title: IARS1_RFP-rep2

city: EA Utrecht

first: Imre

last: Schene

state: Utrecht

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI37) using BWA41 package (mem –t 7 –c 100 –M –R ) (Li, H., and Durbin, R. Fast and accurate short read alignment with Burrows – Wheeler transform. Bioinformatics 25, 1754–1760 (2009)).
RNA sequencing was analyzed using DESeq2 in Rstudio (Love, M. I., Huber, W., & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014)).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file, raw read counts of all samples included

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained and split every 4-5 days in standard medium, consisting of DMEM+GlutaMAX (1x, Gibco), 10% FBS (Gibco), and PenStrep (1x, Gibco).

extract_protocol:
Total RNA was isolated using Trizol LS reagent (Invitrogen) and stored at –80°C until further processing. mRNA was isolated using Poly(A) Beads (NEXTflex).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex) and sequenced on a NextSeq500 (Illumina) to produce 75 base long reads (Utrecht DNA Sequencing Facility).

treatment_protocol: HEK293T cells were plated in standard medium at a density of 50,000 cells per well in a 96 wells plate one day prior to transfection. HEK293T cells were transfected with 0.1 µg fluoPEER plasmid, 0.25 µg prime editor plasmid, 0.1 µg pegRNA plasmid, and optionally 0.05 µg nicking-gRNA plasmid in a mix of 25 µl OptiMEM and 0.5 µl lipofectamine 2000 for each well. Organoids and cell lines were harvested and dissociated to single cells using TrypLE (Gibco) or Trypsin (Gibco), respectively, after which cells were resuspended in FACS buffer (phosphate-buffered saline with 2 mM ethylenediaminetetraacetic acid and 0.5% bovine serum albumin). Prior to FACS, cells were filtered through a 5 ml Falcon polystyrene test tube (Corning). Flow cytometry was performed on the FACS Fortessa (BD) and sorting was performed on the FACS FUSION (BD) using FACS Diva software (BD).

tag: transfection

tag: fluopeer

value: RFP


title: IARS1_RFP-rep1

status: Public on Feb 03 2022

type: SRA

country: Netherlands

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: 12hour R1

city: Belfast

first: Aditi

last: Singh

state: Please Select State

address: 97 Lisburn Road, Belfast

department: The Wellcome-Wolfson Institute for Experimental Medicine, SMDBS

country: United Kingdom

institute: Queen's University Belfast

description:
ES ND1 12h +Dox H3K27ac R1
ChIP-seq in ES

library_source: genomic

data_processing:
ChIP-sequencing files in fastq format were subjected to quality control using FASTQC. Bowtie2 was used with local parameter for soft clipping of reads and align the reads to the mouse mm10 genome using UCSC.
Aligned sam files were sorted, indexed, and converted to the bam format using SAMTOOLS v0.1.19. Peak calling was performed using MACS2 and taking Input as a control.
Peaks were merged from all samples as well as replicates to retain all the regions of interest for differential occupancy.
qCount from QuasR was used to count reads from all samples in the merged peak regions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: K27Reads_mergedPeaks.csv: Comma-separated text file includes read counts from all samples.

molecule: genomic DNA

organism: Mus musculus

source_name: A2Lox cell line

growth_protocol: Murine ESCs were cultured at 37°C, 7% CO2 and 88% relative air humidity in 8 ml ES medium (DMEM supplemented with 10% fetal calf serum, 1X MEM NEAA, 2mM L-glutamine and LIF on feeders (inactivated MEFs)). For further experiments, feeders were removed by splitting mESCs every 2 days on tissue-culture dishes coated with 0.2% gelatin with daily media change. Experiments were performed at feeder-free five state.

extract_protocol:
Cells were cross-linked in medium containing 1% formaldehyde for 10 min at room temperature, neutralized with 0.125M glycine, scraped off and rinsed twice with cold 10 ml 1X PBS. Cells were pelleted by centrifugation for 7 min at 4°C at 600g. Pellets were resuspended in 10 mL of Buffer L1 (50mM Hepes KOH, pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP-40, 0.25% Triton-X 100) and incubated at 4°C for 10 min. This was followed by centrifugation for 5 min at 4°C at 1300g. The pellet was again resuspended in 10 ml of Buffer L2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0) and incubated at room temperature for 10 min, followed by centrifugation for 5 min at 4°C at 1300g. The pellet was then resuspended in 900 µl Buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate, 0.17mM N-Lauroyl sarcosine) containing protease inhibitors and incubated at 4°C for overnight following sonication using Bioruptor plus (Diagenode). After clearing cellular debris by spinning at 14,000 g for 10 min at 4°C DNA 60 µg of chromatin were incubated at 4 °C overnight with respective antibodies after 1h of preclearing. The mixture was then incubated with 40 µl protein A-Sepharose beads preblocked with tRNA and BSA for 3 h at 4°C. Beads were washed twice with 1 ml buffer L3 and once with 1 ml DOC buffer (10 mM Tris (pH 8.0), 0.25 M LiCl, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA), and bound chromatin was eluted in 1% SDS/0.1 M NaHCO3. This followed treatment with RNase A (0.2mg/ml) for 30 min at 37°C and then with Proteinase K (50 µg/ml) for 2.5 h at 55°C. The crosslinking was reversed at 65°C overnight with gentle shaking. DNA was purified by phenol-chloroform extraction followed by ethanol precipitation and recovered in 40 µl TE buffer.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ectopic NeuroD1 expression was induced with Doxycycline (500 ng/ml final. conc.) for 48 hours.

tag: cell type

value: ES cells

tag: treatment

value: plusDox (NeuroD1 induction)

tag: time point

value: 12 hour

tag: chip antibody


title: CTNNB1_RFP-rep2


title: Survivor, 293T

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

data_processing:
Library strategy: CRISPR screen
extraction of sgRNA sequences with cutadapt
sgRNA counting and comparison with MAGeCK and the Brunello CRISPR library
Genome_build: hg38
Supplementary_files_format_and_content: gene-level summary

extract_protocol:
Genomic DNA (gDNA) of cell pellets was isolated using a Quick-DNA Miniprep Plus kit (Zymo Research).
PCR was performed on gDNA to construct Illumina sequencing libraries, each containing 5 μg gDNA, according to the Broad Institute protocol for PCR of sgRNAs for Illumina sequencing.

tag: rounds of infection


title: CTNNB1_RFP-rep1


title: IARS1_GFP-rep2

value: GFP


title: CTNNB1_GFP-rep1


title: IARS1_GFP-rep1


title: CTNNB1_GFP-rep2


title: HUDEP1 cells H2AK119Ub

city: Boston

first: Grant

last: Rowe

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
library strategy: CUT&RUN
Bowtie2 alignment (human specimens)
FastQC and CUT&RUNTools (Bowtie2, Trimmomatic, Picard, Samtools)
E. coli spike-in normalization with Bowtie2
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: bigwig files

growth_protocol: HUDEP1 were cultured in StemSpan SFEM with SCF, EPO, dexamethasone, and doxycycline prior to processing.  Mouse HSPCs were purified from fresh tissue and processed immediately.

extract_protocol:
Per Epicypher CUTANA kit instructions
Per Epicypher CUTANA kit and New England Biolabs next generation library instructions

treatment_protocol: No treatments

value: human neonatal erythroblast cell line

tag: cut&run antibody

value: Cell Signal rabbit anti-H2AK199Ub (8240S)

tag: molecule subtype

value: CUT&RUN DNA


title: HUDEP1 cells H3K4me3

value: Epicypher anti-H3K4me3 positive control antibody


title: RF_liver_rep3

city: Ithaca

first: Pat

last: Johnson

state: New York

address: 507 Tower Rd

department: Animal Science

institute: Cornell University

data_processing:
Sequencing quality of the data was determined using FastQC.
Reads were aligned to UCSC Galgal4 using Tophat (v2.0.13).
Transcripts were counted using cuffdiff (v.2.2.1)
Differentially expression analysis was conducted using edgeR.
Genome_build: Galgal4
Supplementary_files_format_and_content: count table for each gene and sample

organism: Gallus gallus

source_name: Liver

extract_protocol:
RNA was extracted from the frozen liver of 3 FF and 3 RF broiler breeder hens using an RNeasy Mini Kit with on-column DNase digestion (Qiagen Inc., Valencia CA) according to manufacturer guidelines. RNA quality was analyzed on an Aligent Bioanalyzer (Aligent Technologies, Santa Clara, CA) and all samples had RIN values > 8.
Strand-Specific RNA sequencing library preparation was done in the laboratory of Dr. James Giovannoni at the Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, according to a previously described protocol.

treatment_protocol: Starting at 38 weeks of age, hens were given a dietary treatment of either ad libitum (FF) or restricted (RF) feed allowance.

value: RF


title: RF_liver_rep1


title: K562 cells IgG

value: Erythroleukemia

value: Epicypher control IgG


title: FF_liver_rep2

value: FF


title: HUDEP1 cells IgG


title: FF_liver_rep1


city: Tarrytown

first: Yu

last: Bai

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description:
largescale JK line microglia like cell wild type day66 repeat 2
raw_gene_counts_matrix.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing reads were mapped to the human genome (hg19) using the OmicSoft ArrayStudio software with two mismatches allowed
Gene expressions were quantified from raw sequencing reads using the OmicSoft ArrayStudio RNA-seq analysis pipeline. Reads that uniquely mapped to the exons of a gene were identified and counted. The resulting read counts were summarized at the gene level as raw expression.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human iPSC derived cell

extract_protocol:
Cells were homogenized in TRIzol and chloroform was used for phase separation. The aqueous phase, containing total RNA, was purified using MagMAX-96 for Microarrays Total RNA Isolation Kit and genomic DNA was removed using RNase-free DNase Set
Strand- specific RNA-seq libraries were prepared from 500 ng of RNA using KAPA Stranded mRNA- Seq Kit and amplified by 12-cycle PCR.

value: human iPSC derived microglia like cell

tag: timepoint

tag: genotype

value: wild type

tag: cell line id

value: JK

tag: clone id


description:
largescale JK line microglia like cell wild type day66 repeat 4
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day66 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day66 repeat 1
raw_gene_counts_matrix.txt


title: DBR1_KO_C19

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St, Box G

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

data_processing:
Reads originating from lariats were identified in the sequenced reads using the branchpoint detection algorithm described in Taggart et al (2012)
Genome_build: hg19
Supplementary_files_format_and_content: BED - each mapped lariat read is listed with the start and end coordinates being the 5' splice site and branchpoint (or vice versa if the the lariat maps to the negative strand); additionally, the read ID, inferred branchpoint nucleotide, and nearest 3' splice site are listed in the name field

growth_protocol: DMEM media +10% FBS with 1% pen-strep, 5% CO2, 37 deg. C

extract_protocol:
Trizol
Illumina with rRNA depletion

value: DBR1 -


title: HEK293T_wildtype_rep3 (DBR1_KO control)


title: HEK293T_wildtype_rep2 (DBR1_KO control)


description:
largescale JK line microglia like cell wild type day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day62 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day59 repeat 4
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day62 repeat 4
raw_gene_counts_matrix.txt


title: K562 H2AK119Ub


description:
largescale JK line microglia like cell wild type day59 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day59 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day59 repeat 2
raw_gene_counts_matrix.txt


title: HEK293T_wildtype_rep1 (DBR1_KO control)


title: RF_liver_rep2


description:
largescale JK line microglia like cell wild type day55 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day55 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell wild type day55 repeat 1
raw_gene_counts_matrix.txt


title: DBR1_KO_C22


description:
largescale JK line microglia like cell P525LHom day66 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day66 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day62 repeat 4
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day59 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day55 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day66 repeat 4
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day55 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day59 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day62 repeat 4
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day62 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day66 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day66 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day66 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day59 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day59 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day55 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day59 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day62 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day55 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day66 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day66 repeat 3
raw_gene_counts_matrix.txt

value: engineered control


description:
largescale JK line microglia like cell P525LHet day55 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day66 repeat 4
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day66 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day66 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day62 repeat 4
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHet day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day59 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell P525LHom day55 repeat 3
raw_gene_counts_matrix.txt


title: GFP rep2

status: Public on Feb 04 2022

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Basecalling carried out by NovaSeq 6000: 3.4.4 and bcl2fastq v2.20.0.422
Paired-end reads were merged, trimmed and filtered by size using bbmerge and bbduk, merged reads longer and 34 base-pairs were retained for analysis
umi_tools was used to separate UMI from reads with the following command: umi_tools extract --bc-pattern=NNNXXXXXXNNNNN -I {Input.fastq.gz} --3prime
flexbar was used to split biological replicates from each other with the command: flexbar -r {reads.fastq.gz} -b  new_flash_barcodes.fa --barcode-trim-end --barcode-error-rate 0.2 --zip-output GZ
Internal replicates were merged (taR1, taR10, taR15, taR16 for rep1 of C9orf78 and GFP; taR2, taR4, taR7, taR9 for rep2 of C9orf78 and GFP, these files are provided)
Reads were mapped to the human genome (hg38) with bowtie2 and bbmap
umi_tools was used remove PCR duplicates: umi_tools dedup -I {in.bam} -S {out.bam} --spliced-is-unique --soft-clip-threshold 3
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage from deepTools2

source_name: Flp-In™ T-REx™ 293 Cell Line

growth_protocol: Flp-In T-REx HEK293 expression cell lines are maintained in DMEM with Glutamax, high glucose and Na-pyruvate (Thermo Fisher #31966), that is supplemented with 10% FBS and penicillin-streptomycin, and kept under blasticidin (15µg/ml) and hygromycin (150µg/ml) selection.

extract_protocol:
Cells were solubilized with 1X PBS with additional 0.3M NaCl 1% Triton™ X-100 and 0.2% TWEEN® 20
Flp-In™ T-REx™ 293 cells expressing either 3xFLAG-BIO tagged C9ORF78 or 3xFLAG-BIO tagged GFP were induced with 0.1µg/mL doxycycline for ~16hrs and UV-crosslinked with 0.2mJ/cm2 UV-C light. Target proteins were purified using MyONE C1 streptavidin beads, after a partial RNase digestion using RNAse1 and end-repair with T4 PNK, uniquely barcoded s-oligos were ligated to each sample (2 biological replicates). After several stringent washes (up to 1% SDS), biological replicates are merged, and bead-bound RNA was released with proteinase K and purified with Oligo Clean and Concentrator columns. RNA was then reverse-transcribed and treated with RNaseH to phosphorylate 5’-ends of cDNA. The cDNA was then circularized with CircLigaseII, amplified with Q5 polymerase and sequenced on an Illumina platform (100bp, PE sequencing).
FLASH (Ilik et al., 2020)

treatment_protocol: Cells were UV-crosslinked with 200mJ/cm2 UV-C on 15 cm plates

value: Flp-In T-REx 293 Human Embryonic Kidney Cell Line

value: 200mJ/cm2 UV-C

tag: expressing

value: 3xFLAG-BIO tagged GFP


description:
largescale JK line microglia like cell engineered control day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day59 repeat 3
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day59 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day59 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day55 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day55 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day66 repeat 7
raw_gene_counts_matrix.txt

value: AG

value: parental


description:
largescale AG line microglia like cell wild type day66 repeat 4
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day66 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day66 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day66 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day62 repeat 4
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day62 repeat 6
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day62 repeat 5
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day62 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day59 repeat 7
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day59 repeat 6
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day59 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day59 repeat 2
raw_gene_counts_matrix.txt


description:
largescale JK line microglia like cell engineered control day62 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day59 repeat 5
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day59 repeat 4
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day55 repeat 7
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day59 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day66 repeat 5
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day55 repeat 6
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day66 repeat 6
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day55 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day66 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day66 repeat 4
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day55 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day62 repeat 7
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day66 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day62 repeat 4
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day59 repeat 4
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day62 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day66 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day59 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day59 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day59 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day55 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day55 repeat 4
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day55 repeat 5
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell wild type day55 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day66 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day62 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day66 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day66 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day55 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day59 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day59 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day55 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day59 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell engineered control day66 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day55 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day55 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell engineered control day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHom day62 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell P525LHet day55 repeat 2
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell engineered control day62 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell engineered control day55 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day111 repeat 4
raw_gene_counts_matrix.txt

value: human iPSC derived myeloid progenitor

value: FUS KO


description:
largescale AG line microglia like cell engineered control day59 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day111 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day111 repeat 3
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell engineered control day55 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 8
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day111 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day111 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day111 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day111 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day111 repeat 1
raw_gene_counts_matrix.txt


description:
largescale AG line microglia like cell engineered control day59 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day111 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day111 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day111 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day111 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day75 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day75 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day111 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 8
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 8
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day111 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 8
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day75 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day75 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day75 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day75 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day75 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day75 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day75 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day75 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day75 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day75 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day65 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day65 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day65 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day75 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 8
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day65 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 8
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day65 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day65 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day75 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day65 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day65 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day65 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day65 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day65 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day55 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day65 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day55 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day55 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day55 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day65 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day55 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell FUS KO day55 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day65 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day55 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day55 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day55 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day55 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 6
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 7
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 8
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHom day55 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day55 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 4
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day55 repeat 2
raw_gene_counts_matrix.txt


description:
pilot progenitor cell P525LHet day55 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day55 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day55 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day115 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day115 repeat 3
raw_gene_counts_matrix.txt


description:
pilot progenitor cell engineered control day55 repeat 1
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day55 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day115 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day115 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day115 repeat 5
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day115 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day115 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day115 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day115 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day115 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day115 repeat 7
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 5
raw_gene_counts_matrix.txt


description:
pilot progenitor cell wild type day55 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 8
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 7
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day115 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day115 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day115 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day115 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day72 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day115 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day115 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day115 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day115 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day115 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day72 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 5
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day72 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 8
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 7
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day72 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 7
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 5
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 8
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day72 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day72 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day72 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day72 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day72 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day72 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day72 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day62 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day72 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day72 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day62 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day62 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day62 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day62 repeat 7
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day62 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day62 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day62 repeat 5
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day62 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day62 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day62 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day62 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day62 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day62 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day62 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day62 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day62 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day62 repeat 7
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day62 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day62 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day62 repeat 5
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day52 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day52 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day52 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day72 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day62 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day62 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day62 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day62 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day52 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell FUS KO day62 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day52 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day52 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 5
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 8
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day52 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day52 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 7
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day52 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day52 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 6
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHet day52 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day52 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell engineered control day52 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day52 repeat 3
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day52 repeat 1
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day52 repeat 4
raw_gene_counts_matrix.txt


description:
pilot microglia like cell wild type day52 repeat 2
raw_gene_counts_matrix.txt


description:
pilot microglia like cell P525LHom day52 repeat 5
raw_gene_counts_matrix.txt


title: M-19-3921_157-C_SI-GA-H5_S8: iPS XXXY,48 KS Single cell RNAseq

city: Jeddah

first: Antonio

last: Adamo

state: Not in US

address: 4700 KAUST, Thuwal

department: Biological and Environmental Science and Engineering Division, BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology, KAUST

description:
Single cell RNAseq
M-19-3921_157-C_SI-GA-H5_S8_L008

data_processing:
Bulk RNA-Seq data validation, pairing and FastQC quality control was followed by trimming using BBDuk by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were mapped against the reference genome (GrCh38 release 91) using the STAR end-to-end alignment method and gene expression quantification performed with featureCounts. Data normalization was performed with the Trimmed Mean of M-values (TMM) method
The pre-processing of single cell RNA-Seq data that includes the identification of cell barcodes and the steps of UMI detection, extraction and processing was performed using UMI-tools 1.0.1. Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and BBDuk with default options of minimum size 35 bp and minimum quality score 25 to perform adapter and quality trimming. To align the filtered reads to a human genome reference (GrCh38 release 91) STAR 2.7.3a was used, while FeatureCounts 1.6.3 package was used to assign reads to genes.
Data from single cell RNA-sequencing were then analyzed using the R packages: SC3 for clustering methods, differential expression analysis and gene marker detection algorithm and Scater 1.16.0 was used for expression data pre-processing, quality control, normalization and visualization through the t-distributed stochastic neighbor embedding (t-SNE) analysis. The package scImpute 0.0.9 was used to correct dropout values.
Genome_build: GrCh38 release 91 was used fo bulk and scRNA-SEQ analysis
Supplementary_files_format_and_content: File including FPKM values for each Sample
Supplementary_files_format_and_content: Rdata file includes single cell experiment objects

source_name: iPS

growth_protocol: hiPSC lines were adapted to feeder-free conditions on matrigel-coated plates in E8 medium

extract_protocol:
For bulk RNA-Seq libraries the RNA has been extracted using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions
Bulk RNA libraries were generated using the human mRNA TruSeq Stranded library preparation KIT from Illumina, and profiled using a HiSeq4000 system with 150 bp paired-end sequencing method

treatment_protocol: Before RNA extraction hiPSCs were adapted to Vitronectin (VTN-N) coated plates  in presence of E8 medium and passaged with Versene.

value: human induced pluripotent stem cell

tag: karyotype

value: XXXY,48 KS

tag: name in the manuscript

value: KS7 #A


title: M-19-3917_321-H_SI-GA-D5_S4: iPS XX,46 Single cell RNAseq

description:
Single cell RNAseq
M-19-3917_321-H_SI-GA-D5_S4_L004

value: HM #B


title: M-19-3916_323-E2_SI-GA-C5_S3: iPS XY,46 Single cell RNAseq

description:
Single cell RNAseq
M-19-3916_323-E2_SI-GA-C5_S3_L003

value: KS4 #E


title: M-19-3920_157-A_SI-GA-G5_S7: iPS XXXXY,49 KS Single cell RNAseq

description:
Single cell RNAseq
M-19-3920_157-A_SI-GA-G5_S7_L007

value: XXXXY,49 KS

value: KS7 #B


title: M-19-3914_326-E_SI-GA-A5_S1: iPS XXXXY,49 KS Single cell RNAseq

description:
Single cell RNAseq
M-19-3914_326-E_SI-GA-A5_S1_L001

value: KS1 #D


description:
pilot microglia like cell engineered control day52 repeat 1
raw_gene_counts_matrix.txt

value: human iPSC derived microglia like cell


title: M_19_1095_1581_AD009: iPS XXXXY,49 KS Bulk RNAseq

description:
Bulk RNAseq
M_19_1095_1581_AD009_L001


title: M-19-3918_807-A_SI-GA-E5_S5: iPS XXY,47 KS Single cell RNAseq

description:
Single cell RNAseq
M-19-3918_807-A_SI-GA-E5_S5_L005

value: XXY,47 KS

value: KS6 #B


title: M-19-3919_807-G_SI-GA-F5_S6: iPS XY,46 Single cell RNAseq

description:
Single cell RNAseq
M-19-3919_807-G_SI-GA-F5_S6_L006

value: KS6 #A


title: M_18_3208_1295_AD013: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3208_1295_AD013_L006


title: M_18_3205_1292_AD002: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3205_1292_AD002_L006

value: KS4 #F


title: M_18_3324_1375_AD018: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3324_1375_AD018_L001

value: KS4 #D


title: M_18_3325_1376_AD019: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3325_1376_AD019_L001


title: M_18_3337_1388_AD014: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3337_1388_AD014_L003

value: KS3 #A


title: M_18_3339_1390_AD016: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3339_1390_AD016_L003

value: KS3 #B


title: M_18_3338_1389_AD015: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3338_1389_AD015_L003


title: M_18_3323_1374_AD013: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3323_1374_AD013_L001

value: KS4 #C


title: M_18_3333_1384_AD019: iPS XXXXY,49 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3333_1384_AD019_L002

value: human induced pluripotent stem cell


title: M_19_1117_1397_AD003: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_19_1117_1397_AD003_L004

value: KS5 #A


title: M_18_3335_1386_AD004: iPS XXXY,48 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3335_1386_AD004_L003

value: XXXY,48 KS

value: KS7 #A


title: M_19_1094_1580_AD008: iPS XXXXY,49 KS Bulk RNAseq

description:
Bulk RNAseq
M_19_1094_1580_AD008_L001


title: M-19-4034_Pool50-Sample6674C_SI-GA-E6_S3: iPS XXY,47 KS Single cell RNAseq

description:
Single cell RNAseq
M-19-4034_Pool50-Sample6674C_SI-GA-E6_S3_L003


title: M_18_3326_1377_AD007: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3326_1377_AD007_L002


title: M_18_3327_1378_AD012: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3327_1378_AD012_L002


title: M_18_3334_1385_AD002: iPS XXXY,48 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3334_1385_AD002_L003


title: Duodenum_Sham_VSG_PF_rep3

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 3

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3.0.187) including median polish and Sketch-Quantile normalisation

label: biotin

organism: Rattus norvegicus

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 3

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Mini kit including on-column digestion of DNA (Qiagen, Valencia, CA, USA)  (Qiagen, Valencia, CA, USA)

treatment_protocol: As described in the paper. Briefly, the day prior to surgery solid food was replaced with liquid diet (Osmolite). Under isoflurane/O2 mixture anesthesia, all animals received a midline incision in the ventral abdominal wall and the stomach was exposed. For VSG, approximately 80% of the stomach was transected along the greater curvature using an Endopath ETS-FLEX 35mm Stapler (Ethicon endo-surgery) creating a sleeve-like gastric remnant. For sham surgery, pressure was applied on the stomach imitating the VSG-transection line with nontoothed blunt forceps. The abdominal wall was closed using continuous absorbable 5-0 Vicryl Rapide sutures.

tag: tissue

value: Duodenum

tag: strain

value: Long-Evans

tag: age

value: 8-10 weeks

tag: gender

value: male

value: WT


title: M_18_3332_1383_AD018: iPS XXXXY,49 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3332_1383_AD018_L002

tag: cell type

value: XXXXY,49 KS

value: KS7 #B


title: Duodenum_Sham_VSG_PF_rep4

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 4

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 4


title: Duodenum_Sham_VSG_rep5

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 5

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 5


title: Duodenum_Sham_VSG_rep4

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 4

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 4


title: Duodenum_Sham_VSG_PF_rep2

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 2

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 2


title: Duodenum_Sham_VSG_rep6

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 6

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 6


title: Duodenum_Sham_VSG_PF_rep5

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 5

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 5


title: Duodenum_Sham_VSG_rep3

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 3

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 3


title: Duodenum_VSG_rep6

description: Gene expression data from duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 6

source_name: Duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 6


title: Duodenum_Sham_VSG_rep1

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 1

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 1


title: Duodenum_Sham_VSG_PF_rep6

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 6

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 6


title: Duodenum_Sham_VSG_rep2

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 2

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG, biological replicate 2


title: Duodenum_Sham_VSG_PF_rep1

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 1

source_name: Duodenum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 1


title: M_18_3336_1387_AD005: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3336_1387_AD005_L003

value: XXY,47 KS


title: M_18_3321_1372_AD006: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3321_1372_AD006_L001

value: KS2 #B


title: M_18_3320_1371_AD005: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3320_1371_AD005_L001


title: M_18_3319_1370_AD004: iPS XXY,47 KS Bulk RNAseq

description:
Bulk RNAseq
M_18_3319_1370_AD004_L001

value: KS2 #A


title: Duodenum_VSG_rep5

description: Gene expression data from duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 5

source_name: Duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 5


title: M_18_3330_1381_AD015: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3330_1381_AD015_L002

value: KS6 #A


title: M-19-3759_1785_AD008: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M-19-3759_1785_AD008_L008

value: KS4 #A


title: M-19-3757_1783_AD001: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M-19-3757_1783_AD001_L008


title: M_18_3200_1287_AD012: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3200_1287_AD012_L005

value: HB #B


title: M-19-3758_1784_AD003: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M-19-3758_1784_AD003_L008

value: human induced pluripotent stem cell


title: M_18_3201_1288_AD014: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3201_1288_AD014_L005

value: HB #C


title: M_18_3202_1289_AD016: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3202_1289_AD016_L005


title: M_18_3331_1382_AD016: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3331_1382_AD016_L002


title: Duodenum_VSG_rep2

description: Gene expression data from duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 2

source_name: Duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 2


title: Duodenum_VSG_rep3

description: Gene expression data from duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 3

source_name: Duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 3


title: M_18_3199_1286_AD007: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3199_1286_AD007_L005

source_name: iPS


title: Duodenum_VSG_rep4

description: Gene expression data from duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 4

source_name: Duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 4


title: Duodenum_Sham_RYGB_rep5

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 5

source_name: Duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 5


title: Duodenum_Sham_RYGB_rep2

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 2

source_name: Duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 2


title: M_18_3197_1284_AD004: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3197_1284_AD004_L005

value: HB #A


title: Duodenum_Sham_RYGB_rep4

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 4

source_name: Duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 4


title: Duodenum_Sham_RYGB_rep3

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 3

source_name: Duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 3


title: Duodenum_Sham_RYGB_rep1

description: Gene expression data from duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 1

source_name: Duodenum tissue derived from rats treated with sham surgery for RYGB, biological replicate 1


title: Duodenum_RYGB_rep6

description: Gene expression data from duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 6

source_name: Duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 6


title: Duodenum_RYGB_rep5

description: Gene expression data from duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 5

source_name: Duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 5


title: Undifferentiated ESC_rep1

city: Montreal

first: Massimiliano

last: Paganelli

state: QC

address: 3175 Ch. Cote-Ste-Catherine

country: Canada

institute: CHU Sainte-Justine

description:
figS1E_heatmap.txt
figS1E_raw_counts.txt [12016]
figS1E_heatmap_samples_rename.txt

data_processing:
For heatmaps, prior to all analysis, the raw gene counts were normalized using the logCPM method by dividing each column by the total sum of its counts, multiply by a million and followed by the application of a log10-transform.
For UMAP analysis, raw counts from different RNA-seq datasets were normalized (divided by the total count, multiplied by 1 million and natural-log transformed using log1p) and center-scaled.
For DGE (Fig. S4), annotation with Salmon’s quasi-mapping and Ensebl EnsDb.Hsapiens.v86, quantification of gene expression was performed with Salmon
Genome_build: GRCh37/hg19

growth_protocol: See differentiation protocol in paper

extract_protocol:
ReliaPrep RNA Miniprep system (Promega)
TruSeq RNA v2 mRNA Sample Prep Kit

value: ESC


title: M_18_3198_1285_AD005: iPS XY,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3198_1285_AD005_L005


title: Undifferentiated ESC_rep2

description:
figS1E_heatmap.txt
figS1E_raw_counts.txt [12017]
figS1E_heatmap_samples_rename.txt


title: Duodenum_RYGB_rep2

description: Gene expression data from duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 2

source_name: Duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 2

value: Duodenum


title: Duodenum_RYGB_rep4

description: Gene expression data from duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 4

source_name: Duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 4

value: Long-Evans


title: Undifferentiated iPSC_pop1

description:
figS1E_heatmap.txt
figS1E_raw_counts.txt [11999]
figS1E_heatmap_samples_rename.txt

source_name: human iPSC

value: iPSC


title: Duodenum_VSG_rep1

description: Gene expression data from duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 1

source_name: Duodenum tissue derived from rats treated VSG bariatric surgery, biological replicate 1

value: 8-10 weeks

value: male


title: M_18_3209_1301_AD014: iPS XX,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3209_1301_AD014_L006

value: HM #A


title: iPSC-derived bipotent hepatoblsts_rep1

description:
fig5B_heatmap.txt
fig5B_raw_counts.txt [12021]

value: iPSC-derived liver progenitor cells


title: M_19_1146_1305_AD025: iPS XX,46 Bulk RNAseq

description:
Bulk RNAseq
M_19_1146_1305_AD025_L007

value: HM #B


title: M_19_1100_1306_AD027: iPS XX,46 Bulk RNAseq

description:
Bulk RNAseq
M_19_1100_1306_AD027_L002


title: TargetSeq_Sample_91

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Library strategy: TargetSeq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human reference genome using BWA-MEM v0.7.17.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Excel for base subtitutions

source_name: 293FT-NT:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-NT:4 hHEK1_OT_sites,4 hEMX1_OT_sites;

growth_protocol: 293FT cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination.

extract_protocol:
72 hours after transfection, the genomic DNA was extracted from the transfected cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre)
Target genomic sequences were PCR amplified by high-fidelity DNA polymerase PrimeSTAR HS (Clonetech) with primer sets flanking examined gRNA target sites. The gRNA target sequences and PCR primer sequences are listed in Supplementary Table 2. Indexed DNA libraries were prepared by using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina. After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina Hiseq X Ten (2×150) at Omics Core of Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Shanghai, China.

treatment_protocol: 293FT cells were seeded in a 24-well plate at a density of 1E+5 per well and transfected with 250 μl serum-free Opti-MEM that contained LIPOFECTAMINE LTX (Life, Invitrogen), LIPOFECTAMINE plus (Life, Invitrogen) and expression vector. After 24 hr, puromycin (ant-pr-1, InvivoGen) was added to the medium at the final concentration of 4 μg/ml. After another 48 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) for subsequent sequencing analysis

tag: cell line

value: 293FT cells

tag: treatment


title: M_18_3210_1302_AD016: iPS XX,46 Bulk RNAseq

description:
Bulk RNAseq
M_18_3210_1302_AD016_L006


title: TargetSeq_Sample_90


title: iPSC-derived bipotent hepatoblsts_rep2

description:
fig5B_heatmap.txt
fig5B_raw_counts.txt [12023]


title: Undifferentiated iPSC_pop2

description:
figS1E_heatmap.txt
figS1E_raw_counts.txt [10121]
figS1E_heatmap_samples_rename.txt


title: Duodenum_RYGB_rep1

description: Gene expression data from duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 1

source_name: Duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 1

value: WT


title: iPSC-derived HLC standard protocol_rep4

description:
Included only in UMAP analysis
figS4BC_raw_counts.csv [12038]
figS4BC_DGE.csv

value: iPSC-derived HLC


title: Ileum_Sham_VSG_PF_rep4

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 4

source_name: Ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 4

value: Ileum


title: Ileum_Sham_VSG_rep6

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 6

source_name: Ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 6


title: Ileum_Sham_VSG_rep5

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 5

source_name: Ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 5


title: Ileum_Sham_VSG_PF_rep5

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 5

source_name: Ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 5


title: iPSC-derived HLC standard protocol_rep2

description:
fig5B_heatmap.txt
fig5B_raw_counts.txt [9792]
figS4BC_raw_counts.csv [9792]
figS4BC_DGE.csv


title: Ileum_Sham_VSG_PF_rep2

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 2

source_name: Ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 2


title: Ileum_Sham_VSG_PF_rep1

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 1

source_name: Ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 1


title: Ileum_Sham_VSG_PF_rep3

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 3

source_name: Ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 3


title: Duodenum_RYGB_rep3

description: Gene expression data from duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 3

source_name: Duodenum tissue derived from rats treated RYGB bariatric surgery, biological replicate 3


title: Ileum_Sham_VSG_rep4

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 4

source_name: Ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 4


title: Ileum_Sham_VSG_PF_rep6

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 6

source_name: Ileum tissue derived from rats treated with sham surgery for VSG and paired feeding, biological replicate 6


title: TargetSeq_Sample_89


title: TargetSeq_Sample_88

source_name: 293FT-Cas9:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-Cas9:4 hHEK1_OT_sites,4 hEMX1_OT_sites;


title: Ileum_VSG_rep6

description: Gene expression data from ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 6

source_name: Ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 6


title: iPSC-derived HLC standard protocol_rep3

description: Included only in UMAP analysis


title: iPSC-derived HLC standard protocol_rep1

description:
fig5B_heatmap.txt
fig5B_raw_counts.txt [9791]
figS4BC_raw_counts.csv [9791]
figS4BC_DGE.csv


title: Ileum_Sham_VSG_rep1

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 1

source_name: Ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 1


title: Ileum_Sham_VSG_rep2

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 2

source_name: Ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 2


title: iPSC-derived HLC new protocol_rep2

description:
fig5B_heatmap.txt
fig5B_raw_counts.txt [12026]
figS4BC_raw_counts.csv [12026]
figS4BC_DGE.csv

source_name: human iPSC


title: TargetSeq_Sample_87


title: Ileum_VSG_rep5

description: Gene expression data from ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 5

source_name: Ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 5


title: Ileum_VSG_rep4

description: Gene expression data from ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 4

source_name: Ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 4


title: Ileum_VSG_rep3

description: Gene expression data from ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 3

source_name: Ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 3


title: Ileum_Sham_VSG_rep3

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 3

source_name: Ileum tissue derived from rats treated with sham surgery for VSG, biological replicate 3


title: iPSC-derived HLC new protocol_rep1

description:
fig5B_heatmap.txt
fig5B_raw_counts.txt [12024]
figS4BC_raw_counts.csv [12024]
figS4BC_DGE.csv


title: Ileum_VSG_rep2

description: Gene expression data from ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 2

source_name: Ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 2


title: Ileum_Sham_RYGB_rep5

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 5

source_name: Ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 5


title: Ileum_VSG_rep1

description: Gene expression data from ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 1

source_name: Ileum tissue derived from rats treated VSG bariatric surgery, biological replicate 1


title: TargetSeq_Sample_86


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS4 #E M_18_3207_1294_AD012

description:
Homo sapiens iPS XXY,47 KS Bulk RNAseq
Bulk RNAseq

data_processing:
Bulk RNA-Seq data validation, pairing and FastQC quality control was followed by trimming using BBDuk by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were mapped against the reference genome (GrCh38 release 91) using the STAR end-to-end alignment method and gene expression quantification performed with featureCounts. Data normalization was performed with the Trimmed Mean of M-values (TMM) method
The pre-processing of single cell RNA-Seq data that includes the identification of cell barcodes and the steps of UMI detection, extraction and processing was performed using UMI-tools 1.0.1. Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and BBDuk with default options of minimum size 35 bp and minimum quality score 25 to perform adapter and quality trimming. To align the filtered reads to a human genome reference (GrCh38 release 91) STAR 2.7.3a was used, while FeatureCounts 1.6.3 package was used to assign reads to genes.
Genome_build: GrCh38 release 91 was used fo bulk and scRNA-SEQ analysis
Supplementary_files_format_and_content: File including FPKM values for each Sample

source_name: iPS

value: XXY,47 KS

value: KS4 #E


title: TargetSeq_Sample_85

source_name: 293FT-PE3:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-PE3-del:4 hHEK1_OT_sites,4 hEMX1_OT_sites;


title: TargetSeq_Sample_84


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS5 #A M_19_1116_1396_AD001

value: human induced pluripotent stem cell

value: KS5 #A


title: Ileum_Sham_RYGB_rep6

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 6

source_name: Ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 6


title: Ileum_Sham_RYGB_rep4

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 4

source_name: Ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 4


title: Ileum_Sham_RYGB_rep3

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 3

source_name: Ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 3


title: Ileum_Sham_RYGB_rep2

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 2

source_name: Ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 2


title: TargetSeq_Sample_83


title: TargetSeq_Sample_82

source_name: 293FT-hA3A-BE3:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-PE3-ins:4 hHEK1_OT_sites,4 hEMX1_OT_sites;


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS5 #B M_19_1107_1395_AD022

value: KS5 #B


title: TargetSeq_Sample_81


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS5 #A M_19_1118_1398_AD008


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS4 #C M_18_3322_1373_AD007

value: KS4 #C


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS2 #A M_18_3318_1369_AD002

value: KS2 #A


title: Ileum_RYGB_rep6

description: Gene expression data from ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 6

source_name: Ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 6

value: Long-Evans


title: TargetSeq_Sample_80


title: TargetSeq_Sample_79

source_name: NT:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-NT:hLSP1,hHEK1,hEMX1,4 hLSP1_OT_sites;


title: TargetSeq_Sample_78


title: Ileum_RYGB_rep3

description: Gene expression data from ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 3

source_name: Ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 3

value: 8-10 weeks


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS4 #G M_18_3204_1291_AD019

value: KS4 #G


title: ChIP_cNK_T-bet-1

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
ChIP-Seq and DNase-Seq reads (50 bp) were mapped to mm10 genome with Bowtie2 (Langmead and Salzberg, 2012). Only non-redundant reads with MAPQ >=10 were used for follow-up analysis. DNase-Seq peaks were called by MACS2 (Zhang et al., 2008) with settings of --nomodel--extsize 75.
Genome_build: mm10
Supplementary_files_format_and_content: Aligned unique high quality reads single end (BED files) and paired-end (BEDPE files). Peaks (narrowPeak files) were called for limited samples.

source_name: cNK

growth_protocol: To prepare Th1 cells, naïve CD4 T cells are cultured in conditions: α-CD3, α-CD28, α-IL-4, IL-12 and IL-2. After 4 days, cells were harvested.

extract_protocol:
Detailed procedures for DNase-Seq (in duplicates) were reported previously (Jin et al., 2015).
Dnase and ChIP DNA were end-repaired using an End-It DNA End-Repair kit (Epicentre), universal adaptors were then ligated. The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 16 cycles. The fragments between 180bp to 350bp were isolated on E-gel and subjected to sequencing on Illumina instruments.

value: cNK

value: Spleen

tag: markers

tag: chip antibody

value: anti-T-bet


title: DNase-seq_LTi-2

source_name: Lti

value: Lti

value: Small intestine


title: Ileum_RYGB_rep5

description: Gene expression data from ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 5

source_name: Ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 5

value: male

value: WT


title: bulked RNAseq of root tips growning with nitrate replicate 2

city: Guangzhou

middle: Xu

last: Hui

state: Guangdong

address: #10 Shiliugang

institute: Guangdong Academy of Science

data_processing:
The raw reads were aligned to the B73 reference genome, and gene expression was quantified using the Cell Ranger pipelines (v3.1, 10× Genomics).
Genome_build: Zea_mays.B73_RefGen_v4.42
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and ervey cell or sample

organism: Zea mays

source_name: root tips growning with nitrate

growth_protocol: The seedlings were incubated at 25℃/22℃ with an 8h light/16h dark cycle for 4 days.

extract_protocol:
primary roots were sampled and cut into small pieces of approximately 0.5mm and then digested in protoplasting solution (1.25% cellulase R10, 0.3% macerozyme R10, 400 mM mannitol, 20 mM 4-morpholineethanesulfonic acid, 20 mM KCl, 10 mM CaCl2 and 0.1% BSA).
RNA library were perpared with the Chromium Single Cell 3’ Reagent Kit v3 according to the manufacturer's protocol.

treatment_protocol: Twenty sterilized B73 seeds (sterilized with 1% sodium hypochlorite) were placed on germination paper, which was soaked in nutrient solution (nitrate+) with 4 mM Ca(NO3)2, 0.75 mM K2SO4, 0.65 mM MgSO4, 0.1 mM KCl, 0.25 mM KH2PO4, 0.01 mM H3BO3, 0.001 mM MnSO4, 0.0001 mM CuSO4, 0.001 mM ZnSO4, 0.000001 mM (NH4)6Mo7O24, and 0.1 mM FeNa-EDTA . Then, the germination papers were rolled and placed vertically in a sealed plastic bag. The paper roll was incubated at 25℃/22℃ with an 8h light/16h dark cycle for 4 days. For nitrate deficiency treatment (nitrate-), the Ca(NO3)2 in nutrient solution had been replaced by an equal concentration of CaCl2.

value: 2cm root tips

value: four days after germination


title: Ileum_RYGB_rep2

description: Gene expression data from ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 2

source_name: Ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 2

value: Ileum


title: bulked RNAseq of root tips growning with nitrate replicate 1


title: bulked RNAseq of root tips growning without nitrate replicate 2

source_name: root tips growning without nitrate


title: bulked RNAseq of root tips growning without nitrate replicate 1


title: Ileum_RYGB_rep1

description: Gene expression data from ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 1

source_name: Ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 1


title: TargetSeq_Sample_77

value: 293FT cells


title: Ileum_RYGB_rep4

description: Gene expression data from ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 4

source_name: Ileum tissue derived from rats treated RYGB bariatric surgery, biological replicate 4


title: Ileum_Sham_RYGB_rep1

description: Gene expression data from ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 1

source_name: Ileum tissue derived from rats treated with sham surgery for RYGB, biological replicate 1


title: TargetSeq_Sample_76

source_name: Cas9:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-Cas9:hLSP1,hHEK1,hEMX1,4 hLSP1_OT_sites;


title: ChIP_cNK_T-bet-2


title: DNase-seq_ILC1-2

value: Liver


title: DNase-seq_ILC2-1


title: DNase-seq_ILC2-2


title: TargetSeq_Sample_75


title: DNase-seq_ILC1-1


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS4 #F M_18_3206_1293_AD007

source_name: iPS

value: human induced pluripotent stem cell

value: XXY,47 KS

value: KS4 #F


title: Homo sapiens iPS XY,46 Bulk RNAseq KS4 #B M-19-3760_1845_AD020

description:
Homo sapiens iPS XY,46 Bulk RNAseq
Bulk RNAseq

value: KS4 #B


title: ChIP_Th1_T-bet-1

value: Naive CD4 T cell

tag: cell culture condition


title: TargetSeq_Sample_74


title: DNase-seq_LTi-1


title: DKO Lung RNA 4

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

description: RNA Seq

data_processing:
RNA-Seq were quality trimmed with trimgalore
and the reads were aligned to STAR mm10 genome
DESeq2 were used for differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: differential expression results

source_name: Lung ECs

growth_protocol: Mouse heart and lungs were perfused, excised, minced,  digested with type I collagenase, and then were mechanically disrupted and filtered  through a 70 um cell strainer to get a single cell suspension. Cells were immediately  stained for FACS analysis. CD31+/CD45- cells were isolated as endothelial cells for  downstream analyses.

extract_protocol:
Cell lysates were isolated using the Roche HighPure RNA isolation kit. 1ug of RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: VE-Cad Cre KLF2F/F KLF4F/F + Tamox

value: 2 months

value: Lung ECs


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq KS4 #G M_18_3203_1290_AD018

value: KS4 #G


title: TargetSeq_Sample_73

source_name: PE3:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-PE3-del:hLSP1,hHEK1,hEMX1,4 hLSP1_OT_sites;


title: DNase-seq_Vitro_Th17-1


title: Homo sapiens iPS XY,46 Bulk RNAseq KS4 #B M-19-3761_1846_AD021


title: DNase-seq_Vitro_Th17-2


title: DKO Lung RNA 2

description: RNA Seq


title: DKO Lung RNA 3

description: RNA Seq


title: DNase-seq_Vitro_Th1-1


title: TargetSeq_Sample_71


title: DKO Lung RNA 1

description: RNA Seq


title: DNase-seq_Vitro_Th2-1


title: TargetSeq_Sample_72


title: DNase-seq_Vitro_Th1-2


title: DNase-seq_Vitro_Th2-2


title: DNase-seq_Naive_CD4-1

source_name: Naïve CD4 T cell

value: lymph node


title: TargetSeq_Sample_70

source_name: hA3A-BE3:hRNF2,hFANCF,hSEC61B,4 hRNF2_OT_sites,4 hFANCF_OT_sites,4 hSEC61B_OT_sites;293FT-PE3-ins:hLSP1,hHEK1,hEMX1,4 hLSP1_OT_sites;


title: TargetSeq_Sample_69


title: DNase-seq_Naive_CD4-2


title: DNase-seq_cNK-1

value: cNK


title: Cre Lung RNA 4

description: RNA Seq

value: VE-Cad Cre


title: DNase-seq_cNK-2


title: Cre Lung RNA 3

description: RNA Seq


title: TargetSeq_Sample_68


title: Cre Lung RNA 2

description: RNA Seq


title: ATACseq_male_rep7

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

description: ATACseq

data_processing:
Adapters were trimmed from the raw reads using Trimmomatic version 0.39.
The raw reads were aligned to the hg19 genome using Bowtie2 version 2.3.4.2 using default parameters.
MACS2 v2.1.1.20160309 was used to call peaks using default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: bedGraph files were genarated from MACS2

source_name: Umbilical cord blood CD14+ monocyte

extract_protocol:
According to previously published ATAC-seq protocol (Buenrostro J, Wu B, Chang H, Greenleaf W. ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol, 2015, 109: 21.29.1-21.29.9).
According to previously published ATAC-seq protocol (Buenrostro J, Wu B, Chang H, Greenleaf W. ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol, 2015, 109: 21.29.1-21.29.9). Libraries were sequenced on an Illumina Novaseq S1 according to the manufacturer's instructions.

tag: Sex

value: Male

value: Neonate

value: Umbilical cord blood CD14+ monocyte


title: ATACseq_female_rep3

description: ATACseq

value: Female


title: ATACseq_male_rep6

description: ATACseq


title: ATACseq_male_rep5

description: ATACseq


title: ATACseq_male_rep4

description: ATACseq


title: Cre Lung RNA 1

description: RNA Seq

tag: genotype


title: ATACseq_male_rep3

description: ATACseq


title: ATACseq_female_rep2

description: ATACseq


title: ATACseq_male_rep2

description: ATACseq


title: TargetSeq_Sample_67

source_name: PE3-300ng+24h-4:hRNF2;PE3+_+103_nicking sgRNA-4:hSEC61B;PE3 del+_+104_nicking sgRNA-4:hLSP;

value: 293FT cells

value: 293FT-Apobec KO92-1-PE3-300ng+24h-4(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+103_nicking sgRNA-4(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+104_nicking sgRNA-4(Target_gene:hLSP);


title: ATACseq_male_rep1

description: ATACseq


title: Pol II Lung 2

data_processing:
Processed using TaRGET-II ATAC-Seq Pipeline
After initial quality checking with fastgc (0.11.90, we used TaRGET-II ATAC-Seq pipeline (https://github.com/Zhang-lab) for analysis. TaRGET-II includes quality trimming using cutadapt and trimmed reads (>36bp minimum alignment length) were mapped against the mm10 genome using BWA aligner. We used de-duplicated and uniquely mapped reads for peak calling analysis after excluding black-list regions defined by ENCODE. The candidate peaks were predicted by callpeak implemented in MACS2. We used predicted open chromatin peaks where at least two biological replicates were reproducible for the downstream analysis using an IDR cutoff of 0.05. We also applied limma based edgeR method to determine differentially accessible regions (DARs); cutoff: log2FC >1.0, CPM>2, p-value <0.01.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 for peakcalling

source_name: Heart ECs

extract_protocol:
Flow-sorted endothelial cells were fixed using 1% formaldehyde. 200,000 cells were lysed and frozen in 100ul SDS lysis buffer (50mM Tris/HCl, 0.5% SDS, and 10mM EDTA) supplemented with 1x cOmplete EDTA-free protease inhibitor (Roche) (n=3 mice of each genotype, n=6 for heart H3K27ac). For ChIP-seq, anti-FLAG (Cell Signaling Technologies, #8146), anti-Pol II (Sigma, 05-623), anti-p300 (Cell Signaling Technologies, 54062), or anti-H3K27ac (Abcam, ab4729) antibodies were added to Protein A/G-coupled Dynabeads (Bimake, B23202) in PBS with 0.5% BSA and incubated with rotation for 4hr at 4 degrees. For 100,000-150,000 cells, 25 ul of beads were incubated with 5ug antibody per ChIP. Aliquots were diluted with SDS lysis buffer and 100 ul containing the appropriate number of cells were processed. Cells were sonicated for 12 cycles of 30s on/30s off on high power using a Bioruptor Pico (Diagenode). To neutralize the SDS, Triton-X-100 was added to a final concentration of 1% along with 50x cOmplete protease inhibitor (final concentration: 1x). Samples were incubated at room temperature for 10min and 5% aliquots were saved for preparation of input controls. Antibody-coated Dynabeads were washed with PBS and mixed with cell lysate and incubated overnight at 4 degrees with rotation. Immunoprecipitated chromatin was washed with 150ul low-salt buffer (50mM Tris/HCl, 150mM NaCl, 0.1% SDS, 0.1% NaDOC, 1% Triton-X-100, and 1mM EDTA), high-salt buffer (500mM NaCl), and LiCl buffer (10mM Tris/HCl, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% NaDOC, and 1mM EDTA), followed by two washes with TE buffer and two washes with ice cold Tris/HCl (pH 8, 10mM). For tagmentation, bead-bound chromatin was resuspended in 30ul of tagmentation buffer, 1ul of transposase (Nextera, Illumina) was added and samples were incubated at 37 degrees for 10min, followed by two washses with low-salt buffer. For standard reverse crosslinking, chromatin complexes were diluted with 200ul ChIP elution buffer (10mM Tris/HCl, 0.5% SDS, 300mM NaCL, and 5mM EDTA) and 2ul of 20ug/ml proteinase K (Thermo Scientific). Samples were vortexed and incubated overnight at 65 degrees. After reverse crosslinking, 1 ul 20ug/ml RNase (Sigma) was added and incubated at 37 degrees for 30min. DNA purification was carried out using Qiagen MinElute PCR Purification Kit.
15ul of PCR master mix and 5ul of primer mix (Nextera, Illumina) were added to 20ul of eluted DNA and libraries were amplified. After PCR amplification, library cleanup was done using Agencourt AmPureXP eads (Beckman Coulter) at a ratio of 1:1. DNA concentrations in purified samples were measured using the Qubit dsRNA HS Kit (Invitrogen). Libraries were pooled and single-end sequenced (50 cycles) using the NextSeq500 platform (Illumina). Analysis was performed as described in the ATAC-seq pipeline

value: WT C57bl/6J

tag: chip target

value: Pol II ChIP Seq


title: ATACseq_female_rep1

description: ATACseq


title: Pol II Lung 3


title: TargetSeq_Sample_64

source_name: PE3-300ng+24h-1:hRNF2;PE3+_+103_nicking sgRNA-1:hSEC61B;PE3 del+_+104_nicking sgRNA-1:hLSP;

value: 293FT-Apobec KO92-1-PE3-300ng+24h-1(Target_gene:hRNF2);293FT-Apobec KO92-1-PE3+_+103_nicking sgRNA-1(Target_gene:hSEC61B);293FT-Apobec KO92-1-PE3 del+_+104_nicking sgRNA-1(Target_gene:hLSP);


title: NCI-H510A siSCRAMBLED LURBI rep1

city: Colmenar Viejo

first: Javier

middle: Díez

last: Pérez

state: Madrid

address: Avda. De los Reyes, 1

department: I+D

country: Spain

institute: Pharma Mar

data_processing:
Processed using nf-core RNA-Seq pipeline v1.3.3
Alingment with  HISAT 2.1.0
Read count with Subread featureCounts v1.6.4
DEG analisyed with Deseq2 from featurecounts matrix
FPKM calculated with Stringtie 1.3.5
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: Cell lines were cultured in Waymouth’s medium (DMS‑53) or RPMI medium (NCI‑H82 and NCI‑H510A and supplemented with 10%FBS, 2nmol/L L-glutamine, and penicillin-streptomycin mix.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer’s recommendations.
Total RNA was extracted from cells using the RNeasy kit (Qiagen, Germantown, MD). On-column DNase treatment was given following the procedure provided by the manufacturer.  Strand-specific library was prepared using Illumina TruSeq stranded RNA library prep kit (Illumina, San Diego, CA) according to manufacturer’s protocols.

treatment_protocol: DMS-53, NCI-H82 and NCI-H510A cells were treated with 50 nM of lurbinectedin, 50nM of cisplatin or 20µM cisplatin for 4 hours.

value: cell line

value: LURBINECTEDIN

tag: dose


title: NCI-H510A siSCRAMBLED UNTREATED rep2

value: UNTREATED


title: NCI-H510A siSCRAMBLED LURBI rep2


title: Pol II Lung 1

value: 2 months

value: Lung ECs


title: OCI-Ly18 - CAR19 AND DMSO treatment

city: Philadelphia

first: Puneeth

last: Guruprasad

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
The median absolute deviation (MAD)-based definition of outliers was used to remove putative low-quality cells from the dataset. Here, any cells with fewer than 200 expressed genes, with an unusually high number of unique molecular identifier counts (above 3 M.A.D.s), or with high mitochondrial RNA expression (above 3 MADs) were discarded from downstream analysis
To compare the OCI-Ly18 cells between the two treatment conditions, the two libraries from the CART19 and CART19 + venetoclax samples were first merged and batch-corrected using the IntregrateData function in Seurat. The data were normalized and scaled using the NormalizeData and ScaleData functions. Variable features were identified using the FindVariableGenes function, and the principal components were calculated using the RunPCA function. An elbow plot, generated from the ElbowPlot function, determined the number of significant principal components (PCs) required for cell clustering. The top 15 PCs were used to drive unsupervised clustering analysis via uniform manifold and approximation (UMAP) using the RunUMAP function (resolution = 0.4).
To determine differentially expressed genes (DEGs) between the two treatment conditions for each cluster, the FindMarkers function was used with threshold values of min.pct = 0.1 and log fold change = 0.25. Gene Ontology gene sets were downloaded from the MSigDB Database, and pathway analysis was performed in R using the gseGO function under default parameters
Gene Set Enrichment Analysis (GSEA) was performed using the clusterProfiler interface 79. The CellCycleScoring function was also used to confirm a phase of cell cycle to each cluster in the UMAP
Genome_build: Feature-barcode matrices were obtained after aligning reads to the pre-built GRCh38 human reference genome.
Supplementary_files_format_and_content: Normalized Counts Matrices

source_name: Diffuse large B cell lymphoma (DLBCL) cell line

growth_protocol: Cells were grown and cultured at a concentration of 1x106 cells/mL of standard culture media (RPMI 1640 + 10% FBS, 1% penicillin/streptomycin, 1% HEPES, 1% GlutaMAX) at 37°C in 5% ambient CO2

extract_protocol:
Subcutaneous tumor xenografts of OCI-Ly18 were resected from two mice on day 14 of treatment with either CART19 (Sample 1) or CART19 + Venetoclax (Sample 2). Resected tumors were minced and dissociated into single-cell suspensions using a 0.45 µm filter
Libraries for single-cell RNA sequencing were prepared using the Chromium Single Cell 5' Reagent Kit with v1.1 Chemistry (10x Genomics) according to the manufacturer's instructions. After library construction, both libraries were sequenced together on the Illumina NovaSeq 6000. The raw scRNA-seq data were pre-processed using the Cell Ranger software (version 5.0.1) (10x Genomics). Feature-barcode matrices were obtained after aligning reads to the pre-built GRCh38 human reference genome. Filtered gene expression was processed using the Seurat package (version 4.0.1)

treatment_protocol: 5e6 OCI-Ly18 cells were subcutaneously injected into the right flank of 100-200 mm3. CAR19 cells were thawed overnight prior to infusion (2.5e6 CAR+ T cells per mouse), and the mouse treated with Venetoclax received 50mg/kg/day of Venetoclax through oral gavage for 14 days.

tag: host

value: NSG murine model

value: OCI-Ly18 tumor

value: CAR19 AND DMSO


title: OCI-Ly18 - CAR19 AND Venetoclax treatment

value: CAR19 AND Venetoclax


title: iPSC-derived HLC standard protocol_rep5

description:
Included only in UMAP analysis
figS4BC_raw_counts.csv [12039]
figS4BC_DGE.csv

source_name: human iPSC

value: iPSC-derived HLC