title: R08

city: Edinburgh

first: Amy

last: Buck

address: Ashworth Labs, Charlotte Auerbach Road

department: IIIR

institute: The University of Edinburgh

description:
small RNAs
Hb_EvU_Un_2

data_processing:
Sequence quality using FastQC
Adapters were removed using cutadapt
Genome alignments of sequences using bowtie to the host genome mus musculus (version GRCm38, with additional RefSeq rRNA, as all mouse rRNA genes are not present in the genome) and  T. muris (GCA_000612645.2) requiring perfect matches.
miRNAs were predicted using miDeep2 v2.0.0.8 utilizing sequences from miRBase v22 and additional nematode miRNA sequences from Brugia pahangi.
RNA biotypes were identified using the genome version PRJEB126 TMUE3.0  downloaded from WormBase ParaSite, miRNA identified as above, rRNA using cmsearch from the infernal [v1.1.2], (Friedländer et al., 2012); rRNAs using cmsearch from the infernal [v1.1.2] (Nawrocki et al., 2013) suite to search for eukaryotic rRNAs using covariance models from Rfam [version 14.1], tRNAs using tRNA-scan-SE [v1.1.1], snRNA, protein-coding exons, and protein-coding introns were extracted from publicly available GFF3 annotation on WormBase ParaSite genome PREJEB126.

organism: Heligmosomoides polygyrus bakeri

source_name: Secretion product

growth_protocol: T. muris were cultured for 22 hr in RPMI supplemented with 500 U/ml penicillin and 500 μg/ml, conditioned media was collected at 4 hr, discarded and replaced. Conditioned media from 4-22hr was collected, spun at 720 x g for 15 minutes and filtered through a 0.2μm filter. EVs were isolated using ultracentrifugation at 100,000 x g for 2 hr, and washed twice using PBS. EV pellets were re-suspendedin 6 ml of PBS and stored frozen until required. EVs concentrated to 185 μl using a 5kDa MWCO vivapspin and RNA extracted using Qiagen miRNeasy mini kit. Some samples were treated with either polyphosphatase, DNase or both. Small RNA libraries were prepared using CleanTag small RNA library preparation kit from Trilink using 18 PCR cycles. For H.bakeri EVs, the filtered HES were concentrated in a Vivaspin 20 MWCO 3kDa concentrator (Sartorius, Göttingen, Germany). 400 μL of HES (concentration 5mg/mL) was separated into 1 ml fractions by size exclusion chromatography using a Superdex 200 10/300 GL column (GE Healthcare) in PBS with an AKTA basic FPLC system (GE Healthcare). Libraries were prepared using the CleanTag small RNA Library prep kit (Trilink) following manufacturer’s instructions.  Adapters were diluted 1:12 and 18 PCR cycles used. Quantification and size analysis of H. bakeri EVs was performed using the qNano Gold platform (Izon Science).

extract_protocol:
Qiagen miRNeasy mini kit
CleanTag small RNA library prep kit, 18 PCR cycles

tag: product type

value: Extracellular vesicle

tag: developmental stage

value: Adult parasites


title: R09

status: Public on Aug 01 2020

type: SRA

country: United Kingdom

description:
small RNAs
Hb_EvU_Un_3

library_source: transcriptomic

molecule: total RNA


title: CB20070111-06-016_resistant

type: RNA

city: Beijing

first: Haizhao

last: Yi

address: No. 52 Fucheng Rd., Haidian District

country: China

institute: Peking University Cancer Hospital & Institute

description: Gene expression data from rectal cancer tissue

hyb_protocol: The labeled cRNA targets were then hybridized on the slides

scan_protocol: After hybridization, slides were scanned by GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, US).

data_processing: Data were extracted with Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US). Raw data were normalized by the MAS 5.0 algorithm, and Gene Spring Software v12.6.1 (Agilent technologies, Santa Clara, CA, US).

label: biotin

organism: Homo sapiens

source_name: RECTAL CANCER

label_protocol: RNA samples of each group were subsequently used to generate fluorescence-labeled cRNA targets for the Affymetrix Human U133 Plus 2 arrays .

growth_protocol: All the tumor tissues were stored at -80°C before extraction

extract_protocol: Total RNA was  isolated using TRIzol reagent (Life technologies, Carlsbad, CA, US), according to the manufacturer’s instructions, and purified by using the RNeasy Mini Kit (Qiagen, GmBH, Germany)

treatment_protocol: Pre-treatment tumor staging was performed in all patients using endorectal ultrasonography, pelvic magnetic resonance imaging, or computed tomography. The radiotherapy regimen consisted of a 50.6 Gy dose delivered in 22 fractions with concurrent capecitabine treatment for 5 weeks

tag: disease state

value: rectal cancer

tag: tissue

value: rectal cancer biopsy

tag: sensitivity

value: resistant

tag: patient age

tag: tumor stage


title: LSO-3

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: ARS1

organism: Capra hircus

extract_protocol:
Goat oocyte cells samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: breed

value: Ji'ning grey goat

value: Oocyte

tag: treatment

value: LSO


title: NPC48h_DMSO_H3K36me3_rep1

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: RELACS ChIP-Seq

library_source: genomic

data_processing:
fastq files were demultiplexed on RELACS barcodes and aligned to the mm10 genome assembly using snakePipes (v1.1.1 and v1.2.2). QC metrix and further downstream files were also generated using snakepipes (Bhardwaj at al, 2018).
We use gencode M18 as reference gene model annotation
ChIP-Seq BW files were generated on filtered bam files (mapq>=5, UMI-deduplicated) using a bin size of 25bp, and sequencing depth normalized (for normalization, MT and scaffold chromosmes were excluded). RNA-Seq BW were RPKM normalized. ATAC-Seq BW were normalized using Deseq2 scaling factors computed on the locally enriched locy (identified using MACS2)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig, normalized coverage

molecule: genomic DNA

organism: Mus musculus

source_name: neural progenitor cells

growth_protocol: mESC were cultured on inactivated MEFs up to p3, and in feeder-free condition from p4 onwards, in ESC complete medium + LIF (leukemia inhibitor factor) (1/1000) + beta-Mercapto-EtOH (1/500). Cells were splitted every 2-3 days upon reach of ~ 70% confluence. NPC were derived from mESC following Bibel et al. (2007)

extract_protocol:
formaldehyde fixed chromatin was preprocessed following RELACS high-thoughput ChIP-seq protocol (Arrigoni et al., 2019) using Covaris sonicator. For end repair, a-tailing, barcoding, and adaptor ligation we use reagents from the NEBNext Ultra II kit. RNA was extracted using RNeasy Mini Kit and processed using TrueSeq Stranded mRNA kit.  ATAC-seq was generated following the protocol of Buerostro et al. 2015.
Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After illumina adapter ligation, library was PCR amplified (15 cycles). Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on HiSeq3000 (RELACS ChIP-Seq, ATAC-Seq) and NextSeq HIGH (RNA-Seq) following manufacturer's protocols.

treatment_protocol: mESC growing in feeder-free plates were treated with either DMSO or EPZ5676 for 48 hours. NPC were treated  with either DMSO or EPZ5676 for 48 hours immediately after embryoid bodies disaggregation in complete N2 medium

tag: cell type

value: Dot1l-HA-FLAG ES-derived neural progenitor cells

value: DMSO

tag: passage

tag: chip ab / kit


title: NPC48h_DMSO_H3K27me3_rep2

description: RELACS ChIP-Seq


title: Hb_EV_monop_2

description:
small RNAs
Hb_EvS_Un_2


title: Hb_EV_monop_1

description:
small RNAs
Hb_EvS_Un_1


title: CB20070111-06-015_resistant


title: LSO-1


title: LMO-5

value: LMO


title: LSO-2


title: NPC48h_DMSO_H3K36me3_rep2

description: RELACS ChIP-Seq


title: Hb_EV_polyp_2

description:
small RNAs
Hb_EvS_Pp_2


title: CB20070111-06-014_resistant


title: E14.5 Embryonic Periphery

city: Marseille

first: Serge

middle: Alexander

last: van de Pavert

address: 163 Av de Luminy, case 906

department: CIML

country: France

institute: Inserm

data_processing:
FASTQ raw files were processed using Cell Ranger software (v3, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes, features and matrix files in .zip file

molecule: polyA RNA

source_name: E14.5 Embryonic Periphery

extract_protocol:
C57BL/6J E13.5 and E14.5 embryonic peripheries and FL were collected and cell suspension were prepared. CD45+ cells were enriched using CD45 magnetic microbeads on the autoMACS Pro separator. Cells were subsequently stained and alive CD45+ F4/80- IL7Rα+ LTi cells were sort-purified using the BD FACS ARIA III sorter.
Sorted-purified cells were subsequently prepared for single-cell sequencing using the Chromium Single Cell 3’ kit from 10X genomics (v2 for periphery and v3 for FL (120267 and 1000092 respectively– California, USA) for the library preparation and the NextSeq 500/550 High Output Kit v2 (75 cycles) cartridges from Illumina for the sequencing. The quality and concentration of the cDNA was determined with the bioanalyzer using the High Sensitivity DNA Analysis Kit (Agilent 5067-4626) and Qubit fluorometer using the Qubit dsDNA HS Assay Kit.

tag: strain

value: Embryos


title: NPC48h_DMSO_H3K27ac_rep2

description: RELACS ChIP-Seq


title: CB20070111-06-010_sensitive

value: sensitive


title: CB20070111-06-007_sensitive


title: CB20070111-06-008_unknown

value: unknown


title: R07

description:
small RNAs
Hb_EvU_Un_1


title: Hb_EV_polyp_1

description:
small RNAs
Hb_EvS_Pp_1


title: NPC48h_DMSO_H3K27ac_rep1

description: RELACS ChIP-Seq


title: CB20070111-06-018_sensitive


title: E13.5 Embryonic Periphery

source_name: E13.5 Embryonic Periphery


title: NPC48h_DMSO_H3K27me3_rep1

description: RELACS ChIP-Seq


title: LMO-3


title: LMO-4


title: E14.5 Fetal Liver

source_name: E14.5 Fetal Liver


title: Hb_pellet_polyp_2

description:
small RNAs
Hb_Ev_Pp_2


title: Hb_pellet_polyp_1

description:
small RNAs
Hb_Ev_Pp_1


title: mESC_EPZ_Input_rep2

description: RELACS ChIP-Seq

source_name: mouse embryionic stem cells

value: Dot1l-HA-FLAG C57BL/6 mouse embryonic stem cells


title: f LTiP [10333546_S8_R1_001.AHVYCNBGX2]

description:
170831_NB501865_0025_AHVYCNBGX2_clean.count
FLP2

data_processing:
Sequencing was performed using a NextSeq 550, in 2 runs of 14 multiplexed samples. NextSeq 500 data were demultiplexed individually per sample. Furthermore, the raw fastq files were processed to trim the molecular barcodes, the end of reads depending on quality, and the potential remaining illumina adapters. A sequencing Quality Control (QC) step was run twice on the fastq file: before and after the trimming of the reads. Afterwards, alignments were performed using STAR vs GRCm38 ensemble transcriptome resulting in a BAM which was qualified by Qualimap RNAseq. Detection and elimination of duplicated reads were done using MarkDuplicates. Finally, one table count by run was obtained using FeatureCount.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: E13.5 Fetal Liver

extract_protocol:
E13.5 embryos from RORγt-eGFP mice were digested for 20 min at 37C with Liberase/DNase . All subsequent procedures were at 0–4°C. Cells were enriched using anti-CD45 microbeads and an AutoMACS magnetic cell separator according to manufacturer’s instructions and stained and sorted based on the presence of surface markers CD45, IL7Rα, α4β7, RORγt, CD4. Lineage positive cells were excluded using F4/80, CD3e, CD19, CD8a, Ly6G. Cell viability was evaluated using LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit (Life Technologies). LTi cells and precursors were sorted using a FACSAria III. RNA was isolated using a RNA purification kit (Norgen Biotek Corp. 51800) and the quality and concentration of the RNA was determined with the bioanalyzer using RNA 6000 pico kit (Agilent 5067-1513) and Qubit fluorometer (ThermoFisher) using the Qubit dsDNA HS Assay Kit (ThermoFisher Q32854). Only those samples with a RIN value above 8 were used for subsequent library preparation. Samples were pre-amplified with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).
Pre-amplification of 8 samples with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were generated with samples’ barcode and molecular indexing, the latter being used in order to provide an absolute digital measurement of genes expression levels.


title: mESC_EPZ_Input_rep1

description: RELACS ChIP-Seq


title: LMO-1


title: HetIP_Cochlea1

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

country: USA

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller.
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner.
Reads counts were calculated for each sample.
Differential expression of genes were computed between wild type and mutant samples.
Genome_build: M. musculus GRCm38
Supplementary_files_format_and_content: *.cpm.txt: Tab-delimited text files include counts per million reads (CPM) for each sample.

growth_protocol: Room temperature 18-23°C, 12 hour light/dark cycle.

extract_protocol:
The hair cell translatome was enriched for by ribosome immunoprecipitation using an HA antibody (see protocol outlined in Sanz et al., 2009).
Gfi1Cre;RiboTag IP RNA-seq libraries were prepared in biological triplicates from cochlear tissues using the Ovation® Ultralow Library Preparation Kit (NuGEN), and vestibular tissues using the NEBNext® Ultra™ Directional RNA Library Prep Kit (New England BioLabs) per manufacturers' instructions.

tag: genotype/variation

tag: age

value: Cochlea

value: hair cells (enriched)

tag: antibody

value: HA


title: mESC_EPZ_H3K9me3_rep2

description: RELACS ChIP-Seq


title: 86 WT gWAT

city: St Louis

first: Irfan

middle: J

last: Lodhi

state: MO

address: 660 S Euclid Ave Campus box 8127

institute: Washington University School of Medicine in St. Louis

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were then aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.52. Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.133.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.34
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights7.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Genome_build: Aligned to m_musculus reference build Ensembl_R76

source_name: Gonadal white adipose tissue

growth_protocol: Female Med19-iAKO and control mice were grown to 12-weeks of age.

extract_protocol:
Total RNA was isolated using a combination of TRIzol reagent (Invitrogen 15596026) and PureLink RNA Mini Kit (Invitrogen 12183018A).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12-week old MED19-iAKO mice were injected with 100mg/kg of tamoxifen for 5 days. 14 days post tamoxifen gWAT was harvested for RNA isolation

value: Gonadal white adipose tissue

value: 12 weeks

tag: Sex

value: female

tag: genotype

value: WT


title: Scn1a +/+ Mouse 23

city: Huntsville

first: Gregory

middle: S

last: Barsh

state: ALABAMA

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: 3' RNA-seq

data_processing:
The raw fastq reads were trimmed using TrimGalore (https://github.com/FelixKrueger/TrimGalore).
The UMI sequence was clipped from each read and was added to the fastq header using in-house scripts to enable deduplication at a later stage.
The reads were aligned to the mouse genome build GRCm38.p6 using STAR aligner (version 2.7.0d)
The reads were deduped in the bam file using the program umi_tools (version 1.0.0)
HTseq (v0.11.2) was used to generate counts for genes from the alignments
DESeq2 (v1.22.1) was used to obtain the normalized table of counts for all 8 samples
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: text file  with table of counts for all 8 samples

source_name: Brain

extract_protocol:
Total RNA was extracted using Norgen Biotek Corp Animal Tissue RNA purification kit (Cat # 25700) using the manufacturer supplied protocol.
RNA-seq libraries were constructed using Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina using Unique molecular identifiers (UMIs) as per the manufacturers protocol

treatment_protocol: The mice were anesthetized by Fatal-plus (Vortech) and perfused with 0.9 % saline. Brain tissue was then dissected and frozen.

value: Whole Brain

value: Scn1a +/+


title: f CLP [10333545_S7_R1_001.AHVYCNBGX2]

description:
170831_NB501865_0025_AHVYCNBGX2_clean.count
FLP1

tag: developmental stage


title: LLO-5

value: Ji'ning grey goat

value: Oocyte

value: LLO


title: E13.5 Fetal Liver


title: mESC_EPZ_H3K9me3_rep1

description: RELACS ChIP-Seq


title: e LTiP [10333538_S14_R1_001.AHVYCNBGX2]

description:
170831_NB501865_0025_AHVYCNBGX2_clean.count
EP2


title: LLO-4


title: Scn1a +/+ Mouse 22

description: 3' RNA-seq


title: e CLP [10333537_S13_R1_001.AHVYCNBGX2]

description:
170831_NB501865_0025_AHVYCNBGX2_clean.count
EP1


title: LLO-3


title: mESC_EPZ_H3K79me2_rep2

description: RELACS ChIP-Seq

value: H3K79me2 (abcam, ab3594)


title: e LTi0 [10333535_S11_R1_001.AHVYCNBGX2]

description:
170831_NB501865_0025_AHVYCNBGX2_clean.count
EP3


title: mESC_EPZ_H3K79me2_rep1

description: RELACS ChIP-Seq


title: Scn1a +/- Mouse 8

description: 3' RNA-seq

value: Scn1a +/-


title: e LTi4 [10333536_S12_R1_001.AHVYCNBGX2]

description:
170831_NB501865_0025_AHVYCNBGX2_clean.count
EP4


title: Scn1a +/+ Mouse 4

description: 3' RNA-seq


title: Scn1a +/+ Mouse 5

description: 3' RNA-seq


title: LMO-2

value: LMO


title: Scn1a +/- Mouse 27

description: 3' RNA-seq


title: mESC_EPZ_H3K4me3_rep2

description: RELACS ChIP-Seq


title: LLO-2


title: Scn1a +/- Mouse 2

description: 3' RNA-seq


title: mESC_EPZ_H3K4me1_rep2

description: RELACS ChIP-Seq


title: HSO-4

value: HSO


title: Scn1a +/- Mouse 1

description: 3' RNA-seq


title: e LTiP [10333530_S6_R1_001.AHVYCNBGX2]


title: e CLP [10333533_S9_R1_001.AHVYCNBGX2]


title: mESC_EPZ_H3K4me1_rep1

description: RELACS ChIP-Seq

value: Dot1l-HA-FLAG C57BL/6 mouse embryonic stem cells


title: mESC_EPZ_H3K4me3_rep1

description: RELACS ChIP-Seq


title: HSO-3


title: mESC_EPZ_H3K36me3_rep2

description: RELACS ChIP-Seq


title: e CLP [10333529_S5_R1_001.AHVYCNBGX2]


title: HSO-1


title: P1ovary

first: Allan

last: Spradling

address: 3520 San Martin Drive

institute: Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science

description: single cell RNA

data_processing:
Raw 10X sequencing data was processed into a matrix employing the standard 10X Cell Ranger pipeline.
Briefly, base call files were fastq format which were aligned to the mm10 reference genome followed by nUMI and barcode counting, constructing the nUMI count matrices.
nUMI matrices were filtered, centered and normalized using Seurat (Butler et al., 2018; Macosko et al., 2015).
Data was then log scaled, centered and normalized to nUMI.
Genome_build: mm10.3
Supplementary_files_format_and_content: TSV; MTX

source_name: Postnatal Ovary

growth_protocol: Individual ovary isolated from WT mice

extract_protocol:
Perinatal ovaries were dissected and placed in 1X PBS on ice, then dissociated into single cells using 0.25% Trypsin at 37°C with pipet trituration at intervals. E11.5 and E12.5 ovaries were dissociated for 20 min, E14.5 and E16.5 ovaries for 40 min, E18.5 ovaries for 1h, P1 and P5 ovaries for 80 min. After neutralized with 10% FBS, dissociated cells were passed through 70 μm and 30 μm cell strainer, separately.
Approximately 10,000 live cells were loaded per sample onto the 10x Genomics Chromium Single Cell system using the v2 chemistry per manufacturer’s instructions.  Single cell RNA capture and library preparations were performed according to manufacturer’s instructions. Sample libraries were sequenced on the NextSeq 500 (Illumina). Sequencing output was processed through the Cell Ranger 3.1.0 mkfastq and count pipelines using default parameters. Reads were quantified using the mouse reference index provided by 10x Genomics (refdata-cellranger-mm10v3.0).
single cell RNA seq

treatment_protocol: No treatment

tag: strain/background

value: Ovary


title: P5ovary

description: single cell RNA


title: mESC_EPZ_H3K36me3_rep1

description: RELACS ChIP-Seq


title: HMO-5

tag: tissue

value: HMO


title: e LTi0 [10333527_S3_R1_001.AHVYCNBGX2]


title: mESC_EPZ_H3K27me3_rep2

description: RELACS ChIP-Seq


title: e LTiP [10333534_S10_R1_001.AHVYCNBGX2]


title: LLO-1


title: E18.5ovary

description: single cell RNA

source_name: Prenatal Ovary


title: e LTiP [10333526_S2_R1_001.AHVYCNBGX2]


title: mESC_EPZ_H3K27me3_rep1

description: RELACS ChIP-Seq


title: HMO-4


title: HSO-5


title: E16.5ovary

description: single cell RNA


title: E14.5ovary

description: single cell RNA


title: HMO-3


title: e CLP [10333525_S1_R1_001.AHVYCNBGX2]


title: E12.5ovary

description: single cell RNA


title: HMO-2


title: f LTi4 [10333552_S14_R1_001.AHVW33BGX2]

description:
170905_NB501865_0026_AHVW33BGX2.count
FLP4


title: mESC_EPZ_H3K27ac_rep1

description: RELACS ChIP-Seq


title: E11.5gonad

description: single cell RNA

source_name: Prenatal gonad

value: Gonad


title: HMO-1


title: e LTi4 [10333528_S4_R1_001.AHVYCNBGX2]


title: mESC_DMSO_Input_rep2

description: RELACS ChIP-Seq

value: DMSO


title: HL-1 siCtrl

city: Hannover

first: Christian

last: Bär

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hannover Medical School

data_processing:
Casava1.7 (Illumina) was used for basecalling.
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were taken for further analysis.
Peaks were called using SICER algorithms at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp
Peak filtering was performed by removing false ChIP-Seq  peaks as defined within the ENCODE blacklist.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Signal files in bigwig format

extract_protocol:
HL-1 cells were fixed using Formaldehyde solution and harvested. Chromatin was isolated and the DNA sheared to an average length of 300-500bp. Resulting DNA was quantified on a NanoDrop spectrophotometer. 30µg of chromatin was precleared with protein A agarose beads. Genomic DNA regions of interest were isolated using 4 ug of antibody against H3K27me3 (# 39155, Active Motif, Carlsbad, CA, USA). Crosslinks were reversed and ChIP DNA was purified.
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500.

tag: cell line

value: transfected with siCtrl

tag: chip antibody

value: H3K27me3 (Active Motif, # 39155)


title: HLO-5

value: HLO


title: f LTiP [10333550_S12_R1_001.AHVW33BGX2]

description:
170905_NB501865_0026_AHVW33BGX2.count
FLP2


title: mESC_DMSO_Input_rep1

description: RELACS ChIP-Seq


title: HL-1 siH19

value: transfected with siRNA for H19 KD


title: HLO-4


title: f CLP [10333549_S11_R1_001.AHVW33BGX2]

description:
170905_NB501865_0026_AHVW33BGX2.count
FLP1


title: HLO-3


title: HL-1 pLV+H19

value: transduced with lentivirus inducing H19 expression


title: mESC_DMSO_H3K9me3_rep2

description: RELACS ChIP-Seq


title: mESC_DMSO_H3K9me3_rep1

description: RELACS ChIP-Seq


title: f LTi4 [10333548_S10_R1_001.AHVW33BGX2]


title: HL-1 pLV+empty

value: transduced with lentivirus inducing expression of a control sequence


title: HLO-2

value: Ji'ning grey goat

value: Oocyte


title: mESC_EPZ_H3K27ac_rep2

description: RELACS ChIP-Seq


title: f LTi0 [10333547_S9_R1_001.AHVW33BGX2]

description:
170905_NB501865_0026_AHVW33BGX2.count
FLP3


title: mESC_DMSO_H3K79me2_rep2

description: RELACS ChIP-Seq

value: H3K79me2 (abcam, ab3594)


title: HLO-1


title: Treg.15wk.M.VAT.fat1562_immunized.C

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: visceral adipose tissue

extract_protocol:
1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: Treg cells from pooled spleen and lymph nodes of vTreg53 TCR transgenic mice were transferred into CD45.1 B6 mice. Six weeks later, the recipient mice were immunized subcutaneously with CFA/Fat1562, followed by a boost with IFA/Fat1562 intraperitoneally one week later. The clonotype+ Tregs from the spleen/lymph nodes and VAT of recipient mice were double sorted and processed for RNA-seq

tag: group

value: immunized

value: Treg

value: visceral adipose tissue

value: vTreg53 Tg+


title: f LTi4 [10333544_S6_R1_001.AHVW33BGX2]


title: f LTi0 [10333551_S13_R1_001.AHVW33BGX2]


title: mESC_DMSO_H3K4me3_rep2

description: RELACS ChIP-Seq

value: Dot1l-HA-FLAG C57BL/6 mouse embryonic stem cells


title: LSG-10_Ovarian granulosa cells

description: The group information is prefixed with LSG-10 in the column of processed data file

source_name: LSG-10_Ovarian granulosa cells

extract_protocol:
Granulosa cells samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: breed

value: Ovarian granulosa cells

value: LSG


title: f LTiP [10333542_S4_R1_001.AHVW33BGX2]


title: Treg.15wk.M.VAT.fat1562_immunized.A


title: Treg.15wk.M.VAT.fat1562_immunized.B


title: mESC_DMSO_H3K4me3_rep1

description: RELACS ChIP-Seq

tag: treatment

value: DMSO


title: Treg.15wk.M.VAT.PBS_unimmunized.B

value: unimmunized

tag: cell type


title: LSG-8_Ovarian granulosa cells

description: The group information is prefixed with LSG-8 in the column of processed data file

source_name: LSG-8_Ovarian granulosa cells


title: f CLP [10333541_S3_R1_001.AHVW33BGX2]


title: Treg.15wk.M.VAT.PBS_unimmunized.A


title: mESC_DMSO_H3K4me1_rep2

description: RELACS ChIP-Seq

tag: passage


title: LSG-7_Ovarian granulosa cells

description: The group information is prefixed with LSG-7 in the column of processed data file

source_name: LSG-7_Ovarian granulosa cells


title: Treg.15wk.M.SpLN.fat1562_immunized.C

source_name: Spleen and lymph nodes

value: Spleen and lymph nodes


title: e LTi4 [10333540_S2_R1_001.AHVW33BGX2]

description:
170905_NB501865_0026_AHVW33BGX2.count
EP4


title: e LTi0 [10333539_S1_R1_001.AHVW33BGX2]

description:
170905_NB501865_0026_AHVW33BGX2.count
EP3


title: mESC_DMSO_H3K4me1_rep1

description: RELACS ChIP-Seq

tag: chip ab / kit


title: LSG-5_Ovarian granulosa cells

description: The group information is prefixed with LSG-5 in the column of processed data file

source_name: LSG-5_Ovarian granulosa cells


title: mESC_DMSO_H3K36me3_rep2

description: RELACS ChIP-Seq


title: LMG-10_Ovarian granulosa cells

description: The group information is prefixed with LMG-10 in the column of processed data file

source_name: LMG-10_Ovarian granulosa cells

value: LMG


title: e LTi4 [10333532_S8_R1_001.AHVW33BGX2]

tag: strain


title: mESC_DMSO_H3K79me2_rep1

description: RELACS ChIP-Seq


title: Treg.15wk.M.SpLN.fat1562_immunized.B


title: e LTi0 [10333531_S7_R1_001.AHVW33BGX2]


title: Treg.15wk.M.SpLN.fat1562_immunized.A


title: mESC_DMSO_H3K27me3_rep2

description: RELACS ChIP-Seq


title: LMG-9_Ovarian granulosa cells

description: The group information is prefixed with LMG-9 in the column of processed data file

source_name: LMG-9_Ovarian granulosa cells


title: Treg.15wk.M.SpLN.PBS_unimmunized.C


title: mESC_DMSO_H3K27me3_rep1

description: RELACS ChIP-Seq


title: f LTi0 [10333543_S5_R1_001.AHVW33BGX2]


title: LMG-7_Ovarian granulosa cells

description: The group information is prefixed with LMG-7 in the column of processed data file

source_name: LMG-7_Ovarian granulosa cells


title: LSG-9_Ovarian granulosa cells

description: The group information is prefixed with LSG-9 in the column of processed data file

source_name: LSG-9_Ovarian granulosa cells


title: LMG-8_Ovarian granulosa cells

description: The group information is prefixed with LMG-8 in the column of processed data file

source_name: LMG-8_Ovarian granulosa cells


title: Treg.15wk.M.SpLN.PBS_unimmunized.A


title: Treg.15wk.M.SpLN.PBS_unimmunized.B


title: LMG-5_Ovarian granulosa cells

description: The group information is prefixed with LMG-5 in the column of processed data file

source_name: LMG-5_Ovarian granulosa cells


title: mESC_DMSO_H3K36me3_rep1

description: RELACS ChIP-Seq

source_name: mouse embryionic stem cells


title: mESC_DMSO_H3K27ac_rep1

description: RELACS ChIP-Seq


title: LLG-10_Ovarian granulosa cells

description: The group information is prefixed with LLG-10 in the column of processed data file

source_name: LLG-10_Ovarian granulosa cells

value: LLG


title: Group_IV_rep_6

city: Leiden

first: Rob

last: Mariman

address: Zernikedreef 9

country: Netherlands

institute: TNO

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq2 Conversion Software v2.20
Gene expression profiles in the mouse lungs were obtained by RNAseq. Therefore, libraries for the Illumina NextSeq were generated using the TruSeq Stranded mRNA Library Prep Kit using 400 ng of total RNA as input according to the manufacturer’s instructions. Briefly, the mRNA fraction was purified from total RNA by polyA capture, fragmented and subjected to first-strand cDNA synthesis with random hexamers in the presence of Actinomycin D. The second-strand synthesis was performed incorporating dUTP instead of dTTP. Barcoded DNA adapters were ligated to both ends of the double-stranded cDNA and subjected to PCR amplification. Libraries were subsequently validated for fragment size on a QiaXcel (Qiagen) and quantified using RT-qPCR with a Kapa-kit (Roche Sequencing Store). In each sequencing run, 24 libraries were pooled at equimolar concentrations and sequenced using the Illumina NextSeq 500/550 High Output Kit v2.5 (single-end, 75 Cycles).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: .xlsx files with statisticsal analysis, normalized counts and raw counts

source_name: Lung

extract_protocol:
Total RNA was extracted from the caudal lobes (right lungs) using phenol extraction in combination with the Mirneasy RNA isolation kit (Qiagen, Hilden, Germany). 3 µg BioPM were chosen as representative dose to study gene expression in lungs of OVA/Sal and OVA/OVA mice. In short, murine lung tissue was homogenized by using the bead homogenization (MP Biomedicals, Illkirch, France) in 600 µl Trizol (Thermofisher, Landsmeer, The Netherlands). RNA isolation was carried out according to the manufacturer’s instructions.
Gene expression profiles in the mouse lungs were obtained by RNAseq. Therefore, libraries for the Illumina NextSeq were generated using the TruSeq Stranded mRNA Library Prep Kit using 400 ng of total RNA as input according to the manufacturer’s instructions. Briefly, the mRNA fraction was purified from total RNA by polyA capture, fragmented and subjected to first-strand cDNA synthesis with random hexamers in the presence of Actinomycin D. The second-strand synthesis was performed incorporating dUTP instead of dTTP. Barcoded DNA adapters were ligated to both ends of the double-stranded cDNA and subjected to PCR amplification. Libraries were subsequently validated for fragment size on a QiaXcel (Qiagen) and quantified using RT-qPCR with a Kapa-kit (Roche Sequencing Store). In each sequencing run, 24 libraries were pooled at equimolar concentrations and sequenced using the Illumina NextSeq 500/550 High Output Kit v2.5 (single-end, 75 Cycles)

value: Lung

tag: sensitization

value: OVA

tag: challenge

value: PM 3ug


title: LLG-9_Ovarian granulosa cells

description: The group information is prefixed with LLG-9 in the column of processed data file

source_name: LLG-9_Ovarian granulosa cells

value: Ji'ning grey goat


title: LLG-8_Ovarian granulosa cells

description: The group information is prefixed with LLG-8 in the column of processed data file

source_name: LLG-8_Ovarian granulosa cells


title: LLG-7_Ovarian granulosa cells

description: The group information is prefixed with LLG-7 in the column of processed data file

source_name: LLG-7_Ovarian granulosa cells


title: ASR2_6a_rep2

city: Stony Brook

first: Xinxin

last: Yang

state: New York

address: 100 Nicolls Road

department: Chemistry

institute: Stony Brook University

description: Biological replicate 1 of 3

data_processing:
Raw sequence data in FASTQ format were assessed for quality (FastQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ribosomal RNA content (sortmeRNA, http://bioinfo.lifl.fr/RNA/sortmerna/).
NovoAlign (Novocraft, http://novocraft.com) was used to align reads to a set of transcript sequences. Alignments to the genome were performed using STAR (https://github.com/alexdobin/STAR).
The genome alignment loci from all samples were combined and clustered to generate genomic loci (“patches”) with contiguous read coverage. Patches overlapping reference genome annotation loci were labelled as such.
For each transcript or patch, the RPKM expression value was calculated for each sample. These RPKM values are the basis for expression comparison and statistics generation.
For each replicate group, the mean and coefficient of variation for each transcript or patch were calculated across the expression values for the samples in that group. These means were considered to be the expression values for the replicate group. P-values were calculated between the means of each pair of replicate groups using a Welch’s t-test corrected for FDR by the method of Benjamini-Hochberg.
Genome_build: Mycobacterium tuberculosis CDC1551
Supplementary_files_format_and_content: matrix table

organism: Mycobacterium tuberculosis

source_name: in vitro culture

growth_protocol: Mycobacterium tuberculosis cultures were grown to OD ~0.6 at 37°C.

extract_protocol:
Total RNA was extracted using TriZol, with chloroform back extraction and 70% ethanol precipitation. RNA was purified by RNeasy kit (Qiagen) with DNAse treatment.
Ribo-depletion, NGS libraries were prepared for sequencing using standard Illumina protocols (Cofactor Genomics, Inc.)

treatment_protocol: Cultures were treated with 30 μM of 4a or 6a or vehicle control for 6h.

value: compound 6a

value: whole organism from in vitro culture


title: ASR2_6a_rep3

description: Biological replicate 1 of 3


title: ASR2_4a_rep3

description: Biological replicate 1 of 3

value: compound 4a


title: Group_IV_rep_2


title: Group_IV_rep_4


title: ASR2_6a_rep1

description: Biological replicate 1 of 3


title: Group_IV_rep_5


title: Group_IV_rep_1


title: mESC_DMSO_H3K27ac_rep2

description: RELACS ChIP-Seq


title: ASR2_4a_rep2

description: Biological replicate 1 of 3


title: LLG-5_Ovarian granulosa cells

description: The group information is prefixed with LLG-5 in the column of processed data file

source_name: LLG-5_Ovarian granulosa cells


title: OO 2016

type: genomic

city: Columbus

first: Michael

last: Brooker

state: OH

address: 590 Woody Hayes Drive

department: Food, Agricultural, and Biological Engineering

institute: The Ohio State Unviersity

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA)

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) and transform the data to the natural logarithmic form

organism: uncultured soil bacterium

source_name: floodplain soil collected from OO ditch

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Genomic DNA was extracted using the MoBio PowerSoil DNA kit (QIAGEN, Valencia, CA)

treatment_protocol: Soils were collected from the field, transported on ice, and stored at -20°C until processing

tag: land use

value: agricultural

tag: collection site

value: a ditch in the Oak Openings Ecoregion


title: Group_III_rep_6

value: no PM


title: CHLP 2016

source_name: floodplain soil collected from CHLP ditch

value: a ditch in the Clayey, High-Lime Till Plains Ecoregion


title: OO rep#2 2015


title: PP 2016

source_name: floodplain soil collected from PP ditch

value: a ditch in the Paulding Plains Ecoregion


title: ASR2_4a_rep1

description: Biological replicate 1 of 3


title: CHLP rep#2 2015


title: HSG-9_Ovarian granulosa cells

description: The group information is prefixed with HSG-9 in the column of processed data file

source_name: HSG-9_Ovarian granulosa cells

value: Ovarian granulosa cells

value: HSG


title: Group_III_rep_5


title: ASR2_control_rep3

description: Biological replicate 1 of 3

value: no


title: Group_III_rep_4


title: S_99

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of Prunus persica and Monilinia laxa with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Prunus persica NCBIv2, Monilinia laxa ASM293894v1
Supplementary_files_format_and_content: Monilinia_Peach_primary_transcripts.counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism: Prunus persica

source_name: Inoculated fruit

extract_protocol: Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

tag: ripening stage

value: Mature

value: Monilinia laxa Inoculated

tag: time point (hours post inoculation)


title: S_100


title: S_97


title: HSG-5_Ovarian granulosa cells

description: The group information is prefixed with HSG-5 in the column of processed data file

source_name: HSG-5_Ovarian granulosa cells


title: PP rep#2 2015


title: HSG-10_Ovarian granulosa cells

description: The group information is prefixed with HSG-10 in the column of processed data file

source_name: HSG-10_Ovarian granulosa cells


title: ASR2_control_rep1

description: Biological replicate 1 of 3


title: S_96

value: Healthy


title: ASR1_6a_rep3

description: Biological replicate 1 of 3


title: HMG-10_Ovarian granulosa cells

description: The group information is prefixed with HMG-10 in the column of processed data file

source_name: HMG-10_Ovarian granulosa cells

value: HMG


title: Group_III_rep_2

value: Lung

value: OVA


title: CHLP rep#1 2015


title: S_95


title: Group_III_rep_1


title: HMG-9_Ovarian granulosa cells

description: The group information is prefixed with HMG-9 in the column of processed data file

source_name: HMG-9_Ovarian granulosa cells

value: Ji'ning grey goat


title: Group_II_rep_6

value: saline

value: PM 3ug


title: ASR1_6a_rep2

description: Biological replicate 1 of 3

value: compound 6a

value: whole organism from in vitro culture


title: Group_III_rep_3

value: no PM


title: HSG-7_Ovarian granulosa cells

description: The group information is prefixed with HSG-7 in the column of processed data file

source_name: HSG-7_Ovarian granulosa cells


title: ASR1_6a_rep1

description: Biological replicate 1 of 3


title: S_93


title: Group_II_rep_5


title: HMG-8_Ovarian granulosa cells

description: The group information is prefixed with HMG-8 in the column of processed data file

source_name: HMG-8_Ovarian granulosa cells


title: S_92


title: Group_II_rep_3

source_name: Lung


title: ASR1_4a_rep3

description: Biological replicate 1 of 3

value: compound 4a


title: S_91


title: ASR1_4a_rep2

description: Biological replicate 1 of 3


title: S_89


title: Group_II_rep_2


title: HMG-5_Ovarian granulosa cells

description: The group information is prefixed with HMG-5 in the column of processed data file

source_name: HMG-5_Ovarian granulosa cells


title: ASR1_4a_rep1

description: Biological replicate 1 of 3


title: Group_II_rep_1


title: S_88


title: ASR1_control_rep3

description: Biological replicate 1 of 3


title: HLG-10_Ovarian granulosa cells

description: The group information is prefixed with HLG-10 in the column of processed data file

source_name: HLG-10_Ovarian granulosa cells

value: HLG


title: PP rep#1 2015

value: agricultural

value: a ditch in the Paulding Plains Ecoregion


title: HLG-9_Ovarian granulosa cells

description: The group information is prefixed with HLG-9 in the column of processed data file

source_name: HLG-9_Ovarian granulosa cells

value: Ovarian granulosa cells


title: S_87

value: Mature


title: HLG-8_Ovarian granulosa cells

description: The group information is prefixed with HLG-8 in the column of processed data file

source_name: HLG-8_Ovarian granulosa cells


title: Group_I_rep_5


title: Group_I_rep_6


title: S_85


title: Group_I_rep_4


title: ASR1_control_rep2

description: Biological replicate 1 of 3

source_name: in vitro culture

value: no


title: S_84

value: Monilinia laxa Inoculated


title: HLG-7_Ovarian granulosa cells

description: The group information is prefixed with HLG-7 in the column of processed data file

source_name: HLG-7_Ovarian granulosa cells


title: CDC1551_6a_rep3

description: Biological replicate 1 of 3


title: HMG-7_Ovarian granulosa cells

description: The group information is prefixed with HMG-7 in the column of processed data file

source_name: HMG-7_Ovarian granulosa cells

value: HMG


title: HLG-5_Ovarian granulosa cells

description: The group information is prefixed with HLG-5 in the column of processed data file

source_name: HLG-5_Ovarian granulosa cells


title: ASR1_control_rep1

description: Biological replicate 1 of 3


title: S_83


title: CDC1551_6a_rep2

description: Biological replicate 1 of 3


title: Group_I_rep_2

value: Lung


title: Group_I_rep_3


title: S_81


title: CDC1551_6a_rep1

description: Biological replicate 1 of 3


title: Group_I_rep_1


title: Mammary gland cells, KD553-2

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with  KD553_1 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of -m 0 -x 1000 -s 40 -l 35 -v 3 -r 2. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR 0.001 and an absolute value of log2Ratio1 to judge the significance of gene expression difference.
Genome_build: ARS1
Supplementary_files_format_and_content: FPKMs

extract_protocol:
goat mammary gland cells were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: Lanshan dairy goat

value: mammary gland cells cultured in 3D condition

tag: genotype

value: lncRNA55666 knockdown


title: Mammary gland cells, KD553-1

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with  KD553_3 in the column of processed data file


title: S_80

value: Healthy


title: S_78


title: Mammary gland cells, Lv3NC-2

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with  Lv3NC_2 in the column of processed data file


title: CDC1551_4a_rep2

description: Biological replicate 1 of 3

tag: tissue


title: PRO-Seq E14 LBH589 6hrs  REP2

city: LEICESTER

first: RICHARD

middle: DAVID WILLIAM

last: KELLY

address: LANCASTER ROAD

department: BIOCHEMISTRY

institute: UNIVERSITY OF LEICESTER

description:
total RNA (nascent)
LBH-6hr.minus.ucsc.bedgraph
LBH-6hr.plus.ucsc.bedgraph
LBH6_gb_change.txt
LBH6_pindex_change.txt
LBH589_6hr_Enhancer_change.txt

data_processing:
Library strategy: PRO-Seq
Quality control: reads not passing Illumina QC were removed.
Trimming: adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Alignment: Reverse complements of the trimmed reads were aligned to the mouse genome mm10 using Bowtie2.
Downstream analysis: Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
Genome_build: mm10
Supplementary_files_format_and_content: gb_change.txt = transcription changes of gene body regions across two conditions; pindex_change.txt = pausing index changes across two conditions; Enhancer_change.txt = transcription change of enhancers across two conditions; For PROseq genome coverage was normalized and calculated for each strand separately and reported in bedGraph format.

source_name: E14 Embryonic stem cells

growth_protocol: ES cell lines were maintained on gelatinized plates in standard ES cell medium consisting of Knockout DMEM (Invitrogen), 15% fetal calf serum (FCS), 1_ glutamine/penicillin/streptomycin (Invitrogen), 100 _M _-mercaptoethanol (Sigma-Aldrich), and Leukemia inhibitory factor (LIF) under feeder free conditions. wild type (Ctrl/0hr) E14 ESC were compared to ESC treate with Panobinostat/LBH589 (50nM) for 2hr and 6hr or JQ1 for 2hrs. .  Each time points were analyzed in duplicate.

extract_protocol:
Briefly, 30 million nuclei were used for each run-on assay. In vitro nuclear run-on assays were carried out in the presence of ATP, UTP, GTP, and biotin-11-CTP and 0.5% Sarkosyl at 30°C for 3 min. Total nuclear RNA was extracted using Trizol  and ethanol precipitation. RNA was resuspended and hydrolyzed with 0.2 N NaOH, and biotinylated RNA was purified by streptavidin bead binding, which was followed by 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification. DNA libraries were PAGE purified and submitted for sequencing.
Mahat, D. B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc 11, 1455-1476, doi:10.1038/nprot.2016.086 (2016).

treatment_protocol: To inhibit HDAC activity , E14 ESC were treated with Panobinostat/LBH589 (50nM) for 2hr and 6hr or JQ1 for 2hrs.

tag: cell line

value: embryonic stem cells

tag: Sex

value: Male

value: LBH589 6hrs


title: PRO-Seq E14 LBH589 6hrs  REP1


title: Mammary gland cells, Lv3NC-1

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with  Lv3NC_1 in the column of processed data file


title: CDC1551_4a_rep1

description: Biological replicate 1 of 3

value: compound 4a

value: whole organism from in vitro culture


title: S_76

source_name: Inoculated fruit


title: PRO-Seq E14 LBH589 2hrs  REP2

description:
total RNA (nascent)
LBH-2hr.minus.ucsc.bedgraph
LBH-2hr.plus.ucsc.bedgraph
LBH2_gb_change.txt
pindex_change.txt
LBH589_2hr_Enhancer_change.txt

value: LBH589 2hrs


title: CDC1551_control_rep3

description: Biological replicate 1 of 3


title: Mammary gland cells, OV55666-1

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with OV55666_1 in the column of processed data file

value: lncRNA55666 overexpression


title: S_74


title: CDC1551_control_rep2

description: Biological replicate 1 of 3


title: Mammary gland cells, Lv5NC-2

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with  Lv5NC_2 in the column of processed data file


title: OO rep#1 2015

source_name: floodplain soil collected from OO ditch

value: agricultural

value: a ditch in the Oak Openings Ecoregion


title: S_73

value: Mature


title: PRO-Seq E14 JQ1 2hrs  REP2

description:
total RNA (nascent)
JQ1-2hr.minus.ucsc.bedgraph
JQ1-2hr.plus.ucsc.bedgraph
JQ1-2_gb_change.txt
JQ1-2_pindex_change.txt
JQ1_2hr_Enhancer_change.txt

value: JQ1 2hrs


title: CDC1551_4a_rep3

description: Biological replicate 1 of 3


title: PRO-Seq E14 JQ1 2hrs  REP1


title: Mammary gland cells, Lv5NC-1

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with Lv5NC_1 in the column of processed data file


title: CDC1551_control_rep1

description: Biological replicate 1 of 3

value: no


title: S_72


title: S_71


title: PRO-Seq CTRL E14 REP2

description:
total RNA (nascent)
control.minus.ucsc.bedgraph
control.plus.ucsc.bedgraph

value: control


title: Mammary gland cells, Blank-1

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with Blank_1 in the column of processed data file

value: Lanshan dairy goat

value: Blank


title: Mammary gland cells, Blank-2

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with Blank_2 in the column of processed data file

value: mammary gland cells cultured in 3D condition


title: PRO-Seq CTRL E14 REP1


title: Mammary gland cells, OV55666-2

description:
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with OV55666_2 in the column of processed data file


title: S_77

value: Healthy


title: MCF-7T-3-IP

city: Zhengzhou

first: Weihua

last: Gong

state: Henan

address: ZZ

institute: Zhengzhou University

description: Breast cancer drug-resistant cells MCF-7 / Taxol_rep3

data_processing:
Off-Line Basecaller software (OLB V1.8)
MeDIP-seq reads were aligned to human genome (UCSC hg19) using Hisat2 software
The trimmed reads were aligned to reference genome with Hisat2 software.
Aligned reads were used for peak calling, LncRNA, mRNA and Small ncRNA associated MeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value threshold of 10阈 5 by MACS2 software
Genome_build: hg19

source_name: Breast cancer  cells

growth_protocol: The human breast cancer cells (MCF-7) were purchased from the American Type Culture Collection (ATCC, USA). Low concentration gradient induction method was used to establish breast cancer Taxol-resistant cells MCF-7 / Taxol. MCF-7 cells were cultured in a complete RPMI 1640 (Solarbio, China) medium containing 10% fetal bovine serum (BI, USA). MCF-7 / Taxol cells were stably cultured in complete RPMI 1640 medium containing 85.50 nmol• L-1 Taxols (Xi 'an Haoxuan bio-tech Co., Ltd., China). All cells were cultured aseptically in a humidified atmosphere of 5%CO2 at 37° C.

extract_protocol:
Genomic DNA was sonicated to ～200-800bp fragments, and 1 μg of fragmented sample was ligated to Illumina’s genomic adapters, following the manufacturer’s instructions. ～300-900 bp ligated DNA fragments were further immunoprecipitated by anti-5-Methylcytosine antibody. The enriched DNA was amplified by PCR and purified by AMPure XP beads.
DNA samples were fragmented to a size range of ～200-800bp with a Diagenode Bioruptor. About 1 μg of fragmented DNA was prepared for Illumina NovaSeq 6000 sequencing as the following steps: 1) End repair of DNA samples; 2) A single ‘A’ base was added to the 3’ ends; 3) Ligation of Illumina’s genomic adapters to DNA fragments; 4) MeDIP to enrich Methylated DNA by anti-5-Methylcytosine antibody; 5) PCR amplification to enrich precipitated fragments; 6) Size selection of ～300-900bp DNA fragments using AMPure XP beads. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Illumina NovaSeq 6000 following the NovaSeq 6000 S4 Reagent Kit (300 cycles) protocol.

value: Breast cancer drug-resistant cells

value: treated with Taxol for 16 days


title: MCF-7T-3-input

treatment_protocol: MCF-7 / Taxol cells were stably cultured in complete RPMI 1640 medium containing 85.50 nmol• L-1 Taxols


title: PRO-Seq E14 LBH589 2hrs  REP1

value: embryonic stem cells

value: Male


title: S_70


title: MCF-7T-2-input

description: Breast cancer drug-resistant cells MCF-7 / Taxol_rep2

value: treated with Taxol for 15 days


title: MCF-7T-2-IP


title: input DNA 56

city: Rijeka

first: Felix

middle: M.

last: Wensveen

address: Braće Branchetta 20

department: Histology & Embryology

country: Croatia

institute: University of Rijeka

description: Pooled input from Eomes_ChIP5 and Eomes_ChIP6

data_processing:
STAR was used for the mapping to the mouse genome (GRCm38/mm10 assembly), indexed using STAR with the fasta obtained from UCSC
The findPeaks program from the Homer suit of programs was used for the peak calling using the default parameters
Homer was used to find motifs
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: Activated OT-1 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with antibody.
ChIPseq libraries were prepared by using Followed Rubicon ThruPLEX® DNA-seq Kit (CAT. NO. R400427).

value: Activated OT-1 cells_high Eomes

tag: passages

value: Primary

tag: chip antibody


title: input DNA 12

description: Pooled input from Eomes_ChIP1 and Eomes_ChIP1

value: Activated OT-1 cells_low Eomes


title: vdrko_9

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description: Genisphere Flashtag

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Post-processing of array signal data (rma) was performed with Partek Genomics Suite 6.6 (Partek, St Louis, MO)

source_name: macrophage culture supernatant

label_protocol: Genisphere Flashtag

growth_protocol: Murine peritoneal monocytes were isolated as previously described (Oh, J. et al. Deletion of macrophage Vitamin D receptor promotes insulin resistance and monocyte cholesterol transport to accelerate atherosclerosis in mice. Cell Reports 10, 1872-1886, doi:10.1016/j.celrep.2015.02.043 (2015); Weng, S. et al. Vitamin D deficiency induces high blood pressure and accelerates atherosclerosis in mice. PloS One 8, e54625, doi:10.1371/journal.pone.0054625 (2013))and were cultured in DMEM plus 10% FBS at 37 C in a 5% CO2 atmosphere.

extract_protocol: RNA was extracted from cell culture supernatants (macrophage media), processed, and hybridized to Affymetrix GeneChip miRNA 4.0 microarrays by Washington University’s Genome Technology Access Center

value: Lyz2Cre/Vdr(fl/fl) (KODMAC)


title: MCF-7T-1-input

description: Breast cancer drug-resistant cells MCF-7 / Taxol_rep1

tag: treatment

value: treated with Taxol for 14 days


title: S_34

value: Immature

value: Monilinia laxa Inoculated


title: Eomes_ChIPSeq 6

tag: cell type

value: Eomes (Abcam, ab23345)


title: vdrko_8

description: Genisphere Flashtag


title: Eomes_ChIPSeq 5


title: vdrko_7

description: Genisphere Flashtag


title: S_32


title: MCF-7T-1-IP


title: Eomes_ChIPSeq 2


title: S_31


title: vdrko_6

description: Genisphere Flashtag


title: MCF-7-3-input

description: Breast cancer sensitive cells MCF-7_rep3

value: Breast cancer sensitive cells

value: untreated


title: Eomes_ChIPSeq 1


title: S_29


title: MCF-7-3-IP


title: vdrko_5

description: Genisphere Flashtag


title: S_36


title: vdrko_4

description: Genisphere Flashtag


title: MCF-7-2-input

description: Breast cancer sensitive cells MCF-7_rep2


title: S_26


title: MCF-7-1-input

description: Breast cancer sensitive cells MCF-7_rep1


title: S_33


title: vdrko_3

description: Genisphere Flashtag


title: S_24


title: S_25


title: batch2_Patient-Tumor-3_S15

city: Durham

first: Jennifer

last: Freedman

address: 905 South Lasalle Street

institute: Duke Cancer Institute

data_processing:
Base-calling was done on the instrument using RTA v3.3.3.
Demultiplexing was done using bcl2fatq v2.20.0.422
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic v0.36
Reads were mapped to human hg38 genome using STAR v2.6.1db and quantified to features using HT-Seq built in the STAR aligner.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with read counts per gene

source_name: TUMOR

growth_protocol: All animal studies were performed under a Duke University Animal Care and Use Committee (IACUC) approved protocol. Briefly, tissues were washed with phosphate buffered saline (PBS) and then minced into pieces approximately 2mm in size and injected into the flanks of 8-10-week-old JAX NOD.CB17-PrkdcSCID-J (SCID) or NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice obtained from the Duke University Rodent Genetic and Breeding Core to develop subcutaneous tumors

extract_protocol: Mice were sacrificed once tumors exceeded 10 x 10 mm and tissue was harvested at 150mg/mL in PBS for serial passaging and for testing therapeutic response. To test therapeutic response, tissue was dissociated with the MACS GentleMACS Dissociater and 200μL of the suspension was injected into each new mouse with a 19-guage needle

treatment_protocol: Enzalutamide, docetaxel and cisplatin were acquired from the Duke University Pharmacy stockroom. Enzalutamide was diluted in 1:20 DMSO in ultrapure distilled water and delivered at 10mg/kg by oral gavage five times per week. Docetaxel was diluted in 1:20 DMSO and cisplatin was diluted in DPBS and administered by intraperitoneal injection twice per week at 8mg/kg and 3.5mg/kg, respectively as standard doses

value: TUMOR

value: Patient-Tumor


title: S_27


title: MCF-7-2-IP


title: S_23

value: Healthy


title: S_21


title: batch2_Patient-Tumor-2_S14


title: wt_9

description: Genisphere Flashtag

value: wild-type


title: vdrko_1

description: Genisphere Flashtag


title: Hep3B_hypoxia_48hr_rep2

city: Xi'an

first: Kangsheng

last: Tu

address: 277 Yanta West Road

department: Department of Hepatobiliary Surgery

institute: First Affiliated Hospital of Xi'an Jiaotong University

description: The expression of human lncRNAs and protein-coding transcripts in Hep3B cells after 48hr hypoxia culture

hyb_protocol: Kit and Instruments: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). Hybridization Chamber, stainless (Agilent p/n G2534A). Hybridization Chamber gasket slides (Agilent p/n G2534-60003). Hybridization oven (Agilent p/n G2545A). Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029). 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2. Equilibrate water bath to 60°C. 3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube. 4. Mix well but gently on a vortex mixer. 5. Incubate at 60°C for exactly 30 minutes to fragment RNA. 6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. 7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9. Place sample on ice and load onto the array as soon as possible. 10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner. 12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. 13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14. Hand-tighten the clamp onto the chamber. 15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17. Hybridize at 65°C for 17 hours.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (Agilent p/n G2565BA). 1. Assemble the slides into an slide holder. 2. Place assembled slide holders into scanner carousel. 3. Verify scan settings for one-color scans. 4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: Hep3B, 48hr, hypoxia, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hep3B cells were cultured in the normoxic incubator (20% O2, Thermo Scientific) and hypoxic incubator (1% O2, SANYO) for 48 hours.

extract_protocol: Total RNA was isolated from Hep3B cells using TRIzol reagent (Invitrogen) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: hepatocellular carcinoma

tag: stress

value: hypoxia


title: batch2_Patient-Tumor-1_S13


title: vdrko_2

description: Genisphere Flashtag


title: wt_7

description: Genisphere Flashtag


title: wt_8

description: Genisphere Flashtag


title: S_19


title: Hep3B_hypoxia_48hr_rep3

source_name: Hep3B, 48hr, hypoxia, replicate 3


title: batch2_Enzalutamide-3_S6

source_name: Prostate Cancer Patient Derived Explant (PDX)

value: Enzalutamide


title: Hep3B_normoxia_48hr_rep2

description: The expression of human lncRNAs and protein-coding transcripts in Hep3B cells after 48hr normoxia culture

source_name: Hep3B, 48hr, normoxia, replicate 2

value: normoxia


title: Hep3B_normoxia_48hr_rep3

source_name: Hep3B, 48hr, normoxia, replicate 3


title: MCF-7-1-IP


title: ASR2_control_rep2

description: Biological replicate 1 of 3

value: no

value: whole organism from in vitro culture


title: S2

city: Fontenay aux roses

first: Pierre

last: Fouchet

address: 10, route du panorama

institute: CEA

description: Gene expression data from a mixture of somatic tissue

hyb_protocol: Following fragmentation, 3,6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Affymetrix® Human Gene 2.1 ST Array GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 Scanner.

data_processing: Data were normalized using RMA and statistical analysis was realized on R usin CDF file V24.

source_name: somatic tissues

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation PicoV2 protocol from 500 pg total RNA.

growth_protocol: Adult human testis biopsies

extract_protocol: Cell suspension was analysed and sorted by flow cytometry according to the side population phenotype, DNA content and the α-6 integrin, Thy-1 and β-2 microglobulin cell markers. Sorted cells were retrieved in the lysis buffer from the the RNeasy micro kit from Qiagen and RNA repared according to the manufacturer's instructions. A somatic RNA reference sample (Ctrl somatic) was prepared from a mixture of CD45-positive blood cell RNA, prepuce tissue RNA and esophageal tissue RNA.

treatment_protocol: Testicular single-cell suspensions were prepared after incubateion in a buffer containing PBS (1X) without Ca2+ and Mg2+, collagenase (final concentration, 1 mg/ml), and DNase I (final concentration, 0.02 mg/ml) for 20 minutes at 37°C.

value: ctrl somatic

value: testicular biopsy


title: wt_5

description: Genisphere Flashtag


title: Hep3B_hypoxia_48hr_rep1

source_name: Hep3B, 48hr, hypoxia, replicate 1


title: batch2_Enzalutamide-2_S5

value: Prostate Cancer Patient Derived Explant (PDX)


title: S_18

value: Immature

value: Monilinia laxa Inoculated


title: batch2_Enzalutamide-1_S4


title: S_17


title: wt_4

description: Genisphere Flashtag


title: wt_6

description: Genisphere Flashtag


title: S_15


title: HSG-8_Ovarian granulosa cells

city: Qingdao

first: Yong

last: Zhao

address: 700 Changcheng Road

institute: Qingdao Agricultural University

description: The group information is prefixed with HSG-8 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: ARS1

source_name: HSG-8_Ovarian granulosa cells

tag: breed

value: Ji'ning grey goat

value: Ovarian granulosa cells

value: HSG


title: batch2_Docetaxel-3_S18

value: Docetaxel


title: S_14

value: Healthy


title: wt_3

description: Genisphere Flashtag

value: wild-type


title: S_13


title: batch2_Docetaxel-2_S17


title: S20

description: Gene expression data from 2N

source_name: flow sorted adult germinal cells

value: Mixture of CD45-positive blood cell RNA, prepuce tissue RNA and esophageal tissue RNA


title: S21

description: Gene expression data from N

value: N


title: wt_1

description: Genisphere Flashtag


title: wt_2

description: Genisphere Flashtag


title: S_12


title: S18

description: Gene expression data from B2M-SPa6medThy-1-Sphase


title: S1


title: batch2_Docetaxel-1_S16


title: S19


title: batch2_Control-Enza-3_S3

value: Control-Enza


title: S17

description: Gene expression data from N


title: Hep3B_normoxia_48hr_rep1

source_name: Hep3B, 48hr, normoxia, replicate 1

value: hepatocellular carcinoma

value: normoxia


title: batch2_Control-Enza-2_S2


title: S_10


title: S_8


title: batch2_Control-Chemo-3_S9

value: Control-Chemo


title: S_7


title: batch2_Control-Chemo-2_S8


title: S15

description: Gene expression data from 2N


title: batch2_Control-Chemo-1_S7


title: WT_2_1

city: Nagoya

first: Chieko

last: Sugita

state: Aichi

address: Chikusa-ku Furo-cho

department: Center for Gene Research

country: Japan

institute: Nagoya University

description: Gene expression of WT protonema cells

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >16.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Sure Scan using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent) using default parameters (protocol GE1-1105_Oct12 and Grid: 084494_D_F_20161121) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Physcomitrium patens

source_name: 4 day old WT protonemata

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick-Amp WT Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: protonemal tissue was grown on cellophane-overlaid BCD media supplemented with 50mM ammonium tartarate  and 0.5% glucose under continuous light (30 micromole photons m-2 sec-1)at 25ºC

extract_protocol: Total cellular RNA was extracted with Isogen II (Nippon gene), purified with phenol/chloroform/isoamyl alcohol, and treated with DNase I (TaKaRa).

value: wild type

value: protonemata


title: WT_1_1

description: Gene expression of WT protonema cells


title: S14

description: Gene expression data from N

value: testicular biopsy


title: S_6

source_name: Inoculated fruit

value: Immature


title: 31KO12_1_4

description: Gene expression of 31KO-12 protonema cells

source_name: 4 day old 31KO-12 protonemata

value: PpPPR_31 Knock OUT mutant #12


title: S16


title: 31KO14_2_4

description: Gene expression of 31KO-14 protonema cells

source_name: 4 day old 31KO-14 protonemata

value: PpPPR_31 Knock OUT mutant #14


title: S12

description: Gene expression data from B-2M-SPa6medThy-1-


title: 5ng RNA input rep2

city: chongqing

first: peng

last: zhou

address: 重庆市大渡口区天安数码城5栋10层

institute: First Affiliated Hospital of Army Medical University

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 mm8 whole genome using Hisat2 v2.1.0 with parameters -p 16
Use featurecount to calculate the count to each gene
Genome_build: mm20
Supplementary_files_format_and_content: tab-delimited text files include row count values for each Sample

source_name: 5ng RNA

extract_protocol:
RNA was isolated from different number of  cell samples  by using the Direct-zolTM RNA MiniPrep Kit
The qualified RNA samples were added with 1 µl of SuperScript III reverse transcriptase, 4 µl of Superscript III first strand synthesis buffer , 1 µl of dNTP mixture, 1 µl of Oligo 30 (dT) primer , 1 µl of RNase inhibitor and 1 µl of DTT (0.1M) to construct 20 µl reaction system for RNA reverse transcription by heating the mixtures for 50 ℃ for 90 min, 70 ℃ for 15min, and a final hold at 4 ℃. For second strand cDNA synthesis, the 20 µl products of reverse transcription were directly mixed into reaction buffer on ice to obtain dsDNA samples with the help of DNA polymerase I and T4 DNA ligase, following the manufacturer’s recommendations . dsDNA products obtained from the synthesis were purified with 144 µl (1.8 ×) of Agencourt AMPure XP Beads  through magnetic separation. The purified dsDNA samples were then dissolved into nuclease-free water and diluted to 1 ng/µl following Qubit 2.0 measurement . 1 ng of dsDNA, and 4 µl of 5 × TTBL and 5 µl of TTE Mix V1 were used to in the Tn5 tagmentation reaction system. Reaction was performed for 10 mintues at 55℃ and quenched with 5 µl of pre-mixed 5 × TS to avoid excessive DNA fragmentation. Samples were then barcoded following the protocol of TruePrep DNA Library Prep Kit for Illumina with P5/P7 adapter primers , and amplicon purified via the VAHTSTM DNA clean beads kit.

tag: strain

tag: age


title: batch2_Cisplatin-3_S12

value: Prostate Cancer Patient Derived Explant (PDX)

value: Cisplatin


title: 1ng RNA input rep3

address: 重庆市大渡口区天安数码城5栋10层

source_name: 1ng RNA


title: batch2_Cisplatin-2_S11


title: S10

description: Gene expression data from 2N


title: 1ng RNA input rep2

address: 重庆市大渡口区天安数码城5栋10层


title: 5ng RNA input rep3

address: 重庆市大渡口区天安数码城5栋10层


title: 1ng RNA input rep1

address: 重庆市大渡口区天安数码城5栋10层


title: 0.5ng RNA input rep3

address: 重庆市大渡口区天安数码城5栋10层

source_name: 0.5ng RNA


title: 0.5ng RNA input rep1

address: 重庆市大渡口区天安数码城5栋10层


title: batch1_Patient-Tumor-2_S14

source_name: TUMOR

value: TUMOR

value: Patient-Tumor


title: batch1_Patient-Tumor-3_S15


title: 5ng RNA input rep1

address: 重庆市大渡口区天安数码城5栋10层


title: 0.5ng RNA input rep2

address: 重庆市大渡口区天安数码城5栋10层


title: S7

description: Gene expression data from 4N


title: batch1_Patient-Tumor-1_S13


title: S11

description: Gene expression data from 4N


title: batch1_Enzalutamide-3_S6

value: Enzalutamide


title: S9

description: Gene expression data from B-2M-SPa6+Thy-1+


title: S13


title: 25_S_japonica_1

city: Gimcheon

first: Mohammad

last: Vatanparast

address: 167, Yongjeon-ro

department: Plant quarantine technology center

country: South Korea

institute: Animal and Plant Quarantine Agency

data_processing:
HiSeq 4000 System (Illumina, San Diego, USA) used for basecalling.
Quality-filtered and adapter-trimmed using Trimmomatic v0.38. FastQC v0.11.7 was used to check data quality before and after trimming. de novo transcriptome assembly was performed using Trinity version trinity rnaseq r20140717, bowtie 1.1.2. Trinity groups transcripts into clusters based on shared sequence content. For assembled genes, longest contigs of the assembled contigs are filtered and clustered into the non-redundant transcripts using CD-HIT version 4.6. ORF prediction for unigenes was performed using TransDecoder version 3.0.1. For the differentially expressed gene analysis, the abundances of unigenes across samples were estimated into read count as an expression measure by RSEM algorithm (RSEM version v1.2.29, bowtie 1.1.2.
Unigenes were searched against Kyoto Encyclopedia of Genes and Genomes (KEGG) v20190104 (http://www.genome.jp/kegg/ko.html), NCBI Nucleotide (NT) v20180116 (https://www.ncbi.nlm.nih.gov/nucleotide/), Pfam v20160316 (https://pfam.xfam.org/), Gene ontology (GO) v20180319 (http://www.geneontology.org/),  NCBI non-redundant Protein (NR) v20180503 (https://www.ncbi.nlm.nih.gov/protein/), UniProt v20180116 (http://www.uniprot.org/), and EggNOG (http://eggnogdb.embl.de/) using BLASTN of NCBI BLAST and BLASTX of DIAMOND version 0.9.21 (https://github.com/bbuchfink/diamond) with an E-value default cutoff of E-value 10-5.
Significant unigene results were analyzed as Up and Down-regulated count by FC ≥ 2, ≤ -2, distribution of expression level between two groups was plotted as Volcano plot and simple bar plots.
The twenty genes in response to cold treatment (9_S_japonica) were chosen for validation using qRT-PCR. To do that, S. japonica adults were incubated at 9 and 25°C in two separated group including 10 ants, for 24 h.
Genome_build: merge_Trinity_Unigene.fasta
Supplementary_files_format_and_content: read counts, FPKM values etc, for each Sample

organism: Solenopsis japonica

growth_protocol: Ant colonies were maintained at 25±1℃. Each test colony plastic trays were placed in larger holding trays. Talcum powder was dusted on 10 cm top edge of the trays and in the bottom of the larger holding trays so that any ants escaping would not happen and would not interfered other test colonies. Ants were fed with 20% sucrose solution and mealworm (Tenebrio molitor larvae) and an artificial diet

extract_protocol:
RNAs samples were extracted from whole body of S. japonica adults using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instruction. After RNA extraction, it was resuspended in nuclease-free water and quantified using a spectrophotometer (NanoDrop, Thermo Scientific, Wilmington, DE, USA). cDNA was then synthesized from RNA (1 μg) using RT PreMix (Intron Biotechnology, Seoul, Korea) containing oligo dT primer according to the manufacturer's instruction. After RNA extraction, it was resuspended in nuclease-free water and quantified using a spectrophotometer (NanoDrop, Thermo Scientific, Wilmington, DE, USA). cDNA was then synthesized from RNA (1 μg) using RT PreMix (Intron Biotechnology, Seoul, Korea) containing oligo dT primer according to the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To perform transcriptomic analysis medium workers were incubated at 9 and 25℃ for 24 h as the temperature treatment groups. Incubated ants at 25℃ were considered as control group.

value: Fire ant

value: Whole body

value: Adult ant

value: Wild type


title: S6


title: MCF7-3

city: Shenyang

first: Ming

last: Zhang

state: China

address: Department of Pharmacology, School of Pharmacy

institute: China Medical University

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm.

source_name: BRCA_ADR sensitive

label_protocol: The total RNA was reverse transcribed into double stranded cDNA, and then the cDNA labeled with Cyanine-3-CTP (Cy3) was synthesized. The labeled cRNA was hybridized with the chip.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

value: breast cancer (BRCA) cell line

tag: phenotype

value: ADR sensitive


title: S8


title: 0.1ng RNA input rep2

address: 重庆市大渡口区天安数码城5栋10层

source_name: 0.1ng RNA


title: MCF7-2


title: S5


title: S4

description: Gene expression data from 4N


title: MCF7-1


title: 9_S_japonica_1

value: 9℃


title: MCF7_Adr-3

source_name: BRCA_ADR resistant

value: ADR resistant


title: MCF7_Adr-2


title: batch2_Cisplatin-1_S10

source_name: Prostate Cancer Patient Derived Explant (PDX)


title: batch1_Enzalutamide-2_S5


title: MCF7_Adr-1


title: 0.1ng RNA input rep1

address: 重庆市大渡口区天安数码城5栋10层


title: Nutlin_Peg6_exp2_rep3

city: Boulder

first: Dylan

last: Taatjes

state: CO

address: 3415 Colorado Ave JSC Biotechnology Building Campus Box 596

department: Biochemistry

institute: University of Colorado at Boulder

description: RNA-seq from HCT116 cells

data_processing:
Read trimming using bbduk (options: ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=25 tpe tbo literal=AAAAAAAAAAAAAAAAAAAAAAA)
Reads were mapped to hg38 using hisat2 (options: --very-sensitive)
Reads over hg38 refseq gene annotations were counted using bedtools multibamcov and then RPKM normalized.
Highest average RPKM isoform (across replicates and treatments) was retained in cases where multiple isoform annotations existed
Batch correction performed using limma removeBatchEffect function where batch corresponded to replicate number
Genome_build: hg38

source_name: wild type HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy's media (Gibco, 16600082) with Gibco 100x Antibiotic-Antimycotic (Fisher Sci, 15240062) penicillin-streptomycin and 10% fetal bovine serum (FBS) supplementation.

extract_protocol:
To isolate the nuclei, cells were resuspended in 10 mL lysis buffer (10 mM Tris-HCl, pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol) and thoroughly mixed. The nuclei were then spun down at 1,000xg for 10 minutes, the lysis buffer was removed and 1 mL of TRIzol was added. The RNA was isolated as described in the TRIzol instructions, except an additional phenol/chloroform extraction and chloroform only extraction were performed to reduce contaminants that would negatively affect qPCR. RNA was precipitated and washed twice with 75% ethanol to further remove contaminants. The RNA was then converted to cDNA using the High Capacity cDNA kit from Thermo Fisher Scientific and qPCR was performed with the SYBR Select Mast Mix from Applied Biosystems.
Protocol for NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420S) was used in combination with NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (E6310L)

treatment_protocol: Cells were then trypsinized, washed with PBS and resuspended in 150 µL Neon Buffer R.  The cells were then split into three groups:  No peptide, 1 µM peptide and 10 µM peptide.  The cells were then drawn into a 10 µL Neon pipet tip, electroporated and ejected into 2 mL of McCoy’s 5A media without antibiotic.  For each peptide concentration, two cell electroporations went into media containing either 0.1% DMSO or 0.1% DMSO and 10 µM Nutlin-3a.  For wells containing cells electroporated with peptide, an additional 200 nM peptide was added to allow for peptide uptake during p53 target gene expression.  The 6-well plates of cells were then placed back at 37 °C for 3 hours.

value: colorectal carcinoma

value: 10uM Nutlin3a + 10uM bivalent peptide

tag: treatment delivery method

value: electroporation with neon transfection system invitrogen


title: batch1_Enzalutamide-1_S4


title: Smal RNA library from H.bakeri EVs following size exclusion + polyphosphatase

city: Edinburgh

first: Amy

last: Buck

address: Ashworth Labs, Charlotte Auerbach Road

institute: The University of Edinburgh

description:
small RNAs
Hb_F3_Pp

data_processing:
Sequence quality using FastQC
Adapters were removed using cutadapt
Genome alignments of sequences using bowtie to the host genome mus musculus (version GRCm38, with additional RefSeq rRNA, as all mouse rRNA genes are not present in the genome) and  T. muris (GCA_000612645.2) requiring perfect matches.
miRNAs were predicted using miDeep2 v2.0.0.8 utilizing sequences from miRBase v22 and additional nematode miRNA sequences from Brugia pahangi.
RNA biotypes were identified using the genome version PRJEB126 TMUE3.0  downloaded from WormBase ParaSite, miRNA identified as above, rRNA using cmsearch from the infernal [v1.1.2], (Friedländer et al., 2012); rRNAs using cmsearch from the infernal [v1.1.2] (Nawrocki et al., 2013) suite to search for eukaryotic rRNAs using covariance models from Rfam [version 14.1], tRNAs using tRNA-scan-SE [v1.1.1], snRNA, protein-coding exons, and protein-coding introns were extracted from publicly available GFF3 annotation on WormBase ParaSite genome PREJEB126.

source_name: Secretion product

extract_protocol:
Qiagen miRNeasy mini kit
CleanTag small RNA library prep kit, 18 PCR cycles

tag: product type

value: Extracellular vesicle

tag: developmental stage

value: Adult parasites


title: Smal RNA library from H.bakeri EVs following size exclusion

description:
small RNAs
Hb_F3_Un


title: batch1_Docetaxel-3_S18

value: Prostate Cancer Patient Derived Explant (PDX)

value: Docetaxel


title: Nutlin_Peg6_exp2_rep2

description: RNA-seq from HCT116 cells


title: e4cell input rep3

address: 重庆市大渡口区天安数码城5栋10层

source_name: 10000 cells

value: spleen T cell


title: e4cell input rep2

address: 重庆市大渡口区天安数码城5栋10层


title: batch1_Docetaxel-2_S17


title: Nutlin_Peg6_exp2_rep1

description: RNA-seq from HCT116 cells


title: e4cell input rep1

address: 重庆市大渡口区天安数码城5栋10层


title: e3cell input rep3

address: 重庆市大渡口区天安数码城5栋10层

source_name: 1000 cells


title: batch1_Control-Enza-3_S3

value: Control-Enza


title: Nutlin_H2O_exp2_rep3

description: RNA-seq from HCT116 cells

value: 10uM Nutlin3a + water


title: batch1_Docetaxel-1_S16


title: Nutlin_H2O_exp2_rep2

description: RNA-seq from HCT116 cells


title: e3cell input rep2

address: 重庆市大渡口区天安数码城5栋10层


title: S3

source_name: somatic tissues

value: ctrl somatic

value: testicular biopsy


title: e3cell input rep1

address: 重庆市大渡口区天安数码城5栋10层


title: batch1_Control-Enza-1_S1


title: Monocytes, breast cancer bone metastasis, JWP41

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

description: Gene expression data from monocytes sorted from breast cancer bone metastasis

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array according to manufacturers recommendations.

scan_protocol: Scanning was performed according to manufacturers recommendations.

data_processing:
Data were processed and normalized using the oligo package. Annotation information was obtained from the Bioconductor MoGene 2.0 transcript cluster database and Affymetrix control probes were removed from the annotation and the transcript cluster data.
Normalized expresssion values. Mouse gene symbols are given. Mean expression was used for multiple probes.

source_name: Bone metastasis from mice bearing MetBo2 breast cancer bone metastasis

label_protocol: cDNAs were labelled with biotin.

growth_protocol: MetBo2 is a selected bone homing clone of murine breast cancer cell line Met-1, which derived from Polyoma Middle T Oncoprotein (PyMT) tumour previously. Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco) and 1% penicillin-streptomycin (P/S) (Gibco). Cells were maintained at 37°C with 5% CO2 in incubator.

extract_protocol: Bone marrow macrophages and Ly6C+ inflammatory monocytes from mice bearing MetBo2 bone metastasis  and  from healthy bone marrow.  Total RNA was extracted from these sorted cells using RNeasy Mini kit (QIAGEN),  and their quality were determined using Pico Chip with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Bone metastasis was generated through intra-cardiac injection of 1x105 tumour cells into 4-week-old female mice of respective strains described above. Mice were not treated.

value: breast cancer bone metastasis

tag: sorted cell type

value: Monocytes


title: DMSO_Peg6_exp2_rep3

description: RNA-seq from HCT116 cells

value: 0.1% DMSO + 10uM bivalent peptide


title: Nutlin_H2O_exp2_rep1

description: RNA-seq from HCT116 cells


title: Monocytes, breast cancer bone metastasis, JWP39


title: DMSO_Peg6_exp2_rep2

description: RNA-seq from HCT116 cells


title: batch1_Control-Chemo-2_S8

value: Control-Chemo


title: 500cells input rep1

address: 重庆市大渡口区天安数码城5栋10层

source_name: 500 cells


title: batch1_Control-Chemo-1_S7


title: Monocytes, breast cancer bone metastasis, JWP42


title: Monocytes, breast cancer bone metastasis, JWP38


title: batch1_Control-Chemo-3_S9


title: DMSO_Peg6_exp2_rep1

description: RNA-seq from HCT116 cells


title: 100cells input rep3

address: 重庆市大渡口区天安数码城5栋10层

source_name: 100 cells


title: batch1_Cisplatin-3_S12

value: Cisplatin


title: DMSO_H2O_exp2_rep3

description: RNA-seq from HCT116 cells

value: colorectal carcinoma

value: 0.1% DMSO + water


title: Monocytes, healthy bone, JWP36

description: Gene expression data from monocytes sorted from healthy bone marrow

source_name: Healthy bone from mice

value: healthy bone


title: Monocytes, healthy bone, JWP35


title: batch1_Control-Enza-2_S2


title: DMSO_H2O_exp2_rep2

description: RNA-seq from HCT116 cells

value: electroporation with neon transfection system invitrogen


title: Monocytes, healthy bone, JWP33


title: 100cells input rep2

address: 重庆市大渡口区天安数码城5栋10层


title: Monocytes, healthy bone, JWP32


title: 500cells input rep3

address: 重庆市大渡口区天安数码城5栋10层


title: batch1_Cisplatin-2_S11


title: Monocytes, healthy bone, JWP31


title: 500cells input rep2

address: 重庆市大渡口区天安数码城5栋10层


title: DMSO_H2O_exp2_rep1

description: RNA-seq from HCT116 cells


title: batch1_Cisplatin-1_S10


title: Nutlin_Peg6_exp1_rep2

description: RNA-seq from HCT116 cells

value: 10uM Nutlin3a + 10uM bivalent peptide


title: Macrophages, breast cancer bone metastasis, JWP30

description: Gene expression data from macrophages sorted from breast cancer bone metastasis

value: Macrophages


title: Nutlin_Peg6_exp1_rep1

description: RNA-seq from HCT116 cells


title: Nutlin_H2O_exp1_rep2

description: RNA-seq from HCT116 cells


title: Nutlin_H2O_exp1_rep1

description: RNA-seq from HCT116 cells


title: DMSO_Peg6_exp1_rep2

description: RNA-seq from HCT116 cells


title: 2505NFA

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For subsequent adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_06 was used.
Cleaned read sequences were aligned with STAR version 2.5.4a
Read counting for exonic regions was performed with subread featureCounts version 1.6.0.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count data in featureCounts default output format, see description at http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

source_name: ishikawa cells

growth_protocol: A well differentiated endometrial carcinoma cell line (Ishikawa cells, ECACC #99040201, Sigma Aldrich) was cultured in a humidified atmosphere of 5% CO2 at 37 ºC in Dulbecco’s modified Eagle’s medium F-12 (DMEM: F12) phenol free supplemented with 10% (v/v) FBS, 1% antibiotic/antimycotic solution and 0.25% L-Glutamine (Invitrogen, Germany), which was replenished every 48h.   Cells were passaged when the confluency reached at 80%. When performing experiments, cells were cultured in DMEM: F12 phenol free supplemented with 2% (v/v) FBS, 0.25% L-Glutamine and 1% antibiotic/antimycotic solution overnight. .

extract_protocol:
Total RNA samples were extracted by using miRNeasy Mini kit (QIAGEN, Germany) according to the manufacturer’s protocol. RNA concentration and quality were measured by using a Nanodrop (Eppendorf µCuvette® G1.0, Microvolume measuring cell for Eppendorf BioPhotometer® and BioSpectrometer®, Eppendorf, Germany). RNA quality was assessed with an Agilent 2100 Bioanalyzer system. Samples with high RNA integrity number >8 were selected for library construction.
Sequencing libraries have been prepared with New England Biolabs NEBNext Ultra II Directional RNA Library Prep following the manufacturer's handbook.

treatment_protocol: Ishikawa cells were plated in 6-well plates at a density of 200,000 cells per well in 2% (v/v) FBS, 0.25% L-Glutamine and 1% antibiotic/antimycotic solution . Ishikawa cells were transfected with plasmid DNA (11ng/ul) encoding human NFAT5 in pcDNA6V5-HisC vector or empty vector plasmid by using VIROMER RED (#230155, Biozym, Germany) according to the manufacturer’s protocol for 24h.

tag: transfection


title: Macrophages, breast cancer bone metastasis, JWP29

tag: tissue


title: DMSO_Peg6_exp1_rep1

description: RNA-seq from HCT116 cells

tag: cell line


title: 100cells input rep1

address: 重庆市大渡口区天安数码城5栋10层


title: Macrophages, breast cancer bone metastasis, JWP27


title: DMSO_H2O_exp1_rep2

description: RNA-seq from HCT116 cells


title: Macrophages, breast cancer bone metastasis, JWP28


title: 2704NFA


title: 2505Cont

value: control


title: Macrophages, breast cancer bone metastasis, JWP26