title: Vector

city: XI'AN

first: wang

address: Yanta Street

institute: Department of Endocrinology

data_processing:
Basecalls performed using fastx(version 0.0.14)
Reads were aligned to the hg19 using Bowtie(version 1.0.0)
Data filtering was performed using trim(version 0.3.7)
peaks were called using MACS(version 1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using Bowtie(version 1.0.0)

source_name: BCPAP cells

growth_protocol: BCPAP cells were cultured in RPMI 1640 medium supplemented with bovine calf serum to a final concentration of 10% at 37°C. Atmosphere: air, 95%;

extract_protocol:
Cells were fixed with 1.0% formaldehyde at room temperature for 15 min, after which glycine was added to the medium. The cells were then lysed and the mouse monoclonal antibodies against Myc (Millipore,#05-724MG) was used for the ChIP assay using the Pierce™ Magnetic ChIP Kit (Thermo, Inc., MA, USA) according to the instructions of manufacturer. Immunoprecipitated DNA (20 ng) was subjected to size selection of fragments around 200-bp in length.
Sequencing libraries were consequently constructed by adaptor ligation and PCR. Sequencing was carried out with an Illumina HiSeq2500 system according to the manufacturer's protocol.

treatment_protocol: BCPAP cells were transfected with a pcDNA3.1-Vector (contains Myc tag) and pcDNA3.1-TBX1 (contains Myc tag).

value: BCPAP

value: Papillary thyroid carcinoma

tag: transfected with

tag: passages

value: Anti-Myc Tag Antibody, clone 4A6 (Millipore,#05-724MG)


title: TBX1

status: Public on May 01 2018

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: chip antibody


title: CCND1-1

city: BOSTON

first: Teresa

last: Davoli

state: MA

address: 12 Aberdeen Street, 2

country: USA

institute: BRIGHAM AND WOMEN S Hospital

library_source: transcriptomic

data_processing:
HISAT2 (Kim et al., Nat Method, 2015)
Aligned reads were annotated using a matched build of all known gene transcripts and spliceforms.
Sorted bam files from this alignment were then assessed for transcript frequency using the featureCounts application of the Subread suite, defining features at the exon-level (Liao et al. Bioinformatics, 2014)
We filtered raw counts to remove transcripts that had less than 20 reads across all samples.
Counts were then normalized with Limma’s voom function and differential expression was determined with Limma’s general linear model.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: txt files that include counts normalized with Limma’s voom function.

molecule: polyA RNA

source_name: hTERT human mammary epithelial cells (hMEC)

growth_protocol: HMECs (Lonza cat # CC-2551) were immortalized with hTERT, and were maintained in MEGM (Lonza cat # CC-3150).

extract_protocol:
Cells were lysed and RNA extracted using the Qiagen RNeasy kit per manufacturer’s instructions. Poly-A tailed mRNAs were enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module per manufacturer’s instructions.
Poly-A tailed mRNAs were then prepped into RNA-Seq libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina. RNA-Seq libraries were amplified and indexed using NEBNext® Multiplex Oligos for Illumina® per manufacturer’s instructions.
Libraries were sequenced on an Illumina HiSeq 2500.

treatment_protocol: Cells plated at equal density, treated with 100 ng/ml dox for 96 hours.

value: cells overexpressing CCND1

tag: sample type


title: 1eCeN21

type: genomic

city: Beijing

first: Qun

last: Gao

state: Beijing

address: Shuang Qing Road

department: Environmental sicence and engineering

institute: Tsinghua University

description: GeoChip data for soil sample collected at elevated CO2, elevated N

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

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

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

organism: soil metagenome

source_name: Soil microbes in BioCON plots

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: In August 2009, soil samples were collected from all of the plots. Soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: different carbon and nitrogen levels

value: elevated CO2, elevated N


title: CD anti-TNF non-responder 2

type: RNA

city: Erlangen

first: Heike

last: Schmitt

address: Ulmenweg 18

department: First Department of Medicine

country: Germany

institute: University of Erlangen-Nuremberg

description: Gene expression of CD anti-TNF non-responder

hyb_protocol: Following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent 026652 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2505C Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.5.1. (Agilent Technologies Germany). Data extraction using protocol GE1_1105_0ct12

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.6 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in both replicates in at least one conditions were selected by filtering  on data present. Entitie lists were further filtered by selection of genes which do not change their expression in all conditions. This list was subtracted from the entities present in at least one conditions  by means of VENN diagramms. Entities differentially expressed  in anti-TNF non responders compared to anti-TNF responders  were obtained by Volcano plot analysis (fold change >=2, p-value <=0.05, Benjamini Hochberg fals discovery fals positive correction).

molecule: total RNA

source_name: CD anti-TNF non-responder, replicate 2

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 100ng total RNA (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Intestinal biopsies or gut resections from Crohn’s disease patients were used for microarray.

extract_protocol: RNA was isolated from intestinal biopsies using the Nucleo Spin II kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: CD patients were classified as responders to anti-TNF therapy, if they had ongoing anti-TNF therapy (infliximab or adalimumab) for over 3 months and a Simple Endoscopic Score for Crohn's Disease (SES-CD)27,28 <5 during the endoscopic examination where the biopsy was taken. Non-response was defined by a SES-CD ≥5 to ongoing anti-TNF therapy (over 3 months), or if the surgical intestinal specimen used, had a segmental SES-CD ≥5. If clinical response to anti-TNF therapy was additionally defined as an evaluation criterion, the respective condition is stated in the text. Concomitant medication of the patients included salicylates, corticosteroids or azathioprine.

tag: patient

value: CD anti-TNF non- responder

tag: tissue

value: Intestine


title: 1eCeN22

treatment_protocol: In August 2009, soil samples were collected from all of the plots. Soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.


title: 1eCeN17


title: 1eCeN18


title: 1eCeN16


title: 1eCeN23


title: MYC-1

value: cells overexpressing MYC

value: pInducer-rtTA-Neo and pHAGE-TRE-BC-MYC


title: 1eCeN14


title: 1eCeN20


title: 1eCeN15


title: 1eCeN13


title: 1eCeN19


title: CCND1-2


title: 1eCeN12


title: MYC-2


title: 1eCeN10


title: 1eCeN11


title: ch12_wt_mRNA_rep4

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description:
mRNA-Seq
ch12_wt_mRNA_merged.bw

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer runnning with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer  between the  end of the primer and the restriction sites  used  in  the  corresponding  experiment.
4C-Seq: mapping: bowtie-1.1.1/bowite -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to DPNII/CSP6i fragment to calculate fraction of restriction fragments for which 4C reads were found
ChIAPET: followed the process described in Li et al.,2010
ChIAPET: interaction call by chiapettool v2 program with default parameter
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
local HiC: preprocess & normalization: juicer.sh using default parameter
local HiC: 5kb resolution matrices extraction: juicebox dump obsevered NONE .hic BP 5000
local HiC: R & custom script: generate genome wide contact matrix as in Sanborn et al. PNAS 2015
local HiC: estimation of number of in silico spike-ins: median of the genome-wide per-bin coverage of the local HiC matrix at the targeted region
local HiC: reconstruct HiC matrix: combine the targeted region local HiC with the global CH12 wt matrix which matched to spike-ins
local HiC: re-normalization: Knight-Ruiz balancing algorithm with the juicebox pre -r 5000
ChromRNA_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChromRNA_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
ChromRNA_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content:
ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Gro-Seq: .wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh
ChIAPET: bed12 format by editting the result of chiapettool by restricting to show only interactions having more than or equal to 3 PETs
4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window
mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
ChromRNA: strand-specific density tracks are generated by using bedtools genomecov program divided by library size in millions to obtain normalized read density (rpm)

organism: Mus musculus

source_name: CH12 B cell line

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: we used the same protocol for in situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)
Gro-seq: Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation. Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis was performed the next day as described in (Wang et al., 2011). However, for reverse transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA  was  religated  in  a  7 ml  volume  (1,000 U  T4  DNA  Ligase,  Roche).  Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C.  Bait was amplified with inverse PCR primers as follows: 3RR with DpnII:_4C 5'-GCTTATCTGTAAAGAATGGGTC-3', 3RR_Csp6i 5'-GGCCTTAGAAGGCTCTGTAC-3'. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 106 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated .
local Hi-C: 500ng of Hi-C library (8 cycles of amplification) was mixed with 2.5 µg of mouse Cot-1 DNA and 10µg of salomon sperm DNA in a total volume of 25µl. The sample was heated to 95℃ for 5 minutes. Next the temperature was diminished to 65℃ and the samples incubated for at least 5 minutes at 65℃. In the meantime 6µl of a RNA probe mixture (500ng of RNA probes, 20U of supreRNAseIn) and 33µl of hybridization buffer (10xSSPE, 10xDenhardt buffer, 10mM EDTA, 0.2% SDS) were incubated at 65℃. Next, the hybridization buffer and the RNA probe mixture were added to the sample. The final mix was incubated at 65℃ for 24 hours. Following the hybridization, 50 µl of MyOne Streptavidin T1 beads were washed 3 times with Bind-and-Wash buffer (1M NaCl, 10 mM Tris-HCl, pH=7.5, 1mM EDTA) and then resuspended in 134 µl of Bind-and-Wash buffer and added to the sample. The mixture was incubated for 30 minutes at room temperature with occasional swirling. Next, beads were separated using a magnet and the supernatant discarded. Beads were then washed once with 200µl of low-stringency buffer (1xSSC, 0.1%SDS) and incubated for 15 minutes at RT. Beads were separated and washed 3 times with high stringency.
ChromRNA-seq: chromatin RNA fraction was prepared from 3*10^6 cells following the method previously described (Pandya-Jones & Black, RNA, 2009) with some modifications. The pellet was lysed in a cytoplasm lysis buffer (20mM Hepes-KOH pH 7.6, 2mM MgCl2, 10% glycerol, 0.1% NP40, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). The lysate was then layered on top of a sucrose buffer in order to isolate the nuclei fraction from the cytoplasmic one (10mM Hepes-KOH pH7.6, 10mM NaCl, 1.5mM MgCl2, 10% glycerol, 0.5mM EDTA, 0.5mM DTT, 34% sucrose w/v with protease inhibitor, phosphatase inhibitor and RNase inhibitor).
ChromRNA-seq: The nuclei fraction was resuspended and lysed in a nuclear lysis buffer (10mM Hepes-KOH pH 7.6, 100mM NaCl, 0.5mM EDTA, 50% glycerol, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). Chromatin was precipitated by adding a Urea c

treatment_protocol: Myc floxed allele was obtained from Douglas Green (St. Jude Children’s research hospital). Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice). The deletion of floxed allele was checked by PCR or intracellular staining of Myc protein.

tag: genotype

value: WT

value: lymphoma cell line


title: 1eCeN6


title: 16aCeN11

description: GeoChip data for soil sample collected at ambient CO2, elevated N

value: ambient CO2, elevated N


title: 16aCeN9


title: 16aCeN10


title: 16aCeN4


title: 1eCeN1


title: 16aCeN12


title: 16aCeN7


title: 9aCeN15


title: 9aCeN14


title: 1eCeN5


title: 16aCeN6


title: 1eCeN7


title: 16aCeN3


title: 16aCeN5


title: ch12_wt_mRNA_rep1

description:
mRNA-Seq
ch12_wt_mRNA_merged.bw


title: 16aCeN1


title: ch12_wt_mRNA_rep3

description:
mRNA-Seq
ch12_wt_mRNA_merged.bw


title: 16aCeN2


title: 1eCeN3


title: ch12_wt_mRNA_rep2

description:
mRNA-Seq
ch12_wt_mRNA_merged.bw


title: ch12_CTCFZF9to11_mRNA_rep7

description:
mRNA-Seq
ch12_CTCFZF9to11_mRNA_merged.bw


title: ch12_CTCFZF9to11_mRNA_rep6


title: ch12_CTCFZF9to11_mRNA_rep3


title: 9aCeN13


title: ch12_CTCFZF9to11_mRNA_rep4


title: 9aCeN11


title: 1eCeN9


title: ch12_CTCFZF9to11_mRNA_rep2


title: 9aCeN10


title: esc_wt_CTCF_rep5

source_name: ES cell

value: blastocyst

value: anti-CTCF (EMD Millipore; 07-729)


title: esc_wt_CTCF_rep3


title: esc_wt_CTCF_rep4


title: 9aCeN12


title: 9aCeN9


title: 9aCeN8


title: esc_wt_CTCF_rep1


title: 9aCeN6


title: ch12_wt_input_rep2

tag: activation treatment

value: input


title: 9aCeN7


title: ch12_CTCFZF9to11_mRNA_rep1


title: esc_wt_CTCF_rep6


title: ch12_ZF9to11_CTCF_rep1


title: 4aCeN15


title: 9aCeN4


title: 9aCeN5


title: 1VPMR

first: pei

middle: pei

last: WU

address: Zhongguancun South Street

institute: Chinese Academy of Agricultural Sciences

data_processing:
The raw sequencing reads generated were quality controlled using software Trimmomatic v0.36
The clean reads were aligned to the Chinese Spring whole genome assembly sequences (IWGSC WGS v1, NRGene DeNovoMAGIC, Seq Repository of Wheat Portal on URGI, INRA, France)
The read alignments were masked for PCR duplications and split for reads spanning introns before they were used to call SNPs and InDels using module “HaplotypeCaller” software GATK v3.6
The resulting single nucleotide polymorphism (SNPs) and InDels with sequencing depth less than 6 were discarded, and the remaining ones were applied to BSA. Only variants with allele frequency difference (AFD) > 0.6 and P-value of Fisher’s exact test on read count data < 1e-8 were classified as resistance-associated variants and used as templates for marker development.
Genome_build: http://www.wheatgenome.org/News/Latest-news/RefSeq-v1.0-URGI
Supplementary_files_format_and_content: fa file including the different SNPs of the resistant pool and the susceptible pool

organism: Triticum aestivum

source_name: leaf

growth_protocol: The BSR-seq approach was performed on selected F2:3 families from the mapping population of VPM1/7*Bainong 3217 F4 × Bainong 3217 cross.

extract_protocol:
Total RNA of the two bulks of leaf samples was separately extracted using the Illumina TruSeq RNA Sample Prep Kit
The library was created using phenotypically contrasting bulks of leaf samples  which were created by pooling equal size of the primary leaf from each representative plant two-leaf-old of 50 homozygous resistant and 50 homozygous susceptible F2:3 families.

tag: phenotype

value: Resistant to powdery mildew

value: leaf


title: 9aCeN1


title: 9aCeN3


title: 4aCeN14


title: 9aCeN2


title: 2VPMS

value: Sensitive to powdery mildew


title: Foetus rep4

city: Cambridge

first: Aurora

last: Gomez-Duran

state: Cambridge

address: Welcome Trust/MRC Building

department: Department of Clinical Neurosciences

country: United Kingdom

institute: Cambridge University

data_processing:
Alignment: start 2.5.2b
Normalised abundance: DESeq2
Genome_build: cavPor3
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited ASCII file.
Supplementary_files_format_and_content: normalisedcounts.csv: Comma-separated text file includes normalised counts.

organism: Cavia porcellus

source_name: heart - left ventricle

growth_protocol: Adult male and female guinea pigs (Dunkin Hartley; Envigo UK) were housed under standard 12 hour day/night cycles and fed ad libitum. Non-pregnant and time-mated term (day 66-67) pregnant guinea pigs were killed by anesthetic overdose.

extract_protocol:
Hearts isolated from the animals were immediately flushed with excess cardioplegic solution (glucose 227.5mM, mannitol 34.5mM, KCl 30mM, NaHCO3 25mM, pH 7.4) by retrograde perfusion via the aorta to clear all blood. The left ventricular walls were dissected out, frozen in liquid nitrogen and tissues stored until use at -80degC. Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing with standard Illumina protocols using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold, Illumina.

treatment_protocol: No treatment.

tag: strain/background

value: Dunkin Hartley

tag: age

value: Fetus, gestation day 67

value: heart, left ventricle


title: Foetus rep2


title: Foetus rep1


title: Foetus rep3


title: ch12_ZF9to11_CTCF_rep2


title: ch12_wt_input_rep1


title: 4aCeN13


title: 1eCeN4

value: elevated CO2, elevated N


title: 16aCeN8


title: 4aCeN11


title: 4aCeN12


title: Adult rep4

value: Adult, non-pregnant


title: 4aCeN9


title: 4aCeN10


title: 4aCeN8


title: 4aCeN6


title: 4aCeN7


title: Adult rep3


title: Adult rep2


title: 4aCeN5


title: Adult rep1


title: ctrlu2: Patients with BPH

type: other

city: Philadelphia

first: Sagarika

last: Banerjee

address: 3610 Hamilton Walk

institute: University of Pennsylvania

description: Germ free human B cell line for dye compensation

hyb_protocol: Using Agilent 2X HI-RPM Hybridization buffer and blocking agents, hybridization was done at 65 degree for 40 hours as per the protocol of Agilent Oligonucleotide Array-Based CGH for genomic DNA Analysis.

scan_protocol: Scanned on SureScan Agilent scanner G2600D, scan protocol Agilent G3_CGH (resolution 3um) Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and normalization. We calculated scale factor using the signals of green and red channels for human probes. Scale factors are the sum of green/sum of red signal ratios of human probes. Then we used scale factors to obtain normalized signals for all other probes. For all probes except human probes, normalized signal is log2 transformed of green signals / scale factors modified red signals (log2 g – log2 scale factor * r).

molecule: other

source_name: control samples from 5 BPH patients pooled together; formalin fixed paraffin embedded tissue section

label_protocol: 1microgram of amplified DNA/RNA which was amplified by WTA-2 kit from Sigma was labelled with SureTag DNA Labeling Kit (Agilent). Amplified DNA/RNA from the FFPE tumor/control tissyes were labelled with Cy3 and that of BJAB cells were labelled with Cy5. Labelled samples werec purified with Sure Tag purification columns (Agilent).

growth_protocol: Formalin fixed paraffin embedded (FFPE) prostate tumor and control tissues were provided to us. The human B cells were grown in RPMI media supplemented with 10% FBS.

extract_protocol: We used AllPrep DNA/RNA FFPE Kit from Qiagen for simultaneous extraction of DNA and RNA from each of the FFPE tissue samples.

value: Non cancerous prostate tissue

tag: molecule

value: cDNA+gDNA

source_name: microbiome free human B cell line BJAB

value: BJAB, a human B cell line


title: ctrlu3: Patients with BPH


title: ctrlu1: Patients with BPH


title: 1047: Prostate cancer patient 49

source_name: individual sample; formalin fixed paraffin embedded tissue section

value: Prostate tumor tissue


title: 1048: Prostate cancer patient 50


title: 1050: Prostate cancer patient 48


title: 1049: Prostate cancer patient 47


title: 1046: Prostate cancer patient 46


title: 4aCeN1


title: 1045: Prostate cancer patient 45


title: 1aCeN32


title: 1eCeN2


title: 4aCeN3


title: 1041: Prostate cancer patient 44


title: 1aCeN26


title: 4aCeN2


title: 1aCeN31


title: 1aCeN30


title: 4aCeN4


title: 1aCeN29


title: 1aCeN28


title: 1eCeN8


title: 1aCeN27


title: 1aCeN25


title: 1044: Prostate cancer patient 43


title: 1043: Prostate cancer patient 42


title: 1042: Prostate cancer patient 41


title: 1aCeN24


title: 1040: Prostate cancer patient 40


title: 1039: Prostate cancer patient 39


title: 1038: Prostate cancer patient 38


title: 1aCeN23


title: 1037: Prostate cancer patient 37


title: 1aCeN22


title: 1036: Prostate cancer patient 36


title: 1aCeN21


title: 1035: Prostate cancer patient 35


title: 1aCeN20


title: 1034: Prostate cancer patient 34


title: 1033: Prostate cancer patient 33


title: 1031: Prostate cancer patient 31


title: 1032: Prostate cancer patient 32


title: 1aCeN17


title: 1aCeN19


title: 1aCeN18


title: 1aCeN16


title: Day 7

city: Maebashi

first: Tsukasa

last: Oda

state: Gunma

address: Showa-machi, 3-39-15

department: IMCR

country: Japan

institute: Gunma University

description: SAMPLE 4

hyb_protocol: 65C, 17 hr, 10 rpm, Gene Expression Hybridization kit <5188-5242> (Agilent Technologies) and hybridization oven <G2545A, G2530 60029> (Agilent Technologies).

scan_protocol: Scanner <G2539A> (Agilent Technologies).

data_processing: Scan Control <version A.8.5.1> (Agilent Technologies).

source_name: DOX-treatment, Day 7

label_protocol: Low Input Quick Amp labeling kit, one-color <5190-2305> (Agilent Technologies) and Agilent RNA Spike In kit <5188 5282> (Agilent Technologies).

extract_protocol: RNeasy mini kit (74106, Qiagen).

value: hTERT-immortalized human fibroblasts expressing doxycycline-inducible shRNA targeting HSF1

tag: treatment

value: DOX

tag: day


title: 1aCeN14

value: ambient CO2, elevated N


title: Day 1

description: SAMPLE 2

source_name: DOX-treatment, Day 1


title: 1aCeN13


title: 1aCeN15


title: Day 3

description: SAMPLE 3

source_name: DOX-treatment, Day 3


title: 1029: Prostate cancer patient 29


title: Day 0

description: SAMPLE 1

source_name: vehicle-treatment

value: vehicle


title: 1aCeN11


title: 1028: Prostate cancer patient 28


title: 1027: Prostate cancer patient 27


title: 1aCeN12


title: Dermis from healthy skin, sample 4, set 2

city: Lille

first: Denis

middle: A

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

country: France

institute: INSERM

description:
Gene expression in human healthy dermis
CN4Dh

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was hybridized with Human Gene Expression Microarray 8x60K chip (Agilent Technologies) according to manufacturer's protocol

scan_protocol: Slides were scanned with the Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1). Data were background-corrected with 'normexp' option and quantile normalized using limma R package.

source_name: Human healthy dermis (laser capture microdissection), sample 4

label_protocol: 10 ng RNA were amplified with ExpressArt Kit and labeled (Cy3) with One-color microarray-based Gene Expression Analysis Low Input Quick Amp WT Labeling (Agilent Technologies) according to manufacturer's protocol

extract_protocol: RNA was isolated with Arcturus Picopure RNA isolation Kit according to manufacturer's protocol

tag: disease state

value: control

value: dermis

tag: gender

value: female


title: Lesional dermis from psoriatic skin, sample 14, set 2

description:
Gene expression in human lesional psoriatic dermis
PN14DL

source_name: Human lesional psoriatic dermis (laser capture microdissection), sample 14

value: psoriasis

value: male


title: 1aCeN10


title: Dermis from healthy skin, sample 2, set 2

description:
Gene expression in human healthy dermis
CN2Dh

source_name: Human healthy dermis (laser capture microdissection), sample 2


title: 1030: Prostate cancer patient 30


title: 1026: Prostate cancer patient 26


title: 1aCeN9


title: 1025: Prostate cancer patient 25


title: Lesional dermis from psoriatic skin, sample 10, set 2

description:
Gene expression in human lesional psoriatic dermis
PN10DL

source_name: Human lesional psoriatic dermis (laser capture microdissection), sample 10


title: 1024: Prostate cancer patient 24


title: 1aCeN8

source_name: Soil microbes in BioCON plots


title: fog-2_D_hex

city: College Park

first: Eric

middle: S.

last: Haag

address: 4094 Campus Drive

department: Department of Biology

institute: University of Maryland

description: random hexamer-primed cDNA synthesis

data_processing:
base-calling: Cassava 1.8.2 (Illumina)
de-multiplexing: Cassava 1.8.2 (Illumina)
read-mapping to the C. elegans reference genome: TopHat, implemented in Cufflinks 2.1.1
differential expression analysis: cuffdiff, implemented in Cufflinks 2.1.1, with per-condition dispersion option.
Genome_build: WBcel215
Supplementary_files_format_and_content: cuffdiff output files in Excel format, including comparison of total

organism: Caenorhabditis elegans

source_name: whole XX adult female

growth_protocol: Grown on NGM agar plates at 20 C, using OP50 E. coli bacteria as food.

extract_protocol:
Total RNA was extracted using Trizol (Ambion), chloroform, and isopropanol precipitation according the manufacturer's protocol.
Libraries were produced using the Illumina TotalScript kit.

tag: strain

value: strain JK574

tag: genotype/variation

value: fog-2(q71) homozygous mutant


title: fog-2_B_hex

description: random hexamer-primed cDNA synthesis


title: 1023: Prostate cancer patient 23


title: 1022: Prostate cancer patient 22


title: fog-2_A_hex

description: random hexamer-primed cDNA synthesis


title: 1021: Prostate cancer patient 21


title: 1aCeN7


title: Lesional dermis from psoriatic skin, sample 7, set 2

description:
Gene expression in human lesional psoriatic dermis
PN7DL

source_name: Human lesional psoriatic dermis (laser capture microdissection), sample 7


title: 1aCeN6


title: Dermis from healthy skin, sample 6, set 1

description:
Gene expression in human healthy epidermis
CN6Dh

source_name: Human healthy dermis (laser capture microdissection), sample 6


title: 1aCeN3


title: Dermis from healthy skin, sample 7, set 1

description:
Gene expression in human healthy epidermis
CN7Dh

source_name: Human healthy dermis (laser capture microdissection), sample 7


title: N2_D_hex

description: random hexamer-primed cDNA synthesis

source_name: whole XX adult hermaphrodite

value: strain N3

value: wildtype


title: 1aCeN5


title: N2_C_hex

description: random hexamer-primed cDNA synthesis

value: strain N2


title: 1020: Prostate cancer patient 20

value: cDNA+gDNA


title: 1019: Prostate cancer patient 19

value: BJAB, a human B cell line


title: N2_A_hex

description: oligo-dT-primed cDNA synthesis


title: Lesional dermis from psoriatic skin, sample 8, set 1

description:
Gene expression in human lesional psoriatic epidermis
PN8DL

source_name: Human lesional psoriatic dermis (laser capture microdissection), sample 8


title: 1aCeN4


title: fog-2_D_dT

description: oligo-dT-primed cDNA synthesis


title: 16eCaN12

description: GeoChip data for soil sample collected at elevated CO2, ambient N

value: elevated CO2, ambient N


title: Lesional dermis from psoriatic skin, sample 6, set 1

description:
Gene expression in human lesional psoriatic epidermis
PN6DL

source_name: Human lesional psoriatic dermis (laser capture microdissection), sample 6


title: 1aCeN1


title: 1017: Prostate cancer patient 17

source_name: individual sample; formalin fixed paraffin embedded tissue section

value: Prostate tumor tissue

source_name: microbiome free human B cell line BJAB


title: 1016: Prostate cancer patient 16


title: 16eCaN10


title: fog-2_A_dT

description: oligo-dT-primed cDNA synthesis


title: 1015: Prostate cancer patient 15


title: 16eCaN9


title: 1aCeN2


title: N2_D_dT

description: oligo-dT-primed cDNA synthesis


title: 1014: Prostate cancer patient 14


title: 1018: Prostate cancer patient 18


title: 16eCaN8


title: N2_C_dT

description: oligo-dT-primed cDNA synthesis


title: N2_A_dT

description: oligo-dT-primed cDNA synthesis


title: 1012: Prostate cancer patient 12


title: fog-2_B_dT

description: oligo-dT-primed cDNA synthesis


title: CCD8Lu with CFIm25 siRNA P3

city: Irvine

first: Lei

last: Li

state: CA

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
RNA-seq reads were mapping to human hg19 genome using STAR (version:2.4.1) with default parameters
The sorted BAM files were then converted to wig format using samtools (version: 0.1.19)
The wig files were further converted to bigwig format using wigtobigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format

source_name: lung fibroblasts

growth_protocol: CCD8-Lu was cultured in Eagle's Minimum Essential Medium (EMEM) supplement with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
RNA was extracted with miRNeasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with control or CFIm25 siRNA using RNAimax.

value: lung

tag: passages

tag: sirnas

value: CFIm25 siRNA


title: CCD8Lu with CFIm25 siRNA P2


title: 1013: Prostate cancer patient 13


title: 16eCaN11

tag: different carbon and nitrogen levels


title: 16eCaN6


title: 1011: Prostate cancer patient 11


title: 16eCaN4


title: 16eCaN7


title: 1010: Prostate cancer patient 10


title: 16eCaN5


title: 16eCaN2


title: CCD8Lu with control siRNA P2

value: control siRNA


title: 16eCaN1


title: 1007: Prostate cancer patient 7


title: 1006: Prostate cancer patient 6


title: 1008: Prostate cancer patient 8


title: 1005: Prostate cancer patient 5


title: 1004: Prostate cancer patient 4


title: 16eCaN3


title: 9eCaN14


title: 9eCaN13


title: 1009: Prostate cancer patient 9


title: 1002: Prostate cancer patient 2


title: CCD8Lu with control siRNA P3


title: 9eCaN15


title: 9eCaN10


title: 9eCaN12


title: 9eCaN11


title: 1003: Prostate cancer patient 3


title: 9eCaN8


title: 1001: Prostate cancer patient 1


title: DLBCL_MC_F927_JHS

city: Boston

first: Björn

last: Chapuy

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004) using Brainarray custom chip definition files (Version 16) based on Ensemble IDs.

label: biotin

source_name: DLBCL

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: 10-20 x 20 um sections from snap-frozen tumor specimens from newly diagnosed previously untreated samples were directly transferred to Trizol.

extract_protocol: For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols.

tag: tissue type

value: primary Diffuse Large B-cell Lymphoma


title: 9eCaN6


title: 9eCaN9


title: DLBCL_MC_F990_MNA


title: DLBCL_MC_F959_ERM


title: 9eCaN5


title: 9eCaN4


title: 9eCaN3


title: 9eCaN1


title: DLBCL_MC_F886_EJH


title: DLBCL_MC_F925_DLR


title: DLBCL_MC_F729_MAN


title: 9eCaN7


title: 4eCaN15


title: DLBCL_MC_F739_AMA3


title: 4eCaN12


title: DLBCL_MC_F648_JKW


title: 4eCaN14


title: 4eCaN13


title: DLBCL_MC_F606_DMJ


title: 9eCaN2


title: DLBCL_MC_F815_BAT


title: 4eCaN11


title: DLBCL_MC_F519_ALT


title: DLBCL_MC_F502_RFK


title: 4eCaN10


title: DLBCL_MC_F500_ECU


title: 4eCaN8


title: DLBCL_MC_F496DMP


title: 4eCaN7


title: DLBCL_MC_F358_WDS


title: 4eCaN6


title: 4eCaN4


title: DLBCL_MC_F344_CJS


title: DLBCL_MC_F339_JPS2


title: DLBCL_MC_F307_JPS


title: 4eCaN2


title: 4eCaN5


title: DLBCL_MC_F362_MJB1


title: DLBCL_MC_F300_TBF


title: 4eCaN9


title: DLBCL_MC_F262_WLC


title: SKNSH_WN.1

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

description:
SKNSH cells treated with 1 µM WN for 24h, replicate1
SAMPLE 16

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Expression values were log2 transformed and quantile normalized using the limma R package

source_name: SKNSH, WN, 1µM, 24h, replicate1

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

growth_protocol: IMR-32 and SK-N-SH cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum and L-glutamine (1 mM).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacterer's protocol.

value: WN

tag: cell line

value: SKNSH


title: P_r_N_s25_exp3

city: Rome

first: domenico

last: raimondo

address: Viale Regina Elena 324

department: Molecular Medicine

country: Italy

institute: Sapienza University of Rome

description: sample 25

hyb_protocol: In accordance with the experimental protocol, 4 μL of total RNA was incubated with 1 μL of SuperScript VILO Master Mix (Invitrogen, Life Technologies, Carlsbad, CA) at 25°C for 10 minutes, then at 42°C for 60 minutes, and finally at 85°C for 5 minutes to perform RNA reverse transcription (RT). Then, cDNA was denaturated at 94°C for 10 minutes and, after the addition of 1 μL of pooled MTE

scan_protocol: To quantify mRNA targets, each cartridge was scanned in 550 field-of-view by means of the automatic nCounter Digital Analyzer primers and 5 μL of TaqMan Pre Amp Master Mix (Applied Biosystems, Life Technology), amplified by 18 PCR cycles at 94°C for 15 seconds and 60°C for 4 minutes. After denaturation (94°C for 2 minutes, then on ice), the amplification product was hybridized for 18 hours at 65°C in the presence of both reporter and capture probes. The nCounter Prep Station was then used to purify and immobilize the resulting hybrid onto the internal surface of a cartridge.

data_processing: Raw count data were preprocessed with the NanoStringNorm R package, a set of tools for normalizing, running diagnostics, and visualizing NanoString nCounter data. Specifically, geometric mean-based scaling normalization was performed to account for technical assay variation, which involved choosing the geo.mean setting in the CodeCount R option. The background subtracted from each sample was calculated by setting mean.2sd in the background option. The method used to normalize for RNA content (i.e., pipetting fluctuations) entailed selecting the “housekeeping.geo.mean” setting in the SampleContent R option via all internal annotated housekeeping genes. All data were grouped in four classes based on cell sample subtype: naïve healthy donors (N-HDs), naïve patients (N-Ps), effector cells in healthy donors (Eff-HDs), and effector cells in patients (Eff-Ps). We did not consider genes that are not expressed in any sample, thereby excluding them from further analysis. This resulted in an analysis set of 401 unique genes and 26 samples.

source_name: CD8+ T lymphocytes

label_protocol: The nCounter® Single Cell Human Immunology v2 Kit contains fluorescent barcoded probes that are complementary to both 571immune-response and inflammation–associated genes, and 13 housekeeping genes (used as internal controls).

growth_protocol: Perypheral blood mononuclear cells (PBMCs) were isolated from healthy donors and patients, and CD8+ T cells subsets of interest (specific for apoptotic epitopes) were sorted with FACS AriaIII.

extract_protocol: The RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) was used to extract RNA from 130 sorted cells from all samples.

treatment_protocol: Samples were stored at -80 °C until the assays were performed.

tag: diagnosis

value: rheumatoid arthritis

tag: patient status

value: responder patient

tag: cell type

value: CD8+ T lymphocytes

value: naive cells


title: 4eCaN1


title: SKNSH_WN.3

description:
SKNSH cells treated with 1 µM WN for 24h, replicate3
SAMPLE 18

source_name: SKNSH, WN, 1µM, 24h, replicate3


title: SKNSH_WN.2

description:
SKNSH cells treated with 1 µM WN for 24h, replicate2
SAMPLE 17

source_name: SKNSH, WN, 1µM, 24h, replicate2


title: 1eCaN31


title: DLBCL_MC_F349_BJJ


title: P_r_N_s23_exp3

description: sample 23


title: DLBCL_MC_F210_GWC


title: 4eCaN3


title: 1eCaN32


title: 1eCaN30


title: SKNSH_WA.2

description:
SKNSH cells treated with 1 µM WA for 24h, replicate2
SAMPLE 14

source_name: SKNSH, WA, 1µM, 24h, replicate2

value: WA


title: DLBCL_MC_F139_LJF


title: P_r_N_s6_exp5

description: sample 6


title: 1eCaN29

source_name: Soil microbes in BioCON plots


title: DLBCL_MC_F139_AD


title: Lesional dermis from psoriatic skin, sample 4, set 1

description:
Gene expression in human lesional psoriatic epidermis
PN4DL

source_name: Human lesional psoriatic dermis (laser capture microdissection), sample 4

value: psoriasis

tag: tissue

value: dermis

value: female


title: SKNSH_WA.1

description:
SKNSH cells treated with 1 µM WA for 24h, replicate1
SAMPLE 13

source_name: SKNSH, WA, 1µM, 24h, replicate1


title: 1eCaN28


title: SKNSH_DMSO.3

description:
SKNSH cells treated with DMSO for 24h, replicate3
SAMPLE 12

source_name: SKNSH, DMSO, 24h, replicate3

value: DMSO


title: P_r_N_s5_exp7

description: sample 5


title: DLBCL_MC_F132_MLM


title: P_r_Eff_s23_exp3

description: sample 23

value: effector cells


title: P_r_Eff_s24_exp3

description: sample 24


title: P_nr_N_s22_exp3

description: sample 22

value: non responder patient


title: P_nr_N_s21_exp5

description: sample 21


title: P_r_Eff_s6_exp5

description: sample 6


title: DLBCL_MC_F089_HCZ


title: 1eCaN25

value: elevated CO2, ambient N


title: DLBCL_MC_F089_MLB


title: IMR32_WN.2

description:
IMR32 cells treated with 1 µM WN for 24h, replicate2
SAMPLE 8

source_name: IMR32, WN, 1µM, 24h, replicate2


title: 1eCaN26


title: DLBCL_LS88


title: SKNSH_DMSO.1

description:
SKNSH cells treated with DMSO for 24h, replicate1
SAMPLE 10

source_name: SKNSH, DMSO, 24h, replicate1


title: SKNSH_DMSO.2

description:
SKNSH cells treated with DMSO for 24h, replicate2
SAMPLE 11

source_name: SKNSH, DMSO, 24h, replicate2


title: IMR32_WN.1

description:
IMR32 cells treated with 1 µM WN for 24h, replicate1
SAMPLE 7

source_name: IMR32, WN, 1µM, 24h, replicate1


title: DLBCL_MC_F064AB


title: DLBCL_MC_F218_RAP


title: 1eCaN23


title: IMR32_WN.3

description:
IMR32 cells treated with 1 µM WN for 24h, replicate3
SAMPLE 9

source_name: IMR32, WN, 1µM, 24h, replicate3


title: P_nr_N_s9_exp5

description: sample 9


title: 1eCaN27


title: P_nr_N_s8_exp5

description: samle 8


title: IMR32_WA.3

description:
IMR32 cells treated with 1 µM WA for 24h, replicate3
SAMPLE 6

source_name: IMR32, WA, 1µM, 24h, replicate3


title: 1eCaN24


title: P_nr_N_s7_exp7

description: sample 7


title: DLBCL_LS297


title: DLBCL_C_D_1163_NULLPAIR


title: P_nr_Eff_s22_exp3

description: sample 22


title: P_nr_Eff_s21_exp5

description: sample 21


title: DLBCL_MC_F231_CAO


title: 1eCaN22


title: 1eCaN20


title: DLBCL_LS1065


title: IMR32_WA.1

description:
IMR32 cells treated with 1 µM WA for 24h, replicate1
SAMPLE 4

source_name: IMR32, WA, 1µM, 24h, replicate1


title: 1eCaN21


title: 1eCaN19


title: P_nr_Eff_s8_exp5

description: sample 8


title: DLBCL_C_D_1162_NULLPAIR

source_name: DLBCL


title: 1eCaN17


title: IMR32_DMSO.3

description:
IMR32 cells treated with DMSO for 24h, replicate3
SAMPLE 3

source_name: IMR32, DMSO, 24h, replicate3


title: 1eCaN18

description: GeoChip data for soil sample collected at elevated CO2, ambient N


title: IMR32_WA.2

description:
IMR32 cells treated with 1 µM WA for 24h, replicate2
SAMPLE 5

source_name: IMR32, WA, 1µM, 24h, replicate2


title: DLBCL_C_D_1159_NULLPAIR


title: P_r_Eff_s25_rep_exp8

description: sample 25

source_name: CD8+ T lymphocytes


title: DLBCL_C_D_1158_NULLPAIR


title: 1eCaN15


title: IMR32_DMSO.1

description:
IMR32 cells treated with DMSO for 24h, replicate1
SAMPLE 1

source_name: IMR32, DMSO, 24h, replicate1


title: 1eCaN14


title: HDs_N_s15_exp8

description: sample 15 rep exp8

value: healthy


title: SKNSH_WA.3

description:
SKNSH cells treated with 1 µM WA for 24h, replicate3
SAMPLE 15

source_name: SKNSH, WA, 1µM, 24h, replicate3


title: DLBCL_C_D_1157_NULLPAIR


title: DLBCL_C_D_1156_NULLPAIR


title: HDs_N_s14_exp6

description: sample 14


title: DLBCL_C_D_1155_NULLPAIR


title: HDs_N_s13_exp6

description: sample 13


title: P_nr_Eff_s9_exp5

description: sample 9


title: DLBCL_C_D_1154_NULLPAIR


title: HDs_N_s12_exp6

description: sample 12


title: 1eCaN12

source_name: Soil microbes in BioCON plots


title: 1eCaN13


title: HDs_Eff_s15_rep_exp8

description: sample 15 rep exp8


title: HDs_N_s11_exp6

description: sample 11


title: DLBCL_C_D_1153_NULLPAIR


title: DLBCL_C_D_1150_NULLPAIR


title: HDs_Eff_s13_exp6

description: sample 13


title: IMR32_DMSO.2

description:
IMR32 cells treated with DMSO for 24h, replicate2
SAMPLE 2

source_name: IMR32, DMSO, 24h, replicate2


title: 1eCaN10


title: HDs_Eff_s12_exp6

description: sample 12


title: 1eCaN9


title: DLBCL_C_D_1149_NULLPAIR


title: HDs_Eff_s10_exp6

description: sample 10


title: 1eCaN8


title: DLBCL_C_D_1148_NULLPAIR


title: DLBCL_C_D_1147_NULLPAIR


title: DLBCL_C_D_1151_NULLPAIR


title: 1eCaN11


title: SDS treated sample 150 minutes exposure, replicate 2

city: Warsaw

first: Ewa

middle: M

last: Furmanczyk

address: Pawinskiego 5a

department: Institute of Biochemistry and Biophysics

country: Poland

institute: Polish Academy of Sciences

data_processing:
base-caling CASAVA v1.8.2
quality (q30), lenght (l>40) filtering and adaptor removal, Cutadapt script
filtering, outfiltering the 16S rRNA, SortMeRNA
alignment, Bowtie2
further processing, filtering, counting, - samtools v1.2-10, HTSeq v0.6.1
differental expression analysis, DESeq2
Genome_build: Genbank: MUJK00000000
Supplementary_files_format_and_content: count table - htseq-count output for all samples

organism: Pseudomonas laurylsulfativorans

source_name: cultured strain

growth_protocol: For the transcriptomic analysis the P. laurylsulfatovorans AP3_22T strain was precultured overnight in LB medium. Then washed with minimal medium and diluted in the fresh 0.1 LB medium with or without SDS (5 g/L) to the initial OD600=0.4 and cultured in 30°C with 140 rpm agitation. Every 30 minutes the cultures OD600 and SDS concentration were measured and the samples for RNA isolation were collected.

extract_protocol:
Pellets from 5 ml of culture from each time point were resuspended in 1 ml of TE buffer and transferred to new tube with 250 μl of zirconia beads. One ml of TRIzol was added and each sample was mixed by vortexing for 3 minutes followed by adding 200 μl of chloroform and short mixing (30s vortex). After 30 minutes of incubation in RT the samples were centrifuged (10 minutes, 14000 rpm, 4°C). RNA was precipitated with isopropanol and sodium acetate for 30 minutes, pellet was centrifuged (20 minutes, 14000 rpm, 4°C), washed two times with 75% ethanol and resuspended in 40 μl of water. The concentration and purity of RNA solutions were determined by NanoDrop. The RNA quality was evaluated by agarose gel electrophoresis. Ten μg of RNA was treated with TURBO DNase (ThermoFisher) according to manufacturer protocol followed by phenol/chloroform extraction. The purified samples were stored in -80°C.
RNA libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit. 2,5 µg of total RNA was used as input. rRNA was removed using Ribo-Zero rRNA Removal Kit (Bacteria). Fragmentation and priming were done in 94°C for 8 minutes. The libraries were verified using a 2100 Bioanalyzer (Agilent) High-Sensitivity DNA Assay and KAPA Library Quantification Kit for the Illumina. Sequencing was performed using an Illumina NextSeq (2x75 bp).

tag: timepoint

value: SDS

tag: replicate


title: SDS treated sample 150 minutes exposure, replicate 3

tag: treatment


title: SDS treated sample 150 minutes exposure, replicate 1


title: 1eCaN7


title: 1eCaN4


title: 1eCaN5


title: moderately obese subject (BMI, 27.5~30 kg/m2), rep6

city: Daegu

first: Un Ju

address: 1370, Sankyuk-dong, Buk-gu

department: Center for Food & Nutritional Genomics

country: South Korea

institute: Kyungpook National University

description:
replicate 6
B6

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing:
Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)
All probe signal value was transformed by logarithm and normalized by quantile method. The 1-way anova test, tukey HSD test and fold change were applied. Statistical significance was adjusted by the Benjamini-Hocbherg multiple-testing correction with false discovery rate(FDR). All data analysis was conducted using R 2.15.1 (www.r-project.org)

source_name: human peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: 28 volunteers aged 20~59 years were recruited from Daegu and its suburbs in the Republic of Korea.  Subjects were classified as normal weight (BMI, 18.5~23 kg/m2, n=4), mildly obese (BMI, 25~27.5 kg/m2, n=7), and moderately obese (BMI, 27.5~30 kg/m2, n=7).

extract_protocol: Total RNA was extracted from the adipose tissue using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

tag: ethnic group

value: Korean

tag: development stage

value: adult

value: men

tag: bmi

tag: age

value: 20~59 years

value: peripheral blood mononuclear cells


title: DLBCL_C_D_1146_NULLPAIR

value: primary Diffuse Large B-cell Lymphoma


title: DLBCL_C_D_1145_NULLPAIR


title: 1eCaN6


title: moderately obese subject (BMI, 27.5~30 kg/m2), rep4

description:
replicate 4
B4

tag: gender


title: moderately obese subject (BMI, 27.5~30 kg/m2), rep7

description:
replicate 7
B7


title: 1eCaN16


title: DLBCL_C_D_1144_NULLPAIR


title: Control sample 150 minutes exposure, replicate 3

value: control


title: 1eCaN3


title: DLBCL_C_D_1142_NULLPAIR


title: 1eCaN2


title: moderately obese subject (BMI, 27.5~30 kg/m2), rep1

description:
replicate 1
B1


title: DLBCL_C_D_1141_NULLPAIR


title: moderately obese subject (BMI, 27.5~30 kg/m2), rep5

description:
replicate 5
B5


title: mildly obese subejct (BMI, 25~27.5 kg/m2), rep7

description:
replicate 7
A7


title: mildly obese subejct (BMI, 25~27.5 kg/m2), rep6

description:
replicate 6
A6


title: moderately obese subject (BMI, 27.5~30 kg/m2), rep2

description:
replicate 2
B2


title: 1eCaN1


title: DLBCL_C_D_1140_NULLPAIR


title: SDS treated sample 60 minutes exposure, replicate 3


title: 16aCaN12

description: GeoChip data for soil sample collected at ambient CO2, ambient N

value: ambient CO2, ambient N


title: SDS treated sample 60 minutes exposure, replicate 1


title: Control sample 150 minutes exposure, replicate 2


title: SDS treated sample 60 minutes exposure, replicate 2


title: Control sample 150 minutes exposure, replicate 1


title: DLBCL_C_D_1139_NULLPAIR


title: mildly obese subejct (BMI, 25~27.5 kg/m2), rep4

description:
replicate 4
A4


title: mildly obese subejct (BMI, 25~27.5 kg/m2), rep3

description:
replicate 3
A3


title: Control sample 60 minutes exposure, replicate 2


title: 16aCaN11


title: DLBCL_C_D_1138_NULLPAIR


title: 16aCaN10


title: DLBCL_C_D_1136_NULLPAIR


title: mildly obese subejct (BMI, 25~27.5 kg/m2), rep1

description:
replicate 1
A1


title: mildly obese subejct (BMI, 25~27.5 kg/m2), rep5

description:
replicate 5
A5


title: DLBCL_C_D_1135_NULLPAIR


title: 16aCaN9


title: Control sample 60 minutes exposure, replicate 3


title: mildly obese subejct (BMI, 25~27.5 kg/m2), rep2

description:
replicate 2
A2


title: 16aCaN8


title: normal weight subject, rep4

description:
replicate 4
C4


title: Control sample 60 minutes exposure, replicate 1


title: SDS treated sample 30 minutes exposure, replicate 3


title: 16aCaN7


title: DLBCL_C_D_1131_NULLPAIR


title: 16aCaN6


title: SDS treated sample 30 minutes exposure, replicate 2


title: DLBCL_C_D_1132_NULLPAIR


title: normal weight subject, rep2

description:
replicate 2
C2


title: DLBCL_C_D_1130_NULLPAIR


title: normal weight subject, rep3

description:
replicate 3
C3


title: moderately obese subject (BMI, 27.5~30 kg/m2), rep3

description:
replicate 3
B3


title: SDS treated sample 30 minutes exposure, replicate 1


title: 16aCaN4


title: DLBCL_C_D_1133_NULLPAIR


title: normal weight subject, rep1

description:
replicate 1
C1


title: DLBCL_C_D_1129_NULLPAIR


title: Control sample 30 minutes exposure, replicate 2


title: DLBCL_C_D_1128_NULLPAIR


title: 16aCaN5


title: Control sample 30 minutes exposure, replicate 1


title: SDS treated sample beginning time point, replicate 3


title: DLBCL_C_D_1127_NULLPAIR


title: DLBCL_C_D_1124_NULLPAIR


title: 16aCaN3


title: DLBCL_C_D_1125_NULLPAIR


title: Control sample 30 minutes exposure, replicate 3


title: DLBCL_C_D_1123_NULLPAIR


title: SDS treated sample beginning time point, replicate 1


title: SDS treated sample beginning time point, replicate 2


title: 9aCaN14


title: Control sample beginning time point, replicate 3


title: 9aCaN13


title: 16aCaN2


title: 9aCaN15


title: DLBCL_C_D_1121_NULLPAIR


title: 16aCaN1


title: DLBCL_C_D_1120_NULLPAIR


title: 9aCaN12


title: Control sample beginning time point, replicate 2


title: Control sample beginning time point, replicate 1


title: 9aCaN11


title: surface1 WGBS

city: Bethesda

first: Aniket

last: Gore

address: Bldg 6B center drive

institute: National Institute of child health and human development

data_processing:
For WGBS: Raw single-end sequence data was trimmed for quality and adapter sequence using Trimmomatic software, trimming leading or trailing bases at quality < 5 as well as using a sliding window requiring a 4 bp average of quality > 15. Reads trimmed below 50 bp were discarded. Following trimming, reads were aligned using Bismark software against a bisulfite converted Pachon cavefish genome using non-directional alignment.
For RNA seq: Paired-end reads were trimmed using trimmomatic and aligned to Pachon cavefish genome using RNA-STAR, quantitation performed with subread featureCounts and differential expression analysis performed with count data via DESeq2.
log2 fold change values were calculated by comparing normalized RNA seq reads between cavefish (samples cave1,cave2) and surface fish (samples surface1,surface2) eyes.
Supplementary_files_format_and_content: Tab Delimited Text and DEseq2 quantitations for RNA seq and BISMARK quantitation for differential methylation for WGBS.

organism: Astyanax mexicanus

source_name: isolated surface morph eyes

extract_protocol:
Eyes were extracted at around 54hpf in 1X PBS without ca and mg. RNA and DNA was isolated using Zymo Duet Kit
WGBS libraries were generated using illumina's TruSeq DNA methylation kit  and RNA seq libraries were constructed using TruSeq Standard mRNA library prep kit after poly A enrichment and sequenced using Illumina HiSeq 2500

value: isolated eye

tag: genotype

value: Wild type

tag: morphs

value: surface fish


title: cave1 WGBS

source_name: isolated cave morph eyes

value: cave fish


title: surface1 RNA-Seq

source_name: isolated surface morph (S1) eyes


title: surface2 RNA-Seq

source_name: isolated surface morph (S2) eyes


title: DLBCL_C_D_1118_NULLPAIR


title: DLBCL_C_D_1119_NULLPAIR


title: 9aCaN10

tag: different carbon and nitrogen levels


title: DLBCL_C_D_1117_NULLPAIR

tag: tissue type


title: DLBCL_C_D_1113_NULLPAIR


title: DLBCL_C_D_1115_NULLPAIR


title: cave2 RNA-Seq

source_name: isolated cave morph (C2) eyes


title: DLBCL_C_D_1114_NULLPAIR


title: 9aCaN7


title: cave1 RNA-Seq

source_name: isolated cave morph (C1) eyes


title: 9aCaN9


title: 9aCaN8


title: DLBCL_C_D_1112_NULLPAIR


title: 9aCaN6


title: 9aCaN5


title: 9aCaN4


title: ALG-2 IP rep2

city: La Jolla

first: Amy

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

description: ALG-2 IP rep2

data_processing:
Basecalling with Illumina's software RTA2
Adapter sequences were removed with Cutadapt, and using miRDeep2 small RNA sequences were mapped to the C. elegans genome (WS261) and quantified based on miRNA annotations from miRBase release 21
Calculated the normalized reads (reads per million in the library) and only miRNAs with equal to or more then 1000 reads across the libraries were included
Genome_build: WS261
Supplementary_files_format_and_content: csv files were generated with quantifier (miRDeep2), normalized (reads per million in the library) and only miRNAs with =>1000 reads across all replicates were included

source_name: whole organism

growth_protocol: Synchronized FLAG::GFP::ALG-1 (PQ530) and FLAG::RFP::ALG-2 (PQ582)  animals cultured on OP50 bacteria at 20°C were collected at adult day 5 after removing eggs and progeny larvae.

extract_protocol:
ALG-1 or ALG-2 was immunoprecipitated from D5 C.elegans from PQ530 and PQ582 resopectively, RNA was extracted with Trizol and DNAse treated from the immunoprecipitated complexes.
Libraries were prepared according to Illumina's TruSeq Small RNA (15004197 Rev. A). Briefly 3' and 5' adapters were ligate on, the library was PCR amplified and the small RNA portion of the cDNA library purified and isolated before sequencing.

treatment_protocol: No special treatment

tag: developmental stage

value: adult day 5 (D5)

value: FLAG::RFP::ALG-2 (PQ582)

tag: ip antibody

value: FLAG (Signa F1804)


title: ALG-2 IP rep1

description: ALG-2 IP rep1


title: ALG-1 IP rep2

description: ALG-1 IP rep2

value: FLAG::GFP::ALG-1 (PQ530)


title: ALG-1 IP rep1

description: ALG-1 IP rep1


title: DLBCL_C_D_1104_NULLPAIR

source_name: DLBCL


title: DLBCL_C_D_1107_NULLPAIR


title: DLBCL_C_D_1108_NULLPAIR


title: DLBCL_C_D_1106_NULLPAIR


title: DLBCL_MAYO_DLBCL_5613


title: DLBCL_C_D_1105_NULLPAIR


title: 9aCaN2

first: Qun

address: Shuang Qing Road

institute: Tsinghua University

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

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.


title: 9aCaN1


title: 4aCaN12


title: 4aCaN11


title: 4aCaN10


title: DLBCL_MAYO_DLBCL_7359


title: DLBCL_C_D_1109_NULLPAIR


title: 4aCaN13


title: severe_WS_rep2

city: Pathumthani

first: Yuwares

last: Malila

address: 113 Thailand Science Park Phahonyothin Road Khlong Nueng, Khlong Luang

country: Thailand

institute: National Center for Genetic Engineering and Biotechnology

description: Gene expression of breast meat that showed severe white striping defect

hyb_protocol: 600 ng purified cRNA was hybridized onto the Aglient SurePrint array at 65°C for 17 h. The array was subsequently washed for 1 min at room temperature in Gene Expression Washing buffer I (Agilent), followed by another minute at 37°C in Washing buffer II (Agilent).

scan_protocol: The array was gently blotted dry using Kimwipe® and scanned using Agilent High Resolution Microarray Scanner (C Model, Agilent).

data_processing: The scan image were analyzed by Agilent Feature Extraction Software version V10.7.1.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  If the signal intensities were flaged as not-detected and data were missed across arrays more than 50% of total arrays within group, that probes were discarded from analysis.

organism: Gallus gallus

source_name: Breast meat with severe white striping defect, replicate 2

label_protocol: A total of 40 arrays (8 slides) were hybridized in this project. One hundred nanograms of total RNA was labeled using One-color Low Input Quick Amp Labeling Kit (Agilent) the manufacturer's recommendations. In brief, total RNA was reverse transcribed into double-stranded cDNA by priming with Oligo(dT) primer. The synthesized cDNA was subjected to an In vitro transcription using T7 RNA polymerases to produce cyanine 3CTP labeled complementary RNA (cRNA). The cRNA was purified using Qiagen RNeasy kit (Qiagen) and quantified using Nanodrop.

growth_protocol: Commercial broilers (ROSS) were raised under a uniform industrial standard practice at five different farms located around the central of Thailand. When reach the desirable slaughter age, the birds were transferred to an industrial abattoir located in Saraburi province (Thailand) and harvested according to a standard industry practice. The pectoralis major muscle from one side of the breasts was collected and snap frozen in liquid nitrogen and stored at -80C until RNA isolation.

extract_protocol: Total RNA was isolated from chicken muscle samples using TRIzolTM Reagent (Invitrogen) according to the manufacturer’s instruction. The isolated RNA was precipitated by mixing 500 μL of the aqueous phase with an equal volume of isopropanol. The pellet of the total RNA was collected by centrifugation and subsequently resuspended using sterile deionized water. Quantity and integrity of total RNA was determined using a Nanodrop and Bioanalyzer, respectively. The RNA samples with RIN exceed 7.0 were used in this study.

treatment_protocol: Breast meat samples were classified as “non-defect”, “WS” or “WB” based on their appearance. The defective samples were further classified based on different defect severity.  For WS, there were 3 severity levels, i.e. mild, moderate and severe. For WB, 2 severity levels, moderate and severe, were classified.

value: chicken breast muscle

tag: wooden breast defect

value: severe

tag: white striping defect

value: no

value: male


title: moderate_WS_rep3

description: Gene expression of breast meat that showed moderate white striping defect

source_name: Breast meat with moderate white striping defect, replicate 3

tag: tissue

value: moderate


title: 4aCaN9

city: Beijing

last: Gao


title: moderate_WS_rep6

source_name: Breast meat with moderate white striping defect, replicate 6


title: severe_WS_rep4

source_name: Breast meat with severe white striping defect, replicate 4


title: 4aCaN15


title: severe_WS_rep3

source_name: Breast meat with severe white striping defect, replicate 3


title: 9aCaN3

source_name: Soil microbes in BioCON plots


title: DLBCL_C_D_1111_NULLPAIR


title: severe_WS_rep1

source_name: Breast meat with severe white striping defect, replicate 1


title: moderate_WS_rep4

source_name: Breast meat with moderate white striping defect, replicate 4


title: moderate_WS_rep5

source_name: Breast meat with moderate white striping defect, replicate 5


title: WT vs KO

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: embryonic stem cells, untreated,

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: WT

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Conventional ES growth medium with LIF and 2i

extract_protocol: Total RNA was isolated from ES Cells samples using RNeasy Mini kit (QIAGEN).

tag: cell type

value: Embryonic stem cells

tag: genotype/variation

value: wild type

source_name: KO


title: DLBCL_C_D_1103_NULLPAIR

value: primary Diffuse Large B-cell Lymphoma


title: 4aCaN14

value: ambient CO2, ambient N


title: B6 Tfh 3

city: Gainesville

first: Laurence

last: Morel

state: FL

address: 1395 Center Drive, D6-6

department: Pathology and Immunology

institute: University of Florida

hyb_protocol: Labeled cDNA was hybridized to microarrays according to Affymetrix (currently Thermo Fisher) instructions. Prehybridization mix was applied for 30 minutes, after which  5.2 ug of ss-DNA was injected and hybridized to the MTA 1.0 chips for 16 hours at 45C at 60 rpm.

scan_protocol: GeneChip Scanner 3000 7G using AGCC software

data_processing: Data was analyzed using Partek Genomic Suite version 6.6. Raw CEL files were imported and normalized by RMA with quantile normalization and median polish. Statistical testing was performed with Student's unpaired test between SLE and HC groups.

source_name: unimmunized mouse

label_protocol: ss-cDNA was fragmented with UDG and APE1.  Labeling used TdT with biotin reagent followed by streptavidin/phycoerythrin usign the Affymetrix DNA labeling kit.

growth_protocol: Tfh cells were not grown in vitro

extract_protocol: RNA from cell pellet extracted with Qiagen Rneasy mini kit, using 2-mercaptoethanol and manufacturer instructions

treatment_protocol: No specific treatment, PD-1, CXCR5 antibody staining for sorting

value: T follicular helper (Tfh) cells

tag: cell population

value: CD4+ CXCR5+ PD-1+ T cell

value: 8 to 11 months


title: moderate_WS_rep2

source_name: Breast meat with moderate white striping defect, replicate 2


title: DLBCL_MAYO_DLBCL_3653


title: B6 Tfh 1


title: 4aCaN8


title: TC Tfh 5

value: Triple Congenic

value: 7 months


title: TC Tfh 4


title: TC Tfh 2


title: 4aCaN6


title: DLBCL_LS951


title: DLBCL_MAYO_DLBCL_234


title: mild_WS_rep7

description: Gene expression of breast meat that showed mild white striping defect

source_name: Breast meat with mild white striping defect, replicate 7

value: mild


title: B6 Tfh 2


title: moderate_WS_rep1

source_name: Breast meat with moderate white striping defect, replicate 1


title: 4aCaN7


title: DLBCL_LS762


title: 4aCaN5


title: DLBCL_LS4616


title: DLBCL_LS4592


title: 4aCaN3


title: mild_WS_rep3

source_name: Breast meat with mild white striping defect, replicate 3


title: mild_WS_rep5

source_name: Breast meat with mild white striping defect, replicate 5


title: TC Tfh 1


title: mild_WS_rep4

source_name: Breast meat with mild white striping defect, replicate 4


title: mild_WS_rep6

source_name: Breast meat with mild white striping defect, replicate 6


title: mild_WS_rep1

source_name: Breast meat with mild white striping defect, replicate 1


title: 4aCaN1


title: 4aCaN4


title: mild_WS_rep2

source_name: Breast meat with mild white striping defect, replicate 2


title: 4aCaN2


title: TC Tfh 3


title: DLBCL_LS4618

source_name: DLBCL


title: DLBCL_LS4619


title: RNA- seq analyses in a Cas9 deletion in OD1.5_PPM+media

description: Sample 4 NH_35

data_processing:
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Adapter trimming using cutadapt (Martin, 2011) version 1.7.1 (R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, R2: GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT), discard empty reads
Size filtering: discard read pairs with at least one read shorter than 12 nt (READemption 0.3.5, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0 (READemption 0.3.5, Förstner et al., 2014),Coverage calculation based on uniquely mapped reads (READemption 0.3.5, Förstner et al., 2014)
Genome_build: NC_017501.fa
Supplementary_files_format_and_content: wiggle

organism: Neisseria meningitidis 8013

source_name: Cas9 deletion in OD1.5_PPM+media

extract_protocol:
Samples for RNA-Seq were collected from bacterial cul- tures grown to optical densities (OD)600 of 0.5 or 1.5, corre- sponding to the mid logarithmic and late logarithmic/early stationary growth phase, respectively. Samples were fixated by the addition of STOP Mix [95% (vol/vol) EtOH and 5% (vol/vol) phenol], frozen in liquid nitrogen and subsequently stored at−80◦C untilRNA preparation. For RNA extraction frozen bacterial cultureswere thawed on ice, cen- trifuged and cell pellets were resuspended in a lysis solution consisting of 800 ?l of 0.5 mg/ml lysozyme in Tris-EDTA (TE) buffer (pH 8.0) and 80 ?l 10% sodium dodecyl sul- phate (SDS). Bacterial cells were lysed by placing the sam- ples for 1–2 min at 65◦C in a water bath. Total RNA was extracted fromthe lysates using the hot phenol method. N. meningitidis expressing either 3× FLAG-tagged- or wild-type (WT) Cas9 protein were grown in the presence of kanamycin until an OD600 of 0.5 and 1.5, respectively. For each strain cells equivalent to an OD600 of 50 were collected and subjected to Cas9 coIP and control coIP as described in detail in ref.14 and briefly in the Supplementary Materials and Methods.
cDNA libraries of RNA-seq and RIP-seq samples were constructed by Vertis Biotechnology AG, Munich, Germany. cDNA libraries were pooled and sequenced using a MiSeqmachine  in the single-read mode.
RNA-seq with wild type and Cas9 mutant and RIP-seq RNA co-immunoprecipitation (coIP) with Cas9

tag: description

value: deletion Cas9 in OD1.5_PPM+media

value: deletion Cas9


title: RNA- seq analyses in a Cas9 deletion in OD0.5_PPM+media

description: Sample 3 NH_34

source_name: Cas9 deletion in OD0.5_PPM+media

value: deletion Cas9 in OD0.5_PPM+media


title: CoIP_Cas9 chromosomally Flag tagged (negative) OD600 0.5

description: Sample 5 NH_55

source_name: CoIP_Cas9 chromosomally Flag

value: wild type OD600 0.5 (negative)


title: DLBCL_LS4323


title: RNA- seq analyses in a Cas9 wild type in OD1.5_PPM+media

description: Sample 2 NH_33

source_name: Cas9 wild type in OD1.5_PPM+media

value: wild type in OD1.5_PPM+media


title: non_defective_WS_rep4

description: Gene expression of breast meat that white striping defect did not occur

source_name: Breast meat without white striping defect, replicate 4

value: chicken breast muscle

value: no

value: male


title: DLBCL_LS4054


title: DLBCL_LS378


title: 1aCaN31

source_name: Soil microbes in BioCON plots


title: non_defective_WS_rep2

source_name: Breast meat without white striping defect, replicate 2


title: 1aCaN27


title: CoIP_Cas9 chromosomally Flag tagged (negative) OD600 1.5

description: Sample 7 NH_57

value: wild type OD600 1.5 (negative)


title: DLBCL_LS3809

value: primary Diffuse Large B-cell Lymphoma


title: CoIP_Cas9 chromosomally Flag tagged (positive) OD600 0.5

description: Sample 6 NH_56

value: Cas9-Flag chromosomally tagged;  CoIP(positive) at OD600 0.5


title: non_defective_WS_rep1

source_name: Breast meat without white striping defect, replicate 1


title: severe_WB_and_mild_WS_rep2 b

description: Gene expression of breast meat that showed severe wooden breast defect plus mild white striping defect

source_name: Breast meat with severe wooden breast defect plus mild white striping defect, ≤45 days, replicate 2

value: severe

value: 45 days or under


title: 1aCaN28

value: ambient CO2, ambient N


title: 1aCaN26


title: RNA- seq analyses in a Cas9 wild type in OD0.5_PPM+media

description: Sample 1 NH_32

source_name: Cas9 wild type in OD0.5_PPM+media

value: wild type in OD0.5_PPM+media

value: wild type


title: severe_WB_and_mild_WS_rep3 b

source_name: Breast meat with severe wooden breast defect plus mild white striping defect, ≤45 days, replicate 3

value: mild


title: severe_WB_and_mild_WS_rep1 b

source_name: Breast meat with severe wooden breast defect plus mild white striping defect, ≤45 days, replicate 1


title: 1aCaN32


title: non_defective_WS_rep3

source_name: Breast meat without white striping defect, replicate 3


title: 11963a.skin

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

data_processing:
Illumina Hi-Seq 2000 was used to sequence all samples
raw reads were trimmed and filtered using a custom Perl script,The reads were truncated based on similarity to library adaptor sequences. Then, low-scoring sections of each read were removed, preserving the longest remaining fragment
Filtered reads are mapped to the Xiphophorus transcriptome using GSNAP
Gene expression were quantified using eXpress.
Genome_build: Xiphophorus maculatus Ensembl 80
Supplementary_files_format_and_content: Format: .csv; Content: gene expression profiles

organism: Xiphophorus maculatus x Xiphophorus hellerii

source_name: skin

growth_protocol: Fish utilized were 9 month old melanoma-bearing BC1 interspecies hybrids between X. maculatus and X. hellerii. All fish were housed in the Xiphophorus Genetic Stock Center following standard animal mainteince protocol.

extract_protocol:
RNA isolation was performed following the Qiagen RNeasy RNA isolation protocol (Qiagen, Valencia, CA, USA). Skin and melanoma samples harvested from fish were first homogenized using a hand-held homogenizer in a 1.5 mL microcentrifuge tube while the sample remained frozen in TRI Reagent (Sigma Inc., St Louis, MO, USA). After homogenization, 300 μL of fresh 4°C TRI Reagent was added to the samples followed by incubation (rt) for 5 min. Chloroform extraction was performed by adding 120 μL chloroform and shaken for 15 sec. Samples were centrifuged (16,100 rcf for 5 min at 4°C) for phase partition. The aqueous layer was transferred to a new 1.5 mL microcentrifuge tube and a second chloroform extraction performed (300 μL TRI Reagent, 60 μL chloroform). After extraction, nucleic acids in the aqueous phase were precipitated with 500 μL 70% EtOH in diethylpyrocarbonate (DEPC) treated water. The sample was then transferred to a Qiagen RNeasy mini spin column and on-column DNase treatment was performed for 15 min at 25°C. RNA samples were then washed and eluted in 100 μL RNase free water. RNA concentration was measured with a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY, USA). To further assess the RNA quality, a RNA integrity (RIN) score was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All samples processed for RNA sequencing had a RIN score above 8.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

tag: strain

value: interspecies hybrid


title: DLBCL_LS3749


title: 1aCaN29

growth_protocol: In August 2009, soil samples were collected from all of the plots. Soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.


title: 1aCaN25


title: 1aCaN24


title: 11963g.tumor

source_name: tumor

value: spontaneous melanoma


title: DLBCL_LS3866


title: DLBCL_LS3615


title: CoIP_Cas9 chromosomally Flag tagged (positive) OD600 1.5

description: Sample 8 NH_58

value: Cas9-Flag chromosomally tagged;  CoIP(positive) at OD600 1.5


title: 11963d.tumor


title: DLBCL_LS3820


title: 1aCaN23


title: DLBCL_LS4085


title: 11963d.skin


title: DLBCL_LS3387


title: severe_WB_and_moderate_WS_rep3

description: Gene expression of breast meat that showed severe wooden breast defect plus moderate white striping defect

source_name: Breast meat with severe wooden breast defect plus moderate white striping defect, 49 days, replicate 3

value: moderate

value: 49 days


title: DLBCL_LS3309

source_name: DLBCL


title: DLBCL_LS3271


title: 11963g.skin


title: 11963a.tumor


title: severe_WB_and_moderate_WS_rep2

source_name: Breast meat with severe wooden breast defect plus moderate white striping defect, 49 days, replicate 2

value: chicken breast muscle


title: 1aCaN22


title: 11969b.tumor


title: DLBCL_LS3499


title: severe_WB_and_moderate_WS_rep1

source_name: Breast meat with severe wooden breast defect plus moderate white striping defect, 49 days, replicate 1

value: male


title: 1aCaN20


title: DLBCL_LS3245


title: severe_WB_and_mild_WS_rep2

source_name: Breast meat with severe wooden breast defect plus mild white striping defect, 49 days, replicate 2


title: 1aCaN21


title: DLBCL_LS3219


title: 1aCaN30


title: severe_WB_and_mild_WS_rep1

source_name: Breast meat with severe wooden breast defect plus mild white striping defect, 49 days, replicate 1


title: non_WB_but_severe_WS_rep4

description: Gene expression of breast meat that showed severe  white striping defect and without wooden breast defect

source_name: Breast meat with severe white striping defect but without wooden breast defect, ≤45 days, replicate 4

value: no


title: 1aCaN19

source_name: Soil microbes in BioCON plots


title: non_WB_but_severe_WS_rep2

source_name: Breast meat with severe white striping defect but without wooden breast defect, ≤45 days, replicate 2


title: 11960b.skin


title: 11960a.tumor


title: 11960a.skin


title: non_WB_but_severe_WS_rep3

source_name: Breast meat with severe white striping defect but without wooden breast defect, ≤45 days, replicate 3


title: DLBCL_LS3204

value: primary Diffuse Large B-cell Lymphoma


title: 11949q.skin


title: 1aCaN17


title: 11949l.skin


title: 11949l.tumor


title: non_WB_but_moderate_WS_rep4

description: Gene expression of breast meat that showed moderate  white striping defect and without wooden breast defect

source_name: Breast meat with moderate white striping defect but without wooden breast defect, 49 days, replicate 4


title: 1aCaN16


title: DLBCL_LS2978


title: 1aCaN18


title: DLBCL_LS2848


title: non_WB_but_severe_WS_rep1

source_name: Breast meat with severe white striping defect but without wooden breast defect, ≤45 days, replicate 1


title: non_WB_but_moderate_WS_rep2

source_name: Breast meat with moderate white striping defect but without wooden breast defect, 49 days, replicate 2


title: 1aCaN14


title: DLBCL_LS3085


title: non_WB_but_moderate_WS_rep3

source_name: Breast meat with moderate white striping defect but without wooden breast defect, 49 days, replicate 3


title: DLBCL_LS2596


title: non_WB_but_moderate_WS_rep1

source_name: Breast meat with moderate white striping defect but without wooden breast defect, 49 days, replicate 1


title: 1aCaN12


title: 11949h.skin

source_name: skin


title: 1aCaN13


title: 1aCaN15


title: DLBCL_LS3200


title: DLBCL_LS2599


title: 11949g.tumor

source_name: tumor


title: DLBCL_LS2590


title: non_WB_but_mild_WS_rep2

description: Gene expression of breast meat that showed mild  white striping defect and without wooden breast defect

source_name: Breast meat with mild white striping defect but without wooden breast defect, 49 days, replicate 2


title: 1aCaN10


title: non_WB_but_mild_WS_rep1

source_name: Breast meat with mild white striping defect but without wooden breast defect, 49 days, replicate 1


title: 11949h.tumor


title: DLBCL_LS2367

source_name: DLBCL


title: 1aCaN11


title: DLBCL_LS2357


title: 11949g.skin


title: non_WB_but_mild_WS_rep3

source_name: Breast meat with mild white striping defect but without wooden breast defect, 49 days, replicate 3


title: DLBCL_LS2328


title: 11949f.tumor


title: 1aCaN9


title: 11949f.skin


title: DLBCL_LS2258


title: 11949d.tumor


title: 11949c.tumor


title: 1aCaN8


title: 11949c.skin


title: 1aCaN7


title: DLBCL_LS2245


title: 1aCaN6


title: VIMN_N121_CD206-

city: Seville

first: Benoit

middle: Raymond

last: Gauthier

state: Seville

address: Americo Vespucio Avenue

department: Stem Cells

country: Spain

institute: Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)

description: The mouse presented healthy appearance

hyb_protocol: Following fragmentation, 5.5 ug of double-stranded cDNA were hybridized for 14 hr at 40C on Clariom™ S Assay, Mouse. GeneChips were washed and stained in the GeneChip® Fluidics Station 450  according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix GCOS software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package of R/Bioconductor project.

source_name: Primary pancreatic FACS-sorted cells from immunized vehicle treated mice

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 1 ng total RNA Labeling Protocol (The Ambion WT Expression kit for Affymetrix 3’-IVT Pico, Life Technologies Corporation, 2009).

growth_protocol: Standard feeding

extract_protocol: RNA from FACS-sorted cells, obtained from different pool of mice per group, in triplicates was isolated using the RNAesay micro kit according to the manufacturer´s protocol (Qiagen).

treatment_protocol: Animals were maintained under standard conditions, immunized  with pre-proinsulin and BL001- or Vehicle-treated for 8 weeks

value: 4 month old

value: Pancreatic macrophages

tag: treatment

value: vehicle


title: 1aCaN4

value: ambient CO2, ambient N


title: DLBCL_LS2208


title: VIMN_N408_CD206+

description: The mouse presented healthy appearance

tag: age


title: VIMN_N690_CD206-

description: The mouse presented healthy appearance


title: VIMN_N690_CD206+

description: The mouse presented healthy appearance


title: DLBCL_LS2089


title: DLBCL_LS2154


title: 1aCaN3


title: BLIMN_BLS77_CD206+

description: The mouse presented healthy appearance

source_name: Primary pancreatic FACS-sorted cells from immunized BL001 treated mice

value: pre-proinsulin and BL001


title: 11949b.tumor


title: 1aCaN5


title: 1aCaN1


title: 11949a.skin


title: DLBCL_LS1921


title: BLIMN_BLS77_CD206-

description: The mouse presented healthy appearance


title: 11949a.tumor


title: 11949b.skin


title: BLIMN_N785_CD206-

description: The mouse presented healthy appearance


title: DLBCL_LS1757


title: DLBCL_LS1899


title: VIMN_N121_CD206+

description: The mouse presented healthy appearance


title: VIMN_N408_CD206-

description: The mouse presented healthy appearance


title: 1aCaN2


title: 11935f.skin


title: BLIMN_N785_CD206+

description: The mouse presented healthy appearance


title: DLBCL_LS1683


title: 11935e.skin


title: BLIMN_I693_CD206+

description: The mouse presented healthy appearance


title: BLIMN_I693_CD206-

description: The mouse presented healthy appearance


title: DLBCL_LS1546


title: 11935d.tumor


title: 11935f.tumor


title: DLBCL_LS1620


title: 11935e.tumor


title: 11935d.skin


title: DLBCL_LS1583


title: Gb_lncRNA

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality sequence and the percentage of unknown bases (N) is greater than 10%. At last, the obtained “clean bases” for further analysis.
Clean reads were processed with Ribo-Zero rRNA Removal Kits (Epicentre, Madison, WI, USA) to deplete ribosomal RNA (rRNA)
Then filtered reads were mapped to G. biloba genome (GigaDB) using HISAT (Kim et al. 2015), with three base mismatches allowed.
Subsequently, the mapped reads were used to assemble transcripts using StringTie. Expression levels of the assembled transcripts were calculated and normalized using Fragments Per Kilobase of transcript per million fragments mapped (FPKM) by StringTie.
The assembled transcripts were annotated using the gffcompare program (Pertea et al. 2016).
Transcripts with lengths ≥ 200 nt, exons number ≥ 2 and FPKM ≥ 0.1 were retained as lncRNA candidates.
Then lncRNA candidates were further screened using the CPC (Coding Potential Calculator) / CNCI (Coding-Non-Coding-Index) / CPAT (Coding-Potential Assessment Tool) / Pfam (protein family database) to obtain high-confidence novel lncRNAs.
Finally, the Cuffcompare program was used to categorize the identified lncRNAs into lincRNAs ("u"), intronic lncRNAs ("I"), sense ("o") and anti-sense lncRNAs ("x").
Genome_build: GigaDB database (BioProject: PRJNA307642)
Supplementary_files_format_and_content: Text file includes transcript_id, length, strand, locus, gene_id, code, FPKM, count.

organism: Ginkgo biloba

source_name: leaves

growth_protocol: A healthy G. biloba tree (20 years old) used in this study was grown under natural conditions at Yangzhou University.

extract_protocol:
The leaves were collected in April, May, June, July, August, September, and October, and was extracted and purified as previous menthod (Lu et al., 2017).
Strand-specific RNA library was generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA) according to the manufacturer’s protocol.

tag: developmental stages

value: seven developmental stages of  leaves


title: indrops_nextseq01: visual cortices

status: Public on Apr 30 2018

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
We used the published inDrops sequencing read mapping Python pipeline from Klein et al. (Klein et al., 2015)(https://github.com/indrops/indrops) with default parameters (umi quantification - m:10, u:1, d:600, split-ambigs:False, min_non_polyA:15, bowtie [v 1.1.1] - m:200, n:1, l:15, e:80, trimmomatic [v 0.33] - LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16", max_low_complexity_fraction : 0.50) on a custom built transcriptome (made with default parameters of same Python pipeline using the GRCm38.p5 mouse genome assembly with the Ensembl transcript annotation build 85) The data were clustered using Seurat (Satija et al., 2015). Nuclei with at least 500 unique molecular identifiers (UMIs) with at least 200 genes covered were retained for analyses and genes expressed in at least 3 nuclei were kept for analyses. Furthermore, nuclei with greater than 15,000 UMIs or nuclei in which >10% of UMI came from mitochrondial genes were excluded from the analyses. T-distributed stochastic neighbor embedding (t-SNE) plots were generated using the “TSNEplot” function. Gene expression overlays were visualized using the  “FeaturePlot” function. We used known neuronal and non-neuronal markers “Slc17a7”, “Gad1”, “Aldoc”, “Olig1”, ”Cx3cr1”, “Cldn5”, “Mrc1” and “Vtn” genes, to identify potential doublets. All nuclei expressing more than one of the above markers were excluded from the analyses. Furthermore, nuclei that expressed more that one of either “Sst”, ”Pvalb” and “Vip” genes were marked as potential doublets of inhibitory neurons and excluded from the analyses.  Average normalized gene expression in Pv and Vip expressing nuclei was quantified using Monocle (Trapnell et al., 2014),
Genome_build: mm10
Supplementary_files_format_and_content: Normalized gene expression levels in all Pv and Vip expressing nuclei. All data from the same genotype were merged. Column 1: Gene name; Column 2: Gene expression in wild type Pv neurons; Column 3: Gene expression in mutant Pv neurons; Column 4: Gene expression in wild type Vip neurons; Column 5: gene expression in mutant Vip neurons.

source_name: Visual cortex

growth_protocol: Adult mice were dark-reared for one week prior to dissecting the visual cortices to reduce variation in transcription caused by light exposure (Mardinly et al., 2016). Nuclei from Dnmt3a cKO and Mecp2 KO visual cortices along with those from the respective littermate wild type controls were isolated as previously described (Mo et al., 2015).

extract_protocol:
SUN1-GFP expressing nuclei were isolated as previously described (Mo et al., 2015) using GFP antibodies (Fisher G10362) coupled with Protein G Dynabeads (Invitrogen 10003D). RNasein Plus RNase Inhibitors (Promega N2611) were added to the buffers to prevent degradation of RNA.
Co-encapsulation into microfluidic droplets of nuclei, polyacrylamide gels containing barcoded reverse transcription primers, reverse-transcriptase enzyme, and lysis buffer were performed as previously described to generate barcoded cDNA from single nuclei (Klein et al., 2015; Zilionis et al., 2017). We added 57µL of FD pre-mix (5µL 10X FD buffer; 45µL ddH20; 3µL ExoI (NEB M0293S, 20U/µL); 4µL HinFI (Thermo FD0804) to every 40 µl of sample. Samples were filtered through a 0.45 µm cellulose acetate filter, and incubated at 30 min at 37 °C. Samples were purified with 1.2X volume Agencourt AMPure XP beads (Beckman Coulter A63881). Second strand complementary DNA synthesis was performed by adding 10X NEB Second Strand Synthesis Buffer and NEB Second Strand Synthesis Enzyme Mix (New England Biolabs E6111S) and incubated at 16°C for 2.5 hours, then heat inactivated at 65 °C for 20min. In vitro transcription was performed with NEB T7 High Yield 10X Buffer, dNTPs, NEB T7 High Yield Enzyme Mix (NEB E2040S) and incubating at 37 °C for 13 hours. Samples were purified with 1.3X volume AMPure beads. RNA was fragmented with Fragmentation reagent (Ambion AM8740) by incubating at at 70°C for 3 min, stopped with the STOP mix, and purified with the 1.2X volume AMPure beads. Reverse transcription was performed using random hexamers: Fragmented RNA were incubated with 10 µM primers (TCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNN) and 10mM dNTPs for 3 min at 70°C. Then added RNase Inhibitor, 5X PrimeScript Buffer, 0.5 µL PrimeScript Reverse Transcriptase (Takara Clontech 2680A), and incubated at 30 °C for 10 min, 42 °C for 1 hour, then 70 °C for 15 min. The product was purified with 1.2X volume AMPure beads. The product was amplified using 2X KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601), 5 µM primer mix (PE1: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA; PE2: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAAC) using the following conditions 98°C 2 min, 2 cycles of (98°C 20sec, 55°C 30sec, 72°C 40sec), 9 to 14 cycles of (98°C 20sec, 65°C 30sec, 72°C 40sec), 72°C 5 min, 4°C hold.

tag: background

value: 10 week

value: Visual cortex

tag: genotype

value: mixed sample (non-demultiplexed)