title: Tpd single pollen drive 128

description: single-pollen-tpd.drive.vcf.gz

data_processing:
library strategy: DNA-seq
Adapter trimming was performed with Cutadapt v3.1 and read quality was assessed using FastQC v0.11.9. Paired-end reads were aligned to the to the W22 reference genome with BWA-MEM v0.7.17. Alignments were filtered by mapping quality (mapQ≥30) and PCR duplicates were removed using Samtools v1.10. SNP calling was performed using Freebayes v1.3.2. Putative SNP calls were filtered by quality, depth, and allele frequency (AF=1) to obtain a high-confidence mexicana marker set that was subsequently validated against the TPD assembly. For BSA analysis, SNP calls were filtered against the gold-standard TPD marker set.
All calls at validated marker sites were extracted and encoded in a sparse matrix format (rows = markers, columns = samples) and encoded (1 = alt allele, -1 = ref allele, 0 = missing). To assess mexicana introgression in individual pollen grains, mean SNP signal was calculated in 100kb bins across the genome. A sliding window (1Mb window, 200kb step) was applied in order to smooth the data and identify regions with mexicana SNP density. To identify genomic intervals overrepresented in surviving Tpd pollen grains, aggregate allele frequency was calculated across all pollen grains at each marker site.
Assembly: Zm-W22-REFERENCE-NRGENE-2.0; Zm-TPD-1.0
Supplementary files format and content: single-pollen-tpd.fertile.vcf.gz

source_name: pollen


title: Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 1 (ATAC-seq)

status: Public on Jul 25 2023

type: SRA

city: Seattle

first: Kathleen

last: Abadie

state: Washington

address: 3720 15th Ave NE

department: Bioengineering

country: USA

institute: University of Washington

library_source: genomic

data_processing:
Raw fastq files were processed and aligned to the mm10 mouse genome using the  PEPATAC (v0.10.3) pipeline, which uses bowtie2 for alignment. Unmapped, unpaired, and mitochondrial reads were removed.
Following alignment, peak calling, merging across all samples, and annotation was performed using HOMER (v4.10). The peaks.txt processed data files represent the individual sample peak counts prior to identifying consensus peaks. The HOMER commands used to generate peak counts from bam files were: makeTagDirectory, findPeaks (parameters: -style factor -o auto), mergePeaks (parameters: -d 150), annotatePeaks.pl (parameters: mm10 -size "given" -raw -d)
Differentially accessible regions were identified using DESeq2.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: The peaks.txt file for each sample was generated from HOMER findPeaks and contains columns with peakID, peak information, and normalized counts.

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Sorted cells were centrifuged and frozen in ATAC freezing buffer and stored at -80°C. For processing, cells were thawed, centrifuged, washed with PBS and lysed. Nuclei were then subjected to tagementation and purification.
Purfied tagmented DNA was PCR amplifed using Illumina indexed primers and NEBNext High-Fidelity 2X PCR Master Mix. Pooled libraries were sequenced on a NextSeq 500 High150 cycle kit with paired end sequencing (read 1: 74 cycles, read 2: 74 cycles, index 1: 10 cycles, index 2: 10 cycles)

tag: tissue

value: spleen

tag: cell type

value: CD8+ T cell


title: Control 45 Pancreas

city: Heidelberg

first: Alicia

last: Alonso de la Vega

address: Im Neuenheimer Feld 280

country: Germany

institute: Deutsches Krebsforschungszentrum, DKFZ

library_source: transcriptomic

data_processing:
R
Sequence reads were ere mapped to GrCM38/mm10
Read count extraction and normalization were performed using R
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for Samples (1-12) and counts for Samples (13-28)

molecule: total RNA

source_name: Pancreas

extract_protocol:
RNA was harvested using AllPrep DNA/RNA Mini (Qiagen, 80204). 1.2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded RNA kit following manufacturer's protocols.

treatment_protocol: Animals were fed with 625 ppm dox impregnated food pellets for 10-15 days.

value: Pancreas

tag: genotype

value: A3B + CAGS-rtTA

tag: treatment time

value: 10 days


title: Tpd single pollen drive 126

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description: single-pollen-tpd.drive.vcf.gz

organism: Zea mays subsp. mays x Zea mays subsp. mexicana

growth_protocol: The TPD lineage traces to teosinte mexicana collected near Copándaro, Michoacán, Mexico in December 1993. Gamete a, plant 4 of collection 107 was used in an initial outcross to the Mid-western US dent inbred W22 and subsequently backcrossed. Tpd1;Tpd2 (BC8S3) homozygous lines were used for whole-genome sequencing and de novo genome assembly. All additional experiments were performed using Tpd1/tpd1; Tpd2/tpd2 (BC11-BC13) plants or populations derived from maternal segregation of these lines. The lbl1-rgd1 and dcl2-mu1 alleles were backcrossed to W22 ≥ 4 times. All genetic experiments used segregating wild-type progeny as experimental controls. Plants were grown under greenhouse and field conditions. In the greenhouse, starter flats were transplanted to pots containing divot mix and a single scoop of Osmocote 19-6-12. Once established, pots were on an irrigation drip of 20-20-20 at 0.8 EC (200 PPM Nitrogen) with a weekend water flush. Marathon was added as a drench and biweekly sprays of insecticides were applied as needed. Long day (6:00 AM until 10:00 PM) conditions were maintained at a 28˚C set point with cooling to 24˚C at night.

extract_protocol:
Pollen grains from Tpd1/tpd1; Tpd2/tpd2 plants were suspended in ice-cold PBS on a microscope slide under a dissecting scope. Individual plump, viable pollen grains were deposited into the 0.2mL wells of a 96-well plate using a p20 pipette. Lysis and whole genome amplification were performed using the REPLI-g single-cell kit (Qiagen, cat#150345) with the following modifications; 1/4th the specified volume of amplification mix was deposited in each well and isothermal amplification was limited to 5 hours. All steps prior to amplification were performed in a UV-decontaminated PCR hood. WGA products were cleaned up using a Genomic DNA Clean & Concentrator kit (Zymo Research, cat#D4067) and yields were quantified using with the QuantiFluor dsDNA system (Promega, cat#E2670) in a 96-well microplate format.
Libraries were prepared using the TruSeq Nano DNA High Throughput kit (Illumina, cat#20015965) with 200ng input. Samples were sequenced on a NextSeq500 platform using 2x150bp high output run.

value: pollen


title: Day11Gata6-derivedtomatopositive40

city: London

first: Fiona

middle: Mary

last: Watt

address: Great Maze Road

country: United Kingdom

institute: Kings College London

description:
Day11Gata6-derivedtomatopositive40
day11g6.txt

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Read quality was checked and alinged to GRCm38 reference genome using STAR version 2.2.
Gene specific counts were calculated using featureCounts from Rsubread 2.7 with mm10 Refseq.
All the downstream analysis was performed using Seurat version 3.2.2 and monocle 2.18.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Seurat object with annotations for every sample/cell.

source_name: Epidermis

extract_protocol:
Single keratinocytes from mouse epidermis were isolated by flow sorting using appropriate markers. Cells were sorted into individual wells of a 96-well plate containing 2ul lysis buffer (0.8% (volume/volume) Triton X-100 and 2U/ul recombinant RNase inhibitor
Libraries were prepared for sequencing using standard Illumina protocols with SmartSeq2 followed by Nextera XT protocol.

treatment_protocol: For lineage-tracing experiments, mice received a topical dose of 4-hydroxy-tamoxifen (1 mg dissolved in 100 µl acetone) applied to clipped back skin

tag: strain

value: Epidermis

tag: age

value: Days 11 post-wounding

value: Cre (+/-) tdTomato (+/-)

tag: treatment


title: Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3, 2 (ATAC-seq)


title: Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3, 1 (ATAC-seq)


title: Sample 125 Pancreas


title: Tpd single pollen drive 124

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 125

description: single-pollen-tpd.drive.vcf.gz


title: Day11Gata6-derivedtomatopositive41

description:
Day11Gata6-derivedtomatopositive41
day11g6.txt


title: Tpd single pollen drive 127

description: single-pollen-tpd.drive.vcf.gz


title: Sample 137 Pancreas


title: Day3 effector, 1 (ATAC-seq)


title: Day11Non-Gata6tomatonegative40

description:
Day11Non-Gata6tomatonegative40
day11ng6.txt


title: Tpd single pollen drive 123

description: single-pollen-tpd.drive.vcf.gz


title: Splenocyte antigen-experienced, 1 (ATAC-seq)


title: Sample 153 Pancreas


title: Sample 53 Pancreas


title: Splenocyte naïve, 1 (ATAC-seq)


title: Day11Non-Gata6tomatonegative37

description:
Day11Non-Gata6tomatonegative37
day11ng6.txt


title: Day11Non-Gata6tomatonegative38

description:
Day11Non-Gata6tomatonegative38
day11ng6.txt


title: Day11Non-Gata6tomatonegative39

description:
Day11Non-Gata6tomatonegative39
day11ng6.txt


title: Day11Gata6-derivedtomatopositive42

description:
Day11Gata6-derivedtomatopositive42
day11g6.txt


title: Sample 44 Pancreas


title: Tpd single pollen drive 121

description: single-pollen-tpd.drive.vcf.gz


title: Control 168 Liver

source_name: Liver

value: Liver


title: Day11Non-Gata6tomatonegative36

description:
Day11Non-Gata6tomatonegative36
day11ng6.txt


title: Tpd single pollen drive 120

description: single-pollen-tpd.drive.vcf.gz


title: SVE-6257

city: Houston

first: Christine

middle: B.

last: Peterson

state: TX

address: 1400 Pressler St.

department: Biostatistics

institute: University of Texas MD Anderson Cancer Center

data_processing:
Cell line data: Quality control was performed on the read data using the FastQC software.
Cell line data: Reads were aligned to human genome data hg38 using TopHat.
Cell line data: SAM Tools was used to sort the BAM files by read name and convert to SAM files.
Cell line data: HTseq was used to summarize the reads per gene from the aligned BAM files.
Cell line data: The count data were normalized using the variance stabilizing transformation in the DEseq2 R package.
Murine tumor data: Quality control was performed on the read data using the FastQC software.
Murine tumor data: The BBTools Repair utility was used to fix order of paired reads in the samples.
Murine tumor data: Reads were aligned to mouse reference genome GRCm38 using the Star RNASeq alignment software.
Murine tumor data: HTseq was used to summarize the reads per gene from the aligned BAM files.
Murine tumor data: The count data were normalized using the rlog transformation in the DEseq2 R package.
Assembly: Cell line data: hg38
Assembly: Murine tumor data: GRCm38
Supplementary files format and content: csv files with normalized counts for each sample

source_name: Kidney

growth_protocol: 786-O cells were maintained in DMEM containing 10% fetal bovine serum at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol: none provided

treatment_protocol:
786-O cells were untreated (Control) or treated with 25nM LY2603618 for 48 hrs.
Renca cells (5 × 105) were suspended in 100 µL Matrigel matrix (Corning, 354234) diluted with PBS at a 1:1 ratio and subcutaneously injected into the backs of mice. After the tumors were palpable (i.e., tumor volume reached approximately 100 mm3), the mice were left untreated or treated with VE822 (60 mg/kg, 5 consecutive days per week) via oral gavage.

value: Kidney

value: SETD2 KD


title: SVE-6264


title: Tpd single pollen drive 119

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 118

description: single-pollen-tpd.drive.vcf.gz


title: SVE-6252


title: Day11Non-Gata6tomatonegative33

description:
Day11Non-Gata6tomatonegative33
day11ng6.txt


title: Day11Non-Gata6tomatonegative34

description:
Day11Non-Gata6tomatonegative34
day11ng6.txt


title: Sample 48 Liver


title: Sample 49 Pancreas


title: SVE-6253


title: Sample 153 Liver


title: Sample 125 Liver


title: SVE-6249


title: Tpd single pollen drive 117

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 122

description: single-pollen-tpd.drive.vcf.gz


title: Day11Gata6-derivedtomatopositive39

description:
Day11Gata6-derivedtomatopositive39
day11g6.txt


title: Tpd single pollen drive 116

description: single-pollen-tpd.drive.vcf.gz


title: SUT-6240

value: Untreated


title: Sample 49 Liver


title: Tpd single pollen drive 115

description: single-pollen-tpd.drive.vcf.gz


title: Day11Gata6-derivedtomatopositive38

description:
Day11Gata6-derivedtomatopositive38
day11g6.txt


title: Sample 137 Liver


title: Tpd single pollen drive 114

description: single-pollen-tpd.drive.vcf.gz


title: Sample 44 Liver


title: Control 45 Liver


title: Day11Gata6-derivedtomatopositive36

description:
Day11Gata6-derivedtomatopositive36
day11g6.txt


title: Day11Non-Gata6tomatonegative35

description:
Day11Non-Gata6tomatonegative35
day11ng6.txt


title: SUT-6234


title: Tpd single pollen drive 113

description: single-pollen-tpd.drive.vcf.gz


title: Sample 74 Lung

source_name: Lung

value: Lung


title: Day11Gata6-derivedtomatopositive35

description:
Day11Gata6-derivedtomatopositive35
day11g6.txt


title: SUT-6233


title: Tpd single pollen drive 112

description: single-pollen-tpd.drive.vcf.gz


title: SUT-6232


title: Sample 69 Lung


title: WVE-6270

value: WT


title: Control 91 Lung

value: 15 days


title: Tpd single pollen drive 111

description: single-pollen-tpd.drive.vcf.gz


title: Day11Gata6-derivedtomatopositive32

description:
Day11Gata6-derivedtomatopositive32
day11g6.txt


title: SUT-6239


title: Tpd single pollen drive 109

description: single-pollen-tpd.drive.vcf.gz


title: Control 88 Lung


title: SUT-6237


title: Day11Non-Gata6tomatonegative32

description:
Day11Non-Gata6tomatonegative32
day11ng6.txt


title: WVE-6267


title: WVE-6260


title: Day11Non-Gata6tomatonegative31

description:
Day11Non-Gata6tomatonegative31
day11ng6.txt


title: Day11Gata6-derivedtomatopositive37

description:
Day11Gata6-derivedtomatopositive37
day11g6.txt


title: Control 87 Lung

value: CAGs


title: Sample 70 Liver


title: Day11Non-Gata6tomatonegative30

description:
Day11Non-Gata6tomatonegative30
day11ng6.txt


title: Tpd single pollen drive 107

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 106

description: single-pollen-tpd.drive.vcf.gz


title: Day11Gata6-derivedtomatopositive34

description:
Day11Gata6-derivedtomatopositive34
day11g6.txt


title: WVE-6247


title: Sample 70 Lung


title: Day11Gata6-derivedtomatopositive33

description:
Day11Gata6-derivedtomatopositive33
day11g6.txt


title: Tpd single pollen drive 110

description: single-pollen-tpd.drive.vcf.gz


title: Day11Non-Gata6tomatonegative29

description:
Day11Non-Gata6tomatonegative29
day11ng6.txt


title: Sample 28 Liver

value: 14 days


title: Tpd single pollen drive 105

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 108

description: single-pollen-tpd.drive.vcf.gz


title: Sample 23 Liver


title: Day11Non-Gata6tomatonegative28

description:
Day11Non-Gata6tomatonegative28
day11ng6.txt


title: WVE-6245


title: Control 92 Liver


title: Tpd single pollen drive 103

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 104

description: single-pollen-tpd.drive.vcf.gz


title: WVE-6251


title: WUT-6210


title: Control 91 Liver


title: Day11Non-Gata6tomatonegative27

description:
Day11Non-Gata6tomatonegative27
day11ng6.txt


title: Tpd single pollen drive 102

description: single-pollen-tpd.drive.vcf.gz


title: WUT-6208


title: Day11Non-Gata6tomatonegative26

description:
Day11Non-Gata6tomatonegative26
day11ng6.txt


title: Day11Non-Gata6tomatonegative25

description:
Day11Non-Gata6tomatonegative25
day11ng6.txt


title: Control 11 Liver


title: Tpd single pollen drive 101

description: single-pollen-tpd.drive.vcf.gz


title: WUT-6207


title: WUT-6205


title: Tpd single pollen drive 100

description: single-pollen-tpd.drive.vcf.gz


title: WUT-6204


title: Tpd single pollen drive 99

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative24

description:
Day9Non-Gata6tomatonegative24
day9ng6.txt

value: Days 9 post-wounding


title: Day9Non-Gata6tomatonegative23

description:
Day9Non-Gata6tomatonegative23
day9ng6.txt


title: Day9Non-Gata6tomatonegative22

description:
Day9Non-Gata6tomatonegative22
day9ng6.txt


title: WUT-6202


title: Day9Non-Gata6tomatonegative21

description:
Day9Non-Gata6tomatonegative21
day9ng6.txt


title: Tpd single pollen drive 98

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 96

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative20

description:
Day9Non-Gata6tomatonegative20
day9ng6.txt


title: Day9Non-Gata6tomatonegative19

description:
Day9Non-Gata6tomatonegative19
day9ng6.txt


title: UG, biological replicate 3

city: San Francisco

first: Eunice

middle: Y

last: Lee

address: 505 Parnassus Ave

institute: University of California, San Francisco

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1
Assembly: mm10, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
For mice, dorsal skin was isolated, subcutaneous fat was removed, and was cut into small pieces prior to digestion with 0.25% collagenase type IV in Dulbecco’s Modified Eagle Medium at 37C for 1 hour in a shaking incubator. Collagenase was neutralized with Advanced RPMI 1640 Medium + 10% FBS and the digested skin was passed through a 70um strainer. The flow through was rinsed twice with centrifugation at 350g, 4C. Single-cell suspensions were stained with anti-CD45-FITC antibody and propidium iodide. CD45+, propidium iodide- cells were isolated via FACS. For human samples, human scalp biopsies were digested using the Whole Skin Dissociation Kit and its accompanying protocol, which involved the use of a gentleMACS Dissociator. Cells were resuspended and washed in 2% FBS in Cell Staining Buffer, then stained with DRAQ5 and SYTOX-Green prior to FACS isolation for DRAQ5- SYTOX-Green- live cells.
Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits (version 2 for mouse, version 3 for human samples) according to the manufacturer’s instructions, with a target of 5000 cells and 350 million reads

value: Skin

value: Immune cells

tag: disease state

value: No disease


title: AA, biological replicate 3

description: 10x Genomics

value: Total hair loss


title: Tpd single pollen drive 95

description: single-pollen-tpd.drive.vcf.gz

value: pollen


title: Day9Non-Gata6tomatonegative18

description:
Day9Non-Gata6tomatonegative18
day9ng6.txt

value: Epidermis


title: AA, biological replicate 2

description: 10x Genomics


title: UG, biological replicate 2

description: 10x Genomics


title: AA, biological replicate 1

description: 10x Genomics


title: Day9Gata6-derivedtomatopositive23

description:
Day9Gata6-derivedtomatopositive23
day9_g6.txt

value: Cre (+/-) tdTomato (+/-)


title: Tpd single pollen drive 92

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative17

description:
Day9Non-Gata6tomatonegative17
day9ng6.txt


title: UG, biological replicate 1

description: 10x Genomics


title: Tpd single pollen drive 97

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive22

description:
Day9Gata6-derivedtomatopositive22
day9_g6.txt


title: Tpd single pollen drive 91

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 94

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 90

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive21

description:
Day9Gata6-derivedtomatopositive21
day9_g6.txt


title: Day9Gata6-derivedtomatopositive20

description:
Day9Gata6-derivedtomatopositive20
day9_g6.txt


title: ES-1: Ctrl embryos

city: Darlinghurst

first: David

middle: Thomas

last: Humphreys

address: 405 Liverpool Street

department: Genome core

country: Australia

institute: Victor Chang Cardiac Research Institute

description: 10x Genomics

data_processing:
Sequenced read were processed, aligned to human genome (GRCh38.96/hg38), counted and filtered using Cell Ranger (v3.1.0)
Supplementary files format and content: mm10_GRCm38.96
Supplementary files format and content: filtered counts of sequencing reads.

source_name: whole embryonic heart at 12.5dpc (4 embryos pooled: eb4, eb5, eb6, eb18)

extract_protocol:
Sorted cardiac nuclei were directed processed according to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 protocol (PN-1000121).
Libraries were made according to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 protocol (PN-1000121).

value: whole embryonic heart at 12.5dpc (4 embryos pooled:eb4, eb5, eb6, eb18)

value: All cell types from cardiac tissue

value: Sox7(fl/fl):Cre negative embryos


title: ES-2: Sox7 iECKO (inducible endothelial cell knock out) embryos

description: 10x Genomics

source_name: whole embryonic heart at 12.5dpc (4 embryos pooled: eb3, eb11, eb12, eb16)

value: whole embryonic heart at 12.5dpc (4 embryos pooled:eb3, eb11, eb12, eb16)

value: Sox7(fl/fl):Cre positive embryos


title: Tpd single pollen drive 93

description: single-pollen-tpd.drive.vcf.gz


title: Mutant 3

city: Tel Aviv

first: Ruth

last: Ashery-Padan

department: Department of Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel-Aviv University

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a
Counting proceeded over genes annotated in Ensembl release 88, using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: retina

growth_protocol: Tissue taken from P2 old mice

extract_protocol:
Rneasy mini-kit
Inhouse poly A based RNA seq

value: retina


title: Day9Gata6-derivedtomatopositive19

description:
Day9Gata6-derivedtomatopositive19
day9_g6.txt


title: WUT-6203

value: Kidney

value: WT

value: Untreated


title: Mutant 2


title: Day9Gata6-derivedtomatopositive18

description:
Day9Gata6-derivedtomatopositive18
day9_g6.txt

value: Days 9 post-wounding


title: Tpd single pollen drive 87

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 88

description: single-pollen-tpd.drive.vcf.gz


title: Mutant 1


title: Tpd single pollen drive 89

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive17

description:
Day9Gata6-derivedtomatopositive17
day9_g6.txt


title: Tpd single pollen drive 86

description: single-pollen-tpd.drive.vcf.gz


title: Control 3

value: Control


title: Day9Gata6-derivedtomatopositive16

description:
Day9Gata6-derivedtomatopositive16
day9_g6.txt


title: Tpd single pollen drive 85

description: single-pollen-tpd.drive.vcf.gz


title: Control 2


title: Tpd single pollen drive 84

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative16

description:
Day9Non-Gata6tomatonegative16
day9ng6.txt


title: Control 1


title: Day9Non-Gata6tomatonegative15

description:
Day9Non-Gata6tomatonegative15
day9ng6.txt


title: Tpd single pollen drive 83

description: single-pollen-tpd.drive.vcf.gz


title: AID, male, 10 mM, replicate 3

city: Bloomington

first: Lesley

middle: Nicole

last: Weaver

state: IN

address: 1001 E. 3rd Street

department: Biology

institute: Indiana University

data_processing:
Reads obtained from sequencing were aligned to the D. melanogaster reference genome using the TopHat read alignment tool.
The reference sequences were downloaded from the Ensembl project website (useast.ensembl.org).
TopHat alignments were used to generate read counts for each gene using HTSeq, which were subsequently used to generate the differential expression results using the DESeq2 R package.
Enriched genes with a corrected P value less than 0.05 were considered significant.
Assembly: ensembl_drosophila_melanogaster_bdgp6_gca_000001215_4
Supplementary files format and content: Tab-delimited excel file contains raw counts for each Sample

organism: Drosophila melanogaster

source_name: Whole body

extract_protocol:
Whole body samples were flash frozen in liquid nitrogen and lysed in 500 µl of lysis buffer from the RNAqueous-4PCR DNA-free RNA isolation for RT-PCR kit (Ambion). RNA samples were sent to Novogene for sequencing.
The cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: Twenty 2-to-4-day old flies were starved for 16 hours prior to transfer to 0 mM (4% sucrose (m/v), 1.5% yeast extract (m/v), 1 mM NaOH) or 10 mM (4% sucrose (m/v), 1.5% yeast extract (m/v), 10 mM auxin) liquid food for 48 hours.

value: Whole body

value: w[1118]; tubP-TIR1-T2A-Gal80.AID

value: 10 mM


title: Tpd single pollen drive 82

description: single-pollen-tpd.drive.vcf.gz

value: pollen


title: AID, male, 10 mM, replicate 2


title: AID, male, 10 mM, replicate 1


title: Day9Non-Gata6tomatonegative14

description:
Day9Non-Gata6tomatonegative14
day9ng6.txt

value: Epidermis


title: Tpd single pollen drive 81

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 80

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative12

description:
Day9Non-Gata6tomatonegative12
day9ng6.txt

value: Cre (+/-) tdTomato (+/-)


title: Day9Non-Gata6tomatonegative13

description:
Day9Non-Gata6tomatonegative13
day9ng6.txt


title: Tpd single pollen drive 79

description: single-pollen-tpd.drive.vcf.gz


title: AID, male, 0 mM, replicate 2

value: 0 mM


title: Day9Non-Gata6tomatonegative10

description:
Day9Non-Gata6tomatonegative10
day9ng6.txt


title: AID, male, 0 mM, replicate 1


title: Day9Non-Gata6tomatonegative9

description:
Day9Non-Gata6tomatonegative9
day9ng6.txt


title: AID, male, 0 mM, replicate 3


title: Tpd single pollen drive 78

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 77

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative11

description:
Day9Non-Gata6tomatonegative11
day9ng6.txt


title: Tpd single pollen drive 76

description: single-pollen-tpd.drive.vcf.gz


title: AID, female, 10 mM, replicate 2


title: FHRCC06Ca

type: genomic

city: Chengdu

first: Zhenhua

last: Liu

state: Sichuan

address: 37# Guoxue Alley

department: Urology

country: China

institute: West China Hospital Sichuan University

description: Hereditary leiomyomatosis and renal cell cancer patient No.06 derived tumor sample

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

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

data_processing: GenomeStudio and ChAMP with default settings

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

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

value: Tumor

value: hereditary leiomyomatosis and renal cell cancer patient


title: FHRCC01Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.01 derived tumor sample


title: FHRCC02Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.02 derived tumor sample


title: AID, female, 10 mM, replicate 3


title: Day9Gata6-derivedtomatopositive15

description:
Day9Gata6-derivedtomatopositive15
day9_g6.txt


title: Tpd single pollen drive 75

description: single-pollen-tpd.drive.vcf.gz


title: FHRCC05Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.05 derived tumor sample


title: Day9Gata6-derivedtomatopositive14

description:
Day9Gata6-derivedtomatopositive14
day9_g6.txt


title: FHRCC19Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.19 derived tumor sample


title: AID, female, 10 mM, replicate 1


title: Day9Gata6-derivedtomatopositive13

description:
Day9Gata6-derivedtomatopositive13
day9_g6.txt


title: Tpd single pollen drive 74

description: single-pollen-tpd.drive.vcf.gz


title: AID, female, 0 mM, replicate 3


title: Day9Gata6-derivedtomatopositive12

description:
Day9Gata6-derivedtomatopositive12
day9_g6.txt


title: AID, female, 0 mM, replicate 2


title: Tpd single pollen drive 73

description: single-pollen-tpd.drive.vcf.gz


title: FHRCC09Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.09 derived tumor sample


title: FHRCC03Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.03 derived tumor sample


title: Day9Gata6-derivedtomatopositive11

description:
Day9Gata6-derivedtomatopositive11
day9_g6.txt


title: FHRCC15Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.15 derived tumor sample


title: FHRCC25Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.25 derived tumor sample


title: FHRCC07N

description: Hereditary leiomyomatosis and renal cell cancer patient No.07 derived normal sample

value: Normal


title: FHRCC02N

description: Hereditary leiomyomatosis and renal cell cancer patient No.02 derived normal sample


title: FHRCC10Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.10 derived tumor sample


title: AID, female, 0 mM, replicate 1


title: FHRCC10N

description: Hereditary leiomyomatosis and renal cell cancer patient No.10 derived normal sample


title: FHRCC04N

description: Hereditary leiomyomatosis and renal cell cancer patient No.04 derived normal sample


title: FHRCC08Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.08 derived tumor sample


title: FHRCC13Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.13 derived tumor sample


title: FHRCC04Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.04 derived tumor sample


title: Tpd single pollen drive 71

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, male, 10 mM, replicate 3


title: Day9Gata6-derivedtomatopositive9

description:
Day9Gata6-derivedtomatopositive9
day9_g6.txt


title: Tpd single pollen drive 70

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, male, 10 mM, replicate 2


title: Day9Gata6-derivedtomatopositive8

description:
Day9Gata6-derivedtomatopositive8
day9_g6.txt


title: FHRCC09N

description: Hereditary leiomyomatosis and renal cell cancer patient No.09 derived normal sample


title: Tpd single pollen drive 69

description: single-pollen-tpd.drive.vcf.gz


title: FHRCC16N

description: Hereditary leiomyomatosis and renal cell cancer patient No.16 derived normal sample


title: FHRCC07Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.07 derived tumor sample


title: Tpd single pollen drive 68

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, male, 0 mM, replicate 3


title: FHRCC16Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.16 derived tumor sample


title: Intestine, Vibrio cholerae V52

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

data_processing:
Raw base call files were demultiplexed and reads aligned to the Zebrafish reference genome (Ensemble GRCz11) using Cell Ranger v3.0.2
Supplementary files format and content: barcodes and features as TSV files
Supplementary files format and content: feature matrix as MTX file

organism: Danio rerio

source_name: Intestine

extract_protocol:
Intestinal tissue was dissociated enzymatically and mechanically followed by removal of debris and dead cells using OptiPrep™ Density Gradient Medium (Sigma).
single cell RNA libraries from freshly collected cells were prepared and barcoded with a 10X genomics Chromium Next GEM Single Cell 3' Reagents Kit v3.

value: Intestine

value: 9 months post fertilization

value: dissociated intestine

value: TL

value: Vibrio cholerae V52

tag: indices

value: SI-GA-B8 AAAGTGCT GCTACCTG TGCTGTAA CTGCAAGC


title: Tpd single pollen drive 67

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, male, 0 mM, replicate 2


title: Day9Non-Gata6tomatonegative7

description:
Day9Non-Gata6tomatonegative7
day9ng6.txt

value: Days 9 post-wounding


title: Intestine, uninfected, Mock

value: PBS

value: SI-GA-B7 AAACCTCA GCCTTGGT CTGGACTC TGTAGAAG


title: Tpd single pollen drive 72

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, male, 10 mM, replicate 1

value: Whole body

value: 10 mM


title: VK00040, male, 0 mM, replicate 1


title: Tpd single pollen drive 66

description: single-pollen-tpd.drive.vcf.gz

value: pollen


title: Day9Non-Gata6tomatonegative6

description:
Day9Non-Gata6tomatonegative6
day9ng6.txt

value: Epidermis

value: Cre (+/-) tdTomato (+/-)


title: Day9Non-Gata6tomatonegative5

description:
Day9Non-Gata6tomatonegative5
day9ng6.txt


title: H146 Dec2 RNA-Seq

city: Cleveland

first: Sudipta

last: Biswas

state: Ohio

address: 9500 Euclid Ave

department: Translational Hematology & Oncology Research

institute: Cleveland Clinic

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 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.
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. Since strand-specific library preparation was performed, the reads were strand-specifically counted.
STAR aligner v.2.5.2b
After extraction of gene hit counts, the gene hit counts table, provided as Table S5, was used for downstream differential expression analysis. Using DESeq257, a comparison of gene expression between vehicle and decitabine-treated H146 and F1339 SCLC cells was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes.
Subread package v.1.5.2
Assembly: GRCh38
Supplementary files format and content: DESeq2

source_name: lung

growth_protocol: H146 and F1339 cells were maintained in RPMI media supplemented with 10% FBS and antibiotics at 37C incubator with 5% CO2.

extract_protocol:
Human SCLC (H146) and murine SCLC (F1339) were treated with decitabine 0.5 µM for 96 and 72 hours respectively in duplicate for gene expression analyses by RNA-sequencing. RNA-extraction and library preparation from the cell pellet, sequencing and data processing was performed by an external vendor, Azenta Life Sciences.
RNA

value: lung

tag: cell line

value: SCLC

value: Decitabine


title: H146 Veh2 RNA-Seq

value: Vehicle


title: Tpd single pollen drive 65

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative8

description:
Day9Non-Gata6tomatonegative8
day9ng6.txt


title: FHRCC08N

description: Hereditary leiomyomatosis and renal cell cancer patient No.08 derived normal sample

value: Normal

value: hereditary leiomyomatosis and renal cell cancer patient


title: VK00040, female, 10 mM, replicate 3


title: FHRCC22Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.22 derived tumor sample

value: Tumor


title: FHRCC15N

description: Hereditary leiomyomatosis and renal cell cancer patient No.15 derived normal sample


title: H146 Dec1 RNA-Seq


title: Day9Non-Gata6tomatonegative4

description:
Day9Non-Gata6tomatonegative4
day9ng6.txt


title: Tpd single pollen drive 64

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, female, 10 mM, replicate 2


title: H146 Veh1 RNA-Seq


title: Tpd single pollen drive 63

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive10

description:
Day9Gata6-derivedtomatopositive10
day9_g6.txt


title: Day9Non-Gata6tomatonegative3

description:
Day9Non-Gata6tomatonegative3
day9ng6.txt


title: Ly1R decitabine-3

city: Madison

first: Lixin

last: Rui

state: WI - Wisconsin

address: 1111 Highland Ave R.4060

department: Medicine

institute: University of Wisconsin-Madison

data_processing:
human reference genome (UCSC hg38) with HISAT2. Transcripts/genes were assembled with StringTie. Differential expressions were analyzed with DESeq2. GSEA was performed locally by GSEA software (V4.0.3)
Supplementary files format and content: RNA-seq (txt file: gene TPM)

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using GeneJET RNA Purification Kit (ThermoFisher, K0731) according to the manufacturer’s protocol
DNBSEQ stranded mRNA library

value: DLBCL

value: Venetoclax resistant


title: VK00040, female, 0 mM, replicate 3

value: 0 mM


title: Ly1R decitabine-2


title: Day9Non-Gata6tomatonegative2

description:
Day9Non-Gata6tomatonegative2
day9ng6.txt

value: Days 9 post-wounding


title: Tpd single pollen drive 62

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, female, 10 mM, replicate 1


title: Day9Non-Gata6tomatonegative1

description:
Day9Non-Gata6tomatonegative1
day9ng6.txt


title: Tpd single pollen drive 61

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, female, 0 mM, replicate 2


title: Tpd single pollen drive 60

description: single-pollen-tpd.drive.vcf.gz


title: VK00040, female, 0 mM, replicate 1


title: Ly1R DMSO-3

value: DMSO


title: FHRCC21Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.21 derived tumor sample


title: Day9Gata6-derivedtomatopositive6

description:
Day9Gata6-derivedtomatopositive6
day9_g6.txt


title: Day9Gata6-derivedtomatopositive7

description:
Day9Gata6-derivedtomatopositive7
day9_g6.txt


title: FHRCC22N

description: Hereditary leiomyomatosis and renal cell cancer patient No.22 derived normal sample


title: Tpd single pollen drive 59

description: single-pollen-tpd.drive.vcf.gz


title: Oregon-R, male, 10 mM, replicate 3

value: Whole body

value: Oregon-R


title: Ly1R DMSO-2


title: FHRCC21N

description: Hereditary leiomyomatosis and renal cell cancer patient No.21 derived normal sample


title: Oregon-R, male, 10 mM, replicate 2

value: 10 mM


title: Day9Gata6-derivedtomatopositive4

description:
Day9Gata6-derivedtomatopositive4
day9_g6.txt

value: Epidermis


title: Tpd single pollen drive 58

description: single-pollen-tpd.drive.vcf.gz

value: pollen


title: Oregon-R, male, 10 mM, replicate 1


title: Ly1R DMSO-1


title: Tpd single pollen drive 57

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive3

description:
Day9Gata6-derivedtomatopositive3
day9_g6.txt

value: Cre (+/-) tdTomato (+/-)


title: Ly1R decitabine-1


title: Oregon-R, male, 0 mM, replicate 3


title: Decitabine-2

value: Parental


title: Tpd single pollen drive 56

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive2

description:
Day9Gata6-derivedtomatopositive2
day9_g6.txt


title: Day9Gata6-derivedtomatopositive5

description:
Day9Gata6-derivedtomatopositive5
day9_g6.txt


title: Decitabine-3

value: Decitabine


title: Oregon-R, male, 0 mM, replicate 2


title: Tpd single pollen drive 55

description: single-pollen-tpd.drive.vcf.gz


title: Decitabine-1


title: Tpd single pollen drive 54

description: single-pollen-tpd.drive.vcf.gz


title: DMSO-3


title: Oregon-R, male, 0 mM, replicate 1


title: Day9Gata6-derivedtomatopositive1

description:
Day9Gata6-derivedtomatopositive1
day9_g6.txt


title: Tpd single pollen drive 53

description: single-pollen-tpd.drive.vcf.gz


title: Oregon-R, female, 10 mM, replicate 3


title: Day9A1Blank

description:
Day9A1Blank
day9_g6.txt


title: Oregon-R, female, 10 mM, replicate 2


title: Tpd single pollen drive 52

description: single-pollen-tpd.drive.vcf.gz


title: DMSO-2


title: Tpd single pollen drive 51

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative47

description:
Day9Non-Gata6tomatonegative47
day9ng6.txt


title: Day9H12Blank

description:
Day9H12Blank
day9ng6.txt


title: Tpd single pollen drive 50

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, input, rep1

city: Kunming City

first: Jiangyang Li

last: Jingyang Li

state: Yunnan Province

address: School of Life Science, Yunnan University, Chenggong District

department: School of Life Science

institute: Yunnan Universiity

data_processing:
ChIP-seq reads were processed with Trim Galore  (v0.6.6) to remove adaptors and low-quality reads with the parameter  “-q30
ChIP-seq reads mapped to human genome (UCSC hg38) using Bowtie2 (v2.3.4.1) with default parameters.
Duplicate reads were by Picard (v2.25.7).
Bigwig files were generated with deeptools v3.5.1.
Peaks called by MACS2 v2.2.7.1
Assembly: hg38
Supplementary files format and content: BigWig files, Peak files(narrow peak)

source_name: HCT116 INTS11-AID

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
15cm plate cells were fixed with 1% formaldehyde for 10 min. The glycine crosslinking at 0.125M was terminated for 10min, the lysates were incubated on ice for 20min, and the chromatin was ultrasonically interrupted by ME220 focused ultrasound (Covaris)
The chip-seq library was prepared using the general DNA library construction kit (Vazyme, NDM607-02), and 100ng of DNA was taken as the starting material of the input sample and IP sample. The library was cyclically amplified 13 times on the thermal circulator. The DNA magnetic beads were recovered with 2% agarose gel, and the amplified library sizes of 250-400bp were selected. Library concentrations were measured using the Qubit™ ssDNA Assay Kit (Invitrogen, Q10212). Q-seq detects library fragment size

treatment_protocol: FBS-free DNEM was treated for 14h, 500uM IAA for 1h, 100ng/ul EGF Protein, Human, recombinant Protein (ECD)(Solarbio,10605-HNAE) for 30min, and 2000U IFN-beta Protein(Sino Biological Inc.,50708-mccH) for 1h

value: HCT116 INTS11-AID

value: colon cancer cell

tag: chip antibody


title: Day9Non-Gata6tomatonegative46

description:
Day9Non-Gata6tomatonegative46
day9ng6.txt


title: Oregon-R, female, 0 mM, replicate 3


title: INTS11-AID cells, input, rep2


title: Day9Non-Gata6tomatonegative45

description:
Day9Non-Gata6tomatonegative45
day9ng6.txt


title: Tpd single pollen drive 49

description: single-pollen-tpd.drive.vcf.gz


title: Oregon-R, female, 0 mM, replicate 2


title: INTS11-AID cells, Ser2P, IAA, CST, rep2


title: Day9Non-Gata6tomatonegative44

description:
Day9Non-Gata6tomatonegative44
day9ng6.txt


title: DMSO-1


title: Oregon-R, female, 0 mM, replicate 1


title: Day9Non-Gata6tomatonegative43

description:
Day9Non-Gata6tomatonegative43
day9ng6.txt


title: INTS11-AID cells, Ser2P, IAA, CST, rep1


title: Tpd single pollen drive 47

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 48

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative42

description:
Day9Non-Gata6tomatonegative42
day9ng6.txt


title: Tpd single pollen drive 46

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, Ser2P, Control, CST, rep2


title: Tpd single pollen drive 45

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative41

description:
Day9Non-Gata6tomatonegative41
day9ng6.txt


title: INTS11-AID cells, Ser2P, Control, CST, rep1


title: FHRCC23N

description: Hereditary leiomyomatosis and renal cell cancer patient No.23 derived normal sample

value: Normal

value: hereditary leiomyomatosis and renal cell cancer patient


title: H82 DNMT1 Cut&Tag no3

data_processing:
methods
Data processing was on the Galaxy platform (usegalaxy.org)54. To trim the adapters, we used Cutadapt. Sequencing reads were mapped to mm10 or GRCh37/hg19 genomes using Bowtie255. Heatmaps of coverage around gene transcription start sites were created using EASEQ56
Assembly: mm10 or GRCh37/hg19
Library strategy: Cut & Tag

growth_protocol: H82 and F1339 cells were maintained in RPMI media supplemented with 10% FBS and antibiotics at 37C incubator with 5% CO2.

extract_protocol: The Cleavage Under Targets and Tagmentation (CUT&Tag) procedure in triplicate, following the manufacturer’s protocol for the CUT&Tag-ITTM Assay Kit from Active Motif (cat no # 53165), and using DNMT1 antibody (Active Motif cat no # 39204), was applied to murine F1339 and human H82 SCLC cells. Libraries were amplified and normalized with the Illumina Nextera DNA Library prep kit (FC-121–1031) according to the manufacturer’s protocols. Sequencing on NextSeq 550 followed the manufacturer’s protocols through the Genomics Core Facility at Case Western Reserve University.

value: lung

value: SCLC


title: FHRCC12N

description: Hereditary leiomyomatosis and renal cell cancer patient No.12 derived normal sample


title: H82 DNMT1 Cut&Tag no2


title: FHRCC20Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.20 derived tumor sample

value: Tumor


title: Day9Gata6-derivedtomatopositive47

description:
Day9Gata6-derivedtomatopositive47
day9_g6.txt

value: Days 9 post-wounding


title: FHRCC23Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.23 derived tumor sample


title: Tpd single pollen drive 44

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, Tyr1P, IAA, Activemotive, rep1

value: Tyr1P (Activemotive, 61383)


title: Day9Gata6-derivedtomatopositive46

description:
Day9Gata6-derivedtomatopositive46
day9_g6.txt


title: INTS11-AID cells, Tyr1P, IAA, Activemotive, rep2


title: Tpd single pollen drive 43

description: single-pollen-tpd.drive.vcf.gz


title: A673 EF low Exp3

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

country: Spain

institute: INSTITUTO DE SALUD CARLOS III - IIER

data_processing:
fastq.gz files were analyzed by using RNA-Seq Alignment (BaseSpace Workflow) 1.1.0 and Isis (Analysis Software) 2.6.25.18
Briefly, mapping, alignment and annotation were  performed with the following softwares: STAR_2.5.0b (using GRCh37 as transcriptome reference), Isaac Variant Caller 2.3.13, IONA (Annotation Service) 1.0.10.37 and BEDTools 2.17.0
Transcript abundance was calculated with Cufflinks 2.2.1
Differences among expressed features (FPKM) were calculated with DESeq2 1.6.3
Assembly: GRCh37
Supplementary files format and content: DESeq2 result tables represent the differential expression among control cells (untreated cells, EWSR1::FLI1 high expression)  and cells treated with doxycycline (EWSR1::FLI1 low expression)
Supplementary files format and content: tab-delimited text files include FPKM values

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and antibiotics (Blasticidine and Zeocin)

extract_protocol:
Total RNA was isolated with Trizol reagent and additionally cleaned-up with RNAeasy minielute columns.
RNA libraries were prepared for sequencing using standard protocols for  ScriptSeq v2 RNA-seq library preparation kit (Epicentre, Catalogue number ssv21124). Ribosomic RNA depletion was performed with Ribo-zero rRNA removal kit (Catalogue number RZH110424)

treatment_protocol: Doxycycline 1 ug/mL during 72 hours

value: Ewing sarcoma cell line

value: enginereed with a EWSR1::FLI1 shRNA (doxycycline inducible)

value: doxicicline 72h (shEF expression)


title: FHRCC12Ca

description: Hereditary leiomyomatosis and renal cell cancer patient No.12 derived tumor sample


title: A673 EF low Exp2


title: INTS11-AID cells, Tyr1P, Control, Activemotive, rep2


title: Day9Gata6-derivedtomatopositive45

description:
Day9Gata6-derivedtomatopositive45
day9_g6.txt

value: Epidermis


title: A673 EF low Exp1


title: INTS11-AID cells, Tyr1P, Control, Activemotive, rep1


title: Day9Gata6-derivedtomatopositive44

description:
Day9Gata6-derivedtomatopositive44
day9_g6.txt


title: H82 DNMT1 Cut&Tag no1


title: A673 EF high Exp3

value: untreated


title: A673 EF high Exp2


title: Tpd single pollen drive 41

description: single-pollen-tpd.drive.vcf.gz

value: pollen


title: Tpd single pollen drive 40

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive42

description:
Day9Gata6-derivedtomatopositive42
day9_g6.txt

value: Cre (+/-) tdTomato (+/-)


title: Tpd single pollen drive 39

description: single-pollen-tpd.drive.vcf.gz


title: A673 EF high Exp1


title: Day9Gata6-derivedtomatopositive41

description:
Day9Gata6-derivedtomatopositive41
day9_g6.txt


title: Human ES-cell derived NPCs [NPC_Bys012_H3K27ac]

city: Boston

first: Gilbert

middle: Joseph

last: Rahme

state: MA

address: 365 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq data were aligned to hg19 or mm10 using BWA aln 0.7.4, requiring minimal mapping quality of 10.
PCR duplicates were removed with picard tools 2.9.2
ChIP-Seq density tracks were generated by bedgraph to BigWig format after RPM normalization
Assembly: hg19 for human samples, mm10 for mouse samples
Supplementary files format and content: ChIP-seq density tracks in bigwig format, and peak files in bed format

source_name: NPCs

growth_protocol: Human NPCs (Bys012) were cultured wiith ATCC formluated media following manufacturer's guidelines. Mouse NPCs were culture with DMEM:F12, 1X N2, 1X B27, 1% penicillin/streptomycin, 20 ng/ml of EGF, 20 ng/ml FGF2, and 1 μg/ml laminin. Mouse OPCs were cultured with DMEM:F12, 1X N2, 1X B27, 1% penicillin/streptomycin, 10 ng/ml PDGFB, 20 ng/ml FGF2 , and 1 μg/ml laminin.

extract_protocol:
For ChIP-seq, cultured cells were fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80 C for at least overnight. Sonication of tumor specimens and cultured cells was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418).  H3K27ac was immunoprecipitated with an antibody from Active Motif (cat 39133).
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3' A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

value: H3K27ac (Active motif 39133)

value: NPCs


title: Tpd single pollen drive 38

description: single-pollen-tpd.drive.vcf.gz

data_processing:
library strategy: DNA-seq
Adapter trimming was performed with Cutadapt v3.1 and read quality was assessed using FastQC v0.11.9. Paired-end reads were aligned to the to the W22 reference genome with BWA-MEM v0.7.17. Alignments were filtered by mapping quality (mapQ≥30) and PCR duplicates were removed using Samtools v1.10. SNP calling was performed using Freebayes v1.3.2. Putative SNP calls were filtered by quality, depth, and allele frequency (AF=1) to obtain a high-confidence mexicana marker set that was subsequently validated against the TPD assembly. For BSA analysis, SNP calls were filtered against the gold-standard TPD marker set.
All calls at validated marker sites were extracted and encoded in a sparse matrix format (rows = markers, columns = samples) and encoded (1 = alt allele, -1 = ref allele, 0 = missing). To assess mexicana introgression in individual pollen grains, mean SNP signal was calculated in 100kb bins across the genome. A sliding window (1Mb window, 200kb step) was applied in order to smooth the data and identify regions with mexicana SNP density. To identify genomic intervals overrepresented in surviving Tpd pollen grains, aggregate allele frequency was calculated across all pollen grains at each marker site.
Assembly: Zm-W22-REFERENCE-NRGENE-2.0; Zm-TPD-1.0
Supplementary files format and content: single-pollen-tpd.fertile.vcf.gz


title: INTS11-AID cells, Pol II, Control, ABACM

value: HCT116 INTS11-AID

value: colon cancer cell

value: Pol II (Abcam, ab26721)


title: Day9Gata6-derivedtomatopositive40

description:
Day9Gata6-derivedtomatopositive40
day9_g6.txt


title: SK-LMS-1_3

first: Nicola

last: Biondi

state: Baden-Württemberg

address: Im Neuenheimer Feld 581

department: Functional and Structural Genomics

institute: German Cancer Research Center (DKFZ)

description: ATAC-Seq

data_processing:
Sequencing reads were processed using the CWL-based ATAC-Seq workflow available at https://github.com/CompEpigen/ATACseq_workflows
Peak calling on individual samples was performed with MACS2 with parameters -- nomodel  -- keep_dup all --broad --gsize 2736124973 --qvalue 0.05.
The DiffBind protocol to obtain a consensus read count matrix from MACS2 peak sets
Peaks were annotated to nearest gene using the ``annotatePeak" function in "ChIPseeker" package in R
Assembly: hg38
Supplementary files format and content: _fragment.macs2_peaks.xls

growth_protocol: SK-UT-1 and SK-UT-1B were cultured in MEM medium supplemented with 10% FBS; MES-SA cells were cultured in McCoy’s medium supplemented with 10% FBS; SK-LMS-1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS. All media were supplemented with 1% penicillin/streptomycin and 1% L-glutamine.

extract_protocol:
50.000 cells per replicate were collected by centrifugation at 500 x g for 5 min at 4°C. Cell pellets were resuspended in 50 μL ice-cold lysis buffer A (see Supplementary file 1 of the manuscript) and incubated on ice for 3 min, after which 500 μL ice-cold lysis buffer B (see Supplementary file 1 of the manuscript) were added. Cell nuclei were pelleted by centrifugation at 500 x g for 10 min at 4°C. The supernatant was removed carefully and nuclei pellets were resuspended in 47.5 μL ice-cold transposition buffer and 2.5 μL Tagment DNA TDE1 enzyme (Illumina). The transposition mix was incubated at 37°C for 30 mins at 1000 rpm. After adding 20 µL 5 M guanidinium thiocyanate, tagmented DNA was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter).
ATAC-Seq libraries for SK-UT-1, SK-UT-1B, MES-SA, and SK-LMS-1 were prepared in triplicate according to the Omni-ATAC protocol.

value: leiomyosarcoma


title: INTS11-AID cells, Pol II, IAA, ABACM, rep2


title: INTS11-AID cells, Pol II, IAA, ABACM


title: Day9Non-Gata6tomatonegative40

description:
Day9Non-Gata6tomatonegative40
day9ng6.txt


title: Tpd single pollen drive 42

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 37

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative39

description:
Day9Non-Gata6tomatonegative39
day9ng6.txt


title: SK-LMS-1_2

description: ATAC-Seq


title: Tpd single pollen drive 36

description: single-pollen-tpd.drive.vcf.gz


title: SK-LMS-1_1

description: ATAC-Seq


title: Day9Gata6-derivedtomatopositive43

description:
Day9Gata6-derivedtomatopositive43
day9_g6.txt


title: INTS11-AID cells, Pol II, IAA+EGF, ABACM


title: INTS11-AID cells, Pol II, EGF, ABACM


title: INTS11-AID cells, Pol II, IAA, ABACM, rep1


title: Tpd single pollen drive 35

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative38

description:
Day9Non-Gata6tomatonegative38
day9ng6.txt


title: INTS11-AID cells, Pol II, Control, ABACM, rep2


title: Day9Non-Gata6tomatonegative37

description:
Day9Non-Gata6tomatonegative37
day9ng6.txt


title: Tpd single pollen drive 33

description: single-pollen-tpd.drive.vcf.gz


title: Tpd single pollen drive 34

description: single-pollen-tpd.drive.vcf.gz


title: MES-SA_3

description: ATAC-Seq

source_name: MES-SA

value: MES-SA


title: MES-SA_2

description: ATAC-Seq


title: Tpd single pollen drive 32

description: single-pollen-tpd.drive.vcf.gz

source_name: pollen


title: INTS11-AID cells, Pol II, Control, ABACM, rep1


title: CPSF73-AID cells, +IAA, steady [CPSF73_IAA4h_rep3]

description:
chromatin associate RNA
CPSF73.txt
CPSF73_IAA4h_rep3

data_processing:
Raw reads were processed with Trim Galore  (v0.6.6) to remove adaptors and low-quality reads with the parameter  “-q30
Ribosomal RNA contaminations were removed using Bowtie (v1.3.0) with “-un”.
Remaining reads were aligned to the human genome (UCSC hg38) with STAR (v2.7.9a), whose results were converted to BAM file with SAMtools (v1.7).
Gene expression quantification was performed with featureCounts tool of Subread (v2.0.1). Differential expression analysis was performed using DESeq2 R package (v1.34.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each samples

extract_protocol:
After 1h treatment with IAA, PBS was washed away for three times and replaced with fresh medium for 7h culture, and chromatin RNA was extracted to construct library
Library Construction using universal RNA-seq library prep kit (Vazyme, NRM605-02). 500ng of Chromatin RNA was used for the construction of sequencing libraries.

treatment_protocol:
FBS-free DNEM was treated for 14h, 500uM IAA for 1h, 100ng/ul EGF Protein, Human, recombinant Protein (ECD)(Solarbio,10605-HNAE) for 30min, and 2000U IFN-beta Protein(Sino Biological Inc.,50708-mccH) for 1h
Chromatin was extracted by Chromatin RNA separation and chromatin RNA was extracted by Trizol. Construction of chromatin RNA libraries

value: auxin(IAA)

tag: time


title: Day9Non-Gata6tomatonegative35

description:
Day9Non-Gata6tomatonegative35
day9ng6.txt

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Read quality was checked and alinged to GRCm38 reference genome using STAR version 2.2.
Gene specific counts were calculated using featureCounts from Rsubread 2.7 with mm10 Refseq.
All the downstream analysis was performed using Seurat version 3.2.2 and monocle 2.18.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Seurat object with annotations for every sample/cell.

value: Days 9 post-wounding


title: MES-SA_1

description: ATAC-Seq


title: CPSF73-AID cells, +IAA, steady [CPSF73_IAA4h_rep2]

description:
chromatin associate RNA
CPSF73.txt
CPSF73_IAA4h_rep2


title: Day9Non-Gata6tomatonegative36

description:
Day9Non-Gata6tomatonegative36
day9ng6.txt


title: Day9Non-Gata6tomatonegative34

description:
Day9Non-Gata6tomatonegative34
day9ng6.txt


title: Oregon-R, female, 10 mM, replicate 1

value: Whole body

value: Oregon-R

value: 10 mM


title: CPSF73-AID cells, +IAA, steady [CPSF73_CTRL_rep3]

description:
chromatin associate RNA
CPSF73.txt
CPSF73_CTRL_rep3

value: DMSO


title: SK-UT1-B_2

description: ATAC-Seq


title: Tpd single pollen drive 30

description: single-pollen-tpd.drive.vcf.gz

extract_protocol:
Pollen grains from Tpd1/tpd1; Tpd2/tpd2 plants were suspended in ice-cold PBS on a microscope slide under a dissecting scope. Individual plump, viable pollen grains were deposited into the 0.2mL wells of a 96-well plate using a p20 pipette. Lysis and whole genome amplification were performed using the REPLI-g single-cell kit (Qiagen, cat#150345) with the following modifications; 1/4th the specified volume of amplification mix was deposited in each well and isothermal amplification was limited to 5 hours. All steps prior to amplification were performed in a UV-decontaminated PCR hood. WGA products were cleaned up using a Genomic DNA Clean & Concentrator kit (Zymo Research, cat#D4067) and yields were quantified using with the QuantiFluor dsDNA system (Promega, cat#E2670) in a 96-well microplate format.
Libraries were prepared using the TruSeq Nano DNA High Throughput kit (Illumina, cat#20015965) with 200ng input. Samples were sequenced on a NextSeq500 platform using 2x150bp high output run.


title: CPSF73-AID cells, +IAA, steady [CPSF73_IAA4h_rep1]

description:
chromatin associate RNA
CPSF73.txt
CPSF73_IAA4h_rep1


title: Tpd single pollen drive 29

description: single-pollen-tpd.drive.vcf.gz


title: SK-UT1-B_1

description: ATAC-Seq


title: CPSF73-AID cells, +IAA, steady [CPSF73_CTRL_rep2]

description:
chromatin associate RNA
CPSF73.txt
CPSF73_CTRL_rep2


title: Day9Gata6-derivedtomatopositive39

description:
Day9Gata6-derivedtomatopositive39
day9_g6.txt

extract_protocol:
Single keratinocytes from mouse epidermis were isolated by flow sorting using appropriate markers. Cells were sorted into individual wells of a 96-well plate containing 2ul lysis buffer (0.8% (volume/volume) Triton X-100 and 2U/ul recombinant RNase inhibitor
Libraries were prepared for sequencing using standard Illumina protocols with SmartSeq2 followed by Nextera XT protocol.

value: Epidermis


title: Tpd single pollen drive 28

description: single-pollen-tpd.drive.vcf.gz


title: SK-UT-1_3

description: ATAC-Seq


title: Day9Gata6-derivedtomatopositive38

description:
Day9Gata6-derivedtomatopositive38
day9_g6.txt


title: SK-UT-1_2

description: ATAC-Seq


title: Tpd single pollen drive 27

description: single-pollen-tpd.drive.vcf.gz


title: INTS9-AID cells, +IAA, starvation [INTS9_IAA_rep2]

description:
chromatin associate RNA
INTS9.txt
INTS9_IAA_rep2


title: Day9Gata6-derivedtomatopositive37

description:
Day9Gata6-derivedtomatopositive37
day9_g6.txt


title: Tpd single pollen drive 31

description: single-pollen-tpd.drive.vcf.gz


title: SK-UT1-B_3

description: ATAC-Seq


title: Day9Gata6-derivedtomatopositive36

description:
Day9Gata6-derivedtomatopositive36
day9_g6.txt


title: Tpd single pollen drive 26

description: single-pollen-tpd.drive.vcf.gz


title: SK-UT-1_1

description: ATAC-Seq


title: Tpd single pollen drive 25

description: single-pollen-tpd.drive.vcf.gz


title: INTS9-AID cells, +IAA, starvation [INTS9_IAA_rep1]

description:
chromatin associate RNA
INTS9.txt
INTS9_IAA_rep1


title: HOM_B4: FACS sorted endothelial cells from SOX7ECKO at 10.5dpc

description:
10x Genomics
HOM_B4

data_processing:
Smart-Seq 2 method as described in (Picelli et al., 2014).Sequencing was performed using the Illumina NextSeq500 (NextSeq control software v2.1.0 / Real Time Analysis v2.4.11). The library pool was diluted and denatured according to the standard NextSeq protocol (Document # 15048776 v04) and sequenced to generate single-end 76 bp reads using a 75 cycle NextSeq500/550 High Output reagent Kit v2 (illumina, FC-404-2005). After sequencing, fastq files were generated using bcl2fastq2 (v2.18.0).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  Trimmomatic
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR Aligner
Read count extraction and normalization were performed edgeR and DEseq2
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: whole embryo

growth_protocol: Tamoxifen injection was performed at 9.5dpc on Sox7fl/fl Cdh5CreERT2 transgenic mice. Embryos were harvested at 10.5dpc,, after inidvidual genotyping, single cell resuspended embryo were used to FACS out endothelial cells.

extract_protocol:
To validate the Sox7iECKO E10.5 RNA-Seq, staged matched (31-33ss) sibling controls and Sox7iECKO embryos were harvested from pregnant dams treated as specified with tamoxifen at E9.5. Whole embryos were subjected to single cell isolation using 0.071 mg/ml liberase in PBS buffer. CD31+ endothelial cells were isolated using Alexa 488 conjugated rat anti-CD31 (1:800, 563607, BD Pharmigen), live/dead cells were detected by 7AAD (1:1000, Invitrogen). Cell sorting was performed on a BD FACSAria Cell Sorter. RNA was harvested using Trizol (Thermo-Fisher) and purified with DirectZol RNA microprep kit (R2060, Zymo research).
RNA-Seq libraries were prepared from polyA selected RNA and cDNA generated by the Smart-Seq2 protocol using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096). For each sample, 0.5 ng of cDNA was used as input for the Nextera XT library prep, with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Agilent Bioanalyzer with the High Sensitivity DNA kit (Agilent Technologies, 5067-4626). Libraries were pooled in equimolar ratios.

value: whole embryo

value: Endothelial cells


title: Day9Gata6-derivedtomatopositive35

description:
Day9Gata6-derivedtomatopositive35
day9_g6.txt

value: Cre (+/-) tdTomato (+/-)


title: Tpd single pollen drive 24

description: single-pollen-tpd.drive.vcf.gz

value: pollen


title: Day9Non-Gata6tomatonegative33

description:
Day9Non-Gata6tomatonegative33
day9ng6.txt


title: HOM_B2: FACS sorted endothelial cells from SOX7ECKO at 10.5dpc

description:
10x Genomics
HOM_B2


title: Tpd single pollen drive 23

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive34

description:
Day9Gata6-derivedtomatopositive34
day9_g6.txt


title: INTS11-AID cells, +IAA+IFNB, starvation [INTS11_IFNB_IAA_IFNB_rep2]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_IAA_IFNB_rep2

value: auxin(IAA)+IFNB


title: Tpd single pollen drive 22

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive33

description:
Day9Gata6-derivedtomatopositive33
day9_g6.txt


title: CPSF73-AID cells, +IAA, steady [CPSF73_CTRL_rep1]

description:
chromatin associate RNA
CPSF73.txt
CPSF73_CTRL_rep1


title: WT_D3: FACS sorted endothelial cells from WT Ctrl at 10.5dpc

description:
10x Genomics
WT_D3

value: WT


title: Day9Gata6-derivedtomatopositive32

description:
Day9Gata6-derivedtomatopositive32
day9_g6.txt


title: INTS11-AID cells, +IAA+IFNB, starvation [INTS11_IFNB_IAA_IFNB_rep1]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_IAA_IFNB_rep1

value: colon cancer cell


title: INTS11-AID cells, +IFNB, starvation [INTS11_IFNB_IFNB_rep2]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_IFNB_rep2

value: IFNB


title: WT_B7: FACS sorted endothelial cells from WT Ctrl at 10.5dpc

description:
10x Genomics
WT_B7


title: Day9Non-Gata6tomatonegative32

description:
Day9Non-Gata6tomatonegative32
day9ng6.txt


title: Tpd single pollen drive 21

description: single-pollen-tpd.drive.vcf.gz


title: WT_B1: FACS sorted endothelial cells from WT Ctrl at 10.5dpc

description:
10x Genomics
WT_B1


title: INTS9-AID cells, Control, starvation [INTS9_CTRL_rep2]

description:
chromatin associate RNA
INTS9.txt
INTS9_CTRL_rep2


title: Tpd single pollen drive 20

description: single-pollen-tpd.drive.vcf.gz


title: HOM_B3: FACS sorted endothelial cells from SOX7ECKO at 10.5dpc

description:
10x Genomics
HOM_B3


title: INTS9-AID cells, Control, starvation [INTS9_CTRL_rep1]

description:
chromatin associate RNA
INTS9.txt
INTS9_CTRL_rep1


title: Tpd single pollen drive 19

description: single-pollen-tpd.drive.vcf.gz


title: RNA_Cre_3xFLAG-deltapro#3_adipocytes_day7_LPS_rep2

city: Tokyo

first: Yuta

last: Hiraike

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: The University of Tokyo

data_processing:
The sequence reads were aligned to the mm9 genome using STAR (Galaxy Version 2.7.8a+galaxy0).
Assembly and quantification were performed using StringTie (Galaxy Version 2.1.1).
Assembly: mm9
Supplementary files format and content: txt files showing FPKM value of each samples.

source_name: ingSVF-derived adipocytes

growth_protocol: SVF cells were mainteined in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Techologies) and RNeasy Mini Kit (Qiagen).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 μM dexamethosone, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. When indicated, 20ng/mL LPS was added to the dish 8 hours before sample collection.

value: ingSVF-derived adipocytes

tag: time-course

value: day 7

value: LPS


title: Day9Non-Gata6tomatonegative31

description:
Day9Non-Gata6tomatonegative31
day9ng6.txt

source_name: Epidermis

value: Days 9 post-wounding


title: RNA_Cre_3xFLAG-deltapro#3_adipocytes_day7_LPS_rep3


title: Day9Non-Gata6tomatonegative30

description:
Day9Non-Gata6tomatonegative30
day9ng6.txt


title: Tpd single pollen drive 18

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative29

description:
Day9Non-Gata6tomatonegative29
day9ng6.txt


title: INTS11-AID cells, +IAA, starvation [INTS11_IFNB_IAA_rep1]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_IAA_rep1

value: auxin(IAA)


title: INTS11-AID cells, +IFNB, starvation [INTS11_IFNB_IFNB_rep1]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_IFNB_rep1


title: Tpd single pollen drive 17

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative28

description:
Day9Non-Gata6tomatonegative28
day9ng6.txt


title: INTS11-AID cells, Control, starvation [INTS11_IFNB_CTRL_rep2]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_CTRL_rep2


title: Tpd single pollen drive 16

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, Control, starvation [INTS11_IFNB_CTRL_rep1]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_CTRL_rep1


title: Tpd single pollen drive 15

description: single-pollen-tpd.drive.vcf.gz


title: RNA_Cre_3xFLAG-NFIA_adipocytes_day7_LPS_rep3

value: NFIA-KO, 3xFLAG-NFIA-expressing


title: RNA_Cre_3xFLAG-NFIA_adipocytes_day7_LPS_rep2


title: RNA_Cre_3xFLAG-deltapro#3_adipocytes_day7_LPS_rep1


title: Day9Non-Gata6tomatonegative27

description:
Day9Non-Gata6tomatonegative27
day9ng6.txt


title: INTS11-AID cells, +IAA+EGF, starvation [INTS11_EGF_IAA_EGF_rep2]

description:
chromatin associate RNA
EGF.txt
INTS11_EGF_IAA_EGF_rep2

value: auxin(IAA)+EGF


title: Tpd single pollen drive 14

description: single-pollen-tpd.drive.vcf.gz


title: Day9Non-Gata6tomatonegative26

description:
Day9Non-Gata6tomatonegative26
day9ng6.txt


title: INTS11-AID cells, +IAA, starvation [INTS11_IFNB_IAA_rep2]

description:
chromatin associate RNA
IFNB.txt
INTS11_IFNB_IAA_rep2


title: RNA_Cre_3xFLAG-NFIA_adipocytes_day7_LPS_rep1


title: Day9Non-Gata6tomatonegative25

description:
Day9Non-Gata6tomatonegative25
day9ng6.txt


title: Tpd single pollen drive 13

description: single-pollen-tpd.drive.vcf.gz


title: RNA_flox_adipocytes_day7_LPS_rep3

value: flox


title: Day9Gata6-derivedtomatopositive31

description:
Day9Gata6-derivedtomatopositive31
day9_g6.txt

value: Epidermis


title: INTS11-AID cells, +EGF, starvation [INTS11_EGF_EGF_rep2]

description:
chromatin associate RNA
EGF.txt
INTS11_EGF_EGF_rep2

value: EGF


title: Tpd single pollen drive 12

description: single-pollen-tpd.drive.vcf.gz


title: Day9Gata6-derivedtomatopositive30

description:
Day9Gata6-derivedtomatopositive30
day9_g6.txt


title: INTS11-AID cells, +EGF, starvation [INTS11_EGF_EGF_rep1]

description:
chromatin associate RNA
EGF.txt
INTS11_EGF_EGF_rep1


title: RNA_flox_adipocytes_day7_LPS_rep2


title: Day9Gata6-derivedtomatopositive29

description:
Day9Gata6-derivedtomatopositive29
day9_g6.txt


title: Tpd single pollen drive 11

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, +IAA, rescue [INTS11_steady_RESCUE_rep2]

description:
chromatin associate RNA
steady.txt
INTS11_steady_RESCUE_rep2

value: auxin(IAA)+remove auxin(IAA)


title: RNA_flox_adipocytes_day7_LPS_rep1


title: Tpd single pollen drive 10

description: single-pollen-tpd.drive.vcf.gz


title: RNA_Cre_3xFLAG-deltapro#3_adipocytes_day7_rep3


title: RNA_Cre_3xFLAG-deltapro#3_adipocytes_day7_rep2


title: INTS11-AID cells, +IAA, rescue [INTS11_steady_RESCUE_rep1]

description:
chromatin associate RNA
steady.txt
INTS11_steady_RESCUE_rep1


title: INTS11-AID cells, +IAA, steady [INTS11_steady_IAA_rep2]

description:
chromatin associate RNA
steady.txt
INTS11_steady_IAA_rep2


title: Day9Gata6-derivedtomatopositive28

description:
Day9Gata6-derivedtomatopositive28
day9_g6.txt

value: Cre (+/-) tdTomato (+/-)


title: Tpd single pollen drive 9

description: single-pollen-tpd.drive.vcf.gz

value: pollen


title: RNA_Cre_3xFLAG-deltapro#3_adipocytes_day7_rep1


title: Day9Gata6-derivedtomatopositive27

description:
Day9Gata6-derivedtomatopositive27
day9_g6.txt


title: INTS11-AID cells, +IAA, steady [INTS11_steady_IAA_rep1]

description:
chromatin associate RNA
steady.txt
INTS11_steady_IAA_rep1


title: Tpd single pollen drive 8

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, +IAA+EGF, starvation [INTS11_EGF_IAA_EGF_rep1]

description:
chromatin associate RNA
EGF.txt
INTS11_EGF_IAA_EGF_rep1


title: Day9Gata6-derivedtomatopositive26

description:
Day9Gata6-derivedtomatopositive26
day9_g6.txt


title: Tpd single pollen drive 7

description: single-pollen-tpd.drive.vcf.gz


title: RNA_Cre_3xFLAG-NFIA_adipocytes_day7_rep3


title: Tpd single pollen drive 6

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, Control, steady [INTS11_steady_CTRL_rep2]

description:
chromatin associate RNA
steady.txt
INTS11_steady_CTRL_rep2

value: DMSO


title: RNA_Cre_3xFLAG-NFIA_adipocytes_day7_rep2


title: Day9Gata6-derivedtomatopositive25

description:
Day9Gata6-derivedtomatopositive25
day9_g6.txt


title: INTS11-AID cells, Control, steady [INTS11_steady_CTRL_rep1]

description:
chromatin associate RNA
steady.txt
INTS11_steady_CTRL_rep1


title: Day9Gata6-derivedtomatopositive24

description:
Day9Gata6-derivedtomatopositive24
day9_g6.txt


title: Tpd single pollen drive 5

description: single-pollen-tpd.drive.vcf.gz


title: RNA_Cre_3xFLAG-NFIA_adipocytes_day7_rep1


title: Tpd single pollen drive 4

description: single-pollen-tpd.drive.vcf.gz


description:
CtrlUnwoundedGata6-derivedtomatopositive30
control_g6.txt

value: Day 0 post-wounding


title: INTS11-AID cells, +IAA, starvation [INTS11_starvation_IAA_rep3]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_IAA_rep3

value: colon cancer cell


title: Tpd single pollen drive 3

description: single-pollen-tpd.drive.vcf.gz


title: INTS11-AID cells, +IAA, starvation [INTS11_starvation_IAA_rep4]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_IAA_rep4


title: INTS11-AID cells, +IAA, starvation [INTS11_starvation_IAA_rep2]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_IAA_rep2


description:
CtrlUnwoundedGata6-derivedtomatopositive29
control_g6.txt


title: Tpd single pollen drive 2

description: single-pollen-tpd.drive.vcf.gz


description:
CtrlUnwoundedGata6-derivedtomatopositive31
control_g6.txt


title: INTS11-AID cells, +IAA, starvation [INTS11_starvation_IAA_rep1]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_IAA_rep1


description:
CtrlUnwoundedGata6-derivedtomatopositive28
control_g6.txt


title: RNA_flox_adipocytes_day7_rep1


description:
CtrlUnwoundedGata6-derivedtomatopositive27
control_g6.txt


title: Tpd single pollen drive 1

description: single-pollen-tpd.drive.vcf.gz


title: ChIP_H3K27Ac_Cre_3xFLAG-deltapro#3_adipocytes_day7_LPS

data_processing:
The sequence reads were mapped to UCSC build mm9 (NCBI Build 37) assembly using bowtie2 (Galaxy version 2.3.4) with default parameters.
Peak calling was performed using MACS2 (Galaxy version 2.1.1.20160309)
Assembly: mm9
Supplementary files format and content: bigWig files showing the peaks of each samples.

extract_protocol:
Samples were treated by nuclear extraction buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 minutes and immediately cross-linked with 1% formaldehyde for 7.5 minutes at room temperature. Cross-linking was quenched using 125 mM glycine for 5 minutes. The chromatin was sheared by probe sonicator (Branson) and was spun at 15,000rpm for 5 minutes. Antibodies were added for overnight incubation at 4C. Mix of Protein A and Protein G magnetic beads (Thermo Scientific) were added to samples for 4h at 4C. Subsequent procedures were performed as described previously (Hiraike Y., Waki H.et.al. 2017).
ChIP-seq libraries were prepared using KAPA hyper prep kit (KAPA Biosystems) according to the manufacturer's instructions.


title: RNA_flox_adipocytes_day7_rep2


title: INTS11-AID cells, Control, starvation [INTS11_starvation_CTRL_rep4]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_CTRL_rep4


title: INTS11-AID cells, Control, starvation [INTS11_starvation_CTRL_rep3]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_CTRL_rep3


description:
CtrlUnwoundedGata6-derivedtomatopositive26
control_g6.txt


title: ChIP_H3K27Ac_Cre_3xFLAG-NFIA_adipocytes_day7_LPS


title: INTS11-AID cells, Control, starvation [INTS11_starvation_CTRL_rep2]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_CTRL_rep2


title: F1339 Dec2 RNA-Seq

value: lung

value: SCLC

value: Decitabine


title: ChIP_H3K27Ac_flox_adipocytes_day7_LPS

value: ingSVF-derived adipocytes

value: day 7

value: LPS


title: ChIP_H3K27Ac_Cre_3xFLAG-deltapro#3_adipocytes_day7


title: INTS11-AID cells, Control, starvation [INTS11_starvation_CTRL_rep1]

description:
chromatin associate RNA
starvation.txt
INTS11_starvation_CTRL_rep1


title: RNA_flox_adipocytes_day7_rep3


description:
CtrlUnwoundedGata6-derivedtomatopositive24
control_g6.txt


title: F1339 Veh1 RNA-Seq

value: Vehicle


title: CtrlUnwoundednon-Gata6tomatonegative24

description:
CtrlUnwoundednon-Gata6tomatonegative24
controlng6.txt


title: ChIP_H3K27Ac_flox_adipocytes_day7


title: CtrlUnwoundednon-Gata6tomatonegative23

description:
CtrlUnwoundednon-Gata6tomatonegative23
controlng6.txt


title: Zymoseptoria ardabiliae Za17, incompatible wheat infection stage A, 10 days post inoculation, replicate 2

city: Kiel

first: Janine

last: Haueisen

address: Am Botanischen Garten 1-9

department: Botanical Institute

institute: Christian-Albrechts University of Kiel

data_processing:
We assessed the quality of the sequencing data with FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/) and applied a stringent trimming and filtering protocol using FASTX‐toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_ toolkit/) and Trimmomatic (Bolger, Lohse, & Usadel, 2014) v0.33.
Reads were mapped to the reference genome assemblies (Feurtey et al., 2020; Goodwin et al., 2011) using hisat2 v2.2.0 (Kim et al., 2019).
Read alignments were stored in SAM format, and indexing, sorting, and conversion to BAM format were performed using SAMtools v1.10 (Li et al., 2009).
Relative abundances of transcripts for predicted genes were calculated in RPKM using Cuffdiff2 v2.2.1 (Trapnell et al., 2013).
Total read counts per gene were estimated with HTSeq v0.11.3 (Anders et al., 2015).
Assembly: SMRT-seq assembled genomes of Za17 & Zp13: https://doi.org/ 10.5281/zenodo.3820378
Supplementary files format and content: Za17_expression_values.csv: csv file, contains normalized RPKM values calculated using Cuffdiff2
Supplementary files format and content: Zp13_expression_values.csv: csv file, contains normalized RPKM values calculated using Cuffdiff2

organism: Zymoseptoria ardabiliae

source_name: Infected leaf tissue of Triticum aestivum Obelisk

growth_protocol: Cells of Z. pseudotritici and Z. ardabiliae were inoculated from cryostocks onto YMS agar (0.4% [w/v] yeast extract, 0.4% [w/v] malt extract, 0.4% [w/v] sucrose, 2% [w/v] bacto agar) and grown at 18°C for 5 days. Single cells were grown in liquid YMS (200 rpm, 18°C) and harvested by centrifugation (3500 rpm for 10 min).

extract_protocol:
Total RNA from Zymoseptoria spp.‐infected wheat material collected during one infection experiment was isolated using the TRIzol™ reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer's instructions. One biological sample consists of material from three inoculated second leaves that were pooled and homogenized in liquid nitrogen. One hundred milligram of the resulting powder was used for RNA extraction.
Preparation of strand‐specific RNA‐seq libraries including polyA enrichment was performed at the Max Planck Genome Center, Cologne, Germany (http://mpgc.mpipz. mpg.de), using the NEBNext UltraTM Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocol (New England Biolabs, Frankfurt/Main, Germany) with an input of 1 µg total RNA.

treatment_protocol: Seedlings of the Triticum aestivum cultivar Obelisk (Wiersum Plantbreeding, Winschoten, Netherlands) were cultivated, maintained and brush-inoculated as described in (Fagundes et al., 2020). Fungal inoculum was adjusted to 10x8 cells/ml in 0.1% [v/v] Tween 20 (Roth, Karlsruhe, Germany). Plants were grown with a 16-h light period and either maintained in a plant growth chamber environment (22°C [day]/20°C [night], 70% humidity) for up to 4 weeks post inoculation.

value: Infecting hyphae

value: WT

value: incompatible wheat infection 10 dpi


title: Zymoseptoria ardabiliae Za17, incompatible wheat infection stage A, 10 days post inoculation, replicate 1

value: Infected leaf tissue of Triticum aestivum Obelisk


title: CtrlUnwoundednon-Gata6tomatonegative22

description:
CtrlUnwoundednon-Gata6tomatonegative22
controlng6.txt

value: Epidermis


title: ChIP_FLAG_Cre_3xFLAG-deltapro#3_adipocytes_day7_LPS

value: FLAG M2


title: OrthoE, Infected, replicate 3

city: Palo Alto

first: Tamar

middle: P

last: Feldman

state: CA

address: 240 Pasteur Dr

institute: Stanford University

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Data were assessed for quality with FastQC. Adapters were trimmed using TrimGalore. BBTools suite was used to remove human and parasite rRNA reads.
Reads were aligned to a concatenation of the human (GRCh38) and Plasmodium (ASM276v2) genomes using STAR with default settings. Gene counts were generated by the -quantMode flag in STAR.
Assembly: GRCh38, ASM276v2
Supplementary files format and content: tab-delimited text file contains raw gene counts for all samples

organism:
Plasmodium falciparum
Homo sapiens

source_name: Orthochromatic erythroblast

extract_protocol:
Cells were sorted directly into Buffer RLT (Qiagen) for total RNA extraction with the Rneasy Micro kit (Qiagen).
Paired-end libraries were prepared using the Tecan Trio RNA-seq for low-input samples on the Agilent BRAVO. Custom AnyDeplete probes (Tecan) were added against the human mitochondrial genome, HBB, EEFA1, MALAT1, and HSP90aa1.

value: Orthochromatic erythroblast

tag: day of differentiation

value: Day 14

value: Infected


title: ChIP_FLAG_Cre_3xFLAG-NFIA_adipocytes_day7_LPS

value: NFIA-KO, 3xFLAG-NFIA-expressing


title: CtrlUnwoundednon-Gata6tomatonegative21

first: Fiona

last: Watt

institute: Kings College London

description:
CtrlUnwoundednon-Gata6tomatonegative21
controlng6.txt

value: Day 0 post-wounding

value: Cre (+/-) tdTomato (+/-)


title: RL382_2016_11_06_MEFirrediated_020816

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

institute: The University of Western Australia

description: mouse embryonic feeder as control population

data_processing:
adapter trimming using Methpipe pipeline as described in Lister et al Science 2013
mapping reads to mm10 genome using Bowtie  as described in Lister et al Science 2013
merging mapped runs, convert to .slam, sort, collapse, trim reads using Methpipe pipeline as described in Lister et al Science 2013
stack creation and hammer correction using Methpipe pipeline as described in Lister et al Science 2013
make allC tables and count global statistics using Methpipe pipeline as described in Lister et al Science 2013
convert stacks to bedgraph files using simple awk script
generate bigwigs using bedgraphtobigwig v4
Genome_build: mm10
Supplementary_files_format_and_content: stacks.txt files containing all mapped methylated and total cytosines, bigWigs for coverage containing all mapped cytosines, bigWigs for mC containing percentage of methylated cytosines for contexts CG and CH

source_name: mouse embryonic feeder

growth_protocol: mESC cells lines R1 and G4 were maintained on gamma-irradiated mouse embryonic fibroblasts in mESC medium with LIF. Cells were fed daily and split based on confluency. Neural differentiation was initiated by dissociating the mESC colonies using Accutase and excess feeder cells were removed from the cell suspensions by panning on gelatin-coated plates. Dissociated cells were counted and transferred to ultra-low attachment cell culture plates at a dilution of 220,000 cells/ml, in differentiation medium. Neural induction was continued for 8 days, medium was changed every two days, and supplemented with 5 µM retinoic acid for the final 4 days. Cell aggregates were dissociated using Accutase, single cell selected through a 40 µm cell strainer, and plated onto poly-ornithine / laminin-coated plates in N2 medium. After 2 days, cells were changed into N2B27 which was changed every 4 days for 12 days, following which 50% media changes were performed for the remaining culture time.

extract_protocol:
Quiagen Blood and Tissue DNA Extraction kit with extended Pretinase K and RNAsA treatment steps.
Lucigen Nxseq Ampfree Low DNA Library Kit and Zymo EZ DNA Methylation Direct Kit for MethylC libraries.

treatment_protocol: High potassium-mediated depolarisation was performed by washing cells with low K+ buffer, transferring to high K+ buffer for 5 min, washed again in low K+ buffer and either harvested directly for RNA, immediately fixed for ICC, or chased in growth medium for the appropriate times prior to fixation or RNA extraction.

value: primary

value: embryonic feeder

tag: protocol

value: irradiated


title: ChIP_FLAG_flox_adipocytes_day7_LPS

value: ingSVF-derived adipocytes

value: flox

value: day 7

value: LPS


title: OrthoE, Infected, replicate 4


city: London

address: Great Maze Road

description:
CtrlUnwoundedGata6-derivedtomatopositive25
control_g6.txt


title: F1339 Dec1 RNA-Seq

value: lung

value: SCLC

value: Decitabine


title: RL383_2017_01_30_G4fans_130616_Day38neuNplus

description: ESC-derived wild type neural differentiation, sorted NeuN positive fraction

source_name: mESC neural diff 8 days induction

value: mESC neural diff 8 days induction

tag: cell culture

value: in vitro

value: 38 days


title: CtrlUnwoundednon-Gata6tomatonegative20

description:
CtrlUnwoundednon-Gata6tomatonegative20
controlng6.txt

value: Epidermis


title: RL381_2016_11_06_R1p36_170716_Day8

description: ESC-derived wild type neural differentiation

value: 8 days


title: F1339 Veh2 RNA-Seq

value: Vehicle


title: RL380_2016_11_06_R1p36_170716_Day6

source_name: mESC neural diff 6 days induction

value: mESC neural diff 6 days induction

value: 6 days


title: ChIP_FLAG_Cre_3xFLAG-deltapro#3_adipocytes_day7

value: FLAG M2


title: CtrlUnwoundednon-Gata6tomatonegative19

description:
CtrlUnwoundednon-Gata6tomatonegative19
controlng6.txt

value: Day 0 post-wounding

value: Cre (+/-) tdTomato (+/-)


title: OrthoE, Infected, replicate 1

value: Orthochromatic erythroblast

value: Day 14

value: Infected


title: RL379_2016_11_06_R1p36_150716_Day4

source_name: mESC neural diff 4 days induction

value: mESC neural diff 4 days induction

value: 4 days


title: ChIP_FLAG_Cre_3xFLAG-NFIA_adipocytes_day7

value: ingSVF-derived adipocytes

value: NFIA-KO, 3xFLAG-NFIA-expressing

value: day 7


title: ChIP_H3K27Ac_Cre_3xFLAG-NFIA_adipocytes_day7


title: PolyE, Infected, replicate 5

source_name: Polychromatic erythroblast

value: Polychromatic erythroblast


title: RL384_2016_11_06_G4fans_130616_Day38neuNneg

description: ESC-derived wild type neural differentiation, sorted NeuN negative fraction

value: mESC neural diff 8 days induction

value: in vitro

value: 38 days


title: CtrlUnwoundednon-Gata6tomatonegative18

description:
CtrlUnwoundednon-Gata6tomatonegative18
controlng6.txt

value: Epidermis


title: ChIP_FLAG_flox_adipocytes_day7

value: flox


title: PolyE, Infected, replicate 4


title: CtrlUnwoundednon-Gata6tomatonegative17

description:
CtrlUnwoundednon-Gata6tomatonegative17
controlng6.txt


title: EB3-derived cells, NUP98-HOXA9#2

city: Bunkyo-ku

first: Yuya

last: Nagaoka

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the mouse (GRCm38) reference genome using STAR v2.7.10a
Transcripts per million (TPM) and Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated using RSEM v1.3.3
Differential expression analysis were performed with DESeq2 v1.36.0
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each sample
Supplementary files format and content: As a supplemental file, we provide the differential expression genes list.

growth_protocol: Mouse embryonic cells were maintained on gelatin-coated dish  in DMEM supplemented with 10% FBS, 10 mM MEM non-essential amino acids, 100 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, and LIF at 37°C in 5% CO2 atmosphere.

extract_protocol:
RNA was isolated using ReliaPrep™ RNA Cell Miniprep System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

value: mESC


title: PolyE, Infected, replicate 3


title: OrthoE, Infected, replicate 2


title: PolyE, Infected, replicate 2


description:
CtrlUnwoundedGata6-derivedtomatopositive22
control_g6.txt

value: Day 0 post-wounding


title: RL375_2016_11_06_G4p34_170716_Day6

value: mESC neural diff 6 days induction

value: 6 days


title: PolyE, Infected, replicate 1

value: Day 14


title: EB3-derived cells, Empty vec control

value: WT(empty vec)


title: EB3-derived cells, NUP98-HOXA9#1


title: RL376_2016_11_06_G4p34_190716_Day8

value: 8 days


description:
CtrlUnwoundedGata6-derivedtomatopositive21
control_g6.txt

value: Cre (+/-) tdTomato (+/-)


title: RL374_2016_11_06_G4p34_150716_Day4

value: mESC neural diff 4 days induction

value: 4 days


title: EB3 cells, Parental ES

value: WT


description:
CtrlUnwoundedGata6-derivedtomatopositive20
control_g6.txt


title: BasoE, Infected, replicate 4

source_name: Basophilic erythroblast

value: Basophilic erythroblast

value: Day 7

value: Infected


title: BasoE, Infected, replicate 3


description:
CtrlUnwoundedGata6-derivedtomatopositive19
control_g6.txt


title: RL373_2016_11_06_G4p34_130716_Day2

source_name: mESC neural diff 2 days induction

value: mESC neural diff 2 days induction

value: in vitro

value: 2 days


title: RL372_2016_11_06_G4p34_110716_Day0

source_name: mESC

value: mESC

value: passage 34


title: RNA_NFIA-Tg_adipocytes_day7_rep3

treatment_protocol: At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 μM dexamethosone, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 μM rosiglitazone.

value: NFIA-Tg

tag: time course

value: day 7

value: ingSVF-derived adipocytes


title: RL378_2016_11_06_R1p36_130716_Day2


title: RNA_NFIA-Tg_adipocytes_day7_rep2

tag: tissue


title: BasoE, Infected, replicate 2

tag: cell type


description:
CtrlUnwoundedGata6-derivedtomatopositive18
control_g6.txt

value: Epidermis

value: Day 0 post-wounding

tag: genotype


title: RL377_2016_11_06_R1p36_110716_Day0

value: passage 36


description:
CtrlUnwoundedGata6-derivedtomatopositive17
control_g6.txt

value: Cre (+/-) tdTomato (+/-)


title: BasoE, Infected, replicate 1


description:
CtrlUnwoundedGata6-derivedtomatopositive23
control_g6.txt


title: RNA_NFIA-Tg_adipocytes_day7_rep1


title: RL272_2016_06_10_G4p31_240316_Day33

description: wild type control

value: mESC neural diff 8 days induction

value: 33 days


title: ProE, Infected, replicate 4

source_name: Proerythroblast

value: Proerythroblast


description:
CtrlUnwoundedGata6-derivedtomatopositive16
control_g6.txt


title: ProE, Infected, replicate 3

value: Day 7


title: RL271_2016_06_22_R1p22_240516_Day27

description: wild type control

value: 27 days


title: RL270_2016_06_10_R1p22_070516_Day10

description: wild type control

value: 10 days


title: RNA_WT_adipocytes_day7_rep1

value: WT


title: CtrlUnwoundednon-Gata6tomatonegative16

description:
CtrlUnwoundednon-Gata6tomatonegative16
controlng6.txt


title: ProE, Infected, replicate 2

value: Infected


title: RL273_2016_06_10_G4p31_170316_Day26lowK

description: low K+

value: in vitro

value: 26 days


title: CtrlUnwoundednon-Gata6tomatonegative15

description:
CtrlUnwoundednon-Gata6tomatonegative15
controlng6.txt


title: RNA_NFIA-Tg_adipocytes_day0_rep3

value: NFIA-Tg

value: day 0


title: ProE, Infected, replicate 1


title: RL269_2016_06_10_R1p22_050516_Day8

description: wild type control

value: 8 days


title: RL268_2016_06_10_G4p17_240516_Day27

description: wild type control


title: CtrlUnwoundednon-Gata6tomatonegative14

description:
CtrlUnwoundednon-Gata6tomatonegative14
controlng6.txt

value: Epidermis


title: CtrlUnwoundednon-Gata6tomatonegative13

description:
CtrlUnwoundednon-Gata6tomatonegative13
controlng6.txt

value: Day 0 post-wounding


title: M_24h_Rep3_exp1

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

description:
exp1
M_24h_Rep3

data_processing:
Reads were trimmed with cudadapt (v. 1.18) to remove Illumina adapter sequences.
Reads were mapped to the ribosomal RNA sequences extracted from ensembl AgamP4 genome using the Ensembl AgamP4 annotation (release 48) with STAR (v. 2.7.3a) with the following parameters: outFilterMultimapNmax 1000000 outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Reads mapping to rRNA were discarded and unmapped reads are used in downstream processing.
Reads were mapped to the ensembl AgamP4 genome using the Ensembl AgamP4 annotation (release 48) together with lncRNA annotation from 10.1186/s12864-015-1507-3 with STAR (v. 2.7.3a) using the following parameters: outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Only uniquely mapped reads were used for downstream analysis.
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v. 1.9) and DeepTools (v. 3.1.0)
Primary alignments were assigned to features using subread (v. 1.6.5) with the AgamP4 annotation (release 48) combined with lncRNA annotation 10.1186/s12864-015-1507-3 as a reference.
Assembly: AgamP4
Supplementary files format and content: tab-delimited text file containing raw counts for each sample, bigWig files containing CPM normalized coverage signals of primary alignments

organism: Anopheles gambiae

source_name: embryo

growth_protocol: A. gambiae mosquitoes were maintained in standard insectary conditions (26–28°C, 75–80% humidity, and 12-/12-h light/dark cycle).

extract_protocol:
RNA was extracted using Trizol  (Fisher Scientific, Cat. No.15-596-026) and the Direct-zol RNA MicroPrep Kit (Zymo Research, Cat. No. R2062).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (June 2020) (Document # 1000000124518 v00).

value: embryo

tag: developmental stage

tag: Sex

value: male


title: RL267_2016_06_10_G4p17_070516_Day10

description: wild type control

value: mESC neural diff 8 days induction

tag: age


title: RNA_NFIA-Tg_adipocytes_day0_rep2

value: ingSVF-derived adipocytes


title: M_24h_Rep2_exp1

description:
exp1
M_24h_Rep2


title: RNA_NFIA-Tg_adipocytes_day0_rep1


title: RNA_WT_adipocytes_day7_rep3

value: day 7


title: CtrlUnwoundednon-Gata6tomatonegative12

description:
CtrlUnwoundednon-Gata6tomatonegative12
controlng6.txt

tag: strain

value: Cre (+/-) tdTomato (+/-)

tag: treatment


title: RL266_2016_06_22_G4p17_050516_Day8

description: wild type control


title: RNA_WT_adipocytes_day7_rep2


title: CtrlUnwoundednon-Gata6tomatonegative11

description:
CtrlUnwoundednon-Gata6tomatonegative11
controlng6.txt


title: Cortical_14div_56mMKCl_6hmedia

description: 14 div +56mMKCl for 5 minutes +6h growth medium

source_name: E18 primary neurons

value: primary

value: cortex


title: RNA_WT_adipocytes_day0_rep2

value: WT


title: F_24h_Rep4_exp1

description:
exp1
F_24h_Rep4

value: female


title: Cortical_14div_50mMKCl_6h

description: 14 div + 50mMKCl for 6 hr


title: CtrlUnwoundednon-Gata6tomatonegative10

description:
CtrlUnwoundednon-Gata6tomatonegative10
controlng6.txt


title: F_24h_Rep2_exp1

description:
exp1
F_24h_Rep2


title: CtrlUnwoundednon-Gata6tomatonegative9

description:
CtrlUnwoundednon-Gata6tomatonegative9
controlng6.txt


title: RNA_NFIA-Tg_iWAT_rep3

source_name: iWAT

value: iWAT


title: Cortical_14div

description: 14 div


title: F_24h_Rep1_exp1

description:
exp1
F_24h_Rep1


title: RNA_WT_adipocytes_day0_rep3


description:
CtrlUnwoundedGata6-derivedtomatopositive15
control_g6.txt


title: M_20h_Rep2_exp1

description:
exp1
M_20h_Rep2


title: HPC_14div_56mMKCl_6hmedia

value: hippocampus


title: M_24h_Rep1_exp1

description:
exp1
M_24h_Rep1


title: Cortical_1div

description: 1 div


description:
CtrlUnwoundedGata6-derivedtomatopositive13
control_g6.txt


title: RNA_NFIA-Tg_iWAT_rep2

value: NFIA-Tg