title: DLD1 CRISPRi sublib2, SAM24482910_24, MOI Low (~0.3), GEX

city: South San Francisco

first: Jake

last: Yeung

email: yeungj3@gene.com, jakeyeung@gmail.com

address: 1 DNA Way

department: Genentech Research & Early Development

institute: Genentech Inc.

description:
Library name: LIB6266257_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.

data_processing:
Raw sequencing reads were demultiplexed and aligned to the GRCh38-2020-A reference genome using Cell Ranger v9.0.1 (10x Genomics) with intron counting enabled.
Hashtag demultiplexing was performed using MULTI-seq CMO counts to assign cells to MOI conditions.
Guide RNA assignments were determined from the sgRNA capture library counts.
Quality control filtering included nuclear fraction estimation (DropletQC) and removal of low-quality cells.
Differential expression analysis was performed using limma-voom on pseudobulk counts aggregated per perturbation target, with perturbation-matched control cells (perturbmatch). MENG guides were excluded. Outputs are genes x perturbations matrices of log-fold-change (lfc), standard error (se), z-score (lfc/se), and pairwise cosine similarity between perturbation z-score profiles.
Assembly: GRCh38-2020-A (10x Genomics pre-built reference)
Supplementary files format and content: HDF5 files containing filtered and raw feature-barcode count matrices (Cell Ranger output). Each .h5 file contains barcodes, gene features, and UMI count data.
Supplementary files format and content: Processed SCE objects: assays.h5 files contain HDF5-serialized count matrices from SingleCellExperiment objects (genes x cells) after QC, hashtag demultiplexing, and guide assignment. se.rds files contain the full R SummarizedExperiment with cell-level metadata (colData) and gene annotations (rowData). Pilot objects are split by MOI condition (MOI_0.1 through MOI_5.0). SubLib2 objects are split by MOI level (Low, Med, High).
Supplementary files format and content: DE result matrices: gzipped CSV files (csv.gz) containing differential expression results from limma-voom weighted GLM with perturbation-matched controls. Four matrix types per condition: lfc_matrix (log-fold-change, genes x perturbations), se_matrix (standard error), zscore_matrix (lfc/se), and cosine_sim (pairwise cosine similarity between perturbation z-score profiles, perturbations x perturbations).
Supplementary files format and content: Hashing UMI-corrected count matrices: HDF5 files (.hashing.umi_correct.h5) containing MULTI-seq CMO hashtag barcode counts per cell, used for sample demultiplexing. sgRNA capture UMI-corrected count matrices: HDF5 files (.crispr.umi_correct.h5) containing guide RNA barcode counts per cell, used for perturbation assignment.

growth_protocol: DLD-1 cells stably expressing TET-DD-inducible Zim3-dCas9 were maintained in standard culture conditions.

extract_protocol:
After 5 days of doxycycline and Shield-1 induction, cells from each MOI condition were harvested, labeled with MULTI-seq CMO hashtag barcodes, pooled, and sorted by FACS. Sorted cells were resuspended and loaded onto 10x Genomics Chromium GEM-X chips targeting ~50,000 cells per channel.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3' GEM-X v4 kit according to the manufacturer's instructions. Three libraries were constructed per 10x channel: gene expression (GEX), sgRNA capture, and MULTI-seq CMO (cell multiplexing oligo) hashing. For the scaled experiment (sub-library 2), 44 10x channels were used (Low MOI: 24, Medium MOI: 12, High MOI: 8). For the pilot experiment, 4 10x channels were used.

treatment_protocol: Cells were transduced with lentiviral CRISPRi guide RNA libraries at specified MOI levels. For the pilot experiment, a 94-guide library was used at MOI 0.1, 0.2, 0.5, 1.0, 3.0, and 5.0. For the scaled experiment, a 6,455-guide CRISPRi sub-library 2 was used at MOI ~0.3 (Low), ~3 (Medium), and ~10 (High), with 5% non-targeting control (NTC) guides spiked in. Cells were treated with 250 ng/mL doxycycline and Shield-1 ligand (1:500) to induce Zim3-dCas9 expression for 5 days. Cells from each MOI pool were labeled with MULTI-seq cell multiplexing oligo (CMO) barcodes, pooled, and sorted by FACS.

value: colorectal adenocarcinoma

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 6455-guide sub-library 2; MOI Low (~0.3); 5% NTC spike-in; MULTI-seq CMO hashing


title: DLD1 CRISPRi sublib2, SAM24482910_23, MOI Low (~0.3), GEX

status: Public on Jul 10 2026

type: SRA

state: CA

country: USA

description:
Library name: LIB6266256_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: TBL60_batch_3_ROI_1_anno_Other

city: Los Angeles

first: Jonathan

last: Perrie

address: 610 Charles E Young Dr S

department: Bioinformatics

institute: University of California, Los Angeles

description:
Library name: TBL60_batch_3_ROI_1
None

library_source: transcriptomic

data_processing:
Analysis began with GeoMx DCC files and followed the pre-processing and normalization steps outlined in the GeoMxWorkflows R vignette.
ROIs were filtered to exclude those detecting less than 5% of total genes from the Whole Transcriptome Atlas. Genes were subsequently filtered to exclude those detected in fewer than 5% of ROIs.
The raw expression matrix was normalized using the 75th percentile normalization.
Assembly: hg38
Supplementary files format and content: DCC files: digital count conversion format per ROI
Supplementary files format and content: geomx_ptb_metadata.csv: ROI attributes after pre-processing
Supplementary files format and content: geomx_ptb_negprobes.csv: negative probe counts
Supplementary files format and content: geomx_ptb_q3_data.csv: quantile normalized counts
Supplementary files format and content: geomx_ptb_raw_data.csv: raw counts
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: Lymph

extract_protocol:
Lung FFPE tissue sections were mounted on glass slides, deparaffinized, and rehydrated following the GeoMx DSP manufacturer’s protocol. Slides were hybridized overnight at 37 °C with the GeoMx Human Whole Transcriptome Atlas probe set. Tissue morphology markers were revealed by fluorescent immunostaining to guide the selection of ROIs.
Barcoded oligonucleotide probes were photocleaved from selected ROIs by UV exposure and collected into separate wells. Oligos were uniquely indexed, and paired-end reads were generated by Illumina sequencing, then aligned and quantified using NanoString’s DSP analysis pipeline.

tag: tissue

value: Lymph

tag: region

value: Other

tag: batch


title: DLD1 CRISPRi sublib2, SAM24482910_22, MOI Low (~0.3), GEX

description:
Library name: LIB6266255_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207097320046_R05C01

type: genomic

city: San Francisco

first: Sebastián

last: Cruz-González

state: California

institute: UCSF

hyb_protocol: DNA methylation was quantified using the Illumina Infinium MethylationEPIC BeadChip (EPIC v1.0, ~850K CpG sites) according to the manufacturer's standard Infinium HD Assay protocol.

scan_protocol: BeadChips were scanned on an Illumina iScan system to generate raw IDAT files.

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: whole blood

label_protocol: Bisulfite conversion of genomic DNA was performed prior to hybridization following standard protocols for the Illumina Infinium MethylationEPIC BeadChip array. Samples were randomized across plates and chips to ensure that ancestry, age, and sex were not confounded with each batch.

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

tag: Sex

value: Female

tag: disease state

value: Healthy control

value: whole blood

tag: ethnicity

value: HISPANIC

tag: cohort

value: PERUVIAN

tag: age


title: DLD1 CRISPRi sublib2, SAM24482910_21, MOI Low (~0.3), GEX

description:
Library name: LIB6266254_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC CONTROL, 64yo M, 207219770097_R05C01

value: Male


title: PTB222_batch_3_ROI_27_anno_Alveoli

description:
Library name: PTB222_batch_3_ROI_27
Alveoli | PTB 22.2 | 27

source_name: Lung

value: Lung

value: Alveoli


title: DLD1 CRISPRi sublib2, SAM24482910_19, MOI Low (~0.3), GEX

description:
Library name: LIB6266252_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_26_anno_Alveoli

description:
Library name: PTB222_batch_3_ROI_26
Alveoli | PTB 22.2 | 26


title: DLD1 CRISPRi sublib2, SAM24482910_20, MOI Low (~0.3), GEX

description:
Library name: LIB6266253_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482910_18, MOI Low (~0.3), GEX

description:
Library name: LIB6266251_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC AD, 68yo M, 207080910117_R06C01

value: Alzheimer's disease


title: A673_VTP50469_tumor_rep1

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

description:
Library name: KB46
Raw counts for samples in batch 3

data_processing:
The quality of the sequencing data was analyzed with FastQC.
Adaptor fragments, low quality ends and short sequences were removed with Trim Galore.
Trimmed sequences were aligned to the reference genome, GRCh38, and gene counts generated with STAR (Batches 1-2, 4) or Salmon (Batch 3).
Additional quality control was performed with MultiQC.
Differentially expressed genes were identified with DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab delimited raw count files using STAR for read counts for batches 1,2 and 4
Supplementary files format and content: Tab delimited raw count files using Salmon for read counts for batch 3

source_name: tumor

growth_protocol:
All cell lines were grown in RPMI1640 + 10% FBS + 2 mM L-glutamine.
1e6 A673 MEN1-KO (A673 gMEN1 1-3, A673 gMEN1 5-1, gMEN1 5-2) or A673 control (A673 gControl 1) cells were injected subcutaneously in NSG mice and tumors were collected 28 days later and flash frozen.

extract_protocol:
Total RNA was collected using a Qiagen RNeasy kit
The polyA enrichment library was prepared using NEBNext Ultra II RNA Library Prep kit and sequencing with the Illumina Novaseq6000 or NovaSeq X Plus sequencer utilizing a paired-end 150 bp (PE150) sequencing strategy

treatment_protocol:
A673 and TC32 cells were treated with 10 µM VTP50469 or 0.1% DMSO (control) for 72 hours.
5e4 A673 and TC32 cells were injected into the tail vein of NSG mice and treated for 5 or 6 weeks respectively with 0.1% VTP50469 mouse chow compared to control mouse chow and liver tumors were flash frozen.

value: tumor

value: Ewing sarcoma cell line

value: 0.1% VTP50469 mouse chow


title: DLD1 CRISPRi sublib2, SAM24482910_17, MOI Low (~0.3), GEX

description:
Library name: LIB6266250_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_25_anno_Core

description:
Library name: PTB222_batch_3_ROI_25
Core | PTB 22.2 | 25

value: Core


title: Whole blood DNA methylation, HISPANIC AD, 70yo M, 207097420153_R01C01


title: DLD1 CRISPRi sublib2, SAM24482910_16, MOI Low (~0.3), GEX

description:
Library name: LIB6266249_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.

value: colorectal adenocarcinoma


title: IGROV-1/CP cisplatin + nelfinavir biol replicate 3

city: Montreal

first: Benjamin

last: Forgie

state: Quebec

address: 3775 Rue University

country: Canada

institute: McGill University

description: Library name: CN3_MPS12351762_B09

data_processing:
Base calling and demultiplexing were performed using BCL Convert v4.2.4 to generate FASTQ files.
FASTQ files were processed using the DRAGEN RNA-seq pipeline.
For samples requiring additional sequencing to reach the requested read depth, FASTQ files from the initial and repeat sequencing read sets were combined during DRAGEN analysis to generate the final gene-level count matrix.
Assembly: GRCh38
Supplementary files format and content: CSV file containing a gene-level normalized count matrix for all 12 IGROV-1/CP RNA-seq samples. Rows correspond to genes and columns correspond to individual biological replicate samples.

growth_protocol: IGROV-1/CP platinum-resistant ovarian cancer cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and antibiotics at 37°C with 5% CO2. Cells were cultured under standard adherent mammalian cell culture conditions prior to treatment and RNA collection.

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy Plus Universal Mini Kit according to the manufacturer’s instructions. Briefly, QIAzol lysis reagent was added to the cell samples, and homogenization was performed by passing the lysate 15 times through a 20-gauge needle attached to a sterile 3 mL syringe. RNA was eluted in 35 uL of the buffer provided with the extraction kit. Total RNA was quantified and RNA integrity was assessed using the 5K/RNA/Charge Variant Assay LabChip and RNA Assay Reagent Kit.
Libraries were generated from 250 ng of total RNA using the Illumina Stranded mRNA Prep Kit, including mRNA enrichment, according to the manufacturer’s recommendations. Libraries were quantified using the KAPA Library Quantification Kit, and average fragment size was determined using a Fragment Analyzer 5300. Libraries were normalized, pooled, denatured in 0.02 N NaOH, neutralized with pre-load buffer, and loaded at 170 pM onto an Illumina NovaSeq X Plus 25B lane for 2 x 100 bp paired-end sequencing. A PhiX control library was spiked in at 1%.

treatment_protocol: IGROV-1/CP cells were treated with vehicle, 10 uM cisplatin (CDDP) for 3 h followed by culture in drug-free medium until 24 h, 20 uM nelfinavir (NFV) for 24 h, or 10 uM CDDP for 3 h followed by culture in medium containing 20 uM NFV until 24 h. Cell pellets were then collected and submitted to Genome Quebec for RNA extraction, library preparation, and sequencing.

value: ovarian cancer cell

value: Not genetically modified

value: cisplatin + nelfinavir


title: PTB222_batch_3_ROI_24_anno_Core

description:
Library name: PTB222_batch_3_ROI_24
Core | PTB 22.2 | 24


title: DLD1 CRISPRi sublib2, SAM24482910_14, MOI Low (~0.3), GEX

description:
Library name: LIB6266247_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 6455-guide sub-library 2; MOI Low (~0.3); 5% NTC spike-in; MULTI-seq CMO hashing


title: DLD1 CRISPRi sublib2, SAM24482910_15, MOI Low (~0.3), GEX

description:
Library name: LIB6266248_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC AD, 87yo F, 207097420011_R02C01

value: Female


title: PTB222_batch_3_ROI_23_anno_Other

description:
Library name: PTB222_batch_3_ROI_23
Other | PTB 22.2 | 23

value: Other


title: DLD1 CRISPRi sublib2, SAM24482910_13, MOI Low (~0.3), GEX

description:
Library name: LIB6266246_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: TBL60_batch_3_ROI_11_anno_Other

description:
Library name: TBL60_batch_3_ROI_11
None

value: Lymph


title: Whole blood DNA methylation, HISPANIC AD, 74yo M, 207097420040_R07C01

value: whole blood

value: HISPANIC

value: PERUVIAN


title: Whole blood DNA methylation, HISPANIC AD, 74yo F, 207097420047_R06C01


title: DLD1 CRISPRi sublib2, SAM24482910_12, MOI Low (~0.3), GEX

description:
Library name: LIB6266245_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: IGROV-1/CP nelfinavir biol replicate 3

description: Library name: NFV3_MPS12351762_G08

value: nelfinavir


title: DLD1 CRISPRi sublib2, SAM24482910_11, MOI Low (~0.3), GEX

description:
Library name: LIB6266244_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_21_anno_Core

description:
Library name: PTB222_batch_3_ROI_21
Core | PTB 22.2 | 21

value: Lung


title: DLD1 CRISPRi sublib2, SAM24482910_10, MOI Low (~0.3), GEX

description:
Library name: LIB6266243_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: IGROV-1/CP cisplatin biol replicate 3

description: Library name: CDDP3_MPS12351762_D08

value: cisplatin


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207080910085_R03C01

value: Healthy control


title: DLD1 CRISPRi sublib2, SAM24482910_9, MOI Low (~0.3), GEX

description:
Library name: LIB6266242_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_20_anno_Core

description:
Library name: PTB222_batch_3_ROI_20
None


title: PTB222_batch_3_ROI_19_anno_Other

description:
Library name: PTB222_batch_3_ROI_19
Other | PTB 22.2 | 19


title: DLD1 CRISPRi sublib2, SAM24482910_7, MOI Low (~0.3), GEX

description:
Library name: LIB6266240_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: TBL60_batch_3_ROI_8_anno_Other

description:
Library name: TBL60_batch_3_ROI_8
None


title: Whole blood DNA methylation, HISPANIC AD, 90yo F, 207097420079_R02C01

value: Alzheimer's disease


title: DLD1 CRISPRi sublib2, SAM24482910_6, MOI Low (~0.3), GEX

description:
Library name: LIB6266239_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_18_anno_Core

description:
Library name: PTB222_batch_3_ROI_18
None

value: Core


title: DLD1 CRISPRi sublib2, SAM24482910_5, MOI Low (~0.3), GEX

description:
Library name: LIB6266238_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.

value: colorectal adenocarcinoma


title: Whole blood DNA methylation, HISPANIC AD, 79yo F, 207097420080_R06C01


title: DLD1 CRISPRi sublib2, SAM24482910_8, MOI Low (~0.3), GEX

description:
Library name: LIB6266241_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC AD, 84yo F, 207097320021_R06C01


title: DLD1 CRISPRi sublib2, SAM24482910_3, MOI Low (~0.3), GEX

description:
Library name: LIB6266236_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482910_1, MOI Low (~0.3), GEX

description:
Library name: LIB6266234_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC AD, 81yo F, 207097420114_R07C01


title: 293_DMSO_rep3

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

description: Library name: 293_DMSO_rep3

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq v2.20 conversion software. Reads were subsequently trimmed with TrimGalore, mapped to the hg38 transcriptome, and quantified using Salmon. Differentially expressed genes were identified using DESeq2.
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: raw counts, and Transcribe per milion in CSV format

source_name: cell line

growth_protocol: HEK293Tcells were obtained from ATCC (CRL-3216, Batch#70049877) and grown in 10 cm BioLite™   Cell Culture   Treated   Dishes   (Catalog# 12-556-002 Thermo   Scientific)   in Dulbecco’s Modified Eagle Medium, high glucose (Catalog# 11965092, Gibco). HEK293T experiments were conducted on cells between passage 10-25. THP-1 monocytes were obtained from ATCC (TIB-202 Batch# 62454382) and propagated in T-75 flasks between 0.2 and 1 × 10e6 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP-1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
E.Z.N.A.® Total RNA Kit I (Catalog# R6834-01, Omega), with 100% ethanol instead of 70% at the binding step to enrich small RNA.
Libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) and sequenced on two 25B lanes for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

treatment_protocol: siRNA and ASO transfected using Lipofectamine® RNAiMax (cat # 13778150) with standard protocol, Overexpression sample are transfected using Lipofectamine 3000 (cat #L3000015)

value: cell line

value: DMSO


title: PTB222_batch_3_ROI_17_anno_Other

description:
Library name: PTB222_batch_3_ROI_17
Other | PTB 22.2 | 17


title: PTB222_batch_3_ROI_16_anno_Other

description:
Library name: PTB222_batch_3_ROI_16
Other | PTB 22.2 | 16


title: DLD1 CRISPRi sublib2, SAM24482910_2, MOI Low (~0.3), GEX

description:
Library name: LIB6266235_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482910_4, MOI Low (~0.3), GEX

description:
Library name: LIB6266237_SAM24482910
10x Chromium Single Cell 3' v4 GEX library. MOI Low (~0.3) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482911_12, MOI Medium (~3), GEX

description:
Library name: LIB6266269_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 6455-guide sub-library 2; MOI Medium (~3); 5% NTC spike-in; MULTI-seq CMO hashing


title: Whole blood DNA methylation, HISPANIC AD, 77yo F, 207097420153_R03C01


title: DLD1 CRISPRi sublib2, SAM24482911_11, MOI Medium (~3), GEX

description:
Library name: LIB6266268_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC AD, 75yo M, 207097420191_R02C01

value: Male


title: PTB222_batch_3_ROI_15_anno_Other

description:
Library name: PTB222_batch_3_ROI_15
Other | PTB 22.2 | 15


title: DLD1 CRISPRi sublib2, SAM24482911_10, MOI Medium (~3), GEX

description:
Library name: LIB6266267_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482911_9, MOI Medium (~3), GEX

description:
Library name: LIB6266266_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: TBL60_batch_3_ROI_4_anno_Other

description:
Library name: TBL60_batch_3_ROI_4
None


title: PTB222_batch_3_ROI_14_anno_Other

description:
Library name: PTB222_batch_3_ROI_14
Other | PTB 22.2 | 14


title: DLD1 CRISPRi sublib2, SAM24482911_7, MOI Medium (~3), GEX

description:
Library name: LIB6266264_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC CONTROL, 65yo F, 207097420065_R05C01

value: Female


title: DLD1 CRISPRi sublib2, SAM24482911_6, MOI Medium (~3), GEX

description:
Library name: LIB6266263_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC CONTROL, 65yo M, 207097420112_R08C01


title: PTB222_batch_3_ROI_13_anno_Other

description:
Library name: PTB222_batch_3_ROI_13
Other | PTB 22.2 | 13

value: Other


title: DLD1 CRISPRi sublib2, SAM24482911_8, MOI Medium (~3), GEX

description:
Library name: LIB6266265_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482911_5, MOI Medium (~3), GEX

description:
Library name: LIB6266262_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207097420010_R01C01


title: PTB222_batch_3_ROI_11_anno_Other

description:
Library name: PTB222_batch_3_ROI_11
Other | PTB 22.2 | 11


title: DLD1 CRISPRi sublib2, SAM24482911_3, MOI Medium (~3), GEX

description:
Library name: LIB6266260_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_12_anno_Mantle

description:
Library name: PTB222_batch_3_ROI_12
Mantle | PTB 22.2 | 12

value: Mantle


title: DLD1 CRISPRi sublib2, SAM24482911_4, MOI Medium (~3), GEX

description:
Library name: LIB6266261_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482911_2, MOI Medium (~3), GEX

description:
Library name: LIB6266259_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo M, 207097420102_R06C01

value: whole blood


title: DLD1 CRISPRi sublib2, SAM24482911_1, MOI Medium (~3), GEX

description:
Library name: LIB6266258_SAM24482911
10x Chromium Single Cell 3' v4 GEX library. MOI Medium (~3) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_10_anno_Core

description:
Library name: PTB222_batch_3_ROI_10
Core | PTB 22.2 | 10


title: Whole blood DNA methylation, HISPANIC CONTROL, 79yo F, 207097420191_R07C01

value: HISPANIC

value: CuADI


title: DLD1 CRISPRi sublib2, SAM24482912_7, MOI High (~10), GEX

description:
Library name: LIB6266276_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 6455-guide sub-library 2; MOI High (~10); 5% NTC spike-in; MULTI-seq CMO hashing


title: PTB222_batch_3_ROI_9_anno_Other

description:
Library name: PTB222_batch_3_ROI_9
None

value: Lung


title: DLD1 CRISPRi sublib2, SAM24482912_8, MOI High (~10), GEX

description:
Library name: LIB6266277_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.


title: DLD1 CRISPRi sublib2, SAM24482912_6, MOI High (~10), GEX

description:
Library name: LIB6266275_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC CONTROL, 64yo F, 207097420010_R05C01


title: PTB222_batch_3_ROI_8_anno_Other

description:
Library name: PTB222_batch_3_ROI_8
Other | PTB 22.2 | 08


title: Whole blood DNA methylation, HISPANIC AD, 87yo M, 207080910085_R05C01


title: DLD1 CRISPRi sublib2, SAM24482912_3, MOI High (~10), GEX

description:
Library name: LIB6266272_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_7_anno_Other

description:
Library name: PTB222_batch_3_ROI_7
Other | PTB 22.2 | 07


title: DLD1 CRISPRi sublib2, SAM24482912_5, MOI High (~10), GEX

description:
Library name: LIB6266274_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.


title: Whole blood DNA methylation, HISPANIC CONTROL, 83yo F, 207080910117_R07C01


title: DLD1 CRISPRi sublib2, SAM24482912_2, MOI High (~10), GEX

description:
Library name: LIB6266271_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.


title: PTB222_batch_3_ROI_6_anno_Alveoli

description:
Library name: PTB222_batch_3_ROI_6
None

value: Alveoli


title: Whole blood DNA methylation, HISPANIC CONTROL, 86yo F, 207097420192_R03C01

value: Healthy control


title: AID-CDK8 #9 + sgCDK19 #3-17 - Combo-2

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Library name: AID-CDK8_9+sgCDK19_3-17_Combo-2

data_processing:
Trim Galore was used for quality and adapter trimming. STAR was employed to align the reads onto the human genome, SAMtools was employed to sort the alignments, and HTSeq Python package was employed to count reads per gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene read counts for each sample

source_name: Muscle

growth_protocol: A-673 AIDCDK8; CDK19-KO clone 1 (#3-28) and clone 2 (#3-17) were maintained in RPMI-1640 media supplemented with 10% FBS, 1% Pen-Strep and 1% L-glutamine in humidified atmosphere with 5% CO2 at 37°C .

extract_protocol:
Total RNA were extracted using TRIzol reagent and purified with Direct-zol miniRNA prep plus kit (Zymo).
RNA libraries were prepared with poly A enrichment, and the first strand cDNAs were synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cells were treated with vehicle (DMSO), 300 nM 5-ph-IAA, 100 nM SW393109 or the combination for 24 hrs in replicate.

value: Muscle

value: Ewing Sarcoma cell


title: AID-CDK8 #9 + sgCDK19 #3-17 - Combo-1

description: Library name: AID-CDK8_9+sgCDK19_3-17_Combo-1


title: PTB222_batch_3_ROI_5_anno_Alveoli

description:
Library name: PTB222_batch_3_ROI_5
Alveoli | PTB 22.2 | 05


title: AID-CDK8 #9 + sgCDK19 #3-17 - 5-ph-IAA-2

description: Library name: AID-CDK8_9+sgCDK19_3-17_5-ph-IAA-2


title: Whole blood DNA methylation, HISPANIC CONTROL, 76yo F, 207080920105_R04C01


title: AID-CDK8 #9 + sgCDK19 #3-17 - 5-ph-IAA-1

description: Library name: AID-CDK8_9+sgCDK19_3-17_5-ph-IAA-1


title: Whole blood DNA methylation, HISPANIC AD, 64yo F, 207080910117_R01C01

value: Alzheimer's disease


title: AID-CDK8 #9 + sgCDK19 #3-17 - SW393109-2

description: Library name: AID-CDK8_9+sgCDK19_3-17_SW393109-2


title: AID-CDK8 #9 + sgCDK19 #3-17 - SW393109-1

description: Library name: AID-CDK8_9+sgCDK19_3-17_SW393109-1


title: PTB222_batch_3_ROI_4_anno_Alveoli

description:
Library name: PTB222_batch_3_ROI_4
Alveoli | PTB 22.2 | 04


title: AID-CDK8 #9 + sgCDK19 #3-17 - DMSO-2

description: Library name: AID-CDK8_9+sgCDK19_3-17_DMSO-2


title: PTB222_batch_3_ROI_3_anno_Core

description:
Library name: PTB222_batch_3_ROI_3
Core | PTB 22.2 | 03

value: Core


title: Whole blood DNA methylation, HISPANIC CONTROL, 91yo M, 207097420191_R06C01


title: PTB222_batch_3_ROI_2_anno_Alveoli

description:
Library name: PTB222_batch_3_ROI_2
Alveoli | PTB 22.2 | 02


title: AID-CDK8 #9 + sgCDK19 #3-17 - DMSO-1

description: Library name: AID-CDK8_9+sgCDK19_3-17_DMSO-1


title: Whole blood DNA methylation, HISPANIC CONTROL, 82yo F, 207097420080_R05C01


title: AID-CDK8 #6 + sgCDK19 #3-28 - Combo-1

description: Library name: AID-CDK8_6+sgCDK19_3-28_Combo-1


title: PTB222_batch_3_ROI_1_anno_Alveoli

description:
Library name: PTB222_batch_3_ROI_1
Alveoli | PTB 22.2 | 01


title: AID-CDK8 #6 + sgCDK19 #3-28 - 5-ph-IAA-2

description: Library name: AID-CDK8_6+sgCDK19_3-28_5-ph-IAA-2


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097420015_R01C01


title: AID-CDK8 #6 + sgCDK19 #3-28 - 5-ph-IAA-1

description: Library name: AID-CDK8_6+sgCDK19_3-28_5-ph-IAA-1


title: NTC_batch_3_ROI_NA_anno_NA

description:
Library name: NTC_batch_3_ROI_NA
None

source_name: Control

value: Control


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207097420015_R05C01


title: AID-CDK8 #6 + sgCDK19 #3-28 - SW393109-2

description: Library name: AID-CDK8_6+sgCDK19_3-28_SW393109-2


title: AID-CDK8 #6 + sgCDK19 #3-28 - SW393109-1

description: Library name: AID-CDK8_6+sgCDK19_3-28_SW393109-1


title: TBL7_batch_2_ROI_12_anno_Other

description:
Library name: TBL7_batch_2_ROI_12
None

value: Lymph


title: Whole blood DNA methylation, HISPANIC CONTROL, 79yo F, 207219770097_R06C01


title: AID-CDK8 #6 + sgCDK19 #3-28 - DMSO-2

description: Library name: AID-CDK8_6+sgCDK19_3-28_DMSO-2


title: AID-CDK8 #6 + sgCDK19 #3-28 - DMSO-1

description: Library name: AID-CDK8_6+sgCDK19_3-28_DMSO-1


title: TBL7_batch_2_ROI_11_anno_Other

description:
Library name: TBL7_batch_2_ROI_11
None


title: ML6_25uM_4h_3_NormalDepth

description: Library name: THP1_ML6_3_NormalDepth

extract_protocol:
E.Z.N.A.® Total RNA Kit I (Catalog# R6834-01, Omega), with 100% ethanol instead of 70% at the binding step to enrich small RNA.
Libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) and sequenced on two 10B lanes for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

value: cell line


title: Whole blood DNA methylation, HISPANIC CONTROL, 63yo F, 207080910061_R04C01

value: Female


title: ML6_25uM_4h_2_NormalDepth

description: Library name: THP1_ML6_2_NormalDepth


title: DMSO_3_NormalDepth

description: Library name: THP1_DMSO_3_NormalDepth


title: TBL7_batch_2_ROI_9_anno_Other

description:
Library name: TBL7_batch_2_ROI_9
None

value: Other


title: Whole blood DNA methylation, HISPANIC AD, 74yo F, 207097420082_R06C01


title: Whole blood DNA methylation, HISPANIC AD, 83yo F, 207097420047_R02C01


title: DMSO_2_NormalDepth

description: Library name: THP1_DMSO_2_NormalDepth


title: DMSO_1_NormalDepth

description: Library name: THP1_DMSO_1_NormalDepth


title: CHX_10ug_per_ml_4.5h_ML625uM_4h_3_NormalDepth

description: Library name: THP1_CHX_ML6_3_NormalDepth


title: CHX_10ug_per_ml_4.5h_ML625uM_4h_1_NormalDepth

description: Library name: THP1_CHX_ML6_1_NormalDepth


title: Whole blood DNA methylation, HISPANIC AD, 84yo M, 207097320046_R04C01

value: Male

value: PRADI


title: CHX_10ug_per_ml_4.5h_3_NormalDepth

description: Library name: THP1_CHX_3_NormalDepth


title: TBL7_batch_2_ROI_6_anno_Other

description:
Library name: TBL7_batch_2_ROI_6
None


title: CHX_10ug_per_ml_4.5h_ML625uM_4h_2_NormalDepth

description: Library name: THP1_CHX_ML6_2_NormalDepth


title: TBL7_batch_2_ROI_7_anno_Other

description:
Library name: TBL7_batch_2_ROI_7
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 80yo M, 207097320052_R08C01

value: whole blood

value: HISPANIC


title: CHX_10ug_per_ml_4.5h_1_NormalDepth

description: Library name: THP1_CHX_1_NormalDepth


title: MAF1_OE_48h_3_NormalDepth

description: Library name: MAF1_OE_3_NormalDepth


title: Whole blood DNA methylation, HISPANIC AD, 88yo M, 207080910133_R05C01


title: MAF1_OE_48h_2_NormalDepth

description: Library name: MAF1_OE_2_NormalDepth


title: TBL7_batch_2_ROI_4_anno_Other

description:
Library name: TBL7_batch_2_ROI_4
None


title: control_eGFP_OE_48h_3_NormalDepth

description: Library name: eGFP_OE_3_NormalDepth


title: control_eGFP_OE_48h_2_NormalDepth

description: Library name: eGFP_OE_2_NormalDepth


title: TBL7_batch_2_ROI_3_anno_Other

description:
Library name: TBL7_batch_2_ROI_3
None


title: control_eGFP_OE_48h_1_NormalDepth

description: Library name: eGFP_OE_1_NormalDepth


title: Whole blood DNA methylation, HISPANIC AD, 89yo M, 207097420112_R05C01


title: Whole blood DNA methylation, HISPANIC AD, 73yo F, 207097320046_R01C01


title: Scramble_ASO_200nM_48h_3_NormalDepth

description: Library name: ASOPOLR3G_control_3_NormalDepth


title: DLD1 CRISPRi sublib2, SAM24482912_1, MOI High (~10), GEX

description:
Library name: LIB6266270_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.

value: colorectal adenocarcinoma

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 6455-guide sub-library 2; MOI High (~10); 5% NTC spike-in; MULTI-seq CMO hashing


title: TBL42_batch_2_ROI_12_anno_Other

description:
Library name: TBL42_batch_2_ROI_12
None


title: Whole blood DNA methylation, HISPANIC AD, 54yo F, 207219770097_R04C01

value: CuADI


title: AID-CDK8 #6 + sgCDK19 #3-28 - Combo-2

description: Library name: AID-CDK8_6+sgCDK19_3-28_Combo-2


title: TBL42_batch_2_ROI_11_anno_Other

description:
Library name: TBL42_batch_2_ROI_11
None


title: siPOLR3GL_siE8_25nM_48_h_1_NormalDepth

description: Library name: siPOLR3GL_siE8_1_NormalDepth

value: siPOLR3GL_siE8_25nM 48 h_1


title: Whole blood DNA methylation, HISPANIC AD, 89yo M, 207097420153_R06C01


title: TBL42_batch_2_ROI_10_anno_Other

description:
Library name: TBL42_batch_2_ROI_10
None


title: TBL7_batch_2_ROI_10_anno_Other

description:
Library name: TBL7_batch_2_ROI_10
None


title: TBL7_batch_2_ROI_8_anno_Other

description:
Library name: TBL7_batch_2_ROI_8
None


title: ML6_25uM_4h_1_NormalDepth

description: Library name: THP1_ML6_1_NormalDepth


title: siPOLR3GL_siE6_25nM_48_h_2_NormalDepth

description: Library name: siPOLR3GL_siE6_2_NormalDepth

value: siPOLR3GL_siE6_25nM 48 h_2


title: Whole blood DNA methylation, HISPANIC AD, 79yo F, 207080910133_R02C01


title: Whole blood DNA methylation, HISPANIC AD, 85yo F, 207097420192_R04C01


title: CHX_10ug_per_ml_4.5h_2_NormalDepth

description: Library name: THP1_CHX_2_NormalDepth


title: TBL42_batch_2_ROI_9_anno_Other

description:
Library name: TBL42_batch_2_ROI_9
None


title: TBL7_batch_2_ROI_5_anno_Other

description:
Library name: TBL7_batch_2_ROI_5
None


title: siPOLR3GL_siE6_25nM_48_h_1_NormalDepth

description: Library name: siPOLR3GL_siE6_1_NormalDepth

value: siPOLR3GL_siE6_25nM 48 h_1


title: siPOLR3GL_siE4_25nM_48_h_3_NormalDepth

description: Library name: siPOLR3GL_siE4_3_NormalDepth

value: siPOLR3GL_siE4_25nM 48 h_3


title: Whole blood DNA methylation, HISPANIC AD, 77yo F, 207080920105_R02C01

value: Alzheimer's disease


title: MAF1_OE_48h_1_NormalDepth

description: Library name: MAF1_OE_1_NormalDepth


title: siPOLR3GL_siE4_25nM_48_h_2_NormalDepth

description: Library name: siPOLR3GL_siE4_2_NormalDepth

value: siPOLR3GL_siE4_25nM 48 h_2


title: Whole blood DNA methylation, HISPANIC AD, 81yo F, 207097420010_R02C01


title: TBL42_batch_2_ROI_8_anno_Other

description:
Library name: TBL42_batch_2_ROI_8
None

value: Lymph


title: siPOLR3GL_siE4_25nM_48_h_1_NormalDepth

description: Library name: siPOLR3GL_siE4_1_NormalDepth

value: cell line

value: siPOLR3GL_siE4_25nM 48 h_1


title: Whole blood DNA methylation, HISPANIC AD, 67yo M, 207080910004_R07C01

value: PERUVIAN


title: control_siRNA_25nM_48_h_3_NormalDepth

description: Library name: siPOLR3GL_control_3_NormalDepth

value: control siRNA 25nM 48 h_3


title: TBL42_batch_2_ROI_7_anno_Other

description:
Library name: TBL42_batch_2_ROI_7
None

value: Other


title: TBL7_batch_2_ROI_2_anno_Other

description:
Library name: TBL7_batch_2_ROI_2
None


title: control_siRNA_25nM_48_h_2_NormalDepth

description: Library name: siPOLR3GL_control_2_NormalDepth

value: control siRNA 25nM 48 h_2


title: Whole blood DNA methylation, HISPANIC AD, 81yo F, 207097420114_R02C01

value: Female

value: whole blood

value: HISPANIC


title: POLR3G_siRNA_200nM_48_h_3_NormalDepth

description: Library name: siPOLR3G_si3G_3_NormalDepth


title: TBL42_batch_2_ROI_6_anno_Other

description:
Library name: TBL42_batch_2_ROI_6
None


title: control_siRNA_25nM_48_h_1_NormalDepth

description: Library name: siPOLR3GL_control_1_NormalDepth

value: control siRNA 25nM 48 h_1


title: POLR3G_ASO_200nM_48h_3_NormalDepth

description: Library name: ASOPOLR3G_ASO3G_3_NormalDepth

value: POLR3G_ASO_200nM_ 48h_3


title: TBL7_batch_2_ROI_1_anno_Other

description:
Library name: TBL7_batch_2_ROI_1
None


title: POLR3G_ASO_200nM_48h_2_NormalDepth

description: Library name: ASOPOLR3G_ASO3G_2_NormalDepth

value: POLR3G_ASO_200nM_ 48h_2


title: POLR3G_ASO_200nM_48h_1_NormalDepth

description: Library name: ASOPOLR3G_ASO3G_1_NormalDepth

value: POLR3G_ASO_200nM_ 48h_1


title: POLR3G_siRNA_200nM_48_h_2_NormalDepth

description: Library name: siPOLR3G_si3G_2_NormalDepth


title: Whole blood DNA methylation, HISPANIC AD, 78yo M, 207097420065_R02C01

value: Male


title: TBL42_batch_2_ROI_5_anno_Other

description:
Library name: TBL42_batch_2_ROI_5
None


title: POLR3G_siRNA_200nM_48_h_1_NormalDepth

description: Library name: siPOLR3G_si3G_1_NormalDepth


title: Whole blood DNA methylation, HISPANIC AD, 81yo F, 207097420011_R05C01

value: Alzheimer's disease


title: control_siRNA_200nM_48_h_3_NormalDepth

description: Library name: siPOLR3G_control_3_NormalDepth


title: TBL42_batch_2_ROI_4_anno_Other

description:
Library name: TBL42_batch_2_ROI_4
None


title: control_siRNA_200nM_48_h_2_NormalDepth

description: Library name: siPOLR3G_control_2_NormalDepth


title: siPOLR3GL_siE8_25nM_48_h_3_NormalDepth

description: Library name: siPOLR3GL_siE8_3_NormalDepth

value: siPOLR3GL_siE8_25nM 48 h_3


title: Whole blood DNA methylation, HISPANIC AD, 74yo M, 207219770097_R03C01

value: PRADI


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207080910004_R04C01


title: TBL42_batch_2_ROI_3_anno_Other

description:
Library name: TBL42_batch_2_ROI_3
None

value: Lymph


title: control_siRNA_200nM_48_h_1_NormalDepth

description: Library name: siPOLR3G_control_1_NormalDepth

value: cell line


title: Scramble_ASO_200nM_48h_1_NormalDepth

description: Library name: ASOPOLR3G_control_1_NormalDepth

value: Scramble_ASO_200nM_ 48h_1


title: Scramble_ASO_200nM_48h_2_NormalDepth

description: Library name: ASOPOLR3G_control_2_NormalDepth

value: Scramble_ASO_200nM_ 48h_2


title: Whole blood DNA methylation, HISPANIC AD, 62yo F, 207097420082_R04C01

value: PERUVIAN


title: TBL42_batch_2_ROI_2_anno_Other

description:
Library name: TBL42_batch_2_ROI_2
None

value: Other


title: H293T_ML6_2_fastgro

description: Library name: H293T_ML6_2_fastgro

data_processing:
Reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: Bigwig

molecule: nuclear RNA

growth_protocol: THP−1 cells were propagated in T-75 flasks between 0.2 and 1 × 106 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP−1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
FastGro sequencing experiment are performed following https://doi.org/10.17504/protocols.io.bbmgik3w
The small RNA were treated with Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).The libraries were sequenced on one 10B lane for 101 cycles from one end of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

treatment_protocol: 10 million THP1 nuclei are used per experiment; freshly isolated nuclei are pretreated with 50nM final concentration ML-60218 (Catalog# 557403-10MG, SigmaAldrich) or DMSO for 10 min and in vitro run-on is carried out with 25nM ML-60218 or DMSO.


title: Whole blood DNA methylation, HISPANIC AD, 62yo F, 207097320052_R04C01

value: Female


title: siPOLR3GL_siE8_25nM_48_h_2_NormalDepth

description: Library name: siPOLR3GL_siE8_2_NormalDepth

value: siPOLR3GL_siE8_25nM 48 h_2


title: H293T_ML6_1_fastgro

description: Library name: H293T_ML6_1_fastgro


title: H293T_DMSO_2_fastgro

description: Library name: H293T_DMSO_2_fastgro

value: DMSO


title: TBL42_batch_2_ROI_1_anno_Other

description:
Library name: TBL42_batch_2_ROI_1
None


title: Whole blood DNA methylation, HISPANIC AD, 65yo F, 207097420152_R02C01

value: whole blood

value: HISPANIC


title: H293T_DMSO_1_fastgro

description: Library name: H293T_DMSO_1_fastgro


title: TBL16_batch_2_ROI_12_anno_Other

description:
Library name: TBL16_batch_2_ROI_12
None


title: G9_ML6_3_fastgro

description: Library name: G9_ML6_3_fastgro


title: G9_ML6_2_fastgro

description: Library name: G9_ML6_2_fastgro


title: TBL16_batch_2_ROI_11_anno_Other

description:
Library name: TBL16_batch_2_ROI_11
None


title: Whole blood DNA methylation, HISPANIC AD, 53yo F, 207097420047_R04C01


title: G9_ML6_1_fastgro

description: Library name: G9_ML6_1_fastgro


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207080910085_R06C01

value: CuADI


title: TBL16_batch_2_ROI_10_anno_Other

description:
Library name: TBL16_batch_2_ROI_10
None


title: siPOLR3GL_siE6_25nM_48_h_3_NormalDepth

description: Library name: siPOLR3GL_siE6_3_NormalDepth

value: siPOLR3GL_siE6_25nM 48 h_3


title: Whole blood DNA methylation, HISPANIC AD, 74yo F, 207097320046_R06C01


title: G9_DMSO_3_fastgro

description: Library name: G9_DMSO_3_fastgro


title: G9_DMSO_1_fastgro

description: Library name: G9_DMSO_1_fastgro


title: TBL16_batch_2_ROI_9_anno_Other

description:
Library name: TBL16_batch_2_ROI_9
None


title: G8_ML6_3_fastgro

description: Library name: G8_ML6_3_fastgro


title: G8_ML6_2_fastgro

description: Library name: G8_ML6_2_fastgro


title: Whole blood DNA methylation, HISPANIC AD, 80yo M, 207080910104_R04C01

value: Male


title: TBL16_batch_2_ROI_8_anno_Other

description:
Library name: TBL16_batch_2_ROI_8
None


title: G8_ML6_1_fastgro

description: Library name: G8_ML6_1_fastgro


title: TBL16_batch_2_ROI_7_anno_Other

description:
Library name: TBL16_batch_2_ROI_7
None


title: Whole blood DNA methylation, HISPANIC AD, 68yo F, 207097420080_R03C01

value: Alzheimer's disease


title: G8_DMSO_3_fastgro

description: Library name: G8_DMSO_3_fastgro


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207097420079_R01C01

value: Healthy control


title: G8_DMSO_2_fastgro

description: Library name: G8_DMSO_2_fastgro


title: G8_DMSO_1_fastgro

description: Library name: G8_DMSO_1_fastgro


title: TBL16_batch_2_ROI_5_anno_Other

description:
Library name: TBL16_batch_2_ROI_5
None


title: TBL16_batch_2_ROI_4_anno_Other

description:
Library name: TBL16_batch_2_ROI_4
None


title: A7_DMSO_3_fastgro

description: Library name: A7_DMSO_3_fastgro


title: Whole blood DNA methylation, HISPANIC CONTROL, 85yo M, 207097320046_R03C01


title: Whole blood DNA methylation, HISPANIC AD, 68yo F, 207097320052_R01C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207097420114_R08C01


title: d6_142_mix_G_2

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: d6_142_mix_G_2

data_processing:
FASTQ files were preprocessed using the nf-core RNA-seq pipeline (v3.14.0) with default parameters, except for UMI extraction, which was done using the following options: --with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*".
Briefly, paired-end reads were aligned to the human genome (Ensembl release 110) using STAR, and transcript quantification was performed with Salmon.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

source_name: skin

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, and penicillin/streptomycin supplemented with the JAK inhibitor ruxolitinib (10 μM).

extract_protocol:
5000-10000 cells were sorted into RLT lysis buffer. RNA was exracted with the miRNeasy Tissue/Cells Advanced Kit according to manufacturer's protocol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit by Takara.

treatment_protocol: HDFs were trasduced on day -1 and/or transfected with PIB-encoding mRNAs and miRNA mimics on day 0 of reprogramming. Cells were sorted on day 3 or 6 by FACS.

value: skin

value: human dermal fibroblast

value: WT

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on days 0 and 3 of reprogramming.

tag: time

value: Cells were collected on day 6 of reprogramming.

tag: sorted cells

value: live (DAPI-) and CD45+


title: A7_DMSO_1_fastgro

description: Library name: A7_DMSO_1_fastgro


title: TBL16_batch_2_ROI_3_anno_Other

description:
Library name: TBL16_batch_2_ROI_3
None

value: Lymph

value: Other


title: Whole blood DNA methylation, HISPANIC CONTROL, 69yo M, 207097420040_R04C01


title: A7_DMSO_2_fastgro

description: Library name: A7_DMSO_2_fastgro


title: A7_ML6_3_fastgro

description: Library name: A7_ML6_3_fastgro


title: d6_142_mix_SC_2

description: Library name: d6_142_mix_SC_2


title: Whole blood DNA methylation, HISPANIC AD, 79yo F, 207097420049_R02C01

value: Female

value: PERUVIAN


title: TBL16_batch_2_ROI_2_anno_Other

description:
Library name: TBL16_batch_2_ROI_2
None


title: DLD1 CRISPRi sublib2, SAM24482912_4, MOI High (~10), GEX

description:
Library name: LIB6266273_SAM24482912
10x Chromium Single Cell 3' v4 GEX library. MOI High (~10) condition multiplexed via MULTI-seq CMO hashing.

value: colorectal adenocarcinoma

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 6455-guide sub-library 2; MOI High (~10); 5% NTC spike-in; MULTI-seq CMO hashing


title: d6_124_3p_L_2

description: Library name: d6_124_3p_L_2

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-124-3p mimic on days 0 and 3 of reprogramming.


title: d6_SCR_L_2

description: Library name: d6_SCR_L_2

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and a scrambled miRNA mimic on days 0 and 3 of reprogramming.


title: Whole blood DNA methylation, HISPANIC AD, 70yo M, 207097320053_R06C01

value: Male

value: whole blood

value: HISPANIC


title: d6_SCR_G_2

description: Library name: d6_SCR_G_2

value: skin


title: PTB211_batch_1_ROI_12_anno_Alveoli

description:
Library name: PTB211_batch_1_ROI_12
Alveoli | PTB 21.1 | 12

value: Lung

value: Alveoli


title: d6_PIB_AG_SCR_L_2

description: Library name: d6_PIB_AG_SCR_L_2

value: human dermal fibroblast

value: WT

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and transfected with a scrambled miRNA mimic on days 0 and 3 of reprogramming.


title: PTB211_batch_1_ROI_11_anno_Alveoli

description:
Library name: PTB211_batch_1_ROI_11
Alveoli | PTB 21.1 | 11


title: d6_PIB_AG_SCR_G_2

description: Library name: d6_PIB_AG_SCR_G_2

value: Cells were collected on day 6 of reprogramming.

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207097420061_R05C01

value: Female

value: Healthy control


title: d3_GFP_L_2

description: Library name: d3_GFP_L_2

value: Cells were transfected with mRNAs coding for GFP and a scrambled miRNA mimic on day 0 of reprogramming.

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and GFP+


title: Whole blood DNA methylation, HISPANIC AD, 60yo M, 207080910117_R04C01

value: Alzheimer's disease

value: PERUVIAN


title: d3_GFP_G_2

description: Library name: d3_GFP_G_2


title: PTB211_batch_1_ROI_9_anno_Alveoli

description:
Library name: PTB211_batch_1_ROI_9
Alveoli | PTB 21.1 | 09


title: Whole blood DNA methylation, HISPANIC AD, 81yo F, 207097420191_R08C01

value: whole blood


title: G9_DMSO_2_fastgro

description: Library name: G9_DMSO_2_fastgro

value: DMSO


title: d3_142_mix_SC_2

description: Library name: d3_142_mix_SC_2

value: skin

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on day 0 of reprogramming.


title: Whole blood DNA methylation, HISPANIC CONTROL, 84yo M, 207080920090_R01C01

value: Male

value: HISPANIC


title: d3_124_3p_L_2

description: Library name: d3_124_3p_L_2

value: human dermal fibroblast

value: WT

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-124-3p mimic on day 0 of reprogramming.


title: PTB211_batch_1_ROI_7_anno_Other

description:
Library name: PTB211_batch_1_ROI_7
Other | PTB 21.1 | 07

value: Lung

value: Other


title: PTB211_batch_1_ROI_6_anno_Mantle

description:
Library name: PTB211_batch_1_ROI_6
Mantle | PTB 21.1 | 06

value: Mantle


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo M, 207097420114_R06C01

value: Healthy control


title: d3_124_3p_SC_2

description: Library name: d3_124_3p_SC_2

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo M, 207080910061_R06C01


title: PTB211_batch_1_ROI_8_anno_Core

description:
Library name: PTB211_batch_1_ROI_8
Core | PTB 21.1 | 08

value: Core


title: d3_124_3p_G_2

description: Library name: d3_124_3p_G_2


title: d3_GFP_SC_2

description: Library name: d3_GFP_SC_2

value: Cells were transfected with mRNAs coding for GFP and a scrambled miRNA mimic on day 0 of reprogramming.

value: live (DAPI-) and GFP+


title: d3_SCR_G_2

description: Library name: d3_SCR_G_2

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and a scrambled miRNA mimic on day 0 of reprogramming.


title: PTB211_batch_1_ROI_5_anno_Alveoli

description:
Library name: PTB211_batch_1_ROI_5
Alveoli | PTB 21.1 | 05

value: Alveoli


title: d3_142_mix_G_2

description: Library name: d3_142_mix_G_2

value: skin

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on day 0 of reprogramming.


title: Whole blood DNA methylation, HISPANIC CONTROL, 67yo F, 207080910133_R08C01

value: Female

value: whole blood

value: HISPANIC

value: PERUVIAN


title: d3_SCR_SC_2

description: Library name: d3_SCR_SC_2

value: human dermal fibroblast

value: WT


title: d3_PIB_AG_SCR_L_2

description: Library name: d3_PIB_AG_SCR_L_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) on day -1 of reprogramming and transfected with a scrambled miRNA mimic on day 0.


title: PTB211_batch_1_ROI_4_anno_Core

description:
Library name: PTB211_batch_1_ROI_4
Core | PTB 21.1 | 04

value: Lung


title: d3_PIB_AG_SCR_SC_2

description: Library name: d3_PIB_AG_SCR_SC_2

value: Cells were collected on day 3 of reprogramming.


title: d3_PIB_AG_SCR_G_2

description: Library name: d3_PIB_AG_SCR_G_2

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC CONTROL, 77yo M, 207097320021_R03C01

value: Male

value: Healthy control


title: PTB211_batch_1_ROI_3_anno_Core

description:
Library name: PTB211_batch_1_ROI_3
Core | PTB 21.1 | 03

value: Core


title: d6_142_mix_L_1

description: Library name: d6_142_mix_L_1

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on days 0 and 3 of reprogramming.

value: Cells were collected on day 6 of reprogramming.


title: d6_142_mix_G_1

description: Library name: d6_142_mix_G_1

value: skin


title: d6_142_mix_SC_1

description: Library name: d6_142_mix_SC_1


title: PTB211_batch_1_ROI_2_anno_Mantle

description:
Library name: PTB211_batch_1_ROI_2
Mantle | PTB 21.1 | 02

value: Mantle


title: Whole blood DNA methylation, HISPANIC CONTROL, 86yo M, 207097420048_R01C01


title: d6_124_3p_L_1

description: Library name: d6_124_3p_L_1

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-124-3p mimic on days 0 and 3 of reprogramming.


title: d6_124_3p_G_1

description: Library name: d6_124_3p_G_1


title: Whole blood DNA methylation, HISPANIC CONTROL, 72yo F, 207097420152_R05C01

value: Female

value: whole blood


title: NTC_batch_1_ROI_NA_anno_NA

description:
Library name: NTC_batch_1_ROI_NA
None

value: Control


title: d6_SCR_L_1

description: Library name: d6_SCR_L_1

value: human dermal fibroblast

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and a scrambled miRNA mimic on days 0 and 3 of reprogramming.


title: Whole blood DNA methylation, HISPANIC CONTROL, 78yo M, 207097420032_R06C01

value: HISPANIC

value: PERUVIAN


title: d6_SCR_G_1

description: Library name: d6_SCR_G_1

value: WT


title: d6_SCR_SC_1

description: Library name: d6_SCR_SC_1

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC CONTROL, 78yo M, 207097420040_R08C01

value: Male


title: d6_PIB_AG_SCR_L_1

description: Library name: d6_PIB_AG_SCR_L_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and transfected with a scrambled miRNA mimic on days 0 and 3 of reprogramming.


title: HTO_Pool1

city: Oxford

first: Ling-Pei

last: Ho

address: Headley Way

department: MRC Human Immunology Unit

country: United Kingdom

institute: University of Oxford

description:
Library name: Pool1 Hashtag
Pool 1: with samples T1_run1 (Blood),T2_run1 (BAL) T3_run1 (Blood), T4_run1 (BAL).

library_source: other

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format
Fastq files were processed using 10x Genomics Cellranger software
Assembly: hg38
Supplementary files format and content: compressed raw UMI counts matrices for mRNA and HTO.
Library strategy: CITE-seq

molecule: protein

source_name: BAL and blood

extract_protocol:
BAL samples were centrifuged to obstain cell pellet, underwent RBC lysis, centrifuged and resuspended in RPMI 1640 media supplemented with 10% fetal bovine serum (FBS). Peripheral blood mononuclear cells (PBMCs) were seperated  from whole blood samples by density grandient seperation, centrifuged and resuspended in RPMI 1640 and supplemented with FBS 10%. BAL and PBMCs from HC and IPF samples were filtered through a 70um filter and stained with TotalSeq™-A anti-human Hashtag antibodies numbers 1-8 (BioLegendTM London, UK) according to manufacturer’s instructions. Cells were washed and counted before loading on to the 10X platform for single-cell RNA sequencing.
Samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX) and  Hashtag oligo (HTO(  library amplification and indexing.

value: BAL and blood

value: Immune

tag: sample

value: T1_run1 (IPF,M),T2_run1 (IPF,M) T3_run1 (IPF,M), T4_run1 (IPF,M).

tag: chemistry

value: 3' Chemistry

tag: library type

value: HTO

tag: hto


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097420065_R06C01

value: Healthy control


title: d6_PIB_AG_SCR_G_1

description: Library name: d6_PIB_AG_SCR_G_1

value: skin

tag: cell type

value: Cells were collected on day 6 of reprogramming.


title: d6_PIB_AG_SCR_SC_1

description: Library name: d6_PIB_AG_SCR_SC_1

tag: genotype


title: GEX_Pool2

description:
Library name: Pool2
Pool 2: with samples T1 (Blood),T2 (Blood) T3 (Blood), T4 (Blood),T5 (BAL), T6 (BAL), T7 (BAL), T8 (BAL).

value: mRNA


title: d3_GFP_L_1

description: Library name: d3_GFP_L_1

value: human dermal fibroblast

tag: treatment

value: Cells were transfected with mRNAs coding for GFP and a scrambled miRNA mimic on day 0 of reprogramming.

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and GFP+


title: A7_ML6_2_fastgro

description: Library name: A7_ML6_2_fastgro

tag: cell line


title: TBL16_batch_2_ROI_6_anno_Other

description:
Library name: TBL16_batch_2_ROI_6
None

tag: tissue

value: Lymph

tag: region

value: Other


title: Whole blood DNA methylation, HISPANIC CONTROL, 80yo F, 207097420192_R08C01

tag: Sex

value: Female

value: whole blood

value: HISPANIC

value: PERUVIAN


title: PTB211_batch_1_ROI_1_anno_Mantle

description:
Library name: PTB211_batch_1_ROI_1
Mantle | PTB 21.1 | 01

value: Lung

value: Mantle

tag: batch


title: A7_ML6_1_fastgro

description: Library name: A7_ML6_1_fastgro


title: d3_GFP_G_1

description: Library name: d3_GFP_G_1

value: WT


title: GEX_Pool1

description:
Library name: Pool1
Pool 1: with samples T1_run1 (Blood),T2_run1 (BAL) T3_run1 (Blood), T4_run1 (BAL).

value: BAL and blood

value: Immune

value: T1_run1 (IPF,M),T2_run1 (IPF,M) T3_run1 (IPF,M), T4_run1 (IPF,M).

value: 3' Chemistry


title: d6_124_3p_SC_1

description: Library name: d6_124_3p_SC_1

value: skin

value: human dermal fibroblast

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-124-3p mimic on days 0 and 3 of reprogramming.

value: Cells were collected on day 6 of reprogramming.

value: live (DAPI-) and CD45+


title: d3_GFP_SC_1

description: Library name: d3_GFP_SC_1

value: Cells were transfected with mRNAs coding for GFP and a scrambled miRNA mimic on day 0 of reprogramming.

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and GFP+


title: Whole blood DNA methylation, HISPANIC AD, 85yo F, 207097420152_R04C01

value: Female

tag: disease state

value: Alzheimer's disease

value: whole blood

tag: ethnicity

value: HISPANIC

value: CuADI


title: d6_142_mix_L_2

description: Library name: d6_142_mix_L_2

value: WT

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on days 0 and 3 of reprogramming.


title: d3_142_mix_L_1

description: Library name: d3_142_mix_L_1

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on day 0 of reprogramming.


title: HSkM, mechanical stretch, rep 6

city: Jyväskylä

first: Riikka

last: Kivelä

address: Rautpohjankatu 8

country: Finland

institute: University of Jyväskylä

description:
Library name: HSkM_12
Column name in counts_all.tsv: HSkM_12

data_processing:
Sequence reads were trimmed at Novogene by removing adapter reads, removing reads containing >10% of unsolvable bases and removing reads containing >50% of low quality bases (Qphred ≤ 5)
Read alignment was done with Bowtie2 software with human GRCh38.95 genome build as reference
Aligned reads were quantified with featureCounts in Rsubread
Quantified reads normalized with CPM with edgeR and lowly expressed genes were filtered
Differential gene expression analysis was done with R/Bioconductor limma-voom pipeline
Assembly: GRCh38.95
Supplementary files format and content: Tab-delimited text file contains raw counts for all cell lines (12 samples per cell line). File named "counts_all.tsv"

source_name: HSkM

extract_protocol:
RNA was collected with a column-based RNA isolation kit (NucleoSpin RNA, Macherey-Nagel).
Library construction, quality control and sequencing was carried out at Novogene (Cambridge, United Kingdom)

treatment_protocol: 5h cyclic uniaxial mechanical loading (1Hz, 12% elongation) with C-stretch device (IonOptix).

value: HSkM

value: mechanical loading


title: d3_142_mix_G_1

description: Library name: d3_142_mix_G_1

value: skin

value: human dermal fibroblast


title: Whole blood DNA methylation, HISPANIC CONTROL, 76yo F, 207080920105_R06C01

value: Healthy control

tag: cohort

tag: age


title: Whole blood DNA methylation, HISPANIC CONTROL, 79yo M, 207097420049_R05C01

value: Male

value: PERUVIAN


title: HSkM, mechanical stretch, rep 5

description:
Library name: HSkM_11
Column name in counts_all.tsv: HSkM_11


title: d3_124_3p_L_1

description: Library name: d3_124_3p_L_1

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-124-3p mimic on day 0 of reprogramming.

tag: time

value: Cells were collected on day 3 of reprogramming.

tag: sorted cells

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC CONTROL, 69yo F, 207097420047_R03C01

value: Female


title: Whole blood DNA methylation, AA AD, 81yo F, 207215830114_R06C01

value: Alzheimer's disease

value: whole blood

value: AA

value: REAAADI


title: 22Rv1, Lactate, Rep4

city: Florence

first: Paola

last: Chiarugi

state: Florence

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: Library name: 146763_ID3399_14-4B

data_processing:
Sequence reads were trimmed for adaptor/low quality sequence using fastp
Trimmed sequence reads were mapped to GRCh38 using STAR
Read count extraction was performed using HTSeq count
Differential Expression analysis was performed by DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw count for each sample

growth_protocol: 22Rv1 cells were manteined in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using RNeasy Kit (#74104; Qiagen) and RNA-seq was performed starting from 800 ng of RNA from each sample.
Universal Plus mRNA-Seq kit

treatment_protocol: 22Rv1 cells were treated with Lactate 20 mM and/or OICR-9429 10 μM; RNA was extracted 48h after treatments

value: Epithelial cell line

value: WT

value: Lactate


title: d6_124_3p_G_2

description: Library name: d6_124_3p_G_2

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-124-3p mimic on days 0 and 3 of reprogramming.

value: Cells were collected on day 6 of reprogramming.


title: Whole blood DNA methylation, NHW CONTROL, 80yo M, 207215820044_R07C01

value: NHW


title: Whole blood DNA methylation, HISPANIC AD, 68yo M, 207097420061_R08C01

value: HISPANIC


title: TBL16_batch_2_ROI_1_anno_Other

description:
Library name: TBL16_batch_2_ROI_1
None

value: Lymph

value: Other


title: NTC_batch_2_ROI_NA_anno_NA

description:
Library name: NTC_batch_2_ROI_NA
None

value: Control


title: d6_SCR_SC_2

description: Library name: d6_SCR_SC_2

value: skin

value: human dermal fibroblast

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and a scrambled miRNA mimic on days 0 and 3 of reprogramming.


title: d3_124_3p_G_1

description: Library name: d3_124_3p_G_1

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-124-3p mimic on day 0 of reprogramming.

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC AD, 75yo F, 207097320021_R01C01

value: Female

value: Alzheimer's disease

value: whole blood

value: PERUVIAN


title: HSkM, mechanical stretch, rep 4

description:
Library name: HSkM_10
Column name in counts_all.tsv: HSkM_10

value: HSkM

value: mechanical loading


title: d3_124_3p_SC_1

description: Library name: d3_124_3p_SC_1

value: WT


title: HTO_Pool2

description:
Library name: Pool2 Hashtag
Pool 2: with samples T1 (Blood),T2 (Blood) T3 (Blood), T4 (Blood),T5 (BAL), T6 (BAL), T7 (BAL), T8 (BAL).

value: BAL and blood

value: Immune

tag: sample

tag: chemistry

value: 3' Chemistry

value: HTO

value: TotalSeq™-A anti-human Hashtag antibodies numbers 1-8


title: Whole blood DNA methylation, HISPANIC AD, 73yo M, 207080910061_R01C01

value: Male

value: HISPANIC


title: d3_SCR_L_1

description: Library name: d3_SCR_L_1

value: skin

value: human dermal fibroblast

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and a scrambled miRNA mimic on day 0 of reprogramming.


title: HSkM, mechanical stretch, rep 3

description:
Library name: HSkM_9
Column name in counts_all.tsv: HSkM_9


title: d3_SCR_G_1

description: Library name: d3_SCR_G_1

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC CONTROL, 65yo M, 207097420048_R04C01

value: Healthy control

value: whole blood


title: d6_PIB_AG_SCR_SC_2

description: Library name: d6_PIB_AG_SCR_SC_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and transfected with a scrambled miRNA mimic on days 0 and 3 of reprogramming.

value: Cells were collected on day 6 of reprogramming.


title: d3_SCR_SC_1

description: Library name: d3_SCR_SC_1

value: WT


title: HSkM, mechanical stretch, rep 2

description:
Library name: HSkM_8
Column name in counts_all.tsv: HSkM_8

value: HSkM

value: mechanical loading


title: d3_PIB_AG_SCR_G_1

description: Library name: d3_PIB_AG_SCR_G_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) on day -1 of reprogramming and transfected with a scrambled miRNA mimic on day 0.


title: HSkM, static control, rep 6

description:
Library name: HSkM_6
Column name in counts_all.tsv: HSkM_6

value: static control


title: Whole blood DNA methylation, HISPANIC CONTROL, 67yo F, 207097420032_R07C01

value: Female

value: PERUVIAN


title: Whole blood DNA methylation, HISPANIC CONTROL, 65yo M, 207097320021_R07C01

value: Male

value: HISPANIC


title: d3_PIB_AG_SCR_L_1

description: Library name: d3_PIB_AG_SCR_L_1

value: skin

value: human dermal fibroblast


title: Whole blood DNA methylation, HISPANIC CONTROL, 66yo F, 207097420010_R03C01


title: M4-11 cells, DMSO, 6h, biol. replicate 2

city: Darmstadt

first: Alexander

last: Loewer

address: Schnittspahnstrasse 13

department: Biologie

country: Germany

institute: Technical University Darmstadt

description:
Library name: DMSO_2
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name

data_processing:
Raw FASTQ reads were quality-filtered using fastp v1.3.2 to remove adapters, low-quality bases (Phred ≤5 in >50% of read) and poly-N regions (>10% N bases), retaining reads with Q20 ≥95% and Q30 ≥90%. GC content was calculated for clean reads.
Paired-end clean reads were aligned to the genome reference using HISAT2 v2.2.1, guided by GTF annotation.
Gene counts were quantified using featureCounts v2.0.6.
Assembly: Human reference genome GRCh38
Supplementary files format and content: tab-delimited file containing read counts for each sample
Supplementary files format and content: tab-delimited file containing FKPM values for each sample

source_name: lymphoblast

growth_protocol: MV4-11 cells were maintained in RPMI-1640 medium with 10%FBS, 1% Pen/Strep and 1% Glutamax

extract_protocol:
RNA was isolated using the Monarch Total RNA Isolation Kit (NEB).  RNA quality was assessed using an Agilent TapeStation.
mRNA  was isolated with magnetic oligo d(T) beads, randomly fragmented, and transcribed to cDNA using random hexamers . CDNA was purified followed by end-repair, A-tailing and adapter ligation. Fragments of the appropriate size were enriched by PCR, where indexed P5 and P7 primers were introduced, and final products were purified.The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 5400 for size distribution.

treatment_protocol: Cells were treated with the indicated compounds for 6h.

value: lymphoblast

value: macrophage


title: M4-11 cells, DMSO, 6h, biol. replicate 3

description:
Library name: DMSO_3
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: HSkM, static control, rep 5

description:
Library name: HSkM_5
Column name in counts_all.tsv: HSkM_5


title: M4-11 cells, DMSO, 6h, biol. replicate 1

description:
Library name: DMSO_1
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: M4-11 cells, 1nM b3c-neg, 6h, biol. replicate 4

description:
Library name: SKD13_4
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: Whole blood DNA methylation, HISPANIC CONTROL, 74yo F, 207097420080_R07C01

value: Healthy control


title: M4-11 cells, 1nM b3c-neg, 6h, biol. replicate 3

description:
Library name: SKD13_3
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: M4-11 cells, 1nM b3c-neg, 6h, biol. replicate 2

description:
Library name: SKD13_2
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: Whole blood DNA methylation, HISPANIC AD, 75yo M, 207097420048_R03C01

value: Alzheimer's disease

value: whole blood


title: M4-11 cells, 1nM b3c-neg, 6h, biol. replicate 1

description:
Library name: SKD13_1
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: M4-11 cells, 500nM JQ1, 6h, biol. replicate 3

description:
Library name: JQ1_3
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: Whole blood DNA methylation, HISPANIC CONTROL, 72yo F, 207097420082_R08C01


title: M4-11 cells, 1nM b3c, 6h, biol. replicate 3

description:
Library name: b3c_3
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: HSkM, static control, rep 1

description:
Library name: HSkM_1
Column name in counts_all.tsv: HSkM_1


title: Whole blood DNA methylation, HISPANIC CONTROL, 69yo F, 207080910117_R02C01


title: M4-11 cells, 1nM b3c, 6h, biol. replicate 2

description:
Library name: b3c_2
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: M4-11 cells, 1nM b3c, 6h, biol. replicate 1

description:
Library name: b3c_1
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: Whole blood DNA methylation, AA CONTROL, 79yo M, 207215820062_R05C01

value: AA

value: REAAADI


title: HCMEC, mechanical stretch, rep 6

description:
Library name: HCMEC_12
Column name in counts_all.tsv: HCMEC_12

source_name: HCMEC

value: HCMEC


title: HSkM, static control, rep 2

description:
Library name: HSkM_2
Column name in counts_all.tsv: HSkM_2

value: HSkM


title: M4-11 cells, 10nM a1dj, 6h, biol. replicate 3

description:
Library name: a1dj_3
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name

value: WT


title: HCMEC, mechanical stretch, rep 5

description:
Library name: HCMEC_11
Column name in counts_all.tsv: HCMEC_11

value: mechanical loading


title: M4-11 cells, 10nM a1dj, 6h, biol. replicate 1

description:
Library name: a1dj_1
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: Whole blood DNA methylation, HISPANIC CONTROL, 74yo M, 207097420102_R02C01


title: Whole blood DNA methylation, HISPANIC AD, 78yo M, 207097420015_R08C01


title: WW-3

city: Qingdao

first: Junyi

last: Mu

address: No. 72, Binhai Road, Jimo District, Qingdao City

country: China

institute: Shandong Unoversity

description: Library name: Mu24

data_processing:
The construction and sequencing of the mRNA library were performed on the DNBSEQ platform at the high-throughput laboratory of Wuhan Huada Gene Technology Service Co., LTD, with a sequencing length of PE150. Sequencing data was filtered using the software SOAPnuke. The quality-controlled clean reads were then aligned to the reference genome (IWGSC RefSeq v1.1) using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) and Bowtie2.
\
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Triticum aestivum

source_name: leaf

growth_protocol: These materials were grown in a greenhouse with white light at 400 μmol·m-2·s-1, with a relative humidity of 50%, and a photoperiod of 16 hours of daylight (22°C) and 8 hours of nighttime (16°C). After germinating for 3 days under normal growth conditions, the endosperm was removed, and the seedlings were transferred to wheat nutrient culture medium containing 1.5 mM KCl, 1 mM MgSO4, 0.2 mM KH2PO4, 0.1 mM Fe(III)-EDTA, 1 µM H3BO3, 1µM ZnSO4, 1 µM MnSO4, 0.5 µM CuSO4, 0.05 µM Na2MoO4, 2.5 mM Ca(NO3)2 or CaCl2, pH = 6.0.

extract_protocol:
The leaves of wheat were collected and subjected to total RNA extraction using the TriZol RNA extraction kit (TransGen Biotech).
mRNA enrichment from total RNA was performed using Oligo(dT) magnetic beads to isolate polyA-tailed mRNA. The RNA was fragmented, reverse-transcribed with random N6 primers, and converted into double-stranded cDNA. The DNA ends were blunt-ended, 5'-phosphorylated, and A-tailed, followed by ligation to a bubble-shaped adapter with a 3'-T overhang. The ligated products were PCR-amplified, heat-denatured into single strands, and circularized using a bridge primer to generate single-stranded circular DNA libraries. After quality control, qualified libraries were sequenced.

treatment_protocol: For drought tolerance analysis, wheat seedlings were germinated under normal conditions and transplanted into soil tanks once the first leaf emerged from the coleoptile (each tank contained 12 identical small black pots, with nine seedlings per pot, in a mixture of vermiculite and Pindstrup substrate peat soil at a 3:1 ratio, 2 L wheat growth medium per tank with 5 mM nitrate;  no additional water was supplied, allowing natural evapotranspiration).  Soil moisture content and above-ground fresh weight were measured every three days from one random pot. For survival rate analysis, seedlings were considered to be under drought stress when soil moisture content fell below 5%, and after one day of drought, they were re-watered with 2 L of wheat growth medium containing either 0- or 5- mM nitrate per tank.  For RW (re-watering) or RWN (re-watering with nitrate) analysis, wheat seedlings subjected to one day of drought were re-watered with wheat growth medium containing 0- or 5- mM nitrate.

value: leaf


title: WW-2

description: Library name: Mu23


title: HCMEC, mechanical stretch, rep 4

description:
Library name: HCMEC_10
Column name in counts_all.tsv: HCMEC_10


title: Whole blood DNA methylation, HISPANIC CONTROL, 74yo F, 207097420112_R07C01

value: Female

value: PERUVIAN


title: WW-1

description: Library name: Mu22


title: primordial germ cell-like cells (PGCLC), RNA-seq, R3

city: Bethesda

first: Astrid

middle: D

last: Haase

state: MD

address: 50 South Dr

department: LCDB

institute: NIDDK

description:
Library name: RNAseq PGCLC R3
raw_gene_counts.xlsx

data_processing:
RNA-seq reads were mapped to the human T2T-CHM13v2 reference genome using STAR v2.7.10b with up to 100 alignments per read and a maximum mismatch ratio of 0.05. Gene-level counts were obtained using featureCounts (v2.20.0).
For small RNA-seq reads, the 3′ adapter sequence (see 'description column' for 3' adapter sequences of sample) was trimmed, and reads were collapsed by sequence to remove PCR duplicates. Unique molecular identifiers (UMIs, 8 nt at the 5’ end and 2 nt at the 3’ end) were then excised. Adapter, UMIs, and artificial calibrator sequences (CUCAUGGUUGUAAGUCCCGGUAAUCU, UCAUGGUUGUAAGUCCCGGUAAUCUA, AUGGUUGUAAGUCCCGGUAAUCUACG, and GGUUGUAAGUCCCGGUAAUCUACGUC; present only in iPSC R1/R2, PGCLC R1/R2, and VT xrTestes R1) were removed using Cutadapt v4.4. Reads shorter than 20 nt were discarded. Structural RNAs were removed. Remaining reads were mapped to the human genome (T2T-CHM13v2) with splicing disabled, allowing up to 100 alignments per read and a maximum of one mismatch per alignment, using STAR v2.7.10b. FASTQ quality was assessed with FastQC v0.11.9. BAM files were sorted and indexed using Samtools v1.17. Reads overlapping snRNA and tRNA loci (RepeatMasker-derived annotations, extended ±10 bp) were additionally removed.
Assembly: Human T2T-CHM13v2
Supplementary files format and content: Raw gene counts for total RNA-seq, normalized read length distributions file, format: .xlsx

source_name: primordial germ cell-like cells

extract_protocol:
Total RNA-seq and small RNA-seq libraries were generated for induced Pluripotent Stem Cells (iPSCs), primordial germ cell-like cells (PGCLCs), xrSpermatogonia (xrSpgn) and xrTestes (total), with three biological replicates per sample. RNA was isolated using the PureLink miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The long RNA fraction (>200 nt) was retained and further purified with TRIzol. Small RNAs were extracted using the same kit in combination with TRIzol, following the manufacturer’s protocol.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library Prep kit with rRNA depletion following the manufacturer's instructions. Small RNAs for small RNA-seq were prepared for sequencing as described in Konstantinidou et al. (2024).

value: primordial germ cell-like cells


title: HCMEC, mechanical stretch, rep 3

description:
Library name: HCMEC_9
Column name in counts_all.tsv: HCMEC_9


title: Rw5N5d-3

description: Library name: Mu21


title: Whole blood DNA methylation, HISPANIC AD, 84yo F, 207097420048_R05C01

value: HISPANIC


title: d3_142_mix_SC_1

description: Library name: d3_142_mix_SC_1

value: skin

value: human dermal fibroblast

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on day 0 of reprogramming.

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: Rw5N5d-2

description: Library name: Mu20


title: HCMEC, mechanical stretch, rep 2

description:
Library name: HCMEC_8
Column name in counts_all.tsv: HCMEC_8


title: Rw5N5d-1

description: Library name: Mu19


title: Rw5N3h-3

description: Library name: Mu18


title: Whole blood DNA methylation, HISPANIC CONTROL, 67yo F, 207080910104_R05C01

value: Healthy control

value: whole blood


title: HCMEC, mechanical stretch, rep 1

description:
Library name: HCMEC_7
Column name in counts_all.tsv: HCMEC_7


title: Rw5N3h-2

description: Library name: Mu17


title: Whole blood DNA methylation, HISPANIC CONTROL, 66yo F, 207080920105_R05C01


title: HCMEC, static control, rep6

description:
Library name: HCMEC_6
Column name in counts_all.tsv: HCMEC_6

value: static control


title: Rw5N1d-3

description: Library name: Mu15


title: Whole blood DNA methylation, HISPANIC CONTROL, 63yo F, 207097320053_R08C01


title: HCMEC, static control, rep5

description:
Library name: HCMEC_5
Column name in counts_all.tsv: HCMEC_5

value: HCMEC


title: Rw5N1d-1

description: Library name: Mu13


title: Rw5N1d-2

description: Library name: Mu14


title: HSkM, mechanical stretch, rep 1

description:
Library name: HSkM_7
Column name in counts_all.tsv: HSkM_7

value: HSkM


title: Rw0N5d-3

description: Library name: Mu12


title: Whole blood DNA methylation, HISPANIC AD, 59yo M, 207097420153_R07C01

value: Male

value: Alzheimer's disease


title: Whole blood DNA methylation, HISPANIC CONTROL, 69yo M, 207097420079_R05C01


title: HCMEC, static control, rep4

description:
Library name: HCMEC_4
Column name in counts_all.tsv: HCMEC_4


title: Rw0N5d-1

description: Library name: Mu10

value: leaf


title: Rw0N3h-3

description: Library name: Mu9


title: Whole blood DNA methylation, HISPANIC CONTROL, 64yo M, 207080910004_R02C01


title: HCMEC, static control, rep3

description:
Library name: HCMEC_3
Column name in counts_all.tsv: HCMEC_3


title: HCMEC, static control, rep2

description:
Library name: HCMEC_2
Column name in counts_all.tsv: HCMEC_2


title: Rw0N1d-3

description: Library name: Mu6


title: Rw0N3h-1

description: Library name: Mu7


title: HCMEC, static control, rep1

description:
Library name: HCMEC_1
Column name in counts_all.tsv: HCMEC_1


title: Whole blood DNA methylation, HISPANIC AD, 62yo F, 207097420102_R04C01

value: Female


title: Rw0N1d-2

description: Library name: Mu5


title: HSkM, static control, rep 3

description:
Library name: HSkM_3
Column name in counts_all.tsv: HSkM_3


title: Rw0N1d-1

description: Library name: Mu4


title: Dr-3

description: Library name: Mu3


title: Whole blood DNA methylation, HISPANIC AD, 82yo M, 207097420032_R05C01

value: CuADI


title: HUVEC, mechanical stretch, rep 5

description:
Library name: HUVEC_11
Column name in counts_all.tsv: HUVEC_11

source_name: HUVEC

value: HUVEC

value: mechanical loading


title: Dr-2

description: Library name: Mu2


title: Dr-1

description: Library name: Mu1


title: Whole blood DNA methylation, HISPANIC CONTROL, 76yo F, 207097420011_R01C01

value: HISPANIC


title: HUVEC, mechanical stretch, rep 4

description:
Library name: HUVEC_10
Column name in counts_all.tsv: HUVEC_10


title: ht1080.revio

city: Singapore

first: XIAORAN

last: CHAI

address: 8 College Rd, Singapore 169857

country: Singapore

institute: Duke-NUS Medical School

description: Library name: ht1080.revio

library_source: genomic

data_processing:
For HiFi sequenicng and Revio sequencing, consensus HiFi reads were generated on-instrument using the default CCS function.
For Nanopore sequencing, base calling was performed using dorado-0.9.5 with “super accurate” mode.
Assembly: CHM13-v2.0
Supplementary files format and content: tab-delimited text file includes telomere/subtelomere length and number of TRF1/TRF2 binding sites on each read.

extract_protocol:
Genomic DNA from cultured cells was extracted using the Gentra Puregene Genomic DNA Purification Kit (Qiagen)
For HiFi and Revio sequencing, SMRTBELL EXPRESS TEMPLATE PREP KIT 2.0 was used. For Nanopore sequencing, Ligation Sequencing Kit V14 was used.

value: human fibrosarcoma cell line


title: Whole blood DNA methylation, HISPANIC AD, 67yo F, 207097420079_R04C01


title: HSkM, static control, rep 4

description:
Library name: HSkM_4
Column name in counts_all.tsv: HSkM_4


title: hct116.revio

description: Library name: hct116.revio

value: human colorectal carcinoma cell line


title: mouse_late.2C_ONT

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

country: Japan

institute: Kyoto University

description: Library name: Sample1

data_processing:
Mouse and bovine Fast5 files were basecalled using MinKNOW (v6.0.14) or Dorado (v0.6.3 or v0.7.3) to generate FASTQ files. The FASTQ reads were then processed and mapped to reference genomes using the wf-transcriptomes pipeline in EPI2ME (v1.7.1) (https://github.com/epi2me-labs/wf-transcriptomes) to obtain GTF files. The mouse reference genome (mm10) and annotation data were downloaded from Illumina iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn), while the bovine reference genome and annotation data were downloaded from the UCSC Genome Browser database (https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/).
Assembly: mm10 or bosTau9
Supplementary files format and content: GTF files generated by EPI2ME (v1.7.1).

organism: Mus musculus

source_name: Late 2-cell stage embryo

growth_protocol: Superovulated mouse oocytes (Slc:ICR) were in vitro fertilized and resulting embryos were cultured in KSOM up to late two-cell stage (36 hpi). Bovine oocytes were recovered from the ovaries of Japanese Black or Japanese Black × Holstein F1 bovine. In vitro matured oocytes were subjected to IVF with sperm from a Japanese Black bull. At 72 h post-insemination, 8-cell to 16-cell stage bovine embryos were collected.

extract_protocol:
Total RNA was extracted from approximately 200 embryos per each group, by using TRIzol reagent (Thermo Fisher Scientific Inc.) according to the manufacturer’s manual.
The cDNA-PCR Sequencing Kit (SQK-PCS114; Oxford Nanopore Technologies Plc., Oxford, UK) was used for reverse transcription and library preparation according to the manufacturer's protocol. After reverse transcription, cDNA was amplified using LongAmp Hot Start Taq 2X Master Mix (New England Biolabs) with 14 cycles. Amplified cDNA was purified using AMPure XP beads (Beckman Coulter, Inc., Brea, CA) and quantified using a Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.). Each library was separately loaded into an R10.4.1 flow cell (Oxford Nanopore Technologies Plc.) and sequenced on a MinION sequencer (Oxford Nanopore Technologies Plc.).

value: Late 2-cell stage embryo

value: in vitro produced


title: HUVEC, mechanical stretch, rep 3

description:
Library name: HUVEC_9
Column name in counts_all.tsv: HUVEC_9


title: 17-CL1_shTENT5AB_2

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

description: Library name: Sample 2

data_processing:
Base calling was done with Guppy version 5.0.10.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Assembly: mm10 assembly annotated with GENCODE vM17 genes
Supplementary files format and content: Comma-separated value file with polyA tail length, mapping transcript, and replicate information for each read.

growth_protocol: Mouse 17-CL1 cells were cultured in DMEM (Life Technologies) media supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The 17-CL1 cells were cultured at 37ºC and in 5% CO2.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Cat. No. 74104, Qiagen). Poly(A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) from 5 μg of total RNA.
Poly(A) mRNA from each shTENT5A/B knockdown cell line was used for library preparation.  Libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). Libraries were loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies), and run on a MinION sequencer.

treatment_protocol: Cells were infected with lentivirus encoding shRNAs against Tent5a and Tent5b (shTENT5A/B).


title: M4-11 cells, 500nM JQ1, 6h, biol. replicate 2

description:
Library name: JQ1_2
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name

value: lymphoblast

value: macrophage

value: WT


title: Whole blood DNA methylation, HISPANIC AD, 66yo F, 207097420080_R04C01

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

value: whole blood


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097320052_R02C01

value: Healthy control

value: PERUVIAN


title: M4-11 cells, 500nM JQ1, 6h, biol. replicate 1

description:
Library name: JQ1_1
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: HUVEC, mechanical stretch, rep 2

description:
Library name: HUVEC_8
Column name in counts_all.tsv: HUVEC_8


title: 17-CL1_shTENT5AB_1

description: Library name: Sample 1


title: PIB_142_SC_2

description: Library name: PIB_142_SC_2

data_processing:
FASTQ files were preprocessed using the nf-core smRNA-seq pipeline (v2.4.0) with default parameters, except for UMI extraction, which was done using the following options: --umitools_extract_method regex --umitools_bc_pattern '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)
Assembly: Reference list of human mature miRNA sequences from miRbase
Supplementary files format and content: smRNA.counts.csv.gz

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, penicillin/streptomycin. Dendritic cell controls were sorted directly after enrichment and sorting from peripheral blood.

extract_protocol:
5000-10000 cells were sorted in RLT lysis buffer. RNA was exracted with the miRNeasy Tissue/Cells Advanced Kit according to manufacturer's protocol.
Libraries were prepared using the QIAseq miRNA UDI Library Kit by Qiagen.

treatment_protocol: HDFs were trasduced on day -1 of reprogramming and sorted on day 9 by FACS.

value: skin

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and for the miR-142 hairpin on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.

value: alive (DAPI-) and CD45+


title: Whole blood DNA methylation, HISPANIC AD, 72yo M, 207097420102_R07C01

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

value: Male

value: Alzheimer's disease

value: PRADI


title: M4-11 cells, 10nM a1dj, 6h, biol. replicate 2

description:
Library name: a1dj_2
Column name in gene_count.txt and gene_fpkm.txt corresponds to library name


title: Whole blood DNA methylation, HISPANIC AD, 74yo M, 207097420102_R01C01

value: HISPANIC


title: HUVEC, mechanical stretch, rep 1

description:
Library name: HUVEC_7
Column name in counts_all.tsv: HUVEC_7

value: HUVEC

value: mechanical loading


title: PIB_142_L_1

description: Library name: PIB_142_L_1


title: PIB_142_SC_1

description: Library name: PIB_142_SC_1


title: induced Pluripotent Stem Cells (iPSC), RNA-seq, R2

description:
Library name: RNA-seq iPSC R2
raw_gene_counts.xlsx

source_name: induced Pluripotent Stem Cells

value: induced Pluripotent Stem Cells


title: PIB_142_L_2

description: Library name: PIB_142_L_2


title: HUVEC, static control, rep6

description:
Library name: HUVEC_6
Column name in counts_all.tsv: HUVEC_6

value: static control


title: PIB_142_G_2

description: Library name: PIB_142_G_2

value: WT


title: PIB_142_G_1

description: Library name: PIB_142_G_1


title: HUVEC, static control, rep5

description:
Library name: HUVEC_5
Column name in counts_all.tsv: HUVEC_5


title: Whole blood DNA methylation, HISPANIC AD, 74yo M, 207097320053_R01C01

value: whole blood


title: Whole blood DNA methylation, HISPANIC AD, 76yo F, 207097420192_R05C01

value: Female


title: HUVEC, static control, rep4

description:
Library name: HUVEC_4
Column name in counts_all.tsv: HUVEC_4


title: PIB_124_SC_2

description: Library name: PIB_124_SC_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and for the miR-124 hairpin on day -1 of reprogramming.


title: PIB_124_L_2

description: Library name: PIB_124_L_2

value: skin


title: PIB_124_SC_1

description: Library name: PIB_124_SC_1

value: human dermal fibroblast


title: PIB_124_L_1

description: Library name: PIB_124_L_1


title: Whole blood DNA methylation, HISPANIC AD, 81yo F, 207097420011_R06C01


title: PIB_124_G_2

description: Library name: PIB_124_G_2


title: Whole blood DNA methylation, HISPANIC AD, 62yo F, 207097420032_R01C01

value: CuADI


title: PIB_SCR_SC_2

description: Library name: PIB_SCR_SC_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and for a scrambled miRNA hairpin on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.


title: HUVEC, static control, rep2

description:
Library name: HUVEC_2
Column name in counts_all.tsv: HUVEC_2


title: PIB_124_G_1

description: Library name: PIB_124_G_1

value: alive (DAPI-) and CD45+


title: HUVEC, static control, rep3

description:
Library name: HUVEC_3
Column name in counts_all.tsv: HUVEC_3


title: Whole blood DNA methylation, HISPANIC AD, 81yo M, 207080910085_R02C01

value: Male

value: Alzheimer's disease


title: PIB_SCR_SC_1

description: Library name: PIB_SCR_SC_1


title: PIB_SCR_L_2

description: Library name: PIB_SCR_L_2


title: HUVEC, static control, rep1

description:
Library name: HUVEC_1
Column name in counts_all.tsv: HUVEC_1


title: PIB_SCR_L_1

description: Library name: PIB_SCR_L_1


title: Whole blood DNA methylation, HISPANIC AD, 83yo F, 207097420152_R03C01

value: HISPANIC


title: PIB_SCR_G_2

description: Library name: PIB_SCR_G_2


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo F, 207097420082_R02C01

value: Healthy control

value: PRADI


title: PIB_SCR_G_1

description: Library name: PIB_SCR_G_1


title: Rw5N3h-1

description: Library name: Mu16

value: leaf