title: KNF1F2-H3K27ac,  replicate HiChIP 2

status: Public on Sep 21 2024

city: Salt Lake City

first: Katherine

last: Gillis

state: UT

address: 2000 CIRCLE OF HOPE DR

institute: Snyder Lab at Huntsman Cancer Institute

data_processing:
The paired-end HiChIP sequencing reads were aligned to the mouse genome mm10 with the HiC-Pro pipeline (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x ).
HiC-DC+ was used to call chromatin loops by binning the genome into 5kb bins (https://www.nature.com/articles/s41467-021-23749-x#citeas).
Chromatin loops were removed if the qvalue < 0.05 or anchors overlapped with ENCODE blacklist regions (https://www.nature.com/articles/s41598-019-45839-z ).
Assembly: build mm10
Supplementary files format and content: allValidPairs file containing H3K27ac interactions for all samples.
Library strategy: HiChIP

source_name: lung

extract_protocol:
KN and KNF1F2 tumor-bearing mice were euthanized at 14 weeks post tumor initiation and the rib-cage was dissected to reveal the trachea and heart. Lungs were perfused with cold PBS, removed, and snap frozen in liquid nitrogen. Flash-frozen lungs were minced on ice in 2 ml of ice-cold PBS for 3 – 5 min. Minced lungs were dounced 10 times with a large 7 ml homogenizer (Wheaton) and centrifuged for 5 min at 4°C (300G). Tissue was crosslinked in 2 mM DSG buffer (1X PBS, 1 mM MgCl2) for 35min, then formaldehyde was added to final concentration of 1% and incubated for 10min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. After fixation, lung samples were resuspended in 2 – 3 ml of TST buffer (Slyper et al. 2020) with protease inhibitors for 5 min. During this time, samples were dounced an additional 5 times in a small 2 ml homogenizer (Wheaton) to extract nuclei. Lysis was quenched with 5 ml of 1X ST buffer (Slyper et al. 2020) plus protease inhibitors. Nuclei were washed in cold PBS and resuspended in 5 – 10 ml cold PBS supplemented with DAPI and protease inhibitors. Nuclei suspension was then sequentially filtered through a 70 μm and 35 μm cell strainer. Nuclei were sorted using BD FACSAria with the 85 μm nozzle for GFP-positive, DAPI-positive nuclei. Samples were sorted into 1 ml of cold PBS with 1% BSA and 10X protease inhibitor. Approximately 10 million nuclei were sorted for HiChIP experiments.
HiChIP protocol based on Mumbach et al., 2016, Nature Methods. Cross-linked chromatin was digested with the MboI restriction enzyme followed by end-repair with dNTPs including biotin labeled dATP, ligation using T4 DNA ligase, and sonication to obtain 1kb chromatin fragments using Qsonica (Q800). To enrich for chromatin interactions occurring at active regulatory elements, an anti-H3K27ac antibody (Abcam, ab4729, rabbit polyclonal, 7.5ug/HiChIP) was used for DNA fragment capture. Streptavidin magnetic beads were used to pull down ligated DNA fragments and HiChIP libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Kit. Sequencing was performed with the Illumina Nextera Library preparation.

treatment_protocol: Mice were treated with tamoxifen (Sigma) dissolved in corn oil at a dose of 120mg/kg. Mice received 4 injections over the course of 5 days. One day following injections, mice were given pellets supplemented with 500mg/kg (Envigo) tamoxifen for 7 days. Tumors were harvested 8 weeks post tamoxifen treatment and nuclei were sorted for GFP+ DAPI+ population.

value: lung

tag: chip-antibody

value: H3K27ac (Active Motif, 39133)

value: KrasFSF-G12D/+; Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F; FoxA1F/F; FoxA2F/F

value: tamoxifen


title: KN-H3K27ac, replicate HiChIP 2

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: 3 day KN tumor, replicate methyl-seq 3

data_processing:
Fastq reads were aligned to the mouse genome (build mm10) with Novocraft novoalign (version 4.03.01) in bisulfite mode (-b 4) with the following options: set penalty for unconverted CHG or CHH cytosines (option -u) to 12, hard clip 3’ bases to quality 20 (option -H), adapter trimming (option -a), and performance tuning set to ‘NOVOSEQ’.
Extreme coverage regions were identified using depth-normalized (Reads Per Million) mean coverage of replicates and MACS2 bdgpeakcall with an absolute depth cutoff of 2 RPM (mean depth was < 0.1), length 200 bp, and gap 500 bp. Alignments overlapping extreme regions were excluded from further analysis. Duplicate alignments were removed using samtools (version 1.16) fixmate and markdup (mode -s).
Alignments were processed with USeq NovoalignBisulfiteParser (version 9.3.0) to collect converted and non-converted C counts with minimum mapping quality score (-q) of 13 and minimum base quality score (options -b and -c) of 20. Measured lambda phage DNA conversion efficiency was typically > 99.7%.
BisMark compatible coverage files were generated from the Converted and NonConverted .useq files using the useq2bismark_methylation_extractor application (https://github.com/tjparnell/HCI-Scripts/blob/master/Methylation/useq2bismark_methylation_extractor.pl).
Assembly: build mm10
Supplementary files format and content: Bismark compatible coverage files containing counts of coverted and non-coverted CpGs for each sample. BigWig CpG fraction methylation files for each sample.

growth_protocol: Organoid cultures grown in 50% L-WRN conditioned media (Miyoshi and Stappenbeck, 2013).

extract_protocol:
DNA was extracted using the Dneasy Blood and Tissue (Qiagen).
DNA libraries were prepped using the NEBNext® Enzymatic Methyl-seq Kit with at least 10 ng of genomic DNA

treatment_protocol: Organoid cultures treated with 4-OH tamoxifen or ethanol for 48hr to delete Foxa1/2 conditional alleles. Cell pellets were collected two weeks post-deletion for DNA extraction. Mice were treated with tamoxifen (Sigma) dissolved in corn oil at a dose of 120mg/kg. Mice received 4 injections over the course of 5 days. One day following injections, mice were given pellets supplemented with 500mg/kg (Envigo) tamoxifen for 7 days. Tumors were harvested 8 weeks post tamoxifen treatment and cells were sorted for GFP+ DAPI- population.


title: 3 day KN tumor, replicate methyl-seq 2


title: 2 week KN tumor, replicate methyl-seq 2


title: 3 day KN tumor, replicate methyl-seq 1


title: 7 day KN tumor, replicate methyl-seq 1


title: 2 week KN tumor, replicate methyl-seq 3


title: 2 week KN tumor, replicate methyl-seq 1


title: Alkb-Treated-Input-for-mouseICC-TRACseq

status: Public on Sep 22 2024

city: Guangzhou

first: Haining

last: Liu

address: Zhongshan road 2

country: China

institute: The first affiliated hospital of sun yat-sen university

library_source: transcriptomic

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Assembly: hg38
Supplementary files format and content: RNA-Seq RPKMs
Supplementary files format and content: TRAC-Seq RPMs
Library strategy: TRAC-Seq

molecule: total RNA

source_name: intrahepatic cholangiocarcinoma tissue

growth_protocol: Human ICC cell lines were  cultured in RMPI 1640 medium. LTP-C9 mouse ICC cell line was cultred in DMEM medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃. Mouse ICC tissues was established by hydrodynamic transfection of myrAKT and YAPS127A

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: Mettl1 gene knockdown was mediated by short hairpin RNA. Mettl1 gene knockout was mediated by CRISPR-Cas9 system

value: wild type

tag: sample type

value: small RNA-TRAC-Seq

value: intrahepatic cholangiocarcinoma tissue


title: 7 day KN tumor, replicate methyl-seq 2


title: KNF1F2-TET2-Input, replicate 2

data_processing:
Fastq reads were pre-processed by merging the third Fastq containing the Unique Molecular Index with Read1 and Read2 using the merge_umi_fastq application from the UMIScripts package (https://github.com/HuntsmanCancerInstitute/UMIScripts)
Reads were aligned using Bowtie2 version 2.4.4 to the standard chromosomes of the mouse genome (build mm10). Duplicate alignments based on the UMI code were removed using the bam_umi_dedup application (UMIScripts) allowing for 1 mismatch.
Peaks were called using MACS2 version 2.2.7 with a significance of q-value < 0.05. Coverage tracks were generated with MACS2 as Reads Per Million.
Assembly: build mm10
Supplementary files format and content: bigWig, BED files (except for Input samples)

extract_protocol:
For all organoid experiments, two 24-well plates (approximately 4 – 8 million cells) were collected in Cell Recovery Solution (500 µl per dome). Organoids were submerged in ice for 30 min before centrifugation at 4°C (300G). Cells were washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). After the third wash, organoids were resuspended in 2 mM DSG buffer (1X PBS, 1 mM MgCl2) and rotated at room temperature for 35 min. Formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were washed with cold PBS, then frozen at -80. Cell pellets were thawed on ice for 5 min then lysed in 1 ml of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) for all TF experiments or 400 ul of Chromatrap Hypotonic buffer (catalog #100007) for all histone experiments. Samples were centrifuged at 4°C (1000G) then resuspended in 1ml of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) or 100 µl of Chromatrap Lysis buffer (catalog #100005) for TF and histone ChIPs respectively. Chromatin extract was sonicated with QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 min; amplitude: 70%) then was brought up to a volume of 1 ml with RIPA lysis buffer. Chromatin from all samples was immunoprecipitated with antibodies premixed with Protein A Dynabeads: FoxA1 (Abcam, ab170933, rabbit monoclonal, 5 µg/ChIP).
For in vivo experiments, KN and KNF1F2 tumor-bearing mice were euthanized at 14 weeks post tumor initiation and the rib-cage was dissected to reveal the trachea and heart. Lungs were perfused with cold PBS, removed, and snap frozen in liquid nitrogen. Flash-frozen lungs were minced on ice in 2 ml of ice-cold PBS for 3 – 5 min. Minced lungs were dounced 10 times with a large 7 ml homogenizer (Wheaton) and centrifuged for 5 min at 4°C (300G). Tissue was crosslinked in 2 mM DSG buffer and 1% Formaldehyde as previously described (In vitro organoid ChIP-seq). After fixation, lung samples were resuspended in 2 – 3 ml of TST buffer (Slyper et al. 2020) with protease inhibitors for 5 min. During this time, samples were dounced an additional 5 times in a small 2 ml homogenizer (Wheaton) to extract nuclei. Lysis was quenched with 5 ml of 1X ST buffer (Slyper et al. 2020) plus protease inhibitors. Nuclei were washed in cold PBS and resuspended in 5 – 10 ml cold PBS supplemented with DAPI and protease inhibitors. Nuclei suspension was then sequentially filtered through a 70 μm and 35 μm cell strainer. Nuclei were sorted using BD FACSAria with the 85 μm nozzle for GFP-positive, DAPI-positive nuclei. Samples were sorted into 1 ml of cold PBS with 1% BSA and 10X protease inhibitor. Approximately 3 million nuclei were sorted for histone ChIP-seq and 10 million for TF ChIP-seq experiments.  After sorting, nuclei were pelleted for 10 min at 4°C (500G) then resuspended in Chromatrap Hypotonic and Lysis buffers and sonicated as previously described (In vitro organoid ChIP-seq). Chromatin was immunoprecipitated with antibodies premixed with Protein A Dynabeads: FoxA1 (Abcam, ab170933, rabbit monoclonal, 5 µg/ChIP), TET3 (Sigma, ABE290, rabbit polyclonal, 5 µg/ChIP) and H3K27ac (Active Motif, 39133, rabbit polyclonal, 5 µg/ChIP).
ChIP-seq libraries were prepared using the ChIP-Seq with NEBNext Ultra II DNA Library Prep Kit. 10ng of DNA was used as strating material for input and IP samples.

treatment_protocol: For in vitro experiments, organoid cultures treated with ethanol for 48hr, then collected two weeks post treatment for ChIP. Mice were treated with tamoxifen (Sigma) dissolved in corn oil at a dose of 120mg/kg. For in vivo experiments, mice received 4 injections over the course of 5 days. One day following injections, mice were given pellets supplemented with 500mg/kg (Envigo) tamoxifen for 7 days. Tumors were harvested 8 weeks post tamoxifen treatment and nuclei were sorted for GFP+ DAPI+ population.

value: TET2 (CST D6C7K)


title: KNF1F2-TET2-Input, replicate 1


title: KN-TET2-Input, replicate 2


title: Input-CT1-KO

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Assembly: hg38
Supplementary files format and content: RNA-Seq RPKMs
Supplementary files format and content: TRAC-Seq RPMs

molecule: polyA RNA

organism: Homo sapiens

source_name: intrahepatic cholangiocarcinoma cell line

value: Mettl1 knockout

value: RNA-Seq

tag: cell line

tag: cell type

value: intrahepatic cholangiocarcinoma cell


title: KN-FoxA2, replicate 2

value: FoxA2 (CST D56D6)


title: KN-TET2, replicate 1


title: KN-FoxA2-Input, replicate 2


title: BMDM, R3-2

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

data_processing:
All the reads were mapped to the mouse reference genome (GRCm38/mm10) using STAR aligner (v2.5.0c)
Alignments were guided by a Gene Transfer File (Ensembl GTF version GRCm38.74) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126)
The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4).
Read count tables were generated using HTSeq (v0.6.0) normalized based on their geometric library size factors using DESeq2 (v3.0) and Deferential Expression (DE) analyses were performed.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Bone marrow

growth_protocol: For mouse bone marrow derived macrophages (BMDMs), BMDMs were obtained from bone marrow of the tibia and femur, and cultured in DMEM with 10% FBS, 20 ng/ml mouse M-CSF (PeproTech), and 1% penicillin/streptomycin for 6 d and then replated and used for experiments.

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (QIAGEN, CA).
RNA-seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA).

treatment_protocol: Mouse BMDMs were treatment with 100 µM deoxycholic acid or butyrate for 24h.

value: Bone marrow

value: BMDM

value: macrophage

value: deoxycholic acid


title: KN-FoxA2, replicate 1


title: KNF1F2-TET2, replicate 2


title: BMDM, NC-2


title: KN-FoxA2-Input, replicate 1


title: BMDM, NC-1


title: KNF1F2-TET2, replicate 1


title: 7 day KN tumor, replicate methyl-seq 3


title: BMDM, WT-2


title: BMDM, But-2

value: butyrate


title: BMDM, But-1


title: BMDM, WT-1


title: In vivo sorted tumor Ptges KO2

city: Philadelphia

first: Il-Kyu

last: Kim

state: Pennsylvania

address: 421 Curie Blvd.

department: Department of Medicine

institute: University of Pennsylvania

data_processing:
Salmon v1.8.0
DESeq2
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: excel files include TPM values for each sample

source_name: Pancreas

growth_protocol: 6419c5 pancreatic cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% Glutamine, and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using the NucleoSpin RNA Kit (Takara Bio)
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocol

treatment_protocol: In vitro samples were prepared at a steady state, and in vivo bulk and sorted tumor samples were from subcutaneously inoculated tumors

value: Pancreas

value: Epithelial pancreatic cancer cells

value: Ptges KO


title: In vivo sorted tumor Ptges KO4


title: In vivo sorted tumor EP4 KO4

value: EP4 (Ptger4) KO


title: In vivo sorted tumor Ptges KO3


title: In vivo sorted tumor Ptges KO1


title: In vivo sorted tumor EP4 KO3


title: KN-TET2, replicate 2

value: lung

value: tamoxifen


title: In vivo sorted tumor EP4 KO1


title: In vivo sorted tumor EP4 KO2


title: KN-TET2-Input, replicate 1


title: In vivo sorted tumor control2

value: WT


title: In vivo sorted tumor control4


title: In vivo sorted tumor control1


title: In vitro Ptges KO2


title: BMDM, R3-1

value: wild type


title: In vitro Ptges KO3


title: In vitro EP4 KO3


title: In vitro EP4 KO2


title: In vitro Ptges KO1


title: In vitro EP4 KO1


title: In vitro control2


title: In vitro control3


title: In vivo bulk Ptges KO4


title: In vivo bulk Ptges KO3


title: In vivo bulk Ptges KO2


title: In vivo bulk EP4 KO4


title: In vivo sorted tumor control3


title: In vivo bulk EP4 KO1


title: In vivo bulk control1


title: In vivo bulk Ptges KO1


title: In vivo bulk control5


title: In vivo bulk EP4 KO2


title: In vivo bulk EP4 KO3


title: In vivo bulk control4


title: In vivo bulk control2


title: In vivo bulk control3


title: LUNG_GEX, 10x scRNAseq, Gene Expression

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description: 10x Genomics

data_processing:
Bulk RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3. Differential gene expression was analyzed using edgeR.
scRNA-seq: 10x Genomics Cellranger v7.0.0 was used to process fastq files and generate matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.1 in R v4.1.3/ Rstudio.
Assembly: mm10
Supplementary files format and content: Bulk RNAseq: TPM expression matrix files were extracted from RSEM gene-results and initially filtered for expressed protein-coding genes.
Supplementary files format and content: scRNAseq: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz; analyzed LUNG only seurat object in rds file.
Library strategy: scRNAseq: HTO hashtags + Gene Expression

source_name: LUNG+BALF

growth_protocol: Flow-sorted Bone marrow neutrophils were stimulated in vitro with control supernatant (s.n.) or ILC2 s.n for 1 hour. Flow-sorted lung ILC2s were cultured with IL-2 and IL-7, plus vehicle, NmU23, IL-25 or IL-33 for 72 hours.

extract_protocol:
DNA and RNA were extracted from cells using AMPure XP beads (Backman)
Bulk RNAseq: Full-length Smart-seq2; scRNAseq: 10x Genomics Chromium Next GEM Single Cell 3’ v3.1

treatment_protocol: Il5cre/+Hilpda+/+ and Il5cre/+Hilpdaflox/flox mice were intranasally challenged with IL-33 for three days.

value: LUNG+BALF

value: primary immune cell

value: CD45+CD3-CD19- cells

tag: strain

value: Balb/c

value: intranasally challenged with IL-33


title: In vivo bulk Ptges KO5


title: In vitro control1


title: KO_2

city: wuhan

first: wang

last: Xuhong

address: 1277 Jiefang Avenue

institute: Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: heart

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Establishing a myocardial infarction model in mouse hearts by ligating the left anterior descending coronary artery and collecting samples after 7 days.

value: heart

value: TSLPR KO

tag: time

value: Day 7

value: Ligation of left anterior descending coronary artery


title: KO_3


title: ILC2_IL2+IL7+IL25_72h_2

data_processing:
Bulk RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3. Differential gene expression was analyzed using edgeR.
scRNA-seq: 10x Genomics Cellranger v7.0.0 was used to process fastq files and generate matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.1 in R v4.1.3/ Rstudio.
Assembly: mm10
Supplementary files format and content: Bulk RNAseq: TPM expression matrix files were extracted from RSEM gene-results and initially filtered for expressed protein-coding genes.
Supplementary files format and content: scRNAseq: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz; analyzed LUNG only seurat object in rds file.

source_name: Lung

value: Lung

value: cultured with IL2, IL7 and IL25


title: ILC2_IL2+IL7+IL33_72h_2

value: cultured with IL2, IL7 and IL33


title: ILC2_IL2+IL7+IL33_72h_1


title: WT_3


title: KO_1


title: In vivo bulk EP4 KO5

value: Pancreas

value: Epithelial pancreatic cancer cells

value: EP4 (Ptger4) KO


title: ILC2_IL2+IL7+IL25_72h_1

value: WT


title: WT_2


title: WT_1


title: Ctrl3-sup

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

library_source: transcriptomic single cell

data_processing:
The data matrix processed by Seurat is output through R language
Assembly: mm10
Supplementary files format and content: tab delimited text file includes data value for each sample
Supplementary files format and content: text file includes data value for each sample

source_name: kidney

extract_protocol:
Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence.
The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification
scRNA-seq,snRNA-seq

value: kidney

value: wide type

value: Control


title: ASO3

value: sodium oxalate


title: ILC2_IL2+IL7+NmU23_72h_1

value: primary immune cell

value: cultured with IL2, IL7 and NmU23


title: ILC2_IL2+IL7_72h_1

value: cultured with IL2 and IL7


title: Neu_ILC2_s.n._1

value: Bone marrow

value: Neutrophil

value: in vitro stimulated with ILC2 supernatant


title: Neu_ILC2_s.n._3


title: Neu_Ctrl_s.n._2

value: in vitro stimulated with control supernatant


title: Neu_ILC2_s.n._2


title: Neu_Ctrl_s.n._1


title: Neu_Ctrl_s.n._3


title: LUNG_FB, 10x scRNAseq, HTO Hashtags

description: 10x Genomics

library_source: other

molecule: other

value: LUNG+BALF

value: CD45+CD3-CD19- cells

value: Balb/c

value: intranasally challenged with IL-33


title: intestine, cKO, rep1

city: Beijing

first: Meng

middle: zhen

last: Li

address: 2 West Yuanmingyuan Road

department: College of biological science

institute: China Agricultural University

data_processing:
none provided
Supplementary files format and content: counts
Supplementary files format and content: fpkm

source_name: intestine

extract_protocol: none provided

value: intestine

value: intestinal epithelial cells

value: Rictor Flox; Villin-Cre


title: intestine, cKO, rep2


title: intestine, cKO, rep3


title: intestine, cKO, rep4


title: intestine, WT, rep4

value: Villin-Cre


title: intestine, WT, rep1


title: intestine, WT, rep2


title: intestine, WT, rep3


title: ILC2_IL2+IL7+NmU23_72h_2

value: Lung

value: WT


title: ILC2_IL2+IL7_72h_2

value: primary immune cell


title: CC_130

city: Moscow

first: Arsenia

last: Alekseeva

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Assembly: Assembly: hg38
Supplementary files format and content: white-space delimited text file includes normalized counts for each Sample

source_name: cancer

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-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: age

value: not collected

tag: Sex

value: cancer


title: CC_23

value: Female


title: CC_25


title: CC_127


title: CC_24


title: CC_21


title: CC_22


title: CC_26


title: CC_27


title: MZsn-dome_biol rep 3

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

country: Germany

institute: University of Freiburg

data_processing:
Novaseq 6000 base calling software RTA3
Trimming: FASTQ paired 150bp files were trimmed for adapter sequence. Low quality reads (Q<30), unpaired reads and reads less than 25 bp were removed, the rest was cropped to 30 bp from the start of the read. All the operations were done using Trimmomatics software on the european Galaxy server.
Mapping: The paired reads were mapped with Bowtie2 on the european Galaxy server, with the option "allow mate dovetailing". The maximum fragment length for valid paired-end alignment was set to 1000 bp. Raw files in our submission come from this step.
Filtering: BAM files were filtered using BAMtools on the european Galaxy server with the parameters {'filters': [{'id': '1', 'isProperPair': 'true', 'isDuplicate': 'false', 'reference': '!chrM', 'mapQuality': '>=30'}]}. Then the fragment ends were shifted as appropriate for ATAC-seq, and only the paired reads with the length less the 110bp ( less than one nucleosome) were kept for further processing . This step was using the "alighmentsieve" program from deeptools suite on the european Galaxy server.
Generation of bigwig files for visualization and scoring: BAM files for all replicates from one stage and genotype were merged using Picard merge command and filtered. Bigwig files were generated with BAM coverage utility ( deeptools), with the parameters bin size =10, normalization method RPKM.
Assembly: danrer11
Supplementary files format and content: Supplementary files format and content: bigwig files, ATAC-seq scores for merged biological replicates for each stage and genotype

organism: Danio rerio

source_name: whole embryo

growth_protocol: embryos were obtained from the natural matings and incubated at 28.5° until the desired stage

extract_protocol:
Chorions were removed by 15 - min. incubation in Pronase E. 3. 30 embryos were deyolked manually with an eyebrow needle in Danieaus medium, centrifuged (500 x g, 5 min, 4°C), resuspended in 100 µl ice-cold PBS and centrifuged again. The cells were resuspended by pipetting in 50 µl ice-cold lysis buffer: (ATAC-RSB (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2), with 0.1% NP40, 0.1% Tween20, and 0.01% digitonin)) and incubated on ice for 5 minutes, then diluted with dilution buffer (1 ml, ATAC-RSB containing 0.1% Tween-20). Nuclei were pelleted at 500 x g, 10 min, 4°C, and resuspended in 16.5 µl PBST.
Tagmentation reaction was assembled according to the manufacturer instructions for Illumina small Tn5 buffer and enzyme kit in 50µl volume and incubated in a thermomixer for 30 min, 37°C, 800 RPM. The samples were purified using Qiagen PCR MinElute Purification kit. The purified transposed mix was pre-amplified for 5 cycles using NEBNext 2x Master Mix (NEB) and Nextera adapters and put on ice. To determine the number of additional cycles, 5 µl of the pre-amplified mixture was used to run a 15 ml qPCR. The amplified libraries were purified using SPRI beads (Beckmann) according to the manufacturer instructions.
Omni-ATAC-seq

treatment_protocol: no treatment

value: whole embryo

tag: developmental stage

value: dome

value: mixed

value: MZsn

value: MZsox19bnanog m1434, m1435


title: MZsn-dome_biol rep 2


title: MZpn-dome_biol rep 2

value: MZpn

value: MZspgnanog m793, m1435


title: MZsn-dome_biol rep 1


title: CC_30

value: Male


title: MZpn-dome_biol rep 1


title: MZnanog-dome_biol rep 2

value: MZnanog

value: MZnanog m1435


title: CC_31


title: CC_29


title: CC_9


title: MZtriple-dome-biol rep 4

value: MZtriple

value: MZsox19bspgnanog m793, m1434,m1435


title: CC_36


title: MZtriple-dome-biol rep 3


title: CC_32


title: MZtriple-dome-biol rep 2


title: CC_37


title: CC_38


title: MZtriple-dome-biol rep 1

value: MZsox19bspgnanog m793, m1434, m1435


title: MZtriple-oblong-biol rep 3

value: oblong


title: CC_49


title: MZtriple-oblong-biol rep 1


title: CC_52


title: MZpn-oblong_biol rep 2


title: MZpn-oblong_biol rep1


title: MZnanog-oblong_biol rep 1


title: MZnanog-oblong_biol rep 2


title: CC_57


title: CC_55


title: CC_58


title: MZtriple-1k-biol rep 3

value: blastomere


title: MZtriple-1k-biol rep 1


title: CC_13

value: cancer


title: CC_59


title: CC_53


title: CC_54

value: Female


title: WT-1k-biol rep 4

value: whole embryo

value: wild-type

value: AB/TL strain


title: WT-1k-biol rep 2


title: CC_86


title: CC_91


title: WT-1k-biol rep 1


title: MZtriple-1k-biol rep 2


title: MZnanog-dome_biol rep 1

value: dome

value: mixed


title: MZtriple-oblong-biol rep 2


title: WT-1k-biol rep 3


title: CC_60


title: CC_96


title: CC_111


title: La_6B

value: not collected


title: La_2B


title: CC_51


title: La_24B


title: Luc 119


title: OpC 5


title: NC 7


title: LC 8


title: PrC 12


title: LuC 118


title: La_5B


title: MKN1_siCont_2

type: RNA

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

country: Japan

institute: Miyagi Cancer Center

description: MKN1, control

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MKN1, control

label_protocol: 100 ng of total RNA was labeled using Low Input Quick Amp Labeling Kit

extract_protocol: RNA from cells was purified using RNeasy Mini Kits (Qiagen, Canada)

value: control


title: MsC 1


title: CC_19

value: Male


title: MKN1_si58_1

description: MKN1, BEX2 knock down

source_name: MKN1, BEX2 knock down


title: CC_20_1


title: MKN1_si57_2

description: MKN1, BEX2 knock down


title: La_15B


title: MKN1_si57_1

description: MKN1, BEX2 knock down


title: GCIY_siCont_2

description: GCIY, control

source_name: GCIY, control

value: GCIY


title: GCIY_siCont_3

description: GCIY, control


title: MKN1_siCont_1

description: MKN1, control


title: GCIY_si58_1

description: GCIY, BEX2 knock down

source_name: GCIY, BEX2 knock down


title: MKN1_si58_2

description: MKN1, BEX2 knock down


title: MKN1_siCont_3

description: MKN1, control


title: MKN1_siCont_4

description: MKN1, control


title: KC 109


title: GCIY_si57_2

description: GCIY, BEX2 knock down


title: GCIY_siCont_4

description: GCIY, control


title: La_25B


title: C.2

city: Lanzhou

first: Xuewen

last: Kang

state: Gansu

address: No. 82, Cuiying Gate, Chengguan District, Lanzhou City, Gansu Province

institute: Lanzhou University Second Hospital

data_processing:
Data processing involved several steps: 1) Quality control using fastp (v0.23.2) including adapter removal, removal of reads with ambiguous bases, quality filtering, and sliding window quality trimming. 2) Removal of rRNA sequences using Bowtie2 (v2.4.5). 3) Alignment of clean reads to the reference genome (Rat Genome, version Rnor_6.0) using HISAT2 (v2.2.1). 4) Conversion of SAM files to BAM files, sorting, and duplicate read filtering using Samtools. 5) Gene expression quantification using RSEM (version 1.3.3) and differential expression analysis using DESeq2 (v1.34.0).
Assembly: The reference genome used was the Rat Genome, version Rnor_6.0.
Supplementary files format and content: Processed data files include SAM and BAM formats, containing alignment information. Final expression data are presented as TPM values. Additional data include PCA plots, correlation coefficient heat maps, and expression heatmaps.

organism: Rattus norvegicus

source_name: Nucleus pulposus

extract_protocol:
Total RNA was extracted from cultured NPCs using the TRIzol Reagent (AG RNAex Pro Reagent, China). RNA degradation and contamination were assessed by electrophoresis on a 1% agarose gel. The quantity of RNA was measured using both the Qubit 4.0 Fluorometer (Thermo Fisher Scientific, Waltham, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific, MA, USA). RNA integrity was accurately determined using the Agilent 4200 TapeStation system (Agilent Technologies, Waldbron, Germany).
Library construction was performed using the ALFA-SEQ RNA Library Prep Kit (Alfa Genetics, China). The key steps included: a) Purification of mRNA from total RNA using poly-T oligo-attached magnetic beads. b) Fragmentation of mRNA using the RT Buffer provided in the ALFA-SEQ RNA Library Prep Kit. c) First-strand cDNA synthesis using random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. d) Terminal repair and 3' terminal adenylation. e) Adapter ligation, fragment selection, and purification. f) PCR amplification using Hi-Fi PCR Mix and primers. g) Purification of PCR products with magnetic beads, followed by evaluation of library fragment size using the Qsep400 high-throughput nucleic acid protein analysis system (Hangzhou Houze Biotechnology Co., LTD., China). The concentration of the final library was measured using the Qubit 4.0 Fluorometer (Thermo Fisher Scientific, Waltham, USA).

value: Nucleus pulposus

value: Primary cells

value: control group (no treatment)


title: MT 5


title: C.3


title: La_1B


title: GCIY_si58_2

description: GCIY, BEX2 knock down


title: B2R.3

value: ntervened with 10 μM BK


title: GCIY_si57_1

description: GCIY, BEX2 knock down


title: GCIY_siCont_1

description: GCIY, control


title: CC_14


title: B2R.2


title: B2R.1


title: La_26B


title: CC_149


title: JY1621, 36-hours germinated seeds at 8℃, rep3

city: Hang Zhou

first: Guangyu

last: Wu

address: No. 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
The cleaned reads were aligned to the reference genome ZS11.v0 using HISAT2 v2.2.1
The raw read counts for each gene were calculated using featureCounts v2.0.6 with pair-end counting mode
Pairwise differential expression analyses were performed using DESeq2 v1.42.0 with the input of raw read counts for each gene
Assembly: ZS11.v0
Supplementary files format and content: Tab-delimited txt file includes raw counts for each sample

organism: Brassica napus

source_name: Seed

extract_protocol:
100 seeds of each sample were used for total RNA extraction, and about 1μg of total RNA was used for the construction of sequencing libraries.
RNA quality examination and sequencing libraries construction were conducted in Biomarker Technologies Co., Ltd. in China following the manufacturer's protocol.

value: Seed


title: JY1621, 36-hours germinated seeds at 8℃, rep2


title: AS_2


title: C.1


title: JY1621, 36-hours germinated seeds at 8℃, rep1


title: PC_44


title: oc_68


title: la_12B


title: JY1621, 8-hours germinated seeds at 8℃, rep3


title: JY1621, 8-hours germinated seeds at 8℃, rep2


title: la_27b


title: la_16B


title: JY1621, 36-hours germinated seeds at 25℃, rep2


title: JY1621, 36-hours germinated seeds at 25℃, rep3


title: JY1621, 8-hours germinated seeds at 8℃, rep1


title: CC_15


title: la_11B


title: JY1621, 8-hours germinated seeds at 25℃, rep3


title: Muscle_Treatment_8

city: Chungnamdo

first: Ki Choon Choi

last: Choi

state: Cheonan

address: Seonghwan-eup

department: Grassland and Forage

country: South Korea

institute: National Institute of Animal Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to ARS-UCD1.2(NCBI) whole genome using Tophat
FPKM calculation using Cufflink
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Bos taurus

source_name: Muscle tissue

growth_protocol: Twelve Hanwoo steers were obtained at 13 months old and were kept in individual cages located at the Daum Hanwoo farm, Jeongeup, Jeollabuk-do, South Korea.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: The animals were divided into two groups: normal diet feed (NF) and alternative diet feed (AF). There are six animals per group (n=6) in each group. Initial body weights for normal diet feed animals were 376.4 kg, whereas for alternate diet feed animals were 415 kg. According to Korean Feeding Standards, NF group hanwoo received rice straw and concentrate, while AF group hanwoo received IRG and WCC silage along with fermented grains for 13 months. As part of early patterning peroids, NF group received rice straw 3.5kg and concentrate 8kg, whereas AF group received IRG silage, WCC silage, and fermented grains (3.0, 5.86, and 7.43 kg, respectively) without concentrate. In late patterning, NF group hanwoo received 1.79 kg of rice straw and 12.57 kg of concentrate, while AF group hanwoo received 0.79 kg of rice straw, 1.29 kg of IRg silage, 0.43 kg of WCC silage, and 8.86 kg of fermented grains. Ad libitum access to water was provided to all animals. The experimental feed was fed twice daily at 9:00 am and 16:00 pm to the animals. An average body weight & daily gain, and feed intake were measured

value: Muscle tissue


title: La_28B

value: cancer


title: JY1621, 8-hours germinated seeds at 25℃, rep2


title: CC_146


title: Muscle_Control_7


title: LpS 6


title: JY1621, 8-hours germinated seeds at 25℃, rep1


title: la_4B


title: Muscle_Control_4


title: OC 63


title: Muscle_Treatment_1


title: JY1621, 36-hours germinated seeds at 25℃, rep1


title: JY1621, Dry seeds, rep2


title: CC_20_2


title: Miyazaki2(M2)

city: Jinzhou

first: Jing

last: Tian

state: Liaoning

address: Linghe District

institute: Jinzhou Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include genecount, TPM, and FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: NBV-MB


title: Miyazaki3(M3)


title: JY1621, Dry seeds, rep1


title: JY1605, 36-hours germinated seeds at 8℃, rep3


title: La_21B


title: Miyazaki1(M1)


title: MENK-Miyazaki3(MM3)

value: MENK-NBV-MB


title: La_3B


title: Liver_Control_7

source_name: Liver tissue

value: Liver tissue


title: JY1605, 36-hours germinated seeds at 8℃, rep2


title: LS 11


title: MENK-Miyazaki2(MM2)


title: Liver_Treatment_1


title: La_20B


title: Adipose_Treatment_2

source_name: Adipose tissue

value: Adipose tissue


title: La_17B


title: JY1621, Dry seeds, rep3


title: JY1605, 8-hours germinated seeds at 8℃, rep3


title: la_10B


title: Adipose_Control_7


title: Liver_Treatment_8


title: CC_150


title: JY1605, 8-hours germinated seeds at 8℃, rep2


title: JY1605, 8-hours germinated seeds at 8℃, rep1


title: JY1605, 36-hours germinated seeds at 25℃, rep3


title: GC 53


title: NC 6


title: Adipose_Control_1


title: Cph, Overexpression, Replicate2

city: Heidelberg

first: Nick

last: Hirschmüller

address: Meyerhofstrasse

department: Genome Biology

institute: European Molecular Biology Laboratory

description: 10x Genomics

data_processing:
Single cell count matricies were generated using CellRanger "count" command with the "include-introns" option (version 7.0.1). Quality control and analyses were conducted using Seurat (version 4.3.0). Raw gene expression count matrices were pre-processed and filtered using scran (version 1.24.0). In brief, droplets with RNA content below each library's inflection point were removed, along with cells meeting any of the following criteria: (a) fewer than 250 detected genes, (b) ranking in the top 1 percentile of cells by UMI count, or (c) a high percentage of mitochondrial reads. One replicate of the NotchRNAi and NotchRNAiCphRNAi condition showed an unusually high content of mitochondrial reads and were removed from subsequent analyses.
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

extract_protocol:
Flies were starved for 3h and placed in vials with filter paper containing 5% sucrose for 16h. 20 midguts were dissected from respective condition in ice-cold PBS, taking care to remove the hindgut, Malpighian tubules and proventriculus. Samples were digested in 1 mg /ml Elastase (Sigma, #E0258) solution at 25°C for 45 min at 1000RPM and vortexed every 15min. Samples were then pelleted and resuspended in PBS and dissociated cells were then passed through a 40uM than 20uM cell strainer and subsequently counted. Approximately 20,000 live cells were used for scRNA-seq with 10X Genomics 5’ V2 kit following the manufacturers protocol for library generation. Prior to sequencing, library fragment size was determined using an Agilent Bioanalyzer high-sensitivity chip and quantified using Qubit. Libraries were multiplexed and sequenced using a Nextseq 550 at the Deep Sequencing Facility, BioQuant, Heidelberg University.
Library preperation was performed according to manufacturers instructions (10X Genomics 5’ V2 kit for knockdown experiments and 10X Genomics 3’ V2 kit for knockout experiments).

value: intestine

value: CphUp


title: Adipose_Treatment_4


title: Cph, Overexpression, Replicate1

description: 10x Genomics


title: CC_16


title: 72hpa BR1

city: Vienna

first: Alexander

middle: Wilhelm

last: Stockinger

address: Dr. Bohr Gasse 9

department: Max Perutz Labs Vienna

country: Austria

institute: University of Vienna

data_processing:
Read alignment and quantification: Cellranger v. 7.0.1 was used to align reads to the Platynereis draft genome (Genbank ID: GCA_026936325.1), prepared using a custom reference (cellranger mkref)
Samples were then imported to Seurat (v. 4.1.3, Butler et al, 2019) and processed using a pipeline adapted from Steger, Cole, Denner, et al., 2022
Assembly: Platynereis draft genome (Genbank ID: GCA_026936325.1)
Supplementary files format and content: A single, processed Seurat object (scd.RData), with several assays and metadata slots relevant to the study. The original sequencing samples are found in sdc@orig.ident according to sample column "description".

organism: Platynereis dumerilii

source_name: posterior trunk segment

extract_protocol:
A single cell suspension was produced following the ACME (ACetic acid MEthanol protocol, Garcia-Castro et al, 2021)
Libraries were prepared using the 10X Genomics Chromium platform, using 10X Dual Index Kit TT

value: posterior trunk segment

value: multiple celltypes

value: PIN strain wildtype

value: 72h post amputation


title: JY1605, 36-hours germinated seeds at 25℃, rep2


title: JY1605, 36-hours germinated seeds at 8℃, rep1


title: 48hpa BR2

value: 48h post amputation


title: JY1605, 36-hours germinated seeds at 25℃, rep1


title: SUDHL4_Parental_BR2

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

data_processing:
Illumina Casava1.7 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR with default paramenters. Genes' Expression have been quantified using HT-Seq count using gencode v22 as gtf.
Read counts have been normalized with TMM algorithm, and converted into log2 counts per million of mapped reads (cpm)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (Raw_Counts sheet)

source_name: B-cell

extract_protocol:
Trizol reagent
Total RNA samples were prepared for RNA-Seq with the NEBNext rRNA Depletion kit, the NEBNext Ultra Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.).

value: B-cell

tag: replicate

tag: phenotype

value: Parental


title: SUDHL4_Parental_BR1


title: La_18B

value: not collected


title: 48hpa BR1


title: La_30B


title: SUDHL4_IMGN529_BR2

value: resistant to IMGN529


title: JY1605, 8-hours germinated seeds at 25℃, rep3

value: Seed


title: 24hpa BR2

value: 24h post amputation


title: SUDHL4_IMGN529_BR1


title: 72hpa BR2


title: La_19B

value: cancer


title: JY1605, 8-hours germinated seeds at 25℃, rep2


title: 24hpa BR1


title: La_7B


title: JY1605, Dry seeds, rep3


title: La_9B


title: 12hpa BR1

value: 12h post amputation


title: SUDHL2_Parental_BR2


title: JY1605, 8-hours germinated seeds at 25℃, rep1


title: La_8B


title: 0hpa BR2

value: 0h post amputation


title: 0hpa BR1

description: trunk


title: SUDHL2_IMGN529_BR2


title: SUDHL2_IMGN529_BR1


title: JY1605, Dry seeds, rep2


title: JY1605, Dry seeds, rep1


title: La_23B


title: HC_T_NT_R9

status: Public on Sep 20 2024

city: Atlanta

first: Erica

middle: L

last: Johnson

state: GA

address: 720 Westview Drive SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R9_NT_T.Read.Count

data_processing:
Data Filtering: SOAPnuke v1.5.2 (parameters: -l 15 -q 0.2 -n 0.05)
Structure Variation Detection: HISAT2 v2.2.1 (parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF), Ericscript v0.5.5-5, rMATS v4.1.1
RNA Identification: Bowtie2 v2.4.4 (parameters: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200)
Gene Quantification: RSEM v1.2.28 (parameters: --forward-prob 0)
Assembly: GRCh38
Supplementary files format and content: CSV format containing read counts for mRNA, miRNA, miscRNA, and ncRNA.

source_name: Human placental tissue (cell culture)

growth_protocol: Human placental tissue samples were used to isolate Hofbauer cells. Human placentae from early/mid-gestation (between 18 and 21.6 weeks of gestation) and human term placentae (>37 weeks gestation) were collected from hepatitis B, HIV-1 seronegative women (>18 years of age) immediately after elective cesarean section without labor. Hofbauer cells were cultured in complete RPMI medium consisting of 1x RPMI (Corning Cellgro, Corning, NY, USA), 10% FBS (Optima, Atlanta Biologics), 2mM L-glutamine (Corning), 1mM sodium pyruvate (Corning), 1x Non-essential Amino Acids (Corning), 1x antibiotics (penicillin, streptomycin, amphotericin B; Corning) at 37°C and 5% CO2.

extract_protocol:
RNA was isolated from Hofbauer cells using the RNAeasy kit (Qiagen, Hilden, Germany). Nucleic acid concentration and purity were assessed using a Nanodrop (Thermo Fisher) and Bioanalyzer (Agilent). RNA integrity numbers (RIN) <7 were excluded from further analysis.
Stranded mRNA libraries were constructed involving mRNA enrichment, RNA fragmentation, cDNA synthesis, end repair, A-tailing, adaptor ligation, PCR amplification, single-strand separation, cyclization, and DNA nanoball synthesis.

treatment_protocol: Hofbauer cells were exposed to either HIV-1BaL, CMV strain TB40/E, ZIKV or no virus (NT) for 24h. Cells were cultured in complete RPMI medium.

value: Human placental tissue (cell culture)

value: Hofbauer cells

value: NT

tag: group

value: Term


title: HC_T_NT_R5

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R5_NT_T.Read.Count


title: HC_T_HIV_R6

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R6_HIV_T.Read.Count

value: HIV


title: HC_T_ZIKV_R7

description:
Hofbauer cells isolated from placenta exposed to ZIKV strain (cell culture)
R7_ZIKV_T.Read.Count

value: ZIKV


title: HC_T_CMV_R8

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R8_CMV_T.Read.Count

value: CMV


title: HC_T_ZIKV_R3

description:
Hofbauer cells isolated from placenta exposed to ZIKV strain (cell culture)
R3_ZIKV_T.Read.Count


title: HC_T_NT_R36

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R36_NT_T.Read.Count


title: HC_eg_NT_R34

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R34_NT_eg.Read.Count

value: Early gestation


title: HC_eg_NT_R35

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R35_NT_eg.Read.Count


title: SUDHL2_Parental_BR1

value: B-cell


title: HC_eg_NT_R32

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R32_NT_eg.Read.Count


title: HC_T_HIV_R2

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R2_HIV_T.Read.Count


title: HC_eg_NT_R33

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R33_NT_eg.Read.Count


title: HC_eg_HIV_R28

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R28_HIV_eg.Read.Count


title: HC_eg_HIV_R26

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R26_HIV_eg.Read.Count


title: HC_eg_CMV_R29

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R29_CMV_eg.Read.Count


title: HC_eg_NT_R27

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R27_NT_eg.Read.Count


title: HC_eg_CMV_R24

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R24_CMV_eg.Read.Count


title: HC_eg_NT_R25

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R25_NT_eg.Read.Count


title: HC_eg_NT_R21

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R21_NT_eg.Read.Count


title: HC_T_CMV_R20

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R20_CMV_T.Read.Count


title: HC_T_CMV_R4

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R4_CMV_T.Read.Count


title: HC_eg_ZIKV_R23

description:
Hofbauer cells isolated from placenta exposed to ZIKV strain (cell culture)
R23_ZIKV_eg.Read.Count


title: HC_eg_HIV_R21

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R21_HIV_eg.Read.Count


title: HC_T_HIV_R19

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R19_HIV_T.Read.Count


title: HC_T_NT_R18

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R18_NT_T.Read.Count


title: HC_T_NT_R1

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R1_NT_T.Read.Count


title: HC_T_CMV_R14

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R14_CMV_T.Read.Count


title: HC_T_HIV_R16

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R16_HIV_T.Read.Count


title: HC_T_CMV_R17

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R17_CMV_T.Read.Count


title: HC_T_NT_R15

description:
Hofbauer cells isolated from placenta exposed to NT strain (cell culture)
R15_NT_T.Read.Count


title: HC_T_HIV_R10

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R10_HIV_T.Read.Count


title: HC_T_CMV_R11

description:
Hofbauer cells isolated from placenta exposed to CMV strain (cell culture)
R11_CMV_T.Read.Count


title: HC_T_HIV_R13

description:
Hofbauer cells isolated from placenta exposed to HIV strain (cell culture)
R13_HIV_T.Read.Count


title: MLL_46959_bone marrow_MPN-U_diagnosis

city: München

first: Torsten

last: Haferlach

address: Max-Lebsche-Platz 31

institute: MLL Munich leukemia laboratory

data_processing:
BaseSpace’s RNA-seq Alignment app (v2.0.1) with default parameters
Reads were mapped with STAR aligner (v2.5.0a)
Gene specific read abundance was calculated with Cufflinks (v2.2.1)
Assembly: hg19
Supplementary files format and content: gene expression data, raw gene counts

source_name: bone marrow

extract_protocol:
RNA was extracted using the Roche MagNA Pure 96 System with the MagNA Pure 96 Cellular RNA LV Kit following the manufacturer’s recommendations
For transcriptome analysis the TruSeq Total Stranded RNA kit was used, starting with 250ng of total RNA, to generate RNA libraries following the manufacturer’s recommendations

value: bone marrow

value: diagnosis


title: MLL_54460_bone marrow_MPN-U_diagnosis


title: MLL_54449_bone marrow_MPN-U_diagnosis


title: MLL_54469_bone marrow_MPN-U_diagnosis


title: MLL_18222_bone marrow_MPN-U_diagnosis


title: MLL_13900_bone marrow_PV_diagnosis


title: MLL_54461_bone marrow_MPN-U_diagnosis


title: MLL_16193_bone marrow_MPN-U_diagnosis


title: MLL_17332_bone marrow_MPN-U_diagnosis


title: MLL_22472_bone marrow_MPN-U_diagnosis


title: MLL_13903_bone marrow_ET_diagnosis


title: MLL_14221_bone marrow_PV_diagnosis


title: MLL_18230_peripheral blood_PMF_diagnosis

source_name: peripheral blood

value: peripheral blood


title: MLL_30022_bone marrow_PMF_diagnosis


title: MLL_18229_peripheral blood_PMF_diagnosis


title: MLL_54467_bone marrow_MPN-U_diagnosis


title: MLL_18239_bone marrow_MPN-U_diagnosis


title: MLL_18238_bone marrow_MPN-U_diagnosis


title: MLL_18226_bone marrow_ET_diagnosis


title: MLL_18225_bone marrow_PV_diagnosis


title: MLL_18233_peripheral blood_PMF_diagnosis


title: MLL_18220_bone marrow_MPN-U_diagnosis


title: MLL_18227_bone marrow_PV_diagnosis


title: MLL_54450_bone marrow_MPN-U_diagnosis


title: MLL_54451_bone marrow_MPN-U_diagnosis


title: MLL_22173_bone marrow_PV_diagnosis


title: MLL_14217_bone marrow_ET_diagnosis


title: MLL_14220_bone marrow_ET_diagnosis


title: MLL_19702_bone marrow_ET_diagnosis


title: MLL_13982_bone marrow_PV_diagnosis


title: MLL_19691_bone marrow_ET_diagnosis


title: MLL_19546_bone marrow_ET_diagnosis


title: MLL_17971_bone marrow_PV_diagnosis


title: MLL_19556_bone marrow_ET_diagnosis


title: MLL_18552_bone marrow_ET_diagnosis


title: MLL_14445_bone marrow_PV_diagnosis


title: MLL_18562_bone marrow_PV_diagnosis


title: MLL_14115_bone marrow_PV_diagnosis


title: MLL_19687_bone marrow_ET_diagnosis


title: MLL_19304_bone marrow_ET_diagnosis


title: MLL_18566_peripheral blood_PMF_diagnosis


title: MLL_18564_bone marrow_ET_diagnosis


title: MLL_17967_bone marrow_PV_diagnosis


title: Liver_Control_2

value: Liver tissue


title: MLL_18551_bone marrow_ET_diagnosis


title: MLL_10227_peripheral blood_PMF_diagnosis


title: MLL_17965_bone marrow_MPN-U_diagnosis


title: MLL_13973_bone marrow_PV_diagnosis


title: MLL_18567_bone marrow_PV_diagnosis


title: MLL_18556_peripheral blood_PMF_diagnosis


title: MLL_18560_peripheral blood_PMF_diagnosis


title: MLL_16779_bone marrow_PV_diagnosis


title: MLL_18558_bone marrow_ET_diagnosis


title: MLL_17970_bone marrow_ET_diagnosis


title: MLL_13981_bone marrow_PV_diagnosis


title: MLL_18557_bone marrow_ET_diagnosis


title: MLL_10223_peripheral blood_PMF_diagnosis


title: MLL_18561_bone marrow_PV_diagnosis


title: MLL_17963_bone marrow_ET_diagnosis


title: MLL_18565_bone marrow_ET_diagnosis


title: MLL_19974_bone marrow_ET_diagnosis


title: MLL_18553_bone marrow_MPN-U_diagnosis


title: MENK-Miyazaki1(MM1)

value: MENK-NBV-MB


title: MLL_17859_bone marrow_PV_diagnosis


title: MLL_21383_bone marrow_ET_diagnosis


title: MLL_17857_bone marrow_PV_diagnosis


title: MLL_18548_bone marrow_PV_diagnosis


title: MLL_18218_bone marrow_PV_diagnosis


title: MLL_17858_bone marrow_PV_diagnosis


title: MLL_19472_bone marrow_ET_diagnosis


title: MLL_14451_bone marrow_ET_diagnosis


title: MLL_10218_peripheral blood_PMF_diagnosis


title: MLL_17979_bone marrow_ET_diagnosis


title: MLL_13979_bone marrow_ET_diagnosis


title: MLL_12490_bone marrow_PV_diagnosis


title: MLL_21521_bone marrow_ET_diagnosis


title: MLL_21520_bone marrow_ET_diagnosis


title: MLL_55544_bone marrow_PMF_diagnosis


title: MLL_10215_peripheral blood_PMF_diagnosis


title: MLL_21519_bone marrow_PV_diagnosis


title: MLL_17847_bone marrow_PV_diagnosis


title: MLL_10216_peripheral blood_PMF_diagnosis


title: LS_12

value: not collected

value: cancer


title: MLL_21381_bone marrow_PV_diagnosis


title: MLL_21518_bone marrow_ET_diagnosis


title: MLL_14450_bone marrow_ET_diagnosis


title: MLL_19680_bone marrow_ET_diagnosis


title: MLL_19683_bone marrow_PV_diagnosis


title: MLL_20412_bone marrow_PV_diagnosis


title: MLL_21382_bone marrow_ET_diagnosis


title: MLL_20391_bone marrow_PV_diagnosis


title: MLL_21379_bone marrow_PV_diagnosis


title: MLL_14441_bone marrow_CML_diagnosis


title: MLL_20411_bone marrow_MPN-U_diagnosis


title: MLL_14745_bone marrow_CML_diagnosis


title: MLL_20404_bone marrow_PV_diagnosis


title: MLL_20387_bone marrow_ET_diagnosis


title: MLL_19698_bone marrow_PV_diagnosis


title: MLL_20199_bone marrow_ET_diagnosis


title: MLL_14449_bone marrow_ET_diagnosis


title: MLL_19692_bone marrow_PV_diagnosis


title: MLL_19693_bone marrow_MPN-U_diagnosis


title: MLL_22730_peripheral blood_PMF_diagnosis


title: MLL_20193_bone marrow_PV_diagnosis


title: MLL_19982_bone marrow_MPN-U_diagnosis


title: MLL_16354_bone marrow_ET_diagnosis


title: MLL_55874_peripheral blood_CML_diagnosis


title: MLL_10211_peripheral blood_PMF_diagnosis


title: MLL_21378_bone marrow_ET_diagnosis


title: MLL_19981_bone marrow_PV_diagnosis


title: MLL_55525_bone marrow_PMF_diagnosis


title: MLL_19978_bone marrow_PV_diagnosis


title: MLL_22728_bone marrow_MPN-U_diagnosis


title: MLL_19679_bone marrow_PV_diagnosis


title: MLL_12468_bone marrow_ET_diagnosis


title: MLL_20603_bone marrow_PV_diagnosis


title: MLL_19400_bone marrow_ET_diagnosis


title: MLL_19547_bone marrow_PV_diagnosis


title: MLL_19980_bone marrow_ET_diagnosis


title: MLL_20195_bone marrow_ET_diagnosis


title: MLL_55873_bone marrow_CML_diagnosis


title: MLL_15379_bone marrow_PV_diagnosis


title: MLL_19287_bone marrow_ET_diagnosis


title: MLL_19291_bone marrow_ET_diagnosis


title: MLL_14437_bone marrow_CML_diagnosis


title: MLL_14438_peripheral blood_CML_diagnosis


title: MLL_19688_peripheral blood_PMF_diagnosis


title: MLL_14447_peripheral blood_CML_diagnosis


title: MLL_19973_bone marrow_MPN-U_diagnosis


title: MLL_16353_peripheral blood_CML_diagnosis


title: MLL_19877_bone marrow_ET_diagnosis


title: MLL_19870_bone marrow_PV_diagnosis


title: MLL_20394_bone marrow_ET_diagnosis


title: MLL_19866_bone marrow_ET_diagnosis


title: MLL_14439_bone marrow_CML_diagnosis


title: MLL_55523_bone marrow_ET_diagnosis


title: MLL_55552_bone marrow_ET_diagnosis


title: MLL_20410_bone marrow_PV_diagnosis


title: MLL_55524_bone marrow_ET_diagnosis


title: MLL_19869_bone marrow_ET_diagnosis


title: MLL_55543_bone marrow_ET_diagnosis


title: MLL_15380_bone marrow_CML_diagnosis


title: MLL_19979_bone marrow_ET_diagnosis


title: MLL_54455_bone marrow_ET_diagnosis


title: MLL_19868_bone marrow_MPN-U_diagnosis


title: MLL_10204_peripheral blood_PMF_diagnosis


title: MLL_19865_bone marrow_PV_diagnosis


title: MLL_14878_peripheral blood_CML_diagnosis


title: MLL_14877_peripheral blood_CML_diagnosis


title: MLL_55869_bone marrow_CML_diagnosis


title: MLL_55551_bone marrow_ET_diagnosis


title: MLL_20407_bone marrow_MPN-U_diagnosis


title: MLL_12467_bone marrow_ET_diagnosis


title: MLL_55521_bone marrow_PV_diagnosis


title: MLL_55522_bone marrow_ET_diagnosis


title: MLL_20192_bone marrow_MPN-U_diagnosis


title: MLL_20386_bone marrow_PV_diagnosis


title: MLL_55550_bone marrow_ET_diagnosis


title: MLL_10203_peripheral blood_PMF_diagnosis


title: MLL_20188_bone marrow_PMF_diagnosis


title: MLL_55541_bone marrow_ET_diagnosis


title: MLL_14756_bone marrow_CML_diagnosis


title: MLL_55549_bone marrow_PV_diagnosis


title: MLL_14753_bone marrow_PV_diagnosis


title: MLL_19876_bone marrow_MPN-U_diagnosis


title: MLL_12558_peripheral blood_CML_diagnosis


title: MLL_21955_bone marrow_MPN-U_diagnosis


title: MLL_54619_bone marrow_ET_diagnosis


title: MLL_55542_peripheral blood_PMF_diagnosis


title: MLL_55540_bone marrow_ET_diagnosis


title: MLL_20181_bone marrow_PMF_diagnosis


title: MLL_12557_peripheral blood_CML_diagnosis


title: MLL_55519_bone marrow_ET_diagnosis


title: MLL_12562_peripheral blood_CML_diagnosis


title: MLL_13976_peripheral blood_CML_diagnosis


title: MLL_12563_peripheral blood_CML_diagnosis


title: MLL_55539_bone marrow_ET_diagnosis


title: MLL_55868_bone marrow_CML_diagnosis


title: MLL_12560_bone marrow_CML_diagnosis


title: MLL_55518_bone marrow_ET_diagnosis


title: MLL_55538_bone marrow_ET_diagnosis


title: MLL_55537_bone marrow_PV_diagnosis


title: MLL_13898_bone marrow_CML_diagnosis


title: MLL_13416_bone marrow_CML_diagnosis


title: MLL_55536_bone marrow_ET_diagnosis


title: MLL_55535_bone marrow_ET_diagnosis


title: MLL_10201_peripheral blood_PMF_diagnosis


title: MLL_55520_bone marrow_ET_diagnosis


title: MLL_55866_bone marrow_PV_diagnosis


title: MLL_55865_bone marrow_ET_diagnosis


title: MLL_12543_peripheral blood_CML_diagnosis


title: MLL_55867_bone marrow_ET_diagnosis


title: MLL_55864_bone marrow_PV_diagnosis


title: MLL_55863_bone marrow_PV_diagnosis


title: MLL_55862_bone marrow_ET_diagnosis


title: MLL_55861_bone marrow_PV_diagnosis


title: MLL_11995_bone marrow_CML_diagnosis


title: MLL_12007_bone marrow_CML_diagnosis


title: MLL_20191_bone marrow_PV_diagnosis


title: MLL_55860_bone marrow_ET_diagnosis


title: MLL_55859_bone marrow_PV_diagnosis


title: MLL_55857_bone marrow_PV_diagnosis


title: MLL_55855_bone marrow_PV_diagnosis


title: MLL_55853_bone marrow_PV_diagnosis


title: MLL_55854_bone marrow_PV_diagnosis


title: MLL_20180_bone marrow_MPN-U_diagnosis


title: MLL_55856_bone marrow_PV_diagnosis


title: MLL_55852_bone marrow_PV_diagnosis


title: MLL_22149_bone marrow_MPN-U_diagnosis


title: MLL_55692_bone marrow_ET_diagnosis


title: MLL_55690_bone marrow_ET_diagnosis


title: MLL_10200_peripheral blood_PMF_diagnosis


title: MLL_55688_bone marrow_PV_diagnosis


title: MLL_55689_bone marrow_PV_diagnosis


title: MLL_55687_bone marrow_ET_diagnosis


title: MLL_55686_bone marrow_ET_diagnosis


title: MLL_11993_peripheral blood_CML_diagnosis


title: MLL_55685_bone marrow_PV_diagnosis


title: MLL_20189_bone marrow_MPN-U_diagnosis


title: MLL_55684_bone marrow_PV_diagnosis


title: MLL_55858_bone marrow_PV_diagnosis


title: MLL_12005_bone marrow_CML_diagnosis


title: MLL_12004_bone marrow_CML_diagnosis


title: MLL_55691_bone marrow_PV_diagnosis


title: MLL_10198_peripheral blood_PMF_diagnosis


title: MLL_12003_bone marrow_CML_diagnosis


title: MLL_10199_peripheral blood_PMF_diagnosis


title: MLL_11994_bone marrow_CML_diagnosis


title: MLL_55682_bone marrow_PV_diagnosis


title: MLL_55680_bone marrow_ET_diagnosis


title: MLL_55679_bone marrow_CML_diagnosis


title: MLL_55678_bone marrow_CML_diagnosis


title: MLL_55677_bone marrow_PV_diagnosis


title: MLL_55681_bone marrow_PV_diagnosis


title: MLL_55676_peripheral blood_CML_diagnosis


title: MLL_55673_bone marrow_PV_diagnosis


title: MLL_54435_bone marrow_PV_diagnosis


title: MLL_12006_peripheral blood_CML_diagnosis


title: MLL_20183_peripheral blood_PMF_diagnosis


title: MLL_55671_bone marrow_CML_diagnosis


title: MLL_17753_bone marrow_PMF_diagnosis


title: MLL_55670_bone marrow_PV_diagnosis


title: MLL_55666_bone marrow_CML_diagnosis


title: MLL_55683_bone marrow_PV_diagnosis


title: MLL_19732_bone marrow_MPN-U_diagnosis


title: MLL_12002_bone marrow_CML_diagnosis


title: MLL_55669_peripheral blood_CML_diagnosis


title: MLL_55668_peripheral blood_CML_diagnosis


title: MLL_21284_peripheral blood_PMF_diagnosis


title: MLL_55664_bone marrow_CML_diagnosis


title: MLL_55667_bone marrow_CML_diagnosis


title: MLL_17977_bone marrow_PMF_diagnosis


title: MLL_55662_bone marrow_CML_diagnosis


title: MLL_12001_peripheral blood_CML_diagnosis


title: MLL_19729_bone marrow_PMF_diagnosis


title: MLL_12530_peripheral blood_CML_diagnosis


title: MLL_12000_bone marrow_CML_diagnosis


title: MLL_19731_bone marrow_PMF_diagnosis


title: MLL_17748_peripheral blood_PMF_diagnosis


title: MLL_55675_bone marrow_PV_diagnosis


title: MLL_55661_bone marrow_CML_diagnosis


title: MLL_19728_bone marrow_MPN-U_diagnosis


title: MLL_19399_bone marrow_MPN-U_diagnosis


title: MLL_54623_peripheral blood_PMF_diagnosis


title: MLL_19726_bone marrow_PMF_diagnosis


title: MLL_54624_bone marrow_ET_diagnosis


title: MLL_19724_bone marrow_MPN-U_diagnosis


title: MLL_17976_bone marrow_PMF_diagnosis


title: MLL_11992_bone marrow_CML_diagnosis


title: MLL_20599_bone marrow_PMF_diagnosis


title: MLL_19478_bone marrow_PMF_diagnosis


title: MLL_17853_bone marrow_PMF_diagnosis


title: MLL_54616_bone marrow_PMF_diagnosis


title: MLL_10190_peripheral blood_PMF_diagnosis


title: MLL_19723_bone marrow_PMF_diagnosis


title: MLL_20375_peripheral blood_PMF_diagnosis


title: MLL_10189_peripheral blood_PMF_diagnosis


title: MLL_10192_peripheral blood_PMF_diagnosis


title: MLL_20371_bone marrow_MPN-U_diagnosis


title: MLL_19721_bone marrow_MPN-U_diagnosis


title: MLL_20373_bone marrow_MPN-U_diagnosis


title: MLL_19398_bone marrow_MPN-U_diagnosis


title: MLL_20374_peripheral blood_PMF_diagnosis


title: MLL_10188_peripheral blood_PMF_diagnosis


title: MLL_20372_bone marrow_PMF_diagnosis


title: MLL_21375_bone marrow_PMF_diagnosis


title: MLL_12506_bone marrow_CML_diagnosis


title: MLL_19189_bone marrow_PMF_diagnosis


title: MLL_21269_peripheral blood_PMF_diagnosis


title: MLL_19202_bone marrow_MPN-U_diagnosis


title: MLL_14754_bone marrow_CML_diagnosis


title: MLL_19204_bone marrow_MPN-U_diagnosis


title: MLL_12502_peripheral blood_CML_diagnosis


title: MLL_12505_peripheral blood_CML_diagnosis


title: MLL_12529_bone marrow_CML_diagnosis


title: MLL_19203_bone marrow_MPN-U_diagnosis


title: MLL_55659_peripheral blood_CML_diagnosis


title: MLL_55657_peripheral blood_CML_diagnosis


title: MLL_14887_bone marrow_CML_diagnosis


title: MLL_55652_bone marrow_CML_diagnosis


title: MLL_19195_bone marrow_PMF_diagnosis


title: MLL_12545_bone marrow_CML_diagnosis


title: MLL_12518_bone marrow_CML_diagnosis


title: MLL_55656_bone marrow_CML_diagnosis


title: MLL_55654_bone marrow_CML_diagnosis


title: MLL_21283_bone marrow_MPN-U_diagnosis


title: MLL_14323_bone marrow_CML_diagnosis


title: MLL_55647_peripheral blood_CML_diagnosis


title: MLL_10182_peripheral blood_PMF_diagnosis


title: MLL_14322_bone marrow_CML_diagnosis


title: MLL_55651_bone marrow_CML_diagnosis


title: MLL_19193_bone marrow_MPN-U_diagnosis


title: MLL_14886_peripheral blood_CML_diagnosis


title: MLL_19194_bone marrow_PMF_diagnosis


title: MLL_19188_bone marrow_MPN-U_diagnosis


title: MLL_17845_bone marrow_PMF_diagnosis


title: MLL_12515_bone marrow_CML_diagnosis


title: MLL_12521_peripheral blood_CML_diagnosis


title: MLL_55645_bone marrow_CML_diagnosis


title: MLL_12508_peripheral blood_CML_diagnosis


title: MLL_55644_bone marrow_CML_diagnosis


title: MLL_55653_bone marrow_CML_diagnosis


title: MLL_19191_bone marrow_PMF_diagnosis


title: MLL_17849_bone marrow_PMF_diagnosis


title: MLL_12524_peripheral blood_CML_diagnosis


title: MLL_12014_bone marrow_CML_diagnosis


title: MLL_10178_peripheral blood_PMF_diagnosis


title: MLL_19187_bone marrow_PMF_diagnosis


title: MLL_55642_peripheral blood_PMF_diagnosis


title: MLL_14320_peripheral blood_CML_diagnosis


title: MLL_55636_peripheral blood_CML_diagnosis


title: MLL_13897_bone marrow_CML_diagnosis


title: MLL_55640_bone marrow_CML_diagnosis


title: MLL_19182_bone marrow_MPN-U_diagnosis


title: MLL_13024_bone marrow_CML_diagnosis


title: MLL_10170_peripheral blood_PMF_diagnosis


title: MLL_18792_bone marrow_MPN-U_diagnosis


title: MLL_19184_bone marrow_PMF_diagnosis


title: MLL_55641_peripheral blood_CML_diagnosis


title: MLL_19183_bone marrow_PMF_diagnosis


title: MLL_55637_bone marrow_CML_diagnosis


title: MLL_55639_bone marrow_CML_diagnosis


title: MLL_18798_bone marrow_PMF_diagnosis


title: MLL_14318_peripheral blood_CML_diagnosis


title: MLL_14746_bone marrow_CML_diagnosis


title: MLL_19185_bone marrow_MPN-U_diagnosis


title: MLL_18793_bone marrow_PMF_diagnosis


title: MLL_13022_bone marrow_CML_diagnosis


title: MLL_18797_bone marrow_PMF_diagnosis


title: MLL_55638_bone marrow_CML_diagnosis


title: MLL_10169_peripheral blood_PMF_diagnosis


title: MLL_54615_peripheral blood_PMF_diagnosis


title: MLL_13017_peripheral blood_CML_diagnosis


title: MLL_14313_bone marrow_CML_diagnosis


title: MLL_10172_peripheral blood_PMF_diagnosis


title: MLL_14316_peripheral blood_CML_diagnosis


title: MLL_54622_peripheral blood_PMF_diagnosis


title: MLL_18799_peripheral blood_PMF_diagnosis


title: MLL_17974_bone marrow_MPN-U_diagnosis


title: MLL_18790_bone marrow_MPN-U_diagnosis


title: MLL_54614_peripheral blood_PMF_diagnosis


title: MLL_55310_peripheral blood_PMF_diagnosis


title: MLL_13423_bone marrow_CML_diagnosis


title: MLL_14216_peripheral blood_CML_diagnosis


title: MLL_55631_bone marrow_CML_diagnosis


title: MLL_54621_peripheral blood_PMF_diagnosis


title: MLL_10165_peripheral blood_PMF_diagnosis


title: MLL_55628_peripheral blood_CML_diagnosis


title: MLL_55627_peripheral blood_CML_diagnosis


title: MLL_18794_bone marrow_MPN-U_diagnosis


title: MUC_00458_bone marrow_CML_diagnosis


title: MLL_55629_bone marrow_CML_diagnosis


title: MLL_18789_bone marrow_MPN-U_diagnosis


title: MLL_10161_peripheral blood_PMF_diagnosis


title: MLL_10160_peripheral blood_PMF_diagnosis


title: MLL_54965_peripheral blood_PMF_diagnosis


title: MLL_55625_bone marrow_CML_diagnosis


title: MUC_00157_bone marrow_CML_diagnosis


title: MLL_10166_peripheral blood_PMF_diagnosis


title: MLL_21748_peripheral blood_ET_diagnosis


title: MLL_19302_peripheral blood_ET_diagnosis


title: MLL_54620_peripheral blood_PMF_diagnosis


title: MLL_13008_peripheral blood_CML_diagnosis


title: MLL_10214_peripheral blood_PMF_diagnosis


title: MLL_18563_peripheral blood_PV_diagnosis


title: MLL_55626_peripheral blood_CML_diagnosis


title: MLL_19300_bone marrow_MPN-U_diagnosis


title: MLL_19481_bone marrow_MPN-U_diagnosis


title: MLL_20196_bone marrow_PV_diagnosis


title: MLL_19479_bone marrow_MPN-U_diagnosis


title: MLL_10212_peripheral blood_PMF_diagnosis


title: MLL_55870_bone marrow_CML_diagnosis


title: MLL_20409_bone marrow_PMF_diagnosis


title: MLL_20187_bone marrow_MPN-U_diagnosis


title: MLL_10191_peripheral blood_PMF_diagnosis


title: MLL_12510_bone marrow_CML_diagnosis


title: MLL_55871_bone marrow_CML_diagnosis


title: MLL_19200_peripheral blood_PMF_diagnosis


title: MLL_55872_bone marrow_CML_diagnosis


title: MLL_10181_peripheral blood_PMF_diagnosis


title: MLL_10162_peripheral blood_PMF_diagnosis


title: MLL_17848_peripheral blood_PMF_diagnosis


title: MLL_55663_bone marrow_CML_diagnosis


title: MLL_10177_bone marrow_PMF_diagnosis


title: ZC3H3_doxycycline_rep1

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
We aligned reads to the human genome version GRCh38 with annotation version Gencode v40 using STAR (v2.7.1a).
Bam files were then filtered to include only read1 values using samtools (v1.16) with option “view -hbf 64.”
C-to-U edit sites were obtained using SAILOR.
Edits were divided by the featurecounts (v1.5.2) output for each gene’s exons to generate EPR values based on GENCODE v40 annotations.
Assembly: GRCh38
Supplementary files format and content: Bam files and EPR (edits-per-read) quantification

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 5% CO2 and 37C.

extract_protocol:
Total RNA was extracted using the Promega Maxwell RSC simplyRNA tissue kit, cat# AS1340.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA library prep kit, cat# 20020595 with the IDT for Illumina TruSeq RNA UD Index set, cat# 20040871, following the manufacturers protocol and using 1ug of RNA for each sample.
Finally, samples were pooled in an equimolar fashion and sequenced on an Illumina NovaSeq 6000 S4 flow cell, generating 100 base-pair paired end reads.

treatment_protocol: HEK293T cells were seeded onto 12-well plates at 0.1X106 cells per well in 1ml of culture medium (DMEM, LifeTech cat# 11995065, 10% FBS), and grown overnight. The next day, the medium was replaced with fresh medium containing 8 ug/ml polybrene (Hexadimethrine bromide - Sigma Aldrich cat# H9268) and 100ul of lentivirus specific to ZNF ORFs. After 24hrs, the lentiviral medium was removed and replaced with fresh medium containing 4ug/ml Puromycin and incubated for two days. On day 3, the puromycin medium was replaced with fresh medium containing 2ug/ml Doxycycline (Sigma Aldrich cat# D9891) + Puromycin and incubated for two days.

value: Human embryonic kidney

value: doxycycline


title: WBP4_untreated_rep2

value: untreated


title: ZC3H3_untreated_rep2


title: ZC3H3_doxycycline_rep2


title: ZC3H3_untreated_rep1


title: MLL_12511_bone marrow_CML_diagnosis


title: WBP4_untreated_rep1


title: RNF14_untreated_rep2


title: RNF14_doxycycline_rep2


title: RNF14_doxycycline_rep1


title: RNF113A_untreated_rep1


title: WBP4_doxycycline_rep2


title: RNF14_untreated_rep1


title: Nontargeting_control_doxycycline_rep2


title: RNF113A_doxycycline_rep1


title: RNF113A_doxycycline_rep2


title: Nontargeting_control_untreated_rep1


title: WBP4_doxycycline_rep1


title: Nontargeting_control_doxycycline_rep1


title: MBNL1_untreated_rep2


title: MBNL1_untreated_rep1


title: RNF113A_untreated_rep2


title: Nontargeting_control_untreated_rep2


title: MBNL1_doxycycline_rep2


title: FUS_doxycycline_rep1


title: FUS_doxycycline_rep2


title: FUS_untreated_rep2


title: ERI2_untreated_rep2


title: MBNL1_doxycycline_rep1


title: FUS_untreated_rep1


title: ERI2_doxycycline_rep2


title: CPSF4_untreated_rep1


title: CPSF4_untreated_rep2


title: ERI2_doxycycline_rep1


title: ERI2_untreated_rep1


title: CPSF4_doxycycline_rep2


title: CNOT4_untreated_rep2


title: CNOT4_untreated_rep1


title: CNOT4_doxycycline_rep2


title: CNOT4_doxycycline_rep1


title: CPSF4_doxycycline_rep1


title: ZXDC_rep1

data_processing:
We aligned reads to the human genome version GRCh38 with annotation version Gencode v40 using STAR (v2.7.1a). Gene expression levels were quantified using RSEM (v1.3.0), in which the TPM values were used to calculate Pearson correlation coefficient between replicates. Samples meeting specific criteria were selected for further analysis: only those with unique aligned reads greater than 10M and a Pearson correlation coefficient between replicates of 0.9 or higher were considered. Samples with fewer reads were re-sequenced to ensure an adequate count, while those with lower correlation were repeated. Plus and minus strand bigwig files were generated using bedGraphToBigWig (v2.9). Transcript abundance was quantified using Salmon (v1.9.0) with the –gcBias option. CQN (v1.40.0) was employed to normalize gene-level GC content and length biases. Transcript merging to genes was performed using Tximport (v1.22.0).
Assembly: GRCh38
Supplementary files format and content: Bam files and salmon quant files

treatment_protocol: HEK293T cells were seeded onto 12-well plates at 0.1X106 cells per well in 1ml of culture medium (DMEM, LifeTech cat# 11995065, 10% FBS), and grown overnight. The next day, the medium was replaced with fresh medium containing 8 ug/ml polybrene (Hexadimethrine bromide - Sigma Aldrich cat# H9268) and 100ul of lentivirus specific to ZNF ORFs. After 24hrs, the lentiviral medium was removed and replaced with fresh medium containing 4ug/ml Puromycin and incubated for two days.

tag: batch


title: ZNHIT3_rep1


title: ZNHIT3_rep2


title: ZRANB2_rep2


title: ZRANB2_rep1


title: ZNF770_rep2


title: ZNF800_rep2


title: ZXDC_rep2


title: ZNF473_rep1


title: ZNF800_rep1


title: ZNF706_rep2


title: ZNF593_rep2


title: ZNF706_rep1


title: ZNF473_rep2


title: ZNF385C_rep2


title: ZNF354A_rep2


title: ZNF317_rep2


title: ZNF354A_rep1


title: ZNF317_rep1


title: ZNF346_rep1


title: ZNF385C_rep1


title: ZNF346_rep2


title: ZNF277_rep2


title: ZNF22_rep2


title: ZNF593_rep1


title: ZNF770_rep1


title: ZNF277_rep1


title: ZNF214_rep2


title: ZNF214_rep1


title: ZNF2_rep2


title: ZNF16_rep2


title: ZNF169_rep2


title: ZMAT3_rep2


title: ZMAT2_rep2


title: ZNF184_rep1


title: ZMAT5_rep2


title: ZNF184_rep2


title: ZNF16_rep1


title: ZMAT2_rep1


title: ZIC3_rep2


title: ZIC3_rep1


title: ZFP36L1_rep2


title: ZFP36L1_rep1


title: ZDHHC5_rep2


title: ZCWPW1_rep2


title: ZNF22_rep1


title: ZFP37_rep1


title: ZDHHC5_rep1


title: ZNF169_rep1


title: ZNF2_rep1


title: ZCCHC9_rep2


title: ZCRB1_rep1


title: ZCWPW1_rep1


title: ZMAT5_rep1


title: ZMAT3_rep1


title: ZCCHC24_rep1


title: ZCCHC7_rep1


title: ZCCHC24_rep2


title: ZC3HC1_rep2


title: ZCRB1_rep2


title: ZCCHC10_rep1


title: ZCCHC10_rep2


title: ZC3H8_rep2


title: ZCCHC9_rep1


title: ZCCHC7_rep2


title: ZC3H7A_rep1


title: ZC3H7A_rep2


title: ZC3HC1_rep1


title: ZFP37_rep2


title: ZC3H3_rep2


title: ZC3H8_rep1


title: ZC3H3_rep1


title: ZC3H18_rep2


title: WBP4_rep2


title: YAF2_rep2


title: YAF2_rep1


title: WBP4_rep1


title: USP39_rep2


title: USP44_rep1


title: USP44_rep2


title: UBR7_rep2


title: U2AF1L4_rep2


title: U2AF1_rep2


title: TUT1_rep1


title: TUT1_rep2


title: TTF2_rep1


title: TTF2_rep2


title: U2AF1_rep1


title: UBR7_rep1


title: USP39_rep1


title: TRIP4_rep2


title: ZC3H18_rep1


title: TRIM28_rep1


title: TRIP4_rep1


title: TRIM32_rep2


title: TRIM28_rep2


title: TRIM2_rep1


title: TRIM2_rep2


title: TAF15_rep2


title: TAF15_rep1


title: SNRNP48_rep1


title: SNRNP48_rep2


title: U2AF1L4_rep1


title: TRMU_rep2


title: SEC23B_rep2


title: RNF43_rep2


title: RNF41_rep2


title: RYBP_rep2


title: RYBP_rep1


title: SEC23B_rep1


title: RNF43_rep1


title: RNF26_rep1


title: TRMU_rep1


title: RNF214_rep2


title: RNF41_rep1


title: RNF214_rep1


title: RNF31_rep1


title: TRIM32_rep1


title: RNF20_rep1


title: RFFL_rep2


title: RNF113A_rep1


title: RNF113A_rep2


title: RNF150_rep2


title: RNF20_rep2


title: RFFL_rep1


title: RC3H2_rep1


title: RC3H2_rep2


title: RBM5_rep2


title: REPIN1_rep1


title: REPIN1_rep2


title: RNF31_rep2


title: RNF26_rep2


title: RBM5_rep1


title: RBBP6_rep2


title: PML_rep2


title: PRR3_rep1


title: PHF7_rep2


title: PHF14_rep2


title: RBM4B_rep1


title: PRR3_rep2


title: PHF11_rep2


title: PHF14_rep1


title: PML_rep1


title: RBBP6_rep1


title: RNF150_rep1


title: PIAS4_rep2


title: PAN3_rep1


title: PHF7_rep1


title: Nontargeting_control_rep15


title: Nontargeting_control_rep16


title: RBM4B_rep2


title: PCGF1_rep2


title: PAN3_rep2


title: PHF11_rep1


title: Nontargeting_control_rep14


title: NUFIP1_rep2


title: NUFIP1_rep1


title: PIAS4_rep1


title: Nontargeting_control_rep11


title: Nontargeting_control_rep7


title: Nontargeting_control_rep12


title: Nontargeting_control_rep6


title: Nontargeting_control_rep10


title: Nontargeting_control_rep8


title: Nontargeting_control_rep5


title: Nontargeting_control_rep9


title: Nontargeting_control_rep4


title: Nontargeting_control_rep2


title: NR5A2_rep3


title: Nontargeting_control_rep1


title: NR5A2_rep4


title: Nontargeting_control_rep3


title: NR5A2_rep1


title: Nontargeting_control_rep13


title: NR5A2_rep2


title: NDUFS6_rep2


title: NR3C1_rep1


title: NDUFS6_rep1


title: MNAT1_rep1


title: MCM10_rep2


title: MCM10_rep1


title: MBNL2_rep2


title: MBNL2_rep1


title: IGHMBP2_rep2


title: LITAF_rep1


title: LIN28B_rep1


title: MAZ_rep1


title: LIN28B_rep2


title: IGHMBP2_rep1


title: KDM5A_rep1


title: NR3C1_rep2


title: IRF2BP1_rep2


title: GTF3C4_rep1


title: LITAF_rep2


title: GTF3C4_rep2


title: MNAT1_rep2


title: IRF2BP1_rep1


title: MAZ_rep2


title: GIN1_rep2


title: FUS_rep1


title: FUS_rep2


title: EGLN1_rep1


title: EGLN1_rep2


title: G2E3_rep1


title: LYAR_rep1


title: LYAR_rep2


title: DZIP3_rep2


title: G2E3_rep2


title: KDM5A_rep2


title: DTX3L_rep2


title: GIN1_rep1


title: DTX3L_rep1


title: CPSF4_rep1


title: CXXC1_rep1


title: CNBP_rep2


title: CISD2_rep2


title: DDX59_rep1


title: CNOT4_rep1


title: CNOT4_rep2


title: CPSF4_rep2


title: CISD2_rep1


title: CISD1_rep2


title: CNBP_rep1


title: CTCF_rep2


title: CISD1_rep1


title: DZIP3_rep1


title: CDCA7_rep1


title: CDCA7_rep2


title: BRCA1_rep1


title: CXXC1_rep2


title: DDX59_rep2


title: BMI1_rep1


title: BRCA1_rep2


title: BL_rep1


title: ARIH1_rep1


title: ARIH1_rep2


title: APEX2_rep2


title: CTCF_rep1


title: APEX2_rep1


title: BMI1_rep2


title: BL_rep2


title: esophageal cancer, organoid, 191

city: Southampton

first: Ian

last: Reddin

address: Tremona Road

department: School of Cancer Sciences

country: United Kingdom

institute: University of Southampton

data_processing:
The raw fastq data for a total of 8 samples (2 CAFs, 3 Organoid and 3 assembloid co-cultures) were quality-checked using fastQC (v0.12.1), and aligned to the reference genome (GRCh38) using Star aligner (V2.7.10b)
The processed count matrices were generated using Htseq-count (V2.0.3).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files containing the raw read counts for each gene for each individual sample.

source_name: Esophageal Adenocarcinoma

growth_protocol: Organoids were grown in esophageal cancer-specific organoid media consisting of advanced DMEM/F12 containing 10mM HEPES, GlutaMAX, N-2 and B-27 supplements, 100ng/ml noggin, 1.25mM N-acetyl-cysteine, 10mM nicotinamide, 50ng/mL EGF, 500nM A83-01, 3µM SB202190 and 100ng/mL FGF-10, with 20% R-Spondin1-Fc 293T conditioned media and 50% L-Wnt3a conditioned media. Fibroblasts and assembloids were grown in complete DMEM containing 10% fetal calf serum, 4mM L-glutamine, 100U/mL penicillin, 100ug/mL streptomycin and 250ng/mL amphotericin B.

extract_protocol:
Total RNA from CAFs was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA library preparation was outsourced to Novogene.

value: Esophageal Adenocarcinoma

value: Organoid


title: esophageal cancer, assembloid, 005 + 669

value: Assembloid


title: ZNF706 knockdown 8hr-chase replicate 2

data_processing:
Reads were aligned to hg38 using SlamDunk (v0.4.3) with inclusion of multi-mapping reads.
Assembly: hg38
Supplementary files format and content: C->T conversion counts within 3' UTR regions output by SlamDunk

extract_protocol:
Total RNA was extracted with the Direct-Zol RNA miniprep kit (Zymo) with DTT added to the buffers.
RNA was alkylated using the SLAMseq kit per manufacturer’s instructions. Libraries were then prepared using the QuantSeq 3’ mRNA-seq Library Prep Kit for Illumina (Lexogen) and sequenced using the Novaseq 6000 platform (Illumina) to approximately 20M SE150 reads per sample.

treatment_protocol: HEK293T cells (3 biological replicates per knockdown, per timepoint) were transduced with lentivirus, puromycin-selected, and confirmed by qPCR. 4SU treatment and alkylation were performed using the SLAMseq Kinetics Kit, Catabolic Module (Lexogen). All steps were performed in the dark under a red light. Cells were treated with 10 uM 4SU for 24 hr with media changes every 8 hr. Then the media was replaced with fresh media containing 1 mM uridine. Cells were incubated for 0, 2, 4, or 8 hr in the presence of excess uridine. At the end of incubation, cells were immediately lysed using Trizol.


title: esophageal cancer, fibroblast, 1412

value: Cancer Associated Fibroblast


title: esophageal cancer, organoid, 005


title: esophageal cancer, organoid, 195


title: ZNF706 knockdown 8hr-chase replicate 3


title: ZNF706 knockdown 0hr-chase replicate 3


title: ZNF706 knockdown 2hr-chase replicate 1


title: ZNF706 knockdown 0hr-chase replicate 2


title: ZNF706 knockdown 4hr-chase replicate 3


title: ZNF706 knockdown 4hr-chase replicate 2


title: ZNF706 knockdown 8hr-chase replicate 1


title: ZNF706 knockdown 2hr-chase replicate 2


title: ZNF706 knockdown 4hr-chase replicate 1


title: esophageal cancer, fibroblast, 669


title: ZNF277 knockdown 8hr-chase replicate 3


title: ZNF277 knockdown 8hr-chase replicate 2


title: ZNF706 knockdown 0hr-chase replicate 1


title: PCGF1_rep1


title: ZNF277 knockdown 4hr-chase replicate 3


title: ZNF277 knockdown 4hr-chase replicate 2


title: ZNF277 knockdown 4hr-chase replicate 1


title: esophageal cancer, assembloid, 191 + 669


title: esophageal cancer, assembloid, 195 + 669


title: ZNF277 knockdown 2hr-chase replicate 3


title: ZNF706 knockdown 2hr-chase replicate 3


title: ZNF277 knockdown 2hr-chase replicate 1


title: ZNF277 knockdown 2hr-chase replicate 2


title: ZNF277 knockdown 0hr-chase replicate 2


title: ZNF277 knockdown 0hr-chase replicate 3


title: ZNF277 knockdown 0hr-chase replicate 1


title: ZMAT5 knockdown 8hr-chase replicate 2


title: ZMAT5 knockdown 8hr-chase replicate 3


title: ZMAT5 knockdown 8hr-chase replicate 1


title: ZNF277 knockdown 8hr-chase replicate 1


title: ZMAT5 knockdown 2hr-chase replicate 3


title: ZMAT5 knockdown 2hr-chase replicate 1


title: ZMAT5 knockdown 0hr-chase replicate 3


title: ZMAT3 knockdown 8hr-chase replicate 2


title: ZMAT5 knockdown 0hr-chase replicate 2


title: ZMAT3 knockdown 4hr-chase replicate 3


title: ZMAT5 knockdown 4hr-chase replicate 1


title: ZMAT3 knockdown 2hr-chase replicate 2


title: ZMAT3 knockdown 4hr-chase replicate 1


title: ZMAT5 knockdown 4hr-chase replicate 2


title: ZMAT5 knockdown 2hr-chase replicate 2


title: ZMAT5 knockdown 0hr-chase replicate 1


title: ZMAT3 knockdown 2hr-chase replicate 3


title: ZMAT3 knockdown 8hr-chase replicate 1


title: ZMAT3 knockdown 8hr-chase replicate 3


title: ZMAT3 knockdown 2hr-chase replicate 1


title: ZMAT3 knockdown 0hr-chase replicate 3


title: ZMAT3 knockdown 0hr-chase replicate 2


title: ZMAT3 knockdown 0hr-chase replicate 1


title: ZMAT5 knockdown 4hr-chase replicate 3


title: ZFP36L1 knockdown 8hr-chase replicate 3


title: ZFP36L1 knockdown 8hr-chase replicate 1


title: ZFP36L1 knockdown 4hr-chase replicate 3


title: ZFP36L1 knockdown 4hr-chase replicate 2


title: ZFP36L1 knockdown 0hr-chase replicate 3


title: ZFP36L1 knockdown 4hr-chase replicate 1


title: ZMAT3 knockdown 4hr-chase replicate 2


title: PHF7 knockdown 8hr-chase replicate 2


title: ZFP36L1 knockdown 2hr-chase replicate 2


title: PHF7 knockdown 8hr-chase replicate 1


title: ZFP36L1 knockdown 2hr-chase replicate 3


title: ZFP36L1 knockdown 2hr-chase replicate 1


title: PHF7 knockdown 4hr-chase replicate 1


title: PHF7 knockdown 2hr-chase replicate 1


title: ZFP36L1 knockdown 0hr-chase replicate 2


title: PHF7 knockdown 0hr-chase replicate 1


title: ZFP36L1 knockdown 0hr-chase replicate 1


title: NT knockdown 8hr-chase replicate 2


title: PHF7 knockdown 4hr-chase replicate 3


title: NT knockdown 8hr-chase replicate 1


title: PHF7 knockdown 4hr-chase replicate 2


title: PHF7 knockdown 8hr-chase replicate 3


title: PHF7 knockdown 2hr-chase replicate 3


title: PHF7 knockdown 0hr-chase replicate 3


title: PHF7 knockdown 2hr-chase replicate 2


title: PHF7 knockdown 0hr-chase replicate 2


title: NT knockdown 8hr-chase replicate 3


title: NT knockdown 2hr-chase replicate 2


title: NT knockdown 4hr-chase replicate 3


title: NT knockdown 2hr-chase replicate 1


title: NT knockdown 0hr-chase replicate 2


title: NT knockdown 4hr-chase replicate 2


title: NT knockdown 2hr-chase replicate 3


title: MAZ knockdown 8hr-chase replicate 2


title: NT knockdown 4hr-chase replicate 1


title: MAZ knockdown 4hr-chase replicate 2


title: MAZ knockdown 2hr-chase replicate 3


title: MAZ knockdown 4hr-chase replicate 1


title: MAZ knockdown 2hr-chase replicate 1


title: NT knockdown 0hr-chase replicate 1


title: MAZ knockdown 8hr-chase replicate 1


title: MAZ knockdown 4hr-chase replicate 3


title: MAZ knockdown 0hr-chase replicate 3


title: MAZ knockdown 0hr-chase replicate 2


title: MAZ knockdown 0hr-chase replicate 1


title: CNOT4 knockdown 8hr-chase replicate 2


title: ZFP36L1 knockdown 8hr-chase replicate 2


title: CNOT4 knockdown 4hr-chase replicate 3


title: CNOT4 knockdown 2hr-chase replicate 2


title: CNOT4 knockdown 0hr-chase replicate 3


title: CNOT4 knockdown 8hr-chase replicate 1


title: CNOT4 knockdown 4hr-chase replicate 2


title: CNOT4 knockdown 2hr-chase replicate 3


title: CNOT4 knockdown 4hr-chase replicate 1


title: CNOT4 knockdown 0hr-chase replicate 2


title: CNOT4 knockdown 2hr-chase replicate 1


title: NT knockdown 0hr-chase replicate 3


title: MAZ knockdown 8hr-chase replicate 3


title: BRCA1 knockdown 8hr-chase replicate 1


title: BRCA1 knockdown 8hr-chase replicate 3


title: CNOT4 knockdown 0hr-chase replicate 1


title: MAZ knockdown 2hr-chase replicate 2


title: BRCA1 knockdown 4hr-chase replicate 3


title: CNOT4 knockdown 8hr-chase replicate 3


title: BRCA1 knockdown 4hr-chase replicate 1


title: BRCA1 knockdown 2hr-chase replicate 2


title: BRCA1 knockdown 2hr-chase replicate 1


title: BRCA1 knockdown 4hr-chase replicate 2


title: BRCA1 knockdown 0hr-chase replicate 3


title: CNBP RBD-deleted replicate 1 eCLIP IP

description: CNBP_DEL.reproducible_enriched_windows.tsv.gz

data_processing:
eCLIP data was analyzed using Skipper with default settings. The kDa of each ORF was matched to the closest input sample beginning at that range; for example, a 78 kDa ORF would be paired with the input sample covering the range of 75 to 150 kDa.
Assembly: hg38
Supplementary files format and content: Reproducible enriched peaks output by Skipper

extract_protocol: eCLIP experiments were performed as previously described using a V5 antibody (Bethyl A190-120A); see Blue et al. 2022 doi:10.1038/s41596-022-00680-z

treatment_protocol: V5-tagged zinc finger ORFs were transfected using Lipofectamine 3000 (Thermo Fisher). One 10cm dish was used for each biological replicate. After 72hr incubation, cells were UV crosslinked on ice at 400 mJoules/cm2 with 254 nm radiation. Cells were then scraped on ice and pelleted at °C, and the supernatant was discarded before the samples were snap-frozen and stored at -80°C. To minimize variability, all samples were prepared in two batches from the same thaw of cells.

value: CNBP RBD-deleted

value: Bethyl A190-120A


title: BRCA1 knockdown 0hr-chase replicate 1


title: CISD2 RBD-deleted replicate 2 eCLIP IP

description: CISD2_DEL.reproducible_enriched_windows.tsv.gz

value: CISD2 RBD-deleted