [9769100124_R04C02]

description:
9769100124_R04C02
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

value: Frozen

tag: age

tag: Sex

tag: mcf


title: Sample_57 [9769100107_R06C02]

description:
9769100107_R06C02
CLL

value: Test set


title: G217B 37 C

description: Library name: 37_G217B_C

tag: genotype


title: Plasma EV miRNA from healthy control 1

description:
Library name: HC_C1
Plasma EV miRNA profiling

value: plasma

value: EV

tag: batch


title: Sample_4 [9769100124_R05C02]

description:
9769100124_R05C02
CLL

value: Ref set

value: F


title: IL17_PA_3

description:
Library name: Sample 3
RNA-seq

value: Skin

tag: cell line

tag: treatment


title: hos2delta 37 B

description: Library name: 37_hos2_B

tag: replicate

value: B

tag: temperature


title: Ulcerative colitis patient 2 - terminal ileum biopsy, and rectum biopsy [UC02_TL_RE]

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description:
Library name: Ulcerative colitis patient 2 - terminal ileum biopsy, and rectum biopsy
Two samples are located on the slide: terminal ileum biopsy, and rectum biopsy
Visium slide serial numbe: H1-P7CQ3M6
Visium capture area identifier : A1

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger v3.0.0 pipeline to generate gene-expression matrix per each slide.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expressin count data in Matrix Market Exchange Format
Supplementary files format and content: HE.tif : H&E brightfield image
Supplementary files format and content: CytAssist.tif : Brightfield image generated by the CytAssist instrument
Supplementary files format and content: aligned.json : Alignment file produced by the Loupe Browser manual alignment step
Supplementary files format and content: tissue_hires_image.png : hi-res image of tissue
Supplementary files format and content: tissue_lowers_image.png : low-res image of tissue
Supplementary files format and content: scalefactors_json : scalefactors in json format
Supplementary files format and content: tissue_positions.parquet : spot-level table of tissue positions in parquet format
Library strategy: Spatial Transcriptomics

source_name: terminal ileum, colon

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tissue sections, 5 µm thick, were mounted on Visium HD slides (10x Genomics) using the CytAssist instrument according to the manufacturer’s protocol.
Sections were deparaffinized, rehydrated, and subjected to hematoxylin and eosin (H&E) staining following the 10x Genomics Visium HD FFPE tissue preparation guidelines. After imaging, RNA molecules were released and hybridized to slide-bound barcoded capture probes, enabling in situ capture of spatially resolved transcriptomes.

value: terminal ileum, colon

tag: subject status

value: Ulcerative colitis patient


title: E-1

description:
Library name: 1
commen method

value: serum

value: Sedentary


title: Sample_27 [9721367080_R05C01]

description:
9721367080_R05C01
CLL


title: Sample_5 [9721367075_R03C02]

description:
9721367075_R03C02
CLL

value: M


title: G217B RT B

description: Library name: RT_G217B_B

value: RT

value: fungal cell


title: IL17_PA_GCDCA_3

description:
Library name: Sample 6
RNA-seq

value: HaCaT

value: Keratinocytes

value: Immortalized cell line


title: hos2delta RT A

description: Library name: RT_hos2_A

value: A


title: QGP1_Apilimod_Rep1

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

description: Library name: 38892

data_processing:
Raw sequencing reads demultiplexing was performed using Illumina’s bcl2fastq software v2.20, and quality control was conducted using FastQC. Adapters and low-quality bases were moved out with Trimmomatic. Transcript-level quantifications were summarized to gene-level counts, which were normalized using TMM normalization (calcNormFactors in edgeR). Genes with low expression (mean TPM < 1 across all groups) were filtered out. Differential expression analysis was conducted using DESeq2 to identify differentially expressed genes (DEGs) between PIKfyve knockdown vs. NC cell lines or Apilimod vs. DMSO-treated QGP-1 cells.
Assembly: hg38
Supplementary files format and content: csv files including CPM values for each samples

extract_protocol:
Total RNA was extracted from cells using miRNeasy Kit (QIAGEN) following the manufacturer’s instructions after cells were lysed in QIAzol Lysis Reagent. RNA concentration and purity were assessed using NanoDrop.
RNA integrity was assessed using the Agilent Bioanalyzer with the Eukaryote Total RNA Nano Kit (Agilent Technologies, #5067-1511). Ribosomal RNA was removed enzymatically using the KAPA RNA HyperPrep Kit with RiboErase HMR (Roche; catalog #08098140702), followed by heat fragmentation of RNA to ~200–300 bp in fragmentation buffer. First-strand cDNA synthesis was performed using reverse transcriptase and random primers, and double-stranded cDNA was generated through second-strand synthesis. End-repair and adapter ligation were carried out using New England Biolabs (NEB) adapters, and libraries were amplified with KAPA HiFi HotStart mix and NEB dual barcodes.

value: neuroendocrine tumor cell

value: WT


title: Sample_23 [9769100107_R02C02]

description:
9769100107_R02C02
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

value: Test set

value: Frozen


title: Sample_55 [9769100025_R01C01]

description:
9769100025_R01C01
CLL


title: rpd3delta 37 B

description: Library name: 37_rpd3_B

value: B


title: Sample_29 [9721367080_R06C01]

description:
9721367080_R06C01
CLL


title: Sample_19 [9704031036_R06C02]

description:
9704031036_R06C02
CLL


title: Ulcerative colitis patient 1 - terminal ileum biopsy, and sigmoid colon biopsy [UC01_TI_SCA40]

description:
Library name: Ulcerative colitis patient 1 - terminal ileum biopsy, and sigmoid colon biopsy
Two samples are located on the slide: terminal ileum biopsy, and sigmoid colon biopsy
Visium slide serial numbe: H1-P7CQ3M6
Visium capture area identifier : D1

value: terminal ileum, colon

value: Ulcerative colitis patient


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Day_rep3

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

description: Library name: D3SC

data_processing:
The RNA-seq count matrix was analyzed using the DESeq2 v1.40.2 package (Love et al., 2014). Genes with less than one read in 10% of the samples were removed before normalization and were considered non-expressed. To perform principal component analysis (PCA), normalized counts were transformed using the vst function in DESeq2, and the top 500 genes with the most variation were used to calculate the principal components with the plotPCA function. The samples were colored based on cell types and sampling times. For differential analysis, the model used in DESeq2 considered the cell type, sampling time, and interaction between the two covariates. The p-values were adjusted (p-adj) using the FDR method implemented in the results function. Genes with a log2-fold change greater than 0.58 and a p-adj smaller than 0.05, were considered differentially expressed genes (DEGs). Three p-adj cut-offs (0.001, 0.01, and 0.05) were used to characterize the significance intensity.
Assembly: “Zea_mays.B73_RefGen_v4.dna.toplevel.fa.gz” from the B73 v4 version, Downloaded on https://ftp.gramene.org/maize/v4/fasta/zea_maysb73v4/dna/ )
Supplementary files format and content: tab delimited text with read count for each samples

organism: Zea mays

source_name: Leaves

growth_protocol: Maize B104 seeds were germinated and transferred to potting soil, as previously described. The plants were grown in a phytotron under a 16/8 h light/dark cycle (25/22 °C) and a daytime light intensity of 200 mmol. m−2. s−1 at the top of the leaves. Humidity was maintained between 60% and 70% in the growth chamber.

extract_protocol:
On the day before the microdissection, the peeled epidermal strips were freeze-dried at -40 °C for 10 h under pressure of 10 Pa in a Labconco® Free-Zone Plus freeze-drier. At the end of the process, the temperature slightly increased to room temperature for 3 h. A few drops of absolute ethanol were placed on the strips to flatten them. The samples were stored in a desiccator under vacuum at room temperature until microdissection, to avoid rehydration. GCs and SCs were collected using a PALM MicroBeam system (Carl Zeiss MicroImaging GmbH). GCs or SCs were selected using Zeiss software and cut using a laser. After cutting, cells were pressure catapulted and collected immediately in a tube with an adhesive cap (Carl Zeiss™ 415190-9211-000). Approximately 1500 cells were collected in one tube, and two tubes were used to collect cells for each sample. After cell collection, 175 µL of lysis buffer with 1% (v/v) β-mercaptoethanol was immediately added to each tube with two steel beads. The tubes were shaken at maximum speed for 30 s with an MM2 mixer mill (Retsch) and then inverted for 5 min to improve the lysis yield, followed by a short spin to remove air bubbles. Tubes from the same sample were mixed in one tube that was stored at -20 °C until RNA extraction. In total, 16 samples were microdissected with two cell types (GCs and SCs), two sampling time (day and night) and four replicates. Microdissection was performed at approximately 19 °C and 30% relative humidity. RNA extraction was performed using RNeasy Plus Micro Kits (Qiagen) following the manufacturer’s instructions. Total RNA was eluted with 14 µL of nuclease-free water and stored at -80 °C until further use.
cDNA amplification was prepared from 10.5 µl (about 10pg) total RNA with Takara SMART-Seq® v4 Ultra® Low Input RNA Kit. Libraries were prepared from 150ng cDNA using Nextera XT DNA Library Preparation Kit and Nextera index Kit V2. The sequencing was carried out at the LCSB sequencing platform (RRID: SCR_021931) at the University of Luxembourg. The pooled libraries were sequenced on an Illumina NextSeq500 (NextSeq 500/550 High Output Kit v2.5 (300 Cycles)) to generate 100 base-pairs paired-end reads. FASTQ files were imported in pairs in CLC genomics workbench v11.0.1 discarding poor-quality reads (<Q30). For each library, reads were trimmed and filtered using the following criteria: sequence quality score <0.01, no ambiguous nucleotides, minimum read length >35 nucleotides, trimming against the Illumina adaptor sequence and polyN>8, and finally a hard trim of 20 nucleotides at the 5’ end and 2 nucleotides at the 3’ end. The filtered reads were aligned on the genome contained in the file “Zea_mays.B73_RefGen_v4.dna.toplevel.fa.gz” from the B73 v4 version (downloaded on https://ftp.gramene.org/maize/v4/fasta/zea_maysb73v4/dna/ ), as the annotations for this version were more stable.

treatment_protocol: Epidermal strips were peeled from the third leaf of two-week-old maize seedlings. They were placed on microscope glass slides (plain microscope slides 76x26mm, 0.8 mm x 1.00 mm, AGL4242) and flash-frozen with liquid nitrogen. The samples were immediately stored at -80 °C until microdissection. The samples were collected at two times, i.e., day (two hours after the light onset) and night (two hours after the light offset). Four independent collections were carried out.

value: Leaves

value: Day


title: IL17_PA_2

description:
Library name: Sample 2
RNA-seq

value: Skin


title: Sample_67 [9769100042_R02C02]

description:
9769100042_R02C02
CLL

value: Ref set

value: F


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Dayst_rep3

description: Library name: N3SC

value: Night


title: IL17_PA_GW4064_2

description:
Library name: Sample 8
RNA-seq

value: HaCaT

value: Keratinocytes

value: Immortalized cell line


title: IL17_PA_1

description:
Library name: Sample 1
RNA-seq


title: Sample_1 [9704031036_R06C01]

description:
9704031036_R06C01
CLL


title: IL17_PA_GCDCA_1

description:
Library name: Sample 4
RNA-seq


title: QGP1_DMSO_Rep2

description: Library name: 38894

value: neuroendocrine tumor cell

value: WT

value: DMSO


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Dayst_rep1

description: Library name: N1SC


title: Sample_61 [9704031036_R05C02]

description:
9704031036_R05C02
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

value: M


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Dayst_rep2

description: Library name: N2SC


title: rpd3delta 37 A

description: Library name: 37_rpd3_A

value: A

value: fungal cell


title: G217B 37 A

description: Library name: 37_G217B_A


title: QGP1_DMSO_Rep1

description: Library name: 38890


title: G217B 37 B

description: Library name: 37_G217B_B

value: B


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Day_rep4

description: Library name: D4SC

value: Leaves

value: Day


title: IL17_PA_GCDCA_2

description:
Library name: Sample 5
RNA-seq

value: Skin


title: QGP1_Apilimod_Rep2

description: Library name: 38896


title: Sample_5 [9704031036_R04C02]

description:
9704031036_R04C02
CLL

value: Ref set

value: Frozen

value: Sample 33


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Dayst_rep4

description: Library name: N4SC

value: Night


title: transduced cells, sorted on FLAG surface expression

description: Library name: Naïve tapasin-TM library

value: Adrenal mass

value: neuroblastoma

value: anti FLAG antibody (L5)


title: QGP1_sgPIKFYVE_1_Rep2

description: Library name: 38818

value: neuroendocrine tumor cell

value: PIKFYVE knockdown


title: QGP1_sgPIKFYVE_1_Rep1

description: Library name: 38814


title: hos2delta 37 A

description: Library name: 37_hos2_A


title: 4R PLSF-het cells, DIV15, biological replicate 1

city: Munich

first: Dominik

last: Paquet

state: Bavaria

address: Feodor-Lynen-Str. 17

department: Institute for Stroke and Dementia Research

country: Germany

institute: University Hospital LMU Munich

description: Library name: P2H6_DIV15_I

data_processing:
Data preprocessing including quality control, trimming and alignment were performed using nf-core/rnaseq (v 3.20)
Alignment with STAR (2.7.9a) usign standard parameters
Reads were counted using Salmon (1.10.1)
Reads mapped to each transcript against the RefSeq hs38
Low-expression genes with fewer than 10 total counts across all samples were filtered prior to analysis.
Assembly: GRCh38p13
Supplementary files format and content: txt file includes filtered raw count table

extract_protocol:
500 000 cells were collected for each independent replicate during differentiation at DIV15 and DIV35, snap frozen in liquid nitrogen and stored at -80°C. RNA was isolated from frozen cell pellets using the RNeasy Mini Kit (Qiagen 74104) according to manufacturer’s instructions.
250ng total RNA was used to generate NGS libraries and 100bp paired end sequencing was performed using a DNBseq platform.

treatment_protocol: For Nocodazole treated samples, media was supplemented with nocodazole to a final concentration of 3 nM Nocodazole for 36h prior to the timepoint of collection.

value: neuronal precursor cells

value: MAPT WT/4R P301L S320F


title: QGP1_Torin1_Rep1

description: Library name: 38891

value: WT


title: QGP1_sgNC_Rep2

description: Library name: 38817


title: 4R PLSF-het cells, DIV35, biological replicate 3

description: Library name: P2H6_DIV35_III

value: early neurons


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Day_rep2

description: Library name: D2SC


title: 4R PLSF-het cells, DIV35, biological replicate 2

description: Library name: P2H6_DIV35_II


title: 4R PLSF-het cells, DIV35, biological replicate 1

description: Library name: P2H6_DIV35_I


title: Maize_B104_Laser_Dissected_Guard_Cells_Night_rep1

description: Library name: N1GC


title: Sample_33 [9704031036_R04C01]

description:
9704031036_R04C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

value: F

value: Sample 32


title: Sample_15 [9721367075_R02C01]

description:
9721367075_R02C01
CLL

value: Ref set


title: QGP1_sgNC_Rep1

description: Library name: 38813


title: 4R cells, DIV35, biological replicate 2

description: Library name: P1H4_DIV35_II

value: MAPT WT/4R


title: Maize_B104_Laser_Dissected_Subsidiary_Cells_Day_rep1

description: Library name: D1SC

value: Leaves

value: Day


title: Sample_37 [9704031036_R01C02]

description:
9704031036_R01C02
CLL

value: Test set

value: Frozen

value: M


title: BON1_Day14_B

description: Library name: 39343

data_processing:
Raw reads (paired-end fastq files) were modified, swapping mates such that R1 contains the reverse primer end of the DNA fragment.
Counting was performed on modified R1 reads using mageck count v 0.5.9.5 with the --reverse-complement option.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing sgRNA annotation (ID, pool, sequence) and sample counts.
Library strategy: CRISPR Screen

extract_protocol:
Both day 0 and day 14 samples were harvested for genomic DNA (gDNA) isolation using DNAeasy blood and tissue kit (Qiagen) in accordance with the manufacturer’s protocol.
For the amplification procedure, Herculase II Fusion DNA Polymerase (Agilent Technologies) was applied to each sample starting from 5 µg gDNA. First-round forward primer: TTTGCATATACGATACAAGGCTG; First-round reverse primer: TCAAGATCTAGTTACGCCAAGC; Second-round forward primer: TTTCTTGGGTAGTTTGCAGTTTT; Second-round reverse primer: TCAAGATCTAGTTACGCCAAGC. Then the amplified DNA was purified by Select-a-Size DNA Clean & Concentrator kit (Zymo Research) and 6% Novex TBE gel (Thermo). After isolating PCR products from gel using Gel Breaker Tubes and Gel Filters (BioChain), the end-repair and A-tail were added for New England Biolabs (NEB) adapter ligation for library establishment. At last, 2 × KAPA HiFi HotStart mix and NEB dual code barcode were used to enrich adapter-ligated DNA fragments for final library preparation, which was sequenced using an Illumina NovaSeq 6000.

value: neuroendocrine tumor cell

tag: time (days)


title: Maize_B104_Laser_Dissected_Guard_Cells_Day_rep4

description: Library name: D4GC


title: Sample_17 [9704031029_R05C02]

description:
9704031029_R05C02
CLL


title: QGP1_Torin1_Rep2

description: Library name: 38895


title: 4R PLSF-het cells, DIV15, biological replicate 3

description: Library name: P2H6_DIV15_III


title: 4R cells, DIV15, biological replicate 1

description: Library name: P1H4_DIV15_I


title: BON1_Day0_A

description: Library name: 39321


title: Maize_B104_Laser_Dissected_Guard_Cells_Night_rep3

description: Library name: N3GC

value: Night


title: G217B DMSO RT day 2 C

description: Library name: RTC_D2

data_processing:
Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Histoplasma G217B transcriptome (S5 Data of Gilmore et al. 2015).  Relative abundances (reported as TPM values and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.2. Further analysis was restricted to transcripts with estimated counts ≥ 10 in at least four samples.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.46.0.  Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 2x (absolute log2 fold change ≥ 1) for a given contrast.
Assembly: Version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PMID:26177267)
Supplementary files format and content: The results of the LIMMA analysis are in processed data file Table_S6.txt, an Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the ucsf_hc.01_1.G217B systematic gene name. The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), and HcG217B_acc (UCSF1 gene accessions [PMID:35089059]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_ChIP (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  The next 7 columns give LIMMA BH-adjusted p-values for differential expression in each of the 7 contrasts, and the corresponding LIMMA-fit log2 ratios are given in the final 7 columns.  The next 21 columns give KALLISTO estimated counts for each transcript in each sample. GWEIGHT is a place-holder column for JavaTreeView compatibility.  The estimated counts in this file are sufficient to recapitulate the LIMMA analysis.

extract_protocol:
Total RNA was extracted from fungal cells as previously described [18-19] with Qiazol (Qiagen 79306). Frozen cell pellets were resuspended in equal volumes of Qiazol and subjugated to bead beating with 0.5 µM zirconia beads (Spectrum Chemical 140-19990-E1) and extraction using chloroform. The resulting aqueous phase was transferred to Epoch SpinTM RNA columns (Epoch Life Sciences 1940-250) to isolate RNA and subjected to sequential washes with 3 M NaOAc (pH = 5.5) and 10 mM TrisCl (pH = 7.5) in 80 % ethanol. The columns were then treated with Purelink DNAse (Invitrogen 12185010) and subjected to additional washes with 3 M NaOAc (pH = 5.5) and 10 mM TrisCl (pH = 7.5) in 80 % ethanol before being eluted with RNAse-free water. The organic phases of each sample were reserved at -20 °C for total protein extraction.  Equal amounts of total RNA (between 5-10 ng) across all samples were used for mRNA isolation. These samples were subjected to a second round of DNAse treatment (Turbo DNAse, Fisher Scientific AM1907) and their quality was assessed with an RNA 6000 Nano Bioanalyzer Kit (Agilent Technologies 5067-1511). Three rounds of poly-A selection using oligo-dT Dynabeads® (Invitrogen 61005) was used to purify mRNA, and mRNA enrichment was verified with an RNA 6000 Nano Bioanalyzer chip.
Poly-A-selected RNA was used to generate libraries with the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S). Each sample was dual indexed with unique primers (UCSF Center For Advanced Technology (CAT)) compatible for multiplexed sequencing. Library quality and size was assessed with the Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent Technologies 5067-4626) to ensure proper fragment size (~300-400 bp) and the absence of contaminating adapters. Final library concentrations were measured using a Qubit HS dsDNA assay kit (Life Technologies Q33230) and equal amounts were pooled into a final library for sequencing. Pooled libraries were used for paired-end sequencing using one NextSeq 2000 lane at the Chan-Zuckerberg Biohub.

tag: additive

value: DMSO

value: RT

tag: day

value: C

value: fungal cell


title: 4R PLSF-het cells, DIV15, biological replicate 2

description: Library name: P2H6_DIV15_II

tag: cell type

value: neuronal precursor cells

value: MAPT WT/4R P301L S320F


title: Sample_39 [9704031036_R03C02]

description:
9704031036_R03C02
CLL

tag: tissue

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

value: F


title: 4R cells, DIV35, biological replicate 1

description: Library name: P1H4_DIV35_I

value: early neurons

value: MAPT WT/4R


title: Sample_15 [9704031036_R02C01]

description:
9704031036_R02C01
CLL

tag: group

value: Sample 16


title: 4R cells, DIV35, biological replicate 3

description: Library name: P1H4_DIV35_III


title: BRCA_8_4_8

city: Melbourne

first: Dale

last: Garsed

address: 305 Grattan St

department: Cancer Research

institute: Peter MacCallum Cancer Centre

description: Library name: BRCA_8_4_8

data_processing:
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8)
Reads were trimmed for low quality, adapters, N content and poly-A tails using fastq-mcf (v1.05)
Contamination was checked using FastQ Screen (v0.11.4)
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b)
Mapped reads were sorted using Picard Tools (v2.17.3)
Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4)
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the “intersection-nonempty” mode
Assembly: hg19
Supplementary files format and content: Raw counts, gene by sample matrix. The GeneID column is in the format "EnsemblID|Chromosome|Start|End|Strand|Whole_Gene_Length|Exon_Only_Length|Gene_Symbol|Gene_Biotype", eg.. "ENSG00000000003|X|99883667|99894988|-|11322|2968|TSPAN6|protein_coding"
Supplementary files format and content: TMM normalized log2 counts, gene by sample matrix. The raw counts were first filtered to only contain protein coding genes. Genes were further filtered to only contain genes with a CPM of > 0.5 in at least 10 samples. The data was then TMM normalized using edgeR (v3.28.1) and batch corrected for strand orientation differences (library_strand_orientation) while retaining comparison survival group differences (survival_group_LTS) by limma's (v3.42.2) removeBatchEffect function [i.e. limma::removeBatchEffect(log2_tmm_data, batch = library_batch, design = model.matrix(~survival_group))].

source_name: Primary Tumour

extract_protocol:
RNA was isolated from frozen tissue sections using either the miRNeasy Mini Kit (Qiagen), AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), or mirVana miRNA Isolation Kit (Ambion/Life Technologies)
Quality assessment was performed using the Bioanalyzer RNA 6000 Nano assay (Agilent), finding a median RNA integrity number of 9.0 (range 4.7 to 10). Total RNA (1 ug) was used for library preparation using Illumina Stranded mRNA Prep and 150 bp paired-end sequencing was performed to a minimum of 100 million reads on Illumina NovaSeq 6000 instruments at the AGRF in accordance with the manufacturer’s instructions.

value: Primary Tumour

tag: sample id

tag: case id

tag: survival group

value: Poor

tag: library batch

value: BadBRCA


title: Maize_B104_Laser_Dissected_Guard_Cells_Night_rep2

description: Library name: N2GC

value: Leaves

tag: genotype


title: Maize_B104_Laser_Dissected_Guard_Cells_Night_rep4

description: Library name: N4GC

value: Night


title: Maize_B104_Laser_Dissected_Guard_Cells_Day_rep3

description: Library name: D3GC

value: Day


title: BON1_Day0_B

description: Library name: 39342

value: neuroendocrine tumor cell


title: Maize_B104_Laser_Dissected_Guard_Cells_Day_rep2

description: Library name: D2GC


title: Sample_47 [9704031022_R02C01]

description:
9704031022_R02C01
CLL

value: Test set

tag: material

value: Frozen

tag: age

tag: Sex

tag: mcf


title: Maize_B104_Laser_Dissected_Guard_Cells_Day_rep1

description: Library name: D1GC

tag: treatment


title: Sample_11 [9704031036_R02C02]

description:
9704031036_R02C02
CLL

value: M

value: Sample 31


title: Sample_31 [9704031022_R05C01]

description:
9704031022_R05C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Ref set


title: 4R cells, DIV15, biological replicate 3

description: Library name: P1H4_DIV15_III

tag: cell line

value: neuronal precursor cells


title: BON1_Day14_A

description: Library name: 39322

tag: time (days)


title: TCGA-GR-A4D6-01 [9305216060_R06C01]

description:
9305216060_R06C01
DLBCL_N

source_name: Diffuse large B-cell lymphoma GCB

value: Diffuse large B-cell lymphoma GCB

value: Lymph node

value: F

value: TCGA


title: PLSF cells, DIV35, biological replicate 3

description: Library name: P1B8_DIV35_III

value: early neurons


title: 4R cells, DIV15, biological replicate 2

description: Library name: P1H4_DIV15_II

value: MAPT WT/4R


title: PLSF cells, DIV35, biological replicate 2

description: Library name: P1B8_DIV35_II


title: TCGA-GR-A4D9-01 [9305216060_R05C01]

description:
9305216060_R05C01
DLBCL_EN

source_name: Diffuse large B-cell lymphoma

value: Diffuse large B-cell lymphoma


title: G217B DMSO RT day 1 A

description: Library name: RTA_D1

tag: additive

value: DMSO

tag: temperature

value: RT

tag: replicate

value: A

value: fungal cell


title: Sample_17 [9704031022_R05C02]

description:
9704031022_R05C02
CLL

tag: tissue

value: Blood

value: Test set

value: Frozen

value: Sample 34


title: PLSF cells, DIV35, biological replicate 1

description: Library name: P1B8_DIV35_I

tag: cell type


title: PLSF cells, DIV15, biological replicate 2

description: Library name: P1B8_DIV15_II


title: BRCA_3_4_X

description: Library name: BRCA_3_4_X

value: Primary Tumour

tag: sample id

value: Poor

value: BadBRCA


title: G217B DMSO RT day 2 B

description: Library name: RTB_D2

tag: day

value: B


title: Sample_6 [9704031016_R02C01]

description:
9704031016_R02C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

tag: group

value: Ref set

value: F


title: G217B DMSO RT day 1 C

description: Library name: RTC_D1

value: C


title: Sample_9 [9704031022_R03C01]

description:
9704031022_R03C01
CLL


title: BRCA_9_4_1

description: Library name: BRCA_9_4_1

tag: case id

tag: survival group

tag: library batch


title: BRCA_24_4_9

description: Library name: BRCA_24_4_9


title: G217B DMSO RT day 1 B

description: Library name: RTB_D1

tag: genotype


title: WT cells, Nocodoazole treated, DIV35, biological replicate 3

description: Library name: Noco_DIV35_III

value: early neurons

value: WT

value: 3 uM Nocodazole, 72h


title: BRCA_6_4_0

description: Library name: BRCA_6_4_0


title: TCGA-FF-8047-01 [7786915146_R06C02]

description:
7786915146_R06C02
DLBCL_N

source_name: Diffuse large B-cell lymphoma ABC(CD10neg, BCL6pos,MUM1 pos)

value: Lymph node

tag: material

tag: age

tag: Sex

value: TCGA


title: BRCA_4_4_3

description: Library name: BRCA_4_4_3


title: PLSF cells, DIV15, biological replicate 3

description: Library name: P1B8_DIV15_III

tag: cell line

value: neuronal precursor cells

tag: treatment


title: WT cells, Nocodoazole treated, DIV15, biological replicate 3

description: Library name: Noco_DIV15_III


title: BRCA_7_4_4

description: Library name: BRCA_7_4_4


title: G217B DMSO RT day 2 A

description: Library name: RTA_D2

tag: additive

value: DMSO

value: RT

value: A

value: fungal cell


title: PLSF cells, DIV15, biological replicate 1

description: Library name: P1B8_DIV15_I


title: G217B 50mM Entinostat 37C day 2 C

description: Library name: Ent50C_D2

value: 50mM Entinostat

tag: temperature


title: BRCA_2_4_6

description: Library name: BRCA_2_4_6

value: Primary Tumour

value: Poor

value: BadBRCA


title: WT cells, Nocodoazole treated, DIV15, biological replicate 1

description: Library name: Noco_DIV15_I


title: TCGA-RQ-A68N-01 [9305216060_R02C01]

description:
9305216060_R02C01
DLBCL_EN

value: Diffuse large B-cell lymphoma

value: Brain

value: Test set

value: Frozen

value: M

tag: mcf


title: Sample_8 [6929793152_R06C01]

description:
6929793152_R06C01
CLL

tag: tissue

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood


title: G217B 50mM Entinostat 37C day 1 A

description: Library name: Ent50A_D1

tag: replicate

tag: cell type


title: BRCA_22_4_1

description: Library name: BRCA_22_4_1

tag: sample id


title: BRCA_19_4_4

description: Library name: BRCA_19_4_4


title: WT cells, Nocodoazole treated, DIV35, biological replicate 1

description: Library name: Noco_DIV35_I

value: early neurons

value: WT

value: 3 uM Nocodazole, 72h


title: G217B 50mM Entinostat 37C day 2 B

description: Library name: Ent50B_D2

tag: day

value: B


title: WT cells, Nocodoazole treated, DIV15, biological replicate 2

description: Library name: Noco_DIV15_II

value: neuronal precursor cells


title: 4R PLSF-hom cells, DIV35, biological replicate 2

description: Library name: A1_DIV35_II

value: MAPT 4R P301L S320F/MAPT 4R P301L S320F


title: G217B 50mM Entinostat 37C day 1 C

description: Library name: Ent50C_D1

value: 50mM Entinostat

value: C

value: fungal cell


title: BRCA_20_4_4

description: Library name: BRCA_20_4_4

value: Primary Tumour

tag: case id

value: Poor

value: BadBRCA


title: TCGA-FF-8046-01 [7786923062_R02C01]

description:
7786923062_R02C01
DLBCL_N

value: Diffuse large B-cell lymphoma GCB

value: Salivary gland

tag: group

value: Ref set

value: TCGA


title: BRCA_23_4_5

description: Library name: BRCA_23_4_5

tag: survival group

tag: library batch


title: BRCA_15_4_X

description: Library name: BRCA_15_4_X


title: 4R PLSF-hom cells, DIV15, biological replicate 2

description: Library name: A1_DIV15_II

tag: genotype


title: BRCA_21_4_8

description: Library name: BRCA_21_4_8


title: WT cells, Nocodoazole treated, DIV35, biological replicate 2

description: Library name: Noco_DIV35_II


title: G217B 50mM Entinostat 37C day 2 A

description: Library name: Ent50A_D2

value: A


title: G217B 10mM Entinostat 37C day 2 C

description: Library name: Ent10C_D2

value: 10mM Entinostat


title: BRCA_16_4_3

description: Library name: BRCA_16_4_3


title: TCGA-FF-8042-01 [7786915146_R06C01]

description:
7786915146_R06C01
DLBCL_N

source_name: Diffuse large B-cell lymphoma ABC(CD10n,BCL6 n, MUM1 NA)

value: Lymph node

tag: material

value: Frozen

tag: age

value: F


title: BRCA_18_4_0

description: Library name: BRCA_18_4_0


title: BRCA_17_4_7

description: Library name: BRCA_17_4_7


title: Sample_20 [6929793152_R03C01]

description:
6929793152_R03C01
CLL

source_name: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Blood

tag: Sex

value: M


title: TCGA-FF-8043-01 [7786915146_R01C01]

description:
7786915146_R01C01
DLBCL_EN

source_name: Diffuse large B-cell lymphoma, ABC

value: Diffuse large B-cell lymphoma, ABC

value: Caecum


title: Sample_19 [6929793152_R02C01]

description:
6929793152_R02C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma


title: 4R PLSF-hom cells, DIV35, biological replicate 3

description: Library name: A1_DIV35_III

tag: cell line

value: early neurons

value: MAPT 4R P301L S320F/MAPT 4R P301L S320F

tag: treatment


title: Sample_18 [6929793152_R01C01]

description:
6929793152_R01C01
CLL


title: G217B 10mM Entinostat 37C day 1 C

description: Library name: Ent10C_D1

tag: additive

tag: temperature

value: C

value: fungal cell


title: Sample_21 [6929793152_R04C01]

description:
6929793152_R04C01
CLL

tag: tissue

tag: mcf


title: G217B 10mM Entinostat 37C day 1 B

description: Library name: Ent10B_D1

tag: replicate

value: B

tag: cell type


title: G217B 50mM Entinostat 37C day 1 B

description: Library name: Ent50B_D1

value: 50mM Entinostat

tag: day


title: Sample_36 [6929793152_R04C02]

description:
6929793152_R04C02
CLL

value: Ref set


title: G217B DMSO 37C day 1 C

description: Library name: 37C_D1

value: DMSO


title: 4R PLSF-hom cells, DIV35, biological replicate 1

description: Library name: A1_DIV35_I


title: WT cells, DIV35, biological replicate 2

description: Library name: A18_DIV35_II

value: WT


title: G217B 10mM Entinostat 37C day 2 B

description: Library name: Ent10B_D2

value: 10mM Entinostat


title: Sample_7 [6929793152_R01C02]

description:
6929793152_R01C02
CLL

value: Frozen


title: Sample_37 [6929793144_R03C02]

description:
6929793144_R03C02
CLL


title: Sample_24 [6929793144_R03C01]

description:
6929793144_R03C01
CLL

value: F


title: Sample_35 [6929793152_R03C02]

description:
6929793152_R03C02
CLL

value: Blood


title: BRCA_14_4_6

description: Library name: BRCA_14_4_6

value: Primary Tumour

tag: sample id

tag: case id

value: Poor

value: BadBRCA


title: BRCA_12_4_9

description: Library name: BRCA_12_4_9

tag: survival group


title: G217B 10mM Entinostat 37C day 2 A

description: Library name: Ent10A_D2

value: A


title: BRCA_1_4_2

description: Library name: BRCA_1_4_2

tag: library batch


title: 4R PLSF-hom cells, DIV15, biological replicate 1

description: Library name: A1_DIV15_I

value: neuronal precursor cells

tag: genotype


title: WT cells, DIV35, biological replicate 3

description: Library name: A18_DIV35_III

value: early neurons


title: G217B DMSO 37C day 2 C

description: Library name: 37C_D2

value: C


title: Sample_25 [6929793144_R04C01]

description:
6929793144_R04C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

tag: group

tag: material


title: G217B DMSO 37C day 2 B

description: Library name: 37B_D2

value: B

value: fungal cell


title: BRCA_10_4_1

description: Library name: BRCA_10_4_1


title: 4R PLSF-hom cells, DIV15, biological replicate 3

description: Library name: A1_DIV15_III

value: MAPT 4R P301L S320F/MAPT 4R P301L S320F


title: BRCA_11_4_5

description: Library name: BRCA_11_4_5


title: WT cells, DIV35, biological replicate 1

description: Library name: A18_DIV35_I


title: BRCA_13_4_2

description: Library name: BRCA_13_4_2


title: Sample_23 [6929793144_R02C01]

description:
6929793144_R02C01
CLL

value: Ref set

tag: age

tag: Sex

value: M


title: A5NRK_4

city: Paris

first: Thierry

last: Galli

address: 102 Rue de la Sante

country: France

institute: Institute of Psychiatry and Neuroscience of Paris

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq
Assembly: Illumina Stranded mRNA Prep Ligation - Reference Guide - PN 1000000124518
Supplementary files format and content: .txt file containing ensembl gene id and raw reads

source_name: Normal Rat Kidney

growth_protocol: Cells were grown in complete growh medium

extract_protocol:
RNA was extracted using RNA-easy Kit from Qiagen
RNA-Seq libraries were generated from 600 ng of total RNA using Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA) according to manufacturer's instructions. Following polyA selection, mRNAs were fragmented at 94oC for 8minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France).  The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: No treatment

tag: cell line

value: Normal Rat Kidney

value: Epithelial


title: F2-4_shKANSL2_I_2

city: Capital federal

first: Carolina

last: Perez-Castro

state: Argentina

address: Godoy Cruz 2090

department: Cell plasticity

country: Argentina

institute: IBioBA (Instituto de investigacion en Biomedicina de Buenos Aires - Instituto partner de la sociedad Max Planck)

description:
Library name: Sample11
Column name in HTSeq_counts.txt: F2-4_shKANSL2_I_2

data_processing:
Quality control of the sample was performed using the FastQC software.
Alignment with the reference genome (GRCh38) using HISAT2.
Processing of BAM files with SAMtools.
Gene expression quantification with HTSeq-count
Differential expression analysis with DESeq2 in Bioconductor
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was extracted using a QIAGEN RNeasy Kit. The integrity of the RNAs was assessed using the Agilent RNA 6000 Pico Kit and the Agilent 2100 Bioanalyzer System. The total amount of RNA sent to the company for each condition was 1 µg.
The libraries were made using the NEBNext® Ultra Directional RNA Library Kit.

value: GBM derived


title: G217B 10mM Entinostat 37C day 1 A

description: Library name: Ent10A_D1

source_name: fungal cell

tag: additive

value: 10mM Entinostat


title: WT cells, DIV15, biological replicate 2

description: Library name: A18_DIV15_II

value: WT

tag: treatment


title: G217B DMSO 37C day 1 B

description: Library name: 37B_D1

value: DMSO

tag: temperature


title: Sample_9 [6929793144_R01C02]

description:
6929793144_R01C02
CLL

data_processing: BeadStudio software v3.2

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: Blood

value: Frozen

value: F

tag: mcf


title: F2-4_shNT_2

description:
Library name: Sample10
Column name in HTSeq_counts.txt: F2-4_shNT_2

tag: cell type

value: shNT


title: G217B DMSO 37C day 2 A

description: Library name: 37A_D2

tag: day

tag: replicate

value: A


title: WT cells, DIV15, biological replicate 1

description: Library name: A18_DIV15_I

value: neuronal precursor cells


title: F2-4_shKANSL2_III_2

description:
Library name: Sample12
Column name in HTSeq_counts.txt: F2-4_shKANSL2_III_2


title: Sample_22 [6929793144_R01C01]

description:
6929793144_R01C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma


title: WT cells, DIV15, biological replicate 3

description: Library name: A18_DIV15_III


title: ASK1_2

city: Guangzhou

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Sun Yat-Sen University

description: Library name: Sample 11

data_processing:
After library quality control, different libraries were pooled based on the effective concentration and targeted data amount. 5'-end of each library was phosphorylated and cyclized. Subsequently, loop amplification was performed to generate DNA nanoballs. We ultimately loaded these DNA nanoballs into flow cytometry cells with DNBSEQ-T7 or Illumina HiSeq 2000 for 2×150bp paired-end sequencing  following the vendor's recommended protocol.
Quality control.Clean datas were obtained by removing low quality reads with Fastp.
Reads mapping.Clean reads were mapped to human reference genome hg38 by hisat2.
Differential expression analysis of two conditions/groups was performed using the feartureCounts.
Assembly: hg38
Supplementary files format and content: xlsx

source_name: human monocyte-derived macrophages

growth_protocol: Human peripheral blood mononuclear cells were isolated from healthy volunteer donors by Percoll density gradient centrifugation, and were then differentiated into HMDMs in RPMI-1640 medium supplemented with 10% fetal calf serum, 1% HEPES, 1% penicillin/streptomycin, and 100 ng/ml of macrophage colony-stimulating factor.

extract_protocol:
Total RNA extraction was conducted by TRlzol Reagent. RNA detect concentration using qubit (Thermo Fisher Scientific, Q33226). RNA purity was checked using the NanoDrop PR-1(Thermo Fisher Scientific,CHEM-PR1-KIT). RNA integrity was assessed using the Qsep1 system (Qsep1 Technologies, CA, China).
Messenger RNA was purified from total RNA using attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: HMDMs were transfected with TRIM21, NFATc3, and ASK1 plasmids for 48 hours, respectively, with the pCMV6 expression vector used as a control.

value: human monocyte-derived macrophages

value: Transfection of ASK1 vector


title: WTNRK_4

value: Wildtype


title: F2-4_shKANSL2_III_1

description:
Library name: Sample9
Column name in HTSeq_counts.txt: F2-4_shKANSL2_III_1


title: ASK1_3

description: Library name: Sample 12


title: G217B DMSO 37C day 1 A

description: Library name: 37A_D1

value: fungal cell


title: V7NRK_4

value: Normal Rat Kidney


title: Sample_10 [6929793144_R02C02]

description:
6929793144_R02C02
CLL

value: Test set

value: M


title: F2-4_shKANSL2_I_1

description:
Library name: Sample8
Column name in HTSeq_counts.txt: F2-4_shKANSL2_I_1

value: GBM derived


title: Sample_12 [6929793134_R06C02]

description:
6929793134_R06C02
CLL

value: Ref set


title: V7NRK_3

value: Epithelial


title: ASK1_1

description: Library name: Sample 10


title: Sample_73 [6929793134_R05C01]

description:
6929793134_R05C01
CLL

value: Blood

value: Sample 39


title: Sample_11 [6929793134_R05C02]

description:
6929793134_R05C02
CLL

value: Frozen

value: F


title: F18-1_shKANSL2_I_2

description:
Library name: Sample5
Column name in HTSeq_counts.txt: F18-1_shKANSL2_I_2


title: NFATc3_2

description: Library name: Sample 8

value: Transfection of NFATc3 vector


title: Sample_26 [6929793134_R04C02]

description:
6929793134_R04C02
CLL


title: NFATc3_3

description: Library name: Sample 9


title: WTNRK_3


title: F2-4_shNT_1

description:
Library name: Sample7
Column name in HTSeq_counts.txt: F2-4_shNT_1

value: shNT


title: Sample_59 [6929793134_R01C01]

description:
6929793134_R01C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Sample 38


title: F18-1_shKANSL2_III_2

description:
Library name: Sample6
Column name in HTSeq_counts.txt: F18-1_shKANSL2_III_2


title: NFATc3_1

description: Library name: Sample 7

value: human monocyte-derived macrophages


title: TRIM21_2

description: Library name: Sample 5

value: Transfection of TRIM21 vector


title: Sample_69 [6929793134_R03C01]

description:
6929793134_R03C01
CLL


title: TRIM21_1

description: Library name: Sample 4


title: Sample_75 [6929793133_R05C02]

description:
6929793133_R05C02
CLL

value: Sample 43


title: A5NRK_3

value: Normal Rat Kidney


title: F18-1_shKANSL2_I_1

description:
Library name: Sample2
Column name in HTSeq_counts.txt: F18-1_shKANSL2_I_1


title: WTNRK_2

value: Wildtype


title: A5NRK_2


title: Control_3

description: Library name: Sample 3

value: Transfection of pCMV6 vector


title: TRIM21_3

description: Library name: Sample 6


title: Sample_53 [6929793133_R05C01]

description:
6929793133_R05C01
CLL

value: Test set


title: Sample_71 [6929793133_R03C02]

description:
6929793133_R03C02
CLL

value: Ref set

value: M

value: Sample 42


title: A5NRK_1

value: Epithelial


title: Sample_45 [6929793133_R03C01]

description:
6929793133_R03C01
CLL

value: Blood

value: Frozen

value: Sample 41


title: V7NRK_2


title: WTNRK_1


title: F18-1_shKANSL2_III_1

description:
Library name: Sample3
Column name in HTSeq_counts.txt: F18-1_shKANSL2_III_1

value: GBM derived


title: MCF10DCIS CD63-NanoLuC 738 Brain 28 days post-implantation replicate 2

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

description: Library name: MCF10DCIS CD63-NLuc 738 Brain 28 dpi 2

data_processing:
Samples were normalized and pooled onto a 150-paired end run on Illumina’s NextSeq 2000 Platform to obtain 10 M reads per sample. The fastq files were aligned with the Mus musculus genome build GRCm39, and differentially expressed genes were identified using ROSALIND software (version 3.39.26.7). Genes with ≥ 1.5- or ≤ 1.5-fold change at adjusted P < 0.05 were considered significantly differentially expressed.
Assembly: Mus musculus GRCm39
Supplementary files format and content: tab-delimited text file includes normalized mRNA read counts for all samples

organism: Mus musculus

source_name: brain

extract_protocol:
Total RNA was isolated from homogenized brain tissue collected at 3 and 28 dpi from mice implanted with MCF10DCIS CD63-NLuc cells using TRIzol reagent and purified using a Monarch Total RNA MiniPrep Kit (NEB, T2010S). Following purification,  RNA was checked for quality using the Agilent TapeStation and concentrations from ThermoFisher’s NanoDrop readings were used.
Stranded RNA-seq libraries were constructed using the NEBNext poly(A) mRNA isolation kit followed directly by the IDT XGen Broad Range RNA Library Prep Kit and the established protocols. Library construction was performed using 1 µg of RNA. Each library was indexed during library construction for multiplex sequencing, quantified using Invitrogen’s Qubit 4 fluorometer, and checked for size and quality on Agilent’s TapeStation.

value: brain

value: ductal carcinoma in situ


title: MCF10DCIS CD63-NanoLuC 749 Brain 28 days post-implantation replicate 3

description: Library name: MCF10DCIS CD63-NLuc 749 Brain 28 dpi 3


title: V7NRK_1


title: TG_6 stool microbiome

city: Nanning

first: Lingzhang

last: Meng

state: Guangxi

address: Qingxiu District

institute: Guangxi Academy of Medical Sciences

description:
Library name: ZTPSN25DC319-TG_6
16S rRNA sequencing of rat stool sample

library_source: other

data_processing:
Raw sequencing reads demultiplexed according to index/barcode sequences.
Reads quality-filtered; primer and adapter sequences removed.
Denoising (DADA2) or OTU clustering (Vsearch) performed; ASV/OTU table generated.
Taxonomic annotation assigned; alpha and beta diversity calculated.
Differential abundance and functional prediction performed.
Assembly: 16S rRNA gene reference databases (e.g., SILVA, Greengenes)
Supplementary files format and content: dnasequences.fasta
Supplementary files format and content: featuretable.tsv
Supplementary files format and content: samplemetadata.tsv
Supplementary files format and content: taxonomyfiltered.xls
Library strategy: 16S rRNA-seq

molecule: other

source_name: Intestinal contents

growth_protocol: Rats housed under standard laboratory conditions, stool samples collected at the indicated experimental time points.

extract_protocol:
Total DNA extracted from stool samples using validated microbiome DNA extraction method; DNA quality assessed via Nanodrop and 1.2% agarose gel electrophoresis.
PCR amplification of 16S rRNA gene variable regions using primers with sample-specific barcodes; PCR products purified with magnetic beads; libraries prepared using Illumina TruSeq Nano DNA LT kit; final libraries quantified and size-selected using Agilent Bioanalyzer.

treatment_protocol: Model group rats induced with radiation enteritis; TG group received therapeutic intervention; control group untreated.

value: Intestinal contents

value: wild-type

value: TCM treatment

tag: batch


title: MCF10DCIS CD63-NanoLuC 726 Brain 28 days post-implantation replicate 1

description: Library name: MCF10DCIS CD63-NLuc 726 Brain 28 dpi 1


title: Control_2

description: Library name: Sample 2

value: human monocyte-derived macrophages


title: MCF10DCIS CD63-NanoLuC 737 Brain 3 days post-implantation replicate 2

description: Library name: MCF10DCIS CD63-NLuc 737 Brain 3 dpi 2


title: Sample_49 [5854945040_R06C01]

city: Wantirna South

first: Rust

last: Turakulov

address: u23 105 Mountain Hwy

institute: AGRF

description:
5854945040_R06C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma


title: TG_5 stool microbiome

description:
Library name: ZTPSN25DC318-TG_5
16S rRNA sequencing of rat stool sample


title: MCF10DCIS CD63-NanoLuC 746 Brain 3 days post-implantation replicate 3

description: Library name: MCF10DCIS CD63-NLuc 746 Brain 3 dpi 3


title: Sample_43 [6929793133_R01C01]

description:
6929793133_R01C01
CLL

value: Sample 40


title: TG_4 stool microbiome

description:
Library name: ZTPSN25DC317-TG_4
16S rRNA sequencing of rat stool sample


title: F18-1_shNT_2

description:
Library name: Sample4
Column name in HTSeq_counts.txt: F18-1_shNT_2

value: shNT


title: Sample_63 [6929793133_R01C02]

description:
6929793133_R01C02
CLL

value: Test set


title: DG_3_Day

city: Hefei

first: daoming

last: cheng

state: Anhui

address: No. 96 Jinzhai Road, Baohe District, Hefei, Anhui, 230026, P.R. China.

institute: 中国科学技术大学附属第一医院的英文名称是 The First AfUniversity of Science and Technology of China

description:
Library name: Sample 12
DG_3_Day

data_processing:
Reads were aligned to the GRCm39 genome using STAR v2.7.x. Gene counts were obtained using featureCounts v2.0.x.
Assembly: GRCm39
Supplementary files format and content: Supplementary_files_fomat_and_content_processed data.xls

source_name: hippocampus tissue

growth_protocol: ICR mice were housed in a specific pathogen-free facility under a 12-hour light/dark cycle (lights on at 7:00 AM, ZT0) with free access to food and water.

extract_protocol:
Total RNA was extracted from approximately 20-30 mg of frozen brain tissue using the RNeasy Mini Kit, Qiagen, including the on-column DNase I digestion step according to the manufacturer's instructions. RNA integrity was verified by an Agilent 2100 Bioanalyzer, and all samples had an RNA Integrity Number (RIN) > 8.0. RNA concentration was measured using a NanoDrop spectrophotometer.
Strand-specific RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB, following the manufacturer's protocol. Briefly, mRNA was enriched from 1 μg total RNA using poly-T oligo-attached magnetic beads, fragmented, and first-strand cDNA was synthesized. After second-strand synthesis, adaptors were ligated, and the libraries were amplified with 12-14 cycles of PCR. Final libraries were size-selected (300-400 bp) and quantified by qPCR (KAPA Library Quantification Kit) before pooling for sequencing.

treatment_protocol: Mice were deeply anesthetized at the designated time points (Day: ZT6; Dark: ZT14) and transcardially perfused with ice-cold phosphate-buffered saline (PBS). The brain was rapidly removed, and the DG and CA1 regions were microdissected on a chilled plate, then immediately frozen in liquid nitrogen and stored at -80°C until use.

value: hippocampus tissue

tag: strain

value: ICR

value: dentate gyrus granule cells

value: WT


title: MCF10DCIS CD63-NanoLuC 728 Brain 3 days post-implantation replicate 1

description: Library name: MCF10DCIS CD63-NLuc 728 Brain 3 dpi 1


title: Sample_48 [5854945040_R05C02]

description:
5854945040_R05C02
CLL

value: Blood

value: Frozen

value: F


title: Sample_44 [5998789035_R01C02]

description:
5998789035_R01C02
CLL

value: M


title: DG_3_Dark

description:
Library name: Sample 11
DG_3_Dark


title: Sample_50 [5854945040_R06C02]

description:
5854945040_R06C02
CLL


title: DG_1_Day

description:
Library name: Sample 8
DG_1_Day


title: Control_1

description: Library name: Sample 1

value: Transfection of pCMV6 vector


title: ApoE ko western diet ischemic muscle

city: Montreal

first: Alain

last: Rivard

state: Qc

address: 900 rue St-Denis

country: Canada

institute: CRCHUM

description:
Library name: ApoE ISCH MUSCLE
Column name in ISCH_Muscle_Processed_DATA.csv: ISCHMuscle_ApoE and CPM_ISCHMuscle_ApoE
ISCH_Muscle_Processed_DATA.csv

data_processing:
Sequenced fragments (R1 read only when appplicable) were trimmed in 3' for sequencing adapters and candidates longer than 20bp where mapped to the reference genome GRCh38 using STAR version 2.7.1a and ENCODE alignment parameters for smallRNA analysis. Known miRNA extracted from miRBase version 22 were then quantified by counting the number of reads that fall into each of their location on the genome, discriminating between 3p and 5p portion of the hairpin miRNA.
Assembly: GRCm38:mm10
Supplementary files format and content: csv files include raw counts and CPM values

source_name: Hind limb muscle

extract_protocol:
Muscle : RNA extraction with the mirVana miRNA Isolation Kit (Thermo) Evs : RNA extraction with the miRNeasy Mini kit (Qiagen)
Muscle : Truseq Small RNA
sEVs : Qiaseq small RNA
lEVs : TriLink SmallRNA

treatment_protocol: ApoE-/- (Jax#2052) mice on Western diet (TD.88137)for 4 weeks prior to hind limb ischemia induction vs C57Bl/6 mice on regular chow

value: Hind limb muscle

value: ApoE ko

tag: diet

value: Western Diet

value: hind limb ischemia


title: TG_3 stool microbiome

description:
Library name: ZTPSN25DC316-TG_3
16S rRNA sequencing of rat stool sample

value: Intestinal contents

tag: genotype

value: wild-type

value: TCM treatment


title: DG_2_Day

description:
Library name: Sample 10
DG_2_Day


title: Sample_46 [5854945040_R03C02]

description:
5854945040_R03C02
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

tag: group

value: Ref set


title: F18-1_shNT_1

description:
Library name: Sample1
Column name in HTSeq_counts.txt: F18-1_shNT_1

value: GBM derived

value: shNT


title: Model_5 stool microbiome

description:
Library name: ZTPSN25DC312-Model_5
16S rRNA sequencing of rat stool sample

value: radiation enteritis model


title: DG_2_Dark

description:
Library name: Sample 9
DG_2_Dark

value: hippocampus tissue

value: ICR

value: dentate gyrus granule cells

value: WT


title: CA1_3_Dark

description:
Library name: Sample 5
CA1_3_Dark

value: CA1 pyramidal neurons


title: Sample_45 [5854945040_R01C02]

description:
5854945040_R01C02
CLL

value: Blood

tag: material

value: Frozen

value: F


title: CA1_2_Day

description:
Library name: Sample 4
CA1_2_Day


title: Model_4 stool microbiome

description:
Library name: ZTPSN25DC311-Model_4
16S rRNA sequencing of rat stool sample


title: DG_1_Dark

description:
Library name: Sample 7
DG_1_Dark


title: TG_2 stool microbiome

description:
Library name: ZTPSN25DC315-TG_2
16S rRNA sequencing of rat stool sample


title: Sample_47 [5854945040_R05C01]

description:
5854945040_R05C01
CLL

tag: age


title: TG_1 stool microbiome

description:
Library name: ZTPSN25DC314-TG_1
16S rRNA sequencing of rat stool sample


title: Sample_25 [5773184018_R05C02]

description:
5773184018_R05C02
CLL

value: Test set

tag: Sex

value: Sample 54


title: TCGA-AB-2956-03 [5775446062_R02C01]

description:
5775446062_R02C01
AML_KMT2A

source_name: Acute myelogenous leukemia

value: Acute myelogenous leukemia

value: M

value: TCGA


title: Model_6 stool microbiome

description:
Library name: ZTPSN25DC313-Model_6
16S rRNA sequencing of rat stool sample

value: Intestinal contents

value: wild-type


title: BRCA_5_3_3

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina Infinium HD Methylation protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings.

data_processing:
Methylation data quality control assessment and processing were performed using the R package minfi (v1.32.0). Probes failing detection (P > 0.01), SNP positions, and cross reactive probes (as collected in https://github.com/sirselim/illumina450k_filtering) were excluded. Data was normalized using the minfi function "preprocessFunnorm" and beta values were generated. Probes were annotated to the Ensembl release GRCh37.92 GTF annotation and output file "betaVals.all.txt.gz" was generated. Beta values for samples from EPIC and 450k arrays were combined to contain shared probes and batch corrected for platform differences using the "ComBat" function in the R package sva (v3.34.0) to generate output file "betaVals.platform_corrected_by_combat.txt.gz".
Beta value

label: Cy3 and Cy5

label_protocol: Illumina Infinium HD Methylation Assay

extract_protocol: DNA was isolated from frozen tissue sections using either the Gentra Puregene Tissue Kit (Qiagen), DNeasy Blood and Tissue Kit (Qiagen), or AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

value: Primary Tumour

tag: case id


title: CA1_1_Dark

description:
Library name: Sample 1
CA1_1_Dark


title: CA1_1_Day

description:
Library name: Sample 2
CA1_1_Day


title: Model_1 stool microbiome

description:
Library name: ZTPSN25DC308-Model_1
16S rRNA sequencing of rat stool sample

value: radiation enteritis model


title: C57Bl/6 control ischemic muscle

description:
Library name: C57 ISCH MUSCLE
Column name in ISCH_Muscle_Processed_DATA.csv: ISCHMuscle_C57 and CPM_ISCHMuscle_C57
ISCH_Muscle_Processed_DATA.csv

value: Hind limb muscle

value: Regular diet

value: hind limb ischemia


title: Sample_13 [5854945040_R04C02]

description:
5854945040_R04C02
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Ref set


title: BRCA_7_3_1


title: BRCA_9_3_X


title: BRCA_3_3_5


title: CA1_3_Day

description:
Library name: Sample 6
CA1_3_Day

value: hippocampus tissue

value: ICR

value: CA1 pyramidal neurons

value: WT


title: CA1_2_Dark

description:
Library name: Sample 3
CA1_2_Dark


title: Sample_35 [5773184018_R04C01]

description:
5773184018_R04C01
CLL

value: Blood

value: Test set

value: Frozen

value: Sample 53


title: BRCA_8_3_0


title: Model_3 stool microbiome

description:
Library name: ZTPSN25DC310-Model_3
16S rRNA sequencing of rat stool sample

value: Intestinal contents


title: Control_5 stool microbiome

description:
Library name: ZTPSN25DC306-Control_5
16S rRNA sequencing of rat stool sample

value: wild-type

value: control


title: BRCA_6_3_2

value: Primary Tumour


title: GSNOR KO-1

city: Beijing

first: Xinhua

last: Qiao

state: 北京市

address: 15# Datun Road,Chaoyang District, Chaoyang District

institute: Institute of Biophysics，Chinese Academy of Sciences

description: Library name: Mouse_H581-T04

data_processing:
Sequence reads were trimmed for adaptor sequence and low-quality sequence using CLC Genomics Workbench v11.0.1 (parameter: Quality limit: 0.05).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC Genomics Workbench (parameters: mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8).
Read count extraction was performed using CLC Genomics Workbench.
Normalization was performed using CLC Genomics Workbench to generate FPKM values.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files containing raw read counts for each sample, and CSV files containing FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each sample.

source_name: inguinal white adipose tissue (iWAT)

extract_protocol:
Total RNA was extracted from snap-frozen iWAT using TRIzol reagent followed by isopropanol precipitation, and its integrity was verified by Bioanalyzer analysis prior to library construction.
mRNA enrichment (poly-T magnetic beads), random primer reverse transcription, fragment selection (200-250 bp), Illumina adapter ligation, PCR amplification library construction.

value: inguinal white adipose tissue (iWAT)

value: C57BL/6J-GSNOR KO


title: Sample_49 [5773184018_R01C01]

state: Victoria

description:
5773184018_R01C01
CLL

value: M

value: Sample 51


title: Control_3 stool microbiome

description:
Library name: ZTPSN25DC304-Control_3
16S rRNA sequencing of rat stool sample


title: Model_2 stool microbiome

description:
Library name: ZTPSN25DC309-Model_2
16S rRNA sequencing of rat stool sample

value: radiation enteritis model


title: Control_6 stool microbiome

description:
Library name: ZTPSN25DC307-Control_6
16S rRNA sequencing of rat stool sample


title: Control_4 stool microbiome

description:
Library name: ZTPSN25DC305-Control_4
16S rRNA sequencing of rat stool sample


title: BRCA_23_3_7


title: Sample_79 [5773184018_R03C01]

description:
5773184018_R03C01
CLL

value: Chronic lymphocytic leukaemia/small lymphocytic lymphoma

value: Ref set

value: Sample 52


title: TCGA-AB-3005-03 [5771955084_R02C02]

description:
5771955084_R02C02
AML_KMT2A

value: Acute myelogenous leukemia

value: TCGA


title: WT-3

description: Library name: Mouse_H581-T03


title: BRCA_4_3_4


title: Control_2 stool microbiome

description:
Library name: ZTPSN25DC303-Control_2
16S rRNA sequencing of rat stool sample


title: GSNOR KO-2

description: Library name: Mouse_H581-T05


title: GSNOR KO-3

description: Library name: Mouse_H581-T06


title: Sample_51 [5773184018_R01C02]

description:
5773184018_R01C02
CLL

value: Blood

value: Test set


title: BRCA_20_3_X


title: Control_1 stool microbiome

description:
Library name: ZTPSN25DC302-Control_1
16S rRNA sequencing of rat stool sample


title: WT-2

description: Library name: Mouse_H581-T02


title: Col-0 ISX+PEP3 rep2

city: Marburg

first: Timo

last: Engelsdorf

address: Karl-von-Frisch-Str. 8

institute: Marburg University

description: Library name: Sample 11

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing poly-N and low-quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Assembly: Index of the TAIR10 reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: xls file includes FPKM data for all samples

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Surface-sterilized seeds were grown in half-strength Murashige and Skoog liquid medium [Murashige and Skoog Basal Medium (2.1 g/liter), MES salt (0.5g/liter), and 1% sucrose, pH 5.7]. Seedling cultures were established in a 24-well plate with 6 seeds per well. Seedlings were grown under a 16-hour light (22°C) / 8-hour dark (20°C) cycle and a photon flux density of 110μmol m−2 s−1.

extract_protocol:
Total RNA was isolated using a NucleoSpin Plant and Fungi RNA Mini Kit (Macherey-Nagel). One microgram of total RNA was treated with RNase-Free DNase (Thermo Scientific) and used for complementary DNA (cDNA) synthesis with a RevertUP II Reverse Transcriptase Kit (Biotechrabbit).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: 10-day-old seedlings were subjected to the following treatments in fresh liquid growth medium at the indicated final concentrations: 600 nM isoxaben (ISX; Supelco 36138), 10 nM AtPEP3 (EIKARGKNKTKPTPSSGKGGKHN), 600 nM ISX + 10 nM AtPEP3 (combined treatment of ISX and AtPEP3). Equal amounts of DMSO were present in all treatments, including mock treatments.

value: whole seedlings


title: TCGA-AB-2894-03 [5771955069_R05C01]

description:
5771955069_R05C01
AML_KMT2A

value: Frozen

value: F


title: TCGA-AB-2819-03 [5771955072_R02C02]

description:
5771955072_R02C02
AML_RUNX1


title: BRCA_24_3_6

source_name: Primary Tumour


title: TCGA-AB-2883-03 [5771955069_R01C02]

description:
5771955069_R01C02
AML_KMT2A


title: Col-0 ISX+PEP3 rep3

description: Library name: Sample 12


title: WT E12.5 fetal liver, Lin- cells, ChIP-seq

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

institute: Kyushu University

description: Library name: WT1_E12.5FL

data_processing:
Raw paired-end ChIP-seq reads were trimmed for adapters and filtered for quality using Cutadapt. Trimmed reads were aligned to the mouse genome (mm10 or CNS11mut-modified mm10) with Bowtie2 (v2.2.5). Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were filtered out using Samtools. Normalized coverage tracks (bigWig) were generated with deepTools bamCoverage using CPM normalization.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: 12.5 fetal liver

extract_protocol:
Fetal liver were separated under a stereo microscope, and single-cell suspension was generated by robustly pipetting with a 1000-μl pipette. Lineage-negative cells were isolated by negative selection with the MojoSort magnetic cell separation system.
Sequence libraries were constructed with NEBNext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina (New England Biolabs).

value: 12.5 fetal liver

value: Lin-

value: WT

tag: antibody

value: CBFβ


title: TCGA-AB-2910-03 [5771955042_R03C02]

description:
5771955042_R03C02
AML_KMT2A


title: BRCA_21_3_9

value: Primary Tumour


title: WT-1

description: Library name: Mouse_H581-T01

value: inguinal white adipose tissue (iWAT)


title: Col-0 ISX+PEP3 rep1

description: Library name: Sample 10

tag: treatment


title: lEVs from C57Bl/6 control ischemic muscle

description:
Library name: lEVs C57
Column name in lEVs_Processed_DATA.csv: lEVs_C57_READs and lEVs_C57_CPM
lEVs_Processed_DATA.csv

source_name: lEVs from Hind limb muscle

value: lEVs from Hind limb muscle

value: Regular diet

value: hind limb ischemia


title: lEVs from ApoE ko western diet ischemic muscle

description:
Library name: lEVs ApoE
Column name in lEVs_Processed_DATA.csv: lEVs_ApoE_READs and lEVs_ApoE_CPM
lEVs_Processed_DATA.csv

value: ApoE ko

value: Western Diet