title: Day9-2Gata6-derivedtomatopositive41

description:
Day9-2Gata6-derivedtomatopositive41
WTCHG_945384_72025274


title: Day9-2Non-Gata6tomatonegative41

status: Public on Jul 25 2023

type: SRA

city: London

first: Fiona

middle: Mary

last: Watt

address: Great Maze Road

country: United Kingdom

institute: Kings College London

description:
Day9-2Non-Gata6tomatonegative41
WTCHG_945384_72095281

library_source: transcriptomic

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
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

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

tag: tissue

value: Epidermis

tag: age

tag: genotype

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

tag: treatment


title: Day9-2Non-Gata6tomatonegative39

description:
Day9-2Non-Gata6tomatonegative39
WTCHG_945384_71995271


title: Day9-2Gata6-derivedtomatopositive40

description:
Day9-2Gata6-derivedtomatopositive40
WTCHG_945384_72015273


title: Day9-2Non-Gata6tomatonegative37

description:
Day9-2Non-Gata6tomatonegative37
WTCHG_945384_71975269


title: Day9-2Non-Gata6tomatonegative36

description:
Day9-2Non-Gata6tomatonegative36
WTCHG_945384_71965268


title: Tpd pollen small RNA Dcl2 rep1

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

country: USA

institute: Cold Spring Harbor Laboratory

description: srna-tpd-pollen.dcl2t-dcl2mu1-dcl2.shortstack-counts.txt

data_processing:
Adapters (5’-TGGAATTCTCGGGTGCCAAGG -3’) were trimmed using cutadapt (Marcel 2011) and the 4bp UMI sequences on either side of each read were removed.
Reads were filtered using pre-alignment to a maize structural RNA consensus database using bowtie2. Alignment and de novo identification of small RNA loci was performed with ShortStack. For any given biological comparison, reads from all samples were merged while simultaneously retaining sample-specific information. This allowed for the identification of a maximum number of putative small RNA loci (CPM≥5). Degradation productions are frequently mis-classified as sRNA producing loci. To avoid this, only clusters with clear size bias (21, 22, or 24nt) were retained in downstream analysis. This set of high-confidence sRNA annotations, along with edgeR, were used to determine differential sRNA accumulation between genotypes or tissues (log2FC ≥ 2, FDR ≤ 0.01). The accumulation of size and strand-biased hp-siRNAs was used to identify hairpin loci throughout the genome. For each locus, the underlying primary sequence was tested for reverse complementarity and RNA secondary structure prediction was performed using RNAfold. Non-hairpin siRNA targets were only retained if they showed negligible strand-bias (i.e., evidence of a dsRNA template for processing by a Dicer-like enzyme).
Assembly: Zm-W22-REFERENCE-NRGENE-2.0; Zm-TPD-1.0

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

source_name: pollen

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:
For comparisons between Tpd1+/-;Tpd2+/-, Tpd1+/-;tpd2 and tpd1;tpd2 pollen, three biological replicates were used. Two biological replicates were used for dcl2T-/- and dcl2-mu1-/- pollen samples.   Tissue was collected, snap frozen in liquid nitrogen, and stored at -80˚C. Samples were ground into a fine powder using a mortar and pestle on liquid nitrogen. 800ul of pre-extraction buffer (100mM Tris-HCl pH 8.0, 150mM LiCl, 50mM EDTA pH 8.0, 1.5% v/v SDS, 1.5% 2-mercaptoethanol) was added and mixed by vortexing. 500ul of acid phenol:chloroform (pH 4.7-5.0) was added and samples were mixed then spun down at 13,000 x g for 15 minutes at 4˚C. The aqueous layer was extracted and 1ml Trizol per 200mg input tissue of was added. Samples were mixed by vortex and incubated at RT for 10 minutes. 200ul chloroform per 1ml Trizol was added and samples were mixed by vortexing then incubated at RT for 2 minutes. Samples were then spun down at 13,000 x g for 15 minutes at 4˚C. The aqueous phase was extracted and cleaned up using the Zymo RNA Clean and Concentrator-5 kit (Zymo Research, cat#R1013). Only samples with RNA integrity (RIN) scores ≥9 were used for qPCR and sequencing.
Libraries were constructed with the NEXTFLEX Small RNA-Seq V3 kit (PerkinElmer, cat#NOVA-5132-06) using 2ug of total RNA input per library and the gel-free size selection protocol. The size distribution of completed libraries was assessed using an Agilent Bioanalyzer, and quantification was performed using a KAPA Library Quantification kit (Roche, cat#KK4824). Libraries were sequenced on a NextSeq500 platform using a 1x76bp run.

value: pollen


title: Tpd pollen small RNA dcl2T-/- rep2


title: Tpd pollen small RNA dcl2-mu1 rep2


title: Tpd pollen small RNA dcl2-mu1 rep1


title: Tpd pollen small RNA dcl2T-/- rep1


title: Day9-2Non-Gata6tomatonegative35

description:
Day9-2Non-Gata6tomatonegative35
WTCHG_945384_71955267


title: Tpd leaf small RNA drive rep1

description:
srna-tpd-leaf.drive.leaf.22nt.pos.bw
srna-tpd-leaf.drive.leaf.22nt.neg.bw

source_name: leaf

value: leaf


title: Tpd leaf small RNA drive rep2


title: Day9-2Non-Gata6tomatonegative34

description:
Day9-2Non-Gata6tomatonegative34
WTCHG_945384_71945266


title: Day9-2Non-Gata6tomatonegative33

description:
Day9-2Non-Gata6tomatonegative33
WTCHG_945384_71935265


title: Tpd leaf small RNA fertile rep3

description:
srna-tpd-leaf.fertile.leaf.22nt.pos.bw
srna-tpd-leaf.fertile.leaf.22nt.neg.bw


title: Day11-2Gata6-derivedtomatopositive39

description:
Day11-2Gata6-derivedtomatopositive39
WTCHG_945384_71925168


title: Tpd pollen small RNA Dcl2 rep2


title: Tpd leaf small RNA fertile rep2


title: Tpd leaf small RNA fertile rep1


title: Day11-2Gata6-derivedtomatopositive38

description:
Day11-2Gata6-derivedtomatopositive38
WTCHG_945384_71915167


title: Day11-2Gata6-derivedtomatopositive36

description:
Day11-2Gata6-derivedtomatopositive36
WTCHG_945384_71895165


title: Day11-2Gata6-derivedtomatopositive37

description:
Day11-2Gata6-derivedtomatopositive37
WTCHG_945384_71905166


title: Tpd pollen small RNA sterile rep1

description:
srna-tpd-pollen.sterile.22nt.pos.bw
srna-tpd-pollen.sterile.22nt.neg.bw


title: Tpd pollen small RNA drive rep3

description:
srna-tpd-pollen.drive.22nt.pos.bw
srna-tpd-pollen.drive.22nt.neg.bw


title: Tpd pollen small RNA sterile rep2


title: Day11-2Gata6-derivedtomatopositive34

description:
Day11-2Gata6-derivedtomatopositive34
WTCHG_945384_71875163


title: Day11-2Non-Gata6tomatonegative32

description:
Day11-2Non-Gata6tomatonegative32
WTCHG_945384_71845160


title: Day11-2Non-Gata6tomatonegative31

description:
Day11-2Non-Gata6tomatonegative31
WTCHG_945384_71835159


title: Day11-2Gata6-derivedtomatopositive33

description:
Day11-2Gata6-derivedtomatopositive33
WTCHG_945384_71865162


title: Day11-2Non-Gata6tomatonegative30

description:
Day11-2Non-Gata6tomatonegative30
WTCHG_945384_71825158


title: Tpd pollen small RNA fertile rep2

description:
srna-tpd-pollen.fertile.22nt.pos.bw
srna-tpd-pollen.fertile.22nt.neg.bw


title: Tpd pollen small RNA fertile rep1


title: Tpd pollen small RNA fertile rep3


title: Day11-2Non-Gata6tomatonegative29

description:
Day11-2Non-Gata6tomatonegative29
WTCHG_945384_71815157


title: Tpd pollen small RNA sterile rep3


title: Day11-2Non-Gata6tomatonegative28

description:
Day11-2Non-Gata6tomatonegative28
WTCHG_945384_71805156


title: Day11-2Non-Gata6tomatonegative27

description:
Day11-2Non-Gata6tomatonegative27
WTCHG_945384_71795155


title: Tpd pollen total RNA drive rep5

description: total-rna.drive.bdg.gz

data_processing:
Trimmed reads were aligned to the W22 reference with STAR in two-pass alignment mode. Read counts were assigned to annotated features using featureCounts. For transposable element expression, multi-mapping reads were assigned fractional counts based on the number of identical alignments. Differential expression analysis was performed using edgeR. To avoid false positives, a stringent cutoff (log2FC ≥ 2, FDR ≤ 0.001) was used to call differentially expressed genes. Gene ontology (GO) analysis (Fisher’s exact test, p<0.01) was performed using topGO, and the results were visualized using rrvgo. For data visualization, alignment files were converted to a strand-specific bigwig format using deepTools.
Assembly: Zm-W22-REFERENCE-NRGENE-2.0

extract_protocol:
Tissue was collected, snap frozen in liquid nitrogen, and stored at -80˚C. Samples were ground into a fine powder using a mortar and pestle on liquid nitrogen. 800ul of pre-extraction buffer (100mM Tris-HCl pH 8.0, 150mM LiCl, 50mM EDTA pH 8.0, 1.5% v/v SDS, 1.5% 2-mercaptoethanol) was added and mixed by vortexing. 500ul of acid phenol:chloroform (pH 4.7-5.0) was added and samples were mixed then spun down at 13,000 x g for 15 minutes at 4˚C. The aqueous layer was extracted and 1ml Trizol per 200mg input tissue of was added. Samples were mixed by vortex and incubated at RT for 10 minutes. 200ul chloroform per 1ml Trizol was added and samples were mixed by vortexing then incubated at RT for 2 minutes. Samples were then spun down at 13,000 x g for 15 minutes at 4˚C. The aqueous phase was extracted and cleaned up using the Zymo RNA Clean and Concentrator-5 kit (Zymo Research, cat#R1013). Only samples with RNA integrity (RIN) scores ≥9 were used for qPCR and sequencing.
Five biological replicates were prepared for each biological condition (Tpd1/tpd1; Tpd2/tpd2 and tpd1; tpd2 siblings). 5ug of total RNA was ribosome depleted using the RiboMinus Plant Kit (ThermoFisher, cat#A1083808), and libraries were prepared using the NEXTFLEX Rapid Directional RNA-seq kit (PerkinElmer, cat#NOVA-5138-08). The size distribution of completed libraries was assessed using an Agilent Bioanalyzer, and quantification was performed using a KAPA Library Quantification kit (Roche, cat#KK4824). Libraries were sequenced on a NextSeq500 platform using a 2x150bp high output run.


title: Day11-2Non-Gata6tomatonegative25

description:
Day11-2Non-Gata6tomatonegative25
WTCHG_945384_71775153


title: Day11-2Non-Gata6tomatonegative26

description:
Day11-2Non-Gata6tomatonegative26
WTCHG_945384_71785154


title: Day11-2Gata6-derivedtomatopositive31

description:
Day11-2Gata6-derivedtomatopositive31
WTCHG_945384_71765152


title: Tpd pollen total RNA drive rep3

description: total-rna.drive.bdg.gz


title: Tpd pollen small RNA drive rep2


title: Tpd pollen total RNA fertile rep5

description: total-rna.fertile.bdg.gz


title: Tpd pollen total RNA drive rep1

description: total-rna.drive.bdg.gz


title: Tpd pollen total RNA drive rep2

description: total-rna.drive.bdg.gz


title: Day11-2Gata6-derivedtomatopositive35

description:
Day11-2Gata6-derivedtomatopositive35
WTCHG_945384_71885164


title: Day11-2Gata6-derivedtomatopositive32

description:
Day11-2Gata6-derivedtomatopositive32
WTCHG_945384_71855161


title: Tpd pollen small RNA drive rep1


title: Day11-2Gata6-derivedtomatopositive29

description:
Day11-2Gata6-derivedtomatopositive29
WTCHG_945384_71745150


title: Tpd pollen total RNA fertile rep3

description: total-rna.fertile.bdg.gz


title: Tpd pollen total RNA fertile rep4

description: total-rna.fertile.bdg.gz


title: Tpd pollen total RNA drive rep4

description: total-rna.drive.bdg.gz


title: Day11-2Gata6-derivedtomatopositive27

description:
Day11-2Gata6-derivedtomatopositive27
WTCHG_945384_71725148


title: Tpd pollen total RNA fertile rep1

description: total-rna.fertile.bdg.gz


title: Day11-2Gata6-derivedtomatopositive26

description:
Day11-2Gata6-derivedtomatopositive26
WTCHG_945384_71715147


title: Day11-2Gata6-derivedtomatopositive25

description:
Day11-2Gata6-derivedtomatopositive25
WTCHG_945384_71705146


title: Day11-2Gata6-derivedtomatopositive30

description:
Day11-2Gata6-derivedtomatopositive30
WTCHG_945384_71755151


title: Day11-2Gata6-derivedtomatopositive24

description:
Day11-2Gata6-derivedtomatopositive24
WTCHG_945384_71695145


title: Tpd pollen iPARE fertile rep3

description: ipare-fertile.norm.bdg.gz

data_processing:
library strategy: iPARE-seq
Cutadapt (Marcel 2011) was used to search and recover the adapter sequence in both 5’ and 3’ orientation (forward in read1 or read2 respectively). Read1 adapter reads were trimmed for the 3’ adapter if present, and the 5’ iPARE adapter was subsequently removed. Potential polyA tails were also removed, and only reads ≥20nt were retained. Read2 adapter reads were processed in an identical fashion. Filtered reads were mapped using Bowtie2 (Langmead and Salzberg 2012) and the 5’ position of each read (the cloned 5’ monophosphate) was extracted using BEDtools (Quinlan and Hall 2010) with CPM normalization. Small RNA target prediction was performed using psRNATarget (Dai et al. 2018).
Assembly: Zm-W22-REFERENCE-NRGENE-2.0; Zm-TPD-1.0

molecule: polyA RNA

extract_protocol:
Tissue was collected, snap frozen in liquid nitrogen, and stored at -80˚C. Samples were ground into a fine powder using a mortar and pestle on liquid nitrogen. 800ul of pre-extraction buffer (100mM Tris-HCl pH 8.0, 150mM LiCl, 50mM EDTA pH 8.0, 1.5% v/v SDS, 1.5% 2-mercaptoethanol) was added and mixed by vortexing. 500ul of acid phenol:chloroform (pH 4.7-5.0) was added and samples were mixed then spun down at 13,000 x g for 15 minutes at 4˚C. The aqueous layer was extracted and 1ml Trizol per 200mg input tissue of was added. Samples were mixed by vortex and incubated at RT for 10 minutes. 200ul chloroform per 1ml Trizol was added and samples were mixed by vortexing then incubated at RT for 2 minutes. Samples were then spun down at 13,000 x g for 15 minutes at 4˚C. The aqueous phase was extracted and cleaned up using the Zymo RNA Clean and Concentrator-5 kit (Zymo Research, cat#R1013). Only samples with RNA integrity (RIN) scores ≥9 were used for qPCR and sequencing.
For iPARE-seq libraries, 40ug of total RNA was poly(A) selected using a Dynabeads mRNA Purification Kit (ThermoFisher, cat#61006). 1ug of poly(A) RNA was ligated to the 5’ PARE adapter (100pmol) in 10% DMSO, 1mM ATP, 1X T4 RNA ligase 1 buffer (New England Biolabs, cat#B0216L), 25% PEG8000 with 1ul (40U) of RNaseOUT (ThermoFisher, cat#10777019) and 1ul T4 RNA ligase 1 (New England Biolabs, cat#M0204S) in a reaction volume of 100ul. Ligation reactions were performed for 2 hours at 25˚C followed by overnight incubation at 16˚C. Samples were then purified using RNA Clean XP beads (Beckman Coulter, cat#A63987) and eluted in 18ul dH20. Chemical fragmentation of ligated RNA to ≤200nt was performed using the Magnesium RNA fragmentation kit (New England Biolabs, cat#E6150S). 2ul RNA Fragmentation Buffer was added and samples were incubated at 94˚C for 5 minutes followed by a transfer to ice and the addition of 2ul of RNA Stop solution. Samples were purified using the RNA Clean & Concentrator-5 kit (Zymo Research, cat#R1013) and eluted in 11ul H20. Reverse-transcription was performed as follows: 10ul of RNA, 1ul 10mM dNTP, and 2ul random primer mix (New England Biolabs, cat#S1330S) were mixed and incubated for 10 minutes at 23˚C then put on ice for 1 minute. The following was then added: 4ul 5X SuperScript IV buffer, 1ul 100mM DTT, 1ul RNaseOUT, and 1ul Superscript IV (200U). The reaction was incubated for 10 minutes at 23˚C followed by 10 minutes at 50˚C. 80ul of TE was then added to this mixture.  Target indirect capture was performed with 100ul Dynabeads MyOne Streptavidin T1 beads (ThermoFisher, cat#65601) as per manufacturer instructions. 100ul of the RT reaction was used as input, and captured cDNA molecules were eluted in 50ul. Second-strand synthesis was performed using 5U Klenow fragment (New England Biolabs, cat#M0210S) with 100uM dNTPs and 1uM of iPARE adapter primer (5’-NNNNTCTAGAATGCATGGGCCCTCCAAG-3’) for 1 hour at 37˚C, incubation at 75˚C for 20 minutes. Samples were purified with a 1:1 ratio of AMPure XP SPRI beads (Beckman Coulter – cat#A63880) and resuspended in 51ul EB. 50ul of sample was used for library preparation with the NEB Ultra DNA library kit (New England Biolabs, cat# E7370S). Barcoded samples were sequenced with a NextSeq500 2x150bp high output run. Use of the directional iPARE adapter allows for the retention of directionality even when using a non-directional DNA-seq kit.


title: Day11-2Non-Gata6tomatonegative24

description:
Day11-2Non-Gata6tomatonegative24
WTCHG_945384_71685144


title: Tpd pollen iPARE fertile rep2

description: ipare-fertile.norm.bdg.gz


title: Tpd pollen iPARE fertile rep1

description: ipare-fertile.norm.bdg.gz


title: Day11-2Non-Gata6tomatonegative22

description:
Day11-2Non-Gata6tomatonegative22
WTCHG_945384_71665142


title: Tpd pollen iPARE drive rep3

description: ipare-drive.norm.bdg.gz


title: Tpd pollen iPARE drive rep1

description: ipare-drive.norm.bdg.gz


title: Day11-2Non-Gata6tomatonegative23

description:
Day11-2Non-Gata6tomatonegative23
WTCHG_945384_71675143


title: Day11-2Non-Gata6tomatonegative19

description:
Day11-2Non-Gata6tomatonegative19
WTCHG_945384_71635139


title: Tpd maternal BSA drive bulk 18

description: bsa.vcf.gz

library_source: genomic

data_processing:
library strategy: WGS
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. Reference and alternate allele frequencies at each marker were calculated and average signal was consolidated into 100kb bins. ∆SNPindex was then calculated for each bin in a sliding window.
Assembly: Zm-W22-REFERENCE-NRGENE-2.0; Zm-TPD

molecule: genomic DNA

extract_protocol:
High molecular weight (HMW) genomic DNA was used as input for all Nanopore and bulk Illumina sequencing experiments. For extraction, bulked seedlings were dark treated for 1 week prior to tissue collection. Four grams of frozen tissue was ground under liquid N2 and pre-washed twice with 1.0M sorbital. The tissue was then transferred to 20ml pre-warmed lysis buffer (100mM Tris-HCl pH 9.0, 2% w/v CTAB, 1.4M NaCl, 20mM EDTA, 2% PVP-10, 1% 2-mercaptoethanol, 0.1% sarkosyl, 100ug/mL proteinase K), mixed gently, and incubated for 1 hour at 65˚C. Organic extraction in phase-lock tubes was performed using 1 vol phenol:chloroform:isoamyl alcohol (25:24:1) followed by 1 vol chloroform:isoamyl alcohol. DNA was precipitated by adding 0.1 vol 3M NaOAc pH 5.2 followed by 0.7 vol isopropanol. HMW DNA was hooked out with a pasteur pipette and washed with 70% EtOH, air dried for 2 minutes, and resuspended in 200ul Tris-Cl pH 8.5 (EB). The solution was treated with 2ul 20mg/ml RNase A at 37˚C for 20 minutes followed by 2ul 50mg/ml proteinase K at 50˚C for 30 minutes. 194ul EB, 100ul NaCl, and 2ul 0.5M EDTA were added and organic extractions were performed as before. DNA was precipitated with 1.7 vol EtOH, hooked out of solution with a pasteur pipette, washed with 70% EtOH, and resuspended in 50ul EB.
HMW DNA from separately maintained Tpd1;Tpd2 lineages (BC5S3, BC8S3) and bulk segregation analysis (BSA) pools were extracted as detailed above. Libraries were prepared using the Illumina TruSeq DNA PCR-Free kit (Illumina, cat#20015962) with 2ug of DNA input.


title: Tpd maternal BSA drive bulk 16

description: bsa.vcf.gz


title: Tpd maternal BSA drive bulk 19

description: bsa.vcf.gz


title: Day11-2Non-Gata6tomatonegative18

description:
Day11-2Non-Gata6tomatonegative18
WTCHG_945384_71625138


title: Day11-2Gata6-derivedtomatopositive28

description:
Day11-2Gata6-derivedtomatopositive28
WTCHG_945384_71735149


title: Tpd maternal BSA drive bulk 13

description: bsa.vcf.gz


title: Day11-2Non-Gata6tomatonegative17

description:
Day11-2Non-Gata6tomatonegative17
WTCHG_945384_71615137


title: Tpd maternal BSA drive bulk 11

description: bsa.vcf.gz


title: Tpd pollen total RNA fertile rep2

description: total-rna.fertile.bdg.gz


title: Tpd maternal BSA drive bulk 10

description: bsa.vcf.gz


title: Day11-2Gata6-derivedtomatopositive23

description:
Day11-2Gata6-derivedtomatopositive23
WTCHG_945384_71605136


title: Tpd maternal BSA sterile bulk 12

description: bsa.vcf.gz


title: Tpd pollen iPARE drive rep2

description: ipare-drive.norm.bdg.gz


title: HOU, SSR42

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

data_processing:
Raw data files (.fastq.gz) were exported from the Illumina BaseSpace Server
Raw data files (.fastq.gz) were imported into Qiagen Bioinformatics software platform (version 22) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were caculated using RNA-Seq Analysis function with experimental fold change feature in Qiagen Bioinformatics software, specifying TPM output
Expression values and fold change comparisons were exported in excel format
Assembly: The accession number for the Genbank genome file used as references was NC_010079.1
Supplementary files format and content: Expression values calculated for each gene are presented as TPM values in excel format

organism: Staphylococcus aureus

source_name: SSR42 deletion mutant bacterial cells, pelleted

growth_protocol: Overnight S. aureus cultures were used to inoculate fresh TSB broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh TSB medium at OD600 0.05. After 15 hour of growth, 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria.
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were pelleted and stored at -80°C prior to RNA extraction.

value: SSR42 deletion

tag: cell type

value: bacterial cell

tag: growth medium

value: TSB

tag: growth conditions


title: Day11-2Gata6-derivedtomatopositive22

description:
Day11-2Gata6-derivedtomatopositive22
WTCHG_945384_71595135


title: HOU, WT

source_name: HOU wildtype bacterial cells, pelleted

value: Wildtype parental


title: Female_SoaRSoaR_RNA-seq_Rep4

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Female_SoaRSoaR_Rep4
counts_pupae_SOAR_RNA.tsv

data_processing:
Reads were mapped to the ensembl AgamP4 genome, ERCCs and elements of the SOA-R and SOA-Ki cassettes (DsRed from SOA-R cassette, mTurquoise2 from SOA-KI cassette, SOA-HA-tag: element of SOA-KI cassette, integrated in front of the endogenous SOA locus), SV40 terminator (part of the SOA-R transgene) using the Ensembl AgamP4 annotation (release 48) together with lncRNA annotation from 10.1186/s12864-015-1507-3 and elements of SOA-KI and SOA-R cassettes. The mapping was performed 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 (v1.9) and DeepTools (v3.1.0)
Primary alignments were assigned to features using subread (v1.6.5) with the AgamP4 annotation (release 48) combined with lncRNA annotation 10.1186/s12864-015-1507-3 combined with the fragments of SOA-Ki and SOA-R cassettes as a reference.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Supplementary files format and content: tab-delimited text file with featureCounts count table output

organism: Anopheles gambiae

source_name: whole pupa

growth_protocol: A. gambiae pupae 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: whole pupa

tag: Sex

value: Female

value: SoaRSoaR


title: Tpd maternal BSA sterile bulk 8

description: bsa.vcf.gz


title: Day11-2Gata6-derivedtomatopositive20

description:
Day11-2Gata6-derivedtomatopositive20
WTCHG_945384_71575133


title: Day11-2Gata6-derivedtomatopositive21

description:
Day11-2Gata6-derivedtomatopositive21
WTCHG_945384_71585134


title: Tpd maternal BSA sterile bulk 2

description: bsa.vcf.gz


title: Female_SoaRSoaR_RNA-seq_Rep3

description:
Female_SoaRSoaR_Rep3
counts_pupae_SOAR_RNA.tsv


title: Tpd maternal BSA sterile bulk 1

description: bsa.vcf.gz


title: Day11-2Non-Gata6tomatonegative21

description:
Day11-2Non-Gata6tomatonegative21
WTCHG_945384_71655141


title: Day11-2Non-Gata6tomatonegative20

description:
Day11-2Non-Gata6tomatonegative20
WTCHG_945384_71645140


title: Day11-2Gata6-derivedtomatopositive19

description:
Day11-2Gata6-derivedtomatopositive19
WTCHG_945384_71565132


title: Tpd maternal BSA fertile bulk 24

description: bsa.vcf.gz


title: Tpd maternal BSA sterile bulk 5

description: bsa.vcf.gz


title: Tpd maternal BSA fertile bulk 23

description: bsa.vcf.gz


title: Female_SoaRSoaR_RNA-seq_Rep2

description:
Female_SoaRSoaR_Rep2
counts_pupae_SOAR_RNA.tsv


title: Tpd maternal BSA fertile bulk 22

description: bsa.vcf.gz


title: Female_SoaRSoaR_RNA-seq_Rep1

description:
Female_SoaRSoaR_Rep1
counts_pupae_SOAR_RNA.tsv


title: Tpd maternal BSA fertile bulk 21

description: bsa.vcf.gz


title: Day11-2Gata6-derivedtomatopositive18

description:
Day11-2Gata6-derivedtomatopositive18
WTCHG_945384_71555131


title: Tpd maternal BSA fertile bulk 17

description: bsa.vcf.gz


title: Female_WT_RNA-seq_Rep3

description:
Female_WT_Rep3
counts_pupae_SOAR_RNA.tsv

value: WT


title: Day11-2Gata6-derivedtomatopositive17

description:
Day11-2Gata6-derivedtomatopositive17
WTCHG_945384_71545130


title: Tpd maternal BSA fertile bulk 9

description: bsa.vcf.gz


title: Tpd homozygous BC5S2 WGS

description: dna-wgs-snps.bed.gz

value: Tpd1;Tpd2 (BC5S2)


title: Female_WT_RNA-seq_Rep2

description:
Female_WT_Rep2
counts_pupae_SOAR_RNA.tsv


title: Tpd homozygous BC8S3 WGS

description: dna-wgs-snps.bed.gz

value: Tpd1;Tpd2 (BC8S3)


title: Day11-2Gata6-derivedtomatopositive16

description:
Day11-2Gata6-derivedtomatopositive16
WTCHG_945384_71535129


title: Female_WT_RNA-seq_Rep1

description:
Female_WT_Rep1
counts_pupae_SOAR_RNA.tsv


title: Tpd maternal BSA sterile bulk 7

description: bsa.vcf.gz


title: Tpd single pollen fertile 32

description: single-pollen-tpd.fertile.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

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: Day11-2Non-Gata6tomatonegative15

description:
Day11-2Non-Gata6tomatonegative15
WTCHG_945384_71515127


title: Tpd single pollen fertile 31

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


title: SoaR_female_IgG_Rep1

data_processing:
library strategy: CUT&Tag
Reads were trimmed with cutadapt (v4.0).
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.4.5)
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.10) and DeepTools (v3.5.1)
Peaks were called with MACS2 (v2.1.2).
A greylist was generated from IgG samples and applied for peak filtering
DiffBind (v3.0.15) was use to determine differential binding, with normalization to background bins (15000 bp). Only peaks with FDR<0.05 in were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments

extract_protocol:
The experiment was performed with flash frozen tissues, which were homogenized in cold PBS and passed through a cell strainer. The cell suspension was counted and 0.4 Mio cells were used for each reaction. The libraries were generated according to the following protocol: dx.doi.org/10.17504/protocols.io.bcuhiwt6). Antibodies are listed with the respective samples. We used pA-Tn5 prepared by the IMB protein production core facilty.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.

tag: developmental stage

value: Pupa

tag: antibody

value: IgG control Rabbit (Abcam ab37415)

value: SoaR


title: Tpd single pollen fertile 28

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


title: Tpd single pollen fertile 29

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


title: Tpd single pollen fertile 27

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


title: Day11-2Non-Gata6tomatonegative14

description:
Day11-2Non-Gata6tomatonegative14
WTCHG_945384_71505126

value: Epidermis


title: Tpd single pollen fertile 30

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


title: WT_female_IgG_Rep2


title: Day11-2Non-Gata6tomatonegative13

description:
Day11-2Non-Gata6tomatonegative13
WTCHG_945384_71495125

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


title: SoaR_female_SOA_Rep2

value: abSOA


title: Tpd single pollen fertile 24

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

value: pollen


title: Day11-2Non-Gata6tomatonegative12

description:
Day11-2Non-Gata6tomatonegative12
WTCHG_945384_71485124


title: Tpd single pollen fertile 22

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


title: Tpd single pollen fertile 23

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


title: Tpd single pollen fertile 21

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


title: Day11-2Non-Gata6tomatonegative11

description:
Day11-2Non-Gata6tomatonegative11
WTCHG_945384_71475123


title: Tpd single pollen fertile 20

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


title: Tpd single pollen fertile 19

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


title: WT_female_SOA_Rep2


title: Day11-2Non-Gata6tomatonegative10

description:
Day11-2Non-Gata6tomatonegative10
WTCHG_945384_71465122


title: Day6Non-Gata6tomatonegative20

description:
Day6Non-Gata6tomatonegative20
WTCHG_945385_70685044


title: Day11-2Non-Gata6tomatonegative16

description:
Day11-2Non-Gata6tomatonegative16
WTCHG_945384_71525128


title: WT_female_IgG_Rep1


title: Tpd single pollen fertile 26

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


title: Tpd single pollen fertile 25

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


title: Day11-2Gata6-derivedtomatopositive15

description:
Day11-2Gata6-derivedtomatopositive15
WTCHG_945384_71445120


title: Tpd single pollen fertile 16

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


title: Day11-2Non-Gata6tomatonegative9

description:
Day11-2Non-Gata6tomatonegative9
WTCHG_945384_71455121


title: mybless_HA_Rep2

data_processing:
library strategy: CUT&Tag
Reads were trimmed with cutadapt (v4.0).
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.4.5)
Mapped reads were filtered for duplicates and multimapping reads using Samtools (v1.10) and BamUtil (v1.0.14).
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.10) and DeepTools (v3.5.1)
Peaks were called with MACS2 (v2.1.2).
A greylist was generated from IgG samples and applied for peak filtering
DiffBind (v3.0.15) was use to determine differential binding, with normalization to background bins (15000 bp). Only peaks with FDR<0.05 in were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments

source_name: Ag55 cell line

growth_protocol: Ag55 cells were cultured in Leibovitz L15 media with 10% FBS (Gibco, 10270-10,6 Lot: 2260092) and 1x penicillin-streptomycin (Gibco, 15140122) at 27°C at 80% humidity.

extract_protocol:
The cell suspension was counted and 0.4 Mio cells were used for each reaction. The experiment was performed following the native protocol dx.doi.org/10.17504/protocols.io.bcuhiwt6. Antibodies are listed with the respective samples. We used pA-Tn5 prepared by the IMB protein production core facilty.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.

treatment_protocol: 2 Mio. Ag55 cells were seeded in a 6-well plate. After 16 hours, 600 μl of a selected baculovirus in Sf-900 media was added to the cells. After 6 hours the media was changed to fresh L15. Cells were collected for further processing 48h from the addition of the baculovirus.

tag: cell line

value: Ag55 cell line

value: HA.11 Mouse (Biolegend, BLD-901502)

tag: ectopic expression

value: HA-tagged myblessSOA (112-1265)


title: Tpd single pollen fertile 17

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


title: Tpd single pollen fertile 14

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


title: mybless_HA_Rep1


title: Day11-2Gata6-derivedtomatopositive14

description:
Day11-2Gata6-derivedtomatopositive14
WTCHG_945384_71435119


title: Tpd single pollen fertile 12

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


title: Tpd single pollen fertile 15

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


title: SoaR_female_SOA_Rep1


title: empty_HA_Rep2

value: HA-tagged empty control


title: Tpd single pollen fertile 11

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


title: Day11-2Gata6-derivedtomatopositive13

description:
Day11-2Gata6-derivedtomatopositive13
WTCHG_945384_71425118


title: empty_HA_Rep1


title: Tpd single pollen fertile 10

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


title: Tpd single pollen fertile 18

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


title: Day11-2Gata6-derivedtomatopositive11

description:
Day11-2Gata6-derivedtomatopositive11
WTCHG_945384_71405116


title: longSOA_HA_Rep1

value: HA-tagged SOA (1-1265)


title: Day11-2Gata6-derivedtomatopositive12

description:
Day11-2Gata6-derivedtomatopositive12
WTCHG_945384_71415117


title: longSOA_HA_Rep2


title: Tpd single pollen fertile 6

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


title: Tpd single pollen fertile 8

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


title: Tpd single pollen fertile 7

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


title: WT_female_SOA_Rep1

value: Female

value: whole pupa


title: Tpd single pollen fertile 9

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


title: Day11-2Gata6-derivedtomatopositive9

description:
Day11-2Gata6-derivedtomatopositive9
WTCHG_945384_71385114


title: longSOA_IgG_Rep2


title: Tpd single pollen fertile 4

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


title: Tpd single pollen fertile 3

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


title: Day11-2Gata6-derivedtomatopositive10

description:
Day11-2Gata6-derivedtomatopositive10
WTCHG_945384_71395115


title: Day11-2Gata6-derivedtomatopositive8

description:
Day11-2Gata6-derivedtomatopositive8
WTCHG_945384_71375113


title: Tpd single pollen fertile 5

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


title: longSOA_IgG_Rep1


title: Tpd single pollen fertile 1

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


title: Tpd single pollen fertile 2

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


title: Tpd single pollen fertile 13

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


title: IgG_WT_Male_Rep3

data_processing:
Reads were trimmed with cutadapt (v4.0) to remove Illumina adapter sequences.
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.4.5)
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.10) and DeepTools (v3.5.1)
Peaks were called with MACS2 (v2.1.2) using the corresponding IgG samples as controls.
A greylist was generated from IgG samples and applied for peak filtering
DiffBind (v3.4.0) was used to determine differential binding, with normalization to background bins (15000 bp). Only peaks with FDR<0.05 were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Supplementary files format and content: DiffBind result file: diffbind_all_sites.xlsx
Library strategy: CUT&Tag

source_name: whole organism

extract_protocol:
The experiment was performed with flash frozen tissues, which were homogenized in cold PBS and passed through a cell strainer. The cell suspension was counted and 0.4 Mio cells were used for each reaction. 400 000 cells were used for each reaction. The libraries were generated according to the following protocol: dx.doi.org/10.17504/protocols.io.bcuhiwt6). Antibodies are listed with the respective samples. We used pA-Tn5 prepared by the IMB protein production core facilty.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.

value: IgG

value: Male

value: WT

value: whole organism


title: Tpd single pollen drive 345

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


title: Day11-2Non-Gata6tomatonegative8

description:
Day11-2Non-Gata6tomatonegative8
WTCHG_945384_71365112


title: Tpd single pollen drive 344

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


title: Tpd single pollen drive 343

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


title: Day11-2Non-Gata6tomatonegative7

description:
Day11-2Non-Gata6tomatonegative7
WTCHG_945384_71355111


title: IgG_WT_Male_Rep4

value: Pupa


title: Tpd single pollen drive 342

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


title: Tpd single pollen drive 341

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


title: abSOA_WT_Male_Rep4


title: Tpd single pollen drive 339

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


title: Day11-2Non-Gata6tomatonegative6

description:
Day11-2Non-Gata6tomatonegative6
WTCHG_945384_71345110


title: Day11-2Non-Gata6tomatonegative5

description:
Day11-2Non-Gata6tomatonegative5
WTCHG_945384_71335109


title: Tpd single pollen drive 337

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


title: Tpd single pollen drive 336

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


title: IgG_SoaKI_Female_Rep2

value: SoaKI


title: Tpd single pollen drive 338

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


title: abSOA_WT_Male_Rep3


title: IgG_SoaKI_Female_Rep1


title: Day11-2Non-Gata6tomatonegative2

description:
Day11-2Non-Gata6tomatonegative2
WTCHG_945384_71305106

value: Epidermis


title: Day11-2Non-Gata6tomatonegative4

description:
Day11-2Non-Gata6tomatonegative4
WTCHG_945384_71325108

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


title: Day11-2Non-Gata6tomatonegative3

description:
Day11-2Non-Gata6tomatonegative3
WTCHG_945384_71315107


title: IgG_SoaKI_Male_Rep2


title: Tpd single pollen drive 328

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


title: Tpd single pollen drive 330

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


title: IgG_WT_Female_Rep1


title: IgG_SoaKI_Male_Rep1


title: Day11-2Non-Gata6tomatonegative1

description:
Day11-2Non-Gata6tomatonegative1
WTCHG_945384_71295105


title: IgG_WT_Female_Rep2


title: Tpd single pollen drive 329

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


title: Tpd single pollen drive 327

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


title: Day11-2Gata6-derivedtomatopositive7

description:
Day11-2Gata6-derivedtomatopositive7
WTCHG_945384_71285104


title: Tpd single pollen drive 326

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


title: Tpd single pollen drive 340

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


title: Tpd single pollen drive 332

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


title: Tpd single pollen drive 333

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


title: Tpd single pollen drive 334

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


title: Tpd single pollen drive 335

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


title: Tpd single pollen drive 331

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


title: Day11-2Gata6-derivedtomatopositive6

description:
Day11-2Gata6-derivedtomatopositive6
WTCHG_945384_71275103


title: Tpd single pollen drive 325

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


title: IgG_WT_Male_Rep2


title: Tpd single pollen drive 324

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


title: Day11-2Gata6-derivedtomatopositive5

description:
Day11-2Gata6-derivedtomatopositive5
WTCHG_945384_71265102


title: Tpd single pollen drive 322

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


title: Day11-2Gata6-derivedtomatopositive4

description:
Day11-2Gata6-derivedtomatopositive4
WTCHG_945384_71255101


title: Day11-2Gata6-derivedtomatopositive3

description:
Day11-2Gata6-derivedtomatopositive3
WTCHG_945384_71245100


title: IgG_WT_Male_Rep1


title: abSOA_SoaKI_Female_Rep2

value: abSOA


title: Tpd single pollen drive 321

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

value: pollen


title: Tpd single pollen drive 323

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


title: Tpd single pollen drive 319

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


title: abSOA_SoaKI_Female_Rep1


title: Day11-2Gata6-derivedtomatopositive2

description:
Day11-2Gata6-derivedtomatopositive2
WTCHG_945384_71235099


title: abSOA_SoaKI_Male_Rep2


title: Tpd single pollen drive 317

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


title: Tpd single pollen drive 318

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


title: Tpd single pollen drive 320

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


title: Day11-2Gata6-derivedtomatopositive1

description:
Day11-2Gata6-derivedtomatopositive1
WTCHG_945384_71225098


title: Tpd single pollen drive 315

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


title: abSOA_SoaKI_Male_Rep1


title: Tpd single pollen drive 314

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


title: Day11-2Non-Gata6tomatonegative47

description:
Day11-2Non-Gata6tomatonegative47
WTCHG_945384_71195191


title: abSOA_WT_Female_Rep2


title: Day11-2Non-Gata6tomatonegative46

description:
Day11-2Non-Gata6tomatonegative46
WTCHG_945384_71185190


title: Tpd single pollen drive 313

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


title: Tpd single pollen drive 312

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


title: abSOA_WT_Female_Rep1


title: Tpd single pollen drive 310

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


title: Tpd single pollen drive 311

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


title: Day11-2Non-Gata6tomatonegative45

description:
Day11-2Non-Gata6tomatonegative45
WTCHG_945384_71175189


title: Tpd single pollen drive 309

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


title: abSOA_WT_Male_Rep2


title: Day11-2Non-Gata6tomatonegative44

description:
Day11-2Non-Gata6tomatonegative44
WTCHG_945384_71165188


title: Tpd single pollen drive 316

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


title: Tpd single pollen drive 307

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


title: Tpd single pollen drive 308

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


title: Tpd single pollen drive 306

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


title: abSOA_WT_Male_Rep1


title: Day11-2Non-Gata6tomatonegative42

description:
Day11-2Non-Gata6tomatonegative42
WTCHG_945384_71145186


title: Day11-2Non-Gata6tomatonegative43

description:
Day11-2Non-Gata6tomatonegative43
WTCHG_945384_71155187


title: RNA Male_SoaKi_Rep4

data_processing:
Reads were trimmed with cudadapt (v1.18) 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 (v2.7.3a) 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  (v2.7.3a) 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 (v1.9) and DeepTools (v3.1.0)
Primary alignments were assigned to features using subread (v1.6.5) 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
Supplementary files format and content: bigWig files containing CPM normalized coverage signals of primary alignments

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).


title: Tpd single pollen drive 305

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


title: Tpd single pollen drive 304

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


title: Tpd single pollen drive 302

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


title: RNA Male_SoaKi_Rep3


title: Day11-2Non-Gata6tomatonegative41

description:
Day11-2Non-Gata6tomatonegative41
WTCHG_945384_71135185


title: Tpd single pollen drive 303

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


title: Tpd single pollen drive 301

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


title: RNA Male_SoaKi_Rep2


title: RNA Male_SoaKi_Rep1


title: Tpd single pollen drive 298

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


title: Tpd single pollen drive 300

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


title: Day11-2Gata6-derivedtomatopositive46

description:
Day11-2Gata6-derivedtomatopositive46
WTCHG_945384_71115183


title: Tpd single pollen drive 297

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


title: RNA Male_WT_Rep4


title: Tpd single pollen drive 299

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


title: Tpd single pollen drive 296

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


title: Tpd single pollen drive 295

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


title: Tpd single pollen drive 294

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


title: Tpd single pollen drive 293

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


title: Day11-2Gata6-derivedtomatopositive44

description:
Day11-2Gata6-derivedtomatopositive44
WTCHG_945384_71095181


title: Tpd single pollen drive 292

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


title: RNA Male_WT_Rep2


title: Day11-2Gata6-derivedtomatopositive47

description:
Day11-2Gata6-derivedtomatopositive47
WTCHG_945384_71125184


title: Day11-2Gata6-derivedtomatopositive43

description:
Day11-2Gata6-derivedtomatopositive43
WTCHG_945384_71085180


title: Tpd single pollen drive 291

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


title: Day11-2Gata6-derivedtomatopositive42

description:
Day11-2Gata6-derivedtomatopositive42
WTCHG_945384_71075179


title: Tpd single pollen drive 289

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


title: Tpd single pollen drive 290

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


title: Day11-2Gata6-derivedtomatopositive41

description:
Day11-2Gata6-derivedtomatopositive41
WTCHG_945384_71065178


title: RNA Male_WT_Rep1


title: Tpd single pollen drive 288

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


title: Day11-2Gata6-derivedtomatopositive45

description:
Day11-2Gata6-derivedtomatopositive45
WTCHG_945384_71105182


title: Tpd single pollen drive 286

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


title: Day11-2Gata6-derivedtomatopositive40

description:
Day11-2Gata6-derivedtomatopositive40
WTCHG_945384_71055177


title: Day11-2Non-Gata6tomatonegative40

description:
Day11-2Non-Gata6tomatonegative40
WTCHG_945384_71045176


title: imb_keller_2022_03_12_IgG_empty_Rep2

data_processing:
Reads were trimmed with cutadapt (v1.18) to remove Illumina adapter sequences.
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.3.4)
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.9) and DeepTools (v3.1)
Peaks were called with MACS2 (v2.1.2) using the corresponding IgG samples as controls.
A greylist was generated from IgG samples and applied for peak filtering
DiffBind (v3.0.5) was use to determine differential binding, with normalization to background bins (15000 bp). Only peaks with FDR<0.05 in were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments

extract_protocol:
The cell suspension was counted and 0.4 Mio cells were used for each reaction. The experiment was performed following the native protocol dx.doi.org/10.17504/protocols.io.bcuhiwt6. Antibodies are listed with the respective samples. We used pA-Tn5 prepared by the IMB protein production core facilty.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.
OTHER: CUT&Tag

value: Ag55 cell line

value: IgG control Rabbit (Abcam ab37415)


title: Tpd single pollen drive 285

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


title: imb_keller_2022_03_11_IgG_longSoa_Rep2


title: imb_keller_2022_03_10_abHA_empty_Rep2

value: HA.11 Mouse (Biolegend, BLD-901502)


title: RNA Male_WT_Rep3


title: Day11-2Non-Gata6tomatonegative39

description:
Day11-2Non-Gata6tomatonegative39
WTCHG_945384_71035175


title: Tpd single pollen drive 284

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


title: Tpd single pollen drive 282

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


title: imb_keller_2022_03_9_abHA_longSoa_Rep2


title: Tpd single pollen drive 287

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


title: Day11-2Non-Gata6tomatonegative38

description:
Day11-2Non-Gata6tomatonegative38
WTCHG_945384_71025174


title: Tpd single pollen drive 280

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


title: Tpd single pollen drive 281

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


title: Tpd single pollen drive 279

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


title: Day11-2Non-Gata6tomatonegative37

description:
Day11-2Non-Gata6tomatonegative37
WTCHG_945384_71015173


title: Tpd single pollen drive 283

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


title: imb_keller_2022_03_5_IgG_longSoa_Rep1


title: Tpd single pollen drive 278

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


title: Tpd single pollen drive 277

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


title: Tpd single pollen drive 276

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


title: imb_keller_2022_03_4_abHA_empty_Rep1

value: HA-tagged empty control


title: Day11-2Non-Gata6tomatonegative36

description:
Day11-2Non-Gata6tomatonegative36
WTCHG_945384_71005172


title: Tpd single pollen drive 275

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


title: Tpd single pollen drive 273

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


title: Tpd single pollen drive 274

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


title: imb_keller_2022_03_3_abHA_longSoa_Rep1

value: HA-tagged SOA (1-1265)


title: Day11-2Non-Gata6tomatonegative35

description:
Day11-2Non-Gata6tomatonegative35
WTCHG_945384_70995171


title: imb_keller_2022_03_6_IgG_empty_Rep1


title: Tpd single pollen drive 269

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


title: Female_SoaKI_Rep2

data_processing:
Reads were trimmed with cutadapt (v4.0) to remove Illumina adapter sequences.
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.4.5)
Multimapping and duplicate reads were discarded using BamUtil (v1.0.14) and Samtools (v1.10)
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.10) and DeepTools (v3.5.1)
Peaks were called with MACS2 version (v2.1.2).
DiffBind (v3.4.0) was used to determine differential binding, with normalization by full library size. Only peaks with FDR<0.05 were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments

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:
The experiment was performed with flash frozen tissues, which were homogenized in cold PBS and passed through a cell strainer. The cell suspension was counted and 50,000 cells were used for each reaction. The libraries were generated according to the following protocol: 10.1002/0471142727.mb2129s109. We used Tn5 prepared by the IMB protein production core facilty.
ATAC-seq libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.

value: Female


title: Day11-2Non-Gata6tomatonegative34

description:
Day11-2Non-Gata6tomatonegative34
WTCHG_945384_70985170


title: Tpd single pollen drive 272

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


title: Tpd single pollen drive 271

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


title: Brain cell,24month,female

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

country: China

institute: Fudan University

library_source: transcriptomic single cell

data_processing:
Single-cell FASTQ sequencing reads from each sample were processed, and converted to digital gene expression matrices after mapping to the reference genome using the Cell Ranger Single Cell Software Suite (v2.1.0) provided on 10x genomics website.
Individual datasets were aggregated using the CellRanger aggr command without subsampling normalization.
The aggregated dataset was then analyzed using the R package Seurat (v 3.2.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
The brain without cerebellum were cut into pieces and then dissociated in 8U/mL papain lysis buffer containing 125 U/mL DNaseI) for 20 minutes at 37 ℃ with mild shaking. This process was then terminated by adding a 10% ovomucoid in L15 culture medium (2 mg/mL). After digestion, cell clusters were removed by filtering through 70 um nylon cell strainers (Faclon). Myelin and cell debris were removed from the mixed cell through the density gradient centrifugation in 37% Percol (SolarBio). after acquiring the mixed brain cells, the mixed cell were resuspended using FACS buffer. Next, mixed cells were stained with antibody against CD45 (1:100, clone 30-F11, BD Pharmingen, cat: 553080) and CD11b (1:100, clone M1/70, BD Pharmingen, cat: 557657). Death cells were labeled by 7-AAD (1:80, BD Pharmingen, cat: 559925).  The harvested cells were then used for scRNA-seq, bulk RNA-seq or ATAC-seq based on different purpose.
The single-cell library was constructed using the ChromiumTM Controller and ChromiumTM Single Cell 3' Reagent Version 2 Kit (10x Genomics, Pleasanton, CA).Briefly, single cells, reagents and Gel Beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized GEMs (Gel Bead in emulsion) using the GemCode Technology. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM. Post RT-GEMs were cleaned up and DNA were amplified. cDNA was fragmented and fragments end were repaired, as well A-tailing was added to the 3' end. The adaptors were ligated to fragments which were double sided SPRI selected. Another double sided SPRI selecting was carried out after sample index PCR. The final library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final products were sequenced using the Illumina Hiseq 4000.

value: Brain

value: 24 months

value: female


title: Female_SoaKI_Rep3


title: Tpd single pollen drive 270

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


title: Day11-2Non-Gata6tomatonegative33

description:
Day11-2Non-Gata6tomatonegative33
WTCHG_945384_70975169


title: Tpd single pollen drive 268

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


title: Male_SoaKI_Rep3

value: Male


title: Male_SoaKI_Rep4

value: whole organism


title: Tpd single pollen drive 264

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


title: Tpd single pollen drive 266

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


title: Tpd single pollen drive 267

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


title: Brain cell,3month,female

value: 3 months

value: WT


title: Tpd single pollen drive 265

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


title: Tpd single pollen drive 262

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


title: Tpd single pollen drive 263

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


title: Female_SoaKI_Rep4

value: Pupa

value: SoaKI


title: Female_WT_Rep3


title: Male_SoaKI_Rep1


title: Tpd single pollen drive 258

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


title: Tpd single pollen drive 260

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


title: Tpd single pollen drive 261

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


title: Female_WT_Rep2


title: microglia,3xPLX

source_name: brain

extract_protocol:
The brain without cerebellum were cut into pieces and then dissociated in 8U/mL papain lysis buffer containing 125 U/mL DNaseI) for 20 minutes at 37 ℃ with mild shaking. This process was then terminated by adding a 10% ovomucoid in L15 culture medium (2 mg/mL). After digestion, cell clusters were removed by filtering through 70 um nylon cell strainers (Faclon). Myelin and cell debris were removed from the mixed cell through the density gradient centrifugation in 37% Percol (SolarBio). after acquiring the mixed brain cells, the mixed cell were resuspended using FACS buffer. Next, mixed cells were stained with antibody against CD45 (1:100, clone 30-F11, BD Pharmingen, cat: 553080) and CD11b (1:100, clone M1/70, BD Pharmingen, cat: 557657). Death cells were labeled by 7-AAD (1:80, BD Pharmingen, cat: 559925). Followed by cell staining, CD45+CD11b+7-ADD-microglia were sorted and collected using BD FACSAria III (BD Biosiences). The harvested cells were then used for scRNA-seq, bulk RNA-seq or ATAC-seq based on different purpose.
The single-cell library was constructed using the ChromiumTM Controller and ChromiumTM Single Cell 3' Reagent Version 2 Kit (10x Genomics, Pleasanton, CA).Briefly, single cells, reagents and Gel Beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized GEMs (Gel Bead in emulsion) using the GemCode Technology. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM. Post RT-GEMs were cleaned up and DNA were amplified. cDNA was fragmented and fragments end were repaired, as well A-tailing was added to the 3' end. The adaptors were ligated to fragments which were double sided SPRI selected. Another double sided SPRI selecting was carried out after sample index PCR. The final library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final products were sequenced using the Illumina Hiseq 4000.

value: brain

value: microglia

value: PLX5622 diet


title: microglia,Control

value: CD diet


title: Tpd single pollen drive 257

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

value: pollen


title: Tpd single pollen drive 256

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


title: microglia,14month,female,LPS

value: 14 month

value: LPS


title: Tpd single pollen drive 255

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


title: Male_WT_Rep4


title: microglia,24month,female,PBS

value: 24 month

value: PBS


title: Tpd single pollen drive 253

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


title: Tpd single pollen drive 252

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


title: Tpd single pollen drive 251

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


title: Tpd single pollen drive 250

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


title: Male_WT_Rep2


title: microglia,14month,female,PBS


title: Tpd single pollen drive 259

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


title: microglia,24month,female,LPS


title: Male_WT_Rep3


title: imb_keller_2021_07_17_longSoa_200_Rep3

data_processing:
Reads were trimmed with cudadapt (v1.18) to remove Illumina adapter sequences.
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  (v2.7.3a) 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 were generated using Samtools (v1.9) and DeepTools (v3.1.0).
Primary alignments were assigned to features using subread (v1.6.5) 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
Supplementary files format and content: bigWig files containing CPM normalized coverage signals of primary alignments

treatment_protocol: 0.75 Mio. cells were seeded per each well of a 24-well plate. After 16 hours, 200 μl of baculovirus in Sf-900 media was added. After 6 hours the media was changed to fresh L15. Cells were collected for extraction after 48h from the addition of the baculovirus.

value: Ag55 cell line

value: male SOA (1-1265) HA-tagged


title: Tpd single pollen drive 247

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


title: Female_WT_Rep1

value: Female


title: Tpd single pollen drive 246

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


title: microglia,3month,female,LPS

value: 3 month

value: female


title: Day11Gata6-derivedtomatopositive30

description:
Day11Gata6-derivedtomatopositive30
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.

value: Epidermis

value: Days 11 post-wounding

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


title: imb_keller_2021_07_15_shSoa_200_Rep3

value: female SOA (1-229) HA-tagged


title: imb_keller_2021_07_13_empty_200_Rep3

value: empty control (HA-tagged)


title: Tpd single pollen drive 248

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


title: Tpd single pollen drive 245

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


title: Tpd single pollen drive 244

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


title: Tpd single pollen drive 254

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


title: Day11Gata6-derivedtomatopositive28

description:
Day11Gata6-derivedtomatopositive28
day11g6.txt


title: Day11Gata6-derivedtomatopositive31

description:
Day11Gata6-derivedtomatopositive31
day11g6.txt


title: Tpd single pollen drive 242

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


title: Tpd single pollen drive 241

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


title: imb_keller_2021_07_09_shSoa_200_Rep2


title: Tpd single pollen drive 249

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


title: microglia,3month,female,PBS

value: brain

value: microglia

value: WT


title: Day11Gata6-derivedtomatopositive27

description:
Day11Gata6-derivedtomatopositive27
day11g6.txt


title: imb_keller_2021_07_07_empty_200_Rep2


title: Tpd single pollen drive 239

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

value: pollen


title: Tpd single pollen drive 238

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


title: Tpd single pollen drive 237

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


title: Day11Gata6-derivedtomatopositive26

description:
Day11Gata6-derivedtomatopositive26
day11g6.txt


title: Tpd single pollen drive 236

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


title: Tpd single pollen drive 243

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


title: Day11Gata6-derivedtomatopositive29

description:
Day11Gata6-derivedtomatopositive29
day11g6.txt


title: Day11Gata6-derivedtomatopositive25

description:
Day11Gata6-derivedtomatopositive25
day11g6.txt


title: Tpd single pollen drive 235

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


title: imb_keller_2021_07_11_longSoa_200_Rep2


title: imb_keller_2021_07_03_shSoa_200_Rep1


title: Day11Gata6-derivedtomatopositive24

description:
Day11Gata6-derivedtomatopositive24
day11g6.txt


title: Tpd single pollen drive 233

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


title: Day11Non-Gata6tomatonegative24

description:
Day11Non-Gata6tomatonegative24
day11ng6.txt


title: Tpd single pollen drive 232

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


title: Tpd single pollen drive 234

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


title: imb_keller_2021_07_01_empty_200_Rep1


title: M_L1_Rep4_exp2

description:
exp2
M_L1_Rep4

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

source_name: L1 larva

value: L1 larva

value: male


title: Day11Non-Gata6tomatonegative23

description:
Day11Non-Gata6tomatonegative23
day11ng6.txt


title: Tpd single pollen drive 231

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


title: Tpd single pollen drive 240

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


title: Tpd single pollen drive 226

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


title: imb_keller_2021_07_05_longSoa_200_Rep1


title: Tpd single pollen drive 228

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


title: Tpd single pollen drive 229

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


title: M_L1_Rep3_exp2

description:
exp2
M_L1_Rep3


title: Tpd single pollen drive 225

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


title: M_L1_Rep2_exp2

description:
exp2
M_L1_Rep2


title: Tpd single pollen drive 227

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


title: Day11Non-Gata6tomatonegative21

description:
Day11Non-Gata6tomatonegative21
day11ng6.txt


title: M_L1_Rep1_exp2

description:
exp2
M_L1_Rep1


title: Day11Non-Gata6tomatonegative22

description:
Day11Non-Gata6tomatonegative22
day11ng6.txt


title: Tpd single pollen drive 224

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


title: Tpd single pollen drive 223

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


title: Tpd single pollen drive 230

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


title: F_L1_Rep4_exp2

description:
exp2
F_L1_Rep4


title: Tpd single pollen drive 222

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


title: Day11Non-Gata6tomatonegative20

description:
Day11Non-Gata6tomatonegative20
day11ng6.txt


title: Day11Non-Gata6tomatonegative19

description:
Day11Non-Gata6tomatonegative19
day11ng6.txt


title: F_L1_Rep3_exp2

description:
exp2
F_L1_Rep3


title: Tpd single pollen drive 220

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


title: Tpd single pollen drive 221

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


title: Day11Non-Gata6tomatonegative18

description:
Day11Non-Gata6tomatonegative18
day11ng6.txt


title: Tpd single pollen drive 219

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


title: F_L1_Rep2_exp2

description:
exp2
F_L1_Rep2


title: F_L1_Rep1_exp2

description:
exp2
F_L1_Rep1


title: Tpd single pollen drive 216

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


title: Tpd single pollen drive 217

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


title: Tpd single pollen drive 218

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


title: Day11Gata6-derivedtomatopositive23

description:
Day11Gata6-derivedtomatopositive23
day11g6.txt


title: Day11Non-Gata6tomatonegative17

description:
Day11Non-Gata6tomatonegative17
day11ng6.txt


title: Tpd single pollen drive 214

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


title: Tpd single pollen drive 212

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


title: Tpd single pollen drive 215

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


title: Tpd single pollen drive 213

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


title: M_14h_Rep4_exp2

description:
exp2
M_14h_Rep4

source_name: embryo

value: embryo


title: M_14h_Rep3_exp2

description:
exp2
M_14h_Rep3


title: Day11Gata6-derivedtomatopositive21

description:
Day11Gata6-derivedtomatopositive21
day11g6.txt


title: Tpd single pollen drive 210

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


title: F_14h_Rep4_exp2

description:
exp2
F_14h_Rep4


title: Day11Gata6-derivedtomatopositive20

description:
Day11Gata6-derivedtomatopositive20
day11g6.txt


title: Day11Gata6-derivedtomatopositive19

description:
Day11Gata6-derivedtomatopositive19
day11g6.txt


title: Day11Gata6-derivedtomatopositive22

description:
Day11Gata6-derivedtomatopositive22
day11g6.txt


title: Tpd single pollen drive 209

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


title: Tpd single pollen drive 208

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


title: Tpd single pollen drive 207

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


title: F_14h_Rep3_exp2

description:
exp2
F_14h_Rep3


title: M_ZGA_late_Rep2_exp2

description:
exp2
M_ZGA_late_Rep2


title: M_ZGA_late_Rep1_exp2

description:
exp2
M_ZGA_late_Rep1


title: Day11Gata6-derivedtomatopositive17

description:
Day11Gata6-derivedtomatopositive17
day11g6.txt


title: Tpd single pollen drive 205

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


title: Tpd single pollen drive 204

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


title: Tpd single pollen drive 211

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


title: Tpd single pollen drive 203

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


title: Day11Gata6-derivedtomatopositive16

description:
Day11Gata6-derivedtomatopositive16
day11g6.txt


title: Tpd single pollen drive 202

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


title: Tpd single pollen drive 201

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


title: Tpd single pollen drive 200

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


title: Tpd single pollen drive 199

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


title: Day11Non-Gata6tomatonegative16

description:
Day11Non-Gata6tomatonegative16
day11ng6.txt


title: Day11Non-Gata6tomatonegative15

description:
Day11Non-Gata6tomatonegative15
day11ng6.txt


title: Day11Non-Gata6tomatonegative14

description:
Day11Non-Gata6tomatonegative14
day11ng6.txt


title: F_ZGA_late_Rep1_exp2

description:
exp2
F_ZGA_late_Rep1


title: Tpd single pollen drive 198

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


title: M_ZGA_early_Rep3_exp2

description:
exp2
M_ZGA_early_Rep3


title: Tpd single pollen drive 196

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


title: Tpd single pollen drive 197

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


title: Tpd single pollen drive 206

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


title: Day11Non-Gata6tomatonegative13

description:
Day11Non-Gata6tomatonegative13
day11ng6.txt


title: Tpd single pollen drive 193

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


title: Tpd single pollen drive 194

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


title: Day11Gata6-derivedtomatopositive18

description:
Day11Gata6-derivedtomatopositive18
day11g6.txt


title: M_ZGA_early_Rep1_exp2

description:
exp2
M_ZGA_early_Rep1


title: Day11Non-Gata6tomatonegative12

description:
Day11Non-Gata6tomatonegative12
day11ng6.txt


title: Tpd single pollen drive 192

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


title: Tpd single pollen drive 191

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


title: F_ZGA_late_Rep2_exp2

description:
exp2
F_ZGA_late_Rep2


title: F_ZGA_late_Rep3_exp2

description:
exp2
F_ZGA_late_Rep3


title: F_ZGA_early_Rep2_exp2

description:
exp2
F_ZGA_early_Rep2


title: F_ZGA_early_Rep1_exp2

description:
exp2
F_ZGA_early_Rep1


title: Tpd single pollen drive 188

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


title: Day11Non-Gata6tomatonegative11

description:
Day11Non-Gata6tomatonegative11
day11ng6.txt


title: Tpd single pollen drive 190

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


title: Tpd single pollen drive 195

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


title: M_ZGA_early_Rep2_exp2

description:
exp2
M_ZGA_early_Rep2


title: M_preZGA_Rep6_exp2

description:
exp2
M_preZGA_Rep6

value: preZGA


title: Tpd single pollen drive 187

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


title: Tpd single pollen drive 185

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


title: Day11Non-Gata6tomatonegative9

description:
Day11Non-Gata6tomatonegative9
day11ng6.txt


title: Tpd single pollen drive 184

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


title: Day11Non-Gata6tomatonegative10

description:
Day11Non-Gata6tomatonegative10
day11ng6.txt


title: Tpd single pollen drive 183

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


title: Day11Gata6-derivedtomatopositive15

description:
Day11Gata6-derivedtomatopositive15
day11g6.txt


title: Tpd single pollen drive 186

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


title: M_preZGA_Rep4_exp2

description:
exp2
M_preZGA_Rep4


title: M_preZGA_Rep5_exp2

description:
exp2
M_preZGA_Rep5


title: Day11Gata6-derivedtomatopositive14

description:
Day11Gata6-derivedtomatopositive14
day11g6.txt


title: Tpd single pollen drive 182

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


title: M_preZGA_Rep3_exp2

description:
exp2
M_preZGA_Rep3


title: Tpd single pollen drive 180

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


title: Tpd single pollen drive 181

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


title: Day11Gata6-derivedtomatopositive13

description:
Day11Gata6-derivedtomatopositive13
day11g6.txt


title: Tpd single pollen drive 179

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


title: M_preZGA_Rep2_exp2

description:
exp2
M_preZGA_Rep2


title: Tpd single pollen drive 189

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


title: Tpd single pollen drive 178

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


title: Day11Gata6-derivedtomatopositive12

description:
Day11Gata6-derivedtomatopositive12
day11g6.txt


title: Tpd single pollen drive 177

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


title: M_preZGA_Rep1_exp2

description:
exp2
M_preZGA_Rep1


title: Day11Gata6-derivedtomatopositive11

description:
Day11Gata6-derivedtomatopositive11
day11g6.txt


title: Tpd single pollen drive 175

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


title: Tpd single pollen drive 176

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


title: Tpd single pollen drive 174

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


title: Tpd single pollen drive 173

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


title: F_preZGA_Rep5_exp2

description:
exp2
F_preZGA_Rep5


title: Day11Gata6-derivedtomatopositive10

description:
Day11Gata6-derivedtomatopositive10
day11g6.txt


title: Tpd single pollen drive 172

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


title: Day11Gata6-derivedtomatopositive9

description:
Day11Gata6-derivedtomatopositive9
day11g6.txt


title: F_preZGA_Rep3_exp2

description:
exp2
F_preZGA_Rep3


title: Tpd single pollen drive 171

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


title: Tpd single pollen drive 169

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


title: Day11Gata6-derivedtomatopositive8

description:
Day11Gata6-derivedtomatopositive8
day11g6.txt


title: Tpd single pollen drive 168

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


title: Tpd single pollen drive 167

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


title: Tpd single pollen drive 170

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


title: Tpd single pollen drive 166

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


title: Day11Non-Gata6tomatonegative8

description:
Day11Non-Gata6tomatonegative8
day11ng6.txt


title: F_preZGA_Rep1_exp2

description:
exp2
F_preZGA_Rep1


title: F_preZGA_Rep2_exp2

description:
exp2
F_preZGA_Rep2


title: Tpd single pollen drive 165

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


title: Day11Non-Gata6tomatonegative7

description:
Day11Non-Gata6tomatonegative7
day11ng6.txt


title: Tpd single pollen drive 163

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


title: Tpd single pollen drive 164

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


title: Day11Non-Gata6tomatonegative6

description:
Day11Non-Gata6tomatonegative6
day11ng6.txt


title: Tpd single pollen drive 162

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


title: Trizina strain [T7]

city: Athens

first: John

last: Vontas

state: Attica

address: Iera Odos 75

department: Department of Crop Science

country: Greece

institute: Agricultural University of Athens

data_processing:
RNA-seq reads were mapped using hisat2 2.1.0
Sam files were converted to bam and then sorted bam files using samtools 1.10
Expression was quantified at the gene level using featureCounts 1.6.0
PCA analysis was performed using the edgeR package. No samples were excluded.
Differential expression analysis was performed using edgeR (Trinity-bundled perl scripts)
Genome_build: Tetranychus urticae London genome (Grbic et al., 2011)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tables with the differentially expressed genes (log2|FC| > 1.5, p-value < 10E-3, FDR < 0.05) between Trz and S-1 (London), and Trz and S-2 (BC2018-14)

organism: Tetranychus urticae

source_name: Whole-body

growth_protocol: All strains were reared on 3-week old potted kidney bean plants (Phaseolus vulgaris L.) at 25 ± 1 °C, 16:8 light: dark photoperiod and maintained without exposure to insecticides.

extract_protocol:
RNA extraction using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions
mRNA paired-end library construction using the Illumina Truseq stranded mRNA sample preparation kit (100 bp reads)

treatment_protocol: All samples were untreated.

value: Trizina strain

value: untreated


title: Day11Non-Gata6tomatonegative5

description:
Day11Non-Gata6tomatonegative5
day11ng6.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.


title: Trizina strain [T6]


title: F_preZGA_Rep4_exp2

description:
exp2
F_preZGA_Rep4


title: Tpd single pollen drive 161

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


title: Tpd single pollen drive 160

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


title: Trizina strain [T5]


title: Day11Non-Gata6tomatonegative4

description:
Day11Non-Gata6tomatonegative4
day11ng6.txt


title: Trizina strain [T4]


title: Tpd single pollen drive 158

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


title: Tpd single pollen drive 159

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


title: Tpd single pollen drive 157

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


title: Day11Non-Gata6tomatonegative3

description:
Day11Non-Gata6tomatonegative3
day11ng6.txt


title: BC2018-14 strain (S-2) [Sp_e]

value: BC2018-14 strain


title: Tpd single pollen drive 156

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


title: Tpd single pollen drive 155

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


title: Tpd single pollen drive 153

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


title: Day11Non-Gata6tomatonegative1

description:
Day11Non-Gata6tomatonegative1
day11ng6.txt


title: BC2018-14 strain (S-2) [Sp_b]


title: Tpd single pollen drive 154

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


title: Tpd single pollen drive 152

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


title: Day11Gata6-derivedtomatopositive7

description:
Day11Gata6-derivedtomatopositive7
day11g6.txt


title: Tpd single pollen drive 151

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


title: Tpd single pollen drive 150

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


title: BC2018-14 strain (S-2) [Sp_c]


title: Day11Gata6-derivedtomatopositive5

description:
Day11Gata6-derivedtomatopositive5
day11g6.txt


title: Tpd single pollen drive 147

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


title: Tpd single pollen drive 148

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


title: Tpd single pollen drive 149

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


title: BC2018-14 strain (S-2) [Sp_a]


title: London strain (S-1) [L5]

value: London strain


title: Day11Gata6-derivedtomatopositive4

description:
Day11Gata6-derivedtomatopositive4
day11g6.txt

value: Epidermis


title: Tpd single pollen drive 145

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


title: Day11Gata6-derivedtomatopositive6

description:
Day11Gata6-derivedtomatopositive6
day11g6.txt

value: Days 11 post-wounding


title: London strain (S-1) [L4]


title: London strain (S-1) [L3]


title: Tpd single pollen drive 146

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


title: Day11Non-Gata6tomatonegative2

description:
Day11Non-Gata6tomatonegative2
day11ng6.txt

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


title: Day11Gata6-derivedtomatopositive3

description:
Day11Gata6-derivedtomatopositive3
day11g6.txt


title: Tpd single pollen drive 144

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


title: London strain (S-1) [L2]


title: WES_Control 168 Pancreas

city: Heidelberg

first: Alicia

last: Alonso de la Vega

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum, DKFZ

data_processing:
SpeedSeq; Picard
Sequence reads were ere mapped to GrCM38/mm10 using SpeedSeq
PCR duplicates were removed using Picard
reads realinged using gatk indel realigner. Mutect2 was used to create pool of normals using the normal samples
Somatic mutations agains the pool of normals were called using mutect2 for each sample
Assembly: mm10
Supplementary files format and content: vcf files with mutation calls
Library strategy: exome-seq

source_name: Pancreas

extract_protocol:
DNA was harvested using AllPrep DNA/RNA Mini (Qiagen, 80204). 0.5 ug of total DNA was used for the construction of sequencing libraries.
DNA libraries for WES were prepared using Agilent Low Input Exom-Seq Mouse kit following manufacturer's protocols.

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

value: Pancreas

value: 10 days


title: WES_Control 45 Pancreas


title: Day11Gata6-derivedtomatopositive2

description:
Day11Gata6-derivedtomatopositive2
day11g6.txt


title: Day11Gata6-derivedtomatopositive1

description:
Day11Gata6-derivedtomatopositive1
day11g6.txt


title: Tpd single pollen drive 143

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


title: Day11A1Blank

description:
Day11A1Blank
day11ng6.txt


title: WES_Sample 153 Pancreas

value: A3B + CAGS-rtTA


title: WES_Sample 137 Pancreas


title: UKF313_T_SPTCR9

city: Freiburg im Breisgau

first: Jasim

last: Kada Benotmane

state: - Select -

address: Breisacherstraße 64

department: Clinic for Neurosurgery

institute: Albert-Ludwigs-University Freiburg

data_processing:
SPTCR-seq Pipeline was performed on raw FASTQ Files
Supplementary files format and content: comma separated text files including VDJ Arrangements & Counts for spatial Barcode Spot
Library strategy: SPTCR-seq

organism: Homo sapiens

source_name: Brain Tumor

extract_protocol:
RNA was harvested from fresh frozen tissue samples of primary glioblastoma followed by Library preparation using 10X Visium protocol. Subsequently libraries were target enriched following the SPTCR-seq protocol.
cDNA Libraries were prepared up to the manufacturers instructions for SQK-LSK110 Library Preparation Protocol. Prepared Libraries were sequenced on ONT MINION ( flow cellFLO-MIN106D) and signal was basecalled using Guppy GPU v4.0 to generate reported raw FASTQs.

tag: disease state

value: Glioblastoma

tag: idh-status

value: IDH-WT

value: m

value: Glioblastoma, Brain Tumor

tag: brain region

value: temporal

value: primary


title: UKF334_T_SPTCR14

value: f


title: Day11H12Blank

description:
Day11H12Blank
day11g6.txt


title: UKF304_T_SPTCR17


title: Tpd single pollen drive 142

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

value: pollen


title: Tpd single pollen drive 141

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


title: UKF296_T_SPTCR20

value: Occipital


title: WES_Sample 49 Pancreas


title: WES_Sample 125 Pancreas


title: Tpd single pollen drive 139

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


title: Tpd single pollen drive 140

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


title: Day11Non-Gata6tomatonegative46

description:
Day11Non-Gata6tomatonegative46
day11ng6.txt


title: UKF275_T_SPTCR16

value: frontal


title: Tpd single pollen drive 138

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


title: UKF269_T_SPTCR2


title: WES_Sample 53 Pancreas


title: Day11Non-Gata6tomatonegative45

description:
Day11Non-Gata6tomatonegative45
day11ng6.txt


title: WES_Sample 44 Pancreas


title: Tpd single pollen drive 137

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


title: UKF259_T_SPTCR12


title: Tpd single pollen drive 136

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


title: Day11Non-Gata6tomatonegative47

description:
Day11Non-Gata6tomatonegative47
day11ng6.txt


title: WES_Control 45 Liver

source_name: Liver

value: Liver


title: Day11Non-Gata6tomatonegative43

description:
Day11Non-Gata6tomatonegative43
day11ng6.txt

value: Epidermis


title: Tpd single pollen drive 135

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


title: UKF248_T_SPTCR15


title: WES_Sample 153 Liver


title: Day11Non-Gata6tomatonegative42

description:
Day11Non-Gata6tomatonegative42
day11ng6.txt

value: Days 11 post-wounding


title: WES_Sample 48 Liver


title: Tpd single pollen drive 134

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


title: Tpd single pollen drive 133

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


title: WES_Control 168 Liver


title: UKF260_T_SPTCR13


title: WES_Sample 49 Liver


title: WES_Sample 125 Liver


title: Tpd single pollen drive 132

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


title: Day11Gata6-derivedtomatopositive46

description:
Day11Gata6-derivedtomatopositive46
day11g6.txt

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


title: Tpd single pollen drive 131

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


title: WES_Sample 137 Liver


title: Day11Non-Gata6tomatonegative44

description:
Day11Non-Gata6tomatonegative44
day11ng6.txt


title: Day11Non-Gata6tomatonegative41

description:
Day11Non-Gata6tomatonegative41
day11ng6.txt


title: WES_Sample 44 Liver


title: Day11Gata6-derivedtomatopositive45

description:
Day11Gata6-derivedtomatopositive45
day11g6.txt


title: Day11Gata6-derivedtomatopositive44

description:
Day11Gata6-derivedtomatopositive44
day11g6.txt


title: Tpd single pollen drive 130

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


title: intact Hi-C from mucosa of descending colon (ENCLB383USQ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR206OUF/
***************
biological replicate number: 1
technical replicate number: 2
description: w80-mucosa-of-descending-colon-intact dnase HiC
experiment encode accession: ENCSR206OUF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB383USQ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female adult (61 years) mucosa of descending colon tissue, preserved by flash-freezing

value: mucosa of descending colon

value: tissue

tag: biosample encode accession

tag: encode accession

value: female

tag: health state

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

tag: dev stage

value: adult

value: 61 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS915BJX at ENCODE; https://www.encodeproject.org/ENCBS915BJX/

value: derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Tpd single pollen drive 129

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

tag: tissue

value: pollen

tag: genotype


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

city: Seattle

first: Kathleen

last: Abadie

state: Washington

address: 3720 15th Ave NE

department: Bioengineering

institute: University of Washington

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.

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)

value: spleen

tag: cell type

value: CD8+ T cell


title: Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 3 (ATAC-seq)


title: Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 3 (ATAC-seq)


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


title: Day11Gata6-derivedtomatopositive43

description:
Day11Gata6-derivedtomatopositive43
day11g6.txt

source_name: Epidermis

tag: strain

tag: age

tag: treatment


title: Control 168 Pancreas

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)

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.

value: Pancreas

value: A3B + CAGS-rtTA

tag: treatment time

value: 10 days


title: intact Hi-C from mucosa of descending colon (ENCLB010FFQ)

description:
https://www.encodeproject.org/experiments/ENCSR206OUF/
***************
biological replicate number: 1
technical replicate number: 1
description: w80-mucosa-of-descending-colon-intact dnase HiC
experiment encode accession: ENCSR206OUF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB010FFQ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

tag: Sex


title: Day11Gata6-derivedtomatopositive47

description:
Day11Gata6-derivedtomatopositive47
day11g6.txt

value: Epidermis

value: Days 11 post-wounding

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


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