title: ATACseq_mES_TIR1_ARID1A_mAID_6h_auxin rep_3

description:
AAG57-6h_ATAC_norm.bw
AAG57-6h-3


title: ATACseq_mES_TIR1_ARID1A_mAID_54h_auxin rep_1

status: Public on Oct 24 2021

type: SRA

city: Dundee

first: Tom

last: Owen-Hughes

state: Tayside

address: Dow Street

department: School of Lifesciences, Gene Regulation and Expression

country: United Kingdom

institute: University of Dundee

description:
AAG57-54h_ATAC_norm_1.2.bw
AAG57-54h-1

library_source: genomic

data_processing:
TT-seq: Fastq files were trimmed using Trim Galore 0.5.0 and CutAdapt 2.4 with default parameters   ATAC-seq: Fastq files were trimmed using trimmomatic-0.36 (CROP: 66) Mnase-seq: Fastq files were aligned to the mouse mm10 genome using bowtie2 with the parameter –X 1000 –x mm10. For each time point three different runs with two replicates each were used.
TT-seq:Sequence reads were aligned using STAR to the reference indexed GRCm38 genome including splice junctions (parameters: -outSAMtype BAM SortedByCoordinate -outSAMattributes All –quantMode GeneCounts TranscriptomeSAM) –outSAMFlagOR 243 –outSAMFlagAND 3852)    ATAC-seq: Alignment was performed using bowtie2-2.1.0 with the parameter –X 1000 –x mm10
ATAC-seq: Filtering was performed: samtools-0.1.18/samtools view -F 3852,
Normalisation was performed: RPM for mapped reads
ATAC-seq: Peaks were called using MACS2 callpeak function with the following parameters: -t "$1".bam -f BAM -n "$1"_MACS -g 1.87e9 -q 0.05 --broad -B ChIP-seq (EP300): macs2 callpeak -c Input.bam -t "$1".bam -f BAMPE -n "$1" -g 1.87e9 -q 0.2 (H3K27Ac) macs2 callpeak -c Input.bam -t "$1".bam -f BAMPE -n "$1" -g 1.87e9 -q 0.05 (H3K27me3) macs2 callpeak -c Input.bam -t "$1".bam -f BAMPE -n "$1" -g 1.87e9 -q 0.05 -broad
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of combined replicates, normalised between time points

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells E14

extract_protocol:
http://dx.doi.org/10.1038/protex.2017.096
Libraries were prepared according to Omni-ATAC-seq protocol (=extract protocol) using the Illumina Nextera DNA Library Prep Kit #15028212

tag: cell type

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57

tag: treatment

value: 54h auxin

tag: molecule subtype

value: genomic DNA


title: ATACseq_mES_TIR1_ARID1A_mAID_6h_auxin rep_1

description:
AAG57-6h_ATAC_norm.bw
AAG57-6h-1

value: 6h auxin


title: ATACseq_mES_TIR1_ARID1A_mAID_0h_auxin rep_3

description:
AAG57-0h_ATAC_norm.bw
AAG57-0h-3

value: 0h auxin


title: ATACseq_mES_TIR1_ARID1A_mAID_2h_auxin rep_3

description:
AAG57-2h_ATAC_norm_1.1.bw
AAG57-2h-3

value: 2h auxin


title: ATACseq_mES_TIR1_ARID1A_mAID_6h_auxin rep_2

description:
AAG57-6h_ATAC_norm.bw
AAG57-6h-2


title: ATACseq_mES_TIR1_ARID1A_untagged_0h_auxin rep_2

description:
ET-905-0h_ATAC_norm.bw
ET-905-0h-2

value: mES TIR1 clone # 905


title: TTseq_mES_TIR1_ARID1Ako_rep4

description:
ARID1A_ko_TT_filtnorm.bw
ARID1Ako4

library_source: transcriptomic

molecule: total RNA

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) following the manufacturers’ instructions. RNA was treated with DNase using the TURBO DNA-free kit (Ambion) according to the manufacturer but increasing the amount of DNase to 6U and the inactivation reagent to 0.2 volumes. After DNase treatment the beads were removed using QIAshredder columns (QIAGEN). Fragmentation, biotinylation and purification of nascent RNA as in Blumli et al.
Libraries were prepared using the NEB Next Ultra II Directional RNA library prep Kit for Illumina according to the protocol

value: mES TIR1 clone # 905, homozygous ARID1A ko

value: no auxin

value: nascent RNA


title: ATACseq_mES_TIR1_ARID1A_mAID_2h_auxin rep_2

description:
AAG57-2h_ATAC_norm_1.1.bw
AAG57-2h-2


title: ATACseq_mES_TIR1_ARID1A_untagged_0h_auxin rep_1

description:
ET-905-0h_ATAC_norm.bw
ET-905-0h-1


title: ATACseq_mES_TIR1_ARID1A_mAID_18h_auxin rep_2

description:
AAG57-18h_ATAC_norm_1.125.bw
AAG57-18h-2

value: 18h auxin


title: ATACseq_mES_TIR1_ARID1A_mAID_0h_auxin rep_2

description:
AAG57-0h_ATAC_norm.bw
AAG57-0h-2


title: TTseq_mES_TIR1_ARID1Ako_rep3

description:
ARID1A_ko_TT_filtnorm.bw
ARID1Ako3


title: ATACseq_mES_TIR1_ARID1A_mAID_0h_auxin rep_1

description:
AAG57-0h_ATAC_norm.bw
AAG57-0h-1


title: TTseq_mES_TIR1_ARID1A_untagged_18h_auxin rep_3

description:
ET905_18h_TT_filtnorm.bw
ET90518h_3


title: TTseq_mES_TIR1_ARID1Ako_rep1

description:
ARID1A_ko_TT_filtnorm.bw
ARID1Ako1


title: TTseq_mES_TIR1_ARID1A_untagged_2h_auxin rep_2

description:
ET905_2h_TT_filtnorm.bw
ET9052h_2


title: ATACseq_mES_TIR1_ARID1A_mAID_2h_auxin rep_1

description:
AAG57-2h_ATAC_norm_1.1.bw
AAG57-2h-1


title: TTseq_mES_TIR1_ARID1A_untagged_18h_auxin rep_4

description:
ET905_18h_TT_filtnorm.bw
ET90518h_4


title: TTseq_mES_TIR1_ARID1A_untagged_18h_auxin rep_2

description:
ET905_18h_TT_filtnorm.bw
ET90518h_2


title: TTseq_mES_TIR1_ARID1A_untagged_2h_auxin rep_3

description:
ET905_2h_TT_filtnorm.bw
ET9052h_3


title: TTseq_mES_TIR1_ARID1A_untagged_2h_auxin rep_4

description:
ET905_2h_TT_filtnorm.bw
ET9052h_4


title: TTseq_mES_TIR1_ARID1A_untagged_2h_auxin rep_1

description:
ET905_2h_TT_filtnorm.bw
ET9052h_1


title: TTseq_mES_TIR1_ARID1A_untagged_18h_auxin rep_1

description:
ET905_18h_TT_filtnorm.bw
ET90518h_1


title: TTseq_mES_TIR1_ARID1Ako_rep2

description:
ARID1A_ko_TT_filtnorm.bw
ARID1Ako2


title: TTseq_mES_TIR1_ARID1A_untagged_0h_auxin rep_4

description:
ET905_0h_TT_filtnorm.bw
ET9050h_4


title: TTseq_mES_TIR1_ARID1A_untagged_0h_auxin rep_3

description:
ET905_0h_TT_filtnorm.bw
ET9050h_3


title: TTseq_mES_TIR1_ARID1A_untagged_0h_auxin rep_2

description:
ET905_0h_TT_filtnorm.bw
ET9050h_2


title: ATACseq_mES_TIR1_ARID1A_mAID_18h_auxin rep_1

description:
AAG57-18h_ATAC_norm_1.125.bw
AAG57-18h-1


title: TTseq_mES_TIR1_ARID1A_mAID_162h_auxin rep_4

description:
AAG57_162h_TT_filtnorm.bw
AAG57162h_4

value: 162h auxin


title: TTseq_mES_TIR1_ARID1A_untagged_0h_auxin rep_1

description:
ET905_0h_TT_filtnorm.bw
ET9050h_1


title: TTseq_mES_TIR1_ARID1A_mAID_162h_auxin rep_2

description:
AAG57_162h_TT_filtnorm.bw
AAG57162h_2


title: TTseq_mES_TIR1_ARID1A_mAID_162h_auxin rep_3

description:
AAG57_162h_TT_filtnorm.bw
AAG57162h_3


title: TTseq_mES_TIR1_ARID1A_mAID_162h_auxin rep_1

description:
AAG57_162h_TT_filtnorm.bw
AAG57162h_1


title: TTseq_mES_TIR1_ARID1A_mAID_54h_auxin rep_4

description:
AAG57_54h_TT_filtnorm.bw
AAG5754h_4


title: TTseq_mES_TIR1_ARID1A_mAID_54h_auxin rep_2

description:
AAG57_54h_TT_filtnorm.bw
AAG5754h_2


title: Covid01 050520 ROI 016 well B05

city: Seattle

first: Tyler

last: Hether

state: WA

address: 530 Fairview Ave N

department: Translational Sciences

country: USA

institute: NanoString Technologies, Inc.

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation

data_processing:
Library strategy: GeoMx Seq
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: olfactory bulb

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: patient id

tag: roi number

tag: segment type

value: PanCK+

tag: viral

value: Infected

tag: type

value: Epithelium

tag: level

value: High

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: raw reads

tag: trimmed reads

tag: stitched reads

tag: aligned reads

tag: deduplicated reads

tag: sequencing saturation


title: Covid01 050520 ROI 014 well B03

value: Rarely Infected

value: Low


title: ATAC-seq in sea urchin whole embryos at 48 hpf, replicate 2

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

data_processing:
Alignment: reads were aligned to the reference genome using Bowtie2 software
Filtering duplicates: duplicated pairs were removed using Samtools software
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Strongylocentrotus purpuratus 2019 Assembly (strPur5/GCF_000002235.5)
Supplementary_files_format_and_content: narrowPeak files with peaks called using MACS2 with q<0.01; BigWig

organism: Strongylocentrotus purpuratus

source_name: whole embryo at 48 hpf

growth_protocol: Embryos were grown at 15°C in ASW until desired developmental stage

extract_protocol:
Wild type embryos were lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

tag: developmental stage

value: 48 hpf

tag: tissue

value: whole embryo

tag: genotype

value: wt


title: Covid01 050520 ROI 017 well B06

tag: patient id

tag: roi number


title: ATAC-seq in sea urchin whole embryos at 48 hpf, replicate 1


title: Soleus LRT CTRL rep3

city: Robina

first: Jamie-Lee

middle: May

last: Thompson

state: QLD

address: 14 University Drive

department: Health Sciences and Medicine

country: Australia

institute: Bond University

data_processing:
Base calls performed using Illumina Real Time Analysis v2.4.11
Low-quality reads and 3' adapters were trimmed with BBDuk and then quasi-mapped to Ensembl Rnor_6.0 release 91 (cDNA and ncRNA) using Salmon v0.9.1
Transcript reads were imported into R/Bioconductor and summarised at the gene level using the tximport package
Genome_build: rn6

organism: Rattus norvegicus

source_name: Soleus muscle

extract_protocol:
Plantaris muscle (50-80mg) were homogenized in QIAzol with steel beads in a Bullet Blender. Total RNA was harvested using the miRNeasy minikit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. The same method was performed separately for soleus muscle.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hindlimb immobilisation of the gastrocnemius and soleus muscles was performed to induce atrophy of the plantaris and soleus muscles. After 3 days the plantaris and soleus muscles were excised, weighed and snap frozen in liquid nitrogen.

tag: line

value: LRT

value: soleus

tag: age

value: 14 months

tag: Sex

value: female

tag: treatment

value: control (CTRL)

tag: line generation

tag: rin


title: Soleus LRT CTRL rep6


title: Covid01 050520 ROI 012 well B01

tag: segment type

tag: viral

value: Lightly Infected

tag: type

tag: level

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: raw reads


title: TTseq_mES_TIR1_ARID1A_mAID_54h_auxin rep_3

description:
AAG57_54h_TT_filtnorm.bw
AAG5754h_3

tag: cell type

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57

value: 54h auxin

tag: molecule subtype

value: nascent RNA


title: TTseq_mES_TIR1_ARID1A_mAID_54h_auxin rep_1

description:
AAG57_54h_TT_filtnorm.bw
AAG5754h_1


title: Soleus LRT CTRL rep5

tag: tissue


title: Soleus LRT CTRL rep4

tag: line


title: Covid01 050520 ROI 015 well B04

tag: patient id

tag: roi number

value: PanCK+

value: Infected

tag: trimmed reads

tag: stitched reads

tag: aligned reads

tag: deduplicated reads

tag: sequencing saturation


title: Covid01 050520 ROI 011 well A12

tag: segment type

tag: viral

tag: type

value: Epithelium

value: Mid


title: Soleus LRT CTRL rep2

tag: age

tag: Sex

tag: treatment

tag: line generation

tag: rin


title: Covid01 050520 ROI 013 well B02

value: Uninfected

tag: level

value: No

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: raw reads


title: Covid01 050520 ROI 010 well A11

tag: patient id

tag: roi number

value: Rarely Infected

value: Low

tag: trimmed reads

tag: stitched reads


title: Covid01 050520 ROI 009 well A10

tag: segment type

tag: aligned reads

tag: deduplicated reads

tag: sequencing saturation


title: TTseq_mES_TIR1_ARID1A_mAID_18h_auxin rep_1

description:
AAG57_18h_TT_filtnorm.bw
AAG5718h_1

tag: cell type

value: 18h auxin

tag: molecule subtype


title: Covid01 050520 ROI 008 well A09

tag: viral

tag: type


title: Covid01 050520 ROI 007 well A08

tag: level

value: High


title: Soleus LRT CTRL rep1

tag: line

value: LRT

tag: tissue

value: soleus

tag: age

value: 14 months

tag: Sex

tag: treatment

tag: line generation

tag: rin


title: Covid01 050520 ROI 006 well A07

tag: patient id

tag: roi number

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: raw reads

tag: trimmed reads

tag: stitched reads


title: Soleus LRT HI rep6

value: female

value: hindlimb immobilisation (HI)


title: TTseq_mES_TIR1_ARID1A_mAID_6h_auxin rep_3

description:
AAG57_6h_TT_filtnorm.bw
AAG576h_3

tag: cell type

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57

value: 6h auxin

tag: molecule subtype


title: TTseq_mES_TIR1_ARID1A_mAID_6h_auxin rep_1

description:
AAG57_6h_TT_filtnorm.bw
AAG576h_1

value: nascent RNA


title: Covid01 050520 ROI 005 well A06

tag: segment type

value: PanCK+

tag: viral

value: Infected

tag: type

tag: level

tag: aligned reads

tag: deduplicated reads

tag: sequencing saturation


title: TTseq_mES_TIR1_ARID1A_mAID_18h_auxin rep_3

description:
AAG57_18h_TT_filtnorm.bw
AAG5718h_3

tag: treatment


title: Covid01 050520 ROI 004 well A05

tag: patient id

tag: roi number

value: Epithelium


title: Covid01 050520 ROI 001 well A02

tag: area

tag: roi x coordinate


title: Soleus LRT HI rep4

tag: line

tag: tissue

tag: age

tag: Sex

tag: line generation

tag: rin


title: Covid01 050520 ROI 002 well A03

tag: segment type

tag: viral

value: Uninfected

tag: roi y coordinate

tag: raw reads

tag: trimmed reads

tag: stitched reads


title: TTseq_mES_TIR1_ARID1A_mAID_2h_auxin rep_1

description:
AAG57_2h_TT_filtnorm.bw
AAG572h_1

tag: cell type

tag: treatment

value: 2h auxin

tag: molecule subtype


title: E14.5_placenta_female_wt2_RRBS

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

institute: Olivia Newton-John Cancer Research Institute

description:
RRBS
163_5_RRBS

data_processing:
as described in Wanigasuriya, Gouil et al. 2020 (https://doi.org/10.7554/eLife.55529)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: gene counts matrices. RRBS/WGBS: bismark coverage reports of mC and C counts (total and by allele)

source_name: E14.5 placenta

tag: strain

tag: mating

value: B6 SMCH/MMTV-Cre ♀ (FL/FL, +/+) X Cast ♂

value: placenta

tag: genotype

value: wt


title: Covid01 050520 ROI 003 well A04

tag: patient id

tag: roi number

tag: type

tag: level

value: High

tag: area

tag: roi x coordinate

tag: aligned reads

tag: deduplicated reads

tag: sequencing saturation


title: E14.5_placenta_female_wt1_RRBS

description:
RRBS
162_3_RRBS

extract_protocol: as described in Wanigasuriya, Gouil et al. 2020 (https://doi.org/10.7554/eLife.55529)

tag: Sex

tag: age

tag: tissue


title: Soleus LRT HI rep3

tag: line

value: LRT

tag: treatment

tag: line generation

tag: rin


title: TTseq_mES_TIR1_ARID1A_mAID_2h_auxin rep_3

description:
AAG57_2h_TT_filtnorm.bw
AAG572h_3

tag: cell type

tag: molecule subtype


title: E14.5_placenta_female_wt3_RRBS

description:
RRBS
163_7_RRBS

tag: strain

tag: mating

tag: genotype


title: Soleus LRT HI rep2

value: soleus


title: AB9926

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

extract_protocol:
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

tag: ad genotype

value: AD

tag: trem2 genotype

tag: organ

value: Brain

value: myeloid

tag: selection marker

tag: mouse sex

value: Male

tag: mouse age

value: 8.5 month


title: Soleus LRT HI rep1

tag: age

value: 14 months

tag: Sex

value: female

value: hindlimb immobilisation (HI)


title: TTseq_mES_TIR1_ARID1A_mAID_0h_auxin rep_1

description:
AAG57_0h_TT_filtnorm.bw
AAG570h_1

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57

value: 0h auxin

value: nascent RNA


title: Soleus HRT CTRL rep6

tag: line

value: HRT

tag: tissue

value: control (CTRL)


title: E14.5_placenta_female_matdel1_RRBS

description:
RRBS
133_2_RRBS

value: B6 SMCH/MMTV-Cre ♀ (DEL/FL, T/+) X Cast ♂

value: placenta

value: matdel


title: E14.5_placenta_female_matdel2_RRBS

description:
RRBS
133_6_RRBS


title: naive_pdl1_etreg_04

city: Philadelphia

first: Christopher

last: Hunter

state: PA

address: 301 S University Ave

department: Pathobiology

institute: University of Pennsylvania

description: Mice were treated with 1mg of anti-PDL1 antibody 72 hours prior to sacrifice

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Kallisto package.
Abundance files were summarized to genes using biomaRt
Expression data was normalized using the VOOM function in the Limma package in R
Genes with no transcripts in 3 or more samples were excluded from analysis
Differentially expressed genes (³0.3-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

source_name: Splenic Tregs

growth_protocol: C57BL/6 mice were obtained from Jackson Laboratories

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen) and processed according to manufacturer’s instructions.
libraries were prepared using the Clontech SMART Seq HT kit according to manufacturer's instructions.

treatment_protocol: 8 week old mice were treated intraperitoneally with 1mg of mouse IgG2b isotype control or anti-PDL1 antibody. Spleenocytes were harvested 72 hours following treatment. cTregs and eTregs were FACS sorted and suspended in RNAlater Plus prior to freezing at -80C.

tag: background strain

value: Spleen

value: etreg

value: wild-type

tag: treatment

value: anti-PD-L1 antibody


title: Soleus HRT CTRL rep5

value: soleus

tag: line generation

tag: rin


title: naive_pdl1_ctreg_04

description: Mice were treated with 1mg of mouse IgG2b isotype antibody 72 hours prior to sacrifice

tag: cell type

value: ctreg


title: AB9924

tag: strain

value: AD

value: Brain

value: myeloid

value: Female

value: 8.5 month


title: Soleus LRT HI rep5

value: LRT

value: 14 months

value: female

value: hindlimb immobilisation (HI)


title: naive_pdl1_etreg_03

tag: genotype


title: Soleus HRT CTRL rep4

value: HRT

value: control (CTRL)


title: naive_pdl1_etreg_02

value: Spleen


title: TTseq_mES_TIR1_ARID1A_mAID_0h_auxin rep_3

description:
AAG57_0h_TT_filtnorm.bw
AAG570h_3

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57

value: 0h auxin

tag: molecule subtype

value: nascent RNA


title: Soleus HRT CTRL rep3

value: soleus


title: AB9923

tag: ad genotype

tag: trem2 genotype


title: naive_pdl1_ctreg_02

value: ctreg

value: wild-type

value: anti-PD-L1 antibody


title: E14.5_placenta_female_matdel3_RRBS

description:
RRBS
133_7_RRBS

tag: mating

value: B6 SMCH/MMTV-Cre ♀ (DEL/FL, T/+) X Cast ♂

value: placenta

value: matdel


title: naive_pdl1_etreg_01

value: etreg


title: E14.5_placenta_female_matdel4_RRBS

description:
RRBS
133_9_RRBS


title: AB9921

value: AD

tag: organ

value: Brain

value: myeloid

tag: selection marker

tag: mouse sex

value: Male

value: 8.5 month


title: AB9922

value: Female

tag: mouse age

value: 7 month


title: naive_pdl1_ctreg_01

value: Spleen


title: Soleus HRT CTRL rep1

tag: line

value: HRT

tag: age

value: 14 months

tag: Sex

value: female

value: control (CTRL)


title: naive_iso_etreg_04

tag: background strain

tag: tissue

value: wild-type

tag: treatment

value: Isotype antibody


title: naive_iso_ctreg_03

tag: cell type

value: ctreg


title: AB9925

tag: strain


title: naive_iso_etreg_03

tag: genotype


title: AB9919


title: naive_iso_etreg_02


title: Soleus HRT HI rep5

value: soleus

value: hindlimb immobilisation (HI)

tag: line generation

tag: rin


title: naive_iso_etreg_01

value: etreg


title: AB9917

tag: ad genotype

value: AD

tag: trem2 genotype

value: Brain


title: naive_iso_ctreg_02


title: Soleus HRT HI rep3


title: AB9916

tag: organ

value: myeloid


title: Soleus HRT HI rep2


title: Soleus HRT HI rep1


title: AB8086

value: Leukocytes

tag: selection marker

value: Male

value: 9 month


title: Plantaris LRT CTRL rep6

source_name: Plantaris muscle

value: LRT

value: plantaris


title: Soleus HRT CTRL rep2

value: HRT

value: 14 months


title: Plantaris LRT CTRL rep5

value: female

value: control (CTRL)


title: AB8085

tag: mouse sex


title: naive_iso_ctreg_01

value: Spleen

value: wild-type

value: Isotype antibody


title: naive_iso_ctreg_04

value: ctreg


title: AB8084

tag: mouse age


title: AB8083


title: E14.5_placenta_female_patdelwt_4

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1246-4_S20

tag: mating

value: Cast ♀ X B6 SMCH/MMTV-Cre ♂(DEL/FL, T/+)

value: placenta

value: patdelwt


title: Soleus HRT HI rep4

tag: line

value: soleus

tag: age

value: hindlimb immobilisation (HI)


title: AB8082

value: WT

value: Brain

value: Leukocytes

value: Male

value: 9.5 month


title: Soleus HRT HI rep6

value: HRT

value: 14 months

tag: Sex


title: AB9918

value: AD

value: myeloid

value: Female

value: 8.5 month


title: E14.5_placenta_female_patdel3

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1183-1_S17

value: female

tag: tissue

value: patdel


title: E14.5_placenta_female_patdel4

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1187-4_S18

value: Cast ♀ X B6 SMCH/MMTV-Cre ♂(DEL/FL, T/+)

value: placenta


title: E14.5_placenta_female_patdel1

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1187-2_S15


title: E14.5_placenta_female_patdelwt_3

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1246-1_S19

value: patdelwt


title: E14.5_placenta_female_patdel2

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1181-3_S16


title: Plantaris LRT CTRL rep2

value: LRT

value: plantaris

tag: treatment

value: control (CTRL)


title: AB8080

value: Brain

tag: cell type

value: Leukocytes

value: 9 month


title: Plantaris LRT CTRL rep1


title: AB8069

tag: strain

value: Infiltrating Leukocytes

value: Male


title: AB8079

value: WT

value: 9.5 month


title: E14.5_placenta_female_patdelwt_2

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1187-1_S14

tag: genotype


title: Plantaris LRT HI rep6

value: 14 months

value: hindlimb immobilisation (HI)

tag: line generation


title: E14.5_placenta_female_patdelwt_1

description:
RNA-seq
E14.5pl_female_patdel_RNA_seq_raw_counts.tsv
1181-5_S13

value: female


title: Plantaris LRT HI rep5

tag: rin


title: E14.5_placenta_female_wt2_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
162_3_RNA

value: B6 SMCH/MMTV-Cre ♀ (FL/FL, +/+) X Cast ♂

value: wt


title: AB8068

tag: ad genotype

value: AD


title: Plantaris LRT HI rep4


title: E14.5_placenta_female_wt3_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
162_7_RNA

value: placenta


title: E14.5_placenta_female_wt1_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
162_1_RNA


title: AB7532

tag: trem2 genotype

value: 6.5 month


title: AB7524

tag: organ

value: IgG

value: Female

value: 6 month


title: AB8081

value: Brain

tag: selection marker


title: E14.5_placenta_female_wt5_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
163_3_RNA


title: Plantaris LRT CTRL rep4

value: LRT

value: plantaris

value: control (CTRL)


title: Plantaris LRT HI rep3


title: E14.5_placenta_female_matdel5_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
133_9_RNA

value: B6 SMCH/MMTV-Cre ♀ (DEL/FL, T/+) X Cast ♂

value: matdel


title: E14.5_placenta_female_matdel4_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
133_7_RNA


title: E14.5_placenta_female_wt6_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
163_9_RNA


title: Plantaris LRT CTRL rep3

value: 14 months


title: E14.5_placenta_female_matdel3_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
133_6_RNA


title: Plantaris LRT HI rep2

value: hindlimb immobilisation (HI)


title: Plantaris LRT HI rep1

value: female


title: AB7523

value: Leukocytes

tag: mouse sex


title: Plantaris HRT CTRL rep6

value: HRT


title: AB7522

value: AD

tag: mouse age


title: Plantaris HRT CTRL rep5


title: AB8067

value: Infiltrating Leukocytes

value: Male

value: 9 month


title: AB7521

value: Female


title: UNx db/db ReninAAV 2

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

country: Denmark

institute: Gubra

data_processing:
bcl2fastq v 2.20.0.422 (basecalling)
STAR v2.5.2a (alignment)
Genome_build: GRCm38_89
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney Cortex

growth_protocol: Not applicable

extract_protocol:
RNA from snap-frozen kidney cortex samples (∼15 mg per animal) stored at −80°C was extracted using a NucleoSpin 8 RNA kit (MachereyNagel) and a vacuum manifold
cDNA library preparation was performed using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, NEG, Ipswich, MA, USA). The number of cycles used for cDNA amplification was 16. The sequencing of cDNA libraries was performed using an NS 500 high Output Kit v2 (75 cycles) (Illumina, San Diego, CA, USA) on an Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA).

treatment_protocol: Not applicable

value: Kidney Cortex

value: 24 weeks of age


title: UNx db/db ReninAAV 4


title: UNx db/db ReninAAV 3


title: UNx db/db ReninAAV 1


title: Plantaris HRT CTRL rep4


title: AB7520

value: Brain

value: IgG

value: 6 month


title: UNx db/db LacZAAV 12


title: UNx db/db LacZAAV 11


title: UNx db/db LacZAAV 13


title: UNx db/db LacZAAV 10


title: AB7519


title: AB7518


title: Plantaris HRT CTRL rep3

value: plantaris

value: control (CTRL)


title: Plantaris HRT CTRL rep2

value: 14 months


title: UNx db/db LacZAAV 9


title: UNx db/db LacZAAV 8


title: UNx db/db LacZAAV 7


title: AB7517


title: E14.5_placenta_female_matdel2_RNA

description:
RNA-seq
E14.5pl_female_matdel_RNA_seq_raw_counts.tsv
133_2_RNA

tag: mating

value: B6 SMCH/MMTV-Cre ♀ (DEL/FL, T/+) X Cast ♂

value: placenta

value: matdel


title: UNx db/db ReninAAV 5


title: Plantaris HRT CTRL rep1

tag: line

value: HRT

value: female


title: UNx db/db LacZAAV 6

tag: age


title: AB7516

value: AD

value: Leukocytes

value: 6.5 month


title: Plantaris HRT HI rep6

tag: Sex

value: hindlimb immobilisation (HI)


title: UNx db/db LacZAAV 5

tag: tissue

value: Kidney Cortex


title: UNx db/db LacZAAV 4

value: 24 weeks of age


title: UNx db/db LacZAAV 3


title: Plantaris HRT HI rep5

tag: treatment


title: UNx db/db LacZAAV 2


title: AB7515

value: Brain

tag: cell type

value: Male


title: Plantaris HRT HI rep4


title: UNx db/db LacZAAV 1

tag: strain


title: AB7514


title: Healthy db/m control 12


title: Healthy db/m control 10


title: AB6433

value: IgG


title: Healthy db/m control 9


title: Healthy db/m control 11


title: Plantaris HRT HI rep3

value: plantaris


title: AB6432


title: Plantaris HRT HI rep2


title: Healthy db/m control 8


title: AB6431


title: Healthy db/m control 6


title: Healthy db/m control 7


title: AB6430


title: Plantaris HRT HI rep1


title: Healthy db/m control 4


title: Healthy db/m control 5


title: grh-1 overexpressor replicate 3

city: Schwerzenbach

first: Fabian

last: Fischer

address: Schorenstrasse 16

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
Bioinformatic analysis was performed using the R package ezRun (github.com/uzh/ezRun) within the data analysis framework SUSHI (PMID 27255077).
Raw reads were quality checked using Fastqc and FastQ Screen (PMID 30254741).
Quality controlled reads (adaptor trimmed, first and last 4 bases hard trimmed, minimum average quality Q10, minimum tail quality Q10, minimum read length 20 nt) were aligned to the reference genome (Ensembl WBcel235) using the STAR aligner (PMID 23104886).
Expression counts were computed using featureCounts in the Bioconductor package Subread (PMID 23558742).
Differential expression analysis was performed using the Bioconductor DESeq2 package, where raw read counts were normalized using the quantile method, and differential expression was computed using the quasi-likelihood (QL) F-test (PMID 25516281).
Gene ontology (GO) enrichment analysis was performed using Bioconductor packages goseq (PMID 20132535) and GOStats (PMID 17098774).
Quality checkpoints (PMID 26813401), such as quality control of the alignment and count results, were implemented in ezRun and applied throughout the analysis workflow to ensure correct data interpretation.
Genome_build: Ensembl WBcel235 (GCA_000002985.3)
Supplementary_files_format_and_content: Two Excel tables (.xlsx), one containing raw counts for all samples and one containing normalized counts and FPKMs + additional information for all samples

organism: Caenorhabditis elegans

source_name: grh-1 overexpressor_whole nematodes

growth_protocol: Adult nematodes (wild-type N2 or grh-1 overexpressors) were allowed to lay eggs for four to nine hours and the resulting eggs incubated for 64 h at 20 °C on NGM agar plates inoculated with E. coli OP50 bacteria to obtain a synchronized population of young adult nematodes. The resulting synchronized populations were incubated for an additional 48 h at 20 °C with continuous supply of OP50 bacteria as a food source.

extract_protocol:
For C. elegans total RNA isolation, nematodes collected from synchronized plates were washed three times with ice-cold S-Buffer and flash-frozen in liquid nitrogen. Afterwards, 500 µl ice-cold TRI Reagent (Molecular Research Center, #TR118) was added to the ground pellet. RNA was extracted based on the phenol-chloroform extraction method. Concentration of the resulting RNA was measured with an LVis plate on a CLARIOstar microplate reader (BMG LABTECH) and stored at -80 °C until further use.
The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies) and a Bioanalyzer 2100 (Agilent). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq RNA Sample Prep Kit v2 (Illumina, #RS-122-2001/2) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10 nM in Tris-Cl 10 mM, pH 8.5 with 0.1% Tween 20.

tag: strain/genotype

value: 48 h post-developmental

value: Whole nematodes


title: AB6429

value: Female


title: Healthy db/m control 3


title: AB6428


title: Healthy db/m control 2


title: Mnase-seq-mES_TIR1_ARID1A_mAID_2h_auxin rep_2_Run3

description:
AAG_2h_all.bw
AAG_2-2_Run3

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched for 5 min with 125 mM glycine at room temperature. After washing cells with cold PBS, cells were lysed using cold NP40-lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40, 0.15 mM spermine, 0.5 mM spermidine) for 5 min on ice. Cells were pelleted and washed with MNase digestion buffer (10 mM Tris pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2, 0.15 mM spermine, 0.5 mM spermidine) and resuspended in 50 μl MNase digestion buffer. For the digest, 7.5 units MNase S7 (Roche) were added to ~4 x 106 cells and incubated for 14 min at 37°C. The digest was stopped adding 1/10 vol 10% SDS and 1/10 vol 250 mM EDTA. 0.24M NaCl and 10 μg RNase A was added to reverse the crosslinking at 65°C for 2 hrs. The samples were treated with 20 μg proteinase K overnight at 65°C, followed by phenol-chloroform extraction and purification using NEB Monarch PCR purification kit.
The resulting DNA fragments were used for Illumina library preparations using PreCR Repair Mix (NEB M0309), followed by NEBNext End Prep (NEB E7442) and NEBNext Adaptor for Illumina (NEB E7335) ligation according to the manufacturer’s protocol. DNA was purified using AMpure beads and amplified by PCR using NEBNext Q5 Hot Start HiFi Master Mix (NEB E6625AA), NEB Universal Primer and NEB Index Primer for 7 cycles. PCR was cleaned up using AMpure beads

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57

value: 2h auxin

tag: molecule subtype

value: genomic DNA


title: Mnase-seq-mES_TIR1_ARID1A_mAID_2h_auxin rep_1_Run3

description:
AAG_2h_all.bw
AAG_2-1_Run3


title: AB6427

value: 7 month


title: Wild-type N2 replicate 3

source_name: Wild-type N2_whole nematodes

value: Wild-type N2 (Bristol)


title: AB6426

value: AD

value: Leukocytes


title: Mnase-seq-mES_TIR1_ARID1A_mAID_0h_auxin rep_2_Run3

description:
AAG_0h_all.bw
AAG_0-2_Run3

value: 0h auxin


title: Mnase-seq-mES_TIR1_ARID1A_mAID_0h_auxin rep_1_Run3

description:
AAG_0h_all.bw
AAG_0-1_Run3


title: Wild-type N2 replicate 2


title: Wild-type N2 replicate 1


title: AB6425


title: Mnase-seq-mES_TIR1_ARID1A_mAID_2h_auxin rep_1_Run2

description:
AAG_2h_all.bw
AAG_2-1_Run2


title: AB6424


title: Mnase-seq-mES_TIR1_ARID1A_mAID_0h_auxin rep_1_Run2

description:
AAG_0h_all.bw
AAG_0-1_Run2


title: Mnase-seq-mES_TIR1_ARID1A_mAID_0h_auxin rep_2_Run2

description:
AAG_0h_all.bw
AAG_0-2_Run2


title: Mnase-seq-mES_TIR1_ARID1A_mAID_2h_auxin rep_2_Run2

description:
AAG_2h_all.bw
AAG_2-2_Run2


title: Mnase-seq-mES_TIR1_ARID1A_mAID_2h_auxin rep_1_Run1

description:
AAG_2h_all.bw
AAG_2-1_Run1


title: AB6297

value: 6.5 month


title: Mnase-seq-mES_TIR1_ARID1A_mAID_0h_auxin rep_2_Run1

description:
AAG_0h_all.bw
AAG_0-2_Run1


title: grh-1 overexpressor replicate 2


title: AB6298


title: Mnase-seq-mES_TIR1_ARID1A_mAID_0h_auxin rep_1_Run1

description:
AAG_0h_all.bw
AAG_0-1_Run1


title: Mnase-seq-mES_TIR1_ARID1A_mAID_2h_auxin rep_2_Run1

description:
AAG_2h_all.bw
AAG_2-2_Run1


title: Healthy db/m control 1

value: Kidney Cortex

value: 24 weeks of age


title: TTseq_mES_TIR1_ARID1A_mAID_18h_auxin rep_4

description:
AAG57_18h_TT_filtnorm.bw
AAG5718h_4

value: 18h auxin

value: nascent RNA


title: grh-1 overexpressor replicate 1


title: TTseq_mES_TIR1_ARID1A_mAID_6h_auxin rep_4

description:
AAG57_6h_TT_filtnorm.bw
AAG576h_4

value: 6h auxin


title: AB10060

value: Brain

value: myeloid

value: Male

value: 8.5 month


title: TTseq_mES_TIR1_ARID1A_mAID_6h_auxin rep_2

description:
AAG57_6h_TT_filtnorm.bw
AAG576h_2

value: mES TIR1, ARID1A-mini-auxin-inducible-GFP-tagged clone#57


title: TTseq_mES_TIR1_ARID1A_mAID_2h_auxin rep_2

description:
AAG57_2h_TT_filtnorm.bw
AAG572h_2

value: 2h auxin


title: TTseq_mES_TIR1_ARID1A_mAID_0h_auxin rep_4

description:
AAG57_0h_TT_filtnorm.bw
AAG570h_4


title: TTseq_mES_TIR1_ARID1A_mAID_0h_auxin rep_2

description:
AAG57_0h_TT_filtnorm.bw
AAG570h_2


title: Non-low temperature treatment of Hosta ventricosa roots_rep3

city: Jilin

first: chen

last: shaopeng

address: 77 Hanlin Road, Economic and Technological Development Zone, Jilin City, Jilin Province

country: China

institute: Jilin Agricultural Science and Technology College

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 (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Hosta ventricosa

source_name: root

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root


title: AB10057

value: Female


title: AB10058

value: AD


title: TTseq_mES_TIR1_ARID1A_mAID_18h_auxin rep_2

description:
AAG57_18h_TT_filtnorm.bw
AAG5718h_2


title: AB10056

value: 7 month


title: Non-low temperature treatment of Hosta ventricosa roots_rep2


title: AB10062


title: KA194A0383-H006S94X_L001

city: Beijing

first: Zhixiu

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

description: F2 duck population

data_processing:
To obtain high-quality clean reads, the reads were filtered using fastp (version 0.18.0).  Reads were removed if they contained adapters, more than 10% unknown nucleotides (N), or more than 50% low-quality (Q-value ≤ 20) bases.
The clean reads were mapped to the duck reference genome using HISAT2.2.4.
The mapped reads of each sample were assembled using StringTie v1.3.1
For each transcription region, the fragments per kilobase of transcript per million mapped reads (FPKM) were analyzed to quantify expression abundance.
RNA differential expression analysis was performed using DESeq2 software.
Genome_build: Anas platyrhynchos (mallard) CAU__Wild1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Anas platyrhynchos

source_name: Breast muscle

growth_protocol: All ducks were farmed under the same breeding conditions. Food and water were provided ad libitum.

extract_protocol:
Breast muscles 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: 42 day after birth

tag: duck  type

value: duck with the low breast muscle ratios (LB)


title: HCT116 SH1

city: Zhengzhou

first: Zhuoyu

last: Gu

address: Jianshe East Road

institute: The First Affiliated Hospital, Zhengzhou 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.

organism: Homo sapiens

source_name: colorectal adenocarcinoma

extract_protocol:
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

tag: cell line

value: colorectal adenocarcinoma

value: Fifth generation

tag: genotype

value: hnRNPK knockdown


title: AB10061

tag: ad genotype

tag: trem2 genotype

tag: organ


title: KA194A0382-H006S94X_L001

description: F2 duck population


title: TTseq_mES_TIR1_ARID1A_mAID_2h_auxin rep_4

description:
AAG57_2h_TT_filtnorm.bw
AAG572h_4

value: nascent RNA


title: HCT116 NC2

value: hnRNPK shNC


title: HCT116 SH2


title: HCT116 NC1


title: AB10059

value: Brain

tag: selection marker

tag: mouse sex

tag: mouse age


title: HK296_Fluoxetine_rep1

city: La Jolla

first: Paul

last: Mischel

state: CA

address: 9500 Gilman Drive, CMME-2021

institute: University of California, San Diego

data_processing:
RNA-seq reads were uploaded to the galaxy platform (https://usegalaxy.org/).
RNA-Seq reads were aligned to the human reference transcriptome (GRCh38 release-98) and quantified in the units of transcripts per million (TPM) and raw read counts using the Salmon software.
Fragment GC bias correction was performed to estimate a correction factor for systematic biases commonly present in RNA-seq data.
Genome_build: GRCh38 release-98
Supplementary_files_format_and_content: Tabular files include transcripts per million (TPM) and raw read for each sample

source_name: GBM patient-derived neurosphere cells

growth_protocol: All patient-derived neurosphere cell lines were cultured in DMEM/F12 medium supplemented with 1x B27, 20 ng/ ml of EGF, 20 ng/ ml of FGF, 1 µg/ ml heparin and 1x Glutamax (Gibco) and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA extraction was performed using an RNeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO or 5 µM fluoxetine for 42 hours

value: GBM cancer cells

value: Fluoxetine


title: AB10055

value: myeloid

value: Male

value: 8.5 month


title: Non-low temperature treatment of Hosta ventricosa roots_rep1

value: root


title: KA194A0381-H006S94X_L001

description: F2 duck population

tag: age


title: HK296_Fluoxetine_rep2


title: HK296_DMSO_rep2

value: DMSO


title: Low temperature treatment of Hosta ventricosa roots_rep3


title: KA194A0380-H006S94X_L001

description: F2 duck population


title: AB10053

value: AD

value: Female


title: HK296_DMSO_rep1


title: Low temperature treatment of Hosta ventricosa roots_rep2


title: AB10052


title: Low temperature treatment of Hosta ventricosa roots_rep1


title: HK301_Fluoxetine_rep2


title: AB10051


title: KA194A0377-H006S94X_L001

description: F2 duck population

value: 42 day after birth

value: duck with the high breast muscle ratios (HB)


title: KA194A0379-H006S94X_L001

description: F2 duck population

value: duck with the low breast muscle ratios (LB)


title: KA194A0378-H006S94X_L001

description: F2 duck population


title: HK301_Fluoxetine_rep1


title: flavodoxin3

city: Chengdu

first: Peiyao

last: Wu

address: Renmin South road

institute: Sichuan University

data_processing:
The libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500) and 150 bp/125bp paired-end reads were generated.
Duplicated sequences, ambiguous reads, and low-quality reads (Q > 20) were removed and assembled from the raw reads. Then the clean reads were mapped to the reference genomes from NCBI for P. gingivalis W83. The numbers of reads were calculated by using Reads Per Kilobase per Million Mapped Reads (RPKM).
The Upper Quartile (UQ) normalization factors were applied to the samples and multiplied by the mean upper quartile by applying the FDR adjustment with the threshold of < 0.05 q-values to compare different experiments or samples using Rockhooper2.
Genome_build: reference genomes from NCBI for P. gingivalis W83
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Porphyromonas gingivalis

source_name: flavodoxin mutant strain

growth_protocol: P. gingivalis W83 and DPG_RS08170 were cultured in anaerobic 37oC condition with 10% H2, and 10% CO2, 80% N2, and in brain-heart infusion (BHI) medium (Oxoid, Basingstoke, USA), supplemented with hemin (5 mg/ml), and menadione (1 mg/ml) (Sigma, St Louis, USA), 5% defibrinated sheep blood (Beiruite Biotechnology, Zhengzhou, China) on blood agar plate.

extract_protocol:
RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PG_RS08170 deletion mutant


title: flavodoxin2


title: AB10050

value: 7 month


title: AB10054


title: AB10049


title: flavodoxin1


title: KA194A0375-H006S94X_L001

description: F2 duck population


title: AB10047


title: GBM39_Fluoxetine_rep2


title: KA194A0374-H006S94X_L001

description: F2 duck population


title: WT3

source_name: P. gingivalis W83

value: W83 Wild-type


title: HK301_DMSO_rep2


title: WT2


title: KA194A0373-H006S94X_L001

description: F2 duck population


title: KA194A0372-H006S94X_L001

description: F2 duck population


title: AB10044


title: HK301_DMSO_rep1


title: AB10045


title: GBM39_DMSO_rep1


title: AB10046


title: KA194A0376-H006S94X_L001

description: F2 duck population


title: biological rep3 for sro 4-5mm inflorescence

status: Public on Oct 23 2021

type: RNA

city: Shanghai

first: Xu

last: wei

state: Shanghai

address: 800 Dong Chuan Road

department: Life Science

institute: SJTU

description: Microarray data of genome-wide gene expression profile

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

label: boitin

organism: Oryza sativa

source_name: inflorescence in 4-5mm length

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual Affymetrix).

growth_protocol: Rice was grown in the paddy field

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

treatment_protocol: No special treatment

value: the sro mutant

value: rice inflorescence


title: KC from HFD mouse 2 treated with Vehicle

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the human genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: mm10
Supplementary_files_format_and_content: CSV files include mRNA molecule count values and single cell barcodes for each Sample

source_name: sorted kupffer cells

extract_protocol:
Qiagen Rneasy micro kit
KAPA mRNA HyperPrep Kit

treatment_protocol: Purified kupffer cells were treated wth DMSO or DPI (500nM) for 24hrs

value: liver

value: kupffer

value: vehicle

tag: diet

value: HFD


title: KC from HFD mouse 4 treated with DPI

tag: tissue

value: DPI


title: KC from HFD mouse 2 treated with DPI

tag: treatment


title: KC from HFD mouse 3 treated with Vehicle

tag: cell type


title: KC from normal diet mouse 1

value: normal


title: KC from HFD mouse 1 treated with Vehicle


title: KC from HFD mouse 1 treated with DPI


title: KC from normal diet mouse 2


title: KC from HFD mouse 3 treated with DPI


title: Astro3

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

institute: UNIGE

data_processing:
Reads (100 bp) were mapped using TopHat.
Biological quality control and summarization were done with PicardTools v1.80.
Counts (total number of reads aligning to each genomic feature) were generated by HTSeq v.0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ex vivo sample

extract_protocol:
QIAGEN column extraction for mRNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: strain

tag: tissue/cell type

value: astrocytes


title: Astro2


title: biological rep2 for sro 4-5mm inflorescence


title: Astro1


title: biological rep3 for wild type 4-5mm inflorescence

value: wild type


title: biological rep2 for wild type 4-5mm inflorescence


title: biological rep1 for wild type 4-5mm inflorescence


title: SAMPLE 2_R02C01_HC

type: genomic

city: Changsha

first: Zhenghao

last: He

address: 139 Renmin Middle Road

institute: Second Xiangya Hospital, Central South University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: CHAMP

label: biotin

source_name: b cell, HC, blood

label_protocol: Standard Illumina Protocol

growth_protocol: blood in SLE patients and human control

extract_protocol: Sorting out B cells by magnetic beads

tag: subject status

value: control

tag: gender

value: male

value: blood


title: biological rep1 for sro 4-5mm inflorescence


title: BAL3

value: whole tissue


title: SAMPLE 6_R06C01_SLE

source_name: b cell, SLE, blood

value: systemic lupus erythematosus (SLE)


title: BAL2


title: SAMPLE 5_R05C01_SLE

value: female


title: Control1


title: Control2


title: BAL1


title: Control3


city: Ipswich

first: Bo

last: Yan

address: County Road

institute: New England Biolabs

description:
Jurkat, Re-Cappable-seq control library, replicate 1
J_Con.tsscount.gtf (Jurkat control combined replicate 1 and replicate 2 TSS counting)

data_processing:
adapter sequence was trimmed using trim_galore
The trimmed reads were mapped to the human genome using STAR
Downsample to 45 million primary mappable reads for TSS counting
The number of reads starting at any position were counted using a customized script, starting from 45 million mappable reads
Genome_build: gencode GRCh38.p5 Release 24
Supplementary_files_format_and_content: Tab-delimited gtf files (TSS counts)

source_name: Jurkat, Re-Cappable-seq control library

extract_protocol:
Total RNA was purified using Trizol, Thermo AM7858
NEB Small RNA library prep
5'end sequencing of total RNA

treatment_protocol: ReCappable-seq protocol

tag: cell line

value: Jurkat cancer cell


description:
Jurkat, Re-Cappable-seq enrich library, replicate 2
J_En_rep2.tsscount.gtf  (Jurkat enrich replicate 2 TSS counting)

source_name: Jurkat, Re-Cappable-seq enrich library


title: K562, CIP treatment, Re-Cappable-seq control library, replicate 2

extract_protocol:
Total RNA was purified using Trizol, Thermo AM7832
NEB Small RNA library prep
5'end sequencing of CIP treated total RNA

treatment_protocol: CIP treatment, ReCappable-seq protocol

value: K562 cancer cell


description:
K562, Re-Cappable-seq enrich library, replicate 2
K_En_rep2.tsscount.gtf  (K562 enrich replicate 2 TSS counting)

source_name: K562, Re-Cappable-seq enrich library

extract_protocol:
Total RNA was purified using Trizol, Thermo AM7832
NEB Small RNA library prep
5'end sequencing of total RNA


description:
K562, Re-Cappable-seq control library, replicate 2
K_Con.tsscount.gtf (K562 control combined replicate 1 and replicate 2 TSS counting)

source_name: K562, Re-Cappable-seq control library


description:
Jurkat, CIP treatment, Re-Cappable-seq enrich library, replicate 1
J_CIP_En.tsscount.gtf (Jurkat CIP treatment, enrich combined replicate 1 and replicate 2 TSS counting)

extract_protocol:
Total RNA was purified using Trizol, Thermo AM7858
NEB Small RNA library prep
5'end sequencing of CIP treated total RNA


title: Jurkat, CIP treatment, Re-Cappable-seq control library, replicate 2


description:
K562, Re-Cappable-seq enrich library, replicate 1
K_En_rep1.tsscount.gtf (K562 enrich replicate 1 TSS counting)


description:
K562, Re-Cappable-seq control library, replicate 1
K_Con.tsscount.gtf (K562 control combined replicate 1 and replicate 2 TSS counting)


description:
Jurkat, CIP treatment, Re-Cappable-seq enrich library, replicate 2
J_CIP_En.tsscount.gtf (Jurkat CIP treatment, enrich combined replicate 1 and replicate 2 TSS counting)


description:
Jurkat, Re-Cappable-seq control library, replicate 2
J_Con.tsscount.gtf (Jurkat control combined replicate 1 and replicate 2 TSS counting)


title: SAMPLE 4_R04C01_HC


title: Jurkat, CIP treatment, Re-Cappable-seq control library, replicate 1


description:
K562, CIP treatment, Re-Cappable-seq enrich library, replicate 2
K_CIP_En.tsscount.gtf (K562 CIP treatment, enrich combined replicate 1 and replicate 2 TSS counting)


description:
K562, CIP treatment, Re-Cappable-seq enrich library, replicate 1
K_CIP_En.tsscount.gtf (K562 CIP treatment, enrich combined replicate 1 and replicate 2 TSS counting)


description:
Jurkat, Re-Cappable-seq enrich library, replicate 1
J_En_rep1.tsscount.gtf  (Jurkat enrich replicate 1 TSS counting)


title: SAMPLE 8_R08C01_SLE


title: SAMPLE 3_R03C01_HC


title: SI_Fig_5d_HEK5_del_HOPE_rep1

first: Hao

address: HaiDian, Beijing

department: Peking University

institute: Peking University

description: Amplified from the human HEK5 locus

data_processing:
Removed-adapter reads were aligned to corresponding amplicon reference with BWA MEM algorithm (v0.7.17-r1188).
After alignment, mapped reads were sorted by positions and converted into mpileup format with samtools (v1.10).
Targeted amplicon sequencing data was analyzed using the published toolkit CRlSPResso2 (v2.0.45).
Graphpad prism 9 was used to analyze the data.
Sanger sequencing data was analyzed using the Snapgene.
The.mpileup files were converted into.bmat files by Python scripts of "Detect-Seq" pipeline (http://detect-seq.com/).
Potential off-target sites were predicted using Cas-OFFinder (V2.4).
Genome_build: WT amplicon sequences were used as WT amplicon genome references, HDR amplicon sequences were used as HDR (insertion and deletion) amplicon references.
Supplementary_files_format_and_content: MPILEUP format: mutation information.

source_name: HCT116 cells

growth_protocol: HEK293T cells were cultured and maintained at 37 °C in DMEM medium plus additional 10% FBS. For HCT116 cells, they were maintained in RPMI medium supplementing with 10% FBS.

extract_protocol:
Genomic DNA was extracted with CWBIO universal genomic DNA kit (CWbiotech, CW2298M) following the manufacturer’s protocol.
Genomic sites to be identified were amplified from genomic DNA samples and sequenced on the Illumina NovaSeq platform.
Targeted amplicon based high throughput sequencing

treatment_protocol: Plasmid transfections into HEK293T or HCT116 cells were conducted with lipofectamine 2000 as the manufacturer’s instructions.

value: human colorectal carcinoma cells

value: transfected with HOPE vectors for 72 h

value: HCT116 cells


title: SI_Fig_5d_HEK5_del_cor_PE3_rep2

description: Amplified from the human HEK5 locus

value: transfected with PE3 vectors for 72 h


title: SI_Fig_5d_HEK5_del_cor_PE3_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_5d_HEK5_del_HOPE_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_5d_HEK5_del_HOPE_rep2

description: Amplified from the human HEK5 locus


title: SAMPLE 7_R07C01_SLE


title: SI_Fig_5d_HEK5_del_AS_PE2_rep2

description: Amplified from the human HEK5 locus

value: transfected with PE2 vectors for 72 h


title: SI_Fig_5c_FANCF_subs_opti_PE3_rep2

description: Amplified from the human FANCF locus


title: SI_Fig_5c_FANCF_subs_cor_PE3_rep2

description: Amplified from the human FANCF locus


title: SI_Fig_5c_FANCF_subs_HOPE_rep3

description: Amplified from the human FANCF locus


title: SI_Fig_5d_HEK5_del_S_PE2_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_5d_HEK5_del_AS_PE2_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_5d_HEK5_del_AS_PE2_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_5c_FANCF_subs_cor_PE3_rep1

description: Amplified from the human FANCF locus


title: SI_Fig_5c_FANCF_subs_opti_PE3_rep3

description: Amplified from the human FANCF locus


title: SI_Fig_5c_FANCF_subs_AS_PE2_rep3

description: Amplified from the human FANCF locus


title: SI_Fig_5c_FANCF_subs_cor_PE3_rep3

description: Amplified from the human FANCF locus


title: SI_Fig_5d_HEK5_del_S_PE2_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_5c_FANCF_subs_HOPE_rep2

description: Amplified from the human FANCF locus


title: SI_Fig_5c_FANCF_subs_HOPE_rep1

description: Amplified from the human FANCF locus


title: SI_Fig_5d_HEK5_del_cor_PE3_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_5c_FANCF_subs_AS_PE2_rep2

description: Amplified from the human FANCF locus


title: SAMPLE 1_R01C01_HC


title: SI_Fig_5c_FANCF_subs_AS_PE2_rep1

description: Amplified from the human FANCF locus


title: SI_Fig_5d_HEK5_del_S_PE2_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_5c_FANCF_subs_S_PE2_rep2

description: Amplified from the human FANCF locus


title: SI_Fig_5c_FANCF_subs_opti_PE3_rep1

description: Amplified from the human FANCF locus


title: SI_Fig_3d_PCIF1_subs_cor_PE3_rep3

description: Amplified from the human PCIF locus

source_name: HEK293T cells

value: human embryonic kidney 293 cells

value: HEK293T cells


title: SI_Fig_5c_FANCF_subs_S_PE2_rep3

description: Amplified from the human FANCF locus


title: SI_Fig_3d_PCIF1_subs_cor_PE3_rep2

description: Amplified from the human PCIF locus


title: SI_Fig_5c_FANCF_subs_S_PE2_rep1

description: Amplified from the human FANCF locus


title: SI_Fig_3d_PCIF1_subs_HOPE_rep3

description: Amplified from the human PCIF locus


title: SI_Fig_3d_PCIF1_subs_AS_PE2_rep3

description: Amplified from the human PCIF locus


title: SI_Fig_3c_HEK5_del_cor_PE3_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3d_PCIF1_subs_S_PE2_rep3

description: Amplified from the human PCIF locus


title: SI_Fig_3d_PCIF1_subs_S_PE2_rep2

description: Amplified from the human PCIF locus


title: SI_Fig_3d_PCIF1_subs_cor_PE3_rep1

description: Amplified from the human PCIF locus


title: SI_Fig_3d_PCIF1_subs_HOPE_rep2

description: Amplified from the human PCIF locus


title: SI_Fig_3c_HEK5_del_cor_PE3_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_HOPE_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3d_PCIF1_subs_AS_PE2_rep1

description: Amplified from the human PCIF locus


title: SI_Fig_3c_HEK5_del_AS_PE2_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_HOPE_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_cor_PE3_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_AS_PE2_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_S_PE2_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_AS_PE2_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_S_PE2_rep2

description: Amplified from the human HEK5 locus


title: GBM39_Fluoxetine_rep1

value: GBM cancer cells

value: Fluoxetine


title: GBM39_DMSO_rep2

value: DMSO


title: SI_Fig_3c_HEK5_del_S_PE2_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_HOPE_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_HOPE_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_cor_PE3_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_cor_PE3_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_cor_PE3_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_HOPE_rep1

description: Amplified from the human HEK5 locus


title: WT1

tag: genotype

value: W83 Wild-type


title: SI_Fig_3b_HEK5_ins_AS_PE2_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3c_HEK5_del_HOPE_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_AS_PE2_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_AS_PE2_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_S_PE2_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_cor_PE3_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3b_HEK5_ins_S_PE2_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_cor_PE3_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_AS_PE2_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_HOPE_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_HOPE_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_AS_PE2_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_HOPE_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_S_PE2_rep2

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_cor_PE3_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_S_PE2_rep3

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_AS_PE2_rep1

description: Amplified from the human HEK5 locus


title: SI_Fig_3a_HEK5_subs_S_PE2_rep1

description: Amplified from the human HEK5 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_13_rep3

description: Amplified from the human HEK3 locus


title: K562, CIP treatment, Re-Cappable-seq control library, replicate 1


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_11_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_14_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_10_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_8_rep3

description: Amplified from the human HEK3 locus


title: SI_Fig_3b_HEK5_ins_S_PE2_rep3

description: Amplified from the human HEK5 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_6_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_7_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_2_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_3_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_5_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_4_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_1_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_12_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_11_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_10_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_13_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_7_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_5_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_8_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_3_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_1_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_4_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_12_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_13_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_2_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_12_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_11_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_14_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_8_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_6_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_4_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_10_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_14_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_7_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_5_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_3_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis2_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_1_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis2_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_14_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_12_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis2_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_6_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_PE3_ins_AS_mis3_2_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_11_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_13_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_10_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_5_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_7_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_3_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_1_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_6_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_14_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_13_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_4_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_2_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_12_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_10_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_8_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_11_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_4_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_5_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_6_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_3_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_8_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_14_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_12_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_13_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_1_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_10_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_8_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_11_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_6_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_4_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_2_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_3_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_7_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_1_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_8_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_6_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_7_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis2_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_5_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis2_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis2_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_4_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_2_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_3_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_2_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_5_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5b_HEK3_HOPE_ins_AS_mis3_7_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_7_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_8_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_6_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_4_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_1_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_2_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_5_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_3_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_6_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_8_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_4_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_1_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis0_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis0_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_1_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_8_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_7_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_3_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis0_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_5_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_2_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_1_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_7_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_8_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_7_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_5_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_4_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_3_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_6_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_2_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_7_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_5_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_3_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_PE3_ins_S_mis3_2_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_5_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_8_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_4_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_6_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_3_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_6_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis0_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_1_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_4_rep3

description: Amplified from the human HEK3 locus


title: ExFig_4i_HEK_site4_ins_S_PE2_TL25nt

description: Amplified from the human HEK site4 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_2_rep1

description: Amplified from the human HEK3 locus


title: ExFig_4i_HEK_site4_ins_S_PE2_TL30nt


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis0_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis0_rep2

description: Amplified from the human HEK3 locus


title: ExFig_4i_HEK_site4_ins_S_PE2_TL55nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL55nt_asTL69nt


title: ExFig_4i_HEK_site4_ins_S_PE2_TL20nt


title: Ex_Fig_5a_HEK3_HOPE_ins_S_mis3_1_rep2

description: Amplified from the human HEK3 locus


title: ExFig_4i_HEK_site4_ins_HOPE_sTL55nt_asTL55nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL55nt_asTL62nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL55nt_asTL66nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL30nt_asTL66nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL30nt_asTL69nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL25nt_asTL69nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL30nt_asTL55nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL25nt_asTL55nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL25nt_asTL62nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL20nt_asTL66nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL20nt_asTL69nt


title: ExFig_4i_HEK_site4_ins_HOPE_sTL20nt_asTL55nt


title: ExFig_4i_HEK_site4_ins_AS_PE2_TL62nt


title: ExFig_4i_HEK_site4_ins_AS_PE2_TL55nt


title: ExFig_4h_METTL3_subs_S_PE2_TL15nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_HOPE_sTL22nt_asTL14nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_HOPE_sTL18nt_asTL17nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_HOPE_sTL18nt_asTL14nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_HOPE_sTL22nt_asTL21nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_HOPE_sTL15nt_asTL21nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_HOPE_sTL18nt_asTL21nt

description: Amplified from the human METTL3 locus


title: ExFig_4i_HEK_site4_ins_HOPE_sTL30nt_asTL62nt


title: ExFig_4h_METTL3_subs_HOPE_sTL15nt_asTL17nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_HOPE_sTL15nt_asTL14nt

description: Amplified from the human METTL3 locus


title: ExFig_4i_HEK_site4_ins_HOPE_sTL25nt_asTL66nt


title: ExFig_4h_METTL3_subs_AS_PE2_TL14nt

description: Amplified from the human METTL3 locus


title: ExFig_4h_METTL3_subs_AS_PE2_TL21nt

description: Amplified from the human METTL3 locus


title: ExFig_4g_FANCF_subs_S_PE2_TL48nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_S_PE2_TL27nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_S_PE2_TL24nt

description: Amplified from the human FANCF locus


title: ExFig_4i_HEK_site4_ins_HOPE_sTL20nt_asTL62nt


title: ExFig_4g_FANCF_subs_S_PE2_TL21nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL48nt_asTL48nt

description: Amplified from the human FANCF locus


title: ExFig_4i_HEK_site4_ins_AS_PE2_TL69nt


title: ExFig_4i_HEK_site4_ins_AS_PE2_TL66nt


title: ExFig_4g_FANCF_subs_HOPE_sTL48nt_asTL24nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL48nt_asTL27nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL48nt_asTL21nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL24nt_asTL24nt

description: Amplified from the human FANCF locus


title: ExFig_4h_METTL3_subs_S_PE2_TL18nt

description: Amplified from the human METTL3 locus


title: ExFig_4g_FANCF_subs_HOPE_sTL24nt_asTL27nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL24nt_asTL48nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL21nt_asTL48nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL21nt_asTL24nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL21nt_asTL21nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL21nt_asTL27nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_HOPE_sTL24nt_asTL21nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_AS_PE2_TL48nt

description: Amplified from the human FANCF locus


title: ExFig_4g_FANCF_subs_AS_PE2_TL24nt

description: Amplified from the human FANCF locus


title: ExFig_4f_PCIF_subs_S_PE2_TL25nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_S_PE2_TL23nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_S_PE2_TL19nt

description: Amplified from the human PCIF locus


title: ExFig_4g_FANCF_subs_AS_PE2_TL21nt

description: Amplified from the human FANCF locus


title: ExFig_4f_PCIF_subs_S_PE2_TL14nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL25nt_asTL17nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL25nt_asTL22nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_S_PE2_TL17nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL25nt_asTL26nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL25nt_asTL19nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL23nt_asTL22nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL23nt_asTL26nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL19nt_asTL19nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL23nt_asTL19nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL23nt_asTL17nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL19nt_asTL17nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL17nt_asTL17nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL17nt_asTL26nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL17nt_asTL19nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL19nt_asTL22nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL19nt_asTL26nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_AS_PE2_TL26nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL14nt_asTL17nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL14nt_asTL26nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL17nt_asTL22nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_HOPE_sTL14nt_asTL22nt

description: Amplified from the human PCIF locus


title: ExFig_4f_PCIF_subs_AS_PE2_TL17nt

description: Amplified from the human PCIF locus


title: ExFig_4e_EMX1_subs_S_PE2_TL27nt

description: Amplified from the human EMX1 locus


title: ExFig_4f_PCIF_subs_AS_PE2_TL22nt

description: Amplified from the human PCIF locus


title: ExFig_4e_EMX1_subs_S_PE2_TL41nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_S_PE2_TL23nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL41nt_asTL44nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL41nt_asTL41nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL41nt_asTL37nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL41nt_asTL30nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL41nt_asTL23nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL27nt_asTL44nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL27nt_asTL41nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL27nt_asTL37nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL27nt_asTL30nt

description: Amplified from the human EMX1 locus


title: ExFig_4f_PCIF_subs_HOPE_sTL14nt_asTL19nt

description: Amplified from the human PCIF locus


title: ExFig_4e_EMX1_subs_HOPE_sTL27nt_asTL27nt

description: Amplified from the human EMX1 locus


title: ExFig_4f_PCIF_subs_AS_PE2_TL19nt

description: Amplified from the human PCIF locus


title: ExFig_4e_EMX1_subs_HOPE_sTL27nt_asTL23nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL23nt_asTL30nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL23nt_asTL23nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL23nt_asTL41nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_AS_PE2_TL44nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL23nt_asTL27nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL23nt_asTL44nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_HOPE_sTL23nt_asTL37nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_AS_PE2_TL27nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_AS_PE2_TL30nt

description: Amplified from the human EMX1 locus


title: ExFig_4e_EMX1_subs_AS_PE2_TL37nt

description: Amplified from the human EMX1 locus


title: ExFig_4d_ABE21_subs_S_PE2_TL23nt

description: Amplified from the human ABEsite21 locus


title: ExFig_4d_ABE21_subs_S_PE2_TL17nt


title: ExFig_4d_ABE21_subs_S_PE2_TL13nt


title: ExFig_4d_ABE21_subs_S_PE2_TL29nt


title: ExFig_4e_EMX1_subs_HOPE_sTL41nt_asTL27nt

description: Amplified from the human EMX1 locus


title: ExFig_4d_ABE21_subs_S_PE2_TL15nt


title: ExFig_4d_ABE21_subs_S_PE2_TL10nt


title: ExFig_4d_ABE21_subs_HOPE_sTL29nt_asTL9nt


title: ExFig_4d_ABE21_subs_HOPE_sTL29nt_asTL20nt


title: ExFig_4d_ABE21_subs_HOPE_sTL29nt_asTL22nt


title: ExFig_4d_ABE21_subs_HOPE_sTL29nt_asTL17nt


title: ExFig_4d_ABE21_subs_HOPE_sTL29nt_asTL28nt


title: ExFig_4d_ABE21_subs_HOPE_sTL29nt_asTL12nt


title: ExFig_4e_EMX1_subs_AS_PE2_TL41nt

description: Amplified from the human EMX1 locus


title: ExFig_4d_ABE21_subs_HOPE_sTL23nt_asTL22nt


title: ExFig_4d_ABE21_subs_HOPE_sTL23nt_asTL17nt


title: ExFig_4e_EMX1_subs_AS_PE2_TL23nt

description: Amplified from the human EMX1 locus


title: ExFig_4d_ABE21_subs_HOPE_sTL23nt_asTL20nt


title: ExFig_4d_ABE21_subs_HOPE_sTL23nt_asTL9nt


title: ExFig_4d_ABE21_subs_HOPE_sTL23nt_asTL14nt


title: ExFig_4d_ABE21_subs_HOPE_sTL29nt_asTL14nt


title: ExFig_4d_ABE21_subs_HOPE_sTL23nt_asTL28nt


title: ExFig_4d_ABE21_subs_HOPE_sTL23nt_asTL12nt


title: ExFig_4d_ABE21_subs_HOPE_sTL19nt_asTL28nt


title: ExFig_4d_ABE21_subs_HOPE_sTL19nt_asTL20nt


title: ExFig_4d_ABE21_subs_HOPE_sTL19nt_asTL9nt


title: ExFig_4d_ABE21_subs_HOPE_sTL19nt_asTL17nt


title: ExFig_4d_ABE21_subs_HOPE_sTL19nt_asTL12nt


title: ExFig_4d_ABE21_subs_HOPE_sTL19nt_asTL14nt


title: ExFig_4d_ABE21_subs_HOPE_sTL15nt_asTL9nt


title: ExFig_4d_ABE21_subs_HOPE_sTL15nt_asTL28nt


title: ExFig_4d_ABE21_subs_HOPE_sTL15nt_asTL20nt


title: ExFig_4d_ABE21_subs_HOPE_sTL15nt_asTL14nt


title: ExFig_4d_ABE21_subs_HOPE_sTL15nt_asTL22nt


title: ExFig_4d_ABE21_subs_HOPE_sTL15nt_asTL17nt


title: ExFig_4d_ABE21_subs_HOPE_sTL13nt_asTL9nt


title: ExFig_4d_ABE21_subs_HOPE_sTL15nt_asTL12nt


title: ExFig_4d_ABE21_subs_HOPE_sTL13nt_asTL28nt


title: ExFig_4d_ABE21_subs_HOPE_sTL13nt_asTL22nt


title: ExFig_4d_ABE21_subs_HOPE_sTL13nt_asTL20nt


title: ExFig_4d_ABE21_subs_HOPE_sTL13nt_asTL14nt


title: ExFig_4d_ABE21_subs_HOPE_sTL13nt_asTL17nt


title: ExFig_4d_ABE21_subs_HOPE_sTL13nt_asTL12nt


title: ExFig_4d_ABE21_subs_HOPE_sTL10nt_asTL9nt


title: ExFig_4d_ABE21_subs_HOPE_sTL19nt_asTL22nt


title: ExFig_4d_ABE21_subs_HOPE_sTL10nt_asTL17nt


title: ExFig_4d_ABE21_subs_HOPE_sTL10nt_asTL22nt


title: ExFig_4d_ABE21_subs_HOPE_sTL10nt_asTL20nt


title: ExFig_4d_ABE21_subs_HOPE_sTL10nt_asTL28nt


title: ExFig_4d_ABE21_subs_HOPE_sTL10nt_asTL12nt


title: ExFig_4d_ABE21_subs_AS_PE2_TL28nt


title: ExFig_4d_ABE21_subs_HOPE_sTL10nt_asTL14nt


title: ExFig_4d_ABE21_subs_AS_PE2_TL9nt


title: ExFig_4d_ABE21_subs_AS_PE2_TL22nt


title: ExFig_4d_ABE21_subs_AS_PE2_TL17nt


title: ExFig_4c_PDCD1_site2_subs_S_PE2_TL17nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_S_PE2_TL29nt

description: Amplified from the human PDCD1 locus


title: ExFig_4d_ABE21_subs_AS_PE2_TL19nt


title: ExFig_4d_ABE21_subs_AS_PE2_TL14nt


title: ExFig_4c_PDCD1_site2_subs_S_PE2_TL23nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_S_PE2_TL15nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL29nt_asTL9nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL29nt_asTL22nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_S_PE2_TL13nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL29nt_asTL19nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL29nt_asTL28nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL29nt_asTL17nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL23nt_asTL28nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL29nt_asTL14nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL23nt_asTL19nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL29nt_asTL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL23nt_asTL22nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL23nt_asTL14nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL23nt_asTL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL17nt_asTL9nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL23nt_asTL9nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL23nt_asTL17nt

description: Amplified from the human PDCD1 locus


title: ExFig_4d_ABE21_subs_AS_PE2_TL10nt


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL17nt_asTL19nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL17nt_asTL28nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL17nt_asTL22nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_S_PE2_TL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL17nt_asTL14nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL17nt_asTL17nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL15nt_asTL22nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL15nt_asTL17nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL17nt_asTL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL15nt_asTL19nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL15nt_asTL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL15nt_asTL9nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL13nt_asTL9nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL15nt_asTL14nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL13nt_asTL28nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL13nt_asTL22nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL13nt_asTL17nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL13nt_asTL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL13nt_asTL19nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL13nt_asTL14nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL10nt_asTL28nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL10nt_asTL19nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL10nt_asTL22nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL10nt_asTL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL15nt_asTL28nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL10nt_asTL14nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_AS_PE2_TL9nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL10nt_asTL9nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_AS_PE2_TL22nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_AS_PE2_TL19nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_AS_PE2_TL10nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_AS_PE2_TL14nt

description: Amplified from the human PDCD1 locus


title: ExFig_4c_PDCD1_site2_subs_AS_PE2_TL28nt

description: Amplified from the human PDCD1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm44_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_S_tm32_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_S_tm43_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_S_tm26_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_S_tm40_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_S_tm40_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_S_tm32_rep2

description: Amplified from the human EMX1 locus