title: 4d-H3_Control_H3

first: Vasu

last: Punj

address: Biggy Street

institute: USC

data_processing:
Basecalls, demultiplexing and fastq generation was carried out using CASAVA v 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using BWA (Burrough Wheel Aligner). PCR duplicate and reads corresponding to adaptor Seq were excluded
The genome was divided into 1Kb bins and aligned reads  were considered to be within a window of the midpoint of its estimated fragment. The genomic bins which contained statistically significant ChIP-Seq tags were identified by comparison to a Poisson background model, assuming that background reads are spread randomly throughout the genome.
genome build: mm9
processed data files format and content: bedgraph files were generated.

source_name: Primary mouse OCP cells (Anet al. 2014 J Biol Chem 289: 24366-24373)

growth_protocol: Bone marrow (BM) cells from 6- to 8-week-old C57BL/6 mice, were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml).

extract_protocol:
After treatment with M-CSF, floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells. On day 3, the cells were stained for tartrate-resistant acid phosphatase (TRAP). The TRAP-positive multinucleated cells containing three or more nuclei are referred as osteoclasts.Chromatin was acetylated with acetic anhydride (20 mM final). cetylated chromatin was immunoprecipitated with an H3K14ac-specific antibody (Active Motif) or an H3 C-terminal (H3CT) antibody (Abcam).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired and blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters.  After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq  following the manufacturer's protocols.sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

treatment_protocol: Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days.

value: Primary mouse osteoclast cells

value: C57BL/6 mice

tag: age

value: 4 d

value: H3 C-terminal (H3CT) antibody


title: 0d-Input

status: Public on Feb 02 2016

type: SRA

city: Los Angeles

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: strain

value: 0 d

tag: chip antibody

value: input


title: 4d-Ac_Control_H3K14ac

value: H3K14ac-specific antibody


title: 0d-H3_MMP-9KD_H3


title: Rvb2 WT replicate 1

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to SacCer3 whole genome using tophat version 2.0.3
Read counts for each gene were calculated with Rsubread 1.16.1, normalized counts were obtained using DESeq2 1.6.3
FPKM values were calculated with DESeq2 1.6.3
Genome_build: SacCer3

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast cells tagged with Rvb1

growth_protocol: 5 ml yeast cells were grown to an OD600 of 1.2 to 1.5 in YPD media by shaking at 30 °C, harvested and used for isolation of total RNA.

extract_protocol:
Standard protocols were followed to extract total RNA from yeast cells using the yeast RNA purification kit (Epicenter, Madison, WI) followed by enrichment of poly(A)+ RNA by oligo(dT) selection.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wild type


title: 0d-AC_MMP9KD_H3K14ac


title: Rvb1 WT replicate 1


title: MMP9_KO

data_processing:
Illumina Casava1.7 software (illumina) or IndexDPGenomic (Helicos) used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Differential expression was calculated at a significance of p<0.05 after Benjamini and Hochberg correction using a null model.
Genome_build: mm9
Supplementary_files_format_and_content: TXT file (File_1_normalized_RPKM_RNA-Seq_Vasu_Woojin.txt) include RPKM values for each Sample.

source_name: MMP9_KO cells

extract_protocol:
Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells. On day 3, the cells were stained for tartrate-resistant acid phosphatase (TRAP). The TRAP-positive multinucleated cells containing three or more nuclei are referred as osteoclasts.
RNA extracted from cells was polyA+ labelled and used to generate libraries following the manufacturer’s protocols (Illumina). The modified cDNA molecules were subjected to sequencing by Illumina Hiseq 2500 system

treatment_protocol: Both Control and MMP9_KO cells were trated with RANKL for thre days

value: Primary osteoclast cells

tag: genotype/variation

value: MMP9 KO

tag: treatment

value: RANKL


title: Control

source_name: Control cells

value: control


title: Leaves of plants well watered and infected with Grapevine rupestris stem pitting-associated virus

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

description: shortRNA

data_processing:
Removed adaptors. Sequences without adaptor matches were discarded.
Sequences were counted and ordered
Supplementary_files_format_and_content: Tabular format. Counts of each species of sRNA in the library

organism: Vitis vinifera

source_name: Vitis vinifera cv. Bosco

growth_protocol: Samples were collected from plants grown in plots under controlled conditions the vegetative start.

extract_protocol: TrueSeq sRNA Illumina kit's instructions

tag: cultivar

value: Bosco

tag: tissue

value: leaves

tag: viral status

value: GRSPaV-infected

tag: watering conditions

value: well watered


title: Leaves of plants water stressed and infected with Grapevine rupestris stem pitting-associated virus

description: shortRNA

value: water stress


title: Leaves of plants well watered and NOT infected with Grapevine rupestris stem pitting-associated virus

description: shortRNA

value: GRSPaV-free


title: WT_ZT04_13016GP32

city: Philadelphia

first: Georgios

middle: K

last: Paschos

state: PA

address: 10-102 Translational Research Center, 3400 Civic Center Boulevard, Building 421

department: Pharmacology

institute: University of Pennsylvania, School of Medicine

data_processing:
CASAVA was used to convert the bcl file to fastq and demultiplex the samples. Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-seq data were aligned to the mouse genome build mm9 by STAR (version 2.4.0f1) with the following parameters "--outFilterType BySJout --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMunmapped Within". Junction information from RefSeq gene models was provided using the "--sjdbGTFfile" argument.
Data were normalized using a resampling strategy, the code is available at https://github.com/itmat/Normalization . We performed gene-level normalization in strand-specific mode using default parameters for the mm9 genome.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: FINAL_master_list_of_genes_counts_MIN.sense.George_WT_v_KO_timecourse.txt: Tab-delimited text file from gene-level normalization contains counts from Unique reads that only map to one gene.

source_name: Liver, WT, ZT4

growth_protocol: All mice were housed under 12h:12h LD conditions with free access to food and water unless specified. All procedures were approved by the University of Pennsylvania Institutional Animal Care and Use Committee. Bmal1 knockout mice (cKO) were obtained from C. Bradfield (University of Wisconsin, Madison, WI, USA). Three mice per genotype were sacrificed every 4h for 20h (6 time points).

extract_protocol:
Liver was extracted every four hours (0, 4, 8, 12, 16, and 20 h) and stored at -80C. Total RNA was extracted using the TruSeq Stranded mRNA Sample Prep Kit Set A.
Library construction was carried out using Illumina TruSeq Stranded mRNA Sample Prep Kit Set A. Samples were barcoded using kit adapters. 13 cycles of PCR selectively amplified cDNA with adapter molecules on both ends. Using the molarity from Bioanalyzer (DNA 1000), libraries were diluted to 10nM. Libraries at 10nM were run on Bioanalyzer again (HighSensitivity DNA) and taking the lowest molarity, six samples with distinct barcodes were pooled. Clustering was carried out on the cBot using the TruSeq PE Cluster Kit v3-cBot-HS. Template DNA was prepared by diluting pooled libraries to 2 nM. The template DNA was denatured to single strands by mixing with NaOH. During this step, DNA is diluted to 20 pM. Denatured DNA was further diluted to desired pM input amount and spike in phiX. PhiX spike in varies by lane. Templates were loaded into an 8 strip tube which was loaded onto the cBot and protocol PE_Amp_Lin_Block_Hyb_v8.9 was used.

tag: strain/background

value: WT

tag: Sex

value: male

value: 13.9 weeks

tag: weight

value: 25 gram

tag: cage number

value: liver

tag: sample collection time


title: KO_ZT00_13016GP30

source_name: Liver, Bmal1 KO, ZT0

value: Bmal1 KO

value: female

value: 19.7 gram


title: KO_ZT08_13016GP27

source_name: Liver, Bmal1 KO, ZT8

value: 8 weeks

value: 22.6 gram


title: KO_ZT12_13016GP28

source_name: Liver, Bmal1 KO, ZT12

value: 18.4 gram


title: Leaves of plants water stressed and NOT infected with Grapevine rupestris stem pitting-associated virus

description: shortRNA

value: Bosco


title: WT_ZT04_13016GP25

value: 21.5 gram


title: WT_ZT20_13016GP23

source_name: Liver, WT, ZT20


title: KO_ZT00_13016GP26

value: 25.2 gram


title: WT_ZT00_13016GP31

source_name: Liver, WT, ZT0

value: 25.4 gram


title: KO_ZT04_13016GP20

source_name: Liver, Bmal1 KO, ZT4

value: 21.1 gram


title: WT_ZT16_13016GP22

source_name: Liver, WT, ZT16

value: 6.4 weeks

value: 23.3 gram


title: KO_ZT16_13016GP36

source_name: Liver, Bmal1 KO, ZT16

value: 10.9 weeks

value: 19.1 gram


title: KO_ZT00_13016GP18

value: male

value: 9.3 weeks

value: 26.5 gram


title: KO_ZT16_13016GP21

value: Bmal1 KO

value: 13.9 weeks

value: 22.5 gram

value: liver


title: Rvb1 WT replicate 3

value: wild type


title: WT_ZT00_13016GP15

value: WT

value: female

value: 21.6 gram


title: WT_ZT08_13016GP35

source_name: Liver, WT, ZT8

value: 8 weeks

value: 23 gram


title: WT_ZT20_13016GP16

value: 10.4 weeks

value: 23.6 gram


title: WT_ZT08_13016GP14

value: 28.4 gram


title: KO_ZT20_13016GP34

source_name: Liver, Bmal1 KO, ZT20

value: 15.7 gram


title: KO_ZT08_13016GP33

value: 22.1 gram


title: KO_ZT20_13016GP13

value: male

value: 25.4 gram


title: WT_ZT16_13016GP29

value: 10.9 weeks

value: 24.3 gram


title: KO_ZT12_13016GP24

value: Bmal1 KO

value: 13.9 weeks

value: 18.1 gram


title: KO_ZT08_13016GP12

value: 24.8 gram

value: liver


title: KO_ZT04_13016GP10

value: 22.7 gram


title: WT_ZT16_13016GP06

value: WT

value: 8 weeks


title: WT_ZT00_13016GP19

value: 6.4 weeks

value: 23.7 gram


title: KO_ZT20_13016GP09

value: female

value: 22.6 gram


title: WT_ZT20_13016GP02

value: 23.3 gram


title: STAT2_NULL_UNT_REP1

city: Stanford

first: Gokul

last: Ramaswami

address: 300 Pasteur Drive Alway M305

institute: Stanford University

data_processing:
Library strategy: mmPCR-seq
Paired-end sequencing reads were combined and mapped as single-end reads onto a combination of the mm9 genome and exonic sequences surrounding known splicing junctions using BWA samse.
We used samtools mpileup to count the number of 'A' and 'G' reads at each editing site to calculate the editing levels.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files contain editing level measurements. The columns are formatted: editing site chromosome, editing site position, editing site gene, editing site strand, editing site annotation1, editing site annotation2, sequencing coverage, number of edited reads, editing level.

extract_protocol:
Total RNA was extracted from cells
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.

value: Mouse Embryonic Fibroblasts

tag: replicate

value: untreated


title: WT_ZT12_13016GP05

source_name: Liver, WT, ZT12

value: male

tag: age

value: 10.9 weeks

value: 29.2 gram


title: KO_ZT16_13016GP17

value: Bmal1 KO

value: 23.5 gram


title: Rvb1 TAH1 deletion replicate 3


title: STAT2_NULL_UNT_REP2

tag: cell type


title: WT_ZT08_13016GP01

value: 13.9 weeks


title: KO_ZT12_13016GP04

value: 13.7 gram

value: liver


title: STAT2_NULL_IFN_REP2

value: interferon


title: STAT1_NULL_IFN_REP2


title: P150_KO_UNT_REP2


title: STAT1_NULL_UNT_REP2


title: STAT1_NULL_IFN_REP1


title: WT_ZT12_13016GP11

value: WT

value: 19.8 gram


title: STAT1_NULL_UNT_REP1


title: P150_KO_IFN_REP2


title: P150_KO_UNT_REP1


title: WT_ZT04_13016GP08

value: 10.4 weeks

value: 23.9 gram


title: P150_KO_IFN_REP1


title: ADAR2_NULL_UNT_REP2


title: ADAR2_NULL_UNT_REP1


title: ADAR1_WT_UNT_REP2


title: KO_ZT04_13016GP03

value: female

value: 8 weeks

value: 20.5 gram


title: WT_ZT12_13016GP07

value: 22.4 gram


title: ADAR2_NULL_IFN_REP2

value: Mouse Embryonic Fibroblasts


title: ADAR1_WT_IFN_REP1


title: ADAR1_WT_IFN_REP2


title: ADAR1_WT_UNT_REP1

value: untreated


title: STAT2_NULL_IFN_REP1


title: ADAR1_NULL_UNT_REP2


title: ADAR1_NULL_UNT_REP1


title: ADAR1_NULL_IFN_REP2


title: MEF Replicate 2

city: Chicago

first: Amy

last: Kenter

address: 835 South Wolcott

department: Microbiology and Immunology

institute: University of Illinois College of Medicine

data_processing:
Genome_build: mm9
5C products were analyzed by Solexa paired-end deep sequencing. A virtual genome of all potential 5C products was created using DNA sequence adjacent to Hind III restriction fragment sites. Reads were aligned to the virtual genome using Novoalign (http://www.novocraft.com). Each paired-end read was mapped independently and only paired-ends for which one end mapped to a 5C forward primer and the other to a 5C reverse primer were considered. Reads that mapped to more than one location were discarded.
Supplementary_files_format_and_content: Files are tab-delimited text tables. Comment header lines give sequence alignment statistics. Data lines have the following columns: (1) forward primer and genomic coordinates, (2) reverse primer and genomic coordinates, (3) number of reads, (4) value = 1 (unused)

source_name: murine embryonic fibroblast

extract_protocol: Bone marrow pro-B cells were expaned in IL7 for four days and then used in 5C assays.  MEF cells were used directly from cell culture.  CD43- resting splenic B cells were isolated directly from the spleen using MACS beads and used in 5C assays.

value: murine embryonic fibroblast


title: Rag2 deficient Pro-B cell Replicate 2

source_name: pro-B cell

value: Bone marrow


title: Rag2 deficient Pro-B cell Replicate 1


title: Resting B cell Replicate 1

source_name: CD43- resting splenic B cells

value: Spleen


title: MEF Replicate 1


title: ADAR1_NULL_IFN_REP1


title: Control-2

city: West Lafayette

first: Joseph

last: Irudayaraj

state: IN

address: 225 S. University Street

department: Bindley Bioscience Center

institute: Purdue University

data_processing:
Sequence reads were aligned with tophat-2.0.8.
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts were calculated with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes row counts and counts per million reads from edgeR.

organism: Homo sapiens

growth_protocol: TK6 human lymphoblastoid cells (ATCC, Manassas, VA) were maintained in the log phase of cell growth by culturing in RPMI-1640 (Life Technologies, Grand Island, NY) medium supplemented with 10% Fetal Bovine Serum (Atlanta Biologicals, Flowery Branch, GA) and 1% Penicillin/Streptomycin (Life Technologies, Grand Island, NY) at 37 °C in 5% CO2 and 95% air

extract_protocol:
Total RNA was extracted from duplicates of cells subjected to stimulated microgravity and static control using RNA-STAT-60 (Tel-Test,Inc., Friendswood, TX) using the manufacturer’s instructions. Briefly, 1ml of RNA-STAT solution was added per 10^6 cells and homogenized for 5 minutes over ice. 1ml of chloroform was added, contents shaked vigorously and centrifuged at 12,000g at 4ºC for 15 minutes. The aqueous solution was transferred to a clean corex tube and 0.8 ml isopropanol added. After incubation of 10 minutes, the contents were centrifuged at 12,000g for another 10 minutes to precipitate the RNA. The RNA pellet was washed with 75% ethanol and centriguged ar 7500g for 5 minutes at 4ºC. The ethanol was aspirated and the RNA pellet dried. The RNA pellet was finally resuspended in DEPC water.
RNA was converted into cDNA and  was end-repaired using repair solution (combination of T4 DNA polymerase, E. coli DNA Pol I large fragment and T4 polynucleotide kinase). A-tailing was obtained by incubating the end repaired DNA with dA-tailing mix. Blunt end ligation was performed by incubating the A-tailed DNA samples (1 μg) with adapters (IDT Inc., Coralville, IA), unmethylated version of Truseq adapters (Illumina Inc., San Diego, CA) for multiplexing. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the illumina hiseq2000 following the manufacturer's protocols.

treatment_protocol: For ground-based simulation of microgravity, HARV rotating suspension culture bioreactors (Synthecon, Houston, TX) were used. Actively growing (96–98% viable) TK6 cells were seeded in the bioreactor at 2 X 10^5 cells/ml and rotated at 12 rpm/min. For control, cells (at the same cellular density i.e 2 X 10^5 cells/ml) were maintained in bioreactors in a normal gravity (static) condition as controls

tag: cell line

value: human lymphoblastoid cells

value: heterozygous at the thymidine kinase (TK) locus

tag: exposed to

value: static (control)


title: Control-1


title: Simulated Microgravity-2

source_name: TK6_simulated microgravity

value: 12 rpm (micro-gravity condition)


title: Simulated Microgravity-1


title: ADAR2_NULL_IFN_REP1

tag: genotype

value: interferon


title: sw480 replicate 2

status: Public on Feb 01 2016

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

data_processing:
trimmed adaptors using Trimmomatic
tophat -g 1  -G genes.gtf GATK/hg19 <fastq.gz>
RNASEQC to generate RPKM measurements
Genome_build: hg19
Supplementary_files_format_and_content: RPKM and coutns

molecule: polyA RNA

source_name: epithelial colon cancer cell lines

growth_protocol: The cell lines used in this study were SW480 cells, D2.15 (SW480+pEF-mycAPC) and R38.7 (SW480+pEF). The cells were thawed from liquid nitrogen and grown in RPMI supplemented with 1.08% thioglycerol, 50mg/ml hydrocortisone, 100U/ml insulin, 10% foetal calf serum and 1% penicillin/streptomycin (SW480 cells) plus 1.5mg/ml G418 (D2.15 and R38.7cells).

extract_protocol:
Seventy two hours later RNA was extracted from the cells using RNAspin Mini RNA isolation kit (Illustra 25-0500-70).
TrueSeq

treatment_protocol: Cells were passaged three times before being plated onto 100mm tissue culture plates at a density of 3.35x105 (SW480 and R38.7) and 2x105(D2.15) in triplicate.


title: sw480 replicate 3


title: sw480 replicate 1


title: microgMe

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to human reference genome hg19 using BWA v 0.6.2
Quality metrics generated using MEDIPS v1.0 and custom R scripts
Peak calling software SPP v1.10 [31], was used to call peaks and rank them based on significance of enrichment
The differentially methylated/hydroxymethylated regions identified by IDR analyses were then annotated with their chromosomal locations and feature types for further biological interpretation using custom perl scripts of MeDUSA package, BEDTools
Genome_build: hg19
Supplementary_files_format_and_content: The normalized RPM (reads per million) in tiled windows across the genome are provided as gzip compressed wig files

source_name: lymphoblastoid cells

extract_protocol:
Lysates were clarified from sonicated nuclei and methylated/hydroxymethylated DNA enrichment was done with antibody.
DNA was end-repaired using repair solution (combination of T4 DNA polymerase, E. coli DNA Pol I large fragment and T4 polynucleotide kinase). A-tailing was obtained by incubating the end repaired DNA with dA-tailing mix. Blunt end ligation was performed by incubating the A-tailed DNA samples (1 μg) with adapters (IDT Inc., Coralville, IA), unmethylated version of Truseq adapters (Illumina Inc., San Diego, CA) for multiplexing. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the illumina hiseq2000 following the manufacturer's protocols.

treatment_protocol: For ground-based simulation of microgravity, HARV rotating suspension culture bioreactors (Synthecon, Houston, TX) were used. Actively growing (96–98% viable) TK6 cells were seeded in the bioreactor at 2 X 105 cells/ml and rotated at 12 rpm/min. For control, cells (at the same cellular density i.e 2 X 105 cells/ml) were maintained in bioreactors in a normal gravity (static) condition as controls

tag: antibody

value: 5-mC monoclonal antibody


title: microgHm

value: 5-hmC monoclonal antibody


title: sw480+CONTROL replicate 3


title: controlHm


title: controlMe


title: sw480+CONTROL replicate 2


title: GSH rep2

city: Sydney

first: Jim

last: Manos

state: NSW

address: Camperdown

institute: University of Sydney

data_processing:
Quality control of raw RNA-seq reads was performed on Illumina BaseSpace using the FastQ Toolkit (v2.0). Raw reads were trimmed of Illumina TruSeq sequencing adapters, filtered for an average Phred Q score minimum of >30 and minimum read length of 32nt after trimming. Reads were further processed by trimming 3’ ends of bases with <Q30 scores
Filtered RNA-seq reads were aligned to the AES-1R genome using Bowtie2 (v2.2.5) using --very-sensitive-local and aligned reads outputted in .sam file.
Samtools (v0.1.19) was used to name sort .sam files to output .bam files
HTSeq (v0.6.1) was used to count reads mapping to features in union mode against a .gtf for AES-1R
Genome_build: AES-1R
Supplementary_files_format_and_content: tab-delimited text files include raw number of reads mapping to features for each sample

organism: Pseudomonas aeruginosa AES-1R

source_name: 80 hour biofilm

growth_protocol: Overnight cultures of AES-1R grown in LB broth were diluted to a MacFarland standard of 0.5, and inoculated in artificial CF sputum media (ASMDM+) at 5µL/mL just under the surface. Cultures were incubated at 37oC for 72 hours. Cultures were treated as below and allowed to incubate for a further 8 hours.

extract_protocol:
Cultures were pooled in technical triplicate to reduce biological variance. 1× PBS was added to pooled cultures and vortex to dislodge biofilms from the ASMDM+. Cultures were spun at 12000g at 4oC for 20 minutes. The ASMDM+ was washed off the resulting cell pellet with 1× PBS. RNA was extracted from cell pellets using the miRNeasy Kit (Qiagen) according to manufacturer's protocols.
Total RNA was then depleted of rRNA using the Ribo-Zero Gold (Bacteria) kit (EpiCentre), according to manufacturer’s specifications. cDNA library preparation for RNA-sequencing was performed using the Illumina TruSeq Stranded kit (#RS-122-2101) according to manufacturer’s specifications, with the following modifications: preparation began at fragmentation, and the number of PCR cycles was reduced from 15 to 12.
RNA-seq was performed on the NextSeq 500 platform, using NextSeq500 v2 reagents (#FC-404-2001) with 75bp paired-end (PE) reads, for a total of 30M reads per sample at the Ramaciotti Centre for Genomics, UNSW, Australia.

treatment_protocol: Cultures were either treated with 1× PBS (WT) or 2mM GSH (GSH).

tag: strain

tag: culture age

value: 80 hours

tag: media

value: ASMDM+


title: WT rep1


title: GSH rep1


title: WT rep2


title: sw480+CONTROL replicate 1


title: Resting B cell Replicate 2

tag: tissue


title: sw480+APC replicate 3


title: J4-control RNA-seq, replicate  2

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
Replicate 2
GSKJ4-2uM_DESeq2_table.txt
GSKJ4_2uM_DESeq2_dds.R

data_processing:
Alignment using Tophat2 (v2.0.12) with default parameters, guided by GTF file from Ensembl release 75
Assignment of reads to transcripts from Ensembl release 75 GTF using htseq-count (v0.6.1p1)
Fold change analysis using DESeq2 to compare two treatment replicates to two control replicates
Results list trimmed to remove transcripts with no associated reads
Raw read counts added to fold change table and exported as text file
DESeqDataSet object exported to file using the R save() command
Genome_build: NCBI 37/hg19
Supplementary_files_format_and_content: Text format table containing differential expression and raw count data. File containing DESeq2 analysis object dumped from R.

source_name: Jurkat cells treated with vehicle control

growth_protocol: RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin and 100 mg/ml streptomycin

extract_protocol:
RNeasy Mini extraction kit from Qiagen with the added step of DNAseI digestion
Illumina TruSeq stranded mRNA library kit

treatment_protocol: Vehicle (DMSO) added to medium for 72h

value: Jurkat

tag: treatment

value: Vehicle (DMSO)


title: sw480+APC replicate 2


title: Merged_Control_ERRa_ChIP-seq

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

institute: Université Laval

description: genomic DNA enriched following ERRa chromatin immunoprecipitation

data_processing:
Sequences were aligned to the human genome database (Hg19) using BWA v0.5.9 (Li and Durbin, 2009)
Significant DNA binding (peak) was determined using MACS v1.4.1 software (Zhang et al., 2008).
Peak annotation, tag directory, bed file generation, and de novo motif discovery were performed with the Homer package v3.18.
Genome_build: hg19
Supplementary_files_format_and_content: data are presented as bigwig and annotated peak lists in excel from the merged of two samples for control condition and two samples for AICAR-treated cells. Additionnally, we included fastq data for each sample. All samples were run twice so there is 2 fastq files per sample (except ERRa_ChIP_AICAR_replicate 1 that has 3 fastq files).

source_name: BT474 human breast cancer cell line treated with vehicle for 90 minutes

growth_protocol: Cells were cultured in regular DMEM. 24h after seeding, media was changed and fresh media with vehicle or AICAR 0.5mM

extract_protocol:
After 90min treatment with vehicle or AICAR, nuclei were isolated and subjected to chromatin immunoprecipitation. Following ERRa ChIP, genomic DNA was purified with QIAGEN DNA extraction kit.
Libraries were performed at the Génome Québec Innovation Centre (McGill University) using standard protocol for HiSeq - Illumina Single reads 50bp sequencing lane

treatment_protocol: Reagents were simply added to the media for cell treatment in regular 6cm culture dish.

tag: tissue type

value: Breast tumor

tag: chip antibody

value: ERRa


title: UTX-KD RNA-seq, replicate  2

description:
Replicate 2
UTX_KD_DESeq_table.txt
UTX_KD_DESeq2_dds.R

source_name: Jurkat cells expressing a Dox-inducible shRNA against UTX with Dox addition

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G425

treatment_protocol: Doxycycline added to medium at 5µg/ml for 72h

value: Dox-induced UTX-KD


title: Merged_AICAR_ERRa_ChIP-seq

source_name: BT474 human breast cancer cell line treated with AICAR for 90 minutes


title: J4-2uM RNA-seq, replicate  1

description:
Replicate 1
GSKJ4-2uM_DESeq2_table.txt
GSKJ4_2uM_DESeq2_dds.R

source_name: Jurkat cells with addition of GSK-J4

treatment_protocol: GSKJ4 added to medium at 2µM for 72h

value: GSK-J4, 2µM


title: Input_ERRa_ChIP-seq

description: input genomic DNA from BT474 cells

source_name: Input DNA from BT474 breast cancer cell line


title: sw480+APC replicate 1


title: J4-control RNA-seq, replicate  1


title: UTX-KD RNA-seq, replicate  1

description:
Replicate 1
UTX_KD_DESeq_table.txt
UTX_KD_DESeq2_dds.R

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G424


title: TAL1-KD RNA-seq, replicate  2

description:
Replicate 2
TAL1_KD_DESeq_table.txt
TAL1_KD_DESeq2_dds.R

source_name: Jurkat cells expressing a Dox-inducible shRNA against TAL1 with Dox addition

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G421

value: Dox-induced TAL1-KD


title: UTX-control RNA-seq, replicate  2

source_name: Jurkat cells expressing a Dox-inducible shRNA against UTX without Dox addition

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G423


title: TAL1-control RNA-seq, replicate  2

source_name: Jurkat cells expressing a Dox-inducible shRNA against TAL1 without Dox addition

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G419


title: TAL1-control RNA-seq, replicate  1

description:
Replicate 1
TAL1_KD_DESeq_table.txt
TAL1_KD_DESeq2_dds.R

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G418


title: J4-2uM RNA-seq, replicate  2


title: TAL1-KD RNA-seq, replicate  1

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G420


title: UTX-control RNA-seq, replicate  1

growth_protocol: RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G422


title: H3K27me3 ChIP-seq TAL1-KD

data_processing:
Reads mapped with bowtie2 (v2.2.4)
We have essentially only mapped reads, as no peak calling protocol was used for this publication. Instead we used the mapped ChIP-seq reads to compare aggregate methylation profiles across a number of loci, presented in figures in the associated paper.
Genome_build: NCBI37/hg19
Supplementary_files_format_and_content: BED file of mapped reads

extract_protocol:
ChIP-seq using protocol from Nature Protocols 3 (3): 398-409, 2008. H3K27me3 antibody: Millipore Cat#07-449. Lot#2475696
KAPA ChIP library kit (KAPA Biosystems)

treatment_protocol: Addition of 5µg/ml Doxycycline to medum of TAL1-KD sample.


title: 3-2 96hai

city: Shenyang

first: Jingjing

last: Chen

state: Liaoning

address: #120  Dongling Road

department: Department of Horticulture

country: China

institute: Shenyang Agricultural University

data_processing:
Illumina HiSeqTM 2000 used for basecalling
all raw reads were filtered by removing reads with adaptors and low-quality reads.sequencing reads were mapped to the reference database for the B. rapa genome (Version 1.2, http://brassicadb.org/brad/) using TopHat
Reads Per Kilo base per Million mapped reads (RPKM) (Mortazavi et al., 2008) was used to estimated gene expression levels of all eight libraries
The EBSeq software was used to identify differentially expressed genes in pair-wise comparison, and the results of all statistical tests were corrected for multiple testing with the Benjamini–Hochberg false discovery rate (FDR<0.01)
Genome_build: v.1.2 at: http://brassicadb.org/brad/;
ftp://brassicadb.org/Brassica_rapa/Bra_Chromosome_V1.2/
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values, length,position etc. for each gene; GeneID searchable at http://brassicadb.org/cgi-bin/gbrowse/Brassica/

organism: Brassica rapa

extract_protocol: plants roots were sampled after inoculation with P. brassicae,RNA was extracted using Trizol reagent. cDNA libraries were prepared for sequencing using standard Illumina protocols

value: Chinese cabbage

tag: background line

value: NIL (near-isogenic line) BJN3-2

tag: genotype/variation

value: clubroot-susceptible line

value: 30 days

value: root

tag: inoculated with

value: Plasmodiophora brassicae

tag: time point

value: 96 hour post inoculation


title: H3K27me3 ChIP-seq TAL1-ctl


title: 3-2 12hai

tag: age

value: 12 hour post inoculation


title: 3-2 0hai

value: 0 hour post inoculation


title: 3-2 72hai

value: 72 hour post inoculation


title: 222 96hai

source_name: CR BJN3-2_root

value: clubroot-resistant line (CR)


title: 222 12hai


title: Input ChIP-seq TAL1-ctl

value: Jurkat


title: 222 72hai


title: 7SK ChIRP-seq - HeLa - Even Probes

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

description:
Affinity purified genomic DNA
processed data file: hg19_7SK_ChIRP-seq_HeLa.bw

data_processing:
Library strategy: ChIRP-seq
After demultiplexing, reads were stripped adaptors and mapped to the mouse (mm9) or human (hg19) genome using Bowtie2. Even and Odd datasets were merged as described previously (PMID:21963238) and visualized as bigWig files. Peaks from the merged datasets were called using MACS2.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: bigWig files of merged (even and odd probe sets) 7SK ChIRP-seq read density

source_name: HeLa cells

growth_protocol: mES cells were grown on gelatin plates with serum and LIF. Human ES cells were grown on matrigel plates. HeLa cells were grown on untreated plates

extract_protocol:
Lysates were produced from soncated cell material and 7SK snRNA enriched with antisense oligonucleotide enrichment.
Libraries were prepared according to the standard ChIRP-seq protocol (PMID: 21963238)

treatment_protocol: All cells were fixed with 1% gluteraldehyde for 10 minutes at room temperature.

tag: cell type

value: Cervical cancer cells

value: HeLa

tag: gender

value: female


title: 7SK ChIRP-seq - HeLa - Odd Probes

tag: cell line


title: 7SK ChIRP-seq - H1 hES - Odd Probes

description:
Affinity purified genomic DNA
processed data file: hg19_7SK_ChIRP-seq_H1.bw

source_name: Embryonic Stem Cells

value: ES cells

value: male


title: 7SK ChIRP-seq - HeLa - Input

description:
Affinity purified genomic DNA
processed data file: hg19_7SK_ChIRP-seq_HeLa_Input.bw


title: 222 0hai

value: Chinese cabbage


title: CD4_90-110y_3 RNA-seq

city: Shanghai

first: Hanqi

last: Yin

state: Shanghai

address: libing road 151

institute: shanghai biochip corporation

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the Ensembl-RNA reference sequence 38 using FanSe2 with parameters: -L110 -E7 -U0 -S10; miRNA-seq reads were aligned to the mirBase 19 using bowtie with parameters: -N 0; MeDIP-seq reads were  aligned to human Hg18 genome using SOAPaligner version 2.21 with parameters -s 34 -v 2 -g 0 -r 1 -M 4.
Gene and miRNA abundance measurements were generationed and normalized using DESeq version 1 ; The normalized standard were condition-dependent per-gene value (CDPV); DMR measurements were generationed and normalized with SOAPaligner
Differential gene and miRNA expression were analysed using DEGseq function package in R program version 2.15.3; Differential DMR were analysed  using MACS version 1.4.0
Genome_build: UCSC human Hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized CDPV, TMP or DMR values and raw fragment counts for each Sample

source_name: CD4+ T cell

growth_protocol: All subjects acceded to a basic physical examination and chest X-rays when the blood samples were harvested. Primary criteria for inclusion in the study were the absence of overt systemic diseases, such as cancer, cardiovascular events, autoimmune diseases or dementia. Furthermore, the long-lived subjects had to be able to perform some daily living activities, and even simple farm work and answer a health and family history questionnaire.

extract_protocol: Total RNA was extracted with Qiagen RNeasy RNA mini kit. Library preparation following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from the pooled blood samples using density gradient centrifugation and CD4+ T cells were isolated by positive selection using CD4 beads

value: long-lived subjects

value: CD4+ T cell


title: CD4_40-55y_2 RNA-seq

value: middle-aged


title: CD4_40-55y_3 RNA-seq


title: CD4_90-110y_1 RNA-seq


title: 7SK ChIRP-seq - H1 hES - Even Probes


title: CD4_90-110y_2 RNA-seq


title: CD4_0y_1 RNA-seq

value: Newborn


title: CD4_40-55y_1 RNA-seq


title: CD4_0y_2 RNA-seq


title: UTX_ChIP

description: UTX ChIP

data_processing:
Basecalling was performed with Illumina RTA 1.12.4.2
ChIP-Seq reads were aligned to the hg19 genome assembly using BWA (version 0.6.2)
Reads mapping to more than 2 locations on the genome were removed with Samtools (version 0.1.18)
Reads mapping to the same genomic location more than once, or duplicated reads, were removed with Samtools (version 0.1.18)
MACS (version 2.0.10) was used to detect tag enrichment of ChIP-Seq experiment, using default values and using a p-value cutoff of 10^-10
Genome_build: hg19
Supplementary_files_format_and_content: WIG files represent the read coverage of the ChIP-Seq over the genome. The files were generated from unique reads without duplicates from the alignment with BWA using the UCSC genome browser standalone tools for Unix. BED files represent the genomic location of ChIP-Seq enrichment peaks as determined by MACS.

source_name: cell line purchased from Invitrogen

growth_protocol: cultured in RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin and 100 mg/ml streptomycin

extract_protocol:
Binding of UTX transcription factor was measured using a ChIP protocol as previously described (Palii, 2011). Chromatin from 1x10^8 cells was fragmented to a size range of 100-300 bases with a Bioruptor (Diagenode) at 4 degrees C. Solubilized chromatin was immunoprecipitated with an antibody against UTX (home made 9838P mixed with A302-374A) or an isotype IgG control. Antibody-chromatin complexes were pulled-down using Dynabeads-Protein A, washed and eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform.
ChIPed DNA was amplified using the Illumina protocol with modifications described in (Palii, 2011).

treatment_protocol: no treatment

value: Jurkat cells_T-ALL


title: Mock_ChIP

description: Mock ChIP

value: IgG control


title: 7SK ChIRP-seq - H1 hES - Input

description:
Affinity purified genomic DNA
processed data file: hg19_7SK_ChIRP-seq_H1_Input.bw


title: 63_sALS

city: La Jolla

first: Ranjan

last: Batra

state: California

address: 2880 Torrey Pines Scenic Drive

institute: University of California San Diego

description: sporadic amyotrophic lateral sclerosis

data_processing:
Raw reads were adaptor-trimmed and aligned to the human genome (UCSC version hg18) using bowtie (parameters: -l 20 -m 5 -k 5 --best -q hg18). Aligned reads were assigned to a custom annotation of human genes [36], [48], and gene expression values were calculated as RPKMs [28].
Control versus sALS patient datasets were compared in a pairwise fashion, calculating ratio fold-changes for all possible 117 disease versus control pairs. For Median Percentile Rank (MPR) analysis, each set of fold-changes were sorted and given a percentile rank, and the median percentile rank for each gene was determined and plotted as a histogram. The local minima near the down-regulated edge, 0.15 was taken as the down-regulated cutoff, and a mirrored cutoff of 0.85 was taken for the up-regulated cutoff, and these gene sets were used for subsequent GO analysis.
Genome_build: hg18
Supplementary_files_format_and_content: Fastq files were aligned to the UCSC genome build (mm9, mm10, or hg19) using BWA, novoaligner (HITS-CLIP) or Olego (polyA-seq). The resulting .sam files were converted to bed files using samtools (HITS-CLIP) or Olego (PolyA-seq). The resulting .bed files were filtered to remove PCR duplicates (HITS-CLIP) and internal A-stretches (polyA-seq). BedGraph files (wiggles) were generated from bedfiles using bedtools (HITS-CLIP) or tag2profile tool from Olego (polyA-seq). Olego is an open source software by Chaolin Zhang lab from Columbia University.

source_name: Human Lumbar spinal cord motor neurons

extract_protocol:
Laser capture microdissection was done according to the protocol described previously (Rabin et al). Briefly, Thirty-five to 50 sections of frozen OCT-embedded human lumbar spinal cord were cut at a thickness of 9 µm in a -18C cryotome and placed onto uncharged glass slides. The sections were returned immediately to -78C after production, and maintained at that temperature for a minimum of three hours. Staining with cresyl violet acetate was accomplished in a 10-step, timed, nuclease-free immersion process. Motor neurons were microdissected from each slide using a Pixcell IIe Laser Capture Microdissection (LCM) System (Arcturus Bioscience) and CapSureTM Macro LCM Caps (Applied Biosystems). Each LCM session had an upper time limit of 2.5 hours. In addition to the motor neuron enriched LCM material, the remaining anterior horn region was collected to create a second parallel pool.
RNA isolation was carried out in each using an RNeasy Micro kit (Qiagen), which employs guanadinium isothiocyanate and 2-mercaptoethanol extraction and column purification, including an on-column DNase I digestion step. Aliquots of each RNA pool were analyzed for quality and quantity on a Bioanalyzer RNA Pico chip (Agilent) and only those samples with RNA Integrity Numbers (RINs) > 5 or evidence of 28S peaks on the electropherogram tracings were advanced to the next step.
Total RNA (10 ng) was amplified to cDNA using random priming with the Ovation® RNA-Seq System (NuGEN).  This procedure involved initial generation of double-stranded cDNA followed by amplification through production of single-stranded cDNA using the SPIA® process.   The single-stranded cDNA was then copied into double-stranded cDNA and quantified using the PicoGreen kit (Invitrogen) assayed with the FUSION system (Packard Biosciences), resulting in a total yield of 3-4 ug amplified cDNA’s.  Standard concentration curves using bacteriophage lambda DNA were generated for each PicoGreen analysis, and the samples were diluted by 10-fold serial dilutions.  QC of the amplified cDNA was determined using a Bioanalyzer running an RNA 6000 Nano LabChip (Agilent).  Double-stranded cDNA (1-2 ug) was fragmented to 150-200 bp sizes using Adaptive Focused AcousticsTM (Covaris, Inc., Woburn, MA), and QC of the fragmented cDNA was performed using a Bioanalyzer DNA Chip 1000 (Agilent).   Fragmented cDNA’s were concentrated using the QIAquick PCR Purification Kit (Qiagen) and 200 ng of the fragmented cDNA’s (determined following PicoGreen quantitation) were end-repaired, followed by adaptor ligation onto the fragments and amplification using the Encore® NGS Library System I (NuGEN).  Library QC was performed using a Bioanalyzer DNA Chip 1000.

value: Laser Capture microdissected MNs from post-mortem spinal cord


title: 84_sALS

description: sporadic amyotrophic lateral sclerosis


title: 89_sALS

description: sporadic amyotrophic lateral sclerosis


title: 48_sALS

description: sporadic amyotrophic lateral sclerosis


title: 27_sALS

description: sporadic amyotrophic lateral sclerosis


title: 34_sALS

description: sporadic amyotrophic lateral sclerosis


title: 85_sALS

description: sporadic amyotrophic lateral sclerosis


title: 16_sALS

description: sporadic amyotrophic lateral sclerosis


title: 79_sALS

description: sporadic amyotrophic lateral sclerosis


title: 21_sALS

description: sporadic amyotrophic lateral sclerosis


title: 62_sALS

description: sporadic amyotrophic lateral sclerosis


title: 60_sALS

description: sporadic amyotrophic lateral sclerosis


title: 88_Control

description: Control


title: 76_Control

description: Control


title: 44_Control

description: Control


title: 67_Control

description: Control


title: 65_Control

description: Control


title: 78_Control

description: Control


title: CD4_0y_3 RNA-seq


title: 10_Control

description: Control


title: 82_sALS

description: sporadic amyotrophic lateral sclerosis


title: 39_Control

description: Control


title: gfp(RNAi) N2 L4

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

country: Spain

institute: IDIBELL

data_processing:
To generate BAM files, more than 50 millions of reads (length of 73 bp) for sample were mapped against the C. elegans worm version WS236 following GEMTools pipeline (http://gemtools.github.io/).
These BAM files were analyzed using the SeqSolve software, which use Cufflinks/Cuffdiff for differential gene/transcript expression analyses (Trapnell et al. 2012)
Genome_build: WS236
Supplementary_files_format_and_content: xls format. Contain a list of genes up and down regulated in ham-3(RNAi) and swsn-2.2(RNAi) animals versus the control population treated with gfp(RNAi).
Supplementary_files_format_and_content: ham-3 & swsn-2.2 RNAi processed data-FPKMs.xlsx contains data for all genes

organism: Caenorhabditis elegans

source_name: wild type N2

growth_protocol: synchronized N2 L1 larvae fed for 36 hours at 35 °C with the RNAi clones of gfp, ham-3, swsn-2.2

extract_protocol:
RNA was isolated with TRI Reagent (MRC, Inc.), and purified by using the Purelink RNA Mini kit (Ambion) and Purelink DNAse (Ambion)
Poly(A) enriched samples were multiplexed in libraries through the CNAG (Centro Nacional de Análisis Genómico) sequencing facility
paired-end RNA-Sequencing on Illumina Hiseq 2000 platform. FASTQs are in standard format with Sanger qualities (Phred+33). read lenght of 73 bp. More than 50 millions of reads per sample

treatment_protocol: RNAi by feeding on plates

tag: developmental stage

value: Larva 4


title: swsn-2.2(RNAi) N2 L4


title: hrde-1_p15C_G3_rep2_sRNAseq

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description: small RNA

data_processing:
The raw reads were processed by trimming 4-nt inline barcode at the 5' end and linker sequence from the 3' end
The processed reads were aligned to the C. elegans annoated gene database (spliced) using bowtie[0.12.7]
The siRNA expression level for each gene was calculated by counting the number of reads that were aligned to the antisense strand of the gene. One pseudo-count was added to each gene to avoid zero counts. The counts were normalized by the sequencing depth (in millions) for each sample.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: A single excel file containing the sRNA expression levels (rpkm) in all 24 samples for all C. elegans genes

source_name: Young adult whole animal

growth_protocol: C. elegans strain N2 and hrde-1 (tm1200) were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 15°C prior to the multigenerational temperature-shift experiment.   For the multigenerational temperature-shift experiment, synchronized worms were cultured at 15°C for three generations, and then 23°C for six generations, followed by 15°C for three generations.  Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10cm NGM OP50 plate (approximately 4500 L1s per plate) at each generation.  Ten L1s from each generation were single picked for the brood size assay. For the 15°C generations (15C-G1-G3 and p15C-G1-G3), young gravid adults were collected 114-120 hours after L1s were released onto the OP50 plates.  For the 23°C generations (23C-G1-G6), young gravid adults were collected 50-55 hours after L1s were released

extract_protocol:
Total small RNA was extracted from frozen synchronized adult worm grinds with the mirVana microRNA (miRNA) isolation kit (Ambion).
small RNA was first ligated to the IDT linker-1 oligo (5' rAppCTGTAGGCACCATCAAT/3ddC/ 3') using T4 RNA ligase 2, truncated  from NEB, and then treated with antarctic phosphatase (NEB) to remove the mono- or tri-phosphate at the 5' end of the small RNAs. Antartic phosphatase was heat-inactivated and T4 polynucleotide kinase reaction  (with ATP) was used to add 5-mono-phosphate group to the small RNA. 33-54 nt small RNA-linker-1 ligation product was gel purified using 8% PAGE with 7.5M urea. A linker oligo with 4 nt barcode (/5AmMC6/ ACG CTC TTC CGA TCT r#r#r#r#-3') was ligated to the 5' end of the small RNA-linker-1 ligation product. cDNA was synthesized with primer (5'-GGAGTTCAGACGTGTGCTCTTCCGATCTATTGATGCTGGCTACAG-3') and SuperScript® III Reverse Transcriptase from Invitrogen. cDNA was PCR amplified with primers:5'- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' and 5'-CAAGCAGAAGACGGCATACGAGAT ###### GTGACTGGAGTTCAGACGTGTGCTCTTCC -3' ( ######: 6 nt multiplexing index sequence). Small RNA library was then purfiled using 3% agarose gel.

tag: genotype

tag: temperature

value: 15˚C (post heat stress)

tag: generation

tag: repeat number


title: ham-3(RNAi) N2 L4

tag: strain


title: hrde-1_p15C_G1_rep2_sRNAseq

description: small RNA


title: hrde-1_p15C_G2_rep2_sRNAseq

description: small RNA


title: hrde-1_23C_G6_rep2_sRNAseq

description: small RNA


title: hrde-1_23C_G5_rep2_sRNAseq

description: small RNA


title: hrde-1_23C_G3_rep2_sRNAseq

description: small RNA


title: hrde-1_23C_G2_rep2_sRNAseq

description: small RNA


title: hrde-1_23C_G4_rep2_sRNAseq

description: small RNA


title: hrde-1_15C_G3_rep2_sRNAseq

description: small RNA

value: 15˚C (before heat stress)


title: hrde-1_15C_G2_rep2_sRNAseq

description: small RNA


title: hrde-1_23C_G1_rep2_sRNAseq

description: small RNA


title: WT_23C_G5_rep2_sRNAseq

description: small RNA

value: WT (N2)


title: WT_p15C_G1_rep2_sRNAseq

description: small RNA


title: WT_23C_G6_rep2_sRNAseq

description: small RNA


title: WT_p15C_G3_rep2_sRNAseq

description: small RNA


title: hrde-1_15C_G1_rep2_sRNAseq

description: small RNA


title: WT_23C_G2_rep2_sRNAseq

description: small RNA


title: WT_23C_G4_rep2_sRNAseq

description: small RNA


title: WT_23C_G3_rep2_sRNAseq

description: small RNA


title: WT_15C_G1_rep2_sRNAseq

description: small RNA


title: WT_23C_G1_rep2_sRNAseq

description: small RNA


title: WT_15C_G2_rep2_sRNAseq

description: small RNA


title: hrde-1_p15C_G3_rep2_mRNAseq

data_processing:
The raw reads were processed by trimming 4-nt inline barcode at the 5' end and linker sequence from the 3' end
The processed reads were aligned to the C. elegans annoated gene database (spliced) using bowtie[0.12.7]
The mRNA expression level for each gene was calculated by counting the number of reads that were aligned to the sense strand of  the gene. One pseudo-count was added to each gene to avoid zero counts. The counts were normalized by the sequencing depth (in millions) for each sample.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: A single excel file containing the mRNA expression levels (rpkm) in all 48 samples for all C. elegans genes

extract_protocol:
Total RNA was extracted from frozen synchronized adult worm grinds (100-200 μl, pulverized in liquid nitrogen by grinding) using Trizol reagent (Life Technologies). mRNA was enriched using Poly(A)Purist MAG kit (Life Technologies).
0.5-1 μg of mRNA was used for each mRNA-seq library. DNA was removed from the RNA sample by DNase I treatment according to manufacture’s instruction (New England Biolabs).  RNA was then fragmented using Fragmentation Reagents (Ambion).  To prepare pre-mRNA libraries, fragmented RNA was treated T4 polynucleotide kinase (New England Biolabs).  The 3’ end of RNA was ligated to an adenylated DNA oligo  (IDT linker-1: 5’-rAppCTGTAGGCACCATCAATC-3’) using T4 RNA ligase 1 (New England Biolabs) without ATP. ~35-60 nt RNA captured by the 3’ linker oligo was purified using 8 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea, followed by a 5’ end ligation reaction using a DNA-RNA hybrid oligo (5’-ACGCTCTTCCGATCTrNrNrNrN-3’, rNrNrNrN as 4-nt barcode) using T4 RNA ligase 1 (New England Biolabs) with ATP.  cDNA was synthesized by using SuperScript III Reverse transcriptase (Life Technologies) and primer SG460 (5’-GGAGTTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3’), followed by  PCR amplification with primers SG-465 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and SG-46X (5’-CAAGCAGAAGACGGCATACGAGAT[6-nt index]GTGACTGGAGTTCAGACGTGTGCTCTTCC-3’). To ensure that amplified DNA is still annealed to a true complement and avoid reannealing-distortion in the resulting libraries, PCR reactions were titrated with increasing cycle numbers; cycle numbers for which product levels have not saturated (i.e. product levels still able to increase substantially with additional cycles) were selected. After separating PCR products on 3 % agarose gels, DNA bands of the expected size were extracted (QIAchange® Gel Extraction Kit [Invitrogen]; omitting the 50°C heating step), followed by massive parallel DNA sequencing (Illumina HiSeq2000).


title: hrde-1_p15C_G2_rep2_mRNAseq


title: hrde-1_23C_G6_rep2_mRNAseq


title: hrde-1_p15C_G1_rep2_mRNAseq


title: hrde-1_23C_G5_rep2_mRNAseq


title: hrde-1_23C_G4_rep2_mRNAseq


title: hrde-1_23C_G3_rep2_mRNAseq


title: hrde-1_23C_G2_rep2_mRNAseq


title: hrde-1_23C_G1_rep2_mRNAseq


title: WT_p15C_G2_rep2_sRNAseq

description: small RNA


title: hrde-1_15C_G3_rep2_mRNAseq


title: hrde-1_15C_G2_rep2_mRNAseq


title: WT_p15C_G3_rep2_mRNAseq


title: WT_23C_G6_rep2_mRNAseq


title: WT_p15C_G2_rep2_mRNAseq


title: WT_p15C_G1_rep2_mRNAseq


title: hrde-1_15C_G1_rep2_mRNAseq


title: WT_23C_G4_rep2_mRNAseq


title: WT_15C_G3_rep2_sRNAseq

description: small RNA


title: WT_23C_G1_rep2_mRNAseq


title: WT_23C_G5_rep2_mRNAseq


title: WT_15C_G3_rep2_mRNAseq


title: hrde-1_p15C_G2_rep1_mRNAseq


title: WT_23C_G3_rep2_mRNAseq


title: WT_15C_G2_rep2_mRNAseq


title: hrde-1_23C_G6_rep1_mRNAseq


title: hrde-1_23C_G5_rep1_mRNAseq


title: hrde-1_23C_G4_rep1_mRNAseq


title: hrde-1_23C_G3_rep1_mRNAseq


title: hrde-1_p15C_G1_rep1_mRNAseq


title: hrde-1_p15C_G3_rep1_mRNAseq


title: hrde-1_23C_G1_rep1_mRNAseq


title: hrde-1_23C_G2_rep1_mRNAseq


title: hrde-1_15C_G1_rep1_mRNAseq


title: hrde-1_15C_G2_rep1_mRNAseq


title: WT_p15C_G3_rep1_mRNAseq


title: hrde-1_15C_G3_rep1_mRNAseq


title: WT_p15C_G2_rep1_mRNAseq


title: WT_23C_G2_rep2_mRNAseq


title: WT_p15C_G1_rep1_mRNAseq


title: WT_15C_G1_rep2_mRNAseq


title: WT_23C_G5_rep1_mRNAseq


title: WT_23C_G4_rep1_mRNAseq


title: WT_23C_G3_rep1_mRNAseq


title: WT_15C_G3_rep1_mRNAseq


title: WT_23C_G2_rep1_mRNAseq


title: WT_15C_G2_rep1_mRNAseq


title: WT_15C_G1_rep1_mRNAseq


title: hrde-1_23C_G4_rep2_H3K9me3ChIP

description: DNA extracted from immunoprecipitated chromatin

data_processing:
50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7].
rpkm value for each gene is calculated by the number of reads that perfectly aligned to both strands of the gene and 300 bp flanking sequence on each site normalized by the size of the gene and the sequencing depth of the library.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: .xlsx file containing rpkm values of all genes for all 24 ChIP-seq libraries and 12 ChIP input libraries.

extract_protocol:
100-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions

tag: antibody

value: Anti-Histone H3 (tri methyl K9)


title: hrde-1_23C_G6_rep2_H3K9me3ChIP


title: hrde-1_23C_G2_rep2_H3K9me3ChIP


title: hrde-1_p15C_G1_rep2_H3K9me3ChIP


title: WT_23C_G6_rep2_H3K9me3ChIP


title: WT_p15C_G1_rep2_H3K9me3ChIP


title: WT_23C_G2_rep2_H3K9me3ChIP


title: hrde-1_15C_G3_rep2_H3K9me3ChIP


title: WT_23C_G4_rep2_H3K9me3ChIP


title: WT_15C_G3_rep2_H3K9me3ChIP


title: WT_p15C_G2_rep2_H3K9me3ChIP


title: WT_23C_G6_rep1_mRNAseq


title: hrde-1_23C_G2_rep2_S2ChIP

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2)


title: hrde-1_15C_G3_rep2_S2ChIP


title: hrde-1_23C_G6_rep2_S2ChIP


title: hrde-1_23C_G4_rep2_S2ChIP


title: hrde-1_p15C_G2_rep2_S2ChIP


title: WT_23C_G1_rep1_mRNAseq


title: WT_p15C_G2_rep2_S2ChIP


title: hrde-1_p15C_G1_rep2_S2ChIP


title: WT_23C_G6_rep2_S2ChIP


title: hrde-1_p15C_G2_rep2_H3K9me3ChIP


title: WT_23C_G2_rep2_S2ChIP


title: WT_15C_G3_rep2_S2ChIP


title: hrde-1_p15C_G2_rep2_ChIPinput

description: DNA extracted from fragmented chromatin

value: ChIP input


title: hrde-1_p15C_G1_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: WT_23C_G4_rep2_S2ChIP


title: hrde-1_23C_G4_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: hrde-1_23C_G6_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: hrde-1_15C_G3_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: WT_15C_G3_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: WT_23C_G6_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: WT_p15C_G2_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: hrde-1_23C_G2_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: M2 NK cells

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

data_processing:
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs were retained. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they did not express or expressed at a very low level in all cell types.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene in each library.

source_name: Spleen

growth_protocol: Samples 1-6 were isolated from spleen and grown in IL-15 for 7 days before RNA isolation. Samples 7-9 were sorted from spleen and RNA isolated.

extract_protocol:
Total RNA from NK cells was purified using RNeasy mini columns (Qiagen).
SuperScript II reverse transcriptase (Roche) was used for first-strand cDNA synthesis according to the manufacturer’s instructions.

treatment_protocol: No treatment

tag: tissue

value: Spleen

value: NK cell

value: Wild type


title: WT_23C_G4_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: WT_p15C_G1_rep2_S2ChIP


title: Immature NK cells


title: Id2-null NK cells rep2


title: Wild-type NK cells rep1


title: Wild-type NK cells rep2


title: Id2-null NK cells rep1


title: Wild-type NK cells rep3


title: RAW_LPS_ChIPSeq

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

description:
Chromatin IP against TFE3
LPS

data_processing:
Illumina Casava1.8 software used for basecalling and demultiplexing.
Sequenced reads were mapped to mm9 whole genome using Bowtie (Langmead et al, 2009).
TFE3 Peaks were called using MACS2  (Zhang et al, 2008), with qvalue of 0.05, --gsize mm, and the rest were defualt setting.
Genome_build: mm9
Supplementary_files_format_and_content: peak files in bed formats and BigWig files

growth_protocol: RAW 264.7 macrophages were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, samples were sonicated and lysates were cleared from sonicated nuclei and used for immunoprecipitation.
Cells were cross-linked in 1% formaldehyde and processed according to Myers Lab ChIP-seq protocol for adherent cells. Purified DNA was processed according to manufacturer's protocol.

treatment_protocol: For activation, cells were treated with 1ug/ml LPS for 24 hours or starved in Earle's balanced salt solution for 2 hours.

value: Activated Macrophage

tag: chip antibody


title: Id2-null NK cells rep3


title: WT_p15C_G1_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: RAW_Control_ChIPSeq

description:
Chromatin IP against TFE3
Control

value: Macrophage


title: RAW_Starvation_ChIPSeq

description:
Chromatin IP against TFE3
Starvation


title: NFkB2_CD40_6h_3

city: New York

first: Ulf

last: Klein

state: NY

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

description: RNAseq data

data_processing:
RTA (Illumina) is used for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming.
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat (version 2.0.4) infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Relative abundance (aka expression level) of genes and splice isoforms is estimated using cufflinks 2.0.2 with default settings.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: TXT files and reads

source_name: Splenic B lymphocytes

growth_protocol: 10% FBS in RPMI and anti-CD40 antibodies for 6 hours.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
poly-A pull-down were used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). For library preparation, the Illumina TruSeq RNA prep kit was used. Libraries were sequenced on the Illumina HiSeq2000 at the Columbia University Genome Center. Samples were multiplexed in each lane, which yields the targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: Splenic B cells from 12-week old nfkb2fl/flCD19-Cre and CD19-Cre littermate mice isolate by magnetic cell separation from splenic mononuclear cells and stimulated with anti-CD40 for 6 hours.

value: MACS-purified B cells

tag: treatment

value: CD40 in vitro activated (6h)


title: NFbK2_CD40_6h_2

description: RNAseq data


title: WT_23C_G2_rep2_ChIPinput

description: DNA extracted from fragmented chromatin


title: NFkB2_CD40_6h_1

description: RNAseq data


title: WT_CD40_6h_2

description: RNAseq data


title: WT_CD40_6h_1

description: RNAseq data


title: RAW_Background Control_ChIPSeq

description:
Chromatin IP against IgG
Negative Control

value: Rabbit IgG (Santa Cruz, Catalog# sc-806, Lot# F0908)


title: NFkB2_BAFF_6h_2

description: RNAseq data

growth_protocol: 10% FBS in RPMI and BAFF for 6 hours.

treatment_protocol: Splenic B cells from 12-week old nfkb2fl/flCD19-Cre and CD19-Cre littermate mice isolate by magnetic cell separation from splenic mononuclear cells and stimulated with BAFF for 6 hours.

value: BAFF in vitro activated (6h)


title: NFkB2_BAFF_6h_3

description: RNAseq data


title: WT__BAFF_6h_2

description: RNAseq data


title: WT_BAFF_6h_3

description: RNAseq data


title: M1 NK cells


title: MEF_Tunicamycin_ChIPSeq

description:
Chromatin IP against TFE3
Tunicamycin - MEF
Stimulated mouse embryonic fibroblasts

data_processing:
Illumina Casava1.8 software used for basecalling and demultiplexing.
Sequenced reads were mapped to mm9 whole genome using Bowtie (Langmead et al, 2009).
TFE3 Peaks were called using MACS2  ( Zhang et al, 2008), with qvalue of 0.05, --gsize mm, and the rest were defualt setting.
Genome_build: mm9
Supplementary_files_format_and_content: peak files in bed format (Chr, Start, End , ID, Score for display, NA, Fold-Change, -log10pvalue, -log10qvalue, relative summit position to peak start) and BigWig files

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, samples were sonicated and lysates were cleared from sonicated nuclei and used for immunoprecipitation.
For ChIPSeq, cells were cross-linked in 1% formaldehyde and processed according to Myers Lab ChIP-seq protocol for adherent cells. Purified DNA was processed according to manufacturer's protocol.

treatment_protocol: For stimulation cells were treated with 0.1ug/ml Tunicamycin for 16 hours or starved in Earle's balanced salt solution for 2 hours.

value: MEF

tag: stress

value: tunicamycin

value: TFE3 (Sigma, Catalog# HPA023881, Lot# E96562)


title: MEF_Starvation_ChIPSeq

description:
Chromatin IP against TFE3
Starvation - MEF
Stimulated mouse embryonic fibroblasts

value: starvation


title: NFkB2_BAFF_6h_1

description: RNAseq data


title: MEF_Full_ChIPSeq

description:
Chromatin IP against TFE3
Full - MEF
Mouse embryonic fibroblasts

value: control


title: MEF_Background Control_ChIPSeq

description:
Chromatin IP against IgG
Negative Control - MEF
Mouse embryonic fibroblasts

value: background control


title: Ctl-3

city: Paris

first: PONTIS

last: Julien

address: 35, rue Hélène BRION

country: France

institute: UMR7216 CNRS

description: PolyA RNA

data_processing:
Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1.8) giving FASTQ formatted reads. Those reads were cleaned from adapter sequences and sequences of low quality using an in-house program (https://github.com/baj12/clean_ngs). Sequences with a minimum length of 25 nucleotides were considered for further analysis. Tophat (version 1.4.1.1, default parameters) was used to align to the reference genome (mm9). HTseq-count (parameters: -m intersection-nonempty, -s yes, -t exon) was used for counting genes (Trapnell et al. 2009 and Anders et al. 2010). Dseq2 package (Love MI, Huber W and Anders S (2014). "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." Genome Biology) was used for statistical analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files: Raw-Counts.txt, Deregulated_genes_upon_knock-down_of_Setdb1_in_C2C12.txt.

source_name: C2C12, Ctl

growth_protocol: C2C12 myoblast cell line was grown in high-glucose Dulbecco’s modified Eagle's medium (DMEM; Invitrogen) with 1% penicillin/streptomycin, sodium pyruvate and 20% Fetal Calf Serum (FCS, PAA).

extract_protocol:
RNA was isolated as described above.
Polyadenylated messenger RNA was purified from 1 µg RNA and the library was generated using the TruSeq stranded mRNA library prep Kit, set A and B (Illumina, #RS-122-2101 & #RS-122-2102). The obtained directional libraries were controlled by Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified by spectrofluorimetry (QuantiT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen).

treatment_protocol: Differentiation was initiated at 80-90% confluence in high-glucose DMEM containing penicillin/streptomycin, 1% sodium pyruvate (PAA) and 2% horse serum (Gibco), for the indicated period of time. C2C12 cells were transfected at 80-90% confluence using HiPerFect transfection reagent (Qiagen) to achieve a final siRNA concentration of 33 nM. Differentiation of cells was started immediately after first transfection as described above. For siMyogenin experiments, cells were transfected with a pool of two siRNA and processed 24 h after transfection. For siSetdb1 experiments, a second transfection was performed 24 h after the first transfection. Cells were incubated 72 h post first transfection before being processed for analysis.

tag: sirna


title: siRNA-3

description: PolyA RNA

source_name: C2C12, Setdb1 siRNA


title: siRNA-1

description: PolyA RNA


title: Ctl-2

description: PolyA RNA


title: WT_CD40_6h_3

description: RNAseq data


title: siRNA-2

description: PolyA RNA


title: Ctl-1

description: PolyA RNA


title: Input H3K9me3

data_processing:
Illumina Casava1.7 software used for basecalling
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v0.12.7 with parameters : -t -q -p 8 -S -n 2 -e 70 -l 50 --maxbts 125 -k 1 - m 1
Peaks were call with MACS v1.4 using paramters : --shiftsize 50 --nomodel
Setdb1-peaks
H3K9me3-peaks
Genome_build: mm9
Supplementary_files_format_and_content: XLSX; Standard MACS peak calling output file.
Supplementary_files_format_and_content: chr, start, end: genomic coordinate of the peaks; length: length of the peak; summit: position of the maximal number of reads in the peak; tags: number of reads in the peak; p-value: p-value; Fold enrichment: over the Input; FDR: false discovery rate.

growth_protocol: C2C12 myoblast cell line was grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) with penicillin/streptomycin, sodium pyruvate and 20% fetal calf serum (FCS) (all from PAA).

extract_protocol:
FA (Sigma) was added to culture medium to a final concentration of 1%. Crosslinking was allowed to proceed for 10 min at RT and stopped by addition of glycine at a final concentration of 0.125 M. Fixed cells were washed and harvested with PBS. Cells were lysed in Buffer 1 (50 mM Hepes/KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton). The resulting pellet was resuspended in Buffer 2 (200 mM NaCl; 1mM EDTA; 0.5mM EGTA; 10 mM Tris pH 8). Each resuspension step was followed by 10 min incubation at 4°C. Nuclei were then pelleted by centrifugation, resuspended in Buffer 3 (50 mM Tris pH 8; 0.1% SDS; 1% NP-40; 0.1% Na-Deoxycholate; 10 mM EDTA; 150 mM NaCl). All buffers were supplemented with phosphatase and protease inhibitors (Sigma) prior to usage. Samples were sonicated with Bioruptor Power-up (Diagenode) yielding genomic DNA fragments with a bulk size of 150-300 bp. Chromatin was precleared with Protein A/G ultralink beads (#53133, Thermo Fisher Scientific) for 1h at 4°C and immunoprecipitation with the specific antibodies overnight at 4°C. Immunocomplexes were recovered by adding protein A/G ultralink beads, preblocked with BSA and incubated for 2 h at RT. Beads were washed twice with Low salt buffer (0.1% SDS; 1% Triton; 2 mM EDTA; 20 mM Tris pH 8; 150 mM NaCl), twice with High salt buffer (0.1% SDS; 1% Triton; 2 mM EDTA; 20 mM Tris pH 8; 500 mM NaCl), once with LiCl buffer (10 mM Tris pH 8.0; 1% Na-deoxycholate; 1% NP- 40, 250 mM LiCl; 1 mM EDTA) and twice with TE buffer + 50mM NaCl. All buffers were supplemented with phosphatase and protease inhibitors (Sigma). Chromatin was eluted with Elution buffer (50mM Tris, pH8; 1mM EDTA; 1%SDS; 0,2M NaCl) at 65°C and crosslinking was reversed O/N at 65°C using Proteinase K (Sigma). The eluted material was phenol/chloroform-extracted and ethanol-precipitated.
Five to fifteen ng of ChIPed DNA or whole cell extract (Input) were prepared for sequencing on Illumina Hiseq 2000. We used the library kit (Truseq DNA sample prep kit V2, Illumina) according to the manufacturers’ instructions with the following modifications: DNA fragments were repaired to blunt ends, purified with magnetic beads (Agencourt AMPure XP, Beckman coulter) and a step of A-tailing was performed before ligating to Illumina adapters. Two steps of DNA purification on magnetic beads were carried out to eliminate non-ligated adaptors and then amplified with 15 PCR cycles. To remove non-ligated left adapters and large DNA fragments, DNA libraries were selected on E-Gel (2% SizeSelect, Invitrogen) to obtain 280-330 bp DNA fragments (including 130 bp of adapters). To ensure high quality of the library, samples were tested using the DNA high sensitivity chip (Agilent Technologies) and for positive target enrichment by qPCR. Furthermore, samples were then quantified by qPCR and PicoGreen (Qubit® 2.0 Fluorometer, Invitrogen).

treatment_protocol: When indicated C2C12 myoblasts were treated with 50 ng/ml Wnt-3a (#1324-WN, R&D systems) for 24 h.


title: 7SK ChIRP-seq - mES - JQ1 Even Probes

description:
Affinity purified genomic DNA
mm9_7SK_ChIRP-seq_mES_JQ1.bw

data_processing:
After demultiplexing, reads were stripped adaptors and mapped to the mouse (mm9)  genome using Bowtie2. Even and Odd datasets were merged as described previously (PMID:21963238) and visualized as bigWig files. Peaks from the merged datasets were called using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of merged (even and odd probe sets) 7SK ChIRP-seq read density

value: ES cells

value: male


title: 7SK ChIRP-seq - mES - Input

description:
Affinity purified genomic DNA
processed data file: mm9_7SK_ChIRP-seq_mES_Input.bw


title: 7SK ChIRP-seq - mES - JQ1 Odd Probes


title: 7SK ChIRP-seq - mES - Even Probes

description:
Affinity purified genomic DNA
processed data file: mm9_7SK_ChIRP-seq_mES_WT.bw


title: WT_BAFF_6h_1

description: RNAseq data


title: 7SK ChIRP-seq - mES - Odd Probes


title: Setdb1+DMSO-C2C12

data_processing:
Illumina Casava1.7 software used for basecallin
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v0.12.7 with parameters : -t -q -p 8 -S -n 2 -e 70 -l 50 --maxbts 125 -k 1 - m 1
Peaks were call with MACS v1.4 using paramters : --shiftsize 50 --nomodel
Setdb1-peaks
H3K9me3-peaks
Genome_build: mm9
Supplementary_files_format_and_content: XLSX; Standard MACS peak calling output file.
Supplementary_files_format_and_content: chr, start, end: genomic coordinate of the peaks; length: length of the peak; summit: position of the maximal number of reads in the peak; tags: number of reads in the peak; p-value: p-value; Fold enrichment: over the Input; FDR: false discovery rate.

extract_protocol:
FA (Sigma) was added to culture medium to a final concentration of 1%. Crosslinking was allowed to proceed for 10 min at RT and stopped by addition of glycine at a final concentration of 0.125 M. Fixed cells were washed and harvested with PBS. Cells were lysed in Buffer 1 (50 mM Hepes/KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton). The resulting pellet was resuspended in Buffer 2 (200 mM NaCl; 1mM EDTA; 0.5mM EGTA; 10 mM Tris pH 8). Each resuspension step was followed by 10 min incubation at 4°C. Nuclei were then pelleted by centrifugation, resuspended in Buffer 3 (50 mM Tris pH 8; 0.1% SDS; 1% NP-40; 0.1% Na-Deoxycholate; 10 mM EDTA; 150 mM NaCl). All buffers were supplemented with phosphatase and protease inhibitors (Sigma) prior to usage. Samples were sonicated with Bioruptor Power-up (Diagenode) yielding genomic DNA fragments with a bulk size of 150-300 bp. Chromatin was precleared with Protein A/G ultralink beads (#53133, Thermo Fisher Scientific) for 1h at 4°C and immunoprecipitation with the specific antibodies overnight at 4°C. Immunocomplexes were recovered by adding protein A/G ultralink beads, preblocked with BSA and incubated for 2 h at RT. Beads were washed twice with Low salt buffer (0.1% SDS; 1% Triton; 2 mM EDTA; 20 mM Tris pH 8; 150 mM NaCl), twice with High salt buffer (0.1% SDS; 1% Triton; 2 mM EDTA; 20 mM Tris pH 8; 500 mM NaCl), once with LiCl buffer (10 mM Tris pH 8.0; 1% Na-deoxycholate; 1% NP- 40, 250 mM LiCl; 1 mM EDTA) and twice with TE buffer + 50mM NaCl. All buffers were supplemented with phosphatase and protease inhibitors (Sigma). Chromatin was eluted with Elution buffer (50mM Tris, pH8; 1mM EDTA; 1%SDS; 0,2M NaCl) at 65°C and crosslinking was reversed O/N at 65°C using Proteinase K (Sigma). The eluted material was phenol/chloroform-extracted and ethanol-precipitated
Five to fifteen ng of ChIPed DNA or whole cell extract (Input) were prepared for sequencing on Illumina Hiseq 2000. We used the library kit (Truseq DNA sample prep kit V2, Illumina) according to the manufacturers’ instructions with the following modifications: DNA fragments were repaired to blunt ends, purified with magnetic beads (Agencourt AMPure XP, Beckman coulter) and a step of A-tailing was performed before ligating to Illumina adapters. Two steps of DNA purification on magnetic beads were carried out to eliminate non-ligated adaptors and then amplified with 15 PCR cycles. To remove non-ligated left adapters and large DNA fragments, DNA libraries were selected on E-Gel (2% SizeSelect, Invitrogen) to obtain 280-330 bp DNA fragments (including 130 bp of adapters). To ensure high quality of the library, samples were tested using the DNA high sensitivity chip (Agilent Technologies) and for positive target enrichment by qPCR. Furthermore, samples were then quantified by qPCR and PicoGreen (Qubit® 2.0 Fluorometer, Invitrogen)

value: Setdb1 Santa Cruz (H-300 sc-66884)


title: H3K9me3-C2C12

value: H3K9me3 Diagenode (pAb-056-050)


title: Setdb1-C2C12


title: CD4_40-55y_2 MeDIP-seq

extract_protocol: Total DNA was extracted with Qiagen AllPrep DNA Kit

value: middle-aged

value: CD4+ T cell


title: CD4_90-110y_2 MeDIP-seq

value: long-lived subjects


title: CD4_90-110y_3 MeDIP-seq


title: CD4_90-110y_1 MeDIP-seq


title: CD4_40-55y_1 MeDIP-seq


title: Input Setdb1


title: CD4_0y_1 MeDIP-seq

value: Newborn


title: Setdb1+Wnt3a-C2C12


title: CD4_90-110y_3 small RNA-seq


title: CD4_90-110y_2 small RNA-seq


title: CD4_90-110y_1 small RNA-seq


title: CD4_40-55y_1 small RNA-seq


title: CD4_0y_3 small RNA-seq


title: CD4_0y_2 small RNA-seq


title: CD4_40-55y_3 MeDIP-seq


title: 0 min post cdc7-4 release of Mcm6-SuOn cells

first: Xiaolan

last: Zhao

address: 430 East 67th Street, RRL 917D

department: Molecular Biology Program

institute: Memorial Sloan-Kettering Cancer Center

description: Mutant_0 min

data_processing:
Reads were mapped onto the S288c reference genome (SGD June 2008 assembly (SacCer2)) to generate coverage maps
reads mapped to repetitive sequences were excluded, then were summed in 1 kb bins. Windows containing fewer than 600 reads in either sample were excluded.
absolute copy numbers were generated by dividing the read counts from the replicating sample by counts from the non-replicating sample (0 min post release) for each strain
relative copy number was generated by normalizing the absolute copy number to the read number in the two corresponding samples to give a genome-wide mean value of 1 for each chromosome.
adjusted copy number was generated by using FACS data to correct for the proportion of DNA that is replicated.
The map of adjusted copy number was further smoothed with the ‘‘loess’’ function in R
Genome_build: S288c reference genome (SGD June 2008 assembly (SacCer2)
Supplementary_files_format_and_content: tab-delimited text files for each chromosome and time point

source_name: Genomic DNA from cdc7-4 post release cells

growth_protocol: cells were grown to early log phase in YPD media at 24˚C before treatment

extract_protocol:
genomic DNA was purified from the lysate of cells by CsCl ultracentrifugation at 90K for 9hrs
Libraries were prepared according to instructions accompanying KAPA’s library kit

treatment_protocol: Cells were first arrested in G2/M by nocodazole at 24˚C and then 1 mM IAA was added to degrade Mcm6-aid, followed by shifting the temperature to 37˚C to inactivate cdc7-4 and achieve tight G1/S arrest. Cells were then released into S phase by rapid cooling to 24˚C and samples were collected at  0 min, 15 min, 30 min, 40 min post cdc7-4 release.

value: cdc7-4/cdc7-4 Mcm6-SuOn::KAN/+ Mcm6-aid::HIS3/+ ADH1-TIR::URA/+

tag: ID

tag: protocol

value: cdc7-4 release

tag: time

value: 0 min


title: 40 min post cdc7-4 release of Mcm6-ctrl cells

description: WT_40 min

value: cdc7-4/cdc7-4 Mcm6-ctrl::KAN/+ Mcm6-aid::HIS3/+ ADH1-TIR::URA/+

value: 40 min


title: 40 min post cdc7-4 release of Mcm6-SuOn cells

description: Mutant_40 min


title: 30 min post cdc7-4 release of Mcm6-SuOn cells

description: Mutant_30 min

value: 30 min


title: 15 min post cdc7-4 release of Mcm6-SuOn cells

description: Mutant_15 min

value: 15 min


title: CD4_0y_2 MeDIP-seq

tag: age

tag: cell type


title: 15 min post cdc7-4 release of Mcm6-ctrl cells

description: WT_15 min


title: CD4_0y_3 MeDIP-seq


title: 0 min post cdc7-4 release of Mcm6-ctrl cells

description: WT_0 min


title: zebrafish crestin EGFP + 15 ss

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to Zv9 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: Zv9
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

organism: Danio rerio

source_name: crestin_1kb:EGFP transgenic zebrafish embryos

growth_protocol: Transgenic zebrafish (crestin_1kb:EGFP) were spawned, and embryos grown under standard conditions at 28C in E3 buffer until 15 SS stage.  These were homogenized, filtered, and sorted using FACS into PBS, collecting ~5,500 EGFP (+) cells and 100K EGFP (-) cells

extract_protocol:
Total RNA was again collected using Trizol and GenElute LPA carrier per manufacturer instructions
Libraries were prepared using Ribogone kit (Clontech) and the SMARTer Universal Low RNA Kit (Clontech) and sequenced on the Illumina Hiseq 2500

value: crestin + neural crest cells at 15 SS

tag: developmental stage

value: embryo


title: zebrafish crestin EGFP neg

value: crestin - cells from 15 SS embryo

tag: genotype


title: MiniCoopR;mitf:EGFP tumor input

description: ChIP'ed genomic DNA

data_processing:
ChIP-Seq aligned to zebrafish Zv9 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: Zv9
Supplementary_files_format_and_content: called peaked in narrowPeak bed file

source_name: zebrafish primary melanoma tumor

growth_protocol: Zebrafish melanoma cells were grown to confluence in DMEM + 10% FCS, and ~ 3-5X10^7 cells were formaldehyde crosslinked and collected.  The primary melanoma was generated in a p53/BRAF/Na zebrafish injected with MiniCoopR;mitf:EGFP control Tol2 plasmid as in Ceol, Houvras, et al, Nature, 2011.  The bulk tumor was carefully dissected and manually dissociated with a razor blade and trypsinized prior to formaldehyde crosslinking.

extract_protocol:
ChIP was performed using the methods of T. I. Lee, S. E. Johnstone, R. A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc. 1, 729–748 (2006).
Libraries were prepared using the NEBNext Multiplex Oligos for Illumina kit (NEB) and run on an Illumina Hi-Seq2000.

value: zebrafish primary melanoma tumor

tag: genotype of founder fish

value: p53/BRAF/Na; MiniCoopR;mitf:EGFP


title: zcrest 1 50K cell

data_processing:
Library strategy: ATAC-Seq
We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Genome_build: Zv9
Supplementary_files_format_and_content: bed file of called peaks

source_name: zebrafish melanoma cell line

growth_protocol: Zebrafish melanoma cell lines were grown to 80% confluence, trypsinized, and counted.

extract_protocol:
50,000 cells were lysed and subjected to “tagmentation” reaction and library construction as described in J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, W. J. Greenleaf, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Meth. 10, 1213–1218 (2013).
Library construction as described in J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, W. J. Greenleaf, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Meth. 10, 1213–1218 (2013).

value: melanoma cell line

tag: passages

value: >20 passages

value: p53/BRAF/Na; crestin:EGFP, MiniCoopR alone


title: MiniCoopR;mitf:EGFP tumor H3K27Ac

description: ChIP'ed genomic DNA

value: H3K27Ac (ab4729) (Abcam)


title: Zcrest input for H3K27Ac

description: ChIP'ed genomic DNA

source_name: zebrafish melanoma tumor cell line zcrest 2

value: zebrafish melanoma tumor cell line

value: > 20 passages


title: zcrest 2 50K cells


title: CD4_40-55y_3 small RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the Ensembl-RNA reference sequence 38 using FanSe2 with parameters: -L110 -E7 -U0 -S10; miRNA-seq reads were aligned to the mirBase 19 using bowtie with parameters: -N 0; MeDIP-seq reads were  aligned to human Hg18 genome using SOAPaligner version 2.21 with parameters -s 34 -v 2 -g 0 -r 1 -M 4.
Gene and miRNA abundance measurements were generationed and normalized using DESeq version 1 ; The normalized standard were condition-dependent per-gene value (CDPV); DMR measurements were generationed and normalized with SOAPaligner
Differential gene and miRNA expression were analysed using DEGseq function package in R program version 2.15.3; Differential DMR were analysed  using MACS version 1.4.0
Genome_build: UCSC human Hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized CDPV, TMP or DMR values and raw fragment counts for each Sample

extract_protocol: Total RNA was extracted with Qiagen RNeasy RNA mini kit. Library preparation following "TruSeq RNA Sample Preparation Guide".

value: middle-aged

value: CD4+ T cell


title: Zcrest H3K27Ac

description: ChIP'ed genomic DNA

source_name: zebrafish melanoma tumor cell line zcrest 1


title: CD4_40-55y_2 small RNA-seq


title: ExposednoNic_5

city: Tuxedo

first: Dana

last: Lauterstein

address: 57 Old Forge Rd

department: Environmental Medicine

institute: New York University

description: Exposed to E-cigarettes with No Nicotine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Samples with reads spanning multiple lanes were merged.
The sequencing reads were aligned to the mouse genome (UCSC build mm9) using the Bowtie aligner.
Likely PCR duplicates were removed with Samtools tool.
HTSeq was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
Counts were normalized and tested for differential expression with the DESeq2 R package.
Genome_build: mm9
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: Brain Tissue

extract_protocol:
Offspring (~1-mo-old) were sacrificed in accordance with IACUC protcol. At the time of sacrifice, brains were sectioned, snap frozen in liquid nitrogen, and stored at -80°C until RNA was extracted from the frontal cortex samples.
A standard protocol for RNA isolation using TRIzol Reagent (Invitrogen) was used, and the RNA samples were subsequently purified using a RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
RNA was quantified using a NanoDrop ND-1000 fluorospectrometer (Thermo Scientific, Waltham, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: tissue compartment

value: Frontal Cortex

tag: Sex

value: Female


title: ExposednoNic_4

tag: strain


title: ExposednoNic_3

tag: tissue


title: CD4_0y_1 small RNA-seq

source_name: CD4+ T cell

value: Newborn


title: 30 min post cdc7-4 release of Mcm6-ctrl cells

description: WT_30 min

value: cdc7-4/cdc7-4 Mcm6-ctrl::KAN/+ Mcm6-aid::HIS3/+ ADH1-TIR::URA/+

value: cdc7-4 release

value: 30 min


title: ExposednoNic_2


title: ExposednoNic_1


title: ExposedNic_5

description: Exposed to Nicotine Containing E-cigarettes (13-16mg/ml)


title: ExposedNic_3


title: Zcrest input for sox10

description: ChIP'ed genomic DNA

source_name: zebrafish melanoma tumor cell line zcrest 4

tag: chip antibody


title: ExposedNic_2


title: Control6

description: Filtered Air Controls


title: ExposedNic_1


title: ExposedNic_6


title: Zcrest sox10

description: ChIP'ed genomic DNA

source_name: zebrafish melanoma tumor cell line zcrest 3

value: SOX10 (Santa Cruz Biotechnology, sc-17342x).


title: Control2

description: Filtered Air Controls


title: Control1

description: Filtered Air Controls


title: Control3

description: Filtered Air Controls


title: Control4

description: Filtered Air Controls


title: ExposedNic_22M

value: Male


title: ExposednoNic_4M


title: ExposedNic_19M


title: ExposednoNic_3M


title: ExposedNic_21M


title: ExposednoNic_5M


title: Mouse

city: Rotterdam

first: Martin

last: Hoogduijn

address: 's-Gravendijkwal 230

country: Netherlands

institute: Erasmus MC

description:
M
negative control, mouse mRNA
MSC_Hoogduijn_allsamples_gene_counts.txt
toptags_I_vs_C.txt

data_processing:
Basecalling: Illumina RTA 1.17.21.3
Demultiplexing: Illumina CASAVA 1.8.4
alignment: tophat_largeindex (tophat2 version 2.0.13)
regenerate input fastq from tophat alignment results (accepted_hits.bam and unmapped.bam) using picard-tools SamToFastq, with options "RC=true INCLUDE_NON_PRIMARY_ALIGNMENTS=false". This was done for sample 06, where the raw sequencer result fastq was inadvertedly lost.
ReadCounting: custom R script, based on IRanges package
Differential expression analysis: R and edgeR package, with model including terms for group and donor
Filtering for mouse-human cross alignment: custom R analysis on toptags result for I vs C comparison
Genome_build: hg19_mm10 combined genome consisting of all human and mouse chromosomes
Supplementary_files_format_and_content: MSC_Hoogduijn_allsamples_gene_counts.txt: tab separated text file, one gene per line, one column per sample
Supplementary_files_format_and_content: toptags*txt: tab separated text file, with toptags listing as produced by R/edgeR. 5 columns: logFC, logCPM, LR, Pvalue, FDR. Data lines have geneID as rowIDs. Header line has one column less than data lines, as is customary for R write.table()

source_name: Lung tissue

growth_protocol: MSC were isolated from adipose tissue and expanded to passage 3 in alpha minimal essential medium with 15% foetal calf serum and 1% p/s

extract_protocol:
mRNA was isolated by Trizol reagent
Illumina TruSeq RNA

tag: sample type

value: negative control


title: ExposedNic_16M


title: ExposedNic_15M


title: Control39M_1

description: Filtered Air Controls


title: ExposedNic_17M


title: Control37M_1

description: Filtered Air Controls


title: Control38M_1

description: Filtered Air Controls


title: Control30M_1

description: Filtered Air Controls


title: GRO-seq - mES - 12hr KD, Control ASO rep2

city: Stanford

institute: Stanford University

description:
nascent RNA
processed data file: mm9_GRO-seq_12hrControlASO_pos.bw, mm9_GRO-seq_12hrControlASO_neg.bw

data_processing:
Library strategy: GRO-Seq
After demultiplexing, reads were stripped adaptors, mapped to a custon index of repetitive RNAs (PMID: 25411354), mapped to the mouse (mm9) genome using Bowtie2, and processed as previously described (PMID: 24843027)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of merged biological replicates split for positive and negative strand reads of GRO-seq read density

growth_protocol: mESCs were grown on gelatin plates with serum and LIF.

extract_protocol:
Nuclei were isolated and run-on reactions performed as described previously (PMID: 24843027).
Run-on RNA (labeled with BrU) was isolated as previously described (PMID: 24843027) and deep sequencing libraries generated.

treatment_protocol: Cells were depleted of 7SK by nucleofecting antisense oligonucleotides for either 6 or 12 hours.

value: ES cells

tag: cell line

tag: gender

value: male


title: GRO-seq - mES - 12hr KD, Control ASO rep1