title: cfDNA_I_16

description: Library name: CEG1554-EL01-D1278-016


title: F1196_002, nonAD, rep1

status: Public on Dec 02 2025

type: SRA

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

country: USA

institute: PreCyte, Inc.

description:
Library name: 09_09_13_17
library name V2: 09_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

library_source: transcriptomic

data_processing:
Step 1: RNA-seq data were processed using R packages using a custom workflow using SnakeMake workflow management system for reproducibility. The workflow included adapter read trimming using Trimmomatic (Bolger, Lohse and Usadel, 2014).
Step 2: Sequences were reference aligned to GRCh using STAR (Dobin et al., 2013)
Step 3: Transcripts were quantified at gene-level resolution using the R software package featureCounts (Liao, Smyth and Shi, 2014). Read duplicates were removed by using –ignoreDups setting in R:featureCounts.
Step 4: RNA-seq QC was performed using MultiQC, dupRadar and GATK estimate of library complexity.
Step 5: Next, data for some samples were excluded based on data quality (technical omissions) as indicated in the methods section of the manuscript. Data were omitted for three reasons:  1) RNA quality score (RQS) < 8; 2) low RNA integrity (RIN) <6 and 3) low RNA-seq quality based on the analysis of metrics in Step 4.
Step 6: RNA-seq data from all 24 AD-iCAP batches were merged into a single file and several preprocessing steps were performed in R to detect and correct technical noise in the data to reduce error as described below in the following steps. First, genes were filtered to remove those below the limit of detection. To do this, ERCC controls were removed and a histogram of expression levels for each gene across all patient samples was generated, showing a bimodal curve indicating some genes were below the limit of detection. A threshold was selected to separate the curves corresponding to 35 counts and genes were filtered to remove those below this threshold for greater than 10% of the samples.
Step 7: Next, data for a subset of samples were excluded based on patient class uncertainty. Samples with class uncertainty included those with conflicting amyloid beta (Aβ) pathology from cerebrospinal fluid (CSF) and positron emission tomography (PET) imaging, CSF Aβ₄₂ values near the diagnostic threshold, or absence of Aβ data at the time of blood draw. Codes include: F1, those with conflicting PET and CSF data for presence of AB pathology;  F2, no AB pathology data at time of blood draw or only CSF AB42 data that is close to threshold; F3, longitudinal AB data show transition from AD  to normal pathology; F4, CSF AB42 value is close to threshold of pathogenic levels.
Step 8: Counts were adjusted to correct for GC bias using either full quantile normalization (FQN) or conditional quantile normalization (CQN) determined by the R-EdgeR package.
Step 9: Data were normalized for heteroskedasticity by variance transformation (VST) using the DESeq2 package and batch corrected using the removeBatchEffect function from the R package Limma (Ritchie et al., 2015).
Step 10: For RNA-seq data generated with mouse plasma, differential expression analysis was performed using R-DESeq2 (Love, Huber and Anders, 2014). GSEA analysis was applied using the R-fgsea package. Raw gene-level counts were normalized using the median-of-ratios method, and a negative binomial generalized linear model was fit with design ~ condition. Wald tests were used to evaluate pairwise contrasts between conditions, and p-values were adjusted using the Benjamini–Hochberg method to control the false discovery rate. Genes with FDR < 0.05 were considered differentially expressed.
Assembly: GRCh
Supplementary files format and content: For RNA-seq data generated with human plasma, processed data included are: 1) feature_counts data containing raw feature counts (ADSBIRII.completeData.20180223.rds) and 2) processed/normalized data (as described) (all.cqn.vst_12032024_2.rds). Both are R data files.
Supplementary files format and content: For RNA-seq data generated with mouse plasma, processed data included are: 1) feature_counts data containing  raw feature counts (feature_counts_GEO2.csv and feature_counts_GEO.csv) and  2) results of differential expression analysis ( log2 fold change and FDR values). Both are .csv files with filenames corresponding to experimental condition (e.g. 2wk,29HEMI_NCAR,cqn.csv)

molecule: polyA RNA

organism: Homo sapiens

source_name: iCell Neurons

growth_protocol: Indicator cells were a commercially available, pan-neuronal population of human neurons (glutamatergic and GABAergic) derived from induced pluripotent stem cells (iPSCs) (iCell Neurons from Fujifilm (formerly Cellular Dynamics International (CDI)). Cells were grown according to manufacturer’s instructions with a modification to the culture duration described below. 12-well Eppendorf moat plates were coated with 0.01% poly-L-ornithine solution (Sigma P4957) for 1 h followed by 3.3 µg/mL laminin (Sigma L2020) for 1 h. Next, iCell neurons were thawed and plated a density of 488,875 cells/well in a total volume of 1 mL/well. Medium was exchanged 24 h after plating. Cells were treated after culturing for a total of 48 h.

extract_protocol:
For experiments with human plasma samples, RNA was isolated manually using an RNeasy Micro kit (Qiagen) and for experiments with mouse plasma samples, automated RNA isolation was performed using a MagMax mirVana kit (Invitrogen, A27828) on either a KingFisher Flex or a Kingfisher Duo Prime liquid handling robot as per the manufacturer’s recommendation (Thermo Fisher Scientific). Total RNA was stored at -80°C.
100 - 250 ng of total RNA from each iCAP sample was used for automated library preparation and RNA sequencing (RNA-seq) performed by Covance/Labcorp. Strand-specific library prep was performed with PolyA selection using TruSeq RNA Library Prep kit (Illumina) with unique dual indices (IDT) and resulting DNA samples were pooled and spread evenly across lanes and sequenced on a HiSeq 4000 (Illumina) with paired-end 150 bp reads yielding 20-30 M total reads per sample.

treatment_protocol: Cells were exposed to 5% plasma containing 0.2 mg/mL heparin sodium salt (Stem Cell Technologies, 07980) in PBS for 6 h.

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 021

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: Whole mammary gland involution day 1 replicate 1

city: Paris

first: Jérémy

last: Chantrel

state: Ile-de-France

address: 25-28 rue du Dr. Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

description:
Library name: Sample 4
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F04

data_processing:
Quality Control and Preprocessing Raw sequencing reads were subjected to quality control using FastQC (v0.11.9). Low-quality bases and adapter sequences were trimmed using TrimGalore (v0.6.7) with the following parameters: --stringency 4. Reads passing the quality filters were retained for further analysis.
Quantification of Gene Expression Gene expression levels were quantified using RSEM (v1.3.3) against the Mus musculus reference genome GRCm39.
Assembly: GRCm39
Supplementary files format and content: rsem_results_FPKM_counts_original.txt contains the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each sample, generated using RSEM. rsem_results_raw_counts_original.txt contains the raw read counts for each sample, generated using RSEM.

molecule: total RNA

organism: Mus musculus

source_name: Mammary gland

growth_protocol: Mammary glands were collected and snap freezed in liquid nitrogen then kept at -80°C.

extract_protocol:
Total RNA from mammary tissues were extracted with Trizol Reagent following manufacturer's instructions Reagent [Invitrogen #15596026] or RNeasy Micro Kit (Qiagen) following manufacturer’s instructions
250-300 bp insert cDNA library, library type BGISEQ-500 RNA-Seq

tag: tissue

value: Mammary gland

tag: genotype

value: WT


title: F56_004, nonAD, rep1

description:
Library name: 06_09_13_17
library name V2: 06_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions


title: F1586_001, MCI, rep1

description:
Library name: 08_09_13_17
library name V2: 08_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number


title: Whole mammary gland involution day 3 replicate 2

description:
Library name: Sample 8
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F08


title: F757_003, preAD, rep1

description:
Library name: 07_09_13_17
library name V2: 07_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number


title: reference_001, reference, rep55

description:
Library name: 15_09_13_17
library name V2: 15_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: reference


title: Whole mammary gland involution day 0 replicate 3

description:
Library name: Sample 3
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F03


title: F549_003, MCI, rep1

description:
Library name: 04_09_13_17
library name V2: 04_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: F1627_001, normal, rep1

description:
Library name: 05_09_13_17
library name V2: 05_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: reference_001, reference, rep54

description:
Library name: 02_09_13_17
library name V2: 02_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type


title: Whole mammary gland involution day 0 replicate 2

description:
Library name: Sample 2
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F02

tag: tissue

tag: genotype


title: F109_003, nonAD, rep1

description:
Library name: 03_09_13_17
library name V2: 03_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type


title: F182_004, normal, rep1

description:
Library name: 01_09_13_17
library name V2: 01_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: Whole mammary gland involution day 0 replicate 1

description:
Library name: Sample 1
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F01


title: cfDNA_I_12

city: Cambridge

first: Fabio

last: Puddu

address: The Trinity Building

country: United Kingdom

institute: biomodal

description: Library name: CEG1554-EL01-D1278-012

library_source: genomic

data_processing:
Library strategy: duet evoC
Trimming and read resolution: internal proprietary software v0.2.0
Alignment: BWA-MEM2 v2.2.1
Duplicate Marking: samtools  v1.19.2
Methylation quantification: internal proprietary softwares 0.5.3 and 0.2.5
Assembly: GRCh38
Supplementary files format and content: bedmethyl file for modC
Supplementary files format and content: bedmethyl file for hmC
Supplementary files format and content: bedmethyl file for mC

molecule: genomic DNA

source_name: cfDNA

extract_protocol:
Where possible, blood was sampled before colonoscopy. 10 mL blood was drawn into a K2 EDTA blood tube, placed on ice, and processed within 4 hours. Samples were centrifuged (2,000g for 10 min at room temperature). The plasma layer was transferred to a clean tube and was again centrifuged (2,000g for 10 min at room temperature) to remove any remaining cellular material. Double-spun plasma was aliquoted into tubes in volumes of at least 1 mL and then immediately frozen and stored at −80°C. cfDNA was extracted using the chemagic™ cfDNA 5k Kit (Revvity) using between 1 and 7 mL of plasma. Resulting cfDNA was quantified using a Qubit Fluorometer (Life Technologies) and quality was assessed using Agilent TapeStation, with samples included if they had >70% for the %cfDNA quality metric on the Cell-free DNA ScreenTape assay.
The duet evoC assay was run according to manufacturer’s instructions. In brief, 10ng of each cfDNA sample was end-repaired, A-tailed, and ligated to hairpin adapters. Adaptors were digested and the 3’ hydroxyl group was extended by a DNA polymerase to generate molecules with the original sample DNA strand connected to its (copied) complementary strand. Y-shaped sequencing adapters were then ligated to molecules. Methylation at 5mC was enzymatically copied across the CpG unit to the C on the copy strand using a DNA methyltransferase, whereas 5hmC was enzymatically glycosylated to prevent such a copy. 5mC on both the original and copy strands was then protected from subsequent deamination. Unmodified Cs were then deaminated to uracil, subsequently read as thymine.

value: cfDNA


title: cfDNA_CONTROL_13

description: Library name: CEG1554-EL01-D1278-011


title: F572_003, nonAD, rep1

description:
Library name: 24_09_07_17
library name V2: 24_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: Aim 2 Batch 020

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: RNASeq QC


title: RNaseA-T1-rep1

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

country: China

institute: Fudan University Shanghai Cancer Center

data_processing:
Reads were trimmed using Cutadapt
mapped to hg38  use STAR
Gene count were generated using featureCounts
Gene TPM were generated using kallisto
Assembly: hg38
Supplementary files format and content: tab-delimited text file include TPM for each Sample

source_name: kidney

growth_protocol: HEK 293T cells were cultured in DMEM high glucose (GIBCO) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin and 100 μg/mL of streptomycin. Cells were kept under standard 37 ℃ and 5% CO2 conditions

extract_protocol:
RNA was amplified in-situ, not extracted from the cultured cells.
For AMOUR: Cells (> 97% viability) were fixed with 4% PFA and immobilized with Concanavalin A beads. The bead-bound cells underwent three washes with AMOUR-wash buffer (PBS, 1 mM ATP, 0.2 U μL-1 RNase inhibitor). Subsequently, the beads were resuspended in PBS with RNase Inhibitor (40 U μL-1) and annealed with T7N9 oligo (0.25 μM). The reaction mixture was incubated at 42 °C for 2 min, followed by ramping to 25 °C and a 5-min hold. After washing, linear amplification with T7 RNA Polymerase occurred at 37 °C for 2 h with shaking at 1,200 rpm. The resulting RNA was purified using Dynabeads MyOne Silane beads. For GWA-Pd and WGA-T: HEK293T cells were collected with (WGA-T) or without 0.25% trypsin treatment (WGA-Pd), and blocked with Egg white avidin and yeast tRNA. Following buffer removal, 500 µg of biotin-WGA was added to the cells and incubated at 37 ℃ for 15 min. After centrifugation at 500 × g, 4 ℃ for 5 min to eliminate excess biotin-WGA, cells were washed with PBS. Lysis was performed with ice-cold lysis buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 1% DDM, and 0.001% GDN with 0.1% CHS, 200 U mL-1 RNase inhibitor, 1 × proteinase inhibitor). Dynabeads MyOne Streptavidin C1 were utilized for capturing membrane-associated RNA, extracted using Buffer RLT, and subsequently purified using silane beads. For RT-Amp: Cells were harvested, fixed, and immobilized utilizing ConA beads, followed by T7N9 oligo annealing through the "AMOUR" strategy. Reverse transcription (RT) was performed on beads employing HiScript II Reverse Transcriptase. Following RT, the cDNA product underwent purification with the DNA Clean Concentrator. Subsequent second-strand synthesis was achieved with Klenow exo- and P5N6 Oligo, and dsDNA was purified using silane beads. Linear amplification was executed using T7 RNA Polymerase. The resulting amplified RNA was purified with silane beads. The purified RNA was ligated to 3'adapter and reverse transcribed. The cDNA was ligated with cDNA adapter and subjected to limited cycle PCR, ready for sequencing.

treatment_protocol: HEK 293T cells were subjected to different strategies of AMOUR, WGA-Pd,WGA-T, and RT-Amp to profile surface RNAs.

value: kidney

tag: cell line

value: Human embryonic kidney


title: cfDNA_I_13

description: Library name: CEG1554-EL01-D1278-013


title: cfDNA_I_17

description: Library name: CEG1566-AM01-D1302-001


title: RNaseA-T1-rep2


title: cfDNA_CONTROL_12

description: Library name: CEG1554-EL01-D1278-010


title: F529_005, preAD, rep1

description:
Library name: 22_09_07_17
library name V2: 22_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: cfDNA_I_14

description: Library name: CEG1554-EL01-D1278-014


title: Cell-lysis-rep2

tag: cell type


title: cfDNA_I_15

description: Library name: CEG1554-EL01-D1278-015

tag: tissue


title: cfDNA_I_11

description: Library name: CEG1553-EL01-D1278-008


title: F1547_001, MCI, rep1

description:
Library name: 19_09_07_17
library name V2: 19_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F126_003, nonAD, rep1

description:
Library name: 20_09_07_17
library name V2: 20_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type


title: F915_001, nonAD, rep1

description:
Library name: 18_09_07_17
library name V2: 18_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: cfDNA_I_10

description: Library name: CEG1553-EL01-D1278-007


title: F1537_001, MCI, rep1

description:
Library name: 17_09_07_17
library name V2: 17_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: Cell-lysis-rep1

tag: cell line

tag: genotype


title: CellsOnly_001, CellsOnly, rep11

description:
Library name: 12_09_07_17
library name V2: 12_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: CellsOnly


title: F1575_001, MCI, rep1

description:
Library name: 23_09_07_17
library name V2: 23_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: sequencing plate_name

tag: rna-seq date


title: cfDNA_I_9

description: Library name: CEG1553-EL01-D1278-006

tag: tissue


title: AMOUR-Ctrl-rep1


title: F1522_001, MCI, rep1

description:
Library name: 14_09_07_17
library name V2: 14_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F1572_001, MCI, rep1

description:
Library name: 21_09_07_17
library name V2: 21_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: F412_005, normal, rep1

description:
Library name: 16_09_07_17
library name V2: 16_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: THP-1 Histone treated-2

data_processing:
Reads were trimmed using Trimmomatic v0.39
mapped to hg38/GRCh38  use STAR
Gene counts were generated using featureCounts
DESeq2 Bioconductor package was used on the RNA-Seq data to conduct differential expression analyse
Assembly: hg38/GRCh38
Supplementary files format and content: tab-delimited text file include raw count for each Sample

source_name: Peripheral blood

growth_protocol: The human monocyte cell line THP-1 was cultured in RPMI-1640 medium (Gibco) supplemented with 2.5 mM glutamine, 10% (v/v) FBS (Gibco), and 100 U mL-1 penicillin-streptomycin (Sangon Biotech). The cultures were maintained in a 5% CO2 incubator at 37 °C.

extract_protocol:
Total RNA was extracted by Trizol in accordance with the manufacturer’s protocol. mRNA were purified by VAHTS mRNA capture beads (Vazyme)
Libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme)

treatment_protocol: THP-1 cells (2.5 × 10^5 cells mL-1) in 48-well plates were differentiated into THP-1 macrophages with 100 ng mL-1 PMA for 48 h followed by 24 h of rest post PMA removal.Then Cells underwent a 6-hour incubation with 50 μg mL-1 calf thymus histones in FBS-free RPMI-1640 medium.

value: Peripheral blood

tag: cell line

value: Human Acute Monocytic Leukemia Cells

tag: treatment

value: Histone


title: THP-1 Histone treated-1


title: reference_001, reference, rep53

description:
Library name: 15_09_07_17
library name V2: 15_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

value: human

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: THP-1 NC-2

tag: tissue

tag: cell type

value: Control


title: F308_005, normal, rep1

description:
Library name: 10_09_07_17
library name V2: 10_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: F487_002, nonAD, rep1

description:
Library name: 08_09_07_17
library name V2: 08_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: cfDNA_CONTROL_10

description: Library name: CEG1471-SY01-D977-020


title: F1440_001, MCI, rep1

description:
Library name: 09_09_07_17
library name V2: 09_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: F1425_001, MCI, rep1

description:
Library name: 05_09_07_17
library name V2: 05_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: AMOUR-Ctrl-rep2

tag: cell line

tag: genotype

value: WT


title: F342_001, nonAD, rep1

description:
Library name: 13_09_07_17
library name V2: 13_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: sample cohort

tag: plasma class


title: F280_005, normal, rep1

description:
Library name: 06_09_07_17
library name V2: 06_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: sequencing plate_name


title: cfDNA_CONTROL_11

description: Library name: CEG1553-EL01-D1278-002

tag: tissue

value: cfDNA


title: cfDNA_I_8

description: Library name: CEG1553-EL01-D1278-005


title: F110_002, nonAD, rep1

description:
Library name: 04_09_07_17
library name V2: 04_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 020

tag: rna-seq date


title: cfDNA_IV_11

description: Library name: CEG1471-SY01-D977-017


title: cfDNA_I_7

description: Library name: CEG1553-EL01-D1278-004


title: THP-1 NC-1

tag: treatment


title: reference_001, reference, rep52

description:
Library name: 02_09_07_17
library name V2: 02_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: reference

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F1462_001, MCI, rep1

description:
Library name: 11_09_07_17
library name V2: 11_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: cfDNA_I_6

description: Library name: CEG1471-SY01-D977-001


title: F1636_001, nonAD, rep1

description:
Library name: 24_08_31_17
library name V2: 24_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: Aim 2 Batch 019

tag: sample cohort

tag: plasma class

value: low RIN


title: cfDNA_CONTROL_9

description: Library name: CEG1469-SY01-D978-019

tag: tissue


title: BJ sgRNA-PURPL#1-input

city: Xi'an

first: Wei

last: Sun

state: Shaanxi

address: No. 229 Taibai North Road, Beilin District

department: College of Life Sciences and Medicine

institute: Northwest University

description: Library name: sgRNA-PURPL#1-input

data_processing:
For ChIP-seq analysis, quality control and removal of sequencing adapters were same as RNA-seq. The trimmed reads were aligned to the reference genome hg38 (GRCh38.p13) using Bowtie2 (v2.4.2) with default parameters. PCR duplicates were removed using GATK MarkDuplicates (v4.1.9.0). Peaks were then called using MACS2 (v2.2.9.1) with the parameters: macs2 callpeak -f BAMPE -g hs --broad --broad-cutoff 0.1. To identify differential peak regions, we used MACS2 with the parameter: macs2 bdgdiff -C 2. Biological replicates’ BAM files were merged and then converted to BigWig files using deepTools (v3.5.1) with the parameters: bamCoverage -bs 10 --normalizeUsing CPM. BigWig files were visualized using Integrative Genomics Viewer (IGV, v2.16.1).
Assembly: hg38
Supplementary files format and content: BigWig, all samples

source_name: BJ

extract_protocol:
ChIP assays were carried out as previously described. Briefly, BJ cells were fixed with 1% formaldehyde (F8775, Sigma) for 10 min at room temperature, and a final concentration of 125 mM glycine was used to quench the reaction. Cells were washed twice with cold PBS and collected in cold PBS by scraping, then resuspended in hypotonic lysis buffer (20 mM Hepes, pH 7.9, with 10 mM KCl, 10% glycerol, 1 mM DTT and a protease inhibitor cocktail (04693124001, Roche)). The pellet of nuclei was resuspended in RIPA buffer (10 mM Tris-HCl, pH 8.0, with 140 mM NaCl, 1% Triton X-100, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and Protease Inhibitor). Nuclear extracts were sonicated to generate chromatin fragment on a Covaris M220 Focused-ultrasonicator (Insert, microTUBE 130 µL; Temperature, 7°C; Peak Incident Power, 75W; Duty Factor, 5%; Treatment Time, 300s). The chromatin was cleaned by centrifugation at 14,000×g for 10 min at 4 °C and diluted with 1 mL RIPA buffer per reaction. Then the chromatin was precleared with Protein G Sepharose 4 Fast Flow (17061801, GE) for 2 hours, 30 µL of sample was set aside as an input and subjected to immunoprecipitation with antibody against H3K9me3 (abcam, ab8898) overnight. On the following day, Pierce Protein A/G Plus Agarose beads (Thermo Fisher Scientific, 20423) that were blocked with RIPA containing 0.5% bovine serum albumin (BSA) were added into the samples followed by incubation for 2 hours in cold room under rocking. The beads were then washed three times with RIPA buffer, followed by two times in RIPA buffer with 0.5 M NaCl, oncein LiCl buffer [250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630,0.1% sodium deoxycholate, and 10 mM tris-HCl (pH 8.0)], and twice in ice-cold Tris- EDTA (TE) buffer. Each time, the beads were sustaining for 5 min with a gentle rock. After washing, both the beads and input sample were added with 150 μL of extraction buffer (1% SDS in 1× TE, 12 μL of 5 M NaCl, and 10 μg of RNAse A) and incubated at 37°C for 1 hour with a shaking. Next, 20 μg of Proteinase K was added to the samples for incubation at 65°C overnight with thermoshaking.
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit for Illumi-na (NEB, E7645).

tag: cell line

value: BJ

value: Human skin fibroblast cell


title: BJ sgRNA-PURPL#1-H3K9me3

description: Library name: sgRNA-PURPL#1-H3K9me3


title: F1355_001, preAD, rep1

description:
Library name: 07_09_07_17
library name V2: 07_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: sequencing plate_name


title: cfDNA_I_5

description: Library name: CEG1469-SY01-D978-002


title: F1293_001, preAD, rep1

description:
Library name: 23_08_31_17
library name V2: 23_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rna-seq date


title: BJ sgRNA-PURPL#2-H3K9me3

description: Library name: sgRNA-PURPL#2-H3K9me3


title: F264_005, normal, rep1

description:
Library name: 01_09_07_17
library name V2: 01_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: cfDNA_IV_10

description: Library name: CEG1461-SY01-D978-017


title: F540_007, MCI, rep1

description:
Library name: 21_08_31_17
library name V2: 21_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: rna-seq covance/genewiz_id

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BJ sgRNA-PURPL#2-input

description: Library name: sgRNA-PURPL#2-input


title: BJ sgCtrl-H3K9me3

description: Library name: sgCtrl-H3K9me3


title: F1419_001, normal, rep1

description:
Library name: 20_08_31_17
library name V2: 20_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma shipment_batch

tag: sample cohort


title: BJ sgCtrl-input

description: Library name: sgCtrl-input

tag: cell line


title: F1340_001, preAD, rep1

description:
Library name: 03_09_07_17
library name V2: 03_09_07_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma class


title: F1637_001, MCI, rep1

description:
Library name: 22_08_31_17
library name V2: 22_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)


title: F386_001, preAD, rep1

description:
Library name: 18_08_31_17
library name V2: 18_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: sequencing plate_name


title: F1311_001, preAD, rep1

description:
Library name: 16_08_31_17
library name V2: 16_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: rna-seq date


title: reference_001, reference, rep51

description:
Library name: 15_08_31_17
library name V2: 15_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number


title: BJ PURPL#2-OE,rep3

description: Library name: PURPL#2-OE,rep3

data_processing:
For RNA-seq analysis, quality control of the raw data was performed using FastQC (v0.11.9). Sequencing adapters were subsequently removed using Cutadapt (v3.3). The trimmed reads were aligned to the human reference genome hg38 (GRCh38.p13) using HISAT2 (v2.1.0) with default parameters. The aligned reads were converted to BAM format and sorted using SAMtools (v1.11). The sorted aligned reads were quantified using Subread featureCounts (v2.0.1) based on the GENCODE v40 annotation. Genes with a total raw count greater than 18 across the three replicates in both the treatment and control groups (i.e., an average of at least 3 counts per sample) were retained for further analysis to filter out lowly expressed genes. Differentially Expressed Genes (DEGs) using DESeq2 (v1.34.0) with threshold: log2-transformed fold change ≥ 0.75 and Adjust P-values < 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include RNA-seq three biological replicates raw counts for sgRNA-PURPL sample in BJ cells
Supplementary files format and content: tab-delimited text file include RNA-seq three biological replicates raw counts for PURPL-OE in BJ cells

extract_protocol:
Total RNA was isolated with TRIzol reagent (15596018, Invitrogen) from cultured cells
For RNA-seq library preparation, poly (A)+ RNA was selected using the NEB-Next Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) to perform the LM-seq procedure. including that isolated mRNA is fragmented in reverse transcription buffer with heat and then reverse-transcribed with SmartScribe reverse transcriptase (Clontech) using a random hexamer oligo (HZG883). After reverse transcription, RNA is removed by RNaseA and RNaseH treatment. A partial adaptor (HZG885) is then ligated to the single stranded cDNA using T4 RNA ligase 1 (NEB) and incubated overnight at 22℃. After purification, ligated cDNA is amplified by 18 cycles of PCR using oligos that contain full BGI adaptors. Last, the resultant libraries were purified using the DNA Clean Beads, followed by sequencing using the DNBSEQ-T7 PE150  platform  (Biopharmaceutical PublicService Platform, Nanjing).

tag: cell type


title: cfDNA_CONTROL_8

description: Library name: CEG1457-SY01-D977-021

tag: tissue


title: cfDNA_IV_8

description: Library name: CEG1461-SY01-D978-014


title: F1309_001, normal, rep1

description:
Library name: 17_08_31_17
library name V2: 17_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: cfDNA_IV_7

description: Library name: CEG1457-SY01-D977-018


title: COM, KTC replicate3

city: Beijing

first: Shuting

last: Ye

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

description:
Library name: COMK3
MD5 Checksums.xls

data_processing:
Basecalling was performed using a software developed for DNBSEQ-T7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al.,  Genome Research, 1997.
Assembly: GCA_000182925.2
Supplementary files format and content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: Mycelium

growth_protocol: Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Ketoconazole (Sigma) was added, with final concentration of 1 μg/mL.

value: Mycelium

tag: genotype

value: cax-9 complementing

tag: treatment

value: Ketoconazole


title: BJ PURPL#2-OE,rep1

description: Library name: PURPL#2-OE,rep1

tag: cell line


title: F1296_001, nonAD, rep1

description:
Library name: 14_08_31_17
library name V2: 14_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: F1366_001, normal, rep1

description:
Library name: 13_08_31_17
library name V2: 13_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: sequencing plate_name


title: BJ PURPL#2-OE,rep2

description: Library name: PURPL#2-OE,rep2

tag: cell type


title: cfDNA_IV_9

description: Library name: CEG1461-SY01-D978-015

tag: tissue


title: COM, KTC replicate1

description:
Library name: COMK1
MD5 Checksums.xls

value: cax-7 complementing


title: F1384_001, normal, rep1

description:
Library name: 19_08_31_17
library name V2: 19_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rna-seq date


title: BJ PURPL#1-OE,rep2

description: Library name: PURPL#1-OE,rep2

tag: cell line


title: cfDNA_I_4

description: Library name: CEG1457-SY01-D977-002


title: COM, control replicate3

description:
Library name: COMC3
MD5 Checksums.xls

tag: genotype

value: cax-6 complementing

tag: treatment

value: No treatment


title: CellsOnly_001, CellsOnly, rep10

description:
Library name: 12_08_31_17
library name V2: 12_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: no plasma, 6 h

tag: plasma shipment_batch

tag: sample cohort

value: CellsOnly

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: cfDNA_CONTROL_6

description: Library name: CEG1451-SY01-D977-023

value: cfDNA


title: COM, control replicate2

description:
Library name: COMC2
MD5 Checksums.xls

value: cax-5 complementing


title: F1259_001, normal, rep1

description:
Library name: 10_08_31_17
library name V2: 10_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 019

tag: plasma class

value: low RIN

value: pass


title: F1269_001, preAD, rep1

description:
Library name: 11_08_31_17
library name V2: 11_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: sequencing plate_name


title: cfDNA_CONTROL_7

description: Library name: CEG1451-SY01-D977-024

tag: tissue


title: BJ PURPL#1-OE,rep1

description: Library name: PURPL#1-OE,rep1

tag: cell line

value: BJ

value: Human skin fibroblast cell


title: F549_001, normal, rep1

description:
Library name: 09_08_31_17
library name V2: 09_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rna-seq date

value: RNASeq QC


title: KO, KTC replicate3

description:
Library name: KOK3
MD5 Checksums.xls

value: Mycelium

tag: genotype

value: cax-4 knockout

tag: treatment

value: Ketoconazole


title: F1241_001, normal, rep1

description:
Library name: 08_08_31_17
library name V2: 08_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

value: human

tag: plasma shipment_batch

tag: sample cohort

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BJ PURPL#1-OE,rep3

description: Library name: PURPL#1-OE,rep3


title: cfDNA_CONTROL_5

description: Library name: CEG1451-SY01-D977-022


title: COM, control replicate1

description:
Library name: COMC1
MD5 Checksums.xls

value: cax-4 complementing

value: No treatment


title: BJ Ctrl,rep3

description: Library name: Ctrl,rep3


title: BJ Ctrl,rep2

description: Library name: Ctrl,rep2


title: COM, KTC replicate2

description:
Library name: COMK2
MD5 Checksums.xls

value: cax-8 complementing


title: cfDNA_IV_5

description: Library name: CEG1451-SY01-D977-019

value: cfDNA


title: BJ Ctrl,rep1

description: Library name: Ctrl,rep1


title: F214_003, normal, rep1

description:
Library name: 07_08_31_17
library name V2: 07_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma class

value: #N/A


title: cfDNA_IV_6

description: Library name: CEG1457-SY01-D977-015

tag: tissue


title: KO, KTC replicate2

description:
Library name: KOK2
MD5 Checksums.xls


title: BJ sgRNA-PURPL#2,rep3

description: Library name: sgRNA-PURPL#2,rep3

tag: cell line

tag: cell type


title: F315_003, nonAD, rep1

description:
Library name: 06_08_31_17
library name V2: 06_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: Aim 2 Batch 019

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sequencing plate_name


title: KO, control replicate3

description:
Library name: KOC3
MD5 Checksums.xls

tag: genotype

tag: treatment


title: cfDNA_IV_4

description: Library name: CEG1451-SY01-D977-016


title: BJ sgRNA-PURPL#2,rep2

description: Library name: sgRNA-PURPL#2,rep2


title: KO, KTC replicate1

description:
Library name: KOK1
MD5 Checksums.xls


title: F549_002, nonAD, rep1

description:
Library name: 05_08_31_17
library name V2: 05_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma shipment_batch

tag: sample cohort

tag: rna-seq date

value: low RIN


title: BJ sgRNA-PURPL#2,rep1

description: Library name: sgRNA-PURPL#2,rep1


title: KO, control replicate2

description:
Library name: KOC2
MD5 Checksums.xls


title: BJ sgRNA-PURPL#1,rep3

description: Library name: sgRNA-PURPL#1,rep3


title: cfDNA_CONTROL_3

description: Library name: CEG1437-SY01-D978-023


title: F1225_001, normal, rep1

description:
Library name: 04_08_31_17
library name V2: 04_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: cfDNA_IV_3

description: Library name: CEG1437-SY01-D978-018

tag: tissue


title: F386_002, MCI, rep1

description:
Library name: 03_08_31_17
library name V2: 03_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma class


title: WT, KTC replicate3

description:
Library name: WTK3
MD5 Checksums.xls

tag: genotype

value: WT


title: cfDNA_I_2

description: Library name: CEG1437-SY01-D978-003


title: F1157_001, nonAD, rep1

description:
Library name: 01_08_31_17
library name V2: 01_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sequencing plate_name


title: cfDNA_CONTROL_2

description: Library name: CEG1407-SY01-D894-008


title: cfDNA_CONTROL_4

description: Library name: CEG1437-SY01-D978-024


title: BJ sgRNA-PURPL#1,rep2

description: Library name: sgRNA-PURPL#1,rep2

tag: cell line

value: BJ

value: Human skin fibroblast cell


title: WT, KTC replicate2

description:
Library name: WTK2
MD5 Checksums.xls

value: Mycelium

tag: treatment


title: cfDNA_I_3

description: Library name: CEG1451-SY01-D977-003


title: BJ sgRNA-PURPL#1,rep1

description: Library name: sgRNA-PURPL#1,rep1


title: WT, KTC replicate1

description:
Library name: WTK1
MD5 Checksums.xls


title: reference_001, reference, rep50

description:
Library name: 02_08_31_17
library name V2: 02_08_31_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma shipment_batch

tag: sample cohort

value: reference

tag: rna-seq date


title: WT, control replicate2

description:
Library name: WTC2
MD5 Checksums.xls


title: WT, control replicate3

description:
Library name: WTC3
MD5 Checksums.xls


title: BJ sgCtrl,rep1

description: Library name: sgCtrl,rep1


title: CellsOnly_001, CellsOnly, rep9

description:
Library name: 21_08_23_17
library name V2: 21_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 018

value: CellsOnly

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F1283_001, preAD, rep1

description:
Library name: 22_08_23_17
library name V2: 22_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

value: 5% plasma, 6 h

value: human

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma class


title: cfDNA_IV_2

description: Library name: CEG1407-SY01-D894-006

tag: tissue


title: KO, control replicate1

description:
Library name: KOC1
MD5 Checksums.xls

tag: genotype

value: cax-4 knockout

value: No treatment


title: F1881_001, normal, rep1

description:
Library name: 20_08_23_17
library name V2: 20_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: #N/A

tag: sequencing plate_name


title: WT, control replicate1

description:
Library name: WTC1
MD5 Checksums.xls

tag: treatment


title: cfDNA_I_1

description: Library name: CEG1407-SY01-D894-001

value: cfDNA


title: BJ P11_DMSO,rep2

description: Library name: P11_DMSO,rep2

data_processing:
For RNA-seq analysis, quality control of the raw data was performed using FastQC (v0.11.9). Sequencing adapters were subsequently removed using Cutadapt (v3.3). The trimmed reads were aligned to the human reference genome hg38 (GRCh38.p13) using HISAT2 (v2.1.0) with default parameters. The aligned reads were converted to BAM format and sorted using SAMtools (v1.11). The sorted aligned reads were quantified using Subread featureCounts (v2.0.1) based on the GENCODE v40 annotation. Genes with a total raw count greater than 18 across the three replicates in both the treatment and control groups (i.e., an average of at least 3 counts per sample) were retained for further analysis to filter out lowly expressed genes. Differentially Expressed Genes (DEGs) using DESeq2 (v1.34.0) with threshold: log2-transformed fold change ≥ 0.75 and Adjust P-values < 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include RNA-seq three biological replicates raw counts for each sample in BJ cells

tag: cell line


title: BJ sgCtrl,rep2

description: Library name: sgCtrl,rep2


title: CellsOnly_001, CellsOnly, rep8

description:
Library name: 19_08_23_17
library name V2: 19_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma shipment_batch

tag: sample cohort

tag: rna-seq date


title: F1416_003, nonAD, rep1

description:
Library name: 18_08_23_17
library name V2: 18_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BJ sgCtrl,rep3

description: Library name: sgCtrl,rep3

tag: cell type


title: MN_H9

city: Xi 'an

first: Kun

last: Chen

address: No.169 Changle West Road

institute: Fourth Military Medical University

description: Library name: MN_H9

data_processing:
fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: FASTQ\EXCEL

source_name: MN

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. 1 ug of total RNA was used for the construction of sequencing libraries.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.

value: MN


title: BJ P11_DMSO,rep3

description: Library name: P11_DMSO,rep3


title: cfDNA_CONTROL_1

description: Library name: CEG1407-SY01-D894-007

tag: tissue


title: MN_H4B

description: Library name: MN_H4B


title: SKMEL28, ctrl, rep2B, simulation

city: Amsterdam

first: Arno

last: Velds

address: Plesmanlaan 121

department: Genomics Core Facility

country: Netherlands

institute: The Netherlands Cancer Institute

description:
Library name: SKMEL28_ctrl_2A_SIM
Simulation run using the bulkl recording of the RNA002 run

data_processing:
RNA004  POD5 files were basecalled using Dorado version 0.8.0 using rna004_130bps_hac@v5.1.0 cobined with m5C, inosine_m6A and pseU modifications. RNA002 data was live basecalled using the SUP model in MinKNOW 23.11.7
Reads were aligned to the tRNA reference fille using BWA-mem using the following settings "-t8 -Y -h30,200 -W13 -k6 -xont2d -T20 -u" from the bam source using a helper program available from
Read mapping quality adjustment and tRNA quantification was performed using trnamaprecal available from
Modification pileups were generated using modkit version 0.4.1 (https://github.com/nanoporetech/modkit) with the following settings: "--chunk-size 1 --num-reads 500000 --filter-percentile .4 --max-depth 100000"
Assembly: hg19
Supplementary files format and content: -counts-q4.txt files. TAB separated filles containing the counts for the different tRNA reference sequences grouped by mapping quality. Only reads with a quality score >= 4.0 are used.
Supplementary files format and content: -mod-q4-q1.bed - Modkit pileup of modification data using modkit v0.4.1. Only reads with a quality score > 4.0 and a mapping quality >= 1 are used.
Supplementary files format and content: codon counts are generated by summing the mapq > 0 reads and the mapq == 0 reads that map to the same codon target and are represented in a table in codon-counts-raw.txt

growth_protocol: PC3 and DU145 cells were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI 1640, Gibco) supplemented with 10% fetal bovine serum (Gibco), 100 U/ml penicillin–streptomycin (Gibco). HEK293T, A375, SK-MEL-28, SNB-19, HT29 and MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum and 100 U/ml penicillin–streptomycin

extract_protocol:
For tRNA extraction, total RNA was isolated using Trizol reagent (Invitrogen), according to manufacturer’s instructions. The samples were treated with Turbo DNase (Thermo Fisher Scientific) and small RNA fraction containing tRNAs (≤200 nt) was retained using a Zymo RNA Clean and Concentrator-5 kit (Zymo Research). For deacylation, the retained fraction incubated in 50 mM Tris-HCl (pH 9.0) at 37 °C for 30 minutes and recovered using a Zymo RNA Clean and Concentrator-5 kit (Zymo Research). The tRNA profiles were confirmed using Agilent 2100 Bioanalyzer, RNA 6000 Nano assay
tRNAs libraries were prepared as previously described (figure 1a) and according to nanopore direct RNA sequencing protocols with some adjustments. The libraries were prepared using either  SQK-RNA002 kit (ONT) or SQK-RNA004 kit (ONT) and all oligos used were acquired from Integrated DNA Technologies (IDT). In short, deacylated tRNA samples were ligated to an annealed adapter set that is complementary to the 3’ NCCA tRNA overhang and contains short poly(A) tail, using T4 RNA ligase 2 (New England Biolabs) for 2h at room temperature Then, DNA oligonucleotides with identical sequence to ONT RTA adapters were annealed and ligated using T4 DNA ligase (New England Biolabs) for 30 minutes at room temperature. The ligated tRNA samples were converted into cDNA using Maxima H Minus Reverse Transcriptase cDNA synthesis kit (Life Technologies). After each ligation step, annealed tRNAs were cleaned and recovered using CleanNGS kit (CNGS-0050, GC biotech) according to the manufacturer protocol, measured on nanodrop and their profiles were confirmed using Agilent 2100 Bioanalyzer, Small RNA analysis (Supplementary figure S1a). Finally, the samples were ligated to either ONT RMX sequencing adapters according to SQK-RNA002 kit (ONT) protocol or to RNA Ligation Adapter (RLA) according to SQK-RNA004 kit (ONT) and recovered using CleanNGS kit (CNGS-0050, GC biotech). The library was prepared for loading according to protocol then loaded on the appropriate RNA MinION Flow Cell (RNA002 or RNA004). Simulation runs were performed on the bulk recorded data of the RNA002 flow cells

treatment_protocol: Arginine deiminase (ADI) was used at a final concentration of 250ng/ml and etoposide (Selleckchem) was used at a final concentration of 10μM. All treatments were given for 48 hours before downstream analyses.

value: control

tag: batch


title: F1687_001, nonAD, rep1

description:
Library name: 17_08_23_17
library name V2: 17_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma class

value: pass


title: MN_1A6

description: Library name: MN_1A6


title: SKMEL28, ctrl, rep1A, simulation

description:
Library name: SKMEL28_ctrl_1A_SIM
Simulation run using the bulkl recording of the RNA002 run

tag: cell line

tag: treatment


title: BJ P11_DOX_50ngml,rep3

description: Library name: P11_DOX_50ngml,rep3

value: BJ


title: F985_004, preAD, rep1

description:
Library name: 16_08_23_17
library name V2: 16_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma shipment_batch

tag: sample cohort

tag: sequencing plate_name


title: A375, ctrl, rep1B, simulation

description:
Library name: A375_ctrl_2A_SIM
Simulation run using the bulkl recording of the RNA002 run


title: BJ P11_DOX_50ngml,rep2

description: Library name: P11_DOX_50ngml,rep2

value: Human skin fibroblast cell


title: BJ P11_DMSO,rep1

description: Library name: P11_DMSO,rep1


title: BJ P11_DOX_50ngml,rep1

description: Library name: P11_DOX_50ngml,rep1


title: F1850_001, normal, rep1

description:
Library name: 15_08_23_17
library name V2: 15_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rna-seq date


title: SKMEL28, ctrl, rep2B

description: Library name: SKMEL28_ctrl_2A

tag: batch


title: MNP_1A6

description: Library name: MNP_1A6

source_name: MNP

tag: cell type

value: MNP


title: MNP_H4B

description: Library name: MNP_H4B


title: SKMEL28, ctrl, rep1A

description: Library name: SKMEL28_ctrl_1A


title: MNP_H9

description: Library name: MNP_H9


title: reference_001, reference, rep49

description:
Library name: 14_08_23_17
library name V2: 14_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: reference

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BJ P33,rep3

description: Library name: P33,rep3

tag: cell line


title: F249_004, preAD, rep1

description:
Library name: 13_08_23_17
library name V2: 13_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: rna-seq covance/genewiz_id

tag: plasma class


title: A375, ctrl, rep1A, simulation

description:
Library name: A375_ctrl_1A_SIM
Simulation run using the bulkl recording of the RNA002 run

tag: treatment


title: BJ P33,rep2

description: Library name: P33,rep2


title: iPSC_H9

description: Library name: iPSC_H9

source_name: iPSC

value: iPSC


title: A375, ctrl, rep1B

description: Library name: A375_ctrl_2A


title: BJ P33,rep1

description: Library name: P33,rep1


title: A375, ctrl, rep1A

description: Library name: A375_ctrl_1A


title: CellsOnly_001, CellsOnly, rep7

description:
Library name: 11_08_23_17
library name V2: 11_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

value: no plasma, 6 h

value: Aim 2 Batch 018

tag: plasma shipment_batch

tag: sample cohort

tag: sequencing plate_name


title: iPSC_H4B

description: Library name: iPSC_H4B


title: F1977_001, normal, rep1

description:
Library name: 12_08_23_17
library name V2: 12_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: cfDNA_IV_1

description: Library name: CEG1407-SY01-D894-005

tag: tissue


title: F250_004, preAD, rep1

description:
Library name: 10_08_23_17
library name V2: 10_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: 5% plasma, 6 h

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rna-seq date


title: SNB19, etop, rep1

description: Library name: SNB19_etop_1

tag: cell line

tag: batch


title: BJ P30,rep3

description: Library name: P30,rep3


title: SNB19, etop, rep2

description: Library name: SNB19_etop_2


title: BJ P30,rep1

description: Library name: P30,rep1


title: BJ P30,rep2

description: Library name: P30,rep2


title: iPSC_1A6

description: Library name: iPSC_1A6


title: F1346_001, normal, rep1

description:
Library name: 08_08_23_17
library name V2: 08_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: human

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma class

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: SCCE-P1

city: Shijiazhuang

first: Xiaolei

last: Yin

address: No. 169, Tianshan Road

institute: Fourth Hospital of Hebei Medical University

description: Library name: SCCE-P1

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with Cell Ranger v7.0.1 (10x Genomics) using the multi pipeline and the Human Transcriptome Probe Set reference. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis  of our  single  cell RNA-seq  data .All functions were run with default parameters, unless specified otherwise. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression  of mitochondria  genes  was  calculated  using  PercentageFeatureSet  function  of  the seurat package  . To remove low activity cells, cells with more than  10 percent expression of mitochondria  genes  were  excluded.  The  normalized  data  (NormalizeData  function  in  Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying‘anchors ’between datasets using.  FindIntegrationAnchors and IntegrateData in the seurat package. Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the  clusters  on  a 2D map produced with  t-distributed  stochastic neighbor embedding (t-SNE). Identification of cell types and subtypes by nonlinear dimensional reduction (t-SNE) Cells were  clustered using  graph-based  clustering  of the  PCA reduced  data with  the  Louvain Method after computing a shared nearest neighbor graph. For sub-clustering, we applied the same procedure  of scaled,  dimensionality reduction,  and  clustering  to the  specific  set  of data (usually restricted to one type of cell.)    For each cluster, we used the Wilcoxon Rank-Sum Test to find significant deferentially expressed genes comparing the remaining clusters. SingleR and known marker genes were used to identify cell type.
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed data files include a digital gene expression matrix (matrix.mtx.gz), barcodes (barcodes.tsv.gz), and features (features.tsv.gz).

molecule: nuclear RNA

source_name: esophagus

extract_protocol:
50 μm FFPE curls were dissociated with the Bioyou® Nuclei lsolation Kit for FFPE Tissue (52301-10, Shanghai Biotechnology Corporation). Approximately 600,000 nucleus were washed, counted, and resuspended, loading 16,000 nucleus per each of four GEM wells (targeting 10,000 recovered cells) on a single Chromium X chip. Sequencing libraries were generated following the User Guide (CG000477). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). Libraries were sequenced on an Illumina NovaSeq6000 (Illumina) using 2x150 chemistry.
50 μm FFPE curls were dissociated with the Bioyou® Nuclei lsolation Kit for FFPE Tissue (52301-10, Shanghai Biotechnology Corporation). Approximately 600,000 nucleus were washed, counted, and resuspended, loading 16,000 nucleus per each of four GEM wells (targeting 10,000 recovered cells) on a single Chromium X chip. Sequencing libraries were generated following the User Guide (CG000477). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). Libraries were sequenced on an Illumina NovaSeq6000 (Illumina) using 2x150 chemistry.

value: esophagus

value: primary tumor cells


title: SNB19, ctrl, rep2

description: Library name: SNB19_ctrl_2

tag: treatment


title: SNB19, ctrl, rep1

description: Library name: SNB19_ctrl_1


title: BJ P24,rep3

description: Library name: P24,rep3


title: SCCE-P3

description: Library name: SCCE-P3


title: SCCE-P2

description: Library name: SCCE-P2


title: F121_004, normal, rep1

description:
Library name: 07_08_23_17
library name V2: 07_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma shipment_batch

tag: sample cohort

value: #N/A

tag: sequencing plate_name


title: 20240621_C_HTO

city: Copenhagen N

first: NNF CBMR

last: Single-Cell Omics Platform

address: Blegdamsvej 3B

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description:
Library name: 20240621_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
Binary base call (BCL) sequence files were demultiplexed into FASTQ files using BCL Convert v4.0.3.
Reads were pseudoaligned using Salmon Alevin v1.10.3 with the flags --read-geometry 2[1-15] --bc-geometry 1[1-16] --umi-geometry 1[17-26] set.
RNA libraries were pseudoaligned to the GENCODE vM33 reference transcriptome, distinguishing between spliced and unspliced transcripts. Alevin-fry v0.9.0 was used to quantify both the RNA and HTO libraries.
Assembly: mm10/hg39
Supplementary files format and content: mtx file with read counts
Supplementary files format and content: barcodes.txt file with 10x droplet barcodes
Supplementary files format and content: features.txt gene IDs
Supplementary files format and content: feature_README.txt containes sample/HTO information and treatment groups for samples
Supplementary files format and content: barcode_data.csv.gz information on individual barcodes
Library strategy: CITE-seq

molecule: protein

source_name: Skeletal muscle

extract_protocol:
The injured part (medial part) of the gastrocnemius muscle as previously confirmed by immunohistochemistry was dissected, minced and transferred to 1.5 ml nonstick tubes containing 1.5 ml of lysis buffer (Pure lysis buffer [L9286-180 ml; Sigma], 0.1% DTT [43816-10 ml; Sigma] and 1% Triton [T1565-1.7 ml; Sigma]). Samples were resuspended for 5 min in an ice box and centrifuged for 5 minutes at 750g and 4°C using rotor swing arms. The supernatant was removed, and the pellet was resuspended in 1 ml nuclei buffer (PBS, 10% BSA (SRE0036-25 ml; Sigma), 1M MgCl₂ [M1028-100 ml; Sigma] and 0.1 % Protector RNase inhibitor 40 U/μl [3335399001; Sigma]). Samples were then filtered through a 40 μm strainer (43-10040-40; pluriSelect) into a 1.5 ml tube and incubated on ice for 10 minutes. After incubation, samples were centrifuged for 5 minutes at 750g and 4°C. The supernatant was removed, and the pellet was resuspended in 100 µl nuclei buffer. Each sample received 1 µl of individual TotalSeq-A antibodies (BioLegend) from 0.5 μg/μl stocks to enable multiplexing. Samples were incubated on ice for 30 minutes. Following this, 1 ml nuclei buffer was added, and the samples were centrifuged for 10 minutes at 1000g and 4°C. The supernatant was discarded, and the pellet was resuspended in 200 µl nuclei buffer for fluorescence-activated cell sorting (FACS) and library preparation.
snRNA-seq was performed by the Single-Cell Omics platform at the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, using the 10x Genomics Chromium single-cell 3′ reagent kit. Libraries were sequenced on an Illumina NovaSeq 6000.

treatment_protocol: Twelve-week-old male C57BL/6NCrl mice were randomly assigned to an injury protocol consisting of 30 electrically-evoked lengthening contractions or to a control procedure (i.e., no lengthening contractions). Experiments started at day 0 with an initial torque measurement immediately followed by the injury or control protocol. Torque production was measured before and 2, 4, 7, 14, and 28 days after injury. Gastrocnemius muscle was collected for single-nucleus RNA sequencing (snRNA-seq) analysis.

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

value: Mixed sample (day 0 - 14)

tag: batch within_date

value: C

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type

value: HTO


title: F1335_001, preAD, rep1

description:
Library name: 06_08_23_17
library name V2: 06_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rna-seq date

value: pass


title: BJ P24,rep2

description: Library name: P24,rep2

tag: cell line

value: BJ

value: Human skin fibroblast cell


title: SKMEL28, ctrl, rep1

description: Library name: SKMEL28_ctrl_1

tag: treatment

value: control

tag: batch


title: BJ P24,rep1

description: Library name: P24,rep1


title: 20240621_B_HTO

description:
Library name: 20240621_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

tag: date of_reaction

tag: batch within_date

value: B

tag: sample state


title: F44_004, normal, rep1

description:
Library name: 05_08_23_17
library name V2: 05_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: Aim 2 Batch 018

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BJ P11,rep3

description: Library name: P11,rep3

tag: cell line


title: 20240621_A_HTO

description:
Library name: 20240621_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: treatment

value: A

tag: included samples

tag: included htos

tag: library type


title: SKMEL28, ADI, rep1

description: Library name: SKMEL28_ADI_1

tag: batch


title: F338_004, normal, rep1

description:
Library name: 09_08_23_17
library name V2: 09_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rna-seq date


title: F51_004, normal, rep1

description:
Library name: 04_08_23_17
library name V2: 04_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: SKMEL28, ADI, rep2

description: Library name: SKMEL28_ADI_2

tag: cell line

tag: treatment


title: F863_006, normal, rep1

description:
Library name: 03_08_23_17
library name V2: 03_08_23_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240621_C_mRNA

description:
Library name: 20240621_C_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

tag: date of_reaction

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: BJ P11,rep1

description: Library name: P11,rep1

tag: cell type


title: F1950_001, normal, rep1

description:
Library name: 22_08_18_17
library name V2: 22_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 017

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: #N/A

tag: rna-seq date

value: RNASeq QC


title: BJ P11,rep2

description: Library name: P11,rep2

tag: cell line


title: 20240621_B_mRNA

description:
Library name: 20240621_B_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

tag: sample state


title: PC3, TYW2, KO, rep2

description: Library name: PC3_TYW2_KO_2

tag: batch


title: SKMEL28, ctrl, rep2

description: Library name: SKMEL28_ctrl_2


title: PC3, TYW2, KO, rep1

description: Library name: PC3_TYW2_KO_1


title: F852_004, preAD, rep1

description:
Library name: 21_08_18_17
library name V2: 21_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BJ P3,rep2

description: Library name: P3,rep2

tag: cell line


title: 20240620_C_HTO

description:
Library name: 20240620_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

value: C

value: frozen

tag: included samples

tag: included htos

tag: library type

value: HTO


title: PC3, ctrl, rep2

description: Library name: PC3_ctrl_2

tag: treatment


title: F671_004, normal, rep1

description:
Library name: 20_08_18_17
library name V2: 20_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date

value: pass


title: 20240621_A_mRNA

description:
Library name: 20240621_A_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: tissue

tag: date of_reaction

tag: batch within_date

tag: sample state


title: BJ P3,rep1

description: Library name: P3,rep1

tag: cell line

value: BJ

tag: cell type

value: Human skin fibroblast cell


title: F1228_004, MCI, rep1

description:
Library name: 19_08_18_17
library name V2: 19_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: PC3, ctrl, rep1

description: Library name: PC3_ctrl_1

tag: treatment

value: control

tag: batch


title: 20240620_A_HTO

description:
Library name: 20240620_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

value: A

tag: included samples

tag: included htos

tag: library type


title: HT29, TYW2, rep2

description: Library name: HT29_TYW2_2


title: Hela2

source_name: Human uterus

growth_protocol: Hela cells were cultured in DMEM high glucose (GIBCO) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin and 100 μg/mL of streptomycin. Cells were kept under standard 37 ℃ and 5% CO2 conditions

treatment_protocol: Hela cells were subjected to different strategies of AMOUR, WGA-Pd,WGA-T, and RT-Amp to profile surface RNAs.

tag: tissue

value: uterus

value: Hela

tag: genotype

value: WT


title: F499_003, normal, rep1

description:
Library name: 18_08_18_17
library name V2: 18_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

value: 5% plasma, 6 h

value: human

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date


title: Hela1

tag: cell line


title: 20240618_B_HTO

description:
Library name: 20240618_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: date of_reaction

tag: treatment

tag: batch within_date

value: B

tag: sample state


title: inVivo_mm_WT_3

city: Philadelphia

first: Michael

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

description: Library name: inVivo_mm_WT_3

data_processing:
Reads were mapped to the mouse GRCm38 (mm10) reference genome using STAR (v.2.5.1b). Raw read counts were generated with STAR using the GeneCounts function. Differential expression in RNA-seq was analyzed using the R package DESeq2 (Love et al. 2014).
Assembly: mm10
Supplementary files format and content: ReadsPerGene.out.tab

source_name: Bone marrow

extract_protocol:
RNA was extracted from indicated cell populations using the Zymo Direct-zol RNA MicroPrep kit.
RNA sequencing was performed by Novogene using polyA enrichment and sequencing on a Novoseq X (20M reads/sample).

value: Bone marrow

value: HSPC


title: F1380_001, normal, rep1

description:
Library name: 17_08_18_17
library name V2: 17_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: Aim 2 Batch 017

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BJ P3,rep3

description: Library name: P3,rep3

tag: cell type


title: HT29, TYW2, rep1

description: Library name: HT29_TYW2_1

tag: batch


title: inVivo_mm_WT_2

description: Library name: inVivo_mm_WT_2

tag: tissue


title: HT29, ctrl, rep2

description: Library name: HT29_ctrl_2


title: F498_003, normal, rep1

description:
Library name: 16_08_18_17
library name V2: 16_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date


title: HT29, ctrl, rep3

description: Library name: HT29_ctrl_3

tag: cell line

tag: treatment


title: 20240614_C_HTO

description:
Library name: 20240614_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

value: Skeletal muscle

tag: date of_reaction

value: Mixed sample (day 0 - 14)

tag: batch within_date

value: C

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type

value: HTO


title: HT29, ctrl, rep1

description: Library name: HT29_ctrl_1

value: control

tag: batch


title: 20240620_B_HTO

description:
Library name: 20240620_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: tissue


title: DU145, etop, rep2

description: Library name: DU145_etop_2


title: F573_004, normal, rep1

description:
Library name: 13_08_18_17
library name V2: 13_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: F639_004, preAD, rep1

description:
Library name: 15_08_18_17
library name V2: 15_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date


title: inVivo_mm_Taf5l_SgRNA2_2

description: Library name: inVivo_mm_Taf5l_SgRNA2_2

tag: tissue

tag: cell type


title: reference_001, reference, rep48

description:
Library name: 14_08_18_17
library name V2: 14_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: reference


title: inVivo_mm_Taf5l_SgRNA1_3

description: Library name: inVivo_mm_Taf5l_SgRNA1_3


title: DU145, etop, rep1

description: Library name: DU145_etop_1

tag: cell line

tag: treatment

tag: batch


title: 20240620_C_mRNA

description:
Library name: 20240620_C_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: F811_004, preAD, rep1

description:
Library name: 12_08_18_17
library name V2: 12_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: RNASeq QC


title: inVivo_mm_Taf5l_SgRNA1_1

description: Library name: inVivo_mm_Taf5l_SgRNA1_1

tag: tissue

tag: cell type


title: 20240620_B_mRNA

description:
Library name: 20240620_B_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

tag: included samples


title: CellsOnly_001, CellsOnly, rep6

description:
Library name: 11_08_18_17
library name V2: 11_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: no plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma shipment_batch

value: CellsOnly

tag: rna-seq date


title: DU145, ctrl, rep2

description: Library name: DU145_ctrl_2

tag: cell line

tag: batch


title: inVivo_mm_WT_1

description: Library name: inVivo_mm_WT_1

tag: tissue

value: Bone marrow

tag: cell type

value: HSPC


title: F1409_001, preAD, rep1

description:
Library name: 10_08_18_17
library name V2: 10_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

value: Aim 2 Batch 017

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240614_B_HTO

description:
Library name: 20240614_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

value: Skeletal muscle

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

value: B

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: DU145, ctrl, rep1

description: Library name: DU145_ctrl_1

tag: cell line

value: control

tag: batch


title: 20240618_B_mRNA

description:
Library name: 20240618_B_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: tissue

value: frozen


title: F318_003, normal, rep1

description:
Library name: 09_08_18_17
library name V2: 09_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma shipment_batch

tag: rna-seq date

value: pass


title: 20240620_A_mRNA

description:
Library name: 20240620_A_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: treatment

tag: batch within_date

value: A

tag: sample state

tag: included samples

tag: included htos

value: mRNA


title: inVivo_mm_Tada2b_SgRNA2_3

description: Library name: inVivo_mm_Tada2b_SgRNA2_3

tag: tissue

tag: cell type


title: 20240618_A_HTO

description:
Library name: 20240618_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: library type

value: HTO


title: 20240614_A_HTO

description:
Library name: 20240614_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: inVivo_mm_Tada2b_SgRNA2_2

description: Library name: inVivo_mm_Tada2b_SgRNA2_2


title: A375, URM1, KO, rep1

description: Library name: A375_URM1_KO_1

tag: cell line

tag: batch


title: 20240618_A_mRNA

description:
Library name: 20240618_A_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: A375, URM1, KO, rep2

description: Library name: A375_URM1_KO_2


title: inVivo_mm_Tada2b_SgRNA1_2

description: Library name: inVivo_mm_Tada2b_SgRNA1_2


title: F645_004, preAD, rep1

description:
Library name: 08_08_18_17
library name V2: 08_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240614_C_mRNA

description:
Library name: 20240614_C_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

value: C

tag: sample state

tag: included samples

tag: included htos


title: A375, TYW2, KO, rep2

description: Library name: A375_TYW2_KO_2

tag: cell line

tag: batch


title: 20240614_B_mRNA

description:
Library name: 20240614_B_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: library type


title: A375, ctrl, rep2

description: Library name: A375_ctrl_2


title: F98_003, normal, rep1

description:
Library name: 07_08_18_17
library name V2: 07_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma shipment_batch

tag: rna-seq date


title: 20240614_A_mRNA

description:
Library name: 20240614_A_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

tag: included samples


title: inVivo_mm_Tada2b_SgRNA1_1

description: Library name: inVivo_mm_Tada2b_SgRNA1_1

value: Bone marrow

tag: cell type


title: inVivo_mm_Tada2b_SgRNA1_3

description: Library name: inVivo_mm_Tada2b_SgRNA1_3

value: HSPC


title: F287_003, normal, rep1

description:
Library name: 05_08_18_17
library name V2: 05_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: A375, TYW2, KO, rep1

description: Library name: A375_TYW2_KO_1

tag: cell line

tag: batch


title: 20240613_C_HTO

description:
Library name: 20240613_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

tag: included htos

tag: library type


title: inVivo_mm_Rosa26_sgRNA_2

description: Library name: inVivo_mm_Rosa26_sgRNA_2


title: F496_003, normal, rep1

description:
Library name: 04_08_18_17
library name V2: 04_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 017

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma shipment_batch

tag: rna-seq date


title: inVivo_mm_Rosa26_sgRNA_3

description: Library name: inVivo_mm_Rosa26_sgRNA_3

tag: cell type


title: A375, ADI, rep2

description: Library name: A375_ADI_2

tag: treatment


title: A375, ctrl, rep1

description: Library name: A375_ctrl_1


title: 20240613_B_HTO

description:
Library name: 20240613_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: date of_reaction

tag: batch within_date

tag: sample state

tag: included samples


title: A375, ADI, rep1

description: Library name: A375_ADI_1

tag: cell line

tag: batch


title: inVivo_mm_Tada2b_SgRNA2_1

description: Library name: inVivo_mm_Tada2b_SgRNA2_1

tag: tissue


title: 20240613_A_HTO

description:
Library name: 20240613_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: included htos

tag: library type


title: reference_001, reference, rep47

description:
Library name: 02_08_18_17
library name V2: 02_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

value: reference

tag: sequencing plate_name

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: WT_Tada2b_2_KO_sgRNA2

description: Library name: WT_Tada2b_2_KO_sgRNA2

tag: cell type


title: F773_003, normal, rep1

description:
Library name: 03_08_18_17
library name V2: 03_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma shipment_batch

tag: rna-seq date


title: 20240612_B_HTO

description:
Library name: 20240612_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: F55_003, preAD, rep1

description:
Library name: 01_08_18_17
library name V2: 01_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class


title: 231, TYW2, rep2

description: Library name: 231_TYW2_2

tag: cell line

value: control

tag: batch


title: 20240612_A_HTO

description:
Library name: 20240612_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

value: frozen


title: CellsOnly_001, CellsOnly, rep5

description:
Library name: 24_08_02_17
library name V2: 24_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

value: no plasma, 6 h

value: Aim 2 Batch 016

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma shipment_batch

value: CellsOnly

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240610_B_HTO

description:
Library name: 20240610_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: B

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: HTO


title: Taf5l_g3_1

description: Library name: Taf5l_g3_1


title: 231, ctrl, rep2

description: Library name: 231_ctrl_2

tag: cell line

tag: batch


title: 20240610_A_HTO

description:
Library name: 20240610_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

tag: date of_reaction

value: A


title: 231, ctrl, rep1

description: Library name: 231_ctrl_1

tag: treatment


title: F2045_001, normal, rep1

description:
Library name: 22_08_02_17
library name V2: 22_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

value: pass


title: Taf5l_g1_4

description: Library name: Taf5l_g1_4

value: Bone marrow

value: HSPC


title: inVivo_mm_Rosa26_sgRNA_1

description: Library name: inVivo_mm_Rosa26_sgRNA_1


title: 20240613_C_mRNA

description:
Library name: 20240613_C_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: batch within_date

value: C

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: F741_004, normal, rep1

description:
Library name: 06_08_18_17
library name V2: 06_08_18_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

value: Aim 2 Batch 017

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma shipment_batch

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Taf5l_g1_1

description: Library name: Taf5l_g1_1

tag: tissue

tag: cell type


title: non (control)  irradiated and XRT

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

description: Library name: DIA4

data_processing:
scRNA-seq: cwl-runner v.2.0 was used to obtain counts
Samples are tagged with sample tag (see feature Readme)
Assembly: hg38
Supplementary files format and content: barcodes, features, matrix contain the raw unfiltered data as result from Rhapsodys cwl runner v2.0
Supplementary files format and content: rds file contains the filtered cells already as Seurat object, feature_readme contains the single sample_tag assignment

source_name: lung

extract_protocol:
BD Rhapsody per protocol on one lane
Library was performed according to the manufacturer’s instructions

treatment_protocol: epithelial-fibroblast spheroids were cultured under standard conditions, irradiated and total RNA was isolated prior RNAseq, for scRNAseq lung organoids were enzymatically digested and sc analyses were perfomed (non-irradiated and irradiated condition) and

value: lung

tag: cell line

value: HBEC3-KT/ HS-5

value: various lung cell types

tag: genotype

value: unknown

tag: treatment

value: Control plus XRT


title: Tada2b_g3_4

description: Library name: Tada2b_g3_4


title: 20240613_B_mRNA

description:
Library name: 20240613_B_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

value: Skeletal muscle

tag: date of_reaction

value: Mixed sample (day 0 - 14)

value: B

value: frozen


title: F62_007, preAD, rep1

description:
Library name: 20_08_02_17
library name V2: 20_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 016

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

value: low RIN

value: pass


title: Taf5l_g3_3

description: Library name: Taf5l_g3_3

tag: tissue

value: Bone marrow

value: HSPC


title: Tada2b_g3_3

description: Library name: Tada2b_g3_3

tag: cell type


title: F1557_002, nonAD, rep1

description:
Library name: 19_08_02_17
library name V2: 19_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma shipment_batch

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 231, TYW2, rep1

description: Library name: 231_TYW2_1

tag: cell line

tag: treatment

value: control

tag: batch