title: P2242_N708-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S508

status: Public on Apr 09 2020

type: SRA

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
full-lenght RNA-seq
P2242.tsv

library_source: transcriptomic

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Human: Gencode release 27, assembly GRCh38
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Freshly harvested epithelial tumor cells from PDO18 and PDO17 xenografts were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 22 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 140 pg of the amplified cDNA were fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera® libraries from 384 cells was carried out in one lane on a Illumina HiSeq2500 v4.
Full-length single-cell RNA sequencing libraries were prepared using the Smart-seq2 protocol
single cell RNA-seq (scRNA-seq)

tag: protocol

tag: cell type

value: Colorectal cancer

tag: treatment

value: PDOX


title: P2242_N710-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S505

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S506

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N709-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N706-S508

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N706-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N706-S506

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N706-S517

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N706-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N706-S505

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N706-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S517

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S508

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S505

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S517

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S508

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S506

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S505

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S506

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N708-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N703-S517

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N703-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N705-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N703-S508

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N703-S505

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N703-S506

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N703-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N703-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S517

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N707-S517

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S508

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S505

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S506

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N701-S517

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N701-S508

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N702-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N704-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N701-S507

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N701-S505

description:
full-lenght RNA-seq
P2242.tsv


title: P2242_N701-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2241_N712-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2242_N701-S502

description:
full-lenght RNA-seq
P2242.tsv


title: P2241_N712-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N712-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N712-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2242_N703-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2241_N712-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N712-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N712-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N712-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N711-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N711-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N711-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N711-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N711-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2242_N706-S504

description:
full-lenght RNA-seq
P2242.tsv


title: P2241_N711-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N711-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N710-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N710-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N710-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2242_N701-S503

description:
full-lenght RNA-seq
P2242.tsv


title: P2241_N710-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N710-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N710-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N710-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N707-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N707-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N707-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N707-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2242_N701-S506

description:
full-lenght RNA-seq
P2242.tsv


title: P2241_N707-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N711-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N707-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N709-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N707-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N707-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N708-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N706-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N704-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N705-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N704-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N704-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N704-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N704-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N703-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N703-S508

description:
full-lenght RNA-seq
P2241.tsv


title: Liver_batch2_control_replicate 1

type: RNA

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: #35 Keyan Road

country: Taiwan

institute: National Health Research Institutes

description: Gene expression data from adult wild-type zebrafish, sample 1 of batch 2

hyb_protocol: An automated Hyb-Wash-Scan workflow with ZebGene1.1ST Array Plate was performed with the GeneTitan™ Multi-Channel (MC) Instrument (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 702933 Rev. 2).

scan_protocol: Hybridized arrays were washed and the signal intensity of the chip was scanned using a "High Throughput Array Scanner" .

data_processing: Data analysis was performed by Transcriptome Analysis Console (TAC) Software 4.0 (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 703150 Rev. 6).

label: biotin

molecule: total RNA

organism: Danio rerio

label_protocol: Target cRNA and ss-cDNA samples were prepared stepwise from 100 ng of total RNA diluted into 3 ul of volume using GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 703147 Rev. 3). The resulting purified ss-cDNA samples were fragmented and labelled with terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin (Thermo Fisher Scientific, US).

growth_protocol: The AB zebrafish strain (Danio rerio) were used and growth for 6 months.

extract_protocol: Total RNA was isolated by NucleoSpin® RNA kit (MACHEREY-NAGEL, US) following the manufacturer manual, and RNA samples was eluted in 40 μl RNase-free water. RNA quantity and purity were assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7.

treatment_protocol: 5-month-old wild-type fish (N = 40) were divided into 2 groups, either no treatment (mock) or OF administrations via an oral gavage with OF (300 mg/kg) thrice a week for one month. The fish were sacrificed and the hepatic tissue was immediately frozen in liquid nitrogen and stored at −80 °C for later RNA extraction and hybridization on Affymetrix microarrays. Two batches of wild-type fish fed with OF were performed.

tag: tissue

value: Liver

tag: feeding

value: no treatment (mock)

tag: age

value: 6 months


title: P2241_N710-S517

description:
full-lenght RNA-seq
P2241.tsv


title: Liver_batch2_control_replicate 2

description: Gene expression data from adult wild-type zebrafish, sample 2 of batch 2.


title: P2241_N704-S506

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N704-S505

description:
full-lenght RNA-seq
P2241.tsv


title: Liver_batch1_fucoidan_replicate 2

description: Gene expression data from adult wild-type zebrafish feed with oligo-fucoidan, sample 2 of batch 1.

value: oral gavage with OF (300 mg/kg) thrice a week for one month


title: Liver_batch2_fucoidan_replicate 1

description: Gene expression data from adult wild-type zebrafish feed with oligo-fucoidan, sample 1 of batch 2.


title: Liver_batch1_fucoidan_replicate 1

description: Gene expression data from adult wild-type zebrafish feed with oligo-fucoidan, sample 1 of batch 1.


title: Control_vs_treated_ 24h_rep1

city: San Diego

first: Livia

middle: Soares

last: Zaramela

state: California

address: 9500 Gilman Drive

department: Pediatrics

country: USA

institute: University of San Diego

hyb_protocol: The hybridization was developed using 825ng of labelled cRNA, mixed on fragmentation buffer, and kept at 60°C for 30 min. The reaction was stopped with the addition of 2x Hi-RPM buffer (Agilent Technologies). Then, the samples were loaded into the Agilent SureHyb chambers and took to a hybridization oven at 65°C for 17h.

scan_protocol: Scanned on an GenePix 4000B scanner.

data_processing: Agilent Feature Extraction Software (v.9.5.3.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

label_protocol: The cDNA synthesis and the following labelling and synthesis of cRNA from cDNA were performed using a Quick Amp Labelling kit (Agilent Technologies).

growth_protocol: Adult male Wistar rats (120±12 days of age) from the institutional animal care facility (São Paulo Federal University – UNIFESP, procedures approved and registered – 1604/2007) were maintained on a 12:12-h light-dark cycle, with standard show and water ad libitum.

extract_protocol: Total RNA was extracted from C3d cells using Trizol following manufacturer's instructions

treatment_protocol: Testosterone proprionate (TP - single dose, 4mg/kg, in 1mL/kg of corn oil, s.c., Sigma Aldrich, St. Louis, MO)

tag: strain

value: Wistar

tag: gender

value: male

tag: agent

value: control

tag: time

tag: cell line

value: castrated rat cells (C3d)

source_name: Treat_24h (C3dpt24h)

value: testosterone


title: Control_vs_treated_ 24h_rep4


title: P2241_N703-S506

description:
full-lenght RNA-seq
P2241.tsv


title: Control_vs_treated_ 8h_rep2

source_name: Treat_8h (C3dpt8h)


title: Liver_batch2_fucoidan_replicate 2

description: Gene expression data from adult wild-type zebrafish feed with oligo-fucoidan, sample 2 of batch 2.


title: Control_vs_treated_ 24h_rep2


title: Liver_batch1_control_replicate 2

description: Gene expression data from adult wild-type zebrafish, sample 2 of batch 1.


title: Control_vs_treated_ 8h_rep3


title: P2241_N703-S507

description:
full-lenght RNA-seq
P2241.tsv


title: Liver_batch1_control_replicate 1

description: Gene expression data from adult wild-type zebrafish, sample 1 of batch 1.


title: Control_vs_treated_ 8h_rep4


title: Control_vs_treated_ 24h_rep3


title: lung, H7N9_3D

city: Shanghai

first: Yongquan

last: He

address: No.2901 Caolang Road

country: China

institute: Fudan University

hyb_protocol: follow the guide of Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.Genespring V12.5(Agilent)was used for normalized and further processed.

organism: Mus musculus

label_protocol: RNA were labelled by Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) and QC by RNeasy Mini Kit (Qiagen p/n 74104)

extract_protocol: RNA were then extracted using RNAzol (Molecular Research Center Inc., USA) in couple with Direct-zol RNA MiniPrep Kit (Zymo Research, Irvine, CA, USA). The quality of RNA was ensured by measurement on an Agilent Bioanalyzer 2100 using RNA NanoChip.

treatment_protocol: Mice were intranasally (i.n) inoculated with either 3.5x10e5 TCID50 of H7N9 virus, or 1.7x10e7 EID50 of H9N2 virus in a volume of 50 microliters

value: lung

tag: challenge


title: lung, H7N9_7D


title: P2241_N704-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N703-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N703-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N703-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N702-S508

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N702-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N702-S506

description:
full-lenght RNA-seq
P2241.tsv


title: lung, Blank

source_name: control

value: Blank


title: P2241_N702-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N702-S517

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N702-S503

description:
full-lenght RNA-seq
P2241.tsv


title: lung, H7N9_1D


title: lung, H7N9_2D


title: P2241_N703-S503

description:
full-lenght RNA-seq
P2241.tsv


title: Control_vs_treated_ 8h_rep1


title: lung, H7N9_6H


title: lung, H9N2_3D


title: lung, H9N2_14D


title: P2241_N701-S517

description:
full-lenght RNA-seq
P2241.tsv


title: lung, H9N2_7D


title: P2241_N701-S506

description:
full-lenght RNA-seq
P2241.tsv


title: Microglia_Phagocytosis_24h_Rep1

city: Leioa

first: Amanda

last: Sierra

address: Parque Científico (UPV/EHU) Barrio Sarriena s/n

institute: Achucarro Basque Center for Neuroscience

description: Microglia primary culture, fms-EGFP mice, phagocytosis of human SH-SY5Y cell line 24h, replicate 1

hyb_protocol: Samples were analyzed using Agilent SurePrint G3 Mouse GE 8x60K microarrays (Design ID 028005) (Agilent Technologies), with 55,681 mouse features represented.  600 ng of labeled cRNA samples were hybridized at 65 ºC for 17 h in a SureHyb hybridization chamber (Agilent Technologies).

scan_protocol: The arrays were scanned immediately after washing on a G2565CA DNA microarray scanner, with ozone-barrier slide covers (Agilent Technologies) using one-color AgilentG3_GX_1color scanner protocol for HD microarray formats (scanner settings Dye channel: Green, Scan Region: Agilent HD (61x21.6 mm), Scan resolution 3 um, Tiff file dynamic range 20 bit, Green PMT gain 100 %)

data_processing: The scanned images were analyzed with Feature Extraction Software v 10.7.3.1.  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data from Feature Extraction software was subsequently processed on GeneSpring GX 13 (Agilent Technologies). GeneSprings transforms all FE Flags to a single Detection Flag and calculates the geometric mean of replicated probes.

label_protocol: RNA samples were labeled and hybridized following standard Agilent Protocol One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) v 6.5. Briefly, 50 ng of total RNA were retrotranscribed and labeled using Low imput Quick Amp Labeling kit one color (Agilent Technologies) following manufacturer instructions. First, total RNA was retrotranscribed with AffinityScript Reverse Transcriptase (Agilent Technologies), using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT was in vitro transcribed by T7 RNA pol in the presence of Cy3-CTP to generate amplified and labeled cRNA. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen, Hilden, Germany). After labeling and purification, cRNA was quantified with NanoDrop 1000 spectrophotometer in order to determine the yield and specific activity of each reaction.

growth_protocol: Primary microglia cultures were performed as previously described (Abiega et al., 2016; Beccari et al., 2018). Postnatal day 0-1 (P0-P1) fms-EGFP mice pup brains were extracted and the meninges were peeled off. The olfactory bulb and cerebellum were discarded and the rest of the brain was then mechanically homogenized by careful pipetting and enzymatically digested with papain (20U/ml, Sigma), a cysteine protease enzyme, and deoxyribonuclease (DNAse; 150U/µl, Invitrogen) for 15min at 37ºC. The resulting cell suspension was then filtered through a 40μm nylon cell strainer (Fisher) and transferred to a 50ml Falcon tube quenched by 5ml of 20% Fetal Bovine Serum (FBS; Gibco) in HBSS. Afterwards, the cell suspension was centrifuged at 200g for 5min, the pellet was resuspended in 1ml Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) complemented with 10% FBS and 1% Antibiotic/Antimycotic (Gibco), and seeded in Poly L-Lysine-coated (15μl/ml, Sigma) culture flasks with a density of two brains per flask. Medium was changed the day after and then every 3–4 days (d), always enriched with granulocyte-macrophage colony stimulating factor (5ng/ml GM-CSF, Sigma), which promotes microglial proliferation. After confluence (at 37°C, 5% CO2 for approximately 14d), microglia cells were harvested by shaking at 100-150rpm, 37°C, 4h. Isolated cells were counted and plated in a density of 1.000.000 cell/dish on coated Petri dishes for RT-qPCR. Microglia were allowed to settle for at least 24h before any experiment.

extract_protocol: Phagocytic and naïve primary microglia cultures (> 500,000 cells) were lysed and stored at-80°C until processed. Total RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), following manufacturer’s instructions, no DNAse treatment step was performed. RNA was quantified in a Nanodrop 2000

treatment_protocol: Microglia were allowed to rest and settle for at least 24h before phagocytosis experiments. Primary microglia cells were fed for different time points with SH-SY5Y. The cell line was previously labeled with the membrane marker CM-DiI (5μM; 10min at 37°C, 15min at 4°C; Invitrogen) and treated with staurosporine (STP, 3µM, 4h; Sigma) to induce apoptosis. Only the floating dead cell fraction was collected from the supernatant and added to the primary microglia cultures in a proportion of 1:1 approximately. Apoptotic cells were visualized and quantified by trypan blue in a Neubauer chamber. Because cell membrane integrity is still maintained in early induced apoptotic cells, cells not labeled with trypan blue were considered apoptotic.

value: Microglia primary culture from brain

tag: genotype

value: fms-EGFP

value: Phagocytosis of human SH-SY5Y cell line


title: P2241_N702-S504

description:
full-lenght RNA-seq
P2241.tsv


title: BCELL_INPUT

city: New York

first: Julia

middle: Nanyi

last: Zhao

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.8 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet --solexa1.3-quals
Peak calling was done using MACS 2.1.0 with the following configurations: -f BAM -g mm -B -q 0.01 --bw 300
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were produced using bamCoverage in the deeptools package

molecule: genomic DNA

source_name: Primary mouse lymphoma

growth_protocol: Lymphoma cells were maintained in B Cell growth meidum: 500ml DMEM (Hyclone #30022.01, DMEM with high glucose, with 4.0mM L-glutamine, without Sodium Pyruvate) +500ml IMDM (Lonza #12-722F) +10% FBS +Penicillin/streptomycin +0.1mM Asparagine +2mM L-glutamine +11ug IL7 +2.2ul B-mercaptoethanol +Non-essential amino acids (100uM each of Glycine, L-alanine, L-asparagine, L-aspartic acid, L-glutamic acid, L-proline, L-serine)

extract_protocol:
Lysates were clarified from sonicated cells and histone-DNA complexes were enriched using PRDM15 antibody. Antibody is an in-house produced rabbit polyclonal antibody against PRDM15.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: Cells were fixed using 1% formaldehyde, collected in SDS lysis buffer and frozen for ChIP. Detailed experimental procedures can be found in the supplemental method section of the paper.

value: Primary mouse lymphoma

value: B cells

tag: genotype/variation

value: E mu-Myc transgenic

tag: antibody

value: input


title: Microglia_Phagocytosis_3h_Rep3

description: Microglia primary culture, fms-EGFP mice, phagocytosis of human SH-SY5Y cell line 3h, replicate 3

source_name: GSM3716450     Microglia_Phagocytos...  Apr 09, 2020   approved  None


title: P2241_N702-S502

description:
full-lenght RNA-seq
P2241.tsv

value: Colorectal cancer

value: PDOX


title: lung, H9N2_2D


title: P2241_N701-S508

description:
full-lenght RNA-seq
P2241.tsv


title: Microglia_Phagocytosis_24h_Rep3

description: Microglia primary culture, fms-EGFP mice, phagocytosis of human SH-SY5Y cell line 24h, replicate 3

source_name: GSM3716453     Microglia_Phagocytos...  Apr 09, 2020   approved  None


title: lung, H9N2_6H


title: Microglia_Control_0min_Rep3

description: Microglia primary culture, fms-EGFP mice, no phagocytic stimuli, replicate 3

source_name: GSM3716447     Microglia_Control_0m...  Apr 09, 2020   approved  None

value: naïve control (no treatment)


title: lung, H9N2_1D


title: P2239_N712-S517

description:
full-lenght RNA-seq
P2239.tsv


title: Microglia_Phagocytosis_24h_Rep2

description: Microglia primary culture, fms-EGFP mice, phagocytosis of human SH-SY5Y cell line 24h, replicate 2


title: Microglia_Phagocytosis_3h_Rep2

description: Microglia primary culture, fms-EGFP mice, phagocytosis of human SH-SY5Y cell line 3h, replicate 2


title: BCELL_PRDM15

value: PRDM15 antibody


title: P2241_N701-S505

description:
full-lenght RNA-seq
P2241.tsv


title: P2239_N712-S506

description:
full-lenght RNA-seq
P2239.tsv


title: P2241_N701-S503

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N701-S502

description:
full-lenght RNA-seq
P2241.tsv


title: P2241_N701-S504

description:
full-lenght RNA-seq
P2241.tsv


title: P2239_N712-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N711-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N712-S502

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N712-S503

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N711-S517

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N712-S507

description:
full-lenght RNA-seq
P2239.tsv


title: Microglia_Phagocytosis_3h_Rep1

description: Microglia primary culture, fms-EGFP mice, phagocytosis of human SH-SY5Y cell line 3h, replicate 1


title: P2241_N701-S507

description:
full-lenght RNA-seq
P2241.tsv


title: P2239_N711-S508

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N711-S503

description:
full-lenght RNA-seq
P2239.tsv


title: Microglia_Control_0min_Rep2

description: Microglia primary culture, fms-EGFP mice, no phagocytic stimuli, replicate 2


title: Control replicate 4

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, Galaxy built-in reference genome) with RNA STAR Galaxy Version 2.6.0b-2 (default parameters) using the Gencode annotation file (Gencode 31, release June 2019
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL release 97 (July 2019) (Human genes, GRCh38.p12, download on 08/31/2019). Genes with 0 reads were removed from the analysis. Based on ENSEMBL gene types, genes were filtered for protein coding genes and small RNAs (lncRNA, miRNA, miscRNA, scRNA, snoRNA, snRNA, sRNA). Genes coding for ribosomal or mitochondrial proteins were removed from the analysis. After principal component analysis, differential gene expression with Benjamini-Hochberg adjusted (adj.) p-values was analyzed using the R package DESeq2 Version 1.22.2 (default parameters)
Genome_build: hg38

source_name: Retinal pigment epithelium, choroidea

extract_protocol:
CNV membranes for RNA-Seq were obtained from 4 patients by the currently obsolete technique of subretinal CNV extraction. Following a 20-gauge vitrectomy, we performed retinotomy temporal to the macula and surgically extracted the CNV membrane using a flexed forceps. The diagnosis was made after a thorough funduscopic examination of both eyes. Only patients exhibiting a CNV associated with AMD changes, such as drusen and RPE alterations, were included in the study. CNV membranes from patients with other diseases, such as myopia or a history of central serous chorioretinopathy, were not included in this study. Control RPE/choroid samples for RNA-Seq were obtained from the macula region of four enucleated eyes suffering from ciliary body melanoma. Fifteen 4-µm-thick FFPE sections from each CNV membrane were collected and stored in tubes prior to RNA extraction. FFPE eyes of patients with ciliary body melanoma were melted and halved and the macular region was carefully examined under the microscope. The retina of the macula was removed and the RPE/choroid carefully scraped and stored in tubes until RNA extraction was performed. RNA isolation from FFPE specimens was carried out as previously described. Briefly, total RNA was extracted from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research). Following DNAse I digestion using the Baseline-ZERO Kit (Epicentre), the RNA concentration was quantified using the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies). RNA quality was determined via the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer). The fragment size of all RNA samples ranged between 120 and 150 bp.
The preparation of massive analysis of cDNA ends (MACE) libraries was carried out by GenXPro GmbH using 1 µg of total RNA as previously described. Briefly, eight barcoded libraries (four CNV membranes and four RPE-choroidal control tissues) were sequenced simultaneously on the NextSeq 500 (Illumina) with 1 × 75 bp.

value: Retinal pigment epithelium, choroidea

tag: patient diagnosis

value: ciliary body melanoma


title: P2239_N711-S506

description:
full-lenght RNA-seq
P2239.tsv


title: Microglia_Control_0min_Rep1

description: Microglia primary culture, fms-EGFP mice, no phagocytic stimuli, replicate 1

value: control


title: P2239_N711-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N712-S505

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N711-S505

description:
full-lenght RNA-seq
P2239.tsv


title: MB2 miRNA-seq

first: Saihua

last: Huang

address: 399 Wanyuan Rd, Minhang, Shanghai

institute: Children’s Hospital of Fudan University

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads
the trimmed reads were aligned to merged pre-miRNA databases,using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression
The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.
Genome_build: miRBase v21
Supplementary_files_format_and_content: text files include TPM values for each Sample

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps：1) 3'-adaptor ligation;2) 5'-adaptor ligation3) cDNA synthesis;4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).

tag: disease state

value: medulloblastoma

value: exosomes from blood plasma


title: Control replicate 3


title: P2239_N710-S517

description:
full-lenght RNA-seq
P2239.tsv

tag: protocol


title: CK4 miRNA-seq

value: healthy control


title: CK1 miRNA-seq


title: MB1 miRNA-seq


title: P2239_N711-S502

description:
full-lenght RNA-seq
P2239.tsv

tag: cell type


title: P2239_N710-S508

description:
full-lenght RNA-seq
P2239.tsv

tag: treatment


title: Control replicate 2


title: Control replicate 1


title: CNV replicate 3

source_name: CNV membrane

value: CNV membrane

value: AMD


title: P2239_N710-S505

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N710-S506

description:
full-lenght RNA-seq
P2239.tsv


title: CNV replicate 2


title: CNV replicate 1


title: P2239_N710-S503

description:
full-lenght RNA-seq
P2239.tsv


title: Ctrl_Chip_2

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

data_processing:
Drop-seq tools package on the EPFL SCITAS HPC platform. After trimming and sequence tagging, reads were aligned to the human  reference genome (hg38) using STAR (version 2.7.0.e). https://github.com/mccrowjp/Dropseq
Following the alignment, the gene annotation was added, bead synthesis errors were corrected and cell barcodes extracted. Subsequently, the BAM files containing the processed data were used to obtain digital gene expression matrices. Only cell barcodes with at least 50 UMI (Unique Molecular Identifier) were retained.
Downstream data analysis was carried out using R (version 3.5.0), with DESeq2 (version 1.22.2), for identifying differentially expressed genes in pair-wise comparison.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPM values for each Sample ...

source_name: Jurkat T cells

growth_protocol: The human T-lymphocytes Jurkat cell line was cultured in suspension in a Roswell Park Memorial Institute (RPMI) medium supplemented 10% fetal bovine serum and 1% antibiotics (L-Glutamine-penicillin-streptomycin).

extract_protocol:
Recovered cells were centrifuged at 600g for 5 min and supernatant was replaced with 25 µl of PBS containing 0.01 % bovine serum albumin (Sigma). Subsequently 25 ml of lysis buffer were added, containing 0.1 % Sarkosyl (Sigma), 5 mM EDTA (Life Technologies), 0.1 M Tris (pH 7.5, Sigma) and 25 mM 1,4-Dithioreitol (DTT, Sigma), 800 units/ml RNase inhibitor (NEB) and 500 Drop-Seq beads (Beads, Lot 120817, ChemGenes). All beads pelleting steps were carried out at 1000 g for 1 min in 1.5 ml microtubes (Axygen). Reverse transcription (RT), exonuclease I (ExoI) treatment and PCR were performed as described Macosko et al. with minor adaptations30. Lysed cells were incubated at 1400 rpm for 5 min at room temperature and subsequently washed twice with 1 ml of 6x SSC buffer (Sigma).
Reverse transcription was performed for 90 min at 42°C in 50 µl of 1 mM dNTPs (Clontech), 2.5 µM template switch oligo (see Table 1), 1250 units/ml RNase inhibitor, 1x Maxima RT buffer and 10,000 units/ml Maxima H minus reverse transcriptase (Thermo Fisher Scientific). Drop-seq beads were washed twice with 0.5 % SDS (Applichem) in 10 mM Tris (TE‑SDS), twice with 0.01 % Tween‑20 (Sigma) in 10 mM Tris (TE‑TW) and once with 10 mM Tris pH 7.5. The Drop-seq beads pellet was then incubated with 50 µl of exonuclease mix containing 1x Exonuclease I Buffer and 1000 units/ml Exonuclease I (NEB), and incubated at 37°C for 45 min at 1,400 rpm). Drop-seq beads were washed twice with TE‑SDS, twice with TE‑TW and once with double-distilled H2O. Beads were amplified by PCR in 25 µL of 1x Hifi HotStart Readymix (Kapa Biosystems) and 0.8 µM TSO-PCR primer (Table 1) at 95 C 3 min; 4 cycles of: 98 C for 20 sec, 65 C for 45 sec, 72 C for 3 min; then 16 cycles of: 98°C for 20 sec, 67°C for 20 sec, 72°C for 3 min and an extension step of 5 min. Libraries were purified using Ampure XP beads (0.6x ratio to remove small fragments), cDNA was quantified using a Qubit HS kit (Thermo Fisher Scientific) and integrity analyzed on a Fragment Analyzer (Agilent). Libraries were prepared using in-house produced Tn5 loaded with adapters, as described31. Size selected and purified libraries were sequenced paired-end on a NextSeq 500 system (Illumina) in High-Output mode following recommendations from the original protocol (read 1 20 bp and read 2 50 bp)

value: Jurkat T

value: Processed + DEP through microfluidics chip


title: P2239_N709-S517

description:
full-lenght RNA-seq
P2239.tsv


title: Ctrl_Chip_3


title: P2239_N710-S502

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N709-S508

description:
full-lenght RNA-seq
P2239.tsv


title: Ctrl_Chip_1


title: DEP_Chip_2

value: Processed through microfluidics chip


title: CNV replicate 4


title: P2239_N709-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N709-S505

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N709-S506

description:
full-lenght RNA-seq
P2239.tsv


title: DEP_Chip_1


title: P2239_N709-S503

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N709-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N710-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N709-S502

description:
full-lenght RNA-seq
P2239.tsv


title: Input_2

value: Untreated


title: Act_3

value: PMA/Ionomycin treated


title: P2239_N708-S517

description:
full-lenght RNA-seq
P2239.tsv

value: Colorectal cancer


title: Input_1


title: DEP_Chip_3


title: P2239_N710-S507

description:
full-lenght RNA-seq
P2239.tsv

value: PDOX


title: Act_2


title: Act_1


title: Input_3


title: P2239_N708-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N708-S503

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N708-S505

description:
full-lenght RNA-seq
P2239.tsv


title: Chromatin-associated RNA, delta-ICP27, 8h p.i., Rep 2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description:
Chromatin-associated RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600526_937H

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Expression of cellular protein-coding and lincRNAs was quantified in terms of fragments per kilobase of exons per million mapped reads (FPKM)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKMs

molecule: nuclear RNA

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 15 were infected with HSV-1 strain 17 or its ICP27-null mutant at an MOI of 10

extract_protocol:
Subcellular RNA fractions were prepared combinig the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013)
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina)  with Ribo-Zero Human/Mouse/Rat (only for total RNA).
NextSeq 500 sequencing 75bp paired-end reads

treatment_protocol: Cells were infected for 15 min using an MOI of 10. 15 min after infection (time point 0h), cell culture media was replaced with fresh media. Cells were harvested prior to or at 8h p.i. Subcellular RNA fractions were prepared and subjected to standard RNA-seq including rRNA deplation

value: human foreskin fibroblasts (HFFs)

tag: infection

value: ICP27-null mutant of HSV-1 strain 17

tag: time post-infection

value: 8h p.i.

tag: subcellular rna fraction

value: Chromatin-associated RNA

tag: replicate


title: P2239_N708-S508

description:
full-lenght RNA-seq
P2239.tsv


title: Nucleoplasmic RNA, delta-ICP27, 8h p.i., Rep 2

description:
Nucleoplasmic RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600522_937N

source_name: Nucleoplasmic RNA, delta-ICP27, 8h p.i.

value: Nucleoplasmic RNA


title: Cytoplasmic RNA, delta-ICP27, 8h p.i., Rep 2

description:
Cytoplasmic RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600518_937C

molecule: cytoplasmic RNA

source_name: Cytoplasmic RNA, delta-ICP27, 8h p.i.

value: Cytoplasmic RNA


title: Total RNA, delta-ICP27, 8h p.i., Rep 2

description:
Total RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600514_937T

source_name: Total RNA, delta-ICP27, 8h p.i.

value: Total RNA


title: MP Intercept

city: Quebec City

first: Patrick

last: Provost

state: QC

address: 2705 Blvd Laurier, Room T1-65

department: CHUQ Research Center / CHUL Pavilion

country: Canada

institute: Université Laval

description:
MP-G4
Primary cells

data_processing:
Clean reads: Illumina HiSeq Real-time base calling and quality filtering.
Adaptor trimmed reads: Removal of adaptor sequence from the reads.
Alignment to reference genome: Classification and distribution of small RNAs. Annotation and tag counts of miRNAs.
Normalization: Tags per million of aligned miRNA (TPM).
Standard analysis: Differentially expressed miRNAs and novel miRNA prediction.
Genome_build: miRBase 21
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

source_name: Blood

extract_protocol:
Total RNA was isolated using Trizol LS and suspended in DEPC-treated DNase-RNase-free water prior to RNA purification and subsequent on-column DNase treatment using RNeasy mini-kit following the manufacturer protocol.
Total RNA was used to prepare the microRNA sequencing library, which included the following steps: 1) 3’-adapter ligation; 2) 5’-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; and 5) size selection of PCR amplified fragments of  ~130–150 base pairs (corresponding to small RNAs of ~15–35 nucleotides). The complete libraries were quantified by Agilent 2100 Bioanalyzer.

value: Platelet microparticles (MPs)

value: Intercept


title: PLT Intercept

description:
PLT-G4
Primary cells

value: Platelets


title: PLT Additive solution

description:
PLT-G3
Primary cells

value: Additive solution


title: PLT Mirasol

description:
PLT-G2
Primary cells

value: Mirasol


title: MP Control

description:
MP-G1
Primary cells

value: Control


title: MP Additive solution

description:
MP-G3
Primary cells


title: P2239_N707-S508

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N707-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N708-S502

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N707-S506

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N707-S517

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N708-S506

description:
full-lenght RNA-seq
P2239.tsv


title: PLT Control

description:
PLT-G1
Primary cells


title: P2239_N707-S505

description:
full-lenght RNA-seq
P2239.tsv


title: MP Mirasol

description:
MP-G2
Primary cells


title: P2239_N708-S504

description:
full-lenght RNA-seq
P2239.tsv


title: Chromatin-associated RNA, delta-ICP27, 8h p.i., Rep 1

description:
Chromatin-associated RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600205_963_HR


title: Nucleoplasmic RNA, delta-ICP27, 8h p.i., Rep 1

description:
Nucleoplasmic RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600204_963_NR


title: Total RNA, delta-ICP27, 8h p.i., Rep 1

description:
Total RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600202_963_TR


title: Cytoplasmic RNA, delta-ICP27, 8h p.i., Rep 1

description:
Cytoplasmic RNA isolated from delta-ICP27 infected HFF at 8h p.i.
FPKM_loc.txt
L1600203_963_CR


title: P2239_N712-S508

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N707-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N707-S502

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N706-S517

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N707-S503

description:
full-lenght RNA-seq
P2239.tsv


title: Chromatin-associated RNA, Mock, Rep 2 (re-analyzed)

description:
Chromatin-associated RNA isolated from mock infected HFF
FPKM_loc.txt
L1600523_934H

source_name: Chromatin-associated RNA, Mock

value: Mock


title: Nucleoplasmic RNA, HSV-1 8h p.i., Rep 2 (re-analyzed)

description:
Nucleoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600520_935N

source_name: Nucleoplasmic RNA, HSV-1 8h p.i.

value: wild-type HSV-1 strain 17


title: P2239_N706-S505

description:
full-lenght RNA-seq
P2239.tsv

value: Colorectal cancer


title: P2239_N706-S503

description:
full-lenght RNA-seq
P2239.tsv

value: PDOX


title: P2239_N705-S517

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N706-S508

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N706-S506

description:
full-lenght RNA-seq
P2239.tsv


title: Nucleoplasmic RNA, HSV-1 8h p.i., Rep 1 (re-analyzed)

description:
Nucleoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600196_961_NR

value: human foreskin fibroblasts (HFFs)


title: Total RNA, HSV-1 8h p.i., Rep 2 (re-analyzed)

description:
Total RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600512_935T

source_name: Total RNA, HSV-1 8h p.i.


title: P2239_N706-S502

description:
full-lenght RNA-seq
P2239.tsv


title: Nucleoplasmic RNA, Mock, Rep 2 (re-analyzed)

description:
Nucleoplasmic RNA isolated from mock infected HFF
FPKM_loc.txt
L1600519_934N

source_name: Nucleoplasmic RNA, Mock


title: Total RNA, Mock, Rep 2 (re-analyzed)

description:
Total RNA isolated from mock infected HFF
FPKM_loc.txt
L1600511_934T

source_name: Total RNA, Mock


title: Chromatin-associated RNA, HSV-1 8h p.i., Rep 2 (re-analyzed)

description:
Chromatin-associated RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600524_935H

source_name: Chromatin-associated RNA, HSV-1 8h p.i.


title: P2239_N705-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N705-S508

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N705-S506

description:
full-lenght RNA-seq
P2239.tsv


title: Cytoplasmic RNA, Mock, Rep 2 (re-analyzed)

description:
Cytoplasmic RNA isolated from mock infected HFF
FPKM_loc.txt
L1600515_934C

source_name: Cytoplasmic RNA, Mock


title: Cytoplasmic RNA, HSV-1 8h p.i., Rep 1 (re-analyzed)

description:
Cytoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600195_961_CR

source_name: Cytoplasmic RNA, HSV-1 8h p.i.


title: P2239_N705-S505

description:
full-lenght RNA-seq
P2239.tsv


title: Total RNA, HSV-1 8h p.i., Rep 1 (re-analyzed)

description:
Total RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600194_961_TR


title: Chromatin-associated RNA, Mock, Rep 1 (re-analyzed)

description:
Chromatin-associated RNA isolated from mock infected HFF
FPKM_loc.txt
L1600193_960_HR


title: P2239_N706-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N706-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N705-S503

description:
full-lenght RNA-seq
P2239.tsv


title: Chromatin-associated RNA, HSV-1 8h p.i., Rep 1 (re-analyzed)

description:
Chromatin-associated RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600197_961_HR


title: Total RNA, Mock, Rep 1 (re-analyzed)

description:
Total RNA isolated from mock infected HFF
FPKM_loc.txt
L1600190_960_TR


title: P2239_N704-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N704-S517

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N704-S506

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N704-S508

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N704-S505

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N705-S504

description:
full-lenght RNA-seq
P2239.tsv


title: Cold-insensitive POA neurons Replicate 3

city: New Haven

first: Viktor

last: Feketa

state: CT

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

institute: Yale University

data_processing:
Primary analysis performed using Illumina's CASAVA 1.8.2 software suite.
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.36 (Bolger et al., 2014) with default parameters
Filtered high-quality reads from all samples were aligned to the mouse reference genome (Gencode; Release M16 [GRCm38.p6]; all files accessed on 2/23/2018) using STAR aligner v2.5.4b with default parameters (Dobin et al., 2013).
Aligned reads were counted by featureCounts program within the Subread package v1.6.2 with default parameters (Liao et al., 2014).
Differential expression of genes based on read counts and fold-change between cold-sensitive and -insensitive neurons was determined by EdgeR v3.22.3 (Robinson et al., 2010) using the following parameters: features with zero counts in at least one sample were excluded prior to statistical analysis; statistical analysis was performed using the GLM approach and the quasi-likelihood F-test; features with less than 1 normalized read/million in at least one sample were excluded post statistical analysis; features were filtered to include only those with the adjusted p-value ≤ 0.05 and sorted by the largest fold-change.
Genome_build: The reference genome and the gene annotation were obtained from the Gencode project (Release M16 [GRCm38.p6]; all files accessed on 2/23/2018).  Reference genome: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M16/GRCm38.primary_assembly.genome.fa.gz;  Gene annotation: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M16/gencode.vM16.annotation.gff3.gz;
Supplementary_files_format_and_content: The output file (RNASeq_Feketa_2019.xlsx) is based on EdgeR output and additional processing in R. It includes the following columns: Gene Symbol, from the output of featureCounts, based on the supplied GenCode annotation; Fold-Change: fold-change in mean normalized read counts between cold-sensitive and cold-insensitive groups; PValue: p-value, calculated by EdgeR using the GLM approach and quasi-likelihood F-test; NormMean_NonCold and NormMean_Cold: mean normalized counts (reads/million) for the cold-sensitive and cold-insensitive groups respectively; S2/S4/S6_NonCold_raw_counts & S1/S3/S7_Cold_raw_counts: raw counts for 3 cold-insensitive samples (S2, S4, S6) and 3 cold-sensitive samples (S1, S3, S7); S2/S4/S6_NonCold_norm_counts & S1/S3/S7_Cold_norm_counts: normalized counts (reads/million) for 3 cold-insensitive samples (S2, S4, S6) and 3 cold-sensitive samples (S1, S3, S7) as calculated by EdgeR. After exclusion of low-expressed genes, the final list contains 9583 features (genes).

source_name: Neurons from the pre-optic area of hypothalamus

growth_protocol: Mice were housed under standard conditions.

extract_protocol:
Primary neurons were isolated from the POA of hypothalamus following a published protocol (Vazirani RP, Fioramonti X, Routh VH. Membrane potential dye imaging of ventromedial hypothalamus neurons from adult mice to study glucose sensing. J Vis Exp. 2013;(81):50861. Published 2013 Nov 27. doi:10.3791/50861) with modifications. Mice were euthanized by isoflurane inhalation overdose followed by cardiac perfusion with the Brain Perfusion Solution. Brain was dissected and brain slices were cut on a vibratome. A brain slice containing the POA was identified by the presence of the anterior commissure crossover, and 2 successive 300-µm slices containing the POA were collected. A square region approximately 2x3 mm between the optic chiasm and anterior commissure crossover containing the POA was microdissected from the brain slices. Tissue was digested in custom formulation of Hibernate A medium containing 20 U/ml papain in a shaking water bath at 34°C for 30 min and dissociated by mechanical trituration. Cell suspension was centrifuged over 8% bovine serum albumin layer, resuspended in custom formulation of Neurobasal-A medium, plated on poly-D-lysine/laminin-coated and cultured in an incubator at 34°C in 5% CO2. POA neurons acutely cultured on coverslips were loaded with 10 µM Fura 2-AM and 0.02% Pluronic F-127 in the Recording Solution. Cold sensitivity of POA neurons was determined as the amplitude of response to cooling from room temperature to ~10°C by live-cell ratiometric calcium imaging. Following the identification of cold-sensitive POA neurons single cold-sensitive and -insensitive neurons were separately collected and pooled for subsequent transcriptomic analysis. Cold-sensitive neurons, defined as those in the top 7% by cold response amplitude, as well as cold-insensitive neurons, in the bottom 14%, were targeted for collection. Collected neurons were deposited into the RNA Lysis Buffer (Quick-RNA Microprep Kit, Zymo). Cell collection was repeated with each coverslip (5-6 total per one neuron isolation procedure) using a different aspiration pipette and collected cells of the same type (cold-sensitive and -insensitive) from each coverslip were pooled together in one tube. Samples were then stored at -80°C until RNA isolation. The procedure was repeated with 2-6 independent neuronal isolations and cell collection sessions until ~100-200 cells were collected to obtain 1 biological replicate, with a total of 3 biological replicates. All samples of one type within each biological replicate were then pooled together and RNA was isolated using the Quick-RNA Microprep Kit (Zymo) according to manufacturer’s instructions. RNA concentration and integrity were assessed by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). RNA concentrations were in the range of 58-211 pg/µl and RIN values were in the range of 4.0-8.9.
Library preparation and sequencing were carried out at the Yale Center for Genome Analysis. Sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Cat. #635005, Clontech/Takara Bio, Mountain View, CA) including rRNA depletion.

treatment_protocol: Naïve wild-type C57Bl/6J mice were used for the study.

tag: tissue

tag: neuron type

value: Cold-insensitive

tag: age

value: 6-14 weeks

tag: strain


title: Cold-insensitive POA neurons Replicate 2

value: Neurons from the pre-optic area of hypothalamus


title: P2239_N704-S503

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N704-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N703-S508

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N703-S505

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N703-S503

description:
full-lenght RNA-seq
P2239.tsv


title: Cold-sensitive POA neurons Replicate 3

value: Cold-sensitive


title: Cytoplasmic RNA, HSV-1 8h p.i., Rep 2 (re-analyzed)

description:
Cytoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.
FPKM_loc.txt
L1600516_935C

value: 8h p.i.

value: Cytoplasmic RNA


title: Cold-insensitive POA neurons Replicate 1


title: Cold-sensitive POA neurons Replicate 2


title: P2239_N704-S502

description:
full-lenght RNA-seq
P2239.tsv


title: Nucleoplasmic RNA, Mock, Rep 1 (re-analyzed)

description:
Nucleoplasmic RNA isolated from mock infected HFF
FPKM_loc.txt
L1600192_960_NR

value: Nucleoplasmic RNA


title: Cold-sensitive POA neurons Replicate 1


title: P2239_N703-S504

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N703-S506

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N703-S517

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N703-S507

description:
full-lenght RNA-seq
P2239.tsv


title: Cytoplasmic RNA, Mock, Rep 1 (re-analyzed)

description:
Cytoplasmic RNA isolated from mock infected HFF
FPKM_loc.txt
L1600191_960_CR


title: P2239_N705-S502

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N703-S502

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N702-S517

description:
full-lenght RNA-seq
P2239.tsv


title: HIV4 HIV-specific Memory B Cells

city: Bethesda

first: James

middle: Wesley

last: Austin

state: MD

address: 9000 Rockville Pike, Bldg 10, Room 6A05

institute: NIH

data_processing:
bcl files were converted to FASTQ using bcl2fastq v 2.17.1.14
Reads were mapped and counted using STAR v2.5.2
Variance stabilized gene counts and differential gene expression was determined by DEseq2
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text file contains raw read counts for all samples

source_name: Lymph node

extract_protocol:
Cells were FACS sorted directly into Trizol LS and RNA was isolated using the Zymo Clean and Concentrator kit
Libraries were constructed using the NuGen Ovation SoLo RNA-seq system per the manufacturer's instructions

value: HIV-specific IgG switched Memory B Cell

value: HIV-infected

tag: donor


title: HIV4 IgG+ Memory B Cells

value: IgG switched Memory B Cell


title: HIV4 Memory B Cells

value: Memory B Cell


title: P2239_N702-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N702-S506

description:
full-lenght RNA-seq
P2239.tsv


title: HIV4 HIV-specific GC

value: HIV-specific IgG switched Germinal Center B Cell


title: P2239_N702-S505

description:
full-lenght RNA-seq
P2239.tsv


title: HIV4 Unswitched Memory

value: Unswitched Memory B Cell


title: P2239_N702-S504

description:
full-lenght RNA-seq
P2239.tsv


title: HIV4 IgG+ GC

value: IgG switched Germinal Center B Cell


title: HIV3 IgG+ Memory B Cells


title: HIV3 Naive B Cells

value: Naive B Cell


title: HIV3 Memory B Cells


title: HIV3 HIV-specific Memory B Cells


title: HIV3 HIV-specific GC


title: HIV4 GC

value: Germinal Center B Cell


title: P2239_N702-S503

description:
full-lenght RNA-seq
P2239.tsv

value: Colorectal cancer

value: PDOX


title: HIV3 Unswitched Memory


title: P2239_N701-S505

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N701-S506

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N701-S504

description:
full-lenght RNA-seq
P2239.tsv


title: HIV4 Naive B Cells


title: P2239_N701-S508

description:
full-lenght RNA-seq
P2239.tsv


title: HIV3 IgG+ GC


title: HIV3 GC


title: P2239_N702-S502

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N701-S503

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N701-S507

description:
full-lenght RNA-seq
P2239.tsv


title: P2239_N702-S508

description:
full-lenght RNA-seq
P2239.tsv


title: Exp_229_AU565 Torkinib_n_1

city: Melbourne

first: David

last: Goode

state: Victoria

address: 305 Grattan Street

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing: RNA sequencing data consisted of 50bp paired-end reads generated from an Illumina HiSeq 2500 instrument (Illumina, CA, USA). Reads were mapped to hg19 (GRCh37.73) using HISAT2 v2.04 (62).  Transcript counts were obtained using HTSeq v0.6.1 (63) and the GENCODE v7 transcript models (64) from the Ensembl annotation database v62(65). Normalised values and log2 ratios relative to parental lines were obtained by using limma-voom v3.34.9 (57). Depth of coverage was >100-fold in 80% of the targeted regions in all samples, rising to >100-fold in 90% of the targeted regions for 21/24 samples (88%).

source_name: Human breast cancer cell line

growth_protocol: Untreated controls were cultured as follows: 94T778 cells and SKBR3 were grown in RPMI 1640 Gibco supplemented with penicillin, streptomycin, L-glutamine and 10% fetal bovine serum (FBS). AU565 were grown in RPMI complete media supplemented with 1mM sodium pyruvate and 1.5g/L sodium bicarbonate. A375 cells were grown in DMEM Gibco media supplemented with penicillin, streptomycin, L-glutamine and 10% fetal bovine serum (FBS). SKMEL28 were grown in MEM Gibco supplemented with penicillin, streptomycin, L-glutamine and 10% fetal bovine serum (FBS).

extract_protocol: Qiagen RNeasy midi kit

treatment_protocol: Drug concentrations were selected to halt cell cycle progression without affecting cell viability: 94T778 10 µM, A375, SKMEL28 and AU565 4 µM, SKBR3 0.8 µM. The pharmacologic inhibition of MTOR repressed expression of the homologous recombination (HR) and Fanconi Anemia (FA) pathways, and selectively high-fidelity but not error-prone DNA polymerases  in all cancer cell lines sequenced

tag: cell line

value: 4 uM Torkinib

tag: sample name


title: HIV2 Memory B Cells


title: Exp_229_AU565 Torkinib_n_2


title: P2239_N701-S502

description:
full-lenght RNA-seq
P2239.tsv


title: HIV2 HIV-specific Memory B Cells


title: HIV2 IgG+ Memory B Cells


title: Exp_229_SKBR3 Torkinib_n_1

value: 0.8 uM Torkinib


title: Exp_229_SKBR3 Torkinib_n_2


title: P2239_N701-S517

description:
full-lenght RNA-seq
P2239.tsv


title: HIV2 Naive B Cells


title: HIV2 Unswitched Memory


title: Exp_229_SKMEL28 Torkinib_n_2

source_name: Human melanoma cell line


title: Exp_229_SKMEL28 Torkinib_n_1


title: HIV2 HIV-specific GC


title: Exp_229_A375 Torkinib_n_2


title: Exp_229_A375 Torkinib_n_1


title: Exp_229_778 Torkinib_n_2

source_name: Human well differentiated liposarcoma

value: 10 uM Torkinib


title: HIV2 GC


title: HIV1 IgG+ Memory B Cells


title: HIV1 HIV-specific Memory B Cells


title: HIV1 Naive B Cells


title: HIV1 Memory B Cells


title: HIV1 Unswitched Memory


title: Exp_229_AU565 untreated_n_2

value: untreated


title: HIV1 HIV-specific GC


title: Exp_229_AU565 untreated_n_1


title: HIV1 IgG+ GC


title: Exp_229_SKBR3 untreated_n_2


title: Day 4 adult injured 4x, bio rep 3

city: Dallas

first: Peter

middle: M

last: Douglas

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

description:
PD11041544C
Caenorhabditis_D4-9
Day 4 adult C. elegans injured 4x

hyb_protocol: Standard protocol.

scan_protocol: Standard protocol.

data_processing: Data were processed with Bioconductor according to the GC-RMA method, including quantile normalization, chip averaging, and background adjustment.

organism: Caenorhabditis elegans

source_name: Day 4 adult C. elegans

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: Egg synchronization by hypochlorite treatment followed by growth at 25C.

extract_protocol: Qiazol extraction followed by purification with RNeasy mini kit.

treatment_protocol: Paralytic Injury on Precellys 24 (max settings, 20 sec) in M9 or only incubation in M9 (uninjured).

value: Day 4 adult

value: All tissues

value: Paralytic injury 4x


title: Day 4 adult injured 4x, bio rep 2

description:
PD11041544B
Caenorhabditis_D4-8
Day 4 adult C. elegans injured 4x


title: Exp_229_SKBR3 untreated_n_1


title: Day 4 adult injured, bio rep 3

description:
PD11041541C
Caenorhabditis_D4-6
Day 4 adult C. elegans injured at day 4

value: Paralytic injury


title: Day 4 adult injured 4x, bio rep 1

description:
PD11041544A
Caenorhabditis_D4-7
Day 4 adult C. elegans injured 4x


title: Day 4 adult injured, bio rep 2

description:
PD11041541B
Caenorhabditis_D4-5
Day 4 adult C. elegans injured at day 4


title: Exp_229_SKMEL28 untreated_n_2


title: HIV1 GC

value: HIV-infected


title: Exp_229_778 Torkinib_n_1


title: Day 1 adult injured, bio rep 3

description:
PD11041511C
Caenorhabditis_D1-6
Day 1 adult C. elegans injured at day 1

source_name: Day 1 adult C. elegans

value: Day 1 adult


title: Exp_229_A375 untreated_n_2


title: Day 4 adult uninjured, bio rep 1

description:
PD11041540A
Caenorhabditis_D4-1
Day 4 adult C. elegans without injury

value: Uninjured


title: BV173 OR21 treated

type: genomic

city: Saga

first: Shinya

last: Kimura

address: 5-1-1 Nabeshima

department: Drug Discovery and Biomedical Sciences, Faculty of Medicine

country: Japan

institute: Saga University

description: OR21 treated 96hrs

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
Genome Studio software (V2011.1 Methylation module 1.9.0) and MethylationEPIC_v-1-0_B4 was used.  Beta values were obtained after background correction and normalization to internal controls.
[OR21forMDS_normalized_data.txt]  normalized Average Beta
[non-normalized_data.txt] Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Chronic Myeloid Leukemia

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using QIAamp DNA Kit (Qiagen)

value: Chronic Myeloid Leukemia


title: Exp_229_SKMEL28 untreated_n_1


title: HD5 Unswitched Memory

value: Unswitched Memory B Cell

value: Uninfected


title: BV173 control

description: control

value: control


title: Day 4 adult injured, bio rep 1

description:
PD11041541A
Caenorhabditis_D4-4
Day 4 adult C. elegans injured at day 4


title: Day 4 adult uninjured, bio rep 2

description:
PD11041540B
Caenorhabditis_D4-2
Day 4 adult C. elegans without injury


title: HD5 Memory B Cells

value: Memory B Cell


title: HD5 Naive B Cells

value: Naive B Cell


title: Day 1 adult injured, bio rep 1

description:
PD11041511A
Caenorhabditis_D1-4
Day 1 adult C. elegans injured at day 1


title: Day 1 adult injured, bio rep 2

description:
PD11041511B
Caenorhabditis_D1-5
Day 1 adult C. elegans injured at day 1


title: K562 OR21 treated

description: OR21 treated 96hrs


title: HD4 Memory B Cells


title: K562 control

description: control


title: Day 1 adult uninjured, bio rep 2

description:
PD11041510B
Caenorhabditis_D1-2
Day 1 adult C. elegans without injury


title: Exp_229_778 untreated_n_2


title: Exp_229_778 untreated_n_1


title: Day 4 adult uninjured, bio rep 3

description:
PD11041540C
Caenorhabditis_D4-3
Day 4 adult C. elegans without injury


title: HD4 Naive B Cells


title: Day 1 adult uninjured, bio rep 3

description:
PD11041510C
Caenorhabditis_D1-3
Day 1 adult C. elegans without injury


title: Day 1 adult uninjured, bio rep 1

description:
PD11041510A
Caenorhabditis_D1-1
Day 1 adult C. elegans without injury


title: Bladder_healthy_PBS_exp2

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Gene expression data from healthy mice bladder

hyb_protocol: 6ug of fragmented and labelled cRNA was hybridized onto Mouse Genome 430 PM array strips (Affymetrix) for 16 hours at 45 °C, washed, stained (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Scanning was done using the GeneAtlas system (Affymetrix).

data_processing: Transcriptomic data was normalized using Robust Multi Average implemented in the Transcriptome Analysis Console software (v.4.0.1.36, Applied Biosystems, ThermoFisher Scientific).

source_name: Mice healthy bladder

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented (GeneChip 3´IVT Express Kit). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 cells. On day 0, bladders were preconditioned by intravesical instillation of poly-L-lysine followed by instillation of MB49 mouse bladder carcinoma cells.

extract_protocol: Frozen bladder tissue was pulverized using liquid nitrogen, total RNA was extracted (RNeasy Mini kit, Qiagen), according to the manufacturer's instructions.

treatment_protocol: The treatment group received alpha1-oleate by intravesical instillation (1.7 mM, 8.5 mM or 17 mM) on days 3, 5, 7, 9 and 11, sham treated animals received PBS.

tag: gender

value: female

value: bladder

tag: agent

value: PBS

tag: dose

tag: cancer model

tag: disease

value: healthy

tag: sacrifice time

tag: experiment


title: HD4 Unswitched Memory

tag: cell type

tag: infection


title: Bladder_healthy_17mM_24h_exp2

description: Gene expression data from healthy mice bladder 24h after treatment with 17mM of alpha1-oleate

source_name: Mice healthy bladder treated with 17mM alpha1-oleate, 24h


title: 778 R Tunicamycin 04/02/2014

data_processing: RNA sequencing data consisted of 50bp paired-end reads generated from an Illumina HiSeq 2500 instrument (Illumina, CA, USA). Reads were mapped to hg19 (GRCh37.73) using HISAT2 v2.04 (62).  Transcript counts were obtained using HTSeq v0.6.1 (63) and the GENCODE v7 transcript models (64) from the Ensembl annotation database v62(65). Normalised values and log2 ratios relative to parental lines were obtained by using limma-voom v3.34.9.

growth_protocol: Untreated cells were cultured in  in RPMI 1640 Gibco supplemented with penicillin, streptomycin, L-glutamine and 10% fetal bovine serum

treatment_protocol: 94T778 cells were exposed to nutlin-3a 2.5µM, palbociclib 7µm and tunicamycin 0.14 µM. Cells were harvested during the early phase of the adaptive evolution in 94T778 cells exposed to palbociclib (P), nutlin-3a (N) and tunicamycin (T) sampled at 10 weeks for P and N and at 9 weeks post-bottleneck for T condition.

value: 94T778 cells

tag: treatment

value: tunicamycin 0.14 uM


title: HD4 GC

value: Germinal Center B Cell


title: HL60 OR21 resistant AZA treated

description: AZA treated 96hrs

source_name: Acute Myeloid Leukemia

tag: disease state

value: Acute Myeloid Leukemia

value: HL60 OR21-resistant

value: AZA


title: HL60 OR21 resistant control

description: control


title: HL60 OR21 resistant OR21 treated

description: OR21 treated 96hrs


title: Bladder_tumor_PBS_exp2

description: Gene expression data from MB49-induced bladder cancer mice sham-treated

source_name: Mice bladder cancer treated with PBS

tag: tissue

value: MB49 bladder cancer

value: bladder cancer


title: Bladder_healthy_17mM_7d_exp2

description: Gene expression data from healthy mice bladder 7d after treatment with 17mM of alpha1-oleate

source_name: Mice healthy bladder treated with 17mM alpha1-oleate, 7d


title: HL60 AZA resistant OR21 treated

description: OR21 treated 96hrs

value: HL60 AZA-resistant


title: 778 R CDK4i 03/01/2014

value: palbociclib 7um


title: HL60 AZA resistant control

description: control

value: control


title: HL60 AZA resistant AZA treated

description: AZA treated 96hrs


title: HD3 Naive B Cells

value: Uninfected


title: 778 R Nutlin 04/02/2014

value: nutlin-3a 2.5uM


title: HD3 Unswitched Memory

value: Unswitched Memory B Cell


title: HD5 GC


title: Exp_229_A375 untreated_n_1

value: untreated


title: Bladder_healthy_PBS_exp1

value: female

value: bladder

value: PBS


title: 778 R Nutlin 03/01/2014

value: 94T778 cells


title: 778 R CDK4i 04/02/2014


title: Bladder_tumor_PBS_exp1


title: HD3 Memory B Cells

value: Memory B Cell


title: MDS-L OR21 treated

description: OR21 treated 96hrs

source_name: Myelodysplastic Syndrome

value: Myelodysplastic Syndrome

value: MDS-L


title: HD3 GC

value: Germinal Center B Cell


title: MDS-L control

description: control


title: 778 parental 24/03/2014


title: HD2 Memory B Cells


title: A549 cells, pSV1.0_3

hyb_protocol: Follow the guide of Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.Genespring V13.1(Agilent)was used for normalized and further processed.

source_name: A549 cell

treatment_protocol: The plasmids expressing wild-type IFN-κ or IFN-κDual, or empty vector (mock) were individually transfected into A549 by TurboFect (Thermo Scientific, R0531)

tag: transfection


title: 778 parental 16/05/2014


title: HL60 Parent OR21 treated

description: OR21 treated 96hrs

value: Acute Myeloid Leukemia

value: HL60 Parent


title: Bladder_tumor_1.7mM_exp1

description: Gene expression data from MB49-induced bladder cancer mice treated with 1.7mM of alpha1-oleate

source_name: Mice bladder cancer treated with 1.7mM alpha1-oleate

tag: strain

value: MB49 bladder cancer

value: bladder cancer


title: HL60 Parent AZA treated

description: AZA treated 96hrs

value: AZA


title: 778 parental 04/02/2014


title: HL60 Parent control

description: control

value: control


title: HD2 GC

value: Uninfected

tag: donor


title: HD2 Unswitched Memory

value: Unswitched Memory B Cell


title: 5.0BAA894 lpxM

city: wuxi

first: Hua

last: Jingjing

address: 1800 Lihu Road

institute: Jiangnan University

description: BAA894_PH7_37-VS-5.0BAA894 lpxM.GeneDiffExp

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCF_000982825.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Cronobacter sakazakii

source_name: strain cells

growth_protocol: C. sakazaki was inoculated into fresh LB and grown to reach middle exponential growth phase at 37℃

extract_protocol:
Total RNA was extracted from cultures using an RNA extraction kit (BioFlux, Beijing, China).mRNA was purified from total RNA using Dynabeads mRNA direct micro kit (Thermo Fisher Scientific, Waltham, USA)
RNA-seq libraries were constructed using the Illumina Paired End Sample Prep kit and all samples were sequenced using the Illumina HiSeq 2000 (BGI Shenzhen, China).

tag: genotype

value: lpxM muntant


title: HD1 Memory B Cells


title: UG5

city: Socorro

first: Rebecca

last: Reiss

state: NM

address: 801 Leroy Place

department: Biology

institute: New Mexico Institute of Mining and Technology

description:
72 h growth on Ultrafine Grain substrate replicate 2
NanoTi_E1_processed_data.csv

data_processing:
The libraries were run in a single lane of a flow cell on an Illumina HiSeq 2000 using manufacturer’s protocols for single-end 50 bp reads. Basecalling was done by Casava v1.8.
Fastq files were uploaded into the data management program Luminogix. Read quality was checked with fastqc.
The Genomic Short-read Nucleotide Alignment Program (GSNAP) was used to align reads to the mouse reference genome GRCm38. HTSeq-count was used to generate read counts per gene.
Read count files were normalized and statistically analyzed with empirical analysis of digital gene expression data in R (EdgeR).
Output from statistical analysis were loaded into JMP v 11 (JMP, Cary, NC) for selection of genes for subsequent enrichment analysis and visualization protocols.
Data mining, enrichment analyses, and network visualization were performed with Cytoscape v3.4.0 app ClueGO v2.3.2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma separated value EdgeR output containing Esembl Gene id, Direction, Position, Gene Symbol, Title, log fold-change (FC), log counts per million (CPM), p-value, FDR, Raw counts for CG2, Raw counts for CG3, Raw counts for UG4, Raw counts for UG5

source_name: Bone/Calvaria

growth_protocol:
Commercially pure Grade 4 titanium  Carpenter Technology Corporation (Reading, Pennsylvania), subjected to ECAP-C,  8 passes of route Bc at 200 C° to 350 C°
Mouse Preosteoblast MC3T3 sub-clone 4 cells (ATCC® CRL-2593™) were grown in Alpha Minimum Essential Medium with ribonucleosides, deoxyribonucleosides and 2mM L-glutamine (MEM α, GIBCO, Grand Island, NY) with 10% fetal bovine serum (FBS, GIBCO), supplemented with 1% penicillin/streptomycin (Cellgro, Manassas, VA). Plates were maintained at 37º C with a constant 5% CO2 atmosphere.

extract_protocol:
RNA was extracted with a Direct-zol RNA Mini Prep kit using the standard protocol (Zymo Research Corp., R2050) and included the treatment of the RNA with DNase I to eliminate genomic DNA. RNA concentrations and quality were determined using a Nanodrop 2000 UV-Vis Spectrophotometer (Thermo Scientific). RNA concentrations were confirmed with the Qubit RNA HS assay kit (ThermoFisher Scientific, Q32852). RNA size and integrity was measured using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Replicates for each treatment (UG, CG) were chosen for library preparation based on RNA quality.  Ribosomal RNA subtraction was done using the Ribo-Zero® Gold rRNA Removal Kit (Illumina, San Diego). Next generation sequencing libraries preparation utilized an Illumina TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego). Unique indexes were added to each of the nine samples during library construction.

treatment_protocol: One mm thick disks were cut from rods of 13.5 mm in diameter. Disks were polished to a 2 nm average surface roughness (Ra).  A 2 mm flat section was ground on diametrically opposed edges of the otherwise circular disks. Disks were arrayed in 24-well culture untreated culture disk using a block design. Wells seeded with 3 x 104 cells, refed after 24 hours, and harvested by removing discs to new plate with trypsin.  Four wells consolidated per sample. Stored in RNA later, -80.

tag: cell

value: preosteoblast

tag: cell line

value: MC3T3-E1 Subclone 4

tag: biosource provider

value: ATCC CRL-2593

tag: substrate

value: ultrafine grain


title: BAA894_PH7_37

tag: protocol

value: grow at pH 7.0

value: wildtype


title: HD1 Naive B Cells

source_name: Lymph node

value: Naive B Cell


title: A549 cells, IFN-κDual_3

value: IFN-κDual


title: UG4

description:
72 h growth on Ultrafine Grain substrate replicate 1
NanoTi_E1_processed_data.csv


title: A549 cells, pSV1.0_2


title: A549 cells, pSV1.0_1


title: 778 parental 08/04/2014

value: 94T778 cells


title: 5.0BAA894pmrA

value: pmrA muntant


title: A549 cells, IFN-κDual_2


title: A549 cells, IFN-κDual_1


title: CG3

description:
72 h growth on Coarse Grain substrate replicate 2
NanoTi_E1_processed_data.csv

growth_protocol:
Commercially pure Grade 4 titanium Carpenter Technology Corporation (Reading, Pennsylvania), As-received
Mouse Preosteoblast MC3T3 sub-clone 4 cells (ATCC® CRL-2593™) were grown in Alpha Minimum Essential Medium with ribonucleosides, deoxyribonucleosides and 2mM L-glutamine (MEM α, GIBCO, Grand Island, NY) with 10% fetal bovine serum (FBS, GIBCO), supplemented with 1% penicillin/streptomycin (Cellgro, Manassas, VA). Plates were maintained at 37º C with a constant 5% CO2 atmosphere.

value: coarse grain


title: HD1 Unswitched Memory


title: 5.0BAA894eptA

value: eptA muntant


title: Bladder_tumor_17mM_exp1

description: Gene expression data from MB49-induced bladder cancer mice treated with 17mM of alpha1-oleate

source_name: Mice bladder cancer treated with 17mM alpha1-oleate

tag: gender

value: female

value: bladder

tag: agent

tag: dose

tag: cancer model

value: MB49 bladder cancer

tag: disease

value: bladder cancer


title: A549 cells, IFN-κ_3

value: IFN-κ


title: HD1 GC

tag: cell type

value: Germinal Center B Cell

tag: infection

value: Uninfected


title: CG2

description:
72 h growth on Coarse Grain substrate replicate 1
NanoTi_E1_processed_data.csv

value: preosteoblast

value: MC3T3-E1 Subclone 4

value: ATCC CRL-2593


title: 5.0BAA894

value: grow at pH 5.0

value: wildtype


title: CEPH1408-H1

status: Public on Apr 08 2020

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
cell line: CEPH1408 cells
experiment: N/A

data_processing:
Library strategy: Exome-Seq
Alignment using Picard (http://broadinstitute.github.io/picard)
SNV calling using MuTect v1.1.4 (Cibulskis et al., 2013) and annotation using Varient Effect Predictor (VEP, McLaren et al., 2010). MuTect was run in paired mode pairing the tumor samples to the project normal, CEPH 1408.
Indel calling using GATK
Variant annotation using OncoAnnotate
CNV calling using RobustCNV. RobustCNV relies on localized changes in mapping depth of sequenced reads in order to identify changes in copy number. Observed values are normalized against the mapping depth in a panel of normals (PON) sampled with the same capture bait set. Normalized coverage data are then segmented using Circular Binary Segmentation (Olshen et al., 2004) with the DNAcopy Bioconductor package. Finally, segments are assigned gain, loss, or normal-copy calls using a cutoff derived from the within-segment standard deviation and a tuning parameter set based on comparisons to array-CGH calls in separate validation experiments.
Genome_build: b37
Supplementary_files_format_and_content: SNV and indel report contains variants with genomic coordinates, gene, DNA and protein change, allele fraction, coverage, and annotations from dbSNP, COSMIC, and gnomAD. CNV report contains gene level calls, with genomic coordinates and coverage levels, and chromosome arm-level calls.

source_name: normal control

growth_protocol: Cells were lentivirally infected with the ClonTracer barcode library (Bhang et al., 2015). Barcoded cells were passaged in vitro in the presence of drug or injected orthotopically into mammary fat pads of NOG mice to produce xenografts.

extract_protocol:
DNA was extracted from frozen cultured cells and xenografts using the AllPrep DNA/RNA Mini Kit or the QIAamp DNA Mini Kit (Qiagen). Equal amounts of DNA were pooled from replicates for library construction.
DNA was fragmented to 250 bp (Covaris ultrasonication) and further purified using Agencourt AMPure XP beads. Size-selected DNA was ligated to sequencing adaptors with sample-specific barcodes using the KAPA Hyper Prep Kit. Libraries were pooled and sequenced on an Illumina MiSeq nano flow cell to estimate the library DNA concentration based on the number of barcode reads per sample. Libraries were pooled and captured using SureSelectXT Human All Exon v5 (Agilent) in 7 x 3-plex and 1 x 2-plex. Captures were performed using the SureSelectXT Reagent Kit (Agilent).

treatment_protocol: Cells were grown in vitro in the presence of DMSO, JQ1 (100 nM), paclitaxel (0.6 nM), palbociclib (160 nM), JQ1+paclitaxel, or JQ1+palbociclib, in triplicates, for up to 18 passages. Mice were treated for up to 2 weeks with vehicle, JQ1 (30-50 mg/kg daily), palbociclib (75 mg/kg daily), paclitaxel (10 mg/kg twice weekly), JQ1+palbociclib, or JQ1+paclitaxel, or for 1 week with JQ1 followed by 1 week with paclitaxel, 1 week with paclitaxel followed by 1 week with JQ1, or 1 week with JQ1+paclitaxel followed by 1 week with vehicle, with 5 mice per group.

value: CEPH1408 cells

tag: treatment


title: A549 cells, IFN-κ_2

first: Yongquan

last: He

address: No.2901 Caolang Road

institute: Fudan University

extract_protocol: RNA were then extracted using RNAzol (Molecular Research Center Inc., USA) in couple with Direct-zol RNA MiniPrep Kit (Zymo Research, Irvine, CA, USA). The quality of RNA was ensured by measurement on an Agilent Bioanalyzer 2100 using RNA NanoChip.

tag: transfection


title: J-4-G3

description: experiment: JQ1+palbociclib in vivo

source_name: breast cancer cells SUM159


title: C-4-E3

description: experiment: JQ1+palbociclib in vivo

value: vehicle


title: PJ-4-H3

description: experiment: JQ1+palbociclib in vivo


title: P-4-F3

description: experiment: JQ1+palbociclib in vivo

value: palbociclib


title: A549 cells, IFN-κ_1


title: T-J-3-C3

description: experiment: JQ1+paclitaxel in vivo


title: JT-3-H2

description: experiment: JQ1+paclitaxel in vivo


title: J-T-3-B3

description: experiment: JQ1+paclitaxel in vivo


title: Pre-3-D2

description: experiment: JQ1+paclitaxel in vivo

value: pre-treatment


title: T-3-F2

description: experiment: JQ1+paclitaxel in vivo

value: paclitaxel


title: J-3-G2

description: experiment: JQ1+paclitaxel in vivo


title: HD2 Naive B Cells

value: Naive B Cell


title: C-3-E2

description: experiment: JQ1+paclitaxel in vivo


title: 10X_scRNAseq_WT_EA

city: Leuven

first: Carmen

last: Bravo González-Blas

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

description: Three experiments analyzed with Cell Ranger (v2.0.2), aggregating samples with 'cellranger aggr --normalize=mapped'

data_processing:
The 10X eye-antennal disc samples were processed (alignment, barcode assignment and UMI counting) with the Cell Ranger (version 2.0.2) count pipeline, using the cellranger aggr command with --normalize=mapped, and building the reference index upon the 3rd 2017 FlyBase release (D. melanogaster r6.16).
Lowly expressed genes detected in less than 11 cells (0.3% of the cells) and with less 32 UMI counts across the data set (3 counts in 0.3% of the cells) were filtered, resulting in a data set with 8,744 genes and 3,531 cells.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited file containing cell barcodes as columns, genes as rows, and raw UMI counts as values. The number at the end of the cell barcode indicates the sequencing run.

organism: Drosophila melanogaster

source_name: L3 Drosophila eye-antennal disc

growth_protocol: All flies were raised and crossed at 25°C on a yeast based medium.

extract_protocol:
Wandering third instar larvae were collected and a total of ~30 eye-antennal discs were dissected and transferred into a tube containing 200 µl of ice-cold PBS. The sample was centrifuged at 800 g for 5 minutes, and after removing the supernatant, 50 µl of dispase (3mg/ml; Sigma-Aldrich_D4818-2mg) and 70 µl of collagenase (100 mg/mL; Invitrogen_17100-017) were added. The tissue was dissociated during 45-60 minutes at 25°C at 550 rpm, pipetting up and down every 15 minutes to disrupt clumps of cells. Cells were washed with 1 mL of ice-cold PBS, and resuspended in 400 µl of PBS 0.04% BSA. The cells were passed through a 10 µm pluriStrainer (ImTec Diagnostics_435001050) and cell viability and concentration were assessed by the LUNA-FL Dual Fluorescence Cell Counter
Single-cell libraries were generated using the GemCode Single-Cell instruments and the Single Cell 3' Library & Gel Bead Kit v2 and ChIP Kit from 10X Genomics, following the protocol provided by the manufacturer. Briefly, the eye-antennal disc cells were suspended in PBS 0.04% BSA. About 8,700 cells were added in each reaction with a targeted cell recovery of 5,000 cells. Following the generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch  Thermal Cycler (Bio Rad) programed at 53°C for 45 min, 85°C for 5 min, and hold at  4°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified with a C1000 Touch Thermal Cycler programed at 98°C for 3 min, 12 cycles of (98°C for 15 s, 67°C for 20 s, 72°C for 1 min), 72°C for 1 min, and held at 4°C twice. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect Reagent Kit (Beckman Coulter) with cleanup in between steps. Post-ligation product was amplified with a C1000 Touch Thermal Cycler programed at 98°C for 45 s, 14 cycles of (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), 72°C for 1 min, and hold at 4°C. The sequencing-ready library was cleaned up with SPRIselect beads.

tag: strain

value: Hybrid of DGRP-551, DGRP-360, DGRP-907 and DGRP-913

tag: sequencing method

value: 10X Genomics Single-cell Gene Expression Solution (v2)


title: JTV-3-D3

description: experiment: JQ1+paclitaxel in vivo


title: J-2-B2

description: experiment: JQ1+palbociclib in vitro


title: PJ_2-C2

description: experiment: JQ1+palbociclib in vitro


title: C-2-G1

description: experiment: JQ1+palbociclib in vitro

value: DMSO


title: T-1-D1

description: experiment: JQ1+paclitaxel in vitro


title: JT-1-F1

description: experiment: JQ1+paclitaxel in vitro


title: J-1-E1

description: experiment: JQ1+paclitaxel in vitro


title: C-1-C1

description: experiment: JQ1+paclitaxel in vitro


title: P-2-A2

description: experiment: JQ1+palbociclib in vitro


title: GMR-GAL4_UAS-TTK88

description: Omni-ATAC-seq protocol as described by Corces et al. (2017)

data_processing:
ATAC-seq reads were first cleaned for adapters using fastq-mcf. (ea-utils v1.12) and a list of sequencing primers. Cleaned reads (FastQC v0.1) were then mapped to the 3rd 2017 FlyBase release (D. melanogaster r6.16) genome using Bowtie2 (v2.2.5) with default parameters, with the single end option (to compare with the WT sample, which was single-end sequenced).
Sorted bam files were produced using using SAMtools (v1.2). Normalized bigwigs were generated using the Kent software (UCSC). Peaks were called on mapped reads using MACS2 (v2.1.2.1) with the following options: -g dm –nomodel –bdg -t Sample/Control -c Sample/Control (depending on whether we want to determine upregulated or downregulated peaks).
Genome_build: dm6
Supplementary_files_format_and_content: Bigwig files containing the normalized coverage profiles of each experiment.

extract_protocol:
Briefly, ~10 eye-antennal discs were dissected and lysed using 50 µl of cold ATAC-Resupension Buffer (RSB) (see Corces et al. for composition) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubating the cells for 3 min on ice. The lysis was washed out by adding 1 mL of cold ATAC-RSB containing 0.1% Tween-20 and inverting the tube three times.
Nuclei were pelleted at 500 RCF for 10 min at 4°C, the supernatant was carefully removed and nuclei were resuspended in 50 µl of transposition mixture (25 µl 2x TD buffer (see Corces et al. for composition), 2.5 µl transposase (100 nM), 16.5 µl DPBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O) by pipetting six times up and down, followed by 30 minutes incubation at 37°C at 1000 RPM mixing rate. After MinElute clean-up and elution in 21 µl elution buffer, the transposed fragments were pre-amplified with Nextera primers by mixing 20 µl of transposed sample, 2.5 µl of both forward and reverse primers (25 µM) and 25 µl of 2x NEBNext Master Mix (program: 72°C for 5 min, 98°C for 30 sec and 5 cycles of [98°C for 10 sec, 63 °C for 30 sec, 72°C for 1 min] and hold at 4°C). To determine the required number of additional PCR cycles, a qPCR was performed (see Buenrostro et al.83 for the determination of the number of cycles to be added). The final amplification was done with the additional number of cycles, samples were cleaned-up by MinElute and libraries were prepped using the KAPA Library Quantification Kit as previously described82. Samples were sequenced on a NextSeq500 High Output chip, with 50bp single-end reads.
Omni-ATAC-seq (Corces et al., 2017)

value: Omni-ATAC-seq


title: 10X_scATACseq_WT_EA

description: Two experiments analyzed with Cell Ranger ATAC (v1.0.1), with customized parameters.

data_processing:
The 10X scATAC-seq eye-antennal disc samples were processed (alignment and barcode assignment) with a customized version of the Cell Ranger ATAC (version 1.0.0) pipeline, in which the parameter PEAK_MERGE_DISTANCE was set to 50 (instead of 500) and the parameter PEAK_ODDS_RATIO was set to 4 (instead of 1/5). In addition, the reference index was built upon the 3rd 2017 FlyBase release (D. melanogaster r6.16).
Fragments within defined regulatory regions (such as ctx regions) were counted, resulting in a matrix with 129,553 regulatory regions and 15,387 cells, after filtering out a total of 379 cells based on the number of fragments within bulk peaks and the total number of fragments.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited file containing cell barcodes as columns, ctx regions as rows, and number of fragments as values. The number at the end of the cell barcode indicates the sequencing run.

extract_protocol:
Wandering third instar larvae were collected and a total of ~30 eye-antennal discs were dissected and transferred into a tube containing 200 µL of ice-cold PBS. The sample was centrifuged at 800 g for 5 minutes, and after removing the supernatant, resuspended in 500 µl of nuclei lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1% BSA, and water) and transferred to a dounce homogenizer (Sigma-Aldrich-D8938_2mL). After incubating the sample for 5 minutes on ice, 25 strokes were applied with the loose pestle. The sample was incubated for 10 minutes on ice and after applying 25 strokes with the tight pestle, transferred to a 2 mL tube. The homogenizer and the pestle were rinsed with wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3mM MgCl2, 0.1% Tween-20, 1% BSA and water), and the solution was also transferred to the 2mL tube. The sample was washed once with wash buffer and resuspended on 50 µl of 1X diluted nuclei buffer (10X Genomics). The nuclei were passed through a 10 µm pluriStrainer (ImTec Diagnostics_435001050) and cell viability and nuclei concentration were assessed by the LUNA-FL Dual Fluorescence Cell Counter.
Single-cell libraries were generated using the GemCode Single-Cell instruments and the Single Cell ATAC Library & Gel Bead Kit and ChIP Kit from 10X Genomics, following the protocol provided by the manufacturer. Briefly, the eye-antennal disc nuclei were suspended in 1X diluted nuclei buffer (10X Genomics). About 8,700 nuclei were added in each reaction with a targeted nuclei recovery of 5,000 nuclei. The samples were incubated at 37°C for 1 hour with 10 µl of transposition mix (per reaction, 7 µl ATAC Buffer and 3 µl ATAC Enzyme (10X Genomics)). Following the generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio Rad) programed at 72°C for 5 min, 98°C for 30 sec, 12 cycles of 98°C for 10 sec, 59°C for 30 sec and 72°C for 1 min, and held at 15°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified with a C1000 Touch Thermal Cycler programed at 98°C for 3 min, 12 cycles of (98°C for 15 s, 67°C for 20 s, 72°C for 1 min), 72°C for 1 min, and held at 4°C twice. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect Reagent Kit (Beckman Coulter) with cleanup in between steps. Post-ligation product was amplified with a C1000 Touch Thermal Cycler programed at 98°C for 45 s, 14 cycles of (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), 72°C for 1 min, and hold at 4°C. The sequencing-ready library was cleaned up with SPRIselect beads.

value: 10X Genomics Single-cell ATAC Solution


title: GMR-GAL4_UAS-PROS_L

value: P{w[+mC]=UAS-pros.L}L3a, w[*]


title: GMR-GAL4_UAS-LZ


title: GMR-GAL4_UAS-PSQ


title: GMR-GAL4_UAS-SP1


title: GMR-GAL4_UAS-LOLA_T


title: GMR-GAL4_UAS-TTK69


title: GMR-GAL4_UAS-L3NEO38


title: GMR-GAL4_UAS-LOLA_L


title: GMR-GAL4_UAS-FRU9280