title: In vitro refolded rep3

description: Multiplexed cDNA amplicon sequencing

data_processing:
After bcl conversion and demultiplexing with Illumina bcl2fastq, adaptor sequences are further trimmed using cutadapt107. Overlapping paired-end reads are merged using BBMerge108. Trimmed and merged reads are aligned to indexed reference of amplicon sequences using Bowtie2 with the following parameters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 --mp 3,1 --rdg 5,1 --dpad 30109. Alignments are filtered to have at least 4 mutations with minimum PHRED estimate of 30 (quality cutoff for substitutions only) and minimum length 150nt. Co-occurrence of modifications at more than 4 positions is considered highly unlikely and assumed to be PCR jackpots. Duplicates are grouped using Hamming distance and directional network algorithm for clustering as implemented for UMIs in umi_tools110. The consensus reads are then parsed and counted for different classes of mutations using functions in ShapeMapper 2 library111. This mutational profiling data processing pipeline results in a matrix of mutation counts, where rows are each nucleotide position of the amplicons and columns are the different samples.  For each amplicon, the counts are first normalized by TMM96. As a quality filter, we require that the average pairwise Pearson correlations between replicate samples for both conditions must be greater than 0.65 for the amplicon to be further analyzed. For statistical significance of differential mutation rates between ATP depletion and untreated conditions at each nucleotide, we use voom-limma which models mean-variance bias and calculates moderated T-statistics112,113. To analyze per-window accessibility pattern differences, for each sliding window of 11nt, we calculate Anderson-Darling statistic between per-nucleotide T-statistic values of the window versus per-nucleotide T-statistic values of the whole amplicon. False discovery rates are estimated by Benjamini-Hochberg procedure. Overlapping significant windows above the chosen cutoff are merged.
Supplementary_files_format_and_content: Text file includes the normalized reactivity values at each nucleotide

source_name: E14 ES cells

extract_protocol:
100 h5UTRs were chosen for amplicon sequencing based on coverage profiles from ENCODE E14 mESC RNA-seq data. A total of 384 primer pairs were designed across these h5UTRs using ThermoAlign and following parameters (others are left at default): primer_size_range=16-40, GC_range=25-75, Tm_range=64-72, primer_conc=300, Na=0, K=75, Tris=10, Mg=2, dNTPs=1.2, amplicon_size_min=250, amplicon_size_max=250. Primers were split into 4 pools of 96 pairs using PrimerPooler106. A final set of 380 pairs were synthesized by Eurofins Genomics. 10x106 mESCs were incubated for 10min in ATP depletion media: DMEM without glucose (ThermoFisher Scientific, A1443001), 10mM 2-Deoxy-D-glucose (MilliporeSigma, 25972), 10mM sodium azide (MilliporeSigma, 71289). The cells were washed, trypsinized and harvested using PBS, trypsin, and finally resuspended in 3.5mL mESC media all containing 10mM 2DG and 10mM NaN3. 1mL 1M bicine (Millipore Sigma, B3876), titrated to pH 8.5 at 25°C, is added to resuspended cells (250mM final bicine concentration). 500uL 16% dimethyl sulfate (MilliporeSigma, D186309) in ethanol is added (1.6% final concentration). Cells are mixed and incubated for 6min at 37°C. 2.5mL ice-cold 30% BME (MilliporeSigma, M3148) in ethanol is added to quench the reaction. Following centrifuge to remove the supernatant, the cells are lysed in Trizol (ThermoFisher Scientific, 15596026). For the untreated condition without ATP depletion treatment, all procedures are the same except for initial 10min incubation in ATP depletion media and inclusion of 2DG and NaN3 in all media. Three independent samples were collected for each condition. Total RNA is phase extracted with chloroform and aqueous phase is purified on silica columns (Zymo, R1013). 10-20ug RNA is DNase treated at 37°C for 30min using 0.2U/uL TURBO DNase (ThermoFisher Scientific, AM2238) with 1U/uL Superase-In (ThermoFisher Scientific, AM2696) in 60uL and purified again on silica column.
1ug RNA is mixed with 1uL 1uM 96x primer pool (96x1uM amplicon reverse primers for total of 1uM oligos) and denatured in 6.25uL total volume (with H2O) at 65°C for 2min, then chilled to 4°C. Reverse transcription reaction conditions are as follows: 20mM Tris-HCl pH7.5, 75mM KCl, 10mM MgCl2, 5mM DTT, 500nM TGIRT (InGex, TGIRT50), 1U/uL Superase-In; 19uL total reaction volume. The RT reaction is preincubated for 25°C for 30min, then initiated with addition of 1uL 12.5mM dNTP each. After incubation at 60°C for 1hour, 1uL 2.5M NaOH is added and the reaction is heated at 95°C for 3min. 1uL 2.5M HCl and 1uL 500mM Tris-HCl pH 7.5 is added to neutralize. 29uL SPRIselect beads (Beckman Coulter, B23318) is used for purification of cDNA; elution volume is 6uL. 4x96 pooled reactions for a total of 384 targets are performed for each sample. To each set of 96 pool cDNA, multiplex PCR is performed with 5uL cDNA, 0.2mM dNTP, 2uM 96x forward primer pool (96x2uM each primer for total of 2uM oligos), 2uM reverse primer pool, 1x SYBR Green I (ThermoFisher Scientific, S7563), Q5 Hot Start DNA polymerase (NEB, M0493S), 1x Q5 Hot Start Reaction Buffer, 1x Q5 Hot Start High GC Enhancer, in total 30uL reaction volume. Cycling conditions are: 98°C 30s initial denaturation, followed by 15-25 cycles (terminated before plateau) of 98°C 10s, 56°C 40s, 76°C 10s. PCR is run for 15-25 cycles. Each 96 pool multiplex PCR reaction is then used in a master mix of second PCR with 96 individual primer pair reactions: 0.2mM dNTP, 500nM forward primer, 500nM reverse primer, 1x SYBR Green I, Q5 Hot Start DNA polymerase, 1x Q5 Hot Start Reaction Buffer, 1x Q5 Hot Start High GC Enhancer, in total 6uL reaction volume. Cycling conditions are: 98°C 30s initial denaturation, followed by 20 cycles of 98°C 10s, 62°C 10s, 76°C 10s. 384 individual reactions are pooled and purified on silica columns (NEB, T1030S). Amplicon pool is end-prepared, Illumina adaptor sequences are ligated, adaptor-ligated DNA is size selected with SPRIselect beads for 370bp, and 3 cycle barcoding PCR is performed (NEB, E7645S). 2x150bp paired end sequencing data is generated on Illumina HiSeq 4000 at Novogene.


title: retina, PKD + PBS (rep4)

status: Public on Jan 29 2021

type: RNA

city: Mannheim

first: Matthias

last: Kolibabka

state: Baden-Wurttemberg

address: Theodor-Kutzer-Ufer 1-3

department: 5th Medical Department

country: Germany

institute: University Hospital Mannheim

data_processing:
Threshold quantification cycles (Cq) were obtained using the manufacturer's Viia7 software and analyzed in the ArrayStudio software package (Version 9, Omicsoft Corporation).
Gene expression levels were obtained by subtracting the average normalization value of four reference genes (18S, B2m, Mrlp19 and Ywhaz) from the individual Cq values.
Fold change 2^-ΔΔCq, where -ΔΔCq = -[ΔCqtest -MV(ΔCqReferenceGenes)]
Samples where transcripts did not reach the threshold within 35 cycles were excluded from the calculation for this particular gene.
Fold Change worksheet reports PKD/SD and PKD + Clodronate/PKD ratios (Reference genes excluded).

label: FAM

molecule: total RNA

organism: Rattus norvegicus

source_name: retina, PBS

label_protocol: cDNA was generated using a high capacity RNA-to-cDNA Kit according to manufacturer's protocol. A quantitative pre-amplification step of 14 cycles was performed using a Taqman Preamp Master Mix Kit according to the manufacturer's protocol. Real-time PCR was performed in parallel using TaqMan microfluidic card technology in a Viia7 thermocycler with a maximum of 40 cycles.

growth_protocol: At 4 and 8 weeks of age, Sprague Dawley and PKD2(HA-1/703-CMV-247) rats were injected with 3 µl solution according to the treatment groups. Uninjected animals served as control groups. Animals were housed with a 12-/12-h light/dark cycle with free access to food and water. Termination occured at 9 weeks of age, 1 week after the second injection.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Enucleated Eyes were snapp frozen in liquid nitrogen and stored at -80°C till further preperation. Extraction of the retina was performed at 0°C and immediately suspended in Trizol.

tag: strain

tag: treatment

value: PBS


title: retina, PKD + PBS (rep3)


title: FCtx_S1209_snRNAseq

type: SRA

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: 35 Convent Drive

department: National Institute on Aging

country: USA

institute: National Institutes of Health

description: snRNAseq_Sample 15

library_source: transcriptomic

data_processing:
10x Genomics cellranger count algorithm (v3.1.0) was used to align fastqs and count reads mapping to the genome.
Genome_build: GRCh38-3.0.0.premrna-
Supplementary_files_format_and_content: tar archive containing barcode file (TSV, column indices), feature file (TSV, row indices), and barcode-feature count matrix (MTX).

organism: Homo sapiens

source_name: frozen frontal cortex tissue

extract_protocol:
Nuclei were extracted from frozen tissue by ultracentrifugation using the Nuclei PURE Prep nuclei isolation kit from Sigma Aldrich.
Libraries were constructed according to the Chromium Single Cell 3' Gene Expression Reagent Kits User Guide (v3 Chemistry) from 10x Genomics.

tag: rs76904798 genotype

value: CT

tag: tissue

value: frontal cortex

tag: differentiation protocol

tag: cell line

tag: rna population

value: nuclear RNA


title: FCtx_S4724_snRNAseq

description: snRNAseq_Sample 14


title: In vitro refolded rep1

city: Stanford

first: Gun Woo

last: Byeon

state: CA

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

description: Multiplexed cDNA amplicon sequencing

organism: Mus musculus

tag: genotype


title: DCS

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
Neurons from the Right Side of DMV in LAD surgery animal
BioMark-RTqPCR

data_processing: Samples were normalized through centering aound the median of all genes that passed quality control through melt curve analysis.

label: EvaGreen

source_name: DMV neurons

label_protocol: cDNA labeled with SYBR green according to manufacture's protocol.

extract_protocol: Brainstems were extracted and frozen in OCT, sectioned on a cryostat at 10 um, sections were prepared with rapid IHC for DAPI and NeuN in less than 15 minutes, single neurons were captured using Arcturus CapSure system according to manufacture protocols.  Single cells or cell pools (2-5 single cells) were indiviually lysed and PCR performed according to Fluidigm's Biomark preparation protocols.

treatment_protocol: Male sprague dawley rats were subjected to ligation of the left anterior decending artery after exteriorizing the heart through a small left thoracotomy. Sham surgery included ketamine/xylazine anesthesia and surgical exposure without ligation. n=3-4 biological replicates. All samples were collected after either 1 week or 3 weeks post surgery.

value: Sprague Dawley

tag: animal number

value: DC

tag: side of brain stem

value: R

tag: surgery type

value: LAD

tag: time point

value: 1 Week


title: FCtx_S1135_snRNAseq

description: snRNAseq_Sample 13


title: DCC


title: Untreated rep3

description: Multiplexed cDNA amplicon sequencing


title: DCA


title: retina, PKD + PBS (rep1)


title: FCtx_S4924_snRNAseq

description: snRNAseq_Sample 12

value: TT


title: Untreated rep2

description: Multiplexed cDNA amplicon sequencing


title: KB2

city: Tianjin

first: Long

last: Shen

address: 22 Qixiangtai Road

country: China

institute: School of Basic Medical Sciences, Tianjin Medical University

description: BMDMs.txt

data_processing:
Basecalls performed using MGISEQ-2000.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to GCF_000001635.26_GRCm38.p6 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include fpkm and read_count values for each Sample

source_name: bone marrow derived macrophage

extract_protocol:
Wild type and PHGDH knockout BMDMs, as well as RAW264.7 cells transfected with siControl or siPHGDH were washed with cold PBS for twice, then collected to extract total RNA using Trizol reagent.
RNA libraries were prepared for sequencing using  oligo -dT beads

value: macrophage

value: PHGDH knockout


title: Untreated rep1

description: Multiplexed cDNA amplicon sequencing


title: FCtx_S4022_snRNAseq

description: snRNAseq_Sample 11


title: retina, SD + Clodronate (rep6)

source_name: retina, clodronate

value: Clodronate


title: KB1

description: BMDMs.txt


title: DCQ


title: FCtx_S1584_snRNAseq

description: snRNAseq_Sample 10

value: CC


title: retina, SD + Clodronate (rep5)


title: ATP depleted rep3

description: Multiplexed cDNA amplicon sequencing


title: In vitro refolded rep2

description: Multiplexed cDNA amplicon sequencing


title: WB3

description: BMDMs.txt

value: wild type


title: FCtx_S630_snRNAseq

description: snRNAseq_Sample 9


title: DCD

description:
Neurons from the Left Side of DMV in LAD surgery animal
BioMark-RTqPCR

value: L


title: WB2

description: BMDMs.txt


title: KB3

description: BMDMs.txt


title: ATP depleted rep2

description: Multiplexed cDNA amplicon sequencing


title: retina, PKD + PBS (rep2)


title: retina, SD + Clodronate (rep3)


title: retina, SD + Clodronate (rep4)


title: FCtx_S5123_snRNAseq

description: snRNAseq_Sample 8


title: ATP depleted rep1

description: Multiplexed cDNA amplicon sequencing


title: retina, SD + Clodronate (rep2)


title: WB1

description: BMDMs.txt


title: NLPC_Qk-/-_Input

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq
ChIP-seq reads (only R1) were aligned to the mm10 genome assembly using bowtie (version 1.2.2)
peaks were called using macs2(v2.1.2) with the following setting: macs2 callpeak -f BAM -g mm -q 0.05 -t ChIP.bam -n NAME -c INPUT.bam
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using macs2

molecule: genomic DNA

growth_protocol: Neural stem cell-derived lens progenitor-like cells (NLPCs) were differentiated from neural stem cells in DMEM/F-12 supplemented with 0.05% BSA, 1% nonessential amino acids, 50 units/mL penicillin G, and 50 μg/mL streptomycin, 1X N2 and 1X B27 with two-step growth factor treatment, 1st step with 100 ng/ml Noggin and 2nd step with 100 ng/ml bFGF, 20 ng/ml BMP4, and 20 ng/ml BMP7.

extract_protocol:
Cells were crosslinked, sonicated and  then incubated with Qki-5, Pol II, and Srebp2 antibodies. Protein-DNA complex were washed and ChIP'ed DNA were isolated for library preparation.
Libraries were prepared by KAPA Hyper Prep Kit (KK8504, Kapa Biosystems).

tag: cell type

value: Neural stem cell-derived lens progenitor-like cells (NLPCs) differentiated from neural stem cells

tag: passages

value: FvB/C57BL6 hybrid

tag: chip antibody


title: FCtx_S1363_snRNAseq

description: snRNAseq_Sample 7


title: S3

source_name: cell line

value: siPHGDH


title: retina, SD + Clodronate (rep1)


title: FCtx_S1672_snRNAseq

description: snRNAseq_Sample 6

value: CT

value: frontal cortex


title: NLPC_WT_Input

source_name: Neural stem cell-derived lens progenitor-like cells (NLPCs)


title: retina, SD (rep6)

source_name: retina, control

value: Sprague Dawley

value: Control


title: FCtx_S1027_snRNAseq

description: snRNAseq_Sample 5

value: nuclear RNA


title: S1


title: FCtx_S794_snRNAseq

description: snRNAseq_Sample 4


title: NLPC_Qk-/-_Pol II

value: RNA polymerase II CTD repeat YSPTSPS (Abcam, Cat# ab817)


title: FCtx_S5079_snRNAseq

description: snRNAseq_Sample 3


title: NLPC_WT_Pol II


title: retina, SD (rep4)


title: C3

value: scramble control


title: C2


title: NLPC_WT_Srebp2

value: Srebp2 (10007663, Cayman Chemical)


title: NLPC_Qk-/-_Srebp2


title: FCtx_S1230_snRNAseq

description: snRNAseq_Sample 1

value: TT


title: retina, SD (rep3)


title: FCtx_S1274_snRNAseq

description: snRNAseq_Sample 2


title: NLPC_WT_Qki-5

value: Qki-5 (home-made)


title: B40_ILC2_CD45RA_il33-tslp-dex

status: Public on Jan 28 2021

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Reads were aligned using HISAT2 v2.0.4. (RNA-seq) with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization
RPKM generation, sample scaling and statistical analysis were performed using HOMER and its implementation of the R package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: RPKM expression values

source_name: Peripheral blood

growth_protocol: Sorted ILC2s were cultured in Yssel's medium with 1% normal human serum. 2000-5000 cells were stimulated for 7 days with IL-2 (10 U/mL), IL-33 (50 ng/mL) and TSLP (both 50 ng/mL). When indicated, dexamethasone was added to the culture medium (10-7 M, Sigma Aldrich) at day 0.

extract_protocol:
ILC2s were isolatd by FACS as Lineage-CD127+CRTH2+ cells peripheral blood samples (buffy coats) of 4 healthy volunteers.
RNA-Seq: Smart-seq2 library construction (as described in Picelli et al. Nature Methods (2013))

value: FACS-purified lymphocytes

tag: culture conditions

value: 7 days with IL-2, IL-33, TSLP and dexamethasone


title: C1

value: macrophage


title: retina, SD (rep1)


title: retina, SD (rep2)


title: B35_ILC2_CD45RA_il33-tslp

value: 7 days with IL-2, IL-33 and TSLP


title: B36_ILC2_CD45RA_il33-tslp


title: retina, SD (rep5)


title: B33_ILC2_CD45RA_il33-tslp-dex


title: Caco-2-Null

city: New York

first: Anil

middle: K.

last: Rustgi

state: New York

address: 1130 St. Nicholas Avenue

institute: Columbia University

data_processing:
FASTQ files from Illumina sequencer were trimmed by Trimmomatic 0.32 to remove low quality bases.
The trimmed reads were mapped to mm10 mouse reference genome using bowtie2 version 2.3.4.1
The mapped reads were filtered by MAPQ >10 and sorted, and the duplicated reads were removed afterwards for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The Bigwig files were generated using HOMER function make UCSC file which the total counts were normalized to 10e7 per sample.
Supplementary_files_format_and_content: MACS2 algorithm was used to call peaks. CDX2 binding peaks were identified by applying FDR cutoff 0.05.

growth_protocol: culture 2 x 10e7 Caco-2 parental and LIN28B knockdown cells per sample

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 mins at 37°C, washed in cold PBS, resuspended in lysis buffer, and sonicated to obtain chromatin fragments between 200 bp and 1000 bp. Sonicated chromatin was resuspended in IP buffer,  and incubated overnight at 4 °C with magnetic beads conjugated to CDX2 (Bethyl BL3194). The IP was washed 5 times with RIPA buffer and the DNA recovered by reversing the crosslink in 1% SDS, 0.1 M NaHCO3 for 8 h at 65°C. DNA was purified and quantified by Qubit.
libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer cells

value: CDX2(Bethyl BL3194)

value: LIN28B knockdown


title: B36_ILC2_CD45RA_il33-tslp-dex


title: Caco-2-WT

value: parental


title: S2

value: siPHGDH


title: B40_ILC2_CD45RA

value: no culture


title: B35_ILC2_CD45RA_il33-tslp-dex


title: B33_ILC2_CD45RA_il33-tslp


title: B35_ILC2_CD45RA


title: B40_ILC2_CD45RA_il33-tslp


title: B33_ILC2_CD45RA


title: FibroblastT90Exp2_rep2

city: Dallas

first: Nicole

middle: Janell

last: De Nisco

state: Texas

address: 6000 Harry Hines Blvd, NA5.146, NA5.146

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

description:
dS_T90
FB_dS_t90_2

data_processing:
Basecalls performed using bcl2fastq/1.8.4
Reads were trimmed using fastq-mcf (ea-utils/1.1.2-806)
Trimmed reads were mapped using TopHat 2 (2.0.12)
Raw reads were counted using featureCounts (subread/1.4.6)
Normalized counts were generated using edgeR (3.2.4)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file reports normalized counts

molecule: polyA RNA

growth_protocol: Primary human fibroblasts were seeded onto 6-well plates at a density of 1x10^5 cells/mL and grown for 18-20 hours to ~80% confluency in ATCC Primary Fibroblast Basal Medium plus Low Serum Growth Kit. V. para cultures were grown over night at 30C in MLB and then normalized to an OD600 of 0.2 and subcultured to OD600 = 0.6.

extract_protocol:
At 90 minutes post-infection, RNAprotect Cell Reagent (Qiagen) was added. Cells were harvested by scraping, pooled and pellets were resuspended in RLT-plus buffer (Qiagen) and stored at -80C. Cells were lysed with 27G1/2 needles before homogenization with QiAshredder columns (Qiagen). Total RNA was then purified using the RNAeasy Plus Kit (Qiagen).
RNA concentration was determined with a Qubit fluorimeter prior to library prep.  4μg of total DNAse treated RNA were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. In brief, polyadenylated RNA was purified and fragmented before strand specific cDNA synthesis.  cDNA was A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent 2100 Bioanalyzer.

treatment_protocol: V. para cultures were pelleted, resuspended in unsupplemented DMEM and grown at 37°C for 30 minutes to pre-induce T3SS1 expression. Primary Fibroblasts were washed with unsupplemented DMEM and then infected with pre-induced V. para strains at a multiplicity of infection (MOI) of 10. Plates were centrifuged at 1000xg for 5 minutes to synchronize infection and incubated at 37°C, 5% CO2

tag: infection strain

value: V. parahaemolyticus POR3 ΔvopS

tag: infection time

value: 90 minutes

value: Primary Adult Dermal Fibroblast


title: FibroblastT90Exp2_rep1

description:
dS_T90
FB_dS_t90_1


title: FibroblastT90Exp1_rep1

description:
dQ_T90
FB_dQ_t90_1

value: V. parahaemolyticus POR3 ΔvopQ


title: FibroblastT90Exp1_rep2

description:
dQ_T90
FB_dQ_t90_2


title: FibroblastT90Exp1_rep3

description:
dQ_T90
FB_dQ_t90_3


title: FibroblastT90Cntrl_rep3

description:
P3_T90
FB_P3_t90_3

value: V. parahaemolyticus POR3


title: FibroblastT90Cntrl_rep1

description:
P3_T90
FB_P3_t90_1


title: FibroblastT90Cntrl_rep2

description:
P3_T90
FB_P3_t90_2


title: FibroblastT0Cntrl_rep3

description:
UN
FB_UN_3


title: FibroblastT0Cntrl_rep1

description:
UN
FB_UN_1


title: FibroblastT0Cntrl_rep2

description:
UN
FB_UN_2


title: Adrenal_Control

city: Munich

first: Alon

last: Chen

department: Department of Stress Neurobiology and Neurogenetics

institute: Max Planck Institute of Psychiatry

description: Single-cell RNA-Seq (10X Genomics)

data_processing:
Pre-processing of the data was done using the 10X Genomics Cell Ranger software version 2.1.1 in default mode. The 10X Genomics supplied reference data for the mm10 assembly and corresponding gene annotation was used for alignment and quantification.
All further analysis were performed using SCANPY (18) (version 1.4.4.post1), following guidelines from an established best practices workflow (19).
For quality control we looked at the distribution of count depth, number of genes and mitochondrial read fraction per sample. Since distributions were fairly homogeneous, we chose to pick the same thresholds for all samples (tissues and conditions). Specifically, we filtered out (1) cells with less than 1,000 counts, (2) less than 400 genes detected, and (3) percentage of mitochondrial gene counts higher than 25%. Additionally, genes expressed in less than 20 cells were removed as well. This resulted in a dataset of 21,723 single cells, of which 6,966 cells and 16,168 genes were from the PVN, 9,879 cells and 15,437 genes for the pituitary, and 4,878 cells and 13,997 genes for the adrenal gland.
The size factors used for normalization were obtained using scran (68) (version 1.14.5) and the data was log1p-transformed. Each dataset was batch-corrected using Combat (69), available in Scanpy. For each tissue, we selected the top 4,000 highly variable genes using the highly_variable_genes function. Dimensionality reduction was performed using PCA computed on highly variable genes and taking the first 50 PCs. Finally, we computed a KNN-graph (k=15) on the low-dimensional embedding, necessary for UMAP visualization.
Genome_build: mm10 assembly
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene per cell-type.

source_name: Adrenal Gland

extract_protocol:
Dissociation protocol: Mice were anesthetized lethally using isoflurane and perfused with cold PBS in order to get rid of undesired blood cells in target tissues. Brains, pituitaries, and adrenal glands were quickly dissected and immediately transferred to ice-cold oxygenated artificial cerebral spinal fluid (aCSF) (brains), ice-cold HBSS (pituitaries) or ice-cold PBS (adrenals) and kept in the same solutions during dissection and dissociation. The aCSF was oxygenated throughout the experiment with a mixture of 5% CO2 in O2. Sectioning of the brain was performed using a 0.5 mm stainless steel adult mouse brain matrix (Kent Scientific) and a Personna Double Edge Prep Razor Blade. A slide (approximately -0.58 mm Bregma to -1.22 mm Bregma) was obtained from each brain and the extended PVN was manually dissected under the microscope. Two cell suspensions were prepared for each of the three tissues with one pool for controls and one pool for stressed mice. The PVN from five different mice were pooled and dissociated for 35 min using the Papain dissociation system (Worthington) following the manufacturer’s instructions. Similarly, the pituitaries from five mice were pooled and dissociated for 15 min using papain. Finally, the adrenal glands from five mice were pooled and dissociated for 55 min using a 0.2% collagenase II solution. All cell suspensions were incubated at 37°C using a shaking water bath. After this, cell suspensions were filtered with 30 μm filters (Partec) and kept in cold aCSF, HBSS, or PBS.
Cell suspensions with approximately 1.000.000 cells/μL were used. Each pool was loaded onto individual lanes of a 10X Genomics Chromium chip, as per factory recommendations. For all three tissues, the control and stress cell-suspensions were loaded and processed together in the same chip, in order to avoid batch effects by condition. Reverse transcription and library preparation were performed using the 10X Genomics Single Cell v2.0 kit following the 10X Genomics protocol. Molar concentration and fragment length of libraries was quantified by qPCR using KAPA Library Quant (Kapa Biosystems) and Bioanalyzer (Agilent high sensitivity DNA kit), respectively. Each library was sequenced on a single lane of an Illumina HiSeq4000 system generating 100bp paired-end reads at a depth of ~340 million reads per sample.
All libraries were prepared using the 10X Genomics Single Cell v2.0 kit following the 10X Genomics protocol.

treatment_protocol: Behavior: Chronic social defeat stress paradigm (21 days)

value: Adrenal Gland

tag: strain

tag: condition

value: Control

tag: age

value: 10 weeks old


title: Pituitary_Stress

description: Single-cell RNA-Seq (10X Genomics)

source_name: Pituitary Gland

tag: tissue

value: Pituitary Gland

value: Chronic Stress (CSDS)


title: Adrenal_Stress

description: Single-cell RNA-Seq (10X Genomics)


title: PVN_Control

description: Single-cell RNA-Seq (10X Genomics)

source_name: Paraventricular nucleus of the hypothalamus (PVN)


title: Pituitary_Control

description: Single-cell RNA-Seq (10X Genomics)


title: B36_ILC2_CD45RA

value: FACS-purified lymphocytes


title: PVN_Stress

description: Single-cell RNA-Seq (10X Genomics)

value: Paraventricular nucleus of the hypothalamus (PVN)


title: FibroblastT90Exp2_rep3

description:
dS_T90
FB_dS_t90_3


title: zebrafish Nodal explants 4hpf

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11 or GRCz10) using the 10x Genomics CellRanger pipeline (version 2.1.1) with default parameters.
Genome_build: GRCz11/GRCz10
Supplementary_files_format_and_content: tar compressed  files included filtered_gene_bc_matrices after running CellRanger pipeline

organism: Danio rerio

source_name: zebrafish cells

growth_protocol: explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium

extract_protocol: Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 (10x Genomics, PN-120237) according to the manufacturer’s protocol for 10000 cells recovery.

treatment_protocol: 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at 128 cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage, then, were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf, 5hpf, 6hpf, 8hpf, 10hpf and 24hpf (corresponding to embryonic developmental stage) separately.

value: AB

value: embryonic cells

tag: treatment

value: injected with 10pg ndr2 mRNA


title: zebrafish Nodal explants 5hpf


title: zebrafish Nodal explants 8hpf


title: zebrafish Nodal explants 10hpf


title: zebrafish Nodal explants 24hpf


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 5hpf rep3

data_processing:
The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR, and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package.
Genome_build: GRCz11
Supplementary_files_format_and_content: comma-delimited csv files included read counts  of each sample and each gene

extract_protocol:
Total RNAs was extracted using TRIzol following the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10pg, 6pg, 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at 128 cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA, 20min after the injection, half of the samples were treated with Cycloheximide (50μg/μl ,MCE, CAS No. 66-81-9) until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage, then, were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf, 5hpf, 6hpf (corresponding to embryonic developmental stage) separately.


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep1


title: zebrafish Nodal explants 6hpf


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 5hpf rep2


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep2


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 6hpf rep3


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 4hpf rep2


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 5hpf rep1


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 4hpf rep3


title: zebrafish explants injected with 10pg ndr2 mRNA 5hpf rep3


title: zebrafish explants injected with 10pg ndr2 mRNA 5hpf rep2


title: zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep2


title: zebrafish explants injected with 10pg ndr2 mRNA and treated with CHX 4hpf rep1


title: zebrafish explants injected with 10pg ndr2 mRNA 4hpf rep2


title: zebrafish explants injected with 10pg ndr2 mRNA 4hpf rep3


title: zebrafish explants injected with 10pg ndr2 mRNA 5hpf rep1


title: zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep1


title: zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep3

value: injected with 6pg ndr2 mRNA


title: zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep1


title: zebrafish explants injected with 10pg ndr2 mRNA 4hpf rep1


title: zebrafish explants injected with 6pg ndr2 mRNA 6hpf rep2


title: zebrafish explants injected with 6pg ndr2 mRNA 5hpf rep2


title: zebrafish explants injected with 6pg ndr2 mRNA 4hpf rep2


title: zebrafish explants injected with 6pg ndr2 mRNA 4hpf rep1


title: zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep3

value: injected with 2pg ndr2 mRNA


title: zebrafish explants injected with 6pg ndr2 mRNA 5hpf rep3


title: zebrafish explants injected with 6pg ndr2 mRNA 4hpf rep3


title: zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep1


title: zebrafish explants injected with 2pg ndr2 mRNA 6hpf rep2


title: zebrafish explants injected with 2pg ndr2 mRNA 5hpf rep1


title: zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep3


title: zebrafish explants injected with 2pg ndr2 mRNA 5hpf rep3


title: zebrafish explants injected with 2pg ndr2 mRNA 4hpf rep3


title: zebrafish explants injected with 2pg ndr2 mRNA 5hpf rep2


title: zebrafish explants injected with 2pg ndr2 mRNA 4hpf rep2


title: zebrafish explants injected with 2pg ndr2 mRNA 4hpf rep1


title: zebrafish explants control 6hpf rep3

value: control


title: zebrafish explants control 6hpf rep1


title: zebrafish explants control 5hpf rep1


title: zebrafish explants control 5hpf rep2


title: zebrafish explants control 4hpf rep2


title: zebrafish explants control 4hpf rep1


title: zebrafish explants control 4hpf rep3


title: zebrafish explants control 6hpf rep2


title: zebrafish explants injected with 6pg ndr2 mRNA 5hpf rep1


title: ChIP_A375_KDM2BKO_H3K36me2

city: San Diego

first: Nathan

middle: E.

last: Lewis

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

data_processing:
FASTQ files from sequencing experiments were mapped to the hg38 genome using Bowtie2 with default parameters (Langmead and Salzberg, 2012).
Normalized tag counts were computated using HOMER annotatePeaks.pl script with parameter "-norm 1e7". Histone marks were counted within +/- 3000 bp around KDM2B peaks
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file containing histone counts around KDM2B peaks.

source_name: human melanoma cell line

growth_protocol: A375 cells [ATCC® CRL-1619™) were grown in DMEM (gibco) supplemented with 10% FBS (gibco) and 1% Penicillin/Streptomycin (10,000 U/mL, gibco) at 37˚C with 5% CO2.

extract_protocol:
Culture media was removed and plates were washed once with PBS and then fixed for 10 minutes with 1% formaldehyde (Thermo Fisher Scientific) in PBS at room temperature and reaction was then quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then scraped into supernatant using a rubber policeman, pelleted for 5 minutes at 400xG at 4°C. Cells were transferred to Eppendorf DNA Lobind tubes and pelleted at 700xG for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-seq protocol preparation. Samples were sonicated using a probe sonicator in 500 µl lysis buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% deoxycholate, 0.5% sarkozyl, 1 × protease inhibitor cocktail). After sonication, 10% Triton X-100 was added to 1% final concentration and lysates were spun at full speed for 10 minutes. 1% was taken as input DNA, and immunoprecipitation was carried out overnight with 20 µl Protein A Dynabeads (Invitrogen) and 2 µg specific antibodies. Beads were washed three times each with wash buffer I (20mM Tris/HCl, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), wash buffer II (10mM Tris/HCl, 250mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1mM EDTA), TE 0.2% Triton X-100 and TE 50mM NaCl and subsequently resuspended 25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20 and sequencing libraries were prepared on the Dynabeads as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit (NEB) as previously described (Heinz et al., 2018). DNA was polished, polyA-tailed and ligated after which dual UDI (IDT) or single (Bioo Scientific) barcodes were ligated to it. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction 16 µl water, 4 µl 10% SDS, 4.5 µl 5M NaCl, 3 µl 0.5 M EDTA, 4 µl 0.2M EGTA, 1 µl RNAse (10 mg/ml) and 1 µl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 75C for 30 minutes in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries were cleaned up by adding 2 µl SpeedBeads 3 EDAC (Thermo) in 124 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 12.25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. Libraries were size selected using TBE gels for 200 – 500 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).

treatment_protocol: After CRISPR knockdown, cells were left untreated.

tag: cell line

value: melanoma

value: KDM2B KO

tag: antibody


title: hESC ZNF91 ko13 ZNF611 ko55 rep 1

city: Amsterdam

first: Frank

last: Jacobs

address: Science Park 904

department: Sammerdam Institute for Life Sciences

institute: University of Amsterdam

description: RNAseq_ZNF91_ZNF611_hESC_scaled_counts_ZNF91-KO_ZNF91-ZNF611-dKO_ZNF611-KO_SVA.csv

data_processing:
Read quality assessment using FASTQC
Trimmomatic (Bolger et al. 2014) was used to clip adapter sequences and trim low quality reads.
Reads were aligned to the human genome (Hg19 version) using STAR (Dobin et al. 2013) with default settings except: outFilterMismatchNmax=2 and outFilterMultimapNmax=10, outWigType=bedGraph, outSAMtype=BAM SortedByCoordinate
Raw read counts of genes were determined with FeatureCounts (Liao et al. 2014) using Hg19 KnownGenes.GTF from UCSC for annotation (downloaded 12th September 2016). Only properly paired reads were counted (-B) and the library was reversely stranded (-s 2). Genes were summarized at metalevel (default), whereas TEs were summarized at the feature level (-f)
DEseq2 (Love et al. 2014) was used to normalize raw counts, perform principal component analysis and differential expression analysis of genes and repeats. For differential expression analysis of SVA elements Log2FC >3 was considered differentially expressed, because SVA expression levels were too low to determine adjusted p values adequately
Hg19
tab-delimited text files include scaled read counts for each Sample
Tab-delimited text/csv DEseq2 output files

source_name: hESCs

growth_protocol: H9 human embryonic stem cells were grown on matrigel (Corning) coated dishes. They were cultured in hESC medium that was incubated with mouse embryonic fibroblasts (MEFs) for 24 hours. HESC medium consisted of: DMEM/F12 supplemented with 2mM L-glutamine (Invitrogen), 20% knockout serum replacement (Gibco), penicillin/streptomycin (Invitrogen), non-essential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Invitrogen). Medium was supplemented with basic fibroblast growth factor (sigma, 8ng/μl) and changed daily to secure pluripotency of hESCs. For maintenance of the culture, cells were grown in colonies and passaged manually by cutting the colonies with a needle

extract_protocol:
Total RNA was isolated using Trizol according to the manufacturer's protocol, followed by a DNAse treatment and RNA purification using the RNA clean and concentrator kit (Zymo research). Ribosomal RNA was depleted from total RNA with the rRNA depletion kit (NEB# E6310)
NEB Next Ultra Directional RNA Library Prep Kit (NEB #E7420) was used to prepare Samples for sequencing at an illumina Hiseq 4000 device.
RNA seq on a Hiseq 4000 device

treatment_protocol: ZNF91 ko-13 H9 hESCs were transfected with two gRNAs targeting ZNF611 cloned into pX330-SpCas9-HF1 and clonally expanded

value: H9 Human embryonic stem cells

tag: genotype

value: ZNF91 ko and ZNF611 ko

tag: crispr clone

value: ZNF91 ko13 ZNF611 ko55


title: ChIP_A375_KDM2BKO_H3K4me3_rep2


title: hESC ZNF91 ko13 ZNF611 ko54 rep 1

value: ZNF91 ko13 ZNF611 ko54


title: ChIP_A375_KDM2BKO_Input

value: input


title: ChIP_A375_WT_H3K4me3_rep2

value: WT


title: ChIP_A375_WT_H3K36me2


title: ChIP_A375_WT_Input


title: ChIP_A375_KDM2BKO_H3K4me3_rep1


title: hESC ZNF91 ko13 ZNF611 wt 31 rep 1

value: ZNF91 ko and ZNF611 wt

value: ZNF91 ko13 ZNF611 wt31


title: hESC ZNF611 wt11 RNA seq rep1

treatment_protocol: H9 hESCs were transfected with two gRNAs targeting ZNF611 cloned into pX330-SpCas9-HF1 and clonally expanded

value: ZNF611 wt


title: hESC ZNF611 ko4 RNA seq rep1

value: ZNF611 ko


title: zebrafish explants control 5hpf rep3

value: AB

value: embryonic cells


title: hESC ZNF91 ko19 RNA seq rep 2

description: RNAseq_ZNF91_hESC_DEseq2_ko9-13-19_vs_wt5-30_Basemean>10reads-in-1samp_SVAs.txt  RNAseq_ZNF91_hESC_DEseq2_ko9-13-19_vs_wt5-30_genes.csv  RNAseq_ZNF91_hESC_scaled_counts_wt5_wt30_ko9-13-19_genes.txt  RNAseq_ZNF91_hESC_scaled_counts_wt5_wt30_ko9-13-19_repeats-all.txt  RNAseq_ZNF91_hESC_scaled_counts_wt5_wt30_ko9-13-19_SVAs-all.txt

treatment_protocol: H9 hESCs were transfected with two gRNAs targeting ZNF91 cloned into pX330-SpCas9-HF1 and clonally expanded

value: ZNF91 ko


title: hESC ZNF91 ko13 RNA seq rep 1


title: hESC ZNF91 ko13 RNA seq rep 2


title: hESC ZNF91 ko19 RNA seq rep 3


title: hESC ZNF91 ko9 RNA seq rep 2


title: hESC ZNF91 ko9 RNA seq rep 1


title: hESC ZNF91 wt30 RNA seq rep 2

value: ZNF91 wt


title: hESC ZNF91 wt5 RNA seq rep 2


title: hESC ZNF91 wt30 RNA seq rep 3


title: hESC ZNF91 wt5 H3K27acChIP rep1

description: ZNF91_hESC_H3K27ac-ChIP_wt5_peaks_BED.csv

data_processing:
Read quality assessment using FASTQC
Trimmomatic (version 0.38) (Bolger et al. 2014) was used to clip adapter sequences and trim low quality reads
Bowtie2 (version 1.0.1) (Langmead and Salzberg 2012) in –end-to-end –very-sensitive mode was used to map reads to the human genome (Hg19 version). Fragment length for valid paired end fragments was set to a minimum of 80 (-I) and a maximum of 500 (-X).
sam files were converted to bam files sorted by coordinate using Samtools (version 1.7). The rmdup function of Samtools was used to remove potential PCR duplicates
Peak calling was done with MACS2 (version 2.1.1.20160309) (Zhang et al. 2008). All tags at a given location were included (--keep-dup all) and subpeaks were determined (--call-summits)
Hg19
MACS output files (.txt or .csv) and for ZNF91-ChIP a file where a filtering treshold was applied: rep1 MACS score >50 and rep2 MACS score >100. The file shows the peaks present in both replicates.

extract_protocol:
hESC colonies were detached from a 60mm dish with a cell scraper and crosslinked immediately after harvest.Cells were lysed and chromatin was shared to fragments ~500bp. Antibody-coated beads were used to extract chromatin
Truseq ChIP sample prep (Illumina, Lot 20194738) was used for library preparation. Provided protocol was followed with the following adjustments: DNA clean & concentrator-5 kit (Zymo research) instead of beads was used for DNA purification. DNA fragment size selection with 2% agarose size selections gels (Invitrogen) using E-Gel sizeSelect II (Invitrogen) was done before and after PCR amplification of indexed ChIP DNA to obtain the 400-500bp fraction.
ChIP seq 150 paired end reads on a Hiseq 4000 device

value: 5 μg rabbit anti-H3K27ac (abcam, ab4729, lot GR3205521-1)


title: hESC ZNF91 wt5 RNA seq rep 1


title: hESC ZNF91 ko13 H3K27acChIP rep1

description: ZNF91_hESC_H3K27ac-ChIP_ko13_peaks_BED.csv


title: ChIP_A375_WT_H3K4me3_rep1

value: melanoma


title: D8_S36

city: Palermo

first: Simone

last: Di Franco

address: Via del Vespro, 131

department: Surgical Oncological and Oral Sciences

country: Italy

institute: University of Palermo

data_processing:
FastQC was used to assess the quality of reads.
Reads were trimmed using Trimmomatic v0.39.
Reads were mapped to the hg19 human genome using STAR.
Raw gene counts were obtained using featureCounts v1.6.4.
The quality of results were assessed using multiQC.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw count data for each sample.

source_name: colorectal cancer

growth_protocol: Sphere cells were cultured in serum-free stem cell medium supplemented with EGF and b-FGF.

extract_protocol:
Cellular pellets were resuspended with TRIzol (Thermo Fisher cat. #15596026Ambion #15596018), and total RNA was extracted according to the manufacturer’s instructions. Contaminating genomic DNA was removed by DNase (Qiagen cat. #79254) digestion. RNA quality and concentration were assed with the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. # Q33226), respectively.
Total RNA-seq libraries were prepared using the Illumina TruSeq library kit (20020597) using 150 ng of total RNA. Libraries were pooled together, and sequenced as single reads with the Illumina HiSeq4000.

treatment_protocol: Purification and propagation of sphere cells was assessed from primary tumor specimens from colorectal cancer patients undergoing colon resection.

tag: disease state

value: primary colorectal cancer cell line

tag: cetuximab resistance

value: resistant

tag: mutation (wt, braf, kras)

value: KRAS

tag: cd44v6 expression (high, medium, low)

value: high


title: hESC ZNF91 ko13 ZNF611 wt 15 rep 1

tag: cell type

value: H9 Human embryonic stem cells

value: ZNF91 ko13 ZNF611 wt15


title: hESC ZNF611 ko16 RNA seq rep1


title: C8_S35


title: B8_S34

value: sensitive

value: wt

value: medium


title: H1 hESC, 8w, rep3

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0
alignment to GRCh38 genome using STAR v2.6.0c
reads counted on GENCODE 27 gene models with htseq-count 0.9.1
Genome_build: GRCh38
Supplementary_files_format_and_content: htseq-count output, two-column text file with Ensembl gene identifier and read count columns

source_name: dopaminergic neuronal culture

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq RNA Library Prep Kit

tag: status

value: control

tag: timepoint

value: 8 weeks


title: E7_S29

value: nd


title: B7_S26


title: F7_S30


title: H7_S32


title: D7_S28


title: A7_S25


title: H6_S24


title: G6_S23


title: E6_S21

value: low


title: D6_S20


title: C6_S19


title: B6_S18


title: H5_S16


title: G5_S15


title: E5_S13


title: A6_S17


title: D5_S12


title: C5_S11


title: B5_S10


title: A8_S33


title: A5_S9


title: G7_S31


title: H4_S8


title: C7_S27


title: F4_S6


title: G4_S7


title: B4_S2


title: D4_S4


title: E4_S5


title: C4_S3


title: A4_S1


title: H3_S24


title: F6_S22


title: G3_S23


title: E3_S21


title: F3_S22


title: D3_S20


title: B3_S18


title: A3_S17


title: F5_S14


title: H2_S16


title: C3_S19


title: E2_S13


title: C2_S11


title: A2_S9


title: H1_S8


title: B2_S10


title: G1_S7


title: F1_S6

value: BRAF


title: D1_S4


title: E1_S5


title: C1_S3


title: A1_S1


title: Cas9, 2

data_processing:
RNA-Seq quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic (Bolger et al. 2014).
Sequence alignment was performed using STAR (Dobin et al. 2013) against the Human genome (GRCH.38; GCF_000001405.38) with the default parameters.
The expression of each gene was quantified using Salmon (Patro et al. 2017). The raw gene expressions were normalized using the estimateSizeFactors function in the DESeq2, and the normalized gene expression further performed differential gene expression analysis using DESeq2 (Anders and Huber 2010).
Genome_build: Human genome (GRCH.38; GCF_000001405.38)
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: A375 (Wild type)

extract_protocol:
For each replicate, genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen), and crRNA barcodes were amplified through nested PCR. For this, genomic DNA extracts were split into portions of 2 µg and diluted with ddH2O to a volume of 67 µL, and mixed with 33 µL of PCR#1 master mix (20 µL Q5-reaction buffer (NEB), 2 µL 10 mM dNTPs (NEB), 5 µL 10 µM primer F1 (Shalem et al., 2014), 5 µL 10 µM primer R1 (Shalem et al., 2014), 1 µL Q5 (NEB)).
PCR#1 was run at 70˚C annealing temperature for 18 cycles. After completion, all reactions were pooled, and 5 µL of the PCR#1 pool were diluted with 62 µL ddH2O, and mixed with 33 µL PCR#2 master mix (20 µL Q5-reaction buffer (NEB), 2 µL 10 mM dNTPs (NEB), 5 µL 10 µM primer F0x (Shalem et al., 2014), 5 µL 10 µM primer R0y (Shalem et al., 2014), 1 µL Q5 (NEB)). PCR#2 was run at 70˚C annealing temperature for 24 cycles. PCR products were gel-purified (QIAquick Gel Extraction kit, Qiagen) and submitted for sequencing on a HiSeq 4000 (Illumina).

treatment_protocol: For the resistance screen, two replicates of 1x107 GeCKO-transduced A375 cells were seeded on 175 cm2 plates (Corning) and treated with 10 nM guanidinylated neomycin (GNeo) [Ref] the next day. Cells were kept in GNeo for 4 days, after which the media was replaced with toxin-free DMEM, and cells were grown for another 8 days before harvesting. Two control replicates were grown in parallel, treated with PBS (gibco), and passaged every two days before harvesting. For the FACS screen, two replicates of 1x107 GeCKO-transduced A375 cells were grown on 175 cm2 plates for two days, harvested, recollected in PBS, and subject to FACS on a FACSCalibur cell analyzer (BD).

value: melanoma cells


title: 18855_3_D_RNA-seq

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 N. Fifth Street

department: Integrated Cancer genomics division

institute: Translational Genomics Research Institute

data_processing:
RNA-seq reads were trimmed and mapped to hg19 using subread (Liao et al. 2014).
RNA-seq reads were re-mapped using WASP (van de Geijn et al. 2015) to remove mapping biases.
The number of filtered reads mapping to genes was quantified using featureCounts within subread
Only autosomal genes are retained.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq counts for autosomal genes for all individuals

growth_protocol: iPSC-derived cardiomyocytes were maintained in Cardiomyocyte Maintenance Media  [500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (S1200-500, Genemate), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1M HEPES (SH3023701, ThermoFisher Scientific), 5 mL Glutamax (35050-061, ThermoFisher Scientific), 5 mL Penicillin/Streptomycin)].

extract_protocol:
RNA was extracted from ~1.5 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA). Samples had a median RIN score of 8.5
Samples were combined into 5 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit.  Libraries were sequenced on the HiSeq2500 or HiSeq4000 following the manufacturer's protocols.

treatment_protocol: Four conditions were collected per individual: A- normoxia at 10% oxygen, B- hypoxia at 1% oxygen for 6 hours, C- 6 hours hypoxia and re-oxygenation at 10% oxygen for 6 hours and D- 6 hours hypoxia and re-oxygenation at 10% oxygen for 24 hours.

tag: subject id

tag: Sex

value: Female

tag: population

value: Yoruba

value: induced pluripotent stem cell-derived cardiomyocytes


title: Cas9, 1


title: KDM2B, 2

source_name: A375 (KDM2B knock-out)


title: 18855_3_B_RNA-seq

source_name: iPSC-derived cardiomyocytes_hypoxia

tag: condition

value: hypoxia


title: B1_S2

value: primary colorectal cancer cell line

value: resistant


title: 18852_3_D_RNA-seq


title: KDM2B, 1


title: KDM2B, 3


title: 18852_3_B_RNA-seq


title: G2_S15

value: KRAS

value: high


title: 18855_3_C_RNA-seq


title: 18855_3_A_RNA-seq

source_name: iPSC-derived cardiomyocytes_normoxia

value: normoxia


title: F2_S14


title: 18852_3_A_RNA-seq


title: 18511_3_D_RNA-seq


title: 18511_3_A_RNA-seq


title: 18855_2_D_RNA-seq


title: 18511_3_B_RNA-seq


title: 18511_3_C_RNA-seq


title: 18855_2_C_RNA-seq


title: 18855_2_B_RNA-seq


title: Cas9, 3


title: 18852_2_A_RNA-seq


title: 18855_2_A_RNA-seq


title: 18852_2_D_RNA-seq


title: 18852_2_C_RNA-seq


title: 18852_3_C_RNA-seq


title: 18852_2_B_RNA-seq


title: D2_S12


title: 19160_D_RNA-seq

value: Male


title: 18511_2_A_RNA-seq


title: 19160_C_RNA-seq


title: 19160_B_RNA-seq


title: 18511_2_D_RNA-seq


title: 18511_2_C_RNA-seq


title: 19128_C_RNA-seq


title: 18511_2_B_RNA-seq


title: 19116_C_RNA-seq


title: 19128_B_RNA-seq


title: 19128_A_RNA-seq


title: 19128_D_RNA-seq


title: 19116_D_RNA-seq


title: 19116_B_RNA-seq


title: 19116_A_RNA-seq


title: 19108_D_RNA-seq


title: 19108_C_RNA-seq


title: 19108_A_RNA-seq


title: 19101_D_RNA-seq


title: 19101_C_RNA-seq


title: 19101_B_RNA-seq


title: 19098_D_RNA-seq


title: 19098_A_RNA-seq


title: 19101_A_RNA-seq


title: 19160_A_RNA-seq


title: 18912_D_RNA-seq


title: 19098_B_RNA-seq


title: 19098_C_RNA-seq


title: 18912_B_RNA-seq


title: 18870_C_RNA-seq


title: 18912_A_RNA-seq


title: 18870_A_RNA-seq


title: 18870_D_RNA-seq


title: 18858_D_RNA-seq


title: 18870_B_RNA-seq


title: 18858_C_RNA-seq


title: 18858_B_RNA-seq


title: 18855_B_RNA-seq


title: 18858_A_RNA-seq


title: 18855_A_RNA-seq


title: 18852_D_RNA-seq


title: 18855_D_RNA-seq


title: 19108_B_RNA-seq


title: 18855_C_RNA-seq


title: 18852_C_RNA-seq


title: 18852_B_RNA-seq


title: 18520_C_RNA-seq


title: 18852_A_RNA-seq


title: 18520_B_RNA-seq


title: 18912_C_RNA-seq


title: 18520_A_RNA-seq


title: 18511_A_RNA-seq


title: 18505_C_RNA-seq


title: 18505_D_RNA-seq


title: 18511_C_RNA-seq


title: 18499_D_RNA-seq


title: 18499_C_RNA-seq


title: 18499_B_RNA-seq


title: 18499_A_RNA-seq


title: 19160_C_ATAC-seq

data_processing:
Paired-end sequencing reads were aligned to hg19 using bowtie2 with default settings (Langmead and Salzberg 2012).
Reads were filtered using Picard Tools (https://broadinstitute.github.io/picard/) to remove duplicate reads, and reads mapping to the mitochondrial genome.
Reads were then remapped using the WASP (van de Giejn et al., 2015)
To generate a unified list of regions with accessible chromatin across conditions and samples, we first used MACS2 (Zhang et al 2008) to identify peaks within each sample independently. Next, we used BEDtools (Quinlan and Hall 2010) with the multiIntersectBed function to identify overlapping peaks within each condition separately. Within each condition, we retained peaks with support from more than three individuals and used the mergeBed function to create a condition-specific consensus. We then combined and merged the bed files across the four conditions to make a final consensus file containing all the filtered accessible regions.
The number of reads mapping to accessible chromatin regions was quantified using featureCounts within subread (Liao, 2014).
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq counts for regions across for all individuals

extract_protocol:
Nuclei were extracted from cell pellets (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA630, dH2O). Nuclei were resuspended in Nextera DNA transposition mix and the transposition reaction performed at 37°C for 30 min
ATAC-seq libraries were prepared using the Illumina Nextera DNA sample kit. Libraries were amplified for 10-16 cycles depending on the amplification rate of each library. Libraries were purified using Agencourt AMPure XP beads (A63880, Beckman Coulter, IN, USA), and bioanalyzed to determine library quality. 12 or 16 samples were pooled together to generate four master mixes. Each master mix was sequenced 50 bp paired-end on the HiSeq4000 according to the manufacturer’s instructions.


title: 19128_D_ATAC-seq


title: 19160_B_ATAC-seq


title: 18520_D_RNA-seq


title: 19128_A_ATAC-seq


title: 19116_D_ATAC-seq


title: 19116_C_ATAC-seq


title: 19108_D_ATAC-seq


title: 18511_D_RNA-seq


title: 19108_B_ATAC-seq


title: 19108_A_ATAC-seq


title: 19116_B_ATAC-seq


title: 19101_D_ATAC-seq


title: 18505_A_RNA-seq


title: 18505_B_RNA-seq


title: 19160_D_ATAC-seq


title: 19098_D_ATAC-seq


title: 19101_B_ATAC-seq


title: 19101_A_ATAC-seq


title: 19101_C_ATAC-seq


title: 19128_B_ATAC-seq


title: 18912_D_ATAC-seq


title: 19098_A_ATAC-seq


title: 19098_B_ATAC-seq


title: 18912_B_ATAC-seq


title: 18870_B_ATAC-seq


title: 18870_D_ATAC-seq


title: 18870_A_ATAC-seq


title: 18855_C_ATAC-seq


title: 18855_D_ATAC-seq


title: 18855_B_ATAC-seq


title: 19160_A_ATAC-seq


title: 18855_A_ATAC-seq


title: 19128_C_ATAC-seq


title: 18852_D_ATAC-seq


title: 18870_C_ATAC-seq


title: 19108_C_ATAC-seq


title: 18852_C_ATAC-seq


title: 18852_B_ATAC-seq


title: 19116_A_ATAC-seq


title: 18520_D_ATAC-seq


title: 18520_B_ATAC-seq


title: 18511_D_ATAC-seq


title: 18912_C_ATAC-seq


title: 18852_A_ATAC-seq


title: 18520_A_ATAC-seq


title: 19098_C_ATAC-seq


title: 18511_C_ATAC-seq


title: 18912_A_ATAC-seq


title: 18511_B_ATAC-seq


title: 18505_D_ATAC-seq


title: 18505_B_ATAC-seq


title: 18505_A_ATAC-seq


title: 18505_C_ATAC-seq


title: 18499_D_ATAC-seq


title: 18511_A_ATAC-seq


title: 18499_C_ATAC-seq


title: 18499_B_ATAC-seq


title: 18499_A_ATAC-seq


title: 18520_C_ATAC-seq


title: Sample856.Big brown bat.204529320130_R02C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Skin species=Big brown bat

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Eptesicus fuscus

source_name: Skin

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: tissue

value: Skin

tag: canbeusedforagingstudies

value: yes

tag: age (years)

tag: confidenceinageestimate


title: Sample857.Big brown bat.204529320130_R03C02


title: Sample848.Big brown bat.204529320118_R06C02


title: Sample858.Big brown bat.204529320130_R04C02


title: Sample842.Big brown bat.204529320118_R06C01


title: Sample850.Big brown bat.204529320130_R02C01


title: Sample859.Big brown bat.204529320130_R05C02


title: Sample855.Big brown bat.204529320130_R01C02


title: Sample851.Big brown bat.204529320130_R03C01


title: Sample840.Big brown bat.204529320118_R04C01


title: Sample860.Big brown bat.204529320130_R06C02


title: Sample836.Big brown bat.204529320125_R06C02


title: Sample852.Big brown bat.204529320130_R04C01


title: Sample837.Big brown bat.204529320118_R01C01


title: Sample854.Big brown bat.204529320130_R06C01


title: Sample838.Big brown bat.204529320118_R02C01


title: Sample853.Big brown bat.204529320130_R05C01


title: Sample843.Big brown bat.204529320118_R01C02


title: Sample844.Big brown bat.204529320118_R02C02


title: Sample834.Big brown bat.204529320125_R04C02


title: Sample846.Big brown bat.204529320118_R04C02


title: Sample849.Big brown bat.204529320130_R01C01


title: Sample841.Big brown bat.204529320118_R05C01


title: Sample839.Big brown bat.204529320118_R03C01


title: Sample832.Big brown bat.204529320125_R02C02


title: Sample835.Big brown bat.204529320125_R05C02


title: Sample833.Big brown bat.204529320125_R03C02


title: Sample845.Big brown bat.204529320118_R03C02


title: Sample847.Big brown bat.204529320118_R05C02


title: Sample831.Big brown bat.204529320125_R01C02


title: 18511_B_RNA-seq


title: Sample824.Big brown bat.204529320127_R06C02


title: Sample825.Big brown bat.204529320125_R01C01


title: Sample829.Big brown bat.204529320125_R05C01


title: Sample827.Big brown bat.204529320125_R03C01


title: Sample822.Big brown bat.204529320127_R04C02


title: Sample830.Big brown bat.204529320125_R06C01


title: Sample828.Big brown bat.204529320125_R04C01


title: Sample817.Big brown bat.204529320127_R05C01


title: Sample819.Big brown bat.204529320127_R01C02


title: Sample818.Big brown bat.204529320127_R06C01


title: Sample821.Big brown bat.204529320127_R03C02


title: Sample826.Big brown bat.204529320125_R02C01


title: Sample820.Big brown bat.204529320127_R02C02


title: Sample823.Big brown bat.204529320127_R05C02


title: Sample816.Big brown bat.204529320127_R04C01


title: Sample811.Noctule.203877620068_R05C02

description: genomic DNA methylation from tissue=Skin species=Noctule

organism: Nyctalus noctula

value: no


title: Sample809.Grey-headed flying fox.203877620068_R03C02

description: genomic DNA methylation from tissue=Skin species=Grey-headed flying fox

organism: Pteropus poliocephalus


title: Sample807.Indian fruit bat.203877620068_R01C02

description: genomic DNA methylation from tissue=Skin species=Indian fruit bat

organism: Pteropus vampyrus


title: Sample808.Indian fruit bat.203877620068_R02C02


title: Sample803.Big brown bat.203877620068_R03C01


title: Sample812.Egyptian fruit bat.203877620068_R06C02

description: genomic DNA methylation from tissue=Liver species=Egyptian fruit bat

organism: Rousettus aegyptiacus

source_name: Liver

value: Liver


title: Sample815.Big brown bat.204529320127_R03C01


title: Sample814.Big brown bat.204529320127_R02C01


title: Sample806.Jamaican fruit bat.203877620068_R06C01

description: genomic DNA methylation from tissue=Skin species=Jamaican fruit bat

organism: Artibeus jamaicensis


title: Sample804.Big brown bat.203877620068_R04C01


title: Sample810.Evening bat.203877620068_R04C02

description: genomic DNA methylation from tissue=Skin species=Evening bat

organism: Nycticeius humeralis


title: Sample813.Big brown bat.204529320127_R01C01


title: Sample800.Egyptian fruit bat.203877620074_R06C02

description: genomic DNA methylation from tissue=Skin species=Egyptian fruit bat


title: Sample798.Noctule.203877620074_R04C02


title: Sample795.Grey-headed flying fox.203877620074_R01C02


title: Sample796.Lesser long-nosed bat.203877620074_R02C02

description: genomic DNA methylation from tissue=Skin species=Lesser long-nosed bat

organism: Leptonycteris yerbabuenae


title: Sample793.Lesser long-nosed bat.203877620074_R05C01


title: Sample791.Grey-headed flying fox.203877620074_R03C01


title: Sample789.Noctule.203877620074_R01C01


title: Sample802.Egyptian fruit bat.203877620068_R02C01


title: Sample801.Common vampire bat.203877620068_R01C01

description: genomic DNA methylation from tissue=Liver species=Common vampire bat

organism: Desmodus rotundus


title: Sample792.Grey-headed flying fox.203877620074_R04C01


title: Sample788.Indian fruit bat.203877620017_R06C02


title: Sample797.Common vampire bat.203877620074_R03C02

description: genomic DNA methylation from tissue=Skin species=Common vampire bat


title: Sample794.Noctule.203877620074_R06C01


title: Sample790.Indian fruit bat.203877620074_R02C01


title: Sample787.Big brown bat.203877620017_R05C02


title: Sample786.Egyptian fruit bat.203877620017_R04C02


title: Sample779.Grey-headed flying fox.203877620017_R03C01


title: Sample785.Egyptian fruit bat.203877620017_R03C02


title: Sample778.Lesser long-nosed bat.203877620017_R02C01


title: Sample776.Rodriguez flying fox.203877620029_R06C02

description: genomic DNA methylation from tissue=Skin species=Rodriguez flying fox

organism: Pteropus rodricensis


title: Sample783.Lesser long-nosed bat.203877620017_R01C02


title: Sample775.Big brown bat.203877620029_R05C02


title: Sample781.Grey-headed flying fox.203877620017_R05C01


title: Sample780.Egyptian fruit bat.203877620017_R04C01


title: Sample782.Fish-eating bat.203877620017_R06C01

description: genomic DNA methylation from tissue=Skin species=Fish-eating bat

organism: Myotis vivesi


title: Sample805.Grey-headed flying fox.203877620068_R05C01


title: Sample765.Big brown bat.203877620029_R01C01


title: Sample772.Pallas's mastiff bat.203877620029_R02C02

description: genomic DNA methylation from tissue=Skin species=Pallas's mastiff bat

organism: Molossus molossus


title: Sample764.Fish-eating bat.203877620003_R06C02


title: Sample777.Big brown bat.203877620017_R01C01


title: Sample767.Egyptian fruit bat.203877620029_R03C01


title: Sample773.Velvety free-tailed bat.203877620029_R03C02

description: genomic DNA methylation from tissue=Liver species=Velvety free-tailed bat


title: Sample769.Big brown bat.203877620029_R05C01


title: Sample762.Egyptian fruit bat.203877620003_R04C02


title: Sample766.Egyptian fruit bat.203877620029_R02C01


title: Sample771.Indian fruit bat.203877620029_R01C02


title: Sample757.Lesser long-nosed bat.203877620003_R05C01


title: Sample759.Grey-headed flying fox.203877620003_R01C02


title: Sample768.Fish-eating bat.203877620029_R04C01


title: Sample755.Common vampire bat.203877620003_R03C01


title: Sample761.Evening bat.203877620003_R03C02


title: Sample784.Velvety free-tailed bat.203877620017_R02C02


title: Sample756.Egyptian fruit bat.203877620003_R04C01


title: Sample749.Egyptian fruit bat.203877620015_R03C02


title: Sample774.Common vampire bat.203877620029_R04C02


title: Sample751.Egyptian fruit bat.203877620015_R05C02


title: Sample754.Egyptian fruit bat.203877620003_R02C01


title: Sample758.Egyptian fruit bat.203877620003_R06C01


title: Sample760.Egyptian fruit bat.203877620003_R02C02


title: Sample747.Big brown bat.203877620015_R01C02


title: Sample748.Grey-headed flying fox.203877620015_R02C02


title: Sample746.Grey-headed flying fox.203877620015_R06C01


title: Sample770.Lesser long-nosed bat.203877620029_R06C01


title: Sample745.Common vampire bat.203877620015_R05C01


title: Sample763.Evening bat.203877620003_R05C02


title: Sample753.Big brown bat.203877620003_R01C01


title: Sample750.Indian fruit bat.203877620015_R04C02


title: Sample752.Grey-headed flying fox.203877620015_R06C02


title: Sample742.Evening bat.203877620015_R02C01


title: Sample743.Grey-headed flying fox.203877620015_R03C01


title: Sample738.Grey-headed flying fox.203877620055_R04C02


title: Sample744.Lesser long-nosed bat.203877620015_R04C01


title: Sample741.Pallas's mastiff bat.203877620015_R01C01


title: Sample734.Big brown bat.203877620055_R06C01


title: Sample733.Big brown bat.203877620055_R05C01


title: Sample726.Evening bat.203877620065_R04C02


title: Sample728.Grey-headed flying fox.203877620065_R06C02


title: Sample724.Jamaican fruit bat.203877620065_R02C02


title: Sample719.Lesser long-nosed bat.203877620065_R03C01


title: Sample739.Egyptian fruit bat.203877620055_R05C02


title: Sample717.Egyptian fruit bat.203877620065_R01C01


title: Sample737.Jamaican fruit bat.203877620055_R03C02


title: Sample799.Lesser long-nosed bat.203877620074_R05C02


title: Sample732.Egyptian fruit bat.203877620055_R04C01


title: Sample731.Jamaican fruit bat.203877620055_R03C01


title: Sample736.Big brown bat.203877620055_R02C02


title: Sample729.Noctule.203877620055_R01C01


title: Sample720.Rodriguez flying fox.203877620065_R04C01


title: Sample714.Proboscis bat.203877620066_R04C02

description: genomic DNA methylation from tissue=Skin species=Proboscis bat

organism: Rhynchonycteris naso


title: Sample730.Grey-headed flying fox.203877620055_R02C01


title: Sample740.Big brown bat.203877620055_R06C02


title: Sample723.Common vampire bat.203877620065_R01C02


title: Sample718.Lesser long-nosed bat.203877620065_R02C01


title: Sample706.Greater horseshoe bat.203877620066_R02C01

description: genomic DNA methylation from tissue=Skin species=Greater horseshoe bat

organism: Rhinolophus ferrumequinum


title: Sample710.Greater horseshoe bat.203877620066_R06C01


title: Sample712.Mexican free-tailed bat.203877620066_R02C02

description: genomic DNA methylation from tissue=Skin species=Mexican free-tailed bat

organism: Tadarida brasiliensis


title: Sample704.Proboscis bat.203675320050_R06C02


title: Sample735.Grey-headed flying fox.203877620055_R01C02


title: Sample721.Lesser long-nosed bat.203877620065_R05C01


title: Sample705.Greater horseshoe bat.203877620066_R01C01


title: Sample725.Big brown bat.203877620065_R03C02

description: genomic DNA methylation from tissue=Skin species=Big brown bat


title: Sample722.Big brown bat.203877620065_R06C01


title: Sample711.Greater horseshoe bat.203877620066_R01C02


title: Sample716.Proboscis bat.203877620066_R06C02


title: Sample702.Greater horseshoe bat.203675320050_R04C02


title: Sample727.Rodriguez flying fox.203877620065_R05C02


title: Sample703.Pallid bat.203675320050_R05C02

description: genomic DNA methylation from tissue=Skin species=Pallid bat

organism: Antrozous pallidus


title: Sample707.Greater horseshoe bat.203877620066_R03C01


title: Sample715.Proboscis bat.203877620066_R05C02


title: Sample698.Pallid bat.203675320050_R06C01


title: Sample713.Pallid bat.203877620066_R03C02


title: Sample708.Proboscis bat.203877620066_R04C01


title: Sample709.Greater horseshoe bat.203877620066_R05C01


title: Sample694.Pallid bat.203675320050_R02C01


title: Sample700.Proboscis bat.203675320050_R02C02


title: Sample693.Proboscis bat.203675320050_R01C01


title: Sample695.Proboscis bat.203675320050_R03C01


title: Sample682.Mexican free-tailed bat.203675320049_R02C01


title: Sample691.Mexican free-tailed bat.203675320049_R05C02


title: Sample687.Proboscis bat.203675320049_R01C02


title: Sample686.Proboscis bat.203675320049_R06C01


title: Sample688.Proboscis bat.203675320049_R02C02


title: Sample697.Pallid bat.203675320050_R05C01


title: Sample684.Greater horseshoe bat.203675320049_R04C01


title: Sample690.Mexican free-tailed bat.203675320049_R04C02


title: Sample677.Mexican free-tailed bat.203675320052_R03C02


title: Sample701.Proboscis bat.203675320050_R03C02


title: Sample683.Mexican free-tailed bat.203675320049_R03C01


title: Sample676.Mexican free-tailed bat.203675320052_R02C02


title: Sample699.Pallid bat.203675320050_R01C02


title: Sample681.Proboscis bat.203675320049_R01C01


title: Sample689.Pallid bat.203675320049_R03C02


title: Sample696.Mexican free-tailed bat.203675320050_R04C01


title: Sample692.Mexican free-tailed bat.203675320049_R06C02


title: Sample685.Greater horseshoe bat.203675320049_R05C01


title: Sample680.Mexican free-tailed bat.203675320052_R06C02


title: Sample669.Greater horseshoe bat.203675320052_R01C01


title: Sample668.Straw-colored fruit bat.203675320053_R06C02

description: genomic DNA methylation from tissue=Skin species=Straw-colored fruit bat

organism: Eidolon helvum


title: Sample679.Proboscis bat.203675320052_R05C02


title: Sample678.Pallid bat.203675320052_R04C02


title: Sample675.Mexican free-tailed bat.203675320052_R01C02


title: Sample674.Pallid bat.203675320052_R06C01


title: Sample667.Greater horseshoe bat.203675320053_R05C02


title: Sample673.Pallid bat.203675320052_R05C01


title: Sample670.Proboscis bat.203675320052_R02C01


title: Sample663.Proboscis bat.203675320053_R01C02


title: Sample671.Pallid bat.203675320052_R03C01


title: Sample664.Greater horseshoe bat.203675320053_R02C02


title: Sample660.Greater horseshoe bat.203675320053_R04C01


title: Sample672.Mexican free-tailed bat.203675320052_R04C01


title: Sample666.Proboscis bat.203675320053_R04C02


title: Sample665.Mexican free-tailed bat.203675320053_R03C02


title: Sample659.Proboscis bat.203675320053_R03C01


title: Sample662.Greater horseshoe bat.203675320053_R06C01


title: Sample658.Mexican free-tailed bat.203675320053_R02C01


title: Sample652.Proboscis bat.203877620022_R02C02


title: Sample657.Proboscis bat.203675320053_R01C01


title: Sample653.Pallid bat.203877620022_R03C02


title: Sample661.Mexican free-tailed bat.203675320053_R05C01


title: Sample655.Straw-colored fruit bat.203877620022_R05C02


title: Sample646.Greater horseshoe bat.203877620022_R02C01


title: Sample643.Pallid bat.203877620013_R05C02


title: Sample651.Greater horseshoe bat.203877620022_R01C02


title: Sample645.Pallid bat.203877620022_R01C01


title: Sample644.Proboscis bat.203877620013_R06C02


title: Sample648.Mexican free-tailed bat.203877620022_R04C01


title: Sample654.Greater horseshoe bat.203877620022_R04C02


title: Sample649.Mexican free-tailed bat.203877620022_R05C01


title: Sample640.Mexican free-tailed bat.203877620013_R02C02


title: Sample647.Mexican free-tailed bat.203877620022_R03C01


title: Sample642.Mexican free-tailed bat.203877620013_R04C02


title: Sample641.Pallid bat.203877620013_R03C02


title: Sample639.Greater horseshoe bat.203877620013_R01C02


title: Sample637.Greater horseshoe bat.203877620013_R05C01


title: Sample636.Pallid bat.203877620013_R04C01


title: Sample638.Greater horseshoe bat.203877620013_R06C01


title: Sample626.Pallid bat.203877620096_R06C01


title: Sample635.Pallid bat.203877620013_R03C01


title: Sample634.Proboscis bat.203877620013_R02C01


title: Sample631.Greater horseshoe bat.203877620096_R05C02


title: Sample633.Greater horseshoe bat.203877620013_R01C01


title: Sample624.Pallid bat.203877620096_R04C01


title: Sample632.Mexican free-tailed bat.203877620096_R06C02


title: Sample628.Pallid bat.203877620096_R02C02


title: Sample625.Proboscis bat.203877620096_R05C01


title: Sample629.Mexican free-tailed bat.203877620096_R03C02


title: Sample619.Little brown bat.203877620097_R05C02

description: genomic DNA methylation from tissue=Skin species=Little brown bat

organism: Myotis lucifugus


title: Sample621.Pallid bat.203877620096_R01C01


title: Sample623.Greater horseshoe bat.203877620096_R03C01


title: Sample622.Greater horseshoe bat.203877620096_R02C01


title: Sample620.Little brown bat.203877620097_R06C02


title: Sample650.Pallid bat.203877620022_R06C01


title: Sample617.Greater sac-winged bat.203877620097_R03C02

description: genomic DNA methylation from tissue=Skin species=Greater sac-winged bat

organism: Saccopteryx bilineata


title: Sample618.Little golden-mantled flying fox.203877620097_R04C02

description: genomic DNA methylation from tissue=Skin species=Little golden-mantled flying fox

organism: Pteropus pumilus


title: Sample613.Greater sac-winged bat.203877620097_R05C01


title: Sample608.Little brown bat.203877620070_R06C02


title: Sample614.Little golden-mantled flying fox.203877620097_R06C01


title: Sample609.Little golden-mantled flying fox.203877620097_R01C01


title: Sample612.Little golden-mantled flying fox.203877620097_R04C01


title: Sample604.Little golden-mantled flying fox.203877620070_R02C02


title: Sample605.Greater sac-winged bat.203877620070_R03C02


title: Sample656.Mexican free-tailed bat.203877620022_R06C02


title: Sample616.Little golden-mantled flying fox.203877620097_R02C02


title: Sample603.Little golden-mantled flying fox.203877620070_R01C02


title: Sample611.Little golden-mantled flying fox.203877620097_R03C01


title: Sample606.Little golden-mantled flying fox.203877620070_R04C02


title: Sample630.Proboscis bat.203877620096_R04C02


title: Sample592.Greater sac-winged bat.203877620064_R02C02


title: Sample585.Little golden-mantled flying fox.203877620064_R01C01


title: Sample597.Little golden-mantled flying fox.203877620070_R01C01


title: Sample607.Little golden-mantled flying fox.203877620070_R05C02


title: Sample586.Greater sac-winged bat.203877620064_R02C01


title: Sample595.Little golden-mantled flying fox.203877620064_R05C02


title: Sample602.Little golden-mantled flying fox.203877620070_R06C01


title: Sample582.Greater sac-winged bat.203877620006_R04C02


title: Sample599.Little golden-mantled flying fox.203877620070_R03C01


title: Sample600.Little brown bat.203877620070_R04C01


title: Sample593.Little brown bat.203877620064_R03C02


title: Sample588.Little brown bat.203877620064_R04C01


title: Sample581.Little golden-mantled flying fox.203877620006_R03C02


title: Sample589.Little brown bat.203877620064_R05C01


title: Sample579.Little golden-mantled flying fox.203877620006_R01C02


title: Sample584.Greater sac-winged bat.203877620006_R06C02


title: Sample596.Little golden-mantled flying fox.203877620064_R06C02


title: Sample578.Little golden-mantled flying fox.203877620006_R06C01


title: Sample583.Little golden-mantled flying fox.203877620006_R05C02


title: Sample590.Little brown bat.203877620064_R06C01


title: Sample601.Little golden-mantled flying fox.203877620070_R05C01


title: Sample627.Pallid bat.203877620096_R01C02


title: Sample591.Greater sac-winged bat.203877620064_R01C02


title: Sample594.Little golden-mantled flying fox.203877620064_R04C02


title: Sample598.Little brown bat.203877620070_R02C01


title: Sample576.Little brown bat.203877620006_R04C01


title: Sample587.Little golden-mantled flying fox.203877620064_R03C01


title: Sample577.Greater sac-winged bat.203877620006_R05C01


title: Sample572.Greater sac-winged bat.203877620050_R06C02


title: Sample569.Little golden-mantled flying fox.203877620050_R03C02


title: Sample562.Greater sac-winged bat.203877620050_R02C01


title: Sample574.Little golden-mantled flying fox.203877620006_R02C01


title: Sample580.Little golden-mantled flying fox.203877620006_R02C02


title: Sample570.Greater sac-winged bat.203877620050_R04C02


title: Sample575.Little golden-mantled flying fox.203877620006_R03C01


title: Sample560.Greater sac-winged bat.203877620018_R06C02


title: Sample565.Greater sac-winged bat.203877620050_R05C01


title: Sample563.Little golden-mantled flying fox.203877620050_R03C01


title: Sample571.Little golden-mantled flying fox.203877620050_R05C02


title: Sample568.Little brown bat.203877620050_R02C02


title: Sample558.Little golden-mantled flying fox.203877620018_R04C02


title: Sample564.Greater sac-winged bat.203877620050_R04C01


title: Sample566.Greater sac-winged bat.203877620050_R06C01


title: Sample561.Greater spear-nosed bat.203877620050_R01C01

description: genomic DNA methylation from tissue=Liver species=Greater spear-nosed bat

organism: Phyllostomus hastatus


title: Sample557.Little brown bat.203877620018_R03C02


title: Sample567.Little golden-mantled flying fox.203877620050_R01C02


title: Sample559.Little golden-mantled flying fox.203877620018_R05C02


title: Sample556.Little golden-mantled flying fox.203877620018_R02C02


title: Sample573.Greater sac-winged bat.203877620006_R01C01


title: Sample615.Greater sac-winged bat.203877620097_R01C02


title: Sample554.Greater sac-winged bat.203877620018_R06C01


title: Sample552.Greater sac-winged bat.203877620018_R04C01


title: Sample610.Little golden-mantled flying fox.203877620097_R02C01


title: Sample555.Greater sac-winged bat.203877620018_R01C02


title: Sample550.Little golden-mantled flying fox.203877620018_R02C01


title: Sample548.Greater sac-winged bat.203877620016_R06C02


title: Sample547.Little brown bat.203877620016_R05C02


title: Sample553.Greater sac-winged bat.203877620018_R05C01


title: Sample545.Little golden-mantled flying fox.203877620016_R03C02


title: Sample546.Little brown bat.203877620016_R04C02


title: Sample538.Greater sac-winged bat.203877620016_R02C01


title: Sample551.Little golden-mantled flying fox.203877620018_R03C01


title: Sample544.Little golden-mantled flying fox.203877620016_R02C02


title: Sample542.Greater sac-winged bat.203877620016_R06C01


title: Sample540.Greater sac-winged bat.203877620016_R04C01


title: Sample535.Little golden-mantled flying fox.203877620019_R05C02


title: Sample549.Little golden-mantled flying fox.203877620018_R01C01


title: Sample531.Little brown bat.203877620019_R01C02


title: Sample524.Greater mouse-eared bat.203531420009_R06C02

description: genomic DNA methylation from tissue=Skin species=Greater mouse-eared bat

organism: Myotis myotis


title: Sample528.Little golden-mantled flying fox.203877620019_R04C01


title: Sample537.Greater sac-winged bat.203877620016_R01C01


title: Sample517.Greater mouse-eared bat.203531420009_R05C01


title: Sample530.Little golden-mantled flying fox.203877620019_R06C01


title: Sample523.Greater mouse-eared bat.203531420009_R05C02


title: Sample520.Greater mouse-eared bat.203531420009_R02C02


title: Sample534.Greater sac-winged bat.203877620019_R04C02


title: Sample516.Greater mouse-eared bat.203531420009_R04C01


title: Sample541.Little golden-mantled flying fox.203877620016_R05C01


title: Sample513.Greater mouse-eared bat.203531420009_R01C01


title: Sample527.Little brown bat.203877620019_R03C01


title: Sample533.Greater sac-winged bat.203877620019_R03C02


title: Sample539.Little golden-mantled flying fox.203877620016_R03C01


title: Sample521.Greater mouse-eared bat.203531420009_R03C02


title: Sample532.Little brown bat.203877620019_R02C02


title: Sample526.Little golden-mantled flying fox.203877620019_R02C01


title: Sample536.Little golden-mantled flying fox.203877620019_R06C02


title: Sample529.Little brown bat.203877620019_R05C01


title: Sample522.Greater mouse-eared bat.203531420009_R04C02


title: Sample514.Greater mouse-eared bat.203531420009_R02C01


title: Sample543.Greater sac-winged bat.203877620016_R01C02


title: Sample525.Greater sac-winged bat.203877620019_R01C01


title: Sample518.Greater mouse-eared bat.203531420009_R06C01


title: Sample515.Greater mouse-eared bat.203531420009_R03C01


title: Sample519.Greater mouse-eared bat.203531420009_R01C02


title: Sample512.Greater mouse-eared bat.203531420040_R06C02


title: Sample510.Greater mouse-eared bat.203531420040_R04C02


title: Sample506.Greater mouse-eared bat.203531420040_R06C01


title: Sample509.Greater mouse-eared bat.203531420040_R03C02


title: Sample502.Greater mouse-eared bat.203531420040_R02C01


title: Sample511.Greater mouse-eared bat.203531420040_R05C02


title: Sample505.Greater mouse-eared bat.203531420040_R05C01


title: Sample496.Greater mouse-eared bat.203531420037_R02C02


title: Sample498.Greater mouse-eared bat.203531420037_R04C02


title: Sample494.Greater mouse-eared bat.203531420037_R06C01


title: Sample508.Greater mouse-eared bat.203531420040_R02C02


title: Sample491.Greater mouse-eared bat.203531420037_R03C01


title: Sample492.Greater mouse-eared bat.203531420037_R04C01


title: Sample504.Greater mouse-eared bat.203531420040_R04C01


title: Sample497.Greater mouse-eared bat.203531420037_R03C02


title: Sample501.Greater mouse-eared bat.203531420040_R01C01


title: Sample499.Greater mouse-eared bat.203531420037_R05C02


title: Sample507.Greater mouse-eared bat.203531420040_R01C02


title: Sample495.Greater mouse-eared bat.203531420037_R01C02


title: Sample503.Greater mouse-eared bat.203531420040_R03C01


title: Sample488.Greater mouse-eared bat.203531420065_R06C02


title: Sample500.Greater mouse-eared bat.203531420037_R06C02


title: Sample490.Greater mouse-eared bat.203531420037_R02C01


title: Sample485.Greater mouse-eared bat.203531420065_R03C02


title: Sample487.Greater mouse-eared bat.203531420065_R05C02


title: Sample493.Greater mouse-eared bat.203531420037_R05C01


title: Sample484.Greater mouse-eared bat.203531420065_R02C02


title: Sample483.Greater mouse-eared bat.203531420065_R01C02


title: Sample486.Greater mouse-eared bat.203531420065_R04C02


title: Sample489.Greater mouse-eared bat.203531420037_R01C01


title: Sample480.Greater mouse-eared bat.203531420065_R04C01


title: Sample477.Greater mouse-eared bat.203531420065_R01C01


title: Sample476.Greater horseshoe bat.203203210004_R06C02


title: Sample482.Greater mouse-eared bat.203531420065_R06C01


title: Sample478.Greater mouse-eared bat.203531420065_R02C01


title: Sample479.Greater mouse-eared bat.203531420065_R03C01


title: Sample475.Greater horseshoe bat.203203210004_R05C02


title: Sample474.Greater horseshoe bat.203203210004_R04C02


title: Sample481.Greater mouse-eared bat.203531420065_R05C01


title: Sample469.Greater horseshoe bat.203203210004_R05C01


title: Sample471.Greater horseshoe bat.203203210004_R01C02


title: Sample472.Greater horseshoe bat.203203210004_R02C02


title: Sample462.Greater horseshoe bat.203203210007_R04C02


title: Sample465.Greater horseshoe bat.203203210004_R01C01


title: Sample461.Greater horseshoe bat.203203210007_R03C02


title: Sample463.Greater horseshoe bat.203203210007_R05C02


title: Sample464.Greater horseshoe bat.203203210007_R06C02


title: Sample458.Noctule.203203210007_R06C01

description: genomic DNA methylation from tissue=Muscle species=Noctule

organism: Nyctalus noctula

source_name: Muscle

value: Muscle


title: Sample468.Greater horseshoe bat.203203210004_R04C01


title: Sample459.Noctule.203203210007_R01C02

description: genomic DNA methylation from tissue=Liver species=Noctule


title: Sample460.Noctule.203203210007_R02C02

description: genomic DNA methylation from tissue=Brain species=Noctule

source_name: Brain

value: Brain


title: Sample467.Greater horseshoe bat.203203210004_R03C01


title: Sample470.Greater horseshoe bat.203203210004_R06C01


title: Sample456.Noctule.203203210007_R04C01


title: Sample466.Greater horseshoe bat.203203210004_R02C01


title: Sample454.Noctule.203203210007_R02C01


title: Sample453.Noctule.203203210007_R01C01


title: Sample473.Greater horseshoe bat.203203210004_R03C02


title: Sample452.Noctule.203203210011_R06C02


title: Sample457.Noctule.203203210007_R05C01


title: Sample455.Noctule.203203210007_R03C01


title: Sample451.Noctule.203203210011_R05C02


title: Sample450.Noctule.203203210011_R04C02


title: Sample447.Brandt's bat.203203210011_R01C02

description: genomic DNA methylation from tissue=Liver species=Brandt's bat

organism: Myotis brandtii


title: Sample448.Brandt's bat.203203210011_R02C02

description: genomic DNA methylation from tissue=Brain species=Brandt's bat


title: Sample445.Brandt's bat.203203210011_R05C01


title: Sample446.Brandt's bat.203203210011_R06C01

description: genomic DNA methylation from tissue=Muscle species=Brandt's bat


title: Sample449.Noctule.203203210011_R03C02


title: Sample442.Brandt's bat.203203210011_R02C01


title: Sample433.Lesser short-nosed fruit bat.203203210005_R05C01

description: genomic DNA methylation from tissue=Skin species=Lesser short-nosed fruit bat

organism: Cynopterus brachyotis


title: Sample431.Lesser short-nosed fruit bat.203203210005_R03C01


title: Sample435.Big brown bat.203203210005_R01C02

description: genomic DNA methylation from tissue=Liver species=Big brown bat

organism: Eptesicus fuscus


title: Sample428.Lesser short-nosed fruit bat.203203210033_R05C02


title: Sample444.Brandt's bat.203203210011_R04C01


title: Sample439.Brandt's bat.203203210005_R05C02


title: Sample441.Brandt's bat.203203210011_R01C01


title: Sample434.Big brown bat.203203210005_R06C01


title: Sample426.Lesser short-nosed fruit bat.203203210033_R03C02


title: Sample438.Brandt's bat.203203210005_R04C02


title: Sample432.Big brown bat.203203210005_R04C01

description: genomic DNA methylation from tissue=Muscle species=Big brown bat


title: Sample429.Lesser short-nosed fruit bat.203203210005_R01C01


title: Sample427.Big brown bat.203203210033_R04C02


title: Sample436.Big brown bat.203203210005_R02C02

description: genomic DNA methylation from tissue=Brain species=Big brown bat


title: Sample440.Brandt's bat.203203210005_R06C02


title: Sample425.Big brown bat.203203210033_R02C02


title: Sample443.Brandt's bat.203203210011_R03C01


title: Sample423.Lesser short-nosed fruit bat.203203210033_R05C01


title: Sample421.Lesser short-nosed fruit bat.203203210033_R03C01


title: Sample418.Big brown bat.203203210212_R04C02


title: Sample419.Lesser short-nosed fruit bat.203203210212_R05C02


title: Sample437.Brandt's bat.203203210005_R03C02


title: Sample430.Big brown bat.203203210005_R02C01


title: Sample424.Lesser short-nosed fruit bat.203203210033_R01C02


title: Sample422.Big brown bat.203203210033_R04C01


title: Sample420.Lesser short-nosed fruit bat.203203210033_R01C01


title: Sample417.Lesser short-nosed fruit bat.203203210212_R03C02


title: Sample416.Seba's short-tailed bat.203203210212_R02C02

description: genomic DNA methylation from tissue=Skin species=Seba's short-tailed bat

organism: Carollia perspicillata


title: Sample406.Seba's short-tailed bat.203203210186_R04C02


title: Sample413.Seba's short-tailed bat.203203210212_R05C01


title: Sample398.Seba's short-tailed bat.203203210186_R02C01


title: Sample404.Seba's short-tailed bat.203203210186_R02C02


title: Sample415.Seba's short-tailed bat.203203210212_R01C02


title: Sample414.Seba's short-tailed bat.203203210212_R06C01


title: Sample401.Seba's short-tailed bat.203203210186_R05C01


title: Sample409.Seba's short-tailed bat.203203210212_R01C01


title: Sample402.Seba's short-tailed bat.203203210186_R06C01


title: Sample407.Seba's short-tailed bat.203203210186_R05C02


title: Sample405.Seba's short-tailed bat.203203210186_R03C02


title: Sample411.Seba's short-tailed bat.203203210212_R03C01


title: Sample392.Seba's short-tailed bat.203203210207_R02C02


title: Sample393.Seba's short-tailed bat.203203210207_R03C02


title: Sample395.Seba's short-tailed bat.203203210207_R05C02


title: Sample390.Seba's short-tailed bat.203203210207_R06C01


title: Sample400.Seba's short-tailed bat.203203210186_R04C01


title: Sample410.Seba's short-tailed bat.203203210212_R02C01


title: Sample403.Seba's short-tailed bat.203203210186_R01C02


title: Sample412.Seba's short-tailed bat.203203210212_R04C01


title: Sample399.Seba's short-tailed bat.203203210186_R03C01


title: Sample386.Seba's short-tailed bat.203203210207_R02C01


title: Sample396.Seba's short-tailed bat.203203210207_R06C02


title: Sample391.Seba's short-tailed bat.203203210207_R01C02


title: Sample389.Seba's short-tailed bat.203203210207_R05C01


title: Sample397.Seba's short-tailed bat.203203210186_R01C01


title: Sample387.Seba's short-tailed bat.203203210207_R03C01


title: Sample408.Seba's short-tailed bat.203203210186_R06C02


title: Sample394.Seba's short-tailed bat.203203210207_R04C02


title: Sample388.Seba's short-tailed bat.203203210207_R04C01


title: Sample376.Straw-colored fruit bat.202894750016_R04C01

description: genomic DNA methylation from tissue=Skin species=Straw-colored fruit bat


title: Sample383.Straw-colored fruit bat.202894750016_R05C02


title: Sample367.Big brown bat.202897220105_R01C02

description: genomic DNA methylation from tissue=Skin species=Big brown bat


title: Sample364.Rodriguez flying fox.202897220105_R04C01

description: genomic DNA methylation from tissue=Skin species=Rodriguez flying fox

organism: Pteropus rodricensis


title: Sample382.Big brown bat.202894750016_R04C02


title: Sample372.Big brown bat.202897220105_R06C02


title: Sample371.Rodriguez flying fox.202897220105_R05C02


title: Sample378.Pallas's mastiff bat.202894750016_R06C01

description: genomic DNA methylation from tissue=Skin species=Pallas's mastiff bat

organism: Molossus molossus


title: Sample366.Pallas's mastiff bat.202897220105_R06C01


title: Sample380.Fish-eating bat.202894750016_R02C02

description: genomic DNA methylation from tissue=Skin species=Fish-eating bat

organism: Myotis vivesi


title: Sample373.Fish-eating bat.202894750016_R01C01


title: Sample369.Fish-eating bat.202897220105_R03C02


title: Sample368.Fish-eating bat.202897220105_R02C02


title: Sample365.Big brown bat.202897220105_R05C01


title: Sample377.Big brown bat.202894750016_R05C01


title: Sample384.Big brown bat.202894750016_R06C02


title: Sample385.Seba's short-tailed bat.203203210207_R01C01


title: Sample374.Rodriguez flying fox.202894750016_R02C01


title: Sample360.Big brown bat.202897220007_R06C02


title: Sample375.Pallas's mastiff bat.202894750016_R03C01


title: Sample381.Rodriguez flying fox.202894750016_R03C02


title: Sample362.Fish-eating bat.202897220105_R02C01


title: Sample358.Big brown bat.202897220007_R04C02


title: Sample359.Fish-eating bat.202897220007_R05C02


title: Sample361.Big brown bat.202897220105_R01C01


title: Sample363.Straw-colored fruit bat.202897220105_R03C01


title: Sample370.Straw-colored fruit bat.202897220105_R04C02


title: Sample350.Rodriguez flying fox.202897220007_R02C01


title: Sample349.Straw-colored fruit bat.202897220007_R01C01


title: Sample356.Big brown bat.202897220007_R02C02


title: Sample357.Pallas's mastiff bat.202897220007_R03C02


title: Sample352.Big brown bat.202897220007_R04C01


title: Sample353.Straw-colored fruit bat.202897220007_R05C01


title: Sample351.Straw-colored fruit bat.202897220007_R03C01


title: Sample354.Big brown bat.202897220007_R06C01


title: Sample345.Fish-eating bat.202897220103_R03C02


title: Sample347.Fish-eating bat.202897220103_R05C02


title: Sample346.Straw-colored fruit bat.202897220103_R04C02


title: Sample340.Fish-eating bat.202897220103_R04C01


title: Sample342.Pallas's mastiff bat.202897220103_R06C01


title: Sample343.Big brown bat.202897220103_R01C02


title: Sample355.Big brown bat.202897220007_R01C02


title: Sample344.Big brown bat.202897220103_R02C02


title: Sample328.Straw-colored fruit bat.202897220075_R04C01


title: Sample332.Rodriguez flying fox.202897220075_R02C02


title: Sample379.Straw-colored fruit bat.202894750016_R01C02


title: Sample348.Big brown bat.202897220103_R06C02


title: Sample333.Rodriguez flying fox.202897220075_R03C02


title: Sample341.Straw-colored fruit bat.202897220103_R05C01


title: Sample321.Pallas's mastiff bat.202897220044_R03C02


title: Sample338.Rodriguez flying fox.202897220103_R02C01


title: Sample330.Pallas's mastiff bat.202897220075_R06C01


title: Sample329.Straw-colored fruit bat.202897220075_R05C01


title: Sample325.Pallas's mastiff bat.202897220075_R01C01


title: Sample327.Straw-colored fruit bat.202897220075_R03C01


title: Sample320.Big brown bat.202897220044_R02C02


title: Sample319.Rodriguez flying fox.202897220044_R01C02


title: Sample339.Pallas's mastiff bat.202897220103_R03C01


title: Sample331.Straw-colored fruit bat.202897220075_R01C02


title: Sample318.Fish-eating bat.202897220044_R06C01


title: Sample336.Rodriguez flying fox.202897220075_R06C02


title: Sample326.Big brown bat.202897220075_R02C01


title: Sample324.Big brown bat.202897220044_R06C02


title: Sample334.Pallas's mastiff bat.202897220075_R04C02


title: Sample335.Big brown bat.202897220075_R05C02


title: Sample323.Rodriguez flying fox.202897220044_R05C02


title: Sample322.Big brown bat.202897220044_R04C02


title: Sample337.Big brown bat.202897220103_R01C01


title: Sample317.Rodriguez flying fox.202897220044_R05C01


title: Sample316.Rodriguez flying fox.202897220044_R04C01


title: Sample315.Fish-eating bat.202897220044_R03C01


title: Sample314.Straw-colored fruit bat.202897220044_R02C01


title: Sample313.Fish-eating bat.202897220044_R01C01


title: Sample312.Straw-colored fruit bat.202897220073_R06C02


title: Sample308.Pallas's mastiff bat.202897220073_R02C02


title: Sample311.Straw-colored fruit bat.202897220073_R05C02


title: Sample309.Fish-eating bat.202897220073_R03C02


title: Sample310.Big brown bat.202897220073_R04C02


title: Sample307.Pallas's mastiff bat.202897220073_R01C02


title: Sample291.Fish-eating bat.202897220074_R03C01


title: Sample300.Straw-colored fruit bat.202897220074_R06C02


title: Sample298.Pallas's mastiff bat.202897220074_R04C02


title: Sample290.Rodriguez flying fox.202897220074_R02C01


title: Sample294.Big brown bat.202897220074_R06C01


title: Sample302.Straw-colored fruit bat.202897220073_R02C01


title: Sample304.Big brown bat.202897220073_R04C01


title: Sample305.Rodriguez flying fox.202897220073_R05C01


title: Sample303.Fish-eating bat.202897220073_R03C01


title: Sample292.Straw-colored fruit bat.202897220074_R04C01


title: Sample295.Straw-colored fruit bat.202897220074_R01C02


title: Sample297.Straw-colored fruit bat.202897220074_R03C02


title: Sample287.Pale spear-nosed bat.202897220046_R05C02

description: genomic DNA methylation from tissue=Skin species=Pale spear-nosed bat

organism: Phyllostomus discolor


title: Sample301.Big brown bat.202897220073_R01C01


title: Sample296.Fish-eating bat.202897220074_R02C02


title: Sample299.Rodriguez flying fox.202897220074_R05C02


title: Sample306.Big brown bat.202897220073_R06C01


title: Sample289.Pallas's mastiff bat.202897220074_R01C01


title: Sample288.Common vampire bat.202897220046_R06C02

description: genomic DNA methylation from tissue=Skin species=Common vampire bat

organism: Desmodus rotundus


title: Sample283.Pale spear-nosed bat.202897220046_R01C02


title: Sample281.Pale spear-nosed bat.202897220046_R05C01


title: Sample280.Pale spear-nosed bat.202897220046_R04C01


title: Sample284.Common vampire bat.202897220046_R02C02


title: Sample285.Pale spear-nosed bat.202897220046_R03C02


title: Sample278.Pale spear-nosed bat.202897220046_R02C01


title: Sample276.Pale spear-nosed bat.202897220006_R06C02


title: Sample271.Pale spear-nosed bat.202897220006_R01C02


title: Sample274.Pale spear-nosed bat.202897220006_R04C02


title: Sample273.Common vampire bat.202897220006_R03C02


title: Sample282.Pale spear-nosed bat.202897220046_R06C01


title: Sample286.Pale spear-nosed bat.202897220046_R04C02


title: Sample293.Fish-eating bat.202897220074_R05C01


title: Sample267.Pale spear-nosed bat.202897220006_R03C01


title: Sample263.Common vampire bat.202894750032_R05C02


title: Sample279.Common vampire bat.202897220046_R03C01


title: Sample265.Pale spear-nosed bat.202897220006_R01C01


title: Sample272.Common vampire bat.202897220006_R02C02


title: Sample269.Pale spear-nosed bat.202897220006_R05C01


title: Sample266.Common vampire bat.202897220006_R02C01


title: Sample277.Common vampire bat.202897220046_R01C01


title: Sample275.Common vampire bat.202897220006_R05C02