title: rad30, DSB, biol rep1

description: Library name: rad30 biol rep1


title: Muscle, Young, biol rep3, GEX

status: Public on May 09 2025

type: SRA

city: Shatin, NT

first: CHUHAN

last: LI

state: shatin

address: The Chinese University of Hong Kong, Central Ave

country: Hong Kong

institute: CUHK

description:
10x Genomics
Young_3_barcodes.tsv.gz
Young_3_features.tsv.gz
Young_3_matrix.mtx.gz

library_source: transcriptomic

data_processing:
Cell Ranger ARC v2.0.1 count functions to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz
Subsequently, the processed matices were read in by Seurat 5.0.1 and Signac 1.12.0 for following analysis.
Assembly: hg38
Supplementary files format and content: CellRanger ARC output files: Tab-separated values files and matrix files
Library strategy: single-cell multiome (RNA+ATAC)

molecule: nuclear RNA

organism: Homo sapiens

source_name: hamstring muscle

extract_protocol:
Whole live muscle mononuclear cells were freshly isolated by FACs sorting
whole muscle cells were isolated with an additional step of viability validation by 7-AAD (Thermo Scientific, 00-6993-50) staining. Red blood cells were eliminated by ACK buffers (150M NH4Cl, 100mM KHCO3, 10mM EDTA-2Na) before sorting. After sorting, live cells were washed with 0.04% BSA in PBS twice and resuspended in the BSA solution. Nuclei were isolated from the suspended cells according to the manufacturer’s instruction CG000366 • Rev D. Isolated nuclei were counted under a microscope and Typan blue was used to examine the number and integrity. The isolated nuclei were then resuspended at an appropriate concentration (5000-10000 nuclei/μl). Library construction was performed following the manufacturer’s instructions for generation of Gel Bead-In Emulsions (GEMs) using the 10x Chromium system. The single-cell multiome (RNA+ATAC) library were sequenced by Illumina NovaSeq S4 instrument.

tag: tissue

value: hamstring muscle

tag: group

value: Young

tag: cell type

value: muscle mononuclear cell


title: csm3, DSB, biol rep2

city: Boston

first: Kaifu

last: Chen

address: 300 Longwood Ave

department: Cardiology

country: USA

institute: Boston Children's Hospital

description: Library name: csm3 biol rep2

library_source: genomic

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: mutant isogenic to JKM139

extract_protocol:
All colonies on YP-galactose plates were collected, combined, and mixed vigorously. Approximately 80 μL cells were spun down for isolating genomic DNA. Standard glass beads-phenol/chloroform/isoamyl alcohol (25:24:1) method. The DNA was dissolved in water and adjusted to a concentration of 10 ng/μL. The construction of the amplicon sequencing library was adapted from Illumina’s protocol #15044223 Rev. B. Briefly, the sequencing libraries were constructed with two rounds of PCR using KAPA HiFi HotStart ReadyMix polymerase (Roche, 7958927001). For the first round of PCR, 3.2 μL genomic DNA and 0.5 μL 10 μM primers were used for a total volume of 25 μL. The forward and reverse primers targeting the MATa locus are located 11 bp upstream or 18 bp downstream of the HO cleavage site respectively, containing Illumina adapter sequence and 3 bases unique home index as described (7). The thermocycling conditions were: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. After the first round of PCR, 18μL PCR product was purified with an equal volume of AMPure XP beads (Beckman Coulter, A63880). The DNA was eluted with 52.5 μL of 10 mM Tris (pH 8.5) and used as the templates for the second round of PCR. For the second round of PCR, 5 μl template DNA, 5 μL index primer N7xx and 5 μL index primer S5xx from Nextera XT V2 Index kit (Illumina, FC-131-2001) were used for the total volume of 50 μL. The following conditions were used for the second round of PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. Then, the PCR product was purified with 1.2x volume of AMPure XP beads and eluted with 10 mM Tris pH 8.5. The average size of each sample was measured with TapeStation and the DNA concentration was measured with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850)
The DNA was diluted to a concentration of 4 nM. An equal volume of DNA from ~20 samples was pooled into the library. The 0.2 M NaOH was used to denature the pooled library and PhiX library (Illumina, FC‐110‐3001). After diluting the libraries with pre-chilled HT1 to 12 pM, pooled library and PhiX library were mixed with the ratio 9:1, further denatured by incubating at 96 °C for 2 min and immediately put in an ice-water bath for 5 min

value: mutant isogenic to JKM139

tag: genotype


title: rrm3, DSB, biol rep2

description: Library name: rrm3 biol rep2


title: rad24, DSB, biol rep2

description: Library name: rad24 biol rep2


title: Muscle, Young, biol rep2, GEX

description:
10x Genomics
Young_2_barcodes.tsv.gz
Young_2_features.tsv.gz
Young_2_matrix.mtx.gz


title: rad24, DSB, biol rep1

description: Library name: rad24 biol rep1


title: mec1 tel1 sml1, DSB, biol rep2

description: Library name: mec1 tel1 sml1 biol rep2

value: mec1 tel1 sml1


title: mec1 tel1 sml1, DSB, biol rep1

description: Library name: mec1 tel1 sml1 biol rep1


title: yen1ON, DSB, biol rep1

description: Library name: yen1ON biol rep1


title: yen1 mus81, DSB, biol rep2

description: Library name: yen1 mus81 biol rep2

value: yen1 mus81


title: mph1, DSB, biol rep2

description: Library name: mph1 biol rep2


title: yen1 mus81, DSB, biol rep1

description: Library name: yen1 mus81 biol rep1


title: Muscle, Young, biol rep1, GEX

description:
10x Genomics
Young_1_barcodes.tsv.gz
Young_1_features.tsv.gz
Young_1_matrix.mtx.gz


title: rad54, DSB, biol rep1

description: Library name: rad54 biol rep1


title: rad54, DSB, biol rep2

description: Library name: rad54 biol rep2


title: rad52, DSB, biol rep4

description: Library name: rad52 biol rep4


title: Dorsal, Ventral D35, rep2, HTO

city: Frederick

first: Tomozumi

last: Imamichi

state: MD

address: Frederick National Laboratory for Cancer Research

department: Applied and Developmental Research Directorate

institute: National Institutes of Health

description:
Library name: Dorsal_Ventral_D35_HTO
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
BCL Convert Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files from BCL files together with barcodes information. Transcript reads were analyzed using 10x Genomics Cell Ranger (v7.2.0) with GRCh38-2020-A as the reference genome, to obtain single-cell gene expression count matrices. For quality control, we excluded cells predicted to be multiplets by the Cell Ranger pipeline, as well as cells that had <1000 detected genes and >10% mitochondrial transcripts.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz. features_reference.csv
Library strategy: CITE-seq

molecule: other

source_name: Cerebral Organoid

extract_protocol:
Single-cell suspensions were processed using the 10X Genomics Chromium platform, and scRNA-seq libraries were sequenced according to the manufacturer’s protocol (Illumina NovaSeqXPlus).
Each paired-end read contains a cell barcodes and a UMI in Read 1, and the transcript-specific read in Read 2 with a read length of 151 nt.  Separately, each cell generates a hashtag oligo count vector for the hashtags used, allowing the cells to be assigned to the organoid samples they come from.

value: Cerebral Organoid

tag: cell line

value: stem cells

value: iPSC

tag: treatment

value: mixed samples

tag: hto

value: 10X CMO305 (Dorsal_C1_D35_rep2), 10X CMO306 (Ventral_C1_D35_rep2), 10X CMO307 (Dorsal_M1_D35), 10X CMO308 (Ventral_M1_D35),


title: rad52, DSB, biol rep2

description: Library name: rad52 biol rep2


title: Ventral, D77, HTO

description:
Library name: Ventral_D77_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0251 anti-human Hashtag 1 (Ventral_C2_D77),  TotalSeq-B0252 anti-human Hashtag 2 (VentraL_C1_D77),  TotalSeq-B0253 anti-human Hashtag 3 (Ventral_M1_no_rap_D77),  TotalSeq-B0254 anti-human Hashtag 4 (Ventral_M1_rap_D77),  TotalSeq-B0255 anti-human Hashtag 5 (Ventral_M2_no_rap_D77),  TotalSeq-B0256 anti-human Hashtag  (Ventral_M2_rap_D77)


title: Dorsal, Ventral,  D35, rep2, GEX

description:
Library name: Dorsal_Ventral_D35_mRNA
polyA RNA (GEX)

library_source: transcriptomic single cell

data_processing:
BCL Convert Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files from BCL files together with barcodes information. Transcript reads were analyzed using 10x Genomics Cell Ranger (v7.2.0) with GRCh38-2020-A as the reference genome, to obtain single-cell gene expression count matrices. For quality control, we excluded cells predicted to be multiplets by the Cell Ranger pipeline, as well as cells that had <1000 detected genes and >10% mitochondrial transcripts.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz. features_reference.csv

molecule: polyA RNA


title: rad52, DSB, biol rep3

description: Library name: rad52 biol rep3


title: rad52, DSB, biol rep1

description: Library name: rad52 biol rep1


title: Ventral, D77, GEX

description:
Library name: Ventral_D77_mRNA
polyA RNA (GEX)


title: Ventral, D35, rep1, HTO

description:
Library name: Ventral_D35_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0251 anti-human Hashtag 1 (Ventral_C2_D35),  TotalSeq-B0252 anti-human Hashtag 2 (Ventral_C1_D35_rep1),  TotalSeq-B0253 anti-human Hashtag 3 (Ventral_M1_no_rap_D35),  TotalSeq-B0254 anti-human Hashtag 4 (Ventral_M1_rap_D35),  TotalSeq-B0255 anti-human Hashtag 5 (Ventral_M2_no_rap_D35),  TotalSeq-B0256 anti-human Hashtag  (Ventral_M2_rap_D35)


title: mph1, DSB, biol rep1

description: Library name: mph1 biol rep1


title: rad51, DSB, biol rep4

description: Library name: rad51 biol rep4


title: Ventral, D35, rep1, GEX

description:
Library name: Ventral_D35_mRNA
polyA RNA (GEX)


title: Dorsal, D77, HTO

description:
Library name: Dorsal_D77_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0251 anti-human Hashtag 1 (Dorsal_C2_D77),  TotalSeq-B0252 anti-human Hashtag 2 (Dorsal_C1_D77),  TotalSeq-B0253 anti-human Hashtag 3 (Dorsal_M1_no_rap_D77),  TotalSeq-B0254 anti-human Hashtag 4 (Dorsal_M1_rap_D77),  TotalSeq-B0255 anti-human Hashtag 5 (Dorsal_M2_no_rap_D77),  TotalSeq-B0256 anti-human Hashtag  (Dorsal_M2_rap_D77)


title: rad51, DSB, biol rep3

description: Library name: rad51 biol rep3


title: Dorsal, D35, rep1, HTO

description:
Library name: Dorsal_D35_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0251 anti-human Hashtag 1 (Dorsal_C2_D35),  TotalSeq-B0252 anti-human Hashtag 2 (Dorsal_C1_D35_rep1),  TotalSeq-B0253 anti-human Hashtag 3 (Dorsal_M1_no_rap_D35),  TotalSeq-B0254 anti-human Hashtag 4 (Dorsal_M1_rap_D35),  TotalSeq-B0255 anti-human Hashtag 5 (Dorsal_M2_no_rap_D35),  TotalSeq-B0256 anti-human Hashtag  (Dorsal_M2_rap_D35)


title: rad51, DSB, biol rep2

description: Library name: rad51 biol rep2


title: Dorsal, D77, GEX

description:
Library name: Dorsal_D77_mRNA
polyA RNA (GEX)


title: Dorsal, D35, rep1, GEX

description:
Library name: Dorsal_D35_mRNA
polyA RNA (GEX)


title: exo1, DSB, biol rep2

description: Library name: exo1 biol rep2


title: rad51, DSB, biol rep1

description: Library name: rad51 biol rep1


title: WT_EMT_1h_rep2

city: Heidelberg

first: Bastian

last: Linder

address: Meyerhofstraße 1

department: Genome Biology Unit

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

data_processing:
reads were adapter-trimmed and aligned using STAR. Expression levels at 0h, 1h and 3h of actinomycin D treatment were calculated and RNA decay rates were calculated using custom R scripts.
Assembly: GRCm38
Supplementary files format and content: tsv file with mRNA decay rates

molecule: total RNA

organism: Mus musculus

source_name: Embryonic Stem Cells

growth_protocol: mES cells were grown in knockout DMEM (ThermoFisher, 10829018) supplemented with 15% heat-inactivated FBS, 10U/mL Penicillin-Streptomycin (ThermoFisher, 15140122), 1x GlutaMax (ThermoFisher, 35050061), 500 µM β-mercaptoethanol (ThermoFisher, 21985023), 1x Nonessential amino acid (ThermoFisuer, 11140076), 103 U/mL LIF (MilliporeSigma, ESG1107), 3 uM CHIR99021 (ThermoFisher, 501013679), and 1 uM PD0325901 (ThermoFisher, 501013147).  Cells were seeded on a plate coated with EmbryoMax™ 0.1% Gelatin Solution (MilliporeSigma, ES-006-B).  Cells were passaged every day using with TrypLE Express (ThermoFisuer, 12604039) according to the manufacture’s instruction.

extract_protocol:
Total RNA was collected using TRIzol reagent (ThermoFisher, 10296010) according to the manufacture’s instruction.  Purified RNA was quantified using Qubit4 Fluorometer (ThermoFisher).  1 µg of RNA was mixed with ERCC RNA Spike-In Mix (ThermoFisher, 4456740).  Ribosomal RNA was first depleted using NEBNext®rRNA Depletion Kit(NEB, E6310X).
NEBNext®Ultra™II Directional RNA Library Prep Kit (NEB, E7760L)

treatment_protocol: Cells were grown in the absence or the presence of 10 ug/mL actinomycin D (SigmaAldrich, A1410-10MG) for 1 or 3 h.

tag: strain

value: Embryonic Stem Cells

value: WT

tag: emetine treatment

value: emetine

tag: actinomycind time


title: WT_EMT_3h_rep2


title: WT_EMT_0h_rep2


title: IMR-90, Ctrl

data_processing:
The raw data were first pre-processed by initial quality assessment, adapters trimming, and low-quality filtering and then mapped to the mouse reference genome (mm10) using bowtie2, and only the non-redundant reads were kept.
The protein DNA-binding peaks (sites) were identified using MACS2. During the peak calling, candidate peaks were compared with the background, dynamic programming was used to determine λ of Poisson distribution, and the P-value cutoff was set to 0.001 for JunB ChIP-Seq experiment.
Assembly: hg38
Supplementary files format and content: *.bedGraph
Supplementary files format and content: *.narrowPeak
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN assay was conducted according to the manufacturer’s instructions. (Cell Signaling Technology, 86652)
Library construction was according to the manufacturer’s instructions(NEB, E7645S).

value: Human fibroblast

tag: chip antibody

value: JUNB antibody (CST, #3753)

value: No treatment


title: IMR-90, ETO

value: ETO-treated


title: WT_noEMT_3h_rep2

value: mock


title: WT_noEMT_1h_rep2


title: WT_EMT_3h_rep1


title: mre11-H125N, DSB, biol rep2

description: Library name: mre11-H125N biol rep2

value: mutant isogenic to JKM139


title: WT_EMT_1h_rep1


title: WT_noEMT_0h_rep2


title: mre11-H125N, DSB, biol rep1

description: Library name: mre11-H125N biol rep1


title: H2

type: genomic

city: Dublin

first: Alexandra

middle: V

last: Tuzova

address: Belfield

country: Ireland

institute: University College Dublin

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Samples were scanned using an Illumina iScan system

data_processing: Raw IDAT files were preprocessed and converted to β-values using the SeSame package.

label: Cy5 and Cy3

source_name: FFPE tissue

label_protocol: Standard Illumina Protocol

growth_protocol: Material was mantained as FFPE tissue slides prior to extraction

extract_protocol: Genomic DNA extraction was performed using the QIAamp DNA FFPE Tissue kit

tag: gender

value: Male

tag: gleason score (macrodissected tissue)

tag: tnm classification (radical prostatectomy)

tag: assigned risk group

value: High-Risk Prostate Cancer

value: prostate cancer tissue sample


title: WT_EMT_0h_rep1


title: WT_noEMT_3h_rep1


title: sae2, DSB, biol rep4

description: Library name: sae2 biol rep4


title: WT_noEMT_0h_rep1


title: WT_noEMT_1h_rep1


title: sae2, DSB, biol rep3

description: Library name: sae2 biol rep3


title: METTL3KO_EMT_3h_rep2


title: exo1, DSB, biol rep1

description: Library name: exo1 biol rep1


title: METTL3KO_EMT_1h_rep2


title: H9


title: sae2, DSB, biol rep2

description: Library name: sae2 biol rep2


title: METTL3KO_EMT_0h_rep2


title: H11


title: H12


title: H7


title: METTL3KO_noEMT_3h_rep2


title: H1


title: METTL3KO_noEMT_1h_rep2


title: H14


title: L7

value: Low-Risk Prostate Cancer


title: H8


title: L13


title: METTL3KO_EMT_0h_rep1


title: METTL3KO_EMT_1h_rep1


title: sgs1, DSB, biol rep2

description: Library name: sgs1 biol rep2


title: METTL3KO_EMT_3h_rep1


title: L12


title: WT, DSB, biol rep6

description: Library name: WT biol rep6

source_name: S. cerevisiae haploid strain

value: S. cerevisiae haploid strain


title: L2


title: H5


title: sae2, DSB, biol rep1

description: Library name: sae2 biol rep1


title: L11


title: L10


title: H4


title: ath_ev_rep3

city: New York

first: Ji

last: Huang

state: NY

address: 12 Waverly Place

department: Center for Genomics & Systems Biology

institute: New York University

data_processing:
Raw fastq files were trimmed by fastp 0.21.0. The clean fastq ﬁles were aligned to TAIR10 genome using hisat2.2.1 with default parameters. The read counts matrix was generated by featureCounts v2.0.1 from the aligned bam ﬁles. The DESeq2 was used to identify differentially expressed genes between AtDIV1 and empty vector with False Discovery Rate (FDR) less than 0.05.
Assembly: TARI10
Supplementary files format and content: tab-delimited text file includes the DE genes from DESeq2.

organism: Arabidopsis thaliana

source_name: 4-week old rosette leaves

growth_protocol: Arabidopsis (Col-0) was grown in the growth chamber for four weeks.

extract_protocol:
Rosette leaves were harvested, sliced with a razor, and incubated in enzyme solution (1 % cellulase R10, 0.2 % macerozyme R10 (Yakult Honsha), 0.4 M mannitol, 20 mM MES pH 5.7, 20 mM KCl, 10 mM CaCl2, and 0.1 % BSA) for 90 min. Cells were strained through a 70 µM filter, collected by centrifugation at 300 g, and washed with W5 buffer (150 mM NaCl, 125 mM CaCl2, 5 mM KCl, 2 mM MES pH 5.7, 5 mM glucose). Cells were collected by centrifugation and transferred to MMg solution (400 mM mannitol, 10 mM MgCl2, 4 mM MES pH 5.7) for transfection. Cells were diluted to a cell density of 6 x 105 cells/ml with MMg and mixed with 20 µl plasmid DNA (20-50 µg DNA) in a 2 mL microcentrifuge tube. 120 ul PEG solution (40 % PEG4000, 200 mM mannitol, 100 mM CaCl2) was added to the cells and mixed by inversion. After incubating for 2-5 min, W5 buffer was added, and the cells were washed twice in W5 buffer. Cells were then transferred to a 48-well plate and incubated overnight with shaking
Illumina library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L) with NEBNext Multiplex Oligos for Illumina (NEB #E6609S) according to the manufacturer’s instructions.

value: 4-week old rosette leaves


title: H10


title: METTL3KO_noEMT_0h_rep2


title: METTL3KO_noEMT_1h_rep1


title: sgs1, DSB, biol rep1

description: Library name: sgs1 biol rep1


title: H6


title: H3


title: B13

value: Histologically Benign Prostate

value: prostate tissue sample


title: ath_ev_rep4


title: ath_ev_rep2


title: METTL3KO_noEMT_0h_rep1

value: Embryonic Stem Cells


title: WT, DSB, biol rep3

description: Library name: WT biol rep3

value: WT


title: ath_ev_rep1


title: METTL3KO_noEMT_3h_rep1


title: 19_D30_Skin

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

description: 10X genomics

data_processing:
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10x Genomics) to demultiplex FASTQ reads, align reads to the mouse reference genome (mm10, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: mm10
Supplementary files format and content: raw_feature_bc_matrix.h5 files includes the UMI counts for all droplets for each sample in .h5 format

source_name: Skin

extract_protocol:
For Lymph nodes, organs were mashed through 70µm cell strainers before lysed with RBC lysis buffer (00-4333-57; eBioscience). For ear and tail skin, separated dorsal and ventral halves were minced and digested at 37 °C for 30 min, with HBSS solution with 1 mg/ml collagenase A (11088785103; Roche) and 40 μg/ml DNase I (10104159001; Roche) before being filtered through 70µm cell strainers. Cells were washed 3 times and kept in PBS supplemented with 2% FBS. OT-1 T cells were then sorted by FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

tag: timepoint


title: L6


title: WT, DSB, biol rep2

description: Library name: WT biol rep2


title: WT, DSB, biol rep5

description: Library name: WT biol rep5


title: L9


title: WT, DSB, biol rep4

description: Library name: WT biol rep4


title: L1


title: L8


title: ath_div1_rep4


title: B12


title: L4


title: 18_D60_Skin

description: 10X genomics


title: 17_D30_Skin

description: 10X genomics


title: YY172, DSB, , biol rep 1

description: Library name: YY172 biol rep 1


title: ath_div1_rep2


title: QL22, DSB, , biol rep 1

description: Library name: QL22 biol rep 1


title: 16_D60_LN

description: 10X genomics

source_name: lymph node

value: lymph node


title: WT, DSB, biol rep1

description: Library name: WT biol rep1


title: 15_D30_LN

description: 10X genomics


title: ath_div1_rep1


title: 14_D45_Skin

description: 10X genomics


title: ath_div1_rep3


title: QL21, DSB, , biol rep 1

description: Library name: QL21 biol rep 1


title: QL20, DSB, , biol rep 1

description: Library name: QL20 biol rep 1


title: EGFP 3 week Mouse liver #2

city: Woburn

first: Hsin-I

last: Jen

state: Massachusetts

address: 19 presidential way

department: Analytical Development

institute: Ultragenyx

data_processing:
CCS reads with length >200 bp and average quality score of 99% were used for mapping and alignment. Reference sequences of expression cassette, residual plasmid DNA were used for mapping.
To get the size of residual plasmid DNA and residual host cell DNA, CCS reads were first mapped to expression cassette (excluding ITR sequences) by MiniMap2 and unmapped reads were extracted by Samtools and mapped to plasmid backbone sequence including AAV2 Rep, Hu37 Cap, KanR and the rest of the Ad genes from helper plasmids. The unmapped reads were then mapped to human genomic DNA sequences. Sizes of reads that mapped to different reference sequences were checked by FastQC. The reads mapped to different impurities and human genome DNA sequences were remapped to ITR sequences via MiniMap2 to quantify the percentage of reads containing ITR.
To identify the genomic loci for the impurity host cell DNA, the PacBio reads that mapped to the human genome (hg38) were annotated using Homer annotatePeak.pl. The results were then further analyzed using JMP.
For RNA-seq, Adapters and short reads (<50 bps) and read with more than 4 ‘Ns’ were removed using Flexbar FASTQ Read Trimmer. The quality and size of the reads were checked with FastQC. The processed reads were mapped to mouse genome mm10 using Bowtie2 FASTQ Read Mapping. The unmapped reads were extracted using Samtools and Bedtools. The unmapped reads were then mapped to EGFP reference genome using Bowtie2 FASTQ Read Mapper, to identify reads mapped to EGFP. Same Samtools and Bedtools commands were used to extract reads that are not mapped to either mouse genome mm10 or EGFP reference genome. The FASTQ files for the unmapped reads were then mapped to pAAV2/8 and then to pAdF6 using Bowtie2 FASTQ Read Mapper.
Assembly: hg38
Supplementary files format and content: txt - mapped bed files

source_name: Liver

extract_protocol:
2 weeks and 3 weeks later, mice were perfused, and liver tissues were isolated. The whole median lobe was collected. Three 3-4mm punches from the Median Lobe were collected and placed in separate cryotubes, snap frozen in liquid nitrogen, and stored in -80°C. Remains from the median lobe were placed in a cryotube, snap frozen in liquid nitrogen, and stored in -80°C.
To prepare viral DNA for long-read sequencing,100 uL of rAAV material was digested in proteinase K reaction at 55°C for 30 minutes followed by deactivation of proteinase K at 80°C for 15 minutes, and gradually dropping the temperature to 4°C to allow single stranded DNA to anneal to double stranded DNA. After this, DNA was purified by Monarch DNA and PCR Purification Kit (NEB, Cat: #T1130) following the manufacturing protocol starting mixture of one volume of sample buffer and three volumes of binding buffer.  DNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and sample purity and integrity was checked using Nanodrop and Agilent TapeStation. Following quality control, PacBio SMRTbell amplicon libraries for PacBio Sequel were constructed using SMRTbell prep kit 3.0 (PacBio, Menlo Park, CA, USA) using the manufacturer recommended protocol. Primer annealing, polymerase binding, and complex cleanup was performed using the Sequel binding kit 3.1 & cleanup beads (PacBio) and loaded onto PacBio Sequel IIe. Sequencing was performed on PacBio Sequel IIe SMRT cell with AAV Mode enabled. Sequel IIe sequencing generated subread files, as well as HiFi reads via on-board circular consensus sequencing (CCS) analysis.RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Cat: 74881). RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). ERCC Ex-fold RNA reagent (Cat: 4456739) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. Samples were treated with TURBO DNase (Thermo Fisher Scientific, Cat: AM2238) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Cat: 334386), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina (NEB, Cat: E7770) by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: C56BL/6 adult male mice between 7 to 8 weeks old were used for this study. Individual doses for AAVhu37-CAG-EGFP were calculated based on individual body weights for intravenous tail vein administration. Each mice received 2.0E14 vg/kg.

value: Liver

value: All Liver cells

value: AAVhu37-GFP treated for 3 weeks


title: B11


title: 13_D20_Skin

description: 10X genomics


title: Leaf from family NE74, plant #8

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

description:
Library name: E74.8_L
Leaf from Family NE74, plant #8, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

data_processing:
Processed file "MuSeq2 count data for bulk pollen outcross experiments.csv.gz" was generated by mapping the Mu sequencing reads to the W22 V2 genome using Bowtie2 and bam files were converted to txt files which were then imported into R. Sample txt files were filtered and combined into a large matrix, containing unique molecules detected per sample per genome location across all MuSeq2 samples in the dataset.
Processed file "Transmitted Mu insertions from bulk pollen outcross experiments.csv.gz" was generated from "MuSeq2 count data for bulk pollen outcross experiments.csv.gz" by normalizing molecule counts to CPM, and called inherited insertions if they were at a CPM >=500 in a tissue and >=200 CPM in the matched tissue. For parental endosperm samples, inherited insertions were called for insertions present in the offspring and >=200 CPM in the parental endosperm.
Assembly: W22 Version 2
Supplementary files format and content: Processed data file "MuSeq2 count data for bulk pollen outcross experiments.csv.gz is a csv table generated in R, containing the number of molecules detected per sample (column) per genome location (row).
Supplementary files format and content: Processed data file "Transmitted Mu insertion from bulk pollen outcross experiment.csv.gz" is a csv table generated in R, consisting of samples in the columns and Mu insertion locations in the rows. 1's indicate that the insertion site is an inherited site in that sample, and 0's indicate that the insertion site is not inherited in that sample.

organism: Zea mays

source_name: Leaf

growth_protocol: All Mu-Active seeds were chipped and grown in soil. The first leaf tissue was harvested 10-13 days after sowing, at the V3 stage seedling.

extract_protocol:
DNA was extracted from leaves using Qiagen Dneasy plant mini kit according to manufacturers instructions. DNA from Endosperm samples were extracted using a modified CTAB DNA extraction protocol (see methods). All DNA samples were then sheared to a mean of 1000 bp using a Covaris E220 Evolution.
Libraries were constructed for all samples by first ligating a custom Museq Adapter, and then subsequent PCR reactions to selectively amplify genomic regions adjacent to Mu insertions. See Methods for details

value: Leaf

tag: sample group

value: Leaf from family NE74


title: Leaf from family NE74, plant #7

description:
Library name: E74.7_L
Leaf from Family NE74, plant #7, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

tag: tissue


title: EGFP 3 week Mouse liver #1


title: QL19, DSB, , biol rep 1

description: Library name: QL19 biol rep 1

value: mutant isogenic to JKM139


title: EGFP 3 week Mouse liver #3


title: 12_D45_LN

description: 10X genomics


title: Leaf from family NE74, plant #6

description:
Library name: E74.6_L
Leaf from Family NE74, plant #6, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: B10

value: Male


title: 10_D5_Skin

description: 10X genomics


title: QL17, DSB, , biol rep 1

description: Library name: QL17 biol rep 1


title: 11_D20_LN

description: 10X genomics


title: EGFP 2 week Mouse liver #2

value: AAVhu37-GFP treated for 2 weeks


title: QL18, DSB, , biol rep 1

description: Library name: QL18 biol rep 1


title: Leaf from family NE74, plant #5

description:
Library name: E74.5_L
Leaf from Family NE74, plant #5, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: EGFP 2 week Mouse liver #3


title: Leaf from family NE74, plant #4

description:
Library name: E74.4_L
Leaf from Family NE74, plant #4, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: B8


title: EGFP 2 week Mouse liver #1


title: QL16, DSB, , biol rep 1

description: Library name: QL16 biol rep 1


title: 9_D5_LN

description: 10X genomics


title: Control Mouse liver #3

value: no


title: 8_D15_Skin

description: 10X genomics


title: Leaf from family NE74, plant #2

description:
Library name: E74.2_L
Leaf from Family NE74, plant #2,  generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: B7


title: Leaf from family NE74, plant #3

description:
Library name: E74.3_L
Leaf from Family NE74, plant #3, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: QL13, DSB, , biol rep 1

description: Library name: QL13 biol rep 1


title: Leaf from family NE73, plant #9

description:
Library name: E73.9_L
Leaf from Family NE73, plant #9, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

value: Leaf from family NE73


title: HEK293_total_RNA_miCLIP

data_processing:
reads were adapter-trimmed and aligned using STAR. miCLIP data analysis was performed using custom snakemake and R scripts.
Assembly: hg38
Supplementary files format and content: bed file of called m6A sites

growth_protocol: HEK293T cells were cultured in 15cm dishes in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37C and 5% CO2.

extract_protocol:
total RNA was extracted using 10ml Trizol
libraries were constructed using the iCLIP cloning process, as previously described (see GSE63753). Replicates were barcoded using barcoded iCLIP RT primers.


title: QL14, DSB, , biol rep 1

description: Library name: QL14 biol rep 1


title: Leaf from family NE74, plant #1

description:
Library name: E74.1_L
Leaf from Family NE74, plant #1, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: 7_D10_Skin

description: 10X genomics


title: 5_D0_Naive

description: 10X genomics


title: B9


title: Control Mouse liver #1


title: 6_D10_LN

description: 10X genomics


title: Control Mouse liver #2


title: JL116, DSB, , biol rep 1

description: Library name: JL116 biol rep 1


title: HCT116_Rep2_Mouse3_T1_Cas9

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

data_processing:
Sequenced files were demultiplexed from illumina
Read counts were calculated using the package from Li, et al. Genome Biology 15:554 (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Library strategy: amplicon sequencing

source_name: Colon

growth_protocol: 7x10^8 cells were infected at an MOI of 0.3 with a viral custom library containing 2 guides for each of the selected SDL hits with non-targeting controls as explained in Cunningham et al.  Infected cells were selected for with puromycin.  T0 replicates (x2) of 2.5x10^7 cells were collected and injected into mice. For replicate 1, four mice was used and for replicate 2, three mice were used for both +/- Cas9 cells

extract_protocol:
genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194)
libraries were constructed following the previously described method in Shalem O et al Science 2014

treatment_protocol: invivo pooled screen of the selected sgRNAs were treated as explained in Cunningham et al

value: Colon

tag: condition

value: T1 Biological Replicate 2 Technical Replicate 3

value: With Cas9


title: B4

value: Histologically Benign Prostate

value: prostate tissue sample


title: QL12, DSB, , biol rep 1

description: Library name: QL12 biol rep 1

tag: cell type


title: 4_D25_Skin

description: 10X genomics

value: Skin


title: Leaf from family NE73, plant #7

description:
Library name: E73.7_L
Leaf from Family NE73, plant #7, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

tag: genotype


title: HCT116_Rep2_Mouse2_T1_Cas9

tag: cell line

value: T1 Biological Replicate 2 Technical Replicate 2


title: Leaf from family NE73, plant #8

description:
Library name: E73.8_L
Leaf from Family NE73, plant #8, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: JL133, DSB, , biol rep 1

description: Library name: JL133 biol rep 1


title: B5


title: B3


title: Leaf from family NE73, plant #4

description:
Library name: E73.4_L
Leaf from Family NE73, plant #4, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: JL134, DSB, , biol rep 1

description: Library name: JL134 biol rep 1


title: 3_D25_LN

description: 10X genomics

value: lymph node


title: JL88, DSB, , biol rep 1

description: Library name: JL88 biol rep 1


title: 1_D2_LN

description: 10X genomics


title: Leaf from family NE73, plant #2

description:
Library name: E73.2_L
Leaf from Family NE73, plant #2, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: QL15, DSB, , biol rep 1

description: Library name: QL15 biol rep 1


title: Y7

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

country: China

institute: Tsinghua University

description: small RNA-seq of  homo sapiens: oral cancer patient's plasma; Provided by Beijing Stomatological Hospital (CMU, Beijing).

data_processing:
Clean fastq files were sequentially mapped to human transcriptome by Bowtie2 v2.3.5 (parameters: -k 100 --norc --end-to-end --no-unal): rRNA, primary miRNA, lncRNA, mRNA, piRNA, snoRNA, snRNA, srpRNA, tRNA, transcript of unknown coding potential RNA (TUCP RNA), and Y RNA (yRNA).
Cell-free RNA peak bed file for each sample were called from bam file by cfPeak v1.0.0 (parameters: call_peaks_localmax --boundary background --mode local --max-iter 100 --permutate-pval 0.05 --poisson-pval 0.05 --bin-width 10 --min-peak-length 10 --max-peak-length 200 --thread 6 --decay 0.5 --min-cov 2).
Recurrent/consensus peak bed file was obtained by merging all peak regions in each sample above given threshold of sample recurrence.
Recurrent/consensus peak count matrix file was obtained by counting all reads in recurrent/consensus peak file and merging all samples.
Assembly: hg38
Supplementary files format and content: Peak bed.txt file in each sample: transcript, start, end, name, probability to be false peak (0-1), strand
Supplementary files format and content: Recurrent/consensus peak count matrix file: value represent read count in each peak regions; first column represents peak name, other columns represent all sample IDs

source_name: plasma

extract_protocol:
Cell-free RNAs were extracted using miRNeasy serum/plasma miRNA isolation kit (QIAGEN, Shanghai, China), and DNA contamination was removed by Recombinant DNase I (RNase-free) (TAKARA, Beijing, China).
Small libraries were prepared according to the manual of QIAseq miRNA library kit (QIAGEN, Shanghai, China).

value: plasma

tag: subject status

value: patient with oral squamous cell carcinoma (OSCC)

value: F

tag: age

value: Metastatic

tag: molecule subtype

value: cell-free small RNA


title: HCT116_Rep2_Mouse1_T1_Cas9

value: T1 Biological Replicate 2 Technical Replicate 1


title: 2_D15_LN

description: 10X genomics


title: Leaf from family NE72, plant #9

description:
Library name: E72.9_L
Leaf from Family NE72, plant #9, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

value: Leaf

value: Leaf from family NE72


title: B6

value: Male


title: Leaf from family NE73, plant #3

description:
Library name: E73.3_L
Leaf from Family NE73, plant #3, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

value: Leaf from family NE73


title: HCT116_Rep1_Mouse3_T1_Cas9

value: Colon

value: T1 Biological Replicate 1 Technical Replicate 3


title: HCT116_Rep1_Mouse4_T1_Cas9

value: T1 Biological Replicate 1 Technical Replicate 4

value: With Cas9


title: Leaf from family NE73, plant #1

description:
Library name: E73.1_L
Leaf from Family NE73, plant #1, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: YY529, DSB, , biol rep 2

description: Library name: YY529 biol rep 2

value: mutant isogenic to JKM139


title: YY529, DSB, -, biol rep 1

description: Library name: YY529 biol rep 1 exp1


title: B2

value: Histologically Benign Prostate

value: prostate tissue sample


title: HCT116_Rep1_Mouse2_T1_Cas9

value: T1 Biological Replicate 1 Technical Replicate 2


title: HCT116_Rep1_Mouse1_T1_Cas9

value: T1 Biological Replicate 1 Technical Replicate 1


title: JL69, DSB, , biol rep 3

description: Library name: JL69 biol rep 3


title: Leaf from family NE72, plant #8

description:
Library name: E72.8_L
Leaf from Family NE72, plant #8, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: Leaf from family NE72, plant #5

description:
Library name: E72.5_L
Leaf from Family NE72, plant #5, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: Y6

value: plasma

value: patient with oral squamous cell carcinoma (OSCC)

value: F


title: HCT116_Rep1_T0_Cas9

value: T0 Timepoint Replicate 1


title: Y4

value: M

value: Metastatic

value: cell-free small RNA


title: B1

value: Male


title: dnm1, DSB, , biol rep 2

description: Library name: dnm1 biol rep 2


title: HCT116_Rep2_T0_Cas9

value: Colon

value: T0 Timepoint Replicate 2


title: HCT116_Rep2_Mouse3_T1_noCas9

value: T1 Biological Replicate 2 Technical Replicate 3

value: No Cas9


title: Y3


title: Y2


title: Leaf from family NE72, plant #4

description:
Library name: E72.4_L
Leaf from Family NE72, plant #4, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

value: Leaf

value: Leaf from family NE72


title: dnm1, DSB, , biol rep 1

description: Library name: dnm1 biol rep 1

value: mutant isogenic to JKM139


title: HCT116_Rep2_Mouse2_T1_noCas9

value: T1 Biological Replicate 2 Technical Replicate 2


title: Leaf from family NE72, plant #3

description:
Library name: E72.3_L
Leaf from Family NE72, plant #3, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: Y1


title: Y5


title: Leaf from family NE72, plant #2

description:
Library name: E72.2_L
Leaf from Family NE72, plant #2, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: Leaf from family NE72, plant #1

description:
Library name: E72.1_L
Leaf from Family NE72, plant #1, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: mgm1, DSB, , biol rep 1

description: Library name: mgm1 biol rep 1


title: W7

value: Localized


title: HCT116_Rep1_Mouse4_T1_noCas9

value: T1 Biological Replicate 1 Technical Replicate 4


title: YY529, DSB, , biol rep 1

description: Library name: YY529 biol rep 1


title: HCT116_Rep1_Mouse3_T1_noCas9

value: T1 Biological Replicate 1 Technical Replicate 3


title: Leaf from family NE71, plant #8

description:
Library name: E71.8_L
Leaf from Family NE71, plant #8, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

value: Leaf from family NE71


title: W5

value: plasma

value: patient with oral squamous cell carcinoma (OSCC)


title: Leaf from family NE71, plant #6

description:
Library name: E71.6_L
Leaf from Family NE71, plant #6, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: Leaf from family NE71, plant #7

description:
Library name: E71.7_L
Leaf from Family NE71, plant #7, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: W4

value: M


title: HCT116_Rep1_Mouse1_T1_noCas9

value: T1 Biological Replicate 1 Technical Replicate 1


title: W3

value: F

value: cell-free small RNA


title: JL19, DSB, , biol rep 3

description: Library name: JL19 biol rep 1 exp12


title: HCT116_Rep1_Mouse2_T1_noCas9

value: Colon

value: T1 Biological Replicate 1 Technical Replicate 2


title: JL19, DSB, , biol rep 1

description: Library name: JL19 biol rep 1 exp10


title: W2


title: Leaf from family NE71, plant #4

description:
Library name: E71.4_L
Leaf from Family NE71, plant #4, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: HCT116_Rep1_T0_noCas9

value: T0 Timepoint Replicate 1

value: No Cas9


title: HCT116_Rep2_T0_noCas9

value: T0 Timepoint Replicate 2


title: W6


title: mgm1, DSB, , biol rep 2

description: Library name: mgm1 biol rep 2

value: mutant isogenic to JKM139


title: HCT116_Rep2_Mouse1_T1_noCas9

value: T1 Biological Replicate 2 Technical Replicate 1


title: W1

value: Metastatic


title: JKM139, DSB, MMPB, biol rep 1

description: Library name: JKM139 biol rep 1 exp11

value: S. cerevisiae haploid strain

tag: treatment


title: JL19, DSB, - , biol rep 1

description: Library name: JL19 biol rep1 exp14


title: Leaf from family NE71, plant #2

description:
Library name: E71.2_L
Leaf from Family NE71, plant #2, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

value: Leaf


title: Leaf from family NE71, plant #3

description:
Library name: E71.3_L
Leaf from Family NE71, plant #3,  generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen

value: Leaf from family NE71


title: F1, pif1-m2 dna2

data_processing:
A gene-count matrix was then processed using edgeR v3.40.2  for differential expression (DE) analysis in R v 4.2.2 and subsequently gene ontology enrichment analyses were performed using clusterProfiler v4.6.2
Assembly: S288C_reference_genome_R64-1-1_20110203
Supplementary files format and content: gene count matrix.  Each column represents : "Gene ID",  "Raw count"

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen, #217004) according to manufacturer instructions. Briefly, cells were lysed in a bead miller with acid-washed glass beads and Qiagen Buffer RLT. One volume of 70% ethanol was added to the homogenized lysate and the sample was purified using the RNeasy spin column and eluted in RNAse-free water
The cDNA library preparation and sequencing were conducted by Novogene following manufacturer's protocols using a paired-end 150 bp sequencing strategy on the Illumina NovaSeq 6000 platform

tag: strain name

value: pif1-m2 dna2


title: JKM139, DSB, 3mM Fe 6hr, biol rep 2

description: Library name: JKM139 biol rep 2 exp10

value: WT + Fe

value: 3mM Fe 6hr


title: JL19, DSB, MMPB, biol rep 2

description: Library name: JL19 biol rep 1 exp13


title: Leaf from family NE71, plant #5

description:
Library name: E71.5_L
Leaf from Family NE71, plant #5, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: Leaf from family NE71, plant #1

description:
Library name: E71.1_L
Leaf from Family NE71, plant #1, generated from a bulk pollen cross betweena Mu-inactive W22 ear and Mu-Active W22 pollen


title: JKM139, DSB, 3mM Fe 6hr, biol rep 1

description: Library name: JKM139 biol rep 1 exp10


title: E3B, pif1-m2


title: E3, pif1-m2


title: JL19, DSB, , biol rep 2

description: Library name: JL19 biol rep 1 exp11


title: E2, pif1-m2


title: D3, ugo1


title: G1B, pif1-m2 dna2


title: JKM139, DSB, BPS, biol rep 1

description: Library name: JKM139 biol rep 1 exp8

value: WT + BPS

value: 250uM BPS Overnight


title: PVSCs, old

city: Shanghai

first: Xiaoxi

last: Pan

address: 197 Ruijin 2nd Road, Shanghai, China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: sample2
10x Genomics

data_processing:
Single-cell expression data was analyzed using the Cell Ranger Single Cell Software Suite (v1.3.1) to perform quality control, sample de-multiplexing, barcode processing, and single-cell 3’ gene counting).
Assembly: mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: perivascular adipose tissue

extract_protocol:
Young and old perivascular adipose tissues (PVAT) were dissected from aorta and cut into small pieces, which then digested with 0.2% collagenase at 37°C for 45 min. The cell suspension was filtered through 70-um Nylon cell strainer for twice to remove tissue debris. The stromal cells were resuspended in red blood cell lysis buffer and maintained in 1% bovine serum albumin (BSA)/ PBS.
The scRNA-seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol.

value: perivascular adipose tissue

value: primary perivascular stromal cells

value: WT

value: old


title: JKM139, DSB, 10mM GSH 6hr, biol rep 1

description: Library name: JKM139 biol rep 1 exp7

value: 10mM GSH 6hr


title: JKM139, DSB, Room temperature, biol rep 1

description: Library name: JKM139 biol rep 1 exp6

value: Room temperature


title: PVSCs, young

description:
Library name: sample1
10x Genomics

value: young


title: D2, ugo1

value: mutant isogenic to JKM139


title: Endosperm from plant ND66-2, father of family NE71

description:
Library name: D66.2_E
Endosperm sample from the Mu-active father of Family NE71, generated from a cross between a Mu-Inactive W22 ear and Mu-Active W22 pollen

source_name: Endosperm

value: Endosperm


title: Endosperm from family NE74, plant #2

description:
Library name: E74.2_E
Endosperm from Family NE74, plant #2, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm from family NE74


title: D1, ugo1


title: JKM139, DSB, 500nM ConcA 6hr, biol rep 1

description: Library name: JKM139 biol rep 1 exp5

value: S. cerevisiae haploid strain

value: 500nM ConcA 6hr


title: JKM139, DSB, BPS, biol rep 2

description: Library name: JKM139 biol rep 1 exp9


title: Endosperm from plant ND67-51, father of family NE72

description:
Library name: D67.51_E
Endosperm sample from the Mu-active father of Family NE72, generated from a cross between a Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Endosperm from plant ND67-40, father of family NE73

description:
Library name: D67.40_E
Endosperm sample from the Mu-active father of Family NE73, generated from a cross between a Mu-Inactive W22 ear and Mu-Active W22 pollen


title: C2, fzo1


title: Wild-type_colon_fibroblasts [GA05768]

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA v1.18.64 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 10000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: colon

extract_protocol:
Total RNA was extracted from cells using RLT Biffer with 2-ME and a miRNeasy kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: colon

value: PDGFRalpha+ Ly6C+ fibroblasts

value: wild type


title: Endosperm from family NE74, plant #8

description:
Library name: E74.8_E
Endosperm from family NE74, plant #8, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Endosperm from family NE71, plant #5

description:
Library name: E71.5_E
Endosperm from Family NE71, plant #5, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm from family NE71


title: C1B, fzo1


title: Endosperm from plant ND67-35, father of family NE74

description:
Library name: D67.35_E
Endosperm sample from the Mu-active father of Family NE74, generated from a cross between a Mu-Inactive W22 ear and Mu-Active W22 pollen


title: JKM139, DSB, 500nM ConcA 4hr, biol rep 1

description: Library name: JKM139 biol rep 1 exp4

value: 500nM ConcA 4hr


title: eWAT_NC

type: RNA

city: Tokushima-city

first: Masashi

last: Kuroda

state: Tokushima

address: 3-18-15, Kuramoto-cho

institute: Tokushima University

description: *** Submitter states that missing raw files are due to file loss ***

hyb_protocol: Following fragmentation, cRNA was used to probe Genechip Mouse430_2 microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: Scanned with a Hewlett Packard confocal laser scanner and visualized with Affymetrix Genechip 3.1 software.

data_processing: The scaned images were analyzed with Genechip Analysis Suite software version 4.0 (Affymetrix). Processed data were normalized using MAS4.0 algorithm. Since this experiment was conducted 20 years ago, no available raw data currently exists.

label: biotin

source_name: eWAT of a mouse fed a normal chow diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA.

growth_protocol: All the animals were maintained in a room with a controlled temperature (22 ± 2°C), humidity (40-60%), and a 12-h-light, 12-h-dark cycle. they were fed ad libitum on tap water and food (regular food) until dietary challenge was initiated at 9 weeks of age.

extract_protocol: Collected adipose tissue was homogenized with Trizol reagent (invitrogen). The homogenate was mixed with chloroform and centrifuged to separate the aqueous phase containing RNA. Total RNA was precipitated with isopropanol and dissolved in Rnase-free water.

tag: Sex

value: male

tag: strain

value: epididymal white adipose tissue

value: normal chow diet


title: JKM139, DSB, 500nM ConcA 2hr, biol rep 1

description: Library name: JKM139 biol rep 1 exp3

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

value: WT

value: 500nM ConcA 2hr


title: CT26WT_siRNA-1 + VSV

city: Montreal

first: Dominic

middle: Guy

last: Roy

state: Quebec

address: 333 rue St-Antoine E, CRCHUM, Room R10.720

institute: Centre de Recherche du CHUM

description: Gene expression data from CT26WT cells transfected with siRNA-1 and infected with VSV

hyb_protocol: 16hr at 45'C. Washing FS450_0002. Microarray processing was performed by StemCore Laboratories at the Ottawa Hospital Research Institute

scan_protocol: Affymetrix GeneChip Scanner 3000. Microarray processing was performed by StemCore Laboratories at the Ottawa Hospital Research Institute

data_processing: Expression console

label: Biotin Allonamide Triphosphate

source_name: VSV-infected mouse CT26WT cells

label_protocol: Biotin Allonamide Triphosphate. Microarray processing was performed by StemCore Laboratories at the Ottawa Hospital Research Institute.

growth_protocol: CT26 cells were cultured for 24h in DMEM+10%FBS

extract_protocol: RNA was extracted using a RNEasy kit (QIAGEN)

treatment_protocol: Cells were transfected with 50uM of the indicated siRNAs followed by infection with VSV 48h post-transfection. Samples were collected 16h post-infection.

value: siRNA-1 and VSV


title: Endosperm from family NE74, plant #7

description:
Library name: E74.7_E
Endosperm from family NE74, plant #7, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: JKM139, DSB, DMSO 6hr, biol rep 1

description: Library name: JKM139 biol rep 1 exp2

extract_protocol:
All colonies on YP-galactose plates were collected, combined, and mixed vigorously. Approximately 80 μL cells were spun down for isolating genomic DNA. Standard glass beads-phenol/chloroform/isoamyl alcohol (25:24:1) method. The DNA was dissolved in water and adjusted to a concentration of 10 ng/μL. The construction of the amplicon sequencing library was adapted from Illumina’s protocol #15044223 Rev. B. Briefly, the sequencing libraries were constructed with two rounds of PCR using KAPA HiFi HotStart ReadyMix polymerase (Roche, 7958927001). For the first round of PCR, 3.2 μL genomic DNA and 0.5 μL 10 μM primers were used for a total volume of 25 μL. The forward and reverse primers targeting the MATa locus are located 11 bp upstream or 18 bp downstream of the HO cleavage site respectively, containing Illumina adapter sequence and 3 bases unique home index as described (7). The thermocycling conditions were: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. After the first round of PCR, 18μL PCR product was purified with an equal volume of AMPure XP beads (Beckman Coulter, A63880). The DNA was eluted with 52.5 μL of 10 mM Tris (pH 8.5) and used as the templates for the second round of PCR. For the second round of PCR, 5 μl template DNA, 5 μL index primer N7xx and 5 μL index primer S5xx from Nextera XT V2 Index kit (Illumina, FC-131-2001) were used for the total volume of 50 μL. The following conditions were used for the second round of PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. Then, the PCR product was purified with 1.2x volume of AMPure XP beads and eluted with 10 mM Tris pH 8.5. The average size of each sample was measured with TapeStation and the DNA concentration was measured with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850)
The DNA was diluted to a concentration of 4 nM. An equal volume of DNA from ~20 samples was pooled into the library. The 0.2 M NaOH was used to denature the pooled library and PhiX library (Illumina, FC‐110‐3001). After diluting the libraries with pre-chilled HT1 to 12 pM, pooled library and PhiX library were mixed with the ratio 9:1, further denatured by incubating at 96 °C for 2 min and immediately put in an ice-water bath for 5 min

value: DMSO 6hr


title: CT26WT_siRNA control + VSV

description: Gene expression data from CT26WT cells transfected with control siRNA and infected with VSV

value: control siRNA and VSV


title: Quant-seq, CTU2_STM_rep2

description: Library name: CTU2_STM_rep2

data_processing:
Raw sequencing reads were processed by removing the poly-A at the 3’ end using cutadapt (v3.7) after the 12nt UMI were extracted. Clean reads were mapped to human genome(hg38) using STAR (v2.7.10b). PCR duplicate reads were removed using UMI-tools (v1.1.2). Read counts for each gene were quantified using featureCounts (v2.0.3) with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts for each gene in each sample

source_name: HEK 293T

growth_protocol: HEK 293T wild-type cells and derivates thereof were grown in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) with antibiotics and glutamine supplement in a humified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the phenol:chloroform method.
Libraries were prepared using the Qant Seq protocol (Lexogen).

treatment_protocol: Cells were treated with 10µM STM2457 for 4h or 1% DMSO (CTRL) before harvesting.

value: HEK 293T

value: Human embryonic kidney cells

value: CTU2 KO

value: STM treated


title: Endosperm from family NE74, plant #6

description:
Library name: E74.6_E
Endosperm from family NE74, plant #6, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm

value: Endosperm from family NE74


title: eWAT_HFD

source_name: eWAT of a mouse fed a high-fat diet for 7 weeks

value: high-fat diet


title: Quant-seq, CTU2_STM_rep3

description: Library name: CTU2_STM_rep3


title: B2, mgm1

source_name: mutant isogenic to JKM139

value: mutant isogenic to JKM139


title: Quant-seq, CTU2_STM_rep1

description: Library name: CTU2_STM_rep1


title: Endosperm from family NE74, plant #5

description:
Library name: E74.5_E
Endosperm from family NE74, plant #5, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: JKM139, DSB, , biol rep 1

description: Library name: JKM139 biol rep 1 exp1

value: S. cerevisiae haploid strain


title: Otud3_colon_fibroblasts [GA05769]

value: colon

value: PDGFRalpha+ Ly6C+ fibroblasts


title: B1, mgm1


title: Endosperm from family NE74, plant #4

description:
Library name: E74.4_E
Endosperm from family NE74, plant #4, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: JL5, DSB, -, biol rep 1

description: Library name: JL5 biol rep 1

value: spt3 mgm1


title: Quant-seq, CTU2_CTRL_rep3

description: Library name: CTU2_CTRL_rep3

value: untreated


title: Quant-seq, CTU2_CTRL_rep2

description: Library name: CTU2_CTRL_rep2


title: Endosperm from family NE74, plant #3

description:
Library name: E74.3_E
Endosperm from family NE74, plant #3, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: A3B, WT

value: WT


title: A2B, WT


title: JL270, DSB, -, biol rep 2

description: Library name: JL270 biol rep 2

value: aft1 nuc1


title: JL270, DSB, -, biol rep 1

description: Library name: JL270 biol rep 1


title: Endosperm from family NE74, plant #1

description:
Library name: E74.1_E
Endosperm from family NE74, plant #1, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Quant-seq, CTU2_CTRL_rep1

description: Library name: CTU2_CTRL_rep1


title: JL11, DSB, -, biol rep 1

description: Library name: JL11 biol rep 1

value: yku70 mgm1


title: Endosperm from family NE73, plant #9

description:
Library name: E73.9_E
Endosperm from family NE73, plant #9, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm from family NE73


title: B3, mgm1


title: Quant-seq, ELP1_STM_rep3

description: Library name: ELP1_STM_rep3

value: HEK 293T

value: ELP1 KO


title: JL252, DSB, -, biol rep 3

description: Library name: JL252 biol rep 3

value: apn1 apn2 mgm1


title: Endosperm from family NE73, plant #8

description:
Library name: E73.8_E
Endosperm from family NE73, plant #8, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Endosperm from family NE73, plant #7

description:
Library name: E73.7_E
Endosperm from family NE73, plant #7, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Quant-seq, ELP1_STM_rep1

description: Library name: ELP1_STM_rep1

value: Human embryonic kidney cells

value: STM treated


title: Quant-seq, ELP1_STM_rep2

description: Library name: ELP1_STM_rep2


title: Direct RNA sequence of siCtrl HEK293T cell replicate 2

city: GuangZhou

first: Zhijun

last: Ren

address: Sun Yat-sen University

institute: Sun Yat-sen University

description:
Library name: HEK293T_siCtrl_Rep2
Direct RNA sequence

data_processing:
For direct RNA sequencing data, base calling was performed on each raw FAST5 file to generate FASTQ files using Guppy (v3.1.3) in high accurate mode.
The reads with mean quality score exceeded 7 were aligned to human GRCm38/hg38 reference transcriptome (GENCODE V32) using minmap2 (Li, 2018). The multi-mapped reads were removed using samtools (Li et al., 2009). The expression of transcripts was calculated based on uniquely mapped reads.
Subsequently, the reads and nanopore current were mapped to their corresponding positions of transcripts by the eventalign module of Nanopolish (version 0.13.2) (Simpson et al., 2017). Simultaneously, the mean, standard deviation, and dwelling time of ionic current from all the reads mapped to the same continuously segmented 5-mers were extracted by Nanopolish (version 0.13.2) (Simpson et al., 2017). Based on the extracted ionic current signals, m6Aiso (Supplementary related manuscript) was used to predict m6A modification at single-molecular level. Only the GLORI annotated m6A sites with read coverages ≥ 20 and modified reads ≥ 10 in gene level were used for the downstream analyses.
Assembly: hg38
Supplementary files format and content: tab-sparated counts files
Supplementary files format and content: tab-sparated m6A files

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Corning, #10-013-CVRC) supplemented with 10% fetal bovine serum (FBS; QuaCell, #B21001). The cells were maintained at 37 °C in a humidified chamber with 5% CO2 and were verified to be free of mycoplasma contamination.

extract_protocol:
Total RNA was extracted from the HEK293T cell line using TRIzol reagent (Invitrogen, #15596018), according to the manufacturer’s instructions.
RNA concentrations and RNA integrity were measured using a NanoDrop 2000 Spectrophotometer and Agilent 4200 TapeStation, respectively. A 20-μg aliquot of total RNA was subjected to poly(A)+ RNA selection using the Dynabeads mRNA DIRECT purification kit (Invitrogen, #61011) following the manufacturer’s instructions. Subsequently, approximately 500 ng of poly(A)+ RNA was used for direct RNA library preparation. The libraries were generated following the standard ONT SQK-RNA002 protocol with the reverse transcription step included. The libraries were loaded onto R9.4.1 flow cells (ONT, FLO-PRO002) and sequenced on PromethION 2 Solo (ONT, PRO-SEQ002).

treatment_protocol: Small interfering RNAs targeting UPF1 or a non-targeting control siRNA were transfected into the cells 24 h after seeding using RNAiMAX following the manufacturer's instructions at a final concentration of 20 nM. Cells were harvested 48 h after transfection for further analysis.

value: siCtrl


title: Direct RNA sequence of UPF1 knockdown HEK293T cell replicate 2

description:
Library name: HEK293T_siUPF1_Rep2
Direct RNA sequence


title: Quant-seq, ELP1_CTRL_rep3

description: Library name: ELP1_CTRL_rep3


title: Endosperm from family NE73, plant #4

description:
Library name: E73.4_E
Endosperm from family NE73, plant #4, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm


title: JL252, DSB, -, biol rep 1

description: Library name: JL252 biol rep 1

value: mutant isogenic to JKM139


title: Quant-seq, ELP1_CTRL_rep2

description: Library name: ELP1_CTRL_rep2


title: Direct RNA sequence of siCtrl HEK293T cell replicate 1

description:
Library name: HEK293T_siCtrl_Rep1
Direct RNA sequence


title: Endosperm from family NE73, plant #3

description:
Library name: E73.3_E
Endosperm from family NE73, plant #3, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: JL274, DSB, -, biol rep 2

description: Library name: JL274 biol rep 2


title: JL243, DSB, -, biol rep 1

description: Library name: JL243 biol rep 1

value: apn1 apn2


title: Quant-seq, ELP1_CTRL_rep1

description: Library name: ELP1_CTRL_rep1


title: A1, WT

value: S. cerevisiae haploid strain


title: Endosperm from family NE73, plant #2

description:
Library name: E73.2_E
Endosperm from family NE73, plant #2, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: scRNA-Seq-Mex3aWT_4wk_Zone1

first: Rachel

last: Duffié

address: Jerome L Greene Sciene Building

department: Biochemistry and Molecular Biophysics

institute: Columbia University

description: Mex3a flox/flox (Alvarez-Varela et al. 2022) (No Cre Driver) zone 1 dissection (dorsal zone of olfactory epithelium), 4 weeks old

data_processing:
libraries were aligned with 10X Cell Ranger software
Seurat was used to analyze aligned data
Assembly: mm10
Supplementary files format and content: 10X Cell Ranger outs: barcodes.txt
Supplementary files format and content: 10X Cell Ranger outs: features.txt
Supplementary files format and content: 10X Cell Ranger outs: matrix.txt

source_name: main olfactory epithelium

growth_protocol: mice had access to food and water ad libitum

extract_protocol:
cells were isolated using papain enzymatic treatment (Worthington). Cells were extracted as part of the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (samples KO and WT 1 and 2); v3 for the zonal dissection experiment
libraries were created with the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (samples KO and WT 1 and 2); v3 for the zonal dissection experiment

value: main olfactory epithelium

value: zonally dissected olfactory epithelium, many cell types

value: Mex3a flox/flox


title: Quant-seq, WT_STM_rep3

description: Library name: WT_STM_rep3

value: WT


title: JL252, DSB, -, biol rep 2

description: Library name: JL252 biol rep 2


title: Direct RNA sequence of UPF1 knockdown HEK293T cell replicate 1

description:
Library name: HEK293T_siUPF1_Rep1
Direct RNA sequence


title: scRNA-Seq-Mex3aKO_4wk_Zone5

description: Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016), zone 5 dissection (ventral zone of the olfactory epithelium), 4 weeks old

value: Mex3a flox/flox; Foxg1iresCre


title: JL218, DSB, 3mM Fe 6hr, biol rep 3

description: Library name: JL218 biol rep 3 exp1

value: 3mM Fe 6hr


title: Quant-seq, WT_STM_rep2

description: Library name: WT_STM_rep2


title: scRNA-Seq-Mex3aKO_4wk_Zone1

description: Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016), zone 1 dissection (dorsal zone of olfactory epithelium), 4 weeks old


title: Endosperm from family NE72, plant #8

description:
Library name: E72.8_E
Endosperm from family NE72, plant #8, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm from family NE72


title: scRNA-Seq-Mex3aWT_PN12_rep2

description: Mex3a flox/flox (Alvarez-Varela et al. 2022) (No Cre Driver) whole olfactory epithelium postnatal day 12

value: whole olfactory epithelium, many cell types


title: JL218, DSB, 3mM Fe 6hr, biol rep 1

description: Library name: JL218 biol rep 1 exp1


title: Endosperm from family NE72, plant #5

description:
Library name: E72.5_E
Endosperm from family NE72, plant #5, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Quant-seq, WT_CTRL_rep3

description: Library name: WT_CTRL_rep3

value: HEK 293T

value: untreated


title: CT26WT_siRNA-2 + VSV

description: Gene expression data from CT26WT cells transfected with siRNA-2 and infected with VSV

value: siRNA-2 and VSV


title: scRNA-Seq-Mex3aKO_PN12_rep2

description: Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016), whole olfactory epithelium postnatal day 12


title: JL229, DSB, -, biol rep 1

description: Library name: JL229 biol rep 1

value: aft1 grx5


title: scRNA-Seq-Mex3aWT_4wk_Zone5

description: Mex3a flox/flox (Alvarez-Varela et al. 2022) (No Cre Driver) zone 5 dissection (ventral zone of olfactory epithelium), 4 weeks old


title: JL218, DSB, 3mM Fe 6hr, biol rep 2

description: Library name: JL218 biol rep 2 exp1


title: Quant-seq, WT_CTRL_rep2

description: Library name: WT_CTRL_rep2

value: Human embryonic kidney cells


title: Endosperm from family NE72, plant #4

description:
Library name: E72.4_E
Endosperm from family NE72, plant #4, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm


title: scRNA-Seq-Mex3aWT_PN12_rep1


title: Endosperm from family NE73, plant #1

description:
Library name: E73.1_E
Endosperm from family NE73, plant #1, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm from family NE73


title: JL274, DSB, -, biol rep 1

description: Library name: JL274 biol rep 1

value: mutant isogenic to JKM139


title: JL228, DSB, -, biol rep 1

description: Library name: JL228 biol rep 1

value: aft1 mgm1


title: Endosperm from family NE72, plant #3

description:
Library name: E72.3_E
Endosperm from family NE72, plant #3, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Quant-seq, WT_CTRL_rep1

description: Library name: WT_CTRL_rep1


title: CTU2_STM_Di

description: Library name: CTU2_STM_Di

data_processing:
Ribosome profiling reads were processed by clipping the adapter sequence (CTGTAGGCACCATCAAT) using cutadapt (v4.1) and trimming the 3 and 6 randomized nucleotides at the 5' and 3' end, respectively. Processed reads were mapped to ncRNA(rRNA, tRNA, snoRNA, snRNA) using bowtie version 1.2.1.1. Residual reads were uniquely mapped to CDS with 21 nucleotides extension at both ends.
Assembly: hg38
Supplementary files format and content: tab-delimited text files including A site coverage for each codon for each sample
Library strategy: Ribo-Seq

extract_protocol:
Total RNA was extracted using the phenol:chloroform method. Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Disomes were similarly purified by size selection from the same samples. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.
Ribosome-protected footprints were purified from monosome and disome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification. The protocol is published in Sharma et al., 2021 (DOI: 10.1038/s41467-021-25411-y).

value: CTU2 KO

value: STM treated


title: JL71, DSB, -, biol rep 1

description: Library name: JL71 biol rep 1

value: dnm1 mgm1


title: Endosperm from family NE72, plant #9

description:
Library name: E72.9_E
Endosperm from family NE72, plant #9, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: MexKO-OMP-rep3_clonetech

description:
Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016); OMP-ires-GFP (Shykind et al. 2004)
Mex3aKO_experiment_count_matrix.txt

data_processing:
libraries were quality checked with fastqc, then cutadapt was used to remove adapter sequences
lirbaries were aligned with STAR with a .bam file as output
.bam files were loaded into R studio and analyzed with DESeq2
Assembly: mm10
Supplementary files format and content: TE_RNASeq_Measurements_Raw.tsv (raw and normalized counts as well as translation efficiency score): Cells from this experiment were divided - one part for ribosome profiling,   one part for RNA-Seq. The RNA-Seq is an internal control for the ribosome   profiling, and as such is all part of the same experiment. The processed   data file is intended to be easy for any user to compare translation   efficiency and RNA abundance in the same sample.

source_name: Main olfactory epithelium

extract_protocol:
RNA was extracted using TRIzol reagent, followed by standard 1-Bromo-3-chloropropane/isopropanol methods, or with a DirectZol kit from Zymo (ribosome profiling RNA control libraries)
libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara), except for TetO-Mex3a experiment samples, which were prepared with the TruSeq Stranded Total RNA (Illumina) kit

treatment_protocol: cells were isolated using papain enzymatic treatment (Worthington)

value: Main olfactory epithelium

value: OMP-GFP+; Mex3a KO cells

value: Mex3a fl/fl; Foxg1iresCre; OMP-ires-Cre


title: Endosperm from family NE72, plant #2

description:
Library name: E72.2_E
Endosperm from family NE72, plant #2, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm from family NE72


title: JL121, DSB, -, biol rep 1

description: Library name: JL121 biol rep 1 exp1


title: CTU2_CTRL_Di

description: Library name: CTU2_CTRL_Di


title: Quant-seq, WT_STM_rep1

description: Library name: WT_STM_rep1

value: WT


title: Endosperm from family NE72, plant #1

description:
Library name: E72.1_E
Endosperm from family NE72, plant #1, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: MexKO-OMP-rep2_clonetech


title: JL121, DSB, , biol rep 1

description: Library name: JL121 biol rep 1


title: Endosperm from family NE71, plant #8

description:
Library name: E71.8_E
Endosperm from family NE71, plant #8, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm from family NE71


title: ELP1_CTRL_Di

description: Library name: ELP1_CTRL_Di

value: HEK 293T

value: ELP1 KO

value: untreated


title: scRNA-Seq-Mex3aKO_PN12_rep1

description: Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016), whole olfactory epithelium, postnatal day 12

value: main olfactory epithelium

value: whole olfactory epithelium, many cell types

value: Mex3a flox/flox; Foxg1iresCre


title: MexKO-OMP-rep1_clonetech


title: Endosperm from family NE71, plant #7

description:
Library name: E71.7_E
Endosperm from family NE71, plant #7, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen

value: Endosperm


title: JL112, DSB, , biol rep 1

description: Library name: JL112 biol rep 1

value: mutant isogenic to JKM139


title: MexWT-OMP-rep3_clonetech

description:
Mex3a flox/flox or Mex3a flox/+  (Alvarez-Varela et al. 2022) (no Cre driver); OMP-ires-GFP (Shykind et al 2004)
Mex3aKO_experiment_count_matrix.txt

value: OMP-GFP+; Mex3a WT cells

value: Mex3a fl/fl; OMP-ires-GFP


title: JL118, DSB, , biol rep 1

description: Library name: JL118 biol rep 1


title: WT_STM_Di

description: Library name: WT_STM_Di

value: Human embryonic kidney cells

value: STM treated


title: JL100, DSB, , biol rep 1

description: Library name: JL100 biol rep 1


title: Endosperm from family NE71, plant #4

description:
Library name: E71.4_E
Endosperm from family NE71, plant #4, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: WT_CTRL_Di

description: Library name: WT_CTRL_Di


title: Endosperm from family NE71, plant #6

description:
Library name: E71.6_E
Endosperm from family NE71, plant #6, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: JL109, DSB, , biol rep 1

description: Library name: JL109 biol rep 1


title: MexWT-OMP-rep1_clonetech

value: Main olfactory epithelium


title: CTU2_STM_rep3

description: Library name: CTU2_STM_rep3_Mono

value: CTU2 KO


title: Endosperm from family NE71, plant #3

description:
Library name: E71.3_E
Endosperm from family NE71, plant #3, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: OMP-MexWT-rep2-RiboControl

description:
Mex3a flox/flox or Mex3a flox/+  (Alvarez-Varela et al. 2022) (no Cre driver); OMP-ires-GFP (Shykind et al 2004)
TE_RNASeq_Measurements_Raw.tsv


title: YY182, DSB, , biol rep 1

description: Library name: YY182 biol rep 1


title: OMP-MexWT-rep1-RiboControl


title: CTU2_STM_rep2

description: Library name: CTU2_STM_rep2_Mono


title: YY111, DSB, , biol rep 1

description: Library name: YY111 biol rep 1


title: CTU2_STM_rep1

description: Library name: CTU2_STM_rep1_Mono


title: Endosperm from family NE71, plant #2

description:
Library name: E71.2_E
Endosperm from family NE71, plant #2, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: Endosperm from family NE71, plant #1

description:
Library name: E71.1_E
Endosperm from family NE71, plant #1, generated from bulk pollen cross between Mu-Inactive W22 ear and Mu-Active W22 pollen


title: OMP-MexKO-rep2-RiboControl

description:
Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016); OMP-ires-GFP (Shykind et al. 2004)
TE_RNASeq_Measurements_Raw.tsv

value: OMP-GFP+; Mex3a KO cells

value: Mex3a fl/fl; Foxg1iresCre; OMP-ires-Cre


title: ELP1_STM_Di

description: Library name: ELP1_STM_Di


title: JL107B, DSB, , biol rep 1

description: Library name: JL107B biol rep 1

value: avt4 (respiration competent)


title: CTU2_CTRL_rep2

description: Library name: CTU2_CTRL_rep2_Mono

value: HEK 293T


title: JL107C, DSB, , biol rep 2

description: Library name: JL107A, C biol rep 2

value: avt4 (respiration deficient)


title: OMP-MexKO-rep1-RiboControl


title: Leaf 83, MuActive Plant ND58-83 diluted 1 part in 30 with MuInactive Leaf 3, Plant ND59-3

state: Georgia

address: 120 East Green St

department: Genetics

institute: University of Georgia, Athens

description:
Library name: L83_30xDilution
MuSeq2 Leaf sample from MuActive plant ND58-83 diluted 1 in 30 with MuSeq2 Leaf sample from MuInactive plant ND59-3

data_processing:
Processed file "MuSeq2 data for maize tissues.csv.gz" was generated by mapping the Mu sequencing reads to the W22 V2 genome using Bowtie2 and bam files were converted to txt files which were then imported into R. Sample txt files were filtered and combined into a large matrix, containing unique molecules detected per sample per genome location across all MuSeq2 samples in the dataset.
Processed file "'MuSeq2 data for maize tissues _ separated Left and Right transposon borders.tar'" was generated from "MuSeq2 data for maize tissues.csv.gz" by separating the molecules based on transposon border. Each row represents the chromosome, position, and direction for each molecule detected.
Assembly: W22 Version 2
Supplementary files format and content: To generate processed file "MuSeq2 data for maize tissues.csv.gz", Sequencing reads were mapped to the W22 V2 genome with Bowtie2. Reads were then converted to molecule counts using both the adapter ligation position and a unique molecular identifier (UMI) incorporated during adapter ligation. Molecule counts mapping to both sides of the transposon border were combined. The rownames in this file are listed as chromosome:position1,position2 where positions 1 and 2 are the first genomic coordinate immediately adjacent to the the left and right side of the transposon insertion (respectively).
Supplementary files format and content: Processed file "MuSeq2 data for maize tissues separated Left and Right transposon borders.tar” data was generated as an intermediate in calculating "MuSeq2 data for maize tissues.csv.gz". This contains two csv files with the molecule counts separated for left and right side of the transposon. The rownames are given as chromosome:position where the position is the genomic coordinate immediately adjacent to the transposon border.

growth_protocol: All Mu-Active plants were first grown in vermiculite and transplanted 10-13 days after sowing to soil, where they were grown in maturity in a greenhouse. Mu-Inactive samples were grown in soil and grown for 10-13 days until the V2 stage before being harvested.

extract_protocol:
Leaf and root samples were extracted using a Qiagen Dneasy plant mini kit according to manufacturers instructions. DNA from Pollen and Endosperm samples were extracted using a modified CTAB DNA extraction protocol (see methods). All DNA samples were then sheared to a mean of 1000 bp using a Covaris E220 Evolution.
Libraries were constructed for all samples by first ligating a custom Museq Adapter, and then subsequent PCR reactions to selectively amplify genomic regions adjacent to Mu insertions. See Methods for details

value: Leaf

value: W22 Mu-Active, W22 Mu-Inactive


title: MexWT-OMP-rep2_clonetech


title: Ngn-MexWT-rep2-RiboControl

description:
Mex3a flox/flox or Mex3a flox/+  (Alvarez-Varela et al. 2022) (no Cre driver); Ngn1-GFP (Magklara et al. 2011)
TE_RNASeq_Measurements_Raw.tsv

value: Ngn-GFP+; Mex3a WT cells

value: Mex3a fl/fl; Ngn1-GFP


title: Leaf 83, MuActive Plant ND58-83 diluted 1 part in 10 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L83_10xDilution
MuSeq2 Leaf sample from MuActive plant ND58-83 diluted 1 in 10 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: JL107A, DSB, , biol rep 1

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: JL107A, C biol rep 1


title: Leaf 83, MuActive Plant ND58-83 diluted 1 part in 3 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L83_3xDilution
MuSeq2 Leaf sample from MuActive plant ND58-83 diluted 1 in 3 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: ELP1_STM_rep2

description: Library name: ELP1_STM_rep2_Mono

value: ELP1 KO


title: Ngn-MexKO-rep2-RiboControl

description:
Mex3a flox/flox (Alvarez-Varela et al. 2022); Foxg1iresCre (Kawaguchi D et al 2016) Ngn1-GFP (Magklara et al. 2011)
TE_RNASeq_Measurements_Raw.tsv

value: Ngn-GFP+; Mex3a cKO cells

value: Mex3a fl/fl; Foxg1iresCre; Ngn1-GFP


title: Ngn-MexWT-rep1-RiboControl


title: ELP1_CTRL_rep2

description: Library name: ELP1_CTRL_rep2_Mono

value: untreated


title: JL173, DSB, , biol rep 3

description: Library name: JL173 biol rep 3

value: mutant isogenic to JKM139


title: Leaf 79, MuActive Plant ND58-79 diluted 1 part in 30 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L79_30xDilution
MuSeq2 Leaf sample from MuActive plant ND58-79 diluted 1 in 30 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: JL173, DSB, , biol rep 2

description: Library name: JL173 biol rep 2


title: ELP1_STM_rep1

description: Library name: ELP1_STM_rep1_Mono

value: Human embryonic kidney cells

value: STM treated


title: Leaf 79, MuActive Plant ND58-79 diluted 1 part in 3 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L79_3xDilution
MuSeq2 Leaf sample from MuActive plant ND58-79 diluted 1 in 3 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: GFPTg_omp-rep2-Truseq

description:
tetracycline transactivator allele that turn on in mOSNs (OMP-tTA- Yu et al. 2004) were bred to mice that carried a transgenic allele of GFP
tetO-Mex_experiment_count_matrix.txt
exon_readcounts_TetOMex3a.txt
intron_readcounts_TetOMex3a.txt

value: Main olfactory epithelium

value: tetO-GFP+ cells; OMP-tTA driver

value: OMP-tTA; tetO-GFP


title: Leaf 79, MuActive Plant ND58-79 diluted 1 part in 10 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L79_10xDilution
MuSeq2 Leaf sample from MuActive plant ND58-79 diluted 1 in 10 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: Ngn-MexKO-rep1-RiboControl


title: JL113, DSB, , biol rep 1

description: Library name: JL113 biol rep 1


title: ELP1_CTRL_rep1

description: Library name: ELP1_CTRL_rep1_Mono


title: JL173, DSB, , biol rep 1

description: Library name: JL173 biol rep 1


title: WT_STM_rep2

description: Library name: WT_STM_rep2_Mono

value: WT


title: Root 75, MuActive Plant ND58-75

description:
MuSeq2 Root sample from MuActive plant ND58-75
Library name: R75

source_name: Root

extract_protocol:
Leaf and root samples were extracted using a Qiagen Dneasy plant mini kit according to manufacturers instructions. DNA from Pollen and Endosperm samples were extracted using a modified CTAB DNA extraction protocol (see methods). All DNA samples were then sheared to a mean of 1000 bp using a Covaris E220 Evolution.
Libraries were constructed for all samples by first ligating a custom Museq Adapter, and then subsequent PCR reactions to selectively amplify genomic regions adjacent to Mu insertions. See Methods for details
A universal adapter was ligated onto the sheared DNA, then DNA fragments spanning the genome-transposon junction were amplified by PCR and sequenced using the MuSeq2 protocol.

value: Root

value: W22 MuActive


title: GFPTg_omp-rep1-Truseq


title: JKM139, DSB, , biol rep 2

description: Library name: JKM139 biol rep 1 exp12

source_name: S. cerevisiae haploid strain

value: S. cerevisiae haploid strain


title: CTU2_CTRL_rep1

description: Library name: CTU2_CTRL_rep1_Mono

value: HEK 293T

value: CTU2 KO


title: Root 69, MuActive Plant ND58-69

description:
MuSeq2 Root sample from MuActive plant ND58-69
Library name: R69


title: GFPTg_gg8omp-rep2-Truseq

description:
tetracycline transactivator alleles that turn on in INP/iOSNs (gg8-tTA - Nguyen et al. 2008), and in mOSNs (OMP-tTA- Yu et al. 2004) were bred to mice that carried a transgenic allele of GFP
tetO-Mex_experiment_count_matrix.txt

value: tetO-GFP+ cells; gg8-tTA; OMP-tTA drivers

value: gg8-tTA; OMP-tTA; tetO-GFP


title: JL142, DSB, , biol rep 1

description: Library name: JL142 biol rep 1


title: WT_CTRL_rep2

description: Library name: WT_CTRL_rep2_Mono


title: JL142, DSB, , biol rep 2

description: Library name: JL142 biol rep 2


title: JL142, DSB, -, biol rep 1

description: Library name: JL142 biol rep 1 exp1


title: Root 74, MuActive Plant ND58-74

description:
MuSeq2 Root sample from MuActive plant ND58-74
Library name: R74


title: WT_STM_rep1

description: Library name: WT_STM_rep1_Mono


title: WT_CTRL_rep1

description: Library name: WT_CTRL_rep1_Mono


title: JL70, DSB, , biol rep 1

description: Library name: JL70 biol rep 1


title: Root 65, MuActive Plant ND58-65

description:
MuSeq2 Root sample from MuActive plant ND58-65
Library name: R65


title: Root 63, MuActive Plant ND58-63

description:
MuSeq2 Root sample from MuActive plant ND58-63
Library name: R63


title: MexMutTg_omp-rep2-Truseq

description:
tetracycline transactivator allele that turns on in mOSNs (OMP-tTA- Yu et al. 2004) were bred to mice that carried a transgenic allele of Mex3a with four point mutations in the RING domain that disrupt the cross-brace structure (made for this study). The allele is knicknamed "TMexF6" in filenames
tetO-Mex_experiment_count_matrix.txt

value: tetO-Mex3a mutant RING mCherry+ cells; OMP-tTA driver

value: OMP-tTA; tetO-Mex3a-mutantRING-mCherry


title: MexMutTg_omp-rep1-Truseq


title: RKO cells day0 control, replicate 3, lane4

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

institute: DKFZ

data_processing:
.fastq.gz: sequence reads of sgRNA expression cassette integrated into RKO genome
custom amplicon-seq on the PCR product consist of sgRNA expression cassette.
the raw sequencing data were transformed into a table of the absolute amount of sgRNA read detected from each sample using MAGeCK package
differential gene expression was called from the normalized and log-transformed sgRNA counts from each sample using LIMMA package.
Assembly: custom sgRNA library
Library strategy: Amplicon-seq

source_name: colorectal cancer

growth_protocol: RKO colorectal cancer cells were cultured in RPMI 1640 supplemented with 10 % FCS, 2 mM L-glutamine, 1 % Penicillin/Streptomycin, and 1x Glutamax.

extract_protocol:
gDNA from RKO was isolated using QIAGEN Blood & Cell Culture DNA Maxi Kit. PCR was performed on the purified gDNA to amplify the sgRNA expression cassette.
as previously described in Henkel, L., Rauscher, B., Schmitt, B., Winter, J., & Boutros, M. (2020). Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library. BMC biology, 18, 1-21.

treatment_protocol: After sgRNA library transduction and puromycin selection, the RKO cells were expanded for a period of time before FACS-sorted into 3 subpopulation according different level of CPY-CA/EGFP signal ratio.

value: colorectal cancer

value: RKO

value: adherent

tag: phenotype

value: control


title: GFPTg_gg8omp-rep1-Truseq

value: Main olfactory epithelium


title: JL69, DSB, , biol rep 2

first: Kaifu

last: Chen

description: Library name: JL69 biol rep 2

value: mutant isogenic to JKM139


title: RKO cells day0 control, replicate 3, lane3


title: MexTg_omp-rep2-Truseq

description:
tetracycline transactivator allele that turns on in mOSNs (OMP-tTA - Yu et al. 2004) were bred to mice that carried a transgenic allele of Mex3a (made for this study). Two distinct founders (different insertion site of Mex3a in the genome) were used for RNA-Seq analysis: knicknamed "TMexF1" and "TMexF2" in the filenames
tetO-Mex_experiment_count_matrix.txt
exon_readcounts_TetOMex3a.txt
intron_readcounts_TetOMex3a.txt

value: tetO-Mex3a mCherry+ cells; OMP-tTA driver

value: OMP-tTA; tetO-Mex3a-mCherry


title: RKO cells day0 control, replicate 3, lane2

value: WT


title: Root 61, MuActive Plant ND58-61

description:
MuSeq2 Root sample from MuActive plant ND58-61
Library name: R61

value: Root

value: W22 MuActive


title: MexTg_omp-rep1-Truseq


title: JL69, DSB, , biol rep 1

description: Library name: JL69 biol rep 1


title: JL218C, DSB, , biol rep 1

description: Library name: JL218C biol rep 1

value: aft1 (respiration competent)


title: RKO cells day0 control, replicate 3, lane1


title: Pollen 99, MuActive Plant ND58-85

description:
MuSeq2 Pollen sample from MuActive plant ND58-99
Library name: P99

source_name: Pollen

value: Pollen


title: JL218A, DSB, , biol rep 1

description: Library name: JL218A biol rep 1


title: MexMutTg_gg8omp-rep2-Truseq

description:
tetracycline transactivator alleles that turn on in INP/iOSNs (gg8-tTA - Nguyen et al. 2008), and in mOSNs (OMP-tTA- Yu et al. 2004) were bred to mice that carried a transgenic allele of Mex3a with four point mutations in the RING domain that disrupt the cross-brace structure (made for this study). The allele is knicknamed "TMexF6" in filenames
tetO-Mex_experiment_count_matrix.txt

value: tetO-Mex3a mutant RING mCherry+ cells; gg8-tTA; OMP-tTA driver


title: Pollen 85, MuActive Plant ND58-85

description:
MuSeq2 Pollen sample from MuActive plant ND58-85
Library name: P85


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 3, lane4

value: low CPY-CA/EGFP signal ratio


title: Pollen 83, MuActive Plant ND58-83

description:
MuSeq2 Pollen sample from MuActive plant ND58-83
Library name: P83


title: JL218B, DSB, , biol rep 1

description: Library name: JL218B biol rep 1

value: aft1 (respiration deficient)


title: MexMutTg_gg8omp-rep1-Truseq


title: Pollen 79 Technical Replciate, MuActive Plant ND58-79

description:
MuSeq2 Pollen sample Technical Replicate split after DNA shearing from MuActive plant ND58-79
Library name: P79T


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 3, lane3


title: MexTg_gg8omp-rep2-Truseq

description:
tetracycline transactivator alleles that turn on in INP/iOSNs (gg8-tTA - Nguyen et al. 2008), and in mOSNs (OMP-tTA- Yu et al. 2004) were bred to mice that carried a transgenic allele of Mex3a (made for this study). Two distinct founders (different insertion site of Mex3a in the genome) were used for RNA-Seq analysis: knicknamed "TMexF1" and "TMexF2" in the filenames
tetO-Mex_experiment_count_matrix.txt

value: tetO-Mex3a mCherry+ cells gg8-tTA; OMP-tTA drivers

value: gg8-tTA; OMP-tTA; tetO-Mex3a-mCherry


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 3, lane2

value: colorectal cancer

value: RKO


title: JL179, DSB, 3mM Fe 6hr, biol rep 1

description: Library name: JL179 biol rep 1 exp1

value: 3mM Fe 6hr


title: Pollen 79, MuActive Plant ND58-79

description:
MuSeq2 Pollen sample from MuActive plant ND58-79
Library name: P79


title: JL179, DSB, , biol rep 2

description: Library name: JL179 biol rep 2


title: MexTg_gg8omp-rep1-Truseq

description:
tetracycline transactivator alleles that turn on in INP/iOSNs (gg8-tTA - Nguyen et al. 2008), and in mOSNs (OMP-tTA- Yu et al. 2004) were bred to mice that carried a transgenic allele of Mex3a (made for this study). Two distinct founders (different insertion site of Mex3a in the genome) were used for RNA-Seq analysis: knicknamed "TMexF1" and "TMexF2" in the file names
tetO-Mex_experiment_count_matrix.txt

value: Main olfactory epithelium


title: JL179, DSB, , biol rep 1

description: Library name: JL179 biol rep 1

value: mutant isogenic to JKM139


title: OMP-rep2-Truseq

description:
OMP-ires-GFP (Shykind et al 2004) marks mature OSNs with GFP
tetO-Mex_experiment_count_matrix.txt

value: OMP-GFP+ cells (mature OSNs)

value: OMP-ires-GFP


title: OMP-rep1-Truseq


title: RKO cells with "low" CPY-CA/EGFP signal ratio, replicate 3, lane1

value: adherent

value: WT


title: Pollen 75, MuActive Plant ND58-75

description:
MuSeq2 Pollen sample from MuActive plant ND58-75
Library name: P75

value: W22 MuActive


title: JL266, DSB, , biol rep 2

description: Library name: JL266 biol rep 2


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 3, lane3

value: high CPY-CA/EGFP signal ratio


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 3, lane4


title: Ngn1-rep2-Truseq

description:
Ngn1-GFP (Magklara et al. 2011) was used to mark INP/iOSN cells. Two GFP+ populations are present, and the brightest one was collected for this experiment, which corresponds to less differentiated Ngn1+ cells
tetO-Mex_experiment_count_matrix.txt

value: Ngn-GFP+ (Immediate Neuronal Progenitor/immature OSN)


title: JL266, DSB, , biol rep 1

description: Library name: JL266 biol rep 1


title: Pollen 76, MuActive Plant ND58-76

description:
MuSeq2 Pollen sample from MuActive plant ND58-76
Library name: P76

value: Pollen


title: Pollen 74, MuActive Plant ND58-74

description:
MuSeq2 Pollen sample from MuActive plant ND58-74
Library name: P74


title: Ngn1-rep1-Truseq


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 3, lane2


title: RKO cells with "high" CPY-CA/EGFP signal ratio, replicate 3, lane1


title: Pollen 69, MuActive Plant ND58-69

description:
MuSeq2 Pollen sample from MuActive plant ND67-69
Library name: P69


title: JL119, DSB, , biol rep 1

description: Library name: JL119 biol rep 1


title: Mash1-rep2-Truseq

description:
Ascl1CreERT2*/+ (Kim et al. 2011); Ai14 tdTomato*/+ (Madisen et al 2010) mice were injected with Tamoxifen between the ages of PN2 and PN4, and red cells were sorted 48 hours later
tetO-Mex_experiment_count_matrix.txt

value: Ascl1/Mash1+ (Globose Basal Cells)

value: Ascl1CreERT2; Ai14 tdTomato


title: JL120, DSB, , biol rep 1

description: Library name: JL120 biol rep 1


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 3, lane4

value: basal CPY-CA/EGFP signal ratio


title: Pollen 52, MuActive Plant ND67-52

description:
MuSeq2 Pollen sample from MuActive plant ND67-52
Library name: P52


title: JL195, DSB, , biol rep 3

description: Library name: JL195 biol rep 3


title: RKO cells with "basal" CPY-CA/EGFP signal ratio, replicate 3, lane3


title: Pollen 78, MuActive Plant ND58-78

description:
MuSeq2 Pollen sample from MuActive plant ND58-78
Library name: P78


title: JL195, DSB, , biol rep 2

description: Library name: JL195 biol rep 2