title: NPC_Day7_Rep1_4SUseq

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

description:
4SU incorporated RNA
The library was barcoded with NEBNext® Multiplex Oligos for Illumina® - Index Primers Set 1 (Catalogue no. E7335S). Primer: INDEX_8. Barcode: ACTTGA.

data_processing:
Basecalling and quality scoring was performed directly using the NextSeq 550 software (RTAv2).
Base called data was de-multiplexed and converted in to FASTQ files using 'bcl2fastq' v2.20.0.422 with the following parameters:  Allowed barcode mismatches - 0   Minimum trimmed read length - 35   Mask short adapter reads - 35   Adapter stringency - 0.9   Adapter trimming method - Sliding window   Ignore missing BCLs - YES   Ignore missing filters - YES   Ignore missing positions - YES   Ignore missing controls - YES   Include non-PF clusters - NO   Create FASTQs for index reads - NO
Alignment. For each de-multiplexed sample, multiple fastq files were merged using the ‘cat’ function for both read 1 and 2. Merged files were the aligned to the mouse genome (mm9) using bowtie2 v2.2.6 with standard parameters for paired end sequence data to generate .SAM files.
Further processing. Aligned read data was processed using HOMER v4.8. SAM files were converted into tag directories using ‘makeTagDirectory’ with the following parameters: -format sam -flip –sspe. Genomic intervals which extended beyond the end of the chromosomes were removed using ‘removeOutOfBoundsReads.pl’. Strand specific browser track files (bigwig format; ‘.bigWig’ or ‘.bw’) for each replicate were generated using ‘makeUCSCfile’ with the following parameters: -fsize 1e20 -strand + (or -) -norm 1e8 -color 25,50,200. Browser tracks of merged replicates were generated by combining replicate tag directories with the ‘makeTagDirectory’ function and then running ‘makeUCSCfile’ on the combined data as described above.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are in bigwig format. Those with extension '.bigWig' represent individual 4SU-seq replicates and those with ‘.bw‘ are combined replicates. Positive and negative strand files are denoted by ‘*PosStr*‘ or ‘*NegStr*‘ respectively.

source_name: 4SU incorported RNA prepared from cells at day 7 of ES to NPC differentiation (parental mESCs - 46c Sox1-GFP reporter line)

growth_protocol: 46C mouse embryonic stem cells (mESCs) derived from E14tg2A (129/Ola) containing a GFP insertion into the Sox1 locus (Ying et al., 2003; PMID: 12524553) were cultured on 0.1% gelatin (Sigma - catalogue no. G1890) coated Corning flasks in GMEM BHK-21 (Gibco - catalogue no. 21710-025) supplemented with 10 % foetal calf serum (FCS; Sigma - catalogue no. F-7524), 1,000 units/ml LIF, non-essential amino acids (Sigma - catalogue no. M7145), sodium pyruvate (Sigma - catalogue no. S8636), 50 μM 2-β-mercaptoethanol (Gibco - catalogue no. 31350-010) and L-glutamine. ESCs were differentiated into NPCs essentially as described previously (Ying et al., 2003 PMID: 12524553 and Pollard et al., 2006 PMID: 17141035). To ensure a homogeneous starting population of ESCs, cells were harvested using trypsin 24 h prior to initiating differentiation and seeded at 3x106 on 0.1% gelatin coated Corning flasks. Differentiation media (1:1 DMEM/F12:Neurobasal medium (Gibco – catalogue no. 31330-032 and 21103-049 respectively) supplimented with 0.5x B27 (Invitrogen – catalogue no. 17504044), 0.5x N2 (Invitrogen –catalogue no. 17502048), L-Glutamine and 50 μM 2-β-mercaptoethanol (Gibco - catalogue no. 31350-010)) was prepared fresh on the day of differentiation. On day 0, ESCs were harvested, washed twice with PBS and twice with differentiation media then seeded at a density of 1x106 ESCs on 0.1% gelatin coated T75 Corning flasks (gelatin coated at RT for 3-6 h and washed twice with PBS prior to seeding). Cells were then cultured for 7 days with media changes each day after day 2. NPC differetiation was monitored microscopically through the expression of the GFP reporter.

extract_protocol:
4SUseq was performed essentially as described previously (Rabani et al., 2011 PMID: 21516085). Briefly, 4-thiouridine (4SU; Sigma - catalogue no. T4509) was added to ESCs / NPCs in  culture to a final concentration of 500 µM and incubated at 37°C for 20 min. Cells were harvested by trypsinisation and washed twice with PBS at RT. Total RNA was isolated from 5x106  cells using trizol according to the manufacturer’s instructions (Invitrogen - catalogue no. 15596026). Following precipitation, purified RNA was resuspended in 100 μl RNase-free water and DNase treated using the TURBO DNA-free kit according to the manufacturer’s instructions (Invitrogen - catalogue no. AM1907M). Residual inactivation beads were removed by spinning the RNA sample through a QIAshredder column at 1000 g for 1 min (Qiagen- catalogue no. 79654). Following quantification, 50 μg of RNA was incubated for 1.5 h at RT with 100 μg of Biotin-HPDP (Pierce - catalogue no. 21341; reconstituted in Dimethylformamide at 1 mg/ml) in 1x Biotinylation Buffer (10 mM Tris pH 7.4 and 1 mM EDTA) to a total volume of 500 μl. Uncoupled biotin was removed through two consecutive rounds of 1:1 v/v chloroform extraction followed by isopropanol/NaCl precipitation. RNA was resuspended in 100 μl of RNase free water and mixed 1:1 w/w with µMacs Streptavidin beads (miltenyi - catalogue no. 130-074-101) and incubated for 15 min at RT with rotation. The RNA / bead mixture was applied to a µMacs column following pre-equilibration with wash buffer (100 mM Tris pH 7.5, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). The captured beads were then washed with 3 x 900 µl of 65 oC wash buffer and 3 x 900 µl RT wash buffer. RNA was then eluted from the column by adding two consecutive rounds of 100 mM DTT. The eluate was added to 700 µl Buffer RLT (RNeasy MinElute Cleanup Kit; Qiagen catalogue no. 74204) and then purified according to the manufacturer’s instructions. Prior to library preparation, ribosomal RNA was depleted from the purified 4SU incorporate RNA using the low Input RiboMinus Eukaryote System v2 kit according to the manufacturer’s instructions (Ambion - catalogue no. A15027).
Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina according to the protocol for ribosome depleted RNA and with a 10 min RNA fragmentation step (NEB - catalogue no. E7760). Library PCRs were supplemented with 2x SYBR dye (Sigma – catalogue no. S9430) so that amplification could be monitored by quantitative PCR on a Roche lightcycler 480. To allow for sample multiplexing, PCRs were performed using index primers (NEBNext Multiplex Oligos for Illumina - Set 1. Catalogue no. E7335) and amplified to linear phase.  Libraries were purified and then combined into 4 sample equimolar pools containing the indexes 1, 3, 6 and 8.

value: ES-derived neural progenitor cells (differentiation day 7)


title: NPC_Day7_Rep2_4SUseq

status: Public on Jan 12 2019

type: SRA

city: Edinburgh

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain


title: BINPSK_ChIPseq

city: San Francisco

first: Melanie

last: Ott

state: CA

address: 1650 Owens Street, 5th Floor

department: Virology and Immunology

country: USA

institute: Gladstone Institutes

description: Replicate 2

library_source: genomic

data_processing:
FastQC was used to detect quality control and determine read length for alignment
Skewer Version 0.1.124 was used to remove barcodes with default parameters and -m function
Bowtie Version 1.1.2 was used for aligning reads using the default paramters and the -a -l 55 -n 2 -m 1 functions
MACS2 Version 2.1.0.20150731 was used for peak calling, normalization and genreation of bedgraph pileup files. Callpeak function was used with -B -SPMR to generate normalized bedgraph files.
bedGraphToBigWig Version 4 was used to convert bedgraph files to bigwigs
Genome_build: mm10
Supplementary_files_format_and_content: BigWig Files created from immunoprecipitated samples or created from input samples

molecule: genomic DNA

source_name: Embryonic Fibroblasts

growth_protocol: NIH3T3 cells were grown in 10% Bovine Calf Serum supplemented with L-Glutamine and Pen/Strep at 1x concentration. Cells were not treated with shRNAs, treated with scrambled shRNAs or RPRD1B shRNAs (indicated in sample section), and selected appropriately with puromycin for at 1 week.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes, thoroughly washed with DPBS, and resuspended in ChIP lysis buffer #1 (10mM Tris pH 7.4, 10mM NaCl, 0.5% NP-40, 1x HALT, 30nM Panobinostat and 5μM Nicotinamide). After sitting on ice for 10 minutes, cells were briefly vortexed and nuclei were pelleted. Nuclei were treated with MNase (NEB, M0247S) for 25 minutes at RT, pelleted and resuspended on ice in ChIP lysis buffer #2 (50mM Tris HCl pH 8.0, 10mM EDTA, 0.5% SDS, 1x HALT, 30nM Panobinostat and 5μM Nicotinamide). Chromatin was further sheared by sonication using the Sonic Dismembrator 500 (ThermoFisher Scientific) and preserved at -80oC until immunoprecipitation. 20-40ug chromatin was used for each IP
2ng of immunoprecipitated DNA from each reaction was used to create libraries using the Ovation Ultra-Low Library prep kit (Nugen, 0344-32) following manufacturer recommendations and libraries were deep sequenced on the HIseq 4000 or NextSeq 500 using single-end 50bp or single-end 75bp sequencing, respectively.

treatment_protocol: Naïve NIH3T3, RPRD1B or Scrambled shRNA selected NIH3T3 cells were treated for 2 hours with complete DMEM containing KDAC inhibitors (30nM Panobinostat, 5uM Nicotinamide) or vehicle controls.

tag: treatment

value: KDAC inhibitor

tag: background

value: Scrambled shRNA treated NIH3T3 Cells


title: NPC_Day5_Rep2_4SUseq

description:
4SU incorporated RNA
The library was barcoded with NEBNext® Multiplex Oligos for Illumina® - Index Primers Set 1 (Catalogue no. E7335S). Primer: INDEX_6. Barcode: GCCAAT.

source_name: 4SU incorported RNA prepared from cells at day 5 of ES to NPC differentiation (parental mESCs - 46c Sox1-GFP reporter line)

value: ES-derived neural progenitor cells (differentiation day 5)


title: AINPSV_ChIPseq

description: Replicate 1

value: Vehicle


title: AINPBV_ChIPseq

description: Replicate 1

value: RPRD1B shRNA treated NIH3T3 Cels


title: AINPBK_ChIPseq

description: Replicate 1


title: NPC_Day3_Rep1_4SUseq

description:
4SU incorporated RNA
The library was barcoded with NEBNext® Multiplex Oligos for Illumina® - Index Primers Set 1 (Catalogue no. E7335S). Primer: INDEX_3. Barcode: TTAGGC.

source_name: 4SU incorported RNA prepared from cells at day 3 of ES to NPC differentiation (parental mESCs - 46c Sox1-GFP reporter line)

value: ES-derived neural progenitor cells (differentiation day 3)


title: ESC_Rep2_4SUseq

description:
4SU incorporated RNA
The library was barcoded with NEBNext® Multiplex Oligos for Illumina® - Index Primers Set 1 (Catalogue no. E7335S). Primer: INDEX_1. Barcode:ATCACG

source_name: 4SU incorported RNA prepared from undifferentiated mouse ESCs (46c Sox1-GFP reporter line)

value: Mouse ESCs


title: NPC_Day3_Rep2_4SUseq


title: B4H8BV_ChIPseq

description: Replicate 2

tag: chip antibody

value: Pol II (4H8) - Abcam, ab5408


title: NPC_Day5_Rep1_4SUseq


title: AINPSK_ChIPseq

description: Replicate 1


title: DHFR - 270 min - Replicate 4

city: Kaiserslautern

first: Johannes

last: Herrmann

address: Erwin-Schrodinger-Strasse 13

department: Cell Biology

country: Germany

institute: University of Kaiserslautern

data_processing:
Reads were quality trimmed using Trimmomatic (version 0.36)
STAR (version 2.5.0a) was used to align reads to the S. cerevisiae R64-1-1 reference genome
BAM files were indexed using SAMtools
Reads per gene were quantified to the Ensembl R64 GTF annotation file with HTSeq
Genome_build: Ensembl S. cerevisiae R64-1-1 reference genome (GCA_000146045.2)
Supplementary_files_format_and_content: Processed files are raw read counts per gene as outputted from HTSeq
Supplementary_files_format_and_content: QCreports_FastQC.tar contains quality control reports for all samples in the dataset (output of the FastQC software).
Supplementary_files_format_and_content: RNAseqQC.pdf includes graphical representations of basic QC statistics of the data.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: DHFR - 270 min , whole cell lysate

growth_protocol: Cells were grown in minimal synthetic selective medium containing 2% lactate as respiratory carbon source

extract_protocol:
Total RNA was purified from clarified cell lysates using phenol-chloroform extraction. DNA was removed with the Turbo DNA free kit (Ambion).
Barcoded stranded mRNA-seq libraries were prepared from total RNA (300 ng) using the Illumina TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA, USA) implemented on the liquid handling robot Beckman FXP2.

treatment_protocol: Clogger expression was induced by addition of 0.5% galactose

value: YPH499 <delta>arg4

tag: time

value: 270 min

tag: genotype

value: DHFR

value: whole cell


title: B4H8BK_ChIPseq

description: Replicate 2


title: ESC_Rep1_4SUseq


title: b2delta-DHFR - 270 min - Replicate 4

source_name: b2delta-DHFR - 270 min , whole cell lysate


title: B4H8SK_ChIPseq

description: Replicate 2


title: B4H8SV_ChIPseq

description: Replicate 2


title: A4H8BV_ChIPseq

description: Replicate 1


title: empty vector - 270 min - Replicate 4

source_name: empty vector - 270 min , whole cell lysate

value: empty vector


title: b2-DHFR - 270 min - Replicate 4

source_name: b2-DHFR - 270 min , whole cell lysate


title: BINPBV_ChIPseq

description: Replicate 2


title: b2delta-DHFR - 90 min - Replicate 4

source_name: b2delta-DHFR - 90 min , whole cell lysate

value: 90 min


title: BINPBK_ChIPseq

description: Replicate 2


title: A4H8BK_ChIPseq

description: Replicate 1


title: A4H8SV_ChIPseq

description: Replicate 1


title: BINPSV_ChIPseq

description: Replicate 2


title: DHFR - 90 min - Replicate 4

source_name: DHFR - 90 min , whole cell lysate


title: b2-DHFR - 90 min - Replicate 4

source_name: b2-DHFR - 90 min , whole cell lysate


title: BK7acBV_ChIPseq

description: Replicate 2

value: Pol II (K7ac) - Custom, Polyclonal


title: A4H8SK_ChIPseq

description: Replicate 1


title: empty vector - 90 min - Replicate 4

source_name: empty vector - 90 min , whole cell lysate


title: BK7acSV_ChIPseq

description: Replicate 2


title: AK7acBV_ChIPseq

description: Replicate 1


title: empty vector - 30 min - Replicate 4

source_name: empty vector - 30 min , whole cell lysate

value: 30 min


title: DHFR - 10 min - Replicate 4

source_name: DHFR - 10 min , whole cell lysate

value: 10 min


title: AK7acSV_ChIPseq

description: Replicate 1


title: BK7acBK_ChIPseq

description: Replicate 2

value: KDAC inhibitor


title: b2-DHFR - 30 min - Replicate 4

source_name: b2-DHFR - 30 min , whole cell lysate


title: BK7acSK_ChIPseq

description: Replicate 2

value: Scrambled shRNA treated NIH3T3 Cells


title: b2delta-DHFR - 30 min - Replicate 4

source_name: b2delta-DHFR - 30 min , whole cell lysate


title: b2delta-DHFR - 10 min - Replicate 4

source_name: b2delta-DHFR - 10 min , whole cell lysate


title: AK7acBK_ChIPseq

description: Replicate 1

source_name: Embryonic Fibroblasts


title: AK7acSK_ChIPseq

description: Replicate 1


title: b2-DHFR - 10 min - Replicate 4

source_name: b2-DHFR - 10 min , whole cell lysate


title: empty vector - 10 min - Replicate 4

source_name: empty vector - 10 min , whole cell lysate


title: B8WG16BV_ChIPseq

description: Replicate 2

value: Pol II (8WG16) - Abcam, ab817


title: B8WG16SV_ChIPseq

description: Replicate 2

value: Vehicle


title: b2delta-DHFR - 0 min - Replicate 4

source_name: b2delta-DHFR - 0 min , whole cell lysate

value: 0 min


title: b2-DHFR - 0 min - Replicate 4

source_name: b2-DHFR - 0 min , whole cell lysate


title: DHFR - 270 min - Replicate 3

source_name: DHFR - 270 min , whole cell lysate


title: B8WG16SK_ChIPseq

description: Replicate 2


title: A8WG16BK_ChIPseq

description: Replicate 1

value: RPRD1B shRNA treated NIH3T3 Cels


title: A8WG16BV_ChIPseq

description: Replicate 1


title: empty vector - 0 min - Replicate 4

source_name: empty vector - 0 min , whole cell lysate


title: B8WG16BK_ChIPseq

description: Replicate 2


title: DHFR - 30 min - Replicate 4

source_name: DHFR - 30 min , whole cell lysate


title: b2delta-DHFR - 270 min - Replicate 3

source_name: b2delta-DHFR - 270 min , whole cell lysate


title: A8WG16SV_ChIPseq

description: Replicate 1


title: b2-DHFR - 270 min - Replicate 3

source_name: b2-DHFR - 270 min , whole cell lysate


title: B4H8V_ChIPseq

description: Replicate 2

value: Naïve NIH3T3 Cells


title: A4H8K_ChIPseq

description: Replicate 1

value: Pol II (4H8) - Abcam, ab5408


title: b2delta-DHFR - 90 min - Replicate 3

source_name: b2delta-DHFR - 90 min , whole cell lysate

value: YPH499 <delta>arg4


title: A4H8V_ChIPseq

description: Replicate 1


title: DHFR - 90 min - Replicate 3

source_name: DHFR - 90 min , whole cell lysate


title: b2-DHFR - 90 min - Replicate 3

source_name: b2-DHFR - 90 min , whole cell lysate


title: empty vector - 90 min - Replicate 3

source_name: empty vector - 90 min , whole cell lysate


title: DHFR - 0 min - Replicate 4

source_name: DHFR - 0 min , whole cell lysate


title: CK7acK_ChIPseq

description: Replicate 3


title: CK7acV_ChIPseq

description: Replicate 3


title: DHFR - 30 min - Replicate 3


title: BK7acV_ChIPseq

description: Replicate 2


title: BK7acK_ChIPseq

description: Replicate 2


title: b2-DHFR - 30 min - Replicate 3

source_name: b2-DHFR - 30 min , whole cell lysate


title: b2delta-DHFR - 30 min - Replicate 3

source_name: b2delta-DHFR - 30 min , whole cell lysate


title: A8WG16SK_ChIPseq

description: Replicate 1

source_name: Embryonic Fibroblasts


title: DHFR - 10 min - Replicate 3

source_name: DHFR - 10 min , whole cell lysate


title: C8WG16K_ChIPseq

description: Replicate 3


title: B8WG16V_ChIPseq

description: Replicate 2


title: C8WG16V_ChIPseq

description: Replicate 3


title: empty vector - 30 min - Replicate 3

source_name: empty vector - 30 min , whole cell lysate


title: b2delta-DHFR - 10 min - Replicate 3

source_name: b2delta-DHFR - 10 min , whole cell lysate


title: b2-DHFR - 10 min - Replicate 3

source_name: b2-DHFR - 10 min , whole cell lysate


title: empty vector - 270 min - Replicate 3

source_name: empty vector - 270 min , whole cell lysate

value: 270 min


title: B8WG16K_ChIPseq

description: Replicate 2


title: B4H8K_ChIPseq

description: Replicate 2


title: empty vector - 10 min - Replicate 3

source_name: empty vector - 10 min , whole cell lysate


title: DHFR - 0 min - Replicate 3

value: DHFR


title: Ex2_48h_CD62L_Low_2_2

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Sorted
20170213_countsMatrix.csv

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Illumina (bcl2fastq v2.17.1.14) software used for basecalling
Quality control is assessed by FastQC (v0.11.7)
Read mapping by STAR (Dobin, et al., 2013)(v2.5.2b)
Gene count calculation a HTSeq (Anders, et al., 2015)(0.9.1)
Genome_build: mm9
Supplementary_files_format_and_content: csv text files include mRNA molecule count values for each Sample

source_name: CD4 T cells

growth_protocol: T cells were cultured in complete RPMI and activated using antiCD3/antiCD28 beads

extract_protocol:
10^4-2*10^4 cells from each T cell subpopulation were sorted in 100 ul of Lysis/Binding Buffer (Life technologies), lysed for 5 min and frozen at -80°C. Cell lysates were thawed and mRNA was captured with 12 ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines. Purified messenger RNA was eluted at 82°C with 10 ul of 10 mM Tris-Cl pH 7.5 and stored at -80°C
cDNA was generated from 6ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated with UMI containing-indexed polyT primers at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM Illumina adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). Libraries were sequenced using an Illumina Nextseq.
3' MARseq  Jaitin et al, 2014

treatment_protocol: cells were cultured without addition of cytokines for the indicated time points

tag: organ

value: spleen

tag: selection markers

tag: time (h)

tag: initial cell concentration (cells/ml)


title: Ex2_72h_Low_1_2

description:
Sorted
20170213_countsMatrix.csv


title: b2delta-DHFR - 0 min - Replicate 3

source_name: b2delta-DHFR - 0 min , whole cell lysate

value: whole cell


title: Ex2_30h_Low_2_2

description:
Sorted
20170213_countsMatrix.csv


title: b2delta-DHFR - 270 min - Replicate 2

source_name: b2delta-DHFR - 270 min , whole cell lysate


title: empty vector - 0 min - Replicate 3

source_name: empty vector - 0 min , whole cell lysate

value: empty vector


title: b2-DHFR - 0 min - Replicate 3

source_name: b2-DHFR - 0 min , whole cell lysate


title: b2-DHFR - 270 min - Replicate 2

source_name: b2-DHFR - 270 min , whole cell lysate


title: Ex2_Naive_1_1

description:
Sorted
20170213_countsMatrix.csv


title: empty vector - 270 min - Replicate 2


title: b2delta-DHFR - 90 min - Replicate 2

source_name: b2delta-DHFR - 90 min , whole cell lysate

value: 90 min


title: Ex2_72h_High_3_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_18h_High_2_1

description:
Sorted
20170213_countsMatrix.csv


title: b2-DHFR - 90 min - Replicate 2

source_name: b2-DHFR - 90 min , whole cell lysate


title: DHFR - 270 min - Replicate 2

source_name: DHFR - 270 min , whole cell lysate


title: Ex2_72h_Low_2_2

description:
Sorted
20170213_countsMatrix.csv


title: DHFR - 90 min - Replicate 2

source_name: DHFR - 90 min , whole cell lysate


title: Ex2_48h_CD62L_High_1_1

description:
Sorted
20170213_countsMatrix.csv


title: DHFR - 30 min - Replicate 2

source_name: DHFR - 30 min , whole cell lysate

value: 30 min


title: Ex2_72h_CD62L_High_1_2

description:
Sorted
20170213_countsMatrix.csv


title: empty vector - 90 min - Replicate 2

source_name: empty vector - 90 min , whole cell lysate


title: Ex2_72h_High_2_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_48h_CD62L_Low_1_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_18h_High_3_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_72h_High_1_1

description:
Sorted
20170213_countsMatrix.csv


title: b2delta-DHFR - 30 min - Replicate 2

source_name: b2delta-DHFR - 30 min , whole cell lysate


title: b2-DHFR - 30 min - Replicate 2

source_name: b2-DHFR - 30 min , whole cell lysate


title: Ex2_72h_CD62L_Low_3_2

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_48h_High_1_2

description:
Sorted
20170213_countsMatrix.csv


title: empty vector - 30 min - Replicate 2

source_name: empty vector - 30 min , whole cell lysate


title: b2-DHFR - 10 min - Replicate 2

source_name: b2-DHFR - 10 min , whole cell lysate

value: 10 min


title: DHFR - 10 min - Replicate 2

source_name: DHFR - 10 min , whole cell lysate


title: Ex2_18h_Low_3_1

description:
Sorted
20170213_countsMatrix.csv

source_name: CD4 T cells


title: b2delta-DHFR - 10 min - Replicate 2

source_name: b2delta-DHFR - 10 min , whole cell lysate


title: DHFR - 0 min - Replicate 2

source_name: DHFR - 0 min , whole cell lysate


title: DHFR - 270 min - Replicate 1


title: Ex2_48h_CD62L_High_2_1

description:
Sorted
20170213_countsMatrix.csv


title: empty vector - 10 min - Replicate 2

source_name: empty vector - 10 min , whole cell lysate


title: b2delta-DHFR - 0 min - Replicate 2

source_name: b2delta-DHFR - 0 min , whole cell lysate


title: b2-DHFR - 270 min - Replicate 1

source_name: b2-DHFR - 270 min , whole cell lysate


title: Ex2_18h_Low_1_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_72h_CD62L_Low_2_1

description:
Sorted
20170213_countsMatrix.csv


title: empty vector - 0 min - Replicate 2

source_name: empty vector - 0 min , whole cell lysate


title: Ex2_48h_Low_3_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_18h_Low_2_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_48h_CD62L_Low_3_2

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_48h_High_3_2

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_30h_Low_1_2

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_72h_CD62L_Low_1_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_30h_High_1_2

description:
Sorted
20170213_countsMatrix.csv


title: DHFR - 90 min - Replicate 1


title: Ex2_Naive_2_1

description:
Sorted
20170213_countsMatrix.csv


title: b2delta-DHFR - 90 min - Replicate 1

source_name: b2delta-DHFR - 90 min , whole cell lysate


title: Ex2_48h_Low_2_1

description:
Sorted
20170213_countsMatrix.csv


title: empty vector - 90 min - Replicate 1


title: b2delta-DHFR - 270 min - Replicate 1

source_name: b2delta-DHFR - 270 min , whole cell lysate


title: Ex2_48h_Low_1_2

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_30h_High_3_2

description:
Sorted
20170213_countsMatrix.csv


title: b2-DHFR - 0 min - Replicate 2

source_name: b2-DHFR - 0 min , whole cell lysate


title: Ex2_30h_High_2_2

description:
Sorted
20170213_countsMatrix.csv


title: empty vector - 270 min - Replicate 1

source_name: empty vector - 270 min , whole cell lysate


title: DHFR - 30 min - Replicate 1

source_name: DHFR - 30 min , whole cell lysate


title: Ex2_72h_CD62L_High_3_1

description:
Sorted
20170213_countsMatrix.csv


title: b2-DHFR - 30 min - Replicate 1


title: Ex2_18h_High_1_1

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_48h_CD62L_High_3_1

description:
Sorted
20170213_countsMatrix.csv


title: b2delta-DHFR - 30 min - Replicate 1

source_name: b2delta-DHFR - 30 min , whole cell lysate


title: Ex2_48h_High_2_2

description:
Sorted
20170213_countsMatrix.csv


title: Ex2_Naive_3_1

description:
Sorted
20170213_countsMatrix.csv


title: b2delta-DHFR - 10 min - Replicate 1


title: empty vector - 10 min - Replicate 1


title: Ex2_72h_CD62L_High_2_1

description:
Sorted
20170213_countsMatrix.csv


title: DHFR - 10 min - Replicate 1


title: DHFR - 0 min - Replicate 1


title: Ex1_Mature-3

description:
MACS enrichment
20160314_CountsMatrix.csv


title: Ex1_Naive-3


title: Ex1_Naive-2


title: b2-DHFR - 90 min - Replicate 1

source_name: b2-DHFR - 90 min , whole cell lysate


title: b2delta-DHFR - 0 min - Replicate 1


title: Ex1_Naive-1


title: Ex1_Mature-2


title: Ex2_30h_Low_3_2

description:
Sorted
20170213_countsMatrix.csv


title: b2-DHFR - 0 min - Replicate 1


title: Ex1_Mature-1


title: empty vector - 0 min - Replicate 1


title: Ex1_72_CD62L_low.3

description:
Sorted
20160314_CountsMatrix.csv


title: Ex1_72_CD62L_low.2

description:
Sorted
20160314_CountsMatrix.csv


title: empty vector - 30 min - Replicate 1

source_name: empty vector - 30 min , whole cell lysate


title: Ex1_72_CD62L_high.1

description:
Sorted
20160314_CountsMatrix.csv


title: Ex1_72_CD62L_low.1

description:
Sorted
20160314_CountsMatrix.csv


title: b2-DHFR - 10 min - Replicate 1

source_name: b2-DHFR - 10 min , whole cell lysate


title: Ex1_72_CD62L_high.2

description:
Sorted
20160314_CountsMatrix.csv


title: Ex1_72_CD62L_high.3

description:
Sorted
20160314_CountsMatrix.csv


title: S00151400

city: Liverpool

first: Simon

last: Jochems

address: Pembroke Place

institute: Liverpool School of Tropical Medicine

data_processing:
Quality control of raw sequencing data was done using fastQC.
Mapping and generation of read counts to a human reference genome assembly (GRCh38) was done using Kallisto
Transcript counts were summarised to the gene level using the package tximport (R/Bioconductor).
The R/Bioconductor package DESeq2 was used to identify differentially expressed genes among the samples. Genes with an FDR value < 0.05 and an absolute fold change (FC) > 2 were identified as differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

organism: Homo sapiens

source_name: nasal cells

extract_protocol:
Nasal cells were collected in RNALater (ThermoFisher) at -80C until extraction. Extraction was performed using the RNEasy micro kit (Qiagen) with on column DNA digestion.
Sample integrity and quantity assessment, library preparation and RNA-sequencing (Illumina Hiseq4000, 20M reads) were performed at the Sanger Institute (Cambridge, UK).

tag: subject id

tag: timepoint

tag: challenge strain

value: 6B Spn

tag: carriage status

value: NonCarrier


title: Ex1_48_CD62L_low.2

description:
Sorted
20160314_CountsMatrix.csv

source_name: CD4 T cells


title: S00151088


title: S00151036


title: Ex1_48_CD62L_high.3

description:
Sorted
20160314_CountsMatrix.csv


title: S00151087


title: Ex1_48_CD62L_low.1

description:
Sorted
20160314_CountsMatrix.csv


title: S00151035


title: S00151033


title: Ex1_48_CD62L_high.1

description:
Sorted
20160314_CountsMatrix.csv


title: S00150631


title: S00151032

value: Carrier


title: S00151368


title: Ex1_48_CD62L_high.2

description:
Sorted
20160314_CountsMatrix.csv


title: S00151369


title: S00150632


title: S00151086


title: 12 h_Rep 3_sigJ deletion

city: Stockton

first: Douglas

middle: D

last: Risser

state: California

address: 3601 Pacific Ave

department: Biology

institute: University of the Pacific

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence at the University of California Berkeley QB3 Vincent J. Coates Genomics Sequencing Laboratory prior to dissemination of data to the end user
Alignment, normalization, and transcript abundance was performed using the Rockhopper software package with default settings
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Nostoc%20punctiforme
Supplementary_files_format_and_content: Excel file with transcript abundance. The gene IDs are publicly available and match the NCBI locus tags.

organism: Nostoc punctiforme PCC 73102

source_name: N. punctiforme

growth_protocol: Nostoc punctiforme strains were cultured in Allan and Arnon medium diluted four fould (AA/4), in the absence of a source of fixed nitrogen, as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) with the exception that cultures were supplemented with 4 mM sucralose to suppress hormognium development prior to induction as previously described (Splitt and Risser, 2016. The non-metabolizable sucrose analog sucralose is a potent inhibitor of hormogonium differentiation in the filamentous cyanobacterium Nostoc punctiforme. Arch Microbiol. 2016 Mar;198(2):137-47)

extract_protocol:
RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256)
Total RNA was ribodepleted using the Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, Inc.). cDNA was synthesized from the rRNA depleted samples, sheared to a library size of 200 bp, and appended with adapters following standard protocols at the University of California Berkeley QB3 Vincent J. Coates Genomics Sequencing Laboratory .

treatment_protocol: For hormogonium induction, culutres were harvested at 1000xg for 5 min, washed 3x with AA/4 to remove sucralose, and resuspended in AA/4 without sucralose

value: ATCC 29133; sigJ deletion

tag: filament type

value: developing hormogonia

tag: time following hormogonium induction


title: S00150717


title: 18 h_Rep 3_sigJ deletion


title: PPARg:RXRa_30nM:10nM_Ab_anti-RXR

type: protein

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

hyb_protocol: Microarray DNA double stranding and basic PBM protocols are as previously described (Berger & Bulyk, 2009)

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner and fluorescence was quantified using GenePix Pro 7.2

data_processing: Exported data were normalized using MicroArray LINEar Regression

label: alexa fluor 488 conjugated antibody

molecule: protein

source_name: PPARg (purchased from Protein One #P1050-01); RXRa (purchased from Active Motif #81082)

label_protocol: Protein samples were then incubated on the array for 1 h in a binding reaction containing: PBS pH7.4 with 0.02% TritonX-100, 1mM DTT, 0.2 mg/mL bovine serum albumin, and 0.4 mg/ml salmon testes DNA (Sigma D7656). See extended methods for protein concentration. Following the protein incubation, microarrays were washed with PBS containing 0.5% Tween-20 for 3 min, then in PBS containing 0.01% Triton X-100 for 2 min followed by a brief PBS rinse. Microarrays were then incubated with 20 μg/ml of primary antibody in 2% milk in PBS for 20 min. For heterodimers, separate experiments were run using Anti-RXRɑ antibody (Active Motif 61029) and Anti-His antibody (Sigma H1029), except for PBM experiments probing PPARɑ which were performed with an Alex488-conjugated anti-GST antibody (Life Tech A11131). Excess primary antibody was removed by washing with PBS containing 0.05% Tween-20 for 3 min and then in PBS containing 0.01% Triton X-100 for 2 min. Arrays were next incubated with 10 μg/ml of Alexa488-conjugated secondary antibody (Anti-mouse A488, Life Tech A1100) in 2% milk in PBS for 20min (PPARɑ was probed with an Alex488-conjugated anti-GST primary antibody and did not require a secondary antibody). Excess antibody was removed by washing 2x with PBS containing 0.05% Tween-20 for 3 min and then in PBS for 2 min.

extract_protocol: Standard Protein extraction kit

treatment_protocol: See individual sample descriptions

value: untreated

tag: target protein

value: RXRa

tag: protein concentrations in pbm

value: PPARg 30 nM; RXRa 10 nM

tag: primary antibody

value: Anti-RXRa (Active Motif 61029)

tag: primary antibody concentration

tag: secondary antibody

value: Alexa488-conjugated anti-mouse (Life Tech A1100)

tag: secondary antibody concentration


title: PPARg:RXRa_90nM:30nM_Ab_anti-RXR

tag: treatment

value: PPARg 90 nM; RXRa 30 nM


title: PPARg:RXRa_270nM:90nM_Ab_anti-RXR

value: PPARg 270 nM; RXRa 90 nM


title: Ex1_48_CD62L_low.3

description:
Sorted
20160314_CountsMatrix.csv

tag: strain

tag: organ

value: spleen


title: 6 h_Rep 3_sigJ deletion

value: 6 h


title: 1 h_Rep 3_sigJ deletion

value: 1 h


title: PPARg_DBDmut:RXRa_IVT_Ab_anti-PPARg

source_name: PPARg_DBDmut (IVT in our lab); RXRa (purchased from Active Motif #81082)

value: PPARg_DBDmut 270 nM; RXRa 90 nM

value: Anti-PPARg (Abcam 41928)


title: S00150013

value: 6B Spn


title: 0 h_Rep 3_sigJ deletion

value: vegetative

value: 0 h


title: 12 h_Rep 2_sigJ deletion

value: ATCC 29133; sigJ deletion


title: S00150629

value: Carrier


title: S00149857

value: NonCarrier


title: 6 h_Rep 2_sigJ deletion

value: developing hormogonia


title: PPARg_DBDmut_IVT_Ab_anti-PPARg

source_name: PPARg_DBDmut (IVT in our lab)

value: untreated

value: PPARg_DBDmut 270 nM


title: 12 h_Rep 1_sigJ deletion


title: 6 h_Rep 1_sigJ deletion


title: 18 h_Rep 1_sigJ deletion


title: 0 h_Rep 2_sigJ deletion


title: 1 h_Rep 2_sigJ deletion


title: RXRa_DBDmut_IVT_Ab_anti-RXR

source_name: RXRa_DBDmut (IVT in our lab)

value: RXRa_DBDmut 90 nM

value: Anti-RXRa (Active Motif 61029)

value: Alexa488-conjugated anti-mouse (Life Tech A1100)


title: S00151034


title: PPARg:RXRa_IVT_Ab_anti-PPARg

source_name: PPARg_DBD (IVT in our lab); RXRa (purchased from Active Motif #81082)

value: PPARg

value: PPARg  270 nM; RXRa 90 nM


title: 1 h_Rep 1_sigJ deletion

value: 1 h


title: S00150011


title: S00150037


title: PXR_Ab_anti-His

source_name: PXR (purchased from Protein One #P1082-02)

value: PXR

value: PXR 270 nM

value: Anti-His-tag (Sigma H1029)


title: 18 h_Rep 3_sigF deletion

value: ATCC 29133; sigF deletion


title: 0 h_Rep 1_sigJ deletion

value: vegetative

value: 0 h


title: VDR_Ab_anti-His

source_name: VDR (purchased from Protein One #P1084-02)

value: VDR

value: VDR 270 nM


title: 18 h_Rep 2_sigJ deletion

value: ATCC 29133; sigJ deletion

value: developing hormogonia


title: 6 h_Rep 3_sigF deletion

value: 6 h


title: 12 h_Rep 3_sigF deletion


title: S00149406

value: 6B Spn

value: NonCarrier


title: S00149859


title: S00149244


title: PPARg:RXRa_DBDmut_IVT_Ab_anti-RXR

source_name: PPARg (purchased from Protein One #P1050-01); RXRa_DBDmut (IVT in our lab)

value: untreated

value: PPARg 180 nM; RXRa_DBDmut 90 nM

value: Anti-RXRa (Active Motif 61029)

value: Alexa488-conjugated anti-mouse (Life Tech A1100)


title: 1 h_Rep 3_sigF deletion

value: 1 h


title: 12 h_Rep 2_sigF deletion


title: RARb_Ab_anti-His

source_name: RARb (purchased from Protein One #P1056-01)

value: RARb

value: RARb 270 nM


title: 0 h_Rep 2_sigF deletion

value: ATCC 29133; sigF deletion


title: 18 h_Rep 1_sigF deletion


title: 18 h_Rep 2_sigF deletion


title: THRa_Ab_anti-His

source_name: THRa (purchased from Protein One #P1052-02)

value: THRa

value: THRa 90 nM

value: Anti-His-tag (Sigma H1029)


title: S00149245


title: 6 h_Rep 2_sigF deletion


title: S00149384


title: S00149858


title: LXRb_Ab_anti-His

source_name: LXRb (purchased from Abcam #ab81924)

value: LXRb

value: LXRb 270 nM


title: RARa_Ab_anti-His

source_name: RARa (purchased from Protein One #P1054-01)

value: RARa

value: RARa 270 nM


title: 1 h_Rep 2_sigF deletion

value: developing hormogonia


title: 12 h_Rep 1_sigF deletion


title: LXRa_Ab_anti-His

source_name: LXRa (purchased from Protein One #P1045-01)

value: LXRa

value: LXRa 270 nM


title: S00149856

value: 6B Spn

value: NonCarrier


title: 0 h_Rep 3_sigF deletion

value: vegetative

value: 0 h


title: 6 h_Rep 1_sigF deletion

value: 6 h


title: S00149461


title: 0 h_Rep 1_sigF deletion


title: 1 h_Rep 1_sigF deletion

value: 1 h


title: NP1_3

city: Hangzhou

first: li

last: lei

address: xiashas street num 6

country: China

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC，including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database，Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Supplementary_files_format_and_content: tab-delimited text files includeTPM values for each Sample

organism: Cunninghamia lanceolata

source_name: Root

growth_protocol: The experimental material was the 1-year clone cuttings of Chinese fir K62. From the end of 2017 to June 2018, sand culture experiment was carried out in the plastic greenhouse of research institute of subtropical forestry,CAF.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: With normal water management, the 1-year clone Chinese fir were transplanted into a plastic greenhouse and growed for 6 months. The fertilization test was started at the beginning of June 2018. The concentration of nitrogen fertilizer or phosphate fertilizer was 0.7 % . 80 hours later, roots from different groups were cleaned and cut as samples. These samples were frozen by liquid nitrogen and transferred to -80 ℃ until RNA extraction.

tag: tissue

value: Root

value: nitrogen and phosphorus


title: NP1_2


title: 12 h_Rep 3_sigC deletion

value: ATCC 29133; sigC deletion


title: 18 h_Rep 3_sigC deletion


title: PPARa:RXRa_Ab_anti-GST

source_name: PPARa (purchased from Abcam #ab81925); RXRa (purified from E. coli in our lab)

value: untreated

value: PPARa

value: PPARa 270 nM; RXRa 90 nM

value: Alexa488-conjugated anti-GST-tag (Life Tech A11131)


title: PPARg_Ab_anti-His

source_name: PPARg (purified from E. coli in our lab)

value: PPARg

value: PPARg 180 nM

value: Anti-His-tag (Sigma H1029)

value: Alexa488-conjugated anti-mouse (Life Tech A1100)


title: NP1_1


title: 6 h_Rep 3_sigC deletion

source_name: N. punctiforme

value: developing hormogonia


title: PPARa:RXRa_Ab_anti-RXR

value: RXRa

value: Anti-RXRa (Active Motif 61029)


title: 1 h_Rep 3_sigC deletion


title: LXRb:RXRa_Ab_anti-His

source_name: LXRb (purchased from Abcam #ab81924); RXRa (purified from E. coli in our lab)

value: LXRb

value: LXRb 270 nM; RXRa 90 nM


title: P1_2

value: phosphorus


title: P1_3

value: Root


title: 18 h_Rep 2_sigC deletion


title: LXRb:RXRa_Ab_anti-RXR


title: P1_1


title: VDR:RXRa_Ab_anti-His

source_name: VDR (purchased from Protein One #P1084-02); RXRa (purified from E. coli in our lab)

value: VDR

value: VDR 270 nM; RXRa 90 nM


title: RARg_Ab_anti-His

source_name: RARg (purchased from Protein One #P1055-02)

value: untreated

value: RARg

value: RARg 270 nM


title: N1_3

value: nitrogen


title: VDR:RXRa_Ab_anti-RXR


title: PXR:RXRa_Ab_anti-His

source_name: PXR (purchased from Protein One #P1082-02); RXRa (purified from E. coli in our lab)

value: PXR

value: PXR 270 nM; RXRa 90 nM


title: PXR:RXRa_Ab_anti-RXR


title: 0 h_Rep 3_sigC deletion

value: ATCC 29133; sigC deletion

value: vegetative

value: 0 h


title: N1_1


title: Ck1_3

value: control


title: N1_2


title: 1 h_Rep 2_sigC deletion

value: developing hormogonia

value: 1 h


title: 0 h_Rep 2_sigC deletion


title: RARb:RXRa_Ab_anti-His

source_name: RARb (purchased from Protein One #P1056-01); RXRa (purified from E. coli in our lab)

value: RARb

value: RARb 270 nM; RXRa 90 nM

value: Anti-His-tag (Sigma H1029)

value: Alexa488-conjugated anti-mouse (Life Tech A1100)


title: 12 h_Rep 2_sigC deletion


title: Ck1_2

value: Root


title: THRa:RXRa_Ab_anti-His

source_name: THRa (purchased from Protein One #P1052-02); RXRa (purified from E. coli in our lab)

value: untreated

value: THRa

value: THRa 90 nM; RXRa 90 nM


title: RARb:RXRa_Ab_anti-RXR

value: RXRa

value: Anti-RXRa (Active Motif 61029)


title: 18 h_Rep 1_sigC deletion


title: 6 h_Rep 1_sigC deletion

value: 6 h


title: 12 h_Rep 1_sigC deletion

value: ATCC 29133; sigC deletion


title: MLAZA_5

city: State College

first: Sally

middle: A

last: Mackenzie

state: PA

address: 362 North Frear

institute: Penn State University

description: memory line treated with 5-azacytidine

data_processing:
Illumina for basecalling
Alignments were performed using RUM 2.0.5_06 (default parameters and min-length = 70) (Grant et al., 2011) keeping only uniquely mapped reads
The read count data were generated from the SAM files by using QoRTs software package (Hartley and Mullikin, 2015) --stranded --singleEnded --minMAPQ 25 --dropChrom Pt,Mt
DESeq2 (Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 2014) was used for gene count normalization and to identify differentially expressed genes (FDR < 0.05, |log2FC| > 0.5. GTF file TAIR10.37
Genome_build: TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with DESeq2

organism: Arabidopsis thaliana

source_name: memory line treated with 5-azacytidine

extract_protocol:
total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
These libraries were sequenced with the 100-bp reads option, in Hi-Seq 4000 analyzer (Illumina, USA) at BGI-Tech (Shenzhen, China).

treatment_protocol: The 5-azacytidine treatment protocol was adopted from Griffin et al  and Yang et al . Col-0 wild type and msh1 memory line seeds were surface-sterilized in 10% (v/v) sodium hypochlorite, rinsed thoroughly with sterile water, and sown in 8-oz clear cups (Fabri-Kal, USA) containing 30 mL 0.5 M Murashige and Skoog medium (Sigma, USA) supplemented with 1% (w/v) agar and 0 (control) or 100 μM 5-azacytidine (Sigma, USA). 10 days old plant were collected for RNAseq

tag: replicate type

value: biological rep 2; technical rep 3

value: whole plant with root

tag: genotype

value: msh1 memory line

tag: background ecotype

tag: age

value: 10 days old


title: 6 h_Rep 2_sigC deletion

value: developing hormogonia


title: Ck1_1

value: control


title: 0 h_Rep 1_sigC deletion

value: vegetative

value: 0 h


title: MLAZA_4

description: memory line treated with 5-azacytidine

growth_protocol: Col-0 wild type and msh1 memory line seeds were surface-sterilized in 10% (v/v) sodium hypochlorite, rinsed thoroughly with sterile water, and sown in 8-oz clear cups (Fabri-Kal, USA) containing 30 mL 0.5 M Murashige and Skoog medium (Sigma, USA) supplemented with 1% (w/v) agar and 0 (control) or 100 μM 5-azacytidine (Sigma, USA).

value: biological rep 2; technical rep 2


title: 18 h_Rep 3_wildtype


title: MLAZA_3

description: memory line treated with 5-azacytidine

value: biological rep 2; technical rep 1


title: RARa:RXRa_Ab_anti-RXR

source_name: RARa (purchased from Protein One #P1054-01); RXRa (purified from E. coli in our lab)

value: untreated

value: RARa 270 nM; RXRa 90 nM

value: Alexa488-conjugated anti-mouse (Life Tech A1100)


title: input_exo1_sgs1_0

city: Martinsried/Munich

first: Susanne

middle: Charlotte Sophie

last: Bantele

state: Bavaria

address: Am Klopferspitz 18

department: NWG

institute: Max Planck Institute of Biochemistry

data_processing:
Raw datas quality was check using the fastqc tool (v. 0.11.2)
the raw data was mapped to the S. cerevisiae genome, excluding multimapped reads (option -m 1)
Using the R (v. 3.22) package GenomicRanges (v. 1.22) the files converted into binned table with a windows size of 1000bp.
the regions in the bam files overlapped the binned regions of the genome were normalized using the TMM normalisation from the edgeR packge (v. 3.12.0)
the table were than converted into wig files for better visulization
Genome_build: Ensembl, build R64-1-1
Supplementary_files_format_and_content: wig files were generated using the R software suite.

extract_protocol:
bead beater lysis, shearing by sonication, RNAseA digest, de-crosslinking, phenol-chloroform extraction
MicroPlex Library Preparation kit v2 (Diagenode)

tag: background strain

tag: genotype/variation

value: exo1delta sgs1delta

tag: time point

value: before DSB induction

tag: antibody


title: RARa:RXRa_Ab_anti-His

tag: target protein

value: RARa

tag: protein concentrations in pbm

value: Anti-His-tag (Sigma H1029)


title: input_exo1_sgs1_4

value: after 4 hours of DSB induction


title: 12 h_Rep 3_wildtype

tag: filament type

tag: time following hormogonium induction


title: 1 h_Rep 1_sigC deletion

value: ATCC 29133; sigC deletion

value: 1 h


title: FXR:RXRa_Ab_anti-RXR

source_name: FXR (purchased from Protein One #P1044-01); RXRa (purified from E. coli in our lab)

value: RXRa

value: FXR 270 nM; RXRa 90 nM

tag: primary antibody

value: Anti-RXRa (Active Motif 61029)

tag: primary antibody concentration

tag: secondary antibody

tag: secondary antibody concentration


title: FXR:RXRa_Ab_anti-His

tag: treatment

value: FXR


title: input_WT_4

value: WT


title: MLAZA_2

description: memory line treated with 5-azacytidine

tag: replicate type

value: biological rep 1; technical rep 2

tag: tissue

value: whole plant with root

value: msh1 memory line

value: 10 days old


title: MLAZA_1

description: memory line treated with 5-azacytidine

value: biological rep 1; technical rep 1

tag: genotype

tag: background ecotype


title: 6 h_Rep 3_wildtype

tag: strain

value: developing hormogonia

value: 6 h


title: THRa:RXRa_Ab_anti-RXR

value: untreated

value: THRa 90 nM; RXRa 90 nM

value: Alexa488-conjugated anti-mouse (Life Tech A1100)


title: ML_6

description: memory line

source_name: memory line

value: biological rep 2; technical rep 3

tag: age


title: 1 h_Rep 3_wildtype

value: 1 h


title: siGATA2 -enz Replicate 3

type: RNA

city: Cambridge

first: Lewis

last: Chaytor

address: Hutchison/MRC Research Centre, Cambridge biomedical campus

department: Department of Oncology

institute: Cambridge University

description:
siGATA2 -enz Replicate 3 - 200307970024_K_Grn.idat
GATA2 targetting siRNA (siGATA2) transfected cells treated with DMSO contol

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array processing, background correction, normalisation and quality control checks were performed using the R package ‘Lumi’. Probe intensity values were converted to VSD (variance stabilized data) using variance stabilising transformation. The robust spline normalization (RSN) was used as an array normalisation method. Poor quality probes (detection threshold < 0.01), and probes that are not detected at all in the remaining arrays were removed prior to downstream analysis. The remaining probe (22,380) normalised intensity was used in the differential expression analysis

label: biotin

source_name: CWR22Rv1 cell line

label_protocol: According to manufacturer (Illumina) specifications.

growth_protocol: CWR22Rv1 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or a GATA2 targeting siRNA (siGATA2) 48 hours prior to harvest using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM in steroid depleted conditions. Cells were grown for 72 hours in steroid depleted conditions total -/+ 10 µM enzalutamide for 24 hours before RNA extraction

extract_protocol: RNA was extracted with TRIzol reagent (Life Technologies) following manufacturers instructions.

tag: cell type

value: Human castrate-resistant prostate cancer carcinoma cell line

tag: cell line


title: siScr +enz Replicate 3

description:
siScr +enz Replicate 3 - 200307970024_J_Grn.idat
Control siRNA (siSCR) transfected cells treated with enzalutamide


title: siGATA2 +enz Replicate 3

description:
siGATA2 +enz Replicate 3 - 200307970024_L_Grn.idat
GATA2 targetting siRNA (siGATA2) transfected cells treated with enzalutamide


title: siGATA2 +enz Replicate 2

description:
siGATA2 +enz Replicate 2 - 200307970024_H_Grn.idat
GATA2 targetting siRNA (siGATA2) transfected cells treated with enzalutamide


title: siScr +enz Replicate 2

description:
siScr +enz Replicate 2 - 200307970024_F_Grn.idat
Control siRNA (siSCR) transfected cells treated with enzalutamide


title: siScr -enz Replicate 3

description:
siScr -enz Replicate 3 - 200307970024_I_Grn.idat
Control siRNA (siSCR) transfected cells treated with DMSO control


title: siGATA2 +enz Replicate 1

description:
siGATA2 +enz Replicate 1 - 200307970024_D_Grn.idat
GATA2 targetting siRNA (siGATA2) transfected cells treated with enzalutamide


title: siGATA2 -enz Replicate 2

description:
siGATA2 -enz Replicate 2 - 200307970024_G_Grn.idat
GATA2 targetting siRNA (siGATA2) transfected cells treated with DMSO contol


title: siScr -enz Replicate 2

description:
siScr -enz Replicate 2 - 200307970024_E_Grn.idat
Control siRNA (siSCR) transfected cells treated with DMSO control


title: siScr +enz Replicate 1

description:
siScr +enz Replicate 1 -200307970024_B_Grn.idat
Control siRNA (siSCR) transfected cells treated with enzalutamide


title: siGATA2 -enz Replicate 1

description:
siGATA2 -enz Replicate 1 -200307970024_C_Grn.idat
GATA2 targetting siRNA (siGATA2) transfected cells treated with DMSO contol


title: LXRa:RXRa_Ab_anti-His

source_name: LXRa (purchased from Protein One #P1045-01); RXRa (purified from E. coli in our lab)

tag: target protein

value: LXRa

value: LXRa 270 nM; RXRa 90 nM

value: Anti-His-tag (Sigma H1029)


title: siScr -enz Replicate 1

description:
siScr -enz Replicate 1 -200307970024_A_Grn.idat
Control siRNA (siSCR) transfected cells treated with DMSO control


title: RARg:RXRa_Ab_anti-His

source_name: RARg (purchased from Protein One #P1055-02); RXRa (purified from E. coli in our lab)

value: RARg

tag: protein concentrations in pbm

value: RARg 270 nM; RXRa 90 nM


title: exo1∆ sgs1∆ 4h gamma-H2A

description:
input used: input_exo1_sgs1_4
IP against gamma-H2A

source_name: exo1∆ sgs1∆ 4h gamma-H2A

tag: background strain

tag: genotype/variation

value: exo1delta sgs1delta

tag: time point

value: after 4 hours of DSB induction

tag: antibody


title: 0 h_Rep 3_wildtype

tag: filament type

value: vegetative

tag: time following hormogonium induction

value: 0 h


title: RARg:RXRa_Ab_anti-RXR

tag: treatment

value: RXRa

tag: primary antibody

value: Anti-RXRa (Active Motif 61029)

tag: primary antibody concentration

tag: secondary antibody

tag: secondary antibody concentration


title: 6 h_Rep 2_wildtype

tag: strain

value: developing hormogonia

value: 6 h


title: ML_5

description: memory line

tag: replicate type

value: biological rep 2; technical rep 2

tag: tissue

value: whole plant with root

tag: genotype

value: msh1 memory line

tag: background ecotype

tag: age

value: 10 days old


title: exo1∆ sgs1∆ 0h gamma-H2A

description:
input used: input_exo1_sgs1_0
IP against gamma-H2A

source_name: exo1∆ sgs1∆ 0h gamma-H2A

tag: background strain

value: before DSB induction


title: WT 4h gamma-H2A

description:
input used: input_WT_4
IP against gamma-H2A

source_name: WT 4h gamma-H2A

tag: genotype/variation

value: WT


title: LXRa:RXRa_Ab_anti-RXR

value: untreated

tag: target protein

tag: protein concentrations in pbm

value: LXRa 270 nM; RXRa 90 nM

value: Alexa488-conjugated anti-mouse (Life Tech A1100)


title: 1 h_Rep 2_wildtype

source_name: N. punctiforme

tag: filament type

value: 1 h


title: ML_4

description: memory line

value: biological rep 2; technical rep 1


title: exo1∆ sgs1∆ 0h RPA

description:
input used: input_exo1_sgs1_0
IP against RPA

source_name: exo1∆ sgs1∆ 0h RPA

value: exo1delta sgs1delta

tag: time point

tag: antibody

value: RPA


title: input_WT_0


title: 0 h_Rep 2_wildtype

value: vegetative

tag: time following hormogonium induction

value: 0 h


title: 12 h_Rep 2_wildtype

value: developing hormogonia


title: PPARg:RXRa_Ab_anti-PPAR_rep2

source_name: PPARg (purified from E. coli in our lab); RXRa (purified from E. coli in our lab)

tag: treatment

value: PPARg

value: PPARg 180 nM; RXRa 90 nM

tag: primary antibody

value: Anti-PPARg (Abcam 41928)

tag: primary antibody concentration


title: ML_3

description: memory line

value: biological rep 1; technical rep 3

value: whole plant with root

value: msh1 memory line


title: Col0AZA_9

description: Wild type treated with 5-azacytidine

source_name: Wild type treated with 5-azacytidine

value: biological rep 3; technical rep 3

value: wildtype

value: 10 days old


title: 18 h_Rep 2_wildtype

tag: strain


title: Col0AZA_8

description: Wild type treated with 5-azacytidine

tag: replicate type

value: biological rep 3; technical rep 2


title: ML_2

description: memory line

value: biological rep 1; technical rep 2

tag: tissue


title: RXRa_Ab_anti-RXR_rep2

source_name: RXRa (purified from E. coli in our lab)

value: untreated

value: RXRa

value: RXRa 180 nM

value: Anti-RXRa (Active Motif 61029)

tag: secondary antibody

value: Alexa488-conjugated anti-mouse (Life Tech A1100)

tag: secondary antibody concentration


title: 18 h_Rep 1_wildtype

value: developing hormogonia


title: Col0AZA_6

description: Wild type treated with 5-azacytidine

value: biological rep 2; technical rep 3

tag: genotype

tag: background ecotype

tag: age


title: 12 h_Rep 1_wildtype


title: ML_1

description: memory line

value: biological rep 1; technical rep 1


title: RXRa_Ab_anti-RXR

tag: target protein


title: Col0AZA_7

description: Wild type treated with 5-azacytidine

value: biological rep 3; technical rep 1


title: Col0AZA_5

description: Wild type treated with 5-azacytidine

value: biological rep 2; technical rep 2


title: WT 4h RPA

description:
input used: input_WT_4
IP against RPA

source_name: WT 4h RPA

tag: background strain

tag: genotype/variation

value: WT

value: after 4 hours of DSB induction

value: RPA


title: WT 0h RPA

description:
input used: input_WT_0
IP against RPA

source_name: WT 0h RPA

tag: time point

value: before DSB induction


title: PPARg:RXRa_Ab_anti-PPAR

value: PPARg

tag: protein concentrations in pbm

value: PPARg 180 nM; RXRa 90 nM

value: Anti-PPARg (Abcam 41928)


title: 1 h_Rep 1_wildtype

tag: filament type

tag: time following hormogonium induction

value: 1 h


title: WT 0h gamma-H2A

description:
input used: input_WT_0
IP against gamma-H2A

source_name: WT 0h gamma-H2A

tag: antibody


title: HFD20 - input

first: Marcus

middle: James

last: Lyall

state: Lothian

address: The Queen's Medical Research Institute, 47 Little France Crescent

department: University/British Heart Foundation Centre for Cardiovascular Science

institute: University of Edinburgh

description: mapped reads (mm10) were binned across 200bp windows.

data_processing:
Reads mapped to mm10 mouse build
Data binned into 150bp windows across the genome
Data converted into mm9 build and into a wiggle (.bedgraph) file
data normalised by read count
enriched (5hmC) datasets normalised to mean input dataset to generate enrichment over background dataset
Genome_build: mm9
Supplementary_files_format_and_content: .bedgraph file

source_name: liver

extract_protocol:
Sheared gDNA was enriched using antibodies against 5hmC (Active Motif , cat# 39769) prior to enrichment through magnetic IgG beads. Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 18 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

treatment_protocol: Diet commenced at weaning.  Following 17 weeks of dietary intervention mice were sacrificed cervical dislocation and livers frozen on dry ice.

value: liver

tag: gender

value: Male

tag: strain background

tag: treatment

value: high fat diet

value: 5-hmC - Active Motif (cat# 39769)


title: Col0AZA_4

description: Wild type treated with 5-azacytidine

tag: replicate type

value: biological rep 2; technical rep 1

tag: tissue

value: whole plant with root

value: wildtype

value: 10 days old


title: 0 h_Rep 1_wildtype

tag: strain

value: vegetative

value: 0 h


title: HFD20


title: 6 h_Rep 1_wildtype

value: developing hormogonia

value: 6 h


title: SHAM rep3

city: Canterbury

first: Lucian

last: Duvenage

address: Giles Lane

department: School of Biosciences

institute: University of Kent

description:
untreated vs SHAM.txt
wild-type treated with SHAM

data_processing:
Illumina NextSeq500 used for basecalling
Sequence quality was assessed using FASTQC. No trimming was performed
Each raw fastq data file was used to map reads to Assembly 21 of C. albicans SC5314 using HISAT2 v1.01. BAM files for technical replicates were merged using Picard (Galaxy version 1.1.2), in order to generate a single BAM file for each biological replicate
Gene differential expression testing was performed to compare groups using three biological replicates each, using Cuffdiff v. 2.2.1.1. with the following parameter changes from default: multi-read correction: yes, perform bias correction: yes (C. albicans SC5314 genome Assembly 21)
Genome_build: C. albicans SC5134 Assembly 21
Supplementary_files_format_and_content: Tab-delimited test files Cuffdiff output for gene differential expression testing comparing untreated sample group ("WT") with each other sample group. Including FPKM, log2(fold_change), test_stat, p value, q-value

organism: Candida albicans

source_name: whole cells

growth_protocol: Inoculation of YPD with overnight cultures to final OD600 nm of 0.2, followed by 5 h shaking incubation 30 °C

extract_protocol:
E.Z.N.A.® Yeast RNA Kit (Omega Bio-tek, Norcross, GA) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Addition of 1mM SNP,  0.5 mM SHAM, or 1 mM SNP+ 0.5 mM SHAM, 30 °C shaking incubation for 30 min, followed by RNA extraction

tag: genotype

value: wild-type


title: SS rep 2

description:
untreated  vs SNP+SHAM.txt
wild-type treated with SNP+SHAM


title: SS rep 1


title: Col0AZA_3

description: Wild type treated with 5-azacytidine

value: biological rep 1; technical rep 3

tag: background ecotype


title: HFD16


title: HFD16 - input


title: SHAM rep 2


title: HFD15 - input


title: SS rep 3


title: L5-3

city: Taizhou

first: Baoying

last: Qian

state: Zhejiang

address: 1139 Shifu Road, Jiaojiang, Taizhou, Zhejiang 318000, P. R. China

department: School of life science

institute: Taizhou University

data_processing:
Output statistics, such as raw sequence data, and then generate clean reads from raw reads after remove reads with adaptors, remove reads with unknown nucleotides larger than 5% and remove low quality reads which the percentage of low quality bases(base quality≤10) is more than 20%.
Transcriptome de novo assembly is carried out with short reads assembling program - Trinity.
Unigene function annotation. Unigene sequences are firstly aligned by blastx to protein databases like NR, Swiss-Prot, KEGG and COG (e-value<0.00001), and aligned by blastn to nucleotide databases nt(evalue<  0.00001), retrieving proteins with the highest sequence similarity with the given Unigenes along with their protein functional annotations,the results about this are inculding in  the folder annotation.
Unigene GO Classification, Metabolic Pathway Analysis, Protein Coding Region Prediction (CDS), Unigene SSR Analysis and Heterozygous SNP Analysis
GO Classification of Differentially Expressed Unigene and Pathway Analysis,
Genome_build: danRer7
Supplementary_files_format_and_content: the xls. files include RPKM values, log2FoldChange, Padj, p-value and anotation in 7 functional database (NR ,NT,GO ,KOG ,KEGG ,SwissProt and InterPro) for each Sample

organism: Micropterus salmoides

source_name: Liver

extract_protocol:
Livers were removed, stored in the liquid of RNAstore (CWBIO, China), and RNA was harvested using Trizol reagent. Seqencing libraries were constructed from 1 ug of total RNA using Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Juvenile largemouth bass (mean weight 3 ± 0.2 g) were purchased from Chinese freshwater fish hatchery (Huzhou, Zhejiang) and maintained in the aquatic toxicology lab of Taizhou University, Zhejiang, China. Fish were randomly divided into 9 groups, and each groups acclimated in water aerated tanks (9 tanks in total and 30 fish in every tank) with a flow-through dechlorinated tap water at the temperature of 28 °C under the photoperiod of 13 h daylight and 11 h dark. They were fed with largemouth bass compound feed for 14 days of acclimation period (3 times every day). A total of 90 juvenile largemouth bass in three tanks were regarded as one lead concentration gradient, and every gradient treated with the concentration of lead 0, 17.8, 100 mg/L for 96 h, respectively.

value: Liver

tag: treatment time

value: treated with 100 mg/L lead exposure


title: L5-2


title: SHAM repR


title: HFD15


title: Col0AZA_2

description: Wild type treated with 5-azacytidine

value: biological rep 1; technical rep 2

tag: age


title: Col0AZA_1

description: Wild type treated with 5-azacytidine

value: biological rep 1; technical rep 1


title: SNP rep3

description:
untreated vs SNP.txt
wild-type treated with SNP


title: L5-1


title: SNP rep2


title: Col0_6

description: Wild type

source_name: Wild type

value: biological rep 3; technical rep 2


title: SNP rep1


title: L2-3

value: treated with 17.8 mg/L lead exposure


title: Col0_5

description: Wild type

value: biological rep 3; technical rep 1


title: control 9 - input

value: liver

value: Male

value: control diet

value: 5-hmC - Active Motif (cat# 39769)


title: HFD12

value: high fat diet


title: WT rep3

description: untreated wild-type


title: L2-2


title: L0-3

value: no treatment


title: control 9


title: Col0_3

description: Wild type

value: biological rep 2; technical rep 1

value: whole plant with root

value: wildtype

value: 10 days old


title: Col0_4

description: Wild type

value: biological rep 2; technical rep 2


title: L2-1

value: Liver


title: control 2 - input


title: Col0_2

description: Wild type

value: biological rep 1; technical rep 2


title: L0-2


title: WT rep1

description: untreated wild-type

value: wild-type


title: control 2


title: Col0_1

description: Wild type

value: biological rep 1; technical rep 1


title: L0-1


title: 445 CB TI

status: Public on Jan 11 2019

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description:
processed data file: mES_445_peaks.bed
processed data file: ZFP445_CB_1.bed

data_processing:
Raw fastq were quality checked with FastQC (version 0.11.5), followed by adapter and base quality trimming with TrimGalore (version 0.2.7). Reads post-QC were aligned using bowtie2 (v2.3.3, --end-to-end).
Potential PCR duplicates were removed with Picard tools (“MarkDuplicates” function).
Peak were called on mapped data using MACS v.2.1.0 with broad peak option using only uniquely aligned reads (MAPQ>10).
For KAP1 ChIP, peaks were filtered for score > 100.
Genome_build: hg19 (GRCh37) and mm10 (GRCm38)
Supplementary_files_format_and_content: *.bed: bed files contain unfiltered raw peaks.

source_name: Embryonic stem cells (Cast/Black6)

growth_protocol: Naive murine embryonic stem cells were cultured in N2B27 medium with 1x MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1x penicillin/streptomycin, 25µg/mL Bovine serum albumin, leukaemia inhibitory factor (LIF), and 2i containing 1µM MEK inhibitor PD 0325901 (Axon 1408) and 3µM GSK3 inhibitor CHIR 99021 (Axon 1386). Cells were grown on 0.1% gelatin-coated plates and split every two days. Cells were transduced, selected with 4μg/mL puromycin and collected after 5 days.

extract_protocol:
Cells were harvested, washed with Episerf (LifeTechnologies, #10732), fixed in 10mL per 1x10^7 cells (10 min in 1% formaldehyde), quenched with TrisHCl in 50mL (at 250 mM final), washed with PBS, and pelleted. Each pellet containing 1x10^7 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65°C, RNase A at 1μg/μL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 1x10^7 cells with Dynabeads (ThermoFisher) in IP buffer (16.25 mM Tris at pH 8.1, 137.5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1.25% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65°C, Proteinase K at 400ng/μL, overnight) and DNA was further extracted for analysis.
Single-end libraries were prepared and sequenced in 150bp reads runs according to Illumina instructions.

tag: strain/background

tag: cell type

value: Embryonic stem cells (ESCs)

value: overexpressing HA-tagged ZFP445

tag: chip antibody


title: 445 BC TI rep2

description:
processed data file: mES_445_peaks.bed
processed data file: ZFP445_BC_2.bed

source_name: Embryonic stem cells (Black6/Cast)

tag: genotype/variation


title: 445 CB ChIP

value: HA (Covance, MMS-101P)


title: 445 TI

description: processed data file: hES_445_HA_ChIP_S2_vs_hES_445_Ti_S1_peaks.bed

source_name: H1 hESCs

growth_protocol: H1 ESCs (WA01, WiCell) were maintained in mTesRI (StemCell Technologies) on hES-qualified Matrigel (BD Biosciences). For transduction, hES were detached using TryPLE Express (Invitrogen), split at 40,000 cells/cm2 and maintained at least 12 hrs with ROCK inhibitor (Y-27632) to increase viability.

extract_protocol:
Cells were harvested, washed 2x (in KO medium), fixed in 10mL per 1x10^7 cells (10 min in 1% formaldehyde), quenched with TrisHCl in 50mL (at 250 mM final), washed with PBS, and pelleted. Each pellet containing 1x10^7 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65°C, RNase A at 1μg/μL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 1x10^7 cells with Dynabeads (ThermoFisher) in IP buffer (16.25 mM Tris at pH 8.1, 137.5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1.25% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65°C, Proteinase K at 400ng/μL, overnight) and DNA was further extracted for analysis.
Paired-end libraries were prepared and sequenced in 75bp reads runs according to Illumina instructions.

tag: cell line

value: overexpressing HA-tagged ZNF445


title: 445 ChIP


title: Br16_6 #2

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.4.2; parameters : --phred33 --length 36 --clip_R1 9).
Mapping using STAR (v 2.5.2a; parameters:  --runMode alignReads --genomeLoad LoadAndExit) to a combined human (GRCh38) and mouse (GRCm38) genome reference
The gene-level expression counts computed with featureCounts (v1.5.1) using the gene annotations obtained from RefSeq (release 70).
To normalize gene counts for cell-specific biases, we used size factors computed utilizing the deconvolution strategy developed by Lun et al. (2016) implemented in the scran (v1.6.5) package available on R/Bioconductor
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.txt are tab-delimited files containing the gene counts as obtained from featureCounts; processed_normalized_matrix.txt contain normalized counts for human genes, using the method implemented in scran R/bioconductor package

extract_protocol:
RNA was captured on beads conjugated with oligo-dT primer according to Macauley et al. Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nat Protoc 11, 2081-2103 (2016).
Libraries were prepared with Smart -Seq2 protocol. Sequencing libraries were generated and indexed from 0.25 ng of cDNA per sample using the Nextera XT DNA Library Preparation Kit (Illumina, Cat# FC-131-2001) according to manufacturer’s instructions

tag: origin

value: patient

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

value: CTC-cluster

value: CTC

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: mouse type

tag: donor


title: Br16_5 #2

tag: treatment


title: WT repR

description: untreated wild-type

tag: strain

tag: genotype


title: Br7_5 #2

value: CTC-single

tag: cell type


title: Br7_2 #2


title: Br16_3 #2


title: Br16_4 #2


title: exo1∆ sgs1∆ 4h RPA

description:
input used: input_exo1_sgs1_4
IP against RPA

source_name: exo1∆ sgs1∆ 4h RPA

tag: background strain

tag: genotype/variation

value: exo1delta sgs1delta

tag: time point

value: after 4 hours of DSB induction

tag: antibody

value: RPA


title: Br7_1_SG #2

tag: origin

tag: number of cells

tag: number of ctc


title: HFD12 - input

tag: tissue

value: liver

tag: gender

value: Male

tag: strain background

value: high fat diet

value: 5-hmC - Active Motif (cat# 39769)


title: Brx50_NSG_CTC_A7 #2

value: xenograft

tag: number of wbc attached

tag: sample type

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat


title: Brx50_NSG_CTC_A6 #2

tag: cell type

tag: mouse type

tag: donor

tag: treatment


title: Brx50_NSG_CTC_A5 #2


title: Brx50_NSG_CTC_A4 #2


title: Br7_7_12 #2


title: Brx50_NSG_CTC_A3 #2


title: Brx50_NSG_CTC_A2 #2


title: 445 BC ChIP rep2

tag: strain/background

tag: genotype/variation

tag: chip antibody


title: Br61_CTC_6 #2

tag: origin

tag: number of cells

tag: number of ctc


title: Br61_CTC_4 #2


title: Br61_CTC_38 #2


title: Br61_CTC_35 #2


title: Br61_CTC_23 #2


title: Br61_CTC_34 #2


title: Br16_1 #2


title: Br61_CTC_20 #2


title: Br61_CTC_22 #2


title: Br61_CTC_25 #2


title: Br61_CTC_18 #2


title: Br57_CTC_9 #2


title: Br61_CTC_13 #2


title: Br57_CTC_8 #2


title: Br61_CTC_10 #2


title: Br57_CTC_7 #2


title: Br57_CTC_3 #2


title: Br57_CTC_17 #2


title: Br57_CTC_15 #2


title: Br57_CTC_14 #2


title: Br57_CTC_2 #2


title: Br57_CTC_11 #2


title: Br57_CTC_10 #2


title: Br53_CTC_1 #2


title: Br45_CTC_3 #2


title: Br61_CTC_24 #2


title: Br45_CTC_2 #2


title: Br11_8 #2


title: Br11_7 #2


title: Br11_9 #2


title: Br61_CTC_45 #2


title: Br57_CTC_4 #2


title: Br11_19 #2


title: Br11_2 #2


title: Br11_18 #2


title: Br11_4 #2


title: Br57_CTC_16 #2


title: Br11_1 #2


title: Br11_17 #2


title: Br39_1 #2


title: Br39_23 #2


title: Br39_16 #2


title: Br39_28 #2


title: Br57_CTC_12 #2


title: Br39_15 #2


title: Br38_12 #2


title: Br44_3 #2


title: Br23_28 #2


title: Br23_27 #2


title: Br11_6 #2


title: Br23_26 #2


title: Br23_23 #2


title: Br38_6 #2


title: Br23_20 #2


title: Br11_3 #2


title: Br38_5 #2


title: Br37_2 #2


title: Br11_10 #2


title: Br37_1 #2


title: Br11_11 #2


title: Br16_C11 #2


title: Br16_C13 #2


title: Br16_C33 #2


title: Br16_C34 #2


title: Br16_C10 #2


title: Br16_C12 #2


title: Br16_C8 #2


title: Br16_C5 #2


title: Br16_C4 #2


title: Br16_C7 #2


title: Br57_CTC_13 #2


title: Br16_C2 #2


title: Br16_B61 #2


title: Br16_C6 #2


title: Br16_C1 #2


title: Br16_C3 #2


title: Br16_B59 #2


title: Br16_B58 #2


title: Br16_B57 #2


title: Br16_B56 #2


title: Br16_B60 #2


title: Br16_B52 #2


title: Br16_B55 #2


title: Br16_B51 #2


title: Br16_B33 #2


title: Br16_B29 #2


title: Br16_B49 #2


title: Br16_B34 #2


title: Br16_B28 #2

value: CTC-cluster-WBC


title: Br16_B46 #2


title: Br16_B31 #2


title: Br16_B30 #2


title: Br16_B25 #2


title: Br16_B24 #2


title: Br16_B32 #2


title: Br16_B17 #2


title: Br16_B19 #2


title: Br16_B45 #2


title: Br16_B26 #2


title: Br16_B11 #2


title: Br16_B20 #2


title: Br16_B16 #2


title: Br16_B23 #2


title: Br16_B53 #2


title: Br16_B7 #2


title: Br16_B50 #2


title: Br16_B5 #2


title: Br16_B3 #2


title: Br16_B4 #2


title: Br16_B6 #2


title: Br16_B2 #2


title: Br16_B12 #2


title: Br16_AC19 #2


title: Br16_AC33 #2


title: Br16_AC18 #2


title: Br16_AC40 #2


title: Br16_AC37 #2


title: Br16_AC15 #2


title: Br16_AC34 #2


title: Br16_B10 #2


title: Br16_AC9 #2


title: Br16_AC8 #2


title: Br16_AC38 #2


title: Br16_AC20 #2


title: Br16_AC6 #2


title: Br16_AC14 #2


title: Br16_AC5 #2


title: Br16_AC39 #2


title: Br16_AC1 #2


title: LM2_G15 #2


title: Br16_AC4 #2


title: Br16_AC7 #2


title: Br16_AC10 #2


title: LM2_G13 #2


title: Br16_B8 #2


title: LM2_G11 #2


title: LM2_G10 #2


title: LM2_G14 #2


title: Br16_AC16 #2


title: Br16_AC17 #2


title: LM2_G9 #2


title: LM2_G1 #2


title: LM2_E5 #2


title: LM2_E1 #2


title: LM2_E2 #2


title: LM2_A94 #2


title: LM2_A93 #2


title: LM2_E7 #2


title: LM2_E4 #2


title: LM2_A89 #2


title: LM2_A83 #2


title: LM2_G12 #2


title: R50_71

value: cell line

value: Rigosertib 50 nM


title: LM2_A90 #2


title: LM2_A85 #2


title: siRNF168_2 NEC

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: NEC cells

growth_protocol: cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the qiagen RNA exaction kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: cells were treated with 50nM siRNF168 or siControl

value: esophagus cancer cell

tag: passages

value: 15-18 passage

value: RNF168 knockdown


title: LM2_A81 #2

tag: number of wbc attached


title: siRNF168_1 NEC


title: siRNF168_3 NEC


title: LM2_E6 #2

tag: sample type


title: Control_2 NEC

value: control


title: Control_3 NEC


title: R50_51

tag: ctc-cluster size


title: Control_1 NEC


title: R50_61

tag: ctc-cluster id


title: R50_7

tag: sample cell type

value: Rigosertib 20 nM


title: 97-gem-Day3-OEA115

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were trimmed to 51bp with Trim Galore v0.4.4. Trimmed data was mapped to the C. elegans WBCel235 genome assembly using HISAT2 v2.1.0 guided by splice junctions taken from Ensembl v75. Mapped positions with MAPQ < 20 and all non-primary alignments were discarded before the data was analyzed. All libraries were mapped as non directional single-end. Only exactly overlapping reads were assigned to a gene and transcript isoforms were merged. Raw counts were generated using Seqmonk and all subsequent analysis was performed in R.
Genome_build: WBCel235
Raw counts were generated using Seqmonk (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and all subsequent analysis was performed in R (http://www.R-project.org). The DESeq2 package (Love et al., 2014) was used to generate normalized counts. Normalized counts were then log-transformed and rounded to two decimal places to generate the values in the processed data file. Processed data is presented as a CSV file with sample ID as column name and gene name as row name.

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
Samples of at least 1000 worms were washed 3X in M9 by settling then snap-frozen in Trizol and kept at -80C until library-prep. Samples were freeze-thawed 10 times to break worm cuticle and RNA was precipitated using chloroform-isopropanol. RNA was treated with 10U DNase I (Roche #04716728001) for 20 minutes at 37°C and purified on Qiagen RNeasy columns (QIAGEN 15596-026).
Libraries were prepared using combined protocols from SuperScript II Reverse Transcriptase (Invitrogen 18064-014), NEBNext mRNA Second Strand Synthesis Module (E6111), and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB-E7645). Half reactions were used for all steps except the final PCR amplification. Briefly, Oligo d(T)25 beads (NEB-S1419S) were washed and resuspended in 2X RNA Binding Buffer (2 M LiCl
, 80 mM Tris HCl (pH 7.5), 4 mM EDTA
, 0.2% Triton X-100) in a 1:1 ratio and 500ng of total RNA was added. RNA was denatured by incubating at 65C for 5 minutes and mRNA was allowed to bind to beads. Beads were washed twice in Wash Buffer (150 mM LiCl
, 20 mM Tris HCl (pH 7.5), 1.0 mM EDTA
, 0.01% Triton X-100) and mRNA eluted in 10 mM Tris Buffer by incubating at 80C for 2 minutes. An equal volume of Binding Buffer was added, washed once more, and the mRNA was eluted into a First Strand Synthesis Reaction Buffer containing 4μl 5X First-Strand Buffer (Invitrogen), 1μl 50µM Random hexamers (Invitrogen N8080127), 0.5μl 10mM dNTP mix, and 1.5μl 0.1M DTT. 0.5μl RNaseOUT (Invitrogen 10777-019), 2.5μl 0.1μg/μl Actinomycin D (Sigma A1410), and 0.5μl SuperScript II Reverse Transcriptase were added and samples were incubated in a thermal cycler for 10 minutes at 25°C, 15 minutes at 42°C, and 15 minutes at 70°C. Second strand synthesis was performed immediately using the NEBNext mRNA Second Strand Synthesis Module.
Libraries were then generated using the NEBNext Ultra II DNA Library Prep Kit. For PCR library enrichment, 13 cycles of amplification were performed. Library quality was assessed on a Bioanalyzer High Sensitivity DNA Chip (Agilent 5067-4626) and concentration was determined using KAPA Library Quantification Kit (KK4824). Libraries were sequenced on an Illumina HiSeq 2500 system by the Babraham Sequencing Facility.

tag: tissue

value: whole organism

tag: age

value: 97 hours

tag: genotype


title: LM2_E3 #2

value: CTC-single

tag: cell type

value: CTC

tag: sample cell type cat

tag: mouse type

tag: donor


title: LM2_A86 #2

value: CTC-cluster

tag: treatment


title: R50_6

tag: origin


title: o50_6

tag: number of cells

value: Ouabain 20 nM


title: d50_7

tag: number of ctc

value: Digitoxin 20 nM


title: 97-gem-Day3-OEA087


title: d50_6


title: 97-fem-Day3-OEA140

value: fem-3(q20) IV


title: o50_7


title: 89-gem-Day3-OEA128

value: 89 hours


title: 97-fem-Day3-OEA088


title: 89-gem-Day3-OEA085


title: R16_61


title: d50_5


title: R16_7


title: 89-gem-Day3-OEA113


title: 89-fem-Day3-OEA127


title: 89-fem-Day3-OEA072


title: 89-fem-Day3-OEA129


title: o16_6


title: o16_5


title: R16_6


title: R16_5


title: 73-gem-Day2-OEA075

value: 73 hours


title: 73-gem-Day2-OEA104


title: 73-fem-Day2-OEA105


title: d16_6

value: cell line


title: 73-fem-Day2-OEA083


title: 97-fem-Day3-OEA133


title: d16_5


title: d16_7


title: 73-fem-Day2-OEA070


title: 65-gem-Day2-OEA122

value: 65 hours


title: 65-gem-Day2-OEA100


title: 50_77

value: Control


title: 50_76


title: 50_75


title: 65-gem-Day2-OEA080


title: 65-fem-Day2-OEA101


title: 50_66

value: Rigosertib 100 nM


title: 50_65


title: 49-gem-Day1-OEA107

value: 49 hours


title: 50_27

value: Ouabain 100 nM


title: 49-fem-Day1-OEA098


title: 50_26


title: 73-gem-Day2-OEA082


title: o16_7


title: 50_17

value: Digitoxin 100 nM


title: 49-fem-Day1-OEA079

value: whole organism


title: 50_16


title: 16_77


title: 49-fem-Day1-OEA066


title: 41-gem-Day1-OEA092

value: 41 hours


title: 16_76


title: 41-gem-Day1-OEA135


title: 41-fem-Day1-OEA136


title: 16_27


title: 16_25


title: 41-fem-Day1-OEA093


title: 41-fem-Day1-OEA117


title: 50_67


title: 49-gem-Day1-OEA097


title: 65-fem-Day2-OEA068


title: 16_16


title: 257-gem-Day10-OEA144

value: 257 hours


title: 16_15


title: 257-gem-Day10-OEA142


title: 257-fem-Day10-OEA145


title: 137-gem-Day5-OEA110

value: 137 hours


title: 117-gem-Day4-OEA106

value: 117 hours


title: 137-gem-Day5-OEA094


title: 41-gem-Day1-OEA116


title: 137-fem-Day5-OEA141


title: 16_75


title: 137-fem-Day5-OEA074


title: 117-fem-Day4-OEA091


title: Adipocytes_shNF1_Rosi_3

city: Philadelphia

first: Chunjie

last: Jiang

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

data_processing:
ChIP-seq reads were aligned to human reference genome (hg19) using Bowtie2. Only unique mapped reads were considered for further analysis. Aligned reads from biological replicates were pooled together and peak calling was performed by HOMER with normalized tag count >=6, p value < 0.00001 and fold change >= 4 for each patient. After that peaks from each patient were merged together using BEDTools, and then resized to 200 bp.
RNA-seq reads were aligned to human reference genome (hg19) using Hisat2 with default parameters. Only unique mapped reads were considered for further analysis. Normalized expression value, fragments per kilobase of exon per million reads mapped (FPKM), was calculated for each gene using StringTie
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using HORMER V4.9; Normalized abundance measurement was generated using StringTie.

source_name: Adipocytes

growth_protocol: hASCs at passage P3-P4 were cultured in DMEM medium. Confluent hASCs were then transferred into adipogenic medium for 14 days. Then, cells were further cultured in maintenance medium another 7 days.

extract_protocol:
Total RNA was extracted by using Qiagen RNeasey Mini kit. Ribosomal RNA was depleted by Ribo-Zero gold kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit. ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.

treatment_protocol: hASC-derived adipocytes were treated with rosiglitazone for 48h beginning at day 21

value: hASC-derived adipocytes


title: 50_15


title: 117-gem-Day4-OEA090


title: Adipocytes_shNF1_DMSO_3


title: 117-fem-Day4-OEA073


title: 257-fem-Day10-OEA143


title: Adipocytes_shNF1_Rosi_1


title: Adipocytes_shNF1_DMSO_2


title: Adipocytes_shNF1_DMSO_1


title: D319N ERK2, rep 3

city: Peoria

first: Sejeong

last: Shin

state: Illinois

address: 1 illini drive

institute: University of Illinois at Chicago

description: DD

hyb_protocol: Following fragmentation,  60 uL of cDNA were hybridized for 16 hr at 45 C on GeneChip Human Transcriptome 2.0 Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing:
The data were analyzed with using Affymetrix Expression Console ver 1.4 using Analysis algorithm RMA.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HTA-2_0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

source_name: MCF10A D319N ERK2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA using amplification kit WT PLUS, Lot # 4224182, followed by labeling 5.5 ug cDNA using kit WT PLUS, Lot # 4224182.

growth_protocol: MCF-10A cells are grown on standard tissue culture plastic in a 5% CO2 humidified incubator at 37 °C. The growth medium is composed of DMEM/F12 supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor (EGF), 10 μg/ml insulin, 0.5 μg/ml hydrocortisone, 100 ng/ml cholera toxin

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen)

treatment_protocol: Vector control, D319N ERK2, and Y261A ERK2 expression was induced by doxycycline in Tet-on MCF10A cell systems.

tag: cell line

value: breast epithelial cells

tag: genotype/variation

value: expressing D319N ERK2


title: Vec control, rep 2

description: FF

source_name: MCF10A vec control

value: expressing vector control


title: Y261A ERK2, rep 3

description: JJ

source_name: MCF10A Y261A ERK2

value: expressing Y261A ERK2


title: Y261A ERK2, rep 1

description: HH


title: Y261A ERK2, rep 2

description: II


title: Adipocytes_Scramble_Rosi_3


title: Vec control, rep 1

description: EE


title: Adipocytes_Scramble_Rosi_2


title: CFT073 stimulatedFibroblast 6 hours rep 2

city: örebro

first: isak

last: demirel

address: campus usö

country: Sweden

institute: örebro University

description: Gene expression after 6 hours of CFT073 stimulated human fibroblasts

hyb_protocol: Labelled samples were hybridized onto G4851C SurePrint G3 Human Gene Expression v3 8x60K Microarray glass slides (Agilent)

scan_protocol: Microarrays were scanned with a G2565 CA array laser scanner (Agilent) followed by image analysis and data extraction with Feature Extraction Software version 10.7.3.1 (Agilent).

data_processing: 75th percentile shift normalization and baseline adjusted

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the low input quick amp labeling kit,one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary human renal fibroblasts were derived from a healthy woman and cultured in Dulbecco's modified eagle medium (DMEM) containing 10% foetal bovine serum (FBS), 2 mM L-glutamine, 1mM non-essential amino acids, 50 U/mL penicillin and 50 ml/mL streptomycin at 37°C in a 5% CO2 atmosphere. The cells were serum starved overnight in DMEM containing 2 mM L-glutamine, 1mM non-essential amino acids and 50 µg/ml Gentamicin (Sigma-Aldrich, St. Louis, MO, USA). During experiments, the medium was replaced with DMEM containing 1% FBS, 1 mM non-essential amino acids and 2 mM L-glutamine.

extract_protocol: Total RNA was isolated from the primary renal fibroblasts using the RNeasy Mini Kit (Qiagen Technologies) according to manufacturer instructions. RNA quality and integrity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) according to manufacturer instructions.

treatment_protocol: The renal fibroblasts were stimulated with CFT073 at a multiplicity of infection (MOI) of 10 for 6 hours and incubated at 37ºC with 5% CO2.

value: Primary human renal fibroblasts

value: uropathogenic E.coli (CFT073)


title: Vec control, rep 3

description: GG


title: Adipocytes_Scramble_DMSO_1


title: D319N ERK2, rep 2

description: CC


title: P5_Adipose_PPARg_ChIP

source_name: Adipose tissue

value: Adipose

tag: chip antibody

value: PPARg(Santa Cruz Biotechnology, Cat# sc-7196)


title: TPM_Sample_A11_20160407000

city: Iowa City

first: John

last: Engelhardt

state: Iowa

address: 51 Newton Rd, 1-111 BSB

department: Developmental and Cellular Biology

institute: University of Iowa

description:
Sample_A11_20160407000
A11_20160407000_S79_L006

data_processing:
TPM quantification via RSEM
Transcripts were collated by gene via summing transcript expression
Remove cells with <60% cellular RNA relative to exogenous RNAspike-in
multiply mRNAs by 1e6 then divide by the sum RNAspike-in TPM
Normalize to upper quartile TPM, removing samples whose upper quartile value was zero.
Remove genes with less than 1% of cells expressing at >=5 normalized TPM
Genome_build: human mRNA (Ensembl V87) with added Ambion RNAspike sequences
Supplementary_files_format_and_content: tab-delimited text file containing normalized TPM values for each included sample

source_name: Human 4

growth_protocol: After receipt of islets from the integrated islet distribution program (IIDP), islets were cultured overnight in RPMI supplemented with 10mM glucose, 10% FBS, and 1% Penn/Strep prior to scRNAseq.

extract_protocol:
Fluidigm C1 microfluidics chip
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

value: individual 4

tag: ethnicity

value: White

value: Pancreatic islet

tag: gender

value: female

tag: bmi


title: Unstimulated Fibroblast 6 hours rep 3

description: Gene expression after 6 hours of unstimulated human fibroblasts

source_name: Unstimulated Fibroblast 6 hours rep 3

value: control


title: Adipocytes_Scramble_Rosi_1


title: CFT073 stimulated Fibroblast 6 hours rep 1


title: CFT073 stimulated Fibroblast 6 hours rep 3


title: MCF-7-TNR_HOTAIRsi.2 RNA-SEQ

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

data_processing:
FASTQ files were trimmed using systemPipeR Bioconductor package,
rsem-calculate-expression --star --star-gzipped-read-file --output-genome-bam -p 48 --paired-end
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MCF-7-TNR_CTLsi.1.results.tsv: Tab-separated value text file includes TPM and FPKM values.
Supplementary_files_format_and_content: MCF-7-TNR_CTLsi.2.results.tsv: Tab-separated value text file includes TPM and FPKM values.
Supplementary_files_format_and_content: MCF-7-TNR_HOTAIRsi.1.results.tsv: Tab-separated value text file includes TPM and FPKM values.
Supplementary_files_format_and_content: MCF-7-TNR_HOTAIRsi.2.results.tsv: Tab-separated value text file includes TPM and FPKM values.

source_name: Breast Cancer Cell Line

growth_protocol: MCF-7-TNR cells were cultured in DMEM with 10% FBS.

extract_protocol:
Total cell RNA was extracted when cells were ~80% confluent using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: HOTAIR-specific siRNA or control siRNA was transfected into MCF-7-TNR cells using RNAiMAX.

value: Breast cancer cell line

tag: sirna

value: HOTAIRsi


title: Adipocytes_Scramble_DMSO_2


title: P4_Adipose_PPARg_ChIP

tag: tissue