title: strain 1cA657V-7B1, biological replicate 1

description: Library name: 2327312_ksb010

value: fungal strain


title: strain 1cADdel-10A, biological replicate 3

status: Public on Jul 28 2025

type: SRA

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 262 Danny Thomas Place, Mail Stop 313, Room I5200

department: Pharmacy & Pharmaceutical Sciences

country: USA

institute: St. Jude Children's Research Hospital

description: Library name: 2327311_ksb009

library_source: transcriptomic

data_processing:
Data were analyzed using the Galaxy web platform public server at usegalaxy.org.
Read quality was assessed and reads were quality-trimmed with a PHRED cutoff of 20 using FastP.
Reads were then mapped to the C. auris B8441 reference assembly (NCBI GCA_002759435.2) using RNA Star with default parameters followed by quantification using featureCounts and assessment of differential expression using DESeq2.
Transcriptional overlap between strains was assessed using either UpsetR R Package or DiVenn 2.0.
Assembly: GCA_002759435.2
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

molecule: total RNA

organism: Candidozyma auris

source_name: fungal strain

growth_protocol: For RNA isolation an aliquot of cells from an overnight culture of each strain was used to inoculate 10 ml MOPS-buffered RPMI + 2% glucose (pH 7.0) to a OD600=0.08-0.12, and the diluted culture was incubated at 35degC in a shaking incubator (220 rpm) until it reached mid-log phase (6 hrs).

extract_protocol:
Cells were collected by centrifugation, supernatants removed, and the cell pellets stored at -80degC until RNA isolation. Cell cultures were grown in triplicate. Cell pellets were thawed and resuspended in 100 µl FE Buffer (98% formamide, 0.01 M EDTA) at room temperature. Fifty microliters of 1 mm RNase-free glass beads was added, and the cells were disrupted in a vortex disruptor for 5 min at room temperature followed by snap-cooling on ice. The cell lysate was centrifuged to remove cell debris, and the crude RNA extract collected from the supernatant. The extract was DNase-treated for 30 min and precipitated by isopropanol precipitation. RNA integrity was confirmed through agarose gel electrophoresis using the bleach gel method, and concentrations were approximated by Nanodrop.
RNA sequencing was performed using Illumina NextSeq for stranded mRNA. Libraries were prepared with paired-end adapters using Illumina chemistries per manufacturer’s instructions, with read lengths of approximately 150 bp with at least 50 million raw reads per sample.

tag: cell type

tag: genotype


title: donor2_CBE

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Library name: Gen-EBES1_6RNA

data_processing:
Read quality was assessed using FastQC [version 0.11.9]. Adapter sequences and low-quality bases (Q < 20) were trimmed from raw reads with BBDuk [version 38.92]; moreover, the first 10 nucleotides were force-trimmed for low quality. Reads shorter than 35 bp post-trimming were discarded.
Trimmed reads were aligned to the human reference genome (hg38) using STAR [version 2.7.9a]. Raw gene counts were generated in R-4.1.1 using the featureCounts function of the Rsubread package [version 2.8.1] and the GENCODE 44 basic gene annotation for hg38 reference genome.
Raw gene counts were normalized to counts per million mapped reads (CPM) and to fragments per kilobase of exon per million mapped reads (FPKM) using the edgeR R package [version 3.36.0]; only genes with a CPM greater than 1 in at least 3 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: FPKM obtained using edgeR

organism: Homo sapiens

source_name: Bone marrow

growth_protocol: Cells were cultured in pre-activation medium for 48 h before electroporation and 48 h after the electroporation

extract_protocol:
Total RNA was isolated from control or edited bone marrow derived-SCD HSPCs using the quick-DNA/RNA miniprep kit (Zymo)
RNA-seq libraries were prepared starting from 30 ng to 50 ng of total RNA using Watchmaker RNA kit with Polaris Depletion - rRNA/Globin (HMR) as recommended by the manufacturer.

treatment_protocol: Cells were electroporated with a combination of base editors mRNA or Cas9 nuclease RNP and sgRNA targeting the+58-kb and the +55-kb enhancers of BCL11A, and then cultured for 2 additional days. Cells electroporated with TE buffer only were used as controls.

tag: tissue

value: Bone marrow

value: SCD CD34+ HSPCs

value: SCD

tag: treatment

value: electroporated with AncBE4max mRNA and GATA_bs_1 and ATF4_bs_2 sgRNA


title: WT_stageII_oocyte_rep2

city: Beijing

first: Xiaotong

last: Wu

address: Haidian

country: China

institute: Tsinghua University

data_processing:
RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low-quality reads.
The filtered data were then mapped to the zebrafish reference genome (danRer11) by STAR (version: STAR_2.5.3a_modified).
The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1).
Assembly: danRer11
Supplementary files format and content: tab-delimited ext file includes FPKM values for each samples
Supplementary files format and content: The RNA-seq data were first processed using Trim Galore! with default parameters to trim the adapter-containing and low-quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer11) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilter-MultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to FPKM values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).

molecule: polyA RNA

organism: Danio rerio

source_name: oocyte

extract_protocol:
In the context of the current investigation, a protocol for the isolation of oocytes from juvenile female fish was developed, aimed at maximizing yield and maintaining cellular integrity. The first step involved the euthanization of the WT and znf706-/- juvenile female fish (3-month-old) by submerging them in an ice-water mixture. After euthanization, the abdominal cavity of the fish was carefully opened using surgical scissors and the ovaries were bilaterally detached from the abdomen by utilizing forceps. The excised ovaries were promptly transferred into a 6-well plate preloaded with 2 ml digestive buffer (cell dissociation buffer, PCM, PC-33689) and incubated for 2-3 hrs at a temperature of 28.5℃. To enhance the efficacy of the digestive process, the 6-well plate was shaken every half hour during incubation. Once the digestion period was complete, the L-15 medium, which had been preheated to 28.5℃, was added to the digestive buffer to halt the digestion process effectively. To eliminate residual impurities, the oocytes were subjected to a series of washing steps involving the addition of fresh L-15 medium, followed by gentle resuspension of the oocytes, a process repeated 2-3 times to ensure thorough cleansing. Approximately 600 stage I oocytes and 150 stage II oocytes were collected manually with a pipette.
All the liquid nitrogen-freezing samples (stages I and II oocytes) were sent to Novogene for RNA-seq library preparation

value: oocyte

value: Wild type


title: donor2_TE

description: Library name: Gen-EBES1_5RNA

value: electroporated with TE buffer only


title: WT_stageII_oocyte_rep1


title: Tendon cells,21 days post-injury,negative

city: Hefei

first: Chao

last: Peng

state: 安徽Anhui

address: 81 Meishan Road

institute: Anhui Medical University

description: Library name: Sample6

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Achilles tendon

extract_protocol:
We have established a controlled longitudinal cohort comprising Gli1-CreERT2; Ai9 reporter mice with tamoxifen induction (n = 24, equal sex distribution). Mice were stratified into three experimental groups: uninjured controls (n = 8) and tenotomy-injured cohorts at 7- and 21-days post-injury (n = 8/group). All samples were collected and subjected to FACS for isolation of Gli1⁺ and Gli1⁻ cells. These sorted cells were lysed and prepared for scRNA-seq.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Achilles tendon

value: Tendon cells


title: strain 1cADdel-10A, biological replicate 1

description: Library name: 2327309_ksb007


title: Tendon cells,21 days post-injury,positive

description: Library name: Sample5


title: strain 1cADdel-10A, biological replicate 2

description: Library name: 2327310_ksb008


title: donor1_DBE

description: Library name: Gen-EBES1_3RNA

value: electroporated with TadDE mRNA and GATA_bs_1 and ATF4_bs_2 sgRNA


title: znf706_stageI_oocyte_rep2


title: Tendon cells,7 days post-injury,negative

description: Library name: Sample4


title: znf706_stageI_oocyte_rep1


title: WT_stageI_oocyte_rep2


title: strain 1c, biological replicate 3

description: Library name: 2327308_ksb006


title: Tendon cells,uninjured control,negative

description: Library name: Sample2


title: donor1_CBE

description: Library name: Gen-EBES1_2RNA


title: WT_stageI_oocyte_rep1


title: Tendon cells,7 days post-injury,positive

description: Library name: Sample3


title: strain 1c, biological replicate 2

description: Library name: 2327307_ksb005


title: Tendon cells,uninjured control,positive

description: Library name: Sample1


title: donor1_Cas9

description: Library name: Gen-EBES1_4RNA

value: electroporated with Cas9-nuclease RNP and GATA_bs_4 and ATF4_bs_4 sgRNA


title: Acas_WGBS

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Library name: WGBS_2

library_source: genomic

data_processing:
WGBS data was mapped to the reference genome using BS-seeker2 with Bowtie2 as a back-end aligner. The resulting bam file was then deduplicated with Sambamba, and the methylation calling done with CGmapTools.
Assembly: Acanthamoeba castellanii: https://zenodo.org/records/6800059, Naegleria gruberi: https://github.com/AlexdeMendoza/6mA_evolution/blob/main/Genomes/Naegleria_gruberi.medakaRagTag.genome.fasta.gz
Supplementary files format and content: CGmap files are described in the BS-Seeker2 github repository: https://github.com/BSSeeker/BSseeker2?tab=readme-ov-file#44-bs_seeker2-call_methylationpy

molecule: genomic DNA

organism: Acanthamoeba castellanii

source_name: axenic culture

growth_protocol: Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712. Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034.

extract_protocol:
DNA was extracted using Monarch
Whole Genome Bisulfite sequencing (EZ DNA Methylation-Gold Kits coupled with EM-seq library prep modules). Includes CpG methylated pUC19 control and unmethylated lambda phage genome control.

treatment_protocol: No treatments were performed.

value: axenic culture

tag: cell line

value: Neff

value: amoeba

value: 23C growth 5 days


title: donor1_TE

description: Library name: Gen-EBES1_1RNA


title: benchmarking_HEK293T_roboATAC_rep8_illumina

status: Public on Jul 27 2025

city: Stanford

first: Betty

middle: B

last: Liu

state: CA

address: 279 Campus Dr W

department: Genetics

institute: Stanford University

description: Library name: SV03_08_illumina

data_processing:
All preprocessing code is available at https://github.com/GreenleafLab/snakeATAC_singularity, following previously described ATAC-seq preprocessing steps. Briefly, we trimmed the Nextera adapter sequences from the reads using the SeqPurge tool from the ngs-bits package (https://github.com/imgag/ngs-bits, v2018_04), aligned reads to the hg38 reference genome using bowtie2 (v2.3.4.3) with standard parameters and a maximum fragment length of 2,000, deduplicated reads with Picard (http://broadinstitute.github.io/picard, v2.25.6), then filtered for high quality (MAPQ ≥ 30), non-mitochondrial chromosome, non-Y chromosome, non-ENCODE blacklist, and properly paired reads using samtools (v1.7) and bedtools (v2.30.0). We called both narrow and broad peaks per sample using Macs2 (v2.1.4) and generated bigwig tracks with deeptools (v3.2.1). The pipeline computes the TSS enrichment ratio using a custom script. The fraction of reads in peaks was calculated as the fraction of reads assigned to the narrow peaks feature set using the featureCounts tool from subread (v2.0.1). We used the SE branch of the Github repository to process single-ended reads generated from Ultima and the main branch to process regular paired-end reads from illumina.
Assembly: hg38
Supplementary files format and content: narrow peaks called from Macs2 and insertion count bigwigs

growth_protocol: HEK293T cells were cultured in DMEM + 10% FBS + 1% PenStrep media. K562, SUDHL5 and Jurkat cells were cultured in RPMI-1640 + 10% FBS + 1% PenStrep media. MCF7 cells were grown in EMEM (ATCC #30-2003) + 10% FBS + 1% PenStrep + 0.01mg/ml insulin media. All cells were incubated at 37C with 5% CO2.

extract_protocol:
OmniATAC: follows standard OmniATAC protocol in Corces et al Nat Methods 2017. RoboATAC: A 96-well plate of cells in media was directly placed on an Agilent Bravo liquid handling platform to begin the automated RoboATAC workflow. Briefly, after removing the media, each well of roughly 50,000 HEK293T cells were lifted in 30uL trypsin for 3 min at 37C, neutralized with 120uL media, and pulled down from trypsin:media solution by binding to 10uL Concanavalin A beads for 10min at room temperature and magnetically separating and removing the supernatant. We added 50uL cold OmniATAC lysis buffer directly to the nuclei pellet, incubated for 3min at 4C, then quenched with 150uL cold OmniATAC wash buffer, magnetically separated and removed the supernatant, added 50uL OmniATAC transposition buffer directly to the pellet, and incubated at 37C for 30min with 1300rpm shaking. For suspension cells, we skipped the trypsinization steps and proceeded directly to ConA bead binding to cells in media.
OmniATAC: follows standard OmniATAC protocol in Corces et al Nat Methods 2017. RoboATAC: To clean up the transposition product, we added 165uL Qiagen buffer RLT directly into the transposition mix, magnetically separated the supernatant from the ConA beads, and transferred the supernatant containing the transposition product into a new plate. We added 10uL Silane beads and 225uL 100% Isopropanol into each well of transposition product, incubated for 2min at room temperature, magnetically separated and removed the supernatant. We washed the pellet twice with 300uL 70% Isopropanol and air dried the pellet for 5 min at room temperature. We eluted the cleaned transposition product with 20uL of H2O for 5min at room temperature, then performed PCR following standard OmniATAC setup for 10 cycles total (72C x 5m, 98C x 30s, then 10 cycles of 98C x 10s + 63C x 30 + 72C x 30s, hold at 4C). The PCR products were cleaned using SPRI beads at a 1.2x ratio following standard SPRI cleanup protocol. TF dose RoboATAC libraries were converted for sequencing on the Ultima Genomics UG 100 sequencer via a conversion PCR reaction (Ultima Protocol Guide D1001055 Rev 01) using 10ng of input DNA, sample-specific UG indexing primers targeting the Nextera Read 1 sequence, and a UG universal primer targeting the Nextera Read 2 sequence. Converted libraries were purified using a SPRI bead ratio of 1.5x.

tag: assay

value: roboATAC


title: benchmarking_HEK293T_roboATAC_rep6

description: Library name: BL146


title: strain 1c, biological replicate 1

description: Library name: 2327306_ksb004

value: fungal strain


title: benchmarking_HEK293T_roboATAC_rep3

description: Library name: BL139


title: benchmarking_HEK293T_roboATAC_rep4

description: Library name: BL140


title: benchmarking_HEK293T_omniATAC_rep3

description: Library name: BL141

value: omniATAC


title: benchmarking_HEK293T_roboATAC_rep7_illumina

description: Library name: SV03_07_illumina


title: benchmarking_Jurkat_roboATAC

description: Library name: BL220

source_name: Jurkat

value: Jurkat


title: benchmarking_HEK293T_roboATAC_rep1

description: Library name: BL137


title: benchmarking_HEK293T_omniATAC_rep1

description: Library name: BL135


title: benchmarking_K562_omniATAC_rep2

description: Library name: BL020


title: benchmarking_K562_roboATAC_rep2

description: Library name: BL024


title: benchmarking_Jurkat_omniATAC

description: Library name: BL218


title: benchmarking_K562_omniATAC_rep3

description: Library name: BL041


title: benchmarking_K562_omniATAC_rep1

description: Library name: BL019


title: benchmarking_K562_roboATAC_rep1

description: Library name: BL023


title: benchmarking_HEK293T_roboATAC_rep5

description: Library name: BL145


title: benchmarking_HEK293T_omniATAC_rep2

description: Library name: BL136


title: benchmarking_HEK293T_omniATAC_rep4

description: Library name: BL142


title: benchmarking_MCF7_roboATAC_rep6

description: Library name: BL162


title: benchmarking_MCF7_roboATAC_rep3

description: Library name: BL159


title: benchmarking_MCF7_roboATAC_rep5

description: Library name: BL161


title: benchmarking_MCF7_roboATAC_rep4

description: Library name: BL160


title: benchmarking_K562_omniATAC_rep4

description: Library name: BL042


title: benchmarking_MCF7_roboATAC_rep2

description: Library name: BL148


title: benchmarking_MCF7_omniATAC_rep4

description: Library name: BL158


title: benchmarking_HEK293T_roboATAC_rep2

description: Library name: BL138


title: benchmarking_SUDHL5_roboATAC_rep3

description: Library name: BL245


title: benchmarking_MCF7_omniATAC_rep2

description: Library name: BL144


title: benchmarking_SUDHL5_omniATAC_rep2

description: Library name: BL238


title: benchmarking_SUDHL5_omniATAC_rep1

description: Library name: BL214


title: benchmarking_MCF7_omniATAC_rep3

description: Library name: BL157


title: benchmarking_MCF7_roboATAC_rep1

description: Library name: BL147


title: benchmarking_SUDHL5_omniATAC_rep3

description: Library name: BL239


title: benchmarking_SUDHL5_roboATAC_rep2

description: Library name: BL244


title: benchmarking_SUDHL5_roboATAC_rep1

description: Library name: BL216


title: benchmarking_MCF7_omniATAC_rep1

description: Library name: BL143


title: RNA_KO_Ibd1_C2

city: Toronto

first: Alejandro

last: Saettone

state: Ontario

address: 686 Bay Street

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
Library name: KO Ibd1C2 RNA-Seq
Fillingham_005_Plate1_Strip1_E01_Ibd1_C2__S52

data_processing:
ChIP-seq reads were assessed for quality using fastqc
ChIP-Seq reads were aligned using BWA and SAMtools
Heursitic method: Peak calling from the genetic and intergenic regions were respectively counted and extracted
MACS2 was use for narrow peaks calling
Peaks normalization and Fold enrichment calculations were performed
Assembly: T_thermophila_June2014_assembly.fasta
Supplementary files format and content: .txt files containing peaks and fold enrichmet were generated using heuristic method and MACS2.
RNA-seq reads were assessed for quality using fastqc
Differentially expression analysis for IBD1 KO RNA-seq data was carried out using DESeq2 (ver 3.11)
on gene counts generated using STAR and the Tetrahymena genome annotation
Genes with less than 10 counts across the sum of all RNA-seq samples were filtered out.
Assembly: T_thermophila_June2014_assembly.fasta
Supplementary files format and content: tsv files with TPKM counts and DEG with fold changes file

organism: Tetrahymena thermophila

source_name: CU428 Ibd1 KO

growth_protocol: 30C; 100rpm; SPP liquid media

extract_protocol:
ChIP-Seq: Lysates were clarified from sonicated nuclei and Ibd1-FZZ-histone-DNA complexes were isolated with ANTI-FLAG® M2 Affinity Gel (Sigma) RNA-Seq: Lysates were used on NEB poly A mRNA magnetic module kit
ChIP-Seq: Illumina's  TruSeq ChIP Sample Preparation Kit (cat# IP-202-1012) RNA-Seq: NEBHI  ultra II directional RNA library prep

value: CU428 Ibd1 KO

value: Vegetative Growth

value: Mpr/Mpr (VII, mp-s) KO bd1

value: Whole cell extraction


title: RNA_WTB

description:
Library name: WTB RNA-Seq
Fillingham_001_Plate1_Strip1_A01_WTB_veg_S26

value: Mpr+/Mpr+ (II, mp-s)


title: RNA_KO_Ibd1_B

description:
Library name: KO Ibd1B RNA-Seq
Fillingham_003_Plate1_Strip1_C01_Ibd1_B__S50

source_name: B2086 Ibd1 KO

value: B2086 Ibd1 KO

value: Mpr+/Mpr+ (II, mp-s) KO Ibd1


title: RNA_WTC

description:
Library name: WTC RNA-Seq
Fillingham_002_Plate1_Strip1_B01_WTC_veg_S27

value: Mpr/Mpr (VII, mp-s)


title: Plate3_TF_MYC_P3D11_dose0.05_rep2

description: Library name: P3D11

data_processing:
All preprocessing code is available at https://github.com/GreenleafLab/RoboATAC. We used cutadapt (v3.5) to trim the TruSeq read 2 adapter from RNA reads and ran the command kallisto quant from the kallisto package (v0.46.2) to efficiently quantify transcript levels. Normalized transcript abundance is reported in TPM.
Assembly: hg38
Supplementary files format and content: transcript abundance reported in both raw counts and TPM, output from kallisto

extract_protocol:
At 48 hours post transfection, we removed the media, added 32uL Trizol to the cells in each well to extract RNA, mixed thoroughly by pipetting, snap froze in dry ice + EtOH and stored the plate at -80C until ready for RNA purification. After thawing the Trizol prepped cells on ice, we used the Zymo Direct-zol-96 RNA kits (Zymo #R2056) to purify RNA.
For RNA library preparation, we sent the total RNA to Novogene for bulk unstranded mRNA library preparation with PolyA enrichment and sequencing on an Illumina NovaSeq X Plus (paired end 150 cycles).

treatment_protocol: We seeded 30k HEK293T cells per well in a 96-well plate with 100uL media per well. Two identical plates were prepared for RoboATAC and RNA-seq. After 24 hours, we transfected each well with a different ratio of TF:GFP plasmids in duplicates while keeping the total amount of plasmids transfected per well at 1ug (ratios: 1:0, 0.75:0.25, 0.5:0.5, 0.25:0.75, 0.05:0.95, 0:1). This ensures a consistent transfection efficiency across different doses. We transfected the cells using FUGENE HD (DNA ug to FUGENE uL ratio = 1:3).


title: Plate3_TF_SPI1_P3F11_dose0.05_rep2

description: Library name: P3F11


title: Plate3_TF_SPI1_P3G11_dose0.05_rep3

description: Library name: P3G11


title: Plate3_TF_GFP_P3A12_dose1_rep1

description: Library name: P3A12


title: Plate3_TF_SPI1_P3H11_dose0.05_rep4

description: Library name: P3H11


title: RNA_KO_Ibd1_C

description:
Library name: KO Ibd1C RNA-Seq
Fillingham_004_Plate1_Strip1_D01_Ibd1_C__S51

value: Mpr/Mpr (VII, mp-s)  KO Ibd1


title: Plate3_TF_SPI1_P3E11_dose0.05_rep1

description: Library name: P3E11


title: Plate3_TF_MYC_P3C11_dose0.05_rep1

description: Library name: P3C11


title: Plate3_TF_GFP_P3B12_dose1_rep2

description: Library name: P3B12


title: Plate3_TF_SPI1_P3H10_dose0.25_rep4

description: Library name: P3H10


title: Plate3_TF_SOX2_P3B11_dose0.05_rep2

description: Library name: P3B11


title: Plate3_TF_SOX2_P3A11_dose0.05_rep1

description: Library name: P3A11


title: Plate3_TF_SPI1_P3F10_dose0.25_rep2

description: Library name: P3F10


title: Plate3_TF_SPI1_P3G10_dose0.25_rep3

description: Library name: P3G10


title: Plate3_TF_SPI1_P3E10_dose0.25_rep1

description: Library name: P3E10


title: Plate3_TF_MYC_P3D10_dose0.25_rep2

description: Library name: P3D10


title: Plate3_TF_SPI1_P3H9_dose0.5_rep4

description: Library name: P3H9


title: Plate3_TF_MYC_P3C10_dose0.25_rep1

description: Library name: P3C10


title: Plate3_TF_MYC_P3D9_dose0.5_rep2

description: Library name: P3D9


title: Plate3_TF_SPI1_P3E9_dose0.5_rep1

description: Library name: P3E9


title: Plate3_TF_MYC_P3C9_dose0.5_rep1

description: Library name: P3C9


title: Plate3_TF_SOX2_P3B9_dose0.5_rep2

description: Library name: P3B9


title: Plate3_TF_SPI1_P3G9_dose0.5_rep3

description: Library name: P3G9


title: Plate3_TF_SPI1_P3F9_dose0.5_rep2

description: Library name: P3F9


title: iAlg11ATc_3

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

description: Library name: Sample 6

data_processing:
1. Data quality control. Rawdata (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
2. Reads mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools.
3. Novel transcripts prediction. The mapped reads of each sample were assembled by StringTie (v2.2.3) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
4. Quantification of gene expression level feature. Counts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
5. Differential expression analysis. For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.42.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1. For edgeR without biological replicates: Prior to differential gene expression analysis, for each sequencing library, read counts were adjusted using the edgeR R package (4.0.16) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis. The resulting P value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Assembly: ToxoDB_68_TgondiiGT1_Genome
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Toxoplasma gondii

source_name: Tachyzoites

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.  RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Non strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Clustering and sequencing After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing. The basic principle of sequencing is "Sequencing by Synthesis", where fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the sequencing flow cell for amplification. As each sequencing cluster extends its complementary strand, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence signal. The sequencer captures these fluorescence signals and converts them into sequencing peaks through computer software, thereby obtaining the sequence information of the target fragment.

value: Tachyzoites

value: ATc


title: Plate3_TF_SOX2_P3A9_dose0.5_rep1

description: Library name: P3A9


title: Plate3_TF_SOX2_P3A10_dose0.25_rep1

description: Library name: P3A10


title: iAlg11ATc_2

description: Library name: Sample 5


title: Plate3_TF_SOX2_P3B10_dose0.25_rep2

description: Library name: P3B10


title: Plate3_TF_SPI1_P3H8_dose0.75_rep4

description: Library name: P3H8


title: Plate3_TF_SPI1_P3F8_dose0.75_rep2

description: Library name: P3F8


title: iAlg11_3

description: Library name: Sample 3

value: DMSO


title: iAlg11_2

description: Library name: Sample 2


title: iAlg11_1

description: Library name: Sample 1


title: Plate3_TF_SPI1_P3E8_dose0.75_rep1

description: Library name: P3E8


title: Plate3_TF_SPI1_P3G8_dose0.75_rep3

description: Library name: P3G8


title: Plate3_TF_MYC_P3C8_dose0.75_rep1

description: Library name: P3C8


title: Plate3_TF_SOX2_P3B8_dose0.75_rep2

description: Library name: P3B8


title: Plate3_TF_SOX2_P3A8_dose0.75_rep1

description: Library name: P3A8


title: Plate3_TF_SPI1_P3F11_dose0.05_rep2

description: Library name: P3F11


title: Plate3_TF_SPI1_P3H11_dose0.05_rep4

description: Library name: P3H11


title: Plate3_TF_GFP_P3A12_dose1_rep1

description: Library name: P3A12


title: Plate3_TF_SPI1_P3G11_dose0.05_rep3

description: Library name: P3G11


title: Plate3_TF_SPI1_P3E11_dose0.05_rep1

description: Library name: P3E11


title: iAlg11ATc_1

description: Library name: Sample 4


title: Plate3_TF_SPI1_P3F7_dose1_rep2

description: Library name: P3F7


title: Plate3_TF_MYC_P3D11_dose0.05_rep2

description: Library name: P3D11


title: Plate3_TF_SPI1_P3G7_dose1_rep3

description: Library name: P3G7


title: Plate3_TF_MYC_P3D7_dose1_rep2

description: Library name: P3D7


title: Plate3_TF_SPI1_P3H7_dose1_rep4

description: Library name: P3H7


title: Plate3_TF_MYC_P3C11_dose0.05_rep1

description: Library name: P3C11


title: Plate3_TF_SPI1_P3E7_dose1_rep1

description: Library name: P3E7


title: Plate3_TF_SOX2_P3A11_dose0.05_rep1

description: Library name: P3A11


title: Plate3_TF_SOX2_P3B11_dose0.05_rep2

description: Library name: P3B11


title: Plate3_TF_SPI1_P3H10_dose0.25_rep4

description: Library name: P3H10


title: Plate3_TF_GFP_P3B12_dose1_rep2

description: Library name: P3B12


title: Plate3_TF_MYC_P3D8_dose0.75_rep2

description: Library name: P3D8


title: Plate3_TF_MYC_P3C7_dose1_rep1

description: Library name: P3C7


title: Plate3_TF_SPI1_P3G10_dose0.25_rep3

description: Library name: P3G10


title: Plate3_TF_SOX2_P3A7_dose1_rep1

description: Library name: P3A7


title: Plate3_TF_SPI1_P3F10_dose0.25_rep2

description: Library name: P3F10


title: Plate3_TF_KLF1_P3H6_dose0.05_rep4

description: Library name: P3H6


title: Plate3_TF_MYC_P3D10_dose0.25_rep2

description: Library name: P3D10


title: Plate3_TF_SPI1_P3E10_dose0.25_rep1

description: Library name: P3E10


title: Plate3_TF_KLF1_P3F6_dose0.05_rep2

description: Library name: P3F6


title: Plate3_TF_KLF1_P3G6_dose0.05_rep3

description: Library name: P3G6


title: Plate3_TF_KLF1_P3E6_dose0.05_rep1

description: Library name: P3E6


title: Plate3_TF_KLF4_P3C6_dose0.05_rep1

description: Library name: P3C6


title: Plate3_TF_MYC_P3C10_dose0.25_rep1

description: Library name: P3C10


title: Plate3_TF_KLF4_P3D6_dose0.05_rep2

description: Library name: P3D6


title: Plate3_TF_SOX2_P3B7_dose1_rep2

description: Library name: P3B7


title: Plate3_TF_SPI1_P3G9_dose0.5_rep3

description: Library name: P3G9


title: Plate3_TF_SOX2_P3A10_dose0.25_rep1

description: Library name: P3A10


title: Plate3_TF_SOX2_P3B10_dose0.25_rep2

description: Library name: P3B10


title: Plate3_TF_SPI1_P3H9_dose0.5_rep4

description: Library name: P3H9


title: Plate3_TF_OCT4_P3B6_dose0.05_rep2

description: Library name: P3B6


title: Plate3_TF_SPI1_P3E9_dose0.5_rep1

description: Library name: P3E9


title: Plate3_TF_KLF1_P3H5_dose0.25_rep4

description: Library name: P3H5


title: Plate3_TF_KLF1_P3G5_dose0.25_rep3

description: Library name: P3G5


title: Plate3_TF_OCT4_P3A6_dose0.05_rep1

description: Library name: P3A6


title: Plate3_TF_MYC_P3D9_dose0.5_rep2

description: Library name: P3D9


title: Plate3_TF_SOX2_P3B9_dose0.5_rep2

description: Library name: P3B9


title: Plate3_TF_KLF1_P3F5_dose0.25_rep2

description: Library name: P3F5


title: Plate3_TF_SPI1_P3H8_dose0.75_rep4

description: Library name: P3H8


title: Plate3_TF_SPI1_P3G8_dose0.75_rep3

description: Library name: P3G8


title: Plate3_TF_KLF1_P3E5_dose0.25_rep1

description: Library name: P3E5


title: Plate3_TF_OCT4_P3A5_dose0.25_rep1

description: Library name: P3A5


title: Plate3_TF_OCT4_P3B5_dose0.25_rep2

description: Library name: P3B5


title: Plate3_TF_KLF4_P3D5_dose0.25_rep2

description: Library name: P3D5


title: Plate3_TF_KLF4_P3C5_dose0.25_rep1

description: Library name: P3C5


title: Plate3_TF_SPI1_P3F9_dose0.5_rep2

description: Library name: P3F9


title: Plate3_TF_SPI1_P3F8_dose0.75_rep2

description: Library name: P3F8


title: Plate3_TF_MYC_P3D8_dose0.75_rep2

description: Library name: P3D8


title: Plate3_TF_KLF1_P3F4_dose0.5_rep2

description: Library name: P3F4


title: Plate3_TF_KLF1_P3H4_dose0.5_rep4

description: Library name: P3H4


title: Plate3_TF_KLF1_P3G4_dose0.5_rep3

description: Library name: P3G4


title: Plate3_TF_MYC_P3C9_dose0.5_rep1

description: Library name: P3C9


title: Plate3_TF_KLF1_P3E4_dose0.5_rep1

description: Library name: P3E4


title: Plate3_TF_MYC_P3C8_dose0.75_rep1

description: Library name: P3C8


title: Plate3_TF_SOX2_P3B8_dose0.75_rep2

description: Library name: P3B8


title: Plate3_TF_KLF4_P3C4_dose0.5_rep1

description: Library name: P3C4


title: Plate3_TF_KLF4_P3D4_dose0.5_rep2

description: Library name: P3D4


title: Plate3_TF_SOX2_P3A9_dose0.5_rep1

description: Library name: P3A9


title: Plate3_TF_SPI1_P3H7_dose1_rep4

description: Library name: P3H7


title: Plate3_TF_SOX2_P3A8_dose0.75_rep1

description: Library name: P3A8


title: Plate3_TF_OCT4_P3A4_dose0.5_rep1

description: Library name: P3A4


title: Plate3_TF_SPI1_P3G7_dose1_rep3

description: Library name: P3G7


title: Plate3_TF_SPI1_P3F7_dose1_rep2

description: Library name: P3F7


title: Plate3_TF_SPI1_P3E8_dose0.75_rep1

description: Library name: P3E8


title: Plate3_TF_OCT4_P3B4_dose0.5_rep2

description: Library name: P3B4


title: Plate3_TF_KLF1_P3H3_dose0.75_rep4

description: Library name: P3H3


title: Plate3_TF_SPI1_P3E7_dose1_rep1

description: Library name: P3E7


title: Plate3_TF_KLF1_P3F3_dose0.75_rep2

description: Library name: P3F3


title: Plate3_TF_MYC_P3C7_dose1_rep1

description: Library name: P3C7


title: Plate3_TF_KLF1_P3E3_dose0.75_rep1

description: Library name: P3E3


title: Plate3_TF_MYC_P3D7_dose1_rep2

description: Library name: P3D7


title: Plate3_TF_SOX2_P3A7_dose1_rep1

description: Library name: P3A7


title: Plate3_TF_SOX2_P3B7_dose1_rep2

description: Library name: P3B7


title: Plate3_TF_KLF4_P3C3_dose0.75_rep1

description: Library name: P3C3


title: Plate3_TF_KLF4_P3D3_dose0.75_rep2

description: Library name: P3D3


title: Plate3_TF_KLF1_P3H6_dose0.05_rep4

description: Library name: P3H6


title: Plate3_TF_OCT4_P3A3_dose0.75_rep1

description: Library name: P3A3


title: Plate3_TF_KLF1_P3G6_dose0.05_rep3

description: Library name: P3G6


title: Plate3_TF_KLF1_P3F6_dose0.05_rep2

description: Library name: P3F6


title: Plate3_TF_OCT4_P3B3_dose0.75_rep2

description: Library name: P3B3


title: Plate3_TF_KLF1_P3H2_dose1_rep4

description: Library name: P3H2


title: Plate3_TF_KLF1_P3E6_dose0.05_rep1

description: Library name: P3E6


title: Plate3_TF_KLF1_P3G2_dose1_rep3

description: Library name: P3G2


title: Plate3_TF_KLF1_P3G3_dose0.75_rep3

description: Library name: P3G3


title: Plate3_TF_OCT4_P3B6_dose0.05_rep2

description: Library name: P3B6


title: Plate3_TF_KLF1_P3E2_dose1_rep1

description: Library name: P3E2


title: Plate3_TF_OCT4_P3A6_dose0.05_rep1

description: Library name: P3A6


title: Plate3_TF_KLF4_P3C2_dose1_rep1

description: Library name: P3C2


title: Plate3_TF_OCT4_P3B2_dose1_rep2

description: Library name: P3B2


title: Plate3_TF_KLF1_P3F2_dose1_rep2

description: Library name: P3F2


title: Plate3_TF_KLF4_P3D2_dose1_rep2

description: Library name: P3D2


title: Plate3_TF_OCT4_P3A2_dose1_rep1

description: Library name: P3A2


title: Plate3_TF_KLF1_P3G5_dose0.25_rep3

description: Library name: P3G5


title: Plate3_TF_KLF1_P3F5_dose0.25_rep2

description: Library name: P3F5


title: Plate2_TF_GFP_P2B12_dose1_rep2

description: Library name: P2B12


title: Plate3_TF_KLF4_P3D6_dose0.05_rep2

description: Library name: P3D6


title: Plate2_TF_MXD1_P2H11_dose0.05_rep2

description: Library name: P2H11


title: Plate3_TF_KLF4_P3C6_dose0.05_rep1

description: Library name: P3C6


title: Plate2_TF_GFP_P2A12_dose1_rep1

description: Library name: P2A12


title: Plate3_TF_KLF4_P3C5_dose0.25_rep1

description: Library name: P3C5


title: Plate3_TF_KLF4_P3D5_dose0.25_rep2

description: Library name: P3D5


title: Plate3_TF_OCT4_P3B5_dose0.25_rep2

description: Library name: P3B5


title: Plate3_TF_KLF1_P3E5_dose0.25_rep1

description: Library name: P3E5


title: Plate2_TF_TCF3_P2F11_dose0.05_rep2

description: Library name: P2F11


title: Plate2_TF_MXD1_P2G11_dose0.05_rep1

description: Library name: P2G11


title: Plate3_TF_KLF1_P3H5_dose0.25_rep4

description: Library name: P3H5


title: Plate2_TF_ALX4_P2D11_dose0.05_rep2

description: Library name: P2D11


title: Plate2_TF_TCF3_P2E11_dose0.05_rep1

description: Library name: P2E11


title: Plate3_TF_KLF1_P3G4_dose0.5_rep3

description: Library name: P3G4


title: Plate3_TF_KLF1_P3F4_dose0.5_rep2

description: Library name: P3F4


title: Plate2_TF_XBP1_P2B11_dose0.05_rep2

description: Library name: P2B11


title: Plate2_TF_XBP1_P2A11_dose0.05_rep1

description: Library name: P2A11


title: Plate3_TF_KLF1_P3E4_dose0.5_rep1

description: Library name: P3E4


title: Plate2_TF_MXD1_P2G10_dose0.25_rep1

description: Library name: P2G10


title: Plate2_TF_MXD1_P2H10_dose0.25_rep2

description: Library name: P2H10


title: Plate2_TF_ALX4_P2C11_dose0.05_rep1

description: Library name: P2C11


title: Plate3_TF_OCT4_P3B4_dose0.5_rep2

description: Library name: P3B4


title: Plate2_TF_TCF3_P2E10_dose0.25_rep1

description: Library name: P2E10


title: Plate3_TF_KLF1_P3H3_dose0.75_rep4

description: Library name: P3H3


title: Plate3_TF_OCT4_P3A5_dose0.25_rep1

description: Library name: P3A5


title: Plate3_TF_KLF1_P3H4_dose0.5_rep4

description: Library name: P3H4


title: Plate2_TF_ALX4_P2C10_dose0.25_rep1

description: Library name: P2C10


title: Plate3_TF_KLF1_P3G3_dose0.75_rep3

description: Library name: P3G3


title: Plate2_TF_ALX4_P2D10_dose0.25_rep2

description: Library name: P2D10


title: Plate2_TF_XBP1_P2A10_dose0.25_rep1

description: Library name: P2A10


title: Plate3_TF_KLF4_P3C3_dose0.75_rep1

description: Library name: P3C3


title: Plate2_TF_MXD1_P2H9_dose0.5_rep2

description: Library name: P2H9


title: Plate2_TF_MXD1_P2G9_dose0.5_rep1

description: Library name: P2G9


title: Plate3_TF_KLF4_P3D4_dose0.5_rep2

description: Library name: P3D4


title: Plate3_TF_KLF4_P3C4_dose0.5_rep1

description: Library name: P3C4


title: Plate3_TF_OCT4_P3A3_dose0.75_rep1

description: Library name: P3A3


title: Plate2_TF_TCF3_P2F10_dose0.25_rep2

description: Library name: P2F10


title: Plate2_TF_TCF3_P2E9_dose0.5_rep1

description: Library name: P2E9


title: Plate3_TF_OCT4_P3B3_dose0.75_rep2

description: Library name: P3B3


title: Plate2_TF_TCF3_P2F9_dose0.5_rep2

description: Library name: P2F9


title: Plate2_TF_ALX4_P2D9_dose0.5_rep2

description: Library name: P2D9


title: Plate2_TF_XBP1_P2B9_dose0.5_rep2

description: Library name: P2B9


title: Plate3_TF_OCT4_P3A4_dose0.5_rep1

description: Library name: P3A4


title: Plate2_TF_ALX4_P2C9_dose0.5_rep1

description: Library name: P2C9


title: Plate3_TF_KLF1_P3G2_dose1_rep3

description: Library name: P3G2


title: Plate3_TF_KLF1_P3E2_dose1_rep1

description: Library name: P3E2


title: Plate3_TF_KLF1_P3H2_dose1_rep4

description: Library name: P3H2


title: Plate2_TF_XBP1_P2A9_dose0.5_rep1

description: Library name: P2A9


title: Plate2_TF_XBP1_P2B10_dose0.25_rep2

description: Library name: P2B10


title: Plate3_TF_KLF1_P3E3_dose0.75_rep1

description: Library name: P3E3


title: Plate3_TF_KLF4_P3D3_dose0.75_rep2

description: Library name: P3D3


title: Plate2_TF_MXD1_P2H8_dose0.75_rep2

description: Library name: P2H8


title: Plate3_TF_KLF1_P3F3_dose0.75_rep2

description: Library name: P3F3


title: Plate3_TF_KLF4_P3C2_dose1_rep1

description: Library name: P3C2


title: Plate3_TF_KLF4_P3D2_dose1_rep2

description: Library name: P3D2


title: Plate2_TF_TCF3_P2F8_dose0.75_rep2

description: Library name: P2F8


title: Plate2_TF_MXD1_P2G8_dose0.75_rep1

description: Library name: P2G8


title: Plate3_TF_KLF1_P3F2_dose1_rep2

description: Library name: P3F2


title: Plate3_TF_OCT4_P3A2_dose1_rep1

description: Library name: P3A2


title: Plate2_TF_TCF3_P2E8_dose0.75_rep1

description: Library name: P2E8


title: Plate3_TF_OCT4_P3B2_dose1_rep2

description: Library name: P3B2


title: Plate2_TF_ALX4_P2D8_dose0.75_rep2

description: Library name: P2D8


title: Plate2_TF_GFP_P2B12_dose1_rep2

description: Library name: P2B12


title: Plate2_TF_XBP1_P2B8_dose0.75_rep2

description: Library name: P2B8


title: Plate2_TF_MXD1_P2H11_dose0.05_rep2

description: Library name: P2H11


title: Plate2_TF_GFP_P2A12_dose1_rep1

description: Library name: P2A12


title: Plate2_TF_TCF3_P2F11_dose0.05_rep2

description: Library name: P2F11


title: Plate2_TF_ALX4_P2C8_dose0.75_rep1

description: Library name: P2C8


title: Plate2_TF_MXD1_P2H7_dose1_rep2

description: Library name: P2H7


title: Plate2_TF_MXD1_P2G7_dose1_rep1

description: Library name: P2G7


title: Plate2_TF_XBP1_P2A8_dose0.75_rep1

description: Library name: P2A8


title: Plate2_TF_ALX4_P2D11_dose0.05_rep2

description: Library name: P2D11


title: Plate2_TF_TCF3_P2F7_dose1_rep2

description: Library name: P2F7


title: Plate2_TF_TCF3_P2E11_dose0.05_rep1

description: Library name: P2E11


title: Plate2_TF_XBP1_P2B11_dose0.05_rep2

description: Library name: P2B11


title: Plate2_TF_ALX4_P2C7_dose1_rep1

description: Library name: P2C7


title: Plate2_TF_ALX4_P2D7_dose1_rep2

description: Library name: P2D7


title: Plate2_TF_ALX4_P2C11_dose0.05_rep1

description: Library name: P2C11


title: Plate2_TF_TCF3_P2E7_dose1_rep1

description: Library name: P2E7


title: Plate2_TF_XBP1_P2A11_dose0.05_rep1

description: Library name: P2A11


title: Plate2_TF_MXD1_P2H10_dose0.25_rep2

description: Library name: P2H10


title: Plate2_TF_MXD1_P2G11_dose0.05_rep1

description: Library name: P2G11


title: Plate2_TF_XBP1_P2B7_dose1_rep2

description: Library name: P2B7


title: Plate2_TF_MXD1_P2G10_dose0.25_rep1

description: Library name: P2G10


title: Plate2_TF_PRDM1_P2H6_dose0.05_rep2

description: Library name: P2H6


title: Plate2_TF_TCF3_P2F10_dose0.25_rep2

description: Library name: P2F10


title: Plate2_TF_TCF3_P2E10_dose0.25_rep1

description: Library name: P2E10


title: Plate2_TF_PRDM1_P2G6_dose0.05_rep1

description: Library name: P2G6


title: Plate2_TF_ALX4_P2D10_dose0.25_rep2

description: Library name: P2D10


title: Plate2_TF_NR4A1_P2F6_dose0.05_rep2

description: Library name: P2F6


title: Plate2_TF_ALX4_P2C10_dose0.25_rep1

description: Library name: P2C10


title: Plate2_TF_NR4A1_P2E6_dose0.05_rep1

description: Library name: P2E6


title: Plate2_TF_LEF1_P2D6_dose0.05_rep2

description: Library name: P2D6


title: Plate2_TF_MXD1_P2H9_dose0.5_rep2

description: Library name: P2H9


title: Plate2_TF_XBP1_P2B10_dose0.25_rep2

description: Library name: P2B10


title: Plate2_TF_MXD1_P2G9_dose0.5_rep1

description: Library name: P2G9


title: Plate2_TF_IKZF2_P2B6_dose0.05_rep2

description: Library name: P2B6


title: Plate2_TF_XBP1_P2A7_dose1_rep1

description: Library name: P2A7


title: Plate2_TF_LEF1_P2C6_dose0.05_rep1

description: Library name: P2C6


title: Plate2_TF_IKZF2_P2A6_dose0.05_rep1

description: Library name: P2A6


title: Plate2_TF_XBP1_P2A10_dose0.25_rep1

description: Library name: P2A10


title: Plate2_TF_NR4A1_P2F5_dose0.25_rep2

description: Library name: P2F5


title: Plate2_TF_NR4A1_P2E5_dose0.25_rep1

description: Library name: P2E5


title: Plate2_TF_ALX4_P2C9_dose0.5_rep1

description: Library name: P2C9


title: Plate2_TF_PRDM1_P2G5_dose0.25_rep1

description: Library name: P2G5


title: Plate2_TF_LEF1_P2D5_dose0.25_rep2

description: Library name: P2D5


title: Plate2_TF_PRDM1_P2H5_dose0.25_rep2

description: Library name: P2H5


title: Plate2_TF_TCF3_P2E9_dose0.5_rep1

description: Library name: P2E9


title: Plate2_TF_XBP1_P2A9_dose0.5_rep1

description: Library name: P2A9


title: Plate2_TF_XBP1_P2B9_dose0.5_rep2

description: Library name: P2B9


title: Plate2_TF_ALX4_P2D9_dose0.5_rep2

description: Library name: P2D9


title: Plate2_TF_LEF1_P2C5_dose0.25_rep1

description: Library name: P2C5


title: Plate2_TF_MXD1_P2H8_dose0.75_rep2

description: Library name: P2H8


title: Plate2_TF_MXD1_P2G8_dose0.75_rep1

description: Library name: P2G8


title: Plate2_TF_IKZF2_P2B5_dose0.25_rep2

description: Library name: P2B5


title: Plate2_TF_IKZF2_P2A5_dose0.25_rep1

description: Library name: P2A5


title: Plate2_TF_TCF3_P2F8_dose0.75_rep2

description: Library name: P2F8


title: Plate2_TF_TCF3_P2F9_dose0.5_rep2

description: Library name: P2F9


title: Plate2_TF_TCF3_P2E8_dose0.75_rep1

description: Library name: P2E8


title: Plate2_TF_PRDM1_P2H4_dose0.5_rep2

description: Library name: P2H4


title: Plate2_TF_PRDM1_P2G4_dose0.5_rep1

description: Library name: P2G4


title: Plate2_TF_NR4A1_P2F4_dose0.5_rep2

description: Library name: P2F4


title: Plate2_TF_ALX4_P2D8_dose0.75_rep2

description: Library name: P2D8


title: Plate2_TF_NR4A1_P2E4_dose0.5_rep1

description: Library name: P2E4


title: Plate2_TF_ALX4_P2C8_dose0.75_rep1

description: Library name: P2C8


title: Plate2_TF_IKZF2_P2B4_dose0.5_rep2

description: Library name: P2B4


title: Plate2_TF_XBP1_P2B8_dose0.75_rep2

description: Library name: P2B8


title: Plate2_TF_LEF1_P2D4_dose0.5_rep2

description: Library name: P2D4


title: Plate2_TF_MXD1_P2H7_dose1_rep2

description: Library name: P2H7


title: Plate2_TF_MXD1_P2G7_dose1_rep1

description: Library name: P2G7


title: Plate2_TF_ALX4_P2D7_dose1_rep2

description: Library name: P2D7


title: Plate2_TF_TCF3_P2E7_dose1_rep1

description: Library name: P2E7


title: Plate2_TF_PRDM1_P2H3_dose0.75_rep2

description: Library name: P2H3


title: Plate2_TF_TCF3_P2F7_dose1_rep2

description: Library name: P2F7


title: Plate2_TF_IKZF2_P2A4_dose0.5_rep1

description: Library name: P2A4


title: Plate2_TF_PRDM1_P2G3_dose0.75_rep1

description: Library name: P2G3


title: Plate2_TF_XBP1_P2A8_dose0.75_rep1

description: Library name: P2A8


title: Plate2_TF_PRDM1_P2H6_dose0.05_rep2

description: Library name: P2H6


title: Plate2_TF_LEF1_P2C3_dose0.75_rep1

description: Library name: P2C3


title: Plate2_TF_XBP1_P2B7_dose1_rep2

description: Library name: P2B7


title: Plate2_TF_IKZF2_P2B3_dose0.75_rep2

description: Library name: P2B3


title: Plate2_TF_NR4A1_P2E3_dose0.75_rep1

description: Library name: P2E3


title: Plate2_TF_NR4A1_P2F6_dose0.05_rep2

description: Library name: P2F6


title: Plate2_TF_LEF1_P2C4_dose0.5_rep1

description: Library name: P2C4


title: Plate2_TF_NR4A1_P2F3_dose0.75_rep2

description: Library name: P2F3


title: Plate2_TF_ALX4_P2C7_dose1_rep1

description: Library name: P2C7


title: Plate2_TF_PRDM1_P2H2_dose1_rep2

description: Library name: P2H2


title: Plate2_TF_PRDM1_P2G6_dose0.05_rep1

description: Library name: P2G6


title: Plate2_TF_XBP1_P2A7_dose1_rep1

description: Library name: P2A7


title: Plate2_TF_NR4A1_P2E6_dose0.05_rep1

description: Library name: P2E6


title: Plate2_TF_LEF1_P2D3_dose0.75_rep2

description: Library name: P2D3


title: Plate2_TF_PRDM1_P2G2_dose1_rep1

description: Library name: P2G2


title: Plate2_TF_LEF1_P2D6_dose0.05_rep2

description: Library name: P2D6


title: Plate2_TF_NR4A1_P2F2_dose1_rep2

description: Library name: P2F2


title: Plate2_TF_IKZF2_P2B6_dose0.05_rep2

description: Library name: P2B6


title: Plate2_TF_NR4A1_P2E2_dose1_rep1

description: Library name: P2E2


title: Plate2_TF_LEF1_P2C6_dose0.05_rep1

description: Library name: P2C6


title: Plate2_TF_IKZF2_P2A6_dose0.05_rep1

description: Library name: P2A6


title: Plate2_TF_PRDM1_P2H5_dose0.25_rep2

description: Library name: P2H5


title: Plate2_TF_IKZF2_P2B2_dose1_rep2

description: Library name: P2B2


title: Plate2_TF_LEF1_P2C2_dose1_rep1

description: Library name: P2C2


title: Plate2_TF_IKZF2_P2A3_dose0.75_rep1

description: Library name: P2A3


title: Plate2_TF_IKZF2_P2A2_dose1_rep1

description: Library name: P2A2


title: Plate2_TF_NR4A1_P2F5_dose0.25_rep2

description: Library name: P2F5


title: Plate2_TF_NR4A1_P2E5_dose0.25_rep1

description: Library name: P2E5


title: Plate1_TF_GFP_P1B12_dose1_rep2

description: Library name: P1B12


title: Plate1_TF_GFP_P1A12_dose1_rep1

description: Library name: P1A12


title: Plate1_TF_IRF4_P1H11_dose0.05_rep2

description: Library name: P1H11


title: Plate2_TF_LEF1_P2D5_dose0.25_rep2

description: Library name: P2D5


title: Plate2_TF_LEF1_P2C5_dose0.25_rep1

description: Library name: P2C5


title: Plate1_TF_IRF4_P1G11_dose0.05_rep1

description: Library name: P1G11


title: Plate2_TF_IKZF2_P2A5_dose0.25_rep1

description: Library name: P2A5


title: Plate2_TF_LEF1_P2D2_dose1_rep2

description: Library name: P2D2


title: Plate2_TF_IKZF2_P2B5_dose0.25_rep2

description: Library name: P2B5


title: Plate1_TF_FOXP3_P1E11_dose0.05_rep1

description: Library name: P1E11


title: Plate1_TF_FOXP3_P1F11_dose0.05_rep2

description: Library name: P1F11


title: Plate2_TF_PRDM1_P2H4_dose0.5_rep2

description: Library name: P2H4


title: Plate1_TF_FOXO1_P1D11_dose0.05_rep2

description: Library name: P1D11


title: Plate1_TF_FOXO1_P1C11_dose0.05_rep1

description: Library name: P1C11


title: Plate2_TF_PRDM1_P2G4_dose0.5_rep1

description: Library name: P2G4


title: Plate1_TF_BACH2_P1B11_dose0.05_rep2

description: Library name: P1B11


title: Plate2_TF_PRDM1_P2G5_dose0.25_rep1

description: Library name: P2G5


title: Plate2_TF_NR4A1_P2E4_dose0.5_rep1

description: Library name: P2E4


title: Plate1_TF_BACH2_P1A11_dose0.05_rep1

description: Library name: P1A11


title: Plate2_TF_LEF1_P2D4_dose0.5_rep2

description: Library name: P2D4


title: Plate1_TF_IRF4_P1H10_dose0.25_rep2

description: Library name: P1H10


title: Plate1_TF_IRF4_P1G10_dose0.25_rep1

description: Library name: P1G10


title: Plate2_TF_LEF1_P2C4_dose0.5_rep1

description: Library name: P2C4


title: Plate2_TF_IKZF2_P2B4_dose0.5_rep2

description: Library name: P2B4


title: Plate2_TF_IKZF2_P2A4_dose0.5_rep1

description: Library name: P2A4


title: Plate1_TF_FOXP3_P1F10_dose0.25_rep2

description: Library name: P1F10


title: Plate1_TF_FOXP3_P1E10_dose0.25_rep1

description: Library name: P1E10


title: Plate2_TF_PRDM1_P2H3_dose0.75_rep2

description: Library name: P2H3


title: Plate1_TF_FOXO1_P1D10_dose0.25_rep2

description: Library name: P1D10


title: Plate2_TF_PRDM1_P2G3_dose0.75_rep1

description: Library name: P2G3


title: Plate1_TF_FOXO1_P1C10_dose0.25_rep1

description: Library name: P1C10


title: Plate2_TF_NR4A1_P2F4_dose0.5_rep2

description: Library name: P2F4


title: Plate2_TF_NR4A1_P2F3_dose0.75_rep2

description: Library name: P2F3


title: Plate2_TF_NR4A1_P2E3_dose0.75_rep1

description: Library name: P2E3


title: Plate1_TF_BACH2_P1B10_dose0.25_rep2

description: Library name: P1B10


title: Plate1_TF_IRF4_P1H9_dose0.5_rep2

description: Library name: P1H9


title: Plate1_TF_BACH2_P1A10_dose0.25_rep1

description: Library name: P1A10


title: Plate2_TF_IKZF2_P2B3_dose0.75_rep2

description: Library name: P2B3


title: Plate1_TF_FOXP3_P1F9_dose0.5_rep2

description: Library name: P1F9


title: Plate2_TF_LEF1_P2D3_dose0.75_rep2

description: Library name: P2D3


title: Plate1_TF_IRF4_P1G9_dose0.5_rep1

description: Library name: P1G9


title: Plate2_TF_IKZF2_P2A3_dose0.75_rep1

description: Library name: P2A3


title: Plate1_TF_FOXO1_P1C9_dose0.5_rep1

description: Library name: P1C9


title: Plate2_TF_LEF1_P2C3_dose0.75_rep1

description: Library name: P2C3


title: Plate1_TF_FOXO1_P1D9_dose0.5_rep2

description: Library name: P1D9


title: Plate2_TF_PRDM1_P2H2_dose1_rep2

description: Library name: P2H2


title: Plate1_TF_BACH2_P1B9_dose0.5_rep2

description: Library name: P1B9


title: Plate2_TF_PRDM1_P2G2_dose1_rep1

description: Library name: P2G2


title: Plate2_TF_NR4A1_P2F2_dose1_rep2

description: Library name: P2F2


title: Plate1_TF_FOXP3_P1E9_dose0.5_rep1

description: Library name: P1E9


title: Plate2_TF_LEF1_P2C2_dose1_rep1

description: Library name: P2C2


title: Plate2_TF_NR4A1_P2E2_dose1_rep1

description: Library name: P2E2


title: Plate1_TF_BACH2_P1A9_dose0.5_rep1

description: Library name: P1A9


title: Plate2_TF_LEF1_P2D2_dose1_rep2

description: Library name: P2D2


title: Plate2_TF_IKZF2_P2B2_dose1_rep2

description: Library name: P2B2


title: Plate1_TF_IRF4_P1G8_dose0.75_rep1

description: Library name: P1G8


title: Plate2_TF_IKZF2_P2A2_dose1_rep1

description: Library name: P2A2


title: Plate1_TF_FOXP3_P1E8_dose0.75_rep1

description: Library name: P1E8


title: Plate1_TF_GFP_P1B12_dose1_rep2

description: Library name: P1B12


title: Plate1_TF_FOXO1_P1D8_dose0.75_rep2

description: Library name: P1D8


title: Plate1_TF_IRF4_P1G11_dose0.05_rep1

description: Library name: P1G11


title: Plate1_TF_IRF4_P1H11_dose0.05_rep2

description: Library name: P1H11


title: Plate1_TF_IRF4_P1H7_dose1_rep2

description: Library name: P1H7


title: Plate1_TF_BACH2_P1A8_dose0.75_rep1

description: Library name: P1A8


title: Plate1_TF_FOXO1_P1C8_dose0.75_rep1

description: Library name: P1C8


title: Plate1_TF_BACH2_P1B8_dose0.75_rep2

description: Library name: P1B8


title: Plate1_TF_FOXP3_P1F11_dose0.05_rep2

description: Library name: P1F11


title: Plate1_TF_FOXP3_P1E11_dose0.05_rep1

description: Library name: P1E11


title: Plate1_TF_IRF4_P1G7_dose1_rep1

description: Library name: P1G7


title: Plate1_TF_FOXO1_P1D11_dose0.05_rep2

description: Library name: P1D11


title: Plate1_TF_FOXP3_P1F7_dose1_rep2

description: Library name: P1F7


title: Plate1_TF_IRF4_P1H8_dose0.75_rep2

description: Library name: P1H8


title: Plate1_TF_FOXO1_P1C11_dose0.05_rep1

description: Library name: P1C11


title: Plate1_TF_FOXP3_P1E7_dose1_rep1

description: Library name: P1E7


title: Plate1_TF_FOXP3_P1F8_dose0.75_rep2

description: Library name: P1F8


title: Plate1_TF_BACH2_P1B11_dose0.05_rep2

description: Library name: P1B11


title: Plate1_TF_FOXO1_P1D7_dose1_rep2

description: Library name: P1D7


title: Plate1_TF_BACH2_P1A11_dose0.05_rep1

description: Library name: P1A11


title: Plate1_TF_FOXO1_P1C7_dose1_rep1

description: Library name: P1C7


title: Plate1_TF_BACH2_P1B7_dose1_rep2

description: Library name: P1B7


title: Plate1_TF_BACH2_P1A7_dose1_rep1

description: Library name: P1A7


title: Plate1_TF_IRF4_P1H10_dose0.25_rep2

description: Library name: P1H10


title: Plate1_TF_IRF4_P1G10_dose0.25_rep1

description: Library name: P1G10


title: Plate1_TF_GFP_P1A12_dose1_rep1

description: Library name: P1A12


title: Plate1_TF_GATA1_P1G6_dose0.05_rep1

description: Library name: P1G6


title: Plate1_TF_FOXP3_P1F10_dose0.25_rep2

description: Library name: P1F10


title: Plate1_TF_FOXP3_P1E10_dose0.25_rep1

description: Library name: P1E10


title: Plate1_TF_FOXO1_P1D10_dose0.25_rep2

description: Library name: P1D10


title: HTO_ADT of 017_023_027_029_pooled_whole

city: New Haven

first: Yulong

last: Wei

state: CT

address: 295 Congress Avenue

department: Microbial Pathogenesis

institute: Yale University

description:
Library name: PT3_HTO_ADT
ADT HTO feature barcoding

library_source: other

data_processing:
RTA3 was used for basecalling
Cellranger-Arc count (v2.0)
Cellranger count (v5.0.1)
Assembly: hg38
Supplementary files format and content: HTO_ADT feature barcoding and RNA raw feature_bc_matrices from cellranger; cellranger_antiboy_list_with_barcode.csv; hashing_info.txt
Supplementary files format and content: ATAC raw feature_bc_matrices from cellranger-arc; atac_cut_sites.bigwig; atac_fragments.tsv.gz; atac_fragments.tsv.gz.tbi; atac_peak_annotation.tsv; atac_peaks.bed; per_barcode_metrics.csv

molecule: other

source_name: colon

extract_protocol:
Refer to Mimitou et al., Nature Biotechnology 2021 for nuclear DNA extraction, cytoplasmic RNA, and surface protien capture in DOGMA-seq protocol.
RNA, ATAC, and ADT_HTO libraries  were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Library construction kit following manufacturer's protocols.

value: colon

value: colon primary cells

tag: disease state

value: HIV-1 positive

value: Antiretroviral therapy


title: HTO_ADT of 008_012_015_pooled_whole

description:
Library name: PT2_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_FOXP1_P1E6_dose0.05_rep1

description: Library name: P1E6


title: Plate1_TF_BACH2_P1B10_dose0.25_rep2

description: Library name: P1B10

value: roboATAC


title: HTO_ADT of 361_pooled_whole

description:
Library name: PT4_HTO_ADT
ADT HTO feature barcoding

value: HIV-1 negative


title: Plate1_TF_FOXO1_P1C10_dose0.25_rep1

description: Library name: P1C10


title: HTO_ADT of HD363_C_whole

description:
Library name: B363C_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_ELF1_P1D6_dose0.05_rep2

description: Library name: P1D6


title: HTO_ADT of 035_037_040_pooled_whole

description:
Library name: PT1_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_GATA1_P1H6_dose0.05_rep2

description: Library name: P1H6


title: HTO_ADT of HD363_B_whole

description:
Library name: B363B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_BACH2_P1A10_dose0.25_rep1

description: Library name: P1A10


title: HTO_ADT of HD363_A_whole

description:
Library name: B363A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_FOXP1_P1F6_dose0.05_rep2

description: Library name: P1F6


title: Plate1_TF_IRF4_P1H9_dose0.5_rep2

description: Library name: P1H9


title: HTO_ADT of HD360_B_whole

description:
Library name: B360B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_ELF1_P1C6_dose0.05_rep1

description: Library name: P1C6


title: Plate1_TF_SP4_P1B6_dose0.05_rep2

description: Library name: P1B6


title: HTO_ADT of HD357_C_whole

description:
Library name: B357C_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_IRF4_P1G9_dose0.5_rep1

description: Library name: P1G9


title: Plate1_TF_FOXP3_P1F9_dose0.5_rep2

description: Library name: P1F9


title: HTO_ADT of HD357_B_whole

description:
Library name: B357B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_GATA1_P1H5_dose0.25_rep2

description: Library name: P1H5


title: Plate1_TF_SP4_P1A6_dose0.05_rep1

description: Library name: P1A6


title: HTO_ADT of HD351_C_whole

description:
Library name: B351C_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_FOXP3_P1E9_dose0.5_rep1

description: Library name: P1E9


title: HTO_ADT of HD351_B_whole

description:
Library name: B351B_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of HD357_A_whole

description:
Library name: B357A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_GATA1_P1G5_dose0.25_rep1

description: Library name: P1G5


title: Plate1_TF_FOXO1_P1D9_dose0.5_rep2

description: Library name: P1D9


title: HTO_ADT of HD351_A_whole

description:
Library name: B351A_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of HD361_B_CD3

description:
Library name: B361B_HTO_ADT
ADT HTO feature barcoding

value: primary CD3+ T cells


title: Plate1_TF_FOXP1_P1F5_dose0.25_rep2

description: Library name: P1F5


title: HTO_ADT of HD360_C_whole

description:
Library name: B360C_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of HD360_A_whole

description:
Library name: B360A_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of HD361_C_CD3

description:
Library name: B361C_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_FOXP1_P1E5_dose0.25_rep1

description: Library name: P1E5


title: HTO_ADT of HD361_A_CD3

description:
Library name: B361A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_BACH2_P1B9_dose0.5_rep2

description: Library name: P1B9


title: Plate1_TF_ELF1_P1D5_dose0.25_rep2

description: Library name: P1D5


title: Plate1_TF_FOXO1_P1C9_dose0.5_rep1

description: Library name: P1C9


title: HTO_ADT of PLWH040_A_CD3

description:
Library name: B040A_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH037_B_CD3

description:
Library name: B037B_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH040_B_CD3

description:
Library name: B040B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_ELF1_P1C5_dose0.25_rep1

description: Library name: P1C5


title: HTO_ADT of PLWH037_A_CD3

description:
Library name: B037A_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH035_B_CD3

description:
Library name: B035B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_IRF4_P1H8_dose0.75_rep2

description: Library name: P1H8


title: Plate1_TF_SP4_P1B5_dose0.25_rep2

description: Library name: P1B5


title: Plate1_TF_BACH2_P1A9_dose0.5_rep1

description: Library name: P1A9


title: HTO_ADT of PLWH035_A_CD3

description:
Library name: B035A_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH029_B_CD3

description:
Library name: B029B_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH029_A_CD3

description:
Library name: B029A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_IRF4_P1G8_dose0.75_rep1

description: Library name: P1G8


title: HTO_ADT of PLWH027_B_CD3

description:
Library name: B027B_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH027_A_CD3

description:
Library name: B027A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_GATA1_P1H4_dose0.5_rep2

description: Library name: P1H4


title: Plate1_TF_FOXP3_P1E8_dose0.75_rep1

description: Library name: P1E8


title: HTO_ADT of PLWH023_A_CD3

description:
Library name: B023A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_GATA1_P1G4_dose0.5_rep1

description: Library name: P1G4


title: Plate1_TF_FOXO1_P1D8_dose0.75_rep2

description: Library name: P1D8


title: HTO_ADT of PLWH017_B_CD3

description:
Library name: B017B_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH015_A_CD3

description:
Library name: B015A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_FOXO1_P1C8_dose0.75_rep1

description: Library name: P1C8


title: HTO_ADT of PLWH012_B_CD3

description:
Library name: B012B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_ELF1_P1D4_dose0.5_rep2

description: Library name: P1D4


title: Plate1_TF_BACH2_P1B8_dose0.75_rep2

description: Library name: P1B8


title: HTO_ADT of PLWH012_A_CD3

description:
Library name: B012A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_BACH2_P1A8_dose0.75_rep1

description: Library name: P1A8


title: HTO_ADT of PLWH008_B_CD3

description:
Library name: B008B_HTO_ADT
ADT HTO feature barcoding


title: HTO_ADT of PLWH008_A_CD3

description:
Library name: B008A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_FOXP3_P1F8_dose0.75_rep2

description: Library name: P1F8


title: HTO_ADT of PLWH017_A_CD3

description:
Library name: B017A_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_SP4_P1A5_dose0.25_rep1

description: Library name: P1A5


title: Plate1_TF_SP4_P1B4_dose0.5_rep2

description: Library name: P1B4


title: Plate1_TF_IRF4_P1H7_dose1_rep2

description: Library name: P1H7


title: ATAC-Seq of 017_023_027_029_pooled_whole

description:
Library name: PT3_ATAC
scATAC-seq

library_source: genomic single cell


title: ATAC-Seq of 361_pooled_whole

description:
Library name: PT4_ATAC
scATAC-seq


title: ATAC-Seq of 008_012_015_pooled_whole

description:
Library name: PT2_ATAC
scATAC-seq


title: HTO_ADT of PLWH015_B_CD3

description:
Library name: B015B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_IRF4_P1G7_dose1_rep1

description: Library name: P1G7


title: Plate1_TF_FOXP1_P1E4_dose0.5_rep1

description: Library name: P1E4


title: Plate1_TF_SP4_P1A4_dose0.5_rep1

description: Library name: P1A4


title: ATAC-Seq of 035_037_040_pooled_whole

description:
Library name: PT1_ATAC
scATAC-seq


title: ATAC-Seq of HD363_C_whole

description:
Library name: B363C_ATAC
scATAC-seq


title: Plate1_TF_FOXP3_P1F7_dose1_rep2

description: Library name: P1F7


title: Plate1_TF_GATA1_P1H3_dose0.75_rep2

description: Library name: P1H3


title: ATAC-Seq of HD363_B_whole

description:
Library name: B363B_ATAC
scATAC-seq


title: Plate1_TF_ELF1_P1C4_dose0.5_rep1

description: Library name: P1C4


title: Plate1_TF_FOXP3_P1E7_dose1_rep1

description: Library name: P1E7


title: ATAC-Seq of HD363_A_whole

description:
Library name: B363A_ATAC
scATAC-seq


title: Plate1_TF_GATA1_P1G3_dose0.75_rep1

description: Library name: P1G3


title: Plate1_TF_FOXO1_P1D7_dose1_rep2

description: Library name: P1D7


title: ATAC-Seq of HD360_A_whole

description:
Library name: B360A_ATAC
scATAC-seq


title: Plate1_TF_FOXP1_P1F3_dose0.75_rep2

description: Library name: P1F3


title: Plate1_TF_FOXP1_P1E3_dose0.75_rep1

description: Library name: P1E3


title: ATAC-Seq of HD357_B_whole

description:
Library name: B357B_ATAC
scATAC-seq


title: ATAC-Seq of HD357_A_whole

description:
Library name: B357A_ATAC
scATAC-seq


title: Plate1_TF_ELF1_P1D3_dose0.75_rep2

description: Library name: P1D3


title: ATAC-Seq of HD351_B_whole

description:
Library name: B351B_ATAC
scATAC-seq


title: Plate1_TF_BACH2_P1A7_dose1_rep1

description: Library name: P1A7


title: ATAC-Seq of HD351_A_whole

description:
Library name: B351A_ATAC
scATAC-seq


title: ATAC-Seq of HD360_C_whole

description:
Library name: B360C_ATAC
scATAC-seq


title: ATAC-Seq of HD361_C_CD3

description:
Library name: B361C_ATAC
scATAC-seq


title: Plate1_TF_FOXP1_P1F4_dose0.5_rep2

description: Library name: P1F4


title: ATAC-Seq of HD361_B_CD3

description:
Library name: B361B_ATAC
scATAC-seq


title: Plate1_TF_SP4_P1B3_dose0.75_rep2

description: Library name: P1B3


title: ATAC-Seq of HD360_B_whole

description:
Library name: B360B_ATAC
scATAC-seq


title: Plate1_TF_FOXO1_P1C7_dose1_rep1

description: Library name: P1C7


title: Plate1_TF_SP4_P1A3_dose0.75_rep1

description: Library name: P1A3


title: Plate1_TF_GATA1_P1G6_dose0.05_rep1

description: Library name: P1G6


title: ATAC-Seq of HD357_C_whole

description:
Library name: B357C_ATAC
scATAC-seq


title: ATAC-Seq of PLWH040_A_CD3

description:
Library name: B040A_ATAC
scATAC-seq


title: ATAC-Seq of PLWH040_B_CD3

description:
Library name: B040B_ATAC
scATAC-seq


title: Plate1_TF_FOXP1_P1F6_dose0.05_rep2

description: Library name: P1F6


title: ATAC-Seq of PLWH037_A_CD3

description:
Library name: B037A_ATAC
scATAC-seq


title: Plate1_TF_GATA1_P1G2_dose1_rep1

description: Library name: P1G2


title: ATAC-Seq of PLWH035_B_CD3

description:
Library name: B035B_ATAC
scATAC-seq


title: Plate1_TF_GATA1_P1H6_dose0.05_rep2

description: Library name: P1H6


title: Plate1_TF_BACH2_P1B7_dose1_rep2

description: Library name: P1B7


title: Plate1_TF_FOXP1_P1E6_dose0.05_rep1

description: Library name: P1E6


title: ATAC-Seq of PLWH037_B_CD3

description:
Library name: B037B_ATAC
scATAC-seq


title: Plate1_TF_FOXP1_P1F2_dose1_rep2

description: Library name: P1F2


title: Plate1_TF_FOXP1_P1E2_dose1_rep1

description: Library name: P1E2


title: ATAC-Seq of PLWH035_A_CD3

description:
Library name: B035A_ATAC
scATAC-seq


title: ATAC-Seq of PLWH027_B_CD3

description:
Library name: B027B_ATAC
scATAC-seq


title: Plate1_TF_GATA1_P1H2_dose1_rep2

description: Library name: P1H2


title: ATAC-Seq of HD351_C_whole

description:
Library name: B351C_ATAC
scATAC-seq


title: ATAC-Seq of PLWH023_B_CD3

description:
Library name: B023B_ATAC
scATAC-seq


title: Plate1_TF_ELF1_P1D6_dose0.05_rep2

description: Library name: P1D6


title: Plate1_TF_ELF1_P1C2_dose1_rep1

description: Library name: P1C2


title: ATAC-Seq of PLWH029_A_CD3

description:
Library name: B029A_ATAC
scATAC-seq


title: ATAC-Seq of PLWH027_A_CD3

description:
Library name: B027A_ATAC
scATAC-seq


title: HTO_ADT of PLWH023_B_CD3

description:
Library name: B023B_HTO_ADT
ADT HTO feature barcoding


title: Plate1_TF_GATA1_P1H5_dose0.25_rep2

description: Library name: P1H5


title: Plate1_TF_ELF1_P1D2_dose1_rep2

description: Library name: P1D2


title: ATAC-Seq of HD361_A_CD3

description:
Library name: B361A_ATAC
scATAC-seq


title: Plate1_TF_ELF1_P1C3_dose0.75_rep1

description: Library name: P1C3


title: Plate1_TF_ELF1_P1C6_dose0.05_rep1

description: Library name: P1C6


title: Plate1_TF_SP4_P1A6_dose0.05_rep1

description: Library name: P1A6


title: ATAC-Seq of PLWH017_A_CD3

description:
Library name: B017A_ATAC
scATAC-seq


title: ATAC-Seq of PLWH023_A_CD3

description:
Library name: B023A_ATAC
scATAC-seq


title: Plate1_TF_SP4_P1B2_dose1_rep2

description: Library name: P1B2


title: Plate1_TF_GATA1_P1G5_dose0.25_rep1

description: Library name: P1G5


title: Plate1_TF_SP4_P1A2_dose1_rep1

description: Library name: P1A2


title: ATAC-Seq of PLWH029_B_CD3

description:
Library name: B029B_ATAC
scATAC-seq


title: ATAC-Seq of PLWH012_A_CD3

description:
Library name: B012A_ATAC
scATAC-seq


title: Plate1_TF_SP4_P1B6_dose0.05_rep2

description: Library name: P1B6


title: ATAC-Seq of PLWH012_B_CD3

description:
Library name: B012B_ATAC
scATAC-seq


title: ATAC-Seq of PLWH008_B_CD3

description:
Library name: B008B_ATAC
scATAC-seq


title: ATAC-Seq of PLWH015_B_CD3

description:
Library name: B015B_ATAC
scATAC-seq


title: Plate1_TF_FOXP1_P1E5_dose0.25_rep1

description: Library name: P1E5


title: ATAC-Seq of PLWH008_A_CD3

description:
Library name: B008A_ATAC
scATAC-seq


title: LoVo, WT, replicate1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
RNA-seq reads were first processed by trimmomatic (version 0.39, parameters: ILLUMINACLIP: TruSeq3PE-2.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50) to remove low quality bases and adaptor sequences.
Next, trimmed RNA-seq reads were mapped to GRCh38/hg38 human reference genome with the GENCODE (version 41) by using HISAT2 (version 2.1.0 parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k 10).
The HISAT2-mapped sam ﬁles were transferred to bam format by samtools (version 1.9).
Gene expression levels were computed with FPKM (Fragments Per Kilobase of transcript per Million mapped reads) by normalized gene counts from featureCounts (version 2.0.1, parameters: -T 12 -t exon -g gene_name -O --fraction).
In addition, circRNA expression levels were quantified as FPB (Fragments Per Base) using CIRCexplorer3/CLEAR (version 1.0.0, parameters: clear_quant -1 R1. fq -2 R2. fq -g hg38.fa -i HISAT2_Index -j Bowtie_Index -G annotation.gtf) with the same reference genome and annotation file.
Assembly: hg38
Supplementary files format and content: zip file including linear RNA and circRNA expression

source_name: LoVo

extract_protocol:
Total RNAs from scramble and circMAN1A2(2,3,4,5) KD samples of HT29, DLD-1, HeLa, A549, and 293FT cells were processed with the KAPA RiboErase Kit (HMR) to deplete rRNAs for sequencing.
ribo-RNA-seq libraries of HT29, DLD-1, HeLa, A549 and 293FT cells were prepared using the KAPA RNA HyperPrep Kit (Roche), followed by size selection using KAPA Pure Beads (Roche). The size-selected libraries were quantified with the Agilent Bioanalyzer 2100 (Agilent) and Qubit dsDNA HS Assay Kit (ABP Biosciences), and then subjected to deep sequencing with the Illumina NovaSeq 6000 system at Sequanta Technologies, Shanghai, China. ribo-RNA-seq libraries of LoVo WT cells were prepared using the Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. The libraries were then size-selected with AmpureXP beads (Agencourt) and quantified using the Agilent Bioanalyzer 2100 and Qubit high-sensitivity dsDNA assay (Invitrogen). Size-selected libraries were subjected to deep sequencing with the Illumina HiSeq X Ten at Azenta Life Science, Suzhou, China. All the above raw read qualities were evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).

value: LoVo

value: WT


title: RNA-Seq of 361_pooled_whole

description:
Library name: PT4_RNA
scRNA-seq

molecule: cytoplasmic RNA


title: LoVo, WT, replicate2


title: ATAC-Seq of PLWH017_B_CD3

description:
Library name: B017B_ATAC
scATAC-seq


title: ATAC-Seq of PLWH015_A_CD3

description:
Library name: B015A_ATAC
scATAC-seq


title: Plate1_TF_ELF1_P1D5_dose0.25_rep2

description: Library name: P1D5


title: RNA-Seq of 008_012_015_pooled_whole

description:
Library name: PT2_RNA
scRNA-seq


title: Mono-mac-6-sgDDX6.2-Rep2

city: Duarte

first: Rui

last: Su

address: 1500 E Duarte Rd

institute: City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the TPM were calculated using RSEM 1.2.31 with default parameters
Assembly: GRCh38
Supplementary files format and content: RSEM output file containing the expression of genes

growth_protocol: Human Mono-mac-6 cell line was grown in RPMI 1640 media supplemented with 10% FBS ,1% Penicillin-Streptomycin , 2 mM L-glutamine ,1x non-essential amino acids , 1 mM sodium pyruvate , 10 μg /ml human insulin,10mM HEPES and 0.1%Plasmocin™ Prophylactic

extract_protocol:
Total mRNA was extracted using TRIZOL reagent
FastTrack MAG Maxi mRNA isolation kit

treatment_protocol: Mono-mac-6 cells were havested at 8 days after virius infection.

value: AML

value: carry MLL-AF9 fusion gene


title: RNA-Seq of 035_037_040_pooled_whole

description:
Library name: PT1_RNA
scRNA-seq


title: Plate1_TF_ELF1_P1C5_dose0.25_rep1

description: Library name: P1C5


title: RNA-Seq of HD363_C_whole

description:
Library name: B363C_RNA
scRNA-seq


title: RNA-Seq of HD363_A_whole

description:
Library name: B363A_RNA
scRNA-seq


title: RNA-Seq of HD363_B_whole

description:
Library name: B363B_RNA
scRNA-seq


title: Mono-mac-6-sgNS-Rep2

value: sgNS


title: Plate1_TF_SP4_P1B5_dose0.25_rep2

description: Library name: P1B5


title: RNA-Seq of HD360_C_whole

description:
Library name: B360C_RNA
scRNA-seq


title: Mono-mac-6-sgDDX6.1-Rep2


title: Plate1_TF_FOXP1_P1F5_dose0.25_rep2

description: Library name: P1F5


title: RNA-Seq of HD360_A_whole

description:
Library name: B360A_RNA
scRNA-seq


title: Plate1_TF_SP4_P1A5_dose0.25_rep1

description: Library name: P1A5


title: Mono-mac-6-sgDDX6.2-Rep1


title: RNA-Seq of HD357_C_whole

description:
Library name: B357C_RNA
scRNA-seq


title: Plate1_TF_GATA1_P1H4_dose0.5_rep2

description: Library name: P1H4


title: Mono-mac-6-sgDDX6.1-Rep1


title: RNA-Seq of HD360_B_whole

description:
Library name: B360B_RNA
scRNA-seq


title: Mono-mac-6-sgNS-Rep1


title: RNA-Seq of HD357_B_whole

description:
Library name: B357B_RNA
scRNA-seq


title: RNA-Seq of HD351_C_whole

description:
Library name: B351C_RNA
scRNA-seq


title: RNA-Seq of HD357_A_whole

description:
Library name: B357A_RNA
scRNA-seq


title: Plate1_TF_GATA1_P1G4_dose0.5_rep1

description: Library name: P1G4


title: Plate1_TF_FOXP1_P1F4_dose0.5_rep2

description: Library name: P1F4


title: RNA-Seq of HD351_B_whole

description:
Library name: B351B_RNA
scRNA-seq


title: RNA-Seq of HD361_C_CD3

description:
Library name: B361C_RNA
scRNA-seq


title: Plate1_TF_FOXP1_P1E4_dose0.5_rep1

description: Library name: P1E4


title: PDX2263_day5_sgNeg_rep2

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

data_processing:
Sequencing reads were aligned to human genome hg38 using STAR Aligner. Raw read counts were generated via HTSeq-count.
Assembly: hg38
Supplementary files format and content: txt, tab, raw read counts

source_name: human AML PDX-2263

growth_protocol: MOLM-13 and MV4-11 were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Fetal Serum (FBS) and 1% Penicillin/ Streptomycin. PDX-2263 cells were cultured in BM media (IMDM supplemented with 15% Fetal Bovine Serum (FBS), 1% P/S, 1% GlutaMAX) and human cytokines, including 1:1000 dilution of the10ng/μl human IL-3 (Peprotech#200-03), 10ng/μl human FLT3 (Peprotech#300-19), 100ng/μl human SCF (Peprotech#300-07), 20ng/μl human IL-6 (Peprotech#200-06), and 10 ng/μl human TPO (Peprotech#300-18) stock.

extract_protocol:
Total RNA was isolated from 0.5~5 million cells using Direct-zol RNA Miniprep Plus kit (ZYMO) or RNeasy Mini Kit (Qiagen) with DNase I treatment in column.
For MOLM-13 and MV4;11 cells, RNA-seq libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen) with 0.5-2 µg of total RNA according to the manufacturer's protocol. For PDX-2263 cells, RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina. Library quality was checked by High Sensitivity Bioanalyzer (Agilent) and libraries with different barcodes were pooled and sequenced on the Nextseq 500 platform with 75 or 150 bp single-end reads.

treatment_protocol: MOLM-13 and MV4-11 cells were harvested on day 5 post-infection of sgRNA for GAP45-KO; PDX-2263 was harvested on day 5 post-electroporation of CRISPR-RNP. For drug treatment, MOLM-13 was harvesed on day 6 post-infection and day 3 post-treatment.

value: human AML PDX-2263


title: Plate1_TF_ELF1_P1D4_dose0.5_rep2

description: Library name: P1D4


title: PDX2263_day5_sgNeg_rep3


title: PDX2263_day5_sgNeg_rep1


title: RNA-Seq of HD361_A_CD3

description:
Library name: B361A_RNA
scRNA-seq


title: RNA-Seq of PLWH040_A_CD3

description:
Library name: B040A_RNA
scRNA-seq


title: Plate1_TF_ELF1_P1C4_dose0.5_rep1

description: Library name: P1C4


title: PDX2263_day5_sgGAP45_4_rep3


title: RNA-Seq of HD351_A_whole

description:
Library name: B351A_RNA
scRNA-seq


title: RNA-Seq of PLWH037_B_CD3

description:
Library name: B037B_RNA
scRNA-seq


title: PDX2263_day5_sgGAP45_4_rep2


title: Plate1_TF_SP4_P1B4_dose0.5_rep2

description: Library name: P1B4


title: RNA-Seq of PLWH040_B_CD3

description:
Library name: B040B_RNA
scRNA-seq


title: RNA-Seq of PLWH035_B_CD3

description:
Library name: B035B_RNA
scRNA-seq


title: RNA-Seq of PLWH037_A_CD3

description:
Library name: B037A_RNA
scRNA-seq


title: Plate1_TF_GATA1_P1H3_dose0.75_rep2

description: Library name: P1H3


title: Plate1_TF_SP4_P1A4_dose0.5_rep1

description: Library name: P1A4


title: RNA-Seq of PLWH029_A_CD3

description:
Library name: B029A_RNA
scRNA-seq


title: RNA-Seq of PLWH027_A_CD3

description:
Library name: B027A_RNA
scRNA-seq


title: PDX2263_day5_sgGAP45_3_rep2


title: PDX2263_day5_sgGAP45_3_rep3


title: Plate1_TF_GATA1_P1G3_dose0.75_rep1

description: Library name: P1G3


title: RNA-Seq of PLWH027_B_CD3

description:
Library name: B027B_RNA
scRNA-seq


title: PDX2263_day5_sgGAP45_4_rep1


title: RNA-Seq of HD361_B_CD3

description:
Library name: B361B_RNA
scRNA-seq


title: RNA-Seq of PLWH029_B_CD3

description:
Library name: B029B_RNA
scRNA-seq


title: Plate1_TF_FOXP1_P1F3_dose0.75_rep2

description: Library name: P1F3


title: RNA-Seq of PLWH023_A_CD3

description:
Library name: B023A_RNA
scRNA-seq


title: RNA-Seq of PLWH023_B_CD3

description:
Library name: B023B_RNA
scRNA-seq


title: RNA-Seq of PLWH017_B_CD3

description:
Library name: B017B_RNA
scRNA-seq


title: PDX2263_day5_sgGAP45_3_rep1


title: Plate1_TF_FOXP1_P1E3_dose0.75_rep1

description: Library name: P1E3


title: MOLM13-SgNeg-veh-3

source_name: human AML MOLM-13 cell line

value: human AML MOLM-13 cell line


title: RNA-Seq of PLWH035_A_CD3

description:
Library name: B035A_RNA
scRNA-seq


title: RNA-Seq of PLWH017_A_CD3

description:
Library name: B017A_RNA
scRNA-seq


title: RNA-Seq of PLWH015_B_CD3

description:
Library name: B015B_RNA
scRNA-seq


title: MOLM13-SgNeg-veh-2


title: Plate1_TF_ELF1_P1D3_dose0.75_rep2

description: Library name: P1D3


title: RNA-Seq of PLWH012_B_CD3

description:
Library name: B012B_RNA
scRNA-seq


title: RNA-Seq of PLWH012_A_CD3

description:
Library name: B012A_RNA
scRNA-seq


title: RNA-Seq of PLWH015_A_CD3

description:
Library name: B015A_RNA
scRNA-seq


title: RNA-Seq of PLWH008_B_CD3

description:
Library name: B008B_RNA
scRNA-seq


title: Plate1_TF_SP4_P1B3_dose0.75_rep2

description: Library name: P1B3


title: Plate1_TF_ELF1_P1C3_dose0.75_rep1

description: Library name: P1C3


title: 293FT, shRNA2 circMAN1A2(2,3,4,5) KD, replicate2

value: circMAN1A2(2,3,4,5) knockdown

value: circMAN1A2(2,3,4,5) shRNA KD


title: 293FT, shRNA2 circMAN1A2(2,3,4,5) KD, replicate1


title: MOLM13-SgNeg-MBQ-3


title: RNA-Seq of PLWH008_A_CD3

description:
Library name: B008A_RNA
scRNA-seq


title: MOLM13-SgNeg-MBQ-2


title: Plate1_TF_SP4_P1A3_dose0.75_rep1

description: Library name: P1A3


title: MOLM13-SgNeg-MBQ-1


title: Plate1_TF_GATA1_P1H2_dose1_rep2

description: Library name: P1H2


title: Plate1_TF_GATA1_P1G2_dose1_rep1

description: Library name: P1G2


title: 293FT, shRNA1 circMAN1A2(2,3,4,5) KD, replicate1


title: 293FT, scramble, replicate1

value: scramble


title: MOLM13-SgGAP45_4-veh-3


title: A549, shRNA2 circMAN1A2(2,3,4,5) KD, replicate2


title: 293FT, scramble, replicate2


title: Plate1_TF_FOXP1_P1F2_dose1_rep2

description: Library name: P1F2


title: A549, shRNA2 circMAN1A2(2,3,4,5) KD, replicate1


title: A549, shRNA1 circMAN1A2(2,3,4,5) KD, replicate2


title: MOLM13-SgGAP45_4-veh-2


title: MOLM13-SgNeg-veh-1


title: A549, shRNA1 circMAN1A2(2,3,4,5) KD, replicate1


title: MOLM13-SgGAP45_4-veh-1


title: CAU3

city: 广州市

first: 心怡

last: 任

state: 广东省

address: 黄埔大道601号

institute: 暨南大学

description: replicate biosample 3

data_processing:
The clean reads were mapped to the reference genome using HISAT2 . After that, Ericscript (v0.5.5)  and rMATS (V3.2.5)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.12) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.44.0) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include different gene for each group

source_name: ovarian

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

value: ovarian

value: xenograft tumors of the breast cancer cell line MDA-MB-231 in female BALB/c nude mice

value: caulerpin


title: A549, scramble, replicate2


title: CAU2

description: replicate biosample 2


title: MOLM13-SgGAP45_4-MBQ-3


title: Plate1_TF_ELF1_P1D2_dose1_rep2

description: Library name: P1D2


title: Plate1_TF_ELF1_P1C2_dose1_rep1

description: Library name: P1C2


title: Plate1_TF_SP4_P1B2_dose1_rep2

description: Library name: P1B2


title: CAU1

description: replicate biosample 1


title: MOLM13-SgGAP45_4-MBQ-2


title: CTX3

description: replicate biosample 3

value: cyclophosphamide (CTX)


title: HeLa, shRNA2 circMAN1A2(2,3,4,5) KD, replicate2

source_name: HeLa

value: HeLa


title: MOLM13-SgGAP45_4-MBQ-1


title: Plate1_TF_SP4_P1A2_dose1_rep1

description: Library name: P1A2

value: roboATAC


title: CTX2

description: replicate biosample 2


title: MOLM13-SgGAP45_3-veh-3


title: HeLa, shRNA2 circMAN1A2(2,3,4,5) KD, replicate1


title: CTX1

description: replicate biosample 1


title: benchmarking_HEK293T_roboATAC_rep8_ultima

description: Library name: SV03_08_ultima


title: Plate1_TF_FOXP1_P1E2_dose1_rep1

description: Library name: P1E2


title: HeLa, shRNA1 circMAN1A2(2,3,4,5) KD, replicate2


title: benchmarking_HEK293T_roboATAC_rep7_ultima

description: Library name: SV03_07_ultima


title: UT3

description: replicate biosample 3


title: MOLM13-SgGAP45_3-veh-1


title: HeLa, shRNA1 circMAN1A2(2,3,4,5) KD, replicate1


title: ChiP2-Ibd2

description: Library name: Ibd2 ChIP-Seq2

source_name: B2086 Ibd2-FZZ

value: B2086 Ibd2-FZZ

value: Vegetative Growth

value: Mpr+/Mpr+ (II, mp-s) Ibd2-FZZ

value: Immunoprecipitation


title: HeLa, scramble, replicate2

value: WT


title: A549, scramble, replicate1


title: UT1

description: replicate biosample 1


title: ChIP1-Ibd2

description: Library name: Ibd2 ChIP-Seq1


title: UT2

description: replicate biosample 2


title: HeLa, scramble, replicate1


title: MOLM13-SgGAP45_3-MBQ-2

value: AML


title: MOLM13-SgGAP45_3-MBQ-1


title: DLD-1, shRNA2 circMAN1A2(2,3,4,5) KD, replicate2


title: CM-IR-3

city: MONROVIA

first: Yahuei

last: Kuo

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to mm10 using Tophat2 with default settings
Gene expression level of RefSeq mm10 coding genes were quantified using HTSeq v0.6.1p1
Assembly: mm10
Supplementary files format and content: tab delimited text file gene expression raw counts
Supplementary files format and content: tab delimited text file gene expression RPKM

source_name: LSK

extract_protocol:
Total RNA was isolated from LSK using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, 80224)
RNA-seq with KAPA RNA HyperPrep with RiboErase
stranded RNA-seq with Ribosomal RNA removal

treatment_protocol: The LSK population (Lin-Sca1+ckit+) was sorted out from the bone marrow of preleukemic stage Cbfb-MYH11 mice and wild-type mice and exposed to irridiation (3.5Gy). Twenty-four hours after the irridiation, cells were harvested and sujected to RNA extraction. LSK cells went through the same incubation process without irridiation were collected as control.

tag: library type

value: mRNA

value: LSK

value: CM

value: IR


title: MOLM13-SgGAP45_3-MBQ-3

value: human AML MOLM-13 cell line


title: MV411_sgGAP45_3

source_name: human AML MV4-11 cell line

value: human AML MV4-11 cell line


title: INPUT2-Ibd2

description: Library name: Ibd2 Input-Seq2

value: Whole cell extraction


title: CM-IR-2


title: MOLM13-SgGAP45_3-veh-2


title: INPUT1-Ibd2

description: Library name: Ibd2 Input-Seq1


title: DLD-1, shRNA1 circMAN1A2(2,3,4,5) KD, replicate2

value: circMAN1A2(2,3,4,5) knockdown

value: circMAN1A2(2,3,4,5) shRNA KD


title: 293FT, shRNA1 circMAN1A2(2,3,4,5) KD, replicate2


title: CM-IR-1


title: MV411_sgGAP45_1_rep2


title: wild type

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

description: Library name: WT

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: 10x Genomics 2024-A
Supplementary files format and content: CellRanger output files: filtered_peak_bc_matrix.h5 , fragments.tsv.gz

source_name: spleen

growth_protocol: Spleen were harvested from WT and p52ki/ki mice (1 each) on day 9 post immunisation with NP-OVA and alum.

extract_protocol:
These sorted B cells (1 wt and 1 p52 ki/ki) were sent to immunogenomics facility at SIgN to be processed for single cell ATAC-seq on the 10x Genomics Chromium platform.
Their protocol: Briefly, nuclei were prepared from sorted cells as per the 10x Genomics Demonstrated Protocol CG000169 followed by processing with the Chromium Single Cell ATAC Kit v2 following the manufacturer’s protocol, targeting the capture of up to 5000 nuclei. After quantification on the Agilent Bioanalyzer, ATAC-seq libraries were pooled for sequencing on the Illumina NovaSeq X, with the cycle configuration of Read 1N-151 cycles; i7 index-8 cycles, i5 index-16 cycles; Read 2N-151 cycles, targeting about 200 million reads-pairs/sample.

treatment_protocol: B cells were isolated from spleen cells and stained for FACs. Naive (CD19+IgD+) and activated B cells  (CD19+IgD-) were sorted and mixed at 1:3 ratio.

value: spleen

value: B cells


title: MV411_sgGAP45_1_rep1


title: p52: ETS1 interaction disrupted mice, p52ki/ki mice

description: Library name: K11


title: control-IR-3


title: DLD-1, shRNA1 circMAN1A2(2,3,4,5) KD, replicate1


title: A+R 3

city: Jinan

first: Chen

last: He

address: Wenhua Road

institute: Shandong University

data_processing:
llumina Casava1.7 sotware used for bascealing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000182965.3 whole genome using hisat2
Fragment Per Kilobase per Million bases of library size (FPKM) were calculated using cufflinks v2.2.1
The differentially expressed genes were detected as previously described based on the parameters of DeSeq2: Fold change > = 2.00 and Probability > = 0.8 with a significant false discovery rate-adjusted P value (FDR) <0.05
Assembly: GCF_000182965.3
Supplementary files format and content: tab delimited text files include FPKM values for each Sample.

organism: Candida albicans

growth_protocol: Overnight grown C. albicans SC5314  was diluted to E6 cells per mL in RPMI1640 medium, and treated with 0.5μg/mL Amb alone or plus 8μg/mL rimonabant at 30℃ for 6 h.  The same volume of dimethyl sulfoxide-treated cells were set as control group.

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 0.5μg/mL Amb and 8ug/mL Rimonabant


title: DLD-1, scramble, replicate2

value: scramble


title: control-IR-2


title: MV411_sgNeg_rep2


title: A+R 2


title: DLD-1, scramble, replicate1


title: DLD-1, shRNA2 circMAN1A2(2,3,4,5) KD, replicate1


title: MV411_sgNeg_rep1


title: CM-NIR-3

value: NIR


title: A+R 1


title: CM-NIR-2


title: A3

value: 0.5μg/mL Amb


title: HT29, shRNA2 circMAN1A2(2,3,4,5) KD, replicate1


title: MOLM13_sgGAP45_3_rep2


title: MOLM13_sgGAP45_3_rep1


title: CM-NIR-1


title: MOLM13_sgGAP45_1_rep2


title: A2


title: control-NIR-3

value: WT


title: HT29, shRNA1 circMAN1A2(2,3,4,5) KD, replicate2


title: control K3

value: without drug treatment


title: RNA-Seq of 017_023_027_029_pooled_whole

description:
Library name: PT3_RNA
scRNA-seq

value: colon

value: colon primary cells

value: HIV-1 positive

value: Antiretroviral therapy


title: control-NIR-2

value: mRNA

value: LSK


title: HT29, shRNA1 circMAN1A2(2,3,4,5) KD, replicate1


title: control K2


title: HT29, scramble, replicate2


title: control-IR-1

value: IR


title: control-NIR-1


title: MOLM13_sgNeg_rep1

value: human AML MOLM-13 cell line

value: AML


title: HT29, shRNA2 circMAN1A2(2,3,4,5) KD, replicate2

value: circMAN1A2(2,3,4,5) knockdown

value: circMAN1A2(2,3,4,5) shRNA KD


title: control K1


title: HT29, scramble, replicate1


title: RL95-2 cells, 10 nM 11KDHT Biol. Repl 2

status: Public on Jul 26 2025

city: Ljubljana

first: Marija

last: Gjorgoska

state: Outside North America

address: Vrazov trg 2

country: Slovenia

institute: Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana

description:
Library name: Sample 17
Column name in FPKM_All_Samples.txt: RL95-2_11KDHT_10nM_B

data_processing:
Raw reads were processed with fastp software to remove adapter sequences, poly-N reads, and low-quality reads. Clean reads were aligned to the reference genome (Homo Sapiens [GRCh38/hg38]) using HISAT2 v2.0.5.
Gene-level counts were generated using featureCounts v1.5.0-p3, and gene expression was quantified as FPKM.
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
Assembly: GRCh38

growth_protocol: Ishikawa cells were maintained in Eagle’s Minimum Essential Medium (#M5650, Gibco) with 5% FBS. RL95-2 cells were maintained in DMEM/F12 (#D6421, Sigma Aldrich GmbH) with 10% FBS, 2.5 mM L-glutamine. Cells were maintained in humidified athmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Macherey Nagel RNA extraction kit ((#740933.5, Macherey-Nagel GmbH&Co, Germany).
mRNA sequencing was performed at Novogene Inc. mRNA was enriched using poly-T oligo-attached magnetic beads and fragmented. First-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand synthesis using dTTP for non-directional libraries. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Library quality was assessed by Qubit, real-time PCR, and Bioanalyzer to determine concentration and fragment size distribution. Libraries were pooled and sequenced on an Illumina platform using paired-end 150 bp (PE150) reads, generating approximately 12 Gb of raw data per sample.

treatment_protocol: Ishikawa cells were seeded at cell density 3.5 x 10^5/well in 6-well plates in complete culture medium. RL95-2 cells were seeded at cell density 3.5 millions/well in 6-well plates in complete culture media. After 24h, the culture media was replaced with phenol-red free, steroid-free culture media with L-glutamine as a supplement. 5 uL of steroid in ethanol/well was added. Cells were incubated for 72h in humidified athmosphere with 5% CO2 at 37C.

value: Endometrial cancer cell line

value: Wild type

value: 10 nM 11-keto-dihydrotestosterone (11KDHT)

tag: batch


title: RL95-2 cells, 10 nM 11KDHT Biol. Repl 3

description:
Library name: Sample 18
Column name in FPKM_All_Samples.txt: RL95-2_11KDHT_10nM_C


title: MOLM13_sgGAP45_1_rep1


title: RL95-2 cells, 10 nM DHT Biol. Repl 3

description:
Library name: Sample 15
Column name in FPKM_All_Samples.txt:RL95-2_DHT_10nM_C

value: 10 nM dihydrotestosterone (DHT)


title: RL95-2 cells, 10 nM 11KDHT Biol. Repl 1

description:
Library name: Sample 16
Column name in FPKM_All_Samples.txt: RL95-2_11KDHT_10nM_A


title: MOLM13_sgNeg_rep2


title: RL95-2 cells, 10 nM DHT Biol. Repl 1

description:
Library name: Sample 13
Column name in FPKM_All_Samples.txt: RL95-2_DHT_10nM_A


title: RL95-2 cells, 10 nM DHT Biol. Repl 2

description:
Library name: Sample 14
Column name in FPKM_All_Samples.txt: RL95-2_DHT_10nM_B