title: sample_995

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-20, biol rep: 4


title: MZsox19bspg_rep2_5hpf [re-analysis]

status: Public on Aug 02 2023

type: SRA

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

country: Germany

institute: University of Freiburg

library_source: transcriptomic

data_processing:
Clean raw data were uploaded into Galaxy EU (https://galaxy.uni-freiburg.de) and passed fastQC quality check. Following analysis are all performed on Galaxy server.
Clean raw data were trimmed on 5' end for 5bp by Trim Galore! according to the sequencing quality.
Trimmed reads were mapped to GRCz11/danRer11 ensGene using RNA STAR.
Number of reads for each gene was counted in Featurecount using GRCz11/danRer11 ensGene reference genome.
All Featurecount reads from each sample were normalized in Deseq2. We used genotypes as factor level 1. The rest parameters are default.
Data has been run in 2 groups: first one with WT/MZsox19b/MZspg/MZnanog/MZsox19bnanog/MZsox19bspg (WT/MZsox19b/MZspg/MZsox19bspg data is from Series GSE137424), second group include WT/Mznanogspg/triple mutants.
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: text files with normalized reads for each Sample

molecule: total RNA

organism: Danio rerio

source_name: whole zebrafish embryos

extract_protocol:
40-45 zebrafish embryos were collected, sorted and fixed in liquid nitrogen for each time point. Total RNA was isolated with QIAGEN RNeasy kit following the user’s manual.  RNA was eluted in ddH2O.
Eukaryotic Poly-A enriched library preparation

tag: Stage

tag: genotype

tag: biological replicates number


title: sample_298

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

country: USA

institute: Washington University

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-25, biol rep: 2

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: Tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

organism: Cryptococcus neoformans

growth_protocol: Strains were removed from -80C to YPD agar no more than 5 days before the experiment, grown at 30C for 2 nights , and a single colony was inoculated into 4 mL YPD and grown overnight  at 30C shaking at 230 rpm. One day before the experiment, 1 mL of the ON culture was inoculated into 100 mL YPD and grown as above. At the beginning of the experiment, this culture was spun down, washed in 25 mL PBS, and resuspended in 10 mL PBS. 2 x 10^8 cells were then inoculated into each of four T75 flasks containing preconditioned medium  and incubated under the conditions specified for the experiment. A single flask was harvested for each time point (30, 90, 180, and 1440 min after inoculation), with 1.5 mL of culture removed for imaging and the remaining 18.5 mL used for RNA-Seq. The latter was transferred into a tube on ice containing 2 mL RNA Stop solution (5% tris-saturated phenol in ethanol), the cells were sedimented (3000g, 5 min, 4C), supernatant fraction decanted, and the pellet was frozen in liquid nitrogen and stored at -80C. All flasks were prepared and then preconditioned for 24 hours at the designated temperature and pH concentration before use. Cultures were then inoculated as above and the T75 flasks (MIDSCI TP90076) incubated without rotation. DMEM (Sigma D6429) RPMI (Sigma R8758) was used as purchased except in “buffer” conditions, where sterile 1M HEPES pH 7.0 was added to a final concentration of 25 mM

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

tag: cell line

tag: cell type

value: yeast cell

value: WT

tag: medium

value: YPD

tag: atmosphere

tag: temperature

tag: treatment

value: cAMP none; HEPES buffer pH 7.0 25 mM

tag: time

value: 180 min


title: Cas9 opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

library_source: genomic

data_processing:
Data analyzed withthe CRISPResso2 pipeline:
Reads were trimmed using the Trimmomatic
Trimmed sequences were mapped to the input amplicon reference (by providing also the sequence for the sgRNA, and the base editor nucleotide change) and the quantification window was set to 3
Computed alleles were quantified by measuring the number of reads and their relative abundance based on total read counts
Assembly: Custom reference vector AAV sequence and guide
Supplementary files format and content: Tab-separated results of the different allele found with corresponding quantifications
Library strategy: amplicon sequencing

molecule: genomic DNA

organism: Homo sapiens

source_name: mobilized peripheral blood

extract_protocol:
gDNA was isolated with QIAamp DNA Micro Kit (QIAGEN) according to the manufacturer’s instructions.
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA.The first PCR step was performed using the following amplification protocol: 95°C x 10’, (95°C x 30’’, 59°C x 30’’, 72°C x 20’’) x 20 cycles, 72°C x 10’. The second PCR step was performed using the same reagents of the first step, 5 μl of the PCR product and the following amplification protocol: 95°C x 10’, (95°C x 30’’, 59°C x 30’’, 72°C x 20’’) x 20 cycles, 72°C x 10’. Primers used for the second PCR step contained P5/P7 sequences, i5/i7 Illumina tags to allow multiplexed sequencing and R1/R2 primer binding sites. The PCR amplicon from each sample was separately purified by QIAquick PCR Purification Kit (QIAGEN). Concentration and quality of amplicons were assessed by QuantiFluor ONE dsDNA system and 4200 Tapestation System (Agilent). Amplicons from up to 25 differently tagged samples were multiplexed at equimolar ratios.

tag: tissue

value: mobilized peripheral blood

value: mPB CD34

value: Cas9 opt

tag: target locus

tag: editing time

value: day 3

tag: time of_collection

value: day 7


title: MZsox19bspg_rep2_4.5hpf [re-analysis]


title: sample_937

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-06-01, biol rep: 3


title: sample_1001

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-02-20, biol rep: 4


title: sample_304

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-02-25, biol rep: 2


title: Cas9 at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_91

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-05-25, biol rep: 1


title: ABE8.20-m opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: ABE8.20-m opt


title: MZsox19bspg_rep2_3.5hpf [re-analysis]


title: MZsox19bspg_rep2_4hpf [re-analysis]


title: sample_953

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-10, biol rep: 3

value: cAMP 20 mM

value: 90 min


title: ABE8.20-m at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: MZsox19bspg_rep2_3hpf [re-analysis]


title: BE4max opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: BE4max opt


title: sample_254

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-04, biol rep: 1


title: sample_3628

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2021-09-08, biol rep: 4

value: 30 min


title: MZsox19bspg_rep1_5.5hpf [re-analysis]


title: sample_947

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-10, biol rep: 2


title: BE4max at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_79

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-05-25, biol rep: 1


title: sample_1302

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-23, biol rep: 4


title: MZsox19bspg_rep2_2.5hpf [re-analysis]


title: ABE8.20-m at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: Cas9 opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_1296

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-23, biol rep: 3


title: sample_925

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-06-01, biol rep: 3


title: MZsox19bspg_rep1_5hpf [re-analysis]


title: Cas9 at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep


title: sample_260

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-04, biol rep: 1


title: sample_338

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-29, biol rep: 1


title: sample_350

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-29, biol rep: 2


title: sample_1308

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-23, biol rep: 4


title: MZsox19bspg_rep1_4hpf [re-analysis]


title: sample_959

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-10, biol rep: 3


title: ABE8.20-m at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_266

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-04, biol rep: 1


title: sample_965

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-10, biol rep: 3


title: MZsox19bspg_rep1_4.5hpf [re-analysis]


title: sample_344

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-29, biol rep: 2


title: sample_1314

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-23, biol rep: 4


title: ABE8.20-m opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: MZsox19bspg_rep1_3.5hpf [re-analysis]


title: BE4max opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_357

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-29, biol rep: 2


title: sample_3218

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-05-13, biol rep: 5

value: RPMI

value: room air

value: cAMP none


title: MZsox19bspg_rep1_3hpf [re-analysis]


title: MZsox19bspg_rep1_2.5hpf [re-analysis]


title: sample_1906

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-09-28, biol rep: 4

value: yeast cell

value: WT


title: BE4max at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: MZspg_rep2_6hpf [re-analysis]

value: MZspg


title: sample_1655

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-09-21, biol rep: 3


title: sample_1403

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-10-17, biol rep: 2


title: sample_3300

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-06-04, biol rep: 6


title: sample_464

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-10-15, biol rep: 1


title: sample_3212

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-05-13, biol rep: 5


title: MZspg_rep2_5.5hpf [re-analysis]


title: MZspg_rep2_5hpf [re-analysis]


title: Cas9 at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_1643

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-09-21, biol rep: 3


title: ABE8.20-m opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_1894

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-09-28, biol rep: 4


title: sample_3306

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-06-04, biol rep: 6


title: MZspg_rep2_4.5hpf [re-analysis]


title: sample_452

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-10-15, biol rep: 1


title: ABE8.20-m at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_1918

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-09-28, biol rep: 3

value: 180 min


title: sample_1391

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-10-17, biol rep: 2


title: BE4max opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: mobilized peripheral blood


title: sample_3224

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-05-13, biol rep: 4


title: sample_3312

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-06-04, biol rep: 5


title: MZspg_rep2_3.5hpf [re-analysis]


title: BE4max opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: mPB CD34


title: BE4max at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: MZspg_rep2_3hpf [re-analysis]


title: sample_476

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-10-15, biol rep: 1


title: sample_1667

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-09-21, biol rep: 2


title: MZspg_rep2_2.5hpf [re-analysis]


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep5

value: Mock electro


title: Cas9 at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: day 3


title: sample_106

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-10, biol rep: 1

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: Cas9 opt at IL2RG locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: Cas9 opt

value: day 7


title: sample_3725

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 4


title: sample_874

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2019-12-19, biol rep: 2

value: 90 min


title: sample_3724

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 3


title: ABE8.20-m opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: ABE8.20-m opt


title: Cas9 opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_3631

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2021-09-08, biol rep: 4

value: 30 min


title: MZspg_rep2_4hpf [re-analysis]


title: sample_3230

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-05-13, biol rep: 1

value: RPMI


title: MZspg_rep1_4.5hpf [re-analysis]


title: MZspg_rep1_5hpf [re-analysis]


title: MZspg_rep1_4hpf [re-analysis]


title: sample_868

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2019-12-19, biol rep: 2

value: room air


title: sample_3318

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-06-04, biol rep: 2

value: cAMP none


title: MZspg_rep1_5.5hpf [re-analysis]


title: sample_2244

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-06, biol rep: 3

value: yeast cell


title: sample_100

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-10, biol rep: 1

value: WT


title: sample_2256

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-06, biol rep: 3


title: sample_880

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2019-12-19, biol rep: 2


title: BE4max opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: BE4max opt


title: ABE8.20-m at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: MZspg_rep1_3.5hpf [re-analysis]

value: MZspg


title: sample_3734

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-15, biol rep: 4


title: sample_2250

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-06, biol rep: 3


title: MZspg_rep1_6hpf [re-analysis]


title: MZspg_rep1_3hpf [re-analysis]


title: sample_112

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-10, biol rep: 1

value: 180 min


title: BE4max at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: mobilized peripheral blood

value: mPB CD34


title: sample_886

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2019-12-19, biol rep: 2


title: sample_2262

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-01-06, biol rep: 3


title: BE4max at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: day 3


title: MZspg_rep1_2.5hpf [re-analysis]


title: Cas9 opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_118

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-01-10, biol rep: 1

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: sample_3331

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2021-06-08, biol rep: 7

value: cAMP 20 mM


title: sample_3036

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2021-04-07, biol rep: 6


title: Cas9 at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: day 7


title: MZsox19b_rep2_6hpf [re-analysis]


title: MZsox19b_rep2_5.5hpf [re-analysis]


title: sample_1212

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-07-02, biol rep: 4

value: 90 min


title: sample_2608

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2020-12-22, biol rep: 5


title: sample_1161

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-07-22, biol rep: 3


title: ABE8.20-m opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: ABE8.20-m opt


title: sample_427

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-08-09, biol rep: 2


title: sample_399

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-06-20, biol rep: 1


title: sample_3325

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2021-06-08, biol rep: 6

value: 30 min


title: MZsox19b_rep2_4.5hpf [re-analysis]


title: sample_3030

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2021-04-07, biol rep: 5

value: RPMI


title: MZsox19b_rep2_5hpf [re-analysis]


title: sample_1205

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-02, biol rep: 4

value: room air


title: BE4max at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep7

value: B2M ex1


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep4

value: Mock electro


title: sample_1155

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-22, biol rep: 3

value: yeast cell

value: WT


title: MZsox19b_rep2_4hpf [re-analysis]


title: ABE8.20-m at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep7


title: sample_421

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-08-09, biol rep: 2


title: sample_393

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-06-20, biol rep: 1


title: Cas9 at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep7


title: MZsox19b_rep2_3hpf [re-analysis]


title: BE4max at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep6


title: MZsox19b_rep2_2.5hpf [re-analysis]


title: sample_3042

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2021-04-07, biol rep: 6


title: sample_2614

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2020-12-22, biol rep: 5


title: sample_1167

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-22, biol rep: 3


title: MZsox19b_rep1_6hpf [re-analysis]


title: sample_433

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-08-09, biol rep: 2


title: sample_1219

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-02, biol rep: 4


title: Cas9 at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep6


title: MZsox19b_rep1_5.5hpf [re-analysis]


title: sample_405

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-06-20, biol rep: 1


title: sample_3718

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-09-15, biol rep: 4


title: MZsox19b_rep2_3.5hpf [re-analysis]


title: MZsox19b_rep1_5hpf [re-analysis]


title: ABE8.20-m at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep6


title: sample_3343

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-06-08, biol rep: 3


title: sample_1227

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-07-02, biol rep: 1


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep2


title: MZsox19b_rep1_4.5hpf [re-analysis]


title: sample_3337

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2021-06-08, biol rep: 7


title: sample_3048

description: medium: RPMI, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-04-07, biol rep: 2


title: MZsox19b_rep1_4hpf [re-analysis]


title: sample_3983

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-11-08, biol rep: 7

value: cAMP none


title: MZsox19b_rep1_3.5hpf [re-analysis]


title: ABE8.20-m at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep5


title: BE4max at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep5


title: sample_3305

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-06-04, biol rep: 6


title: sample_1904

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-09-28, biol rep: 4


title: sample_3217

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-05-13, biol rep: 5


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_1401

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-10-17, biol rep: 2


title: ABE8.20-m at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep4


title: sample_462

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-10-15, biol rep: 1


title: sample_3981

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-11-08, biol rep: 7


title: BE4max at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep4


title: MZsox19b_rep1_2.5hpf [re-analysis]


title: sample_3299

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-06-04, biol rep: 6


title: sample_3211

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-05-13, biol rep: 5


title: WT_rep4_5.5hpf [re-analysis]

value: wild-type


title: WT_rep4_6hpf [re-analysis]


title: Cas9 at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep5

value: mobilized peripheral blood


title: sample_1641

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-09-21, biol rep: 3


title: WT_rep4_5hpf [re-analysis]


title: sample_450

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-10-15, biol rep: 1


title: Cas9 at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep4

value: mPB CD34


title: sample_1892

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-09-28, biol rep: 4


title: MZsox19b_rep1_3hpf [re-analysis]


title: WT_rep4_4hpf [re-analysis]


title: sample_1916

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-09-28, biol rep: 3

value: 180 min


title: sample_1665

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-09-21, biol rep: 2


title: Cas9 at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: day 3


title: sample_3311

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-06-04, biol rep: 5


title: ABE8.20-m at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_1653

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-09-21, biol rep: 3


title: WT_rep4_4.5hpf [re-analysis]


title: sample_3985

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-11-08, biol rep: 6


title: Cas9 at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_474

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-10-15, biol rep: 1


title: sample_3223

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-05-13, biol rep: 4


title: ABE8.20-m at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: BE4max at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_3317

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-06-04, biol rep: 3


title: sample_1389

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-10-17, biol rep: 2


title: sample_3987

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-11-08, biol rep: 4


title: WT_rep4_2.5hpf [re-analysis]


title: sample_1423

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2020-10-17, biol rep: 1


title: Cas9 at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: WT_rep4_3hpf [re-analysis]


title: sample_2249

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-06, biol rep: 3

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: sample_873

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2019-12-19, biol rep: 2


title: sample_3229

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-05-13, biol rep: 2


title: ABE8.20-m at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: day 7


title: WT_rep3_6hpf [re-analysis]


title: sample_105

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-10, biol rep: 1

value: 90 min


title: WT_rep3_5hpf [re-analysis]


title: WT_rep3_5.5hpf [re-analysis]


title: WT_rep4_3.5hpf [re-analysis]


title: sample_2243

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-06, biol rep: 3


title: sample_99

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-10, biol rep: 1


title: sample_867

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2019-12-19, biol rep: 2


title: sample_2255

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-06, biol rep: 3


title: sample_879

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2019-12-19, biol rep: 2


title: BE4max at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: Cas9 at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep6


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep12


title: WT_rep3_4.5hpf [re-analysis]


title: WT_rep3_3.5hpf [re-analysis]


title: sample_111

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-10, biol rep: 1


title: WT_rep3_4hpf [re-analysis]


title: sample_885

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2019-12-19, biol rep: 2


title: Cas9 at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep5


title: sample_2607

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2020-12-22, biol rep: 5

value: cAMP 20 mM


title: WT_rep3_3hpf [re-analysis]


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep11


title: sample_3035

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2021-04-07, biol rep: 6


title: sample_2261

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-01-06, biol rep: 3


title: sample_1211

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-07-02, biol rep: 4


title: sample_117

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-01-10, biol rep: 1


title: sample_1160

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-07-22, biol rep: 3


title: WT_rep2_5.5hpf [re-analysis]


title: sample_426

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-08-09, biol rep: 2


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep10


title: Cas9 at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep7


title: WT_rep2_5hpf [re-analysis]


title: sample_3630

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2021-09-08, biol rep: 4

value: 30 min


title: sample_3324

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2021-06-08, biol rep: 6

value: RPMI


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep9


title: sample_3330

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2021-06-08, biol rep: 7

value: room air


title: BE4max at B2M ex1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: B2M ex1


title: sample_3029

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2021-04-07, biol rep: 5


title: sample_1204

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-02, biol rep: 4


title: Cas9 at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: WT_rep2_4.5hpf [re-analysis]


title: sample_3733

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-15, biol rep: 4


title: Cas9 at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep4


title: WT_rep3_2.5hpf [re-analysis]


title: sample_420

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-08-09, biol rep: 2


title: WT_rep2_6hpf [re-analysis]


title: sample_1154

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-22, biol rep: 3


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep8


title: WT_rep2_4hpf [re-analysis]


title: sample_398

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-06-20, biol rep: 1


title: WT_rep2_3.5hpf [re-analysis]


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7


title: sample_392

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-06-20, biol rep: 1


title: sample_3336

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-06-08, biol rep: 5


title: WT_rep2_3hpf [re-analysis]


title: sample_3041

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-04-07, biol rep: 4


title: Cas9 at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_1218

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-02, biol rep: 3


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep7


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep8


title: WT_rep2_2.5hpf [re-analysis]


title: sample_432

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-08-09, biol rep: 2


title: sample_404

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-06-20, biol rep: 1


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep7


title: WT_rep1_5hpf [re-analysis]


title: sample_1226

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-07-02, biol rep: 2


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep6


title: sample_3108

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-04-23, biol rep: 6


title: sample_3047

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-04-07, biol rep: 3


title: WT_rep1_4.5hpf [re-analysis]


title: sample_412

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-06-20, biol rep: 1


title: WT_rep1_5.5hpf [re-analysis]


title: sample_2708

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-01-26, biol rep: 5


title: sample_1506

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-11-02, biol rep: 4


title: sample_1241

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2019-08-19, biol rep: 3


title: WT_rep1_4hpf [re-analysis]


title: sample_3342

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-06-08, biol rep: 4


title: sample_3102

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-04-23, biol rep: 7


title: WT_rep1_3.5hpf [re-analysis]


title: sample_807

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2019-08-22, biol rep: 2


title: sample_2702

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-01-26, biol rep: 6


title: sample_581

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2019-08-15, biol rep: 1


title: WT_rep1_3hpf [re-analysis]


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep4


title: WT_rep1_2.5hpf [re-analysis]


title: sample_1547

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-12-18, biol rep: 5


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_1235

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2019-08-19, biol rep: 3


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep4


title: sample_801

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2019-08-22, biol rep: 2


title: MZnanog_rep3_6hpf

value: MZnanog


title: sample_575

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2019-08-15, biol rep: 1

value: yeast cell


title: sample_1494

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-11-02, biol rep: 4

value: WT


title: MZnanog_rep3_5.5hpf


title: MZnanog_rep3_5hpf


title: sample_3114

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-04-23, biol rep: 6

value: cAMP none


title: sample_2714

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-01-26, biol rep: 5


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep5


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep6


title: sample_1571

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-12-18, biol rep: 4


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep5


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep1

value: Mock electro


title: sample_1518

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-11-02, biol rep: 3


title: sample_1247

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2019-08-19, biol rep: 2


title: MZnanog_rep3_4.5hpf


title: Cas9 at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: mobilized peripheral blood


title: sample_3727

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 5


title: sample_3726

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 4


title: sample_587

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2019-08-15, biol rep: 1


title: MZnanog_rep3_4hpf


title: MZnanog_rep3_3.5hpf


title: sample_3625

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-09-08, biol rep: 3


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: mPB CD34


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_3440

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-07-06, biol rep: 2


title: MZnanog_rep2_6hpf


title: MZnanog_rep3_3hpf


title: sample_2720

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-01-26, biol rep: 1


title: sample_911

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-06-01, biol rep: 3


title: sample_988

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-20, biol rep: 4


title: sample_291

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-25, biol rep: 2


title: BE4max at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_65

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-05-25, biol rep: 1


title: sample_982

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-20, biol rep: 4


title: MZnanog_rep2_5hpf


title: sample_899

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-06-01, biol rep: 3


title: sample_285

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-25, biol rep: 2


title: sample_53

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-05-25, biol rep: 1


title: MZnanog_rep2_4.5hpf


title: HET : 3 : 1220 PC [PLS_Ali_MSp]

type: RNA

city: RIVERSIDE

first: Declan

last: McCole

state: CA

address: 3401 Watkins Drive

department: Biomedical Sciences

institute: University of California Riverside

description: 50ug of total RNA was used for each sample. WT samples were used as reference samples for comparison in analysis.

hyb_protocol: 50 ng of total RNA was used in the hybridization from each sample following manufacturer's guidelines (18 hours at 65°C). Samples were loaded into a AutoImmune Profiling Nanostring panel with the addition of 30 custom targets screening for markers of host-bacteria interaction, autophagy, immune response and iron transport (PLS_Ali_MSp).

scan_protocol: Scanning of the panels was performed by nCounter SPRINT Profiler and data analysis by nSolver Analysis Software 4.0.

data_processing: Results from each panel were normalized in nSolver software 4.0. using the advanced analysis 2.0 function which relies on the gNorm algorithm. nSolver-generated principal component analysis and heat maps were used to evaluate specific sample clustering and to identify covariants. Principal component analysis identified that at least of set of littermates (co-housing) clustered together, hence data analysis was normalized taking into account littermate effect as a covariate. The same analysis was performed to identify sex differences but none was found. Then, the normalized data from each intestinal segment was consolidated using the MultiRLF function and used for differential expression between genotypes to identify specific targets that exhibit significantly increased or decreased gene expression. p-value was set at 0.05. Benjamini-Yekutieli test was used to calculate the false discovery rate for multiple comparisons analysis. Q-value was set at 0.1.

label: codeset probes

organism: Mus musculus

source_name: Isolated Proximal colon IECs

label_protocol: Samples were labelled with panel-specific codesets, or barcodes, probes designed by Nanostring.

extract_protocol: Proximal colon sections were cut opened longitudinally and immersed in 500uL of Cell Recovery Solution (Corning, Cat. No. 354253) for two hours on ice, and then shaken with forceps to release the intestinal crypts/villi into the solution. Samples were centrifuged at 1.5xG for 10 minutes at 4°C. The supernatant was aspirated and IECs washed with ice-cold PBS (x2). Samples were stored in RNA later and frozen at -80°C until day of experiment. RNA later was removed and cells lysed with syringe and needle (22G). Total RNA was isolated using QIAGEN RNeasy mini kit. RNA estimation was done using Qubit 2.0. Sample purity was assessed by NanoDrop absorbance 260/280 ratio.

value: HET

tag: littermate group

tag: mouse number

tag: Sex

value: Male


title: sample_994

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-20, biol rep: 4

value: cAMP none; HEPES buffer pH 7.0 25 mM

value: 180 min


title: WT : 3 : 1219 PC [PLS_Ali_MSp]


title: MZnanog_rep2_4hpf

tag: Stage


title: sample_923

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-06-01, biol rep: 3

tag: genotype


title: MZnanog_rep2_3.5hpf

tag: biological replicates number


title: sample_77

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-05-25, biol rep: 1

tag: cell line


title: sample_297

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-25, biol rep: 2

tag: cell type


title: ABE8.20-m at AAVS1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: day 3

value: day 7


title: sample_3721

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-15, biol rep: 5

tag: medium


title: MZnanog_rep2_3hpf


title: HET : 3 : 1215 PC [PLS_Ali_MSp]

value: Female


title: sample_3637

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-08, biol rep: 4

value: RPMI

tag: atmosphere


title: WT : 3 : 1216 PC [PLS_Ali_MSp]


title: sample_1000

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-02-20, biol rep: 3

tag: temperature


title: MZnanog_rep2_2.5hpf


title: sample_935

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-06-01, biol rep: 2

tag: treatment


title: MZnanog_rep2_5.5hpf


title: KO : 3 : 1214 PC [PLS_Ali_MSp]

value: KO


title: MZnanog_rep1_6hpf


title: sample_89

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-05-25, biol rep: 1

tag: time


title: sample_1301

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-23, biol rep: 4

value: cAMP 20 mM

value: 90 min


title: sample_343

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-29, biol rep: 2

value: yeast cell


title: sample_952

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-10, biol rep: 3

value: WT


title: WT : 2 : 1402 PC [PLS_Ali_MSp]


title: sample_253

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-04, biol rep: 1


title: MZnanog_rep1_5.5hpf

value: MZnanog


title: HET : 2 : 1403 PC [PLS_Ali_MSp]


title: sample_1295

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-23, biol rep: 4

value: 30 min


title: KO : 3 : 1218 PC [PLS_Ali_MSp]


title: MZnanog_rep1_5hpf


title: MZnanog_rep1_4.5hpf


title: sample_337

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-29, biol rep: 2


title: sample_946

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-10, biol rep: 3


title: KO : 2 : 1405 PC [PLS_Ali_MSp]

description: 50ug of total RNA was used for each sample. WT samples were used as reference samples for comparison in analysis.


title: sample_247

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-04, biol rep: 1


title: MZnanog_rep1_4hpf


title: HET : 1 : 1245 PC [PLS_Ali_MSp]


title: MZnanog_rep1_3.5hpf


title: sample_349

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-29, biol rep: 2


title: sample_259

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-04, biol rep: 1


title: MZnanog_rep1_3hpf


title: sample_958

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-10, biol rep: 3


title: WT : 1 : 1244 PC [PLS_Ali_MSp]


title: HET : 3 : 1220 DC [PLS_Ali_MSp]

source_name: Isolated Distal colon IECs

extract_protocol: Distal colon sections were cut opened longitudinally and immersed in 500uL of Cell Recovery Solution (Corning, Cat. No. 354253) for two hours on ice, and then shaken with forceps to release the intestinal crypts/villi into the solution. Samples were centrifuged at 1.5xG for 10 minutes at 4°C. The supernatant was aspirated and IECs washed with ice-cold PBS (x2). Samples were stored in RNA later and frozen at -80°C until day of experiment. RNA later was removed and cells lysed with syringe and needle (22G). Total RNA was isolated using QIAGEN RNeasy mini kit. RNA estimation was done using Qubit 2.0. Sample purity was assessed by NanoDrop absorbance 260/280 ratio.


title: KO : 1 : 1243 PC [PLS_Ali_MSp]


title: sample_356

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-29, biol rep: 2


title: sample_1313

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-23, biol rep: 4


title: sample_964

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-10, biol rep: 3


title: MZsox19bnanog_rep2_6hpf


title: sample_265

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-04, biol rep: 1


title: MZsox19bnanog_rep2_5.5hpf


title: WT : 3 : 1219 DC [PLS_Ali_MSp]


title: KO : 3 : 1218 DC [PLS_Ali_MSp]


title: MZsox19bnanog_rep2_5hpf


title: sample_2707

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-01-26, biol rep: 4

value: cAMP none


title: sample_3107

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-04-23, biol rep: 5


title: sample_1504

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-11-02, biol rep: 3


title: sample_1307

description: medium: RPMI, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-23, biol rep: 4


title: sample_1240

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2019-08-19, biol rep: 2


title: MZsox19bnanog_rep2_4.5hpf


title: MZsox19bnanog_rep2_4hpf


title: sample_1545

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-12-18, biol rep: 5


title: HET : 3 : 1215 DC [PLS_Ali_MSp]


title: sample_806

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2019-08-22, biol rep: 1


title: sample_1492

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-11-02, biol rep: 4


title: MZsox19bnanog_rep2_3.5hpf


title: sample_800

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2019-08-22, biol rep: 2


title: KO : 3 : 1214 DC [PLS_Ali_MSp]

description: 50ug of total RNA was used for each sample. WT samples were used as reference samples for comparison in analysis.


title: WT : 2 : 1402 DC [PLS_Ali_MSp]


title: MZsox19bnanog_rep2_3hpf


title: sample_3113

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-04-23, biol rep: 5


title: MZsox19bnanog_rep2_2.5hpf


title: KO : 2 : 1405 DC [PLS_Ali_MSp]


title: HET : 2 : 1403 DC [PLS_Ali_MSp]


title: WT : 3 : 1216 DC [PLS_Ali_MSp]


title: sample_1516

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-11-02, biol rep: 4


title: MZsox19bnanog_rep1_5.5hpf


title: sample_586

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2019-08-15, biol rep: 1


title: sample_1246

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2019-08-19, biol rep: 3


title: sample_812

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2019-08-22, biol rep: 2


title: sample_3101

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-04-23, biol rep: 6


title: MZsox19bnanog_rep1_5hpf


title: sample_3623

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-09-08, biol rep: 4


title: HET : 1 : 1245 DC [PLS_Ali_MSp]


title: MZsox19bnanog_rep1_4.5hpf


title: sample_3186

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-04-23, biol rep: 3


title: KO : 1 : 1243 DC [PLS_Ali_MSp]


title: sample_3119

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-04-23, biol rep: 2


title: WT : 1 : 1244 DC [PLS_Ali_MSp]


title: MZsox19bnanog_rep1_4hpf


title: sample_1234

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2019-08-19, biol rep: 3


title: sample_2719

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-01-26, biol rep: 1


title: sample_574

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2019-08-15, biol rep: 1


title: sample_987

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-20, biol rep: 4


title: sample_909

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-06-01, biol rep: 3


title: sample_290

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-25, biol rep: 2


title: HET : 3 : 1220 [PLS_Ali_MSp]

source_name: Isolated Cecum IECs

extract_protocol: Cecum sections were cut opened longitudinally and immersed in 500uL of Cell Recovery Solution (Corning, Cat. No. 354253) for two hours on ice, and then shaken with forceps to release the intestinal crypts/villi into the solution. Samples were centrifuged at 1.5xG for 10 minutes at 4°C. The supernatant was aspirated and IECs washed with ice-cold PBS (x2). Samples were stored in RNA later and frozen at -80°C until day of experiment. RNA later was removed and cells lysed with syringe and needle (22G). Total RNA was isolated using QIAGEN RNeasy mini kit. RNA estimation was done using Qubit 2.0. Sample purity was assessed by NanoDrop absorbance 260/280 ratio.


title: MZsox19bnanog_rep1_3.5hpf


title: MZsox19bnanog_rep1_3hpf


title: WT : 3 : 1219 [PLS_Ali_MSp]


title: sample_63

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-05-25, biol rep: 1


title: sample_981

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-20, biol rep: 4


title: KO : 3 : 1218 [PLS_Ali_MSp]

description: 50ug of total RNA was used for each sample. WT samples were used as reference samples for comparison in analysis.


title: sample_897

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-06-01, biol rep: 3


title: sample_284

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-25, biol rep: 2


title: MZsox19bnanog_rep1_2.5hpf


title: sample_51

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-05-25, biol rep: 1


title: L8_MZnanogspg_B8_6hpf

value: Mznanogspg


title: WT : 3 : 1216 [PLS_Ali_MSp]


title: sample_993

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-20, biol rep: 4


title: sample_921

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-06-01, biol rep: 3


title: L7_MZnanogspg_B8_5.5hpf


title: sample_75

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-05-25, biol rep: 1


title: sample_3636

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-08, biol rep: 4


title: HET : 3 : 1215 [PLS_Ali_MSp]

value: HET


title: sample_999

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-02-20, biol rep: 3


title: KO : 3 : 1214 [PLS_Ali_MSp]


title: sample_933

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-06-01, biol rep: 2


title: L6_MZnanogspg_B8_5hpf


title: WT : 2 : 1402 [PLS_Ali_MSp]


title: L5_MZnanogspg_B8_4.5hpf


title: L4_MZnanogspg_B8_4hpf


title: sample_1300

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-23, biol rep: 4


title: HET : 2 : 1403 [PLS_Ali_MSp]


title: L3_MZnanogspg_B8_3.5hpf


title: KO : 2 : 1405 [PLS_Ali_MSp]


title: sample_951

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-10, biol rep: 3


title: sample_252

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-04, biol rep: 1


title: HET : 1 : 1245 [PLS_Ali_MSp]


title: sample_342

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-29, biol rep: 2


title: L2_MZnanogspg_B8_3hpf


title: sample_1294

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-23, biol rep: 4


title: WT : 1 : 1244 [PLS_Ali_MSp]


title: sample_945

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-10, biol rep: 3


title: sample_336

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-29, biol rep: 2


title: KO : 1 : 1243 [PLS_Ali_MSp]

description: 50ug of total RNA was used for each sample. WT samples were used as reference samples for comparison in analysis.


title: sample_296

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-25, biol rep: 2


title: sample_246

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-04, biol rep: 1


title: Small-Int-Ep, Z00000436 reanalysis

city: Jerusalem

first: Benjamin

middle: P

last: Berman

address: Ein Kerem campus

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

description:
Small-Int-Ep, Z00000436
GSM5652380

data_processing:
BAM files were re-processed with the nf-core/methylseq pipeline using the biscuit aligner (https://github.com/ekushele/methylseq/blob/master/main_bams.nf ). The quality of fastQ files was assessed using FastQC (v0.11.9). TrimGalore (v0.6.4_dev) was used to trim adapters from all samples with the following parameters: ‘clip_r1 = 10 clip_r2 = 15 three_prime_clip_r1 = 10 three_prime_clip_r2 = 10’. We aligned the trimmed samples to the hg19 genome assembly, using the biscuit aligner (v0.3.15.20200318), with ‘-b 1’ for directional library. Duplicates were marked using samblaster (v0.1.24) with ‘--addMateTags’. Then, BAM files were sorted and indexed using Samtools (v1.9). The sorted and indexed BAMs were given as an input to ‘biscuit pileup’, to generate VCF files. We implemented a custom approach to filtering SNPs and generating Biscuit epiread files which contained a merged version of the two ends of each paired-end read. The code is available at https://github.com/ekushele/methylseq
Assembly: hg19
Supplementary files format and content: tab delimited file with the following columns: chromosome, start position, end position, read name, pair (1/2), strand,  CpG positions, methylation pattern, SNP positions, SNP patterns

source_name: Jejunum

extract_protocol:
refer to GSE186458
refer to GSE186458

tag: tissue

value: Jejunum


title: K8_WT_B8_6hpf

value: wild-type


title: sample_1306

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-23, biol rep: 4

value: 180 min


title: sample_957

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-10, biol rep: 3


title: sample_258

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-04, biol rep: 1


title: sample_87

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-05-25, biol rep: 1

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: K7_WT_B8_5.5hpf


title: K6_WT_B8_5hpf


title: sample_348

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-29, biol rep: 2


title: Small-Int-Ep, Z000000UW reanalysis

description:
Small-Int-Ep, Z000000UW
GSM5652378

source_name: Small intestine

value: Small intestine


title: sample_1312

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-23, biol rep: 4


title: sample_963

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-10, biol rep: 3


title: K5_WT_B8_4.5hpf


title: sample_355

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-29, biol rep: 2


title: Small-Int-Ep, Z0000042V reanalysis

description:
Small-Int-Ep, Z0000042V
GSM5652376


title: sample_264

description: medium: RPMI, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-04, biol rep: 1


title: K4_WT_B8_4hpf


title: Colon-Ep, Z0000043C reanalysis

description:
Colon-Ep, Z0000043C
GSM5652375

source_name: Colon

value: Colon


title: sample_3924

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-09-28, biol rep: 46

value: PBS

value: room air

value: 0 min


title: L1_MZnanogspg_B8_2.5hpf


title: K3_WT_B8_3.5hpf


title: sample_3295

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-06-04, biol rep: 44


title: sample_3296

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-06-04, biol rep: 45


title: Colon-Ep, Z0000043B reanalysis

description:
Colon-Ep, Z0000043B
GSM5652374


title: Small-Int-Ep, Z000000UY reanalysis

description:
Small-Int-Ep, Z000000UY
GSM5652379


title: sample_3207

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-05-13, biol rep: 42


title: Colon-Ep, Z0000044T reanalysis

description:
Colon-Ep, Z0000044T
GSM5652373


title: sample_3098

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-04-23, biol rep: 41


title: K1_WT_B8_2.5hpf


title: sample_3097

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-04-23, biol rep: 40


title: Colon-Ep, Z0000044J reanalysis

description:
Colon-Ep, Z0000044J
GSM5652372


title: Small-Int-Ep, Z000000RT reanalysis

description:
Small-Int-Ep, Z000000RT
GSM5652377


title: sample_3025

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-04-07, biol rep: 38


title: sample_3026

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-04-07, biol rep: 39


title: J8_MZnanogspg_B9_6hpf


title: J7_MZnanogspg_B9_5.5hpf


title: Colon-Ep, Z000000VA reanalysis

description:
Colon-Ep, Z000000VA
GSM5652371


title: sample_1884

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-09-28, biol rep: 35


title: sample_2240

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-01-06, biol rep: 37


title: sample_2239

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-01-06, biol rep: 36


title: Colon-Ep, Z0000044S reanalysis

description:
Colon-Ep, Z0000044S
GSM5652370


title: Colon-Ep, Z000000V0 reanalysis

description:
Colon-Ep, Z000000V0
GSM5652368


title: sample_1635

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-09-21, biol rep: 34


title: sample_1539

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-12-18, biol rep: 32


title: sample_3208

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-05-13, biol rep: 43


title: J5_MZnanogspg_B9_4.5hpf


title: sample_1633

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-09-21, biol rep: 33


title: Colon-Ep, Z000000V8 reanalysis

description:
Colon-Ep, Z000000V8
GSM5652369


title: K2_WT_B8_3hpf


title: sample_1486

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-11-02, biol rep: 30


title: Gastric-Ep, Z00000438 reanalysis

description:
Gastric-Ep, Z00000438
GSM5652367

source_name: Gastric

value: Gastric


title: J4_MZnanogspg_B9_4hpf


title: sample_1484

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-11-02, biol rep: 29

value: yeast cell


title: J3_MZnanogspg_B9_3.5hpf


title: sample_1383

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-10-17, biol rep: 28

value: WT


title: Gastric-Ep, Z00000437 reanalysis

description:
Gastric-Ep, Z00000437
GSM5652366


title: sample_1290

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-10-23, biol rep: 26


title: sample_1381

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-10-17, biol rep: 27


title: J2_MZnanogspg_B9_3hpf


title: sample_1231

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-08-19, biol rep: 25


title: Gastric-Ep, Z000000SR reanalysis

description:
Gastric-Ep, Z000000SR
GSM5652365

source_name: Gastric antrum

value: Gastric antrum


title: sample_1230

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-08-19, biol rep: 24


title: J1_MZnanogspg_B9_2.5hpf


title: J6_MZnanogspg_B9_5hpf


title: I8_WT_B9_6hpf


title: sample_1150

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-07-22, biol rep: 23


title: Gastric-Ep, Z000000SP reanalysis

description:
Gastric-Ep, Z000000SP
GSM5652364


title: sample_977

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-02-20, biol rep: 21


title: Gastric-Ep, Z000000SF reanalysis

description:
Gastric-Ep, Z000000SF
GSM5652363


title: sample_978

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-02-20, biol rep: 22


title: I7_WT_B9_5.5hpf


title: Gastric-Ep, Z000000ST reanalysis

description:
Gastric-Ep, Z000000ST
GSM5652362

source_name: Gastric body

value: Gastric body


title: sample_941

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-11-10, biol rep: 19

value: cAMP none


title: sample_942

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-11-10, biol rep: 20


title: sample_1537

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-12-18, biol rep: 31


title: I6_WT_B9_5hpf


title: sample_889

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-06-01, biol rep: 17


title: I5_WT_B9_4.5hpf


title: I4_WT_B9_4hpf


title: sample_797

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-08-22, biol rep: 14


title: sample_863

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-12-19, biol rep: 15


title: Gastric-Ep, Z000000SV reanalysis

description:
Gastric-Ep, Z000000SV
GSM5652359

source_name: Gastric fundus

value: Gastric fundus


title: sample_571

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-08-15, biol rep: 13


title: sample_444

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-10-15, biol rep: 11


title: I3_WT_B9_3.5hpf


title: sample_417

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-08-09, biol rep: 10


title: sample_570

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-08-15, biol rep: 12


title: I2_WT_B9_3hpf


title: sample_389

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-06-20, biol rep: 9


title: Gastric-Ep, Z000000SK reanalysis

description:
Gastric-Ep, Z000000SK
GSM5652358


title: Gastric-Ep, Z000000RX reanalysis

description:
Gastric-Ep, Z000000RX
GSM5652357


title: Gallbladder, Z00000432 reanalysis

description:
Gallbladder, Z00000432
GSM5652356

source_name: Gallbladder

value: Gallbladder


title: sample_388

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-06-20, biol rep: 8


title: Gastric-Ep, Z000000SM reanalysis

description:
Gastric-Ep, Z000000SM
GSM5652361


title: sample_864

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-12-19, biol rep: 16


title: sample_280

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-02-25, biol rep: 5


title: sample_96

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-01-10, biol rep: 4


title: Gastric-Ep, Z000000SD reanalysis

description:
Gastric-Ep, Z000000SD
GSM5652360


title: sample_332

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-10-29, biol rep: 6


title: sample_891

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-06-01, biol rep: 18


title: sample_95

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-01-10, biol rep: 3


title: D6_MZnanogspg_B7_5hpf

value: Mznanogspg


title: Lung-Ep-Alveo, Z000000VE reanalysis

description:
Lung-Ep-Alveo, Z000000VE
GSM5652354

source_name: Lung alveolar

value: Lung alveolar


title: Lung-Ep-Alveo, Z000000VC reanalysis

description:
Lung-Ep-Alveo, Z000000VC
GSM5652353


title: sample_45

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-05-25, biol rep: 2


title: sample_43

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2020-05-25, biol rep: 1


title: D5_MZnanogspg_B7_4.5hpf


title: Lung-Ep-Alveo, Z000000T1 reanalysis

description:
Lung-Ep-Alveo, Z000000T1
GSM5652352


title: sample_3304

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-06-04, biol rep: 6

value: DMEM

value: 90 min


title: sample_3216

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-05-13, biol rep: 5


title: D4_MZnanogspg_B7_4hpf


title: I1_WT_B9_2.5hpf

value: wild-type


title: sample_333

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2019-10-29, biol rep: 7


title: Breast-Basal-Ep, Z0000043E reanalysis

description:
Breast-Basal-Ep, Z0000043E
GSM5652351

source_name: Breast

value: Breast


title: D3_MZnanogspg_B7_3.5hpf


title: D7_MZnanogspg_B7_5.5hpf


title: sample_1399

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-10-17, biol rep: 2


title: sample_1902

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-09-28, biol rep: 4


title: D8_MZnanogspg_B7_6hpf


title: Breast-Basal-Ep, Z000000VG reanalysis

description:
Breast-Basal-Ep, Z000000VG
GSM5652349


title: Breast-Basal-Ep, Z000000VL reanalysis

description:
Breast-Basal-Ep, Z000000VL
GSM5652350


title: sample_460

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-10-15, biol rep: 1


title: sample_3298

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-06-04, biol rep: 6

value: 30 min


title: Lung-Ep-Alveo, Z0000042B reanalysis

description:
Lung-Ep-Alveo, Z0000042B
GSM5652355

source_name: Lung pleural

value: Lung pleural


title: D1_MZnanogspg_B7_2.5hpf


title: sample_3210

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-05-13, biol rep: 5

value: room air


title: Breast-Basal-Ep, Z000000V6 reanalysis

description:
Breast-Basal-Ep, Z000000V6
GSM5652348


title: D2_MZnanogspg_B7_3hpf


title: C8_WT_B7_6hpf


title: sample_1890

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-09-28, biol rep: 4


title: sample_1387

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-10-17, biol rep: 2


title: sample_1639

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-09-21, biol rep: 3


title: Breast-Luminal-Ep, Z000000VN reanalysis

description:
Breast-Luminal-Ep, Z000000VN
GSM5652347


title: sample_448

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-10-15, biol rep: 1


title: C7_WT_B7_5.5hpf


title: sample_3713

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-09-15, biol rep: 5

value: 180 min


title: sample_1651

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-09-21, biol rep: 3

value: yeast cell


title: Breast-Luminal-Ep, Z000000VJ reanalysis

description:
Breast-Luminal-Ep, Z000000VJ
GSM5652346


title: sample_3310

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-06-04, biol rep: 3

value: WT


title: Breast-Luminal-Ep, Z000000V2 reanalysis

description:
Breast-Luminal-Ep, Z000000V2
GSM5652345


title: sample_3222

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-05-13, biol rep: 2


title: C5_WT_B7_4.5hpf


title: sample_1663

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-09-21, biol rep: 1


title: Bladder-Ep, Z00000450 reanalysis

description:
Bladder-Ep, Z00000450
GSM5652344

source_name: Bladder

value: Bladder


title: Bladder-Ep, Z0000044L reanalysis

description:
Bladder-Ep, Z0000044L
GSM5652343


title: C3_WT_B7_3.5hpf

source_name: whole zebrafish embryos


title: sample_3446

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-07-06, biol rep: 3


title: C4_WT_B7_4hpf


title: sample_3711

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 4


title: sample_3316

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-06-04, biol rep: 2


title: Bladder-Ep, Z0000043F reanalysis

description:
Bladder-Ep, Z0000043F
GSM5652342


title: sample_3228

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-05-13, biol rep: 1


title: Bladder-Ep, Z000000QP reanalysis

description:
Bladder-Ep, Z000000QP
GSM5652341


title: Bladder-Ep, Z000000QM reanalysis

description:
Bladder-Ep, Z000000QM
GSM5652340


title: C1_WT_B7_2.5hpf


title: C2_WT_B7_3hpf


title: sample_872

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2019-12-19, biol rep: 2

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: T3_triple_B12_6hpf


title: sample_2248

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-06, biol rep: 3


title: SNU719 7.5uM DEC 72h a

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
ATAC-Seq raw reads were aligned using bowtie against the Human gammaherpesvirus 4 NC_007605.1, followed by HOMER to generate bigwig files
Assembly: Viral Genome Human gammaherpesvirus 4 NC_007605.1
Supplementary files format and content:ATAC-Seq raw reads were aligned using bowtie against the Human gammaherpesvirus 4 NC_007605.1, followed by HOMER to generate bigwig files

organism: human gammaherpesvirus 4

extract_protocol:
1 × 105 cells (>95% viability) were washed in 50 ml cold PBS, spun down at 500 x g and 4°C for 5min
Cells were resuspended in 50 ml cold ATAC-Resuspension Buffer (RSB) (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL CA-630, 0.1% Tween-20 and 0.01% Digitonin. Resuspended cells were kept on ice for 3 min, then washed with 1 ml cold ATAC-RSB containing 0.1% Tween-20 but no IGEPAL CA-630 or Digitonin.  Pellet nuclei at 500 x g and 4°C for 10 min, and the supernatant was removed. The pellet was then resuspended in a 50 ml Tn5 transposase reaction mixture following the manufacturer’s protocol (Illumina Tagment DNA Enzyme and Buffer, Illumina) and incubated at 37°C for 30 min in a thermomixer with 300 rpm mixing. DNA was purified using a MinElute PCR purification kit (Qiagen) and eluted in 10 ml Elution Buffer for library amplification.  PCR amplification of fragmented DNA was done using the NEBNext HiFi PCR mastermix (New England Bioloabs) with a universal forward and sample-specific reverse oligo for sample barcoding using the following PCR conditions: initial incubations of 72°C for 5 min and 98°C for 30 s, followed by 5 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.  Additional number of cycles was determined for each sample through a “side” qPCR reaction using an aliquot of the PCR as template to determine the number of cycles needed to reach 1/3 of the max fluorescence.  PCR products were run on a 1% agarose gel, regions from ~50 bp to ~1 kb were excised, and DNA was extracted using a gel extraction kit (Qiagen).

value: Gastric Cancer

value: 7.5uM DEC

tag: time point


title: SNU719 7.5uM DEC 24h b


title: Prostate-Ep, Z0000045G reanalysis

description:
Prostate-Ep, Z0000045G
GSM5652339

source_name: Prostate

value: Prostate


title: SNU719 7.5uM DEC 24h a


title: C6_WT_B7_5hpf


title: SNU719 DMSO 2

value: DMSO


title: sample_3609

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-09-08, biol rep: 4

value: cAMP none


title: Prostate-Ep, Z0000045F reanalysis

description:
Prostate-Ep, Z0000045F
GSM5652338


title: R7_triple_B12_5hpf


title: SNU719 DMSO 1


title: R8_triple_B12_5.5hpf


title: sample_3629

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2021-09-08, biol rep: 4

value: DMEM


title: SNU719 7.5uM DEC 72h b


title: Prostate-Ep, Z000000S3 reanalysis

description:
Prostate-Ep, Z000000S3
GSM5652337


title: R6_triple_B12_4.5hpf


title: sample_2242

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-06, biol rep: 3


title: Prostate-Ep, Z000000RV reanalysis

description:
Prostate-Ep, Z000000RV
GSM5652336


title: YCCEL1 7.5uM DEC 72h b


title: R5_triple_B12_4hpf


title: Lung-Ep-Bron, Z000000S5 reanalysis

description:
Lung-Ep-Bron, Z000000S5
GSM5652335

source_name: Lung bronchus

value: Lung bronchus


title: sample_866

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2019-12-19, biol rep: 2


title: Lung-Ep-Bron, Z000000RZ reanalysis

description:
Lung-Ep-Bron, Z000000RZ
GSM5652334


title: sample_98

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-10, biol rep: 1


title: YCCEL1 7.5uM DEC 72h a


title: YCCEL1 7.5uM DEC 24h b


title: R4_triple_B12_3.5hpf


title: YCCEL1 7.5uM DEC 24h a


title: R3_triple_B12_3hpf


title: Lung-Ep-Bron, Z000000QD reanalysis

description:
Lung-Ep-Bron, Z000000QD
GSM5652333


title: YCCEL1 DMSO2


title: sample_104

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-10, biol rep: 1

value: 90 min


title: R2_triple_B12_2.5hpf


title: Head-Neck-Ep, Z0000044A reanalysis

description:
Head-Neck-Ep, Z0000044A
GSM5652332

source_name: Pharynx

value: Pharynx


title: YCCEL1 DMSO1


title: T1_WT_B12_6hpf

value: wild-type


title: Head-Neck-Ep, Z00000426 reanalysis

description:
Head-Neck-Ep, Z00000426
GSM5652331

source_name: Esophagus

value: Esophagus


title: sample_110

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-10, biol rep: 1

value: room air


title: GM14385/HG002 Fiber-seq

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

description: assembly: Verkko-assembled autosomes and X chromosome from GM24385/HG00256, as well as the Y chromosome from CHM13 v2.0

data_processing:
CCS reads generated using CCS --hifi-kinetics (v6.4.0).
CCS reads aligned to the reference genome with pbmm2 -N1 (v1.9.0)
Subreads aligned to CCS reads using actc (v0.2.0).
ipdRatios generated for reach molecule using ipdSummary(v3.0).
primrose (v1.3.0) udentified per-molecule 5mCpG sites using CCS reads.
Custom scripts then used ipdRatio output to identify m6A sites using a Gaussian Mixture model.
Custom scripts then utilized per-molecule m6A calls to identify nucleosome footprints.
Supplementary files format and content: single-molecule Nucleosome calls, Methyltransferase Accesible Patch calls, m6A calls, and 5mC calls (CpG) in a bed12 format.
Supplementary files format and content: bam files containing alignment information for single molecules to appropriate reference genome.
Library strategy: Fiber-seq

extract_protocol:
DNA extracted using the Promega Wizard HMW DNA Extraction Kit A2920
PacBio SMRTbell library construction

value: Lymphoblastoid cell line

value: HG002/GM24385 nuclei treated with 200U Hia5 for 10min at 25C, 15kb shearing and pippin size selection


title: Q8_WT_B12_5.5hpf


title: sample_3732

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-15, biol rep: 3

value: yeast cell

value: WT


title: Head-Neck-Ep, Z000000PZ reanalysis

description:
Head-Neck-Ep, Z000000PZ
GSM5652330


title: Q7_WT_B12_5hpf


title: CHM1 Fiber-seq

description: assembly: T2T CHM1 (chm1_cens_v21.fa)

value: Complete hydatidiform mole cell line

value: CHM1 nuclei treated with 200U Hia5 for 10min at 25C, 15kb shearing and pippin size selection


title: sample_2260

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-01-06, biol rep: 2

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: Head-Neck-Ep, Z000000QB reanalysis

description:
Head-Neck-Ep, Z000000QB
GSM5652329

source_name: Larynx

value: Larynx


title: CHM13 Fiber-seq

description: assembly: T2T CHM13 v1.0

value: CHM13 nuclei treated with 200U Hia5 for 10min at 25C, 15kb shearing and pippin size selection


title: Q6_WT_B12_4.5hpf


title: Q5_WT_B12_4hpf


title: Head-Neck-Ep, Z0000044B reanalysis

description:
Head-Neck-Ep, Z0000044B
GSM5652328

source_name: Tongue

value: Tongue


title: SNU719EBNA1 3

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the Human gammaherpesvirus 4 NC_007605.1
DESeq2 was used to normalize the reads and obtain the differentially expressed genes
Assembly: Viral Genome Human gammaherpesvirus 4 NC_007605.1
Supplementary files format and content: bw

extract_protocol:
RNA was extracted from cell pellets using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol and included the on column DNAse I treatment
Libraries were prepared using the QuantSeq (Lexogen) library preparation. This was generated by oligo-dT priming to produce strand specific libraries that were sequenced on NextSeq500 (Illumina) to generate paired-end 2x42 bp reads.

value: Gastric Cancer

tag: agent


title: Q4_WT_B12_3.5hpf


title: sample_3329

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2021-06-08, biol rep: 5

value: DMEM

value: cAMP 20 mM


title: Head-Neck-Ep, Z00000449 reanalysis

description:
Head-Neck-Ep, Z00000449
GSM5652326


title: sample_116

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-01-10, biol rep: 1


title: sample_2254

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-06, biol rep: 3

value: 180 min


title: SNU719EBNA1 2


title: SNU719EBNA1 1


title: sample_2606

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2020-12-22, biol rep: 3

value: 90 min


title: sample_878

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2019-12-19, biol rep: 2


title: Q3_WT_B12_3hpf

value: wild-type


title: sample_3034

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2021-04-07, biol rep: 4

value: room air


title: YCCEL1EBNA1 3


title: Head-Neck-Ep, Z000000QV reanalysis

description:
Head-Neck-Ep, Z000000QV
GSM5652325


title: sample_1159

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-07-22, biol rep: 2


title: Head-Neck-Ep, Z000000S1 reanalysis

description:
Head-Neck-Ep, Z000000S1
GSM5652324

source_name: Tonsil pharyngeal

value: Tonsil pharyngeal


title: sample_397

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-06-20, biol rep: 1


title: YCCEL1EBNA1 2


title: Head-Neck-Ep, Z000000Q9 reanalysis

description:
Head-Neck-Ep, Z000000Q9
GSM5652323


title: sample_3323

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2021-06-08, biol rep: 6

value: 30 min


title: P7_triple_B11_5.5hpf


title: YCCEL1EBNA1 1


title: SNU719 7.5uM DEC 3


title: Head-Neck-Ep, Z0000044F reanalysis

description:
Head-Neck-Ep, Z0000044F
GSM5652327


title: P6_triple_B11_5hpf


title: Q2_WT_B12_2.5hpf


title: P5_triple_B11_4.5hpf


title: sample_3028

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2021-04-07, biol rep: 5

value: yeast cell


title: Head-Neck-Ep, Z000000RP reanalysis

description:
Head-Neck-Ep, Z000000RP
GSM5652321

source_name: Tonsil palatine

value: Tonsil palatine


title: SNU719 7.5uM DEC 1


title: sample_1203

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-02, biol rep: 4

value: WT


title: SNU719 7.5uM DEC 2


title: sample_419

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-08-09, biol rep: 2


title: sample_1153

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-22, biol rep: 3


title: P4_triple_B11_4hpf


title: Blood-B, Z0000041K reanalysis

description:
Blood-B, Z0000041K
GSM5652318

source_name: Blood

value: Blood


title: P3_triple_B11_3.5hpf


title: Blood-B, Z0000041J reanalysis

description:
Blood-B, Z0000041J
GSM5652317


title: P2_triple_B11_3hpf


title: SNU719 DMSO 2

value: DMSO


title: Head-Neck-Ep, Z000000QF reanalysis

description:
Head-Neck-Ep, Z000000QF
GSM5652320


title: sample_391

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-06-20, biol rep: 1


title: Head-Neck-Ep, Z000000RR reanalysis

description:
Head-Neck-Ep, Z000000RR
GSM5652322


title: sample_3335

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2021-06-08, biol rep: 5


title: P1_triple_B11_2.5hpf


title: Blood-B, Z000000UR reanalysis

description:
Blood-B, Z000000UR
GSM5652316


title: YCCEL1 7.5uM DEC 3


title: sample_3040

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2021-04-07, biol rep: 4


title: Blood-B, Z000000UB reanalysis

description:
Blood-B, Z000000UB
GSM5652315


title: P8_triple_B11_6hpf


title: YCCEL1 7.5uM DEC 2


title: sample_1165

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-22, biol rep: 3


title: Epid-Kerat, Z00000424 reanalysis

description:
Epid-Kerat, Z00000424
GSM5652319

source_name: Skin

value: Skin


title: Blood-B, Z000000TX reanalysis

description:
Blood-B, Z000000TX
GSM5652314


title: SNU719 DMSO 3


title: O7_WT_B11_5.5hpf


title: O6_WT_B11_5hpf


title: Blood-Granul, Z000000UT reanalysis

description:
Blood-Granul, Z000000UT
GSM5652313


title: YCCEL1 7.5uM DEC 1


title: YCCEL1 DMSO 3


title: sample_431

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-08-09, biol rep: 2


title: sample_403

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-06-20, biol rep: 1


title: O5_WT_B11_4.5hpf


title: sample_3719

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-09-15, biol rep: 5


title: O4_WT_B11_4hpf


title: Blood-Granul, Z000000TZ reanalysis

description:
Blood-Granul, Z000000TZ
GSM5652311


title: Blood-Mono+Macro, Z0000044E reanalysis

description:
Blood-Mono+Macro, Z0000044E
GSM5652310

source_name: Lung interstitial

value: Lung interstitial


title: SNU719 DMSO 1


title: YCCEL1 DMSO 2


title: YCCEL1 DMSO 1


title: sample_3615

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-09-08, biol rep: 4


title: O2_WT_B11_3hpf