title: 3NCRNApol2

city: St Louis

first: Tiandao

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
Raw sequences generated from Illumina/Solexa sequencer were aligned using ELAND software to UCSC mm10 of the mouse genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 250 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format.
Genome_build: mm10
Supplementary_files_format_and_content: wig files

source_name: Neu-positive mouse mammary tumor

growth_protocol: Neu-positive mouse mammary tumor were harvested and made into a single cell suspension. The cell line was grown in appropriate medium at 37°C in a humidified 5% CO2 incubator.

extract_protocol: One hundred million cells were cross-linked for 10 min at 37°C using 0.7% formaldehyde, 0.125 M glycine. Cells were washed twice with PBS, re-suspended in lysis buffer and incubated for 5 minutes. Cells were collected by centrifugation and cell pellets were frozen in liquid nitrogen and stored at minus 80°C. Cell pellets were thawed in lysis buffer, collected by centrifugation and cell nuclei were re-suspended in RIPA buffer. Chromatin was sonicated using conditions determined empirically for MCF-7 cells to achieve an optimal fragment length between 100 to 400 bp. After sonication, samples were centrifuged at 20,000 × g for 10 min at 4°C. The supernatant containing cross-linked DNA/histones was diluted with IP dilution buffer to 2 mg/ml. The sample was immunoprecipitated with 10 μg of TFAP2A with the addition of Dynal sheep anti-mouse Dynabeads and allowed to recognize their antigens overnight at 4°C with rotation. Protein/antibody/DNA complexes were collected magnetically followed by washing and elution. Protein/DNA cross-links were reversed using 200 mmol/L NaCl at 65°C overnight. DNA was treated with Proteinase K and RNase A and was recovered with QIAquick PCR Kit (Qiagen) according to manufacturer's suggested protocol. Purified DNA was quantified by using a NanoDrop ND-1000 (NanoDrop, Wilmington, DE). 100 ng of ChIPed DNA was end-repaired, followed by the addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing.

tag: antibody source

value: Millipore 05-623-Z

value: mammary tumor


title: RBL67_mono_1

status: Public on Mar 31 2015

type: SRA

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

library_source: transcriptomic

data_processing:
Illumina raw data reads (100 bp) were separated by barcode and mapped against the genome of RBL67 (GenBank accession no. CP004346) or Salmonella Typhimurium LT2 (GenBank accession no. AE006468) using CLC Genomics Workbench 6.5.1 (http://www.clcbio.com), applying the default settings. Maximum allowance of mismatches was set at 2, minimum length fraction at 0.9 and minimum similarity fraction at 0.8. The raw data provided are the total counts per gene, not normalized against gene length or library size.
Genome_build: CP004346 (ASM34769v1) and AE006468 (ASM694v1)
Supplementary_files_format_and_content: The processed data files contain a table with in the first column the locus_tag of the gene as it is stored in NCBI Genbank (<locus_tag>), in the second and third column the position on the chromosome(<start><stop>), in the fourth column the strand (<strand>), in the fifth column the length of the encoded protein in amino acids (<length (AA)>), and the sixth column the protein ID as it is stored in the NCBI databases (<ProteinID>). The last column contains the total counts resulting from the RNA mapping (<Total count>).

molecule: total RNA

organism: Bifidobacterium thermophilum

source_name: B. thermophilum RBL67 mono culture

growth_protocol: Two sets of fermentations were performed, each set consisting of six fermentations. The first set was composed of three RBL67 mono-cultures and three RBL67-N15 co-cultures. The second set consisted of three N-15 mono-cultures and three N-15-RBL67 co-cultures. Bacteria were cultured in 350 mL scale Sixfors bioreactors (Infors AG, Bottmingen, Switzerland) using 310 mL YCFA medium  supplemented with 6 g/L glucose (Sigma-Aldrich Chemie GmbH, Buchs, Switzerland). Fermentations were performed for 24 h at 38°C with stirring at 200 rpm. A constant pH of 6.0 was maintained by automated addition of 2.5 M NaOH. Anaerobic conditions were ensured by purging the headspace with CO2. Both, mono- and co-culture fermentations were inoculated with 4 % (v/v) of a 16 h grown pre-culture. Pre-cultures were prepared by twice propagating RBL67 and N-15 in 10 mL YCFA medium in Hungate tubes to adapt the strains to the medium and anaerobic conditions. The pre-cultures were centrifuged (6000 x g, 5 min), washed in 0.1 % peptone water reduced with 0.05 % L-cysteine hydrochloride (VWR International AG, Dietikon, Switzerland) and resuspended in 2 mL peptone water before inoculation to the fermenter.

extract_protocol:
RNA was extracted from culture samples taken after 5 h (N-15) or 5 h (RBL67) for mono-and co-cultures. RBL67 and N-15 mono- and co-culture samples were subjected to different procedures to allow optimal RNA extraction of both RBL67 and N-15. Mono- and co-culture samples of N-15 cultures (20 mL each) were directly transferred to 20 mL 60 % glycerol (Sigma-Aldrich Chemie GmbH, Buchs, Switzerland) at -40°C, kept on ice for 20 min and centrifuged for 15 min (3220 x g, 4°C). The supernatant was discarded and the resulting pellets were immediately frozen at -80°C until RNA extraction. Mono- and co-culture samples of RBL67 cultures were shortly centrifuged (10000 x g, 20 s). The RBL67 mono-culture pellets were resuspended in 400 μl MRS-C and transferred to a pre-chilled screw cap tube, containing 500 mg glass beads (0.1 mm; Biospec Products Inc., Bartlesville, USA), 500 μl chloroform/phenol (1:1, v/v), 30 μl 3 M Na-acetate (pH 5.2) and 30 μl SDS 10 %. The pellet of the RBL67 co-culture was resuspended in 12 mL of RNAprotect® Bacteria Reagent (Qiagen AG, Basel, Switzerland), incubated for 5 min at room temperature and centrifuged again (10000 x g, 20 s). Both samples were then rapidly frozen in liquid nitrogen and stored at -80°C until RNA extraction. Frozen pellets from N-15 samples were resuspended in 200 μl 10 mM Tris-buffer (pH 8.0). Total RNA was extracted using the High Pure RNA isolation kit (Roche Diagnostics, Rotkreuz, Switzerland), according to the manufacturer’s instructions. Total RNA of RBL67 mono- and co-culture samples was extracted using a phenol/chloroform extraction method, followed by a purification using the High Pure RNA isolation kit (Roche Diagnostics). Prior to RNA extraction the sample from the RBL67 co-culture was resuspended in MRS-C medium and transferred to a pre-chilled mix of 500 mg glass beads (Biospec Products Inc.) and TRI Reagent® (Life Technologies Europe BV, Zug, Switzerland). RNA quantity and purity was determined on a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, Washington, USA) and RNA integrity was tested with an Agilent 2100 Bioanalyzer (Agilent, Basel, Switzerland). Depletion of ribosomal RNA from 10 μg total RNA was performed using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Life Technologies Europe BV, Zug, Switzerland) according to the manufacturer’s instructions. Additionally, EDTA (1 mM) was added to chelate divalent cations present in the RNA solution.
RNA-sequencing was performed on an Illumina HiSeq 2000 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v3-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 100 bp was done using the TruSeq SBS Kit v3-HS (Illumina). Each set of samples (n=6) was analyzed in a separate sequencing lane.

tag: strain

tag: fermentation

value: RBL67 mono-culture


title: RBL67_co_1

source_name: B. thermophilum RBL67 -S. Typhimurium N-15 co-culture

value: RBL67-N15 co-culture


title: N15_co_3

organism: Salmonella enterica subsp. enterica serovar Typhimurium

value: N15-RBL67 co-culture


title: 1NCAP2C

status: Public on Apr 01 2015

last: Li

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: antibody

value: Millipore 05-909

tag: tissue


title: ArgR (-arg) rep1 and rep2

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description: ChIP-exo

data_processing:
Basecalls performed using CASAVA version 1.4
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
To capture target protein binding sites corresponding genomic position of mapped reads start position (MRSP) was counted and stored for visual inspection using in-house scripts.
Supplementary_files_format_and_content: gff file is generated by in-house script

organism: Escherichia coli str. K-12 substr. MG1655

source_name: ArgR (-arg) rep1 and rep2

growth_protocol: All strains used are E. coli K-12 MG1655 and its derivatives. Glycerol stock of the E. coli strain was inoculated into 3 mL Luria broth supplemented with 150 μg kanamycin and cultured overnight at 37°C with constant agitation.

extract_protocol:
Cultured cells (50 mL) were cross-linked with 1% formaldehyde at room temperature for 30 min and added 2 mL of 2.5M glycine to quench the unused formaldehyde. After washing  three times with 50 mL of ice-cold Tris-buffered saline (TBS), the washed cells were resuspended in 0.5 mL of lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 μg/mL RNaseA, protease inhibitor cocktail and 1 kU Ready-Lyse lysozyme (Epicentre, Madison, WI) and incubated at 37oC for 30 min. The cells were then treated with 0.5 mL of 2×IP buffer (100 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 2%(v/v) Triton X-100, and protease inhibitor cocktail), followed by incubation on ice for 30 min. The lysate was then sonicated in an ice bath using Sonic Dismembrator Model 500 (four times for 20 s each, output level, 2.5). Size distribution of the fragmented DNAs was confirmed using agarose gel electrophoresis (200-400 bp) after removing cell debris by centrifugation.
The cross-linked DNA-ArgR complexes in the supernatant were then immunoprecipitated by adding 10 µL of Anti-myc (9E10) (Santa Cruz, Dallas, TX). For mock-IP control, 2 µg of normal mouse IgG (Santa Cruz) was added into the supernatant in parallel. They were then incubated overnight at 4oC with constant rotation. The cross-linked DNA-protein and antibody complexes were selectively captured by adding 50 µL of Dynabeads Pan Mouse IgG magnetic beads (Invitrogen, Grand Island, NY). Then, DNAs were end-polished using T4 DNA polymerase (NEB, Ipswich, MA), ligated with the annealed adaptor 1 (5’- Phospho-AACTGCCCCGGGTTGCTCTTCCGATCT and 5’- OH-AGATCGGAAGAGC-OH), nick-repaired using phi29 polymerase (NEB), and digested with λ exonuclease (NEB) as reported previously. Then, protein-DNA complexes were reverse-cross-linked by heating at 65°C overnight and proteins were degraded by 8 µg of protease K (Invitrogen). The purified DNAs were denatured at 95°C and extended by P1 primer (5’-OH-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT), further ligated with the annealed adaptor 2 (5’-OH-ACACTCTTTCCCTACACGACGCTCTTCCGATCT and 5’-OH-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG). The ligated DNA products were purified using Qiagen PCR purification kit and were PCR-amplified by P2 primer (5’-OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and P3 primer (5’-OH-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT). The degenerative sequence (the underlined 6Ns) in the P3 primer indicates the index sequence for the Illumina next-generation sequencing (Illumina, San Diego, CA). The PCR-amplified DNA products were then loaded onto 2% agarose gel and extracted using QIAquick gel purification columns.

treatment_protocol: The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh M9 medium containing 2 g/L glucose in either the presence or absence of 1 g/L arginine and continued to culture at 37°C until reaching an appropriate cell density (OD600 ≈ 0.5).

tag: chip antibody

tag: substrain


title: RBL67_mono_2


title: N15_co_2


title: RBL67_mono_3


title: RBL67_co_3


title: N15_mono_3

source_name: S. Typhimurium N-15 mono culture

value: N-15 mono-culture


title: N15_co_1


title: N15_mono_1


title: M376-Yers-4

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
We mapped the short reads to the human genome (hg19) using Subread (default parameters).
We obtained the read counts for each Ensembl protein-coding gene (biotype: “protein_coding”) with featureCounts, which sums the reads falling in the union of all exons of a gene and discards reads mapping to more than one gene (default parameters, except that we provided the Ensembl annotation file as described).
We removed genes with fewer than one count per million exonic reads in fewer than six samples.
We normalized the samples using the weighted trimmed mean of M-values algorithm (TMM) in edgeR.
We converted the counts to log counts per million using the cpm function in edgeR (default parameters).
We removed the effect of RNA quality (RIN) score and extraction batch using removeBatchEffect from limma.
Genome_build: hg19
Supplementary_files_format_and_content: table-s1.txt is a tab-delimited text file that contains the batch-corrected log2 counts per million for each of the 156 samples, as well as the Ensembl gene ID and gene name.

organism: Homo sapiens

source_name: monocyte-derived macrophages

growth_protocol: First, we collected buffy coats (~50 mL). Next we isolated peripheral blood mononuclear cells (PBMCs) via Ficoll-Paque centrifugation nd enriched for monocytes via positive selection with beads containing CD14 antibodies. Then we differentiated the monocytes into macrophages by culturing for 6-7 days in RPMI buffer supplemented with macrophage colony-stimulating factor (M-CSF).

extract_protocol:
We extracted RNA using the QIAgen miRNeasy kit. There were a total of 13 batches of 12 samples each (6 individuals x 9 conditions x 3 timepoints, minus 48 hours post-infection with Staphylococcus epidermidis). We designed the batches to maximally partition the variables of interest (individual, condition, timepoint) in order to minimize the introduction of biases due to batch processing.
In batches of 12 samples (the same 13 from the extraction protocol), we added barcoded adapters (Illumina TruSeq RNA Sample Preparation Kit v2)

treatment_protocol: For each bacterial infection, we treated the macrophages with a multiplicity of infection (MOI) of 2:1. After one hour, we washed the macrophages five times with phosphate-buffered saline (PBS) and treated them with gentamycin (50 µg/µL) to kill all extracellular bacteria. After one hour of antibiotic treatment, we changed the medium to a lower concentration of gentamycin (5 µg/µL), which marked the zero timepoint of the study. We allowed the cells to grow for 4, 18, or 48 hours before lysing them before lysing them with QIAzol Lysis Reagent and then storing them at -80° C.

tag: individual

tag: agent

value: Yers

tag: time point

tag: batch

tag: rin


title: ArgR (+arg) rep1 and rep2

description: ChIP-exo

source_name: ArgR (+arg) rep1 and rep2

value: Anti-myc (9E10) (Santa Cruz, Dallas, TX)


title: M373-Smeg-4

value: Smeg


title: RBL67_co_2


title: M373-GC-48

value: GC


title: M373-Rv-4

value: Rv


title: M372-Rv+-18

value: Rv+


title: M375-Rv-4


title: M377-Smeg-4


title: M375-GC-48


title: M376-Yers-18


title: M374-Yers-18


title: M373-BCG-18

value: BCG


title: M375-BCG-18


title: M374-Salm-18

value: Salm


title: M373-BCG-4


title: M376-Yers-48


title: M375-Salm-18


title: M376-Rv+-18


title: M374-Yers-48


title: M375-Rv-48


title: N15_mono_2


title: M374-Rv+-18


title: M377-none-4


title: M377-GC-4


title: M374-Smeg-18


title: M373-GC-4


title: M372-Salm-48


title: M372-Yers-4


title: M376-Smeg-18


title: M375-Yers-4


title: M373-none-4


title: M377-Salm-48


title: M373-Yers-4


title: M376-Rv-48


title: M375-Rv+-18


title: M372-Rv+-4


title: M375-GC-4


title: M374-none-18


title: M376-BCG-4


title: M373-Rv-48


title: M377-Smeg-48


title: M372-Rv-18


title: M376-Rv+-4


title: M374-GC-4


title: M377-none-18


title: M377-Rv-18


title: M376-none-18


title: M374-Rv+-48


title: M375-Smeg-18


title: M377-BCG-4


title: M374-BCG-18


title: M373-Smeg-18


title: M374-Rv-48


title: M374-Salm-48


title: M372-none-18


title: M374-Smeg-48


title: M375-Rv+-48


title: M376-Salm-48


title: M376-Staph-4

value: Staph


title: M374-BCG-4


title: M372-Staph-4


title: M377-none-48


title: M376-Smeg-48


title: M374-Staph-18


title: M375-GC-18


title: M376-Staph-18


title: M374-GC-18


title: M375-Salm-4


title: M377-BCG-18


title: M372-Salm-4


title: M372-Rv-4


title: M377-Rv-4


title: M373-Smeg-48


title: M375-BCG-48


title: M373-BCG-48


title: M376-none-4


title: M377-Yers-48


title: M373-Rv+-18


title: M376-Salm-18


title: M375-Smeg-4


title: M373-none-48


title: M372-Smeg-4


title: M377-Rv+-18


title: M372-Yers-48


title: M372-Salm-18


title: Evo_0min_1

city: Jena

first: Fabian

last: Horn

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI)

data_processing:
FASTQ files were received from GATC, Konstanz, Germany
Sequenced reads were trimmed for low-quality regions (btrim windowsize 15 average  phredscore20)
Mapping of read pairs using TopHat (v2.0.6; -G GFF from Candida Genome Database (CGDB http://www.candidagenome.org/); -maxintronlength 10000)
Read counting using htseq-count (-mode union, -s no, -type CDS)
Calculation of RPKM values using raw counts, sum of totally mapped reads and sum of CDS length using CGDB GFF file
For SNP calling mapping of trimmed reads with BWA,  removal of duplicates, realignment arround INDELs, counting of bases with bamreadcount
Genome_build: Candida albicans SC5314 (http://www.candidagenome.org/)
Supplementary_files_format_and_content: rpkm

organism: Candida albicans

source_name: yeast

growth_protocol: C. albicans was grown in YPD medium at 30°C and 180 rpm for 14-16 h.

extract_protocol:
1x107 cells of the log-phase cultures were collected by centrifugation and frozen in liquid nitrogen until RNA extraction. After incubation under filament-inducing condition, medium and non-adherent cells were removed and 5 ml ice-cold PBS was added. The cells were collected by scraping and then centrifuged for 5 min at 6,000 rpm and 4°C. Cell pellets were snap frozen in liquid nitrogen. Total RNA was isolated using the Ribopure-Yeast Kit (Ambion) and treated with Turbo DNase (Ambion). RNA quality was determined in a Bioanalyzer with an RNA 6000 Nano LabChip Kit (Agilent Technologies) according to the manufacturer's protocol. RNA concentration was determined with a Nanodrop ND1000 (Peqlab)
tagged random primed cDNA libraries were prepared from fragmented polyA-RNA using standard illumina protocols

treatment_protocol: For yeast promoting condition, cells were grown in YPD medium at 30°C and 180 rpm for 4 h (=0 min time point). 1x107 cells of the log-phase cultures were incubated for 75 min under filament-inducing conditions (DMEM + 10% FBS at 37°C and 5% CO2 in a 75 cm2 cell culture flask).

tag: genotype

tag: time

value: 4 h

tag: medium

value: YPD

tag: incubation

value: air, 30°C, 180 rpm


title: Evo_75min_3

source_name: germ tube

value: 75 min

value: 5% CO2, 37°C, static


title: Evo_0min_4


title: Evo_75min_1


title: cph1/efg1_0min_3


title: cph1/efg1_75min_1


title: cph1/efg1_75min_3


title: cph1/efg1_0min_4


title: Evo_0min_3


title: cph1/efg1_75min_4


title: cph1/efg1_0min_1


title: M374-none-4


title: M375-none-48


title: M373-Rv+-4


title: wild type

city: shanghai

first: Gang

last: Wang

state: Shanghai

address: No. 333 of Nanchen Road

department: College of Life Science

country: China

institute: Shanghai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl plants release‐15 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: seedling

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: seedling

tag: age

value: 14 DAG

value: wild type


title: pro1 mutant


title: Evo_75min_4


title: M372-none-48


title: M372-Staph-18


title: Library_189

city: Newark

first: Carl

middle: Joseph

last: Schmidt

state: De

address: 531 S. College Ave.

department: Animal and Food Sciences

institute: University of Delaware

data_processing:
CASAVA
Erange for RNA-SEQ alignment and qualitation
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: galGal3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Gallus gallus

source_name: Pectoralis Major

extract_protocol:
Pectoralis major tissue was removed, flash frozen in liquid nitrogen, and RNA was harvested using the Qiagen RNeasy Fibrous Tissue Mini Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: Illinois

value: post-hatch D21

value: skeletal muscle


title: Library_191


title: Library_190


title: M374-GC-48

value: GC


title: Library_186


title: Library_183


title: Library_184


title: M373-Salm-4


title: Library_182


title: M377-Staph-18


title: M376-GC-48


title: Library_181


title: M374-Rv-18

value: Rv


title: Library_162

value: post-hatch D6


title: Library_164


title: Library_179


title: Library_161


title: M376-Salm-4


title: M377-Rv+-4

value: Rv+


title: Library_187


title: Library_160


title: Library_163


title: M372-BCG-48

value: BCG


title: Library_159


title: Library_155


title: M374-Rv+-4


title: Library_156


title: Library_157


title: Library_154


title: M377-Rv-48


title: M375-none-18


title: Library_152


title: Library_153


title: M372-GC-18


title: M373-none-18


title: M375-Rv-18


title: M372-Rv-48


title: Library_180


title: Sth1 degron nucleosome

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

data_processing:
De-multiplexed Fastq files from the Illumina pipeline were aligned to the Saccharomyces cerevisiae genome release 64 (UCSC SacCer3) using Novoalign version 2.8 (http://www.novocraft.com), allowing for one random repeat, base recalibration, and a minimum alignment quality score of 13. Alignments were converted to sorted, indexed Bam files using samtools. Separate sequence lanes from the same sample were merged using samtools.
Proper paired-end alignments were filtered for an insert size of 99-195 bp using the BioToolBox (http://code.google.com/p/biotoolbox/) extra program split_bam_by_isize, using the --at option. Midpoint and fragment coverage normalized maps were generated using the BioToolBox program bam2wig using the --pos option of mid and span, respectively, combined with the options --pe and --rpm. Wig files were converted to bigWig files using UCSC utilities.
Difference maps were calculated using the MACS2 (http://pypi.python.org/pypi/MACS2) bdgcmp mode. High level gene analysis was performed using BioToolBox programs get_datasets and get_relative_data.
Genome_build: SacCer3
Supplementary_files_format_and_content: Nucleosome coverage spanning paired-ends of filtered bam alignments, normalized to fragments per million mapped.

organism: Saccharomyces cerevisiae

source_name: MNase-digested mononucleosome

growth_protocol: Yeast cultures were grown in 100 ml SC -ura media with 1% raffinose and 50 mM CuSO4 at 27C with agitation until optical density of 0.8. Galactose was added to the media to 1% final concentration to induce UBR1 expression. After 1 hour of induction, the incubator was shifted to 37C to induce Sth1 protein degradation. After 2 hours of high temperature, cells were harvested. Cells were crosslinked for 5 minutes by addition of formaldehyde to 1% final concentration in the media and quenched by the addition of 1M glycine to 0.1M final concentration. Cells were harvested by centrifugation and washed twice with Tris-Buffered Saline. Cells were stored at -80C until preparation.

extract_protocol:
Cells (equivalent to 50 ml culture) were suspended in spheroplasting solution (1M sorbitol, 10 mM Tris pH 7.5, 10 mM 2-MercaptoEthanol, protease inhibitors) and incubated with prepared zymolyase (Sigma) at 37C until the optical density of a 1:100 dilution in 1% SDS dropped to 0.01. Spheroplasts were gently harvested by low-speed centrifugation and stored on ice until ready. Spheroplasts were resuspended with MNase Digestion buffer (50 mM Tris pH 7.5, 100 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.1% Triton X-100) and digested with MNase at 37C for 25 minutes. The amount of MNase was empirically determined to yield an estimated 60% mono-, 30% di-, and 10% tri-nucleosomes. MNase digestion was stopped by the addition of 0.1X volumes of stop solution (250 mM EDTA. 5% SDS). Proteinase K was added to the samples, incubated at 37C for 2 hours, and then 65C overnight to reverse cross links. Protein was precipitated from the samples by addition of 8M potassium acetate to 1.2M final concentration, cooling on ice, and centrifugation. DNA was recovered by ethanol precipitation. Mononucleosome DNA was isolated by RNAase treatment, electrophoresis on a 1.2% agarose gel, excision, and purification with a Qiagen Gel Extraction Kit.
Mononucleosome DNA was phosphorylated with T4 kinase (NEB) prior to ligation of adaptors using Illumina Tru-Seq library construction kit according to manufacturers instructions. No other end repair was performed (fill-in, etc). After limited PCR amplification, samples were size selected on agarose gel and fragments corresponding to mononucleosomes were excised and purified.

tag: strain

tag: genotype/variation

value: Sth1td pGal-UBR1


title: Sth1 control nucleosome

value: Sth1td ubr1-null


title: M376-GC-18


title: M374-Staph-4

value: Staph


title: Snf2 ChIP

description:
Snf2 ChIP
8378X8

data_processing:
De-multiplexed Fastq files from the Illumina pipeline were aligned to the Saccharomyces cerevisiae genome release 64 (UCSC SacCer3) using Novoalign version 2.8 (http://www.novocraft.com), allowing for one random repeat, base recalibration, and a minimum alignment quality score of 13. Alignments were converted to sorted, indexed Bam files using samtools.
Proper paired-end alignments were filtered for an insert size of 99-195 bp using the BioToolBox (http://code.google.com/p/biotoolbox/) extra program split_bam_by_isize, using the --at option. Midpoint and fragment coverage normalized maps were generated using the BioToolBox program bam2wig using the --pos option of mid and span, respectively, combined with the options --pe and --rpm. Wig files were converted to bigWig files using UCSC utilities.
ChIP enrichment was calculated using MACS2 (http://pypi.python.org/pypi/MACS2) with the callpeak mode options '--keep-dup all --shift-control -g 12.1e6 --slocal 0 --llocal 0'. Tracks representing QValue FDR scores and Fold Enrichment were generated with the MACS2 bdgcmp mode. High level gene analysis was performed using BioToolBox programs get_datasets and get_relative_data.
Genome_build: SacCer3
Supplementary_files_format_and_content: Log2 Fold Enrichment of ChIP over Input as generated by MACS2

source_name: Immunoprecipitated chromatin

growth_protocol: Cells were grown in standard synthetic complete media with 2% glucose at 30C until an optical density at 600 nm of 1.0. Cells were cross-linked by addition of formaldehyde to the media to 1% final concentration for 30 minutes and quenched by the addition of 1M glycine to 0.1M final concentration. Cells were harvested by centrifugation and washed twice with Tris-Buffered Saline. Cells were stored at -80C until preparation.

extract_protocol:
Cells were lysed by resuspending the cells in lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, protease inhibitors) and bead beating with 0.7 mm zirconium beads for six rounds of 2 minutes, interspersed with cooling on ice. Cells were collected by centrifugation, the supernatant was discarded, and the pellet resuspended in MNase Digestion buffer (50 mM Tris pH 7.5, 100 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.1% Triton X-100). Chromatin was digested with MNase at 37C for 15 minutes. The amount of MNase was empirically determined to yield an estimated 60% mono-, 30% di-, and 10% tri-nucleosomes. MNase digestion was stopped by the addition of 0.1X volumes of 10X MNase ChIP Stop Buffer (50 mM Tris pH 7.5, 500 mM NaCl, 100 mM EDTA, 20 mM EGTA, 10% Triton X-100, 1% sodium deoxycholate). Cell debris was removed by centrifugation and the soluble chromatin was added to prepared beads. For immunoprecipitation, anti-mouse magnetic Dynabeads (Invitrogen) were prepared by incubating with anti-cMyc (9E11) in phosphate-buffered saline containing 5 mg/ml BSA for several hours with rotation. Normalized amounts of protein was then incubated with the prepared beads in ChIP buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate). Immunoprecipitations were performed at 4C overnight with gentle rotation. Beads were harvested by magnetic field and washed twice with ChIP buffer, twice with ChIP buffer supplemented to 500 mM NaCl, twice with LiCl wash buffer (10 mM Tris pH 8, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and once with TE. Captured complexes were eluted and cross-links reversed by incubating the beads in buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5% SDS) at 65C overnight. DNA was purified using Qiagen PCR Clean-up columns using the manufacturer's protocol.
ChIP eluate DNA and Input DNA were phosphorylated with T4 kinase (NEB) prior to ligation of adaptors using Illumina Tru-Seq library construction kit according to manufacturers instructions. No other end repair was performed (fill-in, etc). After limited PCR amplification, samples were size selected on agarose gel and fragments corresponding to mononucleosomes were excised and purified.

value: Anti-c-Myc antibody [9E11]

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: M377-Staph-4


title: Ioc3 ChIP

description:
Ioc3 ChIP
8378X7

tag: chip antibody


title: Sth1 ChIP

description:
Sth1 ChIP
8378X1


title: M375-Rv+-4


title: M376-Smeg-4

value: Smeg


title: Sth1 Input

description:
Sth1 Input
8378X2

source_name: Input chromatin


title: M376-BCG-48


title: M373-Yers-48

value: Yers


title: M372-GC-48


title: M374-Smeg-4


title: M375-BCG-4


title: M372-BCG-4


title: M373-Rv-18


title: M377-Salm-18

value: Salm


title: M377-GC-48


title: M375-Yers-48


title: M376-GC-4


title: M373-Staph-18


title: M372-Smeg-18


title: M377-Smeg-18


title: M374-Salm-4


title: M376-Rv+-48


title: M372-GC-4


title: M375-Salm-48


title: Ioc3 Snf2 Input

description:
Ioc3 Snf2 Input
8378X9


title: M373-Salm-18


title: M372-Rv+-48


title: M373-Salm-48


title: M376-Rv-18


title: M375-Staph-18


title: M376-none-48


title: M373-Staph-4


title: M374-none-48


title: M374-Yers-4


title: M377-Salm-4


title: M375-Yers-18


title: M375-Staph-4


title: Grain_224

city: College Park

first: Jose

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

data_processing:
Illumina HiSeq 2000 sequencer for basecalling
Alignment to the reference genome (Bos_taurus_UMD3.1/bosTau6) obtained from the UCSC (http://genome.ucsc.edu/) was performed employing Bowtie (Ultrafast, memory-efficient short read aligner). During this step, the first 15 bases of each read (50 bp) were trimmed to avoid low Phred quality scores, resulting in 35 bp tags
Counting of reads per gene was executed by the summarizeOverlaps function implemented in R
The identification of differentially expressed genes was achieved employing the edgeR software package and the included generalized linear model (GLM) approach, which requires a design matrix to describe the treatment conditions (grass-fed and grain-fed).
Genome_build: Bos_taurus_UMD3.1/bosTau6
Supplementary_files_format_and_content: RumenCountNormalizededgeR.xls- Normalized reads count per gene using edgeR
Supplementary_files_format_and_content: RumenSigensembl_edgeRGLM.xls- Differentially expressed genes, with statistical measurement obtained from edgeR using GLM approach

organism: Bos taurus

source_name: Ruminal Wall

growth_protocol: The animals were born, raised and maintained at the Wye Angus farm. All animals received the same diet until weaning

extract_protocol:
Total RNA was extracted individually (two animals per group) using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Invitrogen, Carlsbad, CA, USA). The RNA sample was dissolved in RNAse-free H2O; the integrity and quality of RNA were then checked by a NanoDrop 1000 spectrophotometer and by resolution on a 1.5% non-denaturing agarose gel
Each library was identified by adding 6-bp adaptors and sequenced at 50 bp/sequence read using an Illumina HiSeq 2000 sequencer

treatment_protocol: After weaning, the calves were randomly assigned to one diet and exclusively received that regimen until termination. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain

tag: breed

value: Aberdeen Angus

tag: treatment

value: Grain-fed

tag: tissue

value: Ruminal wall


title: Grain_184


title: M376-BCG-18

tag: individual

tag: agent

tag: time point


title: M373-Rv+-48

tag: batch

tag: rin


title: Grass_104

value: Grass-fed


title: M377-Yers-4


title: M372-BCG-18


title: M372-Yers-18


title: Grass_222


title: Glucose time course, 336 hour time point, biological replicate 3, rRNA not depleted

city: Austin

first: Jeffrey

middle: E.

last: Barrick

state: TX

address: 2500 Speedway, Stop A4800

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Trimmed adaptor sequences from reads using Flexbar 2.31
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0
Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq.
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format

organism: Escherichia coli

source_name: REL606_glucose-limited minimal medium_336 hr_rRNA not depleted

growth_protocol: Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter.

extract_protocol:
RNAsnap
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research).

value: 336 hours

tag: molecule subtype

value: total RNA


title: Glucose time course, 48 hour time point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_48 hr_rRNA not depleted

value: 48 hours


title: Glucose time course, 168 hour time point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_168 hr_rRNA not depleted

value: 168 hours


title: Glucose time course, 24 hour time point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_24 hr_rRNA not depleted

value: 24 hours


title: M374-Rv-4

value: Rv


title: M376-Rv-4


title: Glucose time course, 8 hourt ime point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_8 hr_rRNA not depleted

value: 8 hours


title: Glucose time course, 6 hour time point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_6 hr_rRNA not depleted

value: 6 hours


title: M377-BCG-48

value: BCG


title: Glucose time course, 5 hour time point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_5 hr_rRNA not depleted

value: 5 hours


title: M373-Yers-18

source_name: monocyte-derived macrophages


title: M372-Smeg-48

value: Smeg


title: Glucose time course, 336 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_336 hr

extract_protocol:
RNAsnap followed by RiboZero rRNA removal kit for gram-negative bacteria (Epicentre)
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research).

value: rRNA-depleted total RNA


title: Glucose time course, 168 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_168 hr


title: M375-none-4


title: Glucose time course, 4 hour time point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_4 hr_rRNA not depleted

value: 4 hours


title: M374-BCG-48


title: Glucose time course, 48 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_48 hr


title: M373-GC-18

value: GC


title: Glucose time course, 24 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_24 hr


title: M375-Smeg-48


title: M372-none-4


title: Glucose time course, 8 hourt ime point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_8 hr


title: Glucose time course, 5 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_5 hr


title: Glucose time course, 3 hour time point, biological replicate 3, rRNA not depleted

source_name: REL606_glucose-limited minimal medium_3 hr_rRNA not depleted

value: 3 hours


title: Glucose time course, 3 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_3 hr


title: GTtoH_H3K27ac

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq:  Illumina's HiSeq Control Software
Each fastq file was mapped to human genome (hg18) with Bowtie. We allow up to 2 mismatches. The mapping results for two biological replicates were merged for downstream analysis. To generate the wig file, we first extended each read to 300 bp along 5' end. We then cut the genome into 100 bp bins and count how many reads fall into each bin. Finally, the wig files were converted to bigwig by using the wigToBigwig software.
Genome_build: hg18
Supplementary_files_format_and_content: To generate the wig file, we extend each read to 300 bp.

source_name: Hepatic endoderm

growth_protocol: hESC media was comprised of DMEM/F12 (Mediatech or Life Technologies) supplemented with 10% (vol/vol) KnockOut™ Serum Replacement XenoFree (Life Technologies), 0.1 mM MEM non-essential amino acids (Life Technologies), 1X GlutaMAX™ I (Life Technologies), 1% (vol/vol) penicillin/streptomycin (Life Technologies), 0.1mM 2-mercaptoethanol (Life Technologies), 10 ng/ml Activin A (R&D Systems), and 10 ng/ml Heregulin-β1  (PeproTech).

extract_protocol:
ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).
Libraries were prepared according to Illumina's instruction or cited literatures.

treatment_protocol: Pancreatic differentiation was performed as previously described (D'Amour et al., 2006; Kroon et al., 2008; Schulz et al., 2012). Gut tube derived hepatic endoderm was derived by treating the primtive gut tube stage (Day 5),with 50ng/ml BMP4 (Millipore) and 10ng/ml FGF2 (Millipore) in RPMI media (Mediatech) supplemented with 0.2% (vol/vol) FBS (HyClone) with daily feeding for three days. Suspension culture was used.

tag: cell line

tag: cell types

value: gut tube derived hepatic endoderm

value: Active motif


title: Glucose time course, 6 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_6 hr


title: Glucose time course, 168 hour time point, biological replicate 2


title: ES_D10_FOXA1

source_name: Pancreatic endoderm

value: hESC derived pancreatic endoderm

value: Abcam


title: ES_D7_FOXA2

source_name: Posterior foregut

value: hESC derived posterior foregut

value: Santa Cruz


title: ES_D5_FOXA2

source_name: Primitive gut tube

value: hESC derived primitive gut tube


title: M377-Rv+-48

value: Rv+


title: ES_D10_FOXA2


title: Glucose time course, 48 hour time point, biological replicate 2

value: 48 hours


title: ES_D2_FOXA2

source_name: Definitive Endoderm

value: hESC derived definitive endoderm


title: M377-GC-18


title: ES_D2_FOXA1


title: Glucose time course, 336 hour time point, biological replicate 2

value: 336 hours


title: Glucose time course, 5 hour time point, biological replicate 2

value: 5 hours


title: Glucose time course, 8 hour time point, biological replicate 2

value: 8 hours


title: Glucose time course, 4 hour time point, biological replicate 3

source_name: REL606_glucose-limited minimal medium_4 hr

value: rRNA-depleted total RNA


title: GTtoH_input


title: ES_D5_FOXA1


title: Glucose time course, 6 hour time point, biological replicate 2

value: 6 hours


title: Glucose time course, 3 hour time point, biological replicate 2


title: Glucose time course, 24 hour time point, biological replicate 2

value: 24 hours


title: Islet_input

data_processing:
fastq:  Illumina's HiSeq Control Software
Each fastq file was mapped to human genome (hg18) with Bowtie. We allow up to 2 mismatches. The mapping results for two biological replicates were merged for downstream analysis. To generate the wig file, we first extended each read to 300 bp along 5' end. We then cut the genome into 100 bp bins and count how many reads fall into each bin. Finally, the wig files were converted to bigwig by using the wigToBigwig software
Genome_build: hg18
Supplementary_files_format_and_content: Experiments with two biological replicates were merged first. To generate the wig file, we extend each read to 300 bp. In cases of merged replicates, the wig data is linked to the first replicate (rep1).

source_name: Islet

treatment_protocol: Pancreatic differentiation was performed as previously described (D'Amour et al., 2006; Kroon et al., 2008; Schulz et al., 2012). Hepatic endoderm was derived by treating the definitive endoderm stage (Day 2),with 50ng/ml BMP4 (Millipore) and 10ng/ml FGF2 (Millipore) in RPMI media (Mediatech) supplemented with 0.2% (vol/vol) FBS (HyClone) with daily feeding for six days. Suspension culture was used.

value: IIDP/donor 790

value: Cadaveric Islet

tag: antibody


title: Islet_H3K27ac

value: H3K27ac, Activemotif 39133


title: Glucose time course, 4 hour time point, biological replicate 2

tag: strain

value: 4 hours


title: Glucose time course, 168 hour time point, biological replicate 1

value: 168 hours


title: ES_D7_FOXA1

value: hESC derived posterior foregut

value: Abcam


title: PDX1_chip

value: hESC derived pancreatic endoderm

value: PDX1, BCBC goat anti-PDX1


title: Glucose time course, 24 hour time point, biological replicate 1


title: Glucose time course, 5 hour time point, biological replicate 1


title: Glucose time course, 48 hour time point, biological replicate 1

value: 48 hours


title: PDX1_input


title: PE-shPDX1

description: hES-derived PE transduced with lentivirus conatining shRNA targeting Pdx1


title: PE-shSCRAM

description: hES-derived PE transduced with lentivirus containing scrambled shRNA controls


title: Glucose time course, 8 hour time point, biological replicate 1


title: ES_D10_Input_rep2


title: Glucose time course, 6 hour time point, biological replicate 1


title: ES_D10_GRO_seq

data_processing:
Library strategy: GRO-Seq
fastq:  Illumina's HiSeq Control Software
Each fastq file was mapped to human genome (hg18) with Bowtie. We allow up to 2 mismatches. The mapping results for two biological replicates were merged for downstream analysis. To generate the wig file, we first extended each read to 300 bp along 5' end. We then cut the genome into 100 bp bins and count how many reads fall into each bin. Finally, the wig files were converted to bigwig by using the wigToBigwig software
Genome_build: hg18
Supplementary_files_format_and_content: Experiments with two biological replicates were merged first. To generate the wig file, we extend each read to 300 bp. In cases of merged replicates, the wig data is linked to the first replicate (rep1).


title: ES_D10_H3K4me1_rep2

value: H3K4me1, Abcam ab8895


title: ES_D10_H3K4me1_rep1


title: ES_D10_H3K27ac_rep2


title: ES_D10_Input_rep1


title: HE_H3K27ac

value: hESC derived hepatic endoderm


title: HCC_362T

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

institute: astrazeneca

data_processing:
Illumina HiSeq Control Software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by illumina HiSeq Analysis Software
Raw fastq data was mapped to human genome(Human.B37) and transcriptome(Gene model:RefGene) by ArrayStudiuo V7.0
Sequenced Fragments Per Kilobase of exon per Million fragments mapped to human genome (FPKM) were calculated using ArrayStudiuo V7.0. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Human NCBI genome build 37 and Gene model:RefGene
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample.

source_name: hepatocyte

extract_protocol:
Total RNA were extracted from the snap-frozen HCC or adjacent normal liver tissues.  25 ug total RNA prepared for sequencing for each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tumor status

value: Tumor

tag: age

tag: gender

value: M

value: liver


title: HCC_363T


title: HCC_361T


title: HE_input


title: ES_D10_H3K27ac_rep1


title: HCC_360T


title: Glucose time course, 4 hour time point, biological replicate 1

value: rRNA-depleted total RNA


title: ES_D7_GRO_seq


title: ES_D7_Input_rep2


title: HCC_359T

value: F


title: ES_D7_H3K4me1_rep2


title: HCC_358T


title: HCC_357T


title: HCC_356T


title: ES_D7_H3K27ac_rep2


title: ES_D7_H3K27ac_rep1


title: HCC_353T


title: HCC_354T


title: Glucose time course, 3 hour time point, biological replicate 1

value: 3 hours


title: ES_D7_H3K4me1_rep1


title: ES_D5_Input_rep2

value: hESC derived primitive gut tube


title: ES_D5_GRO_seq


title: HCC_352T


title: HCC_350T


title: HCC_351T


title: ES_D5_H3K27ac_rep1

value: H3K27ac, Activemotif 39133


title: HCC_346T


title: HCC_347T


title: ES_D2_GRO_seq

source_name: Definitive endoderm

value: hESC derived definitive endoderm


title: HCC_345T


title: ES_D2_Input_rep2


title: HCC_349T


title: M377-Yers-18

source_name: monocyte-derived macrophages

value: Yers


title: ES_D5_H3K27ac_rep2


title: ES_D5_H3K4me1_rep1


title: ES_D7_Input_rep1

value: hESC derived posterior foregut


title: HCC_342T


title: HCC_355T


title: ES_D2_H3K4me1_rep1


title: HCC_348T


title: HCC_339T


title: HCC_337T


title: ES_D5_H3K4me1_rep2


title: ES_D5_Input_rep1


title: HCC_335T


title: ES_D2_H3K27ac_rep1


title: Glucose time course, 336 hour time point, biological replicate 1

source_name: REL606_glucose-limited minimal medium_336 hr

value: 336 hours


title: ES_D0_GRO_seq

source_name: hESC

value: Undifferentiated hESCs


title: ES_D2_Input_rep1


title: ES_D2_H3K4me1_rep2


title: ES_D0_Input_rep2


title: HCC_330T


title: HCC_329T


title: ES_D2_H3K27ac_rep2


title: HCC_328T


title: ES_D0_Input_rep1


title: ES_D0_H3K4me1_rep2


title: HCC_326T


title: HCC_336T


title: HCC_332T


title: HCC_325T


title: ES_D0_H3K27ac_rep2


title: HCC_327T


title: Rsc8 Input

description:
Rsc8 Input
7018X1

source_name: Input chromatin

tag: genotype/variation


title: ES_D0_H3K27ac_rep1


title: HCC_333T


title: ES_D0_H3K4me1_rep1


title: HCC_322T


title: HCC_334T


title: HCC_320T


title: Rsc8 ChIP

description:
Rsc8 ChIP
7018X2

source_name: Immunoprecipitated chromatin

tag: chip antibody

value: Anti-c-Myc antibody [9E11]

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: HCC_323T

tag: tissue


title: HCC_321T


title: Glomerulus, replicate #5

city: Bethesda

first: Jae Wook

last: Lee

address: 10 Center Drive, 6N314

institute: National Institutes of Health

data_processing:
Base-calling was performed using on-instrument real-time analysis (RTA) pipeline provided by Illumina HiSeq 2000.
Individual pair of FASTQ sequences was inspected and nucleotides with phred33 score lower than 30 were trimmed with Trimmomatic 0.32 (http://www.usadellab.org/cms/?page=trimmomatic) using the following command: java -jar trimmomatic-0.32.jar PE -threads 8 -phred33 sample_1.fastq.gz sample_2.fastq.gz sample1_p1.fastq. sample1_up1.fastq sample2_p2.fastq sample2_pup2.fastq TRAILING:30 MINLEN:35
Pairs of FASTQ sequences that survived the trimming process were mapped to rat reference genome (rn5) with STAR 2.3.0-r192 using the following command: STAR --genomeDir <genome directory> --readFilesIn sample_p1.fastq sample_p2.fastq --runThread 8 --outFilterMismatchNmax 3 --genomeLoad LoadAndKeep --outSamstrandField intronMotif --alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
HOMER software package was used to calculate RPKMs.
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: RPKM.without.PAseq.txt is a tab-delimited text file that contains a matrix of reads per kilobase exons per million mapped reads (RPKMs) for RefSeq transcripts without information from PA-seq study. RPKM.with.PAseq.txt is a tab-delimtied text file that contains a matrix of revised RPKMs after including the information on alternative polyadenylation from PA-seq study. Bedgraph files for individual tubule segments, in bedgraph format, contain median read counts at each nucleotide normalized to million uniquely mapped reads. These files can be uploaded onto the UCSC genome browser for visualization. PAseq.peak.rn5 bedgraph files for the forward and reverse strand contain information on polyadenylation peaks in the whole kidney across the rat genome. These files can be uploaded onto the UCSC genome browser to examine the location and intensity of polyadenylation peaks.

organism: Rattus norvegicus

source_name: Microdissected from rat kidney

growth_protocol: Male Sprague-Dawley rats were grown and maintained in the Animal Facility of the NHLBI. Normal rat chow was fed to the animals. For vasopressin-escape experiment, 5-week-old rats were used.

extract_protocol:
Dissected tubules were lysed in buffer containing RNase inhibitors and universal primers. Reverse transcription was started in this cell lysate. See Tang F. et al. (2010). "RNA-Seq analysis to capture the transcriptome landscape of a single cell" Nature Protocol 5(3):517-35.
We followed an RNA-seq protocol developed for single-cell RNA-seq. See Tang F. et al. (2010). "RNA-Seq analysis to capture the transcriptome landscape of a single cell" Nature Protocol 5(3):517-35. cDNAs were sheared and made into adapter-ligated RNA-seq libraries using NuGen Mondrian machine and Ultralow Library System.
We sequenced from both ends of a cDNA molecule, 50 nucleotides each.

treatment_protocol: For vasopressin-escape experiment, subcutaneous minipumps containing DDAVP (5ng/hr) were implanted into the back of the rats. These rats received either water load ("WL", 50 mL/day) or normal amount of water ("C", 25 mL/day) in the form of gelled food. After 4 days of water load, the cortical collecting duct was microdissected.

value: Adult

tag: Sex

value: male

value: Sprague-Dawley

value: glomerulus


title: Glomerulus, replicate #3


title: HCC_319T

value: Tumor

value: liver


title: HCC_312T

value: F


title: HCC_314T

value: M


title: Glomerulus, replicate #2


title: Glomerulus, replicate #1


title: HCC_315T


title: Cortical collecting duct, Water-loaded rat #3

source_name: Microdissected cortical collecting duct_water-loaded

tag: stress

value: water-loaded

value: cortical collecting duct


title: Cortical collecting duct, Water-loaded rat #2


title: HCC_309T


title: Glomerulus, replicate #4


title: Cortical collecting duct, Control rat #2

source_name: Microdissected cortical collecting duct_control

value: control


title: Cortical collecting duct, Water-loaded rat #1


title: HCC_311T


title: HCC_308T


title: Cortical collecting duct, Control rat #1


title: HCC_310T


title: Cortical collecting duct, Control rat #3


title: Cortical collecting duct, Control rat #4


title: HCC_317T


title: HCC_316T


title: HCC_305T


title: Soleus muscle

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
FastX Toolkit: fastq_quality_trimmer -t 20 -l 18: >Q20, length > 18
FastX Toolkit: fastx_collapser: remove duplicates (to accelerate analyses; still counted later)
Remove long reads: length < 29
Cluster reads which are completely included in each other or which differ by the  last 5' base only
Blastn vs. miRBase 20 Mus Musculus miRNAs: blastn -num_alignments 15 -word_size 7 -evalue 10 -dust no -strand plus
Trim microRNA names to refer to families only
Keep only miRNA sequences with a meaningful number of counts/family (>5% of the most abundant sequence) to reduce mismatching due to sequencing errors
Keep only miRNA families with a minimum count of 5
Genome_build: miRBase 20 Mus Musculus miRNAs
Supplementary_files_format_and_content: tab-delimited text file includes miRNA expression per million mapped reads

source_name: Soleus

extract_protocol:
PureLink® miRNA Isolation Kit (Life Technologies)
Ion Total RNA-Seq Kit  (Life Technologies)
Chapter 3: Prepare Small RNA Libraries

value: soleus muscle

value: adult

tag: genotype

value: wild type


title: Cortical collecting duct, Water-loaded rat #4


title: HCC_304T


title: HCC_307T


title: Polyadenylated mRNA-seq (PA-seq), replicate #6

description:
DNA-free total RNA from the whole kidney was used to create a strand-specific paired-end library. For detailed information, see Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615. 50 nucleotides from each end of a cDNA were sequenced. Burrows-Wheeler Aligner and in-house python script was used to call polyadenylation peaks.
PAseq6

data_processing:
Base-calling was performed using on-instrument real-time analysis (RTA) pipeline provided by Illumina HiSeq 2000.
Individual pair of FASTQ sequences was inspected and nucleotides with phred33 score lower than 30 were trimmed with Trimmomatic 0.32 (http://www.usadellab.org/cms/?page=trimmomatic) using the following command: java -jar trimmomatic-0.32.jar PE -threads 8 -phred33 sample_1.fastq.gz sample_2.fastq.gz sample1_p1.fastq. sample1_up1.fastq sample2_p2.fastq sample2_pup2.fastq TRAILING:30 MINLEN:35
Pairs of FASTQ sequences that survived the trimming process were mapped to rat reference genome (rn5) with STAR 2.3.0-r192 using the following command: STAR --genomeDir <genome directory> --readFilesIn sample_p1.fastq sample_p2.fastq --runThread 8 --outFilterMismatchNmax 3 --genomeLoad LoadAndKeep --outSamstrandField intronMotif --alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
HOMER software package was used to calculate RPKMs.
PA-seq data were mapped to Rn5 using Burrows-Wheeler Aligner. Peaks were called using in-house software written in Python. See Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615.
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: RPKM.without.PAseq.txt is a tab-delimited text file that contains a matrix of reads per kilobase exons per million mapped reads (RPKMs) for RefSeq transcripts without information from PA-seq study. RPKM.with.PAseq.txt is a tab-delimtied text file that contains a matrix of revised RPKMs after including the information on alternative polyadenylation from PA-seq study. Bedgraph files for individual tubule segments, in bedgraph format, contain median read counts at each nucleotide normalized to million uniquely mapped reads. These files can be uploaded onto the UCSC genome browser for visualization. PAseq.peak.rn5 bedgraph files for the forward and reverse strand contain information on polyadenylation peaks in the whole kidney across the rat genome. These files can be uploaded onto the UCSC genome browser to examine the location and intensity of polyadenylation peaks.

source_name: Whole kidney

growth_protocol: Male Sprague-Dawley rats were grown and maintained in the Animal Facility of the NHLBI. Normal rat chow was fed to the animals. Rats weighing 200-250 g were used for this study.

treatment_protocol: The left kidney of a male Sprague-Dawley rat was isolated from the circulation and perfused with 1x dissection solution and collagenase solution. The chunks of the kidney were digested in the same collagenase solution at 37 C for 25 minutes (cortex), 50 minutes (outer medulla), or 90 minutes (inner medulla).

value: whole kidney


title: Polyadenylated mRNA-seq (PA-seq), replicate #5

description:
DNA-free total RNA from the whole kidney was used to create a strand-specific paired-end library. For detailed information, see Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615. 50 nucleotides from each end of a cDNA were sequenced. Burrows-Wheeler Aligner and in-house python script was used to call polyadenylation peaks.
PAseq5


title: Polyadenylated mRNA-seq (PA-seq), replicate #7

description:
DNA-free total RNA from the whole kidney was used to create a strand-specific paired-end library. For detailed information, see Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615. 50 nucleotides from each end of a cDNA were sequenced. Burrows-Wheeler Aligner and in-house python script was used to call polyadenylation peaks.
PAseq7


title: Polyadenylated mRNA-seq (PA-seq), replicate #3

description:
DNA-free total RNA from the whole kidney was used to create a strand-specific paired-end library. For detailed information, see Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615. 50 nucleotides from each end of a cDNA were sequenced. Burrows-Wheeler Aligner and in-house python script was used to call polyadenylation peaks.
PAseq3


title: Polyadenylated mRNA-seq (PA-seq), replicate #4

description:
DNA-free total RNA from the whole kidney was used to create a strand-specific paired-end library. For detailed information, see Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615. 50 nucleotides from each end of a cDNA were sequenced. Burrows-Wheeler Aligner and in-house python script was used to call polyadenylation peaks.
PAseq4


title: HCC_356N

value: Adjacent Normal tissue


title: Polyadenylated mRNA-seq (PA-seq), replicate #2

description:
DNA-free total RNA from the whole kidney was used to create a strand-specific paired-end library. For detailed information, see Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615. 50 nucleotides from each end of a cDNA were sequenced. Burrows-Wheeler Aligner and in-house python script was used to call polyadenylation peaks.
PAseq2


title: Inner medullary collecting duct, replicate #8

description:
mRNA released from cell lysate
IMCD8

source_name: Microdissected renal tubule segment

value: Inner medullary collecting duct


title: HCC_302N


title: HCC_355N


title: Inner medullary collecting duct, replicate #7

description:
mRNA released from cell lysate
IMCD7

value: Adult


title: Inner medullary collecting duct, replicate #6

description:
mRNA released from cell lysate
IMCD6

value: male


title: HCC_301N


title: SAT22_T3

city: Paris

first: Laurence

last: Tiret

address: 91 Bd de l'Hôpital

country: France

institute: INSERM

description: sequenced twice in 2 different lanes

data_processing:
Filtering of bad quality reads using fastq_illumina_filter
Trimming  using sickle with default parameters (quality threshold=20, length threshold=20).
Quality of reads  checked using FastQC
Paired-end reads mapped to the human transcriptome using Bowtie2 v2.1.0 .
Quantification of transcript abundance  using eXpress
Genome_build: Reference human transcriptome  generated from the UCSC reference genome (hg19) and the Illumina iGenome annotation file of transcripts using RSEM
Supplementary_files_format_and_content: Data used for analysis are the eff_counts provided by eXpress. Data are provided at the gene level by summing isoform counts for each gene.
Supplementary_files_format_and_content: Rows of the matrix correspond to genes identified by Gene symbol and Ensembl identifier. Columns correspond to individuals at each time point (T0 or T3)

source_name: subcutaneous adipose tissue

extract_protocol:
Total RNA was extracted from SAT using the mirVana™ miRNA Isolation Kit (Ambion®). 500 ng of total RNA were used to prepare the library with TruSeq RNA sample Prep Kit V2 (Illumina). Briefly, mRNA was selected from total RNA by poly-T oligo-attached magnetic beads and fragmented. Reverse transcription was done with random hexamers by SuperScript II reverse transcriptase.
RNA libraries were prepared for sequencing using standard Illumina protocols.The generated libraries were submitted to quality control on High Sensitivity DNA chip from the Agilent Bioanalyzer 2100 (Agilent Technologies, Wokingham, UK) and quantified by fluorimetry using the Quant-iT™ dsDNA Assay Kit (Life Technology). A dilution at 10nM was performed for each library and pools of 12 libraries were constituted. Each pool included the libraries from 3 individuals for the 2 time points, each library being identifiable by a specific index. The resulting pools were loaded on a High Sensitivity DNA chip (Agilent) and quantified by integration. 9 pM of this solution was used for cluster generation using the TruSeq PE Cluster Kit v3 (Illumina) on a CBot instrument. A 75 bp paired-end run was performed on the Illumina HiSeq2000 platform with the TruSeq SBS kit V3 (Illumina). Sequencing was performed on two 8-laned flow cells. Each flow cell included 4 pools sequenced twice in 2 different lanes.

treatment_protocol: SAT samples were obtained by needle biopsy from the peri-umbilical area under local anesthesia (1% xylocaïne)

tag: time

tag: type of surgical procedure

value: Roux-en-Y gastric bypass


title: SAT21_T3

description: sequenced twice in 2 different lanes

value: adjustable gastric banding


title: SAT19_T3

description: sequenced twice in 2 different lanes


title: SAT20_T3

description: sequenced twice in 2 different lanes


title: Inner medullary collecting duct, replicate #4

description:
mRNA released from cell lysate
IMCD4

value: Sprague-Dawley


title: Inner medullary collecting duct, replicate #3

description:
mRNA released from cell lysate
IMCD3


title: Inner medullary collecting duct, replicate #5

description:
mRNA released from cell lysate
IMCD5


title: SAT17_T3

description: sequenced twice in 2 different lanes


title: SAT16_T3

description: sequenced twice in 2 different lanes


title: SAT18_T3

description: sequenced twice in 2 different lanes


title: Inner medullary collecting duct, replicate #2

description:
mRNA released from cell lysate
IMCD2


title: SAT15_T3

description: sequenced twice in 2 different lanes


title: Outer medullary collecting duct, replicate #6

description:
mRNA released from cell lysate
OMCD6

value: Outer medullary collecting duct


title: Polyadenylated mRNA-seq (PA-seq), replicate #1

description:
DNA-free total RNA from the whole kidney was used to create a strand-specific paired-end library. For detailed information, see Ni, T., Y. Yang, et al. (2013). "Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy." BMC Genomics 14:615. 50 nucleotides from each end of a cDNA were sequenced. Burrows-Wheeler Aligner and in-house python script was used to call polyadenylation peaks.
PAseq1


title: SAT14_T3

description: sequenced twice in 2 different lanes


title: SAT13_T3

description: sequenced twice in 2 different lanes


title: Outer medullary collecting duct, replicate #4

description:
mRNA released from cell lysate
OMCD4


title: Outer medullary collecting duct, replicate #5

description:
mRNA released from cell lysate
OMCD5


title: Outer medullary collecting duct, replicate #7

description:
mRNA released from cell lysate
OMCD7


title: SAT12_T3

description: sequenced twice in 2 different lanes


title: SAT11_T3

description: sequenced twice in 2 different lanes


title: Outer medullary collecting duct, replicate #2

description:
mRNA released from cell lysate
OMCD2


title: SAT10_T3

description: sequenced twice in 2 different lanes


title: Outer medullary collecting duct, replicate #3

description:
mRNA released from cell lysate
OMCD3


title: SAT09_T3

description: sequenced twice in 2 different lanes


title: NCOR2_ChIPSeq

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: unstimulated bone marrow derived macrophages

data_processing:
Sequencing was performed on an Illumina Genome Analyzer, and the raw image data were processed using the Illumina Genome Analysis Pipeline Software on a dedicated sequence data processing system
ChIP-Seq reads were aligned to the mouse genome (NCBI37/mm9; July 2007) using the ELAND alignment software (Illumina). We have used our in-house pipeline to identify regions where the ChIP signals were enriched relative to the normal rabbit serum (NRS) control.
The peaks were identiﬁed as a binding location if and only if all the three conditions were simultaneously satisﬁed: i) the ChIP-Seq signal in the NCOR2/HDAC3-speciﬁc IP was at least ﬁve times the control ChIP-Seq signal (ii) the ChIP-Seq signal in the NCOR2/HDAC3-speciﬁc IP was at least two fragments per million; and (iii) the ChIP-Seq signal in the NCOR2/HDAC3-speciﬁc IP corresponded to at least six overlapping fragments (extended reads) at that peak.
Genome_build: NCBI37/mm9; July 2007
Supplementary_files_format_and_content: BAR file obtained by converting the processed data files; Tags per million; Used for visualizing in the Integrated Genome Browser (IGB)

source_name: Bone-marrow derived macrophages

growth_protocol: BMMs were isolated from femurs  of C57BL/6 mice and plated on non–tissue culture–treated plastic in complete RPMI medium containing 10% (vol/vol) FBS (Hyclone Laboratories), 2 mM L-glutamine, 100 IU/ml of penicillin and 100 g/ml of streptomycin (all from Cellgro, Mediatech) and supplemented with recombinant human macrophage colony-stimulating factor (50 ng/ml; Peprotech).

extract_protocol:
For ChIP-Seq analysis, formalin-fixed cells were sonicated and processed for immunoprecipitation. Briefly, 1.5 X 10^7 BMMs were crosslinked for 10 min. in 1% paraformaldehyde, washed and lysed. Chromatin was sheared by sonication (5 x 60 s at 30% maximum potency) to fragments of approximately 150bp. The sheared chromatin was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with antibodies against either HDAC3 or NCOR2, washed and eluted. The eluted chromatin was reverse-cross-linked, and DNA was purified using phenol/chloroform/isoamyl extraction. The purified ChIP DNA was prepared for sequencing with the Illumina ChIPSeq Sample Prep kit and processed in according to the manufacturer’s protocol. Sequencing was performed by Covance, Seattle, WA.
Libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: NCOR2  (PA1-843) (Thermo Scientific)


title: HDAC3_ChIPSeq

value: unstimulated bone marrow derived macrophages

value: HDAC3 (sc-11417) (Santa Cruz Biotechnology)


title: Cortical collecting duct, replicate #11

description:
mRNA released from cell lysate
CCD11

value: Cortical collecting duct


title: Cortical collecting duct, replicate #10

description:
mRNA released from cell lysate
CCD10


title: Mecp2-null Microglia #3

description: Mecp2-null microglia, 3 pooled mice 10-12wks old

data_processing:
Basecalls performed using CASAVA
Data were aligned to the mm9 genome using STAR version 2.3.0
Aligned reads were counted against genes from the UCSC mm9 annotation using the htseq-count python library
Data were normalized for library size using the DESeq2 median ratio normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R.
Genome_build: mm9
Supplementary_files_format_and_content: Counts of reads aligning to genes from the mm9 annotation as output from htseq-count

source_name: Microglia

extract_protocol:
Cells were acutely isolated from mouse tissues and sorted via AutoMACS prior to RNA isolation. Qiagen Rneasy mini kit (Cat #74106) was used per manufacturer's protocol for RNA isolation.
RNA-Seq Poly A selection using NEBNext library prep modules

value: Acutely isolated microglia


title: SAT07_T3

description: sequenced twice in 2 different lanes


title: Cortical collecting duct, replicate #9

description:
mRNA released from cell lysate
CCD9


title: Inner medullary collecting duct, replicate #1

description:
mRNA released from cell lysate
IMCD1


title: WT Microglia #6

description: Wild type microglia, 3 pooled mice 10-12wks old

value: Wild type


title: SAT06_T3

description: sequenced twice in 2 different lanes


title: Cortical collecting duct, replicate #8

description:
mRNA released from cell lysate
CCD8


title: SAT05_T3

description: sequenced twice in 2 different lanes


title: SAT04_T3

description: sequenced twice in 2 different lanes


title: WT Microglia #5


title: WT Microglia #3


title: Cortical collecting duct, replicate #6

description:
mRNA released from cell lysate
CCD6


title: WT Microglia #4


title: Cortical collecting duct, replicate #7

description:
mRNA released from cell lysate
CCD7


title: Mecp2-null Resident peritoneal macrophages

description: Mecp2-null resident peritoneal macrophages, 6 pooled mice 10-12wks old

source_name: Resident peritoneal macrophages

value: Acutely isolated resident peritoneal macrophages


title: SAT02_T3

description: sequenced twice in 2 different lanes


title: Outer medullary collecting duct, replicate #1

description:
mRNA released from cell lysate
OMCD1


title: Cortical collecting duct, replicate #5

description:
mRNA released from cell lysate
CCD5


title: Cortical collecting duct, replicate #4

description:
mRNA released from cell lysate
CCD4


title: SAT01_T3

description: sequenced twice in 2 different lanes


title: Mecp2-null Microglia #2


title: Cortical collecting duct, replicate #3

description:
mRNA released from cell lysate
CCD3


title: WT Resident peritoneal macrophages

description: Wild type resident peritoneal macrophages, 6 pooled mice 10-12wks old


title: SAT08_T3

description: sequenced twice in 2 different lanes


title: Mecp2-null Microglia #1


title: Cortical collecting duct, replicate #2

description:
mRNA released from cell lysate
CCD2


title: SAT21_T0

description: sequenced twice in 2 different lanes


title: SAT20_T0

description: sequenced twice in 2 different lanes


title: Cortical collecting duct, replicate #1

description:
mRNA released from cell lysate
CCD1


title: Connecting tubule, replicate #6

description:
mRNA released from cell lysate
CNT6

value: Connecting tubule


title: SAT19_T0

description: sequenced twice in 2 different lanes


title: WT Microglia #1


title: Connecting tubule, replicate #5

description:
mRNA released from cell lysate
CNT5


title: SAT18_T0

description: sequenced twice in 2 different lanes


title: SAT03_T3

description: sequenced twice in 2 different lanes


title: SAT17_T0

description: sequenced twice in 2 different lanes


title: Connecting tubule, replicate #4

description:
mRNA released from cell lysate
CNT4


title: WT replictae 3

first: Lana

last: Schaffer

address: 10550 North Torrey Pines Road

department: DNA ARRAY CORE

institute: TSRI

description: Mixed pool of 4 mice.

data_processing:
Sequence using HiSeq2000 and pipeline Casava 1.8.2
Cleaned the reads using the program called cutadapt (https://code.google.com/p/cutadapt/wiki/Downloads?tm=2) to trim the 3' adapter sequence, quality scores less than 24, and eliminate reads less than 35 in length.
Aligned to Mus.Musculus build mm10 using program tophat version 2.0.8b,
exon/gene annotations I am currently using Partek.
Partek® software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA is used for the mRNA annotation.
Significantly changed reads using edgeR Bioconductor software package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html)
Biological significant pathways using Gene Set Enrichment Analysis (GSEA) (http://www.broadinstitute.org/gsea)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Excel and Count Per Million reads (CPM)

source_name: FACS sorted LSK CD34-CD150+CD48-Flk2- LT-HSC

extract_protocol:
RNeasy Micro kits (Quiagen)
The NuGEN Ovation RNA-Seq System V2 was used to prepare RNAseq libraries following manufacturer’s protocols. Input RNA was estimated at 1-5 ng based on the Agilent Bioanalyzer RNA Pico assay. RNA was of high quality with RIN scores either >9 (3 samples) or not called due to low input. For samples without RIN scores, the traces were similar to the samples with RIN scores of 9.

treatment_protocol: For each of 3 replicate ItpkB-/- or wt samples, we enriched Lin- cells from BM of 4 pooled age-matched mice with Rapidspheres (Stemcell Technologies), FACS-sorted ≥10,000 LSK CD34-CD150+CD48-Flk2- LT-HSC into lysis buffer and prepared RNA with RNeasy Micro kits (Quiagen).

tag: genetic background

value: WT

tag: allele

value: Litter mate control


title: Connecting tubule, replicate #2

description:
mRNA released from cell lysate
CNT2

tag: strain


title: SAT16_T0

description: sequenced twice in 2 different lanes


title: IPTKB-/- replicate 3

description: Mixed pool of 4 mice.

value: IPTKB-/-

value: ENU-induced Ms T-less


title: WT replictae 2

description: Mixed pool of 4 mice.


title: WT replictae 1

description: Mixed pool of 4 mice.


title: SAT22_T0

description: sequenced twice in 2 different lanes


title: SAT15_T0

description: sequenced twice in 2 different lanes


title: IPTKB-/- replicate 2

description: Mixed pool of 4 mice.


title: Distal convoluted tubule, replicate #8

description:
mRNA released from cell lysate
DCT8

value: Adult

value: male

value: Distal convoluted tubule


title: SAT14_T0

description: sequenced twice in 2 different lanes

value: Roux-en-Y gastric bypass


title: Connecting tubule, replicate #1

description:
mRNA released from cell lysate
CNT1

value: Sprague-Dawley


title: IPTKB-/- replicate 1

description: Mixed pool of 4 mice.


title: WT Microgia #2


title: SAT13_T0

description: sequenced twice in 2 different lanes

value: adjustable gastric banding


title: SAT12_T0

description: sequenced twice in 2 different lanes


title: IgG_ChipSeq

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using BOWTIE version 0.12.7 with following parameters  -q -m 1 -v 2 --best --strata
Peaks where called using MACS version 1.4 with default parameters. Final coordinates were reassigned as it is described in the paper
Genome_build: mm9

source_name: pancreatic beta cells

growth_protocol: DMED media (25mmol/l glucose) contains 15%FBS and 70Um 2-Mercaptoethanol, 1:3 passage every one week.

extract_protocol:
Chromatin were sonicated and protein-DNA complexes were isolated with indicated antibody.
Starting from 10-20ng of ChIP-DNA, the following library preparation steps are performed for each sample: end-repair, a-tailing, adapter ligation, gel purification and a final PCR enrichment. After quality control of the sequencing library on an Agilent Bioanalyzer and quanrtification of the final library on a Qubit, we proceeded with cluster generation and sequencing.

tag: background mouse strain

value: mix of C57BL/6, 129/ola and CBA/J

value: Established from islets of 6 weeks old RIP1-Tag2 transgenic mice

tag: passages

value: IgG


title: Foxa2_ChipSeq

value: Foxa2 (sc-6554, Santa Cruz Biotechnology)


title: Neurod1_ChipSeq

value: Neurod1 (#4373, Cell Signaling Technology, Danvers, MA)


title: Connecting tubule, replicate #3

description:
mRNA released from cell lysate
CNT3

tag: age


title: SAT10_T0

description: sequenced twice in 2 different lanes


title: Insm1_ChipSeq

value: Insm1 (Welcker et al , 2013)


title: Distal convoluted tubule, replicate #5

description:
mRNA released from cell lysate
DCT5


title: Distal convoluted tubule, replicate #3

description:
mRNA released from cell lysate
DCT3


title: Distal convoluted tubule, replicate #4

description:
mRNA released from cell lysate
DCT4


title: SAT08_T0

description: sequenced twice in 2 different lanes


title: Distal convoluted tubule, replicate #2

description:
mRNA released from cell lysate
DCT2


title: Cortical thick ascending limb, replicate #6

description:
mRNA released from cell lysate
cTAL6

value: Cortical thick ascending limb


title: Distal convoluted tubule, replicate #1

description:
mRNA released from cell lysate
DCT1


title: SAT06_T0

description: sequenced twice in 2 different lanes


title: Cortical thick ascending limb, replicate #7

description:
mRNA released from cell lysate
cTAL7


title: SAT07_T0

description: sequenced twice in 2 different lanes


title: SAT05_T0

description: sequenced twice in 2 different lanes


title: Cortical thick ascending limb, replicate #4

description:
mRNA released from cell lysate
cTAL4


title: SAT02_T0

description: sequenced twice in 2 different lanes


title: SAT04_T0

description: sequenced twice in 2 different lanes


title: SAT11_T0

description: sequenced twice in 2 different lanes


title: Cortical thick ascending limb, replicate #2

description:
mRNA released from cell lysate
cTAL2


title: Distal convoluted tubule, replicate #6

description:
mRNA released from cell lysate
DCT6


title: Cortical thick ascending limb, replicate #3

description:
mRNA released from cell lysate
cTAL3


title: Cortical thick ascending limb, replicate #5

description:
mRNA released from cell lysate
cTAL5


title: SAT01_T0

description: sequenced twice in 2 different lanes


title: Cortical thick ascending limb, replicate #1

description:
mRNA released from cell lysate
cTAL1


title: 0401_Responder_RNA-seq

city: Miami

first: Maria

middle: E

last: Figueroa

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and the quality of reads obtained was evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the hg18 whole genome or to the ERCC spike-in reference sequence using TopHat v2.0.8 with parameters -g 20 -p 10.
Gene counts or ERCC spike-in counts were collected by HTseq v0.5.4p5 with parameters --mode=union --stranded=no.
Gene counts were normalized by the scaling factors of ERCC spike-in controls, and then Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated.
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: RPKM_samples.txt: Abundance measurements: tab-delimited text file includes RPKM values for all Samples.

source_name: Bone marrow mononuclear cells, responder

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA kit from Qiagen (Valencia, CA) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer's instructions (San Diego, CA).

value: bone marrow mononuclear cells (BM MNC)

tag: resonse to decitabine

value: responder

tag: type of chronic myelomonocytic leukemia

tag: cytogenetics

value: 46 XY

tag: mutation

value: mutant

tag: gender


title: Medullary thick ascending limb, replicate #7

description:
mRNA released from cell lysate
mTAL7

value: Adult

tag: Sex

tag: tissue

value: Medullary thick ascending limb


title: Medullary thick ascending limb, replicate #6

description:
mRNA released from cell lysate
mTAL6

value: male


title: SAT09_T0

description: sequenced twice in 2 different lanes


title: 0305_Responder_RNA-seq

tag: response to decitabine

value: wild type


title: 0801_Responder_RNA-seq

value: non methaphasis


title: AG_Responder_RNA-seq

value: female


title: Medullary thick ascending limb, replicate #5

description:
mRNA released from cell lysate
mTAL5

value: Sprague-Dawley


title: 0802_Responder_RNA-seq


title: Medullary thick ascending limb, replicate #4

description:
mRNA released from cell lysate
mTAL4


title: Distal convoluted tubule, replicate #7

description:
mRNA released from cell lysate
DCT7

value: Distal convoluted tubule


title: 1203_Non-responder_RNA-seq

source_name: Bone marrow mononuclear cells, non-responder

value: non-responder


title: 0503_Responder_RNA-seq


title: Medullary thick ascending limb, replicate #2

description:
mRNA released from cell lysate
mTAL2


title: SAT03_T0

description: sequenced twice in 2 different lanes

tag: time

value: Roux-en-Y gastric bypass


title: Medullary thick ascending limb, replicate #3

description:
mRNA released from cell lysate
mTAL3


title: 0601_Non-responder_RNA-seq


title: 1401_Non-responder_RNA-seq


title: Medullary thick ascending limb, replicate #1

description:
mRNA released from cell lysate
mTAL1


title: 1302_Non-responder_RNA-seq


title: Thin ascending limb, replicate #7

description:
mRNA released from cell lysate
tAL7

value: Thin ascending limb


title: 0205_Non-responder_RNA-seq


title: Thin ascending limb, replicate #5

description:
mRNA released from cell lysate
tAL5


title: Thin ascending limb, replicate #6

description:
mRNA released from cell lysate
tAL6


title: 0108_Responder_RNA-seq


title: Thin ascending limb, replicate #4

description:
mRNA released from cell lysate
tAL4


title: Thin ascending limb, replicate #3

description:
mRNA released from cell lysate
tAL3


title: Thin ascending limb, replicate #2

description:
mRNA released from cell lysate
tAL2


title: Thin ascending limb, replicate #1

description:
mRNA released from cell lysate
tAL1


title: 1204_Responder_ERRBS

description:
ERRBS
32872

data_processing:
Reads were created by CASAVA 1.8.2 from the HiSeq 2000, and these are all reads which pass filter.
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR -- flexible adapter remover. FAR project website (2011)) (http://sourceforge.net/projects/theflexibleadap/).
Reads were aligned to the whole genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X and at most 500X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis.
*myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs.
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: myCpG.txt: Methylation calls; tab-delimited text file with the following column headers: chrBase, chr, base, strand, coverage, freqC, freqT

extract_protocol:
Genomic DNA was isolated using the AllPrep DNA/RNA kit from Qiagen (Valencia, CA) according to manufacturer's instructions.
ERRBS libraries were constructed as described in Akalin A et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 2012;8(6):e1002781.


title: 1204_Responder_RNA-seq


title: 0503_Responder_ERRBS

description:
ERRBS
32870


title: Descending thin limb of long-loop nephron of inner medulla, replicate #4

description:
mRNA released from cell lysate
LDLIM4


title: Bovine_H3K4me3_tough

data_processing:
[Alignment] Maq Version 0.7.1., Alignment policies of Maq were modified from default. A valid alignment could have a maximum of one mismatch and redundant reads were removed before further analysis to avoid amplification bias. If a read aligned equally well to multiple locations in the genome, this read was discarded to obtain the unique alignment. Only unique reads and unique aligned reads were chosen to perform further analysis
[Counting] Read counts were summarized using non-overlapping windows of 200 bp for visualization on the UCSC genome browser. For the purpose of comparison between tender and tough group, summary counts in each sample were normalized to per million mapped reads in the corresponding sample
[Peak identification] SICER V1.1, The source code was modified to support the bovine genome. Fragment length was specified to be about 190 bp as estimated from our ChIP-Seq experiments. A window size of 200 (default) and gap size of 400 bp was used for the analysis. The E-value for estimating significant peaks was set to 100. After filtering the scoreisland files, the final peaks could be seen in the bed files.
Genome_build: bosTau4
Supplementary_files_format_and_content: SICER V1.1-generated bedgraph and scoreisland files. Bedgraph file: a summary graph file obtained from the redundancy-removed bed file with window size 200bp in bedGraph format. Scoreisland file: Delineation of significant islands controlled by E-value of 100, in "chrom start end score" format.

source_name: Longissimus Dorsi

extract_protocol:
Nineteen purebred Angus steers were obtained from the Wye Farm. At approximately 12 months of age, the animals were serially harvested. Immediately after harvest, samples of longissimus dorsi (LD) from the right side of the carcass were obtained and placed in RNAlater solution at -80°C. The carcass were stored at 4°C for a total of 14 days. After this period, steaks were obtained from the LD at the level of the 12th intercostal space and then frozen. For measurement of the WBSF, steaks were thawed at room temperature to an internal temperature of 4°C. Then, the steaks were cooked to a core temperature of 70°C. The cooked steaks were then cooled down to room temperature. Using a sharp cylinder, especially designed for muscle, six cores (1.27 cm in diameter) were sampled parallel to the muscle fiber orientation. The Warner-Bratzler shear forces (WBSF) of the cores were obtained. The average WBSF of the six cores was calculated and used as the WBSF for the samples. From these 19 steers, 4 with the lowest WBSF values (6.77±0.56 kg) were identified as tender and 5 samples with the largest WBSF values (19.93±0.39 kg) labeled as tough.
LD samples from 4 tender and 5 tough were chopped into pieces in cold 1×PBS, and then crosslinked and sonicated. Briefly, after chromatin was prepared for all 9 samples, equal aliquots of chromatin from each individual were pooled to create tender or tough chromatins. Thirty microgram tender or tough chromatins were digested with Micrococcal Nuclease to produce mono-nucleosomes. Then chromatin was immunoprecipitated with H3K4me3 antibody (Millipore) and purified to obtain immunoprecipitated DNA.  After checked the quality by PCR, the IP-DNA was end-repaired, added A and ligated with a pair of Solexa adaptors (Illumina, San Diego, CA). After performed PCR on the DNA using the adaptor primers, fragments with a length of approximately 200-400 bp (mononucleosome + adaptors) were isolated from the agarose gel. Sequencing analysis using the purified DNA was performed on the Solexa 1G Genome Analyzer (Illumina) following the manufacturer’s protocols.

tag: breed

value: Aberdeen Angus

value: Longissimus Dorsi

tag: wbsf value

tag: chip antibody

value: H3K4me3 antibody (Millipore, cat# 07-449)


title: Bovine_H3K4me3_tender


title: 0901_Responder_ERRBS

description:
ERRBS
32866

tag: cell type

value: bone marrow mononuclear cells (BM MNC)

value: responder


title: Descending thin limb of long-loop nephron of inner medulla, replicate #2

description:
mRNA released from cell lysate
LDLIM2

tag: strain


title: 1103_Responder_ERRBS

description:
ERRBS
32864

value: mutant


title: Descending thin limb of long-loop nephron of inner medulla, replicate #3

description:
mRNA released from cell lysate
LDLIM3

value: Adult


title: 0108_Responder_ERRBS

description:
ERRBS
32862


title: Descending thin limb of long-loop nephron of outer medulla, replicate #9

description:
mRNA released from cell lysate
LDLOM9


title: 0404_Non-responder_ERRBS

description:
ERRBS
32860


title: 1102_Responder_ERRBS

description:
ERRBS
32858

value: 46 XY


title: 0404_Non-responder_RNA-seq


title: Descending thin limb of long-loop nephron of outer medulla, replicate #7

description:
mRNA released from cell lysate
LDLOM7

value: male


title: Descending thin limb of long-loop nephron of outer medulla, replicate #6

description:
mRNA released from cell lysate
LDLOM6


title: Descending thin limb of long-loop nephron of outer medulla, replicate #8

description:
mRNA released from cell lysate
LDLOM8


title: 0802_Responder_ERRBS

description:
ERRBS
28578


title: Descending thin limb of long-loop nephron of outer medulla, replicate #4

description:
mRNA released from cell lysate
LDLOM4


title: Descending thin limb of long-loop nephron of outer medulla, replicate #5

description:
mRNA released from cell lysate
LDLOM5


title: 0601_Non-responder_ERRBS

description:
ERRBS
28566


title: Descending thin limb of long-loop nephron of outer medulla, replicate #3

description:
mRNA released from cell lysate
LDLOM3


title: Descending thin limb of long-loop nephron of outer medulla, replicate #2

description:
mRNA released from cell lysate
LDLOM2


title: Descending thin limb of long-loop nephron of outer medulla, replicate #1

description:
mRNA released from cell lysate
LDLOM1


title: 0305_Responder_ERRBS

description:
ERRBS
28264

value: wild type


title: 0401_Responder_ERRBS

description:
ERRBS
28266


title: 0701_Responder_ERRBS

description:
ERRBS
32868


title: Descending thin limb of long-loop nephron of inner medulla, replicate #1

description:
mRNA released from cell lysate
LDLIM1


title: 0801_Responder_ERRBS

description:
ERRBS
28262

value: non methaphasis


title: Descending thin limb of short-loop nephron, replicate #7

description:
mRNA released from cell lysate
SDL7


title: AG_Responder_ERRBS

description:
ERRBS
28260

value: female


title: Descending thin limb of short-loop nephron, replicate #8

description:
mRNA released from cell lysate
SDL8

value: Sprague-Dawley


title: 0507_Non-responder_ERRBS

description:
ERRBS
28258


title: 1203_Non-responder_ERRBS

description:
ERRBS
28254


title: Descending thin limb of short-loop nephron, replicate #9

description:
mRNA released from cell lysate
SDL9


title: Descending thin limb of short-loop nephron, replicate #5

description:
mRNA released from cell lysate
SDL5


title: 1401_Non-responder_ERRBS

description:
ERRBS
27932


title: 0203_Non-responder_ERRBS

description:
ERRBS
28256

value: tris 19 and tris 13


title: 0302_Non-responder_ERRBS

description:
ERRBS
28568

value: non-responder

value: complex karyotype, t(1;3), t(20;21), 20q-


title: Descending thin limb of short-loop nephron, replicate #6

description:
mRNA released from cell lysate
SDL6


title: 0204_Non-responder_ERRBS

description:
ERRBS
27930


title: 1101_Responder_ERRBS

description:
ERRBS
25685

value: tris 8


title: 1201_Non-responder_ERRBS

description:
ERRBS
28580


title: Descending thin limb of short-loop nephron, replicate #1

description:
mRNA released from cell lysate
SDL1


title: Descending thin limb of short-loop nephron, replicate #3

description:
mRNA released from cell lysate
SDL3


title: Descending thin limb of short-loop nephron, replicate #4

description:
mRNA released from cell lysate
SDL4


title: S3 proximal tubule, replicate #7

description:
mRNA released from cell lysate
S3_7

value: S3 proximal tubule


title: 1301_Non-responder_ERRBS

description:
ERRBS
25681


title: Descending thin limb of short-loop nephron, replicate #2

description:
mRNA released from cell lysate
SDL2


title: 1003_Non-responder_ERRBS

description:
ERRBS
28268


title: Descending thin limb of short-loop nephron, replicate #10

description:
mRNA released from cell lysate
SDL10


title: S3 proximal tubule, replicate #6

description:
mRNA released from cell lysate
S3_6


title: 0205_Non-responder_ERRBS

description:
ERRBS
25677


title: 1501_Responder_ERRBS

description:
ERRBS
25673


title: 0506_Non-responder_ERRBS

description:
ERRBS
25675

value: other alteration than common


title: 0105_Responder_ERRBS

description:
ERRBS
13621


title: S3 proximal tubule, replicate #4

description:
mRNA released from cell lysate
S3_4


title: S3 proximal tubule, replicate #5

description:
mRNA released from cell lysate
S3_5


title: 1001_Responder_ERRBS

description:
ERRBS
13619


title: S3 proximal tubule, replicate #3

description:
mRNA released from cell lysate
S3_3


title: S3 proximal tubule, replicate #2

description:
mRNA released from cell lysate
S3_2


title: 0103_Responder_ERRBS

description:
ERRBS
13617


title: S3 proximal tubule, replicate #1

description:
mRNA released from cell lysate
S3_1


title: 1302_Non-responder_ERRBS

description:
ERRBS
25683


title: S2 proximal tubule, replicate #7

description:
mRNA released from cell lysate
S2_7

value: S2 proximal tubule


title: 0403_Responder_ERRBS

description:
ERRBS
13613

value: bone marrow mononuclear cells (BM MNC)


title: 0502_Responder_ERRBS

description:
ERRBS
13615

value: responder