title: CEMBA190207_5J_1_CEMBA190207_5J_2_A7_ad001


title: T16_Xenograft_Generation_2

status: Public on Oct 01 2020

type: genomic

city: Luxembourg

first: Ann-Christin

last: Hau

address: 1, Rue Louis Rech

department: National Center of Pathology

country: Luxembourg

institute: Laboratoire National de sante

hyb_protocol: Similarly treated amounts of reference; Female or Male gDNA pool (Promega) were processed as sample genomic DNAs and hybridized with the Agilent Oligo aCGH Hybridization Kit to the corresponding platform array at 65°C for 24h or 48h respectively.

scan_protocol: Microarray slides were scanned using an Agilent 2565C DNA scanner

data_processing:
The tif images were analyzed with Agilent Feature Extraction version 12.5, using default settings
normalised log ratio Cy5/Cy3 representing test/reference; transformed logratio matrix with 0 - unaltered, 1 - gain, -1 - loss, 2 - amplification, -2 - deletion

molecule: genomic DNA

organism: Homo sapiens

source_name: Xenotransplant

label_protocol: For Agilent-021529 platform 2µg, for Agilent-021850 and Agilent-028081 platform 1µg, for Agilent-030587 platform 500ng and for Agilent-021924 platform 250ng of genomic DNA  were digested with RSA1 and Alu1 (Agilent) to generate 200-500bp large fragments. The BioPrime aCGH Genomic labeling Kit (Life Technologies) and Cy3 and Cy5 dyes (GE Healthcare) were used following standard protocols for Agilent aCGH (CGH enzymatic protocol v6.2; Ref # G4410-90010).

growth_protocol: patient specimen were: 1) flash frozen on dry ice after surgical removal or 2) mechanically cut, seeded on agar coated flasks (0.85%) and allowed to form spheroids for up to 2 weeks at 37°C under 5% CO2 and atmospheric oxygen in DMEM medium, 10% FBS, 2mM L-Glutamine, 0.4mM NEAA and 100U/ml Pen-Strep (all from Lonza).  Spheroids (generation 0) with a diameter of 300-1000 µm were then implanted in the brain of immunodeficient mice (NOD/Scid, Nude or NSG; 6 spheroids per mice). Cell lines were derived from xenotransplanted mice by papain-based enzymatic digestion of PDOX tissue and cultured in serum-free medium based on  Neurobasal® base medium (Life Technologies) supplemented with 1 x B27 (Life Technologies) 2 mM L-Glutamine, 30 U/ml Pen-Step, 1 U/ml Heparin (Sigma), 20 ng/ml bFGF (Miltenyi, 130-093-841) and 20 ng/ml EGF (Provitro, 1325950500).

extract_protocol: Genomic DNA was isolated from patient tissue, spheroid cultures or cell lines using the AllPrep DNA/RNA Mini Kit® (Qiagen) following manufacturer’s instructions for “Simultaneous purification of genomic DNA and total RNA from animal tissues”.

tag: sample type

value: Xenotransplant

tag: gender

value: Female

source_name: Reference DNA

value: Reference DNA

tag: catalog no


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A7_ad004

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CP

tag: Sex

value: male

tag: age

tag: strain


title: P158_cell-line_passage_12

source_name: Cell Line

value: Cell Line


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A7_ad008


title: P158_Xenograft_Generation_3


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A7_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A6_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A6_ad007


title: T158_patient_sample_1

source_name: Primary patient sample

value: Primary patient sample


title: Human_ST_51_Nod1-FL-plusDOX

type: RNA

city: Seattle

first: Naeha

last: Subramanian

state: Wa

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: Labeled target from sixty submitted samples was combined with 2X hybridization buffer, 3nM B2 control oligo (Affymetrix 900457), 20X spike in (Affymetrix 51214), and DMSO making a final volume of 100ul for the sixty individual hybridizations to the commercial Affymetrix GeneChip Human 1.0 ST containing the human genome.  The hybridization cocktail, including the components listed above, was denatured for five minutes at 94◦C then transferred to a 45◦C heat block for an additional five minutes before transferring 80ul of the cocktail into the chip.  The hybridization was carried out at a constant temperature of 45◦C for approximately seventeen hours using the 500k approved, Affymetrix 640 oven. Upon completion of the hybridization each sample was removed from the chip and archived according to the Chip ID issued to processing project NS_1.  Each chip was filled with ~100ul of wash buffer A, and then processed on the fluidics station 450.  The reagents for the stain mixture consisted of 2X MES stain buffer, 50mg/ml of BSA, 1mg/ml of streptavidin phycoerythrin and water to make up 600ul total volume for each stain and a holding buffer added to make up 800ul total volume for storage and scanning.

scan_protocol: Upon completion of the fluidics process, each sample was scanned using the Affymetrix GeneChip 3000 7Gplus scanner to create the image files (dat).  Expression console (EC, v1.1 Affymetrix) was used to convert the dat files to intensity (cel) files.

data_processing: Data was analyzed using R/Bioconductor. Normalization was conducted using the rma function in the oligo package. Low intensity probes, probes without gene names, and probes mapping to more than one gene were then filtered. Finally, for genes with multiple probe sets the probe with the max variation for each gene was used.

label: biotin

molecule: total RNA

label_protocol: cRNA labeling was performed with the GeneChip one-cycle target labeling and control reagents kit (Affymetrix)

growth_protocol: THP-1 cells were obtained from ATCC and cultured in RPMI (Lonza) supplemented with  2 mM glutamine (Gibco), 10 mM HEPES (Corning) and 10% FCS (RPMI-10) in a  humidified atmosphere of 5% CO 2 at 37°C. Vectors for gateway cloning namely  pEN_TmiRc3 entry vector and pSLIK_Neo destination vector were kindly provided by  Dr. Iain Fraser, NIAID, NIH. Primers and probes used for detection of endogenous and  3X FLAG NOD1 and NLRP4 are listed in Table S1 of the publication. For generation of stable cell lines, 3X FLAG-tagged NOD1 and NLRP4 were cloned into  an entry vector (pEN_TmiRc3) driven by a tetracycline-inducible (TRE) promoter and  recombined into a lentiviral expression vector (pSLIK_Neo). Lentiviruses were produced  in modified HEK-293T cells by co-transfecting plasmid DNA of interest along with pRSV,  pVSV and pMDL plasmids as previously described (Shin et al., 2006). Virus was  concentrated from the supernatant and used to infect THP-1 cells at low copy to ensure  <30% infection frequency such that majority of the transduced cells contain a single viral  integration. Stable cell lines were selected with 1 mg/ml G418 (Invivogen). Expression  of NOD1 and NLRP4 was induced by treatment with 1 μg/ml doxycycline (DOX; Sigma)  for 6 h.

extract_protocol: Total RNA was isolated from 4 replicates per treatment using the RNeasy miniprep kit (Qiagen)

treatment_protocol: THP-1 cells were seeded at a density of 50,000 cells per well in a 96-well plate and  treated with 1 ug/ml DOX for 6 hours to induce NOD1 or NLRP4 expression.

tag: cell line

tag: transduced with

value: NOD1 coding sequence

tag: treated with

value: 1 μg/ml doxycycline (DOX) for 6 h


title: Human_ST_52_Nod1-FL-plusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A6_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A6_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A6_ad010


title: T101_Xenograft_Generation_5_Sample_2

value: Male


title: P8_patient_sample_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A6_ad002


title: Human_ST_47_Nod1-FL-minusDOX

value: none (uninduced control)


title: P8_Xenograft_Generation_8


title: P8_Xenograft_Generation_4


title: P3_Xenograft_Generation_9


title: Human_ST_48_Nod1-FL-minusDOX


title: P13_cell-line_passage_9


title: T16_patient_sample_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A6_ad008


title: T101_patient_sample_2


title: P3_patient_sample_1


title: P13_Xenograft_Generation_2


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A5_ad012


title: Human_ST_45_Nod1-FL-minusDOX


title: P3_patient_sample_2


title: T101_Xenograft_Generation_2


title: P8_patient_sample_2


title: Human_ST_49_Nod1-FL-plusDOX


title: Human_ST_36_Nalp4-FL-plusDOX

value: NLRP4 coding sequence


title: P13_patient_sample_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A5_ad007


title: T101_Xenograft_Generation_6


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A5_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A5_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A5_ad002


title: T16_Xenograft_Generation_3_Sample_2


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A4_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A4_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A4_ad010


title: Human_ST_35_Nalp4-FL-plusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A4_ad006


title: Human_ST_31_Nalp4-FL-minusDOX


title: Human_ST_46_Nod1-FL-minusDOX


title: Human_ST_29_Nalp4-FL-minusDOX


title: Human_ST_32_Nalp4-FL-minusDOX


title: Human_ST_34_Nalp4-FL-plusDOX


title: Human_ST_30_Nalp4-FL-minusDOX


title: Human_ST_33_Nalp4-FL-plusDOX


title: Human_ST_08_Control-C-plusDOX

source_name: Control-C-plusDOX

value: empty vector alone


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A4_ad002


title: Human_ST_07_Control-C-plusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A3_ad007


title: Human_ST_04_Control-C-minusDOX

source_name: Control-C-minusDOX


title: Human_ST_05_Control-C-plusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A3_ad010


title: Human_ST_02_Control-C-minusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A3_ad008


title: Human_ST_06_Control-C-plusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A3_ad004


title: Human_ST_03_Control-C-minusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A4_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A5_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad007


title: Human_ST_50_Nod1-FL-plusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad006


title: Human_ST_01_Control-C-minusDOX


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A3_ad006


title: KL Null_3

city: Indianapolis

first: Kenneth

middle: E.

last: White

state: IN

address: 635 Barnhill Dr, MS 5012

institute: Indiana University School of Medicine

hyb_protocol: Labeled RNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays for 17 hours then washed using the Affymetrix standard protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay, rev. 5)

scan_protocol: Arrays were scanned using

data_processing: Data were imported into Partek Genomics Suite version 6.2 (Partek, Inc. St. Louis, Mo). Robust Multichip Average signals (RMA) (21) were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish using Partek Genomics Suite. Summarized signals for each probe set were log2 transformed.

source_name: kidney

label_protocol: The RNA was labeled following the standard WT protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay, rev. 5, www.affymetrix.com).

extract_protocol: Trizol

treatment_protocol: KL-null mice (20) and wild type littermates (N=4-6) were maintained on standard diet for 5-8 weeks and given one intraperitoneal injection of 500 ng/g body weight recombinant HBEGF (R&D System), 500 ng/g body weight recombinant FGF23 (R&D System) or 100 µl saline vehicle i.p., then sacrificed after one hour.

tag: tissue

value: kidney

tag: genotype

value: KL null

tag: treatment

value: injected with 100ul saline vehicle


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad002


title: KL Null_2


title: WT-Vehicle_3

value: WT


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad004


title: KL Null_1


title: WT-Vehicle_2


title: WT-Vehicle_4


title: KL Null_4


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad008


title: WT-FGF23_4

value: injected with 500 ng/g body weight recombinant FGF23


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A12_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A12_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A12_ad006


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A12_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A12_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A12_ad004


title: T16_Xenograft_Generation_0

value: Xenotransplant

value: Female


title: T16_patient_sample_3

value: Reference DNA


title: WT naïve CD4+ T cells [CK36]

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

library_source: transcriptomic

data_processing:
Raw reads obtained from bcl2fastq (Illumina) were aligned to the Mus musculus reference genome (GRCm38) using STAR v.2.7 in paired-end mode with 2-pass mapping.
Mapped reads were summarized at the gene level using featureCounts (R Subread package v1.6).
Raw feature counts were normalized using DESeq2 (version 1.24.0) in R (version 3.6.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized gene counts for each sample

molecule: polyA RNA

source_name: WT naïve CD4+ T cells

extract_protocol:
Total RNA was extracted from FACS-sorted FYN-TRAF3IP2-induced mouse lymphoma cells using AllPrep DNA/RNA mini kit (Qiagen #80204). Briefly, we sorted CD4+ GFP+ lymphoma cells into appropriate volume of RLT plus buffer and isolated nucleic acid from the lysate according to the kit manufacturer’s protocol. We used RNeasy mini kit (Qiagen #74104) to extract total RNA in naïve CD4+ T cells, isolated from wild type C57BL/6 mouse spleen via magnetic bead-based negative selection cell depletion (Miltenyi Biotec #130-104-453).
RNAseq libraries were prepared and sequenced on Illumina HiSeq platform by GENEWIZ. Briefly, sequencing libraries were prepared using Illumina Nextera XT library from the full-length cDNA synthesized and amplified by SMART-Seq v4 Ultra Low Input Kit (Clontech, Mountain View, CA).

tag: strain background

value: FYN-TRAF3IP2;GFP;Tet2 -/-

value: spleen

tag: cell type

value: CD4+ T Lymphocytes


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A12_ad001

value: CP

value: male


title: Secondary of Lymphoma #5 CD4+ GFP+ sorted [CK16]

source_name: Secondary of Lymphoma CD4+ GFP+ sorted


title: WT naïve CD4+ T cells [CK37]


title: WT-FGF23_3


title: Secondary of Lymphoma #2 CD4+ GFP+ sorted [CK15]


title: WT-FGF23_2


title: Secondary of Lymphoma #4 CD4+ GFP+ sorted [CK17]


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A11_ad010


title: WT-FGF23_1


title: WT-Vehicle_1


title: Lymphoma #6 CD4+ GFP+ sorted [CK40]

source_name: Lymphoma CD4+ GFP+ sorted

value: FYN-TRAF3IP2;GFP;Tet2 fl/fl


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A11_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A11_ad004


title: Lymphoma #5 CD4+ GFP+ sorted [CK27]


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A11_ad002


title: Lymphoma #3 CD4+ GFP+ sorted [CK39]


title: Lymphoma #2 CD4+ GFP+ sorted [CK01]


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A10_ad010


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A10_ad008


title: Lymphoma #1 CD4+ GFP+ sorted [CK07]


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A10_ad007


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A10_ad004


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A10_ad006


title: T16_Xenograft_Generation_3_Sample_1


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A11_ad008


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A10_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A10_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A11_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A1_ad001


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A1_ad012


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A1_ad007


title: WT naïve CD4+ T cells [CK38]


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A1_ad006


title: Lymphoma #4 CD4+ GFP+ sorted [CK26]


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A5_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H9_ad010

value: PIR


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H9_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H9_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H9_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H9_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H9_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H8_ad002


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A1_ad008


title: LCL Gene Expression Sample 26

city: Los Angeles

first: Anil

last: Ori

state: Verenigde Staten van Amerika

address: 695 Charles E Young Drive South

department: Center for Neurobehavioral Genetics

institute: University of California, Los Angeles

hyb_protocol: standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: 24h exposure 20uM clozapine

label_protocol: Standard Illumina Protocol

extract_protocol: RNA was extracted and purified from LCL samples using Qiagen RNeasy Kit according to standard instructions

value: 24h exposure 20uM clozapine

value: lymphoblast cell line model

tag: rin

tag: percentagelivecells


title: LCL Gene Expression Sample 31

source_name: control - no exposure

value: control - no exposure


title: LCL Gene Expression Sample 28

source_name: 24h exposure 1x DMSO

value: 24h exposure 1x DMSO


title: LCL Gene Expression Sample 22


title: LCL Gene Expression Sample 30

source_name: 24h exposure 100x DMSO

value: 24h exposure 100x DMSO


title: LCL Gene Expression Sample 21


title: LCL Gene Expression Sample 29

source_name: 24h exposure 10x DMSO

value: 24h exposure 10x DMSO


title: LCL Gene Expression Sample 25

source_name: 24h exposure 2uM clozapine

value: 24h exposure 2uM clozapine


title: LCL Gene Expression Sample 24

source_name: 24h exposure 100uM clozapine

value: 24h exposure 100uM clozapine


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H9_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H8_ad010


title: LCL Gene Expression Sample 18


title: LCL Gene Expression Sample 20


title: LCL Gene Expression Sample 19


title: LCL Gene Expression Sample 15


title: LCL Gene Expression Sample 14


title: LCL Gene Expression Sample 13


title: LCL Gene Expression Sample 17


title: LCL Gene Expression Sample 27


title: LCL Gene Expression Sample 11


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H8_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H8_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H7_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H7_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H7_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H7_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H8_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H7_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H8_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H7_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H8_ad008


title: LCL Gene Expression Sample 7


title: LCL Gene Expression Sample 8


title: LCL Gene Expression Sample 3


title: LCL Gene Expression Sample 16


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H7_ad010


title: LCL Gene Expression Sample 10


title: SC-25

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Limma package was used to process the IDAT files. Genes that were absent (dection p value>0.05) in more than 50% of the samples were removed. The rest of the genes were background corrected, log-transformed, and normalized to have the same median expression value per sample.

source_name: small cell carinoma (SCC)

label_protocol: biotinylated primers were used in the conversion of RNA to cDNA

extract_protocol: RNA was isolated using the MasterPure Complete DNA and RNA Purification Kit (Epicenter Biotechnologies, Madison, WI, USA)

tag: subject age

value: 58 years

tag: subject gender

value: bladder

tag: tissue type

value: small cell carinoma (SCC)


title: LCL Gene Expression Sample 4


title: LCL Gene Expression Sample 2


title: LCL Gene Expression Sample 1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad004

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: SC-22

value: 62 years


title: SC-24

value: 72 years


title: SC-23

value: 90 years

value: female


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad006

tag: Sex

value: male


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad002

value: PIR

tag: age


title: SC-21

value: 34 years


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad008

tag: strain


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H5_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H5_ad006


title: SC-20

value: 67 years


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H5_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H5_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H5_ad010


title: LCL Gene Expression Sample 9

value: lymphoblast cell line model


title: SC-17


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H4_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H4_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H5_ad004


title: SC-14

value: 71 years


title: SC-18

value: 57 years


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H4_ad004


title: SC-11

value: 76 years


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H6_ad007


title: SC-12


title: SC-15

value: 65 years


title: CEMBA190207_5J_1_CEMBA190207_5J_2_A2_ad001

value: CP


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H4_ad007


title: SC-7

value: 79 years


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H4_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H3_ad012


title: SC-19

value: bladder


title: SC-8

value: 60 years

value: small cell carinoma (SCC)


title: SC-4

value: 72 years


title: SC-9


title: SC-2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H4_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H3_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H3_ad006


title: SC-13


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H3_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H3_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad012


title: SC-10

value: 41 years


title: SC-3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H3_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad012


title: LCL Gene Expression Sample 5

value: 24h exposure 100x DMSO


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad010

value: male


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H3_ad004

value: PIR


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H2_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H4_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad007


title: genomic DNA patient T347 [T470_X]

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation Beadchips using standard Illumina protocol. Processing of HumanMethylationEPIC BeadChip arrays was performed by the Helmholtz Zentrum Muenchen (Research Unit of Molecular Epidemiology/Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany. Illumina HumanMethylation450 BeadChips were processed at the German Cancer Research Center (DFKZ) Genomics and Proteomics Core Facility.

scan_protocol: The arrays were scanned with the Illumina HiScan SQ scanner.

data_processing: The R package ʹRnBeadsʹ was used to generate individual 450k and EPIC RnBeadSets that were normalized using the ʹBMIQʹ method. Both platforms were combined using the ʹrnb.combine.arraysʹ function in order to extract only common sites present in both objects with corresponding DNA methylation level. The DNA methylation level for each locus was measured as a β-value score.

label: Cy5 and Cy3

source_name: xenograft

tag: source subject status

value: glioma patient

tag: source patient id

tag: sample type

value: xenograft


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad002


title: genomic DNA patient T434 [T434_X]


title: genomic DNA patient T476 [T476_B]

source_name: patient sample

value: patient sample


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H12_ad001


title: genomic DNA patient T394 [T394_X]


title: genomic DNA patient T394 [T407_C]

source_name: cell line

value: cell line


title: genomic DNA patient T394 [T394_C]


title: SC-16

value: 71 years

tag: tissue


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad012


title: genomic DNA patient T476 [T476_X]


title: genomic DNA patient T394 [T407_B]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad008


title: genomic DNA patient T361 [T361_B]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad007


title: genomic DNA patient T434 [T434_B]


title: genomic DNA patient T367 [T367_B]


title: genomic DNA patient T394 [T394_B]


title: genomic DNA patient T331 [T331_X]


title: genomic DNA patient T394 [T407_X]


title: genomic DNA patient T361 [T361_X]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad004


title: genomic DNA patient T386 [T386_X]


title: genomic DNA patient T347 [T347_X]


title: genomic DNA patient T347 [T347_B]


title: genomic DNA patient T367 [T367_X]


title: genomic DNA patient T341 [T341_X]


title: genomic DNA patient T341 [T337_B]


title: genomic DNA patient T347 [T470_B]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H11_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad002


title: genomic DNA patient T192 [T251_X1]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H10_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad007


title: genomic DNA patient T192 [T233_X]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad001


title: genomic DNA patient T0238 [T238_X]


title: genomic DNA patient T331 [T331_B]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad004


title: 3seq-S2R+-Rbp9WT-rep2

first: Seungjae

last: Lee

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

data_processing:
Data were mapped onto the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6).
3′ end clusters were derived and quantified within a 25 bp window as described (Sanfilippo et al., 2017).
Genome_build: dm6
Supplementary_files_format_and_content: S2R+ 3seq gene expression table and bigwig

organism: Drosophila melanogaster

growth_protocol: S2R+ cells were maintained at 25℃ in standard Schneider insect medium supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNAs were extracted from S2R+ cells transfected as described above using Trizol.
3’-end sequencing libraries were prepared using a custom method as described (Sanfilippo et al., 2017). Briefly, 3’-end sequencing libraries were prepared using 2 ug of total RNA as starting material.

treatment_protocol: S2R+ cells were transfected with wildtype Elav, Rbp9, Fne and RRM mutant versions of Elav, Rbp9, Fne using Qiangen Effectene according to manufacture' s instructions.

tag: cell line

value: Rbp9WT overexpression

tag: protocol

value: 3’-end sequencing


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad010


title: 3seq-S2R+-Rbp9WT-rep1

tag: treatment


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad008


title: genomic DNA patient T192 [T233_B]


title: genomic DNA patient T192 [T251_B1]


title: 3seq-S2R+-Rbp93X-rep1

value: Rbp93Xmut overexpression


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G9_ad012


title: genomic DNA patient T192 [T192_B]


title: genomic DNA patient T192 [T192_X]


title: 3seq-S2R+-FneWT-rep2

value: FneWT overexpression


title: genomic DNA patient T158 [T158_X]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G9_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad006


title: 3seq-S2R+-FneWT-rep1


title: genomic DNA patient T0238 [T238_B]


title: 3seq-S2R+-Fne3X-rep1

value: Fne3Xmut overexpression


title: genomic DNA patient T188 [T188_X]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G9_ad004


title: genomic DNA patient P8 [P8_X]


title: 3seq-S2R+-ElavWT-rep1

value: ElavWT overexpression


title: CEMBA190205_6D_3_CEMBA190205_6D_4_H1_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G9_ad007


title: genomic DNA patient T16 [T16_C]


title: genomic DNA patient T186 [T186_X]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G9_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G9_ad008


title: genomic DNA patient T101 [T101_X]


title: 3seq-S2R+-ElavWT-rep2


title: genomic DNA patient T186 [T186_B]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G8_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G8_ad007


title: genomic DNA patient T158 [T158_B]


title: 3seq-S2R+-Elav3X-rep1

value: Elav3Xmut overexpression


title: 3seq-S2R+-rep1


title: genomic DNA patient P13 [P13_X]


title: 3seq-S2R+-Elav3X-rep2


title: genomic DNA patient P13 [P13_C]


title: 3seq-S2R+-rep2


title: RNAseq-L1CNS-elav5fne-rep3

data_processing:
Total RNA-seq data were mapped to the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6), HISAT2 aligner was used for the alignment with default parameters.
Genome_build: dm6
Supplementary_files_format_and_content: gene expression table and bigwig

growth_protocol: Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant flies were maintained at 25℃.

extract_protocol:
Total RNAs were extracted from dissected CNS from homozygous 1st insta larvae of Canton-S, elav5 single mutant, and elav5/fne double mutant
Total RNA-seq libraries of L1CNS samples were prepared using TruSeq Stranded Total RNA Library Preparation Kit (Illumina) with 0.1 ug total RNA as starting materials for each sample.

treatment_protocol: Viable homozygous 1st insta larvae of Canton-S, elav5 single mutant, and elav5/fne double mutant were manually picked based on visualized marker, CNS were dissected from whole viable homozygous 1st instar larvae

tag: developmental stage

value: CNS

tag: genotype


title: RNAseq-L1CNS-elav5fne-rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G8_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G7_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G8_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G7_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G7_ad007


title: genomic DNA patient P8 [P8_B]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G8_ad004


title: RNAseq-L1CNS-CantonS-rep3

value: Canton-S


title: RNAseq-L1CNS-elav5-rep2


title: RNAseq-L1CNS-elav5-rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G8_ad006


title: genomic DNA patient P3 [P3_C1]


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G7_ad010


title: RNAseq-L1CNS-CantonS-rep2


title: genomic DNA patient P3 [P3_C]


title: 3seq-L1CNS-elav5fne-rep3

data_processing:
Data were mapped onto the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6).
3′ end clusters were derived and quantified within a 25 bp window as described (Sanfilippo et al., 2017).
Genome_build: dm6
Supplementary_files_format_and_content: L1CNS 3seq gene expression table and bigwig

extract_protocol:
Total RNAs were extracted from dissected CNS from homozygous 1st insta larvae of Canton-S, elav5 single mutant, and elav5/fne double mutant
Total 3'-end sequencing libraries of L1CNS samples were prepared using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina with 40 ng total RNA as starting materials for each sample

treatment_protocol: Viable homozygous 1st insta larvae of Canton-S, elav5 single mutant, and elav5/fne double mutant were manually picked based on visualized marker, CNS were dissected from whole viable homozygous 1st insta larvae

value: 3'-end sequencing


title: RNAseq-L1CNS-elav5fne-rep2


title: 3seq-L1CNS-elav5fne-rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G7_ad002

value: male


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G7_ad008

value: PIR


title: 3seq-L1CNS-elav5fne-rep1


title: 3seq-L1CNS-elav5-rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G6_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G7_ad006


title: 3seq-L1CNS-CantonS-rep2


title: 3seq-L1CNS-CantonS-rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G6_ad008


title: GP-18: 3-80: PA3_phage-80min_rep3

city: Chongqing,

first: Qiu

last: Zhong

address: Daping Changjiang street 10#

department: Department of Clinical Laboratory

country: China

institute: Third Military Medical University

data_processing:
The sequenced libraries were mapped against predicted transcripts from the  Pseudomonas aeruginosa PAO1 genome using TopHat v2.0.4
The transcript  abundance (FPKM, Fragments Per Kilobase of exon per  Million fragments mapped) and significant changes in  transcript expression were estimated using Cufflinks  v2.0.2
Transcripts with p-values less than 0.05,  determined using CuffDiff
Genome_build: NC_002516.2 and NC_004466.2 were used as the reference genomes
Supplementary_files_format_and_content: processed data are bam files

organism: Pseudomonas aeruginosa

source_name: Transcriptome after phage infection of 80min

growth_protocol: PA3 with or wihout phage infection was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol:
Total RNA was isolated using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Barcoded sequencing libraries. Pooled libraries were enriched for the exome using hybridization (TruSeq Exome Enrichment Kit, Illumina), quantified using quantitative PCR and pooled in 1:1 ratio for pairedend sequencing on a HiSeq2500 (Illumina)

treatment_protocol: Bacterial culture were infected with phage PaP3 at MOI of 10 for 5min, 10min, 20min,30min,80min.The uninfected samples served as reference.

tag: host

value: Pseudomonas aeruginosa PA3

tag: agent

value: Pseudomonas aeruginosa bacteriophage PaP3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G6_ad006


title: 3seq-L1CNS-elav5-rep2


title: 3seq-L1CNS-elav5-rep1


title: 3seq-L1CNS-CantonS-rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad001


title: GP-16: 1-80: PA3_phage-80min_rep1


title: GP-15: 3-30: PA3_phage-30min_rep3

source_name: Transcriptome after phage infection of 30min


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G6_ad004


title: GP-14: 2-30: PA3_phage-30min_rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad004


title: GP-13: 1-30: PA3_phage-30min_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G6_ad010


title: GP-12: 3-20: PA3_phage-20min_rep3

source_name: Transcriptome after phage infection of 20min


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad010


title: genomic DNA patient T188 [T188_B]

value: glioma patient

value: patient sample


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G6_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G5_ad008


title: GP-17: 2-80: PA3_phage-80min_rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G4_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G4_ad010


title: GP-11: 2-20: PA3_phage-20min_rep2


title: GP-09: 3-10: PA3_phage-10min_rep3

source_name: Transcriptome after phage infection of 10min


title: GP-08: 2-10: PA3_phage-10min_rep2


title: GP-10: 1-20: PA3_phage-20min_rep1


title: GP-06: 3-5: PA3_phage-5min_rep3

source_name: Transcriptome after phage infection of 5min


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G4_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G4_ad006


title: GP-05: 2-5: PA3_phage-5min_rep2


title: GP-07: 1-10: PA3_phage-10min_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G4_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G4_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G4_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G3_ad012


title: GP-04: 1-5: PA3_phage-5min_rep1


title: GP-02: 2-0: PA3_phage-0min_rep2

source_name: Transcriptome without phage infection


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G3_ad007


title: GP-03: 3-0: PA3_phage-0min_rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G3_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G3_ad010


title: GP-01: 1-0: PA3_phage-0min_rep1


title: Brain_E16.5_SNORD115_116_KO_3

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Whole cell RNA from tissue

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: Mouse rDNA (18S, 28S, 5.8S, 5S). The reference sequences are in Supplementary_Data_1.fasta
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

source_name: Brain

extract_protocol:
Tissues were homogenized and whole cell RNA was extracted using Tri-Reagent (Euromedex) according to the manufacturers instructions.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

value: Brain

value: SNORD115/116 KO


title: Brain_E16.5_SNORD115_116_KO_2

description: Whole cell RNA from tissue


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G3_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G3_ad002


title: Brain_adult_SNORD115_KO_3

description: Whole cell RNA from tissue

value: SNORD115 KO

value: adult


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad012


title: Brain_adult_SNORD115_KO_2

description: Whole cell RNA from tissue


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad001


title: Brain_E16.5_SNORD115_116_KO_1

description: Whole cell RNA from tissue


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad004


title: CR-pretreatment plus myocardial ischemic rat 1

city: Yantai

first: Defang

last: Li

address: No. 346 Guanhai, Laishan District

institute: Binzhou Medical University

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer.After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
tRF & tiRNA ID will be divided into four parts by the horizontal line, eg: 'tRF-Gly-TCC-001'. The following is a brief description of these fields:(1) tRF or tiRNA, The type of tRF & tiRNA, eg: tRF; (2) amino acid, Type of amino acid, eg: Gly; (3) anticodon, Type of anticodon, eg: TCC; (4) Serial, The serial number of tRF & tiRNA derived from the tRNA of the same anticodon, eg: 001
The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb, tRFdb
Supplementary_files_format_and_content: Supplementary_files_format_and_content: text file with abundance

organism: Rattus norvegicus

source_name: Heart tissue

extract_protocol:
Total RNAs that were extracted from left heart ventricle tissue were pretreated with rtStar tRF & tiRNA Pretreatment Kits to remove RNA modifications that interfere with the construction of small RNA-seq libraries.
The cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, 134–160-bp PCR-amplified fragments (corresponding to small RNAs that were each 14–40 nt in length) were extracted and purified from an agarose gel.

treatment_protocol: Total RNA samples are pretreated to remove some RNA modifications that interfere with small RNA-seq library construction.

value: left heart ventricle tissue

value: Sprague-Dawley

value: caloric restriction plus isoproterenol


title: CR-pretreatment plus myocardial ischemic rat 4


title: CR-pretreatment plus myocardial ischemic rat 2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad002


title: Myocardial ischemic rat 5

value: isoproterenol


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G12_ad012


title: Myocardial ischemic rat 4


title: CR-pretreatment plus myocardial ischemic rat 5


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G12_ad010


title: Myocardial ischemic rat 3


title: Myocardial ischemic rat 2


title: Normal rat 5

value: untreated


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G12_ad007


title: Myocardial ischemic rat 1


title: Normal rat 4


title: CR-pretreatment plus myocardial ischemic rat 3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G12_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G12_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G3_ad006


title: Normal rat 3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G12_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad012


title: genomic DNA patient P3 [P3_X]

value: xenograft


title: Normal rat 2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G2_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad010


title: Normal rat 1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G9_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad007


title: CRS_WKY_1

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Reads, in FASTQ format, were trimmed using cutadapt v1.14.
Trimmed reads were aligned to the Rattus norvegicus (rn6) genome using TopHat  v2.1.0 using mostly default parameters with the exception of --library-type, which was set to "firststrand", due to Ion Proton library construction.
Genes were quantified and differential expression was performed using Cufflinks v2.2.1.
Cufflinks results were processed and visualized using CummeRbund.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each Sample

source_name: Wistar

growth_protocol: Adult male Fischer 344 (F344) and Wistar Kyoto (WKY) rats (approximately 3 months old) were obtained for the current study from Envigo (Indianapolis, IN) and for the microarray study carried out previously from Charles River Laboratories (Wilmington, MA), respectively. All animals were housed in a temperature-controlled environment with 12 h light/dark cycles and allowed feed and water ad–libitum. They were allowed to acclimate to their new environment for 2 weeks before beginning experimentation.

extract_protocol:
Immediately upon sacrifice, fresh blood was collected into PAXgene Blood RNA Tubes (PreAnalytiX, Qiagen, Hombrechtikon, Switzerland) and stored at -80 ºC after 1-day incubation at room temperature. Total RNA was isolated from the blood samples using the PAXgene Blood RNA Kit (PreanalytiX, Switzerland) according to the manufacturer’s protocol). This RNA was used for RNA-Seq and quantitative RT-PCR expression analyses.
RNA libraries were prepared for sequencing using standard Ion Proton protocols

treatment_protocol: Adult, 70-90 days old, F344 and WKY male rats were tested in the first contextual fear conditioning (FC) paradigm after which they were returned to their home cages for four weeks. Then, half of the animals were exposed to chronic restrain stress (CRS) daily, for two weeks while the other half remained in the home cage, undisturbed (No Stress; NS). CRS was performed by individually restraining the rats in breathable decapicone bags for 2 hours each day for two weeks. After each CRS treatment, the rats were returned to their home cage. Body weight was recorded before and after CRS treatment. All animals were exposed to a second FC test and the rats were sacrificed by quick decapitation at 24 h after the second day of the second FC testing

value: Wistar Kyoto

value: Chronic Restraint Stress (CRC)


title: CRS_WKY_2

value: male


title: CRS_WKY_3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad004

value: PIR


title: CRS_F344_3

source_name: Fischer

value: Fischer 344


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad002


title: RNAseq-L1CNS-CantonS-rep1

value: CNS

value: Canton-S


title: CRS_F344_2


title: Control_WKY_3

value: No Stress (NS)


title: CRS_F344_1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G10_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G10_ad008


title: Control_WKY_2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G10_ad006


title: Control_F344_3


title: Control_WKY_1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G10_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G10_ad001


title: Control_F344_2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G11_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad010


title: A549 cells_BM-MSC treated 4d_rep2

city: Hsinchu

first: Jia-Lin

address: 101, Sec. 2, Kuang Fu Road

country: Taiwan

institute: National Tsing Hua University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (Dye channel: R ; Scan resolution : 10 um; Tiff: 16-bit; Red PMT gain: 100%; XDR: 100 10) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: Lung cancer cell line A549

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

value: A549 lung cancer cells

value: BM-MSC

tag: time


title: A549 cells_BM-MSC treated 4d_rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G10_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad008


title: A549 cells_BM-MSC treated 3d_rep2


title: Control_F344_1


title: A549 cells_BM-MSC treated 4d_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F9_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F9_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F9_ad012


title: A549 cells_BM-MSC treated 3d_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F9_ad006


title: A549 cells_BM-MSC treated 2d_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F9_ad004


title: A549 cells_BM-MSC treated 1d_rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F9_ad002


title: A549 cells_BM-MSC treated 1d_rep2


title: A549 cells_BM-MSC treated 2d_rep2


title: A549 cells_BM-MSC treated 1d_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F9_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F8_ad012


title: A549 cells_BM-MSC treated 3d_rep3


title: A549 cells_BM-MSC treated 16h_rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F8_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G1_ad004


title: A549 cells_BM-MSC treated 16h_rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F8_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F8_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F8_ad002


title: A549 cells_BM-MSC treated 8h_rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F8_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F7_ad012


title: A549 cells_BM-MSC treated 8h_rep2


title: A549 cells_BM-MSC treated 16h_rep1


title: A549 cells_BM-MSC treated 4h_rep3


title: A549 cells_BM-MSC treated 8h_rep1


title: A549 cells_BM-MSC treated 4h_rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F7_ad007


title: A549 cells_BM-MSC treated 4h_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F7_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F7_ad002


title: t1

city: Beijing

first: qianqian

last: li

address: No. 11, Bei San Huan Dong Lu, Chaoyang District

department: School of Traditional Chinese Medicine

institute: Beijing University of Chinese Medicine

source_name: MXSG group

growth_protocol: Eight or nine-week-old Male SD rats (110±10 g) were maintained under specific pathogen-free conditions according to agency guidelines. The rats were kept with a 12-h light/dark cycle and with access to water and food ad libitum. After three days of adaptive breeding, 30 rats were randomly divided into three groups (n=10): normal group, pneumonia model group, Ma Xing Shi Gan Decoction (MXSG) group.

extract_protocol:
Add 600 μL Lysis/Binding Buffer to the tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min .Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
the library was detected by Agilent 2100 Bioanalyzer, Illumina HiSeqTM 2 sequencer was used to sequence the library, and 125bp or 150bp double-ended data were generated.

treatment_protocol: The pneumonia model group and MXSG group were received given 0.5 mg/mL LPS nebulization intervention, 30 min per day for three consecutive days. After 3 days, the MXSG group were intragastrically administered of MXSG once a day for 3 consecutive days (According to clinical guidelines, all doses were converted according to the equivalent dose of 0.018 for human and rat). The model group and the control group received an equal volume of saline accordingly.

value: Ma Xing Shi Gan (MXSG) Decoction

value: lung


title: t2

value: Sprague-Dawley


title: t3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F7_ad008


title: n3

source_name: normal group

tag: group

value: normal

value: saline


title: A549 cells_BM-MSC treated 2h_rep3


title: n2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad012

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: A549 cells_BM-MSC treated 2h_rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad001

tag: Sex


title: A549 cells_BM-MSC treated 2h_rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F7_ad001

tag: age


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad010

tag: strain


title: n1


title: A549 cells_BM-MSC treated 2d_rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad004


title: p2

source_name: pneumonia model group

value: LPS-induced ALI model


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F7_ad004


title: p1


title: JF41

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. The offspring F1, F2 and F3 generations were all aged to 90 days of age and bred within the generation and within the jet fuel lineage. F1- F3 generation control and jet fuel lineages were housed in the same room and racks with lighting, food and water. All the animals were aged to 1 year and euthanized for pathology and sperm collected for epigenetic analyses.

extract_protocol:
The epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm. The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing. An appropriate amount of rat sperm suspension was used for DNA extraction. Previous studies have shown mammalian sperm heads are resistant to sonication unlike somatic cells. Somatic cells and debris were therefore removed by brief sonication (Fisher Sonic Dismembrator, model 300, power 25), then centrifugation and washing 1-2 times in 1X PBS. The resulting pellet was resuspended in 820 µL DNA extraction buffer and 80 µl 0.1M DTT added, then incubated at 65°C for 15 minutes. 80 µl proteinase K (20 mg/ml) was added and the sample was incubated at 55°C for 2-3 hours under constant rotation. Protein was removed by addition of protein precipitation solution (300 µl, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500 rpm for 30 minutes at 4°C. One ml of the supernatant was precipitated with 2 µl of glycoblue (Invitrogen, AM9516) and 1 ml of cold 100 % isopropanol. After incubation, the sample was spun at 13,500 x g for 30 min at 4°C, then washed with 70% cold ethanol. The pellet was air-dried for about 5 minutes then resuspended in 100 µl of nuclease free water. Genomic DNA was sonicated and run on 1.5% agarose gel for fragment size verification. The sonicated DNA was then diluted with 1X TE buffer to 400 μl, then heat-denatured for 10min at 95˚C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100 μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml), and incubated for 2-3 hours on a rotator at 55˚C. DNA clean-up was performed using a Phenol-Chloroform-Isoamyl-Alcohol extraction, and the supernatant precipitated with 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol in -20˚C freezer for one to several hours. The DNA precipitate was pelleted, washed with 70% ethanol, then dried and resuspended in 20μl H2O or 1X TE. DNA concentration was measured in Qubit (Life Technologies) with the ssDNA kit (Molecular Probes Q10212).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina. The samples were sequenced on the Illumina HiSeq 2500 at PE50, with a read size of approximately 50 bp and approximately 20 million reads per pool. Twelve libraries were run in one lane.

treatment_protocol: Timed-pregnant females on days 8 through 14 of gestation [53] were administered daily intraperitoneal injections of JP-8 hydrocarbon (jet fuel obtained from Lt Dean Wagner, Dayton, OH), 500 mg/kg/BW/day, or dimethyl sulfoxide (DMSO) with an equal volume of sesame oil (Sigma) to prevent irritation at the injection site.

value: Hsd:Sprague Dawley SD (Harlan)

value: Sperm

tag: f0 treatment

value: Jet fuel

value: 1 year

tag: disease


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad008

value: PIR

value: male


title: JF40


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F5_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad007


title: p3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F5_ad007


title: JF37

description: jetfuel.multiple.results.csv.gz

value: testis, prostate


title: JF39

description:
jetfuel.kidney.results.csv.gz
jetfuel.latePuberty.results.csv.gz
jetfuel.multiple.results.csv.gz
jetfuel.obesity.results.csv.gz


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F5_ad004


title: JF34


title: JF33


title: JF38

description: jetfuel.multiple.results.csv.gz

value: prostate, obesity


title: JF35


title: JF32

description: jetfuel.latePuberty.results.csv.gz

value: late puberty


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F4_ad012


title: JF31


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F5_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F5_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F4_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F5_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F6_ad002


title: JF29


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F5_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F4_ad004


title: JF28

description: jetfuel.kidney.results.csv.gz

value: kidney


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F4_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F4_ad008


title: JF27


title: JF36

description: jetfuel.kidney.results.csv.gz


title: JF26


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad001


title: JF25


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F4_ad001


title: JF30


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad010


title: JF21

value: testis


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad002


title: JF20

description: jetfuel.obesity.results.csv.gz

value: obesity


title: JF18

description: jetfuel.multiple.results.csv.gz

value: early puberty, kidney


title: JF17


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F2_ad012


title: JF16


title: JF23

description: jetfuel.obesity.results.csv.gz


title: JF22


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F2_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F2_ad010


title: JF15


title: JF14

description:
jetfuel.kidney.results.csv.gz
jetfuel.latePuberty.results.csv.gz


title: JF24


title: JF13

description: jetfuel.obesity.results.csv.gz


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F2_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F2_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F3_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_G12_ad008


title: JF19


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad010


title: JF9

description: jetfuel.latePuberty.results.csv.gz


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad007


title: JF11


title: JF8

description: jetfuel.multiple.results.csv.gz

value: late puberty, obesity


title: JF7


title: JF6

description: jetfuel.latePuberty.results.csv.gz


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F12_ad001


title: JF4


title: JF3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F2_ad006


title: JF12

description: jetfuel.kidney.results.csv.gz


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F2_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F11_ad010


title: JF1

description: jetfuel.obesity.results.csv.gz


title: JF2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F11_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F11_ad006


title: JF10


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F11_ad004


title: FS_30_27_094_F

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 (10mg/m3 dose) or MINLEN:60 (30mg/m3 dose).
All sequences were aligned to the Rattus norvegicus Rnor 6.0 genome from NCBI downloaded July 31, 2015 using HiSat2/2.1.0.
Raw gene counts were assigned using Samtools/1.8, Python/2.7.3 and HTSeq/0.6.1.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

source_name: lung

growth_protocol: Male Sprague-Dawley rats (Hilltop Lab Animals, Scottdale, PA), weighing approximately 200-250 g were used in this study which was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in pairs and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and HaCXan Teklad Global 18% protein rodent diet (Harlan Teklad; Madison, WI).

extract_protocol:
Total RNA was isolated from a piece of the lung tissue using the RNeasy Mini Kit (Qiagen, Inc, Valencia, CA) following the procedure provided by the manufacturer.
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep (Illumina, Inc., San Diego, CA) following the manufacturer's protocol.  Briefly, following depletion of ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis.  The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers.  While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA.  After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. The rats were exposed by inhalation to filtered air or fracking sand dust (10 or 30 mg/m3, 6 hours/day for 4 days). At post exposure time intervals of 1, 7, and 27 days, the air and fracking sand dust exposed rats were euthanized (n=5 for the 10 mg/m3 post exposure intervals 1 and 7 days; n=4 for 10 mg/m3 post exposure interval 27 days, and n=6 for the 30 mg/m3 fracking sand dust at all post exposure intervals).

value: Sprague-Dawley

tag: post-exposure timepoint (days)


title: FS_30_27_096_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F11_ad001

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: JF5

description: jetfuel.kidney.results.csv.gz

tag: tissue


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F10_ad012


title: FS_30_27_091_F


title: FS_30_27_092_F


title: FS_30_27_090_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F11_ad002


title: FS_30_27_085_A

value: air


title: FS_30_27_089_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F10_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F10_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F11_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F10_ad004


title: FS_30_27_087_A


title: FS_30_27_084_A


title: FS_30_27_083_A


title: FS_30_27_082_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F10_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F10_ad010


title: FS_30_27_081_A


title: FS_30_07_079_F


title: FS_30_07_077_F


title: Brain_adult_SNORD115_KO_1

description: Whole cell RNA from tissue

value: Brain

value: SNORD115 KO

value: adult


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad001


title: FS_30_07_075_F


title: FS_30_07_076_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad007


title: FS_30_07_074_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad004


title: FS_30_07_073_F


title: FS_30_07_071_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad002


title: FS_30_07_070_A


title: FS_30_07_068_A


title: FS_30_07_069_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E9_ad007


title: FS_30_07_066_A


title: FS_30_07_065_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E9_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E9_ad001


title: FS_30_01_062_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad010


title: FS_30_01_061_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E9_ad012


title: FS_30_01_060_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad007


title: FS_30_01_058_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F1_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E9_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad010


title: FS_30_01_053_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad004


title: FS_30_01_055_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E9_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad008


title: FS_30_01_052_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad012


title: FS_30_01_049_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad001


title: FS_30_01_051_A


title: FS_10_27_016_F


title: FS_30_01_059_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad004


title: FS_10_27_013_F


title: FS_10_27_014_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad002


title: FS_30_01_057_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad008


title: FS_30_01_054_A


title: FS_10_27_006_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E8_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad001


title: FS_10_07_048_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad007


title: FS_10_27_005_A


title: FS_10_27_003_A


title: FS_10_27_001_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad010


title: FS_10_07_047_F


title: FS_10_07_045_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad006


title: FS_10_07_044_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E7_ad006


title: FS_10_07_043_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E5_ad001


title: FS_10_07_039_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad002


title: FS_10_07_037_A


title: FS_10_07_036_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E5_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad008


title: FS_10_07_034_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_F10_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E5_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E5_ad006


title: FS_10_01_031_F


title: FS_10_01_032_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E5_ad002


title: FS_10_07_033_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad012


title: FS_10_01_030_F


title: FS_10_01_029_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E5_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E6_ad004


title: FS_10_01_027_F


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad007


title: FS_10_01_021_A


title: FS_10_01_020_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad006


title: FS_10_01_019_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E5_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad002


title: FS_10_01_018_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E3_ad004


title: FS_10_01_017_A


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E2_ad001


title: bZIP30-input

city: Yangling

first: Xianhang

last: Wang

state: Shaanxi

address: No.3 Taicheng Road

department: State Key Laboratory of Crop Stress Biology in Arid Areas

institute: Northwest A&F University

data_processing:
The clean reads were then aligned to reference genome sequences using the bwa program
using macs2 software for callpeak with cutoff qvalue < 0.05.
Peaks were annotated by using homer's annotatePeaks.pl.
Genome_build: V. vinifera reference genome (http://plants.ensembl.org/index.html)
Supplementary_files_format_and_content: peak

organism: Vitis vinifera

source_name: grapevine

growth_protocol: Four-month-old transgenic grapevine overexpressing VlbZIP30 as a fusion with a 3 × FLAG-tag under the control of the CaMV35S grown in an illumination incubator (25°C, 16-h photoperiod and a light intensity of 200 μmol m–2 s–1), were subjected to drought stress by withholding water for 20 days. The first to third leaf from the top of the grapevine were harvested, immediately frozen in liquid nitrogen and stored at -80°C, prior to use in ChIP-seq analysis.

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
the ChIP DNA and NEBNext® Ultra™II DNA Library Prep Kit for Illumina (#E7645S, New England Biolabs) was used to generate sequencing libraries, according to the manufacturer’s instructions.

treatment_protocol: Drought treatment for 20 day

value: drought treatment

tag: chip antibody

value: IgG (Sigma-Aldrich) antibody

value: leaves


title: bZIP30-flag

value: anti-FLAG M2 antibody (#F1804, Sigma-Aldrich)


title: CK1-rep1

city: Hangzhou

first: Dan

last: Hou

address: 666 Wusu street, Lin'an District, Hangzhou

institute: A&F university

data_processing:
Illumina Novaseq™ 6000 used for RNA-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Phyllostachys edulis reference genome
FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) were caculated
Genome_build: Phyllostachys edulis reference genome
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt includes count and FPKM values for all genes

organism: Phyllostachys violascens

source_name: spring shoot

extract_protocol:
The middle parts of 6 shoots for each repetition (about 10 cm) were sampled and rapidly frozen in the liquid nitrogen and stored at -80℃. Total RNA was extracted using RNAiso Plus (Takara, Japan) according to the protocol, and after quality testing, was used for library construction and transcriptome sequencing by Illumina Novaseq™ 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A total of ~120 shoots (four biological replicate, 30 shoots together for each repeat) were treated under low temperature (4℃). The polyethylene bags were used to pack shoots to keep the humidity around 60%-70%.

value: young shoots about 30-40 cm height

value: middle part of shoot

tag: time point

tag: protocol

value: 4degreeC treatment


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E2_ad010

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: PIR

value: male


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E2_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E2_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E2_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad012


title: T3-3-L

city: Chengdu

first: Liming

last: Chang

state: Sichuan

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

institute: Chengdu Institute of Biology

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;The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
Genome_build: de novo
Supplementary_files_format_and_content: FPKMs; fasta file includes the sequences of all unigenes across samples.

organism: Rana omeimontis

source_name: Liver

extract_protocol:
Total RNA of each sample was extracted and purified using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. After purified with poly-T oligo-attached magnetic beads, the mRNAs were fragmented.
First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H−). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 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 a 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. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 2500 platform by NovoGene (Beijing), and paired-end reads were generated.

tag: collection site

value: Anzihe Natural Reserve (103.459885° E, 30.744614° N, 701 m) in Sichuan Province, China

tag: developmental stage

value: Metamorphic stage

value: Liver


title: T3-3-T

source_name: Tail

value: Tail


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad010

city: La Jolla

last: Ecker


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E2_ad002


title: T3-2-T


title: T3-2-L


title: T3-1-T


title: CK-3-L

value: Pro-metamorphic stage


title: CK-3-T


title: T3-1-L


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E2_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad006


title: CK-2-L


title: CK-2-T


title: CK-1-L


title: CK-1-T


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad001


title: UNC-3_Input

first: Paschalis

last: Kratsios

department: Department of Neurobiology

institute: University of Chicago

description: Total genomic DNA was purified from whole worm lysates

data_processing:
ChIP-Seq reads were alligned to the ce10 genome with bowtie2
Peak calling was performed with MACS2
Genome_build: ce10
Supplementary_files_format_and_content: bed files including peaks called with MACS2
Supplementary_files_format_and_content: bigWig files were generated by normalizing read counts to 1x genome coverage

organism: Caenorhabditis elegans

source_name: Whole worms

growth_protocol: Worms were grown on NGM (Nematode Growth Medium) plates seeded with OP50 at 20 °C

extract_protocol:
Lysates were clarified from sonicated worm tissue and UNC-3-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole worms

tag: antibody


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad012


title: UNC-3_ChIPSeq

description: ChIP DNA was isolated with GFP antibody from whole worm lysates

value: Anti-GFP antibody - ChIP grade (ab290)


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad007


title: LT-20d-rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad006


title: LT-20d-rep3


title: LT-20d-rep4


title: LT-6d-rep4


title: LT-20d-rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad004


title: LT-6d-rep3


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad010


title: LT-6d-rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E12_ad004


title: LT-6d-rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad008


title: LT-2d-rep4


title: LT-2d-rep3


title: LT-2d-rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad004


title: LT-2d-rep1


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E11_ad010


title: CK4-rep4


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E1_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E1_ad010


title: CK3-rep3


title: CK2-rep2


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E1_ad008


title: 5571AA_MSCB-192

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

description:
cryopreserved HCA reference
In total, 4 sample pools were analyzed with 192 cells/pool. Each of the groups should be considered identical except for batch correction during the statistical analysis.

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the genome reference  for human, mouse and canine cells. Smart-seq2 libraries were equally mapped as paired-end reads.
For MARS-seq samples, gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Human: Gencode release 27, assembly GRCh38;  mouse: Gencode release M15, assembly GRCm38; dog:  Ensembl v90, assembly CanFam3.1
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts (MARS-Seq) for each cell (columns).

organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

extract_protocol:
Human cell line HEK293 (human embryonic kidney cells) was acquired from the German Collection of Microorganisms and Cell Cultures (DSMZ). NIH3T3 (mouse embryo fibroblasts) were kindly provided by Dr. Manel Esteller (IDIBELL, Spain). HEK293, NIH3T3 and MDCK were maintained in DMEM (10% Fetal Bovine Serum, FBS; 1% Penicillin/Streptomycin) at 37ºC (5% CO2).    For cryopreservation, cells were trypsinized, pelleted and resuspended in freezing solution I (10% DMSO; 10% heat-inactivated FBS; 80% DMEM) or solution II (10% DMSO; 90% non-inactivated FBS). Subsequently, cells were frozen with gradually decreasing temperatures (1ºC/min) to -80ºC (cryopreserved).For single cell analysis, cryopreserved cells were rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Fresh cells were trypsinized, pelleted and resuspended in 1x HBSS. Before sorting, cells from both conditions were filtered (70 µm nylon mesh) and propidium iodide staining identified dead/damaged cells.    Whole blood was collected from a healthy donor into EDTA tubes (Becton, Dickinson and Co). Separation of peripheral blood mononuclear cells (PBMC) was performed with Ficoll-Paque PREMIUM (GE Healthcare) according to manufacturer's instructions. Briefly, for density gradient separation, 4 ml of blood was added onto 3 ml of Ficoll-Paque PREMIUM. Centrifuged at 400 x g for 30 minutes at 18ºC without brake. PBMC layer was recuperated and washed twice with PBS at 400g for 15 minutes at 18ºC. PBMC were resuspended in freezing solution (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to ‑80ºC (cryopreserved). After storage for one week at -80ºC, the cryopreserved sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. To avoid batch effects, fresh PBMC were sorted in parallel with the cryopreserved material and distributed over the same sequencing pools. Therefore, blood from the same donor was isolated as described above and directly resuspended in DMEM. Dead and damaged cells were identified by propidium iodide staining.    Primary mouse colon was dissected from an athymic nu/nu mouse and placed on ice. The sample was divided and half of the colon was immediately prepared for single cell separation, while the other half was minced on ice, placed into freezing solution II (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to ‑80ºC (cryopreserved). After storage for one week at -80ºC, the sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. For single cell separation the fresh and conserved samples were minced on ice and enzymatically digested in 5 ml 1x HBSS and 83 µl collagenase IV (10,000 U/ml) for 10 min at 37ºC. Single cells were separated by passing the sample through a 0.9 mm needle and filtration (70 µm nylon mesh). Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. Dead and damaged cells were identified by propidium iodide staining.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014).  This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes. Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

tag: cell type

value: human PBMC and mouse colon (80%), HEK293 (10%), NIH3T3 (10%), MDCK (< 1%)

tag: sample pool


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E1_ad004


title: 5571AA_MSCB-191


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad012


title: 5571AA_MSCB-190


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E1_ad012


title: 5571AA_MSCB-187


title: 5571AA_MSCB-186


title: 5571AA_MSCB-189


title: 5571AA_MSCB-185


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E10_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad004


title: 5571AA_MSCB-184


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad002


title: 5571AA_MSCB-182


title: 5571AA_MSCB-181


title: CEMBA190205_6D_3_CEMBA190205_6D_4_E1_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad012


title: 5571AA_MSCB-188


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad007


title: 5571AA_MSCB-179


title: 5571AA_MSCB-180


title: 5571AA_MSCB-177


title: 5571AA_MSCB-178


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad002


title: 5571AA_MSCB-175


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D8_ad008


title: 5571AA_MSCB-176


title: 5571AA_MSCB-171


title: 5571AA_MSCB-183


title: 5571AA_MSCB-173


title: 5571AA_MSCB-172


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D7_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D7_ad001


title: 5571AA_MSCB-170


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D7_ad007


title: 5571AA_MSCB-169


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D9_ad008


title: 5571AA_MSCB-168


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D7_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D7_ad006


title: 5571AA_MSCB-167


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D7_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D7_ad008


title: 5571AA_MSCB-174


title: 5571AA_MSCB-166


title: 5571AA_MSCB-165


title: 5571AA_MSCB-164


title: 5571AA_MSCB-162


title: 5571AA_MSCB-163


title: 5571AA_MSCB-161


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad007


title: 5571AA_MSCB-159


title: 5571AA_MSCB-160


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad004


title: 5571AA_MSCB-158


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad007


title: 5571AA_MSCB-155


title: 5571AA_MSCB-154


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad010


title: 5571AA_MSCB-153


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad012


title: 5571AA_MSCB-152


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D6_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad008


title: 5571AA_MSCB-157


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D5_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad001


title: 5571AA_MSCB-156


title: 5571AA_MSCB-147


title: 5571AA_MSCB-148


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad010


title: 5571AA_MSCB-149


title: 5571AA_MSCB-150


title: 5571AA_MSCB-145


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad006


title: 5571AA_MSCB-144


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad007


title: 5571AA_MSCB-143


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad002


title: 5571AA_MSCB-151


title: 5571AA_MSCB-141


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D3_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D4_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D3_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D3_ad008


title: 5571AA_MSCB-139


title: 5571AA_MSCB-140


title: 5571AA_MSCB-146


title: 5571AA_MSCB-137


title: 5571AA_MSCB-138


title: 5571AA_MSCB-136


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D3_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D3_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D2_ad012


title: 5571AA_MSCB-135


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D3_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D2_ad010


title: 5571AA_MSCB-134


title: 5571AA_MSCB-142


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D3_ad006


title: 5571AA_MSCB-131


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D2_ad004


title: 5571AA_MSCB-130


title: 5571AA_MSCB-129


title: 5571AA_MSCB-132


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D2_ad002


title: 5571AA_MSCB-127


title: 5571AA_MSCB-128


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D2_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D12_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D12_ad010


title: 5571AA_MSCB-133


title: 5571AA_MSCB-125


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D12_ad007


title: 5571AA_MSCB-123


title: 5571AA_MSCB-124


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D12_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D2_ad007


title: 5571AA_MSCB-122


title: 5571AA_MSCB-121


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D12_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D12_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D2_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D12_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad012


title: 5571AA_MSCB-119


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad010


title: 5571AA_MSCB-120


title: 5571AA_MSCB-118


title: 5571AA_MSCB-117


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad006


title: 5571AA_MSCB-116


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad002


title: 5571AA_MSCB-114


title: 5571AA_MSCB-115


title: 5571AA_MSCB-113


title: 5571AA_MSCB-110


title: 5571AA_MSCB-112


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad012


title: 5571AA_MSCB-108


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad001


title: 5571AA_MSCB-111


title: 5571AA_MSCB-107


title: 5571AA_MSCB-106


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad004


title: 5571AA_MSCB-105


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad007


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad008


title: 5571AA_MSCB-103


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C9_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad004


title: 5571AA_MSCB-102


title: 5571AA_MSCB-101


title: 5571AA_MSCB-100


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C9_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C9_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C9_ad002


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C9_ad008


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D1_ad006


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C8_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C8_ad001


title: CEMBA190205_6D_3_CEMBA190205_6D_4_D10_ad001


title: 5571AA_MSCB-104


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C8_ad010


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C9_ad012


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C8_ad006


title: 5571AA_MSCB-094


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C8_ad004


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C8_ad008


title: 5571AA_MSCB-092


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad012


title: 5571AA_MSCB-093


title: 5571AA_MSCB-109


title: 5571AA_MSCB-091


title: 5571AA_MSCB-090


title: 5571AA_MSCB-089


title: 5571AA_MSCB-098


title: FS_10_27_015_F

tag: treatment

value: Sprague-Dawley


title: CEMBA190205_6D_3_CEMBA190205_6D_4_C7_ad010

tag: brain region