title: MSC_CEBPaVeh_rep2


title: MSC_H3K9Ac125_rep2

status: Public on Jul 11 2016

type: SRA

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

country: USA

institute: University of Wisconsin-Madison

library_source: genomic

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and MACS.
HOMER analysis was run using the default settings for peak finding.  Histone peaks were called with a 2-fold enrichment over input instead of 4-fold (for transcription factors) given the nature of histone chip-seq.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: mm9
Supplementary_files_format_and_content: *.bed files contain the ChIP-seq peak locations, *.bedgraph files are for display in the UCSC genome browser

molecule: genomic DNA

organism: Mus musculus

source_name: marrow derived MSC

growth_protocol: Marrow derived MSC (mdMSC) were obtained from Dr. Janet Rubin, cryopreserved and expanded no more than 10 passages.  The MSCs were cultured in minimum Eagle’s medium alpha (MEMα) modification supplemented with 10% fetal bovine serum from Hyclone (Logan, UT), and 1% penicillin-streptomycin from Invitrogen.  For differentiation, cells were grown to confluency and then transferred to either osteogenic differentiation media (10 mM β–glycerophosphate and 50 µg/mL ascorbic acid) or adipogenic differentiation media (5 µg/mL insulin, 50 µM indomethacin, 0.1 µM dexamethasone) for the indicated lengths, replenishing the media every 2-3 days until assay.

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Meyer MB, Mol Endo. 2012). Briefly, samples were subjected to immuno-precipitation using either a control IgG antibody or the indicated experimental antibody (VDR, RXR, H3K4me1, H3K4me2, H3K4me3, H3K27Ac, H3K5Ac, H3K9Ac, H4K20me1, H3K36me3, or H3K9me3).  To remove the calcified matrix from the differentiated cells, the cells were subjected to three 15 minute 300mM EDTA washes following fixation. Subsequently, matrix mix was subjected to 2x10 pulses with a Polytron Homogenizer (Power Gen 125, Fisher Scientific) while in NCP 1 buffer (Hepes 10mM pH 6.5, EDTA 10mM, EGTA 0.5mM, Triton X-100 0.25%).  Resulting cell pellet was resuspended in NCP 2 buffer (Hepes 10mM pH 6.5, EDTA 1mM, EGTA 0.5mM, NaCl 200mM) and remainder of protocol was followed.  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols.  ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencers by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver.  3) on an Illumina cBot (Illumina, Carlsbad, CA) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver.  3). Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina Carlsbad, CA) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  The ChIP samples were repeated in biological replicate in the same manner (minimum of 2 replicates). Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Where indicated, MSC cells were treated with 100nM of 1,25(OH)2D3 for 3 hours prior to ChIP assay.

tag: cell type

value: marrow-derived mesenchymal stem cells

tag: differentiation time point (day)

tag: differentiation media

tag: treatment

tag: antibody


title: MSC_PPARgVeh_rep1

value: vehicle


title: MSC_PPARgVeh_rep2


title: MSC_H4K5AcVeh_rep1


title: MSC_CEBPbVeh_rep2

value: C/EBPβ (Santa Cruz, C-19, sc-150, lot# F3011)


title: MSC_CEBPaVeh_rep1


title: MSC_Runx2Veh_rep2

value: RUNX2 (Santa Cruz, M-70, sc10758, lot# D1411)


title: MSC_Runx2Veh_rep1


title: MSC_H3K4me1125_rep1


title: MSC_VDR125_rep2

value: VDR (Santa Cruz, C-20, sc-1008, lot# A0912)


title: MSC_H3K9AcVeh_rep1


title: MSC_H3K9Ac125_rep1


title: MSC_VDR125_rep1


title: MSC_H4K5AcVeh_rep2


title: MSC_RXR125_rep2

value: RXR (Santa Cruz, ΔN-197, sc-774, lot# G2310)


title: MSC_RXR125_rep1


title: MSC_RXRVeh_rep1


title: MSC_H4K5Ac125_rep1


title: MSC_VDRVeh_rep1


title: MSC_H4K5Ac125_rep2


title: MSC_VDRVeh_rep2


title: Prop1 df/df 26291

city: ann arbor

first: Sally

middle: A

last: Camper

state: MICHIGAN

address: 1241 E catherine st

institute: university of michigan

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10  whole genome using bowtie v2.1.0
Differential expression was assessed using cufflinks version 2.1.1. and the cuffdiff command.  Defaults were used for cuffdiff as well except for the multi-read-correct option which helps accurately weight reads that map to multiple locations.  Data are output as FPKM values as defined by cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2FC of mutant vs control(Wt Prop1 vs Prop1 df/df and Wt Pit1 vs Pit1dw/dw). Also log2FC unique to each mutant.

molecule: total RNA

source_name: pituitary CFUs

growth_protocol: Anterior pituitaries from Prop1+/+, Prop1df/df, Pit1+/+, and Pit1dw/dw mice were collected and dissociated into a single-cell suspension following incubation in enzyme mix (0.5% w/v Collagenase type 2 (Lorne Laboratories), 0.1X Trypsin (Invitrogen), 50 µg/ml DNase I (Worthington) and 2.5 µg/ml Fungizone (Invitrogen) in Hank’s Balanced Salt Solution (HBSS) (Gibco) for 4h at 37°C.  Following washes in HBSS, cells were suspended in stem cell medium UltraCulture (LONZA) containing 5% Fetal Bovine Serum (Gibco), 20 ng/ml bFGF (R&D Systems) and 50 ng/ml cholera toxin (Sigma), counted and plated in six-well plates at a density of 8,000 cells per well.

extract_protocol:
After 10 days in culture, the cells were harvested and RNA was extracted using Rneasy kit from Qiagen
RNA libraries were prepared for sequencing using Encore® Complete RNA-Seq Library Systems (NuGen, 0333 and 0334)

tag: strain

value: non-inbred stock (DF/B)

tag: tissue

value: pituitary

tag: age

value: post natal day 13

tag: genotype

value: Prop1 df/df

value: Pituitary Colony forming cells


title: MSC_RXRVeh_rep2


title: Prop1 df/df 26289


title: Prop1 df/df 26290


title: MSC_H3K9AcVeh_rep2


title: Wt Prop1 +/+ 26288

value: wild type


title: Wt Prop1 +/+ 26287


title: Wt Pit1+/+ 26282

value: (inbred DW/J-Pit1dw x CAST/EiJ) F2


title: Pit dw/dw 26283

value: Pit1 dw/dw


title: Pit dw/dw 26285


title: MSC_CEBPbVeh_rep1


title: Wt Pit1+/+ 26281


title: Wt Pit1+/+ 26280


title: Wt Prop1 +/+ 26286


title: input DNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtiev0.12.7
peaks were called using MACS v2.0.10
Peaks were annotated using HOMERv4.6
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: pituitary cell line

growth_protocol: GHFT1 cells (Dr Pamela Mellon, University of San Diego, La Jolla, CA) were maintained at 37ºC/5% CO2 in Dulbecco's Modified Eagle Medium (Invitrogen, Carlsbad, CA) supplemented with 10% heat inactivated fetal bovine serum (Hyclone, Logan, UT) and 100 units/ml penicillin-streptomycin (Invitrogen). To make stable cell lines, transfected cells were incubated with 1.4 mg/ml G-418 solution (Roche) and 5 µg/ml Puromycin (Sigma) for selection of BirA and Prop1-Tag respectively.

extract_protocol:
Lysates were clarified from sonicated nuclei and biotinylated PROP1-DNA complexes were isolated with streptavidin beads.
Libraries were prepared according to Rubicon ThruPlex kit protocol (CAT. NO. R40012).

tag: cell line

tag: passages

tag: ChIP

value: input DNA


title: Prop1Tag BirA

description: cells were transfected with Prop1Tag and BirA expressing vectors and stable cell line was generated.

value: streptavidin beads


title: Single macrophage #24

city: New York

first: F.

middle: Nina

last: Papavasiliou

state: New York

address: 1230 York Ave.

institute: Rockefeller University

description: processed data file: Macs_CU_list.xlsx

data_processing:
Raw reads for the bulk RNA-seq datasets were pre-processed with TrimGalore! V.0.2.5 using the following command: trim_galore -q 20 -a  GATCGGAAGAGCACACGTCTGAACTCCAGTCAC --stringency 5 --length 20
Reads from bulk RNA-seq were then aligned to UCSC mm10, providing the genes.gtf file and Bowtie index files from Illumina iGenomes, with Tophat2 with the following command: tophat2 -p 8 -G genes.gtf --segment-mismatches 2 --segment-length 20 -g 1 --no-coverage-search --library-type fr-firststrand
Raw reads from the single cell RNA-seq were not trimmed before alignment. Those reads were directly mapped to UCSC mm10 with Tophat2 with the same command used with the bulk, except with the flag set to --library-type fr-unstranded
Resulting alignments for both the bulk and single cell RNA-seq datasets were deduplicated with Picard tools
Custom Python and shell scripts were then deployed to perform the RNA editing analysis on the deduplicated bulk BAM files, by detecting C-to-U transitions in the WT, but not in the Apobec1 -/-, samples. Editing levels for the sites identified from the bulk data were then assessed in the single cell data.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: High confidence lists of editing for macrophages (from bulk, and single cell data) in spreadsheets containing region, gene, coordinate, coverage, and editing rate for each site.

molecule: polyA RNA

source_name: Macrophage

growth_protocol: To obtain bone marrow-derived macrophages, cells were cultured in DMEM, supplemented with FBS, non-essential amino acids, beta-mercaptoethanol, and 20 ng/mL M-CSF (Peprotech, Rocky Hill, NJ) on bacterial plates. One day after initial isolation, the cells were replated at 2 million cells per 10 mL media (per 100mm dish). Half of the media was replaced every 3-4 days. 7-9 days after initial isolation, the cells were checked for matura- tion by FACS (Cd11b+, F4/80), and harvested.

extract_protocol:
Wildtype macrophages were flowed into a C1 IFC for mRNA seq (10-17 μm) chip using the Fluigidm system. Lysis, reverse, transcription and PCR were performed using the SMARTer Kit designed for the C1 (Clontech, Mountain View, CA). The efficiency of chip loading (capture) was confirmed by microscopy and any of the wells that contained either none or more than one cell were noted and discarded from further library preparation and analysis. 24 wildtype single cDNA libraries were selected for library preparation on the basis of concentration and size range, as determined via Agilent Bioanalyzer.
Sequencing libraries were made from the cDNA using the Nextera XT DNA Sample Preparation Kit (Illumina).

value: bone marrow

value: macrophage


title: Single macrophage #23

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #17

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #21

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #20

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #19

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #15

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #18

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #14

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #16

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #13

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #11

description: processed data file: Macs_CU_list.xlsx


title: Pit dw/dw 26284


title: Single macrophage #7

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #9

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #6

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #8

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #10

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #22

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #5

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #3

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #12

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #1

description: processed data file: Macs_CU_list.xlsx


title: Single macrophage #2

description: processed data file: Macs_CU_list.xlsx


title: Bulk WT macrophages

description: processed data file: Macs_CU_list.xlsx

source_name: Macrophages

extract_protocol:
Total RNA was extracted using Trizol
1 μg of the total RNA was treated with DNase, and then processed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA).

value: macrophages


title: Bulk Apo1 KO macrophages

description: processed data file: Macs_CU_list.xlsx

value: Apobec1 -/-


title: STHSC rep 4

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Short-Term Hematopoietic Stem Cell

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and aligned to mm9. Transcript abundances were estimated using RSEM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Short-Term Hematopoietic Stem Cell

extract_protocol:
RNA isolation was performed according to manufacturer protocols (Qiagen) using DNase treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone Marrow

value: 6-12 weeks

value: WT


title: STHSC rep 3

description: Short-Term Hematopoietic Stem Cell


title: STHSC rep 2

description: Short-Term Hematopoietic Stem Cell


title: STHSC Bulk Tumor rep 1

description: Short-Term Hematopoietic Stem Cell Bulk-Derived Tumor Cell


title: STHSC Bulk Tumor rep 2

source_name: Short-Term Hematopoietic Stem Cell Bulk-Derived Tumor Cell


title: STHSC Bulk Tumor rep 3


title: STHSC rep 5

description: Short-Term Hematopoietic Stem Cell


title: MPP Bulk Tumor rep 5

description: Multipotent Progenitor Cell-Derived Bulk Tumor Cell


title: MPP Bulk Tumor rep 2

source_name: Multipotent Progenitor Cell-Derived Bulk Tumor Cell


title: Single macrophage #4

description: processed data file: Macs_CU_list.xlsx


title: MPP rep 6

description: Multipotent Progenitor Cell

source_name: Multipotent Progenitor Cell


title: MPP Bulk Tumor rep 1


title: MPP rep 5

description: Multipotent Progenitor Cell


title: MPP Bulk Tumor rep 3


title: MPP rep 3

description: Multipotent Progenitor Cell


title: MEP rep 4

description: Megakaryocyte-Erythrocyte Progenitor Cell


title: MPP rep 1

description: Multipotent Progenitor Cell


title: MEP rep 2


title: MPP rep 4

description: Multipotent Progenitor Cell


title: LTHSC rep 4

description: Long-Term Hematopoietic Stem Cell

source_name: Long-Term Hematopoietic Stem Cell


title: MEP rep 3


title: LTHSC rep 1

description: Long-Term Hematopoietic Stem Cell


title: LTHSC rep 3

description: Long-Term Hematopoietic Stem Cell


title: LTHSC rep 2

description: Long-Term Hematopoietic Stem Cell


title: MEP rep 1


title: MPP Bulk Tumor rep 6


title: MPP rep 2

description: Multipotent Progenitor Cell


title: STHSC rep 1

description: Short-Term Hematopoietic Stem Cell


title: LTHSC rep 5

description: Long-Term Hematopoietic Stem Cell


title: MPP Bulk Tumor rep 4


title: GMP Bulk Tumor rep 6

description: Granulocyte-Macrophage Progenitor Cell-Derived Bulk Tumor Cell


title: GMP Bulk Tumor rep 3

source_name: Granulocyte-Macrophage Progenitor Cell-Derived Bulk Tumor Cell


title: GMP rep 4

description: Granulocyte-Macrophage Progenitor Cell

source_name: Granulocyte-Macrophage Progenitor Cell


title: GMP Bulk Tumor rep 2


title: GMP Bulk Tumor rep 4


title: GMP rep 5

description: Granulocyte-Macrophage Progenitor Cell


title: CMP Bulk Tumor rep 3

description: Commom Myelooid Progenitor Cell-Derived Bulk Tumor Cell


title: CMP Bulk Tumor rep 4

source_name: Commom Myelooid Progenitor Cell-Derived Bulk Tumor Cell


title: GMP rep 1

description: Granulocyte-Macrophage Progenitor Cell


title: GMP rep 2

description: Granulocyte-Macrophage Progenitor Cell


title: GMP Bulk Tumor rep 1


title: GMP Bulk Tumor rep 5


title: CMP rep 5

description: Commom Myelooid Progenitor Cell

source_name: Commom Myelooid Progenitor Cell


title: GMP rep 3

description: Granulocyte-Macrophage Progenitor Cell


title: CMP Bulk Tumor rep 2


title: STHSC Bulk Tumor rep 1

description: Short Term Hematopoietic Stem Cell-Derived Bulk Tumor Cell

data_processing:
Library strategy: ATAC-seq
Libraries were sequenced on the Illumina HiSeq 2000 platform generating 2x150bp paired end reads at a sequencing depth of ~30-50 million reads per sample.
Reads were aligned to the mouse mm9 assembly using bowtie2. Only reads that uniquely mapped to the genome were used in subsequent analysis. Duplicate reads were eliminated to avoid potential PCR amplification artifacts and to eliminate mtDNA duplicates. Samples with <10 million uniquely aligned reads were considered noisy and were excluded from the analysis.
ATAC-seq peaks in each sample were identified using MACS2 with the following settings: MACS2-2.1.0.20140616/bin/macs2 callpeak -t <input tag file> -f BED -n <output peak file> -g 'mm' --nomodel --shift -100 --extsize 200 -B –broad.
Peak annotation was performed via HOMER v4.6 annotatePeaks.pl for the mm9 assembly.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include HOMER Peak Score values for each Sample

extract_protocol:
Cryopreserved leukemic bone marrow samples were thawed, and 50,000 bulk leukemia (GFP+) cells were sorted by FACSAria (BD). Samples were placed at 37oC and 5% CO2 in IMDM plus 10% fetal calf serum for 30 minutes, then harvested, washed with 1X PBS, and ATAC-seq libraries were prepared as described in Buenrostro et al (Buenrostro et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Nature Methods 10, 1213-1218, doi:10.1038/nmeth.2688)
ATAC-seq libraries were prepared as described in Buenrostro et al (Buenrostro et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Nature Methods 10, 1213-1218, doi:10.1038/nmeth.2688


title: CMP rep 4

description: Commom Myelooid Progenitor Cell


title: CMP rep 1

description: Commom Myelooid Progenitor Cell


title: CMP rep 3

description: Commom Myelooid Progenitor Cell


title: STHSC Bulk Tumor rep 2

source_name: Short Term Hematopoietic Stem Cell-Derived Bulk Tumor Cell


title: CMP rep 2

description: Commom Myelooid Progenitor Cell


title: MPP Bulk Tumor rep 1


title: MPP Bulk Tumor rep 2


title: GMP Bulk Tumor rep 1


title: GMP Bulk Tumor rep 2


title: CMP Bulk Tumor rep 1

description: Common Myeloid Progenitor Cell-Derived Bulk Tumor Cell


title: CMP Bulk Tumor rep 2

source_name: Common Myeloid Progenitor Cell-Derived Bulk Tumor Cell


title: Sample91.WT.In-vivo-wound.RNA-seq.Wounded.Day14 reads FPKM

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 (NCBI 37) genome using default parameter for bowtie (RNA-Star, respectively). Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and other analyses in the study.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), text files (RNA-Seq data).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

source_name: in-vivo wound

growth_protocol: Bone marrow was extracted and differentiated for 5 - 7 days in 30% L929 cells, 20% fetal bovine serum (FBS)/RPMI-1640 containing 100U/ml penicillin/streptomycin in petri dishes supplemented with MCSF 1 after 4 days and replated after this time in 10% fetal bovine serum (FBS)/RPMI-1640 with 100U/ml penicillin/streptomycin supplemented with MCSF

extract_protocol: RNA-Seq: RNA was isolated using TRIzol LS (ThermoFisher Scientific) and resuspended with UltraPure water (ThermoFisher Scientific) supplemented with 1U/μL SUPERase (Ambion) treated with TURBO DNA-free kit (Ambion). Poly(A) selection was performed using the MicroPoly(A)Purist kit (Invitrogen) according to the manufacturer’s instructions. Poly(A) RNA was fragmented using RNA Fragmentation Reagents (Ambion) 10 min at 70°C and purified by running through a Micro Bio-Spin P-30 column (Bio-Rad) according to the manufacturer’s instructions. 30 nanograms RNA was utilized for subsequent library preparation.

treatment_protocol: For ChIP-seq experiments, cells were left untreated or treated by adding 100ng/ml KDO2-lipid A ("KLA"), or 1ng/ml tumor growth factor β  ("TGFγ"), or replacing the seeding media with fresh, warm media ("vehicle") or warm tissue homogenate. For RNA-seq experiments, cell media was replaced with fresh, warm media (no treatment) or that containing 300ng/ml Pam3CSK4 ("Pam3"), 50ng/ml polyinosinic:polycytidylic acid ("PolyIC"), 100ng/ml KDO2-Lipid A ("KLA"), 100ng/ml KDO2-Lipid A plus 10 U/ml recombinant interferon γ ("KLA-IFNγ"), 20ng/ml interleukin 4 ("IL4"), or 1ng/ml tumor growth factor β ("TGFβ") for the indicated treatment times.


title: Sample92.WT.In-vivo-wound.RNA-seq.Wounded.Day14 reads FPKM


title: CMP Bulk Tumor rep 1


title: Sample90.WT.In-vivo-wound.RNA-seq.Wounded.Day8 reads FPKM


title: Sample88.WT.In-vivo-wound.RNA-seq.Wounded.Day4 reads FPKM


title: Sample87.WT.In-vivo-wound.RNA-seq.Wounded.Day4 reads FPKM


title: Sample86.WT.In-vivo-wound.RNA-seq.Wounded.Day4 reads FPKM


title: Sample85.WT.In-vivo-wound.RNA-seq.Wounded.Day4 reads FPKM


title: Sample89.WT.In-vivo-wound.RNA-seq.Wounded.Day8 reads FPKM


title: Sample81.WT.In-vivo-wound.RNA-seq.Unwounded reads FPKM


title: Sample84.WT.In-vivo-wound.RNA-seq.Wounded.Day1 reads FPKM


title: Sample83.WT.In-vivo-wound.RNA-seq.Wounded.Day1 reads FPKM


title: Sample80.WT.In-vivo-wound.RNA-seq.Unwounded reads FPKM


title: Sample82.WT.In-vivo-wound.RNA-seq.Unwounded reads FPKM


title: Sample78.ReverbDKO.BMDM.RNA-seq.TGF.29h reads FPKM

source_name: bone marrow-derived macrophages

value: ReverbDKO

value: TGF 29h


title: Sample77.ReverbDKO.BMDM.RNA-seq.TGF.29h reads FPKM


title: Sample76.ReverbDKO.BMDM.RNA-seq.TGF.29h reads FPKM


title: Sample75.ReverbDKO.BMDM.RNA-seq.TGF.9h reads FPKM

value: TGF 9h


title: Sample70.WT.BMDM.RNA-seq.TGF.29h reads FPKM


title: Sample74.ReverbDKO.BMDM.RNA-seq.TGF.9h reads FPKM


title: B_rapa_MethylC-seq

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: Whole Genome Bisulphite Sequencing of B. rapa (FPsc)

data_processing:
For MethylC-seq data: Reads were trimmed, aligned, and methylation called using the methylpy pipeline (Schultz et al. 2015). The genome is converted into a forward strand reference (all Cs to Ts) and a reverse strand reference (all Gs to As). Cutadapt (Martin et al. 2011) is used to trim adaptor sequences and then bowtie (Langmead et al. 2009) aligns reads to the two converted reference genomes. Only uniquely aligned reads are retained and the non-conversion rate calculated from unmethylated reads aligned to the chloroplast genome or spiked in unmethylated lambda DNA.
For RNA-seq data: Raw FASTQ reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32 (Bolger et al. 2014). Reads were aligned using Tophat v2.0.13 (Trapnell et al. 2010) supplied with a reference GFF file and the following arguments: -I 50000 --b2-very-sensitive --b2-D 50. Transcripts were then quantified using Cufflinks v2.2.1 (Trapnell et al. 2012) supplied with a reference GFF file.
For CHIP-seq data: Raw ChIP reads were trimmed for adapters and low-quality bases using Trimmomatic version 0.32 (Bolger et al. 2014). Reads were trimmed for TruSeq version 3 single-end adapters with maximum of two seed mismatches, palindrome clip threshold of 30 and simple clip threshold of 10. Additionally, leading and trailing bases with quality less than 10 were removed; reads shorter than 50 bp were discarded. Trimmed reads were mapped to the TAIR10 genome using bowtie2 version 2.2.3 (Langmead et al. 2012) with default options. Mapped reads were sorted using samtools verison 1.2 (Li et al. 2009) then clonal duplicates were removed using samtools version 0.1.9 (Li et al. 2009). BAM files were then converted to BED files using bedtools v2.21.1 (Quinlan and Hall 2010).
Genome_build: A. thaliana = TAIR10; A. lyrata = v1.0; B. rapa = FPsc v1.3 (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_BrapaFPsc);  B. oleracea = TO1000 v1.0 (GCF_000695525.1); C. rubella = v1.0 (GCF_000375325.1);  E. salsugineum = v1.0 (GCF_000478725.1)
Supplementary_files_format_and_content: MethylC-seq data (marked as “allc_total.tsv”) column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0
Supplementary_files_format_and_content: RNAseq data column 1 = gene_ID = gene identifier; column 2 = FPKM = gene expression in fragments per kilobase per million (FPKM)
Supplementary_files_format_and_content: BED file of H2A.Z CHIP-Seq data

organism: Brassica rapa

growth_protocol: All plants with the exception of met1/sdg7/sdg8 mutants and their controls were sown onto soil and grown in growth chamber under 18 hr light, 6 hr dark at 23-25C. met1/sdg7/sdg8 mutants and their wild-type controls were sown and germinated on MS media.

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).
RNA-seq: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.
CHIP-seq: Immunoprecipitated DNA was end repaired using the End-It DNA Repair Kit (Epicentre, Madison, WI) according to the manufacturer’s instructions. DNA was purified using Sera-Mag (Thermo Scientific, Waltham, MA) at a 1:1 DNA to beads ratio. The reaction was then incubated for 10 minutes at room temperature, placed on a magnet to immobilize the beads, and the supernatant was removed. The samples were washed two times with 500µL of 80% ethanol, air dried at 37C and then resuspended in 50ul of 10 mM Tris-Cl pH8.0. Finally, the samples were incubated at room temperature for 10 minutes, placed on the magnet, and the supernatant was transferred to a new tube, which contained reagents for “A-tailing.” A-tailing reactions were performed at 37C according to the manufacturers instructions (New England Biolabs, Ipswich, MA). The samples were cleaned using Sera-Mag beads as previously described. Next, adapter ligation was performed using Illumina Truseq Universal Y-adapters and T4 DNA ligase (New England Biolabs, Ipswich, MA) overnight at 16C. A double clean-up using the Sera-Mag beads was performed to remove any adapter-adapter dimers and the elution was used for 15 rounds of PCR. Lastly, samples were cleaned up one final time using the procedures described above.

tag: accession

value: FPsc

value: leaf


title: B_oleracea_MethylC-seq

description: Whole Genome Bisulphite Sequencing of B. oleracea (TO1000)

organism: Brassica oleracea


title: Sample69.WT.BMDM.RNA-seq.TGF.9h reads FPKM


title: E_salsugineum_shandong_MethylC-seq

description: Whole Genome Bisulphite Sequencing of E. salsugineum (Shandong)

organism: Eutrema salsugineum

value: Shandong


title: Sample68.WT.BMDM.RNA-seq.TGF.9h reads FPKM


title: Sample71.WT.BMDM.RNA-seq.TGF.29h reads FPKM


title: Transfection of HeLa cells with NORAD over-expression plasmid

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were aligned to the human genome (hg19 assembly) using STAR Aligner
Read counts for individual genes (defined as overlapping sets of RefSeq transcripts annotated with their Entrez Gene identifier) were counted using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: Counts for individual genes (Entrez Gene, and where not available, RefSeq identifiers)

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: Human cell lines U2OS (osteosarcoma) and HeLa (cervical carcinoma) were routinely cultured in DMEM containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using TRI reagent (MRC)
Strand-specific mRNA-seq libraries were prepared from U2OS cells using the TruSeq Stranded mRNA Library Prep Kit (Illumina). Strand-specific mRNA-seq libraries for HeLa cells were prepared as described in Guo et al. Nature 2010.

treatment_protocol: Plasmid transfections were performed using PolyEthylene Imine (PEI)35 (PEI linear, Mr 25000 from Polyscience Inc). In order to overexpress NORAD, the full transcript of the lincRNA was amplified from human genomic DNA (ATCC NCI-BL2126) using the primers TGCCAGCGCAGAGAACTGCC (Fw) and GGCACTCGGGAGTGTCAGGTTC (Rev), and cloned into a ZeroBlunt TOPO vector (Invitrogen), and then subcloned into the pcDNA3.1(+) vector (Invitrogen). PUM1 and PUM2 were over-expressed using pEF-BOS vectors34 (a kind gift of Prof. Takashi Fujita). As controls in over-expression experiments we used pBluescript II KS+ (Stratagene). Plasmids were used in the amount of 0.1µg per 100,000 cells in 24 well plates for 24 h before cells were harvested. Gene knockdown was achieved using siRNAs directed against NORAD, PUM1, and PUM2 genes (all from Dharmacon, Supplementary Table 1), while as control we used the mammalian non-targeting siRNA (Lincode Non-targeting Pool, Dharmacon), at final concentration of 50nM for 24h or 48h prior to further experimental procedures. The transfections into U2OS cells were conducted using the PolyEthylene Imine.  siRNA transfection into HeLa cells were conducted using 100 nM siRNA and Dharmafect (Dharmacon) transfection reagent and using siRNA buffer only as a control, and transfection of pCDNA3.1-NORAD was into HeLa cells was peformed using Lipofectamine 2000.

value: HeLa

tag: sample treatment

value: NORAD plasmid


title: Transfection of HeLa cells with siRNA buffer

value: siRNA buffer


title: Sample79.WT.In-vivo-wound.RNA-seq.Unwounded reads FPKM


title: siHOXC11 rep4

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

data_processing:
de-multiplex of raw data was performed using customized scripts
short reads were mapped to the reference genome using tophat program version 1.2.0
Not all the raw data passed our initial QC. Only samples s_1_scr2 (scrHOXC11 rep1),  s_2_scr3 (scrHOXC11 rep2), s_1_si3 (siHOXC11 rep1) & s_2_si2 (siHOXC11 rep2) passed and were used for further analysis.
differential expression test was performed using cutfflink/cuffdiff program version 1.0.2
Genome_build: Ensembl GRCh37 release 64 (hg19)
Supplementary_files_format_and_content: differential expression targets from cuffdiff output, including gene ids, locus, FPKM, fold changes, p-values.
The processed file is the output results from CuffDiff. The fields "value_1" and "value_2" correspond to an average FPKM expression of two samples (Value_1 = ave. s_1_scr2 & s_2_scr3; Value_2 = ave. s_1_si3 & s_2_si2).

source_name: LY2 cells

growth_protocol: MCF7-derived LY2 (Bronzert et al., 1985) were maintained in phenol red-free Eagle’s minimum essential medium with 2 mM L-glutamine and supplemented with charcoal dextran stripped fetal bovine serum, 10% (Invitrogen, Paisley, UK).

extract_protocol:
RNA was extracted using an RNeasy (Qiagen, UK) according to manufacturer's instractions.
Libraries were perepared according to standard Illumina protocols.  Four independent biological libraries were prepared for each sample to facilitate the expression detection and variance estimation. Multiplexing was achieved using in-house designed barcoding adapters Four biological replicates of either siHOXC11 or scrHOXC11 sample were sequenced on a flow cell. Two replicates, one from each sample, were multiplexed and loaded on a single lane.

treatment_protocol: LY2 cells were seeded at a density of 2.5x10e5 and incubated overnight under standard conditions. HOXC11 was silenced by transient transfection using an experimentally verified pool of siRNA (Flexitube, Qiagen, UK) (2μg siRNA/6well) .  All transfections were carried out using Lipofectamine 2000 transfection reagent according to manufacturer’s instructions (Invitrogen, UK) and a non-targeting siRNA negative control (Ambion, UK) was used as a control for all siRNA experiments.  Both siRNA and scambled controls were treated with tamoxifen (10-8M) (24 hours) before cells were pelleted and RNA extracted,

tag: origin

value: breast epithelial

tag: sirna

value: MCF7-derived LY2


title: Sample67.WT.BMDM.RNA-seq.TGF.9h reads FPKM


title: siHOXC11 rep3


title: siHOXC11 rep2


title: scrHOXC11 rep3

value: scrambled CONTROL


title: scrHOXC11 rep4


title: scrHOXC11 rep2


title: Sample63.ReverbDKO.BMDM.RNA-seq.tissuehomogenate.6h reads FPKM

value: tissuehomogenate 6h


title: siHOXC11 rep1


title: Sample64.ReverbDKO.BMDM.RNA-seq.tissuehomogenate.24h reads FPKM

value: tissuehomogenate 24h


title: Sample65.ReverbDKO.BMDM.RNA-seq.tissuehomogenate.24h reads FPKM


title: Sample72.WT.BMDM.RNA-seq.TGF.29h reads FPKM


title: Sample73.ReverbDKO.BMDM.RNA-seq.TGF.9h reads FPKM


title: ChIP_3xFLAG WT ZNF335

city: Singapore

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

description: Anti-FLAG ChIP, 3xFLAG WT ZNF335

data_processing:
Base calling performed using RTA; demulitplexed FASTQ files were generated using CASAVA 1.8.2.
Illumina adapter sequences were trimmed from reads using cutadapt 1.4.1. Trimmed reads were aligned to the hg19 genome assembly using bwa.
Reads aligned with a MAPQ score of less than 20 were filtered out using samtools.
Peaks were called using MACS2 (parameters: -g hs --bw=300 –q 0.05).
Aligned sequence reads were filtered with samtools rmdup and used for generating normalized pileup tracks with MACS2 callpeak --SPMR (fragment pileup per million reads), which were then converted to the bigWig format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: normalized signal tracks; narrowPeak: peaks called by MACS2

source_name: Jurkat cells

growth_protocol: Jurkat T-REx cells, cultured in 10% FBS RPMI-1640 media, were electroporated with 3xFLAG-hZfp335-IRES-GFP pcDNA4/TO plasmid and clonal lines of stable transfectants were established by limiting dilution coupled with drug selection (10 mg/ml blasticidin, 200 mg/ml Zeocin). GFP+ clones were identified by flow cytometry analysis and expression of full-length protein verified by Western blotting.

extract_protocol:
Chromatin was fragmented by a combination of sonication and MNase digestion. Chromatin immunoprecipitation was performed using anti-FLAG M2 bound to Protein G Dynabeads. Beads were washed in low salt buffer, high salt buffer, LiCl buffer and TE buffer. Protein/DNA complexes were eluted, reverse-crosslinked overnight at 65°C and treated with RNase A and proteinase K. ChIP DNA was purified using Qiaquick PCR Purification kit (Qiagen).
Approximately 150 ng DNA was used for library construction according to Illumina’s TruSeq protocol. Libraries were size-selected (200–500 bp) by agarose gel purification, assessed for quality using the High Sensitivity DNA Bioanalyzer kit (Agilent). Libraries were sequenced on the Illumina HiSeq 2000 platform as 50 bp single-end reads

treatment_protocol: To induce expression, cells were treated with 1 mg/ml doxycycline overnight.

value: Jurkat T-REx

tag: protein expression

value: 3xFLAG WT ZNF335

tag: chip antibody

value: anti-FLAG M2 mouse monoclonal (Sigma)


title: ChIP_3xFLAG bloto (R1092W) ZNF335

description: Anti-FLAG ChIP, 3xFLAG bloto ZNF335

value: 3xFLAG bloto (R1092W) ZNF335


title: Transfection of HeLa cells with a pool of siRNAs against NORAD

value: siRNA pool against NORAD


title: Input_WT_3xFLAG WT ZNF335

description: input, 3xFLAG WT ZNF335


title: Input_control

description: input, Jurkat control


title: ChIP_control

description: Anti-FLAG ChIP, Jurkat control


title: scrHOXC11 rep1


title: Input_3xFLAG bloto (R1092W) ZNF335

description: input, 3xFLAG bloto ZNF335


title: Sample62.ReverbDKO.BMDM.RNA-seq.tissuehomogenate.6h reads FPKM

value: ReverbDKO


title: Sample60.WT.BMDM.RNA-seq.tissuehomogenate.24h reads FPKM


title: Sample59.WT.BMDM.RNA-seq.tissuehomogenate.24h reads FPKM


title: Sample61.ReverbDKO.BMDM.RNA-seq.tissuehomogenate.6h reads FPKM


title: Strain-rep2

city: Münster

first: Sara

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: Tophat2 alignment

data_processing:
Fastqc (0.11.2) was used for basecalling.
Adapters were removed using Cutadapt (1.5)
Fastq files were mapped to the combined ERCC and H. sapiens genome (GRCh37) using Tophat2 (2.0.13).
Reads were counted from the bam files using the featureCount algorithm from the SubRead software package (1.4.2). Then read counts were normalized to ERCC reference RNAs.
Differential gene expression was analyzed using the DESeq2 (1.8.1). Adjusted p-values ≤ 0.05 have been computed.
Genome_build: GRCh37
Supplementary_files_format_and_content: Read_sum.csv reports counts before and after normalization

source_name: epidermis

growth_protocol: NHEKs were purchased LifeTechnologies and cultured according to manufacturers instruction

extract_protocol:
RNA was isolated with RNEasy Mini Plus Kit (Qiagen) according to manufacturer's instructions. ERCC ExFold RNA Spike-In Mixes (Ambion) were added to all samples according to the manufacturer’s instructions.
Libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Cells were exposed to biaxial cyclic strain at 100 mHz

tag: cell type

value: keratinocyte

value: wt

tag: stress

value: biaxial cyclic strain at 100 mHz


title: Strain-rep3

description: Tophat2 alignment


title: Sample66.ReverbDKO.BMDM.RNA-seq.tissuehomogenate.24h reads FPKM

tag: treatment


title: Strain-rep1

description: Tophat2 alignment


title: ctrl-rep3

description: Tophat2 alignment

value: control


title: RNA-seq si-CBX3 T0 rep1

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

country: Spain

institute: CRG-Centre for Genomic Regulation

description: small interfering (si) knock-down of CBX3 before treatment with R5020 (synthetic analog of the progesterone) (replicate #1)

data_processing:
RNA-seq reads were trimmed using Trimmomatic to remove sequencing adapters with parameters: sequencing type=PE, seedMismatches=2, palindromeClipThreshold=30, simpleClipThreshold=12, minAdapterLength=1, keepBothReads=True, minQual=3, minLength=36 (all other parameters as default)
RNA-seq reads were aligned to hg19 using STAR with parameters: outFilterType "BySJout", outFilterMultimapNmax 20, alignSJoverhangMin 8, alignSJDBoverhangMin 1, outFilterMismatchNmax 999, outFilterMismatchNoverLmax 0.04, alignIntronMin 20, alignIntronMax 1000000, alignMatesGapMax 1000000 (all other parameters as default)
Gene expression was measured as per-gene read counts using featureCounts treating reads as reversely stranded (all other parameters as default)
Genome_build: hg19
Supplementary_files_format_and_content: txt files with gene raw read counts (featureCounts standard output format)

source_name: Breast cancer cells

extract_protocol:
Extraction protocol not provided.
Library construction protocol not provided.

tag: small interfering knock-down

tag: time after r5020

value: 0 hours


title: ctrl-rep2

description: Tophat2 alignment


title: Sample57.WT.BMDM.RNA-seq.tissuehomogenate.6h reads FPKM

tag: strain


title: Sample55.WT.BMDM.RNA-seq.tissuehomogenate.6h reads FPKM


title: ctrl-rep1

description: Tophat2 alignment


title: Sample56.WT.BMDM.RNA-seq.tissuehomogenate.6h reads FPKM


title: Sample58.WT.BMDM.RNA-seq.tissuehomogenate.24h reads FPKM


title: Sample109.Reverb.DKO.BMDM.RNA-seq.PolyIC.6h

description: N\A

extract_protocol:
RNA-Seq: Total RNA was isolated using TRIzol LS (ThermoFisher Scientific) and resuspended
with UltraPure water (ThermoFisher Scientific) supplemented with 1U/μL SUPERase-In
 (Ambion) then treated with TURBO DNA-free kit (Ambion). Poly(A) selection was performed
using the MicroPoly(A)Purist kit (Invitrogen) according to the manufacturer’s instructions.
Poly(A) RNA was fragmented using RNA Fragmentation Reagents (Ambion) for 10 min at 70°C
and purified by running through a Micro Bio-Spin P-30 column (Bio-Rad) according to the
manufacturer’s instructions. 30ng RNA was utilized for subsequent library preparation.
ChIP-Seq:Briefly, for cFos, p65, Nrf2, and Smad3 ChIPs, macrophages were first cross-linked in 2mM dissuccinimidyl glutarate (Pierce 20593) in PBS for 30 minutes, followed by subsequent 1% formaldehyde (Sigma) cross-linking in PBS for 10 minutes at room temperature. For H3K27ac ChIPs, cells were cross-linked using 1% formaldehyde in PBS for 10 minutes at room temperature. After cross-linking, glycine (Sigma) was added to a final concentration of 0.2625 M to quench the reaction. Subsequently, cross-linked macrophages were centrifuged (5 minutes, 1200 rpm, 4°C), washed twice with PBS, and pellets snap frozen and stored at -80°C. For ChIP of H3K27Ac, p65, and Smad3, frozen cell pellets were resuspended in cell lysis buffer (10 mM HEPES/KOH pH 7.9, 85 mM KCl, 1 mM EDTA, 1.0% IGEPAL CA-630 (Sigma), 1x protease inhibitor cocktail (Roche), 1 mM PMSF). After five minutes lysis on ice, cells were centrifuged (5 minutes, 4000 rpm, 4°C), and the supernatant was removed. The pellet was then resuspended in nuclear lysis buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF) and the chromatin was sheared by sonication on wet ice with a Bioruptor Standard Sonicator (Diagenode) for three 15 min cycles each alternating 30 sec on and 30 sec off on the high setting. Additional Triton X-100 was added to the sonicated chromatin to 10% of the final volume and the lysate was cleared by centrifugation (5 minutes, 14000 rpm, 4˚C). Input was then saved for subsequent analysis. For cFos ChIP, pellets were suspended in 50 mM Tris pH 8.0, 60 mM KCl, 0.5% IGEPAL, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF, followed by 10 minutes of incubation on ice and centrifugation at 2,000 x g for 3 minutes at 4°C. The pellet was then suspended in 0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris pH 8.0, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF. The chromatin suspension was sheared by sonication on wet ice with a Bioruptor Standard Sonicator (Diagenode) for three 15 min cycles each alternating 30 sec on and 30 sec off on the high setting, followed by centrifugation for 10 minutes at maximum speed at 4°C. The chromatin was diluted 5x with 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris pH 8.0, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF. An input sample was saved for subsequent analysis.
ChIP-Seq: Antibodies against p65 (sc-372), cFos (sc-7202) and Nrf2 (sc-13032) were purchased from Santa Cruz Biotechnology, against Smad3 (ab28379) from Abcam, and against H3K27ac (39135) from Activ Motif. Protein A or G dynabeads (Invitrogen) pre-bound with antibody was added to the diluted cell lysate overnight at 4˚C. Immunoprecipitated complexes were washed three times with 20 mM Tris/HCl pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, three times with 10 mM Tris/HCl pH 7.4 at 20°C, 250 mM LiCl, 1% Triton X-100, 1% sodium deoxycholate, 1 mM EDTA, and two times with Tris-EDTA plus 0.1% Tween-20 before eluting two times with 50 µL elution buffer (TE, 1% SDS, 30 and 10 minutes, room temperature). Elution buffer was also added to the input. After pooling the eluted samples, the sodium concentration was adjusted to 300 mM and cross-links were reversed overnight at 65°C. Samples were treated with 0.5 mg/ml proteinase K for 1 hour at 55˚C and 0.25 mg/ml RNase A for 1 hour at 37˚C before DNA was isolated using the ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions. For library preparation, NEXTflex DNA barcode adaptors (BioO Scientific) were ligated to the genomic DNA. Polymerase chain reaction mediated library amplification was performed and final libraries were size selected on 10% TBE gels (Invitrogen). Libraries were PCR-amplified for 12-14 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.

value: PolyIC 6h

tag: chip (antibody)


title: Sample108.ReverbDKO.BMDM.RNA-seq.no.treatment.24h

description: N\A

value: no treatment 24h


title: Sample110.Reverb.DKO.BMDM.RNA-seq.PolyIC.6h

description: N\A


title: Sample52.ReverbDKO.BMDM.RNA-seq.KLA+IFNg.24h reads FPKM

value: KLA IFNg 24h


title: Sample53.ReverbDKO.BMDM.RNA-seq.KLA.6h reads FPKM

value: KLA 6h


title: Sample107.ReverbDKO.BMDM.RNA-seq.no.treatment.6h

description: N\A

value: no treatment 6h


title: Sample106.ReverbDKO.BMDM.RNA-seq.Pam3CSK4.6h

description: N\A

value: Pam3CSK4 6h


title: Sample105.ReverbDKO.BMDM.RNA-seq.Pam3CSK4.6h

description: N\A


title: Sample104.ReverbDKO.BMDM.RNA-seq.KLA+IFNg.24h

description: N\A


title: Sample48.ReverbDKO.BMDM.RNA-seq.IL4.24h reads FPKM

value: Il4 24h


title: Sample51.ReverbDKO.BMDM.RNA-seq.KLA+IFNg.24h reads FPKM


title: Sample47.ReverbDKO.BMDM.RNA-seq.untreated reads FPKM

value: no treatment


title: Sample103.ReverbDKO.BMDM.RNA-seq.KLA.6h

description: N\A


title: Sample101.WT.BMDM.RNA-seq.PolyIC.6h

description: N\A


title: Sample100.WT.BMDM.RNA-seq.PolyIC.6h

description: N\A


title: Sample46.ReverbDKO.BMDM.RNA-seq.untreated reads FPKM


title: Sample99.WT.BMDM.RNA-seq.no.treatment.24h

description: N\A


title: Sample45.WT.BMDM.RNA-seq.KLA.6h reads FPKM


title: Sample102.ReverbDKO.BMDM.RNA-seq.Il4.24h

description: N\A


title: Sample97.WT.BMDM.RNA-seq.Pam3CSK4.6h

description: N\A


title: Sample98.WT.BMDM.RNA-seq.no.treatment.6h

description: N\A


title: Sample96.WT.BMDM.RNA-seq.Pam3CSK4.6h

description: N\A


title: Sample54.ReverbDKO.BMDM.RNA-seq.KLA.6h reads FPKM


title: Sample95.WT.BMDM.RNA-seq.KLA+IFNg.24h

description: N\A


title: Sample94.WT.BMDM.RNA-seq.KLA.6h

description: N\A


title: Sample43.WT.BMDM.RNA-seq.KLA+IFNg.24h reads FPKM


title: Sample50.ReverbDKO.BMDM.RNA-seq.PolyIC.6h reads FPKM


title: Sample93.WT.BMDM.RNA-seq.Il.24h

description: N\A


title: Sample114.WT.BMDM.input.nrf2.tissuehomogenate.6h

description: DSG and formaldehyde cross-linked

value: tissuehomogenate 6h


title: Sample42.WT.BMDM.RNA-seq.KLA+IFNg.24h reads FPKM


title: Sample113.WT.BMDM.chip.nrf2.tissuehomogenate.6h

description: DSG and formaldehyde cross-linked

value: Nrf2  (Vendor:Santa Cruz, cat# sc-13032X, lot# I1311)


title: Sample39.WT.BMDM.RNA-seq.IL4.24h reads FPKM


title: Sample111.WT.BMDM.chip.nrf2.vehicle.6h

description: DSG and formaldehyde cross-linked

value: vehicle 6h


title: Sample112.WT.BMDM.input.nrf2.vehicle.6h

description: DSG and formaldehyde cross-linked


title: Sample38.WT.BMDM.RNA-seq.untreated reads FPKM


title: Wild-type Ebola Campothecin

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: RNA sequencing

data_processing:
Following adapter removal with cutadapt and base quality trimming to remove 3’ ends if more than 20 bases with Q<20 were present, reads were mapped to the human (hg19) and Ebola  virus (H.sapiens-tc/COD/1976/Yambuku-Mayinga, NC_002549) reference genomes using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: human monocytic cell line

growth_protocol: Cells were maintained in culture at 37 °C with 5% CO2 in Dulbecco's minimal essential medium (DMEM, Gibco, Life Technologies) supplemented with 2 mM glutamine (Life Technologies), 10% FBS (Hyclone), 100 U/mL penicillin (Life technologies) and 100 μg/mL streptomycin (Gibco, Life Technologies).

extract_protocol: 1 ug of RNA was treated using the Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat, Illumina), and purified post-depletion with 1.6x ratio of AMPureXP beads. Directional RNA libraries were prepared using NEBNext Ultra Directional RNA library prep kit for Illumina (New England BioLabs Inc.), according to manufacturer’s instruction. Fragment size distribution and concentration of the PCR amplified libraries were assessed using the Qubit and the Agilent Bioanalyzer. Finally, samples were sequenced on the HiSeq2500 platform in a 100bp single-end read format.

treatment_protocol: Camptothecin (CPT, Sigma) was dissolved in a 4:1 mixture of chloroform:methanol at the concentration of 0.5 mM, heated at 55 °C until fully dissolved and then added to cells in DMEM medium at the final concentration of 0.5 M. Infections with the Ebola virus were performed in THP-1 cells, a human monocytic cell line that naturally expresses several Pattern Recognition Receptors. We used the wild-type Ebola Zaire-Mayinga strain and its VP-35 mutant, which fails to block the type I Interferon response in the host (52). Cells were recovered 24 hours after Ebola infection.

value: Campothecin


title: Sample37.WT.BMDM.RNA-seq.untreated reads FPKM


title: Wild-type Ebola DMSO

description: RNA sequencing

value: DMSO


title: Sample36.Input for Smad3 ChIP-Seq TGFb 4h

description: DSG and formaldehyde cross-linked

extract_protocol:
ChIP-Seq: Briefly, for cFos, p65, and Smad3 ChIPs, macrophages were first cross-linked in 2mM dissuccinimidyl glutarate (Pierce 20593) in PBS for 30 minutes, followed by subsequent 1% formaldehyde (Sigma) cross-linking in PBS for 10 minutes at room temperature. For H3K27ac ChIPs, cells were cross-linked using 1% formaldehyde in PBS for 10 minutes at room temperature. After cross-linking, glycine (Sigma) was added to a final concentration of 0.2625 M to quench the reaction. Subsequently, cross-linked macrophages were centrifuged (5 minutes, 1200 rpm, 4°C), washed twice with PBS, and pellets snap frozen and stored at -80°C. For ChIP of H3K27Ac, p65, and Smad3, frozen cell pellets were resuspended in cell lysis buffer (10 mM HEPES/KOH pH 7.9, 85 mM KCl, 1 mM EDTA, 1.0% IGEPAL CA-630 (Sigma), 1x protease inhibitor cocktail (Roche), 1 mM PMSF). After five minutes lysis on ice, cells were centrifuged (5 minutes, 4000 rpm, 4°C), and the supernatant was removed. The pellet was then resuspended in nuclear lysis buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF) and the chromatin was sheared by sonication on wet ice with a Bioruptor Standard Sonicator (Diagenode) for three 15 min cycles each alternating 30 sec on and 30 sec off on the high setting. Additional Triton X-100 was added to the sonicated chromatin to 10% of the final volume and the lysate was cleared by centrifugation (5 minutes, 14000 rpm, 4˚C). Input was then saved for subsequent analysis. For cFos ChIP, pellets were suspended in 50 mM Tris pH 8.0, 60 mM KCl, 0.5% IGEPAL, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF, followed by 10 minutes of incubation on ice and centrifugation at 2,000 x g for 3 minutes at 4°C. The pellet was then suspended in 0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris pH 8.0, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF. The chromatin suspension was sheared by sonication on wet ice with a Bioruptor Standard Sonicator (Diagenode) for three 15 min cycles each alternating 30 sec on and 30 sec off on the high setting, followed by centrifugation for 10 minutes at maximum speed at 4°C. The chromatin was diluted 5x with 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris pH 8.0, 1x protease inhibitor cocktail (Roche), and 1 mM PMSF. An input sample was saved for subsequent analysis.
ChIP-Seq: Antibodies against p65 (sc-372) and cFos (sc-7202) were purchased from Santa Cruz Biotechnology, against Smad3 (ab28379) from Abcam, and against H3K27ac (39135) from Activ Motif. Protein A or G dynabeads (Invitrogen) pre-bound with antibody was added to the diluted cell lysate overnight at 4˚C. Immunoprecipitated complexes were washed three times with 20 mM Tris/HCl pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, three times with 10 mM Tris/HCl pH 7.4 at 20°C, 250 mM LiCl, 1% Triton X-100, 1% sodium deoxycholate, 1 mM EDTA, and two times with Tris-EDTA plus 0.1% Tween-20 before eluting two times with 50 µL elution buffer (TE, 1% SDS, 30 and 10 minutes, room temperature). Elution buffer was also added to the input. After pooling the eluted samples, the sodium concentration was adjusted to 300 mM and cross-links were reversed overnight at 65°C. Samples were treated with 0.5 mg/ml proteinase K for 1 hour at 55˚C and 0.25 mg/ml RNase A for 1 hour at 37˚C before DNA was isolated using the ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions. For library preparation, NEXTflex DNA barcode adaptors (BioO Scientific) were ligated to the genomic DNA. Polymerase chain reaction mediated library amplification was performed and final libraries were size selected on 10% TBE gels (Invitrogen). Libraries were PCR-amplified for 12-14 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.

value: TGFb 4h


title: Delta 4

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: pancreatic delta cells rep 4

data_processing:
Reads were aligned to the GRCm38/Ensembl V54 transcriptome using Tophat v2.0.8 with default parameter
Raw and normalised counts using CuffLinks v2.2.1 with --max-bundle-frags 50000000
Differential gene expression was determined by EdgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: fastq files for raw data and FPKM values in tab-delimted txt format

source_name: Pancreatic Islets

extract_protocol:
RNA was extracted from FACS isolated cells using Qiagen RNasy Plus micro kit according to manufacturer's manual
RNA was subjected to whole-transcriptome amplification using NuGEN RNAseq v2 System followed by fragmentation to 200bp with a Diagenode Bioruptor Pico sonicator, The resulting fragments were then used to make bar-coded libraries using NuGEN Ovation Rapid DR Multiplex System

treatment_protocol: Pancreatic alpha, beta and delta cells were isolated using a BD Influx cell sorter iinstrument based on fluorescence of Venus and EFYP

tag: genotype

tag: cell-type

value: Pancreatic delta cells


title: Delta 2

description: pancreatic delta cells rep 2


title: Delta 1

description: pancreatic delta cells rep 1


title: Delta 5

description: pancreatic delta cells rep 5


title: Delta 3

description: pancreatic delta cells rep 3


title: Sample35.Smad3 ChIP-Seq TGFb 4h

description: DSG and formaldehyde cross-linked

value: Smad3 (Vendor:Abcam, cat# ab28379)


title: Sample44.WT.BMDM.RNA-seq.KLA.6h reads FPKM


title: Beta 4

description: pancreatic beta cells rep 4

value: Glu-Venus

value: Pancreatic beta cells


title: Delta 6

description: pancreatic delta cells rep 6


title: Mutated Ebola Campothecin

description: RNA sequencing


title: Beta 3

description: pancreatic beta cells rep 3


title: Sample34.Input for Smad3 ChIP-Seq no treatment

description: DSG and formaldehyde cross-linked


title: Sample33.Smad3 ChIP-Seq no treatment

description: DSG and formaldehyde cross-linked


title: Beta 2

description: pancreatic beta cells rep 2


title: Mock DMSO

description: RNA sequencing


title: Mock Campothecin

description: RNA sequencing


title: Beta 1

description: pancreatic beta cells rep 1


title: Sample41.WT.BMDM.RNA-seq.PolyIC.6h reads FPKM

value: PolyIC 6h


title: Alpha 5

description: pancreatic alpha cells rep 5

value: Pancreatic alpha cells


title: Sample32.Input for p65 ChIP-Seq no treatment

description: DSG and formaldehyde cross-linked


title: RNAPII uninfected campothecin

description: ChIP-sequencing

data_processing:
ChIP-Seq reads were trimmed for adapter sequences using 'cutadapt'. Reads were then filtered using 'sickle' with a minimum quality threshold of 20 and retaining only sequences containing at least 20 bases. QC-filtered reads were then aligned against the human reference genome (GRCh37) using STAR, selecting only non-ambiguous alignments and allowing up to 5 mismatches for each alignment. The resulting BAM files were processed using the R package "Pasha" with default parameters in order to exclude artefactual enrichments, estimate fragments elongation, and prepare genome-wide read coverage tracks in variable-step WIG format. WIG scores were finally rescaled for each sample by dividing all values by the average genome wide enrichment value.
Genome_build: GRCh37
Supplementary_files_format_and_content: Wig variable step

source_name: adenocarcinomic human alveolar basal epithelial cells

extract_protocol: Crosslinking was performed for 10 minutes. For sonication, we used a refrigerated Bioruptor (Diagenode), which we optimized to generate DNA fragments of approximately 200– 1,000 base pair (bp). Lysates were pre-cleared for 3 hours using the appropriate isotype-matched control antibody (rabbit IgG; Cell Signaling) or anti-mouse IgG (Cell Signaling). The anti-RNA polymerase II (RNAPII) (clone 8WG16; Covance/BioLegend) antibodies were coupled with magnetic paramagnetic beads (Dynabeads® M-280 Sheep anti- 21 Mouse IgG; ThermoFisher Scientific) bound to anti–mouse IgG or anti–rabbit IgG for 6 hours. Antibody-bound beads and chromatin were then immune-precipitated overnight at 4 °C with rotation. After washing, reverse crosslinking was carried out overnight at 65°C. After digestion with RNase and proteinase K (Roche), DNA was isolated with a MinElute kit (Qiagen) and used for downstream applications.

treatment_protocol: Camptothecin (CPT, Sigma) was dissolved in a 4:1 mixture of chloroform:methanol at the concentration of 0.5 mM, heated at 55 °C until fully dissolved and then added to cells in DMEM medium at the final concentration of 0.5 microM.

tag: viral strain

value: campothecin

tag: timepoint

value: uninfected


title: RNAPII uninfected DMSO

description: ChIP-sequencing


title: Sample30.Input for p65 ChIP-Seq TGFb 6h

description: DSG and formaldehyde cross-linked

value: TGFb 6h


title: Alpha 4

description: pancreatic alpha cells rep 4


title: Sample28.Input for p65 ChIP-Seq KLA 6h

description: DSG and formaldehyde cross-linked

value: KLA 6h


title: Mutated Ebola DMSO

description: RNA sequencing


title: Sample29.p65 ChIP-Seq TGFb 6h

description: DSG and formaldehyde cross-linked

value: NFkB p65 (Vendor:Santa Cruz, cat# sc-372X, lot# A0314)


title: Alpha 2

description: pancreatic alpha cells rep 2


title: Alpha 3

description: pancreatic alpha cells rep 3


title: Sample26.Smad3 ChIP-Seq tissue homogenate 6h

description: DSG and formaldehyde cross-linked

value: tissuehomogenate 6h

value: Smad3 (Vendor:Abcam, cat# ab28379, lot# GR188908-1)


title: Sample27.p65 ChIP-Seq KLA 6h

description: DSG and formaldehyde cross-linked


title: FLAG ctrl

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

data_processing:
ChIP-seq reads aligned to mm10 using bowtie2 (version 2.0.6) with extra parameters (-k 2 -N 1).
bigWig density profiles were created with in-house script incorporating UCSC's wigToBigWig utility.
Peaks were called using macs2 (version 2.0.10).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig – read density profile, BED – peaks file

source_name: KSL

growth_protocol: Lin-Sca-1+c-Kit+ cells were maintained for 5 days in basal OP9 medium supplemented with 50 ng/ml SCF, 10 ng/ml IL-7, 10 ng/ml Flt3L and 5 ng/ml IL-3.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Lin-Sca-1+c-Kit+ cells were infected on retronectin coated plates with either a MigR1 control or a MigR1-3xFLAG-Hlf/Hlf virus

tag: animal age

value: 8-10 weeks

tag: tissue

value: blood

tag: cell markers

tag: transgene

value: MigR1 empty vector

value: anti-FLAG (Sigma F3165)


title: Sample25.Smad3 ChIP-Seq vehicle 6h

description: DSG and formaldehyde cross-linked

value: vehicle 6h


title: Sample24.Input for p65, Smad3, and Fos ChIP-Seq tissue homogenate 6h

description: DSG and formaldehyde cross-linked


title: RNAPII 06hpi DMSO

description: ChIP-sequencing

value: A/PR/8/34 deltaNS1

value: DMSO

value: 06 hours post-infection


title: RNAPII 06hpi campothecin

description: ChIP-sequencing


title: ChIPseq_input_siCTR_siMYC

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
ChIPseq:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned o the human genome usingBowtie v0.12.8. with default settings. For siRNA-treated samples, reads were trimmed 5bp from the 3' end.
Samples were normalized to the same number of aligned reads.
Bam files were generated using Samtools v0.1.18.
For the generation of wiggle files MACS v1.4.2 was used with a fixed step of 10bp and the "keep-dup" parameter was set to 3.
Genome_build: hg19
Supplementary_files_format_and_content: fixedStep wiggle files

source_name: U2OS cells

growth_protocol: U2OS cells were grown in DMEM (Sigma) suppelmented with 10% FCS (Biochrom) and penicillin/streptomycin (Sigma).

extract_protocol: For ChIP-seq in MYC-induced U2OS cells, libraries from GEO record GSE44672 were used and sequenced deeper. For ChIP-seq in MYC-depleted U2OS cells, cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using phenol-chloroform extraction and ethanol precipitation.  Libraries were constructed following manufacturer's instructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay.

tag: antibody

tag: sirna treatment

value: siCTR and siMYC

tag: doxycycline [ng/µl]


title: FLAG-HLF

value: MigR1 3xFLAG-HLF/HLF

tag: chip antibody


title: Sample31.p65 ChIP-Seq no treatment

description: DSG and formaldehyde cross-linked

tag: treatment

value: no treatment


title: Sample23.p65 ChIP-Seq tissue homogenate 6h

description: DSG and formaldehyde cross-linked


title: ELAVL2_GFP1

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Single-end unstranded reads were aligned in a staged manner. Reads were aligned with segemehl using default options to a reference sequence comprised of mitochondrial DNA (h19/GRCh37 from Ensembl).
RNA-seq Counts values were quantified using R and confirmed by Htseq-Count, providing transcript database and gtf file related to GRCh37 from Ensembl.
RNA-seq RPKM values were then quantified using R.
Gene counts were used for differentially expression. Gene-level RPKMs quantifications were used for the remaining downstream processing.
Genome_build: Human h19/GRCh37 from Ensembl
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

source_name: Neural progenitor cells_ELAVL2_GFP

growth_protocol: Differentiated human neural progenitors were used

extract_protocol:
All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent). Samples were randomized for RNA extractions and sequencing. 1ug of total RNA were treated with Ribo-zero Removal Kit according to the manufacturer’s instructions to remove ribosomal RNA.
Libraries were prepared using an Illumina TruSeq kit according to the manufacturer’s instructions.

treatment_protocol: RNA was extracted after three days post-transduction using Qiagen’s miRNeasy Kit according to the manufacturer’s instructions.

tag: tissue source

value: mid-gestation fetal brain

tag: cell type

value: primary human neural progenitor cells

tag: transfected with

value: control shRNA

tag: genotype/variation

value: GFP control

tag: time point

value: differentiated into neurons for 4 weeks and then harvested


title: ChIPseq_MYC_siMYC

value: c-MYC N262 (Santa Cruz, sc764)

value: siMYC


title: ELAVL2_5

source_name: Neural progenitor cells_ELAVL2

value: shRNA targeting ELAVL2

value: ELAVL2 knockdown


title: ELAVL2_GFP2


title: ELAVL2_GFP4


title: ELAVL2_GFP3


title: ELAVL2_GFP5


title: Sample21.p65 ChIP-Seq vehicle 6h

description: DSG and formaldehyde cross-linked

tag: strain

tag: chip (antibody)

value: NFkB p65 (Vendor:Santa Cruz, cat# sc-372X, lot# A0314)


title: Alpha 1

description: pancreatic alpha cells rep 1

tag: genotype

value: Glu-Venus

tag: cell-type

value: Pancreatic alpha cells


title: ELAVL2_4


title: Sample20.Input for Fos ChIP-Seq KLA 6h

description: DSG and formaldehyde cross-linked

value: KLA 6h


title: Sample19.Fos ChIP-Seq KLA 6h

description: DSG and formaldehyde cross-linked

value: cFos (Vendor:Santa Cruz, cat# Sc-7202, lot# )


title: ChIPseq_MYC_siCTR

value: siCTR


title: ELAVL2_2


title: ELAVL2_3


title: Ribo-seq following transfection of siRNA 1 against NORAD

description: Ribo-seq

tag: cell line

tag: sample treatment

value: siRNA1 against NORAD


title: ELAVL2_1


title: Ribo-seq following transfection of siRNA 2 against NORAD

description: Ribo-seq

value: siRNA2 against NORAD


title: NORAD OE, 24h post-transfection, replicate 1

value: NORAD plasmid


title: Sample17.Fos ChIP-Seq no treatment

description: DSG and formaldehyde cross-linked

value: no treatment


title: NORAD OE, 24h post-transfection, replicate 2


title: Sample18.Input for Fos ChIP-Seq no treatment

description: DSG and formaldehyde cross-linked


title: Sample16.Input for Fos ChIP-Seq tissue homogenate 6h

description: DSG and formaldehyde cross-linked

value: tissuehomogenate 6h


title: met1_sdg78_RNAseq_5

description: RNA-seq for A. thaliana met1sdg7/sdg8 replicate 5

organism: Arabidopsis thaliana

tag: accession

tag: tissue

value: aerial


title: Sample14.Input for Fos ChIP-Seq vehicle 6h

description: DSG and formaldehyde cross-linked

value: vehicle 6h


title: NORAD siRNA 1 transfection, 48h post-transfection


title: Control transfection for siRNA2, 48h post-transfection

value: Control siRNA


title: Sample12.Input for PU.1 ChIP-Seq tissue homogenate 6h

description: formaldehyde cross-linked


title: met1_sdg78_RNAseq_2

description: RNA-seq for A. thaliana met1sdg7/sdg8 replicate 2


title: met1_sdg78_RNAseq_1

description: RNA-seq for A. thaliana met1sdg7/sdg8 replicate 1


title: Ribo-seq following transfection of a control siRNA, 48h post-transfection

description: Ribo-seq


title: Sample11.PU.1 ChIP-Seq tissue homogenate 6h

description: formaldehyde cross-linked

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# F1214)


title: met1_sdg78_RNAseq_3

description: RNA-seq for A. thaliana met1sdg7/sdg8 replicate 3


title: Control transfection for siRNA1, 48h post-transfection


title: WT_RNAseq_3

description: RNA-seq for A. thaliana Col-0 WT replicate 3 (for comparison to met1/sdg7/sdg8 mutants)


title: Sample9.PU.1 ChIP-Seq vehicle 6h

description: formaldehyde cross-linked


title: WT_RNAseq_2

description: RNA-seq for A. thaliana Col-0 WT replicate 2 (for comparison to met1/sdg7/sdg8 mutants)


title: Control plasmid over-expression, 24 hr post-transfection

value: Control plasmid


title: NORAD KD using a pool of siRNAs, 24h post-transfection, replicate 2

value: siRNA pool against NORAD


title: Sample15.Fos ChIP-Seq tissue homogenate 6h

description: DSG and formaldehyde cross-linked


title: Sample10.Input for PU.1 ChIP-Seq vehicle 6h

description: formaldehyde cross-linked


title: WT_RNAseq_1

description: RNA-seq for A. thaliana Col-0 WT replicate 1 (for comparison to met1/sdg7/sdg8 mutants)


title: Sample7.H3K27Ac ChIP-Seq wouldhomogenate 3h

description: formaldehyde cross-linked

value: tissuehomogenate 3h

value: H3K27Ac (Vendor:Activ Motif, cat# 39135, lot#17513002)


title: Sample6.Input for H3K27Ac ChIP-Seq vehicle 3h

description: formaldehyde cross-linked

value: vehicle 3h


title: met1_sdg78_RNAseq_4

description: RNA-seq for A. thaliana met1sdg7/sdg8 replicate 4


title: Over-expression of PUM2, replicate 2

value: PUM2 plasmid


title: Over-expression of PUM2, replicate 1


title: NORAD siRNA 2 transfection, 48h post-transfection


title: Over-expression of PUM1, replicate 2

value: PUM1 plasmid


title: Sample13.Fos ChIP-Seq vehicle 6h

description: DSG and formaldehyde cross-linked

value: cFos (Vendor:Santa Cruz, cat# Sc-7202, lot# )


title: Over-expression of PUM1, replicate 1


title: NORAD KD using a pool of siRNAs, 24h post-transfection, replicate 1


title: Sample4.Input for H3K27Ac ChIP-Seq tissue homogenate 6h

description: formaldehyde cross-linked


title: Control siRNA transfection, 24 h post-transfection


title: siRNA-mediated knockdown of PUM2, replicate 2

value: siRNA pool against PUM2


title: siRNA-mediated knockdown of PUM2, replicate 1


title: HKBd_BioRep2

city: Vermillion

first: Joseph

last: Madison

state: SD

address: 414 East Clark St

department: Biology

institute: University of South Dakota

data_processing:
Illumina CASAVA v1.8.2 softwre was used for base-calling
Alignment was done by uploading raw data to the Rockhopper platform for analysis of bacterial RNA-seq data. Alignment utilized a Burrows-wheeler index of the Serratia marcescens WW4 reference genome. All parameters for this step utilized the default settings in Rockhopper.
Normalization of transcript abundance between samples was also done within Rockhopper using upper-quartile normalization after exclusion of genes showing zero expression. All parameters for this step utilized the default settings in Rockhopper.
Genome_build: Serratia marcescens strain WW4 reference genome; NC_020211.1
Supplementary_files_format_and_content: All processed data files are in tab-delimited format. All operon.txt files include predicted operon structure and relative abundance. All trascripts.txt files include relative transcript abundance normalized using upper-quartile based normalization. All summary_xxx.txt files include a summary of alignment results.

organism: Serratia marcescens

source_name: whole cell

growth_protocol: Serratia marcescens was grown in tryptone hyrolyzed gelatin lactose broth at 20C with the three different experimental treatments (control, Bd, heat-killed Bd).

extract_protocol:
RNA was extracted in bacterial exponential growth phase. RNA extraction was done by initially stabilizing bacterial RNA with the RNAprotect bacteria reagent (Qiagen). Enzymatic lysis was subsequently used using an EDTA(buffered in Tris)/lysozyme solution. RNA purification was then carried out using an RNAeasy kit (Qiagen) following standard protocols. Subsequent rRNA reduction of total-RNA for both bacteria and fungi (contaminating bacterial sample) was accomplished using a modified protocol for a Ribo-Zero rRNA Removal Kit (Illumina). The modified protocol included probes from both the yeast and bacterial rRNA Removal Kits which were combined in a 1:1 ratio to the recommended concentration for a one probe kit. Clean-up of the rRNA reduced RNA was done using a Zymogen RNA-Clean and Concentrator kit following a standard protocol.
Library preparation for sequencing utilized the Illumina ScriptSeq RNA-Seq Library Kit. Indices were added for a six sample multiplex on a one lane flowcell. The indices used were as follows: Bd3-TGACCA, Bd13_2-TAGCTT, C2- ATCACG, C13_1-ACAGTG, HKBd1-ACTTGA, HKBd13_2-GGCTAC.

treatment_protocol: The three treatments used in this study were inoculation of the bacterial culture with live Batrachochytrium dendrobatidis zoospores, heat-killed Batrachochytrium dendrobatidis zoospores, and a control treamtent that had no zoospores.

tag: organism host

value: Agalychnis annae


title: siRNA-mediated knockdown of PUM1, replicate 2

value: siRNA pool against PUM1


title: siRNA-mediated knockdown of PUM1, replicate 1


title: Bd_BioRep1

value: Batrachochytrium dendrobatidis


title: Bd_BioRep2


title: Sample8.Input for H3K27Ac ChIP-Seq tissue homogenate 3h

description: formaldehyde cross-linked


title: HKBd_BioRep1


title: Control_BioRep2

value: control


title: Sample5.H3K27Ac ChIP-Seq vehicle 3h

description: formaldehyde cross-linked


title: siMTS_ATAC_Seq

status: Public on Jul 10 2016

city: Frankfurt

first: Matthias

middle: S

last: Leisegang

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe-University

data_processing:
library strategy: ATAC-seq
Read quality trimming with Trimmomatic 0.33 (LEADING:3 TRAILING:3 SLIDINGWINDOW:5:20 CROP:500 MINLEN:30)
Random subsampling of reads to 27 million per sample
Mapping of reads versus human genome version hg19 using STAR 2.4.2a (--outFilterMismatchNoverLmax 0.1 --alignIntronMin 2 --alignIntronMax 1 --alignEndsType EndToEnd --outFilterMultimapNmax 1)
Deduplication of reads using Picard 1.136
Peak calling using MUSIC version Dec. 2015 (punctate mode, qvalue < 0.2)
Removal of peaks overlapping ENCODE blacklisted regions
Merging of peaks of all samples to a unified set
Recount of reads per union peaks per sample
Normalization of union peak counts using DESeq
Annotation of peaks based on GENCODE v19 (most closely located TSS +-5000 nt of the peak center)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of DESeq normalized unified peaks

source_name: HUVEC

growth_protocol: HUVECs were cultivated in a humidified atmosphere of 5% CO2 at 37°C on Fibronectin-coated dishes. Endothelial growth medium (EGM), consisting of endothelial basal medium and human recombinant epidermal growth factor, EndoCGS-Heparin, 8% fetal calf serum, penicillin (50 U/ml) and streptomycin (50 µg/ml) was used.

extract_protocol:
Transposition of native chromatin for multimodal regulatory analysis and personal epigenomics; Nat Methods. 2013 December ; 10(12): 1213–1218. doi:10.1038/nmeth.2688.
Transposition of native chromatin for multimodal regulatory analysis and personal epigenomics; Nat Methods. 2013 December ; 10(12): 1213–1218. doi:10.1038/nmeth.2688.

treatment_protocol: HUVECs (80–90% confluent) were transfected with GeneTrans II according to the instructions provided by MoBiTec (Göttingen, Germany) with scrambled or MANTIS siRNA for 48 hours.

value: human umbilical vein endothelial cells (HUVEC)

tag: knockdown

value: MANTIS siRNA


title: Control_BioRep1


title: siSCR_ATAC_Seq

value: scrambled siRNA


title: Control_3

city: Beijing

first: Bao

last: Yi

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Basecalls performed using CASAVA version 1.7
The adaptor sequences were removed and data were Q20, Q30 filtered
Fragments Per Kilobase of transcript per Million mapped fragments (FPKM) was calculated using bowtie2
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: Breast muscle

extract_protocol:
Total RNA of breast muscle was isolated with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. mRNA was extracted from total RNA using oligo (dT) magnetic beads (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Arbor Acres

tag: Sex

value: male

tag: age

value: 42-day old

value: breast muscle

tag: ammonia exposure

value: 3 ± 3 ppm


title: Control_2


title: Control plasmid transfection for the PUM1/2 OE 2

value: Control siRNA


title: Control plasmid transfection for the PUM1/2 OE 1


title: MK5D_Runx1

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with -m 1 and default parameters
Uniquely aligned reads were filtered using SICER v1.1 to keep 1 copies at each genomic location
Wiggle files were generated using MACS v1.4
Wiggle files were normalized to the same scale
Genome_build: mm9

source_name: Mature Megakaryocytes

extract_protocol:
Individual lineages were isolated by depleting other lineages using TER119, GR1, CD41, and CD11b (B-D Pharmingen) monoclonal antibodies (mAb) and immunomagnetic Dynabeads (Invitrogen) or by positive selection using GR1 or TER119 mAb for flow cytometry. MK isolations included additional passage over triple (4%, 3%, 1.5%) gradients of bovine serum albumin, with collection of the pellet. Cell isolations were monitored by viewing May-Grünwald-Giemsa stains of cytocentrifuged preparations with an Olympus BX41 microscope and by flow cytometry using the above-listed mAb. Transcription factors were pulled down with the respective antibodies after crosslinking + sonication of the cells.
At least 20 ng of precipitated or input DNA from pools of at least 3 replicates was processed for deep sequencing using different library preparation kits for cells (TruSeq, Illumina) and progenitors (TruPLEX-FD, Rubicon Genetics), following the manufacturers’ instructions. ChIP-seq libraries were sequenced using Illumina HiSeq2000 and tags were mapped to mouse genome build mm9.

value: liver

tag: cell type

value: Mature Megakaryocytes

tag: genome/variation

value: wild-type

tag: antibody

value: Runx1, antibody vendor, cat#, lot #:Abcam, ab23980, gr25538-1


title: MK5D_Fli1

value: Fli-1, antibody vendor, cat#, lot #:Abcam, ab15289, gr1478-2


title: Control_1


title: Sample2.Input for H3K27Ac ChIP-Seq vehicle 6h

description: formaldehyde cross-linked

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 (NCBI 37) genome using default parameter for bowtie (RNA-Star, respectively). Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and other analyses in the study.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), text files (RNA-Seq data).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

source_name: bone marrow-derived macrophages

tag: treatment

value: vehicle 6h


title: Sample1.H3K27Ac ChIP-Seq vehicle 6h

description: formaldehyde cross-linked

tag: strain

value: H3K27Ac (Vendor:Activ Motif, cat# 39135, lot#17513002)


title: Treatment_1

value: 75 ± 3 ppm


title: Treatment_2


title: AdLacZ_Input

city: Suita

first: Shuichiro

last: Higo

address: 2-2, Yamadaoka

department: Dpt. of Cardiovascular Medicine

country: Japan

institute: Osaka University

data_processing:
Unfiltered sequence reads were aligned to the rat reference genome (rn4) using Bowtie (ChIP-seq).
The peak calling of Myc and pol II and the generation of WIG formatted files were performed using MACS (Model-based Analysis for ChIP-Seq).
Genome_build: rn4
Supplementary_files_format_and_content: wig

organism: Rattus norvegicus

source_name: AdLacZ, Input

growth_protocol: Neonatal rat hearts were incubated in 0.25% trypsin/EDTA (Sigma) at 4 °C overnight and then digested with collagenase type II (Worthington). The cardiomyocyte fraction was collected after differential plating for 70 min at 37 °C, seeded and incubated with DMEM (Dulbecco’s Modified Eagle Medium, Gibco) containing 10% fetal bovine serum (FBS, Gibco) and penicillin, streptomycin and glutamine (Gibco).

extract_protocol:
Twenty-four h after transduction, chromatin fractions were extracted and immunoprecipitated with the specific antibodies.
Libraries were prepared according to the manufacture's instructions (Life Technologies and Illumina).

treatment_protocol: Primary cultured rat neonatal cardiomyocytes were transduced with adenovirus encoding Myc or LacZ.

value: Wistar

value: neonatal cardiomyocyte

tag: transduction

value: adenovirus encoding LacZ control

tag: chip antibody


title: Treatment_3

value: Arbor Acres


title: AdLacZ_ChIPMyc_2

source_name: AdLacZ, ChIP Myc


title: AdMyc_ChIPpolII_2

source_name: AdMyc, ChIP polII

value: adenovirus encoding Myc

value: RNA polymerase II (clone 8WG16) (Millipore, catalog# 05-952, lot# 2073109)


title: AdLacZ_ChIPpolII_2

source_name: AdLacZ, ChIP polII


title: AdMyc_Input

source_name: AdMyc, Input


title: MK5D input


title: Sample3.H3K27Ac ChIP-Seq tissue homogenate 6h

first: Christopher

last: Glass

description: formaldehyde cross-linked

value: tissuehomogenate 6h

tag: chip (antibody)


title: AdMyc_ChIPMyc_2

source_name: AdMyc, ChIP Myc


title: AdLacZ_ChIPMyc_1


title: AdLacZ_ChIPpolII_1


title: AdMyc_ChIPpolII_1


title: Sample22.Input for p65, Smad3, and Fos ChIP-Seq vehicle 6h

description: DSG and formaldehyde cross-linked


title: iPSC_CONTROL_COVE_3_7

city: Los Angeles

first: Daniel

middle: H.

last: Geschwind

state: California

address: 2309 Gonda Bldg, 695 Charles E. Young Dr. South

department: Neurology

institute: UCLA

data_processing:
Basecalls and demultiplexing: CASAVA version 1.8.2 using default settings
Alignment: TopHat v2.0.5 with default settings except: 1) allowing up to 10 alignments for a given read; 2) expected inner distance between paired reads: 100; 3) alignment is supplied with Homo sapiens GRCh37 gene model annotations
Expression levels: read counts were summarized to Genecode11 gene models using htseq-count version 0.5.4 with intersection-nonempty model option
Genome_build: Human reference genome from the 1000 Genomes Project (human_g1k_v37)
Supplementary_files_format_and_content: tab-delimited text file includes read counts for all the samples

source_name: iPSCs

growth_protocol: The iPSCs were growing in Matrigel (BD Biosciences)-coated plates, and maintained in mTeSR media (Stem Cell Technologies).

extract_protocol:
Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA).
1000 ng of total RNAs were used for library preparation using Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: Differentiation protocol: The iPSC colonies were plated on Matrigel (BD Biosciences)-coated plates and maintained for 5 days in mTSeR media (Stem Cell Technologies). On the fifth day, the media was changed to N2 media [DMEM/F12 media supplemented with 1X N2 supplement (Invitrogen) and 1X B27 supplement (Invitrogen). After 2 days, the colonies were removed from the plate and cultured in suspension as embryoid bodies (EBs) for 2 weeks using NPC media with dorsomorphin during the entire procedure. The EBs were then gently dissociated with accutase (Gibco), plated on Matrigel-coated dishes, and maintained in NBF media (DMEM/F12 media supplemented with 1X N2, 1X B7 supplements, 20 ng/mL FGF2 and 1% penicillin/streptomycin). The rosettes that emerged after 3 or 4 days were manually selected, gently dissociated with accutase, and plated in dishes coated with 10 μg/mL poly-ornithine and 5 μg/mL laminin. This NPC population was expanded using NBF media. To differentiate the NPCs into neurons, the cells were re-plated in the absence of FGF2, with regular media changes every 3 or 4 days.

value: iPSCs

tag: patient id

value: COVE

tag: group

value: CONTROL

tag: iPSc clone

tag: age at biopsy

tag: gender

value: Male

tag: total brain volume

tag: scan age, years

tag: ados total score at biopsy


title: iPSC_CONTROL_COVE_3_1


title: iPSC_CONTROL_COVE_3_6


title: iPSC_CONTROL_CLUE_4_7

value: CLUE


title: iPSC_CONTROL_CLAY_1_2

value: CLAY


title: iPSC_CONTROL_CLUE_4_12


title: iPSC_CONTROL_CHAP_1_5

value: CHAP


title: iPSC_CONTROL_CENT_3_6

value: CENT


title: iPSC_CONTROL_CHAP_1_2


title: iPSC_CONTROL_CENT_3_3


title: iPSC_CONTROL_CAPE_1_8

value: CAPE


title: iPSC_ASD_ARCH_1_2

value: ARCH

value: ASD

value: 18 (Pre-verbal/Single Words)


title: iPSC_ASD_AVID_5_20

value: AVID

value: 16 (Fluent Speech - Child/Adolescent)


title: iPSC_ASD_ACAI_3_2

value: ACAI

value: 13 (Fluent Speech - Child/Adolescent)


title: iPSC_ASD_AHOY_5_4

value: AHOY

value: 20 (Fluent Speech - Adolescent/Adult)


title: iPSC_ASD_AHOY_5_13

value: iPSCs


title: iPSC_ASD_AHOY_5_19


title: iPSC_ASD_AVID_5_5


title: AdMyc_ChIPMyc_1

value: Wistar

value: neonatal cardiomyocyte

value: adenovirus encoding Myc


title: NPC_CONTROL_COVE_3_1

source_name: iPSC-derived neural progenitors

value: iPSC-derived neural progenitors

value: COVE

value: CONTROL

value: Male


title: iPSC_ASD_ABLE_3_12

value: ABLE

value: 16 (Pre-verbal/Single Words)


title: iPSC_ASD_ABLE_3_6

value: ASD


title: iPSC_ASD_AQUA_3_9

value: AQUA

value: 13 (Fluent Speech -Chld/Adolescent)


title: iPSC_ASD_APEX_5_15

value: APEX

value: 18 (Fluent Speech - Adolescent/Adult)


title: NPC_CONTROL_CLUE_4_7

value: CLUE


title: iPSC_ASD_ARCH_1_6

value: ARCH

value: 18 (Pre-verbal/Single Words)


title: iPSC_ASD_AQUA_3_3

value: iPSCs


title: NPC_CONTROL_CLAY_1_1

value: CLAY


title: NPC_CONTROL_CHAP_1_5

value: CHAP


title: NPC_CONTROL_CHAP_1_2

value: iPSC-derived neural progenitors


title: NPC_CONTROL_CENT_3_6

value: CENT


title: NPC_CONTROL_CLAY_1_2

value: CONTROL


title: NPC_CONTROL_CENT_3_3

value: Male


title: NPC_ASD_AVID_5_20

value: AVID

value: 16 (Fluent Speech - Child/Adolescent)


title: iPSC_ASD_ACAI_1_1

value: ACAI

value: ASD

value: 13 (Fluent Speech - Child/Adolescent)


title: iPSC_ASD_AERO_3_13

value: AERO

value: 20 (Fluent Speech - Child/Adolescent)


title: iPSC_ASD_APEX_5_4

value: APEX

value: 18 (Fluent Speech - Adolescent/Adult)


title: NPC_CONTROL_CAPE_1_8

value: CAPE


title: iPSC_ASD_ABLE_3_8

value: iPSCs

value: ABLE

value: 16 (Pre-verbal/Single Words)


title: NPC_ASD_APEX_5_4

value: iPSC-derived neural progenitors


title: NPC_ASD_AQUA_3_3

value: AQUA

value: 13 (Fluent Speech -Chld/Adolescent)


title: NPC_ASD_ARCH_1_6

value: ARCH

value: Male

value: 18 (Pre-verbal/Single Words)


title: NPC_ASD_AHOY_5_4

value: AHOY

value: 20 (Fluent Speech - Adolescent/Adult)


title: NPC_ASD_ARCH_1_2

value: ASD


title: NPC_ASD_ARCH_1_1


title: NPC_ASD_ACAI_1_1

value: ACAI

value: 13 (Fluent Speech - Child/Adolescent)


title: NPC_ASD_AQUA_3_9


title: NPC_ASD_AERO_3_13

value: AERO

value: 20 (Fluent Speech - Child/Adolescent)


title: NPC_ASD_AERO_3_14


title: NPC_ASD_AHOY_5_13


title: NPC_ASD_AHOY_5_19


title: NPC_ASD_ABLE_3_6


title: NPC_ASD_ABLE_3_12


title: NPC_ASD_ACAI_3_2


title: Neuron_CONTROL_COVE_3_1

source_name: iPSC-derived neurons

value: iPSC-derived neurons

value: COVE

value: CONTROL


title: Neuron_CONTROL_CLUE_4_7

value: CLUE


title: Neuron_CONTROL_CLAY_1_2

value: CLAY


title: Neuron_CONTROL_COVE_3_7


title: NPC_ASD_AERO_3_6

value: iPSC-derived neural progenitors


title: NPC_ASD_AVID_5_5

value: AVID

value: 16 (Fluent Speech - Child/Adolescent)


title: NPC_ASD_ARCH_1_2_Replicate2

value: ARCH

value: Male


title: Neuron_ASD_AVID_5_5


title: Neuron_CONTROL_CENT_3_3

value: CENT


title: Neuron_ASD_ARCH_1_1

value: 18 (Pre-verbal/Single Words)


title: Neuron_CONTROL_CENT_3_6


title: Neuron_ASD_ARCH_1_2

value: ASD


title: Neuron_ASD_ARCH_1_6


title: Neuron_ASD_AERO_3_7


title: Sucralose

city: Sydney

first: Qiaoping

last: Wang

state: NSW

address: Johns Hopkins Dr

department: Charles Perkins Centre

country: Australia

institute: University of Sydney

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences, percentage of unknown bases (N)>10% and low quality reads
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, A., B. A. Williams, et al . Nature Methods. 5(7): 621-8.
Genome_build: Drosophila melanogaster reference genome,Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

organism: Drosophila melanogaster

source_name: Head

growth_protocol: 4-7 days adult flies grew on stardard control diet or control diet plus sucralose

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6 days pretreatment with control diet or sucralose diet

tag: age

value: 10-14 days adult

tag: fed with

value: control plus sucralose diet

tag: tissue

value: head


title: Control

value: control diet


title: Neuron_ASD_AERO_3_6

tag: cell type

value: iPSC-derived neurons

value: AERO

value: 20 (Fluent Speech - Child/Adolescent)


title: Neuron_ASD_AHOY_5_13

value: AHOY

value: 20 (Fluent Speech - Adolescent/Adult)


title: Neuron_ASD_AQUA_3_9

value: AQUA

value: 13 (Fluent Speech -Chld/Adolescent)


title: Neuron_ASD_AHOY_5_4


title: Neuron_ASD_AQUA_3_3


title: Neuron_ASD_APEX_5_4

value: APEX

value: 18 (Fluent Speech - Adolescent/Adult)


title: Neuron_ASD_AHOY_5_19

value: Male


title: Neuron_ASD_ABLE_3_12

value: ABLE

value: 16 (Pre-verbal/Single Words)


title: Neuron_ASD_ACAI_1_1

value: ACAI

value: ASD

value: 13 (Fluent Speech - Child/Adolescent)


title: BZJ_4_T

city: Yangling

first: Sihuan

last: Zhang

state: Shaanxi

address: No. 22 Xinong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

description: treatment group

data_processing:
Illumina CASAVA version1.8+ soft were used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The transcript and unigene assembly was carried out using the short assembly program Trinity methodthen (MG Grabherr, 2011).
The gene expression level was computed by bowtie 0.12.8 soft using single-end mapping method, and further measured by the Reads Per Kilobase of exon model per Million mapped reads value (RPKM), which can be calculated as follow: RPKM=Total exon reads/[mapped read (millions) * exon length (KB)] (Mortazavi et al., 2008).
All assembled unigenes were compared with public database, NCBI non-redundant protein sequences (NR), SWISS-PROTProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), euKaryotic Ortholog Groups (KOG) and Pfam, to make functional annotation by similarity analysis. Sequences alignment using BLAST software.
Genome_build: De novo assembly
Supplementary_files_format_and_content: tab-delimited text files

organism: Capra hircus

source_name: Longissimus thoracis

growth_protocol: Five goats were feed on the same fodderand with similar body weight

extract_protocol:
The longissimus thoracis were collected immediately after slaughtering, and were snap-frozen in liquid nitrogen, then stored at -80oC until RNA extraction.Total RNA was extracted from the sample using Trizol reagent (Takara, Dalian, China) according to the manufacturer’s instructions.
RNA samples with a RIN value greater than 8.0 (8.0 out of 10.0), OD260/ OD280 ratio greater than 1.9 and OD260/ OD230 ratio is no less than 1.7 were selected for deep sequencing.The RNA was treated with DNase I for 30 min at 37oC to remove residual DNA. Then enrich and purify mRNA using beads with oligo (dT).The purified mRNA was fragmented to approximately 350 nt fragments using the RNA fragmentation kit. The first strand cDNA was synthesized using purified RNA fragments as template and hexamer primers. After the first strand was synthesized, the buffer (Invitrogen, 20 μL), dNTPs (0.25 mM / μL), RNaseH (0.05 U / μL) and DNA polymerase I (0.5 U / μL) were added to synthesize the second strand cDNA (Zhang et al., 2015). The short cDNA fragments were further purified using the QIAQuick PCR extraction kit (LianChuan Sciences, Hangzhou, China). The samples were then subjected to 3’ end repaired, a single “A” base and an adaptor ligation. Agarose gel electrophoresis was used to filter the suitably sized fragments (350 ± 50 bp), which would be used as the templates for the PCR amplification and RNA-seq library generation. Then the sequencing of the libraries was performed using Illumina HiSeq 2000 (LianChuan Sciences, Hangzhou, China).

treatment_protocol: The goats in the treatment group were ovariectomized at the beginning of the experiment and the goats in control group were untreated. All the five goats were slaughtered at the 50th day.

tag: sample source

value: ovariectomized goat

tag: breed

value: Hybrid goats (Boer goat(male) and Guan Zhong dairy goat(female))

tag: Sex

value: female

tag: experimental treatment (ovariectomy) age

value: about 5 months old

tag: slaughter age

value: after treatment 50th days


title: BZJ_5_T

description: treatment group