title: PlasmidPool-for-Cas13b-TwoVector

city: Shenyang

first: Teng

last: Fei

state: Liaoning

address: 195 Chuangxin Rd. Life Sciences Building A426. Hunnan District.

department: College of Life and Health Sciences

institute: Northeastern University, China

description: Pcr product from plasmid pool

data_processing:
Read count table generated by MAGeCK 0.5.9.4
MAGeCK count command was used to collect read count from the fastq file
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

organism: synthetic construct

source_name: Plasmid pool

growth_protocol: A375 cells were regularly tested negative for mycoplasma contamination and maintained in DMEM (SEVEN Biotech) supplemented with 10% fetal bovine serum (ExCell) and 1% penicillin–streptomycin (Solarbio). Cells were passaged every 2-4 days to maintain exponential growth and were kept in a humidity-controlled incubator at 37°C with 5% CO2. Protein-coding gene and lncRNA-targeting plasmid libraries under lentiviral backbone were firstly transfected along with pCMV8.74 and pMD2.G packaging plasmids into 293FT cells using Lipofectamine™ 2000 Transfection Reagent to generate crRNA-expressing lentivirus. Harvest virus-containing media at 72 hours post-transfection, and spin down the media at 1000 g for 5 min to remove the floating cells and cell debris. Carefully collect the virus supernatant, aliquot and store them at -80°C for further use. Test the virus titer and MOI (multiplicity of infection) before proceeding to the screen.

extract_protocol:
The regions encompassing the sgRNAs were firstly PCR-amplified for around 20-23 cycles . The second round of PCR were employed to attach the illumina adaptors and index for around 10-12 cycles. These PCR products were gel purified and pooled for high-throughput sequencing to identify sgRNA abundance on illumina PE150 sequencing platform (Novogene, China).
The pooled synthesized oligos (Synbio Technologies, China) were PCR amplified and then cloned into pLentiGuideDR-puro vector (for expressing Cas13b/d crRNA) via BsmBI site by Gibson Assembly. The ligated Gibson Assembly mix was transformed into self-prepared electrocompetent Stable E. coli cells by electro-transformation to reach the efficiency with at least 100X coverage representation of each clone in the designed library. The transformed bacteria were cultured directly in liquid LB medium for 16~20 hours at temperature 30°C to minimize the recombination events in E. coli. The library plasmids were then extracted with EndoFree Maxi Plasmid Kit (TIANGEN, Cat no. 4992194).
Ensembl gene and lncRNA annotations (version: GRCh38) are used to extract the sequences of corresponding genes or lncRNAs. For genes (or lncRNAs) with multiple transcripts, the transcripts that have the corresponding RefSeq ID are used. We first enumerate all possible guides (22bp for Cas13d and 30bp for Cas13b) that span the entire transcript, then remove guides that (1) map to more than one location in the human genome and transcriptome (allowing up to 1 mismatch) or (2) contains BsmBI digestion sites (“CGTCTC” or “GAGACG”). The remaining guides are randomly selected if they hit the greatest number of transcripts (“common” guides) within the same gene/lncRNA. If all the guides that hit the greatest number of transcripts are selected, the remaining guides that hit the second greatest number of transcripts will be randomly selected, and so on. For essential and non-essential genes, 35 guides are designed per gene. For other genes or lncRNAs, 15 guides are designed per gene or lncRNA.

treatment_protocol: Cas13b/d-expressing A375 cells were firstly generated by lentiviral infection of Cas13b/d (pLentiCas13b/d-NES-blast) and then amplified to a number around 3x10^7. Then, these cells were infected with Cas13b/d crRNA-expressing lentiviral CRISPR library with MOI ~0.3. Two days later, select the infected cells with puromycin (1 µg/mL) for three days to get rid of any non-infected cells before changing back to normal media. At least ~300x coverage of cells were collected as Day 5 sample and stored at -80°C for later genomic DNA isolation. The rest of cells were continually cultured until Day 33 before harvesting as the end point sample.

tag: sample type

value: PlasmidPool

tag: infection

tag: time


title: LentivirusPool-for-Cas13b-TwoVector-R1

status: Public on Oct 09 2023

type: SRA

country: China

description: Pcr product from cdna from viral RNA of  lentivirus pool

library_source: other

molecule: other

source_name: Lentivirus pool

value: LentivirusPool

tag: tissue

tag: cell line


title: LentivirusPool-for-Cas13d-TwoVector-R2


title: LentivirusPool-for-Cas13d-TwoVector-R1


title: SV18359-1065

city: Boston

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

country: USA

institute: Mass General Brigham

library_source: transcriptomic

data_processing:
The ExceRpt pipeline was used for quality control (QC) of the RNA-seq data
miRNAs with less than five mapped reads in at least 50% of subjects were removed prior to analysis
subjects with less than 100k mapped reads were dropped.
Assembly: hg38, miRBase v22
Supplementary files format and content: tab-delimited text file with raw counts of miRNA x Sample.

molecule: total RNA

organism: Homo sapiens

source_name: serum

extract_protocol:
Total RNA was isolated from archival serum samples using the miRNeasy kit (Qiagen, Germantown, MD) according to the manufacturer's instructions
small RNA-seq libraries were prepared by using the Norgen Biotek Small RNA Library Prep Kit (Norgen Biotek, Therold, Canada), and sequenced on the Illumina NextSeq 500 platform.
NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cylce Kit)

value: serum

tag: batch

tag: age

tag: Sex

value: F

tag: pctpred fev1_pre_bd

tag: inhaled steroids

tag: bdrbase


title: SV18359-1062

value: M


title: LentivirusPool-for-Cas13b-TwoVector-R2


title: SV18359-1060


title: SV18359-1061


title: SV18359-1073


title: HB115

city: Ithaca

first: Hao

last: Wu

state: NY

address: 236 Tower Rd, Plant Science Building Room #236

institute: Cornell University

description: 75 bp SE

library_source: genomic

data_processing:
DAP-seq reads were trimmed using trimmomatic with the following parameters: ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Trimmed reads were mapped to the maize reference genome using bowtie2.3.3
Mapped reads were filtered for reads containing > MAPQ30 using samtools
Peaks were called using GEM v2.5 with default thresholds
Assembly: B73 RefGen_v3
Supplementary files format and content: narrowPeak
Library strategy: DAP-Seq

molecule: genomic DNA

organism: Zea mays

source_name: 14-d old seedlings

extract_protocol:
DNA was extracted from maize B73 14-day old seedlings. Five grams of tissue was ground in liquid nitrogen and the genomic DNA was extracted in a phenol/chloroform/IAA extract cocktail. The DNA pellet was resuspended and diluted in EB (10mM Tris-HCl pH 8.5).
The EB diluted DNA was sheared to 200bp fragments using a Covaris S2 sonicator. DNA was purified using AmpureXP beads with a 2:1 bead to DNA ratio, and then end-repaired using an End-It kit (Lucigen) according to the manufacturer’s recommendations. Samples were cleaned using a Qiaquick PCR purification kit (Qiagen), A-tailed using Klenow (3’ to 5’ exo-), cleaned with Qiaquick and ligated overnight with a truncated Illumina Y-adapter. Final libraries were purified using AMPureXP beads with a 1:1 bead to DNA ratio and eluted in 30ul of EB. DNA concentration was determined using the Qubit HS kit.

value: 14-d old seedlings

tag: cultivar

tag: cell type

value: Plant seedling cells


title: GBF1

description: 75 bp SE


title: SV18359-1057


title: SV18359-1059


title: SV18359-1058


title: LentivirusPool-for-Cas13d-OneVector-R2


title: SynXI v36 RNA-seq

city: New York

first: Jitong

last: Cai

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

description: v36 - S. cerevisiae with synXI; debugged synXI strain; homozygous diploid.

data_processing:
First, we pre-processed the Illumina unstranded paired-end reads by trimming adapters and remove low quality bases.
Then, we built a reference synXI genome by replacing the wild type BY4742 chrXI with the synXI_9.11 and created a reference transcriptome by considering only protein-coding genes. Importantly, when a gene in the synthetic chromosome was deleted, we replaced it with the corresponding wild type one; this allows us to readily cross check for sample mislabelling, since no expression is expected from a deleted locus.
We then used transcriptomes and reads to quantify gene expression using kallisto quant with sequence based bias correction (Bray et al., 2016).
Successively, differentially expressed genes were identified with edgeR (Robinson et al., 2010), using the exactTest method with dispersion parameter set to 0.22 to account for the lack of replicates. Finally, we reported as significantly differentially expressed all the genes with False Discovery Rate (FDR) less or equal to 0.01.
Assembly: S288C
Supplementary files format and content: comma-delimited csv file contains a list of differential expression genes and related statistics
Supplementary files format and content: tab-delimited txt file contains the raw read count for each gene

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: We grew cells in YPD or YPG medium at 30 °C until mid-exponential growth phase (OD600 ~2).

extract_protocol:
Cell culture corresponding to ~3 x 10^8 cells was harvested by centrifugation, washed in 0.8% physiological salt solution and resuspended in 500 µl solution of 1M sorbitol and 100 mM ethylenediaminetetraacetic acid (EDTA). We generated spheroplasts by digesting cells with 50U zymolyase (Zymo Research) at 30 °C for 30 minutes. We then collected spheroplasts by centrifugation and isolated RNA using the NucleoSpin RNA Plus kit (Macherey-Nagel). We evaluated RNA quality and integrity by Qubit fluorometry using an RNA BR Assay Kit (Thermo), spectrophotometry with a NanoDrop (Thermo) and on a 2100 Bioanalyser using an RNA 2000 Nano Kit (Agilent).
RNA sequencing was performed by Novogene Co. Briefly, mRNA was purified from total RNA with poly-T oligo-attached magnetic beads prior to cDNA synthesis, adaptor ligation and sequencing on an Illumina platform.

tag: strain

value: Cell culture

tag: genotype

value: SynXI


title: SynXI v1 RNA-seq

description: v1 - S. cerevisiae with synXI; initial synXI strain with some bugs; haploid.


title: SV18359-1055


title: SV18359-1056


title: Wildtype RNA-seq

description: WT - S. cerevisiae BY4742+HIS, haploid.

value: WT


title: SV18359-1053


title: SV18359-1054


title: SV18359-1063


title: LentivirusPool-for-Cas13d-OneVector-R1


title: SV18359-1050


title: SV18359-1051


title: BY4741_wildtype RNA-seq replicate 1

data_processing:
Reads were processed using Trimmomatic to remove Illumina barcodes and adapter sequences, then aligned to the S288C reference with Kallisto (Bolger, Lohse, and Usadel 2014; Bray et al., n.d.).
Analysis was performed using the Sleuth package in R (Pimentel et al. 2017). Log2 fold change values were calculated and tested for significance with Wald’s test using an adjusted p-value with corrections for multiple hypothesis testing (Benjamini-Hochberg method).
Assembly: S288C
Supplementary files format and content: comma-delimited csv file contains a list of differential expression genes and related statistics
Supplementary files format and content: tab-delimited txt file contains the raw read count for each gene

source_name: wildtype strain BY4741 as control

growth_protocol: Single yeast colonies were inoculated in 3 mL of YPD at 30°C with rotation overnight, then diluted to A600 = 0.1 in 5 mL of fresh YPD medium. Cells were harvested after reaching A600 = 0.8-1.0.

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit (Qiagen, 74106).
And 1 µg of total RNA was used as input for RNA library preparation (NEB E7770).


title: ySLL185_SynVIII RNA-seq replicate 3

source_name: SynVIII strain ySLL217

value: SynVIII


title: BY4741_wildtype RNA-seq replicate 2


title: ySLL185_SynVIII RNA-seq replicate 2


title: NACTF49

description: 75 bp SE


title: SV18359-1048


title: SV18359-1046


title: SV18359-1045


title: HSFTF10

description: 75 bp SE


title: SV18359-1044


title: SV18359-1049


title: E14 WT cells, Day4, batch2 replicate 47 (SMARTseq2_EpiLC)

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

library_source: transcriptomic single cell

data_processing:
Paired-end reads were trimmed with trim Galore (v0.6.5) in order to remove adapter sequences and Ns nucleotides from both side of the read.
Cleaned reads were aligned onto a concatenated genome (the Mouse reference genome mm10 + fasta file with the ERCC spike-in sequences) with STAR (v2.7.5a) reporting random alignment with at most 6 % of mismatches. ERCCs, genes and TE families-based quantification was performed with featureCounts (v1.5.1) using a concatenated file with repeatMasker, ERCC spike-in and Gencode vM25 annotations. Filtering of cells was performed with the following criteria: cells with less than 7500 genes with at least one read and cells with more than 2% of mitochondrial reads or more than 10% of ribosomal reads were filtered out.
Assembly: GRCm38/mm10
Supplementary files format and content: Text file with quantification per gene

organism: Mus musculus

growth_protocol: ESCs were grown for at least two weeks on fibronectin-coated plates (1/60 dilution in PBS) in 2i+VitC medium (N2B27 (50% Neurobasal medium and 50% DMEM/F12 (Gibco) complemented with 2mM L-glutamine, 0.1mM β-Mercaptoethanol, N2 supplement (Gibco) and B27 serum-free supplement (Gibco)), complemented with 1000U/ml LIF, 2i (3μM Gsk3 inhibitor and 1μM of MEK inhibitor), and vitamin C 100µg/ml final (Sigma)) and passed with accutase (GIBCO) every 2-3 days.

extract_protocol:
Single cells were index-sorted individually by FACS (SONY SH800) into wells of a 96-well PCR plate containing 2.3 µl of lysis buffer (200U/µL SUPERase-IN (LifeTechnologies), 10% Triton X100, RNAse free H2O). scRNA-seq SMARTseq2 was performed as previously described (Picelli et al., 2014).
The Illumina Nextera XT DNA kit was used to prepare libraries that were sequenced on the Illumina HiSeq 4000 (paired-end 50bp). Samples from all cell lines were included in each sequencing lane, to control for technical lane effects

treatment_protocol: To initiate EpiLC differentiation, 2i+VitC-grown ESCs were first split with accutase (Gibco) and plated on fibronectin-coated 6-well/plates at a density of 0.20x106 cells/well. The next day, the medium was replaced with AF medium: N2B27 medium supplemented with 12ng/ml Fgf2 (R&D) and 20ng/ml Activin A (R&D), 1% Knock-out Serum Medium (Gibco), to drive EpiLC differentiation. cells were harvested at Day 0, 1, 2, and 4 of differentiation, with an additional splitting step at D4 with accutase to reduce cell density.

value: Embryonic stem cells (murine)

tag: treatment

value: EpiLC differentiation


title: E14 TKO cells, Day4, batch2 replicate 48 (SMARTseq2_EpiLC)


title: SV18359-1043


title: SV18359-1042


title: ySLL185_SynVIII RNA-seq replicate 1


title: E14 WT cells, Day4, batch2 replicate 48 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 46 (SMARTseq2_EpiLC)


title: SV18359-1047


title: SV18359-1041


title: SV18359-1052


title: E14 WT cells, Day4, batch2 replicate 46 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 47 (SMARTseq2_EpiLC)


title: SV18359-1040


title: BY4741_wildtype RNA-seq replicate 3


title: E14 WT cells, Day4, batch2 replicate 45 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 44 (SMARTseq2_EpiLC)


title: SV18359-1039


title: SV18359-1037


title: SV18359-1038


title: E14 WT cells, Day4, batch2 replicate 44 (SMARTseq2_EpiLC)


title: SV18359-1036


title: E14 TKO cells, Day4, batch2 replicate 43 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 42 (SMARTseq2_EpiLC)


title: SV18359-1035


title: E14 TKO cells, Day4, batch2 replicate 41 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 43 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 42 (SMARTseq2_EpiLC)


title: SV18359-1031


title: SV18359-1034


title: E14 TKO cells, Day4, batch2 replicate 39 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 41 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 40 (SMARTseq2_EpiLC)


title: SV18359-1033


title: SV18359-1030


title: E14 TKO cells, Day4, batch2 replicate 40 (SMARTseq2_EpiLC)


title: SV18359-1032


title: SV18359-1029


title: E14 WT cells, Day4, batch2 replicate 39 (SMARTseq2_EpiLC)


title: SV18359-1027


title: SV18359-1028


title: SV18359-1026


title: E14 WT cells, Day4, batch2 replicate 38 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 38 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 37 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 45 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 37 (SMARTseq2_EpiLC)


title: SV18359-1022


title: SV18359-1023


title: SV18359-1025


title: E14 WT cells, Day4, batch2 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-1021


title: E14 WT cells, Day4, batch2 replicate 35 (SMARTseq2_EpiLC)


title: SV18359-1020


title: E14 TKO cells, Day4, batch2 replicate 34 (SMARTseq2_EpiLC)


title: SV18359-1019


title: E14 WT cells, Day4, batch2 replicate 34 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-1017


title: E14 TKO cells, Day4, batch2 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-1014


title: E14 TKO cells, Day4, batch2 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-1013


title: SV18359-1018


title: SV18359-1012


title: SV18359-1016


title: SV18359-1015


title: E14 TKO cells, Day4, batch2 replicate 31 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 36 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-1024


title: SV18359-1011


title: E14 WT cells, Day4, batch2 replicate 31 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 30 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 29 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 29 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 35 (SMARTseq2_EpiLC)


title: SV18359-1009


title: SV18359-1004


title: SV18359-1007


title: E14 TKO cells, Day4, batch2 replicate 28 (SMARTseq2_EpiLC)


title: SV18359-1002


title: E14 WT cells, Day4, batch2 replicate 26 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-1000


title: SV18359-1006


title: E14 WT cells, Day4, batch2 replicate 28 (SMARTseq2_EpiLC)


title: SV18359-1008


title: E14 TKO cells, Day4, batch2 replicate 27 (SMARTseq2_EpiLC)


title: SV18359-1005


title: E14 WT cells, Day4, batch2 replicate 27 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 26 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 30 (SMARTseq2_EpiLC)


title: SV18359-1003


title: SV18359-0994


title: SV18359-1001


title: SV18359-0992


title: E14 WT cells, Day4, batch2 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0999


title: E14 TKO cells, Day4, batch2 replicate 24 (SMARTseq2_EpiLC)


title: SV18359-0998


title: SV18359-0997


title: SV18359-0990


title: E14 WT cells, Day4, batch2 replicate 24 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 23 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 20 (SMARTseq2_EpiLC)


title: SV18359-0996


title: SV18359-0988


title: E14 WT cells, Day4, batch2 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0995


title: SV18359-0993


title: E14 TKO cells, Day4, batch2 replicate 21 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 21 (SMARTseq2_EpiLC)


title: SV18359-0986


title: SV18359-0991


title: E14 TKO cells, Day4, batch2 replicate 20 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 22 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 17 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 16 (SMARTseq2_EpiLC)


title: SV18359-0983


title: E14 TKO cells, Day4, batch2 replicate 19 (SMARTseq2_EpiLC)


title: SV18359-0981


title: SV18359-0980


title: E14 WT cells, Day4, batch2 replicate 19 (SMARTseq2_EpiLC)


title: SV18359-0987


title: E14 WT cells, Day4, batch2 replicate 18 (SMARTseq2_EpiLC)


title: SV18359-0985


title: E14 WT cells, Day4, batch2 replicate 22 (SMARTseq2_EpiLC)


title: SV18359-0984


title: SV18359-0977


title: SV18359-0989


title: E14 TKO cells, Day4, batch2 replicate 17 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 14 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 13 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 13 (SMARTseq2_EpiLC)


title: SV18359-0982


title: E14 TKO cells, Day4, batch2 replicate 15 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 18 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 16 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 12 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0973


title: SV18359-0979


title: E14 WT cells, Day4, batch2 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0978


title: SV18359-0976


title: E14 WT cells, Day4, batch2 replicate 10 (SMARTseq2_EpiLC)


title: SV18359-0975


title: E14 TKO cells, Day4, batch2 replicate 12 (SMARTseq2_EpiLC)


title: SV18359-0969


title: SV18359-0972


title: SV18359-0967


title: E14 TKO cells, Day4, batch2 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0964


title: E14 WT cells, Day4, batch2 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0970


title: SV18359-0971


title: E14 TKO cells, Day4, batch2 replicate 10 (SMARTseq2_EpiLC)


title: SV18359-0968


title: E14 TKO cells, Day4, batch2 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0974


title: E14 WT cells, Day4, batch2 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0966


title: E14 WT cells, Day4, batch2 replicate 8 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 5 (SMARTseq2_EpiLC)


title: SV18359-0960


title: E14 TKO cells, Day4, batch2 replicate 8 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 7 (SMARTseq2_EpiLC)


title: SV18359-0965


title: SV18359-0963


title: E14 TKO cells, Day4, batch2 replicate 6 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 6 (SMARTseq2_EpiLC)


title: SV18359-0957


title: SV18359-0961


title: E14 WT cells, Day4, batch2 replicate 7 (SMARTseq2_EpiLC)


title: SV18359-0958


title: SV18359-0962


title: E14 TKO cells, Day4, batch2 replicate 3 (SMARTseq2_EpiLC)


title: SV18359-0956


title: E14 WT cells, Day4, batch2 replicate 3 (SMARTseq2_EpiLC)


title: SV18359-0954


title: E14 WT cells, Day4, batch2 replicate 4 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 5 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 1 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0953


title: SV18359-0955


title: SV18359-0959


title: SV18359-0952


title: E14 TKO cells, Day4, batch2 replicate 4 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch2 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0950


title: E14 TKO cells, Day2, batch2 replicate 48 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch2 replicate 1 (SMARTseq2_EpiLC)


title: SV18359-0951


title: SV18359-0949


title: SV18359-0948


title: SV18359-0945


title: SV18359-0946


title: E14 WT cells, Day2, batch2 replicate 48 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 47 (SMARTseq2_EpiLC)


title: SV18359-0944


title: E14 WT cells, Day2, batch2 replicate 46 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 47 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 46 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 45 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 45 (SMARTseq2_EpiLC)


title: SV18359-0942


title: SV18359-0939


title: E14 TKO cells, Day2, batch2 replicate 44 (SMARTseq2_EpiLC)


title: SV18359-0943


title: SV18359-0940


title: SV18359-0941


title: E14 TKO cells, Day2, batch2 replicate 43 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 44 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 42 (SMARTseq2_EpiLC)


title: SV18359-0938


title: SV18359-0937


title: SV18359-0947


title: SV18359-0935


title: E14 TKO cells, Day2, batch2 replicate 40 (SMARTseq2_EpiLC)


title: SV18359-0936


title: E14 WT cells, Day2, batch2 replicate 41 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 41 (SMARTseq2_EpiLC)


title: SV18359-0934


title: SV18359-0932


title: SV18359-0931


title: E14 TKO cells, Day2, batch2 replicate 39 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 40 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 43 (SMARTseq2_EpiLC)


title: SV18359-0933


title: E14 TKO cells, Day2, batch2 replicate 38 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 42 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 39 (SMARTseq2_EpiLC)


title: SV18359-0927


title: SV18359-0929


title: SV18359-0928


title: E14 WT cells, Day2, batch2 replicate 37 (SMARTseq2_EpiLC)


title: SV18359-0926


title: SV18359-0925


title: E14 TKO cells, Day2, batch2 replicate 35 (SMARTseq2_EpiLC)


title: SV18359-0924


title: E14 WT cells, Day2, batch2 replicate 35 (SMARTseq2_EpiLC)


title: SV18359-0923


title: SV18359-0922


title: E14 TKO cells, Day2, batch2 replicate 34 (SMARTseq2_EpiLC)


title: SV18359-0921


title: E14 WT cells, Day2, batch2 replicate 34 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0930


title: SV18359-0919


title: SV18359-0920


title: E14 WT cells, Day2, batch2 replicate 33 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0917


title: E14 TKO cells, Day2, batch2 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0916


title: SV18359-0918


title: E14 TKO cells, Day2, batch2 replicate 31 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0913


title: E14 TKO cells, Day2, batch2 replicate 37 (SMARTseq2_EpiLC)


title: SV18359-0915


title: E14 TKO cells, Day2, batch2 replicate 33 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 29 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 30 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 29 (SMARTseq2_EpiLC)


title: SV18359-0911


title: E14 TKO cells, Day2, batch2 replicate 30 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 28 (SMARTseq2_EpiLC)


title: SV18359-0908


title: E14 WT cells, Day2, batch2 replicate 28 (SMARTseq2_EpiLC)


title: SV18359-0909


title: E14 TKO cells, Day2, batch2 replicate 27 (SMARTseq2_EpiLC)


title: SV18359-0906


title: SV18359-0903


title: E14 WT cells, Day2, batch2 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0901


title: E14 WT cells, Day2, batch2 replicate 24 (SMARTseq2_EpiLC)


title: SV18359-0899


title: E14 TKO cells, Day2, batch2 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0898


title: E14 TKO cells, Day2, batch2 replicate 22 (SMARTseq2_EpiLC)


title: SV18359-0907


title: E14 WT cells, Day2, batch2 replicate 22 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 31 (SMARTseq2_EpiLC)


title: SV18359-0905


title: E14 WT cells, Day2, batch2 replicate 27 (SMARTseq2_EpiLC)


title: SV18359-0904


title: E14 TKO cells, Day2, batch2 replicate 26 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 26 (SMARTseq2_EpiLC)


title: SV18359-0895


title: SV18359-0894


title: SV18359-0914


title: E14 TKO cells, Day2, batch2 replicate 25 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0902


title: SV18359-0893


title: SV18359-0900


title: SV18359-0910


title: SV18359-0897


title: SV18359-0896


title: E14 TKO cells, Day2, batch2 replicate 24 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 19 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 18 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 21 (SMARTseq2_EpiLC)


title: SV18359-0890


title: SV18359-0887


title: E14 TKO cells, Day2, batch2 replicate 17 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 20 (SMARTseq2_EpiLC)


title: SV18359-0886


title: E14 WT cells, Day2, batch2 replicate 20 (SMARTseq2_EpiLC)


title: SV18359-0892


title: E14 TKO cells, Day2, batch2 replicate 19 (SMARTseq2_EpiLC)


title: SV18359-0891


title: E14 TKO cells, Day2, batch2 replicate 21 (SMARTseq2_EpiLC)


title: SV18359-0883


title: SV18359-0881


title: SV18359-0882


title: E14 TKO cells, Day2, batch2 replicate 14 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0879


title: E14 TKO cells, Day2, batch2 replicate 16 (SMARTseq2_EpiLC)


title: SV18359-0885


title: SV18359-0878


title: SV18359-0889


title: E14 WT cells, Day2, batch2 replicate 13 (SMARTseq2_EpiLC)


title: SV18359-0888


title: E14 TKO cells, Day2, batch2 replicate 12 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 18 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 16 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0874


title: SV18359-0875


title: E14 WT cells, Day2, batch2 replicate 15 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0873


title: SV18359-0880


title: E14 TKO cells, Day2, batch2 replicate 13 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 17 (SMARTseq2_EpiLC)


title: SV18359-0877


title: E14 WT cells, Day2, batch2 replicate 12 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 9 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 10 (SMARTseq2_EpiLC)


title: SV18359-0872


title: SV18359-0871


title: SV18359-0884


title: SV18359-0876


title: SV18359-0869


title: E14 WT cells, Day2, batch2 replicate 8 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 8 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 9 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 7 (SMARTseq2_EpiLC)


title: SV18359-0870


title: E14 WT cells, Day2, batch2 replicate 7 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 11 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 10 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 6 (SMARTseq2_EpiLC)


title: SV18359-0864


title: SV18359-0863


title: E14 WT cells, Day2, batch2 replicate 6 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 5 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 5 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0860


title: E14 TKO cells, Day2, batch2 replicate 3 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 4 (SMARTseq2_EpiLC)


title: SV18359-0856


title: SV18359-0855


title: E14 WT cells, Day2, batch2 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0868


title: SV18359-0867


title: SV18359-0866


title: SV18359-0854


title: E14 TKO cells, Day1, batch2 replicate 48 (SMARTseq2_EpiLC)


title: SV18359-0853


title: SV18359-0851


title: E14 WT cells, Day1, batch2 replicate 47 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 4 (SMARTseq2_EpiLC)


title: SV18359-0865


title: SV18359-0861


title: SV18359-0859


title: SV18359-0850


title: E14 WT cells, Day2, batch2 replicate 3 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 46 (SMARTseq2_EpiLC)


title: SV18359-0858


title: SV18359-0848


title: E14 WT cells, Day1, batch2 replicate 46 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch2 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0845


title: E14 TKO cells, Day2, batch2 replicate 1 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 43 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch2 replicate 1 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 42 (SMARTseq2_EpiLC)


title: SV18359-0842


title: SV18359-0840


title: E14 WT cells, Day1, batch2 replicate 42 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 41 (SMARTseq2_EpiLC)


title: SV18359-0838


title: E14 TKO cells, Day1, batch2 replicate 40 (SMARTseq2_EpiLC)


title: SV18359-0837


title: SV18359-0836


title: SV18359-0862


title: SV18359-0852


title: E14 WT cells, Day1, batch2 replicate 48 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 38 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0832


title: SV18359-0857


title: SV18359-0831


title: SV18359-0849


title: E14 WT cells, Day1, batch2 replicate 37 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 45 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 44 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 45 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 47 (SMARTseq2_EpiLC)


title: SV18359-0828


title: SV18359-0844


title: SV18359-0827


title: E14 TKO cells, Day1, batch2 replicate 35 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0826


title: SV18359-0843


title: E14 TKO cells, Day1, batch2 replicate 34 (SMARTseq2_EpiLC)


title: SV18359-0825


title: E14 WT cells, Day1, batch2 replicate 43 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 34 (SMARTseq2_EpiLC)


title: SV18359-0841


title: SV18359-0847


title: SV18359-0824


title: SV18359-0823


title: SV18359-0846


title: SV18359-0839


title: E14 WT cells, Day1, batch2 replicate 41 (SMARTseq2_EpiLC)


title: SV18359-0822


title: E14 TKO cells, Day1, batch2 replicate 32 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 44 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0835


title: E14 WT cells, Day1, batch2 replicate 40 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 31 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 39 (SMARTseq2_EpiLC)


title: SV18359-0834


title: SV18359-0833


title: E14 TKO cells, Day1, batch2 replicate 37 (SMARTseq2_EpiLC)


title: SV18359-0830


title: SV18359-0818


title: SV18359-0829


title: E14 TKO cells, Day1, batch2 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0814


title: E14 WT cells, Day1, batch2 replicate 35 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 39 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 28 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-0821


title: E14 TKO cells, Day1, batch2 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-0810


title: E14 WT cells, Day1, batch2 replicate 26 (SMARTseq2_EpiLC)


title: SV18359-0820


title: SV18359-0819


title: E14 TKO cells, Day1, batch2 replicate 31 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0806


title: E14 TKO cells, Day1, batch2 replicate 24 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 30 (SMARTseq2_EpiLC)


title: SV18359-0817


title: SV18359-0816


title: E14 TKO cells, Day1, batch2 replicate 29 (SMARTseq2_EpiLC)


title: SV18359-0805


title: E14 TKO cells, Day1, batch2 replicate 30 (SMARTseq2_EpiLC)


title: SV18359-0804


title: SV18359-0803


title: SV18359-0815


title: E14 TKO cells, Day1, batch2 replicate 23 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 29 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0813


title: E14 WT cells, Day1, batch2 replicate 22 (SMARTseq2_EpiLC)


title: SV18359-0812


title: SV18359-0799


title: SV18359-0811


title: E14 TKO cells, Day1, batch2 replicate 27 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 24 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 27 (SMARTseq2_EpiLC)


title: SV18359-0795


title: SV18359-0809


title: SV18359-0808


title: E14 TKO cells, Day1, batch2 replicate 28 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 26 (SMARTseq2_EpiLC)


title: SV18359-0807


title: E14 WT cells, Day1, batch2 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0802


title: SV18359-0791


title: E14 TKO cells, Day1, batch2 replicate 22 (SMARTseq2_EpiLC)


title: SV18359-0801


title: SV18359-0800


title: E14 TKO cells, Day1, batch2 replicate 21 (SMARTseq2_EpiLC)


title: SV18359-0798


title: E14 WT cells, Day1, batch2 replicate 21 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 20 (SMARTseq2_EpiLC)


title: SV18359-0797


title: SV18359-0796


title: E14 TKO cells, Day1, batch2 replicate 19 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 20 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 19 (SMARTseq2_EpiLC)


title: SV18359-0794


title: SV18359-0787


title: E14 TKO cells, Day1, batch2 replicate 18 (SMARTseq2_EpiLC)


title: SV18359-0793


title: E14 TKO cells, Day1, batch2 replicate 17 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0786


title: E14 TKO cells, Day1, batch2 replicate 13 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0783


title: SV18359-0782


title: E14 WT cells, Day1, batch2 replicate 18 (SMARTseq2_EpiLC)


title: SV18359-0792


title: E14 WT cells, Day1, batch2 replicate 17 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 12 (SMARTseq2_EpiLC)


title: SV18359-0789


title: SV18359-0790


title: E14 WT cells, Day1, batch2 replicate 13 (SMARTseq2_EpiLC)


title: SV18359-0788


title: E14 WT cells, Day1, batch2 replicate 16 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 16 (SMARTseq2_EpiLC)


title: SV18359-0779


title: E14 WT cells, Day1, batch2 replicate 11 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0778


title: E14 WT cells, Day1, batch2 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0776


title: SV18359-0785


title: E14 TKO cells, Day1, batch2 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0781


title: SV18359-0774


title: E14 WT cells, Day1, batch2 replicate 12 (SMARTseq2_EpiLC)


title: SV18359-0780


title: SV18359-0777


title: E14 WT cells, Day1, batch2 replicate 8 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 10 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 8 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 10 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 7 (SMARTseq2_EpiLC)


title: SV18359-0784


title: E14 TKO cells, Day1, batch2 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0769


title: SV18359-0767


title: E14 TKO cells, Day1, batch2 replicate 5 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0775


title: E14 WT cells, Day1, batch2 replicate 4 (SMARTseq2_EpiLC)


title: SV18359-0773


title: SV18359-0772


title: E14 WT cells, Day1, batch2 replicate 3 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0761


title: SV18359-0771


title: E14 WT cells, Day1, batch2 replicate 6 (SMARTseq2_EpiLC)


title: E14 WT cells, Day1, batch2 replicate 7 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch2 replicate 1 (SMARTseq2_EpiLC)


title: SV18359-0759


title: SV18359-0770


title: SV18359-0758


title: E14 TKO cells, Day1, batch2 replicate 6 (SMARTseq2_EpiLC)


title: SV18359-0765


title: SV18359-0757


title: SV18359-0768


title: E14 WT cells, Day1, batch2 replicate 5 (SMARTseq2_EpiLC)


title: SV18359-0766


title: SV18359-0756


title: E14 TKO cells, Day1, batch2 replicate 4 (SMARTseq2_EpiLC)


title: SV18359-0764


title: SV18359-0755


title: E14 TKO cells, Day1, batch2 replicate 3 (SMARTseq2_EpiLC)


title: SV18359-0762


title: E14 WT cells, Day1, batch2 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0760


title: SV18359-0754


title: E14 WT cells, Day1, batch2 replicate 1 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 48 (SMARTseq2_EpiLC)


title: SV18359-0752


title: E14 TKO cells, Day0, batch2 replicate 45 (SMARTseq2_EpiLC)


title: SV18359-0750


title: E14 WT cells, Day0, batch2 replicate 48 (SMARTseq2_EpiLC)


title: SV18359-0763


title: E14 TKO cells, Day0, batch2 replicate 44 (SMARTseq2_EpiLC)


title: SV18359-0749


title: E14 TKO cells, Day0, batch2 replicate 46 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 43 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 47 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 44 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 47 (SMARTseq2_EpiLC)


title: SV18359-0753


title: SV18359-0746


title: E14 WT cells, Day0, batch2 replicate 45 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 42 (SMARTseq2_EpiLC)


title: SV18359-0748


title: SV18359-0745


title: SV18359-0751


title: SV18359-0747


title: E14 WT cells, Day0, batch2 replicate 43 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 41 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 42 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 41 (SMARTseq2_EpiLC)


title: SV18359-0742


title: E14 WT cells, Day0, batch2 replicate 46 (SMARTseq2_EpiLC)


title: SV18359-0743


title: SV18359-0744


title: SV18359-0740


title: SV18359-0739


title: E14 WT cells, Day0, batch2 replicate 39 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 39 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 40 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 37 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 37 (SMARTseq2_EpiLC)


title: SV18359-0736


title: SV18359-0735


title: E14 WT cells, Day0, batch2 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0734


title: SV18359-0737


title: SV18359-0732


title: E14 WT cells, Day0, batch2 replicate 36 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 35 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0733


title: SV18359-0741


title: E14 WT cells, Day0, batch2 replicate 40 (SMARTseq2_EpiLC)


title: SV18359-0730


title: SV18359-0731


title: E14 WT cells, Day0, batch2 replicate 35 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 34 (SMARTseq2_EpiLC)


title: SV18359-0728


title: E14 TKO cells, Day0, batch2 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0727


title: SV18359-0726


title: E14 TKO cells, Day0, batch2 replicate 33 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 32 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-0724


title: E14 WT cells, Day0, batch2 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0723


title: E14 TKO cells, Day0, batch2 replicate 31 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 31 (SMARTseq2_EpiLC)


title: SV18359-0722


title: SV18359-0720


title: SV18359-0719


title: SV18359-0721


title: E14 WT cells, Day0, batch2 replicate 30 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 30 (SMARTseq2_EpiLC)


title: SV18359-0718


title: E14 TKO cells, Day0, batch2 replicate 29 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 28 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 34 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 28 (SMARTseq2_EpiLC)


title: SV18359-0717


title: SV18359-0716


title: SV18359-0725


title: SV18359-0713


title: E14 WT cells, Day0, batch2 replicate 27 (SMARTseq2_EpiLC)


title: SV18359-0715


title: SV18359-0714


title: E14 TKO cells, Day0, batch2 replicate 26 (SMARTseq2_EpiLC)


title: SV18359-0711


title: SV18359-0712


title: E14 TKO cells, Day0, batch2 replicate 25 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 26 (SMARTseq2_EpiLC)


title: SV18359-0710


title: E14 WT cells, Day0, batch2 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0709


title: E14 TKO cells, Day0, batch2 replicate 24 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0706


title: E14 WT cells, Day0, batch2 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0705


title: E14 TKO cells, Day0, batch2 replicate 27 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 22 (SMARTseq2_EpiLC)


title: SV18359-0704


title: E14 TKO cells, Day0, batch2 replicate 21 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 22 (SMARTseq2_EpiLC)


title: SV18359-0703


title: SV18359-0702


title: SV18359-0700


title: SV18359-0693


title: E14 TKO cells, Day0, batch2 replicate 20 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 19 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 21 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 20 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 19 (SMARTseq2_EpiLC)


title: SV18359-0691


title: SV18359-0701


title: E14 WT cells, Day0, batch2 replicate 29 (SMARTseq2_EpiLC)


title: SV18359-0692


title: E14 TKO cells, Day0, batch2 replicate 18 (SMARTseq2_EpiLC)


title: SV18359-0708


title: SV18359-0690


title: E14 WT cells, Day0, batch2 replicate 24 (SMARTseq2_EpiLC)


title: SV18359-0689


title: E14 WT cells, Day0, batch2 replicate 18 (SMARTseq2_EpiLC)


title: SV18359-0688


title: E14 TKO cells, Day0, batch2 replicate 17 (SMARTseq2_EpiLC)


title: SV18359-0707


title: SV18359-0687


title: SV18359-0686


title: E14 TKO cells, Day0, batch2 replicate 16 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 17 (SMARTseq2_EpiLC)


title: SV18359-0685


title: E14 TKO cells, Day0, batch2 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0684


title: E14 WT cells, Day0, batch2 replicate 16 (SMARTseq2_EpiLC)


title: SV18359-0683


title: E14 TKO cells, Day0, batch2 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0682


title: E14 WT cells, Day0, batch2 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0681


title: E14 TKO cells, Day0, batch2 replicate 13 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0680


title: E14 WT cells, Day0, batch2 replicate 13 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 12 (SMARTseq2_EpiLC)


title: SV18359-0679


title: SV18359-0678


title: SV18359-0677


title: SV18359-0675


title: E14 TKO cells, Day0, batch2 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0674


title: E14 WT cells, Day0, batch2 replicate 11 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 10 (SMARTseq2_EpiLC)


title: SV18359-0671


title: SV18359-0670


title: E14 WT cells, Day0, batch2 replicate 10 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0668


title: E14 TKO cells, Day0, batch2 replicate 8 (SMARTseq2_EpiLC)


title: SV18359-0669


title: E14 WT cells, Day0, batch2 replicate 8 (SMARTseq2_EpiLC)


title: SV18359-0667


title: E14 WT cells, Day0, batch2 replicate 7 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 6 (SMARTseq2_EpiLC)


title: SV18359-0665


title: SV18359-0662


title: SV18359-0661


title: E14 WT cells, Day0, batch2 replicate 6 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 12 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 5 (SMARTseq2_EpiLC)


title: SV18359-0659


title: E14 TKO cells, Day0, batch2 replicate 4 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 4 (SMARTseq2_EpiLC)


title: SV18359-0672


title: SV18359-0658


title: E14 TKO cells, Day0, batch2 replicate 3 (SMARTseq2_EpiLC)


title: SV18359-0657


title: E14 TKO cells, Day0, batch2 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0656


title: E14 TKO cells, Day0, batch2 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0664


title: SV18359-0663


title: E14 WT cells, Day0, batch2 replicate 3 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 7 (SMARTseq2_EpiLC)


title: SV18359-0655


title: SV18359-0654


title: E14 WT cells, Day0, batch2 replicate 2 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day0, batch2 replicate 1 (SMARTseq2_EpiLC)


title: SV18359-0653


title: E14 WT cells, Day0, batch2 replicate 1 (SMARTseq2_EpiLC)


title: E14 WT cells, Day0, batch2 replicate 5 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 48 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 48 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 47 (SMARTseq2_EpiLC)


title: SV18359-0650


title: SV18359-0649


title: SV18359-0651


title: SV18359-0648


title: E14 WT cells, Day4, batch1 replicate 47 (SMARTseq2_EpiLC)


title: SV18359-0646


title: E14 WT cells, Day4, batch1 replicate 46 (SMARTseq2_EpiLC)


title: SV18359-0644


title: SV18359-0643


title: E14 WT cells, Day4, batch1 replicate 45 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 44 (SMARTseq2_EpiLC)


title: SV18359-0641


title: E14 TKO cells, Day4, batch1 replicate 46 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 44 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 45 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 43 (SMARTseq2_EpiLC)


title: SV18359-0652


title: SV18359-0639


title: E14 WT cells, Day4, batch1 replicate 43 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 42 (SMARTseq2_EpiLC)


title: SV18359-0642


title: E14 WT cells, Day4, batch1 replicate 42 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 41 (SMARTseq2_EpiLC)


title: SV18359-0636


title: E14 TKO cells, Day4, batch1 replicate 41 (SMARTseq2_EpiLC)


title: SV18359-0640


title: SV18359-0634


title: SV18359-0635


title: E14 TKO cells, Day4, batch1 replicate 40 (SMARTseq2_EpiLC)


title: SV18359-0633


title: SV18359-0632


title: E14 TKO cells, Day4, batch1 replicate 39 (SMARTseq2_EpiLC)


title: SV18359-0631


title: E14 WT cells, Day4, batch1 replicate 40 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 39 (SMARTseq2_EpiLC)


title: SV18359-0630


title: E14 TKO cells, Day4, batch1 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0628


title: SV18359-0638


title: SV18359-0637


title: E14 WT cells, Day4, batch1 replicate 37 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0626


title: E14 WT cells, Day4, batch1 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0627


title: SV18359-0622


title: SV18359-0624


title: E14 WT cells, Day4, batch1 replicate 35 (SMARTseq2_EpiLC)


title: SV18359-0621


title: E14 WT cells, Day4, batch1 replicate 34 (SMARTseq2_EpiLC)


title: SV18359-0629


title: SV18359-0619


title: E14 TKO cells, Day4, batch1 replicate 37 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-0617


title: SV18359-0623


title: E14 TKO cells, Day4, batch1 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0625


title: E14 TKO cells, Day4, batch1 replicate 31 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 34 (SMARTseq2_EpiLC)


title: SV18359-0618


title: E14 WT cells, Day4, batch1 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0616


title: E14 WT cells, Day4, batch1 replicate 31 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 35 (SMARTseq2_EpiLC)


title: SV18359-0611


title: E14 WT cells, Day4, batch1 replicate 30 (SMARTseq2_EpiLC)


title: SV18359-0614


title: SV18359-0609


title: SV18359-0610


title: SV18359-0608


title: E14 TKO cells, Day4, batch1 replicate 29 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 29 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 28 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 27 (SMARTseq2_EpiLC)


title: SV18359-0604


title: SV18359-0605


title: E14 WT cells, Day4, batch1 replicate 27 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 26 (SMARTseq2_EpiLC)


title: SV18359-0603


title: SV18359-0606


title: E14 TKO cells, Day4, batch1 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0612


title: E14 WT cells, Day4, batch1 replicate 28 (SMARTseq2_EpiLC)


title: SV18359-0602


title: SV18359-0607


title: SV18359-0660


title: E14 WT cells, Day4, batch1 replicate 26 (SMARTseq2_EpiLC)


title: SV18359-0601


title: SV18359-0600


title: SV18359-0620


title: SV18359-0599


title: E14 TKO cells, Day4, batch1 replicate 24 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0597


title: SV18359-0598


title: E14 WT cells, Day4, batch1 replicate 25 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 22 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 21 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 24 (SMARTseq2_EpiLC)


title: SV18359-0596


title: E14 TKO cells, Day4, batch1 replicate 33 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 22 (SMARTseq2_EpiLC)


title: SV18359-0594


title: E14 WT cells, Day4, batch1 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0593


title: E14 TKO cells, Day4, batch1 replicate 21 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 20 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 20 (SMARTseq2_EpiLC)


title: SV18359-0592


title: SV18359-0595


title: E14 TKO cells, Day4, batch1 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0591


title: SV18359-0590


title: E14 TKO cells, Day4, batch1 replicate 19 (SMARTseq2_EpiLC)


title: SV18359-0589


title: E14 WT cells, Day4, batch1 replicate 19 (SMARTseq2_EpiLC)


title: SV18359-0587


title: E14 TKO cells, Day4, batch1 replicate 18 (SMARTseq2_EpiLC)


title: SV18359-0586


title: E14 WT cells, Day4, batch1 replicate 18 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 30 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 17 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 17 (SMARTseq2_EpiLC)


title: SV18359-0584


title: E14 WT cells, Day4, batch1 replicate 16 (SMARTseq2_EpiLC)


title: SV18359-0581


title: SV18359-0585


title: SV18359-0583


title: SV18359-0580


title: E14 TKO cells, Day4, batch1 replicate 14 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0582


title: E14 WT cells, Day4, batch1 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0579


title: E14 WT cells, Day4, batch1 replicate 15 (SMARTseq2_EpiLC)


title: SV18359-0578


title: E14 TKO cells, Day4, batch1 replicate 13 (SMARTseq2_EpiLC)


title: SV18359-0577


title: SV18359-0576


title: E14 WT cells, Day4, batch1 replicate 13 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 12 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 16 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 12 (SMARTseq2_EpiLC)


title: SV18359-0575


title: E14 TKO cells, Day4, batch1 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0573


title: E14 TKO cells, Day4, batch1 replicate 10 (SMARTseq2_EpiLC)


title: SV18359-0572


title: SV18359-0571


title: SV18359-0570


title: E14 WT cells, Day4, batch1 replicate 10 (SMARTseq2_EpiLC)


title: SV18359-0567


title: E14 TKO cells, Day4, batch1 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0566


title: SV18359-0568


title: E14 TKO cells, Day4, batch1 replicate 8 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 7 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 7 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 8 (SMARTseq2_EpiLC)


title: SV18359-0564


title: SV18359-0569


title: E14 TKO cells, Day4, batch1 replicate 6 (SMARTseq2_EpiLC)


title: SV18359-0563


title: E14 WT cells, Day4, batch1 replicate 9 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 6 (SMARTseq2_EpiLC)


title: SV18359-0574


title: E14 WT cells, Day4, batch1 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0561


title: E14 TKO cells, Day4, batch1 replicate 5 (SMARTseq2_EpiLC)


title: SV18359-0565


title: E14 TKO cells, Day4, batch1 replicate 4 (SMARTseq2_EpiLC)


title: SV18359-0560


title: SV18359-0559


title: SV18359-0558


title: E14 TKO cells, Day4, batch1 replicate 3 (SMARTseq2_EpiLC)


title: SV18359-0557


title: E14 WT cells, Day4, batch1 replicate 4 (SMARTseq2_EpiLC)


title: SV18359-0554


title: SV18359-0553


title: E14 TKO cells, Day4, batch1 replicate 1 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 3 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day4, batch1 replicate 2 (SMARTseq2_EpiLC)


title: SV18359-0552


title: E14 WT cells, Day4, batch1 replicate 1 (SMARTseq2_EpiLC)


title: SV18359-0615


title: E14 TKO cells, Day2, batch1 replicate 48 (SMARTseq2_EpiLC)


title: SV18359-0551


title: E14 WT cells, Day4, batch1 replicate 2 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 47 (SMARTseq2_EpiLC)


title: SV18359-0549


title: E14 WT cells, Day2, batch1 replicate 48 (SMARTseq2_EpiLC)


title: E14 WT cells, Day4, batch1 replicate 5 (SMARTseq2_EpiLC)


title: SV18359-0548


title: E14 WT cells, Day2, batch1 replicate 47 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 46 (SMARTseq2_EpiLC)


title: SV18359-0547


title: SV18359-0546


title: SV18359-0545


title: E14 WT cells, Day2, batch1 replicate 46 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 45 (SMARTseq2_EpiLC)


title: SV18359-0544


title: SV18359-0556


title: SV18359-0555


title: E14 WT cells, Day2, batch1 replicate 45 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 44 (SMARTseq2_EpiLC)


title: SV18359-0542


title: E14 TKO cells, Day2, batch1 replicate 43 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 44 (SMARTseq2_EpiLC)


title: SV18359-0540


title: E14 TKO cells, Day2, batch1 replicate 42 (SMARTseq2_EpiLC)


title: SV18359-0539


title: SV18359-0538


title: E14 WT cells, Day2, batch1 replicate 43 (SMARTseq2_EpiLC)


title: SV18359-0537


title: SV18359-0536


title: E14 WT cells, Day2, batch1 replicate 41 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 42 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 41 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 40 (SMARTseq2_EpiLC)


title: SV18359-0533


title: SV18359-0534


title: E14 WT cells, Day2, batch1 replicate 40 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 39 (SMARTseq2_EpiLC)


title: SV18359-0532


title: SV18359-0535


title: E14 WT cells, Day2, batch1 replicate 39 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0531


title: SV18359-0530


title: SV18359-0543


title: SV18359-0541


title: E14 WT cells, Day2, batch1 replicate 38 (SMARTseq2_EpiLC)


title: SV18359-0529


title: E14 WT cells, Day2, batch1 replicate 37 (SMARTseq2_EpiLC)


title: SV18359-0528


title: SV18359-0527


title: E14 TKO cells, Day2, batch1 replicate 37 (SMARTseq2_EpiLC)


title: SV18359-0526


title: E14 TKO cells, Day2, batch1 replicate 36 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 36 (SMARTseq2_EpiLC)


title: SV18359-0525


title: E14 TKO cells, Day2, batch1 replicate 35 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 35 (SMARTseq2_EpiLC)


title: SV18359-0524


title: SV18359-0523


title: SV18359-0522


title: E14 TKO cells, Day2, batch1 replicate 34 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 34 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-0521


title: SV18359-0519


title: E14 TKO cells, Day2, batch1 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0518


title: SV18359-0520


title: SV18359-0517


title: E14 WT cells, Day2, batch1 replicate 32 (SMARTseq2_EpiLC)


title: SV18359-0516


title: E14 TKO cells, Day2, batch1 replicate 31 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 31 (SMARTseq2_EpiLC)


title: SV18359-0515


title: SV18359-0514


title: SV18359-0513


title: E14 TKO cells, Day2, batch1 replicate 30 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 30 (SMARTseq2_EpiLC)


title: SV18359-0512


title: E14 WT cells, Day2, batch1 replicate 29 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 29 (SMARTseq2_EpiLC)


title: SV18359-0510


title: SV18359-0509


title: E14 TKO cells, Day2, batch1 replicate 28 (SMARTseq2_EpiLC)


title: SV18359-0508


title: E14 WT cells, Day2, batch1 replicate 27 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 28 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 33 (SMARTseq2_EpiLC)


title: SV18359-0507


title: SV18359-0562


title: SV18359-0506


title: SV18359-0505


title: SV18359-0504


title: E14 WT cells, Day2, batch1 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0503


title: E14 TKO cells, Day2, batch1 replicate 24 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 26 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 25 (SMARTseq2_EpiLC)


title: SV18359-0502


title: SV18359-0501


title: SV18359-0511


title: SV18359-0500


title: SV18359-0499


title: E14 TKO cells, Day2, batch1 replicate 22 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 23 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 27 (SMARTseq2_EpiLC)


title: SV18359-0498


title: SV18359-0497


title: E14 TKO cells, Day2, batch1 replicate 26 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 22 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 21 (SMARTseq2_EpiLC)


title: SV18359-0496


title: E14 WT cells, Day2, batch1 replicate 21 (SMARTseq2_EpiLC)


title: SV18359-0495


title: SV18359-0494


title: E14 TKO cells, Day2, batch1 replicate 20 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 19 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 20 (SMARTseq2_EpiLC)


title: SV18359-0493


title: E14 WT cells, Day2, batch1 replicate 19 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 18 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 24 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 23 (SMARTseq2_EpiLC)


title: SV18359-0490


title: SV18359-0491


title: E14 WT cells, Day2, batch1 replicate 18 (SMARTseq2_EpiLC)


title: SV18359-0492


title: SV18359-0488


title: E14 WT cells, Day2, batch1 replicate 17 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day2, batch1 replicate 17 (SMARTseq2_EpiLC)


title: SV18359-0489


title: SV18359-0487


title: E14 TKO cells, Day2, batch1 replicate 16 (SMARTseq2_EpiLC)


title: A375_NUTF2_u_11-EGFP sgTRAC C

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing pipeline:  Paired-end reads were processed in a single run by nf-core/rnaseq pipeline v2.0 (https://nf-co.re/rnaseq/2.0), a pipeline implemented in Nextflow. Below there is a brief description of the main steps. nf-core documentation provides detail of all the individual steps in the pipeline. Parameters: --aligner star_rsem
Pipeline manager:  nextflow 20.10.0
Adapter and quality trimming:  Reads are trimmed using trimgalore 0.6.6
Mapping:  Reads mapped to reference using STAR aligner
Deduplication:  BAM files generated by STAR are deduplicated using picard (2.23.8) markDuplicates
Scaling:  Gene counts and TPM estimated with RSEM 1.3.1
BigWig file generation:  BigWig files were generated from mapped BAM files using deepTools (v3.3.2) bamCoverage --normalizeUsing BPM --filterRNAStrand reverse and forward, respectively
Assembly: genome build:  hg38 (Homo_sapiens_UCSC_hg38.tar.gz - Illumina iGenomes: http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg38/Homo_sapiens_UCSC_hg38.tar.gz )
Supplementary files format and content: processed data files format and content:  BigWig files with read profiles.

growth_protocol: Cells were grown in Gibco DMEM (ThermoFisher Scientific, 10569010) supplemented with 10% FBS (Sigma-Aldrich, F7524)

extract_protocol:
One million cells were then harvested by trypsinization and pelleted by centrifugation at 500 x g for three minutes. Pellets were washed once with PBS (Sigma-Aldrich, D8537), flash frozen and stored at -80C until use. The pellet was resuspended in 350ul RLT buffer (Qiagen, 74106)  supplemented with 1% beta-mercaptoethanol. The lysate was homogenised using the Qiashredder column (Qiagen, 79654) and RNA extracted utilising the RNeasy Plus Mini Kit (Qiagen, 74136) according to manufacturer’s instructions. RNA concentration was measured with  the Qubit RNA HS assay kit (Life Technologies, Q32852) according to  manufacturer’s instructions and methanol flash frozen.
RNA-seq libraries were generated and sequence through BGI service for strand specific RNA-seq with PolyA selection (DNBseq Eukaryotic Transcriptome De novo Sequencing).

treatment_protocol: 80,000 cells per well were seeded in a 24- well plate and transfected with the respective synthetic sgRNA (Synthego) in triplicate wells one day after seeding using Lipofectamine™ RNAiMAX (ThermoFisher Scientific, 13778075) according to the manufacturer’s protocol. Cells were transferred into a 6-well plate one day post-transfection and expanded until three days post-transfection.

value: A375 Malignant Melanoma Cell Line

tag: transgene

value: TRAC control sgRNA


title: E14 WT cells, Day2, batch1 replicate 16 (SMARTseq2_EpiLC)


title: SV18359-0484


title: A375_NUTF2_u_11-EGFP sgTRAC A


title: A375_NUTF2_u_11-EGFP sgNUTF2_u_11 B

value: NUTF2_u_11 sgRNA


title: E14 TKO cells, Day2, batch1 replicate 15 (SMARTseq2_EpiLC)


title: A375_NUTF2_u_11-EGFP sgNUTF2_u_11 C


title: A375_NUTF2_u_11-EGFP sgNUTF2_u_11 A


title: A375_CENPBD2P_p_13-EGFP sgTRAC C


title: SV18359-0483


title: E14 TKO cells, Day2, batch1 replicate 14 (SMARTseq2_EpiLC)


title: A375_CENPBD2P_p_13-EGFP sgTRAC A


title: E14 WT cells, Day2, batch1 replicate 15 (SMARTseq2_EpiLC)


title: A375_CENPBD2P_p_13-EGFP sgCENPBD2P_p_13 B

value: CENPBD2P_p_13 sgRNA


title: A375_CENPBD2P_p_13-EGFP sgCENPBD2P_p_13 C


title: A375_CENPBD2P_p_13-EGFP sgTRAC B


title: A375_DSE_u_63-EGFP sgTRAC C


title: SV18359-0481


title: A375_NUTF2_u_11-EGFP sgTRAC B


title: A375_DSE_u_63-EGFP sgTRAC B


title: SV18359-0479


title: E14 TKO cells, Day2, batch1 replicate 13 (SMARTseq2_EpiLC)


title: A375_DSE_u_63-EGFP sgDSE_u_63 C

value: DSE_u_63 sgRNA


title: SV18359-0480


title: SV18359-0486


title: A375_CENPBD2P_p_13-EGFP sgCENPBD2P_p_13 A


title: E14 WT cells, Day2, batch1 replicate 13 (SMARTseq2_EpiLC)


title: SV18359-0478


title: A375_DSE_u_63-EGFP sgDSE_u_63 B


title: E14 TKO cells, Day2, batch1 replicate 12 (SMARTseq2_EpiLC)


title: SV18359-0482


title: A375_DSE_u_63-EGFP sgDSE_u_63 A


title: E14 WT cells, Day2, batch1 replicate 12 (SMARTseq2_EpiLC)


title: A375 Cas9 sgTRAC C


title: A375 Cas9 sgTRAC B


title: A375 Cas9 sgTRAC A


title: SV18359-0477


title: E14 WT cells, Day2, batch1 replicate 14 (SMARTseq2_EpiLC)


title: SV18359-0476


title: E14 TKO cells, Day2, batch1 replicate 11 (SMARTseq2_EpiLC)


title: SV18359-0475


title: A375 Cas9 sgNUTF2_u_11 C


title: A375_DSE_u_63-EGFP sgTRAC A


title: A375 Cas9 sgNUTF2_u_11 A


title: A375 Cas9 sgNUTF2_u_11 B


title: SV18359-0474


title: A375 Cas9 sgCENPBD2P_p_13 C


title: SV18359-0473


title: E14 WT cells, Day2, batch1 replicate 10 (SMARTseq2_EpiLC)


title: SV18359-0472


title: E14 WT cells, Day2, batch1 replicate 11 (SMARTseq2_EpiLC)


title: A375 Cas9 sgDSE_u_63 C


title: A375 Cas9 sgDSE_u_63 B


title: E14 TKO cells, Day2, batch1 replicate 9 (SMARTseq2_EpiLC)


title: Total RNA from iKO MEFs grown in galactose medium - Rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Basic QC and mapping were performed using snakePipes v.2.5.1
Reads were trimmed using cutadapt and aligned to the hg38 or mm10 genome assembly using STAR.
Counts for individual genes were obtained using featureCounts.
Differential expression analysis was performed using DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: DESeq2 LFC output in tsv format

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Both MEFs and HDFs were cultured in High Glucose DMEM supplemented with GlutaMax, 10 % FBS and penicillin-streptomycin at 37 °C and 5 % CO2.

extract_protocol:
Total RNA was collected using Trizol and purified using Zymo Research DirectZol RNA Mini Prep Kit.
Libraries were prepared according to the instructions of Illumina's Stranded RNA with RiboZero Plus kit.

treatment_protocol: For glucose/galactose adaption experiment in primary MEFs, cells were cultured in no-glucose growth medium supplemented with either 25 mM glucose or galactose for 2 weeks followed by 4-OHT treatment for additional 4 days.

value: Galactose +Tamoxifen

value: MOF fl/fl, Cre-ERT2 T/+

tag: disease state

value: MOF KO


title: Total RNA from iKO MEFs grown in galactose medium - Rep1


title: E14 WT cells, Day2, batch1 replicate 9 (SMARTseq2_EpiLC)


title: SV18359-0471

value: serum

value: F


title: E14 TKO cells, Day2, batch1 replicate 8 (SMARTseq2_EpiLC)


title: Total RNA from iWT MEFs grown in galactose medium - Rep1

value: MOF fl/fl, Cre-ERT2 -/-

value: MOF WT


title: Total RNA from iKO MEFs grown in glucose medium - Rep2

value: Glucose +Tamoxifen


title: Total RNA from iWT MEFs grown in galactose medium - Rep2


title: SV18359-0469

value: M


title: Total RNA from iKO MEFs grown in glucose medium - Rep1


title: Total RNA from iWT MEFs grown in glucose medium - Rep2


title: A375 Cas9 sgCENPBD2P_p_13 A


title: A375 Cas9 sgCENPBD2P_p_13 B


title: E14 TKO cells, Day2, batch1 replicate 10 (SMARTseq2_EpiLC)

value: WT


title: Total RNA from iWT MEFs grown in glucose medium - Rep1


title: SV18359-0468


title: A375 Cas9 sgDSE_u_63 A


title: E14 WT cells, Day2, batch1 replicate 7 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: E14 WT cells, Day2, batch1 replicate 8 (SMARTseq2_EpiLC)

value: EpiLC differentiation


title: rdr1-1 TuMV-6K2:Scarlet inoculation 16 dpi rep 1

city: Vienna

first: Ruben

last: Gutzat

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute GmbH

data_processing:
Reads were trimmed to 21 - to 24-nt in length (cutadapt v 1.18) with parameters "cutadapt -a AACTGTAGGCACCATCAAT -g GTTCAGAGTTCTACAGTCCGACGATC -m 21 -M 24 --discard-untrimmed"
Trimmed reads are aligned to Arabidopsis TAIR 10 Genome using bowtie2 (v 2.3.5.1) with parameters "bowtie2 -k 1000 --no-unal"
Raw count table was achieved by using featureCounts from subread (v 2.0.1) with parameter "featureCounts -s 0 -M --fraction -t gene,transposable_element"
Raw counts were normalized to read per million (RPM)
Assembly: TAIR10
Supplementary files format and content: Matrix table with normalized read per million for every gene and transposon for every sample. The table contains GeneID, 21nt, 22nt, 23nt and 24nt RPM count of col-0 control replica 1, col-0  control replica 2, col-0 TuMV infection rep 1, col-0 TuMV infection rep 2, rdr1 control replica 1, rdr1 control replica 2, rdr1 TuMV infection rep 1, rdr1 TuMV infection rep 2

organism: Arabidopsis thaliana

source_name: Inflorescence apices (apical stem + meristem + youngest flower buds)

growth_protocol: Plants were grown in soil under LED illumination and 12h light/12h darkness cycles, watering twice a week. At 25 days after germination plants were inoculated and transferred to 16h light/8h dark to induce flowering.

extract_protocol:
RNA was extracted with TRI reagent and chloroform, acqueous phase added to 1 vol isopropanol and precipitation allowed O/N. After centrifugation, pellett was washed twice with 80% EtOH, dried and resuspended in RNAse-free water.
QIAGEN miRNA-seq #331502

treatment_protocol: Inoculum consisted of N. benthamiana leaves systemically infected by TuMV-6K2:Scarlet following agro-inoculation with the corresponding plasmid. Inoculum was stored at -80C. To inoculate Arabidopsis, first the inoculum was pulverized in liquid nitrogen and resuspended in sodium phosphate pH 7.2 50 mM + 0.2% sodium sulfite, cleared by centrifugation and kept on ice. Leaves were sprinkled with Celite and inoculum was rubbed with cotton swabs.

tag: ecotype

value: TuMV-6K2:Scarlet rub inoculation


title: E14 TKO cells, Day2, batch1 replicate 7 (SMARTseq2_EpiLC)

tag: time


title: SV18359-0470

tag: tissue


title: Output 3ABri

city: Barcelona

first: Mariano

last: Martín

address: c/ Baldiri Reixac 10-12

country: Spain

institute: IBEC

description:
PCR amplicon
from plasmid library

data_processing:
FastQ files from paired-end sequencing of each library library before (‘input’) and after selection (‘output’) were processed using the DiMSum pipeline (https://github.com/lehner-lab/DiMSum)
Supplementary files format and content: aa_seq = amino acid sequence, ID= Mutation identifier, mean_count= mean read count of the input replicates, nscore_c= Merged nucleation score centered to WT, nscore[1,2,3]_c= Nucleation score for [1,2,3] replicates, sigma= Merged error over nucleation score.

source_name: yeast culture

growth_protocol: Yeast cells were transformed with the plasmid libraries in 3 biological replicas. A minimum of 60,000 yeast transformants were used for each replicate to ensure the coverage of the full library and reaching therefore a >50x coverage of each variant. Once the culture reached the exponential phase, cells were resuspended in 100mL protein inducing medium (-URA, 20% glucose, 100uM Cu2SO4) at OD600=0.05. Selection was performed afterwards. After 24h 5ml input pellets were collected and stored at -20C for later DNA extraction (input pellets). In parallel, 1 million cells/replicate were plated on -ADE-URA selection medium in 145cm2 plates. Plates were incubated at 30 C for 7 days inside an incubator. Finally colonies were scraped off the plates with PBS 1x, harvested by centrifugation and stored at -20C for later DNA extraction (output pellets).

extract_protocol:
The input and output pellets (3 biological replicates) were thawed and resuspended in 2ml extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris pH 8, 1mM EDTA pH 8), and underwent two cycles of freezing and thawing in an ethanol-dry ice bath (10 min) and at 62C (10min).  Samples were then vortexed together with 1.5ml of phenol:chloroform:isoamyl 25:24:1 and 1.5g of glass beads (sigma). The aqueous phase was recovered by centrifugation and mixed again with 1.5ml phenol:chloroform:isoamyl 25:24:1. DNA precipitation was performed by adding 1:10V of 3M NaOAc and 2.2V of 100% cold ethanol to the aqueous phase and incubating the samples at -20C for 1h. After a centrifugation step, pellets were dried overnight at room temperature. Pellets were resuspended in 1ml resuspension buffer (10mM Tris pH 8, 1mM EDTA pH 8) and treated with 7.5ul RNase A (Thermo Scientific) for 30min at 37C. The DNA was finally purified using 75ul of silica beads (QIAEX II Gel Extraction Kit, Qiagen), washed and eluted in 375ul elution buffer.
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 25 million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Ilumina sequencing primers. PCR products from the first step were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. DNA concentration was then quantified by means of a Quant-iT™ PicoGreen® dsDNA Assay Kit (Promega). All replicates were pooled together in an equimolar ratio. Finally, the pooled sequencing library was run on a 2% agarose gel, purified and sent for 125 bp paired-end Illumina sequencing.
Libraries were synthesized by Integrated DNA Techonologies (IDT) as oligo pools covering the ADan and/or ABri 102 nt sequence, flanked by 25 nt upstream and 21 nt downstream constant regions for cloning.

value: yeast culture

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)


title: Input 2ABri

description:
PCR amplicon
from plasmid library


title: Input 3ABri

description:
PCR amplicon
from plasmid library


title: Output 2ABri

description:
PCR amplicon
from plasmid library


title: E14 TKO cells, Day2, batch1 replicate 6 (SMARTseq2_EpiLC)

tag: cell line


title: rdr1-1 mock inoculation 16 dpi rep 2

value: Inflorescence apices (apical stem + meristem + youngest flower buds)

value: Mock inoculation (buffer only)


title: Input 1ABri

description:
PCR amplicon
from plasmid library


title: E14 WT cells, Day2, batch1 replicate 6 (SMARTseq2_EpiLC)


title: Output 3ADan

description:
PCR amplicon
from plasmid library


title: rdr1-1 mock inoculation 16 dpi rep 1


title: E14 TKO cells, Day2, batch1 replicate 5 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 5 (SMARTseq2_EpiLC)


title: rdr1-1 TuMV-6K2:Scarlet inoculation 16 dpi rep 2


title: Input 2ADan

description:
PCR amplicon
from plasmid library


title: Input 1ADan

description:
PCR amplicon
from plasmid library


title: WT TuMV-6K2:Scarlet inoculation 16 dpi rep 1


title: WT TuMV-6K2:Scarlet inoculation 16 dpi rep 2


title: Output 2ADan

description:
PCR amplicon
from plasmid library


title: Output 1ABri

description:
PCR amplicon
from plasmid library


title: Sclerotinia sclerotiorum rapeseed, treated, Day2, biol  rep 3

city: chongqing

first: binnian

last: tian

address: tianshenglu

institute: binniantian

data_processing:
Sclerotinia sclerotiorum Genomics
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Sclerotinia sclerotiorum genomic benchwork
Trimmed sequence reads were mapped to Sclerotinia sclerotiorum genomic benchwork
Read count extraction and normalization were performed using Sclerotinia sclerotiorum genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sclerotinia sclerotiorum

source_name: Rapeseed stem

growth_protocol: wheat and rapeseed seedlings grow on MS

extract_protocol:
RNA was harvested using TRIzol Plus RNA Purification Kit (Takara). 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Rapeseed stem

value: QingYou 1

value: Sclerotinia sclerotiorum

value: Day 2


title: Input 3ADan

description:
PCR amplicon
from plasmid library


title: WT mock inoculation 16 dpi rep 2


title: Sclerotinia sclerotiorum rapeseed, treated, Day2, biol  rep 2


title: Sclerotinia sclerotiorum rapeseed, treated, Day2, biol  rep 1


title: E14 TKO cells, Day2, batch1 replicate 4 (SMARTseq2_EpiLC)


title: E14 WT cells, Day2, batch1 replicate 4 (SMARTseq2_EpiLC)


title: WT mock inoculation 16 dpi rep 1


title: Sclerotinia sclerotiorum wheat, treated, Day2, biol  rep 3

source_name: Wheat root

value: Wheat root

value: Zheng 9023


title: E14 TKO cells, Day2, batch1 replicate 3 (SMARTseq2_EpiLC)


title: Sclerotinia sclerotiorum wheat, treated, Day2, biol  rep 2


title: Sclerotinia sclerotiorum wheat, treated, Day2, biol  rep 1


title: E14 WT cells, Day2, batch1 replicate 3 (SMARTseq2_EpiLC)


title: Output 1ADan

description:
PCR amplicon
from plasmid library


title: Sclerotinia sclerotiorum, Control, Day2, biol  rep 3

source_name: mycelium

value: mycelium

value: control


title: 94_95_CTRL (reanalysis)

city: New Haven

first: John

last: McDonough

state: CT

address: 300 Cedar St

institute: Yale School of Medicine

data_processing:
Basecalling was performed with Ion Torrent Suite 5.0.5.
After quality control for adapter contamination and trimming, fastq files were mapped on human genome (Hg38) by combinations of Tophat and Bowtie2 softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1.
Assembly: hg38
Supplementary files format and content: Matrix table with FPKM gene counts for every gene and every sample.

source_name: Lung

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen) from each core according to the manufacturer protocol. RNA concentration and integrity were measured by using NanoDrop ND-2000 and 2200 Tape Station.
20 ng RNA input was used for library preparation by AmpliSeq Transcriptome Human Gene Expression kit. The cDNA was then amplified and barcoded using the Ion Xpress RNA-Seq Barcode 1-16 Kit (Life Technologies 4475485). The Ion Chip Kit v2 BC (Life Technologies 4484270) was then loaded using the Ion Chef System (Life Technologies 4484177) with the Ion PI IC 200 Kit (Life Technologies 4488377). Afterwards, the chips were run on the Ion Proton System for Next-Generation Sequencing (Life Technologies 4476610) using the Ion PI IC 200 Kit.

treatment_protocol: Following explantation, lungs were inflated to 30 cm H2O and held at 10 cm H2O pressure inflation while frozen over liquid nitrogen vapor. The frozen lung was imaged using a high resolution CT scanner and cut into 2 cm thick slices along the transverse plane for sampling. Cores were systematically sampled from each slice using a 1.4 cm diameter coring drill. For this study, 4 cores were randomly selected per lung.

value: Lung

tag: disease

value: Control (donor)

tag: subject

tag: surface density

tag: tissue percentage

tag: terminal bronchioles/ ml

tag: smoking ever

value: no

tag: age transplant

tag: gender

value: Male


title: 94_82_CTRL (reanalysis)


title: E14 TKO cells, Day2, batch1 replicate 2 (SMARTseq2_EpiLC)

tag: cell type

value: Embryonic stem cells (murine)

value: WT

value: EpiLC differentiation


title: Sclerotinia sclerotiorum, Control, Day2, biol  rep 1

tag: genotype


title: 94_48_CTRL (reanalysis)


title: E14 TKO cells, Day2, batch1 replicate 1 (SMARTseq2_EpiLC)

tag: treatment


title: 94_42_CTRL (reanalysis)


title: rdr1-1 TuMV-6K2:Scarlet inoculation 16 dpi rep 1

city: Potsdam

first: Marco

last: Incarbone

address: 1 Am Muehlenberg

institute: Max Planck Institute of Molecular Plant Physiology

data_processing:
Smart-seq3 sequencing libraries were generated and sequencing reads were processed with nf-core/rnaseq. Due to the redundancy of the TAIR annotations "transposable element" and "transposable element gene," we used a custom annotation file containing TAIR10 features plus “transposable elements” without “transposable element genes” and added sequences of transgenes (see DOI 10.1101/2022.01.25.477718 for details).
The following specifications deviated from the default of the rnaseq pipeline: --additional_fasta (containing the sequence for Clover and TuMV_6K2_Scarlet), --clip_r1 19, --three_prime_clip_r1 2.
Differential gene expression analysis was performed with DESeq2. Visualization of the data was achieved using R and Bioconductor including the packages tidyverse and ggplot2
Raw counts were normalized to transcripts per million (TPM)
Assembly: TAIR10
Supplementary files format and content: Table with transcripts per million(TPM) and log2 fold enrichment in indicated pairwise comparisons between genotypes/conditions, with relative p value and adjusted p value, for every gene and transposon of the samples. The table contains GeneID, col-0 mock replica 1, col-0  mock replica 2, col-0 TuMV infection rep 1, col-0 TuMV infection rep 2, rdr1 mock replica 1, rdr1 mock replica 2, rdr1 TuMV infection rep 1, rdr1 TuMV infection rep 2

extract_protocol:
RNA was extracted with TRI reagent and chloroform, acqueous phase added to 1 vol isopropanol and precipitation allowed O/N. After centrifugation, pellett was washed twice with 80% EtOH, dried and resuspended in RNAse-free water.
Smartseq3 (DOI 10.1038/s41587-020-0497-0)

value: Inflorescence apices (apical stem + meristem + youngest flower buds)

value: TuMV-6K2:Scarlet rub inoculation


title: rdr1-1 mock inoculation 16 dpi rep 1

value: Mock inoculation (buffer only)


title: E14 WT cells, Day2, batch1 replicate 2 (SMARTseq2_EpiLC)


title: rdr1-1 mock inoculation 16 dpi rep 2


title: WT TuMV-6K2:Scarlet inoculation 16 dpi rep 2


title: rdr1-1 TuMV-6K2:Scarlet inoculation 16 dpi rep 2


title: 63_98_CTRL (reanalysis)


title: 63_69_CTRL (reanalysis)


title: E14 TKO cells, Day1, batch1 replicate 48 (SMARTseq2_EpiLC)


title: WT mock inoculation 16 dpi rep 1


title: WT TuMV-6K2:Scarlet inoculation 16 dpi rep 1


title: WT mock inoculation 16 dpi rep 2


title: 63_63_CTRL (reanalysis)


title: E14 WT cells, Day1, batch1 replicate 48 (SMARTseq2_EpiLC)


title: Sclerotinia sclerotiorum, Control, Day2, biol  rep 2


title: Cor-15 snRNA

city: Singapore

first: Meng

last: Liu

state: Singapore

address: 11 Mandalay road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
Both snATAC and snRNA sequenced reads were aligned to the Hg38 with Cell ranger ARC 2.0.2
The output files of Cellranger ARC are used for cell clustering with Seurat and Signac
Supplementary files format and content: Hg38
Supplementary files format and content: The snATAC fragments files and snRNA matrix file

molecule: nuclear RNA

source_name: kidney organoid

growth_protocol: Kidney organoids were generated based on the Low et al., 2019 Cell stem cell protocol

extract_protocol:
All of the organoids were treated with 5um FSK for 3 days before collection. The protocol for nuclei isolation is modified based on 10x Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000375). Breifly, the organoids were treated with 0.1% NP40 lysis buffer and homogenized with Dounce tissue grinder (KIMBLE KONTES; 885500-0019) for 5 mins on ice. The suspension was further filtered through a 40 μm cell strainer (pluriSelect) and centrifuged at 500 × g for 5 min at 4 °C. The supernatant was removed. The pellet was washed with wash buffer for three times, then resuspended in pre-cooled nuclei buffer.
10x Chromium Next GEM Single-Cell Multiome ATAC + Gene Expression kit  was used for library preparation according to the instruction
10X single nuclei multiomics kit is suitable to sequencing both ATAC and RNA library from the same cell.

treatment_protocol: Kidney organoids were treated with Forskolin for 3 days

value: kidney organoid

value: PKD patient-derived iPSCs

value: PKHD1 correction

value: Forskolin

value: 3 days


title: Epi-17KIF3AKO snRNA

value: PKHD1 mutation, KIF3A mutation


title: Epi-17 KIF3AKO snATAC

description: nuclear chromation open region

library_source: genomic single cell


title: 63_28_CTRL (reanalysis)


title: E14 WT cells, Day1, batch1 replicate 47 (SMARTseq2_EpiLC)


title: Epi-17 snATAC

description: nuclear chromation accessible region

value: PKHD1 mutation


title: E14 TKO cells, Day1, batch1 replicate 47 (SMARTseq2_EpiLC)


title: 222_65_CTRL (reanalysis)

value: Lung

value: Female


title: 222_77_CTRL (reanalysis)

value: Control (donor)

value: no


title: E14 WT cells, Day2, batch1 replicate 1 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)


title: E14 WT cells, Day1, batch1 replicate 46 (SMARTseq2_EpiLC)

value: WT


title: E14 TKO cells, Day1, batch1 replicate 46 (SMARTseq2_EpiLC)

value: EpiLC differentiation


title: Breast Cancer, T2N1M0, 3' single-cell

city: Pleasanton

first: Stephen

middle: Richardson

last: Williams

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

description: 10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranfer v7.0.1 or Space Ranger v2022.0705.1 pipelines to generate FASTQ files
Sequences were aligned to human genome GRCh38-2020-A or probe set reference to obtain gene expression counts using Cell or Space Ranger's default settings
Assembly: Human reference, GRCh38

source_name: Disassociated Breast Cancer

extract_protocol:
For the Chromium Flex workflow, two 25 μm curls were pooled as a single replicate. 5 μm sections from Sample #1 were taken from the FFPE tissue using a microtome. Two replicate 5 μm sections were taken each for Visium CytAssist and Xenium. Corresponding dissociated tumor cells for Sample #1, fresh frozen (FF) in liquid nitrogen, were also sampled from the same 2.5 cm biopsy.  A 5 μm section was also taken from Sample #2 for Xenium.
Library prep was performed according to 10x Genomics protocols.  5' GEX: https://www.10xgenomics.com/support/single-cell-immune-profiling/documentation/steps/library-prep/chromium-single-cell-5-reagent-kits-user-guide-v-2-chemistry-dual-index; 3' GEX: https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry-dual-index; scFFPE-seq (Flex): https://www.10xgenomics.com/support/single-cell-gene-expression-flex/documentation/steps/library-prep/chromium-single-cell-gene-expression-flex-reagent-kits-for-singleplexed-samples-optional-with-feature-barcode-technology-for-cell-surface-protein; Visium CytAssist: https://www.10xgenomics.com/support/spatial-gene-and-protein-expression/documentation/steps/library-construction/visium-cytassist-spatial-gene-and-protein-expression-reagent-kits;

value: Disassociated Breast Cancer


title: Breast Cancer, T2N1M0, 5' single-cell

description: 10x Genomics


title: 222_56_CTRL (reanalysis)


title: Breast Cancer, Visium CytAssist Spatial Gene Expression

description: 10x Genomics

source_name: 5 µm section Breast Cancer

value: 5 µm section Breast Cancer


title: Breast Cancer, Single Cell Gene Expression Flex

description: 10x Genomics


title: E14 TKO cells, Day1, batch1 replicate 45 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 2200mGy, input, rep4

city: Chalk River

first: Richard

middle: B.

last: Richardson

state: Ontario

address: 286 Plant Rd

department: Radiobiology and Health

country: Canada

institute: Canadian Nuclear Laboratories

data_processing:
Quality control was conducted using FastQ Screen (v0.4.1) and FastQC (v0.11.9).
Trimming was performed using TrimGalore (v0.6.6) with parameters: --clip_R1 1; --clip_R2 1; --three_prime_clip_R1 1; - three_prime_clip_R2 1; --trim-n; --length 50; -q 20 and --stringency 5. Quality of trimmed filtered reads was revaluated using FastQC (v0.11.9).
Alignment to the human reference genome GRCh38 was conducted using BWA (v0.7.17) in the paired-end mode of the BWA-MEM algorithm with the default parameter settings.
Mapped read files (*.sam) were converted to sorted BAM files by SAMtools (v1.11). Unmapped reads were filtered out using SAMtools (v1.11).
Bioconductor package MEDIPS (v1.40.0) was used to identify differentially methylated regions (DMRs) between controls and irradiated cells for both regimens with ws=50 bp; shift=0 and uniq=1.
Differential coverage was calculated using the edgeR function in MEDIPS with minRowSum=5 and quantile normalization. P-values were adjusted for multiple testing using the FDR method. Statistically significant methylation coverage results were selected using the criteria of FDR<0.05.
Genomic annotation was carried out using HOMER (v4.11). Neighboring significant regions located within the same chromosome, and with the same annotation and Gene ID, were merged using an in-house Python script.
Assembly: GRCh38
Supplementary files format and content: Bam files include only mapped sorted reads for each sample
Supplementary files format and content: RData files include differential coverage results using the edgeR function (mr.edgeR). When available, it also includes specific data extracted from the "mr.edgeR" file as follows:  differential coverage results with unadjusted P value<0.05 (mr.edgeR.sna), differential coverage results with FDR<0.1 (mr.edgeR.s0.1), differential coverage results with FDR<0.05 (mr.edgeR.s), differential coverage results with FDR<0.05 of hyperDMRs (mr.edgeR.s.gain), differential coverage results with FDR<0.05of hypoDMRs (mr.edgeR.s.lost)

growth_protocol: WI-38 cells were maintained in EMEM medium supplemented with 10% fetal bovine serum (FBS), 50 U/mL Penicillin, 50 µg/mL Streptomycin, and 2 mM L-Glutamine in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total DNA was extracted using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol with minor modifications.
Cell pellets were resuspended in PBS and treated with proteinase K and RNase A. The DNA-loaded spin columns were washed three times with buffer AW2. DNA was then eluted in Tris-EDTA (TE) buffer (low EDTA, pH 8.0) after 5 m at RT. DNA samples displayed A260/A280 ratios in the range of 1.8 to 2.0 and A260/A230 ratios higher than 2.1.
DNA was sheared into ~200 bp fragments using a Covaris S220 focused ultrasonicator. Libraries were constructed with 1.2 μg of DNA using a NEBNext Ultra II DNA library prep kit for Illumina following the manufacturer’s guidelines. Immunoprecipitation with a 5mC antibody was conducted using a Diagenode MagMeDIP kit as described in the manufacturer’s protocol with starting volume of 15 µL. The immunoprecipitated adaptor-ligated DNA and Input fraction were purified with a Diagenode IPure kit v2 according to the manufacturer’s instructions.
The libraries from the Input fraction and IP DNA were linked to unique dual index primers (New England Biolabs) and amplified by PCR using a NEBNext Ultra II DNA library prep kit for Illumina with 7 cycles for the Input and 8 for the IP samples. The PCR products were further purified and size selected using NEBNext sample purification beads. Libraries were quantified using a KAPA library quantification kit.

treatment_protocol:
Cells were irradiated to seven doses of americium-241 α-sources ranging from 2.0 to 2,200 mGy using two exposure regimens, a single-fraction where the total dose was given at once, and a multi-fraction method, where the total dose was equally distributed over 14 consecutive days.
Cells in both exposure regimens were trypsinized and collected after the last irradiation following 1 h incubation at 37 °C in a 5% CO2 humidified atmosphere. Collected cells were immediately flash-frozen in liquid nitrogen and subsequently stored at -80 °C.

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

tag: dose (mgy)

tag: radiation regimen

value: multi-fraction

tag: total number_of_fractions

tag: antibody


title: WI-38 cells, multi-fraction, 2200mGy, input, rep3


title: 191_95_CTRL (reanalysis)

tag: tissue


title: WI-38 cells, multi-fraction, 2200mGy, input, rep2

tag: cell line


title: Cor-15 snATAC

description: nuclear chromation open region

value: kidney organoid

value: PKD patient-derived iPSCs

value: PKHD1 correction


title: E14 WT cells, Day1, batch1 replicate 45 (SMARTseq2_EpiLC)

tag: time


title: WI-38 cells, multi-fraction, 2200mGy, input, rep1


title: Epi-17 snRNA

value: Forskolin

value: 3 days


title: 191_71_CTRL (reanalysis)

value: Lung

tag: disease

tag: subject


title: WI-38 cells, multi-fraction, 1100mGy, input, rep4


title: E14 WT cells, Day1, batch1 replicate 44 (SMARTseq2_EpiLC)


title: E14 TKO cells, Day1, batch1 replicate 44 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 1100mGy, input, rep1


title: 191_30_CTRL (reanalysis)

tag: surface density

tag: tissue percentage

value: Female


title: WI-38 cells, multi-fraction, 1100mGy, input, rep3


title: WI-38 cells, multi-fraction, 220mGy, input, rep4


title: WI-38 cells, multi-fraction, 1100mGy, input, rep2


title: E14 TKO cells, Day1, batch1 replicate 43 (SMARTseq2_EpiLC)


title: 222_42_CTRL (reanalysis)

value: Control (donor)

tag: terminal bronchioles/ ml

tag: smoking ever


title: 293FT, RNAseq, Cas13d, R3

data_processing:
The RNA-seq reads were aligned against the hg38 human reference genome using HISAT2.
Count table generated by htseq-count using gencode.v38.basic.annotation.gtf
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each gene

source_name: human embryonal kidney cells

growth_protocol: 293FT cells were regularly tested negative for mycoplasma contamination and maintained in DMEM (SEVEN Biotech) supplemented with 10% fetal bovine serum (ExCell) and 1% penicillin–streptomycin (Solarbio). Cells were passaged every 2-4 days to maintain exponential growth and were kept in a humidity-controlled incubator at 37°C with 5% CO2.

extract_protocol: Total RNA from cells is isolated using The Invitrogen Life Technologies TRIzol Reagent (Total RNA Isolation Reagent)

treatment_protocol: Plasmid expressing Cas9 or Cas13 protein were  transfected into 293FT cells using Lipofectamine™ 2000 Transfection Reagent.

value: kidney

tag: transfection

value: Day 3 after transient transfection


title: 293FT, RNAseq, Cas13d, R2


title: WI-38 cells, multi-fraction, 220mGy, input, rep3

tag: cell type


title: 175_58_CTRL (reanalysis)

value: yes

tag: age transplant

tag: gender

value: Male


title: WI-38 cells, multi-fraction, 220mGy, input, rep2

tag: treatment

tag: dose (mgy)


title: 175_67_CTRL (reanalysis)


title: E14 WT cells, Day1, batch1 replicate 43 (SMARTseq2_EpiLC)

value: Embryonic stem cells (murine)

tag: genotype

value: WT

value: EpiLC differentiation


title: E14 WT cells, Day1, batch1 replicate 42 (SMARTseq2_EpiLC)


title: 175_22_CTRL (reanalysis)


title: E14 TKO cells, Day1, batch1 replicate 42 (SMARTseq2_EpiLC)


title: 293FT, RNAseq, Cas13d, R1


title: 175_45_CTRL (reanalysis)


title: E14 TKO cells, Day1, batch1 replicate 41 (SMARTseq2_EpiLC)


title: 293FT, RNAseq, Cas13b, crNT, R3


title: 293FT, RNAseq, Cas13b, crNT, R2


title: 145_4_CTRL (reanalysis)

value: no


title: WI-38 cells, multi-fraction, 110mGy, input, rep3

value: Human fibroblast from 3-month-old female lung tissue

value: alpha-irradiation

tag: radiation regimen

value: multi-fraction

tag: total number_of_fractions

tag: antibody


title: 191_37_CTRL (reanalysis)

tag: tissue


title: 293FT, RNAseq, Cas13b, crNT, R1

tag: cell line

tag: time


title: E14 WT cells, Day1, batch1 replicate 41 (SMARTseq2_EpiLC)


title: WI-38 cells, multi-fraction, 110mGy, input, rep2