title: 12K MPRA experiment on AML12 (5prime library, AML12, rep 2, Plasmid)

data_processing:
For the 5' enhancer-barcode assignments eads were first processed with fastqc (v0.11.8) to assess their quality, and then trimmed using cutadapt witih options -g TGTCCCCAGTGCAAGTGCAG --discard-untrimmed -m 12 -l 12 for read 1 to extract the enhancer barcode and options -g AATTAATTCGGGCCCCGGTCC...GATCGGCGCGCCTGCTCG -j 10 --discard-untrimmed -m 17 -M 17 for read 2 to extract the plasmid barcode. For read 2, we then used seqkit (v0.10.2), with options seq -r -p, to get the reverse complement sequence. Reads were filtered to keep only those with quality > 30 using fastp (v0.20.0). This resulted in 8,835,050 enhancer-barcode assignments for the 5’ 12K library, with 78.3% barcodes assigned to a unique enhancer. For the 3' enhancer-barcode assignments, Raw signal fast5 files were re-basecalled using Guppy v6.0.7 using the super-accuracy model (dna_r10.4_e8.1_sup). To process the reads, we first generated a synthetic genome consisting of the plasmid sequence (with 100bp flanks) with all possible enhancers inserted. Reads were mapped using minimap2 (v2.22) with options -ax map-ont –secondary=no -N 1 -f 500 and a bam file was generated using SAMTools (v1.11). Next, we used the R package GenomicAlignments (v1.24.0) to extract the sequences overlapping the enhancer sequence and the enhancer barcodes from the reads and calculate the number of mismatches. This resulted in a librariy with 723,805 nique enhancer-barcode assignments, with 85.5% barcodes assigned to a unique enhancer. CHEQ-seq barcodes were extracted from the plasmid and cDNA samples (read 2) using cutadapt with parameters with options  -g TTATCATGTCTGCTCGAAGC...GATCGGCGCGCCTGCTCG --discard-untrimmed -m 17 -M 17 and seqkit (v0.10.2), with options seq -r -p, was used to get the reverse complement sequence. Reads were filtered to keep only those with quality > 30 using fastp (v0.20.0). Reads were assigned to enhancers based on the corresponding enhancer-barcode assignments, resulting in a count matrix with number of reads per enhancer and sample.
Assembly: mm10
Supplementary files format and content: AML12_MPRA/processed/AML12_MPRA_counts.tsv.gz:  Tab separated file containing bulk MPRA samples as columns, tested enhancers as rows and assigned reads per sample as value.
Library strategy: CHEQ-seq

growth_protocol: Culture of AML12 cells: The AML12 cell line was purchased from ATCC (CRL-2254).  AML12 cells were cultured in DMEM-F12 medium. All media were supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 50 µg/mL penicillin/streptomycin (Thermo Fisher Scientific).  Cell cultures were kept at 37°C, with 5% CO2.

extract_protocol:
Enhancer library cloning: The pSA293-CHEQseq plasmid (Addgene 174669), containing a SCP1 promoter, a chimeric intron and the Venus cDNA, was used as a reporter plasmid for MPRA. Two different versions of that plasmid were used for the cloning of the 12k library: pSA293-CHEQseq-5’BC contains a random 17 bp barcode (BC) upstream of the chimeric intron and pSA293-CHEQseq-3’BC-1 contains a random 17 bp BC between the Venus and the poly(A) tail. The oligonucleotide libraries were resuspended according to the manufacturer’s recommendation and amplified via PCR with the primers ‘CHEQ_liver_For’ and ‘CHEQ_liver_Rev’. To clone the amplified enhancer library upstream of the SCP1 promoter, the vectors were linearized via inverse PCR with primers ‘CHEQ_lin_For’ and ‘CHEQ_lin_Rev’. Amplified libraries and the corresponding linearized vector were combined in an NEBuilder reaction with a vector to insert ratio of 1:5. The NEBuilder reactions were dialyzed against water in a 6 cm Petri dish with a membrane filter MF-Millipore 0.05 µm (Merck, Kenilworth, NJ) for 1 hr. Reactions were recovered from the membrane, and 2.5 µL of the reaction was transformed into 25 µL of Lucigen Endura ElectroCompetent Cells (Biosearch Technologies, Hoddesdon, UK). Before culture for maxiprep, 1:100,000 of the transformed bacteria was plated on an LB-agar dish with carbenicillin to estimate the complexity of the cloned library. A volume of bacteria corresponding to a complexity of 500 BCs per enhancer was put in culture for maxiprep. Maxiprep was performed with the Nucleobond Xtra endotoxin-free maxiprep kit (Macherey-Nagel). Bulk MPRA in vitro: The MPRA libraries were transfected in HepG2 cells by use of the Lipofectamine 3000 reagent (Thermo Fisher Scientific). Briefly, 4 million HepG2 cells were seeded in a 10 cm cell culture dish. The next day, when cells reach 70-90% confluency, a tube A with 500 µL opti-MEM (Thermo Fisher Scientific) and 25 µL Lipofectamine 3000 reagent and a tube B with 500 µL opti-MEM and 15 µL of the liver enhancer library were prepared and incubated for 5 min at RT. Tube B was mixed carefully with tube A and incubated for 15 min at RT. The medium of the HepG2 cells was also changed to opti-MEM medium and finally the mixture was added dropwise to the cells. 48 hours post-transfection, cells were detached from the plate using trypsin (Thermo Fisher Scientific). One-fifth of the cells was used for plasmid DNA extraction (Qiagen). The remaining cells were used for RNA extraction using the innuPREP RNA Mini Kit 2.0 (Analytik Jena), followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion) and cDNA synthesis using the GoScript RT Kit and oligo dT primer (Promega). To amplify the random 5’ and 3’ BC from the plasmid DNA or cDNA sample, a PCR was performed for 16 cycles with ‘CHEQseq_barcode_5’_For’, ‘CHEQseq_barcode_5’_Rev’ and ‘CHEQseq_barcode_3’_For’, ‘CHEQseq_barcode_3’_Rev’, respectively. To add Illumina sequencing adaptors, all samples were finally amplified by PCR for 6 cycles with the primers ‘i5_Indexing_For’ and ‘i7_Indexing_Rev. Bulk MPRA in vivo: For intrahepatic delivery of the liver MPRA libraries, 8 to 10-week-old mice were secured and hydrodynamically injected with 20 µg of the libraries via the lateral tail vein. All libraries were diluted in sterile filtered 0.9% NaCl, and the total volume was adjusted to 10% (in mL) of the total body weight (in grams). 24 hours post-injection, mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50 mg/kg) and whole livers were isolated. Liver tissues were homogenized by using M tubes (Miltenyi Biotec) and the GentleMACS Dissociator (Miltenyi Biotec). RNA and plasmid DNA extraction, mRNA purification and cDNA prep, and barcode amplification, were done as described for MPRA in vitro.
For the liver library cloned in the pSA293-CHEQseq-5’BC plasmid, a PCR amplification (12 cycles) of the enhancer, together with the random BC, was done with the primers ‘Enh_BC_5’_For’ and ‘Enh_BC_5’_Rev'. Illumina sequencing adaptors were added during a second round of PCR with the primers ‘i5_Indexing_For’ and ‘i7_Indexing_Rev’. Before sequencing, the fragment size of every library was analyzed using the Bioanalyzer high-sensitivity chip. All libraries were sequenced on a NextSeq2000 instrument (Illumina) with the following sequencing parameters: 51 bp read 1 – 8 bp index 1 – 8 bp index 2 – 51 bp read 2. For the liver libraries cloned in the pSA293-CHEQseq-3’BC plasmids, we performed Nanopore sequencing as follows. A total of 1.5 µg of the library was linearized by digestion with NcoI according to the manufacturer’s protocol. We next processed 200 ng of the cleaned up and linearized plasmid with an Oxford Nanopore Technologies Q20+ ligation sequencing kit early-access SQK-LSK112 following the manufacturer’s protocol (Genomic DNA by Ligation; revision GDE_9141_v112_revC_01Dec2021). A total amount of 10 fmol of the prepared library was loaded onto a MinION R10.4 flow cell and sequenced for at least 72 hr (MinKNOW ≥ v21.11.09).


title: 12K MPRA experiment on AML12 (5prime library, AML12, rep 2, cDNA)

status: Public on Sep 07 2023

type: SRA

city: Leuven

first: Carmen

last: Bravo Gonzalez-Blas

address: Herestraat 49

country: Belgium

institute: VIB-KU Leuven Center for Brain & Disease Research

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue


title: Bulk ATAC-seq on Hepa16

data_processing:
Adapters were removed with fastq-mcf (ea-utils v1.12), cleaned reads were mapped to the hg19 (HepG2) or mm10 (AML12 and Hepa16) genome  using Bowtie2 (v2.3.5.1) and and bigwig files were generated using deepTools bamCoverage function (v3.5.0, with --normalizeUsing CPM --binSize 1 as parameters). Coverage heatmaps were done using deepTools (v3.5.0).
Assembly: hg19 for HepG2 and mm10 for AML12 and Hepa16
Supplementary files format and content: CLE__e257b6__27092021_HepG2wt_OmniATAC_S4_q4_sorted.bw: Bigwig containing HepG2 ATAC-seq profile. MLV__babe04__OmniATAC_Hepa1-6_S3_q4_sorted.bw: Bigiwg containing Hepa16 ATAC-seq profile. CLE__77d534__27092021_AML12wt_OmniATAC_S3_q4_sorted.bw:  Bigwig containing AML12 ATAC-seq profile.
Library strategy: OmniATAC-seq

extract_protocol:
The HepG2, Hepa1-6 and AML12 cell lines were purchased from ATCC (HB-8065, CRK-1830 and CRL-2254, respectively). HepG2 cells were cultured in Eagle’s Minimum Essential Medium (EMEM, Thermo Fisher Scientific), Hepa1-6 cells were clustered in Dulbecco’s Modified Eagle’s Medium (DMEM), and AML12 in DMEM-F12 medium. All media were supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 50 µg/mL penicillin/streptomycin (Thermo Fisher Scientific).  Cell cultures were kept at 37°C, with 5% CO2.
Omni-assay for transposase-accessible chromatin using sequencing (OmniATAC-seq) was performed as described previously. Briefly, 50,000 cells obtained after FACS were resuspended in 50 µL of cold ATAC-seq resuspension buffer (RSB; 10 mM TrisHCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 µL of transposition mix (25 µL 2x TD buffer, 2.5 µL transposase (Nextera Tn5 transposase, Illumina), 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermoblock. Reactions were cleaned-up by MinElute (Qiagen). Transposed DNA was amplified with primers 'i5_Indexing_For’ and ‘i7_Indexing_Rev’ (Supplementary Table 4). Number of PCR cycles was based on quantitative real-time PCR as described previously. All libraries were sequenced on a NextSeq2000 instrument (Illumina) with the following sequencing parameters: 51 bp read 1 – 8 bp index 1 – 8 bp index 2 – 51 bp read 2.


title: Input for Tbx3 ChIP-seq experiment

data_processing:
Reads were mapped to the mm10 genome using Bowtie2 (v2.3.5.1), peaks were called with MACS2 (v2.2.7.1, with --format BAM --gsize mm --qvalue 0.01 --call-summits as options) and bigwig files were generated using deepTools bamCoverage function (v3.5.0, with --normalizeUsing CPM --binSize 1 as parameters).
Assembly: mm10
Supplementary files format and content: MLV__0a3a08__ChIPseq_mouse_hepatocytes_anti-TBX3_Bethyl_rabbit_S29_q4_sorted.bw: Bigwig containing Tbx3 ChIP-seq profile. MLV__232339__ChIPseq_mouse_hepatocytes_input_S31_q4_sorted.bw: Bigiwg containing input ChIP-seq profile. MLV__0a3a08__ChIPseq_mouse_hepatocytes_anti-TBX3_Bethyl_rabbit_S29_VS_CONTROL_peaks.narrowPeak: MACS narrowPeak file.

source_name: Liver (P56)

extract_protocol:
For intrahepatic delivery of the liver MPRA libraries, 8 to 10-week-old mice were secured and hydrodynamically injected with 20 µg of the libraries via the lateral tail vein. All libraries were diluted in sterile filtered 0.9% NaCl, and the total volume was adjusted to 10% (in mL) of the total body weight (in grams). 48 hours post-injection, mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50 mg/kg). Livers were perfused for 5 minutes with 40 mL of perfusion medium SC-1 (8 g/L Nacl, 400 mg/L KCl, 75.5 mg/L NaH2PO4, 120.5 mg/L Na2HPO4, 2,38 g/L HEPES, 350 mg/L NaHCO3, 190 mg/L EGTA, 900 mg/L D-(+)-Glucose, 1.2 mL Phenol Red solution) to remove the blood, followed by perfusion with 40 mL of SC-2 medium (8 g/L Nacl, 400 mg/L KCl, 75.5 mg/L NaH2PO4, 120.5 mg/L Na2HPO4, 2,38 g/L HEPES, 350 mg/L NaHCO3, 560 mg/L CaCl2.2H2O, 1.2 mL Phenol Red solution) containing 10 mg of collagenase P (Merck) for 5 minutes. Each lobe was dissected off and minced into small pieces in a beaker containing 39 mL SC-2 supplemented with 1 mL DNase I (Sigma-Aldrich) and 20 mg collagenase P, followed by rotating incubation for 15 min at 37°C. Hepatocytes were centrifuged for 2 min at 50 g, washed with PBS, centrifuged again for 2 min at 50 g, resuspended in 3 ml Hoechst buffer (DMEM + 10% FBS + 10 mM HEPES) and filtered through a 70 µm strainer.
ChIP-seq was performed by following the Myers Lab ChIP-seq Protocol v011014 on 2x107 hepatocytes. Bethyl rabbit anti-TBX3 Ab (Sanbio A303-098A) was used for ChIP. 10 ng of immunoprecipitated DNA was used to perform library preparation according to the Illumina TruSeq DNA Sample preparation guide. Briefly, the immunoprecipitated DNA was end-repaired, A-tailed, and ligated to diluted sequencing adapters (1/100). After PCR amplification (18 cycles) and bead purification (Agencourt AmpureXP, Analis), the libraries with fragment size of 300-500 bp were sequenced using the NextSeq2000 (Illumina).

value: Liver (P56)

tag: genotype

tag: chip antibody


title: PML knockdown, MDA231, rep2

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

library_source: transcriptomic

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine.
Sequencing adapters were removed using trimmomatic v0.39.
Trimmed sequence reads were mapped to the human genome assembly GRCh38 (hg38) using the STAR aligner v2.5.3a.
Annotation of genomic features was performed using the featureCounts tool v1.6.4 using the GENCODE v31 Gene transfer format (GTF). Differential gene expression was evaluated in R/BioConductor using the DeSeq2 package.
Assembly: hg38
Supplementary files format and content: tab delimited text of normalized counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was isolated using the RNAeasy mini kit (Qiagen)
RNA libraries were prepared using the TruSeq stranded mRNA protocol (Illumina).

treatment_protocol: Silencing of PML was performed via lentiviral shRNA

tag: cell line

tag: cell type

value: Human breast cancer

value: PML knockdown

tag: treatment

value: shPML


title: KPC organoid Il1b stimulation 72h RNA-seq replicate 1

city: Milano

first: Renato

last: Ostuni

address: Via Olgettina 58

institute: San Raffaele Telethon Institute for Gene Therapy

description:
Smart-seq2
Organoids_KPC_IL1B_72h_Sample1
Organoids_KPC_counts_matrix.csv.gz

data_processing:
Reads were aligned using STAR aligner (v STAR_2.5.3a). Read counts matrices were computed using the featureCounts function from Rsubread package (v 2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-separated counts file (gzipped format)

molecule: polyA RNA

source_name: KPC organoid Il1b stimulation 72h

growth_protocol: KC (DT6606) and KPC (K8484) cell lines were previously established from tumors arising in genetically engineered mouse models carrying the G12D oncogenic mutation in the Kras gene (KrasLSL-G12D/+;Pdx1Cre/WT for KC) and the missense point R720H mutation in the Tpr53 gene (KrasLSL-G12D/+;Tpr53LSL-R270H/+;Pdx1Cre/WT for KPC) and were cultured under standard conditions. KPC organoids were previously established from tumors arising in KPC genetically engineered mouse model (Kras+/LSLG12D Trp53fl/f lp48+/Cre) and were cultured following already published protocols.

extract_protocol:
Total RNA was purified using the ReliaPrep RNA Cell Miniprep System.
RNA-Seq libraries were generated using the Smart-seq2 method with minor modification. Briefly, five ng of RNA were retrotranscribed, cDNA was PCR-amplified (15 cycles) and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 minutes at 55°C and the enrichment PCR was carried out using 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0, assessed for fragment size distribution on an Agilent 4200 TapeStation system.

treatment_protocol: KC and KPC cells were stimulated with IL-1b (10 ng/mL) for 24, 48 or 96 hours. KPC organoids were stimulated with IL-1b (10 ng/mL) for 8, 24, 48 or 72 hours. Controls were left untreated.

tag: strain

value: PDAC tumor organoids

value: Kras+/LSLG12D Trp53fl/f lp48+/Cre

value: IL-1b (10 ng/mL)

tag: time


title: PML knockdown, MDA231, rep1


title: 12K MPRA experiment on AML12 (5prime library, AML12, rep 1, Plasmid)


title: Tbx3 ChIP-seq

value: Bethyl rabbit anti-TBX3 Ab (Sanbio A303-098A)


title: KPC organoid control 48h RNA-seq replicate 1

description:
Smart-seq2
Organoids_KPC_UT_48h_Sample1
Organoids_KPC_counts_matrix.csv.gz

source_name: KPC organoid control 48h

value: untreated


title: KPC organoid control 48h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_UT_48h_Sample2
Organoids_KPC_counts_matrix.csv.gz


title: 10x multiome (RNA) on the mouse liver (rep 2)

data_processing:
The generated fastq files were processed with cellranger-arc (v1.0.0) count function, with include introns =True option. Reads were aligned to Mus musculus reference genome (ata-cellranger-arc-mm10-2020-A-2.0.0).
Data was processed as the other multiome samples and combined with the other multiome samples and analyzed using VSN-pipelines (for the snRNA-seq layer) and pycisTopic (for the scATAC-seq layer, using 100 topics).
Assembly: mm10
Supplementary files format and content: TEW__872466__dedf23__Multiome_Liver_CTRL1_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample CTRL1
Supplementary files format and content: TEW__95843a__0f8200__Multiome_Liver_CTRL2_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample CTRL2
Supplementary files format and content: multiome_validation_rna_counts.tsv.gz: tab seperated flat text file containing genes as rows, cells as columns and counts for each gene in each cell as values.
Library strategy: Single-cell Multiome (10X Genomics)

extract_protocol:
We used a modified protocol from the Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (CG000375) from 10x Genomics. Briefly, 100 mg of fresh mouse liver tissue was chopped and transferred to a Dounce homogenizer cylinder containing 1 mL of ice-cold homogenization buffer (10 mM NaCl, 10 mM Tris 7.4, 3 mM MgCl2, 0,1% IGEPAL CA-63, 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)). The tissue was homogenized with 5 strokes of pestle A and 10 strokes of pestle B until a homogeneous nuclei suspension was achieved. The resulting homogenate was filtered through a 70-μm cell strainer (Corning). The homogenizer and the filter were rinsed with an additional 0.5 μL of homogenization buffer. The tissue material was spun down at 500 x g for 5 min and the supernatant was discarded. The tissue pellet was resuspended in wash buffer (1% BSA in PBS + 1 U/µlL of Protector RNase inhibitor (Sigma)). Nuclei were stained with 7AAD (Thermo Fisher Scientific) and viability sorted on a BD FACS Fusion into 5 mL low bind Eppendorf tube containing BSA with RNase inhibitor. The sorted nuclei were spun down at 500 x g for 5 min and the supernatant was discarded. Next, the nuclei were permeabilized by resuspending the pellet in 0.1x lysis buffer (10 mM NaCl, 10 mM Tris 7.4, 3 mM MgCl2, 0.1% IGEPAL CA-63, 0.01% Digitonin, 1% BSA, 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)) and incubated on ice for 2 min. 1 mL Wash Buffer (10 mM NaCl, 10 mM Tris 7.4, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)) was added. The nuclei were spun down at 500 x g for 5 min and the supernatant was discarded. The nuclei pellet was resuspended in diluted nuclei buffer (1x Nuclei buffer Multiome kit (10x Genomics)), 1 mM DTT, 1 U/µL of Protector RNase inhibitor (Sigma)).
Single-nuclei libraries were generated using the 10x Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocol. In brief, the single mouse liver nuclei were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanolitre-scale gel bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 37°C for 45 min, 25°C for 30 min and hold at 4°C. Incubation of the GEMs produced 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). Next quenching reagent (Multiome 10x kit) was used to stop the reaction. After quenching, single-cell droplets were dissolved, and the transposed DNA and full-length cDNA were isolated using Cleanup Mix containing Silane Dynabeads. To fill gaps and generate sufficient mass for library construction, the transposed DNA and cDNA were amplified via PCR: 72°C for 5 min; 98°C for 3 min; 7 cycles of 98°C for 20 s, 63°C for 30 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. The pre-amplified product was used as input for both ATAC library construction and cDNA amplification for gene expression library construction. Illumina P7 sequence and a sample index were added to the single-strand DNA during ATAC library construction via PCR: 98°C for 45 s; 7-9 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready ATAC-seq library was cleaned up with SPRIselect beads (Beckman Coulter). Barcoded, full-length pre-amplified cDNA was further amplified via PCR: 98°C for 3 min; 6-9 cycles of 98°C for 15 s, 63°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end- repaired, A-tailed and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 5-16 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s. 72°C for 1 min; and hold at 4°C. The sequencing-ready GEX library was cleaned up with SPRIselect beads. Before sequencing, the fragment size of every library was analyzed using the Bioanalyzer high-sensitivity chip. All 10x Multiome ATAC libraries were sequenced on NextSeq2000 instruments (Illumina) with the following sequencing parameters: 50 bp read 1 – 8 bp index 1 (i7) – 16 bp index 2 (i5) - 49 bp read 2. All 10x Multiome GEX libraries were sequenced on NovaSeq6000 instruments with the following sequencing parameters: 28 bp read 1 – 10 bp index 1 (i7) – 10 bp index 2 (i5) – 75 bp read 2.


title: 12K MPRA experiment on HepG2 (3prime library, rep 2, cDNA)

data_processing:
For the 5' enhancer-barcode assignments reads were first processed with fastqc (v0.11.8) to assess their quality, and then trimmed using cutadapt with options -g TGTCCCCAGTGCAAGTGCAG --discard-untrimmed -m 12 -l 12 for read 1 to extract the enhancer barcode and options -g AATTAATTCGGGCCCCGGTCC...GATCGGCGCGCCTGCTCG -j 10 --discard-untrimmed -m 17 -M 17 for read 2 to extract the plasmid barcode. For read 2, we then used seqkit (v0.10.2), with options seq -r -p, to get the reverse complement sequence. Reads were filtered to keep only those with quality > 30 using fastp (v0.20.0). This resulted in 8,835,050 enhancer-barcode assignments for the 5’ 12K library, with 78.3% barcodes assigned to a unique enhancer. For the 3' enhancer-barcode assignments, Raw signal fast5 files were re-basecalled using Guppy v6.0.7 using the super-accuracy model (dna_r10.4_e8.1_sup). To process the reads, we first generated a synthetic genome consisting of the plasmid sequence (with 100bp flanks) with all possible enhancers inserted. Reads were mapped using minimap2 (v2.22) with options -ax map-ont –secondary=no -N 1 -f 500 and a bam file was generated using SAMTools (v1.11). Next, we used the R package GenomicAlignments (v1.24.0) to extract the sequences overlapping the enhancer sequence and the enhancer barcodes from the reads and calculate the number of mismatches. This resulted in a library with 723,805 unique enhancer-barcode assignments, with 85.5% barcodes assigned to a unique enhancer. CHEQ-seq barcodes were extracted from the plasmid and cDNA samples (read 2) using cutadapt with parameters with options -g TTATCATGTCTGCTCGAAGC...GATCGGCGCGCCTGCTCG --discard-untrimmed -m 17 -M 17 and seqkit (v0.10.2), with options seq -r -p, was used to get the reverse complement sequence. Reads were filtered to keep only those with quality > 30 using fastp (v0.20.0). Reads were assigned to enhancers based on the corresponding enhancer-barcode assignments, resulting in a count matrix with number of reads per enhancer and sample.
Assembly: mm10
Supplementary files format and content: 12K_MPRA_counts.tsv: Tab-separated text file containing bulk MPRA samples as columns, tested enhancers as rows and assigned reads per sample as value.
Library strategy: CHEQ-seq

growth_protocol: Culture of HepG2 cells: The HepG2 cell line was purchased from ATCC (HB-8065). HepG2 cells were cultured in Eagle’s Minimum Essential Medium (EMEM, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 50 µg/mL penicillin/streptomycin (Thermo Fisher Scientific). Cell cultures were kept at 37°C, with 5% CO2.

extract_protocol:
Enhancer library cloning: The pSA293-CHEQseq plasmid (Addgene 174669), containing a SCP1 promoter, a chimeric intron and the Venus cDNA, was used as a reporter plasmid for MPRA. Two different versions of that plasmid were used for the cloning of the 12k library: pSA293-CHEQseq-5’BC contains a random 17 bp barcode (BC) upstream of the chimeric intron and pSA293-CHEQseq-3’BC-1 contains a random 17 bp BC between the Venus and the poly(A) tail. The oligonucleotide libraries were resuspended according to the manufacturer’s recommendation and amplified via PCR with the primers ‘CHEQ_liver_For’ and ‘CHEQ_liver_Rev’. To clone the amplified enhancer library upstream of the SCP1 promoter, the vectors were linearized via inverse PCR with primers ‘CHEQ_lin_For’ and ‘CHEQ_lin_Rev’. Amplified libraries and the corresponding linearized vector were combined in an NEBuilder reaction with a vector to insert ratio of 1:5. The NEBuilder reactions were dialyzed against water in a 6 cm Petri dish with a membrane filter MF-Millipore 0.05 µm (Merck, Kenilworth, NJ) for 1 hr. Reactions were recovered from the membrane, and 2.5 µL of the reaction was transformed into 25 µL of Lucigen Endura ElectroCompetent Cells (Biosearch Technologies, Hoddesdon, UK). Before culture for maxiprep, 1:100,000 of the transformed bacteria was plated on an LB-agar dish with carbenicillin to estimate the complexity of the cloned library. A volume of bacteria corresponding to a complexity of 500 BCs per enhancer was put in culture for maxiprep. Maxiprep was performed with the Nucleobond Xtra endotoxin-free maxiprep kit (Macherey-Nagel). Bulk MPRA in vitro: The MPRA libraries were transfected in HepG2 cells by use of the Lipofectamine 3000 reagent (Thermo Fisher Scientific). Briefly, 4 million HepG2 cells were seeded in a 10 cm cell culture dish. The next day, when cells reach 70-90% confluency, a tube A with 500 µL opti-MEM (Thermo Fisher Scientific) and 25 µL Lipofectamine 3000 reagent and a tube B with 500 µL opti-MEM and 15 µL of the liver enhancer library were prepared and incubated for 5 min at RT. Tube B was mixed carefully with tube A and incubated for 15 min at RT. The medium of the HepG2 cells was also changed to opti-MEM medium and finally the mixture was added dropwise to the cells. 48 hours post-transfection, cells were detached from the plate using trypsin (Thermo Fisher Scientific). One-fifth of the cells was used for plasmid DNA extraction (Qiagen). The remaining cells were used for RNA extraction using the innuPREP RNA Mini Kit 2.0 (Analytik Jena), followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion) and cDNA synthesis using the GoScript RT Kit and oligo dT primer (Promega). To amplify the random 5’ and 3’ BC from the plasmid DNA or cDNA sample, a PCR was performed for 16 cycles with ‘CHEQseq_barcode_5’_For’, ‘CHEQseq_barcode_5’_Rev’ and ‘CHEQseq_barcode_3’_For’, ‘CHEQseq_barcode_3’_Rev’, respectively. To add Illumina sequencing adaptors, all samples were finally amplified by PCR for 6 cycles with the primers ‘i5_Indexing_For’ and ‘i7_Indexing_Rev. Bulk MPRA in vivo: For intrahepatic delivery of the liver MPRA libraries, 8- to 10-week-old mice were secured and hydrodynamically injected with 20 µg of the libraries via the lateral tail vein. All libraries were diluted in sterile filtered 0.9% NaCl, and the total volume was adjusted to 10% (in mL) of the total body weight (in grams). 24 hours post-injection, mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50 mg/kg) and whole livers were isolated. Liver tissues were homogenized by using M tubes (Miltenyi Biotec) and the GentleMACS Dissociator (Miltenyi Biotec). RNA and plasmid DNA extraction, mRNA purification and cDNA prep, and barcode amplification, were done as described for MPRA in vitro.
For the liver library cloned in the pSA293-CHEQseq-5’BC plasmid, a PCR amplification (12 cycles) of the enhancer, together with the random BC, was done with the primers ‘Enh_BC_5’_For’ and ‘Enh_BC_5’_Rev'. Illumina sequencing adaptors were added during a second round of PCR with the primers ‘i5_Indexing_For’ and ‘i7_Indexing_Rev’. Before sequencing, the fragment size of every library was analyzed using the Bioanalyzer high-sensitivity chip. All libraries were sequenced on a NextSeq2000 instrument (Illumina) with the following sequencing parameters: 51 bp read 1 – 8 bp index 1 – 8 bp index 2 – 51 bp read 2. For the liver libraries cloned in the pSA293-CHEQseq-3’BC plasmids, we performed Nanopore sequencing as follows. A total of 1.5 µg of the library was linearized by digestion with NcoI according to the manufacturer’s protocol. We next processed 200 ng of the cleaned up and linearized plasmid with an Oxford Nanopore Technologies Q20+ ligation sequencing kit early-access SQK-LSK112 following the manufacturer’s protocol (Genomic DNA by Ligation; revision GDE_9141_v112_revC_01Dec2021). A total amount of 10 fmol of the prepared library was loaded onto a MinION R10.4 flow cell and sequenced for at least 72 hr (MinKNOW ≥ v21.11.09).


title: 12K MPRA experiment on HepG2 (3prime library, rep 2, Plasmid)


title: control, MDA231, rep3

value: control

value: shCTRL


title: 12K MPRA experiment on HepG2 (3prime library, rep 1, Plasmid)


title: 12K MPRA experiment on AML12 (5prime library, AML12, rep 1, cDNA)


title: control, MDA231, rep2


title: 12K MPRA experiment on HepG2 (3prime library, rep 1, cDNA)


title: KPC organoid Il1b stimulation 48h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_IL1B_48h_Sample2
Organoids_KPC_counts_matrix.csv.gz

source_name: KPC organoid Il1b stimulation 48h


title: 12K MPRA experiment on the mouse liver (3prime library, mouse 3, rep 1, Plasmid)


title: human_blastoid_day14

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

country: USA

institute: Washington University School of Medicine

data_processing:
Raw sequencing data were converted to fastq format using the cellranger mkfastq command (v.5.0.0).
scRNA-seq reads were aligned to the GRCh38 (hg38) reference genome and quantified using the cellranger count command.
Assembly: hg38
Supplementary files format and content: Processed data files contain matrix with counts, barcodes and features provided as standard output by cellranger.

source_name: WIBR3 (OCT4-GFP)

growth_protocol: 7 day blastoid sample aggregated in 5i/L/A media 1 day, N2B27+NaPy 2 days, and BAM for 4 days at 5% oxygen in Aggrewell 400 plates. 14 day blastoids were collected at day 7 from the previous protocol and transferred into 96 round bottom plates with a 3D matrix of 50% matrigel and 50% GFR geltrex. They were maintained for 7 days (with daily media changes) in N2B27+NaPy+Estradiol (10nM) at 5% oxygen.

extract_protocol:
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.
GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits (v3 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v3 (PN-1000075), Chromium Single Cell B Chip Kit (PN-1000153), and Dual Index Kit TT Set A (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.
Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28x10x10x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library

treatment_protocol: Papain dissociation

tag: culture condition

tag: passage


title: human_blastoid_day7

value: BAM


title: 12K MPRA experiment on the mouse liver (3prime library, mouse 3, rep 1, cDNA)


title: control, MDA231, rep1


title: 12K MPRA experiment on the mouse liver (3prime library, mouse 2, rep 1, Plasmid)


title: KPC organoid control 24h RNA-seq replicate 3

description:
Smart-seq2
Organoids_KPC_UT_24h_Sample3
Organoids_KPC_counts_matrix.csv.gz

source_name: KPC organoid control 24h


title: H3K27ac, PML knockdown, MDA231, rep2

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine.
ChIP-seq reads were trimmed using BBDuk from BBTools suite version 37.36 with suggested settings (ktrim=r k=23 mink=11 hdist=1).
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA-MEM version 0.7.12-r1039 . Uniquely mapped reads were selected with MarkDuplicates from Picard Tools version 1.104
Filtering was done on reads mapping in regions present in the ENCODE hg38 blacklist and regions flagged as not primary alignment or with mapping quality score less than 15.
For H3K4me3 and H3K27ac ChIP-seq peaks were detected using MACS2 v2.2.7.1. For PML, LMNB1, H3K9me3 and H3K27me3 mapped reads were used to call domain using the Enriched Domain Detector.
Assembly: bigWig files were generated using bamCompare from Deeptools.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for H3K27me3 samples) , EDD peaks (except for Input samples)

extract_protocol:
Cells were fixed with 2 mM Di(N-succinimidyl) glutarate for 45 min at RT and with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor 300.
ChIP-seq libraries were prepared using ChIPSeq Illumina protocol. Libraries were validated using the High Sensitivity D5000 ScreenTape (Agilent Technologies).

value: anti-H3K27ac Cell Signaling Technologies D5E4


title: KPC organoid Il1b stimulation 48h RNA-seq replicate 1

description:
Smart-seq2
Organoids_KPC_IL1B_48h_Sample1
Organoids_KPC_counts_matrix.csv.gz


title: 12K MPRA experiment on the mouse liver (3prime library, mouse 2, rep 1, cDNA)


title: 12K MPRA experiment on the mouse liver (3prime library, mouse 1, rep 1, Plasmid)


title: H3K27ac,control, MDA231, rep2


title: KPC organoid control 24h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_UT_24h_Sample2
Organoids_KPC_counts_matrix.csv.gz


title: H3K27ac, PML knockdown, MDA231, rep1


title: KPC organoid control 24h RNA-seq replicate 1

description:
Smart-seq2
Organoids_KPC_UT_24h_Sample1
Organoids_KPC_counts_matrix.csv.gz


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 2, rep 2, cDNA)


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 1, rep 2, Plasmid)


title: H3K27ac,control, MDA231, rep1


title: KPC organoid Il1b stimulation 24h RNA-seq replicate 3

description:
Smart-seq2
Organoids_KPC_IL1B_24h_Sample3
Organoids_KPC_counts_matrix.csv.gz

source_name: KPC organoid Il1b stimulation 24h


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 2, rep 1, Plasmid)


title: H3K4me3, PML knockdown, MDA231, rep2

value: anti-H3K4me3 Cell Signaling Technologies C42D8


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 1, rep 1, Plasmid)


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 2, rep 1, cDNA)


title: H3K4me3, PML knockdown, MDA231, rep1


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 1, rep 1, cDNA)


title: KPC organoid Il1b stimulation 24h RNA-seq replicate 1

description:
Smart-seq2
Organoids_KPC_IL1B_24h_Sample1
Organoids_KPC_counts_matrix.csv.gz


title: H3K4me3,control, MDA231, rep2


title: KPC organoid control 8h RNA-seq replicate 3

description:
Smart-seq2
Organoids_KPC_UT_8h_Sample3
Organoids_KPC_counts_matrix.csv.gz

source_name: KPC organoid control 8h


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, CD71 Low, rep 4, cDNA)

data_processing:
For the 3' enhancer-barcode assignments, Raw signal fast5 files were re-basecalled using Guppy v6.0.7 using the super-accuracy model (dna_r10.4_e8.1_sup). To process the reads, we first generated a synthetic genome consisting of the plasmid sequence (with 100bp flanks) with all possible enhancers inserted. Reads were mapped using minimap2 (v2.22) with options -ax map-ont –secondary=no -N 1 -f 500 and a bam file was generated using SAMTools (v1.11). Next, we used the R package GenomicAlignments (v1.24.0) to extract the sequences overlapping the enhancer sequence and the enhancer barcodes from the reads and calculate the number of mismatches. This resulted in a library with 723,805 unique enhancer-barcode assignments, with 85.5% barcodes assigned to a unique enhancer. CHEQ-seq barcodes were extracted from the plasmid and cDNA samples (read 2) using cutadapt with parameters with options -g TTATCATGTCTGCTCGAAGC...GATCGGCGCGCCTGCTCG --discard-untrimmed -m 17 -M 17 and seqkit (v0.10.2), with options seq -r -p, was used to get the reverse complement sequence. Reads were filtered to keep only those with quality > 30 using fastp (v0.20.0). Reads were assigned to enhancers based on the corresponding enhancer-barcode assignments, resulting in a count matrix with number of reads per enhancer and sample.
Assembly: mm10
Supplementary files format and content: Bulk_455_MPRA_counts.tsv: Tab-separated text file containing bulk MPRA samples as columns, tested enhancers as rows and assigned reads per sample as value.
Supplementary files format and content: FACS_455_MPRA_counts.tsv: Tab-separated text file containing FACS bulk MPRA samples as columns, tested enhancers as rows and assigned reads per sample as value.
Library strategy: CHEQ-seq

extract_protocol:
Enhancer library cloning: The pSA293-CHEQseq plasmid (Addgene 174669), containing a SCP1 promoter, a chimeric intron and the Venus cDNA, was used as a reporter plasmid for MPRA. The 455 library was cloned in a newly generated pSA293-CHEQseq-3'BC-2 containing an 18 bp BC optimized for ONT sequencing with the following pattern: NNNYRNNNYRNNNYRNNN. The oligonucleotide libraries were resuspended according to the manufacturer’s recommendation and amplified via PCR with the primers ‘CHEQ_liver_For’ and ‘CHEQ_liver_Rev’. To clone the amplified enhancer library upstream of the SCP1 promoter, the vectors were linearized via inverse PCR with primers ‘CHEQ_lin_For’ and ‘CHEQ_lin_Rev’. Amplified libraries and the corresponding linearized vector were combined in an NEBuilder reaction with a vector to insert ratio of 1:5. The NEBuilder reactions were dialyzed against water in a 6 cm Petri dish with a membrane filter MF-Millipore 0.05 µm (Merck, Kenilworth, NJ) for 1 hr. Reactions were recovered from the membrane, and 2.5 µL of the reaction was transformed into 25 µL of Lucigen Endura ElectroCompetent Cells (Biosearch Technologies, Hoddesdon, UK). Before culture for maxiprep, 1:100,000 of the transformed bacteria was plated on an LB-agar dish with carbenicillin to estimate the complexity of the cloned library. A volume of bacteria corresponding to a complexity of 500 BCs per enhancer was put in culture for maxiprep. Maxiprep was performed with the Nucleobond Xtra endotoxin-free maxiprep kit (Macherey-Nagel). Bulk MPRA in vitro: The MPRA libraries were transfected in HepG2 cells by use of the Lipofectamine 3000 reagent (Thermo Fisher Scientific). Briefly, 4 million HepG2 cells were seeded in a 10 cm cell culture dish. The next day, when cells reach 70-90% confluency, a tube A with 500 µL opti-MEM (Thermo Fisher Scientific) and 25 µL Lipofectamine 3000 reagent and a tube B with 500 µL opti-MEM and 15 µL of the liver enhancer library were prepared and incubated for 5 min at RT. Tube B was mixed carefully with tube A and incubated for 15 min at RT. The medium of the HepG2 cells was also changed to opti-MEM medium and finally the mixture was added dropwise to the cells. 48 hours post-transfection, cells were detached from the plate using trypsin (Thermo Fisher Scientific). One-fifth of the cells was used for plasmid DNA extraction (Qiagen). The remaining cells were used for RNA extraction using the innuPREP RNA Mini Kit 2.0 (Analytik Jena), followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion) and cDNA synthesis using the GoScript RT Kit and oligo dT primer (Promega). To amplify the random 5’ and 3’ BC from the plasmid DNA or cDNA sample, a PCR was performed for 16 cycles with ‘CHEQseq_barcode_5’_For’, ‘CHEQseq_barcode_5’_Rev’ and ‘CHEQseq_barcode_3’_For’, ‘CHEQseq_barcode_3’_Rev’, respectively. To add Illumina sequencing adaptors, all samples were finally amplified by PCR for 6 cycles with the primers ‘i5_Indexing_For’ and ‘i7_Indexing_Rev. Bulk MPRA in vivo: For intrahepatic delivery of the liver MPRA libraries, 8- to 10-week-old mice were secured and hydrodynamically injected with 20 µg of the libraries via the lateral tail vein. All libraries were diluted in sterile filtered 0.9% NaCl, and the total volume was adjusted to 10% (in mL) of the total body weight (in grams). 24 hours post-injection, mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50 mg/kg) and whole livers were isolated. Liver tissues were homogenized by using M tubes (Miltenyi Biotec) and the GentleMACS Dissociator (Miltenyi Biotec). RNA and plasmid DNA extraction, mRNA purification and cDNA prep, and barcode amplification, were done as described for MPRA in vitro. FACS MPRA in vivo: For intrahepatic delivery of the liver MPRA libraries, 8- to 10-week-old mice were secured and hydrodynamically injected with 20 µg of the libraries via the lateral tail vein. All libraries were diluted in sterile filtered 0.9% NaCl, and the total volume was adjusted to 10% (in mL) of the total body weight (in grams). 48 hours post-injection, mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50 mg/kg). Livers were perfused for 5 minutes with 40 mL of perfusion medium SC-1 (8 g/L Nacl, 400 mg/L KCl, 75.5 mg/L NaH2PO4, 120.5 mg/L Na2HPO4, 2,38 g/L HEPES, 350 mg/L NaHCO3, 190 mg/L EGTA, 900 mg/L D-(+)-Glucose, 1.2 mL Phenol Red solution) to remove the blood, followed by perfusion with 40 mL of SC-2 medium (8 g/L Nacl, 400 mg/L KCl, 75.5 mg/L NaH2PO4, 120.5 mg/L Na2HPO4, 2,38 g/L HEPES, 350 mg/L NaHCO3, 560 mg/L CaCl2.2H2O, 1.2 mL Phenol Red solution) containing 10 mg of collagenase P (Merck) for 5 minutes. Each lobe was dissected off and minced into small pieces in a beaker containing 39 mL SC-2 supplemented with 1 mL DNase I (Sigma-Aldrich) and 20 mg collagenase P, followed by rotating incubation for 15 min at 37°C. Hepatocytes were centrifuged for 2 min at 50 g, washed with PBS, centrifuged again for 2 min at 50 g, resuspended in 3 ml Hoechst buffer (DMEM + 10% FBS + 10 mM HEPES) and filtered through a 70 µm strainer. The protocol for hepatocyte staining was adapted from Ben-Moshe S. et al. After counting the cells on a LUNA cell counter, the concentration was adjusted to 5 million cells in 1 mL of Hoechst buffer. To determine the ploidy of hepatocytes, DNA was stained with Hoechst (Thermo Fisher Scientific) (15 µg/mL). Reserpine (5 µM) was also supplemented to prevent Hoechst expulsion from the cells. Cells were incubated for 30 min at 37°C. Hepatocytes were centrifuged for 5 min at 1,000 rpm at 4°C and the supernatant was discarded. Cells were resuspended in cold PBS in a concentration of 1 million cells in 100 µL. After spinning down (1,000 rpm for 5 min at 4°C), cells were resuspended in FACS buffer (2 mM EDTA, pH 8, and 0.5% BSA in 1x PBS) at a concentration of 1 million cells in 100 µL. Cells were stained with the following antibodies (BioLegend) at a dilution of 1:300: PE anti-mouse/human CD324 E-cadherin (catalogue no. 147304) and APC anti-mouse CD73 (catalogue no. 127210). FcX blocking solution (BioLegend catalogue no. 101319) was added at a dilution of 1:50. Cells were sorted by FACS-Aria-Fusion (BD Biosciences) using a 100 µm nozzle. FSC-A and SSC-A were used for hepatocytes size selection. Cells containing the library were selected based on GFP. Tetraploid hepatocytes were selected based on Hoechst stain. CD73 and Ecad were used to select hepatocytes bins along the porto-central axis, obtaining 100,000-200,000 cells per bin. RNA extraction, mRNA purification and cDNA prep were done as described for MPRA in vitro. To amplify the enhancer barcode on the cDNA small modifications were made. To amplify the random 3’ BC, a PCR with 24 cycles was performed. To add Illumina sequencing adaptors, a PCR with 10 cycles was done.
For the liver libraries cloned in the pSA293-CHEQseq-3’BC plasmids, we performed Nanopore sequencing as follows. A total of 1.5 µg of the library was linearized by digestion with NcoI according to the manufacturer’s protocol. We next processed 200 ng of the cleaned up and linearized plasmid with an Oxford Nanopore Technologies Q20+ ligation sequencing kit early-access SQK-LSK112 following the manufacturer’s protocol (Genomic DNA by Ligation; revision GDE_9141_v112_revC_01Dec2021). A total amount of 10 fmol of the prepared library was loaded onto a MinION R10.4 flow cell and sequenced for at least 72 hr (MinKNOW ≥ v21.11.09). All cDNA/Plasmid libraries were sequenced on a NextSeq2000 instrument (Illumina) with the following sequencing parameters: 51 bp read 1 – 8 bp index 1 – 8 bp index 2 – 51 bp read 2.


title: 12K MPRA experiment on the mouse liver (3prime library, mouse 1, rep 1, cDNA)


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, CD71 Low, rep 2, cDNA)


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, CD71 High, rep 4, cDNA)


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 2, rep 2, Plasmid)


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, CD71 Low, rep 3, cDNA)


title: KPC organoid control 8h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_UT_8h_Sample2
Organoids_KPC_counts_matrix.csv.gz


title: H3K27me3, PML knockdown, MDA231, rep2

value: anti-H3K27me3 Abcam 6002


title: 12K MPRA experiment on the mouse liver (5prime library, mouse 1, rep 2, cDNA)


title: H3K27me3, PML knockdown, MDA231, rep1


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, CD71 High, rep 3, cDNA)


title: KPC organoid control 8h RNA-seq replicate 1

description:
Smart-seq2
Organoids_KPC_UT_8h_Sample1
Organoids_KPC_counts_matrix.csv.gz


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, CD71 High, rep 2, cDNA)


title: KPC organoid Il1b stimulation 8h RNA-seq replicate 3

description:
Smart-seq2
Organoids_KPC_IL1B_8h_Sample3
Organoids_KPC_counts_matrix.csv.gz

source_name: KPC organoid Il1b stimulation 8h


title: KPC organoid Il1b stimulation 24h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_IL1B_24h_Sample2
Organoids_KPC_counts_matrix.csv.gz


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, CD73, rep 1, cDNA)


title: H3K27me3,control, MDA231, rep2


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, Ecad Low, rep 4, cDNA)


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, Ecad Low, rep 3, cDNA)


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, Ecad Low, rep 2, cDNA)


title: KPC organoid Il1b stimulation 8h RNA-seq replicate 2

description:
Smart-seq2
Organoids_KPC_IL1B_8h_Sample2
Organoids_KPC_counts_matrix.csv.gz


title: KPC organoid Il1b stimulation 8h RNA-seq replicate 1

description:
Smart-seq2
Organoids_KPC_IL1B_8h_Sample1
Organoids_KPC_counts_matrix.csv.gz


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, Ecad Low, rep 1, cDNA)


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, Ecad High, rep 4, cDNA)


title: H3K4me3,control, MDA231, rep1


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, Ecad High, rep 2, cDNA)


title: DT6606 KC cell line control 96h RNA-seq replicate 3

description:
Smart-seq2
DT6606_UT_96h_Sample3
K8484_DT6606_counts_matrix.csv.gz

source_name: DT6606 KC cell line control 96h

value: PDAC tumor cell

value: Kras G12D mutation


title: 455 MPRA experiment on FACS populations of the mouse liver (3prime library, Ecad High, rep 1, cDNA)

value: Liver (P56)


title: H3K9me3, PML knockdown, MDA231, rep1

value: Human breast cancer

value: anti-H3K9me3 Abcam 8898


title: 455 MPRA experiment on HepG2 (3prime library, bulk Hepg2 - 3, rep 3, Plasmid)


title: DT6606 KC cell line control 96h RNA-seq replicate 2

description:
Smart-seq2
DT6606_UT_96h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: H3K9me3,control, MDA231, rep1


title: H3K9me3,control, MDA231, rep2


title: DT6606 KC cell line control 96h RNA-seq replicate 1

description:
Smart-seq2
DT6606_UT_96h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: 455 MPRA experiment on HepG2 (3prime library, bulk Hepg2 - 2, rep 3, Plasmid)


title: DT6606 KC cell line Il1b stimulation 96h RNA-seq replicate 3

description:
Smart-seq2
DT6606_IL1B_96h_Sample3
K8484_DT6606_counts_matrix.csv.gz


title: 455 MPRA experiment on HepG2 (3prime library, bulk Hepg2 - 2, rep 3, cDNA)


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 3, rep 3, Plasmid)


title: 455 MPRA experiment on HepG2 (3prime library, bulk Hepg2 - 1, rep 3, Plasmid)


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 2, rep 3, Plasmid)


title: 455 MPRA experiment on HepG2 (3prime library, bulk Hepg2 - 3, rep 3, cDNA)


title: H3K27me3,control, MDA231, rep1


title: LMNB1, PML knockdown, MDA231, rep1

value: anti-LMNB1 Abcam 16048


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 1, rep 3, Plasmid)


title: DT6606 KC cell line Il1b stimulation 96h RNA-seq replicate 1

description:
Smart-seq2
DT6606_IL1B_96h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: H3K9me3, PML knockdown, MDA231, rep2


title: 455 MPRA experiment on HepG2 (3prime library, bulk Hepg2 - 1, rep 3, cDNA)


title: LMNB1, PML knockdown, MDA231, rep2


title: DT6606 KC cell line Il1b stimulation 96h RNA-seq replicate 2

description:
Smart-seq2
DT6606_IL1B_96h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: LMNB1, control, MDA231, rep2


title: LMNB1, control, MDA231, rep1


title: DT6606 KC cell line control 48h RNA-seq replicate 2

description:
Smart-seq2
DT6606_UT_48h_Sample2
K8484_DT6606_counts_matrix.csv.gz

source_name: DT6606 KC cell line control 48h


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 1, rep 2, cDNA)


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 3, rep 2, cDNA)


title: DT6606 KC cell line control 48h RNA-seq replicate 1

description:
Smart-seq2
DT6606_UT_48h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 5, rep 1, cDNA)


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 4, rep 1, cDNA)


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 3, rep 1, cDNA)


title: PML, MDA231, rep3

value: anti-PML Santa Cruz Biotechnology 71910


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 2, rep 1, cDNA)


title: DT6606 KC cell line Il1b stimulation 48h RNA-seq replicate 3

description:
Smart-seq2
DT6606_IL1B_48h_Sample3
K8484_DT6606_counts_matrix.csv.gz


title: Bulk ATAC-seq on FACS populations from the mouse liver (CD73 high)

description:
ATAC_CD73_High
OmniATAC-seq

data_processing:
Adapters were removed with fastq-mcf (ea-utils v1.12) and cleaned reads were mapped to the mm10 genome using Bowtie2 (v2.3.5.1). A fragment count matrix was generated using the liver scATAC-seq consensus peaks using SubRead (v1.6.3).
Assembly: mm10
Supplementary files format and content: FACS_ATAC_counts.tsv: Tab-separated text file containing bulk ATAC-seq samples as columns, consensus liver peaks as rows and fragments in the regions as values.

extract_protocol:
Mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50 mg/kg). Livers were perfused for 5 minutes with 40 mL of perfusion medium SC-1 (8 g/L Nacl, 400 mg/L KCl, 75.5 mg/L NaH2PO4, 120.5 mg/L Na2HPO4, 2,38 g/L HEPES, 350 mg/L NaHCO3, 190 mg/L EGTA, 900 mg/L D-(+)-Glucose, 1.2 mL Phenol Red solution) to remove the blood, followed by perfusion with 40 mL of SC-2 medium (8 g/L Nacl, 400 mg/L KCl, 75.5 mg/L NaH2PO4, 120.5 mg/L Na2HPO4, 2,38 g/L HEPES, 350 mg/L NaHCO3, 560 mg/L CaCl2.2H2O, 1.2 mL Phenol Red solution) containing 10 mg of collagenase P (Merck) for 5 minutes. Each lobe was dissected off and minced into small pieces in a beaker containing 39 mL SC-2 supplemented with 1 mL DNase I (Sigma-Aldrich) and 20 mg collagenase P, followed by rotating incubation for 15 min at 37°C. Hepatocytes were centrifuged for 2 min at 50 g, washed with PBS, centrifuged again for 2 min at 50 g, resuspended in 3 ml Hoechst buffer (DMEM + 10% FBS + 10 mM HEPES) and filtered through a 70 µm strainer. The protocol for hepatocyte staining was adapted from Ben-Moshe S. et al. After counting the cells on a LUNA cell counter, the concentration was adjusted to 5 million cells in 1 mL of Hoechst buffer. To determine the ploidy of hepatocytes, DNA was stained with Hoechst (Thermo Fisher Scientific) (15 µg/mL). Reserpine (5 µM) was also supplemented to prevent Hoechst expulsion from the cells. Cells were incubated for 30 min at 37°C. Hepatocytes were centrifuged for 5 min at 1,000 rpm at 4°C and the supernatant was discarded. Cells were resuspended in cold PBS in a concentration of 1 million cells in 100 µL. After spinning down (1,000 rpm for 5 min at 4°C), cells were resuspended in FACS buffer (2 mM EDTA, pH 8, and 0.5% BSA in 1x PBS) at a concentration of 1 million cells in 100 µL. Cells were stained with the following antibodies (BioLegend) at a dilution of 1:300: PE anti-mouse/human CD324 E-cadherin (catalogue no. 147304) and APC anti-mouse CD73 (catalogue no. 127210). FcX blocking solution (BioLegend catalogue no. 101319) was added at a dilution of 1:50. Cells were also stained with Alexa Fluor 488 Zombie Green (BioLegend) to enable the detection of viable cells by FACS. Zombie Green was added at a dilution of 1:500 and cells were kept in a rotator in the dark at room temperature for 15 min. Cells were sorted by FACS-Aria-Fusion (BD Biosciences) using a 100 µm nozzle. FSC-A and SSC-A were used for hepatocytes size selection. Viable cells were selected based on the Zombie Green signal. Tetraploid hepatocytes were selected based on Hoechst stain. CD73 and Ecad were used to select hepatocytes bins along the porto-central axis, obtaining 20,000-50,000 cells per bin. Omni-assay for transposase-accessible chromatin using sequencing (OmniATAC-seq) was performed as described previously.
Cells obtained after FACS were resuspended in 50 µL of cold ATAC-seq resuspension buffer (RSB; 10 mM TrisHCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 µL of transposition mix (25 µL 2x TD buffer, 2.5 µL transposase (Nextera Tn5 transposase, Illumina), 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermoblock. Reactions were cleaned-up by MinElute (Qiagen). Transposed DNA was amplified with primers 'i5_Indexing_For’ and ‘i7_Indexing_Rev’. Number of PCR cycles was based on quantitative real-time PCR as described previously. All libraries were sequenced on a NextSeq2000 instrument (Illumina) with the following sequencing parameters: 51 bp read 1 – 8 bp index 1 – 8 bp index 2 – 51 bp read 2.


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 1, rep 1, cDNA)


title: Bulk ATAC-seq on FACS populations from the mouse liver (CD73 low)

description:
ATAC_CD73_Low
OmniATAC-seq


title: PML, MDA231, rep1


title: DT6606 KC cell line Il1b stimulation 48h RNA-seq replicate 1

description:
Smart-seq2
DT6606_IL1B_48h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: DT6606 KC cell line Il1b stimulation 48h RNA-seq replicate 2

description:
Smart-seq2
DT6606_IL1B_48h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: DT6606 KC cell line control 24h RNA-seq replicate 3

description:
Smart-seq2
DT6606_UT_24h_Sample3
K8484_DT6606_counts_matrix.csv.gz

source_name: DT6606 KC cell line control 24h


title: Input, PML knockdown, MDA231

value: none (input)


title: Bulk ATAC-seq on FACS populations from the mouse liver (Ecad low)

description:
ATAC_Ecad_Low
OmniATAC-seq


title: 455 MPRA experiment on the mouse liver (3prime library, bulk mouse 2, rep 2, cDNA)


title: Input, control, MDA231


title: DT6606 KC cell line control 24h RNA-seq replicate 2

description:
Smart-seq2
DT6606_UT_24h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: ADAR1 KD RNA-seq 2

city: Fort Collins

first: Cali

middle: Madison

last: McEntee

state: CO

address: 910 Moby Dr

department: Health and Exercise Science

institute: Colorado State University

data_processing:
Reads trimmed by Fastp.
Reads aligned to the hg38 genome using STAR.
Repetitive elements were identified using RepeatMasker annotation files with RepEnrich2.
Differential expression of genes/repetitive elemsnts was analyzed using DESeq2.
Assembly: hg38

source_name: astrocytes

growth_protocol: Tissue culture dishes were coated with poly-L-lysine prior to seeding, and astrocytes were grown in complete astrocyte growth medium at 37 °C and 5% CO2 in a humidified incubator.

extract_protocol:
RNA was isolated using Direct-zol RNA MicroPrep from Zymo Research.
RNA libraries for RNA-seq were prepared using Zymo Total RNA library preparation kits following manufacturer's protocols.

treatment_protocol: Astrocytes were transfected with siRNAs (scramble or ADAR1) at a concentration of 15 nM.

value: astrocytes

value: WT

value: ADAR1 siRNA transfection


title: DT6606 KC cell line Il1b stimulation 24h RNA-seq replicate 2

description:
Smart-seq2
DT6606_IL1B_24h_Sample2
K8484_DT6606_counts_matrix.csv.gz

value: IL-1b (10 ng/mL)


title: ADAR1 KD RNA-seq 3


title: PML, MDA231, rep2


title: ADAR1 KD RNA-seq 1


title: scramble RNA-seq 3

value: scramble siRNA transfection


title: scramble RNA-seq 2


title: K8484 KPC cell line control 96h RNA-seq replicate 3

description:
Smart-seq2
K8484_UT_96h_Sample3
K8484_DT6606_counts_matrix.csv.gz

source_name: K8484 KPC cell line control 96h

value: Kras G12D and Tpr53 R720H mutations

value: untreated


title: HSC_shMTA1_sh2_rep2

type: RNA

city: Lund

first: Kristijonas

last: Zemaitis

address: BMC A12

country: Sweden

institute: Lund University

description: RMA expression value derived from Affymetrix GeneChip Expression Console v1.4 Software

hyb_protocol: Labeled ss cDNA samples were hybridized to Affymetrix Human Gene 2.0 arrays for 16 h at 45 ° C and 60 rpm in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated

label: biotin

source_name: pooled UCB units

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT Pico Reagent Kit User Guide (Affymetrix, Inc., Santa Clara, CA, USA). Samples were labeled with biotin.

growth_protocol: CD34 positive cells were isolated from UCB and then CD34+CD38-CD90+CD45RA- cells were enriched by sorting. Cells were cultured in SFEM medium supplemented with SCF, TPO and FLT3L cytokines.

extract_protocol: Total RNA was extracted from sorted human cells stabilized in RLT buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored in RLT buffer and shipped on dry ice. After thawing the samples were homogenized by vortexing for1 min. Next one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns, followed by an on-column DNase digestion and several wash steps. Finally total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).

treatment_protocol: Cells were lentivirally transduced with shRNAs and cultured for 60 h before GFP+ cells were sorted.

value: Umbilical cord blood


title: K8484 KPC cell line control 96h RNA-seq replicate 1

description:
Smart-seq2
K8484_UT_96h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: mEC-TW3-YMK6

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

data_processing:
Sequenced reads were aligned to the Mus musculus reference genome GRCm39 (mm39) with STAR v.2.7.6a. Then mRNA expression counts were quantified from the aligned reads by using STAR –quantMode option.
Assembly: mm39
Supplementary files format and content: csv file contains gene count matrix, each row represents one gene, each column represents one sample.

source_name: Skeletal muscle ECs

extract_protocol:
ECs from skeletal muscles (gastrocnemius, tibialis anterior, or quadriceps) from hindlimbs were isolated and stained with specific antibodies of CD31 and CD45, and  the pure muscle ECs (CD31+CD45-DAPI-) were sorted using MoFlo Astrios (Beckman Coulter) as mentioned above. The sorted ECs were used for total RNA extraction by TRIzol Reagent (Invitrogen, 15596026) and the RNA was treated with DNase and its quality was evaluated with gel QC.
Bulk RNA sequencing for 4-6 samples (each sample indicates a mouse) with 4 time points was performed with oligo-dT mRNA directional using Illumina Novaseq (HiSeq SR50) for coding genes at Genomic Facility in University of Chicago.

value: Skeletal muscle ECs

value: Tumor


title: DT6606 KC cell line control 24h RNA-seq replicate 1

description:
Smart-seq2
DT6606_UT_24h_Sample1
K8484_DT6606_counts_matrix.csv.gz

value: PDAC tumor cell

value: Kras G12D mutation


title: Bulk ATAC-seq on FACS populations from the mouse liver (Ecad high)

description:
ATAC_Ecad_high
OmniATAC-seq

value: Liver (P56)


title: human_blastoid_day21

library_source: transcriptomic single cell

growth_protocol: The 21 day blastoid sample was aggregated in 5i/L/A media for 1 day, N2B27+NaPy for 2 days, and BIM for 4 days at 5% oxygen in Aggrewell 400 plates. The 14 day blastoids were collected at day 7 from the previous protocol and transferred into 96 round bottom plates containing a 3D matrix of 50% matrigel and 50% GFR geltrex. The 21 day blastoid sample was generated using Cultrex Ultrimatrix, which provided an alternative 3D matrix for post-implantation blastoid culture that supported robust development of embryonic and extraembryonic structures. These post-implantation blastoid samples were maintained after aggregation in BIM (with daily media changes) for an additional 7 days and 14 days, respectively, in N2B27+NaPy+Estradiol (10nM) at 5% oxygen.

extract_protocol:
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration.
GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell3’ Reagent Kits(v3Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v3 (PN-1000075), Chromium Single Cell B Chip Kit (PN-1000153), and Dual Index Kit TT Set A (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.
Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a28x10x10x150sequencing recipe according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene ExpressionLibrary

tag: sequencing platform


title: mEC-TW3-YMK5


title: L31432_K562_endogenous_RNA_IFNA_replicate6

city: Durham

first: Rachel

middle: A

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

data_processing:
Reads were trimmed with Trim Galore (Trim Galore version 0.6.4_dev; Cutadapt version 2.3) to remove basepairs with a Phred score less than 20, and end sequences that matched at least two basepairs of the adapter sequence. Only trimmed reads longer than 25 basepairs were retained.
We used the STAR package (version 2.5.0) (Dobin et al., 2013) two-pass mapping to map the filtered reads to the hg38 genome. We retained uniquely mapped reads by filtering the output SAM file to keep reads with MAPQ = 255.
We then used htseq (version 0.6.0) (Anders et al., 2014) to quantify read counts per gene.
We only retained genes that had TPM > 3 in at least 3 of 6 samples in at least one of the three conditions (baseline, IFNA, or dex).
Only protein-coding genes were retained for final analysis, resulting in a total of 10,676 testable genes.
Assembly: hg38
Supplementary files format and content: Tab delimited text file with data matrix of raw read counts mapping to a gene, where each row represents a gene, and each column represents a biological replicate (i.e., library). Only protein-coding genes that had transcripts per million > 3 in at least 3 of 6 samples in at least 1 of the 3 conditions (baseline, IFNA, or dex) are included.

growth_protocol: We made 18 replicate T75 flasks, each containing 12 million K562s. 42 hours later, K562s were stimulated with treatment, and cells were collected 6 hours post-treatment.

extract_protocol:
We extracted RNA from the separately aliquoted cells using the Qiagen RNEasy kit.
We prepared RNA-Seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: In this data set, 6 replicate flasks of K562 cells were treated for 6 hours with each of the following treatments: dexamethasone (1 uM), IFNA2b (2,000U/ml), or vehicle control (media). Cells were then collected for mRNA-Seq to assess the endogenous gene expression response of K562 cells to treatment.

value: Lymphoblast cells

value: wildtype

value: IFNA


title: HSC_shMTA1_sh1_rep2


title: HSC_shMTA1_sh1_rep1


title: HSC_shMTA1_sh2_rep1


title: HSC_shMTA1_sh2_rep3


title: mEC-TW3-YMK4


title: HSC_shScr_sh0_rep1


title: HSC_shScr_sh0_rep3


title: HSC_shScr_sh0_rep2


title: HSC_shMTA1_sh1_rep3


title: mEC-TW3-YMK3


title: DT6606 KC cell line Il1b stimulation 24h RNA-seq replicate 1

description:
Smart-seq2
DT6606_IL1B_24h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: mEC-TW2-YMK6


title: K8484 KPC cell line control 96h RNA-seq replicate 2

description:
Smart-seq2
K8484_UT_96h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: K8484 KPC cell line Il1b stimulation 96h RNA-seq replicate 3

description:
Smart-seq2
K8484_IL1B_96h_Sample3
K8484_DT6606_counts_matrix.csv.gz


title: K8484 KPC cell line Il1b stimulation 96h RNA-seq replicate 1

description:
Smart-seq2
K8484_IL1B_96h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: mEC-TW2-YMK4


title: L31430_K562_endogenous_RNA_baseline5

value: baseline


title: K8484 KPC cell line control 48h RNA-seq replicate 3

description:
Smart-seq2
K8484_UT_48h_Sample3
K8484_DT6606_counts_matrix.csv.gz

source_name: K8484 KPC cell line control 48h


title: scramble RNA-seq 1

value: astrocytes


title: L31433_K562_endogenous_RNA_baseline_replicate6


title: L31429_K562_endogenous_RNA_IFNA_replicate5


title: mEC-TW2-YMK3


title: K8484 KPC cell line control 48h RNA-seq replicate 2

description:
Smart-seq2
K8484_UT_48h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: mEC-TW1-YMK5


title: mEC-TW1-YMK6


title: mEC-TW1-YMK4


title: L31428_K562_endogenous_RNA_Dex_replicate5

value: Dex


title: K8484 KPC cell line Il1b stimulation 96h RNA-seq replicate 2

description:
Smart-seq2
K8484_IL1B_96h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: K8484 KPC cell line control 48h RNA-seq replicate 1

description:
Smart-seq2
K8484_UT_48h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: mEC-TW1-YMK2


title: mEC-TW1-YMK3


title: L31427_K562_endogenous_RNA_baseline_replicate3


title: mEC-TW1-YMK1


title: K8484 KPC cell line Il1b stimulation 48h RNA-seq replicate 3

description:
Smart-seq2
K8484_IL1B_48h_Sample3
K8484_DT6606_counts_matrix.csv.gz


title: mEC-C-YMK5

value: PBS


title: L31431_K562_endogenous_RNA_Dex_replicate6


title: L31426_K562_endogenous_RNA_IFNA_replicate4


title: K8484 KPC cell line Il1b stimulation 48h RNA-seq replicate 2

description:
Smart-seq2
K8484_IL1B_48h_Sample2
K8484_DT6606_counts_matrix.csv.gz

value: IL-1b (10 ng/mL)


title: mEC-C-YMK4


title: mEC-TW2-YMK5


title: L31425_K562_endogenous_RNA_Dex_replicate4


title: K8484 KPC cell line Il1b stimulation 48h RNA-seq replicate 1

description:
Smart-seq2
K8484_IL1B_48h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: mEC-C-YMK2


title: mEC-C-YMK3


title: L31424_K562_endogenous_RNA_baseline_replicate3


title: mEC-C-YMK1


title: K8484 KPC cell line control 24h RNA-seq replicate 3

description:
Smart-seq2
K8484_UT_24h_Sample3
K8484_DT6606_counts_matrix.csv.gz

source_name: K8484 KPC cell line control 24h


title: L31423_K562_endogenous_RNA_IFNA_replicate3


title: L31422_K562_endogenous_RNA_Dex_replicate3


title: e13.5heart_wildtype_male_rep5

city: Houston

first: Ashish

last: Kapoor

state: TX

address: 1825 Pressler St. Rm SRB 530C

institute: University of Texas Health Science Center at Houston

data_processing:
Illumina RNA-seq paired-end read fastq files were quality checked using FASTQC (version: 0.11.5) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then processed using Trimmomatic (version: 0.36), for removing adapters and other Illumina-specific sequences from the reads, and, for performing a sliding-window based trimming of low quality bases from each read (ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).  For estimating gene and isoform expression levels, we first extracted reference transcript sequences from the mouse genome (GRCm38, primary assembly) based on the GENCODE (http://www.gencodegenes.org/mouse_releases/current.html) primary assembly gene annotation (release M10) and built STAR aligner indices using the RSEM software package (version: 1.2.31).  Trimmed paired-end reads from each sample were then aligned to the reference transcript sequences by calling the STAR aligner within RSEM and using alignment parameters from the ENCODE STAR-RSEM long RNA-seq pipeline (--outSAMunmapped Within --outFilterType BySJout  --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM).  Gene and isoform expression levels were then estimated in each sample from these transcriptome alignments using RSEM keeping in mind the strandedness of the prepared RNA-seq libraries (--forward-prob 0.0).  Gene-level read count data generated by RSEM was compared between wildtype and mutant mice to assess differential gene expression using the DESeq software (version: 1.24.0).  Only those genes where the sum of read counts across the 10 samples was >1, were retained for differential gene expression analysis.  Although, release M10 of the GENCODE primary assembly gene annotation has 48,526 genes, we limited differential gene expression comparison to only protein coding genes (22,098). To address multiple hypothesis testing, observed P-values were adjusted based on Benjamini-Hochberg FDR procedure.
Assembly: mm10
Supplementary files format and content: Text (.txt) file with differential gene expression analysis results using DESeq.

source_name: heart

extract_protocol:
Total RNA was isolated from e13.5 heart tissue using RNeasy Mini Kit following manufacturers’ recommendations (Qiagen, MD) that included the on-column DNase digestion using RNase-Free DNase set (Qiagen, MD). KAPA Stranded mRNA-Seq kit (KAPA Biosystems, MA) was used to generate indexed Illumina platform sequencing libraries.  Briefly, polyA RNA was captured from 1µg total RNA using magnetic oligo-dT beads.  After elution from the magnetic beads, polyA RNA was fragmented to generate inserts ranging in size from 100-200 bp, followed by random priming and reverse transcription to generate double-stranded cDNA.  Next, after performing a 1.8× SPRI cleanup using AMPure XP beads (Agencourt, IN), dAMP was added to 3’-ends of the cDNA fragments.
Indexed 3’-dTMP Illumina TruSeq adapters were ligated to cDNA fragments.  Ligated fragments were subsequently size selected using PEG/NaCl SPRI solution and underwent PCR amplification (12 cycles) to generate the sequencing libraries.  After performing a 1× SPRI cleanup using AMPure XP beads (Agencourt, IN), a sample from each library was used to assess library fragment size distribution by electrophoresis using BioAnalyzer High Sensitivity DNA Assay (Agilent Technologies, CA) and to assess library concentration by qPCR using KAPA library quantification kit (KAPA Biosystems, MA).  Equimolar amounts of libraries were pooled and sequenced on an Illumina HiSeq 2500 instrument using standard protocols for paired end 100 bp sequencing with a desired sequencing depth of ~30 million paired end reads per library.

value: heart

tag: age

value: embryonic day 13.5

tag: Sex

value: male


title: e13.5heart_Nos1ap_null_male_rep3


title: e13.5heart_wildtype_male_rep4


title: K8484 KPC cell line control 24h RNA-seq replicate 1

description:
Smart-seq2
K8484_UT_24h_Sample1
K8484_DT6606_counts_matrix.csv.gz

value: Kras G12D and Tpr53 R720H mutations

value: untreated


title: e13.5heart_Nos1ap_null_male_rep5


title: e13.5heart_Nos1ap_null_male_rep2


title: L31421_K562_endogenous_RNA_baseline_replicate2


title: L31420_K562_endogenous_RNA_IFNA_replicate2


title: e13.5heart_wildtype_male_rep2


title: K8484 KPC cell line control 24h RNA-seq replicate 2

description:
Smart-seq2
K8484_UT_24h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: K8484 KPC cell line Il1b stimulation 24h RNA-seq replicate 1

description:
Smart-seq2
K8484_IL1B_24h_Sample1
K8484_DT6606_counts_matrix.csv.gz


title: e13.5heart_Nos1ap_null_male_rep1


title: K8484 KPC cell line Il1b stimulation 24h RNA-seq replicate 2

description:
Smart-seq2
K8484_IL1B_24h_Sample2
K8484_DT6606_counts_matrix.csv.gz


title: e13.5heart_wildtype_male_rep1


title: e13.5heart_Nos1ap_null_male_rep4


title: L31419_K562_endogenous_RNA_Dex_replicate2


title: HuR KO-Hy-TRG-179

city: New Haven

first: Timur

middle: O

last: Yarovinsky

state: CT

address: 300 George Street, 7th floor Cardiology Bender lab

department: Yale Cardiovascular Research Center

institute: Yale University

data_processing:
Library strategy: translating ribosome affinity purification (TRAP)
Multiplex (8 samples/lane) paired-end (75 bp) sequencing was carried out using Illumina HiSeq 2500 at Yale Center for Genome Analyses.
Raw sequencing data were trimmed for quality and aligned to the Mus musculus reference genome GRCm38 using HiSAT.
The alignments were processed using ballgown, and per-gene counts were obtained.
The raw counts were processed using DESeq2 and R.
Subsequent analyses used Transcripts Per kilobase Million (TPM). TMP Log2FC of total and translated poly(A) in hypoxia relative to normoxia was calculated for each sample.
Genome_build: Mus musculus reference genome GRCm38
Supplementary_files_format_and_content: Matrix table with TPM counts for every transcript and sample as well as Log2FC for inter-related samples.

source_name: fetal liver derived macrophages

growth_protocol: Fetal liver cells were isolated from day E14.4 embryos and cultured for 6 days in presence of conditioned medium from L cells to obtain differentiated macrophages.

extract_protocol:
Macrophages were lysed in two steps using the lysis buffer with 1% NP-40, low speed centrifugation, and addition of 1,2-diheptanoyl-sn-glycero-phosphocholine (30 mM). After preclearing by high-speed centrifugation, the lysates were divided for total RNA isolation and  affinity purification of translated RNA using EGFP-tagged ribosomal protein L10a. Both RNA fractions were isolated using Direct-Zol RNA MiniPrep Plus (Zymo Research).
Poly(A) enriched cDNA libraries were prepared according to low input Illumina's protocol.

treatment_protocol: Separate plates were subjected to hypoxia (1% O2, 5% CO2) while control plates remain in normoxia (20% O2, 5% CO2).

tag: hur/elavl1 genotype

value: fl/fl

value: hypoxia

value: fetal liver derived macrophages

tag: molecule subtype

value: L10a-TRAP translated RNA


title: HuR KO-Hy-INPG-179

data_processing:
Multiplex (8 samples/lane) paired-end (75 bp) sequencing was carried out using Illumina HiSeq 2500 at Yale Center for Genome Analyses.
Raw sequencing data were trimmed for quality and aligned to the Mus musculus reference genome GRCm38 using HiSAT.
The alignments were processed using ballgown, and per-gene counts were obtained.
The raw counts were processed using DESeq2 and R.
Subsequent analyses used Transcripts Per kilobase Million (TPM). TMP Log2FC of total and translated poly(A) in hypoxia relative to normoxia was calculated for each sample.
Genome_build: Mus musculus reference genome GRCm38
Supplementary_files_format_and_content: Matrix table with TPM counts for every transcript and sample as well as Log2FC for inter-related samples.

value: total RNA


title: L31418_K562_endogenous_RNA_baseline_replicate1

value: Lymphoblast cells

value: wildtype


title: 6 hour phenylarsine oxide 47

city: Birmingham

first: Kyle

middle: Hartley

last: Moore

state: Alabama

department: Division of Nephrology

institute: University of Alabama at Birmingham

description:
6 hour phenylarsine oxide
10X Genomics

data_processing:
Processed following 10X Genomics protocol for CellRanger
Assembly: mm10

source_name: kidney

extract_protocol:
Nuclei were isolated, purified, and sequenced per 10x genomics suggestion
single nuclei RNA sequencing

value: kidney

tag: gender

tag: disease state

value: Acute Kidney Injury


title: HuR KO-No-INPG-179

value: normoxia


title: HuR KO-No-TRG-179


title: 6 hour phenylarsine oxide 43

description:
6 hour phenylarsine oxide
10X Genomics

tag: tissue


title: L31417_K562_endogenous_RNA_IFNA_replicate1

tag: genotype

value: IFNA


title: HuR KO-Hy-TRG-94


title: 6 hour phenylarsine oxide 45

description:
6 hour phenylarsine oxide
10X Genomics


title: e13.5heart_wildtype_male_rep3


title: L31416_K562_endogenous_RNA_Dex_replicate1

value: Dex


title: HuR KO-Hy-INPG-94


title: HuR KO-No-TRG-94


title: 24 hour phenylarsine oxide 42

description:
24 hour phenylarsine oxide
10X Genomics


title: Patient PDAC_60 Peripheral blood scRNAseq

description: 10X Genomics

data_processing:
Fastq files were processed with Cell Ranger (v 4.0.0), using default parameters
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (gzipped format)

source_name: Peripheral blood

extract_protocol:
Freshly resected human PDAC samples were minced in small pieces and digested with the Tumor Dissociation kit, human (Miltenyi Biotec). For the patient LiMeT PDAC15, cells were enriched in the myeloid fraction as CD45+CD3-CD19- by sorting into FACSAria instrument (BD Biosciences). Human PB samples were incubated with Red Blood Cell (RBC) lysis buffer (Biolegend) for 10 minutes on ice and washed with Phosphate Buffered Saline (PBS). Cells were centrifuged for 5 minutes at 450 x g and resuspended in the appropriate buffer for down-stream application.
scRNA-Seq libraries were generated using a microfluidics-based approach on Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v3.1, according to the manufacturers’ instructions

value: Peripheral blood


title: HuR KO-No-INPG-94


title: HuR KO-No-TRG-84


title: HuR KO-Hy-TRG-84


title: Patient PDAC_51 Peripheral blood scRNAseq

description: 10X Genomics


title: HuR KO-No-INPG-84


title: HuR WT-Hy-TRG-281


title: HuR KO-Hy-INPG-84


title: Patient PDAC_55 Peripheral blood scRNAseq

description: 10X Genomics


title: 24 hour phenylarsine oxide 39

description:
24 hour phenylarsine oxide
10X Genomics


title: 24 hour phenylarsine oxide 41

description:
24 hour phenylarsine oxide
10X Genomics


title: Patient PDAC_50 Peripheral blood scRNAseq

description: 10X Genomics


title: HuR WT-No-TRG-281


title: HuR WT-No-INPG-281


title: 6 hour vehicle 37

description:
6 hour vehicle
10X Genomics


title: 24 hour phenylarsine oxide 38

description:
24 hour phenylarsine oxide
10X Genomics


title: Patient PDAC_48 Peripheral blood scRNAseq

description: 10X Genomics


title: 6 hour vehicle 35

description:
6 hour vehicle
10X Genomics


title: HuR WT-Hy-TRG-280


title: HuR WT-Hy-INPG-280


title: Patient PDAC_47 Peripheral blood scRNAseq

description: 10X Genomics


title: 24 hour vehicle 34

description:
24 hour vehicle
10X Genomics


title: HuR WT-No-TRG-280


title: Patient PDAC_60 Tumor scRNAseq

description: 10X Genomics

source_name: Primary tumor

value: Primary tumor


title: HuR WT-No-INPG-280


title: KO-H-TRG-301

description: L10a-TRAP translated RNA

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow cells were isolated from 8-12 wk old mice and cultured for 6 days in presence of conditioned medium from L cells to obtain differentiated macrophages.

extract_protocol:
Macrophages were lysed in two steps using the lysis buffer with 1% NP-40, low speed centrifugation, and addition of 1,2-diheptanoyl-sn-glycero-phosphocholine (30 mM). After preclearing by high-speed centrifugation, the lysates were divided for total RNA isolation and  affinity purification of translated RNA using EGFP-tagged ribosomal protein L10a. Both RNA fractions were isolated using Direct-Zol RNA MiniPrep Plus (Zymo Research).
Poly(A) enriched cDNA libraries were prepared according to standard Illumina's protocol.

value: bone marrow derived macrophages


title: 24 hour vehicle 33

description:
24 hour vehicle
10X Genomics

value: male


title: KO-H-INPG-301

description: total RNA


title: Patient PDAC_55 Tumor scRNAseq

description: 10X Genomics


title: 24 hour vehicle 31

description:
24 hour vehicle
10X Genomics


title: Patient PDAC_51 Tumor scRNAseq

description: 10X Genomics


title: KO-N-TRG-301

description: L10a-TRAP translated RNA


title: KO-N-INPG-301

description: total RNA


title: HuR WT-Hy-INPG-281


title: KO-H-INPG-281

description: total RNA


title: CD349

first: David

last: Crossman

state: AL

address: 720 20th Street South

department: Genetics

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Extracted lungs were infused with 1 ml digestion solution (dispase with 0.2 mg/ml DNase I). Lungs were incubated at room temperature for 45 min with gentle agitation and tissue was gently teased apart with forceps into 1-2 mm fragments and incubated in digestion buffer for 15 min. Solution was filtered through a 70 µm cell strainer, washed with DMEM containing 5% FBS, centrifuged, and RBCs lysed with ACK lysing buffer. Resulting single cell suspension was filtered twice through a 40 µm cell strainer with DMEM containing 5% FBS. Cells were counted after staining with 7-AAD for exclusion of nonviable cells, cell viability exceeded 95%.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: lung

value: WT C57BL/6J

value: Cadmium + Streptococcus pneumoniae


title: KO-N-TRG-281

description: L10a-TRAP translated RNA

value: fl/fl


title: Patient PDAC_48 Tumor scRNAseq

description: 10X Genomics


title: CD345

description: 10x Genomics

value: Streptococcus pneumoniae


title: CD343

description: 10x Genomics

value: Cadmium


title: KO-N-TRG-176

description: L10a-TRAP translated RNA


title: Patient LPDAC_30 Tumor scRNAseq

description: 10X Genomics


title: MCH Treated 4, replicate 4, RNA-seq

first: Kristofer

middle: James

last: Davie

department: Center for Brain and Disease Research

institute: Vlaams Instituut voor Biotechnologie

data_processing:
Raw reads were pre-processed, mapped and quantified against the GRCm38 Mus musculus genome using the nf-core/rnaseq pipeline (v3.0, https://doi.org/10.5281/zenodo.1400710)
Salmon quantifications from the nf-core/rnaseq pipeline were imported into R v4.0.3 using the tximport library. Resulting counts were normalised and differential analysis was performed using DEseq2 (v.1.13.0). Genes were tested for differential expression between vehicle treated and MCH treated samples and those with an adjusted p-value (Benjamini & Hochberg) <0.05 were deemed significant.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values file

source_name: hippocampal neurons

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen 74104).
Briefly, 1ug of total RNA extract per sample was enriched for mRNA molecules using poly-T oligo attached magnetic beads. The enriched poly-A mRNA species is subjected to fragmentation and reverse transcriptions using random primers and the subsequent library processing was done using standard Illumina TruSeq Stranded mRNA Sample Prep Kit (protocol version 15031047 Rev.E).

treatment_protocol: 4 hours incubation of peptide or control vehicle

tag: model

value: Alzheimer’s disease (AD)

value: hippocampal neurons

value: C57/Bl6 wild type

value: MCH


title: KO-H-TRG-176

description: L10a-TRAP translated RNA

value: hypoxia


title: KO-N-INPG-281

description: total RNA

value: normoxia


title: KO-H-INPG-176

description: total RNA


title: KO-N-INPG-176

description: total RNA


title: MCH Treated 3, replicate 3, RNA-seq


title: HET-H-TRG-129

description: L10a-TRAP translated RNA

value: +/fl


title: Patient LPDAC_26 Tumor scRNAseq

description: 10X Genomics


title: HET-H-INPG-129

description: total RNA


title: HET-N-TRG-129

description: L10a-TRAP translated RNA


title: MCH Treated 2, replicate 2, RNA-seq


title: HET-N-INPG-129

description: total RNA


title: Patient LPDAC_25 Tumor scRNAseq

description: 10X Genomics


title: MCH Treated 1, replicate 1, RNA-seq


title: Patient PDAC_50 Tumor scRNAseq

description: 10X Genomics


title: HET-H-TRG-102

description: L10a-TRAP translated RNA


title: KO-H-TRG-281

description: L10a-TRAP translated RNA


title: HET-N-TRG-102

description: L10a-TRAP translated RNA


title: Differentiated cells, CHIR+PUR+RA, Bio rep 3 [CPR3]

city: Shanghai

first: Ting

last: Xu

address: 1239 Siping Road

country: China

institute: Tongji University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle  with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2.
The mapped reads of each sample were assembled by StringTie in a reference-based approach
Assembly: homo_sapiens GRCh38 V101
Supplementary files format and content: tab-delimited text files includeTPM values for each Sample

extract_protocol:
Total RNA was extracted from the cells using TRIzol® Reagent, about  1ug of total RNA was used for the construction of sequencing libraries.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA).

tag: cell line

value: Neural stem cells

value: WT

value: treat with CHIR, Purmorphamine and RA


title: HET-N-INPG-102

description: total RNA

tag: cell type

value: bone marrow derived macrophages


title: Control sample 4, replicate 4, RNA-seq

tag: treatment


title: HET-H-INPG-102

description: total RNA


title: HET-H-TRG-97

description: L10a-TRAP translated RNA


title: Control sample 3, replicate 3, RNA-seq


title: Differentiated cells, CHIR+PUR+RA, Bio rep 2 [CPR2]


title: Patient PDAC_47 Tumor scRNAseq

description: 10X Genomics

value: Primary tumor


title: HET-H-INPG-97

description: total RNA


title: Differentiated cells, CHIR+PUR+RA, Bio rep 1 [CPR1]


title: HET-N-INPG-97

description: total RNA


title: Differentiated cells, CHIR+RA, Bio rep 3 [CR3]

value: treat with CHIR and RA


title: Control sample 1, replicate 1, RNA-seq


title: HET-N-TRG-97

description: L10a-TRAP translated RNA


title: Control sample 2, replicate 2, RNA-seq