title: iPSCDA neuron PET3, replicate 2


title: PAWRVC_Dx_scRNA

status: Public on Nov 20 2023

type: SRA

city: Vancouver

first: Marco

last: Marra

state: BC

address: 675 West 10th Avenue

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Research Centre

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
1. Raw sequencing data was processed using Cellranger (V3.1) mkfastq to generate fastq files. Fastq files were aligned to hg38 and quantified using CellRanger (V3.1) count applying standard settings. Libraries with poor sequencing quality (as determined by Cellranger metrics: e.g. base quality, percentage of valid barcodes, valid unique molecular identifiers (UMIs) and cluster density) were discarded.
2. Cells were filtered with less than 1000 UMIs, less than 500 covered genes or more than 15% mitochondrial reads.
3. Using Seurat (V4.0.1), data were log normalized to 10,000 counts and subsequently scaled. Considering the uniform treatment of the cohort and uniform processing of samples, batch effect correction was not applied to avoid overcorrection of patient-to-patient differences. The uwot implementation of Uniform Manifold Approximation and Projection (UMAP) (V0.1.1), was used to visualize scRNA-seq data after initialization using principal component analysis (PCA) and calculation of nearest neighbors (nn) by applying the annoy algorithm.
Assembly: HG38
Supplementary files format and content: Tab-separated values files and matrix files containing: unfiltered files that have not been processed after alignament using cellranger including genes, barcodes and matrix files with the raw counts and filtered files containing the matrices, genes and barcodes for filtered cells, having processed counts. Each sample also contains a metadata file for the processed cells containing, in order: cell and sample IDs, Quality statistics (counts, genes covered, mitochondiral reads) , cell classification including celltype identified using scPRED (see manuscript for details), cluster identified using Seurat and Malignancy status (see manuscript for details), and various patient information.

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
At diagnosis, remission or relapse, bone marrow or blood samples were taken and Ficoll-enrichment was performed followed by viable cryopreservation of the cells (in FBS + DMSO) and long-term storage in liquid nitrogen at the COG biorepository.Cryopreserved samples were taken from liquid nitrogen and thawed in thawing media (50% FBS (ThermoFisher Scientific) + 40% HBSS (Stemcell Technologies) + 100ug/ml DNAseI (Sigma)). Cells were centrifuged (300g for 5 minutes), and washed once with 10ml of ice-cold HBSS + 10% FBS. A second wash with 1ml of HBSS + 10% FBS was performed followed by passing the cell suspension through a 40µm FlowMi filter (SP Bel-Art) into a new 1.5ml Eppendorf tube
Single-cell 3’ RNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.0 (10X Genomics) following the manufacturer’s protocol.Library quality was assessed using the Agilent High Sensitivity DNA kit and libraries were quantified using the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled and converted using the MGIEasy Universal Library Conversion Kit (MGI Americas) following the manufacturer's protocol

treatment_protocol: For this study, a cohort of 28 patients who were enrolled in the Children’s Oncology Group (COG) Phase III AAML1031 trial (clinicaltrials.gov, NCT01371981) were studied using single cell sequencing. For the generation of the single cell datasets, patients were selected from Arm B (Standard Chemotherapy (ADE 10+3+5) + Bortezomib (n=24)) or Arm C (Standard Chemotherapy (ADE 10+3) + Sorafenib (n=4)). Four patients that were taken from Arm B were long-term remission patients (no event for at least five years after treatment). None of the patients that were sequenced longitudinally underwent stem cell transplantation.

tag: cell type

value: Blood cells

tag: tissue

value: Blood

tag: treatment

value: Arm B


title: PAVBCV_Rem_scRNA

description: 10x Genomics


title: iPSCDA neuron CHE6, replicate 2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

library_source: transcriptomic

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the hg19 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: 38444 iPSC derived neurons

growth_protocol: Dopaminergic neurons were differentiated directly from iPSCs using the Kriks et al protocol https://www.nature.com/articles/nature10648

extract_protocol: Cells were dissociated using Trizol and the Zymo RNA clean and concentrate kit was used for RNA preparation

tag: cell line

value: 38444 iPSC derived neurons

value: dopmainergic

tag: genotype

value: LRRK2 mutation

tag: time

value: 45 days


title: Cell line Exon 11partc-2 Ola Pool1 Replicate 1

city: Frederick

first: Shyam

last: Sharan

state: MD

address: Building 560, Room 32-33

institute: Mouse Cancer Genetics Program

library_source: genomic

data_processing:
The paired end reads were aligned to the reference sequence using the Needleman-Wunsch alignment algorithm after the reads were demultiplexed using bcl2fastq (Illumina), generation of fastq files, and merging using FLASH.
The total number of aligned reads were quantified using CRISPResso2 http://crispresso.pinellolab.org/submission. Iindividual unique alignments were annotated with a custom-made variant caller modified from ANNOVAR (64) (release 2019-10-21) and the R/Bioconductor Biostrings package in R version 4.1.2 https://bioconductor.org/packages/Biostrings. Merged reads containing “N” bases were removed from the analysis.
Abundances of SNVs were quantified when the reads contained a single-nucleotide substitution. Read counts for each SNVs were then normalized to the total read coverage of the sequencing library after adding a pseudocount of 1 to all reads for all conditions. Individual variants with a read count of more than 1 in 1,000 reads in the M15 condition were used for further analysis. Dropout or enrichment scores were calculated by taking the ratio of frequency of SNV after HAT, cisplatin, or olaparib treatment over that in M15.
The scores were expressed in log2 scale, which we define as the functional scores of SNVs in HAT, cisplatin, and olaparib. The functional scores, averaged between independent replicates (2-4), were used to calculate the the probabilities of impact on function (PIF) for all the variants in the data set.
Assembly: GRCh38
Supplementary files format and content: xlsx: Excel files include PIF and function scores for all variants.
Library strategy: Amplicon sequencing

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Genomic DNA was extracted from the cell pellets using Zymo Genomic DNA Extraction kit
DNA libraries were prepared using TruSeq Nano DNA Library Prep kit

value: Embryonic stem cell

value: Olaparib


title: HE2-Low-Rep4

city: Birmingham

first: Benjamin

last: Edginton-White

address: Medical School

department: ICGS

country: United Kingdom

institute: University of Birmingham

description: Higher read depth sequencing than original experiments

data_processing:
Paired end sequencing reads were trimmed using Trim Galore (Krueger F, 2021) with the parameters --nextera --length 70 –paired.
The reads were then aligned to the mm10 genome using bowtie2 using parameters --very-sensitive --fr --no-discordant -X 600 --no-mixed.
Aligned reads were filtered for only those which were properly paired and with a mapq score of over 40 using Samtools and output as a bedpe file.
This was further converted to a bed file of enhancer fragments by taking the first co-ordinate of read 1 and the final co-ordinate of read 2 for each pair. Duplicate fragments were removed using the uniq functionin bash and fragments were further filtered using the intersect function on Bedtools for any which had 100% overlap with an off target background fragment list which was created by producing a library from un-transfected cells. The fragments were further filtered by the same method against the input plasmid libraries.
The fragments were then filtered using Bedtools intersect for those which were found in open chromatin, defined by ATAC-Seq peaks in the correct differentiation stage in HM-1 cells.
Finally, the enhancer fragments were annotated using the annotatePeaks function of Homer for those within 1.5 kb of a TSS (promoter fragments) and distal fragments representing genuine enhancers.
Assembly: mm10
Supplementary files format and content: Bed files of filtered distal enhancer fragment co-ordinates
Supplementary files format and content: Bed files of filtered promoter fragment co-ordinates
Library strategy: Enhancer Reporter Sequencing

source_name: Hemogenic Endothelium 2 (HE2)

growth_protocol: A genome-wide enhancer reporter assay was designed based on an enhancer reporter system designed by Wilkinson et al. (2013). Briefly the enhancer reporter functions by inserting a fragment of interest upstream of a HSP68 minimal promoter and Venus-YFP reporter by Gateway® cloning. The reporter construct is then transfected into the HM-1 ES cell line which has a non-functional HPRT locus. Using HPRT homology arms the report cassette becomes integrated into the HPRT locus by homologous recombination, also repairing the locus, enabling selection of clones with successful recombination. This enhancer reporter system was modified and optimised for genome-wide screening. To obtain genome-wide enhancer fragments for cloning into the reporter we isolated tn5 tagmented open-chromatin fragments based on the ATAC-Seq protocol 33 from cells of the five differentiation stages. Cells were obtained (2.5x105) from each differentiation stage (ES, HB, HE1, HE2, HP) as detailed in the serum IVD method. Cells were pelleted in 5 aliquots of 50x103 cells and following the ATAC-Seq protocol each cell pellet had a transposition mix added (2x TD Buffer 25µl, TN5 Transposase 2.5 µl, PBS 16.5 µl, 1% Digitonin 0.5 µl, 10 % Tween-20 0.5 µl, H2O 5 µl) and cells were gently resuspended by pipetting. The transposition reaction was then incubated in a shaker at 700 RPM, 37°C for 30 minutes. The 5 reactions were then combined and DNA purified using the Qiagen MinElute® Reaction Clean-up kit and eluted in 26.5 µl H2O. One fifth of the purified reaction from each stage was used to produce ATAC-Seq libraries for direct sequencing and the remainder had linkers added incorporating AttB Gateway® cloning sites to enable insertion into a Gateway® donor vector (pDONR 221). The linkers were designed based on the tn5 transposase sequence and added by PCR in 2 steps. Initially 5 cycles of PCR were performed (Transposed DNA 20 µl, H2O 20 µl, 25 µM AttB tn5 Fwd primer 5 µl, 25 µM AttB tn5 Rev primer 5 µl, NEBNext Master Mix 50 µl) with the following conditions, 72°C for 5 minutes, 98°C for 30 seconds, 5 cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute and a final hold at 4°C.  To optimize the required cycle number, the material from the initial PCR reaction was split and a 5 µl was used for a separate qPCR reaction (0.125 µM AttB tn5 Fwd Primer, 0.125 µM AttB tn5 Rev Primer, 1 x SYBR Green I, NEBNext Master Mix) with the following conditions: 72°C for 5 minutes, 98°C for 30 seconds, 35 cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute using a StepOnePlus™ Real-Time PCR System (Thermo Fisher). Using the raw data from the cyan channel the number of cycles for 25% amplification was calculated. The number of cycles obtained from the qPCR side reaction was then used to amplify the remainder of the material as follows, 98°C for 30 seconds, cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute with a final hold at 4°C. The resulting material was size selected, to optimise for material originating from enhancers, for fragments between 350 and 650 bp by electrophoresis on a 1.2% agarose gel with ethidium bromide and gel extraction was performed using the Qiagen MinElute® Gel Extraction Kit following manufactures protocol. To generate attL-flanked entry clones compatible with cloning into the reporter vector the size selected material was cloned into the pDONR™221 (Thermo Fisher) by BP Gateway® reaction (100 fmol pDONR221, 100 fmol PCR material, 2 µl BP Clonase II, made up to 20µl with TE buffer (pH 8.0) the reaction was incubated for 18 hours at 25°C and ended by treatment with 0.2µg proteinase K and incubation at 37°C for 10 minutes. NEB 10-beta Electrocompetent cells were transformed with the plasmid by electroporation with a Bio-Rad GenePulser using program EC1 (2.0 kV, 200 Ohm, 25 µF), after addition of outgrowth media and incubation at 37°C, 250 rpm for 1 hour the bacteria were spread onto 150 mm agar plates containing 50 µg/ml kanamycin. Following overnight incubation at 37°C, 10 ml of LB was added to each plate and the bacterial lawn scraped off using a cell scraper. Plasmid DNA was extracted from the collected bacteria by Maxi-prep using the NucleoBond Xtra Midi EF kit following manufacturer’s instructions. The resulting product was eluted in 500 µl H2O.  The chromatin fragments were then transferred into the enhancer reporter cassette in the pSKB-GW-Hsp68-Venus vector 1 by Gateway® LR reaction (150ng Entry clone (pDONR), 150 ng pSKB, 2 µl LR Clonase II, made up to 10µl with TE buffer (pH 8.0) ) the reaction was incubated for 1 hour at 25°C and ended by treatment with 0.2 µg proteinase K and incubation at 37°C for 10 minutes. As with the BP reaction product, NEB 10-beta Electrocompetent cells were transformed with the material and after overnight incubation on agar plates containing 200 µg/ml ampicillin the bacteria were collected and the plasmid library extracted by Maxi-Prep. To obtain the highest possible diversity of fragments the cloning was carried out 10 times for material from each differentiation stage with the pDONR 221 library material  being combined before moving to the LR clonase reaction.  The HM-1 ES cell line was cultured on gelatinised culture plates in ES-Media (DMEM, 15% FCS, 1 mM Sodium pyruvate, 1x Pen/Strep, 1x L-glutamine, 0.15 mM MTG, 25 mM Hepes buffer and 1u/ml ESGRO LIF (Sigma-Aldrich)) at 37 °C, 10% CO2 and split every 48 hours to maintain healthy cells. Prior to transfection the cells were treated for 1 week with 1 x 6-TG to remove any cells with a functional HPRT locus. The plasmid libraries were mixed and digested with PmeI (NEB) to linearise the plasmids prior to transfection. To obtain optimum homologous recombination efficiency CRISPR guides were designed flanking the region and cloned into the PX458 Cas9 and sgRNA expression vector. For each experiment, 500x106 cells were transfected using a Nucleofector®-4D (Lonza) with the P3 Primary Cell X kit with 5x106 per cuvette 10 ug pSKB enhancer reporter plasmid and 10 ug of PX458-HPRT CRISPR plasmid using program CG-104. Following electroporation, the cells were plated on gelatinised plates in ES-media with the addition of 50 µM SCR7 pyrazine (Sigma) to inhibit Non-homologous end joining, promoting homologous recombination following cutting by Cas9. After 12 hours the media was changed and 1 x HAT (Hypoxanthine-Aminopterin-Thymidine (Sigma)) was added to select for clones with successful recombination. The cells were then maintained in media containing HAT for one week and HT (hypoxanthine and thymidine (Sigma)) for a further 2 passages to prevent the cells from dying after the withdrawal of HAT, whereby all cells were kept and replated after splitting. The selected cells were then put into IVD cultures and differentiated into HB, HE1, HE2 and HP (as described in Obier et al (2016)) and sorted by FACS. In addition to the previously mentioned gating for obtaining the cell populations the cells were also sorted into negative, low, medium and high Venus-YFP populations representing the activity of the enhancer fragment driven minimal promoter. The YFP-Venus negative population was gated based on a cell line containing a reporter construct with only the minimal promoter and reporter with no enhancer fragment.

extract_protocol:
Genomic DNA was extracted from the sorted cell populations using the Qiagen DNA Micro kit following manufacturer’s instructions.
To amplify the fragments contained in the reporter cassettes and add sequencing adaptors a PCR using indexed primers compatible with Illumina sequencing and targeted against the tn5 transposase sequence ((0.5 µM Nextera PCR Primer i5, 0.5 µM Nextera PCR Primer i7, 25 µl NEBNext Master Mix). Dependant on the amount of DNA obtained from the sorted cells between 25 and 30 PCR cycles were performed with the following conditions 98°C for 30 seconds, cycles of 98°C 10 seconds, 63°C 30 seconds and 72°C 1 minute with a final hold at 4°C. Libraries were quantified using a Bioanalyzer 2100 (Agilent) with a High Sensitivity DNA Chip and pooled at equal concentration for sequencing. The final pool concentration and size was then confirmed by Kappa Library Quantification Kit (Roche) and Bioanalyzer. The pooled libraries were sequenced on a Next-Seq 550 as a paired end run with a 150 cycle High Output kit by the Genomics Birmingham Sequencing Facility.

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells

value: In Vitro Differentiation


title: PAVBCV_Dx_scRNA

description: 10x Genomics

source_name: Marrow

value: Bone marrow cells

value: Marrow


title: HP-Negative-Rep4

source_name: Hematopeitic Porgenitor (HP)

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells


title: iPSCDA neuron CHE6, replicate 1


title: HE2-Negative-Rep4


title: Cell line Exon 11partc-2 Ola Pool1 Replicate 2


title: Cell line Exon 11partc-2 Cis Pool1 Replicate 1

value: Cisplatin


title: PAULSL_Dx_scRNA

description: 10x Genomics

value: Arm B (long-term remission)


title: Cell line Exon 11partc-2 HAT Pool1 Replicate 2

value: HAT


title: iPSCDA neuron 5-1, replicate 2

source_name: UKERfRJO-X-001 iPSC derived neurons

value: UKERfRJO-X-001 iPSC derived neurons

value: sporadic PD


title: iPSCDA neuron 6-5, replicate 1

source_name: UKERfM89-X-001 iPSC derived neurons

value: UKERfM89-X-001 iPSC derived neurons

value: dopmainergic


title: PAULSL_Rem_scRNA

description: 10x Genomics


title: iPSCDA neuron 6-5, replicate 2

value: 45 days


title: HE1-High-Rep4

source_name: Hemogenic Endothelium 1 (HE1)

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: Cell line Exon 11partc-2 Cis Pool1 Replicate 2

value: Embryonic stem cell


title: iPSCDA neuron 5-1, replicate 1


title: PAXGDG_Rel_scRNA

description: 10x Genomics

value: Blood cells

value: Blood

value: Arm B


title: PAVBCV_Rel_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Marrow


title: PAWUAE_Rem_scRNA

description: 10x Genomics


title: iPSCDA neuron 4-18, replicate 2

source_name: UKERf1JF-X-001 iPSC derived neurons

value: UKERf1JF-X-001 iPSC derived neurons

value: control


title: HC7 [CL190821]

city: London

first: Ahsen

last: Ustaoglu

state: England

address: Blizard Institute

institute: Queen Mary University of London

description:
Partek_GC-AU-9942_Normalization_TPM.txt
Partek_GC-AU-9942_Normalization_Median_ratio_for_DEseq2.txt

data_processing:
Sequencing analysis was conducted using Partek Flow software
FASTQ files were demultiplexed and underwent pre-alignment QC to ensure that the collected data did not have any obvious systematic errors before alignment
Next, Spliced Transcripts Alignment to a Reference (STAR) was used to align sequenced reads to the hg38 human genome
Adapter sequence overrepresentation was insignificant, so trimming was not necessary. Post-alignment QC was performed to check the quality of alignment. All samples had more than 97% alignment to the genome
Aligned genes were normalised using median ratio for DEseq2 on Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalised median ratio values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: oesophageal mucosa

extract_protocol:
Endoscopic biopsies from the distal oesophagus were placed in RNA later solution (Sigma, Cat. Number R0901-100ml) and kept at -80ºC until RNA extraction. A total of 9-10 biopsy samples were selected for sequencing from each GORD phenotype. RNA isolation was performed using the RNeasy Mini Kit (Qiagen, Cat. Number 74016). A maximum of 30 mg of tissue was used for each RNA extraction to ensure sufficient RNA yield for sequencing.
Nanodrop and bioanalyzer were used to perform quality control (QC) checks of RNA supplied to the Genome Centre. RNA samples with RNA integrity less than 7 were excluded from library preparation. cDNA libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit with the mRNA isolation module using the manufacturer’s instructions (Illumina). Briefly, RNA samples were first diluted to 20ng/μl using RNAse-free water. First strand synthesis reaction buffer was prepared and left on ice until reaction. NEBNext oligo d(T) beads were washed with RNA binding buffer, placed on a plate and subsequently resuspended in RNA binding buffer on a magnetic rack. The plate was then sealed and placed on a thermal cycler with the lid heated to 75°C, at 65°C for 5min to denature RNA and facilitate binding of the poly-A mRNA to the beads. Following centrifugation, resuspension, and washing of the beads, the plate was placed on the magnetic rack again and supernatant was discarded. Next, 50μl of Tris buffer was added per well, plate sealed and incubated at 80°C for 2min with the lid heated to 90°C. The plate was removed when the temperature reached 25°C, centrifuged, and 50μl RNA binding buffer added per well to allow mRNA to re-bind beads. The supernatant was removed using the magnetic rack, and mRNA eluted from the beads by adding 11.5μl of the first strand synthesis buffer and placing in the thermal cycler with the lid heated to 105°C for 10min at 94°C. Following completion of incubation, the plate was removed from the thermal cycler, centrifuged, and purified mRNA collected by transferring 10μl of supernatant to a clean nuclease-free PCR plate. The plate was then placed on ice and first strand cDNA synthesis was immediately started.  The first strand enzyme mastermix (composed of NEBNext strand specificity reagent and NEBNext first strand synthesis enzyme mix) was added to the fragmented and primed mRNA, gently mixed, and the plate sealed and placed in the thermal cycler with the heated lid set to 80°C using the following conditions: 25°C for 10min, 42°C for 50min, 70°C for 15min, hold at 4°C. Plate was then removed, briefly centrifuged, and second strand cDNA synthesis reaction began immediately. Next, 60μl second strand mastermix (composed of nuclease free water, NEBNext second strand synthesis buffer, and NEBNext second strand synthesis enzyme mix) was added to the first strand synthesis reaction. The plate was sealed and placed in thermal  107  cycler for 60min at 16°C. AMPure XP beads were resuspended and added to the second strand synthesis reaction to purify the double-stranded cDNA. The supernatant was subsequently discarded and washed in 80% ethanol, airdried, and the DNA target was eluted from the beads by adding 53μl 0.1x TE buffer to the beads. The end prep mastermix was prepared by combining NEBNext Ultra II end prep reaction buffer and NEBNext Ultra II end prep enzyme mix, and added to the purified cDNA. The sealed plate was then placed in a thermal cycler at 20°C for 30min, and 65°C for 30min, and removed when the incubation reached 4°C.  Following adaptor ligation and purification using AMPure XP beads, the PCR library was enriched by adding 25μl of NEBNext Q5 Hot start HiFi PCR master mix and 10μl of pre-assigned index primer to each well and incubation. The thermal cycler lid was heated to 105°C, and samples went through: 1 cycle of 98°C for 30sec, 98°C for 10sec, 13 cycles of 65°C for 75sec, 1 cycle of 65°C for 5min, and held at 4°C. The PCR reaction was then purified using Agencourt AMPure XP beads. All resulting libraries were quantified using the Qubit HS dsDNA kit and qualified on the appropriate 1000bp ScreenTape according to concentration.  Paired end mRNA sequencing was performed using the NextSeq 500 High Output Kit (Blizard Genome Centre) with 20M reads and a read length of 75bp per sample.

value: oesophageal mucosa

value: squamous epithelial

value: Female

tag: group

value: healthy control (HC)


title: PAXGDG_Dx_scRNA

description: 10x Genomics


title: HC8 [TG010921]

value: Male


title: HC6 [MG050821]


title: HE1-Low-Rep4

value: In Vitro Differentiation


title: PAWUAE_Rel_scRNA

description: 10x Genomics


title: HE1-Negative-Rep4


title: iPSCDA neuron 4-18, replicate 1

value: dopmainergic

value: 45 days


title: HB-Medium-Rep4

source_name: Hemangioblast Cell (HB)

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: HC5 [ZP290721]


title: PAWUAE_Dx_scRNA

description: 10x Genomics


title: iPSCDA neuron 30-1, replicate 2

source_name: UKERfO3H-X-001 iPSC derived neurons

value: UKERfO3H-X-001 iPSC derived neurons


title: HE1-Medium-Rep4

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: HC4 [AV140721]


title: HB-Low-Rep4


title: HC3 [BB260521]


title: iPSCDA neuron 30-1, replicate 1


title: PAUURD_Rem_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Arm B (long-term remission)


title: PAUURD_Dx_scRNA

description: 10x Genomics

value: Marrow


title: HC2 [MV120521]


title: ES-High-Rep4

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell

value: HM-1 ES cell


title: HB-High-Rep4


title: HB-Negative-Rep4


title: iPSCDA neuron 23-1, replicate 1

source_name: UKERfAY6-X-001 iPSC derived neurons

value: UKERfAY6-X-001 iPSC derived neurons

value: sporadic PD


title: iPSCDA neuron 23-1, replicate 2


title: BO 9 [JB110320]

value: oesophageal mucosa

value: squamous epithelial

value: BO


title: PAVJXG_Rem_scRNA

description: 10x Genomics

value: Arm B


title: ES-Medium-Rep4


title: iPSCDA neuron 21-2, replicate 2

source_name: UKERf33Q-X-001 iPSC derived neurons

value: UKERf33Q-X-001 iPSC derived neurons

value: dopmainergic

value: control

value: 45 days


title: BO 8 [RC110320]

value: Male


title: PAVJXG_Dx_scRNA

description: 10x Genomics


title: BO 7 [GK190220]


title: iPSCDA neuron 21-2, replicate 1


title: PAVJXG_Rel_scRNA

description: 10x Genomics


title: ES-Low-Rep4


title: ES-Negative-Rep4


title: PAWNPU_Rem_scRNA

description: 10x Genomics


title: NERD 10 [JI050220]

value: Female

value: NERD


title: HP-High-Rep3

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells

value: In Vitro Differentiation


title: HP-Medium-Rep3


title: ERD 10 [CB050220]

value: ERD


title: MCF10A_WT_mock_r3

city: Seattle

first: Amanda

last: Paulovich

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina Bcl2fastq v2.16
Genome_build: UCSC hg19
Supplementary_files_format_and_content: .gct (cpm)

source_name: ATCC CRL-10317 (mammary gland; breast; epithelium)

growth_protocol: The cell lines were maintained at 37 °C in 5% CO2 and cultured in DMEM/F-12 medium (Gibco, 11320) supplemented with 5% horse serum (Gibco, 16050), cholera toxin (Sigma-Aldrich, C8052) to a final concentration of 1 ng/mL, insulin (Sigma-Aldrich, I6634) to a final concentration of 10 ug/mL, human epidermal growth factor (PeproTech, AF-100-15) to a final concentration of 10 ng/mL, hydrocortisone (Sigma-Aldrich, C8052) to a final concentration of 0.5 ug/mL, and 1% Pen Strep (Gibco, 15140). All cell line identities were confirmed by DNA fingerprinting using STR (Short Tandem Repeats) CODIS (Combined DNA Index System) typing.

extract_protocol: Total RNA was extracted from cells treated with or without methyl methanesulfonate in growth medium for 3 hours using the RNeasy Mini Kit (Qiagen, 74104) coupled with the QIAshredder homogenizers (Qiagen, 79654). RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA was only accepted if the RNA Integrity Number (RIN) was >9.0. 1.0 ug of total RNA from each sample was then polyA selected and chemically fragmented to ?200 bp, and cDNA was created using random hexamer primers. Library preparation followed the TruSeq Illumina protocol with each individual library receiving a unique Illumina barcode. RNA-seq was performed on an Illumina HiSeq 2500 machine with six libraries multiplexed per lane using 50-bp paired-end reads. This resulted in an average of 250 million reads per lane, with an average of 43 million reads per sample. Each sample had three biological replicates that were prepared on three separate days.

treatment_protocol: Two days prior to cell line lysis, cells were plated in 100 mm culture dishes using an equal number of cells per dish (example: 1 million cells per 100 mm culture dish). 48 hours later, the growth medium was replaced with growth medium containing 0.5 mM of methyl methanesulfonate (MMS, Sigma-Aldrich, 129925) or growth medium containing no MMS (mock treatment). The cells were incubated for 3 hours at 37 °C in 5% CO2. At the end of the incubation time, the growth medium was removed, and the adherent cells were rinsed with Dulbecco's Phosphate-Buffered Saline (DPBS, Gibco, 14190). The cells were detached using 0.25% Trypsin-EDTA (Gibco, 25200) and placed in the incubator at 37 °C in 5% CO2 for 15-20 minutes. The Trypsin-EDTA solution was inactivated by adding Trypsin Neutralization Solution (TNS, DMEM:F-12 SILAC media containing 5% dialyzed horse serum) and the remaining attached cells were scraped off the plate with a cell scraper. The cells were transferred to pre-cooled 50 mL conical tubes, spun at 400 × g for 8 min at 4C to remove the medium, and washed twice with ice-cold DPBS.

value: WT

value: untreated

tag: cell line catalog #

value: ATCC CRL-10317


title: MCF10A_PTEN-KO_MMC_r3

source_name: MCF10A CELLS PTEN (-/-)

value: 0.5 mM methyl methanesulfonate - 3 hours

value: Sigma Aldrich (catalog # CLLS1046)


title: HP-Low-Rep3


title: healthy control (HC) 1 [HF040320]

value: oesophageal mucosa

value: squamous epithelial

value: healthy control (HC)


title: PAWNPU_Dx_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Marrow

value: Arm B


title: PAUWUZ_Rem_scRNA

description: 10x Genomics

value: Arm B (long-term remission)


title: ERD 9 [SM050220]

value: Female


title: MCF10A_PTEN-KO_mock_r3


title: PAUWUZ_Dx_scRNA

description: 10x Genomics


title: MCF10A_p53-KO_MMC_r3

source_name: MCF10A CELLS TP53 (-/-)

value: Sigma Aldrich (catalog # CLLS1045)


title: NERD 9 [E6]

value: Male

value: NERD


title: HP-Negative-Rep3

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells

value: In Vitro Differentiation


title: NERD 8 [E4]


title: HE2-Medium-Rep3

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: MCF10A_WT_MMC_r3

value: WT

value: 0.5 mM methyl methanesulfonate - 3 hours

value: ATCC CRL-10317


title: PAWWXU_Rem_scRNA

description: 10x Genomics


title: MCF10A_WT_MMC_r2


title: MCF10A_p53-KO_mock_r3

value: untreated


title: HE2-Low-Rep3


title: MCF10A_WT_mock_r2


title: PAWWXU_Dx_scRNA

description: 10x Genomics

value: Bone marrow cells


title: FH 9 [NE8]

value: oesophageal mucosa

value: squamous epithelial

value: FH


title: PAWNPU_Rel_scRNA

description: 10x Genomics

value: Marrow

value: Arm B


title: FH 8 [NE4-2]

value: Male


title: MCF10A_PTEN-KO_MMC_r2

value: Sigma Aldrich (catalog # CLLS1046)


title: PAVDYE_Rem_scRNA

description: 10x Genomics


title: MCF10A_PTEN-KO_mock_r2


title: PAVDYE_Rel_scRNA

description: 10x Genomics


title: HE2-Negative-Rep3


title: HE1-High-Rep3

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: FH 6 [AE161118]


title: HE2-High-Rep3

value: In Vitro Differentiation


title: NERD 7 [LJ300319]

value: Female

value: NERD


title: PAWWXU_Rel_scRNA

description: 10x Genomics


title: ERD 8 [BT150519]

value: ERD


title: MCF10A_p53-KO_MMC_r2

value: 0.5 mM methyl methanesulfonate - 3 hours

value: Sigma Aldrich (catalog # CLLS1045)


title: PAVDYE_Dx_scRNA

description: 10x Genomics


title: PAWNYX_Rem_scRNA

description: 10x Genomics


title: HE1-Low-Rep3


title: FH 5 [EB120419]


title: PAWNYX_Dx_scRNA

description: 10x Genomics

source_name: Blood

value: Blood cells

value: Blood


title: HE1-Negative-Rep3


title: FH 4 [CB120419]

value: oesophageal mucosa


title: HB-Medium-Rep3

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: MCF10A_p53-KO_mock_r2

value: untreated


title: HB-High-Rep3


title: FH 7 [RM120419]

value: squamous epithelial

value: FH


title: PAUZRT_Rem_scRNA

description: 10x Genomics

value: Arm B


title: MCF10A_WT_MMC_r1

value: WT

value: ATCC CRL-10317


title: MCF10A_WT_mock_r1


title: PAWNYX_Rel_scRNA

description: 10x Genomics

value: Bone marrow cells

value: Marrow


title: HE1-Medium-Rep3

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells

value: In Vitro Differentiation


title: ERD 7 [PJ281118]

value: Female

value: ERD


title: MCF10A_PTEN-KO_MMC_r1

value: 0.5 mM methyl methanesulfonate - 3 hours

value: Sigma Aldrich (catalog # CLLS1046)


title: BO 6 [BA221019]

value: oesophageal mucosa

value: BO


title: MCF10A_PTEN-KO_mock_r1

value: untreated


title: PAUZRT_Rel_scRNA

description: 10x Genomics


title: PAUZRT_Dx_scRNA

description: 10x Genomics


title: BO 5 [PB091019]

value: squamous epithelial


title: HB-Negative-Rep3

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: MCF10A_p53-KO_MMC_r1

value: Sigma Aldrich (catalog # CLLS1045)


title: ERD 6 [MS161118]

value: Male


title: FH 3 [SG131119]

value: FH


title: ES-Medium-Rep3

value: Embryonic Stem Cell

value: HM-1 ES cell


title: ES-High-Rep3


title: HB-Low-Rep3


title: BO 4 [SH061119]


title: polII_TGF+_ChIP-Seq

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: MCF10A cells treated with TGF-β1 and subjected to ChIP using an anti-RNA polymerase II antibody

data_processing:
Prepared libraries were sequenced using a HiSeq 2500 platform (Illumina), and 75 bp single-end reads were obtained.
Raw reads of FASTQ files were employed for ChIP-Seq analysis using StrandNGS version 3.0 software (Strand Life Sciences). Reads were mapped onto the Homo sapiens hg19 reference genome using the COBWeb algorithm.
Peak calling was performed using the enriched region detection algorithm with default settings. Genes located within 5 kb of the detected peaks were listed.
Processed data were visualized with Integrative Genome Browser software.
Genome_build: Sequence reads were aligned to the human genome (hg19).
Supplementary_files_format_and_content: bigWig files were generated for processed data containing chromosome, regions

growth_protocol: MCF10A cells were purchased from the American Type Culture Collection (Manassas, VA, USA) and maintained in Dulbecco’s Modified Eagle's Medium (DMEM) supplemented with 5% horse serum, Ham’s F12 Nutrient Mixture (Thermo Fisher Scientific), 20 ng/ml epidermal growth factor, 100 ng/ml cholera toxin, 500 ng/ml hydrocortisone, and 5 μg/ml insulin.

extract_protocol:
ChIP was performed using a SimpleChIP Plus Kit (CST) according to the manufacturer’s instructions.
The ChIP-Seq library of precipitated DNAs was prepared using KAPA Library Preparation Kits for Illumina (Kapa Biosystems).

treatment_protocol: MCF10A cells treated with or without TGF-β1  (10 ng/ml) for 48 h were fixed in 1% formaldehyde, which was quenched by incubation with 125 mM glycine for 5 min. Lysed cell extracts were subjected to ChIP.

value: human epithelial MCF10A cells

tag: agent

tag: antibody

value: anti-RNA polymerase II


title: ES-Negative-Rep3


title: ES-Low-Rep3


title: SC3_24h_combi_rep2

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 control vs 2 drug-treated samples (2 drug-treated vs 2 control with 2 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes, featureCount read count for all samples

source_name: Jurkat cells

growth_protocol: TAL1-FKBP12 Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBSEQ platform were performed at the BGI Genomics.

treatment_protocol: The cells were treated with DMSO, dTAG-13, GSI or combination of dTAG-13 and GSI.  Total RNA were harvested after 24 hours.

value: Jurkat

value: T-ALL

tag: protein depletion

value: Combi

tag: timepoint


title: BO 3 [CF231019]

value: Female


title: WCL_Jurkat_DMSO

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with --no-unal.
Aligned ChIP-seq reads were removed of duplicates with Picard MarkDuplicate package.
ChIP-Seq peaks were called with MACS2 software version 2.2.7.1 with --keep-dup=1 --SPMR -p 1e-3 -f BAM --broad --broad-cutoff 1e-3.
The output bedGraph data were normalized by subtracting the corresponding background values using MACS2 bdgcmp -m subtract.
BedGraph signal were further floored to 0.1, then convert to bigWig format using UCSC bedGraphToBigWig tool
Assembly: hg19
Supplementary files format and content: Peak bed files of TAL1-HA
Supplementary files format and content: bigWig files of TAL1-HA

extract_protocol:
Library construction from the HA ChIP-seq samples and sequencing of paired-end 150-bp-long reads by the DNBSEQ platform were performed at BGI Genomics.
Paired-end ChIP-Seq sequencing

treatment_protocol: The cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei.  Protein-DNA complexes were isolated with anti-HA antibody.  A sample of whole cell extract (input) was sequenced and used as the background to determine enrichment.

tag: chip target

value: WCL


title: IgG_TGF+_ChIP-Seq

description: MCF10A cells treated with TGF-β1 and subjected to ChIP using an anti-IgG antibody

value: anti-IgG


title: BO 2 [SM211019]

value: oesophageal mucosa

value: BO


title: IgG_TGF-_ChIP-Seq

description: MCF10A cells treated without TGF-β1 and subjected to ChIP using an anti-IgG antibody


title: polII_TGF-_ChIP-Seq

description: MCF10A cells treated without TGF-β1 and subjected to ChIP using an anti-RNA polymerase II antibody


title: TAL1_HA_Jurkat_DMSO


title: HP-High-R2

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells

value: In Vitro Differentiation


title: HP-Medium-R2


title: SC3_24h_gsi_rep2

value: GSI


title: ERD 5 [WB081019]

value: squamous epithelial

value: Male

value: ERD


title: MCF10A_p53-KO_mock_r1

value: untreated

value: Sigma Aldrich (catalog # CLLS1045)


title: WCL_Jurkat_dTAG

value: Jurkat


title: HP-Low-R2


title: Large preB cell, IKDN, NIPBL, rep2

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Read alignment was performed on the mm10 assembly with the STAR 5.02 genome alignment algorithm (--alignIntronMax 1 --alignEndsType EndToEnd) on the DNAnexus platform (https://www.dnanexus.com/)
Picard-tools 4.0.3 (Broad Institute) were used to remove PCR duplicates.
Peak calling was performed using MACS2 2.1.1 (Zhang et al., 2008) with input chromatin as control and with a q-value (minimum FDR) cutoff of 0.05. Model building with --mfold of 5, 50 was used for transcription factors, H3K4me3and H3K27ac. The –broad flag was used to identify enriched regions for spreading histone marks such as H3K4me1, H3K27ac, H3K9me3.
Normalized “pileup.bedgraphs” were used after indexing for browser visualization.
Bigwigs were obtained from the “pileup” files for visualization using bedGraphToBigWig v4.
Assembly: mm10

source_name: mouse large pre-B cell (CD19+CD43+BP1+)

growth_protocol: Sorted large pre-B cells were cultured on OP9 stroma in DMEM ( D-5671; Sigma) supplemented with 10% FBS (2442; Sigma), 50 μM 2-mercaptoethanol, 100 μg/ml penicillin, 100 μg/ml streptomycin, 1× Glutamax (35050-062; Gibco), 10 mM HEPES (156-30-80; Gibco) and 1× sodium pyruvate (11360-070; Gibco) in the presence of 5ng/ml of IL-7. Stroma adherent large pre-B cells from WT or IKDN cultures were detached with 0.2% trypsin (EDTA free) for 2 minutes at room temperature. Large pre-B cells were ~ 99% of the cells in suspension as determined by flow cytometry.

extract_protocol:
ChIP-seq experiments was performed as previously described (Hu et al, Genes Dev. 2016). Briefly, cells were first crosslinked with 2mM DSG for 45 min and then with 1% formaldehyde for 10 min at room temperature. Cells were then lysed and sonicated in RIPA buffer containing 0.2% SDS (50mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.2% SDS, 0.5 mM PMSF, and 1x Protease inhibitor cocktail (Roche). Chromatin was cleared by centrifugation at 18,000xg for 20 minutes, and then incubated with 5 μg of antibodies pre-bound to Dynabeads protein G (Life technologies). After extensive washing on beads, bound chromatin was eluted and de-crosslinked in elution buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS, 0.3M NaCl) overnight at 65°C and purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Purified ChIP DNA was end repaired, end adenylated, and then ligated with Illumina Truseq indexed adaptors. The ligated DNA was purified with AMPure XP beads (Beckman Coulter) and then amplified with KAPA HiFi DNA Polymerase (KAPA Biosystems) for 8 to 13 cycles. After amplification, the library DNA was size selected with AMPurex XP beads to 200-600 bp range, and the purified libraries were multiplexed for sequencing in house with an Illumina NextSeq 550 system.

value: mouse large pre-B cell (CD19+CD43+BP1+)

value: IkE5D/D (IKE5 fl/fl, Cd2-cre)

tag: chip antibody

value: NIPBL (Proteintech 18792-1-AP)


title: SC3_24h_dt_rep2

value: T-ALL

value: dTAG


title: TAL1_HA_Jurkat_dTAG


title: Large preB cell, WT, NIPBL, rep2

value: Wild-type (IKE5 fl/fl, Cre-)


title: HP-Negative-R2

source_name: Hematopeitic Porgenitor (HP)


title: SC3_24h_DM_rep2

value: control


title: NERD 5 [SV210819]

value: oesophageal mucosa

value: Female

value: NERD


title: Large preB cell, IKDN, NIPBL, rep1


title: HE2-High-R2

source_name: Hemogenic Endothelium 2 (HE2)

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells

value: In Vitro Differentiation


title: Barrett's oesophagus (BO) 1 [JW140819]

value: squamous epithelial

value: Male

value: Barrett's oesophagus (BO)


title: Large preB cell, WT, NIPBL, rep1


title: SC3_24h_gsi_rep1

value: Jurkat

value: GSI


title: HE2-Medium-R2


title: SC3_24h_dt_rep1


title: NERD 6 [DS120919]


title: NERD 4 [AO190719]


title: HE2-Negative-R2


title: ERD 4 [RM250619]

value: ERD


title: NERD 3 [SC160519]


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D3, Input

extract_protocol:
Cells were fixed in 1% of fresh formaldehyde for 10 minutes at room temperature, quenched with glycine and washed twice with ice-cold PBS. Cells were re-suspended in lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 minutes at 4°C, pelleted, and then re-suspended in lysis buffer 2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH8) for 5 minutes at 4°C. Cells were finally re-suspended in RIPA buffer (50mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Nadeoxycholate, 0.2% SDS, 0.5 mM PMSF, and 1x Protease inhibitor cocktail (Roche)) to a final concentration of 5x107 cells/ml. Chromatin was sonicated to an average size of 350bp with a Branson Sonifier 450 equipped with a micro probe. Chromatin was cleared by centrifugation at 20,000xg for 10 minutes, and then incubated with 5-10μg of antibodies pre-bound to Dynabeads protein G (Life technologies) and rotated overnight at 4°C. After extensive washing on beads, bound chromatin was eluted and de-crosslinked in 300μl of elution buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS, 0.3M NaCl) overnight at 65°C. Proteinases K was added to a final concentration of 200 μg/ml and incubated at 45°C for 2 hours. DNA was ethanol precipitated, re-suspended in TE and purified using the DNA Clean & Concentrator-5 kit (Zymo Research).
Purified ChIP DNA was end repaired, end adenylated, and then ligated with Illumina Truseq indexed adaptors. The ligated DNA was purified with AMPure XP beads (Beckman Coulter) and then amplified with KAPA HiFi DNA Polymerase (KAPA Biosystems) for 8 to 13 cycles. After amplification, the library DNA was size selected with AMPurex XP beads to 200-600 bp range, and the purified libraries were multiplexed for sequencing in house with an Illumina NextSeq 550 system.

treatment_protocol: To induce IkE5 deletion in the incucible IkE5 deletion large preB cells (IkE5 fl/fl, Rosa26-ERT2-Cre), 4-OHT (Sigma H7904, final concentration 0.2 μM ) or an equal volume of DMSO as control were added into the medium; and cells were harvested at Day 3 and D12 post induction.

value: mouse large pre-B cell (CD19+CD43+BP1+)

value: IkE5 fl/fl, Rosa26-ERT2-Cre


title: SC3_24h_DM_rep1

value: T-ALL


title: HE1-High-R2

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: ERD 3 [SSG130319]

value: oesophageal mucosa


title: HE1-Medium-R2


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D3, CTCF, rep2

value: CTCF (Abcam, ab188488)


title: HE1-Low-R2


title: FH 2 [JU130319]

value: Female

value: FH


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D12, CTCF, rep2


title: 16h_DMSO_rep2

data_processing:
RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 DMSO control vs 2 dTAG KD samples for each of the timepoint (2 DMSO control vs 2 dTAG KD samples with 2 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes, featureCount read count for all samples

treatment_protocol: The cells were treated with DMSO or dTAG-13 for 1h, 2h, 4h, 8h, 16h, 24h, 48h or 72h.  Total RNAs were then harvested.

value: DMSO


title: NERD 2 [BA060319]

value: NERD


title: Large preB cell, inducible IkE5 deletion, DMSO/Induction D0, input


title: Large preB cell, inducible IkE5 deletion, DMSO/Induction D0, CTCF, rep2


title: HE1-Negative-R2

value: In Vitro Differentiation


title: 16h_dTAG_rep2

value: dTAG


title: 16h_dTAG_rep1


title: HE2-Low-R2

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: ERD 2 [JM010319]

value: squamous epithelial

value: Male


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D12, Input

value: mouse large pre-B cell (CD19+CD43+BP1+)


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D12, CTCF, rep1

value: IkE5 fl/fl, Rosa26-ERT2-Cre


title: SC3_24h_combi_rep1

value: Jurkat

value: T-ALL

value: Combi


title: 16h_DMSO_rep1


title: HB-High-R2

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: Nonerosive reflux disease (NERD) 1 [DS200219]

value: oesophageal mucosa

value: Nonerosive reflux disease (NERD)


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D3, CTCF, rep1

value: CTCF (Abcam, ab188488)


title: 8h_dTAG_rep2


title: Functional heartburn (FH) 1 [AG200219]

value: Functional heartburn (FH)


title: 8h_dTAG_rep1


title: Large preB cell, inducible IkE5 deletion, DMSO/Induction D0, CTCF, rep1


title: Erosive reflux disease (ERD) 1 [JG120219]

value: Erosive reflux disease (ERD)


title: HB-Low-R2

value: In Vitro Differentiation


title: 8h_DMSO_rep2

value: DMSO


title: HB-Negative-R2


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D12, H3K27ac, rep2

value: H3K27ac (Abcam, ab4729)


title: 8h_DMSO_rep1


title: 1_Full

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: 10X genomics

data_processing:
Samples were sequenced paired-end 100bp by Illumina NovaSeq 6000 platform and preliminary sequencing results were converted to FASTQ files with Cell Ranger
The 10x Genomics standard seq protocol by trimming the barcode and unique molecular identifier (UMI) end to 28 bp, and the mRNA end to 91 bp.
The FASTQ files were aligned to the human reference genome (GRCh38).
Quality control of the processed expression matrix were performed by evaluating detected transcripts, detected counts, cell doublets, mito-ratio.
Normalization were performed by scTransform.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene expression matrix for each Sample

source_name: Human intestinal stem cells from human pluripotent stem cell-drived 3D intestinal organoids

extract_protocol:
(scRNA-Seq has nothing to do with this step)
Library construction was performed using the 10X Chromium Single Cell 3’ Reagent Kits v3.1.

value: Human intestinal stem cells


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D3, H3K27ac, rep2


title: IL17NG_D6_input

city: Slough

first: Andrew

middle: James

last: Skelton

address: 208 Bath Road

department: Translational Bioinformatics

institute: UCB

data_processing:
Alignment with Bowtie2 (v2.3.5.1)
Peak Calling with MACS2 (v .2.7.1)
Merge with Bed Tools (v2.28)
Normalisation and Differential with DiffBind (v3.0.9)
Genome_build: GRCh38

source_name: IL17 Negative Cells

growth_protocol: PBMCs were cultured in X-VIVO15 media with anti-CD3/CD28 stimulation with IL-1b and IL-23 for 72 hours.

extract_protocol:
The formaldehyde fixed and FACS sorted Th17 cells (~100k) were lysed in ChIP lysis buffer and sonicated until the DNA fragment length sheared to the range of 200-600 bp. The supernatant containing the soluble sonicated chromatin was collected by centrifugation.
NEBNext ultra II DNA library prep kit (NEB) was used to prepare the illumina sequencing libraries, following the manufacturer guidelines. The DNA libraries were dual indexed with NEBNext multiplex oligos (NEB) and were sequenced (single end) on Illumina Miseq platform. For each sample, approximately 30 million reads were sequenced

treatment_protocol: Activated, cytokine secreting cells were captured using bispecific antibodies to CD45/IL-17A or CD45/IL-17F to anchor the cytokine to the cell. Subsets were purified by FACS sorting and fixed in formaldehyde.

tag: donor

tag: class

value: Input


title: ES-High-R2

value: Embryonic Stem Cell

value: HM-1 ES cell


title: 72h_dTAG_rep2

value: Jurkat

value: dTAG


title: 72h_dTAG_rep1

value: T-ALL


title: IL17NG_D5_input


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D12, H3K27ac, rep1

value: mouse large pre-B cell (CD19+CD43+BP1+)

value: IkE5 fl/fl, Rosa26-ERT2-Cre


title: ES-Low-R2


title: ES-Medium-R2


title: 72h_DMSO_rep2


title: Large preB cell, inducible IkE5 deletion, 4OHT induction D3, H3K27ac, rep1


title: IL17NG_D5

value: Ab


title: HB-Medium-R2

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: Large preB cell, inducible IkE5 deletion, DMSO/Induction D0, H3K27ac, rep1


title: ES-Negative-R2


title: IL17NG_D4_input


title: 6h_dTAG_rep2


title: HP-High-R1

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells


title: 72h_DMSO_rep1


title: Large preB cell, IKDN, H3K36me3

value: IkE5D/D (IKE5 fl/fl, Cd2-cre)

value: H3K36me3 (Abcam, ab9050)


title: IL17NG_D4


title: Large preB cell, WT, H3K36me3

value: Wild-type (IKE5 fl/fl, Cre-)


title: Large preB cell, inducible IkE5 deletion, DMSO/Induction D0, H3K27ac, rep2

value: H3K27ac (Abcam, ab4729)


title: IL17NG_D6


title: HP-Medium-R1

value: In Vitro Differentiation


title: 6h_dTAG_rep1


title: Large preB cell, IKDN, SMC1A, rep2

value: SMC1A (Bethyl, A300-055A)


title: 6h_DMSO_rep1

value: DMSO


title: Large preB cell, WT, SMC1A, rep2


title: 6h_DMSO_rep2

value: Jurkat


title: HP-Low-R1


title: IL17NG_D2_input

value: Input


title: HE2-High-R1

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells


title: Large preB cell, IKDN, SMC1A, rep1

value: mouse large pre-B cell (CD19+CD43+BP1+)


title: IL17NG_D2

value: Ab


title: HE2-Medium-R1


title: 4h_dTAG_rep1

value: T-ALL

value: dTAG


title: Large preB cell, WT, SMC1A, rep1


title: 4h_dTAG_rep2


title: HE2-Low-R1


title: IL17NG_D1_input


title: Large preB cell, IKDN, CTCF, rep2

value: CTCF (Abcam, ab188488)


title: 4h_DMSO_rep1


title: Large preB cell, WT, CTCF, rep2


title: IL17NG_D1


title: 4h_DMSO_rep2


title: IL17NG_D3


title: IL17F_D6_input

source_name: IL17F Positive Cells


title: HP-Negative-R1

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells


title: HE1-High-R1

source_name: Hemogenic Endothelium 1 (HE1)

value: Hemogenic Endothelium 1 (HE1)

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: 48h_dTAG_rep2


title: LAC_camSΔ69-391_rep3

city: Leicester

first: Katrin

last: Schilcher

state: Leicestershire

address: University Road

department: Genetics and Genome Biology

institute: University of Leicester

data_processing:
Qiagen CLC Genomics Workbench v 20.0.4
Raw sequencing reads in fastq format were imported, adapter sequences trimmed and the reads were mapped to the USA300 FPR3757 reference genome using Qiagen CLC Genomics Workbench with default settings.
Trim settings: Automatic removal of read-through adapter sequences. Removal of low quality sequence (limit = 0.05).
Trimmed sequence reads were mapped to NC_007793 using CLC Genomics Workbench (Mapping settings: mismatch cost: 2 insertion cost: 3, deletion cost: 3, length fraction: 0.8 similarity fraction: 0.8)
Read count extraction was performed using CLC Genomics Workbench.
Assembly: NC_007793
Supplementary files format and content: tab-deliminated text file for each sample
Supplementary files format and content: tab-deliminated text files contain information regarding gene name, chromosome, region, expression value, TPM, RPKM, gene length, unique gene reads and total gene reads

organism: Staphylococcus aureus

source_name: bacterial

extract_protocol:
RNA was extracted using a RNeasy Mini Kit with the following modifications. Cells were lysed by incubation with 100 mM TRIS-HCL with 800 ng/µl lysostaphin for 25 min at 37 °C. Subsequently, 700 µl RLT buffer containing β-mercaptoethanol were added and samples were transferred to lysing matrix B tubes and the samples were subjected to three bead beating steps (30 sec x 3; 1 min on ice in between). RNA was treated with turbo DNAse kit according to manufacturers instructions.
Depletion of ribosomal RNA and library preparations were performed at the Genomics Core at the University of Colorado Anschutz Medical Campus using the Illumina Ribo-ZeroTm Plus rRNA depletion kit and the Zymo-Seq RiboFree total RNA library kit.

value: bacterial


title: IL17F_D6


title: 48h_dTAG_rep1


title: HE1-Medium-R1

value: In Vitro Differentiation


title: IL17F_D5_input


title: LAC_camSΔ69-391_rep2


title: HE1-Low-R1


title: HE1-Negative-R1


title: 48h_DMSO_rep1


title: 48h_DMSO_rep2


title: LAC_camS::camS_rep2


title: IL17F_D5


title: LAC_camSΔ69-391_rep1


title: HB-High-R1

source_name: Hemangioblast Cell (HB)

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: HB-Medium-R1


title: HB-Low-R1


title: IL17F_D4_input


title: IL17F_D3_input


title: 2h_dTAG_rep2

value: Jurkat


title: 2h_dTAG_rep1


title: HE2-Negative-R1


title: LAC_camS::camS_rep1


title: 2h_DMSO_rep2

value: DMSO


title: IL17F_D3


title: HB-Negative-R1


title: LAC_ΔcamS_rep3

value: [delta]camS


title: LAC_ΔcamS_rep2


title: ES-High-R1

source_name: Embryonic Stem Cell (ES)

value: Embryonic Stem Cell (ES)

value: HM-1 ES cells


title: 2h_DMSO_rep1


title: 24h_dTAG_rep2


title: IL17NG_D3_input

value: Input


title: LAC_camS::camS_rep3


title: IL17F_D2

value: Ab


title: IL17F_D1_input


title: IL17F_D2_input


title: 24h_dTAG_rep1

value: T-ALL

value: dTAG


title: LAC_wt_rep3

value: wild type


title: IL17A_D6_input

source_name: IL17A Positive Cells


title: ES-Medium-R1


title: LAC_wt_rep1


title: IL17F_D4


title: HP Rep 2

description: HP

data_processing:
RNA-Seq reads were first filtered using RiboDetector (v0.2.7) (Deng et al., 2022)using options -t 70 -l 75 -e norrna --chunk_size 256 to remove any residual rRNA reads from the libraries.
The reads were then filtered for quality and length using Trimmomatic (Bolger et al., 2014) with options LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20.
The trimmed reads were aligned to the mouse genome (mm10) using Hisat2 (v2.2.1) (Kim et al., 2019) using default options.
Raw counts were obtained using featureCounts (Liao et al., 2014) with gene models from (ensembl as the reference transcriptome. Counts were normalized using the edgeR package (v3.40.2)(Robinson et al., 2010) in R (v4.2.3).
Differential gene expression analysis was carried out using the Limma-Voom (v3.17) (Law et al., 2014) method.
Assembly: mm10
Supplementary files format and content: Raw counts obtained using featureCounts (Liao et al., 2014) with gene models from ensembl as the reference transcriptome.

molecule: nuclear RNA

growth_protocol: A HM-1 targeting ES cell line (Magin et al., 1992) was cultured on gelatinised tissue culture plates in DMEM-ES media (DMEM (Merk.,D5796), 15% FSC, 1mM sodium pyruvate (Merck, S8636), 1x penicillin /Streptomycin (Merck, P4333), 1 x L-Glutamine (Merck, G7513), 1 x Non-Essential amino acids (Merck, M7145), 1000 U/ml ESGRO®LIF (Merck, ESG1107), 0.15 mM MTG and 25 mM Hepes buffer (Merck, H0887)) at 37 °C and 5% CO2. Every 48h cell colonies were disociated with TrypLE™ Express (ThermoFisher, 12605010)and replated onto gelatinised tissue culture plates at 1.2 x104 per cm2.

extract_protocol:
Nuclear enriched RNA extracted with the Cytoplasmic and Nuclear RNA Purification kit (Norgen, 21000,37400) based on manufacturers instructions.
RNA-Seq libraries were then prepared using the NEBNext® Ultra ™ II Directional RNA Library Prep Kit (NEB, E7760) total RNA with rRNA depletion protocol using 100 ng of input RNA. Libraries were sequenced using a Nova-Seq 6000 SP 200 cycle flow cell.

treatment_protocol: Hematopoietic in vitro differentiation (I.V.D) using serum was performed as described in (Obier et al., 2016) and (Edginton-White et al., 2023). First, ES cell colonies being cultured on gelatinised plates were dissociated to form a single cell suspension using TrypLE™ Express (ThermoFisher, 12605010). DMEM-ES media was then added at a 1:1 ratio to stop the trypsin activity. The cells were then centrifuged at 300g for 5 minutes before being resuspended at 2.5 × 104/ml in I.V.D media (IMDM (Merck, I3390), 15% FCS, 1 x Penicillin/Streptomycin (Merck, P4333), 1 x L-Glutamine (Merck, G7513), 0.15 mM MTG, 50 µg/ml Ascorbic acid and 180 µg/ml Human transferrin (Merck, T8158)) and then plated onto non-adherent dishes (ThermoFisher, 501 V). he cells were then incubated at 37 °C, 5% CO2 for 3 days to allow for the formation of floating embryoid bodies (EBs). The floating EBs were then transferred to 50 ml centrifuge tubes and the EBs were allowed to settle by gravity over 5 minutes. The EBs were then washed with PBS before being allowed to settle again over 5 minutes. The EBs were then dissociated with TrypLE™ Express (ThermoFisher, 12605010) with gentle pipetting.  The dissociated cells were sorted for the FLK1 surface marker (forming the population referred to as the HB). The dissociated cells were incubated with a FLK1 biotin-coupled antibody (1:200) (eBioscience, 13-5821-82), and then with MACS anti-biotin beads (Miltenyi Biotec, 130-090,485). FLK1 expressing cells were sorted for by separation using a MACS LS column (Miltenyi Biotec, 130-042-401). FLK1 expressing HB cells were then taken for flow cytometry analysis and sequencing experiments as well as further differentiation in blast culture into HE1, HE2 and HP populations. To achieve this FLK1+ HB cells were plated onto gelatine coated tissue culture flasks at a concentration of 1.6 × 104 cells per cm2 in Blast media (IMDM (Merck, I3390), 10% FCS, 1 x Penicillin/Streptomycin (Merck, P4333), 1 x L-Glutamine (Merck, G7513), 0.45 mM MTG, 25 µg/ml Ascorbic acid, 180 µg/ml Human transferrin (Merck, T8158), 20% D4T Conditioned Media, 5 ng/ml VEGF(PeproTech, 450-32), 10 ng/ml IL-6 (PeproTech, 216-16)) and were left to incubate for 2.5 days at 37 °C, 5% CO2. HE1, HE2 and HP populations were FACS sorted after incubation with KIT-APC (1:100)(BD Pharmingen, 553356), TIE2-PE (1:200)(eBioscience, 12-5987-82) and CD41-PECY7 (1:100)(eBioscience, 25-0411-82) antibodies into HE1 (KIT+, TIE2+, CD41-), HE2 (KIT+, TIE2+, CD41+) and HP (KIT+, TIE2-, CD41 +) populations.

value: Hematopeitic Porgenitor (HP)

value: HM-1 ES dervied Hematopetic progenitor cells


title: 24h_DMSO_rep1


title: 24h_DMSO_rep2


title: IL17F_D1


title: 1h_dTAG_rep2


title: LAC_ΔcamS_rep1


title: ES-Low-R1


title: IL17A_D6


title: LAC_wt_rep2


title: 1h_dTAG_rep1


title: HP Rep 1

description: HP


title: 1h_DMSO_rep2


title: IL17A_D5_input


title: Infection, ORA_CIT, Liver11

city: Copenhagen

first: Jingren

last: Zhong

state: Frederiksberg

address: Dyrlægevej 68 DK-1870

country: Denmark

institute: University of Copenhagen

data_processing:
The libraries were sequenced on the Illumina NovaSeq 6000 S4 flowcell with PE150.
Quality and adapter trimming of raw reads were performed using fastp software.
Raw data are stored in FASTQ (fq) format files which contain sequences of reads and corresponding base quality.
Alignments were performed with HISAT2 to the reference. The annotated gene information of porcine genome was obtained from Ensembl (release 109).
The featureCounts was used to generate a gene-count matrix, followed by analyses of DEGs using DESeq2 .
Assembly: Sscrofa11.1
Supplementary files format and content: xls of read counts.
Supplementary files format and content: xls of FPKM counts.

organism: Sus scrofa

source_name: Liver

growth_protocol: Preterm pigs were gained by C-section and kept in NICU incubators for 14h. Pigs were nourished with standard parenteral nutrition.

extract_protocol:
Total RNA of homogenized liver tissues was extracted using RNeasy Mini Kit (Qiagen, Copenhagen, Denmark).
Construction of RNA-Seq libraries was done using Novogene NGS RNA Library Prep Set (PT042)

treatment_protocol: Preterm pigs were supplemented with intravenous/oral citrulline and inoculated with live Staphylococcus epidermidis

value: Liver

value: Infection, ORA_CIT


title: Infection, ORA_CIT, Liver12


title: Infection, ORA_CIT, Liver10


title: HE2 Rep 1

value: Hemogenic Endothelium 2 (HE2)

value: HM-1 ES dervied Hemogenic Endothelium 2 cells

value: In Vitro Differentiation


title: ES-Negative-R1


title: IL17A_D5


title: 1h_DMSO_rep1

value: Jurkat


title: Infection, ORA_CIT, Liver9


title: IL17A_D4_input


title: C25-DOX_rep2

data_processing:
RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 DOX overexpression vs 2 DMSO control samples (2 DOX overexpression vs 2 DMSO control with 2 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes

source_name: HPB-ALL cells

growth_protocol: HPB-ALL cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

treatment_protocol: HPB-ALL cells were infected with TAL1/LMO1-expressing lentiviruses. At 48 hours post infection, drug selection was carried out for 36 hours.  The cells were then treated with doxycycline to induce overexpression.  Total RNA were harvested.

value: HPB-ALL

tag: overexpress

value: TAL1/LMO1 overexpression


title: Infection, ORA_CIT, Liver8


title: HE1 Rep 2

value: Hemogenic Endothelium 1 (HE1)

tag: cell type

value: HM-1 ES dervied Hemogenic Endothelium 1 cells


title: HE1 Rep 1

tag: tissue


title: IL17A_D4


title: HE2 Rep 2

tag: treatment


title: IL17A_D3_input

value: Input


title: C25-DMSO_rep2

tag: cell line


title: Infection, ORA_CIT, Liver7


title: HB Rep 1

description: HB

value: Hemangioblast Cell (HB)

value: HM-1 ES dervied Hemangioblast cells


title: L4-DOX_rep2

value: T-ALL

value: LMO1 overexpression


title: Infection, ORA_CIT, Liver6


title: IL17A_D3

value: Ab


title: HB Rep 2

description: HB


title: ES Rep 2

description: ES

value: Embryonic Stem Cell (ES)

value: HM-1 ES cells


title: T5-DOX_rep2

value: TAL1 overexpression


title: ES Rep 1

description: ES


title: IL17A_D2


title: Infection, ORA_CIT, Liver3

value: Liver

value: Infection, ORA_CIT


title: Infection, ORA_CIT, Liver4


title: T5-DMSO_rep2


title: IL17A_D1_input


title: Mouse, lung, mixed Cre_Neg and Cre_Pos cells, sublibrary 4

city: Nashville

first: Jessica

last: Blackburn

address: 1611 21st Ave MCN

institute: VUMC

description: PARSE Biosciences- SPLIT-seq

data_processing:
Parse Biosciences analysis pipeline (split-pipe command, version 1.1.0 ) was used to demulitplex fastq files. Reads were mapped to a mouse reference genome (Mouse GRCm39 genome) and further processed using default parameters. The pipeline generated an unfiltered Digital Gene Expression (DGE) matrix.
Assembly: mouse GRCm39
Supplementary files format and content: cell_metadata.csv - spreadsheet with cell barcode, species, sample, well in each round of barcoding, and number of transcripts and genes
Supplementary files format and content: all_genes.csv - spreadsheet with gene name, gene id, and genome for each column in DGE.mtx
Supplementary files format and content: count_matrix.mtx - (aka DGE.mtx) sparse matrix with all cell-gene counts. Each row is a cell and each column is a gene.

source_name: lung

extract_protocol:
Lungs were perfused with PBS and extracted from mice. Lungs were digested in DMEM containing collagenase I (1mg/mL), dispase II (1mg/mL), DNase I (1.25 uU/mL), Aprotinin (20 ug/mL), Pepstatin A (10ug/mL), Leupeptin Hemisulfate (10mg/mL), and PMSF (1 mM). EDTA (5mM) and PMSF (1mM) in DMEM were added to quench the reaction. Single cell suspensions were treated with ACK lysing buffer followed by maganetic bead based depletion of CD45+ cells and enrichment for Epcam+ cells. A cell sorter was used to enrich for live cells based on negative DAPI staining.
Parse Evercode Cell Fixation kit v2 and Evercode WT v2 kits were used to prepare cells for sequencing with UDI barcodes.

value: lung

tag: strain

tag: age

value: 8 weeks

tag: genotype


title: WT ID8TB

city: St. Louis

first: Katherine

last: Fuh

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
Read alignment, gene expression estimation, normalizeation and quality control were performed using the Cell ranger Single-Cell Software Suite (10x Genomics)
Cellranger count was used to align samples to the reference genome (mm10), quantify reads and filter reads with a quality score below 30.
Downstream analysis was performed using the seurat package in R
Assembly: mm10
Supplementary files format and content: rds file with filtered and normalized data

source_name: whole omental tumor  ID8 p53-/- BRCA2-/- model in C57bl6 mice

extract_protocol:
Omental ID8TB-/- tumors from WT mice were collected and dissociated in media containing 1mg/ml collagenase III (Worthington LS004182), 1mg/ml hyaluronidase (Worthington LS002592) and 0.2mg/ml DNAse Type IV (Sigma D5025). Mechanical dissociation was performed for 1min at 500rpm using the gentlemacs dissociator (Miltenyi Biotec 130-096-427) and enzymatic digestion was performed for 30min at 37°C and 150rpm. Cells were filtered using a 70μm filter and red blood cells were lysed using RBC lysis buffer (Biolegend 420301). Dead cell removal was performed (Miltenyi Biotec 130-090-101). Cells were resuspended in FACS buffer (PBS, 1mM EDTA, 4% FBS) and counted.
Libraries were prepared for sequencing using standard protocols

value: WT C57bl6


title: Infection, ORA_CIT, Liver2


title: IL17A_D1


title: C25-DMSO_rep1

value: HPB-ALL

value: TAL1/LMO1 overexpression


title: L4-DMSO_rep2


title: Infection, ORA_CIT, Liver1


title: L4-DOX_rep1


title: Mouse, lung, mixed Cre_Neg and Cre_Pos cells, sublibrary 2

description: PARSE Biosciences- SPLIT-seq


title: Mouse, lung, mixed Cre_Neg and Cre_Pos cells, sublibrary 3

description: PARSE Biosciences- SPLIT-seq


title: IL17A_D2_input


title: Infection, IV_CIT, Liver10

value: Infection, IV_CIT


title: L4-DMSO_rep1


title: Infection, IV_CIT, Liver11


title: IL17AF_D6

source_name: IL17AF Positive Cells


title: Infection, IV_CIT, Liver9


title: Mouse, lung, mixed Cre_Neg and Cre_Pos cells, sublibrary 1

description: PARSE Biosciences- SPLIT-seq


title: T5-DOX_rep1


title: IL17AF_D5


title: SCR-2 mutant 3_GD5

city: HOUSTON

first: Vineet

middle: Kumar

last: Maurya

state: TX

address: ONE BAYLOR PLAZA

department: Molecular & Cell Biology

institute: BAYLOR COLLEGE OF MEDICINE

description: SRC-2d/d -3

data_processing:
Raw sequenced reads in Ilumina fastq file format were aligned to the mouse genome (Genome Reference Consortium Mouse Build 39 (NCBI)) through use of the hierarchical indexing for spliced alignment of transcripts (HISAT2). The number of reads aligned to known genes was determined by the Python-based software package HTSeq  (http://www-huber.embl,de/users/anders/HTSeq).
The Bioconductor package DESeq was applied to the gene expression data to detect differentially expressed genes between the two groups.
Fragments per kilobase of transcript per million (FPKM) values of transcripts were used for hierarchical clustering; the pheatmap package in R was used to draw the clustered heatmap.
Assembly: mouse genome (Genome Reference Consortium Mouse Build 39
Supplementary files format and content: tab-delimited text file include FPKM values for each samples

source_name: Uterus

extract_protocol:
Uterine tissues were lysed inRNeasyPlusRNA lysis bufferand total RNA was isolated using theQiagen RNeasyPlus Mini kit.
Sequencing libraries were prepared from 250ng of RNA using the TruSeq Stranded mRNA kit (Illumina Inc, # 20020594).

value: Uterus


title: Infection, IV_CIT, Liver8


title: C25-DOX_rep1


title: SCR-2 mutant 2_GD5

description: SRC-2d/d -2


title: IL17AF_D4_input

value: Input


title: Jurkat_dTAG_H3K27ac_Hi-CHIP

data_processing:
Hi-ChIP data were aligned and processed using HiC-Pro pipeline version 2.11.1, and the reads in the fastq files were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 version 2.4.1.
The restriction sites ^GATC and G^ANTC across the human genome were cut and utilized by HiC-Pro using the HiC-Pro Utilities Python script “digest genome”.
HiC-Pro configuration on ligation site were set to be ^GATC and G^ANTC optimize for ARIMA kit data. The aligned data were further processed using hichipper to call interactions.
Hichipper version 2.7.9 was used to extract the valid interactions from the HiC-Pro data and generate the bedpe interaction file by utilizing anchors from peaks called by MACS2 broadPeak using the dangling-end and self-cycle Hi-ChIP read pairs with the following parameters: --keep-dup all -p 1e-9 --extsize 147 --nomodel -f bed.
Hichipper used to process interactions using the following parameters: -l 50 -mi 5000 -ma 2000000.
Assembly: hg19
Supplementary files format and content: *_allValidPairs: txt file output from HiC-Pro
Supplementary files format and content: *.intra.loop_counts.bedpe: bedpe file output from hichipper
Supplementary files format and content: *.anchors.bed: anchor used by hichipper
Library strategy: Hi-ChIP

source_name: Jurkat cells

extract_protocol:
Library construction from the H3K27ac Hi-ChIP-seq samples and sequencing of paired-end 100-bp-long reads by the DNBSEQ platform were performed at BGI Genomics.
Paired-end Hi-ChIP

treatment_protocol: The cells were cross-linked with formaldehyde, lysed with Hi-C buffer, and then sonicated. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. Post-ChIP DNA was tagmented with Tn5 enzyme follwed by PCR amplification library synthesis.

value: dTAG

value: H3K27ac Antibody (Abcam; ab4729)


title: Infection, IV_CIT, Liver7


title: SCR-2 mutant 1_GD5

description: SRC-2d/d -1


title: T5-DMSO_rep1

value: T-ALL


title: IL17AF_D4

value: Ab


title: Infection, IV_CIT, Liver6


title: SRC-2 control 3_GD5

description: SRC-2f/f -3


title: IL17AF_D3_input


title: Infection, IV_CIT, Liver5


title: IL17AF_D3


title: IL17AF_D5_input


title: IL17AF_D6_input


title: Jurkat_DMSO_H3K27ac_Hi-CHIP

value: DMSO


title: IL17AF_D2_input


title: delta-asf1, input control for C35

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

country: Germany

institute: Ruhr-University Bochum

data_processing:
Sequence reads were trimmed with fastp (Chen et al. 2018, Bioinformatics 34:i884-i890) and mapped with bowtie2 (Langmead and Salzberg 2012, Nat Methods 9:357-359). MACS2callpeak was used to call broad peaks (Zhang et al. 2008, Genome Biol 9:R137).
Assembly: Sordaria macrospora genome version 4, BioProject ID: PRJNA744349, acc. no. for the seven chromsomes are CP083903-CP083909
Supplementary files format and content: The .bed files were generated by broad peak calling with MACS2 and contain the following columns (tab-delimited): 1. name of chromosome, 2. start position of peak on chromosome, 3. end position of peak on chromosome, 4. name of peak, 5. score (indicates how dark a peak will be displayed in a browser), 6. strand ("." denotes not orientation was assigned), 7. signal value (measurement of overall enrichment for the region), 8. pvalue (measurement of statistical significance, given as -log10), 9. qvalue (measurement of statistical significance using false discovery rate, given as -log10)

organism: Sordaria macrospora

source_name: mycelium

growth_protocol: Strains were grown in liquid complete medium at 27 °C in constant light for 2 days (wild type) or 3 days (delta-asf1, the slower-growing mutant was grown longer to reach the same developmental stage)

extract_protocol:
Mycelia were harvested by filtering, washed and ground to powder in liquid nitrogen.
Crosslinking was performed in 1% formaldehyde for 15 minutes, followed by 15 minutes of quenching by addition of glycerin. The powder was washed multiple times in isotonic buffer. Lysis was performed on ice, by addition of an NP-40 based lysis buffer with proteinase inhibitors. Clear chromatin extracts were harvested by multiple centrifugation steps. MNase based shearing was done under Ca2+ rich conditions with 230 U MNase per ml sample for 105 minutes at 37°C. After stopping with EDTA, 10 µl Histone H3K56ac antibody #39281 (Active Motif) was added to 1 ml samples and incubated at 4 °C over night on a spinning wheel. Pull down was performed after incubation of the solution with 40 µl of Protein A/G PLUS-Agarose: sc-2003 (Santa Cruz Biotechnology, Dallas, TX, USA). After washing, the DNA fragments were extracted by incubation of the beads with an SDS rich buffer, overnight decrosslinking and phenol / chloroform extraction.

value: mycelium


title: SRC-2 control 1_GD5

description: SRC-2f/f -1


title: SRC-2 control 2_GD5

description: SRC-2f/f -2


title: splenic folliculaar B cell, WT, rep2

data_processing:
Alignment to the mouse mm10 assembly was conducted by STAR 5.02 (Dobin et al., 2013) on the DNAnexus platform
Normalization and differential expression by  DESeq2 were performed through a HOMER v4.10.4 implementation of the package in R.
Assembly: mm10

molecule: polyA RNA

source_name: splenic folliculaar B cell (CD19+, CD23+, CD21 mid)

extract_protocol:
Total RNAs were prepared using the Direct-zol RNA Miniprep (Zymo Research) and 1mg of total RNA was used for the construction of sequencing libraries.
The TruSeq Stranded mRNA Library prep kit was used for construction of cDNA libraries for RNA-sequencing (Illumina). The cDNA libraries were ligated with indexed primers and amplified by PCR for 10 cycles, multiplexed and sequenced in house with an Illumina NextSeq550 system.

value: Wild-type


title: Infection, IV_CIT, Liver3

value: Liver


title: wild type, input control for C34

value: wild type


title: delta-asf1, input control for C33


title: Infection, ORA_CIT, Liver5

value: Infection, ORA_CIT


title: Infection, IV_CIT, Liver2


title: IL17AF_D2


title: IL17AF_D1_input


title: splenic folliculaar B cell, WT, rep1

value: splenic folliculaar B cell (CD19+, CD23+, CD21 mid)


title: delta-asf1, H3K56ac, replicate 2


title: splenic marginal zone B cell, WT, rep 2

source_name: splenic marginal zone B cell (CD19+, CD23-, CD21 high)


title: Infection, IV_CIT, Liver1


title: IL17AF_D1


title: Infection, NO_CIT, Liver11

value: Infection, NO_CIT


title: splenic marginal zone B cell, WT, rep 1

value: splenic marginal zone B cell (CD19+, CD23-, CD21 high)


title: delta-asf1, H3K56ac, replicate 1


title: Infection, IV_CIT, Liver4


title: Infection, NO_CIT, Liver10


title: 7694

city: Madison

first: Hugo

last: Lee

state: WI

address: 440 Henry Mall

institute: University of Wisconsin-Madison

description: KO 3

data_processing:
Illumina BCL2fastq v2.20
Adapter trimming with Skewer v0.1.123 and parameters -m pe -q 20 -k 15 -l 25
Alignment with STAR v2.5.3a and parameters
Expression estimation with RSEM v1.2.31
Differential expression with edgeR v3.16.15
Assembly: GRCm38.p5
Supplementary files format and content: Microsoft Excel files containing results of edgeR analysis

source_name: pancreatic islets

growth_protocol: Housed under a 12:12-hr light/dark cycle, with unrestricted access to food and drinking water in an animal housing facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.

extract_protocol:
Islets were isolated using the standard collagenase/protease digestion method. The pancreatic duct was cannulated and distended with 4°C collagenase/protease solution. Islets were separated from the exocrine tissue using Histopaque-1077. RNA from sorted beta cells was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce Cre recombinase activity, tamoxifen was dissolved in sterilized corn oil  by shaking overnight at 37°C. The solution was protected from light, and1 mg/ml tamoxifen was administrated to pups via intragastric injection once/day from p1-p3.

value: pancreatic islets

value: sorted beta cells

value: tamoxifen injection to induce deletion


title: splenic B1a cell, WT, rep2

source_name: splenic B1a cell (CD19+, CD5+, B220 low)


title: 7693

description: KO 2


title: wild type, H3K56ac, replicate 1


title: splenic B1a cell, WT, rep1

value: splenic B1a cell (CD19+, CD5+, B220 low)


title: wild type, input control for C32


title: splenic immature B cell, WT, rep2

source_name: splenic immature B cell (CD19+, B220+, CD5-, CD23-, CD21 low/-)


title: wild type, 2 days, replicate 2

data_processing:
Reads were trimmed with fastp (Chen et al. 2018, Bioinformatics 34:i884-i890) and mapped with bwa-mem (Li H. 2013, arXiv:1303.3997).
Valid ligation events were recorded with pairtools parse, sorted with pairtool sort, deduplicated with pairtools dedup and files splitted by using pairtools split (Open2C Revision 1e8d5188).
Samtools sort and samtools index were used to generate indexed mapped files (Danecek et al. 2021, Gigascience 10:giab008). The contact matrices were generated and visualized by using juicertools1.22.01 (Durand et al. 2016, Cell Syst 3:99-101).
Assembly: Sordaria macrospora genome version 4, BioProject ID: PRJNA744349, acc. no. for the seven chromsomes are CP083903-CP083909
Supplementary files format and content: The .hic files are contact matrices generated by juicertools1.22.01; briefly, this 3D matrix is divided into bins, and the interactions between the bins is reported.

growth_protocol: Strains were grown in liquid complete medium at 27 °C in constant light for the indicated time.

extract_protocol:
Mycelia were harvested by filtering, washed and ground to powder in liquid nitrogen.
Hi-C and library prepration was performed according to the Dovetail Genomics (Scotts Vallex, CA, USA) Omni-C Kit (Non-mammalian samples protocol 1.2A).

value: 2 days


title: 7690

description: WT 4


title: 7689

description: KO 1


title: wild type, 5 days, replicate 2

value: 5 days


title: splenic immature B cell, WT, rep1

value: splenic immature B cell (CD19+, B220+, CD5-, CD23-, CD21 low/-)


title: 7369

description: WT 3


title: Infection, NO_CIT, Liver8


title: Infection, NO_CIT, Liver9


title: Infection, NO_CIT, Liver7


title: Infection, NO_CIT, Liver6


title: 7370

description: WT 2


title: delta-asf1, 3 days, replicate 1

value: 3 days


title: Infection, NO_CIT, Liver5


title: wild type, H3K56ac, replicate 2


title: Spleen, homozygous R594C/R594C, HTO-derived cDNA

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes_VBO003.tsv.gz
features_VBO003.tsv.gz
matrix_VBO003.mtx.gz
feature_reference_VBO_Ire1KI.csv
seuratObj_Ire1KI_paper_merge.rds

library_source: other

data_processing:
The Cell Ranger pipeline (10x Genomics, v5.0.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1 and read 2 for the gene expression and cell surface protein libraries. Read 2 of the gene expression libraries was mapped to the reference genome (mouse mm10) using STAR. Subsequent barcode processing, unique molecular identifiers filtering and gene counting was performed using the Cell Ranger suite. CITE-seq reads were quantified using the feature-barcoding functionality.
Pre-processing of the RNA UMI matrix was done by the scater and scran R packages (v1.14.6) according to the workflow proposed by the Marioni lab. Subsequent processing was done with Seurat v3.1.4 (gene filtering, SCTransform, clustering, dimensionality reduction, differential gene expression analysis).
DoubletFinder (v2.0.2) was performed to predict any remaining doublets in the dataset.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files for individual samples: barcodes_VBO001.tsv.gz, barcodes_VBO002.tsv.gz, barcodes_VBO003.tsv.gz, features_VBO001.tsv.gz, features_VBO002.tsv.gz, features_VBO003.tsv.gz, matrix_VBO001.mtx.gz, matrix_VBO002.mtx.gz, matrix_VBO003.mtx.gz
Supplementary files format and content: ADT feature and HTO overview: feature_reference_VBO_Ire1KI.csv
Supplementary files format and content: Seurat object for the three genotypes merged together: seuratObj_Ire1KI_paper_merge.rds
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Spleen

extract_protocol:
Splenocytes of the mice were sorted with DAPI.
Sorted single-cell suspensions were resuspended at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version NextGEM 3.1 (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primer (3 nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos. Size selection with SPRIselect Reagent Kit (Beckman Coulter) was used to separate amplified cDNA molecules for 3’ gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index PCR using Illumina’s Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 70:20:10 ratio for the combined 3’ gene expression, cell surface protein samples and HashTag-Oligo (HTO) data, respectively.

value: Spleen

value: Total splenocytes

tag: library type

value: HTO

value: Homozygous R594C/R594C

tag: antibodies/tags

value: See Custom feature_type in feature_reference_VBO_Ire1KI.csv (Anti CD45 + Anti MHC classI :Replicate 1 = TotalSeq-A0301 ; Replicate 2 = TotalSeq-A0302)


title: 7363

description: WT 1


title: wild type, 5 days, replicate 1

value: mycelium

value: wild type


title: Spleen, homozygous R594C/R594C, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes_VBO003.tsv.gz
features_VBO003.tsv.gz
matrix_VBO003.mtx.gz
seuratObj_Ire1KI_paper_merge.rds

value: mRNA


title: wild type, 2 days, replicate 1


title: Spleen, heterozygous R594C/+, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes_VBO002.tsv.gz
features_VBO002.tsv.gz
matrix_VBO002.mtx.gz
feature_reference_VBO_Ire1KI.csv
seuratObj_Ire1KI_paper_merge.rds

value: Heterozygous R594C/+

value: See Custom feature_type in feature_reference_VBO_Ire1KI.csv (Anti CD45 + Anti MHC classI :Replicate 1 = TotalSeq-A0301 ; Replicate 2 = TotalSeq-A0302 ; Replicate 3 = TotalSeq-A0303 ; Replicate 4 = TotalSeq-A0304)


title: Infection, NO_CIT, Liver3

value: Liver

value: Infection, NO_CIT


title: Pancreatic tumor, Combination, replicate 2

city: Houston

first: Arthur

last: Liu

address: 7455 Fannin Street

institute: UT MD Anderson Cancer Center

data_processing:
An average of 64 million reads per sample were captured
Sequencing quality was examined using FastQC (v0.11.9)
Trimmomatic (version 0.39) was used to remove adapters, low quality bases, and short reads
Sequencing data was aligned ot the mouse genome (GRCm39)) using Kallisto (v.46.1)
R and Bioconductor packages LIMMA (v3.48.3) and edgeR (v3.34.0) were used to normalize reads and identify differentially expressed genes
Assembly: GRCm39
Supplementary files format and content: Matrix table with log2 filtered counts per million normalized gene counts for every gene and every sample

source_name: Bulk tumor

extract_protocol: Tumors were resected and processed into single cell suspension and counted. 5 million total cells were flash frozen per sample before RNA was extracted using qiagen RNeasy Mini kit. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice bearing orthotopic MT4-LA tumors were treated with or without TH-302, aVEGFR-2, or the combination

value: Bulk tumor

value: Tumor cell

value: Combination


title: Pancreatic tumor, Combination, replicate 3


title: delta-asf1, input control for C31

extract_protocol:
Mycelia were harvested by filtering, washed and ground to powder in liquid nitrogen.
Crosslinking was performed in 1% formaldehyde for 15 minutes, followed by 15 minutes of quenching by addition of glycerin. The powder was washed multiple times in isotonic buffer. Lysis was performed on ice, by addition of an NP-40 based lysis buffer with proteinase inhibitors. Clear chromatin extracts were harvested by multiple centrifugation steps. MNase based shearing was done under Ca2+ rich conditions with 230 U MNase per ml sample for 105 minutes at 37 °C. After stopping with EDTA, 10 µl Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 antibodies (Cell Signaling, Danvers, MA, USA) or Histone H3 Antibody (ChIP Formulated) #2650 (Cell Signaling) were added to 1 ml samples and incubated at 4 °C over night on a spinning wheel. Pull down was performed after incubation of the solution with 40 µl of Protein A/G PLUS-Agarose: sc-2003 (Santa Cruz Biotechnology, Dallas, TX, USA). After washing, the DNA fragments were extracted by incubation of the beads with an SDS rich buffer, overnight decrosslinking and phenol / chloroform extraction.


title: Spleen, heterozygous R594C/+, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
barcodes_VBO002.tsv.gz
features_VBO002.tsv.gz
matrix_VBO002.mtx.gz
feature_reference_VBO_Ire1KI.csv
seuratObj_Ire1KI_paper_merge.rds

value: ADT

value: See Antibody Capture feature_type in feature_reference_VBO_Ire1KI.csv


title: Pancreatic tumor, Combination, replicate 1


title: Infection, NO_CIT, Liver2


title: delta-asf1, 3 days, replicate 2

value: 3 days


title: Infection, NO_CIT, Liver1


title: Spleen, heterozygous R594C/+, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes_VBO002.tsv.gz
features_VBO002.tsv.gz
matrix_VBO002.mtx.gz
seuratObj_Ire1KI_paper_merge.rds

value: Spleen

value: Total splenocytes


title: delta-asf1, input control for C30


title: Non-infection, ORA_CIT, Liver3

value: Non-infection, ORA_CIT


title: Pancreatic tumor, VEGFR-2, replicate 2


title: Pancreatic tumor, VEGFR-2, replicate 3


title: Spleen, homozygous R594C/R594C, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
barcodes_VBO003.tsv.gz
features_VBO003.tsv.gz
matrix_VBO003.mtx.gz
feature_reference_VBO_Ire1KI.csv
seuratObj_Ire1KI_paper_merge.rds

value: Homozygous R594C/R594C


title: wild type, input control for C28

value: mycelium


title: Spleen, WT, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
barcodes_VBO001.tsv.gz
features_VBO001.tsv.gz
matrix_VBO001.mtx.gz
feature_reference_VBO_Ire1KI.csv
seuratObj_Ire1KI_paper_merge.rds

value: HTO

value: WT


title: Non-infection, ORA_CIT, Liver2


title: wild type, input control for C27

value: wild type


title: Spleen, WT, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
barcodes_VBO001.tsv.gz
features_VBO001.tsv.gz
matrix_VBO001.mtx.gz
seuratObj_Ire1KI_paper_merge.rds

value: mRNA


title: Non-infection, ORA_CIT, Liver1

value: Liver


title: Infection, NO_CIT, Liver4

value: Infection, NO_CIT


title: Pancreatic tumor, TH-302, replicate 3

value: Bulk tumor


title: Spleen, WT, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
barcodes_VBO001.tsv.gz
features_VBO001.tsv.gz
matrix_VBO001.mtx.gz
feature_reference_VBO_Ire1KI.csv
seuratObj_Ire1KI_paper_merge.rds


title: Pancreatic tumor, VEGFR-2, replicate 1

value: Tumor cell


title: wild type, input control for C26


title: dHeps isolated from CCl4-injured mice, 5C-S, Day16 [14.5C-S RNA-seq]

city: Beijing

first: pengyan

last: lin

state: Beijing

address: No.5 Yiheyuan Road Haidian

department: College of Future Technology,

country: China

institute: Peking university

data_processing:
Bulk RNA-seq data were processed to obtain a gene count matrix of all samples using the featureCounts tool of the subread software. The count matrix was used for differential analysis with DESeq2 (Love et al., 2014).
Assembly: Mus musculus genome GRCm39
Supplementary files format and content: tab-delimited text files include RPKM and count values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using  EasyPure® RNA Kit (TransGen)
RNA libraries for RNA-seq were prepared using NEBNext@ Ultra™  RNA Library Prep Kit for Illumina@ (#E7530) following manufacturer's protocols.

value: liver

value: hepatocytes

value: 5C.S in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: Non-infection, IV_CIT, Liver2

value: Non-infection, IV_CIT


title: dHeps isolated from CCl4-injured mice, 5C-E, Day16 [6.5C-E RNA-seq]

value: 5C.E in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: wild type, input control for C29


title: Pancreatic tumor, TH-302, replicate 1


title: Pancreatic tumor, untreated, replicate 3

value: Untreated


title: dHeps isolated from CCl4-injured mice, 5C-E, Day16 [5.5C-E RNA-seq]


title: delta-asf1, input control for C24


title: dHeps isolated from CCl4-injured mice, 5C-C, Day16 [10.5C-C RNA-seq]

value: 5C.C in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: Pancreatic tumor, untreated, replicate 2


title: Non-infection, NO_CIT, Liver3

value: Non-infection, NO_CIT


title: delta-asf1, histone H3, replicate 2

value: mycelium


title: Non-infection, NO_CIT, Liver2


title: dHeps isolated from CCl4-injured mice, 5C-C, Day16 [9.5C-C RNA-seq]


title: Pancreatic tumor, untreated, replicate 1


title: delta-asf1, H3K27me3, replicate 2


title: wild type, H3K27me3, replicate 2


title: wild type, histone H3, replicate 2


title: liver cells isolated from CCl4-injured mice

description: 10x Genomics

data_processing:
Raw reads were processed to generate gene expression profiles using an in-house pipeline. Briefly, after filtering all read one sequences lacking a poly T tail, cell barcodes, and UMI were extracted. Adapters and poly-A tails were trimmed (fastp V1) before aligning read two to GRCh38 with ensemble version 92 gene annotation (fastp 2.5.3a and feature Counts 1.6.2). Reads with the same cell barcode, UMI, and gene were grouped to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
After perfusion with EGTA, Pronase (14 mg per mouse), and Collagenase (3.7 U per mouse), liver specimens were further digested by Pronase/Collagenase and purified via Nycodenz density gradient centrifugation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: whole liver cells

value: Col1a2CreER:Rosa26tdTomato mice


title: dHeps isolated from CCl4-injured mice, 5C-F, Day16 [12.5C-F RNA-seq]

value: WT

value: 5C.F in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: dHeps isolated from CCl4-injured mice, 5C-F, Day16 [11.5C-F RNA-seq]


title: Non-infection, IV_CIT, Liver3

value: Liver


title: Pancreatic tumor, TH-302, replicate 2


title: liver cells isolated from healthy mice

description: 10x Genomics


title: wild type, histone H3, replicate 1

value: wild type


title: pig 13 skin, site 6b, no ID IL-15

city: St. Louise

first: CANXIN

last: XU

address: 4340 Duncan Ave

department: Pharmacology

institute: Aclaris Therapeutics, Inc.

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl Sscrofa11.1.99
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: skin

extract_protocol:
Total RNA was extracted using RNeasy lipid tissue mini kit (QIAGEN).
RiboZero Gold

treatment_protocol: IL-15 (200ng in100ul saline) (Abcam) was injected intradermally in prepared grids on Yorkshire swine skin. After 3 hours, the injected site was biopsied and the entire biopsy piece was placed into 0.4ml Trizol (ThemoFisher) and immediately the tube containing the biopsy was put into dry ice/EtOH and frozen until RNA extraction.

value: skin

value: Control


title: pig 13 skin, site 7b, no ID IL-15


title: delta-asf1, input control for C25


title: Non-infection, NO_CIT, Liver1

source_name: Liver


title: Non-infection, IV_CIT, Liver1


title: dHeps isolated from CCl4-injured mice, 5C-G, Day16 [8.5C-G RNA-seq]

value: liver

value: 5C.G in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days