title: siYTHDC1 SRSF3 RIP Rep-2

description: RIP SRSF3 Poly(A)

data_processing:
After adaptor trimming with Cutadapt (v1.4.1) and quality control, 50 bp sequence reads were mapped to the human genome (hg19) using TopHat (v.2.0.11) and Bowtie (v1.0.1).
RIP-seq and RNA-seq differential expression was quantified between replicate experiments using Cufflinks (v.2.2.1)
Genome_build: hg19 (human)
Supplementary_files_format_and_content: Differential enrichment in siControl vs siYTHDC1 was assessed in repliacte using Cufflinks (v.2.2.1), including normalization to input samples under each condition.

extract_protocol:
RIP was performed according to literature procedure (Peritz et al., 2006) using polyA selected RNA following treatment with two uique siRNA sequences as biological replicates.
RIP-seq and subcellular RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA kit.

tag: antibody

value: MBL Code No. RN080PW Anti-SRSF3 (SRp20) pAb


title: siYTHDC1 NXF1 RIP Rep-1

status: Public on Oct 12 2017

type: SRA

city: Chicago

first: Ian

last: Roundtree

state: IL

address: 929 E 57th Street E307

department: Department of Chemistry

country: USA

institute: University of Chicago

description: RIP NXF1 Poly(A)

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: HeLa transfected with YTHDC1 siRNA

growth_protocol: HeLa cells (ATCC CCL-2) were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep.

treatment_protocol: Transfections were carried out using Lipofectamine RNAiMAX according to manufacturers protocol in the absence of antibiotics.

tag: cell line

value: HeLa

tag: culture media

value: DMEM

value: Abcam ab129160 Anti-NXF1 antibody [EPR8009]

tag: strain

value: ATCC CCL-2


title: siYTHDC1 SRSF3 RIP Rep-1

description: RIP SRSF3 Poly(A)


title: siControl SRSF3 RIP Rep-1

description: RIP SRSF3 Poly(A)

source_name: HeLa transfected with control siRNA


title: siControl NXF1 RIP Rep-2

description: RIP NXF1 Poly(A)


title: siYTHDC1 Input Rep-1

description: RIP input


title: siControl Input Rep-2

description: RIP input


title: siYTHDC1 Input Rep-2

description: RIP input

source_name: HeLa transfected with YT521 siRNA


title: IR_PB2

city: Hangzhou

first: Haiyan

last: Lin

state: Zhejiang

address: No 28, Rice Road, Fuyang Dist

country: China

institute: China National Rice Research Insititution

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: OS-Nipponbare-IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

growth_protocol: Rice submergence-intolerant variety IR64 plants were grown in plastic pots (25 cm in length, 18cm in width, and 8 cm in height) filled with 2.0 kg mixture of dry paddy soil and special seedling substrate (NPK content ≥ 5%, organic material ≥ 15%) in a 4:1 ratio, a 24-15-15 (N-P2O5-K2O) fertilizer was applied at 0.8 g per pot rate once before seeding. Thirty IR64 pre-germination seeds were sown in each pot. Irrigation was applied as needed to prevent any visible drought stress during seedling growth. Plants were thinned to twenty seedlings per pot 10 days after sowing.

extract_protocol:
Total RNA was extracted from leaves of seedlings using the Trizol (Invitrogen, Carlsbad, U.S.A.) according to the manufacturer’s protocols. The total RNA quantity and purifity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Labchip Kit (Agilent, CA, USA) with RIN number>7. 0.5 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen, Carlsbad, U.S.A.). The mRNA is fragmented into small pieces using divalent-cation under elevated temperature after purification, then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, U.S.A.), the average insert size for the paired-end libraries was 300 bp (±50 bp).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.

tag: variety

tag: genotype/phenotype

value: submergence-intolerant variety

tag: treated with

value: Paclobutrazol (PB)

tag: condition

value: four days in submergence

tag: tissue

value: leaves


title: siYTHDC1 Total

description: siYTHDC1 Total

data_processing:
After adaptor trimming with Cutadapt (v1.4.1) and quality control, 50 bp sequence reads were mapped to the human genome (hg19) using TopHat (v.2.0.11) and Bowtie (v1.0.1). 150 bp reads from paired-end sequencing were mapped directly to the mouse genome (mm9) using TopHat.
PAR-CLIP peaks were called using PARalyzer (v.1.5) with default parameters.
RIP-seq and RNA-seq differential expression was quantified between replicate experiments using Cufflinks (v.2.2.1)
Differential splicing was analyzed using MATS (v3.0.8) (rMATS) below a FDR of 0.05.
Genome_build: hg19 (human), mm9 (mouse)

growth_protocol: HeLa cells (ATCC CCL-2) were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep. mESCs (CGR8) were cultured in GMEM supplemented with 10% FBS, Non-Essential Amino Acids, 1 mM sodium pyruvate, 1 mM 2-mercaptoethanol and 1,000 U/mL LIF. All cells were cultured at 37 degrees C in 5% CO2 incubators.

extract_protocol:
PAR-CLIP was performed as previously described (Xu et al., 2014). Breifly, Flag-tagged YTHDC1 was immunoprecipitated from transfected HeLa cells and treated with Rnase. Bound RNA fragments were isolated with TriZol following Proteinase K digestion and subject to ibrary construction.
RIP was performed according to literature procedure (Peritz et al., 2006) using polyA selected RNA and ribosomal RNA depleted RNA as biological replicates.
HeLa cells were fractionated using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Scientific) according to manufacturer protocol with the following modifications: following cytoplasmic isolation, nuclei were washed extensively (4 x 200 μL) with PBS. RNA from each portion was collected using Directzol RNA miniprep (Zymo Research) and treated with DNaseI. Samples were depleted of ribosomal RNA prior to sequencing.
mESC mRNA was isolated using TriZol reagent and purified using poly-T oligo magnetic beads.
PAR-CLIP libraries were constructed using Illumina TruSeq Small RNA (Rep 1) or NEBNext Small RNA (Rep 2) library construction kits. RIP-seq and subcellular RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA kit. mESC mRNA libraries were constructed using the NEBNext Ultra Directional RNA library construction kit.

treatment_protocol: Transfections were carried out using Lipofectamine 2000, Lipofectamine LTX (multiple plasmids) or Lipofectamine RNAiMAX according to manufacturers protocol in the absence of antibiotics.


title: siYTHDC1 Nucleus

description: siYTHDC1 Nucleus


title: siYTHDC1 Cytoplasm

description: siYTHDC1 Cytoplasm


title: siControl Nucleus re

description: siControl Nucleus re


title: IR_CK2

value: ethanol solvent (untreated control)


title: siYT521 Total

description: siYT521 Total


title: siYT521 Nucleus

description: siYT521 Nucleus


title: siControl Cytoplasm

description: siControl Cytoplasm


title: siControl Total

description: siControl Total


title: siYT521 Cytoplasm

description: siYT521 Cytoplasm


title: siControl Nucleus

description: siControl Nucleus


title: siControl SRSF3 RIP Rep-2

description: RIP SRSF3 Poly(A)


title: siYTHDC1 NXF1 RIP Rep-2

description: RIP NXF1 Poly(A)


title: YTHDC1 IP Ribo(-)

description: RIP YTHDC1 Ribo(-)

source_name: HeLa transfected with YTHDC1-Flag

value: Sigma anti-FLAG M2


title: siControl NXF1 RIP Rep-1

description: RIP NXF1 Poly(A)


title: Input Ribo(-)

description: RIP input


title: Input Poly(A)

description: RIP input


title: siControl Total re

description: siControl Total re


title: YTHDC1 PAR-CLIP Rep 2

description: PAR-CLIP


title: ESC (alternative genotype) Hdac3-/- Input

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

library_source: genomic

data_processing:
Fastq files were aligned to the mm9 reference genome using STAR with the following parameters --alignIntronMax 1 --alignEndsType EndToEnd
Duplicate reads were marked and removed using Picard Tools and Bamtools
Replicates were merged and downsampled using PicardTools
Peaks were called using EDD using the following parameters  '--bin-size auto --fdr 5 -g 10 '
Coverage tracks were created using DeepTools BamCompare
Genome_build: mm9
Supplementary_files_format_and_content: Input normalized coverage wiggle files and EDD peak bedfiles

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic Stem Cell

growth_protocol: Embryonic stem cells (ESCs) were derived from CMV-creERT; Hdac3f/f mice as previously described {Nagy, 2002 #108}. Briefly, blastocysts were collected at E3.5 and cultured on STO feeder cells in standard ESC media + leukemia inhibitory factor (LIF) + 50µM MEK1 inhibitor (Cell Signaling #9900) for 7 days until the blastocyst hatches and forms colony. Individual colonies were subcultured for about 1 week when MEK1 inhibitor is removed and cells passaged as a normal ESC line. Cardiac differentiation from these cells was adapted from published protocols {Christoforou, 2008 #9;Kattman, 2011 #18}. Briefly, ESCs were cultured and maintained on a feeder layer of mitotically inactivated MEFs in DMEM with 15% FBS (Fisher Scientific # SH3007003) and ESGRO LIF. Differentiation through hanging droplets method was initiated following ESC dissociation and suspension at 5 x 104 cells/ml in DMEM with 10% FBS (Atlanta Biologicals #S11550) without LIF in 20 µl drops. Two days after droplets formation, embryoid bodies (EBs) were transferred in suspension onto poly-HEMA coated dishes. After another two days, EBs were plated on gelatin coated dishes in cardiac differentiation media (StemPro-34 SF medium (Invitrogen #10639-011) supplemented with 5ng/ml VEGF (R&D systems), 10ng/ml bFGF (R&D systems), 12.5ng/ml FGF10 (R&D systems), 2.5µM XAV939 (Cayman Chemical #13596), 1mM Ascorbic Acid (Sigma #A4403) and 2mM Glutamax (Invitrogen #35050-061)). Beating cells were visible within 24-48 hours. Hdac3 knockout in CMV-creERT; Hdac3f/f ES cells were performed using 4-Hydroxytamoxifen (Sigma #T176) dissolved in 100% ethanol. Cells were treated with 1 µg/ml tamoxifen for 24 hour to delete Hdac3.

extract_protocol:
Murine ESCs and ESC-derived CMs were crosslinked in culture by addition of methanol-free formaldehyde (ThermoFisher; final 1% v/v) and incubated at room temperature for 10 minutes with gentle rotation. Crosslinking was quenched by addition of glycine (final 125mM) and incubated at room temperature for 5 minutes with gentle rotation. Media was discarded and replaced with PBS; cells were scraped and transferred to conical tubes and pelleted by centrifugation (250xg, 5 minutes at room temperature). Supernatant was removed, and pellets were flash frozen on dry ice and stored at -80C.    Six hours before lysing cells, 30uL protein G magnetic beads (per ChIP sample) were washed 3 times in blocking buffer (0.5% BSA in PBS); beads were resuspended in 250uL blocking buffer and 2ug antibody (Lamin B: sc6217 [Santa Cruz]; H3K9me2: ab1220 [Abcam]) and rotated at 4C for at least 6 hours. Crude nuclei were isolated from frozen crosslinked cells as follows: cell pellet (from 10cm plate) was resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP‐40, 0.25% Triton X‐100, and protease inhibitors), and rotated at 4C for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and the pellet was resuspended in 10mL cold Lysis Buffer 2 (10mM Tris‐HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors), and rotated at room temperature for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and nuclei were resuspended/lysed in 1mL cold Lysis Buffer 3 (10mM Tris‐HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na‐Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris) Samples were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Lysates were transferred to tubes and Triton X-100 was added (final 1%) followed by centrifugation (top speed, 10 minutes at 4C in microcentrifuge). Supernatant was transferred to a new tube; protein concentration was measured by Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer, resuspended in 50uL blocking buffer and added to 500ug input protein for overnight incubation with rotation at 4C. 50ug lysate was aliquoted and stored at -20C for input. On day 2, beads were washed 5 times in 1mL RIPA buffer (50mM HEPES‐KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP‐40, 0.7% Na‐Deoxycholate) with 2-minute incubation at room temperature with rotation for each wash. Beads were washed in 1mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes with rotation at room temperature before final resuspension in 210uL elution buffer (50mM Tris‐HCl pH 8.0, 10mM EDTA, 1% SDS). To elute, beads were incubated with agitation at 65C for 30 minutes. 200uL eluate was removed to a fresh tube, and all samples (ChIP and reserved inputs) were reverse-crosslinked overnight at 65C with agitation for a minimum of 12 hours, but not more than 18 hours. 200uL 1xTE was added to reverse crosslinked DNA to dilute SDS, and samples were RNaseA treated (final 0.2mg/mL RNase; 37C for 2 hours) and Proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours) before phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.
ChIP and input DNA was quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for multiplex sequencing. Library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems). Libraries were pooled for multiplex sequencing, requantified, and sequenced on the Illumina NextSeq500 platform (vII; 75bp single end sequencing; Illumina).

treatment_protocol: For differentiation of wild-type cells related to LaminB and H3K9me2 ChIP-seq experiments, the protocol was slightly modified: mESCs were cultured in serum-free, feeder-free 2i media (50% DMD-F12 (Invitrogen); 50% Neurobasal medium (Invitrogen); 0.5 x N2 supplement (Invitrogen); 0.5 x B27 supplement (Invitrogen); 0.05% BSA (Invitrogen); L-Glutamine (Invitrogen); Penicilin/Streptomycin (Invitrogen) and 150 uM ß-mercaptoethanol (Sigma); 20 ng/ml LIF (eBioscience), 3 µM CHIR (Stemgent) and 1 µM PD325901 (Stemgent). ESCs were differentiated as EBs to the cardiomyocyte lineage. EBs were generated at day 0 of differentiation in SF-D media (75% IMDM (Invitrogen); 25% Ham’s F12 (Invitrogen); 0.5 x N2 supplement (Invitrogen); 0.5 x B27 supplement (Invitrogen); 0.05% BSA (Invitrogen); L-Glutamine (Invitrogen); Penicillin/Streptomycin (Invitrogen) and 150 µM beta-mercaptoethanol (Sigma) with ascorbic acid (0.5 mM) and monothioglycerol (0.4 mM). On day 2, EBs were collected, dissociated, and reaggregated in SF-D media with VEGF (5 ng/ml, R&D Systems), Activin A (8 ng/ml, R&D Systems), and BMP4 (1 ng/ml, R&D Systems) to induce cardiac mesoderm formation. At day 4 EBs were collected, washed (with IMDM), and cultured in StemPro (Invitrogen) with VEGF (5 ng/ml, R&D Systems), bFGF (10 ng/ml, R&D SYstems), and XAV (10 µM, Stemgent) to induce cardiomyocyte differentiation. Subsequent media changes were done in the same media without XAV, and cells were collected on day 10 of differentiation.

tag: cell type

value: Embryonic Stem Cell

tag: genotype

value: CMV-creERT; Hdac3f/f

tag: chip antibody


title: YTHDC1 PAR-CLIP Rep 1

description: PAR-CLIP


title: ESC (alternative genotype) Hdac3-/- LaminB ChIP-seq rep2

description:
mESC_HDAC3-ERCre_PlusTamoxSet2_LB1
mESC_LB1_ds.bw
mESC_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed

value: Lamin B:sc6217 [Santa Cruz]


title: UVB-TBPT-rep3

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
gene_exp.diff: UV_2
genes.read_group_tracking: UV_2

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--no-novel-juncs) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: Melanocyte stem cells

growth_protocol: Mice were raised under standard conditions

extract_protocol:
Cells were sorted through FACS, and total RNA was isolated using Trizol LS reagent
RNA-seq libraries were prepared from 500 ng total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Chemical Depilation or UVB irradiation

tag: protocol

value: UVB

value: Skin

tag: age

value: Postnatal 10 weeks

value: TBPT


title: siControl Cytoplasm re

description: siControl Cytoplasm re

value: HeLa


title: Active-TBPT-rep1

description:
gene_exp.diff: A_0
genes.read_group_tracking: A_0

value: Active


title: Active-TBPT-rep2

description:
gene_exp.diff: A_1
genes.read_group_tracking: A_1


title: ESC (alternative genotype) Hdac3-/- LaminB ChIP-seq rep1

description:
mESC_HDAC3-ERCre_PlusTamoxSet1_LB1
mESC_LB1_ds.bw
mESC_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed


title: Quiescent-TBPT-rep2

description:
gene_exp.diff: Q_1
genes.read_group_tracking: Q_1

value: Quiescent


title: Quiescent-TBPT-rep3

description:
gene_exp.diff: Q_2
genes.read_group_tracking: Q_2


title: siControl Input Rep-1

description: RIP input

value: DMEM

value: ATCC CCL-2


title: UVB-TBPT-rep1

description:
gene_exp.diff: UV_0
genes.read_group_tracking: UV_0


title: UVB-TBPT-rep2

description:
gene_exp.diff: UV_1
genes.read_group_tracking: UV_1


title: Active-TBPT-rep3

description:
gene_exp.diff: A_2
genes.read_group_tracking: A_2


title: ESC (alternative genotype) H3K9me2 ChIP-seq rep2

description:
mESC_HDAC3-ERCre_MinusTamoxSet2_H3K9me2
mESC_H3K9me2.bw
mESC_H3K9me2_g_10_bin_auto_fdr_5_peaks.bed

value: H3K9me2:ab1220 [Abcam]


title: Quiescent-TBPT-rep1

description:
gene_exp.diff: Q_0
genes.read_group_tracking: Q_0


title: ESC (alternative genotype) LaminB ChIP-seq rep1

description:
mESC_HDAC3-ERCre_MinusTamoxSet1_LB1
mESC_LB1_ds.bw
mESC_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed


title: ESC (alternative genotype) LaminB ChIP-seq rep2

description:
mESC_HDAC3-ERCre_MinusTamoxSet2_LB1
mESC_LB1_ds.bw
mESC_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed


title: ESC (alternative genotype) Input

description:
mESC_HDAC3-ERCre_MinusTamoxSet1_Input
mESC_Input_filter.bw


title: YTHDC1 IP Poly(A)

description: RIP YTHDC1 IP Poly(A)


title: ESC LaminB ChIP-seq rep2

description:
mESC_LB1_Lib42
mESC_LB1_ds.bw
mESC_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed

value: WT


title: 112N

city: Shijiazhuang

first: Li

last: Meng

address: 12# Jiankang road

institute: colon tissues

data_processing:
bcl2fastq-2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 â€“r 70 --library-type fr-unstranded
Transcripts per million (TPM) were calculated using a protocol from Günter P. Wagner, Koryu Kin, Vincent J. Lynch. Theory Biosci. (2012) 131:281285.
Genome_build: hg19
Supplementary_files_format_and_content: gene_exp.txt: Tab-delimited text file includes COUNT and TPM values for each Sample.

source_name: colon

extract_protocol:
Samples were immediately frozen in liquid nitrogen and stored at  -80℃ until further use.RNA was harvested using Trizol reagent.  NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
rRNAs were removed from Total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA) and fragmented to approximately 200bp. Subsequently, the purified  RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).

tag: pair id

value: nontumor colon tissue

tag: Sex

value: male

tag: Stage


title: ESC LaminB ChIP-seq rep1

description:
mESC_LB1_Lib19
mESC_LB1_ds.bw
mESC_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed


title: ESC Input

description:
mESC_Input_Lib20
mESC_Input_filter.bw


title: ESC H3K9me2 ChIP-seq rep2

description:
mESC_H3K9me2_Lib41
mESC_H3K9me2.bw
mESC_H3K9me2_g_10_bin_auto_fdr_5_peaks.bed


title: ESC H3K9me2 ChIP-seq rep1

description:
mESC_H3K9me2_Lib18
mESC_H3K9me2.bw
mESC_H3K9me2_g_10_bin_auto_fdr_5_peaks.bed


title: 111N

value: female


title: 111C

value: colon cancer tissue


title: 101C


title: CM LaminB ChIP-seq rep1

description:
CM_LB1_Lib23
CM_LB1_ds.bw
CM_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed

source_name: Cardiomyocytes

value: Cardiomyocytes


title: 94N


title: CM H3K9me2 ChIP-seq rep1

description:
CM_H3K9me2_Lib22
CM_H3K9me2.bw
CM_H3K9me2_g_10_bin_auto_fdr_5_peaks.bed


title: 94C


title: ESC (alternative genotype) H3K9me2 ChIP-seq rep1

description:
mESC_HDAC3-ERCre_MinusTamoxSet1_H3K9me2
mESC_H3K9me2.bw
mESC_H3K9me2_g_10_bin_auto_fdr_5_peaks.bed

value: Embryonic Stem Cell

value: CMV-creERT; Hdac3f/f


title: CM H3K9me2 ChIP-seq rep2

description:
CM_H3K9me2_Lib44
CM_H3K9me2.bw
CM_H3K9me2_g_10_bin_auto_fdr_5_peaks.bed


title: 101N


title: CM Input


title: TRV8

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

country: Spain

institute: Centro de Edafología y Biología Aplicada del Segura

description: small RNAs

data_processing:
Basecalls performed using CASAVA version 1.4
Adapters were trimmed and small RNAs were filtered by length (20 to 26 nts) using in-house Perl scripts
Rfam mappings were removed using Bowtie
sRNAs were mapped against TRV1 genome or against TAIR10 cDNAs using Bowtie
sRNAs were collapsed using in-house Perl scripts
Supplementary_files_format_and_content: tab delimited files containing sRNA sequences mapping to either TRV1 or Arabidopsis cDNAs and counts per each sRNA sequence

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Arabidopsis plants were grown in chambers at 22-24 ºC and with a 16h photoperiod

extract_protocol:
Total RNA was extracted using Trizol according to manufacturer’s instructions
Libraries were prepaired according to Illumina TruSeq Small RNA Library Prep Kit

treatment_protocol: Rossette leaves were rub inoculated with buffer or with a TRV-infected N. benthamiana extract

tag: ecotype

tag: treatment

value: Infected with TRV

tag: timepoint

value: 8 dpi


title: OAB-49

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

description: piglets from three sows (Danish Landrace x Large White x Duroc) were caesarean-delivered at preterm (d 106 or 90% of gestation)

data_processing:
Raw sequencing data were processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 30% ‘N’s or more than 10% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the NCBI pig reference genome (Sscrofa10.2) using the BSMAP v2.73, to identify methylcytosine (mC).
The uniquely mapped reads that contained at least one enzyme digestion site in the ends were used for further analysis.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Cout files include chromosome ID,C sites' coordinate, the number of methylated reads and non-methylated reads:
(1) chromosome
(2) coordinate (1-based)
(3) strand (+/-)
(4) type (CG/CHH/CHG)
(5) sequence context (2nt upstream to 2nt downstream in Watson strand direction)
(6) methylation ratio, calculated as #C_counts / #eff_CT_counts
(7) number of effective total C+T counts on this locus (#eff_CT_counts)
(8) number of total C counts on this locus (#C_counts)
(9) number of total C+T counts on this locuso (#CT_counts)
(10) number of total G counts on this locus of reverse strand (#rev_G_counts)
(11) number of total G+A counts on this locus of reverse strand (#rev_GA_counts)
(12) lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.
(13) upper bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.

organism: Sus scrofa

source_name: OAB

extract_protocol:
Piglets were euthanized by sodium pentobarbital (200 mg/kg, i.a.). The gastrointestinal tract was immediately removed. The small intestine was carefully emptied of its contents and weighed. From the middle of distal small intestine, small pieces were snap frozen in liquid nitrogen and kept at −80°C for later analysis of DNA methylome and inflammatory cytokines.
Genomic DNA from the above 14 distal intestinal tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen) and was subjected to RRBS library preparation. Briefly, 1.5 µg of genomic DNA was digested with MspI enzymes (NEB), followed by end-repairing, A-base tailing and 5-methylcytosine modified adapter ligation. Size selection was performed to obtain DNA fractions of 40-250bp ranges of MspI digested products. Afterwards, bisulfite treatment was conducted using ZYMO EZ DNA Methylation-Gold Kit™ following the manufacturer’s instructions. 12 cycles of PCR were performed to enrich the DNA fragments, in which each library was integrated with DNA index. The libraries were analyzed by Agilent 2100 Bioanalyzer and QPCR for quality control. Libraries were then subjected to paired-end 125bp multiplex sequencing on Hiseq 2500 platform.

tag: maternal breed

value: Danish Landrace x Large White x Duroc

tag: developmental stage

value: piglet

value: broad-spectrum antibiotics

value: distal small intestine


title: OAB-47


title: OAB-18


title: 91N


title: OAB-16


title: 57N


title: 91C


title: CM LaminB ChIP-seq rep2

description:
CM_LB1_Lib45
CM_LB1_ds.bw
CM_LB1_ds_g_10_bin_auto_fdr_5_peaks.bed

value: Lamin B:sc6217 [Santa Cruz]


title: OAB-15


title: 112C


title: OAB-10


title: 55N


title: OAB-06


title: 57C


title: CON-45

source_name: CON

value: control


title: 55C


title: CON-44


title: MOCK8

description: small RNAs

value: Healthy


title: 48N


title: CON-37


title: CON-26


title: CON-20


title: 29N


title: 34N


title: CON-11


title: CON-04


title: 29C


title: Input DNA

city: Ann Arbor

first: Jean-Francois

middle: Michel

last: Rual

state: Mi

address: 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan

data_processing:
Sequenced reads were preprocessed to trim adaptor sequences (Trimmomatic)
Aligned to human reference genome (hg19) using BWA software (version 0.7.15). Only uniquely mapped reads were used in downstream analyses.
Duplicated ChIP-seq samples were processed with Model-based Analysis for ChIP-seq 2 (MACS2) to identify peaks using the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: MDA-MB-231, Input DNA

growth_protocol: MDA-MB-231 cells were cultivated in RPMI1640 medium supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
Multiplexed ChIP-seq libraries were prepared at University of Michigan DNA Sequencing Core. 50-cycle single-end sequencing runs were performed on Illumina HiSeq 2500 at a sequencing depth of 30-40 million aligned reads per sample. Sequenced reads were preprocessed to trim adaptor sequences (Trimmomatic) and then aligned to human reference genome (hg19) using BWA software (version 0.7.15).

tag: cell line


title: 34C


title: L3MBTL3 ChIP-seq

source_name: MDA-MB-231, L3MBTL3 ChIP-seq

value: anti-L3MBTL3 (Bethyl, Catalog# A302-854A, Lot# 1)


title: RBPJ ChIP-seq

source_name: MDA-MB-231, RBPJ ChIP-seq

value: RBPSUH(D10A4) (Cell Signaling, Catalog# 5313s, lot# 3)


title: HKE293-Post-DRB-GRO-Rep2

city: Nanjing

first: Jia-Yu

last: Chen

state: CA

address: No 163 of XianlinAvenue, Qixia District

department: School of Life Sciences

institute: Nanjing University

description: RNA

data_processing:
R-ChIP and GRO-seq sequence reads were mapped to the human genome (hg19) via default --local mode of Bowtie2
Repeatedly-mapped reads, reads with low mapping quality (-q 30 for R-ChIP and -q 2 for GRO-seq) and PCR duplicates were discarded according to Samtools
R-ChIP reads were extended to 150 nt (which corresponds to the average size of gel-isolated DNA fragments). We then used MACS2 with default settings to call narrow (or broad when necessary) R-loop peaks. Only confident R-loop peaks with ≥5 folds enrichment and with q-value ≤ 0.001 (or 0.0001 for broad peak) over background were kept for subsequent analyses. GRO-seq reads were extended to 90 nt and were used to estimate the expression level. The expression level in promoter proximal regions was quantified as RPKM in the region -30 to +300 bp from TSS, while the overall gene expression level was defined as RPKM in the downstream region from +300 bp of TSS to gene end.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1X penicillin-streptomycin; K562 cells were cultured in RPMI1640 with 10% FBS, 2mM sodium pyruvate and 1X penicillin-streptomycin.

extract_protocol:
For R-ChIP, cells expressing mutant RNASEH1 were fixed followed by nuclei extraction. Chromatin DNA was sheared to 250-600 bp in size by sonication followed by incubation with magnetic beads conjugated with anti-V5 antibody overnight at 4°C. Beads were sequentially washed in high salt buffers to remove non-specifically bound protein and chromtin complexes. The enriched RNASEH1-RNA/DNA complex was eluted and decrosslinked overnight at 65°C. After sequential RNase A and Proteinase K treatment, the precipitated hybrid was cleaned by phenol and phenol:chloroform:isoamyl alcohol, followed by ethanol precipitation. The recovered fragment was subjected to library construction. For GRO-seq, the intact nuclei were extracted and mixed with run-on reaction buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 200 U/ml RNaseOut, 1% Sarkosyl, 500 μM ATP, 500 μM GTP, 500 μM Br-UTP and 2 μM CTP) for in vitro run-on reaction and Br-U labeling for 5 min at 30°C. The reaction was stopped by adding TRIzol LS reagent (Thermo Fisher). RNA was then extracted followed by treatment wtih DNase I (Promega) and antarctic phosphatase (NEB). For immunopurification, equilibrated and blocked anti-BrdU agarose beads (Santa Cruz) were mixed with RNA for 1 hr at 4°C. After binding, beads were thoroughly washed and BrU-incorporated RNAs were eluted. The BrU-RNA end was repaired by T4 PNK (NEB) and then subjected to poly-A tailing reaction. Tailed RNAs were reverse transcribed into cDNA by using superscript III (Thermo Fisher) and the GRO-seq RT primer (5’-pAGATCGGAAGAGCGTCGTGTAG;GCAGAAGACGGCATACGAGATTTTTTTTTTTTTTTTTTTTVN-3’), where p indicates 5’ phosphate; ‘;’ indicates the abasic dSpacer furan, and VN indicates degenerate nucleotides. The cDNA products were treated with Exonuclease I (NEB) for 1 hr at 37°C to eliminate excessive primer. The resultant cDNA was resolved in 10% polyacrylamide TBE-urea gel and the fraction in the size range of 100-400 bp was excised and recovered.
For R-ChIP library construction, DNA from precipitated RNA/DNA hybrids was used as the template to generate dsDNA by random priming using a tail-containing N9 primer (5’- /invddt/CAAGCAGAAGACGGCATACGAGNNNNNNNNN-3’). An “A” base was then added to the 3’ end and the standard Illumina adaptor was ligated to one end of the resultant dsDNA. After purification,PCR were performed and the libraries in the size range of 130-350 bp were gel-isolated and purified. For GRO-seq library construction, cDNA was circularized and re-linearized. the libraries were amplified by PCR reaction. the final products were resolved in a non-denaturing 10% polyacrylamide TBE gel and libraries with the size 130-250 bp were recovered.
R-ChIP and GRO-seq

treatment_protocol: DRB (100 mM) was added to the medium to the final concentration of 100 μM. Cells were incubated for 2 hrs. To wash off DRB, the DRB-containing medium was aspirated, followed by washing with PBS. Fresh medium was then added and the cells were incubated for 30 min before harvest.

value: After DRB removal for 30min


title: Estrogen_84h (41-153)

city: Davis

first: Grace

middle: E

last: Berryhill

address: One Shields Avenue

department: Animal Science

institute: University of California, Davis

description:
CountLate_use.txt
Late_RPKM_export_07_09_2016.txt

data_processing:
Data were imported into the CLC Genomics Workbench. Demultiplexed libraries were concatenated to a single file for each sample ID.
Adapter sequences were trimmed from the reads using the CLC Genomics Workbench. Quality Control reports were created and inspected for each sample.
Reads were mapped to the mouse genome (Mus musculus GRCm38.84) using the CLC Genomics Workbench.
Matrix files with raw counts and RPKM for each gene were exported from the CLC Genomics Workbench.
Genome_build: Mus musculus GRCm38.84
Supplementary_files_format_and_content: tab delimited text files containing RPKM for each sample, and tab delimited text files containing raw counts.

growth_protocol: Balb/cJ mice were ovariectomized at 21d of postnatal age.

extract_protocol:
The lymph node was removed from one #4 inguinal mammary gland and the tissue proximal to the teat and extending to the region where the lymph node was excised was flash frozen in liquid nitrogen. Tissues were stored at -80C until further processing. Total RNA was extracted using TriReagent (Qiazol) and DNase treated in solution followed by an on-column clean-up. RNA integrity was assesed using automated gel electrophoresis (Bio-Rad Experion). Samples with an RQI between 7.5-9.4 (mean 8.7) were submitted for library preparation.
Libraries were constructed by the UC Davis DNA Technologies Core using the Stranded mRNA-Seq Kit for Illumina platforms with poly-A enrichment with 10 cycles of PCR. All libraries were pooled and sequenced across 4 lanes. There were an average of 39 million reads per library.

treatment_protocol: After a 7d recovery period, mice were fed either a defined control diet (AIN 93G based) or the control diet with 2.7% fat as conjugated linoleic acid (CLA). Another group was fed the control diet and administered estrogen in the drinking water (200 nM). Mice were euthanized by CO2 inhalation 60, 84, 108, or 132h after starting treatment.

tag: strain

value: Balb/cJ

value: mammary gland

tag: reproductive status

value: OVX at 21d

tag: agent

value: Estrogen

tag: time


title: Estrogen_84h (41-152)

tag: tissue


title: Estrogen_60h (41-163)

description:
CountEarly_use.txt
Early_RPKM_export_07_09_2016.txt


title: Estrogen_60h (41-164)


title: HKE293-Post-DRB-GRO-Rep1

description: RNA


title: HKE293-DRB(+)-GRO-Rep1

description: RNA

value: DRB


title: HKE293-DRB(-)-GRO-Rep2

description: RNA


title: Estrogen_84h (41-151)


title: Estrogen_60h (41-150)


title: HKE293-DRB(-)-GRO-Rep1

description: RNA


title: Estrogen_60h (41-148)


title: 48C

value: colon cancer tissue

value: female


title: Estrogen_60h (41-149)


title: Estrogen_84h (41-139)


title: HKE293-DRB(+)-V5ChIP-Rep1

description: RNA-DNA hybird

tag: rnaseh mutant

tag: antibody


title: Estrogen_84h (41-138)


title: HKE293-DRB(+)-GRO-Rep2

description: RNA


title: CLA_132h (41-121)

value: CLA


title: HKE293-DRB(+)-V5ChIP-Rep2

description: RNA-DNA hybird


title: Control_132h (41-120)

value: Control


title: HKE293-DRB(-)-V5ChIP-Rep1

description: RNA-DNA hybird


title: CLA_108h (41-117)


title: K562-D210N-Input

description: DNA


title: K562-D210N-V5ChIP-Rep2

description: RNA-DNA hybird


title: K562-D210N-V5ChIP-Rep1

description: RNA-DNA hybird


title: CLA_108h (41-118)


title: Control_108h (41-114)


title: Control_108h (41-115)


title: Control_84h (41-112)


title: CLA_132h (41-94)


title: Control_132h (41-91)


title: HKE293-WKKD-V5ChIP

description: RNA-DNA hybird


title: Control_108h (41-116)


title: HKE293-ΔHC-V5ChIP

description: RNA-DNA hybird

value: delta-HC


title: HKE293-Post-DRB-V5ChIP-Rep1

description: RNA-DNA hybird


title: HKE293-DRB(-)-V5ChIP-Rep2

description: RNA-DNA hybird


title: Control_132h (41-92)


title: HKE293-WKKD-Input

description: DNA


title: Control_84h (41-88)


title: v1_IP_ribo_tes

city: Moscow

first: Sergey

middle: A

last: Lavrov

address: Kurchatov sq. 2

department: DMBC

country: Russia

institute: IMG

description: βNACtes-precipitated ribosomes

data_processing:
Basecalling by Illumina Casava1.8 software
Preprocessing: Sequenced reads were converted to Sanger quality scores type by Galaxy tool FASTQ Parallel Groomer (Galaxy Version 0.3.1) for subsequent manipulations. Sequencing artefacts were removed by Galaxy tool Remove sequencing artifacts. Quality trimming, adapter trimming and short reads removal were done by Flexbar (2.5) in Galaxy (Max uncalled:1, Phred-trimming treshold:30, Adapter removal:on, Trim-end mode:Any, Min-overlap:5, Threshold:3, Minimum read length:18), using adapter sequences from "2011-08-03 Illumina Adapter Sequence Letter". rRNA sequences were removed by assembly of RNA-seq reads to Drosophila rDNA sequences using Bowtie2 with default parameters and taking nonaligned sequences for further analysis.
Mapping: Transcripts were assembled by TopHat v2.0.14 (Galaxy tool) using preprocessed reads and dm3 R5 Drosophila genome as a reference. Parameters list: (Max realign edit distance:0, Max edit distance:2, Library Type:FR Unstranded, Final read mismatches:2, Use bowtie -n mode:No, Anchor length:8, Maximum number of mismatches that can appear in the anchor region of spliced alignment:0, The minimum intron length:29, The maximum intron length:167000, Allow indel search:No, Maximum number of alignments to be allowed:20, Minimum intron length that may be found during split-segment (default) search:29, Maximum intron length that may be found during split-segment (default) search:167000, Number of mismatches allowed in each segment alignment for reads mapped independently:2, Minimum length of read segments:20, Use Coverage Search:Yes, Minimum intron length that may be found during coverage search:29, Maximum intron length that may be found during coverage search:167000, Use Microexon Search:No, Do Fusion Search:No, Set Bowtie2 settings:Yes, Use Preset options:Yes, Preset option:Very sensitive).
FPKM calculation: Was done by Cufflinks v2.2.1(Galaxy Tool) using Tophat bam output and dm3_genes.gtf dm3 genes list from Ensemble. Parameters: Max Intron Length:167000, Min Isoform Fraction:0.1, Pre MRNA Fraction:0.15, Reference Annotation: dm3_genes.gtf, Count hits compatible with reference RNAs only: Yes, Perform Bias Correction:Yes, Reference sequence data: Using reference genome:dm3, Use multi-read correct:Yes. Genes output tables from Cufflinks were used for gene-level FPKM data.
The gene IDs and FPKM values from Cufflinks output tables were imported into FlexArray 1.6.3 software package (McGill University and Genome Quebec Innovation Centre) as custom normalized data for further processing and visualization. Genes with zero FPKM in all samples were removed, and the average between-replica FPKM values for IP and Total (control) were used for fold change (log2(IP/Total)) calculation.
Genome_build: D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3)
Supplementary_files_format_and_content: Comma-separated text file with header. Columns: "Gene" gene name, "FBID" Flybase Gene ID,  "IP_RIBO_TES" - average FPKM values of immunoprecipitated samples, "TOTAL_RIBO_TES" - average FPKM values of control (total ribosomal RNA) samples, "LOG2(IP/TOTAL)" log2-transformed ratio of immunoprecipitation to control.

organism: Drosophila melanogaster

source_name: testes

growth_protocol: Flies were maintained on standart media at 25C

extract_protocol:
1000 frozen testes were homogenized in ice-cold LB (25 mM HEPES, pH 7.6, 100 mM KCL, 5 mM MgCl2, 1 mM DTT, 1 х Complete protease inhibitor mix (Roche), 200 units/ml RNase inhibitor RiboLock (Thermo Scientific), 0.015% digitonin (Sigma), 1% NP-40, 0.5% deoxycholate sodium, 100 µg/ml  cycloheximide (Sigma)), cell debris was removed by centrifugation at 14000 rpm in Eppendorf microcentrifuge at 4C for 20 min. A post-mitochondrial supernatant was then centrifugated for 4h at 39000 rpm in a swinging bucket rotor (Beckman SW40 Ti) at 4C. Pellet was washed with LB buffer and dissolved in a buffer for immunoprecipitation (IPB: 50 mM Tris pH 8.0, 150 mM NaCl, 1 х Complete protease inhibitor mix (Roche), 40 units/ml RNase inhibitor RiboLock (Thermo Scientific), 1% NP-40, 0.5% deoxycholate sodium, 0.5% CHAPS). Part of ribosome extract (tesRb) was used for testes total ribosome RNA preparation by standard TRIZOL extraction (Total RNA) and the other for ab-NACtes immunoprecipitation. Ab-NACtes-conjugated Dynabeads Protein G magnetic beads (Life Technologies) were prepared according to the recommendation and used for immunoprecipitation. 300 μl of ribosome extract containing 2 μg protein/ml was added to 50 μl Ab-NACtes-conjugated Protein G Dynabeads, the suspension was incubated on rotating platform 1 h at 20C and then washed 5-6 times in PBS containing 0.1% Tween-20. 500 μl TRIZOL reagent (Life Technology) was added to magnetic particles, thoroughly stirred, then 1/10 volume CHCl3 was added, samples left for 10 minutes on ice and centrifugated at 10000 rpm for 5 minutes at 4C in Eppendorf microfuge.  1 μg of glycogen was added to the aqueous phase and RNA (IP RNA) was precipitated by adding an equal volume of isopropanol and incubation overnight at -20C. RNA was washed with 70% ethanol and dissolved in DEPC- treated water. RNA amount was quantified using NanoDrop 1000 spectrophotometer (Thermo Scientific).
Testis ribosome-associated RNA samples from IP βNACtes ribosome extract (IP1, IP3, IP4) and from total testis ribosome extract (T2, T5) were prepared according to the standard Illumina protocol [TruSeq RNA Sample Prep Kit after rRNA depletion by RiboZero rRNA Removal Kit (Human/Mouse/Rat), Epicentre] and sequenced on the Illumina HiSeq2000. The following sequencing parameters were used: single-end reading, read length 50 bp, approximately 2-4x10^7 reads per sample.

treatment_protocol: Testes of 1-2 old adult male flies were dissected in phosphate-buffered saline (PBS) at 4°C and snap-frozen in liquid nitrogen.

value: Batumi

value: IP

tag: cell fraction

value: ribosome extract


title: Control_60h (41-82)


title: v5_RNA_ribo_tes 2

description: Control, total ribosomes

value: control


title: Control_60h (41-81)


title: Control_60h (41-80)


title: v2_RNA_ribo_tes

description: Control, total ribosomes


title: Control_84h (41-20)


title: v4_IP_ribo_tes 3

description: βNACtes-precipitated ribosomes


title: CLA_132h (41-43)


title: Control_108h (41-26)


title: Control_60h (41-78)


title: CLA_132h (41-42)


title: Control_84h (41-17)


title: CLA_132h (41-39)


title: Control_132h (41-37)


title: 1999BM

status: Public on Oct 11 2017

city: Gainesville

first: Thomas

middle: C

last: Foster

state: FL

address: 1149 S Newell Dr.

department: Neuroscience

institute: University of Florida

description: Exosomal RNA

data_processing:
Reads were trimmed based on size such that reads below 15 bp and reads above 35 bp were discarded. Following trimming, reads were aligned using Bowtie (version 1.0.0) against the human genome reference (hg38).
Gene annotation was completed with the miRBase mature microRNAs model (release version 21) and normalization was performed on total counts.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated values files which contain the normalized counts for each sample.

source_name: Blood Plasma

extract_protocol:
Peripheral blood samples from  male and female (44-92 years) were collected into EDTA Tubes- Plasma (Cat# 367863) were inverted five times, stored on ice and processed within 30 minutes of blood draw. The blood samples were centrifuged at 1600 x g for 15 minutes at 4°C and the plasma was isolated. Exosomal RNA was isolated using exoRNeasy Serum/Plasma Maxi kit (Cat# 77064, Qiagen) according to the manufacturer’s instructions with the final elution volume of 12 ul.
Sequencing libraries were constructed using ~2ng of total exosomal RNA with the library preparation kit Ion Total RNA-Seq kit v2 (Thermo Fisher, Cat# 4475936)

value: Blood Plasma

tag: gender

value: Male

tag: age

tag: moca score


title: v3_IP_ribo_tes 2

description: βNACtes-precipitated ribosomes


title: CLA_108h (41-34)


title: Control_132h (41-35)


title: CLA_108h (41-31)


title: Control_108h (41-28)


title: CLA_108h (41-32)


title: TBMd

city: Yangling

first: Hao

last: Feng

state: Shaanxi

address: Taicheng Road 3#

department: State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection

institute: Northwest A&F University

data_processing:
Library strategy: degradome sequencing
Raw data (raw reads) were first processed through custom Perl and Python scripts to obtain clean data.
The clean data were mapped to the reference sequence in miRBase21.0 by Bowtie, without mismatch to look for known miRNAs.
the other reads were integrated to predict novel miRNAs using the available software miREvo and mirdeep2.
The miRNA counts as well as base bias were identified using custom scripts.
The miFam.dat (http://www.mirbase.org/ftp.shtml) was used to look for families of known miRNAs. The novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
The psRobot_tarin psRobot was performed to predict target genes of miRNA.
target transcripts of differentially expressed miRNAs were analyzed by Gene Ontology Functional Annotation Suite (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)
Genome_build: https://phytozome.jgi.doe.gov/pz/portal.html#info?alias  =Org Mdomestica
Supplementary_files_format_and_content: BMd and TBMd were generated using the twig bark tissuses inoculated with PDA to identified the miRNAs and the corresponding target genes; IVm and TBVm were gengerated using the twig bark tissuses inoculated with Valsa mali to identified the miRNAs and the corresponding target genes.

organism: Malus domestica

source_name: twig

growth_protocol: “Fuji” apple plants (Malus domestica Borkh) were grown in a greenhouse with 25 ℃ and natural daylight conditions

extract_protocol:
According to the instruction of TrizolTM Reagent (Invitrogen, Carlsbad, CA), total RNA was extracted from each sample, and RNA purity was evaluated using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) were used to assess RNA concentration and integrity.
Three repeats of control samples and inoculation samples were mixed for small RNA library construction, respectively. Three μg of total RNA per sample was used as input material for the small RNA library. Small RNA library construction was proceeded following the detailed protocol provided by the genome sequencing company (Novogene, China).
The detailed protocol of miRNA-seq was provided by the genome sequencing company (Novogene, China) and the protocol of degradome sequnce was followed with  the published parallel analysis of RNA Ends (PARE) protocol (German et al., 2009)..

treatment_protocol: The twigs were inoculated with Vm as described by Li et al. (2015). The samples of lesion borders were collected at 0, 12 and 48 hours post-inoculation (hpi).

tag: tisse

value: bark

value: inoculated with PDA


title: 1894LS

description: Exosomal RNA


title: BMd

data_processing:
Raw data (raw reads) were first processed through custom Perl and Python scripts to obtain clean data.
The clean data were mapped to the reference sequence in miRBase21.0 by Bowtie, without mismatch to look for known miRNAs.
the other reads were integrated to predict novel miRNAs using the available software miREvo and mirdeep2.
The miRNA counts as well as base bias were identified using custom scripts.
The miFam.dat (http://www.mirbase.org/ftp.shtml) was used to look for families of known miRNAs. The novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
The psRobot_tarin psRobot was performed to predict target genes of miRNA.
target transcripts of differentially expressed miRNAs were analyzed by Gene Ontology Functional Annotation Suite (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)
Genome_build: https://phytozome.jgi.doe.gov/pz/portal.html#info?alias  =Org Mdomestica
Supplementary_files_format_and_content: BMd and TBMd were generated using the twig bark tissuses inoculated with PDA to identified the miRNAs and the corresponding target genes; IVm and TBVm were gengerated using the twig bark tissuses inoculated with Valsa mali to identified the miRNAs and the corresponding target genes.

tag: treatment


title: IVm

value: inoculated with Valsa mali


title: Control_60h (41-11)

value: Balb/cJ

value: mammary gland

value: OVX at 21d


title: TBVm


title: 1879ESK

description: Exosomal RNA

value: Female


title: HKE293-Post-DRB-V5ChIP-Rep2

description: RNA-DNA hybird

value: After DRB removal for 30min


title: 1885WB

description: Exosomal RNA


title: 1873JXL

description: Exosomal RNA


title: Control_84h (41-19)


title: 1870CFB

description: Exosomal RNA


title: 1865PXW

description: Exosomal RNA


title: 1876HXM

description: Exosomal RNA


title: 1878RXW

description: Exosomal RNA


title: 1877PXH

description: Exosomal RNA


title: 1855SXB

description: Exosomal RNA


title: 1871WXS

description: Exosomal RNA


title: 1830DXE

description: Exosomal RNA


title: 1874DXA

description: Exosomal RNA


title: 1842JXJ

description: Exosomal RNA


title: 1856CXX

description: Exosomal RNA


title: 1838GB

description: Exosomal RNA


title: 1814LP

description: Exosomal RNA


title: 1776JHC

description: Exosomal RNA


title: 1748OW

description: Exosomal RNA


title: 1709KDC

description: Exosomal RNA


title: 1756EXF

description: Exosomal RNA


title: 1714JXT

description: Exosomal RNA


title: 1681PH

description: Exosomal RNA


title: 1663FXC

description: Exosomal RNA


title: 1857JXV

description: Exosomal RNA


title: 1659CK

description: Exosomal RNA


title: 1651JXS

description: Exosomal RNA


title: 1641MXS

description: Exosomal RNA


title: 1638KK

description: Exosomal RNA


title: 1827BXJ

description: Exosomal RNA


title: 1701AA

description: Exosomal RNA


title: 1823LXM

description: Exosomal RNA


title: 1593VS

description: Exosomal RNA


title: 1588FL

description: Exosomal RNA


title: 1561MK

description: Exosomal RNA


title: 1620PTB

description: Exosomal RNA


title: 1606JW

description: Exosomal RNA


title: 1617BXJ

description: Exosomal RNA


title: 1692GS

description: Exosomal RNA


title: 1553JDP

description: Exosomal RNA


title: 1576MXP

description: Exosomal RNA


title: 1565RXP

description: Exosomal RNA


title: 1544LXW

description: Exosomal RNA


title: 1546PC

description: Exosomal RNA


title: 1586EXP

description: Exosomal RNA


title: 1573SXW

description: Exosomal RNA


title: 1543FM

description: Exosomal RNA


title: 1542SMB

description: Exosomal RNA


title: 1540JAE

description: Exosomal RNA


title: 1530LXD

description: Exosomal RNA


title: 1521JXW

description: Exosomal RNA


title: 1536PW

description: Exosomal RNA


title: 1534FXC

description: Exosomal RNA


title: 1516FXE

description: Exosomal RNA


title: 1524CXC

description: Exosomal RNA


title: 1489BXQ

description: Exosomal RNA


title: 1537JXM

description: Exosomal RNA


title: 1496JT

description: Exosomal RNA


title: 1497FH

description: Exosomal RNA


title: 1515AXE

description: Exosomal RNA


title: 1492WC

description: Exosomal RNA


title: 1500TB

description: Exosomal RNA


title: 1457RO

description: Exosomal RNA


title: 1454GTL

description: Exosomal RNA


title: 1441ML

description: Exosomal RNA


title: 1440JL

description: Exosomal RNA


title: 1453HB

description: Exosomal RNA


title: 1444RES

description: Exosomal RNA


title: 1491EXW

description: Exosomal RNA


title: 1433JM

description: Exosomal RNA


title: 1435HRG

description: Exosomal RNA


title: 1431JAM

description: Exosomal RNA


title: 1413JK

description: Exosomal RNA


title: 1316JXC

description: Exosomal RNA


title: 1107DHG

description: Exosomal RNA


title: 1305EDP

description: Exosomal RNA


title: 1037HMV

description: Exosomal RNA


title: 1040NM

description: Exosomal RNA


title: 1046RW

description: Exosomal RNA


title: 1024LC

description: Exosomal RNA


title: 1471PJT

description: Exosomal RNA


title: 1016GH

description: Exosomal RNA


title: 1044IKM

description: Exosomal RNA


title: 1045PG

description: Exosomal RNA


title: 1039AG

description: Exosomal RNA


title: 1434VG

description: Exosomal RNA


title: 1442ESW

description: Exosomal RNA


title: Sample18_MeA_CTL_C

city: Los Angeles

first: Ye

middle: Emily

last: Wu

address: 635 Charles E. Young Dr. South

institute: UCLA

description:
Cells from saline injected control mice. In the associated publication, these cells were used for comparison of immediate early gene expression between conventional dissociation method and Act-Seq (Figure 6).
processed data file:
MeA_Act-Seq_vs_Conventional_DGE.txt

data_processing:
Demultiplexing was performed with bcl2fastq2 v2.17.1.14
Cell barcodes and UMI were extracted using Drop-seq_tools v1.12
Read 2 was aligned with STAR v2.5.0a
Each aligned read was tagged with its mate-pair UMI and cell barcode
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell
20,679 cells expressing > 450 genes and > 700 transcripts from Samples 1-6 and 8-17 were merged into a single matrix (MeA_AllCells_DGE.txt).  These cells were used for the major cell type clustering analysis in the associated publication (Figure 1). Raw UMI counts for 16,233 genes detected in > 10 cells with > 15 transcripts were included in the matrix. rRNA, tRNA, and mitochondrial genes were removed.
PCA, tSNE, and Louvain-Jaccard clustering were performed to identify major cell types
Neuronally enriched genes were identified by comparing neurons to all the other cell types combined with a binomial test. 3,237 genes with fold change ≥ 1.3, FDR < 0.05, and expressed in ≥ 0.3% neurons were selected. 2,444 neurons with > 600 transcripts of these genes were merged into a single matrix (MeA_Neurons_DGE.txt). These neurons were used for neuronal subtype clustering analysis in the associated publication (Figure 2). Raw UMI counts for the 3,237 neuronally enriched genes as well as 106 immediate early genes detected in the neurons were included in the matrix.
Neuronal subclustering was performed using BackSPIN.
8,071 cells expressing > 550 genes and > 700 transcripts from Samples 7-9 and 18-19 were merged into a single matrix (MeA_Act-Seq_vs_Conventional_DGE.txt).  These cells were used for the comparison between Act-seq and conventional dissociation method in dectecting seizure-induced immediate early gene expression changes in MeA cells in the associated publication (Figure 6A). Raw UMI counts for 15,299 genes detected in > 10 cells with > 15 transcripts were included in the matrix. rRNA, tRNA, and mitochondrial genes were removed.
Genome_build: mm10
Supplementary_files_format_and_content: flat text files with tab delimiters; digital gene expression matrices of raw UMI counts for each gene in each cell; cells in columns and genes in rows; cells named as X_Y_Z  or X_Y where X is cell barcode, Y is sample name, and Z is major cell type or neuronal subcluster.

source_name: Medial amygdala

growth_protocol: Mice were housed with a reverse light cycle (12 hr light/12 hr dark) and ad libitum access to food and water.

extract_protocol:
Single-cell suspensions were generated using the Act-Seq protocol (Samples 1-17) or conventional dissociation protocol (Samples 18-19), and processed through Drop-Seq to produce single-cell cDNA libraries attached to microbeads. cDNAs were amplified by PCR and prepared for sequencing through tagmentation.
Sequencing libraries were generated through tagmentation using Illumina Nextera XT DNA Library Prep Kit.

value: 8 weeks

tag: Sex

value: male

tag: treatment group

value: saline-injected control mice

value: Medial amygdala (MeA)

tag: single-cell dissociation method

value: Conventional


title: Sample19_MeA_SZ_C

description:
Cells from seizure-affected mice. In the associated publication, these cells were used for comparison of immediate early gene expression between conventional dissociation method and Act-Seq (Figure 6).
processed data file:
MeA_Act-Seq_vs_Conventional_DGE.txt

value: seizure-affected mice


title: Sample17_MeA_O_4

description:
Cells from additional mice used for cell type clustering in the associated publication. The mice were acutely exposed to odors. In the associated publication, expression data of genes excluding IEGs from these cells were only used for cell type clustering analysis (Figures 1-3); these cells were not used in any differential expression analysis for immediate early genes (Figures 6-7).
processed data file:
MeA_AllCells_DGE.txt
MeA_Neurons_DGE.txt

value: Act-Seq


title: 1027LG

description: Exosomal RNA

value: Blood Plasma


title: Sample16_MeA_O_3


title: Sample13_MeA_IM_4

description:
Cells from mice acutely stressed by immobilization. In the associated publication, these cells were used for both cell type clustering analysis (Figures 1-3) and differential expression analysis for immediate early genes between different experimental groups (Figure 7).
processed data file:
MeA_AllCells_DGE.txt
MeA_Neurons_DGE.txt

value: acutely stressed by immobilization


title: Sample14_MeA_O_1

value: 9 weeks


title: Sample15_MeA_O_2


title: Sample12_MeA_IM_3


title: 1033ET

description: Exosomal RNA


title: 1743CB

description: Exosomal RNA

value: Male


title: Sample10_MeA_IM_1


title: Sample9_MeA_SZ_2

description:
Cells from seizure-affected mice. In the associated publication, these cells were used for both cell type clustering analysis (Figures 1-3) and differential expression analysis for immediate early genes between different experimental groups and between conventional dissociation method and Act-Seq (Figures 6-7).
processed data file:
MeA_AllCells_DGE.txt
MeA_Neurons_DGE.txt
MeA_Act-Seq_vs_Conventional_DGE.txt


title: Sample11_MeA_IM_2


title: Sample8_MeA_SZ_1


title: Sample7_MeA_CTL_7

description:
Cells from saline injected control mice. In the associated publication, these cells were used for differential expression analysis for immediate early genes between different experimental groups and between conventional dissociation method and Act-Seq (Figure 6).
processed data file:
MeA_Act-Seq_vs_Conventional_DGE.txt


title: Sample6_MeA_CTL_6

description:
Cells from naïve control mice. In the associated publication, these cells were used for both cell type clustering analysis (Figures 1-3) and differential expression analysis for immediate early genes between different experimental groups (Figures 6-7).
processed data file:
MeA_AllCells_DGE.txt
MeA_Neurons_DGE.txt

value: naïve control mice


title: Sample5_MeA_CTL_5


title: Sample4_MeA_CTL_4


title: Sample2_MeA_CTL_2


title: Sample3_MeA_CTL_3


title: S141210.82_Ly6D+

city: Basel

first: Llucia

last: Alberti-Servera

state: Basel stat

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: Uni Basel

description:
Single-cell RNA-Seq
Processed data file: counts_selected_365.tsv

data_processing:
The analysis was performed using the open source software R accessed via RStudio server (R version 3.2.0).
Sequencing reads were aligned to the mouse genome assembly, version mm9 (downloaded from UCSC http://genome.ucsc.edu), with SpliceMap, included in the R/Bioconductor package QuasR version 1.14.0. Parameters: -max_intron 400000 -min_intron 20000 -max_multi_hit 10 -selectSingleHit TRUE -seed_mismatch 1 -read_mismatch 2 -try_hard yes.
The count table with gene expression levels was generated using the qCount function from QuasR package version 1.14.0 and coordinates of RefSeq mRNA genes (http://genome.ucsc.edu , downloaded in December 2013). The expression level was defined as a number of reads that started within any annotated exon of a gene (exon-union model). Parameters used in the qCount function: reportLevel="gene", selectReadPosition=start, orientation=any, useRead=first.
During the quality control, cells having less than 60% of mapped reads, less than 2x10e5 counts, or less than 800 detected genes were filtered out from further analysis. In total, 152 Ly6D+ and 213 TN passed these criteria, which are the samples provided herein.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: counts_selected_365.tsv: Tab-delimited text file includes the raw counts of each gene (rows) per sample (single-cell, columns). The first column corresponds to the gene length.

source_name: Ly6D+ EPLM subpopulation

extract_protocol:
Single cells were captured from ex-vivo sorted hematopoietic progenitors (from Flt3Ltg mice) on a small-sized (5-10μm) C1 chip using the Fluidigm C1 system. Cells were washed, lysed, the polyA containing mRNA molecules were hybridized to oligo-dT and whole-transcriptome full-length amplified cDNA was prepared by template switching on the C1 chip using the SMARTer Ultra Low RNA kit for the Fluidigm C1 System.
Illumina single-cell libraries were constructed in 96-well plates using the Nextera XT DNA Library Preparation Kit (Illumina) following the protocol supplied by Fluidigm (“Using C1 to Generate Single-Cell cDNA Libraries for mRNA Sequencing”).

tag: strain/background

value: 2-pooled C57BL/6 Flt3Ltg mice

tag: tissue origination

value: bone marrow (femur)

tag: cell type

value: ex-vivo sorted hematopoietic progenitor

tag: eplm subpopulation

tag: run


title: Sample1_MeA_CTL_1

tag: strain

tag: tissue


title: 1846DXB

description: Exosomal RNA

value: Female


title: S141210.76_Ly6D+


title: S141210.72_Ly6D+


title: S141210.89_Ly6D+


title: S141210.66_Ly6D+


title: S141210.83_Ly6D+


title: S141210.53_Ly6D+


title: S141210.90_Ly6D+


title: S141210.78_Ly6D+


title: S141210.42_Ly6D+


title: S141210.58_Ly6D+


title: S141210.60_Ly6D+


title: S141210.22_Ly6D+


title: S141210.71_Ly6D+


title: S141210.96_Ly6D+


title: S141210.65_Ly6D+


title: S141210.41_Ly6D+


title: S141210.30_Ly6D+


title: S141210.77_Ly6D+


title: S141210.12_Ly6D+


title: S141210.11_Ly6D+


title: S141210.73_Ly6D+


title: S141210.6_Ly6D+


title: S141210.91_Ly6D+


title: S141210.92_Ly6D+


title: S141210.79_Ly6D+


title: S141210.51_Ly6D+


title: S141210.86_Ly6D+


title: S141210.74_Ly6D+


title: S141210.16_Ly6D+


title: S141210.23_Ly6D+


title: S141210.87_Ly6D+


title: S141210.81_Ly6D+


title: S141210.75_Ly6D+


title: S141210.61_Ly6D+


title: S141210.67_Ly6D+


title: S141210.49_Ly6D+


title: S141210.45_Ly6D+


title: S141210.85_Ly6D+


title: S141210.33_Ly6D+


title: S141210.27_Ly6D+


title: 1866DXS

description: Exosomal RNA


title: S141210.68_Ly6D+


title: S141210.44_Ly6D+


title: S141210.63_Ly6D+


title: S141210.1_Ly6D+


title: S141210.26_Ly6D+


title: S141210.2_Ly6D+


title: S141209.82_Ly6D+


title: S141209.95_Ly6D+


title: S141209.88_Ly6D+


title: S141209.89_Ly6D+


title: 1818PXR

description: Exosomal RNA


title: S141210.31_Ly6D+


title: S141209.90_Ly6D+


title: S141209.53_Ly6D+


title: S141209.58_Ly6D+


title: S141210.13_Ly6D+


title: S141209.84_Ly6D+


title: S141209.64_Ly6D+


title: S141209.30_Ly6D+


title: S141209.10_Ly6D+


title: S141209.48_Ly6D+


title: S141209.77_Ly6D+


title: S141209.22_Ly6D+


title: S141210.9_Ly6D+


title: S141210.8_Ly6D+


title: S141210.14_Ly6D+


title: S141209.42_Ly6D+


title: S141209.41_Ly6D+


title: S141209.35_Ly6D+


title: S141209.4_Ly6D+


title: S141209.47_Ly6D+


title: 1437WF

description: Exosomal RNA


title: S141209.34_Ly6D+


title: S141209.12_Ly6D+


title: S141209.23_Ly6D+


title: S141209.17_Ly6D+


title: S141209.91_Ly6D+


title: S141209.5_Ly6D+


title: S141209.63_Ly6D+


title: S141209.52_Ly6D+


title: S141209.73_Ly6D+


title: S141209.85_Ly6D+


title: S141209.28_Ly6D+


title: S141209.92_Ly6D+


title: S141209.57_Ly6D+


title: S141209.86_Ly6D+


title: S141209.39_Ly6D+


title: S141209.81_Ly6D+


title: S141209.67_Ly6D+


title: S141209.80_Ly6D+


title: S141209.74_Ly6D+


title: S141209.62_Ly6D+


title: S141209.93_Ly6D+


title: S141209.61_Ly6D+


title: S141209.87_Ly6D+


title: S141209.50_Ly6D+


title: S141209.49_Ly6D+


title: S141209.7_Ly6D+


title: S141209.26_Ly6D+


title: S141209.46_Ly6D+


title: S141209.32_Ly6D+


title: S141209.27_Ly6D+


title: S141209.9_Ly6D+


title: S141209.2_Ly6D+


title: S141209.15_Ly6D+


title: S141209.13_Ly6D+


title: S141209.44_Ly6D+


title: S141209.56_Ly6D+


title: S141209.19_Ly6D+


title: S141209.1_Ly6D+


title: S141209.14_Ly6D+


title: S141209.20_Ly6D+


title: S141127.88_Ly6D+


title: S141127.82_Ly6D+


title: S141127.66_Ly6D+


title: S141127.76_Ly6D+


title: S141127.89_Ly6D+


title: S141127.95_Ly6D+


title: S141127.77_Ly6D+


title: S141127.78_Ly6D+


title: S141127.84_Ly6D+


title: S141127.70_Ly6D+


title: S141209.8_Ly6D+


title: S141127.41_Ly6D+


title: S141127.30_Ly6D+


title: S141127.42_Ly6D+


title: S141127.47_Ly6D+


title: 1472MD

description: Exosomal RNA


title: S141127.29_Ly6D+


title: S141127.35_Ly6D+


title: S141127.23_Ly6D+


title: S141127.85_Ly6D+


title: S141127.40_Ly6D+


title: S141127.46_Ly6D+


title: 1545JAX

description: Exosomal RNA


title: S141127.28_Ly6D+


title: S141127.34_Ly6D+


title: S141127.91_Ly6D+


title: S141127.83_Ly6D+


title: S141127.81_Ly6D+


title: S141127.65_Ly6D+


title: S141127.86_Ly6D+


title: S141127.93_Ly6D+


title: S141127.45_Ly6D+


title: S141127.92_Ly6D+


title: S141127.73_Ly6D+


title: S141127.33_Ly6D+


title: S141127.27_Ly6D+


title: S141127.63_Ly6D+


title: S141127.20_Ly6D+


title: S141127.31_Ly6D+


title: S141127.21_Ly6D+


title: S141125.82_TN

source_name: TN EPLM subpopulation

value: TN (triple negative)


title: S141125.76_TN


title: S141125.88_TN


title: S141125.95_TN


title: S141127.74_Ly6D+


title: S141125.89_TN


title: S141125.83_TN


title: S141127.75_Ly6D+


title: S141125.53_TN


title: S141125.90_TN


title: S141125.52_TN


title: S141125.70_TN


title: S141125.77_TN


title: S141125.36_TN


title: S141125.84_TN


title: S141125.96_TN


title: S141125.30_TN


title: S141125.16_TN


title: S141125.48_TN


title: S141125.4_TN


title: S141125.42_TN


title: S141125.22_TN


title: S141127.19_Ly6D+


title: S141125.64_TN


title: S141125.47_TN


title: S141125.35_TN


title: S141125.72_TN


title: S141125.29_TN


title: S141125.23_TN


title: S141125.60_TN


title: S141125.17_TN


title: S141125.5_TN


title: S141125.46_TN


title: S141125.40_TN


title: S141125.34_TN


title: S141125.28_TN


title: S141125.24_TN


title: S141125.18_TN


title: S141125.12_TN


title: S141125.69_TN


title: S141125.79_TN


title: S141125.6_TN


title: S141125.74_TN


title: S141125.86_TN


title: S141125.80_TN


title: S141125.62_TN


title: S141125.68_TN


title: S141125.93_TN


title: S141125.41_TN


title: S141125.87_TN


title: S141125.11_TN


title: S141125.75_TN


title: S141125.81_TN


title: S141125.61_TN


title: S141125.45_TN


title: S141125.56_TN


title: S141125.7_TN


title: S141125.33_TN


title: S141125.44_TN


title: S141125.32_TN


title: S141125.39_TN


title: S141125.26_TN


title: S141125.91_TN


title: S141125.92_TN


title: S141125.8_TN


title: S141125.2_TN


title: S141125.43_TN


title: S141125.15_TN


title: S141125.9_TN


title: S141023.82_TN


title: S141125.14_TN


title: S141023.76_TN


title: S141023.72_TN


title: S141023.95_TN


title: S141023.89_TN


title: S141023.77_TN


title: S141023.66_TN


title: S141023.83_TN


title: S141023.71_TN


title: S141023.88_TN


title: S141023.70_TN


title: S141023.96_TN


title: S141023.78_TN


title: S141023.65_TN


title: S141125.38_TN


title: S141023.58_TN


title: S141023.52_TN


title: S141023.36_TN


title: S141023.42_TN


title: S141023.22_TN


title: S141023.30_TN


title: S141023.10_TN


title: S141023.35_TN


title: S141023.41_TN


title: S141023.47_TN


title: S141023.40_TN


title: S141023.5_TN


title: S141023.29_TN


title: S141023.34_TN


title: S141023.12_TN


title: S141023.24_TN


title: S141023.28_TN


title: S141023.91_TN


title: S141023.73_TN


title: S141023.85_TN


title: S141023.79_TN


title: S141023.64_TN


title: S141023.51_TN


title: S141023.63_TN


title: S141023.74_TN


title: S141023.68_TN


title: S141023.86_TN


title: S141023.62_TN


title: S141023.4_TN


title: S141023.93_TN


title: S141023.87_TN


title: S141023.80_TN


title: S141023.81_TN


title: S141023.45_TN


title: S141023.46_TN


title: S141023.67_TN


title: S141023.39_TN


title: S141023.6_TN


title: S141023.27_TN


title: S141023.33_TN


title: S141023.26_TN


title: S141023.19_TN


title: S141023.38_TN


title: S141023.32_TN


title: S141023.44_TN


title: S141023.20_TN


title: S141023.8_TN


title: S141023.31_TN


title: S141023.21_TN


title: S141023.37_TN


title: S141023.2_TN


title: S141022.94_TN


title: S141022.82_TN


title: S141022.88_TN


title: S141023.50_TN


title: S141023.25_TN


title: S141022.66_TN


title: S141023.15_TN


title: S141022.76_TN


title: S141022.72_TN


title: S141022.83_TN


title: S141022.60_TN


title: S141022.77_TN


title: S141022.71_TN


title: S141022.65_TN


title: S141022.54_TN


title: S141023.7_TN


title: S141022.59_TN


title: S141022.53_TN


title: S141022.96_TN


title: S141022.78_TN


title: S141022.70_TN


title: S141022.90_TN


title: S141022.64_TN


title: S141022.52_TN


title: S141022.48_TN


title: S141022.42_TN


title: S141022.84_TN


title: S141125.73_TN


title: S141022.47_TN


title: S141022.16_TN


title: S141022.35_TN


title: S141022.10_TN


title: S141022.30_TN


title: S141022.36_TN


title: S141022.23_TN


title: S141022.29_TN


title: S141022.11_TN


title: S141022.5_TN


title: S141022.46_TN


title: S141022.17_TN


title: S141022.24_TN


title: S141022.40_TN


title: S141022.79_TN


title: S141022.34_TN


title: S141022.12_TN


title: S141022.85_TN


title: S141022.69_TN


title: S141022.57_TN


title: S141022.22_TN


title: S141022.51_TN


title: S141022.68_TN


title: S141022.80_TN


title: S141022.92_TN


title: S141022.62_TN


title: S141022.56_TN


title: S141022.50_TN


title: S141022.55_TN


title: S141022.45_TN


title: S141022.27_TN


title: S141022.75_TN


title: S141022.39_TN


title: S141022.93_TN


title: S141022.1_TN


title: S141022.19_TN


title: S141022.38_TN


title: S141022.32_TN


title: S141022.73_TN


title: S141022.37_TN


title: S141022.2_TN


title: S141022.26_TN


title: S141022.63_TN


title: S141022.44_TN


title: S141022.25_TN


title: S141022.21_TN


title: S141022.15_TN


title: S141022.3_TN


title: ProB_4

description: Processed data file: counts_12.tsv

data_processing:
The analysis was performed using the open source software R accessed via RStudio server (R version 3.2.0).
Sequencing reads were aligned to the mouse genome assembly, version mm9 (downloaded from UCSC http://genome.ucsc.edu), with SpliceMap, included in the R/Bioconductor package QuasR version 1.14.0. Parameters: -max_intron 400000 -min_intron 20000 -max_multi_hit 10 -selectSingleHit TRUE -seed_mismatch 1 -read_mismatch 2 -try_hard yes.
The count table with gene expression levels was generated using the qCount function from QuasR package version 1.14.0 and coordinates of RefSeq mRNA genes (http://genome.ucsc.edu , downloaded in December 2013). The expression level was defined as a number of reads that started within any annotated exon of a gene (exon-union model). Parameters used in the qCount function: reportLevel="gene", selectReadPosition=end, orientation=opposite, useRead=first.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: counts_12.tsv: Tab-delimited text file includes the raw counts of each gene (rows) per sample (columns). The first column corresponds to the gene length.

source_name: Pro-B cells

extract_protocol:
Total RNA was extracted from ex-vivo sorted hematopoietic progenitors (from Flt3Ltg mice) using TRIzol-based method.
For the preparation of sequencing libraries, the TruSeq Stranded mRNA LT Sample Preparation kit was used with 500ng of total RNA. Single-end sequencing was performed on the Illumina NextSeq 500 Sequencing System.


title: ProB_3

description: Processed data file: counts_12.tsv


title: ProB_1

description: Processed data file: counts_12.tsv


title: ProB_2

description: Processed data file: counts_12.tsv


title: TN_4

description: Processed data file: counts_12.tsv


title: S141022.9_TN


title: S141022.61_TN


title: Ly6D_2

description: Processed data file: counts_12.tsv


title: Ly6D_1

description: Processed data file: counts_12.tsv


title: TN_3

description: Processed data file: counts_12.tsv


title: TN_2

description: Processed data file: counts_12.tsv


title: Ly6D_3

description: Processed data file: counts_12.tsv


title: S141022.14_TN


title: S141022.8_TN


title: BM-MSC

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human bone marrow samples

growth_protocol: H1 were induced for stepwise mesenchymal stem cells differentiation. First, cells were cultured in DMEM-F12 (Gibco) supplemented with 1%(v/v) FBS (Gibco),4μg/ml TGF-β1(Peprotech), 4μg/ml bFGF(Peprotech), 0.5μM CHIR99021 (Sigma) and 20 nM DAC (Sigma) for 5 days. Second, cells were cultured in   DMEM-F12 (Gibco) supplemented with 1%(v/v) FBS (Gibco) and 20 nM DAC (Sigma) for another 2 days.

extract_protocol:
H1 drived cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: bone marrow MSCs


title: D-d7

source_name: H1 samples collected from day 7 after mesenchymal stem cells differentiation under DOX+ conditions,


title: Ly6D_4

description: Processed data file: counts_12.tsv


title: DS-d7

source_name: H1 samples collected from day 7 after mesenchymal stem cells differentiation under DOX+CC conditions,


title: DS-d5

source_name: H1 samples collected from day 5 after mesenchymal stem cells differentiation under DOX+CC conditions,


title: DS-d1

source_name: H1 samples collected from day 1 after mesenchymal stem cells differentiation under DOX+CC conditions,


title: NT-d0

source_name: Undifferentiated H1 cells


title: DS-d3

source_name: H1 samples collected from day 3 after mesenchymal stem cells differentiation under DOX+CC conditions,


title: Vim KO4

city: Turku

first: Emilia

last: Peuhu

address: Medisiina D5, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of turku

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using Star (v. 2.5.2b) to mm10 mouse genome reference
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: mm10
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

source_name: Mammary gland basal epithelial cells

growth_protocol: Epithelial cells were isolated in two independent experiments from collagenase digested mouse mammary glands (2-3 mice pooled per sample) by differential centrifugation and basal epithelial cells (Live, CD45neg, CD31neg, CD24low, CD49fhi) were sorted by flow cytometry

extract_protocol:
RNA was isolated using NucleoSpin kit (Macherey-Nagel).
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047):

treatment_protocol: Sorted cells were collected directly in RLT lysis buffer (Qiagen) and frozen.

value: Mammary gland

value: 15 week-old

tag: genotype

tag: passage


title: Control-input

city: Stanford

first: Min

last: Huang

address: 265 Campus Drive

department: Internal Medicine

institute: Stanford Cancer Institute

data_processing:
using FASTQ in Galaxy online platform for quality control
Sequencing reads were aligned using Bowtie aligner with default parameters using Galaxy
Peaks were called by MACS version 2.1.0. Peaks were defined as significant with a q value cut-off of 5.00e-02 using Galaxy
ChIP-input samples with or without JQ1 treatment were used to construct a peak matrix using Galaxy
ChIP-seq density heat map and genome-wide occupancy histogram plots were generated using Galaxy.
Genome_build: Human reference genome (hg38)
Supplementary_files_format_and_content: Bigwig files generated by Galaxy

source_name: Control-input

growth_protocol: The OCI-AML3 cell line was maintained in MEM-alpha medium supplemented with 20% heat-inactivated fetal bovine serum (FBS), 2 mM glutamine, 100 U ml-1 penicillin and 100 µg/ml streptomycin. All experiments were initiated at a cell density of 1×10^5 to 4×10^5 cells/ml.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described previously (Lee TI, Johnstone SE, Young RA. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc. 2006;1(2):729-748)
ChIP-seq libraries were prepared according to the Illumina protocol for ChIP-seq

treatment_protocol: OCI-AML3 cells were treated with 500 nM JQ1 for 24 h

value: NPMc+ leukemia OCI-AML3 cells

value: acute myeloid leukemia

value: Control No Treatment

tag: chip antibody


title: JQ1-input

value: JQ1, 500 nM for 24 h


title: WT2

tag: age

value: Vimwt/wt


title: CEBPB-CHIP-control

source_name: CEBPB-CHIP-control

value: CEBPB (sc-7962, H-7, Lot#:E1916, Santa Cruz Biotechnology)


title: CEBPB-CHIP-JQ1

value: CEBPB (sc-7962, H-7, Lot #:E1916, Santa Cruz Biotechnology)


title: Vim KO2


title: Vim KO1


title: S6K1i-HDL replicate 9

city: New York

first: XIANXIAO

last: ZHOU

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

data_processing:
sequencing reads were aligned to human genome hg19 using tophat (v2.1.0) aligner (bowtie2 (v2.2.8))
HTSeq (v0.6.1) was used to quantify the gene expression at the gene level based on GENCODE gene model release 22.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited contain genes and counts

source_name: Atherosclerotic plaque

growth_protocol: Female Apoe-/- mice (B6.129P2-Apoetm1Unc, n=131) were used for this study. Animal care and procedures were based on an approved institutional protocol from Icahn School of Medicine at Mount Sinai. Eight-week-old Apoe-/- mice were purchased from The Jackson Laboratory. All mice were fed a high-cholesterol diet (HCD) (0.2% weight cholesterol; 15.2% kcal protein, 42.7% kcal carbohydrate, 42.0% kcal fat; Harlan TD. 88137) for 12 weeks before the start of the treatments.

extract_protocol:
Laser capture microdisection was performed on aortic root sections (6 µm) per condition. First, 24 frozen sections were dehydrated in graded ethanol solutions (70% / 95% / 100%) and washed with DEPC treated water. Then, 21 sections were stained with Mayer’s hematoxylin and eosin. For every 8 sections, 1 section was used for CD68 staining (Abdserotec, 1:250 dilution) which was used to guide the LCM. CD68 rich areas within the plaques were identified and collected with a ArcturusXT LCM System. The collected cells were used for RNA isolation (PicoPure RNA Isolation Kit, Arcturus) and subsequent RNA amplification and cDNA preparation, following manufacturers protocols (Ovation Pico WTA System, NuGEN).
Quality and concentration of the RNA and cDNA samples were measured with the Agilent 2100 Bioanalyzer and a ThermoFischer NanoDrop system.

treatment_protocol: Each experimental setup was similar: twenty-week-old Apoe-/- mice were randomly assigned to either placebo (saline), empty rHDL nanoparticles, CD40-HDL (5 mg/kg), rapamycin-HDL (rapamycin at 5 mg/kg), or PF-4708671-HDL (PF-4708671 at 5 mg/kg) groups. Mice were treated with 4 intravenous injections over 7 days, while being kept on a HCD. For the targeting and biodistribution experiments, mice received a single intravenous injection. All animals were sacrificed 24 hours after the last injection.


title: WT1


title: TN_1

description: Processed data file: counts_12.tsv


title: S6K1i-HDL replicate 8


title: S6K1i-HDL replicate 7


title: rat_P4_ESC

city: Beijing

first: Qi

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

data_processing:
The sequencing reads were mapped to the rat genome (version rn6) by Bismark v0.13.1 (Babraham Bioinformatics) after trimming by Trim Galore (Babraham Bioinformatics) with the "-rrbs" option.
The methylation levels of covered cytosine sites were calculated by dividing the number of reported C with the total number of reported C and T. CpG sites covered by more than ten reads were used for the analysis.
Genome_build: rn6
Supplementary_files_format_and_content: Methylation percentage of the CpG sites

organism: Rattus norvegicus

growth_protocol: The Dark Agouti (DA)  strain rats were used to establish ES cells and tissue preparation. The established rESCs were cultured in N2B27 medium with 2i and rLIF, and passaged every 2 to 3 days by rat digest solution for 3 min.

extract_protocol:
Genomic DNA was isolated from the tissues and cells with Universal Genomic DNA Extraction Kit (TaKaRa).
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications.Briefly, about 1 ug genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters. Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 2500.

value: Embryonic Stem Cell

value: Dark Agouti


title: rat_P17_ESC


title: rat_Tail tip

source_name: rat_Tail tip

value: one kind of fibroblast isolated from rat tail tip


title: mTORi-HDL replicate 10


title: mTORi-HDL replicate 8


title: mTORi-HDL replicate 7


title: mTORi-HDL replicate 9


title: rat_P14_ESC rep2

data_processing:
Basecalls performed by Casava using default settings
For the bulk cells RNA-Seq data, the clean reads were mapped to at rn6 genome assembly by HISAT (version 0.1.6-beta).
due to the incompleted gene annotation for rat, the transcripts were assembled by Cufflinks (version 2.0.2) with the known annotation as guide.
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks
Genome_build: rn6
Supplementary_files_format_and_content: FPKM files estimated by Cufflinks

growth_protocol: The established rESCs were cultured in N2B27 medium with 2i and rLIF, and passaged every 2 to 3 days by rat digest solution for 3 min.

extract_protocol:
Total RNA was isolated using the RNeasy kit (QIAGEN) and complementary DNA (cDNA) made from 1000ng of RNA using SuperScript III (Invitrogen) and oligo-dT primers.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: rat_P14_ESC rep1


title: rat_sperm

value: rat sperm


title: Vim KO3


title: mTORi-HDL replicate 6


title: mTORi-HDL replicate 5


title: rat_P4_ESC rep1


title: Brd4-CHIP-JQ1

value: Brd4 (A301-985A50, Lot #, 6, BETHYL Laboratories)


title: S6K1i-HDL replicate 5


title: BATF3-JUNB-IRF8-unbound

city: St. Louis

first: Gary

middle: D.

last: Stormo

state: MO

address: 4515 McKinley Ave. Room 4208.

department: Genetics

institute: Washington University School of Medicine

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF3-JUNB-IRF8_processed.txt

data_processing:
Extracting binding sites sequence from raw reads. Each read follows the format of GAGTCGTCTCGTCAGCAC-binding site-CCGTAGAGCACTCAGGTC for samples 1 to 6 and follows the format of GATAGTCTCATTTTCACC-binding site-TTCCATTACAGTATCTGT for samples 7 to 15.
Count read numbers for each variant and classfied by bound or unbound in specseq.
For specseq, calculate the bound/unbound ratio for each variant, then rank variants according to their relative affinities.
Genome_build: N/A
Supplementary_files_format_and_content: Tab delimited text files.

molecule: other

organism: synthetic construct

source_name: Synthesized DNA

extract_protocol:
All EMSA were done in 1X NEB Cutsmart buffer (50mM Potassium Acetate, 20mM Tris-acetate, 10mM Magnesium Acetate, 100μg/ml BSA, pH 7.9@25°C) supplemented with 10% glycerol with 1mM of dsDNA and were incubated for 30 minutes on ice. Electrophoresis mobility assay (EMSA) were done using native 12% PAGE prepared as Tris/Glycine (25mM Tris pH 8.3; 192mM glycine) mini-gels. These gels were first pre-run using 1X Tris/Glycine buffer (25mM Tris pH 8.3; 192mM glycine) at 200V for 30 minutes, then samples were loaded for an additional run of 60 minutes at 200 V at 4°C. After EMSA, the gels were stained with ethidium bromide and visualized using Biorad gel imager. Each band detected in the EMSA were excised with a plastic tool and the DNA in the gel extracted by incubating for 30 mins at 50°C in 50ml acrylamide gel extraction buffer (500mM Ammonium acetate, 10mM Magnesium Acetate, 1mM EDTA, 0.1% SDS). 0.01 pmole of PCR Control DNA with the sequence of GAGTCGTCTCGTCAGCACCGGCGGCGGTTCCCGGAAAGACCGTAGAGCACTCAGGTC (primer binding sites underlined) were added to each extracted sample. Sample in the extraction buffer were purified with QIAquick Nucleotide Removal Kit (Qiagen) following the manufacturer’s instructions. Each fraction of DNA was barcoded and amplified using HotStart PCR Master Mix (Lambda Biotech). DNA was denatured at 94°C for 30 seconds, annealed at 55°C for 30 seconds and extend at 72°C for 45 seconds per round for 12 to 20 rounds with modified Indexed-Illumina primers (PE1-Genetics1/2, PE2.0). The PCR product was then purified again using QIAquick Nucleotide Removal Kit.
DNA library was constructed by mixing the degenerate sequences of interest. DNA library was designed by flanking the degenerate sequences of interest with sequences GAGTCGTCTCGTCAGCAC and CCGTAGAGCACTCAGGTC or GATAGTCTCATTTTCACC and TTCCATTACAGTATCTGT for downstream processing. To make double-stranded DNA (dsDNA) libraries, 100 pmole single-strand degenerate template sequences were mixed with an equal amount of reverse complement primer (GACCTGAGTGCTCTACGG). In the presence of Taq Polymerase, brief 10-sec denaturing followed by 10 min of 55 degree annealing/extension is sufficient to make dsDNA libraries. Because any unextended single-stranded DNA (ssDNA) could contaminate the unbound band, the reaction mix was digested by 1 ml NEB Exo I exo- nuclease (New England Biolabs, Beverly, MA) for 30 min. All final dsDNA products were purified by QIAGEN (Valencia, CA) PCR purification columns.

tag: library

value: DNA oligos


title: S6K1i-HDL replicate 6


title: Brd4-CHIP-control

tag: treatment

value: Brd4 (A301-985A50, Lot #:6, BETHYL Laboratories)


title: BATF3-JUNB-IRF4-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF3-JUNB-IRF4_processed.txt


title: S6K1i-HDL replicate 4


title: S6K1i-HDL replicate 3


title: BATF3-JUNB-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF3-JUNB_processed.txt


title: BATF2-JUNB-IRF8-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF2-JUNB-IRF8_processed.txt


title: S6K1i-HDL replicate 2


title: S6K1i-HDL replicate 1


title: BATF2-JUNB-IRF4-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF2-JUNB-IRF4_processed.txt


title: BATF2-JUNB-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF2-JUNB_processed.txt


title: mTORi-HDL replicate 4


title: BATF-JUNB-IRF4-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF-JUNB-IRF4_processed.txt


title: mTORi-HDL replicate 3


title: BATF-JUNB-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF-JUNB_processed.txt


title: mTORi-HDL replicate 2


title: BATF3-IRF8-Specseq-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF3-IRF8-Specseq_processed.txt


title: mTORi-HDL replicate 1


title: rat_P4_ESC rep2


title: BATF3-IRF4-Specseq-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF3-IRF4-Specseq_processed.txt


title: PBS replicate 10


title: BATF2-IRF8-Specseq-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF2-IRF8-Specseq_processed.txt


title: BATF-JUNB-IRF8-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF-JUNB-IRF8_processed.txt


title: PBS replicate 8


title: PBS replicate 7


title: PBS replicate 9


title: BATF-IRF4-Specseq-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF-IRF4-Specseq_processed.txt


title: BATF-IRF8-Specseq-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF-IRF8-Specseq_processed.txt


title: BATF3-JUNB-IRF8-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF3-JUNB-IRF8_processed.txt


title: PBS replicate 6


title: PBS replicate 5


title: BATF3-JUNB-IRF4-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF3-JUNB-IRF4_processed.txt


title: PBS replicate 3


title: BATF3-JUNB-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF3-JUNB_processed.txt


title: PBS replicate 1


title: TRAF6i-HDL replicate 10


title: PBS replicate 2


title: BATF2-JUNB-IRF4-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF2-JUNB-IRF4_processed.txt


title: BATF2-JUNB-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF2-JUNB_processed.txt


title: TRAF6i-HDL replicate 9


title: BATF-JUNB-IRF8-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF-JUNB-IRF8_processed.txt


title: BATF2-IRF4-Specseq-unbound

description:
Conatins unbound reads needed to calculate the relative binding energy.
BATF2-IRF4-Specseq_processed.txt


title: BATF3-IRF8-Specseq-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF3-IRF8-Specseq_processed.txt


title: BATF-JUNB-IRF4-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF-JUNB-IRF4_processed.txt


title: TRAF6i-HDL replicate 7


title: TRAF6i-HDL replicate 6


title: TRAF6i-HDL replicate 5


title: BATF2-IRF8-Specseq-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF2-IRF8-Specseq_processed.txt


title: BATF2-IRF4-Specseq-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF2-IRF4-Specseq_processed.txt


title: BATF3-IRF4-Specseq-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF3-IRF4-Specseq_processed.txt


title: BATF-IRF8-Specseq-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF-IRF8-Specseq_processed.txt


title: CRS3

first: Carla

last: Nasca

address: 1 Park Avenue

institute: NYU Grossman School of Medicine

data_processing:
FastQC v0.11.3
Trimmomatic v0.33 SE -phred33 ILLUMINACLIP:TruSeq3.fa:2:30:10 TRAILING:3 MINLEN:36
merge fatsq files
Tophat v2.0.9 --library-type  fr-firststrand --GTF mus_musculus_genes_UCSC_igenome_mm10.gtf --min-coverage-intron 50 --max-coverage-intron 20000
htseq-count v0.6.1 -s 'reverse'
EdgeR v3.12.0
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited files with raw counts for each sample

source_name: ventral dentate gyrus

extract_protocol:
Ventral dentate gyrus tissues were dissected and weighed before homogenization and tissue was lysed. Total RNA was extracted using Qiazol reagent and RNeasy mini Kit (Qiagen, US), according to the manufacturer’s instructions. RNA quality was checked using the 2100 Bioanalyzer (Agilent Technologies, US) and quantified spectrophotometrically. The acceptance criteria for RNA quality were a 260/280 ratio ≥ 1.80 and ≤ 2.20.
After checking RNA for quality, Total RNA was extracted according to the manufacturer’s instructions (TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat).

tag: group

value: Chronic Restrained Stress

value: C57black 6


title: TRAF6i-HDL replicate 3


title: TRAF6i-HDL replicate 1


title: AP1_mspecseq_sample2 (unbound)

data_processing:
Methylation property identification
For any particular DNA variant inside library, it carries particular barcode to indicate its methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated. Thus acording to the unique methylation barcode information, each read was identified and sorted to its methylation type.
Variant reads counting and sorting
For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Energy logo visualization
Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions. Futhermore, besides conventional G-T-A-C bases, we used two extra “M" and ”W" to represent methylated cytosine on upper and lower strand of DNA respectively, in which the height of M or W indicate the extra binding energy contribution between methylated and unmethylated base.
Supplementary_files_format_and_content: All processed data were saved in .excel files, including the methylation property, bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.

extract_protocol:
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1 and PE2 PCR primers were used to PCR amplify extracted DNA by at least 8 cycles (95C 15s, 52C 15s, 72C 30s)
For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.

treatment_protocol: All EMSA reactions were done in 9% Tris-glycine gel, 200V, 30mins

value: AP1 Duplex Methylated,AP1 Mspec Top Hemimethylated,AP1 Bottom Hemimethylated,AP1 Unmethylated

tag: recombinant protein

value: BATF and JUNB


title: PBS replicate 4


title: BATF2-JUNB-IRF8-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF2-JUNB-IRF8_processed.txt


title: AP1_mspecseq_sample2 (bound)


title: BATF-IRF4-Specseq-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF-IRF4-Specseq_processed.txt


title: TRAF6i-HDL replicate 2


title: CRS1


title: TRAF6i-HDL replicate 8


title: Ctrl2

value: Not-stressed Controls


title: BATF-JUNB-bound

description:
Conatins bound reads needed to calculate the relative binding energy.
BATF-JUNB_processed.txt


title: AP1_mspecseq_sample1 (unbound)


title: TRAF6i-HDL replicate 4


title: AP1_specseq (unbound)


title: Ctrl1


title: AP1_specseq (bound)