description: Library name: p22286_s014_DHIX_Male_20_21_Group_1_D8_Post_ATI


status: Public on Sep 10 2025

type: SRA

city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

country: USA

institute: Beth Israel Deaconess Medical Center

description: Library name: p22286_s009_DHIX_Male_20_21_Group_1_D2_Post_ATI

library_source: transcriptomic

data_processing:
The quality of the raw reads was assessed using multiQC39. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Data were aligned to the Mmul10-100 assembly and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a.
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
Assembly: Mmul10-100
Supplementary files format and content: siv-reservoir-biomarkers-rawCounts.csv (raw RNA sequencing counts)
Supplementary files format and content: siv-reservoir-biomarkers-normalizedCounts.csv (normalized RNA sequencing counts)

molecule: total RNA

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood samples using the PAXgene Blood RNA Kit IVD (PreAnalytix).
RNA quality was assessed with the Fragment Analyzer (Agilent) and its Standard Sensitivity RNA kit. Total RNA was normalized to 100 ng before random hexamer priming and libraries were generated by the TruSeq Stranded Total RNA—Globin kit (Illumina). The resulting libraries were assessed on the Fragment Analyzer (Agilent) with the High Sense Large Fragment kit and quantified using a Qubit 3.0 fluorometer (Life Technologies). Medium-depth sequencing, with at least 30 million reads per sample, was performed on a NextSeq 500 (Illumina) with a PE100 configuration, paired-end run yielding ~40 million reads per sample.

tag: tissue

value: Whole blood

tag: animal id

value: DHIX

tag: Sex

value: Male

tag: batch

value: BatchA

tag: viral loads_(cp/ml)


title: AD1_CELL

city: Novato

last: Winer

state: CA

address: 8001 Redwood Blvd, Novato, CA 94945

institute: Buck Institute for Research on Aging

description: Library name: AD1_CELL

library_source: other

data_processing:
Raw sequencing data were first processed into a count table of amplicon sequence variants (ASVs) using standard pipelines. This table was then imported into phyloseq in R for downstream analysis. Within phyloseq, relative abundance was calculated on a per-sample basis by dividing the raw counts for each ASV (or higher-level taxonomic grouping, when agglomerated) by the total sequencing depth of that sample. For example, if a sample contained 20,000 total reads and 2,000 of those were assigned to a given ASV, the relative abundance of that ASV would be 2,000   20,000 = 0.10 (10%).
This procedure was applied across all samples to generate a relative abundance matrix, where the values for each sample sum to 1. These relative abundances were then used for downstream statistical analyses and visualization of microbial community.
Assembly: RDP training set (v18)
Supplementary files format and content: csv file of the relative abundance of biota for each sample
Library strategy: 16S rRNA-seq

molecule: other

organism: mouse gut metagenome

source_name: Stool

extract_protocol:
Fecal pellets from 15-month-old mice were subject to the Quick-DNA Fecal/Soil Microbe Microprep kit (Zymo Research. Cat.# D6012).
Sequencing libraries were generated and indexes were added to attribute sequences to each sample. Briefly, PCR amplification of targeted regions was performed by using specific primers connecting with barcodes. The PCR products with proper size were selected by 2% agarose gel electrophoresis. Same amount of PCR products from each sample was pooled, end-repaired, A-tailed and further ligated with Illumina adapters. Libraries were sequenced on a paired-end Illumina platform to generate 250bp paired-end raw reads. Subsequently, library quality was assessed and quantified by QPCR. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: Stool


title: AD1_CTRL

description: Library name: AD1_CTRL


title: Coverslip_1

type: RNA

city: Worcester

first: Travis

middle: E.

last: Faust

address: 366 Plantation Street

department: Neurobiology

institute: University of Massachusetts Chan Medical School

description: male (both samples)

hyb_protocol: The tissue was washed with DAPI and PolyT staining reagent (Vizgen 2030021) for 15 minutes, formamide wash buffer for 10 minutes, and 2X SSC for 2 minutes, all at room temperature.

scan_protocol: MERFISH imaging was performed according to Vizgen MERSCOPE instructions

data_processing:
Raw data were decoded using Vizgen's MERLIN pipeline incorporated in the MERSCOPE. Vizgen's postprocessing tool was applied to obtain the cell segmentation based on the DAPI staining by using the CellPose algorithim.
counts_and_metadata.csv files contain matrices of cell IDs as rows, genes and metadata as columns. Matrix contains raw counts of detected transcripts. Volume metadata is provided in cubic microns. X and Y metadata are provided in microns.

organism: Mus musculus

source_name: Barrel cortex

label_protocol: Tissue on coverslips was fixed for 15 minutes at room temperature in 4% paraformaldehyde in PBS, followed by three washes with PBS. Tissue was then permeabilized in 70% ethanol for 24 hours, during which time the tissue was photobleached for 3 hours to remove autofluorescence using the MERSCOPE Photobleacher (Vizgen 1010003). The tissue was then washed with PBS, and incubated with blocking solution containing 1:10 murine RNAse inhibitor (M0314L New England Biolabs) in blocking buffer (Vizgen 20300100) for 1 hour. This was followed by 1 hour of incubation with the primary antibody, purified rabbit anti-VGluT2 (Abcam 227906) diluted 1:100 in blocking solution. The tissue was then washed three times with PBS and incubated for 1 hour with an oligo-conjugated secondary anti-rabbit antibody (Vizgen 20300102), 1:100 in blocking solution containing 1:10 murine RNAse inhibitor (M0314L New England Biolabs). The sample was washed three times with PBS and fixed for 15 minutes at room temperature in 4% paraformaldehyde in PBS, followed by three washes with PBS. Next, the tissue was washed with 2X saline sodium citrate (SSC) and then formamide wash buffer (30% formamide in 2X saline sodium citrate, or SSC) for 30 minutes at 37°C. Afterwards, a custom MERFISH library mix was added and allowed to hybridize for 48 hours at 37°C in a humidified chamber. Sample was then washed and incubated at 47°C with Formamide Wash Buffer twice for 30 minutes each, and once with 2X SSC for 2 minutes at room temperature. The tissue was then embedded in a polyacrylamide gel (4% 19:1 acrylamide/bis-acrylamide, 17% 5M NaCL, 17% 1M Tris pH 8) followed by incubation with tissue clearing solution (2X SSC, 2% SDS, 0.5% v/v Triton X-100, and proteinase K 1:100) overnight at 37°C.

extract_protocol: Brains were extracted and embedded in OCT for sectioning onto specialized coverslips. Embedded brains were frozen and stored at -80°C. 10 microns coronal sections containing the barrel cortex were collected for analysis by MERFISH

treatment_protocol: Brains were isolated from P5 mice 24 hours after unilateral whisker lesioning on the right side of the mouse's snout at age P4.

tag: genotype

value: 1 wild-type sample and 1 Cx3cl1(-/-) sample

tag: age

value: Barrel cortex

tag: treatment

value: Whisker lesioning of right snout at P4

tag: timepoint

value: 24 hours after whisker lesioning


title: Coverslip_4

description: female (both samples)

value: Female


description: Library name: p22286_s008_DHIX_Male_20_21_Group_1_D0_Post_ATI_BatchB

value: BatchB


title: AD2_CTRL

description: Library name: AD2_CTRL


description: Library name: p22286_s013_DHIX_Male_20_21_Group_1_D7_Post_ATI


title: Coverslip_2

description: male (both samples)


description: Library name: p22286_s011_DHIX_Male_20_21_Group_1_D5_Post_ATI


description: Library name: p22286_s010_DHIX_Male_20_21_Group_1_D4_Post_ATI


description: Library name: p22286_s016_L604_Male_20_21_Group_2_D2_Post_ATI


description: Library name: p22286_s008_DHIX_Male_20_21_Group_1_D0_Post_ATI


title: Coverslip_3

description: female (both samples)


title: R01042RF_IDPN3w

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

country: Spain

institute: Universitat de Barcelona

description: Library name: AN0817

data_processing:
RNAseq reads were mapped to the rat reference genome (Rnor6.0) with STAR/2.5.3a with ENCODE parameters
Genes were quantified with RSEM/1.3.0 with default parameters
The gene annotation file was ensembl92
Assembly: Rnor6.0
Supplementary files format and content: text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Vestibular epithelium

extract_protocol:
Vestibular epithelia were quickly dissected in ice-cold PBS. Two utricles and six crista from each animal were pooled and stored at -80C. Total RNA was extracted using the Qiagen RNeasy mini kit and protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2014) with some modifications. Briefly, reverse transcription of the total RNA input material of 1.8 µl (6-11 ng, in function of the sample availability) was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (2x) (Roche) and 100 nM IS PCR primer (5′-AAG CAG TGG TAT CAA CGC AGA GT-3′) with 8 cycles of PCR amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), the product size distribution and the quantity were assessed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit.

treatment_protocol: Ototoxicity rats were given 20 mM of 3,3'-iminodipropionitrile (CAS# 111-94-4; >98%) in the drinking water for 3 or 7 weeks; control rats received plain drinking water.

value: Vestibular epithelium

value: male

value: Long-Evans

value: Ototoxicity 3 weeks


title: R01042LF_IDPN3w

description: Library name: AN0818


title: R01046NM_IDPN3w

description: Library name: AN0815


description: Library name: p22286_s007_DHGI_Male_20_21_Group_1_D8_Post_ATI

value: DHGI


title: R01041LF_Control

description: Library name: AN0816

value: Control


description: Library name: p22286_s006_DHGI_Male_20_21_Group_1_D7_Post_ATI

value: Whole blood


title: R01041RF_Control

description: Library name: AN0814


title: WT 24hr 3

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Library name: Sample 15

data_processing:
Adapter sequences and low quality reads were filtered by Trimmoatic
Surviving reads were aligned to reference genome using STAR aligner
Assembly: mm39
Supplementary files format and content: TAB file for gene count

molecule: polyA RNA

source_name: liver

extract_protocol:
RNA was isolated from individual WT and MET-KO mice liver samples at 0, 6, and 24hr (n=3) using the TRIzol method. The RNA samples were submitted to Novogene (Sacramento, CA) for quality verification, library preparation and RNA sequencing.
Following Illumina library prep and RNA-seq protocols.

value: liver

value: Wild-type


title: WT 24hr 2

description: Library name: Sample 14


title: KO 24hr 3

description: Library name: Sample 18

value: hepatocyte-specific MET knockout


title: KO 24hr 2

description: Library name: Sample 17


title: R01041NM_Control

description: Library name: AN0813


title: WT 24hr 1

description: Library name: Sample 13


title: KO 6hr 3

description: Library name: Sample 12


description: Library name: p22286_s004_DHGI_Male_20_21_Group_1_D5_Post_ATI

value: Male

value: BatchA


description: Library name: p22286_s005_DHGI_Male_20_21_Group_1_D6_Post_ATI


title: KO 24hr 1

description: Library name: Sample 16


title: R01043RF_IDPN7w

description: Library name: AN0812

value: Ototoxicity 7 weeks


title: R01043LF_IDPN7w

description: Library name: AN0811


title: KO 6hr 1

description: Library name: Sample 10


title: R01046LF_IDPN7w

description: Library name: AN0810


title: SC_D28_1

city: Nanjing

first: Shaoxun

last: Yuan

address: No. 138, Xianlin Avenue, Qixia District

country: China

institute: Nanjing University of Chinese Medicine

description:
SD rats
local bone tissue,28days after tibial fractures

data_processing:
The sequencing data were filtered, and the low-quality data were removed.
The clean reads of each sample were screened, and sRNA within a certain length range was selected for subsequent analysis
The distribution of small Rnas on the reference sequence was analyzed by positioning the length screened srnas to the reference sequence using bowtie
Assembly: Rattus_norvegicus.Rnor_6.0.dna_sm.toplevel.fa
Supplementary files format and content: reads count for each sample (quantitative by featureCounts )

source_name: Spinal cord

extract_protocol:
Rats were anesthetized with 2.5% isoflurane/oxygen.  Right L4-L6 spinal coad was taken from each rat, and the samples were frozen in liquid nitrogen within 3 minutes after leaving the body.  The frozen samples were crushed and dissolved in TRIzol (Invitrogen).  RNA was subsequently extracted from tissues and the RNA were subjected to strict quality control (Agilent 2100 bioanalyzer).
The reference genome is from the ensembl database (rattus_norvegicus_Ensembl_97).  Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.  After the completion of the library construction, Qubit 2.0 was used for preliminary quantification, diluting the library to 1.5ng/ul, and then Agilent 2100 was used to detect the Insert size of the library to ensure the quality of the library.  After qualified library inspection, Illumina PE150 sequencing was conducted by pooling according to effective concentration of library and data output requirements.

value: Spinal cord

tag: cell line

value: spinal cord neuron cells

value: tibial fractures

value: 28days after fracture


title: KO 6hr 2

description: Library name: Sample 11


title: SC_D28_3


description: Library name: p22286_s003_DHGI_Male_20_21_Group_1_D4_Post_ATI


title: SC_D14_3

description:
SD rats
local bone tissue,14days after fracture

value: 14days after fracture


title: SC_D28_2


title: SC_D14_1


description: Library name: p22286_s001_DHGI_Male_20_21_Group_1_D0_Post_ATI_BatchB

value: BatchB


title: WT 6hr 1

description: Library name: Sample 7


title: WT 6hr 3

description: Library name: Sample 9


description: Library name: p22286_s001_DHGI_Male_20_21_Group_1_D0_Post_ATI


title: SC_D7_1

description:
SD rats
local bone tissue,7days after fracture

value: 7days after fracture


title: WT 6hr 2

description: Library name: Sample 8


description: Library name: p22286_s001_DHGI_Male_20_21_Group_1_D0_Post_ATI_BatchC

value: BatchC


title: SC_D3_2

description:
SD rats
local bone tissue,3days after tibial fractures

value: 3days after fracture


title: SC_D7_3


title: SC_D3_1


title: Apollo Study sample 12 t2 NMP

city: Rotterdam

first: Hector

last: Tejeda Mora

address: Doctor Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

description: Library name: FS18

library_source: transcriptomic single cell

data_processing:
CellRanger (v6.0.2) was used to perform the alignment with standard parameters. The option ‘–include-introns’ was activated since the input consisted of nuclei.
Ambient RNA removal with SoupX. Bad quality cells were removed based on general QC parameters.
Data processed and integrated with Seurat, including doublet removal.
For extra methods see publication
Assembly: GRCh38
Supplementary files format and content: Normalized counts as a single tab-delimited (.txt) file from the integrated object

molecule: nuclear RNA

organism: Homo sapiens

source_name: kidney

growth_protocol: Needle kidney biopsies were collected before and afte r2-hour NMP. The biopsies were snap-frozen in liquid nitrogen and stored at –80°C.

extract_protocol:
Kidney tissues were cut in small pieces and isolated by nuclei isolation buffer (Nuclei EZ lysis buffer, N3408-200ML, Sigma-Aldrich) supplemented with Protease and RNase inhibitors. The nuclei were stained with DAPI (D9542-10MG, Sigma-Aldrich) and fluorescence-activated nuclei sorting was performed via Sony SH800 to enrich the nuclei. 18.000 to 20.000 nuclei per sample were loaded into the chromium controller (PN-120223, 10x Genomics) on a Chromium Next GEM Chip G (PN-2000177, 10x Genomics) and processed following the manufacturer’s original protocol.Quality control for the constructed library was performed using a High Sensitivity DNA Assay (5067-4626, Agilent technologies). Libraries were sequenced on NovaSeq6000 (Illumina) targeting 50,000 reads per cell.
The library construction was performed using the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (PN-1000121, 10x Genomics) and Dual Index Kit TT Set A (PN-1000215, 10x Genomics).

treatment_protocol: NMP for 2 hours

value: kidney

value: biopsy

tag: cell type

value: various kidney cell types

value: After NMP


title: SC_D7_2


title: Apollo Study sample 12 t0

description: Library name: FS17

value: Before NMP


description: Library name: p22286_s002_DHGI_Male_20_21_Group_1_D2_Post_ATI

value: Whole blood

value: DHGI

value: Male


title: SC_D0_2

description:
SD rats
Healthy rat,local bone tissue

value: Spinal cord

value: healthy rat

value: 0 day


title: SC_D3_3

value: spinal cord neuron cells

value: tibial fractures


title: KO 0hr 2

description: Library name: Sample 5

value: liver

value: hepatocyte-specific MET knockout


title: KO 0hr 3

description: Library name: Sample 6


title: KO 0hr 1

description: Library name: Sample 4


title: SC_D0_1

description:
SD rats
Healthy rat,local bone tissue


title: SC_D0_3

description:
SD rats
Healthy rat,local bone tissue


title: WT 0hr 3

description: Library name: Sample 3

value: Wild-type


title: Apollo Study sample 10 t2h NMP

description: Library name: FS16


title: SC_D14_2

value: 14days after fracture


title: Apollo Study sample 10 t0

description: Library name: FS15

value: kidney


title: GLI2 WT_2

city: 咸阳市

first: qing

last: he

state: 陕西省

address: 钓台街道西安交大创新港21号楼

institute: xi'an jiaotong university

description: Library name: GLI2 WT_2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-qualty sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
inmmed secuence reads were mapedto GrcM38lmm10 usina Clc oenomic benchwok (carameters- mismath cost.2insenion cost 3 deleton cost 3 lendh facio.. 8 simlarty faction. 0 8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: ensembl_109_danio_rerio_grcz11_primary
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: embyro

extract_protocol:
Zebrafish embryos from each group were manually dechorionated at 24 hpf and immediately used for total RNA extraction with the MiniBEST Universal RNA Extraction Kit (TaKaRa, Cat#9767).
RNA libranies for RNA-seq were prepared using SMARTER mRNA-Seg Librany Prep Kit following manufacturer's protocols.

value: embyro


title: GLI2 WT_3

address: 钓台街道西安交大创新港21号楼

description: Library name: GLI2 WT_3


title: Apollo Study sample 9 t2h NMP

description: Library name: FS14

value: biopsy

value: various kidney cell types


title: GLI2 A543G_3

address: 钓台街道西安交大创新港21号楼

description: Library name: GLI2 A543G_3

value: GLI2-A543G mRNA


title: GLI2 A543G_2

address: 钓台街道西安交大创新港21号楼

description: Library name: GLI2 A543G_2


title: WT 0hr 1

description: Library name: Sample 1


title: GLI2 WT_1

address: 钓台街道西安交大创新港21号楼

description: Library name: GLI2 WT_1


title: Cal33, Metformin, rep3

city: La Jolla

first: Kuniaki

last: Sato

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

description: Library name: Metformin_rep3

library_source: genomic

data_processing:
Next-generation sequencing read counts were processed and aligned using PinAPL-Py to obtain raw read count matrix for each sgRNA.
Raw read counts were analyzed using Mageck-MLE to identify enrichment or depletion of sgRNAs in metformin-treated versus control samples.
Assembly: hg38
Supplementary files format and content: A tab-delimed text file containing gene names, beta-values and statistics
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: The screen was performed by seeding Cal33-Cas9 cells into 245 mm × 245 mm tissue culture dishes (at a seeding density of 12 × 106 cells/plate) divided into two treatment arms: three replicate plates for either vehicle or metformin treatment. A total of 24 × 106 cells were passaged into new plates containing vehicle or 1 mmol/L metformin until the population doubling level reached 18.

extract_protocol:
Genomic DNA was extracted and purified using a QIAGEN DNeasy Blood & Tissue kit.
The human Brunello whole-genome CRISPR pooled library was a gift from David Root and John Doench (Addgene #73178). The library contains 76,441 sgRNAs targeting 19,114 genes (four sgRNAs per gene) and 1000 nontargeting sgRNAs as the negative control. The library DNA was transformed by electroporation using electrocompetent cells. The entirety of isolated genomic DNA was used for subsequent amplification through PCR to ensure capturing the full representation of the libraries. PCR products were sequenced on a HiSeq4000 instrument.

value: Head and neck cancer cell line

value: Metformin


title: Cal33, Metformin, rep1

description: Library name: Metformin_rep1


title: WT 0hr 2

description: Library name: Sample 2


title: Cal33, Metformin, rep2

description: Library name: Metformin_rep2


title: Apollo Study sample 9 t0

description: Library name: FS13

value: Before NMP


title: VCaP, siERG_2

first: Steven

last: Balk

address: 3 Blackfan circle

institute: BIDMC

description: Library name: siERG_2

data_processing:
Assembly: hg19
Raw reads were analyzed using  Visualization Pipeline for RNA-seq analysis (VIPER) based on workflow management system Snakemake
Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters
cufflinks v2.2.1 was used to generate FPKM values
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters
Supplementary files format and content: comma-separated values file includes differential gene expressions (log2(Fold Change) and statistical values)

source_name: Prostate

growth_protocol: VCaP cells (ATCC, Manassas, VA) were maintained in DMEM with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
mRNA libraries were generated using the Illumina TruSeq stranded mRNA sample kit.

value: Prostate

value: VCaP

value: prostate cancer

value: WT

value: ERG siRNA


title: Apollo Study sample 2 t2h NMP

description: Library name: FS12

value: After NMP


title: Cal33, Control, rep3

description: Library name: Control_rep3

value: Vehicle


title: Apollo Study sample 2 t0

description: Library name: FS11


title: VCaP, siCntrl_2

description: Library name: siCntrl_2

value: non-targeted siRNA


title: Cal33, Control, rep1

description: Library name: Control_rep1


title: DNT-Eto-1

city: Beijing

first: Zeyu

last: Wang

address: Gongti South Road No.8

institute: Capital medical university

data_processing:
HiSeq PE Cluster Kit v4-cBot-HS（Illumia）
RNA samples were purified, fragmented, reverse transcribed, end-repaired. After sequenced adapters were added, the target fragments were recovered by magnetic bead screening, and PCR amplification was performed to complete the entire library preparation work.
After the library construction was completed, use Agilent2100 to detect the insert size of the library.
If insert size met the expectation, Bio-RAD CFX 96 fluorescent quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN were used to perform q-PCR to accurately quantify the effective concentration of the library (the effective concentration of the library was > 10nM) to ensure the quality of the library.
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: double negative cells (DNT cells)

growth_protocol: DNT cells were maintained in 1640 medium with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% carbon dioxide at 37 ° C

extract_protocol:
DNT cells were collected after treatment with or without Etomoxir and Trizol reagent was used for collecting total RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: DNT cells were treated with or without Etomoxir 100 μM for 24 hours

value: double negative cells (DNT cells)

value: T cell

value: Etomoxir 100 μM for 24 hours


title: MC38-LM3b-shScramble

city: chengdu

first: Shufang

last: Liang

state: State...

address: chengdu

institute: sichuan university

description: Library name: Sample 1

data_processing:
Cell Ranger software (version 7.1.0) from 10x Genomics was used to align reads, with GRCm39 as the reference genome. The gene information, UMI counts, and barcode matrix obtained from Cell Ranger were used for downstream analysis with the Seurat package (version 5.1.0) in R (version 4.4.1).
Assembly: GRCm39
Supplementary files format and content: The three files obtained after aligning reads with Cell Ranger software are the matrix, genes, and barcodes files.

source_name: Liver

extract_protocol:
Cell suspensions were loaded onto a Chromium Single-Cell Chip (10x Genomics, PN-1000120)
Single-cell library preparation was carried out using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000268).

value: Liver

value: shScramble


title: Br8667_Nac-PI+

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

description: Library name: 19c_Nac_SVB

data_processing:
FASTQ and image data files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38 (10x Genomics 2020 reference version)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and fastq.gz files

source_name: nucleus accumbens

extract_protocol:
Nucleus accumbens samples were dissected from fresh frozen postmortem human brain tissue. 100 micron coronal sections were obtained by cryosectioning (about 70-100 mg of tissue). Nuclei were isolated by homogenizing tissue in Nuclei EZ Lysis Buffer, followed by filtration through a mesh strainer, and three washes. Nuclei pellets from each donor were divided into two groups, one stained with propidium iodide (PI), to select all nuclei, and the other stained with both PI and anti- NeuN antibody, to select only the neuronal nuclei. Fluorescent-activated nuclear sorting (FANS) was performed to obtain PI+ nuclei and PI+NeuN+ nuclei for each donor.
Libraries were prepared using the Chromium Next GEM Single cell 3' v3.1 (dual-index) kit according to manufacturer's instructions (CG000315, revision E, 10x Genomics)

value: nucleus accumbens

value: PI+


title: Br8667_Nac-PI+NeuN+

description: Library name: 20c_Nac_SVB

value: PI+NeuN+


title: Br6522_Nac-PI+NeuN+

description: Library name: 18c_Nac_SVB


title: GLI2 A543G_1

address: 钓台街道西安交大创新港21号楼

description: Library name: GLI2 A543G_1

value: embyro

value: GLI2-A543G mRNA


title: VCaP, siCntrl_1

description: Library name: siCntrl_1

value: Prostate

value: VCaP


title: Cal33, Control, rep2

description: Library name: Control_rep2

value: Head and neck cancer cell line


title: VCaP, siERG_3

description: Library name: siERG_3

value: prostate cancer

value: WT

value: ERG siRNA


title: DNT-Eto-2


title: DNT-Eto-3


title: VCaP, siERG_1

description: Library name: siERG_1


title: MC38-LM3b-shSLAMF3

description: Library name: Sample 2


title: TNBC_PO9

city: Bangkok

first: Pimchanok

last: Phankeaw

state: Bangkok

address: 2 Wanglang Rd., Bangkok Noi, Siriraj

department: Immunology

country: Thailand

institute: Mahidol University

description: Library name: S_TNBC_PO9_F_SP0196_P01_E02

data_processing:
TempO-Seq sequence files were analysed using the Tempo-SeqR software package. The input for TempO-Seq data analysis is a folder of zipped FASTQ files.
Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the STAR algorithm to a pseudo- transcriptome corresponding to the gene panel used in the assay.
For ProbeID, it is composed of gene name along with a numeric identifier, separated by an underscore. Some genes may have multiple ProbeIDs representing assays against isoforms that are not captured by a single probe against the region of maximal overlap of all gene isoforms.
Assembly: Based on hg38 human reference genome using BioClavis TempO-Seq transcriptome probe set.
Supplementary files format and content: Tab-delimited text file containing gene symbols in the first column and raw read counts for each sample in subsequent columns.

source_name: Breast

growth_protocol: FFPE tumor tissue obtained from breast cancer patients. No cell culture was performed.

extract_protocol:
No RNA extraction from FFPE samples
Templated oligo sequencing (TemPo-Seq) libraries were prepared using BioClavis TemPo-Seq Human Whole Transcriptome assay following the manufacturer’s instructions. RNA was hybridized to detector oligos, ligated, and PCR amplified with sample-specific barcodes.

tag: tumor budding

value: High

tag: fap expression

value: Pos

tag: survival

value: Short

value: Breast

tag: subtype

value: TNBC

value: CAF


title: TNBC_PO6

description: Library name: S_TNBC_PO6_F_SP0196_P01_C05

value: Neg

value: Long


title: VCaP, siCntrl_3

description: Library name: siCntrl_3

value: non-targeted siRNA


title: DNT-Control-2

value: double negative cells (DNT cells)

value: T cell


title: DNT-Control-3


title: Br6522_Nac-PI+

description: Library name: 17c_Nac_SVB

value: nucleus accumbens

value: PI+


title: TNBC_PO4

description: Library name: S_TNBC_PO4_F_SP0196_P01_D02


title: Br6471_Nac-PI+NeuN+

description: Library name: 16c_Nac_SVB

value: PI+NeuN+


title: DNT-Control-1


title: TNBC_G06

description: Library name: S_TNBC_G06_F_SP0196_P01_B05

value: Low


title: TNBC_G19

description: Library name: S_TNBC_G19_F_SP0196_P01_G05

value: WT


title: TNBC_G01

description: Library name: S_TNBC_G01_F_SP0196_P01_A05


title: Br6471_Nac-PI+

description: Library name: 15c_Nac_SVB


title: TNBC_G03

description: Library name: S_TNBC_G03_F_SP0196_P01_B03


title: smallRNA_seq_Kitaake_WT_2.5_3

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: Library name: 60

data_processing:
For RNAseq libraries, raw reads were mapped to the Kitaake reference genome v3.1 using HISAT2, version 2.1.1 (Kim et al., 2015). Reads mapped to individual genes were quantified using Stringtie version 2.1.4 (Pertea et. al, 2016).
We preprocessed sRNA reads using cutadapt v3.0 (cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -g GTTCAGAGTTCTACAGTCCGACGATC -u 1 -m 10 -j 0 --max-n 0 -o sequencingfile.fq ) and we quality controlled preprocessed reads using FastQC v0.12. Preprocessed reads were aligned to the Oryza sativa Kitaake genome v3.1 using bowtie alignment software v2.5.2 (bowtie2 -f -N 0 -k 1 --no-1mm-upfront --no-unal --no-sq --norc). To annotate miRNAs from the Kitaake genome, we aligned our reads to Oryza sativa miRNAs in miRbase v22.
Assembly: Kitaake v3.1
Supplementary files format and content: For RNAseq, tab-delimited files contain raw counts for each Sample
Supplementary files format and content: For sRNAseq, tab-delimited files containing raw counts for miRNAs

organism: Oryza sativa

source_name: anther

growth_protocol: Rice plant grown in greenhouse in 16 hours light at 30°C and 8 hours dark at 25°C photoperiod under neon.

extract_protocol:
Total RNA extracted from 20-30 anthers with Tri-reagent (Sigma-Aldrich). RNA precipitates at RT for one hour with glycogen.
For RNA-seq libraries, total RNA was treated with DNAase I (New England Biolabs, CA) and cleaned via precipitation. Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (no. E7765L, New England Biosystems, CA), following the manufacturer's instructions for use with the NEBNext Poly(A) mRNA magnetic isolation module. sRNA libraries were generated using the RealSeq-AC V2 Library Kit for Illumina sequencing (#500-00048, RealSeq Biosciences Inc.), following the manufacturer’s recommendations (10 ng of total RNA, adapter dilution of 1:20, and 16 PCR cycles). sRNA libraries were size selected with an end product of ~150 nt using polyacrylamide gels.

value: anther


title: Br3942_Nac-PI+NeuN+

description: Library name: 12c_NAc_SVB


title: smallRNA_seq_Kitaake_WT_2.0_3

description: Library name: 57


title: Br6432_Nac-PI+

description: Library name: 13c_NAc_SVB


title: PC_B_099

description: Library name: S_PC_B_099_F_SP0196_P01_F02

value: High


title: smallRNA_seq_Kitaake_WT_2.5_2

description: Library name: 59


title: smallRNA_seq_Kitaake_WT_2.5_1

description: Library name: 58


title: B041

description: Library name: S_B041_F_SP0196_P01_H02

value: Pos


title: B166

description: Library name: S_B166_F_SP0196_P01_E05


title: Br3942_Nac-PI+

description: Library name: 11c_NAc_SVB


title: B168

description: Library name: S_B168_F_SP0196_P01_F05


title: PC_B_130

description: Library name: S_PC_B_130_F_SP0196_P01_G02

value: Short


title: UMUC9_4h_Amb_3

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

description: Library name: Sample24

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were trimmed using BBDuk (BB Tools v38.46). The bundled adapter sequences and following parameters were used. Single-end reads: ktrim=r, mink=5, minlength=20, hdist=1. The k parameter was set to 30 or the length of the smallest adapter sequence, whichever is larger. Paired-end reads: ktrim=r, mink=11, hdist=1, k=31.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3).
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27.
Coverages were determined using bedtools 2 v2.28.0 as (1 / read length) for each base in the genome. These base coverages were used to obtain pseudo-read counts in strand-specific regions of interest using bedtools intersect. Reads Per Kilobase per Megabase of library size (RPKM) were calculated for meta-transcripts ("genes") defined by merging exons and intervening intronic spaces from all isoforms of a gene in the GENCODE v27 "basic" annotation. Genes were quantified by summing pseudo-counts falling within the features (exons and intronic spaces) and normalized by the effective gene length (sum of feature lengths) and by the size of the library (uniquely mapped read count).
Assembly: hg38
Supplementary files format and content: bed files are BED6+ regions containing gene-level quantifications. columns: 1 - chr, 2 - start, 3 - end, 4 - Ensembl gene ID, 5 - placeholder of value 0, 6 - strand (+ or -), 7 - gene symbol, 8 - effective length used to compute RPKM, 9 - pseudocounts, 10 - RPKM.
Supplementary files format and content: counts and RPKM are reported in separate matrices (tab-delimited text with headers).  Each matrix contains gene-level annotation in the first 8 columns.
Library strategy: BRU-Seq

growth_protocol: Breast cancer cell lines were cultured in Ham’s F12 supplemented with 50 uM hydrocortisone, ITES (Biowhittaker), and 5% FBS. Bladder cancer cell lines were propagated in DMEM and supplemented with 10% FBS and glutamine.

extract_protocol:
Cells were lysed directly in TRIzol followed by isolation of total RNA. Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2014; Paulsen et al., 2013). This protocol used single-index barcoded ligation adapters and universal primers for PCR. Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first strand synthesis. These strand-specific libraries were made using a universal ligation adapter and dual-index, barcoded primers for PCR. Size selection for all libraries was via agarose gel excision.

treatment_protocol: Both bladder cancer (UMUC5, UMUC9) and breast cancer (BT20, MDA231) cell lines were cultured with either vehicle (ethanol) or 10μM ambrosin for 3.5 hours. Bromouridine (Bru; Aldrich) was added to the culture media s to a final concentration of 2 mM, and cells were incubated at 37 °C for 30 min.

value: Amb


title: smallRNA_seq_Kitaake_WT_2.0_2

description: Library name: 56


title: B031

description: Library name: S_B031_F_SP0196_P01_C02

value: Breast

value: TNBC


title: Br2743_Nac-PI+NeuN+

description: Library name: 10c_NAc_SVB


title: UMUC9_4h_Amb_2

description: Library name: Sample23


title: smallRNA_seq_Kitaake_WT_2.0_1

description: Library name: 55


title: UMUC9_4h_Amb_1

description: Library name: Sample22


title: Br2743_Nac-PI+

description: Library name: 9c_NAc_SVB


title: smallRNA_seq_Kitaake_WT_1.8_3

description: Library name: 54


title: Br6432_Nac-PI+NeuN+

description: Library name: 14c_NAc_SVB


title: UMUC9_4h_Veh_2

description: Library name: Sample20

value: Veh


title: Br6423_Nac-PI+NeuN+

description: Library name: 8c_NAc_SVB


title: UMUC9_4h_Veh_1

description: Library name: Sample19


title: UMUC5_4h_Amb_3

description: Library name: Sample18


title: UMUC5_4h_Amb_2

description: Library name: Sample17


title: UMUC5_4h_Amb_1

description: Library name: Sample16


title: smallRNA_seq_Kitaake_WT_1.8_2

description: Library name: 53


title: Br2720_Nac-PI+

description: Library name: 5c_NAc_SVB


title: UMUC5_4h_Veh_2

description: Library name: Sample14


title: smallRNA_seq_Kitaake_WT_1.8_1

description: Library name: 52


title: UMUC5_4h_Veh_1

description: Library name: Sample13


title: Br2720_Nac-PI+NeuN+

description: Library name: 6c_NAc_SVB


title: Br8492_Nac-PI+NeuN+

description: Library name: 4c_NAc_SVB


title: smallRNA_seq_Kitaake_WT_1.6_3

description: Library name: 51


title: UMUC9_4h_Veh_3

description: Library name: Sample21


title: smallRNA_seq_Kitaake_WT_1.6_2

description: Library name: 50


title: MDA231_4h_Amb_2

description: Library name: Sample11


title: smallRNA_seq_Kitaake_WT_1.6_1

description: Library name: 49


title: MDA231_4h_Amb_1

description: Library name: Sample10


title: MDA231_4h_Amb_3

description: Library name: Sample12


title: MDA231_4h_Veh_2

description: Library name: Sample8


title: smallRNA_seq_Kitaake_WT_1.4_3

description: Library name: 48


title: MDA231_4h_Veh_3

description: Library name: Sample9


title: Br8325_Nac-PI+NeuN+

description: Library name: 2c_NAc_SVB


title: Br6423_Nac-PI+

description: Library name: 7c_NAc_SVB


title: MDA231_4h_Veh_1

description: Library name: Sample7


title: smallRNA_seq_Kitaake_WT_1.4_2

description: Library name: 47


title: UMUC5_4h_Veh_3

description: Library name: Sample15


title: BT20_4h_Amb_3

description: Library name: Sample6


title: Br8325_Nac-PI+

description: Library name: 1c_NAc_SVB


title: BT20_4h_Amb_2

description: Library name: Sample5


title: smallRNA_seq_Kitaake_WT_1.4_1

description: Library name: 46


title: BT20_4h_Amb_1

description: Library name: Sample4


title: BT20_4h_Veh_2

description: Library name: Sample2


title: Hs_Br8667_V13M13-362-C1

description: Library name: 79v_NAc_SVB

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38 (10x Genomics 2020 reference version)
Assembly: GRCh38
Supplementary files format and content: fastq.gz, matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz, aligned_fiducials.jpg, scalefactors_json.json, detected_tissue_image.jpg, tissue_positions_list.csv, hires_image.png, lowres_image.png, tissue_positions_list.csv
Library strategy: Spatial Transcriptomics

extract_protocol:
Nucleus accumbens samples were dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

tag: subject status

value: neurotypical control postmortem human brain donor

tag: sample group


title: smallRNA_seq_Kitaake_WT_1.2_3

description: Library name: 45

tag: tissue


title: BT20_4h_Veh_3

description: Library name: Sample3


title: Br8492_Nac-PI+

description: Library name: 3c_NAc_SVB


title: Healthy control sample 14

city: El Paso

first: Enrique

middle: Ivan

last: Ramos

state: Texas

address: 5001 El Paso Dr.

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: miRBase 22.0
Supplementary files format and content: xlsx file with raw read counts for each sample

source_name: Brain

extract_protocol:
Total RNA including miRNA was extracted from the synaptosomes of AD and control postmortem brain samples usingthe TriZol reagent with some modifications.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system. All extracted RNA was used in the library preparation following Illumina’s TruSeq -small-RNA-sample preparation protocols (Illumina, San Diego, CA, USA). Quality control analysis and quantification of the DNA library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Single-end sequencing 50bp was performed on Illumina’s Hiseq 2500 sequencing system following the manufacture’s recommended protocols

value: Brain


title: smallRNA_seq_Kitaake_WT_1.2_2

description: Library name: 44


title: BT20_4h_Veh_1

description: Library name: Sample1


title: Healthy control sample 11


title: Hs_Br8667_V13M13-362-B1

description: Library name: 78v_NAc_SVB


title: Hs_Br3942_V13M06-379-C1

description: Library name: 75v_NAc_SVB


title: Hs_Br3942_V13M06-379-D1

description: Library name: 76v_NAc_SVB


title: Healthy control sample 13


title: Healthy control sample 12


title: smallRNA_seq_Kitaake_WT_1.0_3

description: Library name: 42


title: smallRNA_seq_Kitaake_WT_1.2_1

description: Library name: 43


title: Healthy control sample 10


title: Healthy control sample 9


title: smallRNA_seq_Kitaake_WT_1.0_2

description: Library name: 41


title: Hs_Br3942_V13M06-379-A1

description: Library name: 73v_NAc_SVB


title: Healthy control sample 8


title: Healthy control sample 7


title: smallRNA_seq_Kitaake_WT_1.0_1

description: Library name: 40


title: Hs_Br2743-Left_V13M06-378-D1

description: Library name: 64v_NAc_SVB


title: Healthy control sample 5


title: Healthy control sample 4


title: Healthy control sample 3


title: smallRNA_seq_Kitaake_WT_0.8_2

description: Library name: 38


title: Healthy control sample 2


title: Hs_Br2743-Left_V13M06-378-C1

description: Library name: 63v_NAc_SVB


title: Hs_Br2743-Left_V13M06-378-B1

description: Library name: 62v_NAc_SVB


title: smallRNA_seq_Kitaake_WT_0.8_1

description: Library name: 37


title: Alzheimer's disease sample 26


title: Alzheimer's disease sample 27


title: Hs_Br3942_V13M06-379-B1

description: Library name: 74v_NAc_SVB


title: smallRNA_seq_Kitaake_WT_0.6_3

description: Library name: 36


title: Alzheimer's disease sample 23


title: Hs_Br2743-Left_V13M06-378-A1

description: Library name: 61v_NAc_SVB


title: Alzheimer's disease sample 25


title: smallRNA_seq_Kitaake_WT_0.6_2

description: Library name: 35


title: Alzheimer's disease sample 24


title: Healthy control sample 6


title: Alzheimer's disease sample 22


title: Alzheimer's disease sample 21


title: smallRNA_seq_Kitaake_WT_0.6_1

description: Library name: 34


title: Hs_Br6471-Left_V13M06-377-D1

description: Library name: 60v_NAc_SVB


title: Hs_Br6471-Left_V13M06-377-C1

description: Library name: 59v_NAc_SVB


title: Alzheimer's disease sample 20


title: smallRNA_seq_Kitaake_WT_0.8_3

description: Library name: 39


title: Hs_Br6471-Left_V13M06-377-B1

description: Library name: 58v_NAc_SVB


title: Healthy control sample 1


title: Alzheimer's disease sample 18


title: smallRNA_seq_Kitaake_WT_0.4_2

description: Library name: 32


title: Alzheimer's disease sample 17


title: Alzheimer's disease sample 19


title: Alzheimer's disease sample 16


title: Alzheimer's disease sample 15


title: smallRNA_seq_Kitaake_WT_0.4_3

description: Library name: 33


title: Hs_Br6432_V11D01-384-C1

description: Library name: 55v_NAc_SVB


title: Hs_Br6432_V11D01-384-D1

description: Library name: 56v_NAc_SVB


title: Alzheimer's disease sample 12


title: Hs_Br6432_V11D01-384-B1

description: Library name: 54v_NAc_SVB


title: RNA_seq_Kitaake_WT_2.5_1

description: Library name: 28


title: Alzheimer's disease sample 10


title: Alzheimer's disease sample 9


title: Alzheimer's disease sample 13


title: Hs_Br6432_V11D01-384-A1

description: Library name: 53v_NAc_SVB


title: RNA_seq_Kitaake_WT_2.5_3

description: Library name: 30


title: Alzheimer's disease sample 14


title: Hs_Br8325_V13M06-376-D1

description: Library name: 52v_Nac_SVB


title: Alzheimer's disease sample 8


title: Alzheimer's disease sample 7


title: RNA_seq_Kitaake_WT_2.0_2

description: Library name: 26


title: Alzheimer's disease sample 6


title: Alzheimer's disease sample 5


title: Hs_Br6471-Left_V13M06-377-A1

description: Library name: 57v_NAc_SVB


title: Hs_Br8325_V13M06-376-B1

description: Library name: 50v_Nac_SVB


title: smallRNA_seq_Kitaake_WT_0.4_1

description: Library name: 31


title: RNA_seq_Kitaake_WT_2.5_2

description: Library name: 29


title: Alzheimer's disease sample 11


title: RNA_seq_Kitaake_WT_2.0_1

description: Library name: 25


title: Alzheimer's disease sample 2


title: Hs_Br8325_V13M06-376-C1

description: Library name: 51v_Nac_SVB


title: Alzheimer's disease sample 3


title: RNA_seq_Kitaake_WT_2.0_3

description: Library name: 27


title: Alzheimer's disease sample 1


title: Hs_Br6423_V13F06-313-D1

description: Library name: 48v_Nac_SVB


title: Master-based nanopore cDNA adaptive sampling on T47D, replicate 1 and 2

city: Philadelphia

first: Lan

last: Lin

address: CTRB 9054 3501 Civic Center Blvd

department: Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine

institute: The Children’s Hospital of Philadelphia

description:
Library name: T47D_master_based_cDNA_AS
Column='T47D_ASmaster_downsampled_ontarget'
T47D_ESPRESSO_downsampled_abundance.esp
T47D_ESPRESSO_downsampled_updated.gtf

data_processing:
For adaptive sampling experiments, reference FASTA files were uploaded and selected under “Enrich or deplete sequences” in the “Adaptive Sampling” section of the experiment set up within MinKNOW. When indicated, adaptive sampling was performed only on channels 1-1500, while channels 1501-3000 performed standard 1D cDNA or direct RNA sequencing.
Basecalling of raw nanopore data was performed using super-high accuracy dorado (v.0.6.0) with the following settings: --emit-fastq --device cuda:all’. The ‘dna_r10.4.1_e8.2_400bps_sup@v4.3.0’ model was used for basecalling of cDNA sequencing data, and ‘rna004_130bps_sup@v3.0.1’ was used for basecalling of direct RNA data. Where adaptive sampling was performed on only a portion of channels on a flow cell, pod5 files were split according to channel number before basecalling was performed.
Basecalled reads were aligned to either the GRCh38/hg39 primary reference genome or to the SIRV-Set4 reference genome using minimap2 (v2.25) with parameters: ‘-ax splice -ub --secondary=no -t 8 -k 14 -w 4’. A bed file containing annotated splice junctions was created using minimap2’s ‘paftools.js gff2bed’ tool and supplied to the aligner with ‘--junc-bed’.
Data from SH-SY5Y, BT549, and T47D cell lines were downsampled to an equal number of on-target reads in each condition, where indicated.
Novel and annotated transcripts were quantified using ESPRESSO (v1.4.0) guided by a gene annotation GTF file using default parameters.
Assembly: GRCh38
Supplementary files format and content: *_abundance.esp files contain transcript isoform quantifications for each sample.
Supplementary files format and content: *_updated.gtf files contain all novel and annotated transcript isoforms output by ESPRESSO.

source_name: T47D human breast cancer cells

growth_protocol: SH-SY5Y human neuroblastoma cells (ATCC, CRL-2266) were cultured in DMEM/F-12 (Gibco, 11330032) with 10% fetal bovine serum (FBS, Corning, MT35010CV) and 100 U/ml penicillin-streptomycin (Gibco, 15140122) at 37°C in 5% CO2. BT459 and T47D breast cancer cell lines were cultured according to ATCC recommendations in RPMI-1640 Medium (Gibco, 11875093) with 10% fetal bovine serum (FBS, Corning, MT35010CV), 0.023 units/mL human insulin (BT549) (Sigma Aldrich, I2643) or 0.2 units/mL bovine insulin (T47D) (Cell Applications, 128100) at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from SH-SY5Y, BT549, and T47D cell lines using TRIzol reagent (Invitrogen, 15596018).
Spike-in RNA variants (SIRV) were added to total SH-SY5Y RNA at a ratio of 1:1200. For whole transcriptome cDNA sequencing, reverse transcription was performed on 300ng of total SH-SY5Y RNA with 250pg SIRV-Set4 spike-in RNA (Lexogen, 141.01) using Maxima H minus reverse transcriptase (Thermo Fisher, EP0752), dNTP (Invitrogen, 18427088), template-switching oligo (TSO) (IDT), and RNase inhibitor (Promega, N2615) at 42°C for 90 min, followed by enzymatic inactivation at 85°C for 5 min. PCR amplification was performed with KAPA HiFi HotStart ReadyMix (Fisher Scientific, 50-196-5217) using the following program: 95°C initial denaturing for 3 minutes, followed by 12 cycles of 98 °C for 20 seconds, 67°C for 20 seconds, 72°C for 5 minutes, and a final extension at 72°C for 8 minutes. Amplified cDNA was purified using 0.7X SPRIselect beads (Beckman Coulter, B23318). Nanopore direct RNA libraries were prepared from 3600ng of total RNA from SY5Y cells with 3ng of spike-in RNAs following the standard SQK-RNA004 protocol. First-strand cDNA was synthesized by incubating RNA with T4 DNA Ligase (2M U/ml - NEB, M0202), Quick Ligation Reaction Buffer (NEB, B6058), RNAseOUT (Invitrogen, 10777019), and the supplied RT Adapter at room temperature for 10 minutes, then 50°C for 50 minutes with 10 mM dNTP mix (Thermo Scientific, 18427013), SuperScript III Reverse Transcriptase and the associated 5X First-strand buffer (Invitrogen, 18080093), and the supplied DTT, followed by a 10 minute enzymatic inactivation at 70°C. The resulting RNA-DNA hybrid was purified with 1.8X Agencourt RNAClean XP beads (Beckman Coulter, A63987). The supplied RNA Ligation Adapter was ligated for at room temperature with NEBNext Quick Ligation Reaction Buffer (NEB, E6056) and T4 DNA Ligase (2M U/ml - NEB, M0202) for 10 minutes, then purified with 0.4X Agencourt RNAClean XP beads (Beckman Coulter, A63987) and supplied Wash Buffer, then eluted with the supplied RNA Elution Buffer. Libraries were immediately loaded onto RNA PromethION flow cells (FLO-PRO004RA) and sequenced on a P2 Solo. Nanopore whole transcriptome libraries were prepared from 200ng of amplified cDNA following the standard ONT SQK-LSK114 protocol. The cDNA products underwent end-repair and dA-tailing with the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, E7546) by incubating at 20°C for 5 minutes and 65°C for 5 minutes. The cDNA was then purified with 1X AMPure XP beads (Beckman Coulter, A63881). Adapter ligation was carried out at room temperature for 10 minutes using NEBNext Quick T4 DNA ligase (NEB, E6056). The ligated libraries were purified with 0.4X volumes of AMPure XP beads (Beckman Coulter, A63881) and the supplied Ligation Adapter and Short Fragment Buffer, then eluted with the supplied Elution Buffer. Replicates for each SY5Y+SIRV-Set4 experiment (cDNA control, gene-based cDNA-AS, master-transcript-based cDNA-AS, transcript-based cDNA-AS, exon-based cDNA-AS, and TEQUILA-seq) as well as BT549/T47D experiments (cDNA control, gene-based cDNA-AS, and master-transcript-based cDNA-AS) were performed on a single R10.4.1 PromethION flow cell (FLO-PRO114M) on a P2 Solo or P24. Flow cells were washed in between replicates using the flow cell wash kit (ONT, EXP-WSH004). BT549 and T47D TEQUILA-seq experiments were sequenced on R9.4.1 flow cells (FLO-MIN106) on a GridION. Unless otherwise specified, 20fmol of each cDNA library was loaded onto the flow cell.

value: T47D human breast cancer cells


title: Gene-based nanopore cDNA adaptive sampling on T47D, replicate 1 and 2

description:
Library name: T47D_gene_based_cDNA_AS
Column='T47D_ASgene_downsampled_ontarget'
T47D_ESPRESSO_downsampled_abundance.esp
T47D_ESPRESSO_downsampled_updated.gtf


title: Nanopore whole transcriptome cDNA-seq on T47D, replicate 1 and 2

description:
Library name: T47D_cDNA_whole_transcriptome
Column='T47D_control_downsampled_ontarget'
T47D_ESPRESSO_downsampled_abundance.esp
T47D_ESPRESSO_downsampled_updated.gtf


title: Master-based nanopore cDNA adaptive sampling on BT549, replicate 1 and 2

description:
Library name: BT549_master_based_cDNA_AS
Column='BT549_ASmaster_downsampled_ontarget'
BT549_ESPRESSO_downsampled_abundance.esp
BT549_ESPRESSO_downsampled_updated.gtf

source_name: BT549 human breast cancer cells

value: BT549 human breast cancer cells


title: Nanopore whole transcriptome cDNA-seq on BT549, replicate 1 and 2

description:
Library name: BT549_cDNA_whole_transcriptome
Column='BT549_control_downsampled_ontarget'
BT549_ESPRESSO_downsampled_abundance.esp
BT549_ESPRESSO_downsampled_updated.gtf


title: RNA_seq_Kitaake_WT_1.6_3

description: Library name: 21


title: Gene-based nanopore direct RNA adaptive sampling on SY5Y, half of a flow cell, replicate 1 and 2

description:
Library name: SY5Y_half_gene_based_dRNA_AS
Column='SY5Y_SIRV_dRNA_GENE_downsampled_ontarget'
SH-SY5Y_ESPRESSO_SIRV_abundance.esp
SH-SY5Y_ESPRESSO_SIRV_updated.gtf

source_name: SH-SY5Y human neuroblastoma cells

value: SH-SY5Y human neuroblastoma cells


title: Hs_Br6423_V13F06-313-A1

description: Library name: 45v_Nac_SVB

value: nucleus accumbens


title: RNA_seq_Kitaake_WT_1.8_1

description: Library name: 22


title: RNA_seq_Kitaake_WT_1.8_2

description: Library name: 23


title: Alzheimer's disease sample 4


title: Hs_Br8325_V13F06-313-C1

description: Library name: 47v_Nac_SVB


title: Hs_Br6423_V13F06-313-B1

description: Library name: 46v_Nac_SVB


title: Hs_Br8325_V13M06-376-A1

description: Library name: 49v_Nac_SVB


title: RNA_seq_Kitaake_WT_1.6_2

description: Library name: 20


title: Master-based nanopore cDNA adaptive sampling on SY5Y, replicate 1 and 2

description:
Library name: SY5Y_master_based_cDNA_AS
Column='SY5Y_SIRV_MASTER_downsampled_ontarget'
SH-SY5Y_ESPRESSO_SIRV_abundance.esp
SH-SY5Y_ESPRESSO_SIRV_updated.gtf


title: RNA_seq_Kitaake_WT_1.4_3

description: Library name: 18


title: Nanopore whole transcriptome direct RNA-seq on SY5Y, half of a flow cell, replicate 1 and 2

description:
Library name: SY5Y_half_dRNA_whole_transcriptome
Column='SY5Y_SIRV_dRNA_CONTROL_downsampled_ontarget'
SH-SY5Y_ESPRESSO_SIRV_abundance.esp
SH-SY5Y_ESPRESSO_SIRV_updated.gtf


title: RNA_seq_Kitaake_WT_1.8_3

description: Library name: 24


title: Hs_Br6522_V12-D07-333-B1

description: Library name: 42v_NAc_SVB


title: RNA_seq_Kitaake_WT_1.4_2

description: Library name: 17


title: RNA_seq_Kitaake_WT_1.6_1

description: Library name: 19


title: Hs_Br6522_V12-D07-333-D1

description: Library name: 44v_NAc_SVB


title: Gene-based nanopore cDNA adaptive sampling on SY5Y, replicate 1 and 2

description:
Library name: SY5Y_gene_based_cDNA_AS
Column='SY5Y_SIRV_GENE_downsampled_ontarget'
SH-SY5Y_ESPRESSO_SIRV_abundance.esp
SH-SY5Y_ESPRESSO_SIRV_updated.gtf


title: Hs_Br6522_V12-D07-333-A1

description: Library name: 41v_NAc_SVB


title: Hs_Br6522_V12-D07-333-C1

description: Library name: 43v_NAc_SVB


title: Nanopore whole transcriptome cDNA-seq on SY5Y, replicate 1, 2, 3, and 4

description:
Library name: SY5Y_cDNA_whole_transcriptome
Column='SY5Y_SIRV_control_downsampled_ontarget'
SH-SY5Y_ESPRESSO_SIRV_abundance.esp
SH-SY5Y_ESPRESSO_SIRV_updated.gtf


title: TEQUILA-seq on SY5Y for splicing factors, replicate 1 and 2

description:
Library name: SY5Y_TEQUILA
Column='SY5Y_SIRV_TEQUILA_downsampled_ontarget'
SH-SY5Y_ESPRESSO_SIRV_abundance.esp
SH-SY5Y_ESPRESSO_SIRV_updated.gtf


title: RNA_seq_Kitaake_WT_1.2_3

description: Library name: 15


title: Gene-based nanopore direct RNA adaptive sampling on SY5Y, half of a flow cell, replicate 2

description:
Library name: SY5Y_half_gene_based_dRNA_AS_rep2
Column='RNA_half_ASgene_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Hs_Br8492_V12D07-078-C1

description: Library name: 39v_NAc_SVB


title: Gene-based nanopore direct RNA adaptive sampling on SY5Y, half of a flow cell, replicate 1

description:
Library name: SY5Y_half_gene_based_dRNA_AS_rep1
Column='RNA_half_ASgene_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Nanopore whole transcriptome cDNA-seq on 40fmol SY5Y, half of a flow cell, replicate 1

description:
Library name: SY5Y_half_cDNA_whole_transcriptome_40fmol_rep1
Column='half_control_40fmol_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Gene-based nanopore cDNA adaptive sampling on BT549, replicate 1 and 2

description:
Library name: BT549_gene_based_cDNA_AS
Column='BT549_ASgene_downsampled_ontarget'
BT549_ESPRESSO_downsampled_abundance.esp
BT549_ESPRESSO_downsampled_updated.gtf


title: RNA_seq_Kitaake_WT_1.4_1

description: Library name: 16


title: Nanopore whole transcriptome direct RNA-seq on SY5Y, half of a flow cell, replicate 1

description:
Library name: SY5Y_half_dRNA_whole_transcriptome_rep1
Column='RNA_half_control_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Gene-based nanopore cDNA adaptive sampling on 20fmol SY5Y, half of a flow cell, replicate 2

description:
Library name: SY5Y_half_gene_based_cDNA_AS_20fmol_rep2
Column='half_ASgene_20fmol_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Nanopore whole transcriptome direct RNA-seq on SY5Y, half of a flow cell, replicate 2

description:
Library name: SY5Y_half_dRNA_whole_transcriptome_rep2
Column='RNA_half_control_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Gene-based nanopore cDNA adaptive sampling on 40fmol SY5Y, half of a flow cell, replicate 2

description:
Library name: SY5Y_half_gene_based_cDNA_AS_40fmol_rep2
Column='half_ASgene_40fmol_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Gene-based nanopore cDNA adaptive sampling on 40fmol SY5Y, half of a flow cell, replicate 1

description:
Library name: SY5Y_half_gene_based_cDNA_AS_40fmol_rep1
Column='half_ASgene_40fmol_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: RNA_seq_Kitaake_WT_1.2_2

description: Library name: 14


title: Hs_Br8492_V12D07-078-A1

description: Library name: 37v_NAc_SVB


title: Nanopore whole transcriptome cDNA-seq on 40fmol SY5Y, half of a flow cell, replicate 2

description:
Library name: SY5Y_half_cDNA_whole_transcriptome_40fmol_rep2
Column='half_control_40fmol_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Gene-based nanopore cDNA adaptive sampling on 20fmol SY5Y, half of a flow cell, replicate 1

description:
Library name: SY5Y_half_gene_based_cDNA_AS_20fmol_rep1
Column='half_ASgene_20fmol_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Hs_Br8492_V12D07-078-B1

description: Library name: 38v_NAc_SVB


title: RNA_seq_Kitaake_WT_1.0_3

description: Library name: 12


title: RNA_seq_Kitaake_WT_1.0_2

description: Library name: 11


title: Hs_Br2720_V12D07-074-D1

description: Library name: Nac_2720_36V_SVB


title: Exon-based nanopore cDNA adaptive sampling on SY5Y, replicate 2

description:
Library name: SY5Y_exon_based_cDNA_AS_rep2
Column='ASexon_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Nanopore whole transcriptome cDNA-seq on 20fmol SY5Y, half of a flow cell, replicate 1

description:
Library name: SY5Y_half_cDNA_whole_transcriptome_20fmol_rep1
Column='half_control_20fmol_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Hs_Br8492_V12D07-078-D1

description: Library name: 40v_NAc_SVB


title: Hs_Br2720_V12D07-074-C1

description: Library name: Nac_2720_35V_SVB


title: RNA_seq_Kitaake_WT_1.0_1

description: Library name: 10


title: Transcript-based nanopore cDNA adaptive sampling on SY5Y, replicate 1

description:
Library name: SY5Y_transcript_based_cDNA_AS_rep1
Column='AStranscript_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Transcript-based nanopore cDNA adaptive sampling on SY5Y, replicate 2

description:
Library name: SY5Y_transcript_based_cDNA_AS_rep2
Column='AStranscript_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Master-based nanopore cDNA adaptive sampling on SY5Y, replicate 2

description:
Library name: SY5Y_master_based_cDNA_AS_rep2
Column='ASmaster_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: RNA_seq_Kitaake_WT_0.8_3

description: Library name: 9


title: Hs_Br2720_V12D07-074-B1

description: Library name: Nac_2720_34V_SVB


title: RNA_seq_Kitaake_WT_1.2_1

description: Library name: 13


title: Gene-based nanopore cDNA adaptive sampling on SY5Y, replicate 2

description:
Library name: SY5Y_gene_based_cDNA_AS_rep2
Column='ASgene_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Master-based nanopore cDNA adaptive sampling on SY5Y, replicate 1

description:
Library name: SY5Y_master_based_cDNA_AS_rep1
Column='ASmaster_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Gene-based nanopore cDNA adaptive sampling on SY5Y, replicate 1

description:
Library name: SY5Y_gene_based_cDNA_AS_rep1
Column='ASgene_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: RNA_seq_Kitaake_WT_0.8_2

description: Library name: 8


title: A549.atacseq.gel_50kpa.brep3

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description: Library name: A549.atacseq.gel_50kpa.brep3

data_processing:
FastQC was used to identify read quality, and adapter reads were trimmed using Trimmomatic v0.32 followed by Bowtie alignment (v1.0) of the reads to the reference genome using the settings: -v 2 –best –strata -m 1 with duplicate reads removed using Picard MarkDuplicates (v1.13) and ENCODE hg38 blacklist reads removed using bedtools2 v2.25.
Peak calling was performed using MACS2 with narrowPeak settings and a threshold of FDR < 0.001, and a master peak set was generated as the union set of all called peaks across every sample analyzed (224,906 unique regions total).
Count matrices were made using featureCounts and DEseq2 v1 was used for differential accessibility analysis.
Annotation of genomic regions was performed using ChIPSeeker, interactive visualization of processed data was done using Degust and Rstudio along with ggplot2 and tidyverse plugins were used to generate data visualizations.
Sequencing-depth normalized ATAC bigWig files were generated using deeptools bamCoverage v3.0.1.
Assembly: hg38
Supplementary files format and content: narrowPeak files containing peak calls for each sample.
Supplementary files format and content: bigwig signal profiles for each sample, normalized by library size

growth_protocol: Primary human neonatal fibroblasts (HFF cells) were acquired from ATCC (CRL-2097) and cultured in DMEM with 10% FBS, 1% AntiAnti, and 1% NEAA (Sigma) on tissue culture plastic. A549 cells were cultured in F-12K Medium from ATCC (30-2004) with 10% FBS. All work was performed within 30 doublings from the initial passage of the vial.

extract_protocol:
Omni-ATAC-seq protocol was used to minimize mitochondrial reads from the preps, however no trypsinization was used and instead on-plate disruption/removal of nuclei (using the digitonin present in the lysis buffer) was used to better preserve nuclear mechanical context and connectivity prior to transposition by the Tn5.
The Omni-ATAC-seq protocol was used to minimize mitochondrial reads from the preps, however no trypsinization was used and instead on-plate disruption/removal of nuclei (using the digitonin present in the lysis buffer) was used to better preserve nuclear mechanical context and connectivity prior to transposition by the Tn5.  Following the final PCR, libraries were cleaned with a 0.5x/1.8x double-sided SPRI clean. Libraries were subjected to quality control by determining the number of cycles required to reach 25% of the peak threshold in the diagnostic PCR, as well as running the amplified libraries out on a High Sensitivity D1000 Tapestation (Agilent) to confirm expected size, and Qubit dsDNA HS assays were performed to determine a final concentration. Libraries were individually diluted to 6nM and then pooled at equal volumes prior to sequencing on an Illumina HiSeq 4000 using a single lane of 50bp single end reads.

treatment_protocol: HFFs were seeded on 35mm Matrigen dishes of varying stiffness (1, 12, 50 kPa elastic modulus) coated with 10ug/mL fibronectin. HFFS were seeded at slightly variable densities to account for reduced cell attachment on softer substrates (70k, 45k, 40k HFF cells seeded per group) and allowed to culture for 20 hours. A549s were seeded in a similar fashion with Matrigen T75 flasks (1, 50 kPa elastic modulus) seeded with either 2 million and 1.25 million cells per flask, respectively and allowed to culture for 20 hours. For Y-27632 ROCKi experiments, the cells were seeded as normal, but 1 hour prior to harvest 10 μM Y-27632 ROCKi (StemCell Tech) in growth media was added to the cells. For verteporfin (Sigma-Aldrich) and CCG-222740 (MedChemExpress) studies, these inhibitors were added 18 hr prior to harvest and used at 0.7 μM and 20 μM, respectively.

value: Tumor-derived lung epithelial cells

value: 50kPa surface


title: RNA_seq_Kitaake_WT_0.8_1

description: Library name: 7


title: Nanopore whole transcriptome cDNA-seq on 20fmol SY5Y, half of a flow cell, replicate 2

description:
Library name: SY5Y_half_cDNA_whole_transcriptome_20fmol_rep2
Column='half_control_20fmol_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: TEQUILA-seq on SY5Y for splicing factors, replicate 2

description:
Library name: SY5Y_TEQUILA_rep2
Column='TEQUILA_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: TEQUILA-seq on SY5Y for splicing factors, replicate 1

description:
Library name: SY5Y_TEQUILA_rep1
Column='TEQUILA_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: RNA_seq_Kitaake_WT_0.6_3

description: Library name: 6


title: Nanopore whole transcriptome cDNA-seq on SY5Y, replicate 4

description:
Library name: SY5Y_cDNA_whole_transcriptome_rep4
Column='control_rep4'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Exon-based nanopore cDNA adaptive sampling on SY5Y, replicate 1

description:
Library name: SY5Y_exon_based_cDNA_AS_rep1
Column='ASexon_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Nanopore whole transcriptome cDNA-seq on SY5Y, replicate 3

description:
Library name: SY5Y_cDNA_whole_transcriptome_rep3
Column='control_rep3'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: Nanopore whole transcriptome cDNA-seq on SY5Y, replicate 2

description:
Library name: SY5Y_cDNA_whole_transcriptome_rep2
Column='control_rep2'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: A549.atacseq.gel_50kpa.brep1

description: Library name: A549.atacseq.gel_50kpa.brep1


title: Nanopore whole transcriptome cDNA-seq on SY5Y, replicate 1

description:
Library name: SY5Y_cDNA_whole_transcriptome_rep1
Column='control_rep1'
SH-SY5Y_ESPRESSO_abundance.esp
SH-SY5Y_ESPRESSO_updated.gtf
SH-SY5Y_ESPRESSO_downsampled_abundance.esp
SH-SY5Y_ESPRESSO_downsampled_updated.gtf


title: RNA_seq_Kitaake_WT_0.6_2

description: Library name: 5


title: A549.atacseq.gel_1kpa.brep3

description: Library name: A549.atacseq.gel_1kpa.brep3

value: 1kPa surface


title: RNA_seq_Kitaake_WT_0.6_1

description: Library name: 4

value: anther


title: Porcine pancreas, rep 1

city: Oberschleissheim

first: Christos

last: Karampelias

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum Munich

description:
Library name: Porcine pancreas scRNASEQ 1
10x Genomics

data_processing:
For the scRNA-seq: The CelRanger software v7.1.0 was used to process sequencing data that were aligned to the Sus Scrofa custom genome annotation or the GRCh38 human genome release. All scRNA-Seq procesing data downstream of CellRanger can be found in teh methods of the corresponding manuscript.
Assembly: Grch38 and the improved Sus Scrofa genome assaembly: sus_scrofa_Sscrofa11.1_custom_release101_egfp
Supplementary files format and content: Bulk_PPDO_RNASEQ_salmon_raw_gene_counts.tsv tab-delimited file containing the raw unaggregated counts of the bulk RNA-Seq experiment
Supplementary files format and content: *barcodes.tsv, *features.tsv and *matrix.mtx files are the output of the CellRanger pipeline for each of the scRNA-Seq samples
Supplementary files format and content: *.h5ad are anndata object files containing the processed scRNA-seq datasets following normalization and cluster annotation. Counts layer of the anndata object contains the raw counts for each file.

organism: Sus scrofa

source_name: Pancreas

extract_protocol:
For the bulk RNA-Seq experiments: PPDO were treated with control and differentiation media followed by 2 washes with PBS 1X. The Arcturus PicoPure RNA kit was used to extract RNA and quality assessed using a Bioanalyzer instrument (all samples had RIN>9). For the scRNA-Seq experiments: porcine pancreas was dispersed into single cell suspension using collagenase V and TrypLE digestion and single alive cells were sorted using a FACSAria III instrument. HPDO and PPDO cells were dissociated using TrypLE express into single cell suspnsions and 10000 alive cells were sorted using the FACSAria III instrument for library preparation.
For the scRNA-seq: the Chromium Single Cell 3' reagent kit v3.1 was used for library construction according to manufacturer's instructions.

value: Pancreas


title: Porcine pancreas, rep 2

description:
Library name: Porcine pancreas scRNASEQ 2
10x Genomics


title: A549.atacseq.gel_1kpa.brep2

description: Library name: A549.atacseq.gel_1kpa.brep2


title: RNA_seq_Kitaake_WT_0.4_3

description: Library name: 3


title: A549.atacseq.gel_1kpa.brep1

description: Library name: A549.atacseq.gel_1kpa.brep1


title: WTR_3

city: Chengdu

first: liming

last: lu

address: No.211 Huimin Street

institute: Sichuan Agricultural University

description:
Library name: WTR_3
Nicotiana tabacum

data_processing:
The library was sequenced using a DNA sequencing instrument (DNBSEQ-T7, MGI Tech Co., Ltd.) and the length of reads is 300bp, We used FastP software to process raw reads, removing low-quality reads to obtain clean reads. Clean reads were aligned to the reference genome using spliced transcripts alignment to a reference (STAR) software to obtain information on sequence locations within the reference genome or gene, as well as the unique sequence features of the sample.
After assembling the sequence using StringTie2 software, known annotated genes were compared with the reference genome using Cuffcompare software for identification of new transcripts.
Supplementary files format and content: FPKM

organism: Nicotiana tabacum

source_name: root

growth_protocol: The tobacco seedlings were allowed to grow to the small cross stage for thinning, leaving one seedling in each well. During this period, the same tobacco-specific seedling fertilizer was cultivated. The cultivation conditions were as follows: 16 h/8 h light dark treatment, 25 °C.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad,USA)following the manufacturer’s protocols.
The library was sequenced using a DNA sequencing instrument (DNBSEQ-T7, MGI Tech Co., Ltd.) and the length of reads is 300bp, We used FastP software to process raw reads, removing low-quality reads to obtain clean reads. Clean reads were aligned to the reference genome using spliced transcripts alignment to a reference (STAR) software to obtain information on sequence locations within the reference genome or gene, as well as the unique sequence features of the sample. After assembling the sequence using StringTie2 software, known annotated genes were compared with the reference genome using Cuffcompare software for identification of new transcripts.

treatment_protocol: The tobacco NtLHT1 mutant was hydroponically cultured in LN solution for 15 days.

value: root


title: Hs_Br2720_V12D07-074-A1

description: Library name: Nac_2720_33V_SVB


title: WTR_2

description:
Library name: WTR_2
Nicotiana tabacum


title: Porcine pancreatic ductal organoids, rep 1

description:
Library name: PPDO scRNASEQ 1
10x Genomics

value: Primary pancreatic ductal organoids


title: HFF.50KPa.DMSO.rep3

description: Library name: HFF.50KPa.DMSO.rep3

source_name: HFF

value: HFF

value: Human foreskin fibroblasts

value: 50kPa surface; DMSO


title: RNA_seq_Kitaake_WT_0.4_2

description: Library name: 2


title: WTR_1

description:
Library name: WTR_1
Nicotiana tabacum


title: TWTR_3

description:
Library name: TWTR_3
Nicotiana tabacum


title: RNA_seq_Kitaake_WT_0.4_1

description: Library name: 1


title: A549.atacseq.gel_50kpa.brep2

description: Library name: A549.atacseq.gel_50kpa.brep2


title: TWTR_2

description:
Library name: TWTR_2
Nicotiana tabacum


title: HFF.50KPa.DMSO.rep2

description: Library name: HFF.50KPa.DMSO.rep2


title: HFF.50KPa.DMSO.rep1

description: Library name: HFF.50KPa.DMSO.rep1


title: TWTR_1

description:
Library name: TWTR_1
Nicotiana tabacum


title: TCR_3

description:
Library name: TCR_3
Nicotiana tabacum


title: WT cells, biofilm, biol rep 3

city: Toronto

first: Delphine

last: Dufour

state: Ontario

address: 124 Edward Street

country: Canada

institute: Faculty of Dentistry, University of Toronto

data_processing:
The Illumina bcl2fastq Conversion software was used for demultiplexing and to convert the base call files generated by the Illumina sequencing into FASTAQ files.
Quality of the raw data was assessed with FastQC (v0.11.9).
Removal of sequencing adapters and low-quality ends was performed using Trim Galore (v0.5.0) and the QC checks were repeated with FastQC to ensure that high-quality data was retained.
The reads were then aligned to S. Mutans UA159 complete genome (NC_004350.2) downloaded from NCBI using STAR aligner (v2.6.0c).
Assembly: NC_004350.2
Supplementary files format and content: htseq files include read counts for each sample

organism: Streptococcus mutans UA159

source_name: bacteria

growth_protocol: S. mutans UA159 WT and DpnII R-M mutant biofilms were developped in BHI broth complemented with 1% (w/v) sucrose at 37C with 5% CO2 for 6 hours.

extract_protocol:
RNA  was harvested using the RiboPure-Bacteria purification kit. 0.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit following manufacturer's protocols.

value: bacteria

value: WT


title: TCR_1

description:
Library name: TCR_1
Nicotiana tabacum


title: TCR_2

description:
Library name: TCR_2
Nicotiana tabacum


title: HFF.50KPa.CCG.rep3

description: Library name: HFF.50KPa.CCG.rep3

value: 50kPa surface + 20 μM CCG-222740


title: WT cells, biofilm, biol rep 2


title: Porcine pancreatic ductal organoids, rep 2

description:
Library name: PPDO scRNASEQ 2
10x Genomics


title: WT cells, biofilm, biol rep 1


title: CR_3

description:
Library name: CR_3
Nicotiana tabacum


title: CR_1

description:
Library name: CR_1
Nicotiana tabacum


title: CR_2

description:
Library name: CR_2
Nicotiana tabacum


title: DpnII R-M mutant cells, biofilm, biol rep 3


title: HFF.50KPa.CCG.rep1

description: Library name: HFF.50KPa.CCG.rep1


title: DpnII R-M mutant cells, biofilm, biol rep 2


title: HFF.50KPa.18hVer.rep3

description: Library name: HFF.50KPa.18hVer.rep3

value: 50kPa surface + 0.7 μM verteporfin (18h)


title: DpnII R-M mutant cells, biofilm, biol rep 1


title: MC38-LM3b-3

description: Library name: Sample 9

data_processing:
Reads were filtered using the SOAPnuke software, and the filtered reads were aligned to the reference genome using HISAT software.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: txt file containing the gene expression TPM values for each sample.

source_name: Colon

extract_protocol:
Total RNA was extracted from the cells using TRIzol
PolyA-tailed mRNA was enriched using Oligo(dT) magnetic beads. The RNA was fragmented and reverse transcribed with random N6 primers to synthesize cDNA. The double-stranded DNA was end-repaired, 5' phosphorylated, and ligated with a connector. The ligation products were PCR amplified, heat-denatured, and circularized using a bridging primer to generate a single-stranded circular DNA library.

value: Colon

value: Epithelial cell


title: HFF.50KPa.18hVer.rep2

description: Library name: HFF.50KPa.18hVer.rep2


title: HFF.50KPa.18hVer.rep1

description: Library name: HFF.50KPa.18hVer.rep1


title: B4585-1

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

department: Pediatrics

institute: GENVIP research group

hyb_protocol: Gene expression was evaluated through the nCounter MAX (NanoString Technologies) and the nCounter Host Response Panel, which includes 785 genes. We followed standard protocols; including 12 RNA hybridization with 5 ul of RNA as input, and hybridization time of 18 hours for all samples. We also mixed controls and ACD patient samples in the same runs to avoid technical sample bias and batch effects.

data_processing: We carried out a quality control (QC) of the raw expression data checking some technical parameters following manufacturer recommendations to verify the absence of technical problems. Samples that did not pass technical QC, or with low number of genes detected, were excluded for downstream analysis.   Genes with counts below the background (defined as the mean + 2 standard deviations [SD] of the negative control spikes in the code set, disregarding negative control C, which typically yields a higher number of counts) were excluded from both normalization and the differential expression analysis. After filtering out genes expressing below the background (maximum expression value < background), we detected a total of 566 and 672 genes (out of the total 785 in the NanoString panel) in ACD patients and healthy controls, respectively. In addition, 553 out of 566 genes in ACD and 648 out of 672 genes in healthy controls.  Data normalization was performed through an iterative strategy that combines both DESeq2 and RUVSeq packages. Control reference genes for data normalization were detected by selecting invariable genes (P-value > 0.1, BaseMean > 100 and |log2FC| < 0.2) after a naïve differential expression analysis between TP1 And TP2 in both ACD and healthy controls separately. Genes expressed below the background were removed. We used a paired-sampling design correcting by subject ID to carry out analysis of transcriptome differences before the musical stimuli (Pretest; time-point one or TP1) and after the musical stimuli (Posttest; TP2).

source_name: Saliva

extract_protocol: RNA from saliva was isolated using 500µl of sample and the RNeasy microkit (Qiagen). We slightly modified the protocol provided by the extraction kit as recommended by the Oragene tubes supplier. RNA concentration step and an additional DNase treatment were undertaken using an RNA clean & concentrator kit (Zymo Research). RNA amount and integrity were checked using TapeStation 4200 (Agilent), and DV200 values were calculated to ensure that >50% of the RNA fragments were above 200nt and to estimate the optimal sample input.

tag: phenotype

value: ACD

tag: gender

value: Female

tag: plate

tag: subject


title: B4585-2


title: HFF.1KPa.DMSO.rep3

description: Library name: HFF.1KPa.DMSO.rep3

value: 1kPa surface; DMSO


title: MC38-LM3b-2

description: Library name: Sample 8


title: B4584-1


title: B4584-2


title: 1137-2


title: 1137-1


title: B4572-1


title: MC38-LM3b-1

description: Library name: Sample 7


title: B4572-2


title: HFF.50KPa.CCG.rep2

description: Library name: HFF.50KPa.CCG.rep2


title: HFF.1KPa.DMSO.rep2

description: Library name: HFF.1KPa.DMSO.rep2


title: MC38-LM3a-3

description: Library name: Sample 6


title: B4570-1

value: Male


title: HFF.1KPa.DMSO.rep1

description: Library name: HFF.1KPa.DMSO.rep1


title: 1122-1

value: CONTROL


title: 1122-2


title: MC38-LM3a-2

description: Library name: Sample 5


title: HFF.1KPa.CCG.rep3

description: Library name: HFF.1KPa.CCG.rep3

value: 1kPa surface + 20 μM CCG-222740


title: 1111-2


title: 1111-1


title: MC38-LM3a-1

description: Library name: Sample 4


title: 1103-2


title: MC38-P-3

description: Library name: Sample 3


title: 1103-1


title: HFF.1KPa.CCG.rep2

description: Library name: HFF.1KPa.CCG.rep2


title: MC38-P-2

description: Library name: Sample 2


title: 1095-2


title: HFF.1KPa.18hVer.rep1

description: Library name: HFF.1KPa.18hVer.rep1

value: 1kPa surface + 0.7 μM verteporfin (18h)


title: 1094-1


title: 1095-1


title: 1094-2


title: hippocampus, 24w, nTg, biol rep3

city: Taichung City

first: Keng-Ying

last: Liao

address: No. 145, Xingda Rd., South Dist.,

department: Department of Veterinary Medicine

country: Taiwan

institute: National Chung Hsing University

description: Library name: n1582

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format.
The obtained raw paired-end reads were filtered by Trimmomatic (v.0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The number of reads mapped to individual genes was counted using FeatureCounts (v.2.0.0), and the expression was normalized using relative log expression methods performed by DESeq2 (v1.26.0) with biological duplicates.
Assembly: Read pairs from each sample were aligned to the reference genome (ie. GRCm38) by the HISAT2 software (v2.1.0).
Supplementary files format and content: xlsx file includes raw read counts of each sample

source_name: hippocampus

extract_protocol:
RNA was extracted using RareRNA kit (Genepure, Taiwan) following the manufacturer’s procedure.
RNA sequencing library was prepared using the KAPA mRNA HyperPrep Kit (Roche, Switzerland) following the manufacturer's protocol.

value: hippocampus

tag: genotype

tag: batch


title: 1086-1


title: 1086-2


title: B4570-2


title: A549.TCP.rep3

description: Library name: A549-TCP-B3

data_processing:
Resulting reads were subjected to adapter trimming using Trimmomatic v0.32, aligned to GRCh38 with the STAR v2.4 aligner, and counts were retrieved using featureCounts from subread version 1.4.6p4 with Gencode v22 gene annotations used as reference.
Differential expression analysis was performed using edgeR quasi-likelihood methodology and data was visualized using Degust and Rstudio.
Genes with significant differential expression were determined using a threshold of FDR < 0.05 and absolute value of Log2(FC) > 1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with gene count measurements calculated with RSEM.

extract_protocol:
RNA was isolated from the cells using the Norgen Total RNA Purification Kit (#17250) according to the manufacturer's protocol, and samples were run on a RNA TapeStation (Agilent) to verify all samples had a RIN score > 8.
cDNA Libraries were built from our RNA inputs using the TruSeq Stranded Library Prep Kit (Illumina #RS-122-2101) according to manufacturer’s instructions. Quality control was performed by running the amplified libraries out on a High Sensitivity D1000 Tapestation (Agilent) to confirm expected size, and Qubit dsDNA HS assays were performed to determine a final concentration. Libraries were diluted to 10nM and pooled together in equal volumes, followed by sequencing performed on an Illumina HiSeq 2500 using a 50bp PE RapidRun kit.

treatment_protocol: 40k HFF cells were seeded on 35mm 50 kPa dishes and TCP dishes, while 70k HFF cells were seeded on 1 kPa 35mm dishes to achieve the same effective plating density due to slightly reduced HFF attachment rates (and spreading) on 1kPa hydrogels. Similarly, A549 cells were seeded on Matrigen T75 flasks (1 kPa and 50 kPa) at slightly variable densities to account for reduced cell attachment on softer substrates (2 million cells and 1.25 million cells, for 1 and 50 kPa flasks). 20 hours after seeding, cells were harvested for RNA.

value: Tumor-derived lung epithelial cells

tag: treatment

value: Tissue culture plastic (TCP)


title: hippocampus, 15w, nTg, biol rep2

description: Library name: n1751


title: A549.TCP.rep2

description: Library name: A549-TCP-B2


title: 1083-2

tag: timepoint


title: 1081-2


title: hippocampus, 24w, nTg, biol rep1

description: Library name: n1841


title: 1081-1


title: 1083-1


title: 1079-2


title: A549.TCP.rep1

description: Library name: A549-TCP-B1

tag: cell line


title: 1079-1


title: HFF.1KPa.18hVer.rep2

description: Library name: HFF.1KPa.18hVer.rep2

value: HFF

tag: cell type

value: Human foreskin fibroblasts


title: 1069-2


title: MC38-P-1

description: Library name: Sample 1


title: hippocampus, 15w, Tg, biol rep3

description: Library name: n1969


title: A549.50Kpa.rep3

description: Library name: A549-50Kpa-B3

value: 50kPa surface


title: 1069-1


title: B4522-2


title: hippocampus, 15w, Tg, biol rep2

description: Library name: n1691


title: A549.50Kpa.rep1

description: Library name: A549-50Kpa-B1


title: 1056-2


title: A549.50Kpa.rep2

description: Library name: A549-50Kpa-B2


title: hippocampus, 15w, Tg, biol rep1

description: Library name: n1585


title: hippocampus, 24w, Tg, biol rep3

description: Library name: n1619


title: 1056-1


title: hippocampus, 24w, Tg, biol rep2

description: Library name: n1587


title: B4522-1


title: B4503-2


title: B4503-1


title: A549.1Kpa.rep2

description: Library name: A549-1Kpa-B2

value: 1kPa surface


title: hippocampus, 24w, Tg, biol rep1

description: Library name: n1904


title: A549.1Kpa.rep1

description: Library name: A549-1Kpa-B1


title: B4491-1


title: Urethra, Adult mus female, LPS treated pool

city: Bengaluru

first: Diya

last: Binoy Joseph

state: Karnataka

address: GKVK - Post, Bellary Rd

country: India

institute: Institute for Stem Cell Science and Regenerative Medicine

description:
Library name: UrLPS
10x Genomics 3' gene expression

data_processing:
Base calling: Illumina bcl2fastq
Barcoding processing and single cell 3' counting: cellranger-8.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes)
Assembly: GRCm39
Supplementary files format and content: filtered feature-barcode matrix, .h5 files

source_name: Urethra

growth_protocol: CD-1 wildtype female mice at 9-10 weeks were used for this study

extract_protocol:
Whole urethras were dissected and washed with HBSS to remove fat and debris. Cells were chopped and digested in Accutase supplemented with DNaseI and 10 uM Rock inhibitor Y-27632 for 1.5 hours. Cells were triturated to generated single suspensions and passed through a 30 micron filter to obtain single cells. Following RBC lysis, cell counts were obtained using a hemocytometer. Single cells were loaded onto the Chromium controller for single cell partitioning and barcoding.
A target of 10,000 cells per sample was loaded on to the 10x Chromium contoller for cell partitioning. Libraries were prepared according to the manufacturers instructions for the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1. Briefly, cells were resuspended in the master mix and loaded along with the partitioning oil and gel beads onto the Chromium Next GeM Chip G to generate gel bead-in emulsions (GEM). Poly-A mRNAs captured by the beads were reverse transcribed to cDNA along with the unique molecular identified (UMI), Illumina R1 primer and the cell barcode. Following reverse transcriptions, GEMs were broken up and cDNAs were pooled. Silane magnetic beads were used to purify first strand cDNA from the RT mixture. Full length cDNA was amplified by PCR. Enzymatic fragmentation and size selection was performed to obtain desired read lengths. Illumina R2 primer, P5 and P7 bridge amplification primers and sample index is introduced using end-repair, A-tailing, ligation and PCR. Librariers were pooled for sequencing.

treatment_protocol: Transurethral instillation with PBS (100 microliter) or bacterial lipopolysaccharide (LPS, 1 mg/ml, 100 microliter)

value: Urethra

tag: Sex

tag: age

value: 9-10 weeks

value: Wildtype

value: Transurethral instillation LPS


title: B4490-2

value: Female


title: Human pancreatic ductal organoids

description:
Library name: HPDO scRNASEQ 1
10x Genomics

data_processing:
The CelRanger software v7.1.0 was used to process sequencing data that were aligned to the GRCh38 human genome release. All scRNA-Seq procesing data downstream of CellRanger can be found in the methods of the corresponding manuscript.
Assembly: Grch38
Supplementary files format and content: *barcodes.tsv, *features.tsv and *matrix.mtx files are the output of the CellRanger pipeline
Supplementary files format and content: *.h5ad are anndata object files containing the processed scRNA-seq datasets following normalization and cluster annotation. Counts layer of the anndata object contains the raw counts for each file.

extract_protocol:
HPDO cells were dissociated using TrypLE express into single cell suspnsions and 10000 alive cells were sorted using the FACSAria III instrument for library preparation.
The Chromium Single Cell 3' reagent kit v3.1 was used for library construction according to manufacturer's instructions.

value: Pancreas

value: Primary pancreatic ductal organoids


title: B4490-1

value: CONTROL


title: B4491-2


title: B4591-2


title: Urethra, Adult mus female, PBS treated pool

description:
Library name: UrPBS
10x Genomics 3' gene expression

value: Transurethral instillation PBS


title: 1007-2


title: A549.1Kpa.rep3

description: Library name: A549-1Kpa-B3


title: 1007-1


title: HOM 4

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

description: Library name: Sample 8

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm39 whole genome using HISAT2 Version 2.1.0
FeatureCounts version 2.0.2 was used for counting reads to genes.
Differential expression analysis between genotypes was performed using the DESeq2 R package (2_1.6.3)
Assembly: mm39
Supplementary files format and content: tab-delimited file includes  the results of the differential expression analysis

source_name: Frontal cortex

extract_protocol:
Bulk RNA was extracted using Qiagen Lipid Tissue kit,  from frontal cortex, of wild type and homozygous TardbpM323K/M323K  male mice at 9-months of age (in an  F1 hybrid genetic background, C57BL/6J- DBA/2J). Quality and quantity was assessed using the 5400 Fragment Analyzer System (Agilent Technologies).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: Frontal cortex