title: WT-DN1_BC_8

value: wild type

value: thymus


title: PFA9_hypox_p3.H3K27me3

status: Public on Jun 27 2022

type: SRA

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

library_source: genomic

data_processing:
ChIP-seq datasets were processed using the ChIP-seq module of GenPipes (v3.1.0 for isogenic cell lines, v3.1.2 for parental cell lines). Raw reads were trimmed using Trimmomatic (v0.32) to remove adaptor and sequencing-primer associated reads then aligned to hg19 using bwa-mem (v0.7.12) with default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard (v2.0.1) to produce uniquely aligned reads. Reads with a mapping quality of 5 or less were then filtered out. For single-end (SE) 50bp datasets, reads were extended by 250bp.
Wiggle tracks are generated using uniquely aligned reads using Homer (v4.9.1). ChIP-seq RPKM values over CGIs and genome-wide 100kb bins for scatterplots were calculated using VisRSeq (v0.9.40).
Rx- and RPKM-normalized BigWig tracks were produced using the “bamCoverage” functionality of deeptools (v3.5.1). Rx ratios were supplied via the ‘--scaleFactor’ option.  Reads flagged as duplicates, mapping to random, mitochondrial or sex chromosomes, as well as low-mappability regions according to ENCODE’s blacklist were discarded.
Assembly: hg19
Supplementary files format and content: bigwig files. Read coverage for each sample over the human genome

molecule: genomic DNA

organism: Homo sapiens

source_name: Posterior fossa

extract_protocol:
Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents. Ffor HTP kit, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adapter ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, at 20°C for 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. For HyperPrep kit, end-repair and A tailing were performed in one reaction: 15ul of ChIP sample was incubated with 45ul end repair+A-tailing mix at 20°C for 30 min, then 65°C for 30 min. Directly proceeded to adapter ligation by adding 5ul of IDT for Illumina Unique Dual Indexes (IDT) adapters and 45ul ligation buffer enzyme mix, incubating at 20°C for 15 min, followed by Ampure XP bead purification. Library enrichment: 10 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: material

value: cell line

tag: histone mark/factor

tag: perturbation

value: Parental


title: ChIPseq_WDR5A-HA_WT_rep1

city: Beijing

first: Yangyang

last: Fan

address: No.5 Yiheyuan Road Haidian District,

country: China

institute: Peking University

description: WDR5A-HA-ChIP from WT rep1

data_processing:
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using bowtie2 (version 2.3.3) with default parameters.
Peak calling was performed using MACS2 (version 2.2.5) with the following parameters: --keep-dup 1 --gsize 1.2e8 --qvalue 0.05.
The alignments were converted to bigWig files using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Supplementary_files_format_and_content: peak text files

organism: Arabidopsis thaliana

source_name: total seedlings

extract_protocol:
2 g of 9-day-old seedlings grown on MS medium were collected and cross-linked with 1% formaldehyde for 20 min under vacuum and then ground into a fine powder in liquid nitrogen. Chromatin was isolated and sheared into fragments (200–500 bp) by sonication. The sonicated chromatin was incubated with antibody-bound Sera-Mag SpeedBeads Protein A/G Magnetic Particles (17152104010150, GE Healthcare) overnight at 4℃. Precipitated DNA was then reverse-crosslinked and digested with RNase A and Proteinase K, after which it was purified with the ChIP DNA Clean & Concentrator kit (D5205, Zymo research) according to the manufacturer’s instructions.
All ChIP-seq libraries were generated with the NEBNext® Ultra II DNA Library Prep Kit for Illumina® (E7645S, NEB) according to the manufacturer’s instructions.

tag: tissue

value: total seedlings

tag: developmental stage

value: 9-day-old seedlings grown under continuous white light

tag: chip antibody

value: WDR5a-HA (anti-HA Magnetic Beads (88837, Thermo))

tag: genotype

value: Col-0 ecotype


title: H3K27me3 CUT&RUN mat del mESC line 2

city: Parkville

first: Natalia

last: Benetti

state: Victoria

address: 1G Royal Parade

country: Australia

institute: WEHI

description:
Maternal deletion with Zp3-Cre
benetti_CUT_RUN_H3K27me3.txt

data_processing:
Library strategy: CUT&RUN
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth library size using Seqmonk.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed read counts normalized by library size within bins created ±2.5kb centered on a list of MACS peaks determined using SeqMonk's MACS-like functionality for each genotype separately.  MACS peaks were called between H3K27me3 ChIP and input samples from Liu et al., 2016 (Nature . 2016 Sep 22;537(7621):558-562.  doi: 10.1038/nature19362.  Epub 2016 Sep 14.). Peak lists from biological replicates were merged before peak calculation.

organism: Mus musculus

source_name: mESC cultured in 2i+LIF medium

growth_protocol: mESCs derived, and cultured as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

extract_protocol:
Fresh cells were subject to CUT&RUN for H3K27me3. DNA was extracted with phenol/chloroform/isoamyl alcohol
NEBNext Ultra II DNA Library Prep Kit for Illumina
CUT&RUN was performed as described in Skene and Henikoff eLife 2017;6:e21856 DOI: 10.7554/eLife.21856 DNA was purified by phenol/chloroform/isoamylalcohol extraction followed by glycogen/ethanol precipitation
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: development stage

value: Pluripotent state

value: Smchd1[del/+] (maternally deleted)

tag: strain

value: C57BL/6/Cast F1

tag: Sex

value: M

tag: cell type

value: mESC


title: WT-DN1_BC_89

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

description:
PolyA RNA
processed data file: barcode_information.xlsx
processed data file: count_matrix.csv
processed data file: expression_matrix_log2(TPM:10+1).csv

library_source: transcriptomic

data_processing:
Unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails.
Next, we removed reads with adapter contaminants and low-quality bases (N>10%).
The cleaned reads were aligned to the mm10 mouse transcriptome (Genocode) using Tophat (version 2.1.1).
Uniquely mapped reads were counted using htseq-count of the HTSeq package. For each gene, duplicated transcripts with the same UMI sequence were removed. For each cell, the transcript copy number of each gene were counted on the basis of the number of distinct UMIs of that gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcode_information.xlsx
Supplementary_files_format_and_content: count_matrix.csv
Supplementary_files_format_and_content: expression_matrix_log2(TPM:10+1).csv

molecule: total RNA

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)

extract_protocol:
Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell RNA-seq. Libraries were prepared using KAPA Hyper Prep Kits (KK8505). The NEB U-shaped adapter was used for ligation. The libraries were sequenced on an Illumina Hiseq x ten platform to generate 150-bp paired-end reads (sequenced by BGI).
Libraries are constructed according to the standard protocol for Smart-seq2.

tag: strain/background

tag: genotype/variation

tag: age

value: 6~8 wks


title: H3K27me3 CUT&RUN mat del mESC line 1


title: ChIPseq_IgG_e2f_rep3

description: IgG-ChIP (negative control) from e2f triple mutant rep3

value: IgG (PP64, Millipore)

value: e2fa e2fb e2fc triple mutant


title: WT-DN1_BC_88


title: PFA4_hypox_p3.H3K27me3


title: PFA2-Rx-XChIP_K27me2


title: H3K27me3 CUT&RUN wt mESC line 3

value: Smchd1[fl/+] (wild-type)


title: H2AK119ub CUT&RUN wt mESC line 1

description: Maternal deletion with Zp3-Cre

data_processing:
Library strategy: CUT&RUN
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth library size using Seqmonk.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed read counts normalized by library size within bins created ±2.5kb centered on a list of MACS peaks determined using SeqMonk's MACS-like functionality for each genotype separately.  MACS peaks were called between H2AK119ub ChIP and input samples from Fursova et al., 2021 (Genes Dev . 2021 May 1;35(9-10):749-770.  doi: 10.1101/gad.347005.120.  Epub 2021 Apr 22) . Peak lists from biological replicates were merged before peak calculation.

extract_protocol:
Fresh cells were subject to CUT&RUN for H2AK119ub. DNA was extracted with phenol/chloroform/isoamyl alcohol
NEBNext Ultra II DNA Library Prep Kit for Illumina
CUT&RUN was performed as described in Skene and Henikoff eLife 2017;6:e21856 DOI: 10.7554/eLife.21856 DNA was purified by phenol/chloroform/isoamylalcohol extraction followed by glycogen/ethanol precipitation
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: PFA5-Rx_cells_ChIP1_Input

value: Input


title: H3K27me3 CUT&RUN wt mESC line 2


title: WT-DN1_BC_87

value: wild type

value: thymus


title: PFA2-Rx_cells_ChIP1_Input

value: cell line

value: Parental


title: ChIPseq_IgG_bte1_rep3

description: IgG-ChIP (negative control) from bte1 mutant rep3

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: bte1 mutant


title: ChIPseq_IgG_e2f_rep1

description: IgG-ChIP (negative control) from e2f triple mutant rep1


title: ChIPseq_IgG_bte1_rep2

description: IgG-ChIP (negative control) from bte1 mutant rep2


title: H3K27me3 CUT&RUN wt mESC line 1

value: Pluripotent state


title: DIPGIV-ACVR1-ko-c129p7-Rx_H3K27me3-C

source_name: Pons

tag: clone or passage


title: PFA4-Rx_cells_ChIP1_Input


title: ChIPseq_IgG_e2f_rep2

description: IgG-ChIP (negative control) from e2f triple mutant rep2


title: ChIPseq_IgG_bte1_rep1

description: IgG-ChIP (negative control) from bte1 mutant rep1


title: DIPGIV-ACVR1-ko-c129p7-Rx_Input


title: WT-DN1_BC_86


title: WT-DN1_BC_85


title: RNAseq mat del mESC day 3 diff line 2 rep 4

description:
Maternal deletion with Zp3-Cre
benetti_ESC_RNAseq_log2PRKM_Hox.txt
benetti_ESC_RNAseq_log2PRKM_diff_factors.txt

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed RPKM counts normalized by sequencing depth for all Hox genes and a list of pluripotency and differentiation factors relevant to mESC to NMP differentiation. Transcript isoforms were merged.

molecule: polyA RNA

source_name: mESC differentiating to NMPs

extract_protocol:
Quick-RNA Miniprep Kit (Zymo)
TruSeq Stranded mRNA kit (Illumina
100ng total RNA extracted with Quick-RNA Miniprep Kit (Zymo) then used as library prep input
TruSeq Stranded or non-stranded mRNA kit (Illumina)

treatment_protocol: mESCSs were differentiated into NMPs as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

value: day 3 differentiation

value: Smchd1[del/+] (maternally deleted)

tag: growth protocol

value: day 3 diff


title: ChIPseq_IgG_WT_rep3

description: IgG-ChIP (negative control) from WT rep3

value: Col-0 ecotype


title: HSJ051-p32.H3K27me2

source_name: Thalamus


title: WT-DN1_BC_84

value: 6~8 wks


title: WT-DN1_BC_83


title: RNAseq mat del mESC day 2 diff line 2 rep 4

value: day 2 differentiation

value: C57BL/6/Cast F1

value: M

value: mESC

value: day 2 diff


title: ChIPseq_IgG_WT_rep2

description: IgG-ChIP (negative control) from WT rep2

value: IgG (PP64, Millipore)


title: DIPGIV-ACVR1-ko-c129p7-Rx_H3K27me2

value: cell line


title: RNAseq mat del mESC day 1 diff line 2 rep 4

value: day 1 differentiation

value: day 1 diff


title: ChIPseq_IgG_WT_rep1

description: IgG-ChIP (negative control) from WT rep1

value: total seedlings

value: 9-day-old seedlings grown under continuous white light


title: WT-DN1_BC_82

value: wild type

value: thymus


title: RNAseq wt mESC day 4 diff line 2 rep 4

value: day 4 differentiation

value: Smchd1[fl/+] (wild-type)

value: day 4 diff


title: WT-DN1_BC_81

value: 6~8 wks


title: PKU2PC IP for m6A-seq

city: Shenzhen

first: Wenli

last: Mao

address: 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

data_processing:
library strategy: m6A-seq; MeRIP-seq
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For RNA-seq: The reads mapped the genome were calculated using HTseq sorftware. For MeRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: hg38
Supplementary files format and content: For RNA-seq reads counts: All.HTSeq.counts.txt
Supplementary files format and content: For MeRIP-seq peak: CAPC_sig_diff_peak_ann.xls

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For RNA-seq: VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction. For MeRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106). The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).

tag: sample name

tag: sample type

value: IP


title: FYZPC IP for m6A-seq

source_name: FYZPC

value: FYZPC


title: WT-DN1_BC_80


title: ChIPseq_E2FA_bte1_rep3

description: E2FA-ChIP from bte1 mutant rep3

value: E2FA (raised in rabbit using full-length E2FA as antigen, Beijing Protein Innovation, 1:1000 dilution)

value: bte1 mutant


title: RNAseq wt mESC day 3 diff line 2 rep 4

value: day 3 differentiation

value: C57BL/6/Cast F1

value: M

value: mESC

value: day 3 diff


title: FHTPC IP for m6A-seq

source_name: FHTPC

value: FHTPC


title: WT-DN1_BC_7


title: RNAseq mat del mESC day 4 diff line 2 rep 4

value: Smchd1[del/+] (maternally deleted)


title: ChIPseq_E2FA_bte1_rep1

description: E2FA-ChIP from bte1 mutant rep1

value: total seedlings

value: 9-day-old seedlings grown under continuous white light


title: ChIPseq_E2FA_bte1_rep2

description: E2FA-ChIP from bte1 mutant rep2


title: RNAseq wt mESC day 2 diff line 2 rep 4

value: day 2 differentiation

value: day 2 diff


title: RNAseq wt mESC day 2.5 diff line 2 rep 4

value: day 2.5 differentiation

value: Smchd1[fl/+] (wild-type)

value: day 2.5 diff


title: PKU2CA IP for m6A-seq

value: IP


title: WT-DN1_BC_78

value: wild type

value: thymus

value: 6~8 wks


title: WT-DN1_BC_79


title: RNAseq wt mESC day 1 diff line 2 rep 4

value: day 1 differentiation

value: C57BL/6/Cast F1

value: day 1 diff


title: FYZCA IP for m6A-seq

source_name: FYZCA

value: FYZCA


title: RNAseq wt mESC DME LIF line 2 rep 4

source_name: Differentiating mESC, in DME + LIF medium

value: day 0 differentation

value: M

value: mESC

value: DME LIF


title: FHTCA IP for m6A-seq

source_name: FHTCA

value: FHTCA


title: ChIPseq_E2FA_WT_rep2

description: E2FA-ChIP from WT rep2

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: E2FA (raised in rabbit using full-length E2FA as antigen, Beijing Protein Innovation, 1:1000 dilution)

value: Col-0 ecotype


title: ChIPseq_E2FA_WT_rep3

description: E2FA-ChIP from WT rep3


title: PKU2PC input for m6A-seq

value: input


title: WT-DN1_BC_77

value: wild type


title: RNAseq mat del mESC day 4 diff line 1 rep 3

value: day 4 differentiation

value: Smchd1[del/+] (maternally deleted)

value: day 4 diff


title: ChIPseq_E2FA_WT_rep1

description: E2FA-ChIP from WT rep1


title: WT-DN1_BC_76

value: thymus

value: 6~8 wks


title: FHTPC input for m6A-seq

value: FHTPC


title: FYZPC input for m6A-seq

value: FYZPC


title: WT-DN1_BC_75


title: RNAseq mat del mESC day 3 diff line 1 rep 3

value: day 3 differentiation

value: C57BL/6/Cast F1

value: M

value: day 3 diff


title: WT-DN1_BC_74


title: ChIPseq_BTE1_e2f_rep2

description: BTE1-ChIP from e2f triple mutant rep2

value: total seedlings

value: BTE1 (raised in rabbit using the N-terminal 214 amino acids of BTE1 as antigen, Beijing Protein Innovation, 1:1000 dilution)

value: e2fa e2fb e2fc triple mutant


title: RNAseq mat del mESC day 2 diff line 1 rep 3

value: day 2 differentiation

value: mESC

value: day 2 diff


title: PKU2CA input for m6A-seq

value: input


title: ChIPseq_BTE1_e2f_rep1

description: BTE1-ChIP from e2f triple mutant rep1

value: 9-day-old seedlings grown under continuous white light


title: FYZCA input for m6A-seq

value: FYZCA


title: ChIPseq_BTE1_bte1_rep3

description: BTE1-ChIP from bte1 mutant rep3

value: bte1 mutant


title: WT-DN1_BC_72

value: wild type

value: thymus

value: 6~8 wks


title: RNAseq wt mESC day 4 diff line 1 rep 3

value: day 4 differentiation

value: Smchd1[fl/+] (wild-type)

value: day 4 diff


title: RNAseq mat del mESC day 1 diff line 1 rep 3

value: day 1 differentiation

value: Smchd1[del/+] (maternally deleted)

value: C57BL/6/Cast F1

value: M

value: day 1 diff


title: RNAseq wt mESC day 3 diff line 1 rep 3

value: day 3 differentiation

value: mESC

value: day 3 diff


title: ChIPseq_BTE1_e2f_rep3

description: BTE1-ChIP from e2f triple mutant rep3

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: BTE1 (raised in rabbit using the N-terminal 214 amino acids of BTE1 as antigen, Beijing Protein Innovation, 1:1000 dilution)

value: e2fa e2fb e2fc triple mutant


title: FHTCA input for m6A-seq

value: FHTCA

value: input


title: PKU2PC for RNA-seq

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For RNA-seq: The reads mapped the genome were calculated using HTseq sorftware. For MeRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: hg38
Supplementary files format and content: For RNA-seq reads counts: All.HTSeq.counts.txt
Supplementary files format and content: For MeRIP-seq peak: CAPC_sig_diff_peak_ann.xls


title: ChIPseq_BTE1_bte1_rep1

description: BTE1-ChIP from bte1 mutant rep1

value: bte1 mutant


title: WT-DN1_BC_71

value: wild type

value: thymus

value: 6~8 wks


title: RNAseq wt mESC day 2.5 diff line 1 rep 3

value: day 2.5 differentiation

value: Smchd1[fl/+] (wild-type)

value: day 2.5 diff


title: FYZPC for RNA-seq

source_name: P-FYZPC

value: FYZPC


title: WT-DN1_BC_70


title: FHTPC for RNA-seq

source_name: P-FHTPC

value: FHTPC


title: RNAseq mat del mESC day 4 diff line 1 rep 2

value: day 4 differentiation

value: Smchd1[del/+] (maternally deleted)

value: C57BL/6/Cast F1

value: M

value: mESC

value: day 4 diff


title: RNAseq wt mESC DME LIF line 1 rep 3

value: day 0 differentation

value: DME LIF


title: ChIPseq_BTE1_WT_rep3

description: BTE1-ChIP from WT rep3

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: BTE1 (raised in rabbit using the N-terminal 214 amino acids of BTE1 as antigen, Beijing Protein Innovation, 1:1000 dilution)

value: Col-0 ecotype


title: PKU2CA for RNA-seq


title: WT-DN1_BC_69

value: wild type

value: thymus

value: 6~8 wks


title: RNAseq mat del mESC day 3 diff line 1 rep 2

value: day 3 differentiation

value: day 3 diff


title: ChIPseq_BTE1_WT_rep2

description: BTE1-ChIP from WT rep2


title: ChIPseq_BTE1_WT_rep1

description: BTE1-ChIP from WT rep1


title: WT-DN1_BC_68


title: WT-DN1_BC_73


title: FYZCA for RNA-seq

source_name: C-FYZCA

value: FYZCA


title: ChIPseq_H3K27me3_bte1_rep3

description: H3K27me3-ChIP from bte1 mutant rep3

value: H3K27me3 (07-449, Millipore)

value: bte1 mutant


title: WT-DN1_BC_67


title: RNAseq mat del mESC day 2.5 diff line 1 rep 2

value: day 2.5 differentiation

value: Smchd1[del/+] (maternally deleted)

value: C57BL/6/Cast F1

value: M

value: day 2.5 diff


title: ChIPseq_BTE1_bte1_rep2

description: BTE1-ChIP from bte1 mutant rep2

value: total seedlings


title: FHTCA for RNA-seq

source_name: C-FHTCA

value: FHTCA


title: ChIPseq_H3K27me3_bte1_rep2

description: H3K27me3-ChIP from bte1 mutant rep2

value: 9-day-old seedlings grown under continuous white light


title: WT-DN1_BC_66


title: RNAseq mat del mESC day 2 diff line 1 rep 2

value: day 2 differentiation

value: mESC

value: day 2 diff


title: WT-DN1_BC_6

value: wild type

value: thymus

value: 6~8 wks


title: ChIPseq_H3K27me3_bte1_rep1

description: H3K27me3-ChIP from bte1 mutant rep1


title: RNAseq mat del mESC day 1 diff line 1 rep 2

value: day 1 differentiation

value: day 1 diff


title: NB4 cells, DMSO 24h, rep1

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes readcount values for each Sample

source_name: NB4 cells, DMSO 24h

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AML cells

tag: cell line

tag: treatment

value: DMSO


title: ChIPseq_H3K27me3_WT_rep3

description: H3K27me3-ChIP from WT rep3

tag: tissue

value: H3K27me3 (07-449, Millipore)

value: Col-0 ecotype


title: NB4 cells, DMSO 24h, rep2


title: NB4 cells, dBET1 24h, rep2

source_name: NB4 cells, dBET1 24h


title: WT-DN1_BC_64


title: RNAseq mat del mESC DME LIF line 1 rep 2

value: day 0 differentation

value: Smchd1[del/+] (maternally deleted)

value: C57BL/6/Cast F1

value: M

value: DME LIF


title: ChIPseq_H3K27me3_WT_rep2

description: H3K27me3-ChIP from WT rep2

source_name: total seedlings

value: total seedlings

tag: developmental stage

value: 9-day-old seedlings grown under continuous white light


title: WT-DN1_BC_62


title: RNAseq wt mESC day 4 diff line 1 rep 2

value: day 4 differentiation

value: Smchd1[fl/+] (wild-type)

value: mESC

value: day 4 diff


title: ChIPseq_H3K27me3_WT_rep1

description: H3K27me3-ChIP from WT rep1

tag: chip antibody


title: RNAseq wt mESC day 3 diff line 1 rep 2

value: day 3 differentiation

tag: genotype

value: day 3 diff


title: NB4 cells, dBET1 24h, rep1

value: AML cells


title: ChIPseq_H3K4me3_bte1_rep3

description: H3K4me3-ChIP from bte1 mutant rep3

value: H3K4me3 (04-745, Millipore)

value: bte1 mutant


title: WT-DN1_BC_61

value: wild type

value: thymus

value: 6~8 wks


title: RNAseq wt mESC day 2.5 diff line 1 rep 2

tag: development stage

value: day 2.5 differentiation

value: C57BL/6/Cast F1

value: day 2.5 diff


title: WT-DN1_BC_60


title: ChIPseq_H3K4me3_bte1_rep2

description: H3K4me3-ChIP from bte1 mutant rep2

value: total seedlings


title: ASH171_DIPG21-pX-Rxx_Input

data_processing:
ChIP-seq datasets were processed using the ChIP-seq module of GenPipes (v3.1.0 for isogenic cell lines, v3.1.2 for parental cell lines). Raw reads were trimmed using Trimmomatic (v0.32) to remove adaptor and sequencing-primer associated reads then aligned to hg19 using bwa-mem (v0.7.12) with default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard (v2.0.1) to produce uniquely aligned reads. Reads with a mapping quality of 5 or less were then filtered out. For single-end (SE) 50bp datasets, reads were extended by 250bp.
Wiggle tracks are generated using uniquely aligned reads using Homer (v4.9.1). ChIP-seq RPKM values over CGIs and genome-wide 100kb bins for scatterplots were calculated using VisRSeq (v0.9.40).
Rx- and RPKM-normalized BigWig tracks were produced using the “bamCoverage” functionality of deeptools (v3.5.1). Rx ratios were supplied via the ‘--scaleFactor’ option.  Reads flagged as duplicates, mapping to random, mitochondrial or sex chromosomes, as well as low-mappability regions according to ENCODE’s blacklist were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files. Read coverage for each sample over the human genome

tag: material

value: Cell line

tag: histone mark/factor

value: Input

tag: crispr

value: Parental

value: PX


title: RNAseq wt mESC day 2 diff line 1 rep 2

value: day 2 differentiation

value: Smchd1[fl/+] (wild-type)

tag: strain

tag: Sex

value: M

tag: cell type

value: mESC

value: day 2 diff


title: HSJ051-p32-Rx_XChIP_Input

tag: clone or passage


title: ChIPseq_H3K4me3_bte1_rep1

description: H3K4me3-ChIP from bte1 mutant rep1

value: 9-day-old seedlings grown under continuous white light

value: H3K4me3 (04-745, Millipore)

value: bte1 mutant


title: WT-DN1_BC_5

tag: strain/background

tag: genotype/variation

value: wild type

value: thymus

tag: age

value: 6~8 wks


title: WT-DN1_BC_65


title: HSJ019_parental_p25_Input


title: RNAseq wt mESC day 1 diff line 1 rep 2

value: day 1 differentiation

value: C57BL/6/Cast F1

tag: growth protocol

value: day 1 diff


title: WT-DN1_BC_63


title: HSJ019_KO_c8p30_Input

value: Cell line

value: Input

value: KO


title: RNAseq wt mESC DME LIF line 1 rep 2

value: day 0 differentation

value: DME LIF


title: ChIPseq_H3K4me3_WT_rep3

description: H3K4me3-ChIP from WT rep3

value: total seedlings

value: Col-0 ecotype


title: ChIPseq_H3K4me3_WT_rep2

description: H3K4me3-ChIP from WT rep2


title: WT-DN1_BC_59


title: DIPG21-pX-Rx_CTCF

value: CTCF

value: Parental

value: PX


title: RNAseq mat del mESC day 4 diff line 1 rep 1

value: day 4 differentiation

value: Smchd1[del/+] (maternally deleted)

value: M

value: mESC

value: day 4 diff


title: HSJ019_KO_c10p29_Input


title: ChIPseq_H3K4me3_WT_rep1

description: H3K4me3-ChIP from WT rep1

value: 9-day-old seedlings grown under continuous white light

value: H3K4me3 (04-745, Millipore)


title: WT-DN1_BC_57

value: wild type

value: thymus

value: 6~8 wks


title: DIPGIV_KO_c9p9_Input

value: Cell line

value: Input

value: KO


title: RNAseq mat del mESC day 3 diff line 1 rep 1

value: day 3 differentiation

value: C57BL/6/Cast F1

value: day 3 diff


title: RNAseq mat del mESC day 2.5 diff line 1 rep 1

value: day 2.5 differentiation

value: day 2.5 diff


title: ChIPseq_H3K4me2_bte1_rep2

description: H3K4me2-ChIP from bte1 mutant rep2

value: total seedlings

value: H3K4me2 (07-030, Millipore)

value: bte1 mutant


title: ChIPseq_H3K4me2_bte1_rep3

description: H3K4me2-ChIP from bte1 mutant rep3


title: WT-DN1_BC_56


title: WT-DN1_BC_55


title: DIPG36_NKO_c1S2_Input

value: NKO


title: RNAseq mat del mESC day 2 diff line 1 rep 1

value: day 2 differentiation

value: Smchd1[del/+] (maternally deleted)

value: M

value: mESC

value: day 2 diff


title: RNAseq mat del mESC day 1 diff line 1 rep 1

value: day 1 differentiation

value: day 1 diff


title: DIPG36_parental_p20_Input

value: Cell line

value: Input

value: Parental


title: WT-DN1_BC_54

value: wild type

value: thymus

value: 6~8 wks


title: ChIPseq_H3K4me2_WT_rep3

description: H3K4me2-ChIP from WT rep3

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: Col-0 ecotype


title: WT-DN1_BC_58


title: WT-DN1_BC_53


title: RNAseq mat del mESC DME LIF line 1 rep 1

value: day 0 differentation

value: C57BL/6/Cast F1

value: DME LIF


title: DIPG21_KO_c7p6_Input

value: KO


title: WT-DN1_BC_51


title: RNAseq wt mESC day 4 diff line 1 rep 1

value: day 4 differentiation

value: Smchd1[fl/+] (wild-type)

value: M

value: mESC

value: day 4 diff


title: DIPG21_NKO_c4p6_Input

value: Cell line

value: Input

value: NKO


title: WT-DN1_BC_50

value: wild type

value: thymus


title: ChIPseq_H3K4me2_WT_rep1

description: H3K4me2-ChIP from WT rep1

value: total seedlings

value: H3K4me2 (07-030, Millipore)


title: WT-DN1_BC_52

value: 6~8 wks


title: RNAseq wt mESC day 3 diff line 1 rep 1

value: day 3 differentiation

value: day 3 diff


title: ChIPseq_H3K4me2_WT_rep2

description: H3K4me2-ChIP from WT rep2

value: 9-day-old seedlings grown under continuous white light

value: Col-0 ecotype


title: HSJ051-p32-Rx_XChIP_H3K27me3-C

value: Parental


title: WT-DN1_BC_4


title: ChIPseq_H3K4me1_bte1_rep2

description: H3K4me1-ChIP from bte1 mutant rep2

value: H3K4me1 (07-436, Millipore)

value: bte1 mutant


title: ChIPseq_H3K4me2_bte1_rep1

description: H3K4me2-ChIP from bte1 mutant rep1


title: RNAseq wt mESC day 2 diff line 1 rep 1

value: day 2 differentiation

value: Smchd1[fl/+] (wild-type)

value: C57BL/6/Cast F1

value: M

value: mESC

value: day 2 diff


title: HSJ051-p32-Rx_XChIP_H3K27ac

value: Cell line


title: RNAseq wt mESC day 2.5 diff line 1 rep 1

value: day 2.5 differentiation

value: day 2.5 diff


title: DIPG36_KO_c2p4_Input

value: Input

value: KO


title: HSJ019_parental_p25_H3K27ac


title: ChIPseq_H3K4me1_bte1_rep1

description: H3K4me1-ChIP from bte1 mutant rep1

value: total seedlings


title: WT-DN1_BC_49

value: wild type

value: thymus

value: 6~8 wks


title: HSJ019_KO_c10p29_H3K27ac


title: WT-DN1_BC_48


title: RNAseq wt mESC day 1 diff line 1 rep 1

value: day 1 differentiation

value: day 1 diff


title: HSJ019_KO_c8p30_H3K27ac


title: ChIPseq_H3K4me1_WT_rep2

description: H3K4me1-ChIP from WT rep2

value: 9-day-old seedlings grown under continuous white light

value: H3K4me1 (07-436, Millipore)

value: Col-0 ecotype


title: RNAseq wt mESC DME LIF line 1 rep 1

value: day 0 differentation

value: Smchd1[fl/+] (wild-type)

value: C57BL/6/Cast F1

value: M

value: DME LIF


title: WT-DN1_BC_47


title: ChIPseq_H3K4me1_WT_rep3

description: H3K4me1-ChIP from WT rep3


title: RNAseq mat del mESC 2i LIF line 3

description: Maternal deletion with Zp3-Cre

source_name: mESC cultured in 2i+LIF medium

value: Pluripotent state

value: Smchd1[del/+] (maternally deleted)

value: mESC

value: 2i LIF


title: DIPGIV_KO_c9p9_H3K27me3

value: Cell line

value: KO


title: ChIPseq_H3K4me1_bte1_rep3

description: H3K4me1-ChIP from bte1 mutant rep3

value: total seedlings

value: bte1 mutant


title: RNAseq mat del mESC 2i LIF line 2

description: Maternal deletion with Zp3-Cre


title: WT-DN1_BC_46

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)

value: wild type

value: thymus

value: 6~8 wks


title: WT-DN1_BC_45


title: DIPGIV_KO_c9p9_H3K27me2

source_name: Pons


title: WT-DN1_BC_43


title: RNAseq mat del mESC 2i LIF line 1

description: Maternal deletion with Zp3-Cre


title: RNAseq wt mESC 2i LIF line 3

description: Maternal deletion with Zp3-Cre


title: WT-DN1_BC_44


title: RNAseq wt mESC 2i LIF line 2

description: Maternal deletion with Zp3-Cre


title: DIPGIV_KO_c9p9_H3K27ac


title: ChIPseq_PolIISer2P_bte1_rep3

description: Ser2P Pol II-ChIP from bte1 mutant rep3

value: 9-day-old seedlings grown under continuous white light

value: Ser2P (ab5095, Abcam)


title: ChIPseq_PolIISer2P_bte1_rep1

description: Ser2P Pol II-ChIP from bte1 mutant rep1


title: DIPG36_NKO_c1S2_H3K27me3

value: NKO


title: DIPG36_KO_c2p4_H3K27me3


title: ChIPseq_H3K4me1_WT_rep1

description: H3K4me1-ChIP from WT rep1

value: H3K4me1 (07-436, Millipore)

value: Col-0 ecotype


title: ChIPseq_PolIISer2P_bte1_rep2

description: Ser2P Pol II-ChIP from bte1 mutant rep2


title: RNAseq wt mESC 2i LIF line 1

description: Maternal deletion with Zp3-Cre

value: Smchd1[fl/+] (wild-type)

value: C57BL/6/Cast F1

value: M


title: WT-DN1_BC_42


title: ChIPseq_PolIISer2P_WT_rep3

description: Ser2P Pol II-ChIP from WT rep3


title: ChIPseq_PolIISer2P_WT_rep2

description: Ser2P Pol II-ChIP from WT rep2


title: RNAseq tailbud 11 somite mat del rep2 female

description:
Maternal deletion with MMTV-Cre
benetti_tailbud_RNAseq_log2RPKM_Hox.txt
benetti_tailbud_RNAseq_DEGs.txt

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed RPKM counts normalized by sequencing depth for all Hox genes. Transcript isoforms were merged. DEGs.

source_name: Tailbud from E8-8.5 embryo

growth_protocol: Tailbud tissue dissected from E8-8.5 mouse embryo and snap frozen until RNA extraction

value: Tailbud from E8-8.5 embryo

value: 11 somites

value: Smchd1[del/+] (maternally deleted)

value: F


title: DIPG36_NKO_c1S2_H3K27me2

value: Cell line


title: RNAseq tailbud 11 somite mat del rep1 male


title: ChIPseq_PolIISer2P_WT_rep1

description: Ser2P Pol II-ChIP from WT rep1

value: total seedlings


title: WT-DN1_BC_40

value: wild type


title: DIPG36_KO_c2p4_H3K27ac

value: KO


title: WT-DN1_BC_3

value: thymus

value: 6~8 wks


title: RNAseq tailbud 11 somite wt rep3 female


title: DIPG36_NKO_c1S2_H3K27ac


title: ChIPseq_PolIISer5P_bte1_rep3

description: Ser5P Pol II-ChIP from bte1 mutant rep3

value: 9-day-old seedlings grown under continuous white light

value: Ser5P (ab5408, Abcam)

value: bte1 mutant


title: RNAseq tailbud 11 somite wt rep2 female


title: WT-DN1_BC_38


title: WT-DN1_BC_36


title: DIPG21_KO_c7p6_H3K27me3


title: RNAseq tailbud 11 somite wt rep1 male


title: DIPG21_NKO_c4p6_H3K27me3

value: NKO


title: DIPG21_KO_c7p6_H3K27me2


title: WT-DN1_BC_37


title: WT-DN1_BC_41


title: DIPG36_KO_c2p4_H3K27me2


title: ChIPseq_PolIISer5P_bte1_rep1

description: Ser5P Pol II-ChIP from bte1 mutant rep1


title: RNAseq tailbud 10 somite mat del rep3 female

value: 10 somites


title: ChIPseq_PolIISer5P_WT_rep3

description: Ser5P Pol II-ChIP from WT rep3

value: Col-0 ecotype


title: ChIPseq_PolIISer5P_WT_rep2

description: Ser5P Pol II-ChIP from WT rep2


title: WT-DN1_BC_35


title: DIPG21_NKO_c4p6_H3K27me2


title: ChIPseq_PolIISer5P_WT_rep1

description: Ser5P Pol II-ChIP from WT rep1


title: RNAseq tailbud 10 somite mat del rep1 male

value: C57BL/6/Cast F1

value: M


title: RNAseq tailbud 10 somite wt rep4 female

value: Tailbud from E8-8.5 embryo

value: Smchd1[fl/+] (wild-type)


title: RNAseq tailbud 10 somite mat del rep2 male

value: Smchd1[del/+] (maternally deleted)


title: ChIPseq_PolII_bte1_rep3

description: Pol II-ChIP from bte1 mutant rep3

value: total Pol II (ab817, Abcam)


title: DIPG21_KO_c7p6_H3K27ac

value: Cell line


title: ChIPseq_PolIISer5P_bte1_rep2

description: Ser5P Pol II-ChIP from bte1 mutant rep2

value: total seedlings


title: WT-DN1_BC_39

value: wild type


title: WT-DN1_BC_34

value: thymus


title: DIPG21_NKO_c4p6_H3K27ac


title: WT-DN1_BC_33

value: 6~8 wks


title: ChIPseq_PolII_bte1_rep2

description: Pol II-ChIP from bte1 mutant rep2

value: 9-day-old seedlings grown under continuous white light


title: RNAseq tailbud 10 somite wt rep3 female

value: F


title: WT-DN1_BC_32


title: RNAseq tailbud 10 somite wt rep2 female


title: WT-DN1_BC_30


title: WT-DN1_BC_31


title: Inflamed

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

country: USA

institute: NYU Langone Health

data_processing:
Reads were processed using 10X’s Cell Ranger version 5.0.0 using the hg19 reference genome, resulting in a filtered HDF5 file
HDF5 files were processing using Seurat version 4.0.3 in R 4.0.4
Inflamed and Non-inflamed samples were separately normalized and 2000 variable features generated for each sample separately
Inflamed and Non-inflamed samples were integrated using the Seurat functions SelectIntegrationFeatures, FindIntegrationAnchors, and IntegrateData
30 principal components were calculated for the integrated data, following which the integrated data were clustered using the Louvain algorithm with resolution parameter 0.4
Dimensional reduction was performed using UMAP
Genome_build: hg19
Supplementary_files_format_and_content: HDF5 (.h5) files generated by CellRanger 5.0.0
Supplementary_files_format_and_content: TSV file contains cell (barcode) metadata from final processed, integrated Seurat object. Includes cluster identities and UMAP embedding coordinates

source_name: Human small intestine

extract_protocol: Standard Illumina/10X protocols

tag: site

value: Inflamed tissue

value: small intestine

tag: patient diagnosis

value: Crohn’s disease


title: RNAseq tailbud 9 somite mat del rep2 female

tag: tissue

value: 9 somites


title: RNAseq tailbud 10 somite wt rep1 male

value: 10 somites

value: C57BL/6/Cast F1


title: H9_KO-IP

first: Haibin

last: Jiang

address: Dongdan Santiao 5#

institute: Peking Union Medical College

data_processing: After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human reference genome HG19 using BOWTIE (V2.2.7). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of two samples, using a p-value threshold of 0.0001. Then the peaks were annotated by the nearest gene using the newest UCSC RefSeq database.

source_name: human embryonic stem cell

growth_protocol: The H9 was cultured in E8 medium

extract_protocol:
Lysates were clarified from enzyme digested nuclei and histone-DNA complexes were isolated with antibody.
10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads.

treatment_protocol: Knockout of ID1 and ID3 by CRISPR-Cas9

tag: cell line

value: human embryonic stem cell

value: ID1 and ID3 double knock out

tag: chip antibody

value: E2A (TCF3) Rabbit mAb (CST, 12258S)


title: ChIPseq_PolII_WT_rep1

description: Pol II-ChIP from WT rep1

tag: developmental stage

value: total Pol II (ab817, Abcam)

tag: genotype

value: Col-0 ecotype


title: RNAseq tailbud 9 somite wt rep3 female

value: Tailbud from E8-8.5 embryo

tag: development stage

value: Smchd1[fl/+] (wild-type)


title: RNAseq tailbud 9 somite mat del rep1 female

value: Smchd1[del/+] (maternally deleted)


title: GROseq_bte1_rep2

data_processing:
Library strategy: GRO-seq
Illumina bcl-convert v3.7.5 software used for basecalling.
GRO-seq raw reads were filtered by removing adapter sequences and low-quality sequences using fastp.
Next, reads mapped to ribosomal RNAs were filtered using bowtie2 and mapped to the Arabidopsis genome (TAIR10) using HISAT2.
The reads were filtered to retain those that had a MAPQ score >10 and were mapped to only one position, after which they were filtered to remove duplicate reads using Picard tools MarkDuplicates version 2.21.3.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 1 --normalizeUsing CPM”.

extract_protocol:
Nuclei from 9-day-old light-grown seedlings were extracted using Honda buffer. Three biological replicates for each sample were subjected to RNA-seq.
Strand-specific RNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR605-02, Vazyme) according to the manufacturer’s instructions and sequenced on a HiSeq X Ten System (Illumina).

value: total seedlings

value: bte1 mutant


title: WT-DN1_BC_2

value: wild type

value: thymus

value: 6~8 wks


title: H9_WT-IP

value: Wild Type


title: GROseq_bte1_rep3

value: 9-day-old seedlings grown under continuous white light


title: ChIPseq_PolII_WT_rep2

description: Pol II-ChIP from WT rep2


title: H9_WT-input

value: none (input)


title: WT-DN1_BC_29


title: H9_KO-input


title: GROseq_bte1_rep1


title: WT-DN1_BC_28


title: 786-O_JMJD6_WT_sgCtrl_RNA_Rep3

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
For RNA-seq: Reads were filtered for adapter contamination using cutadapt (v1.12) and filtered such that at least 90% of bases of each read had a quality score >20. Reads were aligned to the reference genome (hg19) using STAR (v2.5.2b) retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed. Transcript abundance was then estimated using Salmon, and differential expression was detected using DESeq2.
For ChIP: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Sequencing adapters on reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 in paired mode. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. In-house scripts were used to limit potential PCR duplicates by limiting reads with the same sequence to a maximum of 5 copies and discarding the copies beyond that limit. Since the previous filtering steps may remove one end of a read pair but not the other, both read-pair fastq files were synced using in-house scripts to ensure proper order for alignment. Read alignment was done using STAR (v2.5.2b) and options --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. Post-alignment, Samtools (v1.31) and bedtools (2.26) were used to generate bigWig files for downstream analyses. MACS2 (v2.1.2) was used for peak calling on each individual sample with the designated inputs.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.sf: Salmon files are tab-delimited text files with the per-transcript expression.
Supplementary_files_format_and_content: *.bw: BigWig files show the per-base signal across the genome.
Supplementary_files_format_and_content: *.narrowpeak: narrowPeak files contain the peak calls from MACS2.

source_name: 786-O cell line

growth_protocol: 786-O cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, incubated in a 5% CO2 humidified incubator at 37°C. 786-O cells were obtained from Sigma. All cells were used for experiments within 10-20 passages from thawing, and they were mycoplasma-free guaranteed by applying mycoplasma detection kit (Lonza, LT07–218) or mycoplasma elimination reagent-plasmocin (Invivogen, ant-mpt).

extract_protocol:
Total RNA was extracted from 786-O cells (triplicate) infected with control or JMJD6 sgRNA2/4 using the RNeasy® Mini Kit (QIAGEN, 74106), and RNase-Free DNase Set (QIAGEN, 79256) was applied for DNase digestion during RNA purification.
Library preparation, quality control and sequencing were performed by Novogen.

treatment_protocol:
Seed cells (786-O) in 6-well plates to be 60-70% confluent at transfection, followed by transfection using the Invitrogen™ lipofectamine™ RNAiMAX transfection reagent (Thermo Fisher Scientific, 13778150), change medium after 12 h transfection. Incubate cells for 48 h at 37°C. Then further use the cells to perform experiments (immunoblots, cell proliferation assay and soft agar colony formation assay). Non-targeting siRNA was used as control and obtained from Dharmacon (D0012100220). The sequence of main siRNAs used in this study is as below:
JMJD6 siRNA (1): GGAGAGCACUCGAGAUGAU
JMJD6 siRNA (4): GGAUAACGAUGGCUACUCA
Other 2-OG family siRNAs sequence is showed in Supplementary table.

value: JMJD6 WT

tag: sgrna

value: sgCtrl


title: ChIPseq_PolII_bte1_rep1

description: Pol II-ChIP from bte1 mutant rep1


title: WT-DN1_BC_27


title: RNAseq tailbud 9 somite wt rep2 female

value: 9 somites

tag: strain

value: C57BL/6/Cast F1

value: F


title: 786-O_JMJD6_WT_sgCtrl_RNA_Rep2


title: Non-inflamed

value: Adjacent non-inflamed tissue

value: small intestine

value: Crohn’s disease


title: GROseq_WT_rep3

value: Col-0 ecotype


title: RNAseq tailbud 9 somite wt rep1 male

value: Tailbud from E8-8.5 embryo

value: Smchd1[fl/+] (wild-type)

tag: Sex

value: M


title: ChIPseq_PolII_WT_rep3

description: Pol II-ChIP from WT rep3

value: total seedlings

value: total Pol II (ab817, Abcam)


title: RNAseq tailbud 8 somite mat del rep2 female

value: 8 somites

value: Smchd1[del/+] (maternally deleted)


title: GROseq_WT_rep2

value: 9-day-old seedlings grown under continuous white light


title: WT-DN1_BC_25

value: wild type

value: thymus

tag: cell type

value: 6~8 wks


title: 786-O_JMJD6_WT_sgCtrl_RNA_Rep1

value: JMJD6 WT

value: sgCtrl


title: WT-DN1_BC_24


title: MH-seq_bte1_rep3

description: MH-seq from bte1 mutant rep3

value: Micrococcal Nuclease (M0247S, NEB)

value: bte1 mutant


title: 786-O_JMJD6_KO_sg4_RNA_Rep3

value: JMJD6 KO

value: JMJD6 sg4


title: RNAseq tailbud 8 somite wt rep2 male

value: Tailbud from E8-8.5 embryo

value: C57BL/6/Cast F1


title: WT-DN1_BC_22


title: RNAseq tailbud 8 somite wt rep3 female

value: Smchd1[fl/+] (wild-type)

value: F


title: WT-DN1_BC_21


title: WT-DN1_BC_23


title: WT-DN1_BC_26


title: MH-seq_bte1_rep2

description: MH-seq from bte1 mutant rep2

value: total seedlings


title: 786-O_JMJD6_KO_sg2_RNA_Rep3

value: JMJD6 sg2


title: 786-O_JMJD6_KO_sg4_RNA_Rep1


title: MH-seq_WT_rep3

description: MH-seq from WT rep3

value: Col-0 ecotype


title: RNAseq tailbud 7 somite mat del rep2 male

value: 7 somites

value: Smchd1[del/+] (maternally deleted)

value: M


title: MH-seq_bte1_rep1

description: MH-seq from bte1 mutant rep1

value: 9-day-old seedlings grown under continuous white light


title: 786-O_JMJD6_KO_sg2_RNA_Rep2


title: WT-DN1_BC_1

value: wild type

value: thymus

value: 6~8 wks


title: WT-DN1_BC_20


title: GROseq_WT_rep1


title: 786-O_JMJD6_KO_sg2_RNA_Rep1


title: RNAseq tailbud 7 somite mat del rep1 male


title: RNAseq tailbud 7 somite mat del rep3 female


title: RNAseq tailbud 8 somite mat del rep1 female

value: 8 somites


title: 786-O_JMJD6_KO_sg4_RNA_Rep2

value: JMJD6 KO


title: MH-seq_WT_rep1

description: MH-seq from WT rep1

value: Micrococcal Nuclease (M0247S, NEB)


title: WT-DN1_BC_19


title: HeLa_WT_H3K18ub_ChIP_seq_rep

first: Falong

last: Lu

address: 1 West Beichen Road Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Clean reads were aligned to the human reference genome (hg38) and mouse reference genome (mm10), respectively, using Bowtie2 with default parameters.
Unmapped reads, multiple mapped reads and PCR duplicates were removed by samtools and Picard.
HeLa H3K18ub peaks were called using MACS2 with the parameters: --broad -g 2.9e9 -q 0.05 -f BAMPE --nomodel --extsize 147 -B.
E14 H3K18ub peaks were called using SICER with the parameters: --window size 200 --gap size 200.
E14 H3K27me3 peaks were called by SICER with parameters: --window size 200 --gap size 600.
Hela H3K27me3 peaks were called by SICER with parameters: --window size 2000 --gap size 8000.
Genome_build: mm10;hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage(v3.3.1); Scores represent RPKM.
Supplementary_files_format_and_content: peak text files

source_name: Hela

growth_protocol: WT and SUZ12 KO HeLa-S3 cells were grown in Dulbecco’s Modiﬁed Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. WT, Suz12 KO, Uhrf1 KO and Suz12/Uhrf1 DKO E14Tg2a mESCs were cultured on 0.2% gelatin-coated plates in DMEM supplemented with 15% fetal bovine serum, 1% penicillin/streptomycin, 1% nonessential amino acid, 1% sodium pyruvate, β-mercaptoethanol and 1000 U/mL LIF (ESGRO, Millipore).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 minutes. After quenching with 125 mM glycine, the cells were harvested and digested by MNase (NEB, M0247S, 2 U/μL) at 37 °C for 20 minutes to produce soluble chromatin with DNA fragments in the range of 150-300 bp. The lysates were then sonicated for 5 minutes (30 sec on / 30 sec off) using Bioruptor Sonicator (Diagenode, Inc., Denville, NJ) and centrifuged at 21,130 g for 10 minutes. The supernatants were collected and the chromatin content was incubated with Protein A and Protein G Dynabeads pre-linked with antibodies against H3K27me3 or H3K18ub overnight at 4 °C. Bound chromatin was washed extensively, then eluted and reverse-crosslinked at 65 °C overnight using elution buffer. After being treated by RNase A and proteinase K, the samples were extracted by phenol: chloroform and precipitated with ethanol in the presence of linear acrylamide. After dissolving in nuclease free TE buffer, the samples are ready for sequencing library construction.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa

value: WT

value: H3K18ub (custom-made)


title: ChIPseq_input_bte1_rep3

description: input (negative control) from bte1 mutant rep3

value: input (negative control)

value: bte1 mutant


title: RNAseq tailbud 7 somite wt rep4 female

value: Tailbud from E8-8.5 embryo

value: Smchd1[fl/+] (wild-type)

value: C57BL/6/Cast F1

value: F


title: RNAseq tailbud 8 somite wt rep1 male

value: M


title: WT-DN1_BC_18


title: HeLa_WT_H3K27me3_ChIP_seq

value: H3K27me3 (Cell Signaling, cat#9733)


title: ChIPseq_input_WT_rep3

description: input (negative control) from WT rep3

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: Col-0 ecotype


title: ChIPseq_input_bte1_rep2

description: input (negative control) from bte1 mutant rep2


title: RNAseq tailbud 7 somite wt rep2 male

value: 7 somites


title: WT-DN1_BC_17

value: wild type

value: thymus

value: 6~8 wks


title: MH-seq_WT_rep2

description: MH-seq from WT rep2

value: Micrococcal Nuclease (M0247S, NEB)


title: ChIPseq_input_bte1_rep1

description: input (negative control) from bte1 mutant rep1


title: HeLa_WT_H3K18ub_ChIP_seq

value: HeLa

value: WT

value: H3K18ub (custom-made)


title: WT-DN1_BC_14


title: RNAseq tailbud 6 somite mat del rep4 female

value: Tailbud from E8-8.5 embryo

value: 6 somites

value: Smchd1[del/+] (maternally deleted)


title: HeLa_SUZ12_KO_1_input_ChIP_seq

value: none (input)


title: WT-DN1_BC_13


title: ChIPseq_input_WT_rep2

description: input (negative control) from WT rep2

value: input (negative control)


title: HeLa_SUZ12_KO_1_H3K18ub_ChIP_seq


title: RNAseq tailbud 7 somite wt rep3 male

value: Smchd1[fl/+] (wild-type)

value: C57BL/6/Cast F1

value: M


title: HeLa_SUZ12_KO_H3K18ub_ChIP_seq_rep


title: ChIPseq_H2A.Z_bte1_rep3

description: H2A.Z-ChIP from bte1 mutant rep3

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: H2A.Z (ABE1348, Millipore)

value: bte1 mutant


title: WT-DN1_BC_16

value: wild type

value: thymus

value: 6~8 wks


title: RNAseq tailbud 7 somite wt rep1 male

value: 7 somites


title: RNAseq tailbud 6 somite mat del rep3 female

value: F


title: ChIPseq_input_WT_rep1

description: input (negative control) from WT rep1

value: Col-0 ecotype


title: HeLa_SUZ12_KO_2_RNA_seq

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Paired reads were aligned with STAR_2.6.0c to hg38.
Gene expression of RNA-seq data were quantified using Salmon (version 0.12.0) with parameters: -l ISR --seqBias --gcBias --posBias.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include TPM values for all samples.

growth_protocol: WT and SUZ12 KO HeLa-S3 cells were grown in Dulbecco’s Modiﬁed Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNA samples were extracted by Trizol (Life Tech). Barcoded RNA-seq libraries were constructed using NEBNext ultra II directional RNA library prep kit for Illumina according to the manufacturer’s instructions (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa


title: WT-DN1_BC_15


title: RNAseq tailbud 6 somite mat del rep2 female

value: Tailbud from E8-8.5 embryo

value: 6 somites

value: Smchd1[del/+] (maternally deleted)


title: HeLa_WT_RNA_seq

description: WT

value: WT


title: ChIPseq_H2A.Z_bte1_rep2

description: H2A.Z-ChIP from bte1 mutant rep2


title: RNAseq tailbud 6 somite wt rep4 female

value: Smchd1[fl/+] (wild-type)

value: C57BL/6/Cast F1


title: HeLa_WT_H3K27me3_BS_seq

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Bismark v0.19.0 was used to align reads to a reference genome (hg38/mm10) and extract the coverage depth and methylation level of each cytosine
Genome_build: mm10;hg38
Supplementary_files_format_and_content: Coverage files (using 1-based genomic genomic coordinates) that feature methylated and unmethylated counts.

molecule: other

growth_protocol: HeLa-S3 cells were grown in Dulbecco’s Modiﬁed Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
100 ng H3K27me3 ChIP DNA was end-repaired, dA-tailed, and ligated with methylated adaptors. Then a quarter of the sample was amplified by PCR to obtain ChIP-seq library. The rest three quarters of the sample with 1% lambda DNA spike-in sheared by Bioruptor sonicator to size of 400 to 500 bp in length were for bisulfite conversion using an EpiTect fast bisulfite conversion kit (Qiagen), ten minutes were used in both conversion steps.
Bisulfite-converted DNA was then amplified by PCR to obtain the final library. The H3K27me3-BS-seq library was subjected to pair-end (150 bp) sequencing on a Novaseq instrument (Illumina).

value: H3K27me3(Cell Signaling, cat#9733)


title: RNAseq tailbud 6 somite wt rep3 female


title: HeLa_SUZ12_KO_1_RNA_seq


title: WT-DN1_BC_12


title: ChIPseq_H2A.Z_WT_rep3

description: H2A.Z-ChIP from WT rep3

data_processing:
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using bowtie2 (version 2.3.3) with default parameters.
Peak calling was performed using MACS2 (version 2.2.5) with the following parameters: --keep-dup 1 --gsize 1.2e8 --qvalue 0.05.
The alignments were converted to bigWig files using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Supplementary_files_format_and_content: peak text files

value: total seedlings

value: 9-day-old seedlings grown under continuous white light


title: HeLa_SUZ12_KO_2_WGBS

extract_protocol:
Genomic DNA (500 ng) with 1% lambda DNA spike-in was sheared by Bioruptor sonicator to an average size of 350 bp in length. DNA was then end-repaired, dA-tailed, and ligated with methylated adaptors according to the manufacturer’s instruction (NEBNext Ultra DNA Library Prep Kit for Illumina #E7645S). Bisulfite conversion was carried out using an EpiTect fast bisulfite conversion kit (Qiagen) according to the manufacturer’s instructions. Twenty minutes were used in both conversion steps.
Bisulfite-converted DNA was then amplified by PCR to obtain the final library. The WGBS libraries were subjected to pair-end (150 bp) sequencing on a Novaseq instrument (Illumina).


title: RNAseq tailbud 6 somite mat del rep1 female


title: RNAseq tailbud 6 somite wt rep1 female


title: ChIPseq_H2A.Z_WT_rep2

description: H2A.Z-ChIP from WT rep2

value: H2A.Z (ABE1348, Millipore)


title: ChIPseq_H2A.Z_WT_rep1

description: H2A.Z-ChIP from WT rep1


title: ChIPseq_H2A.Z_bte1_rep1

description: H2A.Z-ChIP from bte1 mutant rep1

value: bte1 mutant


title: WT-DN1_BC_10

value: wild type

value: thymus


title: WT-DN1_BC_11

value: 6~8 wks


title: SampleID_2: Gain of Function (GOF) third instar larval brain data

city: Göteborg

first: Vimala

last: Anthonydhason

address: Medicinaregatan 9 a-b

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

data_processing:
Cellranger
Seurat and Scanpy
Assembly: Drosophila melanogaser
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Drosophila melanogaster

source_name: wandering 3rd instar larval brain

extract_protocol: Libraries prepared using the normal workflow for Single Cell 3´ v3 libraries (10X Genomics).

value: brain

value: wandering 3rd instar larval brain

value: GOF


title: RNAseq tailbud 6 somite wt rep2 female

value: Tailbud from E8-8.5 embryo

value: F


title: HeLa_SUZ12_KO_1_WGBS

value: HeLa


title: SampleID_1: Wild type (WT) third instar larval brain data

value: WT


title: N-1

status: Public on Jun 26 2022

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: serum N-1

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: female

tag: condition

value: normal placenta


title: PE-3

source_name: serum PE-3

value: preeclampsia


title: N-3

source_name: serum N-3


title: HeLa_WT_WGBS


title: PE-2

source_name: serum PE-2


title: N-2

source_name: serum N-2


title: PE-1

source_name: serum PE-1


title: MOLT4 cells, 955 0.1 uM, 1 h, Rep3

city: Gainesville

first: Dongwen

last: Lyu

state: FL

address: Basic Science Building, BG-003F, 1345 Center Drive

institute: UF

data_processing:
Raw fastq data were analyzed by using Galaxy (https://usegalaxy.org/)
Human genome (hg38) was used as the reference genome.
Differentially expressed gene was analyzed by using DESeq2 based on a false-discovery rate–adjusted q-value (q< 0.05).
Genes with more than 2-fold change were selected for further analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include logFC, logCPM, F, p, and FDR values for each sample

growth_protocol: MOLT4 cells were cultured in RPMI 1640 medium (Cat No. 22400-089, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS, Cat. No. S11150H, Atlanta Biologicals, Flowery Branch, GA, USA), 100 U/mL penicillin and 100 µg/mL streptomycin (Pen-Strep, Cat. No. 15140122, Thermo Fisher Scientific). The cells were maintained in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Cat. No. 74134).
RNA libraries for RNA-seq were prepared using BGI mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: MOLT4 cells were treated with DMSO, 0.1 uM 955 or 1 uM SNS-032 for the indicated times.

value: T lymphoblast cells

tag: treatment

tag: time

value: 1 h


title: MOLT4 cells, 955 0.1 uM, 6 h, Rep2

value: 6 h


title: MOLT4 cells, SNS-032 1 uM, 6 h, Rep2

value: SNS-032 1 uM


title: MOLT4 cells, 955 0.1 uM, 6 h, Rep3


title: MOLT4 cells, DMSO, 6 h, Rep3

value: DMSO


title: MOLT4 cells, SNS-032 1 uM, 6 h, Rep3


title: MOLT4 cells, 955 0.1 uM, 1 h, Rep2


title: MOLT4 cells, DMSO, 6 h, Rep2


title: P4-tumor

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

hyb_protocol: RNA was prepared, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were hybridized, washed, and stained in Affymetrix fluidics station according to manufacturer's protocols.

data_processing: Raw data (CEL files) were processed using the R package oligo (v1.60.0) and further processed using Robust Multichip Average algorithm.

label: biotin

source_name: Tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: As per manufacturer (Affymetrix)

tag: patient

tag: disease state

value: Colorectal cancer


title: MOLT4 cells, 955 0.1 uM, 6 h, Rep1


title: MOLT4 cells, SNS-032 1 uM, 6 h, Rep1


title: P4-normal

source_name: Normal


title: MOLT4 cells, 955 0.1 uM, 1 h, Rep1


title: P4-metastasis

source_name: Metastasis


title: MOLT4 cells, DMSO, 6 h, Rep1


title: P3-tumor-t8


title: P3-normal


title: P3-tumor-t7


title: genomic DNA from lung normal tissue

type: genomic

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

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

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

data_processing:
BeadStudio software v3.2
Average Beta or normalized (provide the normalization method) Average Beta

label_protocol: Standard Illumina Protocol

growth_protocol: Store in formalin.

extract_protocol: Genomic DNA was extracted and purified from human lung samples using Axygen genomic DNA purification Kit according to standard instructions

value: lung


title: P3-tumor-t4


title: P3-tumor-t6


title: P127

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: Whole blood samples were obtained from 15 pediatric COVID-19 cases with no evidence of MIS-C

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting. Briefly, 600 ng of DNA of the studied samples was used to hybridize the BeadChip 850K microarray and scanned using HiScan SQ system (Illumina)

data_processing:
Raw signal intensity data were initially QC’d and preprocessed from resulting idat files in R statistical environment (v4.0.3) using minfi Bioconductor package (v1.36.0). A number of quality control steps were applied to minimize errors and remove erratic probe signals, such as failed probes (probes with detection P value > 0.01 in at least 10% of samples were removed. If probe P value > 0.01 in less than 10% of samples, the Beta values of those probes in the failed samples were marked as NAs and later imputed using the median), cross-reacting probes, and probes that overlapped SNPs within ±1 bp of CpG sites, followed by background correction and dye-based normalization using ssNoob algorithm (single-sample normal-exponential out-of-band). All analyses were performed under R statistical environment (v4.0.3)
Minfi (v1.36.0) preprocessNoob (single-sample) normalized Average Beta

label: Cy5 and Cy3

source_name: High molecular weight DNA extracted from whole blood samples

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: whole blood

tag: group

tag: biological sex

value: Male

tag: age (years)


title: P126

tag: tissue


title: P3-tumor-t5


title: P2-normal


title: P3-tumor-t3


title: P3-tumor-t1


title: genomic DNA from lung tumor tissue


title: mCRC_076

city: BARCELONA

first: Leire

last: Pedrosa

address: Carrer del Villarroel 170

institute: IDIBAPS

hyb_protocol: Gene Expression RNA CodeSet Hybridization Protocol MAN-10056: Prepare Master Mix adding 70uL of Hybridization Buffer to the tube containing the 42uL of Reporter CodeSet. Add 8 μL of Master Mix to each well of a strip tube, Add 5 µL of sample to each tube containing Master Mix. Mix the Capture ProbeSet tube by inverting or flicking, and briefly spin down the contents. Add 2 μL of Capture ProbeSet to each tube. Cap the strip tubes tightly and mix. Spin briefly and immediately place the tubes in a pre-heated 65°C thermal cycler. Incubate hybridization reactions for 16 hours. Incubate at 4°C and read.

scan_protocol: nCounter Prep Station using nCounter Analysis System User Manual (MAN-C0035), nSolver software

data_processing: The raw data were analyzed with nSolver software. Only the samples that passed the control quality were normalized by nSolver, using default settings and taking into account the positive and negative probes and the housekeeping genes in the panel

source_name: tumour tissue

label_protocol: pathology of study (mCRC) and the order to RNA extraction

extract_protocol: High Pure FFPET RNA isolation kit, Roche

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

value: IV

tag: primary surgery

value: Yes

tag: surgery

value: Right hemicolectomy

tag: date of surgery

tag: adjuvancy

value: No

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

value: FOLFOX

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

value: FOLFIRI-BEV

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: KRAS, TP53

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: high


title: mCRC_077

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Abdominal resection

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: treatment

value: FOLFIRI-AFLI

value: Alive

tag: genotype

value: low


title: P125

tag: tissue

value: whole blood

tag: group

tag: biological sex

tag: age (years)


title: P3-tumor-t2

tag: patient

tag: disease state

value: Colorectal cancer


title: P2-tumor


title: P124

value: Male

value: 0 (4 days)


title: P2-metastasis


title: P1-normal


title: P3-metastasis


title: P123


title: mCRC_075

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Transverse

tag: localization (right or left)

value: right

tag: state at diagnosis

value: IV

tag: primary surgery

value: No

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: Yes

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

value: FOLFOX

tag: response

value: Estable

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

value: CTNB1, KRAS, SMAD4, TP53

tag: number of mutations

tag: mss

tag: gemcad classification


title: P1-tumor

tag: patient

tag: disease state


title: P122

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: P1-metastasis


title: P118


title: P119


title: mCRC_072

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Parcial Response

value: FBXW7, KRAS, TP53

tag: genotype

value: MSS


title: mCRC_073

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Right hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: CIR

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Alive

tag: date of last follow up

tag: mutations

value: BRAF, MET, SMAD4

tag: number of mutations

tag: mss

value: MSI

tag: gemcad classification

value: intermediate


title: mCRC_074

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: right

value: IV

value: No

tag: metastasis

tag: liver metastasis

value: Yes

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: BSC

value: Dead

value: KRAS

tag: genotype

value: high


title: P116

tag: tissue

value: whole blood

tag: group

tag: biological sex

value: Male

tag: age (years)


title: mCRC_071

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

value: FOLFOX

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

value: IRI

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: mCRC_070

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Subtotal colectomy

tag: date of surgery

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Estable

value: IRI-BEV

value: KRAS, PTEN, TP53

tag: genotype


title: P120

tag: tissue

tag: group

tag: biological sex

value: Female

tag: age (years)


title: mCRC_069

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

value: Abdominal resection

tag: date of surgery

tag: adjuvancy

value: No

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification


title: mCRC_068

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: date of surgery

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Dead

value: WT

tag: genotype

value: high


title: P112

description: Whole blood samples and clinical data from 43 patients with MIS-C were retrospectively collected between April 16th, 2020 and August 17th, 2021 from seven Hospitals in Spain. MIS-C was diagnosed based on the case definition provided by the World Health Organization

tag: tissue

value: whole blood

tag: group

value: MIS-C

tag: biological sex

tag: age (years)


title: P111

description: Whole blood samples were obtained from 69 healthy children and adolescents collected during the pre-COVID-19 era (before December 2019)

value: Control


title: P109

value: Female


title: mCRC_062

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Descending

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Left hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: FOLFOX

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

value: CIR

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Alive

tag: date of last follow up

tag: mutations

value: PIK3CA, TP53

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: intermediate


title: mCRC_064

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

value: Right hemicolectomy

tag: date of surgery

value: No

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Not evaluated

value: FOLFOX-PAN

tag: genotype


title: P107

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: mCRC_066

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

value: FOLFIRI-AFLI

tag: status

value: Dead

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification

value: high


title: P121

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: P106


title: mCRC_067

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: XELOX

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: CIR

value: RF

tag: genotype

value: MSS

value: intermediate


title: mCRC_065

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Descending

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

value: Total colectomy

tag: date of surgery

value: FOLFOX

tag: number of liver metastasis

tag: extrahepatic metastasis

value: No

value: FOLFIRI-BEV

tag: response

value: Progression

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

value: BRAF, ERB4, SMAD4, TP53

tag: number of mutations

tag: mss

tag: gemcad classification


title: P104

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: mCRC_057

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

value: IV

tag: primary surgery

tag: surgery

value: Right hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: BSC

value: Not evaluated

value: Dead

value: KRAS, PIK3CA, SMAD4, TP53

tag: genotype

value: high


title: P115

tag: tissue

tag: group

tag: biological sex

value: Male

tag: age (years)


title: mCRC_053

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

value: Left hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: FOLFOX

tag: metastasis

tag: liver metastasis

value: No

tag: number of liver metastasis

tag: extrahepatic metastasis

value: FOLFOX-CET

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Alive

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: intermediate


title: P114

tag: tissue

value: whole blood

tag: group

tag: biological sex

value: Female

tag: age (years)


title: mCRC_063

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Estable

value: FOLFIRI-AFLI

tag: genotype

value: low


title: P113

tag: tissue

tag: group

tag: biological sex

value: Male

tag: age (years)


title: mCRC_061

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: Yes

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: NRAS

tag: number of mutations

tag: mss

tag: gemcad classification

value: high


title: mCRC_059

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Right hemicolectomy

tag: date of surgery

value: No

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: FOLFOX

value: Parcial Response

value: KRAS, NRAS, TP53

tag: genotype


title: P110

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: mCRC_050

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

value: FOLFOX-CET

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

value: WT

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: P117

tag: tissue

tag: group

tag: biological sex

value: Male

tag: age (years)


title: P101


title: P105


title: mCRC_048

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

value: Yes

tag: surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: CAPECITABINA

value: RF

value: Alive

value: KRAS, PIK3CA

tag: genotype

value: low


title: mCRC_058

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Right hemicolectomy

tag: date of surgery

value: No

tag: number of liver metastasis

tag: extrahepatic metastasis

value: BSC

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: BRAF, PIK3CA

tag: number of mutations

tag: mss

value: MSI

tag: gemcad classification

value: high


title: mCRC_060

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

value: left

value: III

value: Sigmoidectomy

tag: adjuvancy

tag: tipe of adjuvancy

value: FOLFOX

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: CIR

tag: genotype

value: MSS

value: intermediate


title: P96

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: mCRC_055

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

value: IV

tag: primary surgery

value: No

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: Yes

tag: number of liver metastasis

tag: extrahepatic metastasis

value: FOLFOX-BEV

tag: response

value: Estable

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

value: BRAF, FBXW7, PIK3CA, SMAD4

tag: number of mutations

tag: mss

tag: gemcad classification


title: P108

tag: tissue

tag: group

tag: biological sex

value: Male

tag: age (years)


title: mCRC_045

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Descending

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Left hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Not evaluated

value: FOLFIRI-BEV

value: Alive

value: KRAS, TP53

tag: genotype


title: mCRC_054

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Right hemicolectomy

tag: date of surgery

tag: number of liver metastasis

tag: extrahepatic metastasis

value: BSC

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: KRAS

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: high


title: mCRC_052

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

value: IV

value: No

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: Yes

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: BRAF, TP53

tag: genotype


title: P98

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: mCRC_044

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

tag: primary surgery

tag: surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

value: FOLFOX

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification

value: intermediate


title: P103

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: P94


title: P102


title: P93


title: mCRC_056

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Estable

value: Dead

tag: genotype


title: mCRC_051

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Abdominal resection

tag: date of surgery

value: CAPECIT

tag: number of liver metastasis

tag: extrahepatic metastasis

value: ND

value: FOLFOX-PAN

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Alive

tag: date of last follow up

tag: mutations

value: WT

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: P90

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: P99

value: Female


title: P100


title: mCRC_042

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

value: Yes

tag: surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: lung metastasis

value: No

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: FOLFOX

value: Complete Response

value: KRAS, TP53

tag: genotype

value: intermediate


title: mCRC_049

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: surgery

value: Sigmoidectomy

tag: date of surgery

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

value: CAP-BEV

tag: status

value: Dead

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification


title: P88

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: P89


title: mCRC_047

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: cea

tag: treatment

value: Estable

value: FOLFIRI-BEV

value: KRAS

tag: genotype

value: MSS

value: high


title: P85

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: P95


title: mCRC_046

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

value: Yes

tag: surgery

tag: date of surgery

tag: adjuvancy

value: No

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

value: BSC

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

value: WT

tag: number of mutations

tag: mss

tag: gemcad classification


title: mCRC_036

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: date of surgery

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX

value: KRAS, TP53

tag: genotype


title: P92

tag: tissue

tag: group

tag: biological sex

value: Male

tag: age (years)


title: mCRC_043

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Abdominal resection

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: cea

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: KRAS, SMAD4, TP53

tag: number of mutations

tag: mss

tag: gemcad classification

value: intermediate


title: P97

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: P91


title: mCRC_041

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

value: No

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: Yes

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: BRAF, FBXW7, MAPK2

tag: genotype

value: MSS

value: high


title: mCRC_035

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma and rectum

tag: localization (right or left)

tag: state at diagnosis

value: II

tag: primary surgery

tag: surgery

value: colectomía total

tag: date of surgery

tag: extrahepatic metastasis

tag: cea

value: FOLFOX

tag: response

value: Complete Response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Alive

tag: date of last follow up

tag: mutations

value: NRAS, TP53

tag: number of mutations

tag: mss

tag: gemcad classification