title: lung, 135C_600_Rm196

description:
raw data file: 2013-09-20_19723135_600PMT_5um_0532.txt
Array C (blocks17-24)

data_processing: Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split into four subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 10240 features on each microarray by subtracting the median local background from the median local foreground for each spot. Visually flagged spots were removed prior to averaging and normalizing.The 95th percentile of the negative control spots was also calculated for each array. The spot intensities and 95th percentile of negative controls (TPT95) were transformed by taking the log (base 2) of each value. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The mean probe intensities for each of the probes on each array were then determined by averaging the triplicate spot intensities. Spots that have an average saturated signal were removed prior to normalization. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the non-saturated human probes above threshold in all samples. The log2-transformed spot intensities for all features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays.

source_name: lung, 80ug MWCNT, 1 mo

label_protocol: The total RNA with was DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitous viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus.

extract_protocol: Total RNA was isolated from mouse lung tissue using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol.

tag: strain

value: 80ug MWCNT

tag: time

value: 1 mo

value: lung


title: mouse_1_zone_7

status: Public on Jul 26 2019

type: RNA

city: Rehovot

first: Shalev

last: Itzkovitz

state: Israel

address: 234 Herzl

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: miRNA expression hepatocytes - mouse 1, zone 7

hyb_protocol: cDNAs were hybridized to according to the Agilent microRNA Hybridization Kit protocol.

scan_protocol: Chips were  scanned using Agilent G2505B array scanner with default parameters.

data_processing: Data were extracted using the Agilent Feature Extraction software with default parameters. miRNAs that were not expressed in at least one zone in all three mice were removed from the analysis. miRNAs that were not annotated as high confidence in miRBase v22 were removed from the analysis. The raw signal for each miRNA (in each chip) was divided by the total signal from all miRNAs in that chip.

molecule: total RNA

organism: Mus musculus

source_name: Mouse 1, Zone 7 hepatocytes

label_protocol: Total RNA was labeled with Cy3 during transformation into cDNA using an RNA Agilent miRNA Labeling Kit and Spike Kit.

growth_protocol: Mice were fed ad libitum and were kept in a reverse light-dark cycle

extract_protocol: See associated paper (Ben Moshe et al., Nat. Metab., 2019) for full details. Liver cells from anesthetized mice were dissociated via liberase perfusion. The cell isolate was immuno-labeled for CD73, E-cadherin, CD45, and CD31 and stained with Hoechst and and a viability stain (Zombie Green). The labeled isolate was depeleted of unviable, CD45+ and CD31+ cells and filtered for tetraploid cells. The remaining 4n hepatocytes were sorted based on CD73 and E-cadherin intensities as a proxy of position along the porto-central axis (zone 1 - most pericentral / higher CD73, zone 8 - most periportal / higher E-cadherin). 50,000 cells were sorted for each population (in each mouse). Total RNA was extracted from the hepatocyte pellet using the Direct-zol RNA Mini-prep kit (Zymo Research, USA).

tag: Sex

value: Male

tag: age

value: 3 months

tag: tissue

value: tetraploid hepatocytes


title: mouse_1_zone_6

description: miRNA expression hepatocytes - mouse 1, zone 6

source_name: Mouse 1, Zone 6 hepatocytes


title: lung, 135A_600_Rm409

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

country: USA

institute: West Virginia University

description:
raw data file: 2013-09-20_19723135_600PMT_5um_0532.txt
Array A (blocks 1-8)

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon Genepix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

label: Oyster-550 fluorescent dye

source_name: lung, 40ug MWCNT, 12 mo

treatment_protocol: Each component consisted of 8 mice per exposure group (dispersion media [DM, negative control]; 1, 10, 40, or 80 μg MWCNT; 120 μg crocidolite asbestos [positive control]) to be sacrificed at 1, 6 or 12 months post-exposure, for a total of 144 mice.

tag: treatment

value: 40ug MWCNT

value: 12 mo


title: lung, 135B_600_Rm298

description:
raw data file: 2013-09-20_19723135_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 1ug MWCNT, 12 mo

value: 1ug MWCNT


title: HMid_R2B

type: SRA

city: Cambridge

first: Heather

middle: P

last: Harding

state: Cambridge

address: Hills Road

department: CIMR Clinical Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
CLB_GCN_O12
Histidinol treated_Medium-dull_sorted_round_2_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
Compressed fastq files containing base calls were produced by the sequencing facility.
The MAGECK program (PMID: 25476604 PMCID: PMC4290824) was used for trimming and mapping the reads to the guide library (see supplementary file 'CHO_library_B_GCN Screen_counts.xls' columns A-F for library).
The raw guide counts were adjusted to total counts per sample to equalize between samples.
Genome_build: The genome used to build the guide list was GCF_000223135.1 (CriGri_1.0). Please see the supplementary file 'CHO_library_B_GCN Screen_counts.xls' columns A-F for the sg guide sequences and genes targeted.
Supplementary_files_format_and_content: *.txt: Tab-delimited text files, column A Guide unique ID, column B normalized guide counts.

molecule: genomic DNA

organism: Cricetulus griseus

source_name: CHO cells

growth_protocol: Cells with a stable ISR reporter (CHOP::GFP) and stable Cas9 expression were infected with lentivirus prepared from pooled sgRNA expression library plasmid and helpers by transfection into HEK293T cells. After selection of the infected cells with puromycin for two weeks the cells were left untreated or treated and then sorted as indicated.

extract_protocol:
Genomic DNA containing the integrated sgRNA viral expression vectors was prepared using the DNAzol method.
Two round of PCR were used to produce barcoded amplicons that were pooled for sequencing. The first round of amplicon used vector directed primers flanking the 20bp sgRNA and the second round added barcodes to the individual samples.

treatment_protocol: Cells were treated with histidinol to inhibit histidinyl-tRNA synthetase at 0.5 mM for 20 hours before collection and replating or sorting for dull cells and then replating. After recovery, some cells were expanded and aliquots saved for DNA prep or an additional round of sorting.

tag: cell line

value: CHO

tag: cell type

value: Chinese hamster ovary cell line

value: Histidinol 0.5 mM, 20hr

tag: selection

value: Survival and sort for medium

tag: round of selection


title: mouse_1_zone_4

description: miRNA expression hepatocytes - mouse 1, zone 4

source_name: Mouse 1, Zone 4 hepatocytes


title: mouse_1_zone_5

description: miRNA expression hepatocytes - mouse 1, zone 5

source_name: Mouse 1, Zone 5 hepatocytes


title: lung, 134C_600_Rm320

description:
raw data file: 2013-09-20_19723134_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, DM, 1 mo

value: DM


title: lung, 134D_600_Rm200

description:
raw data file: 2013-09-20_19723134_600PMT_5um_0532.txt
Array D (blocks 25-32)

source_name: lung, 80ug MWCNT, 12 mo


title: HMid_R2A

description:
CLB_GCN_O11
Histidinol treated_Medium-dull_sorted_round_2_replicate_A
processed data file: CHO_library_B_GCN Screen_counts.xls


title: mouse_1_zone_3

description: miRNA expression hepatocytes - mouse 1, zone 3

source_name: Mouse 1, Zone 3 hepatocytes


title: lung, 134B_600_Rm214

description:
raw data file: 2013-09-20_19723134_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: mouse_1_zone_2

description: miRNA expression hepatocytes - mouse 1, zone 2

source_name: Mouse 1, Zone 2 hepatocytes


title: HUS_R2A

description:
CLB_GCN_O9
Histidinol treated_Unsorted_round_2_replicate_A
processed data file: CHO_library_B_GCN Screen_counts.xls

value: Survival


title: mouse_1_zone_1

description: miRNA expression hepatocytes - mouse 1, zone 1

source_name: Mouse 1, Zone 1 hepatocytes


title: lung, 134A_600_Rm205

description:
raw data file: 2013-09-20_19723134_600PMT_5um_0532.txt
Array A (blocks 1-8)

source_name: lung, 10ug MWCNT, 12 mo

value: 10ug MWCNT


title: HDull_ R1B

description:
CLB_GCN_O8
Histidinol treated_Dull_sorted_round_1_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls

value: Survival and sort for dull


title: HDull_ R1A

description:
CLB_GCN_O7
Histidinol treated_Dull_sorted_round_1_replicate_A
processed data file: CHO_library_B_GCN Screen_counts.xls


title: lung, 133C_600_Rm407

description:
raw data file: 2013-09-20_19723133_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, 10ug MWCNT, 6 mo

value: 6 mo


title: PYO 3

city: Canterbury

first: Lucian

last: Duvenage

address: Giles Lane

department: School of Biosciences

institute: University of Kent

description:
wild-type treated with pyocyanin
untreated vs PYO

library_source: transcriptomic

data_processing:
Illumina NextSeq500 used for basecalling
Sequence quality was assessed using FASTQC. No trimming was performed
Each Fastq file was mapped to Assembly 21 of C. albicans SC5314 using HISAT2 v1.01. BAM file alignments for technical replicates were merged using Picard (Galaxy version 1.12), in order to generate a single BAM file for each biological replicate
Gene differential expression testing was performed usng Cuffdiff v. 2.2.1.1. with the following parameters: multi-read correction: yes, perform bias correction: yes (C. albicans SC5314 genome Assembly 21)
Genome_build: C. albicans SC5134 Assembly 21
Supplementary_files_format_and_content: Tab-delimited test files Cuffdiff output for gene differential expression testing comparing untreated sample group ("WT") with each other sample group. Including FPKM, log2(fold_change), test_stat, p value, q-value

organism: Candida albicans

source_name: whole cells

growth_protocol: Inoculation of YPD with overnight cultures to final OD600 nm of 0.2, followed by 5 h shaking incubation 30 °C

extract_protocol:
E.Z.N.A.® Yeast RNA Kit (Omega Bio-tek, Norcross, GA) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Addition of 0.5 mM SHAM, or 80 µM pyocyanin, 30 °C shaking incubation for 30 min, followed by RNA extraction

tag: genotype

value: wild-type


title: HUS_R1B

description:
CLB_GCN_O6
Histidinol treated_Unsorted_round_1_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls


title: lung, 133D_600_Rm36

description:
raw data file: 2013-09-20_19723133_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: 80ug MWCNT

value: lung


title: PYO 1


title: lung, 133B_600_m2

description:
raw data file: 2013-09-20_19723133_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, DM, 12 mo


title: HUS_R2B

description:
CLB_GCN_O10
Histidinol treated_Unsorted_round_2_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls


title: lung, 133A_600_m35

description:
raw data file: 2013-09-20_19723133_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: UTUS_R1B

description:
CLB_GCN_O4
Untreated_Unsorted_round_1_replicate_B
processed data file: CHO_library_B_GCN Screen_counts.xls

value: Untreated


title: SHAM 3

description:
wild-type treated with SHAM
untreated vs SHAM


title: SHAM 2


title: lung, 620D_600_Rm288

description:
raw data file: 2013-08-23_19718620_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: 2cell HMVEC 24hr #5

description:
2012-05-24_19706187_650PMT_0532.txt
Array # (Block ID): B

data_processing: Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split in to four subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 8816 features on each microarray by subtracting the median local background from the median local foreground for each spot. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The spot intensities and T were transformed by taking the log (base 2) of each value; and all further calculations were performed with the log-transformed values. The spot intensities for the 8760 features associated with an oligonucleotide probe were averaged per probe in order to obtain the mean of the triplicate spots for each probe (i.e. probe intensities). The normalization factor (N) for each microarray was calculated as the 20% trim mean of the average human probes spot intensities above threshold in all samples. The probe intensities were then normalized, by subtracting N from each spot intensity and adding back the grand mean of N across all microarrays. The data was filtered to retain values for the 1718 human microRNA probes on the microarray minus any probes showing an overall saturation of signal.

organism: Homo sapiens

source_name: HMVEC 2cell 1.2ug/ml MWCNT 24hr

label_protocol: The RNA samples were DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through Nanosep 100K columns (Pall Corporation) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: For monoculture exposures, SAEC and HMVEC were plated directly into 100 mm cell culture dishes (Corning, Tewksbury, MA; growth area: 55 cm2), allowed to form intact barriers for 72 h, serum starved overnight, and exposed directly to MWCNT at a concentration of 1.2 µg/mL in 10 mL of their respective media for either 6 or 24 h. DM for 24 h was used as a negative control. Six biological replicates of each SAEC and HMVEC monoculture exposure condition were collected for microarray analysis. Both SAEC and HMVEC in monoculture have been shown to interact with MWCNT (Pacurari et al. 2012; Snyder-Talkington et al. 2013b).    For coculture exposures, SAEC and HMVEC were allowed to form intact epithelial and endothelial barriers for 72 h, serum starved overnight, and SAEC were exposed to MWCNT at a concentration of 1.2 µg/mL in 10 mL of SAEC media for either 6 or 24 h. DM for 24 h was used as a negative control. HMVEC in the coculture system were not directly exposed to MWCNT, and MWCNT are not apparent in HMVEC transmission electron microscopy preparations following SAEC exposure in coculture (Snyder-Talkington et al. 2013a).Six biological replicates of each SAEC and HMVEC coculture at each exposure condition were collected for microarray analysis. The total number of monoculture and coculture samples for microarray analysis was 72.

extract_protocol: Total RNA was isolated from SAEC and HMVEC using RNAprotect Cell Reagent and an RNeasy Mini Kit from Qiagen according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA concentrations were determined using a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For cell culture exposures, MWCNT were prepared in DM. Transmission electron micrographs of MWCNT dispersed in DM determined that DM promoted significant dispersion of MWCNT. MWCNT were prepared in DM, followed by indirect sonication at 4°C for 5 min (Hielscher ultrasonic processor, UIS259L) at amplitude 100% and cycle 1. Following indirect sonication, the suspension was directly sonicated for 5 min at 5W output and 10% duty cycle (Branson Sonifier 450). The stock solution (0.5 mg/mL) of MWCNT was kept at 4°C and used within 2–3 weeks. Prior to cell culture experiments, the MWCNT stock solution was directly sonicated for 1 min at 5W output and 10% duty cycle.

value: HMVEC

tag: culture

value: coculture


title: Liver_uninfection [L1]

city: Nanjing

first: Yangyue

last: Ni

state: Jangsu

address: 101 Longmian Avenue

department: Department of Pathogen Biology

country: China

institute: Nanjing Medical University

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US). Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Male C57BL/6 mice (aged 6 weeks) were purchased from the Animal Core Facility of Nanjing Medical University and fed in a specific pathogen-free environment in the Animal Core Facility of Nanjing Medical University.

extract_protocol: RNA from 3 combined liver samples from mice in the uninfection and infection groups was isolated using RNAiso Plus kits (TaKaRa Biotechnology Co. Ltd., Dalian, China) following the manufacturer’s protocol. RNA integrity and concentration were assessed on a NanoDrop Ultramicro-Spectrophotometer (Thermo Fisher Scientific, MA, USA).

treatment_protocol: 6-week-old male C57BL/6 mice were fed a normal diet . mice in the infection group was infected with 10±1 S. japonicum cercariae and the other, unchallenged, group was used as the normal control.

tag: gender

value: male

value: none (uninfected)

value: liver


title: Liver_infection [L9]

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

value: S. japonicum infection


title: B. cinerea-treated_T2_rep2

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: Gene expression 10 days after the injection (Time 2) in B. cinerea-injected berry pericarps, replicate 2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing  25x Agilent fragmentation buffer and  10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-048771 4x44K Grape all custom microarray chip (GPL22427) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid:048771_D_F_20130410) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Vitis vinifera

source_name: berry pericarp B. cinerea-injected T2 (10 days after injection), replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA).

growth_protocol: Vitis vinifera cv. Muller-Thurgau bunches were harvested in August 2017 in Custoza (Italy) and dehydrated into the withering setting of the “La Prendina” farm located in Monzambano (Mantova, Italy). Muller-Thurgau grapes were collected with a soluble solids content of 18.25 ± 0.05 °Brix and placed into plateaux (about 20 kg each) in a ventilated withering facility (14-15°C, 53-60% of relative humidity). Brix degree and weight loss of berry bunches where monitored weekly during withering. After one month, berry Brix degree was about 24 and the percentage of weight loss was ~30% of the initial weigh. One thousand Muller-Thurgau berries (with pedicels) were sampled, surface sterilized for 5 minutes in 70% Ethanol and dried in sterility.

extract_protocol: Infected/uninfected berry pericarps were ground into liquid nitrogen and total RNA was isolated from 200 mg of powders using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA). The RNA quantity, integrity and purity were controlled using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer Chip RNA 7500 serie II (Agilent).

treatment_protocol: Among the sterilized berries, 200 berries were frozen, divided into three different biological replicates (a pool of 65 berries each) and sampled as time point 0 (T0) of the experiment. Botrytis cinerea B05.10 was cultured and inoculated into 400 berries (1x105 conidia per ml). The remaining 400 berries were water-injected and used as control. Berries were incubated into sterile 24-well plates under controlled conditions (15°C/15h dark; 18°C/9h light) to induced noble rot. Three biological replicates (about 50 berries each) of infected/control berries were collected and frozen 5 days after the injection when inoculated berries were at the initial stage of noble rot development (time point 1, T1). Moreover, infected/control berries were sampled 10 days after the injection when the inoculated berries were at the pourri plain stage of noble rot (time point 2, T2) characterized by a complete and homogeneous chocolate hue.

tag: cultivar

value: Muller-Thurgau

value: Berry pericarps

tag: type of treatment

value: B. cinerea-infected


title: B. cinerea-treated_T2_rep3

description: Gene expression 10 days after the injection (Time 2) in B. cinerea-injected berry pericarps, replicate 3

source_name: berry pericarp B. cinerea-injected T2 (10 days after injection), replicate 3


title: control_T2_rep2

description: Gene expression 10 days after the injection (Time 2) in water-injected berry pericarps, replicate 2

source_name: berry pericarp water-injected T2 (10 days after injection), replicate 2

value: water-injected


title: control_T2_rep1

description: Gene expression 10 days after the injection (Time 2) in water-injected berry pericarps, replicate 1

source_name: berry pericarp water-injected T2 (10 days after injection), replicate 1


title: UTUS_R1A

description:
CLB_GCN_O3
Untreated_Unsorted_round_1_replicate_A
processed data file: CHO_library_B_GCN Screen_counts.xls

source_name: CHO cells

value: CHO

value: Chinese hamster ovary cell line

value: Survival


title: B. cinerea-treated_T2_rep1

description: Gene expression 10 days after the injection (Time 2) in B. cinerea-injected berry pericarps, replicate 1

source_name: berry pericarp B. cinerea-injected T2 (10 days after injection), replicate 1


title: B. cinerea-treated_T1_rep2

description: Gene expression 5 days after the injection (Time 1) in B. cinerea-injected berry pericarps, replicate 2

source_name: berry pericarp B. cinerea-injected T1 (5 days after injection), replicate 2


title: control_T2_rep3

description: Gene expression 10 days after the injection (Time 2) in water-injected berry pericarps, replicate 3

source_name: berry pericarp water-injected T2 (10 days after injection), replicate 3


title: CHO_B

description:
CLB_GCN_O1
Starting library_plasmid
processed data file: CHO_library_B_GCN Screen_counts.xls

organism: synthetic construct

source_name: Starting library

value: Starting library


title: B. cinerea-treated_T1_rep3

description: Gene expression 5 days after the injection (Time 1) in B. cinerea-injected berry pericarps, replicate 3

source_name: berry pericarp B. cinerea-injected T1 (5 days after injection), replicate 3


title: HUS_R1A

description:
CLB_GCN_O5
Histidinol treated_Unsorted_round_1_replicate_A
processed data file: CHO_library_B_GCN Screen_counts.xls

value: Histidinol 0.5 mM, 20hr


title: B. cinerea-treated_T1_rep1

description: Gene expression 5 days after the injection (Time 1) in B. cinerea-injected berry pericarps, replicate 1

source_name: berry pericarp B. cinerea-injected T1 (5 days after injection), replicate 1


title: AOX 1

description:
aox2 deletion mutant
WT vs aox2_del

value: SN152 with homozygous aox2 deletion

value: aox2 deletion Arg-


title: AOX 3

description:
aox2 deletion mutant
WT vs aox2_del


title: Control Garganega berries 3

description: Control Garganega berries, inoculated with water

data_processing:
de-multiplexing: all raw reads related to the same sample (originally spread over multiple FASTQ files) were merged into a single FASTQ file of R1 or R2 reads for the given sample.
data filtering: raw reads were subjected to quality control by using the IlluQC software, that is part of the NGS QC Toolkit [Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619. doi: 10.1371/journal.pone.0030619. Epub 2012 Feb 1. PubMed PMID: 22312429; PubMed Central PMCID: PMC3270013.] with default parameters (i.e.: quality cutoff: 20; required % of nucleotides in reads with quality score at least equal to quality cutoff: 70%).
mapping: filtered reads were mapped against a mixed reference genome (Botrytis cinerea + Vitis vinifera) by using TopHat (version 2.0.11) [Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with  RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16. PubMed PMID: 19289445; PubMed Central PMCID: PMC2672628.].
gene-level summarization: mapped reads were summarized at the gene-level into a count-matrix by using the htseq-count tool from the HTSeq library [Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25. PubMed PMID: 25260700; PubMed Central PMCID: PMC4287950].
gene-level count matrices were then used to perform differential expression analyses by using edgeR [Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11. PubMed PMID: 19910308; PubMed Central PMCID: PMC2796818]. Only genes having at least 3 mapped reads in at least 3 samples of the above count matrix were tested for differential expression.
Genome_build: whole-genome sequences and annotations for Vitis vinifera (genome annotation release: V1) were obtained from the Grape genome database [Vitulo N, Forcato C, Carpinelli EC, Telatin A, Campagna D, D'Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M, Valle G. A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol. 2014 Apr 17;14:99. doi: 10.1186/1471-2229-14-99. PubMed PMID: 24739459; PubMed Central PMCID: PMC4108029]. Whole-genome sequences and annotations for Botrytis cinerea (Ensembl-fungi release 28; Botrytis cinerea strain: B05.10; Genome assembly: ASM15095v2) were obtained from the Ensembl Fungi data portal [Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K,  Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res. 2010 Jan;38(Database issue):D563-9. doi: 10.1093/nar/gkp871. Epub 2009 Nov 1. PubMed PMID: 19884133; PubMed Central PMCID: PMC2808935]. Both sets of genomic data were downloaded on August 5, 2015.
Supplementary_files_format_and_content: file “Gene_level_count matrix_Botrytis cinerea.xls”: Microsoft Excel file including 2 sheets: (1.) “rawCounts__allGenes” = gene-level raw counts matrix produced by the hts-count software for 11702 annotated Botrytis cinerea genes across all 9 samples assayed by RNA-Seq; (2) “normCounts__edgeR_testedGenes” = gene-level matrix of edgeR-normalized counts limited to 10881 genes passing abundance filter (ie: with at least 3 raw counts in at least 3 samples) across 6 samples (ie: 3 replicates of the two conditions under contrast). File “Gene_level_count matrix_Garganega.xls”: Microsoft Excel file including 2 sheets: (1.) “rawCounts__allGenes” = gene-level raw counts matrix produced by the hts-count software for 29970 annotated Vitis vinifera genes across all 9 samples assayed by RNA-Seq; (2) “normCounts__edgeR_testedGenes” = gene-level matrix of edgeR-normalized counts limited to 22253 genes passing abundance filter (ie: with at least 3 raw counts in at least 3 samples) across 6 samples (ie: 3 replicates of the two conditions under contrast).

source_name: berries

growth_protocol: B. cinerea B05.10 liquid cultures were produced in three flasks inoculating 7 x 106 conidia/ml into 125 ml of potato dextrose broth (Formedium, Hunstanton, UK). After 7 days of incubation at 22°C and shaking at 120 rpm, B. cinerea mycelia were recovered by filtration, frozen and ground in liquid nitrogen. Vitis vinifera cv. Garganega bunches were harvested in October 2014 in Monteforte d’Alpone (Verona, Italy) and withered into the Pasqua Vigneti e Cantine winery facility located in Verona. Healthy grapes were collected at the commercial ripening stage (soluble solids content = 18.5 ± 0.25°Brix) and placed into perforated plastic boxes (plateaux, about 5 kg each) in a ventilated withering facility under natural conditions (17–20°C, 78–82% relative humidity).  Randomly selected replicates were subjected weekly to Brix degrees determination using a DBR35 digital refractometer (Giorgio Bormac, Carpi, Italy) while three dedicated plateaux were weighed weekly using a CH50K50 electronic balance (Kern, Balingen, Germany) in order to determine the weight loss of the berry bunches.  After one month of withering, berry Brix degree was about 26.6 and the percentage of weight loss was ~30% of the initial weigh. At this stage, 1000 Garganega berries (with pedicels) were sampled, surface sterilized for 5 minutes in 70% Ethanol and dried in sterility.

extract_protocol:
Infected/uninfected berry pericarps were ground into liquid nitrogen and total RNA was isolated from 200 mg of powders using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA). The RNA quantity, integrity and purity were controlled using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer Chip RNA 7500 serie II (Agilent).
For each sample, unstranded library was prepared from 2.5 µg of total RNA using the Illumina TruSeq Library Prep Kit v2 (Illumina, San Diego, CA).

treatment_protocol: Among the 1000 sterilized berries, 500 berries were inoculated with B. cinerea by syringae injection while the remaining 500 berries were injected with sterile water and were used as negative control.  Garganega berries were then incubated into sterile 24-well plates under controlled conditions (15°C/15h dark; 18°C/9h light) to induced noble rot.

value: berries

tag: sample type

value: control berries

tag: strain/cultivar

value: Vitis vinifera cv. Garganega


title: WT 3

description: untreated wild-type

tag: strain

value: wild-type


title: lung, 620A_600_Rm327

description:
raw data file: 2013-08-23_19718620_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: DM

tag: time

value: 12 mo

value: lung


title: Control Garganega berries 2


title: lung, 620B_600_Rm300

description:
raw data file: 2013-08-23_19718620_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 40ug MWCNT, 12 mo

value: 40ug MWCNT


title: WT 1

description: untreated wild-type


title: control_T1_rep3

description: Gene expression 5 days after the injection (Time 1) in water-injected berry pericarps, replicate 3

source_name: berry pericarp water-injected T1 (5 days after injection), replicate 3

value: Muller-Thurgau

value: Berry pericarps


title: control_T1_rep1

description: Gene expression 5 days after the injection (Time 1) in water-injected berry pericarps, replicate 1

source_name: berry pericarp water-injected T1 (5 days after injection), replicate 1

value: water-injected


title: lung, 616D_600_Rm314

description:
raw data file: 2013-08-23_19718616_600PMT_5um_0532.txt
Array D (blocks 25-32)

source_name: lung, DM, 12 mo


title: Control Garganega berries 1


title: CHO_B_cell

description:
CLB_GCN_O2
Freshly_infected_Untreated_Unsorted
processed data file: CHO_library_B_GCN Screen_counts.xls

value: CHO

value: Chinese hamster ovary cell line

value: Untreated

value: Survival-short term


title: control_T1_rep2

description: Gene expression 5 days after the injection (Time 1) in water-injected berry pericarps, replicate 2

source_name: berry pericarp water-injected T1 (5 days after injection), replicate 2


title: lung, 620C_600_m221

description:
raw data file: 2013-08-23_19718620_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, 80ug MWCNT, 1 mo

value: 80ug MWCNT

value: 1 mo


title: E_sample

status: Public on Jul 25 2019

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

description:
E_CAGATC_L002
processed data file:
CHG_statistica_gene.smk.txt.gz
CHH_statistica_gene.smk.txt.gz
CpG_statistica_gene.smk.txt.gz

data_processing:
The quality of DNA reads obtained from WGBS sequencing was assessed using FastQC v0.11.5. Illumina adapter sequences left in reads were removed using cutadapt v1.15. Low quality reads at the 3′ and 5′ ends of the reads were trimmed with Trimmomatic v0.36. After sequence quality control, an average of 9.7 Gb/sample of Illumina PE reads (approximate sequencing depth = 17x) were separately assembled using Bowtie v2.3.4 based on the Malus x domestica GDDH13 Whole Genome v1.1 apple genome data. DNA methylation analysis and gene clustering analysis to assess methylation patterns were performed with Bismark v0.17.0.
Differential methylation, statistical analysis, DNA methylation distribution plots and gene clustering were performed with SeqMonk v1.41.0, using a bisulphite pipeline over sets of 50 CpGs, CHGs and CHHs. Unreplicated differential methylation was performed with a χ2 test (P < 0.05). Genes that displayed significant differences in DNA methylation in either their promoter or coding regions according to the χ2 test were classified as differentially methylated genes (DMGs). The χ2 test was visualised with an MA plot (Bland-Altman plot) in which the differences between measurements in two samples was assessed by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.
All assembled DMGs (based on the χ2 test) were considered for functional mapping of biological processes, molecular functions and cellular compounds. The functions of all DMGs in the three environments were determined, focusing on biological processes, molecular functions and cellular components of green plants (Viridiplantae), as these might have important roles during in vitro culture by Gene Ontology (GO) annotation. GO annotation was performed with Blast2GO v5.1.12 based on the Malus x domestica GDDH13 Whole Genome v1.1 mRNA sequences. For functional mapping and GO annotation, several databases were used [NCBI Nr: non-redundant protein database; Swissprot-Uniprot database; Kyoto Encyclopedia of Genes and Genomes (KEGG); GO; InterproScan] by BlastX-fast with the E-value cut-off set to 10-3.
Genome_build: Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation (https://doi.org/10.1038/ng.3886):
https://www.rosaceae.org/species/malus/malus_x_domestica/genome_GDDH13_v1.1
Supplementary_files_format_and_content: cov and bedGraph files with methylated and non-methylated cytosine sites from Bismark methylation extractor; smk files with statistical analysis from SeqMonk

organism: Malus domestica

source_name: leaf

growth_protocol: Plant material was collected from three sources. The first source was in vitro leaves from four-week-old in vitro shoot cultures of M. x domestica Borkh. scion cultivars 'McIntosh' and 'Húsvéti rozmaring'. Shoot cultures were maintained for 16 years and subcultured monthly on Murashige and Skoog (MS) basal medium supplemented with 4.4 µM 6-benzyladenine (BA; Sigma-Aldrich, Budapest, Hungary) and 1.48 µM indole-3-butyric acid (IBA; Sigma-Aldrich) under a 16-h photoperiod, a photosynthetic photon flux density of 105 µM s-1 m-2 and at 22±2°C. The second source was in vivo leaves collected from in vivo mother trees of both cultivars from which in vitro cultures had been originally established 16 years earlier. The third source was leaves collected from rooted in vitro apple shoots one year after acclimatization

extract_protocol:
DNA was extracted and purified from all three samples of each cultivar with a NucleoSpin plant II DNA extraction kit (Macherey-Nagel, Düren, Germany), following the manufacturer's instructions.
Bisulfite was applied to determine the status of cytosine methylation with the Pico MethylSeq Library Prep kit (Zymo Research, Irvine, CA, USA) using 100 ng of genomic DNA based on the user manual.

value: Húsvéti rozmaring

value: 16 years

value: in vitro plant

value: leaf

tag: molecule subtype

value: Bisulfite treated genomic DNA


title: D_sample

description:
D_GCCAAT_L002
processed data file:
CHG_statistica_gene.smk.txt.gz
CHH_statistica_gene.smk.txt.gz
CpG_statistica_gene.smk.txt.gz

tag: age

value: 1 year

value: acclimatized plant


title: F_sample

description:
F_CTTGTA_L002
processed data file:
CHG_statistica_gene.smk.txt.gz
CHH_statistica_gene.smk.txt.gz
CpG_statistica_gene.smk.txt.gz

value: 20 years

value: in vivo mother plant

tag: tissue


title: C_sample

description:
C_ACAGTG_L001
processed data file:
CHG_statistica_gene.smk.txt.gz
CHH_statistica_gene.smk.txt.gz
CpG_statistica_gene.smk.txt.gz

value: McIntosh


title: A_sample

description:
A_CGATGT_L001
processed data file:
CHG_statistica_gene.smk.txt.gz
CHH_statistica_gene.smk.txt.gz
CpG_statistica_gene.smk.txt.gz


title: B_sample

description:
B_TGACCA_L001
processed data file:
CHG_statistica_gene.smk.txt.gz
CHH_statistica_gene.smk.txt.gz
CpG_statistica_gene.smk.txt.gz


title: Bin1-WT-M-0178

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

data_processing:
The reads were aligned with the OmicSoft OSA4 to the mouse genome (mm10) and the Ensembl.R84 gene model. Gene counts were estimated using RSEM.  Six samples were removed (one from each cohort, except two samples from WT_Female cohort and zero samples from Heterozygote_Male cohort) due to low fraction of uniquely mapped paired reads and higher than expected duplication.  Of note, these samples with poor technical QC metrics were also clear outliers in PCA.  Normalization and differential expression analysis were carried out with the Bioconductor package DESeq2. Differentially expressed genes (DEGs) were defined as having an average normalized alignment counts > 4, adjpval < 0.05, and |FC| > 1.5.  The lists of DEGs were analyzed for pathway and ontology enrichment using the Ingenuity IPA software.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: Microglia

growth_protocol: Primary mixed glia cell culture was prepared from the cerebrum of P0 pups. Briefly, cortices from pups were removed from the skull and transferred to a 60mm dish with HBSS and 0.37% Glucose and then minced with sterile blade. After adding Trypsin 10X, cortices and incubated at 37°C in 5%CO2 for 20min. Subsequently, complete DMEM (containing 10%FBS and Pen/Strep) was mixed with the cell suspension and transferred to a 15ml tube and spun at 200g for 5min at 20°C. After removing the supernatant, the cell pellet was resuspended in complete DMEM and plated in a T25 flask, where cells were maintained in the presence of murine GM-CSF (2mg/ml) (Cat: 215-GM, R&D Systems). Media was replaced every 3 days. After 10 days, flasks were shaken at 50rpm for 30min at 37°C and floating microglial cells were collected and pooled together by genotype. Cells were counted and plated at 1-2x10e6 in 10cm Primaria plates (Cat:353803, Corning).  The following day, primary-cultured murine microglia were incubated with 10μg/ml of recombinant human Tau for 3h at 37 °C with 5%CO2. The cells were washed twice with DMEM and stimulated with LPS (from E. coli 0111: B4, 1μg/ml, cat: L3024, Sigma-Aldrich) for 3h. After the LPS stimulation, media was removed and the cells were treated with 5mM ATP (Cat: A6559-25UMO, Sigma-Aldrich) for 15min. The conditioned media was then collected, spun at 2,000g for 10min at 4°C, and subsequently at 10,000g for 30min at 4°C, and then resulting EVs were purified by commercial Sepharose Size-Exclusion Chromatography (IZON, MA) as described above. Microglia cells were washed in PBS and lysed in Lysis Buffer (as described above). After 1h incubation on ice, lysates were cleared by spinning at 13,000rpm for 10min at 4°C. Protein concentrations were determined by BCA protein assay.

extract_protocol:
Qiagen All Prep kit (Cat: 80224, Qiagen) was used for RNA extraction from previously frozen microglia cells. Briefly, cells were lysed with RLT Buffer (with β-mercaptoethanol added), and passed through QIA shredder (Cat: 79654, Qiagen). Flow-through from the QIA shredder was then passed through a DNA Mini column to remove the DNA from the lysate. DNA mini columns were stored at 4°C for DNA purification later; and the passed-through lysates were treated with proteinase K. Following treatment, 100% ethanol was added to the lysates and passed through a RNeasy Mini spin column. In-column DNase treatment was also performed. Subsequently, RNA was eluted with RNase-free water, quantified in Nano-drop and stored at -70°C until samples were submitted for sequencing.
500 ng RNA was used as starting input to Illumina TruSeq mRNA stranded library construction according to the manufacturers recommendation. High quality libraries were then pooled and sequenced on an Illumina HiSeq 2500
cDNA from each sample was generated from 5ng of total RNA using SMARTer Ultra Low Input RNA kit v4 (Clontech).  The cDNA was amplified by 9 PCR cycles, followed by QC analysis on BioAnalyzer 2100 (Agilent).  Sequence libraries were produced from 150pg of cDNA using Nextera XT DNA library kit (Illumina), cleaned up with AMPure XP beads, and QC checked with Caliper LabChip GX.  Paired-end sequencing data were generated on an Illumina HiSeq 2500, at a depth of 20 million reads per sample, with read length 50b X 2.

value: WT

value: Male

value: Microglia


title: Bin1-WT-M-0177


title: Bin1-WT-M-0176


title: Bin1-WT-F-0207

value: Female


title: Bin1-Homo-M-0190

value: Homo


title: Bin1-WT-F-0200


title: Mobile_CRISPRi_no_guide

city: San Francisco

first: Neha

last: Prasad

state: CA

institute: UC-San Francisco

data_processing:
Libraries were sequenced in collaboration with the Chan Zuckerberg Biohub in San Francisco on an Illumina MiSeq in 150 bp paired-end runs. Approximately 1,000,000 reads were collected for each of the two samples
Bowtie2 reported ~94% alignment to PA14 WT modified to include the exogenous RFP gene. Note: The genome does not included the chromosomally integrated Mobile-CRSIPRi system because we are interested in the differential expression of genes in response to this integration.
Resultant sam files were used as input for HTSeq, which generated a gene count table
Only genes with a non-normalized read count greater than 1 in both samples were included in analysis, with a coverage of 1286 genes (~20% genome).
Genome_build: NC_008463.1
Supplementary_files_format_and_content: pa14_with_rfp.gtf; reference sequence for PA14 modified with RFP gene (added at the end)
Supplementary_files_format_and_content: htseq_with_guide.txt; gene count table produced by HTSeq count for Mobile-CRISPRi strain with mRFP-targeting sgRNA
Supplementary_files_format_and_content: htseq_no_guide.txt; gene count table produced by HTSeq count for Mobile-CRISPRi strain with non-targeting sgRNA

organism: Pseudomonas aeruginosa

growth_protocol: PA14 Mobile-CRISPRi strains were streaked onto LB agar plates and incubated overnight at 37 °C. One colony from each plate was grown in LB medium at 37 °C for 16 hours with shaking at 250 rpm. Then the strains were subcultured in 400 µL fresh LB medium until the OD600nm reached 1.0.

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy minikit (Qiagen) according to the manufacturer’s instructions with on-column DNase I digestion (Qiagen). The RNA extracts were aliquoted and stored at -80 °C.
10 ng total RNA of each sample was fragmented for 6 min, cDNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#E7770S).

value: with chromosomally encoded mRFP


title: Mobile_CRISPRi_with_guide


title: untreated_T0_rep3

description: Gene expression at time 0 in untreated berry pericarps, replicate 3

source_name: berry pericarp untreated T0, replicate 3

value: Muller-Thurgau

value: Berry pericarps

value: untreated


title: Bin1-Homo-F-0238


title: Bin1-Homo-M-0093


title: untreated_T0_rep2

description: Gene expression at time 0 in untreated berry pericarps, replicate 2

source_name: berry pericarp untreated T0, replicate 2


title: Bin1-Homo-M-0097


title: Bin1-WT-F-0122


title: Bin1-Homo-M-0189


title: Bin1-Homo-M-0109


title: Bin1-Homo-F-0201


title: Bin1-Homo-F-0193


title: Bin1-Homo-F-0234


title: Bin1-Homo-F-0228


title: Bin1-WT-M-0202


title: Bin1-Het-M-0199

value: Het


title: Bin1-Het-M-0203


title: Bin1-Het-M-0210


title: Bin1-Het-M-0197


title: untreated_T0_rep1

description: Gene expression at time 0 in untreated berry pericarps, replicate 1

source_name: berry pericarp untreated T0, replicate 1


title: Bin1-Het-M-0108


title: Bin1-Het-M-0100


title: Bin1-Het-F-0220


title: Bin1-Het-F-0257


title: Bin1-Het-F-0205


title: Bin1-Het-F-0206


title: Bin1-WT-F-0192


title: LOF_Sox9fl_per_cre_scar_heart_LV_RNA_seq_rep2

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

country: Germany

institute: Medizinische Fakultät Mannheim

description: Sox9_scar_heart_LV_RNA_seq_NOiseqBio_diff_expression.xls

data_processing:
Raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using the Trim Galore! wrapper tool
Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star).
Samples were quantified by the use of analyzeRepeats.pl (PMID:20513432)  (mm10 -count exons -strand both and -noadj
Differential expression was performed using normalized mapped reads after trimmed mean of M-values (TMM) and batch correction by the help of NOISeqBIO (PMID: 26184878
bamCoverage was used to normalize the bam file following the parameters ( -bs 20 --smoothLength 40 -p max --normalizeTo1x 2150570000 -e 150)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, raw counts, TMMs

source_name: scar area of left ventricle of 14 to 16-week-old mice

extract_protocol:
total RNA was isolated from infarct scars of Sox9fl/fl (control) and Sox9fl-Per-Cre mice 6 weeks after myocardial infarction using the RNeasy mini kit (Qiagen) following the instruction manual.
The RNA sequencing library was generated from 100ng of total RNA using ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer’s protocols

value: Sox9 deletion in fibroblast (Sox9 fl/perCre)

value: 6 weeks after myocardial infarction

value: heart


title: Control_Sox9fl_fl_scar_heart_LV_RNA_seq_rep2

value: control (Sox9 fl/fl)


title: Control_Sox9fl_fl_scar_heart_LV_RNA_seq_rep3


title: Control_Sox9fl_fl_scar_heart_LV_RNA_seq_rep1


title: RIL_2

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description: protocol: CEL-seq

data_processing:
HiSeq Control Software v2.2 was used for system control and base calling through an integrated primary analysis software RTA (Real Time Analysis. v1.18). The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Quality filtering and adapter removal were performed using Trimmomatic version 0.32.
Reads were mapped to mm10 mouse genome using STAR (version 2.5.2b). Genes were counted via featureCounts (version 1.5).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for each sample

molecule: polyA RNA

source_name: Liver

extract_protocol:
After sacrifice, liver was removed and frozen on dry ice. RNA was extracted from liver tissues with PureLink RNA Mini Kit.
Sequencing libraries were prepared as described in (Hashimshony et al., 2016).

treatment_protocol: Mice were kept on control diet (Purina 5LG6) or the same diet supplied with the certain compounds (ascorbyl-palmitate, KU-0063794, AZD8055 and rilmenidine).

value: liver

tag: compound

value: Rilmenidine

tag: dose

value: 10 ppm

tag: Sex

value: M

value: 4 months

tag: intervention duration

value: 1 month


title: KU_4

description: protocol: CEL-seq


title: KU_1

description: protocol: CEL-seq


title: RIL_1

description: protocol: CEL-seq


title: KU_2

description: protocol: CEL-seq


title: KU_3

description: protocol: CEL-seq


title: RIL_3

description: protocol: CEL-seq


title: CON_7

description: protocol: CEL-seq

value: Control


title: CON_6

description: protocol: CEL-seq


title: CON_4

description: protocol: CEL-seq


title: CON_3

description: protocol: CEL-seq


title: Bin1-Het-F-0208

value: Female

tag: cell type

value: Microglia


title: CON_1

description: protocol: CEL-seq


title: LOF_Sox9fl_per_cre_scar_heart_LV_RNA_seq_rep3

tag: genotype


title: CON_2

description: protocol: CEL-seq


title: LOF_Sox9fl_per_cre_scar_heart_LV_RNA_seq_rep1


title: AZD_3

description: protocol: CEL-seq

value: 20 ppm


title: AZD_2

description: protocol: CEL-seq


title: AZD_1

description: protocol: CEL-seq


title: ASC_4

description: protocol: CEL-seq

value: Ascorbyl-palmitate

value: 6.3 ppm


title: AZD_4

description: protocol: CEL-seq


title: ASC_1

description: protocol: CEL-seq


title: CON_5

description: protocol: CEL-seq


title: SAM24325813 hMAPT-P301S neuron

city: South San Francisco

first: Melanie

last: Huntley

address: 1 DNA Way

institute: Genentech

description: RNA from sorted brain neuron, or astrocyte cells

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: hMAPT-P301S neuron

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

value: hMAPT-P301S transgenic

value: neuron

value: 6 months-old


title: SAM24327051 Non-Tg neuron

source_name: Non-Tg neuron

value: Non-transgenic


title: SAM24325799 Non-Tg astrocyte

source_name: Non-Tg astrocyte

value: astrocyte


title: SAM24325804 hMAPT-P301S astrocyte

source_name: hMAPT-P301S astrocyte


title: SAM24325795 Non-Tg astrocyte


title: SAM24325805 hMAPT-P301S astrocyte


title: SAM24325814 hMAPT-P301S neuron


title: CON_8

description: protocol: CEL-seq

value: liver


title: SAM24325808 Non-Tg neuron


title: SAM24327050 Non-Tg neuron


title: SAM24325815 hMAPT-P301S neuron


title: SAM24325796 Non-Tg astrocyte


title: RIL_4

description: protocol: CEL-seq

value: Rilmenidine


title: SAM24325810 Non-Tg neuron


title: SAM24325818 hMAPT-P301S neuron


title: SAM24325807 Non-Tg neuron


title: SAM24325812 Non-Tg neuron


title: SAM24325800 Non-Tg astrocyte


title: Bin1-WT-M-0258

value: WT

value: Male


title: SAM24325817 hMAPT-P301S neuron


title: SAM24325811 Non-Tg neuron


title: SAM24325797 Non-Tg astrocyte


title: SAM24325809 Non-Tg neuron


title: ASC_2

description: protocol: CEL-seq

value: M

value: 4 months


title: SAM24325801 hMAPT-P301S astrocyte


title: ASC_3

description: protocol: CEL-seq

value: 1 month


title: SAM24325803 hMAPT-P301S astrocyte


title: SAM24325802 hMAPT-P301S astrocyte


title: SAM24325798 Non-Tg astrocyte


title: SAM19937580 PS2APP NeuN

description: RNA from sorted brain neuron, astrocyte or myeloid cells

source_name: PS2APP NeuN

value: PS2APP transgenic mice

value: NeuN+ neurons

value: 11.5 month old


title: SAM19937571 non-Tg CD11b

source_name: non-Tg CD11b

value: non-transgenic

value: Cd11b+ myeloid cells


title: SAM19937573 non-Tg CD11b


title: SAM19937585 PS2APP CD11b

source_name: PS2APP CD11b


title: SAM19937569 non-Tg CD11b


title: SAM19937582 PS2APP NeuN


title: SAM19937583 PS2APP CD11b


title: SAM19937577 non-Tg CD11b


title: SAM22196647 non-Tg Gfap

source_name: non-Tg Gfap

value: Gfap+ astrocytes


title: SAM19937581 PS2APP CD11b


title: SAM22196648 non-Tg Gfap


title: SAM19937579 PS2APP CD11b


title: SAM19937584 PS2APP NeuN


title: SAM19937588 PS2APP NeuN


title: SAM22196653 PS2APP Gfap

source_name: PS2APP Gfap


title: SAM19937574 non-Tg NeuN

source_name: non-Tg NeuN


title: SAM19937587 PS2APP CD11b


title: SAM24325816 hMAPT-P301S neuron

value: hMAPT-P301S transgenic

value: neuron


title: SAM22196650 non-Tg Gfap


title: SAM19937572 non-Tg NeuN


title: SAM19937570 non-Tg NeuN


title: SAM22196652 PS2APP Gfap


title: SAM22196656 PS2APP Gfap


title: SAM22196651 non-Tg Gfap


title: SAM22196654 PS2APP Gfap


title: SAM22196655 PS2APP Gfap


title: SAM19937575 non-Tg CD11b


title: SAM19937576 non-Tg NeuN


title: SAM22196649 non-Tg Gfap


title: SAM19937578 non-Tg NeuN


title: HetU rep5 (control)

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

description: Sample 9

data_processing:
The number of reads per library was between 14.3 and 33.4 million. Fastq files were aligned to mouse genome GRCm38 with TopHat (version 2.0.11; Kim 2013) and default settings (the mapping percentage varied between 96.2 and 98.3%).
Differential expression was performed using Cuffdiff (version 2.1.1; Trapnell 2012) with the following settings; require a minimum of 5 alignments to conduct significance testing, perform bias correction, do initial estimation to weight multi-hits.
Genes identified as differentially expressed with Cuffdiff significance indicated as q value<0.05.  Gene abundance for each sample is provided as FPKM values in a tab-delimited text
Pathway analysis was then determined using DAVID geneontology and REViGO bioinformatic tools.
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

source_name: placenta

extract_protocol:
Total RNA was extracted from placenta using RNeasy Kits (Qiagen – 74134). Quantity and quality were verified using the RNA 6000 Nano Kit (Agilent – 5067-1511) and an Agilent 2100 Bioanalyzer. Only RNA samples with RNA integrity numbers (RIN) >9.0 were used.
Libraries were prepared using TruSeq (Illumina), the barcoded libraries were combined and submitted for sequencing (50bp single ended on a HiSeq2500) through the Wellcome Trust-MRC Institute of Metabolic Science Genomics Core Facility.

tag: developmental stage

value: day 19 of pregnancy

value: Het-U (control)


title: HetU rep2 (control)

description: Sample 6


title: HetU rep1 (control)

description: Sample 5


title: HetU rep4 (control)

description: Sample 8


title: HomP rep2 (mutant)

description: Sample 2

value: Hom-P (mutant)


title: HomP rep3 (mutant)

description: Sample 3


title: HomP rep1 (mutant)

description: Sample 1


title: 1220-Bottom-half

city: La Jolla

first: Luc

last: Teyton

address: 10550 North Torrey Pines Road

institute: TSRI

description:
Sheet number: Sheet15-1220-Bottom-half_summary.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

data_processing:
Post sequencing, adapter trimming was performed by TrimGalore v0.4.1 (F Krueger - A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files (2015): https://github.com/FelixKrueger/TrimGalore). FLASH was used to pair end reads (FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63.)
Cd-hit was used for upstream analysis (Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences (2006) Bioinformatics, v22(13), pages 1658-9.). After counts were generated, sequences with the highest counts and greatest alignment were run through the International Immunogenetics information system (IMGT) ("IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org). Further data analysis utilized a custom R script.
Genome_build: hg19
Supplementary_files_format_and_content: All alpha and beta chains returned from IMGT were placed into a single Excel file. This file has the barcode information of the alpha or beta chain for each single cell as well as metadata. Each "Sheet" in this file is a sorted 96 well plate; thus, by sheet, the alpha and beta chains of a TCR from a single cell can be reassembled. Not all T cells had an alpha and a beta chain that amplified, thus some cells have only one or the other.

source_name: pLN

extract_protocol:
Protocol is detailed in Holt et al. (PMID 29224077). In short, cells stained with tetramer were single cell sorted into single wells that contained lysis buffer from the SuperScript Vilo Master Mix kit. Isolated total RNA was reverse transcribed, pre-amplified and then, utilizing the Fluidigm AccessArray, the TCRalpha and TCRbeta chains for each individual cell were barcoded and amplified again. Then samples were sent to TSRI Genomics Core for library preparation.
Detailed in Holt et al.

tag: strain/background

value: NOD/ShiltJ

value: pLN

tag: tetramer

tag: age in weeks

tag: mouse number

value: No Mouse Number


title: M198_M-3-25-16

description:
Sheet number: Sheet12-032516_TRAC_and_TRBC.xlsx
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

source_name: Islets, pLN

value: mixed sample (non-demultiplexed)


title: M307-05-12-17

description:
Sheet number: Sheet14-TRAC_and_TRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

source_name: Islets, pLN, PBMC


title: M134-072715

description:
Sheet number: Sheet9-TRAC_072315_dataM134.xlsx
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

source_name: Islets

value: Islets


title: M251-092816_M264-092816

description:
Sheet number: Sheet13_092816_TRAC_and_TRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx


title: M230-07-01-16

description:
Sheet number: Sheet8-TRAC_and_TRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

value: Mouse 3


title: 1220-Top-half

description:
Sheet number: Sheet16-1220-Top-half_summary.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx


title: M354-082517

description:
Sheet number: Sheet7-chip082517_TRAC_and_TRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

source_name: Islets, PBMC


title: M134-080515

description:
Sheet number: Sheet10_TRAC_080515.xlsx
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx


title: M354-082417

description:
Sheet number: Sheet5-Chip082417_TRAC_and_TRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

source_name: Spleen, pLN


title: M142-101615

description:
Sheet number: Sheet6-101615_TRAC_90.xlsx
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

value: Mouse 1


title: M198_M-3-23-16

description:
Sheet number: Sheet4-032316_TRAC_and_TRBC.xlsx
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx


title: M230-07-06-16

description:
Sheet number: Sheet2-TRACandTRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

value: Mouse 4


title: HetU rep3 (control)

description: Sample 7

value: Male


title: M225-06-24-16

description:
Sheet number: Sheet3-06-24-16_TRAC_and_TRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx


title: HomP rep4 (mutant)

description: Sample 4


title: SAM19937586 PS2APP NeuN

value: PS2APP transgenic mice

value: NeuN+ neurons

value: 11.5 month old


title: M251-092116_M264-092116

description:
Sheet number: Sheet11-092116_TRAC_and_TRBC.xls
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx


title: CNhi10373.T-Flu_30_-6-1_ACC

city: Yokohama

first: Erik

last: Arner

address: Suehiro-cho 1-7-22

country: Japan

institute: RIKEN

data_processing:
Basecalling was done using Illumina Casava 1.8
Tag extraction and barcode removal was done using inhouse scripts.
Ribosomal sequences were removed using rRNAdust 1.00
bwa and delve was used for mapping with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: The first position of the start of reads mapped on the positive strand, and the last position of the end of reads mapped on the negative strand, were used as the CAGE tag positon and all tags at the same tag position were summed up in s strand specific way to create ctss files for each sample.

growth_protocol: HepG2 and MCF-7 cells were cultured in DMEM high glucose (Gibco) supplemented with 10% inactivated fetal bovine serum (Gibco), 100 U/mL penicillin, 100 μg/mL streptomycin (Gibco) and 1 mM sodium pyruvate (Gibco). THP-1cells were cultured in RPMI-1640 (Gibco) supplemented with 10% inactivated fetal bovine serum (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco).

extract_protocol:
After the treatments, total RNA was extracted from the cells using RNeasy kit (Qiagen).
8-plex nAnT-iCAGE protocol (Murata M, et al. Detecting expressed genes using CAGE. Methods Mol. Biol. 2014;1164:67–85. doi: 10.1007/978-1-4939-0805-9_7.)

treatment_protocol: In the statin treatment, Atorvastatin, Fluvastatin, Rosuvastatin and Simvastatin were added to the culture medium at the final concentration of 30 uM for MCF-7 and THP-1 and 10 uM for HepG2 for 6 and 48 h. In the siRNA treatment, 2 siRNAs against HMGCR gene (HSS104864and HSS179267, Thermo Fisher SCIENTIFIC) and negative control siRNA (Stealth RNAi siRNA Negative Control, Med GC, Thermo Fisher SCIENTIFIC) were transfected using Lipofectamine RNAiMAX　Transfection Reagent (Thermo Fisher Scientific) and incubated for 48 h. The HMGCR knockdown efficiency for HSS104864 and HSS179267 was 80% and 81% (HepG2), 42% and 52% (MCF-7) and 77% and 70% (THP-1), respectively.

tag: cell line

tag: tissue/cell type source

value: monocyte

tag: treatment group

value: Statins

tag: treatment

value: Flu

tag: treatment time

tag: library id

tag: barcode

value: ACC


title: CNhi10373.T-Flu_30_-6-3_AGT

value: AGT


title: CNhi10373.T-Ros_30_-6-3_TAC

value: Ros

value: TAC


title: CNhi10373.T-Flu_30_-6-2_CAC

value: CAC


title: CNhi10373.T-Ros_30_-6-1_GCG

value: GCG


title: CNhi10373.T-Non_0_-48-1_ACG

value: Non

value: ACG


title: CNhi10372.T-Sim_30_-6-1_TAC

value: Sim


title: CNhi10373.T-Ros_30_-6-2_ATG

value: ATG


title: CNhi10372.T-Sim_30_-6-2_ACG


title: CNhi10372.T-Sim_30_-6-3_GCT

value: GCT


title: CNhi10372.T-Non_0_-6-6_CAC


title: CNhi10373.T-Non_0_-48-2_GCT


title: CNhi10372.T-Non_0_-6-5_ACC


title: CNhi10372.T-Ato_30_-6-3_ATG

value: Ato


title: CNhi10372.T-Ato_30_-6-2_GCG


title: CNhi10372.T-Ato_30_-6-1_AGT


title: CNhi10371.T-Non_0_-6-4_GCT


title: CNhi10334.AG_T-104864-540-48-3__AGT

value: siRNA


title: CNhi10334.AJ_T-179267-540-48-3__GCG


title: CNhi10371.T-Non_0_-6-3_ACG


title: CNhi10334.AD_T-NC-540-48-6__CAC

value: NC


title: CNhi10371.T-Non_0_-6-2_TAC

value: monocyte


title: M142-101515

description:
Sheet number: Sheet1-101515_TRAC_90_and_TRBC_90_1.xlsx
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx

value: NOD/ShiltJ

tag: tissue

value: Islets

value: Mouse 2


title: CNhi10334.AC_T-NC-540-48-5__ACC

value: ACC


title: CNhi10333.AI_T-179267-540-48-2__TAC


title: CNhi10333.AB_T-NC-540-48-4__GCG


title: CNhi10332.Z_T-NC-540-48-2__TAC


title: CNhi10333.AF_T-104864-540-48-2__ATG


title: CNhi10333.AA_T-NC-540-48-3__AGT

value: AGT


title: CNhi10371.T-Non_0_-6-1_ATG

value: Statins


title: CNhi10332.AH_T-179267-540-48-1__GCT


title: CNhi10329.T-Ros_30_-48-3_GCT

value: Ros


title: CNhi10328.T-Non_0_-48-4_CAC

value: CAC


title: CNhi10328.T-Non_0_-48-3_ACC

value: Non


title: CNhi10329.T-Sim_30_-48-3_CAC


title: CNhi10329.T-Ros_30_-48-1_TAC

value: TAC


title: CNhi10329.T-Sim_30_-48-2_ACC

value: Sim


title: CNhi10329.T-Ros_30_-48-2_ACG

value: ACG


title: CNhi10329.T-Flu_30_-48-2_GCG

value: Flu

value: GCG


title: CNhi10328.T-Ato_30_-48-2_TAC

value: Ato


title: CNhi10329.T-Flu_30_-48-3_ATG

value: ATG


title: CNhi10329.T-Flu_30_-48-1_AGT

value: monocyte


title: CNhi10328.T-Non_0_-48-5_AGT


title: CNhi10328.T-Ato_30_-48-1_ATG


title: CNhi10328.T-Ato_30_-48-3_ACG


title: CNhi10327.T-Non_0_-48-2_GCT

value: GCT


title: CNhi10327.T-Non_0_-48-1_ACG


title: CNhi10327.T-Ros_30_-6-3_TAC


title: CNhi10327.T-Ros_30_-6-1_GCG


title: CNhi10327.T-Flu_30_-6-3_AGT


title: CNhi10327.T-Flu_30_-6-2_CAC


title: CNhi10326.T-Sim_30_-6-3_GCT


title: CNhi10327.T-Flu_30_-6-1_ACC


title: CNhi10327.T-Ros_30_-6-2_ATG


title: CNhi10332.Y_T-NC-540-48-1__ATG

value: siRNA

value: NC


title: CNhi10332.AE_T-104864-540-48-1__ACG


title: CNhi10326.T-Sim_30_-6-1_TAC


title: CNhi10328.T-Non_0_-48-6_GCG


title: CNhi10328.T-Sim_30_-48-1_GCT


title: CNhi10326.T-Sim_30_-6-2_ACG


title: CNhi10326.T-Non_0_-6-6_CAC


title: CNhi10326.T-Non_0_-6-5_ACC

value: ACC


title: CNhi10326.T-Ato_30_-6-3_ATG


title: CNhi10325.T-Non_0_-6-3_ACG


title: CNhi10326.T-Ato_30_-6-2_GCG


title: CNhi10326.T-Ato_30_-6-1_AGT

value: AGT


title: CNhi10325.T-Non_0_-6-1_ATG

value: Statins


title: CNhi10370.M-179267-540-48-2_GCG

value: breast cancer


title: CNhi10370.M-104864-540-48-3_CAC

value: CAC


title: CNhi10370.M-104864-540-48-2_ACC


title: CNhi10369.M-NC-540-48-6_ACG


title: CNhi10370.M-179267-540-48-3_ATG


title: CNhi10370.M-179267-540-48-1_AGT


title: CNhi10369.M-NC-540-48-5_TAC


title: CNhi10369.M-NC-540-48-4_ATG


title: CNhi10369.M-NC-540-48-3_GCG


title: CNhi10369.M-NC-540-48-1_CAC


title: CNhi10331.M-179267-540-48-3_ATG


title: CNhi10369.M-NC-540-48-1_AGT


title: CNhi10331.M-179267-540-48-1_AGT


title: CNhi10331.M-179267-540-48-2_GCG


title: CNhi10331.M-104864-540-48-3_CAC


title: CNhi10369.M-104864-540-48-1_GCT


title: CNhi10331.M-104864-540-48-2_ACC


title: CNhi10330.M-NC-540-48-6_ACG


title: CNhi10330.M-NC-540-48-4_ATG


title: CNhi10330.M-NC-540-48-5_TAC


title: CNhi10330.M-NC-540-48-3_GCG


title: CNhi10330.M-NC-540-48-2_AGT


title: CNhi10325.T-Non_0_-6-4_GCT

value: Non


title: CNhi10325.T-Non_0_-6-2_TAC

value: TAC


title: CNhi10330.M-104864-540-48-1_GCT


title: CNhi10319.M-Ros_30_-48-3_TAC

value: Ros


title: CNhi10319.M-Ros_30_-48-1_GCG


title: CNhi10318.M-Sim_30_-48-3_GCT

value: Sim


title: CNhi10319.M-Flu_30_-48-2_CAC

value: Flu


title: CNhi10318.M-Sim_30_-48-1_TAC


title: CNhi10318.M-Sim_30_-48-2_ACG

value: ACG


title: CNhi10319.M-Flu_30_-48-3_AGT


title: CNhi10319.M-Ros_30_-48-2_ATG


title: CNhi10319.M-Flu_30_-48-1_ACC


title: CNhi10330.M-NC-540-48-1_CAC


title: CNhi10318.M-Non_0_-48-6_CAC


title: CNhi10317.M-Ros_30_-6-2_CAC


title: CNhi10318.M-Ato_30_-48-2_GCG

value: Ato

value: GCG


title: CNhi10317.M-Ros_30_-6-3_AGT


title: CNhi10316.M-Flu_30_-6-1_TAC


title: CNhi10316.M-Flu_30_-6-2_ACG


title: CNhi10316.M-Sim_30_-6-2_GCG


title: CNhi10316.M-Sim_30_-6-1_AGT


title: CNhi10318.M-Ato_30_-48-3_ATG

value: ATG


title: CNhi10316.M-Ato_30_-6-3_CAC


title: CNhi10316.M-Ato_30_-6-2_ACC


title: CNhi10318.M-Ato_30_-48-1_AGT


title: CNhi10316.M-Flu_30_-6-3_GCT

value: GCT


title: CNhi10317.M-Non_0_-48-2_ATG


title: CNhi10316.M-Sim_30_-6-3_ATG


title: CNhi10317.M-Non_0_-48-1_GCG


title: CNhi10317.M-Non_0_-48-4_ACG


title: CNhi10317.M-Non_0_-48-3_TAC


title: CNhi10315.M-Non_0_-6-4_ATG


title: CNhi10317.M-Ros_30_-6-1_ACC


title: CNhi10317.M-Non_0_-48-5_GCT


title: CNhi10315.M-Ato_30_-6-1_GCT


title: CNhi10315.M-Non_0_-6-5_TAC


title: CNhi10371.H-Ros_30_-48-3_GCG

value: hepatocellular carcinoma


title: CNhi10315.M-Non_0_-6-2_AGT


title: CNhi10315.M-Non_0_-6-6_ACG


title: CNhi10315.M-Non_0_-6-1_CAC


title: CNhi10371.H-Ros_30_-48-2_AGT


title: CNhi10371.H-Ros_30_-48-1_CAC


title: CNhi10315.M-Non_0_-6-3_GCG


title: CNhi10371.H-Flu_30_-48-3_ACC


title: CNhi10357.H-Sim_30_-48-2_TAC


title: CNhi10334.L_H-179267-540-48-3__GCT

value: siRNA


title: CNhi10333.K_H-179267-540-48-2__CAC


title: CNhi10334.I_H-104864-540-48-3__ACG


title: CNhi10333.C_H-NC-540-48-3__ACG

value: NC


title: CNhi10334.E_H-NC-540-48-5__ATG


title: CNhi10333.D_H-NC-540-48-4__GCT


title: CNhi10332.J_H-179267-540-48-1__GCG


title: CNhi10332.G_H-104864-540-48-1__AGT

value: AGT


title: CNhi10333.H_H-104864-540-48-2__ACC

value: ACC


title: CNhi10332.B_H-NC-540-48-2__CAC


title: CNhi10334.F_H-NC-540-48-6__TAC


title: CNhi10325.H-Ros_30_-48-2_AGT

value: Statins


title: CNhi10325.H-Ros_30_-48-1_CAC

value: CAC


title: CNhi10332.A_H-NC-540-48-1__ACC


title: CNhi10325.H-Flu_30_-48-3_ACC


title: CNhi10324.H-Sim_30_-48-3_TAC


title: CNhi10324.H-Flu_30_-48-2_GCT


title: CNhi10324.H-Flu_30_-48-1_ACG


title: CNhi10324.H-Ato_30_-48-2_CAC


title: CNhi10324.H-Ato_30_-48-3_AGT


title: ULG1-66

city: Utrecht

first: Sharon

last: Berendsen

state: Utrecht

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Affymetrix Hybridization, Wash, and Stain Kit

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization in R (package affy)

label: biotin

source_name: human glioblastoma tumor tissue

label_protocol: Genechip 3' IVT Express kit (Affymetrix)

extract_protocol: Nucleospin® TriPrep (Macherey-Nagel, Düren, Germany) and the QIASymphony RNA (Qiagen, Venlo, The Netherlands) kits

treatment_protocol: Glioblastoma tumor tissue was snap-frozen in nitrogen.

tag: tumor contact with subventricular zone yes/no


title: ULG1-60


title: ULG1-59


title: ULG1-55


title: ULG1-68


title: ULG1-61


title: ULG1-69


title: ULG1-67


title: ULG1-65


title: CNhi10324.H-Sim_30_-48-1_GCG


title: ULG1-58


title: ULG1-63


title: ULG1-56


title: CNhi10324.H-Ato_30_-48-1_ACC


title: ULG1-70


title: ULG1-64


title: ULG1-57


title: ULG1-52


title: ULG1-54


title: ULG1-71


title: ULG1-53


title: CNhi10323.H-Ros_30_-6-3_CAC


title: CNhi10323.H-Non_0_-48-6_GCT

value: Non


title: CNhi10323.H-Ros_30_-6-2_ACC


title: CNhi10323.H-Non_0_-48-5_ACG


title: ULG1-50


title: ULG1-62


title: ULG1-51


title: CNhi10323.H-Non_0_-48-4_TAC

value: TAC


title: CNhi10325.H-Ros_30_-48-3_GCG

value: Ros


title: CNhi10323.H-Non_0_-48-3_ATG


title: CNhi10323.H-Non_0_-48-1_AGT


title: CNhi10322.H-Sim_30_-6-2_AGT

value: Sim


title: CNhi10323.H-Non_0_-48-2_GCG


title: CNhi10322.H-Sim_30_-6-3_GCG


title: CNhi10322.H-Sim_30_-6-1_CAC


title: CNhi10322.H-Ros_30_-6-1_GCT


title: CNhi10322.H-Flu_30_-6-2_TAC

value: Flu


title: CNhi10322.H-Flu_30_-6-1_ATG


title: CNhi10322.H-Ato_30_-6-3_ACC


title: CNhi10321.H-Non_0_-6-6_TAC


title: ULG1-49


title: ULG1-44


title: CNhi10321.H-Non_0_-6-5_ATG


title: CNhi10322.H-Flu_30_-6-3_ACG

value: ACG


title: ULG1-46


title: CNhi10321.H-Non_0_-6-4_GCG


title: ULG1-45


title: ULG1-47


title: ULG1-41


title: ULG1-43


title: ULG1-39


title: ULG1-37


title: CNhi10321.H-Non_0_-6-3_AGT


title: CNhi10321.H-Non_0_-6-2_CAC


title: ULG1-40


title: CNhi10321.H-Non_0_-6-1_ACC


title: ULG1-36


title: CNhi10321.H-Ato_30_-6-2_GCT

value: Ato


title: ULG1-34


title: CNhi10321.H-Ato_30_-6-1_ACG


title: CB20

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq 1.8.4 pipeline.
MBD-seq reads were quality trimmed using FastX Toolkit (FastX Toolkit 0.0.14) with a minimum base quality threshold of 20 and minimum read length of 20 nt.
Reads were mapped to the human genome using BWA-MEM (version 0.7.10). Reference human genome (GRCh38 primary assembly) was downloaded from Ensembl alongside Ensembl v84 gene annotation in GTF format
Peak calling was performed using MACS v1.4d(70) software comparing each patient dataset to a pool of inputs we generated previously. Peak size, GC and CpG proportions were determined with a custom BASH script. Reads mapped to peaks were counted using featureCounts (v1.4.2) with mapping quality≥10 and otherwise default settings(71). Peak regions with fewer than 10 reads per sample on average were omitted from downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MBD-seq count matrix of peaks

source_name: heart failure_PBMCs

extract_protocol:
Whole blood was collected into EDTA tubes and DNA was extracted using a by DNeasy Blood & Tissue Kit (Qiagen) and quantified by Qubit fluorometer (Thermo Fisher).
DNA was fragmented by sonication. The MethylMiner Methylated DNA Enrichment Kit (Thermo Fisher) was used to enrich methylated DNA fragments from 500 ng of input material. DNA was eluted from beads with 2 M NaCl solution and was purified by NucleoSpin columns to concentrate DNA and remove salts. Five ng of methyl-enriched DNA underwent library construction using the NEBNext Ultra II DNA Library Prep (New England Biolabs) and the barcoded libraries underwent equimolar pooling

tag: cardiac function

value: Heart Failure

tag: age

value: Peripheral blood mononuclear cells (PBMCs)


title: CB19

tag: cell type


title: ULG1-48


title: CB16


title: ULG1-38


title: ULG1-33


title: ULG1-29


title: ULG1-32


title: ULG1-42


title: ULG1-30


title: ULG1-31


title: ULG1-35


title: ULG1-28


title: CB13


title: CB14


title: CB12


title: CB17


title: CB18


title: CB15


title: CB10

value: Normal


title: ULG1-27


title: CB09


title: ULG1-26


title: ULG1-25


title: CB08


title: ULG1-24


title: CB06


title: ULG1-20


title: CB11


title: ULG1-22


title: ULG1-16


title: CB03


title: ULG1-17


title: CB02


title: ULG1-19


title: ULG1-23


title: ULG1-21


title: ULG1-18


title: ULG1-13


title: ULG1-14


title: ULG1-15


title: ULG1-11


title: ULG1-12


title: CB01


title: CB04


title: CB05


title: 11943X9: HF-06

city: Stanford

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --unpaired, --trim1
Trimmed reads were then aligned with STAR (2.6) to Gencode hg38 reference genome with parameters: $STAR_RUN --genomeDir $GENOME_DIR --readFilesCommand zcat --readFilesIn $INPUT_DIR/fastq/${VAR}.txt.gz --sjdbGTFfile $GENOME_DIR/gencode.v28.annotation.gtf --sjdbOverhang 99 --quantMode GeneCounts --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${RESULTS_DIR}/Alignment/${VAR}_
DESeq2 (1.22.1) within R (3.2.1) was then run to get to final differential expression results comparing failing (HF) to non-failing (NF) hearts.
Genome_build: hg38 (GRCh38.p12.genome.fa)

source_name: Left Ventricle Endocardium

extract_protocol:
Endocardial samples were removed, flash frozen on dry ice, and RNA was harvested using RNEasy® Fibrous tissue reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human heart biopsies taken from left ventricle of patients with end-stage heart failure during Ventricular Assist Device (LVAD) implantation.

value: Left Ventricle Endocardium

tag: diagnosis

value: HF

tag: Sex

value: M

tag: race

value: CAU

tag: molecule subtype

value: genomic RNA


title: CB07


title: 11943X8: HF-05


title: 11943X54: HF-04


title: 11943X48: HF-03


title: 11943X4: HF-02


title: 10931X21: NF-03

value: CON


title: 10931X71: HF-01


title: 10931X11: NF-01

value: F


title: Gata2_SLC6ebs_17788

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: Gata2, replica #1, condition #2

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: hg19
Supplementary_files_format_and_content: IgG_SLC9ips_17784.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ips_17785.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: IgG_SLC6ips_17786.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC6ips_17787.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC6ebs_17788.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ebs_17789.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ips_17785.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC6ips_17787.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC6ebs_17788.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC9ebs_17789.bed (BED, signal enriched regions)

source_name: Embryoid bodies

growth_protocol: hiPSC lines were differentiated via embryoid body (EB) in serum-free condition cultures with the successive addition of BMP4 50 ng/ml (d0-d3), CHIR99021 3µM (d2-d3) and hematopoietic cytokines (d3-d15; SCF 300ng/ml, Flt3 300ng/ml, IL6 and IL3 10ng/ml) and maintained at 37 ºC in 5% CO2

extract_protocol:
Chromatin immunoprecipitation assays were performed using ChIP-IT High Sensitive kit (Active Motif) following the manufacturer's instructions
Libraries were prepared according to Illumina instructions.

treatment_protocol: Doxycycline (Doxi) was added at a final concentration of 1 µg/ml to induce the expression of GATA2 transgene from days 2 to 7 of differentiation

value: iGATA2-hiPSC CL6

tag: chip antibody

value: H-116:sc-9008, Santa Cruz


title: Gata2_SLC6ips_17787

description: Gata, replica #2, condition #1

source_name: Human Induced Pluripotent Stem Cells (hiPSCs)

tag: cell line


title: shKIAA1429-rep1

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

data_processing:
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using BOWTIE software (V2.1.0).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HCC cells

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: intervention


title: shCtrl-rep2

value: shCtrl


title: Gata2_SLC9ips_17785

description: Gata2, replica #1, condition #1

value: iGATA2-hiPSC CL9


title: shCtrl-rep1


title: IgG_SLC9ips_17784

description: IgG, replica #1, condition #1

value: Ab172730, Abcam


title: SAM24360869

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

data_processing:
RNA sequencing (RNAseq) data were analyzed with HTSeqGenie [Pau and Reeder, R package, 2012] in BioConductor [Huber et al, Nat Methods 2015] as follows: reads were trimmed to 75 bp, filtered for quality and rRNA/adapter contamination, and aligned to the reference genome GRCh38
Gene expression was quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample x gene length x size factor).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tables of read counts for all genes and replicates

source_name: cell line

growth_protocol: MDA-MB-134 VI, MDA-MB-330, EFM-19, T-47D, and BT-474 cells were grown in hormone deprivation media for at least 3 days prior to treatment

extract_protocol:
Total RNA was extracted from duplicates using Qiagen RNeasy kit as per manufacturer’s protocol and quality control of RNA samples was done to determine their quantity and quality.
Approximately 500 ng of total RNA was used as an input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). In addition, RNA input of 100 ng was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina)
The libraries were multiplexed and then sequenced on Illumina HiSeq4000 (Illumina) to generate 30M of single end 50 base pair reads

treatment_protocol: Cells were treated with either 1 nM E2, or 1 M 4-OH tamoxifen, GDC-0810, fulvestrant, GNE-274 or GDC-0927 for 24 hours

tag: ligand

tag: concentration

tag: time


title: ULG1-8


title: ULG1-9


title: SAM24360868


title: MDM_CC20

city: Biberach

first: Christian

middle: Thaddaeus

last: Wohnhaas

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

data_processing:
Reads: Read 1: 20 bp (cell barcode and UMI), Read 2: 50 (sequence read)
Raw base BCL files were demultiplexed using bcl2fastq v2.17.1.14 with the parameters “--minimum-trimmed-read-length 20” and “--mask-short-adapter-read 1”. The 50 bp read 2 containing the cDNA sequence was aligned using STAR aligner 2.3.0 against a merged reference of both human hg19 and murine mm10 for the species mixing experiment whereas the reads of MDMs were aligned to the GRCh38 reference genome and annotated according to Ensembl release 86. The STAR genome indices were generated using the parameters “--sjdbOverhang 49” and “--genomeSAsparseD 2”. Drop-seq tools software version 1.12 was then applied to generate a digital expression matrix for each sample.
Genome_build: merged hg19 and mm10 (species mixing), GRCh38 (monocyte-derived macrophages)
Supplementary_files_format_and_content: tab-delimited text files include counts per gene for each cell barcode

source_name: monocyte-derived macrophages

growth_protocol: HEK293 and NIH 3T3 cells were grown in DMEM supplemented with 10 % FCS at 37 °C and 5 % CO2 to approximately 70 % – 80 % confluence. Monocyte-derived macrophages were generated from monocytes isolated from PBMCs. PBMCs were separated with LeucosepTM tubes (Greiner Bio-One, Kremsmünster, Austria) filled withFicoll® Paque Plus (GE Healthcare, Chicago, IL) according to the manufacturer’s instructions. Monoytes were purified from PBMCs by the EasySepTM Human Monocyte Isolation Kit (Stemcell Technologies, Vancouver, BC, Canada) following the manufacturer’s instructions. Monocytes were cultivated in X-VIVOTM 10 Medium (Lonza, Basel, Switzerland) supplemented with 100 ng/ml of GM-CSF (rhGM-CSF, R&D Systems, Minneapolis, MN). On day 6 of the differentiation protocol 50 – 75 % of fresh medium was added per well. Monocyte-derived macrophages were harvested on day 11.

extract_protocol:
Droplet-based single-cell partitioning using Dolomite Bio´s Drop-seq system
Single-cell RNA-Seq libraries were generated using the Drop-seq protocol and Nextera XT DNA sample preparation kit

value: monocyte-derived macrophages

tag: time point

value: week 3

tag: preservation protocol

value: CellCover -20C

tag: experiment

value: human MDMs


title: MDM_DMSO

value: DMSO cryopreservation


title: ULG1-4

tag: tumor contact with subventricular zone yes/no


title: ULG1-6


title: Gata2_SLC9ebs_17789

description: Gata, replica #2, condition #2


title: 10931X16: NF-02

tag: tissue

value: Left Ventricle Endocardium


title: ULG1-1


title: SAM24360867


title: MDM_fresh

value: fresh

value: no preservation


title: ULG1-3


title: SAM24360866


title: ULG1-10


title: HNRNPA2B1 72 hours, replicate 5

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: MCF-7 stably transfected with pcDNA3.1-HNRNPA2B1 for 72h

data_processing:
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1). The FastQC results indicate quality trimming is not necessary since the minimum quality value for all samples is well above Q30 (1 in 1000 error rate).
Preliminary adapter trimming was performed on each of the samples to remove the Qiagen 3’ Adapter sequence with Trimmomatric v0.33.
The trimmed sequences were directly aligned to the human hg19 reference genome assembly using the mapper.pl wrapper of the mirdeep2 package (v 0.0.7).  This script uses bowtie (version 1.1.1), generating alignment files in arf format.
The aligned sequences were then used as inputs into the mirdeep2 package and the script quantifier.pl.  In addition, this script uses the mirBase release 21 mature miRNA and miRNA hairpin sequences downloaded from ftp://mirbase.org/pub/mirbase/CURRENT/. The result is a file containing the number of reads mapping to each of the 2,822 human (hsa) miRs for the specific sample.
After quantification, the resulting counts for each miR in each sample were then combined into a reads matrix, where the rows represent each miR, and the columns represent the non-normalized counts for the miR in a specific sample.
Using the resulting counts table, differentially expressed miRs were determined using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: read count

source_name: MCF-7 cell line

growth_protocol: MCF-7 cells were grown in IMEM medium supplemented with 10% FBS and 5% pen-strep

extract_protocol:
miRNA was isolated using the miRNeasy Mini Ki from Qiagen according to the manufacturer's instructions; miRNA quantity and quality were checked by Agilent Bioanlyzer
Libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN Cat. No. 331502), following manufacturer’s instructions.  a. 3’ ligation: 500 ng of RNA samples (in a volume of 5 µl) were combine with 1 µl 3’ adapter, 1 µl RI, 1 µl 3’ ligase, 2 µl 3’ buffer and 10 µl ligation activator. The reaction mix was incubated for 1 hour at 28°C, then 20 minutes at 65°C. b. 5’ ligation:  To the 3’ ligation reaction, add 15 µl H2O, 2 µl 5’ buffer, 1 µl RI, 1 µl 5’ ligase and 1 µl 5’ adapter. The reaction mix was incubated for 30 minutes at 28°C, then 20 minutes at 65°C. c. Reverse Transcription: Add 2 µl RT initiator to the reaction, incubate 2 minutes each at 75°C, 70°C, 65°C, 60°C, 55°C, then 5 minutes at 37°C, and 5 minutes at 25°C. Add 2 µl RT primer, 2 µl H2O, 12 µl RT buffer, 1 µl RI and 1 µl RT enzyme. The reaction mix was incubated for 1 hour at 50°C, then 15 minutes at 70°C.  d. cDNA cleanup: Reactions were cleaned up with magnetic beads (QIAseq miRNA NGS beads). cDNA was eluted in 15 µl H2O.  e. Library Amplification:  cDNA was amplified in a thermal cycler for 13 cycles at the following temperature 95°C for 15 sec, 60 °C for 30 sec, 72 °C for 15 sec, 72°C for 2 minutes and hold for 4°C. Sample and Barcode Information: Samples were barcoded with QIAseq miRNA NGS ILM IPD primers.

treatment_protocol: MCF-7 cells were plated in six well plates in OPTIMEM and transfected with 2.5 µg of plasmid DNA using Lipofectamine 3000 per the manufacturer's instructions.  Six hours after transfection, the medium was replaced with IMEM + 10% FBS + 5% Pen-Strep for a total of 48 or 72 h prior to miRNA isolation

tag: transfection

tag: barcode

value: QIAseq miRNA NGS ILM IDP5


title: SAM24360865

value: DMSO


title: shKIAA1429-rep2


title: ULG1-5


title: Control

city: Suita

first: Ayumu

last: Asai

address: 2-2 Yamadaoka

institute: Osaka University

hyb_protocol: TaKaRa Hybridization Chamber 5  (#TX711)

scan_protocol: GeneScanner3000 (TORAY）

data_processing:
The value were subtracted with the background value.
The value were corrected at the center value.

label_protocol: Amersham Cy5 Mono-ReactiveDye (GE,#PA25001）

extract_protocol: Isogen (Nippon gene)

treatment_protocol: DICER knockout HCT116 cell which were transfected non-methylated miR200c

tag: cell types

value: human colon cancer cell line


title: ULG1-2


title: SAM24360863


title: SAM24360862


title: SAM24360861


title: 5mC

treatment_protocol: DICER knockout HCT116 cell which were transfected 5mC containing miR200c


title: SAM24360860


title: SAM24360859


title: m6A

treatment_protocol: DICER knockout HCT116 cell which were transfected m6A containing miR 200c


title: 5mC_All

treatment_protocol: DICER knockout HCT116 cell which were transfected all cytosine methylated miR200c


title: HNRNPA2B1 72 hours, replicate 3

value: QIAseq miRNA NGS ILM IDP3


title: HNRNPA2B1 72 hours, replicate 2

value: QIAseq miRNA NGS ILM IDP2


title: HNRNPA2B1 72 hours, replicate 6

value: QIAseq miRNA NGS ILM IDP6


title: SAM24360858


title: HNRNPA2B1 48 hours, replicate 6

description: MCF-7 stably transfected with pcDNA3.1-HNRNPA2B1 for 48h

value: QIAseq miRNA NGS ILM IDP18


title: HNRNPA2B1 48 hours, replicate 5

value: QIAseq miRNA NGS ILM IDP17


title: HNRNPA2B1 48 hours, replicate 4

value: QIAseq miRNA NGS ILM IDP16


title: SAM24360857


title: HNRNPA2B1 48 hours, replicate 3

value: QIAseq miRNA NGS ILM IDP15


title: SAM24360864


title: HNRNPA2B1 72 hours, replicate 4

value: QIAseq miRNA NGS ILM IDP4


title: HNRNPA2B1 48 hours, replicate 2

value: QIAseq miRNA NGS ILM IDP14


title: SAM24360856


title: HNRNPA2B1 48 hours, replicate 1

value: QIAseq miRNA NGS ILM IDP13


title: control, replicate 5

description: MCF-7 control

value: control, pcDNA 3.1

value: QIAseq miRNA NGS ILM IDP11


title: SAM24360855


title: SAM24360854


title: SAM24360853


title: HNRNPA2B1 72 hours, replicate 1

value: QIAseq miRNA NGS ILM IDP1


title: control, replicate 4

description: MCF-7 control

value: QIAseq miRNA NGS ILM IDP10


title: SAM24360850


title: control, replicate 2

description: MCF-7 control

value: QIAseq miRNA NGS ILM IDP8


title: control, replicate 3

description: MCF-7 control

value: QIAseq miRNA NGS ILM IDP9


title: control, replicate 1

description: MCF-7 control

value: QIAseq miRNA NGS ILM IDP7


title: SAM24360849


title: SAM24360851


title: SAM24360848


title: SAM24360846


title: SAM24360847


title: 4OH-Tam-45m_ERa

data_processing:
Fastq sequencing files for all ChIP-seq samples were first filtered for read quality (Phred scores 23+). Reads were then aligned to the human reference genome (NCBI Build 38) and the drosophila reference genome using GSNAP (PMID: 20147302) version ‘2013-10-10’, allowing a maximum of two mismatches per read sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’), followed by removal of duplicate reads.
Reads that aligned to the human genome were used to quantify ER chromatin binding. Peaks of 200 bp width were identified in each sample individually relative to the respective input samples using MACS 2.1.0 (PMID: 18798982) using a cutoff of p=1e-7 and 3-fold increase over input control
An atlas of peaks was generated, encompassing all significant peaks observed in any of the samples and joining overlapping ones.
We quantified the level of chromatin binding within each peak as the number of pseudo-fragments overlapping the peak in question based on the spike-in adjusted BigWig files. Read counts for each sample were normalized based on the number of reads outside of the atlas for each sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tables of peaks with genomic corrdinates, annotations, significance, and pseudo-counts in each condition

growth_protocol: MCF7 cells were cultured in hormone deprivation media for 5 days

extract_protocol:
Cells were fixed by incubation in 11% formaldehyde solution for 15 minutes at room temperature. Fixation was stopped by the addition of a 2.5 M glycine solution. Cells were washed in a 0.5% Igepal-PBS solution prior to snap-freezing.
Active Motif (Carlsbad, CA) performed chromatin isolation, immunoprecipitation reactions, library generation and sequencing. ER ChIP reactions were conducted using 30 μg MCF7 breast cancer cell line chromatin and 4 μg of ER alpha antibody (sc-543, Santa Cruz Biotechnology, Dallas, TX). The ChIP reactions also contained a drosophila chromatin spike in for the normalization of the sequencing data.  Libraries were prepared from each ER ChIP reaction, as well as an input/control DNA sample, and single-end sequencing data were generated on the Illumina platform

treatment_protocol: After 5 days, 1 nM E2 or 100 nM test compound was added for 45 minutes

value: 4OH Tamoxifen


title: G6274-45m_ERa


title: SAM24360844

value: fulvestrant


title: SAM24360843

value: 4-OH tamoxifen


title: SAM24360842


title: control, replicate 6

description: MCF-7 control

value: QIAseq miRNA NGS ILM IDP12


title: Veh-45m_ERa

value: Vehicle


title: SAM24360852

value: DMSO


title: SAM24360845


title: E2-45m_ERa


title: Pooled_Input

description: This input sample was used for all IP samples.

value: none (Input)


title: SAM24360841