title: RNPS1 RNAi biol rep 2

city: Irvine

first: Yoseop

last: Yoon

state: CA

address: 1002 Health Sciences Rd

institute: University of California Irvine

description: Library name: YY14

data_processing:
PAS-seq data analysis was conducted as described by (Wang et al., 2021).
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: All HEK293T cell lines were cultured in DMEM (Dulbecco's Modified Eagle Medium, high glucose, pyruvate) (Gibco, 11995065) supplemented with 10% FBS (fetal bovine serum) (Sigma, F0926-100ML).

extract_protocol:
TRIZOL
2µg of total RNA was used for PAS-seq library preparation, adhering to the protocol detailed in our methodological paper (Yoon et al., 2021).

treatment_protocol: Protein knockdown samples were generated using short targeting RNA (shRNA) plasmids from the MISSION lentiviral collection (Sigma-Aldrich). HEK293XT cells were seeded onto 12-well plates at a density of 0.1x106 cells per well in 1mL of DMEM (LifeTech, 11995065) + 10% FBS and grown overnight. The media was replaced the following day using fresh media containing 8ug/mL polybrene (Hexadimethrine bromide - Sigma Aldrich cat# H9268) and 100ul of lentivirus specific to RBP open reading frames. The lentiviral medium was removed after 24h and replaced with fresh media containing 4ug/mL Puromycin and incubated in a standard tissue culture incubator for 48h.

value: human embryonic kidney cell

value: siRNA

value: A


title: day1died_16

status: Public on Jun 29 2026

type: SRA

city: Tokyo

first: Riho

last: Saito

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

description: Library name: Sample52

library_source: transcriptomic

data_processing:
Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Blood

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads or on a DNBSEQ-G400RS platform with 100 bp single-end reads. For DNBSEQ-G400RS sequencing, adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

tag: tissue

value: Blood

tag: cell type

value: CXCR2+ cells

tag: genotype

value: C57B6J WT

tag: treatment

value: VSV (New Jersey) intranasal infection

tag: batch

tag: group

value: Lethal group


title: CXCR3- lung tumor Treg cells, rep 3

city: New York

first: Nicholas

last: Arpaia

address: 701 W 168TH ST HHSC 906

country: USA

institute: Columbia University Irving Medical Center

description: Library name: NO315

data_processing:
Cells were run on Element Aviti
Base calling was performed utilizing RTA (Illumina). Bclfastq2 (version 2.19) was used to convert BCL to fastq format, coupled with adapter trimming.
Assembly: Ensembl v96, Mouse GRCm38.p6
Supplementary files format and content: tsv

source_name: lung tumor

extract_protocol:
RNA was extracted using a Aliglent RNA 6000 Pico Kit
We utilized the CLONTECH the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) to reverse transcribe and amplify small amounts of RNA. After creating cDNA, the library was prepared using Nextera XT (Illumina)

value: lung tumor

value: Treg (Foxp3+ CD4+) cells

value: C57B6J - Foxp3 GFP males


title: Human Methylome HCMS, PHH Donor1, HBV-CRISPRi, 2

status: Public on Jun 28 2026

city: Boston

first: Jennifer

last: Marlowe

state: Massachusetts

address: 201 Brookline Avenue

institute: nChroma Bio

description: Library name: NGSHC3143

library_source: genomic

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to the human reference genome (GRCh38) using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Assembly: GRCh38
Supplementary files format and content: Bismark methylation bedgraph file
Supplementary files format and content: Bismark methylation coverage file
Library strategy: EM-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

growth_protocol: Primary human hepatocytes (PHH) isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium (dHCGM media [PhoenixBio], 10% FBS). Primary human splenic endothelial cells (HSECs) (Innoprot and Accegen) were cultured in media (endothelial cell medium (ScienCell) with 5% FBS, 1% Pen-Strep, and 1% endothelial cell growth supplement [ScienCell]) and incubated at 37˚C and in 5% CO2. Primary human adrenal cortical cells (HAdCCs) (Accegen) were cultured in media (Mesenchymal Stem Cell Medium (Innoprot) with 5% FBS, 1% Pen-Strep and 1% Mesenchymal Stem Cell Growth Serum (Innoprot) and incubated at 37˚C and in 5% CO2.

extract_protocol:
From each PHH donor, 4 x 105 µL aliquots of lysate were processed for DNA extraction. From each HAdCC and HSEC donor, 4 x 63 µL aliquots of lysate were mixed with 42 µL of additional LBE buffer per aliquot and processed for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter patented SPRI paramagnetic beads to bind total DNA from the cell lysate. DNA-bound beads were then pelleted with a plate magnet, and the supernatants were removed and discarded before DNA-bound beads were treated with RNase in Beckman Coulter WBA buffer, pelleted with a plate magnet, and the supernatants removed. The retained DNA-bound beads were then washed twice with 70% ethanol. gDNA was eluted from the paramagnetic beads in 10 mM Tris pH 8.0, all twelve technical replicate wells combined and transferred to a clean storage plate.
The first step of the Hybrid Capture Methylation Sequencing (HCMS) workflow was the preparation of EM-seq libraries using Twist NGS Methylation Detection System. Samples were normalized in 10 mM Tris pH 8.0 to generate aliquots containing 200 ng of gDNA in 50 µL. Samples were then mechanically sheared on a Covaris R230 Focused Ultrasonicator to a size range of 350 – 450 bp and at least 5% of the samples were evaluated on a D1000 HS ScreenTape to ensure target size range was reached. The second step of the HCMS workflow was enrichment of DNA fragments for sequencing. Target-enrichment for subsequent methylation sequencing was accomplished through a hybridization reaction in which biotinylated DNA probes were used to capture regions of interest from the whole genome EM-seq library. The biotinylated DNA probe panel and capture reagents were supplied by Twist Biosciences and the workflow was performed following the manufacturer’s recommendations. Briefly, the hybridization reaction was carried out by first drying down 8-plex library pools in a mix of the custom biotinylated DNA probe panel, reaction buffer, and universal blocking oligos, which prevent library fragments from annealing to each other at their adapter sequences. The dried reactions were then resuspended in prewarmed hybridization buffer (65˚C) and incubated on a thermocycler for a hybridization time of 16 hours. Following hybridization, biotinylated DNA probes bound to target gDNA sequences were enriched using streptavidin beads. Streptavidin beads bound to the probe-library complex were pelleted on a magnet and unbound (i.e., off panel) fragments removed through a series of heated washes. The final bead slurry was resuspended in water before performing a PCR amplification to enrich the captured library fragments. Following amplification, libraries were purified with Twist Total Purification beads. Final library concentrations were determined by using the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader. Library fragment size was assessed on a High Sensitivity DNA 1000 ScreenTape on the Agilent 4200 Tapestation instrument. Libraries were pooled in an equimolar manner and, to ensure proper quantitation of sequenceable library molecules, qPCR was also performed using the NEBNext Library Quant Kit for Illumina.  Enriched EM-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and a targeted sequencing depth of >200 M read-pairs per library.

treatment_protocol: For PHH, on the day of treatment cells were treated with 500 µL culture media supplemented with 1 µg/mL of rhApoE3 and 0.5 or 1 µg/mL CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HSEC, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of human fibronectin and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of fresh media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HAdCCs, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of Poly-L-Lysine (Sigma-Aldrich) and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). Plates were maintained, cells sub-cultured (cell trypsinization every 3-4 days, followed by transfer of ~10,000 cells to a new 96-well culture plate with fresh media). All cells were collected for extraction 14 days after treatment.

value: Liver

tag: cell line

value: PXB cells

value: Primary Human Hepatocyte


title: Human Methylome HCMS, PHH Donor1, HBV-CRISPRi, 3

description: Library name: NGSHC3151


title: Human Methylome HCMS, PHH Donor1, Mock-treatment, 1

description: Library name: NGSHC3131


title: Human Methylome HCMS, PHH Donor1, HBV-CRISPRi, 1

description: Library name: NGSHC3135


title: Human Methylome HCMS, PHH Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3150


title: Human Methylome HCMS, PHH Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3142


title: Human Methylome HCMS, PHH Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3134


title: Human Methylome HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSHC3152


title: Human Methylome HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSHC3144


title: Human Methylome HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSHC3136


title: Custom Panel2 HCMS, PHH Donor3, Untreated, 4

description: Library name: NGSHC3714


title: Custom Panel2 HCMS, PHH Donor3, PCSK9-EE7000, 4

description: Library name: NGSHC3717


title: Custom Panel2 HCMS, PHH Donor3, Untreated, 3

description: Library name: NGSHC3710


title: Custom Panel2 HCMS, PHH Donor3, Untreated, 2

description: Library name: NGSHC3706


title: Custom Panel2 HCMS, PHH Donor3, Untreated, 1

description: Library name: NGSHC3702


title: Custom Panel2 HCMS, PHH Donor3, PCSK9-EE7000, 3

description: Library name: NGSHC3713


title: Custom Panel2 HCMS, PHH Donor3, PCSK9-EE7000, 2

description: Library name: NGSHC3709


title: Custom Panel2 HCMS, PHH Donor3, Mock-treatment, 4

description: Library name: NGSHC3715


title: Custom Panel2 HCMS, PHH Donor3, Mock-treatment, 3

description: Library name: NGSHC3711


title: Custom Panel2 HCMS, PHH Donor3, PCSK9-EE7000, 1

description: Library name: NGSHC3705


title: Custom Panel2 HCMS, PHH Donor3, Mock-treatment, 2

description: Library name: NGSHC3707


title: Custom Panel2 HCMS, PHH Donor3, Mock-treatment, 1

description: Library name: NGSHC3703


title: Custom Panel2 HCMS, PHH Donor3, HBV-CRISPRi, 4

description: Library name: NGSHC3728


title: Custom Panel2 HCMS, PHH Donor3, HBV-CRISPRi, 3

description: Library name: NGSHC3725


title: Custom Panel2 HCMS, PHH Donor3, HBV-CRISPRi, 2

description: Library name: NGSHC3722


title: Custom Panel2 HCMS, PHH Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSHC3727


title: Custom Panel2 HCMS, PHH Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSHC3718


title: Custom Panel2 HCMS, PHH Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSHC3721


title: Custom Panel2 HCMS, PHH Donor3, HBV-CRISPRi, 1

description: Library name: NGSHC3719


title: Custom Panel2 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3716


title: Custom Panel2 HCMS, PHH Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSHC3724


title: Custom Panel2 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3704


title: Custom Panel2 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3708


title: Custom Panel2 HCMS, PHH Donor3, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSHC3726


title: Custom Panel2 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3712


title: Custom Panel2 HCMS, PHH Donor3, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSHC3723


title: cdk8-1, Shoot, 0mM magnesium sulfate, 10 days, rep1

city: East Lansing

first: Gregg

last: Howe

state: Michigan

address: 612 Wilson Street

institute: Michigan State University

description:
Library name: cdk8_noS_rep1
Column name in TPMs_AllSamples.xlsx: cdk8_noS_Shoot1

data_processing:
RNA-seq was perfomed Novogene Co., Ltd., with a raw data filter step: Remove reads containing adapters; Remove reads containing N > 10%; Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Genome alignment was performed with STAR (v2.7.11b) and Araport11.
Number of reads was determined with featureCounts (v2.0.8) to get raw reads.
Raw reads were normalized through DESeq2 (v1.46) to get normalized counts for differential expression analysis. Raw reads were also normalized using TPM calculations.
Assembly: Araport11
Supplementary files format and content: .xlsx file includes TPM values for each sample

organism: Arabidopsis thaliana

source_name: plate-grown shoot

growth_protocol: A. thaliana seedlings were grown in the Percival chamber at 21˚C under 16-h-light/8-h-dark cycles. For experiments where seedlings were plated on the agar plates, seeds were surface sterilized using 70% ethanol (v/v) for 5 min, 30% bleach with 0.05% Tween 20 for 5 min, washed 3 times with sterile Ultrapure water, and then stratified at 4˚ C in the dark for 2 days. The agar plates were 1% agar containing half-strength Murashige and Skoog medium (Murashige & Skoog, 1962). The Difco agar (fisher scientific, catalog number 214010) was washed 5 times according to the following procedures: 16.5g agar was stirred in 1.5 L Ultrapure water for 1 hour, after which the agar was set in the flask for 20 min before pouring the washed water. After washing 5 times, the agar was collected by vacuum filtration. Washed agar was completely dried in 65˚C oven for 3 days before proceeded to make the half-strength MS medium. 30 mL medium was poured into a 6x6 petri dish (Fisherbrand, 100x100x15mm). S sufficient plates contained 1.5 mM MgSO4 and S deprived plates contained 1.5 mM MgCl2.

extract_protocol:
RNA was extracted using the NucleoSpin RNA Plant Kit (Macherey-Nagel).
RNA-seq library construction was performed by Novogene Co., Ltd., using NEBNext Ultra II Directional RNA Library Prep Kit following the manufacturer's protocols.

treatment_protocol: 10-day-old seedlings were harvested, using a razer blade to dissect the shoot, then flash froze in liquid nitrogen.

value: plate-grown shoot

value: Day 10


title: Custom Panel2 HCMS, PHH Donor3, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSHC3720


title: day1died_11

description: Library name: Sample47


title: clone3_5

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 366449
SMART-Seq v3

library_source: transcriptomic single cell

data_processing:
Alignment was performed using STAR (v.2.7.9a) on GRCm39 and Gencode vM27 with STAR parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --outFilterScoreMinOverLread 0.22, --outFilterMatchNminOverLread 0.22. Note that we only used the R2 reads from paired end sequencing for this analysis. Reads in exonic and intronic regions (Gencode vM27) were counted using the aligned bam files produced by STAR and summarizeOverlaps (GenomicAlignments v1.40.0, R v4.4.0) with singleEnd=TRUE, mode = "IntersectionNotEmpty", ignore.strand = T, inter.feature = T parameters.
Assembly: GRCm39
Supplementary files format and content: Matrix in csv format with columns corresponding to cells and rows to genes. One file for exonic and one file for intronic reads is given.

source_name: cerebral organoid

growth_protocol: mESCs were plated at high density so that colonies covered approximately half of the well area after 2 days of incubation. Medium was changed 1-2 hours prior to dissociation with StemPro Accutase (Thermo Fisher Scientific) or CTS TrypLE (Thermo Fisher Scientific) for 5 min at 37°C. Cells were counted with an automated cell counter, and were only used if >90% of cells were alive based on Trypan blue staining (Thermo Fisher Scientific). mESCs were centrifuged for 5 min at 200 x g, resuspended in Solution 1, and plated at a density of 3500 cells/microwell in a 24w-Aggrewell plate (Stem Cell Technologies). Solution 1 contained G-MEM (Thermo Fisher Scientific), 10% knockout serum replacement (Thermo Fisher Scientific), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin and WNT inhibitor (3 µM, IWR1, Sigma). No SMAD inhibitors were used as they were not required to direct cortical differentiation in mouse. Embryoid bodies were generated by day (D) 1, which were then transferred to 10 cm dishes with fresh Solution 1 and 2% growth factor-reduced Matrigel (Corning). On D5, organoids were gently pipetted to remove Matrigel and Solution 2 was added, containing DMEM/F12 (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin, 1% chemically defined lipid concentrate (Thermo Fisher Scientific), and heparin (1 mg/ml; Sigma). On D7, organoids were transferred to 6-well plates and placed on an orbital shaker at low speed (50 r.p.m.) to prevent organoid fusion. From D9, organoids were grown in medium containing a 50:50 mix of DMEM/F12 and Neurobasal (Thermo Fisher Scientific), 0.5% N2, 1% B27 (Thermo Fisher Scientific), 0.5 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml pen/strep, 1% chemically defined lipid concentrate, and 50 mM 2-mercaptoethanol. Throughout the protocol medium was replaced as necessary every 2-3 days, and orbital shaker speed was increased after D9 (80 r.p.m.). Fused organoids and/or organoids that failed to grow were discarded throughout the procedure. Standard cell culture conditions (37°C with 5% CO2) were applied throughout all procedures.

extract_protocol:
Organoids with MADM clones induced at D13 were collected at D20 for MADM-CloneSeq. The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (PMID: 38968076). Organoids were kept in cell culture membrane (Millicell) in oxygenated (95% O2, 5% CO2) artificial cerebrospinal fluid (ACSF) containing (in mM): 118 NaCl, 2.5 KCl, 1.25 NaH2PO4, 1.5 MgSO4, 1 CaCl2, 10 Glucose, 3 Myo-inositol, 30 Sucrose, 30 NaHCO3 prepared   with ultra-distilled water; pH=7.4, at 35C, until sample collection. All work surface and equipment were cleaned using RNase away solution (Thermo Fisher Scientific) prior to experiments. Single organoids were transferred to a LNscope 240XY miscroscope (Luigs & Neumann) and superfused with ACSF at a rate of 0.5 ml/min at room temperature. Individual clones were visualized under a 20x objective and by using ImageJ software. To observe red or green fluorescence, light was emitted from a LED light source (CoolLED, Andover, UK). Glass pipettes (B150-86-10, Sutter Instrument, Novato, CA) previously autoclaved, were pulled using a P-1000 pipette puller (Sutter Instrument) to generate pipettes with an opening of around 3-5ym. Before use, each pipette was filled with 3.5yl of pipette solution which consisted of RNase inhibitor (Takara, 1.95%) in RNase-free PBS (Invitrogen) filtered through a 0.22mm filter. Red or green fluorescent neurons were approached with the pipette under positive pressure to avoid tissue contamination of the pipette tip. When contact with cell membrane was made, tight seal formation was achieved under IR/DIC visualization. The complete aspiration of the cell body was immediately performed by applying a gentle and steady suction while monitoring under fluorescence and typically takes 5-10 s. The negative pressure was removed immediately once the target cell was collected and the pipette was carefully withdrawn from the acute slice to avoid contamination. The content of each pipette was directly transferred into individual PCR tubes and kept at -80C until cDNA library preparation.
cDNA libraries for individual MADM-CloneSeq cells were were prepared using Smart-seq3 protocol (PMID 32518404) in 3 batches (96well plates).

treatment_protocol: Stock solutions of 4-hydroxytamoxifen (4-OHT, Sigma) were generated by dilution in 100% ethanol to a concentration 1000-fold greater (20-80 µM) than the working solution. A concentration of 60 nM 4-OHT was used for D13. If 4-OHT treatment occurred on a day without medium change, medium was removed from wells containing organoids to be treated and placed in a tube, 4-OHT was added, and medium was added back to wells. After 24 h, medium was completely replaced and organoids were washed 1x with PBS.

value: cerebral organoid

tag: plate

tag: cloneid

tag: color

value: G

tag: clone type

value: N

tag: clone size


title: Custom Panel2 HCMS, PHH Donor2, Untreated, 4

description: Library name: NGSHC3686


title: Custom Panel2 HCMS, PHH Donor2, Untreated, 2

description: Library name: NGSHC3678


title: Custom Panel2 HCMS, PHH Donor2, Untreated, 3

description: Library name: NGSHC3682


title: Custom Panel2 HCMS, PHH Donor2, Untreated, 1

description: Library name: NGSHC3674


title: Custom Panel2 HCMS, PHH Donor2, PCSK9-EE7000, 4

description: Library name: NGSHC3689


title: Custom Panel2 HCMS, PHH Donor2, PCSK9-EE7000, 2

description: Library name: NGSHC3681


title: Custom Panel2 HCMS, PHH Donor2, Mock-treatment, 4

description: Library name: NGSHC3687


title: Custom Panel2 HCMS, PHH Donor2, PCSK9-EE7000, 1

description: Library name: NGSHC3677


title: Custom Panel2 HCMS, PHH Donor2, PCSK9-EE7000, 3

description: Library name: NGSHC3685


title: Custom Panel2 HCMS, PHH Donor2, Mock-treatment, 2

description: Library name: NGSHC3679


title: Custom Panel2 HCMS, PHH Donor2, Mock-treatment, 1

description: Library name: NGSHC3675


title: Custom Panel2 HCMS, PHH Donor2, HBV-CRISPRi, 4

description: Library name: NGSHC3700


title: Custom Panel2 HCMS, PHH Donor2, HBV-CRISPRi, 2

description: Library name: NGSHC3694


title: Custom Panel2 HCMS, PHH Donor2, HBV-CRISPRi, 3

description: Library name: NGSHC3697


title: Custom Panel2 HCMS, PHH Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSHC3699


title: Custom Panel2 HCMS, PHH Donor2, Mock-treatment, 3

description: Library name: NGSHC3683


title: Custom Panel2 HCMS, PHH Donor2, HBV-CRISPRi, 1

description: Library name: NGSHC3691


title: Custom Panel2 HCMS, PHH Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSHC3696


title: Custom Panel2 HCMS, PHH Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSHC3693


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3688


title: Custom Panel2 HCMS, PHH Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSHC3690


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3684


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3680


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSHC3698


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSHC3695


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSHC3701


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3676


title: Custom Panel2 HCMS, PHH Donor1, Untreated, 4

description: Library name: NGSHC3658


title: Custom Panel2 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSHC3692


title: Custom Panel2 HCMS, PHH Donor1, Untreated, 2

description: Library name: NGSHC3650


title: Custom Panel2 HCMS, PHH Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3653


title: Custom Panel2 HCMS, PHH Donor1, Untreated, 1

description: Library name: NGSHC3646


title: Custom Panel2 HCMS, PHH Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3649


title: Custom Panel2 HCMS, PHH Donor1, Mock-treatment, 4

description: Library name: NGSHC3659


title: Custom Panel2 HCMS, PHH Donor1, Mock-treatment, 2

description: Library name: NGSHC3651


title: Retinal Ganglion Cells, 2wks post ONC, scramble shRNA, rep 2

city: Farmington

first: Jacob

last: Brady

state: Connecticut

address: 263 Farmington Avenue

department: Neuroscience

institute: UConn School of Medicine

description: Library name: Sample 2

data_processing:
Trimmomatic v0.39; HISAT2 v2.2.1; SAMtools v1.10; Cufflinks suite (Cuffquant, Cuffnorm, Cuffdiff) v2.2.1
Raw paired-end sequence reads were trimmed for adaptor sequence and low-quality bases using Trimmomatic (parameters- ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:25 TRAILING:25 SLIDINGWINDOW:4:28 MINLEN:45)
Trimmed sequence reads were mapped to GRCm39/mm39 using HISAT2 with default parameters
Aligned reads were sorted by coordinate and indexed using SAMtools
Per-sample transcript abundances were quantified using Cuffquant against the GENCODE vM38 primary assembly annotation
Assembly: mm39 (vM38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: retina

extract_protocol:
Approximately, 5,000 RGCs (for each of the 2 replicates per condition) were collected by FACS and RNA was isolated immediately using the Quick-RNA Microprep Kit (ZR1050, Zymo Research)
cDNA libraries were prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina)

treatment_protocol: Optic nerve surgeries and intravitreal injections were carried out on mice of both sexes 8-12 weeks of age (average body weight 20-26 g) under general anesthesia, as described previously. The viruses included adeno-associated virus serotype 2 (AAV2) vectors expressing anti-miR132-3p (sequence: 5′-CGACCATGGCTGTAGACTGTTA-3′, against the targeted sequence: 5′-TAACAGTCTACAGCCATGGTCG-3′) and scrambled control (sequence: 5’-TCGAGGGCGACTTAACCTTAGG-3’) shRNAs (titers ~1 × 1013 GC/mL; VectorBuilder, Inc.). Both viral vectors co-expressed an mCherry reporter of transduction. Viruses (2 μl per eye) were injected intravitreally, avoiding injury to the lens, in 8-week-old mice, which were randomly assigned to experimental or control conditions, 2 weeks prior to ONC surgery

value: retina

value: Retinal Ganglion Cells

value: WT

value: ONC, scramble shRNA AAV2


title: Custom Panel2 HCMS, PHH Donor1, Mock-treatment, 3

description: Library name: NGSHC3655


title: Retinal Ganglion Cells, 2wks post ONC, anti-miR132-3p shRNA, rep 1

description: Library name: Sample 3

value: ONC, anti-miR132-3p shRNA AAV2


title: shWhite_END-seq

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

country: China

institute: CEMCS, CAS

data_processing:
Adapters were trimmed via cutadapt (v 4.1) with parameters -e 0.1 -O 3 -m 55 --quality-cutoff 25, then using bowtie with parameters s -n 3 -l 50 -k 1 aligned reads to dm6 and TE sequences.  Functions “view” and “sort” of samtools (v 1.9) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further deduplicated by picard (v2.18.7) and only the forward reads were retained. Then the R1.dedup.bam files were converted to bed files by the bedtools (v2.25.0) bamToBed command. BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig.
Assembly: dm6; Drosophila TE consensus sequence
Supplementary files format and content: bigwig
Library strategy: END-seq

organism: Drosophila melanogaster

source_name: pupa 4d hindgut

extract_protocol:
Hindguts were resuspended in cell suspension buffer and embedded in agarose plugs. Cells were lysed in agarose using proteinase K, follwed by RNase treatment. DNA was later precipitated after plug melting and shearing.
The DNA within the plugs was blunted, A-tailed and ligated with a biotin-labelled hairpin adaptor containing a 3' T overhang and Illumina's p5 sequence. Subsequently, DNA was extracted from the melted agarose and sheared by sonication. Biotinylated DNA was enriched by streptavidin coated beads and the DNA fragments were ligated to a second adaptor containing Illumina's p7 sequence followed by PCR amplification with Illumina sequencing primers for 22 cycles.

value: pupa 4d hindgut

value: sh-white


title: clone2_2

description:
Library name: 366442
SMART-Seq v3

value: SN


title: Custom Panel2 HCMS, PHH Donor1, Mock-treatment, 1

description: Library name: NGSHC3647


title: clone3_2

description:
Library name: 366446
SMART-Seq v3


title: clone2_3

description:
Library name: 366443
SMART-Seq v3


title: Custom Panel2 HCMS, PHH Donor1, HBV-CRISPRi, 4

description: Library name: NGSHC3672


title: Custom Panel2 HCMS, PHH Donor1, Untreated, 3

description: Library name: NGSHC3654


title: Custom Panel2 HCMS, PHH Donor1, PCSK9-EE7000, 4

description: Library name: NGSHC3661


title: Custom Panel2 HCMS, PHH Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3657


title: Custom Panel2 HCMS, PHH Donor1, HBV-CRISPRi, 2

description: Library name: NGSHC3666


title: Col-0, Shoot, 0mM magnesium sulfate, 10 days, rep3

description:
Library name: Col0_noS_rep3
Column name in TPMs_AllSamples.xlsx: Col0_noS_Shoot3


title: Custom Panel2 HCMS, PHH Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSHC3671


title: Custom Panel2 HCMS, PHH Donor1, HBV-CRISPRi, 1

description: Library name: NGSHC3663


title: Custom Panel2 HCMS, PHH Donor1, HBV-CRISPRi, 3

description: Library name: NGSHC3669


title: Custom Panel2 HCMS, PHH Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3662


title: Custom Panel2 HCMS, PHH Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3668


title: Custom Panel2 HCMS, PHH Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3665


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3660


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3656


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3652


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3648


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSHC3670


title: RNAseq, HAdCC Donor3, Untreated, 4

description: Library name: NGSRS3259

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38) and gene and transcript counts and normalized counts (TPM) were calculated using the nf-core RNA-seq pipeline using the STAR aligner and RSEM workflow for transcript quantification.
Assembly: GRCh38
Supplementary files format and content: genes.results file generated by RSEM containing the following columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: Adrenal

growth_protocol: Primary human hepatocytes (PHH) from three different human donors isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium (dHCGM media [PhoenixBio], 10% FBS). Primary human splenic endothelial cells (HSECs) (Innoprot and Accegen) from three different human donors were cultured in media (endothelial cell medium (ScienCell) with 5% FBS, 1% Pen-Strep, and 1% endothelial cell growth supplement [ScienCell]) and incubated at 37˚C and in 5% CO2. Primary human adrenal cortical cells (HAdCCs) (Accegen) from three different human donors were cultured in media (Mesenchymal Stem Cell Medium (Innoprot) with 5% FBS, 1% Pen-Strep and 1% Mesenchymal Stem Cell Growth Serum (Innoprot) and incubated at 37˚C and in 5% CO2.

extract_protocol:
For RNA extraction of all donors and sample types, Beckman Coulter RNAdvance v2 Kit was used. For RNA extraction from each PHH donor, two 24-well replicate plates per donor containing 336 µL cell lysate were combined and 4 x 63 µL aliquots of lysate were processed . For RNA extraction from each HAdCC donor, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. For RNA extraction from HSEC, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. The remaining lysate from each cell type was used for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter-patented SPRI paramagnetic beads to bind total RNA from the cell lysate. Bound RNA was then pelleted with a plate magnet, removing the supernatant allowing DNA and other contaminants to be removed through DNase treatment and a series of buffer (Wash WBD) and 70% ethanol washes, respectively. Total RNA was then eluted from the magnetic beads in nuclease-free water (HAdCC and HSEC samples (96-well plate format) were eluted in 22 uL per sample combining the replicates for a total of 44 uL eluate. PHH samples (24-well format) were eluted in 26 uL.).
Total RNA sequencing libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus. Samples were normalized with nuclease-free water to 100 ng in 11 µL total volume. Concentrations of final libraries were determined by using either the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader or the Qubit DNA High Sensitivity kit on the Qubit Flex Fluorometer. Library fragment size was also checked on a DNA D1000 or HSD1000 ScreenTape on the Agilent 4200 Tapestation instrument. To ensure proper quantification of sequenceable library molecules, a qPCR reaction was also performed using the NEBNext Library Quant Kit for Illumina.  Total RNA-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and targeted sequencing depth was >100 M read-pairs per library. Note that PHH Donor 3 sequencing data had a high percentage of duplicates. Therefore, the library prep and sequencing were repeated, with RNA-seq libraries sequenced in the Sponsor’s laboratory on a NextSeq2000 with a 2 x 151 bp configuration and targeted sequencing depth >100 M read-pairs per library.

value: Adrenal

value: HAdCC cells

value: Human Adrenal Cortical Cells


title: RNAseq, HAdCC Donor3, Untreated, 3

description: Library name: NGSRS3258


title: RNAseq, HAdCC Donor3, PCSK9-EE7000, 4

description: Library name: NGSRS3247


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSHC3664

value: Liver

value: PXB cells

value: Primary Human Hepatocyte


title: RNAseq, HAdCC Donor3, PCSK9-EE7000, 1

description: Library name: NGSRS3244


title: RNAseq, HAdCC Donor3, PCSK9-EE7000, 2

description: Library name: NGSRS3245


title: RNAseq, HAdCC Donor3, Untreated, 1

description: Library name: NGSRS3256


title: RNAseq, HAdCC Donor3, Mock-treatment, 3

description: Library name: NGSRS3254


title: RNAseq, HAdCC Donor3, PCSK9-EE7000, 3

description: Library name: NGSRS3246


title: RNAseq, HAdCC Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSRS3243


title: RNAseq, HAdCC Donor3, Mock-treatment, 2

description: Library name: NGSRS3253


title: RNAseq, HAdCC Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSRS3242


title: RNAseq, HAdCC Donor3, Mock-treatment, 4

description: Library name: NGSRS3255


title: RNAseq, HAdCC Donor3, Mock-treatment, 1

description: Library name: NGSRS3252


title: RNAseq, HAdCC Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSRS3241


title: RNAseq, HAdCC Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSRS3240


title: RNAseq, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3248


title: RNAseq, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3249


title: RNAseq, HAdCC Donor2, Untreated, 4

description: Library name: NGSRS3239


title: RNAseq, HAdCC Donor2, Untreated, 3

description: Library name: NGSRS3238


title: RNAseq, HAdCC Donor2, Untreated, 1

description: Library name: NGSRS3236


title: RNAseq, HAdCC Donor2, PCSK9-EE7000, 3

description: Library name: NGSRS3226


title: RNAseq, HAdCC Donor2, PCSK9-EE7000, 2

description: Library name: NGSRS3225


title: RNAseq, HAdCC Donor2, PCSK9-EE7000, 4

description: Library name: NGSRS3227


title: RNAseq, HAdCC Donor2, Mock-treatment, 3

description: Library name: NGSRS3234


title: RNAseq, HAdCC Donor2, PCSK9-EE7000, 1

description: Library name: NGSRS3224


title: RNAseq, HAdCC Donor2, Mock-treatment, 2

description: Library name: NGSRS3233


title: RNAseq, HAdCC Donor2, Mock-treatment, 1

description: Library name: NGSRS3232


title: RNAseq, HAdCC Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSRS3223


title: RNAseq, HAdCC Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSRS3222


title: RNAseq, HAdCC Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSRS3220


title: RNAseq, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3231


title: RNAseq, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3228


title: RNAseq, HAdCC Donor1, Untreated, 4

description: Library name: NGSRS3219


title: RNAseq, HAdCC Donor1, Untreated, 3

description: Library name: NGSRS3218


title: RNAseq, HAdCC Donor1, Untreated, 2

description: Library name: NGSRS3217


title: RNAseq, HAdCC Donor1, Untreated, 1

description: Library name: NGSRS3216


title: RNAseq, HAdCC Donor1, PCSK9-EE7000, 1

description: Library name: NGSRS3204


title: RNAseq, HAdCC Donor1, Mock-treatment, 2

description: Library name: NGSRS3213


title: RNAseq, HAdCC Donor1, Mock-treatment, 4

description: Library name: NGSRS3215


title: RNAseq, HAdCC Donor1, Mock-treatment, 3

description: Library name: NGSRS3214


title: RNAseq, HAdCC Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSRS3203


title: RNAseq, HAdCC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSRS3202


title: RNAseq, HAdCC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSRS3200


title: RNAseq, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3211


title: RNAseq, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3209


title: RNAseq, HSEC Donor3, Untreated, 2

description: Library name: NGSRS3197

source_name: Spleen

value: Spleen

value: HSEC cells

value: Human Splenic Endothelial Cells


title: RNAseq, HSEC Donor3, PCSK9-EE7000, 3

description: Library name: NGSRS3186


title: RNAseq, HSEC Donor3, Mock-treatment, 4

description: Library name: NGSRS3195


title: RNAseq, HSEC Donor3, Mock-treatment, 3

description: Library name: NGSRS3194


title: RNAseq, HSEC Donor3, Mock-treatment, 2

description: Library name: NGSRS3193


title: RNAseq, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3251


title: RNAseq, HSEC Donor3, Mock-treatment, 1

description: Library name: NGSRS3192


title: RNAseq, HAdCC Donor2, Mock-treatment, 4

description: Library name: NGSRS3235


title: RNAseq, HAdCC Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSRS3221


title: RNAseq, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3230


title: RNAseq, HSEC Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSRS3183


title: RNAseq, HSEC Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSRS3182


title: RNAseq, HSEC Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSRS3181


title: RNAseq, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3229


title: RNAseq, HAdCC Donor1, PCSK9-EE7000, 4

description: Library name: NGSRS3207


title: RNAseq, HSEC Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSRS3180


title: RNAseq, HSEC Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3190


title: RNAseq, HAdCC Donor1, PCSK9-EE7000, 2

description: Library name: NGSRS3205


title: RNAseq, HSEC Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3189


title: RNAseq, HSEC Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3188


title: RNAseq, HSEC Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3191


title: RNAseq, HSEC Donor2, Untreated, 4

description: Library name: NGSRS3179


title: RNAseq, HAdCC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSRS3201


title: RNAseq, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3210


title: RNAseq, HSEC Donor2, Untreated, 2

description: Library name: NGSRS3177


title: RNAseq, HSEC Donor2, Untreated, 1

description: Library name: NGSRS3176


title: RNAseq, HSEC Donor3, PCSK9-EE7000, 4

description: Library name: NGSRS3187


title: RNAseq, HSEC Donor3, Untreated, 3

description: Library name: NGSRS3198


title: RNAseq, HSEC Donor3, Untreated, 4

description: Library name: NGSRS3199


title: RNAseq, HSEC Donor2, PCSK9-EE7000, 4

description: Library name: NGSRS3167


title: RNAseq, HSEC Donor2, Mock-treatment, 4

description: Library name: NGSRS3175


title: RNAseq, HSEC Donor2, Mock-treatment, 3

description: Library name: NGSRS3174


title: DZIP3 knockdown, rep2, group A

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Library name: DZIP3-BG293LV06-60

data_processing:
Quality of reads were assessed using fastqc.
Reads were trimmed.
Reads were aligned to hg38 reference and quantified with salmon.
Assembly: hg38
Supplementary files format and content: quant.sf files contain transcript quantifications

growth_protocol: HEK293XT cells were seeded onto 12-well plates at a density of 0.1x106 cells per well in 1mL of DMEM + 10% FBS and grown overnight.

extract_protocol:
RNA extraction was completed using the Maxwell RSC simplyRNA tissue kit .
RNA-seq libraries were prepared using the TruSeq Stranded mRNA library preparation kit and the IDT for Illumina TruSeq RNA UD Index set for samples having greater than 50% knockdown of the RBP.

treatment_protocol: The media was replaced the following day using fresh media containing 8ug/mL polybrene (Hexadimethrine bromide) and 100ul of lentivirus specific to RBP open reading frames. The lentiviral medium was removed after 24h and replaced with fresh media containing 4ug/mL Puromycin and incubated in a standard tissue culture incubator for 48h.

value: human embryonic kidney

value: knockdown


title: RNAseq, HSEC Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSRS3160


title: RNAseq, HSEC Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3171


title: RNAseq, HSEC Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSRS3162


title: RNAseq, HSEC Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSRS3161


title: RNAseq, HSEC Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3170


title: RNAseq, HSEC Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3169


title: RNAseq, HSEC Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3168


title: RNAseq, HSEC Donor1, Untreated, 4

description: Library name: NGSRS3159


title: RNAseq, HSEC Donor1, Untreated, 1

description: Library name: NGSRS3156


title: RNAseq, HSEC Donor1, Untreated, 3

description: Library name: NGSRS3158


title: RNAseq, HSEC Donor1, PCSK9-EE7000, 3

description: Library name: NGSRS3146


title: RNAseq, HSEC Donor1, PCSK9-EE7000, 1

description: Library name: NGSRS3144


title: RNAseq, HSEC Donor1, Mock-treatment, 4

description: Library name: NGSRS3155


title: RNAseq, HSEC Donor1, Mock-treatment, 3

description: Library name: NGSRS3154


title: RNAseq, HSEC Donor1, Mock-treatment, 2

description: Library name: NGSRS3153


title: RNAseq, HSEC Donor1, PCSK9-EE7000, 2

description: Library name: NGSRS3145


title: RNAseq, HSEC Donor1, Mock-treatment, 1

description: Library name: NGSRS3152


title: RNAseq, HSEC Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSRS3143


title: RNAseq, HSEC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSRS3142


title: RNAseq, HSEC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSRS3141


title: RNAseq, HSEC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSRS3140


title: RNAseq, HSEC Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3151


title: RNAseq, HSEC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3149


title: RNAseq, HSEC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3148


title: RNAseq, PHH Donor2, Untreated, 3

description: Library name: NGSRS3084


title: RNAseq, PHH Donor2, Untreated, 2

description: Library name: NGSRS3080


title: RNAseq, HSEC Donor2, PCSK9-EE7000, 2

description: Library name: NGSRS3165


title: RNAseq, HSEC Donor2, PCSK9-EE7000, 3

description: Library name: NGSRS3166


title: RNAseq, HSEC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3150


title: RNAseq, PHH Donor2, Untreated, 1

description: Library name: NGSRS3076


title: RNAseq, PHH Donor2, PCSK9-EE7000, 4

description: Library name: NGSRS3091


title: RNAseq, HSEC Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSRS3163


title: RNAseq, PHH Donor2, PCSK9-EE7000, 2

description: Library name: NGSRS3083


title: RNAseq, PHH Donor2, PCSK9-EE7000, 3

description: Library name: NGSRS3087


title: RNAseq, PHH Donor2, Mock-treatment, 4

description: Library name: NGSRS3089


title: RNAseq, PHH Donor2, PCSK9-EE7000, 1

description: Library name: NGSRS3079


title: RNAseq, PHH Donor2, Mock-treatment, 3

description: Library name: NGSRS3085


title: RNAseq, PHH Donor2, Mock-treatment, 2

description: Library name: NGSRS3081


title: RNAseq, PHH Donor2, Mock-treatment, 1

description: Library name: NGSRS3077


title: RNAseq, PHH Donor2, HBV-CRISPRi, 4

description: Library name: NGSRS3102


title: RNAseq, PHH Donor2, HBV-CRISPRi, 2

description: Library name: NGSRS3096


title: RNAseq, PHH Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSRS3098


title: RNAseq, PHH Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSRS3095


title: RNAseq, PHH Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSRS3092


title: RNAseq, PHH Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3090


title: RNAseq, PHH Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3078


title: RNAseq, PHH Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3082


title: RNAseq, PHH Donor2, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSRS3103


title: RNAseq, PHH Donor2, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSRS3100


title: RNAseq, PHH Donor2, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSRS3097


title: RNAseq, PHH Donor2, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSRS3094


title: RNAseq, PHH Donor1, PCSK9-EE7000, 4

description: Library name: NGSRS3063


title: RNAseq, PHH Donor1, PCSK9-EE7000, 2

description: Library name: NGSRS3055


title: RNAseq, PHH Donor1, Mock-treatment, 3

description: Library name: NGSRS3057


title: RNAseq, PHH Donor2, Untreated, 4

description: Library name: NGSRS3088


title: RNAseq, PHH Donor1, Mock-treatment, 1

description: Library name: NGSRS3049


title: RNAseq, PHH Donor1, HBV-CRISPRi, 4

description: Library name: NGSRS3074


title: RNAseq, PHH Donor2, HBV-CRISPRi, 3

description: Library name: NGSRS3099


title: RNAseq, PHH Donor2, HBV-CRISPRi, 1

description: Library name: NGSRS3093


title: RNAseq, PHH Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSRS3101


title: RNAseq, PHH Donor1, HBV-CRISPRi, 3

description: Library name: NGSRS3071


title: RNAseq, PHH Donor1, HBV-CRISPRi, 2

description: Library name: NGSRS3068


title: RNAseq, PHH Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3086


title: RNAseq, PHH Donor1, HBV-CRISPRi, 1

description: Library name: NGSRS3065


title: RNAseq, PHH Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSRS3073


title: RNAseq, PHH Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSRS3070


title: RNAseq, PHH Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSRS3067


title: RNAseq, PHH Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSRS3064


title: RNAseq, PHH Donor1, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSRS3075


title: RNAseq, PHH Donor1, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSRS3072


title: RNAseq, PHH Donor1, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSRS3069


title: RNAseq, PHH Donor1, PCSK9-EE7000, 3

description: Library name: NGSRS3059


title: RNAseq, PHH Donor1, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSRS3066


title: Whole Genome Methylseq, HAdCC Donor1, Untreated, 3

description: Library name: NGSWGM225

extract_protocol:
Genomic DNA was extracted from PHHs, HSECs, and HAdCCs using a split lysate protocol to extract both RNA and DNA from the same sample lysate (Beckman Coulter).
Genomic DNA was mechanically sheared on a Covaris R230 Focused Ultrasonicator to a size range of 350 – 450 bp. Sequencing libraries were then constructed from the sheared genomic DNA using the NEBNext Enzymatic Methyl-seq (EM-seq) kit plus NEBNext Multiplex Oligos for Enzymatic Methyl-seq. Libraries were then sequenced using an Illumina NovaSeq X instrument with 2 x 151 bp reads to a read-depth of >1 billion read pairs per sample.


title: Whole Genome Methylseq, HAdCC Donor1, Untreated, 2

description: Library name: NGSWGM217


title: Whole Genome Methylseq, HAdCC Donor1, Untreated, 1

description: Library name: NGSWGM209


title: RNAseq, PHH Donor1, PCSK9-EE7000, 1

description: Library name: NGSRS3051


title: RNAseq, PHH Donor1, Mock-treatment, 4

description: Library name: NGSRS3061


title: Whole Genome Methylseq, HAdCC Donor1, PCSK9-EE7000, 3

description: Library name: NGSWGM222


title: Whole Genome Methylseq, HAdCC Donor1, PCSK9-EE7000, 2

description: Library name: NGSWGM214


title: Whole Genome Methylseq, HAdCC Donor1, PCSK9-EE7000, 1

description: Library name: NGSWGM206


title: Whole Genome Methylseq, HAdCC Donor1, Mock-treatment, 3

description: Library name: NGSWGM224


title: RNAseq, HAdCC Donor3, Untreated, 2

description: Library name: NGSRS3257


title: Whole Genome Methylseq, HAdCC Donor1, Mock-treatment, 2

description: Library name: NGSWGM216


title: Whole Genome Methylseq, HAdCC Donor1, Mock-treatment, 1

description: Library name: NGSWGM208


title: Whole Genome Methylseq, HAdCC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSWGM221


title: Whole Genome Methylseq, HAdCC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSWGM205


title: Whole Genome Methylseq, HAdCC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSWGM213


title: Whole Genome Methylseq, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSWGM223


title: Whole Genome Methylseq, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSWGM215


title: Whole Genome Methylseq, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSWGM207


title: Whole Genome Methylseq, HSEC Donor1, Untreated, 3

description: Library name: NGSWGM201


title: Whole Genome Methylseq, HSEC Donor1, Untreated, 2

description: Library name: NGSWGM193


title: RNAseq, PHH Donor1, Mock-treatment, 2

description: Library name: NGSRS3053


title: RNAseq, HAdCC Donor2, Untreated, 2

description: Library name: NGSRS3237


title: Whole Genome Methylseq, HSEC Donor1, Untreated, 1

description: Library name: NGSWGM188


title: Whole Genome Methylseq, HSEC Donor1, PCSK9-EE7000, 3

description: Library name: NGSWGM198


title: Whole Genome Methylseq, HSEC Donor1, PCSK9-EE7000, 1

description: Library name: NGSWGM185


title: Whole Genome Methylseq, HSEC Donor1, PCSK9-EE7000, 2

description: Library name: NGSWGM190


title: Whole Genome Methylseq, HSEC Donor1, Mock-treatment, 3

description: Library name: NGSWGM200


title: Whole Genome Methylseq, HSEC Donor1, Mock-treatment, 2

description: Library name: NGSWGM192


title: Whole Genome Methylseq, HSEC Donor1, Mock-treatment, 1

description: Library name: NGSWGM187


title: Whole Genome Methylseq, HSEC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSWGM197


title: Whole Genome Methylseq, HSEC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSWGM184


title: Whole Genome Methylseq, HSEC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSWGM199


title: Whole Genome Methylseq, HSEC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSWGM189


title: Whole Genome Methylseq, HSEC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSWGM191


title: Whole Genome Methylseq, HSEC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSWGM186


title: Whole Genome Methylseq, PHH Donor1, Untreated, 3

description: Library name: NGSWGM202


title: Whole Genome Methylseq, PHH Donor1, Untreated, 2

description: Library name: NGSWGM194


title: Whole Genome Methylseq, PHH Donor1, Untreated, 1

description: Library name: NGSWGM181


title: Whole Genome Methylseq, PHH Donor1, PCSK9-EE7000, 2

description: Library name: NGSWGM230


title: Whole Genome Methylseq, PHH Donor1, PCSK9-EE7000, 3

description: Library name: NGSWGM231


title: Whole Genome Methylseq, PHH Donor1, PCSK9-EE7000, 1

description: Library name: NGSWGM229


title: Whole Genome Methylseq, PHH Donor1, Mock-treatment, 2

description: Library name: NGSWGM195


title: Whole Genome Methylseq, PHH Donor1, HBV-CRISPRi, 3

description: Library name: NGSWGM227


title: Whole Genome Methylseq, PHH Donor1, Mock-treatment, 3

description: Library name: NGSWGM203


title: Whole Genome Methylseq, PHH Donor1, Mock-treatment, 1

description: Library name: NGSWGM182


title: Whole Genome Methylseq, PHH Donor1, HBV-CRISPRi, 2

description: Library name: NGSWGM219


title: RNAseq, HSEC Donor3, Untreated, 1

description: Library name: NGSRS3196


title: Whole Genome Methylseq, PHH Donor1, HBV-CRISPRi, 1

description: Library name: NGSWGM211


title: Whole Genome Methylseq, PHH Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSWGM226


title: Whole Genome Methylseq, PHH Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSWGM218


title: Whole Genome Methylseq, PHH Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSWGM210


title: Whole Genome Methylseq, PHH Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSWGM204


title: Whole Genome Methylseq, PHH Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSWGM196


title: Whole Genome Methylseq, PHH Donor1, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSWGM220


title: Whole Genome Methylseq, PHH Donor1, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSWGM228


title: Whole Genome Methylseq, PHH Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSWGM183


title: Human Methylome HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3148

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to the human reference genome (GRCh38) using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Assembly: GRCh38
Supplementary files format and content: Bismark methylation bedgraph file
Supplementary files format and content: Bismark methylation coverage file

extract_protocol:
From each PHH donor, 4 x 105 µL aliquots of lysate were processed for DNA extraction. From each HAdCC and HSEC donor, 4 x 63 µL aliquots of lysate were mixed with 42 µL of additional LBE buffer per aliquot and processed for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter patented SPRI paramagnetic beads to bind total DNA from the cell lysate. DNA-bound beads were then pelleted with a plate magnet, and the supernatants were removed and discarded before DNA-bound beads were treated with RNase in Beckman Coulter WBA buffer, pelleted with a plate magnet, and the supernatants removed. The retained DNA-bound beads were then washed twice with 70% ethanol. gDNA was eluted from the paramagnetic beads in 10 mM Tris pH 8.0, all twelve technical replicate wells combined and transferred to a clean storage plate.
The first step of the Hybrid Capture Methylation Sequencing (HCMS) workflow was the preparation of EM-seq libraries using Twist NGS Methylation Detection System. Samples were normalized in 10 mM Tris pH 8.0 to generate aliquots containing 200 ng of gDNA in 50 µL. Samples were then mechanically sheared on a Covaris R230 Focused Ultrasonicator to a size range of 350 – 450 bp and at least 5% of the samples were evaluated on a D1000 HS ScreenTape to ensure target size range was reached. The second step of the HCMS workflow was enrichment of DNA fragments for sequencing. Target-enrichment for subsequent methylation sequencing was accomplished through a hybridization reaction in which biotinylated DNA probes were used to capture regions of interest from the whole genome EM-seq library. The biotinylated DNA probe panel and capture reagents were supplied by Twist Biosciences and the workflow was performed following the manufacturer’s recommendations. Briefly, the hybridization reaction was carried out by first drying down 8-plex library pools in a mix of the custom biotinylated DNA probe panel, reaction buffer, and universal blocking oligos, which prevent library fragments from annealing to each other at their adapter sequences. The dried reactions were then resuspended in prewarmed hybridization buffer (65˚C) and incubated on a thermocycler for a hybridization time of 16 hours. Following hybridization, biotinylated DNA probes bound to target gDNA sequences were enriched using streptavidin beads. Streptavidin beads bound to the probe-library complex were pelleted on a magnet and unbound (i.e., off panel) fragments removed through a series of heated washes. The final bead slurry was resuspended in water before performing a PCR amplification to enrich the captured library fragments. Following amplification, libraries were purified with Twist Total Purification beads. Final library concentrations were determined by using the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader. Library fragment size was assessed on a High Sensitivity DNA 1000 ScreenTape on the Agilent 4200 Tapestation instrument. Libraries were pooled in an equimolar manner and, to ensure proper quantitation of sequenceable library molecules, qPCR was also performed using the NEBNext Library Quant Kit for Illumina. Enriched EM-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and a targeted sequencing depth of >200 M read-pairs per library, to ensure the minimum requirement of >120 M read-pairs for each library

value: CRMA-1001 ES (1ug)


title: Whole Genome Methylseq, PHH Donor1, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSWGM212


title: Human Methylome HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3132


title: Human Methylome HCMS, PHH Donor1, Untreated, 3

description: Library name: NGSHC3146

value: Untreated


title: Human Methylome HCMS, PHH Donor1, Untreated, 2

description: Library name: NGSHC3138


title: Human Methylome HCMS, PHH Donor1, Untreated, 1

description: Library name: NGSHC3130


title: RNAseq, PHH Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3062

extract_protocol:
For RNA extraction of all donors and sample types, Beckman Coulter RNAdvance v2 Kit was used. For RNA extraction from each PHH donor, two 24-well replicate plates per donor containing 336 µL cell lysate were combined and 4 x 63 µL aliquots of lysate were processed . For RNA extraction from each HAdCC donor, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. For RNA extraction from HSEC, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. The remaining lysate from each cell type was used for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter-patented SPRI paramagnetic beads to bind total RNA from the cell lysate. Bound RNA was then pelleted with a plate magnet, removing the supernatant allowing DNA and other contaminants to be removed through DNase treatment and a series of buffer (Wash WBD) and 70% ethanol washes, respectively. Total RNA was then eluted from the magnetic beads in nuclease-free water (HAdCC and HSEC samples (96-well plate format) were eluted in 22 uL per sample combining the replicates for a total of 44 uL eluate. PHH samples (24-well format) were eluted in 26 uL.).
Total RNA sequencing libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus. Samples were normalized with nuclease-free water to 100 ng in 11 µL total volume. Concentrations of final libraries were determined by using either the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader or the Qubit DNA High Sensitivity kit on the Qubit Flex Fluorometer. Library fragment size was also checked on a DNA D1000 or HSD1000 ScreenTape on the Agilent 4200 Tapestation instrument. To ensure proper quantification of sequenceable library molecules, a qPCR reaction was also performed using the NEBNext Library Quant Kit for Illumina. Total RNA-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and targeted sequencing depth was >100 M read-pairs per library. Note that PHH Donor 3 sequencing data had a high percentage of duplicates. Therefore, the library prep and sequencing were repeated, with RNA-seq libraries sequenced in the Sponsor’s laboratory on a NextSeq2000 with a 2 x 151 bp configuration and targeted sequencing depth >100 M read-pairs per library.


title: RNAseq, PHH Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3054


title: RNAseq, PHH Donor1, Untreated, 4

description: Library name: NGSRS3060


title: RNAseq, PHH Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3050


title: RNAseq, PHH Donor1, Untreated, 3

description: Library name: NGSRS3056


title: RNAseq, PHH Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3058


title: RNAseq, PHH Donor1, Untreated, 1

description: Library name: NGSRS3048


title: ZR751 RB1 knockout palbociclib RNAseq rep 3

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample 24
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_sgRB_Palbo_R3

data_processing:
Adapters and low quality reads were removed using BBMap bbduk.sh with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20.
Trimmed reads were aligned to the human reference genome (hg38) using STAR.
Aligned reads were counted using featureCounts with GENCODE (gencode.v35.annotation.gtf )
Assembly: hg38
Supplementary files format and content: CSV file includes raw, non-normalised gene counts for each sample.

growth_protocol: RPMI-1640 supplemented with 10% FBS, 1% GlutaMax, and 1% HEPES, incubated at 37C at 5% CO2.

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using QuantSeq 3’ mRNA-Library Prep Kit FWD (Lexogen). RNA quantity and quality were assessed on TapeStation 4150 (Agilent).

treatment_protocol: Cells were treated with DMSO control or palbociclib 500 nM. MCF7 cells were treated for 5 days; ZR-75-1 cells were treated for 4 day.

value: RB1 knockout

value: Palbociclib

tag: replicate

value: replicate 3


title: Human Methylome HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3140


title: ZR751 RB1 knockout palbociclib RNAseq rep 2

description:
Library name: Sample 23
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_sgRB_Palbo_R2

value: replicate 2


title: ZR751 RB1 knockout palbociclib RNAseq rep 1

description:
Library name: Sample 22
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_sgRB_Palbo_R1

value: replicate 1


title: RNAseq, PHH Donor1, Untreated, 2

description: Library name: NGSRS3052


title: ZR751 RB1 knockout DMSO RNAseq rep 3

description:
Library name: Sample 21
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_sgRB_DMSO_R3

value: DMSO


title: ZR751 RB1 knockout DMSO RNAseq rep 2

description:
Library name: Sample 20
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_sgRB_DMSO_R2


title: ZR751 RB1 knockout DMSO RNAseq rep 1

description:
Library name: Sample 19
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_sgRB_DMSO_R1


title: ZR751 Parent palbociclib RNAseq rep 3

description:
Library name: Sample 18
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_Par_Palbo_R3

value: Parent


title: ZR751 Parent palbociclib RNAseq rep 2

description:
Library name: Sample 17
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_Par_Palbo_R2


title: ZR751 Parent palbociclib RNAseq rep 1

description:
Library name: Sample 16
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_Par_Palbo_R1


title: ZR751 Parent DMSO RNAseq rep 3

description:
Library name: Sample 15
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_Par_DMSO_R3


title: ZR751 Parent DMSO RNAseq rep 1

description:
Library name: Sample 13
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_Par_DMSO_R1


title: ZR751 Parent DMSO RNAseq rep 2

description:
Library name: Sample 14
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: ZR751_Par_DMSO_R2


title: MCF7 RB1 knockout palbociclib RNAseq rep 3

description:
Library name: Sample 12
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_sgRB_Palbo_R3


title: MCF7 RB1 knockout palbociclib RNAseq rep 1

description:
Library name: Sample 10
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_sgRB_Palbo_R1


title: MCF7 RB1 knockout palbociclib RNAseq rep 2

description:
Library name: Sample 11
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_sgRB_Palbo_R2


title: MCF7 RB1 knockout DMSO RNAseq rep 3

description:
Library name: Sample 9
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_sgRB_DMSO_R3


title: MCF7 RB1 knockout DMSO RNAseq rep 2

description:
Library name: Sample 8
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_sgRB_DMSO_R2


title: MCF7 RB1 knockout DMSO RNAseq rep 1

description:
Library name: Sample 7
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_sgRB_DMSO_R1


title: MCF7 Parent palbociclib RNAseq rep 3

description:
Library name: Sample 6
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_Par_Palbo_R3


title: MCF7 Parent palbociclib RNAseq rep 2

description:
Library name: Sample 5
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_Par_Palbo_R2


title: MCF7 Parent palbociclib RNAseq rep 1

description:
Library name: Sample 4
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_Par_Palbo_R1


title: MCF7 Parent DMSO RNAseq rep 3

description:
Library name: Sample 3
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_Par_DMSO_R3


title: MCF7 Parent DMSO RNAseq rep 1

description:
Library name: Sample 1
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_Par_DMSO_R1


title: MCF7 Parent DMSO RNAseq rep 2

description:
Library name: Sample 2
Column name in RNAseq_MCF7_ZR_Par_RBKO_Palbo_rawcounts.csv: MCF7M_Par_DMSO_R2


title: ZR751 RB1 KO Abemaciclib RNAseq replicate 3

description:
Library name: Sample 12
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgRB1_Abemaciclib_Rep3

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
trimmed reads were aligned using STAR (v2.7.5b) to the human reference genome (hg38)
Aligned reads were counted using featurecounts (v2.0.1)  using annotations from GENCODE (gencode.v35.annotation.gtf)
Assembly: hg38
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. RNA quantity and quality were assessed on TapeStation 4150 (Agilent).

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 5 days.

value: Abemaciclib


title: ZR751 RB1 KO Abemaciclib RNAseq replicate 2

description:
Library name: Sample 11
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgRB1_Abemaciclib_Rep2


title: ZR751 RB1 KO Abemaciclib RNAseq replicate 1

description:
Library name: Sample 10
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgRB1_Abemaciclib_Rep1


title: ZR751 RB1 KO DMSO RNAseq replicate 3

description:
Library name: Sample 9
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgRB1_DMSO_Rep3


title: ZR751 RB1 KO DMSO RNAseq replicate 2

description:
Library name: Sample 8
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgRB1_DMSO_Rep2


title: ZR751 RB1 KO DMSO RNAseq replicate 1

description:
Library name: Sample 7
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgRB1_DMSO_Rep1


title: ZR751 sgControl Abemaciclib RNAseq replicate 3

description:
Library name: Sample 6
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgControl_Abemaciclib_Rep3

value: sgControl


title: ZR751 sgControl Abemaciclib RNAseq replicate 2

description:
Library name: Sample 5
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgControl_Abemaciclib_Rep2


title: ZR751 sgControl Abemaciclib RNAseq replicate 1

description:
Library name: Sample 4
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgControl_Abemaciclib_Rep1


title: ZR751 sgControl DMSO RNAseq replicate 2

description:
Library name: Sample 2
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgControl_DMSO_Rep2


title: ZR751 sgControl DMSO RNAseq replicate 3

description:
Library name: Sample 3
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgControl_DMSO_Rep3


title: ZR751 sgControl DMSO RNAseq replicate 1

description:
Library name: Sample 1
Column name in RNAseq_ZR751_Abema_RBKO_rawcounts.csv: sgControl_DMSO_Rep1


title: MCF7_ESR1_Fulv_rep2

description: Library name: Sample 6

data_processing:
Adapters and low-quality reads were removed using BBMap v39.01 bbduk.sh with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20.
Trimmed reads were aligned to the human reference genome (hg38) using STAR.
Aligned reads were counted using featureCounts with GENCODE (gencode.v35.annotation.gtf)
Assembly: hg38
Supplementary files format and content: CSV file includes raw (non-normalised) gene counts for each sample.

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using a QuantSeq 3' mRNA sequencing workflow and sequenced as 101-cycle single-end reads on an Illumina NextSeq 2000.

treatment_protocol: Cells were treated with DMSO control, abemaciclib 500 nM, fulvestrant 10 nM, or a combination of abemaciclib and fulvestrant for 5 days.

value: ESR1 Y537S mutant

value: Fulvestrant


title: MCF7_ESR1_LYFulv_rep1

description: Library name: Sample 7

value: Abemaciclib+Fulvestrant


title: MCF7_ESR1_LYFulv_rep2

description: Library name: Sample 8


title: MCF7_ESR1_Fulv_rep1

description: Library name: Sample 5


title: MCF7_ESR1_LY_rep2

description: Library name: Sample 4


title: MCF7_ESR1_LY_rep1

description: Library name: Sample 3


title: MCF7_ESR1_DMSO_rep1

description: Library name: Sample 1


title: PDX3837 tumour slice, Abemaciclib, IgG DynaTag, biological replicate 2

description:
Library name: DynaTag_PDX3837_Abemaciclib_IgG_Rep2_S15
Matched IgG control for Abemaciclib biological replicate 2.

data_processing:
Adapters and low-quality reads were removed using BBMap BBduk v39.13 with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20.
Reads were aligned with Bowtie2 v2.3.4.1 to a hg38 reference using --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads aligning to mitochondrial, blacklist, unmapped, multimapping, and low-quality reads were filtered. Duplicate reads were marked but retained.
bigWig signal tracks were generated using deepTools bamCoverage v3.5.3 with bin size 20, smooth length 60, read extension, and RLE background-normalisation scale factors generated by DiffBind.
Peaks were called with MACS2 v2.2.7.1 using matched IgG controls, paired-end BAM input (BAMPE), human genome size, and q-value threshold 0.05.
Assembly: hg38
Supplementary files format and content: bigWig files contain RLE-normalised genome-wide DynaTag signal tracks; narrowPeak files contain MACS2 peak calls for the Rb1-targeted libraries.

source_name: PDX3837 tumour slice

growth_protocol: NOD.Cg-Prkdcscid Il2rgtm1Wjl (NSG) mice were used for all in vivo experiments. Mice were housed under specific pathogen-free conditions at 19–21 °C and 40–60% relative humidity with ad libitum access to food and water. Animals were maintained on a 14-h light/10-h dark cycle (lights on at 07:00 and off at 20:00) with 30-min dawn and dusk transitions. Tumour pieces of 1-2 mm^3 were implanted into the thoracic mammary fat pads of 7-week-old NGS female mice implanted with 0.3 mg oestradiol silicon pellets.

extract_protocol:
Cleavage under Dynamic targets and Tagmentation (DynaTag), a modified CUT&Tag method adapted from Hunold, et al., was used21. Briefly, tissue slices were washed in DynaTag Buffer (25 mM HEPES pH 7.5 (Gibco Cat. 15630-080), 110 mM KCl (Invitrogen Cat. AM9640G), 10 mM NaCl (Invitrogen Cat. AM9760G), 1 mM MgCl2 (Invitrogen Cat. AM9530G), 1X Spermidine (CST Cat. 27287S), 1X Protease Inhibitor Cocktail (CST Cat. 7012L)), bound to ConA beads, and incubated overnight at 4°C with primary antibody (Rb (CST #61121) or mouse IgG2a) in Antibody Buffer (DynaTag Buffer + 1% w/v BSA (Sigma Cat. A8577-10ML), Digitonin (CST Cat. 16359L)). Anti-mouse secondary antibody (0.5 μg; Abcam, ab46540) and pre-loaded pA-Tn5 complex (1:100 dilution, Diagenode Cat. C0107001) binding were performed at room temperature for one hour each. Tagmentation was initiated by incubating samples at 37°C for one hour in Antibody Buffer supplemented with 10 mM MgCl2. Upon tagmentation, samples were resuspended in Denaturation Buffer (10 mM Tris-HCl (Invitrogen Cat. 15568-025), 50 mM NaCl (Invitrogen Cat. AM9760G), 0.2% SDS (Invitrogen Cat. 15553-035), 0.15 mg/mL Proteinase K (CST Cat. 10012S), 16.67 mM EDTA (Invitrogen Cat. 15575020)) and incubated at 58°C for 3 hours. Denaturation was stopped by purification of the tagmented DNA fragments using the MinElute PCR Cleanup Kit (Qiagen Cat. 28004), as per manufacturer’s protocol.
DynaTag libraries were prepared using Illumina® DNA/RNA UD Indexes Set A, Tagmentation (Illumina Cat. 20091654) and NEBNext 2× PCR Mix (NEB, M0541L).

treatment_protocol: When tumours reached an average of 250 mm3 (using the formula: width2 × length × 0.5), mice were randomised into two treatment groups: abemaciclib or vehicle control. Abemaciclib and vehicle were prepared as previously described44. Mice were treated with 90 mg/kg abemaciclib by daily oral gavage, five doses in total, and then euthanised by CO2 asphyxiation or cervical dislocation 2 to 4 hours after the last dose.

value: PDX3837 tumour slice

tag: model

value: PDX3837 patient-derived xenograft

tag: antibody

value: IgG


title: MCF7_ESR1_DMSO_rep2

description: Library name: Sample 2


title: PDX3837 tumour slice, Abemaciclib, IgG DynaTag, biological replicate 1

description:
Library name: DynaTag_PDX3837_Abemaciclib_IgG_Rep1_S12
Matched IgG control for Abemaciclib biological replicate 1.


title: PDX3837 tumour slice, Abemaciclib, Rb1 DynaTag, biological replicate 1

description:
Library name: DynaTag_PDX3837_Abemaciclib_Rb1_Rep1_S10
Rb1-targeted DynaTag library.


title: PDX3837 tumour slice, Abemaciclib, Rb1 DynaTag, biological replicate 2

description:
Library name: DynaTag_PDX3837_Abemaciclib_Rb1_Rep2_S13
Rb1-targeted DynaTag library.


title: PDX3837 tumour slice, Vehicle, IgG DynaTag, biological replicate 2

description:
Library name: DynaTag_PDX3837_Vehicle_IgG_Rep2_S9
Matched IgG control for Vehicle biological replicate 2.

value: Vehicle


title: PDX3837 tumour slice, Vehicle, Rb1 DynaTag, biological replicate 2

description:
Library name: DynaTag_PDX3837_Vehicle_Rb1_Rep2_S7
Rb1-targeted DynaTag library.


title: PDX3837 tumour slice, Vehicle, Rb1 DynaTag, biological replicate 1

description:
Library name: DynaTag_PDX3837_Vehicle_Rb1_Rep1_S4
Rb1-targeted DynaTag library.


title: PDX3837 tumour slice, Vehicle, IgG DynaTag, biological replicate 1

description:
Library name: DynaTag_PDX3837_Vehicle_IgG_Rep1_S6
Matched IgG control for Vehicle biological replicate 1.


title: MCF7 siControl DMSO Mouse IgG2a C&R negative control

description: Library name: MCF7_siControl_DMSO_Mouse_IgG2a

data_processing:
Adapters and low quality reads were removed using BBMap bbduk.sh with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20.
Reads were aligned using Bowtie2 v2.3.4.1 to the hg38 genome with parameters --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. hg38 BAM files were retained after removing reads aligned to mitochondrial reads, blacklisted regions, duplicate reads, unmapped reads, and multimapping reads.
bigWig files were created from hg38 final BAM files using deepTools bamCoverage v3.5.3 with --binSize 20, --smoothLength 60, --scaleFactor from DiffBind background RLE normalisation factors, and --extendReads.
Peaks were called with MACS2 v2.2.7.1 callpeak using -f BAMPE -g hs -q 0.05. RB samples used the Mouse IgG2a control and KDM5A samples used the Rabbit IgG control in the MACS2 --control parameter.
Assembly: GCA hg38
Supplementary files format and content: bigWig signal tracks, narrowPeak peak calls
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed using the Cell Signaling Technologies (CST) CUT&RUN Assay Kit (#86652) as per manufacturer's protocol.
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina, following the CST DNA Library Prep Kit protocol for CUT&RUN.

treatment_protocol: Cells were transfected with non-targeting control siRNA or KDM5A siRNA and treated with abemaciclib or equal volume of DMSO control as indicated in the sample table.

tag: sirna

value: Non-targeting

value: Mouse IgG2a (CST 61656)


title: MCF7 siKDM5A DMSO Rabbit IgG C&R negative control

description: Library name: MCF7_siKDM5A_DMSO_Rabbit_IgG

value: Rabbit IgG (CST 66362)


title: MCF7 siKDM5A Abemaciclib RB C&R Rep 2

description: Library name: MCF7_siKDM5A_LY_rep2_RB


title: MCF7 siKDM5A DMSO RB C&R Rep 2

description: Library name: MCF7_siKDM5A_DMSO_rep2_RB


title: RNAseq, HSEC Donor1, PCSK9-EE7000, 4

description: Library name: NGSRS3147

value: Spleen

value: HSEC cells

value: Human Splenic Endothelial Cells


title: MCF7 siKDM5A Abemaciclib RB C&R Rep 1

description: Library name: MCF7_siKDM5A_LY_rep1_RB


title: MCF7 siKDM5A DMSO RB C&R Rep 1

description: Library name: MCF7_siKDM5A_DMSO_rep1_RB

value: DMSO


title: MCF7 siControl Abemaciclib RB C&R Rep 2

description: Library name: MCF7_siControl_LY_rep2_RB


title: MCF7 siControl Abemaciclib RB C&R Rep 1

description: Library name: MCF7_siControl_LY_rep1_RB


title: MCF7 siControl DMSO RB C&R Rep 2

description: Library name: MCF7_siControl_DMSO_rep2_RB


title: MCF7 siControl DMSO RB C&R Rep 1

description: Library name: MCF7_siControl_DMSO_rep1_RB


title: MCF7 siKDM5A DMSO KDM5A C&R Rep 1

description: Library name: MCF7_siKDM5A_DMSO_rep1_KDM5A


title: MCF7 siControl DMSO KDM5A C&R Rep 1

description: Library name: MCF7_siControl_DMSO_rep1_KDM5A


title: MCF7 DMSO Rabbit IgG negative control

description: Library name: Sample 5

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
Reads were aligned using Bowtie2 v2.3.4.1 to the GCA hg38 genome with the following parameters: --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads that aligned to ChIP blacklisted regions were removed, as well as reads aligned to mitrochondria DNA. Duplicates were kept.
bigwigs for treated samples were created using deeptools/3.5.0 bamCoverage function using paramters --binSize 20, --smoothLength 60, --scaleFactor scalefactor, --extendReads, where the scalefactor generated by a background normalisation from DiffBind was used as a normalisation factor. Bigwig for the IgG sample was normalised with BPM.
peaks were called using MACS2 v2.2.7.1 callpeak using the negative input in the --control parameter, --format BAMPE -gsize hs. Peaks for the negative input (IgG) were called without a control parameter.
Assembly: GCA hg38
Supplementary files format and content: bigwigs, narrowPeaks
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed using the Cell Signaling Technologies (CST) CUT&RUN Assay Kit (#86652) as per manufacturer's protocol.
CUT&RUN libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit for Illumina, following the CST DNA Library Prep Kit protocol for CUT&RUN.

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 2 days.

value: Parent


title: MCF7 Abema KDM5A C&R Rep 2

description: Library name: Sample 4

value: Abemaciclib


title: MCF7 Abema KDM5A C&R Rep 1

description: Library name: Sample 3


title: Custom Panel1 HCMS, HAdCC Donor3, Untreated, 3

description: Library name: NGSHC3467

value: Adrenal

value: HAdCC cells

value: Human Adrenal Cortical Cells


title: MCF7 DMSO KDM5A C&R Rep 2

description: Library name: Sample 2


title: MCF7 DMSO KDM5A C&R Rep 1

description: Library name: Sample 1


title: Custom Panel1 HCMS, HAdCC Donor3, Untreated, 4

description: Library name: NGSHC3468


title: Custom Panel1 HCMS, HAdCC Donor3, Untreated, 2

description: Library name: NGSHC3466


title: Custom Panel1 HCMS, HAdCC Donor3, Untreated, 1

description: Library name: NGSHC3465


title: Custom Panel1 HCMS, HAdCC Donor3, PCSK9-EE7000, 4

description: Library name: NGSHC3456


title: Custom Panel1 HCMS, HAdCC Donor3, PCSK9-EE7000, 3

description: Library name: NGSHC3455


title: Custom Panel1 HCMS, HAdCC Donor3, PCSK9-EE7000, 2

description: Library name: NGSHC3454


title: Custom Panel1 HCMS, HAdCC Donor3, PCSK9-EE7000, 1

description: Library name: NGSHC3453


title: Custom Panel1 HCMS, HAdCC Donor3, Mock-treatment, 4

description: Library name: NGSHC3464


title: Custom Panel1 HCMS, HAdCC Donor3, Mock-treatment, 3

description: Library name: NGSHC3463


title: Custom Panel1 HCMS, HAdCC Donor3, Mock-treatment, 2

description: Library name: NGSHC3462


title: Custom Panel1 HCMS, HAdCC Donor3, Mock-treatment, 1

description: Library name: NGSHC3461


title: Custom Panel1 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSHC3452


title: Custom Panel1 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSHC3449


title: Custom Panel1 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSHC3450


title: Custom Panel1 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3460


title: Custom Panel1 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3459


title: Custom Panel1 HCMS, HAdCC Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSHC3451


title: Custom Panel1 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3458


title: Custom Panel1 HCMS, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3457


title: Custom Panel1 HCMS, HAdCC Donor2, Untreated, 4

description: Library name: NGSHC3488


title: Custom Panel1 HCMS, HAdCC Donor2, Untreated, 3

description: Library name: NGSHC3487


title: Custom Panel1 HCMS, HAdCC Donor2, Untreated, 2

description: Library name: NGSHC3486


title: Custom Panel1 HCMS, HAdCC Donor2, Untreated, 1

description: Library name: NGSHC3485


title: Custom Panel1 HCMS, HAdCC Donor2, PCSK9-EE7000, 3

description: Library name: NGSHC3475


title: Custom Panel1 HCMS, HAdCC Donor2, PCSK9-EE7000, 4

description: Library name: NGSHC3476


title: Custom Panel1 HCMS, HAdCC Donor2, PCSK9-EE7000, 1

description: Library name: NGSHC3473


title: Custom Panel1 HCMS, HAdCC Donor2, PCSK9-EE7000, 2

description: Library name: NGSHC3474


title: Custom Panel1 HCMS, HAdCC Donor2, Mock-treatment, 4

description: Library name: NGSHC3484


title: Custom Panel1 HCMS, HAdCC Donor2, Mock-treatment, 3

description: Library name: NGSHC3483


title: Custom Panel1 HCMS, HAdCC Donor2, Mock-treatment, 1

description: Library name: NGSHC3481


title: Custom Panel1 HCMS, HAdCC Donor2, Mock-treatment, 2

description: Library name: NGSHC3482


title: Custom Panel1 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSHC3472


title: Custom Panel1 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSHC3471


title: Custom Panel1 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSHC3470


title: Custom Panel1 HCMS, HAdCC Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSHC3469


title: Custom Panel1 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3480


title: Custom Panel1 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3479


title: Custom Panel1 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3478


title: Custom Panel1 HCMS, HAdCC Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3477


title: Custom Panel1 HCMS, HAdCC Donor1, Untreated, 4

description: Library name: NGSHC3517


title: Custom Panel1 HCMS, HAdCC Donor1, Untreated, 3

description: Library name: NGSHC3511


title: Custom Panel1 HCMS, HAdCC Donor1, Untreated, 2

description: Library name: NGSHC3509


title: Custom Panel1 HCMS, HAdCC Donor1, Untreated, 1

description: Library name: NGSHC3501


title: Custom Panel1 HCMS, HAdCC Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3506


title: Custom Panel1 HCMS, HAdCC Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3503


title: Custom Panel1 HCMS, HAdCC Donor1, PCSK9-EE7000, 4

description: Library name: NGSHC3514


title: Custom Panel1 HCMS, HAdCC Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3498


title: Custom Panel1 HCMS, HAdCC Donor1, Mock-treatment, 4

description: Library name: NGSHC3516


title: Custom Panel1 HCMS, HAdCC Donor1, Mock-treatment, 3

description: Library name: NGSHC3510


title: Custom Panel1 HCMS, HAdCC Donor1, Mock-treatment, 2

description: Library name: NGSHC3508


title: Custom Panel1 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSHC3513


title: Custom Panel1 HCMS, HAdCC Donor1, Mock-treatment, 1

description: Library name: NGSHC3500


title: Custom Panel1 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3505


title: Custom Panel1 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3497


title: Custom Panel1 HCMS, HAdCC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3502


title: Custom Panel1 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3515


title: Custom Panel1 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3504


title: Custom Panel1 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3507


title: Custom Panel1 HCMS, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3499


title: Custom Panel1 HCMS, HSEC Donor3, Untreated, 4

description: Library name: NGSHC3396


title: Custom Panel1 HCMS, HSEC Donor3, Untreated, 3

description: Library name: NGSHC3395


title: Custom Panel1 HCMS, HSEC Donor3, Untreated, 2

description: Library name: NGSHC3394


title: Custom Panel1 HCMS, HSEC Donor3, Untreated, 1

description: Library name: NGSHC3393


title: Custom Panel1 HCMS, HSEC Donor3, PCSK9-EE7000, 4

description: Library name: NGSHC3372


title: Custom Panel1 HCMS, HSEC Donor3, PCSK9-EE7000, 2

description: Library name: NGSHC3370


title: Custom Panel1 HCMS, HSEC Donor3, PCSK9-EE7000, 1

description: Library name: NGSHC3369


title: Custom Panel1 HCMS, HSEC Donor3, Mock-treatment, 4

description: Library name: NGSHC3388


title: Custom Panel1 HCMS, HSEC Donor3, PCSK9-EE7000, 3

description: Library name: NGSHC3371


title: Custom Panel1 HCMS, HSEC Donor3, Mock-treatment, 3

description: Library name: NGSHC3387


title: Custom Panel1 HCMS, HSEC Donor3, Mock-treatment, 2

description: Library name: NGSHC3386


title: Custom Panel1 HCMS, HSEC Donor3, Mock-treatment, 1

description: Library name: NGSHC3385


title: Custom Panel1 HCMS, HSEC Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSHC3363


title: Custom Panel1 HCMS, HSEC Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSHC3364


title: Custom Panel1 HCMS, HSEC Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSHC3362


title: Custom Panel1 HCMS, HSEC Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSHC3361


title: Custom Panel1 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3380


title: Custom Panel1 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3379


title: Custom Panel1 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3378


title: Custom Panel1 HCMS, HSEC Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3377


title: Custom Panel1 HCMS, HSEC Donor2, Untreated, 3

description: Library name: NGSHC3391


title: Custom Panel1 HCMS, HSEC Donor2, Untreated, 4

description: Library name: NGSHC3392


title: Custom Panel1 HCMS, HSEC Donor2, Untreated, 2

description: Library name: NGSHC3390


title: Custom Panel1 HCMS, HSEC Donor2, Untreated, 1

description: Library name: NGSHC3389


title: Custom Panel1 HCMS, HSEC Donor2, PCSK9-EE7000, 3

description: Library name: NGSHC3367


title: Custom Panel1 HCMS, HSEC Donor2, PCSK9-EE7000, 2

description: Library name: NGSHC3366


title: Custom Panel1 HCMS, HSEC Donor2, PCSK9-EE7000, 4

description: Library name: NGSHC3368


title: Custom Panel1 HCMS, HSEC Donor2, Mock-treatment, 4

description: Library name: NGSHC3384


title: Custom Panel1 HCMS, HSEC Donor2, PCSK9-EE7000, 1

description: Library name: NGSHC3365


title: Custom Panel1 HCMS, HSEC Donor2, Mock-treatment, 3

description: Library name: NGSHC3383


title: Custom Panel1 HCMS, HSEC Donor2, Mock-treatment, 2

description: Library name: NGSHC3382


title: Custom Panel1 HCMS, HSEC Donor2, Mock-treatment, 1

description: Library name: NGSHC3381


title: Custom Panel1 HCMS, HSEC Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSHC3360


title: Custom Panel1 HCMS, HSEC Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSHC3358


title: Custom Panel1 HCMS, HSEC Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSHC3357


title: Custom Panel1 HCMS, HSEC Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSHC3359


title: Custom Panel1 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3376


title: Custom Panel1 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3374


title: Custom Panel1 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3373


title: Custom Panel1 HCMS, HSEC Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3375


title: Custom Panel1 HCMS, HSEC Donor1, Untreated, 4

description: Library name: NGSHC3425


title: Custom Panel1 HCMS, HSEC Donor1, Untreated, 3

description: Library name: NGSHC3419


title: Custom Panel1 HCMS, HSEC Donor1, Untreated, 1

description: Library name: NGSHC3409


title: Custom Panel1 HCMS, HSEC Donor1, Untreated, 2

description: Library name: NGSHC3417


title: Custom Panel1 HCMS, HSEC Donor1, PCSK9-EE7000, 4

description: Library name: NGSHC3422


title: Custom Panel1 HCMS, HSEC Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3411


title: Custom Panel1 HCMS, HSEC Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3406


title: Custom Panel1 HCMS, HSEC Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3414


title: Custom Panel1 HCMS, HSEC Donor1, Mock-treatment, 3

description: Library name: NGSHC3418


title: Custom Panel1 HCMS, HSEC Donor1, Mock-treatment, 4

description: Library name: NGSHC3424


title: Custom Panel1 HCMS, HSEC Donor1, Mock-treatment, 2

description: Library name: NGSHC3416


title: Custom Panel1 HCMS, HSEC Donor1, Mock-treatment, 1

description: Library name: NGSHC3408


title: Custom Panel1 HCMS, HSEC Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSHC3421


title: Custom Panel1 HCMS, HSEC Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3413


title: Custom Panel1 HCMS, HSEC Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3410


title: Custom Panel1 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3423


title: Custom Panel1 HCMS, HSEC Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3405


title: Custom Panel1 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3415


title: Custom Panel1 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3412


title: Custom Panel1 HCMS, HSEC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3407


title: Custom Panel1 HCMS, PHH Donor3, Untreated, 4

description: Library name: NGSHC3318

value: Liver

value: PXB cells

value: Primary Human Hepatocyte


title: Custom Panel1 HCMS, PHH Donor3, Untreated, 3

description: Library name: NGSHC3311


title: Custom Panel1 HCMS, PHH Donor3, Untreated, 1

description: Library name: NGSHC3297


title: Custom Panel1 HCMS, PHH Donor3, Untreated, 2

description: Library name: NGSHC3304


title: Custom Panel1 HCMS, PHH Donor3, PCSK9-EE7000, 4

description: Library name: NGSHC3321


title: Custom Panel1 HCMS, PHH Donor3, PCSK9-EE7000, 3

description: Library name: NGSHC3314


title: Custom Panel1 HCMS, PHH Donor3, PCSK9-EE7000, 2

description: Library name: NGSHC3307


title: Custom Panel1 HCMS, PHH Donor3, PCSK9-EE7000, 1

description: Library name: NGSHC3300


title: Custom Panel1 HCMS, PHH Donor3, Mock-treatment, 4

description: Library name: NGSHC3319


title: Custom Panel1 HCMS, PHH Donor3, Mock-treatment, 2

description: Library name: NGSHC3305


title: Custom Panel1 HCMS, PHH Donor3, HBV-CRISPRi, 4

description: Library name: NGSHC3323


title: Custom Panel1 HCMS, PHH Donor3, HBV-CRISPRi, 2

description: Library name: NGSHC3309


title: Custom Panel1 HCMS, PHH Donor3, Mock-treatment, 3

description: Library name: NGSHC3312


title: Custom Panel1 HCMS, PHH Donor3, HBV-CRISPRi, 3

description: Library name: NGSHC3316


title: Custom Panel1 HCMS, PHH Donor3, Mock-treatment, 1

description: Library name: NGSHC3298


title: Custom Panel1 HCMS, PHH Donor3, HBV-CRISPRi, 1

description: Library name: NGSHC3302


title: Custom Panel1 HCMS, PHH Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSHC3322


title: Custom Panel1 HCMS, PHH Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSHC3308


title: Custom Panel1 HCMS, PHH Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSHC3301


title: Custom Panel1 HCMS, PHH Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSHC3315


title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3313


title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3299


title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3306