title: silica_5

city: apex

first: Lyle

last: Burgoon

state: nc

address: 216 kelly west dr

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

data_processing:
Our RNA-sequencing analysis pipeline is focused on measuring the abundance of gene transcripts, giving us a measure of gene expression. We start by using Salmon (v0.12.0) to align and measure the number of RNA molecules. Gene-specific transcript abundance is then calculated using the tximport package in R (v3.4.3).
Genome_build: wFleaBase (http://server7.wfleabase.org/genome/Daphnia_magna/openaccess/genes/Genes/earlyaccess/dmagset7finalt9b.puban.mrna.gz)
Supplementary_files_format_and_content: Table/matrix where first column is the gene symbol, subsequent columns are the individual replicate pools for each of the treatment groups or vehicle control.

organism: Daphnia magna

source_name: Daphnia magna (whole organism)

extract_protocol:
For RNA isolation, the pooled daphnids were placed in a new 2-ml Eppendorf tube containing 600 μl of RLT Buffer, β-mercaptoethanol and one 5-mm stainless steel bead. The daphnids were then homogenized in a tissue lyser for 2 minutes. RNA isolation from pooled D. magna samples was then performed with Qiagen RNA mini kits (Product ID# 74104, Qiagen, Germantown, MD, USA). The RNA isolation procedure followed the instructions in the mini kit and included a step treating the samples with DNase solution. The DNase solution preparation followed the kit handbook instructions. Following RNA isolation, RNA concentrations and purity were determined using a Nanodrop 1000 Spectrophotometer (Thermo Fisher Model ND-1000, Thermo Fisher Scientific Inc., USA), and a qualitative RNA integrity examination was conducted using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were prepared with the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA, USA) as per the manufacturer’s instructions using 125 ng of total RNA per sample. Briefly, the poly-A containing mRNA molecules are purified using magnetic beads, fragmented, and synthesized into first strand cDNA. Next, second strand cDNA is synthesized, a single ‘A’ nucleotide is added to the 3’ ends, the single-index adapters are ligated, and DNA fragments are enriched to prepare the final libraries. The size and purity of the libraries were determined on the D1000 ScreenTape on the Agilent TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA). The quantity of the individual libraries was assessed using the KAPA Library Quantification Kit for Illumina Libraries (Kapa Biosystems, Inc., Wilmington, MA, USA) and confirmed using the dsDNA HS Kit on the Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). The concentrations of the libraries were then normalized. The libraries were pooled together with eight libraries per pool, and the pools were quantified using the dsDNA HS Kit on the Qubit 3.0 Fluorometer, followed by further dilution to 5nM. The pools were then sequenced on the HiSeq 4000 system (Illumina) at 1x150 cycles single-read using the HiSeq 3000/4000 SBS kit following the manufacturer’s instructions.

treatment_protocol: The definitive test was conducted under static-renewal conditions for 21 days following OECD test guideline procedures for chronic daphnia toxicity studies (OECD 2012). Fifteen replicate test vessels (i.e. 125-ml glass borosilicate jars) each containing approximately 90 ml of the appropriate test dispersion were prepared per test level and controls. At test initiation, one daphnid was impartially added to each test vessel. The replicate test vessels were placed into a temperature-controlled water bath according to a computer-generated randomization. The target test temperature was 20 ± 1°C. The photoperiod was set at 16 hours light/8 hours dark per day with a target light intensity not to exceed 1500 lux. Dispersions in the replicate test vessels were renewed every Monday, Wednesday and Friday. Daphnids were fed 0.4 ml Raphidocelis subcapitata, and 0.1 ml YTC (yeast, wheat grass, finfish food suspension) daily from test initiation through test day 6. On test days 7 through 20, the feeding ration was increased from 0.4 ml to 0.5 ml R. subcapitata with 0.1 ml YTC. Daphnids were not fed on day 21. The total organic carbon (C) concentration was determined from representative samples of the two food types. The R. subcapitata and YTC suspensions contained 0.331 mg C/ml and 0.675 mg C/ml, respectively. This resulted in a final feeding ration level of approximately 0.2 mg C/daphnid/day throughout the entire exposure period. Dissolved oxygen, temperature, and pH were measured at test initiation and at each test solution renewal from the bulk test dispersions, including the controls. Water temperature was continuously monitored from one surrogate vessel, containing LDW and located in the test area throughout the study. Alkalinity, hardness, and conductivity were measured at least one time per week from the bulk controls and bulk test dispersions. Light intensity was measured at test initiation and weekly throughout the remainder of the exposure period. Observations were made daily for parent mortality and neonate production. Any abnormal behavior or appearances were recorded, if observed. Neonate production was quantified every Monday, Wednesday and Friday. The time (days) to production of first brood was also recorded.

value: neonates (less than 24hrs old)


title: iR-iHEC-2-2

status: Public on Jul 31 2020

type: SRA

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

library_source: transcriptomic

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: TPM table was a csv file

molecule: polyA RNA

organism: Mus musculus

source_name: induced endothelia hematopoietic cells

growth_protocol: Expression of defined factors in ESC/iPSC led to the production of an hematopoietic cell type

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2(Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

treatment_protocol: The single HCs were sorted for RNAseq analysis.

tag: cell type

value: induced endothelia hematopoietic cells

tag: strain


title: Time 32_PyrkII CLD_Rep 2

type: RNA

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

country: USA

institute: Johns Hopkins University, School of Public Health

description: Gene Expression Data

hyb_protocol: The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate (in triplicate for each treatment condition).

scan_protocol: Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.

data_processing: Txt files from the Feature Extraction software were imported into the Partek Genomics Suite (v7.0; Partek) for detailed analyses of gene expression. Within Partek, the gProcessedSignal was imported, and the intensity values were normalized to the 75th percentile, lower expressed genes were filtered out using a max cutoff of <=0.5, and log transformation base 2.0 was performed.

molecule: total RNA

organism: Plasmodium falciparum

source_name: PyrkII CLD Nf54 attB parasites,Time 32, Rep 2

label_protocol: From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).

growth_protocol: Blood-stage P. falciparum parasites were cultured in human erythrocytes at 2% hematocrit in CMA (Complete Medium with Albumax) containing RPMI 1640 medium with L-glutamine (USBiological Life Sciences), supplemented with 20mM HEPES, 0.2% sodium bicarbonate, 12.5μg/ml hypoxanthine, 0.5μM R-lipoic acid, 5g/L Albumax II (Life Technologies) and 25μg/mL gentamicin. Cultures were maintained in 25cm2 gassed flasks (94% N2, 3% O2, 3% CO2) and incubated at 37°C.

extract_protocol: For each data point, RNA was extracted from 100 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.

treatment_protocol: The CLD-PyrKII parasite line was synchronized via magnetic purification and used to seed a 50mL culture flask at 1% parasitemia and 2% hematocrit. Six hours post synchronization (mid-schizogeny) 500nM Shield1 was added, representing time 0. Media containing 500nM Shield1 was replaced at 16 hours and every 24 hours thereafter.

tag: tissue

value: Blood-stage PyrkII CLD Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit in media containing 500nM Shield1

tag: time

value: Time 32

tag: treatment

value: PyrkII CLD

tag: slide id (array batch)

tag: replicate

value: Rep 2


title: Time 24_PyrkII CLD_Rep 2

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 24, Rep 2

value: Time 24


title: CU-3

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: Nasal

data_processing:
cutadapt
STAR alignment
featureCount, gene-level extraction
Genome_build: hg38
Supplementary_files_format_and_content: tab delimeted format Normalized-log2CPM.csv

organism: Homo sapiens

source_name: Nasal brush biopsy

extract_protocol:
Invitrogen Purelink RNA Minikit, supplemented with the Proteinase K and Rnase-Free Dnaset (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nasal epithelial cells

tag: growth conditions

value: cultured epithelia


title: silica_4

tag: developmental stage


title: CU-2

description: Nasal


title: iR-iHEC-2-18


title: iR-iHEC-2-1


title: silica_3


title: silica_2


title: NBR-5

description: Nasal

value: brushed epithelia


title: iR-iHEC-2-3


title: iR-iHEC-2-17


title: iR-iHEC-2-16


title: Time 16_PyrkII CLD_Rep 2

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 16, Rep 2

value: Time 16


title: iR-iHEC-2-15


title: silica_1


title: Time 08_PyrkII CLD_Rep 2

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 08, Rep 2

value: Time 08


title: Time 0_PyrkII CLD_Rep 2

description: Gene Expression Data

source_name: PyrkII CLD Nf54 attB parasites,Time 0, Rep 2

value: Time 0


title: NBR-3

description: Nasal


title: NBR-4

description: Nasal


title: Time 48_Control_Rep 4 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 48, Rep 4

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

value: Time 48

value: Control

value: Rep 4


title: control_5

value: neonates (less than 24hrs old)


title: iR-iHEC-2-13

value: induced endothelia hematopoietic cells


title: control_4


title: iR-iHEC-2-12


title: NBR-1

description: Nasal


title: NBR-2

description: Nasal


title: control_2


title: Time 32_Control_Rep 4 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 4


title: iR-iHEC-2-11


title: CU-1

description: Nasal


title: EPN_1269

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

data_processing:
UMI count matrices were generated using the 10X Genomics Cell Ranger (3.0.1) pipeline with default parameters.
The Seurat package in R was then used to aggregate the matrices, which were further filtered to exclude cells not passing the following QC measures: at least 200 genes detected (UMI > 0), fewer than 30% of UMIs derived from mitochondia, and fewer than 70,000 UMIs (to exclude putative doublets). . Genes were also excluded if they were not expressed in at least 5 cells (UMI count > 0).
Next, we applied Harmony alignment to correct for inter-sample variation due to experimental or sequencing batch effects.
After alignment, the harmony reduction used for UMAP projection and graph based clustering.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix.

source_name: Ependymoma

extract_protocol:
Surgical material was collected at our institution at the time of surgery with consent (COMIRB 95-500) and processed identically. Samples were rapidly dissociated into single cells using a mechanical process as described previously, viably cryopreserved and banked at <80C for later use. Samples were thawed in 2 batches and flow sorted (Astrios EQ) to obtain viable single cells based on propidium iodide (PI) exclusion. Cells were processed using the 10x chromium platform to generate single cell RNA-Seq libraries, which were sequenced on the Illumina HiSeq or NovaSeq.
10x Genomics 3' end library kit (v2)

value: Ependymoma

tag: subtype


title: control_1


title: EPN_1347


title: control_3


title: nano_high_5


title: iR-iHEC-1-8


title: iR-iHEC-1-7


title: Time 24_Control_Rep 4 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 4


title: nano_high_4


title: iR-iHEC-1-6


title: Time 40_Control_Rep 4 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 4

value: Time 40


title: EPN_1329

value: ST-RELA


title: EPN_1158


title: EPN_1386


title: iR-iHEC-1-4


title: iR-iHEC-1-3


title: EPN_1185

value: ST-YAP


title: EPN_1067

value: PFB


title: Time 16_Control_Rep 4 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 4


title: iR-iHEC-1-9


title: Time 08_Control_Rep 4 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 4


title: nano_high_2


title: nano_high_3


title: nano_high_1


title: nano_low_5


title: iR-iHEC-1-2


title: EPN_1048


title: iR-iHEC-1-1


title: nano_low_4


title: EPN_1010


title: nano_low_3


title: iR-iHEC-1-14


title: EPN_987


title: Time 0_Control_Rep 4 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 4


title: Time 48_Control_Rep 3 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 48, Rep 3

value: Rep 3


title: Time 32_Control_Rep 3 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 3

value: Time 32


title: Time 40_Control_Rep 3 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 3


title: Time 24_Control_Rep 3 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 3

value: Time 24


title: nano_low_2

source_name: Daphnia magna (whole organism)


title: nano_low_1


title: Time 16_Control_Rep 3 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 3

value: Time 16


title: iR-iHEC-1-11

source_name: induced endothelia hematopoietic cells


title: iR-iHEC-1-10


title: Time 08_Control_Rep 3 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 3

value: Time 08


title: EPN_781


title: [CuR+Pip] + AB Rep 3: Combined curcumin and piperine treatment followed by addition of Aβ, biology rep3

city: Subang Jaya

first: Aimi Syamima

last: Abdul Manap

state: Selangor

address: No. 1, Jalan Taylor's

country: Malaysia

institute: Taylor's University

description: Gene expression data from cells treated with combined compound of curcumin and piperine followed by addition of amyloid beta

hyb_protocol: In vitro transcription (IVT) generated cRNA was then purified and subjected to 2nd-cycle single-stranded sense cDNA synthesis which was later fragmented, labeled, and hybridized to Human Clariom S Array for 16 hours at 45°C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Applied Biosystems™ GeneChip™ Scanner 3000 7G.

data_processing: The scanned images were inspected for hybridization efficiency and CEL files generated from GeneChip Command Console Software were imported into Transcriptome Analysis Console v4.0 software for array QC. RMA normalization was performed on the samples to generate the quality control (QC) metrics that we routinely use to determine data quality. These include, All Probeset mean, Background mean (Bgrd_Mean), positive and negative probes (POS vs NEG AUC), bacterial spike controls and Poly-A controls.

label: biotin

source_name: SH-SY5Y Neuroblastoma Cell line

label_protocol: 100ng of total RNA was reverse transcribed to produce cDNA/mRNA hybrid molecule, which was subsequently used as a template to create double stranded cDNA. This double-stranded cDNA was then amplified via in vitro transcription (IVT) to produce cRNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: bone marrow

tag: gender

value: female

tag: cell line

value: Neuroblastoma


title: Time 0_Control_Rep 3 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 3

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

value: Time 0

value: Control


title: [CuR+Pip] + AB Rep 2: Combined curcumin and piperine treatment followed by addition of Aβ, biology rep2


title: Time 40_Control_Rep 2 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 2

value: Time 48

value: Rep 2


title: EPN_727

source_name: Ependymoma

value: Ependymoma


title: [CuR+Pip] + AB Rep 1: Combined curcumin and piperine treatment followed by addition of Aβ, biology rep1


title: EPN_723


title: Pip + AB Rep 3: Individual piperine treatment followed by addition of Aβ, biology rep3

description: Gene expression data from cells treated with individual compound of piperine followed by addition of amyloid beta


title: Pip + AB Rep 1: Individual piperine treatment followed by addition of Aβ, biology rep1


title: EPN_965


title: CuR + AB Rep 3: Individual curcumin treatment followed by addition of Aβ, biology rep3

description: Gene expression data from cells treated with individual compound of curcumin followed by addition of amyloid beta


title: Time 24_Control_Rep 2 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 2


title: Time 16_Control_Rep 2 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 2


title: Time 0_Control_Rep 2 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 2


title: Time 40_Control_Rep 1 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 1

value: Time 40

value: Rep 1


title: Time 32_Control_Rep 2 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 2


title: CuR + AB Rep 1: Individual curcumin treatment followed by addition of Aβ, biology rep1


title: Time 08_Control_Rep 2 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 2


title: CuR + AB Rep 2: Individual curcumin treatment followed by addition of Aβ, biology rep2


title: Max-Soy-48h

city: Aarhus

first: Holger

last: Brueggemann

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
Demultiplexing
Fastq quality trimming: cut-off value of 20 (FastX). Fastq to fasta conversion (FastX)
PolyA clipping (READemption 0.3.0). Size filtering: discarding reads shorter than 12 nt (READemption 0.3.0).
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: JWIX01000001-JWIX01000093
Supplementary_files_format_and_content: wiggle

organism: Clostridium tetani

source_name: Bacterial culture

growth_protocol: Bacterial culture, anaerobic conditions, for 24 h or 48 h in TGY broth or Max-Soy broth

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Inc.). Briefly, after bacterial lysis in prelysis buffer containing 50 mM Tris (pH 8.0), 25% sucrose, and 10 mg of lysozyme/ml, RNA was extracted with Trizol, RNA and precipitated in absolute ethanol and stored until utilization at −80°C. A DNase treatment with TURBO DNA-freeTM kit (Ambion) was performed following the manufacturer's instructions. The absence of DNA contamination on RNA extracts was determined after the DNase treatment by performing a real-time PCR.
The cDNA libraries were constructed as previously described (Dugar et al. 2013). The libraries were constructed by Vertis Biotechnology AG, Germany. The cDNA libraries were sequenced using a HiSeq 2000 machine (Illumina) in single-read mode and 100 cycles.

treatment_protocol: growth in different media (TGY and Max-Soy) for 24 h and 48 h

value: strain A

tag: medium

value: Max-Soy


title: Time 48_Control_Rep 1 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 48, Rep 1


title: 40MPa30min_5min_3

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

country: Japan

institute: Japan Aerospace Exploration Agency

description: Gene expression in 30min after 40 Mpa 5min

hyb_protocol: The labeled cRNA (1.65 µg/sample) was hybridized to a microarray using the Agilent Gene Expression Hybridization Kit at 65°C for 17 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1.

organism: Caenorhabditis elegans

source_name: 30 min after 40 MPa 5min,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: C. elegans were maintained for culture on NGM agar plates or on NGM liquid with E. coli OP50 as food source at 20°C.

extract_protocol: Total RNA was extracted with TRIzol Reagent (Invitrogen Corp.).

treatment_protocol: The synchronized N2 adult hermaphrodites (cultured from L1 larvae for 4 days on Escherichia coli OP-50 NGM plate at 20℃) were exposed to a hydrostatic pressure of 40 mega pascal (MPa) for 5 min with a larger customized high-pressure vessel system (Ripken Seiki s-8/8, WNH3/8, WP-1B). After exposure, the animals were cultured in liquid medium ontaining 2 x freeze-dried OP50 (NemaMetrix) for 30min.

tag: age

value: Adult

value: 40 Mpa, 5 minutes


title: Time 24_Control_Rep 1 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 1

value: Time 24


title: Pip + AB Rep 2: Individual piperine treatment followed by addition of Aβ, biology rep2


title: Time 32_Control_Rep 1 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 1

value: Time 32


title: AB Rep 3: Amyloid beta as control, biology rep3

description: Gene expression data from cells treated with amyloid beta as a control

value: bone marrow


title: hippocampus, Gly

city: HangZhou City

first: Hua

last: Ji

state: Zhejiang

address: No.481 Bingwen road

department: Department of Basic Medicine

institute: Hangzhou medical college

description: Experimental animals were male offspring produced by ICR mice (SLAC, Shanghai, China).

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
The statistical significance of the difference may be conveniently estimated by t-test. lncRNAs having fold changes>2.0 and p-values<0.05 are selected as the significantly differentially expressed.

source_name: hippocampus

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Mouse hippocampus dissected from PND28 mouse brain

extract_protocol: The pregnant ICR mice were randomly allocated in two groups, each group consisting of 8 pregnant mice (Slac, China ). Each group were used for the lncRNA microarray assay. In the control group, pregnant mice were provided with purified water. In the glyphosate treated group, pregnant mice were provided with 0.38% glyphosate in drinking water (1% Roundup®), equivalent to 50 mg of glyphosate/kg/day.

treatment_protocol: not applicable

value: male

value: ICR

value: 4 weeks old

value: brain

value: prenatal glyphosate exposure


title: Max-Soy-24h


title: control_1

description: Gene expression in normal enviroment

source_name: non treat, replicate 1

value: control


title: control_2

description: Gene expression in normal enviroment

source_name: non treat, replicate 2


title: 40MPa30min_5min_2

source_name: 30 min after 40 MPa 5min,replicate 2


title: hippocampus, C


title: AB Rep 2: Amyloid beta as control, biology rep2

source_name: SH-SY5Y Neuroblastoma Cell line

value: female

value: Neuroblastoma


title: TGY-48h

value: TGY


title: 40MPa30min_5min_1

source_name: 30 min after 40 MPa 5min,replicate 1


title: Time 08_Control_Rep 1 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 1

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

value: Time 08

value: Control

value: Rep 1


title: AB Rep 1: Amyloid beta as control, biology rep1


title: Time 0_Control_Rep 1 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 1

value: Time 0


title: TGY-24h

value: strain A


title: RT112 sh2

status: Public on Jul 30 2020

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

country: France

institute: Institut Curie

library_source: genomic

data_processing:
Data were processed for read quality control, mapping, interaction detection, filtering, and matrix normalization using TADbit (Serra et al. 2017, PLoS Comput Biol.).
Reads were quality-controlled using the TADbit implementation of FastQC for Hi-C datasets.
We used a fragment-based strategy for mapping the remaining reads to the reference human genome (GRCh38). Non-informative contacts including self-circles, dangling-ends, errors, random breaks or duplicates were filtered out, resulting in 158-197M valid interactions per condition.
Valid reads were then used to generate genome-wide interaction maps at 100kb and 20kb resolution to segment the genome into A/B compartments, demarcate TADs, and identify changes in chromatin looping.
hic files were generated with HOMER (Heinz et al. 2018, Cell) for visualization with Juicebox (Durand et al. 2016, Cell Syst.).
Genome_build: GRCh38
Supplementary_files_format_and_content: hic files

molecule: genomic DNA

source_name: Bladder cancer cell line

growth_protocol: RT112 bladder cancer cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated FBS (Fetal Bovine Serum) and 1 mM sodium pyruvate.

extract_protocol:
20 million cells per condition were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with MboI, the ends of the restriction fragments were labelled with biotinylated nucleotides, and then ligated. After revearsal of crosslinks, DNA was purified.
Purified DNA was fragmented to obtain fragments of an average size of 300–400 bp using a Bioruptor Pico (Diagenode; 8 cycles; 20 sec ON/60 sec OFF). 3 µg of DNA per condition were used for library preparation. Biotinylated DNA was pulled down with Dynabeads MyOne T1 streptavidin beads. End-repair, A-tailing and the Illumina adaptors ligation were performed on beads. Libraries were amplified by 10 cycles of PCR and purified using AMPure XP beads. The concentration and size distribution of the Hi-C library after PCR amplification were determined using a Qbit fluorometer and visual exploration in an agarose gel. Hi-C libraries were then paired-end sequenced on an Illumina NextSeq500 (200M reads per library).

treatment_protocol: Cells were transduced with control or STAG2-targeting shRNAs and placed in serum-free medium to avoid cell cycle-dependent effects.

tag: shRNA


title: RT112 sh1


title: Time 16_Control_Rep 1 (reanalysis)

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 1

value: Time 16


title: RT112 shNT


title: S8A_10_S10

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

description: 8hr treatement with 1µM of SAHA replicate A

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Trimmed PE reads were aligned to GRCh38 reference genome with HISAT2 2.1.0 reporting up to 10 multimappers in SAM format
Alignments in SAM format were converted to BAM format with Samtools 0.1.19 and the sequences were sorted and duplicate removed by Picard 1.8.0
RNA abundance of transcripts was calculated with Stringtie v1.3.2 and the RNA abundance was converted into a read count table
Differentially-expressed genes were identified with DESeq2 1.24.0
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Comma-separated text file includes raw counts for all samples.

source_name: acute T cell leukemia  (Jurkat)

growth_protocol: JLat 10.6 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 Media (Hyclone SH30027.FS) supplemented with 10% Fetal Bovine Serum (Sigma F4135) and 1% Pen-Strep (MP Biomedicals 1670049). Cells were incubated at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from ~5.00x10^6 cells using the Quick-RNA Miniprep Kit (Zymo R1055) according to manufacturer's instructions. RNA quality was determined with Agilent Tapestation ScreenTape (Agilent 5067-5576).
1µg of total RNA with ERCC Spike-ins (ThermoFisher 4456740) was used to prepare libraries with KAPA stranded RNA-seq kit with RiboErase (HMR) (KAPA Biosystems KK8483) according to manufacturer's instructions. Briefly, total RNA was hybridized and rRNA depleted followed by DNase digestion. RNA is then fragmented to a size of ~100-200bp and primed for first strand synthesis. First and second strand synthesis is performed and the reaction is incubated overnight in A-tailing buffer at 4°C. The next day, A-tailing is performed followed by adapter ligation (NEB E735L) and library amplification for 12 cycles. After final cleanup, libraries are run on Agilent Tapestation DNA D1000 ScreenTape (Agilent 5067-5582) to confirm fragment size and quantified using a Qubit 2.0 fluorometer. Libraries are submitted to the UTSWMC McDermott Center Sequencing Core and 75bp pair-end reads were generated for both libraries.

treatment_protocol: ~16 hrs prior to experiment, cells were suspended at 7.50x10^5cells/mL in fresh complete RPMI and seeded in triplicates in 6-well plates (5mLs/sample). The next morning, cells were treated with 1µM of compounds for the indicated treatment times. Upon completion of treatment, cell pellets were obtained and stored at -80°C.

value: T lymphocyte containing retroviral construct:HIV-R7/E-/GFP; full length HIV 1 minus env, minus nef (JLat 10.6)

tag: passages

value: under 15


title: S8B_11_S11

description: 8hr treatement with 1µM of SAHA replicate B


title: S4C_9_S9

description: 4hr treatement with 1µM of SAHA replicate C


title: S4A_7_S7

description: 4hr treatement with 1µM of SAHA replicate A


title: S2C_6_S6

description: 2hr treatement with 1µM of SAHA replicate C


title: S8C_12_S12

description: 8hr treatement with 1µM of SAHA replicate C


title: S4B_8_S8

description: 4hr treatement with 1µM of SAHA replicate B


title: S0A_1_S1

description: Untreated control SAHA dataset


title: S2B_5_S5

description: 2hr treatement with 1µM of SAHA replicate B


title: S0C_3_S3

description: Untreated control SAHA dataset


title: E16C_3_S12

description: 16hr treatment with 1µM of EPH334 replicate C


title: S0B_2_S2

description: Untreated control SAHA dataset


title: E16B_2_S11

description: 16hr treatment with 1µM of EPH334 replicate B


title: E8C_9_S9

description: 8hr treatment with 1µM of EPH334 replicate C


title: E1C_6_S6

description: 1hr treatment with 1µM of EPH334 replicate C


title: E8A_7_S7

description: 8hr treatment with 1µM of EPH334 replicate A


title: E1B_5_S5

description: 1hr treatment with 1µM of EPH334 replicate B


title: E0B_2_S2

description: Untreated control EPH334 dataset


title: E0C_3_S3

description: Untreated control EPH334 dataset


title: E16A_1_S10

description: 16hr treatment with 1µM of EPH334 replicate A


title: E8B_8_S8

description: 8hr treatment with 1µM of EPH334 replicate B


title: E0A_1_S1

description: Untreated control EPH334 dataset


title: RNA-Seq mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_1_seq2

city: Jerusalem

first: Carmel

last: Braverman-Gross

address: The Edmond J. Safra Campus

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Reads were mapped to the reference genome and annotated using STAR 2.4.0.1 software.
Genome_build: GRCh38 reference genome
Supplementary_files_format_and_content: comma separated values (csv) file contains transcript counts for each sample.

source_name: embryonic stem cells

growth_protocol: Mutant hESC library was cultured at 37 0C and 5% CO2 in feeder-free conditions on Matrigel-coated plates (Corning) in mTeSR1 (STEMCELL Technologies).

extract_protocol:
At the end of each differentiation assay, cells were harvested and total RNA was extracted with a RNeasy Mini Kit (QIAGEN).
mRNA fraction of total RNA was enriched by pulldown of poly(A)-RNA. RNA sequencing libraries were generated using TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol and sequenced using Illumina NextSeq 500 with 75 bp single-end reads.

treatment_protocol: hESCs were plated on Matrigel-coated 6-well plates at density of 200,000 cells per well. The cells were maintaind in mTeSR1 (STEMCELL Technologies, (2 ml/well)  that was replaced every 24 hours for nine days.

value: embryonic stem cells

tag: differentiation stage

value: Embryonic stem cells

value: CRISPR/Cas9 mutant library in h-pES10


title: RNA-Seq mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_2_seq1

tag: cell type


title: RNA-Seq mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_1_seq1

tag: strain


title: RNA-Seq mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_2

treatment_protocol: hESCs were plated on Matrigel-coated 6-well plates at density of 200,000 cells per well. The cells were maintaind in mTeSR1 (STEMCELL Technologies, (2 ml/well)  that was replaced every 24 hours for four days.


title: RNA-Seq mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_2_seq2


title: E1A_4_S4

description: 1hr treatment with 1µM of EPH334 replicate A


title: RNA-Seq mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_3


title: RNA-Seq mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_3_seq1


title: RNA-Seq mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_3_seq2


title: RNA-Seq mutant_hESC_library_CTRL_for_Definitive_Endoderm_undifferentiated_rep_3


title: H1299_Followers_1

type: genomic

city: Atlanta

first: Emily

middle: Rose

last: Summerbell

state: GA

address: Winship Cancer Institute, 1701 Uppergate Dr NE, C4060- Marcus Lab

institute: Emory University

description:
Follower cells from spheroids of H1299 NSCLC cells after 24h invasion in Matrigel, extracted using photoconversion and FACS.
ES007

hyb_protocol: 500ng of DNA was bisulfite converted using the Zymo EZ-96 DNA Methylation Kit (Zymo #D5004) using the Illumina Infinium standard protocol (Illumina, 150191519). Bisulfite converted DNA was amplified, fragmented, and hybridized to the Illumina Infinium MethylationEPIC BeadChip array using standard Illuminum protocols.

scan_protocol: standard Illumina HiScan scanner

data_processing: Data processing was performed using the R studio package ChAMP. Raw intensity values were filtered using standard ChAMP settings (with the exception that all probes on the X and Y chromosomes were retained). Briefly, probe intensity values were filtered to exclude any probes containing the following: a detection p-value < 0.01 in 1 or more samples, bead count < 3 in one or more samples, non-CG probe, probe contains a SNP, or probe aligns to multiple genomic locations. Normalized beta values wer calculated according to the BMIQ method and standard ChAMP settings. Total of 756,997 probes after filtering.

label: Cy5 and Cy3

source_name: Follower cells isolated from invading spheroids of H1299 cell line

label_protocol: Standard Illumina protocol

growth_protocol: After FACS sorting, cells were grown under standard cell culture conditions in RPMI-1640 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 1% kanamycin.

extract_protocol: Genomic DNA was isolated from cell pellets that were stored at -80°C using the All Prep DNA/RNA kit (Qiagen #80204) according to the manufacturer’s standard protocol.

treatment_protocol: No treatment

value: H1299 NSCLC cell line

tag: phenotype

value: Followers


title: RNA-Seq mutant_hESC_library_CTRL_for_Definitive_Endoderm_undifferentiated_rep_2


title: RNA-Seq mutant_hESC_library_Early_Mesoderm_differentiated_rep_3

treatment_protocol: hESCs were plated on Matrigel-coated 6-well plates at density of 500,000 cells per well. The next day, STEMdiff Mesoderm Induction Kit (STEMCELL TECHNOLOGIES, cat. No. 05220) has been used according to manufacturer's instructions.  Differentiation medium (3 ml/well) was replaced every 24 hours for four days.

value: early mesoderm cells

value: Early mesoderm


title: RNA-Seq mutant_hESC_library_Neuroectoderm_differentiated_rep_1_seq2

treatment_protocol: For neuroectoderm differentiation, neural progenitor cells were obtained using a previously established protocol for efficient neural differentiation with slight modification. To generate the NPCs, hESCs were plated on Matrigel-coated 6-well plates at a density of 2 million cells per well. The next day, mTeSR1 medium was replaced by embryoid body (EB) medium (knockout Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% knockout serum replacement (KSR, Thermo Fisher Scientific), 2 mM L-glutamine, 0.1 mM nonessential amino acids, 50 units ml−1 penicillin, 50 µg ml−1 streptomycin and 0.1 mM β-mercaptoethanol) supplemented with 10 µM of SB431542 (Biogems) and 2.5 µM of LDN193189 (Biogems). EB medium (2 ml/well) was replaced every 24 hours for four days. Medium was then changed to a composite medium of EB medium and N-2 medium (Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham (Sigma), 1 x N-2 supplement (Thermo Fisher, cat. no. 17502001), 50 units ml−1 penicillin, 50 µg ml−1 streptomycin, 2 mM L-glutamine, 0.1 M ascorbic acid (Sigma) and 0.16 % D-Glucose) at a 3:1 ratio in the presence of 10 µM of SB431542 and 2.5 µM of LDN193189 for 24 hours.  The next day, medium was changed to a 1:1 ratio mix of EB medium and N-2 medium in the presence of 10 µM of SB431542 and 2.5 µM of LDN193189 for another 24 hours. The following day, the medium was changed to a 1:3 mix of EB medium and N-2 medium in the presence of 10 µM of SB431542 and 2.5 µM of LDN193189 for another 24 hours. Next, the medium was changed to N-2 medium in the presence of 10 µM of SB431542 and 2.5 µM of LDN193189 for another 24 hours and the cells were harvested the following day (9th day) for downstream analyses.

value: neuroectoderm cells

value: Neuroectoderm


title: RNA-Seq mutant_hESC_library_Neuroectoderm_differentiated_rep_2_seq1


title: RNA-Seq mutant_hESC_library_Neuroectoderm_differentiated_rep_3


title: RNA-Seq mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_1_seq1


title: RNA-Seq mutant_hESC_library_Neuroectoderm_differentiated_rep_1_seq1


title: RNA-Seq mutant_hESC_library_Neuroectoderm_differentiated_rep_2_seq2


title: RNA-Seq mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_1_seq2


title: RNA-Seq mutant_hESC_library_Early_Mesoderm_differentiated_rep_2_seq2


title: RNA-Seq mutant_hESC_library_Early_Mesoderm_differentiated_rep_1_seq2


title: RNA-Seq mutant_hESC_library_Early_Mesoderm_differentiated_rep_2_seq1


title: RNA-Seq mutant_hESC_library_Early_Mesoderm_differentiated_rep_1_seq1


title: H1299_Leaders_1

description:
Leader cells from spheroids of H1299 NSCLC cells after 24h invasion in Matrigel, extracted using photoconversion and FACS.
ES013

source_name: Leader cells isolated from invading spheroids of H1299 cell line

value: Leaders


title: TMED9TMED10_mutant_EBs_10days

source_name: mutant embryoid bodies

growth_protocol: hESCs were cultured at 37 0C and 5% CO2 in feeder-free conditions on Matrigel-coated plates (Corning) in mTeSR1 (STEMCELL Technologies).

extract_protocol:
At the end of the differentiation assays, cells were harvested and total RNA was extracted with a RNeasy Mini Kit (QIAGEN).
mRNA fraction of total RNA was enriched by pulldown of poly(A)-RNA. RNA sequencing libraries were generated using TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol and sequenced using Illumina NextSeq 500 with 75 bp single-end reads.

treatment_protocol: hESCs grown on feeder layer MEFs to 50-60% confluency were washed with PBS and gently dissociated using 0.25% Trypsin Solution A (Biological Industries) for 5 min at 37 0C. Dissociated colonies were harvested and transferred on non-adherent 10 cm dishes as suspension in EB medium, composed of knockout Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% knockout serum replacement (KSR, Thermo Fisher Scientific), 2 mM L-glutamine, 0.1 mM nonessential amino acids, 50 units ml-1 penicillin, 50 µg ml-1 streptomycin and 0.1 mM β-mercaptoethanol. The cell aggregates in suspension were gently fed with EB medium every other day until 10th day.

value: mutant embryoid bodies

value: Spontaneous differentiation for 10 days

value: H9 hESCs


title: TMED10_mutant_EBs_10days


title: RNA-Seq mutant_hESC_library_Definitive_Endoderm_differentiated_rep_2

treatment_protocol: hESCs were plated on Matrigel-coated 6-well plates at a density of 2 million cells per well. The next day, STEMdiff Definitive Endoderm Kit (STEMCELL TECHNOLOGIES, cat. No. 05110) has been used according to manufacturer's instructions.  Differentiation medium (2 ml/well) was replaced every 24 hours for four days.

value: definitive endoderm cells

value: Definitive endoderm


title: RNA-Seq mutant_hESC_library_Definitive_Endoderm_differentiated_rep_1


title: H1299_Leaders_3

description:
Leader cells from spheroids of H1299 NSCLC cells after 24h invasion in Matrigel, extracted using photoconversion and FACS.
ES017


title: RNA-Seq mutant_hESC_library_Definitive_Endoderm_differentiated_rep_3


title: TMED9_mutant_EBs_10days


title: H1299_Followers_3

description:
Follower cells from spheroids of H1299 NSCLC cells after 24h invasion in Matrigel, extracted using photoconversion and FACS.
ES011


title: RNA-Seq mutant_hESC_library_CTRL_for_Definitive_Endoderm_undifferentiated_rep_1


title: H1299_Followers_2

description:
Follower cells from spheroids of H1299 NSCLC cells after 24h invasion in Matrigel, extracted using photoconversion and FACS.
ES009


title: DPM3_mutant_EBs_10days


title: S2A_4_S4

description: 2hr treatement with 1µM of SAHA replicate A

value: T lymphocyte containing retroviral construct:HIV-R7/E-/GFP; full length HIV 1 minus env, minus nef (JLat 10.6)


title: H1299_Parental_2

description:
Parental cells extracted from whole spheroids of H1299 NSCLC cells after 24h invasion in Matrigel
ES003

source_name: Parental cells from invading spheroids of H1299 cell line

value: Parental


title: DPM1DPM3_mutant_EBs_10days


title: TMED9TMED10_mutant_EBs_5days

treatment_protocol: hESCs grown on feeder layer MEFs to 50-60% confluency were washed with PBS and gently dissociated using 0.25% Trypsin Solution A (Biological Industries) for 5 min at 37 0C. Dissociated colonies were harvested and transferred on non-adherent 10 cm dishes as suspension in EB medium, composed of knockout Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% knockout serum replacement (KSR, Thermo Fisher Scientific), 2 mM L-glutamine, 0.1 mM nonessential amino acids, 50 units ml-1 penicillin, 50 µg ml-1 streptomycin and 0.1 mM β-mercaptoethanol. The cell aggregates in suspension were gently fed with EB medium every other day until 5th day.

value: Spontaneous differentiation for 5 days


title: TMED10_mutant_EBs_5days


title: TMED9_mutant_EBs_5days


title: H1299_Leaders_2

description:
Leader cells from spheroids of H1299 NSCLC cells after 24h invasion in Matrigel, extracted using photoconversion and FACS.
ES015


title: Empty-vector_EBs_10days

source_name: embryoid bodies

value: embryoid bodies


title: DPM3_mutant_EBs_5days


title: TBL1X_mutant_Neuroectoderm_rep_3

source_name: mutant neuroectoderm cells

value: mutant neuroectoderm cells

value: neuroectoderm


title: Empty-vector_EBs_5days


title: DPM1_mutant_EBs_10days


title: CTRL_sgRNA_EBs_5days


title: DPM1_mutant_EBs_5days


title: TBL1X_mutant_Neuroectoderm_rep_1


title: CTRL_sgRNA_EBs_10days


title: POU3F3_mutant_Neuroectoderm_rep_3


title: TBL1X_mutant_Neuroectoderm_rep_2


title: POU3F3_mutant_Neuroectoderm_rep_1


title: POU3F3_mutant_Neuroectoderm_rep_2


title: POU3F2_mutant_Neuroectoderm_rep_3


title: POU3F2_mutant_Neuroectoderm_rep_1


title: H1299_Parental_3

description:
Parental cells extracted from whole spheroids of H1299 NSCLC cells after 24h invasion in Matrigel
ES005

value: H1299 NSCLC cell line


title: Empty-vector_Neuroectoderm_rep_2

source_name: neuroectoderm cells


title: H1299_Parental_1

description:
Parental cells extracted from whole spheroids of H1299 NSCLC cells after 24h invasion in Matrigel
ES001


title: POU3F2_mutant_Neuroectoderm_rep_2


title: Empty-vector_Neuroectoderm_rep_1


title: Empty-vector_Neuroectoderm_rep_3


title: CTRL_sgRNA_Neuroectoderm_rep_3


title: CTRL_sgRNA_Neuroectoderm_rep_1


title: CTRL_sgRNA_Neuroectoderm_rep_2


title: ZBTB10_mutant_Early_Mesoderm_rep_3

source_name: mutant early mesoderm cells

treatment_protocol: hESCs were plated on Matrigel-coated 6-well plates at density of 500,000 cells per well. The next day, STEMdiffTM Mesoderm Induction Kit (STEMCELL TECHNOLOGIES, cat. No. 05220) has been used according to manufacturer's instructions.  Differentiation medium (3 ml/well) was replaced every 24 hours for four days.

value: mutant early mesoderm cells

value: early mesoderm


title: CDX2_mutant_Early_Mesoderm_rep_2


title: ZBTB10_mutant_Early_Mesoderm_rep_1


title: ZBTB10_mutant_Early_Mesoderm_rep_2


title: Empty-vector_Early_Mesoderm_rep_2

source_name: early mesoderm cells

value: early mesoderm cells


title: CDX2_mutant_Early_Mesoderm_rep_1


title: Empty-vector_Early_Mesoderm_rep_1


title: CTRL_sgRNA_Early_Mesoderm_rep_3


title: HNF4a_mutant_Definitive_Endoderm_rep_2

source_name: mutant definitive endoderm cells

treatment_protocol: hESCs were plated on Matrigel-coated 6-well plates at density of 200,000 cells per well. The next day, STEMdiffTM Mesoderm Induction Kit (STEMCELL TECHNOLOGIES, cat. No. 05220) has been used according to manufacturer's instructions.  Differentiation medium (1.5 ml/well) was replaced every 24 hours for four days.

value: mutant definitive endoderm cells

value: definitive endoderm


title: Empty-vector_Early_Mesoderm_rep_3


title: CTRL_sgRNA_Early_Mesoderm_rep_1


title: Empty-vector_Definitive_Endoderm_rep_1

source_name: definitive endoderm cells

treatment_protocol: hESCs were plated on Matrigel-coated 6-well plates at density of 2 million cells per well. The next day, STEMdiffTM Definitive Endoderm Kit (STEMCELL TECHNOLOGIES, cat. No. 05110) has been used according to manufacturer's instructions.  Differentiation medium (2 ml/well) was replaced every 24 hours for four days.


title: GLIS1_mutant_Definitive_Endoderm_rep_1


title: HNF4a_mutant_Definitive_Endoderm_rep_1


title: Empty-vector_Undifferentiated_rep_3

value: embryonic stem cells


title: CTRL_sgRNA_Definitive_Endoderm_rep_1


title: CTRL_sgRNA_Undifferentiated_rep_3


title: CTRL_sgRNA_Undifferentiated_rep_2


title: Empty-vector_Undifferentiated_rep_2


title: CTRL_sgRNA_Undifferentiated_rep_1


title: mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_3

data_processing:
Alignment: Align the fastq files against the library’s sgRNAs sequences list using Bowtie2
Genome_build: The sgRNAs sequences as appear in Table S1 of Wang, T. et al. Identification and characterization of essential genes in the human genome. Science 350, 1096–1101 (2015).
Supplementary_files_format_and_content: comma separated values (csv) file contains sgRNA counts for each sample.

extract_protocol:
At the end of differentiation assay, cells were harvested and genomic DNA was extracted with a Blood & Cell Culture DNA Midi Kit (QIAGEN).
genomic DNA was extracted with Blood & Cell Culture DNA Midi Kit (QIAGEN) according to manufacturer’s instructions.  The region containing the sgRNA integration was amplified with the following primers that also contain overhang sequences compatible for Nextera DNA library preparations (Illumina): 5’- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNGGCTTTATATATCTTGTGGAAAGGACG – 3’ (forward) and 5’ - GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGACGGACTAGCCTTATTTTAACTTGC - 3’ (reverse). Total genomic DNA for each sample was divided into 50 µl PCR reactions with 4 µg DNA input. PCR settings were described previously. After the purification of the 170 base pair product, a second PCR reaction was performed using Nextera adapter primers in order to generate Nextera DNA library according to manufacturer’s instructions (Illumina). DNA libraries were sequenced using NextSeq 500 (Illumina) with 75 bp single-end reads.

value: Embryonic stem cells

value: CRISPR/Cas9 mutant library in h-pES24


title: Empty-vector_Undifferentiated_rep_1

value: H9 hESCs


title: mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_2

value: CRISPR/Cas9 mutant library in h-pES23


title: CTRL_sgRNA_Definitive_Endoderm_rep_2

value: definitive endoderm cells


title: GLIS1_mutant_Definitive_Endoderm_rep_2


title: CTRL_sgRNA_Early_Mesoderm_rep_2


title: mutant_hESC_library_CTRL_for_Definitive_Endoderm_undifferentiated_rep_3

value: CRISPR/Cas9 mutant library in h-pES21


title: mutant_hESC_library_CTRL_for_Definitive_Endoderm_undifferentiated_rep_1

value: CRISPR/Cas9 mutant library in h-pES19


title: mutant_hESC_library_CTRL_for_Definitive_Endoderm_undifferentiated_rep_2

value: CRISPR/Cas9 mutant library in h-pES20


title: Empty-vector_Definitive_Endoderm_rep_2


title: mutant_hESC_library_Neuroectoderm_differentiated_rep_3

value: neuroectoderm cells

value: Neuroectoderm

value: CRISPR/Cas9 mutant library in h-pES18


title: mutant_hESC_library_Early_Mesoderm_differentiated_rep_3

value: Early mesoderm

value: CRISPR/Cas9 mutant library in h-pES15


title: mutant_hESC_library_Neuroectoderm_differentiated_rep_2

value: CRISPR/Cas9 mutant library in h-pES17


title: mutant_hESC_library_Neuroectoderm_differentiated_rep_1

value: CRISPR/Cas9 mutant library in h-pES16


title: mutant_hESC_library_Definitive_Endoderm_differentiated_rep_3

value: Definitive endoderm

value: CRISPR/Cas9 mutant library in h-pES12


title: mutant_hESC_library_Early_Mesoderm_differentiated_rep_1

value: early mesoderm cells

value: CRISPR/Cas9 mutant library in h-pES13


title: mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_3

value: embryonic stem cells

value: Embryonic stem cells

value: CRISPR/Cas9 mutant library in h-pES27


title: mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_1

value: CRISPR/Cas9 mutant library in h-pES25


title: mutant_hESC_library_Definitive_Endoderm_differentiated_rep_1

value: definitive endoderm cells

value: CRISPR/Cas9 mutant library in h-pES10


title: mutant_hESC_library_CTRL_for_Neuroectoderm_undifferentiated_rep_2

value: CRISPR/Cas9 mutant library in h-pES26


title: ST2_KO_3_P2

city: Gaithersburg

first: Jingya

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

description: ST2 Knockout P2_replicate3

data_processing:
Fastq files were generated using bcl2fastq
Sequencing reads were aligned to mouse reference genome mm10 using Hisat2 (v2.0.2)
Count tables were generated using HTseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

growth_protocol: Adult (12-wk old) female C57Bl/6J mice supplied by Jackson Lab (Jax, #000664). ST2-deficient mice were generated and housed under pathogen-free conditions at MedImmune/AstraZeneca Gaithersburg

extract_protocol:
RNA was isolated using PicoPure RNA isolation kit (Thermo Fisher Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naphthalene (NA) (Sigma-Aldrich) was dissolved in corn oil and injected intra-peritoneally to C57Bl/6J and ST2KO female mice at a dose of 200-250 mg/kg. After injection, mice were maintained in pathogen-free conditions and were monitored daily for signs of distress and they were given gel packs to aid in the recovery. On day 6, mice were euthanized and their lungs were collected and digested for myeloid cell sorting and RNAseq analysis.

tag: Sex

value: female

tag: time

value: Day 6

value: monocyte-derived macrophages (P2)

tag: mouse model

value: ST2 knockout


title: ST2_KO_3_P3

description: ST2 Knockout P3_replicate3

value: resident alveolar macrophages (P3)


title: mutant_hESC_library_Definitive_Endoderm_differentiated_rep_2

value: CRISPR/Cas9 mutant library in h-pES11


title: ST2_KO_2_P2

description: ST2 Knockout P2_replicate2


title: ST2_KO_1_P3

description: ST2 Knockout P3_replicate1


title: ST2_KO_2_P3

description: ST2 Knockout P3_replicate2


title: ST2_KO_2_P1

description: ST2 Knockout P1_replicate2

value: inflammatory monocytes (P1)


title: mutant_hESC_library_CTRL_for_Early_Mesoderm_undifferentiated_rep_1

value: CRISPR/Cas9 mutant library in h-pES22


title: ST2_KO_1_P1

description: ST2 Knockout P1_replicate1


title: ST2_KO_1_P2

description: ST2 Knockout P2_replicate1


title: WT_3_P2

description: wild type P2_replicate3

value: wildtype


title: mutant_hESC_library_Early_Mesoderm_differentiated_rep_2

value: early mesoderm cells

value: Early mesoderm

value: CRISPR/Cas9 mutant library in h-pES14


title: WT_2_P3

description: wild type P3_replicate2


title: WT_2_P2

description: wild type P2_replicate2


title: WT_1_P2

description: wild type P2_replicate1


title: WT_1_P3

description: wild type P3_replicate1


title: WT_3_P1

description: wild type P1_replicate3


title: WT_1_P1

description: wild type P1_replicate1


title: ST2_KO_3_P1

description: ST2 Knockout P1_replicate3


title: Day6_napthalene_P1_monos_2

description: day 6/ napthalene P1 monos_replicate2

source_name: day 6/ napthalene P1 monos

growth_protocol: Adult (12-wk old) female C57Bl/6J mice supplied by Jackson Lab (Jax, #000664)

treatment_protocol: Naphthalene (NA) (Sigma-Aldrich) was dissolved in corn oil and injected intra-peritoneally to C57Bl/6J female mice at a dose of 200-250 mg/kg. After injection, mice were maintained in pathogen-free conditions and were monitored daily for signs of distress and they were given gel packs to aid in the recovery. On day 6, mice were euthanized and their lungs were collected and digested for myeloid cell sorting and RNAseq analysis.


title: Day6_napthalene_P1_monos_1

description: day 6/ napthalene P1 monos_replicate1


title: Day6_napthalene_P1_monos_3

description: day 6/ napthalene P1 monos_replicate3


title: Day6_napthalene_P2_macs_3

description: day 6/ napthalene P2 macs_replicate3

source_name: day 6/ napthalene P2 macs


title: Day6_napthalene_P2_macs_2

description: day 6/ napthalene P2 macs_replicate2


title: Day6_napthalene_P2_macs_1

description: day 6/ napthalene P2 macs_replicate1


title: Day6_napthalene_P3_AAMs_2

description: day 6/ napthalene P3 AAMs_replicate2

source_name: day 6/ napthalene P3 AAMs


title: MOE_051916_DS21

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description: 15 min Drop-seq run, run1

data_processing:
Paired end reads from the fastq files were trimmed, aligned, and tagged via the Drop-seq tools (v1.13) pipeline, using STAR (v2.5.4a) with genomic indices from Ensembl Release 93. The digital gene expression matrix was generated for 4,000 cells for 0126_2, 5,000 cells for 0105, 0126_1, 051916_DS11, 051916_DS12, 051916_DS22, 5,500 cells for 051916_DS21, and 9,500 cells for 0106.
Genome_build: Ensembl Rel 93 (GRCm38.p6)
Supplementary_files_format_and_content: MOE_all_counts.csv.gz contains the counts table for all cells and genes from the 8 samples. MOE_metadata.tsvcontains metadata information about the clusters and UMAP coordinates for each filtered cell used for analysis.

source_name: whole olfactory mucosa

extract_protocol:
Briefly, dissected main olfactory epithelium were cleaned up in 750 µl of EBSS (Worthington) and epithelium tissues were isolated in 750 µL of Papain (20 U/mL in EBSS) and 50 µL of DNase I (2000 U/mL). Tissue pieces were transferred to a 5 mL round-bottom tube (BD) and 1.75 mL of Papain and 450 µL of DNase I were added. After 1–1.5 hour incubation with rocking at 37°C, the suspension was triturated with a 5 mL pipette 15 times and passed through 40 µm cell strainer (BD) and strainer was washed with 1 mL of DMEM + 10 % FBS (Invitrogen). The cell suspension was centrifuged at 300g for 5 min. Cells were resuspended with 4 mL of DMEM + 10 % FBS and centrifuged at 300g for 5 min. Cells were suspended with PBS + 0.01 % BSA and concentration was measured by hemocytometer.
Drop-seq experiments (cell capture, reverse transcription, PCR, tagmentation), were performed as described in Macosko et al. 2015. Microfluidics devices were obtained from FlowJEM and barcode beads were obtained from Chemgenes. 8 replicates of Drop-seq samples were sequenced across 5 runs on an Illumina NextSeq 500 platform.

tag: tissue

value: whole olfactory mucosa

value: 8-12 weeks


title: Day0_sham_naïve_1

description: day 0/ sham(naïve)_replicate1

source_name: day 0/ sham(naïve)

value: Naive cells

value: Day 0


title: Day0_sham_naïve_2

description: day 0/ sham(naïve)_replicate2


title: MOE_051916_DS12

description: 15 min Drop-seq run, run2


title: Day6_napthalene_P3_AAMs_1

description: day 6/ napthalene P3 AAMs_replicate1


title: MOE_051916_DS11

description: 15 min Drop-seq run, run1


title: Day0_sham_naïve_3

description: day 0/ sham(naïve)_replicate3


title: MOE_0126_1

description: 15 min Drop-seq run, run1


title: MOE_0106

description: 15 min Drop-seq run


title: WT_3_P3

description: wild type P3_replicate3


title: MOE_0126_2

description: 15 min Drop-seq run, run2


title: WT_2_P1

description: wild type P1_replicate2


title: MOE_0105

description: 15 min Drop-seq run


title: TKO MT RB1

city: Indianapolis

first: Jaeyeon

last: Kim

state: IN

address: 635 Barnhill Drive, MS4053

department: Department of Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: TKO Metastatic tumor Replicate B1

data_processing:
Reads were adapter trimmed and quality filtered using Trimmomatic ver. 0.33 setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded.
Reads were mapped to Mus musculus genome ver. GRCm38.75 using Tophat2 version 2.1.0.
Number of reads mapping uniquely to each of the annotated genes from GRCm38.75 were quantified using htseq-count ver. 0.6.1p2.
Genome_build: GRCm38.75
Supplementary_files_format_and_content: counts.txt files contain number of uniquely mapped reads for each of the GRCm38.75 annotated genes. These numbers provide a measure of gene expression.

source_name: fallopian tube tissue

extract_protocol:
Total RNA was isolated at different stages of tumor development in DKO and TKO mice: fallopian tubes at premalignant stage (Pre), early-stage fallopian tube tumors (ET). Additionally, RNA was isolated from normal fallopian tubes (Ovid, oviducts) of respective control mice for DKO and TKO mice. Total RNA was isolated using TRIzol (Invitrogen) and purified using RNeasy MinElute Cleanup Kit (Qiagen, Germantown, MD, USA), according to manufacturer’s instructions.
Total RNA (1 -1.2μg) was used for mRNA library preparation. Library preparation was performed using the TruSeq Stranded mRNA HT Library preparation kit (Illumina).

value: metastatic tumors

tag: genotype

value: p53 R172H/+ Dicer fl/fl Pten f/f/ Amhr2 Cre/+

value: p53 Dicer Pten conditional KO


title: TKO PT RB2

description: TKO Primary tumor Replicate B2

value: primary fallopian tube tumors


title: TKO PT RB3

description: TKO Primary tumor Replicate B3


title: TKO MT RB2

description: TKO Metastatic tumor Replicate B2


title: TKO MT RB3

description: TKO Metastatic tumor Replicate B3


title: TKO Ctrl RB1

description: TKO Control Replicate B1

value: Normal fallopian tubes

value: wild type


title: TKO PT RB1

description: TKO Primary tumor Replicate B1


title: DKO MT RB2

description: DKO Metastatic tumor Replicate B2

value: Dicer fl/fl Pten f/f/ Amhr2 Cre/+

value: Dicer Pten conditional KO


title: TKO Ctrl RB3

description: TKO Control Replicate B3


title: DKO PT RB3

description: DKO Primary tumor Replicate B3


title: DKO MT RB1

description: DKO Metastatic tumor Replicate B1


title: DKO PT RB2

description: DKO Primary tumor Replicate B2


title: MOE_051916_DS22

description: 15 min Drop-seq run, run2


title: DKO Ctrl RB3

description: DKO Control Replicate B3


title: DKO PT RB1

description: DKO Primary tumor Replicate B1


title: TKO ET RA2

description: TKO Early Replicate A2

value: Early stage fallopian tubes


title: DKO Ctrl RB1

description: DKO Control Replicate B1


title: TKO ET RA1

description: TKO Early Replicate A1


title: TKO Pre RA2

description: TKO Premalignant Replicate A2

value: premalignant stage fallopian tubes


title: TKO Pre RA3

description: TKO Premalignant Replicate A3


title: DKO Ctrl RB2

description: DKO Control Replicate B2


title: TKO Pre RA1

description: TKO Premalignant Replicate A1


title: TKO Ctrl RA1

description: TKO Control Replicate A1


title: TKO Ctrl RA2

description: TKO Control Replicate A2


title: TKO Ctrl RA3

description: TKO Control Replicate A3


title: TKO Ctrl RB2

description: TKO Control Replicate B2


title: DKO ET RA3

description: DKO Early Replicate A3


title: DKO ET RA2

description: DKO Early Replicate A2


title: DKO MT RB3

description: DKO Metastatic tumor Replicate B3


title: DKO ET RA1

description: DKO Early Replicate A1


title: DKO Pre RA2

description: DKO Premalignant Replicate A2


title: DKO Ctrl RA2

description: DKO Control Replicate A2


title: DKO Pre RA3

description: DKO Premalignant Replicate A3


title: DKO Pre RA1

description: DKO Premalignant Replicate A1


title: DKO Ctrl RA3

description: DKO Control Replicate A3


title: OB_121516_run1

description: 15 min Drop-seq run, run1

data_processing:
UMI counts for each cell were obtained via the Drop-Seq Computational protocol, as described in http://mccarrolllab.org/dropseq/, using Picard and additional java programs as part of the Drop-seq_tools-1-2.0 pipeline. In brief, reads were demultiplexed, tagged with cell and UMI barcodes, and trimmed.
Trimmed reads were aligned to the genome with STAR (v2.4.2a). Exonic reads with unique alignments were tagged merged with their barcodes. Bead synthesis errors were corrected.
The digital gene expression (dge) counts matrix was generated for 8,000 cells per replicate
Genome_build: Ensembl Rel 82 (GRCm38.p4)
Supplementary_files_format_and_content: OB_2016Dec_all_counts.csv.gz contains the counts table for all cells from the 4 samples. Datta_integratedOB_UMAP_noDoublets.csv contains metadata information about the clusters for each filtered cell used for analysis. Linnarsson_integratedOB_UMAP_noDoublets.csv contains metadata information about the cells from Zeisel et al. 2018, downloaded from mousebrain.org/loomfiles_level_L1.html in loom format (l1 olfactory.loom) and available in GSE103840

source_name: Olfactory Bulb

extract_protocol:
Dissected olfactory bulbs (including the accessory olfactory bulb and fractions of the anterior olfactory nucleus) were dissociated in 750 µl of dissociation media (DM: HBSS containing 10mM HEPES, 1 mM MgCl2, 33 mM D-glucose) with 28 U/mL Papain and 386 U/mL DNase I (Worthington). Minced tissue pieces were transferred to a 5 mL round-bottom tube (BD). DM was added to a final volume of 3.3 mL and the tissue was mechanically triturated 5 times with a P1000 pipette tip. After 1-hour incubation with rocking at 37°C, the suspension was triturated with a 10 mL pipette 10 times and 2.3 mL was passed through 40 µm cell strainer (BD). The suspension was then mechanically triturated with a P1000 pipette tip 10 times and 800 µL were filtered on the same strainer. The cell suspension was further triturated with a P200 pipette tip 10 times and filtered. 1 mL of Quench buffer (22 mL of DM, 2.5 mL of protease inhibitor prepared by resuspending 1 vial of protease inhibitor with 32 mL of DM, and 2000U of DNase I) was added to the suspension and centrifuged at 300g for 5 min. Cells were resuspended with 3 mL of Quench buffer and overlaid gently on top of 5 mL of protease inhibitor, then spun down at 70g for 10min. The pellet was resuspended using DM supplemented with 0.04 % BSA, and spun down at 300g for 5 min. Cells were resuspended in 400-500 µL of DM with 0.04% BSA and the concentration was measured by hemocytometer, then diluted by DM with 0.04% BSA at a final concentration of 200 cells/µL.
Drop-seq experiments (cell capture, reverse transcription, PCR, tagmentation), were performed as described in Macosko et al. 2015. Microfluidics devices were obtained from FlowJEM and barcode beads were obtained from Chemgenes. 4 replicates of Drop-seq samples were pooled and sequenced across 3 runs on an Illumina NextSeq 500 platform

value: olfactory bulb


title: DKO Ctrl RA1

description: DKO Control Replicate A1


title: OB_121516_run2

description: 15 min Drop-seq run, run2


title: sNuc_seq_HepDKO

city: Houston

first: Dongyin

last: Guan

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

data_processing:
Cellranger (3.0.2) software (10x Genomics) was run on the raw data using mm10. Output from cellRanger was loaded into R package Seurat (version 3.0). After removing doublets and nuclei with low quality, 18,239 nuclei with more than 500 detected genes and less than 2% mitochondria genes were retained for further analysis.  Unique sequencing reads for each gene were normalized to total Unique Molecular Identifiers (UMIs) in each nucleus to obtain normalized UMI values. Unsupervised clustering was applied after aligning the top 40 dimensions resulting from the PCA  space using a resolution of 0.5.
Genome_build: mm10

source_name: Liver

extract_protocol:
mice were anesthetized, and the livers were perfused with perfusion media though the portal vein. Livers were subjected to dounce homogenization in cold swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In). After centrifugation at 400 g, the nuclei were extracted using lysis buffer (swelling buffer with 10% glycerol and 1% Igepal). After washing once with lysis buffer, the nuclei were resuspended in chilled (4 °C) nuclei wash and resuspension buffer (1X PBS, 1.0% BSA, and 0.2 U/μl RNase Inhibitor) with nuclei concentration of 1000 nuclei/ul.
10,000 nuclei were immediately proceeded with the 10X Genomics Chromium Single-Cell 3’ according to the manufacturer’s instructions. The libraries from control and HepDKO liver were constructed based on the 10X Genomics Chromium Single-Cell 3’ manufacturer’s instructions and sequenced by Nextseq 500.

value: male

tag: diet

value: normal chow

tag: genotype/variation

value: REV-ERB a/b double knockout

value: Liver


title: OB_121316_run2

description: 15 min Drop-seq run, run2

value: 8-12 weeks


title: OB_121316_run1

description: 15 min Drop-seq run, run1

extract_protocol: Dissected olfactory bulbs (including the accessory olfactory bulb and fractions of the anterior olfactory nucleus) were dissociated in 750 µl of dissociation media (DM: HBSS containing 10mM HEPES, 1 mM MgCl2, 33 mM D-glucose) with 28 U/mL Papain and 386 U/mL DNase I (Worthington). Minced tissue pieces were transferred to a 5 mL round-bottom tube (BD). DM was added to a final volume of 3.3 mL and the tissue was mechanically triturated 5 times with a P1000 pipette tip. After 1-hour incubation with rocking at 37°C, the suspension was triturated with a 10 mL pipette 10 times and 2.3 mL was passed through 40 µm cell strainer (BD). The suspension was then mechanically triturated with a P1000 pipette tip 10 times and 800 µL were filtered on the same strainer. The cell suspension was further triturated with a P200 pipette tip 10 times and filtered. 1 mL of Quench buffer (22 mL of DM, 2.5 mL of protease inhibitor prepared by resuspending 1 vial of protease inhibitor with 32 mL of DM, and 2000U of DNase I) was added to the suspension and centrifuged at 300g for 5 min. Cells were resuspended with 3 mL of Quench buffer and overlaid gently on top of 5 mL of protease inhibitor, then spun down at 70g for 10min. The pellet was resuspended using DM supplemented with 0.04 % BSA, and spun down at 300g for 5 min. Cells were resuspended in 400-500 µL of DM with 0.04% BSA and the concentration was measured by hemocytometer, then diluted by DM with 0.04% BSA at a final concentration of 200 cells/µL. Drop-seq experiments (cell capture, reverse transcription, PCR, tagmentation), were performed as described in Macosko et al. 2015. Microfluidics devices were obtained from FlowJEM and barcode beads were obtained from Chemgenes. 4 replicates of Drop-seq samples were pooled and sequenced across 3 runs on an Illumina NextSeq 500 platform


title: ATAC_seq_KC_ZT22_KO_rep3

data_processing:
The ATAC-seq analysis pipeline developed by Anshul Kundaje (Stanford University, Stanford, CA, USA) (https://github.com/kundajelab/atac_dnase_pipelines) was applied. For each sample, adapters were trimmed and aligned to the mouse genome mm9 with Bowtie. The aligned bam files of biological replicates were then merged and subjected to peak calling of open chromatin regions. The tag directories were established, and normalized read counts were measured using Homer.
Genome_build: mm9
Supplementary_files_format_and_content: peak of nucleosome free region (NFR)

source_name: Kupffer cells

extract_protocol:
50,000 isolated ECs or KCs were resuspended in 50 μl of transposase mixture (25 μl of 2× TD buffer, 2.5 μl of TDE1, 0.5 μl of 1% digitonin, and 22 μl of nuclease-free water) (15027865, Illumina). Transposition reactions were incubated at 37 °C for 30 min in an Eppendorf Thermo Mixer with agitation at 300 rpm. Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204), and purified DNA was eluted in 10 μl of elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified as described previously (PMID: 25559105).

tag: gender

value: Kupffer cells


title: ATAC_seq_KC_ZT22_KO_rep4


title: sNuc_seq_Control

value: WT


title: TKO ET RA3

description: TKO Early Replicate A3

value: p53 R172H/+ Dicer fl/fl Pten f/f/ Amhr2 Cre/+


title: ATAC_seq_KC_ZT10_KO_rep4


title: ATAC_seq_KC_ZT22_KO_rep2


title: ATAC_seq_KC_ZT22_WT_rep3


title: ATAC_seq_KC_ZT22_WT_rep4


title: ATAC_seq_KC_ZT22_WT_rep1


title: ATAC_seq_KC_ZT22_WT_rep2


title: ATAC_seq_KC_ZT10_WT_rep3


title: ATAC_seq_KC_ZT10_WT_rep1


title: ATAC_seq_KC_ZT10_WT_rep4


title: ATAC_seq_EC_ZT22_KO_rep4

source_name: Endothelial cells

value: Endothelial cells


title: ATAC_seq_EC_ZT22_KO_rep2


title: ATAC_seq_EC_ZT10_KO_rep3


title: ATAC_seq_EC_ZT22_KO_rep1


title: ATAC_seq_EC_ZT10_KO_rep4


title: ATAC_seq_EC_ZT10_KO_rep1


title: ATAC_seq_EC_ZT22_WT_rep1


title: ATAC_seq_EC_ZT10_KO_rep2


title: ATAC_seq_EC_ZT22_WT_rep4


title: ATAC_seq_EC_ZT22_WT_rep3


title: ATAC_seq_EC_ZT10_WT_rep4


title: ATAC_seq_KC_ZT22_KO_rep1


title: ATAC_seq_KC_ZT10_KO_rep3


title: ATAC_seq_EC_ZT22_KO_rep3


title: ATAC_seq_EC_ZT10_WT_rep3


title: ATAC_seq_EC_ZT10_WT_rep1


title: ATAC_seq_KC_ZT10_KO_rep1


title: ATAC_seq_EC_ZT10_WT_rep2


title: ATAC_seq_KC_ZT10_KO_rep2


title: ATAC_seq_KC_ZT10_WT_rep2


title: RNAseq_KC_KO_ZT22_rep3

data_processing:
RNA-seq reads were aligned to the University of California, Santa Cruz (UCSC) mm9 genome browser using STAR. The tag directories were established and normalized read counts were measured with RefSeq genes using Homer.
Genome_build: mm9

extract_protocol:
Total RNA was extracted from liver tissue or isolated endothelial cells and kupffer cells using Trizol reagent followed by RNeasy Mini Kit (#74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: RNAseq_KC_KO_ZT22_rep1


title: RNAseq_KC_KO_ZT22_rep2


title: RNAseq_KC_KO_ZT16_rep3


title: RNAseq_KC_KO_ZT16_rep2


title: RNAseq_KC_KO_ZT16_rep1


title: RNAseq_KC_KO_ZT10_rep3


title: ATAC_seq_EC_ZT22_WT_rep2


title: RNAseq_KC_KO_ZT10_rep1


title: RNAseq_KC_KO_ZT10_rep2


title: RNAseq_KC_KO_ZT4_rep1


title: RNAseq_KC_WT_ZT22_rep2


title: RNAseq_KC_WT_ZT16_rep2


title: RNAseq_KC_WT_ZT10_rep2


title: RNAseq_KC_WT_ZT16_rep3


title: RNAseq_KC_KO_ZT4_rep2


title: RNAseq_KC_WT_ZT22_rep1


title: RNAseq_KC_WT_ZT22_rep3


title: RNAseq_KC_WT_ZT16_rep1


title: RNAseq_KC_WT_ZT10_rep3


title: RNAseq_KC_WT_ZT10_rep1


title: RNAseq_KC_WT_ZT4_rep3


title: cervical cells, interleukin-1 beta, biological rep1

city: Columbus

first: Douglas

middle: A

last: Kniss

state: Ohio

address: 395 W. 12th Ave

department: Obstetrics and Gynecology

institute: Ohio State University

description: Gene expression data from cervical cells treated with interleukin-1beta.

hyb_protocol: Samples were hybridization to the Affymetrix Human Transcriptome 2.0 array according to the manufacturer’s protocols (16-hour hybridization).

scan_protocol: Hybridized arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Quality control and robust multichip averaging was performed on the feature intensity files using the Affymetrix Expression Console software version 1.4. Gene level differential expression analysis was subsequently performed using the Affymetrix Transcriptome Analysis Console software version 3.0 using the paired sample analytical pipeline (one-way repeated measure ANOVA), and the Benjamini-Hochberg false discovery rate (FDR)-controlling procedure.

label: Biotin

label_protocol: Total RNA (250 ng per sample) was processed using the Ambion WT expression kit and labeled with Affymetrix GeneChip whole-transcript sense target labeling assay.

growth_protocol: Cervical tissues were obtained with informed consent from premenopausal women undergoing hysterectomy for benign gynecological conditions. Primary human cervical stromal fibroblasts were isolated via outgrowth from explanted cervical stromal tissues. The cells were then incubated in experimental medium containing phenol red-free DMEM/F12 (1:1) with 0.5% charcoal-stripped fetal bovine serum in the absence (0.01% ethanol, vehicle control) or presence of 17β-estradiol (10-8 M) for 7 days, which was used to promote nuclear progesterone receptor expression prior to progesterone treatment.

extract_protocol: Total RNA was extracted from harvested cells using TRIzol (Invitrogen). Following the addition of chloroform and centrifugation, the aqueous phase was mixed with an equal volume of 100% ethanol, applied to a miRNeasy spin column (Qiagen) and processed according to the manufacturer's protocol. The extraction procedure included on-column deoxyribonuclease (DNase) digestion using the RNase-Free DNase Set (Qiagen) to remove contaminating genomic DNA. RNA was quantified by absorbance at 260 and 280 nm using a NanoDrop 2000 spectrophotometer (Thermo Scientific).

treatment_protocol: Following estradiol priming, cells were incubated 24 h in the absence or presence of progesterone (10-7 M), followed by challenge for 4 h with 0.2 ng/ml human recombinant interleukin-1β (IL-1β) or an equivalent volume of vehicle (phosphate buffered saline with 0.1% bovine serum albumin).

tag: treatment

tag: progesterone pretreatment time

value: None (vehicle only)

tag: cytokine exposure time

value: 4 h


title: RNAseq_KC_KO_ZT4_rep3


title: RNAseq_KC_WT_ZT4_rep1


title: cervical cells, vehicle, biological rep1

description: Gene expression data from cervical cells treated with vehicle.

source_name: cervical cells treated with vehicle

value: vehicle


title: RNAseq_EC_KO_ZT22_rep2


title: RNAseq_KC_WT_ZT4_rep2


title: RNAseq_EC_KO_ZT22_rep3


title: cervical cells, progesterone, biological rep1

description: Gene expression data from cervical cells treated with progesterone.

value: progesterone


title: cervical cells, progesterone plus interleukin-1 beta, biological rep2

description: Gene expression data from cervical cells treated with progesterone and interleukin-1beta..

value: progesterone and interleukin-1beta


title: cervical cells, interleukin-1 beta, biological rep2

source_name: cervical cells treated with interleukin-1beta


title: cervical cells, vehicle, biological rep2


title: cervical cells, progesterone, biological rep2

source_name: cervical cells treated with progesterone


title: RNAseq_EC_KO_ZT22_rep1


title: RNAseq_EC_KO_ZT16_rep1


title: cervical cells, progesterone plus interleukin-1 beta, biological rep1

source_name: cervical cells treated with progesterone and interleukin-1beta


title: RNAseq_EC_WT_ZT22_rep3


title: RNAseq_EC_KO_ZT4_rep3


title: RNAseq_EC_WT_ZT22_rep1


title: RNAseq_EC_KO_ZT10_rep2


title: RNAseq_EC_KO_ZT10_rep1


title: RNAseq_EC_WT_ZT16_rep1


title: RNAseq_EC_WT_ZT22_rep2


title: RNAseq_EC_KO_ZT4_rep1


title: RNAseq_EC_KO_ZT4_rep2


title: RNAseq_EC_WT_ZT16_rep2


title: RNAseq_EC_KO_ZT16_rep2


title: RNAseq_EC_KO_ZT16_rep3


title: RNAseq_EC_WT_ZT10_rep3


title: RNAseq_EC_KO_ZT10_rep3


title: RNAseq_EC_WT_ZT10_rep2


title: RNAseq_EC_WT_ZT10_rep1


title: RNAseq_EC_WT_ZT4_rep3


title: RNAseq_EC_WT_ZT4_rep1


title: RNAseq_EC_WT_ZT4_rep2


title: RNAseq_RPF_KO_ZT19_rep3


title: RNAseq_RPF_KO_ZT22_rep3


title: RNAseq_RPF_KO_ZT22_rep1


title: RNAseq_RPF_KO_ZT22_rep2


title: RNAseq_RPF_KO_ZT19_rep1


title: RNAseq_RPF_KO_ZT16_rep2


title: RNAseq_RPF_KO_ZT19_rep2


title: RNAseq_RPF_KO_ZT16_rep3


title: RNAseq_RPF_KO_ZT16_rep1


title: RNAseq_RPF_KO_ZT13_rep1


title: RNAseq_RPF_KO_ZT10_rep3


title: RNAseq_RPF_KO_ZT7_rep3


title: RNAseq_RPF_KO_ZT10_rep1


title: RNAseq_RPF_KO_ZT1_rep3


title: RNAseq_RPF_KO_ZT7_rep1


title: RNAseq_RPF_KO_ZT4_rep3


title: RNAseq_RPF_KO_ZT7_rep2


title: RNAseq_RPF_KO_ZT1_rep2


title: RNAseq_RPF_KO_ZT4_rep2


title: RNAseq_RPF_KO_ZT1_rep1


title: RNAseq_RPF_WT_ZT22_rep3


title: RNAseq_RPF_WT_ZT22_rep2


title: RNAseq_RPF_WT_ZT22_rep1


title: RNAseq_RPF_WT_ZT19_rep3


title: RNAseq_RPF_WT_ZT19_rep2


title: RNAseq_RPF_WT_ZT16_rep3


title: RNAseq_RPF_KO_ZT13_rep3


title: RNAseq_RPF_KO_ZT13_rep2


title: RNAseq_RPF_WT_ZT13_rep3


title: RNAseq_RPF_WT_ZT19_rep1


title: RNAseq_RPF_WT_ZT13_rep2


title: RNAseq_RPF_WT_ZT16_rep2


title: RNAseq_RPF_WT_ZT10_rep3


title: RNAseq_RPF_WT_ZT13_rep1


title: RNAseq_RPF_WT_ZT10_rep2


title: RNAseq_RPF_WT_ZT10_rep1


title: RNAseq_RPF_WT_ZT7_rep3


title: RNAseq_RPF_WT_ZT7_rep2


title: RNAseq_RPF_WT_ZT7_rep1


title: RNAseq_RPF_WT_ZT4_rep3


title: RNAseq_RPF_WT_ZT4_rep1


title: RNAseq_RPF_WT_ZT1_rep2


title: RNAseq_RPF_WT_ZT1_rep1


title: RNAseq_RPF_WT_ZT4_rep2


title: RNAseq_Ad_lib_KO_ZT22_rep3


title: RNAseq_Ad_lib_KO_ZT22_rep2


title: RNAseq_Ad_lib_KO_ZT22_rep1


title: RNAseq_Ad_lib_KO_ZT19_rep3


title: RNAseq_Ad_lib_KO_ZT19_rep2


title: RNAseq_Ad_lib_KO_ZT16_rep3


title: RNAseq_Ad_lib_KO_ZT19_rep1


title: RNAseq_RPF_WT_ZT16_rep1


title: RNAseq_Ad_lib_KO_ZT16_rep2


title: RNAseq_Ad_lib_KO_ZT16_rep1


title: RNAseq_Ad_lib_KO_ZT13_rep3


title: RNAseq_Ad_lib_KO_ZT13_rep1


title: RNAseq_Ad_lib_KO_ZT13_rep2


title: RNAseq_Ad_lib_KO_ZT10_rep3


title: RNAseq_RPF_WT_ZT1_rep3


title: RNAseq_Ad_lib_KO_ZT10_rep1


title: RNAseq_Ad_lib_KO_ZT10_rep2


title: RNAseq_Ad_lib_KO_ZT7_rep3


title: RNAseq_RPF_KO_ZT10_rep2


title: NR96_3

city: Charlottesville

first: Jeffrey

last: Smith

state: Virginia

address: 1340 JPA  PO Box 800733 Charlottesville, VA 22908 Telephone:

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Barcoded cDNA was sequenced on an Illumina Nextseq 500. Individual lanes were pooled together for unique samples.
Reads were then mapped to the sacCer3 genome using bowtie2 with default options.
Bam files were then converted into transcript (gene) counts using bedtools.
The counts matrix was annotated with sample names and further analyzed in edgeR (DESeq2, ggplot) and metaboanalyst online program to produce the figures in the paper.
To generate Volcano plots, ggplot was used and only genes <.05 FDR utilized.
Genome_build: sacCer3
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

growth_protocol: All cells were grown in Synthetic Complete (SC) medium with 2% glucose (NR) added at the time of inoculation

extract_protocol:
Cell pellets were obtained, frozen in -80 and RNA was harvested using Trizol reagent. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using standard NEBNext Ultra library RNA library kit for Illumina protocols.

treatment_protocol: CR conditioned medium or NR conditioned medium (filtered and concentrated x10) or water was supplemented to NR (2%) cultures

tag: collection time point

value: 96 hours

value: added NRCM 2% at inoculation


title: RNAseq_Ad_lib_KO_ZT7_rep2


title: NR96_2


title: NR96_1


title: RNAseq_Ad_lib_KO_ZT7_rep1


title: RNAseq_Ad_lib_KO_ZT4_rep3


title: NR24_3

value: 24 hours


title: RNAseq_Ad_lib_KO_ZT4_rep2

value: male


title: NR24_2


title: CD8_KO_2

city: Ann Arbor

first: Yingjie

last: Bian

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on a Mouse Gene ST 2.1 Array, and washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.1.1.

source_name: CD8+ T cell

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Dot1l flox/flox mice were crossed with CD4-Cre mice. Mice were housed and bred in a specific pathogen free (SPF) animal facility. Fresh CD8+ T cells in the peripheral lymph nodes and spleen from Dot1l knockout and wild type mice were isolated by EasySep™ Mouse CD8+ T Cell Isolation Kit (STEMCELL, USA).

extract_protocol: RNA was isolated from these cells using Direct-zolTM RNA miniprep Plus kit (ZOMO research, Irvine, CA, USA).

treatment_protocol: Not applicable

value: Dot1l knockout

value: CD8+ T cell


title: CD8_WT_2

value: wild type


title: RNAseq_Ad_lib_KO_ZT4_rep1

value: normal chow

value: REV-ERB a/b double knockout

value: Liver


title: NR24_1


title: CD8_WT_1


title: CD8_WT_3


title: CD8_KO_1


title: Nrlog_3

value: Log


title: RNAseq_Ad_lib_KO_ZT1_rep2


title: RNAseq_Ad_lib_KO_ZT1_rep3


title: CD8_KO_3


title: RNAseq_Ad_lib_KO_ZT1_rep1


title: RNAseq_Ad_lib_WT_ZT22_rep3

value: WT


title: RNAseq_Ad_lib_WT_ZT22_rep2


title: Nrlog_1


title: CR96_3

value: added CRCM 2% at inoculation


title: RNAseq_EC_WT_ZT16_rep3

value: Endothelial cells


title: dmem_rep5

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Replicate 5 from pig inoculated with DMEM

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: counts

organism: Sus scrofa

source_name: inguinal lymph node

extract_protocol: none provided by the submitter

tag: variant

value: Landrace pig

value: DMEM


title: dmem_rep4

description: Replicate 4 from pig inoculated with DMEM


title: CR96_1


title: RNAseq_Ad_lib_WT_ZT19_rep3


title: dmem_rep3

description: Replicate 3 from pig inoculated with DMEM


title: dmem_rep2

description: Replicate 2 from pig inoculated with DMEM


title: Nrlog_2


title: RNAseq_Ad_lib_WT_ZT19_rep2


title: RNAseq_Ad_lib_WT_ZT19_rep1


title: pprsv_rep5

description: Replicate 5 from pig inoculated with live-attenuated PRRSV strain

value: PPRSV CON KT894735.1


title: pprsv_rep4

description: Replicate 4 from pig inoculated with live-attenuated PRRSV strain


title: RNAseq_Ad_lib_WT_ZT16_rep3


title: CR24_1


title: pprsv_rep3

description: Replicate 3 from pig inoculated with live-attenuated PRRSV strain


title: RNAseq_Ad_lib_WT_ZT16_rep2


title: CRlog_3


title: pprsv_rep1

description: Replicate 1 from pig inoculated with live-attenuated PRRSV strain


title: CRlog_2


title: RNAseq_Ad_lib_WT_ZT16_rep1


title: Th17 RORgt-KO

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality control using Trim Galore v0.4.4.
Clean paired-end reads were mapped to mouse geneme mm10 using Bowtie2 v2.2.9.
Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were filtered by Samtools.
PCR duplicates were removed with picard MarkDuplicates.
Peaks were determined by MACS2.
Peaks with differential accessibility were determined by DEGseq with at least 2 folds of change and FDR adjusted p value of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file with quantitative data for each sample

source_name: Th17 cells

growth_protocol: Naïve CD4+ T cells were isolated and cultured under Th17 polarizing condition.

extract_protocol:
DNA were extracted using TruePrep DNA Library Prep Kit V2 for Illumina.
DNA libraries were constructed with TruePrep DNA Library Prep Kit V2 and TruePrep Index Kit V2 for Illumina.

treatment_protocol: After 3 days culture, T cells were reactivated with anti-CD3 for 4 hours.

value: RORgt fl/fl -CD4cre

tag: age

value: 3 days in vitro

value: Spleen+Lymph nodes

value: Th17 cells


title: Th17 RORgt-WT

value: RORgt fl/fl

tag: cell type


title: CRlog_1

tag: strain


title: Th17 STAT3-WT

value: STAT3 fl/fl


title: RNAseq_Ad_lib_WT_ZT13_rep3

value: male


title: dmem_rep1

description: Replicate 1 from pig inoculated with DMEM


title: CR24_3

value: 24 hours


title: RNAseq_Ad_lib_WT_ZT13_rep2

value: normal chow


title: RNAseq_RPF_KO_ZT4_rep1

value: REV-ERB a/b double knockout

value: Liver


title: Water96_2

value: 96 hours

value: added water at inoculation


title: Water96_1


title: pprsv_rep2

description: Replicate 2 from pig inoculated with live-attenuated PRRSV strain


title: 6-6_mtN23-YZW139-2

city: Ithaca

first: Andrew

last: Clark

state: NY

address: 215 Tower Road

institute: Cornell University

data_processing:
All Scripts Used For Processing + Analysis Can Be Found on github.com/mam737/mitoY_RNASEQ
FastQC v0.11.5 - evaluate quality of raw reads
Trimmomatic v0.36 - remove low qualtiy reads, crop first 10 bp, remove adapters, and drop reads shorter than 20 bp long
Star v2.6- align reads to reference genome
HTSeq-Count v0.11.0 - count reads
DESeq2 - Differential Expression Analsis
Genome_build: Drosophila melanogaster Genome Reference 6.18
Genome_build: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.18_FB2017_05/
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: 10 pooled 3-5 day old whole fly males

growth_protocol: All flies during the crossing process were maintained in vials on standard sucrose-yeast medium in climate controlled growth chambers with a 12:12 hours light:dark cycle at 25℃

extract_protocol:
For each sample, 10 3-5 day old adult males were collected, pooled, and flash frozen on dry ice. RNA was harvested using a Trizol reagent. Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used.
RNA libraries were prepared for sequencing using standard Illumina protocols accompannying the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD

treatment_protocol: N/A - this experiment was only to look at differences between otherwise isogenic lines w/ unique mitochondrial-Y combinations

value: whole fly

tag: mitochondrial haplogroup

value: Global Diversity Line N23

tag: y haplotype

value: Global Diversity Line ZW139

tag: bio replicate

value: B

tag: batch


title: RNAseq_Ad_lib_WT_ZT10_rep3

value: WT

tag: tissue


title: 6-5_mtN23-YZH23-1

tag: Sex

value: Global Diversity Line ZH23

value: A


title: 6-5_mtN23-YZH23-2


title: Water24_3


title: 6-4_mtN23-YN07-2

value: Global Diversity Line N07


title: 6-4_mtN23-YN07-1


title: Th17 STAT3-KO

tag: genotype

value: STAT3 fl/fl -CD4cre

value: 3 days in vitro

value: Spleen+Lymph nodes

value: Th17 cells


title: 6-3_mtN23-YN03-2

value: male

value: Global Diversity Line N03


title: 6-2_mtN23-YB11-2

value: Global Diversity Line B11


title: Water24_2

value: 24 hours


title: Water24_1

value: added water at inoculation


title: Water96_3

value: 96 hours


title: 6-2_mtN23-YB11-1

value: whole fly

value: Global Diversity Line N23


title: RNAseq_Ad_lib_WT_ZT7_rep3

tag: diet

value: normal chow

tag: genotype/variation

value: Liver


title: 6-3_mtN23-YN03-1


title: Waterlog_3

value: Log

tag: treatment


title: 6-6_mtN23-YZW139-1

value: Global Diversity Line ZW139

value: A


title: 6-1_mtN23-YB04-2

value: Global Diversity Line B04

value: B


title: 6-1_mtN23-YB04-1


title: Waterlog_2


title: RNAseq_Ad_lib_WT_ZT7_rep2

tag: gender

value: WT


title: RNAseq_Ad_lib_WT_ZT13_rep1


title: RNAseq_Ad_lib_WT_ZT7_rep1


title: 5-6_mtN02-YZW139-2

value: Global Diversity Line N02


title: Waterlog_1


title: RNAseq_Ad_lib_WT_ZT10_rep2

value: male


title: 5-5_mtN02-YZH23-2

value: Global Diversity Line ZH23


title: 5-6_mtN02-YZW139-1


title: 5-5_mtN02-YZH23-1


title: RNAseq_Ad_lib_WT_ZT4_rep3


title: 5-4_mtN02-YN07-2

value: Global Diversity Line N07


title: RNAseq_Ad_lib_WT_ZT4_rep2


title: RNAseq_Ad_lib_WT_ZT10_rep1


title: 5-4_mtN02-YN07-1


title: IOSE11

city: Brisbane

first: Tracy

last: O'Mara

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
Library strategy: HiChIP-Seq
HiChIP reads (fastq files) were aligned to the human reference genome (hg19) using HiC-Pro version 2.9.0 and default settings used to remove duplicate reads, assign reads to DpnII restriction fragments and filter for valid interactions.
Genome_build: hg19
Supplementary_files_format_and_content: allValidPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.

source_name: Normal immortalized ovarian surface epithelial cells

growth_protocol: Cells were grown in 1:1 MCDB105:Medium 199 with 15% FBS and antibiotics (100 IU/ml penicillin and 100 µg/ml streptomycin)

extract_protocol:
Cell nuclei were extracted from fixed cell pellets and digested overnight with 375U of DpnII . After digestion, nuclei were resuspended in NEB buffer 2 (New England Biolabs) and restriction fragment overhangs were filled in with biotin-dATP using the DNA polymerase I, large Klenow fragment (incubated at 30oC for 2h). Proximity ligation was performed for 4 h at 16oC, then nuclei lysed and chromatin sheared for 9 min using the Covaris S220 Sonicator. For each sample, sheared chromatin was split into two tubes and incubated overnight with 4.6 mg of H3K27Ac antibody (Abcam, EP16602). The next day Protein A beads were used to capture H3K27Ac-associated chromatin which was eluted and purified with Zymo Research concentrator columns (columns were washed twice with 10 ml of water). The DNA concentration of the purified chromatin was to estimate the amount of TDE1 enzyme (Illumina) needed for tagmentation which was performed with biotin-labelled chromatin captured on streptavidin beads.
Sequencing libraries were then generated by PCR of tagmented samples using the Nextera DNA preparation kit (Illumina) as per the manufacturer’s instructions. Afterwards, size selection was performed using Ampure XP beads to capture 300-700 bp fragments. For each cell line, at least two independent sequencing libraries were pooled together to provide 25 ml of library at ≥10 nM for Illumina HiSeq4000

tag: chip antibody

value: H3K27Ac (Abcam, EP16602)

value: normal ovary


title: 5-3_mtN02-YN03-1

value: Global Diversity Line N03


title: RNAseq_Ad_lib_WT_ZT1_rep3


title: RNAseq_Ad_lib_WT_ZT4_rep1


title: 5-2_mtN02-YB11-2

value: whole fly

value: Global Diversity Line B11


title: 5-2_mtN02-YB11-1


title: RNAseq_Ad_lib_WT_ZT1_rep2

value: normal chow