title: ESC_1

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

source_name: embryonic stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The culture of MSCs and iMSCs was carried out in αMEM with GlutaMAX™, 10% fetal bovine serum (Biochrom AG) and penicillin/streptomycin (all from Thermo Fisher Scientific). MSCs and iMSCs were expanded with a seeding density of 1000 cells per cm2. iMSCs were cultured in the same conditions from passage four.  Pluripotent stem cells (iPS-cells and human embryonic stem cells H1 (#WA01) were cultured in StemMACS MSC Expansion Media Kit XF, human (Milteny Biotech) and penicillin/streptomycin (Thermo Fisher Scientific). Passaging of pluripotent stem cells was carried out with a splitting ratio of 1:6. Cell culture dishes coated with Matrigel (BD) were used to culture iPS-cells and hESCs. MSC, iPSC and ESC culture was carried out at 37°C and 5% CO2.in a humidified atmosphere.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: Episomal plasmid-based reprogramming was performed using the Human MSC (Mesenchymal Stem Cell) Nucleofector® Kit (Lonza, VPE-1001) in combination with the Amaxa Nucleofector II® (Lonza) according to the descriptions of the manufacturer. The plasmid combination 7F-2 was delivered to the MSCs as previously described (Megges, M et al., 2016).   Megges, M., Oreffo, R. O. & Adjaye, J. Episomal plasmid-based generation of induced pluripotent stem cells from fetal femur-derived human mesenchymal stromal cells. Stem Cell Res. 16, 128-132 (2016).  .

value: embryonic stem cells


title: BALB/c_24h post Af/12h post air_2

status: Public on Apr 30 2019

type: RNA

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

country: USA

institute: University of Colorado

description: Gene expression data

hyb_protocol: The GeneChip HT MG-430 PM 24 Array Plate consists of 24 single MG-430 PM arrays arranged into standard 96 well plate format. Array hybridization, washing and scanning were performed according to the manufacturer's recommendations on a GeneTitan Instrument.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Data was processed in ArrayStudio and quality was assessed via Almac QC ToolBox. Differential expression of genes with false discovery rate (FDR) adjusted to p<0.05 was included for downstream pathway analysis. Pathway analysis was performed using Metacore and pathways with FDR adjusted p<0.05 were reported.

label: Matrix lysis D fast prep

molecule: total RNA

organism: Mus musculus

source_name: whole lung homogenate

label_protocol: Expression profiling was performed using the NuGEN cDNA RNA Amplification system along with GeneChip HT Mouse430PM 96 Array Plate.

extract_protocol: Animals were sacrificed using a 30G needle, loaded with 200 uL 1:1 Ketamine:Xylazine (100/20 mg/kg). The lungs were perfused with Ca++/Mg++ free PBS. The left lung lobe was collected for RNA extraction in a Matrix lysis D fast prep tube and frozen immediately after collection.

treatment_protocol: Mice received treatment as described for each sample. Ozone exposure (3 ppm) is performed for 2 hours and mice are sacrificed 12 hours later. Control mice received air exposure for 2 hours and are sacrificed 12 hours later. Af sensitization was performed by intraperitoneal injection on day 0 and day 7. Af challenge was performed by intranasal instillation on day 13. Timepoints for each sample indicate the time of euthanasia following Af challenge and/or ozone exposure.

tag: strain

value: Balb/c

tag: Sex

value: male

tag: age

value: 7-8 weeks

tag: tissue

value: whole lung homogenate

tag: treatment

value: 24 hours after Af and 12 hours after air exposure


title: fMSC.iMSC_2

country: Germany

description: replicate 2

label: biotin

organism: Homo sapiens

source_name: mesenchymal stem cells derived from fMSC-iPSC

tag: cell type


title: SOD1 ALS 1 [transcript-level]

city: Baltimore

first: Sean

middle: James

last: Miller

state: MD

address: 855 North Wolfe St.

department: Neurology-Neuromuscular Medicine

institute: Johns Hopkins School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: cerebral cortex

label_protocol: The NuGEN WT-Ovation Exon Module was used according to the manufacturer's protoco in the JHMI Sequencing & Microarray Core facility.

growth_protocol: The care and treatment of animals is in accordance with the NIH Guide for the Care and Use of Laboratory Animals, the Guidelines for the Use of Animals in Neuroscience Research, and the Johns Hopkins University IACUC (protocol M14M089). Mice were housed at standard temperature and in light-controlled environment with ad libitum access to the food and water. No more than 5 mice were kept in a cage, in accordance with Johns Hopkins IACUC.

extract_protocol: Total RNA was isolated from FACS sorted populations using the RNA isolation kit (Qiagen) and the concentrations determined using Nanodrop (Thermo Fisher Scientific) and Bioanalyzer (Agilent Technologies). Only samples with a RNA integrity score greater than 5 were used. Total RNA was lineally amplified and labeled in a NuGEN protocol.

treatment_protocol: SOD1 G93A ALS mice and controls were aged to P120. SOD1 G93A mice that displayed hindleg paralysis at P120 were used for this study. Fluorescent-activated cell sorting (FACS) was performed by first sacrificing mice with an intraperitoneal injection of ketamine xylazine. The entire cortex was immediately dissected and dissociated as previously described (Foo et al. 2011). Single cells were then sorted by using MoFlo high-speed cell sorter and gated based on eGFP fluorescence.

value: cerebral cortex

tag: hind-limb paralysis

value: paralyzed

tag: phenotype

value: ALS


title: 11752X1

type: SRA

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr.

institute: University of Utah

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 + splice junctions
Spliced alignments were converted back to genomic coordinates using USeq_8.8.8 SamTranscriptomeParser
Reads mapping uniquely to features were counted using USeq_8.8.8 DefinedRegionDifferentialSeq (DRDS)
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38 (mm10 from UCSC)
Supplementary_files_format_and_content: raw count table from DRDS

source_name: Wt 1

growth_protocol: 1x10^6 B16f10 tumor cells were injected into the flank of the indicated mice and after 12 days tumors were isolated, digested in accumax solution to obtain a single cell suspension and flow sorted based on the expression of CD11b and F480

extract_protocol: RNA was isolated with miRneasy mini kit, library was prepped.

treatment_protocol: Cells from 3 to 4 mice were pooled per sample, thus each indvidual sample is representative of cells aquired from 3 to 4 individual mice

value: tumor-associated macrophages (TAMs)

tag: genotype

value: WT

tag: cell markers


title: ESC.iMSC

description: replicate 1

source_name: mesenchymal stem cells derived from embryonal stem cells


title: RNAseq_72h_FW_S2

city: Ithaca

first: Karin

middle: Revka Loek

last: van der Burg

state: NY

address: 215 Tower Road, Corson Hall

department: EEB

institute: Cornell University

data_processing:
Alignment to junonia coenia genome using tophat.
Read counts overlapping genes were calculated with bedtools
Differential expression analysis was performed using DESeq2
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: normalized bigwig files were produced using ucsc script
Read counts file (Gene IDs can be found online at lepbase.org)

organism: Junonia coenia

source_name: whole wing tissue

growth_protocol: Caterpillars and pupae were raised at ~27C

extract_protocol:
RNA was isolated from whole wing tissue and poly-A selected using NEB poly-A selection beads
Libraries were prepared using the NEB RNA library prep kit

tag: developmental stage

value: 72 hours after pupation

value: forewing


title: 10625X11

data_processing:
Reads were aligned to mm10 + splice junctions
Spliced alignments were converted back to genomic coordinates using Useq SamTranscriptomeParser
Reads mapping uniquely to features were counted using USeq DefinedRegionDifferentialSeq (DRDS)
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38 (mm10 from UCSC)
Supplementary_files_format_and_content: raw count table from DRDS

source_name: BMM M2 (IL4) 1

growth_protocol: Primary bone marrow macrophages are obtained by plating bone marrow cells in DMEM supplemented with 10% FBS, pen/strep, and L-glut with 20ng/mL M-CSF for six days prior to stimulation.

extract_protocol: RNA was isolated with miRneasy micro kit, library was prepped.

treatment_protocol: M1 conditions = 50ng/mL IFNγ and 10ng/mL LPS, M2 conditions = 100ng/mL IL-4, media only, Cells were treated 6 hours prior to RNA isolation.

value: bone marrow

value: macrophage

value: BMM M2


title: 10625X12

source_name: BMM M2 (IL4) 2


title: 10625X8

source_name: BMM media 2

value: BMM media


title: RNAseq_ann_M_pd2_A

description: This RNA library was used solely for annotation purposes, so no quantitative analyses were done.

source_name: head

value: 2 days after pupation

value: head

tag: gender


title: RNAseq_pp_HW_S3

value: pre pupa

value: hindwing


title: 10625X9

source_name: BMM M1 (LPS/IFNg) 1

value: BMM M1


title: GMPTreated_Rep2

city: Fermoy

first: Rita

last: Hickey

state: County Cork

address: Moorepark

department: Food Bioscience

country: Ireland

institute: Teagasc Food Research Centre

description: Gene expression in HT29 cells exposed to Glycomacropeptide

hyb_protocol: 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies).  Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (AMADID 039494). Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile.

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner

data_processing:
Data was extracted from the scanned image using Feature Extraction 10.7 (Agilent Technologies)
Quantile normalization was applied to the data set. All samples were normalized at once, thus normalized data of all groups can be analyzed together. After normalization, the microarray probes, represented by the column ProbeName, were filtered according to the flag information provided by Feature Extraction 10.7.3.1 software. ProbeNames of an array are flagged and annotated as “Compromised” if they are not distinguishable from the array background (not significantly detectable) or as “Not Detected” if the shape of the spot does not fit to the expectations (unequal saturation, non-uniformity). Filtering on flags was carried out in a way that a ProbeName must be “Detected” or “Not Detected” in at least one out of all samples. Welch’s approximate t-test (“unpaired unequal variance”, parametric) was applied to the comparisons of the different groups. The Welch’s approximate t-test-based p-value was corrected for multiple testing using the algorithm of Benjamini a  nd Hochberg.

source_name: Human colon adenocarcinoma cell line HT-29 exposed to 5mg/ml glycomacropeptide for 24hrs

label_protocol: 100 ng total RNA per sample were introduced into a reverse transcription with subsequent in vitro transcription (RT-IVT) reaction. Prior to RT-IVT, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) The spiked total RNA was reverse transcribed into cDNA and then converted into Cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies).

growth_protocol: Human colon adenocarcinoma cell line HT-29 cells were fgrown in McCoy's 5A modified medium supplemented with 10% fetal bovine serum in 75 cm2 tissue culture flasks at 37 degrees celsium in 5% CO2.The medium was changed every other day and the cells were passaged at 80% confluency. Cells for treatment were grown to 18 passages.

extract_protocol: Following treatment, the culture medium was removed from the cells and replaced with 5ml of RNAlater reagent and the cells detached from the flask using a cell scraper. The suspended cells were centrifuged in a microcentrifuge (14,000 rpm) and the RNAlater supernatant removed. The resulting cell pellets (10 per flask) were stored at -80 degrees celsium until required. Total RNA was extracted from the frozen pellets using a HighPure RNA isolation kit (Roche). The quality and quantity of each RNA sample was determind on a BioAnalyser (Agilent Technologies). Only samples with an A260/A280 ratioo > 2 were used for analysis.

treatment_protocol: 24 hours prior to treatment the culture medium was replaced with McCoy's 5A medium supplemented with 2% Fetal bovine serum. To begin the treatment the culture medium was removed and replaced with McCoys 5A medium supplemented withor Glycomacropeptide (5 mg/ml). Nonsupplemented McCoy's 5A medium was used as a control.

tag: cell line

value: HT29 human epithelial adenocarcinoma cell line

tag: agent

value: glycomacropeptide


title: 11752X2

source_name: Wt 2


title: 10625X4

source_name: Raw 264.7 M1 (LPS/IFNg) 2

value: macrophage cell line

value: RAW M1


title: GMPTreated_Rep3


title: 10625X5

value: RAW M2


title: fMSC_2

description: replicate 2

source_name: fetal mesenchymal stem cells

value: fetal mesenchymal stem cells


title: RNAseq_pp_HW_S1


title: RNAseq_pp_FW_S2


title: 10625X7

source_name: BMM media 1


title: RNAseq_72h_FW_S1

value: 72 hours after pupation


title: RNAseq_5th_HW_S2

value: 5th instar


title: RNAseq_5th_HW_S3


title: RNAseq_pp_FW_S3

value: forewing


title: 10625X6


title: RNAseq_pp_HW_S2


title: 10625X10

source_name: BMM M1 (LPS/IFNg) 2

value: bone marrow

value: macrophage


title: RNAseq_5th_HW_S1


title: RNAseq_5th_FW_S3


title: RNAseq_pp_FW_S1


title: BALB/c_12 hr Ozone_1

description: Gene expression data

source_name: whole lung homogenate

value: Balb/c

value: male

value: 7-8 weeks

value: whole lung homogenate

value: 12 hours after ozone exposure


title: 10625X1

source_name: Raw 264.7 media 1

value: RAW media


title: LW-6-1

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

country: China

institute: Northwest A&F University

data_processing:
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, then mapped to the predicted gene models of B. dothidea PG45 genome (GenBank accession no. NNRO00000000)
A gene expression profile was created using Tophat2 and Cufflinks.
Genes with a significant P-value (< 0.05) and a greater than threefold change (log2) in transcript level were considered to be differently expressed. All P-values were corrected for false discoveries resulting from multiple hypothesis testing using the Benjamini-Hochberg procedure.
Genome_build: reference genome deposited at DDBJ/EMBL/GenBank under the accession NNRO00000000
Supplementary_files_format_and_content: tab-delimited text files include expression profiles

organism: Botryosphaeria dothidea

source_name: mycelium

extract_protocol:
Total RNA was extracted according to the instruction manual of the Trizol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mycelium

tag: Stage


title: fMSC.iPSC

description: replicate 1

source_name: induced pluripotent stem cells from fMSCs


title: LW-1-3


title: 11550X12

source_name: NRE1 KO clone 2 LPS/IFNγ

growth_protocol: Raw 264.7 cells were transfected with CRISPR constructs that targeted flanking regions of NRE1. Cells with both CRISPR constructs were selected based on GFP and Puro expression. Cells were grown from single cell clones and assayed for the deletion of NRE1

treatment_protocol: Cells positive for the deletion of NRE1 were stimulated with media or LPS/IFNγ combination (10ng/mL and 50ng/mL respectively) for six hours prior to RNA isolation

value: Raw 264.7 cells

tag: trt

value: KO M1


title: 10625X2

source_name: Raw 264.7 media 2

value: macrophage cell line


title: A2780_450B_3_small_RNA-Seq

city: Bethesda

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

description:
small RNA
replicate 3
A2780_mature_miRNAs_relative_freq.xlsx A2780_prec_miRNAs_relative_freq.xlsx

data_processing:
For RNA-Seq and small RNA-Seq, the sequence reads were aligned to the human genome h19 using TopHat.Differential expression was performed using Cuffdiff
For AGO 4SU-PAR-CLIP, the analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Genome_build: h19

source_name: ovarian cancer cell line

growth_protocol: A2780 and SKOV-3 were cultivated either in RPMI medium (Gibco, Catalog No. 31800–022) or in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, Catalog No. 11995065), respectively, supplemented with 10% fetal bovine serum (FBS, GE Healthcare, Catalog No. SH30071.03) and 100 units of penicillin and 0,1 mg/ ml of streptomycin (Sigma-Aldrich Co., Catalog No. P4333). Cells were cultivated at 37°C and 5% CO2

extract_protocol:
Total RNA was extracted from three biological replicates from each cell line using TRIzol™ Reagent (Invitrogen, Catalog No. 15596026) second to recommendations from manufacturer. For small RNA cDNA library, we followed the protocol from Farazi et al (Farazi et al., 2012) after RNA extraction. AGO 4SU-PAR-CLIP method was performed as described previously (Benhalevy et al., 2016; Hafner et al., 2010)
All the samples were sequenced on an Illumina HiSeq 3000 machine using the 50 cycle single read protocol.

value: pri-miR-450b overexpression with lentivirus

value: ovarian cancer


title: RNAseq_5th_FW_S1

source_name: whole wing tissue


title: 10625X3

source_name: Raw 264.7 M1 (LPS/IFNg) 1

value: RAW M1


title: GMPTreated_Rep1

value: HT29 human epithelial adenocarcinoma cell line

value: glycomacropeptide


title: fMSC_1

description: replicate 1

value: fetal mesenchymal stem cells


title: Untreated_Rep3

description: Gene expression in untreated HT29 cells

source_name: Human colon adenocarcinoma cell line HT-29 Untreated


title: Untreated_Rep2

description: Gene expression in untreated HT29 cells


title: fMSC.iMSC_1

description: replicate 1

source_name: mesenchymal stem cells derived from fMSC-iPSCs


title: RNAseq_5th_FW_S2

value: 5th instar

value: forewing


title: A2780_450B_2_small_RNA-Seq

description:
small RNA
replicate 2
A2780_mature_miRNAs_relative_freq.xlsx A2780_prec_miRNAs_relative_freq.xlsx


title: LW-0-3


title: ChIP_pp_S2_input

library_source: genomic

data_processing:
Alignment to junonia coenia genome using bowtie 2.
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
Peak calls were performed using MACS2
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: RPKM normalized and input subtracted signal files were produced using Deeptools

molecule: genomic DNA

extract_protocol:
Nuclei from whole wing tissue were sheared with a bioraptor and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions accompanying the NEBNext Ultra DNA Library Prep Kit

value: pre pupa

value: hindwings

tag: chip antibody


title: Untreated_Rep1

description: Gene expression in untreated HT29 cells


title: 11550X10

source_name: NRE1 KO clone 1B LPS/IFNγ


title: RSM_3

city: Ann Arbor

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

data_processing:
Alignment with BWA v 0.7.8-r455
Differential expression analyses were perfomed with limma and edgeR packages in R
Genome_build: Streptococcus pyogenes MEW123, GenBank accession #: CP014139
Supplementary_files_format_and_content: Txt file with cpm values for each gene in each sample. The file MEW123_locustags_key.csv provides a key to the locus tags for each gene ID used in the processed data file.

organism: Streptococcus pyogenes

source_name: Streptococcus pyogenes, RSM deficient

growth_protocol: Cells were grown in C-media at 37C under anaerobic conditions to mid-log phase (OD600 of 0.6)

extract_protocol:
RiboPure RNA Purification Kit, bacteria (AM1925)
Library construction was performed by the University of Michigan Sequencing Core using the Ribo-Zero Magnetic Kit, bacteria for rRNA depletion and the Illumina TruSeq Sample Prep Kit

treatment_protocol: Cell pellets were resuspended in RNAlater and stored at -20C

tag: sample id

tag: strain

value: RSM deficient


title: 11550X11

source_name: NRE1 KO clone 2 media

value: KO media


title: ChIP_pp_S1_input


title: ChIP_pp_S2_ECR

value: dshb  (Developmental Studies Hybridoma Bank, Catalog# 6B7)


title: RSM_2


title: A2780_450B_1_small_RNA-Seq

description:
small RNA
replicate 1
A2780_mature_miRNAs_relative_freq.xlsx A2780_prec_miRNAs_relative_freq.xlsx


title: 11550X8

source_name: NRE1 KO clone 1A LPS/IFNγ


title: 11550X9

source_name: NRE1 KO clone 1B media


title: A2780_450a_3_small_RNA-Seq

value: pri-miR-450a overexpression with lentivirus


title: A2780_450a_1_small_RNA-Seq


title: A2780_pLVX_3_small_RNA-Seq

value: empty lentivirus vector


title: ChIP_pp_S1_ECR


title: StemPRO

city: Helsinki

first: Sippy

last: Kaur

address: PO Box 63

department: Oral and Maxillofacial Diseases

country: Finland

institute: University of Helsinki

description:
miRNA_raw.txt
smRNA_raw.txt
miRNA_spikein_normalized.txt
smRNA_spikein_normalized.txt

data_processing:
Raw data was demultiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.).
To correct PCR bias with UMI information, raw reads were processed as follows: First, cutadapt 1.11  was used on each raw read with the adapter sequence to acquire information about the presence of adapter. Only reads that fulfilled the following criteria were kept: 1) read contained adapters, 2) read had at least 16nt insert sequence length, and 3) read had at least 10nt-long UMI sequence. Second, insert sequences with incomplete UMI sequence were extracted as partial-UMI reads. Third, all unique insert+UMI combinations were identified from reads with full-length UMI and collapsed into a single read. Fourth, collapsed full-length UMI reads and partial-UMI reads were combined.
After UMI-correction, reads were trimmed using cutadapt output and an in-house script.
Reads were mapped using Bowtie 2 (2.2.2) as follows: First, reads mapped to spike-ins or outmapped (mapped to adapter sequences, polyA and polyC homopolymers, or abundant ribosomal or mitochondrial RNA sequences) were filtered out. Perfect match to the reference sequence was required. Second, reads were aligned to mature sequences of miRBase 20, requiring perfect matches. Third, unmapped reads were mapped to either to human GRCh37 or bovine UMD3 reference genome, allowing one mismatch in the first 32 bases of the read. Reads aligned to known miRNA loci in the genome were combined with the miRBase-mapped reads and reads aligned to smallRNA reqions in the Exiqon smallRNA database were classified as smallRNA. Reads mapping to the reference genome outside the miRNA or smallRNA regions were classified as genome-mapped. No indels were allowed in any of the mapping steps.
Read counts were normalized using the external spike-ins (UniSp100-UniSp151) that were present in three relative concentrations of 0.1 (low), 1 (moderate) and 5 (high), reflecting the expected range of miRNAs in the samples. Linear functions with intercept fixed at zero were fitted to the spike-in concentration versus observed counts in each sample. The linear fit was used calculate an estimated relative concentration for each RNA.
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt files contain results of mapping to miRBase 20 and GRCh37 reference genome. miRNA_raw.txt: miRNA raw counts for all samples, smRNA_raw.txt: other smRNA raw counts for all samples, miRNA_spikein_normalized.txt: spike-in normalized miRNA counts for all samples, smRNA_spikein_normalized.txt: spike-in normalized counts for other smRNA for all samples.

organism: other sequences

source_name: Defined serum-free medium extracellular vesicles

extract_protocol:
Two supernatant removal steps were used on 3 ml of culture media to get rid of the un-precipitated material. EV lysis and RNA isolation was performed on 500 µl of media using exoRNeasy Serum/Plasma Maxi Kit (QIAGEN).
Library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). Out of 12µl of isolated RNA, 5µl was converted into microRNA NGS libraries. Adapters containing 12nt-long unique molecular indices (UMIs) were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation quality control was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent). Based on the quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pools were quantified using the qPCR ExiSEQ LNA™ Quant kit (Exiqon). The library pools were then sequenced on a NextSeq500 sequencing instrument according to the manufacturer instructions using 1x75bp reads.

tag: sample type

value: EV

tag: medium

value: Defined serum-free medium

tag: supplier

value: Gibco


title: ChIP_d7_S1_input

value: 6 days after pupation

tag: tissue


title: 11550X6

source_name: NRE1 Wt clone 3 LPS/IFNγ

tag: cell type

value: Raw 264.7 cells

value: WT M1


title: A2780_450a_2_small_RNA-Seq

value: ovarian cancer


title: 11550X4

source_name: NRE1 Wt clone 2 LPS/IFNγ


title: 11550X3

source_name: NRE1 Wt clone 2 media

value: WT media


title: ChIP_72h_S3_ss

value: 72 hours after pupation

value: spineless (gift from M. Perry)


title: RSM_1


title: SKOV3_450a_3_RNA-Seq

description:
total RNA
replicate 3
SKOV3-450A_gene_exp.diff


title: SKOV3_450a_1_RNA-Seq

description:
total RNA
replicate 1
SKOV3-450A_gene_exp.diff


title: 123EC-DM: 12hr 3

city: Pittsburgh

first: Chibueze

middle: Anthony

last: Ihunnah

state: Pennsylvania

address: Lothrop St, Pittsburgh, PA 15213

department: Medicine

institute: University of Pittsburgh

description: Probes hybirdize directly to target molecule in solution. A reporter probe carries the signal, and a capture probe allows the complex to be immobilized for data collection.

hyb_protocol: Probe pairs are placed into a reaction in massive excess to target mRNA to ensure that each target finds a probe pair. Barcoded probes hybridize directly to target molecules in solution. The reporter probe carries the signal and the capture prode allows the complex to be immobilized for data collection.  Samples were hybridized overnight.

scan_protocol: Using the nCounter prep station, magnetic beads derivitized with short nuclei acid sequences that are complementary to the capture probe and the reporter probe are used for immobilization of the complex, followed by a number of wash steps to remove excess probe. Data collection was carried out in the nCounter digital analyzer. At the highest standard data resolution, 600 fields of view are collected per flow cell(Sample).

data_processing: Data processing was carried out using the nSolver software from Nanostring. For nSolver software analysis, raw values were normalized to 10 house-keeping genes including (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, RPL13A,SDHA,TBP,UBC,YWHAZ). Fold induction was calculated as a ratio of normalized drug treated samples versus normalized DMSO treated samples.

label: Proprietary "bar code" for each target sequence

source_name: Human lung microvascular endothelial cells (HMVEC)

label_protocol: A standardized and automated system for conducting nCounter assays (lableing, hybridization, scan, data processing) has been established by Nanostring.  In short nCounter technology is based on digital detection and direct molucular barcoding of target molecules, in this case RNA, through the use of a color coded probe pair. The probe pair consists of a reporter probe and a capture probe. The color codes carry six positions and each postion can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to a target (mRNA transcript).

growth_protocol: Primary human lung microvascular endothelial cells  were cultured using endothelial cell growth medium . Human erythroleukemia cells (K562) ,  were cultured in Iscove’s Modified Dulbecco Medium. Both cell types were grown in a cell culture incubator (Applied Biosystems) under standard conditions at 37° C and 5% CO2.

extract_protocol: RNA was isolated using RNeasy mini kits (Quiagen). Total of 500ng of total RNA was used for Nanostring nCounter assays.

treatment_protocol: For pharmacological experiments cells were culture in DMF (20 uM), CDDO-Me (100 nM) or DMSO for 6-12hrs. All cells were cultured in a cell culture incubator (Applied Biosystems) under standard conditions at 37° C and 5% CO2.

value: Human lung

tag: drug treatment

value: Cells were treated with dimethyl fumarate (DMF, 20mM)


title: 121EC-DM: 12hr 1

value: Human lung microvascular endothelial cells (HMVEC)


title: 11550X1

source_name: NRE1 Wt clone 1 media


title: WT_3

source_name: Streptococcus pyogenes

tag: genotype

value: WT


title: WT_2


title: ChIP_72h_S3_ECR

value: hindwings

value: dshb  (Developmental Studies Hybridoma Bank, Catalog# 6B7)


title: ChIP_d7_S2_ECR


title: WT_1


title: 11550X5

source_name: NRE1 Wt clone 3 media


title: 11550X7

source_name: NRE1 KO clone 1A media

value: KO media


title: ChIP_72h_S2_ss

source_name: whole wing tissue


title: ChIP_72h_S2_input


title: 64EC-DM: 6hr 4


title: 11550X2

source_name: NRE1 Wt clone 1 LPS/IFNγ


title: A2780_450a_3_RNA-Seq

description:
total RNA
replicate 3
A2780-450A_gene_exp.diff

source_name: ovarian cancer cell line

value: pri-miR-450a overexpression with lentivirus


title: ATACseq_d7_HW_S3

data_processing:
Alignment to Junonia coenia genome using bowtie 2.
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
Peak calls were performed with F-seq
Genome_build: jc.gen.v1 (Genome build can be found at lepbase.org; download sequence: http://download.lepbase.org/v4/sequence/; overview: http://ensembl.lepbase.org/Junonia_coenia_jc10/Info/Index)
Supplementary_files_format_and_content: RPKM normalized files were produced using deeptools

growth_protocol: Caterpillars and pupae were raised at ~27C before sampling.

extract_protocol:
Nuclei from whole wing tissue were treated with hyperactive Tn5 as described in the ATAC-seq protocol
Libraries were prepared as described in the ATAC-seq protocol

value: hindwing


title: ATACseq_d7_HW_S2


title: 62EC-DM: 6hr 2


title: 61EC-DM: 6hr 1


title: ChIP_d7_S1_ECR


title: A2780_450a_2_RNA-Seq

description:
total RNA
replicate 2
A2780-450A_gene_exp.diff


title: VAD diet_1

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

data_processing:
Sequence data were mapped against the mm10 genome using TopHat and FPKMs were generated using Cuffdiff with parameters FPKM >10 (50), fold change >2, and adjusted p value <0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file with fpkm for each sample

source_name: Skin

extract_protocol: RNA was extracted from whole mouse skin.

treatment_protocol: Conventional mice on a vitamin A deprived diet

value: Skin

tag: diet

value: Vitamin A deprived diet

tag: treatment


title: A2780_450a_1_RNA-Seq

description:
total RNA
replicate 1
A2780-450A_gene_exp.diff


title: 66EC-DM: 6hr 6


title: D3EC-DM: DMSO 3

value: Cells were treated with DMSO (Vehicle)


title: A2780_pLVX_2_small_RNA-Seq

value: empty lentivirus vector


title: ChIP_d7_S2_input

tag: developmental stage

value: 6 days after pupation


title: A2780_pLVX_1_small_RNA-Seq

tag: cell line

value: ovarian cancer


title: 122EC-DM: 12hr 2


title: SKOV3_pLVX_3_RNA-Seq


title: 65EC-DM: 6hr 5


title: VAD diet_2

value: Conventional mice on a vitamin A deprived diet


title: ATACseq_d7_FW_S3

value: forewing


title: D1EC-DM: DMSO 1

value: Human lung


title: 63EC-DM: 6hr 3

value: Cells were treated with dimethyl fumarate (DMF, 20mM)


title: 12FEC-CD: 12hr 6

value: Human lung microvascular endothelial cells (HMVEC)

value: Cell were treated with CDDO-Me (CDDO, 100nM)


title: SKOV3_450a_2_RNA-Seq

description:
total RNA
replicate 2
SKOV3-450A_gene_exp.diff


title: Germ-free_Staphylococcus aureus_3

treatment_protocol: Germ-free mice treated topically for three days with mid-log phase S.aureus

value: Chow diet


title: ChIP_72h_S2_ECR

value: 72 hours after pupation

value: hindwings

value: dshb  (Developmental Studies Hybridoma Bank, Catalog# 6B7)


title: WT

city: Shanghai

first: Chenguang

last: Zhu

address: Nanchen Road 333

institute: Shanghai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v3 using bowtie 2 v2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. 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: Ensembl plants release-30 zea_mays
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Zea mays

source_name: kernel

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

value: endosperm

tag: age

value: 12 DAP

value: wild type


title: ATACseq_72h_HW_S3

value: hindwing


title: ATACseq_d7_HW_S1


title: Control_3

treatment_protocol: Conventional mice on a chow diet

value: Skin

value: Control Vitamin A diet

value: Conventional mice on a chow diet


title: Germ-free_Staphylococcus aureus_2

value: Germ-free mice treated topically for three days with mid-log phase S.aureus


title: dek40


title: SKOV3_pLVX_2_RNA-Seq

value: empty lentivirus vector

value: ovarian cancer


title: A2780_pLVX_2_RNA-Seq


title: D2EC-DM: DMSO 2

value: Human lung

value: Cells were treated with DMSO (Vehicle)


title: 5mRNA

city: beijing

first: zhanying

last: hu

address: 1# tiantanxili, dongcheng district

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

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 danRer10 whole genome using STAR 2.5.2a
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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: danRer10
Supplementary_files_format_and_content: RPKMs

organism: Danio rerio

source_name: larvae

extract_protocol:
A total amount of 1.5μ g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB

value: 6 day post fertilization

value: injection atg5 mRNA

value: atg5 overexpression


title: ATACseq_72h_HW_S1

value: 72 hours after pupation


title: A2780_pLVX_1_RNA-Seq


title: 12EEC-CD: 12hr 5

value: Human lung microvascular endothelial cells (HMVEC)

value: Cell were treated with CDDO-Me (CDDO, 100nM)


title: ChIP_72h_S3_input

value: hindwings


title: ATACseq_d7_FW_S1

value: 6 days after pupation

value: forewing


title: ATACseq_d7_FW_S2


title: Germ-free_6

treatment_protocol: Germ-free mice with no treatment

value: Skin

value: Chow diet

value: Germ-free mice with no treatment


title: Control_2

value: Control Vitamin A diet

value: Conventional mice on a chow diet


title: ATACseq_72h_HW_S2

value: hindwing


title: Germ-free_5


title: 12BEC-CD: 12hr 2

value: Human lung


title: 12DEC-CD: 12hr 4


title: 12AEC-CD: 12hr 1


title: 12CEC-CD: 12hr 3


title: 6CEC-CD: 6hr 3


title: Control_1


title: Germ-free_4


title: A2780_pLVX_3_RNA-Seq

value: empty lentivirus vector

value: ovarian cancer


title: 5MO

value: AB

value: 6 day post fertilization

value: injection 5MO

value: atg5 knockdown


title: ATACseq_72h_FW_S3

value: 72 hours after pupation


title: Germ-free_3


title: ATACseq_72h_FW_S1


title: WT

value: untreated

value: wildtype


title: ATACseq_72h_FW_S2

value: forewing


title: 6BEC-CD: 6hr 2

value: Human lung microvascular endothelial cells (HMVEC)

value: Cell were treated with CDDO-Me (CDDO, 100nM)


title: Germ-free_Staphylococcus aureus_1

value: Skin

value: Chow diet

value: Germ-free mice treated topically for three days with mid-log phase S.aureus


title: 6AEC-CD: 6hr 1


title: ATACseq_pp_HW_S1

value: pre pupa

value: hindwing


title: D3EC-CD: DMSO 3

value: Human lung

value: Cells were treated with DMSO (Vehicle)


title: ATACseq_pp_HW_S3


title: D2EC-CD: DMSO 2


title: ATACseq_pp_FW_S3


title: SKOV3_pLVX_1_RNA-Seq

value: empty lentivirus vector

value: ovarian cancer


title: ATACseq_pp_FW_S1


title: ATACseq_pp_HW_S2


title: 123K5-CD: 12hr 3

source_name: K562 cells (ATCC)

value: Human erythroleukemia cells


title: ATACseq_5th_HW_S1

value: 5th instar


title: 122K5-CD: 12hr 2


title: ATACseq_5th_HW_S2


title: Germ-free_2

value: Germ-free mice with no treatment


title: 121K5-CD: 12hr 1


title: 66K5-CD: 6hr 6


title: ATACseq_pp_FW_S2


title: ATACseq_5th_HW_S3


title: Germ-free_1


title: 65K5-CD: 6hr 5


title: D1EC-CD: DMSO 1


title: Harrington-Uninoculated-Rep2

city: Fargo

first: Robert

last: Brueggeman

state: ND

address: 306 Walster Hall, North Dakota State University

department: Plant Pathology

institute: North Dakota State University

data_processing:
The Illumina bcl2fastq2 Conversion Software was used to convert basecall (BCL) to FASTQ files and demultiples the reads to each barcodes
Sequnenced reads were trimmed for quality score and ambigious calls using default parameters in CLCgenomics Workbench v8.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) eads Per Kilobase of exon model per Million mapped reads were calculated for reads mapped to pathogen and host gene models in CLC genomics Workbench v8.0
Supplementary_files_format_and_content: tab-delimited text files include total gene reads and RPKM values of host and pathogen genes for each sample

organism: Hordeum vulgare

source_name: Leaf tissues

growth_protocol: Barley variety Harrington were grown for seven days in 6 inch cone

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 following the manufactures standard protocol

treatment_protocol: Barley variety Harrington was swab inoculated with different isolates of fungal pathogen Puccinia graminis f.sp. tritici at two leaf stage

tag: host cultivar

value: Harrington

tag: pathogen isolate

value: (Not applicable)

tag: isolate virulence profile

value: Leaf


title: Harrington-Uninoculated-Rep3


title: ATACseq_5th_FW_S1

value: forewing


title: ATACseq_5th_FW_S2


title: Harrington-Uninoculated-Rep1


title: 64K5-CD: 6hr 4

value: Cell were treated with CDDO-Me (CDDO, 100nM)


title: RSM

data_processing:
Library strategy: DNA-seq
Data processing was performed using RS_Modification_and_Motif_analysis.1 version 2.3.0 from SMRT portal
Genome_build: Streptococcus pyogenes MEW123, GenBank accession #: CP014139
Supplementary_files_format_and_content: HTML and text file with the identified modified motifs

extract_protocol:
Genomic DNA was purified using the Wizard Genomic DNA Purification Kit (Promega)
Library construction was performed by the University of Michigan Sequencing Core, 5kb mean insert size

value: RM system deficient


title: ATACseq_5th_FW_S3


title: 62K5-CD: 6hr 2


title: 61K5-CD: 6hr 1


title: 63K5-CD: 6hr 3


title: D3K5-CD: DMSO 3


title: P84-16

organism:
Hordeum vulgare
Puccinia graminis f. sp. tritici

value: Virulent-Rpg1 and Avirulent rpg4/5


title: R29JB

value: Virulent-rpg4/5 and Avirulent Rpg1


title: R29M


title: AC-12

value: Avirulent-rpg4/5 and Avirulent Rpg1


title: WM1


title: A-5


title: QCCJ

value: QCCJ


title: A-48


title: R29JA


title: R11c


title: A-21


title: 66K5-DM: 6hr 6

value: Cells were treated with dimethyl fumarate (DMF, 20mM)


title: 122K5-DM: 12hr 2


title: 121K5-DM: 12hr 1


title: 65K5-DM: 6hr 5


title: 123K5-DM: 12hr 3


title: D2K5-CD: DMSO 2

value: Cells were treated with DMSO (Vehicle)


title: A-14


title: A-12


title: 62K5-DM: 6hr 2


title: 61K5-DM: 6hr 1


title: 64K5-DM: 6hr 4


title: Leftventricle_Postpartum_2

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Hybridizations to Mouse Gene ST 2.0 chips (Affymetrix / ThermoFisher) were done according to manufacturer protocols using 3.5 ug labeled material appropriate for the 100-format array. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files were imported into Affymetrix Expression Console software and normalization conducted using RMA gene level summarization. Annotated expression data was exported, and the references and controls (i.e., not designated as type main or rescue) were excluded from the data set.

source_name: Left ventricle, female, post-partum, day 1.5

label_protocol: Total RNA (100 ng) was converted into fragmented, biotin-labeled, single stranded cDNA using the WT Plus Reagent Kit (Affymetrix / ThermoFisher) in accordance with manufacturer protocols.

growth_protocol: Age-matched 3-4 month old non pregnant and timed pregnant C57BL/6 mice were purchased from Jackson Laboratories (Bar Harbor, ME).  Animals were housed under standard conditions.  The animal protocol was approved by the University of South Carolina Institutional Animal Care and Use Committee.  Animals were subjected to isoflurane inhalation until toe pinch reflex was lost and subjected to cervical dislocation.

extract_protocol: At sacrifice, the heart was removed and the left ventricle dissected from the rest of the heart, cut into three pieces, snap frozen and then stored at -80 °C until RNA isolation. RNA was isolated from one piece of left ventricle tissue using Trizol reagent (Invitrogen, Thermofisher) and the RNeasy Mini kit (Qiagen).  RNA samples were screened for quality by Expirion (Biorad) RNA analysis chip.

treatment_protocol: Animals were sacrificed according to the following groups:  1) non-pregnant mice in diestrus, 2) mice at 12 days of pregnancy (mid-pregnancy), 3) mice at 18/19 days of pregnancy (late pregnancy), 4) mice at 1.5 days post-partum.

tag: Stage

value: Post-partum, day 1.5

value: left ventricle


title: A-15


title: 63K5-DM: 6hr 3

value: Human erythroleukemia cells


title: D1K5-CD: DMSO 1


title: D3K5-DM: DMSO 3


title: H2AX replicate 2 (tiling2)

type: genomic

city: Bronx

first: Kami

last: Kim

state: New York

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

hyb_protocol: Cy3/5 labelled DNA (input/Experiment) were precipitated with 0.1 vol of 5M NaCl and 0.9 vol Isopropanol. Using NimbleGen Hybridization Kit, manufacturer's instructions were followed for hybridization reaction

scan_protocol: Arrays were scanned at wavelengths (532=cy3, 635=Cy5) with pixel size 5_m at 100% power using Agilent's DNA Microarray Scanner using Agilent scanner software

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Following this a custom R-script was used to convert T. gondii genome version 4 data to version 11 and combine tiling 1 and 2 arrays. Processed files (_ratio.gff and ratio_peaks.gff) are in T. gondii version 11.

organism: Toxoplasma gondii RH

source_name: H2AX ChIP DNA from T. gondii

label_protocol: 1.2_g of Input and Experimental DNA sample were labelled with Cy3 and Cy5 dye respectively (NimbleGen Dual-Color DNA Labelling Kit) using Klenow Fragment 3->5 exo- (NEB) following manufacturer's instructions

growth_protocol: Normal pH7 growth conditions

extract_protocol: Nuclei extracted with high salt buffer and chromatin digested with micrococcal nuclease and digested DNA was incubated with antibodies against H3K4me3, H2AZ, H2AX or anti-Myc followed by protein G Dynabeads (Invitrogen). Immunoprecipitated DNA was amplified using Complete Whole Genome Amplification Kit (SIGMA ALDRICH)

treatment_protocol: Mnase-digestion

value: Tachyzoite

value: Wild type

source_name: Input Mnase-digested DNA

treatment_protocol: Input DNA


title: H2AX replicate 1 (tiling2)


title: D1K5-DM: DMSO 1


title: D2K5-DM: DMSO 2


title: Leftventricle_Pregnant_Ed19_1

source_name: Left ventricle, female, pregnant, embryonic day 19

value: Pregnant, day 19

tag: strain


title: H2AZ replicate 2 (tiling2)

source_name: H2AZ ChIP DNA from T. gondii


title: 81AC46

value: Harrington


title: 81AC28

value: Leaf


title: 79_20


title: LowA4_granulosa-cells_4

city: Lincoln

first: Sarah

last: Romereim

state: NE

address: 3940 Fair Street

department: Animal Science

institute: University of Nebraska-Lincoln

description: Isolated from estrogen-active dominant follicles in ovaries of estrous-synchronized beef cows (75% Red Angus, 25% MARC III) from the physiology herd located at the University of Nebraska Agricultural Research and Development Center. The University of Nebraska-Lincoln Institutional Animal Care and Use Committee approved all procedures and facilities used in this experiment. Estrous cycles of cows were synchronized with a modified Co-Synch protocol using gonadotropin releasing hormone (GnRH) and a controlled internal drug release device (CIDR; 1.38 g progesterone, Zoetis) for 7 days with a PGF2α (25 mg/mL; Lutalyse, Pfizer Animal Health) injection at CIDR removal (Summers et al., 2014). Ovariectomy was performed approximately 36 hours after CIDR removal (Youngquist et al., 1995). Upon ovariectomy, each dominant antral follicle was aspirated/dissected and the granulosa cells (≥ 94% purity) and follicular fluid were isolated as described previously (Summers et al., 2014).

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 42C on Bovine GeneChip Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G using the Affymetrix GeneChip Command Console Software

data_processing: Affymetrix Expression Console software was used to perform GC-RMA normalization and export the linear expression data.

organism: Bos taurus

source_name: bovine ovarian dominant follicle, mural and cumulus granulosa cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Homogenized in Tri-Reagent (Sigma-Aldrich) for total RNA extraction according to the manufacturer's instructions.

tag: androgen-content

value: low


title: Leftventricle_Diestrus_3

source_name: Left ventricle, female, diestrus

value: Diestrus


title: Leftventricle_Diestrus_2


title: 79.2


title: 72-41-SP-2


title: 640C


title: H2AZ replicate 1 (tiling2)


title: CS1AN_UV30min

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

data_processing:
FastQC was conducted for Quality control (QC) of RNA-seq reads
Trimming was performed by seqtk for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads
Trimmed reads were mapped to the Homo Sapiens reference genome by the Hisat 2(version:2.0.4)
String Tie(version:1.3.0) was performed for each gene count from trimmed reads
Gene counts were normalized by trimmed mean of M-values, and fragments per kilobase of transcript per million mapped reads (FPKM) in Perl script
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: fibroblast cell line

growth_protocol: culture in complete DMEM + 10% FBS + 1% Amp/Strep

extract_protocol:
Culture medium was removed and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12J/m2 UV-C irradiation

tag: stress

value: UV


title: CS1AN_un

value: control


title: 45C sample 5

city: New York

first: Jonathan

middle: W.

last: Snow

address: 3009 Broadway

department: Biology

institute: Barnard College

description:
apis_Nc45-5vNcD2
nosema_Nc45-5vNcD2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the A. mellifera and N. ceranae reference genomes available on NCBI using the STAR aligner.
The RNA-seq aligner is executed using a splice aligner, which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step.
Gene hit counts were calculated using Feature counts from the Subread package.
After mapping and total gene hit counts calculation, the total gene hit counts table was used for downstream differential expression analysis using DESeq2 and groups were compared.
Genome_build: Nosema ceranae BRL01
Genome_build: Amel_4.5
Supplementary_files_format_and_content: comma-separated values, normalized read ouns for paired samples

organism:
Apis mellifera
Vairimorpha ceranae

source_name: N. ceranae infected honey bee midgut

extract_protocol:
Midguts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA was submitted to additional quality control analysis before mRNA was enriched by polyA selectio
Llibrary preparation was performed using a NEBNext Ultra RNA library preparation kit. Sequencing was then performed using Illumina HiSeq platform.

value: midgut

tag: infection

value: infected with Nosema ceranae

tag: infection time

value: 8 days post-infection

tag: temperature


title: 72_00

value: Virulent-Rpg1 and Avirulent rpg4/5

tag: tissue


title: 45C sample 4

description:
apis_Nc45-4vNcD3
nosema_Nc45-4vNcD3


title: H3K4me3 replicate 1 (tiling2)

source_name: H3K4me3 ChIP DNA from T. gondii

tag: genotype


title: MRC5_un


title: HighA4_granulosa-cells_2

value: high


title: MRC5_UV30min


title: Leftventricle_Postpartum_4

value: Post-partum, day 1.5


title: 370C

value: Virulent-rpg4/5 and Avirulent Rpg1


title: 79-1


title: Leftventricle_Pregnant_Ed12_2

source_name: Left ventricle, female, pregnant, embryonic day 12

value: Pregnant, day 12

value: left ventricle


title: Leftventricle_Pregnant_Ed19_2


title: 81AC34

value: Avirulent-rpg4/5 and Avirulent Rpg1


title: 35C sample 4

description:
apis_Nc45-1vNcD4
nosema_Nc45-1vNcD4


title: 35C sample 3

description:
apis_Nc45-4vNcD3
nosema_Nc45-4vNcD3


title: LowA4_granulosa-cells_2


title: 35C sample 2

description:
apis_Nc45-5vNcD2
nosema_Nc45-5vNcD2


title: H1_H3K27me3_20181025_icell8_486_(20181025_Pool2_TAGGCATG_ACGCGCAG)

status: Public on Apr 29 2019

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Single-cell CUT&Tag for H3K27me3 in H1 cells using ICELL8 platform

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We extracted fragments from properly paired reads (Supplementary file(s) .bed) .

source_name: Single cell CUT&Tag

extract_protocol:
Single-cell CUT&Tag: Approximately 1 million exponentially growing H1 cells were processed by centrifugation between buffer and reagent exchanges in low-retention tubes throughout. Centrifugations were performed at 600g for 3 min in a swinging bucket rotor for the initial wash and incubation steps, and then at 300g for 3 min after pA-Tn5 binding.  Cells were collected and washed twice with 1ml Wash Buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM Spermidine, 1X Protease inhibitor cocktail) at room temperature. Nuclei were isolated by permeabilizing cells in NP40-Digitonin Wash Buffer (0.01% NP40, 0.01% Digitonin in wash buffer) and resuspended in 0.25 mL of NP40-Digitonin Wash buffer with 1mM EDTA. Antibody was added at a 1:50 dilution and incubated on a rotator at 4°C overnight. Permeabilized cells were then rinsed once with NP40-Digitonin Wash buffer and incubated with anti-Rabbit IgG antibody (1:50 dilution) in 0.5 ml of NP40-Digitonin Wash buffer on a rotator at room temperature for 30 min. Nuclei were then washed 3x for 5 min in 1 ml NP40-Digitonin Wash buffer to remove unbound antibodies. For pA-Tn5 binding, a 1:200 dilution of pA-Tn5 adapter complex was prepared in 0.3 mL NP40-Dig-med-buffer (0.01% NP40, 0.01% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1X Protease inhibitor cocktail), and permeabilized cells were incubated with the pA-Tn5 adapter complex on a rotator at RT for 1 hr. Cells were washed 3x for 5 min in 1 ml NP40-Dig-med-buffer to remove excess pA-Tn5 protein. Cells were resuspended in 150 µL Tagmentation buffer (10 mM MgCl2 in NP40-Dig-med-buffer) and incubated at 37 for 1h. Tagmentation was stopped by adding 50 µL of 4X Stop Buffer (40.4 mM EDTA and 2 mg/ml DAPI) and the sample was held on ice for 30 minutes. The SMARTer ICELL8 single-cell system (Takara Bio USA, Cat. #640000) was used to array single cells as described for scATAC-seq12. DAPI-stained nuclei were visualized under the microscope and if there were clumps, they were strained through 10 micron cell strainers. Cells were counted using a hematocytometer and diluted at 28 cells/µL in 0.5X PBS and 1X Second Diluent (Takara Bio USA, Cat. # 640196). 10000 cells were loaded to 4 wells of the source loading plate. Control wells containing 0.5X PBS (25 µl) and fiducial mix (25 µl) (Takara Bio USA, Cat.  #640196) were also included in the source loading plate. Using the ICELL8 MultiSample NanoDispenser (MSND) FLA program, cells were dispensed into a SMARTer ICELL8 250v chip (Takara Bio USA, Cat. # 640183) at 35 nanoliter per well. After cell dispense was complete, chips were sealed with the imaging film (Takara Bio USA, Cat. #640109) and centrifuged at 400 xg for 5 min at room temperature and imaged using the ICELL8 imaging station (Takara Bio USA). Images were analyzed using automated microscopy image analysis software (CellSelect, Takara Bio USA). Since cells were stained only with DAPI, they were propidium iodide negative, so that permeabilized cells would not be excluded by default software settings. Additional single cells were manually selected for dispensing using a manual triaging procedure (~486 single cells in total). Immediately following imaging, the filter file, which notes single-cell containing wells and control wells, was generated. All of the following reagents were added to the selected set of wells which contained single cells. To index the whole chip, 72 i5 and 72 i7 unique indices [Buenostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486-U264 (2015)] were dispensed at 7.32 µM using ICELL8 MSND FLA program using the index 1 and index 2 filtered dispense tool respectively at 35 nanoliter per well. KAPA PCR mix (168 ul 5X HiFi Buffer + 25.2 ul 10mM dNTPs + 8.4 ul KAPA HiFi Polymerase non-hot start + 8.4 ul NF-water) was dispensed to selected wells using ICELL8 MSND FLA program at 35 nanoliter per well. The chip was sealed and centrifuged at 2250 xg at 4◦C for at least 5 min after each dispense. The chip was sealed with a TE Sealing film (Takara Bio USA, Cat. #640109) and on-chip PCR was performed using a SMARTer ICELL8 Thermal Cycler (Takara Bio USA) as follows: 5 min at 72 ◦C and 1 min at 98 ◦C followed by 15 cycles of 30 sec at 98 ◦C, 5 sec at 55 ◦C, with a final extension at 72 ◦C for 1 min. PCR products were collected by centrifugation at ~2250 xg for 20 min using the supplied SMARTer ICELL8 Collection Kit (Takara Bio USA, Cat.#640048). Pooled libraries were purified using Ampure XP beads (Beckman Counter) in a 1:1.1 ratio. Briefly, libraries were incubated with beads for 15 min at RT, washed twice in 80% ethanol, and eluted in 10 mM Tris pH 8.0. Paired-end 25x8x8x25 bp Illumina sequencing was performed on the pooled barcoded libraries following the manufacturer’s instructions.
Single-cell CUT&Tag

tag: antibody

value: H3K27me3 Cell Signalling #9733

tag: cell type

value: human embryonic stem cells


title: H1_H3K27me3_20181025_icell8_473_(20181025_Pool2_GTGTGGTG_TGATTGTT)


title: H1_H3K27me3_20181025_icell8_481_(20181025_Pool2_TTCCATAT_GTCGGACT)


title: H1_H3K27me3_20181025_icell8_484_(20181025_Pool2_CATCCTGT_GTCGGACT)


title: H1_H3K27me3_20181025_icell8_485_(20181025_Pool2_GGACTCCT_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_482_(20181025_Pool2_CGAGGCTG_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_469_(20181025_Pool2_CGGCCAAT_CGATAGGG)


title: H1_H3K27me3_20181025_icell8_474_(20181025_Pool2_CGGTTCCC_CTAAGCCT)


title: H1_H3K27me3_20181025_icell8_471_(20181025_Pool2_GTGTGGTG_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_483_(20181025_Pool2_TAAGGCGA_TCTGGCGA)


title: H1_H3K27me3_20181025_icell8_468_(20181025_Pool2_GTGTGGTG_GATCATTC)


title: H1_H3K27me3_20181025_icell8_475_(20181025_Pool2_TAAGGCGA_TCCATCAA)


title: 45C sample 1

description:
apis_Nc45-1vNcD4
nosema_Nc45-1vNcD4


title: Leftventricle_Pregnant_Ed12_3


title: H1_H3K27me3_20181025_icell8_480_(20181025_Pool2_TGGATCTG_GCAGCCTC)


title: LowA4_granulosa-cells_1


title: H1_H3K27me3_20181025_icell8_479_(20181025_Pool2_TTATGAAA_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_472_(20181025_Pool2_CGTACTAG_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_476_(20181025_Pool2_CGCGGACA_CCTGCGGG)


title: H1_H3K27me3_20181025_icell8_478_(20181025_Pool2_GGAGTAAG_AGAGATCT)


title: H1_H3K27me3_20181025_icell8_470_(20181025_Pool2_TAGGCATG_ATTGGGTC)


title: H1_H3K27me3_20181025_icell8_466_(20181025_Pool2_CGTACTAG_AGAGATCT)


title: LowA4_granulosa-cells_3


title: H1_H3K27me3_20181025_icell8_465_(20181025_Pool2_GGAGTAAG_ATCGAATG)


title: H1_H3K27me3_20181025_icell8_463_(20181025_Pool2_TAAGGCGA_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_477_(20181025_Pool2_TAGGCATG_GTCGGACT)


title: H1_H3K27me3_20181025_icell8_464_(20181025_Pool2_TAAGGCGA_GGGCTTGG)


title: HighA4_granulosa-cells_1


title: HighA4_granulosa-cells_3


title: H1_H3K27me3_20181025_icell8_445_(20181025_Pool2_GGAGTAAG_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_467_(20181025_Pool2_GGAGTAAG_TACTGACC)


title: HighA4_granulosa-cells_4


title: H1_H3K27me3_20181025_icell8_451_(20181025_Pool2_GTGTGGTG_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_453_(20181025_Pool2_TGGGTTTC_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_458_(20181025_Pool2_TCTTATTA_GGGCTTGG)


title: H1_H3K27me3_20181025_icell8_454_(20181025_Pool2_CAAGAATT_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_461_(20181025_Pool2_CGAGGCTG_CGCCAGAT)


title: H1_H3K27me3_20181025_icell8_444_(20181025_Pool2_CGCGGACA_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_455_(20181025_Pool2_CGGCCAAT_TGGGCGGT)


title: H1_H3K27me3_20181025_icell8_442_(20181025_Pool2_TAGGCATG_TCTGGCGA)


title: H1_H3K27me3_20181025_icell8_441_(20181025_Pool2_ATTGCCGG_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_460_(20181025_Pool2_GGACTCCT_AGGTTGCC)


title: H1_H3K27me3_20181025_icell8_452_(20181025_Pool2_GTTAACAG_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_447_(20181025_Pool2_GGACTCCT_CTAAGCCT)


title: H1_H3K27me3_20181025_icell8_446_(20181025_Pool2_AATGGTAG_TGGGCGGT)


title: H1_H3K27me3_20181025_icell8_462_(20181025_Pool2_CGAGGCTG_AGGTTGCC)


title: H1_H3K27me3_20181025_icell8_440_(20181025_Pool2_CGGTTCCC_GTCGGACT)


title: H1_H3K27me3_20181025_icell8_457_(20181025_Pool2_ATTGCCGG_CTAAGCCT)


title: H1_H3K27me3_20181025_icell8_443_(20181025_Pool2_CGCGGACA_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_456_(20181025_Pool2_CGTACTAG_GTAAGGAG)


title: H1_H3K27me3_20181025_icell8_450_(20181025_Pool2_TACTTGAA_GATTCCCA)


title: H1_H3K27me3_20181025_icell8_434_(20181025_Pool2_CGTACTAG_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_435_(20181025_Pool2_TTATGAAA_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_431_(20181025_Pool2_CGCGGACA_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_448_(20181025_Pool2_CGTACTAG_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_439_(20181025_Pool2_ATTGCCGG_ATGGTCAT)


title: H1_H3K27me3_20181025_icell8_426_(20181025_Pool2_TAGGCATG_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_437_(20181025_Pool2_ACAAAGTG_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_428_(20181025_Pool2_CGTACTAG_GTCGGACT)


title: H1_H3K27me3_20181025_icell8_459_(20181025_Pool2_CGGCCAAT_AGGTTGCC)


title: H1_H3K27me3_20181025_icell8_449_(20181025_Pool2_GACTTAGT_AGAGTAGA)


title: H1_H3K27me3_20181025_icell8_422_(20181025_Pool2_TTGCTAAG_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_424_(20181025_Pool2_GTGTGGTG_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_414_(20181025_Pool2_GATCCAAA_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_438_(20181025_Pool2_ATTGCCGG_TCACATGG)


title: H1_H3K27me3_20181025_icell8_419_(20181025_Pool2_TTCCATAT_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_421_(20181025_Pool2_TGGGTTTC_TACTGACC)


title: H1_H3K27me3_20181025_icell8_423_(20181025_Pool2_GTGTGGTG_AGAGATCT)


title: H1_H3K27me3_20181025_icell8_412_(20181025_Pool2_TAAGGCGA_AAGGAGTA)


title: H1_H3K27me3_20181025_icell8_430_(20181025_Pool2_TAGGCATG_GTGTATCG)


title: H1_H3K27me3_20181025_icell8_410_(20181025_Pool2_CGGCCAAT_CAGCAACG)


title: H1_H3K27me3_20181025_icell8_429_(20181025_Pool2_AAACGGTC_TACTGACC)


title: H1_H3K27me3_20181025_icell8_436_(20181025_Pool2_GCTACGCT_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_406_(20181025_Pool2_CGCGGACA_CCTTATGT)


title: H1_H3K27me3_20181025_icell8_420_(20181025_Pool2_TAAGGCGA_GTGTATCG)


title: H1_H3K27me3_20181025_icell8_416_(20181025_Pool2_CATCCTGT_ATCGAATG)


title: H1_H3K27me3_20181025_icell8_415_(20181025_Pool2_GGTAAACC_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_407_(20181025_Pool2_ATTGCCGG_AGGTTGCC)


title: H1_H3K27me3_20181025_icell8_417_(20181025_Pool2_ACAAAGTG_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_433_(20181025_Pool2_CTTGGGTC_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_418_(20181025_Pool2_TAAGGCGA_AGTCCGAG)


title: H1_H3K27me3_20181025_icell8_402_(20181025_Pool2_AAACGGTC_CGGACTGC)


title: H1_H3K27me3_20181025_icell8_405_(20181025_Pool2_AAACGGTC_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_425_(20181025_Pool2_TAAGGCGA_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_400_(20181025_Pool2_CGGCCAAT_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_399_(20181025_Pool2_CGTACTAG_CTAAGCCT)


title: H1_H3K27me3_20181025_icell8_408_(20181025_Pool2_CGGCCAAT_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_398_(20181025_Pool2_GGACTCCT_CGCCAGAT)


title: H1_H3K27me3_20181025_icell8_397_(20181025_Pool2_TAGGCATG_CCTGCGGG)


title: H1_H3K27me3_20181025_icell8_427_(20181025_Pool2_GGTCATTT_TCTGGCGA)


title: H1_H3K27me3_20181025_icell8_413_(20181025_Pool2_ATTGCCGG_GGGCTTGG)


title: H1_H3K27me3_20181025_icell8_395_(20181025_Pool2_CATCCTGT_GATTCCCA)


title: H1_H3K27me3_20181025_icell8_401_(20181025_Pool2_ACAAAGTG_GTCGGACT)


title: H1_H3K27me3_20181025_icell8_403_(20181025_Pool2_TAGGCATG_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_432_(20181025_Pool2_CGAGGCTG_CCTGCGGG)


title: H1_H3K27me3_20181025_icell8_388_(20181025_Pool2_CCGTTTGT_ATGGTCAT)


title: H1_H3K27me3_20181025_icell8_392_(20181025_Pool2_CGGTTCCC_CCTGCGGG)


title: H1_H3K27me3_20181025_icell8_411_(20181025_Pool2_CCGTTTGT_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_396_(20181025_Pool2_TGGGTTTC_TATTTGCG)


title: H1_H3K27me3_20181025_icell8_387_(20181025_Pool2_TTGCTAAG_ACCGGCCC)


title: H1_H3K27me3_20181025_icell8_394_(20181025_Pool2_TAGGCATG_TGCATACT)


title: H1_H3K27me3_20181025_icell8_409_(20181025_Pool2_CGGCCAAT_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_404_(20181025_Pool2_TTGCTAAG_ACGCGCAG)


title: H1_H3K27me3_20181025_icell8_390_(20181025_Pool2_TAGGCATG_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_383_(20181025_Pool2_TAAGGCGA_AGGTTGCC)


title: H1_H3K27me3_20181025_icell8_386_(20181025_Pool2_TTCCATAT_AGGTTGCC)


title: H1_H3K27me3_20181025_icell8_385_(20181025_Pool2_TAAGGCGA_CGTACCAA)


title: H1_H3K27me3_20181025_icell8_380_(20181025_Pool2_AAACGGTC_CGATAGGG)


title: H1_H3K27me3_20181025_icell8_393_(20181025_Pool2_CGTACTAG_AATCTACA)


title: H1_H3K27me3_20181025_icell8_391_(20181025_Pool2_GACTTAGT_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_381_(20181025_Pool2_TGGGTTTC_ATTGGGTC)


title: H1_H3K27me3_20181025_icell8_389_(20181025_Pool2_CTTGGGTC_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_378_(20181025_Pool2_CGAGGCTG_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_376_(20181025_Pool2_TCTTATTA_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_375_(20181025_Pool2_AAACGGTC_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_374_(20181025_Pool2_GTTAACAG_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_377_(20181025_Pool2_CGAGGCTG_ACCGGCCC)


title: H1_H3K27me3_20181025_icell8_384_(20181025_Pool2_CGAGGCTG_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_372_(20181025_Pool2_GTTAACAG_ACATTCGT)


title: H1_H3K27me3_20181025_icell8_371_(20181025_Pool2_GTTAACAG_ATCGAATG)


title: H1_H3K27me3_20181025_icell8_373_(20181025_Pool2_ACCGGCTA_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_370_(20181025_Pool2_ATTGCCGG_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_382_(20181025_Pool2_GGACTCCT_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_368_(20181025_Pool2_TAGGCATG_TGGAAATC)


title: H1_H3K27me3_20181025_icell8_369_(20181025_Pool2_TAAGGCGA_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_367_(20181025_Pool2_CGCGGACA_CGATAGGG)


title: H1_H3K27me3_20181025_icell8_366_(20181025_Pool2_TACTTGAA_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_379_(20181025_Pool2_GGACTCCT_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_363_(20181025_Pool2_GGTAAACC_GATCATTC)


title: H1_H3K27me3_20181025_icell8_359_(20181025_Pool2_AAACGGTC_TCCATCAA)


title: H1_H3K27me3_20181025_icell8_362_(20181025_Pool2_AATGGTAG_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_355_(20181025_Pool2_TTGCTAAG_ATTGGGTC)


title: H1_H3K27me3_20181025_icell8_360_(20181025_Pool2_CGCGGACA_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_357_(20181025_Pool2_CGGCCAAT_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_358_(20181025_Pool2_CGAGGCTG_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_356_(20181025_Pool2_TAAGGCGA_AGAGTAGA)


title: H1_H3K27me3_20181025_icell8_350_(20181025_Pool2_ACCGGCTA_ATTGGGTC)


title: H1_H3K27me3_20181025_icell8_352_(20181025_Pool2_CGGTTCCC_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_354_(20181025_Pool2_CGTACTAG_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_349_(20181025_Pool2_GGACTCCT_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_348_(20181025_Pool2_TGGGTTTC_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_353_(20181025_Pool2_TAAGGCGA_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_351_(20181025_Pool2_GGAGTAAG_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_346_(20181025_Pool2_AAACGGTC_AGAGATCT)


title: H1_H3K27me3_20181025_icell8_347_(20181025_Pool2_TACTTGAA_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_345_(20181025_Pool2_GGGAATGA_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_343_(20181025_Pool2_CGGCCAAT_AATCTACA)


title: H1_H3K27me3_20181025_icell8_361_(20181025_Pool2_CAAGAATT_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_364_(20181025_Pool2_TAAGGCGA_AATCTACA)


title: H1_H3K27me3_20181025_icell8_341_(20181025_Pool2_TACTTGAA_CCTGCGGG)


title: H1_H3K27me3_20181025_icell8_342_(20181025_Pool2_GAAATGCC_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_339_(20181025_Pool2_TACACCTC_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_344_(20181025_Pool2_GGACTCCT_GATCATTC)


title: H1_H3K27me3_20181025_icell8_365_(20181025_Pool2_GGACTCCT_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_331_(20181025_Pool2_ACAAAGTG_ATGGTCAT)


title: H1_H3K27me3_20181025_icell8_336_(20181025_Pool2_CGGTTCCC_GGGCTTGG)


title: H1_H3K27me3_20181025_icell8_333_(20181025_Pool2_GATCCAAA_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_335_(20181025_Pool2_ACAAAGTG_TACTGACC)


title: H1_H3K27me3_20181025_icell8_325_(20181025_Pool2_CAAGAATT_AATCTACA)


title: H1_H3K27me3_20181025_icell8_326_(20181025_Pool2_AATGGTAG_ATGGTCAT)


title: H1_H3K27me3_20181025_icell8_327_(20181025_Pool2_CGGCCAAT_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_329_(20181025_Pool2_CAAGAATT_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_334_(20181025_Pool2_AAACGGTC_TGCATACT)


title: H1_H3K27me3_20181025_icell8_324_(20181025_Pool2_TGGATCTG_TGATGAAA)


title: H1_H3K27me3_20181025_icell8_330_(20181025_Pool2_TGGATCTG_CCTTATGT)


title: H1_H3K27me3_20181025_icell8_322_(20181025_Pool2_TCTTATTA_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_332_(20181025_Pool2_AATGGTAG_AAGGAGTA)


title: H1_H3K27me3_20181025_icell8_338_(20181025_Pool2_CGGTTCCC_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_319_(20181025_Pool2_TTCCATAT_ATTGGGTC)


title: H1_H3K27me3_20181025_icell8_318_(20181025_Pool2_AAACGGTC_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_316_(20181025_Pool2_ACCGGCTA_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_317_(20181025_Pool2_TAGGCATG_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_315_(20181025_Pool2_GGTCATTT_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_337_(20181025_Pool2_CGGTTCCC_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_321_(20181025_Pool2_CGTACTAG_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_313_(20181025_Pool2_ACCGGCTA_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_314_(20181025_Pool2_TTCCATAT_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_311_(20181025_Pool2_GATCCAAA_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_323_(20181025_Pool2_CCGTTTGT_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_310_(20181025_Pool2_CATCCTGT_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_306_(20181025_Pool2_TAACAACA_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_307_(20181025_Pool2_GGTAAACC_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_309_(20181025_Pool2_CGGTTCCC_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_308_(20181025_Pool2_TTCCATAT_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_297_(20181025_Pool2_GTTAACAG_GCCCACGT)


title: H1_H3K27me3_20181025_icell8_302_(20181025_Pool2_ACCGGCTA_AAGGAGTA)


title: H1_H3K27me3_20181025_icell8_300_(20181025_Pool2_TACACCTC_AACATGAT)


title: H1_H3K27me3_20181025_icell8_320_(20181025_Pool2_CATCCTGT_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_299_(20181025_Pool2_GGAGTAAG_ACCGGCCC)


title: H1_H3K27me3_20181025_icell8_301_(20181025_Pool2_GGGAATGA_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_294_(20181025_Pool2_AATGGTAG_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_295_(20181025_Pool2_ACCGGCTA_TTGCCTAA)


title: H1_H3K27me3_20181025_icell8_303_(20181025_Pool2_GGGAATGA_TCACATGG)


title: H1_H3K27me3_20181025_icell8_305_(20181025_Pool2_TAGGCATG_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_296_(20181025_Pool2_CGCGGACA_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_312_(20181025_Pool2_CCGTTTGT_GTGTATCG)


title: H1_H3K27me3_20181025_icell8_298_(20181025_Pool2_ATTGCCGG_CGTACCAA)


title: H1_H3K27me3_20181025_icell8_304_(20181025_Pool2_TAACAACA_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_340_(20181025_Pool2_GAAATGCC_AACATGAT)


title: H1_H3K27me3_20181025_icell8_290_(20181025_Pool2_TGGATCTG_TGATTGTT)


title: H1_H3K27me3_20181025_icell8_291_(20181025_Pool2_ACAAAGTG_ACGCGCAG)


title: H1_H3K27me3_20181025_icell8_293_(20181025_Pool2_CGCGGACA_TGATTGTT)


title: H1_H3K27me3_20181025_icell8_292_(20181025_Pool2_TCTTATTA_GATTCCCA)


title: H1_H3K27me3_20181025_icell8_289_(20181025_Pool2_CCGTTTGT_ACATTCGT)


title: H1_H3K27me3_20181025_icell8_285_(20181025_Pool2_CGAGGCTG_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_287_(20181025_Pool2_CGGCCAAT_GCCCACGT)


title: H1_H3K27me3_20181025_icell8_286_(20181025_Pool2_TCTTATTA_TACTGACC)


title: H1_H3K27me3_20181025_icell8_282_(20181025_Pool2_GATCCAAA_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_274_(20181025_Pool2_TAAGGCGA_ACCGGCCC)


title: H1_H3K27me3_20181025_icell8_280_(20181025_Pool2_TTATGAAA_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_281_(20181025_Pool2_GGACTCCT_GTGTATCG)


title: H1_H3K27me3_20181025_icell8_284_(20181025_Pool2_TTATGAAA_TCACATGG)


title: H1_H3K27me3_20181025_icell8_275_(20181025_Pool2_TCTTATTA_ATTGGGTC)


title: H1_H3K27me3_20181025_icell8_268_(20181025_Pool2_CCGTTTGT_TGATGAAA)


title: H1_H3K27me3_20181025_icell8_272_(20181025_Pool2_ACCGGCTA_TGATGAAA)


title: H1_H3K27me3_20181025_icell8_267_(20181025_Pool2_GGGAATGA_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_283_(20181025_Pool2_ACAAAGTG_CTAAGCCT)


title: H1_H3K27me3_20181025_icell8_269_(20181025_Pool2_CGGTTCCC_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_271_(20181025_Pool2_ATTGCCGG_CGTAGACC)


title: H1_H3K27me3_20181025_icell8_278_(20181025_Pool2_TGGATCTG_CGTACCAA)


title: H1_H3K27me3_20181025_icell8_270_(20181025_Pool2_CGTACTAG_CGGACTGC)


title: H1_H3K27me3_20181025_icell8_279_(20181025_Pool2_GGGAATGA_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_277_(20181025_Pool2_CTTGGGTC_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_276_(20181025_Pool2_GGTCATTT_GCATTAAG)


title: H1_H3K27me3_20181025_icell8_264_(20181025_Pool2_ATTGCCGG_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_260_(20181025_Pool2_GGTAAACC_CCTGCGGG)


title: H1_H3K27me3_20181025_icell8_259_(20181025_Pool2_TTATGAAA_TGATTGTT)


title: H1_H3K27me3_20181025_icell8_263_(20181025_Pool2_TAACAACA_ACTTAGAA)


title: H1_H3K27me3_20181025_icell8_262_(20181025_Pool2_AATGGTAG_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_261_(20181025_Pool2_AAACGGTC_CGTAGACC)


title: H1_H3K27me3_20181025_icell8_257_(20181025_Pool2_GCTACGCT_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_258_(20181025_Pool2_CTTGGGTC_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_273_(20181025_Pool2_TAACAACA_AATCTACA)


title: H1_H3K27me3_20181025_icell8_256_(20181025_Pool2_CGCGGACA_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_288_(20181025_Pool2_CGAGGCTG_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_265_(20181025_Pool2_CAAGAATT_GATCATTC)


title: H1_H3K27me3_20181025_icell8_255_(20181025_Pool2_TAGGCATG_CGATAGGG)


title: H1_H3K27me3_20181025_icell8_252_(20181025_Pool2_CGTACTAG_TCCATCAA)


title: H1_H3K27me3_20181025_icell8_253_(20181025_Pool2_ACAAAGTG_CGTACCAA)


title: H1_H3K27me3_20181025_icell8_247_(20181025_Pool2_CGAGGCTG_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_251_(20181025_Pool2_GGACTCCT_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_250_(20181025_Pool2_CTTGGGTC_GTAAGGAG)


title: H1_H3K27me3_20181025_icell8_254_(20181025_Pool2_AATGGTAG_TGATGAAA)


title: H1_H3K27me3_20181025_icell8_248_(20181025_Pool2_CCGTTTGT_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_241_(20181025_Pool2_GACTTAGT_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_242_(20181025_Pool2_ATTGCCGG_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_246_(20181025_Pool2_ACAAAGTG_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_245_(20181025_Pool2_CATCCTGT_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_243_(20181025_Pool2_TTATGAAA_GATTCCCA)


title: H1_H3K27me3_20181025_icell8_240_(20181025_Pool2_GAAATGCC_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_238_(20181025_Pool2_TTGCTAAG_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_236_(20181025_Pool2_TACTTGAA_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_237_(20181025_Pool2_CCGTTTGT_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_239_(20181025_Pool2_GGACTCCT_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_235_(20181025_Pool2_GGTAAACC_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_231_(20181025_Pool2_CTTGGGTC_AGTCCGAG)


title: H1_H3K27me3_20181025_icell8_232_(20181025_Pool2_CATCCTGT_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_249_(20181025_Pool2_CGGTTCCC_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_230_(20181025_Pool2_CGAGGCTG_ATGGTCAT)


title: H1_H3K27me3_20181025_icell8_244_(20181025_Pool2_GACTTAGT_CTTTAACA)


title: H1_H3K27me3_20181025_icell8_234_(20181025_Pool2_GAAATGCC_GAACTCGA)


title: H1_H3K27me3_20181025_icell8_227_(20181025_Pool2_CGTACTAG_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_228_(20181025_Pool2_GTTAACAG_CGGACTGC)


title: H1_H3K27me3_20181025_icell8_233_(20181025_Pool2_GACTTAGT_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_225_(20181025_Pool2_GGACTCCT_CCTTATGT)


title: H1_H3K27me3_20181025_icell8_266_(20181025_Pool2_TACACCTC_TACTGACC)


title: H1_H3K27me3_20181025_icell8_224_(20181025_Pool2_GAAATGCC_TCACATGG)


title: H1_H3K27me3_20181025_icell8_226_(20181025_Pool2_TACTTGAA_ACTGCATA)


title: H1_H3K27me3_20181025_icell8_221_(20181025_Pool2_CATCCTGT_CAGCAACG)


title: H1_H3K27me3_20181025_icell8_219_(20181025_Pool2_TACACCTC_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_222_(20181025_Pool2_GGAGTAAG_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_218_(20181025_Pool2_AATGGTAG_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_215_(20181025_Pool2_CCGTTTGT_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_216_(20181025_Pool2_GATCCAAA_ACTGCATA)


title: H1_H3K27me3_20181025_icell8_229_(20181025_Pool2_GATCCAAA_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_214_(20181025_Pool2_AAACGGTC_TGGAAATC)


title: H1_H3K27me3_20181025_icell8_211_(20181025_Pool2_CGGTTCCC_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_212_(20181025_Pool2_CGGCCAAT_TAAGTTAC)


title: H1_H3K27me3_20181025_icell8_209_(20181025_Pool2_ACAAAGTG_GCCCACGT)


title: H1_H3K27me3_20181025_icell8_213_(20181025_Pool2_CTTGGGTC_GATCATTC)


title: H1_H3K27me3_20181025_icell8_223_(20181025_Pool2_GTGTGGTG_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_210_(20181025_Pool2_TACACCTC_TAAGTTAC)


title: H1_H3K27me3_20181025_icell8_328_(20181025_Pool2_TTCCATAT_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_220_(20181025_Pool2_ATTGCCGG_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_206_(20181025_Pool2_GAAATGCC_AAGGAGTA)


title: H1_H3K27me3_20181025_icell8_208_(20181025_Pool2_CGTACTAG_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_204_(20181025_Pool2_ACAAAGTG_CTAGAAGT)


title: H1_H3K27me3_20181025_icell8_203_(20181025_Pool2_TACACCTC_TTAACTTG)


title: H1_H3K27me3_20181025_icell8_207_(20181025_Pool2_GATCCAAA_GTAAGGAG)


title: H1_H3K27me3_20181025_icell8_205_(20181025_Pool2_GGTAAACC_TGATTGTT)


title: H1_H3K27me3_20181025_icell8_199_(20181025_Pool2_ATTGCCGG_TAAGTTAC)


title: H1_H3K27me3_20181025_icell8_200_(20181025_Pool2_CGTACTAG_CTAGAAGT)


title: H1_H3K27me3_20181025_icell8_201_(20181025_Pool2_CCGTTTGT_GATCATTC)


title: H1_H3K27me3_20181025_icell8_198_(20181025_Pool2_TGGGTTTC_GAACTCGA)


title: H1_H3K27me3_20181025_icell8_217_(20181025_Pool2_TTCCATAT_GTGTATCG)


title: H1_H3K27me3_20181025_icell8_194_(20181025_Pool2_ACCGGCTA_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_193_(20181025_Pool2_CGGTTCCC_GATTCCCA)


title: H1_H3K27me3_20181025_icell8_195_(20181025_Pool2_GATCCAAA_ATTGGGTC)


title: H1_H3K27me3_20181025_icell8_190_(20181025_Pool2_GGGAATGA_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_189_(20181025_Pool2_CCGTTTGT_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_196_(20181025_Pool2_CGGTTCCC_CGTACCAA)


title: H1_H3K27me3_20181025_icell8_187_(20181025_Pool2_TACACCTC_TGCATACT)


title: H1_H3K27me3_20181025_icell8_188_(20181025_Pool2_GTTAACAG_GATTCCCA)


title: H1_H3K27me3_20181025_icell8_184_(20181025_Pool2_CAAGAATT_AGTCCGAG)


title: H1_H3K27me3_20181025_icell8_185_(20181025_Pool2_TACACCTC_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_186_(20181025_Pool2_TGGGTTTC_CCTGCGGG)


title: H1_H3K27me3_20181025_icell8_181_(20181025_Pool2_CAAGAATT_CCTTATGT)


title: H1_H3K27me3_20181025_icell8_183_(20181025_Pool2_TGGATCTG_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_180_(20181025_Pool2_CTTGGGTC_CTTTAACA)


title: H1_H3K27me3_20181025_icell8_177_(20181025_Pool2_GGTCATTT_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_176_(20181025_Pool2_GGACTCCT_ACGCGCAG)


title: H1_H3K27me3_20181025_icell8_175_(20181025_Pool2_TTATGAAA_AGAGTAGA)


title: H1_H3K27me3_20181025_icell8_202_(20181025_Pool2_GGTCATTT_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_179_(20181025_Pool2_CAAGAATT_CCACCGTT)


title: H1_H3K27me3_20181025_icell8_178_(20181025_Pool2_ATTGCCGG_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_172_(20181025_Pool2_TTATGAAA_CTAGAAGT)


title: H1_H3K27me3_20181025_icell8_171_(20181025_Pool2_GGACTCCT_TTAACTTG)


title: H1_H3K27me3_20181025_icell8_173_(20181025_Pool2_TAGGCATG_TCCATCAA)


title: H1_H3K27me3_20181025_icell8_191_(20181025_Pool2_TAACAACA_GTAAGGAG)


title: H1_H3K27me3_20181025_icell8_192_(20181025_Pool2_TACACCTC_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_170_(20181025_Pool2_GTTAACAG_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_182_(20181025_Pool2_CAAGAATT_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_169_(20181025_Pool2_GTGTGGTG_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_166_(20181025_Pool2_ACAAAGTG_TCCATCAA)


title: H1_H3K27me3_20181025_icell8_165_(20181025_Pool2_TGGATCTG_GCCCACGT)


title: H1_H3K27me3_20181025_icell8_167_(20181025_Pool2_CTTGGGTC_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_197_(20181025_Pool2_GGTAAACC_ATTACCGT)


title: H1_H3K27me3_20181025_icell8_168_(20181025_Pool2_TACTTGAA_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_164_(20181025_Pool2_CCGTTTGT_AAGGAGTA)


title: H1_H3K27me3_20181025_icell8_161_(20181025_Pool2_GGACTCCT_TCCATCAA)


title: H1_H3K27me3_20181025_icell8_162_(20181025_Pool2_TACTTGAA_TCACATGG)


title: H1_H3K27me3_20181025_icell8_159_(20181025_Pool2_GGTAAACC_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_174_(20181025_Pool2_CTTGGGTC_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_160_(20181025_Pool2_TTGCTAAG_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_157_(20181025_Pool2_TGGGTTTC_AAGGAGTA)


title: H1_H3K27me3_20181025_icell8_156_(20181025_Pool2_TACACCTC_CAGCAACG)


title: H1_H3K27me3_20181025_icell8_158_(20181025_Pool2_TGGATCTG_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_155_(20181025_Pool2_TGGGTTTC_ACATTCGT)


title: H1_H3K27me3_20181025_icell8_152_(20181025_Pool2_TACTTGAA_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_150_(20181025_Pool2_CATCCTGT_TCACATGG)


title: H1_H3K27me3_20181025_icell8_149_(20181025_Pool2_GGACTCCT_AATCTACA)


title: H1_H3K27me3_20181025_icell8_154_(20181025_Pool2_AATGGTAG_TGATTGTT)


title: H1_H3K27me3_20181025_icell8_147_(20181025_Pool2_ACCGGCTA_ACGCGCAG)


title: H1_H3K27me3_20181025_icell8_151_(20181025_Pool2_GCTACGCT_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_144_(20181025_Pool2_CTTGGGTC_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_145_(20181025_Pool2_CATCCTGT_TAAGTTAC)


title: H1_H3K27me3_20181025_icell8_153_(20181025_Pool2_GGTCATTT_ACATTCGT)


title: H1_H3K27me3_20181025_icell8_143_(20181025_Pool2_ACCGGCTA_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_140_(20181025_Pool2_TAGGCATG_ACATTCGT)


title: H1_H3K27me3_20181025_icell8_137_(20181025_Pool2_TCTTATTA_CAGCAACG)


title: H1_H3K27me3_20181025_icell8_148_(20181025_Pool2_TTATGAAA_CTTTAACA)


title: H1_H3K27me3_20181025_icell8_141_(20181025_Pool2_CGGTTCCC_GTAAGGAG)


title: H1_H3K27me3_20181025_icell8_142_(20181025_Pool2_GGACTCCT_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_163_(20181025_Pool2_GGTAAACC_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_138_(20181025_Pool2_TTGCTAAG_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_131_(20181025_Pool2_GGAGTAAG_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_127_(20181025_Pool2_CCGTTTGT_GAACTCGA)


title: H1_H3K27me3_20181025_icell8_128_(20181025_Pool2_GAAATGCC_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_124_(20181025_Pool2_TCTTATTA_CGTAGACC)


title: H1_H3K27me3_20181025_icell8_119_(20181025_Pool2_GCTACGCT_CCACCGTT)


title: H1_H3K27me3_20181025_icell8_133_(20181025_Pool2_CATCCTGT_TTAACTTG)


title: H1_H3K27me3_20181025_icell8_135_(20181025_Pool2_TTATGAAA_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_139_(20181025_Pool2_CTTGGGTC_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_146_(20181025_Pool2_CGTACTAG_GAACTCGA)


title: H1_H3K27me3_20181025_icell8_134_(20181025_Pool2_AAACGGTC_ACTGCATA)


title: H1_H3K27me3_20181025_icell8_136_(20181025_Pool2_ACAAAGTG_CTTTAACA)


title: H1_H3K27me3_20181025_icell8_132_(20181025_Pool2_TAACAACA_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_126_(20181025_Pool2_TTGCTAAG_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_130_(20181025_Pool2_ATTGCCGG_TGATGAAA)


title: H1_H3K27me3_20181025_icell8_120_(20181025_Pool2_GGGAATGA_CTCTCTAT)


title: H1_H3K27me3_20181025_icell8_129_(20181025_Pool2_CGTACTAG_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_116_(20181025_Pool2_AAACGGTC_GCATTAAG)


title: H1_H3K27me3_20181025_icell8_110_(20181025_Pool2_ATTGCCGG_ACGCGCAG)


title: H1_H3K27me3_20181025_icell8_123_(20181025_Pool2_AAACGGTC_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_122_(20181025_Pool2_CCGTTTGT_CTTTAACA)


title: H1_H3K27me3_20181025_icell8_109_(20181025_Pool2_ACAAAGTG_CGCCAGAT)


title: H1_H3K27me3_20181025_icell8_125_(20181025_Pool2_CGGCCAAT_AGAGATCT)


title: H1_H3K27me3_20181025_icell8_114_(20181025_Pool2_ATTGCCGG_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_121_(20181025_Pool2_TAGGCATG_CGTAGACC)


title: H1_H3K27me3_20181025_icell8_111_(20181025_Pool2_GGTCATTT_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_118_(20181025_Pool2_AATGGTAG_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_115_(20181025_Pool2_ACAAAGTG_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_112_(20181025_Pool2_GCTACGCT_ACTGCATA)


title: H1_H3K27me3_20181025_icell8_107_(20181025_Pool2_AATGGTAG_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_105_(20181025_Pool2_GGGAATGA_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_108_(20181025_Pool2_GGACTCCT_TCACATGG)


title: H1_H3K27me3_20181025_icell8_117_(20181025_Pool2_CTTGGGTC_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_104_(20181025_Pool2_CGAGGCTG_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_106_(20181025_Pool2_GGACTCCT_TGGGCGGT)


title: H1_H3K27me3_20181025_icell8_113_(20181025_Pool2_ACCGGCTA_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_102_(20181025_Pool2_GACTTAGT_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_101_(20181025_Pool2_GGTCATTT_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_95_(20181025_Pool2_GGTAAACC_GCATTAAG)


title: H1_H3K27me3_20181025_icell8_100_(20181025_Pool2_TTGCTAAG_AACATGAT)


title: H1_H3K27me3_20181025_icell8_96_(20181025_Pool2_TAGGCATG_AACATGAT)


title: H1_H3K27me3_20181025_icell8_98_(20181025_Pool2_TTCCATAT_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_97_(20181025_Pool2_TGGATCTG_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_94_(20181025_Pool2_TTCCATAT_CCCTTGGA)


title: H1_H3K27me3_20181025_icell8_93_(20181025_Pool2_CATCCTGT_TGCATACT)


title: H1_H3K27me3_20181025_icell8_92_(20181025_Pool2_TACACCTC_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_89_(20181025_Pool2_CGGTTCCC_TAGATCGC)


title: H1_H3K27me3_20181025_icell8_88_(20181025_Pool2_GATCCAAA_CTAAGCCT)


title: H1_H3K27me3_20181025_icell8_90_(20181025_Pool2_GTTAACAG_AGTCCGAG)


title: H1_H3K27me3_20181025_icell8_91_(20181025_Pool2_CAAGAATT_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_87_(20181025_Pool2_TTGCTAAG_ACTGCATA)


title: H1_H3K27me3_20181025_icell8_86_(20181025_Pool2_GCTACGCT_TCCATCAA)


title: H1_H3K27me3_20181025_icell8_81_(20181025_Pool2_ACAAAGTG_CCACCGTT)


title: H1_H3K27me3_20181025_icell8_82_(20181025_Pool2_GACTTAGT_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_80_(20181025_Pool2_GGTCATTT_ACTGCATA)


title: H1_H3K27me3_20181025_icell8_84_(20181025_Pool2_TGGATCTG_AATCTACA)


title: H1_H3K27me3_20181025_icell8_83_(20181025_Pool2_CTTGGGTC_CGCCAGAT)


title: H1_H3K27me3_20181025_icell8_85_(20181025_Pool2_TGGGTTTC_TGATTGTT)


title: H1_H3K27me3_20181025_icell8_78_(20181025_Pool2_GGTCATTT_AAGGAGTA)


title: H1_H3K27me3_20181025_icell8_79_(20181025_Pool2_TTCCATAT_AACATGAT)


title: H1_H3K27me3_20181025_icell8_74_(20181025_Pool2_GTTAACAG_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_75_(20181025_Pool2_TTGCTAAG_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_99_(20181025_Pool2_GGACTCCT_TATCCTCT)


title: H1_H3K27me3_20181025_icell8_76_(20181025_Pool2_CGCGGACA_ACTTAGAA)


title: H1_H3K27me3_20181025_icell8_73_(20181025_Pool2_TTGCTAAG_GAACTCGA)


title: H1_H3K27me3_20181025_icell8_70_(20181025_Pool2_ATTGCCGG_CGGACTGC)


title: H1_H3K27me3_20181025_icell8_72_(20181025_Pool2_TAACAACA_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_103_(20181025_Pool2_GACTTAGT_GGTGAAGG)


title: H1_H3K27me3_20181025_icell8_71_(20181025_Pool2_CGGTTCCC_AATCTACA)


title: H1_H3K27me3_20181025_icell8_69_(20181025_Pool2_CTTGGGTC_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_77_(20181025_Pool2_ATTGCCGG_CGCCAGAT)


title: H1_H3K27me3_20181025_icell8_66_(20181025_Pool2_AATGGTAG_TCAAGAGC)


title: H1_H3K27me3_20181025_icell8_67_(20181025_Pool2_GGGAATGA_ACTTAGAA)


title: H1_H3K27me3_20181025_icell8_68_(20181025_Pool2_CAAGAATT_TCACATGG)


title: H1_H3K27me3_20181025_icell8_64_(20181025_Pool2_ATTGCCGG_AGAGTAGA)


title: H1_H3K27me3_20181025_icell8_63_(20181025_Pool2_GGTAAACC_TCACATGG)


title: H1_H3K27me3_20181025_icell8_65_(20181025_Pool2_ACCGGCTA_TCACATGG)


title: H1_H3K27me3_20181025_icell8_61_(20181025_Pool2_ATTGCCGG_GCAGCCTC)


title: H1_H3K27me3_20181025_icell8_62_(20181025_Pool2_TTGCTAAG_ATCCAGGA)


title: H1_H3K27me3_20181025_icell8_54_(20181025_Pool2_TTATGAAA_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_60_(20181025_Pool2_CCGTTTGT_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_53_(20181025_Pool2_ACAAAGTG_TTAACTTG)


title: H1_H3K27me3_20181025_icell8_51_(20181025_Pool2_CGCGGACA_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_58_(20181025_Pool2_ACCGGCTA_ATGGTCAT)


title: H1_H3K27me3_20181025_icell8_44_(20181025_Pool2_TAAGGCGA_TCACATGG)


title: H1_H3K27me3_20181025_icell8_50_(20181025_Pool2_TGGATCTG_TAAGTTAC)


title: H1_H3K27me3_20181025_icell8_52_(20181025_Pool2_CAAGAATT_CTAAGCCT)


title: H1_H3K27me3_20181025_icell8_47_(20181025_Pool2_GAAATGCC_ACTTAGAA)


title: H1_H3K27me3_20181025_icell8_49_(20181025_Pool2_ACAAAGTG_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_48_(20181025_Pool2_ACAAAGTG_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_46_(20181025_Pool2_CATCCTGT_CGTACCAA)


title: H1_H3K27me3_20181025_icell8_45_(20181025_Pool2_TTCCATAT_CTTTAACA)


title: H1_H3K27me3_20181025_icell8_55_(20181025_Pool2_TTATGAAA_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_43_(20181025_Pool2_GATCCAAA_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_38_(20181025_Pool2_GGGAATGA_TGGAAATC)


title: H1_H3K27me3_20181025_icell8_36_(20181025_Pool2_AAACGGTC_AACATGAT)


title: H1_H3K27me3_20181025_icell8_35_(20181025_Pool2_TGGATCTG_GAACTCGA)


title: H1_H3K27me3_20181025_icell8_33_(20181025_Pool2_TTATGAAA_GGCACGGA)


title: H1_H3K27me3_20181025_icell8_32_(20181025_Pool2_TTGCTAAG_ACTTAGAA)


title: H1_H3K27me3_20181025_icell8_56_(20181025_Pool2_GCTACGCT_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_42_(20181025_Pool2_TAGGCATG_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_40_(20181025_Pool2_CGCGGACA_TCCGAGTT)


title: H1_H3K27me3_20181025_icell8_59_(20181025_Pool2_GGTAAACC_GACGTGGC)


title: H1_H3K27me3_20181025_icell8_29_(20181025_Pool2_TAGGCATG_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_41_(20181025_Pool2_GGTAAACC_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_34_(20181025_Pool2_CGGTTCCC_AACATGAT)


title: H1_H3K27me3_20181025_icell8_39_(20181025_Pool2_CCGTTTGT_CGTAGACC)


title: H1_H3K27me3_20181025_icell8_57_(20181025_Pool2_TGGGTTTC_GCATTAAG)


title: H1_H3K27me3_20181025_icell8_37_(20181025_Pool2_GAAATGCC_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_19_(20181025_Pool2_TGGATCTG_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_25_(20181025_Pool2_GCTACGCT_GCAAATTT)


title: H1_H3K27me3_20181025_icell8_23_(20181025_Pool2_GCTACGCT_CGTAGACC)


title: H1_H3K27me3_20181025_icell8_31_(20181025_Pool2_TGGATCTG_ACGATAAC)


title: H1_H3K27me3_20181025_icell8_28_(20181025_Pool2_TAAGGCGA_TGGAAATC)


title: H1_H3K27me3_20181025_icell8_16_(20181025_Pool2_GTTAACAG_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_27_(20181025_Pool2_GGTAAACC_GCAAATTT)


title: H1_H3K27me3_20181025_icell8_30_(20181025_Pool2_GTTAACAG_GATCATTC)


title: H1_H3K27me3_20181025_icell8_17_(20181025_Pool2_TACACCTC_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_22_(20181025_Pool2_TACACCTC_GCATTAAG)


title: H1_H3K27me3_20181025_icell8_18_(20181025_Pool2_TGGGTTTC_TGATGAAA)


title: H1_H3K27me3_20181025_icell8_26_(20181025_Pool2_TACACCTC_TATTTGCG)


title: H1_H3K27me3_20181025_icell8_15_(20181025_Pool2_GGGAATGA_GGTTCAAT)


title: H1_H3K27me3_20181025_icell8_14_(20181025_Pool2_TACTTGAA_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_21_(20181025_Pool2_GGGAATGA_ACTTGTTG)


title: H1_H3K27me3_20181025_icell8_20_(20181025_Pool2_TGGATCTG_GTAAGGAG)


title: H1_H3K27me3_20181025_icell8_11_(20181025_Pool2_TCTTATTA_TAACCAAG)


title: H1_H3K27me3_20181025_icell8_10_(20181025_Pool2_AAACGGTC_CCACCGTT)


title: H1_H3K27me3_20181025_icell8_24_(20181025_Pool2_GGTAAACC_TTCGTGCA)


title: H1_H3K27me3_20181025_icell8_4_(20181025_Pool2_CAAGAATT_CCAGTTTA)


title: H1_H3K27me3_20181025_icell8_9_(20181025_Pool2_GGTAAACC_AGCCGTTC)


title: H1_H3K27me3_20181025_icell8_12_(20181025_Pool2_ACCGGCTA_GAGACGTG)


title: H1_H3K27me3_20181025_icell8_13_(20181025_Pool2_GATCCAAA_CGTAGACC)


title: H1_H3K27me3_20181025_icell8_7_(20181025_Pool2_CATCCTGT_TGTTCCTG)


title: H1_H3K27me3_20181025_icell8_8_(20181025_Pool2_TGGATCTG_TTTCTAGC)


title: H1_H3K27me3_20181025_icell8_3_(20181025_Pool2_TCTTATTA_TGGAAATC)