title: EMP2 knockout placenta, sample 3

city: LA

first: Madhuri

last: Wadehra

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

data_processing:
The STAR ultrafast universal RNA-seq aligner (v2.3.0) was used to generate the genome index and perform paired-end alignments(15). Reads were aligned to a genome index that includes both the genome sequence (GRCm38.71 primary assembly) and the exon/intron structure of known gene models (Ensembl GRCm38.71 genome annotation).
Alignment files were used to generate strand-specific, gene-level count summaries with HTSeq (using default options for version v0.6.1p2 except  --mode=intersection-strict” and --stranded=reverse), using the Ensembl GRCm38.71 genome annotation as reference.
Genome_build: GRCm38.71
Supplementary_files_format_and_content: Per sample expression estimates in units of RPKMs

source_name: EMP2 knockout placenta

growth_protocol: Day 13.5 placental tissue was isolated from Emp2+/+ and Emp2-/- animals and snap-frozen.

extract_protocol:
Total RNA from each tissue was extracted using theRNAeasy kit
Paired-end stranded RNA-Seq libraries were prepared for sequencing using standard the KAPA Stranded RNA-Seq Kit. Three biological replicates were generated for each genotype

treatment_protocol: placentas from E16.5 mice

tag: strain background

value: EMP2 knockout; Emp2-/-

tag: gender

value: female

value: placenta


title: CS2-4_Del_clone2_TSS1

status: Public on Feb 23 2017

type: SRA

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

country: USA

institute: Washington University in St Louis

library_source: genomic

data_processing:
Reads were aligned to the reference human genome (build hg19) with Bowtie2 2.2.9.
Reads per million for each HindIII fragment were calculated using r3Cseq 1.18.0 and normalized using DESeq 2 1.14.
Statistical analysis for differential interactions between genotypes were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files include average reads per HindIII fragment normalized by DESeq2 in wildtype samples, deletion samples, and the differential signal between deletion and wild-type samples. Bed files include HindIII fragments with significant difference in normalized read counts between genotypes as generated by DESeq2.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
3C DNAs were digested with a second restriction enzyme, DpnII, religated, and purified using Qiagen PCR purification columns. The circularized DNA was amplified using inverse PCR and nested inverse PCR reactions with primers in the anchor HindIII-DpnII fragment. PCR products were used to prepare indexed sequencing libraries. Twelve to fourteen libraries were pooled in one lane for 50 bp single-end deep sequencing (Illumina HiSeq2500).
4C libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Transformed B lymphoblastoid cells

tag: genotype

value: NEK6 CS2-4 homozygote


title: CE1_WT_clone2_TSS1

data_processing:
Reads were aligned to the reference human genome (build hg19) with Bowtie2 2.2.9.
Reads per million for each HindIII fragment were calculated using r3Cseq 1.18.0 and normalized using DESeq2 1.14.
Statistical analysis for differential interactions between genotypes were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files include average reads per HindIII fragment normalized by DESeq2 in wildtype samples, deletion samples, and the differential signal between deletion and wild-type samples. Bed files include HindIII fragments with significant difference in normalized read counts between genotypes as generated by DESeq2.

value: NEK6 CE1 wild-type


title: EMP2 knockout placenta, sample 2

state: CA

institute: UCLA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype/variation

tag: age

tag: tissue


title: CE1_Del_clone1_TSS1

value: NEK6 CE1 homozygote


title: CS2-4_WT_clone2_CE1

value: NEK6 CS2-4 wild-type


title: CE1_Del_clone1_CE1


title: MOLM13.ENL_Flag

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6+B102; Scores represent the ChIP-seq tag numbers

growth_protocol: Cells were maintained in RPMI with 10% FBS, 5% CO2, 37oC.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
Sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.

treatment_protocol: For Flag-tagged stable cell selection, 10 ug/ml blasticidin was used for stable cells selection. For iCas9 induced ENL CRISPR knockout, 1ug/ml of doxycycline was used for induction of 5days before collecting for ChIP.

tag: cell line

tag: treatment

value: Control

tag: antibody

value: Flag M2, Sigma F3165


title: wildtype placenta, sample 2

source_name: wildtype placenta

value: wild type; Emp2+/+


title: wildtype placenta, sample 3


title: EMP2 knockout placenta, sample 1


title: CS2-4_Del_clone2_SE1


title: wildtype placenta, sample 1


title: CS2-4_Del_clone1_SE1


title: CS2-4_Del_clone1_CE1


title: CS2-4_Del_clone2_CE1


title: CE1_WT_clone1_CE1


title: HCT116 NC siRNA

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence, then mapped to hg19 Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bam2rpkm v.0.06 from the University of Liverpool. 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: hg19
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

source_name: colorectal cancer cell line

growth_protocol: HCT116 and HT29 cell lines were cultured with RPMI media

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

treatment_protocol: 15nM of NC siRNA and RPL9, RPL17, RPL27 siRNA transfected with lipofectamine 2000. 48h after transfection cell's total RNA was harvested

value: colon

value: colorectal cancer cell line

value: Negative control siRNA treated


title: CS2-4_WT_clone1_CE1


title: GM12878_TSS1

value: NEK6 CS2-4 and CE1 wild-type (parental)


title: SE1_Del_clone3

data_processing:
RNA-seq reads were aligned to the reference human genome (Ensembl 76) with STAR 2.0.4b.
Gene counts were derived by Subread:featureCounts 1.4.5.
Statistical analysis was performed using edgeR 3.14.0.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene (transcript_count), log2 fold-change of each gene between the average CPM of deletion versus wild-type subclones (logFC), the average expression level of each gene among three wild-type and three deletion subclones, reported as log2 read counts per million mapped reads (logCPM), p-values (PValue), and p-values adjusted by Benjamini-Hochberg procedure (FDR) for each sample.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted (RNeasy, Qiagen). Poly (A) mRNA was purified (Dynabeads mRNA Direct, Thermo Fisher Scientific), reverse-transcribed, and used for preparation of indexed libraries. All six libraries were pooled in one lane for 50 bp single-end deep sequencing (Illumina HiSeq2500).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NEK6 SE1 homozygote


title: GM12878_SE1


title: SE1_WT_clone2

value: NEK6 SE1 wild-type


title: SE1_Del_clone1


title: SE1_Del_clone2


title: SE1_WT_clone1


title: CS2-4_Del_clone1_TSS1


title: Stroma_Input_H3K9ac_cont

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Alignment: Sequence reads were obtained using the Illumina CASAVA v1.8.2. Reads were aligned against the human hg19 reference genome (NCBI Build 37) using the Bowtie aligner. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection and Superenhancer identification were performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated on Homer and can be visualized on the UCSC genome browser; peak files were generated using Homer.

source_name: MIA PaCa-2 cells

growth_protocol: MIAPaCa2 cells were obtained from the American Type Culture Collection and cultured in DMEM containing 10% FBS.

extract_protocol: Standard Illumina DNA library construction

treatment_protocol: Astromal and stromal cultures were generated using the ESI BIO HyStem-C kit (BioTime, Inc.).  Kit components were equilibrated to room temperature, and the suggested volume of degassed H2O was transferred to vials of Extralink, Gelin-S, and Glycosil using a syringe and 25G needle to avoid opening the vials.  Vials were vortexed every 5-10 minutes to aid reconstitution, and all reagents were in solution within 30 minutes.  To generate astromal cultures, PDAC cells were resuspended in a solution of 1:1:1 degassed H2O:Glycosil:Extralink (PEGDA) at a concentration of 5 x 105 cells/ml.  After careful mixing by pipetting, the suspension was added to a culture dish and placed in a 37°C incubator for 30 minutes to polymerize.  To generate stromal cultures, PDAC cells were resuspended in a solution of 1:1:1 Gelin-S (collagens):Glycosil:Extralink (PEGDA) at a concentration of 5 x 105 cells/ml, mixed by pipetting, and added to a culture dish.  After 30 minutes in a 37°C incubator, both astromal and stromal cultures polymerized and the appropriate volume of DMEM containing 10% FBS was layered over the hydrogels.  The next day, media was removed, gels washed twice with sterile PBS, and DMEM containing 2% FBS was added to astromal cultures or conditioned media containing 2% FBS was added to stromal cultures.  Cells appeared in single-cell suspension upon plating and expanded as spheroids over several days in 3D culture.  Conditioned media for human PDAC lines was generated from immortalized stromal myofibroblasts grown out of surgically resected human PDAC.  Stromal cells were grown to confluency and changed to fresh DMEM containing 2% FBS.  After 48 hours, media was collected, spun down at 1000rpm for 5 min to remove dead cells and debris, and added to stromal cultures.

value: MIA PaCa-2

value: pancreatic tumor cells

tag: chip antibody

value: input

value: stromal


title: Astromal_Input_H3K9ac_cont

value: astromal


title: Stromal_H3K27ac_ChIP


title: E3-6

status: Public on Feb 22 2017

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Reads were trimmed for adapters and low quality flanking ends using Trim Galore v0.3.7 and Cutadapt v1.4.2
Pre-processed reads were mapped to the mouse reference genome (mm10) with Bismark
Gene coverages were computed with featureCounts and the Gencode v19 annotation
Differential methylation was tested with analyses of variance and t-tests
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file with differential DNA methylation statistics of EPS versus Control, tab delmited text file with DNA methylation levels of targeted genes (genes along rows, samples along columns)

source_name: EPS, Timepoint 60

growth_protocol: Mouse skeletal muscle cell line C2C12 (ATCC® CRL1772™) were seeded into 6-well plates at a density of 1x105 cells/well, cultured in growth medium containing Dulbecco's Modified Eagle's Medium (DMEM; 25 mM glucose) supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin at 37oC, 5% CO2. After reaching ~90% confluence, differentiation was induced by switching to 2% horse serum. Differentiation medium was changed every day until fully differentiated myotubes was visualized under a light microscope.

extract_protocol:
DNA was isolated with AllPrep DNA/RNA/miRNA universal kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s instructions.
Genomic DNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo Research Corp, CA, USA) according to the manufacturer’s instructions. Bisulfite primers were designed to span the promoter region of Ppard, Ccnd1, and Nr4a3 genes within -3000 to +2000 base pairs relative to transcriptional start site (TSS) (Table 1, Figure 3) using MethPrimer program (Li and Dahiya, 2002)

treatment_protocol: A six-well plate, containing differentiated C2C12 myotubes was connected to C-dish electrode (IonOptix, Milton, MA, USA). The electrical current was discharged from the carbon electrode immersed in 8 ml differentiation medium added 24 hours before the EPS. Then, EPS was applied by C-pace cell culture stimulator (C-pace EP, IonOptix, Milton, MA, USA)

value: EPS

tag: time

value: 60 min

tag: replicate


title: TFAP2A_(3B5)_ChIPSeq_Rep_1

city: Iowa City

first: Robert

middle: A.

last: Cornell

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

data_processing:
LifeScope™ Genomic Analysis Software was used for Basecalling and alignment to hg19 genome
Data processed with default specifications for each program
Data quality is assessed using Phantompeak tools as per the guidelines of the Encode project.
peaks were called using SPP R program with the FDR setting of 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Bed file with Chip-seq peak regions and the columns represent; chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak

source_name: primary melanocytes

growth_protocol: Primary melanocytes were regularly maintained in culture using complete growth medium consisting of Minimum Essential Medium Eagle (MCDB) 153 supplemented with 4% fetal bovine serum, insulin (5 ug/ml), alpha-tocopherol (1 ug/ml), 1% penicillin/streptomycin/amphotericin, human basic fibroblast growth factor (bFGF, 0.6 ng/ml), phorbol 12-myristate 13-acetate (PMA, 8 nM), and bovine pituitary extract (BPE, 13 ug/ml).  For splitting primary melanocytes T-75 cm2 flasks were washed with an EDTA solution for two minutes, solution removed, and then 500 ul of 0.25% trypsin solution added.  Cells were incubated with trypsin solution for two minutes, flasks were tapped to help detach the cells, and then trypsin solution was neutralized with 10 ml of media. In general, one T-75 cm2 flask was split into 4 flasks (2.5 ml cell suspension + 8 ml media).  All ChIP-Seq experiments were conducted on primary cells that had not exceeded 10 passages.

extract_protocol:
For chromatin immunoprecipitation (ChIP) experiments approximately 40 million human primary melanocytes were fixed at room temperature for 10 minutes with 1% formaldehyde diluted in cell culture media (v/v).  Following fixation, formaldehyde was quenched with 1.25M glycine for 5 minutes at room temperature.  Fixed/quenched cells were subsequently spun at 1,200 rpm for 5 minutes, washed with 1x PBS, and respun.  Pelleted cells were then resuspended in 1mL cell lysis buffer (150mM NaCl, 10mM Hepes pH 7.4, 1.5mM MgCl2, 10 mM KCl, 0.5% NP-40, 0.5mM DTT, 1mM EDTA, plus protease inhibitors) and incubated on ice 10 minutes.  Following cell lysis, nuclei were pelleted by spinning down at 5,000 rpm, 5 minutes at 4 degrees Celsius.  Nuclei were then resuspended in 1 part nuclear lysis buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS plus protease inhibitors) and 2 parts ChIP-dilution buffer (150mM NaCl, 16.7mM Tris pH 7.5, 3.3mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% Na-Doc, plus protease inhibitors), and either sonicated on a Covaris (Woburn, MA, Model S220) or with a standard probe-tip sonicator (VirTis Virsonic 600).  Sonication settings were determined empirically to generate fragments ranging from 200-500 bp.  Following sonication samples were spun at 14,000 rpm for 15 minutes and supernatant saved for immunoprecipitation.  For immunoprecipitation, dynabeads (Life Technologies, Grand Island, NY) were first washed 3x with ChIP-dilution buffer and subsequently incubated with equal amounts (5-10ug) of either anti-TFAP2A (3B5, Santa Cruz Biotechnology, Inc., Santa Cruz, CA) or Mouse IgG (Millipore, Billerica, MA) for 2 hrs up to overnight at 4 degrees Celsius.  Following incubation antibody bound beads were washed 3x with ChIP-dilution buffer.  Sonicated chromatin was then equally split between two tubes and brought to approximately 1 mL with ChIP-dilution buffer and used to resuspend antibody bound beads.  Samples were incubated at 4 degrees Celsius overnight.  Following overnight incubation antibody/bead/chromatin complexes were washed with a series of solutions 3x followed by elution with 100 uL elution buffer.  Subsequent to elution crosslinks were reversed overnight at 65 degrees Celsius with 0.2 M NaCl.  DNA was further cleaned using a Qiagen PCR purification kit as per manufacturer's instructions (Qiagen, Valencia, CA).
Post-ChIP a variety of quality control protocols were implemented before sequencing.  Initially, real-time PCR was performed to confirm successful chromatin enrichment at known TFAP2A targets (and lack of enrichment at "off-targets").  Subsequently, total DNA enriched was quantified using a PicoGreen dsDNA assay kit (LifeTechnologies, Grand Island, NY) and shearing efficiency confirmed using a High Sensitivity DNA Analysis Kit and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) on the input sample.  Libraries were then constructed using ABI's SOLiD ChIP-Seq kit with barcoding (rev. 08/06/2010), per manufacturer's instructions (Life Technologies, Grand Island, NY).  Following library construction, samples were sequenced using the ABI SOLiD 3 platform, using a 50bp sequencing run.

tag: passage

value: under 10 passages

value: neonatal foreskin


title: E3-3

source_name: EPS, Timepoint 30

value: 30 min


title: Astromal_H3K27ac_ChIP


title: E3-24

source_name: EPS, Timepoint 240

value: 240 min


title: E3-12

source_name: EPS, Timepoint 120

value: 120 min


title: Astromal_H3K9ac_ChIP


title: Stromal_H3K9ac_ChIP


title: CS2-4_WT_clone1_SE1

value: Transformed B lymphoblastoid cells

value: NEK6 CS2-4 wild-type


title: CS2-4_WT_clone1_TSS1


title: E3-0

source_name: EPS, Timepoint 0

value: 0 min


title: GM12878_CE1

value: NEK6 CS2-4 and CE1 wild-type (parental)


title: E3-18

source_name: EPS, Timepoint 180

value: 180 min


title: SE1_WT_clone3

value: NEK6 SE1 wild-type


title: E2-6


title: Astromal_Input_H3K27ac_cont

value: MIA PaCa-2

value: pancreatic tumor cells


title: IgG_ChIPSeq_Rep_1

value: Mouse IgG (Millipore, Billerica, MA)


title: Stroma_Input_H3K27ac_cont

value: input

value: stromal


title: E1-6

value: EPS

value: 60 min


title: E2-0


title: E1-3


title: E2-18


title: E2-12


title: E1-24


title: E2-24


title: E2-3


title: E1-18


title: E1-12


title: C3-6

source_name: Control, Timepoint 60

value: Control


title: E1-0


title: C3-3

source_name: Control, Timepoint 30

value: 30 min


title: C3-18

source_name: Control, Timepoint 180


title: mv411_dTAG_24h_Pol2_Rx

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Chromatin IP against RNA Pol II

data_processing:
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

source_name: MLL-AF4 rearranged acute myeloid leukemia

growth_protocol:
RPMI, 10% FBS
MV4;11 cells (obtained from the laboratory of Prof. Scott A. Armstrong) were cultured in RPMI supplemented with 10% FBS, penecillin, and streptomycin. ENL-FKBP(F36V)-expressing MV4;11 cells were selected with 2 µg/mL puromycin

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

treatment_protocol: ENL-FKBP(F36V) was degraded with addition of 500 nM dTAG-13 (final DMSO concentration of 0.01%). Control treatments were performed with 0.01% DMSO

value: MV4;11(Cas9; ENL-FKBP(F36V); ENL-/-)

tag: input

value: 0.01% DMSO, 500 nM dTAG-13 for 24 hr

tag: sequencing barcode

value: TTCCAGTG

value: RNA Pol II

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog number


title: C3-0

source_name: Control, Timepoint 0

value: 0 min


title: C2-3


title: C2-24

source_name: Control, Timepoint 240

value: 240 min


title: C2-6


title: C3-12

source_name: Control, Timepoint 120

value: 120 min


title: C1-3


title: C2-0


title: C2-18

value: 180 min


title: C1-6


title: C2-12


title: C1-12


title: C1-24


title: C1-0


title: C1-18


title: C3-24


title: B1369_GATCAG_L006_R1

city: Los Angeles

first: Alexandra

last: Binder

state: California

address: 650 Charles Young Drive, South

department: Department of Epidemiology

institute: University of California Los Angeles

description: Barcode: GATCAG

data_processing:
trimming: trim_galore version 0.2.4 (-f fastq -O 1 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG)
alignment: bismark version 0.7.7 (--directional -q -n 1 -k 2 --best --chunkmbs 512)
SNP and CpG base calling: BisSNP version 0.82.2 (-T BisulfiteGenotyper  -stand_call_conf 20  -stand_emit_conf 0  -mmq 30  -mbq 0)
C/T summarization: BisSNP vcf2bedGraph.pl script ()
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include position and number of reads and percent methylation for each CpG locus

source_name: whole blood

extract_protocol:
Genomic DNA was extracted from human blood using the DNeasy Blood and Tissue Kit from Qiagen (Valencia, CA), mixed well, quantified via NanoDrop (Wilmington, DE), and then aliquoted into samples for rapid multiplexed reduced representation bisulfite sequencing (rmRRBS)
Briefly, we prepared the RRBS libraries as follows. First, we digested200ng of gDNA overnight at 37oC using 10U of MspI restriction endonuclease (C↓CGG) from New England Biolabs (NEB; Ipswitch, MA) generating fragments that each contain at least two CpG loci. We next filled in the 3’ overhangs and added an adenosine residue to each terminus of the DNA fragments via end repairing and A-tailing reagents from NEB. We then ligated indexed, methylated Illumina TruSeq adapters to the A-tailed fragments using a T4 ligase from NEB. All adapters contain universal PCR primer and NGS sequencing primer sequences, but the different adapters have unique six base index sequences, sometimes referred to as barcodes, that allow multiple different RRBS libraries to be sequenced in a single lane and then distinguished bioinformatically after sequencing. We then selected adapter-ligated DNA fragments larger than 100bp using positive selection with 1.2X volume of AMPure XP magnetic beads from Beckman Coulter, which also cleaned up the mRRBS libraries. We next pooled either 6 or 12 libraries, and then treated the pools with sodium bisulfite using the EZ DNA Methylation Gold kit from Zymo according to the manufacturer's instructions. Bisulfite converted library pools, which now contained uracil in place of unmethylated cytosines, were then PCR amplified using the minimum number of cycles (determined using a small scale test reaction with each pool) with a Pfu Turbo Cx Hotstart DNA polymerase from Agilent Technologies. We then cleaned up the final amplified library pools using a 1.8X volume of AMPure XP magnetic beads.
mRRBS libraries were sequenced on an Illumina HiSeq2500 using 75 base-pair single-end reads. All libraries were sequenced at normal cluster density except those prepared from participants C and D, as well as a replicate prepared from participant E, which were run at high cluster density.

tag: gender

value: male

tag: run

tag: individual

value: C

tag: sample input

tag: protocol

value: rmRRBS

tag: lane

value: whole blood


title: C462_GATCAG_L003_R1

description: Barcode: GATCAG

value: H

tag: tissue


title: C554_ACTTGA_L003_R1

description: Barcode: ACTTGA

value: I


title: D07_200ngReg_Ad10_TAGCTT_L006_R1

description: Barcode: TAGCTT

value: J


title: A1850_ATCACG_L001_R1

description: Barcode: ATCACG

value: A


title: A5113_TAGCTT_L001_R1

description: Barcode: TAGCTT

value: B


title: D07_200ngReg_Ad11_GGCTAC_L006_R1

description: Barcode: GGCTAC


title: Col_Q_RNAseq2_TCP-MG_HUVEC_s2

city: Madison

first: Scott

last: Swanson

state: WI

address: 330 N. Orchard St

institute: Morgridge Institute for Research

description:
Human umbilical vein endothelial cells cultured on MG-TCP surface
20_2D_MG_HUVEC

data_processing:
RNA-seq Exp2: Reads filtered and trimmed for adapter sequence and quality. Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Basecalls performed using CASAVA version 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with separate worksheets with separate worksheets for RSEM "Expected Counts" expression estimates and TPM expression estimates

source_name: HUVEC, 2D On Matrigel-TCP, Day 1, s2

growth_protocol: E8 medium: DMEM/F12, L-ascorbic acid-2-phosphate magnesium (64 mg/L), sodium selenium (14 μg/L), FGF2 (100 μg/L), insulin (20 mg/L), NaHCO3 (543 mg/L), transferrin (10.7 mg/L), and TGFβ1 (2 μg/L). E8BA medium: E8 supplemented with 5 μg/L BMP4 and 25 μg/L Activin A. E8BAC medium: E8BA supplemented with 1 μM CHIR99021. E7BVi medium: E7V supplemented with 50 μg/L BMP4 and 5 μM SB431542. E7V medium: E8 minus TGFβ1, but supplemented with 50 μg/L VEGF-A.  Human H1 ES cells were dissociated with Accutase (Invitrogen) and plated on vitronectin-coated plates. H1 ES cells were differentiated into mesoderm by culturing in E8BA or E8BAC medium supplemented with 10 μM Y27632 for the first day. Mesoderm was cultured for three days in E7BVi medium to yield CD31+CD34+ endothelial cells. Endothelial cells were derived from H1 ES cells (Thomson et al, 1998, “Embryonic stem cell lines derived from human blastocysts,” Science 282, 1145) using E8BA mesoderm medium for RNA-Seq experiment #1 (referred to as “H1-EC1”) and from H1-FUCCI ES cells (Leng et al, 2015, “Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments,” Nat Methods 12, 947) in E8BAC mesoderm medium for RNA-Seq experiment #2 (referred to as “H1-EC2”).

extract_protocol:
RNA was extracted using the Rneasy plus mini kit (Qiagen)
cDNA libraries were prepped using the LM-Seq protocol described in  Hou et al 2015 (PMID 25831155).

treatment_protocol: PEG hydrogels were formed by crosslinking 8-arm PEG-norbornene molecules (20,000 MW) with a matrix metalloproteinase (MMP)-degradable peptide (KCGGPQGIWGQGCK). Cell adhesion was promoted using a pendant CRGDS peptide. Cells were suspended in monomer solutions prepared at final concentrations of 40 mg/mL 8-arm PEG-NB (16 mM norbornene arms), 2.8-4.8 mM MMP-degradable peptide (5.6-9.6 mM cysteines, 35-60% molar ratio of cysteines to norbornene groups), 0 or 2 mM CRGDS, and 0.05% (wt/wt) photoinitiator (Irgacure 2959, or I2959) in PBS. Cell/monomer solutions were polymerized for 2 minutes using ~5-10 mW/cm2 UV light centered at ~365 nm. The gels were then immersed in media for the duration of the experiment.  The PEG-norbornene hydrogel platform was first described in Fairbanks et al, “A versatile synthetic extracellular matrix mimic via thiol-norbornene photopolymerization,” Adv Mater 21, 5005-5010 (2009), and modified as described above in Zanotelli et al, “Stable engineered vascular networks from human induced pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels,” Acta Biomater 35, 32-41.

value: HUVEC


title: C1796_TAGCTT_L003_R1

description: Barcode: TAGCTT

value: F


title: B632_CGATGT_L006_R1

description: Barcode: CGATGT

value: E


title: B1587_ACTTGA_L006_R1

description: Barcode: ACTTGA

value: D


title: C359_CTTGTA_L003_R1

description: Barcode: CTTGTA

value: G


title: B632_CGATGT_L002_R1

description: Barcode: CGATGT


title: Col_Y_RNAseq2_In MG_HUVEC_s2

description:
Human umbilical vein endothelial cells 3D culture in gelled Matrigel
19_In_MG_HUVEC

source_name: HUVEC, 3D In Matrigel Gel, Day 1, s2


title: Col_W_RNAseq2_On MG_HUVEC_s2

description:
Human umbilical vein endothelial cells 2D culture ON gelled Matrigel
18_On_MG_HUVEC

source_name: HUVEC, 2D On Matrigel Gel, Day 1, s2


title: ZT0 alpha_1

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description: replicate 1

data_processing:
Sequenced paired-end reads were mapped to the whole genome (mm10) using STAR (Dobin et al., 2013) with default parameters. Genome index was built considering Ensembl annotation.
For each Ensembl gene, all of the exons of the respective annotated protein-coding transcripts were considered. Reads up to one mismatch were counted considering only reads in the right gene orientation and mapped in the defined exons.
Read counts were normalized by the library size (EdgeR, Robinson et al. 2010) and the average size of the transcripts. Normalized reads count (RPKM) were log2 transformed.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include RPKM values for each sample

source_name: mouse alpha cell

extract_protocol:
RNeasy Plus Micro Kit Qiagen
Libraries were prepared according to the Illumina TruSeq Stranded Total RNA kit (with  Ribo-Zero TM gold probes) according to manufacturer's specifications. Input material was from 80 to 100 ng.

tag: cell type

value: pancreatic alpha cell

tag: strain

value: triple reporter mouse

value: islet isolation time ZT0 (7AM)


title: Col_I_RNAseq2_TCP-MG_H1EC_s2

description:
H1 ES cell-derived endothelial cells cultured on MG-TCP surface
15_2D_MG_H1EC

source_name: H1-EC2, 2D on Matrigel-TCP, Day 1, s2


title: Col_S_RNAseq2_On PEG_HUVEC_s2

description:
Human umbilical vein endothelial cells 2D culture ON a PEG hydrogel
16_On_PEG_HUVEC

source_name: HUVEC, 2D On PEG Gel, Day 1, s2


title: Col_U_RNAseq2_In PEG_HUVEC_s2

description:
Human umbilical vein endothelial cells 3D culture in a PEG hydrogel
17_In_PEG_HUVEC

source_name: HUVEC, 3D In PEG Gel, Day 1, s2


title: ZT0 alpha_2

description: replicate 2


title: ZT0 beta_1

description: replicate 1

source_name: mouse beta cell

value: pancreatic beta cell


title: Col_M_RNAseq2_In PEG_H1EC_s2

description:
H1 ES cell-derived endothelial cells 3D culture in a PEG hydrogel
12_In_PEG_H1EC

source_name: H1-EC2, 3D In PEG Gel, Day 1, s2


title: Col_O_RNAseq2_In MG_H1EC_s2

description:
H1 ES cell-derived endothelial cells 3D culture in Matrigel
14_In_MG_H1EC

source_name: H1-EC2, 3D In Matrigel Gel, Day 1, s2


title: ZT0 beta_2

description: replicate 2


title: Col_K_RNAseq2_On PEG_H1EC_s2

description:
H1 ES cell-derived endothelial cells 2D culture ON a PEG hydrogel
11_On_PEG_H1EC

source_name: H1-EC2, 2D On PEG Gel, Day 1, s2


title: ZT12 alpha_2

description: replicate 2

value: islet isolation time ZT12 (7PM)


title: Col_P_RNAseq2_TCP-MG_HUVEC_s1

description:
Human umbilical vein endothelial cells cultured on MG-TCP surface
10_2D_MG_HUVEC

source_name: HUVEC, 2D On Matrigel-TCP, Day 1, s1


title: Col_X_RNAseq2_In MG_HUVEC_s1

description:
Human umbilical vein endothelial cells 3D culture in gelled Matrigel
9_In_MG_HUVEC

source_name: HUVEC, 3D In Matrigel Gel, Day 1, s1


title: Col_V_RNAseq2_On MG_HUVEC_s1

description:
Human umbilical vein endothelial cells 2D culture ON gelled Matrigel
8_On_MG_HUVEC

source_name: HUVEC, 2D On Matrigel Gel, Day 1, s1


title: ZT12 beta_1

description: replicate 1


title: Col_T_RNAseq2_In PEG_HUVEC_s1

description:
Human umbilical vein endothelial cells 3D culture in a PEG hydrogel
7_In_PEG_HUVEC

source_name: HUVEC, 3D In PEG Gel, Day 1, s1


title: Col_R_RNAseq2_On PEG_HUVEC_s1

description:
Human umbilical vein endothelial cells 2D culture ON a PEG hydrogel
6_On_PEG_HUVEC

source_name: HUVEC, 2D On PEG Gel, Day 1, s1


title: Col_N_RNAseq2_In MG_H1EC_s1

description:
H1 ES cell-derived endothelial cells 3D culture in gelled Matrigel
4_In_MG_H1EC

source_name: H1-EC2, 3D In Matrigel Gel, Day 1, s1


title: ZT16 alpha_2

description: replicate 2

value: islet isolation time ZT16 (11PM)


title: Col_H_RNAseq2_TCP-MG_H1EC_s1

description:
H1 ES cell-derived endothelial cells cultured on MG-TCP surface
5_2D_MG_H1EC

source_name: H1-EC2, 2D on Matrigel-TCP, Day 1, s1


title: ZT16 beta_2

description: replicate 2


title: Col_L_RNAseq2_In PEG_H1EC_s1

description:
H1 ES cell-derived endothelial cells 3D culture in a PEG hydrogel
2_In_PEG_H1EC

source_name: H1-EC2, 3D In PEG Gel, Day 1, s1


title: ZT16 beta_1

description: replicate 1


title: Col_D_RNAseq1_HUVEC1

description:
Human umbilical vein endothelial cells (HUVECs) were cultured on vitronectin coated tissue-culture plates and maintained in EGM growth medium (Lonza).
s_27437_60

data_processing:
RNA-seq Exp1: Gene expression estimates obtained using RSEM v 1.1.21, with Bowtie 0.12.9 for alignment. rsem-calc-expression used default parameters, plus: "--seed-length 28 ", EXCEPT sample s_23085, which had parameters "--seed-length 28 -m 20"
Basecalls performed using CASAVA version 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with separate worksheets with separate worksheets for RSEM "Expected Counts" expression estimates and TPM expression estimates

source_name: HUVEC1 on 2D TCP

extract_protocol:
Total RNA was isolated using the RNeasy Kit (Qiagen) and included lysing in 350 μL RLT lysis buffer and the optional DNase treatment.
cDNA libraries were prepared from 50 nanograms of total RNA and indexed with Illumina’s TruSeq RNA Sample Preparation Kit v2 (RS-122-2001 and RS-122-2002).  Final indexed cDNA libraries were pooled with 12 uniquely indexed TruSeq cDNA libraries for a total of 6 samples per lane.  Multiplexed samples were sequenced on an Illumina HiSeq 2500 with a single 51 bp read and a 7 bp index read. Base-calling and demultiplexing were performed using Casava (v1.8.2). Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts. The remaining reads were aligned to 19084 Refseq genes extracted from the Illumina iGenomes reference, selecting only those with ‘NM_’ annotations.  Bowtie (v 0.12.9) was used for alignment, allowing two mismatches in a 28 bp seed [64]. Reads with more than 200 alignments were excluded from further analysis. RSEM (v1.2.3) was used to estimate isoform and relative gene expression levels (transcripts per million or “TPM”)


title: Col_J_RNAseq2_On PEG_H1EC_s1

description:
H1 ES cell-derived endothelial cells 2D culture ON a PEG hydrogel
1_On_PEG_H1EC

source_name: H1-EC2, 2D On PEG Gel, Day 1, s1


title: Col_E_RNAseq1_PC

description:
Human brain vascular pericytes were cultured on poly-L-lysine coated tissue-culture plates and maintained in Pericyte Medium (ScienCell).
s_27438_61

source_name: Pericytes on 2D TCP

value: Pericytes


title: ZT20 alpha_2

description: replicate 2

source_name: mouse alpha cell

value: islet isolation time ZT20 (3AM)


title: Col_N_RNAseq1_H1EC1_ON_MG_d1

description:
H1-EC1 CD31+ cultured on top of 4.5 mg/mL Matrigel for 1 day
s_27441_64

source_name: H1-EC1, 2D on Matrigel, Day 1


title: ZT20 beta_1

description: replicate 1

source_name: mouse beta cell


title: ZT4 alpha_2

description: replicate 2

value: islet isolation time ZT4 (11AM)


title: ZT4 alpha_1

description: replicate 1


title: ZT12 alpha_1

description: replicate 1


title: Col_C_RNAseq1_H1EC1

description:
Purified H1 ES cell-derived CD31+ endothelial cells (H1-EC1) were cultured on recombinant vitronectin-coated plates (1 µg / cm2) and maintained in E7V medium + 1% BSA.
s_27434_57

source_name: H1-EC1 on 2D TCP


title: Col_AD_RNAseq1_Cocult_60PEG_d5

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 60% MMP 2 mM CRGDS PEG hydrogel
s_27429_45

source_name: H1-EC1-PC, PEG w/ 60% MMP crosslinking, 2 mM CRGDS, Day 5


title: Col_AE_RNAseq1_H1EC1_50PEG_d5

description:
H1 ES cell-derived CD31+ endothelial cells cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27430_49

source_name: H1-EC1, PEG w/ 50% MMP, 2 mM CRGDS, Day 5


title: ZT4 beta_2

description: replicate 2


title: ZT4 beta_1

description: replicate 1


title: ZT20 beta_2

description: replicate 2


title: Col_AB_RNAseq1_Cocult_35PEG_d5

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 35% MMP 2 mM CRGDS PEG hydrogel
s_27427_43

source_name: H1-EC1-PC, PEG w/ 35% MMP crosslinking, 2 mM CRGDS, Day 5


title: ZT8 alpha_1

description: replicate 1

value: islet isolation time ZT8 (3PM)


title: Col_AC_RNAseq1_Cocult_50PEG_d5

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 50% MMP 2 mM CRGDS PEG hydrogel
s_27428_44

source_name: H1-EC1-PC, PEG w/ 50% MMP crosslinking, 2 mM CRGDS, Day 5


title: ZT12 beta_2

description: replicate 2


title: ZT8 alpha_2

description: replicate 2


title: Col_Z_RNAseq1_PC_50PEG_d3

description:
Primary human pericytes cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27422_36

source_name: Pericyte, PEG w/ 50% MMP, 2 mM CRGDS, Day 3

value: Pericyte


title: Col_Y_RNAseq1_H1EC1_50PEG_d3

description:
H1 ES cell-derived CD31+ endothelial cells cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27421_35

source_name: H1-EC1, PEG w/ 50% MMP, 2 mM CRGDS, Day 3


title: ZT8 beta_1

description: replicate 1


title: Col_AA_RNAseq1_HUVEC1_50PEG_d3

description:
Human umbilical vein endothelial cells cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27425_39

source_name: HUVEC1, PEG w/ 50% MMP, 2 mM CRGDS, Day 3


title: ZT8 beta_2

description: replicate 2


title: Col_X_RNAseq1_Cocult_MG_d3

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 4.5 mg/mL gelled Matrigel
s_27420_34

source_name: H1-EC1-PC, Matrigel, Day 3


title: Col_W_RNAseq1_Cocult_60PEG_d3

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 60% MMP 2 mM CRGDS PEG hydrogel
s_27418_31

source_name: H1-EC1-PC, PEG w/ 60% MMP crosslinking, 2 mM CRGDS, Day 3


title: Col_V_RNAseq1_Cocult_50PEG_d3

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 50% MMP 2 mM CRGDS PEG hydrogel
s_27417_30

source_name: H1-EC1-PC, PEG w/ 50% MMP crosslinking, 2 mM CRGDS, Day 3


title: Col_U_RNAseq1_HUVEC1_50PEG_d2

description:
Human umbilical vein endothelial cells cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27415_25

source_name: HUVEC1, PEG w/ 50% MMP, 2 mM CRGDS, Day 2


title: Col_T_RNAseq1_PC_50PEG_d2

description:
Primary human pericytes cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27412_22

source_name: Pericyte, PEG w/ 50% MMP, 2 mM CRGDS, Day 2


title: Neo_LN1

city: San Francisco

first: Tiffany

middle: C

last: Scharschmidt

address: 513 Parnassus Ave, 1201B

department: Dermatology

institute: University of California, San Francisco

data_processing:
The primary sequencing output ( FASTQ) is produced by a combination of Illumina software (CASAVA v. 1.8.2) and EA developed tools. Low quality reads, bases, homopolymers and adapter sequences were removed with fastq-mcf (Expression Analysis)
Reads were then mapped to mm10 using the UCSC refFlat gene model
Reads were mapped using  Tophat (v2.0.12) with Bowtie2 (2.1.0.0) and sorted with Samtools (0.1.19.0).
Reads were counted with HTSeq (0.6.1) using the settings union and stranded=no
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value file contains raw counts for each sample

source_name: skin draining lymph node Tregs

extract_protocol:
Sorted cells were pelleted flash frozen in liquid nitrogen. RNA was sent overnight on dry ice to Expression analysis, Quintiles to perform all subsequent processing and sequencing. RNA was isolated using by column purification.
RNA samples were converted into cDNA libraries using the Illumina SMARTer Ultra Low Input sample preparation kit.

value: skin draining lymph node

tag: age

value: 13 days

value: Regulatory T-cells (Tregs)


title: Neo_LN2


title: Neo_Sk1

source_name: neonatal skin Tregs

value: Skin


title: Col_S_RNAseq1_H1EC1_50PEG_d2

description:
H1 ES cell-derived CD31+ endothelial cells cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27411_21

source_name: H1-EC1, PEG w/ 50% MMP, 2 mM CRGDS, Day 2


title: Neo_LN3


title: Col_Q_RNAseq1_Cocult_60PEG_d2

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 60% MMP 2 mM CRGDS PEG hydrogel
s_27408_17

source_name: H1-EC1-PC, PEG w/ 60% MMP crosslinking, 2 mM CRGDS, Day 2


title: Col_R_RNAseq1_Cocult_MG_d2

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 4.5 mg/mL gelled Matrigel
s_27410_20

source_name: H1-EC1-PC, Matrigel, Day 2


title: Col_P_RNAseq1_Cocult_50PEG_d2

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 50% MMP 2 mM CRGDS PEG hydrogel
s_27407_16

source_name: H1-EC1-PC, PEG w/ 50% MMP crosslinking, 2 mM CRGDS, Day 2


title: D005

city: shanghai

first: menghui

last: zhang

address: 800 dongchuan road

country: China

institute: shanghai jiaotong university

data_processing:
The raw Illumina RNA-Seq reads were firstly processed to trim the adapter using Flexbar_v2.4_linux64, and to remove the reads shorter than 30bp or with ‘N’ base using Prinseq-lite-0.20.3.
The quality filtered reads were then mapped to the reference genome, the Mus_musculus genome (download from http://support.illumina.com/sequencing/sequencing_software/igenome.html, Mus_musculus_Ensembl_NCBIM37.tar) by Tophat (version 2.0.10) with default parameters, which allowed up to two mismatches.
The mapped sequences of each sample were assembled by Cufflinks.The transcript abundance was estimated through incorporation of two normalization steps to ensure that the expression levels for different genes and the transcripts can be compared across runs, and was expressed as the unit of measurement fragments per kilobase of transcript per million mapped fragments (FPKM).
The obtained assembles were then merged by Cuffmerge with the reference annotation (download from http://support.illumina.com/sequencing/sequencing_software/igenome.html, Mus_musculus_Ensembl_NCBIM37.tar).
The differential expression analysis of the merged assembles was then performed with Cuffdiff. Genes and transcripts whose folder change (in log2 scale)> 2 and q values <0.05 (FDR adjusted with Benjamini-Hochberg) were picked as significant ones.
Genome_build: Mus_musculus genome (download from http://support.illumina.com/sequencing/sequencing_software/igenome.html, Mus_musculus_Ensembl_NCBIM37.tar)
Supplementary_files_format_and_content: Text file include FPKM values, P_values, adjusted P_values of each group. Group A: NCD+LB; Group B: NCD+B29; Group C: HFD+LB ; Group D: HFD+B29.

source_name: colon cells_HFD+B29

extract_protocol:
The total RNA from the colon tissues was extracted using TRIzol reagent (Invitrogen Life Technologies, Gaithersburg, MD) and purified with RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany), and the experiment was performed according to the manufacturer’s protocol. The integrity and quality of the total RNA were checked by a NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US), respectively. The ODA260/A280 of the RNA sample was between 1.9 and 2.1.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male C57BL/6J germfree mice were purchased from Shanghai SLAC laboratory Animal Co., Ltd. (Shanghai, China) and raised in gnotobiotic isolators with a regular 12-h light cycle and supplied with sterile food and water. Before the age of 6-10 weeks, all mice were fed with a normal chow diet (NCD) and water ad libitum. Then they were randomly divided into four groups , each received one of the following treatments for 16 weeks : (1) NCD+LB group: inoculated 0.1ml sterile LB medium per day for one week and fed with NCD ; (2) NCD+B29 group: inoculated 1010 cells of B29 per mouse in 0.1ml sterile LB medium per day for one week and fed with NCD; (3) HFD+LB group: inoculated 0.1ml sterile LB medium per day for one week and fed with HFD; (4) HFD+B29 group: inoculated 1010 cells of B29 per mouse in 0.1 ml sterile LB medium per day for one week and fed with HFD. At the end of the experiment, all the 24 mice (n=6/group) were killed by decollation. The colon tissues were collected for the mRNA sequencing.

tag: diet

value: High fat diet (HFD)

tag: inoculation

value: colon

tag: genotype

value: wild type

value: male


title: Col_O_RNAseq1_Cocult_35PEG_d2

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 35% MMP 2 mM CRGDS PEG hydrogel
s_27406_15

source_name: H1-EC1-PC, PEG w/ 35% MMP crosslinking, 2 mM CRGDS, Day 2


title: D001


title: D003


title: D004


title: D002


title: Col_M_RNAseq1_HUVEC1_50PEG_d1

description:
Human umbilical vein endothelial cells cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27404_11

source_name: HUVEC1, PEG w/ 50% MMP, 2 mM CRGDS, Day 1


title: ZT16 alpha_1

description: replicate 1

source_name: mouse alpha cell

value: pancreatic alpha cell

value: triple reporter mouse

tag: time


title: D006


title: C004

description: HFD+LB

source_name: colon cells_HFD+LB

value: LB


title: Col_K_RNAseq1_H1EC1_50PEG_d1

description:
H1 ES cell-derived CD31+ endothelial cells cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27400_7

source_name: H1-EC1, PEG w/ 50% MMP, 2 mM CRGDS, Day 1


title: C006

description: HFD+LB


title: Neo_Sk2


title: C001

description: HFD+LB


title: C003

description: HFD+LB


title: Col_F_RNAseq1_Cocult_50PEG_d1_0RGD

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 50% MMP 0 mM CRGDS PEG hydrogel
s_27397_4

source_name: H1-EC1-PC, PEG w/ 50% MMP crosslinking, 0 mM CRGDS, Day 1


title: Col_I_RNAseq1_Cocult_60PEG_d1

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 60% MMP 2 mM CRGDS PEG hydrogel
s_27396_3

source_name: H1-EC1-PC, PEG w/ 60% MMP crosslinking, 2 mM CRGDS, Day 1


title: Col_H_RNAseq1_Cocult_50PEG_d1

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 50% MMP 2 mM CRGDS PEG hydrogel
s_27395_2

source_name: H1-EC1-PC, PEG w/ 50% MMP crosslinking, 2 mM CRGDS, Day 1


title: B005

source_name: colon cells_NCD+B29

value: Normal chow diet (NCD)


title: Col_B_RNAseq1_H1

description:
The H1 human embryonic stem (ES) cell line was maintained in Essential 8 (E8) medium on Matrigel-coated (10 µg/cm2) tissue culture plates and was passaged routinely with EDTA.
s_23085

extract_protocol:
Total RNA was isolated using the RNeasy Kit (Qiagen) and included lysing in 350 μL RLT lysis buffer and the optional DNase treatment.
cDNA libraries were prepared from 80 nanograms of total RNA and indexed with Illumina’s TruSeq RNA Sample Preparation Kit v2 (RS-122-2001 and RS-122-2002).  Final indexed cDNA libraries were pooled with 12 uniquely indexed TruSeq cDNA libraries for a total of 6 samples per lane.  Multiplexed samples were sequenced on an Illumina HiSeq 2500 with a single 51 bp read and a 7 bp index read. Base-calling and demultiplexing were performed using Casava (v1.8.2). Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts. The remaining reads were aligned to 19084 Refseq genes extracted from the Illumina iGenomes reference, selecting only those with ‘NM_’ annotations.  Bowtie (v 0.12.9) was used for alignment, allowing two mismatches in a 28 bp seed [64]. Reads with more than 200 alignments were excluded from further analysis. RSEM (v1.2.3) was used to estimate isoform and relative gene expression levels (transcripts per million or “TPM”)


title: C002

description: HFD+LB


title: Col_G_RNAseq1_Cocult_35PEG_d1

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 35% MMP 2 mM CRGDS PEG hydrogel
s_27394_1

source_name: H1-EC1-PC, PEG w/ 35% MMP crosslinking, 2 mM CRGDS, Day 1


title: B004


title: 15_1_Basal

data_processing:
Reads were trimmed for adapters and low quality flanking ends using Trim Galore v0.3.7 and Cutadapt v1.4.2 on default settings
Pre-processed reads were mapped to the human reference genome (hg19) with tophat2 using the “--b2-very-sensitive” setting
Gene coverages were computed with featureCounts and the Gencode v19 annotation
Differential expression was determined using edgeR v3.12.1 with the glmQLFit/glmQLFTest modeling framework
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file with differential expression statistics (genes along rows, stats along columns), tab delimited text file with gene read coverage (genes along rows, samples along columns)

source_name: Muscle biopsy before exercise

growth_protocol: Human subjects were fasting at biopsy collection

extract_protocol:
Total RNAs were purified from skeletal muscle biopsies with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) following manufacturer’s instructions. The quality of recovered RNA was assessed by using the Agilent RNA 6000 Nano Kit (Agilent Technologies). RNA concentration was determined by spectrophotometry with a NanoDrop 2000. After purification, RNA samples were stored at -80°C until further analysis
Libraries were prepared after ribosomal RNA depletion with the TruSeq Stranded Total Sample Prep Kit with Ribo-Zero Gold (Illumina). Sequencing was done on a HiSeq 2500

treatment_protocol: Skeletal muscle biopsies collected from danish male subjects (age 22.6+/- 0.52, body mas index 23.08+/-0.87) at fasting conditions at rest and four hours after completion of a 15-minute exercise bout. Biopsies were immediately snap-frozen in liquid nitrogen and stored at -80°C for further analyses.

value: Skeletal Muscle

tag: treatment

value: control

value: Basal


title: C005

description: HFD+LB


title: 15_1_240

source_name: Muscle biopsy 240 min after exercise

value: exercise

value: 240 min


title: B003


title: 16_1_240


title: Col_L_RNAseq1_PC_50PEG_d1

description:
Primary human pericytes cultured in 50% MMP 2 mM CRGDS PEG hydrogel
s_27401_8

source_name: Pericyte, PEG w/ 50% MMP, 2 mM CRGDS, Day 1

value: Pericyte


title: Col_J_RNAseq1_Cocult_MG_d1

description:
H1 ES cell-derived CD31+ endothelial cells cocultured with primary human pericytes in 4.5 mg/mL gelled Matrigel
s_27399_6

source_name: H1-EC1-PC, 4.5 mg/mL Matrigel, Day 1


title: A006

description: NCD+LB

source_name: colon cells_NCD+LB


title: 14_1_240


title: 16_1_Basal


title: A005

description: NCD+LB


title: 14_1_Basal


title: B001


title: B002


title: B006


title: A004

description: NCD+LB


title: A003

description: NCD+LB


title: A002

description: NCD+LB


title: 11_1_Basal


title: 11_1_240


title: 13_1_240


title: 9_1_Basal


title: RNA_shTDG_rep2

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

data_processing:
Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7 pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions. Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2. Reads were mapped onto the mm9 assembly of the mouse genome by using Tophat2 and the bowtie aligner3. Quantification of gene expression was performed using HTSeq-0.5.4p3 (http://www-huber.embl.de/users/anders/HTSeq) and gene annotations from Ensembl release 67. Read counts have been normalized across librairies with the statistical method proposed by Anders and Huber4 and implemented in the DESeq Bioconductor library.
Genome_build: mm9
Supplementary_files_format_and_content: Processed expression data were summarized in a single tab-delimited text file containing the following informations: gene name (c1), Gene description (c2), Ensemble_gene_id (c3), shSCR_rep1 raw read count (c4), shSCR_rep2 raw read count (c5), shTDG_rep1 raw read count (c6), shTDG_rep2 raw read count (c7), shSCR_rep1 normalized read count (c8), shSCR_rep2 normalized read count (c9), shTDG_rep1 normalized read count (c10), shTDG_rep2 normalized read count (c11), log2foldchange (c12), p-value (c13), p-value adjusted for multi-testing (c14).

source_name: Mouse embryonic fibroblasts

extract_protocol:
RNA samples were purified using standard methods from subconfluent MEFs cultures.
Libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” .

treatment_protocol: shRNA targeting Tdg or the control shRNA  were cloned into pLKO.1-blast vector (Addgene). To generate lentiviruses, the transducing vectors were cotransfected into 293T cells using Effectene® Transfection Reagent (Qiagen). The supernatant was harvested at 48 hr after transfection. To generate control and Tdg-knockdown cells, MEFs were infected with lentivirus in a 6-well plate. 24 hr after infection, blasticidine (10 µg/ml) was added to the medium (DMEM containing 10% FBS) for selecting infected cells. Cells were selected by blasticidine for 10 days and were split when necessary until being harvested.

value: shTDG treated

value: Embryos were isolated from the uteri of day 12.5 postcoitus pregnant mice


title: A001

description: NCD+LB


title: RNA_shSCR_rep2

value: shSCR treated


title: 9_1_240


title: 8_1_240


title: 7_1_Basal


title: RNA_shTDG_rep1


title: 5caC_shTDG_rep2

description:
anti-5caC immunoprecipitation
5caC_shTDG.wig.gz

data_processing:
Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2. Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2. Peak detection was performed using MACS (http://liulab.dfci.harvard.edu/MACS/) under settings where the input fraction was used as negative control. Detected peak summits were annotated using HOMER (http://biowhat.ucsd.edu/homer/ngs/annotation.html). Heatmaps, global clustering and quantitative comparisons of the DIP-seq data were performed using seqMINER (http://bips.u-strasbg.fr/seqminer/) using datasets representing the average of replicates normalized to 10 millions uniquely mapped reads.
Genome_build: mm9
Supplementary_files_format_and_content: To visualize peaks in the genome browser, wig track files were generated for each dataset using WigMaker. Scores (average of two replicates) were normalized to 10 millions uniquely mapped reads.

extract_protocol: Libraries were prepared according to Illumina's instructions. The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions.

value: Embryos were isolated from the uteri at embryonic day 10.5.

tag: antibody


title: RNA_shSCR_rep1


title: 7_1_240


title: 13_1_Basal


title: 5_1_Basal


title: 5_1_240


title: 4_1_Basal


title: 5hmC_shSCR_rep2

description:
anti-5hmC immunoprecipitation
5hmC_shSCR.wig.gz


title: 5hmC_shTDG_rep2

description:
anti-5hmC immunoprecipitation
5hmC_shTDG.wig.gz


title: 5fC_shSCR_rep2

description:
anti-5fC immunoprecipitation
5fC_shSCR.wig.gz


title: 5fC_shTDG_rep2

description:
anti-5fC immunoprecipitation
5fC_shTDG.wig.gz


title: 4_1_240


title: 5caC_shSCR_rep2

description:
anti-5caC immunoprecipitation
5caC_shSCR.wig.gz


title: 5mC_shTDG_rep2

description:
anti-5mC immunoprecipitation
5mC_shTDG.wig.gz


title: 5mC_shSCR_rep2

description:
anti-5mC immunoprecipitation
5mC_shSCR.wig.gz


title: 5caC_shSCR_rep1


title: Input_shSCR_rep2

description:
Input fraction
Input_shSCR.wig.gz

value: none, Input fraction


title: Input_shTDG_rep2

description:
Input fraction
Input_shTDG.wig.gz


title: 5fC_shTDG_rep1


title: 8_1_Basal


title: 5hmC_shTDG_rep1

extract_protocol: Libraries were prepared according to Illumina's instructions. The libraries ere sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions.


title: 5fC_shSCR_rep1


title: Input_shTDG_rep1

description:
Input fraction
Input_shTDG.wig.gz


title: 5mC_shSCR_rep1


title: Input_shSCR_rep1

description:
Input fraction
Input_shSCR.wig.gz


title: H3K9me3

description: anti-H3K9me3 immunoprecipitation

data_processing:
Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2. Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2. Heatmaps and quantitative comparisons of the ChIP-seq data were performed using seqMINER (http://bips.u-strasbg.fr/seqminer/).
Genome_build: mm9
Supplementary_files_format_and_content: To visualize peaks in the genome browser, we generated wig track files for each data set using WigMaker. Scores represent tag numbers per total uniquely mapped reads.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions.


title: Input-ChIP

description: Input fraction

value: none, Input


title: Pol2

description: anti-Pol2 immunoprecipitation


title: adults female rep 3

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description:
adults female rep 3
f-adu-rep1

data_processing:
5’ and 3’ low-quality ends of raw reads were trimmed using Fastx-tools. Adaptor sequences were also trimmed using Fastx-tools. Reads with over 5 Ns or the length of which is shorter than 80bp were removed. The remained pair-end reads were kept as clean reads, which were used for de novo assembly. Then, the Trinity (v2.0.6) software were used to assemble the clean reads with default parameters. All assemblies were performed on a server with 48 cores and 128 GB of memory. After assembly, the contigs longer than 200 bases were used for subsequent analysis.
The reads from 8 libraries were mapped to the assembled contigs using Bowtie 0.12.7 with no more than 2 mismatches within the ﬁrst 28 bp. The read counts accumulated on the contigs were normalized as fragments per kilobase of exon model per million mappedreads (FPKM) values. Quantitative analysis for each contig was estimated using FPKM values by RSEM (v1.1.17) software with default parameters.
BLASTx  was performed to align the assembled contigs to the NR protein database for functional annotation. The e-value cut-off was set at 1E-5 for further analysis. Each assembled contig was assigned with the gene name and related function based on the best BLASTx hit (the smallest e-value). Assembled contigs assigned to the same gene were further compared, and the contig from the best e-value was adopted. If there was a tie between 2 assembled sequences, the one with the largest sequence identity was selected.
Supplementary_files_format_and_content: .txt file reports FPKM values

organism: Helicoverpa armigera

source_name: adults female

extract_protocol:
RNA was isolated from first instar larvae, fifth instar larvae and adults using the TRIzol (Invitrogen) reagent by following the company manual. Poly(A) mRNA was isolated from 20 µl total RNA using Oligo (dT) magnetic beads and then was broken into short fragments (about 200bp) in the presence of fragmentation buffer at 94 °C for 5 min.
The short fragments (about 200 bp) were used as templates for first-strand cDNA synthesis using random hexamer-primers. Subsequently, second-strand cDNAs were synthesized using buffer, dNTPs, RNaseH, and DNA polymerase I. After purification of short fragments with a QiaQuick PCR Purification Kit (Qiagen), samples werethen washed with EB buffer for end reparation and single nucleotide adenine addition. Finally, the short fragments were connected to sequencing adapters. Suitable fragments (about 200bp), as judged by agarose gel electrophoresis, were enriched with PCR amplification to prepare the sequencing library.

tag: developmental stage

value: adults of eclosion at first day

value: female

value: whole body


title: adults male rep 2

description:
adults male rep 2
m-adu-rep2

source_name: adults male

tag: gender

value: male


title: adults male rep 1

description:
adults male rep 1
m-adu-rep1


title: fifth instar larvae rep4

description:
fifth instar larvae rep4
5-lar-rep4

source_name: fifth instar larvae

value: larvae of fifth instar stage


title: fifth instar larvae rep3

description:
fifth instar larvae rep3
5-lar-rep3


title: fifth instar larvae rep1

description:
fifth instar larvae rep1
5-lar-rep1


title: fifth instar larvae rep2

description:
fifth instar larvae rep2
5-lar-rep2


title: 5caC_shTDG_rep1


title: ZT20 alpha_1

description: replicate 1

source_name: mouse alpha cell

value: pancreatic alpha cell

value: triple reporter mouse

value: islet isolation time ZT20 (3AM)


title: CK_R

first: Fei

last: Gao

address: 27 Zhongguancun South Street

institute: Minzu University of China

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3),
The dataset was further processed with an in-house program,ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Supplementary_files_format_and_content: fasta files with counts

organism: Ammopiptanthus mongolicus

source_name: unstressed roots

growth_protocol: The seeds of Ammopiptanthus mongolicus were collected from Zhongwei city, Ningxia autonomous district, China. The seeds were sown in pots and germinated in an incubator. After one week, the seedlings were transplanted to the growth chambers and grown at 22°C with 16 h of light per day.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) from leaves and roots of A. mongolicus seedlings following the manufacturer’s procedure.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The quantity and purity of total RNA were analyzed using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the manufacturer’s instructions.

treatment_protocol: For drought treatment, one group of four-week-old seedlings were non-irrigated for 14 days when the soil moisture content (SMC) was decreased to 5%. For well-watered control, water was given to seedlings regularly to maintain SMC higher than 70%. For cold treatment, one group of the five-week-old seedlings were transferred to a incubator kept at 4°C ± 0.5°C with16 h of light per day for 7 days.  After stress treatment, the root and leaf tissues of control and stressed groups were collected, frozen in liquid nitrogen and stored at −80 °C for RNA extraction.

value: leaves

tag: stress

value: unstressed


title: DT_R

source_name: drought stressed roots

value: drought


title: 5mC_shTDG_rep1

value: shTDG treated


title: DT_L

source_name: drought stressed leaves


title: CT_L

source_name: cold stressed leaves

value: cold


title: 5hmC_shSCR_rep1

value: shSCR treated


title: Untreated_189

city: Leiden

first: Bas

last: ter Braak

state: Zuid-Holland

address: Einsteinweg 55

department: Toxicology

country: Netherlands

institute: Leiden University/LACDR

data_processing:
No additional trimming or filtering of reads was performed before processing. Raw data obtained in the .bam file format was converted to fastQ format.
Reads were aligned to mouse genome build GRCm38 - Ensembl using Tophat2 (Version 2.0.10).
Reads which could not be aligned using TopHat2 were aligned in an additional step, using Bowtie2 (Version 2-2.10) in the local, very sensitive mode.
Tophat2- and Bowtie2- aligned reads were merged into a single .bam file for each sample before further analysis
Gene expression was quantified using HTSeq-Count (Version 0.6.1), using the default options ( stranded = yes, mode = union).
Differential gene expression was analyzed for a.  Insulin(n=10) versus untreated(n=10), b.  Glargine(n=10) versus untreated(n=10), c.  X10(n=10) versus untreated(n=10), d.  IGF1(n=10) versus untreated(n=10)
differential expression analysis was performed using DESeq2 (Version1.2.10)
Coverage data for the 5 sample groups (Control and treatment) in the bigWig format
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

source_name: Mammary gland tumor

growth_protocol: 8 week old female p53R270H/+WAPCre mice were obtained from an in house breeding project

extract_protocol:
Once the tumors reached a size of 1 cm3 and 24 hours after their last injection the mice were sacrificed. Tumors and other tissues were isolated. ¼ of the tumor was stored in RNALater at 4 degrees Celsius for RNA isolation. A miRNA isolation kit was used to isolate and purify small and large RNA molecules in one fraction
The Ion Total RNA-Seq kit was used to process the samples. Samples were Poly-A selected prior to library preparation. This library preparation included the cDNA synthesis and purification steps with the Ion Total RNA-Seq kit v2 (Life Technologies, UK) according to manufacturer’s instructions. The Ion PI Template OT2 200 Kit v3 and Ion Sequencing 200 kit v3 (both, Life Technologies, UK) were used according to manufactures instructions for sequencing libraries on the PI chip

treatment_protocol: Every other day these mice have been injected (subcutaneously) with either vehicle, insulin, glargine, X10 or IGF1 till tumor development.

value: p53R270HWAPCre mouse model

tag: sequence sample id

value: mammary gland tumor


title: Untreated_186


title: Untreated_187


title: Untreated_182


title: Untreated_194


title: Untreated_195


title: Untreated_161


title: Untreated_162


title: IGF1_147


title: IGF1_145


title: adults female rep 4

description:
adults female rep 4
f-adu-rep2


title: IGF1_158


title: CK_L

source_name: unstressed leaves


title: IGF1_160


title: IGF1_124


title: IGF1_128


title: IGF1_143


title: IGF1_136


title: X10_120


title: Untreated_197


title: IGF1_135


title: IFG1_132


title: X10_116


title: X10_113


title: X10_115


title: X10_118


title: X10_111


title: glargine_78


title: X10_95


title: Serum_1. NEBNext

city: Ghent

first: Alan

last: Van Goethem

address: De Pintelaan 185

country: Belgium

institute: Ghent University

data_processing:
BaseSpace: FASTQ Generation | Version: 1.0.0 was used for FASTQ generation.
Adaptor trimming was performed using Cutadapt v1.8.1. Reads shorter than 15 bp and those in which no adaptor was found were discarded.
For quality control, the FASTX-Toolkit (v0.0.14) was used. A minimum quality score of 20 in at least 80% of bases was applied as a cutoff.
The reads were mapped with Bowtie (v1.1.2) without allowing for mismatches.
Mapped reads were annotated by matching genomic coordinates of each read with genomic locations of miRNAs (obtained from miRBase, v20) and other small RNAs (obtained from UCSC (mouse: GRCm38/mm10) and Ensembl, v84).
Genome_build: miRBase v20; Ensembl v84; GRCm38/mm10
Supplementary_files_format_and_content: *miRs.txt: Tab-delimited text files represent the raw miRNA count table for each sample.
Supplementary_files_format_and_content: *contam.txt: Tab-delimited text files represent other small RNA counts for each sample. Columns: Sample, Read ID, Read counts, Annotation.

source_name: Serum, NEBNext

extract_protocol:
Healthy male and female 129/SVj mice, with ages varying between 2 to 9 months, were sedated using tribromoethanol at a dose of 250 mg/kg injected intraperitoneally. 500 μl to 1 ml of blood per mouse was collected in Safe-Lock micro test tubes (Eppendorf) by cardiac puncture using a 0.45 x 12 mm needle, after which mice were sacrificed by cervical dislocation. Clotted blood samples from healthy SVj mice were centrifuged at 1900 g for 10 min at 4 °C using a swinging bucket rotor. The supernatant, containing the serum, was collected and centrifuged again at 16000 g for 10 min at 4°C in a fixed angle rotor to pellet cellular nucleic acids attached to cell debris. The supernatant was collected and stored at -80 °C. For all serum samples, the degree of hemolysis was determined by measuring levels of free hemoglobin by spectral analysis. Absorbance peaks at 414, 541 and 576 nm are indicative of free hemoglobin.
Serum samples from individual SVj mice were used as input for RNA isolation using the miRNeasy serum/plasma kit (Qiagen) according to the manufacturer's instructions. Total RNA was eluted in 12 μl of RNase-free water.
Small RNA sequencing libraries were prepared using either the TruSeq small RNA library preparation kit v2 (Illumina), the TailorMix miRNA sample preparation kit v2 (Seqmatic) or the NEBNext Multiplex Small RNA library prep kit (New England Biolabs) according to manufacturer's instructions. After PCR amplification, the quality of libraries was assessed using a high sensitivity DNA kit on a Bioanalyzer (Agilent) according to manufacturer's instructions. Size selection was performed using 3% agarose dye-free marker H cassettes on a Pippin Prep (Sage Science) following manufacturer's instructions with a specified collection size range of 125-153 bp. Libraries were further purified and concentrated by ethanol precipitation, resuspended in 10 μl of 10 mM Tris-HCl (pH=8.5) and quantified using qPCR. Based on the qPCR results, equimolar library pools were prepared, quality was assessed as described above and the library was further diluted to 4 nM using 10 mM Tris-HCl (pH=8.5).

tag: strain/background

tag: disease status

value: Healthy

value: Serum

tag: small rna library preparation kit


title: Serum_2. NEBNext

tag: tissue

value: NEBNext Multiplex Small RNA library prep kit (New England Biolabs)


title: X10_107


title: Serum_2. TailorMix

source_name: Serum, TailorMix

value: TailorMix miRNA sample preparation kit v2 (Seqmatic)


title: glargine_73


title: Serum_1. TailorMix


title: glargine_69


title: glargine_70


title: glargine_67


title: Serum_2. Truseq

source_name: Serum, TruSeq

value: TruSeq small RNA library preparation kit v2 (Illumina)


title: glargine_64


title: glargine_63


title: Serum_1. Truseq


title: Serum_Pool_C. tRNA_dep_None

source_name: Serum, undepleted

extract_protocol:
Healthy male and female 129/SVj mice, with ages varying between 2 to 9 months, were sedated using tribromoethanol at a dose of 250 mg/kg injected intraperitoneally. 500 μl to 1 ml of blood per mouse was collected in Safe-Lock micro test tubes (Eppendorf) by cardiac puncture using a 0.45 x 12 mm needle, after which mice were sacrificed by cervical dislocation. Clotted blood samples from healthy SVj mice were centrifuged at 1900 g for 10 min at 4 °C using a swinging bucket rotor. The supernatant, containing the serum, was collected and centrifuged again at 16000 g for 10 min at 4°C in a fixed angle rotor to pellet cellular nucleic acids attached to cell debris. The supernatant was collected and stored at -80 °C. For all serum samples, the degree of hemolysis was determined by measuring levels of free hemoglobin by spectral analysis. Absorbance peaks at 414, 541 and 576 nm are indicative of free hemoglobin.
Serum samples from 3 individual SVj mice were pooled and 200 μl aliquots of the serum pool were used as input for RNA isolation using the miRNeasy serum/plasma kit (Qiagen) according to the manufacturer's instructions. Total RNA was eluted in 12 μl of RNase-free water. After elution from the miRNeasy column, RNA were diluted to a final volume of 38 μl and distributed in 12 μl aliquots.
Small RNA sequencing libraries were prepared using the TruSeq Small RNA Library Preparation kit v2 (Illumina) according to manufacturer's instructions using 6 µl of RNA as input. After PCR amplification (15 cycles), quality of libraries was assessed using a high sensitivity DNA kit on a Bioanalyzer (Agilent) according to manufacturer's instructions. Size selection was performed using 3% agarose dye-free marker H cassettes on a Pippin Prep (Sage Science) following manufacturer's instructions with a specified collection size range of 125-153 bp. Libraries were further purified and concentrated by ethanol precipitation, resuspended in 10 μl of 10 mM Tris-HCl (pH=8.5) and quantified using qPCR. Based on the qPCR results, equimolar library pools were prepared, quality was assessed as described above and the library was further diluted to 4 nM using 10 mM Tris-HCl (pH=8.5).

value: Pooled male and female

tag: trna-halves depleted

value: No

tag: serum pool

value: C


title: glargine_53

tag: strain


title: insulin_37


title: glargine_47


title: glargine_62


title: X10_100


title: insulin_27


title: Serum_Pool_C. tRNA_dep_RNase_H

source_name: Serum, tRNA-halves depleted using RNase H

value: RNase H


title: X10_105


title: Untreated_174


title: insulin_26


title: insulin_21


title: insulin_18


title: Serum_Pool_B. tRNA_dep_None

value: B


title: insulin_15


title: Serum_Pool_C. tRNA_dep_Beads

source_name: Serum, tRNA-halves depleted using beads

value: Beads


title: insulin_14


title: insulin_9


title: Serum_Pool_B. tRNA_dep_RNase_H


title: insulin_13


title: Serum_Pool_A. tRNA_dep_None

value: A


title: Serum_Pool_B. tRNA_dep_Beads


title: Serum_Pool_A. tRNA_dep_RNase_H


title: 5B3

city: Canberra

first: Linda

last: Tabe

state: ACT

address: PO Box 1600

department: Agriculture and Food

country: Australia

institute: CSIRO

description: processed data file: DESeq_2B-5B.csv, DESeq_4B-5B.csv, DESeq_5A-5B.csv, DESeq_5B-5C.csv

data_processing:
Samples were sequenced using Illumina HiSeq 2000, generating approximately 30 million 100 bp single-end reads per sample.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, then aligned against the wheat (Triticum aestivum) Unigene database build #62 (http://www.ncbi.nlm.nih.gov/unigene), comprising 158,028 transcripts, using the BioKanga software (http://code.google.com/p/biokanga). Alignment allowed a mismatch rate of up to 10% of the length of the read. Only reads with a unique best hit were selected for differential expression analysis.
Unigenes were filtered to those with a sum of counts greater than, or equal to, 100 across samples.Genes were considered expressed if more than 0.15 read per kilo base per million reads (RPKM) was detected.
Chromosomal location of each Unigene was determined using BLASTN (best hit, evalue ≤ 105) against the flow-sorted IWGSC chromosome survey sequencing contigs of cultivar Chinese Spring
Read counts were normalized and tested for differential expression, using the R DESeq package v1.12.0 with default parameters. Hierarchical clustering was done using the Euclidian distances on the normalized reads count following DESeq variance stabilizing transformation. 18 pairwise comparisons were completed (between genotypes at each time point and between time points for each genotype). Genes were considered DE for FDR ≤ 0.05 and |log2(FC)| ≥ log2(2), and for FDR ≤ 0.075 and |log2(FC)| ≥ log2(1.8) if already found DE in similar comparisons.
Genome_build: Triticum aestivum Unigene database build #62 (http://www.ncbi.nlm.nih.gov/unigene), comprising 158,028 transcripts
Supplementary_files_format_and_content: Summary file with Normalised read counts for all samples, Output files from DESeq analysis

organism: Triticum aestivum

source_name: seedling leaf

growth_protocol: Seedlings were grown in a microclimate room (22/20 °C day/night) until the two-leaf stage (approximately 2 weeks)

extract_protocol:
For each sample, the first leaf of two seedlings from different pots were pooled and quickly frozen in liquid nitrogen. Total RNA was extracted using the RNeasy Plant Mini Extraction Kit (Qiagen) and RNA integrity was checked on 1.4% agarose gel and on the Agilent 2100 Bioanalyzer. Poly(A) isolation was performed by the sequencing company, Australian Genome Research Facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were inoculated with wheat stem rust Pgt culture 313 (pathotype 34-1,2,3,5,6,7 according to Australian nomenclature) from the Plant Breeding Institute, University of Sydney, Australia. grown in a microclimate room (22/20 °C day/night) until the two-leaf stage (approximately 2 weeks). Inoculation was undertaken by spraying the plants with urediniospores suspended in light mineral oil. Plants were dried for 30 min and incubated for 2 days in incubation cabinets (22/20 °C day/night, high humidity). Finally, plants were transferred to a microclimate room, at a lower temperature (18/17 °C day/night).

tag: stem rust resistance status

value: resistant

value: seedling leaf

tag: time point (days after after inoculation with stem rust)

tag: pathogen

value: Puccinia graminis f. sp. tritici

tag: biological replicate


title: 5C2

description: processed data file: DESeq_2C-5C.csv, DESeq_4C-5C.csv, DESeq_5A-5C.csv, DESeq_5B-5C.csv

tag: genotype


title: 5B2


title: 5C1


title: 5A3

description: processed data file: DESeq_2A-5A.csv, DESeq_4A-5A.csv, DESeq_5A-5B.csv, DESeq_5A-5C.csv

value: Columbus

value: susceptible


title: 5B1


title: 5A1


title: 5A2


title: 4C3

description: processed data file: DESeq_2C-4C.csv, DESeq_4A-4C.csv, DESeq_4B-4C.csv, DESeq_4C-5C.csv


title: NCr Mouse 1069. TimePoint 2.tRNA dep

data_processing:
BaseSpace: FASTQ Generation | Version: 1.0.0 was used for FASTQ generation.
Adaptor trimming was performed using Cutadapt v1.8.1. Reads shorter than 15 bp and those in which no adaptor was found were discarded.
For quality control, the FASTX-Toolkit (v0.0.14) was used. A minimum quality score of 20 in at least 80% of bases was applied as a cutoff.
The reads were mapped with Bowtie (v1.1.2) without allowing for mismatches.
Mapped reads were annotated by matching genomic coordinates of each read with genomic locations of miRNAs (obtained from miRBase, v20) and other small RNAs (obtained from UCSC (human: GRCh37/hg19; mouse: GRCm38/mm10) and Ensembl, v84).
Genome_build: miRBase v20; Ensembl v84; Human: GRCh37/hg19; mouse: GRCm38/mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files represent the raw miRNA count table for each sample created by mapping either to the mouse genome or the human genome.

source_name: Serum, after tumor, tRNA-halves depleted

growth_protocol: Orthotopic neuroblastoma xenografts were generated in four- to six-week-old female athymic immunodeficient mice. Briefly, one million human SH-SY5Y neuroblastoma cells were surgically implanted in beneath the renal capsule. Serum samples were collected before and two weeks after tumor cell injection.

extract_protocol:
100 µl blood was collected by puncture of the jugular vein using a 4 mm lancet and collected in a BD Vacutainer collection tube with a gel separator (BD). All blood samples clotted at room temperature for 45 min. Clotted blood samples were centrifuged at 2000 g for 15 minutes at 4°C in a fixed angle rotor. The supernatant was collected and stored at -80 °C. For all serum samples, the degree of hemolysis was determined by measuring levels of free hemoglobin by spectral analysis. Absorbance peaks at 414, 541 and 576 nm are indicative of free hemoglobin.
RNA was isolated from 50 μl of serum that was collected from Ncr nude mice and eluted in 12 μl of RNase-free water using the miRNeasy serum/plasma kit (Qiagen) according to the manufacturer's instructions. For RNA samples that are depleted for tRNA-halves, biotinylated DNA probes complementary to the 5' tRNA-halves were allowed to hybridize to the target RNA sequences. Magnetic streptavidin beads were used to immobilize the DNA-RNA complexes. Using a magnetic field, the beads and bound DNA-RNA complexes were separated, after which the supernatant, containing tRNA-depleted RNA, was collected and purified using ethanol precipitation and suspended in 7.5 µl RNase-free water.
Small RNA sequencing libraries were prepared using the TruSeq Small RNA Library Preparation kit v2 (Illumina) according to manufacturer's instructions using 6 µl of RNA as input. After PCR amplification (15 cycles), quality of libraries was assessed using a high sensitivity DNA kit on a Bioanalyzer (Agilent) according to manufacturer's instructions. Size selection was performed using 3% agarose dye-free marker H cassettes on a Pippin Prep (Sage Science) following manufacturer's instructions with a specified collection size range of 125-153 bp. Libraries were further purified and concentrated by ethanol precipitation, resuspended in 10 μl of 10 mM Tris-HCl (pH=8.5) and quantified using qPCR. Based on the qPCR results, equimolar library pools were prepared, quality was assessed as described above and the library was further diluted to 4 nM using 10 mM Tris-HCl (pH=8.5).

value: NCr

value: Female

tag: treatment

value: Injection of SH-SY5Y human neuroblastoma cells

value: Yes

tag: mouse id

value: NCr Mouse 1069


title: 4C4


title: 4C2


title: Serum_Pool_A. tRNA_dep_Beads

value: Healthy

tag: gender

value: Pooled male and female

value: Serum


title: 4B1

description: processed data file: DESeq_2B-4B.csv, DESeq_4A-4B.csv, DESeq_4B-4C.csv, DESeq_4B-5B.csv


title: NCr Mouse 1069. TimePoint 2.tRNA undep

source_name: Serum, after tumor, undepleted

value: No


title: 4A3

description: processed data file: DESeq_2A-4A.csv, DESeq_4A-4B.csv, DESeq_4A-4C.csv, DESeq_4A-5A.csv


title: 4B2


title: 4B3


title: NCr Mouse 1047. TimePoint 2.tRNA undep

value: NCr Mouse 1047


title: NCr Mouse 1047. TimePoint 2.tRNA dep


title: NCr Mouse 1046. TimePoint 2.tRNA undep

value: NCr Mouse 1046


title: insulin_8

value: p53R270HWAPCre mouse model

value: mammary gland tumor


title: 5C4

value: resistant

value: seedling leaf


title: 2C3

description: processed data file: DESeq_2A-2C.csv, DESeq_2B-2C.csv, DESeq_2C-4C.csv, DESeq_2C-5C.csv

value: Puccinia graminis f. sp. tritici


title: 4A1

value: Columbus

value: susceptible


title: 2C1


title: NCr Mouse 1069. TimePoint 1.tRNA undep

source_name: Serum, before tumor, undepleted

value: NCr

value: Female


title: NCr Mouse 1069. TimePoint 1.tRNA dep

source_name: Serum, before tumor, tRNA-halves depleted

value: Yes


title: NCr Mouse 1046. TimePoint 2.tRNA dep

value: Injection of SH-SY5Y human neuroblastoma cells


title: 2B1

description: processed data file: DESeq_2A-2B.csv, DESeq_2B-2C.csv, DESeq_2B-4B.csv, DESeq_2B-5B.csv


title: 2A2

description: processed data file: DESeq_2A-2B.csv, DESeq_2A-2C.csv, DESeq_2A-4A.csv, DESeq_2A-5A.csv


title: NCr Mouse 1047. TimePoint 1.tRNA undep


title: 2A1


title: NCr Mouse 1046. TimePoint 1.tRNA undep


title: 4A2


title: Sample 35_IC_cocaine

city: Galveston

first: Thomas

middle: Arthur

last: Green

state: TX

address: 301 University dr.

department: Pharmacology and Toxicology

institute: University of Texas Medical Branch

description: s35; 35_TTAGGC_L008

data_processing:
Illumina Casava software used for basecalling.
More than 100 million reads with 50bp (paired-end reads) were mapped for each rat and quality was checked with FastQC (v0.9.1).
Reads were mapped to the rat reference genome (RN4) using Tophat2 (v2.0.4) and Bowtie2 (v2.0.0.6) software packages.
The R package EdgeR (v.3.0.8) was then used for analysis using the “trimmed mean for M-values” (TMM) method for normalization and tag-wise dispersion using “count” data.
A likelihood ratio F-test was used for generating p-values to compare EC vs. IC rats and cocaine vs. saline.
Genome_build: rn4
Supplementary_files_format_and_content: Excel file containing normalized count data per gene and differential analysis results using edgeR and DESeq

organism: Rattus norvegicus

source_name: IC_cocaine_nucleus accumbens

extract_protocol:
The RNA was extracted by homogenizing in RNA STAT-60 (Teltest, Friendsood, TX). RNA was separated from DNA and protein using chloroform, and the total RNA was precipitated with isopropanol.
cDNA libraries were created by reverse transcribing the RNA and creating the second strand.
Blunt ends were phosphorylated and “a-tailed” so that adapters could be ligated to both ends. Adapters were individually “bar coded” and thus samples were not pooled despite having 4 samples per flow cell, yielding n=7-8 for each condition (total N=30).

treatment_protocol: Male Sprague-Dawley rats (Harlan, Houston, TX, USA) arrived at 21 days of age and were enriched or isolated for 30 days before behavioral testing. Rats were anesthetized with ketamine (100mg/kg, IP) and xylazine (10mg/kg, IP), and implanted with an indwelling Silastic catheter into the jugular vein. One week after catheter surgery, rats were allowed to self-administer 0.5 mg/kg/infusion cocaine (National Institute on Drug Abuse, Bethesda, MD) or saline under a fixed ratio 1 (FR1) schedule for 2 hours/day for 14 days. The session terminated when the rat received 30 infusions to eliminate cocaine intake differences between EC and IC rats. Tissue was harvested 3 hours after the beginning of the last session.

value: Sprague Dawley

value: male

tag: age

value: post natal day 72

tag: exposed to

value: environmental isolation for 30 days

tag: treated with

value: saline for 2 wks

value: Nucleus accumbens (Left)


title: Sample 34_IC_saline

description: s34; 34_GTGGCC_L007

source_name: IC_saline_nucleus accumbens

value: 0.5 mg/kg/infusion cocaine for 2 wks


title: Sample 39_IC_cocaine

description: s39; 39_ACTGAT_L008


title: Sample 38_IC_saline

description: s38; 38_GATCAG_L008


title: Sample 33_IC_cocaine

description: s33; 33_TAGCTT_L007


title: Sample 30_IC_cocaine

description: s30; 30_CAGATC_L006


title: NCr Mouse 1046. TimePoint 1.tRNA dep

tag: strain/background

value: Serum

value: NCr Mouse 1046


title: Sample 32_IC_saline

description: s32; 32_ATCACG_L007


title: Sample 31_IC_cocaine

description: s31; 31_CCGTCC_L006


title: 2C2

value: resistant

value: seedling leaf


title: Sample 27_IC_saline

description: s27; 27_GTGAAA_L005


title: Sample 24_IC_cocaine

description: s24; 24_GCCAAT_L005


title: Sample 28_IC_cocaine

description: s28; 28_CGATGT_L006


title: Sample 25_IC_saline

description: s25; 25_CTTGTA_L005


title: 2B3

description:
Excluded from DESeq analysis because of low correlation with the other 2 biological replicates
processed data file: DESeq_2A-2B.csv, DESeq_2B-2C.csv, DESeq_2B-4B.csv, DESeq_2B-5B.csv

value: Puccinia graminis f. sp. tritici


title: Sample 23_IC_saline

description: s23; 23_ACAGTG_L005


title: 2B2


title: NCr Mouse 1047. TimePoint 1.tRNA dep

value: NCr Mouse 1047


title: Sample 20_EC_cocaine

description: s20; 20_CGTACG_L004

source_name: EC_cocaine_nucleus accumbens

value: environmental enrichment for 30 days


title: Sample 22_IC_cocaine

description: s22; 22_ATTCCT_L004


title: Sample 19_EC_saline

description: s19; 19_GATCAG_L004

source_name: EC_saline_nucleus accumbens


title: 2A3

value: Columbus

value: susceptible


title: Sample 15_EC_saline

description: s15; 15_ACTTGA_L004


title: Sample 17_EC_saline

description: s17; 17_GGCTAC_L004


title: Sample 14_EC_cocaine

description: s14; 14_ATCACG_L004


title: Sample 29_IC_saline

description: s29; 29_TGACCA_L006


title: Sample 12_EC_cocaine

description: s12; 12_CAGATC_L002


title: Sample 13_EC_saline

description: s13; 13_CCGTCC_L002


title: Sample 16_EC_cocaine

description: s16; 16_TAGCTT_L004


title: Sample 7_EC_cocaine

description: s07; 7_CGATGT_L002


title: Sample 1_EC_cocaine

description: s01; 1_ACAGTG_L001


title: Sample 10_EC_saline

description: s10; 10_TGACCA_L002


title: Sample 2_EC_saline

description: s02; 2_GCCAAT_L001


title: L2H_0h_2-6-5

city: Zhoushan

first: Jianhua

last: Liu

state: Zhejiang

address: 10 Tiyu Road, Room 502

department: Ocean Research Centre of Zhoushan

institute: Zhejiang University

data_processing:
Using FastQC to check the qualities of sequenced reads
De novo assembly using Trinity with processed reads (ALL biosamples) (--SS_lib_type FR --CPU 60 --min_contig_length 300 --KMER_SIZE 25)
Transcriptome were annotated by running BLASTX to 6 algal genomes (evalue < 1e-7, length of homology to subject/ full length> 25%) (-max_target_seqs 1 -num_threads 60 -outfmt 6 -evalue 1e-7)
Expression levels of annotated EST were determined using Trinity-bundled perl script align_and_estimate_abundance.pl which utilizes RSEM to calculate FPKM values (--est_method RSEM --aln_method bowtie2 --SS_lib_type FR --thread_count 60 --trinity_mode)
Differentially expressed ESTs were identified using Trinity-bundled perl script run_DE_analysis.pl based on the ESTs counts Matrix
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
Supplementary_files_format_and_content: Non-redundant assembly of D.salina: D.salina_43236.fasta
Supplementary_files_format_and_content: FASTA sequences with annotation in this study: D.salina_annotated_6815.fasta

organism: Dunaliella salina

source_name: CCAP 19/3 algae culture cells

extract_protocol:
Total RNA from Dunaliella salina cells was isolated using RNeasy Plant Mini Kit (Qiagen, Netherlands) according to the manufacturer’s instructions. RNA integrity number (RIN) was measured using RNA 6000 Pico Kit (Agilent, USA) on an Agilent 2100 Bioanalyzer (Schroeder et al., 2006).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: high-salt to low-salt

tag: time point

value: CCAP 19/3


title: L2H_0h_8-4


title: L2H_24h_2-7-5


title: L2H_24h_1-7-5


title: L2H_4h_2-6-5


title: L2H_4h_1-6-5


title: L2H_4h_8-4


title: Sample 18_EC_cocaine

description: s18; 18_TTAGGC_L004

value: Sprague Dawley

value: male

tag: tissue


title: L2H_0h_1-6-5


title: H2L_24h_D1-15-5

value: low-salt to high-salt


title: H2L_24h_1-7-5


title: H2L_24h_2-7-5


title: first instar larvae rep4

description:
first instar larvae rep4
1-lar-rep4

source_name: first instar larvae

tag: developmental stage

value: larvae of first instar stage

value: whole body


title: H2L_4h_2-6-5

tag: strain


title: H2L_4h_D1-14-5


title: H2L_4h_1-6-5


title: H2L_0h_D1-14-5


title: H2L_0h_2-6-5


title: L2H_24h_9-4


title: first instar larvae rep2

description:
first instar larvae rep2
1-lar-rep2


title: first instar larvae rep3

description:
first instar larvae rep3
1-lar-rep3


title: Sample 3_EC_cocaine

description: s03; 3_CTTGTA_L001

value: post natal day 72

value: 0.5 mg/kg/infusion cocaine for 2 wks

value: Nucleus accumbens (Left)


title: Ctrl_36hpf_embryo

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

data_processing:
Illumina bcl2fastq2-v 2.16.0.10 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters -q -p 8 --no-novel-juncs -G -o.
Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Danio rerio

source_name: embryos

extract_protocol:
36hpf zebrafish embryos and 21dpf heart were collected respectively, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Magnetic beads with oligo(dT) were used to enrich the mRNAs, and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first-strand cDNA. Then double-stranded cDNA was synthesized by adding buffer solution, dNTPs and DNA polymeraseΙ. The double-stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions, then repaired at the tail ends, poly(A) added and enriched by PCR amplification. Finally, we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.

value: TU

value: embryo

value: control


title: Zfpm1_36hpf_embryo

value: zfpm1 mutant


title: H2L_0h_1-6-5


title: first instar larvae rep1

description:
first instar larvae rep1
1-lar-rep1


title: pre-iPSCs_A3_Sin3a_rep2

status: Public on Feb 21 2017

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: pre-iPSCs, Nanog (FLAG) + Sin3a, Sin3a-ChIP, replicate 2

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the mouse genome mm9 using the bowtie (v1.0.0) program, with parameters -m 1 -v 2 --best --strata.
The mapped reads were sorted, redundent reads were removed using samtools (v0.1.19)
ChIP-seq reads of biological replicates were merged. Peaks were determined by MACS program (v.2.0.10), using input ChIP-seq as the control data, and all other parameters followed the default settings.
Genome_build: mm9

source_name: Neural stem cell (NSC)-derived pre-iPSCs

growth_protocol: Female neural stem cell (NSC)-derived pre-iPSCs containing an Oct4-GFP-IRES-puro reporter were generated and used for reprogramming. Briefly, pre-iPSCs maintained in standard mESC (“serum + LIF”) culture medium [DMEM high glucose (Gibco), 15% heat inactivated FBS (Corning), Pen/Strep (Gibco), Nucleoside mix (Sigma), L-glutamine (Gibco), MEM Non-essential amino acids (Gibco), β-mercaptoethanol (0.1 mM), and recombinant LIF (20 ng/mL)] on gelatinized cell culture dishes.

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006)
ChIP-seq libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370) and NEBNext Multiplex Oligos for Illumina (E7335) according to the manufacturer’s protocol. Massively parallel sequencing was performed with the Platform: Nextseq 500. Flow cell was Nextseq 500/550 High Output Flow Cell Cartridge V2, reagent was Nextseq 500/550 V2 75 cycles.

treatment_protocol: Pre-iPSCs were stably transfected with combinations of PiggyBac-CAG (PB) transposon vectors along with PB transposase (PBase) in a 1:2 PB:PBase ratio. Transfections for pre-iPSCs were performed in suspension using 1 μL of Lipofectamine 2000 transfection reagent (Invitrogen) per μg of transfected DNA. 24 hours after transfection, stable line selection began with 200-250 μg/mL hygromycin (“Hygro”) and/or 10-20 μg/mL blasticidin S (“Blast”) for 5-7 days, with passaging of cells at least once during drug selection.

tag: ectopic gene

value: Sin3a + Nanog (FLAG)

tag: antibody

value: Sin3a (Abcam ab3479)


title: pre-iPSCs_A3_FLAG_rep2

description: pre-iPSCs, Nanog (FLAG) + Sin3a, FLAG-ChIP, replicate 2

value: Neural stem cell (NSC)-derived pre-iPSCs

value: FLAG (Sigma F1804)


title: pre-iPSCs_A3_Sin3a_rep1

description: pre-iPSCs, Nanog (FLAG) + Sin3a, Sin3a-ChIP, replicate 1


title: pre-iPSCs_A3_FLAG_rep1

description: pre-iPSCs, Nanog (FLAG) + Sin3a, FLAG-ChIP, replicate 1


title: pre-iPSCs_A1_Sin3a_rep2

description: pre-iPSCs, Sin3a + EV, Sin3a-ChIP, replicate 2


title: pre-iPSCs_A2_FLAG_rep1

description: pre-iPSCs, Nanog (FLAG) + EV, FLAG-ChIP, replicate 1

value: Nanog (FLAG)


title: Sample 6_EC_saline

description: s06; 6_GTGAAA_L001

value: Sprague Dawley

value: environmental enrichment for 30 days

value: saline for 2 wks


title: pre-iPSCs_Input

description: pre-iPSCs Input


title: pre-iPSCs_IgG

description: pre-iPSCs IgG-ChIP


title: pre-iPSCs_A2_FLAG_rep2

description: pre-iPSCs, Nanog (FLAG) + EV, FLAG-ChIP, replicate 2


title: pre-iPSCs_A1_Sin3a_rep1

description: pre-iPSCs, Sin3a + EV, Sin3a-ChIP, replicate 1