title: ChIPseq_T3M4_Input

description: Library name: Sample038

data_processing:
Paired or single end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2/2.5.0. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge (samtools/1.18). Bigwig files for individual and merged bam files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage (deeptools/3.3.2) . MACS2 callpeak (python/3.10.11) was used to call the significant peaks with --broad cutoff 0.05 for histone marks and non-broad cutoff of 0.05 for transcription factors while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: merged bigiwg file for each conditiion
Supplementary files format and content: bed file

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep), PaTu8988s (DMEM, 20% FBS, 1% Pen-Strep), GöCDX5 (keratinocyte-SFM media, 10% FBS, 1% Pen-Strep, recombinant epidermal growth factor, bovine pituitary extract) were maintained in humidified 5% CO2 incubator at 37C. GöCDX5, a GöPDX5-derived cell line, was thawed on collagen coated plates and after the first trypsinization were transferred to a normal cell culture plate. PDX models were generated as described in PMID: 36889906.

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted. For GATA6 and Pol II ChIP of PDX tumors, 5 mm3 samples were thawed on ice in a petri dish, washed three times with PBS, cut into small pieces and transferred to a 15 mL falcon. Samples were fixed with 1% formaldehyde rotating on wheel for 20 min and quenched with 1.25 M glycine for 5 min. Samples were washed three times with PBS, resuspended in RPMI 1640 with 210 µg liberase TH per sample and transferred to gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) and incubated (step 1: spin 50 rpm 20 min; step 2: spin 1000 rpm 30 min; step 3: spin -1000 rpm 30 min). Samples were centrifuged and transferred to a new tube and washed three times with lysis buffer, resuspending the nuclear pellet each time. ChIP was continues as described above for cell lines. For H3K27ac ChIP of PDX tumors, 5 mm3 samples were homogenized on dry ice using the Sciences BioMasher II Micro Tissue Homogenizer. ChIP was carried out for the powdered tissue as described for cell lines.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.


title: ChIPseq_TCCPAN2_BI_300nM_H3K27ac_Rep2

status: Public on Jan 14 2025

type: SRA

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description: Library name: Sample033

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: PDAC


title: ChIPseq_TCCPAN2_BI_300nM_H3K27ac_Rep3

description: Library name: Sample034


title: ChIPseq_T3M4_dNp63_Rep2

description: Library name: Sample036


title: ChIPseq_TCCPAN2_BI_0nM_H3K27ac_Rep3

description: Library name: Sample032


title: ChIPseq_HPAFII_BI_300nM_H3K27ac_Rep1

description: Library name: Sample028

value: HPAFII


title: ChIPseq_HPAFII_BI_300nM_H3K27ac_Rep3

description: Library name: Sample030


title: ChIPseq_HPAFII_BI_0nM_H3K27ac_Rep3

description: Library name: Sample027


title: ChIPseq_HPAFII_BI_300nM_H3K27ac_Rep2

description: Library name: Sample029


title: ATACseq_AsPC1_Ctrl_Rep3

description: Library name: Sample41

data_processing:
Paired end sequencing reads were filtered for adapter contamination with cutadapt/2.8 and mapped to the reference genome assembly hg38 using bowtie2 with --dovetail. BamTools Filter was used for removing low quality (mapQ >= 30) and mitochondrial reads. Resulting bam file was converted to a bed file with bedtools/2.30.0 bamtobed. Peak calling and bedgraph generation was performed using macs2 callpeak using shift and extend method to center peaks at 5’ cut site (shift -100 extension size 200). The data was visualized by using bedGraphToBigWig (ucscbigtools/11-Aug-2023).
Assembly: hg38
Supplementary files format and content: bigwigs for each condition, controls normalized to BI 653048 treatment
Supplementary files format and content: peakfile
Supplementary files format and content: Alternative control normalization against siGATA6

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep) and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol: For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.


title: ChIPseq_HPAFII_BI_0nM_H3K27ac_Rep1

description: Library name: Sample025


title: ChIPseq_HPAFII_BI_0nM_H3K27ac_Rep2

description: Library name: Sample026


title: ATACseq_AsPC1_Ctrl_Rep2

description: Library name: Sample40


title: ChIPseq_AsPC1_BI_300nM_H3K27ac_Rep2

description: Library name: Sample023


title: ATACseq_L36pl_DMSO_Rep3

description: Library name: Sample59


title: ChIPseq_AsPC1_BI_300nM_H3K27ac_Rep1

description: Library name: Sample022


title: ChIPseq_T3M4_dNp63_Rep1

description: Library name: Sample035


title: ChIPseq_AsPC1_BI_0nM_H3K27ac_Rep3

description: Library name: Sample021


title: ChIPseq_AsPC1_BI_0nM_H3K27ac_Rep2

description: Library name: Sample020


title: ChIPseq_AsPC1_BI_0nM_H3K27ac_Rep1

description: Library name: Sample019


title: ChIPseq_T3M4_BI_3000nM_GR

description: Library name: Sample018


title: ChIPseq_L36pl_BI_3000nM_GR

description: Library name: Sample017


title: ChIPseq_L36pl_BI_0nM_GR

description: Library name: Sample016


title: ChIPseq_HPAFII_BI_3000nM_GR

description: Library name: Sample015


title: ChIPseq_T3M4_dNp63_Rep3

description: Library name: Sample037


title: ChIPseq_AsPC1_BI_3000nM_GR

description: Library name: Sample014


title: ChIPseq_AsPC1_BI_0nM_GR

description: Library name: Sample013


title: ChIPseq_L36pl_H3K4me1_Rep2

description: Library name: Sample011


title: ChIPseq_L36pl_H3K4me1_Rep3

description: Library name: Sample012


title: ChIPseq_TCCPAN2_BI_0nM_H3K27ac_Rep2

description: Library name: Sample031


title: ChIPseq_L36pl_H3K27me3_Rep2

description: Library name: Sample008


title: ChIPseq_L36pl_H3K4me1_Rep1

description: Library name: Sample010


title: ChIPseq_AsPC1_BI_300nM_H3K27ac_Rep3

description: Library name: Sample024


title: ChIPseq_L36pl_H3K27me3_Rep1

description: Library name: Sample007


title: ChIPseq_AsPC1_H3K4me1_Rep1

description: Library name: Sample004


title: ChIPseq_AsPC1_H3K27me3_Rep3

description: Library name: Sample003


title: RNAseq_L36pl_siNT5_aRep2

description: Library name: Sample109

library_source: transcriptomic

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using STAR (star/2.7.3a). Reverse (sense strand) reads were quantified using htseq-count (htseq/0.9.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

growth_protocol: AsPC1, TCCPAN2 and T3M4 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep), PaTu8988s (DMEM, 20% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C. PDX models were generated as described in PMID: 36889906.

extract_protocol:
Cells were washed twice with PBS after removing cell culture medium and total RNA was extracted from cells by adding 700 µL of QIAzol, incubated for 5 min on rocker, scraped and transferred to a new tube. 140 µL chloroform was added to the samples, vortexed for 15 sec, incubated for 3 min at room temperature, and centrifuged. Aqueous phase was transferred to a new tube and mixed with an equal volume of isopropanol. Samples were incubated at -20°C overnight and centrifuged. RNA pellet was washed twice with 70% ethanol and the pellet was air-dried at room temperature for 5-10 min. 50 µL of RNAse-free water was used to resuspend the pellet.
Before RNA-sequencing, RNA integrity was validated by gel electrophoresis and libraries were prepped using 500 ng following supplier’s protocol TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020595). The library fragment size was determined by TapeStation.


title: ChIPseq_L36pl_H3K27me3_Rep3

description: Library name: Sample009


title: RNAseq_L36pl_siNT5_aRep3

description: Library name: Sample110


title: RNAseq_L36pl_siTP63_aRep2

description: Library name: Sample112


title: RNAseq_L36pl_siTP63_aRep1

description: Library name: Sample111


title: ChIPseq_AsPC1_H3K27me3_Rep2

description: Library name: Sample002


title: RNAseq_L36pl_siNT5_aRep1

description: Library name: Sample108


title: ChIPseq_AsPC1_H3K4me1_Rep2

description: Library name: Sample005


title: RNAseq_T3M4_siTP63_Rep3

description: Library name: Sample107


title: RNAseq_T3M4_siTP63_Rep1

description: Library name: Sample105


title: RNAseq_T3M4_siNT5_Rep3

description: Library name: Sample104


title: RNAseq_L36pl_siTP63_aRep3

description: Library name: Sample113


title: RNAseq_T3M4_siTP63_Rep2

description: Library name: Sample106


title: RNAseq_T3M4_BI653048_Rep3

description: Library name: Sample101


title: RNAseq_T3M4_BI653048_Rep2

description: Library name: Sample100


title: RNAseq_T3M4_BI653048_Rep1

description: Library name: Sample99


title: RNAseq_T3M4_DMSO_Rep3

description: Library name: Sample98


title: RNAseq_T3M4_DMSO_Rep1

description: Library name: Sample96


title: RNAseq_T3M4_DMSO_Rep2

description: Library name: Sample97


title: ChIPseq_AsPC1_H3K4me1_Rep3

description: Library name: Sample006


title: RNAseq_TCCPAN2_siGATA6_Rep3

description: Library name: Sample95


title: RNAseq_TCCPAN2_siGATA6_Rep2

description: Library name: Sample94


title: RNAseq_TCCPAN2_siGATA6_Rep1

description: Library name: Sample93


title: ChIPseq_AsPC1_H3K27me3_Rep1

description: Library name: Sample001


title: RNAseq_TCCPAN2_siNT5_Rep3

description: Library name: Sample92


title: RNAseq_TCCPAN2_siNT5_Rep2

description: Library name: Sample91


title: RNAseq_TCCPAN2_siNT5_Rep1

description: Library name: Sample90


title: RNAseq_TCCPAN2_BI653048_Rep3

description: Library name: Sample89


title: RNAseq_TCCPAN2_BI653048_Rep1

description: Library name: Sample87


title: RNAseq_TCCPAN2_BI653048_Rep2

description: Library name: Sample88


title: RNAseq_TCCPAN2_DMSO_Rep2

description: Library name: Sample85


title: RNAseq_TCCPAN2_DMSO_Rep3

description: Library name: Sample86


title: RNAseq_TCCPAN2_DMSO_Rep1

description: Library name: Sample84


title: RNAseq_HPAFII_BI653048_Rep2

description: Library name: Sample82


title: RNAseq_HPAFII_BI653048_Rep3

description: Library name: Sample83


title: RNAseq_HPAFII_DMSO_Rep3

description: Library name: Sample80


title: RNAseq_HPAFII_BI653048_Rep1

description: Library name: Sample81


title: RNAseq_HPAFII_DMSO_Rep2

description: Library name: Sample79


title: RNAseq_T3M4_siNT5_Rep2

description: Library name: Sample103


title: RNAseq_T3M4_siNT5_Rep1

description: Library name: Sample102


title: RNAseq_HPAFII_DMSO_Rep1

description: Library name: Sample78


title: RNAseq_AsPC1_siLGALS4_aRep2

description: Library name: Sample76


title: RNAseq_AsPC1_siLGALS4_aRep1

description: Library name: Sample75


title: RNAseq_AsPC1_siCDH17_aRep3

description: Library name: Sample74


title: RNAseq_AsPC1_siCDH17_aRep2

description: Library name: Sample73


title: RNAseq_AsPC1_siLGALS4_aRep3

description: Library name: Sample77


title: RNAseq_AsPC1_siCDH17_aRep1

description: Library name: Sample72


title: RNAseq_AsPC1_siNT5_aRep3

description: Library name: Sample71


title: K562 CTCF MNase HiChIP Rep3

city: Boston

first: Martin

last: Aryee

state: MA

address: 3 Blackfan Circle, 11th Floor

department: Data Science

country: USA

institute: Dana Farber Cancer Institute

description: Library name: K562 CTCF MNase HiChIP Rep3

data_processing:
Four replicates of K562 MNase CTCF HiChIP were aligned to the reference genome (hg38) using the BWA-MEM algorithm (with -5SP -T0). Ligation events were then recorded using pairtools parse v. 0.3.0 (with --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --add-columns pos5, pos3, dist_to_5, dist_to_3, read_len). Parsed reads were then sorted (pairtools sort) and PCR duplicates were removed (pairtools dedup). Final pairs and bam files were then generated using pairtools split --nproc-in 8 --nproc-out 8 --output-pairs ${filename}.mapped.pairs --output-sam -|samtools view -bS -@16 | samtools sort -@16 -o ${filename}.mapped.PT.bam; samtools index ${filename}.mapped.PT.bam We used a Terra pipeline to keep data processing consistent. CTCF MNase HiChIP loop calls were then made from the combined replicate pairs file using FitHiChIP Peak to Peak with 2.5kb loop anchor bin size.
Assembly: hg38
Supplementary files format and content: Combined replicate pairs file (k562_ctcf_mapped.pairs) and FitHiChIP loop calls (K562_CTCF_2.5kb.interactions_FitHiC_Q0.01.bed).

growth_protocol: Four MNase K562 CTCF HiChIP (150 bp paired-end) libraries were generated using the Cantata Bio / Dovetail Genomics MNase HiChIP kit.

extract_protocol:
CTCF MNase HiChIP was performed as described in the Dovetail HiChIP MNase Kit protocol v.2.0. Briefly, 5 million K562 cells per sample were crosslinked with 3mM DSG and 1% formaldehyde and digested with 1ul MNase (“YET” samples) or 2ul MNase (“GW” samples) in 100ul of 1X nuclease digestion buffer. Cells were lysed with 1X RIPA containing 0.1% SDS, and CTCF ChIP was performed using 1500ng of chromatin (40-70% mononucleosomes) and 500 ng of CTCF antibody (Cell Signaling, cat #: 3418). Protein A/G beads pull-down, proximity ligation, and library preparation were done according to the protocol.
Libraries were sequenced to a read depth of ~172 million paired end reads per sample on the Illumina Nextseq 2000 platform.

value: Chronic Myeloid Leukemia

tag: genotype

value: WT


title: K562 CTCF MNase HiChIP Rep4

description: Library name: K562 CTCF MNase HiChIP Rep4


title: K562 CTCF MNase HiChIP Rep2

description: Library name: K562 CTCF MNase HiChIP Rep2


title: RNAseq_AsPC1_siNT5_aRep1

description: Library name: Sample69


title: K562 CTCF MNase HiChIP Rep1

description: Library name: K562 CTCF MNase HiChIP Rep1


title: FIX Tile 3 Bin 4, Strep II tag antibody, BioReplicate 1

city: Seattle

first: Nicholas

middle: Anthony

last: Popp

email: poppn@uw.edu, poppn13@gmail.com

state: Washington

address: 3720 15th Avenue NE, S-320

department: Genome Sciences

institute: University of Washington School of Medicine

description:
MultiSTEP_GEO_counts.csv
MultiSTEP_GEO_scores.csv

data_processing:
library strategy: Targeted barcode amplificatiion from genomic DNA
Libraries were sequenced on either a NextSeq 550 or NextSeq 2000 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Barcode sequencing reads were first converted to FASTQ format and demultiplexed using bcl2fastq (v2.20). Forward and reverse barcode reads were paired using PEAR (v0.9.11). Unique barcodes were counted.
To reduce error associated with counting noise, we removed low frequency variants using a frequency threshold of 1x10-6 as well as variants that were observed in fewer than two replicates. FIX variants were then assigned to sequenced barcodes using the barcode-variant map from PacBio sequencing. Any barcode associated with insertions, deletions, or multiple amino acid substitutions in FIX was removed from the analysis.
Secretion and γ-carboxylation scores were calculated using a weighted average of every variant’s frequency in each bin was calculated with the following weights: wbin 1: 0.25, wbin 2: 0.5, wbin 3: 0.75, wbin 4: 1. The weighted average for each variant was then min-max normalized such that the median score of WT barcodes was 1 and the median score of the lowest 5th percentile of missense variants was 0. The final secretion and γ-carboxylation scores for each variant were then averaged across all replicates. Standard errors for each score were calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed.
Assembly: None
Supplementary files format and content: MultiSTEP_F9_barcode_variant_map_singlevars.csv processed data file is a comma-separated text file containing the barcode-variant map determined by PacBio long-read sequencing.
Supplementary files format and content: MultiSTEP_GEO_counts.csv processed data file is a comma-separated text tile containing the read counts and variant frequency for each variant in each biological replicate.
Supplementary files format and content: MultiSTEP_GEO_scores.csv processed data file is a comma-separated text file containing the functional scores for each variant in each biological replicate.

growth_protocol: Freestyle 293F LLP_attB-BFP-iCasp9-BlastR cells were cultured in Freestyle 293 Expression media supplemented with 2 μg/mL doxycycline on a shaking platform at 37°C, 8% CO2, 135 rpm.

extract_protocol:
Genomic DNA was extracted from harvested cell pellets using the DNEasy Blood and Tissue kit (Qiagen) according to the manufacturers’ protocol with the addition of a 30 minute RNase digestion at 56°C during the resuspension step. Two technical PCR replicates were performed on each bin for each sample to assess the variability in barcode counts from sequencing and amplification. For each replicate, 8 identical 50 μL first-round PCRs were prepared, and each PCR contained 2,500 ng genomic DNA, 25 μL Q5 polymerase, and 0.5 μM of NP0492 and NP0546 primers. Cycling conditions were an initial denaturing at 98°C for 30 seconds, followed by 5 cycles of 98°C for 10 seconds, 61°C for 30 seconds, and 72°C for 30 seconds, followed by a final 72°C extension for 2 minutes and a hold at 4°C. PCR products were then cleaned using 0.8x AmpureXP beads (Beckman Coulter) and eluted in 21 μL water following the manufacturer’s instructions. 8 μL of cleaned PCR product was then mixed with 25 μL Q5 polymerase, 0.25 μL of 100x SYBR Green I (ThermoFisher Scientific) 4.75 μL water, and one uniquely indexed forward (NP0595-NP0608) and reverse (NP0551-NP0564) primer at a final concentration of 0.5 μM. Samples were run on the CFX Connect (Bio-Rad) for a maximum of 20 cycles or until all samples were above 3,000 relative fluorescence units. Reactions were denatured at 98°C for 30 seconds, and cycled at 98°C for 10 seconds, 65°C for 30 seconds, and 72°C for 30 seconds, with a final extension at 72°C for 2 minutes. Samples were then run on a 2% agarose gel with 1x SYBR Safe for 2 hours at 120V before gel extraction with a Freeze ‘N Squeeze column (Bio-Rad). After extraction, samples were quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), pooled in equimolar concentrations, and sequenced using custom sequencing primers NP0494, NP0495, NP0497, and NP0550 on a NextSeq 550 using a NextSeq 500/550 High Output v2.5 75 cycle kit (Illumina) or on a NextSeq 2000 using a NextSeq 1000/2000 P3 50 cycle kit.
Site-saturation mutagenesis oligonucleotides were ordered from Twist Biosciences for each position in F9, except position 1. Each position contained one codon for each synonymous or missense variant. 50 ng of each oligonucleotide were resuspended in 10 μL water, and then pooled in equal volumes into three tiled sublibraries encompassing the entire length of F9, including 20 positions of overlap between adjacent sublibraries. Tile 1 sublibrary: positions 2-164; Tile 2 sublibrary: positions 146-318; Tile 3 sublibrary: positions 299-461. pNP0079 was inverse PCR amplified using NP0295 and NP0325 following the standard protocol, and the correct size PCR product was gel extracted. The backbone PCR product was then Gibson assembled with each of the three pooled sublibraries at a 5:1 molar ratio of insert:backbone at 50°C for 1 hour. Gibson assembled products were then cleaned and eluted in 10 μL water (Zymo Clean and Concentrate). 1 μL of cleaned product was then added to 25 μL NEB-10β E. coli in pre-chilled cuvettes and allowed to rest on ice for 30 minutes. 2 electroporation replicates were performed per sublibrary tile, as well as a pUC19 control (10 pg/μL). Cells were then electroporated at 2 kV for 6 milliseconds. After electroporation, cells were immediately resuspended in 100 μL pre-warmed SOC and transferred to a culture tube. Identical replicates were pooled at this step, and pre-warmed SOC was added to a final volume of 1 mL and allowed to recover at 37°C, shaking at 225 rpm, for 1 hour. After recovery, the entire recovery volume was added to 49 mL of LB containing 100 μg/mL carbenicillin and allowed to grow overnight. After 16 hours of overnight growth at 37°C, each 50 mL midiprep culture was spun down for 30 minutes at 4,300xg and midiprepped. To barcode each sublibrary, 1 μg of each sublibrary plasmid was digested at 37°C for 5 hours with NheI-HF and SacI-HF (New England Biolabs), incubated with rSAP for 30 minutes at 37°C, then heat-inactivated at 65°C for 20 minutes. Digested product was then run on a 1% agarose with 1x SYBR Safe (ThermoFisher Scientific) gel for 45 minutes at 100V and gel extracted (Qiagen). A barcode ultramer (NP0490) was ordered from IDT with 18 degenerate nucleotides and resuspended at 10 μM. 1 μL NP0490 was then annealed with 1 μL of 10 μM NP0397 primer, 4 μL CutSmart buffer, and 34 μL water by running at 98°C for 3 minutes, followed by ramping down to 25°C at -0.1°C per second. After annealing, 1.35 μL of 1 mM dNTPs and 0.8 μL Klenow exo- polymerase (New England Biolabs) were added to fill in the barcode oligo. The cycling conditions were 25°C for 15 minutes, 70°C for 20 minutes, and then ramped down to 37°C in -0.1°C per second increments. Once at 37°C, 1 μL each NheI-HF and SacI-HF were added and digested for 1 hour. Digested product was then run on a 4% agarose gel with 1x SYBR Safe for 45 minutes at 100V and gel extracted (Qiagen). Both gel extracted sublibrary and barcode oligonucleotide were cleaned and eluted in 10 μL and 30 μL water, respectively (Zymo Clean and Concentrate). A 7:1 molar ratio of barcode oligonucleotide to sublibrary was ligated overnight at 16°C with T4 DNA ligase (New England Biolabs). Ligated product was then cleaned and eluted in 10 μL water (Zymo). 1 μL of ligation product, ligation controls, or pUC19 was electroporated into NEB-10β E. coli following the same procedure as above. For sublibrary ligation products, 2 independent replicates were pooled before recovery. After recovery, each sublibrary ligation product was bottlenecked by diluting various recovery volumes (500 μL, 250 μL, 125 μL, and 50 μL) into independent 50 mL LB-ampicillin cultures. After 2-3 minutes of shaking, a 200 μL sample from each ligation bottleneck was taken and used for serial dilutions to estimate colony counts on LB-ampicillin plates. Colony counts were then used to estimate the number of barcoded variants present in each sublibrary for each bottleneck. After 16 hours of overnight growth at 37°C, each 50 mL midiprep culture was spun down for 30 minutes at 4,300g and midiprepped.

treatment_protocol: Freestyle 293F LLP_attB-BFP-iCasp9-BlastR cells were plated at 3x105 cells/mL with the addition of 50 nM vitamin K1. After 24 hours, cells were induced with 2 μg/mL doxycycline and grown for an additional 48 hours. On the day of staining, flasks of cells were split into equal 4 mL volumes and spun at 300xg for 3 minutes. Media was aspirated, and 3 washes of 1 mL cold staining buffer were performed, with 300xg spins and supernatant aspiration between. Cells were then resuspended in 100 μL of diluted primary antibodies and incubated at room temperature for 30 minutes, with vortexing at 10 minute intervals. After primary antibody staining, cells were diluted with 1 mL staining buffer and spun at 300xg for 3 minutes. This washing step was repeated twice more before secondary antibody staining. For secondary antibody staining, cells were resuspended in 100 μL of diluted secondary antibodies and incubated at room temperature for 30 minutes in the dark, with vortexing at 10 minute intervals. After secondary antibody staining, cells were again diluted with 1 mL cold staining buffer and spun at 300xg for 3 minutes. This washing step was repeated twice more before a final resuspension in 500 μL staining buffer. At this point, all identical tubes were pooled. Stained cells were sorted using FACS on an Aria III, dividing the library into four approximately equally sized quartile bins based on the ratio of fluorescent antibody to mCherry fluorescence. At least 2 million cells were sorted into each of the four quartile bins. After sorting, each bin of library cells was spun down at 300xg for 5 minutes and then resuspended in 10 mL of Freestyle 293 Expression media and supplemented with 100 U/mL penicillin and 100 ng/mL streptomycin. Cells were harvested once each bin contained at least 20 million cells. To harvest, cells were spun down at 300xg for 10 minutes, the supernatant was aspirated, and the pellet was flash frozen in liquid nitrogen before storage at -20°C.

value: human embryonic kidney

tag: treatment


title: RNAseq_AsPC1_siNT5_aRep2

description: Library name: Sample70


title: FIX Tile 3 Bin 3, Strep II tag antibody, BioReplicate 1


title: FIX Tile 3 Bin 4, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 3, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 4, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 2, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 1, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 3, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 1, Strep II tag antibody, BioReplicate 1


title: FIX Tile 3 Bin 2, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 2, Light chain antibody, BioReplicate 2


title: FIX Tile 3 Bin 3, Light chain antibody, BioReplicate 2


title: FIX Tile 3 Bin 1, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 1, Light chain antibody, BioReplicate 2


title: FIX Tile 3 Bin 4, Light chain antibody, BioReplicate 1


title: FIX Tile 3 Bin 3, Light chain antibody, BioReplicate 1


title: FIX Tile 3 Bin 1, Light chain antibody, BioReplicate 1


title: FIX Tile 3 Bin 4, Heavy chain antibody, BioReplicate 3


title: FIX Tile 3 Bin 2, Light chain antibody, BioReplicate 1


title: FIX Tile 3 Bin 3, Heavy chain antibody, BioReplicate 3


title: FIX Tile 3 Bin 1, Heavy chain antibody, BioReplicate 3


title: FIX Tile 3 Bin 2, Strep II tag antibody, BioReplicate 1


title: FIX Tile 3 Bin 4, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 3, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 4, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 2, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 1, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 3 Bin 3, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 2 Bin 1, Strep II tag antibody, BioReplicate 1


title: FIX Tile 2 Bin 3, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 1, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 4, Strep II tag antibody, BioReplicate 1


title: FIX Tile 2 Bin 4, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 2 Bin 4, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 3, Light chain antibody, BioReplicate 2


title: FIX Tile 2 Bin 2, Strep II tag antibody, BioReplicate 1


title: FIX Tile 2 Bin 2, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 2 Bin 2, Light chain antibody, BioReplicate 2


title: FIX Tile 2 Bin 3, Strep II tag antibody, BioReplicate 1


title: FIX Tile 3 Bin 4, Light chain antibody, BioReplicate 2


title: FIX Tile 2 Bin 2, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 3, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 2 Bin 1, Light chain antibody, BioReplicate 2


title: FIX Tile 2 Bin 4, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 2, Heavy chain antibody, BioReplicate 3


title: FIX Tile 2 Bin 4, Light chain antibody, BioReplicate 2


title: FIX Tile 2 Bin 1, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 2, Heavy chain antibody, BioReplicate 3


title: FIX Tile 3 Bin 2, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 2 Bin 4, Heavy chain antibody, BioReplicate 3


title: FIX Tile 2 Bin 4, Light chain antibody, BioReplicate 1


title: FIX Tile 2 Bin 2, Light chain antibody, BioReplicate 1


title: FIX Tile 2 Bin 1, Light chain antibody, BioReplicate 1


title: FIX Tile 2 Bin 3, Light chain antibody, BioReplicate 1


title: FIX Tile 2 Bin 3, Heavy chain antibody, BioReplicate 3


title: FIX Tile 2 Bin 1, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 1, Heavy chain antibody, BioReplicate 3


title: FIX Tile 3 Bin 1, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 4, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 4, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 3, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 2 Bin 3, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 1 Bin 1, Strep II tag antibody, BioReplicate 1


title: FIX Tile 2 Bin 2, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 2 Bin 2, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 1 Bin 2, Strep II tag antibody, BioReplicate 1


title: FIX Tile 1 Bin 2, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 1 Bin 4, Strep II tag antibody, BioReplicate 1


title: FIX Tile 2 Bin 1, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 1, Carboxylation-sensitive pan-Gla antibody, BioReplicate 4


title: FIX Tile 1 Bin 3, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 4, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 1, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 4, Light chain antibody, BioReplicate 2


title: FIX Tile 1 Bin 1, Light chain antibody, BioReplicate 2


title: FIX Tile 1 Bin 4, Light chain antibody, BioReplicate 1


title: FIX Tile 1 Bin 2, Light chain antibody, BioReplicate 1


title: FIX Tile 1 Bin 2, Heavy chain antibody, BioReplicate 3


title: FIX Tile 1 Bin 3, Light chain antibody, BioReplicate 1


title: FIX Tile 1 Bin 2, Light chain antibody, BioReplicate 2


title: FIX Tile 1 Bin 3, Light chain antibody, BioReplicate 2


title: FIX Tile 1 Bin 3, Strep II tag antibody, BioReplicate 1


title: FIX Tile 1 Bin 2, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 1 Bin 4, Heavy chain antibody, BioReplicate 3


title: FIX Tile 1 Bin 3, Heavy chain antibody, BioReplicate 3


title: FIX Tile 2 Bin 3, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 1, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 1 Bin 1, Heavy chain antibody, BioReplicate 3


title: FIX Tile 1 Bin 3, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: FIX Tile 1 Bin 1, Light chain antibody, BioReplicate 1


title: FIX Tile 1 Bin 2, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 3, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 1 Bin 1, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 4, Strep II tag antibody, BioReplicate 3


title: FIX Tile 1 Bin 2, Carboxylation-sensitive pan-Gla antibody, BioReplicate 3


title: FIX Tile 3 Bin 3, Strep II tag antibody, BioReplicate 2


title: FIX Tile 3 Bin 2, Strep II tag antibody, BioReplicate 3


title: FIX Tile 3 Bin 4, Strep II tag antibody, BioReplicate 2


title: FIX Tile 3 Bin 4, Heavy chain antibody, BioReplicate 2


title: FIX Tile 3 Bin 2, Strep II tag antibody, BioReplicate 2


title: FIX Tile 3 Bin 1, Strep II tag antibody, BioReplicate 2


title: FIX Tile 3 Bin 2, Heavy chain antibody, BioReplicate 2


title: FIX Tile 3 Bin 3, Heavy chain antibody, BioReplicate 2


title: FIX Tile 3 Bin 1, Heavy chain antibody, BioReplicate 2


title: FIX Tile 3 Bin 3, Heavy chain antibody, BioReplicate 1


title: FIX Tile 3 Bin 4, Heavy chain antibody, BioReplicate 1


title: FIX Tile 3 Bin 1, Heavy chain antibody, BioReplicate 1


title: FIX Tile 3 Bin 2, Heavy chain antibody, BioReplicate 1


title: FIX Tile 2 Bin 4, Strep II tag antibody, BioReplicate 3


title: FIX Tile 2 Bin 3, Strep II tag antibody, BioReplicate 3


title: FIX Tile 1 Bin 4, Carboxylation-sensitive FIX Gla antibody, BioReplicate 3


title: FIX Tile 2 Bin 3, Strep II tag antibody, BioReplicate 2


title: FIX Tile 2 Bin 1, Strep II tag antibody, BioReplicate 3


title: H3T20

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

country: China

institute: Yangzhou University

description: Library name: Sample 36

data_processing:
The Fastp software (v0.23.4) was used to perform quality control (QC) on the raw data and obtain clean data with default parameters. The HISAT2 software (v2.2.1) was used to align the obtained clean data referred to the latest reference genome in sheep (ARS-UI_Ramb_v3.0). The Samtools software (v.1.20) was used to sort and convert the SAM files to BAM format. the Stringtie software (v2.1.5) was used to assemble and quantify the transcripts and genes based on read counts.
Assembly: sheep reference genome ARS-UI_Ramb_v3.0
Supplementary files format and content: a excel file named "gene count matrix for RNA-seq.csv" of raw counts  for each sample

molecule: total RNA

organism: Ovis aries

source_name: ovine ruminal epithelial cells

extract_protocol:
Total RNA was extracted from ORECs using the TRNzol Universal reagent (DP424, TIANGEN, Beijing, China) and genomic DNA was removed using DNase I (TaKara).
High-quality RNA sample was used to construct sequencing library using TruSeq RNA Library Prep Kit v2 (Illumina) according to Illumina’s protocol. RNA sequencing was performed using Illumina NovaSeq 6000 (PE150).

value: ovine ruminal epithelial cells

value: Hay-VFAs

tag: time


title: FIX Tile 3 Bin 3, Strep II tag antibody, BioReplicate 3


title: FIX Tile 2 Bin 2, Strep II tag antibody, BioReplicate 2


title: FIX Tile 2 Bin 1, Strep II tag antibody, BioReplicate 2


title: H3T16

description: Library name: Sample 35


title: FIX Tile 3 Bin 1, Strep II tag antibody, BioReplicate 3


title: H3T4

description: Library name: Sample 32


title: FIX Tile 2 Bin 2, Heavy chain antibody, BioReplicate 2


title: FIX Tile 2 Bin 4, Heavy chain antibody, BioReplicate 1


title: FIX Tile 2 Bin 3, Heavy chain antibody, BioReplicate 2


title: H3T8

description: Library name: Sample 33


title: FIX Tile 1 Bin 4, Carboxylation-sensitive FIX Gla antibody, BioReplicate 4


title: H3T12

description: Library name: Sample 34


title: FIX Tile 2 Bin 4, Heavy chain antibody, BioReplicate 2


title: FIX Tile 2 Bin 1, Heavy chain antibody, BioReplicate 2


title: H2T20

description: Library name: Sample 30


title: H2T16

description: Library name: Sample 29


title: FIX Tile 2 Bin 2, Heavy chain antibody, BioReplicate 1


title: FIX Tile 2 Bin 2, Strep II tag antibody, BioReplicate 3


title: H2T8

description: Library name: Sample 27


title: FIX Tile 2 Bin 1, Heavy chain antibody, BioReplicate 1


title: H2T12

description: Library name: Sample 28


title: H2T4

description: Library name: Sample 26


title: FIX Tile 1 Bin 4, Strep II tag antibody, BioReplicate 3


title: H2T0

description: Library name: Sample 25


title: H1T20

description: Library name: Sample 24


title: FIX Tile 1 Bin 3, Strep II tag antibody, BioReplicate 3


title: FIX Tile 1 Bin 1, Strep II tag antibody, BioReplicate 3


title: FIX Tile 1 Bin 2, Strep II tag antibody, BioReplicate 3


title: H1T16

description: Library name: Sample 23


title: FIX Tile 1 Bin 4, Strep II tag antibody, BioReplicate 2


title: H1T12

description: Library name: Sample 22


title: H3T0

description: Library name: Sample 31


title: FIX Tile 2 Bin 3, Heavy chain antibody, BioReplicate 1


title: FIX Tile 1 Bin 3, Strep II tag antibody, BioReplicate 2


title: H1T8

description: Library name: Sample 21


title: FIX Tile 1 Bin 2, Strep II tag antibody, BioReplicate 2


title: H1T0

description: Library name: Sample 19


title: G3T16

description: Library name: Sample 17

value: Grain-VFAs


title: G3T20

description: Library name: Sample 18


title: FIX Tile 1 Bin 1, Strep II tag antibody, BioReplicate 2


title: H1T4

description: Library name: Sample 20


title: FIX Tile 1 Bin 2, Heavy chain antibody, BioReplicate 2


title: FIX Tile 1 Bin 4, Heavy chain antibody, BioReplicate 2


title: FIX Tile 1 Bin 3, Heavy chain antibody, BioReplicate 2


title: G3T12

description: Library name: Sample 16


title: G3T4

description: Library name: Sample 14


title: FIX Tile 1 Bin 1, Heavy chain antibody, BioReplicate 2


title: G3T8

description: Library name: Sample 15


title: G3T0

description: Library name: Sample 13


title: FIX Tile 1 Bin 4, Heavy chain antibody, BioReplicate 1


title: G2T20

description: Library name: Sample 12


title: FIX Tile 1 Bin 1, Heavy chain antibody, BioReplicate 1


title: FIX Tile 1 Bin 2, Heavy chain antibody, BioReplicate 1


title: FIX Tile 1 Bin 3, Heavy chain antibody, BioReplicate 1


title: Control 4 HFD Periportal Bio Rep 3

city: Baton Rouge

first: Tim

last: Heden*

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

description:
Library name: DSP-1001660015952-G-H08
FFPE Spatial Transcriptome Sequencing

data_processing:
The GeoMx NGS Pipeline was used to process FASTQ sequencing files from Nanostring GeoMx libraries to produce digital count conversion files. The DCC files were packed into a zip file and uploaded into the GeoMx Digital Spatial Profiler system for spatially resolved expression analysis and visualizations.
Assembly: Mm10
Supplementary files format and content: Slide_Image_with_ROIs_Study_2_Blk_1.tiff
Supplementary files format and content: Slide_Image_with_ROIs_Study_2_Blk_2.tiff
Supplementary files format and content: Information_Summary_for_each_ROI.xlsx
Supplementary files format and content: GeneExpression_CountData.xlsx
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Liver

extract_protocol:
Formalin Fixed Paraffin Embedded Tissue was sectioned to a 5 micron thickness.
Spatial transcriptome sequencing libraries were prepared with Nanostring GeoMx Mouse NGS Whole Transcritpome Atlas RNA panel.

value: Liver


title: G2T16

description: Library name: Sample 11


title: G2T12

description: Library name: Sample 10


title: Control 4 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-H06
FFPE Spatial Transcriptome Sequencing


title: G2T4

description: Library name: Sample 8


title: Control 4 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-H05
FFPE Spatial Transcriptome Sequencing


title: G1T20

description: Library name: Sample 6


title: Control 4 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-H03
FFPE Spatial Transcriptome Sequencing


title: Control 4 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-H04
FFPE Spatial Transcriptome Sequencing


title: G1T12

description: Library name: Sample 4


title: Control 3 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-H01
FFPE Spatial Transcriptome Sequencing


title: G1T8

description: Library name: Sample 3


title: Control 3 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-G12
FFPE Spatial Transcriptome Sequencing


title: G1T16

description: Library name: Sample 5


title: G1T4

description: Library name: Sample 2


title: FIX Tile 2 Bin 4, Strep II tag antibody, BioReplicate 2


title: C4-2 Enz-R 3

city: Tianjin

first: zhiqun

last: shang

address: Pingjiang road, tianjin

institute: tianjin medical university

description:
Library name: Sample 6
Sample 6

data_processing:
HISAT2 workbench
Assembly: GRCh38
Supplementary files format and content: txt. File with counts

source_name: prostate cancer

extract_protocol:
Total RNA from the cancer cells was extracted with TRIzol (Invitrogen).
Briefly, 1ug purified mRNAs were used for RNA-Seq library generation with the NEBNext® Ultra™ RNA Library Prep Kit (# E7530, NEB, MA, USA) and were subjected to 150 bp paired-end sequencing on an Illumina HiSeq sequencer.

value: prostate cancer

value: C4-2 Enz-R


title: G1T0

description: Library name: Sample 1


title: Control 3 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-G10
FFPE Spatial Transcriptome Sequencing


title: Control 3 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-G09
FFPE Spatial Transcriptome Sequencing


title: C4-2 Enz-R 2

description:
Library name: Sample 5
Sample 5


title: Control 2 HFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-G08
FFPE Spatial Transcriptome Sequencing


title: Control 4 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-H07
FFPE Spatial Transcriptome Sequencing


title: C4-2 parental 3

description:
Library name: Sample 3
Sample 3

value: C4-2 parental


title: Control 2 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-G07
FFPE Spatial Transcriptome Sequencing


title: Control 2 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-G06
FFPE Spatial Transcriptome Sequencing


title: G2T8

description: Library name: Sample 9


title: Control 2 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-G05
FFPE Spatial Transcriptome Sequencing


title: C4-2 parental 2

description:
Library name: Sample 2
Sample 2


title: C4-2 parental 1

description:
Library name: Sample 1
Sample 1


title: G2T0

description: Library name: Sample 7


title: Control 1 HFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-G02
FFPE Spatial Transcriptome Sequencing


title: Control 1 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-G01
FFPE Spatial Transcriptome Sequencing


title: Control 2 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-G04
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from mucosa of descending colon (ENCLB870RYA)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR681ARR/
***************
biological replicate number: 1
technical replicate number: 1
description: W64 mucosa of descending colon
experiment encode accession: ENCSR681ARR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-26
lab: Barbara Wold, Caltech
library encode accession: ENCLB870RYA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (26 years) mucosa of descending colon tissue, preserved by flash-freezing

value: mucosa of descending colon

value: tissue

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: DM:no; HTN:no; CAD:no

tag: dev stage

value: adult

tag: age

value: 26 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS841OTS at ENCODE; https://www.encodeproject.org/ENCBS841OTS/


title: Control 3 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-G11
FFPE Spatial Transcriptome Sequencing


title: Control 1 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-F12
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from heart right ventricle (ENCLB262WJR)

description:
https://www.encodeproject.org/experiments/ENCSR441IDG/
***************
biological replicate number: 1
technical replicate number: 1
description: UW038 heart right ventricle
experiment encode accession: ENCSR441IDG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB262WJR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (55 years) heart right ventricle tissue

value: heart right ventricle

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

value: 55 year

value: Shin Lin

value: ENCBS397EAK at ENCODE; https://www.encodeproject.org/ENCBS397EAK/


title: total RNA-seq from HCT116 (ENCLB750BWO)

description:
https://www.encodeproject.org/experiments/ENCSR945VLG/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-POLR2A-clone1-untreated-new_bulk-B10
experiment encode accession: ENCSR945VLG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB750BWO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A

tag: line

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS038BAW at ENCODE; https://www.encodeproject.org/ENCBS038BAW/


title: Control 3 HFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-H02
FFPE Spatial Transcriptome Sequencing

tag: tissue

value: Liver


title: Control 2 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-G03
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB012HOL)

description:
https://www.encodeproject.org/experiments/ENCSR945VLG/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-POLR2A-clone1-untreated-new_bulk-B10
experiment encode accession: ENCSR945VLG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB012HOL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: male

value: adult

value: ENCBS976NRF at ENCODE; https://www.encodeproject.org/ENCBS976NRF/


title: RIP-seq from K562 (ENCLB296KKL)

description:
https://www.encodeproject.org/experiments/ENCSR433RRS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR433RRS
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB296KKL
fragmentation methods: sonication (generic)
size range: 150-150

source_name: Homo sapiens K562 cell line

tag: antibody

value: CTCF

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Bradley Bernstein, Broad

value: ATCC

value: not applicable

value: ENCBS532KVA at ENCODE; https://www.encodeproject.org/ENCBS532KVA/


title: Control 1 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-F09
FFPE Spatial Transcriptome Sequencing


title: C4-2 Enz-R 1

description:
Library name: Sample 4
Sample 4

value: prostate cancer

tag: cell line

value: C4-2 Enz-R


title: Control 1 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-F10
FFPE Spatial Transcriptome Sequencing


title: Het KO 4 HFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-F08
FFPE Spatial Transcriptome Sequencing


title: RIP-seq from K562 (ENCLB897QGI)

description:
https://www.encodeproject.org/experiments/ENCSR433RRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR433RRS
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB897QGI
fragmentation methods: sonication (generic)
size range: 150-150

value: cell line

value: ENCBS216WMI at ENCODE; https://www.encodeproject.org/ENCBS216WMI/


title: RIP-seq from K562 (ENCLB576IJT)

description:
https://www.encodeproject.org/experiments/ENCSR433RRS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR433RRS
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB576IJT
fragmentation methods: sonication (generic)
size range: 150-150

value: ENCBS323WRW at ENCODE; https://www.encodeproject.org/ENCBS323WRW/


title: total RNA-seq from HCT116 (ENCLB111HGM)

description:
https://www.encodeproject.org/experiments/ENCSR931ATS/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-MED14-clone1-treated-new_bulk-4C
experiment encode accession: ENCSR931ATS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB111HGM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS066LQR at ENCODE; https://www.encodeproject.org/ENCBS066LQR/


title: Het KO 4 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-F06
FFPE Spatial Transcriptome Sequencing

value: Liver


title: Het KO 4 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-F05
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from heart right ventricle (ENCLB934SPI)

description:
https://www.encodeproject.org/experiments/ENCSR889IAP/
***************
biological replicate number: 1
technical replicate number: 1
description: UW036 heart right ventricle
experiment encode accession: ENCSR889IAP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB934SPI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (61 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: male

value: nonischemic (EF 11% LVEDD 7.7; RV severe dilation, severe dysfunction)

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS605FHL at ENCODE; https://www.encodeproject.org/ENCBS605FHL/


title: Het KO 4 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-F07
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from heart left ventricle (ENCLB204LAO)

description:
https://www.encodeproject.org/experiments/ENCSR882RCG/
***************
biological replicate number: 1
technical replicate number: 1
description: UW054 heart left ventricle
experiment encode accession: ENCSR882RCG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB204LAO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (54 years) heart left ventricle tissue

value: heart left ventricle

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: 54 year

value: not applicable

value: ENCBS943DGX at ENCODE; https://www.encodeproject.org/ENCBS943DGX/


title: Het KO 4 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-F04
FFPE Spatial Transcriptome Sequencing


title: Het KO 4 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-F03
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from esophagus mucosa (ENCLB381LKK)

description:
https://www.encodeproject.org/experiments/ENCSR636QDK/
***************
biological replicate number: 1
technical replicate number: 1
description: W71 esophagus mucosa
experiment encode accession: ENCSR636QDK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB381LKK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (47 years) esophagus mucosa tissue, preserved by flash-freezing

value: esophagus mucosa

value: female

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Yiing Lin, MD, PhD

value: ENCBS503WYP at ENCODE; https://www.encodeproject.org/ENCBS503WYP/


title: total RNA-seq from uterus (ENCLB568SHY)

description:
https://www.encodeproject.org/experiments/ENCSR676SRP/
***************
biological replicate number: 1
technical replicate number: 1
description: W73 uterus
experiment encode accession: ENCSR676SRP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB568SHY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (59 years) uterus tissue, preserved by flash-freezing

value: uterus

value: tissue

value: 59 year

value: ENCBS178VYX at ENCODE; https://www.encodeproject.org/ENCBS178VYX/


title: Het KO 3 HFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-F02
FFPE Spatial Transcriptome Sequencing

value: Liver


title: total RNA-seq from psoas muscle (ENCLB567HZE)

description:
https://www.encodeproject.org/experiments/ENCSR870IUI/
***************
biological replicate number: 1
technical replicate number: 1
description: W62 psoas muscle
experiment encode accession: ENCSR870IUI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB567HZE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female child (16 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

value: ENCBS479HPS at ENCODE; https://www.encodeproject.org/ENCBS479HPS/


title: Control 1 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-F11
FFPE Spatial Transcriptome Sequencing


title: Het KO 3 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-E11
FFPE Spatial Transcriptome Sequencing


title: Het KO 3 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-F01
FFPE Spatial Transcriptome Sequencing


title: Het KO 3 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-E12
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from heart right ventricle (ENCLB572AZV)

description:
https://www.encodeproject.org/experiments/ENCSR854VRX/
***************
biological replicate number: 1
technical replicate number: 1
description: UW076 heart right ventricle
experiment encode accession: ENCSR854VRX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB572AZV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (43 years) heart right ventricle tissue

value: heart right ventricle

value: male

value: nonischemic (EF 23%, LVEDD 6.1; RV moderate dilation, normal function)

value: adult

value: 43 year

value: Shin Lin

value: not applicable

value: ENCBS488WUX at ENCODE; https://www.encodeproject.org/ENCBS488WUX/


title: total RNA-seq from ureter (ENCLB304SRT)

description:
https://www.encodeproject.org/experiments/ENCSR619DQO/
***************
biological replicate number: 1
technical replicate number: 1
description: W71 ureter
experiment encode accession: ENCSR619DQO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB304SRT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (47 years) ureter tissue, preserved by flash-freezing

value: ureter

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Yiing Lin, MD, PhD

value: ENCBS604WKC at ENCODE; https://www.encodeproject.org/ENCBS604WKC/


title: total RNA-seq from psoas muscle (ENCLB865QTY)

description:
https://www.encodeproject.org/experiments/ENCSR629HFE/
***************
biological replicate number: 1
technical replicate number: 1
description: W73 psoas muscle
experiment encode accession: ENCSR629HFE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB865QTY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (59 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: 59 year

value: Michael Snyder, Stanford

value: ENCBS200HBA at ENCODE; https://www.encodeproject.org/ENCBS200HBA/


title: RIP-seq from GM12878 (ENCLB426GUK)

description:
https://www.encodeproject.org/experiments/ENCSR593SOD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR593SOD
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR477ECC
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB426GUK
fragmentation methods: none
size range: 150-150

source_name: Homo sapiens GM12878 cell line

value: CTCF

value: cell line

value: unknown

value: Bradley Bernstein, Broad

value: Coriell

value: ENCBS571ZAL at ENCODE; https://www.encodeproject.org/ENCBS571ZAL/


title: Het KO 3 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-E09
FFPE Spatial Transcriptome Sequencing

value: Liver


title: Het KO 2 HFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-E08
FFPE Spatial Transcriptome Sequencing


title: RIP-seq from GM12878 (ENCLB462WBF)

description:
https://www.encodeproject.org/experiments/ENCSR593SOD/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR593SOD
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR477ECC
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB462WBF
fragmentation methods: none
size range: 150-150

value: adult

value: not applicable

value: ENCBS166BUX at ENCODE; https://www.encodeproject.org/ENCBS166BUX/


title: total RNA-seq from heart right ventricle (ENCLB537QJC)

description:
https://www.encodeproject.org/experiments/ENCSR828JSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: UW040 heart right ventricle
experiment encode accession: ENCSR828JSJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB537QJC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (69 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: male

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 69 year

value: Shin Lin

value: ENCBS046OBK at ENCODE; https://www.encodeproject.org/ENCBS046OBK/


title: Het KO 2 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-E07
FFPE Spatial Transcriptome Sequencing

source_name: Liver


title: Het KO 2 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-E06
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB716UQV)

description:
https://www.encodeproject.org/experiments/ENCSR931ATS/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-MED14-clone1-treated-new_bulk-4C
experiment encode accession: ENCSR931ATS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB716UQV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS896ORZ at ENCODE; https://www.encodeproject.org/ENCBS896ORZ/


title: RIP-seq from GM12878 (ENCLB933KGH)

description:
https://www.encodeproject.org/experiments/ENCSR593SOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR593SOD
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR477ECC
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB933KGH
fragmentation methods: none
size range: 150-150

value: CTCF

value: cell line

value: female

value: unknown

value: Bradley Bernstein, Broad

value: Coriell

value: ENCBS866OKF at ENCODE; https://www.encodeproject.org/ENCBS866OKF/


title: Het KO 2 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-E05
FFPE Spatial Transcriptome Sequencing

value: Liver


title: RIP-seq from GM12878 (ENCLB559LZB)

description:
https://www.encodeproject.org/experiments/ENCSR551YTL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR551YTL
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR477ECC
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB559LZB
fragmentation methods: none
size range: 150-150

value: adult

value: not applicable

value: ENCBS571ZAL at ENCODE; https://www.encodeproject.org/ENCBS571ZAL/


title: total RNA-seq from lower lobe of left lung (ENCLB784CDY)

description:
https://www.encodeproject.org/experiments/ENCSR568UGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: W80 lower lobe of left lung
experiment encode accession: ENCSR568UGZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB784CDY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (61 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS921WDE at ENCODE; https://www.encodeproject.org/ENCBS921WDE/


title: RIP-seq from GM12878 (ENCLB804KFL)

description:
https://www.encodeproject.org/experiments/ENCSR551YTL/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR551YTL
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR477ECC
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB804KFL
fragmentation methods: none
size range: 150-150

value: cell line


title: Het KO 2 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-E04
FFPE Spatial Transcriptome Sequencing


title: Het KO 2 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-E03
FFPE Spatial Transcriptome Sequencing


title: Het KO 1 HFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-E02
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB100CAA)

description:
https://www.encodeproject.org/experiments/ENCSR800KLD/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-RAD21-clone1-untreated-new_bulk-C1
experiment encode accession: ENCSR800KLD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB100CAA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS470QIL at ENCODE; https://www.encodeproject.org/ENCBS470QIL/


title: Het KO 1 HFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-E01
FFPE Spatial Transcriptome Sequencing

value: Liver


title: Het KO 3 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-E10
FFPE Spatial Transcriptome Sequencing


title: Het KO 1 HFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-D11
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB816PFW)

description:
https://www.encodeproject.org/experiments/ENCSR800KLD/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-RAD21-clone1-untreated-new_bulk-C1
experiment encode accession: ENCSR800KLD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB816PFW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adult

value: not applicable

value: ENCBS767IFU at ENCODE; https://www.encodeproject.org/ENCBS767IFU/


title: total RNA-seq from heart left ventricle (ENCLB516NAR)

description:
https://www.encodeproject.org/experiments/ENCSR790BBE/
***************
biological replicate number: 1
technical replicate number: 1
description: UW068 heart left ventricle
experiment encode accession: ENCSR790BBE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB516NAR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (56 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: female

value: PGD

value: 56 year

value: Shin Lin

value: ENCBS531TYS at ENCODE; https://www.encodeproject.org/ENCBS531TYS/


title: Het KO 1 HFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-D10
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from right lobe of liver (ENCLB324ONR)

description:
https://www.encodeproject.org/experiments/ENCSR534OAS/
***************
biological replicate number: 1
technical replicate number: 1
description: W82 right lobe of liver
experiment encode accession: ENCSR534OAS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB324ONR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (45 years) right lobe of liver tissue, preserved by flash-freezing

value: right lobe of liver

value: male

value: DM:no; HTN:yes; CAD:no

value: 45 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS280RHQ at ENCODE; https://www.encodeproject.org/ENCBS280RHQ/


title: total RNA-seq from heart left ventricle (ENCLB300DPB)

description:
https://www.encodeproject.org/experiments/ENCSR570DQR/
***************
biological replicate number: 1
technical replicate number: 1
description: UW076 heart left ventricle
experiment encode accession: ENCSR570DQR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB300DPB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (43 years) heart left ventricle tissue

value: nonischemic (EF 23%, LVEDD 6.1; RV moderate dilation, normal function)

value: adult

value: 43 year

value: ENCBS230VLO at ENCODE; https://www.encodeproject.org/ENCBS230VLO/


title: Het KO 1 HFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-D09
FFPE Spatial Transcriptome Sequencing

value: Liver


title: Control 4 LFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-D05
FFPE Spatial Transcriptome Sequencing


title: Control 4 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-D07
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB777AWG)

description:
https://www.encodeproject.org/experiments/ENCSR294AKN/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-CDK7-untreated-new_bulk-A4
experiment encode accession: ENCSR294AKN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB777AWG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: not applicable

value: ENCBS298VZU at ENCODE; https://www.encodeproject.org/ENCBS298VZU/


title: total RNA-seq from HCT116 (ENCLB800UTG)

description:
https://www.encodeproject.org/experiments/ENCSR502PAY/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-CDK7-treated-new_bulk-A4
experiment encode accession: ENCSR502PAY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB800UTG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS806WQS at ENCODE; https://www.encodeproject.org/ENCBS806WQS/


title: total RNA-seq from HCT116 (ENCLB966TKR)

description:
https://www.encodeproject.org/experiments/ENCSR502PAY/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-CDK7-treated-new_bulk-A4
experiment encode accession: ENCSR502PAY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB966TKR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS040KDM at ENCODE; https://www.encodeproject.org/ENCBS040KDM/


title: total RNA-seq from HCT116 (ENCLB652WVK)

description:
https://www.encodeproject.org/experiments/ENCSR275SNI/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-BRD4-clone1-treated-new_bulk-1F
experiment encode accession: ENCSR275SNI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB652WVK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: ENCBS569QUD at ENCODE; https://www.encodeproject.org/ENCBS569QUD/


title: total RNA-seq from HCT116 (ENCLB614QIF)

description:
https://www.encodeproject.org/experiments/ENCSR294AKN/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-CDK7-untreated-new_bulk-A4
experiment encode accession: ENCSR294AKN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB614QIF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS921NBP at ENCODE; https://www.encodeproject.org/ENCBS921NBP/


title: Control 3 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-D02
FFPE Spatial Transcriptome Sequencing


title: Control 4 LFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-D03
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB833KPI)

description:
https://www.encodeproject.org/experiments/ENCSR275SNI/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-BRD4-clone1-treated-new_bulk-1F
experiment encode accession: ENCSR275SNI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB833KPI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adult

value: ENCBS116FGF at ENCODE; https://www.encodeproject.org/ENCBS116FGF/


title: Control 4 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-D06
FFPE Spatial Transcriptome Sequencing


title: Control 4 LFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-D04
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from heart right ventricle (ENCLB949HRC)

description:
https://www.encodeproject.org/experiments/ENCSR278TQR/
***************
biological replicate number: 1
technical replicate number: 1
description: UW067 heart right ventricle
experiment encode accession: ENCSR278TQR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB949HRC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (66 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: 66 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS655VDJ at ENCODE; https://www.encodeproject.org/ENCBS655VDJ/


title: total RNA-seq from HCT116 (ENCLB628LDS)

description:
https://www.encodeproject.org/experiments/ENCSR267FRL/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-BRD4-clone1-untreated-new_bulk-1F
experiment encode accession: ENCSR267FRL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB628LDS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: not applicable

value: ENCBS909MRS at ENCODE; https://www.encodeproject.org/ENCBS909MRS/


title: total RNA-seq from HCT116 (ENCLB170OEZ)

description:
https://www.encodeproject.org/experiments/ENCSR266SBI/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-CTCF-treated-new_bulk-D12
experiment encode accession: ENCSR266SBI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB170OEZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS895NSJ at ENCODE; https://www.encodeproject.org/ENCBS895NSJ/


title: total RNA-seq from HCT116 (ENCLB635BLG)

description:
https://www.encodeproject.org/experiments/ENCSR267FRL/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-BRD4-clone1-untreated-new_bulk-1F
experiment encode accession: ENCSR267FRL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB635BLG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adult

value: ENCBS913PLQ at ENCODE; https://www.encodeproject.org/ENCBS913PLQ/


title: RIP-seq from GM12878 (ENCLB317EQR)

description:
https://www.encodeproject.org/experiments/ENCSR551YTL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR551YTL
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR477ECC
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB317EQR
fragmentation methods: none
size range: 150-150

value: female

value: unknown

value: Bradley Bernstein, Broad

value: Coriell

value: ENCBS166BUX at ENCODE; https://www.encodeproject.org/ENCBS166BUX/


title: Control 4 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-D08
FFPE Spatial Transcriptome Sequencing

value: Liver


title: total RNA-seq from T-helper 1 cell (ENCLB622OQU)

description:
https://www.encodeproject.org/experiments/ENCSR743TJZ/
***************
biological replicate number: 2
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th1 (aIL-4 1ug/ml+IL-12 30ng/ml)(day 14)
experiment encode accession: ENCSR743TJZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB622OQU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (35 years) T-helper 1 primary cell treated with 30 ng/mL Interleukin-12 subunit beta for 36 hours, 30 ng/mL Interleukin-12 subunit alpha for 36 hours, 1 μg/mL Interleukin-4 antibody for 36 hours

value: T-helper 1 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:36; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:36; duration_units:hour; treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS941XOI at ENCODE; https://www.encodeproject.org/ENCBS941XOI/


title: Control 3 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-D01
FFPE Spatial Transcriptome Sequencing


title: Het KO 1 HFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-D12
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from T-helper 1 cell (ENCLB268KWG)

description:
https://www.encodeproject.org/experiments/ENCSR743TJZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th1 (aIL-4 1ug/ml+IL-12 30ng/ml)(day 14)
experiment encode accession: ENCSR743TJZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB268KWG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: male

value: not applicable

value: ENCBS995NLO at ENCODE; https://www.encodeproject.org/ENCBS995NLO/


title: total RNA-seq from HCT116 (ENCLB601FNR)

description:
https://www.encodeproject.org/experiments/ENCSR257FJF/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-POLR2A-clone1-treated-new_bulk-B10
experiment encode accession: ENCSR257FJF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB601FNR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS606HUI at ENCODE; https://www.encodeproject.org/ENCBS606HUI/


title: total RNA-seq from HCT116 (ENCLB228BCP)

description:
https://www.encodeproject.org/experiments/ENCSR266SBI/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-CTCF-treated-new_bulk-D12
experiment encode accession: ENCSR266SBI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB228BCP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS753USK at ENCODE; https://www.encodeproject.org/ENCBS753USK/


title: Control 3 LFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-C11
FFPE Spatial Transcriptome Sequencing

value: Liver


title: Control 2 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-C08
FFPE Spatial Transcriptome Sequencing


title: Control 3 LFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-C09
FFPE Spatial Transcriptome Sequencing


title: Control 2 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-C07
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB553GHK)

description:
https://www.encodeproject.org/experiments/ENCSR257FJF/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-POLR2A-clone1-treated-new_bulk-B10
experiment encode accession: ENCSR257FJF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB553GHK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS141PCL at ENCODE; https://www.encodeproject.org/ENCBS141PCL/


title: Control 2 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-C06
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB685IZF)

description:
https://www.encodeproject.org/experiments/ENCSR729VMM/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-CTCF-untreated-new_bulk-D12
experiment encode accession: ENCSR729VMM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB685IZF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

value: ENCBS242YXD at ENCODE; https://www.encodeproject.org/ENCBS242YXD/


title: Control 2 LFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-C05
FFPE Spatial Transcriptome Sequencing


title: Control 2 LFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-C03
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from activated T-helper 1 cell (ENCLB074ZEJ)

description:
https://www.encodeproject.org/experiments/ENCSR475KPG/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th1 (aIL-4 1ug/ml+IL-12 30ng/ml)(day 13)+beads (1:3) day 1
experiment encode accession: ENCSR475KPG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB074ZEJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (35 years) activated T-helper 1 primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 30 ng/mL Interleukin-12 subunit beta for 36 hours, 10 ng/mL Interleukin-2 for 14 days, anti-CD3 and anti-CD28 coated b...

value: activated T-helper 1 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:36; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:14; duration_units:day; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day; treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; duration:36; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:36; duration_units:hour;

value: ENCBS942GGC at ENCODE; https://www.encodeproject.org/ENCBS942GGC/


title: total RNA-seq from HCT116 (ENCLB893VKV)

description:
https://www.encodeproject.org/experiments/ENCSR729VMM/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-CTCF-untreated-new_bulk-D12
experiment encode accession: ENCSR729VMM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB893VKV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: not applicable

value: ENCBS529HYV at ENCODE; https://www.encodeproject.org/ENCBS529HYV/


title: total RNA-seq from activated T-helper 1 cell (ENCLB894UWQ)

description:
https://www.encodeproject.org/experiments/ENCSR475KPG/
***************
biological replicate number: 2
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th1 (aIL-4 1ug/ml+IL-12 30ng/ml)(day 13)+beads (1:3) day 1
experiment encode accession: ENCSR475KPG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB894UWQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS035SRN at ENCODE; https://www.encodeproject.org/ENCBS035SRN/


title: Control 3 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-C12
FFPE Spatial Transcriptome Sequencing

value: Liver


title: total RNA-seq from heart right ventricle (ENCLB393SOY)

description:
https://www.encodeproject.org/experiments/ENCSR727DPU/
***************
biological replicate number: 1
technical replicate number: 1
description: UW068 heart right ventricle
experiment encode accession: ENCSR727DPU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB393SOY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (56 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: female

value: PGD

value: 56 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS189LQW at ENCODE; https://www.encodeproject.org/ENCBS189LQW/


title: Control 2 LFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-C04
FFPE Spatial Transcriptome Sequencing

source_name: Liver


title: Control 1 LFD Perivenous Bio Rep 3

description:
Library name: DSP-1001660015952-G-B11
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB142YWG)

description:
https://www.encodeproject.org/experiments/ENCSR714CHF/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-SMARCA5-clone1-untreated-new_bulk-E3
experiment encode accession: ENCSR714CHF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB142YWG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS349LBR at ENCODE; https://www.encodeproject.org/ENCBS349LBR/


title: Control 1 LFD Periportal Bio Rep 3

description:
Library name: DSP-1001660015952-G-C02
FFPE Spatial Transcriptome Sequencing


title: Control 1 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-C01
FFPE Spatial Transcriptome Sequencing


title: Control 1 LFD Periportal Bio Rep 1

description:
Library name: DSP-1001660015952-G-B12
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from HCT116 (ENCLB347KUT)

description:
https://www.encodeproject.org/experiments/ENCSR714CHF/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-SMARCA5-clone1-untreated-new_bulk-E3
experiment encode accession: ENCSR714CHF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-12-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB347KUT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: ENCBS913KQH at ENCODE; https://www.encodeproject.org/ENCBS913KQH/


title: Control 3 LFD Perivenous Bio Rep 2

description:
Library name: DSP-1001660015952-G-C10
FFPE Spatial Transcriptome Sequencing

value: Liver


title: total RNA-seq from ovary (ENCLB290ONB)

description:
https://www.encodeproject.org/experiments/ENCSR231ICM/
***************
biological replicate number: 1
technical replicate number: 1
description: W71 ovary
experiment encode accession: ENCSR231ICM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB290ONB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (47 years) ovary tissue, preserved by flash-freezing

value: ovary

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Yiing Lin, MD, PhD

value: not applicable

value: ENCBS557JWA at ENCODE; https://www.encodeproject.org/ENCBS557JWA/


title: RIP-seq from K562 (ENCLB377RKB)

description:
https://www.encodeproject.org/experiments/ENCSR192OSC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR192OSC
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB377RKB
fragmentation methods: sonication (generic)
size range: 150-150

source_name: Homo sapiens K562 cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Bradley Bernstein, Broad

value: ATCC

value: ENCBS005AIZ at ENCODE; https://www.encodeproject.org/ENCBS005AIZ/


title: Control 1 LFD Perivenous Bio Rep 1

description:
Library name: DSP-1001660015952-G-B09
FFPE Spatial Transcriptome Sequencing


title: total RNA-seq from heart right ventricle (ENCLB193UPZ)

description:
https://www.encodeproject.org/experiments/ENCSR197GCF/
***************
biological replicate number: 1
technical replicate number: 1
description: UW054 heart right ventricle
experiment encode accession: ENCSR197GCF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2023-01-25
lab: Barbara Wold, Caltech
library encode accession: ENCLB193UPZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (54 years) heart right ventricle tissue

value: heart right ventricle

value: male

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: 54 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS736NYQ at ENCODE; https://www.encodeproject.org/ENCBS736NYQ/


title: RIP-seq from K562 (ENCLB759ISJ)

description:
https://www.encodeproject.org/experiments/ENCSR192OSC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR192OSC
assay title: RIP-seq
assembly: hg19
possible controls: ENCSR067RXF
encode release date: 2016-05-04
lab: John Rinn, Broad
library encode accession: ENCLB759ISJ
fragmentation methods: sonication (generic)
size range: 150-150

value: cell line

value: adult

value: ENCBS378DFU at ENCODE; https://www.encodeproject.org/ENCBS378DFU/


title: Het KO 4 LFD Periportal Bio Rep 2

description:
Library name: DSP-1001660015952-G-B07
FFPE Spatial Transcriptome Sequencing

value: Liver