title: M_51N [16-51N]

city: Sheffield

first: Nicola

last: Nadeau

address: Western Bank

department: Ecology and Evolutionary Biology

institute: The University of Sheffield

data_processing:
Quality control: Low quality reads (PHRED <33) removed + Illumina adapters clipped (Trimmomatic v. 0.38)
Read Alignment: Trimmed reads aligned to Heliconius reference genomes  (HISAT2 v. 2.1.0)
BAM file generation: Output aligned files sorted and converted to BAM (samtools v. 1.9)
transcript assembly + read quantification: Transcript assembly and read quantification (StringTie version 1.3.5)
Creation of gene count matrix: Gene count matrix designed for EdgeR were created using the python script ‘prepDE.py’ (provided by StringTie)
Genome_build: Heliconius_erato_demophoon_v1
Supplementary_files_format_and_content: Raw counts of reads for all genes and all individuals provided as a matrix

organism: Heliconius erato cyrbia

source_name: wing tissue

growth_protocol: captive populations of butterflies maintained at 25◦C, fed Passiflora biflora

extract_protocol:
QIAgen RNeasy
TruSeq v2 kit

value: anterior-Hindwing

value: Male

tag: %development

tag: individual id


title: D5C6HNJQ-SUR

status: Public on Dec 10 2021

type: RNA

city: Barcelona

first: Fernando

last: Salvador Gómez

address: Balmes 89, 3º 7

country: Spain

institute: SOLTI

description: A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA). Data were log2 transformed and normalized using the housekeeping genes.

hyb_protocol: NOT PROVIDED

scan_protocol: NOT PROVIDED

data_processing: Data were normalized using 5 housekeeping genes (ACTB, MRPL19, PSMC4, RPLP0, and SF3A1), and log2 transformed

label: NOT PROVIDED

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor

label_protocol: NOT PROVIDED

extract_protocol: At baseline, a section of the formalin-fixed paraffin-embedded (FFPE) breast tissue was examined with haematoxylin and eosin (H&E) staining to confirm the presence of invasive tumor cells and to determine the minimum tumor surface area. For samples obtained at Cycle 2 Day 1, those without invasive tumor cells were also profiled. For RNA purification (High Pure FFPET RNA isolation kit, Roche, Indianapolis, IN, USA), at least 1–5 10 μm FFPE slides were used for each tumor specimen, and macrodissection was performed (when needed) to avoid contamination with normal breast tissues. A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA).

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age

tag: er

tag: pr


title: U87 IFNg Expt 1 Duplicatet 2

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

description: RNA expression value derived from Transcriptome Analysis Console software

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data analysis was performed using the Affymetrix software, Transcriptome Analysis Console (TAC) version 4.0

label: biotin

source_name: human glioblastoma

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: U87 cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum and 100 units/ml penicillin as well as 100 ug/ml strepmycin. The IDO1-O/E U87 cells were cultured using the same medium with additional puromycin (1ug/ml) to maintain IDO1 overexpression. Both cell lines are cultured at 37 oC with 5% CO2.

extract_protocol: After the incubation, cells were lysed using RNA Lysis Buffer from the PureLink RNA Mini Kit (Thermo Fisher Scientific, catalog# 12183020)

treatment_protocol: Cells were transfected with 20 nM siRNA using either Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific, catalog# 13778030) or jetPRIME siRNA transfection reagent (Polyplus-transfection) according to the product manual, followed by 100 ng/ml human IFNg treatment (Shenandoah Biotechnology, SKU# 100-77-100ug).

tag: tissue

value: brain

tag: Sex

value: male


title: BLISS_Dox_merged

type: SRA

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

library_source: transcriptomic

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1
barcodes used as follows: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC
reads were aligned with Bowtie2 v2.3.4.1 to hg19
reads were filtered with bedtools intersect v2.26.0
reads were counted for specific regions using the R package exomeCopy v1.18.0
density plots were generated using the R package metagene2 v3.10
Genome_build: hg19
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: SH-EP-MYCNER shEXOSC10

growth_protocol: SH-EP-MYCNER cells stably expressing a Dox-inducible shRNA against EXOSC10 were grown in RPMI-1640 (Thermo Fisher Scientific), supplemented with 10% fetal calf serum (Capricorn Scientific) and 1% penicillin/streptomycin (Sigma Aldrich).

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol. Barcodes used as follows: EtOH: CATCACGC, 4-OHT: GTCGTTCC, Dox: TGATGATC, Dox_4-OHT: ACGACATC

treatment_protocol: Cells were treated with Dox (1 µg/ml) and/or 4-OHT (100 nM) for 96 h

tag: treatment (etoh or 4-oht)

value: EtOH

tag: treatment (etoh or dox)

value: Dox (1 µg/ml)


title: 204088150164_R02C01

type: genomic

city: Boston

first: Olivia

last: Okereke

state: MASSACHUSETTS

address: One bowdoin square, room no. 745

institute: Massachusetts General Hospital

description: Additional sample characteristics of  baseline and follow-up (values: 1=yes, 0=No) were added to reflect baseline sample and 2-year follow-up sample respectively.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadArray technology (Methyl850K chip) using standard Illumina protocol

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

data_processing: Minfi bioconductor package

label: Cy5 and Cy38

molecule: genomic DNA

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood leukocytes (buffy-coat cryotubes had been stored in the vapor phase of liquid nitrogen freezers at ≤−130°C for later use) using the QIAamp® DNA Blood Mini Kit (Qiagen Inc., Valencia, CA), and PicoGreen DNA quantitation was performed using a Molecular Devices 96-well spectrophotometer.

value: peripheral blood leucocytes

tag: gender

value: female

tag: disease status

value: Case

tag: race /ethnicity

value: Non-Hispanic white

tag: baseline

tag: follow-up


title: U87 NT Expt 1 Duplicate 2


title: D5C6HNJQ-2W


title: U87 IFNg Expt 1 Duplicatet 1


title: D5C6HNJQ-SCR

value: Yes

value: Positive

value: Negative


title: BLISS_4-OHT_merged


title: U87 NT Expt 1 Duplicate 1


title: M_50I [13-50I]

middle: J

country: United Kingdom

value: Forewing + posterior Hindwing

tag: %development


title: M_44N [4-44N]

tag: individual id


title: 43BNQ9CW-2W

tag: cellularity


title: KKMFHZEI-2W

tag: tumor infiltrating lymphocytes (tils)


title: MVV2GLYR-SUR

tag: pcrb


title: 4sU_KU-60019.merged

description: nascent RNA

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.2.7. and normalized to the sample with the spike in control (mm10) except for MYCN ChIPseq, which was read normalized
For 4sU-seq, reads were mapped to hg19 with  Bowtie2,  reads mapping to rRNA,exons and blacklist regions were removed, and then normalized based on read depth, except for no chase 4sUseq, which was normalized to spike in control (mm10)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

source_name: SH-EP-MYCNER

growth_protocol: SH-EP-MYCNER cells stably expressing Dox-inducible shRNAs against EXOSC10, TCEA1 or DCP1A were grown in RPMI-1640 (Thermo Fisher Scientific), supplemented with 10% fetal calf serum (Capricorn Scientific) and 1% penicillin/streptomycin (Sigma Aldrich).

extract_protocol:
SH-EP-MYCNER cell lysates were spiked with 4sU-treated mouse T-cell lysates for the no chase 4sU. Total RNA was isolated using QIAzol and purified with miRNeasy columns and biotinylated. This was followed by  4sU-RNA pulldown pulldown using streptavidin-MyOne beads, followed by purification with RNA minElute columns (Qiagen)
4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 10-14 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform.

treatment_protocol: For shRNA experiments, cells were treated for 72 h with Dox (1 µg/ml) before adding 4-OHT (200 nM) for 4 h. For the ATM inhibition 4sU, cells were treated for 4 h with 4-OHT (200 nM) and/or KU-60019 ATM inhibitor (100 nM). For all 4sU experiments, 4sU (500 µM) was added in the last 20 min of treatment.

tag: treatment (etoh ordox)

tag: treatment (dmso or ku-60019)

value: KU-60019 ATM inhibitor (100 nM)

tag: label

value: 20min 4sU

tag: antibody


title: KKMFHZEI-SCR

value: No

tag: age

tag: er

tag: pr


title: 204088150163_R06C01

label: Cy5 and Cy34

tag: tissue

tag: gender

value: Control


title: M_44I [3-44I]

tag: Sex

value: Male


title: 4sU_KU-60019_4-OHT.merged

description: nascent RNA

tag: treatment (etoh or 4-oht)


title: 4sU_4-OHT.merged

description: nascent RNA

value: DMSO


title: M_43N [2-43N]

value: anterior-Hindwing


title: 204088150163_R07C01

label: Cy5 and Cy35

value: male

tag: disease status

tag: race /ethnicity

tag: baseline

tag: follow-up


title: BLISS_Dox_4-OHT_merged

tag: treatment (etoh or dox)

value: Dox (1 µg/ml)


title: M_43I [1-43I]

tag: %development

tag: individual id


title: 4DG1B0AA-2W

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb


title: M_51I [15-51I]


title: 204088150164_R01C01

label: Cy5 and Cy37

value: peripheral blood leucocytes

value: Unsure

tag: age


title: BLISS_EtOH_merged

value: EtOH


title: 4sU_DMSO_EtOH.merged

description: nascent RNA

tag: treatment (etoh ordox)

tag: treatment (dmso or ku-60019)

tag: label

tag: antibody


title: 204088150164_R03C01

label: Cy5 and Cy39

tag: tissue

tag: gender

value: female

value: Case

value: Non-Hispanic white


title: 204088150163_R08C01

label: Cy5 and Cy36

tag: disease status


title: M_50N [14-50N]

tag: Sex


title: M_28N [24-28N]


title: 204088150164_R04C01

label: Cy5 and Cy40

tag: race /ethnicity

tag: baseline


title: M_28I [23-28I]

value: Forewing + posterior Hindwing


title: ChIPRX_pSer2RNAPII_shDCP1A_4-OHT_R2

library_source: genomic

source_name: SH-EP-MYCNER shDCP1A

extract_protocol:
Cells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. DNA fragments were amplified by 12 to 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

tag: treatment (etoh or 4-oht)

value: RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, ab5095


title: ChIPRX_pSer2RNAPII_shDCP1A_EtOH_R2


title: F_25N [22-25N]

value: Female

tag: %development


title: 204088150163_R02C01

label: Cy5 and Cy30

tag: follow-up


title: 7090UB1S-SUR

tag: cellularity

tag: er

tag: pr


title: 204088150163_R05C01

label: Cy5 and Cy33

tag: age


title: 7090UB1S-2W

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb


title: F_25I [21-25I]

tag: individual id


title: 4DG1B0AA-SUR


title: 204088150163_R04C01

label: Cy5 and Cy32


title: 204088150164_R06C01

label: Cy5 and Cy42


title: 7090UB1S-SCR

value: No

value: Positive

value: Negative


title: F_27N [28-27N]


title: F_27I [27-27I]


title: 204088150113_R06C01

label: Cy5 and Cy26


title: 4DG1B0AA-SCR


title: ChIPRX_totalRNAPII_shDCP1A_Dox_R2

tag: treatment (etoh ordox)

tag: treatment (dmso or ku-60019)

tag: label

tag: antibody

value: Pol II antibody (A-10), Santa Cruz Biotechnology, sc-17798


title: NMRIXFYI-SUR


title: 204088150163_R01C01

label: Cy5 and Cy29

tag: tissue

tag: gender

tag: disease status

value: Control


title: ChIPRX_pSer2RNAPII_shDCP1A_Dox_R2

tag: treatment (etoh or 4-oht)


title: Y1K6691V-SCR


title: M_23N [26-23N]

value: anterior-Hindwing

tag: Sex

value: Male

tag: %development


title: NMRIXFYI-2W

tag: cellularity

value: N/A; no information


title: ChIPRX_totalRNAPII_shDCP1A_4-OHT_R2


title: 204088150113_R07C01

label: Cy5 and Cy27

value: peripheral blood leucocytes

tag: race /ethnicity

value: Black

tag: baseline

tag: follow-up


title: 11RLNSX4-2W

tag: tumor infiltrating lymphocytes (tils)

tag: age

tag: er

tag: pr


title: THP-1 cells , rsmY3

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

data_processing:
Basecalls performed using CASAVA version 1.9
Adapters removal with cutadapt software version 1.15
Trimming of the reads using Sickle, with a quality threshold of 20 (-q 20). Reads shorter than 36 nucleotides were removed
The remaining reads were aligned to the Human genome sequence build GRCh38 with STAR assembler and we kept only uniquely mapped reads
Reads count with featureCounts programm (from the Subreads package). We used --primary option and stranded counts (option -s 1)
Differential analysis performed with Sartools version 1.3.0 (DESeq2 methods and "median" option to compute size factors).
Genome_build: GRCh38
Supplementary_files_format_and_content: columns of the TSV result file are tabular separated. This analysis file contains reads count and normalized reads count (norm. ...) for each sample (column 1 to 13). In columns 14 to the end, there are different calculations like fold change, log2 fold change, P-value, adjusted p-value for the comparison between the two conditions (rsmY versus Wt).

organism:
Legionella pneumophila
Homo sapiens

source_name: human THP-1 cells, LprsmY-EVs

growth_protocol: Legionella strains were grown in liquid BYE medium until post-exponential phase (OD 4.2). Human monocyte derived macrophages (THP-1) were cultivated in RPMI 1640+GlutaMAX

extract_protocol:
RNA of THP-1 cells was  extracted using the miRNeasy®Mini kit (Qiagen) and  libraries were constructed according to the manufactures instruction
TruSeq stranded mRNA (Illumina)

treatment_protocol: For Lp-EV purification, Bacterial cells were harvested by centrifugation at 5.000xg, 4°C for 15 min and the supernatant was twice passed through a 0.2µm PES membrane Stericup® Quick Release (Millipore) and re-centrifuged for 15min at 15.000xg, 4°C. The supernatant was treated with RNaseA/T1 (Thermo Scientific) at a final concentration of 2µg/ml RNaseA for 1h at 37°C followed by centrifugation at 150.000xg for 2h at 4°C to pellet the MVs. The MV-pellet was washed, re-centrifuged and resuspended in PBS. THP-1 cells were incubated for 3h with purified Lp-EVs or not at an MOI of 10 according to flow cytometry quantification.

tag: cell line

value: human THP-1 cells

tag: cell type

value: human monocyte derived macrophages

tag: treatment

value: experiment delta-rsmY Lp-Evs


title: ChIPRX_pSer2RNAPII_shDCP1A_Dox_4-OHT_R1

tag: treatment (etoh ordox)

value: Dox (1 µg/ml)

tag: treatment (dmso or ku-60019)

tag: label

tag: antibody


title: 11RLNSX4-SCR

tag: pcrb


title: 204088150113_R08C01

label: Cy5 and Cy28

tag: tissue

tag: gender

value: female

tag: disease status

value: Case


title: 204088150113_R04C01

label: Cy5 and Cy24

value: male

tag: race /ethnicity

value: Non-Hispanic white

tag: baseline


title: 204088150113_R05C01

label: Cy5 and Cy25

tag: follow-up


title: THP-1 cells , rsmY2


title: 4J3PEG02-SUR

label: NOT PROVIDED

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: age


title: 204088150113_R01C01

label: Cy5 and Cy21


title: ChIPRX_pSer2RNAPII_shDCP1A_Dox_4-OHT_R2

tag: treatment (etoh or 4-oht)

value: RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, ab5095


title: 204088150113_R03C01

label: Cy5 and Cy23


title: 4J3PEG02-2W

tag: er

tag: pr


title: ChIPRX_total/pSer2RNAPII_shDCP1A_input_R2

tag: treatment (etoh ordox)


title: ChIPRX_pSer2RNAPII_shDCP1A_Dox_R1

value: EtOH

tag: treatment (dmso or ku-60019)


title: 204088150163_R03C01

label: Cy5 and Cy31


title: THP-1 cells , wt3

source_name: human THP-1 cells, Lpwt-EVs

tag: cell line

tag: cell type

tag: treatment

value: experiment wt Lp-Evs


title: ChIPRX_totalRNAPII_shDCP1A_EtOH_R2

tag: label

tag: antibody

value: Pol II antibody (A-10), Santa Cruz Biotechnology, sc-17798


title: THP-1 cells , wt2


title: THP-1 cells , rsmY1


title: 4J3PEG02-SCR

tag: pcrb

value: No

value: Positive

value: Negative


title: 204088150112_R07C01

label: Cy5 and Cy19

tag: tissue

value: peripheral blood leucocytes

tag: gender

tag: disease status

value: Control

tag: race /ethnicity


title: ChIPRX_total/pSer2RNAPII_shDCP1A_input_R1


title: ChIPRX_pSer2RNAPII_shDCP1A_EtOH_R1


title: ChIPRX_totalRNAPII_shDCP1A_Dox_4-OHT_R1


title: ChIPRX_totalRNAPII_shDCP1A_Dox_R1


title: B. bronchiseptica inside amoeba [AB2]

city: Athens

first: Longhuan

last: Ma

state: Georgia

address: 500 D. W. Brooks Dr.

department: Infectious Diseases

institute: University of Georgia

data_processing:
Preparation of the Illumina sequencing library included depletion of ribosomal RNA from each sample.
Filtering of low-quality reads and trimming of Illumina library adapters were performed using FASTQC and TRIMMOMATIC.
High quality reads were mapped to the genome of B. bronchiseptica RB50 genome assembly NC_002927.3 using “Bowtie2”.
Differential gene expression between two replicates each of intracellular B. bronchiseptica and controls were evaluated using the “EdgeR” package for R implemented in the Bioconductor project.
Genome_build: NC_002927.3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bordetella bronchiseptica

source_name: B. bronchiseptica inside amoeba

growth_protocol: B. bronchiseptica were incubated with unicellular D. discoideum, and a subset of the bacteria wereas incubated in HL/5 medium without amoeba as the negative control. After 2 h of gentamicin treatment, the HL/5 was removed, the unicellular amoebae were washed with PBS, and the samples were suspended in 1 ml of TRIzol for RNA extraction.

extract_protocol:
RNA was extracted from the lysates using TRIzol (Ambion) and the Bacterial RNA isolation Kit (Max Bacterial Enhancement Reagent, Ambion) with implemented PureLink DNase treatment (Invitrogen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: sample group

value: intro-amoeba survived bacteria


title: M_23I [25-23I]

value: Forewing + posterior Hindwing

tag: Sex

value: Male

tag: %development

tag: individual id


title: B. bronchiseptica [B3]

source_name: B. bronchiseptica

value: negative control


title: Y6YUG74V-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: age

tag: er

tag: pr


title: B. bronchiseptica inside amoeba [AB1]


title: W7TBDM1X-2W

value: N/A; no information


title: 204088150113_R02C01

label: Cy5 and Cy22

value: Black

tag: baseline

tag: follow-up


title: ChIPRX_totalRNAPII_shDCP1A_Dox_4-OHT_R2

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

value: Dox (1 µg/ml)

tag: treatment (dmso or ku-60019)

tag: label

tag: antibody


title: 204088150112_R06C01

label: Cy5 and Cy18

tag: tissue

tag: gender

value: female

tag: disease status

value: Case

tag: race /ethnicity

value: Non-Hispanic white


title: 204088150112_R03C01

label: Cy5 and Cy15

value: male


title: W7TBDM1X-SCR

tag: pcrb


title: W7TBDM1X-SUR

tag: cellularity


title: B. bronchiseptica [B1]

tag: strain

tag: sample group


title: Y6YUG74V-SUR

tag: tumor infiltrating lymphocytes (tils)

tag: age

tag: er


title: KKMFHZEI-SUR

tag: pr


title: ChIPRX_totalRNAPII_shDCP1A_EtOH_R1

tag: treatment (etoh or 4-oht)

value: EtOH

value: Pol II antibody (A-10), Santa Cruz Biotechnology, sc-17798


title: ChIPRX_totalRNAPII_shTCEA1_Dox_4-OHT_R2

source_name: SH-EP-MYCNER shTCEA1

tag: treatment (etoh ordox)


title: ChIPRX_pSer2RNAPII_shDCP1A_4-OHT_R1

tag: treatment (dmso or ku-60019)

value: RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, ab5095


title: 204088150112_R05C01

label: Cy5 and Cy17

tag: baseline

tag: follow-up


title: Late stage aggregate released cells replicate 1

city: Cambridge

first: Julia

last: Schwartzman

state: MA

address: 15 Vassar St

department: Civil and Environmental Engineering

institute: MIT

data_processing:
Paired-end Illumina reads were trimmed using Trimmomatic (v0.30) to remove sequencing adapters and low quality reads (phred >30)(Bolger et al., 2014).
The remaining paired reads were checked for quality using FastQC (version 0.11.9) (Brown et al., 2017) and mapped to the predicted coding regions of the V. splendidus 12B01 genome (assembly ASM15276v1) using Bowtie2 (v 2.3.4.1)(Langmead and Salzberg, 2012), outputting SAM files.
SAM files were sorted by position using SAMTools (V 1.9) (Danecek et al., 2021), and mapping was parsed using HTSeq (Anders et al., 2015) to obtain count tables.
Genome_build: Genbank Accession # AAMR00000000.1
Supplementary_files_format_and_content: count tables from HTSeq

molecule: polyA RNA

organism: Vibrio splendidus

source_name: Cells released from aggregates

growth_protocol: Incubation temperature was 25°C. For experimental measurements, precultures were established in a defined minimal medium (Amarnath K, et al. 2021. bioRxiv. doi:10.1101/2021.06.24.449802). Minimal medium contained 10 mM ammonium as sole source nitrogen and carbon source indicated. Precultures were grown with 10 mM glucose to an optical density of 0.4-0.6, as measured at 600 nm with a 1 cm path cuvette on a Genesys 20 Spectrophotometer (Thermo Scientific, Waltham, MA), rinsed by pelleting cells at 5000 rcf for 1 min in a tabletop microcentrifuge (Eppendorf, Hamburg, Germany), and resuspended in carbon-free defined minimal medium such that the final was 1.0. Experimental cultures were initiated by inoculating cells to an initial OD of 0.01 in 250 mL borosilicate glass Erelenmeyer flasks containing 70 mL of alginate minimal medium. Low viscosity alginate (Sigma-Aldrich A1112, St. Louis, MO) was added as the medium carbon source at 700 mg/L (0.07% w/v). Shaking was established by orbital rotation of flasks at setting 2 on an orbital shaker (Model 3500, VWR, Radnor, PA), which corresponds to ~100 rpm.

extract_protocol:
A Qiagen RNeasy kit was used to isolate total RNA, following manufacturer’s protocol, except for the following modifications: cells were resuspended in 15 mg/mL lysozyme in TE buffer, and incubated for room temperature for 30 min, prior to addition of buffer RLT. Samples were lysed by mechanical disruption using lysing matrix B (MPBio, Santa Ana, CA). Samples in lysing matrix shaken in a homogenizer (MPBio) for 10X 30 second intervals, taking care to keep samples from heating up. Samples were treated with DNase digestion using a Turbo DNA free DNAse kit (Ambion, Austin, TX), following manufacturer’s instructions. The integrity and purity of total RNA was assessed running a sample on an Agilent 4200 Tapestation in a HS RNA screen tape (Agilent, Santa Clara, CA). Depletion of rRNA was accomplished using the Ribominus Yeast and Bacteria transcriptome isolation kit (Invitrogen, Waltham, MA) and included ethanol precipitation with glycogen to concentrate remaining mRNA.
Ethanol precipitated samples were resuspended in FPF sample buffer from the TruSeq stranded mRNA-Seq kit reagents (Illumina, San Diego, CA). mRNA abundance was quantified using a Quant-iT RNA Assay kit (Invitrogen) on a Tecan Spark plate reader equipped with a monochrometer, following manufacturer’s instructions (Tecan, Männendorf, Switzeland). The quality of the mRNA was further assessed using an Agilent HS tape. We analyzed resulting samples on a Bioanalyzer to confirm mRNA depletion, and concentrated samples using ethanol precipitation with glycogen. Samples were screened for quality by requiring an RNA integrity number (RIN) or more than 8. mRNA remaining from rRNA depletion of 2-10 µg total RNA was used as template to create sequencing libraries. Sequencing libraries were prepared using an Illumina TruSeq Stranded mRNA library preparation kit (Illumina). Libraries were assessed for quality using screen tapes and fluorescence-based plate reader assays prior to pooling.

treatment_protocol: Cultures were grown an indicated stage of self-organization, as defined by microscopy. 30 mL RNA Protect Bacterial Reagent (Qiagen, Hilden, Germany) was added to 15 mL cultures and incubated at 4 °C overnight. Cells were collected by centrifugation at 5000 rcf and 4°C in a Sorvall Legend XIR centrifuge (Thermo Fisher, Waltham, MA), equipped with a Fiberlite F15-6x100g rotor for 30 min. Supernatant was decanted, leaving pelleted cell material which was frozen at -20°C.

tag: carbon source

value: 0.07% w/v alginate

tag: Stage

value: late stage


title: Late stage aggregate released cells replicate 2


title: 204088150112_R04C01

label: Cy5 and Cy16

tag: tissue

value: peripheral blood leucocytes

tag: gender

tag: disease status


title: 204088150112_R08C01

label: Cy5 and Cy20

value: Unsure

value: Control

tag: race /ethnicity


title: 204088150112_R01C01

label: Cy5 and Cy13


title: ChIPRX_totalRNAPII_shTCEA1_input_R2

tag: label

tag: antibody


title: 204088150112_R02C01

label: Cy5 and Cy14


title: N50SBJ07-2W

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb


title: Late stage aggregate shell replicate 3

source_name: Cell aggregates

tag: strain


title: N50SBJ07-SCR

value: No

tag: age

tag: er

value: Positive

tag: pr

value: Negative


title: ChIPRX_totalRNAPII_shTCEA1_Dox_R2

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

tag: treatment (dmso or ku-60019)


title: Late stage aggregate shell replicate 2

tag: carbon source

tag: Stage


title: Late stage aggregate shell replicate 1


title: ChIPRX_totalRNAPII_shTCEA1_EtOH_R2


title: ChIPRX_totalRNAPII_shTCEA1_4-OHT_R2


title: XHOGUOOX-2W

value: N/A; no information


title: Early stage aggregate replicate 3

value: early stage


title: I4I5IDSJ-2W


title: ChIPRX_totalRNAPII_shTCEA1_input_R1


title: 204088150094_R06C01

label: Cy5 and Cy10

tag: tissue

tag: gender

value: female

tag: baseline

tag: follow-up


title: ChIPRX_totalRNAPII_shDCP1A_4-OHT_R1

tag: label

tag: antibody


title: I4I5IDSJ-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)


title: Early stage aggregate replicate 2

tag: strain


title: Early stage aggregate replicate 1


title: 204088150094_R08C01

label: Cy5 and Cy12

tag: disease status

tag: age

tag: race /ethnicity


title: 204088150094_R07C01

label: Cy5 and Cy11


title: ZI3V7CNV-SUR

tag: pcrb

tag: er

tag: pr


title: ChIPRX_totalRNAPII_shTCEA1_Dox_R1

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

value: Dox (1 µg/ml)

tag: treatment (dmso or ku-60019)


title: ChIPRX_totalRNAPII_shTCEA1_4-OHT_R1


title: ChIPRX_totalRNAPII_shTCEA1_EtOH_R1


title: ZI3V7CNV-2W


title: ZI3V7CNV-SCR


title: ChIPRX_totalRNAPII_shTCEA1_Dox_4-OHT_R1


title: YB8OJ57B-SUR


title: 204088150094_R03C01

label: Cy5 and Cy7

tag: tissue

tag: gender

value: Non-Hispanic white


title: ChIPRX_pSer5RNAPII_shEXOSC10_Dox_4-OHT

value: RNA Polymerase II CTD 4H8 (phosph.Ser5), Covance, # MMS-128P


title: XHOGUOOX-SCR

label: NOT PROVIDED


title: 204088150094_R05C01

label: Cy5 and Cy9

tag: baseline

tag: follow-up


title: ChIPRX_pSer5RNAPII_shEXOSC10_4-OHT

value: EtOH

tag: label

tag: antibody


title: 204088150094_R01C01

label: Cy5 and Cy5

value: male

value: Other/Multiple/Unknown


title: ChIPRX_pSer5RNAPII_shEXOSC10_EtOH


title: YB8OJ57B-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)


title: U4URKCL5-SUR


title: ChIPRX_pSer5RNAPII_shEXOSC10_Dox


title: YB8OJ57B-2W


title: U4URKCL5-2W


title: CSMPWKQ0-SUR


title: ChIPRX_pSer2RNAPII_shEXOSC10_Dox_4-OHT

value: RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, ab5095


title: U4URKCL5-SCR


title: ChIPRX_pSer2RNAPII_shEXOSC10_Dox


title: 204088150094_R02C01

label: Cy5 and Cy6

tag: disease status


title: ChIPRX_pSer5RNAPII_shEXOSC10_input


title: 204088150076_R06C01

label: Cy5 and Cy3

tag: age


title: 204088150076_R07C01

value: Case

tag: race /ethnicity


title: CSMPWKQ0-SCR

tag: pcrb


title: CSMPWKQ0-2W

tag: er


title: OV.0946

city: Rochester

first: Julie

last: Cunningham

state: MN

address: 200 First Street SW

department: Department of Laboratory Medicine and Pathology

institute: Mayo Clinic

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data were normalized separately for the two platforms, and batch correction across the two platforms were performed via COMBAT

label: Cy3, Cy5

source_name: Fresh Frozen Tumor

extract_protocol: genomic DNA extraction

value: Female

tag: histology

value: Ovarian Clear Cell Carcinoma (OCCC)

tag: batch

value: ucla


title: 204088150094_R04C01

label: Cy5 and Cy8

value: peripheral blood leucocytes

value: Control


title: 204088150076_R08C01

label: Cy5 and Cy4


title: ChIPRX_pSer2RNAPII_shEXOSC10_EtOH

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)


title: QAO4H8WA-SUR

tag: pr


title: OV.0623

tag: gender


title: ChIPRX_pSer2RNAPII_shEXOSC10_input

tag: treatment (dmso or ku-60019)


title: 204088150076_R04C01

tag: tissue

tag: baseline

tag: follow-up


title: 204088150076_R05C01


title: ChIPseq_MYCN_shEXOSC10_Dox_4-OHT

tag: label

tag: antibody

value: N-Myc Antibody (B8.4.B), Santa Cruz Biotechnology, sc-53993


title: QAO4H8WA-2W

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)


title: OV.0546


title: QAO4H8WA-SCR

value: No

tag: age

value: Positive

value: Negative


title: ChIPseq_MYCN_shEXOSC10_Dox

value: Dox (1 µg/ml)


title: ChIPRX_pSer2RNAPII_shEXOSC10_4-OHT


title: 204088150076_R02C01

tag: disease status

tag: race /ethnicity

value: Non-Hispanic white


title: OV.0756

tag: histology


title: OV.0453

tag: batch


title: A-028 Post

city: Taipei

first: Hsiang-Fong

last: Kao

state: Please Select

address: No.57, Ln. 155, Sec. 3, Keelung Rd.,

department: Medical Oncology

country: Taiwan

institute: National Taiwan University Cancer Center

hyb_protocol: Per Nanostring manufacturer's instruction.

scan_protocol: Digital data acquisition via the nCounter Digital Analyzer (NanoString Technologies) was performed by Cold Spring Biotech Corporation (Taipei, Taiwan).

data_processing: nSolver 4.0 Analysis Software (NanoString Technologies, USA) and R 3.5.0 were used for data analysis.

label: Nanostring

source_name: Head and neck squamous cell carcinoma

label_protocol: nCounter PanCancer Immune Profiling Panel (NanoString Technologies, USA)

growth_protocol: Tissue biopsy from the patient. The biopsy is fixed in formalin-fixed paraffin-embedded specimen.

extract_protocol: Total RNA was isolated and purified using a Qiagen RNeasy FFPE kit (Qiagen, Valencia, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Gene expression was measured using RNA isolated from formalin-fixed paraffin-embedded (FFPE) biopsy tissue using NanoString technology.

tag: disease state

value: Head and neck squamous cell carcinoma

tag: mtap status

value: Unaltered

tag: treatment status

value: Post-treatment

tag: biomaterial

value: tissue biopsy (FFPE)


title: J94AAF6A-2W

tag: pcrb

tag: er

tag: pr


title: ChIPseq_MYCN_shEXOSC10_4-OHT

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

value: EtOH

tag: treatment (dmso or ku-60019)


title: ChIPseq_MYCN_shEXOSC10_EtOH

tag: label

tag: antibody


title: 204088150076_R03C01

tag: tissue

tag: gender

value: male

value: Case

tag: age

tag: baseline

tag: follow-up


title: 204088150076_R01C01

tag: disease status

tag: race /ethnicity


title: 204088150068_R07C01

value: female

value: Other/Multiple/Unknown


title: A-023 Post

description: nCounter PanCancer Immune Profiling Panel

tag: disease state

tag: mtap status

value: Altered

tag: treatment status


title: 1Q2LAXZY-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er


title: ChIPseq_MYCN_shEXOSC10_input.

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)

tag: treatment (dmso or ku-60019)


title: OV.0340

value: Female

tag: histology

value: Ovarian Clear Cell Carcinoma (OCCC)

tag: batch

value: ucla


title: A-018 Post

tag: biomaterial


title: OV.0306

tag: gender


title: 1Q2LAXZY-SUR

value: N/A; no information

tag: age

tag: pr


title: nochase_spiked_4sU_Dox_4-OHT.merged

description: nascent RNA

tag: label

value: 20min 4sU

tag: antibody


title: OV.1264


title: nochase_spiked_4sU_Dox.merged

description: nascent RNA

value: Dox (1 µg/ml)


title: G0SD5Q8E-SCR

value: No

value: Positive

value: Negative


title: 204088150068_R05C01

tag: tissue

value: peripheral blood leucocytes

tag: disease status

tag: race /ethnicity

value: Non-Hispanic white

tag: baseline

tag: follow-up


title: 204088150068_R02C01

value: Control


title: 204088150068_R04C01

value: male


title: OV.0267


title: J94AAF6A-SUR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er


title: OV.0343

tag: histology


title: A-008 Post

tag: disease state

value: Head and neck squamous cell carcinoma

tag: mtap status

value: Unaltered

tag: treatment status

value: Post-treatment

value: tissue biopsy (FFPE)


title: nochase_spiked_4sU_EtOH.merged

description: nascent RNA

tag: treatment (etoh or 4-oht)

value: EtOH

tag: treatment (etoh ordox)

tag: treatment (dmso or ku-60019)


title: J94AAF6A-SCR

tag: age

tag: pr


title: 204088150068_R06C01

tag: tissue

tag: gender

value: female

tag: disease status

value: Case


title: OV.0997

value: Female

value: Ovarian Clear Cell Carcinoma (OCCC)

tag: batch

value: ucla


title: 204088150068_R03C01

tag: race /ethnicity

tag: baseline

tag: follow-up


title: nochase_spiked_4sU_4-OHT.merged

description: nascent RNA

tag: label

value: 20min 4sU

tag: antibody


title: 204088150068_R08C01

value: Other/Multiple/Unknown


title: 204088150068_R01C01


title: OV.0102

tag: histology


title: chase_4sU_merged.Dox.minus/plus_strand

description: nascent RNA

value: Dox (1 µg/ml)


title: 204088140158_R08C01

value: peripheral blood leucocytes

value: Asian


title: 204088140158_R07C01


title: 204088140158_R03C01

value: Control

value: Non-Hispanic white


title: chase_4sU_merged.Dox_4-OHT.minus/plus_strand

description: nascent RNA


title: X1423004172


title: A-004 Post

tag: disease state

value: Head and neck squamous cell carcinoma

tag: mtap status

value: Altered

tag: biomaterial


title: chase_4sU_merged.4-OHT.minus/plus_strand

description: nascent RNA

tag: treatment (etoh or 4-oht)

tag: treatment (etoh ordox)


title: X1507804994


title: A-002 Post

value: Unaltered

tag: treatment status

value: Post-treatment


title: A-029 Pre

value: Pre-treatment

value: tissue biopsy (FFPE)


title: X1507805022


title: A-006 Post


title: A-028 Pre


title: VEYG3HY8-SUR

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age

tag: er

tag: pr


title: YBAQ1HAV-SUR


title: OV.0774

tag: gender

value: Female

tag: batch


title: VEYG3HY8-2W


title: YBAQ1HAV-2W


title: 204088140158_R04C01

tag: tissue

value: female

tag: disease status

tag: race /ethnicity

tag: baseline

tag: follow-up


title: A-027 Pre

tag: disease state

tag: mtap status

tag: biomaterial


title: chase_4sU_merged.EtOH.minus/plus_strand

description: nascent RNA

tag: treatment (etoh or 4-oht)

value: EtOH

tag: treatment (etoh ordox)

tag: treatment (dmso or ku-60019)

tag: label

tag: antibody


title: X1507804997

tag: histology

value: Ovarian Clear Cell Carcinoma (OCCC)


title: 66GZTW15-2W

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age

tag: er

tag: pr


title: X1507805002

tag: gender

tag: batch


title: X1507805020


title: A-023 Pre

tag: disease state

tag: treatment status


title: X1507805004


title: A-025 Pre

tag: mtap status

tag: biomaterial


title: X1507805018


title: YBAQ1HAV-SCR

value: No

value: Positive

value: Negative


title: OH9GMYUH-SUR


title: OH9GMYUH-2W


title: A-022 Pre


title: Adar1fl/fl;Mist1Cre-ERT/+_LD-Tam + HD-Tam_3

city: St. Louis

first: Jose

middle: Bernardo

last: Saenz

state: Missouri

address: 660 S. Euclid Avenue

department: Medicine

institute: Washington University in St. Louis School of Medicine

hyb_protocol: Following fragmentation, cDNA was hybridized using slides with defined attached probes (GeneChip 2.0).

scan_protocol: Gene chips were scanned using the Affymetrix Genechip 3000.

data_processing: Data were processed using the Transcriptome Analysis Console (TAC; Thermo Fisher).

label: biotin

organism: Mus musculus

source_name: Gastric corpus

label_protocol: RNA was submitted to the Genome Technology Access Center at Washington University in St. Louis. cDNA was prepared according to the standard Affymetrix protocol using at least 1 µg RNA per sample using the WT Plus assay.

extract_protocol: The day after the final vehicle/HD-Tam injection, mouse stomachs were harvested, and the gastric corpora were removed and snap-frozen in liquid nitrogen and stored at -80°C until further use. RNA was isolated from tissue sections using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Wild-type C57BL/6 mice were injected with either vehicle for 24 hours or with two daily injections of HD-Tam (5 mg/20 g body weight). In addition, Adar1fl/fl;Mist1Cre-ERT/+ mice were intra-peritoneally injected with 7 consecutive daily injections of low-dose tamoxifen (LD-Tam; 1 mg/20 g body weight). Four days after the last injection, mice were then injected intra-peritoneally daily for 2 consecutive days with either vehicle (10% ethanol in sunflower seed oil) or high-dose tamoxifen (HD-Tam; 5 mg tamoxifen/20 g body weight). All mice were sacrificed one day after the last injection.

tag: tissue

value: Gastric corpus

tag: genotype

tag: treatment

value: HD-Tam


title: Adar1fl/fl;Mist1Cre-ERT/+_LD-Tam + HD-Tam_4


title: Adar1fl/fl;Mist1Cre-ERT/+_LD-Tam + HD-Tam_2


title: Adar1fl/fl;Mist1Cre-ERT/+_LD-Tam + HD-Tam_1


title: VEYG3HY8-SCR


title: A-021 Pre


title: X1507805011


title: Adar1fl/fl;Mist1Cre-ERT/+_LD-Tam + Vehicle_1

value: Vehicle


title: 204088140158_R02C01

value: peripheral blood leucocytes

value: male

tag: disease status

value: Case

tag: race /ethnicity

value: Non-Hispanic white

tag: baseline

tag: follow-up


title: G0SD5Q8E-2W

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb


title: QB0IICMW-SUR

tag: age

tag: er

tag: pr


title: A-009 Post

tag: disease state

value: Head and neck squamous cell carcinoma

value: Post-treatment


title: 204088140158_R01C01

tag: gender


title: A-020 Pre

tag: mtap status

value: Unaltered

tag: treatment status

value: Pre-treatment

value: tissue biopsy (FFPE)


title: QB0IICMW-2W

value: N/A; no information


title: X1507805006

value: Female

tag: histology

value: Ovarian Clear Cell Carcinoma (OCCC)

tag: batch


title: A-012 Post

tag: biomaterial


title: WT + HD-Tam x 48 hours_2

tag: tissue

tag: genotype

value: WT

tag: treatment


title: A-018 Pre


title: X1507805008


title: WT + HD-Tam x 48 hours_1


title: QB0IICMW-SCR

value: No

value: Positive

value: Negative


title: FOLS5DPI-SUR


title: 204088140158_R05C01

value: female

tag: disease status

tag: race /ethnicity

tag: baseline

tag: follow-up


title: A-026 Pre

value: Altered


title: A-017 Pre


title: X1117104593


title: X1117104583


title: WT + Vehicle x 24 hours_2

value: Gastric corpus

value: Vehicle


title: FOLS5DPI-2W

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: age


title: A-016 Pre

tag: disease state


title: X1507805013

tag: gender


title: FOLS5DPI-SCR

tag: er

tag: pr


title: 204088140158_R06C01

value: peripheral blood leucocytes

value: Case

value: Non-Hispanic white


title: Adar1fl/fl;Mist1Cre-ERT/+_LD-Tam + Vehicle_2


title: X1117103192

tag: histology

tag: batch


title: OH9GMYUH-SCR


title: K8FDIQKH-SUR


title: X1034204686


title: X1034204633


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_992302-3-T)

city: Houston

first: Yuya

last: Sasaki

state: TX

address: 1515 Holcombe Blvd

institute: M.D. Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw-sequencing data from the Illumina platform were converted to a fastq format and aligned to the reference genome (hg19) using the Burroughs–Wheeler Aligner using MEM mode with following parameters: -k 31 -T 100 -t 8 -M.
The aligned BAM files were subjected to mark duplication, realignment, and recalibration, using Picard and GATK with default parameters.
Preprocessed BAM files were then analyzed to detect SNV and small insertions and deletions (indels), using MuTect and Pindel, respectively, against pooled unmatched normal sequences developed in house.
Genome_build: hg19
Supplementary_files_format_and_content: Mutect/Pindel calling tab-separated values matrix

source_name: Bone marrow cells

growth_protocol: Not applicable.

extract_protocol:
Genomic DNA was extracted from bone marrow or peripheral blood samples using a QIAamp DNA Mini kit (QIAGEN, Hilden, Germany).
After sample quality control, targeted capture DNA sequencing using custom designed SureSelect panel of 295 genes (Agilent Technologies, Santa Clara, CA, USA) was performed
Targeted capture DNA sequencing

treatment_protocol: Samples were either bone marrow samples obtained from previously untreated patients.

value: Ph-positive ALL

tag: tissue

value: bone marrow

tag: cell type

value: leukemic cell

tag: Sex

tag: outcome

value: Complete Response


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_923355-6-T)

tag: treatment

value: Female


title: A-011 Pre

value: Head and neck squamous cell carcinoma

tag: mtap status

value: Unaltered

tag: treatment status

value: Pre-treatment

tag: biomaterial

value: tissue biopsy (FFPE)


title: A9GU9DRN-SCR

source_name: Breast tumor

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

value: No

value: Positive

value: Negative


title: A-010 Pre


title: A-009 Pre


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_921072-9-T)

value: Male


title: A-015 Pre


title: A-007 Pre


title: 82SDROMV-2W

value: N/A; no information

tag: pcrb

tag: age


title: C2TAEM62-2W


title: X1034204302

tag: gender

value: Ovarian Clear Cell Carcinoma (OCCC)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_833261-7-T)

tag: disease state


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_760777-6-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_783510-16-T)


title: X1034204228


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_939833-6-T)


title: X1034204285


title: A-004 Pre

value: Altered


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_814440-6-T)


title: WT + Vehicle x 24 hours_1

value: Gastric corpus

tag: genotype

value: WT

value: Vehicle


title: PWCW6PPJ-2W

tag: er

tag: pr


title: A-008 Pre


title: 82SDROMV-SCR


title: A-012 Pre


title: PWCW6PPJ-SCR


title: X1110900577

tag: histology

tag: batch


title: Bone marrow cells - SNP array (AL855A7399M6)

hyb_protocol: According to the hybridazation protocol in manufacture's Reference Guide

scan_protocol: According to the scan protocol in manufacture's  Reference Guide

data_processing:
Genomic DNA extracted from patient-derived leukemic cells was genotyped using Infinium HumanCytoSNP-850K-12 v2.1 BeadChips (Illumina).
The raw log R ratio was used for ASCAT (allele-specific copy number analysis of tumors) algorithm to identify allele-specific copy-number alterations.
The log R ratio (LRR)

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from bone marrow or peripheral blood samples using a QIAamp DNA Mini kit (QIAGEN, Hilden, Germany).

treatment_protocol: Samples were either bone marrow aspirate or peripheral blood obtained from previously untreated patients.

value: Ph-positive ALL

tag: tissue

value: bone marrow

tag: cell type

value: leukemic cell

tag: Sex


title: Bone marrow cells - SNP array (AL819A7292M0)

tag: treatment

tag: outcome

value: Complete Response


title: X1034204266

value: Female


title: X1032303312


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_855377-5-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_921120-4-T)


title: X1034204236


title: X1034204639


title: C2TAEM62-SCR


title: A9GU9DRN-2W


title: A-006 Pre

value: Head and neck squamous cell carcinoma

tag: mtap status

value: Unaltered

tag: treatment status

value: Pre-treatment

tag: biomaterial


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_877105-4-T)


title: Bone marrow cells - SNP array (AL3182A7400M6)


title: 0RGIUUVD-SUR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_805345-5-T)

tag: disease state


title: X1034204214

tag: gender


title: A-002 Pre

value: tissue biopsy (FFPE)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_835209-2-T)


title: K8FDIQKH-2W

tag: age

tag: er


title: HGJRRA5N-SUR

tag: pr


title: Bone marrow cells - SNP array (AL782A7299M3)


title: K8FDIQKH-SCR

value: No

value: Positive

value: Negative


title: Bone marrow cells - SNP array (AL3195A7465M0)

value: Male


title: HGJRRA5N-2W

value: N/A; no information


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_838028-2-T)


title: HGJRRA5N-SCR


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_742316-6-T)


title: X1110900581

tag: histology

value: Ovarian Clear Cell Carcinoma (OCCC)

tag: batch


title: Bone marrow cells - SNP array (AL3170A7363M6)

tag: tissue

tag: cell type


title: A8U6LZ0L-SUR


title: A8U6LZ0L-2W


title: Bone marrow cells - SNP array (AL3186A7421M2)

tag: treatment

tag: Sex


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_362025-4-T)

tag: outcome


title: Bone marrow cells - SNP array (AL3180A7388M6)


title: A8U6LZ0L-SCR


title: Bone marrow cells - SNP array (AL3177A7376M6)


title: Bone marrow cells - SNP array (AL3174A7373M6)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_640560-4-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_766053-7-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_502310-6-T)


title: Bone marrow cells - SNP array (AL2846A7318M8)


title: Bone marrow cells - SNP array (AL2841A7317M0)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_318817-9-T)


title: Bone marrow cells - SNP array (AL2077A3395M5)


title: Z77GBPXV-SUR


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_321826-5-T)


title: Bone marrow cells - SNP array (AL1995A7395M0)


title: Z77GBPXV-2W


title: Z77GBPXV-SCR


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_241561-6-T)


title: Bone marrow cells - SNP array (AL2073A7303M6)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL1660A2339M0-T)


title: Bone marrow cells - SNP array (AL1790A2529M5)


title: J38OQTLS-SUR


title: J38OQTLS-2W


title: A9GU9DRN-SUR


title: Bone marrow cells - SNP array (AL1689A7467M2)


title: Bone marrow cells - SNP array (AL1660A2339M0)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_241237-12-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_984677-4-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_241047-6-T)


title: Bone marrow cells - SNP array (AL1399A7328M7)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_241753-9-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_240615-19-T)


title: 0RGIUUVD-2W


title: ST621FQU-SUR


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL1790A2529M5-T)


title: 0RGIUUVD-SCR


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_237595-10-T)


title: ST621FQU-2W


title: S_61IF

data_processing:
Quality control: Low quality reads (PHRED <33) removed + Illumina adapters clipped (Trimmomatic v. 0.38)
Read Alignment: Trimmed reads aligned to Heliconius reference genomes  (HISAT2 v. 2.1.0)
BAM file generation: Output aligned files sorted and converted to BAM (samtools v. 1.9)
transcript assembly + read quantification: Transcript assembly and read quantification (StringTie version 1.3.5)
Creation of gene count matrix: Gene count matrix designed for EdgeR were created using the python script ‘prepDE.py’ (provided by StringTie)
Genome_build: Heliconius_melpomene_melpomene_Hmel2.5
Supplementary_files_format_and_content: Raw counts of reads for all genes and all individuals provided as a matrix

organism: Heliconius melpomene cythera

source_name: wing tissue

extract_protocol:
QIAgen RNeasy
TruSeq Stranded mRNA-seq kit (H. melpomene)

value: Forewing + posterior Hindwing

tag: %development

tag: individual id


title: S_86IM


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_241163-7-T)


title: S_86AM

value: anterior-Hindwing


title: S_96IF


title: ST621FQU-SCR

tag: cellularity


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_240736-5-T)

value: Ph-positive ALL


title: S_96AF


title: PZ001VUO-SUR

tag: tumor infiltrating lymphocytes (tils)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_239348-3-T)

value: bone marrow


title: PZ001VUO-SCR

tag: pcrb


title: PZ001VUO-2W


title: S_71IM


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_240630-24-T)

tag: disease state

value: leukemic cell


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_238493-17-T)

value: Complete Response


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_235894-23-T)


title: S_71AM


title: J38OQTLS-SCR


title: HZHI5I3X-SUR


title: S_61AF

value: Female


title: HZHI5I3X-2W


title: S_81IM


title: S_81AM


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1035563-6-T)


title: S_91IF


title: S_91AF


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_240462-2-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL3186A7421M2-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1065340-6-T)


title: UMNXPI4D-SUR


title: S_80IM


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_240197-7-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1012121-11-T)


title: S_80AM


title: MOW5ZUC0-SUR


title: BF0XCR0I-2W


title: S_84AF


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL3177A7376M6-T)


title: HZHI5I3X-SCR


title: MOW5ZUC0-SCR


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL3195A7465M0-T)


title: BF0XCR0I-SCR


title: MOW5ZUC0-2W


title: 5N7CWC4J-2W


title: 5N7CWC4J-SCR


title: Colon DSS day14 B cell depleted (BCD)

city: Solna

first: Ludvig

middle: Ale

last: Larsson

state: Stockholm

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: SciLifeLab

data_processing:
Library strategy: Spatial Transcriptomics (Visium)
bcl2fastq command line tool was used for base calling
Sequence reads were trimmed for adapter sequence (Template Switch Oligo) and polyA homopolymers using cutadapt (-g XAAGCAGTGGTATCAACGCAGAGTACATGGG;max_error_rate=0.1 -a AAAAAAAAAA ;max_error_rate=0--overlap 5 -n 2)
Reads were mapped, annotated and demultiplexed using the spaceranger v1.0.0 command line tool
Annotated reads were quantified and mapped to the Hematoxylin and Eosin image using the spaceranger v1.0.0 command line tool
Genome_build: mm10 (Ensembl 93)
Supplementary_files_format_and_content: Matrix with raw counts for every gene and every spot
Supplementary_files_format_and_content: Matrix with raw counts for every gene and every spot, filtered to include spots under tissue
Supplementary_files_format_and_content: Hematoxylin and Eosin (HE) image in TIF format
Supplementary_files_format_and_content: Low resolution Hematoxylin and Eosin (HE) image in PNG format
Supplementary_files_format_and_content: Scalefactors in json format
Supplementary_files_format_and_content: Table with array and pixel coordinates

source_name: Colon

extract_protocol:
Mouse colonic tissues were collected either on day 0 (without any exposure to DSS) or on day14 after exposure to DSS, Swisrolled and frozen in OCT. Mouse colonic tissues (day0 and day14) were cryo-sectioned (10uM) and placed on the already barcoded spots (6.5mm x 6.5mm) on the glass slide.
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol

treatment_protocol: Wild type C57BL/6J mice were exposed to DSS in drinking water for 7 days and then allowed to recover for 7 more days.

tag: strain

value: female

value: colon

tag: genotype

value: wild type


title: 5N7CWC4J-SUR

tag: age

tag: er


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL3182A7400M6-T)


title: UMNXPI4D-SCR

value: Yes

tag: pr


title: XSD5Z32C-SUR


title: TNBC_57

city: Bunkyo-ku

first: Mai

last: Onishi

state: Tokyo

department: Clinical oncology

country: Japan

institute: Juntendo university Graduated schoo;

data_processing: Raw expression data was processed using nSolverAnalysis Software 4.0.70: Background subtraction with geometric mean of negative controls; Normalization with geometric mean of positive controls and standard housekeeping genes; No ratios built

source_name: primary breast cancer

extract_protocol: Glass slide specimens with 10-µm thick sections of FFPE tissue block were prepared. Total RNA was extracted from the samples using RNeasy mini kit (Qiagen, USA) according to manufacture's instructions

value: primary breast cancer

tag: status

value: dead

tag: gender

tag: biopsy method

value: VAB

tag: er status

tag: pgr status

tag: her2 status

tag: t stage

tag: n stage


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1009724-4-T)

tag: treatment

tag: tissue

tag: cell type

tag: Sex

value: Male

tag: outcome


title: TNBC_59

value: alive

value: CNB


title: TNBC_58


title: S_84IF

value: Forewing + posterior Hindwing

tag: %development

tag: individual id


title: WT2 P18 replicate 2

city: beijing

first: shuntai

last: yu

state: beijing

address: 7 Science Park Road ZGC Life Science Park, Beijing

department: transgenic animal center

country: China

institute: NIBS

data_processing:
Library strategy: CUT&Tag
The trimmed reads were mapped to the UCSC mm10 genome assemblies using Bowtie2 v2.2.5 with very-sensitive parameters.
Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.4.3) and visualized in the Integrative Genomics Viewer (IGV version 2.4.9).
Peak calling was carried out using MACS program with default parameters (version 2.2.7.1).
Peaks were annotated to the genomic region and the nearest genes within 2 kb of TSS using Bioconductor package ChIPSeeker (version 1.22.1).
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2; Scores represent signal per million reads for fragment pileup profiles.

source_name: testicular cells

growth_protocol: Mouse testicular cell suspensions were isolated from wild type and Zfp541-EGFP mouse testes. Briefly, the seminiferous tubules were minced and digested at a final concentration of 1 mg/ml collagenase IV and 1mg/ml DNase I at 37°C for 20 min, settled by standing the tube vertically, and washed with DMEM. Cell suspension was subsequently digested with 0.25% Trypsin containing 1mg/ml DNase I 37◦C for 5 min to prepare single-cell suspensions. Enzymatic digestion was quenched with DMEM supplemented with 10% FBS.

extract_protocol:
1×10^5 testicular single cells were washed twice in 1 ml of Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× Protease inhibitor cocktail) and centrifuged at 400 g for 5 min. Concanavalin A-coated magnetic beads were washed twice with binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MnCl2, 1 mM CaCl2). Next, 10 μl of activated beads were added per sample and incubated at room temperature for 15 min. The unbound supernatant was removed and bead-bound cells were resuspended in 50 μl of Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1× Protease inhibitor cocktail) containing 2 mM EDTA, 0.1% BSA and 1 μg rabbit polyclonal GFP antibody. The GFP antibody was incubated on a rotating platform overnight at 4°C, and removed using a magnet stand. Guinea Pig anti-Rabbit IgG (Heavy & Light Chain) secondary antibody was diluted in 100 µl of Dig-wash buffer and cells were incubated for 1 hour. Cells were washed three times with Dig-wash buffer to remove unbound antibody. The Hyperactive pA-Tn5 Transposase adapter complex (TTE mix) was diluted 1:100 (0.04 μM) in Dig-med buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5mM Spermidine, 0.01% Digitonin, 1× Protease inhibitor cocktail). Cells were incubated with 0.04 μM TTE mix at room temperature for 1 hour, washed three times with Dig-med buffer to remove unbound pA-Tn5 protein. Cells were then resuspended in 300 μl of Tagmentation buffer (10 mM MgCl2 in Dig-med buffer) and incubated at 37°C for 1 hour. To terminate tagmentation, 10 μl of 0.5 M EDTA, 3 μl of 10% SDS and 5 μl of 10 mg/ml Proteinase K were added to 300 μl of per sample and incubated at 55 °C for 1 hour. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation as well as RNase A treatment. For library amplification, 24 μl of DNA was mixed with 10 μl of 5×Multiplex PCR Mix,14 μl of ddH2O, as well as 1 μl of uniquely barcoded i5 and i7 primers. A total volume of 50 μl of sample was placed in a PCR amplifier. To purify the PCR products, 1.2× volumes of VAHTS DNA Clean Beads were added and incubated at room temperature for 10 min. Libraries were washed twice with 80% ethanol and eluted in 22 µl of ddH2O. Libraries were sequenced on an Illumina NovaSeq platform and 150-bp paired-end reads were generated.
Libraries were sequenced on an Illumina NovaSeq platform.

tag: genotype

value: Wild type

tag: age

value: Testicular cells

tag: chip-grade antibody

value: GFP (ab290)

tag: 2nd antibody

value: anti-rabbit IgG


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL3180A7388M6-T)

tag: disease state

value: Ph-positive ALL

value: bone marrow

value: leukemic cell

value: Complete Response


title: TNBC_60

tag: status

tag: gender

value: female

tag: biopsy method

tag: er status


title: TNBC_56

tag: pgr status

tag: her2 status

tag: t stage

tag: n stage


title: 81E7Z2UF-SCR

data_processing: Data were normalized using 5 housekeeping genes (ACTB, MRPL19, PSMC4, RPLP0, and SF3A1), and log2 transformed

extract_protocol: At baseline, a section of the formalin-fixed paraffin-embedded (FFPE) breast tissue was examined with haematoxylin and eosin (H&E) staining to confirm the presence of invasive tumor cells and to determine the minimum tumor surface area. For samples obtained at Cycle 2 Day 1, those without invasive tumor cells were also profiled. For RNA purification (High Pure FFPET RNA isolation kit, Roche, Indianapolis, IN, USA), at least 1–5 10 μm FFPE slides were used for each tumor specimen, and macrodissection was performed (when needed) to avoid contamination with normal breast tissues. A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA).

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

value: No

tag: er

value: Negative

tag: pr

value: Positive


title: TNBC_55

tag: tissue

value: primary breast cancer


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL782A7299M3-T)

tag: treatment

tag: cell type

tag: Sex

value: Male

tag: outcome


title: ZFP541-EGFP1 P18 replicate 1

tag: genotype

tag: age

tag: chip-grade antibody

tag: 2nd antibody


title: TNBC_54

tag: status

value: alive

tag: gender

tag: biopsy method

tag: er status

tag: pgr status

tag: her2 status


title: Colon DSS day14 control

tag: strain

value: colon

value: wild type


title: SNDCULO7-2W

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL855A7399M6-T)

tag: disease state

tag: treatment

tag: tissue

tag: cell type

tag: Sex

tag: outcome


title: mRNA-Seq P18 ko replicate 3

data_processing:
Basecalls performed using CASAVA version 1.9.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). 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: GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM (for single-end sequencing samples) or FPKM (for paired-end sequencing samples) values for each Sample.

growth_protocol: Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 7 am to 7 pm).

extract_protocol:
Total RNA of testes was extracted using Trizol reagent (15596026; Invitrogen). Poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L).
Libraries for mRNA abundance examination were prepared by using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

tag: genotype

tag: age

value: Testicular cells


title: 81E7Z2UF-2W


title: WT1 P18 replicate 1

value: Wild type

tag: chip-grade antibody

value: GFP (ab290)

tag: 2nd antibody


title: TNBC_53

tag: status

tag: gender

tag: biopsy method

value: VAB

tag: er status

tag: pgr status

tag: her2 status

tag: t stage

tag: n stage


title: ZFP541-EGFP2 P18 replicate 2

value: anti-rabbit IgG


title: mRNA-Seq P18 ko replicate 1

tag: strain


title: SNDCULO7-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL2073A7303M6-T)

tag: disease state

value: Ph-positive ALL

tag: treatment

tag: tissue

value: bone marrow

tag: cell type

value: leukemic cell

tag: Sex

value: Female

tag: outcome


title: mRNA-Seq P18 ko replicate 2

tag: genotype

tag: age


title: TNBC_52

tag: status

tag: gender

value: female

tag: biopsy method

value: CNB

tag: er status

tag: pgr status

tag: her2 status


title: U784B5T0-SUR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL1399A7328M7-T)

tag: disease state

value: Complete Response


title: SNDCULO7-SUR

tag: er

tag: pr


title: mRNA-Seq P18 het replicate 2

tag: strain

value: Male

tag: cell type


title: TNBC_50

tag: tissue

value: primary breast cancer

value: alive

tag: t stage

tag: n stage


title: AZE9NNMV-SUR

tag: age


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL819A7292M0-T)

tag: treatment

tag: Sex

tag: outcome


title: TNBC_51

tag: status

tag: gender

tag: biopsy method

tag: er status

tag: pgr status


title: U784B5T0-SCR

tag: cellularity

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

value: No

value: Positive

value: Negative


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL3170A7363M6-T)

tag: disease state


title: U784B5T0-2W

value: N/A; no information

tag: er

tag: pr


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL2846A7318M8-T)

tag: tissue

tag: cell type


title: TNBC_49

tag: her2 status

tag: t stage

tag: n stage


title: TNBC_48


title: AZE9NNMV-2W

tag: age


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_966152-2-T)

tag: treatment

tag: Sex

tag: outcome


title: AZE9NNMV-SCR


title: mRNA-Seq P18 het replicate 3

tag: strain

tag: genotype

value: Testicular cells


title: TNBC_47

tag: status

tag: gender

tag: biopsy method

value: VAB

tag: er status

tag: pgr status


title: S_74IM

organism: Heliconius melpomene rosina

value: Forewing + posterior Hindwing

tag: %development

tag: individual id


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_962070-10-T)

tag: disease state

value: Ph-positive ALL

tag: tissue

tag: cell type


title: TNBC_46

tag: her2 status

tag: t stage

tag: n stage


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_AL2841A7317M0-T)

tag: treatment

value: bone marrow

tag: Sex


title: S_74AM

value: anterior-Hindwing


title: LApc_organoid

city: Helsinki

first: Kari

last: Alitalo

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
Reference genome: GRCm38/mm10
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Intestinal organoids

growth_protocol: 7-8 week old mice received two doses of tamoxifen and were analyzed at the time point when they met criteria for euthanization

extract_protocol:
Small intestinal organoids of WT, LApc and LApcL mice (passage 3;day 6) were incubated in trypsin for 40 minutes, washed with adv.DMEM and filtered through a 20 μm mesh. Sorted cells were resuspended into HBSS with 0.04 % BSA.
Sample libraries were sequenced using the Illumina NovaSeq 6000 system (50,000 reads per sample).

treatment_protocol: Two doses of tamoxifen (at 2mg)

tag: strain

value: Intestinal organoids

value: Two doses of tamoxifen (2mg)

tag: analysis (days post tamoxifen injection)

value: 29 dpi

value: Lgr5-CreERT2;Apc fl/fl


title: LApcL_organoid

value: 21 dpi

tag: genotype

value: Lgr5-CreERT2;Apc fl/fl; Lef1 fl/fl


title: LApcL

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
Reference genome: GRCm38/mm10

source_name: Intestinal Epcam+ epithelial cells

extract_protocol:
Small intestine of WT, LApc and LApcL mice was removed and washed with cold PBS. Intestines were cut into 3-4 pieces and incubated in 10 mM EDTA in orbital shaker +4°C for 30 min. Tissues were washed with PBS and cells from luminal surface were scraped off with a glass slide. Cells were then centrifuged 300 rpm +4°C followed by incubation with enzymes (4 mg/ml Dispase II, 1 mg/ml Collagenase I, 1 mg/ml Collagenase H and 1 U/ml Dnase I) for 7 min at 32 °C. Cells were washed with DMEM with 2 % FBS and centrifuged at 300 rpm +4°C for 2 min after which floating cells were collected and filtered through a 40 μm mesh. Remaining cells were centrifuged at 300 rpm +4°C for 5 min, and incubated in trypsin-EDTA with 1 U/ml DNase I for 5 min at 32°C. After a wash with DMEM with 2 % FBS, the cells were centrifuged at 300 rpm +4°C and filtered through a 40 μm mesh. Epithelial cells of WT, LApc and LApcL mice were sorted on BD Influx (BD Biosciences). The epithelial cells were surface-stained with Anti-Mo CD326 (EpCAM) PE (eBioscience, Invitrogen #12-5791-82). Sorted cells were resuspended into HBSS with 0.04 % BSA.
Sample libraries were sequenced using the Illumina NovaSeq 6000 system (50,000 reads per sample).

treatment_protocol: Two doses of tamoxifen (á 2mg)


title: WT_organoid

value: WT


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_934267-2-T)

value: leukemic cell

value: Male

tag: outcome

value: Complete Response


title: LApc


title: TNBC_45

value: primary breast cancer

tag: status

value: dead

tag: gender

value: female

tag: biopsy method

value: CNB


title: TNBC_44

value: alive

tag: er status

tag: pgr status


title: S_85AM

tag: %development

tag: individual id


title: WT


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_653954-14-T)

tag: disease state

value: Ph-positive ALL

tag: tissue

value: bone marrow

tag: cell type


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_924362-4-T)


title: mRNA-Seq P18 het replicate 1

tag: age

value: Testicular cells


title: S_65AM

value: anterior-Hindwing


title: VApcMinL2 intestinal adenoma

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10.
We used the Seurat R package 3.1.1 for data analysis.
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
Genome_build: Reference genome: GRCm38/mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv or features.tsv, matrix.mtx

source_name: Mouse small intestinal adenomas

growth_protocol: Mice were euthanized at 11 weeks of age.

extract_protocol:
For tumor dissociation, 3-10 tumors of approximately same size and from similar locations in the intestines were removed from 11-week-old ApcMin and VApcMinL mice. Tumors were incubated with enzymes (4 mg/ml Dispase II, 1 mg/ml Collagenase I, 1 mg/ml Collagenase H and 1 U/ml DNase I) for 30 min at +32°C, followed by incubation with trypsin-EDTA for 15 min at +37°C. Cells were filtered through 40 μm mesh and subjected to scRNA-seq without FACS sorting.
All samples were analyzed with the Chromium Single-Cell 3’RNA-sequencing platform (10x Genomics, Pleasanton, CA) with the Reagent Kit V2 (ApcMin and VApcMinL) or V3 (ApcMin2 and VApcMinL2) according to the manufacturer’s instructions.
Sample libraries were sequenced using the Illumina NovaSeq 6000 system (50,000 reads per sample).

treatment_protocol: Constitutive deletion.

value: ApcMin/+;Lef1 fl/fl; Villin-Cre

value: Intestinal adenomas

value: 11 weeks


title: TNBC_42

tag: her2 status

tag: t stage

tag: n stage


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_890197-8-T)

tag: treatment

tag: Sex

value: Female


title: TNBC_43


title: TNBC_41

value: VAB


title: S_60IM

value: Forewing + posterior Hindwing


title: S_85IM

value: Male


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_928975-4-T)

value: leukemic cell

tag: outcome

value: Complete Response


title: S_60AM


title: S_90IF


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_813733-9-T)


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_277327-3-T)


title: VApcMinL intestinal adenoma

tag: strain

tag: genotype


title: TNBC_39

value: primary breast cancer

tag: status

tag: gender

tag: biopsy method


title: TNBC_40

value: female

tag: er status

tag: pgr status


title: TNBC_38

value: CNB


title: ApcMin2 intestinal adenoma

value: ApcMin/+;Lef1 +/+


title: ApcMin intestinal adenoma


title: S_90AF

tag: %development

tag: individual id


title: S_65IM

tag: tissue


title: S_78IM


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_322781-8-T)

tag: disease state

value: Ph-positive ALL

tag: cell type


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_729567-3-T)

value: bone marrow


title: TNBC_36

value: alive

tag: her2 status

tag: t stage


title: VApcMinL

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package 3.1.1 for data analysis
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
Reference genome: GRCm38/mm10
Supplementary_files_format_and_content: mtx, barcodes, features

source_name: Intestinal lamina propria Epcam- and CD45- cells

growth_protocol: Mice were euthanized at 11 weeks of age

extract_protocol:
Lamina propria was digested into single cells by EDTA treatment 20min +37°C plus Liberase TL treatment 60min +37°C. FACS: DAPI-Ter119-Epcam-CD45- intestinal stromal cells
All samples were analyzed with the Chromium Single-Cell 3’RNA-sequencing platform (10x Genomics, Pleasanton, CA) with the Reagent Kit v3 according to the manufacturer’s instructions.
Sample libraries were sequenced using the Illumina NovaSeq 6000 system (50,000 reads per sample).

treatment_protocol: Constitutive deletion

value: Intestine

tag: age


title: S_78AM

value: anterior-Hindwing

tag: Sex


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_752316-6-T)

tag: treatment

tag: outcome


title: ApcMin

tag: strain

tag: genotype


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_338863-4-T)


title: TNBC_35

tag: status

tag: gender

tag: n stage


title: S_76IF


title: dhdJ5_K9me3_Ov_rep2

city: Lyon

first: Guillermo

middle: A

last: Orsi

address: 46 allée d'Italie

institute: ENS Lyon/ LBMC-UMR 5239

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
fastq files were trimmered with an offset of 75 (FASTQ Trimmer Galaxy Version 1.1.5).
Trimmed fastq were then aligned to the dm6 genome using Bowtie2 (Galaxy Version 2.4.2+galaxy0) with default parameters.
bam alignments were brought down to the same readcount with the Downsample SAM/BAM tool (Galaxy Version 2.18.2.1)
bedgraph files for all fragments were generated with the bamCoverage tool (Galaxy Version 3.3.2.0.0) without normalizing, using a 25bp bin and paired-end extension.
bedgraph files for short fragments (<120bp) were generated with the bamCoverage tool (Galaxy Version 3.3.2.0.0) without normalizing, using a 10 bp bin and paired-end extension.
Genome_build: dm6
Supplementary_files_format_and_content: bedgraphs showing H3K27me3 or H3K9me3 coverage for all fragments and short fragments (<120 bp) in drosophila ovaries of different genotypes

organism: Drosophila melanogaster

source_name: Ovaries

extract_protocol:
Cut&Run in Drosophila tissues was previously described (Ahmad and Spens, 2019). Briefly, ovaries from 3-day-old flies were dissected in Wash+ Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.9 mM spermidine, 0.1% BSA with Roche cOmplete protease inhibitor) and were bound to BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc). Tissue was then permeabilized for 10min in dbe+ Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.9 mM spermidine, 2 mM EDTA, 0.1% BSA, 0.05% digitonin with Roche cOmplete protease inhibitor). Samples were then incubated with gentle rocking overnight at 4°C with antibody solution (H3K27me3, Cell Signalling Technology #9733, final concentration of 1:100 in dbe+ buffer, or H3K9me3, Abcam #8898, final concentration of 1:50 in dbe+ buffer). Protein A fused to micrococcal nuclease (p-AMNase) was added in dbe+ buffer and samples were incubated with rotation at room temperature for 1 hour. Cleavage was done in WashCa+ buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.9 mM spermidine, 0.1% BSA, 2 mM CaCl2 with Roche cOmplete protease inhibitor) at 0 ̊ for 30 minutes. Digestion was stopped with addition of 2XSTOP Buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 62.5µg/mL RNaseA). Samples were incubated at 37°C for 30 min to digest RNA and release DNA fragments. Cleaved DNA was then recovered with Ampure XP beads (Beckman Coulter) immediately after protease treatment.
Cut&Run samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). Cut&Run-seq libraries were prepared from10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: ovaries

tag: genotype/variation

tag: cut&run antibody


title: TNBC_37

tag: biopsy method

tag: er status

tag: pgr status


title: dhdJ5_K9me3_Ov_rep1

tag: tissue


title: TNBC_34

value: dead

tag: her2 status


title: Ctrl_K9me3_Ov_rep2

value: control


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_242199-8-T)

tag: disease state

tag: cell type

value: Female


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_242032-17-T)

tag: Sex

value: Early Death


title: S_76AF

city: Sheffield

first: Nicola

last: Nadeau

institute: The University of Sheffield

tag: %development

tag: individual id


title: S_62IM

value: Forewing + posterior Hindwing

value: Male


title: Ctrl_K9me3_Ov_rep1


title: TNBC_33

tag: t stage


title: TNBC_32


title: mod(mdg4)KD_RNA-seq_Ov_rep2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover
RNA-seq read alignment: Tophat version 2.1.1, default.
RNA-seq read assignment to genes: feautreCounts 1.4.6, default.
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include read count values for each feature
Supplementary_files_format_and_content: DESeq2 results files in tab-separated format
Supplementary_files_format_and_content: bigwig files for each sample were generated using Deeptools command bamCoverage with the following options -bs 10 -p max --normalizeUsing CPM --smoothLength 30 --minMappingQuality 5 --outFileFormat bigwig

source_name: ovaries

extract_protocol:
RNAs were extracted with the Trizol (Invitrogen, Cat# 15596026) method according to supplier recommendations. RNA concentration wre measured using NanoDrop. RNA integrity was assessed using an Agilent Bioanalyzer. RNA-seq libraries were made from samples with a RNA Integrity Number (RIN) of at least 9.0. RNA-seq library was synthesized according to TruSeq Stranded mRNA Sample Preparation Guide - PN 15031047, version Rev.E Oct 2013
RNA-Seq libraries were generated from 800 ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Number RS-122-2101). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: genotype

value: mod(mdg4) KD (MTD-Gal4>shRNA mod(mdg4))

tag: age

value: 3 day-old


title: TNBC_31

value: primary breast cancer

tag: status

tag: gender

value: female


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_239041-3-T)

tag: treatment

value: leukemic cell

tag: outcome

value: Complete Response


title: S_62AM


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_241830-5-T)

value: Ph-positive ALL

value: bone marrow


title: F_47N [12-47N]

data_processing:
Quality control: Low quality reads (PHRED <33) removed + Illumina adapters clipped (Trimmomatic v. 0.38)
Read Alignment: Trimmed reads aligned to Heliconius reference genomes  (HISAT2 v. 2.1.0)
BAM file generation: Output aligned files sorted and converted to BAM (samtools v. 1.9)
transcript assembly + read quantification: Transcript assembly and read quantification (StringTie version 1.3.5)
Creation of gene count matrix: Gene count matrix designed for EdgeR were created using the python script ‘prepDE.py’ (provided by StringTie)
Genome_build: Heliconius_erato_demophoon_v1
Supplementary_files_format_and_content: Raw counts of reads for all genes and all individuals provided as a matrix

organism: Heliconius erato demophoon

extract_protocol:
QIAgen RNeasy
TruSeq v2 kit


title: mod(mdg4)KD_RNA-seq_Ov_rep1


title: F_47I [11-47I]


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_241537-11-T)


title: Snr1KD_RNA-seq_Ov_rep2

value: Snr1 KD (MTD-Gal4>shRNA Snr1)


title: M_45N [10-45N]

value: anterior-Hindwing


title: TNBC_29

value: alive

tag: biopsy method

value: CNB

tag: n stage


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_236365-32-T)


title: Snr1KD_RNA-seq_Ov_rep1

value: ovaries


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1247996-9-T)

value: Female


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_240516-8-T)


title: TNBC_28

value: dead

tag: er status

tag: pgr status


title: F_40I [7-40I]

tag: tissue

value: Forewing + posterior Hindwing


title: F_40N [8-40N]


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_235735-2-T)

tag: disease state


title: dhdJ5-pW8-dhdDDRE_K27me3_Ov_rep2

tag: genotype/variation

tag: cut&run antibody

value: H3K27me3 (Cell Signaling Technology, 9733)


title: dhdJ5-pW8-dhdDDRE_K27me3_Ov_rep1


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_237407-26-T)

tag: cell type

tag: Sex


title: dhdJ5-pW8-dhdWT_K27me3_Ov_rep2


title: TNBC_26

tag: her2 status

tag: t stage


title: TNBC_25


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1241281-14-T)


title: F_39N [6-39N]

tag: %development

tag: individual id


title: F_39I [5-39I]


title: TNBC_30

tag: status

tag: gender


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_240093-10-T)

tag: treatment

tag: outcome


title: dhdJ5_K27me3_Ov_rep2


title: TNBC_24

tag: biopsy method

tag: n stage


title: dhdJ5-pW8-dhdWT_K27me3_Ov_rep1


title: M_45I [9-45I]

value: Male


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_237705-14-T)


title: dhdJ5_K27me3_Ov_rep1


title: TNBC_27

tag: er status

tag: pgr status


title: M_36I [31-36I]

tag: tissue


title: TNBC_22


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1157117-9-T)

tag: disease state


title: TNBC_20


title: F_20N [30-20N]


title: TNBC_23


title: TNBC_21


title: F_32N [20-32N]


title: F_20I [29-20I]


title: mod_mdg4KD_K27me3_Ov_rep3

tag: genotype/variation

tag: cut&run antibody


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1023797-4-T)

tag: cell type

tag: Sex


title: TNBC_19

tag: her2 status

tag: t stage


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1214391-9-T)


title: Ez_KD_K27me3_Ov_rep1


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1050752-5-T)


title: M_36N [32-36N]

tag: %development

tag: individual id


title: F_31N [18-31N]


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1222650-5-T)


title: F_32I [19-32I]


title: TNBC_16

tag: status

tag: gender


title: mod_mdg4KD_K27me3_Ov_rep2


title: Ez_KD_K27me3_Ov_rep2


title: TNBC_18


title: TNBC_17


title: F_31I [17-31I]


title: mod_mdg4KD_K27me3_Ov_rep1


title: Snr1KD_K27me3_Ov_rep2


title: Snr1KD_K27me3_Ov_rep3


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1187886-16-T)

tag: treatment

tag: outcome


title: Snr1KD_K27me3_Ov_rep1


title: RNaseH_ssDRIP_rep1

city: Hangzhou

first: Xingyu

last: Huang

state: Zhejiang

address: 866 Yuhangtang Road, Hangzhou, Zhejiang Province

institute: Life Sciences Institute (LSI), Zhejiang University (ZJU)

data_processing:
Library strategy: ssDRIP-seq
Trimmomatic fitered the raw reads
ssDRIP-seq reads were aligned to the MH63 genome assembly using bwa mem
Remove multi-mapped reads, filtered using the SAMTOOLS MAPQ20 and filter the  duplication reads
Using samtools to split the filter align file into forward and reverse align file
Peak was calling using MACS2 with callpeak -t <input file> --nomodel --extsize 100 -f BAM –n <output peak file> -B -q 0.05 -g 3.6e+8
Genome_build: MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage
Supplementary_files_format_and_content: peak text files

organism: Oryza sativa

source_name: MH63 seedling

growth_protocol: MH63 (one parent of one of the most widely cultivated rice hybrids in China, Shanyou 63) were used in this study. The germinating seeds were collected by soaking dry seeds in water for 72 h at 37 °C. The germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °C.

extract_protocol:
Genomic DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed at 37 °C overnight using endonucleases (Ssp I, Eco RI, Hind III, Dde I, Msp I and Rsa I; New England Biolabs, Ipswich, MA, USA); the negative control was treated with RNase H (New England Biolabs) at 37 °C overnight. DRIP was performed as described previously. The S9.6 antibody was purified from HB-8730 (ATCC, Manassas, VA, USA). The DRIPed DNA samples were sonicated to a set size of 250 bp with an M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).
The sonicated DNA was denatured at 95 °C for 2 minutes and immediately placed on ice for 2 minutes to obtain ssDNA fragments. The first adapter (Adp1, GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(i7) ATCTCGTATGCCGTCTTCTGCTTG) was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences, Ann Arbor, MI, USA) via a highly efficient, proprietary reaction that tails only the 3’ ends of ssDNA and ligates the first truncated adapter to the 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequenceindependent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter (Adp2, AATGATACGGCGACCACCGAGATCTACAC(i5) ACACTCTTTCCCTACACGACGCTCTTCCGATCT) to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified. The libraries were HiSeq X Ten system.

treatment_protocol: Nuclei were isolated from 3 g of 2-week-old fresh seedlings, followed by SDS/proteinase K treatment at 37℃ overnight.

tag: development stage/tissue

value: seedling

tag: cultivar

value: Minghui 63


title: RNaseH_ssDRIP_rep2


title: Sin3aKD_K27me3_Ov_rep3


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1003312-3-T)


title: TNBC_14

value: primary breast cancer

value: female

tag: biopsy method

tag: er status

tag: pgr status

tag: n stage


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1146473-5-T)

tag: disease state

tag: tissue

value: leukemic cell

value: Complete Response


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1146245-4-T)

value: Ph-positive ALL

value: bone marrow

tag: cell type

tag: Sex


title: Sin3aKD_K27me3_Ov_rep1

tag: genotype/variation

tag: cut&run antibody


title: TNBC_15

tag: her2 status

tag: t stage


title: TNBC_12

tag: status

tag: gender


title: TNBC_13


title: TNBC_11


title: H3_ChRD_rep2

data_processing:
Library strategy: ChRD-PET
FastQC and cutadapt filtered the raw reads
Combine the R1 and R2 by FLASH, and get a "Combine" data and two "NotCombine" data
Finding the linker("CCTCGATACTTGAGCTGACT") in three file by cutadapt. And split data into DNA and RNA data
For length<70 DNA reads were aligned to MH63 genome assembly using bwa aln. For length>70 DNA reads were aligned to MH63 genome assembly using bwa mem. For RNA reads, We use a two-step comparison strategy. Firstly, RNA reads wrer aligned to MH63 using hisat2. And than, get the unmapped and multi-mapped reads and were aligned to MH63 again by bowtie2.
Remove multi-mapped reads, filtered using the SAMTOOLS MAPQ20
Remove reads aligned to rRNA, and combine DNA and RNA aligned result into a bedpe file. Merge records with similar positions(both DNA and RNA) to calculate a highly significant DNA-RNA interaction
Genome_build: MH63
Supplementary_files_format_and_content: bedpe
Supplementary_files_format_and_content: bigWig

extract_protocol:
About 3 g Rice nuclei isolated from dual cross-linked rice MH63 seedlings were  lysed in Buffer S  (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 1% SDS) at 4 °C for 40 min at 12 rpm. Then add 9 volume buffer F (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate) to sample and rotate at 4 °C for 40 min at 12 rpm. The chromatin were then sonicated into 1–3 kb (High level, 28 cycles, 30 s ON, and 50 s OFF) using a Bioruptor (Diagenode). The chromatin fragments were centrifuged at 2800 g for 10 min at 4 °C and the supernatant was transferred to a new tube for chromatin immunoprecipitation (ChIP). To prepare antibody-loaded beads, 40 μL antibody (H3K4me3 antibody, ABclonal cat. no. A2357；H3 antibody, ABclonal cat. no. A2348) was mixed with 750 μL of suspended protein G magnetic beads, followed by incubation at 4 °C for 8 h with rotation at 12 rpm. Then, the mixed fragmented chromatin extract was incubated with antibody-loaded beads and incubated at 4 °C overnight with rotation at 12 rpm. The supernatant was discarded and the beads were washed three times with 1 mL 0.1% SDS FA cell lysis buffer (0.05 M, HEPES-KOH, 0.15 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS), and then washed twice with 1 mL high salt ChIP buffer (0.05 M, HEPES-KOH, 0.35 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS); and once with 1 mL ChIP wash buffer (0.01 M Tris–HCl, 0.25 M LiCl, 0.001 M EDTA, 2.5% NP-40, and 0.5% sodium deoxycholate), and finally washed with 1 mL 1× TE buffer (pH 8.0, Ambion, cat. no. AM9849) twice. DNA of the ChIP complex on beads was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F), and Klenow enzyme (NEB, cat. no. M0212L). To ligate DNA and RNA, we used a specially designed single biotinylated bridge linker: forward strand: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGACT-3′; reverse strand: 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. Then, RNA ends were proximity-ligated by the single biotinylated bridge-linker with the 5′ end adenylated on the forward strand, followed by extension of the reverse strand in the linker into ligated RNA with reverse transcription as first strand cDNA synthesis. Next, the DNA ends with 3’ A-tailing were proximity-ligated by the single biotinylated bridge linker with a 3’ nucleotide T over-hang on the forward strand, followed by second strand cDNA synthesis. (For RNase H treated H3K4me3 ChRD-PET data, RNase H treatment was conducted before DNA end repair and A-tailing.)
The proximity ligation RNA-DNA fragments were reverse cross-linked and fragmented before adding sequencing adaptors simultaneously by using Tn5 transposase (VAHTS, cat. no. TD501). The fragments contained the bridge-linker at ligation junctions were captured by Streptavidin beads, and used as templates for PCR amplification. These DNA products were then subjected to size-selection and paired-end sequencing (2 × 150 bp) using Illumina Hiseq X-Ten.

treatment_protocol: Young leaves of 2-week-old seedlings were collected and immediately preserved in 1× PBS for dual crosslinking with 1% (v/v) formaldehyde (Sigma, F8775) and 1.5 mM ethylene glycol bis (EGS, Thermo Fisher Scientific, 21565). Dual cross-linked samples were rinsed three times with deionised water and immediately frozen in liquid nitrogen. Frozen tissues were kept at -80 °C for no longer than 1 month.

tag: development stage

tag: chip antibody


title: H3_ChRD_rep1

tag: cultivar