title: WT_GR24_rep2

description:
Sample 16
1-13-25 vs. 4-16-28.xlsx
4-16-28 vs. 8-20-32.xlsx
4-16-28 vs. 12-24-36.xlsx


title: Bdkai2-1_mock_rep2

status: Public on May 07 2021

type: SRA

city: CRAWLEY

first: Mark

last: Waters

state: WA

address: 35 Stirling Hwy

department: School of Molecular Sciences

country: Australia

institute: The University of Western Australia

description:
Sample 17
1-13-25 vs. 5-17-29.xlsx
5-17-29 vs. 6-18-30.xlsx
5-17-29 vs. 7-19-31.xlsx
5-17-29 vs. 8-20-32.xlsx

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina Nextseq
Data was trimmed based on read length and quality. Minimum number of nucleotides in reads = 50, Software: CLC Genomics Workbench 11.0
CLC RNA-Seq analysis was carried out. Min. length fraction = 0.8, Min. similarity fraction = 0.8, Maximum number of mismatches allowed 2, Unspecific match limit = 10, Software: CLC Genomics Workbench Tool 11.0
Genome_build: Brachypodium distachyon strain Bd21 v3 27-MAR-2018, NC_016131, NC_016132, NC_016133, NC_016134, NC_016135, NC_011032
Supplementary_files_format_and_content: MS Excel, gene expressions
Supplementary_files_format_and_content: Text file, matrix table with RPKM values for every gene and every sample

molecule: total RNA

organism: Brachypodium distachyon

growth_protocol: Seeds were soaked, de-glumed, and surface sterilized by treating with 70% ethanol for 30s, followed by 10% sodium hypochlorite for 3 min, followed by 4 rinses with sterile deionized water. Seeds were sown on a double layer of saturated, sterile 3MM Whatman paper and sealed in 100 mm square petri dishes. Pllates were incubated at 4 degC in the dark for 72 h. Seeds were then manually transferred to solid 0.5xMS medium (pH 5.9, no sucrose, 0.8% w/v agar) and incubated at 22 degC day, 16 degC night on a 16 h/8h day/night cycle, with broad-spectrum white light supplied at 120 µmol/m2/s, for a further 72 h. Approximately 10 seedlings per sample were transferred to 25 mL liquid 0.5xMS medium (pH 5.9) in a 250-mL conical flask, and shaken at 70 rpm under the same growth conditions, for a further 24 h to acclimatize the seedlings to growth in liquid.

extract_protocol:
Whole seedlings were recovered from flasks, shoot tissue dissected using microscissors and collected in a 2-mL microfuge tube. Tissue was immediately frozen in liquid nitrogen, and ground to a fine powder with a bead mill. RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich).
Paired-end libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturers' protocol.

treatment_protocol: Treatment solutions (acetone, KAR1, KAR2, rac-GR24) were added directly to the flasks by manual pipetting. Incubation and shaking continued for a further 4 h before seedlings were harvested. Treatments within a replicate were peformed in parallel.

tag: strain

tag: genotype

tag: tissue

value: whole shoots

tag: treatment

value: mock

tag: developmental stage

value: four-day-old seedlings


title: WT_KAR2_rep2

description:
Sample 15
1-13-25 vs. 3-15-27.xlsx
3-15-27 vs. 7-19-31.xlsx
3-15-27 vs. 11-23-35.xlsx

value: WT

value: 1 µM KAR2


title: Bdkai2-1_KAR1_rep2

description:
Sample 18
2-14-26 vs. 6-18-30.xlsx
5-17-29 vs. 6-18-30.xlsx

value: 1 µM KAR1


title: WT_KAR1_rep2

description:
Sample 14
1-13-25 vs. 2-14-26.xlsx
2-14-26 vs. 6-18-30.xlsx
2-14-26 vs. 10-22-34.xlsx


title: Bdkai2-2_GR24_rep1

description:
Sample 12
4-16-28 vs. 12-24-36.xlsx
9-21-33 vs. 12-24-36.xlsx

value: 10 µM rac-GR24


title: WT_mock_rep2

description:
Sample 13
1-13-25 vs. 2-14-26.xlsx
1-13-25 vs. 3-15-27.xlsx
1-13-25 vs. 4-16-28.xlsx
1-13-25 vs. 5-17-29.xlsx
1-13-25 vs. 9-21-33.xlsx


title: Bdkai2-2_KAR2_rep1

description:
Sample 11
3-15-27 vs. 11-23-35.xlsx
9-21-33 vs. 11-23-35.xlsx


title: WT_KAR2_rep3

description:
Sample 27
1-13-25 vs. 3-15-27.xlsx
3-15-27 vs. 7-19-31.xlsx
3-15-27 vs. 11-23-35.xlsx


title: Bdkai2-2_mock_rep1

description:
Sample 9
1-13-25 vs. 9-21-33.xlsx
9-21-33 vs. 10-22-34.xlsx
9-21-33 vs. 11-23-35.xlsx
9-21-33 vs. 12-24-36.xlsx


title: Bdkai2-2_KAR1_rep1

description:
Sample 10
2-14-26 vs. 10-22-34.xlsx
9-21-33 vs. 10-22-34.xlsx


title: Bdkai2-2_GR24_rep2

description:
Sample 24
4-16-28 vs. 12-24-36.xlsx
9-21-33 vs. 12-24-36.xlsx


title: Bdkai2-1_GR24_rep1

description:
Sample 8
4-16-28 vs. 8-20-32.xlsx
5-17-29 vs. 8-20-32.xlsx


title: Bdkai2-1_KAR1_rep1

description:
Sample 6
2-14-26 vs. 6-18-30.xlsx
5-17-29 vs. 6-18-30.xlsx


title: Bdkai2-1_KAR2_rep1

description:
Sample 7
3-15-27 vs. 7-19-31.xlsx
5-17-29 vs. 7-19-31.xlsx


title: WT_GR24_rep1

description:
Sample 4
1-13-25 vs. 4-16-28.xlsx
4-16-28 vs. 8-20-32.xlsx
4-16-28 vs. 12-24-36.xlsx


title: Ros77L1B1

city: Wellesley

first: Andrea

last: Sequeira

state: MA

address: 106 Central St

department: Department of Biological Sciences

country: USA

institute: Wellesley College

description:
Adult abdomen tissue prep 1 of Naupactus leucoloma from locality code Ros77.
b2_Nleuc_DEG.csv

data_processing:
sequencing: paired-end reads from the Illumina HiSeq 2500; fastQC to filter sequences with low quality
reference transcriptome assembly: Trinity/bowtie alignment script, see publication methods for further details
alignment: bowtie to align all transcripts to protein sequences in UniProt, retaining best match for annotation
generation of abundance measurements: RSEM for quantification of transcript abundance and gene expression levels from the Trinity assembly
normalization of gene expression & outlier removal: remove low-expression genes with counts per million of less than 1 in all samples; normalize RNA composition via TMM scaling (edgeR package in R); normalized gene counts transformed to log2 (limma package in R); filter out outliers with low numbers of gene detected, low median expression values, or high % reads from top gene
differential gene expression analysis: use the R package limma for comparisons of expression that contain more than one sample in the groups to be compared; for comparisons with one sample per group, generate a table of log2 fold change, deltaFPKM, and log2FC adjusted by mean expression level for each gene that passed prior QC based on median expression. adjusted log2FC of +/-1 and deltaFPKM of > 1 were considered to be differentially expressed.
gene set enrichment analysis: GSEA
Genome_build: FASTA files with transcript sequences included on series record.
Supplementary_files_format_and_content: .csv file including gene expression raw counts, fold change, and annotated transcript identity for the samples corresponding to that comparison.

molecule: polyA RNA

organism: Naupactus leucoloma

source_name: adult abdominal tissue

growth_protocol: Weevils were collected from Argentina in Buenos Aires and Entre Rios Provinces (7 localities) and within the United States in Georgia, Florida, Alabama (6 localities), and California (4 localities) (S1 Table). Adult weevils were maintained in temperature-controlled environmental rooms with 12:12 dark/light cycles at 24-28Â°C and 50% humidity (after Tarrant and McCoy, 1989) for a three-week acclimation period. Each set of weevils was fed their natal host plant. Weevil rearing boxes were checked daily for eggs, and juvenile specimens were separated, allowed to develop for 7-10 days, and frozen before active feeding on plant matter began. Adults were processed three weeks after the acclimation period.

extract_protocol:
Adults and immature (larval) specimens were frozen and preserved in RNAlater (Invitrogen, Carlsbad, CA). RNA extraction was performed using the PureLink RNA Mini Kit (Ambion, Carlsbad, CA). To obtain enough RNA from adult tissues we extracted material from a pool of six weevils for the head and abdomen samples. To extract RNA from immature tissues, between 50 to 100 first instar larvae were pooled, also maintaining the parental host plant and locality of origin. RNA concentration and quality were assessed using a NanoDrop 2000 spectrophotometer (ThermoFisher Scientific, Carlsbad, CA) and a Qubitâ„¢ 4 fluorometer (Invitrogen, Carlsbad, CA).
mRNA sequencing using the standard Illumina Stranded mRNA prep

treatment_protocol: For a set of experimental host switch trials, individual adults were randomly assigned to continue consuming their natal host or to switch to a novel host plant after the three-week acclimation period and processed after an additional three weeks.

tag: experimental host switch

value: no host switch

tag: life stage

value: adult


title: WT_KAR2_rep1

description:
Sample 3
1-13-25 vs. 3-15-27.xlsx
3-15-27 vs. 7-19-31.xlsx
3-15-27 vs. 11-23-35.xlsx


title: Sol82L1A1

description:
Adult head tissue prep 1 of Naupactus leucoloma from locality code Sol82.
b2_Nleuc_DEG.csv

source_name: adult head tissue


title: Bdkai2-1_mock_rep1

description:
Sample 5
1-13-25 vs. 5-17-29.xlsx
5-17-29 vs. 6-18-30.xlsx
5-17-29 vs. 7-19-31.xlsx
5-17-29 vs. 8-20-32.xlsx


title: Fair74L1B1

description:
Adult abdomen tissue prep 1 of Naupactus leucoloma from locality code Fair74.
b1_Nleuc_DEG.csv, b2_Nleuc_DEG.csv


title: FAIR74L1I1

description:
Immature tissue prep 1 of Naupactus leucoloma from locality code Fair74.
b3_L62i_Simple.csv

source_name: immature larval tissue

value: immature


title: Ros77L1A1

description:
Adult head tissue prep 1 of Naupactus leucoloma from locality code Ros77.
b2_Nleuc_DEG.csv


title: POST70L1I1

description:
Immature tissue prep 1 of Naupactus leucoloma from locality code Post70.
b3_L62i_Simple.csv


title: Post70L1B1

description:
Adult abdomen tissue prep 1 of Naupactus leucoloma from locality code Post70.
b1_Nleuc_DEG.csv, b2_Nleuc_DEG.csv


title: WT_KAR1_rep1

description:
Sample 2
1-13-25 vs. 2-14-26.xlsx
2-14-26 vs. 6-18-30.xlsx
2-14-26 vs. 10-22-34.xlsx


title: Post70L1A1

description:
Adult head tissue prep 1 of Naupactus leucoloma from locality code Post70.
b2_Nleuc_DEG.csv


title: Eli80L1A1

description:
Adult head tissue prep 1 of Naupactus leucoloma from locality code Eli80.
b2_Nleuc_DEG.csv


title: RNA_hO_b42

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: scRNA-sequencing data of human oocytes and somatic cells profiled by scChaRM-seq

data_processing:
Processing of the scChaRM-seq DNA data: Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the human reference genome hg19 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Processing of the single-cell RNA-seq data (including data from scChaRM-seq and SCRB-seq): First, raw reads were trimmed by Cutadapt (v1.15). Clean reads for each individual cell were then classified according to cell barcodes on Read#2. Then, Read#1 was aligned to the hg19 human transcriptome by STAR (v2.6.0a) with default parameters. The transcript copy number of each gene was counted by HTseq (v0.10.0) after de-duplication based on UMIs. Cells with fewer than 10,000 transcripts or with fewer than 1,000 detected genes were excluded. Genes with an average count less than 0.1 among all retained cells were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: *bw: bigwig files; hO_scChaRM_count_matix.xls.gz: Count matrix in tab-separated value files; barcodes_and_cell_information.xlsx.gz: Excel data file including sequences of barcodes used and annotations of cells processed by scChaRM-seq.

organism: Homo sapiens

source_name: Ovarian

extract_protocol:
For the isolation of human growing oocytes and ovarian somatic cells, fresh ovarian tissue (~1cm3) was cut into pieces after the blood vessels and cysts were removed. Then, pieces of ovarian tissue were dissociated in 2ml of 1× DPBS (Gibco) with 5% collagenase (Gibco) at 37°C for 1 h, 1000× rpm on a thermo incubator. After the first round dissociation, the sample was filtrated through a 100-µm cell strainer (Biololgix Group). Single cells were centrifuged at 300× g for 5 min and resuspended in 2ml LFP medium (1× L15 medium (Gibco), 10% FBS (Vistec) and 1% penicillin–streptomycin (Gibco)) before picking up. Next, the undissociated tissue sample underwent the second round digestion by 2ml TrypLE™ Express (Gibco) at 37°C for 30 min, 1000× rpm on a thermo incubator. Then the digested sample was filtrated through a 100-µm cell strainer (Biololgix Group). Finally, single cells were centrifuged at 300× g for 5 min and resuspended in 2ml LFP medium before selection. Individual cell was picked and subjected to the scChaRM-seq steps. For mature human oocytes, zona pellucida was removed by Tyrode's Solution (Sigma). Then, oocytes were washed in 1× DPBS with 1% BSA by several times under a stereomicroscope. Individual oocyte was picked and subjected to the scChaRM-seq steps.
For scChaRM-seq, single cells were individually picked into 0.25-ml PCR tubes containing 1.825 µl of ice-cold lysis buffer. Then, in vitro GpC methylation was performed by adding 2.5 U of M.CviPI (New England Biolabs) and 160 μM SAM (New England Biolabs)directly to the single-cell lysate. Samples were incubated at 37°C for 15 min, and the reaction was stopped by adding 5 μl of RLT buffer (Qiagen). Single-cell mRNA was captured by biotin-tagged and barcoded-oligo-dT primer conjugated to magnetic streptavidin beads (Invitrogen), and the gDNA supernatant was transferred into another PCR tube for methylome analysis. The mRNA separated from single cells was subjected to cDNA synthesis, PCR amplification and library construction according to our previously reported protocol. The corresponding gDNA from single cells was first purified by AMPureXP beads (Beckman Coulter), then subjected to bisulfite conversion (Zymo Research) and DNA library construction by our recently published separated (TAILS) method. For SCRB-seq, single cells were picked, lysed and subjected to first-strand cDNA synthesis as reported previously. Then, second-strand cDNA was synthesized, amplified and fragmented. An RNA-seq library was prepared by following the instruction manual of the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs). Finally, the libraries were checked, pooled and sequenced with paired-end 150-bp reads on the Illumina HiSeq X-Ten platform (Novogene).

value: Human oocytes and somatic cells


title: RNA_hO_b34


title: RNA_hO_b38


title: RNA_hO_b39


title: RNA_hO_b37


title: RNA_hO_b36


title: WT_mock_rep1

description:
Sample 1
1-13-25 vs. 2-14-26.xlsx
1-13-25 vs. 3-15-27.xlsx
1-13-25 vs. 4-16-28.xlsx
1-13-25 vs. 5-17-29.xlsx
1-13-25 vs. 9-21-33.xlsx


title: RNA_hO_b41


title: RNA_hO_b33


title: RNA_hO_b35


title: RNA_hO_b32


title: RNA_hO_b31


title: Fair74L1A1

description:
Adult head tissue prep 1 of Naupactus leucoloma from locality code Fair74.
b1_Nleuc_DEG.csv, b2_Nleuc_DEG.csv


title: RNA_hO_b40


title: RNA_hO_b30


title: RNA_hO_b29


title: RNA_hO_b26


title: RNA_hO_b27


title: RNA_hO_b25


title: RNA_hO_b20


title: RNA_hO_b23


title: RNA_hO_b18


title: RNA_hO_b22


title: RNA_hO_b15


title: RNA_hO_b12


title: RNA_hO_b9


title: RNA_hO_b17


title: RNA_hO_b13


title: RNA_hO_b7


title: RNA_hO_b8


title: RNA_hO_b11


title: RNA_hO_b10


title: RNA_hO_b16


title: RNA_hO_b4


title: RNA_hO_b14


title: RNA_hO_b5


title: RNA_hO_b3


title: RNA_hO_b28


title: RNA_hO_b2


title: RNA_hO_b21


title: RNA_hO_b1


title: RNA_hO_b19


title: RNA_hO_b24


title: DNA_Immune_sc20

description: Bisulfite-sequencing data of single human somatic cells profiled by scChaRM-seq

library_source: genomic

molecule: genomic DNA

value: Human somatic cells


title: DNA_Immune_sc19


title: DNA_Immune_sc14


title: DNA_Immune_sc16


title: DNA_Immune_sc17


title: DNA_Immune_sc13


title: DNA_Immune_sc12


title: DNA_Immune_sc9


title: DNA_Immune_sc8


title: DNA_Immune_sc5


title: DNA_Immune_sc11


title: DNA_Immune_sc7


title: DNA_Immune_sc1


title: DNA_Immune_sc2


title: DNA_StromaC2_sc185


title: DNA_StromaC2_sc184


title: DNA_Immune_sc15


title: DNA_StromaC2_sc180


title: DNA_StromaC2_sc182


title: DNA_StromaC2_sc179


title: DNA_StromaC2_sc181


title: DNA_Immune_sc10


title: DNA_StromaC2_sc178


title: DNA_StromaC2_sc177


title: DNA_StromaC2_sc176


title: DNA_Immune_sc4


title: DNA_StromaC2_sc174


title: DNA_StromaC2_sc175


title: DNA_Immune_sc3


title: DNA_Immune_sc6


title: DNA_StromaC2_sc173


title: DNA_StromaC2_sc172


title: DNA_StromaC2_sc169


title: DNA_StromaC2_sc171


title: DNA_StromaC2_sc170


title: DNA_StromaC2_sc167


title: DNA_StromaC2_sc166


title: DNA_StromaC2_sc168


title: DNA_StromaC2_sc165


title: DNA_StromaC2_sc164


title: DNA_StromaC2_sc163


title: DNA_StromaC2_sc162


title: DNA_StromaC2_sc161


title: DNA_StromaC2_sc160


title: DNA_StromaC2_sc158


title: DNA_StromaC2_sc159


title: DNA_StromaC2_sc156


title: DNA_StromaC2_sc157


title: DNA_StromaC2_sc155


title: DNA_StromaC2_sc153


title: gNT enza

status: Public on May 08 2021

city: Amsterdam

first: Sander

last: Palit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
A differential analysis of TLE3KO vs Wildtype samples was done using DESeq2. The DESeq2 result were sorted on the DESeq2 statistic in decreasing order and used as input for GSEA.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: LNCaP

growth_protocol: Library-infected LNCaP cells were cultured in RPMI medium supplemented with 10% FBS, 1% penicillin/streptomycin.

extract_protocol:
RNA extraction using Trizol
gNT_enza: GATCAGA
gTLE3 KO_1_enza: GTTTCGG
gTLE3 KO_2_enza: ATTCCTT

treatment_protocol: Library-infected LNCaP cells were cultured in RPMI medium supplemented with 10% FBS, 1% penicillin/streptomycin in the presence of 10 uM enzalutamide

tag: disease state

value: prostate cancer

tag: genotype/variation

value: wild type

tag: tag


title: DNA_StromaC2_sc149


title: DNA_StromaC2_sc147


title: DNA_StromaC2_sc150


title: DNA_StromaC2_sc152


title: DNA_StromaC2_sc151


title: DNA_StromaC2_sc145


title: DNA_StromaC2_sc148


title: DNA_StromaC2_sc146


title: DNA_StromaC2_sc142


title: DNA_StromaC2_sc141


title: DNA_StromaC2_sc139


title: DNA_StromaC2_sc137


title: DNA_StromaC2_sc136


title: DNA_StromaC2_sc138


title: DNA_StromaC2_sc140


title: DNA_StromaC2_sc133


title: DNA_StromaC2_sc132


title: DNA_StromaC2_sc134


title: DNA_StromaC2_sc131


title: DNA_StromaC2_sc154


title: DNA_StromaC2_sc130


title: DNA_StromaC2_sc129


title: DNA_StromaC2_sc128


title: DNA_StromaC2_sc127


title: DNA_StromaC2_sc143


title: DNA_StromaC2_sc144


title: DNA_StromaC2_sc126


title: DNA_StromaC2_sc135


title: DNA_StromaC2_sc124


title: DNA_StromaC2_sc125


title: DNA_StromaC2_sc119


title: DNA_StromaC2_sc120


title: DNA_StromaC2_sc121


title: DNA_StromaC2_sc123


title: DNA_StromaC2_sc117


title: DNA_StromaC2_sc116


title: DNA_StromaC2_sc113


title: DNA_StromaC2_sc114


title: DNA_StromaC2_sc111


title: DNA_StromaC2_sc112


title: DNA_StromaC2_sc110


title: DNA_StromaC2_sc109


title: DNA_StromaC2_sc115


title: DNA_StromaC2_sc106


title: DNA_StromaC2_sc105


title: DNA_StromaC2_sc104


title: DNA_StromaC2_sc107


title: DNA_StromaC2_sc108


title: DNA_StromaC2_sc102


title: DNA_StromaC2_sc122


title: DNA_StromaC2_sc103


title: DNA_StromaC2_sc101


title: DNA_StromaC2_sc100


title: DNA_StromaC2_sc118


title: DNA_Immune_sc18


title: DNA_StromaC2_sc99


title: DNA_StromaC2_sc94


title: DNA_StromaC2_sc97


title: DNA_StromaC2_sc96


title: DNA_StromaC2_sc95


title: DNA_StromaC2_sc93


title: DNA_StromaC2_sc92


title: DNA_StromaC2_sc90


title: DNA_StromaC2_sc91


title: DNA_StromaC2_sc89


title: DNA_StromaC2_sc88


title: DNA_StromaC2_sc86


title: DNA_StromaC2_sc87


title: DNA_StromaC2_sc80


title: DNA_StromaC2_sc84


title: DNA_StromaC2_sc82


title: DNA_StromaC2_sc85


title: DNA_StromaC2_sc83


title: DNA_StromaC2_sc79


title: DNA_StromaC2_sc78


title: DNA_StromaC2_sc98


title: DNA_StromaC2_sc77


title: DNA_StromaC2_sc74


title: DNA_StromaC2_sc72


title: DNA_StromaC2_sc75


title: DNA_StromaC2_sc73


title: DNA_StromaC2_sc71


title: DNA_StromaC2_sc67


title: DNA_StromaC2_sc69


title: DNA_StromaC2_sc68


title: DNA_StromaC2_sc66


title: DNA_StromaC2_sc65


title: DNA_StromaC2_sc81


title: DNA_StromaC2_sc63

data_processing:
Processing of the scChaRM-seq DNA data: Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the human reference genome hg19 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Processing of the single-cell RNA-seq data (including data from scChaRM-seq and SCRB-seq): First, raw reads were trimmed by Cutadapt (v1.15). Clean reads for each individual cell were then classified according to cell barcodes on Read#2. Then, Read#1 was aligned to the hg19 human transcriptome by STAR (v2.6.0a) with default parameters. The transcript copy number of each gene was counted by HTseq (v0.10.0) after de-duplication based on UMIs. Cells with fewer than 10,000 transcripts or with fewer than 1,000 detected genes were excluded. Genes with an average count less than 0.1 among all retained cells were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: *bw: bigwig files (including aggregated WCG and GCH sites of eight cell types); hO_scChaRM_count_matix.xls.gz: Count matrix in tab-separated value files; barcodes_and_cell_information.xlsx.gz: Excel data file including sequences of barcodes used and annotations of cells processed by scChaRM-seq.


title: DNA_StromaC2_sc61


title: DNA_StromaC2_sc62


title: DNA_StromaC2_sc60


title: DNA_StromaC2_sc76


title: DNA_StromaC2_sc57


title: DNA_StromaC2_sc54


title: DNA_StromaC2_sc58


title: DNA_StromaC2_sc56


title: DNA_StromaC2_sc52


title: DNA_StromaC2_sc51


title: DNA_StromaC2_sc49


title: DNA_StromaC2_sc50


title: DNA_StromaC2_sc70


title: DNA_StromaC2_sc47


title: DNA_StromaC2_sc48


title: DNA_StromaC2_sc64

data_processing:
Processing of the scChaRM-seq DNA data: Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the human reference genome hg19 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Processing of the single-cell RNA-seq data (including data from scChaRM-seq and SCRB-seq): First, raw reads were trimmed by Cutadapt (v1.15). Clean reads for each individual cell were then classified according to cell barcodes on Read#2. Then, Read#1 was aligned to the hg19 human transcriptome by STAR (v2.6.0a) with default parameters. The transcript copy number of each gene was counted by HTseq (v0.10.0) after de-duplication based on UMIs. Cells with fewer than 10,000 transcripts or with fewer than 1,000 detected genes were excluded. Genes with an average count less than 0.1 among all retained cells were filtered out.
Genome_build: hg19


title: DNA_StromaC2_sc46


title: DNA_StromaC2_sc45


title: DNA_StromaC2_sc44


title: DNA_StromaC2_sc183


title: DNA_StromaC2_sc41


title: DNA_StromaC2_sc59


title: DNA_StromaC2_sc39


title: DNA_StromaC2_sc42


title: DNA_StromaC2_sc37


title: DNA_StromaC2_sc36


title: DNA_StromaC2_sc53


title: DNA_StromaC2_sc35


title: DNA_StromaC2_sc55


title: DNA_StromaC2_sc38


title: DNA_StromaC2_sc33


title: DNA_StromaC2_sc34


title: DNA_StromaC2_sc32


title: DNA_StromaC2_sc30


title: DNA_StromaC2_sc43


title: DNA_StromaC2_sc29


title: DNA_StromaC2_sc31


title: DNA_StromaC2_sc27


title: DNA_StromaC2_sc28


title: DNA_StromaC2_sc26


title: DNA_StromaC2_sc25


title: DNA_StromaC2_sc24


title: DNA_StromaC2_sc20


title: DNA_StromaC2_sc40


title: DNA_StromaC2_sc18


title: DNA_StromaC2_sc16


title: DNA_StromaC2_sc21


title: DNA_StromaC2_sc17


title: DNA_StromaC2_sc13


title: DNA_StromaC2_sc15


title: DNA_StromaC2_sc10


title: DNA_StromaC2_sc19


title: DNA_StromaC2_sc9


title: DNA_StromaC2_sc7


title: DNA_StromaC2_sc11


title: DNA_StromaC2_sc22


title: DNA_StromaC2_sc3


title: DNA_StromaC2_sc5


title: DNA_StromaC2_sc4


title: DNA_StromaC2_sc1


title: DNA_StromaC2_sc2


title: DNA_StromaC2_sc6


title: DNA_StromaC1_sc188


title: DNA_StromaC2_sc12


title: DNA_StromaC1_sc186


title: DNA_StromaC1_sc185


title: DNA_StromaC1_sc187


title: DNA_StromaC1_sc189


title: DNA_StromaC2_sc23


title: DNA_StromaC2_sc8


title: RNA_hO_b6


title: DNA_StromaC1_sc184


title: DNA_StromaC1_sc181


title: DNA_StromaC1_sc182


title: DNA_StromaC1_sc183


title: DNA_StromaC1_sc180


title: DNA_StromaC1_sc179


title: DNA_StromaC1_sc178


title: DNA_StromaC1_sc175


title: DNA_StromaC1_sc177


title: DNA_StromaC1_sc171


title: DNA_StromaC1_sc172


title: DNA_StromaC1_sc170


title: DNA_StromaC1_sc166


title: DNA_StromaC1_sc168


title: DNA_StromaC1_sc174


title: DNA_StromaC1_sc162


title: DNA_StromaC1_sc165


title: DNA_StromaC1_sc167


title: DNA_StromaC1_sc176


title: DNA_StromaC1_sc158


title: DNA_StromaC1_sc169


title: DNA_StromaC1_sc164


title: DNA_StromaC1_sc163


title: DNA_StromaC1_sc160


title: DNA_StromaC1_sc159


title: DNA_StromaC1_sc157


title: DNA_StromaC1_sc156


title: DNA_StromaC1_sc161


title: DNA_StromaC1_sc155


title: DNA_StromaC1_sc153


title: DNA_StromaC1_sc152


title: DNA_StromaC1_sc154


title: DNA_StromaC1_sc151


title: DNA_StromaC1_sc149


title: DNA_StromaC1_sc150


title: DNA_StromaC1_sc173


title: DNA_StromaC1_sc147


title: DNA_StromaC1_sc148


title: DNA_StromaC1_sc146


title: DNA_StromaC1_sc145


title: DNA_StromaC1_sc139


title: DNA_StromaC1_sc144


title: DNA_StromaC1_sc140


title: DNA_StromaC1_sc143


title: DNA_StromaC1_sc141


title: DNA_StromaC1_sc142


title: DNA_StromaC1_sc136


title: DNA_StromaC1_sc135


title: DNA_StromaC1_sc134


title: DNA_StromaC1_sc131


title: DNA_StromaC1_sc129


title: DNA_StromaC1_sc128


title: DNA_StromaC1_sc132


title: DNA_StromaC1_sc126


title: DNA_StromaC1_sc125


title: DNA_StromaC1_sc138


title: DNA_StromaC1_sc127


title: DNA_StromaC1_sc130


title: DNA_StromaC1_sc121


title: DNA_StromaC1_sc124


title: DNA_StromaC1_sc123


title: DNA_StromaC1_sc119


title: DNA_StromaC1_sc120


title: DNA_StromaC1_sc118


title: DNA_StromaC1_sc137


title: DNA_StromaC1_sc117


title: DNA_StromaC1_sc116


title: DNA_StromaC1_sc133


title: DNA_StromaC1_sc115


title: DNA_StromaC1_sc112


title: DNA_StromaC1_sc111


title: DNA_StromaC1_sc113


title: DNA_StromaC1_sc109


title: DNA_StromaC1_sc107


title: DNA_StromaC1_sc114


title: DNA_StromaC1_sc106


title: DNA_StromaC1_sc105


title: DNA_StromaC1_sc103


title: DNA_StromaC1_sc104


title: DNA_StromaC1_sc122


title: DNA_StromaC1_sc102


title: DNA_StromaC1_sc101


title: DNA_StromaC1_sc98


title: DNA_StromaC1_sc99


title: DNA_StromaC1_sc95


title: DNA_StromaC1_sc93


title: DNA_StromaC1_sc100


title: DNA_StromaC1_sc96


title: DNA_StromaC1_sc94


title: DNA_StromaC1_sc97


title: DNA_StromaC1_sc90


title: DNA_StromaC1_sc91


title: DNA_StromaC1_sc92


title: DNA_StromaC1_sc108


title: DNA_StromaC1_sc89


title: DNA_StromaC1_sc88


title: DNA_StromaC1_sc84


title: DNA_StromaC1_sc86


title: DNA_StromaC1_sc87


title: DNA_StromaC1_sc83


title: DNA_StromaC1_sc85


title: DNA_StromaC1_sc81


title: DNA_StromaC1_sc79


title: DNA_StromaC1_sc110


title: DNA_StromaC1_sc78


title: DNA_StromaC1_sc75


title: DNA_StromaC1_sc76


title: DNA_StromaC1_sc82


title: DNA_StromaC1_sc74


title: DNA_StromaC1_sc77


title: DNA_StromaC1_sc72


title: DNA_StromaC1_sc73


title: DNA_StromaC1_sc71


title: DNA_StromaC1_sc70


title: DNA_StromaC1_sc65


title: DNA_StromaC1_sc67


title: DNA_StromaC1_sc68


title: DNA_StromaC1_sc69


title: DNA_StromaC1_sc64


title: DNA_StromaC1_sc62


title: DNA_StromaC1_sc80


title: DNA_StromaC1_sc61


title: DNA_StromaC1_sc60


title: DNA_StromaC1_sc56


title: DNA_StromaC1_sc59


title: DNA_StromaC1_sc57


title: DNA_StromaC1_sc55


title: DNA_StromaC1_sc58


title: DNA_StromaC1_sc54


title: DNA_StromaC1_sc53


title: DNA_StromaC1_sc52


title: DNA_StromaC1_sc49


title: DNA_StromaC1_sc50


title: DNA_StromaC1_sc51


title: DNA_StromaC1_sc66


title: DNA_StromaC1_sc48


title: DNA_StromaC1_sc47


title: DNA_StromaC1_sc46


title: DNA_StromaC1_sc45


title: DNA_StromaC1_sc44


title: DNA_StromaC1_sc63


title: DNA_StromaC1_sc43


title: DNA_StromaC1_sc42


title: DNA_StromaC1_sc39


title: DNA_StromaC1_sc41


title: DNA_StromaC1_sc40


title: DNA_StromaC1_sc38


title: DNA_StromaC1_sc37


title: DNA_StromaC1_sc36


title: DNA_StromaC1_sc34


title: DNA_StromaC1_sc32


title: DNA_StromaC1_sc33


title: DNA_StromaC1_sc31


title: DNA_StromaC1_sc29


title: DNA_StromaC1_sc27


title: DNA_StromaC1_sc35


title: DNA_StromaC1_sc30


title: DNA_StromaC1_sc26


title: DNA_StromaC1_sc25


title: DNA_StromaC1_sc24


title: DNA_StromaC1_sc21


title: DNA_StromaC1_sc20


title: DNA_StromaC1_sc22


title: DNA_StromaC1_sc19


title: DNA_StromaC1_sc14


title: DNA_StromaC1_sc11


title: DNA_StromaC1_sc23


title: DNA_StromaC1_sc16


title: DNA_StromaC1_sc12


title: DNA_StromaC1_sc15


title: DNA_StromaC1_sc10


title: DNA_StromaC1_sc8


title: DNA_StromaC1_sc28


title: DNA_StromaC1_sc13


title: DNA_StromaC1_sc7


title: DNA_StromaC1_sc6


title: DNA_StromaC1_sc5


title: DNA_Granulosa_sc92


title: DNA_Granulosa_sc93


title: DNA_StromaC1_sc1


title: DNA_StromaC1_sc3


title: DNA_Granulosa_sc91


title: DNA_StromaC1_sc4


title: DNA_StromaC1_sc18


title: DNA_StromaC1_sc17


title: DNA_StromaC1_sc2


title: DNA_Granulosa_sc90


title: DNA_Granulosa_sc88


title: DNA_Granulosa_sc87


title: DNA_StromaC1_sc9


title: DNA_Granulosa_sc85


title: DNA_Granulosa_sc89


title: DNA_Granulosa_sc81


title: DNA_Granulosa_sc83


title: DNA_Granulosa_sc82


title: DNA_Granulosa_sc80


title: DNA_Granulosa_sc79


title: DNA_Granulosa_sc77


title: DNA_Granulosa_sc74


title: DNA_Granulosa_sc78


title: DNA_Granulosa_sc76


title: DNA_Granulosa_sc75


title: DNA_Granulosa_sc72


title: DNA_Granulosa_sc71


title: DNA_Granulosa_sc65


title: DNA_Granulosa_sc69


title: DNA_Granulosa_sc73


title: DNA_Granulosa_sc66


title: DNA_Granulosa_sc64


title: DNA_Granulosa_sc70


title: DNA_Granulosa_sc68


title: DNA_Granulosa_sc86


title: DNA_Granulosa_sc84


title: DNA_Granulosa_sc67


title: DNA_Granulosa_sc61


title: DNA_Granulosa_sc63


title: DNA_Granulosa_sc59


title: DNA_Granulosa_sc62


title: DNA_Granulosa_sc58


title: DNA_Granulosa_sc57


title: DNA_Granulosa_sc56


title: DNA_Granulosa_sc55


title: DNA_Granulosa_sc53


title: DNA_Granulosa_sc52


title: DNA_Granulosa_sc51


title: DNA_Granulosa_sc50


title: DNA_Granulosa_sc48


title: DNA_Granulosa_sc47


title: DNA_Granulosa_sc46


title: DNA_Granulosa_sc43


title: DNA_Granulosa_sc41


title: DNA_Granulosa_sc40


title: DNA_Granulosa_sc42


title: DNA_Granulosa_sc37


title: DNA_Granulosa_sc39


title: DNA_Granulosa_sc44


title: DNA_Granulosa_sc60


title: DNA_StromaC2_sc14


title: DNA_Granulosa_sc36


title: DNA_Granulosa_sc34


title: DNA_Granulosa_sc32


title: DNA_Granulosa_sc29


title: DNA_Granulosa_sc30


title: DNA_Granulosa_sc31


title: DNA_Granulosa_sc33


title: DNA_Granulosa_sc28


title: DNA_Granulosa_sc35


title: DNA_Granulosa_sc54


title: DNA_Granulosa_sc49


title: DNA_Granulosa_sc25


title: DNA_Granulosa_sc23


title: DNA_Granulosa_sc24


title: DNA_Granulosa_sc22


title: DNA_Granulosa_sc45


title: DNA_Granulosa_sc38


title: DNA_Granulosa_sc20


title: DNA_Granulosa_sc21


title: DNA_Granulosa_sc18


title: DNA_Granulosa_sc14


title: DNA_Granulosa_sc26


title: DNA_Granulosa_sc15


title: DNA_Granulosa_sc17


title: DNA_Granulosa_sc27


title: DNA_Granulosa_sc13


title: DNA_Granulosa_sc12


title: DNA_Granulosa_sc11


title: DNA_Granulosa_sc9


title: DNA_Granulosa_sc8


title: DNA_Granulosa_sc10


title: DNA_Granulosa_sc7


title: DNA_Granulosa_sc5


title: DNA_Granulosa_sc2


title: DNA_Granulosa_sc3


title: DNA_MII_sc90

description: Bisulfite-sequencing data of single human oocytes profiled by scChaRM-seq

value: Human oocytes


title: DNA_MII_sc89


title: DNA_Granulosa_sc1


title: DNA_MII_sc87


title: DNA_MII_sc86


title: DNA_MII_sc88


title: DNA_Granulosa_sc19


title: DNA_MII_sc85


title: DNA_Granulosa_sc16


title: DNA_MII_sc82


title: DNA_MII_sc81


title: DNA_Granulosa_sc6


title: DNA_MII_sc76


title: DNA_MII_sc80


title: DNA_MII_sc77


title: DNA_MII_sc84


title: DNA_MII_sc79


title: DNA_MII_sc72


title: DNA_MII_sc74


title: DNA_MII_sc75


title: DNA_Granulosa_sc4


title: DNA_MII_sc78


title: DNA_MII_sc71


title: DNA_MII_sc73


title: DNA_MII_sc69


title: DNA_MII_sc68


title: DNA_MII_sc61


title: DNA_MII_sc62


title: DNA_MII_sc64


title: DNA_MII_sc63


title: DNA_MII_sc60


title: DNA_MII_sc83


title: DNA_MII_sc70


title: DNA_MII_sc65


title: DNA_MII_sc59


title: DNA_MII_sc58


title: DNA_MII_sc57


title: DNA_MII_sc56


title: DNA_MII_sc52


title: DNA_MII_sc54


title: DNA_MII_sc53


title: DNA_MII_sc51


title: DNA_MII_sc66


title: DNA_MII_sc50


title: DNA_MII_sc49


title: DNA_MII_sc67


title: DNA_MII_sc47


title: DNA_MII_sc48


title: DNA_MII_sc45


title: DNA_MII_sc44


title: DNA_MII_sc46


title: DNA_MII_sc42


title: DNA_MII_sc43


title: DNA_MII_sc37


title: DNA_MII_sc40


title: DNA_MII_sc38


title: DNA_MII_sc36


title: DNA_MII_sc34


title: DNA_MII_sc35


title: DNA_MII_sc30


title: DNA_MII_sc32


title: DNA_MII_sc31


title: DNA_MII_sc29


title: DNA_MII_sc39


title: DNA_MII_sc33


title: DNA_MII_sc27


title: DNA_MII_sc26


title: DNA_MII_sc24


title: DNA_MII_sc25


title: DNA_MII_sc21


title: DNA_MII_sc20


title: DNA_MII_sc19


title: DNA_MII_sc22


title: DNA_MII_sc23


title: DNA_MII_sc18


title: DNA_MII_sc28


title: DNA_MII_sc13


title: DNA_MII_sc16


title: DNA_MII_sc17


title: DNA_MII_sc15


title: DNA_MII_sc14


title: DNA_MII_sc12


title: DNA_MII_sc8


title: DNA_MII_sc7


title: DNA_MII_sc41


title: DNA_MII_sc6


title: DNA_MII_sc4


title: DNA_MII_sc9


title: DNA_MII_sc2


title: DNA_MII_sc3


title: DNA_MII_sc55


title: DNA_MII_sc1


title: DNA_MI_sc155


title: DNA_MII_sc5


title: DNA_MI_sc153


title: DNA_MI_sc154


title: DNA_MII_sc11


title: DNA_MI_sc151


title: DNA_MI_sc152


title: DNA_MI_sc149


title: DNA_MI_sc148


title: DNA_MI_sc147


title: DNA_MII_sc10


title: DNA_MI_sc146


title: DNA_MI_sc143


title: DNA_MI_sc144


title: DNA_MI_sc140


title: DNA_MI_sc139


title: DNA_MI_sc142


title: DNA_MI_sc136


title: DNA_MI_sc138


title: DNA_MI_sc135


title: DNA_MI_sc141


title: DNA_MI_sc132


title: DNA_MI_sc129


title: DNA_MI_sc128


title: DNA_MI_sc131


title: DNA_MI_sc134


title: DNA_MI_sc133


title: DNA_MI_sc121


title: DNA_MI_sc117


title: DNA_MI_sc123


title: DNA_MI_sc126


title: DNA_MI_sc124


title: DNA_MI_sc127


title: DNA_MI_sc130


title: DNA_MI_sc118


title: DNA_MI_sc137


title: DNA_MI_sc122


title: DNA_MI_sc125


title: DNA_MI_sc120


title: DNA_MI_sc115


title: DNA_MI_sc113


title: DNA_MI_sc114


title: DNA_MI_sc116


title: DNA_MI_sc109


title: DNA_MI_sc108


title: DNA_MI_sc119


title: DNA_MI_sc112


title: DNA_MI_sc110


title: DNA_MI_sc104


title: DNA_MI_sc106


title: DNA_MI_sc107


title: DNA_MI_sc103


title: DNA_MI_sc102


title: DNA_MI_sc101


title: DNA_MI_sc111


title: DNA_MI_sc96


title: DNA_MI_sc99


title: DNA_MI_sc94


title: DNA_MI_sc93


title: DNA_MI_sc92


title: DNA_MI_sc98


title: DNA_MI_sc91


title: DNA_MI_sc90


title: DNA_MI_sc150


title: DNA_MI_sc89


title: DNA_MI_sc78


title: DNA_MI_sc79


title: DNA_MI_sc80


title: DNA_MI_sc82


title: DNA_MI_sc85


title: DNA_MI_sc86


title: DNA_MI_sc76


title: DNA_MI_sc87


title: DNA_MI_sc75


title: DNA_MI_sc105


title: DNA_MI_sc88


title: DNA_MI_sc81


title: DNA_MI_sc145


title: DNA_MI_sc84


title: DNA_MI_sc95


title: DNA_MI_sc83


title: DNA_MI_sc77


title: DNA_MI_sc68


title: DNA_MI_sc67


title: DNA_MI_sc100


title: DNA_MI_sc70


title: DNA_MI_sc74


title: DNA_MI_sc97


title: DNA_MI_sc64


title: DNA_MI_sc72


title: DNA_MI_sc71


title: DNA_MI_sc62


title: DNA_MI_sc73


title: DNA_MI_sc59


title: DNA_MI_sc69


title: DNA_MI_sc57


title: DNA_MI_sc56


title: DNA_MI_sc55


title: DNA_MI_sc66


title: DNA_MI_sc49


title: DNA_MI_sc65


title: DNA_MI_sc50


title: DNA_MI_sc48


title: DNA_MI_sc61


title: DNA_MI_sc60


title: DNA_MI_sc47


title: DNA_MI_sc58


title: DNA_MI_sc54


title: DNA_MI_sc53


title: DNA_MI_sc45


title: DNA_MI_sc52


title: DNA_MI_sc43


title: DNA_MI_sc51


title: DNA_MI_sc42


title: DNA_MI_sc44


title: DNA_MI_sc41


title: DNA_MI_sc63


title: DNA_MI_sc39


title: DNA_MI_sc37


title: DNA_MI_sc36


title: DNA_MI_sc33


title: DNA_MI_sc34


title: DNA_MI_sc38


title: DNA_MI_sc31


title: DNA_MI_sc35


title: DNA_MI_sc32


title: DNA_MI_sc29


title: DNA_MI_sc30


title: DNA_MI_sc28


title: DNA_MI_sc46


title: DNA_MI_sc40


title: DNA_MI_sc26


title: DNA_MI_sc25


title: DNA_MI_sc24


title: DNA_MI_sc18


title: DNA_MI_sc23


title: DNA_MI_sc20


title: DNA_MI_sc22


title: DNA_MI_sc21


title: DNA_MI_sc19


title: DNA_MI_sc17


title: DNA_MI_sc16


title: DNA_MI_sc13


title: DNA_MI_sc12


title: DNA_MI_sc14


title: DNA_MI_sc11


title: DNA_MI_sc9


title: DNA_MI_sc8


title: DNA_MI_sc6


title: DNA_MI_sc7


title: DNA_MI_sc27


title: DNA_MI_sc15


title: DNA_FGO_sc81


title: DNA_MI_sc4


title: DNA_FGO_sc80


title: DNA_MI_sc2


title: DNA_MI_sc3


title: DNA_MI_sc1


title: DNA_FGO_sc79


title: DNA_FGO_sc78


title: DNA_MI_sc10


title: DNA_FGO_sc69


title: DNA_FGO_sc66


title: DNA_FGO_sc73


title: DNA_FGO_sc74


title: DNA_FGO_sc67


title: DNA_FGO_sc64


title: DNA_FGO_sc68


title: DNA_FGO_sc71


title: DNA_FGO_sc65


title: DNA_FGO_sc75


title: DNA_FGO_sc76


title: DNA_MI_sc5


title: DNA_FGO_sc63


title: DNA_FGO_sc77


title: DNA_FGO_sc70


title: DNA_FGO_sc60


title: DNA_FGO_sc61


title: DNA_FGO_sc59


title: DNA_FGO_sc57


title: DNA_FGO_sc55


title: DNA_FGO_sc54


title: DNA_FGO_sc58


title: DNA_FGO_sc52


title: DNA_FGO_sc72


title: DNA_FGO_sc51


title: DNA_FGO_sc50


title: DNA_FGO_sc62


title: DNA_FGO_sc47


title: DNA_FGO_sc48


title: DNA_FGO_sc49


title: DNA_FGO_sc45


title: DNA_FGO_sc44


title: DNA_FGO_sc46


title: DNA_FGO_sc42


title: DNA_FGO_sc38


title: DNA_FGO_sc40


title: DNA_FGO_sc39


title: DNA_FGO_sc41


title: DNA_FGO_sc37


title: DNA_FGO_sc56


title: DNA_FGO_sc32


title: DNA_FGO_sc35


title: DNA_FGO_sc34


title: DNA_FGO_sc31


title: DNA_FGO_sc53


title: DNA_FGO_sc28


title: DNA_FGO_sc29


title: DNA_FGO_sc30


title: DNA_FGO_sc25


title: DNA_FGO_sc27


title: DNA_FGO_sc24


title: DNA_FGO_sc43


title: DNA_FGO_sc23


title: DNA_FGO_sc22


title: DNA_FGO_sc21


title: DNA_FGO_sc20


title: DNA_FGO_sc36


title: DNA_FGO_sc19


title: DNA_FGO_sc16


title: DNA_FGO_sc33


title: DNA_FGO_sc15


title: DNA_FGO_sc17


title: DNA_FGO_sc12


title: DNA_FGO_sc13


title: DNA_FGO_sc11


title: DNA_FGO_sc14


title: DNA_FGO_sc9


title: DNA_FGO_sc26


title: DNA_FGO_sc8


title: DNA_FGO_sc10


title: DNA_FGO_sc4


title: DNA_FGO_sc5


title: DNA_FGO_sc3


title: DNA_FGO_sc1


title: DNA_GO2_sc46


title: DNA_GO2_sc45


title: DNA_FGO_sc2


title: DNA_FGO_sc18


title: DNA_GO2_sc44


title: DNA_GO2_sc42


title: DNA_GO2_sc43


title: DNA_GO2_sc41


title: DNA_GO2_sc38


title: DNA_GO2_sc39


title: DNA_GO2_sc36


title: DNA_GO2_sc35


title: DNA_GO2_sc33


title: DNA_GO2_sc34


title: DNA_FGO_sc6


title: DNA_GO2_sc30


title: DNA_FGO_sc7


title: DNA_GO2_sc40


title: DNA_GO2_sc27


title: DNA_GO2_sc31


title: DNA_GO2_sc37


title: DNA_GO2_sc28


title: DNA_GO2_sc25


title: DNA_GO2_sc24


title: DNA_GO2_sc26


title: DNA_GO2_sc22


title: DNA_GO2_sc21


title: DNA_GO2_sc20


title: DNA_GO2_sc18


title: DNA_GO2_sc17


title: DNA_GO2_sc16


title: DNA_GO2_sc23


title: DNA_GO2_sc13


title: DNA_GO2_sc11


title: DNA_GO2_sc10


title: DNA_GO2_sc14


title: DNA_GO2_sc12


title: DNA_GO2_sc19


title: DNA_GO2_sc32


title: DNA_GO2_sc29


title: DNA_GO2_sc8


title: DNA_GO2_sc9


title: DNA_GO2_sc5


title: DNA_GO2_sc6


title: DNA_GO2_sc4


title: DNA_GO2_sc7


title: DNA_GO2_sc1


title: DNA_GO1_sc40


title: DNA_GO2_sc3


title: DNA_GO1_sc39


title: DNA_GO2_sc2


title: DNA_GO1_sc38


title: DNA_GO1_sc37


title: DNA_GO1_sc35


title: DNA_GO1_sc36


title: DNA_GO2_sc15


title: DNA_GO1_sc34


title: DNA_GO1_sc33


title: DNA_GO1_sc31


title: DNA_GO1_sc29


title: DNA_GO1_sc32


title: DNA_GO1_sc28


title: DNA_GO1_sc27


title: DNA_GO1_sc26


title: DNA_GO1_sc25


title: DNA_GO1_sc24


title: DNA_GO1_sc21


title: DNA_GO1_sc20


title: DNA_GO1_sc30


title: DNA_GO1_sc22


title: DNA_GO1_sc17


title: DNA_GO1_sc14


title: DNA_GO1_sc15


title: DNA_GO1_sc18


title: DNA_GO1_sc16


title: DNA_GO1_sc13


title: DNA_GO1_sc10


title: DNA_GO1_sc19


title: DNA_GO1_sc11


title: DNA_GO1_sc9


title: DNA_GO1_sc8


title: DNA_GO1_sc7


title: DNA_GO1_sc12


title: DNA_GO1_sc2


title: DNA_GO1_sc5


title: DNA_GO1_sc1


title: Vec_PHF8_ChIP

city: Shanghai

first: Jian

last: Chen

address: 507 Zhengmin Road

department: Department of thoracic Surgery

institute: Shanghai pulmonary Hospital

data_processing:
All ChIP-seq reads were aligned to the hg38 reference human genome by Bowtie 2 (version 2.2.9)
Enriched PHF8 occupancies were called using MACS (version 2.0) with default settings. And the -B --trackline settings were used for  generating the bedGraph files.
The enriched regions were annotated using the annotatePeaks package from the HOMER suite
Supplementary_files_format_and_content: bedGraph, peaks bed

source_name: RKO cell line

growth_protocol: RKO cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco), L-glutamine, and appropriate antibiotics. Cell cultures were maintained in a 5% CO2 humidified incubator at 37℃.

extract_protocol:
ChIP was performed using the ChIP-IT High Sensitivity (HS) Kit (Active Motif 53040) according to the manufacturer’s recommended protocol.
ChIP-seq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode C05010014) and the Agencourt AMPure XP system (Beckman Coulter A63880) was used to select 350–550 bp libraries. Sequencing was carried out on the Illumina HiSeq Xten platform.

treatment_protocol: RKO cells were transfected with vector or APOC2 overexpression plasmid.

value: vector

tag: cell line

value: RKO cell line

tag: chip antibody


title: APOC2_OV_PHF8_ChIP

value: APOC2 overexpression


title: DNA_GO1_sc3


title: KO_non-Treg

city: Pohang

first: Soeun

last: Kim

address: 77, Cheongam-ro

country: South Korea

institute: POSTECH

description: TCR alpha and beta chain were separately sequenced for a sample. Raw file containing "CGCTCT" in its name is sequencing for alpha chain and "AGCAGC" for beta chain.

data_processing:
Sequencing raw data were analyzed using the iRmap program. Briefly, Sequence reads were de-multiplexed according to both Illumina dual indices incorporated during the amplification process and barcode sequences at the 5’ end of reads from the constant region.
Reads were then trimmed according to their base qualities with a 2-basesliding window. If either quality value in this window is lower than 20, this sequence stretches from the window to 3’ end was trimmed out from the original read.
Trimmed pair-end reads were joined together through overlapping alignment with a modified Needleman-Wunsch algorithm. If paired forward and reverse reads in the overlapping region were not perfectly matched, both forward and reverse reads were thrown out without further consideration.
The merged reads were mapped using a Smith-Waterman algorithm to germline V, D, J and C reference sequences using an IMGT reference library.
To define the complementarity determining regions 3 (CDR3s) region, the position of CDR3 boundaries of reference sequences from the IMGT database was migrated onto reads through mapping results, and the resulting CDR3 regions were extracted and translated into amino acids.
Genome_build: IMGT database (http://www.imgt.org/)
Supplementary_files_format_and_content: The frequency of CDR3 length of alpha and beta chain between samples are presented in CDR3_length_freq_GEO.xlsx file. The list of CDR3, V and J chain used for each CDR3 sequence, and its frequency are presented in each csv file. CTRL_non-Treg alpha chain, 124882_CDR3_list_2.csv; CTRL_non-Treg beta chain, 124879_CDR3_list_2.csv; KO_non-Treg alpha chain, 124881_CDR3_list_2.csv; KO_non-Treg beta chain, 124880_CDR3_list_2.csv; CTRL_Treg alpha chain, 124845_CDR3_list_2.csv; CTRL_Treg beta chain, 124841_CDR3_list_2.csv; KO_Treg alpha chain, 124848_CDR3_list_2.csv; KO_Treg beta chain, 124844_CDR3_list_2.csv.

organism: Mus musculus

source_name: non-Treg (CD4+CD8-GFP-) cells

extract_protocol:
Thymus from each mouse was dissected and homogenized into single-cell suspensions for cell sorting. Treg (CD4+CD8-CD25+GFP+) and non-Treg (CD4+CD8-GFP-) cells were sorted by a MoFlo-XDP (Beckman Coulter) and total RNA was extracted with RiboEx (GeneAll, Seoul, Republic of Korea) according to the manufacturer's protocol.
Reverse transcription and subsequent PCR amplification (RT-PCR1) is performed using Qiagen OneStep RT PCR mix (Qiagen). The cDNA is selected and unused primer is removed by SPRIselect bead selection (Beckman Coulter) followed by a second round of amplification performed with a pair of primers that are specific for communal sites engineered onto the 5’ end of the C- and V- primers used during RT-PCR1. The final constructed library includes Illumina sequencing adapters and a 6-nucleotide internal barcode associated with the C-gene primer.

value: thymus

tag: age


title: CTRL_Treg

description: TCR alpha and beta chain were separately sequenced for a sample. Raw file containing "TGACTA" in its name is sequencing for alpha chain and "TGTATC" for beta chain.

source_name: Treg (CD4+CD8-CD25+GFP+) cells


title: CTRL_non-Treg

description: TCR alpha and beta chain were separately sequenced for a sample. Raw file containing "GTGTCA" in its name is sequencing for alpha chain and "TACGTA" for beta chain.


title: hMONO_R848_20h_ChIP_OCT2_D1

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
To avoid effects derived from different reads lengths, reads were truncated to 51bp using fastx_trimmer from the FASTX-toolkit. Trimmed reads were mapped to the human genome using Bowtie2 v2.3.5.1 with default parameters, and deduplication was performed with markdup of Sambamba v0.6.7. Only reads mapping to the nuclear genome were kept for downstream analyses.
PU.1, C/EBPb and OCT2 peaks were identified using MACS2 v2.2.6 with the following parameters –gsize hs -p 1e-4 –fix-bimodal –call-summits, peaks that overlap with ENCODE blacklist regions were removed with bedtools v2.26.0. ChIP-seq biological with the following parameters -r biological -s 1E-10 -w 1E-6 -m Highest -c 2 replicates peaks were then combined using MSPC
H3K27Ac-enriched regions were identified by MACS2 with parameters –gsize hs  --broad –broad-cutoff 0.1 –nomodel –extsize 146. Peaks overlapping ENCODE blacklist regions were removed and biological replicates were combined by MSPC to construct consensus peaks. Consensus H3K27Ac coordinates were re-centered to the best nucleosome free regions (NFR) within a 200 bp window, using the command “getPeakTags –nfr”, and then resized to 2 kb
Differential H3K27ac occupancy and TFs binding (|log2[fold change]|>1)  and false discovery rare < 0.01 was performed using Bioconductor/R DiffBind v2.14.
Genome_build: Genome Reference Consortium GRCh38, Dec/2013
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated using HOMER

source_name: human CD14+ monocytes

growth_protocol: Granulocytes were isolated from buffy coats of healthy donors and manipulated under endotoxin-free conditions. After Ficoll-Plaque gradient centrifugation, followed by dextran sedimentation and hypotonic lysis of erythrocytes, neutrophils were isolated to reach 99.7 ± 0.2 % purity, by positively removing any eventual contaminating cells using the EasySep neutrophil enrichment kit (StemCell Technology, Vancouver, Canada). Neutrophils were then suspend at 5x106/ml in RPMI 1640 medium supplemented with 10 % low endotoxin FBS (< 0.5 EU/ml; from Sigma, Saint Louis, MO, USA),

extract_protocol:
Protein-DNA cross-linking was achieved by incubating 2.5x106 (for histone modification ChIP), or 107 (for TF ChIP), neutrophils with 1 % formaldehyde for 10 min at room T, under gentle agitation. Cross-linking reaction was stopped by adding glycine to a final concentration of 125 mM, and incubating cells at room T for five more minutes. After fixation, cells were washed with ice-cold PBS, collected by scraping, and finally pelleted by centrifugation (5 min, 300xg, 4°C). Pellets were suspended in 900 l L1 lysis buffer (50 mM Tris, pH 8.0, 2 mM EDTA, 0.1 % IGEPAL, 10 % glycerol) containing protease inhibitors. Nuclei were pelleted at 1000xg at 4°C and resuspended in 300 l L2 lysis buffer (50 mM Tris, pH 8.0, 1 % SDS, 5 mM EDTA) including protease inhibitors. Chromatin was sheared to an average DNA size of 300-400 bp by sonication on wet ice [6 pulses of 15 seconds at the 50 % maximum potency, with 15 second pauses, using a BANDELIN SONOPLUS ultrasonic homogenizers HD 2070 (Bandelin, Berlin, Germany)]. Lysates were then cleared by centrifugation to remove debris (10 min, 13000xg, 12°C), and diluted 10x in dilution buffer (50 mM Tris, 5 mM EDTA, 200 mM, 0.5 % IGEPAL). Immunoprecipitations were carried out overnight at 4°C using 5 µg/ml antibodies. Immune complexes were then collected by adding 15 µl of protein A sepharose-coupled magnetics beads (GE Healthcare, Piscataway, NJ, USA) for 1 h at 4°C under gentle rotation. Beads were then immobilized on a magnetic support and washed three times in washing buffer (20 mM Tris, pH 8.0, 0.1 % SDS, 2 mM EDTA, 1% IGEPAL, 500 mM NaCl) and once in TE. The resulting protein complexes were then eluted in TE containing 2 % SDS, and reversed crosslinked by an overnight incubation at 65°C. The DNA was purified by QiaQuick PCR purification kit (Qiagen) according to the manufacturer’s instructions, and eluted in 50-100 µl.
ChIP DNA was prepared for HiSeq2000 and NextSeq 500 sequencing following TruSeq DNA sample preparation guide (Illumina, Cambridge, UK). In brief, 10-50 ng purified DNA from chromatin immunoprecipitation were adapter-ligated and PCR-amplified according to the manufacturer’s protocol (Illumina).

treatment_protocol: Neutrophils were treated or not with  5 µM R848, seated either in 6/24-well tissue culture plates or in polystyrene flasks (Greiner Bio-One, Kremsmüster, Austria), and cultured at 37°, 5 % CO2 atmosphere.

value: Anti-OCT2 (sc-233)

tag: time

tag: cell type

value: monocyte


title: hMONO_UT_20h_ChIP_OCT2_D1

value: no treatment


title: hPMN_UT_20h_ChIP_OCT2_D1

source_name: human neutrophil

value: neutrophil


title: hPMN_UT_20h_ChIP_H3K27ac_D1

value: Anti-H3K27Ac (Abcam # ab4729)


title: DNA_GO1_sc6


title: hPMN_R848_20h_ChIP_OCT2_D1


title: hPMN_R848_20h_ChIP_CEBPb_D1

value: Anti-C/EBPβ (sc-150)


title: hPMN_R848_20h_ChIP_H3K27ac_D1


title: hPMN_R848_20h_ChIP_PU.1_D1


title: hPMN_UT_20h_ChIP_PU.1_D1


title: hPMN_R848_6h_ChIP_H3K27ac_D1

value: 6 h


title: hPMN_UT_20h_ChIP_CEBPB_D1


title: hPMN_UT_6h_ChIP_H3K27ac_D1


title: DNA_GO1_sc4


title: CLL [G90687_GCLL-0199-T-02]

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

description: RRBS

data_processing:
Libraries were sequenced and aligned to the bisulfite-converted hg19 reference genome using Bismark v0.15.0 (Krueger et al., 2011) and the original methylation sites were inferred based on cytosine-to-thymine conversion.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Methyl call files are in .txt format.

source_name: CLL cells

extract_protocol:
Genomic DNA was isolated and quantified using previously described methods (Boyle et al., 2012).
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.

value: Chronic lymphocytic leukemia

tag: time point

value: After treatment


title: CLL [G90691_GCLL-0313-T-02]

description: RRBS


title: CLL [G90692_GCLL-0105-T-02]

description: RRBS


title: KO_Treg

description: TCR alpha and beta chain were separately sequenced for a sample. Raw file containing "ACTCAT" in its name is sequencing for alpha chain and "ACGTAC" for beta chain.


title: CLL [G90684_GCLL-0287-T-02]

description: RRBS


title: CLL [G90682_GCLL-0236-T-02]

description: RRBS


title: CLL [G90680_GCLL-0157-T-02]

description: RRBS


title: CLL [G90688_GCLL-0042-T-02]

description: RRBS


title: CLL [G90690_GCLL-0115-T-02]

description: RRBS


title: CLL [G90686_GCLL-0125-T-02]

description: RRBS


title: CLL [G90677_GCLL-0265-T-02]

description: RRBS


title: CLL [G90678_GCLL-0237-T-02]

description: RRBS


title: CLL [G90681_GCLL-0048-T-02]

description: RRBS


title: CLL [G90673_GCLL-0135-T-02]

description: RRBS


title: CLL [G90675_GCLL-0164-T-02]

description: RRBS


title: CLL [G90670_GCLL-0255-T-02]

description: RRBS


title: CLL [G90669_GCLL-0257-T-02]

description: RRBS


title: CLL [G90668_GCLL-0260-T-02]

description: RRBS


title: CLL [G90664_GCLL-0192-T-02]

description: RRBS


title: CLL [G90666_GCLL-0233-T-02]

description: RRBS


title: CLL [G90662_GCLL-0186-T-02]

description: RRBS


title: CLL [G90665_GCLL-0071-T-02]

description: RRBS


title: CLL [G90660_GCLL-0068-T-02]

description: RRBS


title: CLL [G90661_GCLL-0285-T-02]

description: RRBS


title: CLL [G90657_GCLL-0168-T-02]

description: RRBS


title: CLL [G90658_GCLL-0142-T-02]

description: RRBS


title: CLL [G90654_GCLL-0101-T-02]

description: RRBS


title: CLL [G90652_GCLL-0146-T-02]

description: RRBS


title: CLL [G90655_GCLL-0060-T-02]

description: RRBS


title: CLL [G90649_GCLL-0289-T-02]

description: RRBS


title: CLL [G90651_GCLL-0176-T-02]

description: RRBS


title: CLL [G90650_GCLL-0182-T-02]

description: RRBS


title: CLL [G90656_GCLL-0049-T-02]

description: RRBS


title: CLL [G90643_GCLL-0024-T-02]

description: RRBS


title: CLL [G90642_GCLL-0208-T-02]

description: RRBS


title: CLL [G90641_GCLL-0011-T-02]

description: RRBS


title: CLL [G90648_GCLL-0017-T-02]

description: RRBS


title: CLL [G90644_GCLL-0286-T-02]

description: RRBS


title: CLL [G90638_GCLL-0022-T-02]

description: RRBS


title: CLL [G90645_GCLL-0085-T-02]

description: RRBS


title: CLL [G90647_GCLL-0166-T-02]

description: RRBS


title: CLL [G90635_GCLL-0045-T-02]

description: RRBS


title: CLL [G90663_GCLL-0089-T-02]

description: RRBS


title: CLL [G88566_GCLL-0259-T-02]

description: RRBS


title: CLL [G88565_GCLL-0106-T-02]

description: RRBS


title: CLL [G88563_GCLL-0132_UNKNOWN_T-02]

description: RRBS


title: CLL [G90646_GCLL-0263-T-02]

description: RRBS


title: CLL [G88561_GCLL-0252-T-02]

description: RRBS


title: CLL [G88560_GCLL-0009-T-02]

description: RRBS


title: CLL [G88558_GCLL-0304-T-02]

description: RRBS


title: CLL [G88556_GCLL-0311-T-02]

description: RRBS


title: CLL [G88548_GCLL-0314-T-02]

description: RRBS


title: CLL [G88554_GCLL-0082-T-02]

description: RRBS


title: CLL [G88546_GCLL-0080-T-02]

description: RRBS


title: CLL [G90636_GCLL-0103-T-02]

description: RRBS


title: CLL [G88545_GCLL-0153-T-02]

description: RRBS


title: CLL [G88567_GCLL-0299-T-02]

description: RRBS


title: CLL [G88535_GCLL-0300-T-02]

description: RRBS


title: CLL [G88541_GCLL-0066-T-02]

description: RRBS


title: CLL [G88540_GCLL-0057-T-02]

description: RRBS


title: CLL [G88542_GCLL-0016-T-02]

description: RRBS


title: CLL [G88544_GCLL-0026-T-02]

description: RRBS


title: CLL [G88530_GCLL-0184-T-02]

description: RRBS


title: CLL [G88547_GCLL-0167-T-02]

description: RRBS


title: CLL [G88528_GCLL-0218-T-02]

description: RRBS


title: CLL [G88543_GCLL-0190-T-02]

description: RRBS


title: CLL [G88532_GCLL-0308-T-02]

description: RRBS


title: CLL [G88529_GCLL-0296-T-02]

description: RRBS


title: CLL [G88534_GCLL-0290-T-02]

description: RRBS


title: CLL [G88559_GCLL-0015-T-02]

description: RRBS


title: CLL [G88526_GCLL-0150-T-02]

description: RRBS


title: CLL [G88527_GCLL-0183-T-02]

description: RRBS


title: CLL [G88525_GCLL-0297-T-02]

description: RRBS


title: CLL [G88557_GCLL-0309-T-02]

description: RRBS


title: CLL [G88521_GCLL-0293-T-02]

description: RRBS


title: CLL [G88520_GCLL-0148-T-02]

description: RRBS


title: CLL [G88518_GCLL-0277-T-02]

description: RRBS


title: CLL [G88519_GCLL-0305-T-02]

description: RRBS


title: CLL [G88516_GCLL-0307-T-02]

description: RRBS


title: CLL [G88515_GCLL-0084-T-02]

description: RRBS


title: CLL [G88513_GCLL-0306-T-02]

description: RRBS


title: CLL [G88511_GCLL-0295-T-02]

description: RRBS


title: CLL [G88510_GCLL-0298-T-02]

description: RRBS


title: CLL [G88508_GCLL-0204-T-02]

description: RRBS


title: CLL [G88507_GCLL-0294-T-02]

description: RRBS


title: CLL [G88506_GCLL-0123-T-02]

description: RRBS


title: CLL [G77967_GCLL-0237-T-02]

description: RRBS


title: CLL [G77967_GCLL-0233-T-02]

description: RRBS


title: CLL [G77967_GCLL-0236-T-02]

description: RRBS


title: CLL [G77967_GCLL-0101-T-02]

description: RRBS


title: CLL [G77967_GCLL-0142-T-02]

description: RRBS


title: CLL [G77967_GCLL-0089-T-02]

description: RRBS


title: CLL [G77967_GCLL-0164-T-02]

description: RRBS


title: CLL [G90634_GCLL-0313-T-01]

description: RRBS

value: Before treatment


title: CLL [G77967_GCLL-0176-T-02]

description: RRBS


title: CLL [G77967_GCLL-0071-T-02]

description: RRBS


title: CLL [G90632_GCLL-0310-T-01]

description: RRBS


title: CLL [G90631_GCLL-0309-T-01]

description: RRBS


title: CLL [G90629_GCLL-0307-T-01]

description: RRBS


title: CLL [G90628_GCLL-0306-T-01]

description: RRBS


title: CLL [G90633_GCLL-0311-T-01]

description: RRBS


title: CLL [G90627_GCLL-0305-T-01]

description: RRBS


title: CLL [G90625_GCLL-0303-T-01]

description: RRBS


title: CLL [G88512_GCLL-0027-T-02]

description: RRBS


title: CLL [G90624_GCLL-0302-T-01]

description: RRBS


title: CLL [G90626_GCLL-0304-T-01]

description: RRBS


title: CLL [G90623_GCLL-0301-T-01]

description: RRBS


title: CLL [G90622_GCLL-0300-T-01]

description: RRBS


title: CLL [G90621_GCLL-0299-T-01]

description: RRBS


title: CLL [G90620_GCLL-0298-T-01]

description: RRBS


title: CLL [G90618_GCLL-0296-T-01]

description: RRBS


title: CLL [G77967_GCLL-0042-T-02]

description: RRBS


title: CLL [G90619_GCLL-0297-T-01]

description: RRBS


title: CLL [G90615_GCLL-0293-T-01]

description: RRBS


title: CLL [G90616_GCLL-0294-T-01]

description: RRBS


title: CLL [G90614_GCLL-0291-T-01]

description: RRBS


title: CLL [G90613_GCLL-0290-T-01]

description: RRBS


title: CLL [G77967_GCLL-0264-T-01]

description: RRBS


title: CLL [G88552_GCLL-0314-T-01]

description: RRBS


title: CLL [G90630_GCLL-0308-T-01]

description: RRBS


title: CLL [G77967_GCLL-0250-T-01]

description: RRBS


title: CLL [G77967_GCLL-0255-T-01]

description: RRBS


title: CLL [G77967_GCLL-0252-T-01]

description: RRBS


title: CLL [G77967_GCLL-0253-T-01]

description: RRBS


title: CLL [G77967_GCLL-0245-T-01]

description: RRBS


title: CLL [G77967_GCLL-0254-T-01]

description: RRBS


title: CLL [G77967_GCLL-0249-T-01]

description: RRBS


title: CLL [G77967_GCLL-0243-T-01]

description: RRBS


title: CLL [G77967_GCLL-0242-T-01]

description: RRBS


title: CLL [G77967_GCLL-0241-T-01]

description: RRBS


title: CLL [G77967_GCLL-0239-T-01]

description: RRBS


title: CLL [G77967_GCLL-0237-T-01]

description: RRBS


title: CLL [G77967_GCLL-0238-T-01]

description: RRBS


title: CLL [G77967_GCLL-0236-T-01]

description: RRBS


title: CLL [G90617_GCLL-0295-T-01]

description: RRBS


title: CLL [G77967_GCLL-0234-T-01]

description: RRBS


title: CLL [G77967_GCLL-0233-T-01]

description: RRBS


title: CLL [G77967_GCLL-0232-T-01]

description: RRBS


title: CLL [G77967_GCLL-0231-T-01]

description: RRBS


title: CLL [G77967_GCLL-0230-T-01]

description: RRBS


title: CLL [G77967_GCLL-0225-T-01]

description: RRBS


title: CLL [G77967_GCLL-0223-T-01]

description: RRBS


title: CLL [G77967_GCLL-0224-T-01]

description: RRBS


title: CLL [G77967_GCLL-0244-T-01]

description: RRBS


title: CLL [G77967_GCLL-0221-T-01]

description: RRBS


title: CLL [G77967_GCLL-0222-T-01]

description: RRBS


title: CLL [G77967_GCLL-0220-T-01]

description: RRBS


title: CLL [G77967_GCLL-0219-T-01]

description: RRBS


title: CLL [G77967_GCLL-0229-T-01]

description: RRBS


title: CLL [G77967_GCLL-0217-T-01]

description: RRBS


title: CLL [G77967_GCLL-0218-T-01]

description: RRBS


title: CLL [G77967_GCLL-0216-T-01]

description: RRBS


title: CLL [G77967_GCLL-0215-T-01]

description: RRBS


title: CLL [G77967_GCLL-0213-T-01]

description: RRBS


title: CLL [G77967_GCLL-0235-T-01]

description: RRBS


title: CLL [G77967_GCLL-0211-T-01]

description: RRBS


title: CLL [G77967_GCLL-0212-T-01]

description: RRBS


title: CLL [G77967_GCLL-0210-T-01]

description: RRBS


title: CLL [G77967_GCLL-0209-T-01]

description: RRBS


title: CLL [G77967_GCLL-0228-T-01]

description: RRBS


title: CLL [G77967_GCLL-0214-T-01]

description: RRBS


title: CLL [G77967_GCLL-0206-T-01]

description: RRBS


title: CLL [G77967_GCLL-0207-T-01]

description: RRBS


title: CLL [G77967_GCLL-0226-T-01]

description: RRBS


title: CLL [G77967_GCLL-0205-T-01]

description: RRBS


title: CLL [G77967_GCLL-0204-T-01]

description: RRBS


title: CLL [G77967_GCLL-0203-T-01]

description: RRBS


title: CLL [G77967_GCLL-0201-T-01]

description: RRBS


title: CLL [G77967_GCLL-0208-T-01]

description: RRBS


title: CLL [G70381_GCLL-0209-T-01]

description: RRBS


title: CLL [G70380_GCLL-0246-T-01]

description: RRBS


title: CLL [G70378_GCLL-0131-T-01]

description: RRBS


title: CLL [G70377_GCLL-0107-T-01]

description: RRBS


title: CLL [G70371_GCLL-0155-T-01]

description: RRBS


title: CLL [G70370_GCLL-0212-T-01]

description: RRBS


title: CLL [G70369_GCLL-0211-T-01]

description: RRBS


title: CLL [G70372_GCLL-0222-T-01]

description: RRBS


title: CLL [G70368_GCLL-0003-T-01]

description: RRBS


title: CLL [G70367_GCLL-0162-T-01]

description: RRBS


title: CLL [G70373_GCLL-0186-T-01]

description: RRBS


title: CLL [G70366_GCLL-0135-T-01]

description: RRBS


title: CLL [G70365_GCLL-0136-T-01]

description: RRBS


title: CLL [G70364_GCLL-0213-T-01]

description: RRBS


title: CLL [G77967_GCLL-0202-T-01]

description: RRBS


title: CLL [G70361_GCLL-0216-T-01]

description: RRBS


title: CLL [G70359_GCLL-0220-T-01]

description: RRBS


title: CLL [G70362_GCLL-0215-T-01]

description: RRBS


title: CLL [G70360_GCLL-0218-T-01]

description: RRBS


title: CLL [G70363_GCLL-0166-T-01]

description: RRBS


title: CLL [G70357_GCLL-0171-T-01]

description: RRBS


title: CLL [G70358_GCLL-0070-T-01]

description: RRBS


title: CLL [G70356_GCLL-0210-T-01]

description: RRBS


title: CLL [G70355_GCLL-0112-T-01]

description: RRBS


title: CLL [G70374_GCLL-0068-T-01]

description: RRBS


title: CLL [G70376_GCLL-0189-T-01]

description: RRBS


title: DNA_GO1_sc23


title: CLL [G70375_GCLL-0289-T-01]

description: RRBS


title: CLL [G70379_GCLL-0261-T-01]

description: RRBS


title: CLL [G70350_GCLL-0072-T-01]

description: RRBS


title: CLL [G70351_GCLL-0223-T-01]

description: RRBS


title: CLL [G70353_GCLL-0031-T-01]

description: RRBS


title: CLL [G70348_GCLL-0141-T-01]

description: RRBS


title: CLL [G70345_GCLL-0074-T-01]

description: RRBS


title: CLL [G70347_GCLL-0226-T-01]

description: RRBS


title: CLL [G70344_GCLL-0139-T-01]

description: RRBS


title: CLL [G70346_GCLL-0255-T-01]

description: RRBS


title: CLL [G70343_GCLL-0153-T-01]

description: RRBS


title: CLL [G70336_GCLL-0230-T-01]

description: RRBS


title: CLL [G70334_GCLL-0098-T-01]

description: RRBS


title: CLL [G70341_GCLL-0142-T-01]

description: RRBS


title: CLL [G70338_GCLL-0042-T-01]

description: RRBS


title: CLL [G70354_GCLL-0221-T-01]

description: RRBS


title: CLL [G70337_GCLL-0228-T-01]

description: RRBS


title: CLL [G70339_GCLL-0158-T-01]

description: RRBS


title: CLL [G70335_GCLL-0034-T-01]

description: RRBS


title: CLL [G70332_GCLL-0039-T-01]

description: RRBS


title: CLL [G70331_GCLL-0046-T-01]

description: RRBS


title: CLL [G70333_GCLL-0077-T-01]

description: RRBS


title: CLL [G70329_GCLL-0231-T-01]

description: RRBS


title: CLL [G70352_GCLL-0138-T-01]

description: RRBS


title: CLL [G70328_GCLL-0236-T-01]

description: RRBS


title: CLL [G70326_GCLL-0144-T-01]

description: RRBS


title: CLL [G70325_GCLL-0056-T-01]

description: RRBS


title: CLL [G70327_GCLL-0266-T-01]

description: RRBS


title: CLL [G70349_GCLL-0281-T-01]

description: RRBS


title: CLL [G70324_GCLL-0146-T-01]

description: RRBS


title: CLL [G70342_GCLL-0253-T-01]

description: RRBS


title: CLL [G70322_GCLL-0272-T-01]

description: RRBS


title: CLL [G70321_GCLL-0147-T-01]

description: RRBS


title: CLL [G70340_GCLL-0214-T-01]

description: RRBS


title: CLL [G70318_GCLL-0149-T-01]

description: RRBS


title: CLL [G70320_GCLL-0201-T-01]

description: RRBS


title: CLL [G70316_GCLL-0054-T-01]

description: RRBS


title: CLL [G70319_GCLL-0224-T-01]

description: RRBS


title: CLL [G70317_GCLL-0048-T-01]

description: RRBS


title: CLL [G70330_GCLL-0173-T-01]

description: RRBS


title: CLL [G70313_GCLL-0015-T-01]

description: RRBS


title: CLL [G70311_GCLL-0082-T-01]

description: RRBS


title: CLL [G70309_GCLL-0012-T-01]

description: RRBS


title: CLL [G70308_GCLL-0185-T-01]

description: RRBS


title: CLL [G70315_GCLL-0081-T-01]

description: RRBS


title: CLL [G70306_GCLL-0097-T-01]

description: RRBS


title: CLL [G70310_GCLL-0007-T-01]

description: RRBS


title: CLL [G70314_GCLL-0001-T-01]

description: RRBS


title: CLL [G70307_GCLL-0111-T-01]

description: RRBS


title: CLL [G70302_GCLL-0157-T-01]

description: RRBS


title: CLL [G70303_GCLL-0151-T-01]

description: RRBS


title: CLL [G70305_GCLL-0238-T-01]

description: RRBS


title: CLL [G70304_GCLL-0150-T-01]

description: RRBS


title: CLL [G70323_GCLL-0237-T-01]

description: RRBS


title: CLL [G70300_GCLL-0256-T-01]

description: RRBS


title: CLL [G70299_GCLL-0127-T-01]

description: RRBS


title: CLL [G70301_GCLL-0002-T-01]

description: RRBS


title: CLL [G70298_GCLL-0229-T-01]

description: RRBS


title: CLL [G70297_GCLL-0160-T-01]

description: RRBS


title: CLL [G70296_GCLL-0004-T-01]

description: RRBS


title: CLL [G70294_GCLL-0234-T-01]

description: RRBS


title: CLL [G70293_GCLL-0125-T-01]

description: RRBS


title: CLL [G70292_GCLL-0073-T-01]

description: RRBS


title: CLL [G70290_GCLL-0052-T-01]

description: RRBS


title: CLL [G70289_GCLL-0143-T-01]

description: RRBS


title: CLL [G70291_GCLL-0240-T-01]

description: RRBS


title: CLL [G70295_GCLL-0043-T-01]

description: RRBS


title: CLL [G70288_GCLL-0257-T-01]

description: RRBS


title: CLL [G70312_GCLL-0225-T-01]

description: RRBS


title: CLL [G70281_GCLL-0164-T-01]

description: RRBS


title: CLL [G70280_GCLL-0050-T-01]

description: RRBS


title: CLL [G70284_GCLL-0161-T-01]

description: RRBS


title: CLL [G70283_GCLL-0006-T-01]

description: RRBS


title: CLL [G70282_GCLL-0163-T-01]

description: RRBS


title: CLL [G70285_GCLL-0235-T-01]

description: RRBS


title: CLL [G70287_GCLL-0036-T-01]

description: RRBS


title: CLL [G70286_GCLL-0075-T-01]

description: RRBS


title: CLL [G70276_GCLL-0010-T-01]

description: RRBS


title: CLL [G70279_GCLL-0239-T-01]

description: RRBS


title: CLL [G70277_GCLL-0028-T-01]

description: RRBS


title: CLL [G70278_GCLL-0009-T-01]

description: RRBS


title: CLL [G70272_GCLL-0192-T-01]

description: RRBS


title: CLL [G70270_GCLL-0083-T-01]

description: RRBS


title: CLL [G70275_GCLL-0019-T-01]

description: RRBS


title: CLL [G70273_GCLL-0011-T-01]

description: RRBS


title: CLL [G70274_GCLL-0023-T-01]

description: RRBS


title: CLL [G70269_GCLL-0117-T-01]

description: RRBS


title: CLL [G70267_GCLL-0242-T-01]

description: RRBS


title: CLL [G70263_GCLL-0190-T-01]

description: RRBS


title: CLL [G70268_GCLL-0013-T-01]

description: RRBS


title: CLL [G70261_GCLL-0014-T-01]

description: RRBS


title: CLL [G70266_GCLL-0022-T-01]

description: RRBS


title: CLL [G70264_GCLL-0250-T-01]

description: RRBS


title: CLL [G70262_GCLL-0118-T-01]

description: RRBS


title: CLL [G70265_GCLL-0244-T-01]

description: RRBS


title: CLL [G70258_GCLL-0024-T-01]

description: RRBS


title: CLL [G70259_GCLL-0020-T-01]

description: RRBS


title: CLL [G70260_GCLL-0018-T-01]

description: RRBS


title: CLL [G70257_GCLL-0085-T-01]

description: RRBS


title: CLL [G70271_GCLL-0241-T-01]

description: RRBS


title: CLL [G70254_GCLL-0025-T-01]

description: RRBS


title: CLL [G70241_GCLL-0243-T-01]

description: RRBS


title: CLL [G70243_GCLL-0258-T-01]

description: RRBS


title: CLL [G70242_GCLL-0121-T-01]

description: RRBS


title: CLL [G70240_GCLL-0093-T-01]

description: RRBS


title: CLL [G70251_GCLL-0079-T-01]

description: RRBS


title: CLL [G70255_GCLL-0177-T-01]

description: RRBS


title: CLL [G70246_GCLL-0092-T-01]

description: RRBS


title: CLL [G70245_GCLL-0232-T-01]

description: RRBS


title: CLL [G70252_GCLL-0251-T-01]

description: RRBS


title: CLL [G70249_GCLL-0252-T-01]

description: RRBS


title: CLL [G70244_GCLL-0165-T-01]

description: RRBS


title: CLL [G70238_GCLL-0268-T-01]

description: RRBS


title: CLL [G70237_GCLL-0260-T-01]

description: RRBS


title: CLL [G70233_GCLL-0026-T-01]

description: RRBS


title: CLL [G70247_GCLL-0067-T-01]

description: RRBS


title: CLL [G70235_GCLL-0063-T-01]

description: RRBS


title: CLL [G70236_GCLL-0095-T-01]

description: RRBS


title: CLL [G70256_GCLL-0078-T-01]

description: RRBS


title: CLL [G70253_GCLL-0087-T-01]

description: RRBS


title: CLL [G70239_GCLL-0259-T-01]

description: RRBS


title: CLL [G70248_GCLL-0089-T-01]

description: RRBS


title: CLL [G70234_GCLL-0140-T-01]

description: RRBS


title: CLL [G70231_GCLL-0106-T-01]

description: RRBS


title: CLL [G70250_GCLL-0080-T-01]

description: RRBS


title: CLL [G70228_GCLL-0262-T-01]

description: RRBS


title: CLL [G70232_GCLL-0167-T-01]

description: RRBS


title: CLL [G70227_GCLL-0109-T-01]

description: RRBS


title: CLL [G70229_GCLL-0096-T-01]

description: RRBS


title: CLL [G70230_GCLL-0027-T-01]

description: RRBS


title: CLL [G70223_GCLL-0132-T-01]

description: RRBS


title: CLL [G70214_GCLL-0265-T-01]

description: RRBS


title: CLL [G70224_GCLL-0099-T-01]

description: RRBS


title: CLL [G70213_GCLL-0267-T-01]

description: RRBS


title: CLL [G70216_GCLL-0029-T-01]

description: RRBS


title: CLL [G70222_GCLL-0100-T-01]

description: RRBS


title: CLL [G70207_GCLL-0174-T-01]

description: RRBS


title: CLL [G70215_GCLL-0172-T-01]

description: RRBS


title: CLL [G70206_GCLL-0254-T-01]

description: RRBS


title: CLL [G70208_GCLL-0035-T-01]

description: RRBS


title: CLL [G70219_GCLL-0201-T-01]

description: RRBS


title: CLL [G70204_GCLL-0176-T-01]

description: RRBS


title: CLL [G70217_GCLL-0168-T-01]

description: RRBS


title: CLL [G70221_GCLL-0044-T-01]

description: RRBS


title: CLL [G70218_GCLL-0102-T-01]

description: RRBS


title: CLL [G70225_GCLL-0091-T-01]

description: RRBS


title: CLL [G70205_GCLL-0037-T-01]

description: RRBS


title: CLL [G70211_GCLL-0071-T-01]

description: RRBS


title: CLL [G70226_GCLL-0152-T-01]

description: RRBS


title: CLL [G70209_GCLL-0032-T-01]

description: RRBS


title: CLL [G70203_GCLL-0178-T-01]

description: RRBS


title: CLL [G70202_GCLL-0069-T-01]

description: RRBS


title: CLL [G70201_GCLL-0103-T-01]

description: RRBS


title: CLL [G70199_GCLL-0156-T-01]

description: RRBS


title: CLL [G70200_GCLL-0196-T-01]

description: RRBS


title: CLL [G70220_GCLL-0264-T-01]

description: RRBS


title: CLL [G70212_GCLL-0084-T-01]

description: RRBS


title: CLL [G70210_GCLL-0030-T-01]

description: RRBS


title: CLL [G70198_GCLL-0269-T-01]

description: RRBS


title: CLL [G70197_GCLL-0263-T-01]

description: RRBS


title: CLL [G70196_GCLL-0133-T-01]

description: RRBS


title: CLL [G70190_GCLL-0104-T-01]

description: RRBS


title: CLL [G70192_GCLL-0016-T-01]

description: RRBS


title: CLL [G70193_GCLL-0008-T-01]

description: RRBS


title: CLL [G70187_GCLL-0194-T-01]

description: RRBS


title: CLL [G70184_GCLL-0040-T-01]

description: RRBS


title: CLL [G70185_GCLL-0288-T-01]

description: RRBS


title: CLL [G70181_GCLL-0154-T-01]

description: RRBS


title: CLL [G70191_GCLL-0273-T-01]

description: RRBS


title: CLL [G70188_GCLL-0227-T-01]

description: RRBS


title: CLL [G70182_GCLL-0183-T-01]

description: RRBS


title: M33942_3

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

data_processing:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA).
PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: CR33942-overexpressing flies 12h post-infection

extract_protocol:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA). PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gal80ts; Tub> NANPI

value: 12 hours after injection of M. luteus

value: adult

tag: Sex

value: male


title: CLL [G70179_GCLL-0270-T-01]

description: RRBS


title: M25C_2

source_name: control flies 12h post-infection

tag: strain

value: Gal80ts; Tub-Gal4/P{CaryP}attP40


title: CLL [G70183_GCLL-0182-T-01]

description: RRBS


title: CLL [G70189_GCLL-0105-T-01]

description: RRBS


title: M25C_3


title: M33942_2


title: M25C_1


title: CLL [G70180_GCLL-0181-T-01]

description: RRBS


title: M33942_1


title: Imida-S3

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

data_processing:
After unplexing and removing adaptors FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used on each sample to assess reads quality.
After unplexing and removing adaptors reads quality was checked for each sample using FastQC. Reads were then filtered based on their length, pairing and quality using Trimmomatic (Bolger et al. 2014). Parameters were set as follows: read length ≥ 76 bp; mean Phred quality score > 30; Phred quality score > 30 across all read (10 bp sliding window).
Trimmed reads (only paired reads) were then mapped to Ae. aegypti genome (AaegL5 assembly) using Strand NGS V2.2 (Strand Life Sciences).
Genome_build: AaegL5 assembly
Supplementary_files_format_and_content: Strand-NGS file of normalized RPKM

organism: Aedes aegypti

source_name: Whole body

extract_protocol:
Three pools of thirty 4th stage larvae from each line (Imida-R, Imida-S and Bora-Bora) not exposed to insecticide were used for RNA extractions using the RNAqueous-4PCR kit (Life technologies) according to manufacturer’s instructions.
Three RNA-seq libraries were prepared per line using the TruSeq Stranded mRNA sample Prep kit (Illumina) following manufacturer’s instructions. After quality check, libraries were sequenced (paired reads) in multiplex on an Illumina GAIIx sequencer by Hybrigenics-Helixio (Clermont-Ferrand, France).

tag: common name

value: yellow fever mosquito

value: Imida-S line

tag: develpment stage

value: 4th stage Larvae


title: CLL [G70178_GCLL-0271-T-01]

description: RRBS

tag: tissue


title: CLL [G70195_GCLL-0179-T-01]

description: RRBS


title: Imida-S2


title: CLL [G70194_GCLL-0180-T-01]

description: RRBS


title: CLL [G70186_GCLL-0038-T-01]

description: RRBS


title: CLL [G70177_GCLL-0249-T-01]

description: RRBS


title: Imida-S1


title: CLL [G70176_GCLL-0101-T-01]

description: RRBS


title: CLL [G70173_GCLL-0128-T-01]

description: RRBS


title: CLL [G70174_GCLL-0041-T-01]

description: RRBS


title: CLL [G70171_GCLL-0207-T-01]

description: RRBS


title: CLL [G70172_GCLL-0148-T-01]

description: RRBS


title: CLL [G70170_GCLL-0045-T-01]

description: RRBS


title: Imida-R1

value: Imida-R line


title: Imida-R3


title: Bora1

value: Bora bora strain


title: Imida-R2


title: Bora2


title: CLL [G70166_GCLL-0184-T-01]

description: RRBS


title: CLL [G70167_GCLL-0094-T-01]

description: RRBS


title: CLL [G70168_GCLL-0108-T-01]

description: RRBS


title: CLL [G70162_GCLL-0110-T-01]

description: RRBS


title: CLL [G70169_GCLL-0017-T-01]

description: RRBS


title: CLL [G70165_GCLL-0047-T-01]

description: RRBS


title: CLL [G70164_GCLL-0187-T-01]

description: RRBS


title: CLL [G70163_GCLL-0137-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – EtOH 24 hrs – rep 1

city: Duluth

first: Matthew

last: Slattery

state: MN

address: 1035 University Drive, SMed 255

department: Biomedical Sciences

institute: University of Minnesota Medical School

description: 08-24hr-E_merged-rep_nonmito_nodup_tn5.bigWig

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
50 bp paired-end sequencing reads were trimmed for adapter sequence and low-quality ends were removed
Mitochondrial reads were removed with BBMap v38.05
Remaining downstream processing was done using the ENCODE ATAC-seq-pipeline v1.1.4 (https://github.com/ENCODE-DCC/atac-seq-pipeline) with default settings, including macs2 peak-calling and IDR peak threshold of 0.1.  Mapping – bowtie2 v 2.2., map quality filtering > 30 – SAMtools v1.2, duplicate read removal – Picard MarkDuplicates v2.10.6, peak calling – macs2 v2.1.
A final ‘master’ peak list across all conditions was generated by combining: 1) all unique peaks (<50% overlap with any other peak), and 2) a set of merged peaks where any peaks with >50% overlap with another peak were merged using bedops version 2.4.35.
tagAlign files (BED format), with locations for all aligned & filtered reads from the ATAC-seq pipeline, for each sample were converted back to BAM alignment files using the bedToBam command of bedtools version 2.27.1, and read counts for each peak in the final ‘master’ peak list were counted across each sample using the multiBamCov command.
The tagAlign-generated BAM files were combined into merged replicates using the SAMtools (v1.9) merge command and then converted into library size-normalized (counts per million) bigwig tracks using the bamCoverage command of deepTools version 3.3.0.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using Tn5-shifted BAM alignments merged across replicates of the same condition; scores/signal represents library size-normalized (counts per million) signal of these merged replicates
Supplementary_files_format_and_content: Tab-delimited matrix table of all ‘master’ IDR peaks across conditions in narrowpeak format, along with read counts for every sample at each of these regions.  Merged peaks include narrowpeak information for all peaks that were combined using a semicolon delimiter

source_name: Breast cancer cell line

growth_protocol: MCF7 cells were grown and maintained in IMEM culture media (Phenol-red free, Gibco) supplemented with 5% fetal bovine serum, 1% penicillin/streptomycin (Invitrogen-Life technologies), 11.25 nM bovine insulin (Sigma-Aldrich) and 2.5 μg/L Plasmocin prophylactic (InvivoGen, San Diego, CA) in humidified air with ~20% oxygen and 5% carbon dioxide.

extract_protocol:
After treatment, cells were harvested, maintained on wet ice, and counted.  50000 cells / ml was used: first washed in ice cold PBS and resuspended in 50 μL ice cold lysis buffer.  Cells were centrifuged at 500 x G for 10 min at 4°C to generate crude nuclei pellets. The crude nuclei pellet was resuspended in 50 μL Nextera Tn5 reaction buffer and transposase (Nextera cat no 15027865-6).  They were then incubated at 37°C for 30 min at 250 RPM, purified with Qiagen MinElute PCR Purification Kit, eluted in 50 μL buffer EB and stored at -20°C until library preparation and sequencing.
DNA libraries were prepared using standard Illumina protocols for Nextera-tagged DNA

treatment_protocol: MCF7 cells were seeded (125,000 cells/ml) in 6 well plates and grown at 37°C for 24 hrs, after which cells were treated with the growth media supplemented with either 0.1% ethanol, 10 μM MEN, or 80 μM TBOOH for 0, 1, 8, or 24 hrs.

tag: treatment

value: 0.1% ethanol

value: 24 hours

tag: replicate


title: ATAC-seq_MCF7 cells – TBOOH 24 hrs – rep 2

description: 10-24hr-T_merged-rep_nonmito_nodup_tn5.bigWig

value: 80 uM tert-butyl hydroperoxide


title: ATAC-seq_MCF7 cells – TBOOH 8 hrs – rep 2

description: 07-8hr-T_merged-rep_nonmito_nodup_tn5.bigWig

value: 8 hours


title: ATAC-seq_MCF7 cells – EtOH 24 hrs – rep 2


title: ATAC-seq_MCF7 cells – MEN 24 hrs – rep 2

description: 09-24hr-M_merged-rep_nonmito_nodup_tn5.bigWig

value: 10 uM menadione


title: ATAC-seq_MCF7 cells – TBOOH 24 hrs – rep 1


title: ATAC-seq_MCF7 cells – TBOOH 8 hrs – rep 1


title: ATAC-seq_MCF7 cells – MEN 24 hrs – rep 1


title: Bora3


title: ATAC-seq_MCF7 cells – MEN 8 hrs – rep 1

description: 06-8hr-M_merged-rep_nonmito_nodup_tn5.bigWig


title: CLL [G70156_GCLL-0005-T-01]

description: RRBS

value: Chronic lymphocytic leukemia


title: ATAC-seq_MCF7 cells – EtOH 8 hrs – rep 1

description: 05-8hr-E_merged-rep_nonmito_nodup_tn5.bigWig


title: ATAC-seq_MCF7 cells – TBOOH 1 hr – rep 2

description: 04-1hr-T_merged-rep_nonmito_nodup_tn5.bigWig

value: 1 hour


title: ATAC-seq_MCF7 cells – MEN 1 hr – rep 2

description: 03-1hr-M_merged-rep_nonmito_nodup_tn5.bigWig


title: CLL [G70155_GCLL-0122-T-01]

description: RRBS

value: Before treatment


title: CLL [G70175_GCLL-0274-T-01]

description: RRBS


title: CLL [G70161_GCLL-0113-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – MEN 8 hrs – rep 2


title: CLL [G70158_GCLL-0088-T-01]

description: RRBS


title: CLL [G70159_GCLL-0275-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – EtOH 8 hrs – rep 2


title: CLL [G70157_GCLL-0021-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – TBOOH 1 hr – rep 1


title: CLL [G70150_GCLL-0277-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – MEN 1 hr – rep 1


title: CLL [G70149_GCLL-0049-T-01]

description: RRBS


title: CLL [G70160_GCLL-0188-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – EtOH 1 hr – rep 1

description: 02-1hr-E_merged-rep_nonmito_nodup_tn5.bigWig


title: ATAC-seq_MCF7 cells – control 0 hr – rep 1

description: 01-0hr-0_merged-rep_nonmito_nodup_tn5.bigWig

value: untreated

value: 0 hours


title: CLL [G70152_GCLL-0159-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – EtOH 1 hr – rep 2


title: CLL [G70148_GCLL-0278-T-01]

description: RRBS


title: CLL [G70151_GCLL-0276-T-01]

description: RRBS


title: ATAC-seq_MCF7 cells – control 0 hr – rep 2


title: CLL [G70154_GCLL-0245-T-01]

description: RRBS


title: CLL [G70153_GCLL-0114-T-01]

description: RRBS


title: MCF7 cells – TBOOH 24 hrs – rep 1

data_processing:
Illumina Casava1.8 software used for basecalling.
50 bp single-end sequencing reads were directly ‘pseudo-mapped’ to a 25 kmer Gencode v27lift37 transcriptome index using quasi-mapping mode with Salmon v0.10.2 using the following parameters: libtype – A, fldMean – 51, fldSD – 1, seqBias enabled, posBias enabled, useVBOpt enabled, rangeFactorizationBins – 4, numGibbsSamples – 1000.
Genome_build: Gencode human release 27lift37 (comprehensive annotation, GRCh37)
Supplementary_files_format_and_content: Compressed tab-delimited Salmon quantification files (quant.sf.txt) with quantifications for all transcripts (by column): transcript length (Length), effective transcript length (EffectiveLength), abundance (TPM), and read counts (NumReads)

extract_protocol:
After treatment, cells were harvested, maintained on wet ice, pelleted and flash frozen in liquid nitrogen.  Samples were kept on dry ice until Qiagen Rneasy kit (Qiagen, cat no. 74104) was utilized to extract total RNA for RNA-seq.  Samples were stored at -20°C until library preparation and sequencing.
RNA libraries were prepared using standard Illumina protocols, including oligo-dT purification


title: MCF7 cells – MEN 24 hrs – rep 1


title: MCF7 cells – TBOOH 24 hrs – rep 2


title: CLL [G70145_GCLL-0203-T-01]

description: RRBS


title: MCF7 cells – EtOH 24 hrs – rep 1


title: MCF7 cells – EtOH 24 hrs – rep 2


title: MCF7 cells – MEN 24 hrs – rep 2


title: CLL [G70147_GCLL-0116-T-01]

description: RRBS


title: CLL [G70144_GCLL-0233-T-01]

description: RRBS


title: CLL [G70143_GCLL-0051-T-01]

description: RRBS


title: MCF7 cells – TBOOH 8 hrs – rep 1


title: MCF7 cells – MEN 8 hrs – rep 2


title: CLL [G70146_GCLL-0170-T-01]

description: RRBS


title: CLL [G70141_GCLL-0119-T-01]

description: RRBS


title: MCF7 cells – TBOOH 8 hrs – rep 2


title: CLL [G70140_GCLL-0217-T-01]

description: RRBS


title: MCF7 cells – MEN 8 hrs – rep 1


title: MCF7 cells – TBOOH 1 hr – rep 2


title: CLL [G70139_GCLL-0219-T-01]

description: RRBS


title: CLL [G70138_GCLL-0279-T-01]

description: RRBS


title: CLL [G70137_GCLL-0055-T-01]

description: RRBS


title: MCF7 cells – EtOH 8 hrs – rep 1


title: MCF7 cells – EtOH 8 hrs – rep 2


title: MCF7 cells – TBOOH 1 hr – rep 1


title: CLL [G70136_GCLL-0120-T-01]

description: RRBS


title: MCF7 cells – MEN 1 hr – rep 2


title: CLL [G70135_GCLL-0126-T-01]

description: RRBS


title: MCF7 cells – MEN 1 hr – rep 1


title: CLL [G70142_GCLL-0115-T-01]

description: RRBS


title: CLL [G70134_GCLL-0280-T-01]

description: RRBS


title: CLL [G70133_GCLL-0282-T-01]

description: RRBS


title: CLL [G70132_GCLL-0086-T-01]

description: RRBS


title: CLL [G70131_GCLL-0191-T-01]

description: RRBS


title: SKMEL2 Sirt5 Knockdown (shRNA 547) Rep 3

city: Ann Arbor

first: David

middle: B

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Ann Arbor

description: sample ID: 73862

data_processing:
Paired-end reads were assessed for various quality metrics before and after trimming via FastQC v.0.11.9 and MultiQC v.1.9.
Reads were trimmed by Trimmomatic v0.39
Trimmed FASTQ files were aligned by STAR v.2.7.3a (96) in paired-end mode against Gencode (GRCh38 Release 34 primary assembly). For each unique sample, all corresponding FASTQ files (i.e. R1/R2, split lanes) were aligned together in a single STAR call via –readFilesIn to yield single sorted BAM files for each sample.
STAR-output BAM files were subsequently counted by the SubRead v.2.0.0 (97) featureCounts command to yield counts.
Count matrices produced by featureCounts were then supplied to the Bioconductor package DESeq2 v.1.28.1 (98) for differential gene expression analysis.
Genome_build: Gencode (GRCh38 Release 34 primary assembly)
Supplementary_files_format_and_content: FPKM values generated from DESeq2

source_name: SKMEL2 Sirt5 Knockdown (shRNA 547)

growth_protocol: A375, A2058, SK-MEL-2 cell lines were purchased from ATCC and grown according to the provided directions.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) 96 hrs. post-transduction from three wells and treated with RNAse-free DNAse I (Roche) for 1 hour at 37ºC, according to manufacturer’s instructions.
RNA libraries were prepared using standard Illumina protocols by the University of Michigan Ann Arbor Advanced Genomics Core

treatment_protocol: Lentiviral plasmids in the pLKO.1 backbone containing shRNAs targeting human SIRT5 were used to generate high-titer lentiviral particles at the Vector Core (UM). A non-silencing control shRNA against Gaussia luciferase was used as the non-targeting control (NT). Lentiviral transduction was carried out in the presence of 8 µg/ml polybrene in complete growth medium for 24 hrs., after which medium was replaced with fresh complete growth medium. Puromycin was added to a final concentration of 1 µg/ml 48 hrs. post-transduction to select for transductants. Successful SIRT5 KD was routinely confirmed by western blotting 48-96 hrs. post-transduction.

value: Melanoma cell line

value: Sirt5 knockdown shRNA 547


title: MCF7 cells – EtOH 1 hr – rep 2


title: MCF7 cells – control 0 hr – rep 1


title: CLL [G70130_GCLL-0057-T-01]

description: RRBS


title: CLL [G70129_GCLL-0199-T-01]

description: RRBS


title: MCF7 cells – EtOH 1 hr – rep 1


title: SKMEL2 Sirt5 Knockdown (shRNA 547) Rep 1

description: sample ID: 73860


title: SKMEL2 Non-targetting Control Rep 3

description: sample ID: 73856

source_name: SKMEL2 Non-targetting Control

value: shRNA non-targeting control


title: SKMEL2 Non-targetting Control Rep 1

description: sample ID: 73854


title: SKMEL2 Sirt5 Knockdown (shRNA 546) Rep 3

description: sample ID: 73859

source_name: SKMEL2 Sirt5 Knockdown (shRNA 546)

value: Sirt5 knockdown shRNA 546


title: SKMEL2 Non-targetting Control Rep 2

description: sample ID: 73855


title: SKMEL2 Sirt5 Knockdown (shRNA 546) Rep 1

description: sample ID: 73857


title: SKMEL2 Sirt5 Knockdown (shRNA 546) Rep 2

description: sample ID: 73858


title: MCF7 cells – control 0 hr – rep 2


title: CLL [G70128_GCLL-0058-T-01]

description: RRBS


title: CLL [G70125_GCLL-0283-T-01]

description: RRBS


title: CLL [G70123_GCLL-0123-T-01]

description: RRBS


title: CLL [G70124_GCLL-0124-T-01]

description: RRBS


title: SKMEL2 Sirt5 Knockdown (shRNA 547) Rep 2

description: sample ID: 73861


title: CLL [G70122_GCLL-0059-T-01]

description: RRBS


title: CLL [G70127_GCLL-0033-T-01]

description: RRBS


title: CLL [G70120_GCLL-0053-T-01]

description: RRBS


title: CLL [G70121_GCLL-0200-T-01]

description: RRBS


title: CLL [G70119_GCLL-0060-T-01]

description: RRBS


title: CLL [G70118_GCLL-0175-T-01]

description: RRBS


title: CLL [G70117_GCLL-0202-T-01]

description: RRBS


title: CLL [G70126_GCLL-0169-T-01]

description: RRBS


title: CLL [G70116_GCLL-0129-T-01]

description: RRBS


title: CLL [G70115_GCLL-0285-T-01]

description: RRBS


title: CLL [G70114_GCLL-0204-T-01]

description: RRBS


title: A375 Sirt5 Knockdown (shRNA 547) Rep 2

description: sample ID: 70420

source_name: A375 Sirt5 Knockdown (shRNA 547)


title: A375 Sirt5 Knockdown (shRNA 546) Rep 2

description: sample ID: 70417

source_name: A375 Sirt5 Knockdown (shRNA 546)


title: A375 Sirt5 Knockdown (shRNA 547) Rep 3

description: sample ID: 70421


title: A375 Sirt5 Knockdown (shRNA 546) Rep 3

description: sample ID: 70418


title: A375 Sirt5 Knockdown (shRNA 546) Rep 1

description: sample ID: 70416


title: A375 Sirt5 Knockdown (shRNA 547) Rep 1

description: sample ID: 70419


title: CLL [G70111_GCLL-0061-T-01]

description: RRBS


title: A375 Non-targetting Control Rep 3

description: sample ID: 70415

source_name: A375 Non-targetting Control


title: CLL [G70113_GCLL-0145-T-01]

description: RRBS


title: CLL [G70108_GCLL-0208-T-01]

description: RRBS


title: CLL [G70110_GCLL-0206-T-01]

description: RRBS


title: A375 Non-targetting Control Rep 1

description: sample ID: 70413


title: A2058 Sirt5 Knockdown (shRNA 546) Rep 2

description: sample ID: 63230

source_name: A2058 Sirt5 Knockdown (shRNA 546)


title: CLL [G70109_GCLL-0062-T-01]

description: RRBS


title: A2058 Sirt5 Knockdown (shRNA 546) Rep 1

description: sample ID: 63229


title: A2058 Sirt5 Knockdown (shRNA 546) Rep 3

description: sample ID: 63231


title: A2058 Sirt5 Knockdown (shRNA 547) Rep 1

description: sample ID: 63232

source_name: A2058 Sirt5 Knockdown (shRNA 547)


title: A2058 Sirt5 Knockdown (shRNA 547) Rep 2

description: sample ID: 63233


title: A375 Non-targetting Control Rep 2

description: sample ID: 70414


title: CLL [G70105_GCLL-0064-T-01]

description: RRBS


title: CLL [G70104_GCLL-0090-T-01]

description: RRBS


title: A2058 Non-targetting Control Rep 2

description: sample ID: 63227

source_name: A2058 Non-targetting Control


title: A2058 Non-targetting Control Rep 3

description: sample ID: 63228


title: CLL [G70106_GCLL-0076-T-01]

description: RRBS


title: A2058 Non-targetting Control Rep 1

description: sample ID: 63226


title: CLL [G70103_GCLL-0287-T-01]

description: RRBS


title: CLL [G70112_GCLL-0205-T-01]

description: RRBS


title: A2058 Sirt5 Knockdown (shRNA 547) Rep 3

description: sample ID: 63234


title: CLL [G70102_GCLL-0130-T-01]

description: RRBS


title: CLL [G70100_GCLL-0066-T-01]

description: RRBS


title: CLL [G70107_GCLL-0286-T-01]

description: RRBS