title: Heart, WT_Sham_06

city: Iowa City

first: Renata

middle: O

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
Reads aligned using HISAT2 version 2.0.6
the number of reads per feature were calculated using HTSeq version 0.7.1
counts were normalized and anlayzed for differential expression using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated table of normalized count data from DESeq2

source_name: Heart

extract_protocol:
mirVana™ miRNA Isolation Kit; totalRNA protocol
Illumina TruSeq Stranded mRNA sample preparation kit

treatment_protocol:
6-week old mice were subjected to transaortic constriction (TAC) using 7-0 Proline suture around a blunt 27-G needle placed between the innominate artery and the left common carotid artery
Cardiac function was assessed two days after surgery and mice sacrificed on the third day. The apex of the heart was used for RNA extraction.

tag: strain

tag: genotype

tag: surgery

value: Sham

tag: age

value: 6 weeks


title: 5_r2: TF5 Zm00001d044785 ChIP-Seq

status: Public on Mar 01 2020

type: SRA

city: Hong Hong

first: Silin

last: Zhong

address: Shatin, N.T.

department: School of Life Sciences

country: China

institute: CUHK

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR

library_source: genomic

data_processing:
For mapping, we aligned the raw reads to the unmasked maize genome (B73 RefGen_v4) using Bowtie 2 (version 2.2.5) under the default parameters with the 3’  100 bp trimming option. Reads with mapping quality >= 10 were kept and PCR duplicates are removed using SAMTools (version 1.3). Deeptools bamcoverage was used to convert the BAM to bigwig files for viewing.
For peak calling, BAM files of biological replicates were used to call peaks with the SPP peak caller using relaxed parameters “-i = <INPUT BAM file>”, “-npeak = 300,000”, with input as control. Peaks in the transformed TF genebody itself are removed. Reproducible peaks were obtained with the IDR (Irreproducible discovery rate) statistical framework (version 2.0.3), as implemented in the PhantomPeakQualTools package, using 1% IDR as the threshold (cut-off).
To identify the high confident target genes of each TF, we used the probabilistic model TIP (Cheng et al., Bioinformatics, 2011, 3221–3227) with FDR 0.05 as cutoff.
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: peak and bigwig files
Supplementary_files_format_and_content: TF_target_TIP.txt: High cofident TF target genes called by TIP

molecule: genomic DNA

organism: Zea mays

source_name: Leaf protoplast

growth_protocol: Leaf protoplast from 1-2 weeks old maize seedlings

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with streptavidin dynabeads.
Libraries were prepared according to Illumina's instructions using purified HS-Tn5 transposase, Tn5-MEA/B adapter as well as N5xx and N7xx PCR primers.

treatment_protocol: PEG mediated protoplast transformation

tag: cultivar

tag: tissue

value: Leaf protoplast

tag: transcription factor


title: 58_r2: TF58 Zm00001d015407 ChIP-Seq


title: RC17_after_mesDA_16_F2

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

library_source: transcriptomic

data_processing:
All reads were aligned to the human (hg19) genome using STAR v2.3.0e (Dobin et al. 2013)
Non-uniquely mapped reads were removed using Samtools
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl ( June 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values are provided as rpkms and counts (comma separated text files)

molecule: polyA RNA

organism: Homo sapiens

source_name: Human graft in rat brain

growth_protocol: Ventral midbrain human embryonic stem cells have been generated following the Nature protocols: Nolbrant et al 2017.

extract_protocol:
Single cells have been extracted from tissue using Papain Dissociation System (Worthington). cDNA was generated from FACS sorted single cells (ventral midbrain human embryonic stem cells before grafting, fetal cells before and after grafting were sorted for size, ventral midbrain human embryonic stem cells after grafting were sorted for GFP expression) using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer.
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

tag: cell type

value: B

tag: sortingmethod

value: GFP

tag: plate


title: FFPE_renal_carcinoma_57

type: RNA

city: Madrid

first: Lucia

last: Trilla-Fuertes

state: Madrid

address: Paseo de la Castellana 261

country: Spain

institute: Hospital Universitario La Paz

description:
US22502514_252182713904_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples

hyb_protocol: One hundred ng of Cy3 labeled RNA were hybridized for 20 hours at 55ºC in a hybridization oven (G2545A, Agilent) set to 20 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer

scan_protocol: The scan was done on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) equipped with extended dynamic range (XDR) software.

data_processing:
Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1.
Only miRNAs with an average intensity over the 20th percentile of the overall intensities and a detectable signal in at least 10 percent of the hybridized samples considered for further analysis.

molecule: total RNA

source_name: renal carcinoma

label_protocol: 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

extract_protocol: FFPE tumor specimens were cut into serial sections with a thickness of 10 µm. Total RNA was then isolated using the miRNEasy Kit (Quiagen). Purified RNA quality control for quantity and purity was assessed using an ND-1000 NanoDrop spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Paraffin samples with at least 50% of tumor cells were selected by a pathologist.

value: renal carcinoma


title: FFPE_renal_carcinoma_55

description:
US22502514_252182713904_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_56

description:
US22502514_252182713904_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_F10


title: RC17_after_mesDA_16_F11


title: FFPE_renal_carcinoma_54

description:
US22502514_252182713904_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 58_r1: TF58 Zm00001d015407 ChIP-Seq


title: 56_r4: TF56 Zm00001d035604 ChIP-Seq


title: FFPE_renal_carcinoma_59

description:
US22502514_252182713904_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_F1


title: RFP_2iL_Rep1

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

data_processing:
Library strategy: Ribosome-profiling
To analyze the ribosome profiling data, FASTQ reads were processed s previously described (Ingolia et al., 2012). Briefly, adaptor sequences were removed using fastx_clipper (fastx_toolkit-0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and by employing the following parameters clipper -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -n –v. Reads were then trimmed using fastx_trimmer (fastx_toolkit-0.0.14) and  -Q33 -f 2 parameters.  Both RNA-seq reads and the trimmed ribosome profiling reads were then aligned against mouse rRNA, tRNA, snRNA, snoRNA, mtRNA sequences using Bowtie (Langmead et al., 2009) and --seedlen=23 to deplete these small RNA contamination. Unmapped reads (cleaned) were then mapped against mouse genome (mm9) using GSNAP (Wu and Watanabe, 2005) and by employing the following parameters:  -B 5 -t 15 -N 1 -E 100 -w 100000 -n 10 -s mm9refGene_splice. Mapped reads were counted in the coding sequence using HTseq-count (Anders et al., 2015) with the settings: -m union -s reverse -t CDS.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth.

organism: Mus musculus

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were maintained in NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore). To test the genome wide binding of Esrrb, Nr5a2 and Klf4, we generated BAC lines expressing the GFP-tagged proteins as described previously by Poser et al (poser I et al Nat. Methods 5, 409–415 (2008). For Nr5a2-null ESCs, cre-recombination was induced by treating with 4-hydroxy tamoxifen (0.5 μM) for 2 days. Cells were confirmed for the correct deletion using PCR. All siRNA experiments were performed for 72h and by using 25pmol stealth siRNAs per well of 6-well plates.

extract_protocol:
Illumina RNA-seq strand specific
Briefly, 500 µg of the ribonucleoproteins (2 biological replicates per sample) were treated with 1000U RNase I (Ambion Cat# AM2295) at 4oC for 50 min with gentle end-over-end rotation followed by incubation with SuperaseIn (Ambion, Cat# AM2696). Monosomes were pelleted by ultracentrifugation in a 34% sucrose cushion at 70,000 rpm in TLA-120.2 rotor (Beckman Coulter) at 4oC for 3h. RNA fragments were extracted with acid phenol (2x), once with chloroform, and precipitated with isopropanol at -20oC in the presence of NaOAc and GlycoBlue (Invitrogen). Purified RNA samples were resolved on a denaturing 15% polyacrylamide-urea gel and the sections corresponding to 28-32 nucleotides containing the ribosome footprints (RFPs) were excised, eluted, and precipitated by isopropanol.
Purified RFPs were dephosphorylated using T4 polynucleotide kinase (New England Biolabs) for 1 h at 37°C. Denatured fragments were resuspended in 10 mM Tris (pH 7) and quantified using the Bio-Analyzer Small RNA assay (Agilent). A sample of 10 pmol of RNA was ligated to the 3′-adaptor with T4 RNA ligase 1 (New England Biolabs) for 2 h at 37°C. Reverse transcription was carried out using oNTI223 adapter (Illumina) and SuperScript III reverse transcriptase (Invitrogen) according to the manufacturer’s instructions. Products were separated from the empty adaptor on a 10% polyacrylamide Tris/Borate/EDTA-urea (TBE-urea) gel and circularized by CircLigase (Epicentre). Ribosomal RNA amounts were reduced by subtractive hybridization using biotinylated rDNA complementary oligos (Ingolia et al., 2012). The RFP libraries were amplified by PCR (11 cycles) using indexed primers and quantified using the Agilent BioAnalyzer High-Sensitivity assay. DNA was then sequenced on the HiSeq-2000 platform with read length of 50 nucleotides (SR50) according to the manufacturer’s instructions, with sequencing primer oNTI202 (5CGACAGGTTCAGAGTTCTACAGTCCGACGATC).

tag: background strain

value: Mouse Embryonic Stem Cells

tag: treatment

value: 2i/LIF culture

tag: cell line


title: Heart, WT_TAC_06

country: USA

value: TAC


title: Heart, IRS2KO_TAC_06

value: alphaMHC-Cre X IRS2-flox


title: FFPE_renal_carcinoma_52

description:
US22502514_252182713900_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: Heart, IRS1KO_TAC_05

value: alphaMHC-Cre X IRS1-flox


title: RC17_after_mesDA_16_E9


title: FFPE_renal_carcinoma_51

description:
US22502514_252182713900_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_E7


title: 56_r1: TF56 Zm00001d035604 ChIP-Seq


title: Heart, IRS1KO_Sham_05


title: RC17_after_mesDA_16_E6


title: Heart, WT_TAC_05


title: FFPE_renal_carcinoma_53

description:
US22502514_252182713900_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: 55_r2: TF55 Zm00001d041576 ChIP-Seq


title: FFPE_renal_carcinoma_49

description:
50_3990_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_50

description:
US22502514_252182713900_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_48

description:
US22502514_252182713900_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: 55_r1: TF55 Zm00001d041576 ChIP-Seq


title: Heart, WT_Sham_05


title: 54_r2: TF54 Zm00001d038683 ChIP-Seq


title: RC17_after_mesDA_16_E3


title: FFPE_renal_carcinoma_47

description:
US22502514_252182713900_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: 56_r3: TF56 Zm00001d035604 ChIP-Seq


title: 56_r2: TF56 Zm00001d035604 ChIP-Seq


title: 54_r1: TF54 Zm00001d038683 ChIP-Seq


title: Heart, IRS2KO_TAC_05


title: RC17_after_mesDA_16_E2


title: 4_r2: TF4 Zm00001d034601 ChIP-Seq


title: Heart, IRS2KO_Sham_04


title: Heart, IRS2KO_Sham_05


title: RC17_after_mesDA_16_E5


title: FFPE_renal_carcinoma_46

description:
US22502514_252182713900_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_E4


title: Heart, IRS2KO_TAC_04


title: RC17_after_mesDA_16_E10


title: FFPE_renal_carcinoma_45

description:
US22502514_252182713900_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_44

description:
US22502514_252182713806_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: 4_r1: TF4 Zm00001d034601 ChIP-Seq


title: RC17_after_mesDA_16_E1


title: 41_r2: TF41 Zm00001d016793 ChIP-Seq


title: FFPE_renal_carcinoma_43

description:
US22502514_252182713806_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: Heart, WT_Sham_04


title: 41_r1: TF41 Zm00001d016793 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: Heart, IRS1KO_Sham_04


title: RC17_after_mesDA_16_D9


title: 40_r2: TF40 Zm00001d014863 ChIP-Seq


title: 5_r3: TF5 Zm00001d044785 ChIP-Seq


title: RC17_after_mesDA_16_D8


title: FFPE_renal_carcinoma_41

description:
US22502514_252182713806_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: 40_r1: TF40 Zm00001d014863 ChIP-Seq


title: FFPE_renal_carcinoma_42

description:
US22502514_252182713806_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: Heart, IRS2KO_Sham_03


title: RC17_after_mesDA_16_E11


title: RC17_after_mesDA_16_D7


title: FFPE_renal_carcinoma_40

description:
US22502514_252182713806_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: Heart, IRS1KO_TAC_06


title: Heart, IRS1KO_TAC_04


title: 3_r2: TF3 Zm00001d031717 ChIP-Seq


title: FFPE_renal_carcinoma_39

description:
US22502514_252182713806_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_F6


title: Heart, IRS2KO_TAC_03


title: RC17_after_mesDA_16_D6


title: 3_r1: TF3 Zm00001d031717 ChIP-Seq


title: Heart, WT_Sham_03


title: RC17_after_mesDA_16_D5


title: Heart, WT_TAC_03


title: RC17_after_mesDA_16_D4


title: RC17_after_mesDA_16_D3


title: Heart, IRS1KO_Sham_03


title: 38_r1: TF38 Zm00001d029875 ChIP-Seq


title: FFPE_renal_carcinoma_38

description:
US22502514_252182713806_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: 38_r2: TF38 Zm00001d029875 ChIP-Seq


title: Heart, IRS2KO_Sham_06


title: FFPE_renal_carcinoma_37

description:
US22502514_252182713806_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_36

description:
US22502514_252182713805_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: Heart, IRS1KO_TAC_03


title: FFPE_renal_carcinoma_35

description:
US22502514_252182713805_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: Heart, IRS1KO_Sham_06


title: Heart, IRS2KO_TAC_02


title: 34_r1: TF34 Zm00001d024644 ChIP-Seq


title: RC17_after_mesDA_16_D11


title: 34_r2: TF34 Zm00001d024644 ChIP-Seq


title: 32_r2: TF32 Zm00001d050816 ChIP-Seq


title: FFPE_renal_carcinoma_33

description:
US22502514_252182713805_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_34

description:
US22502514_252182713805_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: Heart, IRS1KO_TAC_02


title: 32_r1: TF32 Zm00001d050816 ChIP-Seq


title: RC17_after_mesDA_16_C9


title: Heart, IRS2KO_Sham_02


title: Heart, IRS1KO_Sham_02


title: FFPE_renal_carcinoma_31

description:
US22502514_252182713805_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: 30_r2: TF30 Zm00001d016861 ChIP-Seq


title: RC17_after_mesDA_16_C8


title: 30_r1: TF30 Zm00001d016861 ChIP-Seq


title: Heart, WT_Sham_02


title: 2_r2: TF2 Zm00001d013443 ChIP-Seq


title: RC17_after_mesDA_16_D2


title: RC17_after_mesDA_16_C6


title: FFPE_renal_carcinoma_30

description:
30_3990_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: 2_r1: TF2 Zm00001d013443 ChIP-Seq


title: Heart, WT_TAC_02


title: Heart, IRS2KO_TAC_01


title: RC17_after_mesDA_16_C4


title: Heart, IRS2KO_Sham_01


title: 29_r2: TF29 Zm00001d007068 ChIP-Seq


title: FFPE_renal_carcinoma_27

description:
US22502514_252182713804_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_C3


title: RC17_after_mesDA_16_D10


title: FFPE_renal_carcinoma_28

description:
US22502514_252182713805_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 29_r1: TF29 Zm00001d007068 ChIP-Seq


title: Heart, IRS1KO_TAC_01


title: FFPE_renal_carcinoma_32

description:
US22502514_252182713805_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_26

description:
US22502514_252182713804_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: Heart, IRS1KO_Sham_01


title: RC17_after_mesDA_16_C2


title: FFPE_renal_carcinoma_25

description:
US22502514_252182713804_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: 26_r2: TF26 Zm00001d015549 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: RC17_after_mesDA_16_C12


title: RC17_after_mesDA_16_C5


title: Heart, WT_TAC_01


title: FFPE_renal_carcinoma_24

description:
US22502514_252182713804_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_C11


title: 25_r2: TF25 Zm00001d042907 ChIP-Seq


title: FFPE_renal_carcinoma_29

description:
US22502514_252182713805_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_C10


title: Heart, WT_Sham_01


title: FFPE_renal_carcinoma_22

description:
US22502514_252182713804_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_23

description:
US22502514_252182713804_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: 24_r2: TF24 Zm00001d020954 ChIP-Seq


title: 25_r1: TF25 Zm00001d042907 ChIP-Seq


title: RC17_after_mesDA_16_B8


title: FFPE_renal_carcinoma_21

description:
US22502514_252182713804_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: 24_r1: TF24 Zm00001d020954 ChIP-Seq


title: RC17_after_mesDA_16_B7


title: 237_r2: TF237 Zm00001d037221 ChIP-Seq


title: FFPE_renal_carcinoma_19

description:
US22502514_252182713992_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: 26_r1: TF26 Zm00001d015549 ChIP-Seq


title: FFPE_renal_carcinoma_20

description:
US22502514_252182713804_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_C1


title: RC17_after_mesDA_16_B6


title: 237_r1: TF237 Zm00001d037221 ChIP-Seq


title: 235_r2: TF235 Zm00001d017575 ChIP-Seq


title: RC17_after_mesDA_16_B5


title: 235_r1: TF235 Zm00001d017575 ChIP-Seq


title: FFPE_renal_carcinoma_18

description:
US22502514_252182713992_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_B4


title: RC17_after_mesDA_16_B2


title: RC17_after_mesDA_16_B9


title: FFPE_renal_carcinoma_16

description:
US22502514_252182713992_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_15

description:
15_3990_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_17

description:
US22502514_252182713992_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: 226_r2: TF226 Zm00001d043950 ChIP-Seq


title: RC17_after_mesDA_16_B12


title: RC17_after_mesDA_16_B11


title: FFPE_renal_carcinoma_14

description:
US22502514_252182713992_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: 224_r2: TF224 Zm00001d006236 ChIP-Seq


title: 224_r1: TF224 Zm00001d006236 ChIP-Seq


title: 226_r1: TF226 Zm00001d043950 ChIP-Seq


title: FFPE_renal_carcinoma_13

description:
US22502514_252182713992_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_B10


title: RC17_after_mesDA_16_B1


title: FFPE_renal_carcinoma_12

description:
US22502514_252182713992_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: 221_r2: TF221 Zm00001d020025 ChIP-Seq


title: 221_r1: TF221 Zm00001d020025 ChIP-Seq


title: RC17_after_mesDA_16_A8


title: 21_r2: TF21 Zm00001d000184 ChIP-Seq


title: RC17_after_mesDA_16_A6


title: 21_r1: TF21 Zm00001d000184 ChIP-Seq


title: FFPE_renal_carcinoma_09

description:
US22502514_252182713991_S01_miRNA_107_Sep09_2_4
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_A5


title: FFPE_renal_carcinoma_11

description:
US22502514_252182713992_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 219_r2: TF219 Zm00001d005578 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: RC17_after_mesDA_16_A4


title: 219_r1: TF219 Zm00001d005578 ChIP-Seq


title: 202_r2: TF202 Zm00001d021291 ChIP-Seq


title: FFPE_renal_carcinoma_08

description:
US22502514_252182713991_S01_miRNA_107_Sep09_2_3
microRNA expression of renal carcinoma paraffin samples


title: 202_r1: TF202 Zm00001d021291 ChIP-Seq


title: FFPE_renal_carcinoma_06

description:
US22502514_252182713991_S01_miRNA_107_Sep09_2_1
microRNA expression of renal carcinoma paraffin samples


title: FFPE_renal_carcinoma_07

description:
US22502514_252182713991_S01_miRNA_107_Sep09_2_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_A12


title: 199_r2: TF199 Zm00001d012527 ChIP-Seq


title: RC17_after_mesDA_16_A11


title: FFPE_renal_carcinoma_04

description:
US22502514_252182713991_S01_miRNA_107_Sep09_1_4
microRNA expression of renal carcinoma paraffin samples


title: 199_r1: TF199 Zm00001d012527 ChIP-Seq


title: FFPE_renal_carcinoma_10

description:
10_3990_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: RC17_after_mesDA_16_A7


title: 198_r2: TF198 Zm00001d024546 ChIP-Seq


title: FFPE_renal_carcinoma_02

description:
US22502514_252182713991_S01_miRNA_107_Sep09_1_2
microRNA expression of renal carcinoma paraffin samples


title: 198_r1: TF198 Zm00001d024546 ChIP-Seq


title: RC17_after_mesDA_16_A10


title: RC17_after_mesDA_16_A1


title: FFPE_renal_carcinoma_01

description:
US22502514_252182713991_S01_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 196_r1: TF196 Zm00001d009599 ChIP-Seq


title: HiC_UNC4976_4h_rep

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description:
UNC4976_juicer_q30.hic.gz
UNC4976_contact_domains_list.txt.gz
UNC4976_hiccups_loops.txt.gz

data_processing:
Sequencing reads were mapped to human genome using bowtie2.
Redundant reads were filtered out from further analysis.
Peaks of CBX7 ChIP-Seq were called using MACS2 with default parameters. Peaks for ATAC-Seq were called using MACS2 with parameters "--nomodel --shift -100 --extsize 200". Differential peaks between drug-treatment and control conditions were predicted using DESeq2.
RPKM were calucuated to quantify gene expression levels. DESeq2 were used for differential gene expression analysis.
Sequencing reads for HiC experiments from replicates were combined and used for loop domain analysis by Juicer package. HiCCUPS was used for calling loops with parameters “-r 5000,10000,25000 –k KR”. Arrowhead was used for calling contact domains with parameters “-r 25000 –k KR”.
Genome_build: hg18
Supplementary_files_format_and_content: wig files for ATAC-Seq and ChIP-Seq shows tag abundance at genomic loci; tab-delimited text files include expression level (RPKM values) for each gene for RNA-Seq samples; .hic files (compressed binary file) generated using Juicer Tools (Neva C. Durand et al Cell Systems 2016) provides access to the chromatin contact matrices; loop files (tab-delimited text) provide predicted chromatin loops generated by HICCUPS; contact domain files provide predicted contact domains predicted by Arrowhead.

source_name: Lymphocytes

growth_protocol: Elutriated lymphocytes from early male donors were purified according to specification by manufacturer according to the StemCell Technologies Human CD4+ T Cell Enrichment Kit.

extract_protocol:
For HiC experiments, 5-10 million purified CD4+ T lymphocytes were fixed for 10 min with 1 % formaldehyde after 4h treatment with 20 mM UNC4976 (0.2% DMSO) or 0.2% DMSO. The fixing was quenched by adding glycine (100 mM final concentration). After pelleting at 1200g and decanting, cells were resuspended with 10 mL 3e Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP40, and Sigma protease inhibitor cocktail) and incubated at 4 °C for 1 h. The cells were pelleted and resuspended with 400 mL CutSmart Buffer (1X, NEB), adjusted to 0.1% SDS, and heated at 65 °C for 10 min. The mixture was treated with 10 % Triton X-100 (44 mL), and digested with CviQI (20U, NEB) and CviAII (20U, NEB) at room temperature for 20 min. Bfa I was added (20U, NEB) and the mixture was incubated at 37 °C for 20 min. The reaction mixture was quenched with the addition of 600 mL wash buffer (10mM NaCl, 1mM EDTA, 0.1% Triton X-100). The cells were pelleted, and washed again with 600 mL wash buffer.
Blunt-ended DNA fragments were generated by incubating with Klenow Fragment (NEB) for ligation of dCTP, dGTP, dTTP, biotin-dATP, followed by blunt-end ligation with T4 DNA ligase (NEB) at 16 °C overnight. The samples were de-crosslinked, treated with T4 DNA Polymerase, and sheared to a median fragment length of 400 bp with Diagenode sonicator. After DNA End Repair and A-tailing according to standard procedure31 and biotin capture was performed with Streptavidin C1 beads (ThermoFisher) according to manufacturer’s specifications. On-bead ligation was carried out with Paired-End Adaptors (Illumina) and PCR amplification and size selection afforded indexed sequencing libraries with a median fragment length of 500 bp. After 2% E-gel purification (ThermoFisher), libraries were paired-end sequenced on the HiSeq 2500.

treatment_protocol: Purified CD4 T cells were cultured with 20 mM UNC4976 (0.2% DMSO), 20 mM UNC3866 (0.2% DMSO), or 0.2% DMSO and used for subsequent experiments.

value: CD4+ T cells

tag: treatment condition


title: RC17_after_mesDA_16_A3


title: 196_r2: TF196 Zm00001d009599 ChIP-Seq


title: In vivo, AAV-RSPO1-Fc D2

city: Helsinki

first: Marianne

last: Lähde

address: Haartmaninkatu 8

department: Faculty of Medicine, Translational cancer medicine program

country: Finland

institute: University of Helsinki

description:
mouse treated with AAV-RSPO1-Fc D2
MinD12combi.Rdata

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package 3.1.1 for quality control, filtering, and analysis of the data
Cells were filtered based on unique feature counts and the percentage of mitochondrial genes
Cells with more than 15% of mitochondrial genes were filtered out
The expression matrix was further filtered by removing genes with expression in less than five cells and cells with less than 500 distinct expressed genes.
Filtered data was combined for CCA and further analysis, and saved as MinD4combi.Robj for day 4 samples and MinD12combi.Robj for day 1-2 samples (supplementary files have .Rdata extension).
Genome_build: mm10

source_name: Intestinal adenoma

extract_protocol:
Intestinal adenomas of ApcMin/+ mice injected with AAV-RSPO1-Fc or empty vector were collected and incubated in a tissue dissociation solution (collagenase I 1 mg/mL, collagenase H 1 mg/mL, dispase II 4 mg/mL, DNase 4 mg/mL) for 30 min at +32°C. The suspension was incubated with Trypsin-EDTA (0.25%, phenol red, 25200056, Thermo Fisher Scientific) for 15 min at +37°C, gently pipetted to obtain a single-cell suspension and transferred into 0.04% BSA-HBSS.
Single cells were analyzed using the 10x Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA, USA) with the Reagent Kit v2 as instructed by the manufacturer. Briefly, the cells were first loaded into Chromium Single-Cell Chip v2 (10x Genomics, Pleasanton, CA, USA), followed by generation of Gel beads in EMulsion (GEM) aiming at 5000 cell captures per sample. This was followed by cDNA purification, amplification (12 cycles), and library construction (sample index PCR 14 cycles) as instructed by the manufacturer.
The sample libraries were sequenced on an Illumina NovaSeq 6000 sequencer using read lengths of 26bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 91bp (Read 2),  resulting in an average of following reads per cell: 37 547 (ApcMin/+ in vivo D1-2 Ctrl), 47 141 (ApcMin/+ in vivo D1 RSPO1), and 38 871 (ApcMin/+ in vivo D2 RSPO1), 105 926 (ApcMin/+ in vivo D4 Ctrl), and 85 650 (ApcMin/+ in vivo D4 RSPO1). Chromium single-cell 3’ RNA-sequencing barcodes and read data were demultiplexed and converted to FASTQ files, and aligned reads and gene-cell matrices were generated using Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA, USA). Reads were aligned to mouse reference genome mm10.

treatment_protocol: 1x10^12 vp of indicated AAV was injected intraperitoneally

value: ApcMin/+

value: intestinal adenoma

value: 17 weeks

value: AAV-RSPO1-Fc D2


title: In vivo, AAV-Ctrl D1-2

description:
mouse treated with AAV-Ctrl D1-2
MinD12combi.Rdata

value: AAV-Ctrl D1-2


title: RC17_after_mesDA_16_A2


title: In vivo, AAV-RSPO1-Fc D1

description:
mouse treated with AAV-RSPO1-Fc D1
MinD12combi.Rdata

value: AAV-RSPO1-Fc D1


title: In vivo, AAV-RSPO1-Fc D4

description:
mouse treated with AAV-RSPO1-Fc D4
MinD4Combi.Rdata

value: AAV-RSPO1-Fc D4


title: HiC_DMSO_4h_rep

description:
DMSO_juicer_q30.hic.gz
DMSO_contact_domains_list.txt.gz
DMSO_hiccups_loops.txt.gz

value: DMSO (4h)


title: HiC_UNC4976_4h


title: In vivo, AAV-Ctrl D4

description:
mouse treated with AAV-Ctrl D4
MinD4Combi.Rdata

value: AAV-Ctrl D4


title: FFPE_renal_carcinoma_05

description:
5_3990_miRNA_107_Sep09_1_1
microRNA expression of renal carcinoma paraffin samples


title: 195_r1: TF195 Zm00001d044117 ChIP-Seq

value: Leaf protoplast


title: 193_r2: TF193 Zm00001d051458 ChIP-Seq


title: FFPE_renal_carcinoma_03

description:
US22502514_252182713991_S01_miRNA_107_Sep09_1_3
microRNA expression of renal carcinoma paraffin samples

value: renal carcinoma


title: ChIPSeq_input_UNC4976_4h

extract_protocol:
We fixed 10-20 million CD4 T lymphocytes, after 4h treatment with 20 mM UNC4976 (0.2% DMSO) or 0.2% DMSO, with 1% formaldehyde for 12 minutes. After fixation, formaldehyde was quenched by adding glycine to a final concentration of 100 mM. The Fixed cells were washed in ice cold PBS, pelleted at 1200g and after decanting remaining PBS, the pellets were flash frozen with liquid nitrogen. After harvesting fixed nuclei and chromatin was sheared and immunoprecipitated as previously described (Hodges and Stanton et al Nature Struct Mol Biol 2017). For these ChIP studies, rabbit anti-CBX7 antibody (Abcam cat# 21873, Lot number: GR255463-2) was used. After reverse crosslinking, ChIP DNA was phenol-chloroform extracted.
Library preparation was performed as previously described (Love et al. Genome Biol. 2014)


title: 193_r1: TF193 Zm00001d051458 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: ChIPSeq_input_DMSO_4h


title: 191_r2: TF191 Zm00001d029963 ChIP-Seq


title: 191_r1: TF191 Zm00001d029963 ChIP-Seq


title: ChIPSeq_CBX7_UNC4976_4h_rep


title: ChIPSeq_CBX7_UNC4976_4h


title: ChIPSeq_CBX7_DMSO_4h


title: ChIPSeq_CBX7_DMSO_4h_rep


title: 189_r2: TF189 Zm00001d039893 ChIP-Seq


title: 195_r2: TF195 Zm00001d044117 ChIP-Seq


title: 190_r2: TF190 Zm00001d044409 ChIP-Seq


title: HiC_DMSO_4h


title: RNASeq_UNC4976_4h

extract_protocol:
After treatment with CBX7 inhibitor or DMSO control, RNA was harvested from purified 625,000 CD4+ T lymphocytes for each independent experiment with QIAzol (Qiagen) and chloroform extracted.
The Smart-seq2 RNA-seq protocol was used for generation of cDNA, which was fragmented with Diagenode sonication (performed at 4 °C, 25 second pulse followed by 30 second recovery, for 2 x 10 cycles).


title: 190_r1: TF190 Zm00001d044409 ChIP-Seq


title: RNASeq_UNC4976_4h_rep


title: 186_r2: TF186 Zm00001d013399 ChIP-Seq


title: 189_r1: TF189 Zm00001d039893 ChIP-Seq


title: 186_r1: TF186 Zm00001d013399 ChIP-Seq


title: RNASeq_DMSO_4h_rep


title: Cells at T12, biological rep 2

city: Detroit

first: Terrence

last: Monks

state: Michigan

address: 259 Mack Ave, Suite 5148

institute: Wayne State University

description: Gene expression data from ATRA-treated cells

hyb_protocol: Following fragmentation, 5.5ug of cRNA were hybridized for 16 hr at 45C on GeneChip PorGene-1_0-st. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using standard protocols (GeneChip Fluidics Station 450 User’s Guide, 2006, Affymeytrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Transcriptome Analysis Console version 2.0.0.9 using default analysis settings:    Analysis Type: Gene Level Differential Expression Analysis  Array Type: PorGene-1_0-st  Genome Version: sscr2  Annotation File: PorGene-1_0-st-v1.na34.sscr2.transcript.csv    Algorithm Options:   1.) One-Way Between-Subject ANOVA (Unpaired)  Default Filter Criteria:   1.) Fold Change (linear) < -2 or Fold Change (linear) > 2  2.) ANOVA p-value (Condition pair) < 0.05    Conditions:   0hr (3)  1.) 7688_JS_ATRA_0h-R2_(PorGene-1_0-st).rma-gene-full.chp  2.) 7694_JS_ATRA_0h-R3_(PorGene-1_0-st).rma-gene-full.chp  3.) Exp7628_JS-ATRA 0h_(PorGene-1_0-st).rma-gene-full.chp    0.5hr (3)  1.) 7689_JS_ATRA_0.5h-R2_(PorGene-1_0-st).rma-gene-full.chp  2.) 7695_JS_ATRA_0.5h-R3_(PorGene-1_0-st).rma-gene-full.chp  3.) Exp7629_JS-ATRA 0.5h_(PorGene-1_0-st).rma-gene-full.chp    1hr (3)  1.) 7690_JS_ATRA_1h-R2_(PorGene-1_0-st).rma-gene-full.chp  2.) 7696_JS_ATRA_1h-R3_(PorGene-1_0-st).rma-gene-full.chp  3.) Exp7630_JS-ATRA 1h_(PorGene-1_0-st).rma-gene-full.chp    4hr (3)  1.) 7691_JS_ATRA_4h-R2_(PorGene-1_0-st).rma-gene-full.chp  2.) 7697_JS_ATRA_4h-R3_(PorGene-1_0-st).rma-gene-full.chp  3.) Exp7631_JS-ATRA 4h_(PorGene-1_0-st).rma-gene-full.chp    8hr (3)  1.) 7692_JS_ATRA_8h-R2_(PorGene-1_0-st).rma-gene-full.chp  2.) 7698_JS_ATRA_8h-R3_(PorGene-1_0-st).rma-gene-full.chp  3.) Exp7632_JS-ATRA 8h_(PorGene-1_0-st).rma-gene-full.chp    12hr (3)  1.) 7687_JS_ATRA_12h-R1_(PorGene-1_0-st).rma-gene-full.chp  2.) 7693_JS_ATRA_12h-R2_(PorGene-1_0-st).rma-gene-full.chp  3.) 7699_JS_ATRA_12h-R3_(PorGene-1_0-st).rma-gene-full.chp

label: biotin

organism: Sus scrofa

source_name: LLC-PK1 cells

label_protocol: 15ug of cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (GeneChip WT Plus Reagen Kit Manual, 2013, Affymetrix).

growth_protocol: Cells were plated, grown to post confluency, and ATRA added for given time period

extract_protocol: Cells were lysed and total cellular RNA was extracted using an Rneasy kit following the manufacturer's instructions

treatment_protocol: Cells were exposed to ATRA for either 0.5, 1, 4, 8, or 12 hr

tag: time point

value: kidney

tag: morphology

value: epithelial

tag: gender

value: male

tag: breed

value: Hampshire


title: Cells at T12, biological rep 1


title: Cells at T12, biological rep 3


title: Cells at T8, biological rep 3


title: Cells at T8, biological rep 2


title: RNASeq_DMSO_4h


title: ATAC_UNC4976_4h_rep

extract_protocol:
For each independent ATAC-seq experiment, 50,000 CD4+ T cells were washed once with PBS at 4 °C and resuspended in 500 mL lysis buffer (RSB buffer with 0.1% Tween-20) and incubated on ice for 10 min to generate nuclei. After centrifugation at 500g for 10 min, nuclei were resuspended in 54 mL reaction buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.5% IGEPAL CA-630) and mixed with 6 mL 10X transposase mixture (0.5 M Tris-acetate pH 7.5, 1.5 M potassium acetate, 100 mM magnesium acetate, 40 mM spermidine, 2 mL active Tn5 complex. The reaction mixtures were incubated at 37 °C for 30 min, quenched with 500  mL PB Buffer and then purified directly with MinElute PCR purification kit (Qiagen).
Transposase reaction products were amplified with Nextera primers (Illumina), size selected with AMPure XP beads (Beckman Coulter) for fragement between 70bp and 1,000 bp and paired-end sequenced with HiSeq2500 sequencer.


title: Cells at T8, biological rep 1


title: 185_r2: TF185 Zm00001d030678 ChIP-Seq


title: Cells at T4, biological rep 3


title: Cells at T1, biological rep 3


title: ATAC_UNC4976_4h


title: 185_r1: TF185 Zm00001d030678 ChIP-Seq


title: Cells at T4, biological rep 2


title: 184_r2: TF184 Zm00001d032024 ChIP-Seq


title: Cells at T1, biological rep 2


title: Cells at T1, biological rep 1


title: 184_r1: TF184 Zm00001d032024 ChIP-Seq


title: ATAC_UNC3866_4h_rep


title: 183_r2: TF183 Zm00001d048623 ChIP-Seq


title: 183_r1: TF183 Zm00001d048623 ChIP-Seq


title: ATAC_DMSO_4h


title: ATAC_DMSO_4h_rep


title: ATAC_UNC3866_4h


title: 181_r2: TF181 Zm00001d025964 ChIP-Seq


title: Cells at T4, biological rep 1


title: ATAC_UNC4976_1h_rep


title: ATAC_UNC4976_1h


title: 181_r1: TF181 Zm00001d025964 ChIP-Seq


title: 180_r2: TF180 Zm00001d031182 ChIP-Seq


title: IC5S

city: East Melbourne

first: Kylie

middle: L

last: Gorringe

state: Victoria

address: St Andrew's Pl

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: As per manufacturer's recommendations (Affymetrix)

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Analysis of the Human Gene 1.0 ST data was performed using the Partek Gene Expression workflow. CEL files were processed using RMA normalization and batch correction.
CEL files are provided for each sample in the study.

label: BIOTIN

source_name: Ovarian serous cystadenofibroma

extract_protocol: Total RNA was extracted from stroma using the Qiagen Rneasy kit. Concentration was determined by Nanodrop and quality by Bioanalyser kit. 300 ng was used.

value: Tumour stroma

tag: tumour histology

value: Serous cystadenofibroma

tag: diagnosis

value: Benign serous cystadenofibroma


title: Cells at T0.5, biological rep 3


title: IC458S

source_name: Ovarian fibroma

label_protocol: As per manufacturer's recommendations (Affymetrix)

value: Fibroma

value: Benign fibroma


title: IC467S


title: ATAC_UNC3866_1h_rep

value: CD4+ T cells


title: IC591S

source_name: Ovarian serous cystadenoma

value: Serous cystadenoma

value: Benign serous cystadenoma


title: TSA_Sample2

type: genomic

city: Madison

first: Bermans

middle: J

last: Iskandar

state: WI

address: 600 Highland Ave, K4/832

department: Neurological Surgery

institute: University of Wisconsin

description: Genomic DNA was isolated and sonicated prior to MeDIP analysis

hyb_protocol: Labeled MeDIP and Input fractions were co-hybridized to NimbleGen RN34 CpG Island Plus RefSeq Promoter Microarray arrays

scan_protocol: Arrays were scanned with the Axon GenePix 400B scanner and analyzed using NimbleScan software and Bioconductor packages Ringo and limma

data_processing:
Raw data were extracted as pair files by NimbleScan software (v2.5) with median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo http://www.bioconductor.org/packages/release/bioc/html/Ringo.html, limma http://www.bioconductor.org/packages/release/bioc/html/limma.html [38], and MEDME http://www.bioconductor.org/packages/release/bioc/html/MEDME.html. Normalization resulted in log base 2 ratios of the immunoprecipitated and total DNA for each sample, with Spearman correlations ranging from 0.86 to 0.91 between samples within each MeDIP group.
*ratio.gff files include scaled, log2(MeDIP/input) ratio

organism: Rattus norvegicus

source_name: MeDIP of DNA from injured cervical spinal cord, TSA

label_protocol: MeDIP fractions were  labeled with Cy5, Input fractions were labeled with Cy3.

growth_protocol: TSA-treated F3 progeny from F0 treated with folic acid

extract_protocol: Genomic DNA was isolated by proteinase K treatment, phenol-chloroform extraction, ethanol precipitation and RNase digestion. Before carrying out MeDIP, genomic DNA was sonicated using a Bioruptor sonicator (Diagenode, Denville, NJ) at “Low” mode for 10 cycles of 30 seconds “ON” and 30 seconds “OFF” (with an ultrasound wave frequency of 20 kHz) to produce random fragments ranging from 200 to 1,000 bp. Five µg of fragmented DNA was used for a standard MeDIP assay, while 1 µg sheared DNA was used as input. DNA was denatured for 10 minutes at 94 °C and immunoprecipitated for 4 hours at 4 °C with 5 µg anti- 5-methycytidine (Diagenod, Denville, NJ) in a final volume of 500 µl IP buffer (0.5% NP40; 1.1% Triton X-100; 1.5 mM EDTA; 50 mM Tris-HCl; 150 mM NaCl). The mixture was then incubated with 50 µl of BiomagTM magnetic beads coupled anti-mouse IgG for 2 hours at 4 °C, and washed three times with 500 µl IP buffer. DNA was eluted at 65°C for 15 minutes in 200 µl elution buffer (1 mM Tris-HCl, pH 8.0; 0.5 mM EDTA, pH 8.0; 10% SDS). Methylated DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation.

value: cervical spinal cord

tag: generation

value: F3 of F0-folate lineage

source_name: Input DNA from injured cervical spinal cord, TSA


title: Cells at T0.5, biological rep 2


title: IC450S

source_name: Ovarian serous adenomafibroma

value: Serous adenofibroma

value: Benign serous adenofibroma


title: Cells at T0, biological rep 3


title: Cells at T0, biological rep 2


title: IC369S

source_name: Normal ovary

value: Ovarian stroma

value: Normal ovary


title: Cells at T0.5, biological rep 1

value: kidney

value: epithelial


title: IC494S


title: IC425S


title: 180_r1: TF180 Zm00001d031182 ChIP-Seq

tag: cultivar

value: Leaf protoplast


title: TSA_Sample1

tag: tissue


title: 17_r2: TF17 Zm00001d012810 ChIP-Seq

tag: transcription factor


title: IC269S

value: Tumour stroma


title: IC236S


title: Cells at T0, biological rep 1

value: male

value: Hampshire


title: ATAC_DMSO_1h_rep

tag: cell type

value: DMSO (1h)


title: TSA_Sample3


title: EXP6

source_name: MeDIP of DNA from injured cervical spinal cord, FA80

growth_protocol: F3 progeny from F0 treated with folic acid

source_name: Input DNA from injured cervical spinal cord, FA80


title: IC196S

value: Ovarian serous cystadenoma


title: 17_r1: TF17 Zm00001d012810 ChIP-Seq


title: ATAC_DMSO_1h

value: CD4+ T cells


title: EXP5


title: IC181S

value: Fibroma

value: Benign fibroma


title: RNA-Seq analyses with sorted ROSHigh cells

city: Taipei

first: Jeng-Fan

last: Lo

address: No. 155, Section 2, Li-Nong Street, Taipei, 11221, Taiwan

country: Taiwan

institute: National Yang-Ming University

data_processing:
Base calling were conducted by Illumina’s software packages RTA1.17.21.3. Raw reads were processed using the Illumina CAS (v. 1.8.2) to filter out the low-quality reads.
RNA-seq reads were aligned to the GRCh38 genome assembly using CLC Genomics Workbench v8.0 with the following configurations…
Adaptor quality checked using CLC Genomics Workbench v8.0
Reads were aligned to GRCh38 using CLC Genomics Workbench v8.0
Aligned reads were sorted with CLC Genomics Workbench v8.0
Number of reads was counted using  CLC Genomics Workbench v8.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Window size used for peak calling. Tab-delimited text files (CSV) include Expression value,   reads and P-value.

source_name: HNSCC

growth_protocol: Cells were seeded at a density of 7.5×104 live cells/10-mm dish in defined selection medium (DMEM/F12 medium (GIBCO) containing with N2 supplement (GIBCO), 10 ng/mL human recombinant basic fibroblast growth factor-basic (FGF) and 10 ng/mL Epidermal Growth Factor (EGF) (R&D Systems, Minneapolis, MN). The medium was changed every other day until the sphere formation was achieved by approximately 4 weeks

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen), according to the manufacturer's instructions. cDNA synthesis was performed using SuperScriptIII reverse transcriptase (Invitrogen) with random hexamer primers.
RNA-seq libraries were sequenced paired-end (100 bp)

treatment_protocol: We stained the HN-CICs with ROS-indicator dye DCFDA to separate cells into ROSLow, and ROSHigh subpopulations followed by flow cytometry.

value: Sorted ROSHigh cells

tag: origin

value: SAS sphere cells


title: EXP4

value: cervical spinal cord

value: F3 of F0-folate lineage


title: 179_r3: TF179 Zm00001d035907 ChIP-Seq


title: 179_r2: TF179 Zm00001d035907 ChIP-Seq


title: CON3

source_name: MeDIP of DNA from injured cervical spinal cord, control

growth_protocol: F3 progeny from F0 treated with double distilled water

value: F3 of F0-control lineage

source_name: Input DNA from injured cervical spinal cord, control


title: ATAC_UNC3866_1h


title: IC164S

value: Serous cystadenofibroma

value: Benign serous cystadenofibroma


title: 179_r1: TF179 Zm00001d035907 ChIP-Seq

source_name: Leaf protoplast


title: Hypothalamus [JL511]

city: Davis

first: Simon

middle: Jesse

last: Lopez

state: CA

address: One Shields Ave

department: MMI

institute: UC Davis

description:
JL511
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt

data_processing:
WGBS: CpG_me, DMRichR
RNA-seq: htstream, STAR
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: hypothalamus_counts.txt: Gene feature counts output from STAR aligner for each hypothalamus sample.
Supplementary_files_format_and_content: cortex_counts.txt: Gene feature counts output from STAR aligner for each cortex sample.
Supplementary_files_format_and_content: DMRs.xlsx: DMRs for each pair-wise group comparison output from DMRichR.
Supplementary_files_format_and_content: maternal_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for all maternal samples.
Supplementary_files_format_and_content: paternal_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for all paternal samples.
Supplementary_files_format_and_content: control_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for maternal and paternal wild-tpe samples.

source_name: hypothalamus

extract_protocol:
WGBS: Illumina TruSeq DNA Methylation Kit (Illumina EGMK81312).
RNA-seq: NEB NEBNext rRNA Depletion Kit (NEB E6310L) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB E7420S).

tag: parent-of-origin

value: Paternal

tag: time

tag: genotype/variation

value: Deletion

tag: Sex

value: Female

value: Hypothalamus


title: CON2


title: CON1


title: 178_r1: TF178 Zm00001d033378 ChIP-Seq

value: Leaf protoplast


title: Hypothalamus [JL509]

description:
JL509
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt

value: Maternal


title: 177_r2: TF177 Zm00001d002799 ChIP-Seq


title: Hypothalamus [JL508]

description:
JL508
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt

value: Wild-type


title: 178_r2: TF178 Zm00001d033378 ChIP-Seq


title: 177_r1: TF177 Zm00001d002799 ChIP-Seq


title: Hypothalamus [JL507]

description:
JL507
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt


title: RNA-Seq analyses with sorted ROSLow cells

value: Sorted ROSLow cells


title: IC158S

value: Tumour stroma


title: 055_OPU: Granulosa cells_36h_rFSH_GNRHa

city: Køge

first: Liv

middle: la Cour

last: Poulsen

address: Lykkebækvej 14

department: Gynaecology and Obstetrics

country: Denmark

institute: Zealand University Hospital

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
055_OPU

hyb_protocol: RNA was processed using Clariom™ D Pico Assay (Applied Biosystems, Thermo Fisher, USA) according to the manufacturer’s protocol, using the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in the Affymetrix GeneArray 3000 7G scanner to generate fluorescent images. Cell intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC, Affymetrix, Thermo Fisher, USA).

data_processing: The 83 raw CEL-files were imported into Transcriptome Analysis Console (TAC 4.0.1, applied Biosystems, Thermo Fisher Scientific, MA, USA) . Normalization and summarization were performed by the SST-RMA (Robust Multichip Analysis) approach.

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa

label_protocol: Phycoerytrin conjugated streptavidin

growth_protocol: Granulosa cells were isolated from aspirated follicular fluid with a pipette as blood clots and vessels were avoided. The cells were washed through a 4-well dish containing PBS and 0,1% PVA, transferred to a cryotube with minimal PBS, snap frozen in liquid nitrogen and stored at -80⁰C until RNA extraction.

extract_protocol: The Arcturus PicoPure® RNA isolation kit (Applied Biosystems, CA, USA) was used to isolate total RNA from GC according to the manufacturer’s instructions

treatment_protocol: Patients were treated with individually dosed rFSH (Puregon®, MSD, Denmark) or hMG (Menopur®, Ferring, Denmark) starting on day 2-3 of the menstrual cycle. From stimulation day 5-6 a GnRH antagonist (Ganirelix 0,25 mg (Fyremadel®, SUN pharma, Netherlands)) was administered daily. When at least three follicles reached ≥17 mm in diameter, an ovulation trigger (hCG (6500 IU (Ovitrelle®, Merck Serono, Germany) or GNRHa (buserelin 0,5 mg (Suprefact®, Sanofi-Aventis)) was administered and oocyte pick up was planned for 36 hours later.

value: granulosa cells isolated from aspirated follicular fluid

tag: ovulation time point

tag: treatment

value: rFSH

tag: ovulation induction

value: GNRHa


title: IC120S


title: 054_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
054_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with hMG, ovulation induced with GNRHa

value: hMG


title: Hypothalamus [JL506]

description:
JL506
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt


title: 174_r2: TF174 Zm00001d005692 ChIP-Seq


title: IC137S

value: Fibroma

value: Benign fibroma


title: Hypothalamus [JL505]

description:
JL505
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt


title: 054_EP: Granulosa cells_0h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
054_EP

source_name: Granulosa cells collected before induction of ovulation in a patient treated with hMG, ovulation induced with GNRHa


title: Hypothalamus [JL510]

description:
JL510
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt


title: IC149S

source_name: Ovarian serous cystadenofibroma

value: Serous cystadenofibroma


title: 173_r2: TF173 Zm00001d010634 ChIP-Seq


title: IC103S

value: Benign serous cystadenofibroma


title: 055_EP: Granulosa cells_17h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 17 hours after induction of ovulation
055_EP

source_name: Granulosa cells collected 17 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: IC79S

value: Ovarian stroma

value: Normal ovary


title: Hypothalamus [JL504]

description:
JL504
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt

value: Paternal

value: Female


title: IC148S

source_name: Ovarian serous cystadenoma

value: Serous cystadenoma

value: Ovarian serous cystadenoma


title: 173_r1: TF173 Zm00001d010634 ChIP-Seq

value: Leaf protoplast


title: Hypothalamus [JL503]

description:
JL503
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt

value: Maternal

value: Deletion

value: Hypothalamus


title: 053_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
053_OPU

value: granulosa cells isolated from aspirated follicular fluid


title: 050_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
050_OPU

value: rFSH

value: GNRHa


title: 052_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
052_OPU


title: IC24S

value: Tumour stroma


title: 172_r2: TF172 Zm00001d039260 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: Hypothalamus [JL501]

description:
JL501
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt

value: Wild-type


title: IC10S

value: Serous cystadenofibroma


title: Hypothalamus [JL500]

description:
JL500
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt


title: 174_r1: TF174 Zm00001d005692 ChIP-Seq


title: 171_r2: TF171 Zm00001d017726 ChIP-Seq


title: 050_EP: Granulosa cells_12h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 12 hours after induction of ovulation
050_EP

source_name: Granulosa cells collected 12 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: 048_EP: Granulosa cells_12h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 12 hours after induction of ovulation
048_EP

source_name: Granulosa cells collected 12 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG

value: rhCG


title: Hypothalamus [JL411]

description:
JL411
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt


title: 048_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
048_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG


title: 046_EP: Granulosa cells_0h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
046_EP

source_name: Granulosa cells collected before induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: 170_r3: TF170 Zm00001d044232 ChIP-Seq


title: 171_r1: TF171 Zm00001d017726 ChIP-Seq


title: IC33S

source_name: Ovarian fibroma

value: Fibroma

value: Benign fibroma


title: Hypothalamus [JL408]

description:
JL408
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt

value: Paternal


title: IC4S


title: 045_EP: Granulosa cells_0h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
045_EP

value: hMG


title: 045_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
045_OPU


title: Tems_6

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Reads were pseudo-aligned to the transcriptome using Salmon and transcript expression values were summarized using tximport.
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix (raw counts) was obtained using DESeq2.

source_name: cultured with Temsirolimus

growth_protocol: Human CD14+ monocytes were cultured with M-CSF, IL-4 and TNF-a for 5 days, at pH 7.3 or pH 6.5 or in the presence of mTORC1 inhibitor Temsirolimus.

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
cDNA was generated with SMART-Seq v4 Ultra Low Imput RNA Kit for Sequencing (Takara). Multiplexed pair-end libraries 100 nt in length were obtained using Nextera XT kit (Clontech).
Sequencing was performed in the same sequencing unit of NovaSeq (Illumina) (100-nt-length reads, paired end) with an average depth of 15 million reads per sample.

treatment_protocol: Dendritic cells (CD1a+ CD16- cells) were sorted using an Aria cell sorter.

value: monocyte-derived dendritic cells

tag: cultured with

value: M-CSF, IL-4 and TNF-a

tag: condition

value: Temsirolimus


title: 170_r1: TF170 Zm00001d044232 ChIP-Seq

value: Leaf protoplast


title: Hypothalamus [JL407]

description:
JL407
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt

value: Female


title: pH65_6

source_name: cultured at pH 6.5


title: Tems_5


title: pH73_6

source_name: cultured at pH 7.3


title: IC7S

tag: tumour histology

value: Serous cystadenoma

value: Ovarian serous cystadenoma


title: 172_r1: TF172 Zm00001d039260 ChIP-Seq


title: pH73_5


title: Tems_4


title: 16_r2: TF16 Zm00001d018571 ChIP-Seq


title: Hypothalamus [JL403]

description:
JL403
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt

value: Deletion

value: Hypothalamus


title: Hypothalamus [JL409]

description:
JL409
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt


title: Hypothalamus [JL402]

description:
JL402
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt


title: 043_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
043_OPU

value: granulosa cells isolated from aspirated follicular fluid

value: rFSH

value: GNRHa


title: 043_EP: Granulosa cells_0h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
043_EP


title: 16_r1: TF16 Zm00001d018571 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: pH65_4


title: 164_r2: TF164 Zm00001d037605 ChIP-Seq


title: 042_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
042_OPU


title: 164_r1: TF164 Zm00001d037605 ChIP-Seq


title: pH73_4


title: pH65_5


title: 170_r2: TF170 Zm00001d044232 ChIP-Seq


title: Tems_3


title: 041_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
041_OPU


title: 040_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
040_OPU


title: 040_EP: Granulosa cells_0h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
040_EP


title: pH73_3


title: 163_r1: TF163 Zm00001d027846 ChIP-Seq


title: Hypothalamus [JL306]

description:
JL306
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt

value: Maternal

value: Wild-type


title: Hypothalamus [JL310]

description:
JL310
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt


title: 163_r2: TF163 Zm00001d027846 ChIP-Seq


title: Hypothalamus [JL401]

description:
JL401
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt


title: pH65_3


title: Hypothalamus [JL305]

description:
JL305
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt


title: 162_r2: TF162 Zm00001d051439 ChIP-Seq


title: 039_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
039_OPU


title: 039_EP: Granulosa cells_0h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
039_EP


title: 162_r1: TF162 Zm00001d051439 ChIP-Seq


title: Hypothalamus [JL303]

description:
JL303
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt


title: Tems_2


title: 038_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
038_OPU


title: Hypothalamus [JL302]

description:
JL302
processed data file: DMRs.xlsx
processed data file: maternal_background_smoothed_methylation.txt
processed data file: control_background_smoothed_methylation.txt


title: 161_r2: TF161 Zm00001d028625 ChIP-Seq


title: Hypothalamus [JL405]

description:
JL405
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt


title: 036_EP: Granulosa cells_0h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
036_EP


title: pH65_2


title: pH73_2


title: 034_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
034_OPU

value: rhCG


title: pH73_1


title: pH65_1


title: 161_r1: TF161 Zm00001d028625 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: 15_r1: TF15 Zm00001d042609 ChIP-Seq


title: 033_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
033_OPU


title: Mixing

city: San Francisco

first: Aaron

last: Diaz

institute: University of California, San Francisco

description: Single Cell RNA-Seq

data_processing:
For 10x scRNA-Seq and snRNA-Seq data, we utilized CellRanger (version 3.0.2) for data pre-processing and gene expression quantification, following the guidelines from the CellRanger website.
Single-cell data were normalized via the Seurat “LogNormalize” function.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix file (mtx) includes sparse matrix of read counts, unique cell barcode files (tsv), and feature file (tsv)

source_name: Brain

extract_protocol:
Fresh tissue was dissociated mechanically in the presence of collagenase, deoxyribonuclease, trypsin inhibitor, and DPBS. The homogenate was shaken in a thermomixer at 37˚ for 15 minutes, triturated via pipette, and shaken again at 37˚ for 15 minutes. The cells were then filtered through a 70 micron strainer, pelleted, and resuspended in neural basal media with FBS. Frozen tissues were dissociated mechanically and incubated with Nuclei EZ lysis buffer (Sigma) according to the manufacturer’s protocols. Nuclei were then filtered through a 70 micron strainer. Debris was further depleted via a sucrose-based density gradient.
The 10X Chromium single-cell platform (v3 3’-chemistry) was used for cell/nuclei capture and library preparation was performed per 10X Genomics’ protocols.
Sequencing was performed on an Illumina NovaSeq using a paired-end 100bp protocol.

tag: age

tag: gender

value: M/M

tag: idh status

value: Mutant


title: Tems_1

value: monocyte-derived dendritic cells


title: 033_EP: Granulosa cells_0h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
033_EP

tag: tissue


title: 034_EP: Granulosa cells_0h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
034_EP

source_name: Granulosa cells collected before induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG


title: 035_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
035_OPU


title: 15_r2: TF15 Zm00001d042609 ChIP-Seq

source_name: Leaf protoplast

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with streptavidin dynabeads.
Libraries were prepared according to Illumina's instructions using purified HS-Tn5 transposase, Tn5-MEA/B adapter as well as N5xx and N7xx PCR primers.

tag: cultivar

tag: transcription factor


title: SF4324

description: Single Cell RNA-Seq

value: F

value: Wildtype


title: 159_r2: TF159 Zm00001d026398 ChIP-Seq

value: Leaf protoplast


title: S10432

description: Single Cell RNA-Seq


title: 158_r2: TF158 Zm00001d015421 ChIP-Seq


title: 159_r3: TF159 Zm00001d026398 ChIP-Seq


title: SF12199

description: Single Cell RNA-Seq

value: M


title: 032_EP: Granulosa cells_0h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
032_EP


title: 159_r1: TF159 Zm00001d026398 ChIP-Seq


title: 032_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
032_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: 031_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
031_OPU


title: Cortex [JL710]

description:
JL710
processed data file: cortex_counts.txt

source_name: cortex

value: Paternal

value: Female

value: Cortex


title: 157_r2: TF157 Zm00001d021019 ChIP-Seq


title: Cortex [JL708]

description:
JL708
processed data file: cortex_counts.txt


title: 031_EP: Granulosa cells_0h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
031_EP


title: 030_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
030_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with hMG, ovulation induced with GNRHa

value: hMG


title: 029_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
029_OPU

value: granulosa cells isolated from aspirated follicular fluid


title: 153_r2: TF153 Zm00001d018081 ChIP-Seq


title: Cortex [JL709]

description:
JL709
processed data file: cortex_counts.txt

value: Deletion


title: 030_EP: Granulosa cells_0h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
030_EP

source_name: Granulosa cells collected before induction of ovulation in a patient treated with hMG, ovulation induced with GNRHa

value: GNRHa


title: 157_r1: TF157 Zm00001d021019 ChIP-Seq


title: 029_EP: Granulosa cells_12h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 12 hours after induction of ovulation
029_EP

value: rFSH


title: Cortex [JL706]

description:
JL706
processed data file: cortex_counts.txt

value: Wild-type


title: 14_r2: TF14 GRMZM2G017586 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: 153_r1: TF153 Zm00001d018081 ChIP-Seq


title: Cortex [JL707]

description:
JL707
processed data file: cortex_counts.txt


title: 152_r2: TF152 Zm00001d020595 ChIP-Seq


title: 158_r1: TF158 Zm00001d015421 ChIP-Seq


title: Cortex [JL705]

description:
JL705
processed data file: cortex_counts.txt


title: 152_r1: TF152 Zm00001d020595 ChIP-Seq


title: B. subtilis_-t60_choline.addition_rep2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

hyb_protocol: 100 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 12.1.0.1, Agilent Technologies).
signal intensity (gProcessedSignal) obtained by applying the Feature Extraction protocol for 1 color gene expression arrays (GE1_1200_Jun14).
[signal_salt_choline_annotated_genes.txt]  Median scaling were performed using the median of individual probe intensities calculated for GenBank annotated genes and RNA segments reported by Nicolas et al., 2012 (PMID 22383849).

organism: Bacillus subtilis

source_name: B. subtilis_choline added 60 min before NaCl shock

label_protocol:
For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D
(final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye,
GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: B. subtilis BSB1 was grown aerobically at 37 °C in Spizizen minimal medium. Salt stress was induced by addition of NaCl to a final molarity of 0.4 M at OD600nm of 0.3, whereas choline to a final molarity of 1 mM was added immediately, 15, 30 or 60 minutes before salt addition, respectively.

extract_protocol: Cells were harvested 10 min after salt imposition and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

tag: strain

value: Bacillus subtilis BSB1 (Trp+ derivative of strain 168)

value: choline added 60 min before NaCl shock


title: Cortex [JL711]

description:
JL711
processed data file: cortex_counts.txt

tag: parent-of-origin


title: Cortex [JL704]

description:
JL704
processed data file: cortex_counts.txt

tag: time


title: B. subtilis_-t60_choline.addition_rep1


title: 028_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
028_OPU


title: 14_r1: TF14 GRMZM2G017586 ChIP-Seq


title: B. subtilis_-t30_choline.addition_rep1

source_name: B. subtilis_choline added 30 min before NaCl shock

value: choline added 30 min before NaCl shock


title: 028_EP: Granulosa cells_17h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 17 hours after induction of ovulation
028_EP

source_name: Granulosa cells collected 17 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: B. subtilis_-t15_choline.addition_rep1

source_name: B. subtilis_choline added 15 min before NaCl shock

value: choline added 15 min before NaCl shock


title: B. subtilis_t0_choline.addition_rep1

source_name: B. subtilis_simultaneous addition of choline and NaCl


title: 027_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
027_OPU


title: Cortex [JL702]

description:
JL702
processed data file: cortex_counts.txt

tag: genotype/variation


title: B. subtilis_-t15_choline.addition_rep2


title: 026_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
026_OPU


title: B. subtilis_-t30_choline.addition_rep2


title: Cortex [JL701]

description:
JL701
processed data file: cortex_counts.txt

tag: Sex


title: 149_r2: TF149 Zm00001d031044 ChIP-Seq


title: B. subtilis_t0_choline.addition_rep2

value: simultaneous addition of choline and NaCl


title: 149_r1: TF149 Zm00001d031044 ChIP-Seq


title: 027_EP: Granulosa cells_17h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 17 hours after induction of ovulation
027_EP

tag: ovulation time point


title: Cortex [JL703]

description:
JL703
processed data file: cortex_counts.txt


title: 026_EP: Granulosa cells_17h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 17 hours after induction of ovulation
026_EP

tag: treatment


title: 148_r1: TF148 Zm00001d033267 ChIP-Seq


title: Cortex [JL611]

description:
JL611
processed data file: cortex_counts.txt

value: Maternal


title: 024_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
024_OPU

tag: ovulation induction


title: 142_r2: TF142 Zm00001d025141 ChIP-Seq

value: Leaf protoplast


title: Cortex [JL700]

description:
JL700
processed data file: cortex_counts.txt


title: Cortex [JL609]

description:
JL609
processed data file: cortex_counts.txt


title: Cortex [JL608]

description:
JL608
processed data file: cortex_counts.txt


title: 142_r1: TF142 Zm00001d025141 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: 140_r2: TF140 Zm00001d048208 ChIP-Seq


title: 148_r2: TF148 Zm00001d033267 ChIP-Seq


title: 13_r1: TF13 Zm00001d020614 ChIP-Seq


title: Cortex [JL610]

description:
JL610
processed data file: cortex_counts.txt


title: Cortex [JL606]

description:
JL606
processed data file: cortex_counts.txt


title: 13_r2: TF13 Zm00001d020614 ChIP-Seq


title: 140_r1: TF140 Zm00001d048208 ChIP-Seq


title: 022_EP: Granulosa cells_32h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
022_EP

source_name: Granulosa cells collected 32 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG

value: rhCG


title: 136_r2: TF136 Zm00001d024324 ChIP-Seq


title: 024_EP: Granulosa cells_32h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
024_EP

source_name: Granulosa cells collected 32 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: 136_r1: TF136 Zm00001d024324 ChIP-Seq


title: 022_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
022_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG


title: 023_EP: Granulosa cells_17h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 17 hours after induction of ovulation
023_EP

source_name: Granulosa cells collected 17 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG


title: 139_r2: TF139 Zm00001d047017 ChIP-Seq


title: 020_EP: Granulosa cells_0h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
020_EP


title: Cortex [JL603]

description:
JL603
processed data file: cortex_counts.txt


title: 020_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
020_OPU


title: Cortex [JL605]

description:
JL605
processed data file: cortex_counts.txt


title: 021_EP: Granulosa cells_12h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 12 hours after induction of ovulation
021_EP

source_name: Granulosa cells collected 12 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG


title: Cortex [JL604]

description:
JL604
processed data file: cortex_counts.txt


title: Cortex [JL601]

description:
JL601
processed data file: cortex_counts.txt


title: 019_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
019_OPU


title: Cortex [JL602]

description:
JL602
processed data file: cortex_counts.txt


title: 135_r2: TF135 Zm00001d048647 ChIP-Seq


title: Cortex [JL600]

description:
JL600
processed data file: cortex_counts.txt


title: Cortex [JL607]

description:
JL607
processed data file: cortex_counts.txt


title: 019_EP: Granulosa cells_32h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
019_EP


title: Hypothalamus [JL223]

description:
JL223
processed data file: hypothalamus_counts.txt

source_name: hypothalamus

value: Paternal

value: Hypothalamus


title: 023_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
023_OPU


title: 139_r1: TF139 Zm00001d047017 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: 135_r1: TF135 Zm00001d048647 ChIP-Seq


title: Hypothalamus [JL222]

description:
JL222
processed data file: hypothalamus_counts.txt

value: Female


title: 018_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
018_OPU


title: 128_r2: TF128 Zm00001d032265 ChIP-Seq


title: Hypothalamus [JL221]

description:
JL221
processed data file: hypothalamus_counts.txt


title: 021_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
021_OPU


title: 018_EP: Granulosa cells_32h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
018_EP


title: 017_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
017_OPU


title: T-rubrum-2

city: YiWu

first: wang

middle: chuan

last: wen

address: No. 288, Yang Cun road, Chou Jiang Street, Yiwu, Zhejiang

institute: AnnoGene

description: human primary epidermis-derived organoids infected by Trichophyton Rubrum at 24h

data_processing:
Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4  --barcode-mismatches 0
Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
hg19(ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
processed data files format and content: Tab-delimited xls file incluing fpkm of each sample

extract_protocol:
Adherent  cells and suspension cells were extracted from the blood of tissue samples ,then add lysate TRNzol-A+ ,after lysis ,centrifugation with chloroform ,RNA was extracted from supernatant
RNA libraries were prepared for sequencing using standard illumina protocols

value: epidermis

tag: agent

value: Trichophyton Rubrum


title: Hypothalamus [JL220]

description:
JL220
processed data file: hypothalamus_counts.txt


title: 127_r1: TF127 Zm00001d027900 ChIP-Seq


title: 127_r2: TF127 Zm00001d027900 ChIP-Seq


title: Control-2

description: human primary epidermis-derived organoids


title: 016_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
016_OPU

value: granulosa cells isolated from aspirated follicular fluid


title: 016_EP: Granulosa cells_12h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 12 hours after induction of ovulation
016_EP


title: 125_r2: TF125 Zm00001d053859 ChIP-Seq


title: Hypothalamus [JL219]

description:
JL219
processed data file: hypothalamus_counts.txt


title: Hypothalamus [JL218]

description:
JL218
processed data file: hypothalamus_counts.txt


title: 015_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
015_OPU


title: Hypothalamus [JL217]

description:
JL217
processed data file: hypothalamus_counts.txt

value: Deletion


title: Control-1

source_name: human primary epidermis-derived organoids


title: T-rubrum-1

source_name: human primary epidermis-derived organoids infected by Trichophyton Rubrum at 24h


title: PHH_2

data_processing:
bcl2fastq2-v2.19.1 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and  low-quality sequence, then mapped to GRCh38.91 whole genome using hisat2-2.1.0 with default parameters
Reads count was calculated by htseq-count with  parameters -t exon -f bam -s no -a 10
Genome_build: GRCh38.91
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: human adult liver tissue

extract_protocol:
Adherent  cells and suspension cells were extracted from the blood of tissue samples ,then add lysate TRNzol-A+ ,after lysis ,centrifugation with chloroform ,RNA was extracted from supernatant
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human adult liver tissue

tag: cell type

value: primary human hepatocytes

tag: passage


title: Hypothalamus [JL216]

description:
JL216
processed data file: hypothalamus_counts.txt


title: 124_r2: TF124 Zm00001d005892 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR

data_processing:
For mapping, we aligned the raw reads to the unmasked maize genome (B73 RefGen_v4) using Bowtie 2 (version 2.2.5) under the default parameters with the 3’  100 bp trimming option. Reads with mapping quality >= 10 were kept and PCR duplicates are removed using SAMTools (version 1.3). Deeptools bamcoverage was used to convert the BAM to bigwig files for viewing.
For peak calling, BAM files of biological replicates were used to call peaks with the SPP peak caller using relaxed parameters “-i = <INPUT BAM file>”, “-npeak = 300,000”, with input as control. Peaks in the transformed TF genebody itself are removed. Reproducible peaks were obtained with the IDR (Irreproducible discovery rate) statistical framework (version 2.0.3), as implemented in the PhantomPeakQualTools package, using 1% IDR as the threshold (cut-off).
To identify the high confident target genes of each TF, we used the probabilistic model TIP (Cheng et al., Bioinformatics, 2011, 3221–3227) with FDR 0.05 as cutoff.
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: peak and bigwig files
Supplementary_files_format_and_content: TF_target_TIP.txt: High cofident TF target genes called by TIP

source_name: Leaf protoplast


title: PHH_1


title: 014_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
014_OPU

value: rFSH


title: 124_r1: TF124 Zm00001d005892 ChIP-Seq


title: 128_r1: TF128 Zm00001d032265 ChIP-Seq


title: 014_EP: Granulosa cells_0h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
014_EP

source_name: Granulosa cells collected before induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG


title: 123_r2: TF123 Zm00001d026542 ChIP-Seq


title: Hypothalamus [JL215]

description:
JL215
processed data file: hypothalamus_counts.txt


title: hAHOs_2

value: human adult hepatic organoids


title: Hypothalamus [JL214]

description:
JL214
processed data file: hypothalamus_counts.txt

value: Wild-type


title: 013_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
013_OPU


title: hAHOs_1


title: Hypothalamus [JL213]

description:
JL213
processed data file: hypothalamus_counts.txt


title: 123_r1: TF123 Zm00001d026542 ChIP-Seq


title: 013_EP: Granulosa cells_32h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
013_EP


title: hEHOs_P3-2

source_name: human embryonic stem cells

value: human embryonic stem cells

value: human stem/progenitor cells


title: 119_r1: TF119 Zm00001d024679 ChIP-Seq


title: 125_r1: TF125 Zm00001d053859 ChIP-Seq


title: 119_r2: TF119 Zm00001d024679 ChIP-Seq


title: hEHOs_P3-1


title: Hypothalamus [JL211]

description:
JL211
processed data file: hypothalamus_counts.txt

value: Maternal


title: Hypothalamus [JL212]

description:
JL212
processed data file: hypothalamus_counts.txt


title: 117_r2: TF117 Zm00001d052229 ChIP-Seq

value: Leaf protoplast


title: 012_EP: Granulosa cells_0h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
012_EP

value: rhCG


title: 015_EP: Granulosa cells_32h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
015_EP


title: hEHOs_P1-2


title: Hypothalamus [JL210]

description:
JL210
processed data file: hypothalamus_counts.txt


title: 117_r1: TF117 Zm00001d052229 ChIP-Seq


title: 011_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
011_OPU


title: hEHOs_P1-1


title: 011_EP: Granulosa cells_12h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 12 hours after induction of ovulation
011_EP


title: Hypothalamus [JL209]

description:
JL209
processed data file: hypothalamus_counts.txt


title: 115_r2: TF115 Zm00001d050195 ChIP-Seq


title: Hypothalamus [JL208]

description:
JL208
processed data file: hypothalamus_counts.txt


title: HB_2

value: hepatoblasts


title: 115_r1: TF115 Zm00001d050195 ChIP-Seq

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR


title: 010_OPU: Granulosa cells_36h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
010_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with hMG, ovulation induced with GNRHa

value: hMG

value: GNRHa


title: HB_1


title: Hypothalamus [JL207]

description:
JL207
processed data file: hypothalamus_counts.txt

value: Female

value: Hypothalamus


title: 012_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
012_OPU

value: granulosa cells isolated from aspirated follicular fluid


title: 113_r2: TF113 Zm00001d014858 ChIP-Seq


title: HS_2

value: hepatic specification


title: Hypothalamus [JL206]

description:
JL206
processed data file: hypothalamus_counts.txt


title: 009_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
009_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: 009_EP: Granulosa cells_32h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
009_EP


title: Hypothalamus [JL205]

description:
JL205
processed data file: hypothalamus_counts.txt

value: Deletion


title: 111_r2: TF111 Zm00001d038843 ChIP-Seq


title: 113_r1: TF113 Zm00001d014858 ChIP-Seq


title: Hypothalamus [JL204]

description:
JL204
processed data file: hypothalamus_counts.txt


title: 008_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
008_OPU


title: FSCs_2

value: foregut stem cells


title: 111_r1: TF111 Zm00001d038843 ChIP-Seq


title: 007_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
007_OPU

value: rFSH


title: FSCs_1


title: 007_EP: Granulosa cells_17h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 17 hours after induction of ovulation
007_EP

source_name: Granulosa cells collected 17 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: 109_r2: TF109 Zm00001d014995 ChIP-Seq


title: +5dV3_rep3

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

institute: University of Cologne

data_processing:
The reads were mapped to the Arabis alpina reference genome (Assembly Version 5) using HISAT2 package with default settings. The SAM files obtained after mapping were converted into BAM files.
Genes were assembled and quantified in each sample using StringTie package. The raw gene count was obtained by feeding the .gtf file to a python script (prepDE.py) obtained from http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual.
The raw gene counts table was further analysed with DESeq2 to obtain differentially expressed genes.
Differentially expressed genes within 2 conditions with a fold change of 2 and a p-value significance <0.05 were analysed further.
Genome_build: Arabis alpina ( NCBI ID: 17813)
Supplementary_files_format_and_content: .xlsx file containing raw read counts produced with StringTie, normalized FPKM counts produced with TopHat, calculated log2 fold changes and p-value produced by DESeq2, annotation were downloaded from TAIR

organism: Arabis alpina

source_name: lateral buds

growth_protocol: Plants were grown for 8 weeks in long day conditions (16h light at 20°C, 8h dark at 18°C) and vernalized in a growth chamber for 12 weeks (16h light, 8h dark, at 4°C) before transfering them back to long day condition for 5 days

extract_protocol:
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to manufacturer's instructions
The libraries were prepared from 1 µg total RNA with RNA integrity number >8 (Bioanalyzer; Agilent) using the NEBNext Ultra Directional II RNA Library Prep Kit for Illumina (New England Biolabs) at the Cologne Genome Centre and sequencing was carried out using a HiSeq3000 (Illumina) with 1 x 150 bp single reads.

treatment_protocol: Buds of the dormant zone (V2) and buds in the growing zone (V3) were harvested at the end of the vernalization period (+0) and 5 days later (+5d)

tag: arabis alpina ecotype

value: Pajares

tag: time of harvesting

value: 5 days after vernalization (+5d)

tag: zone of the plant


title: 109_r1: TF109 Zm00001d014995 ChIP-Seq

city: Hong Hong

first: Silin

last: Zhong

institute: CUHK

tag: tissue


title: +5dV3_rep2


title: Hypothalamus [JL202]

description:
JL202
processed data file: hypothalamus_counts.txt

value: Wild-type


title: Hypothalamus [JL201]

description:
JL201
processed data file: hypothalamus_counts.txt


title: 010_EP: Granulosa cells_0h_hMG_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
010_EP

source_name: Granulosa cells collected before induction of ovulation in a patient treated with hMG, ovulation induced with GNRHa