title: 1/133_WA

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: RNA expression levels in the blood of patient diagnosed with ulcerative colitis.

hyb_protocol: Standard Illumina hybridization protocol. Hybridization performed in AROS (Denmark) http://arosab.com/services/microarrays/gene-expression/ .

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalised using lumi library in R 2.15.

source_name: Ulcerative colitis, adult

label_protocol: Standard Illumina labeling protocol.

extract_protocol: For RNA extraction, whole blood was collected and total RNA was isolated using the Tempus RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop spectrophotometer, and samples with A260/A280 ratios of 1.8–2.1 were further assessed using an Agilent 2100 Bioanalyzer. Samples used for microarray analysis had RNA integrity numbers in the range 7.6–9.6.

value: ulcerative colitis

tag: age group

value: adult

tag: tissue

value: whole blood


title: BAL Cells not severe biological rep12

status: Public on May 01 2019

type: RNA

city: Pittsburgh

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

country: USA

institute: University of Pittsburgh

description:
1943H
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4X44K array slides

data_processing:
The data was extracted using the Agilent Feature Extraction software 10.7.3.1 (Agilent Technologies)
The data set was normalized by cyclic-LOESS with use of Bioconductor package as described previously (Wu W et. al. 2005). Probes which did not map to an Entrez ID were excluded

molecule: total RNA

organism: Homo sapiens

source_name: Human BAL cells

label_protocol: Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA.  Labeled RNA   was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays.

extract_protocol: Total RNA was extracted from BALF cells the suspended in Trizol solution using the QIACube system (Qiagen, Valencia, CA). RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and only samples with an RIN higher than 7 used for microarray experiments.

tag: condition

value: mild-moderate asmathic

tag: cells

value: BAL cells


title: BAL Cells not severe biological rep7

description:
1784N
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

hyb_protocol: RNA  was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays


title: BAL Cells not severe biological rep3

description:
1751Y
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: LEN-treated rep 2

city: London

first: Andrew

last: Gravett

address: Cranmer Terrace

country: United Kingdom

institute: SGUL

description: replicate 2

hyb_protocol: Arrays were washed and stained with Streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) according to the Illumina Whole Genome Gene Expression Direct Hybridisation manual.

scan_protocol: Arrays were scanned using  BeadArray Reader (Illumina, San Diego, CA) according to the manufacturer's instructions.

data_processing:
Image data were imported into GenomeStudio (Illumina, San Diego, CA) without normalisation. Non-normalised data were exported from GenomeStudio using the ArrayExpress Data Submission Report Plug-in v1.0. Data were quantile normalized in BeadStudio.
The file processed_data.xls includes hierarchical clustering data, normalized data (All Data tab) and averaged replicate data.

label: biotin

source_name: HCT116 colorectal cancer cell

label_protocol: RNA was labelled using Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX) according to the manufacturer's instructions.

growth_protocol: HCT116 cells were obtained from Public Health England and maintained in Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) foetal bovine serum (FBS), 2mM L-glutamine and 1x penicillin/streptomycin (basal culture medium). Cells were incubated in a humidified atmosphere with 5% CO2 in air at 37°C, and discarded at when the passage number exceeded 15.

extract_protocol: RNA was purified using the Qiagen RNA extraction mini-prep kit using manufacturer's instructions.

treatment_protocol: Cells were cultured in media supplemented with 1uM lenalidomide (LEN) dissolved in PBS for 4 hours.

tag: cell line

tag: cell type

value: colorectal cancer


title: 14/29_WA


title: Untreated control rep 2

description: replicate 2

treatment_protocol: Cells were cultured in media supplemented with phosphate buffered saline (PBS) for 4 hours.


title: iHepLPCs-Hep rep1

type: SRA

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

country: China

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

library_source: transcriptomic

data_processing:
Raw data were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks
Read counts of each gene were obtained by htseq-count.
Differentially expressed genes were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Hepatocyte-like cells differentiated from iHepLPCs

growth_protocol: For iHepLPCs, cells  were seeded and kept 2–4 days in TEM until full confluence. For iHepLPCs-Hep, iHepLPCs were seeded and kept 2–4 days in TEM until full confluence. Then the medium was changed to modified Hepatocyte Maturation Medium (mHMM) for another 7-10 days for further maturation; medium was changed every other day. For iHepLPCs-Hep-3D, 1x10^6 iHepLPCs  cells were seeded in the low-attachment 6-well plate. iHepLPCs  formed cellular spheres after 24 hours in TEM. Then the medium was changed to mHMM, and cultured another 7-10 days for further maturation.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following  the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Monolayer differentiated human hepatocyte-derived liver progenitor-like cells

tag: immortal gene

value: HPV16 E6/E7

tag: passages


title: 14/25_WA


title: BAL Cells not severe biological rep1

description:
1685L
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep2

description:
1742X
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep6

description:
1781H
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep38

description:
2310Z
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

value: normal control


title: iHepLPCs rep2

source_name: Immortalized human liver progenitor-like cells

value: human hepatocyte-derived liver progenitor-like cells


title: 18/85_WA


title: 14/37_WA


title: 18/93_WA


title: PAR_THZ1_250NM_3

city: Boston

first: Jun

last: Qi

state: Massachusetts

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber

data_processing:
Fastq files were aligned to human genome build hg19 using HiSat with default parameters.
Transcripts were assembled and FPKM values were generated using cuff quant and cuffnorm from the cufflinks pipeline (Trapnell et al., Nat. Biotechnol. 28, 511-515, 2010).
FPKM values were then normalized to synthetic ERCC spike-in RNAs as described previously (Loven et al., Cell 151, 476-482, 2012).
Genome_build: hg19
Supplementary_files_format_and_content: Moffitt_RNAseq_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

source_name: Mantle cell lymphoma

extract_protocol:
Total RNA was isolated using the Rneasy Plus Mini (Qiagen Cat# 74134) and ERCC spike in controls (Life Technologies, Cat 4456740) were added after total RNA extraction (1ul to 5000ng RNA).
Library prep was conducted using TruSeq Stranded mRNA Library Prep Kit (Illumina Cat #RS-122-2101/2) according to manufacture instruction. RNA sequencing was done on HiSeq 2500v4 high output (50-bp, single-end reads).

treatment_protocol: 1x106 Cells were treated for 6 hours with either 50/250nm THZ1 or DMSO at equal concentration as vehicle control.

tag: treatment

value: 250nM THZ1


title: iHepLPCs rep1


title: 1/210_WY

source_name: Ulcerative colitis, child

value: child


title: PAR_THZ1_250NM_2


title: BAL Cells control biological rep36

description:
2298J
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1/158_WY


title: BAL Cells control biological rep34

description:
2287E
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 18/206_WA


title: PAR_THZ1_250NM_1


title: BAL Cells control biological rep35

description:
2295D
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1/174_WY


title: 1/170_WY


title: 1/132_WY


title: 1/93_WY


title: 1/94_WY


title: 18/89_WA


title: 1/213_WY


title: 1/212_WY


title: BAL Cells control biological rep32

description:
2244M
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: PAR_THZ1_50NM_2

value: 50nM THZ1


title: PAR_THZ1_50NM_1


title: 1/143_WY


title: PAR_DMSO_3


title: BAL Cells control biological rep31

description:
1902T
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep37

description:
2309O
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep33

description:
2252L
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: PAR_DMSO_2


title: BAL Cells control biological rep29

description:
0039X
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 18/36_CA

description: RNA expression levels in the blood of patient diagnosed with crohn’s disease.

source_name: Crohn’s disease, adult

value: Crohn's disease


title: PAR_DMSO_1


title: 1/75_WY

description: RNA expression levels in the blood of patient diagnosed with ulcerative colitis.


title: 1/165_WY


title: 18/105_CA


title: 1/154_WY


title: 1/211_WY


title: BAL Cells control biological rep27

description:
2213B
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: L20_THZ1_250NM_3


title: BAL Cells control biological rep28

description:
2220Y
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 18/94_CA


title: 1/164_WY


title: L20_THZ1_250NM_2


title: 13/144_CA


title: BAL Cells control biological rep26

description:
2170J
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: L20_THZ1_250NM_1


title: 18/99_CA


title: 13/145_CA


title: BAL Cells control biological rep25

description:
2129M
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1/175_CY

source_name: Crohn’s disease, child


title: L20_THZ1_50NM_3


title: 1/189_CY


title: 13/149_CA


title: L20_THZ1_50NM_1


title: 1/205_CY


title: 1/159_CY


title: 1/156_CY


title: L20_THZ1_50NM_2


title: L20_DMSO_3


title: BAL Cells control biological rep23

description:
2096X
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep24

description:
2099D
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1/171_CY


title: 1/191_CY


title: BAL Cells control biological rep21

description:
2106A
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1/202_CY


title: L20_DMSO_2


title: 1/139_CY


title: BAL Cells control biological rep20

description:
2000K
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1/129_CY


title: BAL Cells control biological rep19

description:
1963N
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1/153_CY


title: L20_DMSO_1


title: BAL Cells control biological rep18

description:
1955O
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep22

description:
2052D
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: J4_THZ1_250NM_3


title: 1/151_CY


title: 1/180_CY


title: 1/172_CY


title: 8/57 PBC

description: RNA expression levels in the blood of patient diagnosed with primary biliary cholangitis.

source_name: Primary biliary cholangitis, adult

value: primary biliary cholangitis


title: J4_THZ1_250NM_1


title: J4_THZ1_250NM_2


title: 8/52 PBC


title: J4_THZ1_50NM_3


title: J4_THZ1_50NM_2


title: BAL Cells control biological rep30

description:
1734Y
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 8//22_K

description: RNA expression levels in the blood of control patient.

source_name: Control, adult

value: control


title: BAL Cells control biological rep16

description:
1818E
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 8/43_K


title: 8/33_K


title: J4_THZ1_50NM_1


title: 8//6_K


title: J4_DMSO_3


title: BAL Cells control biological rep14

description:
1325H
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 10/57_K


title: 8/42 PBC


title: 11//31_K


title: BAL Cells control biological rep13

description:
1270I
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep17

description:
1913Y
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 8/44_K


title: BAL Cells control biological rep15

description:
1624R
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep12

description:
1220T
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 8/44 PBC


title: 10//17_K


title: 11//24_K


title: 8//17_K


title: 11//4_K


title: 1/201_CY

description: RNA expression levels in the blood of patient diagnosed with crohn’s disease.


title: 10/51_K


title: J4_DMSO_1


title: J4_DMSO_2


title: I10_THZ1_250NM_3


title: I10_THZ1_250NM_2


title: BAL Cells control biological rep10

description:
1947P
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: PAR_THZ1_50NM_3


title: BAL Cells control biological rep9

description:
1924D
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: I10_THZ1_250NM_1


title: 8/66_PBC


title: 8//24_PBC


title: 8//27_PBC


title: 8/72_PBC


title: 8//6_PBC


title: I10_THZ1_50NM_1


title: BAL Cells control biological rep6

description:
1656E
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep7

description:
1701J
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: I10_DMSO_3


title: BAL Cells control biological rep8

description:
1733W
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 8//5_PBC


title: I10_THZ1_50NM_2


title: BAL Cells control biological rep4

description:
1524N
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 8//9_PBC


title: 12/104_PBC


title: 1/162_WY

description: RNA expression levels in the blood of patient diagnosed with ulcerative colitis.


title: 12/243_PBC

description: RNA expression levels in the blood of patient diagnosed with primary biliary cholangitis.


title: 8/80_PBC


title: BAL Cells control biological rep5

description:
1619Y
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells control biological rep3

description:
1431G
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 12/126_PBC


title: 12/125_PBC


title: 12/66_PBC


title: I10_DMSO_2


title: 12/94_PBC


title: 12/97_PBC


title: BAL Cells control biological rep2

description:
1221V
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 12/359_PBC


title: I10_DMSO_1


title: RL95_2 ATAC-seq replicate 1

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

library_source: genomic

data_processing:
Align to hg19 reference genome using Bowtie 1.0.1
Peak calling to generate signal tracks on on individual replicates using macs2 2.1.1.20160309 with options -B -p 1e-2 --shift -100 --extsize 200
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using deeptools

molecule: genomic DNA

source_name: Endometrial adenosquamous carcinoma

growth_protocol: RL95-2 cells were maintained using DMEM:F12 media; Caov3, OVCAR8 cells were maintained using RPMI 1640; AN3CA, Ishikawa, KLE were maintained using EME; SNU685, JHUCS1 cells were maintained using DME:F12; ACI126, ACI158 cells were maintained using DMEM/F-12; MDA-MB-436, MDA-MB-231 cells were maintained using DMEM-HG without 2mM L glutamine.

extract_protocol:
50,000 cells were lysed in ATAC lysis buffer and tagmented (Illumina Nextera DNA Library Preparation Kit). After adding SDS, the samples were purified with 2X Agencourt AMPure XP beads (Beckman Coulter A63881)
Samples were amplified using NEBNext Q5 Hot Start HiFi PCR Master Mix. The concentration of samples was checked using PicoGreen and median fragment size was checked using the Agilent D1000 screentape on the Agilent Technologies 2200 TapeStation. Samples were sequenced PE50 on a HiSeq 2500.

value: Endometrial adenosquamous carcinoma


title: 18/119_CA


title: 12/309_PBC


title: Z7: thyroid cancer with metastasis

city: Harbin

first: Xiaoyi

last: Huang

state: Heilongjiang

address: Haping Road 150

institute: Harbin Medical University Cancer Hospital

description: miRNA

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia).
After cluster generation, the libraries were sequenced and 50bp single-end reads were generated.
The raw data (raw reads) extracted from FASTQ files were firstly processed through perl and python scripts. In this step, clean data(clean reads) were generated by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data.
Then the clean data were aligned against human miRNA sequences from miRBase (Release 20) and NCBI human genome reference sequences (Release 103) using Bowtie (version 0.12.8) .
miRNA profiling was normalized using read counts of a specific miRNA per million(TPM) mappable miRNA sequences. To find novel miRNAs, the raw data was independently processed by combined use of miRDeep 2 and miREvo. Predicted miRNAs with scores ≥ 2 were considered significant.

source_name: plasma

growth_protocol: plasma exosomal RNA was isolated from petient with benign thyriod nodule, metiastatic thyroid cancer, non-metastatic thyroid cancer, and healty individuals.

extract_protocol:
The miRNAs were extracted from plasma-isolated exosomes using the miRNeasy Micro Kit per the manufacturer’s protocol
Small RNA libraries were constructed as instructed by the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, Ipswich, MA, USA) with minor modifications. Ten ng of small RNA were used as the starting material. After sequential ligation of the Multiplex 3’ SR Adaptor, hybridization of the reverse transcription primer, and ligation of the Multiplex 5’ SR Adaptor, the RNA-Adaptor complex was reversed transcribed into cDNA. Then the small RNA libraries were amplified and the Illumina compatible Index Primers were incorporated with 10 cycles of PCR amplification. The amplified libraries were resolved on a native 5% acrylamide gel (Bio-rad, Hercules, CA). DNA fragments corresponding to 140 - 160 bp (the size comprising the miRNA inserts plus the 3’ and 5’ adaptors) were recovered in 12 µL of Elution Buffer (QIAGEN) and determined with High Sensitivity DNA Chip on Agilent 2100 bioanalyzer. Absolute quantities of each indexed library were determined by real time qPCR using KAPA Library Quantification Kit according to the manufacture’s protocol.

value: thyroid cancer with metastasis

tag: fraction

value: circulating exosomes


title: 12/221_PBC

value: adult

value: whole blood


title: Z8: thyroid cancer with metastasis

description: miRNA


title: 12/177_PBC


title: Z5: thyroid cancer with metastasis

description: miRNA


title: Z4: thyroid cancer with metastasis

description: miRNA


title: OVCAR8 ATAC-seq replicate 2

source_name: High grade ovarian serous adenocarcinoma


title: RL95_2 ATAC-seq replicate 2


title: Z3: thyroid cancer with metastasis

description: miRNA


title: Z6: thyroid cancer with metastasis

description: miRNA


title: BAL Cells control biological rep1

description:
0261T
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

value: BAL cells


title: 12/294_PBC


title: SNU685 ATAC-seq replicate 2

source_name: Uterine carcinosarcoma

value: Uterine carcinosarcoma


title: 12/73_PBC


title: OVCAR8 ATAC-seq replicate 1

value: High grade ovarian serous adenocarcinoma


title: SNU685 ATAC-seq replicate 1


title: MDA_MB_436 ATAC-seq replicate 2

source_name: Breast adenocarcinoma

value: Breast adenocarcinoma


title: 12//30_PBC


title: 1/206_CY


title: MDA_MB_436 ATAC-seq replicate 1


title: Z2: thyroid cancer with metastasis

description: miRNA


title: Z1: thyroid cancer with metastasis

description: miRNA


title: 12/121_PBC


title: 12//27_PBC


title: BAL Cells control biological rep11

description:
0054J
BAL
Control
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

value: normal control


title: 18/183_WA

value: ulcerative colitis


title: 12/195_PBC


title: 18/197_WA


title: 18/168_WA


title: 18/185_WA


title: 18/148_WA


title: Y8: thyroid cancer without metastasis

description: miRNA

value: thyroid cancer without metastasis


title: 18/146_WA


title: 12/240_PBC


title: 18/140_WA


title: 18/141_WA


title: MDA_MB_231 ATAC-seq replicate 2


title: MDA_MB_231 ATAC-seq replicate 1


title: Y6: thyroid cancer without metastasis

description: miRNA


title: KLE ATAC-seq replicate 2

source_name: Endometrial adenocarcinoma

value: KLE

value: Endometrial adenocarcinoma


title: 1/167_WY

value: child


title: KLE ATAC-seq replicate 1


title: Y5: thyroid cancer without metastasis

description: miRNA


title: Y4: thyroid cancer without metastasis

description: miRNA


title: JHUCS_1 ATAC-seq replicate 2


title: Y7: thyroid cancer without metastasis

description: miRNA


title: Y3: thyroid cancer without metastasis

description: miRNA


title: Y2: thyroid cancer without metastasis

description: miRNA


title: JHUCS_1 ATAC-seq replicate 1


title: Y1: thyroid cancer without metastasis

description: miRNA


title: Ishikawa ATAC-seq replicate 1

value: Ishikawa


title: X8: benign thyriod nodule

description: miRNA

value: benign thyriod nodule


title: 1/86_WY


title: Caov3 ATAC-seq replicate 2


title: X7: benign thyriod nodule

description: miRNA


title: 15//12_WY


title: Ishikawa ATAC-seq replicate 2


title: Caov3 ATAC-seq replicate 1


title: 1/145_WY


title: X6: benign thyriod nodule

description: miRNA


title: AN3_CA ATAC-seq replicate 2


title: 12/129_PBC

value: primary biliary cholangitis


title: 1/88_WY


title: X5: benign thyriod nodule

description: miRNA


title: AN3_CA ATAC-seq replicate 1


title: X4: benign thyriod nodule

description: miRNA


title: ACI_158 ATAC-seq replicate 2

source_name: Endometrial serous adenocarcinoma

value: Endometrial serous adenocarcinoma


title: 15/64_WY


title: X3: benign thyriod nodule

description: miRNA

value: circulating exosomes


title: ACI_158 ATAC-seq replicate 1


title: 1/200_WY


title: 1/166_WY


title: 15/51_WY


title: 1/131_WY


title: X2: benign thyriod nodule

description: miRNA


title: ACI_126 ATAC-seq replicate 2


title: 15/71_WY


title: 15/69_WY


title: 15/67_WY


title: 15/74_WY


title: 13/113_CA

value: Crohn's disease

value: adult


title: 13/141_CA

value: whole blood


title: 1/173_CY


title: 13/133_CA


title: 13/134_CA


title: ACI_126 ATAC-seq replicate 1


title: 1/147_CY


title: 1/195_CY


title: 5/35_WY


title: 13/135_CA


title: Cntrl-FLAG-R3_hiseq8

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

description: Control iCLIP Replicate 3

data_processing:
Library strategy: iCLIP
Reads from complete lanes mapping to spiked in PhiX were removed by mapping the PhiX genome using bowtie v1.1.2 with paramteres ‘-v 2 --best --strata -a’
UMI sequences were removed from 5' end of reads using the extract command from UMI-tools v0.5.3 with the parameters '--bc-pattern=NNNXXXXNN'
Reads were adaptor trimmed and demultiplexed using repear version 15-065 keeping only reads longer than 15nt.
Reads were mapped to hg19 using STAR 2.4.2a and a junction database built from ensembl 75. The options to STAR were ‘--outFilterMultimapNmax 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.2 --outFilterScoreMin 0.8 --alignSJDBoverhangMin 1’
Alignments from different sequencing lanes for the same sample were merged and deduplicated using the dedup command from UMI-tools v0.5.3 with parameters `--method=directional`
Bed files of per base tag counts were produced by taking either the 5' most deletion in an alignment or the base immediately 5' of the 5' end of the alignment, accounting for alignement strand using iCLIP2BigWig from iCLIPlib (www.github.com/sudlab/iCLIPlib)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files containing the tag count for each base in the genome. Union files contain counts from the sum of all replicates.

source_name: FlipIn HEK293T cells

growth_protocol: FlpIn-293 cells expressing the FLAG-tagged proteins were generated as described previously (Hautbergue et al., 2009, PMID: 19836239 ) and maintained in DMEM with 10% FBS, 15 µg/mL Blasticidin, and 0.1 mg/mL Hygromycin.

extract_protocol: iCLIP was then performed exactly as described previously (König et al., 2011 PMID: 21559008 ) but using 10 µg of anti-FLAG antibodies (Sigma) and performing the high salt washes of the immunoprecipitation part of the protocol at room temperature (22°C) on a rotating wheel for 5 minutes per wash. Additionally, the following modifications from (Broughton et al., 2013 PMID: 23583680) were used. All nucleic acid pellets were air dry for a maximum of 10 minutes to ease resuspension. Nucleic acids centrifugations after each overnight precipitation were done at 4°C, 16000 x g for 20 minutes and 5 minutes for the EtOH 80% washes. During the cDNA gel purification step, each gel piece was transferred to a 0.5 mL microcentrifuge tube pierced with 3-4 holes made with a 19-gauge needle. The gel-containing 0.5 mL tube was itself inserted inside a 1.5 mL microfuge tube and the assembly was centrifuged at 16000 x g for 2 minutes to efficiently shred the gel piece. After circularisation of the cDNAs, the Circligase was inactivated by heating the samples for 15 minutes at 80°C. To linearize the cDNAs, the standard iCLIP cut_oligo was replaced by a cut_oligo bearing a 3’ dideoxycytosine instead of four adenosines. Libraries for each sample were mixed and the mixture split across multiple sequencing lanes.

treatment_protocol: FLAG-tagged protein expression was induced for 48h in the stable cell lines by addition of tetracycline at 5 ng/mL for Nxf1, and 10 ng/mL for Chtop, and Alyref.

tag: genotype/variation

value: Expresses empty FLAG construct

tag: antibody

value: anti-FLAG (Sigma)


title: 13/124_CA


title: 13/131_CY


title: 1/197_CA


title: 1/199_CY


title: 13/119_CA


title: 1/152_CY


title: Cntrl-FLAG-R3_hiseq7

description: Control iCLIP Replicate 3


title: 1/100_CY


title: ATF1-ChIP-seq

city: Wuhan

first: Tian

last: Jianbo

state: HuBei

address: Hangkong Road13, School of Public Health, Tongji Medical College, HUST

department: Key Laboratory for Environment and Health (Ministry of Education),

institute: Huazhong University of Science and Technology

description: Chip-Seq on HCT116

data_processing:
ChIP-seq fastq files were generated by using Illumina's CASAVA software and mapped to the human genome (hg38) with Bowtie2 tool with default parameters and normalized to the sample with the smallest number of mapped reads. ChIP-Seq bedgraph files were generated using Bedtools and ChIP-seq Peaks were called using the MACS1.4 with mfold 15, tsize of 50, p-vaule of 1e-5.Genome_build: hg38
Supplementary_files_format_and_content: Peak files contains ChIP peal locations and range of scores; Wig format contains genome-wide binding profile

growth_protocol: HCT116 cell line was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (Gibco, USA) and 1% antibiotics at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
ChIP assays were performed using a ChIP assay kit (Cat#10086, Millipore) according to the manufacturer’s instructions. Cells were crosslinked with 1% formaldehyde, and glycine was added to stop fixation. Genomic DNA was extracted from the fixed-chromatin cells and was sonicated to 200-400 bp fragments. Antibodies (5 µg) against  Flag-ATF1 (CST, Cat#14793) and a nonspecific rabbit IgG (Santa Cruz) were subsequently incubated with the cross-linked protein/DNA overnight for immunoprecipitation using protein A/G magnetic beads. DNA fragments were purified and collected by a Dr.GenTLE Precipitation Carrier kit (Takara, Japan).
Libraries were constructed according to Illuminas standard protocol. The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane. Sequencing was performed using Illumina HiSeq 2000.

value: colon adenocarcinoma

value: 3xFlag-ATF1 antibody (CST, Cat#14793)


title: 1/136_WY

value: ulcerative colitis


title: X1: benign thyriod nodule

description: miRNA


title: Input DNA

description: Chip-Seq on HCT116


title: B7992_RTT_TCTX

city: Seattle

first: Kimberly

middle: A

last: Aldinger

state: WA

address: 1900 Nineth Ave

institute: Seattle Children's Research Institute

data_processing:
Illumina FASTQ Generation v1.0.0
STAR v2.5.3a was used for mapping reads to the human reference genome NCBI build 37/hg19
featureCounts v1.6 was used to summarize gene counts
DESeq2 v1.20.0 was used for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including gene counts for each sample
Supplementary_files_format_and_content: comma-delimited text file including regularized-logarithm transformed gene counts for each sample

source_name: Temporal cortex

extract_protocol:
Total RNA was isolated from frozen samples using the Qiagen RNeasy Kit. RNA integrity number >8.0 for all samples.
Illumina TruSeq v2

value: postmortem brain

tag: age

value: 31 years

tag: gender

value: female

tag: pmi

value: 30 hours


title: Cntrl-FLAG-R2_hiseq6

description: Control iCLIP Replicate 2


title: Cntrl-FLAG-R2_hiseq5

description: Control iCLIP Replicate 2


title: 7783_RTT_TCTX

value: 26 years

value: 39 hours


title: HFD-Pair-fed to AM251

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

institute: University of South Carolina School of Medicine

hyb_protocol: Labeled samples were hybridized to miRNA 4.0 chips overnight (16h, 48°C, 60 RPM) then washed and stained on an Affymetrix GCS 3000 system Fluidics station using the FS450_0002 protocol.

scan_protocol: Chips were scanned on a Affymetrix GCS 3000 system scanner.

data_processing:
Affymetrix Expression Console Version 1.4.1.46 was used for quality control, data summarization, and normalization. The processing algorithm used was RMA-DABG. Affymetrix Transcriptome Analysis Console Version 3.1.0.5 was used to perform differential expression analyses. MicroRNAs were considered differentially expressed between the two groups if linear fold change was greater than ±2 and the ANOVA p-value was less than 0.05
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_0
program-name = Expression Console
program-version = 1.3.0.187

label: Biotin

organism: Mus musculus

source_name: Epididymal fat macrophages

label_protocol: 500ng total RNA was used as starting material for labeling according to the Affymetrix FlashTag Biotin HSR RNA Labeling Kit manufacturer protocol.

growth_protocol: Mice were fed a control 10% low-fat diet (LFD) or 60% high fat diet (HFD) for 16 weeks starting at 6 weeks of age. Mice were then treated with vehicle (Veh) or CB1 antagonist (SR141716A "SR", AM251), daily for 4 weeks. Pair-fed controls are denoted as "PF".

extract_protocol: Total RNA was isolated with Qiagen miRNeasy micro kit.

treatment_protocol: Epididymal fat stromal vascular fractions (SVF) were isolated by collagenase digestion. F4/80+ cells (ATMs) were purified by labeling SVF cells with anti-F4/80-PE (clone: BM8) followed by immunomagnetic selection with StemCell EasySep PE Positive Selection Kit. Each biological replicate is pools of ATMs isolated from either 20 NCD-fed mice or 10 HFD-fed mice.

tag: strain

value: Male

value: 22 weeks

tag: diet

value: HFD-Pair-fed to AM251

tag: weeks of diet

value: 16 weeks

tag: treatment duration

value: 4 weeks

value: Epididymal fat macrophages


title: Cntrl-FLAG-R1_hiseq8

description: Control iCLIP Replicate 1

value: Expresses empty FLAG construct


title: HFD+AM251


title: SMB56-GDC0449-2

city: Shanghai

first: Yujie

last: Tang

address: 280 South Chong-qing Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The RNAseq reads were mapped to the hg19 reference  genome using STAR (v2.5.3a)
FPKM was calculated using Cufflinks (v2.2.1)
Differential expression analysis was carried  out using R package DESeq2 (v1.20.0)

source_name: medulloblastoma

growth_protocol: SMB56 and SMB56-shSufu cell lines were cultured (typically 1 × 10E6 cells into a well of 6-well plate) as neurospheres in DMEM/F12 media (Gibco, 11330-032) containing 1×B27(-A) (Gibco, 12587-010) and 1×Antibiotic-Antimycotic (Gibco, 15240-062).

extract_protocol:
Cells were harvested in Trizol and extracted by using mirVana miRNA isolation kit.
RNA libraries were prepared for sequencing by service provider using standard Illumina protocols with Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

treatment_protocol: SMB56 cells were treated with DMSO, 0.1 uM THZ1 or 1 uM GDC-0449 for 8 hours, SMB56-shSufu cells were treated with DMSO or 0.1 uM THZ1 for 8 hours

value: spontaneous medulloblastoma cells from Ptch+/ mice

tag: genotype

value: Ptch+/-

value: Treated with 1uM GDC-0449 for 8hr


title: 7773_RTT_TCTX

tag: tissue

value: 24 years

value: 25 hours


title: 4725_CTL_TCTX

value: postmortem brain

value: 32 years

value: 17 hours


title: SMB56-GDC0449-1

tag: cell line


title: 6355_RTT_TCTX

value: 16 years

value: female

value: 28 hours


title: Cntrl-FLAG-R1_hiseq7

description: Control iCLIP Replicate 1

value: anti-FLAG (Sigma)


title: Nxf1-FLAG-R3_hiseq8

description: Nxf1-FLAG iCLIP Replicate 3

value: Expresses Nxf1-FLAG


title: 2/109_CY

tag: condition

value: Crohn's disease

tag: age group

value: child

value: whole blood


title: SMB56-THZ1-2

tag: cell type

tag: passages

value: Treated with 0.1uM THZ1 for 8hr


title: 4724_CTL_TCTX

value: 15 hours


title: 1/113_CY


title: SMB56-THZ1-1

value: spontaneous medulloblastoma cells from Ptch+/ mice

value: Ptch+/-

tag: treatment


title: Nxf1-FLAG-R3_hiseq7

description: Nxf1-FLAG iCLIP Replicate 3

tag: genotype/variation


title: 2/54_CY


title: SMB56-DMSO-2

value: Treated with DMSO for 8hr


title: 1614_CTL_TCTX

value: 27 years

value: 18 hours


title: Nxf1-FLAG-R2_hiseq6

description: Nxf1-FLAG iCLIP Replicate 2

tag: antibody


title: SMB56-DMSO-1


title: 1038_CTL_TCTX

value: postmortem brain

tag: age

value: 24 years

value: 7 hours


title: B7992_RTT_CCTX

source_name: Cingluate cortex

value: 31 years

tag: gender

value: female

value: 30 hours


title: Nxf1-FLAG-R2_hiseq5

description: Nxf1-FLAG iCLIP Replicate 2

value: Expresses Nxf1-FLAG

value: anti-FLAG (Sigma)


title: 2/91_CY

value: Crohn's disease

value: child


title: 2/110_CY

value: whole blood


title: 2/53_CY


title: Nxf1-FLAG-R1_hiseq8

description: Nxf1-FLAG iCLIP Replicate 1


title: 7783_RTT_CCTX

value: 26 years

tag: pmi

value: 39 hours


title: BulkRNA-seq_murine_p12_ICAM1_Rep2

city: Philadelphia

first: Patrick

last: Seale

address: Smilow Center 3400 Civic Center Blvd. 1

institute: University of Pennsylvania

description:
Bulk RNA-Seq of FACS purified ICAM1+ cells
processed data in files: ResultsICAM1vCD142.csv, ResultsICAM1vDPP4.csv

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using STAR v2.5.2a with parameters --outFilterMultimapNmax 1 --quantmode Genecounts
Raw genecounts were analyzed for differential expression via DeSeq2 in R 3.5.1
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 analysis of differential expression in all pairwise comparisons of DPP4+, ICAM1+, and CD142+ cells.

source_name: Subcutaneous WAT (inguinal + axillary)

extract_protocol:
Whole adipose tissues were manually minced, digested with Collagenase D and Dispase II at 37C for 45 min, and cells were separated into DPP4+, ICAM1+, and CD142+ Populations via FACS. FACS isolated cells were pelleted via centrifugation and lysed in TriZol reagent followed by phenol cholorform extraction/ arctus picopure RNA isolation kit to isolate RNA.
Novogene Paired End Protocol "fter the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment."

tag: strain

value: 12 days

value: Mixed male and female

value: Inguinal + Axillary White Adipose

tag: cell population

tag: developmental stage


title: 7773_RTT_CCTX

value: 25 hours


title: Nxf1-FLAG-R1_hiseq7

description: Nxf1-FLAG iCLIP Replicate 1


title: BulkRNA-seq_murine_p12_ICAM1_Rep1


title: Chtop-FLAG-R3_hiseq8

description: Chtop-FLAG iCLIP Replicate 3

value: Expresses Chtop-FLAG


title: 6355_RTT_CCTX

value: postmortem brain

value: 16 years

value: 28 hours


title: BulkRNA-seq_murine_p12_DPP4_Rep3

description:
Bulk RNA-Seq of FACS purified DPP4+ cells
processed data in files: ResultsCD142vDPP4.csv, ResultsICAM1vDPP4.csv


title: 4725_CTL_CCTX

value: 32 years

value: female

value: 17 hours


title: Chtop-FLAG-R3_hiseq7

description: Chtop-FLAG iCLIP Replicate 3

value: anti-FLAG (Sigma)


title: BulkRNA-seq_murine_p12_DPP4_Rep2


title: BulkRNA-seq_murine_p12_ICAM1_Rep3


title: Chtop-FLAG-R2_hiseq6

description: Chtop-FLAG iCLIP Replicate 2


title: Chtop-FLAG-R2_hiseq5

description: Chtop-FLAG iCLIP Replicate 2


title: 12/244_PBC

value: primary biliary cholangitis

value: adult


title: 4724_CTL_CCTX

value: 15 hours


title: 2/87_CY

value: Crohn's disease

value: child

value: whole blood


title: 2/59_CY


title: BulkRNA-seq_murine_p12_DPP4_Rep1

value: 12 days

value: Mixed male and female


title: BulkRNA-seq_murine_p12_CD142_Rep3

description:
Bulk RNA-Seq of FACS purified CD142+ cells
processed data in files: ResultsCD142vDPP4.csv, ResultsICAM1vCD142.csv

value: Inguinal + Axillary White Adipose


title: 2/55_CY

description: RNA expression levels in the blood of patient diagnosed with crohn’s disease.


title: 11/34_K

description: RNA expression levels in the blood of control patient.

value: control


title: 1038_CTL_CCTX

value: postmortem brain

value: 24 years

value: 7 hours


title: BulkRNA-seq_murine_p12_CD142_Rep2


title: 10/38_K


title: 12/282_PBC


title: 11//28_K


title: 8//21_K


title: 11/40_K


title: 11//14_K


title: Chtop-FLAG-R1_hiseq7

description: Chtop-FLAG iCLIP Replicate 1

value: Expresses Chtop-FLAG


title: BulkRNA-seq_murine_p12_CD142_Rep1


title: Alyref-FLAG-R3_hiseq8

description: Alyref-FLAG iCLIP Replicate 3

value: Expresses Alyref-FLAG


title: Sample_6-fRIP-IPhnK-Run3

city: Houston

first: Vrutant

middle: V

last: Shah

state: TX

address: 1515 Holcombe Blvd #1000

department: EMC

institute: UT MD Anderson Cancer Center

data_processing:
Raw reads were trimmed using flexbar (6) keeping minimum length of 25 base pairs.
Trimmed reads were aligned to human genome assembly 38 using bowtie2. The following options were used for bowtie2: --local –sensitive (-N 1 instead of 0)
The output was collected as .sam format. The .sam files were converted to .bam files using samtools
The .bam files were indexed, sorted and filtered for unique read counts per alignment using samtools.
To obtain differential representation between input and IP, we used cufflinks, cuffmerge and cuffdiff pipeline. q-values were calculated using cuffdiff by comparing input to IP samples using following parameters: --total-hits-norm --library-norm-method geometric --no-effective-length-correction.
Genome_build: human genome assembly 38

source_name: OCI-AML3 cells

growth_protocol: OCI-AML3 cells were grown in RPMI culture media supplemented with 10% FBS and 1% Pencillin/Streptomycin. The cells were cultured in 5% CO2 at 37 °C.

extract_protocol:
100 million OCI-AML3 cells were collected by centrifugation, washed with PBS and fixed using 0.25% formaldehyde. Formaldehyde was quenched using glycine and the fixed cells were lysed using 0.5% NP40 buffer supplemented with protease and RNase inhibitors. The lysate was then flash frozen at minus 80 deg C. The lysate was then sonicated, cleared by centrifugation  and the cleared lysate was used for immunoprecipitation experiments.
Libraries were prepared using TruSeq RNA Library Prepkit v2 and as per the anufacture's recommended protocol.
After library prep, single-read sequencing was performed on an Illumina HiSeq 2000 at a depth of 36 nucleotides per read at the MD Anderson Sequencing Core.

value: OCI-AML3 cells

value: anti-(hnRNP K)


title: Chtop-FLAG-R1_hiseq8

description: Chtop-FLAG iCLIP Replicate 1

value: anti-FLAG (Sigma)


title: Alyref-FLAG-R3_hiseq7

description: Alyref-FLAG iCLIP Replicate 3


title: 1614_CTL_CCTX

value: 27 years

value: female

value: 18 hours


title: Sample_5-fRIP-Input-Run3

value: none (input)


title: Sample_4-fRIP-IP-hnK-Run2


title: ChIP_ST_8C_Setd2_KO_H3K27me3

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

institute: Tsinghua University

description:
processed data file:
ST_8C_Setd2_KO_H3K27me3.bed.gz

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome.

source_name: embryo

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

treatment_protocol: 8-week-old control and Setd2mNull female mice were superovulated by PMSG (5 IU) and hCG (5 IU) injection at 48 hours apart. Denuded oocytes were washed in M2 and incubated in normal M16 medium. Transferring of spindle-chromosome complex of Setd2mNull (or control) donor oocyte and enucleation of control (or Setd2mNull) recipient oocyte were done with a piezo-driven actuator. Then donor spindle-chromosome complex was gently aspirated to a pipette, exposed to the HVJ-E (CosmoBio), and transferred to an enucleated recipient oocyte. About 15 minutes later, reconstructed oocytes were fertilized by intracytoplasmic sperm injection (ICSI). Then reconstructed zygotes were incubated in M16 medium to 8-cell stage.

value: embryo

tag: chip-antibody


title: ChIP_FGO_Setd2_Con_H3K27me3_rep2

description:
processed data file:
FGO_Setd2_Con_H3K27me3.bed.gz

source_name: oocyte

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stage.

value: oocyte

value: FGO

tag: genotype


title: 8/48_PBC

source_name: Primary biliary cholangitis, adult

value: primary biliary cholangitis

value: adult

tag: tissue

value: whole blood


title: 11/32_K

source_name: Control, adult

value: control


title: 11//2_K


title: Sample_3-fRIP-Input-Run2


title: ChIP_ST_8C_Setd2_KO_H3K4me3

description:
processed data file:
ST_8C_Setd2_KO_H3K4me3.bed.gz

value: H3K4me3(home made)


title: 8/54_PBC


title: ChIP_ST_Early2C_Setd2_KO_H3K27me3

description:
processed data file:
ST_Early2C_Setd2_KO_H3K27me3.bed.gz


title: Sample_2-fRIP-IP-hnK-Run1


title: Alyref-FLAG-R1_hiseq8

description: Alyref-FLAG iCLIP Replicate 1

tag: cell line


title: Sample_1-fRIP-Input-Run1


title: 8//9_K

tag: condition


title: 10/48_K

tag: age group


title: Alyref-FLAG-R1_hiseq7

description: Alyref-FLAG iCLIP Replicate 1


title: 8//28_K


title: Alyref-FLAG-R2_hiseq5

description: Alyref-FLAG iCLIP Replicate 2


title: 8/36_K


title: Alyref-FLAG-R2_hiseq6

description: Alyref-FLAG iCLIP Replicate 2


title: 12/396_PSC

description: RNA expression levels in the blood of patient diagnosed with primary sclerosing cholangitis.

source_name: Primary sclerosing cholangitis, adult

value: primary sclerosing cholangitis


title: 12/170_PSC


title: 12/381_PSC


title: MDA-MB-231-FRY rep2

city: Buffalo

first: Jie

last: Wang

state: NY

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
RNA-seq reads were aligned to the hg19 reference sequences and gencode annotation (version v19) using STAR (version 2.4.2a)
Then the alignments were used for the gene quantification using RSEM (version 1.2.23)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: human breast cancer cells

growth_protocol: The human breast cancer cell lines MDA-MB-231 were cultured in Dulbecco's Modified Eagle's medium supplemented with 10 % FBS and 1% penicillin-streptomycin and incubated at 37 °C in a fully humidified atmosphere containing 5% CO2.

extract_protocol:
The extraction of total cellular RNA from cells was carried out using TRIzol Reagent (Thermo Scientific) and purified with an RNeasy Kit (Qiagen). RNA quality was assessed by agarose gel electrophoresis, spectrophotometry, and a BioAnalyzer (Agilent).
The sequencing libraries were generated with a TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions.

tag: expression

value: FRY expression

tag: cell type

value: epithelial

tag: disease

value: adenocarcinoma

tag: immunoprofile

value: ER-, PR-, HER2-


title: ChIP_GO_P7_Setd2_KO_H3K4me3

description:
processed data file:
GO_P7_Setd2_KO_H3K4me3.bed.gz

treatment_protocol: Oocytes (20-30 μm) were harvested from postnatal 7 days females for both Setd2 control and mutant in M2 medium.

value: GO


title: pSTAT3CHIP-TMD8-AZD1480

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

description: Genomic DNA isolicated from immunoprecipitated chromatin using pSTAT3 antibody.

data_processing:
Sequence reads were filtered for average QC score>30. Reads were mapped  with Bowtie2 to the hg19 genome, with default parameters. Reads mapping to identical positions in the genome  were collapsed into one read.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq (bigwig file)

source_name: ABC DLBCL cell line (TMD8)

growth_protocol: TMD8 cells were grown in RPMI1640 media plus 20%FBS,1%  penicillin, 1% streptomycin.

extract_protocol:
ChIP experiments are followed by Rui et al., 2016, PNAS 113(46): E7260-E7267
ChIP library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330)

treatment_protocol: TMD8 cells were treated by eithor DMSO or AZD1480(JAK inhibitor) for 4hrs. Naïve B cells were collected from peripheral blood mononuclear cells by Naive B Cell Isolation kit (miltenyi biotec; 130-091-150), and treated by 10ug/ml α-IgM (southernbiotech; #2020-01) for 24hrs.

tag: antibody

tag: agent

value: ABC DLBCL cell line (TMD8)


title: ChIP_FGO_Dnmt3l_KO_H3K36me3_rep2

description:
processed data file:
FGO_Dnmt3l_Con_H3K36me3.bed.gz
processed data file:
FGO_Setd2_Con_H3K27me3.bed.gz

treatment_protocol:
8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stage.
8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stage.

value: H3K36me3 (Active Motif, Cat.61021)


title: STAT3CHIP-IGMNB

description: Genomic DNA isolicated from immunoprecipitated chromatin using STAT3 antibody.

source_name: Naïve B cell stimulated by α-IgM 10ug/ml for 24hrs

value: alpha-IgM

value: Naive B cell


title: MDA-MB-231-v-ctrl rep2

value: vector-control

tag: gender

value: female


title: MDA-MB-231-v-ctrl rep1


title: ChIP_FGO_Dnmt3l_Con_H3K27me3_rep2

description:
processed data file:
FGO_Dnmt3l_Con_H3K27me3.bed.gz

value: oocyte

value: FGO


title: MDA-MB-231-FRY rep1


title: ChIP_ST_Early2C_Setd2_KO_H3K4me3

description:
processed data file:
ST_Early2C_Setd2_KO_H3K4me3.bed.gz

value: embryo


title: MDA-MB-231-prt rep2

value: parental line


title: ChIP_GO_P7_Setd2_KO_H3K27me3

description:
processed data file:
GO_P7_Setd2_KO_H3K27me3.bed.gz


title: 12/91_PSC

first: Krzysztof

last: Goryca

address: Banacha 2c

data_processing: Quantile normalised using lumi library in R 2.15.

extract_protocol: For RNA extraction, whole blood was collected and total RNA was isolated using the Tempus RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop spectrophotometer, and samples with A260/A280 ratios of 1.8–2.1 were further assessed using an Agilent 2100 Bioanalyzer. Samples used for microarray analysis had RNA integrity numbers in the range 7.6–9.6.

value: adult

value: whole blood


title: STAT3INPUT-IGMNB


title: MDA-MB-231-prt rep1


title: pSTAT3CHIP-TMD8-DMSO

value: DMSO


title: 12/349_PSC

value: primary sclerosing cholangitis


title: T5082

city: Guangzhou

first: YY

last: Xiong

address: Xingangxi Rd

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
raw sequencing reads were aligned to human reference genome (version hg19, downloaded from UCSC Genome Browser website, http://genome.ucsc.edu/) using HISAT2 (v2.0.4). Gene expression quantification were performed by kallisto (v0.43.0), with reference gene annotations of Gencode version 19. We did statistics analysis including normalization and visualization in R (v3.3.2) with package DESeq2 (v1.14.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and TPM values for each Sample ...

source_name: Kidney biopsy

growth_protocol: HRMCs (purchased from ScienCell, USA) were cultivated in Mesangial Cell Medium (ScienCell). HeLa cells (purchased from Cell Bank, Shanghai Institutes for Biological Sciences) were cultivated in Dulbecco’s modified Eagle’s medium（Gibco）containing 10% fetal bovine serum(FBS)(Gibco). All cells were grown at 37。C under an atmosphere of 5% CO2

extract_protocol:
Total RNA was extracted using TRIzol Reagent(Invitrogen). 250 ng of total RNA was reverse transcribed into complementary DNA(cDNA) with PrimeScript RT reagent kit (Takara), and then diluted 5 times. Equal amount of cDNA was amplified with real-time PCR using SYBR® Premix Ex TaqTM (Takara) in an vii7 Real Time PCR System (Applied Biosystems). The endogenous expression of glyceraldehyde-phosphate dehydrogenase (GAPDH) was determined as the internal control. Relative expression levels were calculated with the 2-ΔΔCt method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HRMCs were cultured in 24-well flat-bottomed plates at a concentration of 1×105 cells in 500 μL of complete MCM. HeLa cells were cultured in 24-well flat-bottomed plates at a concentration of 5×104 cells in 500 μL of complete DMEM. All adherent cells placed in plates overnight for experiments follow-up.  Cells were stimulated by type I IFN (PBL Interferon Source) through directly adding into cell culture with definite time and concentration.  Cells were transfected with Lipofectamine RNAimax (Invitrogen) and diluted with Opti-MEM® I Medium (Gibco). Antisense oligonucleotides (ASOs) targeting to lncRNA RP11-2B6.2 and scramble as control (designed by http://sfold.wadsworth.org and synthesized by Sangon Biotech, Shanghai) at final concentration of 200 nM were also diluted with Opti-MEM. After incubation for 20 min at room temperature, the transfection mixture was added to the cell culture for 12 h. And cells were stimulated with type I IFN at the concentration of 1000 U/ml for additional 6 h.

value: Kidney

value: LN


title: ChIP_Sperm_H3K36me3_rep2

description:
processed data file:
Sperm_H3K36me3.bed.gz

source_name: sperm

extract_protocol:
The DNA extraction follows STEM-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

treatment_protocol: 8-week-old PWK males were sacrificed and sperm were collected from caudal epididymides and treated as previously reported (Hisano et al., 2013).

value: sperm

value: WT


title: T5085


title: T5084


title: ChIP_PN3_IVF_H3K36me3

description:
processed data file:
PN3_IVF_H3K36me3.bed.gz

treatment_protocol: MII oocytes from C57BL/6 were inseminated with mature PWK sperm.

value: H3K36me3 (Active Motif, Cat.61021)


title: carnosine_2

city: Leipzig

first: Henry

last: Oppermann

address: Liebigstraße 19

department: Klinik und Poliklinik für Neurochirurgie

country: Germany

institute: Universitätsklinikum Leipzig

data_processing:
Illumina bcl2fastq v2.17.0 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality terminating bases. Paired-end reads overlapping by at least 11 bases were collapsed to one consecutive read.
Trimmed paired-end reads were mapped to hg38 whole genome using HiSat2 v2.1.0 with parameters -q -p 8 --rna-strandness RF --new-summary
Trimmed collapsed reads were mapped to hg38 whole genome using HiSat2 v2.1.0 with parameters -q -p 8 --rna-strandness R --new-summary
Gene counts were generated with HTSeq v0.6.1 (Anders et al. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 2015)  with parameters –stranded=reverse, --type=exon, --idattr=gene_id and --mode=intersection-strict
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample with the corresponsing gene name and ensemble_id

source_name: U87 (ATCC)

growth_protocol: U87 were purchased from ATCC (Manassas, USA) and cultivated in DMEM (4.5 g/L glucose, without pyruvate, Gibco, Thermo scientific, Darmstadt, Germany) supplemented with 10 % fetal bovine serum (FBS superior, Biochrom, Berlin, Germany), 2 mM GlutaMAX (Gibco) and antibiotics (Gibco) at 37°C and 5% CO2 in humidified air in an incubator.

extract_protocol:
After treatment, cells were washed trice with washing buffer (137 mM NaCl, 5.4 mM HCl, 0.41 mM MgSO4, 0.49 mM MgCl2, 0.126 mM CaCl2, 0.33 mM Na2HPO4, 0.44 mM KH2PO4, 2mM HEPES, pH 7.4). Then, Total RNA was extracted using the miRNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions and RNA was stored at -80°C until further use.
To eliminate all traces of genomic DNA DNAse-digestion (TURBO DNA free Kit, Ambion) was performed twice in each sample. Extracted RNA was quantified using a Qubit RNA-Kit and the Qubit 2.0 instrument (Life Technologies). Quality of RNA was analysed on a Bioanalyzer 2100 instrument (Agilent Technologies). For subsequent RNA-sequencing analyses 200 ng RNA per sample was used. Library preparation was conducted using Truseq-Stranded Total RNA Sample Prep kit (Illumina, Inc, San Diego, CA) including an rRNA depletion step according to manufacturers’ protocol. Fragmentation step was performed for 8 min, depending on the quality of the input RNA, following Illuminas recommendation. Quality and quantity of each prepared library was analysed with the Qubit 2.0 instrument (Qubit DNA-Kit) and the Bioanalyzer 2100. Molarity of each library was calculated and equal amounts were pooled and used for subsequent sequencing (10 pM).
Sequencing was performed with 2 x 101-bp paired-end reads using HiSeq Rapid SBS V2 Kit (200 cycles) on a HiSeq 2500 (Illumina). One rapid run flowcells with 2 lanes was sequenced with the pooled libraries (N=4).

treatment_protocol: One million U87 cells were seeded into a 10-mm cell culture dish (TPP, Trasadingen, Switzerland) with 10 ml of medium. After 24 hours of incubation, cells received fresh medium supplemented with or without 50 mM carnosine. After 24 hours of incubation, extraction was performed.

value: U87 (ATCC)

value: glioblastoma

tag: treatment

value: 50 mM carnosine


title: carnosine_1


title: 12/223_PSC

city: Warszawa

institute: Uniwersytet Warszawski


title: 12/168_PSC


title: 12/224_PSC


title: ChIP_FGO_Dnmt3l_Con_H3K27me3_rep1


title: control_2

value: 0 mM carnosine


title: T5078


title: T5079


title: T5072


title: ChIP_Sperm_H3K36me3_rep1


title: 12//360_PSC


title: T5070


title: MethylC_GO_P7_Setd2_KO_5mC_rep1

description:
processed data file:
GO_P7_Setd2_KO_5mC.bed.gz

data_processing:
STEM-seq datasets were trimmed adaptors by Trim galore and then aligned to the mm9 reference genome though BSSeeker2 with the parameters: --bt2-p 8 --XS 0.2,3 --a CCCCCC --m 4. Multiple mapped and duplicated reads were also removed.
Genome_build: mm9
Supplementary_files_format_and_content: For STEM-seq, the bedgraph files contains the average DNA methylation level of 2kb and 100bp bin for GO-P7 and FGO, respectively.

extract_protocol:
The DNA extraction follows STEM-seq protocol
The STEM-seq libraries were generated following the protocol as described previously(Zhang et al., 2018).

value: oocyte


title: MethylC_FGO_Setd2_KO_5mC_rep2

description:
processed data file:
FGO_Setd2_KO_5mC.bed.gz

value: FGO


title: T5048


title: MethylC_GO_P7_Setd2_KO_5mC_rep2


title: control_1


title: RNA_ST_8C_Setd2_KO_RNA_rep2

description:
processed data file:
ST_8C_Setd2_KO_RNA_FPKM.txt.gz

data_processing:
RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat 2.0.11. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The RNA FPKM txt file contains FPKM value for each sample.

extract_protocol:
The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated following the Smart-seq2 protocol with minor modification (Picelli et al., 2014).

value: embryo


title: MethylC_GO_P7_Setd2_Con_5mC

description:
processed data file:
GO_P7_Setd2_Con_5mC.bed.gz


title: 12/192_PSC


title: 12/317_PSC


title: T5042


title: 12/316_PSC


title: RNA_ST_8C_Setd2_KO_RNA_rep1


title: 12/383_PSC


title: EGFR+ Schwann cell stem cell 2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: CEL files were processed using BioConductor’s affy package with Robust Multi-array Average (RMA) normalization procedure.

source_name: EGFR+ Schwann cell stem cell

label_protocol: standard Affymetrix protocol

growth_protocol: No growth condition, from tumor directly, FACS-sorted

extract_protocol: using QIAGEN kit

treatment_protocol: No treatment,

value: Schwann cells

tag: cell type source

value: Tumor initiating-like cell

tag: genotype/variation

value: EGFR+


title: 12/45_PSC

value: adult

value: whole blood


title: 12/382_PSC

value: primary sclerosing cholangitis


title: T4899

value: Kidney

value: LN


title: RNA_ST_8C_Setd2_Con_RNA_rep2

tag: developmental stage


title: RNA_ST_8C_Setd2_Con_RNA_rep1


title: EGFR+ Schwann cell stem cell 1


title: T4891


title: T4865


title: RNA_GO_P7_Setd2_KO_RNA_rep1

description:
processed data file:
GO_P7_Setd2_KO_RNA_FPKM.txt.gz


title: ATACMe_THP1_0.5hrPMA_rep2

city: Nashville

first: Emily

last: Hodges

state: TN

address: 2212 Garland Ave.

department: Biochemistry

institute: Vanderbilt University

description:
ATAC-Me-seq of THP1 Monocytes: 0.5hrs 162nM PMA treatment
ATAC-seq coupled with bisulfite conversion

data_processing:
Trimming: All sequencing library reads were trimmed of adapters using TrimGalore script wrapper for Cutadapt (Martin, 2011) and FastQC. Version: trim_galore 0.4.0. Command: trim_galore --fastqc --fastqc_args "--outdir ${FASTQC_DIR}" --clip_R1 9 --clip_R2 9 --paired --retain_unpaired --output_dir ${TRIM_DIR} ${R1} ${R2}
Mapping: Standard ATAC reads were mapped with bowtie2. Version: bowtie2 2.2.6. Command: bowtie2 -p 8 --no-discordant --no-mixed -X 1000 -x ${INDEX} -1 ${R1} -2 ${R2} -S ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All bisulfite converted samples were mapped with WALT. Version: WALT v1.0. Command: walt -m 8 -t 6 -i ${INDEX} -1 ${R1} -2 ${R2} -o ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All RNA-seq reads were mapped with STAR. Version: STAR_2.6.1a. Command: STAR --runThreadN 4 --genomeDir /data/hodges_lab/human_genome/GRCh38_Gencode24 --sjdbGTFfile /data/hodges_lab/human_genome/GRCh38_Gencode24/gencode.v24.primary_assembly.annotation.gtf --readFilesCommand zcat --readFilesIn --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
ATAC peak calling: All peak calling was done with MACS2. Version: MACS2 2.1.1. Command: macs2 callpeak -t ${MAPPED_DIR}/${MAPPED}.shifted.bam -f BAMPE -n ${MACS_DIR}/${MAPPED} -g hs -q 0.005 -B --SPMR --keep-dup all --broad --broad-cutoff 0.005
DNA methylation analysis: The Methpipe suite of tools was used for all CpG methylation analysis. Version: Methpipe 3.4.3
Differential RNA-seq analysis: DESeq2 was use to calculate differential RNA expression across the time course. Version: DESeq2 1.18.1. R-Version: 3.4.3
Differential ATAC-seq analysis: TCseq was used to calculate differential chromatin accessibility across the time course. Version: 1.6.1. R-version: 3.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are broadPeak output bed files from MACS2, meth files are a tab delimited text file of CpG methylation values for all symmetic CpGs in hg19, meth files are generated as output from Methpipe
Supplementary_files_format_and_content: DEseq2 normalized transcript abundance table

source_name: THP-1 Monocyte

growth_protocol: THP1 monocytes were cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 units penicillin/streptomycin and 1mM sodium pyruvate. During routine culture THP1 cells were maintained at a density of 0.5-2E6 cells/mL. All cells were regularly screened for mycoplasma contamination using the Lonza MycoAlert kit.

extract_protocol: THP1 cell suspension volume corresponding to 2E5 cells was pelleted in a 1.5mL tube at 4°C, 500 R.C.F for 5 minutes. Supernatant was aspirated and the pellet resuspended in 150µL cold ATAC lysis buffer (10mM Tris-HCl pH = 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL-630). This suspension was agitated by pipetting up/down with a 200µL micropipette tip 8 times. Subsequently, this suspension was pelleted at 4°C, 500 R.C.F for 10 minutes. Supernatant was discarded and pellet immediately resuspended in 190µL transposition reaction mix (10mM Tris-HCl pH=7.5, 5mM MgCl2, 10% Dimethylformamide) by pipetting up/down with a 200µL micropipette tip 3 times. After resuspension 10µL of Tn5 transposase pre-assembled with methylated adapters was added. Tube was flicked gently to mix all components and incubated at 37°C, 30 minutes, 700RPM in an Eppendorf Thermomixer. Immediately after the 30-minute incubation ATAC reactions were terminated by adding 1mL Zymo DNA binding buffer and vortexing. This binding buffer and ATAC reaction mixture was purified according to manufacturer instruction in the Zymo DNA Clean and Concentrator-5 kit. Final elution was in 12.5µL nuclease free H2O. After elution gap repair reactions were assembled and incubated as described in “Wang, Q. et al. Tagmentation-based whole-genome bisulfite sequencing. Nature Protocols 8, 2022-2032 (2013)“ with slight modification (11µL ATAC-Me DNA eluate, 2µL 10µM Tn5mC-Repl01 oligo, 2µL 10x ampligase buffer, 2µL dNTPs 2.5mM each)17. 2µL of the gap repair reaction was reserved for a test PCR amplification to confirm successful ATAC nucleosomal laddering. Subsequently, 2µL of 250mM EDTA (pH=8.0) was added to stop the reaction. Gap repaired ATAC-Me material was bisulfite converted according to manufacturer instructions using the EZ DNA Methylation-Lightning Kit (Zymo). Final elution was in 22µL of M-elution buffer supplied by the kit. Gap repaired, bisulfite converted ATAC-Me DNA reactions were PCR amplified with 12 cycles of amplification using HiFi HotStart Uracil + Ready Mix (KAPA) and barcoded primers. Post-amplification PCR reactions were cleaned and concentrated with a DNA Clean and Concentrator-5 column kit (Zymo). Elution was in 22µL nuclease free H2O. Preliminary library analysis for concentration and size distribution was performed using an Agilent 2200 TapeStation with a D5000 screentape.

treatment_protocol: Differentiation of THP1 monocytes was induced with RPMI medium carrying PMA at a concentration of 100ng/mL (162nM). THP1 monocyte PMA stimulation time points were harvested with a combination of aspiration (for suspended cells) and trypsin (for adherent cells). The final collection of each time point was pelleted at 4°C, 500 R.C.F for 5 minutes. After pelleting cells were resuspended in ice cold PBS and cell counted using an automated cell counter (Biorad). This cell suspension was divided as input material for RNA extraction, genomic DNA extraction and ATAC reactions.

tag: pma stimulation time point


title: T4873


title: RNA_GO_P7_Setd2_KO_RNA_rep2

tag: genotype


title: RNA_GO_P7_Setd2_Con_RNA_rep1

tag: tissue


title: T4826


title: ATACMe_THP1_1hrPMA_rep2

description:
ATAC-Me-seq of THP1 Monocytes: 1hrs 162nM PMA treatment
ATAC-seq coupled with bisulfite conversion

value: 1 hr


title: T4844


title: RNA_GO_P7_Setd2_Con_RNA_rep2


title: EGFR- Schwann cell stem cell 4

source_name: EGFR- Schwann cell stem cell

value: EGFR-


title: T4825


title: 12/34_PSC

description: RNA expression levels in the blood of patient diagnosed with primary sclerosing cholangitis.


title: RNA_Th1_rep2

first: Jinyi

address: Yueyang road 320

institute: IPS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were cleaned for trimming adaptor sequence, low-quality sequence (Q<20) from the 3' end, and filtering the reads with the length less than 20.
Cleaned reads were then mapped to mm10 whole genome using HISAT2 (version 2.0.5) with the default parameters for paired-end data.
Fragments Per Kilobase of transcript per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
HTSeq was used to count the reads for each gene. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using TMM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample.

extract_protocol:
Three populations from IFN-γ-YFP reporter mice were isolated by cell sorting (IFN-γ-Tfh: CD4+CD44hiCD62LlowCXCR5hiPD-1hiCXCR3-YFP- ,IFN-γ+Tfh: CD4+CD44hiCD62LlowCXCR5hiPD-1hiCXCR3+YFP+, Th1: CD4+CD44hiCD62LlowCXCR5-CXCR3+YFP+ ).
Total RNA were extracted using Trizol(Thermo),  and sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: IFN-γ-YFP reporter mice were infected by ZIKV with anti-IFNα/β receptor blocking one day before. Spleens and dLNs were harvested 7 dpi

tag: strain

value: Spleen and draining LN

value: IFN-gamma-YFP reporter


title: T4824


title: RNA_Th1_rep1


title: ATACMe_THP1_2hrPMA_rep2

description:
ATAC-Me-seq of THP1 Monocytes: 2hrs 162nM PMA treatment
ATAC-seq coupled with bisulfite conversion

value: 2 hr


title: ATACMe_THP1_0hrPMA_rep2

description:
ATAC-Me-seq of THP1 Monocytes: 0hrs 162nM PMA treatment
ATAC-seq coupled with bisulfite conversion

value: 0 hr


title: EGFR- Schwann cell stem cell 3


title: EGFR- Schwann cell stem cell 1


title: 8//29_PBC

description: RNA expression levels in the blood of patient diagnosed with primary biliary cholangitis.

tag: condition

value: primary biliary cholangitis


title: ATACMe_THP1_24hrPMA_rep2

description:
ATAC-Me-seq of THP1 Monocytes: 24hrs 162nM PMA treatment
ATAC-seq coupled with bisulfite conversion

value: 24 hr


title: EGFR- Schwann cell stem cell 2


title: RNA_Th1-like-Tfh_rep2


title: EGFR+ Schwann cell stem cell 3


title: 8//12_PBC

tag: age group


title: RNA_Th1-like-Tfh_rep1


title: 8/64_PBC


title: T4814


title: 8/62_PBC


title: 8//8_PBC


title: 8//30_PBC


title: T018

value: healthy


title: RNA_Tfh_rep2


title: RNA_Tfh_rep1


title: ATACMe_THP1_0.5hrPMA_rep1


title: T017


title: ATACMe_THP1_24hrPMA_rep1


title: ATACMe_THP1_1hrPMA_rep1


title: T5041


title: T015


title: T4813


title: ChIP_1C_Setd2_KO_H3K27me3

description:
processed data file:
1C_Setd2_KO_H3K27me3.bed.gz

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome. For STEM-seq, the bedgraph files contains the average DNA methylation level of 2kb bin. The RNA FPKM txt file contains FPKM value for each sample.

value: embryo

tag: chip-antibody

value: H3K27me3 (Diagenode,Cat.C15410069)


title: 8/58_PBC


title: 8/50_PBC


title: 8/53_PBC


title: T014


title: 8//31_PBC


title: ATACMe_THP1_0hrPMA_rep1


title: RENAL CELL CARCINOMA7

city: Shenyang

first: Chengcheng

last: Lv

state: Liaoning

address: 44. Xiaoheyan Road

department: Department of Urology Surgery

institute: Liaoning Cancer Hospital and Institute

description:
13875346C
circRNA-Seq

data_processing:
CircRNA-Seq high throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The reads were aligned to the reference genome/transcriptome with STAR software and circRNAs were detected and annotated with DCC software
circBase database and circ2Trait disease database were used to annotated the identified circRNAs. Raw junction reads for all samples were normalized by total reads number and log2 transformed.
Differentially expressed circRNAs were identified by ttest between two groups.
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

source_name: kidney

extract_protocol:
Total RNA was extracted from the frozen kidney tissues with using TRIzol reagent
Total RNA from each sample was used to prepare the circRNA sequencing library  using standard Illumina protocols

value: male

tag: tumor stage

tag: age

value: renal cell carcinoma


title: ChIP_1C_Setd2_KO_H3K4me3

description:
processed data file:
1C_Setd2_KO_H3K4me3.bed.gz

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h.

tag: chip antibody

value: H3K4me3 (home made)


title: T013

tag: disease


title: ChIP_1C_Setd2_Con_H3K4me3

description:
processed data file:
1C_Setd2_Con_H3K4me3.bed.gz


title: RENAL CELL CARCINOMA6

description:
14095024C
circRNA-Seq


title: T012


title: RENAL CELL CARCINOMA5

description:
14057581C
circRNA-Seq

value: female

value: Ⅲ


title: ATACMe_THP1_2hrPMA_rep1


title: T011

value: Kidney


title: ChIP_FGO_Setd2_KO_H3K36me3_rep1

description:
processed data file:
FGO_Setd2_KO_H3K36me3.bed.gz

value: oocyte

value: FGO

value: H3K36me3 (Active Motif, Cat.61021)


title: RENAL CELL CARCINOMA3

description:
13894592C
circRNA-Seq


title: ChIP_FGO_Setd2_Con_H3K36me3_rep2

description:
processed data file:
FGO_Setd2_Con_H3K36me3.bed.gz


title: RENAL CELL CARCINOMA4

description:
13991707C
circRNA-Seq


title: 8//16_PBC

value: adult

value: whole blood


title: 18/139_WA

description: RNA expression levels in the blood of patient diagnosed with ulcerative colitis.

source_name: Ulcerative colitis, adult

value: ulcerative colitis


title: 18/138_WA


title: 8/35_PBC

value: primary biliary cholangitis


title: ChIP_FGO_Setd2_Con_H3K36me3_rep1


title: Leaf, MIR160a CRISPR single nucleotide insertion line (T2), rep1

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043).
Genome_build: None
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Total RNAs were prepared using a Trizol reagent-based method
Small RNA libraries were made using 5 µg total RNA with TruSeq Small RNA Library Prep Kit, and sequenced on the Illumina HiSeq 2500 platform.

value: leaf

tag: ecotype


title: RENAL CELL CARCINOMA2

description:
13935242C
circRNA-Seq

tag: gender


title: Leaf, MIR160a CRISPR control, rep2

value: MIR160a CRISPR control


title: ChIP_FGO_Setd2_KO_H3K27me3_rep2

description:
processed data file:
FGO_Setd2_KO_H3K27me3.bed.gz


title: RENAL CELL CARCINOMA1

description:
13907589C
circRNA-Seq


title: ChIP_FGO_Setd2_KO_H3K36me3_rep2


title: NORMAL KIDNEY7

description:
13875346N
circRNA-Seq

value: normal


title: Leaf, MIR160a CRISPR control, rep1


title: ChIP_FGO_Setd2_KO_H3K27me3_rep1

value: H3K27me3 (Diagenode,Cat.C15410069)


title: Viable_paternal_excess_3 [RNA-Seq]

city: Cambridge

first: satyaki

middle: P

last: Rajavasireddy

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description: mRNA-seq

data_processing:
Sequence data were filtered for quality with “ trim_galore -q 25 --phred64 --fastqc --length 20 --stringency 5”.
Filtered reads were aligned to the TAIR10 genome using “tophat  -i 30 -I 3000 --solexa1.3-quals -p 5 -g 5 --segment-mismatches 1 --segment-length 18 --b2-very-sensitive”
CUFFDIFF with default settings and the ARAPORT11 genome annotation to calculate changes in gene expression and their statistical significance.
We used a custom script (https://github.com/clp90/imprinting_analysis/tree/master/helper_scripts) to identify allele specific reads.
To assess TE transcript levels, we aligned our reads to the REPBASE consensus sequence (Jurka et al., 2005) using “ bowtie -v 2 -m 3 --best --strata -p 5 --phred64” and summed reads mapping to each TE family. META1, ATHILA6A and ATGP8 were precluded from further analyses because of mapping artifacts. Differential expression was identified using DEGSEQ.
Genome_build: TAIR10
Supplementary_files_format_and_content: Cuffdiff output with details of differential expression
Supplementary_files_format_and_content: Allele specific differences in expression between balanced, lethal and viable paternal excess endosperm
Supplementary_files_format_and_content: TE expression differences

molecule: polyA RNA

source_name: Endosperm

growth_protocol: Plants were grown in a growth-chamber with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at seven DAP

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total embryo or endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
DNase I-treated RNA (Invitrogen, Life Technologies Corporation, Carlsbad, CA) was used to prepare mRNA-seq libraries using the SMARTerUltralowPOLYA kit at the Whitehead Institute's Genome Technology Core.

treatment_protocol: no treatment

value: Ler female x 4N Col  nrpd1 male

value: 7 days after pollination


title: ChIP_FGO_Setd2_Con_H3K27me3_rep1

description:
processed data file:
FGO_Setd2_Con_H3K27me3.bed.gz

source_name: oocyte


title: NORMAL KIDNEY6

description:
14095024N
circRNA-Seq

value: male


title: Leaf, MIR160a CRISPR single nucleotide insertion line (T2), rep2


title: 8/40_PBC

source_name: Primary biliary cholangitis, adult


title: 8//28_PBC


title: 18/137_WA


title: 18/135_WA


title: Viable_paternal_excess_2_part2 [RNA-Seq]

description: mRNA-seq


title: 18/129_WA


title: 8//25_PBC


title: ChIP_FGO_Setd2_KO_H3K4me3_rep2

description:
processed data file:
FGO_Setd2_KO_H3K4me3.bed.gz

value: H3K4me3 (home made)


title: 18/128_WA


title: Viable_paternal_excess_2_part1 [RNA-Seq]

description: mRNA-seq


title: 18/125_WA


title: 18/127_WA


title: NORMAL KIDNEY4

description:
13991707N
circRNA-Seq


title: ChIP_FGO_Setd2_KO_H3K4me3_rep1


title: NORMAL KIDNEY3

description:
13894592N
circRNA-Seq

value: female


title: ChIP_FGO_Setd2_Con_H3K4me3_rep2

description:
processed data file:
FGO_Setd2_Con_H3K4me3.bed.gz


title: Viable_paternal_excess_1_part2 [RNA-Seq]

description: mRNA-seq


title: ChIP_FGO_Setd2_Con_H3K4me3_rep1


title: Viable_paternal_excess_1_part1 [RNA-Seq]

description: mRNA-seq


title: Lethal_paternal_excess_3 [RNA-Seq]

description: mRNA-seq

value: Ler female x 4N Col male


title: NORMAL KIDNEY1

description:
13907589N
circRNA-Seq


title: ChIP_FGO_Dnmt3l_KO_H3K27me3_rep2

description:
processed data file:
FGO_Dnmt3l_KO_H3K27me3.bed.gz

value: oocyte


title: 18/124_WA


title: NORMAL KIDNEY5

description:
14057581N
circRNA-Seq


title: Lethal_paternal_excess_2_part2 [RNA-Seq]

description: mRNA-seq


title: ChIP_FGO_Dnmt3l_KO_H3K36me3_rep1

description:
processed data file:
FGO_Dnmt3l_KO_H3K36me3.bed.gz

value: FGO


title: RETS16084

source_name: HeLa

tag: cell line

value: HeLa

value: cancer + ifh 6h + antisense knock down


title: ChIP_FGO_Dnmt3l_Con_H3K36me3_rep2

description:
processed data file:
FGO_Dnmt3l_Con_H3K36me3.bed.gz

value: H3K36me3 (Active Motif, Cat.61021)


title: Lethal_paternal_excess_2_part1 [RNA-Seq]

description: mRNA-seq


title: RETS16082

value: cancer + ifn 6h


title: ChIP_FGO_Dnmt3l_Con_H3K36me3_rep1


title: Lethal_paternal_excess_1_part2 [RNA-Seq]

description: mRNA-seq

value: 8 days after pollination


title: 18/114_WA

value: ulcerative colitis

value: adult

value: whole blood


title: 18/120_WA


title: NORMAL KIDNEY2

description:
13935242N
circRNA-Seq

value: normal


title: ChIP_mESC_500_H3K36me3

description:
processed data file:
mESC_500_H3K36me3.bed.gz

source_name: embryonic stem cell

value: embryonic stem cell


title: Lethal_paternal_excess_1_part1 [RNA-Seq]

description: mRNA-seq

value: 7 days after pollination


title: RETS16081

value: cancer + antisense knowck down


title: Viable_Paternal_excess_2 [miRNA-Seq]

description: sRNA-seq

data_processing:
Analysis of sRNA libraries began with the trimming of low-quality read ends fastq_quality_trimmer -v -t 20 -l 25; (http://hannonlab.cshl.edu/fastx_toolkit/).
Adapters were removed with  cutadapt -a TGGAATTCTCGGGTGCCAAGG  --trimmed-only --quality-base 64 -m 24 -M 40 --max-n 0.5 (https://cutadapt.readthedocs.io/en/stable/)
sRNA libraries prepared using the NEXTflex sRNA-Seq Kit v2 are appended with 4 base randomized barcodes immediately 3’ and 5’ of the sRNA read itself. These barcodes were used to remove PCR duplicates (any read of the same sRNA sequence with identical flanking barcodes on both ends) using prinseq-lite –fastq <infile> -out_format 3 –out_good <outfile> -derep 1
Reads were aligned to TAIR10 using bowtie -v 1 --best  -5 4 -3 4 --sam --phred64-quals  or --phred33-quals
Genome_build: TAIR10
Supplementary_files_format_and_content: un-normalized bedgraph files with 4th column showing read depth at that position. Bedgraph files include reanalysis of data from balanced endosperm previously published by Erdmann etal (2017).

growth_protocol: Plants were grown in a growth-chamber with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at seven days after pollination

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total embryo or endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
The small RNA pool was separated from the larger RNA pool by sequential ethanol addition and filtering. The larger RNA pool was collected on filters after the addition of ethanol equivalent to 60% of the sample volume, and the small RNA pool was collected on filters after the addition of ethanol equivalent to 50% of the flowthrough volume from the larger RNA filter binding step.  Libraries for Illumina sequencing were constructed using the NEXTflex Small RNA-Seq Kit v3 as directed (Bioo Scientific Corporation, Austin, Texas). Final library amplification was carried out for 24 cycles and the resultant libraries were size selected with a pippin prep. 40 base single-end sequencing of sRNA libraries was performed on an Illumina HiSeq 2500 machine.

value: Ler female x 4N Col  nrpd1 male


title: RETS16079

value: cancer


title: ChIP_mESC_10k_H3K36me3

description:
processed data file:
mESC_10k_H3K36me3.bed.gz


title: 18/103_WA


title: ChIP_ICM_H3K36me3_rep2

description:
processed data file:
ICM_H3K36me3.bed.gz

source_name: embryo

value: embryo

value: ICM


title: GECKOv2 plasmid pool A

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

description: plasmid DNA

organism: synthetic construct

source_name: plasmid DNA

growth_protocol: HAP1 and HAP1-derived cell lines and pools were maintained in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% FBS and 100 units/mL penicillin, 100 µg/mL streptomycin (Invitrogen).

extract_protocol:
Genomic DNA was prepared using the Gentra Puregene kit (Qiagen #158767)
Integrated sgRNAs were amplified by PCR for 24 cycles. For sgRNA sequencing, 2 ug of gDNA per PCR reaction was used as template, and four reactions were pooled per sample to ensure sufficient representation of integrated sgRNAs. The resulting amplicon was diluted and further amplified in a second-round PCR to add Illumina adaptor sequences and sample-specific index barcodes.

treatment_protocol: HAP1 cells were transduced with the GECKOv2 lentiviral library, and at 24-hours post infection, puromycin (2.5 ug/ml final concentration) was added to the media to select for transduced cells.

tag: sample type

value: plasmid pool


title: ChIP_ICM_H3K36me3_rep1

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).


title: 5//23_WY

source_name: Ulcerative colitis, child

value: child


title: GECKOv2 plasmid pool B

description: plasmid DNA


title: ChIP_8C_H3K36me3_rep2

description:
processed data file:
8C_H3K36me3.bed.gz


title: Lethal_Paternal_excess_2 [miRNA-Seq]

description: sRNA-seq

value: Ler female x 4N Col male


title: 5//2_WY


title: ChIP_8C_H3K36me3_rep1

description:
processed data file:
8C_H3K36me3.bed.gz

value: H3K36me3 (Active Motif, Cat.61021)


title: Lethal_Paternal_excess_1 [miRNA-Seq]

description: sRNA-seq


title: Viable_paternal_excess_2 [Bisulfite-seq]

description:
Bisulfite sequencing
Viable_paternal_excess_2

data_processing:
Reads that were obtained were filtered for quality with “trim_galore --phred64 --fastqc --stringency 5 --length 15 --paired --clip_R1 2 --clip_R2 2”.
The reads were then aligned to TAIR10 using “bismark  -N 1 -L 20”.
Duplicate reads were removed using bismark.
Bismark methylation extractor was used to obtain unfiltered per base methylation data. Custom scripts previously described  were used to obtain per base methylation and to identify DMRs.
We used a custom script (https://github.com/clp90/imprinting_analysis/tree/master/helper_scripts) to identify allele specific reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Contains output from script for DMR detection and includes methylation per window, significance of difference in tab delimited files. Generated based on data from both biological replicates.
Supplementary_files_format_and_content: List of detected DMRs for CHH, CHG and CG methylation in comparisons between Balanced, Lethal and Viable paternal excess endosperm in bed format. Generated based on data from both biological replicates.Briefly, differences in methylation were calculated genome-wide for 300 bp sliding windows with 200 bp overlaps. To be included, windows had at least 3overlapping cytosines in both genotypes with a read depth of at least 6 reads per cytosine. Windows called as significantly different were at least 10% different between tested genotypes for CHH methylation, 20% for CHG methylation and 30% for CG methylation. Significance of difference was calculated by F.E.T with a Bonferroni- Hochberg correction (p<0.01).
Supplementary_files_format_and_content: Methylation level at single base resolution in CHH,CHG and CG context in Balanced, lethal and viable paternal excess endosperm in tdf format. Only cytosines passing coverage thresholds are included here. Each *tdf file for a genotype includes data from both biological replicates

extract_protocol:
Endosperm was hand dissected from seeds at 7 DAP. DNA was extracted from dissected endosperm using the QiaAMP DNA microkit. Breifly, dissected tissue was incubated in ATL buffer and Proteinase K overnight. 80-100 ng of DNA obtained for each sample was subjected to bisulfite treatment using Methylcode Bisulfite conversion kit (Invitrogen).
Purified, bisulfite converted DNA was used as input for library construction using Illumina Truseq DNA methylation kit.


title: 18/106_WA


title: 101035680075_F

first: Zhiqiang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: As per instructions for Illumina HT12v4.0 BeadArrays.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value. Values below the detection threshold (determined from the P95) value for negative control probes were "floored", i.e., set to the detection threshold value. Probes were then excluded for which <25% of the samples in the dataset exceeded the detection threshold value.

label_protocol: 300 ng of total RNA was reverse-transcribed, biotinylated, and amplified by standard Eberwine labeling with the  Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Cells were maintained in RPMI 1640 medium with L-glutamine supplemented with 5% fetal bovine serum and 1% penicillin/streptomycin. Per replicate, 1 million cells were cultured in 8 mL of  medium. After 24 hr treatment with either DMSO or TAK-243 (25 nM) for 24 hours, cells were collected and washed 2X with PBS for gene expression analysis.

extract_protocol: Total RNA was isolated from harvested cells with the RNeasy Plus Mini Kit (Qiagen, catalog#:74134) with subsequent RNA quality assessment using Agilent 2100 Bioanalyzer.

tag: cell type

value: multiple myeloma

tag: treatment

value: Treated (TAK-243)


title: 101035680075_D


title: 101035680075_E


title: 5//18_WY

extract_protocol: For RNA extraction, whole blood was collected and total RNA was isolated using the Tempus RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop spectrophotometer, and samples with A260/A280 ratios of 1.8–2.1 were further assessed using an Agilent 2100 Bioanalyzer. Samples used for microarray analysis had RNA integrity numbers in the range 7.6–9.6.

value: ulcerative colitis


title: 2/65_WY


title: 5//22_WY


title: 2/136_WY


title: 2/119_WY


title: Viable_Paternal_excess_1 [miRNA-Seq]

description: sRNA-seq

tag: developmental stage


title: 101035680075_C

value: Control (DMSO)


title: Viable_paternal_excess_1 [Bisulfite-seq]

description:
Bisulfite sequencing
Viable_paternal_excess_1

tag: genotype


title: 101035680075_B


title: ChIP_Late_2C_H3K36me3_rep2

description:
processed data file:
Late_2C_H3K36me3.bed.gz

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome.

tag: tissue


title: Lethal_paternal_excess_2 [Bisulfite-seq]

description:
Bisulfite sequencing
Lethal_paternal_excess_2


title: 101035680075_A


title: Lethal_paternal_excess_1 [Bisulfite-seq]

description:
Bisulfite sequencing
Lethal_paternal_excess_1


title: ChIP_1C_H3K36me3_rep2

description:
processed data file:
1C_H3K36me3.bed.gz


title: Balanced_2 [Bisulfite-seq]

description:
Bisulfite sequencing
Balanced_2

value: Ler female x  Col male


title: ATAC_THP1_24hrPMA_rep2

description: ATAC-seq of THP1 Monocytes: 24hrs 162nM PMA treatment

extract_protocol: THP1 cell suspension volume corresponding to 2E5 cells was pelleted in a 1.5mL tube at 4°C, 500 R.C.F for 5 minutes. Supernatant was aspirated and the pellet resuspended in 150µL cold ATAC lysis buffer (10mM Tris-HCl pH = 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL-630). This suspension was agitated by pipetting up/down with a 200µL micropipette tip 8 times. Subsequently, this suspension was pelleted at 4°C, 500 R.C.F for 10 minutes. Supernatant was discarded and pellet immediately resuspended in 190µL transposition reaction mix (10mM Tris-HCl pH=7.5, 5mM MgCl2, 10% Dimethylformamide) by pipetting up/down with a 200µL micropipette tip 3 times. After resuspension 10µL of pre-assembled Tn5 transposome was added. Tube was flicked gently to mix all components and incubated at 37°C, 30 minutes, 700RPM in an Eppendorf Thermomixer. Immediately after the 30-minute incubation ATAC reactions were terminated by adding 1mL Zymo DNA binding buffer and vortexing. This binding buffer and ATAC reaction mixture was purified according to manufacturer instruction in the Zymo DNA Clean and Concentrator-5 kit. Final elution was in 12.5µL nuclease free H2O. Libraries were barcoded and amplified with 8 cycles of PCR amplification

tag: pma stimulation time point

value: 24 hr


title: ChIP_FGO_H3K36me3_rep2

description:
processed data file:
FGO_H3K36me3.bed.gz

value: oocyte

value: FGO


title: 13/110_CA

description: RNA expression levels in the blood of patient diagnosed with crohn’s disease.

source_name: Crohn’s disease, adult

tag: condition

value: Crohn's disease

value: adult

value: whole blood


title: Balanced_1 [Bisulfite-seq]

description:
Bisulfite sequencing
Balanced_1

value: 7 days after pollination


title: ATAC_THP1_0hrPMA_rep2

description: ATAC-seq of THP1 Monocytes: 0hrs 162nM PMA treatment

value: 0 hr