title: IL-10+ CD4+ T-cells small intestine p2_D13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_C23

status: Public on Nov 07 2018

type: SRA

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description: SI.counts.txt

library_source: transcriptomic

data_processing:
After demultiplexing based on Nextera-adapters and the 384-well plate layout, the single-end reads were aligned to the reference genome using STAR
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts in tab delimited text file

molecule: polyA RNA

organism: Mus musculus

source_name: T-cells from small intestine

extract_protocol: Libraries were constructed using the SMART-seq2 protocol

tag: tissue

value: small intestine

tag: treatment


title: MS1222_Nicolaides-Baraitser syndrome

type: genomic

city: London

first: Bekim

last: Sadikovic

state: Ontario

address: 800 Commissioners Rd E

department: Pathology and Laboratory Medicine

country: Canada

institute: University of Western Ontario

description: SAMPLE 10

hyb_protocol: According to the manufacturer's protocol

scan_protocol: iScan

data_processing: Illumina Normalization method with background correction, using minfi package in R 3.4.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Standard DNA extraction from blood

tag: disease state

value: Nicolaides-Baraitser syndrome

value: Whole Blood


title: MS1163_Coffin-Siris Syndrome 3

description: SAMPLE 3

label_protocol: According to the manufacturer's protocol

value: Coffin-Siris syndrome


title: Thorax_D30_control_batch_1_rep_3

type: RNA

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

country: USA

institute: NINDS/NIH

hyb_protocol: Labeled cRNA were hybridized to the DroGene 1.0 ST GeneChip (Affymetrix, Santa Clara, CA) according to the manufacturer’s guidelines.

scan_protocol: The Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate one .CEL file per hybridized cRNA.

data_processing: The Expression Console (Affymetrix) was used to summarize the data contained across all .CEL files and generate 16,322 RMA normalized probe expression values.

label: Biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: D30 control

label_protocol: Extracted RNA were processed and labeled according to the manufacturer’s guidelines for use with the DroGene 1.0 ST GeneChip (Affymetrix, GeneChip Whole Transcript Sense Target Labeling).

growth_protocol: In this study, flies were aged to 3-, 10-, 30-, or 45-days old.  14 male and 10 female newly-eclosed flies were aliquoted into a vial containing standard KD food and a strip of tegocept paper; five sets of 10 vials were collected for each genotype and time point (each replicate consisted of 90-140 male flies).  Flies were maintained at 25°C with a 12 hr∶12 hr light∶dark cycle, and were transferred to fresh vials every three days.  Once at the appropriate age, flies were anesthetized under CO2, then flash frozen in liquid nitrogen; samples were stored at -80°C until all time points were collected. Eppendorf tubes containing frozen flies were transferred into liquid nitrogen to further chill them, then vortexed to separate the heads, wings, and legs from the rest of the bodies.  Keeping the samples cold on dry ice, the heads were manually transferred to a fresh tube.  Thoraces were separated from the abdomen using a surgical blade, and then transferred to their own tube.  Separated tissues were flash frozen and stored at -80°C until all samples were collected.

extract_protocol: Isolated tissue samples were stored at -80°C prior to phenol-chloroform extraction using the TRIzol reagent.  Samples were homogenized in TRIzol, chloroform was added, and the resultant mixture centrifuged; RNA was precipitated from the upper aqueous layer using isopropanol.  Following ethanol washes, the purified RNA was resuspended in RNAse-free water and stored at -80°C.

value: Thorax

tag: genotype

value: control

tag: age

value: 30 Days

tag: Sex

value: male

tag: batch

tag: cross batch technical replicate

value: No


title: Thorax_D10_p35-OE_batch_1_rep_5

value: 10 Days


title: Thorax_D30_control_batch_1_rep_2


title: IL-10+ CD4+ T-cells small intestine p2_C22

description: SI.counts.txt


title: MS1160_Nicolaides-Baraitser syndrome

description: SAMPLE 1


title: Thorax_D30_control_batch_1_rep_1


title: IL-10+ CD4+ T-cells small intestine p2_C20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_C19

description: SI.counts.txt


title: Thorax_D45_control_batch_1_rep_3

source_name: D45 control

value: 45 Days


title: Thorax_D10_p35-OE_batch_1_rep_4


title: IL-10+ CD4+ T-cells small intestine p2_C18

description: SI.counts.txt


title: Thorax_D10_p35-null_batch_1_rep_5

source_name: D10 p35-null


title: IL-10+ CD4+ T-cells small intestine p2_C17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_C16

description: SI.counts.txt


title: Thorax_D10_p35-null_batch_1_rep_2


title: Thorax_D10_p35-OE_batch_1_rep_1


title: Thorax_D10_p35-OE_batch_1_rep_3


title: Thorax_D10_control_batch_1_rep_4

source_name: D10 control


title: Thorax_D10_p35-OE_batch_1_rep_2


title: Thorax_D10_p35-null_batch_1_rep_1


title: Thorax_D10_p35-null_batch_1_rep_3


title: Thorax_D10_control_batch_1_rep_3


title: Thorax_D3_control_batch_1_rep_5

source_name: D3 control

value: 3 Days


title: Thorax_D10_control_batch_1_rep_1

value: Yes


title: Thorax_D3_control_batch_1_rep_4


title: Thorax_D10_p35-null_batch_1_rep_4


title: Thorax_D3_control_batch_1_rep_3


title: Thorax_D10_control_batch_1_rep_5


title: Thorax_D10_control_batch_1_rep_2


title: MS1168_Coffin-Siris Syndrome 4

description: SAMPLE 4


title: Thorax_D10_control_batch_2_rep_2


title: Thorax_D3_control_batch_1_rep_2


title: IL-10+ CD4+ T-cells small intestine p2_C14

description: SI.counts.txt


title: MS1221_Nicolaides-Baraitser syndrome

description: SAMPLE 9


title: IL-10+ CD4+ T-cells small intestine p2_C13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_B24

description: SI.counts.txt


title: Thorax_D3_control_batch_1_rep_1


title: IL-10+ CD4+ T-cells small intestine p2_C15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_B23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_B22

description: SI.counts.txt


title: Head_D10_rescue_batch_2_rep_2

source_name: D10 rescue

value: Head

value: rescue


title: IL-10+ CD4+ T-cells small intestine p2_B20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_B21

description: SI.counts.txt


title: Head_D10_control_batch_2_rep_6


title: Head_D10_control_batch_2_rep_5


title: Head_D10_rescue_batch_2_rep_5


title: Head_D10_control_batch_2_rep_4


title: Thorax_D45_control_batch_1_rep_4


title: Head_D10_control_batch_2_rep_3


title: Head_D45_control_batch_1_rep_4


title: Head_D10_rescue_batch_2_rep_1


title: Head_D45_control_batch_1_rep_5


title: Head_D10_control_batch_2_rep_1


title: Head_D10_rescue_batch_2_rep_4


title: IL-10+ CD4+ T-cells small intestine p2_B18

description: SI.counts.txt


title: Head_D10_control_batch_2_rep_2


title: Head_D10_rescue_batch_2_rep_3


title: Head_D45_control_batch_1_rep_1


title: Head_D45_control_batch_1_rep_2


title: IL-10+ CD4+ T-cells small intestine p2_B16

description: SI.counts.txt


title: Head_D30_control_batch_1_rep_3


title: IL-10+ CD4+ T-cells small intestine p2_B15

description: SI.counts.txt


title: Head_D30_control_batch_1_rep_2


title: IL-10+ CD4+ T-cells small intestine p2_B19

description: SI.counts.txt


title: Head_D30_control_batch_1_rep_4


title: IL-10+ CD4+ T-cells small intestine p2_B14

description: SI.counts.txt


title: Head_D30_control_batch_1_rep_1


title: Head_D10_p35-OE_batch_1_rep_5


title: Head_D10_p35-OE_batch_1_rep_3


title: Head_D45_control_batch_1_rep_3


title: Head_D10_p35-OE_batch_1_rep_4


title: Head_D10_p35-OE_batch_1_rep_2


title: Head_D10_p35-OE_batch_1_rep_1


title: IL-10+ CD4+ T-cells small intestine p2_A24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_A23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_B13

description: SI.counts.txt


title: Head_D30_control_batch_1_rep_5


title: IL-10+ CD4+ T-cells small intestine p2_A22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_B17

description: SI.counts.txt


title: Head_D10_p35-null_batch_1_rep_3


title: Head_D10_p35-null_batch_1_rep_5


title: Head_D10_control_batch_1_rep_5


title: Head_D10_p35-null_batch_1_rep_2


title: Head_D10_control_batch_1_rep_2


title: Head_D10_p35-null_batch_1_rep_1


title: Head_D10_control_batch_1_rep_1


title: Head_D10_control_batch_1_rep_4


title: IL-10+ CD4+ T-cells small intestine p2_A21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_A20

description: SI.counts.txt


title: Head_D10_control_batch_1_rep_3


title: IL-10+ CD4+ T-cells small intestine p2_A19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_A18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_A16

description: SI.counts.txt


title: Head_D3_control_batch_1_rep_4


title: Head_D3_control_batch_1_rep_5


title: Head_D10_p35-null_batch_1_rep_4


title: IL-10+ CD4+ T-cells small intestine p2_A15

description: SI.counts.txt


title: Head_D3_control_batch_1_rep_3


title: IL-10+ CD4+ T-cells small intestine p2_A14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_A13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_A17

description: SI.counts.txt


title: Head_D3_control_batch_1_rep_1


title: Head_D3_control_batch_1_rep_2


title: 4 dpf, reserpine injected at zygote, biological replicate 1

city: Woods Hole

first: Evgeny

middle: G.

last: Ivashkin

state: MA

address: 7 MBL St.

department: Josephine Bay Paul Center

institute: Marine Biological Laboratory

description: Gene expression data from  4-day old larvae injected with reserpine at zygote stage

hyb_protocol: Total RNA wath hybridized to 902007 Affymetrix® Zebrafish Gene 1.0 ST Array with Ambion WT terminal labeling and hybridization protocol

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The data were analysed with MATLAB Bioinformatics Toolbox R2015a, using affygcrma function with default settings

label: biotin

organism: Danio rerio

source_name: 4-day old larvae,  reserpine injected at zygote

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Standard protocol

extract_protocol: Total RNA was extracted from 30-40 2 and 4 dpf zebrafish larvae from each experimental group. Total RNA from each sample was used for the synthesis of cDNA. Trizol extraction and Qiagen RNAeasy Mini Kit protocol were applied.

treatment_protocol: Embryos were dechorionated with Proteinase K. Embryos were injected with solution of 5-HT or reserpine in KCl (reserpine was dissolved in ethanol then in DMSO and finally in water-based injections solution) mixed with TRITC- dextran as a marker. Controls were injected with relevant amount of DMSO and ethanol in TRITC-dextran-containing KCl solution.

value: larvae

value: wildtype, AB line


title: 4 dpf, reserpine injected at zygote, biological replicate 2

description: Gene expression data from  2-day old larvae injected with reserpine at zygote stage


title: 4 dpf, 5-HT injected at zygote, biological replicate 1

description: Gene expression data from  4-day old larvae injected with 5-HT at zygote stage

source_name: 4-day old larvae,  5-HT injected at zygote


title: 4 dpf, 5-HT injected at zygote, biological replicate 2


title: 4 dpf, control, biological replicate 1

description: Gene expression data from normal 4-day old larvae

source_name: 4-day old larvae,  control


title: 2 dpf, reserpine injected at zygote, biological replicate 1

source_name: 2-day old larvae,  reserpine injected at zygote


title: 2 dpf, control, biological replicate 2

description: Gene expression data from normal 2-day old larvae

source_name: 2-day old larvae,  control


title: 4 dpf, control, biological replicate 2


title: sh Mbd3 Day 0

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

hyb_protocol: Fragmented and labelled cDNA was hybridised to GeneChip Mouse Gene 2.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The probe set signals were calculated with the robust multi-array average (RMA) algorithm implemented in GeneSpring GX 12.6.1 software (Agilent Technologies).

source_name: Mbd3 shRNA was introduced into ESCs

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) was used according to Affymetrix protocol.

growth_protocol: ESCs were cultured on 0.1% gelatin-coated dishes. The culture medium for ESCs included GMEM, 10% FBS, 1 mM non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol and 1000 units/ml LIF. For neural differentiation, ESCs were re-aggregated using low-cell-adhesion 96-well plates in G-MEM-based differentiation medium supplemented with 10% KSR.

extract_protocol: Total RNAs were extracted using NucleoSpin RNA kit according to the manufacturer’s protocol. On-column DNase digestion was performed.

treatment_protocol: ESCs were infected with a lentivirus encoding control shRNA or Chd4 shRNA or Mbd3 shRNA.

tag: cell type

value: ESC

value: Mbd3 knockdown

tag: time

value: day 0


title: 2 dpf, 5-HT injected at zygote, biological replicate 1

description: Gene expression data from  2-day old larvae injected with 5-HT at zygote stage

source_name: 2-day old larvae,  5-HT injected at zygote


title: 2 dpf, reserpine injected at zygote, biological replicate 2


title: sh Mbd3 Day 4

source_name: Mbd3 shRNA was introduced into ESCs and neural differentiation was induced for 4 days

value: day 4


title: 2 dpf, control, biological replicate 1


title: Periodontal connective tissue

city: Chiyoda-ku

first: Hodaka

last: Sasaki

address: 2-9-18, Kandamisaki-cho

department: Dept. of Oral and Maxillofacial Implantology

institute: Tokyo Dental College

description:
PCT_Rat230
Gene expression data from periodontal connective tissue collected by laser capture microdissection.

hyb_protocol: Following fragmentation, aRNA products were hybridized on GeneChip® Rat Genome 230 2.0 Array Chips (Affymetrix) for 16 h at 45°C in a GeneChip® Hybridization Oven 640 (Affymetrix). Hybridized arrays were washed and stained by using a GeneChip® Fluidics station 450 (Affymetrix).

scan_protocol: The images were scanned by using a GeneChip® scanner 3000 (Affymetrix).

data_processing: CEL files were generated using the GeneChip® Operating Software version 1.2 (Affymetrix). Data analysis and normalization were performed using GeneSpring® GX software version 12 (Agilent Technologies, Foster City, CA, USA).

organism: Rattus norvegicus

source_name: Periodontal connective tissue collected by laser microdissection

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled aRNA.

growth_protocol: Five-week-old male Sprague-Dawley rats were obtained from Japan SLC Inc. (Tokyo, Japan). After surgery the animals were housed in a room with controlled temperature and humidity and a 12 h light dark cycle and given freely water and diet until sacrificed after 4 weeks.

extract_protocol: Total RNA was extracted from PICT, PCT and OMCT which collected by laser microdissection using an RNeasy® Mini kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: For peri-implant connective tissue (PICT) collection, upper first molars of 5-week-old rats were extracted and titanium alloy implants were placed in the socket immediately and samples were harvested after 4 weeks. Periodontal connective tissue (PCT) was harvested from upper first molar of 9-week-old rats. Oral mucosal connective tissue (OMCT) was harvested from upper first molars 4 weeks after tooth extraction.

tag: strain/background

value: Sprague Dawley

tag: genotype/variation

value: Wild type

tag: gender

value: Male

value: 9 weeks

value: Periodontal connective tissue


title: CKBA rep3

city: Shanghai

first: Jing

last: Bai

state: Shanghai

address: 280# South Chongqing Road

department: School of Medicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapter sequences were removed by using SeqPrep, and then poor quality reads filtered by sickle (version 1.200) for quality control
Quality filtered reads were then mapped to GRCm38 using Hiast2(v2.1.0)
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
GO functional enrichment and KEGG pathway analysis were carried out by Goatools  and KOBAS
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file of expression analysis result of  EdgeR and annotation

source_name: mouse epidermis

growth_protocol: Mouse CD4 naïve T cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS, 500 U penicillin-streptomycin, 55 nM β-mercaptoethanol, 0.02 mM L-Glutamine, MEM Non-essential amino acids, 0.1 mM HEPES, 0.01 mM Sodium pyruvate, anti-CD28 (2 μg/ml), anti-IFN-γ (10 μg/ml), anti-IL-4(5 μg/ml), rhTGF-β1 (10 ng/ml), rmIL-6 (10 ng/ml) and rmIL-23 (10 ng/ml) for 3 days.

extract_protocol:
Cells were collected and total RNA was extracted using TRIzol® Reagent (Invitrogen).
RNA libraries were prepared for sequencing using TruSeq RNA library Prep Kit (Illumina) according to the protocol.

value: epidermis of mouse skin

tag: strain background

value: wild type

value: CD4+ T cells


title: DMSO rep1


title: Ribociclib_300mpk_B

city: San Diego

first: Brad

last: Hirakawa

state: CA

address: 10646 Science Center Drive

department: Drug Safety R&D

institute: Pfizer

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Rat 230_2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing:
The data were analyzed with the Affymetrix Command Console, Applied Biosystems Transcriptome Analysis console and Qiagen Ingenuity Pathways Analsys using default analysis settings and RMA normalization.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: jejunum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix/Applied Biosystems protocol using the IVT Express kit from 150 nM total RNA (Expression Analysis Technical Manual, Affymetrix)

growth_protocol: Male Sprague Dawley rats (CRL/CD SD, Charles River Laboratories, Hollister, CA) 6-8 weeks-old were utilized

extract_protocol: Qiazol extraction of total RNA in a bead mill homogenizer was performed according to the manufacturer's instructions, followed by RNA clean up using Qiagen RNeasy columns based on manufacturer's instructions.

treatment_protocol: Oral gavage dosing, 1 dose per day

tag: strain

value: male

value: 6-8 weeks-old

value: ribociclib (300 mg/kg/day)

value: jejunum mucosal scrapings


title: DMSO rep2


title: Oral mucosa connective tissue

description:
OMCT_Rat230
Gene expression data from oral mucosa connective tissue collected by laser capture microdissection.

source_name: Oral mucosal connective tissue collected by laser microdissection

value: Oral mucosa connective tissue


title: sh Chd4 Day 4

source_name: Chd4 shRNA was introduced into ESCs and neural differentiation was induced for 4 days

value: ESC

value: Chd4 knockdown


title: Peri-implant connective tissue

description:
PICT_Rat230
Gene expression data from peri-implant connective tissue collected by laser capture microdissection.

source_name: Peri-implant connective tissue collected by laser microdissection

value: Peri-implant connective tissue


title: CKBA rep2


title: Ribociclib_300mpk_A


title: Ribociclib_300mpk_C


title: sh Ctrl. Day 0

source_name: Control shRNA was introduced into ESCs

value: control

value: day 0


title: Input_B

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

library_source: genomic

data_processing:
Basecalling was performed using RTA version 2.4.11
Barcodes were demultiplexed allowing 1 mismatch using Bcl2fastq 2.17
Adapter and Quality Trimming was performed using Trimmomatic 0.36 with the following parameters: PE -threads 16 -phred33 –trimlog sample.log read1.fastq read2.fastq read1_trimmed.fastq read2_trimmed.fastq ILLUMINACLIP:Trimmomatic-0.36/adapters/TruSeq2-PE.fa:2:30:10 LEADING:20 TRAILING:20 MINLEN:50
Reads were aligned to hg38 genome using Bowtie2 version 2.2.5 with the following command: Bowtie2 –p 8 –x bowtie2_ref/genome_prefix –1 read1.fastq -2 read2.fastq –S result.sam
Peaks were called with DROMPA3.4.1, PC_SHARP settings
Genome_build: hg38
Supplementary_files_format_and_content: BED files containing peak location information

source_name: A549 lung adenocarcinoma cells

growth_protocol: A549 cell-line (1.6x106 cells) was seeded to a 125 cm2 flask with 10 mL of RPMI1640 supplemented with glutamine and 10% FBS followed by growth at 37°C for two overnights in a CO2 incubator.

extract_protocol:
Cells were washed with 10 ml of intact RPMI1640 media and fixed with 10 ml of fresh 1% paraformaldehyde in RPMI1640 media for 15 min at room temperature with gentle shaking. The fixation was quenched by adding 600 ul of 2.5 M glycine and incubating at room temperature for 5 min. The fixed cells were scraped and then resuspended after adding 1 ml of lysis H buffer (150 mM NaCl, 50 mM HEPES (7.5), 5 mM EDTA, 0.5% (vol/vol) IGEPAL CA-630, 1.0% (vol/vol) Triton-X100). The cells were collected with centrifugation in a 1.5 ml tube/flask at 2 krpm for 5 min at 4°C and washed twice with 500 ul of the cell wash buffer (1/10 diluted Lysis H buffer by HBSS). Resulting cell pellet was stored at -80°C until following analysis (one sample results in two flasks and then two tubes of cell pellets). One tube of cell pellet was washed twice with 1 ml of the lysis H buffer with protease inhibitors and collected with centrifuge. The cell pellet was resuspended with 1.5 ml of 1% SDS in the lysis H buffer. An aliquot (500 ul) of the cell suspension was transferred to a 1.5 ml tube to perform sonication by the BRANSON digital Sonifier (power 40%; pulse ON, 0.7 sec.; interval 1.3 sec.; total 30 min). The resulting lysates were cleared by twice of centrifuges and pooled. For input DNA control, 50 ul of the cleared lysate was saved. All of the left lysate was diluted with 13.5 ml of lysis H buffer with inhibitors, and this was incubated with 90 ul of washed suspension of the Streptavidin sepharose resin at 4°C for one overnight with gentle shacking. The resin was washed with once with 1 ml of the wash buffer I (20 mM Tris-HCl (8.0), 150 mM NaCl, 2mM EDTA, 1% TritonX-100, 0.1% SDS), II (20 mM Tris-HCl (8.0), 500 mM NaCl, 2mM EDTA, 1% TritonX-100, 0.1% SDS), III (20 mM Tris-HCl (8.0), 1mM EDTA, 0.5% Na deoxycholate, 1% IGEPAL), and twice with 1 ml of 100 mM Tris-HCl (pH 8.0), 10 mM EDTA, and then eluted with 90 ul of TESK buffer (25 mM Tris-HCl (pH8.0), 1 mM EDTA, 1% SDS, 20 ug/ml Protease K) by incubation at 55°C for 30 min. After recovering the first elution fraction, the remaining DNAs were further eluted with additional 90 ul of TESK buffer with incubation at 65°C for one overnight. The first elution fraction was also incubated at 65°C for one overnight. Pooled elution solutions (total about 180 ul) was treated with 3.6 ul of 10 mg/ml RNaseA at 37°C for 1 hour and then 9 ul of 10 mg/ml Protease K with presence of 1 mM CaCl2 at 55°C for 1 hour. The resulting solution was subjected to DNA purification by the MinElute PCR kit (Qiagen) with twice of 10 ul elution (total 20 ul).
Libraries were prepared according to Illumina's instructions (Prep kit IP-202-1012)

treatment_protocol: The grown cells were washed with serum free media and treated with 15 uM biotin-PEG-GG-SVS-1 in 10 ml of serum free media for 1 hour at 37°C in a CO2 incubator. In order to remove excess peptides and dead cells, the treated cells were passaged as follows. The media was disposed and cells were washed with 10 ml of serum containing media followed by treatment with 2.5 ml of trypsin solution at 37°C for 10 min. The resulting cells were stripped by pipetting with additional 3 ml of serum containing media and collected by centrifugation at 2 krpm for 5 min at room temperature. The cell pellet was resuspended with 4.2 ml of serum containing media, and 2 ml of the suspension was transferred to two of 125 cm2 flask that has totally 10 ml of the serum containing media, which were incubated at 37°C for one overnight in a CO2 incubator.

tag: ChIP

tag: cell line


title: sh Chd4 Day 0

source_name: Chd4 shRNA was introduced into ESCs


title: 2 dpf, 5-HT injected at zygote, biological replicate 2

tag: tissue

value: larvae

value: wildtype, AB line


title: CKBA rep1


title: Abemaciclib_120mpk_C

value: Sprague Dawley

tag: treatment

value: abemaciclib (120 mg/kg/day)


title: Input_A


title: DMSO rep3

value: epidermis of mouse skin


title: ChIP_A

value: N-terminal biotinylated SVS-1


title: ChIP_B


title: sh Ctrl. Day 4

source_name: Control shRNA was introduced into ESCs and neural differentiation was induced for 4 days

value: day 4


title: Abemaciclib_120mpk_A

value: male


title: IL-10+ CD4+ T-cells small intestine p2_C21

description: SI.counts.txt

source_name: T-cells from small intestine

value: small intestine


title: Abemaciclib_100mpk_B

value: 6-8 weeks-old


title: Abemaciclib_36mpk_C

value: abemaciclib (36 mg/kg/day)

value: jejunum mucosal scrapings


title: Abemaciclib_36mpk_B


title: Abemaciclib_36mpk_A


title: E10.5_rep5

city: Amsterdam

first: Febilla

last: Fernando

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Academic Medical Center

description: SAMPLE 30

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation function in limma package in R

source_name: mice uterus

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: FVB/N

tag: time point


title: E6.5_rep4

description: SAMPLE 29


title: E15.5_rep5

description: SAMPLE 27


title: E17.5_rep5

description: SAMPLE 32


title: Palbociclib_100mpk_B

value: palbociclib (100 mg/kg/day)


title: Palbociclib_100mpk_C


title: shGLO1#1 replicate 3

city: Liège

first: Marie-Julie

last: Nokin

address: Avenue Hippocrate

department: GIGA-Cancer

country: Belgium

institute: University of Liège

data_processing:
Illumina bcl2fastq v2.17 was used to generate fastq files with adapters trimmed
Alignment to human genome with Tophat 2.1.1
Raw read counts generated with HTseq count in union mode
Reference genome and annotations (UCSC hg19) downloaded from Illumina iGenome
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with gene raw counts from HTseq count

source_name: MDA-MB-231 cells

extract_protocol:
RNA was harvested from cell pellets using RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were stably silenced for GLO1 using shRNA

value: MDA-MB-231 cells

tag: cancer type

value: Breast cancer


title: shGLO1#2 replicate 1


title: shGLO1#2 replicate 2


title: shGLO1#1 replicate 1


title: shGLO1#2 replicate 3


title: shGLO1#1 replicate 2


title: Palbociclib_30mpk_A

tag: age

value: palbociclib (30 mg/kg/day)


title: E12.5_rep5

description: SAMPLE 31


title: E12.5_rep4

description: SAMPLE 26


title: Vehicle_C

tag: Sex

value: vehicle (0.5% methyl cellulose)


title: E17.5_rep4

description: SAMPLE 28


title: Palbociclib_100mpk_A


title: E8.5_rep4

description: SAMPLE 25


title: Palbociclib_30mpk_B


title: E10.5_rep4

description: SAMPLE 23


title: shNT(Control) replicate 3


title: Palbociclib_30mpk_C


title: shNT(Control) replicate 2


title: MEF WT

city: Oxford

first: Michal

middle: R.

last: Gdula

address: South Parks Road

country: United Kingdom

institute: Oxford University

description:
genomic DNA Hi-C ditags
BedGraphs for all cytosines: unsorted reads (T), Domesticus-FVB(D), Castaneus and analogical for cytosines covered by at least 3 reads

data_processing:
Whole Genome Bisulfite libraries were mapped with Bismark71, and deduplicated.
With SNPsplit programme6 and confident Cast/FVB SNPs reads were sorted into paternal, maternal and unassigned subsets.
Sorted reads were processed with bismark_methylation_extractor to retrieve methylated cytosines. Cytosines covered by at least 3 reads in allele-specific alignment were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file: UCSC bedgraph heading followed by the table with following columns: chr,start, end, value. Value= %of methylated cytsoines at given locus

source_name: female clonal MEFs

growth_protocol: SmcHD1 WT, MommeD1 MUT cell lines were grown on 5-8x145mm petri dishes in EC10 medium to semi-confluency.

extract_protocol:
Genomic DNA and RNA were extracted from MEF cultures using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer’s instructions. Concentration of DNA was measured on Nanodrop and adjusted to 20ng/ul after which the DNA was sheared to 100-500bp fragments on Covaris sonicator with the following settings: 10% duty cycle, 200 bursts/sec, intensity 4.0, 80sec duration; mode – frequency sweeping). Fragment ends were repaired, A-tailed and ligated with PE Illumina methylated adapter oligos using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB). Adaptor-ligated gDNA fragments were subjected to bisulfite conversion using two-step modification procedure with Imprint™ DNA Modification Kit (Sigma). Converted and purified DNA was amplified for 9-12cycles with KAPA HiFi HS Uracil enzyme mix (Anachem). Precise concentration and size of the libraries were determined by qPCR with universal Illumina primers and also on Agilent 2100 Bioanalyzer (Agilent Technologies) using High Sensitivity DNA assay. Libraries were sequenced on HiSeq2000 system (Illumina) using 100bp Paired End protocol.
Shared DNA fragment ends were repaired, A-tailed and ligated with PE Illumina methylated adapter oligos using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB). Adaptor-ligated gDNA fragments were subjected to bisulfite conversion using two-step modification procedure with Imprint™ DNA Modification Kit (Sigma). Converted and purified DNA was amplified for 9-12cycles with KAPA HiFi HS Uracil enzyme mix (Anachem). Precise concentration and size of the libraries were determined by qPCR with universal Illumina primers and also on Agilent 2100 Bioanalyzer (Agilent Technologies) using High Sensitivity DNA assay. Libraries were sequenced on HiSeq2000 system (Illumina) using 100bp Paired End protocol.

tag: genetic background

value: Inter-specific:F2, M.m.domesticus FVB x M.m.Castaneus

tag: genotype

value: wild-type

tag: clone

value: female

value: MEFs


title: MEF MUT

value: SmcHD1 MomeD1 mutant

tag: cell type


title: E17.5_rep3

description: SAMPLE 24


title: SmcHD1_wt_rep2

description: processed files were generated from merged bam files coming from all replicates and contain density plots (rpm, bigWigs) for both unsorted and allele-specific reads (FVB and M.m.castaneus) seperately fro each strand

data_processing:
Reads were mapped with STAR 2.5b aligner with index generated from FVB-Cast SNP N-masked genome and allele-specificaly sorted with SNPsplit.
For visualisation genome-wide coverage within 50 bp were calculated normalised for sequencing depth (rpm). BigWig files were generated to visualize the data in the UCSC browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
created form bedGraph file (table: chr, start, end, value) with the bedGraphToBigWig utility available form UCSC; scores represent sequencing-depth normalized read density or log2(IP/input)

growth_protocol: SmcHD1 WT, MommeD1 and CRISPR KO cell lines were grown on 5-8x145mm petri dishes in EC10 medium to semi-confluency.

extract_protocol:
WT, SmcHD1 null and acute SmcHD1 null MEFs were grown on 2x145mm petri dishes in EC10 medium to semi-confluency. RNA-Seq enriching for chromatin-bound nuclear RNA was performed according to a modified chromatin RNA-Seq protocol 59 . The cells were trypsinised, collected in EC10 medium and cell number was counted on LUNAII cell counter (Logos Biosystems). 1x10^7 cells for each line were spun down, resuspended in 12ml of ice cold PBS and supplemented with 2.5x10^6 SG4 drosophila cells for calibration. Cells were spun down at 500g, 5 min at 4 0 C and cell pellets were resuspended in 800l of HLBN hypotonic buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 2.5 mM MgCl 2 , 0.05% NP40). 480 μl of buffer HLBNS (HLBN, 25% sucrose) was carefully under-layered to create sucrose cushion, and nuclei were isolated by centrifugation for 5 min at 1000g at 4 0 C. Supernatant containing cytoplasmic debris was discarded and the nuclear pellet was re-suspended in 100 μl of ice-cold buffer NUN1 (20 mM Tris-HCl pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol; 1 mM DTT and cOmplete EDTA free protease inhibitors (Sigma) added fresh). Nuclei were lysed in 1200 μl of ice-cold lysis buffer NUN2 (20 mM HEPES pH7.6, 300 mM NaCl, 7.5 mM MgCl 2 , 0.2 mM EDTA, 1 M urea, 1% NP40; 1 mM DTT) during 15min incubation on ice and RNA-bound chromatin was pelleted at 16000 g for 10min at 40C. Chromatin-RNA pellet was re-suspended in 200 μl of high salt buffer HSB (10 mM Tris-HCl pH 7.5, 500 mM NaCl, 10 mM MgCl 2 ). DNA and proteins were digested with Turbo DNAse (Life Sciences) and proteinase K (10 mg/ml, ThermoFisher, nuclease free), incubating on ThermoMixer at 37 0 C for 10 min and 30min, respectively. RNA was extracted with 1 ml of TRIzol (Life Sciences) according to the manufacturer guidelines. RNA was dissolved in 1xTURBO DNAse buffer, digested with TURBO DNAse for 30 min at 37o C on a ThermoMixer and extracted with TRIzol. RNA was washed three times with 75% ethanol, dissolved in water and quantified using a NanoDrop (ND-1000). RNA quality was checked with RNA 6000 Pico Chip (Agilent Technologies) on Agilent 2100 Bioanalyser (Agilent Technologies). Samples were depleted of ribosomal RNA with Ribo-Zero Gold Kit (MRZG12324, Illumina) according to manufacturer’s guidelines. RNA was isolated from 3 biological replicates. RNA-Seq libraries were prepared with NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420S) using NEBNext® Multiplex Oligos for Illumina for multiplexing (E7335S and E7500S). Libraries were sequenced on HiSeq2000 and NextSeq500 using NextSeq 500 High-Output Kit: 1 lane, 150 cycles, 75 bp paired end sequencing (Illumina).
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®


title: SmcHD1_mut_rep1


title: H3K27me3_mut_rep2_input

data_processing:
ChIP-seq reads were mapped with bowtie2 with SNP N-masked genome index and sorted with SNP-split to separate subsets of reads originating from parental genomes.
For SmcHD1, CTCF and Rad21 ChIP-seqs macs2 was used to detect significant enrichments – narrow peaks, q-value < 0.05.
For visualisation genome-wide coverage within 50 bp were calculated normalised for sequencing depth (rpm, for all samples apart from H3K27me3 where enrichment values were scaled down to equalize the total read number to the sample with smaller number of reads). BigWig files were generated to visualize the data in the UCSC browser.
for SmcHD1 and H3K27me3 ChIP-seq geneome-wide coverages were additionally binned into 500 bp bins and log2(IP/input) tracks were generatad.
Genome_build: mm10
Supplementary_files_format_and_content: bed: Table with three columns: chr, start, end; contains peak coordinates
Supplementary_files_format_and_content: bigWig: created form bedGraph file (table: chr, start, end, value) with the bedGraphToBigWig utility available form UCSC; scores represent sequencing-depth normalized read density or log2(IP/input)

extract_protocol:
Cells were trypsinised, washed in PBS and counted. For SmcHD1 and Rad21 5x107 cells were then crosslinked in 2M Ethylene glycol-bis(succinic acid N-hydroxysuccinimide ester) (EGS, Sigma) in PBS at RT for 1hr followed by 15 min crosslinking in 1% formaldehyde. For H3K27me3 and CTCF 1x107 cells were crosslinked in 1% formaldehyde alone for 15 min at RT. Formaldehyde was quenched by addition of glycine to a final concentration of 125mM and incubation at RT for 3min. Cells were spun down at 700rpm for 4 min at 4oC and lysed in 50mM HEPES pH 7.9, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.25% Triton X100 and 2% NP40. Cellular lysis was assisted by 20 strokes of large clearance pestle in Dounce grinder and subsequent incubation for 10 min at 4oC with constant rotation. Released nuclei were spun down and washed once in 10mM Tris-HCl pH8.0, 200mM NaCl, 1mM EDTA and 0.5mM EGTA. Nuclei were lysed by addition of 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine. All solutions contained cOmplete EDTA-free protease inhibitors (Sigma) added fresh. Chromatin was sonicated on BioRuptor sonicator (Diagenode) to produce fragments of approximately 500 bp. Triton X100 was added to a final concentration of 1%, and insoluble pellet was removed by centrifugation at maximum speed for 10 min at 40C. Chromatin was aliquoted and stored at -80C until use.  Immunoprecipitation was performed overnight at 40C with 3-5g of specific antibody and 100 l of chromatin corresponding to 1x105 (H3K27me3, CTCF) or 5x105 cells (Rad21, SmcHD1) in 20 mM Tris-HCl pH 8.0, 1mM EDTA, 150 mM NaCl and 1% triton-x-100, with proteinase inhibitors. Antibody-bound chromatin was isolated on rProtein A Sepharose Fast Flow beads (GE Healthcare) that had been blocked for 1 h at 4°C with 1 mg/ml bovine serum albumin (NEB) and 1 mg/ml yeast tRNA (Sigma). Agarose beads with immunoprecipitated material were washed thoroughly in low salt buffer (LSB, 20mM Tri-HCl pH8.0, 2mM EDTA, 150mM NaCl, 0.1% SDS, 1% Triton X100), high salt buffer (HSB, the same as LSB but with 500mM NaCl), LiCl buffer (10MM Tris-HCl pH8.0, 1mM EDTA, 0.25 M LiCl, 1% NP40, 1% deoxycholate) and twice in TE buffer, all with proteinase inhibitors. Immunoprecipitated material was eluted from beads in elution buffer (0.1M NaHCO3, 1% SDS) with shaking on Thermomixer at RT for 30min.  Beads were removed by centrifugation, eluted chromatin was reverse cross-linked and treated with RNAse and proteinase K in the presence of 200mM of NaCl at 370C for 2 hrs followed by 650C overnight with shaking at 800rpm for 1 min every 2 min. DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo Research) according to the manufacturer’s instructions.  DNA size was assessed on Bioanalyser (Agilent) and DNA was post-sonicated on Bioruptor Pico sonicator for 18-20 cycles of 30s on/30s off if necessary. DNA Concentration was quantified using PicoGreen® dsDNA Quantitation Kit (Molecular Probes), Bioanalyser High sensitivity DNA assay and/or Qubit dsDNA HS assay kit.
NEBNext (H3K27me3) or NEBNext Ultra II (CTCF, Rad21, SmcHD1) DNA Library Prep Kits for Illumina were used to prepare libraries for sequencing, following the manufacturer’s instructions.

tag: antibody


title: WT_Ribo-seq_BioRep_1 (total RNA)

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
Library strategy: Ribo-Seq
Raw reads were pre-processed to remove low quality bases on 3’ ends by cropping to 101bp using Trimmomatic. Reads were mapped to the human genome (hg19) with Tophat2 v.2.1.1. Parameters used were: reporting at most one alignment per read (-g 1), allowing maximally five mismatches per read (>95% matching), and supplying the Ensembl Release 75 gene annotation. A post-alignment filter removed alignments to mitochondrial DNA (chrM) and non-concordant mate pairs
Genomic alignments were used to quantify transcripts using HTSeq against the Ensembl 75 annotation. Differential expression and gene-level variance-stabilized counts were calculated using DESeq2.
For transcript-level peak calling, canonical transcript sequences were downloaded from the UCSC genome browser and used in the generation of a Bowtie2-based index. Reads were aligned in local alignment mode with Bowtie2. MACS2 was used for peak calling in these alignment files .
For Ribo-Seq analysis, ribosome protected reads were first trimmed of adaptor sequence (5’-CTGTAGGCACCATCAAT) using cutadapt, and reads arising from rRNA were removed from the dataset based on alignment to a set of ribosomal RNA sequences using bowtie2. Remaining reads were then mapped to the UCSC hg19 canonical transcriptome with tophat (v 2.1.1), with the –prefilter-multihits option enabled to screen out reads that may have arisen from elsewhere in the genome. Uniquely mapped reads were then assigned to the specific codon estimated to be within the A-site of the protecting ribosome, based on identification of the P-site offset from the corresponding peak in read density that occurs up-stream of the start codon, with the added constraint that each read was mapped to the nearest in-frame codon and under the assumption that all reads will be in frame with the associated gene. Reads were assigned to the 5’ UTR, CDS or 3’ UTR based on the location of the inferred A-site of the read for purpose of estimating ribosome density in these regions.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq_variance_stabilized_data.csv contains gene-level variance-stabilized counts from DESeq2 for RNA-Seq samples
Supplementary_files_format_and_content: acRIP_peaks.csv contains data for ac4C peaks in UCSC canonical transcripts.
Supplementary_files_format_and_content: RiboSeq_processed_data.csv contains tabulated Ribo-Seq results: mRNA normalized ribosome density summaries across canonical transcripts and by transcript feature (CDS/UTR).

source_name: HeLa cells, total RNA

growth_protocol: Parental and NAT10-/- cells were grown in complete DMEM medium to 80% confluency.

extract_protocol:
Total RNA was purified from cultured cells using Trizol (ThermoFisher) followed by treatment with TurboTM DNAse (ThermoFisher). Enrichment of polyadenylated RNA (poly(A)-RNA) from DNAse-treated total RNA was carried out by two rounds of selection with Oligo-(dT)25 Dynabeads (ThermoFisher) according to the manufacturer’s instructions. Enrichment efficiencies were estimated with Bioanalyzer picoRNA chips (Agilent Technologies, Santa Clara, CA).
Parental and NAT10-/- cells were grown in complete DMEM medium to 80% confluency in three 10 cm plates per sample per replicate. Following quick media aspiration, cells were flash frozen by placing the plates on top of liquid nitrogen and immediately transferred to ice. Cells for each sample were scraped on wet ice into 500 μL lysis buffer (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 2 mM DTT, and 100 μg/mL cycloheximide), which was transferred from one plate to the next to collect the cells from all three plates for each sample. Cells were next triturated 10 times using a 26-gauge needle and the lysates were clarified by centrifugation at 20,000 X g for 10 min at 4°C. For ribosome profiling, 300-450 μL of each lysate were treated with 0.3 U/μL RNase I (ThermoFisher) for 40 min at room temperature, while the remaining lysate was flash frozen in liquid nitrogen for later total RNA isolation. Following the RNase I digestion, 5 μL of Superase-In (ThermoFisher) were added to each sample, and the samples were loaded onto 15-45% w/w sucrose gradients which were prepared, centrifuged, and fractionated as described in (J.E. Smith et al., 2014). Ribosome footprint RNA was isolated from fractions containing 80S monosomes and ribosome profiling libraries were prepared, as described previously, with a few modifications (J.E. Smith et al., 2014).  Briefly, RNA was isolated using two phenol/chloroform/LET (25 mM Tris-HCl, pH 8.0, 100 mM LiCl, 20 mM EDTA, pH 8.0) extractions, and 10 μg was depleted of ribosomal RNA only once, using the human/mouse/rat Ribo-Zero Gold rRNA removal kit (Illumina MRZG12324). For the total RNA fragmented controls, 200 μL LET was added to each 50 μL aliquot of lysate, and total RNA was extracted once with phenol/LET, once with phenol/chloroform/LET, and once with chloroform. Following ethanol precipitation, the total RNA was DNase I treated (Sigma-Aldrich). An RNA Spike-In mix (Thermo Fisher Scientific 4456740) was added to 5 μg of DNase I-treated total RNA according to the manufacturer’s instructions, and ribosomal RNA was depleted using the human/mouse/rat Ribo-Zero Gold rRNA removal kit. Next, the total RNA samples were fragmented in alkaline fragmentation buffer (1 mM EDTA, 50 mM Na2CO3, 50 mM NaHCO3, [pH 9.2] for 40 min at 95°C, as described previously (N.T. Ingolia et al., 2010), and fragments between 26 and 34 nucleotides in size were gel purified and used for library preparation in parallel with the ribosome profiling samples as described above (N.T. Ingolia et al., 2010).
Illumina libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.

value: HeLa cells

value: WT


title: NAT10_KO_Ribo-seq_BioRep_1 (total RNA)


title: NAT10_KO_Ribo-seq_BioRep_2 (protected RNA)

source_name: HeLa cells, Ribosome Protected RNA


title: WT_Ribo-seq_BioRep_2 (protected RNA)


title: NAT10_KO_Ribo-seq_BioRep_2 (total RNA)


title: SmcHD1_wt_rep1


title: NAT10_KO_Ribo-seq_BioRep_1 (protected RNA)


title: WT_Ribo-seq_BioRep_1 (protected RNA)


title: H3K27me3_mut_rep1_input

description: processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) : input, input_FVB, input_Cast


title: E8.5_rep3

description: SAMPLE 22


title: NP_rep4

description: SAMPLE 21

value: NP


title: Vehicle_A

value: Sprague Dawley

value: male

value: 6-8 weeks-old


title: Vehicle_B

value: jejunum mucosal scrapings


title: E17.5_rep1

description: SAMPLE 16

value: FVB/N


title: E8.5_rep2

description: SAMPLE 18


title: E17.5_rep2

description: SAMPLE 20


title: E15.5_rep4

description: SAMPLE 15


title: NP_rep3

description: SAMPLE 17


title: WT_Ribo-seq_BioRep_2 (total RNA)


title: E12.5_rep3

description: SAMPLE 19


title: E12.5_rep2

description: SAMPLE 14


title: SmcHD1_mut_rep2


title: WT condylar cartilage replicate 3

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn Institute of Medicine at Mount Sinai

data_processing:
Adapter removal with cutadapt (Martin, 2011) and base quality trimming to remove 3’ read sequences if more than 20 bases with Q < 20 were present.  Paired-end reads were mapped to the mouse (mm10) reference genome using STAR (Dobin et al., 2013) and gene count summaries were generated using featureCounts (Liao et al., 2014). Raw read counts were then combined into a numeric matrix, with genes in rows and experiments in columns and used as input for differential gene expression analysis with the Bioconductor Limma package (Ritchie et al., 2015) after multiple filtering steps to remove low-expressed genes. First, gene counts were converted to FPKM (fragments per kb per million reads) using the RSEM package (Li et al., 2011) with default settings in strand specific mode and only genes with expression levels above 1 FPKM in at least 50% of samples were retained for further analysis. Additional filtering removed genes with less than 50 total reads across all samples or less than 200 nucleotides in length. Finally, normalization factors were computed on the filtered data matrix using the weighted trimmed mean of M-values (TMM) method, followed by voom (Law et al., 2014) mean-variance transformation in preparation for Limma linear modeling. Data was fitted to a design matrix containing all sample groups and pairwise comparisons were performed between sample groups. eBayes adjusted P-values were corrected for multiple testing using the Benjamin-Hochberg (BH) method and used to select genes with significant expression differences.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing the Gene ID, Chromosome Start and End positions, Strand Type, and Length. BigWig files containing Genome Browser track information.

source_name: WT mandibular condylar cartilage

extract_protocol:
Laser Capture Microdissection was used to isolate tissues from Meckels cartilage, mandibular bone and mandibular condylar cartilage, respectively. RNA was isolated with Arcturus Picopure RNA Isolation Kit as described by the manufacturer and eluted in a final volume of approximately 16 µl of elution buffer. RNA quality and concentration was assessed using the Agilent RNA Pico kit and Agilent Bioanalyzer 2100 as described by the manufacturer.
Libraries were prepared with NuGEN Ovation RNA-Seq System v2 (amplification) and Illumina Nextera XT Library Prep kit. Fragments were sequenced using paired end reads (2×100 bp) on the Illumina HiSeq platform.

tag: disease state

value: control

value: mandibular condylar cartilage

value: embryonic day 16.5


title: H3K27me3_wt_rep1_input


title: WT Meckel's cartilage replicate 3

source_name: WT Meckel's cartilage

tag: gender

value: Meckel's cartilage


title: H3K27me3_wt_rep2_ChIP

value: Inter-specific:F2, M.m.domesticus FVB x M.m.Castaneus


title: WT condylar cartilage replicate 2


title: WT Meckel's cartilage replicate 2


title: WT bone replicate 3

source_name: WT mandibular bone

value: mandibular bone


title: H3K27me3_mut_rep2_ChIP


title: H3K27me3_mut_rep1_ChIP

description: processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) : IP,  log2(IP/input), IP_FVB, log2(IP_FVB/input_FVB), IP_Cast, log2(IP_Cast/input_Cast)


title: NP_rep2

description: SAMPLE 12


title: E10.5_rep3

description: SAMPLE 13


title: E15.5_rep2

description: SAMPLE 10


title: E15.5_rep3

description: SAMPLE 11


title: H3K27me3_wt_rep2_input

value: wild-type


title: E6.5_rep3

description: SAMPLE 8


title: Apert condylar cartilage replicate 3

source_name: Fgfr2S252W mandibular condylar cartilage

value: female

value: Apert syndrome


title: WT Meckel's cartilage replicate 1


title: WT bone replicate 1


title: WT condylar cartilage replicate 1


title: E10.5_rep2

description: SAMPLE 9


title: Apert Meckel's cartilage replicate 3

source_name: Fgfr2S252W Meckel's cartilage


title: Apert bone replicate 3

source_name: Fgfr2S252W mandibular bone


title: Apert condylar cartilage replicate 2


title: NP_rep1

description: SAMPLE 7


title: Apert condylar cartilage replicate 1


title: Apert Meckel's cartilage replicate 1


title: Apert bone replicate 2


title: E10.5_rep1

description: SAMPLE 5


title: WT bone replicate 2


title: E12.5_rep1

description: SAMPLE 3


title: Apert Meckel's cartilage replicate 2


title: E8.5_rep1

description: SAMPLE 2


title: E15.5_rep1

description: SAMPLE 6


title: H3K27me3_wt_rep1_ChIP


title: E6.5_rep2

description: SAMPLE 4


title: E6.5_rep1

description: SAMPLE 1


title: IL-10+ CIR poor splenocytes 2

data_processing:
low quality bases were trimmed with Trimmomatic 0.33 (parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Alignment and summarization were done using Tophat and HTSeq count
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text file containing log2 normalized counts for all samples provided by DESeq2

source_name: Splenic T-cells

extract_protocol:
RNA was extracted using TRIzol LS reagent (Life Technology)
sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina

tag: phenotype

value: poor


title: IL-10+ CIR poor splenocytes 1

description: log.norm.counts.txt


title: IL-10+ CIR rich splenocytes 2

value: rich


title: IL-10+ CIR rich splenocytes 1

description: log.norm.counts.txt


title: eCeT_R4_T1

city: Urbana

first: Elizabeth (Lisa)

last: Ainsworth

state: IL

address: 1201 W Gregory Dr.

department: Plant Biology

institute: University of Illinois Urbana-Champaign

description:
seq_id: P16_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

data_processing:
The library was quantitated by qPCR and sequenced on one MiSeq flowcell for 301 cycles from each end of the fragments using a MiSeq 600-cycle sequencing kit version 3 and analyzed with Casava1.8 (pipeline 1.8)
PhiX DNA is used as a spike-in control for MiSeq runs.  Most PhiX reads are removed in normal Casava processing but a few residual reads may remain. PhiX genome is 3kb in length.
The libraries were quantitated, pooled in equimolar concentration, quantitated by qPCR and sequenced on two lanes for 161 cycles from each end of the fragments on a HiSeq2500 using a TruSeq SBS Rapid sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)
Trinity was used for de novo transcriptome build
Genome_build: Functional annotation of the genes was done by using BLAST against Arabidopsis thaliana, Zea mays, and Setaria italica
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for HiSeq
Supplementary_files_format_and_content: tab-delimited text files include Trinity annotation for MiSeq

organism: Megathyrsus maximus

source_name: Leaf-youngest fully expanded

growth_protocol: As described Britto de Assis Prado et al. (2016)

extract_protocol:
100 ul RNA extracted and shipped to UIUC in 250ul EtOH(100%). EtOH removed. 10ul NaAC (pH 5.5) added with 1 ul glycerol. 30 min spin, remove supernatant. 250 ul EtOH (80%). 15 min spin, EtOH removed. Air dry 10 min. 50ul RNA treated H2O. 5ul aliquot
The libraries were prepared with Illumina's TruSeq Standard RNA sample prep kit. (for the MiSeq library, 500 ng of total RNA from each sample were pooled and prepared with this kit with one modification: RNA was not fragmented). MiSeq Sequencing of pooled RNA: library was quantitated by qPCR and sequenced on one MiSeq flowcell for 301 cycles from each end of the fragments using a MiSeq 600-cycle sequencing kit version 3. HiSeq Sequencing of Pools: libraries were quantitated, pooled in equimolar concentration, quantitated by qPCR and sequenced on two lanes for 161 cycles from each end of the fragments on a HiSeq2500 using a TruSeq SBS Rapid sequencing kit version 1.

value: Leaf-youngest fully expanded

value: combined treatment (elevated [CO2] and elevated temperature)

value: A (30 days)

tag: ring


title: eCeT_R4_T2

description:
seq_id: P16_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

treatment_protocol: As described Britto de Assis Prado et al. (2016)

value: B (50 days)


title: IL-10- CIR rich splenocytes 2


title: T_R4_T2

description:
seq_id: P15_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: elevated temperature


title: Apert bone replicate 1

tag: strain


title: IL-10- CIR poor splenocytes 2


title: IL-10- CIR rich splenocytes 1

description: log.norm.counts.txt


title: IL-10- CIR poor splenocytes 1

description: log.norm.counts.txt


title: Amb_R4_T1

description:
seq_id: P12_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: ambient conditions


title: Amb_R4_T2

description:
seq_id: P12_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: T_R4_T1

description:
seq_id: P15_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eC_R4_T1

description:
seq_id: P11_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: elevated CO2 [600 ppm] and ambient temperature


title: eCeT_R3_T1

description:
seq_id: P14_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: T_R3_T1

description:
seq_id: P13_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: Amb_R3_T2

description:
seq_id: P10_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: Amb_R3_T1

description:
seq_id: P10_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eCeT_R3_T2

description:
seq_id: P14_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eC_R4_T2

description:
seq_id: P11_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eC_R3_T1

description:
seq_id: P9_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: T_R3_T2

description:
seq_id: P13_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eC_R3_T2

description:
seq_id: P9_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: T_R2_T2

description:
seq_id: P7_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eCeT_R2_T2

description:
seq_id: P8_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: UVB_NM105.1 mg/L_rep3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: whole body

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts (40 organisms)

tag: stage of development

value: Adult organisms with well developed clitellum

tag: exposure

value: 1 mg/L TiO2_NM105 + UVA radiation, in ISO reconstituted water, for 5 days


title: UVB_NM104.1 mg/L_rep1

tag: tissue

value: 1 mg/L TiO2_NM104 + UVA radiation, in ISO reconstituted water, for 5 days


title: UVB_NM104.1 mg/L_rep3


title: UVB_NM103.1 mg/L_rep3

value: 1 mg/L TiO2_NM103 + UVA radiation, in ISO reconstituted water, for 5 days


title: UVB_NM105.1 mg/L_rep2


title: UVB_NM103.1 mg/L_rep2


title: UVB_NM105.1 mg/L_rep1


title: Amb_R2_T2

description:
seq_id: P4_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

tag: treatment

tag: time point


title: shNT(Control) replicate 1

tag: cell line

value: MDA-MB-231 cells

tag: cancer type

value: Breast cancer


title: MS0681_Coffin-Siris Syndrome 3

description: SAMPLE 6

data_processing: Illumina Normalization method with background correction, using minfi package in R 3.4.2

extract_protocol: Standard DNA extraction from blood

value: Coffin-Siris syndrome

value: Whole Blood


title: eCeT_R2_T1

description:
seq_id: P8_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: UVB_NM103.1 mg/L_rep1


title: T_R2_T1

description:
seq_id: P7_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eC_R2_T2

description:
seq_id: P3_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eC_R2_T1

description:
seq_id: P3_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: Amb_R2_T1

description:
seq_id: P4_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: eCeT_R1_T2

description:
seq_id: P6_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: UVB_Bulk.1 mg/L_rep3

value: 1 mg/L Bulk TiO2 + UVA radiation, in ISO reconstituted water, for 5 days


title: Control UVB_rep2

value: UVA radiation, in ISO reconstituted water, for 5 days


title: MS0683_Coffin-Siris Syndrome 3

description: SAMPLE 7


title: T_R1_T2

description:
seq_id: P5_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: Leaf-youngest fully expanded


title: UVB_Bulk.1 mg/L_rep1


title: T_R1_T1

description:
seq_id: P5_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: A (30 days)


title: UVB_NM104.1 mg/L_rep2


title: UVB_Bulk.1 mg/L_rep2


title: Control UVB_rep1


title: NoUV_NM105.1 mg/L_rep2

value: 1 mg/L TiO2_NM105 under standard laboratory illumination, in ISO reconstituted water, for 5 days


title: Control UVB_rep3


title: NoUV_NM105.1 mg/L_rep3


title: BRICseq_Nat10_KO2_16hr

data_processing:
Library strategy: BRIC-Seq
Raw reads were pre-processed to remove low quality bases on 3’ ends by cropping to 101bp using Trimmomatic. Reads were mapped to the human genome (hg19) with Tophat2 v.2.1.1. Parameters used were: reporting at most one alignment per read (-g 1), allowing maximally five mismatches per read (>95% matching), and supplying the Ensembl Release 75 gene annotation. A post-alignment filter removed alignments to mitochondrial DNA (chrM) and non-concordant mate pairs
Genomic alignments were used to quantify transcripts using HTSeq against the Ensembl 75 annotation. Differential expression and gene-level variance-stabilized counts were calculated using DESeq2.
For transcript-level peak calling, canonical transcript sequences were downloaded from the UCSC genome browser and used in the generation of a Bowtie2-based index. Reads were aligned in local alignment mode with Bowtie2. MACS2 was used for peak calling in these alignment files .
For Ribo-Seq analysis, ribosome protected reads were first trimmed of adaptor sequence (5’-CTGTAGGCACCATCAAT) using cutadapt, and reads arising from rRNA were removed from the dataset based on alignment to a set of ribosomal RNA sequences using bowtie2. Remaining reads were then mapped to the UCSC hg19 canonical transcriptome with tophat (v 2.1.1), with the –prefilter-multihits option enabled to screen out reads that may have arisen from elsewhere in the genome. Uniquely mapped reads were then assigned to the specific codon estimated to be within the A-site of the protecting ribosome, based on identification of the P-site offset from the corresponding peak in read density that occurs up-stream of the start codon, with the added constraint that each read was mapped to the nearest in-frame codon and under the assumption that all reads will be in frame with the associated gene. Reads were assigned to the 5’ UTR, CDS or 3’ UTR based on the location of the inferred A-site of the read for purpose of estimating ribosome density in these regions.
For BRIC-Seq analysis, raw reads were mapped to a modified human genome (hg19 with the luciferase probe sequence added) using Hisat2 v2.0.5 (Kim et al., 2015). Parameters used were: reads that failed to align were not reported (--no-unal), library strandedness was specified (--rna-strandness FR), and a list of known splice sites was generated from the Ensembl 75 annotation (--known-splicesite-infile). Due to skewed sequencing depth, parental HeLa (WT) Rep-1 T2 was down-sampled to a depth representative of the other samples. Afterwards, genomic alignments were used to quantify transcripts using HTSeq v 0.6.1p1 (Anders et al., 2015) against the edited Ensembl 75 annotation with added probe. Library depth normalized gene expression counts were calculated using DESeq2 (Love et al., 2014). Then, all normalized gene count values in a particular time point were divided by the probe value for that time point. Data was further normalized to the first time point and log transformed. Half-lives were calculated by use of a linear model. Half-lives for HeLa WT and NAT10-/-A were calculated together within one linear model. A maximum half-life value of 24 hours was applied to calculated values exceeding this value. Genes with R2 values of < 0.8 were excluded from further analysis
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq_variance_stabilized_data.csv contains gene-level variance-stabilized counts from DESeq2 for RNA-Seq samples
Supplementary_files_format_and_content: acRIP_peaks.csv contains data for ac4C peaks in UCSC canonical transcripts.
Supplementary_files_format_and_content: RiboSeq_processed_data.csv contains tabulated Ribo-Seq results: mRNA normalized ribosome density summaries across canonical transcripts and by transcript feature (CDS/UTR).
Supplementary_files_format_and_content: BRIC_half_lives.csv contains computed RNA half-lives from BRIC-Seq Experiments

source_name: HeLa cells

extract_protocol:
Cells were incubated in complete DMEM medium containing 150 μM BrU (Sigma-Aldrich) for 24 hr. Cells were washed twice with PBS and medium was replaced with complete DMEM medium containing 150 μM Uridine (Sigma-Aldrich) for 0, 2, 4, 8 and 16 hrs. After each time point, medium was removed and Trizol was added directly to culture dishes.
Illumina libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina
Total RNA was purified from cultured cells using Trizol (ThermoFisher) followed by treatment with TurboTM DNAse (ThermoFisher). Enrichment of polyadenylated RNA (poly(A)-RNA) from DNAse-treated total RNA was carried out by two rounds of selection with Oligo-(dT)25 Dynabeads (ThermoFisher) according to the manufacturer’s instructions. Enrichment efficiencies were estimated with Bioanalyzer picoRNA chips (Agilent Technologies, Santa Clara, CA).


title: NoUV_NM104.1 mg/L_rep1

value: 1 mg/L TiO2_NM104 under standard laboratory illumination, in ISO reconstituted water, for 5 days


title: NoUV_NM104.1 mg/L_rep2


title: MS0679_Coffin-Siris Syndrome 3

description: SAMPLE 4


title: MS0680_Coffin-Siris Syndrome 1

description: SAMPLE 5


title: MS0674_Coffin-Siris Syndrome 1

description: SAMPLE 1


title: Amb_R1_T2

description:
seq_id: P2_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: ambient conditions

value: B (50 days)


title: Amb_R1_T1

description:
seq_id: P2_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: BRICseq_Nat10_KO2_4hr


title: MS0678_Coffin-Siris Syndrome 1

description: SAMPLE 3


title: BRICseq_Nat10_KO2_8hr


title: eCeT_R1_T1

description:
seq_id: P6_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: combined treatment (elevated [CO2] and elevated temperature)


title: eC_R1_T1

description:
seq_id: P1_C1
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt

value: elevated CO2 [600 ppm] and ambient temperature


title: BRICseq_Nat10_KO2_0hr


title: BRICseq_Nat10_KO1_16hr


title: DTF2_exp_2

city: Berlin

first: Paul

last: Schäpe

address: Gustav-Meyer-Allee 25

department: Applied and Molecular Microbiology

institute: TU-Berlin

data_processing:
Sequenced libraries were mapped against predicted transcripts from A. niger CBS 513.88 genome (http://fungi.ensembl.org/) with STAR. Raw counts for reads mapping to unique exons were calculated with Bioconductor packages; GenomicFeatures and GenomicAlignments.
Normalization and differential gene expression analysis were performed with DEseq2.

organism: Aspergillus niger

source_name: mycelium

extract_protocol:
Mycelium was sampled, flash frozen and grinded. RNA was extracted using TRIzol method from Vitrogen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MJK16.5 (derivative of MA169.4)

value: mycelium

tag: age

value: exponential growth phase

value: {delta}MjkB


title: DTF1_exp_2

value: MJK15.4 (derivative of MA169.4)

tag: genotype

value: {delta}MjkA


title: BRICseq_Nat10_KO2_2hr


title: eC_R1_T2

description:
seq_id: P1_C2
GuineaGrass.TMM.txt
GuienaGrass_transcriptome_fpkm.txt


title: BRICseq_Nat10_KO1_8hr


title: BRICseq_Nat10_KO1_4hr


title: DDTF12_exp_2

value: MJK18.1 (derivative of MA169.4)

value: {delta}MjkA/{delta}MjkB


title: BRICseq_Nat10_KO1_2hr


title: DTF1_exp_1


title: BRICseq_Nat10_KO1_0hr


title: BRICseq_Wt_Rep2_T16

value: WT


title: BRICseq_Wt_Rep2_T8


title: NoUV_NM105.1 mg/L_rep1

value: Whole body extracts (40 organisms)

value: Adult organisms with well developed clitellum


title: DDTF12_exp_1


title: NoUV_NM104.1 mg/L_rep3


title: NoUV_NM103.1 mg/L_rep3

value: 1 mg/L TiO2_NM103 under standard laboratory illumination, in ISO reconstituted water, for 5 days


title: TF2OE_exp_2

value: MJK11.17 (derivative of MA169.4)

value: MjkB OE


title: NoUV_Bulk.1 mg/L_rep1

value: 1 mg/L Bulk TiO2 under standard laboratory illumination, in ISO reconstituted water, for 5 days


title: NoUV_Bulk.1 mg/L_rep2


title: NoUV_NM103.1 mg/L_rep1


title: BRICseq_Wt_Rep2_T4


title: TF2OE_exp_1


title: DTF2_exp_1


title: CD3_CD155_48h

city: Tokyo

first: Naoko

last: Negishi

address: 2-1-1 Hongo, Bunkyo-ku

department: Atopy (Allergy) Research Center

institute: Juntendo University Graduate School of Medicine

hyb_protocol: cDNA was hybridized to a SurePrint G3 Mouse Gene Expression Microarray 8x60K v2; Agilent Technologies according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: Spleen CD4 T cell

label_protocol: Total RNA were amplified with Ovation RNA Amplification System V2 (NuGEN Technologies). Amplified cDNA were labeled with Genomic DNA Enzymatic Labeling Kit (Agilent technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: CD4 T cell

value: anti-CD3 and anti-CD155

value: female

value: BALB/c

value: spleen


title: NoUV_Bulk.1 mg/L_rep3


title: DHD_exp_2

value: MJK14.7 (derivative of MA169.4)

value: mycelium

value: exponential growth phase

value: {delta} histone deacetylase


title: CD3_48h


title: BRICseq_Wt_Rep2_T2


title: NoUV_NM103.1 mg/L_rep2


title: BRICseq_Wt_Rep2_T0


title: BRICseq_Wt_Rep1_T16


title: DHD_exp_1


title: TF1OE_exp_2

value: MJK10.12 (derivative of MA169.4)

value: MjkA OE


title: Ubc9Tg 45mins ischemia 6hrs reperfusion rep1

description: Ubc9Tg 45mins ischemia 6hrs reperfusion

hyb_protocol: Labeled cRNA were hybridized to the Mouse Clariom S GeneChip (Affymetrix, Santa Clara, CA) in blinded interleaved fashion.

data_processing: The Expression Console (Affymetrix) was used to summarize the data contained across all .CEL files and generate 28,846 SST-RMA normalized transcript cluster expression values.

source_name: Ubc9Tg 45mins ischemia 6hrs reperfusion

label_protocol: Total RNA was labeled on a sample-by-sample basis according to the manufacturer’s guidelines for use with the Mouse Clariom S GeneChip (Affymetrix, Santa Clara, CA).

growth_protocol: Animal work was approved by the Duke University and the National Institutes of Health (NIH)/National Institute of Neurological Disorders and Stroke (NINDS) Animal Care and Use Committees (ACUC) respectively. Initial studies were performed in C57BL/6 mice obtained from Jackson Lab (Bar Harbor, ME). Experiments in the previously established Ubc9 transgenic mice (Ubc9Tg) were performed in the “H3” and “N2” founder lines [25]. For mesenteric I/R, mice were anesthetized with 1% isoflurane-supplemented by a one-time administration of 80mg/kg ketamine, 5mg/kg xylazine intraperitoneally, and 0.05mg/kg buprenorphine subcutaneously. A midline laparotomy was then made and a 2-3cm ileal loop isolated and rendered ischemic by placing aneurysm clips (Kent Scientific, Torrington,CT) on the peripheral branches of the superior mesenteric artery as well as across the intestine itself to block flow through collaterals. Ischemia was maintained for 15, 30, or 45 minutes when the clamps were removed, and the incision closed. During the procedure, the body temperature was maintained at 37°C rectal temperature using a feedback-controlled heating pad. For the reperfusion phase of injury, mice were kept in a heated box with supplemental oxygen for a variable amount of time (0.5, 1, 3, or 6 hours) without anesthesia. After euthanasia, tissue was rapidly removed and snap frozen in liquid nitrogen for RNA and protein isolation or transferred into 4% paraformaldehyde (PFA) for paraffin embedding. To achieve snapshot images representative of in vivo SUMO expression and distribution, a subset of mice were euthanized, and perfused with 0.9% NaCl (10 ml) followed by 4% PFA (30 ml) via transcardiac puncture. The intestines were then removed, placed in 4% PFA overnight, transferred to PBS, and embedded in paraffin.

extract_protocol: RNA was isolated using a commercially available kit (Macherey-Nagel, Bethlehem, PA), which includes a DNAse digestion step.

treatment_protocol: A subset of animals undergoing I/R (n=4 in 3 hour and 6 hour reperfusion groups) received 0.6 mg/g body weight FITC dextran (4,000 kD at a concentration of 80 mg/ml; Sigma-Aldrich, St. Louis, MO) by gavage 3 hours before euthanasia. At euthanasia, plasma was harvested and the FITC concentration quantitated by fluorometry against a FITC-dextran standard curve.

value: 45mins ischemia 6hrs reperfusion

tag: reperfusion time


title: TF1OE_exp_1


title: BRICseq_Wt_Rep1_T8

value: WT


title: Ubc9Tg 45mins ischemia 6hrs reperfusion rep2

description: Ubc9Tg 45mins ischemia 6hrs reperfusion


title: BRICseq_Wt_Rep1_T4


title: Ubc9Tg 45mins ischemia 6hrs reperfusion rep4

description: Ubc9Tg 45mins ischemia 6hrs reperfusion


title: MS0676_Coffin-Siris Syndrome 1

first: Bekim

last: Sadikovic

institute: University of Western Ontario

description: SAMPLE 2

value: Coffin-Siris syndrome

value: Whole Blood


title: Ubc9Tg 45mins ischemia 6hrs reperfusion rep3

first: Kory

last: Johnson

institute: NINDS/NIH

description: Ubc9Tg 45mins ischemia 6hrs reperfusion


title: WT 45mins ischemia 6hrs reperfusion rep4

description: WT 45mins ischemia 6hrs reperfusion

source_name: WT 45mins ischemia 6hrs reperfusion


title: WT 45mins ischemia 6hrs reperfusion rep3

description: WT 45mins ischemia 6hrs reperfusion


title: BRICseq_Wt_Rep1_T2


title: WT_exp_2

value: MJK17.25 (derivative of MA169.4)

value: wild type


title: WT_exp_1


title: Ciz1NullPrimaryDox_S15

city: York

first: Dawn

last: Coverley

address: Wentworth Way

department: Department of Biology

institute: University of York

description:
sample_fpkms.txt
cuffdiff_results.txt

data_processing:
Libraries were sequenced at the Leeds Institute for Molecular Medicine (LIMM) using Illumina 3000 system, using paired-end sequencing to generate ~50 million reads per sample.
Reads were trimmed using Cutadapt v.1.8.3
Reads were aligned to version GRCm38  of mouse genome using HISAT2 v2.0.5
Transcriptomes were assembled and gene expression quantified using the Tuxedo pipeline (version 2.2.1). Transcriptome assembly, merging, quantification and normalisation to fragments per kilobase per million mapped reads (FPKM) were performed using Cufflinks, Cuffmerge, Cuffquant and Cuffnorm, respectively.
Cuffdiff (version 2.2.1) was used for differential expression analysis.
Genome_build: Genome Reference Consortium Mouse Build 38 (GRCm38)
Supplementary_files_format_and_content: sample_fpkms.txt: FPKM values for all genes in all samples as derived from Cufflinks; cuffdiff_results.txt: log2-fold-change values (lfc), p-values, and q-values derived from Cuffdiff comparisons for 1. WTPrimary_vs_Ciz1NullPrimary (S01-S03 vs S04-S06) 2. WTAdapted_vs_Ciz1NullAdapted (S07-S09 vs S10-S12) 3.   WTPrimary_vs_WTAdapted (S01-S03 vs S07-S09) 4.  Ciz1NullPrimary_vs_Ciz1NullAdapted (S04-S06 vs S10-S12)

growth_protocol: Primary (before passage 5) and culture-adapted derivative cell lines of murine embryonic fibroblasts 13.1, 13.8 and 14.4 (female WT), and 13.15, 13.17, 14.2 and 14.19 (female CIZ1 null) were grown to 80% confluence.

extract_protocol:
RNA was extracted with TRIzol (Ambion 15596-026) following manufacturer’s instructions, then treated with DNase (Roche 04716728001), before quality analysis by agarose gel, NanoDrop spectrophotometer and Agilent 2100 Bioanalyzer.
Libraries were prepared with NEBNext® UltraTM RNA library Prep Kit for Illumina®, and enriched for mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module, which is optimized for production of libraries with 250-400bp inserts.

tag: background strain

tag: Sex

value: Female

tag: cell type

value: Primary embryonic fibroblasts

value: CIZ1 -/- with inducible CIZ1 transgene

value: doxycycline (5-10 μg/ml)


title: Ciz1NullPrimaryDox_S14

description:
sample_fpkms.txt
cuffdiff_results.txt


title: DTF2_post_2

value: MJK16.5 (derivative of MA169.4)

value: post exponential growth phase

value: {delta}MjkB


title: BRICseq_Wt_Rep1_T0

tag: antibody


title: Ciz1NullPrimaryInducible_S13

description:
sample_fpkms.txt
cuffdiff_results.txt


title: NAT10_ac4C_RIP rep 2

data_processing:
Raw reads were pre-processed to remove low quality bases on 3’ ends by cropping to 101bp using Trimmomatic. Reads were mapped to the human genome (hg19) with Tophat2 v.2.1.1. Parameters used were: reporting at most one alignment per read (-g 1), allowing maximally five mismatches per read (>95% matching), and supplying the Ensembl Release 75 gene annotation. A post-alignment filter removed alignments to mitochondrial DNA (chrM) and non-concordant mate pairs
Genomic alignments were used to quantify transcripts using HTSeq against the Ensembl 75 annotation. Differential expression and gene-level variance-stabilized counts were calculated using DESeq2.
For transcript-level peak calling, canonical transcript sequences were downloaded from the UCSC genome browser and used in the generation of a Bowtie2-based index. Reads were aligned in local alignment mode with Bowtie2. MACS2 was used for peak calling in these alignment files .
For Ribo-Seq analysis, ribosome protected reads were first trimmed of adaptor sequence (5’-CTGTAGGCACCATCAAT) using cutadapt, and reads arising from rRNA were removed from the dataset based on alignment to a set of ribosomal RNA sequences using bowtie2. Remaining reads were then mapped to the UCSC hg19 canonical transcriptome with tophat (v 2.1.1), with the –prefilter-multihits option enabled to screen out reads that may have arisen from elsewhere in the genome. Uniquely mapped reads were then assigned to the specific codon estimated to be within the A-site of the protecting ribosome, based on identification of the P-site offset from the corresponding peak in read density that occurs up-stream of the start codon, with the added constraint that each read was mapped to the nearest in-frame codon and under the assumption that all reads will be in frame with the associated gene. Reads were assigned to the 5’ UTR, CDS or 3’ UTR based on the location of the inferred A-site of the read for purpose of estimating ribosome density in these regions.
For BRIC-Seq analysis, raw reads were mapped to a modified human genome (hg19 with the luciferase probe sequence added) using Hisat2 v2.0.5 (Kim et al., 2015). Parameters used were: reads that failed to align were not reported (--no-unal), library strandedness was specified (--rna-strandness FR), and a list of known splice sites was generated from the Ensembl 75 annotation (--known-splicesite-infile). Due to skewed sequencing depth, parental HeLa (WT) Rep-1 T2 was down-sampled to a depth representative of the other samples. Afterwards, genomic alignments were used to quantify transcripts using HTSeq v 0.6.1p1 (Anders et al., 2015) against the edited Ensembl 75 annotation with added probe. Library depth normalized gene expression counts were calculated using DESeq2 (Love et al., 2014). Then, all normalized gene count values in a particular time point were divided by the probe value for that time point. Data was further normalized to the first time point and log transformed. Half-lives were calculated by use of a linear model. Half-lives for HeLa WT and NAT10-/-A were calculated together within one linear model. A maximum half-life value of 24 hours was applied to calculated values exceeding this value. Genes with R2 values of < 0.8 were excluded from further analysis
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq_variance_stabilized_data.csv contains gene-level variance-stabilized counts from DESeq2 for RNA-Seq samples
Supplementary_files_format_and_content: acRIP_peaks.csv contains data for ac4C peaks in UCSC canonical transcripts.
Supplementary_files_format_and_content: RiboSeq_processed_data.csv contains tabulated Ribo-Seq results: mRNA normalized ribosome density summaries across canonical transcripts and by transcript feature (CDS/UTR).
Supplementary_files_format_and_content: BRIC_half_lives.csv contains computed RNA half-lives from BRIC-Seq Experiments

extract_protocol:
Poly(A)-RNA from parental and NAT10-/- HeLa cells (pool of two clones) was fragmented using NEBNext® Magnesium RNA Fragmentation buffer for 5 min at 94 oC. 8 pg of ac4C-RNA probe was spiked into 8 mg of fragmented poly(A)-RNA (8 mg) followed by immunoprecipitation with 1 mg anti-ac4C
Illumina libraries were constructed for inputs (parental vs NAT10-/-) and acRIPs (parental vs NAT10-/-) using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.
Total RNA was purified from cultured cells using Trizol (ThermoFisher) followed by treatment with TurboTM DNAse (ThermoFisher). Enrichment of polyadenylated RNA (poly(A)-RNA) from DNAse-treated total RNA was carried out by two rounds of selection with Oligo-(dT)25 Dynabeads (ThermoFisher) according to the manufacturer’s instructions. Enrichment efficiencies were estimated with Bioanalyzer picoRNA chips (Agilent Technologies, Santa Clara, CA).

value: anti-ac4C (Abcam, lot#H09131602)


title: Ciz1NullAdapted_S12

description:
sample_fpkms.txt
cuffdiff_results.txt

value: Adapted fibroblast cell line


title: DTF2_post_1

value: mycelium


title: Ciz1NullAdapted_S11

description:
sample_fpkms.txt
cuffdiff_results.txt


title: Ubc9Tg 45mins ischemia 3hrs reperfusion rep3

description: Ubc9Tg 45mins ischemia 3hrs reperfusion

source_name: Ubc9Tg 45mins ischemia 3hrs reperfusion

value: 45mins ischemia 3hrs reperfusion


title: WT 45mins ischemia 6hrs reperfusion rep1

description: WT 45mins ischemia 6hrs reperfusion

value: 45mins ischemia 6hrs reperfusion


title: NAT10_Input rep 2


title: Ciz1NullAdapted_S10

description:
sample_fpkms.txt
cuffdiff_results.txt


title: HeLa_ac4C_RIP rep 2

value: WT


title: DTF1_post_1

value: MJK15.4 (derivative of MA169.4)

value: {delta}MjkA


title: Ubc9Tg 45mins ischemia 3hrs reperfusion rep1

description: Ubc9Tg 45mins ischemia 3hrs reperfusion


title: WTAdapted_S09

description:
sample_fpkms.txt
cuffdiff_results.txt

source_name: WTAdapted

value: wild-type CIZ1 +/+


title: WTAdapted_S08

description:
sample_fpkms.txt
cuffdiff_results.txt


title: DDTF12_post_2

value: MJK18.1 (derivative of MA169.4)

value: {delta}MjkA/{delta}MjkB


title: DDTF12_post_1


title: Ubc9Tg 45mins ischemia 3hrs reperfusion rep2

description: Ubc9Tg 45mins ischemia 3hrs reperfusion


title: HeLa_Input

data_processing:
Raw reads were pre-processed to remove low quality bases on 3’ ends by cropping to 101bp using Trimmomatic. Reads were mapped to the human genome (hg19) with Tophat2 v.2.1.1. Parameters used were: reporting at most one alignment per read (-g 1), allowing maximally five mismatches per read (>95% matching), and supplying the Ensembl Release 75 gene annotation. A post-alignment filter removed alignments to mitochondrial DNA (chrM) and non-concordant mate pairs
Genomic alignments were used to quantify transcripts using HTSeq against the Ensembl 75 annotation. Differential expression and gene-level variance-stabilized counts were calculated using DESeq2.
For transcript-level peak calling, canonical transcript sequences were downloaded from the UCSC genome browser and used in the generation of a Bowtie2-based index. Reads were aligned in local alignment mode with Bowtie2. MACS2 was used for peak calling in these alignment files .
For Ribo-Seq analysis, ribosome protected reads were first trimmed of adaptor sequence (5’-CTGTAGGCACCATCAAT) using cutadapt, and reads arising from rRNA were removed from the dataset based on alignment to a set of ribosomal RNA sequences using bowtie2. Remaining reads were then mapped to the UCSC hg19 canonical transcriptome with tophat (v 2.1.1), with the –prefilter-multihits option enabled to screen out reads that may have arisen from elsewhere in the genome. Uniquely mapped reads were then assigned to the specific codon estimated to be within the A-site of the protecting ribosome, based on identification of the P-site offset from the corresponding peak in read density that occurs up-stream of the start codon, with the added constraint that each read was mapped to the nearest in-frame codon and under the assumption that all reads will be in frame with the associated gene. Reads were assigned to the 5’ UTR, CDS or 3’ UTR based on the location of the inferred A-site of the read for purpose of estimating ribosome density in these regions.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq_variance_stabilized_data.csv contains gene-level variance-stabilized counts from DESeq2 for RNA-Seq samples
Supplementary_files_format_and_content: acRIP_peaks.csv contains data for ac4C peaks in UCSC canonical transcripts.
Supplementary_files_format_and_content: RiboSeq_processed_data.csv contains tabulated Ribo-Seq results: mRNA normalized ribosome density summaries across canonical transcripts and by transcript feature (CDS/UTR).

source_name: HeLa cells, polyA RNA

extract_protocol:
Total RNA was purified from cultured cells using Trizol (ThermoFisher) followed by treatment with TurboTM DNAse (ThermoFisher). Enrichment of polyadenylated RNA (poly(A)-RNA) from DNAse-treated total RNA was carried out by two rounds of selection with Oligo-(dT)25 Dynabeads (ThermoFisher) according to the manufacturer’s instructions. Enrichment efficiencies were estimated with Bioanalyzer picoRNA chips (Agilent Technologies, Santa Clara, CA).
Poly(A)-RNA from parental and NAT10-/- HeLa cells (pool of two clones) was fragmented using NEBNext® Magnesium RNA Fragmentation buffer for 5 min at 94 oC. 8 pg of ac4C-RNA probe was spiked into 8 mg of fragmented poly(A)-RNA (8 mg) followed by immunoprecipitation with 1 mg anti-ac4C or IgG pre-coupled Protein G Dynabeads
Illumina libraries were constructed for inputs (parental vs NAT10-/-), acRIPs (parental vs NAT10-/-), and IgG (parental) using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.

value: HeLa cells


title: NAT10_ac4C_RIP


title: DHD_post_2

value: MJK14.7 (derivative of MA169.4)

value: {delta} histone deacetylase


title: WT 45mins ischemia 3hrs reperfusion rep2

description: WT 45mins ischemia 3hrs reperfusion

source_name: WT 45mins ischemia 3hrs reperfusion


title: WT 45mins ischemia 3hrs reperfusion rep3

description: WT 45mins ischemia 3hrs reperfusion


title: WTAdapted_S07

description:
sample_fpkms.txt
cuffdiff_results.txt

value: Female


title: HeLa_ac4C_RIP


title: WT 45mins ischemia 3hrs reperfusion rep4

description: WT 45mins ischemia 3hrs reperfusion


title: DHD_post_1

value: post exponential growth phase


title: Ciz1NullPrimary_S05

description:
sample_fpkms.txt
cuffdiff_results.txt

value: Primary embryonic fibroblasts


title: DTF1_post_2


title: NAT10_Input


title: HeLa_Input rep 2


title: TF1OE_post_2

value: MJK11.17 (derivative of MA169.4)

value: MjkA OE


title: Ciz1NullPrimary_S04

description:
sample_fpkms.txt
cuffdiff_results.txt


title: HeLa_IgG_RIP

value: anti-rabbit IgG (Cell signaling)


title: WTPrimary_S03

description:
sample_fpkms.txt
cuffdiff_results.txt

source_name: WTPrimary


title: TF1OE_post_1

value: mycelium


title: HeLa_RNA-Seq_Rep2

source_name: HeLa cells, total RNA

extract_protocol:
Total RNA was purified from cultured cells using Trizol (ThermoFisher) followed by treatment with TurboTM DNAse (ThermoFisher). Enrichment of polyadenylated RNA (poly(A)-RNA) from DNAse-treated total RNA was carried out by two rounds of selection with Oligo-(dT)25 Dynabeads (ThermoFisher) according to the manufacturer’s instructions. Enrichment efficiencies were estimated with Bioanalyzer picoRNA chips (Agilent Technologies, Santa Clara, CA).
Total RNA was used for library construction with the Illumina TruSeq stranded RNA Protocol RS-122-2201 protocol (Illumina, San Diego, CA), including rRNA depletion via RiboZero


title: Ubc9Tg 0hrs sham rep4

description: Ubc9Tg 0hrs sham

source_name: Ubc9Tg 0hrs sham

value: sham


title: TF2OE_post_2

value: MjkB OE


title: WT 45mins ischemia 3hrs reperfusion rep1

description: WT 45mins ischemia 3hrs reperfusion

value: WT

value: 45mins ischemia 3hrs reperfusion


title: Ubc9Tg 0hrs sham rep3

description: Ubc9Tg 0hrs sham


title: Ubc9Tg 0hrs sham rep2

description: Ubc9Tg 0hrs sham


title: Ciz1NullPrimaryInducible_S06

description:
sample_fpkms.txt
cuffdiff_results.txt

value: CIZ1 -/- with inducible CIZ1 transgene


title: WTPrimary_S02

description:
sample_fpkms.txt
cuffdiff_results.txt

value: wild-type CIZ1 +/+


title: TF2OE_post_1


title: WTPrimary_S01

description:
sample_fpkms.txt
cuffdiff_results.txt


title: MiSeq_pool

description:
seq_id: NA
ambient conditions
GuineaGrass.Assembly.Trinity.txt

value: Leaf-youngest fully expanded

value: ambient conditions


title: WT_post_2

value: MJK17.25 (derivative of MA169.4)

value: wild type


title: NAT10_RNA-Seq_Rep2

value: HeLa cells


title: HeLa_RNA-Seq_Rep1


title: NAT10_RNA-Seq_Rep1


title: WT_post_1

value: post exponential growth phase


title: WT 0hrs sham rep_4

description: WT 0hrs sham

source_name: WT 0hrs sham


title: Ubc9Tg 0hrs sham rep1

description: Ubc9Tg 0hrs sham


title: WT 0hrs sham rep_1

description: WT 0hrs sham


title: Sarcoma [SA0923]

status: Public on Nov 06 2018

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol were attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: Serum

value: Male

tag: disease status

value: Sarcoma

tag: pathological tstage

value: uncertain

tag: pathological grade


title: Sarcoma [SA0874]

description: miRNA


title: Sarcoma [SA0939]

description: miRNA


title: WT 0hrs sham rep_2

city: Bethesda

address: 10/3B01, 9000 Rockville Pike

description: WT 0hrs sham


title: WT 0hrs sham rep_3

description: WT 0hrs sham


title: Sarcoma [SA0850]

description: miRNA

value: Female


title: Sarcoma [SA0829]

description: miRNA


title: Sarcoma [SA0646]

description: miRNA


title: Sarcoma [SA0731]

description: miRNA


title: Sarcoma [SA0682]

description: miRNA


title: Sarcoma [SA0585]

description: miRNA


title: Sarcoma [SA0550]

description: miRNA


title: Sarcoma [SA0580]

description: miRNA


title: Sarcoma [SA0997]

description: miRNA


title: Sarcoma [SA0478]

description: miRNA


title: Sarcoma [SA0492]

description: miRNA


title: Sarcoma [SA0465]

description: miRNA


title: Sarcoma [SA0463]

description: miRNA


title: Sarcoma [SA0456]

description: miRNA


title: Sarcoma [SA0922]

description: miRNA


title: Sarcoma [SA0937]

description: miRNA


title: Sarcoma [SA0802]

description: miRNA


title: Sarcoma [SA0358]

description: miRNA


title: Sarcoma [SA0331]

description: miRNA


title: Sarcoma [SA0287]

description: miRNA


title: Sarcoma [SA0280]

description: miRNA


title: Sarcoma [SA0204]

description: miRNA


title: Sarcoma [SA0237]

description: miRNA


title: Sarcoma [SA0232]

description: miRNA


title: Sarcoma [SA0273]

description: miRNA


title: Sarcoma [SA0263]

description: miRNA


title: Sarcoma [SA0197]

description: miRNA


title: Sarcoma [SA0380]

description: miRNA


title: Sarcoma [SA0148]

description: miRNA


title: Sarcoma [SA0094]

description: miRNA


title: Sarcoma [SA0112]

description: miRNA


title: Sarcoma [SA0074]

description: miRNA


title: Sarcoma [SA0050]

description: miRNA


title: Sarcoma [SA0042]

description: miRNA


title: Prostate Cancer [PR1039]

description: miRNA

value: Prostate Cancer


title: Sarcoma [SA0060]

description: miRNA


title: Sarcoma [SA0048]

description: miRNA


title: Prostate Cancer [PR0993]

description: miRNA


title: Prostate Cancer [PR0984]

description: miRNA


title: Prostate Cancer [PR0909]

description: miRNA


title: Prostate Cancer [PR0951]

description: miRNA


title: Prostate Cancer [PR0879]

description: miRNA


title: Prostate Cancer [PR0840]

description: miRNA


title: Prostate Cancer [PR0849]

description: miRNA


title: Prostate Cancer [PR0828]

description: miRNA


title: Sarcoma [SA0184]

description: miRNA


title: Prostate Cancer [PR0966]

description: miRNA


title: Prostate Cancer [PR0794]

description: miRNA


title: Prostate Cancer [PR0994]

description: miRNA


title: WT 45mins ischemia 6hrs reperfusion rep2

description: WT 45mins ischemia 6hrs reperfusion

value: 45mins ischemia 6hrs reperfusion


title: Prostate Cancer [PR0672]

description: miRNA


title: Prostate Cancer [PR0662]

description: miRNA


title: Prostate Cancer [PR0760]

description: miRNA


title: Prostate Cancer [PR0724]

description: miRNA


title: Prostate Cancer [PR0730]

description: miRNA


title: Prostate Cancer [PR0650]

description: miRNA


title: Prostate Cancer [PR0782]

description: miRNA


title: Prostate Cancer [PR0641]

description: miRNA


title: Prostate Cancer [PR0630]

description: miRNA


title: Prostate Cancer [PR0612]

description: miRNA


title: Prostate Cancer [PR0589]

description: miRNA


title: Prostate Cancer [PR0604]

description: miRNA


title: Prostate Cancer [PR0640]

description: miRNA


title: Prostate Cancer [PR0499]

description: miRNA


title: Prostate Cancer [PR0595]

description: miRNA


title: Prostate Cancer [PR0566]

description: miRNA


title: Prostate Cancer [PR0530]

description: miRNA


title: Prostate Cancer [PR0495]

description: miRNA


title: Prostate Cancer [PR0485]

description: miRNA


title: Prostate Cancer [PR0463]

description: miRNA


title: Prostate Cancer [PR0433]

description: miRNA


title: Prostate Cancer [PR0449]

description: miRNA


title: Prostate Cancer [PR0369]

description: miRNA


title: Prostate Cancer [PR0327]

description: miRNA


title: Prostate Cancer [PR0330]

description: miRNA


title: Pancreatic Cancer [PC0821]

description: miRNA

value: Pancreatic Cancer


title: Pancreatic Cancer [PC0768]

description: miRNA


title: Pancreatic Cancer [PC0830]

description: miRNA


title: Prostate Cancer [PR0279]

description: miRNA


title: Prostate Cancer [PR0322]

description: miRNA


title: Pancreatic Cancer [PC0847]

description: miRNA