title: 28284 pleural

city: Boston

first: Chris

address: 77 avenue louis Pasteur, NRB 652

institute: Brigham and Women's Hospital

data_processing:
Quality-controlled reads are aligned to the human genome (GRCh38/hg38) and to ERCC92 spike-in sequences using a splice-aware aligner (STAR89) with Ensembl. transcriptome annotations.
Differential expression (DE) analysis is performed using RUVSeq to identify unwanted variation followed by edgeR91 and/or DESeq2
Assembly: GRCm39/mm39 and GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HBSS + 10% FBS + 1% pen/strep + 1x glutamax

extract_protocol:
RNA was harvested using RNAeasy (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. ERCC92 spike-in RNA is added to normalize reads.
RNA libraries for RNA-seq were prepared using the Roche KAPA HyperPrep RNA RiboErase Kit following manufacturer's protocols.

value: pleural fluid


title: pat_03_T

status: Public on Oct 04 2023

type: SRA

city: Milan,

first: Raffaella

last: Pini

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

library_source: transcriptomic

data_processing:
The 100-bp single-end reads were aligned to the reference human genome GRCh38 using STAR aligner (version 2.5.3a)
Only uniquely mapped reads were retained. At the gene level, expression counts were estimated using featureCounts (version1.6.3), and annotated according to Gencode basic annotations (Gencode version 28)
Reads per kilobase of transcript per million reads  (RPKM) were computed with edgeR rpkm function
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: tumor

growth_protocol: Not applicable

extract_protocol:
RNA was extracted using the Rneasy Plus Mini (Quiagen).
RNA libraries fro RNA-seq were prepared using the TruSeq Stranded mRNA (Illumina) protocol, following manufacturer's instructions

treatment_protocol: Not applicable

tag: tissue

value: tumor

tag: treatment

value: Chemo-naive


title: Kasumi-1_DMSO-2

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

description:
con2
Kasumi-1_RB98.csv

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RIP-seq)
Peaks were called by macs2(2.2.6) callpeaks algorithm with default set.(RIP-seq)
fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter，used HISAT2 to map reads to the reference genome Homo sapiens (GRCh38)，Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software
Assembly: hg38 for RNA-seq,RIP-seq and m6A seq.
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)
Supplementary files format and content: BigWig files were generated by deeptools(3.5.1) bamCoverge and normalized with BPM(Bins Per Million mapped reads)method .(RIP-seq)
Supplementary files format and content: StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM(m6A-seq)

source_name: Peripheral blood

growth_protocol: Kasumi-1 were cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
After infection by  shCtrl and shRBPMS lenti-virus for 48h, Kasumi-1 cells were selected by puromycine for 48h and then harvested for RNA extraction with TRIzol Reagent (Invitrogen).Kasumi-1 cells were treated with RB98# and then harvested for RNA extraction with TRIzol Reagent (Invitrogen) (RNA-seq)
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. (m6A-seq)
Libraries were generated using the NR605-02 V8 RNA-seq Library Prep Kit for Illumina and sequenced with Illumina NovaSeq6000.(RNA-seq)
Libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina and sequenced with Illumina NovaSeq6000.(RIP-seq)
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs withE. coliDNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.(m6A-seq)

value: Peripheral blood

tag: cell line

tag: cell type

value: myeloblast

tag: genotype

value: leukemic cell line with an 8;21 chromosome translocation

value: DMSO


title: Kasumi-1_RB98-1

description:
5_1
Kasumi-1_RB98.csv


title: Kasumi-1_DMSO-1

description:
con1
Kasumi-1_RB98.csv


title: shRBPMS-3_Kasumi-1_RNA-seq

description:
R_2_2
Kasumi-1_shRNA.csv

value: RBPMS knockdown


title: shRNA control-3_Kasumi-1_RNA-seq

description:
sc_2_2
Kasumi-1_shRNA.csv

value: scramble shRNA control


title: shRNA control-2_Kasumi-1_RNA-seq

description:
sc_2_1
Kasumi-1_shRNA.csv


title: Fresh_CordBlood_MPP

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

country: USA

institute: Indiana University

data_processing:
Fastq files were analyzed for quality using FastQC
Reads were trimmed of adapters and low-quality reads using Cutadapt with the arguments -a CTGTCTCTTATA -A CTGTCTCTTATA --nextseq-trim=20 --minimum-length 50.
Raw genome files downloaded from GENCODE (GRch38 version 41) were used as input to generate genome indices with STAR alignment software using the arguments –sjdbOverhang 99.
Trimmed reads were aligned to the genome using STAR with the arguments --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within.
Aligned reads were assigned to exons and annotated by gene using HTSeq with the arguments -s no -r pos -f bam.
Gene counts were normalized and differential expression was analyzed using DESeq2 R package.
Assembly: hg38
Supplementary files format and content: tab delimited files containing raw counts for each sample

molecule: polyA RNA

source_name: Umbilical Cord Blood

extract_protocol:
HSCs/MPPs were sorted by flow cytometry directly into lysis buffer and RNA was harvested using Qiagen Rneasy Micro Plus Kit.
Libraries were prepared by the Indiana University Center for Medical Genomics using the SMART-Seq v4 Ultra Low Input RNA kit

treatment_protocol: 27-year cryopreserved cord blood was thawed using clinical procedures. Both 27-year cord blood and fresh cord blood were enriched for CD34+ cells before being sorted by flow cytometry.

value: Umbilical Cord Blood

value: Multipotent progenitor cells

tag: condition

value: Fresh

tag: sex (inferred_from_sequencing_data)

value: male

tag: engraftment capacity

value: na-fresh


title: Fresh_CordBlood3_MPP


title: shRNA control-1_Kasumi-1_RNA-seq

description:
sc_1
Kasumi-1_shRNA.csv


title: Fresh_CordBlood1_HSC

value: Hematopoietic stem cells


title: Fresh_CordBlood1_MPP


title: Cryo_CordBlood410HSC

value: 27-year cryopreserved

value: female

value: high


title: Cryo_CordBlood397_HSC

value: low


title: shRBPMS-1_Kasumi-1_RNA-seq

description:
R_1
Kasumi-1_shRNA.csv


title: Fresh_CordBlood2_HSC


title: Cryo_CordBlood239_HSC


title: Cryo_CordBlood397_MPP


title: Cryo_CordBlood410MPP


title: Fresh_CordBlood2_MPP


title: Fresh_CordBlood4_HSC


title: 283AAn (S84), L001

city: 5841 S Maryland Ave. MC3026

first: Eric

middle: M

last: Thompson

state: IL

institute: The University of Chicago

data_processing:
Sample fastq file quality metrics were assessed via FastQC v0.11.9 and MultiQC v1.11. Paired-end reads were aligned to the GRCh38.p14 human reference genome via STAR v2.7.2b with default parameter settings. Post-alignment quality metrics were assessed via the log file output of STAR. Quantification and generation of the raw counts matrix were performed by featureCounts v1.6.3. The raw counts matrix was then normalized, and differential expression was calculated via DeSeq2 R package v1.36.0.
Assembly: GRCh38.p14
Supplementary files format and content: Single .csv file contains gene counts for all 6 samples with each sample containing two entries; one for each sequencing lane (L001 and L002)

growth_protocol: DMEM-12 plus 10% FNS, 1% NEAA, 1% glutamine

extract_protocol:
The Sequencing and Genomic Technologies (SGT) Core Facility at Duke University performed RNA sequencing. The SGT Core Facility extracted total RNA from cell pellets using the RNeasy Plus Mini Kit from Qiagen (catalog #: 74134). mRNA was enriched from total RNA and reverse-transcribed into cDNA to build sequencing libraries using the KAPA mRNA HyperPrep Kit from Roche (KK8581).
Libraries were pooled to equimolar concentrations and sequenced on the NovaSeq 6000 S2 flow cell to produce 50 bp paired-end reads.

value: medulloblastoma cells

value: inactivation of ABL1 and ABL2


title: 283AAn (S84), L002


title: Cryo_CordBlood239_MPP


title: Fresh_CordBlood3_HSC


title: 283AAn (S83), L001


title: 283AAn (S83), L002


title: full-length AR and AR-V7_2

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
Data was aligned to hg38 using RNA-STAR
Data was normalized using TMM
Assembly: hg38
Supplementary files format and content: Excel table with raw counts

source_name: breast

extract_protocol: RNA was extracted using Rneasy plus kit (Qiagen). 1.5ug of RNA was used for the construction of sequencing libraries.

value: breast

value: breast cancer cells

value: full-length AR and AR-V7


title: full-length AR and AR-V7_3


title: 283AAn (S82), L002


title: 283AAn (S82), L001


title: shRBPMS-2_Kasumi-1_RNA-seq

description:
R_2_1
Kasumi-1_shRNA.csv

value: Peripheral blood

value: myeloblast

value: leukemic cell line with an 8;21 chromosome translocation

value: RBPMS knockdown


title: full-length AR_3

value: full-length AR


title: full-length AR_2


title: 283Scn (S80), L002

value: control


title: 283Scn (S80), L001


title: HOPXDam2

city: Wooloongabba

first: Seth

last: Cheetham

state: QLD

address: Level 4, 37 Kent St

country: Australia

institute: Mater Research Institute-University of Queensland

description:
hoxpdamid2_peaks.bed
hopxdamid2.bedgraph.gz

library_source: genomic

data_processing:
Library strategy: DamID-seq
Reads were aligned to hg38 using bowtie2
Reads were binned into GATC fragments
HOPXDam reads were normalised by the corresponding Dam signal using the damid_seq_pipeline
Samples were quantilise normalised to each other
Peaks were called using the DamID peak caller (FDR <0.01)
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files with normalised DamID signal and peak files in bed format

molecule: genomic DNA

source_name: cardiomyocytes

extract_protocol:
Qiagen MicroAmp
DamID seq (Marshall et al., Nat. Protoc., 2016)
NEB UltraII for Illumina

value: cardiomyocytes


title: Dam2


title: Dam1

description:
hoxpdamid1_peaks.bed
hopxdamid1.bedgraph.gz


title: 283Scn (S79), L001


title: HOPXDam3

description:
hoxpdamid3_peaks.bed
hopxdamid3.bedgraph.gz


title: 283Scn (S79), L002


title: HOPXDam1


title: THP-1_IgG_CUT&Tag

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg19 by bowtie2(2.2.5), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads,maximum fragment length 2000.(ATAC-seq)
Peaks were called by macs2(2.2.6) callpeaks algorithm with --nomodel --shift 100 --extsize 200.(ATAC-seq)
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg19 by bowtie2(2.2.5), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(CUT&Tag)
Peaks were called by macs2(2.2.6) callpeaks algorithm with default set.(CUT&Tag)
Assembly: hg19 for CUT&Tag and ATAC-seq,hg38 for RNA-seq
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)
Supplementary files format and content: BigWig files were generated by deeptools(3.5.1) bamCoverge and normalized with BPM (Bins Per Million mapped reads) method .(CUT&Tag)
Library strategy: CUT&Tag

growth_protocol: Kasumi-1 and THP-1 cells were cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
After infection by  shCtrl and shSMARCA5 lenti-virus for 48h, Kasumi-1 and THP-1 cells were selected by puromycine for 48h and then harvested for RNA extraction with TRIzol Reagent (Invitrogen). (RNA-seq)
After infection by  shCtrl and shSMARCA5 lenti-virus for 48h, Kasumi-1 and THP-1 cells were selected by puromycine for 48h and then harvested for gDNA extraction. (ATAC-seq)
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina #RS-122-2001) and sequenced with Illumina NovaSeq6000.(RNA-seq)
Libraries were generated using the Chromatin Profile Kit for Illumina (Novoprotein #N248-01A) and sequenced with Illumina NovaSeq6000.(ATAC-seq)
Library preparation was according to the manufacture’s guidelines (NovoNGS CUT&Tag 3.0 High-Sensitivity Kit for Illumina) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).(CUT&Tag)

value: endogenous CUT&Tag

tag: antibody

value: IgG


title: iFoxA1, mES+48hrs, antiFLAG-ChIP-exo, time-titration, rep1

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecalls were performed using using bcl-convert verison 00.000.000.3.8.2-12-g85770e0b
BWA mem (version 0.7.17-r1188) was used to align paired-end ChIP-exo reads against the mm10 reference genome using the following arguments: “-t 8 -v 1 -T 30 -h 5”.
Picard MarkDuplicates (version 2.7.1) was used to mark duplicate read pair alignments and then samtools view with arguments “-h -b -f 0x1 -F 0x404” was used to filter out duplicated read pairs. While read pairs were used for alignment and deduplication purposes, only read1 alignment information from the deduplicated alignments was retained for downstream analysis (read1 corresponds to the ends of the immunoprecipitated DNA fragments that are subject to exonuclease digestion, whereas read2 information has the same resolution as ChIP-seq).
Initial peak-finding was performed for each ChIP-exo experiment with ChExMix (version 0.52) with the following settings: “--threads 8 --scalewin 1000 --mememinw 6 --mememaxw 18 --q 0.05 --epsilonscale 0.5”, excluding ENCODE blacklist regions, and using MEME (version 4.11.3) internally to discover motifs associated with binding subtypes. To encourage consistency in shared peak coordinates across Fox TFs, we re-ran ChExMix in a mode where the possible binding subtype motifs are pre-initialized and remain fixed during training, using settings: “--threads 8 --scalewin 1000 --q 0.05 --epsilonscale 0.75 --motfile $motifs –noupdateinitmotifs”. The motif set provided as “$motifs” contain the MEME-discovered subtype motifs from the most populous binding subtypes in the initial ChExMix runs.
Assembly: mm10
Supplementary files format and content: bed: BED format files containing ChExMix peak call locations
Supplementary files format and content: bw: bigwig format files with read coverage of mapped ChIP-exo data
Library strategy: ChIP-exo

organism: Mus musculus

growth_protocol: Generation of the mES transgenic cell lines used in this study is described in [PMID: 19796622]. These cell lines were part of NIA (National Institute on Aging/NIH) mouse ES cell collection. Cell lines are derived from MC1 mouse ES cells (129S6/SvEvTac). Doxycycline-repressible expression constructs containing the relevant TF ORF, C-terminally tagged with His6-FLAG, and a puromycin resistance gene were inserted into the expression-competent Rosa26 locus. ES cells were cultured in a gelatin-coated dish with DMEM medium containing 15% FBS, 1000 U/ml LIF, 1 mM sodium pyruvate, 0.1 mM MEM non-essential amino acids, 2 mM glutamate, 0.1 mM ß-mercaptoethanol, 0.2µg/ml Doxycycline and 1.0μg/ml puromycin.

extract_protocol:
Lysis was performed in Farnham cell lysis buffer for 20mins at 4°C. At the 10-min mark, cells were pushed through a 25-gauge needle five times to enhance cellular lysis. Nuclei were then isolated by pelleting at 10,000 rpm for 3 min. Nuclei were resuspended in RIPA buffer (25 million cells to 1 mL of buffer) for an additional 20 min at 4°C and then pelleted again at 10,000 rpm for 3 min. Disrupted nuclei were then finally resuspended in 1× PBS (25 million cells to 1 mL of buffer) and sonicated for 10 cycles (30-on/30-off) in a Diagenode pico.
Solubilized chromatin was pre-cleared by centrifugation at maximum speed for 15 min at 4°C before incubating with 10 μL pAG Dynabeads, preloaded with 3 μg of antibody overnight, then sequentially processed through A-tailing, first adapter ligation, Phi29 fill-in, lambda exonuclease digestion, cross-link reversal, second adapter ligation, and PCR followed by size selection for final high-throughput sequencing.

treatment_protocol: To induce transgene TFs, Dox was removed by washing three times with PBS at 3 hr intervals and cells were grown in DMEM differentiation medium containing 10% FBS for the stated amount of time. Chromatin was crosslinked using 1% formaldehyde for 10 minutes.

value: embryonic stem cells

value: Dox removal +48hrs

tag: chip-seq antibody

value: F1804 Sigma, lot SLBW5142


title: full-length AR and AR-V7_1


title: iFoxA1, mES+24hrs, antiFoxA1-ChIP-exo, time-titration, rep1

value: Dox removal +24hrs


title: Kasumi-1_SMARCA5_CUT&Tag


title: Kasumi-1_IgG_CUT&Tag


title: shSMARCA5_THP-1_ATAC-seq

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg19 by bowtie2(2.2.5), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads,maximum fragment length 2000.(ATAC-seq)
Peaks were called by macs2(2.2.6) callpeaks algorithm with --nomodel --shift 100 --extsize 200.(ATAC-seq)
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg19 by bowtie2(2.2.5), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(CUT&Tag)
Peaks were called by macs2(2.2.6) callpeaks algorithm with default set.(CUT&Tag)
Assembly: hg19 for CUT&Tag and ATAC-seq,hg38 for RNA-seq
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)
Supplementary files format and content: BigWig files were generated by deeptools(3.5.1) bamCoverge and normalized with BPM (Bins Per Million mapped reads) method .(CUT&Tag)

value: SMARCA5 knockdown


title: iFoxA1, mES+48hrs, antiFoxA1-ChIP-exo, time-titration, rep1


title: shCtrl_THP-1_ATAC-seq

value: scramble shRNA control


title: full-length AR_1

value: breast

value: breast cancer cells


title: iFoxA1, mES+12hrs, antiFoxA1-ChIP-exo, time-titration, rep1

value: Dox removal +12hrs


title: iFoxA1, mES+24hrs, antiFLAG-ChIP-exo, time-titration, rep1


title: iFoxA1, mES+12hrs, antiFLAG-ChIP-exo, time-titration, rep1


title: THP-1_SMARCA5_CUT&Tag

value: Peripheral blood

value: myeloblast


title: shSMARCA5_Kasumi-1_ATAC-seq

value: leukemic cell line with an 8;21 chromosome translocation


title: 283Scn (S81), L002

value: medulloblastoma cells


title: Dam3


title: shCtrl_Kasumi-1_ATAC-seq


title: 283Scn (S81), L001

value: control


title: iFoxA1, mES+6hrs, antiFoxA1-ChIP-exo, time-titration, rep1

value: Dox removal +6hrs


title: shSMARCA5-3_THP-1_RNA-seq

description:
THP1_RNA-seq_result.csv
TS3


title: shSMARCA5-2_THP-1_RNA-seq

description:
THP1_RNA-seq_result.csv
TS2


title: iFoxA1, mES+6hrs, antiFLAG-ChIP-exo, time-titration, rep1


title: iFoxA1, mES+0hrs, antiFoxA1-ChIP-exo, time-titration, rep1

value: Dox removal +0hrs


title: iAscl1, mES+48hrs, antiAscl1-ChIP-exo, time-titration, rep1


title: iFoxA1, mES+0hrs, antiFLAG-ChIP-exo, time-titration, rep1


title: shCtrl-3_THP-1_RNA-seq

description:
THP-1_RNA-seq_result.csv
TP3


title: shCtrl-2_THP-1_RNA-seq

description:
THP1_RNA-seq_result.csv
TP2


title: shSMARCA5-1_THP-1_RNA-seq

description:
THP1_RNA-seq_result.csv
TS1


title: shCtrl-1_THP-1_RNA-seq

description:
THP-1_RNA-seq_result.csv
TP1


title: iAscl1, mES+24hrs, antiAscl1-ChIP-exo, time-titration, rep1


title: iAscl1, mES+12hrs, antiAscl1-ChIP-exo, time-titration, rep1


title: shSMARCA5-3_Kasumi-1_RNA-seq

description:
Kasumi-1_RNA-seq_result.csv
hs3


title: shSMARCA5-2_Kasumi-1_RNA-seq

description:
Kasumi-1_RNA-seq_result.csv
hs2


title: shSMARCA5-1_Kasumi-1_RNA-seq

description:
Kasumi-1_RNA-seq_result.csv
hs1


title: shCtrl-3_Kasumi-1_RNA-seq

description:
Kasumi-1_RNA-seq_result.csv
kc3


title: iAscl1, mES+0hrs, antiAscl1-ChIP-exo, time-titration, rep1


title: iAscl1, mES+6hrs, antiAscl1-ChIP-exo, time-titration, rep1


title: EmptyControl, mES+0hrs, antiFoxA1-ChIP-exo, rep2


title: shCtrl-2_Kasumi-1_RNA-seq

description:
Kasumi-1_RNA-seq_result.csv
kc2


title: iFoxP3, mES+24hrs, antiFLAG-ChIP-exo, rep1


title: shCtrl-1_Kasumi-1_RNA-seq

description:
Kasumi-1_RNA-seq_result.csv
kc1


title: EmptyControl, mES+0hrs, antiFLAG-ChIP-exo, rep1


title: LMDP_117lo_W3_FLT3L_rep5

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description:
C4F_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4  was used to align the second reads
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

extract_protocol:
no extraction_cell lysates
Libraries were prepared using the Illumina DNA Prep kit (Illumina) according to the manufacturer’s guidelines.

tag: time


title: LMDP_117lo_W3_FLT3L_rep3

description:
C4F_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxL2, mES+24hrs, antiFLAG-ChIP-exo, rep2


title: LMDP_117lo_W3_FLT3L_rep6

description:
C4F_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W3_FLT3L_rep4

description:
C4F_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxP3, mES+24hrs, antiFLAG-ChIP-exo, rep2


title: LMDP_117lo_W3_FLT3L_rep2

description:
C4F_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxG1, mES+24hrs, antiFLAG-ChIP-exo, rep2


title: LMDP_117lo_W3_TPO_rep3

description:
C4T_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

value: TPO


title: LMDP_117lo_W3_FLT3L_rep1

description:
C4F_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxC1, mES+24hrs, antiFLAG-ChIP-exo, rep2

value: embryonic stem cells


title: iFoxG1, mES+24hrs, antiFLAG-ChIP-exo, rep1


title: LMDP_117lo_W3_TPO_rep2

description:
C4T_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxC1, mES+24hrs, antiFLAG-ChIP-exo, rep1


title: iFoxA1, mES+24hrs, antiFLAG-ChIP-exo, rep3


title: iFoxA1, mES+24hrs, antiFoxA1-ChIP-exo, rep2


title: LMDP_117lo_W3_SCF_rep6

description:
C4S_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

value: SCF


title: LMDP_117lo_W3_TPO_rep1

description:
C4T_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W3_SCF_rep5

description:
C4S_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W3_SCF_rep4

description:
C4S_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W3_SCF_rep3

description:
C4S_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxA1, mES+24hrs, antiFLAG-ChIP-exo, rep1

value: F1804 Sigma, lot SLBW5142


title: iFoxL2, mES+24hrs, RNA-seq, rep2

data_processing:
Basecalls were performed using using bcl-convert verison 00.000.000.3.8.2-12-g85770e0b
Gene expression was quantified by mapping the RNA-seq fastq files to the mouse mm10 GENCODE transcriptome (version 23) using Salmon (version 1.4.0) with the arguments ‘-l A --gcBias --validateMappings’.
Differential gene expression analysis was performed using DESeq2 (version 1.30.1). To account for the fact that there were single-end and paired-end replicates for the induced FoxC1, FoxG1, FoxL2, and FoxP3 cell-line at the 24hr time point, we used a design formula ‘readtype + condition’. For the 0hr time-point, we treated all cell-lines as the same condition, whereas for the 24hr time-point, the condition was the concatenated cell-line and time-point.
Assembly: mm10
Supplementary files format and content: tsv: tab-separated file containing TPM values or read counts for each sample

extract_protocol:
RNA-seq experiments started with 1 μg of total RNA. The NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) was used to enrich for polyA mRNA.
Strand-specific RNA-seq libraries were then prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit.

treatment_protocol: To induce transgene TFs, Dox was removed by washing three times with PBS at 3 hr intervals and cells were grown in DMEM differentiation medium containing 10% FBS for the stated amount of time.

value: Dox removal +24hrs


title: iFoxL2, mES+24hrs, antiFLAG-ChIP-exo, rep1


title: LMDP_117lo_W3_SCF_rep2

description:
C4S_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxP3, mES+24hrs, RNA-seq, rep2


title: LMDP_117lo_W3_SCF_rep1

description:
C4S_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxG1, mES+24hrs, RNA-seq, rep2


title: LMDP_117int_W3_FLT3L_rep5

description:
C3F_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_FLT3L_rep4

description:
C3F_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_FLT3L_rep6

description:
C3F_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxA1, mES+24hrs, RNA-seq, rep3


title: iFoxP3, mES+24hrs, RNA-seq, rep1


title: iFoxC1, mES+24hrs, RNA-seq, rep2


title: iFoxL2, mES+24hrs, RNA-seq, rep1


title: iFoxG1, mES+24hrs, RNA-seq, rep1


title: LMDP_117int_W3_FLT3L_rep3

description:
C3F_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxC1, mES+24hrs, RNA-seq, rep1


title: LMDP_117int_W3_FLT3L_rep2

description:
C3F_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_FLT3L_rep1

description:
C3F_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxA1, mES+24hrs, RNA-seq, rep2


title: LMDP_117int_W3_TPO_rep6

description:
C3T_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxA1, mES+24hrs, RNA-seq, rep1


title: iFoxP3, mES+0hrs, RNA-seq, rep1


title: LMDP_117int_W3_TPO_rep5

description:
C3T_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_TPO_rep4

description:
C3T_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxG1, mES+0hrs, RNA-seq, rep1


title: LMDP_117int_W3_TPO_rep3

description:
C3T_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxC1, mES+0hrs, RNA-seq, rep1


title: LMDP_117int_W3_TPO_rep1

description:
C3T_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_TPO_rep2

description:
C3T_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_SCF_rep6

description:
C3S_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxA1, mES+0hrs, RNA-seq, rep1


title: LMDP_117int_W3_SCF_rep5

description:
C3S_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_SCF_rep4

description:
C3S_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_SCF_rep3

description:
C3S_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117int_W3_SCF_rep2

description:
C3S_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Bisulfite-Seq Sorghum bicolor: Btx623 whole root replicate 2 under low phosphorous condition

city: Cold Spring Harbor

first: Nicholas

last: Gladman

state: NY

address: 1 Bungtown Rd

department: ARS

institute: USDA

description:
cpg_all_differential_methylated_regions.csv
chh_all_differential_methylated_regions.csv
chg_all_differential_methylated_regions.csv

data_processing:
RNA-seq: Paired-end fastq files were trimmed for quality with Trimmomatic and then merged with Samtools before aligning to the v3.4.1 S. bicolor genome with Kallisto package in rStudio v3.6.1. Differential gene expression was deter- mined through DESeq2 after importing Kallisto abundance files with tximport package. Dimensional analysis was performed using the factoextra package. Heatmaps and hierarchical clustering were per- formed with the heatmpap.2 package in rStudio.
ChIP-seq: Paired-end fastq files were trimmed for quality with Trimmomatic and then mapped to the v3.4.1 S. bicolor genome with BWA (bwa mem -q 30, -f 2 -ubhS). Sorted bam files were marked for duplicates with Picard and then merged with Samtools. Tag directories creation and peak calling, peak enrichment comparison was performed through the Homer package. Overlapped peaks were identified through Bedtools (intersectBed). Peak annotation was performed using the annotatePeaks module of the Homer software. Samtools was used to obtain flagstat metrics and perform various file conversion and handling. Various visualization and file creation was performed using the deepTools package (Ramírez et al., 2016); aligned bam files (that were input-controlled) were converted to bigWig format for generating computeMatrix files for plotHeatmap and plotEnrichment outputs. k-means cluster number was determined by selecting the result that generated the distinct read coverage within and around gene models while minimizing clus- ter overlap.
Bisulphite-Seq: Reads were trimmed and quality controlled using Trim Galore and FASTQC respectively (http://www.bioinformatics.babraham.ac.uk/projects/index.html). Reads were aligned and extracted with Bismark (Krueger & Andrews, 2011). Differential methylation quantification and visualiza- tions were done with MethylKit (Akalin et al., 2012). Additional visual- izations were performed with deepTools (Ramírez et al., 2016) after converting Bismark-aligned bam files to bigWig and then generating computeMatrix files for plotHeatmap and plotEnrichment outputs.
Assembly: Sorghum Bicolor BTx623 v 3.1
Supplementary files format and content: RNA-seq: abundance files (*_abundance.tsv) from a kallisto quant run of trimmomatic-trimmed fastq files. These files are used for input into a differential expression analysis program (DESeq2 or edgeR).
Supplementary files format and content: ChIP-seq: these are bigwig files after processing with the Homer package. Aligned read files were marked for duplicates with Picard and then merged with Samtools. Subsequently, tag directories, peak calling, and peak enrichment were performed with Homer. These files are those outputs using the 'genomic DNA as control' samples as input controls for the calling.
Supplementary files format and content: Bisulphite-Seq: the *_all_differential_methylated_regions.csv files were generated from the MethylKit package after aligning the fastq files with Bismark. These files contain differential methylated sites for CPG, CHG, and CHH methylation using normal phosphorus growth conditions as the control. Statistical values for each call are included in the .csv files as well as a MethylKit score.

organism: Sorghum bicolor

source_name: whole root

extract_protocol:
RNA-seq: Root tissue samples were ground in liquid nitrogen and then the RNA was isolated in Trizol reagent (ThermoFisher) followed by purifica- tion using Zymo-spin columns (Directzol RNA kit; Zymo Research). Column-bound RNA was treated with DNase 1 and finally eluted with 50 μl of DNase/RNase-free water. RNA quality was determined using the Bioanalyzer hardware with the Agilent RNA 6000 Nano Kit (Agilent). Poly-A RNA was isolated from total RNA using Dynabeads (ThermoFisher). Libraries for sequencing were created using the ScriptSeq RNA-seq prep kit (Illumina) following manufacturer protocols. Final libraries were amplified with 17 cycles of PCR and assessed on the Bioanalyzer with the High Sensitivity DNA kit (Agilent). Bisulphite-seq: Bisulfite-sequencing was done as described in (Li et al., 2014). The root apices (first two cm) of all primary and lateral roots were excised from plants grown as described above after 10 days of growth on SP and LP media. The root samples from 10 plants constituted one bio- logical replicate. DNA was isolated from root sections and sheared into fragments between 200 and 300 bp in length. These fragments underwent end repair, dA tailing, and ligation to methylated adaptors for subsequent bisulfite conversion. Libraries were PCR amplified, purified, and qual- ity controlled via Agilent DNA 1000 chip. Sequencing was done on a HiSeq 2500 v4 with 125 bp paired-end reads. ChIP-seq: The entire root systems were harvested for ChIP-seq library prepara- tion. The root tissue was cut into sections and fixed in 10-mM dimethyl adipimate (DMA; Sigma-Aldrich) while applying a vacuum. Samples were ground in liquid nitrogen and then placed in extraction buffer, filtered through miracloth and then a 30-mm CellTrics filter (CellTrics). Nuclei were isolated and then chromatin was sheared in 130-ml tubes (Covaris). Shearing was performed on a Covaris S220 sonicator for 5 min at a cycle/burst of 200, peak power of 175, and duty factor of 10. Immunoprecipitation was performed with anti- bodies for H3K27me3 (Millipore), H3K4me3 (Abcam), H3 (Abacam) for input control, and Protein A Dynabeads (ThermoFisher) for input control. Crosslinking was reversed and samples were purified using Chip DNA Clean and Concentrator Kit (Zymo Research).
RNA-seq: Libraries for sequencing were created using the ScriptSeq RNA-seq prep kit (Illumina) following manufacturer protocols. Final libraries were amplified with 17 cycles of PCR and assessed on the Bioanalyzer with the High Sensitivity DNA kit (Agilent). All root tis- sue libraries that were sequenced comprised two biological replicates. Bisulphite-seq: DNA was isolated from root sections and sheared into fragments between 200 and 300 bp in length. These fragments underwent end repair, dA tailing, and ligation to methylated adaptors for subsequent bisulfite conversion. Libraries were PCR amplified, purified, and qual- ity controlled via Agilent DNA 1000 chip. Chip-seq: Libraries were created using the Nextflex ChIP-Seq library prep kit (Bioo Scien- tific) with the NextFlex ChIP-seq Barcodes. Sequencing was done on a HiSeq 2500 v4 with 125 bp paired-end reads

value: whole root

value: low phosphorus


title: Bisulfite-Seq Sorghum bicolor: Btx623 whole root replicate 1 under low phosphorous condition


title: Bisulfite-Seq Sorghum bicolor: Btx623 whole root replicate 2 under high phosphorous condition

value: normal phosphorus


title: iFoxL2, mES+0hrs, RNA-seq, rep1


title: Bisulfite-Seq Sorghum bicolor: Btx623 whole root replicate 1 under high phosphorous condition


title: don_71_Tfh17

data_processing:
The 75-bp single-end reads were aligned to the reference human genome GRCh38 using STAR aligner (version 2.5.3a)
Only uniquely mapped reads were retained. At the gene level, expression counts were estimated using featureCounts (version1.6.3), and annotated according to Gencode basic annotations (Gencode version 28)
Read counts were normalized using the DESeq2 regularized log transformation method
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

source_name: T follicular helper cells

extract_protocol:
RNA was extracted using the Rneasy Plus Mini or Micro kit (Quiagen), based on cell number recovery.
RNA libraries fro RNA-seq were prepared using the SMART-Seq v4 (TaKaRa) protocol, following manufacturer's instructions

value: T follicular helper cells

value: Chemo-naive


title: LMDP_117int_W3_SCF_rep1

description:
C3S_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_FLT3L_rep5

description:
C2F_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_71_Tfh2


title: don_71_Tfh1


title: don_6_Tfh17


title: LMDP_117hi_W3_FLT3L_rep6

description:
C2F_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_FLT3L_rep4

description:
C2F_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_FLT3L_rep2

description:
C2F_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_5_Tfh17


title: LMDP_117hi_W3_FLT3L_rep1

description:
C2F_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: iFoxA1, mES+0hrs, RNA-seq, rep2


title: don_5_Tfh2


title: don_6_Tfh1


title: don_5_Tfh1


title: don_12_Tfh17


title: LMDP_117hi_W3_TPO_rep6

description:
C2T_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_TPO_rep4

description:
C2T_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_TPO_rep3

description:
C2T_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_12_Tfh2


title: don_12_Tfh1


title: LMDP_117hi_W3_TPO_rep5

description:
C2T_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_111_Tfh17


title: LMDP_117hi_W3_SCF_rep6

description:
C2S_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_TPO_rep1

description:
C2T_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_SCF_rep5

description:
C2S_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_111_Tfh1


title: don_111_Tfh2


title: LMDP_117hi_W3_SCF_rep4

description:
C2S_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_6_Tfh2


title: don_110_Tfh2


title: LMDP_117hi_W3_FLT3L_rep3

description:
C2F_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_110_Tfh1


title: don_11_Tfh17


title: LMDP_117hi_W3_SCF_rep2

description:
C2S_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W3_SCF_rep3

description:
C2S_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_FLT3L_rep9

description:
C1F_9
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

source_name: HSC

value: HSC


title: HSC_W3_FLT3L_rep8

description:
C1F_8
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_11_Tfh1


title: HSC_W3_FLT3L_rep7

description:
C1F_7
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_FLT3L_rep6

description:
C1F_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_108_Tfh2


title: HSC_W3_FLT3L_rep5

description:
C1F_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_FLT3L_rep4

description:
C1F_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_108_Tfh17


title: LMDP_117hi_W3_TPO_rep2

description:
C2T_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_107_Tfh17


title: don_108_Tfh1


title: don_107_Tfh2


title: HSC_W3_FLT3L_rep3

description:
C1F_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_110_Tfh17


title: don_99_Tfh17

value: Healthy donors


title: HSC_W3_FLT3L_rep1

description:
C1F_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_FLT3L_rep2

description:
C1F_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_TPO_rep9

description:
C1T_9
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_99_Tfh1


title: don_107_Tfh1


title: HSC_W3_TPO_rep8

description:
C1T_8
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_11_Tfh2


title: LMDP_117hi_W3_SCF_rep1

description:
C2S_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_98_Tfh2


title: don_98_Tfh1


title: don_91_Tfh17


title: HSC_W3_TPO_rep4

description:
C1T_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_TPO_rep3

description:
C1T_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_TPO_rep2

description:
C1T_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_91_Tfh2


title: HSC_W3_TPO_rep1

description:
C1T_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_91_Tfh1


title: don_90_Tfh17


title: HSC_W3_SCF_rep8

description:
C1S_8
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_90_Tfh1


title: don_99_Tfh2


title: HSC_W3_SCF_rep9

description:
C1S_9
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_90_Tfh2


title: don_89_Tfh2


title: don_98_Tfh17


title: HSC_W3_TPO_rep7

description:
C1T_7
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_SCF_rep4

description:
C1S_4
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_89_Tfh17


title: HSC_W3_TPO_rep6

description:
C1T_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_SCF_rep6

description:
C1S_6
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_SCF_rep7

description:
C1S_7
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_TPO_rep5

description:
C1T_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_SCF_rep3

description:
C1S_3
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_SCF_rep2

description:
C1S_2
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_SCF_rep1

description:
C1S_1
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MDC2_34p116p_W3_rep5

description:
W3_P24_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

value: no


title: don_106_Tfh2


title: MDC2_34p116p_W3_rep4

description:
W3_P24_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MDC2_34p116p_W3_rep2

description:
W3_P24_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_105_Tfh17


title: don_106_Tfh1


title: HD-MS275-48h-2

type: RNA

city: Heidelberg

first: Jonas

last: Ecker

address: Im Neuenheimer Feld 430

country: Germany

institute: Hopp Children's Cancer Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GC-RMA normalization

label: biotin

label_protocol: standard Affymetrix protocol

growth_protocol: HD-MB03 cells were cultured in RPMI medium supplemented with 10% FCS

extract_protocol: RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: treatment with 1µM entinostat for 24h and 48h with respective DMSO treated samples (solvent control)

value: MYC amplified MB cells

value: entinostat


title: HSC_W3_SCF_rep5

description:
C1S_5
Cyto.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MDC1_34p115p_W3_rep5

description:
W3_P27_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_89_Tfh1


title: MDC2_34p116p_W3_rep1

description:
W3_P24_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MDC1_34p115p_W3_rep4

description:
W3_P27_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MDC1_34p115p_W3_rep3

description:
W3_P27_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MDC1_34p115p_W3_rep2

description:
W3_P27_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_106_Tfh17


title: MDC1_34p115p_W3_rep1

description:
W3_P27_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_105_Tfh1


title: don_105_Tfh2


title: PDC_34p123p_W3_rep5

description:
W3_P30_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_103_Tfh17


title: HD-MS275-48h-1


title: PDC_34p123p_W3_rep4

description:
W3_P30_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MDC2_34p116p_W3_rep3

description:
W3_P24_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HD-DMSO-48h-3

value: untreated


title: HD-DMSO-48h-2


title: HD-DMSO-48h-1


title: don_103_Tfh2


title: HD-MS275-24h-3


title: PDC_34p123p_W3_rep3

description:
W3_P30_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HD-MS275-24h-2


title: PDC_34p123p_W3_rep2

description:
W3_P30_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_103_Tfh1


title: ELP_R7pB7p7p_W5_rep5

description:
W5_P22_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_102_Tfh17


title: ELP_R7pB7p7p_W5_rep4

description:
W5_P22_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W5_rep2

description:
W5_P22_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W5_rep3

description:
W5_P22_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W4_rep5

description:
W4_P22_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_102_Tfh1


title: ELP_R7pB7p7p_W5_rep1

description:
W5_P22_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PDC_34p123p_W3_rep1

description:
W3_P30_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HD-DMSO-24h-1


title: HD-DMSO-24h-2


title: HD-MS275-24h-1


title: ELP_R7pB7p7p_W4_rep3

description:
W4_P22_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W4_rep4

description:
W4_P22_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W4_rep2

description:
W4_P22_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W3_rep5

description:
W3_P22_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W4_rep1

description:
W4_P22_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PATIENT 27700PH

city: Salamanca

first: Juan

middle: Luis

last: Garcia

state: Type Below

address: Campus Miguel de Unamuno Centro de Investigacion del Cancer, IBSAL

country: Spain

institute: CIC/IBSAL

hyb_protocol: Samples were heated at 95º C in darkness, hybridized, and washed with the robotic HS 4800 Pro system (Tecan®).

scan_protocol: Fluorescence was scanned with a GenePix 4000B (Axon Instruments™) microarray scanner.  Raw data processing was performed with the

data_processing: Image processing was performed using Gene Prix Pro (v. 6.0), and data processing was performed using MEV (MultiExperiment Viewer) and EXpander 6.0

source_name: Monocytes CD14+

label_protocol: 1µg of total RNA was labelled with the Exiqon Kit protocol following the manufacturer´s instructions.

extract_protocol: Total RNA was extracted from CD14+ isolated monocytes and monocyte-derived macrophages using the miRNA easy Micro Kit (Qiagen), following the manufacturer’s instructions. Briefly, RNA was extracted using a phenol-chloroform mixture, precipitated in ethanol, and purified using RNase-free columns.

value: Peripheral blood

value: Monocytes CD14+

value: excessive alcohol drinker


title: PATIENT 29067PH


title: ELP_R7pB7p7p_W3_rep4

description:
W3_P22_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_102_Tfh2


title: don_100_Tfh1


title: ELP_R7pB7p7p_W3_rep3

description:
W3_P22_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_87_Tfh17

value: Chemotherapy-treated


title: PATIENT 27831/27861


title: ELP_R7pB7p7p_W3_rep2

description:
W3_P22_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W5_rep5

description:
W5_P20_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_87_Tfh2


title: ELP_R7pB7p7p_W3_rep1

description:
W3_P22_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PATIENT 27739PH


title: ELP_R7pB7n7n_W5_rep4

description:
W5_P20_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_100_Tfh17


title: PATIENT 26373PM


title: HD-DMSO-24h-3


title: ELP_R7pB7n7n_W5_rep3

description:
W5_P20_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_87_Tfh1


title: ELP_R7pB7n7n_W5_rep2

description:
W5_P20_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PATIENT 28742PM


title: don_100_Tfh2


title: don_86_Tfh17


title: PATIENT 26468PH


title: ELP_R7pB7n7n_W5_rep1

description:
W5_P20_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W4_rep5

description:
W4_P20_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PATIENT 26665PH


title: don_86_Tfh2


title: ELP_R7pB7n7n_W4_rep3

description:
W4_P20_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W4_rep2

description:
W4_P20_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W4_rep4

description:
W4_P20_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_86_Tfh1


title: ELP_R7pB7n7n_W4_rep1

description:
W4_P20_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_85_Tfh17


title: ELP_R7pB7n7n_W3_rep5

description:
W3_P20_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PATIENT 27962PM


title: ELP_R7pB7n7n_W3_rep4

description:
W3_P20_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PATIENT 26266PH


title: ELP_R7pB7n7n_W3_rep3

description:
W3_P20_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_85_Tfh2


title: PATIENT 26118 PM


title: don_85_Tfh1


title: ELP_R7pB7n7n_W3_rep2

description:
W3_P20_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W3_rep1

description:
W3_P20_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W2_rep5

description:
W2_P20_5
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: PATIENT 26406.26046PH


title: ELP_R7pB7n7n_W2_rep4

description:
W2_P20_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: don_84_Tfh17


title: PATIENT 29010 PM


title: CONTROL 26618CH

source_name: monocytes CD14 control

value: control


title: PATIENT 28628PH


title: ELP_R7pB7n7n_W2_rep3

description:
W2_P20_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W2_rep2

description:
W2_P20_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7n7n_W2_rep1

description:
W2_P20_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7p_W2_rep3

description:
W2_P22_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: CONTROL 26924 cH


title: don_84_Tfh1


title: don_83_Tfh17


title: CONTROL 27489 cH


title: ELP_R7pB7p7p_W2_rep1

description:
W2_P22_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W5_rep5

description:
W5_P21_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_83_Tfh2


title: don_83_Tfh1


title: ELP_R7pB7p7n_W5_rep3

description:
W5_P21_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: CONTROL 25833 c H


title: ELP_R7pB7p7n_W5_rep2

description:
W5_P21_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_82_Tfh17


title: CONTROL 26743 c M


title: ELP_R7pB7p7n_W5_rep1

description:
W5_P21_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_84_Tfh2


title: don_82_Tfh2


title: ELP_R7pB7p7n_W4_rep5

description:
W4_P21_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: CONTROL 27521 c H


title: ELP_R7pB7p7p_W2_rep4

description:
W2_P22_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: CONTROL 26215 c M


title: ELP_R7pB7p7n_W4_rep3

description:
W4_P21_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_82_Tfh1


title: ELP_R7pB7p7p_W2_rep2

description:
W2_P22_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W4_rep2

description:
W4_P21_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W3_rep5

description:
W3_P21_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W3_rep4

description:
W3_P21_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W3_rep2

description:
W3_P21_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W3_rep3

description:
W3_P21_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_80_Tfh2


title: ELP_R7pB7p7n_W5_rep4

description:
W5_P21_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_80_Tfh1


title: CONTROL 26163 c M


title: ELP_R7pB7p7n_W3_rep1

description:
W3_P21_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W2_rep5

description:
W2_P21_5
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W2_rep4

description:
W2_P21_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W2_rep3

description:
W2_P21_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: don_59_Tfh17


title: don_59_Tfh2


title: ELP_R7pB7p7n_W2_rep2

description:
W2_P21_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7pB7p7n_W4_rep4

description:
W4_P21_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_59_Tfh1


title: ELP_R7n7p_W5_rep5

description:
W5_P19_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W5_rep4

description:
W5_P19_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W5_rep2

description:
W5_P19_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_58_Tfh17


title: ELP_R7pB7p7n_W4_rep1

description:
W4_P21_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HD-MS275-48h-3


title: ELP_R7n7p_W5_rep3

description:
W5_P19_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W5_rep1

description:
W5_P19_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_80_Tfh17


title: ELP_R7n7p_W4_rep5

description:
W4_P19_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W4_rep3

description:
W4_P19_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_58_Tfh1


title: ELP_R7n7p_W4_rep2

description:
W4_P19_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W4_rep1

description:
W4_P19_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W4_rep4

description:
W4_P19_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: don_101_Tfh2


title: don_101_Tfh17


title: ELP_R7n7p_W3_rep5

description:
W3_P19_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W3_rep4

description:
W3_P19_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W3_rep3

description:
W3_P19_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W3_rep2

description:
W3_P19_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.WT1+KTS.V5.4

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to hg19 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.
Assembly: hg19
Supplementary files format and content: bigWig files

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads (Beckman Coulter) after crosslink reversal, RNase A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: expression

tag: chip antibody


title: don_101_Tfh1


title: ELP_R7pB7p7n_W2_rep1

description:
W2_P21_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W3_rep1

description:
W3_P19_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W2_rep5

description:
W2_P19_5
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W2_rep2

description:
W2_P19_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7p_W2_rep3

description:
W2_P19_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.WT1-KTS.V5.4


title: ELP_R7n7p_W2_rep1

description:
W2_P19_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.WT1+KTS.V5.3


title: don_58_Tfh2


title: ELP_R7n7p_W2_rep4

description:
W2_P19_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.WT1-KTS.V5.3


title: ELP_R7n7n_W5_rep5

description:
W5_P18_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.WT1+KTS.H3K27ac.4


title: ELP_R7n7n_W5_rep4

description:
W5_P18_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W4_rep5

description:
W4_P18_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.WT1+KTS.H3K27ac.3


title: ELP_R7n7n_W5_rep3

description:
W5_P18_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W5_rep1

description:
W5_P18_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W5_rep2

description:
W5_P18_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.WT1-KTS.H3K27ac.4


title: ELP_R7n7n_W4_rep3

description:
W4_P18_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W4_rep4

description:
W4_P18_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W4_rep2

description:
W4_P18_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W4_rep1

description:
W4_P18_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W3_rep5

description:
W3_P18_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWS.YS37.WT1+KTS.YS37.V5.6


title: MeT-5A.WT1-KTS.H3K27ac.3


title: ELP_R7n7n_W3_rep4

description:
W3_P18_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W3_rep3

description:
W3_P18_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWS.YS37.WT1+KTS.YS37.V5.5


title: ELP_R7n7n_W3_rep2

description:
W3_P18_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W3_rep1

description:
W3_P18_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W2_rep5

description:
W2_P18_5
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W2_rep4

description:
W2_P18_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ELP_R7n7n_W2_rep3

description:
W2_P18_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWS.YS37.WT1+KTS.YS37.H3K27ac.5


title: ELP_R7n7n_W2_rep2

description:
W2_P18_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: wing_w1118_H3K4me2_rep1_(210707_JA_Dm_JA352)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Whole-mount CUT&Tag profiling H3K4me2 in w1118 wing discs

data_processing:
Genome_build: dm6
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to the UCSC repeat-masked dm6 Drosophila melanogaster reference sequence. 2. We extracted properly paired reads from the alignments. 3.We used bedtools 2.30.0 genomecov to make a normalized count dm6 track which is the fraction of counts at each base pair scaled by the size of the dm6 reference sequence (137567484) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .dm6.bw)

organism: Drosophila melanogaster

source_name: CUT&Tag

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v3
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: whole wing disc, permeabilized with 0.1% Triton

value: H3K4me2 Epicypher 13-0027


title: MeT-5A.EWS.YS37.WT1-KTS.V5.6


title: ELP_R7n7n_W2_rep1

description:
W2_P18_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWS.YS37.WT1-KTS.V5.5


title: LMDP_117lo_W5_rep3

description:
W5_P11_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W5_rep5

description:
W5_P11_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W5_rep4

description:
W5_P11_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W5_rep2

description:
W5_P11_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: testis_w1118_H3K4me2_rep3_(210318_JA_Dm_JA252)

description: Whole-mount CUT&Tag profiling H3K4me2 in w1118 testis

value: whole testis, permeabilized with 0.1% Triton


title: MeT-5A.EWS.YS37.WT1-KTS.H3K27ac.6


title: MeT-5A.EWS.YS37.WT1-KTS.H3K27ac.5


title: testis_w1118_H3K4me2_rep2_(210318_JA_Dm_JA251)


title: testis_w1118_H3K4me2_rep1_(210318_JA_Dm_JA247)


title: LMDP_117lo_W5_rep1

description:
W5_P11_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W4_rep5

description:
W4_P11_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: testis_bam_H3K4me2_rep3_(210318_JA_Dm_JA257)

description: Whole-mount CUT&Tag profiling H3K4me2 in bam testis


title: testis_bam_H3K4me2_rep2_(210318_JA_Dm_JA256)


title: MeT-5A.EWS.YS37.WT1+KTS.YS37.H3K27ac.6


title: MeT-5A.EWSWT1+KTS.V5.2


title: LMDP_117lo_W4_rep4

description:
W4_P11_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W4_rep3

description:
W4_P11_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWSWT1-KTS.V5.2


title: testis_bam_H3K4me2_rep1_(210223_JA_Dm_JA237)


title: testis_aly_H3K4me2_rep3_(210318_JA_Dm_JA270)

description: Whole-mount CUT&Tag profiling H3K4me2 in aly testis


title: MeT-5A.EWSWT1+KTS.V5.1


title: MeT-5A.EWSWT1-KTS.V5.1


title: LMDP_117lo_W4_rep2

description:
W4_P11_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: testis_aly_H3K4me2_rep2_(210318_JA_Dm_JA269)


title: LMDP_117lo_W4_rep1

description:
W4_P11_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWSWT1+KTS-KTS.V5.2


title: LMDP_117lo_W3_rep5

description:
W3_P11_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: testis_aly_H3K4me2_rep1_(210318_JA_Dm_JA265)


title: LMDP_117lo_W3_rep4

description:
W3_P11_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWSWT1+KTS-KTS.V5.1


title: MS_Veh_13-0148_rep1

city: durham

first: Yiping

last: He

state: NC

address: 199A MSRB1, Research Drive

department: Pathology

institute: Duke University

description: treated with DMSO for 15days

data_processing:
fastq raw data were trimmed by Tim Galore!
aligned to hg38 by Hisat2
reassembled by Stringtie
defferentially expressed genes analyzed by Deseq2

source_name: human primay GBM cell line

extract_protocol:
E.Z.N,A, Total RNA Kit (OMEGA R6834-02)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: treated with DMSO for 15days


title: PC-3_CyclosporinA_2

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

description: CyclosporinA treatment effect on gene expression profile in PC-3 cells

hyb_protocol: Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Following fragmentation, 5.5 μg of fragmented cDNA were hybridized for about 17 h at 45 °C on Human Gene 1.0 ST arrays.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip  Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).  Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

data_processing: Raw data were normalized using the Single Channel Array Normalization (Piccolo et al. 2012, PMID: 22959562) method, which is implemented as a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). As part of the normalization process, a custom chip-definition file (CDF ver. 22) from the BrainArray (http://brainarray.mbni.med.umich.edu/brainarray/) resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated probes.

source_name: Prostate cancer cell line PC-3, CsA treated

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA(GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol performed  using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).

growth_protocol: The cells were maintained under DMEM medium containing 10% FBS.

extract_protocol: Total RNA was extracted from the cells and processed according to the manufacturer’s guideline (Affymetrix). The extracted RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington,  USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA). All samples showed high RNA. Integrity Number values >9.0 and 28S/18S ratios >1.5. RNA extract with A260/A280 and A260 absorbance ratio ranging from 1.8 to 2.1 was used for cDNA synthesis.

treatment_protocol: CyclosporinA was dissolved in ethanol

value: androgen-independent prostate carcinoma cell line

value: CyclosporinA


title: ANA06 C1D14

city: Toronto

first: YU XUAN

last: LUO

state: ON

address: 2075 Bayview Avenue

department: Biological sciences

country: Canada

institute: Sunnybrook research institute

data_processing:
Ion Torrent sequencing was performed for 500 flows on an Ion S5XL Sequencer with Ion 550 Chips.
Ion Torrent platform-specific pipeline software (Torrent Suite version 5.16.0; ThermoFisher Scientific) was used to remove polyclonal, low quality and adapter dimer reads and then separate barcoded reads for each sample.
Ion Torrent platform-specific ampliSeqRNA plug-in (v5.16.0) was used to analyze the sequencing reads.
Reads were aligned to the human transcriptome reference and target regions flle (hg19_AmpliSeq_Transcriptome_21K_v1) With TMAP mapper in Torrent Suite version 5.16.0.
hg19 Human genome reference
Assembly: text files.  Raw read count and normalized reads count (RPM, reads per million).
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes RPM values for each sample

source_name: blood

growth_protocol: Leukemia cells were purified from the blood and RNA was made immediately and frozen until used for RNAseq.

extract_protocol:
RNA was prepared using the RNeasy mini kit (Qiagen, Valencia, CA, USA), and cDNA was synthesized from 2 μg of RNA using Superscript II reverse transcriptase (Invitrogen), according to the instructions of the manufacturer.
Complementary DNA (cDNA) libraries were constructed from the total RNA using the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.
Targeted RNA sequencing

treatment_protocol: CLL cells were isolated from blood by negative selection with the Rosette Sep Human B cell enrichment cocktail (StemCell Technologies, Vancouver BC, Canada) and density centrifugation. This method yields percentages of CD19+ and CD19+/CD5+ cells of >98 and >96%, respectively. Aliquots were cryopreserved until used for RNAseq.

value: blood

value: CLL- B lymphocytes

value: 2 weeks on Anakinra


title: MeT-5A.EWSWT1+KTS-KTS.HA.1

source_name: HA

value: HA


title: LMDP_117lo_W3_rep3

description:
W3_P11_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

value: no


title: PC-3_CyclosporinA_3


title: PC-3_Vehicle_3

description: Vehicle effect on gene expression profile in PC-3 cells

source_name: Prostate cancer cell line PC-3, vehicle control

value: ethanol vehicle


title: PC-3_Vehicle_2


title: ANA06 C1D1

value: Before Anakinra


title: ANA05 C1D14


title: MS_Veh_13-0102_rep2

description: treated with DMSO for 15days


title: LMDP_117lo_W3_rep2

description:
W3_P11_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: PC-3_CyclosporinA_1


title: MS_Veh_13-0102_rep1

description: treated with DMSO for 15days


title: ANA05 C1D1


title: LMDP_117lo_W3_rep1

description:
W3_P11_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWSWT1+KTS-KTS.H3K27ac.2

value: untreated


title: MeT-5A.EWSWT1+KTS-KTS.H3k27ac.1


title: MS_Cle_13-0148_rep2

description:
treated with 4uM clemastine (Cayman #14637)for 15days
Galaxy902 13-0148 master file_V37


title: ANA04 C1D14


title: MS_Veh_13-0148_rep2

description: treated with DMSO for 15days


title: LMDP_117lo_W2_rep5

description:
W2_P10_5
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWSWT1+KTS-KTS.HA.2


title: MS_Cle_13-0148_rep1

value: treated with 4uM clemastine (Cayman #14637)for 15days


title: ANA04 C1D1


title: MeT-5A.EWSWT1-KTS.HA.2


title: LMDP_117lo_W2_rep4

description:
W2_P10_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: ANA03 C1D14


title: MS_Cle_13-0102_rep2

description:
treated with 4uM clemastine (Cayman #14637)for 15days
Galaxy900 13-0102 master file_V37


title: MS_Cle_13-0102_rep1


title: ANA03 C1D1


title: LMDP_117lo_W2_rep1

description:
W2_P10_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117lo_W2_rep2

description:
W2_P10_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: PC-3_Vehicle_1


title: MeT-5A.EWSWT1+KTS.H3K27ac.2


title: MeT-5A.EWSWT1-KTS.HA.1


title: MeT-5A.EWSWT1+KTS.HA.1


title: LMDP_117int_W5_rep5

description:
W5_P10_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWSWT1-KTS.H3K27ac.2


title: L35148, GCA

city: Phoenix

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

library_source: transcriptomic single cell

data_processing:
CellRanger Count v5.0.2 (10x Genomics) was used to align reads to the GRCh38 (Ensembl 98) reference genome.
Assembly: GRCh38 (Ensembl 98)
Supplementary files format and content: Tab-separated values file containing cell barcodes
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Appendiceal_Epithelial_infercnv_HMMi3.rds - Seurat object containing infercnv results in metadata for epithelial cell lineage
Supplementary files format and content: Appendiceal_integratedrpca_alllineages_final.rds - Seurat object integrated with rPCA, contains all cell lineages with annotations

source_name: Peritoneal metastasis

extract_protocol:
Minced tissue (1-3 mm) was digested with 3 -5 ml RMPI medium containing 0.05mg/ml TM Liberase (Sigma Aldrich, 5401119001) and 0.02 mg/ml DNAaseI (ThermoFisher, EN0521) at 37 ° C for 30 mins with rotation at 150 rpm. Cells were filtered through a 70 µM and 37 µM cell strainer to isolate single cells. The cell suspension was centrifuged at 500xg for 10 mins and resuspended with 5 ml ACK lysis buffer (K.D Medical, RGF3015) at room temperature for 3 mins to remove red blood cells. Microbeads (Miltenyi Biotec, 130-090-101) were used for dead cell removal. Cell viability and number were detected using a TC Automated Cell Counter (Bio-Rad Laboratories), and samples with at least 70% cell viability were processed
Cells were captured on a Chromium controller (10xGenomics) using a single cell 3’ Reagent kit V3.1 (10X Genomics, PN-1000121) targeting ~5000-10000 cell/sample

value: Peritoneal metastasis

tag: pathology reviewed

value: Goblet-cell adenocarcinoma

tag: pathology abbreviated

value: GCA

tag: pathology

value: High grade Adenocarcinoma

tag: pathology 2

value: Moderate-High grade appendiceal adenocarcinoma

tag: pathology 3

value: The immunohistochemical staining features are consistent with adenocarcinoma from gastrointestinal tract primary.  Positive staining for synaptophysin and chromogranin raises the possibility of goblet cell adenocarcinoma from appendiceal primary.

tag: Sex

value: Male

tag: age

tag: ethnicity

value: Non-HISPANIC WHITE

tag: clinical diagnosis

value: High grade

tag: status

value: Cancerous

tag: gemextra

value: TP53(M237I); TMB-Low(3mut/Mb); MSS

tag: vus

value: ATR (P1110L) AURKB (V103M) FGF10 (amplification) MET (amplification) MLL2 (Q3764H) PIK3C2G (amplification) PTPRO (amplification) RICTOR (amplification) SDHA (amplification) SMAD4 (R361G)


title: MeT-5A.EWSWT1+KTS.H3K27ac.1

tag: cell line

tag: treatment


title: ANA01 C1D14

tag: tissue

value: blood

tag: cell type

value: CLL- B lymphocytes

value: 2 weeks on Anakinra


title: L35151, LAMN

value: Low-grade appendiceal mucinous neoplasm

value: LAMN

value: Low grade Mucinous Neoplasm

value: Resected tissue is extensively involved by a neoplasm producing abundant mucin.  The mucinous lining is relatively frequent (being present in almost every 2 x low power field) and shows morphological features ranging from bland columnar nuclei with abundant mucin to rounded high-grade nuclei associated with mitotic activity and architectural complexity.  Although most of the tumor colonizes superficial peritoneum, invasion is present and best appreciated in sections from the uterus (block E4), stomach (block J2), colon (block B2) and ovary (block E8).   Per WHO criteria, the mucinous neoplasm involving the peritoneum corresponds to an overall grade 2.

value: Female

value: Low grade

value: GNAS(R201H); KRAS(G13D); U2AF1(S34F); TMB-Low(<1mut/Mb); MSS

value: ADCY8 (R475C) Missense 7 CT47B1 Deletion . ESCO2 (T254fs) Frameshift 5 SPATA31A3 Deletion . SPATA31A6 Deletion . UGT1A8 Deletion .


title: LMDP_117int_W5_rep4

description:
W5_P10_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

tag: time

value: no


title: MeT-5A.EWSWT1+KTS.HA.2

value: untreated

tag: expression

tag: chip antibody

value: HA


title: L35144, LAMN

value: Peritoneal metastasis

tag: pathology reviewed

tag: pathology abbreviated

tag: pathology

value: There are rare foci of glandular epithelium showing more complex architecture and mitoses, raising the possibility of progression.

value: Male

value: Non-HISPANIC WHITE

value: Cancerous

value: ARID2(R1677*); GNAS(R844H); U2AF1(S34F); TMB-LOW(<1mut/Mb); MSS-Stable

value: ADAMTS14 (F140S) Missense 6 ATP10A (L269P) Missense 5 CIT (D1070N) Missense 7 DSG1 (A195T) Missense 6 FNBP1 (R389H) Missense 6 GLI1 (R265W) Missense 6 LOXL2 (R98Q) Missense 5 TPH1 (R230C) Missense 6


title: MeT-5A.EWSWT1-KTS.H3K27ac.1


title: LMDP_117int_W5_rep3

description:
W5_P10_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EV.INPUT

source_name: INPUT

value: EV


title: LMDP_117lo_W2_rep3

description:
W2_P10_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: L49296, LGMA

value: Low-grade mucinous adenocarcinoma

value: LGMA

value: Low grade Adenocarcinoma

tag: pathology 2

value: Low grade appendiceal adenocarcinoma

tag: pathology 3

value: Metastatic well-differentiated mucinous adenocarcinoma of the appendix.

tag: Sex

value: BLACK or AFRICAN-AMERICAN

value: Low-grade Adenocarcinoma

value: GNAS(R201C); KRAS (G12D)

value: AC002398.9 (W36*) Stop Gain 7 NHS (P1452S) Missense 6 PSENEN (W36*) Stop Gain 7 TIAM1 (P940L) Missense 5 USP40 (Q1160fs) Frameshift 5


title: LMDP_117int_W5_rep2

description:
W5_P10_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

value: no


title: L35150, GCA

value: Peritoneal metastasis

value: Goblet-cell adenocarcinoma

value: GCA

value: High grade Adenocarcinoma

value: Moderate-High grade appendiceal adenocarcinoma

value: The positive specimens show pools of mucin and floating clusters of tumor cells with poorly differentiated signet ring cell/goblet cell morphology.

value: Female

tag: age

tag: ethnicity

tag: clinical diagnosis

value: High grade

value: FGFR2(Amplification); MYC(Amplification); TP53(V272L); KMT2C(G2464*); TMB-Low(1mut/Mb); MSS

value: ABCA3 (A1107T) Missense 6 AFF3 (A1134G) Missense 6 ANGPTL3 Deletion . ARID1B (R496K) Missense 10 ATF4 (I141V) Missense 8 BCAR3 (E772K) Missense 11 BEND4 (A126S) Missense 11 BMPR1B (F387C) Missense 10 C1orf43 Amplification . C1orf68 Amplification . CACNA1H (V869I) Missense 8 CBLN2 Amplification . CCDC74A (R149C) Missense 7 CCL21 (M87I) Missense 5 CHTOP Amplification . COG5 (E840Q) Missense 9 CRCT1 Amplification . CREB3L4 Amplification . CRNN Amplification . CRTC2 Amplification . DENND4B Amplification . DUSP8 Amplification . DUSP8 Breakpoint:Duplication . EXD1 (R112H) Missense 10 FAT3 (R4181H) Missense 10 FBXO46 (R470Q) Missense 7 GATAD2B Amplification . HAX1 Amplification . HIRIP3 (R526W) Missense 5 ILF2 Amplification . INTS3 Amplification . ITGB6 (K165I) Missense 7 IVL Amplification . JTB Amplification . KPRP Amplification . KRT28 (R311H) Missense 14 KRTAP5- 1 Amplification . KRTAP5- 2 Amplification . KRTAP5- 3 Amplification . KRTAP5- 4 Amplification . KRTAP5- 5 Amplification . LAMA1 (R162H) Missense 5 LCE1A Amplification . LCE1B Amplification . LCE1C Amplification . LCE1D Amplification . LCE1F Amplification . LCE2A Amplification . LCE2B Amplification . LCE2C Amplification . LCE3D Amplification . LCE3E Amplification . LCE5A Amplification . LCE6A Amplification . LOR Amplification . MEST (L144F) Missense 9 MKRN3 (S133L) Missense 8 MRPL23 Amplification . MRPL23/RP11- 723G8.2 Fused Genes (RNA) . MSTN (R88W) Missense 8 NHS (R373*) Stop Gain 8 NME8 (L581V) Missense 10 NOD2 (W157*) Stop Gain 10 NPR1 Amplification . NSMCE4A Amplification . NUP210L Amplification . OR10S1 (P331S) Missense 6 P2RY13 (V115A) Missense 10 PAX9 (A340V) Missense 7 PCDHGA5 (D557N) Missense 6 PGLYRP3 Amplification . PGLYRP4 Amplification . PLP1 (V267I) Missense 8 POU5F1B Amplification . PTPRJ (L176F) Missense 9 RAB13 Amplification . RBMXL3 (R434H) Missense 10 S100A1 Amplification . S100A13 Amplification . S100A14 Amplification . S100A16 Amplification . S100A2 Amplification . S100A3 Amplification . S100A4 Amplification . S100A5 Amplification . S100A7 Amplification . S100A7A Amplification . S100A8 Amplification . SACS (D829G) Missense 12 SDF4 (R98W) Missense 9 SLC27A3 Amplification . SLC30A3 (P216L) Missense 10 SLC39A1 Amplification . SLC7A10 (A126T) Missense 5 SLC9A6 (E671K) Missense 5 SLX4 (A267V) Missense 9 SMAD7 Amplification . SMAD7/CBLN2 Fused Genes (RNA) . SMCP Amplification . SNAPIN Amplification . SPRR1A Amplification . SPRR1B Amplification . SPRR2A Amplification . SPRR2B Amplification . SPRR2D Amplification . SPRR2E Amplification . SPRR2F Amplification . SPRR2G Amplification . SPRR3 Amplification . SPRR4 Amplification . SRRM4 (R382W) Missense 9 SV2C (G416R) Missense 10 SYNE1 (A4368S) Missense 5 TACC2 (L422R) Missense 5 TCERG1 (I983fs) Frameshift 13 TPM3 Amplification . TSHZ3 (R381W) Missense 5 TTC29 (N473K) Missense 11 TUBGCP4 (T660I) Missense 9 TYR (R278Q) Missense 6 UBAP2L Amplification . WDR47 (N354D) Missense 10 ZNF436 (D41V) Missense 9


title: ANA02 C1D1

value: blood

value: CLL- B lymphocytes

value: Before Anakinra


title: ANA02 C1D14

value: 2 weeks on Anakinra


title: LMDP_117int_W5_rep1

description:
W5_P10_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Pt.3 Con

data_processing:
Ion Torrent sequencing was performed for 500 flows on an Ion S5XL Sequencer with Ion 540 Chips.
Ion Torrent platform-specific pipeline software (Torrent Suite version 5.12.1; ThermoFisher Scientific) was used to remove polyclonal, low quality and adapter dimer reads and then separate barcoded reads for each sample.
Ion Torrent platform-specific ampliSeqRNA plug-in (v5.12.0.1) was used to analyze the sequencing reads.
Reads were aligned to the human transcriptome reference and target regions flle (hg19_AmpliSeq_Transcriptome_21K_v1) With TMAP mapper in Torrent Suite version 5.12.1.
hg19 Human genome reference
Assembly: text files.  Raw read count and normalized reads count (RPM, reads per million).
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes RPM values for each sample

extract_protocol:
RNA was prepared using the RNeasy mini kit (Qiagen, Valencia, CA, USA), and cDNA was synthesized from 2 μg of RNA using Superscript II reverse transcriptase (Invitrogen), according to the instructions of the manufacturer.
Complementary DNA (cDNA) libraries were constructed from the total RNA using the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.

value: CLL-B lymphocytes

value: Control


title: Pt.2 K

value: 300 microg/ml of anakinra for 48h


title: MeT-5A.control.V5.6

value: untreated

value: control


title: L35147, LGMA

value: Peritoneal metastasis

value: Low-grade mucinous adenocarcinoma

value: LGMA

value: Low grade Adenocarcinoma

value: Low grade appendiceal adenocarcinoma

value: Although the vast majority of the tumor mass is composed of mucin devoid of epithelial elements, islands of carcinoma with high-grade nuclear features as well as architectural complexity are multifocally seen, granting a diagnosis of adenocarcinoma..  The greatest amount of tumor is seen within blocks O1 and P1.  Architectural complexity is appreciated in the B1.  This addendum is issued to specify that the morphological features of the peritoneal metastases are those of a grade 2 mucinous adenocarcinoma (in light of the focal presence of high-grade cytological features and architectural complexity).  The findings are concordant with the primary tumor (S20-07602), which was diagnosed as a well-differentiated (low grade) mucinous adenocarcinoma of the appendix

value: Non-HISPANIC WHITE

value: Low grade

tag: status

value: Cancerous

tag: gemextra

value: KRAS (G12V); TMB-Low(1mut/Mb); MSS

tag: vus

value: ADH1B (T374M) Missense 6 ADNP2 (V907I) Missense 17 AJAP1 (T376M) Missense 7 ALPP (A261V) Missense 8 ANGPTL3 Deletion . APBA2 (A207T) Missense 8 APOB (A4473T) Missense 7 BAI1 (R231C) Missense 9 BRCA2 (S3366fs) Frameshift 31 CNGA2 (Q626K) Missense 6 CNKSR1 (R556W) Missense 8 COL3A1/IGKC Fused Genes (RNA) . CTGF (E311K) Missense 5 DCBLD2 (V712M) Missense 6 DDAH2 (P73L) Missense 9 DDC8 (R212W) Missense 7 DST (R2291C) Missense 7 FOXJ1 (S9L) Missense 6 GRIA1 (R509Q) Missense 9 HNRNPH2 (T328fs) Frameshift 6 HSPA12B (V435M) Missense 6 KIAA0100 (R2092C) Missense 7 KIAA1549 (V553M) Missense 7 LRRC59 (L132W) Missense 7 MAOB (S2I) Missense 5 MTOR (R2505Q) Missense 8 NT5C1B (D378G) Missense 7 NT5C1B- RDH14 (D378G) Missense 7 NTM (N148T) Missense 9 OR13D1 (R86C) Missense 7 PTGIR (R229C) Missense 10 RNGTT (R574*) Stop Gain 8 SEZ6L (R861H) Missense 10 SHROOM4 (R722H) Missense 7 SMAD2 (S464*) Stop Gain 16 SMAD3 (S355*) Stop Gain 16 SOCS3 (V120L) Missense 8 UGDH (c.1037+1delG) Splice Donor Variant 8 ZFR2 (S178L) Missense 9 ZNF341 (P172R) Missense 8 ZNF583 (H342Q) Missense 7 MYT1L (E163del) Inframe Deletion 7


title: LMDP_117int_W4_rep5

description:
W4_P10_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

tag: treatment

value: no


title: L35146, LGMA

tag: tissue

value: Viable strips of carcinoma are relatively frequently seen and associated with extensive mucin. There is focal architectural complexity associated with mitotic and apoptotic activity.

value: Male

value: CDKN1B(Deletion); GNAS(R201C); KRAS(G12D); TMB-Low(1mut/Mb); MSS-Stable

value: ARHGEF28 (P353L) Missense 5 BRDT (Q272H) Missense 5 BSN (R2595C) Missense 5 C1orf170 (G145C) Missense 5 C2orf91 (C18*) Stop Gain 6 C4B (R1072W) Missense 11 COL7A1 (A1313T) Missense 7 CSMD2 (R1555Q) Missense 5 CYP11A1 (S195L) Missense 6 DCBLD1 (S275L) Missense 7 DLGAP2 (P109L) Missense 7 EREG (R102*) Stop Gain 6 FGF10 (V123I) Missense 5 FRAS1 (Q2242H) Missense 5 GLB1L (G306E) Missense 5 GNB1L (A271T) Missense 5 GPC6 (G425W) Missense 6 GPR12 (A199V) Missense 6 GRM7 (T675M) Missense 5 HIST1H1C Deletion . HIST1H1E Deletion . HIST1H2AB Deletion . HIST1H2AI Deletion . HIST1H2AK Deletion . HIST1H2BB Deletion . HIST1H2BC Deletion . HIST1H2BD Deletion . HIST1H3D Deletion . HIST1H4E Deletion . HIST1H4H Deletion . HIST2H2AC Deletion . HIST2H2BE Deletion . JMY (R388*) Stop Gain 5 KCNQ3 (D556N) Missense 7 LRP1B (C1103Y) Missense 6 MXRA5 (T2697M) Missense 12 NDUFV2 (V134A) Missense 12 NOX5 (T707M) Missense 5 NYAP1 (T382M) Missense 9 OR10A6 (F211L) Missense 5 PCDHA9 (S601L) Missense 6 RBMXL3 (R379Q) Missense 11 SLC5A3 (Q442H) Missense 6 SRFBP1 (E306K) Missense 5 STAT6 (c.1001+1G>A) Splice Donor Variant 8 TAOK2 (A530V) Missense 5 TNN (R214H) Missense 11 TNN (V953M) Missense 9 TTN (I33593T) Missense 6 TXLNB (R237H) Missense 7 WDR36 (V836L) Missense 6 ZSCAN1 (R374H) Missense 6


title: LMDP_117int_W4_rep4

description:
W4_P10_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

tag: cell type

tag: time


title: MeT-5A.control.V5.4

tag: cell line

value: untreated

tag: expression

value: control

tag: chip antibody


title: LMDP_117int_W4_rep3

description:
W4_P10_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Pt.1 K

value: blood

value: CLL-B lymphocytes

value: 300 microg/ml of anakinra for 48h


title: ANA01 C1D1

value: CLL- B lymphocytes

value: Before Anakinra


title: L49295, MHNA

value: Peritoneal metastasis

tag: pathology reviewed

tag: pathology abbreviated

value: MHNA

tag: pathology

value: High grade Adenocarcinoma

value: Poorly-differentiated adenocarcinoma involving fibroconnective soft tissues

value: Female

value: Non-HISPANIC WHITE

value: TMB-Low(1mut/Mb); MSS

value: ADARB2 (R73H) Missense 10 ATP6V0D1 (N10K) Missense 9 BLVRA (L185F) Missense 10 CAMKK2 (R217W) Missense 7 CILP (R431C) Missense 8 COL16A1 (E1446K) Missense 9 DAAM2 (Q756H) Missense 7 DLG5 (P1918L) Missense 8 DNAH3 (N3022S) Missense 8 EMID1 (P330L) Missense 9 FAM173A (V68fs) Frameshift 9 FAN1 (R658Q) Missense 9 GABRA5 (M182I) Missense 9 HCLS1 (H473Y) Missense 8 IKBKAP (A1191V) Missense 9 KMT2B (R1140H) Missense 8 KRT33A (R75H) Missense 8 LRP1 (N2350S) Missense 11 MSN (R100H) Missense 7 MYO16 (A1317T) Missense 9 NBEAL1 (T624fs) Frameshift 7 NCR1 (A21T) Missense 9 NLRP10 (Y388*) Stop Gain 8 NLRP9 (L135F) Missense 9 OR2J3 (P141S) Missense 6 OR52E4 (R264H) Missense 9 PCNXL2 Breakpoint:Inversion . PEG3 (H1142Q) Missense 7 POLA1 (L742V) Missense 7 PPARD (Q408R) Missense 6 PROC (E98*) Stop Gain 10 SETD1B (E1061del) Inframe Deletion 8 SI (C63Y) Missense 8 SLC41A3 (A196P) Missense 5 TMEM247 (F198L) Missense 9 USH1G (R366C) Missense 10 WFS1 (A602V) Missense 8 ZFYVE26 (L1661del) Inframe Deletion 7


title: L42572, MHNA

value: Metastatic adenocarcinoma, moderately to poorly differentiated

tag: pathology 2

value: Moderate-High grade appendiceal adenocarcinoma

tag: Sex

value: HISPANIC WHITE

value: Cancerous

value: APC(R876*); FBXW7 (R278*); KRAS(G12D); PIK3CA (E545K); LOW (1mut/ Mb); MSS

value: ADAM8 (G65E) Missense 12 AKAP6 (E1835D) Missense 14 ARAP1 (R407W) Missense 14 ARMCX5 (S184F) Missense 14 ASB5 (D193Y) Missense 11 ATF7IP (R363*) Stop Gain 7 ATP11C Breakpoint:Duplication . BRWD3 (Q1134R) Missense 13 C2CD3 (L1594F) Missense 13 CBFA2T2 (P86L) Missense 14 COL5A2 (G309D) Missense 11 COL6A5 (R190W) Missense 14 CRY1 (R109*) Stop Gain 11 CTHRC1 (R146W) Missense 19 EMP1 (R123H) Missense 10 FAM19A1 (R57H) Missense 11 FXR1 (T611N) Missense 13 GAD2 (G60R) Missense 14 GCN1L1 (F2254L) Missense 13 GPR158 (S698I) Missense 12 GREB1 (V1233M) Missense 15 HECTD1 (D1185G) Missense 12 IRX5 (R269fs) Frameshift 11 KIF16B (R1015fs) Frameshift 9 LAMA5 (R2645C) Missense 11 LPAR4 (K38M) Missense 17 MAPK13 (K55E) Missense 8 MLK4 (A141T) Missense 35 MTMR8 (D687Y) Missense 16 NEDD1 (Y134*) Stop Gain 8 PCDHA3 (G430R) Missense 15 PGGT1B (G220V) Missense 16 PJA1 (R309fs) Frameshift 19 PKN3 (T130M) Missense 12 PMEPA1 (C24S) Missense 9 PRPF31 (A415P) Missense 14 RAI1 (E1380K) Missense 15 RAI1 (V692M) Missense 15 RGAG4 (A490T) Missense 13 SHC4 (F19Y) Missense 13 SHROOM4 (R593H) Missense 13 SLC25A44 (R249H) Missense 10 SLC6A15 (P682Q) Missense 15 SOGA2 (R976H) Missense 13 SPEG (R3196*) Stop Gain 9 SZT2 (P3231L) Missense 13 TBCD (Q723*) Stop Gain 13 TLN2 (S314P) Missense 12 TRANK1 (R2551K) Missense 12 TRPM4 (P1101L) Missense 12 TTC7A (A207T) Missense 10 TTN (K34569N) Missense 11 TTN (R24196H) Missense 14 WDR44 (E567K) Missense 11 WNT6 (R299C) Missense 12 ZNF684 (E352K) Missense 17 ZNF70 (E281K) Missense 13 ZNF732 (S156*) Stop Gain 14 ZNF737 (S410del) Inframe Deletion 12


title: MeT-5A.control.V5.3

value: untreated

value: control


title: MeT-5A.control.V5.2


title: Pt.1 Con

value: blood

value: CLL-B lymphocytes

value: Control


title: LMDP_117int_W4_rep2

description:
W4_P10_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

value: no


title: L49294, normal

source_name: Normal Appendix

value: Normal Appendix

value: Normal

tag: pathology 3

value: Benign Appendix

tag: age

tag: ethnicity


title: L35145, MHNA

value: Peritoneal metastasis

value: MHNA

value: Moderate Adenocarcinoma

value: Male

value: Non-HISPANIC WHITE

tag: clinical diagnosis

value: Moderate-high

tag: status

tag: gemextra

value: ABCF2 (R195C) Missense 41 ADD2 (D255N) Missense 24 ADH7 (A318S) Missense 22 AFF1 (H124R) Missense 5 AMER1 (E219*) Stop Gain 49 ANK3 (A713T) Missense 22 ANKRD11 (T150M) Missense 21 AP3B2 (V908M) Missense 35 APOH (T149M) Missense 22 ARC (E276K) Missense 17 ARHGAP30 (R393W) Missense 22 ASCL5 (R12Q) Missense 23 BNIPL (R309W) Missense 24 BOD1L1 (S683L) Missense 22 C17orf47 (R242S) Missense 24 C17orf74 (P145L) Missense 35 C2orf16 (R242Q) Missense 22 C2orf71 (P908T) Missense 21 C6orf163 (K102I) Missense 22 C9orf92 (G23A) Missense 29 CACNG3 (V76M) Missense 20 CAMP (I32T) Missense 22 CASD1 (A658T) Missense 34 CCDC148 (T144P) Missense 24 CDKL4 (L220I) Missense 21 CLVS2 (A73V) Missense 20 COL22A1 (G112R) Missense 15 CTSV (V228G) Missense 26 CUL1 (E439K) Missense 34 DAZL (A2V) Missense 21 DCAF13 (G580E) Missense 44 DCLK1 (R233C) Missense 20 DGKH (P683L) Missense 35 DMXL1 (L1948V) Missense 22 DRD2 (A420T) Missense 22 ELFN1 (T373M) Missense 20 EPPK1 (L2161*) Stop Gain 48 FAM35A (H513L) Missense 25 FBXL7 (P93L) Missense 31 FGF17 (R72H) Missense 24 FGF22 (R102C) Missense 26 FLG (H630Y) Missense 22 GABBR1 (R126Q) Missense 24 GNB2L1 (S115del) Inframe Deletion 9 H2AFY2 (E222K) Missense 14 HECW1 (R32*) Stop Gain 18 HPS3 (R530Q) Missense 21 IGDCC4 (A925V) Missense 30 KIF9 (E645V) Missense 22 KIRREL (H611L) Missense 21 KL (S742F) Missense 40 LATS2 (G200S) Missense 37 LHX6 (D375N) Missense 23 LRFN2 (G415R) Missense 23 LZTS3 (R10H) Missense 27 MAP1LC3A (E40K) Missense 25 MCF2 (Q888*) Stop Gain 43 MRPL10 (R123*) Stop Gain 23 NCKAP5 (T1564fs) Frameshift 23 NIN (K503fs) Frameshift 20 NPAP1 (R121H) Missense 34 NPFFR2 (L225F) Missense 22 NPY (G11R) Missense 17 OR2F2 (H89N) Missense 16 OTOP3 (A31V) Missense 25 OTUD5 (I398V) Missense 8 OTUD6A (C152R) Missense 47 PCCB (T234M) Missense 22 PCNXL3 (P728S) Missense 20 PIM3 (V316M) Missense 23 PMS1 (T926S) Missense 23 POLR3B (R340Q) Missense 22 PROM1 (P336S) Missense 23 ROBO1 (V1444M) Missense 25 RP11- 613M10.9 (Q42fs) Frameshift 18 RYR1 (D1027A) Missense 22 SHB (Q42fs) Frameshift 18 SLC25A4 (A90V) Missense 18 SPIC (N146fs) Frameshift 24 SUPT20H (R759Q) Missense 17 SYP (V205M) Missense 42 TADA1 (R69C) Missense 16 TGFB2 (N302fs) Frameshift 21 THAP11 (Q132dup) Inframe Insertion 12 TIMP3 (R107H) Missense 24 TMEM229A (S89C) Missense 21 TMSB4X (I10del) Inframe Deletion 37 TNRC6B (W858*) Stop Gain 25 TRPC4 (G110R) Missense 16 TTLL6 (P716A) Missense 24 TTN (R35174H) Missense 22 UAP1 (N284fs) Frameshift 20 WDR17 (L1042I) Missense 18 WNT4 (V97I) Missense 25 XYLT2 (R70Q) Missense 22 ZBBX (A427D) Missense 22 ZC3H3 (S593F) Missense 47 ZFP36L2 (A340fs) Frameshift 15 ZFP57 (G255S) Missense 23 ZFYVE20 (R538P) Missense 22 ZNF131 (N364S) Missense 20 ZNF578 (I476V) Missense 22ROBO1 (V1444M) Missense 25 RP11- 613M10.9 (Q42fs) Frameshift 18 RYR1 (D1027A) Missense 22 SHB (Q42fs) Frameshift 18 SLC25A4 (A90V) Missense 18 SPIC (N146fs) Frameshift 24 SUPT20H (R759Q) Missense 17 SYP (V205M) Missense 42 TADA1 (R69C) Missense 16 TGFB2 (N302fs) Frameshift 21 THAP11 (Q132dup) Inframe Insertion 12 TIMP3 (R107H) Missense 24 TMEM229A (S89C) Missense 21 TMSB4X (I10del) Inframe Deletion 37 TNRC6B (W858*) Stop Gain 25 TRPC4 (G110R) Missense 16 TTLL6 (P716A) Missense 24 TTN (R35174H) Missense 22 UAP1 (N284fs) Frameshift 20 WDR17 (L1042I) Missense 18 WNT4 (V97I) Missense 25 XYLT2 (R70Q) Missense 22 ZBBX (A427D) Missense 22 ZC3H3 (S593F) Missense 47 ZFP36L2 (A340fs) Frameshift 15 ZFP57 (G255S) Missense 23 ZFYVE20 (R538P) Missense 22 ZNF131 (N364S) Missense 20 ZNF578 (I476V) Missense 22