title: D4_DnmtWT_dTET1_Zdbf2_H3K27me3_rep2

city: Paris

first: Julien

last: Richard Albert

address: 15 Rue Hélène Brion

country: France

institute: Institut Jacques Monod, CNRS, Université de Paris

data_processing:
WGBS data: as described in Richard Albert et al. 2020 Nature Communications. Reads were mapped to the mm10 genome using Bismark and standard parameters
CUT&Tag data: PCR duplicate removal using BBmap clumpify (Bushnell et al., 2014)(v38.18) and parameters: reorder dedupe=t k=19 passes=6 subs=(0.01 x readlength). Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using Bowtie2 (Langmead et al., 2019)(v2.4.5) for CUT&Tag using parameters: --local –very-sensitive –no-mixed –dovetail –no-discordant –phred33 -I 10 -X 700
Processed bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
Assembly: mm10
Supplementary files format and content: Bigwig format. CUT&Tag: CPM-normalized counts. WGBS: percent methylated Cs at CpG dinucleotides covered by at least 5 reads.

source_name: mouse embryonic stem cells

growth_protocol: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)

extract_protocol:
RNA extraction from cell pellets was performed using the KingFisher Duo Prime Magnetic Particle Processor and the MagMAX mirVana Total RNA kit, according to the manufacturer's instructions. To measure H3K27me3 enrichment after epigenome editing, we used the original CUT&RUN l protocol with minor modifications. Briefly, 2.5-5 x 105 cells per sample were pelleted and washed twice with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine containing protease inhibitor). The cells were then incubated for the binding with Concavalin A magnetic beads (Polysciences) by rotating for 10 min at RT. The antibody incubation was carried out overnight on a rotor at 4ºC in 100 µL antibody solution (wash buffer with 0.1% digitonin and 2 mM EDTA) containing 1 µL of αH3K27me3 Ab (Cell Signaling C36B11). Samples were then washed in dig-wash buffer (wash buffer with 0.1% digitonin), and incubated with pAG-Mnase on a rotor for 10 min followed by two more washes. The Mnase reaction was then activated by adding 2 mM CaCl2. After incubating at 0°C for 30 min the reaction was stopped with 1x final concentration of STOP solution (2x: 340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% digitonin, 1:200 Rnase A). Chromatin was released by incubating samples at 37°C for 10 min. After centrifuging at full speed for 5 min, the supernatant was collected after incubation on magnet stand. Purified DNA was obtained by phenol/chloroform extraction and precipitated with 100% ethanol by centrifugation. The DNA pellet was washed in 70% ethanol, spun down and air-dried before being resuspended in 35 µl of 5 mM Tris-HCl pH 8.5. The pAG-Mnase plasmid was obtained from Addgene (# 123461), and the protein was purified by the Curiecoretech Recombinant Protein Platform.
Total RNA was sent to Novogene Co. for polyA-RNA library constructions and sequencing on an Illumina NovaSeq X (paired-end, 150 nucleotide-long reads).
Sequencing libraries were constructed from purified CUT&RUN DNA fragments using the xGen low-input DNA library preparation kit from IDT (Cat. #10009859) following the supplier's instructions. Library quality was assessed using 4200 TapeStation system (Agilent) and sequenced on an Illumina NovaSeq X (paired-end, 150 nucleotide-long reads) by Novogene Co.

treatment_protocol: Day 0, 4 or 7 post-FGF2/Activin A treatment

value: mouse embryonic stem cells

value: DnmtWT

value: Day 4 post-FGF2/Activin A treatment


title: Bladder,  β‐Catenin positive 18

status: Public on Jul 16 2024

type: SRA

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

library_source: transcriptomic

data_processing:
RNA sequencing reads were aligned to the human reference genome (GRCh38) by using the Subread (version 2.0.3) package
To quantify gene expression levels, we utilized the featureCounts function (Liao et al, 2014) within the Rsubread package.
Assembly: hg38
Supplementary files format and content: featureCounts(.csv)

molecule: total RNA

organism: Homo sapiens

source_name: Human urinary bladder tumor

extract_protocol:
RNA samples were isolated from FFPE samples
Libraries were prepared using an Illumina Truseq RNA Exome Kit (Illumina, San Diego, CA, United States), which is specific for RNA isolated from formalin-fixed paraffin-embedded tissues (FFPE), according to the manufacturer’s recommendations. Paired-end sequencing for total RNA was performed on Illumina NovaSeq 600 with 150 bp read lengths.
Truseq RNA Exome Kit

tag: tissue

value: Human urinary bladder tumor


title: BVLO #1

city: Minato-ku

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

country: Japan

institute: The University of Tokyo

description:
IonXpress_007
20211222.rpm.bcmatrix.txt

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary files format and content: *.rpm.bcmatrix.txt: Tab-delimited text files include RPM values for each sample.

source_name: iPSC derived cells

growth_protocol: The human iPSC lines Ff-I01s04 were kindly provided by Kyoto University. All iPSC lines were maintained on dishes coated with the laminin 511E8 fragment (iMatrix-511TM, Nippi) in StemFit AK02N medium (Ajinomoto, Tokyo, Japan). The use of human iPSCs was approved by the ethics committee of University of Tokyo. Differentiation of hiPSC into Hepatic endoderm (HE), endothelial (EC), and mesenchymal cells (MC) were done as described previously (Takebe T et al. Cell reports 2017).

extract_protocol:
RNA was extracted with PureLink™ RNA Mini Kit (Invitrogen, Waltham, Massachusetts, USA) from planar-cultured cells according to the manufacturer’s instructions. PureLink™ RNA Micro Scale Kit (Invitrogen, Waltham, Massachusetts, USA) was used for RNA extraction from sorted cells.
RNA libraries were prepared using 30 ng of total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific).

treatment_protocol: Generation of hiPSC-derived liver bud was carried out as described previously (Takebe T et al. Cell reports 2017).

tag: cell type

value: iPSC derived organoid


title: Bladder,  β‐Catenin positive 16


title: D4_DnmtWT_dTET1_Celsr2_H3K27me3_rep2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

value: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)

tag: genotype

tag: treatment


title: Prolactin-XL 8D rep 3

city: Boston

first: Kasia

last: Kready

state: MA

address: 200 Longwood Ave

department: Systems Biology

country: USA

institute: Harvard University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1.
UMI-based de-duplication was performed using fastp v.0.23.1 simultaneously.
Trimmed and de-duplicated reads were then mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: Trimmed and de-duplicated reads were then mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes TPM values for each Sample

molecule: polyA RNA

source_name: mammary gland

growth_protocol: All animal work was approved by the Harvard Medical School IACUC under protocol IS00003310. C57bl/6j mice (Jackson; 000664) were mated at 8 weeks of age. On day 7 postpartum, litters were normalized to 5 pups per dam. Pups were weighed daily until they were weaned at day 21 postpartum or they reached endpoint (20% weight loss compared to positive controls).

extract_protocol:
Abdominal mammary glands were harvested and stored in RNAlater (Thermo Fisher Scientific, AM7020) overnight at 4C. Samples were then stored at -80C until submitted to Azenta/Genewiz for standard RNA sequencing. RNA extraction and PolyA selection was peformed by Azenta/Genewiz.
RNA library for RNA sequencing were constructed using the standard RNA sequencing package at Azenta/Genewiz

treatment_protocol: Beginning on day 7 postpartum, and every other day thereafter, dams were administered 5mg/kg dose of Prolactin-XL or a PBS control by subcutaneous. Dams were dosed until their pups were weaned at day 21 postpartum.

value: mammary gland

tag: strain

tag: age/sex

value: 6-20wk old, lactating  female with litter size n=5

value: WT

value: subcutaneous 5mg/kg Prolactin-XL every other day


title: Bladder,  β‐Catenin positive 15


title: Colon_DT_Cre-Positive_07

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

data_processing:
The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).  Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Quality control and adapter trimming of fastq files was performed using Fastp .
Reads were aligned to mouse reference genome (mm10) using HISAT.
Reads were quantified by FeatureCounts and data was normalised to counts per million (TPM)
Assembly: Mm10
Supplementary files format and content: Processed data contains count output as TPM in txt format

source_name: Colon

extract_protocol:
Total RNA extraction was performed using Trizol reagent as of the manufacturers user guide (Thermo Fisher Scientific, Waltham, MA, USA).
Samples were processed by Genewiz for PolyA purification and library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

treatment_protocol: To evaluate the transcriptome after neural ablation colons were excised from mice sacrificed by CO2 inhalation which were then cut along the mesenteric border and pinned on silicon-lined petri dishes. All mice had received laparotomy and injection of DT with India ink, with mice lacking iDTR expression serving as controls. The injection sites were located by staining with India ink and full-thickness specimens of the injection area were dissected and immediately frozen in LN2 for storage.

value: Colon

value: Diptheria toxin


title: Bladder,  β‐Catenin positive 14


title: E13.5 Spinal cord, NFIA, ChIP

city: La Jolla

first: Stacey

middle: Marie

last: Glasgow

state: California

address: 9500 Gilman Dr, 3216 Pacific Hall

institute: University of California San Diego

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (Q >= 25) were used for further  analysis.
Alignments were extended at their 3’-ends to 200 bp,  assigned to 32-nt bins along the genome, and formatted as bigWig files.
Peaks were called using MACS v2.1.0 with a cutoff p-value= 1e-7
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Spinal cord

growth_protocol: Wildtype embryos were harvested at E13.5 and whole spinal cords extracted

extract_protocol:
Spinal cords were homogenized and fixed with 1% formaldehyde for 15 min. After quenching  and lysis, chromatin was sonicated and the DNA sheared to an average length of 300-500 bp using Active Motif’s EpiShear probe sonicator (cat# 53051).
Genomic DNA (Input) was prepared by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). 40 μg of DNA was used as a starting material for input and IP. Libraries were prepared using an automated system (Apollo 42, Wafergen Biosystems/Takara) and sequenced  on  Illumina NovaSeq 6000 sampes. Immunoprecipitation was performed with 30 μL of anti NFIA antibody (Atlas Antibodies, #HPA008884).

value: Spinal cord

value: wildtype

tag: developmental stage

tag: chip antibody

value: NFIA (Atlas Antibodies, #HPA008884)


title: D4_DnmtWT_dTET1_Celsr2_H3K27me3_rep1


title: HE (day8)

description:
IonXpress_020
20210121.rpm.bcmatrix.txt

value: iPSC derived hepatic cell lineage


title: Bladder,  β‐Catenin positive 17


title: Prolactin-XL 9D rep 1


title: Prolactin-XL 8D rep 2


title: Colon_DT_Cre-Positive_06


title: Prolactin-XL 8D rep 1


title: D4_DnmtWT_TET1_Atp4a_H3K27me3_rep2


title: Prolactin-XL 9D rep 2


title: D4_DnmtWT_dTET1_Zdbf2_H3K27me3_rep1


title: Colon_DT_Cre-Positive_05


title: Bladder,  β‐Catenin positive 13


title: D4_DnmtWT_TET1_scrambled_H3K27me3_rep2


title: Bladder,  β‐Catenin positive 10


title: Spinal cord microglia from ATXN2-Q33;TDP-43 animals (Sc10)

city: Utrecht

first: R. Jeroen

last: Pasterkamp

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

description: Microglia Sc10

data_processing:
Sequencing data were pre-processed by removing adapter sequence and trimming away low quality bases with a Phred score below 20 using TrimGalore (v0.4.1).
Quality control was performed using FastQC to ensure high quality data.
Quantification of gene expression was performed by mapping the filtered reads to the mouse genome (mm10) using Tophat2.
The software featureCounts was used to quantify the number of reads mapping to each gene using gene annotation from the Gencode M25.
Counts were normalized and differential expression analysis was performed using DESeq2 in R with an FDR < 0.05.
Assembly: mm10
Supplementary files format and content: Counts, DE

extract_protocol:
Total RNA was isolated using QIAzol Lysis reagent (Qiagen) and miRNeasy mini kit (Qiagen) with DNA digestion on-column, according to the manufacturer's instructions. RNA concentration and integrity was validated using the RNA 6000 Nano Kit on a 2100 Bioanalyser (Agilent)
Samples were rRNA depleted and prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara)
Library size and purity control was performed on a 2100 Bioanalyzer (Agilent) using a High-Sensitivity DNA-Chip. Library concentration was measured using a KAPA Library Quantification Kit.

value: Microglia

value: Knock-in hATXN2-Q33; hTDP-43 (Double mutant, Heterozygous)

value: Untreated


title: D4_DnmtWT_TET1_Arsi_H3K27me3_rep2

value: mouse embryonic stem cells

value: DnmtWT

value: Day 4 post-FGF2/Activin A treatment


title: Colon_DT_Cre-Positive_02


title: Prolactin-XL 9D rep 3


title: Bladder,  β‐Catenin positive 11

value: Human urinary bladder tumor


title: Colon_DT_Cre-Positive_04


title: Bladder,  β‐Catenin positive 12


title: Colon_DT_Cre-Positive_03


title: D4_DnmtWT_TET1_Atp4a_H3K27me3_rep1

value: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)


title: Colon_DT_Cre-Negative_05


title: Bladder,  β‐Catenin positive 7


title: Spinal cord microglia from ATXN2-Q33;TDP-43 animals (Sc12)

description: Microglia Sc12


title: Spinal cord microglia from ATXN2-Q33;TDP-43 animals (Sc8)

description: Microglia Sc8


title: D4_DnmtWT_TET1_Zdbf2_H3K27me3_rep2


title: Bladder,  β‐Catenin positive 6


title: Spinal cord microglia from NTg animals (Sc11)

description: Microglia Sc11

value: Non-transgenic (C57BL/6)


title: Colon_DT_Cre-Positive_01


title: D4_DnmtWT_TET1_Arsi_H3K27me3_rep1


title: Colon_DT_Cre-Negative_03


title: Bladder,  β‐Catenin positive 8


title: Spinal cord microglia from NTg animals (Sc9)

description: Microglia Sc9


title: D4_DnmtWT_TET1_Zdbf2_H3K27me3_rep1


title: Bladder,  β‐Catenin positive 9


title: D4_DnmtWT_TET1_Celsr2_H3K27me3_rep2


title: Colon_DT_Cre-Negative_02


title: D4_DnmtWT_TET1_Celsr2_H3K27me3_rep1


title: P. vulgaris + T. urticae replicate 3

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

state: Madrid

address: Campus Montegarcedo

department: Interacción de las Plantas con el Medio

country: Spain

institute: CBGP-INIA-UPM

description: VuT rep3

data_processing:
FASTQ files were processed to remove adapters, poly-N sequences and reads with low quality from raw data. Paired-end clean reads were mapped against the P. vulgaris or P. lunatus reference genomes (Phytozome genome IDs: 442 and 563, respectively at https://phytozome-next.jgi.doe.gov/) using HISAT2 software (Kim et al., 2015). FeatureCounts was used for the generation of the count data files from sorted BAM files (Liao et al., 2014).
Differential expression analysis was performed with DESeq2 R package (Love et al., 2014) by comparing infested (VuT for P. vulgaris infested samples; LuT for P. lunatus infested samples) against control or non-infested (VuC and LuC, respectively). Differentially expressed genes (DEGs) were considered when p-value adjusted < 0.05 and -1>log2FC >1 were present.
Assembly: P. vulgaris or P. lunatus reference genomes (Phytozome genome IDs: 442 and 563, respectively at https://phytozome-next.jgi.doe.gov/)
Supplementary files format and content: Pv_rawcounts, raw counts obtained from P. vulgaris samples
Supplementary files format and content: Pl_rawcounts, raw counts obtained from P. lunatus samples

organism: Phaseolus vulgaris

source_name: leaves

growth_protocol: Common bean (Phaseolus vulgaris, cultivar California Red Kidney) and lima bean (Phaseolus lunatus var. Peladilla; Semillas Bartle, Spain) were grown for 3 weekson potting soil and vermiculite (3:1) in growth chambers (Aralab D1200PLH) under control conditions (23 °C ± 1 °C, > 60 % relative humidity and a 16 h/8 h day/night photoperiod). A colony of T. urticae, London strain (Acari: Tetranychidae), kindly provided by Dr. Miodrag Grbic (UWO, Canada), was reared on beans (P. vulgaris) and kept in growth chambers (Sanyo MLR-351-H) at 25 °C ± 1 °C, >70% relative humidity and a 16 h/8 h day/night photoperiod.

extract_protocol:
non-infested (control) or infested with T. urticae Phaseolus detached leaves were collected at 24 hpi (hours post infestation) and frozen into liquid N2. Total RNA was extracted using TRIzol reagent (Invitrogen, Boston, MA, USA) following manufacturer´s instructions. Total DNA-free RNA was cleaned using RNeasy Plant Mini Kit purification columns (Qiagen, Hilden, Germany).
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacture’s intructions.

treatment_protocol: Mite infestation was performed in Phaseolus detached leaves with 50 adult females/leaflet

value: leaves

value: First true leaf

value: T. urticae 24hpi


title: D7_DnmtTKO_EzhipKO_RNA_rep2

value: DnmtTKO + EzhipKO

value: Day 7 post-FGF2/Activin A treatment


title: HD,D45,rep1

city: Melbourne

first: Maria Rosaria

last: Nucera

state: VICTORIA

address: 50, Flemington road

department: Paediatrics

country: Australia

institute: University of Melbourne

library_source: transcriptomic single cell

data_processing:
the sequencing data was pre-processed with the Cell Ranger Single-Cell Software Suite  (v.2.1.1, 10x Genomics)
Assembly: Hg38
Supplementary files format and content: count matrix, barcodes and genes lists

growth_protocol: Cells were kept in monolayer on 120-180 µg/ml Geltrex coated cell culture dishes and in feeder-free conditions in mTeSR1 medium added with Penicillin (100 489 U/ml) and Streptomycin (100 μg/ml) (Euroclone, EC3001D). Once a week, hESC colonies were split with a ratio of 1:10 by ReleSR dissociation. Cells were kept in culture for 3 months and then a new batch was thawed.

extract_protocol: The Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V2 User Guide

value: neuronal stem cell

value: CRISPR/Cas9 modification of HD


title: D4_DnmtWT_TET1_scrambled_H3K27me3_rep1


title: D7_DnmtTKO_EzhipKO_RNA_rep1


title: P. vulgaris + T. urticae replicate 2

description: VuT rep2


title: Colon_DT_Cre-Negative_04

value: Colon

value: Diptheria toxin


title: P. vulgaris + T. urticae replicate 1

description: VuT rep1


title: Bladder,  β‐Catenin positive 1


title: HD,D45,rep3


title: Bladder,  β‐Catenin positive 5


title: CTRL,D45,rep1

value: wild type


title: Bladder,  β‐Catenin positive 4


title: Colon_DT_Cre-Negative_01


title: HD,D45,rep2


title: 2 M mice pooled, age 12 weeks

description: 10x Genomics

data_processing:
Output data were processed using the 10X genomics Cell Ranger pipeline to generate barcode and feature count matrices for downstream analysis
Assembly: mm10
Supplementary files format and content: CellRanger output data_barcodes_features_matrix.tsv

source_name: 3D culture

extract_protocol:
Cell were prepared by Accutase digestion of 3D neurospheres for 45 minutes to generate single cell suspensions that were further purified by FACS
Single cells (scRNAseq) 10X Genomics Cell Ranger pipeline

value: 3D culture

tag: gender

value: male

value: Plp1-negative from 3D culture

value: C57BL/6 Plp1::GFP

tag: age

value: 12 weeks


title: shScramble Bio rep 4

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR (version_2.7.5c) in two-pass mode following STAR best practices and recommendations [Dobin et al]. The quality of the data was evaluated using STAR (version 2.7.5c) [Dobin et al] and samtools (version 1.15) [Danecek et al and Bonfield et al]. PCR duplicates were removed from aligned bam files using samtools (version 1.15) [Bonfield et al]. Read counts were extracted from the aligned bam files using subread’s FeatureCounts (version 2.0.3) [Liao et al].
Assembly: hg38
Supplementary files format and content: Tab separated raw reads values

extract_protocol:
Maxwell® Promega. Maxwell® RCS SImplyRNA Cells. REF: AS1390.
TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031058 Rev. E), using “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA Single Indexes (Illumina Inc. Cat. # 20020492 and 20020493)

treatment_protocol: shRNA transduction

value: Prostate cancer cell line

value: shScramble


title: shIER5L Biol rep 4


title: CTRL,D45,rep3


title: Bladder,  β‐Catenin positive 2

value: Human urinary bladder tumor


title: Spinal cord microglia from NTg animals (Sc7)

description: Microglia Sc7

value: Spinal cord

value: Microglia

value: Non-transgenic (C57BL/6)

value: Untreated


title: CTRL,D45,rep2

value: neuronal stem cell


title: shScramble Bio rep 3


title: P. vulgaris control replicate 1

description: VuC rep1

value: leaves

value: First true leaf

value: control


title: P. vulgaris control replicate 3

description: VuC rep3


title: 96 cells per library, ipsc-motor neurons, ATXN2-ALS and healthy control iPSC-derived hMN combined, 2d

data_processing:
Mapping and generation of count tables was performed using the MapAndGo script
Single-cell transcriptomics analysis was done using RaceID2
cel-seq_barcodes.csv contains barcode information used to assign reads to each cell
Assembly: Hg38
Supplementary files format and content: Ollie_384.coutt.csv            (all libraries merged)
Supplementary files format and content: Merge_files_Ollie384_remapped.R (code for merging individual libraries and cell labeling); Ollie_384_remapped.txt.                    (merged document)

source_name: iPSC-derived spinal motor neuron

extract_protocol:
RNA was extracted by 2x heat lysis (65C) in 384 well and immediately used for downstream single cell RNA sequencing reactions (Celseq2) as previously described (Hashimshony et al., 2016 and Muraro et al., 2016).
RNA libraries for RNA-seq were prepared following a SORT-seq pipeline

value: iPSC-derived spinal motor neuron

value: ALS patient carrying ATXN2 intermediate repeat expansions heterozygously (Q22/Q31; ALS-G) and age-matched healthy control (Q22/Q22; OH2.6)


title: P. vulgaris control replicate 2

description: VuC rep2


title: CTRL,co-culture,rep2

value: mixed wild type genotype and CRISPR/Cas9 modification of HD


title: HD,mono-culture,rep1

value: CRISPR/Cas9 modification of HD


title: 96 cells per library, ipsc-motor neurons, ATXN2-ALS and healthy control iPSC-derived hMN combined, 2c


title: control,mono-culture,rep2

value: wild type


title: Bladder,  β‐Catenin positive 3


title: IgG/aIFNg_C57BL/6_MA10_CMO

city: Charlottesville

first: Chaofan

last: Li

state: VA

address: 345 Crispell Drive

department: Division of Infectious Diseases and International Medicine; Carter Immunology Center

institute: University of Virginia

description: 10X Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger.
Assembly: GRCh38, mm10
Supplementary files format and content: fastq file, hd5 file

molecule: other

source_name: BAL

extract_protocol:
For human samples, the whole blood was mixed with phosphate-buffered saline (PBS) and then gently put over on Ficoll-Paque (Cytiva) in a 50-ml tube. Buffy coat generated by centrifuging at 400g for 40 min at RT was collected. For single-cell purification from BAL, BAL was filtered with a 70-μm cell strainer (Falcon) and then centrifuged at 300g for 10 min at 4°C. Mouse BAL cells were obtained from BAL, briefly, alveolar lavages were pooled from BAL washes (PBS with 2 mM EDTA). Single cell suspensions were further passed through 70μm cell strainers once before the next step operation.
10X 5' Library & Gel Bead Kit v1.1 or 3' Library & Gel Bead Kit v3.1were performed for GEX library construction.

value: BAL

tag: library type

value: CMO

tag: hot


title: BALB/c_BAL_naive/MA10_CMO

description:
10X Genomics
BAL_MA10_1_filtered_feature_bc_matrix.h5
BAL_MA10_2_filtered_feature_bc_matrix.h5
BAL_MA10_3_filtered_feature_bc_matrix.h5
BAL_Naive_1_filtered_feature_bc_matrix.h5
BAL_Naive_2_filtered_feature_bc_matrix.h5
BAL_Naive_3_filtered_feature_bc_matrix.h5
feature_reference.csv

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger.
Assembly: GRCh38, mm10
Supplementary files format and content: hd5 file

value: BALB/c

tag: infection

tag: cmo


title: 96 cells per library, ipsc-motor neurons, ATXN2-ALS and healthy control iPSC-derived hMN combined, 2b


title: shScramble Bio rep 1

value: Prostate cancer cell line

value: shScramble


title: HD,co-culture,rep2


title: IgG/aIFNg_C57BL/6_MA10_GEX

description: 10X Genomics


title: control,mono-culture,rep1


title: D7_DnmtTKO_H3K36me3_rep2

description: CUT&Tag

growth_protocol: Day 7 post-FGF2/Activin A treatment

extract_protocol:
We performed CUT&Tag according with the protocol described in (Kaya-Okur et al., 2020), closely following the procedure described in “Bench top CUT&Tag V.2” (S Kaya-Okur and Henikoff, 2019). 500,000 cells were used for each sample and duplicates were performed. The primaries antibodies, anti-H3K27me3 (Cell signal C36B11) 1:100, the anti-H3K36me3 (Invitrogene RM491) 1:100, were incubated overnight at 4ºC on a rotator. Samples were then incubated with a secondary anti-rabbit IgG (ABIN6923140) at room temperature on a rotator.  After an incubation of 1h at room temperature with a pA-Tn5 adapter complex (Addgene #124601), the Tn5 enzyme tagmentation reaction was performed by adding a buffer containing MgCl2 to the samples and incubating for 1h at 37°C. To stop tagmentation and solubilize DNA fragments, we added 10 μL 0.5M EDTA, 3 μL 10% SDS and 2.5 μL 20 mg/mL Proteinase K to each sample and samples were incubated at 50°C for 1h. Purified DNA was obtained by phenol/chloroform extraction and precipitated with 100% ethanol and centrifugation. The DNA pellet was washed in 80% ethanol, spun down and air-dried before being resuspended in 25µl of 1mM Tris-HCl pH8.0.
Nextera primers or indexed primers were used to perform PCR. Library quality was assessed using 4200 TapeStation system (Agilent) and paired-end, 150 bp sequencing on an Illumina Novaseq was performed by Novogene Co.

tag: growth media

value: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)

value: DnmtTKO


title: shIER5L Biol rep 3


title: HD,co-culture,rep1


title: SW620 bulk

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

institute: Erasmus Medical Center

description: single cell

data_processing:
FASTQ files were processed with CellRanger v2.1.1 and reads were aligned to the human transcriptome (GRCh38)
Downstream analysis was performed in R with the Seurat package
Assembly: GRCh38
Supplementary files format and content: CellRanger output files

source_name: colon

growth_protocol: Cell populations were sorted from established colon cancer cell lines grown in standard culture medium.

extract_protocol:
Cells were FACS sorted to enrich for live, single cells. Cells were lysed in droplets using Single Cell 3' v2 chemistry (10X Genomics).
RNA-Seq was performed at the Erasmus MC Center for Biomics (Rotterdam, The Netherlands). The sample was sequenced to an average depth of 50k reads/cell

value: colon

value: cell line

value: No treatment


title: BALB/c_BAL_naive/MA10_GEX

value: GEX


title: shIER5L Biol rep 2


title: NJH29, AZD1775, rep3, untreated

city: Stanford

first: Alexandros

last: Drainas

address: 265 Campus Drive

department: Pediatrics and Genetics

institute: Stanford

description: Samples were Sequenced by Novogene

data_processing:
salmon version 0.8.2
salmon quant -i <transcripts_index> -l A -1 <read1.fastq.gz> -2 <read2.fastq.gz> -p 8 -o <sample_quant>
Assembly: Hg38
Supplementary files format and content: Salmon quantification file

growth_protocol: NCI-H82 and NCI-H69 were purchase from ATCC (HTB-175 and HTB-119). NJH29 cells were developed at Stanford (Jahchan et al., 2013). The SCLC cell lines were grown in RPMI 1640 (Corning, 15-040-CV) medium supplemented with 10% FBS (Thermo Fischer Scientific, 10500064) or BGS (Thermo Fischer Scientifc, SH3054103HI) and 1X Antibiotic-Anti-mycotic (Thermo Fischer Scientific, 15240062) and L-glutamine (Croning, 25-005-CI). 293T (ATCC #CRL-3216) cells were grown in DMEM (Thermo Fischer Scientific, 31966021) medium supplemented with 10% FBS and 1X Antibiotic-Anti- mycotic. All cell lines were maintained in appropriate densities and were incubated in a humidity-controlled environment (37C, 5% CO2). All cell lines tested negative for mycoplasma contamination.

extract_protocol:
RNA extraction conducted by Novogene
Library construction by Novogene

treatment_protocol: 1M cells were treated with 0.4 or 0.8 μM AZD1775 for 24h.

value: epithelia-like cell line derived from small cell lung cancer

value: AZD1775 tolerant

value: DMSO

tag: replicate

tag: time


title: shIER5L Biol rep 1

tag: cell type


title: D7_DnmtTKO_H3K36me3_rep3

description: CUT&Tag


title: 96 cells per library, ipsc-motor neurons, ATXN2-ALS and healthy control iPSC-derived hMN combined, 2a

value: iPSC-derived spinal motor neuron

value: ALS patient carrying ATXN2 intermediate repeat expansions heterozygously (Q22/Q31; ALS-G) and age-matched healthy control (Q22/Q22; OH2.6)


title: D7_DnmtTKO_H3K36me3_rep1

description: CUT&Tag


title: 4C-Seq melanogaster imaginal disc HP6/Umbrea

city: NEW YORK

first: UnJin

last: Lee

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: single run 50bp mixed with bacterial genomic DNA at core facility

data_processing:
trim, then align
calculate virtual fragment library between dpnii and csp6i
calculate coverage using bedtools
N/A
N/A
Assembly: dm6
Supplementary files format and content: BED file, contains fragment boundaries, number of overlapped reads, number of bases with overlap, length of fragment, fraction of bases with non-zero coverage
Supplementary files format and content: N/A
Library strategy: 4C-Seq

organism: Drosophila melanogaster

source_name: imaginal disc

extract_protocol:
imaginal disc tissue is dissected in 1x PBS in 10m intervals, flash frozen. Single nucleus suspension, then double digestion using DpnII and XbaI.
proximity ligation, amplification with divergent hp6/umbrea primers with i5/i7 adapters
double digest with 4-cutters (dpnii, csp6i), proximity ligation, amplification

tag: tissue

value: imaginal disc


title: control,co-culture,rep1

tag: cell line

value: neuronal stem cell

tag: genotype

value: mixed wild type genotype and CRISPR/Cas9 modification of HD


title: D0_DnmtTKO_H3K36me3_rep2

description: CUT&Tag

data_processing:
WGBS data: as described in Richard Albert et al. 2020 Nature Communications. Reads were mapped to the mm10 genome using Bismark and standard parameters
CUT&Tag data: PCR duplicate removal using BBmap clumpify (Bushnell et al., 2014)(v38.18) and parameters: reorder dedupe=t k=19 passes=6 subs=(0.01 x readlength). Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using Bowtie2 (Langmead et al., 2019)(v2.4.5) for CUT&Tag using parameters: --local –very-sensitive –no-mixed –dovetail –no-discordant –phred33 -I 10 -X 700
Processed bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
Assembly: mm10
Supplementary files format and content: Bigwig format. CUT&Tag: CPM-normalized counts. WGBS: percent methylated Cs at CpG dinucleotides covered by at least 5 reads.

growth_protocol: Day 0 post-FGF2/Activin A treatment

tag: strain


title: 2 F mice pooled, age 12 weeks

description: 10x Genomics

value: 3D culture

value: female

value: Plp1-negative from 3D culture

value: C57BL/6 Plp1::GFP

value: 12 weeks


title: shScramble Bio rep 2

value: Prostate cancer cell line

tag: treatment

value: shScramble


title: OMM2.3, shLINC01315, rep1

city: Shanghai, China

first: Zhu

last: Xie

state: China

address: Rm A601, Building for School of Life Sciences Fudan University Jiangwan Campus 2005 Songhu Rd, Shanghai 200433 China

country: China

institute: Fudan university

data_processing:
CLC Genomics Workbench V 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench(parameter-quanlity limit:0.05)
Trimmed sequence reads were mapped to GRCh38.p13/hg38 using CLC Genomics Workbench(parameter-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8 )
Read count extration and normalization were performed using CLC Genomics Workbench
Assembly: hg38
Supplementary files format and content: raw counts and RPKM values for each sample

growth_protocol: OMM2.3 uveal melanoma cells were maintained in RPMI 1640 supplemented with 10% Fetal bovine and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent (Vazyme).5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA sequence were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina following manufacture'protocols.

treatment_protocol: OMM2.3 with target genotype was treated with 1 ug/ml puromycin for 7 days

value: Uveal melanoma cells

value: YAPer-ORF Knockdown

value: Resistance selection


title: OMM2.3, OE-ORF, rep1

value: YAPer-ORF overexpression


title: OMM2.3, shLINC01315, rep2


title: D7_DnmtWT_H3K36me3_rep3

description: CUT&Tag

value: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)

value: DnmtWT


title: Mice Bone Marrow cells, lu-y17005

type: RNA

city: Houston

first: Yong

last: Lu

address: 6565 Fannin St

institute: Houston Methodist

description: Gene expression data from the cells treated with or without p38 inhibitors

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Bone Marrow cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Murine BM cells were cultured and supplemented with mGM-CSF (20 ng/ml) with or without p38 inhibitors. Mice were treated with mCAR-Tcells. In some studies with or without p38 inhibitors.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 0.6 uM of SB203580 was added to the BM cultures on day 0. B6 mice were treated with SB203580 (i.p. 5 mg/kg, once every three days, 7 times in total) after ACT.

value: Mice Bone Marrow cells

value: p38I (in vitro)


title: NJH29, AZD1775, rep2, untreated

description: Samples were Sequenced by Novogene

value: epithelia-like cell line derived from small cell lung cancer

value: AZD1775 tolerant

value: DMSO


title: HD,mono-culture,rep2

value: neuronal stem cell

value: CRISPR/Cas9 modification of HD


title: Mice Bone Marrow cells, lu-y17003

value: Ctrl (in vitro)


title: NJH29, AZD1775, rep3, treated

description: Samples were Sequenced by Novogene


title: D7_DnmtWT_H3K36me3_rep2

description: CUT&Tag


title: OMM2.3, shControl, rep2

value: WT


title: NJH29, AZD1775, rep1, untreated

description: Samples were Sequenced by Novogene


title: D0_DnmtWT_H3K36me3_rep2

description: CUT&Tag


title: Mice Bone Marrow cells, lu-y17006


title: OMM2.3, OE-ORF, rep2


title: D7_DnmtWT_H3K36me3_rep1

description: CUT&Tag


title: NCI-H82, AZD1775, rep2, untreated

description: Samples were Sequenced by Novogene


title: NCI-H82, AZD1775, rep3, untreated

description: Samples were Sequenced by Novogene


title: D7_DnmtTKO_EzhipKO_H3K27me3_rep2

description: CUT&Tag

value: DnmtTKO


title: D0_DnmtTKO_H3K36me3_rep1

description: CUT&Tag


title: Mice Bone Marrow cells, lu-y17004


title: NCI-H82, AZD1775, rep1, untreated

description: Samples were Sequenced by Novogene


title: D7_DnmtTKO_EzhipKO_H3K27me3_rep1

description: CUT&Tag


title: NJH29, DMSO, rep3, untreated

description: Samples were Sequenced by Novogene


title: NJH29, DMSO, rep2, untreated

description: Samples were Sequenced by Novogene


title: OMM2.3, shControl, rep1


title: Mice Bone Marrow cells, lu-y17002


title: Mice tumor cells, lu-y16018

description: Gene expression data from the mice treated with or without p38 inhibitors

source_name: tumor cells

value: Mice tumor cells

value: CAR-T (in vivo)


title: NJH29, AZD1775, rep2, treated

description: Samples were Sequenced by Novogene


title: M1006_CNS

city: Kiel

first: Lennart

middle: TN

last: Lenk

state: SH

address: Rosalind-Franklin-Str. 9

department: Pediatric Hematology/Oncology

country: Germany

institute: UKSH Campus Kiel

data_processing:
Obtained raw reads were subjected to chastity filtering by Illumina and pre-processed using cutadapt (Martin, 2011) and PrinSeq-lite (Schmieder and Edwards, 2011) to eliminate adapters and sequences of low quality.
Alignment to the human genome (hg19/CRCh37, Ensembl GRCh37, hg19 reference genome)  was conducted with TopHat2 (Trapnell et al., 2012).
Transcript levels were quantified using HTSeq (Anders et al., 2015) and differential expression of genes was assessed using the Bioconductor package DESeq2 (Love et al., 2014).
GSEA was performed as described previously (Subramanian et al., 2005).
Assembly: hg38
Supplementary files format and content: a tabular normalizied counts matrix
Supplementary files format and content: a tabular differentially expressed gene matrix

source_name: Blood

growth_protocol: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice were purchased from Charles River and xenografts generated in accordance with governmental regulations (Schleswig-Holstein Ministerium für Energiewende, Landwirtschaft, Umwelt, Natur und Digitalisierung). One million ALL cells were injected intravenously into female NSG-mice (6–10 weeks of age) and leukemic engraftment was followed by detection of human CD45+/murine CD45−/human CD19+ cells in the peripheral blood via flow cytometry analysis. Animals were sacrificed when showing signs of overt leukemia (detection of >75% leukemic blasts in the peripheral blood or clinical signs of leukemia including loss of weight or activity, organomegaly, hind-limb paralysis).

extract_protocol:
RNA was prepared using Direct-zol™ RNA Kit (Zymo Research). RNA integrity was checked using an Agilent Bionanalyzer according to the manufacturer's guidelines.
Library construction was performed employing the TruSeq stranded totalRNA protocol (Illumina) and subsequently sequenced on an Illumina HiSeq 2500 generating paired end reads with 2x125bp while multiplexing 10 samples per lane.

treatment_protocol: For the recovery of ALL cells from murine organs, mice were sacrificed by CO2 inhalation and spleens, hind leg bones and heads were collected. BM cells were isolated by flushing out the bones using a 27 G syringe. For extraction of the meninges, mouse skulls were opened, brains extracted and the meninges were carefully detached from the skull with tweezers. Spleen and CNS were homogenized using a 70 µm Nylon cell strainer. Spleen, BM, and CNS cells were subjected to red blood cell lysis, washed with PBS and purity of ALL cells was assessed via flow cytometry detecting human CD45, murine CD45, and human CD19.

value: Blood

value: Acute Lymphoblastic Leukemia

value: exctracted from CNS


title: MCL-19245-2

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw paired-end sequence data were merged without trimming using the software package PEAR. Merged reads were mapped to the HBV reference DNA sequence (HBV.fa) using Bismark. Methylation status was called at each CpG using Bismark, and total counts, methylated counts, and percent methylation were computed for each CpG position.
Assembly: Custom: HBV genome fasta file GSE242448_HBV.fa.gz from GSE242448
Supplementary files format and content: combined_methyl.txt: Tab-delimited text file of total coverage, methylated read coverage, and percent methylation for each sample.

source_name: Liver

extract_protocol:
RNA were isolated from liver of HBV transgenic mice using the protocol as described by: Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162: 156–159. doi:10.1006/abio.1987.9999.
Bisulfite treatment of protein-free genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning Kit (D5030; Zymo Research, Inc., Irvine, CA, USA) according to the manufacturer's instructions.  The three major viral amplicons covering 62 of the 99 CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite-treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument.  Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps in a protocol termed targeted amplicon sequencing (TAS)  The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’- TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (ii) 5’-ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’ (oligo CS1FP5a; HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), and (iii) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo CS1FP9; HBV nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV nucleotide coordinates 730-712).

tag: agent

value: hepatitis B virus, replication in mouse

value: Liver

tag: host foxa1_genotype

value: f/f

tag: host foxa2_genotype

tag: host foxa3_genotype

tag: host albcre

tag: host sex

value: M


title: NCI-H82, AZD1775, rep3, treated

description: Samples were Sequenced by Novogene

value: epithelia-like cell line derived from small cell lung cancer


title: M1011_CNS


title: Mice tumor cells, lu-y16017


title: NJH29, AZD1775, rep1, treated

description: Samples were Sequenced by Novogene

value: AZD1775 tolerant


title: M1006_Sp

value: exctracted from spleen


title: Mice Bone Marrow cells, lu-y17001

value: Mice Bone Marrow cells


title: D7_DnmtTKO_H3K27me3_rep2

city: Paris

first: Julien

last: Richard Albert

address: 15 Rue Hélène Brion

institute: Institut Jacques Monod, CNRS, Université de Paris

description: CUT&Tag

value: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)


title: M922_CNS


title: Mice tumor cells, lu-y16015

value: p38I (in vivo)


title: M1011_BM

value: exctracted from bone marrow


title: D7_DnmtWT_H3K27me3_rep2

description: CUT&Tag

value: DnmtWT


title: D0_DnmtWT_H3K36me3_rep1

description: CUT&Tag


title: M1011_Sp


title: Mice tumor cells, lu-y16016

value: Mice tumor cells


title: D7_DnmtWT_H3K27me3_rep1

description: CUT&Tag


title: D7_DnmtTKO_H3K27me3_rep1

description: CUT&Tag

value: DnmtTKO


title: MCL-19238-1

value: F


title: NJH29, DMSO, rep1, untreated

description: Samples were Sequenced by Novogene

value: WT

value: DMSO


title: M922_Sp

value: Blood

value: Acute Lymphoblastic Leukemia


title: M917_CNS

value: exctracted from CNS


title: D0_DnmtWT_H3K27me3_rep1

description: CUT&Tag


title: M1006_BM


title: MCL-19221-1

value: hepatitis B virus, replication in mouse

value: Liver

value: f/f


title: Mice tumor cells, lu-y16013

value: Ctrl (in vivo)


title: MCL-19218-2


title: NCI-H82, AZD1775, rep2, treated

description: Samples were Sequenced by Novogene

value: epithelia-like cell line derived from small cell lung cancer

value: AZD1775 tolerant


title: M917_Sp

value: exctracted from spleen


title: MCL-19218-1


title: MCL-19245-1

value: M


title: M915_CNS


title: BVLO, iPSC-derived organoid

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

institute: The University of Tokyo

data_processing:
Raw data processing: Cell by gene count matrices were generated by processing FASTQ files using the Cell Ranger count (version 5.0.1, 10X Genomics) pipeline with the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference for each sample. Gene expression data were processed using the R package Seurat (version 4)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hiPSC-BV-integrated liver organoids (BVLO)

extract_protocol:
BVLO dissociation was done by incubation in digestion medium [0.5 mg/mL collagenase (Sigma-Aldrich), 0.5 mg/mL pronase (Roche, Basel, Switzerland), and 0.25 mg/mL DNase1 (Sigma-Aldrich) in liver digestion medium for 30 minutes at 37°C, on shaker
Library construction was performed according to manufacturer’s instructions (10x genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: hiPSC


title: MCL-19210-2


title: NCI-H82, AZD1775, rep1, treated

description: Samples were Sequenced by Novogene


title: Mice tumor cells, lu-y16014

value: Mice tumor cells


title: MCL-19238-2


title: D0_DnmtTKO_H3K27me3_rep1

description: CUT&Tag

source_name: mouse embryonic stem cells

value: DnmtTKO


title: SUM159PT, sgYES1, 48 hrs, rep 1

city: Cleveland

first: Ruth

last: Keri

state: Ohio

address: 9620 Carnegie Ave

institute: Cleveland Clinic Foundation

data_processing:
Library preparations were sequenced on Illumina platform and paired-end reads were generated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene.
Assembly: hg38
Supplementary files format and content: read counts, txt

source_name: breast cancer

growth_protocol: Cells were seeded into 6 mm dishes at 3 x 10^6 cells/plate in 4 mL complete RMPI (231) or Ham/F12 (SUM159) on day 0.

extract_protocol:
RNA was extracted using the RNAeasy Plus Minikit (Qiagen) per manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: On day 1, cells were transfected using Lipofectamine2000 in Optimem with sgRNA that was non-targeting (sgNTS) or targeted to YES1 (sgYES1). After 6 hrs, equal parts complete media (respective to cell line) was added to plates. At 24 hours, media was completely changed to media appropriate for cell line. Cells were collected 48 hrs after transfection.

value: breast cancer

value: triple negative breast cancer cells


title: NCI-H82, DMSO, rep1, untreated

description: Samples were Sequenced by Novogene

value: WT

value: DMSO


title: D0_DnmtWT_H3K27me3_rep2

description: CUT&Tag

value: DnmtWT


title: MCL-19206-1

value: F


title: N9 ATXN2-ALS  iPSC-derived motor neurons

description:
ALS MN N
Sample name in MN_5vs5_edgeR_counts2.txt: N

data_processing:
Reads were demultiplexed and converted to FASTQ format using CASAVA software from Illumina.
FASTQ files were mapped with TopHat2  using the ‘fr-firststrand’ option for strand orientation to generate BAM-formatted genomic coordinates.
Count data for genes were analyzed in R using the Bioconductor package edgeR version 3.12.152 with the trimmed mean of M323 values (TMM) normalization method 53.
P values adjusted for multiple testing were calculated using Benjamini Hochberg false discovery rate (FDR) and only genes at FDR < 0.05 were considered significantly differentially expressed
Assembly: hg19/GCh37
Supplementary files format and content: MN_5vs5_sigGenesFDR005.txt  (ALS vs HC DESeq analysis)
Supplementary files format and content: MN_5vs5_edgeR_counts2.txt (ALS vs HC raw counts)

extract_protocol:
Total RNA was isolated and extracted using the RNeasy Micro Kit (Qiagen with DNA digestion on-column, according to the manufacturer's instructions. RNA integrity (RIN) was verified in an Agilent 2100 bioanalyzer and only samples with RIN ≥ 8.0 were used for RNA sequencing. rRNA was depleted using the Ribo-Zero Magnetic Kit before library preparation.
Stranded, paired-end sequencing libraries were prepared (Genome Analysis Facility, Groningen, The Netherlands) and sequenced in the Illumina HiSeq2500 platform (Illumina, San Diego, California).

value: iPSC-derived spinal motor neuron

value: ATXN2 intermediate repeat expansions (Q22/Q33)


title: C57BL/6_Young_BAL_MA10_D35_GEX

description: 10X Genomics

value: BAL

tag: age

value: Young

tag: infection

tag: library type

value: GEX


title: NCI-H82, DMSO, rep2, untreated

description: Samples were Sequenced by Novogene

value: epithelia-like cell line derived from small cell lung cancer

tag: replicate


title: SUM159PT, sgNTS, 48 hrs, rep 3

value: sgNTS


title: C57BL/6_Young_BAL_MA10_D21_GEX

description: 10X Genomics

tag: time


title: MCL-19184-2

value: hepatitis B virus, replication in mouse

value: Liver

value: f/f


title: D0_DnmtTKO_H3K27me3_rep2

description: CUT&Tag

tag: growth media

value: DnmtTKO


title: MCL-19221-2

tag: tissue


title: NCI-H82, DMSO, rep3, untreated

description: Samples were Sequenced by Novogene

tag: cell line

tag: cell type


title: D7_WGBS

description: WGBS

extract_protocol:
Total RNA was extracted from the cells with RNEasy Plus Mini kit (Qiagen), according to the manufacturer’s instructions.
From genomic DNA we provided, WGBS libraries were generated using the Accel-NGS Methyl-Seq DNA library Kit (Swift Biosciences) and sequenced on an Illumina Novaseq (paired-end, 150 nucleotide-long reads) by Novogene Co.

tag: strain

value: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)

tag: genotype


title: SUM159PT, sgNTS, 48 hrs, rep 4

value: breast cancer

value: triple negative breast cancer cells

tag: treatment


title: SUM159PT, sgNTS, 48 hrs, rep 2

value: WT


title: M917_BM

value: Blood

value: Acute Lymphoblastic Leukemia

value: exctracted from bone marrow


title: D4_WGBS

description: WGBS

growth_protocol: Day 4 post-FGF2/Activin A treatment

value: DnmtWT


title: SUM159PT, sgYES1, 48 hrs, rep 4


title: SUM159PT, sgNTS, 48 hrs, rep 1


title: B11 ATXN2-ALS  iPSC-derived motor neurons

description:
ALS MN B
Sample name in MN_5vs5_edgeR_counts2.txt: B11

value: iPSC-derived spinal motor neuron

value: ATXN2 intermediate repeat expansions (Q31/Q33)


title: D0_WGBS

description: WGBS


title: M922_BM


title: SUM159PT, sgYES1, 48 hrs, rep 3


title: C57BL/6_Aged_BAL_MA10_D21_GEX

description: 10X Genomics

value: BAL

value: Aged

value: GEX


title: MCL-19210-1

tag: agent

value: hepatitis B virus, replication in mouse

tag: host foxa1_genotype

value: M


title: SUM159PT, sgYES1, 48 hrs, rep 2


title: M915_Sp

value: exctracted from spleen


title: MCL-19179-1

value: Liver

tag: host foxa2_genotype

value: f/f

tag: host foxa3_genotype


title: OH4.6 HC  iPSC-derived motor neurons

description:
Control MN 4
Sample name in MN_5vs5_edgeR_counts2.txt: I35_8

value: Healthy control (Q22/Q22)


title: MDA-MB-231, sgYES1, 48 hrs, rep 2

value: breast cancer

value: triple negative breast cancer cells


title: C57BL/6_Aged_BAL_MA10_D10_GEX

description: 10X Genomics


title: MCL-19206-2

tag: host albcre

tag: host sex

value: F


title: C57BL/6_Aged_BAL_MA10_D0_GEX

description: 10X Genomics

tag: age

tag: infection


title: MCL-19179-2


title: OH2.6 HC iPSC-derived motor neurons

description:
Control MN 2
Sample name in MN_5vs5_edgeR_counts2.txt: OH2


title: M915_BM

value: Blood

value: Acute Lymphoblastic Leukemia


title: MDA-MB-231, sgNTS, 48 hrs, rep 4

value: WT

value: sgNTS


title: GG1 ATXN2-ALS  iPSC-derived motor neurons

description:
ALS MN G
Sample name in MN_5vs5_edgeR_counts2.txt: G1

value: iPSC-derived spinal motor neuron

value: ATXN2 intermediate repeat expansions (Q22/Q31)


title: P1 ATXN2-ALS iPSC-derived motor neurons

description:
ALS MN P
Sample name in MN_5vs5_edgeR_counts2.txt: P

value: ATXN2 intermediate repeat expansions (Q22/Q29)


title: MDA-MB-231, sgNTS, 48 hrs, rep 2


title: MCL-19184-1


title: C57BL/6_Young_BAL_MA10_D10_GEX

description: 10X Genomics

value: BAL

value: Young

tag: library type

value: GEX


title: MCL-19180-2

value: hepatitis B virus, replication in mouse

value: M


title: C57BL/6_Young_BAL_MA10_D0_GEX

description: 10X Genomics

tag: time


title: MDA-MB-231, sgYES1, 48 hrs, rep 4


title: MCL-19135-2

value: Liver

value: f/f


title: MCL-19180-1


title: Strain KPN15_pOXA-48DlysR_rep 2

city: Madrid

first: Alvaro

last: San Millan

address: Darwin, 3

department: Biotecnología Microbiana

institute: Centro Nacional de Biotecnología-CSIC

description:
KPN15_pOXA-48DlysR_2
KPN15_DlysR_featureCounts.tsv
KPN15_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

data_processing:
We trimmed and adapter-removed the reads with Trim Galore v0.6.4 (-q 20 --length 50 --illumina). We assessed the quality of the reads before and after trimming with FastQC v.0.11.9 and MultiQC v1.11.
After annotating the reference genomes with PGAP v2021-07-01.build5508, we mapped the trimmed reads to their corresponding reference genome with BWA-MEM v0.7.17.
We inspected the mappings to confirm the appropriate presence or absence of pOXA-48 in the replicates.
We obtained the raw counts of reads mapping to each genomic feature (including CDS, ncRNA, tRNA, tmRNA, antisense RNA, RNase P and SRP RNA) with featureCounts from the Rsubread v2.14.2 package.
We performed the DE analysis from raw counts using DESeq2 v1.40.1 by comparing the pOXA-48-carrying strain against the pOXA-48-free strain (first dataset) or the pOXA-48ΔlysR-carrying strain (second dataset).
Assembly: SAMN39826502, SAMN32542096, SAMN32542113, SAMN32542116, SAMN32542119, SAMN32542124, SAMN32542126, SAMN14640123, SAMN14640085, SAMN14640188, SAMN14640320, SAMN14640201
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (<strain>_featureCounts.tsv)
Supplementary files format and content: tab-delimited text files include log2FoldChanges, padj and other values for each differential expression analysis (<strain>_DE_results_raw.tsv or <strain>_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv)

organism: Klebsiella pneumoniae

source_name: Enterobacteria

growth_protocol: We grew the cells in LB medium with continuous shaking. When cultures reached a turbidity of 0.5 (first dataset) or 0.2-0.3 (second dataset) at 600 nm, we collected the cells at 4ºC, pelleted them by centrifugation at 4ºC 12,000 g or 11,000 g for 1 min and immediately froze them at -70ºC.

extract_protocol:
We purified the total RNA from each sample using the NZY Total RNA Isolation kit (NZYTECH) (first dataset) or the Total RNA Mini Kit (BioRad’s Aurum) (second dataset). Then, we determined RNAs concentration using the Qubit RNA Broad-Range Assay following the manufacturer's instructions. Additionally, the quality of the RNA was examined using the Tape-Station system (Agilent).
We ribodepleted the RNA and sequenced it at the Wellcome Trust Centre for Human Genetics (WTCHG; Oxford, UK) using the Illumina's NovaSeq6000 platform, resulting in >8 million reads per sample (first dataset), or at SeqCoast Genomics (Portsmouth, NH, USA) with Illumina NextSeq2000, generating >6 million reads per sample (second dataset).

value: Enterobacteria

value: pOXA-48DlysR transconjugant

tag: dataset batch

value: Second dataset


title: FaDu_Empty_2

city: New York

first: Jessie

last: Brown

address: 1130 St. Nicholas Ave, 401B

institute: Columbia University Medical Center

data_processing:
Raw reads were demultiplexed
FASTQ files were generated using bcl2fastq v2.20.0.422 (Illumina)
Reads were aligned to a the human (GRCh38) genome
Gene-count matrices were computed using STAR v2.7.9a
Normalized gene expression was computed and differential expression analysis was performed using the negative binomial distribution to estimate the variance-mean dependence and to test for statistical significance in DESeq2 v1.32.0
Genome_build: hg38

source_name: Head and neck squamous cell carcinoma

growth_protocol: MEM alpha Glutamax plus 10% fetal bovine serum

extract_protocol:
RNeasy Mini Kit (Qiagen, #74106)
NEBNext Ultra RNA Library Prep Kit for Illumina

value: FaDu


title: C57BL/6_Aged_BAL_MA10_D35_GEX

description: 10X Genomics

tag: tissue

value: Aged


title: MDA-MB-231, sgNTS, 48 hrs, rep 3

value: breast cancer

tag: cell line

value: triple negative breast cancer cells

value: WT


title: 35_8 HC iPSC-derived motor neurons

first: R. Jeroen

last: Pasterkamp

address: Universiteitsweg 100

institute: University Medical Center Utrecht

description:
Control MN 5
Sample name in MN_5vs5_edgeR_counts2.txt: OH4

tag: cell type

value: iPSC-derived spinal motor neuron

value: Healthy control (Q22/Q22)


title: MDA-MB-231, sgYES1, 48 hrs, rep 3


title: MCL-19135-1


title: BT8  HC iPSC-derived motor neurons

description:
Control MN 3
Sample name in MN_5vs5_edgeR_counts2.txt: BT8


title: CVD_11_BAL_GEX

description: 10X Genomics

value: BAL


title: MDA-MB-231, sgYES1, 48 hrs, rep 1


title: MCL-19133-1

value: F


title: MCL-19176-2


title: MCL-19094-2


title: A18 ATXN2-ALS iPSC-derived motor neurons

description:
ALS MN A
Sample name in MN_5vs5_edgeR_counts2.txt: A18

value: ATXN2 intermediate repeat expansions (Q33/Q33)


title: Python bivittatus left ventricle, 4DPF 1

city: Boulder

first: Dakota

last: Hunt

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
Sample quality was assessed using FastQC version 0.11.51 (Anders, 2010) and reads in FASTQ format were cleaned up using Trimmomatic version 0.36 (Bolger et al., 2014) with the following parameters: ILLUMINACLIP:/opt/trimmomatic/0.36/adapters/TruSeq3-PE.fa:2:30:10 \AVGQUAL:24 SLIDINGWINDOW:5:20 MINLEN:75.
Trimmed, paired-end reads were mapped to the Python bivittatus reference genome using HISAT2 version 2.1.0 (Kim et al., 2019) with the --sensitive flag.
Samtools version 1.8 (Danecek et al., 2021) was used to convert .sam files to sorted and indexed .bam files.
The Rsubread version 2.0.1 (Liao et al., 2019) featureCounts function was used to generate raw counts for each sample. Gene count normalization and differential gene expression analysis was conducted with DESeq2 version 1.36.0 (Love et al., 2014).
Assembly: Python_molurus_bivittatus-5.0.2
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

organism: Python bivittatus

source_name: Ventricle

growth_protocol: Captive-bred Burmese pythons (Python bivittatus) were purchased from Bob Clark Reptiles, Oklahoma City, OK. The pythons weighed ~2kg for the RNA sequencing and proteomics studies (n = 6) and ~250g for full feeding cohort (n = 28).

extract_protocol:
Frozen ventricular tissue was homogenized in Trizol and then incubated at room temperature for five minutes. Chloroform was added at 1:5 (v/v), the tubes shaken vigorously, and incubated at room temperature for 15 minutes. Samples were centrifuged at 12,000 RCF for 15 minutes and the upper aqueous layer collected and added to an equal volume of isopropanol. Then samples were incubated at -20 °C for 15 minutes and then centrifuged at 12,000 RCF for 10 minutes to pellet the RNA. The RNA pellet was washed twice with ice-cold 75% ethanol and solubilized in RNase-free water.
RNA was sent to Novogene Corporation (Sacramento, CA) for mRNA enrichment and short-read RNA sequencing at a depth of 50 million paired-end reads per sample.

treatment_protocol: Pythons were fasted for 28 days and then fed a rodent meal consisting of 25% python body weight. Pythons were humanely euthanized under deep isoflurane-induced anesthesia at Fasted (28 day fast), 1-, 4-, 6--days post-fed (DPF) and left ventricle tissue was collected and snap frozen in liquid nitrogen and stored at -80 °C.

value: Ventricle

value: 4 Day Post-Fed


title: CVD_10_BAL_GEX

description: 10X Genomics

value: GEX


title: FaDu_Empty_1


title: MCL-19176-1

value: hepatitis B virus, replication in mouse

value: Liver

value: f/f

value: M


title: OH1.5 HC iPSC-derived motor neurons

city: Utrecht

description:
Control MN 1
Sample name in MN_5vs5_edgeR_counts2.txt: OH1


title: Python bivittatus left ventricle, 1DPF 2

value: 1 Day Post-Fed


title: FaDu_TINCRHF_2

value: FaDu


title: MCL-19138-1


title: Strain KPN15_pOXA-48DlysR_rep 3

description:
KPN15_pOXA-48DlysR_3
KPN15_DlysR_featureCounts.tsv
KPN15_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

value: Enterobacteria

value: pOXA-48DlysR transconjugant

value: Second dataset


title: MCL-19138-2


title: CVD_10_PBMC_GEX

description: 10X Genomics

value: Blood

value: PBMC


title: HUH7，IP, ZMAT2

city: Changsha

first: Yaning

last: Zhu

address: No.138, Tongzipo Road

department: Department of Radiology

institute: The Third Xiangya Hospital, Central South University

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated reads were mapped to the reference genome of Homo sapiens GRCh38 using STAR software (version 2.5.3a) with default parameters.
RBP binding genes were identificated by edgeR (version 3.12.1).
The exomePeak(Version 3.8) software was used for peak calling.
Assembly: GRCh38
Supplementary files format and content: bam files of IP and Input sample

extract_protocol:
The cells was treated with cell lysis buffer. The 10% lysis sample was stored and named “Input”, and 80% was used in immunoprecipitation reactions with anti-ZMAT2 antibody（Invitrogen, PA5-118370）and named “IP”, and 10% was incubated with rabbit IgG (Proteintech, 30000-0-AP) as a negative control and named “IgG”，respectively. The RNA of Input and IP was extracted using TRIzol reagent(Invitrogen, cat. NO 15596026).
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit(Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Hepatocellular carcinoma cells


title: FaDu_TINCRHF_1


title: Strain J57c1_rep 2

description:
J57c1.2
J57_featureCounts.tsv
J57_DE_results_raw.tsv

organism: Klebsiella variicola

value: pOXA-48 cured

value: First dataset


title: CVD_9_BAL_GEX

description: 10X Genomics

extract_protocol:
For human samples, the whole blood was mixed with phosphate-buffered saline (PBS) and then gently put over on Ficoll-Paque (Cytiva) in a 50-ml tube. Buffy coat generated by centrifuging at 400g for 40 min at RT was collected. For single-cell purification from BAL, BAL was filtered with a 70-μm cell strainer (Falcon) and then centrifuged at 300g for 10 min at 4°C. Mouse BAL cells were obtained from BAL, briefly, alveolar lavages were pooled from BAL washes (PBS with 2 mM EDTA). Single cell suspensions were further passed through 70μm cell strainers once before the next step operation.
10X 5' Library & Gel Bead Kit v1.1 or 3' Library & Gel Bead Kit v3.1were performed for GEX library construction.

value: BAL


title: MDA-MB-231, sgNTS, 48 hrs, rep 1

value: breast cancer

value: triple negative breast cancer cells

value: WT

value: sgNTS


title: HUH7，Input, ZMAT2

value: Liver


title: Python bivittatus left ventricle, 6DPF 2

value: Ventricle

value: 6 Day Post-Fed


title: CVD_9_PBMC_GEX

description: 10X Genomics

value: GEX


title: Python bivittatus left ventricle, Fasted 1

value: Fasted


title: Python bivittatus left ventricle, 6DPF 1


title: MCL-19133-2

value: hepatitis B virus, replication in mouse

value: f/f

value: F


title: Strain KPN15_pOXA-48DlysR_rep 1

description:
KPN15_pOXA-48DlysR_1
KPN15_DlysR_featureCounts.tsv
KPN15_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

value: Enterobacteria

value: pOXA-48DlysR transconjugant

value: Second dataset


title: MCL-19091-1

value: M


title: Strain KPN15_pOXA-48_rep 2

description:
KPN15_pOXA-48_2
KPN15_DlysR_featureCounts.tsv
KPN15_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

value: pOXA-48 transconjugant


title: Strain KPN15_pOXA-48_rep 3

description:
KPN15_pOXA-48_3
KPN15_DlysR_featureCounts.tsv
KPN15_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv


title: CVD_11_PBMC_GEX

description: 10X Genomics

value: Blood

value: PBMC


title: Strain J57_rep 2

description:
J57.2
J57_featureCounts.tsv
J57_DE_results_raw.tsv

value: WT

value: First dataset


title: CVD_8_PBMC_GEX

description: 10X Genomics


title: CVD_8_BAL_GEX

description: 10X Genomics

value: BAL


title: Strain KPN15_pOXA-48_rep 1

description:
KPN15_pOXA-48_1
KPN15_DlysR_featureCounts.tsv
KPN15_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv


title: Strain J57_rep 1

description:
J57.1
J57_featureCounts.tsv
J57_DE_results_raw.tsv


title: Strain CF13_pOXA-48DlysR_rep 1

description:
CF13_pOXA-48DlysR_1
CF13_DlysR_featureCounts.tsv
CF13_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

organism: Citrobacter freundii

value: pOXA-48 cured, pOXA-48DlysR transconjugant


title: CVD_7_BAL_GEX

description: 10X Genomics


title: MCL-19094-1

value: Liver


title: MCL-19090-1


title: Python bivittatus left ventricle, 4DPF 2

value: Ventricle

value: 4 Day Post-Fed


title: Strain J57c1_rep 3

description:
J57c1.3
J57_featureCounts.tsv
J57_DE_results_raw.tsv

value: pOXA-48 cured


title: Strain CF13_pOXA-48_rep 3

description:
CF13_pOXA-48_3
CF13_DlysR_featureCounts.tsv
CF13_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv


title: Python bivittatus left ventricle, 1DPF 1

value: 1 Day Post-Fed


title: MCL-19080-2

value: hepatitis B virus, replication in mouse

value: f/f

value: F


title: MCL-19092-2


title: Python bivittatus left ventricle, Fasted 2

value: Fasted


title: MCL-19092-1

value: M


title: Strain J57c1_rep 1

description:
J57c1.1
J57_featureCounts.tsv
J57_DE_results_raw.tsv

value: Enterobacteria


title: MCL-19091-2


title: CVD_6_BAL_GEX

description: 10X Genomics

value: GEX


title: Strain CF13_pOXA-48_rep 2

description:
CF13_pOXA-48_2
CF13_DlysR_featureCounts.tsv
CF13_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

value: Second dataset


title: P. lunatus + T. urticae replicate 1

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

address: Campus Montegarcedo

institute: CBGP-INIA-UPM

description: LuT rep1

data_processing:
FASTQ files were processed to remove adapters, poly-N sequences and reads with low quality from raw data. Paired-end clean reads were mapped against the P. vulgaris or P. lunatus reference genomes (Phytozome genome IDs: 442 and 563, respectively at https://phytozome-next.jgi.doe.gov/) using HISAT2 software (Kim et al., 2015). FeatureCounts was used for the generation of the count data files from sorted BAM files (Liao et al., 2014).
Differential expression analysis was performed with DESeq2 R package (Love et al., 2014) by comparing infested (VuT for P. vulgaris infested samples; LuT for P. lunatus infested samples) against control or non-infested (VuC and LuC, respectively). Differentially expressed genes (DEGs) were considered when p-value adjusted < 0.05 and -1>log2FC >1 were present.
Assembly: P. vulgaris or P. lunatus reference genomes (Phytozome genome IDs: 442 and 563, respectively at https://phytozome-next.jgi.doe.gov/)
Supplementary files format and content: Pv_rawcounts, raw counts obtained from P. vulgaris samples
Supplementary files format and content: Pl_rawcounts, raw counts obtained from P. lunatus samples

organism: Phaseolus lunatus

extract_protocol:
non-infested (control) or infested with T. urticae Phaseolus detached leaves were collected at 24 hpi (hours post infestation) and frozen into liquid N2. Total RNA was extracted using TRIzol reagent (Invitrogen, Boston, MA, USA) following manufacturer´s instructions. Total DNA-free RNA was cleaned using RNeasy Plant Mini Kit purification columns (Qiagen, Hilden, Germany).
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacture’s intructions.

value: leaves

value: First true leaf

value: T. urticae 24hpi


title: MCL-19079-1


title: CVD_3_BAL_GEX

first: Chaofan

last: Li

address: 345 Crispell Drive

institute: University of Virginia

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger.
Assembly: GRCh38, mm10
Supplementary files format and content: hd5 file

value: BAL


title: Strain CF13_pOXA-48DlysR_rep 3

description:
CF13_pOXA-48DlysR_3
CF13_DlysR_featureCounts.tsv
CF13_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

value: pOXA-48 cured, pOXA-48DlysR transconjugant


title: P. lunatus control replicate 2

description: LuC rep2

value: control


title: Strain CF13_pOXA-48DlysR_rep 2

description:
CF13_pOXA-48DlysR_2
CF13_DlysR_featureCounts.tsv
CF13_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv


title: MCL-19090-2

value: Liver


title: P. lunatus control replicate 1

description: LuC rep1


title: P. lunatus + T. urticae replicate 3

description: LuT rep3


title: B19243 : F : f/f : f/+ : -/- : +

hyb_protocol: Hybridization of liver RNA to a specifically designed code set as per the manufacturers instructions.

scan_protocol: NanoString nCounter gene expression transcript counting was used to quantify the levels of a panel of genes using a specifically designed code set  as per the manufacturers instructions.

data_processing: Data were quality controlled and normalized using the nSolver Analysis Software 4.0 (NanoString Technologies). RNA expression levels were normalized to mouse Cnot1, Rps29, Slc9a8, Mrps5 and Scarb1 RNA controls.

source_name: liver of HBV transgenic mice

extract_protocol: RNA was isolated from liver of HBV transgenic mice as described (Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162: 156–159. doi:10.1006/abio.1987.9999)

tag: Sex

tag: host foxa1 genotype

tag: host foxa2 genotype

tag: host foxa3 genotype


title: Strain J57_rep 3

description:
J57.3
J57_featureCounts.tsv
J57_DE_results_raw.tsv

tag: genotype

value: WT

value: First dataset


title: B19241 : F : f/f : f/+ : -/- : +


title: P. lunatus + T. urticae replicate 2

description: LuT rep2

source_name: leaves

tag: treatment


title: CVD_6_PBMC_GEX

description: 10X Genomics

value: Blood

value: PBMC


title: MCL-19077-2

tag: agent

value: hepatitis B virus, replication in mouse

tag: host foxa1_genotype

tag: host foxa2_genotype

value: f/f

tag: host foxa3_genotype

value: F


title: P. lunatus control replicate 3

description: LuC rep3


title: MCL-19079-2

tag: host albcre

tag: host sex


title: Strain CF13_pOXA-48_rep 1

description:
CF13_pOXA-48_1
CF13_DlysR_featureCounts.tsv
CF13_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv

value: Enterobacteria


title: CVD_3_PBMC_GEX

description: 10X Genomics

tag: infection

tag: library type

value: GEX


title: Strain MG1655p_rep 2

description:
MG1655p.2
MG1655_featureCounts.tsv
MG1655_DE_results_raw.tsv

organism: Escherichia coli

value: pOXA-48 transconjugant

tag: dataset batch


title: CVD_1_BAL

description: 10X Genomics

tag: tissue


title: CON_4_BAL_GEX

description: 10X Genomics

tag: cell type


title: Strain MG1655p_rep 1

description:
MG1655p.1
MG1655_featureCounts.tsv
MG1655_DE_results_raw.tsv


title: CVD_7_PBMC_GEX

description: 10X Genomics


title: MCL-19078-2


title: CVD_2_BAL_GEX

description: 10X Genomics


title: B19206 : F : f/f : f/+ : -/- : +

tag: Sex


title: MCL-19078-1


title: MCL-19080-1


title: Strain MG1655p_rep 3

description:
MG1655p.3
MG1655_featureCounts.tsv
MG1655_DE_results_raw.tsv


title: CVD_2_PBMC_GEX

description: 10X Genomics


title: Strain MG1655_rep 1

description:
MG1655.1
MG1655_featureCounts.tsv
MG1655_DE_results_raw.tsv


title: B19238 : F : f/f : f/+ : -/- : +

tag: host foxa1 genotype


title: MCL-19077-1


title: B19221 : F : f/f : f/+ : -/- : -

tag: host foxa2 genotype


title: Strain C325c1_rep 3

description:
C325c1.3
C325_featureCounts.tsv
C325_DE_results_raw.tsv

value: pOXA-48 cured


title: CON_4_PBMC_GEX

description: 10X Genomics


title: MCL-19076-2


title: MCL-19076-1


title: Strain MG1655_rep 2

description:
MG1655.2
MG1655_featureCounts.tsv
MG1655_DE_results_raw.tsv


title: B19291 : F : f/f : f/+ : -/- : -

tag: host foxa3 genotype


title: B19184 : F : f/f : f/+ : -/- : +


title: CON_3_BAL_GEX

description: 10X Genomics


title: MCL-19073-2

value: M


title: Vero_Rep2_Unmodified

city: New Haven

first: Nicholas

last: Huston

state: Connecticut

address: 260 Whitney Avenue, YSB 308

institute: Yale University

data_processing:
ShapeMapper
Library strategy: SHAPE-MaP

organism: Chlorocebus aethiops

source_name: Vero Cells

growth_protocol: Vero and C6/36 cells were cultured in 10cm tissue culture plates

extract_protocol:
Trizol
cDNA was prepared from modified RNA using gene-specific RT primers, followed by generation of amplicons with gene-specific primers. Nextera-XT kit was used for library construction

treatment_protocol: At 4dpi, each sample was collected and treated with either 200mM NAI (final) or equivalent volume DMSO

tag: chemical modification

value: dimethyl sulfoxide


title: B19133 : F : f/f : f/+ : -/- : -


title: Strain C325c1_rep 1

description:
C325c1.1
C325_featureCounts.tsv
C325_DE_results_raw.tsv

tag: genotype


title: MCL-19059-2

tag: agent


title: B19218 : F : f/f : f/+ : -/- : -


title: MCL-19057-2

tag: host foxa1_genotype


title: CON_3_PBMC_GEX

city: Charlottesville

description: 10X Genomics


title: MCL-19073-1

tag: host foxa2_genotype


title: Strain C325_rep 2

description:
C325.2
C325_featureCounts.tsv
C325_DE_results_raw.tsv


title: Strain C325c1_rep 2

description:
C325c1.2
C325_featureCounts.tsv
C325_DE_results_raw.tsv


title: Vero_Rep2_Modified

value: 2-methylnicotinic acid imidazolide


title: B19245 : M : f/f : f/+ : -/- : +


title: B19248 : M : f/f : f/+ : -/- : +


title: Strain C325_rep 3

description:
C325.3
C325_featureCounts.tsv
C325_DE_results_raw.tsv


title: B19280 : M : f/f : f/+ : -/- : +


title: B19135 : M : f/f : f/+ : -/- : +


title: Vero_Rep1_Unmodified


title: UV 3 meRIP Input

city: Chongqing

first: Mingwang

last: Zhang

state: Chongqing

address: Department of Dermatology, Southwest Hospital, Army Medical University, 400038 C

institute: Army Medical University

data_processing:
STAR software (version 2.5.3a)
Assembly: GRCm38
Supplementary files format and content: excel files include peak values of all samples
Supplementary files format and content: excel files include count values of all samples
Library strategy: meRIP-Seq

source_name: Skin

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, USA) and qualified by a NanoDropTM 2000 (Thermo Fisher Scientific, USA) instrument.
RNA-seq libraries of m6A antibody-enriched RNAs and input RNAs were constructed by KC-Digital Stranded mRNA Library Prep Kit for Illumina® (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Skin

tag: treatment

value: UV light


title: Strain C325c1, rep 3

data_processing:
We trimmed and adapter-removed the reads with Trim Galore v0.6.4 (-q 20 --length 50 --illumina). We assessed the quality of the reads before and after trimming with FastQC v.0.11.9 and MultiQC v1.11.
We first identified in the genomes all copies of all IS families annotated by PGAP. Then, we masked the sequences of all but one copy of ISs per family (leaving the unmasked single copy preferentially in the chromosome or in the largest plasmid) from the reference genomes, using the bedtools maskfasta tool v2.27.1. This way, reads belonging to an IS family (like IS1) can map with low ambiguity to one region of the genome.
After re-annotating the masked genomes with PGAP v2021-07-01.build5508, we mapped the trimmed reads to their corresponding reference genome with BWA-MEM v0.7.17.
We inspected the mappings to confirm the appropriate presence or absence of pOXA-48 in the replicates. A replicate in K147c1 and in CF13c1 (cured from pOXA-48) actually carried the plasmid, so they were included as an additional replicate of the pOXA-48-carrying strains. The third replicate of C063p had a mutation in pOXA-48 (near the gene repA) that caused an increased plasmid copy number, unlike the other two replicates. Thus, we removed this replicate from the analysis.
We obtained the raw counts of reads mapping to each genomic feature (including CDS, ncRNA, tRNA, tmRNA, antisense RNA, RNase P and SRP RNA) with featureCounts from the Rsubread v2.14.2 package.
We performed the differential expression analysis from raw counts using DESeq2 v1.40.1 by comparing the pOXA-48-carrying strain against the pOXA-48-free strain.
Assembly: SAMN32542096, SAMN32542113, SAMN32542116, SAMN32542119, SAMN32542124, SAMN32542126, SAMN14640123, SAMN14640085, SAMN14640188, SAMN14640201
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (<strain>_featureCounts.tsv)
Supplementary files format and content: tab-delimited text files include log2FoldChanges, padj and other values for each differential expression analysis (<strain>_DE_results_raw.tsv)

growth_protocol: We grew the cells in LB medium with continuous shaking. When cultures reached a turbidity of 0.5 at 600 nm, we collected the cells at 4ºC, pelleted them by centrifugation at 4ºC 12,000 g for 1 min and immediately froze them at -70ºC.

extract_protocol:
We purified the total RNA from each sample using the NZY Total RNA Isolation kit (NZYTECH). Then, we determined RNAs concentration using the Qubit RNA Broad-Range Assay following the manufacturer's instructions. Additionally, the quality of the RNA was examined using the Tape-Station system (Agilent).
We ribodepleted the RNA and sequenced it at the Wellcome Trust Centre for Human Genetics (WTCHG; Oxford, UK) using the Illumina's NovaSeq6000 platform, resulting in >8 million reads per sample.

tag: strain


title: MCL-19057-1

value: Liver

tag: host foxa3_genotype

tag: host albcre

tag: host sex


title: UV 2 meRIP IP


title: UV 3 meRIP IP


title: Strain C325_rep 1

description:
C325.1
C325_featureCounts.tsv
C325_DE_results_raw.tsv

value: WT

tag: dataset batch


title: MCL-19059-1

tag: tissue


title: Strain C325c1, rep 2

tag: cell type


title: Vero_Rep1_Modified


title: Strain C325, rep 2


title: B19094 : M : f/f : f/+ : -/- : -

tag: Sex


title: MCL-19053-1


title: UV 2 meRIP Input


title: MCL-19056-1


title: Strain C325, rep 1


title: MCL-19056-2


title: MCL-19055-2


title: Control 3 meRIP Input

value: Control


title: B19091 : M : f/f : f/+ : -/- : -

tag: host foxa1 genotype


title: B19090 : M : f/f : f/+ : -/- : +

tag: host foxa2 genotype


title: B19261 : M : f/f : f/+ : -/- : -

tag: host foxa3 genotype


title: B19299 : M : f/f : f/+ : -/- : -


title: dark_minusATR_4

city: Köln

first: Debasish

last: Mukherjee

address: Albertus-Magnus-Platz

institute: Universität zu Köln

data_processing:
Analysis was performed with the nf-core RNA-seq pipeline version 3.0, commands are provided below see: https://doi.org/10.5281/zenodo.1400710
nextflow pull nf-core/rnaseq -r 3.0  nextflow run nf-core/rnaseq \     --input design.csv \     --fasta ftp://ftp.ensembl.org/pub/release-103/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz \     --gff ftp://ftp.ensembl.org/pub/release-103/gff3/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.103.gff3.gz \     --gtf_count_type exon --gtf_group_features gene_id --gtf_extra_attributes Name --skip_biotype_qc \     --save_reference \     --additional_fasta ERCC92.fa \     --aligner star_salmon \     -profile docker \     -r 3.0
Differential expression analysis was performed in R v4.0.3 with DESeq2 v1.30.1 Log Fold Change shrinkage estimation was performed with apeglm v1.12.0
Assembly: C. elegans genome WBcel235
Supplementary files format and content: tab delimited text file includes  raw count of each samples
Supplementary files format and content: tab delimited text file includes  TPM value of all samples

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: For an OptIMMuS experiment, myo-3p::ChR2(C128S;H134R)-expressing worms were grown on NGM plates seeded with E. coli OP50 supplemented with or without 0.1 mM all-trans retinal (ATR) from L1 larval stage on at 18°C. In parallel, worms grown without cofactor supplementation served as control, since the expressed ChR2 protein remained non-functional. Once the worms were placed on ATR, all plates were kept in the dark. All worms were grown for the last 16 h to adulthood at 18°C in the OptIMMuS incubator (Sanyo MIR-154) that was equipped in-house with blue LED lights (Hontiey, 2x 100 W).

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen). RNA quality after RNA extraction was determined using the TapeStation system (Agilent) with TapeStation Analysis Software 3.2 (Agilent). 2 µg total RNA was used for construction of sequencing libraries.
RNAseq library preparation and sequencing were performed by the Cologne Center for Genomics (CCG), Germany (https://ccg.uni-koeln.de/). RNAseq library preparation with poly(A) enrichment was performed on 2 μg total RNA with the TruSeq Stranded mRNA Prep kit (Illumina) including ERCC spike-in.

treatment_protocol: The following day, young adult worms were repeatedly illuminated with blue light (455 nm, >10µW/mm²) for 5 s followed by a 20 min dark period. Blue light illumination was controlled by an FY6800 2-channel DDS arbitrary waveform signal generator (FeelElec) with the following settings: square wave generation, frequency 0.833 mHz, amplitude 7 V, duty cycle 0.417%. As control, worms grown on ATR or without ATR supplementation were kept in the dark for the duration of the experiment.

value: whole worm


title: Strain C325c1, rep 1


title: MCL-19055-1


title: Strain C325, rep 3


title: UV 1 meRIP IP


title: MCL-19053-2


title: UV 1 meRIP Input


title: MCL-19052-1


title: dark_plusATR_4


title: Control 2 meRIP Input


title: B19092 : M : f/f : f/+ : -/- : -


title: Control 3 meRIP IP


title: light_minusATR_4


title: Control 2 meRIP IP


title: B19076 : F : +/+ : f/f : -/- : +


title: MCL-19052-2


title: MCL-19020-2


title: MCL-19020-1


title: B19080 : F : +/+ : f/f : -/- : +


title: B19077 : F : +/+ : f/f : -/- : +


title: Control 1 meRIP Input


title: MCL-19017-2


title: Control 1 meRIP IP


title: dark_plusATR_3


title: dark_minusATR_3


title: MCL-19017-1


title: B19057 : F : +/+ : f/f : -/- : +


title: B19020 : F : +/+ : f/f : -/- : -


title: mammary gland macrophages wild type, rep5

city: New Orleans

first: Heather

middle: L

last: Machado

state: LA

address: Louisiana Cancer Research Consortium

institute: Tulane Cancer Center

description:
WT_mac_5
MAC_KO_WT_subread_counts.txt

data_processing:
Churp pipeline to generate subreads count and normalized reads count
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to GrCM38/mm10 HiSat2
Read count extraction and normalization were performed churp pipeline
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include subreads count for each sample

source_name: mammary gland

extract_protocol:
RNA was prepared using TRIzol reagent
RNA libraries for RNA-seq were prepared using DNBSEQ Low Input Smart-Seq Eukaryotic mRNA library kit following manufacturer's protocols.

value: mammary gland

value: mammary gland macrophages

value: wild type


title: B19078 : F : +/+ : f/f : -/- : -

value: F

value: f/f


title: light_minusATR_3


title: B19055 : F : +/+ : f/f : -/- : -


title: MCL-18911-1

extract_protocol:
RNA were isolated from liver of HBV transgenic mice using the protocol as described by: Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162: 156–159. doi:10.1006/abio.1987.9999.
Bisulfite treatment of protein-free genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning Kit (D5030; Zymo Research, Inc., Irvine, CA, USA) according to the manufacturer's instructions.  The three major viral amplicons covering 62 of the 99 CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite-treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument.  Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps in a protocol termed targeted amplicon sequencing (TAS)  The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’- TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (ii) 5’-ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’ (oligo CS1FP5a; HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), and (iii) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo CS1FP9; HBV nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV nucleotide coordinates 730-712).

value: hepatitis B virus, replication in mouse


title: mammary gland macrophages C/EBPb knockdown, rep7

description:
KO_mac_7
MAC_KO_WT_subread_counts.txt

value: C/EBPb knockdown


title: light_plusATR_3


title: MCL-18909-2


title: light_plusATR_4


title: mammary gland macrophages C/EBPb knockdown, rep6

description:
KO_mac_6
MAC_KO_WT_subread_counts.txt


title: MCL-18909-1


title: mammary gland macrophages C/EBPb knockdown, rep5

description:
KO_mac_5
MAC_KO_WT_subread_counts.txt


title: dark_minusATR_2


title: B19210 : M : +/+ : f/f : -/- : +


title: MCL-18908-2


title: dark_plusATR_2


title: MCL-18908-1


title: light_minusATR_2


title: MCL-18906-2


title: light_plusATR_2


title: Mammary epithelial cell wild type, rep3

description:
WT_MEC_3
MEC_WT_subread_counts.txt

value: Mammary epithelial


title: B19138 : M : +/+ : f/f : -/- : +

value: M


title: B18908 : M : +/+ : f/f : -/- : +


title: dark_minusATR_1


title: mammary gland macrophages wild type, rep4

description:
WT_mac_4
MAC_KO_WT_subread_counts.txt


title: B19017 : M : +/+ : f/f : -/- : +


title: MCL-18911-2


title: Mammary epithelial cell wild type, rep1

description:
WT_MEC_1
MEC_WT_subread_counts.txt


title: B19051 : M : +/+ : f/f : -/- : -


title: mammary gland macrophages C/EBPb knockdown, rep4

description:
KO_mac_4
MAC_KO_WT_subread_counts.txt


title: B19052 : M : +/+ : f/f : -/- : -


title: MCL-18906-1


title: MCL-18905-2


title: Mammary epithelial cell C/EBPb knockdown, rep3

description:
Cre_MEC_3
MEC_WT_subread_counts.txt


title: dark_plusATR_1


title: Mammary epithelial cell C/EBPb knockdown, rep1

description:
Cre_MEC_1
MEC_WT_subread_counts.txt


title: B19212 : M : +/+ : f/f : -/- : -


title: MCL-18905-1


title: light_minusATR_1


title: light_plusATR_1


title: B18905 : M : +/+ : f/f : -/- : -


title: Vh-WT-Rep3-2T

status: Public on Jul 15 2024

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

department: Biology

institute: Indiana University

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping (READemption 0.3.0)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: CP000789.1, CP000790.1, CP000791.1
Supplementary_files_format_and_content: wiggle

organism: Vibrio campbellii

source_name: Bacterial lysate

growth_protocol: Cells were grown at 30°C in LM media to an OD600 of 1.0

extract_protocol:
Trizol Reagent followed by Dnase I treatment
For Illumina sequencing  of cDNA molecules, the libraries were constructed by vertis Biotechnology AG, Germany. The cDNA libraries were sequenced using a NextSeq 500 machine (Illumina) in single-read mode

treatment_protocol: When indicated samples were treated with Terminator Exonucleae (TEX; epicentre)

value: Terminator Exonucleae


title: Vh-WT-Rep2T


title: Vh-WT-Rep3-2


title: B18909 : F : +/+ : f/f : -/- : -


title: Vh-WT-Rep2


title: Vh-WT-Rep1


title: Vh-luxR-Rep3-2

value: deltaluxR (KM669)


title: Vh-luxR-Rep3-2T


title: Vh-luxR-Rep1


title: Vh-luxR-Rep1T


title: M229 cells,H3K27ac

city: Los Angeles

first: Xiang

last: Lu

state: CA

address: 10833 Le Conte Ave

department: Department of Molecular and Medical Pharmaacology

institute: University of California, Los Angeles

data_processing:
For ChIP-seq,Reads were mapped to the human genome hg19 by bowtie273. The identical aligned reads were deduplicated to avoid PCR duplicates. Peaks were called on the merged set of all ChIP-seq reads of M397 using MACS2 with the following parameters: --nomodel, --broad74.To visualize peaks in each sample, bed graph file was generated using MACS2 with following parametes: --nomodel, --broad, --bdg, --SPMR. For RNA-seq,Reads were aligned against the human genome (hg19) using STAR (v2.7.3a). Read counts were quantified using htseq-count with known gene annotations from UCSC.The gene expression level was calculated from Fragments Per Kilobase per Million reads (FPKM) normalized expression values
Assembly: hg19
Supplementary files format and content: bdg file includes peak file for each sample

growth_protocol: M-series patient derived cell lines used in this study were generated under UCLA institutional review board approval # 11–003254. Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2 in RPMI 1640 with L-glutamine (Life Technologies), supplemented with 10% fetal bovine serum (Omega), and 0.2% antibiotics (MycoZapTM Plus-CL from Lonza). The cell lines were tested for mycoplasma and were periodically authenticated to its early passage using GenePrint 10 System (Promega).HCC827(Cat.CRL-2868) and HT-29(Cat.HTB-38) were brought from ATCC. Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2.

extract_protocol:
Briefly, cells were cultured to ~80% confluency in a petri dish containing 10 mL of growth media, and then fixed in 1% formaldehyde by adding 275 μl of 37% formaldehyde for 10 minutes to cross-link protein–DNA complexes at room temperature. The unreacted formaldehyde was quenched by adding Glycine to a final concentration 0.125 M. Gently swirl dish to mix. The nuclear pellet was isolated with Cell Lysis Buffer. The pellet was resuspended with 500 μl SDS Lysis Buffer containing 1X Protease Inhibitor Cocktail II before sonication for 4 min (10 s on, 30 s off, 10% strength in a Bioruptor to yield DNA fragments of 0.2-1.0 kb in length. The lysates were cleared by centrifugation (12,000g for 10 min at 4 °C) and diluted tenfold in ChIP dilution buffer to decrease the concentration of SDS. After keeping 10% of the sample as input, 500 μl supernatant was incubated overnight at 4 °C with antibody and 20 μL of fully resuspended protein A/G magnetic beads. The washing, elution, reverse cross-linking, and purification steps were performed according to manufacturer’s description. ChIPed Eluted DNA was quantified by Qubit dsDNA HS Assay Kit.Total RNA was extracted from the cell pellets using AllPrep DNA/RNA kit (Qiagen)
ChIP-seq libraries were prepared with Kapa DNA HyperPrep Kit (Kapa, Cat KK 8700) according to the manufacturer's protocol. Briefly, 5-10 ng of immunoprecipitated DNA was underwent end-repaired, A tailing and adaptor ligation. A 10 cycles of PCR was performed to produce the final sequencing library. As for ATAC, the Tn5 treated DNA was amplified with a 5-cycle PCR in 50µl reaction volume. The tubes were removed from thermocycler and used 5 µl of partially amplified library to perform qPCR to determine how many additional PCR cycles were needed. For the samples in this study, an additional 4-5 cycles of PCR was performed on the remaining 45ul of each partially amplified product. 1.8X AmpurXP beads purification was used for the final PCR cleanup. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit, and quantified with qPCR. For RNA-seq, sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, USA) with minor modifications.mRNA library was constructed with TruSeq RNA Sample Preparation Kit and sequenced on the Illumina Hiseq 2500 with pair-end 150bp reads following the manufacturer's recommendations by Novogene.

treatment_protocol: BRAF inhibitor (vemurafenib) from Selleck Chemicals LLC, were dissolved in DMSO at designated concentrations before applying to cell culture media. Cells were plated in 10cm tissue culture plate at 60% confluency and treated with certain drugs for the specified numbers of days. M397 cells were treated with 3uM of vemurafenib for 59days and at day29, drug were removed and cells were cultured with normal medium for another 35days.HCC827 cells were cultured using ATCC-formulated RPMI-1640 Medium (ATCC 30-2001) and treated with an EGFR inhibitor (erlotinib, SellecChem S1023).ATCC-formulated McCoy's 5a Medium Modified (ATCC 30-2007) was used to culture HT-29 cells and the cells were treated with an anti-EGFR antibody  (Cetuximab, SellecChem A2000) plus a BRAF inhibitor (Dabrafenib, MCE HY-14660)

tag: cell line

value: melanoma cancer cell line

value: untreated


title: M233 cells,H3K4me3

tag: genotype


title: M233 cells,H3K27ac


title: M263 cells,H3K4me3


title: M229 cells,H3K4me3


title: M381 cells,H3K27ac