title: sample_3931

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

value: deletion CKF44_00570


title: sample_3474

status: Public on Aug 02 2023

type: SRA

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

country: USA

institute: Washington University

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 1

library_source: transcriptomic

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

molecule: total RNA

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.

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

tag: genotype

value: deletion CKF44_05081

tag: medium

value: YPD

tag: atmosphere

value: room air

tag: temperature

tag: treatment

value: cAMP none

tag: time

value: 30 min


title: sample_3583

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-09-07, biol rep: 5

value: deletion CKF44_07470


title: sample_3480

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 4

value: WT


title: sample_3945

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-11-08, biol rep: 5

value: 180 min


title: sample_3929

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


title: sample_3478

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 3


title: sample_3947

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


title: sample_3949

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-11-08, biol rep: 7


title: sample_3496

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-19, biol rep: 3


title: sample_3492

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-19, biol rep: 2


title: sample_3490

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-19, biol rep: 1


title: sample_3953

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-11-08, biol rep: 8


title: sample_3959

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-11-08, biol rep: 10


title: sample_3957

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-11-08, biol rep: 9


title: sample_3607

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-09-07, biol rep: 7


title: sample_3603

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-09-07, biol rep: 5


title: sample_3601

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-09-07, biol rep: 4


title: sample_3500

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-19, biol rep: 2


title: sample_3504

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-19, biol rep: 3


title: sample_3942

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-11-08, biol rep: 13

value: RPMI

value: 90 min


title: sample_3940

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-11-08, biol rep: 12


title: sample_3593

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-09-07, biol rep: 4


title: sample_3936

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


title: sample_3590

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-09-07, biol rep: 10


title: sample_3487

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-19, biol rep: 7


title: sample_3584

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-09-07, biol rep: 8


title: sample_3588

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-09-07, biol rep: 9


title: sample_3457

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-15, biol rep: 1


title: sample_3459

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-15, biol rep: 3


title: sample_3483

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-19, biol rep: 6


title: sample_3582

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-09-07, biol rep: 11


title: sample_3932

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-11-08, biol rep: 13


title: sample_3934

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-11-08, biol rep: 14


title: sample_3578

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-09-07, biol rep: 10


title: sample_3460

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-15, biol rep: 4


title: sample_3576

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-09-07, biol rep: 9


title: sample_3481

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-19, biol rep: 5


title: sample_3930

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-11-08, biol rep: 12


title: sample_3477

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 7


title: sample_3605

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-09-07, biol rep: 6


title: sample_3475

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 6


title: sample_3456

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-15, biol rep: 4


title: sample_3455

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-15, biol rep: 3


title: sample_3498

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-19, biol rep: 1


title: sample_3454

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-15, biol rep: 2


title: sample_3453

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-15, biol rep: 1


title: sample_3950

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-11-08, biol rep: 14


title: sample_3458

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-15, biol rep: 2


title: sample_3946

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-11-08, biol rep: 12


title: sample_3944

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


title: sample_3948

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-11-08, biol rep: 13


title: sample_3592

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-09-07, biol rep: 8


title: sample_3596

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-09-07, biol rep: 9


title: sample_3598

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-09-07, biol rep: 10


title: sample_3495

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-19, biol rep: 7


title: sample_3461

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-15, biol rep: 1


title: sample_3463

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-15, biol rep: 3


title: sample_3479

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 8


title: sample_3952

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-11-08, biol rep: 5


title: sample_3473

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 5


title: sample_3958

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-11-08, biol rep: 6


title: sample_3464

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-15, biol rep: 4


title: sample_3466

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-15, biol rep: 2


title: sample_3489

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-19, biol rep: 5


title: sample_3462

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-15, biol rep: 2


title: sample_3452

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-07-15, biol rep: 3

value: 0 min


title: sample_3465

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-15, biol rep: 1


title: sample_3468

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-15, biol rep: 3


title: sample_3450

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-07-15, biol rep: 2


title: sample_3449

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-07-15, biol rep: 1


title: sample_3927

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-11-08, biol rep: 7

value: PBS


title: sample_3926

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-09-30, biol rep: 6


title: sample_3925

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-09-29, biol rep: 5


title: sample_3472

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-07-19, biol rep: 2


title: sample_3573

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-09-07, biol rep: 3


title: sample_3575

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-09-07, biol rep: 4


title: sample_3470

description: medium: PBS, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-07-19, biol rep: 1


title: sample_3491

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-07-19, biol rep: 6


title: sample_2854

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-02-26, biol rep: 2


title: sample_3497

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-19, biol rep: 4


title: sample_2853

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: none, time: 0 min, librarydate: 2021-02-26, biol rep: 1


title: sample_3008

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 90 min, librarydate: 2021-03-20, biol rep: 3

value: cAMP 6 mM


title: sample_2866

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 90 min, librarydate: 2021-02-26, biol rep: 2


title: sample_2736

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 90 min, librarydate: 2020-10-23, biol rep: 1


title: sample_3015

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 180 min, librarydate: 2021-03-20, biol rep: 2


title: sample_2730

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 30 min, librarydate: 2020-10-23, biol rep: 1


title: sample_3007

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 90 min, librarydate: 2021-03-20, biol rep: 3

value: cAMP 3.3 mM


title: sample_2859

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 30 min, librarydate: 2021-02-26, biol rep: 2


title: sample_3001

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 30 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2735

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 90 min, librarydate: 2020-10-23, biol rep: 1


title: sample_2858

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 30 min, librarydate: 2021-02-26, biol rep: 2


title: sample_2872

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 180 min, librarydate: 2021-02-26, biol rep: 1


title: sample_2873

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 180 min, librarydate: 2021-02-26, biol rep: 1


title: sample_3022

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 1440 min, librarydate: 2021-03-20, biol rep: 2


title: sample_3000

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 30 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2880

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 6 mM, time: 1440 min, librarydate: 2021-02-26, biol rep: 1


title: sample_2729

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 30 min, librarydate: 2020-10-23, biol rep: 1


title: sample_2738

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2020-10-23, biol rep: 1

value: cAMP 20 mM


title: sample_3014

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 180 min, librarydate: 2021-03-20, biol rep: 2


title: sample_2732

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2020-10-23, biol rep: 1


title: sample_2875

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-02-26, biol rep: 2


title: sample_2744

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2020-10-23, biol rep: 1


title: sample_2879

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 1440 min, librarydate: 2021-02-26, biol rep: 1


title: sample_3024

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-03-20, biol rep: 2


title: sample_3021

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 1440 min, librarydate: 2021-03-20, biol rep: 2


title: sample_2882

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-02-26, biol rep: 1


title: sample_2865

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 3.3 mM, time: 90 min, librarydate: 2021-02-26, biol rep: 2


title: sample_3009

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 90 min, librarydate: 2021-03-20, biol rep: 3

value: cAMP 11 mM


title: sample_3002

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 30 min, librarydate: 2021-03-20, biol rep: 3

value: yeast


title: sample_3010

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2868

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2021-02-26, biol rep: 2


title: sample_3003

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2021-03-20, biol rep: 2


title: sample_3017

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2881

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 1440 min, librarydate: 2021-02-26, biol rep: 1


title: sample_3016

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 180 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2867

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 90 min, librarydate: 2021-02-26, biol rep: 2


title: sample_2737

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 90 min, librarydate: 2020-10-23, biol rep: 1


title: sample_2860

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 30 min, librarydate: 2021-02-26, biol rep: 2


title: sample_2734

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 90 min, librarydate: 2020-10-23, biol rep: 1

value: cAMP 1.8 mM


title: sample_3023

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 1440 min, librarydate: 2021-03-20, biol rep: 2


title: sample_2874

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 180 min, librarydate: 2021-02-26, biol rep: 2


title: sample_3013

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 180 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2857

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 30 min, librarydate: 2021-02-26, biol rep: 1


title: sample_2871

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 180 min, librarydate: 2021-02-26, biol rep: 2


title: sample_2740

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 180 min, librarydate: 2020-10-23, biol rep: 1


title: sample_2864

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 90 min, librarydate: 2021-02-26, biol rep: 2


title: sample_2999

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 30 min, librarydate: 2021-03-20, biol rep: 2


title: sample_3006

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 90 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2743

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 180 min, librarydate: 2020-10-23, biol rep: 1


title: sample_2878

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 1440 min, librarydate: 2021-02-26, biol rep: 1


title: sample_2731

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 11 mM, time: 30 min, librarydate: 2020-10-23, biol rep: 1


title: sample_3020

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.8 mM, time: 1440 min, librarydate: 2021-03-20, biol rep: 2


title: sample_2863

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 90 min, librarydate: 2021-02-26, biol rep: 1

value: cAMP 1.08 mM


title: sample_2856

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 30 min, librarydate: 2021-02-26, biol rep: 1

value: room air


title: sample_3012

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 180 min, librarydate: 2021-03-20, biol rep: 2


title: sample_2870

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 180 min, librarydate: 2021-02-26, biol rep: 1


title: SW1222_Control_KO_3D_rep1

type: RNA

city: Barcelona

first: Isabel

last: Puig

state: Catalonia

address: C/Natzaret, 115-117

department: Preclinical and Translational Research

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

description: Control cell line expressing scrambled gRNA no treated.

hyb_protocol: Following fragmentation, cRNA were hybridized using the Hybridization Wash and Stain Kit.

scan_protocol: Hybridization data was acquired using Affymetrix GeneChip/GeneTitan platforms.

data_processing: Partek Genomics Suite 6.6 software (Partek Inc.) was used to normalize raw CEL files in different combinations as indicated using Robust Multichip Average (RMA) algorithm.

label: Biotin

organism: Homo sapiens

source_name: CRC SW1222 cells, control KO, 3D culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cell were grown at atmospheric oxygen concentrations (21%) with 5% CO2 at 37ºC.

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

tag: tissue

value: Colorectal cancer (CRC)

value: scrambled gRNA

tag: culture method


title: SW1222_DPPA3_KO_clone66_3D_rep1

description: CRISPR DPPA3 clone 66 cell line no treated.

source_name: CRC SW1222 cells, DPPA3 KO clone 66, 3D culture

value: CRISPR DPPA3


title: SW1222_DPPA3_KO_clone75_3D_rep2

description: CRISPR DPPA3 clone 75 cell line no treated.

source_name: CRC SW1222 cells, DPPA3 KO clone 75, 3D culture


title: SW1222_DPPA3_KO_clone66_3D_rep2


title: SW1222_Control_shRNA_3D_rep3

description: Control cell line for shRNA no treated.

source_name: CRC SW1222 cells, control shRNA, 3D culture

value: shRNA control


title: SW1222_Control_KO_3D_rep2


title: sample_3019

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 1440 min, librarydate: 2021-03-20, biol rep: 2

value: WT


title: SW1222_DPPA3_shRNA_3D_rep2

description: DPPA3 knockdown cell line no treated.

source_name: CRC SW1222 cells, DPPA3 shRNA, 3D culture

value: DPPA3 knockdown


title: SW1222_Control_OE_2D_rep3

description: Control cell line after 4 hours of doxycycline induction.

source_name: CRC SW1222 cells, control-OE, 2D culture, DOX 4 hours

value: control


title: sample_3005

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 90 min, librarydate: 2021-03-20, biol rep: 2

value: RPMI

value: 90 min


title: SW1222_DPPA3_KO_clone75_3D_rep1


title: sample_2998

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 30 min, librarydate: 2021-03-20, biol rep: 2

value: 30 min


title: SW1222_Control_shRNA_3D_rep2

description: Control cell line for shRNA no treated.


title: SW1222_DPPA3_shRNA_3D_rep3

description: DPPA3 knockdown cell line no treated.


title: sample_2855

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 30 min, librarydate: 2021-02-26, biol rep: 2

value: cAMP 0 mM


title: sample_2997

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 30 min, librarydate: 2021-03-20, biol rep: 3


title: sample_2862

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 90 min, librarydate: 2021-02-26, biol rep: 1


title: sample_2727

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 30 min, librarydate: 2020-10-23, biol rep: 1


title: SW1222_DPPA3_shRNA_3D_rep1

description: DPPA3 knockdown cell line no treated.


title: SW1222_Control_OE_2D_rep2


title: SW1222_Control_OE_2D_rep1


title: sample_3004

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 90 min, librarydate: 2021-03-20, biol rep: 2


title: sample_2877

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 1.08 mM, time: 1440 min, librarydate: 2021-02-26, biol rep: 1


title: sample_3011

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 180 min, librarydate: 2021-03-20, biol rep: 3

value: 180 min


title: SW1222_DPPA3_OE_2D_rep2

description: Cell line overexpressing DPPA3 after 4 hours of doxycycline induction.

source_name: CRC SW1222 cells, DPPA3-OE, 2D culture, DOX 4 hours

value: overexpressing DPPA3


title: SW1222_DPPA3_OE_2D_rep1


title: SW1222_DPPA3_OE_2D_rep3


title: SW1222_Control_OE_3D_rep3

description: Control cell line after 5 days of doxycycline treatment.

source_name: CRC SW1222 cells, control-OE, 3D culture, DOX 5 days


title: sample_2739

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 180 min, librarydate: 2020-10-23, biol rep: 1

value: yeast


title: sample_2876

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 1440 min, librarydate: 2021-02-26, biol rep: 1


title: SW1222_Control_shRNA_3D_rep1

description: Control cell line for shRNA no treated.


title: sample_3308

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-06-04, biol rep: 5

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

value: yeast cell

value: YPD

value: cAMP none


title: SW1222_DPPA3_OE_3D_rep3

description: Cell line overexpressing DPPA3 after 5 days of doxycycline induction.

source_name: CRC SW1222 cells, DPPA3-OE, 3D culture, DOX 5 days

value: Colorectal cancer (CRC)


title: SW1222_DPPA3_OE_3D_rep2


title: sample_3220

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-05-13, biol rep: 4

value: room air


title: SW1222_Control_OE_3D_rep1


title: SW1222_DPPA3_OE_3D_rep1


title: Epidermal_piRNAs_Rep3

city: Bayreuth

first: Andreas

last: Pittroff

address: Universitätsstr. 30

department: BIOmac Research Center, NW1

country: Germany

institute: University of Bayreuth

data_processing:
RTA2 was used for base-calling on NextSeq 500
Fastq files were sub-sampled to 1.5 million reads per replicate using seqtk (github.com/lh3/seqtk).
Reads were filtered against rRNA- and tRNA references using SortMeRNA (Kopylova et al., 2021) and bowtie (Langmead et al., 2009) respectively.
Filtered reads were mapped to the planarian genome using bowtie (Langmead et al., 2009).
Mapped reads were filtered for piRNAs (by length) and weighted counts were calculated to account for multi-mapping events. Finally BigWig files were generated using bedtools (Quinlan & Hall, 2010) and bedGraphToBigWig (Kent et al., 2010)
Genome_build: dd_Smes_g4
Supplementary_files_format_and_content: BigWig files contain strand-specific coverage of filtered piRNAs

organism: Schmidtea mediterranea

source_name: planarian epidermis

extract_protocol:
RNA was extracted by guanidinium thiocyanate-phenol-chloroform extraction (TriFast (peqlab)). RNA was then purified and size-selected (<200 nt) using the RNA Clean & Concentrator Kit (Zymo Research Europe) according to the manufacturer’s manual.
Small RNAs were oxidized using  NaIO4. Library preparation with UMI-containing adapters was performed as described (Fu et al., 2018).

treatment_protocol: Worms were skinned by treating with an SDS solution and removing the epidermis mechanically. Epidermal samples of five worms were pooled for each replicate.

value: epidermis


title: sample_468

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


title: Epidermal_piRNAs_Rep2


title: SW1222_Control_OE_3D_rep2


title: sample_2869

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 180 min, librarydate: 2021-02-26, biol rep: 2


title: sample_1407

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


title: sample_1910

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-09-28, biol rep: 3


title: sample_3302

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-06-04, biol rep: 5


title: sample_3214

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-05-13, biol rep: 4


title: sample_1647

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


title: Epidermal_piRNAs_Rep1


title: sample_3018

description: medium: RPMI, atmosphere: room air, temperature: 30C, cAMP: 0 mM, time: 1440 min, librarydate: 2021-03-20, biol rep: 2


title: sample_1395

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


title: Pig vascular endothelial cell,D-malate treatment-3

city: Guangzhou

first: Penglin

last: Li

address: 483 Wushan Road, Tianhe District

country: China

institute: South China Agriculture University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: Beta_vulgaris GCF_000511025.2_RefBeet_1.2.2
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

organism: Sus scrofa

source_name: vascular

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.
RNA libraries were prepared for sequencing using standard illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: vascular

value: vascular endothelial cells

value: primary cell

value: 100 μM D-malate


title: sample_3226

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-05-13, biol rep: 3

value: WT


title: sample_3314

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-06-04, biol rep: 4


title: NSG5 (Affymetrix)

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

hyb_protocol: Hybridization to Affymetrix Human Gene 1.0 ST arrays was performed using standard Affymetrix protocols.

scan_protocol: Arrays were scanned using a GeneChip scanner 3000 and image analysis was performed using the GeneChip Operating Software.

data_processing: Probe summarization and data normalization were performed using Robust Multi-array Analysis (RMA) with the Expression Console Software v1.1.2.

source_name: normal tissue FF

label_protocol: Biotin labled cRNA was synthesized from 200 ng total RNA according to standard Affymetrix protocols.

extract_protocol: Total RNA was isolated using the Trizol reagent (Life Technologies) followed by the RNeasy Mini kit (Qiagen).

value: normal salivary gland tissue

tag: obtained from

value: Sahlgrenska University Hospital

tag: gender

tag: age

tag: tumor grade

value: epithelial


title: sample_1671

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

value: 180 min


title: NSG7 (Affymetrix)


title: NSG2 (Affymetrix)


title: NSG3 (Affymetrix)


title: NSG6 (Affymetrix)


title: Pig vascular endothelial cell,D-malate treatment-2


title: Pig vascular endothelial cell,D-malate treatment-1


title: NSG1 (Affymetrix)


title: sample_3320

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-06-04, biol rep: 6


title: Pig vascular endothelial cell, non-treatment-3

value: no D-malate


title: sample_3232

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-05-13, biol rep: 5


title: ACC77 (Affymetrix)

source_name: tumor tissue FF

value: adenoid cystic carcinoma

value: male


title: NSG4 (Affymetrix)


title: sample_1934

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2020-09-28, biol rep: 4

value: yeast cell

value: YPD


title: sample_1683

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2020-09-21, biol rep: 3

value: cAMP none


title: sample_488

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2020-10-15, biol rep: 1

value: room air


title: sample_1429

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2020-10-17, biol rep: 2


title: Pig vascular endothelial cell, non-treatment-1


title: Pig vascular endothelial cell, non-treatment-2


title: sample_456

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

value: 30 min


title: sample_2252

description: medium: YPD, atmosphere: room air, temperature: 37C, 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

value: 90 min


title: sample_1922

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-09-28, biol rep: 2


title: ACC74 (Affymetrix)


title: ACC73 (Affymetrix)

value: female


title: ACC75 (Affymetrix)


title: sample_876

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


title: ACC72 (Affymetrix)


title: sample_108

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


title: sample_2246

description: medium: YPD, 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: sample_2369

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-16, biol rep: 4


title: sample_2258

description: medium: YPD, 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_102

description: medium: YPD, 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: ACC76 (Affymetrix)


title: sample_3634

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2021-09-08, biol rep: 4


title: sample_882

description: medium: YPD, 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: HET : 3 : 1220 PC [PLS_vinican 32347]

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 PanCancer Pathways Nanostring panel with the addition of 30 custom targets screening for intestinal epithelial cell markers/function (PLS_vinican 32347).

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: WT : 3 : 1219 PC [PLS_vinican 32347]

value: WT


title: KO : 3 : 1218 PC [PLS_vinican 32347]

value: KO

value: Female


title: sample_3736

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

tag: cell line


title: HET : 3 : 1215 PC [PLS_vinican 32347]


title: WT : 3 : 1216 PC [PLS_vinican 32347]


title: sample_2264

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

tag: cell type


title: ACC68 (Affymetrix)

value: Sahlgrenska University Hospital

value: epithelial


title: ACC67 (Affymetrix)

value: adenoid cystic carcinoma


title: ACC71 (Affymetrix)


title: ACC66 (Affymetrix)


title: sample_888

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

tag: genotype


title: WT : 2 : 1402 PC [PLS_vinican 32347]


title: sample_120

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

tag: medium


title: sample_870

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

tag: atmosphere


title: sample_3333

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2021-06-08, biol rep: 4

tag: temperature

value: cAMP 20 mM


title: sample_1163

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

value: yeast cell

tag: treatment


title: HET : 2 : 1403 PC [PLS_vinican 32347]


title: ACC63 (Affymetrix)


title: ACC64 (Affymetrix)


title: sample_429

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

value: YPD

tag: time


title: sample_114

description: medium: YPD, 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: KO : 2 : 1405 PC [PLS_vinican 32347]


title: sample_3032

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

value: room air


title: sample_1207

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

value: 30 min


title: sample_401

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


title: ACC61 (Affymetrix)

tag: tissue


title: ACC62 (Affymetrix)


title: HET : 1 : 1245 PC [PLS_vinican 32347]


title: WT : 1 : 1244 PC [PLS_vinican 32347]


title: KO : 3 : 1214 PC [PLS_vinican 32347]


title: sample_3044

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2021-04-07, biol rep: 5


title: sample_1157

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


title: sample_3339

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2021-06-08, biol rep: 6


title: sample_423

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


title: sample_2616

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2020-12-22, biol rep: 4


title: KO : 1 : 1243 PC [PLS_vinican 32347]

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


title: sample_1221

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-02, biol rep: 3


title: ACC60 (Affymetrix)

value: The University of Texas MD Anderson Cancer Center


title: ACC58 (Affymetrix)


title: sample_1169

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-22, biol rep: 2


title: ACC56 (Affymetrix)

value: male


title: HET : 3 : 1220 DC [PLS_vinican 32347]

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: sample_407

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


title: WT : 3 : 1219 DC [PLS_vinican 32347]


title: sample_1175

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-07-22, biol rep: 2


title: sample_3345

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-06-08, biol rep: 5


title: KO : 3 : 1218  DC [PLS_vinican 32347]


title: sample_1229

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-07-02, biol rep: 3


title: sample_415

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-06-20, biol rep: 1


title: WT : 3 : 1216 DC [PLS_vinican 32347]


title: HET : 3 : 1215 DC [PLS_vinican 32347]


title: ACC55 (Affymetrix)

value: female


title: sample_395

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


title: sample_3307

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-06-04, biol rep: 5

value: cAMP none

value: 90 min


title: sample_3219

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-05-13, biol rep: 4

value: WT


title: WT : 2 : 1402 DC [PLS_vinican 32347]


title: ACC59 (Affymetrix)


title: ACC53 (Affymetrix)


title: sample_1405

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


title: sample_3984

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-11-08, biol rep: 6


title: ACC51 (Affymetrix)


title: ACC54 (Affymetrix)


title: sample_3050

description: medium: YPD, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-04-07, biol rep: 4


title: ACC50 (Affymetrix)


title: HET : 2 : 1403 DC [PLS_vinican 32347]

value: HET


title: sample_3982

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-11-08, biol rep: 5


title: sample_1657

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


title: sample_3301

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-06-04, biol rep: 4


title: KO : 2 : 1405 DC [PLS_vinican 32347]

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

value: KO

value: Female


title: ACC49 (Affymetrix)

value: epithelial


title: sample_3213

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-05-13, biol rep: 3


title: sample_1393

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


title: sample_466

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


title: ACC47 (Affymetrix)

value: adenoid cystic carcinoma


title: WT : 1 : 1244 DC [PLS_vinican 32347]


title: ACC48 (Affymetrix)


title: sample_3313

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-06-04, biol rep: 4


title: sample_454

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


title: KO : 1 : 1243 DC [PLS_vinican 32347]


title: HET : 1 : 1245 DC [PLS_vinican 32347]


title: KO : 3 : 1214 DC [PLS_vinican 32347]


title: sample_3225

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-05-13, biol rep: 3


title: sample_3988

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-11-08, biol rep: 7


title: sample_1669

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


title: sample_3319

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-06-04, biol rep: 6


title: sample_3231

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-05-13, biol rep: 5


title: HET : 3 : 1220 [PLS_vinican 32347]

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.

value: Male


title: ACC46 (Affymetrix)


title: WT : 3 : 1219 [PLS_vinican 32347]


title: ACC44 (Affymetrix)


title: ACC45 (Affymetrix)


title: sample_1932

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2020-09-28, biol rep: 4

value: yeast cell


title: KO : 3 : 1218 [PLS_vinican 32347]


title: sample_1681

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2020-09-21, biol rep: 3

value: YPD


title: ABE8.20-m at BCL11A 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

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.

value: mobilized peripheral blood

value: mPB CD34

tag: target locus

tag: editing time

value: day 3

tag: time of_collection

value: day 7


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

value: Mock electro


title: Cas9 opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep5

value: Cas9 opt

value: B2M ex2


title: ACC43 (Affymetrix)

tag: obtained from

value: The University of Texas MD Anderson Cancer Center

tag: gender

value: female

tag: age


title: Cas9 opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep4


title: sample_478

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

value: WT

value: room air

value: cAMP none

value: 180 min


title: ABE8.20-m opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep5

value: ABE8.20-m opt


title: sample_875

description: medium: YPD, atmosphere: room air, temperature: 30C, 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

value: 90 min


title: sample_2251

description: medium: YPD, 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: yeast cell

value: YPD


title: sample_486

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2020-10-15, biol rep: 1


title: KO : 3 : 1214 [PLS_vinican 32347]

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

value: KO

tag: littermate group

tag: mouse number

value: Female


title: HET : 3 : 1215 [PLS_vinican 32347]

value: HET

tag: Sex


title: sample_2245

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

tag: cell line

tag: cell type

value: 30 min


title: sample_3632

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

tag: genotype

tag: medium


title: sample_107

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

tag: atmosphere

tag: temperature


title: BE4max opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep5

value: mobilized peripheral blood

value: mPB CD34

tag: treatment

value: BE4max opt

value: day 3

value: day 7


title: WT : 3 : 1216 [PLS_vinican 32347]

value: WT


title: BE4max opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep4

tag: tissue

value: B2M ex2


title: sample_2257

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

value: room air

tag: time

value: 180 min


title: WT : 2 : 1402 [PLS_vinican 32347]


title: sample_869

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

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: sample_101

description: medium: YPD, 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: HET : 2 : 1403 [PLS_vinican 32347]


title: Cas9 opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: Cas9 opt

tag: target locus

tag: editing time


title: KO : 2 : 1405 [PLS_vinican 32347]


title: sample_113

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

value: yeast cell


title: sample_3735

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

value: YPD


title: WT : 1 : 1244 [PLS_vinican 32347]


title: sample_2263

description: medium: YPD, 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_881

description: medium: YPD, 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: ABE8.20-m opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: ABE8.20-m opt

tag: time of_collection


title: HET : 1 : 1245 [PLS_vinican 32347]

value: Female


title: sample_887

description: medium: YPD, 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: sample_119

description: medium: YPD, 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: ABE8.20-m opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_3332

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

value: cAMP 20 mM

value: 90 min


title: KO : 1 : 1243 [PLS_vinican 32347]

value: KO


title: sample_3037

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


title: sample_2609

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


title: Cas9 opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: mobilized peripheral blood

value: mPB CD34


title: replicate_3_P2063

city: Houston

first: Lanlan

last: Shen

state: Texas

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

data_processing: none provided by the submitter

source_name: colonic mucosa

extract_protocol:
RNA was extracted using AllPrep DNA/RNA Mini Kit (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using standard BGI protocols (mRNA enrichment by rRNA depletion and oligo dT selection)

value: colonic mucosa

tag: strain

value: ApcMin/+; p16cis/cis

value: 15 wk


title: sample_3986

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-11-08, biol rep: 5

value: WT

value: cAMP none


title: replicate_4_P2059

tag: age


title: BE4max opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: BE4max opt

value: B2M ex2

value: day 3

value: day 7


title: BE4max opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: replicate_2_P2096


title: sample_1162

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

value: yeast cell

value: YPD

value: room air


title: sample_1213

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

value: cAMP 20 mM


title: replicate_1_P2102

value: Male


title: sample_428

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

value: 90 min


title: BE4max opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: mobilized peripheral blood


title: sample_3031

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

value: 30 min


title: sample_3326

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


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep9

value: mPB CD34

value: Mock electro


title: sample_1206

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


title: sample_1156

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


title: BE4max opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: replicate_4_A002

value: colonic mucosa

value: ApcMin/+

value: 15 wk


title: sample_422

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

value: WT


title: BE4max at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: B2M ex2


title: sample_394

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


title: sample_3338

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-06-08, biol rep: 7

value: 180 min


title: Cas9 opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: Cas9 opt

value: day 3

value: day 7


title: replicate_2_A392


title: sample_1220

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-02, biol rep: 4

value: yeast cell

value: YPD

value: room air


title: sample_3043

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-04-07, biol rep: 6

value: cAMP 20 mM


title: Cas9 at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: mobilized peripheral blood


title: sample_400

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

value: 90 min


title: sample_2615

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2020-12-22, biol rep: 5


title: replicate_1_A390

value: Female


title: sample_1168

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-22, biol rep: 3


title: replicate_5_A385


title: ABE8.20-m opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: mPB CD34

value: ABE8.20-m opt


title: ABE8.20-m at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_3049

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-04-07, biol rep: 4


title: sample_434

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


title: Exp 5

city: Boston

first: Scott

middle: C

last: Fligor

state: MA

address: 300 Longwood Ave

department: Surgery

institute: Boston Children's Hospital

data_processing:
mRNA-Seq was performed by Novogene Co. (Sacramento, CA, USA). RNA integrity was assessed with the RNA Nano 6000 Assay kit (Agilent Technologies, CA, USA). All samples had RIN> 4 and passed the established quality thresholds. mRNA was purified using poly-T oligo-attached magnetic beads and library quality was assessed using the Agilent Bioanalyzer 2100 system. RNA-Seq was performed on the Illumina NovaSeq 6000 platform with 150bp paired-end reads. Raw data were cleaned with removal of low-quality reads and then mapped to the Sscrofa11.1 pig genome using Hisat2 v2.0.5. Read counts were then calculated by featureCounts software (v 2.0.3). Differentially expressed genes (DEGs) were identified by using the DESeq2 (v 1.26.0) R package (adjusted p value <=0.05). A principal components analysis was performed and two outliers were excluded from the experimental group.
Assembly: GCF_000003025.6
Supplementary files format and content: Processed data are provided as a tab-delimited text file including read counts for all genes across all samples, including FPKM values

organism: Sus scrofa domesticus

source_name: Liver

extract_protocol:
Liver sections were flash frozen in liquid nitrogen and stored a -80C. RNA was harvested using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene, Inc.

tag: breed

value: Yorkshire

value: Liver

value: Parenteral Nutrition


title: sample_406

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

value: WT


title: Exp 6


title: sample_3344

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-06-08, biol rep: 5


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep8

value: Mock electro


title: sample_1174

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-07-22, biol rep: 2


title: Exp 4


title: sample_1228

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-07-02, biol rep: 3


title: sample_1427

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2020-10-17, biol rep: 2

value: cAMP none


title: Cas9 opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: Cas9 opt

value: CCR5 #2

value: day 3


title: replicate_3_A395

value: colonic mucosa

value: ApcMin/+

value: Male

value: 15 wk


title: sample_3110

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

value: yeast cell

value: YPD

value: 90 min


title: ABE8.20-m opt at B2M ex2 locus on mPB CD34 edited at day 3 collected at day 7 - rep4

value: mobilized peripheral blood

value: mPB CD34

value: ABE8.20-m opt

value: B2M ex2

value: day 7


title: sample_2710

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

value: WT


title: Exp 2

value: Yorkshire

value: Liver

value: Parenteral Nutrition


title: BE4max at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: day 3


title: sample_1510

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-11-02, biol rep: 3

value: cAMP none


title: sample_583

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


title: Exp 1


title: ABE8.20-m opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: CCR5 #2


title: Cas9 at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: Control 3

value: Sow Milk Replacer


title: sample_3104

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

value: 30 min


title: sample_1563

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-12-18, biol rep: 4

value: yeast cell


title: ABE8.20-m at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_1551

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-12-18, biol rep: 3

value: YPD


title: Control 1


title: sample_2704

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-01-26, biol rep: 4


title: sample_1498

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-11-02, biol rep: 2


title: Control 2


title: BE4max opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: BE4max opt


title: sample_414

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

value: room air

value: cAMP 20 mM


title: sample_3116

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-04-23, biol rep: 4

value: 180 min


title: Exp 3


title: XH_1_S100, silk gland_rep 3

city: Zhenjiang

first: Sun

last: Lindan

address: 301 xuefu road

department: School of Life and Sciences

institute: Jiangsu University

data_processing:
The original data were analyzed using fastp version 0.19.5, and clean data with Q30 > 92.93% was obtained from each sample
Compare clean data(reads) with reference genome.
Use assembly software StringTie Version 1.3.3b for reference-based assembly.
The differentially expressed genes were determined at |log2 (fold change)| > 1 and p-adjust < 0.05 using DESeq2 Version 1.24.0
Assembly: StringTie
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Bombyx mori

source_name: Silk gland

growth_protocol: Silkworms of each strain were fed at the same regulated feeding conditions (25℃ and 71% humidity) up to day 5 of the fifth larval instar.

extract_protocol:
The total RNA was extracted from the silk gland using TRIzol (Invitrogen, Carlsbad, CA, USA). 1 µg of total RNA was used for the construction of sequencing libaries.
The RNA libraries were validated according to the manufacturer’s instructions.

value: Silk gland

value: XH

tag: silk gland weight phenotype_1

tag: silk gland weight phenotype_2


title: BE4max at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: mobilized peripheral blood

value: mPB CD34

value: day 7


title: sample_1575

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-12-18, biol rep: 2

tag: cell line

value: WT


title: sample_2716

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-01-26, biol rep: 3

tag: cell type


title: Cas9 opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: Cas9 opt

value: day 3


title: XH_1_S99, silk gland_rep 2


title: sample_1249

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2019-08-19, biol rep: 1

tag: genotype

value: cAMP none


title: sample_1243

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2019-08-19, biol rep: 2

tag: medium

value: 90 min


title: sample_3122

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-04-23, biol rep: 5

tag: atmosphere


title: XH_1_S98, silk gland_rep 1


title: sample_2722

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-01-26, biol rep: 4

tag: temperature


title: 798_1_S97, silk gland_rep 3


title: ABE8.20-m opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

tag: treatment

value: ABE8.20-m opt

value: CCR5 #2


title: ABE8.20-m at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

tag: tissue


title: sample_1237

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2019-08-19, biol rep: 1

value: yeast cell

value: YPD

tag: time

value: 30 min


title: 798_1_S96, silk gland_rep 2


title: sample_821

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2019-08-22, biol rep: 1


title: sample_1255

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2019-08-19, biol rep: 2


title: sample_1534

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2020-11-02, biol rep: 3


title: sample_990

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

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: sample_915

description: medium: YPD, 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: BE4max opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: BE4max opt

tag: target locus


title: 798_1_S95, silk gland_rep 1

value: Silk gland


title: 306_1_S94, silk gland_rep 3


title: sample_69

description: medium: YPD, 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: BE4max at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

tag: editing time


title: sample_293

description: medium: YPD, 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: sample_984

description: medium: YPD, 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: Cas9 opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep3

tag: time of_collection


title: sample_287

description: medium: YPD, 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: Cas9 at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: sample_57

description: medium: YPD, 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: sample_996

description: medium: YPD, 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: 180 min


title: 306_1_S93, silk gland_rep 2

tag: strain


title: sample_927

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


title: Cas9 at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: mobilized peripheral blood


title: sample_299

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


title: sample_81

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


title: ABE8.20-m opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: mPB CD34


title: HSC7E481 in SD-URA

city: Cambridge

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

description: Strand-sepcific RNA-seq using NEBNext Ultra II Directional RNA Library Prep Kit

data_processing:
RNA-seq reads were pre-processed using Trimmomatic v0.36 with the parameters “ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:true SLIDINGWINDOW:4:10 MINLEN:36”. The ILLUMINACLIP parameter identified and eliminated Illumina adapters specified in the Truseq3 library. Using SLIDINGWINDOW:4:10, reads were scanned in a 4 bp window and trimmed when the average quality dropped below 10. The default parameter MINLEN:36 dropped reads below 36 bases long.  After trimming, the quality of the reads were confirmed with FastQC v 0.11.8.
A reference genome was constructed by concatenating chromosome 7 from the human reference genome GrCH38 (GRCh38.p13) and the yeast S288C reference R64 (GCF_000146045.2_R64/). RNA-seq reads were aligned to the reference using STAR v2.7.10a. First, the reference genome was indexed using the following parameters: --runMode genomeGenerate --sjdbGTFfile --sjdbOverhang 60 --sjdbGTFtagExonParentTranscript Parent --genomeSAindexNbases 12. Reads were then aligned to the reference using the following parameters: --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --alignIntronMax 5000.
PCR duplicates were marked using Picard tools v2.18.7 (Broad Institute).
A genome-guided transcriptome assembly from both evolved and naïve DNA was constructed using Cufflinks v0.17.0. The sorted BAM from the STAR alignment was used as input with the following parameters: --no-update-check --overlap-radius 1 --max-intron-length 5000 --library-type fr-firststrand. The output GTF file containing predicted transcripts was imported into the integrative genomics viewer (IGV) genome browser (Broad Institute) for visual analysis.
Assembly: R64 (yeast) and GRCh38.p13 (human)
Supplementary files format and content: GTF file containing cufflinks predicted transcripts
Supplementary files format and content: bigwig file containing RNA-seq read coverage

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast colonies were grown in liquid SD-URA to an OD600 of ~0.3 - 0.6.

extract_protocol:
Total RNA was extracted from liquid yeast cultures using the hot acid phenol method, described previously (https://www.protocols.io/view/rna-isolation-from-yeast-inwcdfe).
Extracted RNA was prepared for strand specific sequencing by the Biomedical Research Centre Sequencing Core (UBC, Vancouver) using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and polyA selection (NEB).

tag: media

value: SD-URA

value: yeast cells

tag: yac clone


title: sample_3722

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

value: WT


title: sample_3638

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


title: BE4max opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: day 3

value: day 7


title: sample_1002

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


title: sample_93

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


title: BE4max at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_903

description: medium: YPD, 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_345

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

value: cAMP 20 mM

value: 90 min


title: Cas9 opt at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: Cas9 opt

value: CCR5 #2


title: sample_954

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

value: yeast cell

value: YPD


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep7

value: Mock electro


title: MZspg_rep3_4.5hpf [re-analysis]

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

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

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

value: MZspg

tag: biological replicates number


title: MZspg_rep3_6hpf [re-analysis]


title: sample_255

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

tag: cell line


title: 306_1_S92, silk gland_rep 1

value: Silk gland

tag: silk gland weight phenotype_1

tag: silk gland weight phenotype_2


title: MZspg_rep3_4hpf [re-analysis]

tag: genotype


title: sample_1297

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-23, biol rep: 3

tag: cell type

tag: medium

tag: atmosphere

value: 30 min


title: sample_948

description: medium: YPD, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-10, biol rep: 2

tag: temperature

tag: treatment


title: Cas9 opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

tag: tissue

value: mobilized peripheral blood

tag: target locus

value: CCR5 #1


title: Cas9 at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: mPB CD34

tag: editing time

tag: time of_collection


title: sample_249

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

tag: time


title: sample_1309

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

value: 180 min


title: MZspg_rep3_5.5hpf [re-analysis]


title: MZspg_rep3_3hpf [re-analysis]


title: ABE8.20-m at CCR5 #2 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: ABE8.20-m opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: ABE8.20-m opt


title: sample_960

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

value: WT


title: sample_1303

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


title: MZspg_rep3_2.5hpf [re-analysis]


title: Cas9 at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: day 3

value: day 7


title: sample_261

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

value: cAMP 20 mM


title: sample_939

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

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: MZsox19b_rep3_6hpf [re-analysis]


title: sample_1315

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


title: MZspg_rep3_5hpf [re-analysis]


title: sample_966

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


title: BE4max opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: BE4max opt


title: ABE8.20-m at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_358

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

value: yeast cell


title: MZsox19b_rep3_5.5hpf [re-analysis]


title: sample_268

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

value: YPD


title: MZspg_rep3_3.5hpf [re-analysis]


title: MZsox19b_rep3_5hpf [re-analysis]


title: MZsox19b_rep3_4.5hpf [re-analysis]


title: BE4max at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep3


title: sample_2709

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

value: cAMP none

value: 90 min


title: sample_3109

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


title: MZsox19b_rep3_4hpf [re-analysis]


title: Cas9 at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2


title: MZsox19b_rep3_3.5hpf [re-analysis]


title: sample_1242

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


title: sample_3103

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


title: sample_808

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


title: Cas9 opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: Cas9 opt


title: sample_1549

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-12-18, biol rep: 3

value: 30 min


title: ABE8.20-m opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: mobilized peripheral blood


title: sample_351

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


title: ABE8.20-m at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: CCR5 #1


title: BE4max opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: mPB CD34


title: sample_576

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


title: sample_2703

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


title: sample_3115

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-04-23, biol rep: 4

value: 180 min


title: MZsox19b_rep3_2.5hpf [re-analysis]


title: WT_rep5_5.5hpf [re-analysis]

value: wild-type


title: sample_1573

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-12-18, biol rep: 2

value: WT


title: WT_rep5_5hpf [re-analysis]


title: sample_1561

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-12-18, biol rep: 3


title: MZsox19b_rep3_3hpf [re-analysis]


title: sample_588

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


title: BE4max at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep2

value: day 3


title: sample_3121

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-04-23, biol rep: 6


title: Cas9 opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: day 7


title: ABE8.20-m opt at BCL11A locus on mPB CD34 edited at day 3 collected at day 7 - rep3

value: ABE8.20-m opt


title: sample_1532

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2020-11-02, biol rep: 4


title: WT_rep5_4.5hpf [re-analysis]


title: sample_1585

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2020-12-18, biol rep: 5


title: WT_rep5_4hpf [re-analysis]


title: sample_820

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2019-08-22, biol rep: 2


title: sample_2715

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-01-26, biol rep: 3


title: WT_rep5_3.5hpf [re-analysis]


title: Cas9 at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_1236

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


title: WT_rep5_3hpf [re-analysis]


title: sample_594

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2019-08-15, biol rep: 1


title: ABE8.20-m opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_292

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

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: ABE8.20-m at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_983

description: medium: YPD, 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: sample_67

description: medium: YPD, 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: BE4max opt at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1

value: BE4max opt


title: sample_989

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

value: yeast cell


title: WT_rep5_2.5hpf [re-analysis]


title: sample_901

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

value: YPD


title: MZsox19bspg_rep2_6hpf [re-analysis]


title: sample_286

description: medium: YPD, 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: sample_55

description: medium: YPD, 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: MZsox19bspg_rep2_5.5hpf [re-analysis]


title: BE4max at CCR5 #1 locus on mPB CD34 edited at day 3 collected at day 7 - rep1


title: sample_913

description: medium: YPD, 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_1254

description: medium: YPD, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2019-08-19, biol rep: 3

value: cAMP none


title: Mock electro on mPB CD34 edited at day 3 collected at day 7 - rep6

value: Mock electro