title: B1240201G_MDCF1_Baseline

value: Male


title: BRCA2_156_TCF7

status: Public on Aug 20 2019

type: SRA

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: TCF7 ChIPseq of breast organoids from BRCA2 mutation carrier

library_source: genomic

data_processing:
ChIPseq aligher, bowtie
ChIPseq peak call, macs2 2.1.1.20160309
motif, homer
CNV analysis, true
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts matrix, BED format

molecule: genomic DNA

organism: Homo sapiens

source_name: breast organoids

extract_protocol:
phenol-chloroform extraction for ChIP DNA
Rubicon ThruPLEX DNA-seq Kit

tag: gender

value: female

tag: tissue

value: breast organoids

tag: genotype/variation

value: BRCA2 mutation

tag: antibody


title: H15D2

city: Wuhan

first: Hong

last: Meiyan

state: Hubei

address: Xudong 2nd Road

department: Oil Crops Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
Sequencing-received raw image data were transformed by base calling into sequence data. Low quality reads and reads with adaptors or N% more than 5% were removed before data analysis using the FastQC tool
After filtering, the remaining high-quality reads “clean reads” stored in FASTQ were used for statistical analyses. The clean reads were then mapped to the Zea mays genome using the TopHat2 tool
The genomic localization results of all sequencing reads data were assembled with the cufflinks package, and then were compared to the known genetic models in order to identify any new genes and alternative splicing events using the cuffcompare package
New genes were aligned by BLASTX (E-value <1e−5) to the NCBI nonredundant, GO (http://www.geneontology.org/), Swiss-Prot (http://www.ebi.ac.uk/uniprot/), KOG (http://www.ncbi.nlm.nih.gov/COG/), and KEGG (Kyoto Encyclopedia of Genes and Genomes; http://www.genome.jp/kegg/) protein databases to annotate the functions.
The gene expression level was determined according to the number of fragments per kilobase of exon per million fragments mapped (RPKM).
Genome_build: B73_RefGen_v4
Supplementary_files_format_and_content: excel file include RPKM values for all Samples

molecule: total RNA

organism: Zea mays

source_name: embryo

extract_protocol:
developing seeds were collected manually at 15-, 20-, 25-, 30-, 35- and 40-DAP in triplicate. Seeds were soaked in water overnight at room temperature and embryos were then dissected from their endosperm and frozen immediately using liquid nitrogen and stored at -80 °C until use.
Thirty six libraries representing the embryos from the two genotypes collected at six developmental stages and in three replicates were constructed for transcriptome sequencing. Total RNA was extracted using a TIANGEN RNA Prep Pure Plant kit (Tiangen Biotech Co. Ltd, Beijing, China), and purified with the Dynabeads® Oligo (dT)25 kit (Life, USA). RNA concentration was measured using nanodrop spectrophotometer (Nanodrop Technologies, USA) and integrity was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The cDNA library was constructed by using a NEBNext® Ultra RNA Library Prep Kit, the quality of retrieved cDNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Finally, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Sequencing was perfomed using an Illumina HiSeq™ 2500 paired-end sequencing system.

tag: line

value: high oil content

tag: developmental stage

value: 15 days after pollination

value: embryo


title: H15D3


title: B187c

city: Cincinnati

first: Zhenhua

last: Luo

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The RNA-seq reads were aligned to the human genome (GRCh37/hg19) using TopHat (version 2.1.0)
Transcript quantifications were performed by Cufflinks v2.2.1
Transcript abundances were normalized in reads per kilobase of exon per million mapped reads (RPKM) for single end RNA-seq and fragments per kilobase of exon per million mapped reads (FPKM) for paired end RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM or FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated from liver biopsies using the miRNeasy Kit (QIAGEN). RNA purity was assessed using the Agilent 2100 Bioanalyzer. Total RNA was converted to cDNA using High-Capacity cDNA Reverse Transcrition Kit (ABI).
The cDNA was then used for Illumina sequencing library preparation by TruSeq Stranded mRNA Library Prep Kit. DNA fragments were further end repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls and adapters were ligated for single end or paired end sequencing on Illumina HiSeq 2500.

tag: disease state

value: Biliary Atresia

value: Liver


title: B186


title: B188c


title: B1240202G_MDCF1_Treatment

type: protein

city: St. Louis

first: Jeanette

last: Gehrig

state: Missouri

address: 4515 McKinley

institute: Washington University School of Medicine

hyb_protocol: Following the manufacturer’s protocol and utilizing SOMAmer reagents immobilized on streptavidin beads, proteins from plasma samples were tagged with NHS-biotin reagent, captured as a SOMAmer reagent/protein complex, cleaved, denatured, eluted and hybridized to a custom Agilent DNA microarray. Additional details can be found at http://www.tandfonline.com/doi/abs/10.1586/erm.10.89 and Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

scan_protocol: Microarrays were scanned with an Agilent SureScan scanner at 5 um resolution, and the Cy3 fluorescence readout was quantified. Additional information can be found in Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

data_processing: Raw signal values were processed using Somalogic's SOMAscan standardization procedures, including hybridization normalization, plate scaling, median scaling, and final somamer calibration as described in http://www.tandfonline.com/doi/abs/10.1586/erm.10.89.

molecule: protein

source_name: non-fasted plasma

extract_protocol: Non-fasting venous blood was collected into EDTA-coated tubes, spun, separated into plasma, aliquoted and snap-frozen at -80C until sample processing.

treatment_protocol: Non-fasting plasma collected in EDTA-coated tubes

tag: group

tag: age

tag: wlz

tag: waz

tag: laz


title: B1238202G_MDCF1_Treatment

label_protocol: Following the manufacturer’s protocol and utilizing SOMAmer reagents immobilized on streptavidin beads, proteins from plasma samples were tagged with NHS-biotin reagent, captured as a SOMAmer reagent/protein complex, cleaved, denatured, eluted and hybridized to a custom Agilent DNA microarray. Additional details can be found at http://www.tandfonline.com/doi/abs/10.1586/erm.10.89 and Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.

value: Female


title: B1238201G_MDCF1_Baseline


title: BRCA1_448_TCF7

description: TCF7 ChIPseq of breast organoids from BRCA1 mutation carrier

value: BRCA1 mutation


title: BRCA1_201_TCF7


title: Tumor_STm_3

city: Bethesda

first: Daniel

middle: L

last: Kastner

state: MD

address: 9000 Rockville Pike

department: NHGRI

institute: NIH

data_processing:
Sequenced reads were mapped against the mouse reference genome (mm10) using TopHat, and gene expression was quantified by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

organism: Mus musculus

source_name: Colon tumor

growth_protocol: C57B6/J mice were given one i.p. injection of AOM (10 mg/kg, Sigma) in the afternoon. The following day, mice were given DSS (1%, MW 35 000-50 000, MP Biochemicals) in the drinking water for 5 days, followed by 16 days normal water. 2 more doses of DSS (1%) were given for 5 day periods. After the 3rd DSS dose, mice recovered for 1 to 2 weeks before starting the STm∆aroA treatment.

extract_protocol:
Qiagen RNeasy Mini kits
TruSeq RNA Library Prep Kit v2

value: Colon tumor


title: Tumor_STm_4


title: B184


title: B1235201G_MDCF1_Baseline


title: B1235202G_MDCF1_Treatment


title: N296_B2_H3K27ac

description: H3K27ac ChIPseq of breast organoids from BRCA2 mutation carrier

data_processing:
ChIPseq aligher, bowtie
ChIPseq peak call, macs2 2.1.1.20160309
motif, homer
CNV analysis, true
Genome_build: hg19
Supplementary_files_format_and_content: Peak calls in BED format

extract_protocol:
RNeasy Mini Kit for RNA extraction, phenol-chloroform extraction for ChIP DNA
Kapa mRNA Hyper Pepe Kit, Rubicon ThruPLEX DNA-seq Kit

tag: cell type


title: B182


title: Tumor_STm_2


title: B181


title: N274_B2_H3K27ac


title: Tumor_STm_1


title: N293_B1_H3K27ac

description: H3K27ac ChIPseq of breast organoids from BRCA1 mutation carrier


title: B18


title: Tumor_NonTreat_4


title: Tumor_NonTreat_3


title: B175


title: B178


title: Tumor_NonTreat_2


title: B173


title: B1234201G_MDCF1_Baseline


title: N250_INPUT

description: Input DNA of breast organoids from normal (control) woman

value: normal (control)

value: none (input)


title: N250 (CD10+CD44+)

data_processing:
RNA-Seq aligner, STAR 2.5.1b
read counts , HTSeq framework (version 0.6.1p1)
Differentially expressed genes, R studio (version 3.3.3), DEseq2
PCA and heatmap, R studio (version 3.3.3)
Gene set enrichment and pathway analysis, Metacore (Thomson Reuters)
ChIPseq aligher, bowtie
ChIPseq peak call, macs2 2.1.1.20160309
motif, homer
CNV analysis, true
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts matrix, BED format

source_name: CD10+CD44+ cells of breast organoids from nulliparous woman

tag: parity

tag: subtype

value: normal reduction

value: CD10+CD44+ cells of breast organoids


title: Tumor_NonTreat_1


title: B1230201G_MDCF1_Baseline


title: B1230202G_MDCF1_Treatment


title: B1219202G_MDCF1_Treatment


title: N250 (CD10+CD44-)

source_name: CD10+CD44- cells of breast organoids from nulliparous woman

value: CD10+CD44- cells of breast organoids


title: B1219201G_MDCF1_Baseline

value: Male


title: DCIS17

source_name: CD10+ cells from human DCIS samples

value: DCIS

value: CD10+ cells


title: B170c


title: B169


title: Normal_STm_3

source_name: Colon epithelium

value: Colon epithelium


title: Normal_STm_4


title: B1218202G_MDCF1_Treatment


title: B1234202G_MDCF1_Treatment


title: DCIS15


title: N250_N_H3K27ac

description: H3K27ac ChIPseq of breast organoids from normal (control) woman

value: breast organoids


title: B1218201G_MDCF1_Baseline


title: B168c


title: Normal_STm_2


title: DCIS280

value: CD10+ and Epcam


title: B1215202G_MDCF1_Treatment


title: B162


title: Normal_STm_1


title: DCIS274


title: B161


title: Normal_NonTreat_5


title: B160


title: B1205202G_MDCF1_Treatment


title: B1215201G_MDCF1_Baseline


title: N296

source_name: CD10+ cells of breast organoids from BRCA2 mutation carrier

tag: mutation

value: normal prophylactic

value: CD10+ cells of breast organoids


title: B157

value: Biliary Atresia

value: Liver


title: B159


title: N280


title: Normal_NonTreat_4


title: Normal_NonTreat_2


title: B15


title: Normal_NonTreat_3


title: Normal_NonTreat_1


title: B1205201G_MDCF1_Baseline

value: Female


title: B1203201G_MDCF1_Baseline


title: N279


title: TET2RTCF7_Dox_D5_3_LD4601_S21

source_name: MCF10DCIS cells with Doxycycline-inducible TCF7 overexpression following 5 days of Doxycycline treament

tag: treatment

value: Dox

tag: expression vector

tag: days

value: MCF10DCIS cells


title: B147

tag: tissue


title: A1169202G_RUSF_Treatment

tag: gender


title: TET2RTCF7_Dox_D5_1_LD4601_S19


title: B146


title: TET2RTCF7_Dox_D5_2_LD4601_S20


title: A1169201G_RUSF_Baseline


title: B145


title: TET2RTCF7_Dox_D3_3_LD4601_S18

source_name: MCF10DCIS cells with Doxycycline-inducible TCF7 overexpression following 3 days of Doxycycline treament


title: TET2RTCF7_Dox_D3_2_LD4601_S17


title: A1168202G_RUSF_Treatment


title: B142


title: TET2RTCF7_Dox_D3_1_LD4601_S16


title: MCF10DCIS_1_LD4601_S22

source_name: MCF10DCIS cells


title: A1162201G_RUSF_Baseline


title: A1162202G_RUSF_Treatment


title: A1157202G_RUSF_Treatment


title: B140


title: Salivary supernatant from healthy control, biological rep3

type: RNA

city: Beijing

first: Yuan

last: Yang

address: 8 Gongti Nanlu, Chaoyang District

institute: Beijing Chaoyang Hospital, Capital Medical University

description:
Gene expression data from salivary supernatant of MPE patients and healthy controls
Control3

hyb_protocol: 21.5 μL biotin-labeled sample were hybridized for 16 hr at 48℃ on miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol. （Affymetrix® Command Console® User Manual (P/N 702569)）

data_processing: Use Expression Console software for data summarization, normalization, and quality control.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix).

growth_protocol: Before saliva collection, all patients and healthy controls were required to avoid from eating, drinking or smoking for at least 2 hours. At least 3mL saliva was collected from each subject.

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

treatment_protocol: All samples were centrifuged at 3000 × g for 15 minutes at 4°C to get rid of the cells. Only the supernatant was transferred into a 2 mL centrifuge tube. Then, to completely remove the cellular components, a further centrifugation of 12000 × g for 10 minutes at 4°C was followed. The supernatant was transferred into a 2 mL centrifuge tube and stored at -80°C until use.

value: control

tag: sample type

value: Salivary supernatant


title: HCSA1: HCT116 cell line treated with Cyclosporine [1]

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: The standard Affymetrix hybridization protocol was used

scan_protocol: Standard Affy scanning protocol

data_processing: Standard RMA processing using Expression console

label: Biotin

label_protocol: Samples were labeled using the Affymetrix Labeling Kit as per manufacturer's protocols.

growth_protocol: SW480 and IRM90 were cultured in DMEM-F12 and HCT116 in McCoy’s 5A (Gibco), supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco) and 1% (v/v) penicillin/streptomycin (Biological Industries). All cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Exosomal RNAs were extracted using miRNeasy Mini KIT (Qiagen) according to the manufacturer’s instructions. The RNA yield and size distribution were analyzed using an Agilent 2100 Bioanalyzer with an RNA 6000 Pico kit (Agilent Technologies). Exosomal RNA concentration was measured by a Qubit® RNA HS Assay Kit (Life Technologies, Thermo Fisher Scientific Inc).

treatment_protocol: Exosomes were isolated from cells cultured in exosome-depleted FBS (Solmeglas), using sequential centrifugations at 800 g for 7 min, 2000 g for 12 min. Supernatants were filtered through 0.1 μm pore filter and ultracentrifuged (Optima L100XP, Beckman) at 100.000 g for 2 h. PBS washing step was done followed by a second ultracentrifugation.

tag: cell line


title: HCSA2: HCT116 cell line treated with Cyclosporine [2]


title: B14

tag: disease state


title: Salivary supernatant from healthy control, biological rep1

description:
Gene expression data from salivary supernatant of MPE patients and healthy controls
Control1


title: shp63_6504_DoxD5_2_LD4601_S12

source_name: MCF10DCIS cells with Doxycycline-inducible p63 knockdown following 5 days of Doxycycline treament

tag: shRNA


title: Salivary supernatant from healthy control, biological rep2

description:
Gene expression data from salivary supernatant of MPE patients and healthy controls
Control2


title: Salivary supernatant from MPE patient, biological rep3

description:
Gene expression data from salivary supernatant of MPE patients and healthy controls
MPE3

source_name: Salivary supernatant from MPE patient

value: Malignant pleural effusion (MPE)


title: Salivary supernatant from MPE patient, biological rep2

description:
Gene expression data from salivary supernatant of MPE patients and healthy controls
MPE2


title: Salivary supernatant from MPE patient, biological rep1

description:
Gene expression data from salivary supernatant of MPE patients and healthy controls
MPE1


title: shp63_6504_DoxD5_1_LD4601_S11


title: MCF10DCIS_2_LD4601_S23


title: A1168201G_RUSF_Baseline

tag: group

tag: age


title: 480UT2: SW480 cell line untreated [2]

description: SW480 cell line untreated [2]

source_name: SW480 cell line untreated


title: shp63_6504_DoxD3_2_LD4601_S10

source_name: MCF10DCIS cells with Doxycycline-inducible p63 knockdown following 3 days of Doxycycline treament


title: B137


title: B144r


title: A1152202G_RUSF_Treatment

tag: wlz

tag: waz


title: B141


title: A1152201G_RUSF_Baseline

tag: laz


title: B138


title: 480UT1: SW480 cell line untreated [1]

description: SW480 cell line untreated [1]


title: 480RA2: SW480 cell line treated with Rapamycin [2]

source_name: SW480 cell line treated with Rapamycin


title: shp63_6504_No_Dox_2_LD4601_S8

source_name: MCF10DCIS cells with Doxycycline-inducible p63 knockdown without Doxycycline treament

tag: cell type


title: B133

source_name: Liver


title: A1157201G_RUSF_Baseline

source_name: non-fasted plasma


title: A1145202G_RUSF_Treatment


title: shp63_6504_DoxD3_1_LD4601_S9


title: B132


title: 480RA1: SW480 cell line treated with Rapamycin [1]


title: B1203202G_MDCF1_Treatment


title: 480CSA2: SW480 cell line treated with Cyclosporine [2]


title: A1142202G_RUSF_Treatment


title: A1145201G_RUSF_Baseline


title: B124c


title: shp63_6504_No_Dox_1_LD4601_S7


title: 480CSA1: SW480 cell line treated with Cyclosporine [1]


title: MCF10DCIS-TetTCF7_TCF7-HA

source_name: TCF7-HA ChIPseq of MCF10DCIScells overexpressing TCF7

tag: subtype

tag: antibody


title: A1127202G_RUSF_Treatment


title: HUT 1: HCT116 cell line untreated [1]

description: HCT116 cell line untreated [1]

source_name: HCT116 cell line untreated


title: MCF10DCIS-TetTCF7_TCF7-HA_input

source_name: input for TCF7-HA ChIPseq of MCF10DCIS cells overexpressing TCF7

tag: treatment

value: input


title: B114


title: MCF10DCIS-TetTCF7_H3K27ac

source_name: H3K27ac ChIPseq of MCF10DCIScells overexpressing TCF7

tag: expression vector


title: B113


title: HUT 2: HCT116 cell line untreated [2]

description: HCT116 cell line untreated [2]


title: B116


title: A1116202G_RUSF_Treatment

value: Male


title: B111


title: HRA 2: HCT116 cell line treated with Rapamycin [2]

source_name: HCT116 cell line treated with Rapamycin


title: HRA 1: HCT116 cell line treated with Rapamycin [1]


title: MCF10DCIS_H3K27ac_input

source_name: input for H3K27ac ChIPseq of MCF10DCIS cells


title: B109


title: B107


title: N350_B2_p63

source_name: p63 ChIPseq of breast organoids from BRCA2 mutation carrier


title: A1114202G_RUSF_Treatment


title: A1116201G_RUSF_Baseline


title: A1142201G_RUSF_Baseline


title: N322_B2_p63


title: B101


title: A1114201G_RUSF_Baseline


title: B100


title: A1111202G_RUSF_Treatment


title: MCF10DCIS_H3K27ac

source_name: H3K27ac ChIPseq of MCF10DCIS cells


title: A1127201G_RUSF_Baseline


title: B10.c-B76


title: N325_B1_p63

source_name: p63 ChIPseq of breast organoids from BRCA1 mutation carrier


title: A1111201G_RUSF_Baseline


title: N323_B1_p63


title: B1


title: MCF10DCIS_p63

source_name: p63 ChIPseq of MCF10DCIS cells


title: A1110202G_RUSF_Treatment


title: 9-0573


title: A1109202G_RUSF_Treatment


title: 3_0698


title: N334_N_p63

source_name: p63 ChIPseq of breast organoids from normal (control) woman

value: Normal


title: N309_N_p63


title: A1109201G_RUSF_Baseline


title: A1110201G_RUSF_Baseline


title: 1-0463


title: N13-0047_a1

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

data_processing:
Reads were aligned to their corresponding genomes using the BWA mem algorithm (version 0.7.17) with default settings. Samtools 1.9 was used to convert and sort the output and featureCounts 1.6.3 summarized the aligned reads. Normalization and statistical calculation of differentially expressed genes was done in R with the EdegR package
Genome_build: NC_019556.1 for LL195, NZ_QYGN00000000.1 for stain N12-0605 and NZ_QYDR00000000.1 for stain N13-1507
Supplementary_files_format_and_content: a .txt file containig following collumns: Geneid;Chromosone or contig;Start;End;Strand;Length;number of counts

organism: Listeria monocytogenes

source_name: culture in BHI plus acid

growth_protocol: growth in BHI at 37 degrees unitl early stationary phase

extract_protocol:
After one hour of acid exposure, or the respective control condition in BHI without acid, all reactions were stopped by the addition of 1 ml of 10 % acid phenol-chlorophorm in ethanol (v/v) to the cultures, which were chilled to 4 ¡C immediately. To extract the total RNA, the cultures were pelleted at 20Õ000 x g at 4 ¡C, resuspended in 200 ml of 10 mM Tris-buffer (Sigma-Aldrich, Buchs, Switzerland) containing 20 mg/ml Lysozyme (Sigma-Aldrich, Buchs, Switzerland) and 50 ml of 20 mg/ml Proteinase K (Qiagen, Venlo, the Netherlands) and subsequently lysed for 30 min at 37 ¡C. Cell lysates were then mixed with 1 ml TRI-Reagent (Invitrogen by Thermo Fischer Scientific, Zug, Switzerland) and bead-beaten for 2 x 60 s with cooling on ice in between in beat-beating tubes containing 1.4 mm ceramic beads (MagNA lyser green tubes, Roche, Rotkreuz, Switzerland). Subsequently the samples were centrifuged at 16Õ000 x g at 4 ¡C and the supernatant was transferred to a new tube, where 500 ml of bromo-chloro-propane (BCP, ACROS Organics, Geel, Belgium) were added. After 10 min incubation at room temperature the tubes were centrifuged for 15 min at 16Õ000 x g at 4 ¡C and the top aqueous layer was transferred into a new tube. Nucleic acids were precipitated overnight in 2.5 ml isopropanol at -80 ¡C. The following day, nucleic acids were pelleted, washed with 5 ml 75 % ethanol, resuspended in nuclease free water and adjusted to 500 ng/ml using a nanodrop (Witec AG, Sursee, Switzerland). 3 ml Turbo DNAse (Invitrogen by Thermo Fischer Scientific, Zug, Switzerland) and its buffer were added to digest the genomic DNA for one hour at 37 ¡C, with the addition of another 3 ml Turbo DNAse after 30 min to ensure complete digestion of genomic DNA. The DNAse treatment was followed by a phenol-chloroform (Fluka, Bucharest, Romania) extraction and RNA precipitation in EtOH with 1.6% (v/v) 3M sodium acetate at -80 ¡C overnight. The RNA was pelleted and washed with 70 % ethanol, dried and resuspended in 100 ml nuclease free water. Total RNA quality was assessed by a nanodrop measurement and an Agilent 2100 Bioanalyzer pico Chip. Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Reagents (Bacteria)-Low Input and the Magnetic Core Kit-Low Input (Illumina, San Diego, USA) according to the manufacturerÕs specifications, and purified using the Agencourt RNAClean XP Kit (Beckman Coulter Inc., Brea, CA). A pico chip run on the bioanalyzer 2100 confirmed the depletion of 16S and 23S rRNA.
Library preparation was done with an Illumina TruSeq RNA stranded kit according to the manufacturers instruction. All samples were pooled and sequenced on one lane of a Novaseq (paired-end, 150bp per read) at the Functional Genomics Centre ZŸrich.

treatment_protocol: Acid stress was performed by adding anequal volume of BHI adjusted to pH 1.6 with HCl

tag: strain

value: acid


title: bone mouse Mac CTX 2

city: Cambridge

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were trimed with 8 bases in 5-prime and aligned to the human genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: bone

growth_protocol: mouse and human macrophages were sorted by flow cytometry based on expression of hCD45-F4/80+CD11b+ and hCD45+CD14+

extract_protocol:
Qiagen RNeasy Micro Kit
SMARTer Universal Low Input RNA Kit

value: macrophages

tag: patient

value: donor 2

value: CTX

tag: tissue

value: bone


title: N13-0047_1

source_name: culture in BHI


title: N293_B1_p63

value: breast organoids


title: N13-0047_a2


title: bone mouse Mac DMSO 2

value: DMSO


title: A1106201G_RUSF_Baseline

tag: gender


title: N342_N_p63


title: 4-0943

value: Biliary Atresia

value: Liver


title: spleen mouse Mac CTX 2

source_name: spleen

value: spleen


title: Sample 14: Control cy5 vs E. coli challenged cy3 for 12h

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-1 Owashi

country: Japan

institute: National Institute of Agrobiololgical Sciences

description: Dye swap of biological replicate 4 of 4 in 12h.

hyb_protocol: Hybridization was performed with 825 ng of Cy3- and Cy5-labeled cRNA with Hi-RPM Gene Expression Hybridization Kit (Agilent) at 65 ˚C for 17 h at 10 rpm.

scan_protocol: The hybridized arrays were washed with Wash Buffer Kit (Agilent) following manufacturer's instructions. Images were scanned at 5 µm resolution using Agilent DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.

organism: Nephotettix cincticeps

source_name: E. coli challenged for 12 hours

label_protocol: Each 400 ng of total RNA was labeled with Quick Amp Labeling Kit, two colour (Agilent) following manufacturer's instructions. Labeled cRNA was purified with RNeasy Mini kit.

growth_protocol: N. cincticeps Tsukuba strain were reared with rice seedlings in the laboratory at 25-26 degree and 16L-8D.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: One day adult N. cincticeps females were pricked with about 1,500 E. coli cells with a glass needle. Control adults were pricked with sterilized water. Five females were collected up to one sample. Total RNA was extracted after 3 h and 12 h incubation respectively.

value: Tsukuba

value: One day adult

source_name: Control


title: N13-0047_2

value: control


title: A1106202G_RUSF_Treatment

source_name: non-fasted plasma


title: 846_Endo_SCE

city: Jouy-en-Josas

first: Mariam

last: Raliou

address: Allée de Vilvert

department: PHASE

country: France

institute: INRAE

hyb_protocol: Labelled cRNA were hybridized on the custom bovine gene expression 8x60K array for 17 hours, centrifuge at 10 rpm for 65°C. Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 μm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.

scan_protocol: The slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 μm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.

data_processing: Raw.tiff images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE1_1010_Sep10” protocol. Median raw expression values were further normalized by quantile method

organism: Bos taurus

label_protocol: RNA labeling was performed according to Agilent protocol “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labelling” version 6.5, May 2010 (Cat # G4140-90050). Complementary RNA (cRNA) samples were linearly amplified and labelled with cyanine 3 starting from 100 ng of total RNA.

extract_protocol: Total RNAof circulating white blood cells was isolated from PAXgene blood samples using the PAXgene Blood RNA system (PreAnalytiX, Qiagen/BD Company, France). Total endometrium RNA was extracted used Qiagen Kit RNA Extraction.

tag: animal status

value: subclinical endometritis (SCE)

tag: stage of postpartum period

value: days 45-55 postpartum

value: Endometrium (Endo)


title: N13-1507_2


title: Sample 12: Control cy5 vs E. coli challenged cy3 for 12h

description: Dye swap of biological replicate 3 of 4 in 12h.


title: bone mouse Mac CTX 1

value: donor 1


title: N13-1507_a1

value: acid


title: 833_Endo_SCE


title: N13-1507_1


title: Sample 13: Control cy3 vs E. coli challenged cy5 for 12h

description: Biological replicate 4 of 4 in 12h.


title: spleen mouse Mac DMSO 2

value: macrophages


title: spleen mouse Mac CTX 1


title: LL195_a3


title: Sample 10: Control cy5 vs E. coli challenged cy3 for 12h

description: Dye swap of biological replicate 2 of 4 in 12h.


title: N13-1507_a2


title: RPTEC subject 2 stimulated with C5a (200078650017_R04C02)

type: genomic

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

description: Renal Proximal Tubular Cells stimulated by C5a

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the HiScan SQ platform using standard recommended Illumina scanner setting

data_processing: Genome Studio v1 Software

label: Cy5 and Cy3

source_name: RPTEC C5a

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from RPTEC samples using Qiagen DNeasy Kit according to standard instructions

tag: individual

value: subject 2

value: Renal Proximal Tubular Cells (RPTEC)

value: stimulated with C5a


title: LL195_a2


title: RPTEC subject 2 stimulated with C5a (200078650017_R06C01)


title: Sample 9: Control cy3 vs E. coli challenged cy5 for 12h

description: Biological replicate 2 of 4 in 12h.


title: RPTEC subject 2 basal condition (200078650017_R03C02)

description: normal Renal Proximal Tubular Cells

source_name: RPTEC

value: basal condition


title: RPTEC subject 2 basal condition (200078650017_R05C01)

description: normal Renal Proximal Tubular Cells


title: Sample 11: Control cy3 vs E. coli challenged cy5 for 12h

description: Biological replicate 3 of 4 in 12h.


title: 836_Endo_SCE


title: LL195_a1


title: 718_Endo_SCE


title: 883_Endo_Healthy

value: healthy


title: Oil and Pathogen Liver 3

city: Ocean Springs

first: Maria

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

data_processing:
Bases called using Illumina CASAVA software
Read quality assessed using Illumina FastQC software; adpater trimming performed using Trimomatic software
Reads were aligned to Larimichthys crocea genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany).
Gene expression (Transcripts per million --TPM) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany)
Genome_build: Larimichthys crocea genome (NCBI genome ID 12197)
Supplementary_files_format_and_content: CSV text files including TPM expression values

organism: Micropogonias undulatus

source_name: Liver

growth_protocol: All organisms were kept at 15 ppt salinity, 23 degrees C, and dissolved oxygen greater than 6 ppm

extract_protocol:
Qiagen RNeasy kit using manufacturer's protocols
Illumina TruSeq Stranded mRNA kit to construct polyA libraries

treatment_protocol: Oil-exposed organisms were subject to exposure for

tag: oil concentration

tag: pathogen concentration

tag: agent

value: Vibrio anguillarum


title: 850_Endo_Healthy


title: Sample 8: Control cy5 vs E. coli challenged cy3 for 12h

description: Dye swap of biological replicate 1 of 4 in 12h.

tag: age


title: Sample 6: Control cy5 vs E. coli challenged cy3 for 3h

description: Dye swap of biological replicate 3 of 3 in 3h.

source_name: E. coli challenged for 3 hours


title: Oil and Pathogen Liver 2


title: RPTEC subject 1 stimulated with C5a (200078650017_R02C01)

value: subject 1


title: Oil and Pathogen Liver 1


title: LL195_3


title: Oil Only Liver 2

value: 0 cfu/mL


title: LL195_1


title: N12-0605_a2


title: Sample 7: Control cy3 vs E. coli challenged cy5 for 12h

description: Biological replicate 1 of 4 in 12h.

value: Tsukuba


title: N12-0605_a3


title: Oil Only Liver 1


title: 841_Endo_Healthy


title: Sample 2: Control cy5 vs E. coli challenged cy3 for 3h

description: Dye swap of biological replicate 1 of 3 in 3h.

value: One day adult


title: Sample 4: Control cy5 vs E. coli challenged cy3 for 3h

description: Dye swap of biological replicate 2 of 3 in 3h.


title: N12-0605_a1


title: 833_WBC_SCE

value: Circulating white blood cells (WBC)


title: Pathogen Only Liver 3

value: 0 ug/L


title: 846_WBC_SCE

value: subclinical endometritis (SCE)

value: days 45-55 postpartum


title: 836_WBC_SCE


title: 718_WBC_SCE


title: LL195_2

value: control


title: RPTEC subject 1 basal condition (200078650017_R01C01)

description: normal Renal Proximal Tubular Cells


title: Oil Only Liver 3


title: 883_WBC_Healthy


title: Sample 8: Uninfected cy5 vs Rickettsia infected cy3

description: Dye swap of biological replicate 4 of 4.

source_name: Rickettsia-infected

treatment_protocol: N. cincticeps Tsukuba strain consist of Rickattsia infected and uninfected indivisuals. One day adult N. cincticeps females were dissected and separated into cephalothoracic region and abdomen. After PCR checked with cephalothoracic DNA, each five uninfected and Rickettsia infected N. cincticeps were extracted total RNA.

source_name: Uninfected


title: Pathogen Only Liver 2


title: Sample 5: Control cy3 vs E. coli challenged cy5 for 3h

description: Biological replicate 3 of 3 in 3h.


title: 877_WBC_Healthy


title: N12-0605_2


title: N12-0605_1


title: Pathogen Only Liver 1


title: 3MIR1: IMR90 fibroblast cell line transfected with miR-6127 [3]

data_processing: Standard RMA processing using oligo bioconductor R package(v.3.6)

growth_protocol: IRM90 were cultured in DMEM-F12 and HCT116 in McCoy’s 5A (Gibco), supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco) and 1% (v/v) penicillin/streptomycin (Biological Industries). All cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Not provided

tag: cell line


title: Control Liver 3


title: 2MIR123: IMR90 fibroblast cell line trasnfected with miR-6127 , miR-6746-5p and miR-6787-5p


title: 1MIR123: IMR90 fibroblast cell line trasnfected with miR-6127 , miR-6746-5p and miR-6787-5p


title: Sample 7: Uninfected cy3 vs Rickettsia infected cy5

description: Biological replicate 4 of 4.


title: N12-0605_3


title: apco_3

city: Hangzhou

first: Xiang

last: Zhou

state: Zhejiang

address: No. 666 Wusu

institute: Zhejiang Agricultural and Forestry University

description: Conidiobolus-infected aphids

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 assembled to contigs using Trinity v2.1.1 with parameters --seqType fq  --max_memory 44G --CPU 8 --output  --min_contig_length 500 --normalize_reads
All the contigs were annotated using blast 2.2.31 with parameters -evalue 1e-5 -num_threads 4 against NR, SwissProtein Database.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values for each Sample

organism: Conidiobolus obscurus

source_name: mycotized cadaver

extract_protocol:
cadaver samples were collected and frozen in liquid nitrogen. RNA extraction was used with the RNAiso Plus kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mycotized cadavers were harvested by conidial innoculation on alive aphids and incubation for 24-48 hours at at 24 ± 1 °C.

value: ARSEF 7217

tag: developmental stage

value: adult

tag: infected host

value: aphids

value: cadavers


title: apco_2

description: Conidiobolus-infected aphids


title: Sample 5: Uninfected cy3 vs Rickettsia infected cy5

description: Biological replicate 3 of 4.


title: bone mouse Mac DMSO 1

tag: cell type

value: macrophages

value: donor 1

value: DMSO

value: bone


title: 841_WBC_Healthy

value: healthy


title: Control Liver 1

value: 0 cfu/mL


title: Sample 4: Uninfected cy5 vs Rickettsia infected cy3

description: Dye swap of biological replicate 2 of 4.

value: Tsukuba


title: Control Liver 2


title: 850_WBC_Healthy


title: 2MIR3: IMR90 fibroblast cell line transfected with  miR-6787-5p[2]


title: apco_1

description: Conidiobolus-infected aphids


title: 1MIR3: IMR90 fibroblast cell line transfected with  miR-6787-5p[1]


title: Sample 3: Uninfected cy3 vs Rickettsia infected cy5

description: Biological replicate 2 of 4.

value: One day adult


title: co_3

source_name: in vitro liquid culture

growth_protocol: the fungus was innoculated into liquid medium of Sabouraud dextrose broth plus yeast extract and incubated for 4 days in a 150-mL flask in a shaker at 120 rev/min at 24 ± 1 °C.

extract_protocol:
fungal cultures were filtered, washed and frozen in liquid nitrogen. RNA extraction was used with the RNAiso Plus kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelium


title: Sample 6: Uninfected cy5 vs Rickettsia infected cy3

description: Dye swap of biological replicate 3 of 4.


title: 3MIR3A: IMR90 fibroblast cell line transfected with miR-6787-5p [3]


title: Oil and Pathogen Spleen 2

source_name: Spleen

value: Vibrio anguillarum


title: co_2


title: Sample 2: Uninfected cy5 vs Rickettsia infected cy3

description: Dye swap of biological replicate 1 of 4.


title: Oil and Pathogen Spleen 3


title: Oil and Pathogen Spleen 1


title: 2MIR2: IMR90 fibroblast cell line transfected with miR-6746-5p [3]


title: co_1


title: Sample 1: Uninfected cy3 vs Rickettsia infected cy5

description: Biological replicate 1 of 4.


title: Oil Only Spleen 2


title: 1MIR2: IMR90 fibroblast cell line transfected with miR-6746-5p [2]


title: 3MIR2: IMR90 fibroblast cell line transfected with miR-6746-5p [1]


title: Pathogen Only Spleen 2

value: 0 ug/L


title: Oil Only Spleen 1


title: HS_1: heat stressed pollen_rep1

city: Gainesville

first: Kevin

last: Begcy

state: Florida

address: 1535 Fifield Hall

institute: University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality trimming and filtering of resulting paired-end RNAseq reads were done using Trimmomatic v.0.35 (Bolger et al., 2014). Data quality was assessed using FastQC. Processed paired-end reads were aligned to the Zea mays reference genome sequence AGPv3 assembly using annotation release-5b+ (corresponds to Gramene AGPv3.27) and a mapping program STAR v. 2.5.2a (Dobin et al., 2013)
Read pairs aligned to exonic regions were summarized per gene using featureCounts (Liao et al., 2014). Reads overlapping with more than one feature (i.e., gene region) were excluded from the analysis. To test for presence/absence of batch effect and outliers, we performed variance stabilizing transformation (VST) of raw counts and analyzed non-merged technical replicates using R package DESeq2 (Love et al., 2014). For pairwise comparisons, differentially expressed genes were identified using DEseq2 (Anders and Huber, 2010) by analyzing the number of reads aligned to the genes. The thresholds for differential expression were set at fold change greater than 2 and P < 0.05 (after the FDR adjustment for multiple testing) for the null hypothesis.
Genome_build: Zea mays reference genome sequence AGPv3 assembly using annotation release-5b+ (corresponds to Gramene AGPv3.27)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Pollen

growth_protocol: Seeds of the maize inbred line B73 were germinated in an incubator, and then transferred in the greenhouse to pots (10 cm diameter, 10 seedlings per pot) containing a standard substrate and soil mixture (1:1, v/v). Maize B73 seedlings were transferred after three weeks to 10 liters pots in the greenhouse and gown under controlled conditions of 14 h of light at 25°C ± 2°C and 10 h of darkness at 21°C ± 2°C, and a constant air humidity of 60-65%. Supplemented light of about 20,000 LUX was provided to adjust day length duration. An automated temperature-water based irrigation system was used to supply water according to plant consumption in a time-based pre-programmed schedule. Plants were fertilized twice a week with 2% Hakaphos and monitored throughout their entire vegetative and reproductive development.

extract_protocol:
Total RNA was isolated from three biological replicates of non-stressed and heat stressed pollen using the RNA Plant Mini kit (Ambion) following the manufacturer’s instructions.
Library preparation and RNA sequencing (RNAseq) were carried out as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina HiSeq 1000 System User Guide (Illumina, Inc.), and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Kapa Biosystems, Inc.).

treatment_protocol: To apply heat stress treatments, plants at the tetrad stage of pollen development were identified using the Leaf Collar Method as described previously (Begcy and Dresselhaus, 2017), and then transferred to walking growth chambers. For heat stress, growth chamber day/night temperature conditions were set at 35/25°C and 60% humidity at 25,000 LUX during 48 h. Correspondingly, non-stressed plants were maintained under a 25/21°C day/night temperature regime and 60% humidity at 25,000 LUX. After 48 h exposure to heat stress, all plants were maintained under greenhouse conditions as described above until pollen maturation. Pollen at the tetrad stage were collected for morphological and physiological analyses from control (non-stressed) and heat stressed plants. Samples for biochemical analysis, RNA sequencing and pollen germination assays were collected upon pollen maturation

tag: inbred line

value: Mature pollen after heat stress tetrad stage


title: HS_3: heat stressed pollen_rep3


title: HS_2: heat stressed pollen_rep2


title: Wild Type2

city: Tianjin

first: Sha

address: Nankai University

department: The State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

data_processing:
Adaptor sequence and low-quality sequence were trimmed by SOAPnuke, then sequence reads were mapped to mm10 genome using Hisat2 .
Reads count were caculated by FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include count values for each Sample.

source_name: Embryonic stem cell

growth_protocol: ESCs were cultured in medium containing DMEM/HIGH GLUCOSE (HyClone, SH30243.01), 15% FBS (HyClone, SH30070.03), 1X MEM NEAA (Gibco, 11140-050), 2 mM L-Glutamine (Solarbio, G0200), 100 U/ml penicillin, 100 µg/ml streptomycin (Solarbio, P1400), 0.11 mM 2-Mercaptoethanol (Sigma, M3148-250ml) and 10 ng/ml mouse LIF (GeneScript, Z03077) on 12 well tissue culture plates (FALCON, 353043) coated with 0.2% gelatin (SIGMA, G1890-100G).

extract_protocol:
Total RNA of cells were extracted by Trizon reagent (CWBIO,CW0580) following the manufacture‘sprotocol. For genes expression analysis, total RNA was treated by DNase I (Thermosentific, EN0521) for 30~45min to remove genome DNA. DNase I was inactivated in 70~75 °C for 10min.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (BGISEQ-500 RNA-Seq (Quantification) Library Preparation Protocol). mRNA were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription , then was followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. PCR is to amplify the cDNA fragments with adaptors from previous step. PCR products are purified with the SPRI beads, and dissolved in EB solution. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library . Library was validating on the Agilent Technologies 2100 bioanalyzer.
Library was prepared with BGISEQ kit and sequenced on BGISEQ-500 with 50bp read length for 24 million reads.

treatment_protocol: ESCs were transfected 0.5 μg Kdm2a gRNA using 3 μl Polyjet (Signagene, SL100688). 2-3 days later, 1.0 × 104 GFP+ cells were sorted by flow cytometry and single ESC clone was expanded for establishing Kdm2a-/- cell line.

tag: genotype

value: wild type


title: Ctrl_3: control pollen_rep3

value: Mature pollen


title: 2MIR1C: IMR90 fibroblast cell line transfected with miR-6127 [2]


title: Kdm2a_Knock out_1

tag: strain

value: Kdm2a knocked down


title: Pathogen Only Spleen 1


title: Ctrl_2: control pollen_rep2


title: Wild Type1


title: 3CT1: IMR90 fibroblast cell line untreated [3]

source_name: IMR90 fibroblast cell line untreated


title: 1MIR1: IMR90 fibroblast cell line transfected with miR-6127 [1]


title: Control Spleen 2


title: 877_Endo_Healthy

value: days 45-55 postpartum

value: Endometrium (Endo)


title: Mutant UV10046 pH 5.5

city: Thanjavur

first: K

last: Anbarasu

state: TN

address: Periyar Nagar, Vallam

country: India

institute: Periyar Maniammai Institute of Science & Technology

data_processing:
Sequencing
The library was loaded onto illumina NextSeq500 sequencing kit and flow-cell for cluster generation and sequencing. During the sequencing run, the library molecules bind to complementary adapter oligos on paired-end flow cell. In paired-end (PE) sequencing, the DNA library fragments are sequenced in both the forward and reverse directions. The sequencing was performed using the 2 x 75 bp run cycles to generate about 3GB raw data per sample.
Alignment Stats
All processed reads were aligned with reference using Tophat-2 .0.13. TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.
We have used Aspergillus carbonarius ITEM 5010, as reference genome for this study.
Assembly:GCA_001990825.1 Aspca3

organism: Aspergillus carbonarius

source_name: Mutant UV10046 pH 5.5

growth_protocol: Aspergillus carbonarius mutant was grown in glucose medium with pH 3 buffered medium and pH 5.5 buffered medium

extract_protocol:
Total RNA was isolated from fungal samples as per the manufacturer protocol of Qiagen Rneasy Plant Mini Kit (#74903)
paired-end sequencing library preparation using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7770S) and NEBNext Singleplex (NEB #E7350) Oligos for Illumina as per the protocol described by the manufacturer
The library preparation was initiated with the capture of mRNA from Total RNA using Oligo dT beads, fragmentation, first Strand cDNA synthesis, second strand synthesis, end-repairof the double-stranded cDNA and Adaptor ligation, indexing and final library  amplification. The libraries were purified using SPRISelect beads. The amplified libraries were analyzed in 4200 TapeStation (Agilent Technologies) using kit as per manufacturer's instructions

treatment_protocol: Strandard microbial culture method was followed with duplicates

tag: condition


title: Ctrl_1: control pollen_rep1

tag: tissue


title: Control Spleen 1


title: Mutant UV10046 pH 3

source_name: Mutant UV10046 pH 3

value: pH 3


title: 2CT2: IMR90 fibroblast cell line untreated [2]


title: 1CT1: IMR90 fibroblast cell line untreated [1]


title: PE0

city: beijing

first: fang

last: Du

state: china

address: zhongguancun south street 12

data_processing:
Illumina Casava1.7 software used for basecalling
Low-quality reads, duplicate sequences, and adapter sequences were removed to obtain high-quality clean reads
Clean paired-end reads were assembled into contigs based on the similarity between overlapping regions using Trinity. The resulting contigs were clustered with TGICL-2.1 [14] with the parameters "-l40-v20".
The transcript isoforms with the longest sequence in each Trinity subcomponent were extracted as a representative sequence of the Trinity subcomponent, called Unigene. All unigenes were pooled to yield the final unigene library
Supplementary_files_format_and_content: Processed data files include FPKM values

organism: Pleurotus tuoliensis

source_name: mycelia

growth_protocol: Mycelia were grown at 25oC in plastic bottles containing 820 g of cultivation substrate in the dark for 37 days, after which the substrate was fully covered by mycelia. We randomly selected three cultivation bottles and took the mycelia (0 day) from cultivation substrate into three corresponding tubes and froze them at -80oC. The remaining plastic bottles were maintained at a temperature of 17oC in the dark for 35 days to induce physiological maturation of mycelia. We then randomly selected three cultivation bottles and transferred the mycelia (35 day) to three corresponding tubes.

extract_protocol:
Mycelia from cultivation substrate were took and total RNA was extracted using TRIzol reagent.cDNA libraries were constructed using the Illumina TruSeq Stranded mRNA LT Library Preparation Kit and then paired-end sequenced on an Illumina HiSeq 2000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelia

value: immature mycelia


title: PE35

value: mature mycelia


title: sheep_low_heart3

status: Public on Aug 19 2019

city: Chengdu

first: Yao

last: Ma

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

data_processing:
Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit. Libraries were assessed using the Agilent 2200 TapeStation and sequenced on the Illumina HiSeq 2500 platforms. Initial bioinformatics analysis (base calling) was performed with CASAVA 1.8 (Illumina) to generate raw reads(in FASTQ form). Next, raw reads were subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and processed sequences were then mapped to corresponding reference genome (i.e.,chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1)) for each species with stringent criteria (less than 1 mismatch along the whole sequence) using Bowtie software. Thereafter, mappable reads were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters. Notably, mature miRNA sequence of chicken and all annotated mammalian species in miRbase21 were selected as reference. miRNAs with greater than or equal to 4 reads across > 40% samples were remained for further analysis.
Genome_build: chicken (Galgal4), pig (Suscrofa 10.2), cattle (UMD3.1), goat (CHIR 1.0), and sheep (Oar v3.1); miRbase 21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with reads

organism: Ovis aries

source_name: heart

extract_protocol:
Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were used (Table 1). Animals were humanely killed to ameliorate suffering. Upon excised from the corpse, a piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were placed immediately frozen in liquid nitrogen, and then stored at −80 °C until use. Of note, the skeletal muscle for pig, cattle, yak sheep were longissimus muscle, and the pectoral muscle for chicken. Total RNA were extracted using a standard TRIzol (Takara, Japan) protocol.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: altitude

value: low

value: heart

value: > 3 year

tag: group

value: Small Tail Han sheep


title: sheep_low_kidney2

source_name: kidney

value: kidney


title: sheep_low_lung3

source_name: lung

value: lung


title: sheep_low_liver3

source_name: liver

value: liver


title: sheep_low_muscle2

source_name: muscle

value: muscle


title: sheep_low_heart2


title: sheep_low_spleen3

source_name: spleen

value: spleen


title: sheep_low_spleen2


title: sheep_low_liver2


title: sheep_low_muscle3


title: sheep_low_lung2


title: Hepa1c1c7_Tmem54

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

institute: National Institute for Environmental Studies

description: Gene expression of Hepa1c1c7 transfected Tmem54 vector

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 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 GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Ver 2.0 Microarrays (G4858A) for 17 hours at 65℃ 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℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k 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 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol included an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Hepa1c1c7 cells were transfected witj Empty, Cd74 or Tmem54 vector.  The cells were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: Hepa1c1c7 cells

tag: transfection


title: sheep_low_heart1


title: sheep_low_kidney1


title: sheep_low_muscle1


title: Hepa1c1c7_Cd74

description: Gene expression of Hepa1c1c7 transfected Cd74 vector


title: Hippocampus_H1

first: Ming

last: Li

address: Ke Yuan Nan lu 88

department: Department of Anesthesiolog

institute: Sichuan University

description:
lncRNA+mRNA
Expression data in aged mice with postoperative cognitive dysfunction.

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

scan_protocol: Agilent DNA Microarray Scanner (part number G2505C) was used to scan the arrays.

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 two out of two samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Mouse hippocampus

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted according to the manufacturer’s instructions from the two groups using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The RNA integrity of each sample was estimated using standard denaturing agarose gel electrophoresis and quantified via a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE, USA).

tag: strain/background

value: hippocampus

value: 16-18 months

tag: gender

value: Male

tag: treatment

value: Control


title: Hepa1c1c7_Empty

description: Gene expression of Hepa1c1c7 transfected empty vector

value: Empty


title: sheep_low_lung1


title: sheep_high_muscle3

value: high

value: Tibetan sheep


title: sheep_high_heart3


title: Hippocampus_H2

value: Surgery


title: sheep_high_spleen3


title: sheep_high_lung3


title: sheep_high_liver3


title: sheep_low_spleen1

value: low


title: Kdm2a_Knock out_2

value: Kdm2a knocked down


title: sheep_high_muscle2

value: > 3 year


title: sheep_high_spleen2


title: sheep_high_lung2


title: sheep_high_muscle1


title: sheep_high_heart1

value: heart


title: sheep_high_liver2


title: sheep_high_kidney1

value: kidney


title: sheep_high_heart2


title: sheep_high_liver1

value: liver


title: sheep_high_spleen1


title: pig_high_muscle3

organism: Sus scrofa

value: muscle

value: > 1 year

value: Tibetan pig


title: pig_high_heart3


title: pig_high_kidney3


title: pig_high_muscle2


title: pig_high_liver3


title: pig_high_spleen3

value: spleen


title: Sample 3: Control cy3 vs E. coli challenged cy5 for 3h

description: Biological replicate 2 of 3 in 3h.

source_name: Control

value: Tsukuba

value: One day adult

source_name: E. coli challenged for 3 hours


title: spleen mouse Mac DMSO 1

value: macrophages

tag: patient

value: donor 1

value: DMSO


title: pig_high_lung3

value: high

value: lung

tag: age


title: pig_high_spleen2


title: sheep_high_lung1

value: Tibetan sheep


title: pig_high_kidney2


title: sheep_high_kidney2


title: pig_high_muscle1


title: pig_high_heart2


title: pig_high_liver2


title: pig_high_spleen1


title: pig_high_liver1


title: pig_high_kidney1


title: pig_high_lung2


title: pig_high_lung1


title: pig_low_kidney3

value: low

value: Rongchang pig


title: pig_high_heart1

value: heart


title: pig_low_spleen3


title: pig_low_muscle3


title: pig_low_heart3


title: pig_low_liver3


title: pig_low_kidney2

value: kidney


title: pig_low_heart2


title: pig_low_muscle1


title: pig_low_lung3


title: pig_low_kidney1


title: pig_low_liver2

value: liver


title: pig_low_lung2


title: pig_low_lung1


title: pig_low_spleen1


title: pig_low_spleen2


title: pig_low_liver1


title: pig_low_heart1


title: DNC48

city: Jinan

first: Xunwei

last: Wu

state: Shandong

address: 44-1 Wenhua West Road

department: School of Stomatology

institute: Shandong University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b).
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1).
Genome_build: ensemble
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: dermal fibroblast

extract_protocol:
Total RNAs were isolated from dermal cells with/without Y-27632 treatment for 12 hours or 48 hours respectively. Then mRNAs were purified from above total RNA
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Y-27632 (Y0503, Sigma-Aldrich) was dissolved in H2O to make 10 mM stock solution kept in -20℃ freezer, and for treatment, the stock solution was added into the culture medium with 1:1000 dilution (final concentration 10 M).

value: skin

value: dermal fibroblast

value: no treat for 48 hours


title: DY12

value: Y-27632 treated for 12 hours


title: DY48

value: Y-27632 treated for 48 hours


title: DHJH_DQ52RSSDNbait_rep2

city: Boston

first: Frederick

middle: W

last: Alt

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.

treatment_protocol: RAG2 retrovirally complemented and then 3 uM STI-571 treated for 4 days for RAG2 deficient v-Abl pro-B cells.

value: DH-JH+/-, Emu-Bcl2, RAG2 deficient


title: DNC12

value: no treat for 12 hours


title: DHJH_DQ52RSSDNbait_rep1

description: aligned to mm9 genome


title: DHJH_DQ52RSSDNbait_rep3

description: aligned to mm9 genome


title: DFL16.1JH4inv_3CBEsdel_DJHRSSbait_rep1

description: aligned to modified mm9 genome with DH-JH region replaced by DFL16.1JH4 join sequence

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_DFL16.1JH4 genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1JH4
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

treatment_protocol: 3 uM STI-571 treated for 4 days

value: v-Abl transformed pro-B cell line


title: JHdel_dCas9_NlaIII_iEmubait_rep3

description: NlaIII digestion, aligned to mm9 genome

data_processing:
Library strategy: 3C-HTGTS
Sequencing reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files

extract_protocol:
Briefly, 10 million cells were cross-linked with 2% formaldehyde at room temperature for 10 minutes, quenched by glycine (final 0.125M), and then lysed with cold cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, one tablet of protease inhibitor in 50 ml) on ice for 10 min. Nuclei were subjected to 0.3% SDS treatment (37oC, 1 hour) and 1.8% Triton X-100 treatment (37 oC, 1 hour) successively, followed by overnight digestion with indicated restriction enzyme (700 units) at 37oC. Restriction enzyme was inactivated at 65oC for 20 min and samples were subjected to ligation under diluted condition with T4 DNA ligase (100 units, NEB, M0202L). Ligated chromatin was de-crosslinked with Proteinase K (56oC, O/N) and treated with RNaseA (37oC, 1 hour). DNA was purified via phenol/chloroform extraction and resuspended in 200 ul 1XT.E. buffer. DNA templates were then subjected to 3C-HTGTS library preparation.
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.

value: JH-del, dCas9 expressing, Emu-Bcl2, RAG2 deficient


title: JHdel_dCas9_NlaIII_iEmubait_rep1

description: NlaIII digestion, aligned to mm9 genome


title: DHJH_NlaIII_iEmubait_rep2

description: NlaIII digestion, aligned to mm9 genome


title: DFL16.1JH4inv_DJHRSSbait_rep3

value: DFL16.1JH4-inv, Emu-Bcl2


title: DFL16.1JH4inv_3CBEsdel_DJHRSSbait_rep3


title: DFL16.1JH4inv_DJHRSSbait_rep4


title: DFL16.1JH4inv_3CBEsdel_DJHRSSbait_rep2


title: JHdel_dCas9_NlaIII_iEmubait_rep2

description: NlaIII digestion, aligned to mm9 genome


title: DHJH_NlaIII_iEmubait_rep1

description: NlaIII digestion, aligned to mm9 genome


title: DFL16.1JH4_DJHRSSbait_rep1

value: DFL16.1JH4, Emu-Bcl2


title: DFL16.1JH4_DJHRSSbait_rep2


title: DFL16.1JH4inv_DJHRSSbait_rep1


title: Ig2bdel_DQ52RSSDNbait_rep2

description: aligned to mm9 genome

data_processing:
Library strategy: Linear-amplificate PCR-mediated HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read   s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read   s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9, mm9_DFL16.1-RSS-U-inversion, mm9_DFL16.1-RSS-D-inversion, mm9_DFL16.1-inversion, mm9_DQ52-inversion, mm9_DH-cluster-inversion, mm9_DQ52-replace-DFL16.1,  mm9_DQ52inv-replace-DFL16.1, mm9_DFL16.1-replace-DQ52, mm9_DFL16.1inv-replace-DQ52, mm9_DFL16.1JH4
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: JH-del, dCas9 expressing, Ig2b-del/del, Emu-Bcl2, RAG2 deficient


title: DFL16.1JH4_DJHRSSbait_rep3


title: Ig2bdel_DQ52RSSDNbait_rep1

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: Ig2bwt_DQ52RSSDNbait_rep2

description: aligned to mm9 genome


title: Ig2bwt_DQ52RSSDNbait_rep3

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

value: JH-delta-dCas9, Emu-Bcl2, RAG2 deficient


title: Ig2bwt_DQ52RSSDNbait_rep1

description: aligned to mm9 genome


title: dCas9Block_DQ52RSSDNbait_rep2

description: aligned to mm9 genome

value: JH-del,dCas9 expressing, Sg1-sgRNA expressing, Emu-Bcl2, RAG2 deficient


title: dCas9Block_DQ52RSSDNbait_rep4

description: aligned to mm9 genome

value: JH-del, dCas9 expressing, Sg1-sgRNA, Emu-Bcl2, RAG2 deficient


title: dCas9Block_DQ52RSSDNbait_rep3

description: aligned to mm9 genome

value: JH-del, dCas9 expressing, Sg1-sgRNA expressing, Emu-Bcl2, RAG2 deficient

value: RAG2 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: DFL16.1JH4inv_DJHRSSbait_rep2


title: dCas9Control_DQ52RSSDNbait_rep4

description: aligned to mm9 genome


title: dCas9Block_DQ52RSSDNbait_rep1

description: aligned to mm9 genome


title: dCas9Control_DQ52RSSDNbait_rep3

description: aligned to mm9 genome


title: dCas9Control_DQ52RSSDNbait_rep1

description: aligned to mm9 genome


title: dCas9Control_DQ52RSSDNbait_rep2

description: aligned to mm9 genome


title: Ig2bdel_DQ52RSSDNbait_rep3

description: aligned to mm9 genome


title: dCas9Block_DQ52RSSDNbait_rep5

description: aligned to mm9 genome


title: dCas9Control_DQ52RSSDNbait_rep5

description: aligned to mm9 genome


title: JH1_DFL16.1inv_replaceDQ52_JH1bait_rep3

description: aligned to modified mm9 genome with DQ52 replaced by DFL16.1 inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1inv-replace-DQ52
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DFL16.1-del, DQ52 replaced by DFL16.1 inversion, Emu-Bcl2, RAG2 deficient


title: JHdel_DQ52RSSDNbait_rep2

description: aligned to mm9 genome

value: JH-del, Emu-Bcl2, RAG2 deficient


title: JH1_DFL16.1inv_replaceDQ52_JH1bait_rep1

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_DFL16.1inv-replace-DQ52 genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1inv-replace-DQ52
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: JHdel_DQ52RSSUPbait_rep2

description: aligned to mm9 genome


title: JHdel_DQ52RSSUPbait_rep3

description: aligned to mm9 genome


title: JHdel_DQ52RSSUPbait_rep1

description: aligned to mm9 genome


title: JH1_DFL16.1replaceDQ52_JH1bait_rep1

description: aligned to modified mm9 genome with DQ52 replaced by DFL16.1

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_DFL16.1-replace-DQ52 genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1-replace-DQ52
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DFL16.1-del, DQ52 replaced by DFL16.1, Emu-Bcl2, RAG2 deficient


title: JH1_DQ52replaceDFL16.1_JH1bait_rep2

description: aligned to modified mm9 genome with DFL16.1 replaced by DQ52

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_DQ52-replace-DFL16.1 genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DQ52-replace-DFL16.1
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DQ52-del, DFL16.1 replaced by DQ52, Emu-Bcl2, RAG2 deficient


title: JH1_DQ52inv_replaceDFL16.1_JH1bait_rep3

description: aligned to modified mm9 genome with DFL16.1 replaced by DQ52 inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_DQ52inv-replace-DFL16.1 genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DQ52inv-replace-DFL16.1
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DQ52-del, DFL16.1 replaced by DQ52-inv, Emu-Bcl2, RAG2 deficient


title: JH1_DQ52replaceDFL16.1_JH1bait_rep3

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_DQ52-replace-DFL16.1 genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9_DQ52-replace-DFL16.1
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)