title: UCLA1 primed hESC, DMSO 1h, ZIC2 ChIP-seq

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

value: Cultured in medium supplemented with DMSO for 1 hour

tag: antibody

value: anti-ZIC2 (Abcam ab150404)

tag: passage description

value: passage 46


title: L001_2_vehicle

status: Public on Aug 20 2024

type: SRA

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 603 Wilson Rd., BCH Building RM#212

department: Biochemistry and Molecular Biology

country: USA

institute: Michigan State University

library_source: transcriptomic single cell

data_processing:
CellRanger 4.0.0 was used to align reads to a custom reference genome which included introns and exons to consider pre-mRNA and mature mRNA present in the nuclei.
Raw counts were further analysed using Scanpy v1.9.3. Each sample was filtered for (i) genes expressed in at least 3 nuclei, (ii) nuclei which express at least 100 genes, and (iii) ≤1% mitochondrial genes
Scrublet v0.2.3 was used to remove putative doublets.
All libraries were integrated using using scVI v0.20.3, while accounting for dose and time as categorical covariates and using a latent variable of 40.
Assembly: mm10
Supplementary files format and content: Processed data files for individual sample are CellRanger filtered_feature_bc_matrix.H5 Hierarchical Data Format version 5 (HDF5) files.
Supplementary files format and content: The HDF5 Annotated Data (.h5ad) file represents the full scVI processed anndata object.

molecule: nuclear RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) - CG000315 Rev A
snRNAseq (Single-Nuclei RNA-Sequencing)

treatment_protocol:
Mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected at 2, 4, 8, 12, 24, or 72 hours following gavage.
Mice given a single bolus dose by oral gavage

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

tag: administration route

value: oral gavage

tag: administration route_ontology

tag: treatment

value: vehicle

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: L002_2_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

value: Liver

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: bedding


title: 1974_D21_DB_pos

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

country: Canada

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

library_source: transcriptomic

data_processing:
Ion Reporter software (version 5.12) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to hg19 whole genome using the Ion Reporter software (version 5.12).
Counting data of referenced clones were generated by the Ion Reporter software (version 5.12).
Genome_build: hg19
Supplementary_files_format_and_content: Coma-separated value files include VDJ genes associated with CDR3 amino acid and nuclotide sequences, read counts, and read proportions for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: T lymphocytes

growth_protocol: Cells were stimulated weekly with LMP2-pulsed dendritic cells and cultured in complete media.

extract_protocol:
FACS-sorted LMP2 multimer-positive and multimer-negative T cells were harvested. RNA was isolated using Trizol reagent in combination with the PureLink RNA mini and microcolumn system.
Oncomine™ TCR Beta-SR Assay for RNA was used for the construction of sequencing libraries. Sequencing was completed on the Ion S5 semiconductor platform using an Ion 540 chip.

treatment_protocol: Cells were treated or not with anti-PD-L1 and anti-TIM3 antibodies.

tag: lmp2 specificity

value: positive

tag: days in culture

tag: treatment

value: PD-L1/TIM3 double blockade


title: 1832_D28_Ctrl_neg

value: negative

value: Untreated


title: L022_4_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

value: hours

value: degree Celcius

value: percent

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

tag: administration route

tag: administration route_ontology

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: 1932_D28_DB_neg

tag: lmp2 specificity

tag: days in culture

tag: treatment


title: UCLA1 primed hESC, DMSO 1h, Input

first: William

middle: A.

last: Pastor

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

library_source: genomic

data_processing:
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks, where necessary. Otherwise reads per 1x genome coverage (RPGC) was used for generating coverage files.
Differentially accessible regions were calculated using csaw.
Deeptools was used to generate coverage tracks.
Assembly: GRCh38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Primed human embryonic stem cells

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in TESR-E8 or mTESR-plus medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 5iLAF  or 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Reverting and naive hESCs were depleted of MEFs by plating of dissociated single cell suspension on 0.1% gelatin for 30 minutes prior to collection for experiments.

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 10 min, and quenched with 0.14 M glycine for 10 min. Cells were then resuspended with 1 ml lysis buffer 1 (10 mM TrisHCl pH 8.0, 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitors (Roche), 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), then rotated 15 minutes. Nuclei were pelleted by centrifugation at 1200g for 5 minutes at 4 °C. Nuclei were then resuspended with 1 ml lysis buffer 2 (10 mM TrisHCl pH 8.0, 200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitor, 1mM NaF, 1mM Na2VO3 and 1mM PMSF) and rotated 10 minutes at 4 °C. Nuclei were then pelleted and resuspended in 900 μl lysis buffer 3 (10 mM Tris-HCL pH 8, 10 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), and chromatin was fragmented using the Covaris M220 sonicator. Chromatin was pre-cleared with ProtA/G beads for 2 hours at  4 °C. Antibodies were then added to pre-cleared lysates and incubated overnight with end-over-end shaking at 4 °C. Immunocomplexes were then immobiilzed on prot A/G beads, which were then washed 2×4 minutes with 500 μl Wash Buffer A (50 mM HEPES pH 7.9, 1% TritonX-100, 0.1% Deoxycholate, 1mM EDTA, 140 mM NaCl), 500 μl Wash Buffer B (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X100, 0.1% Deoxycholate, 1 mM EDTA, 500 mM NaCl), and 500 μl TE buffer (10 mM TrisHCl pH 8.0, 1 mM EDTA). DNA was eluted in 100 μl elution buffer (50 mM TrisHCl pH 8.0, 1 mM EDTA, 1% SDS) after incubation at 65 °C for 10 minutes at 1400 rpm. The elute was collected, and the beads were subjected to a second round of elution with 150 μl elution buffer. The ChIP eluants were pooled, and the input sample was diluted to 250 μl with elution buffer. These samples were incubated 65 °C overnight to promote decrosslinking. The samples were then allowed to cool to room temperature, 15 μg of RNAse A (Purelink, ThermoFisher) was added, and the samples were incubated 30 minutes at 37 °C to degrade RNA. 100 μg Proteinase K was then added and the samples were incubated 56 °C for two hours. DNA was purified using a MinElute PCR Purification kit (Qiagen).
Purified DNA was fragmented to 200 bp by sonication. Following this, libraires were prepared using the Swift DNA library kit or NEBNext Ultra II DNA Library Prep Kit, according to manufacturers' instructions.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate, 1 uM flavopiridol, 500 nM triptolide, 25 uM STM2457 or DMSO of equivalent v/v concentration, where specified for the appropriate period of time.

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

value: Cultured in medium supplemented with DMSO for 1 hour

tag: antibody

tag: passage description

value: passage 46


title: 1974_D21_DB_neg


title: Retina, 75% oxygen, rep6

city: 上海/上海市/杨浦区

first: 青

last: 李

address: 长海路168号

country: China

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.OIR.6
Gene_FPKM.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and trimming low qulity base with Trimmomatic
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: Gene_FPKM.txt

source_name: retina

extract_protocol:
Total RNA was extracted by TRIzol and subjected to RNA-seq analysis. 1ug of total RNA was used for the construction of sequencing libraries.
Poly-A tailed mRNA molecules were captured using attached oligo-dT and subjected to library construction according to the manufacturer’s recommendations.

value: retina

tag: strain

tag: age

value: 75% oxygen


title: 1974_D21_Ctrl_pos

value: positive


title: Retina, 75% oxygen, rep5

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.OIR.5
Gene_FPKM.txt


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, Input, rep2

source_name: Naïve human embryonic stem cells

value: Naïve human embryonic stem cells

value: UCLA1 naive hESCs

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

value: Cultured in medium supplemented with DMSO for 64 hours followed by 100 ng/ml doxycycline for 8 hours

value: passage 26+39+2


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, H3K27me3 ChIP-seq, rep2

value: anti-H3K27me3 (CST 9733)


title: 1832_D28_Ctrl_pos

value: Untreated


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, Input, rep1


title: Retina, 75% oxygen, rep4

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.OIR.4
Gene_FPKM.txt


title: 1932_D21_DB_pos

value: PD-L1/TIM3 double blockade


title: Retina, 75% oxygen, rep3

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.OIR.3
Gene_FPKM.txt


title: 1932_D21_DB_neg

value: negative


title: Retina, 75% oxygen, rep2

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.OIR.2
Gene_FPKM.txt


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, H3K27me3 ChIP-seq, rep1


title: Retina, 75% oxygen, rep1

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.OIR.1
Gene_FPKM.txt


title: Retina, normoxic air, rep6

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.Con.6
Gene_FPKM.txt

value: normoxic air


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, Input (control for H3K27me3 ChIP)

value: Human embryonic stem cells

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 72 hours


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, Flag ChIP-seq

value: anti-Flag M2 (Sigma F3165)

value: passage 26+39+3


title: 1932_D21_Ctrl_pos


title: Retina, normoxic air, rep3

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.Con.3
Gene_FPKM.txt

value: retina


title: Retina, normoxic air, rep5

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.Con.5
Gene_FPKM.txt


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, Input (control for Flag ChIP)


title: 1932_D21_Ctrl_neg


title: Retina, normoxic air, rep4

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.Con.4
Gene_FPKM.txt


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, H3K27me3 ChIP-seq


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, Input, rep2

value: Cultured in medium supplemented with DMSO for 48 hours followed by 100 ng/ml doxycycline for 24 hours


title: 1974_D21_Ctrl_neg


title: 1867_D21_Ctrl_pos

value: positive


title: 1867_D21_Ctrl_neg


title: 1867_D21_DB_neg


title: 1832_D21_DB_pos


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, Flag ChIP-seq

value: Naïve human embryonic stem cells


title: 1832_D21_DB_neg


title: Retina, normoxic air, rep1

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.Con.1
Gene_FPKM.txt


title: Retina, normoxic air, rep2

institute: 中国人民解放军海军军医大学第一附属医院

description:
C57.Con.2
Gene_FPKM.txt


title: 1867_D21_DB_pos


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, H3K27me3 ChIP-seq, rep2

value: UCLA1 naive hESCs


title: heart, IR_SI1  (ischemia 45min, reperfusion 24h, sh-YTHDF2) rep3

city: harbin

first: yu

last: bian

address: baojian road

institute: harbin medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: tissue

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tissue

value: YTHDF2 knockdown

value: cardiac I/R (ischemia 45min, reperfusion 24h) injury


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, Input, rep1

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

value: passage 26+39+2


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, H3K27me3 ChIP-seq, rep1

value: anti-H3K27me3 (CST 9733)


title: 1832_D21_Ctrl_pos

value: Untreated


title: 1832_D21_Ctrl_neg

value: negative


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, Flag ChIP-seq

value: Human embryonic stem cells


title: heart, IR_SI1  (ischemia 45min, reperfusion 24h, sh-YTHDF2) rep2


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, H3K27ac CUT&Tag

data_processing:
Raw reads were trimmed to 50bp using TrimGalore!
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Mitochondrial reads were removed prior to making coverage files.
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in mTESR-plus medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Naive hESCs were depleted of MEFs prior to collection for experiments.

extract_protocol:
Cells were fixed in 0.1% paraformaldehyde for 10 minutes at room temperature and the reaction was quenched with 0.14 M glycine. Cell pellets were resuspended in 200 μl cold nuclear extraction (NE) buffer (20 mM HEPES pH 7.9, 10 mM KCl, 20% glycerol, 0.1% Triton X-100, 0.5 mM spermidine, 0.15 mM spermine and protease inhibitors) and incubated for 5 minutes on ice. Nuclei were resuspended in 50 μl NE buffer and incubated with activated Concanavalin A-coated magnetic beads for 10 minutes at room temperature. Supernatant was removed using a magnetic stand and nuclei resuspended in 25 µL antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.15 mM spermine, 20% glycerol and 2 mM EDTA) containing 0.5 μg primary antibody. Samples were then incubated overnight at 4 °C on a nutator. To remove unbound antibody, bead-nuclei complexes were washed twice with 150 buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.15 mM spermine, 20% glycerol) using a magnetic stand and resuspended in 25 µL 150 buffer containing 0.5 μg anti-mouse or rabbit secondary antibody for CUTANATM CUT&Tag workflows (EpiCypher). Samples were then incubated for 30 minutes at room temperature. After two washes with 150 buffer, bead/nuclei complexes were resuspended in 12 µl 1x pA/G-Tn5 pre-loaded adapter complex (EpiCypher, USA) made in 150 buffer and incubated for 1 hour at room temperature on a nutator. Bead/nuclei complexes were washed twice in 150 buffer, resuspended in 50 μl cold CUTAC-hex buffer (10 mM TAPS, 5 mM MgCl2, 10% 1,6-hexanediol, 20% glycerol and protease inhibitors) and incubated for 2 minutes at 4 °C followed by 20 minutes at 37 °C. To release pAG-Tn5 from tagmented DNA, bead/nuclei complexes were then resuspended in 5 μl 0.1% SDS and incubated for 1 hour at 58 °C. To generate libraries, 15 μl of 0.67% Triton X-100 neutralization solution was added to each sample followed by 2 μl 10 μM universal or barcoded i5 primers, 2 μl 10 μM uniquely barcoded i7 primers and 25 μl NEBNext High-Fidelity buffer (non-hot-start NEBNext formulation; NEB, USA). Samples were then placed in a thermocycler under the following cycling conditions: 5 min at 58 °C, 5 minutes at 72 °C, 45 seconds at 98 °C, 15 seconds at 98 °C (melting) and 10 seconds at 60 °C (annealing and extension). The last 2 steps were repeated for a total of 14-21 cycles followed by a 1-minute final extension at 72 °C. To purify libraries, 25 μl AMPure XP beads (Beckman Coulter, Canada) were added to the reactions and samples were incubated for 10 minutes at room temperature on a nutator. DNA was washed twice with 70% ethanol using a magnetic stand and once with 100% ethanol. DNA was eluted in 15 μl in pre-warmed 10 mM Tris pH 8 buffer using a magnetic stand.
Libraries were constructed by tagmentation such that chromatin upon treatment with Tn5 was simultaneously fragmented and tagged with Illumina-compatible sequencing adapters.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate or DMSO of equivalent v/v concentration, where specified.

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC2-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC3


title: heart, IR_NC1 (ischemia 45min, reperfusion 24h, sh-NC) rep2

value: NC knockdown


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, Input, rep2

value: Cultured in medium supplemented with DMSO for 72 hours


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, Input, rep1


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, H3K27me3 ChIP-seq, rep1


title: overexpressing Glul and treated with LPS C5

city: Shanghai

first: Jianghong

last: Yu

state: State...

address: Dong'an Road

institute: Fudan University

data_processing:
The original image data file obtained by Illumina Hiseq recognition was transformed into the  original sequencing sequence (Sequenced Reads) base on the CASAVA(latest version) base recognition  (Base Calling) analysis
In order to guarantee the data quality which was used to analysis, the  useful Perl script was used to filter the original data (Raw Data). The steps are:  1)Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed  Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both  of the reads must be removed );  2)Remove the contaminated reads for adapters (The contaminated reads for  adapters was defined that the Read Bases contained more than 5bp of adapter  sequences. If either one of the PE Reads was polluted, we will remove both ends  of the reads);  3)Remove the low quality reads (The low quality reads was defined that the number  of Reads Bases whose phred Quality value was less than or equal to 19  accounted for more than 15% . If either one of the PE Reads defined as low  quality, we will remove both ends of the reads);  4)Remove the reads whose N base more than 5% for total bases (If either one of  the PE Reads had high Ns bases, we will remove both ends of the reads);
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes  (DEGs) by using DESeq2-a R package.
Genome_build: Mus_musculus.GRCm38.90.chr

source_name: bone marrow derived macrophages (BMDMs)

growth_protocol: Mouse bone marrow derived macrophages (BMDMs) were allowed to differentiate for 7 days from bone marrow of 8 to 10-week-old mice, which was extracted from femurs and tibia removed from mice after the lysis of erythrocyte. BMDMs were then cultured in RPMI-1640 medium with 10% FBS and 10 ng/mL M-CSF.

extract_protocol:
Total RNAs of bone marrow derived macrophages (BMDMs) (~1x106) were extracted by the manual of TRIzol (TaKaRa).
Preparation of library by using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® and sequencing of transcriptome were implemented with Illumina HiSeq 2500 system

treatment_protocol: BMDMs transfected with control or overexpressing Glul constructed using lentiviral vectors for 36h, followed by stimulating with LPS (100 ng/ml) for 3h

value: bone marrow derived macrophages (BMDMs)


title: lEVs_ACSL4_KD_1

city: Wenzhou

first: Pei-pei

last: Hou

state: Zhejiang

address: Central North Road, Ou'hai District

department: School of Laboratory Medicine and Life Sciences

institute: Wenzhou Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6), afterwards clean reads were obtained and stored in FASTQ format. The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5), and the expression level of genes was calculated by RSEM (v1.3.1).
Assembly: GRCh38.p13
Supplementary files format and content: Ctrl_vs_lEVs_vs_lEVs_ACSL4_KD_raw_counts.txt was generated by integrating raw count value of genes from each sample.

extract_protocol:
Total RNA was extracted by Trizol method. A certain amount of RNA was used for the construction of sequencing libraries.
The library preparation process involved sample quality control, mRNA isolation and fragmentation, followed by the synthesis of double-stranded cDNA fragments. The cDNA fragments were subjected to end-repair, and then a single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments, followed by adapter ligation reactions. The resulting libraries were PCR-enriched and proceeded for quality control protocol. The subsequent steps included denaturation and circularization to produce single-stranded cyclized products. Single-stranded circle DNA molecules were replicated via rolling cycle amplification to create DNA nanoballs (DNBs), each containing multiple copies of a single molecular entity. Sufficient quality DNBs were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced using the combinatorial Probe-Anchor Synthesis (cPAS) method.

value: incubated with lEVs (10 ug/ml) derived from ACSL4 knocking down (ACSL4 KD) Huh7 cells for 3 days


title: heart, IR_NC1 (ischemia 45min, reperfusion 24h, sh-NC) rep1


title: overexpressing Glul and treated with LPS B5


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, H3K27me3 ChIP-seq, rep2

value: Naïve human embryonic stem cells

value: UCLA1 naive hESCs


title: lEVs_ACSL4_KD_3


title: lEVs_2

value: incubated with lEVs (10 ug/ml) derived from control Huh7 cells for 3 days


title: lEVs_3


title: TDP2seq_pUC19_DNA_SPO11_YF_rep2

city: New York

first: Meret

last: Arter

address: 430 E 67th Street

institute: Memorial Sloan Kettering Cancer Center

description: For mapping in vitro SPO11 cleavage sites, pUC19 plasmid DNA digested by SPO11 in vitro was embedded in plugs together with wild type C57BL/6J mouse testis cells (0.5–1 million cells per plug), whose DNA acted as carrier during library preparation

library_source: other

data_processing:
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.
Top- and bottom-strand peaks were separately called as nucleotide positions with >3,000, >10 and >15 RPM of strand-specific read counts using averaged pUC19, E. coli, and S. cerevisiae TDP2-seq data, respectively. Positions with less read counts than those located at –1 and +1 positions on top and bottom strands, respectively, were not defined as peaks because those reads could be false-positively enriched due to incomplete fill-in of 5-prime overhangs at DNA ends before adaptor ligation.
Assembly: mm10, pUC19, ASM584v2, SacCer3
Supplementary files format and content: bigWig files contain read counts at positions of DNA double-strand break ends. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively.
Supplementary files format and content: bed files contain peak locations. If only one file per experiment is submitted, peaks were determined based on average profiles of the two replicates.
Library strategy: TDP2-seq

molecule: other

organism: Cloning vector pUC19

source_name: Mus musculus, plasmid DNA

extract_protocol:
Testis cells from adult mice were obtained as described previously (ref. 1,2). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing. For in vitro SPO11 treated plasmid or genomic DNA samples, the treated DNA was mixed with wild type B6 (C57BL/6J) mouse testis cells right before plug formation to provide carrier DNA during library preparation. Plugs were treated with SDS, Proteinase K and RNAse as described previously (ref. 1,2). In-plug removal of covalently bound SPO11 using human TDP2 was performed as described with minor modifications (ref. 3). In brief, plugs were equilibrated in TDP2 buffer (0.05 M Tris-HCl pH 8, 0.15 M NaCl, 10 mM Mg2Cl, 0.5 mM Dithriothreitol, 30 μg/ml BSA, 2 mM ATP) and incubated with purified human TDP2 protein (490 pmol per plug, TopoGEN) at 37°C for 30 min according to the TopoGEN protocol. DNA ends were filled-in with T4 DNA polymerase (New England Biolabs) and ligated to biotinylated adaptors as described previously (ref. 1,2,4,5). To minimize the loss of small plasmid fragments through diffusion out of the plugs, the washing step after ligation of the first adaptor was reduced from overnight to 1h for samples containing plasmid DNA. After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously with minor modifications (ref. 1,2,4,5). For end repair after DNA shearing, NEBNext End repair Kit (New England Biolabs) was used. (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 2) Kim et al., Optimized methods for mapping DNA double-strand-break ends and resection tracts and application to meiotic recombination in mouse spermatocytes. bioRxiv 2024.08.10.606181; https://doi.org/10.1101/2024.08.10.606181, (2024).(ref. 3) Gittens et al., A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome. Nat Commun 10, 4846 (2019). (ref. 4) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 5) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
After quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina NextSeq 1000 sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes.
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>.
Sequencing reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.


title: treated with LPS C3

description: treated with LPS

value: treated with LPS


title: lEVs_1


title: Ctrl_3

value: incubated without lEVs


title: Salmonella enterica serovar Typhimurium A130 transposon library

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
reads were trimmed and quality filtered on their right (genomic sequence) ends using PRINSEQ with the command: prinseq-lite.pl -fastq stdin -out_good stdout -out_bad null -min_len 30 -trim_tail_right 2 -trim_ns_right 1 -trim_qual_right 20 -trim_qual_window 3
Reads were filtered for 10 bases matching the expected transposon tag sequence, and filtered reads were then mapped against the appropriate reference genome and plasmid sequences, available at https://github.com/Gardner-BinfLab/EnTrI using the Bio-TraDIS pipeline with the following command line options:    bacteria_tradis -v --smalt_r 0 --smalt_k 8 --smalt_s 1 --smalt_y 0.9 -m 0 -f fastqs.txt -t TAAGAGACAG -r ref.fa
For each gene in each organism, we calculated an insertion index as a measure of gene essentiality. The insertion index is calculated as (ng/lg)(nG/lG) where ng is the number of unique insertion sites in the gene, lg is the length of the gene, nG is the number of insertion sites in the genome, and lG is the length of the genome. We calculated the insertion index for each gene after trimming 5% of the sequence from the 5’ end and 20% of the sequence from the 3’ end
To correct for biases in the insertion index, we used fitted values from a generalized additive model (GAM). For each genome, we fitted a GAM curve (using the MGCV package in R) with the formula y ~ s(x) to the distance vs. insertion index plot for distance normalization. The normalized insertion indices were calculated by dividing the insertion indices by the predicted insertion index from the GAM, then multiplying them by the average insertion index. The same procedure was repeated for G-C normalization.
We used the DBSCAN R package (25) to cluster the normalized insertion indices using the DBSCAN function with parameters minPts = 200 and eps = 0.05.
Supplementary files format and content: Ghomi_SI.xslx: essentiality scores for each gene in each organism
Supplementary files format and content: .plot files: read counts per genomic position

organism: Salmonella enterica subsp. enterica serovar Typhimurium

extract_protocol:
Qiagen Genomic-tip 100/G kit
~2 μg of genomic DNA was fragmented to a size of ~300 base-pairs using a Covaris Focused ultrasonicator (Covaris), followed by end repair using the NEBNext End Repair module (NEB), A-tailing using the NEBNext dA-Tailing module (NEB), and adapter ligation using the NEBNext Quick Ligation Module with a custom splinkerette adaptor (SplA5). PCR enrichment of fragments containing transposon sequence was then carried out using transposon- and adaptor-specific primers using Kapa HiFi HotStart ReadyMix (Kapa Biosystems) for 10 to 20 cycles. PCR products were analyzed on an Agilent Bioanalyzer using a High Sensitivity DNA kit (Agilent Technologies), and by SYBR green qPCR (Kapa Biosystems). Sequencing was then performed on an Illumina HiSeq 2000 or MiSeq using transposon-specific primers and a custom dark-cycle sequencing protocol at the Wellcome Sanger Institute or the King Abdullah University of Science and Technology Bioscience Core Laboratory (Salmonella Typhimurium A130 and D23580). All custom adaptors, primers, and sequencing protocols are described in Barquist et al. "The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries" Bioinformatics 2016 and publicly available at  https://github.com/sanger-pathogens/Bio-Tradis/tree/master/recipes.
transposon insertion sequencing

value: transposon mutagenesis


title: Salmonella enterica serovar Typhimurium D23580 transposon library


title: TDP2seq_pUC19_DNA_SPO11_WT_rep2

value: pUC19 plasmid DNA digested by SPO11 in vitro


title: Ctrl_2


title: heart, IR_SI1  (ischemia 45min, reperfusion 24h, sh-YTHDF2) rep1

value: tissue

value: YTHDF2 knockdown

value: cardiac I/R (ischemia 45min, reperfusion 24h) injury


title: heart, IR_NC1 (ischemia 45min, reperfusion 24h, sh-NC) rep3


title: Ctrl_1


title: TDP2seq_pUC19_DNA_SPO11_WT_rep1


title: UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, Flag ChIP-seq

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

value: anti-Flag M2 (Sigma F3165)

value: passage 26+39+2


title: lEVs_ACSL4_KD_2


title: control B1

description: control

value: control


title: GD156_MM1S_DMSO_ctrl_rep2

status: Public on Aug 19 2024

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to human genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: hg38
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

molecule: polyA RNA

growth_protocol: MM cell lines MM.1S (ATCC, CRL-2974) and RPMI8226 (ATCC, CCL-155) were obtained from the American Type Culture Collection (Manassas, VA, USA). Cell lines tested for mycoplasma every six months. Cells were maintained in RPMI-1640 complete media as described previously (PMID: 35205675)

extract_protocol:
Total RNA was extracted using the Qiagen kit (RNeasy Plus Mini Kit, 74134)
RNA-Seq library were prepared by Admera Health (South Plainfield, NJ, USA) using NEBNext Ultra II RNA (Directional)

treatment_protocol: Cells were treated with CB-6644 (MedChemExpress, HY-114429) at concentrations (MM. 1S,120nM; RPMI 8226, 40nM) to assess its impact on cell viability over a 72-hour treatment period

value: DMSO


title: GD157_MM1S_DMSO_ctrl_rep3


title: GD155_MM1S_DMSO_ctrl_rep1


title: TDP2seq_pUC19_DNA_SPO11_YF_rep1


title: GD153_MM1S_CB6644_rep1

value: CB-6644 treatment (120nM,72hrs)


title: treated with LPS B3

description: treated with LPS

value: bone marrow derived macrophages (BMDMs)


title: GD154_MM1S_CB6644_rep2


title: control C1

description: control


title: Escherichia coli NCTC 13441 transposon mutant library

organism: Escherichia coli


title: C57BL/6J NAc, mouse B32, C57 biol rep 5

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

data_processing:
Illumina NextSeq2000
Adapters and poor-quality bases were removed using Fastp (v. 0.22.0)
Trimmed sequences were aligned using STAR (v. 2.7.10b)
Aligned BAM files were sorted by coordinate using Samtools (v. 1.6) and counts were generated using FeatureCounts (Samtools)
Assembly: GRCm39
Supplementary files format and content: comma separated variable file containing counts determined by FeatureCounts

source_name: nucleus accumbens

growth_protocol: Mice were group-housed with free access to food under a 12-hour light/dark cycle in a 21 °C environment.

extract_protocol:
NAc tissue was dissected at time of sacrifice and snap frozen in liquid nitrogen. RNA was extracted using the Qiagen mRNeasy Mini Kit. RNA quality was assessed by Agilent 2100 Bioanalyzer. All samples had RNA integrity (RIN) numbers > 7.
Poly-A library construction was performed by Novogene Bioinformatics Institute according to the company's established protocols.

value: nucleus accumbens

tag: Sex

value: male


title: C57BL/6J NAc, mouse B14, C57 biol rep 1


title: C57BL/6J NAc, mouse B31, C57 biol rep 4


title: C57BL/6J NAc, mouse B24, C57 biol rep 3


title: DBA/2J NAc, mouse D32, DBA biol rep 4


title: DBA/2J NAc, mouse D34, DBA biol rep 5


title: DBA/2J NAc, mouse D11, DBA biol rep 1


title: DBA/2J NAc, mouse D13, DBA biol rep 2


title: mESC_FGFplusCHIR_72h_r2

city: Klosterneuburg

first: Anna

last: Kicheva

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

data_processing:
RNAseq reads were trimmed using Trim galore v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Reads aligned to the GRCm38 genome using STAR aligner v2.6.0c (https://github.com/alexdobin/STAR)
Aligned reads were counted using STAR GeneCounts.
Assembly: GRCm38
Supplementary files format and content: Star counts files

growth_protocol: The differentaition protocol is described in detail in Lehr et al. Cells were treated with bFGF for 48h, then bFGF + CHIR for 24h before being moved to the treatment conditions. All treatment conditions contain RA with the addition of the noted concentration of exogenous BMP4.

extract_protocol:
Cells differentiated on stencils were dissociated into single cells and pelleted by centrifugation. Three biological replicates per timepoint and condition were collected.
Sequencing libraries were prepared by the VBC Sequencing facility using NEB poly-A stranded kit.

treatment_protocol: Cells were treated from 72h (0h, time since BMP) with 0ng/ml (RA), 1.5ng/ml (RAplus0.5ngB4), 3.0ng/ml (RAplus3ngB4) or 5ng/ml (RAplus5ngB4) BMP4

value: mESC

tag: time point

tag: time since_bmp

value: WT

value: FGFplusCHIR


title: C57BL/6J NAc, mouse B21, C57 biol rep 2


title: mESC_RA_80h_r1

value: RA


title: mESC_RAplus1.5ngB4_96h_r1


title: mESC_RAplus1.5ngB4_80h_r3


title: mESC_RAplus1.5ngB4_144h_r2


title: mESC_RAplus1.5ngB4_80h_r2


title: mESC_RAplus5ngB4_144h_r2


title: mESC_RAplus5ngB4_96h_r1


title: mESC_RAplus3ngB4_80h_r1


title: mESC_RA_80h_r3


title: DBA/2J NAc, mouse D22, DBA biol rep 3


title: mESC_RAplus0.5ngB4_96h_r3


title: mESC_RAplus3ngB4_144h_r1


title: mESC_RAplus3ngB4_96h_r2


title: mESC_RAplus0.5ngB4_144h_r2


title: mESC_RAplus1.5ngB4_80h_r1


title: mESC_RAplus1.5ngB4_96h_r3


title: mESC_RAplus0.5ngB4_80h_r3


title: mESC_RAplus0.5ngB4_144h_r1


title: mESC_RAplus1.5ngB4_144h_r1


title: mESC_RA_144h_r3


title: mESC_RAplus5ngB4_96h_r2


title: mESC_RAplus3ngB4_144h_r3


title: mESC_RAplus0.5ngB4_96h_r1


title: mESC_RAplus5ngB4_144h_r3


title: mESC_RA_144h_r1


title: mESC_RAplus1.5ngB4_144h_r3


title: mESC_RAplus5ngB4_80h_r2


title: mESC_RAplus3ngB4_96h_r3


title: mESC_RAplus0.5ngB4_96h_r2


title: mESC_RA_96h_r2


title: mESC_FGFplusCHIR_72h_r1


title: mESC_RAplus0.5ngB4_80h_r1


title: mESC_RAplus3ngB4_80h_r2


title: mESC_RAplus5ngB4_144h_r1


title: mESC_FGFplusCHIR_72h_r3


title: mESC_RAplus5ngB4_80h_r1


title: mESC_RAplus0.5ngB4_80h_r2


title: mESC_RAplus0.5ngB4_144h_r3


title: mESC_RAplus1.5ngB4_96h_r2


title: mESC_RAplus5ngB4_80h_r3


title: mESC_RAplus5ngB4_96h_r3


title: mESC_RA_96h_r3


title: mESC_RA_144h_r2


title: mESC_RAplus3ngB4_144h_r2


title: mESC_RA_96h_r1


title: HEK293T_DTAG_rep13

city: Farmington

first: Jinhong

last: Dong

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description:
HEK_ATAC_dTAG_13
Combined_ATAC_rep9-16_peak_counts.txt

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication:https://github.com/guertinlab/fqdedupv1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation:https://github.com/guertinlab/seqOutBiasv1.3.1
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: peak summit counts files

extract_protocol:
At the time of harvest, cells were moved to ice and scraped in 1mL ice cold PBS, and 100μL (∼5 x 10^4 cells) were transferred to 1.5 mL tubes. Cells were centrifuged at 500 x g for 5 minutes at 4°C, and the pellets were resuspended in 50 μL cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, adjusted to pH 7.4) and incubated on ice for 3 minutes. Samples were washed with 1 mL cold wash buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20). Cells were centrifuged at 500 x g for 10 minutes at 4°C, and pellets were resuspended in the transposition reaction mix (25 μL 2X TD buffer (Illumina), 2.5 μL TDE1 Tn5 transposase (Illumina), 16.5 μL PBS, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 5 μL nuclease-free water) and incubated in a thermomixer at 37°C and 100rpm for 30 minutes. DNA was extracted with the DNA Clean and Concentrator-5 Kit (Zymo Research).
Sequencing adapters were attached to the transposed DNA fragments using NEBNext Ultra II Q5 PCR mix (New England Biolabs), and libraries were amplified with 8 cycles of PCR. PEG-mediated size fractionation (Lis 1980) was performed on the libraries by mixing SPRIs-elect beads (Beckman) with each sample at a 0.5:1 ratio, then placing the reaction vessels on a magnetic stand. The right side selected sample was transferred to a new reaction vessel, and more beads were added for a final ratio of 1.8:1. The final size-selected sample was eluted into nuclease-free water. This size selection protocol was repeated to further remove large fragments.

treatment_protocol: HEK-293T cells were collected after either no treatment or after 30 minutes of 50nM dTAGV-1 treatment

value: 50nM dTAGV-1


title: HEK293T_DTAG_rep14

description:
HEK_ATAC_dTAG_14
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DTAG_rep16

description:
HEK_ATAC_dTAG_16
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DTAG_rep15

description:
HEK_ATAC_dTAG_15
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DTAG_rep12

description:
HEK_ATAC_dTAG_12
Combined_ATAC_rep9-16_peak_counts.txt


title: mESC_RA_80h_r2


title: HEK293T_DTAG_rep10

description:
HEK_ATAC_dTAG_10
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DMSO_rep14

description:
HEK_ATAC_control_14
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DTAG_rep11

description:
HEK_ATAC_dTAG_11
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DMSO_rep15

description:
HEK_ATAC_control_15
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DMSO_rep16

description:
HEK_ATAC_control_16
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DTAG_rep9

description:
HEK_ATAC_dTAG_9
Combined_ATAC_rep9-16_peak_counts.txt


title: mESC_RAplus3ngB4_80h_r3


title: HEK293T_DMSO_rep12

description:
HEK_ATAC_control_12
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DMSO_rep11

description:
HEK_ATAC_control_11
Combined_ATAC_rep9-16_peak_counts.txt


title: HEK293T_DMSO_rep13

description:
HEK_ATAC_control_13
Combined_ATAC_rep9-16_peak_counts.txt


title: mjb-93-026

city: Madrid

first: Leonardo

middle: Daniel

last: Garma

state: Madrid

address: Melchor Fernández Almagro 3

country: Spain

institute: Spanish National Cancer Research Center

data_processing:
Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 from within Local Run Manager (Illumina). The reads were trimmed using bbduk to remove adapter sequences and polyA tails. The reads were then aligned to the GRCh38 genome assembly using STAR 2.7.10b. The results were quantified using the featureCounts tool from the Rsubread 2.0.3 package. The gene counts obtained from different sequencing rounds from the same sample were added together to merge the results.
Assembly: hg38
Supplementary files format and content: comma-separated values of raw counts for each sample

source_name: Breast cancer tumor

extract_protocol:
For RNA extraction, snap-frozen tumor pieces (~50 mm3) were homogenized in TRizol reagent solution (Invitrogen, #AM9738) according to manufacturer’s instructions using Precellys 24 Tissue Homogeneizer (Bertin technologies). Briefly, after homogenization, chloroform was added and the resulting mixture was centrifuged at 12,000g for 10 min at 4ºC. Aqueous phase was transferred to a clean tube and 70% ethanol was added. Then, total volume was filtered through RNeasy column (Qiagen, #74104) and RNA extraction was performed following protocol instructions. RNA quality was determined by Agilent's 2100 Bioanalyzer Lab-Chip technology.
Total RNA samples (approximately 400 ng) were converted into cDNA sequencing libraries with the "QuantSeq 3‘mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, #191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. An UMI (Unique Molecular Identifier) Second Strand Synthesis module was used, in which random primers featuring a 6 nt long Unique Molecular Identifier (UMI) tag are used (to be addressed for bias correction at data analysis). Primers from both steps contain Illumina-adapter sequences. Libraries were completed by PCR and sequenced on an Illumina NextSeq 550 instrument (with v2.5 reagent kits) by following manufacturer’s protocols.

value: Breast cancer tumor


title: mjb-93-021


title: mjb-93-022


title: HEK293T_DMSO_rep9

description:
HEK_ATAC_control_9
Combined_ATAC_rep9-16_peak_counts.txt


title: mESC_RAplus3ngB4_96h_r1


title: mjb-93-020


title: mjb-93-015


title: mjb-93-012


title: mjb-93-011


title: mjb-81-009


title: mjb-93-002


title: mjb-81-008


title: mjb-55-008


title: mjb-55-003


title: mjb-55-007


title: mjb-55-009


title: mjb-93-024


title: HEK293T_DMSO_rep10

description:
HEK_ATAC_control_10
Combined_ATAC_rep9-16_peak_counts.txt


title: mjb-5001-019


title: mjb-5001-009


title: mjb-5001-017


title: mjb-5001-018


title: mjb-5001-014


title: mjb-5001-010


title: mjb-5001-005


title: mjb-5001-015


title: mjb-5001-003


title: mjb-5001-008


title: mjb-5001-006


title: mjb-5001-007


title: mjb-5001-001


title: mjb-5001-002


title: mjb-5-001


title: mjb-44-010


title: mjb-44-006


title: mjb-44-003


title: mjb-44-001


title: mjb-44-004


title: mjb-35-003


title: mjb-5001-016


title: mjb-5001-011


title: mjb-19-003


title: mjb-19-006


title: mjb-155-006


title: mjb-19-001


title: mjb-148-017


title: mjb-148-018


title: mjb-148-016


title: mjb-14-002


title: mjb-148-015


title: mjb-148-005


title: mjb-14-005


title: mjb-44-009


title: mjb-148-004


title: mjb-148-006


title: mjb-137-011


title: mjb-148-007


title: mjb-148-014


title: mjb-148-001


title: mjb-137-009


title: mjb-137-008


title: mjb-137-010


title: mjb-137-006


title: mjb-137-002


title: mjb-137-004


title: mjb-137-005


title: mjb-136-012


title: mjb-136-015


title: mjb-136-011


title: mjb-137-001


title: mjb-137-017


title: mjb-137-015


title: mjb-137-013


title: mjb-137-014


title: mjb-136-009


title: mjb-136-013


title: mjb-136-006


title: mjb-03-001


title: 93-021POST

value: Bevacizumab


title: 93-022POST


title: 81-008POST


title: 93-026POST


title: 55-003POST


title: 55-006POST


title: 55-009POST


title: 5001-016POST


title: 5001-009POST


title: 5001-011POST


title: 5001-007POST


title: 5001-018POST


title: 5001-006POST


title: 81-009POST


title: mjb-136-014


title: 5-001POST


title: 5001-002POST


title: 35-002POST


title: 35-003POST


title: 44-004POST


title: 148-015POST


title: 14-005POST


title: 137-017POST


title: 137-015POST


title: 148-010POST


title: 137-013POST


title: 136-010POST


title: 136-012POST


title: 136-007POST


title: 137-011POST


title: 137-003POST


title: G. max- LMV 105-rep2

city: Knoxville

first: Tarek

last: Hewezi

address: 2621 Morgan Circle

institute: University of Tennessee, Knoxvile

description:
L. Merr.
Nodules were harvested at 25 days post inoculation (DPI)
W82_CL_2

data_processing:
The quality of raw reads was determined using FastQC.
Reads were then mapped against the soybean reference genome (Williams 82 genome assembly v4) using STAR.
The HTSeq tool was utilized to obtain the read count for all transcripts.
Assembly: Williams 82 genome assembly v4
Supplementary files format and content: Read count text files were generated using Htseq.

organism: Glycine max

source_name: Root

extract_protocol:
Total RNA from 25 DPI soybean nodules were isolated using TRIzol® Reagent (Thermo Fisher Scientific, Waltham MA, USA). Contaminating genomic DNA was removed by treating total RNA with DNase I. RNA integrity was determined using Agilent 2100 (Agilent, Technologies, CA). mRNA was isolated and used for construction of non-stranded, nondirectional mRNA libraries.
Libraries were constructed using the Illumina RNA Library Prep Kit.

value: Root

value: Nodule

value: Whole nodule

value: G. max

value: Roots of three-day old seedlings were inoculated with Bradyrhizobial strain LVM 105


title: G. max- LMV 105-rep3

description:
L. Merr.
Nodules were harvested at 25 days post inoculation (DPI)
W82_CL_3


title: 136-005POST


title: G. max- USDA 110-rep3

description:
L. Merr.
Nodules were harvested at 25 days post inoculation (DPI)
W82B1103

value: Roots of three-day old seedlings were inoculated with Bradyrhizobial strain USDA 110


title: 136-003POST


title: G. max- USDA 110-rep1

description:
L. Merr.
Nodules were harvested at 25 days post inoculation (DPI)
W82B1101


title: G. max- LMV 105-rep1

description:
L. Merr.
Nodules were harvested at 25 days post inoculation (DPI)
W82_CL_1


title: vanillin, biol rep 3

city: Campinas

first: Joaquim

last: Martins Junior

state: SP

address: Rua Giuseppe Maximo Scolfaro 10000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
The raw reads generated in the RNA-seq were filtered to remove adapters or low-quality sequences using the fastp tool, and contaminant rRNA reads were removed using sortmeRNA.
High-quality reads were mapped in the X. citri 306 genome (GI: 21240769) using the Bowtie2 tool
Samtools program was used to process the alignment files viewed using the Integrative Genome viewer program
The mapped reads in the X. citri 306 transcripts were counted using the featureCounts tool
The data processed were summarized and plotted by multiQC package
Assembly: GI: 21240769
Supplementary files format and content: TPM_counts.xlsx (tab-delimited TPM counts)
Supplementary files format and content: Raw_counts.xlsx (tab-delimited raw counts)
Supplementary files format and content: DE.table_edgeR.xlsx (tab-delimited differentially expressed genes)

organism: Xanthomonas citri subsp. citri 306

source_name: bacterial cells

growth_protocol: Cells were grown at 30 ºC, 200 rpm in 40 mL XVM2m minimal medium supplemented with six lignin-related aromatic compounds (coniferyl alcohol, 4-hydroxybenzoate, 4-hydroxybenzaldehyde, vanillin, syringaldehyde, and benzaldehyde), three complex mixtures of lignin-derived compounds (LM lignin, Light Bio-oil, and aldehydes mix), or glucose (as a reference). Samples were collected at the mid-exponential phase (OD600 = 0.05-0.1) from four biological replicates. The cells were pelleted, resuspended in 1.2 mL TRIzol™, and stored at -80 ºC until RNA extraction.

extract_protocol:
Total RNA was extracted using the TRIzol™/chloroform method. Samples were treated with RNase-free DNaseI (Invitrogen) and RNaseOUT (Invitrogen) for 30 min, at 37 °C, and purified with the RNeasy Mini Kit (Qiagen), following manufacturer’s recommendations. RNA samples integrity was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies). The rRNA was depleted with Ribo-Zero Plus rRNA Depletion Kit (Illumina Inc.).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina Inc.), following manufacturer’s recommendations.

value: bacterial cells

value: vanillin


title: vanillin, biol rep 4


title: syringaldehyde, biol rep 4

value: syringaldehyde


title: syringaldehyde, biol rep 3


title: syringaldehyde, biol rep 2


title: vanillin, biol rep 1


title: syringaldehyde, biol rep 1


title: aldehyde mixture, biol rep 1

value: aldehyde mixture


title: aldehyde mixture, biol rep 4


title: low molecular weight lignin, biol rep 4

value: low molecular weight lignin


title: aldehyde mixture, biol rep 3

value: WT


title: glucose, reference condition, biol rep 4

value: glucose, reference condition


title: low molecular weight lignin, biol rep 2


title: low molecular weight lignin, biol rep 3


title: 4-hydroxybenzaldehyde, biol rep 3


title: glucose, reference condition, biol rep 2


title: glucose, reference condition, biol rep 1


title: glucose, reference condition, biol rep 3


title: G. max- USDA 110-rep2

description:
L. Merr.
Nodules were harvested at 25 days post inoculation (DPI)
W82B1102


title: low molecular weight lignin, biol rep 1


title: vanillin, biol rep 2


title: 4-hydroxybenzaldehyde, biol rep 1


title: Light Bio-oil, biol rep 3

value: Light Bio-oil


title: benzaldehyde, biol rep 4

value: benzaldehyde


title: Light Bio-oil, biol rep 4


title: benzaldehyde, biol rep 3


title: coniferyl alcohol, biol rep 2

value: coniferyl alcohol


title: benzaldehyde, biol rep 1


title: coniferyl alcohol, biol rep 1


title: coniferyl alcohol, biol rep 4


title: aldehyde mixture, biol rep 2


title: 4-hydroxybenzoate, biol rep 4


title: 4-hydroxybenzoate, biol rep 3


title: 4-hydroxybenzoate, biol rep 2


title: 4-hydroxybenzaldehyde, biol rep 2


title: dtolC tufA::kan, NMM, rep3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
Sequence quality was determined using FASTQC to determine quality per base in each sample
FASTQC was also used to determine GC content per sample
Sequences were trimmed using Trimmomatic v.0.36 to remove possible adapter sequences and poor qualty nucleotides
Assembly: Sequence reads were aligned to the Escherichia coli K-12 MG1655 reference genome on ENSEMBL using Bowtie2 aligner v.2.26
Supplementary files format and content: csv files include raw count values for each sample
Supplementary files format and content: csv files include TPM values for each sample

growth_protocol: Cells were grown in Luria Broth prior to harvesting cells

extract_protocol:
RNA extraction was conducted by Genewiz with rRNA depletion followed by RNA fragmentation and cDNA synthesis
Adaptor ligation was conducted by Genewiz using dual index primers followed by PCR enrichment and sequencing

treatment_protocol: Cells were grown either in the presence or absence of the G-quadruplex stabilizing compound, NMM. Cells were then harvested via centrifugation and flash frozen. Cells were shipped to Genewiz for RNA extraction and preparation for sequencing.

value: bacterial cell

value: tolC and tufA deletion

value: NMM treated


title: 4-hydroxybenzoate, biol rep 1


title: dtolC tufA::kan, NMM, rep1


title: Light Bio-oil, biol rep 2


title: dtolC tufA::kan, rep3


title: Light Bio-oil, biol rep 1


title: dtolC tufA::kan, rep2


title: dtolC, NMM, rep2

value: WT, with tolC deletion


title: dtolC tufA::kan, rep1


title: dtolC, NMM, rep1


title: dtolC, rep1


title: dtolC, rep3


title: dtolC, rep2


title: benzaldehyde, biol rep 2


title: dtolC tufA::kan, NMM, rep2


city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
CRE6 -116 kb, unsorted control pool library6 rep1
E2262 CRE6 -116 kb, unsorted control pool library6 rep1 Rv
mapped_integrations_short_neutral_insert.txt

data_processing:
The full protocol is described in the corresponding manuscript. In short, reads overlapping the SB-genome junction were selected, SB-sequences were trimmed off (using an adapted version of cutadapt) and reads were mapped to the genome (mm10 or an in silico version of mm10 including the hopping launch pad at -116 kb), filtering for mapq >=10. All putative integrations are lifted over to mm10.
Assembly: mm10
Supplementary files format and content: The processed data file reports all putative integrations mapped in a pool or clone (supported by at least one mapping read, filtering in the manuscript can be more strict). Columns: chr = chromosome; start, end = integration location; seq = dinucleotide at integration site (expected for SB: TA); strand = strand of integration (orientation); read_count = total read count, mapq = total mapping quality (of all reads); read_count_1/mapq_1 = forward mapping reads (3' ITR); read_count_2/mapq_2 = reverse mapping reads (5' ITR); all other columns specify and annotate the sequenced sample. There is one processed data file per founder cell line (pool-based experiments) and one for the isolated clones.

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) Sox2 mCherry+/eGFP+ were cultured in Serum+Lif+2i condition. Briefly, cells were cultured on gelatin-coated (0.1%) culture plates in Glasgow minimum essential medium (Sigma-Aldrich, G5154) supplemented with 15% fetal bovine serum (Thermo Fisher Scientific, 10270-106), 1% L-glutamine (Thermo Fisher Scientific, 25030024), 1% sodium pyruvate (Thermo Fisher Scientific, 11360-70), 1% MEM non-essential amino acids (Thermo Fisher Scientific, 11140-50), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15070063), 100 µM ß-mercaptoethanol, 10 x 4 U leukemia inhibitory factor (LIF; esg1107, Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress) in 5% CO2 at 37°C. Cells were passaged every 2 days.

extract_protocol:
Sorted pools and clones were expanded and crude lysates were obtained from a full 96 well plate by lysing with 50 µL DirectPCR Lysis Reagent (102-T, Viagen Biotec) supplemented with 100 µg/mL proteinase K, and incubating 2.5 h at 55 °C and 45 min at 85 °C. For unsorted control cell pools, gDNA was extracted after expansion using the ISOLATE II Genomic DNA Kit (BIO-52067, Bioline).
SBt integrations were mapped by amplifying and sequencing the ITR-genome junction using a tagmentation-based approach. The procedure was similar to {Schep, 2021, 33848455}, but using the following SB-ITR specific primers: MEP009 (5′ ITR, reverse) or LD027 (3′ ITR, forward) for the linear enrichment and MEP011 (5′ ITR, reverse) or MEP034 (3′ ITR, forward) for PCR.Input for one tagmentation reaction was either 100ng gDNA or 3 µL crude lysate. The 72 °C extension times of all PCRs were increased to 1 min. In addition, the composition of the linear enrichment PCR was changed to 10 μL of tagmented DNA, 2 μL of 1 μM primer, 4 μL dNTPs (10mM), 8 μL 5x Phusion® HF Buffer (NEB), 0.5 μL Phusion® HS Flex polymerase (2 U/μL - NEB), in a final volume of 40 μL. For all clones and some experiments with sorted pools (proof-of-principle experiment, third replicate of the reporter hopping) we halved this reaction to a final volume of 20 µL. For the unsorted control pools, 10 separate tagmentation reactions and library preparations were performed, usually using one set of sequencing indices. Libraries were sequenced with 150 bp paired-end reads using either an Illumina MiSeq system (reagent kit v2) or  Illumina NextSeq 550 system (mid-output kit) including 10% of PhiX spike-in.  Primers are described in the corresponding manuscript.

treatment_protocol: SB hopping was induced by transfecting 2.5 to 5 million cells with the bicistronic plasmid (pME07) encoding SB transposase SB100x and the human nerve growth factor receptor (LNGFR), using Lipofectamine 2000 (Invitrogen, 11668019) and 5 µg of plasmid per million cells. After 30 hours, transfected cells were enriched using MACS MS columns (130-042-201, Miltenyi Biotec) and LNGFR MicroBeads (130-091-330, Miltenyi Biotec) according to the manufacturer’s protocol. One week after transfection, 0.2 million SB-transposase-transfected cells were set apart as an unsorted pool and the remaining cells were FACS sorted into pools (of up to 1000 cells) based on reporter expression. Clones were obtained by sorting single cells from previously obtained pools, or sorted directly from the full pool of SB-transposase-transfected cells.

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: control pool


description:
CRE6 -116 kb, unsorted control pool library7 rep1
E2262 CRE6 -116 kb, unsorted control pool library7 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library3 rep1
E2262 CRE6 -116 kb, unsorted control pool library3 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library8 rep1
E2262 CRE6 -116 kb, unsorted control pool library8 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library10 rep1
E2262 CRE6 -116 kb, unsorted control pool library10 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library2 rep1
E2262 CRE6 -116 kb, unsorted control pool library2 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library5 rep1
E2262 CRE6 -116 kb, unsorted control pool library5 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library4 rep1
E2262 CRE6 -116 kb, unsorted control pool library4 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library5 rep1
E2262 CRE6 -116 kb, unsorted control pool library5 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library1 rep1
E2262 CRE6 -116 kb, unsorted control pool library1 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library2 rep1
E2262 CRE6 -116 kb, unsorted control pool library2 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library1 rep1
E2262 CRE6 -116 kb, unsorted control pool library1 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library4 rep1
E2262 CRE6 -116 kb, unsorted control pool library4 rep1 Rv
mapped_integrations_short_neutral_insert.txt


title: dtolC, NMM, rep3


description:
CRE6 -116 kb, unsorted control pool library3 rep1
E2262 CRE6 -116 kb, unsorted control pool library3 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library9 rep1
E2262 CRE6 -116 kb, unsorted control pool library9 rep1 Rv
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library9 rep1
E2262 CRE6 -116 kb, unsorted control pool library9 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library8 rep1
E2262 CRE6 -116 kb, unsorted control pool library8 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library7 rep1
E2262 CRE6 -116 kb, unsorted control pool library7 rep1 Fw
mapped_integrations_short_neutral_insert.txt


description:
CRE6 -116 kb, unsorted control pool library6 rep1
E2262 CRE6 -116 kb, unsorted control pool library6 rep1 Fw
mapped_integrations_short_neutral_insert.txt


title: clone Sox2P-reporter E2270_23_34A_A7 Rv

description:
clone Sox2P-reporter E2270_23_34A_A7
clone Sox2P-reporter E2270_23_34A_A7 Rv
mapped_integrations_Sox2P_clones.txt

value: deletion clone


title: clone Sox2P-reporter E2270_23_34A_A5 Rv

description:
clone Sox2P-reporter E2270_23_34A_A5
clone Sox2P-reporter E2270_23_34A_A5 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A4 Rv

description:
clone Sox2P-reporter E2270_23_34A_A4
clone Sox2P-reporter E2270_23_34A_A4 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A1 Rv

description:
clone Sox2P-reporter E2270_23_34A_A1
clone Sox2P-reporter E2270_23_34A_A1 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A2 Rv

description:
clone Sox2P-reporter E2270_23_34A_A2
clone Sox2P-reporter E2270_23_34A_A2 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2259_23_34A_B12
clone Sox2P-reporter E2259_23_34A_B12 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2259_23_34A_B11
clone Sox2P-reporter E2259_23_34A_B11 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A3 Rv

description:
clone Sox2P-reporter E2270_23_34A_A3
clone Sox2P-reporter E2270_23_34A_A3 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2259_23_34A_B10
clone Sox2P-reporter E2259_23_34A_B10 Fw
mapped_integrations_Sox2P_clones.txt


description:
CRE6 -116 kb, unsorted control pool library10 rep1
E2262 CRE6 -116 kb, unsorted control pool library10 rep1 Fw
mapped_integrations_short_neutral_insert.txt


title: clone Sox2P-reporter E2270_23_34A_A5 Fw

description:
clone Sox2P-reporter E2270_23_34A_A5
clone Sox2P-reporter E2270_23_34A_A5 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_D11
clone Sox2P-reporter E2270_23_34A_D11 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_D12
clone Sox2P-reporter E2270_23_34A_D12 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B8 Fw

description:
clone Sox2P-reporter E2259_23_34A_B8
clone Sox2P-reporter E2259_23_34A_B8 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B9 Fw

description:
clone Sox2P-reporter E2259_23_34A_B9
clone Sox2P-reporter E2259_23_34A_B9 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A9 Fw

description:
clone Sox2P-reporter E2270_23_34A_A9
clone Sox2P-reporter E2270_23_34A_A9 Fw
mapped_integrations_Sox2P_clones.txt

value: ambiguous clone


title: clone Sox2P-reporter E2270_23_34A_A8 Fw

description:
clone Sox2P-reporter E2270_23_34A_A8
clone Sox2P-reporter E2270_23_34A_A8 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B7 Fw

description:
clone Sox2P-reporter E2259_23_34A_B7
clone Sox2P-reporter E2259_23_34A_B7 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A4 Fw

description:
clone Sox2P-reporter E2270_23_34A_A4
clone Sox2P-reporter E2270_23_34A_A4 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_D10
clone Sox2P-reporter E2270_23_34A_D10 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D9 Fw

description:
clone Sox2P-reporter E2270_23_34A_D9
clone Sox2P-reporter E2270_23_34A_D9 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_A10
clone Sox2P-reporter E2270_23_34A_A10 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D4 Fw

description:
clone Sox2P-reporter E2270_23_34A_D4
clone Sox2P-reporter E2270_23_34A_D4 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B3 Fw

description:
clone Sox2P-reporter E2259_23_34A_B3
clone Sox2P-reporter E2259_23_34A_B3 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B2 Fw

description:
clone Sox2P-reporter E2259_23_34A_B2
clone Sox2P-reporter E2259_23_34A_B2 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A7 Fw

description:
clone Sox2P-reporter E2270_23_34A_A7
clone Sox2P-reporter E2270_23_34A_A7 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D6 Fw

description:
clone Sox2P-reporter E2270_23_34A_D6
clone Sox2P-reporter E2270_23_34A_D6 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D8 Fw

description:
clone Sox2P-reporter E2270_23_34A_D8
clone Sox2P-reporter E2270_23_34A_D8 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D5 Fw

description:
clone Sox2P-reporter E2270_23_34A_D5
clone Sox2P-reporter E2270_23_34A_D5 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D7 Fw

description:
clone Sox2P-reporter E2270_23_34A_D7
clone Sox2P-reporter E2270_23_34A_D7 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D3 Fw

description:
clone Sox2P-reporter E2270_23_34A_D3
clone Sox2P-reporter E2270_23_34A_D3 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D1 Fw

description:
clone Sox2P-reporter E2270_23_34A_D1
clone Sox2P-reporter E2270_23_34A_D1 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_C12
clone Sox2P-reporter E2270_23_34A_C12 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_C10
clone Sox2P-reporter E2270_23_34A_C10 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_C11
clone Sox2P-reporter E2270_23_34A_C11 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C9 Fw

description:
clone Sox2P-reporter E2270_23_34A_C9
clone Sox2P-reporter E2270_23_34A_C9 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C7 Fw

description:
clone Sox2P-reporter E2270_23_34A_C7
clone Sox2P-reporter E2270_23_34A_C7 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A3 Fw

description:
clone Sox2P-reporter E2270_23_34A_A3
clone Sox2P-reporter E2270_23_34A_A3 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C6 Fw

description:
clone Sox2P-reporter E2270_23_34A_C6
clone Sox2P-reporter E2270_23_34A_C6 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C5 Fw

description:
clone Sox2P-reporter E2270_23_34A_C5
clone Sox2P-reporter E2270_23_34A_C5 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C8 Fw

description:
clone Sox2P-reporter E2270_23_34A_C8
clone Sox2P-reporter E2270_23_34A_C8 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D2 Fw

description:
clone Sox2P-reporter E2270_23_34A_D2
clone Sox2P-reporter E2270_23_34A_D2 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C4 Fw

description:
clone Sox2P-reporter E2270_23_34A_C4
clone Sox2P-reporter E2270_23_34A_C4 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B9 Fw

description:
clone Sox2P-reporter E2270_23_34A_B9
clone Sox2P-reporter E2270_23_34A_B9 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C1 Fw

description:
clone Sox2P-reporter E2270_23_34A_C1
clone Sox2P-reporter E2270_23_34A_C1 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C2 Fw

description:
clone Sox2P-reporter E2270_23_34A_C2
clone Sox2P-reporter E2270_23_34A_C2 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_B12
clone Sox2P-reporter E2270_23_34A_B12 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B3 Rv

description:
clone Sox2P-reporter E2259_23_34A_B3
clone Sox2P-reporter E2259_23_34A_B3 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B7 Rv

description:
clone Sox2P-reporter E2259_23_34A_B7
clone Sox2P-reporter E2259_23_34A_B7 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_B10
clone Sox2P-reporter E2270_23_34A_B10 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B2 Rv

description:
clone Sox2P-reporter E2259_23_34A_B2
clone Sox2P-reporter E2259_23_34A_B2 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C3 Fw

description:
clone Sox2P-reporter E2270_23_34A_C3
clone Sox2P-reporter E2270_23_34A_C3 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2259_23_34A_B12
clone Sox2P-reporter E2259_23_34A_B12 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2259_23_34A_B10
clone Sox2P-reporter E2259_23_34A_B10 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2259_23_34A_B11
clone Sox2P-reporter E2259_23_34A_B11 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B6 Fw

description:
clone Sox2P-reporter E2270_23_34A_B6
clone Sox2P-reporter E2270_23_34A_B6 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B7 Fw

description:
clone Sox2P-reporter E2270_23_34A_B7
clone Sox2P-reporter E2270_23_34A_B7 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B8 Fw

description:
clone Sox2P-reporter E2270_23_34A_B8
clone Sox2P-reporter E2270_23_34A_B8 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A2 Fw

description:
clone Sox2P-reporter E2270_23_34A_A2
clone Sox2P-reporter E2270_23_34A_A2 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B8 Rv

description:
clone Sox2P-reporter E2259_23_34A_B8
clone Sox2P-reporter E2259_23_34A_B8 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B4 Fw

description:
clone Sox2P-reporter E2270_23_34A_B4
clone Sox2P-reporter E2270_23_34A_B4 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_D12
clone Sox2P-reporter E2270_23_34A_D12 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B3 Fw

description:
clone Sox2P-reporter E2270_23_34A_B3
clone Sox2P-reporter E2270_23_34A_B3 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_D10
clone Sox2P-reporter E2270_23_34A_D10 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_D11
clone Sox2P-reporter E2270_23_34A_D11 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D6 Rv

description:
clone Sox2P-reporter E2270_23_34A_D6
clone Sox2P-reporter E2270_23_34A_D6 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D5 Rv

description:
clone Sox2P-reporter E2270_23_34A_D5
clone Sox2P-reporter E2270_23_34A_D5 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2259_23_34A_B9 Rv

description:
clone Sox2P-reporter E2259_23_34A_B9
clone Sox2P-reporter E2259_23_34A_B9 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D4 Rv

description:
clone Sox2P-reporter E2270_23_34A_D4
clone Sox2P-reporter E2270_23_34A_D4 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D7 Rv

description:
clone Sox2P-reporter E2270_23_34A_D7
clone Sox2P-reporter E2270_23_34A_D7 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_B11
clone Sox2P-reporter E2270_23_34A_B11 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B5 Fw

description:
clone Sox2P-reporter E2270_23_34A_B5
clone Sox2P-reporter E2270_23_34A_B5 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_C12
clone Sox2P-reporter E2270_23_34A_C12 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D8 Rv

description:
clone Sox2P-reporter E2270_23_34A_D8
clone Sox2P-reporter E2270_23_34A_D8 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D2 Rv

description:
clone Sox2P-reporter E2270_23_34A_D2
clone Sox2P-reporter E2270_23_34A_D2 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D3 Rv

description:
clone Sox2P-reporter E2270_23_34A_D3
clone Sox2P-reporter E2270_23_34A_D3 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D9 Rv

description:
clone Sox2P-reporter E2270_23_34A_D9
clone Sox2P-reporter E2270_23_34A_D9 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C6 Rv

description:
clone Sox2P-reporter E2270_23_34A_C6
clone Sox2P-reporter E2270_23_34A_C6 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_C11
clone Sox2P-reporter E2270_23_34A_C11 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C9 Rv

description:
clone Sox2P-reporter E2270_23_34A_C9
clone Sox2P-reporter E2270_23_34A_C9 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C7 Rv

description:
clone Sox2P-reporter E2270_23_34A_C7
clone Sox2P-reporter E2270_23_34A_C7 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C8 Rv

description:
clone Sox2P-reporter E2270_23_34A_C8
clone Sox2P-reporter E2270_23_34A_C8 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C5 Rv

description:
clone Sox2P-reporter E2270_23_34A_C5
clone Sox2P-reporter E2270_23_34A_C5 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B1 Fw

description:
clone Sox2P-reporter E2270_23_34A_B1
clone Sox2P-reporter E2270_23_34A_B1 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_D1 Rv

description:
clone Sox2P-reporter E2270_23_34A_D1
clone Sox2P-reporter E2270_23_34A_D1 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_B12
clone Sox2P-reporter E2270_23_34A_B12 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_C10
clone Sox2P-reporter E2270_23_34A_C10 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C1 Rv

description:
clone Sox2P-reporter E2270_23_34A_C1
clone Sox2P-reporter E2270_23_34A_C1 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_B11
clone Sox2P-reporter E2270_23_34A_B11 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C3 Rv

description:
clone Sox2P-reporter E2270_23_34A_C3
clone Sox2P-reporter E2270_23_34A_C3 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C2 Rv

description:
clone Sox2P-reporter E2270_23_34A_C2
clone Sox2P-reporter E2270_23_34A_C2 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B9 Rv

description:
clone Sox2P-reporter E2270_23_34A_B9
clone Sox2P-reporter E2270_23_34A_B9 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B2 Fw

description:
clone Sox2P-reporter E2270_23_34A_B2
clone Sox2P-reporter E2270_23_34A_B2 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B7 Rv

description:
clone Sox2P-reporter E2270_23_34A_B7
clone Sox2P-reporter E2270_23_34A_B7 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_A12
clone Sox2P-reporter E2270_23_34A_A12 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_B10
clone Sox2P-reporter E2270_23_34A_B10 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B5 Rv

description:
clone Sox2P-reporter E2270_23_34A_B5
clone Sox2P-reporter E2270_23_34A_B5 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B2 Rv

description:
clone Sox2P-reporter E2270_23_34A_B2
clone Sox2P-reporter E2270_23_34A_B2 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_A12
clone Sox2P-reporter E2270_23_34A_A12 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B3 Rv

description:
clone Sox2P-reporter E2270_23_34A_B3
clone Sox2P-reporter E2270_23_34A_B3 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_C4 Rv

description:
clone Sox2P-reporter E2270_23_34A_C4
clone Sox2P-reporter E2270_23_34A_C4 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B4 Rv

description:
clone Sox2P-reporter E2270_23_34A_B4
clone Sox2P-reporter E2270_23_34A_B4 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_A10
clone Sox2P-reporter E2270_23_34A_A10 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B1 Rv

description:
clone Sox2P-reporter E2270_23_34A_B1
clone Sox2P-reporter E2270_23_34A_B1 Rv
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_A11
clone Sox2P-reporter E2270_23_34A_A11 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A9 Rv

description:
clone Sox2P-reporter E2270_23_34A_A9
clone Sox2P-reporter E2270_23_34A_A9 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-55_34 Rv

description:
clone Sox2P-reporter 2-55_34
E2221 clone Sox2P-reporter 2-55_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B6 Rv

description:
clone Sox2P-reporter E2270_23_34A_B6
clone Sox2P-reporter E2270_23_34A_B6 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A1 Fw

description:
clone Sox2P-reporter E2270_23_34A_A1
clone Sox2P-reporter E2270_23_34A_A1 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-46_34 Rv

description:
clone Sox2P-reporter 2-46_34
E2221 clone Sox2P-reporter 2-46_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-44_34 Rv

description:
clone Sox2P-reporter 2-44_34
E2221 clone Sox2P-reporter 2-44_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_B8 Rv

description:
clone Sox2P-reporter E2270_23_34A_B8
clone Sox2P-reporter E2270_23_34A_B8 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-40_34 Rv

description:
clone Sox2P-reporter 2-40_34
E2221 clone Sox2P-reporter 2-40_34 Rv
mapped_integrations_Sox2P_clones.txt

value: insertion clone


title: clone Sox2P-reporter 2-52_34 Rv

description:
clone Sox2P-reporter 2-52_34
E2221 clone Sox2P-reporter 2-52_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-43_34 Rv

description:
clone Sox2P-reporter 2-43_34
E2221 clone Sox2P-reporter 2-43_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-37_34 Rv

description:
clone Sox2P-reporter 2-37_34
E2221 clone Sox2P-reporter 2-37_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-45_34 Rv

description:
clone Sox2P-reporter 2-45_34
E2221 clone Sox2P-reporter 2-45_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-13_34 Rv

description:
clone Sox2P-reporter 2-13_34
E2221 clone Sox2P-reporter 2-13_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-52_34 Fw

description:
clone Sox2P-reporter 2-52_34
E2221 clone Sox2P-reporter 2-52_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter E2270_23_34A_A8 Rv

description:
clone Sox2P-reporter E2270_23_34A_A8
clone Sox2P-reporter E2270_23_34A_A8 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-92_34 Fw

description:
clone Sox2P-reporter 1-92_34
E2221 clone Sox2P-reporter 1-92_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-96_34 Fw

description:
clone Sox2P-reporter 1-96_34
E2221 clone Sox2P-reporter 1-96_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-91_34 Fw

description:
clone Sox2P-reporter 1-91_34
E2221 clone Sox2P-reporter 1-91_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-94_34 Fw

description:
clone Sox2P-reporter 1-94_34
E2221 clone Sox2P-reporter 1-94_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-90_34 Fw

description:
clone Sox2P-reporter 1-90_34
E2221 clone Sox2P-reporter 1-90_34 Fw
mapped_integrations_Sox2P_clones.txt


description:
clone Sox2P-reporter E2270_23_34A_A11
clone Sox2P-reporter E2270_23_34A_A11 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-83_34 Fw

description:
clone Sox2P-reporter 1-83_34
E2221 clone Sox2P-reporter 1-83_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-46_34 Fw

description:
clone Sox2P-reporter 2-46_34
E2221 clone Sox2P-reporter 2-46_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-77_34 Fw

description:
clone Sox2P-reporter 1-77_34
E2221 clone Sox2P-reporter 1-77_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-84_34 Fw

description:
clone Sox2P-reporter 1-84_34
E2221 clone Sox2P-reporter 1-84_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-73_34 Fw

description:
clone Sox2P-reporter 1-73_34
E2221 clone Sox2P-reporter 1-73_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-81_34 Fw

description:
clone Sox2P-reporter 1-81_34
E2221 clone Sox2P-reporter 1-81_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-72_34 Fw

description:
clone Sox2P-reporter 1-72_34
E2221 clone Sox2P-reporter 1-72_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-85_34 Fw

description:
clone Sox2P-reporter 1-85_34
E2221 clone Sox2P-reporter 1-85_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-69_34 Fw

description:
clone Sox2P-reporter 1-69_34
E2221 clone Sox2P-reporter 1-69_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-68_34 Fw

description:
clone Sox2P-reporter 1-68_34
E2221 clone Sox2P-reporter 1-68_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-66_34 Fw

description:
clone Sox2P-reporter 1-66_34
E2221 clone Sox2P-reporter 1-66_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-62_34 Fw

description:
clone Sox2P-reporter 1-62_34
E2221 clone Sox2P-reporter 1-62_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-70_34 Fw

description:
clone Sox2P-reporter 1-70_34
E2221 clone Sox2P-reporter 1-70_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-64_34 Fw

description:
clone Sox2P-reporter 1-64_34
E2221 clone Sox2P-reporter 1-64_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-63_34 Fw

description:
clone Sox2P-reporter 1-63_34
E2221 clone Sox2P-reporter 1-63_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-60_34 Fw

description:
clone Sox2P-reporter 1-60_34
E2221 clone Sox2P-reporter 1-60_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-56_34 Fw

description:
clone Sox2P-reporter 1-56_34
E2221 clone Sox2P-reporter 1-56_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-55_34 Fw

description:
clone Sox2P-reporter 1-55_34
E2221 clone Sox2P-reporter 1-55_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-53_34 Fw

description:
clone Sox2P-reporter 1-53_34
E2221 clone Sox2P-reporter 1-53_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-52_34 Fw

description:
clone Sox2P-reporter 1-52_34
E2221 clone Sox2P-reporter 1-52_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-50_34 Fw

description:
clone Sox2P-reporter 1-50_34
E2221 clone Sox2P-reporter 1-50_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-44_34 Fw

description:
clone Sox2P-reporter 2-44_34
E2221 clone Sox2P-reporter 2-44_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-87_34 Fw

description:
clone Sox2P-reporter 1-87_34
E2221 clone Sox2P-reporter 1-87_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-80_34 Fw

description:
clone Sox2P-reporter 1-80_34
E2221 clone Sox2P-reporter 1-80_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-79_34 Fw

description:
clone Sox2P-reporter 1-79_34
E2221 clone Sox2P-reporter 1-79_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-47_34 Fw

description:
clone Sox2P-reporter 1-47_34
E2221 clone Sox2P-reporter 1-47_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-48_34 Fw

description:
clone Sox2P-reporter 1-48_34
E2221 clone Sox2P-reporter 1-48_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-45_34 Fw

description:
clone Sox2P-reporter 2-45_34
E2221 clone Sox2P-reporter 2-45_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-44_34 Fw

description:
clone Sox2P-reporter 1-44_34
E2221 clone Sox2P-reporter 1-44_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-71_34 Fw

description:
clone Sox2P-reporter 1-71_34
E2221 clone Sox2P-reporter 1-71_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-49_34 Fw

description:
clone Sox2P-reporter 1-49_34
E2221 clone Sox2P-reporter 1-49_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-43_34 Fw

description:
clone Sox2P-reporter 1-43_34
E2221 clone Sox2P-reporter 1-43_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-45_34 Fw

description:
clone Sox2P-reporter 1-45_34
E2221 clone Sox2P-reporter 1-45_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-40_34 Fw

description:
clone Sox2P-reporter 1-40_34
E2221 clone Sox2P-reporter 1-40_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-39_34 Fw

description:
clone Sox2P-reporter 1-39_34
E2221 clone Sox2P-reporter 1-39_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-41_34 Fw

description:
clone Sox2P-reporter 1-41_34
E2221 clone Sox2P-reporter 1-41_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-42_34 Fw

description:
clone Sox2P-reporter 1-42_34
E2221 clone Sox2P-reporter 1-42_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-33_34 Fw

description:
clone Sox2P-reporter 1-33_34
E2221 clone Sox2P-reporter 1-33_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-43_34 Fw

description:
clone Sox2P-reporter 2-43_34
E2221 clone Sox2P-reporter 2-43_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-36_34 Fw

description:
clone Sox2P-reporter 1-36_34
E2221 clone Sox2P-reporter 1-36_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-34_34 Fw

description:
clone Sox2P-reporter 1-34_34
E2221 clone Sox2P-reporter 1-34_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-54_34 Fw

description:
clone Sox2P-reporter 1-54_34
E2221 clone Sox2P-reporter 1-54_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-30_34 Fw

description:
clone Sox2P-reporter 1-30_34
E2221 clone Sox2P-reporter 1-30_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-26_34 Fw

description:
clone Sox2P-reporter 1-26_34
E2221 clone Sox2P-reporter 1-26_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-29_34 Fw

description:
clone Sox2P-reporter 1-29_34
E2221 clone Sox2P-reporter 1-29_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-23_34 Fw

description:
clone Sox2P-reporter 1-23_34
E2221 clone Sox2P-reporter 1-23_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-22_34 Fw

description:
clone Sox2P-reporter 1-22_34
E2221 clone Sox2P-reporter 1-22_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-32_34 Fw

description:
clone Sox2P-reporter 1-32_34
E2221 clone Sox2P-reporter 1-32_34 Fw
mapped_integrations_Sox2P_clones.txt


title: GD2006-Busada_LIR_WT3

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

source_name: Peritoneal macrophages

extract_protocol:
Total RNA was extracted using ORNA was isolated using the Microelute RNA isolation kit (Omega Bio-Tek) with on-column DNase treatment (Omega Bio-Tek) following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using NEBNext Low Input/Single Cell RNA-Seq kit following manufacture's protocols

treatment_protocol: 3 hours vehicle or 10^7 H. pylori PMSS1

value: Peritoneal macrophages

value: vehicle


title: GD2005-Busada_LIR_WT2


title: GD2004-Busada_LIR_WT1


title: GD2007-Busada_LIR_WT4


title: clone Sox2P-reporter 2-40_34 Fw

description:
clone Sox2P-reporter 2-40_34
E2221 clone Sox2P-reporter 2-40_34 Fw
mapped_integrations_Sox2P_clones.txt

value: WT


title: clone Sox2P-reporter 1-21_34 Fw

description:
clone Sox2P-reporter 1-21_34
E2221 clone Sox2P-reporter 1-21_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-38_34 Fw

description:
clone Sox2P-reporter 1-38_34
E2221 clone Sox2P-reporter 1-38_34 Fw
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-20_34 Fw

description:
clone Sox2P-reporter 1-20_34
E2221 clone Sox2P-reporter 1-20_34 Fw
mapped_integrations_Sox2P_clones.txt


title: GD2002-Busada_LIR_KO3

value: B6.Cg-Nr3c1tm1.1Jda/J;Lyz2 cre/+


title: clone Sox2P-reporter 5-88_34 Rv

description:
clone Sox2P-reporter 5-88_34
E2221 clone Sox2P-reporter 5-88_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 5-86_34 Rv

description:
clone Sox2P-reporter 5-86_34
E2221 clone Sox2P-reporter 5-86_34 Rv
mapped_integrations_Sox2P_clones.txt


title: GD2000-Busada_LIR_KO1


title: clone Sox2P-reporter 1-19_34 Fw

description:
clone Sox2P-reporter 1-19_34
E2221 clone Sox2P-reporter 1-19_34 Fw
mapped_integrations_Sox2P_clones.txt


title: GD1999-Busada_LIR_08-GR

value: H. pylori


title: GD2001-Busada_LIR_KO2