title: RB_037

description: Methylation

extract_protocol: Dneasy Blood and Tissue Kit: Qiagen #65904 was used to extract genomic DNA


title: RNA-seq-HPPT_Ruxolitinib_rep3

status: Public on May 11 2021

type: SRA

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

country: USA

institute: National Institutes of Health (NIH)

library_source: transcriptomic

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

molecule: total RNA

organism: Homo sapiens

growth_protocol: Primary Human Renal Proximal Tubule Epithelial Cells (ATCC® PCS-400-010™) were cultured in low-serum medium consisting of Renal Epithelial Cell Basal Medium (ATCC® PCS-400-030™) with Renal Epithelial Cell Growth Kit (ATCC® PCS-400-040™), Penicillin-Streptomycin-Amphotericin B Solution (ATCC® PCS-999-002™) and Phenol Red (ATCC® PCS-999-001™) added.

extract_protocol:
Total RNA was isolated from the cytokine-stimulated cells using PureLink™ RNA Mini Kit (Invitrogen) and libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301).
Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: human primary proximal tubule (HPPT) cells were stimulated with IFNβ, JAK inhibitor (Ruxolitinib) and the combination of IFNb and Ruxolitinib for 12 hours in concentration of 10 ng/ml.

tag: cell type

value: human primary proximal tubule cells

tag: treatment

value: Ruxolitinib


title: RNA-seq-HPPT_Ruxolitinib_rep2


title: 140516_SN163_0555_AC3VYAACXX_L8_GAGTGG

city: Groningen

first: Xiaojing

last: Chu

state: Groningen

address: Antonius Deusinglaan 1

department: Genetics

country: Netherlands

institute: University medical center Groningen

data_processing:
Alignment was performed with HISAT2 using a standard protocol described in Pertea, Mihaela, et al. Nature protocols 11.9 (2016): 1650.
Raw counts were calculated with StringTie using a standard protocol described in Pertea, Mihaela, et al. Nature protocols 11.9 (2016): 1650.
VST normalization and diffentially expressed genes identification were performed with an R package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including VST normalized gene expression value of each sample

source_name: Pseudomonas aeruginosa_4h

growth_protocol: For PBMCs: Blood from healthy individuals were collected in EDTA tubes (BD vacutainer) and isolated by Ficoll.  Gradient centrifugation was performed for 30 minutes at 400g, using no break. After centrifugation, the layer containing PBMCs was collected using a Pasteur pipette. PBMCs were washed twice with PBS, counted (BioRad cell counter) and adjusted to reach the final concentration of 2 million cells/ml in RPMI 1640 (Gibco, ThermoFisher Scientific), supplemented with 10% heat-inactivated Fetal Cow Serum (Gibco, ThermoFisher Scientific), gentamicin 10mg/ml, L-glutamine 10mM and pyruvate 10mM. Cells were seeded into wells to settle overnight before stimulation.  For HUVECs: Pooled donor-HUVECs were purchased (Lonza) and cultured in EBM-2TM medium (Lonza) supplemented with EGM-2 MV SingleQuot Kit Supplements & Growth Factors (Lonza) at 37oC, 5% CO2 and saturating humidity. Passage 3-5, confluent cells were used for all experiments.

extract_protocol:
Cells were harvested and lysed in lysis buffer of MirVanva MagMax RNA isolation kit. RNA was isolated according to the manufactures instructions. RNA concentration was measured based on Optical density (OD260) using the Nanodrop machine (NanoDrop Technologies). RNA integrity was determined using the Bioanalyzer (Agilent D2000). All samples had RIN score >9.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1) PBMC stimulation: PBMCs were stimulated with various pathogens, including heat-killed Streptococcus pneumonia  at 1 million cells/ml, heat-killed Candida albicans (at 1 million cells/ml, heat-killed  Aspergillus fumigatus at 1 million cells/ml, Mycobacterium tuberculosis  at 1 million cells/ml, heat-killed Pseudomonas aeruginosa at 1 million cells/ml 30. Cells were also stimulated with only RPMI 1640 a negative control.  RNA  was isolated from the PBMCs at 4 and 24 hours after stimulation. 2) HUVEC direct stimulation:  HUVECs were stimulated with either Heat-killed Streptococcus Pneumonia ( 1 million cells/ml), Heat-killed Candida albicans( 1milllion cells/ml), LPS  at 1000ng/ml, IL-1β at 10ng/ml, TNF-αat 10ng/ml for 6 or 24 hours. 3) Supernatant effect on HUVEC: The supernatants from activated PBMCs were thawed overnight at 4oC and warmed up shortly to 37oC. Polymyxin B was added to the supernatants at the final concentration of 100µg/ml to neutralize residual LPS 9. The supernatants were then added to HUVECs. To study the effect of IL-1 and TNF-α secreted by activated PBMCs on endothelial cells, LEAF-purified TNF-α Antibody and/or IL-1RA  were added to the supernatants at the final concentration of 4µg/ml and 300ng/ml, respectively, incubated at 37oC for 1 hour before adding to HUVECs. HUVECs were incubated with the supernatants from stimulated PBMCs 6 and 24 hours.

value: PBMC

tag: genotype

value: healthy donor

tag: donor id


title: RB 152

type: genomic

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

description: Methylation

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Methylation Analysis: Raw data files generated by the iScan array scanner were read and preprocessed by using “minfi” Bioconductor package.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: O-PDX

label_protocol: standard Illumina protocol

tag: tissue

value: xenograft

tag: protocol

value: Dneasy Blood and Tissue kit


title: Leaflet sample V9

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina software BaseCaller was used to generate BCL files, which were demultiplexed using CASAVA-1.8.2
STAR version 2.5.2a was used to align the reads to the hg38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in hg38 version 97
Genome_build: hg38 gene version 97
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: NGS 08,  Hancock®, leaflet

extract_protocol:
Conduits for NGS were explanted from the patients during surgical procedures and immediately transferred to RNAlater® (Sigma Aldrich) to inhibit RNA-degradation. Explants were then dissected to isolate the thickened material of the conduit-wall and one of the three valve-leaflets for RNA-isolation. RNA-isolation was performed in an RNase free area using the TRIzol® reagent (ThermoFisher, 15596026) according to manufacturer’s recommendations. Briefly, small tissue-pieces were frozen in liquid nitrogen and then powered using the TissueLyser® (Qiagen). The resulting 50 – 100 mg tissue-powder was lysed in 1mL TRIzol reagent. Then, the lysate was mixed with 0,2 mL Chloroform and centrifuged to create three phases with the RNA accumulating in the upper aqueous phase. RNA was precipitated using isopropylalcohol and washed twice using 75% Ethanol. DNase treatment was performed on RNeasy mini-columns according to the manufacturer’s protocols (Qiagen). RNA quality was evaluated using the NanoDrop (ThermoFisher) and a fragment analyzer.
RNA-seq libraries were performed using 500 ng total RNA of a non stranded RNA Seq, massively-parallel mRNA sequencing approach from Illumina (TruSeq stranded total RNA Library Preparation , Illumina)

value: tissue from Conduit leaflet


title: Leaflet sample V13

source_name: NGS 09, Contegra®, leaflet


title: 140606_SN163_0558_AC4E0YACXX_L5_GGCTAC

source_name: Aspergillus fumigatus_24h


title: Leaflet sample V8

source_name: NGS 07, Melody® in Homograft,  leaflet


title: RB 151

description: Methylation


title: RNA-seq-HPPT_IFNb_Ruxolitinib_rep3


title: RNA-seq-HPPT_Ruxolitinib_rep1


title: 140516_SN163_0555_AC3VYAACXX_L3_ATTCCT


title: AutophagyActivated-replicate1

city: Tokyo

first: Noboru

last: Mizushima

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
Basecalls performed using Illumina bcl2fastq version 1.8.4
Sequenced reads were trimmed for adaptor sequence and random primer sequences using in-house pipeline
The number of reads that completely matched the GeCKO v2 library sequence was calculated
Supplementary_files_format_and_content: tab-delimited text files include read count for each target

growth_protocol: HEK293T cells expressing the GFP-LC3-RFP autophagy flux reporter and Cas9 (HEK293T GFP-LC3-RFP cells) were cultured in 10% fetal bovine serum (S1820-500; biowest) supplemented DMEM (D6546; Sigma-Aldrich). HEK293T GFP-LC3-RFP cells were transfected the GeCKOv2 library at a multiplicity of infection (MOI) of 0.3–0.5 and selected with puromycin. Cells were cultured and expanded for two weeks, and sorted using a cell sorter (MoFlo AstriosEQ; Beckman Coulter). After sorting, the cells were expanded for roughly two weeks. The sorting was repeated four times.

extract_protocol:
Genomic DNA was extracted using Blood & Cell Culture Midi kit (13343; QIAGEN).
A total of 100 - 240 µg genomic DNA (varying between replicates) was extracted, and sgRNA sequences were amplified by PCR using Herculase II Fusion DNA polymerase (600675; Agilent Technologies). Next, the amplicons were subjected to the second PCR to attach Illumina adaptors and barcode samples. The primers used in the first PCR were as follows: F1, 5'-AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG-3', and R1, 5'-CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC-3'. The primers used in the second PCR were as follows: F2, 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-(variable-length sequence, up to 8 bp)-TCTTGTGGAAAGGACGAAACACCG-3'  R2, 5'-CAAGCAGAAGACGGCATACGAGAT-(8-bp barcode)-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCTACTATTCTTTCCCCTGCACTGT-3'. DNA was sequenced on a HiSeq 2500 (Illumina) sequencer. After data acquisition, the number of reads that completely matched the GeCKO v2 library sequence was calculated.

treatment_protocol: Cells were resuspended with HBSS containing 10% FBS, penicillin and streptomycin. Autophagy-activated cells were collected using a cell sorter (MoFlo AstriosEQ; Beckman Coulter).

tag: sorts

tag: cell line

value: Homo sapiens

tag: sequenced molecule

value: Genomic DNA amplicon


title: RB 142

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L8_ATGTCA

source_name: Pseudomonas aeruginosa_24h


title: RB_004

description: Methylation


title: RNA-seq-HPPT_IFNb_Ruxolitinib_rep2


title: Leaflet sample V6

source_name: NGS 05, Contegra®, leaflet


title: Leaflet sample V7

source_name: NGS 06, Hancock®,  leaflet


title: RNA-seq-HPPT_IFNb_Ruxolitinib_rep1


title: RNA-seq-HPPT_IFNb_rep6

value: IFNb


title: 140516_SN163_0555_AC3VYAACXX_L7_ATCACG

source_name: Streptococcus pneumoniae_4h


title: RB 138

description: Methylation


title: RB_001

description: Methylation


title: RNA-seq-HPPT_IFNb_rep5


title: Leaflet sample V5

source_name: NGS 04, Hancock®, leaflet


title: Wall sample W15

source_name: NGS 11, Hancock®, wall

value: tissue from thickened Conduit-Wall


title: Wall sample W14

source_name: NGS 10, Hancock®, wall


title: RNA-seq-HPPT_IFNb_rep4


title: RB_007

description: Methylation


title: Wall sample W13

source_name: NGS 09, Contegra®, wall


title: D1907612

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

description:
mix experiment 5 -biological replicate 2
Sample 115

data_processing:
Library strategy: sWGS
Each genome profile (line view and chro-mosome view) was manually checked for aberrations. All profiles were visualized using the online tool Vivar (http://cmgg.be/vivar/)(Sante et al., 2014).

growth_protocol: Naive UGENT-11/60 hESCs (referred to as C12) were cultured as described previously (Warrier et al., 2017). In brief, naive hESCs were cultured on inactivated (by irradiation) Mouse Embryonic Fibroblasts (MEFs; A34180, Fisher Scientific). MEFs were seeded at a density of 200 000 cells per well of a 6-well plate in MEF media consisting of DMEM 1x (41965-039, Invitrogen) supplemented with 10% fetal calf serum, 1% L-glutamine (25030-025, Invitrogen) and 1% Penicillin/Streptomycin (15140-122, Invitrogen). Cells were allowed to attach and spread prior to use. hESC were subsequently seeded on the attached MEF. Basal naive hESC medium consisted of Knockout DMEM (10829-018, Invitrogen) containing 20% knockout serum replacement (10828-028, Invitrogen), 2mM L-glutamine, 1% Penicillin/Streptomycin, 1% non-essential amino acids (11140-050, Invitrogen), and 0.1mM β-mercapto-ethanol (31350-010, Invitrogen). This basal naive hESC medium is supplemented with 12ng/ml bFGF (100–18B, Peprotech) and 1000U recombinant human LIF (300-05, Sigma) and the small molecules 1μM PD0325903 (13034, Sanbio), 3μM CHIR99021 (1386, Axon Medchem), 10μM Forskolin (F6886, Sigma) and 50ng/ml ascorbic acid (A8960, Sigma) and used as complete media. Naive hESCs were maintained in hypoxic conditions of 5% O2 and 5% CO2 conditions at 37°C. MEF depletion in the hESC culture at passaging was done by discarding the 0.05% trypsin/EDTA (25300-054, Invitrogen) applied to the culture after an incubation of 5min at room temperature. Next, loosened hESC colonies and remaining MEF were resuspended in complete hESC media. Naive colonies were passaged as single cells at a density of 35 000 cells per well of a 6-well plate every three days and were re-plated on inactivated MEFs.   In order to analyse the subtle differences in growth advantage of 17q gained cells over wt cells a co-culture experiments was set up. Here, 15 000 cells of either monoclonally grown C12-cl32 or C12-cl28 cell lines (passage 54 and 53 respectively) were mixed, labelled as “mix 50%”, and seeded in two-fold on the MEF feeder layer. The cells were seeded in complete media either supplemented with 150µM hydroxyurea (HU; H8627-1G, Sigma) or equal amounts of PBS (14190-094, Invitrogen) as control condition. A normal passaging regime, i.e. every three days, was continued and the co-culture was treated as a new cell line. The C12-cl28, C12-cl32 or co-culture were subsequently passaged each time at 30 000 cells/well in control conditions and 40 000 cells/well under HU treatment. At each moment of passaging, samples for genomic DNA, RNA and FACS analysis were isolated.

extract_protocol:
Genomic DNA extraction  Cell pellets were dissolved in 150µl PBS. Genomic DNA was subsequently extracted by QIAcube (Qiagen) using the QiaAmp Blood mini kit (250, Qiagen) consisting of AL, AE, AW1 and AW2 buffers, Qiagen protease, QIAmp mini spin columns and collection tubes. DNA extraction was conducted according to the manufacturer’s instructions. DNA concentrations were measured by using the Dropquant software of the Dropsense. Samples were diluted appropriately and used for exome sequencing, sWGS and ddPCR.
Shallow Whole Genome Sequencing (sWGS)  For shallow depth WGS (sWGS), 312ng of extracted gDNA was first diluted in TE buffer (12090-015, Invitrogen) to a total volume of 50µl. Next the gDNA was sheared with the help of a Covaris LE220+ focused-ultrasonicator (200bp). The sheared gDNA was subsequently transferred to the Hamilton Star® for automated library preparation where after library con-centration measurements were conducted using the Qubit fluorometer HS kit. Finally, the li-brary pools were sequenced using the HiSeq3000. Each genome profile (line view and chro-mosome view) was manually checked for aberrations. All profiles were visualized using the online tool Vivar (http://cmgg.be/vivar/)(Sante et al., 2014).

value: hESC

tag: full id

tag: vivar id

tag: cell line subclass

value: mix

tag: pluripotency

value: naive

tag: feederlayer

value: MEF

value: HU

tag: passage


title: RB_013

description: Methylation


title: Wall sample W8

source_name: NGS 07, Melody® in Homograft, wall


title: 140516_SN163_0555_AC3VYAACXX_L1_TGACCA


title: 140516_SN163_0555_AC3VYAACXX_L6_CGTACG

source_name: Aspergillus fumigatus_4h


title: Wall sample W7

source_name: NGS 06, Hancock®,  wall


title: RB_009

description: Methylation


title: D1907611

description:
mix experiment 5 -biological replicate 2
Sample 114

treatment_protocol: The cells were seeded in complete media either supplemented with 150µM hydroxyurea (HU; H8627-1G, Sigma) or equal amounts of PBS (14190-094, Invitrogen) as control condition.

value: PBS


title: RB_014

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L4_GCCAAT

source_name: Mycobacterium tuberculosis_24h


title: Wall sample W6

source_name: NGS 05, Contegra®, wall


title: 140424_SN163_0548_AC3TJNACXX_L8_CGTACG


title: 140516_SN163_0555_AC3VYAACXX_L8_ACTTGA

source_name: Candida albicans_24h


title: RB_016

description: Methylation

source_name: O-PDX


title: 140516_SN163_0555_AC3VYAACXX_L5_AGTTCC

source_name: Pseudomonas aeruginosa_4h


title: D1911731

description:
mix experiment 5 -biological replicate 2
Sample 112


title: RB 136

description: Methylation


title: Wall sample W5

source_name: NGS 04, Hancock®, wall


title: RB_017

description: Methylation


title: D1911730

description:
mix experiment 5 -biological replicate 2
Sample 111


title: Wall sample W4

source_name: NGS 03, Contegra®, wall


title: 140424_SN163_0548_AC3TJNACXX_L8_GTCCGC


title: 140516_SN163_0555_AC3VYAACXX_L2_GATCAG


title: 140516_SN163_0555_AC3VYAACXX_L8_TTAGGC


title: D1911729

description:
mix experiment 5 -biological replicate 2
Sample 110


title: Wall sample W2

source_name: NGS 02, Contegra®, wall


title: RB_002

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L1_GCCAAT

source_name: Candida albicans_4h


title: D1911728

description:
mix experiment 5 -biological replicate 2
Sample 109


title: D1911732

description:
mix experiment 5 -biological replicate 2
Sample 113


title: RB_019

description: Methylation


title: Wall sample W1

source_name: NGS 01, Hancock®, wall


title: 140424_SN163_0548_AC3TJNACXX_L7_AGTTCC


title: E36-6h-C

city: Linköping

first: Rada

last: Ellegård

state: Ostergotlands Lan

address: Vallmogatan 16

country: Sweden

institute: Linköping University

data_processing:
trimmomatic
STAR
featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: endocervix biopsy

extract_protocol:
MinElute Reaction Cleanup Kit (Qiagen)
Ovation RNA-Seq V2 kit (Tecan)

tag: donor

tag: condition

value: complement opsonized HIV

tag: time


title: Calu3-OMNI_rep2

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using ENCODE pipeline https://github.com/kundajelab/atac-seq-pipeline
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Lung adenocarcinoma cells

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were construced using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion

tag: growth media

value: DMEM + 10percent FBS


title: RB_020

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L5_CGATGT

source_name: Streptococcus pneumoniae_4h

tag: cell type

value: PBMC

tag: genotype


title: D1911727

description:
mix experiment 5 -biological replicate 2
Sample 108

tag: treatment


title: T47D-OMNI_rep2

source_name: Mammary gland ductal carcinoma cells

value: RPMI1640 + 10percent FBS + 0.2U/mL insulin


title: D1911726

description:
mix experiment 5 -biological replicate 2
Sample 107


title: RB_032

description: Methylation

tag: tissue

value: xenograft

tag: protocol


title: D1911725

description:
mix experiment 5 -biological replicate 2
Sample 106

tag: cell line


title: LNCaP-OMNI_rep2

source_name: Prostate carcinoma

value: LNCaP

value: RPMI1640 + 10percent FBS


title: RB_027

description: Methylation

value: Dneasy Blood and Tissue kit


title: 140424_SN163_0548_AC3TJNACXX_L6_GTGAAA

source_name: Aspergillus fumigatus_24h

value: healthy donor

tag: donor id


title: D1911724

description:
mix experiment 5 -biological replicate 2
Sample 105

tag: full id


title: RB_025

description: Methylation


title: T47D-OMNI_rep1


title: D1911723

description:
mix experiment 5 -biological replicate 2
Sample 104

tag: vivar id


title: RB_029

description: Methylation


title: LNCaP-OMNI_rep1


title: 140606_SN163_0558_AC4E0YACXX_L5_GTTTCG

source_name: Streptococcus pneumoniae_24h


title: RB_030

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L1_TAGCTT


title: D1911722

description:
mix experiment 5 -biological replicate 2
Sample 103

tag: cell line subclass


title: 140516_SN163_0555_AC3VYAACXX_L4_TTAGGC


title: D1911721

description:
mix experiment 5 -biological replicate 2
Sample 102

tag: pluripotency


title: RB_038

description: Methylation


title: Calu3-OMNI_rep1


title: DsarA_4.5H_rep2

city: Hanover

first: Liviu

last: Cengher

state: NH

address: 45 Dewey Field Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine

description: sarA knockout mutant replicate at 4h 30 min

data_processing:
Sequenced reads were verified by a fastqc report
reads were mapped using the BWA aligner
Reads were filtered for reads properly paired and sorted by pairs
Read pairs were counted using HTSeq count
Genome_build: Staphylococcus aureus subps, aureus  HG003
Supplementary_files_format_and_content: Excel file include raw counting

organism: Staphylococcus aureus

source_name: RNA cell extract

growth_protocol: After an overnight growth in TSB medium, OD measurement have been made and culture

extract_protocol:
Cells were lyzed with glass beads in a Fast Prep instrument and RNAs extract with Phenol/Chloroform. Ribosomal RNAs were depleted using the Ribo-zero rRNA remmoval kit (bacteria).
NEBNext ultra directional RNA library prep kit (E7420)

tag: strain

value: DsarA HG003

value: transcriptome at 4.5h growth


title: 140424_SN163_0548_AC3TJNACXX_L7_GTCCGC


title: D1911720

description:
mix experiment 5 -biological replicate 2
Sample 101

value: hESC

tag: feederlayer

tag: passage


title: RB 121-1

description: Methylation


title: D1911719

description:
mix experiment 5 -biological replicate 2
Sample 100


title: 140424_SN163_0548_AC3TJNACXX_L6_AGTCAA

source_name: Mycobacterium tuberculosis_4h


title: RB_018

description: Methylation


title: DsarA_4.5H_rep1


title: RB_023

description: Methylation


title: D1911718

description:
mix experiment 5 -biological replicate 2
Sample 99


title: 140516_SN163_0555_AC3VYAACXX_L3_GTTTCG


title: RB_003

description: Methylation


title: WT_4.5H_rep3

description: wild type replicate at 4h 30 min


title: WT_4.5H_rep4


title: D1911717

description:
mix experiment 5 -biological replicate 2
Sample 98


title: 140516_SN163_0555_AC3VYAACXX_L8_CGTACG


title: RB_048

description: Methylation


title: D1911715

description:
mix experiment 5 -biological replicate 2
Sample 96

value: mix


title: WT_4.5H_rep1

description: wild type replicate at 4h 30 min


title: 140516_SN163_0555_AC3VYAACXX_L8_GTGGCC

source_name: Aspergillus fumigatus_4h


title: DsarA_2H_rep3

description: sarA knockout mutant replicate at 2h

value: transcriptome at 2h growth


title: WT_4.5H_rep2

description: wild type replicate at 4h 30 min


title: RB_047

description: Methylation

source_name: O-PDX


title: 140424_SN163_0548_AC3TJNACXX_L4_CAGATC

source_name: Candida albicans_24h


title: DsarA_2H_rep2

description: sarA knockout mutant replicate at 2h


title: 140516_SN163_0555_AC3VYAACXX_L7_GAGTGG


title: RB 127

description: Methylation


title: D1911714

description:
mix experiment 5 -biological replicate 2
Sample 95

value: naive

value: MEF


title: D1911713

description:
mix experiment 5 -biological replicate 2
Sample 94

value: PBS


title: 140516_SN163_0555_AC3VYAACXX_L5_GGCTAC


title: 140424_SN163_0548_AC3TJNACXX_L4_ATCACG


title: 140424_SN163_0548_AC3TJNACXX_L6_GAGTGG

source_name: Mycobacterium tuberculosis_24h


title: RB_005

description: Methylation


title: D1911712

description:
mix experiment 5 -biological replicate 2
Sample 93

value: HU


title: DsarA_2H_rep1

description: sarA knockout mutant replicate at 2h


title: D1911716

description:
mix experiment 5 -biological replicate 2
Sample 97


title: 140424_SN163_0548_AC3TJNACXX_L8_AGTTCC


title: RB_006

description: Methylation


title: WT_2H_rep2

description: wild type replicate at 2h


title: RB 116-1

description: Methylation


title: MAST 216

description: Methylation


title: D1911710

description:
mix experiment 5 -biological replicate 2
Sample 91


title: 140606_SN163_0558_AC4E0YACXX_L5_ATCACG


title: 140516_SN163_0555_AC3VYAACXX_L3_GTGAAA


title: RB_008

description: Methylation


title: W1664_VEH

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: mRNA

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.txt: Raw counts in tab-delimited text file.

organism: Mus musculus

source_name: Aortic arch inner curvature

extract_protocol:
RNA was column-extracted using RNeasy Micro kit (Qiagen).
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Low-density lipoprotein receptor knockout mice were treated 1x daily with 100 mg/kg ABT263 or vehicle by IP injection for 7 days.

value: Ldlr-/-

value: Aortic arch inner curvature

tag: diet

value: LFD

value: Vehicle


title: 140606_SN163_0558_AC4E0YACXX_L5_TAGCTT

value: PBMC


title: D1911755

description:
mix experiment 5 -biological replicate 2
Sample 89


title: RB_010

description: Methylation

value: xenograft


title: W1731_VEH

description: mRNA


title: RB_024

description: Methylation

value: Dneasy Blood and Tissue kit


title: 140516_SN163_0555_AC3VYAACXX_L7_TTAGGC

source_name: Pseudomonas aeruginosa_4h

value: healthy donor


title: 140516_SN163_0555_AC3VYAACXX_L4_CAGATC


title: WT_2H_rep3

description: wild type replicate at 2h


title: D1911754

description:
mix experiment 5 -biological replicate 2
Sample 88


title: D1911711

description:
mix experiment 5 -biological replicate 2
Sample 92


title: D1911753

description:
mix experiment 5 -biological replicate 2
Sample 87


title: MAST 116-2

description: Methylation


title: W1679_ABT

description: mRNA


title: RB_031

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L6_AGTTCC

source_name: Candida albicans_4h


title: RB_026

description: Methylation


title: WT_2H_rep1

description: wild type replicate at 2h


title: W1714_ABT

description: mRNA


title: D1911709

description:
mix experiment 5 -biological replicate 2
Sample 90


title: 140516_SN163_0555_AC3VYAACXX_L3_GTCCGC


title: 140516_SN163_0555_AC3VYAACXX_L2_TAGCTT


title: T229_ABT263

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: Aortic arch plaque

extract_protocol:
RNA was column-extracted using Rneasy Micro kit (Qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Low-density lipoprotein receptor knockout mice were fed high-fat diet (TD88137) for 12 weeks and then switched to LFD for 3 weeks prior to sacrifice. On week 1 one of LFD feeding, mice were treated 1xdaily with 100 mg/kg ABT263 by IP injection.

value: tissue


title: 140516_SN163_0555_AC3VYAACXX_L5_AGTCAA


title: RB_022

description: Methylation


title: T227_ABT263


title: D1911750

description:
mix experiment 5 -biological replicate 2
Sample 84


title: D1911751

description:
mix experiment 5 -biological replicate 2
Sample 85


title: RB_028

description: Methylation


title: D1911752

description:
mix experiment 5 -biological replicate 2
Sample 86


title: 140516_SN163_0555_AC3VYAACXX_L7_GATCAG


title: RB_011

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L5_ATGTCA


title: W1684_VEH

description: mRNA


title: D1911749

description:
mix experiment 5 -biological replicate 2
Sample 83


title: RB_021

description: Methylation


title: RB 90

description: Methylation


title: T254_Vehicle


title: T201_Vehicle


title: 140424_SN163_0548_AC3TJNACXX_L5_TTAGGC


title: D1911746

description:
mix experiment 5 -biological replicate 2
Sample 80


title: T147_Vehicle


title: RB_012

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L4_ACAGTG


title: D1911748

description:
mix experiment 5 -biological replicate 2
Sample 82


title: D1911745

description:
mix experiment 5 -biological replicate 2
Sample 79


title: D1911744

description:
mix experiment 5 -biological replicate 2
Sample 78


title: RB_015

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L4_TGACCA

source_name: Pseudomonas aeruginosa_24h


title: HCT116_8679_3

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Samples were analyzed using the [nfcore/rnaseq](https://github.com/ewels/nf-core-rnaseq) pipeline version 1.0 (nextflow version version 0.31.1)
The gene expression values of each samples generated by stringtie and featurecount prog.
The intial fastq reads of all the samples were processed by Trimmgalore to trim/filter Illumina adapter sequences if any before processing further. 20bp is the minimum length of the reads kept for analysis after trimming (Illumina TruSeq adapter sequences were found in all the samples).
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include raw count values for each gene in each sample

source_name: HCT116 cells

growth_protocol: Cells were grown in McCoy's 5A medium supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, and Penicillin-Streptomycin (100 U/mL)

extract_protocol:
RNA was extracted using RNeasy Plus Minit kit (Qiagen)
RNA libraries were prepared for paired end sequencing using standard Illumina protocols

treatment_protocol: For the siRNA treatment, HCT116 were transfected with the respective siRNAs (Silencer Select siRNA) at 20 nM using Lipofectamine 3000 (forward transfection). For the compound treatment, DMSO or compound (dissolved in DMSO) was added directly to the cell culture medium to a final concentration of 1% DMSO, 50 uM compound.

tag: cancer type

value: colorectal cancer


title: RB 122_Rep_1

description: Methylation


title: T148_ABT263


title: D1911747

description:
mix experiment 5 -biological replicate 2
Sample 81

value: hESC


title: RB 135

description: Methylation


title: D1911743

description:
mix experiment 5 -biological replicate 2
Sample 77


title: D1911742

description:
mix experiment 5 -biological replicate 2
Sample 76


title: 140606_SN163_0558_AC4E0YACXX_L6_ACAGTG


title: 140516_SN163_0555_AC3VYAACXX_L2_TTAGGC


title: D1911741

description:
mix experiment 5 -biological replicate 2
Sample 75


title: HCT116_6853_3


title: RB 133

description: Methylation


title: HCT116_1874_3


title: HCT116_iCRT3_3


title: RB 132-2

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L7_GTTTCG


title: HCT116_DMSO_3

value: DMSO


title: D1911739

description:
mix experiment 5 -biological replicate 2
Sample 73

value: mix


title: RB 130

description: Methylation


title: 140606_SN163_0558_AC4E0YACXX_L5_TTAGGC


title: HCT116_siCTNNB1_3


title: D1911740

description:
mix experiment 5 -biological replicate 2
Sample 74

value: naive


title: RB 129

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L1_ATCACG


title: HCT116_siNeg_3

value: siNeg


title: D1911737

description:
mix experiment 5 -biological replicate 2
Sample 71

value: MEF

value: PBS


title: 140606_SN163_0558_AC4E0YACXX_L5_GAGTGG


title: 140516_SN163_0555_AC3VYAACXX_L1_ACAGTG


title: RB 128

description: Methylation


title: HCT116_8679_2


title: D1911736

description:
mix experiment 5 -biological replicate 2
Sample 70

value: HU


title: RB 124

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L6_GTTTCG


title: 140424_SN163_0548_AC3TJNACXX_L4_TAGCTT


title: D1911735

description:
mix experiment 5 -biological replicate 2
Sample 69


title: RB 135_Rep_1

description: Methylation


title: HCT116_iCRT3_2


title: HCT116_1874_2


title: 140516_SN163_0555_AC3VYAACXX_L6_TTAGGC


title: D1911734

description:
mix experiment 5 -biological replicate 2
Sample 68


title: D1911733

description:
mix experiment 5 -biological replicate 2
Sample 67


title: D1911738

description:
mix experiment 5 -biological replicate 2
Sample 72


title: 140424_SN163_0548_AC3TJNACXX_L6_GTCCGC


title: RB 132-1

description: Methylation


title: RB 133_Rep_1

description: Methylation


title: HCT116_siCTNNB1_2


title: D1911763

description:
mix experiment 5 -biological replicate 2
Sample 66


title: 140516_SN163_0555_AC3VYAACXX_L6_ACTTGA


title: HCT116_siNeg_2


title: RB 130_Rep_1

description: Methylation


title: D1911762

description:
mix experiment 5 -biological replicate 2
Sample 65


title: D1911761

description:
mix experiment 5 -biological replicate 2
Sample 64


title: 140516_SN163_0555_AC3VYAACXX_L7_GTGGCC


title: HCT116_8679_1


title: HCT116_6853_2


title: RB 122

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L7_GTGGCC


title: RB 128_Rep_1

description: Methylation


title: D1911760

description:
mix experiment 5 -biological replicate 2
Sample 63


title: HCT116_6853_1


title: D1905289

description:
mix experiment 5 -biological replicate 2
Sample 62


title: 140424_SN163_0548_AC3TJNACXX_L4_TTAGGC


title: 140516_SN163_0555_AC3VYAACXX_L3_ACTGAT

source_name: Streptococcus pneumoniae_4h


title: HCT116_1874_1


title: HCT116_DMSO_2


title: D1905288

description:
mix experiment 5 -biological replicate 2
Sample 61


title: HCT116_iCRT3_1


title: RB 120

description: Methylation


title: RB 129_Rep_1

description: Methylation


title: D1911759

description:
mix experiment 5 -biological replicate 2
Sample 60


title: HCT116_DMSO_1


title: 140424_SN163_0548_AC3TJNACXX_L4_GATCAG


title: 140516_SN163_0555_AC3VYAACXX_L8_ATCACG


title: D1911758

description:
mix experiment 5 -biological replicate 2
Sample 59


title: D1911757

description:
mix experiment 5 -biological replicate 2
Sample 58


title: Occipital Cortex  sample from subject 43

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

description:
ovariectomized/hysterectomized (OvH)
S43_OC

data_processing:
Sequences raw files were imported into ONPRC's Prime‐Seq, LabKey Server‐based system (Nelson EK, Piehler B, Eckels J, et al. LabKey server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics. 2011;12(1):71.)
Quality control of the sequences was verified through FastQC (v. 0.1.1.2)
Illumina adapter were removed and 3' read ends were trimmed using Trimmomatic (Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114‐2120)
Reads were aligned to the Rhesus Macaque reference genome (Mmul_10, INSDCA Assembly GCA_003339765.3) using the STAR aligner (v. 2.7.3a) allowing for maximum of 3 mismatches and only unique alignments.
Per‐sample gene count tables were generated by STAR using Ensembl gene annotations (Ensembl.Mmul_10.100) and were merged to form a single gene count matrix.
Genes with at least 0.2 CPM (for Occipital Cortex and Amygdala) and 0.3 CPM (in Prefrontal Cortex and Hippocampus) across samples were retained for further analysis. These thresholds translate into roughly 10 reads per minimum library size (10/minimum library size in millions)
Upper quartile normalization was performed using the edgeR (v. 3.28.0)  Bioconductor package.
Differential expression (DE) between the OvH and OvH-HT groups was determined using edgeR’s Fisher’s exact test function, with the option of “tagwise” dispersion.
Genome_build: Mmul10
Supplementary_files_format_and_content: E2_UQ_normalized_counts.csv (upper-quartile normalized counts): format=comma-delimited, content= normalized gene counts with genes in rows and samples in columns

organism: Macaca mulatta

source_name: Brain - Occipital Cortex

extract_protocol:
Genomic DNA and RNA were extracted from each brain region using the All-Prep DNA/RNA/miRNA Universal kit (Qiagen Sciences Inc, Germantown, MD) following the manufacturer’s recommendations. Briefly, each brain section was pulverized, and ~30 mg of tissue was used for DNA/RNA isolation.
For stranded RNA-seq, cDNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA, USA).
RNA-Seq: The libraries were sequenced on a HiSeq 4000 (Genomics & Cell Characterization Core Facility, University of Oregon) using a paired-end run (2 × 150 bases).

value: OvH


title: Pre-Frontal Cortex  sample from subject 43

description:
ovariectomized/hysterectomized (OvH)
S43_PFC

source_name: Brain - Pre-Frontal Cortex


title: HCT116_siCTNNB1_1


title: HCT116_siNeg_1


title: 140516_SN163_0555_AC3VYAACXX_L6_TAGCTT


title: D1911756

description:
mix experiment 5 -biological replicate 2
Sample 57


title: 140516_SN163_0555_AC3VYAACXX_L4_ACAGTG


title: Hippocampus sample from subject 43

description:
ovariectomized/hysterectomized (OvH)
S43_HIP

source_name: Brain - Hippocampus


title: Amygdala  sample from subject 43

description:
ovariectomized/hysterectomized (OvH)
S43_AMYG

source_name: Brain - Amygdala


title: RB 124_Rep_1

description: Methylation


title: D1903652

description:
mix experiment 5 -biological replicate 2
Sample 56

value: start Mix 5 MC C12 mix N LMS #start #start 22/02/2019

value: start


title: 140516_SN163_0555_AC3VYAACXX_L7_ACTTGA

value: PBMC


title: Pre-Frontal Cortex  sample from subject 42

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S42_PFC

value: OvH-HT


title: 140606_SN163_0558_AC4E0YACXX_L5_CGTACG


title: D1903651

description:
mix experiment 5 -biological replicate 2
Sample 55

value: start Mix 5 MC C12 17q N LMS #54+2 #start 22/02/2019


title: 140424_SN163_0548_AC3TJNACXX_L5_ACTTGA

value: healthy donor


title: Occipital Cortex  sample from subject 42

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S42_OC


title: D1903650

description:
mix experiment 5 -biological replicate 2
Sample 54

value: start Mix 5 MC C12 wt N LMS #53+2 #start 22/02/2019


title: D1903351

description:
mix experiment 5 -biological replicate 2
Sample 53

value: defrosted


title: 103453-001-041

source_name: Candida

value: HUVECs from Lonza

value: WT

value: pooled donors


title: 140516_SN163_0555_AC3VYAACXX_L2_CAGATC


title: Amygdala  sample from subject 42

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S42_AMYG


title: Hippocampus sample from subject 42

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S42_HIP


title: Pre-Frontal Cortex  sample from subject 41

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S41_PFC


title: D1903349

description:
mix experiment 5 -biological replicate 2
Sample 52

value: hESC

value: Monocl C12-wt (1)_ LMS - #53+1 –18/02/2019 - fresh started

value: naive


title: D1900669

description:
mix experiment 4 -biological replicate 1
Sample 51

value: HU_Mix 50% wt/17q N MonoCL LMS - #+12 – 11/01/2019 – #12 Mixexp4

value: mix

value: MEF


title: 103453-001-040


title: 103453-001-039

source_name: Spneu


title: D1900667

description:
mix experiment 4 -biological replicate 1
Sample 50

value: HU


title: Occipital Cortex  sample from subject 41

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S41_OC


title: 103453-001-038


title: Hippocampus sample from subject 41

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S41_HIP


title: Amygdala  sample from subject 41

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S41_AMYG


title: D1900665

description:
mix experiment 4 -biological replicate 1
Sample 49


title: 103453-001-036

source_name: LPS


title: N18_shHERVH3-3

type: RNA

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH3-CNKH Replicate 3

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

label_protocol: Manufature's protocol

growth_protocol: Primed human iPSCs were maintained in StemFiT media (Ajinomoto) supplemented with 100 ng/ml bFGF and 1 ug/ml doxycycline on Laminin 511 E8 fragment-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.

extract_protocol: RNA was prepared using the miReasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Pluripotent stem cell line

tag: genotype/variation


title: Pre-Frontal Cortex  sample from subject 40

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S40_PFC


title: N18_shHERVH3-1

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH3-CNKH Replicate 1

tag: cell type


title: N18_shHERVH3-2

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH3-CNKH Replicate 2


title: N18_shHERVH2-2

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH2-CNKH Replicate 2


title: N18_shHERVH2-1

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH2-CNKH Replicate 1


title: 103453-001-035

tag: genotype


title: Occipital Cortex  sample from subject 40

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S40_OC

tag: treatment


title: N18_shHERVH1-3

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH1-CNKH Replicate 3


title: D1900664

description:
mix experiment 4 -biological replicate 1
Sample 47

value: PBS


title: D1900662

description:
mix experiment 4 -biological replicate 1
Sample 46

value: PBS_C12 wt N MonoCL LMS - #49+15 – 11/01/2019 – #12 Mixexp4


title: 103453-001-034


title: Hippocampus sample from subject 40

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S40_HIP

value: OvH-HT


title: N18_shHERVH1-1

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH1-CNKH Replicate 1


title: Amygdala  sample from subject 40

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S40_AMYG


title: 103453-001-033

source_name: TNF


title: D1911795

description:
mix experiment 4 -biological replicate 1
Sample 45


title: D1911794

description:
mix experiment 4 -biological replicate 1
Sample 44


title: 103453-001-037


title: 103453-001-032


title: N18_shHERVH1-2

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH1-CNKH Replicate 2


title: D1900668

description:
mix experiment 4 -biological replicate 1
Sample 48

value: PBS_Mix 50% wt/17q N MonoCL LMS - #+12 – 11/01/2019 – #12 Mixexp4


title: Pre-Frontal Cortex  sample from subject 39

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S39_PFC


title: N18_Mock-2

description: N18 human induced pluripotent stem cell line transduced SB-U6-NC-CNKH Replicate 2


title: N18_shHERVH2-3

description: N18 human induced pluripotent stem cell line transduced SB-U6-shHERVH2-CNKH Replicate 3


title: N18_Mock-3

description: N18 human induced pluripotent stem cell line transduced SB-U6-NC-CNKH Replicate 3


title: D1911793

description:
mix experiment 4 -biological replicate 1
Sample 43


title: 103453-001-031


title: Occipital Cortex  sample from subject 39

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S39_OC


title: D1911792

description:
mix experiment 4 -biological replicate 1
Sample 42


title: Hippocampus sample from subject 39

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S39_HIP


title: Amygdala  sample from subject 39

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S39_AMYG


title: D1911791

description:
mix experiment 4 -biological replicate 1
Sample 41


title: EB KOc23 d16

description: ESRG knockout embrtonic stem cell line clone 23 after 16 days of embryoid body formation

growth_protocol: Primed human pluripotent stem cells were maintained in StemFiT media (Ajinomoto) supplemented with 100 ng/ml bFGF on Laminin 511 E8 fragment-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.   Naive human pluripotent stem cells were cultured in N2B27 media supplemented with 1 μM PD325901, 10 ng/ml of recombinant human leukemia inhibitory factor, 1 μM Gö6983 and 2 μM XAV939.  Embryoid bodies were maintained on an ultra-low binding plate (Corning) in DMEM/F12 containing 20% Knockout Serum Replacement, 1% MEM non-essential amino acids, 1% GlutaMax and 0.1 mM 2-mercaptoethanol. After 8 days of floating culture, we transferred EBs onto a tissue culture plate coated with 0.1% gelatin (EMD Millipore) and maintained in the same media for another 8 days.

value: ESRG

tag: condition

value: embryoid body formation

value: knock out


title: 103453-001-028

value: HUVECs from Lonza

value: WT


title: 103453-001-030

value: pooled donors


title: Pre-Frontal Cortex  sample from subject 38

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S38_PFC


title: 103453-001-027

source_name: RPMI


title: Occipital Cortex  sample from subject 38

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S38_OC


title: W1683_ABT

description: mRNA

value: Ldlr-/-

tag: tissue

value: Aortic arch inner curvature

value: LFD


title: 103453-001-029


title: 103453-001-026


title: N18_Mock-1

description: N18 human induced pluripotent stem cell line transduced SB-U6-NC-CNKH Replicate 1

tag: cell line


title: Hippocampus sample from subject 38

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S38_HIP


title: EB KOc18 d16

description: ESRG knockout embrtonic stem cell line clone 18 after 16 days of embryoid body formation


title: EB KOc10 d16

description: ESRG knockout embrtonic stem cell line clone 10 after 16 days of embryoid body formation


title: 103453-001-025

tag: donor id


title: EB WTc28 d16

description: ESRG wild-type embrtonic stem cell line clone 28 after 16 days of embryoid body formation

value: wild type


title: D1911787

description:
mix experiment 4 -biological replicate 1
Sample 37

value: hESC

tag: full id

value: naive

value: MEF


title: D1911788

description:
mix experiment 4 -biological replicate 1
Sample 38

tag: vivar id

value: mix

value: PBS


title: Amygdala  sample from subject 38

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S38_AMYG

value: OvH-HT


title: D1911786

description:
mix experiment 4 -biological replicate 1
Sample 36

tag: cell line subclass


title: D1911790

description:
mix experiment 4 -biological replicate 1
Sample 40

tag: pluripotency


title: D1911789

description:
mix experiment 4 -biological replicate 1
Sample 39

value: HU


title: Pre-Frontal Cortex  sample from subject 37

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S37_PFC


title: D1911783

description:
mix experiment 4 -biological replicate 1
Sample 35


title: Occipital Cortex  sample from subject 37

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S37_OC


title: 103453-001-024

source_name: Can_sup+ IL1RA+ TNF_Ab


title: D1911782

description:
mix experiment 4 -biological replicate 1
Sample 34


title: 103453-001-023


title: 103453-001-022

source_name: Strep_sup+ IL1RA+ TNF_Ab


title: Hippocampus sample from subject 37

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S37_HIP


title: D1911781

description:
mix experiment 4 -biological replicate 1
Sample 33


title: EB KOc18 d8

description: ESRG knockout embrtonic stem cell line clone 18 after 8 days of embryoid body formation

value: ESRG


title: EB KOc23 d8

description: ESRG knockout embrtonic stem cell line clone 23 after 8 days of embryoid body formation

value: embryoid body formation


title: 103453-001-021


title: EB WTc21 d16

description: ESRG wild-type embrtonic stem cell line clone 21 after 16 days of embryoid body formation


title: EB KOc10 d8

description: ESRG knockout embrtonic stem cell line clone 10 after 8 days of embryoid body formation

value: knock out


title: D1911780

description:
mix experiment 4 -biological replicate 1
Sample 32


title: EB WTc21 d8

description: ESRG wild-type embrtonic stem cell line clone 21 after 8 days of embryoid body formation


title: EB WTc28 d8

description: ESRG wild-type embrtonic stem cell line clone 28 after 8 days of embryoid body formation


title: 103453-001-020

source_name: LPS_sup+ IL1RA+ TNF_Ab

value: HUVECs from Lonza


title: D1911779

description:
mix experiment 4 -biological replicate 1
Sample 31


title: 103453-001-019

value: WT


title: Occipital Cortex  sample from subject 36

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S36_OC


title: D1911778

description:
mix experiment 4 -biological replicate 1
Sample 30


title: EB WTc1 d8

description: ESRG wild-type embrtonic stem cell line clone 1 after 8 days of embryoid body formation


title: 103453-001-018

value: pooled donors


title: Pre-Frontal Cortex  sample from subject 36

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S36_PFC


title: Hippocampus sample from subject 36

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S36_HIP


title: D1911777

description:
mix experiment 4 -biological replicate 1
Sample 29


title: Amygdala  sample from subject 36

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S36_AMYG


title: 103453-001-017


title: 103453-001-016


title: Pre-Frontal Cortex  sample from subject 35

description:
ovariectomized/hysterectomized (OvH)
S35_PFC

value: OvH


title: Amygdala  sample from subject 37

description:
ovariectomized/hysterectomized (OvH) plus hormone therapy (HT)
S37_AMYG


title: D1911776

description:
mix experiment 4 -biological replicate 1
Sample 28


title: 103453-001-015


title: Occipital Cortex  sample from subject 35

description:
ovariectomized/hysterectomized (OvH)
S35_OC


title: D1911775

description:
mix experiment 4 -biological replicate 1
Sample 27


title: 103453-001-014


title: 103453-001-013


title: Amygdala  sample from subject 35

description:
ovariectomized/hysterectomized (OvH)
S35_AMYG


title: 103453-001-012


title: D1911773

description:
mix experiment 4 -biological replicate 1
Sample 25


title: D1911774

description:
mix experiment 4 -biological replicate 1
Sample 26


title: Pre-Frontal Cortex  sample from subject 34

description:
ovariectomized/hysterectomized (OvH)
S34_PFC


title: D1911772

description:
mix experiment 4 -biological replicate 1
Sample 24


title: Naive KOc23

description: ESRG knockout embrtonic stem cell line clone 23 in naive condition

value: naïve


title: Naive KOc18

description: ESRG knockout embrtonic stem cell line clone 18 in naive condition


title: Naive WTc21

description: ESRG wild-type embrtonic stem cell line clone 21 in naive condition


title: Naive WTc28

description: ESRG wild-type embrtonic stem cell line clone 28 in naive condition


title: 103453-001-011


title: Occipital Cortex  sample from subject 34

description:
ovariectomized/hysterectomized (OvH)
S34_OC


title: Primed KOc18

description: ESRG knockout embrtonic stem cell line clone 18 in primed condition

value: primed


title: D1911771

description:
mix experiment 4 -biological replicate 1
Sample 23


title: EB WTc1 d16

description: ESRG wild-type embrtonic stem cell line clone 1 after 16 days of embryoid body formation

value: wild type


title: Primed KOc10

description: ESRG knockout embrtonic stem cell line clone 10 in primed condition


title: Hippocampus sample from subject 34

description:
ovariectomized/hysterectomized (OvH)
S34_HIP


title: D1911770

description:
mix experiment 4 -biological replicate 1
Sample 22

value: hESC


title: 103453-001-010


title: Hippocampus sample from subject 35

description:
ovariectomized/hysterectomized (OvH)
S35_HIP


title: D1911769

description:
mix experiment 4 -biological replicate 1
Sample 21

value: naive


title: Amygdala  sample from subject 34

description:
ovariectomized/hysterectomized (OvH)
S34_AMYG


title: Primed KOc23

description: ESRG knockout embrtonic stem cell line clone 23 in primed condition


title: Naive WTc1

description: ESRG wild-type embrtonic stem cell line clone 1 in naive condition


title: D1911768

description:
mix experiment 4 -biological replicate 1
Sample 20

value: MEF


title: WT_Ctrl4

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

data_processing:
Illumina bcl2fastq (version 2.18.0.12) was used for basecalling
Read quality check was conducted using FastQC (version 0.11.7) and adaptors were trimmed using Trim Galore (version 0.4.2) with parameters --path_to_cutadapt cutadapt --fastqc --keep --output_dir.
EDGE-pro (version 1.3.1) workflow was used for read processing by using implemented Bowtie2 (version 2.3.4.3) to map trimmed reads to the reference genome and to determine read coverage and count for each gene with edge.pl script with parameters -g GCF_002289205.1_ASM228920v1_genomic.fna -p GCF_002289205.1_ASM228920v1.ptt -r GCF_002289205.1_ASM228920v1.rnt -u $SAMPLE.fq.gz -t 2.
Output files from EDGE-pro were formatted using edgeToDeseq.perl script provided in the EDGE-pro and used as input file for DESeq2 (version 1.26.0) to normalize the counts and determine diffential expression between conditions.
Genome_build: Streptococcus agalactiae 874391 (RefSeq assembly accession: GCF_002289205.1).
Supplementary_files_format_and_content: Tab delimited Excel file including raw counts for each gene in each sample.

organism: Streptococcus agalactiae

source_name: Streptococcus agalactiae 874391

growth_protocol: 1mL overnight THB starter cultures were back-diluted 1/100 in 100mL of THB (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

extract_protocol:
Total RNA SV kit (Promega) and removal of trace DNA using Turbo DNA-free (Life Technologies).
Library construction consisted of random fragmentation of the poly(A) mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired and A-tailed, and adaptors were ligated for indexing (with up to 12 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit (Kapa Biosystems, Woburn, Massachusetts) prior to cluster generation. Clusters were generated to yield approximately 725K–825K clusters/mm2. Cluster density and quality was determined during the run after the first base addition parameters were assessed.

treatment_protocol: RNA quality was analysed by RNA LabChip using GX Touch (Perkin Elmer). RNase-free DNase-treated RNA that passed Bioanalyzer 2100 (Agilent) analysis was used for RNA sequencing (RNA-seq) using the Illumina NextSeq 500 platform. We used TruSeq library generation kits (Illumina, San Diego, California).

tag: strain

value: THB


title: Primed WTc21

description: ESRG wild-type embrtonic stem cell line clone 21 in primed condition


title: Pre-Frontal Cortex  sample from subject 33

description:
ovariectomized/hysterectomized (OvH)
S33_PFC


title: Naive KOc10

description: ESRG knockout embrtonic stem cell line clone 10 in pnaive condition


title: Primed WTc28

description: ESRG wild-type embrtonic stem cell line clone 28 in primed condition


title: WT_Ctrl3


title: 103453-001-009


title: Primed WTc1

description: ESRG wild-type embrtonic stem cell line clone 1 in primed condition


title: 103453-001-008


title: Occipital Cortex  sample from subject 33

description:
ovariectomized/hysterectomized (OvH)
S33_OC


title: Hippocampus sample from subject 33

description:
ovariectomized/hysterectomized (OvH)
S33_HIP


title: 103453-001-007


title: 103453-001-006


title: WT_Ctrl2


title: D1911765

description:
mix experiment 4 -biological replicate 1
Sample 17

tag: feederlayer


title: D1911766

description:
mix experiment 4 -biological replicate 1
Sample 18

value: PBS

tag: passage


title: 103453-001-005


title: WT4

description: Control, Wild-type (WT)

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence files were trimmed with TrimGalore version 0.6.2 using parameters --trim-n --trim1 --nextseq 20 --fastqc_args
Trimmed sequence reads were aligned with STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the alignment files using HTSeq-Count version 0.11.3 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 version 1.24.0 was used with default setting following their vignete to normalize and calculate differential expression
Genome_build: GCF_002289205.1_ASM228920v1_genomic
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

source_name: Bacteria

growth_protocol: 1mL overnight THB cultures were back-diluted 1/100 in 100mL of THB (prewarmed at 37°C in 250mL Erlenmeyer flasks) supplemented with 0.25, 0.5, 1.0 or 1.5mM Zn or Cu. Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: Wild-type

tag: culture

value: Pure culture

value: Equivalent culture conditions

tag: agent

value: 0.25 mM Zn


title: D1911764

description:
mix experiment 4 -biological replicate 1
Sample 16


title: D1911767

description:
mix experiment 4 -biological replicate 1
Sample 19

value: HU


title: 103453-001-003

value: HUVECs from Lonza


title: 103453-001-002

value: WT


title: Hippocampus sample from subject 32

description:
ovariectomized/hysterectomized (OvH)
S32_HIP


title: WT2

description: Control, Wild-type (WT)


title: WT3

description: Control, Wild-type (WT)


title: Pooled samples from 3 biological replicates of healthy controls- Group 1

first: Pushpa

last: Pandiyan

address: 2124, Cornell Road

institute: Case Western Reserve University

description: Median age is provided here

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 reference genome using STAR v2.5, mismatch=2
Quantification was done by HTSeq v0.6.1, parameter  -m union
Differential Analysis using Deseq 2,v2_1.6.3, and  EdgeR v3.16.5  normalized abundance of transcripts -and expressed as FPKM
Enrichment Analysis using ClusterProfiler v2.4.3 For GO, DO, KEGG, Reactome enrichment analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab limited text file includes FPKM values for all the 4 samples
Supplementary_files_format_and_content: Tab limited text file with raw gene counts for all the 4 samples

source_name: gingival mucosa

growth_protocol: Gingival biopsies were collected by dentists

extract_protocol:
RNA was isolated  Illumina TruSeq RNA Sample Prep Kit and total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols-mRNA was purified from total RNA using poly-T oligo-attached magnetic beads
NEB library: Then first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-).

treatment_protocol: Cells were obtained after digestion of tissues with collagenase 1A. Cell pellets were frozen in -80C and were sent to Novogene commercial RNA-sequencing facility

tag: disease state

value: healthy

value: gingival mucosa

tag: age


title: Pre-Frontal Cortex  sample from subject 31

description:
ovariectomized/hysterectomized (OvH)
S31_PFC

value: OvH


title: RNA-seq_AB-I-LL-2

city: Potsdam

first: Stephan

last: Greiner

state: Branbenburg

address: Max-Planck-Institute of Molecular Plant Physiology

department: Organelle Biology, Biotechnology and Molecular Ecophysiology

institute: MPI for Molecular Plant Physiology

data_processing:
Ribo-seq & RNA-seq:
Fastq quality control : Quality control of Ribo-seq and RNA-seq sequencing data  was performed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Barcode, Adapter and UMI removal : 3' adapter trimming was applied to both data sets using Flexbar v2.5 (Dodt et al., 2012) with default parameters and the corresponding adapter-barcode-combined sequences. To remove a potential PCR bias from the Ribo-seq data set, we extracted four bases from the 3’- and 5’-unique molecular identifier (UMI) to evaluate their binding to the read identifier.
Alignment step : All Ribo-seq data, as well as RNA-seq data for computing translation efficiency, were then aligned against their respective plastome (I-johSt = AJ271079.4; II-suavG = EU262889.2) using STAR v2.7.0a with slightly  adapted indexing parameters (--genomeSAindexNbases 8, --genomeChrBinNbits 17) (Dobin et al., 2013).
Post mapping processing and filtering : Subsequently, samtools v1.10 was used to remove secondary alignments, to sort and to index them, and to generate mapping, and gene-wise count statistics (flagstat & idxstat, respectively). Conversion of transcriptomic bam  files (harboring only reads mapped to exons) to bed files was done using bamToBed from the bedtools v2.29.2 (Quinlan and Hall, 2010), adding read length as additional column. Usable reads for all follow-up analysis were defined by the following criteria : (i) removing tRNA and rRNA-associated reads as well as reads shorter than 20 bases and longer than 50 bases; (ii) read de-duplication based on chromosomal location and same UMIs (by sorting bed files on the columns scaffold_id, start/end position and both columns having the UMIs using groupBy to take only the first entry of each group identical entries (-o first); (iii) remain only reads with mapping quality equal to 255 (means unique mapped in the context of the STAR mapper). Resulting bed files were loaded into R to generate different types of plots.
Genome_build: https://ncbi.nlm.nih.gov/nuccore/AJ271079.4 and https://ncbi.nlm.nih.gov/nuccore/EU262889.2
Supplementary_files_format_and_content: Ribo-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = <4 bp 3' UMI>:<4 bp 5'UMI>, column 5 = read length, column = strand
Supplementary_files_format_and_content: RNA-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = read identifier, column 5 = mapping quality, column = strand

organism: Oenothera elata subsp. hookeri x Oenothera grandiflora

source_name: rosette leaves, 21-30 day old

growth_protocol:
generation of plant lines: Incompatible, yellow green (AB-I) and compatible, green (AB-II) plants were obtained from F1 seeds of crosses between the wild type (AA-l) or the green chloroplast substitution line (AA-II) of johansen Standard as the seed parent and wild type line grandiflora Tuscaloosa (BB-III) as the pollen parent. Here, AA-I x BB-III yielded AB-I plants, and AA-II x BB-III produced AB-II plants. Selection against the paternally transmitted plastome III was done using appropriate makers markers.
Oenothera plants were cultivated in a glasshouse as previously described (Greiner and Köhl 2014, Front Plant Sci 5: 38).

extract_protocol:
Total RNA isolations from evening primroses were performed employing protocols specially developed for their mucilage and phenolic compound rich tissue, described in Massouh et al. 2016, Plant Cell 28: 911-929. For RNA-seq analyses, total RNA was purified from residual DNA contamination by digestion employing the Ambion® Turbo DNA-freeTM Kit.
monosome, polysome, and ribosome footprint isolation: The procedure for monosome, polysome, and ribosome footprint isolation are precisely described in Zupok et al. (2021) A photosynthesis operon in the chloroplast genome drives speciation in evening primroses. Plant Cell, in press.
Ribo-seq libraries were prepared using the NEXTflex Small RNA-Seq Kit v3.
RNA-seq libraries were prepared using the Zymo Research Zymo-Seq RiboFree Total RNA Library Kit.

treatment_protocol: AA-I, AA-II, AB-I, and AB-II plants were cultivated in soil in growth chambers using a 16-h light/8 h-darkness cycle and 24°C at low light intensities (~150 µE m-2s-1). At the beginning of the early rosette stage (cf. Greiner and Köhl 2014, Front Plant Sci 5: 38), plants were transferred to higher light intensities, i.e., 300 uE m-2s-1 (low light, LL) and 450 uE m-2s-1 (high light, HL) and then kept under the same growth regime.

value: 300 uE, low light

tag: replicate

tag: genotype

value: AB-I

tag: plant type

value: F1 hybrid

tag: phenotype

value: yellow green (lutescent)

tag: nuclear genome type

value: AB

tag: plastome type

value: I

tag: nuclear genome

tag: chloroplast genome

value: I-johSt

tag: nucleus donor strain(s)

value: johansen Standard, grandiflora Tuscaloosa

tag: chloroplast donor strain

value: johansen Standard

tag: barcode

value: ATATGGAT


title: Pre-Frontal Cortex  sample from subject 32

description:
ovariectomized/hysterectomized (OvH)
S32_PFC

tag: treatment


title: D1822789

description:
mix experiment 4 -biological replicate 1
Sample 12

tag: cell type

value: hESC

tag: full id

value: PBS_Mix 50% wt/1q17q N MonoCL LMS - #+6 – 21/12 – #6 Mixexp4

tag: vivar id

tag: cell line

tag: cell line subclass

value: mix

tag: pluripotency

value: naive

tag: feederlayer

value: MEF

value: PBS

tag: passage


title: D1822803

description:
mix experiment 4 -biological replicate 1
Sample 14

value: HU_C12 17q MonoCL N LMS - #50+9 – 21/12 – #6 Mixexp4

value: HU


title: WT1

description: Control, Wild-type (WT)

tag: genotype

value: Wild-type

tag: strain

tag: culture

value: Pure culture

tag: condition

value: Equivalent culture conditions

tag: agent

value: 0.25 mM Zn


title: Occipital Cortex  sample from subject 32

description:
ovariectomized/hysterectomized (OvH)
S32_OC

value: OvH


title: Occipital Cortex  sample from subject 31

description:
ovariectomized/hysterectomized (OvH)
S31_OC


title: Amygdala  sample from subject 32

description:
ovariectomized/hysterectomized (OvH)
S32_AMYG


title: D1822796

description:
mix experiment 4 -biological replicate 1
Sample 15

value: HU_Mix 50% wt/1q17q N MonoCL LMS - #+6 – 21/12 – #6 Mixexp4


title: L1_FLAG-SETDB1_WT

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

data_processing:
All bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program ELAND based on the 5'-side 36-bp sequences.
Signals of ChIP-seq occupancy are presented as reads per million mapped reads (RPM).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files

source_name: 3T3-L1 preadipocytes

growth_protocol: 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol: Libraries were prepared according to Illumina's instructions.

value: 3T3-L1 preadipocytes

value: WT

tag: time

value: Day 0

tag: chip antibody

value: anti-FLAG


title: WT_Ctrl1

value: wild type

value: THB


title: L1_FLAG-SETDB1_K885A


title: D1822783

description:
mix experiment 4 -biological replicate 1
Sample 10

value: hESC

value: PBS_C12 wt N MonoCL LMS - #49+9 – 21/12 – #6 Mixexp4

value: naive


title: Hippocampus sample from subject 31

description:
ovariectomized/hysterectomized (OvH)
S31_HIP


title: D1822790

description:
mix experiment 4 -biological replicate 1
Sample 11

value: PBS_C12 17q MonoCL N LMS - #50+9 – 21/12 – #6 Mixexp4

value: MEF

value: PBS


title: RNA-seq_AB-II-HL-3

value: 450 uE, high light

tag: replicate

value: AB-II

tag: plant type

value: F1 hybrid between chloroplast substitution line and wild type

tag: phenotype

value: green

tag: nuclear genome type

value: AB

tag: plastome type

value: II

tag: nuclear genome

tag: chloroplast genome

value: II-suavG

tag: nucleus donor strain(s)

value: johansen Standard, grandiflora Tuscaloosa

tag: chloroplast donor strain

value: suaveolens Grado

tag: barcode

value: CGGCGTGA


title: 103453-001-004

data_processing:
Alignment was performed with HISAT2 using a standard protocol described in Pertea, Mihaela, et al. Nature protocols 11.9 (2016): 1650.
Raw counts were calculated with StringTie using a standard protocol described in Pertea, Mihaela, et al. Nature protocols 11.9 (2016): 1650.
VST normalization and diffentially expressed genes identification were performed with an R package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including VST normalized gene expression value of each sample

tag: cell type

value: HUVECs from Lonza

tag: genotype

value: WT

tag: donor id

value: pooled donors


title: Amygdala  sample from subject 33

description:
ovariectomized/hysterectomized (OvH)
S33_AMYG

tag: treatment

value: OvH


title: 103453-001-001


title: D1822792

description:
mix experiment 4 -biological replicate 1
Sample 13

value: hESC

tag: full id

value: HU_C12 wt N MonoCL LMS - #49+9 – 21/12 – #6 Mixexp4

tag: vivar id

tag: cell line

tag: cell line subclass

tag: pluripotency

value: naive

tag: feederlayer

value: HU

tag: passage


title: RNA-seq_AB-I-LL-3

value: 300 uE, low light

tag: replicate

value: AB-I

tag: plant type

value: F1 hybrid

tag: phenotype

value: yellow green (lutescent)

tag: nuclear genome type

tag: plastome type

value: I

value: I-johSt

value: johansen Standard

value: GCGCAAGC


title: D1914585

description:
mix experiment 4 -biological replicate 1
Sample 9

value: HU_C12 17q MonoCL N LMS - #50+8 – 18/12 – #5 Mixexp4

value: MEF


title: RNA-seq_AB-I-LL-1

value: AB

tag: nuclear genome

tag: chloroplast genome

tag: nucleus donor strain(s)

value: johansen Standard, grandiflora Tuscaloosa

tag: chloroplast donor strain

tag: barcode

value: CGGACAAC


title: Amygdala  sample from subject 31

description:
ovariectomized/hysterectomized (OvH)
S31_AMYG

tag: treatment

value: OvH


title: D1914583

description:
mix experiment 4 -biological replicate 1
Sample 8

tag: cell type

value: hESC

tag: full id

value: HU_C12 17q MonoCL N LMS - #50+7 – 14/12 – #4 Mixexp4

tag: vivar id


title: RNA-seq_AB-II-HL-2

value: 450 uE, high light

tag: genotype

value: AB-II

value: F1 hybrid between chloroplast substitution line and wild type

value: green

value: II

value: II-suavG

value: suaveolens Grado

value: TGCGGCGT


title: D1914582

description:
mix experiment 4 -biological replicate 1
Sample 7

value: HU_C12 17q MonoCL N LMS - #50+6 – 10/12 – #3 Mixexp4

tag: cell line

tag: cell line subclass

tag: pluripotency

value: naive

tag: feederlayer

value: HU


title: Pre-Frontal Cortex  sample from subject 30

description:
ovariectomized/hysterectomized (OvH)
S30_PFC


title: RNA-seq_AB-I-HL-2

tag: replicate

value: AB-I

tag: plant type

value: F1 hybrid

tag: phenotype

value: yellow green (lutescent)

value: AB

value: I

value: I-johSt

value: johansen Standard

value: GTTCCAAT


title: Occipital Cortex  sample from subject 30

description:
ovariectomized/hysterectomized (OvH)
S30_OC

source_name: Brain - Occipital Cortex

value: OvH


title: Hippocampus sample from subject 30

description:
ovariectomized/hysterectomized (OvH)
S30_HIP


title: RNA-seq_AB-I-HL-1

value: 450 uE, high light

tag: nuclear genome type

tag: plastome type

tag: nuclear genome

value: johansen Standard, grandiflora Tuscaloosa

value: GCAATGCA


title: RNA-seq_AB-I-HL-3

tag: chloroplast genome

tag: nucleus donor strain(s)

tag: chloroplast donor strain

value: ACCTTGGC


title: RNA-seq_AB-II-HL-1

tag: treatment

value: AB-II

value: F1 hybrid between chloroplast substitution line and wild type

value: green

value: II

value: II-suavG

value: suaveolens Grado

tag: barcode

value: GAATGAGA


title: Amygdala  sample from subject 30

description:
ovariectomized/hysterectomized (OvH)
S30_AMYG


title: Ribo-seq_AB-II-HL-3

data_processing:
library strategy: Ribo-seq
Ribo-seq & RNA-seq:
Fastq quality control : Quality control of Ribo-seq and RNA-seq sequencing data  was performed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Barcode, Adapter and UMI removal : 3' adapter trimming was applied to both data sets using Flexbar v2.5 (Dodt et al., 2012) with default parameters and the corresponding adapter-barcode-combined sequences. To remove a potential PCR bias from the Ribo-seq data set, we extracted four bases from the 3’- and 5’-unique molecular identifier (UMI) to evaluate their binding to the read identifier.
Alignment step : All Ribo-seq data, as well as RNA-seq data for computing translation efficiency, were then aligned against their respective plastome (I-johSt = AJ271079.4; II-suavG = EU262889.2) using STAR v2.7.0a with slightly  adapted indexing parameters (--genomeSAindexNbases 8, --genomeChrBinNbits 17) (Dobin et al., 2013).
Post mapping processing and filtering : Subsequently, samtools v1.10 was used to remove secondary alignments, to sort and to index them, and to generate mapping, and gene-wise count statistics (flagstat & idxstat, respectively). Conversion of transcriptomic bam  files (harboring only reads mapped to exons) to bed files was done using bamToBed from the bedtools v2.29.2 (Quinlan and Hall, 2010), adding read length as additional column. Usable reads for all follow-up analysis were defined by the following criteria : (i) removing tRNA and rRNA-associated reads as well as reads shorter than 20 bases and longer than 50 bases; (ii) read de-duplication based on chromosomal location and same UMIs (by sorting bed files on the columns scaffold_id, start/end position and both columns having the UMIs using groupBy to take only the first entry of each group identical entries (-o first); (iii) remain only reads with mapping quality equal to 255 (means unique mapped in the context of the STAR mapper). Resulting bed files were loaded into R to generate different types of plots.
Genome_build: https://ncbi.nlm.nih.gov/nuccore/AJ271079.4 and https://ncbi.nlm.nih.gov/nuccore/EU262889.2
Supplementary_files_format_and_content: Ribo-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = <4 bp 3' UMI>:<4 bp 5'UMI>, column 5 = read length, column = strand
Supplementary_files_format_and_content: RNA-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = read identifier, column 5 = mapping quality, column = strand

value: AB

value: GCCAAT


title: D1914580

description:
mix experiment 4 -biological replicate 1
Sample 5

tag: cell type

value: hESC

tag: full id

value: HU_C12 17q MonoCL N LMS - #50+4 – 3/12 – #1 Mixexp4

tag: vivar id

value: naive

value: MEF

value: HU

tag: passage


title: D1914581

description:
mix experiment 4 -biological replicate 1
Sample 6

value: HU_C12 17q MonoCL N LMS - #50+5 – 7/12 – #2 Mixexp4

tag: cell line

tag: cell line subclass

tag: pluripotency


title: D1821622

description:
mix experiment 4 -biological replicate 1
Sample 3

value: C12 17q MonoCL N LMS - #50+4 – 30/11 – start Mixexp4

tag: feederlayer

value: start


title: Ribo-seq_AB-II-HL-2

value: 450 uE, high light

tag: replicate

tag: genotype

value: AB-II

tag: plant type

tag: phenotype

value: johansen Standard, grandiflora Tuscaloosa

value: ACTTGA


title: Ribo-seq_AB-II-HL-1

value: F1 hybrid between chloroplast substitution line and wild type

value: green

tag: nuclear genome type

tag: plastome type

value: II

tag: nuclear genome

tag: chloroplast genome

value: II-suavG

value: GATCAG


title: Ribo-seq_AB-I-HL-3

tag: treatment

value: AB-I

value: F1 hybrid

value: yellow green (lutescent)

value: AB

value: I

value: I-johSt

tag: nucleus donor strain(s)

tag: chloroplast donor strain

value: johansen Standard

tag: barcode

value: CAACTA


title: D1821621

description:
mix experiment 4 -biological replicate 1
Sample 2

tag: cell type

value: hESC

tag: full id

value: C12 wt N MonoCL LMS - #49+4 – 30/11 – start Mixexp4

tag: vivar id

value: naive

value: MEF

value: start

tag: passage


title: Ribo-seq_AA-II-HL-2

organism: Oenothera elata subsp. hookeri

value: 450 uE, high light

value: AA-II

value: chloroplast substitution line

value: green

value: AA

value: hjohansen Standard.hjohansen Standard

value: suaveolens Grado

value: GCCAAT


title: D1821625

description:
mix experiment 3
Sample 1

value: C12 1q17q N Mixexp3 LMS - #115+9 – 16/11 – start

tag: cell line

tag: cell line subclass

value: polyclonal

tag: pluripotency

tag: feederlayer


title: D1821623

description:
mix experiment 4 -biological replicate 1
Sample 4

value: Mix 50% wt/1q17q N MonoCL LMS - #0 – 30/11 – start Mixexp4

value: mix


title: mPTCL#4

city: Oullins

first: GENESTIER

last: Laurent

address: Faculté de Medecine Lyon Sud. 165 Chemin du petit Revoyet

country: France

institute: INSERM

description: gene expression data from mPTCL#4

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

data_processing: CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix Expression Console software 1.1

label: biotin

source_name: PTCL from CD3KO mice injected with p53KO T cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA were extract with with the Qiagen RNeasy minikit (Qiagen)

treatment_protocol: Lymphoma cells were purified by cell sorting from liver

tag: strain

tag: genotype

tag: tissue/cell type

value: peripheral T-cell lymphoma (PTCL)


title: mPTCL#6

description: gene expression data from mPTCL#6


title: mPTCL#7

description: gene expression data from mPTCL#7


title: Ribo-seq_AB-I-HL-1

tag: replicate

value: AB-I

tag: plant type

value: F1 hybrid

tag: phenotype

value: yellow green (lutescent)

tag: nuclear genome type

value: AB

tag: plastome type

value: I

tag: nuclear genome

value: I-johSt

value: johansen Standard, grandiflora Tuscaloosa

value: johansen Standard

value: TACAGC


title: mPTCL#5

description: gene expression data from mPTCL#5


title: mPTCL#8

description: gene expression data from mPTCL#8


title: mPTCL#3

description: gene expression data from mPTCL#3


title: mPTCL#2

description: gene expression data from mPTCL#2


title: mPTCL#9

description: gene expression data from mPTCL#9


title: L200

status: Public on May 10 2021

city: Aurora

first: Sandy

last: Martin

state: CO

department: Cell and Developmental Biology

institute: University of Colorado School of Medicine

data_processing:
received off sequencer de-multiplexed files from Genewiz
cutadapt with options -m17 -q10 -a AGATCGGAAGAGC -A AGATCGGAAGAGC  (these are the submitted fastq files)
aligned to I. tridecemlinatus mtDNA (hisat2, option --no-spliced-alignment), those that did not align were then aligned to the HiC_Itri_2 genome for gene based quantification using Salmon
salmon assignments were summarized by gene using tximport and normalized using DESeq2's rlog function.
normalized gene-level counts were then filtered to retain only genes with rlog ≥ 7 in at least 4/5 individuals from at least one physiological group
Genome_build: HiC_Itri_2 (https://www.ncbi.nlm.nih.gov/assembly/GCA_004006685.1;  DOI: 10.3389/fphys.2020.624677)
Supplementary_files_format_and_content: csv file with rlog (log2) count matrix from DESeq2

molecule: polyA RNA

organism: Ictidomys tridecemlineatus

source_name: liver

extract_protocol:
RNA extracted by homogenization with polytron in trizol, cleaned up with Direct-zol RNA MiniPrep Kit (Zymo Research)
Strand-specific RNA-seq libraries (TruSeq Stranded mRNA Library Prep Kit, Illumina, constructed at Genewiz)

treatment_protocol: animals implanted with temperature devices, liver tissue collected based on time and body temperature, flash frozen in N2l immediately after dissection and kept continuously below -70oC until RNA extraction

tag: hibernation state

tag: animal number

tag: Sex

value: F

tag: tissue

value: liver


title: L11 (SpD-2)

value: SpD


title: L4 (Ar-4)

value: Ar


title: L9 (Ar-5)


title: L19 (Ar-2)

value: M


title: L24 (Ar-3)


title: 10X_library_WT_12hpf1

city: New York

first: wei

last: wang

state: NY

address: 100 washington square east

department: Biology

institute: New York University

data_processing:
The feature-barcode matrices were generated using 10X Genomic Cell ranger analysis pipelines.
Genome_build: Genome Sequence, Joined-scaffold (KH), http://ghost.zool.kyoto-u.ac.jp/datas/JoinedScaffold.zip;  KH gene models (ver.2013),http://ghost.zool.kyoto-u.ac.jp/datas/KH.KHGene.2013.gff3.zip
Supplementary_files_format_and_content: feature-barcode matrices, non-normalized UMI counts.

organism: Ciona robusta

source_name: Whole embryo_dissociated

growth_protocol: Embryonic time points are indicated at hours post-fertilization (hpf) for embryo development in artificial sea water at 18 °C.

extract_protocol:
10X Chromium Single Cell 3' RNA-Seq
single-cell library was prepared following Chromium Single Cell 3' v2 Reagent kit following the manufacturer's manual.

treatment_protocol: No treatment.

value: Whole embryo

tag: developmental stage


title: L1 (SpD-1)


title: L6 (SpD-5)


title: Ribo-seq_AB-I-HL-2

tag: treatment

value: 450 uE, high light

tag: chloroplast genome

tag: nucleus donor strain(s)

tag: chloroplast donor strain

tag: barcode

value: TATAAT


title: L21 (SpD-4)


title: L23 (Ent-3)

value: Ent


title: L14 (Ar-1)


title: Ribo-seq_AA-II-HL-1

tag: genotype

value: AA-II

value: chloroplast substitution line

value: green

value: AA

value: II

value: hjohansen Standard.hjohansen Standard

value: II-suavG

value: suaveolens Grado

value: ACAGTG


title: L8 (Ent-5)

value: liver


title: L18 (Ent-2)

value: F


title: L3 (Ent-4)


title: L5 (IBA-5)

value: IBA


title: mPTCL#1

description: gene expression data from mPTCL#1

tag: strain

tag: tissue/cell type

value: peripheral T-cell lymphoma (PTCL)


title: L13 (Ent-1)


title: L16 (SpD-3)

value: SpD


title: L20 (IBA-3)


title: L25 (IBA-4)

value: M


title: L7 (SA-5)

value: SA


title: L10 (IBA-1)


title: L15 (IBA-2)


title: L22 (SA-4)


title: L2 (SA-3)


title: L17 (SA-2)


title: 410_IFNg_RNA

city: Los Angeles

first: Yeon Joo

last: Kim

state: CA

address: Center for Health Sciences 54-200

institute: UCLA

data_processing: Data quality was checked on Sequencing Analysis Viewer software (Illumina), and demultiplexing was performed using the bcl2fastq2 Conversion Software v2.17 (Illumina). Raw FASTQ data files were aligned to the hg19 genome using HISAT2 v2.0.4 with default parameters and counted using HTSeq v0.6.1. The raw counts were normalized to fragments per kilobase of exon per million fragments mapped (FPKM).

source_name: Human melanoma cells

extract_protocol:
Extracted from cells using AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions
Library was prepared using the Kapa Stranded mRNA-Seq Kit. The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

tag: cell type

value: Human melanoma cell line

value: treated with IFNg for 2-5 weeks

tag: cell line


title: L12 (SA-1)


title: 370_TNF_RNA

value: treated with TNF for three days


title: 410_TNF_RNA


title: 370_IFNg_RNA


title: MHC-II+ B cells - Fish1

city: Valdeolmos

first: Pedro

last: Perdiguero

state: Madrid

address: Ctra. de Algete a El Casar Km 8.1

department: Animal Health Research Centre

country: Spain

institute: CISA-INIA

description: Chromium Single Cell 5’ Gene Expression

data_processing:
Assembly and count using cellranger-3.0.2. cellranter count --chemistry=fiveprime --r1-lenght=100 --r2-length=100 --expected-cells=1000
Genome_build: Customized reference transcriptome based in Oncorhynchus mykiss genome v1.0 (GCF_002163495.1)
Supplementary_files_format_and_content: Filtered feature bc matrix folder from cell ranger count (barcodes.tsv, features.tsv and matrix.mtx)
Supplementary_files_format_and_content: Reference transcriptome folder from cell ranger mkref

organism: Oncorhynchus mykiss

source_name: Peripheral blood leukocytes (PBLs)

extract_protocol:
Chromium Single Cell 5′ Gel Beads Kit (10x Genomics, CA, USA)
Chromium Single Cell 5’ Library Construction Kit (10x Genomics, CA, USA)

value: PBLs

value: MHC-II+ B cells

value: untreated


title: MHC-II+ B cells - Fish2

description: Chromium Single Cell 5’ Gene Expression


title: 381_d0_RNA

value: Untreated


title: 381_TNF_RNA


title: MHC-II+ B cells - Fish3

description: Chromium Single Cell 5’ Gene Expression


title: 370_d0_RNA


title: 381_IFNg_RNA


title: 257A2_IFNg_RNA


title: 257A2_TNF_RNA


title: 257A2_d0_RNA


title: hda6_chipseq_chip_rep3

city: Shenzhen

first: Xishi

last: Zhou

address: No 7, Pengfei Road

country: China

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

description:
hda6_chipseq_RPKM_gene.txt
H3Ac_peak_hda6_vs_WT.csv

data_processing:
RNA-seq: Illumina CASAVA software was used for basecalling
RNA-seq: sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
RNA-seq: clean reads were mapped to the TAIR10 Arabidopsis genome using TopHat v 2.0.12 program with parameter --b2-very-sensitive
RNA-seq: the differentially expressed genes and TEs were identified using “Cuffdiff” program of Cufflinks v 2.2.1 , which uses the normalized RNA-seq fragment counts to measure the relative abundances of the genes
ChIP-seq: Illumina CASAVA software was used for basecalling
ChIP-seq: sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
ChIP-seq: clean reads were mapped to the TAIR10 Arabidopsis genome using Bowtie v2.4.1 with default parameters
ChIP-seq: PCR duplicates were removed by Sambamba v 0.6.6 program
ChIP-seq: peaks were called using MACS2 v 2.1.1.20160309 program with parameters -g 1.2e8 -B -q 0.05
ChIP-seq:  differentially enriched peaks were determined by DiffBind R package in Bioconductor
ChIP-seq: the read count falling in each gene region which used for generating RPKM(reads per kilobase per million) value for each gene was calculated by “intersect” command from the BEDTools suite.
Genome_build: tair10
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include the log2(fold_change) of normalized read counts and P value for wild type and each mutant to figure out the differentially expressed genes and transposons(TEs)
Supplementary_files_format_and_content: ChIP-seq: tab-delimited text files include RPKM value of each gene for wild type, sant1234-null and hda6, and .csv files include  the log2 (fold_change) of  normalized read counts falling in each peak and FDR value for wild type, sant1234-null and hda6 to figure out the  differentially enriched peaks

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seeds were sown on 1/2 MS medium plates plates under a long-day photoperiod with 16 h of light at 24 °C and 8 h of darkness at 22 °C, and 12-day-old seedlings were harvested for RNA-seq and ChIP-seq experiments.

extract_protocol:
For RNA-seq: seedling samples were harvested and frozen immediately in liquid nitrogen and total RNA was extracted with TRIzol reagent (Invitrogen). For ChIP-seq: histone-DNA complexes were isolated with anti-acetylated Histone H3 antibody .
Both of the RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

value: hda6 T-DNA insertion line

tag: chip antibody

value: anti-acetylated Histone H3 antibody


title: 3998MEL_TNF_RNA


title: 410_d0_RNA


title: 3998MEL_d0_RNA


title: hda6_chipseq_input_rep3


title: 399_IFNg_RNA


title: hda6_chipseq_chip_rep2


title: hda6_chipseq_input_rep2


title: 3998MEL_IFNg_RNA


title: hda6_chipseq_chip_rep1


title: SKOV3ip1 n.c.

city: Suita

first: Aasa

last: Shimizu

state: Osaka

address: 2-2, Yamadaoka

institute: Osaka University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ovarian cancer cell line

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: Total RNA was extracted using TRIzol.

tag: gender

value: female

value: Ovarian cancer cell line SKOV3ip1

value: control


title: SKOV3ip1 Rab27a ND

value: RAB27A knockdown


title: hda6_chipseq_input_rep1


title: ES-2 Rab27a ND

value: Ovarian cancer cell line ES-2


title: 308_TNF_RNA


title: 308_d0_RNA


title: 308_IFNg_RNA


title: 399_d0_RNA


title: 399_TNF_RNA


title: 262_d0_RNA


title: 262_IFNg_RNA


title: ES-2 n.c.


title: sant1234-null_chipseq_chip_rep3

description:
sant1234-null_chipseq_RPKM_gene.txt
H3Ac_peak_sant1234-null_vs_WT.csv

value: sant1234-null quadruple mutants


title: OL_WT_Input_for_Srebp2

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

data_processing:
Basecalls performed using bcl2fastq
ChIP-seq reads (only R1) were aligned to the mm10 genome assembly using bowtie (version 1.2.2)
peaks were called using macs2(v2.1.2) with the following setting: macs2 callpeak -f BAM -g mm -q 0.05 -t ChIP.bam -n NAME -c INPUT.bam
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using macs2

source_name: differentiated oligodendrocyte

growth_protocol: Neural stem cells were differentiated in Neurobasal medium containing B-27, 2 mM GlutaMAX-I, 30 ng/mL 3,3',5-Triiodo-L-thyronine (T3), 50 U/mL penicillin G, and 50 mg/mL streptomycin

extract_protocol:
Cells were crosslinked, sonicated and  then incubated with Qki-5, Srebp2, and Pol II antibodies. Protein-DNA complex were washed and ChIP'ed DNA were isolated for library preparation.
Libraries were prepared by KAPA Hyper Prep Kit (KK8504, Kapa Biosystems).

value: differentiated oligodendrocyte from neural stem cell

tag: passages

value: FvB/C57BL6 hybrid

value: wild type


title: pH 6.0 6h 3

first: Ian

middle: M

last: Cartwright

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

data_processing:
CASAVA software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapping of clean reads to the reference genome was done using STAR software
Fragments Per Kilobase of transcipt per Mllion mapped reads (FPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. Matrix table with raw gene counts for every gene and every sample

source_name: Intestinal epithelia cell

growth_protocol: T84 cells were grown to confluency in 6 well plates following protocol provided by ATCC

extract_protocol:
RNA was harvested using Tizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Media was replaced with Hanks buffered saline at pH 7.4 or 6.0. Cells were exposed for 3 or 6 hours

value: Intestinal epithelia

value: pH 6.0, 6 hour


title: OL_Qk-/-_Srebp2

value: Srebp2 (10007663, Cayman Chemical)


title: OL_Qk-/-_Input_for_Srebp2


title: sant1234-null_chipseq_input_rep3


title: 262_TNF_RNA

value: Human melanoma cell line

value: treated with TNF for three days


title: OL_WT_Srebp2


title: pH 6.0 6h 1


title: OL_Qk-/-_Input_for_Qki-5_and_Pol II


title: OL_WT_Input_for_Qki-5_and_Pol II


title: sant1234-null_chipseq_chip_rep2

value: untreated


title: pH 6.0 3h 3

value: pH 6.0, 3 hour


title: sant1234-null_chipseq_chip_rep1

value: anti-acetylated Histone H3 antibody


title: sant1234-null_chipseq_input_rep2


title: OL_Qk-/-_Qki-5

value: Qki-5 (home-made)


title: OL_Qk-/-_Pol II

value: RNA polymerase II CTD repeat YSPTSPS (Abcam, Cat# ab817)


title: pH 6.0 3h 2


title: pH 6.0 6h 2


title: OL_WT_Qki-5


title: pH 6.0 3h 1


title: sant1234-null_chipseq_input_rep1


title: WT_chipseq_chip_rep3


title: Control 6h 3

value: pH 7.4, 6 hour


title: WT_chipseq_input_rep3


title: Control 6h 2


title: Control 6h 1


title: WT_chipseq_chip_rep2


title: WT_chipseq_chip_rep1


title: Control 3h 2

value: pH 7.4, 3 hour


title: ATAC-seq in HeLa cells in arginine-free DMEM

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using MACS2
Statistical analysis using Diffbind (EdgeR)

source_name: Cervical cancer cell line (HeLa)

growth_protocol: Cells were grown in normal or SILAC RPMI or DMEM medium (with the addition of arginine where indicated), supplemented with 10% FCS and glutamax (Life Technologies)

extract_protocol:
Cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)

treatment_protocol: Human CD4+ T-cells were purified from PBMCs isolated from commercially available leukocyte cones (NHS Blood and Transplant, Bristol, UK) by magnetic-activated cell sorting (MACS) purification using CD4 Microbead kits (Miltenyi Biotec) then stimulated (where indicated) using anti-CD3/CD28 antibodies (Life Technologies). Cells were cultured in full, low (20uM) arginine or arginine-free medium for 72h prior to harvest, with the addition of 20 nM rapamycin where indicated. HeLa cells were cultured in full or arginine-free medium for 72h prior to harvest.

value: Cervical cancer cell line (HeLa)

value: Cells cultured in arginine-free DMEM for 72h

value: Cell line derived from human cervical carcinoma