title: rGBC2_4

city: Ashburn

first: Yuhan

last: Wang

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
The sequence reads were trimmed to 44 bases and mapped to the mouse genome mm9 (NCBI build 37) using Bowtie (Langmead, et al., 2009) (an ultrafast memory-efficient short read aligner) version 0.12.7.(Allowed up to 3 mismatches, but required unique best matches.)
Customized R scripts (http://www.R-project.org/) were used to align and count sequences in exons according to RefSeq mouse gene models. Only reads that uniquely aligned to the genome were counted.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file is tab delimited text file with RPKM values of rGBC2. Published RNAseq data from primary GBCs, rGBC1(Hickey et al., 2013) and mouse pancreatic β cells (GSE54973; Benner et al., 2014) were included for comparison purposes.

source_name: gallbladder reprogrammed, insulin-positive cells (rGBC2)

growth_protocol: Mouse gallbladder cells were isolated from MIPGFP mice (8 weeks of age) and expanded in DMEM/F12 (Life Technologies, Grand Island, Ca) supplemented with 0.5% FBS (Thermo Fisher Scientific, Cambridge, MA), 1% insulin–transferrin–selenium (Roche, Indianapolis, IN), 15 mM HEPES (Thermo Fisher Scientific, Cambridge, MA),  100 U/ml penicillin and 100 μg/ml streptomycin in a 37 °C incubator with 5% CO2, as previous described (Hickey et al., 2013).

extract_protocol:
Insulin positive cells were directly FACS-sorted into TRI-Reagent LSl for RNA isolation.
Indexed sequencing libraries were constructed using the TruSeq RNA library prep Kit v2 per manufacturer’s instructions (illumina, Cat# RS-122-2001).

treatment_protocol: Cells were reprogrammed with transcription factors Pdx1, Ngn3, Mafa and PAX6 and treated with compounds during a 10-days-reprogramming period before FACS-sorted for gene expression profiling. Please find detailed treatment protocol in linked article.

value: B6.Cg-Tg(Ins1-EGFP)1Hara/J (MIP-GFP)

value: 8 weeks

tag: source cell type

value: primary mouse gallbladder cells (GBCs)

value: GBC-derived, FACS-purified MIP-GFP positive insulin-producing cells (namely rGBC2)


title: rGBC2_3

status: Public on Jan 01 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain background

tag: genotype/variation

tag: age

tag: cell type


title: rGBC2_2


title: Lb1N_rep2

city: Baltimore

first: Joseph

last: Tran

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

data_processing:
Low-quality reads are first filtered out.
Then reads were mapped to the mouse genome (mm9) using tophat.
Reads mapped to each genes were counted using custom scripts.
Differentially expressed genes were called using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files: second column- gene name, third column-the number of reads that uniquely mapped to the gene, fourth column- reads that mapped to multiple regions of the genome

source_name: Epicardial cell explant

growth_protocol: E12.5 embryonic hearts (ventricles only) were explanted on gelatinized wells dorsal side down and cultured for 48 hours. Hearts were removed and the explant was allowed to grow for another 72 hours prior to RNA extraction.

extract_protocol:
RNA was extracted using the Arcturus Picopure (Invitrogen) kit according to the manufacturer's instructions
The library was made using the  Illumina TruSeq RNA library Preparation V2 kit according the the manufacturer's protocol

tag: strain

tag: isolation

value: Explant


title: Lb1N_rep3


title: rGBC2_1


title: Lb1N_rep1


title: WT_rep4

value: wild type


title: WT_rep3


title: ESLAM_CTGCTGG

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
Basecalls performed using Illumina's CASAVA software, version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The first 6 bases were trimmed using Trimgalore v0.4.0 and Cutadapt v1.2.1 using the parameters --clip_R1 6 --clip_R2 6 –paired. Trimmed fastq files were aligned using Novoalign version V3.02.10 (www.novocraft.com) to the mouse assembly GRCm38 (mm10). Alignments were done in paired-end mode using the options -b4 (non-directional), -t 20,3 (optimized for SNP concordance), –a (adapter trimming), --hlimit 8 (homopolymer filter), and -H 20 (removes trailing bases with quality ≤ 20), and –u8 (penalty for unconverted CHG or CHH cytosine) as recommended by Novoalign. Aligned reads were output into the BAM format and sorted using SAMtools V0.1.17. Duplicates were marked with Picard V1.31 (http://picard.sourceforge.net).
Methylation of each cytosine was called using SAMtools mpileup (-B -C 0 -q 30 -d 500) followed by Novomethyl V1.01 (-o Consensus -%) (www.novocraft.com). Cytosine calls with Phred quality score ≤15 were discarded. Methylation percentage of each CpG di-nucleotide (found by searching the genome with a custom java script) was calculated by taking a weighted average of each cytosine using the map command from the bedtools suite (Quinlan and Hall, 2010). In most cases, only one base within a CpG dinucleotide had coverage; in these cases, the methylation information of the covered base was extrapolated to the other base.
Genome_build: mm10
Supplementary_files_format_and_content: bed file for CpG methylation. Columns are as follows: chr, start, end, fractional methylation, methylated C's, total C's, # of CpGs covered in the dinucleotide (1=just one, 2=both C and G covered)

molecule: genomic DNA

source_name: Hematopoetic Stem Cell

extract_protocol:
Sorted cells were lysed in 96 well plates in 4 uL of lysis buffer (20 mM Tris-HCl, pH 8.0, 20 mM KCl, 0.3% Triton-X 100, 1 mg/mL Qiagen Protease) for 30 minutes at 50 degrees.
The lysed cells were then spiked-in with 1 uL of 60 fg/uL purified T7 phage DNA (GeneON). The DNA mixture was then bisulfite converted with the MethylEdge Bisulfite Conversion kit (Promega) using a modified bead-based protocol which enables automation (Domanico et al., 2013): 5 uL of the lysis/spike-in mixture was combined with 32.5 uL of MethylEdge Conversion reagent and incubated at 98°C for 8 minutes and 54°C for 60 minutes in a PCR machine. After incubation, the plate was briefly spun down and placed on an Agilent Bravo robot for subsequent steps. The 37.5 uL of bisulfite converted DNA was mixed with 180 uL of MethylEdge Binding Buffer and 1.8 uL of 20 mg/mL MagSi-DNA allround magnetic silica beads (MagnaMedics) and incubated at room temperature for 15 minutes. The beads were then collected on a magnet for 3 minutes and washed twice with 220 uL of 80% ethanol for 30 seconds while on the magnet. 60 uL of MethylEdge desulfonation buffer was added and incubated for 15 minutes. The desulfonation buffer was then removed and the beads were washed twice with 100 uL of 80% ethanol. The beads were then air-dried for 3 minutes, resuspended in 20 uL of Qiagen elution buffer, and incubated at 56°C in a shaking incubator at 2,000 rpm for 15 minutes. The beads were then collected on a magnet for 30 seconds and the supernatant containing the DNA was removed. The bisulfite-converted ssDNA from above was added directly into a mixture containing 1.25 uL of 10 mM dNTPs and 1 uL of 500 uM random hexamers (3’ phosphothioate). The reactions were incubated at 98°C for 1 minute and snap frozen on ice for 2 minutes. A mastermix of 0.5 uL of 50 U/uL Klenow fragment [3’→5’ exo-] (NEB M0212M), and 2.5 uL of 10X NEB Buffer 2 was added on ice and mixed well. The reactions incubated in a PCR machine as follows: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes. The entire reaction was denatured again at 98˚C for 1 minute and snap frozen on ice for 2 minutes. The reaction was transferred on a pre-chilled CoolRack by robot into a new plate containing 5 uL mixture of 20 uM random hexamers (3’ phosphothioate), 0.5 mM dNTPs, 1X NEB buffer and 25 U of Klenow fragment [3’→5’ exo-]. The wells were mixed well and the reaction was cycled once again: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes, and heat-inactivated at 70°C for 10 minutes. 20 uL of Qiagen Elution Buffer was added to each reaction to make it up to 50 uL, and each reaction was purified using 50 uL of Sera-Mag beads before proceeding to the standard illumina adapter ligation library construction protocol. The 25 uL of cleaned-up adapter-ligated fragments were PCR amplified in 50 uL containing 1 U of Phusion U Hot Start DNA Polymerase (Life Technologies F-555S), 1X HF buffer, 3% DMSO, 200 uM dNTPs, 0.5 uM PCR primer 1.0 (need sequence) (IDT), and corresponding 0.5 uM indexing PCR primer 2.0. The reactions were incubated in a PCR machine as follows: initial 98˚C for 1 minute; 10 cycles of 98˚C for 30 seconds, 65˚C for 15 seconds, 72˚C for 15 seconds; and a final extension of 72˚C for 5 minutes. The 50 uL reaction was cleaned up with 40 uL of Sera-Mag beads and eluted in 15 uL.

tag: markers

tag: type

value: Single-cell


title: WT_rep2


title: ESLAM_CTCAGA


title: ESLAM_CTGAATG


title: Day 2.5 Trim33-deficient rep3

city: Ann Arbor

first: Vesa

middle: Matti

last: Kaartinen

state: MI

address: 1011 N. University

department: BMS

institute: University of Michigan

data_processing:
mRNA and sequencing libraries were prepared by the University of Michigan DNA Sequencing Core and single end reads generated on Illumina HiSeq2000.
After quality assessment per sample, single-end, 52 base pair reads were aligned to mm9 (Mus musculus assembly July 2007) using STAR RNA Seq aligner (Dobin et al., 2013).
Read counts for differential expression were obtained using HTSeq program. Differential expression analyses were performed using the DESeq program in R Statistical Package. https://bioconductor.org/packages/3.3/bioc/vignettes/DESeq/inst/doc/DESeq.pdf.
Genome_build: mm9
Supplementary_files_format_and_content: text files with raw counts from HT-seq (available on sample records) and excel files with DESeq output with differentially expressed genes p <=0.05 (available on series record)

source_name: Embryoid bodies - day2.5 in differentiation

growth_protocol: ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were cultured without feeder cells in the presence of LIF and 2i. Embryoid bodies were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were harvested at days 2 and 2.5 respectively.

extract_protocol:
Equivalent amounts/number of embryoid bodies (EBs) were collected at days 2 and 2.5, comprising control and Trim33-deficient (n=3 independent pairs), in 100-200 μl commercially available (Qiagen) RLT buffer. Total RNA was isolated using Qiagen RNeasy Mini Kit Cat. No 74104.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Trim33-deficiency was induced with 4OH-Tamoxifen on day 1 (at 24 hours in differentiation).

tag: passages

value: outbred

tag: tissue

value: embryoid bodies

tag: timepoint

value: day2.5 in differentiation


title: ESLAM_CGATGT


title: Day 2.5 Trim33-deficient rep2


title: Day 2.5 Control rep3

value: wildtype


title: Day 2.5 Trim33-deficient rep1


title: Day 2.5 Control rep2


title: Day 2.5 Control rep1


title: Day 2 Trim33-deficient rep3

source_name: Embryoid bodies - day2 in differentiation

value: day2 in differentiation


title: ESLAM_CCCCATG


title: Day 2 Trim33-deficient rep2


title: ESLAM_CTTCGAA


title: ESLAM_CCCACGC


title: ESLAM_CCACGC


title: Day 2 Control rep1


title: ESLAM_CCAACA


title: ESLAM_CTGGCGC


title: Day 2 Control rep2


title: ESLAM_CACGAT


title: RNA-seq, poly(A) selected, knockdown control

city: Zurich

first: Markus

last: Stoffel

address: Otto-Stern-Weg 7

department: Inst. f. Molecular Health Sciences

country: Switzerland

institute: ETH Zurich

description:
adenoviral shRNA knockdown, RNA-seq
shRNA.CTRL

data_processing:
RNA-seq
removal of adapters with Trimmomatic
alignment against mm10 mouse genome with STAR aligner (Dobin et al., 2013)
annotation and quantification of reads was performed in EdgeR (Robinson et al., 2010) and GenomicRanges (Lawrence et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: fpkm normalized data: Supplementary_file_1_PAR-CLIP_RNA-seq_annotation.txt  columns 8-13 (including log2 fold change calculation to controls).

source_name: primary hepatocytes

growth_protocol: isolated primary hepatocytes

extract_protocol:
poly(A) selection
Illumina TruSeq protocol

treatment_protocol: siRNA knockdown or lentiviral overexpression

tag: treatment

value: knockdown control

tag: rna source

value: poly(A) selected total RNA


title: ESLAM_CAGATC

value: NTC


title: PAR-CLIP Hdlbp/Vigilin replicate 2

description: PAR-CLIP

data_processing:
PAR-CLIP
removal of adapters with cutadapt
alignment against mm10 mouse genome with bowtie 1 (Langmead and Salzberg, 2012)
cluster generation with PARalyzer and the GRCm38 Encode genomic annotation (Corcoran et al., 2011)
Genome_build: mm10
Supplementary_files_format_and_content: cluster annotations and total read count per cluster

extract_protocol:
immunoprecipitation of Hdlbp/Vigilin crosslinked RNA
3' and 5' RNA adapter ligation, cDNA preparation, PCR amplification

treatment_protocol: 4-thiouridine treatment (100 µM) and in RNA-protein vivo crosslinking at 365 nm

value: immunopurified Hdlbp/Vigilin


title: WT_rep1


title: RNA-seq, poly(A) selected, overexpression human HDLBP/Vigilin

description:
adenoviral protein overexpression, RNA-seq
Ad-hVIGILIN

value: overexpression human HDLBP/Vigilin


title: RNA-seq, poly(A) selected, knockdown Hdlbp/Vigilin

description:
adenoviral shRNA knockdown, RNA-seq
sh.VIG

value: knockdown Hdlbp/Vigilin


title: ESLAM_CACAAAC


title: PAR-CLIP Hdlbp/Vigilin replicate 1

description: PAR-CLIP


title: Day2 Trim33-deficient rep1


title: ESLAM_CAAGGAC


title: LL3

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed for adaptors, masked for low-complexity or low-quality sequence, and subsequently mapped to the mouse genome (build mm10, GRCm38) using STAR (version 2.4.0f1)
The SAM/BAM files were further processed using the SAMtools (version 0.1.18) and read count quantitations were obtained using BEDTools multicov (version 2.25.0).
Normalization of read counts and differential expression analysis between genotypes was carried out using the DESeq2 R package in Bioconductor (release 2.13).
Genome_build: mm10

source_name: Breast tumor cells

extract_protocol:
Total RNA from mammary tumor cell lines was extracted using the RNeasy kit (Qiagen) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

tag: cell line

value: breast tumor


title: LL3WT


title: ESLAM_CAAGCGA


title: RNA-seq, poly(A) selected, overexpression control GFP

description:
adenoviral protein overexpression, RNA-seq
Ad-GFP

value: overexpression control GFP


title: Day 2 Control rep3


title: input DNA_D7

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
ChIP-seq reads and FAIRE-seq reads were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
Peaks of ChIP-seq and FAIRE-seq were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-seq of others: Windows (50), Gaps (50), FDR (1e-10); For FAIRE-seq: Windows (50), Gaps (50), E-value (1000)
Paired-end reads of RNA-seq are aligned to the mm9 genome assembly using TopHat (v2.0.10) with default parameters.
Cufflinks (v1.0.3) was used to calculate the fragments per kilo base per million (FPKM) as expression measurements for each gene as annotated in RefSeq with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq data, wig files were generated using in-house script and the scores represent RPKM; For RNA-seq data, tab-delimited text files were generated to include FPKM values for each gene.

source_name: Brown preadipocyte cell_input DNA

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn Pparγf/f or Mll3-/-Mll4f/f mice (Jackson no. 004584) and immortalized with SV40T-expressing retroviruses generated from the pBabepuro-large T plasmid

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, 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 15-18 cycles and library fragments of 200-400 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: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: Pparg-flox/flox

value: imortalized Pparg-flox/flox BAT isolated brown preadipocytes

tag: stage of adipogenesis

value: Mature adipocytes (D7)


title: FAIRESeq_D-3

data_processing:
library strategy: FAIRE-seq
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
ChIP-seq reads and FAIRE-seq reads were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
Peaks of ChIP-seq and FAIRE-seq were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-seq of others: Windows (50), Gaps (50), FDR (1e-10); For FAIRE-seq: Windows (50), Gaps (50), E-value (1000)
Paired-end reads of RNA-seq are aligned to the mm9 genome assembly using TopHat (v2.0.10) with default parameters.
Cufflinks (v1.0.3) was used to calculate the fragments per kilo base per million (FPKM) as expression measurements for each gene as annotated in RefSeq with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq data, wig files were generated using in-house script and the scores represent RPKM; For RNA-seq data, tab-delimited text files were generated to include FPKM values for each gene.

source_name: Brown preadipocyte cell_FAIRESeq

extract_protocol:
Lysates were clarified from sonicated nuclei and the open chromatin was purified by 3 rounds of phenol chloroform extraction.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, 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 15-18 cycles and library fragments of 200-400 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.

value: Proliferating (D-3)


title: ESLAM_CAAGACT

value: Single-cell


title: input DNA_D2

value: Immature adipocytes (D2)


title: FAIRESeq_D7


title: FAIRESeq_D2


title: input DNA_D0

value: Confluent (D0)


title: input DNA_D-3


title: ESLAM_CAACTTG


title: ESLAM_CAAAAG


title: ESLAM_ATGTCA


title: FAIRESeq_D0


title: H3K27ac_ChIPSeq_D2

source_name: Brown preadipocyte cell_H3K27ac_ChIPSeq

tag: chip antibody

value: Anti-Histone H3 (acetyl K27) antibody - ChIP Grade

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: H3K27ac_ChIPSeq_D7

tag: strain background

tag: genotype/variation


title: H3K4me3_ChIPSeq_D2

source_name: Brown preadipocyte cell_H3K4me3_ChIPSeq

tag: cell type

value: Anti-trimethyl-Histone H3 (Lys4) Antibody

value: Millipore


title: H3K27ac_ChIPSeq_D0


title: H3K27ac_ChIPSeq_D-3


title: ESLAM_ATCCTA

tag: strain


title: H3K4me2_ChIPSeq_D2

source_name: Brown preadipocyte cell_H3K4me2_ChIPSeq

value: imortalized Pparg-flox/flox brown preadipocytes

value: Anti-Histone H3 (di methyl K4) antibody - ChIP Grade


title: H3K4me3_ChIPSeq_D7


title: ESLAM_ATCACG

tag: markers


title: H3K4me2_ChIPSeq_D7


title: ESLAM_CAACCCC

tag: type


title: ESLAM_ATACGG


title: H3K4me1_ChIPSeq_D7

source_name: Brown preadipocyte cell_H3K4me1_ChIPSeq

value: Anti-Histone H3 (mono methyl K4) antibody - ChIP Grade


title: H3K4me2_ChIPSeq_D-3


title: H3K4me1_ChIPSeq_D2


title: ESLAM_ATAATT


title: CTCF_ChIPSeq_D7

source_name: Brown preadipocyte cell_CTCF_ChIPSeq

value: Anti-CTCF Antibody


title: H3K4me1_ChIPSeq_D0


title: ESLAM_AGTGAAA


title: H3K4me1_ChIPSeq_D-3


title: CTCF_ChIPSeq_D2


title: ESLAM_AGTTCC


title: ESLAM_CAATAGG


title: CTCF_ChIPSeq_D0


title: H3K4me3_ChIPSeq_D0


title: H3K4me3_ChIPSeq_D-3


title: CTCF_ChIPSeq_D-3


title: H3K4me2_ChIPSeq_D0


title: Pol_II_ChIPSeq_D2

source_name: Brown preadipocyte cell_Pol_II_ChIPSeq

value: ChIPAb+ RNA Pol II


title: Pol_II_ChIPSeq_D7


title: ESLAM_AGTCCGC


title: ESLAM_AGTAGAG


title: Pol_II_ChIPSeq_D0


title: Pol_II_ChIPSeq_D-3


title: ESLAM_AGCGCT


title: ESLAM_AGATAG

value: NTC


title: PPARγ_ChIPSeq_D0

source_name: Brown preadipocyte cell_PPARγ_ChIPSeq

value: Pparg-flox/flox

value: PPARγ Antibody (H-100)

value: Santa Cruz Biotechnology


title: PPARγ_ChIPSeq_D-3

value: Proliferating (D-3)


title: PPARγ_ChIPSeq_D2


title: C/EBPβ_ChIPSeq_D7

source_name: Brown preadipocyte cell_C/EBPβ_ChIPSeq

value: Mature adipocytes (D7)

value: C/EBP β Antibody (C-19)


title: ESLAM_AGAAGA

value: Single-cell


title: C/EBPα_ChIPSeq_D7

source_name: Brown preadipocyte cell_C/EBPα_ChIPSeq

value: C/EBP α Antibody (14AA)


title: C/EBPα_ChIPSeq_D2

value: Immature adipocytes (D2)


title: C/EBPβ_ChIPSeq_D0

value: Confluent (D0)


title: ESLAM_AGAAACC


title: C/EBPα_ChIPSeq_D-3


title: C/EBPα_ChIPSeq_D0


title: RNA_D7

source_name: Brown preadipocyte cell_RNA-Seq

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA wasfurther  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA_D2


title: RNA_D0


title: ESLAM_ACTGCTG

source_name: Hematopoetic Stem Cell


title: ESLAM_AGGCCG


title: RNA_D-3


title: PPARγ_ChIPSeq_D7


title: ESLAM_ACTGAT


title: ESLAM_ACTATAC


title: ESLAM_ACTCAGA


title: C/EBPβ_ChIPSeq_D2


title: ESLAM_ACGATA


title: ESLAM_ACTCTC


title: ESLAM_AGAATAA


title: ESLAM_ACCGTCC


title: C/EBPβ_ChIPSeq_D-3


title: ESLAM_ACCCAG


title: ESLAM_AATGTCA


title: ESLAM_AATAGG


title: ESLAM_ACCGGC


title: ESLAM_AAGCGA


title: ESLAM_AAGATAG


title: ESLAM_ACAAAC


title: ESLAM_AAGGAC


title: ESLAM_AACTTG


title: ESLAM_AACCCAG


title: ESLAM_AAATGC


title: ESLAM_AAGACT


title: ESLAM_AAAGCA


title: ESLAM_AACTGAT


title: ESLAM_AAACAT


title: Genomic_500cell_rep1

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

data_processing:
library strategy: ATAC-seq
Reads in FASTQ format were aligned to GRCm38 (mm10) using Bowtie v1.1.0 (Langmead et al., 2009) with settings –m 1 –X 2000 –chunkmbs 256 in paired-end mode.
Unaligned reads were processed with the Trim galore wrapper for Cutadapt (Martin, 2011) to remove Nextera primer sequences (settings: --nextera –paired –three_prime_clip_R1 1 –three_prime_clip_R2 1), and were then aligned again using Bowtie (settings –m 1 –X 2000 -3 1 –chunkmbs 256).
The Samtools collection (Li et al., 2009) was used to sort, remove PCR duplicates (rmdup), index BAM files, and calculate library statistics (flagstat). We used CollectInsertSizeMetrics.jar from Picard v1.110 (Broad Institute 2015) to analyze fragment size statistics, and preseq v0.1.0 (Daley and Smith, 2013) to analyze library sequencing saturation.
To downsample BAM files to 3.2M reads, the data were sorted by name instead of location using Samtools sort in SAM format, then R sample() was used to select random read pairs, and a custom Perl script then filtered the selected reads. Samtools view was then used to convert files back to BAM format.
After downsampling, aligned reads were analyzed for peak and region enrichment of open chromatin using HotSpot v4.1 (John et al., 2011) with default settings (FDR < 0.01).
DiffBind v1.16.3 (Stark and Brown, 2011,Ross-Innes et al., 2012) was used to calculate merged peak locations, based on the outer boundaries of overlapping peaks from all cell lines analyzed, and peak accessibility scores for each replicate were calculated using DiffBind with the default setting DBA_SCORE_TMM_MINUS_EFFECTIVE, which uses trimmed mean of M-values (TMM) normalization (Robinson and Oshlack, 2010) built into the edgeR package (Robinson et al., 2010) using read counts minus control (genomic) read counts and full library size.
For overall views of aligned data from each cell class, we built merged BAM files using samtools merge and sort.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak: chr, start, and end coordinates from HotSpot peak results
Supplementary_files_format_and_content: broadPeak: chr, start, and end coordinates form HotSpot region results
Supplementary_files_format_and_content: bed: merged peak locations in BED format as calculated by DiffBind
Supplementary_files_format_and_content: tmmScores: A matrix of TMM scores for each merged peak in each sample as calculated by DiffBind

growth_protocol: Animals were provided food and water ad libitum and were maintained at a regular 12 h day/night cycle at no more than 5 adult animals per cage. Animals were maintained on the C57BL/6J background.

extract_protocol:
We used an isoflurane chamber to anesthetize adult male mice (P56 ± 3), decapitated them, removed the brains, and transferred them immediately to freshly prepared, ice-cold artificial cerebrospinal fluid (ACSF: 126 mM NaCl, 20 mM NaHCO3, 20 mM dextrose, 3 mM KCl, 1.25 mM NaH2PO4, 2 mM CaCl2, 2 mM mgCL2, 50 μM DL-AP5 sodium salt, 20 μM DNQX, and 0.1 μM tetrodotoxin, mixed then bubbled with 95% O2/5% CO2 carbogen gas). We sectioned the brains to generate 400 μm–thick sections using a Leica VT1000S vibratome with a chilled chamber, and immediately transferred the slices to a bubbled ACSF-containing chamberat room temperature. Individual slices of interest were microdissected in a Petri dish while submerged in ACSF under a fluorescence dissecting microscope. Dissected tissue was transferred to a microcentrifuge tube containing ACSF with 1 mg/mL pronase (Sigma, Cat#P6911) for 70 min at room temperature. After incubation, with tissue pieces settled at the bottom of the tubes, ACSF with pronase was exchanged twice with ACSF containing 1% fetal bovine serum (FBS). We next dissociated the tissue into a single-cell suspension by trituration through Pasteur pipettes with polished openings of 600 μm-, 300 μm-, and 150 μm-diameter. 500 cells were sorted into a well of an 8-well PCR strip containing 2 μL ACSF on a BD FACSAriaII SORP with a 130 μm nozzle at 10 psi sheath pressure, and in the single-cell sorting mode. We excluded dead cells by labelling with DAPI (DAPI*2HCl, Life Technologies Cat#D1306) added to the single-cell suspension at 2 ng/mL. We retained only cells that had high tdTomato fluorescence and low DAPI labeling.
Immediately after FACS collection, cells were lysed with 25 µL Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1 % IGEPAL CA-630). Nuclei were pelleted by centrifugation at 500 x g for 30 minutes at 4 °C in a refrigerated microcentrifuge. After pelleting, the supernatant was removed and cells were resuspended by repeated pipetting in 25 µL Reaction Mix (12.5 µL Nextera TD Buffer, 2 µL Nextera TD Enzyme, and 10.5 µL water). Samples were then tagmented by incubation at 37 °C for 1 hour on a heat block. After tagmentation, the reactions were stopped with addition of 5 µL Cleanup Buffer (900 mM NaCl, 300 mM EDTA), 2 µL 5% SDS, and 2 µL Proteinase K and incubation at 40 °C for 30 min. Tagmented DNA was purified using AMPure XP beads at a ratio of 1.8:1 beads to reaction volume, with a final resuspension volume of 11 µL. For indexing and amplification, we added 15 µL KAPA HotStart Ready mix (Kapa Biosystems, Cat# KK2602) and 2 µL each of Nextera i5 and i7 indexed amplification primers. These samples were incubated at 72 °C for 3 minutes, then PCR amplified as follows: 95 °C for 3 min; 9 cycles of 98 °C for 20 sec, 65 °C for 15 sec, and 72 °C for 15 sec; 72 °C final extension for 1 min. Samples were then purified using AMPure XP as above, re-amplified for additional 9 cycles under the same conditions, and then purified once more as before using Ampure XP beads to produce 11 µL final volume. Library quality and quantity were assessed using 1 µL of the final, purified DNA on a BioAnalyzer High Sensitivity DNA chip. For mES cell populations, ES cells grown on mouse embryonic fibroblast (MEF) feeders were passaged onto gelatin plates to dilute/remove feeder cells, and they were made into single-cell suspensions by treatment with Trypsin-EDTA (Thermo Fisher Scientific, Cat#25300054). Cells were washed twice in PBS with 1% FBS, then were resuspended in PBS with 1% FBS and 2 ng/mL DAPI. 500-cell populations of DAPI-negative ES cells were sorted into individual wells of an 8-well PCR strip containing 2 uL of PBS.

tag: broad class

value: Input

tag: tissue/cell type

value: mES cells


title: mES_500cell_rep3

value: mES


title: ESLAM_AACTCTC


title: Scnn1a_L4_500cell_rep3

tag: age (days)

tag: cre driver

tag: reporter

value: Glutamatergic

tag: cortical layer

value: Visual cortex


title: Scnn1a_L4_500cell_rep2


title: Genomic_500cell_rep2


title: mES_500cell_rep1


title: Rbp4_L5_500cell_rep2


title: mES_500cell_rep2


title: Rbp4_L5_500cell_rep1


title: Ntsr1_L6_500cell_rep3


title: Gad2_GABA_500cell_rep3

value: GABAergic

value: All


title: Ntsr1_L6_500cell_rep2


title: ESLAM_AACGATA


title: Ntsr1_L6_500cell_rep1


title: Scnn1a_L4_500cell_rep1


title: ESLAM_AAGAAGA


title: Gad2_GABA_500cell_rep2


title: Gad2_GABA_500cell_rep1


title: Cux2_L2/3_500cell_rep3


title: Cux2_L2/3_500cell_rep2


title: Niclosamide_3

city: Pullman

first: Kanako

last: Hayashi

address: BLS345, 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

description: Daily treatment of 200 mg/kg BW niclosamide for 3 weeks

data_processing:
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2500 using a HiSeq SBS sequencing kit version 3.
Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)
Each sample's fastq file run through trimmomatic 0.33 to first remove any remaining standard Illumina TruSeq SE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove reads shorter than 30 bp (parameters ILLUMINACLIP:/home/apps/trimmomatic/trimmomatic-0.33/adapters/TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 MINLEN:30)
NCBI's GRCm38.p3 genome was indexed using STAR 2.4.2a with gene models ref_GRCm38.p3_top_level.gff3.gz (NCBI Mus musculus Annotation Release 105) and parameters --sjdbOverhang 99 and --sjdbGTFtagExonParentGene gene. Each sample was then aligned to the genome again using STAR 2.4.2a with gene models ref_GRCm38.p3_top_level.gff3.gz (NCBI Mus musculus Annotation Release 105) and parameter --sjdbGTFtagExonParentGene gene.
Read counts for each gene were generated using featureCounts (from subread v 1.4.6-p4) with parameters -s 2 -g gene -t exon
Genome_build: NCBI GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text files of raw read counts per gene per sample were used directly in edgeR 3.12.0 for statistical analysis and thus are the "normalized" data.

source_name: Uterine derived endometriotic like lesions

growth_protocol: Lesions were established by dissecting the uterus from a 6 week old B6-GFP positive donor and suturing this tissue to the peritoneal wall of an 8 week old wild type recipient in a matched estrous cycle.  Lesions were allowed 3 days to develop prior to daily vehicle or drug treatment.    Note: CO_1 sample is pooled from 4 different mice, due to amout of RNAs, while all other samples are from a single mouse.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. DNAse digestion was performed using the accompaning RNAse free DNAse set.
Illumina's TruSeq Stranded RNAseq Sample Prep kit was used with 1 ug of total RNA for the construction of sequencing libraries. Indices (barcodes) were included to be able to differentiate the sequences from each sample. The adapter sequence used was AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNN = 6 nt barcode index in .fastq file name)

treatment_protocol: Recipient mice were necropsied 3 weeks after implantation in diestrus.  Uterine derived tissues were separated from the recipient tissues and were homogenized with Trizol reagent at collection and stored at-80C.

tag: tissue

tag: gender

value: female

tag: genotype

value: B6-GFP Positive

tag: treatment

value: niclosamide

tag: bodyweight(g)


title: Niclosamide_1

value: Uterine derived endometriotic like lesions


title: ESLAM_AACCGGC


title: CO_3

description: Daily vehicle treatment for 3 weeks

value: control


title: CO_1

description: Daily vehicle treatment for 3 weeks (this sample is pooled from 4 different mice, due to amout of RNAs.  Therefore, body weight is average of 4 mice).


title: Niclosamide_2


title: Ulcerated mouse 1

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Ulcerated tissue obtained from the stomach corpus of a C57BL6 mouse at post ulceration day 30

data_processing:
Basecalling was through Illumina HiSeq 2500.
Sequenced reads were trimmed of barcodes and primers, mapped to the mm10 genome using UCSC annotations.
RPKM were generated, log2 transformed, normalized using the DESeq algorithm, and baselined to the median of all intact tissues.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing RPKM for each transcript.

source_name: stomach corpus

extract_protocol:
Stomach was removed and open at 30 days post treatment. Tissue was homogenized in TRI Reagent and extracted total RNA was purified by RureLink DNA Mini Kit.
The mRNA was poly-A selected and a single-stranded cDNA library was generated for sequencing using standard Illumina protocols.

treatment_protocol: 99% acetic acid was placed on the exterior surface of the intact stomach via a microcapillary tube for 25 seconds. Following treatment animals were routinely maintained on food and water.

value: stomach

tag: tissue type

value: Ulcerated tissue

tag: age at ulceration

value: 4 months

tag: time after ulceration

value: post ulceration day 30


title: Ulcerated mouse 3

tag: strain


title: RNA_BAT

data_processing:
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
Sequencing reads were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
Aligned reads on exonic regions from RNA-Seq were used to calculate RPKM to measure the gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files were generated to include RPKM values for each gene.

source_name: interscapular brown adipose tissue

value: brown adipose tissue

tag: developmental stage

value: 16 weeks


title: Uninvolved mouse 1

description: Uninvolved tissue obtained from the stomach corpus of a C57BL6 mouse at post ulceration day 30

value: Uninvolved tissue


title: p300_ChIPSeq_D2 in Mll3-/-;Mll4-/-

source_name: Brown preadipocyte cell_p300_ChIPSeq

treatment_protocol:
After immortalization, cells were infected with adenoviral Cre or GFP to generate WT or Mll4 KO cells
For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

tag: strain background

tag: genotype/variation

tag: cell type

value: imortalized Mll3-/-;Mll4flox/flox brown preadipocytes

tag: stage of adipogenesis

value: Immature adipocytes (D2)

tag: infected with

value: GFP to generate Mll4 KO cells

tag: chip antibody

value: p300 Antibody (C-20)

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: p300_ChIPSeq_D2 in Mll3-/-;Mll4flox/flox

value: adenoviral Cre to generate WT cells


title: Ulcerated mouse 2

tag: tissue


title: Uninvolved mouse 2


title: CBP_ChIPSeq_D2 in Mll3-/-;Mll4-/-

source_name: Brown preadipocyte cell_CBP_ChIPSeq

value: CBP (D6C5) Rabbit mAb

value: Cell Signaling Technology


title: CBP_ChIPSeq_D2 in Mll3-/-;Mll4flox/flox


title: input DNA_D-3 in Mll3-/-;Mll4flox/flox

source_name: Brown preadipocyte cell_input DNA

value: Proliferating (D-3)


title: MLL4_ChIPSeq_D-3 in Mll3-/-;Mll4-/-

source_name: Brown preadipocyte cell_MLL4_ChIPSeq

value: Anti-MLL4 #3

value: Home-made


title: Cux2_L2/3_500cell_rep1

tag: age (days)

tag: cre driver

tag: reporter

tag: broad class

value: Glutamatergic

tag: cortical layer

tag: tissue/cell type

value: Visual cortex


title: MLL4_ChIPSeq_D-3 in Mll3-/-;Mll4flox/flox


title: H3K27me3_ChIPSeq_D2

value: Pparg-flox/flox

value: imortalized Pparg-flox/flox BAT isolated brown preadipocytes

value: Anti-trimethyl-Histone H3 (Lys27) Antibody

value: Millipore


title: H3K27me3_ChIPSeq_D7

value: Mature adipocytes (D7)


title: H3K9me2_ChIPSeq_D7

source_name: Brown preadipocyte cell_H3K9me2_ChIPSeq

value: Anti-Histone H3 (di methyl K9) antibody [mAbcam 1220] - ChIP Grade

value: Abcam


title: H3K27me3_ChIPSeq_D0

value: Confluent (D0)


title: Uninvolved mouse 3

value: stomach

tag: tissue type

value: Uninvolved tissue

tag: strain

tag: age at ulceration

value: 4 months

tag: time after ulceration

value: post ulceration day 30


title: H3K9me2_ChIPSeq_D0

tag: strain background

tag: genotype/variation

tag: cell type

tag: stage of adipogenesis


title: H3K9me2_ChIPSeq_D2

value: Immature adipocytes (D2)

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #


title: H3K9me2_ChIPSeq_D-3

value: Proliferating (D-3)

tag: chip antibody lot/batch #


title: CO_2

description: Daily vehicle treatment for 3 weeks

tag: tissue

value: Uterine derived endometriotic like lesions

tag: gender

value: female

tag: genotype

value: B6-GFP Positive

tag: treatment

value: control

tag: bodyweight(g)


title: H3K27me3_ChIPSeq_D-3

value: Pparg-flox/flox

value: imortalized Pparg-flox/flox BAT isolated brown preadipocytes


title: H3K36me3_ChIPSeq_D7

value: Anti-Histone H3 (tri methyl K36) antibody - ChIP Grade


title: H3K36me3_ChIPSeq_D2


title: input DNA_D-3 in Mll3-/-;Mll4-/-

value: imortalized Mll3-/-;Mll4flox/flox brown preadipocytes

tag: infected with

value: GFP to generate Mll4 KO cells


title: H3K36me3_ChIPSeq_D0

value: Abcam


title: si_LARP4B_1

city: Wuerzburg

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Reads were aligned to the human genome (hg19) with BOWTIE v0.12.8.
Differential expression and statistical inference was done using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: The txt-file contains a table showing the differential expression (as log FoldChange) of ensemble annotated genes (ensemble gene ids, in rows) between samples (=experimental conditions) and the calculated p-value and adjusted p-value for each FoldChange.

organism: Homo sapiens

growth_protocol: HEK293 cells were grown in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion 48 h after transfection. Poly-A RNA was isolated from total RNA using the NEBNext Poly(A)mRNA Magnetic Isolation Module (E7490).
Libraries for the RNA-seq samples were constructed using the NEBNext Library Prep Kit (6100) following the instruction manual. Briefly, poly-A RNA was fragmented to generate 200 nucleotides long fragments. First and second strand cDNA synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBNext adaptors. The cDNA was size selected using agarose gels and amplified by PCR. For the resulting RNA-seq libraries, amplicon sizes and quantities were determined using the Biorad Experion system. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacture’s instructions.

treatment_protocol: HEK293 cells were transfected with siRNA targeting LARP4B and firefly luciferase (Thermo Fisher Scientific).

tag: cell line

tag: si-rna

tag: replicate


title: si_luc_2

value: si-luciferase


title: TenenLab_U937_ChIPseq_input

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

data_processing:
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files.
Mapping: reads were mapped on the human hg19 genome using bowtie2 (parameters: --very-sensitive)
Filtering: reads mapping multiple loci were removed by filtering out reads with MAPQ < 10 (using samtools view -q10)
Visualisation: reads pileup were computed and bigwig files were produced using HOMER (program makeUCSCfile, dewfault parameters)
Removing duplicated reads: for input sequencign, dulicated reads (ie possible pcr amplificatino artifact) were removed using samtools rmdup -s ; this was not done for ChIPexo, as we expect reads to stack at the exact locus of the crosslinking after exonuclease treatment
Genome_build: hg19
Supplementary_files_format_and_content: USCS bigwig format (binary track of pile up signal)

growth_protocol: U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Library contruction and sequencign were performed by Peconic LLC (USA)

treatment_protocol: 8.5x106 U937 cells were harvested, washed with ice-cold PBS and cross-linked with 1% formaldehyde (Sigma) for ten minutes at room temperature with gentle agitation. 2M glycine was added to quench the reaction. Cell pellets were obtained by 10 minutes of cold centrifugation at 2,000 rpm and lysed (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS + protease inhibitors (Complete mini catalog # 04693139001, Roche)). The solution was incubated at 4°C for 30 minutes. Cell pellets were collected by 10 minutes of centrifugation at 2,000 rpm at 4°C, resuspended in lysis buffer and sonicated in a Bioruptor Next Gen water bath sonicator (Diagenode) to 200-500bp. Further steps were all performed by Peconic LLC (USA).

value: no antibody (input)


title: TenenLab_U937_ChIPexo_Znf143

value: ZNF143 antibodies produced and generously provided by Dr. Philippe Carbon (see 10.1074/jbc.274.35.25042)


title: Med1_ChIPSeq_D2

source_name: Brown preadipocyte cell_Med1_ChIPSeq

tag: strain background

value: imortalized Pparg-flox/flox brown preadipocytes

value: CRSP1/TRAP220 Antibody

value: Bethyl Laboratories


title: H3K36me3_ChIPSeq_D-3

tag: genotype/variation

value: Proliferating (D-3)


title: si_luc_1


title: Med1_ChIPSeq_D7

tag: cell type

value: Mature adipocytes (D7)


title: EBF2_ChIPSeq_D7

source_name: Brown preadipocyte cell_EBF2_ChIPSeq

tag: stage of adipogenesis

value: Human/Mouse EBF-2 Antibody

value: R&D Systems


title: Med1_ChIPSeq_D0

value: Confluent (D0)

tag: chip antibody


title: EBF2_ChIPSeq_D2

value: Pparg-flox/flox

value: Immature adipocytes (D2)

tag: chip antibody vendor


title: EBF2_ChIPSeq_D-3

tag: chip antibody cat. #


title: si_LARP4B_2


title: si_LARP4B_3


title: Med1_ChIPSeq_D-3

tag: chip antibody lot/batch #


title: si_luc_3


title: CBP_ChIPSeq_D7

value: CBP (D6C5) Rabbit mAb

value: Cell Signaling Technology


title: EBF2_ChIPSeq_D0


title: CBP_ChIPSeq_D2


title: CBP_ChIPSeq_D-3


title: Lung_Sox2-CreER, Kras

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the mouse (mm9) genome with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis
Fragments Per Kilobase of exon per milion mapped reads (FPKM) were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq)
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) annotation (8 to the end) FPKM

source_name: primary lung

extract_protocol:
Primary tissues were isolated from 1-2 month old mice.  Isolated tissues were homogenized with a polytrone in Trizol. The extracted RNA was purified with RNeasy Micro Kit from the homogenates.
RNA library preps were prepared using the Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-zero Gold (cat. no. RS-122-2301). strand specific total RNA-Seq

value: Sox2-CreER, Kras

tag: strain

value: Mixed

tag: tissue

value: primary lung

tag: age

value: 1-2 month


title: Lung_Sox2-CreER, p53fl/+

value: Sox2-CreER, p53fl/+


title: CBP_ChIPSeq_D0

value: imortalized Pparg-flox/flox brown preadipocytes


title: Esophagus_Sox2-CreER, p53fl/+

source_name: primary esophagus

value: primary esophagus


title: Esophagus_Sox2-CreER, Kras


title: Lung_Sox2-CreER


title: Esophagus_Sox2-CreER


title: Stomach_Sox2-CreER, p53fl/+, Kras

source_name: primary forestomach

value: Sox2-CreER, p53fl/+, Kras

value: primary forestomach


title: Stomach_Sox2-CreER, p53fl/+


title: Stomach_Sox2-CreER, Kras


title: Stomach_Sox2-CreER


title: 6_Infected_CD45_P_MMP_P

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: FACS sorted cells

extract_protocol:
Lungs from infected and control uninfected C57BL/6J mice were immersed in cold PBS, cut into small pieces in 5 ml DMEM containing 10% bovine fetal serum (FACS buffer). Cell suspensions were grinded using 1-ml syringe cup on a 70μm cell strainers (BD Falcon). Cells were washed with ice-cold PBS. Remaining red blood cells were lysed using ammonium chloride solution (Sigma). Cells were harvested and immersed in 1ml FACS buffer (PBS+2% FCS, 1mM EDTA). Lung cells were stained with antibodies against multiple surface antigens: PE-conjugated LEM 2/15 (anti-MT1-MMP Ab), PerCP/cy5.5-conjugated anti-mouse CD45 (clone –F11) or Pacific blue-conjugated anti-mouse CD45
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

value: Lung

tag: selection marker

value: CD45 positive

tag: cell population

value: MT1-MMP positive

tag: treatment

value: H1N1 influenza infected


title: 8_Infected_CD45_MMP_P

value: CD45 negative


title: 3_Non_infectded_CD45_MMP_P

value: Naïve


title: 4_Non_infectded_CD45_MMP_P


title: PAO1

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

description: Ribosomal RNA removed.

data_processing:
Alignment (BOWTIE2).
Counts and direct comparison between samples (DESeq).
Genome_build: NC_002516.2
Supplementary_files_format_and_content: CountsRNA6.txt, CountsRNA7.txt: Text files with counts/sample.
Supplementary_files_format_and_content: PseudomonasDESeq.txt: Text file with relative counts between ΔznuA and PAO1.

organism: Pseudomonas aeruginosa PAO1

source_name: Whole cells, WT

growth_protocol: Wild-type PAO1 and the ΔznuA deletion mutant were inoculated at OD600=0.05 from an overnight culture, and grown aerobically to OD600=0.6 in cation-defined media. Three biological replicates were grown on separate days for each strain.

extract_protocol:
Cells were collected and lysed using TRIzol/Chloroform. Subsequent RNA extraction was performed using an Ambion PureLink RNA Isolation kit. RNA was treated with DNase I (Roche) and cleanup on a Ambion PureLink RNA isolation column. Ribosomal RNA was removed using RiboZero Bacterial (Gram-) depletion kit (Illumina). The RNA integrity was assessed on a BioAnalyzer (RIN > 9). Biological replicates were pooled.
Illumina TruSeq Stranded Total RNA LT Sample Prep Kit.

treatment_protocol: All samples were grown in cation-defined media.

tag: strain/background

value: WT

value: whole cells


title: 6_mono_D14PD2

description: processed data in Series supplementary file 20150826_homer.xlsx

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: bowtie2 with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8) from R2 file.
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
20150515_AD.xlsx - Quantifying RNA expression in genes: analyzeRNA.pl rna mm9 -d <tag directory> -count 3utr -norm 1e7 (HOMER)
20150826_exons_homer.xlsx Quantifying RNA expression in genes: analyzeRNA.pl rna mm9 -d <tag directory> -count exons -norm 1e7 (HOMER)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Brain

extract_protocol:
Mice were transcardially perfused with PBS prior to tissue excision. Choroid plexus tissues were isolated under a dissecting microscope (Stemi DV4; Zeiss) from the lateral, third, and fourth ventricles of the brain. Total RNA from the choroid plexus was extracted using the RNA MicroPrep Kit (Zymo Research), and mRNA (1 µg) was converted into cDNA using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science. 3' RNA-seq for digital gene expression quantitation

tag: organ

value: Brain

value: myeloid cells (CD11b+CD45-high)


title: 13_mono_D7PD3


title: 5_mono_D14PD1


title: 12_mono_D7PD2


title: ΔznuA

description: Ribosomal RNA removed.

source_name: Whole cells, ΔznuA

value: delta-znuA


title: 7_mic_D14PD3

value: myeloid cells (CD11b+CD45-low)


title: 11_mono_D7PD1


title: 6_mic_D14PD2


title: Esophagus_Sox2-CreER, p53fl/+, Kras

value: Mixed

value: 1-2 month


title: 13_mic_D7PD3


title: 167-C

city: Exeter

first: Alan

middle: Reid

last: Brown

state: Devon

address: Geoffrey Pope Building, Stocker Road

department: Biosciences

country: United Kingdom

institute: University of Exeter

description: ribosomal-depleted RNA

data_processing:
Paired-end reads were filtered using the fastq-mcf package from the ea-utils suite to remove reads with less than 90% Q20 scores or above and to trim off adaptor sequence.
Tophat v2.0.4 was used to align reads against the reference genome (B. cenocepacia J2315 genome; NC_011001-NC_011003) using Bowtie 1 to remove reads mapping to ERCC spike-in. Abundance of ERCC spike-ins was then checked against predicted values to confirm successful library preparation.
The Bedtools multicov command was used to extract per-gene counts for each gene, and the DESeq suite used to determine statistical significance of differential expression between conditions.
Genome_build: ASM948v1
Supplementary_files_format_and_content: gene_counts.tab; results*txt files (foldChange)

organism: Burkholderia cenocepacia

source_name: Bacterial cells

growth_protocol: Mid log phase cultures in LB broth with or without supplementation with 1.5 mM zinc chloride

extract_protocol:
Total RNA was prepared from mid log-phase cultures using the RiboPure Bacteria Kit (Ambion), and mRNA was enriched by removal of ribosomal RNA using the MICROBExpress kit (Ambion).
Illumina Sequencing libraries were prepared from 50 ng ribosomal-depleted RNA using ScriptSeq v2 with indexing and 15 cycles of PCR amplification using Kapa HiFi DNA polymerase. The amplified libraries were purified using a 1:1 ratio of Ampure XP beads resulting in 45-75nM concentrations and average insert size of 350 bp. Libraries were pooled in equimolar concentrations, denatured and diluted to 6.5 pM before clustering on a cBOT (Illumina).

treatment_protocol: Samples WTZ (A-C) and 167 (A-C) were derived from cultures grown with 1.5 mM zinc chloride

tag: genotype

value: delta-czcRS

tag: culture conditions

value: LB broth + 1.5 mM zinc chloride


title: Lung_Sox2-CreER, p53fl/+, Kras

tag: genotype/variation

value: Sox2-CreER, p53fl/+, Kras

value: primary lung


title: 5_Infected_CD45_P_MMP_P

value: Lung

value: CD45 positive


title: 7_Infected_CD45_MMP_P

value: MT1-MMP positive

value: H1N1 influenza infected


title: 167-A

description: ribosomal-depleted RNA


title: 11_mic_D7PD1


title: WTZ-C

description: ribosomal-depleted RNA

value: Wildtype


title: 12_mic_D7PD2


title: WTZ-B

description: ribosomal-depleted RNA


title: Un-4_M_6

description: processed data in Series supplementary file 20150515_AD.xlsx

source_name: Choroid plexus

value: Choroid plexus

value: whole tissue

value: Untreated


title: Un-3_F_8


title: 167-B

description: ribosomal-depleted RNA


title: WTZ-A

description: ribosomal-depleted RNA


title: Un-1_M_14


title: WTL-B

description: ribosomal-depleted RNA

value: LB broth


title: Un-2_M_14


title: WTL-A

description: ribosomal-depleted RNA


title: IgG-5_F_6

value: IgG control


title: IgG-4_F_7


title: 0714-B

data_processing:
Paired-end reads were filtered using the fastq-mcf package from the ea-utils suite to remove reads with less than 90% Q20 scores or above and to trim off adaptor sequence.
Reads were  aligned to the reference genome (Burkholderia_cenocepacia_J2315_uid57953; NC_011001-NC_011003) using BWA (0.5.9) and converted to BAM format using Samtools. Potential PCR duplicates were removed using the samtools rmdup command.
The MACS package (v1.4) was used to compare and contrast the control and sample data using the –call-subpeaks and –w options
Genome_build: ASM948v1

growth_protocol: Overnight cultures in tryptone soya broth (TSB)

extract_protocol:
Formaldehyde (1%) was added to overnight cultures and placed at room temperature for 15 min, before quenching the reaction with glycine (125 mm) for 5 min. Cells were subsequently lysed in 0.5 ml of lysis solution (10 mM Tris, pH 8.0, 50 mM NaCl, 10 mM EDTA, 20 % sucrose, 10 mg/ml lysozyme) and 0.5 ml of 2× RIPA solution (100 mM Tris, pH 8.0, 300 mM NaCl, 2 % Nonidet P-40, 1 % sodium deoxycholate, 0.2 % SDS). The cell extract was sonicated to fragment DNA to an average size of 500 bp. A 400 μl aliquot of the extract was incubated with 4 μl of monoclonal anti-FLAG M2 antibody (Sigma-Aldrich) at 4°C for 4 h, following which the extract was incubated with EZview Red Protein G Affinity Gel (Sigma-Aldrich) for 1 h at 4 °C. Beads were washed twice with 1× RIPA solution, then twice with LiCl/detergent solution (10 mM Tris, pH 8.0, 250 mm LiCl, 1 mM EDTA, 0.5 % Nonidet P-40, 0.5 % sodium deoxycholate), and finally with TE buffer. The immunoprecipitated material was eluted with 100 μl of elution buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 1 % SDS). Cross-linking of immunoprecipitated DNA was reversed by incubation at 65°C overnight. After Proteinase K treatment, the immunoprecipitated DNA was purified using CTAB extraction, precipitated with ethanol, and resuspended in TE buffer.
Illumina sequencing libraries were prepared from immunoprecipitated DNA using the Nextflex ChIPseq protocol (Bio Scientific) with indexed adapters. Libraries were amplified by 18 cycles PCR, purified using 0.8 volumes Ampure XP beads (Beckman Coulter) and quantified with a Bioanalyzer 7500 assay (Agilent). Libraries were pooled in equimolar concentrations, denatured and diluted to 6.5 pM, clustered  on a flowcell using a cBOT (Illumina) and sequenced on a HiSeq2000 (Illumina).

treatment_protocol: Sample 0714-B was grown in the presence of 1.5 mM zinc chloride

value: TSB + 1.5 mM zinc chloride

value: monoclonal anti-FLAG M2 antibody (Sigma-Aldrich, catalog# F1804, lot# 080M6035)


title: IgG-2_M_14


title: IgG-1_M_14


title: IgG-3_F_10


title: PD1-5_F_6


title: MBA4_MCA_2

city: Hong Kong

first: Jimmy

last: Tsang

address: Pokfulam Road

department: Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Casava1.7 was used for base calling
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and filtered on length, using CLC Genomic Workbench 8.0.2 with defacult setting.
After trimming and filtering, intact paired-end reads were mapped to  B. caribensis MBA4 de novo assembled whole genome using CLC Genomic Workbench 8.0.2 with parameters: map to gene regions only, default alignment parameters, maximum number of hits for a read: 1.
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated as gene's expression valules.
Genome_build: Burkholderia caribensis MBA4 de novo assembled genome. NCBI accession no.: AXDD00000000
Supplementary_files_format_and_content: tab-delimited text files include gene IDs, numbers of reads mapped to genes, RPKM values for each Sample .

organism: Paraburkholderia caribensis

source_name: monochloroacetate-grown cells

growth_protocol: Bacterial cells were cultivated in defined minimal medium with 0.5 g carbon per litre of MCA, glycolate or pyruvate. The cultures were incubated at 30 °C with shaking.

extract_protocol:
Total RNA was extracted using RNAspin Mini kit from GE Healthcare. Ribosomal RNA were removed by bacterial mRNA enrichment kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: log phase

tag: carbon source

value: MCA


title: MBA4_Glc_2

source_name: glycolate-grown cells

value: Glycolate


title: 5_mic_D14PD1

value: Brain

value: myeloid cells (CD11b+CD45-low)


title: PD1-4_F_10


title: PD1-2_M_14


title: WTL-C

description: ribosomal-depleted RNA


title: MBA_Pyr

data_processing:
Casava1.7 was used for base calling
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and filtered on length, using CLC Genomic Workbench 8.0.2 with defacult setting.
After trimming and filtering, intact paired-end reads were mapped to  B. caribensis MBA4 de novo assembled whole genome using CLC Genomic Workbench 8.0.2 with parameters: map to gene regions only, default alignment parameters, maximum number of hits for a read: 1.
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated as gene's expression valules. Normalization of gene's expression valules in three samples were performed using CLC Genomic Workbench 8.0.2 with the normalization method: quantile.
Genome_build: Burkholderia caribensis MBA4 de novo assembled genome. NCBI accession no.: AXDD00000000
Supplementary_files_format_and_content: tab-delimited text files include gene IDs, numbers of reads mapped to genes, RPKM values and  normalized RPKM values for each Sample .

source_name: pyruvate-grown cells

value: pyruvate


title: MBA4_MCA


title: PD1-3_F_10


title: Wild type effector Tregs rep2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Immunoglobulin genes, T-cell receptor genes and genes located on Y chromosome were excluded from analysis. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Empirical Bayes moderated-t P values were adjusted to control the global false discovery rate (FDR) across all comparisons with the ‘global’ option of the limma package. Genes were called differentially expressed if they achieved a FDR of 0.05 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for genes. Raw counts are available on the series record.

source_name: Spleen and lymph node

extract_protocol:
Treg cells were sorted from pooled spleens and peripheral lymph nodes (not including the mesLN) of healthy adult and age matched Myb+/+FoxP3YFP-Cre/YFP-Cre wild type and Mybfl/flFoxP3YFP-Cre/+ mosaic females. Cell suspensions were depleted of CD8 (53-6.7) and CD19 (1D3)-biotin labeled cells using streptavidin magnetic microbeads (Miltenyi), following the manufacturer instructions. Cells were incubated with anti-FcγR for 10 min on ice, stained with CD4-pacific blue, TCRβ-APC, CD62L-PE, ICOS-PECy7, TIGIT-PerCPeFluor710 and Sytox Blue. Sorted cells were collected in PBS with 50% FCS, washed twice in PBS, resuspended in RLT buffer (Qiagen) with β-Mercaptoethanol (Sigma), and kept at -80ºC. RNA was isolated independently from two biological replicates (each replicate being a pool of up to 4 independent sorts) with RNeasyPlus Mini kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

value: Spleen and lymph node

tag: cell type

value: Regulatory T cells (Treg)

value: wild type effector


title: Wild type effector Tregs rep1


title: Wild type activated Tregs rep1

value: wild type activated


title: PD1-1_M_14

value: Choroid plexus


title: Wild type naive Tregs rep2

value: wild type naive


title: Wild type naive Tregs rep1


title: Myb knockout naive Tregs rep1

value: Myb-/- naive


title: Myb knockout naive Tregs rep2


title: 8dA(T3)

city: Utrecht

first: Wieke

middle: R

last: Teertstra

address: Padualaan 8

department: Science, Biology

country: Netherlands

institute: Utrecht University

data_processing:
Illumina Casava pipeline version 1.8.3 was used for base calling
The RNA-Seq pipeline used the TRIMMOMATIC read trimmer version 0.32 (Bolger et al., 2014) to remove low quality regions and the Illumina adapters from the reads
The program Cuffdiff (version 2.2.1), which is part of Cufflinks (Trapnell et al. 2010), was used to identify reads overlapping with the predicted genes and to identify differentially expressed genes.
Genome_build: http://genome.jgi.doe.gov/Aspni7/Aspni7.home.html
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Aspergillus niger

source_name: conidia

growth_protocol: Aspergillus niger strain N402  was grown at 30 °C on 20 ml minimal medium with 2 % glucose and 1.5 % agar.

extract_protocol:
Frozen conidia in Saline/tween were homogenized in a stainless steel grinding jar using a TissueLyser II (Qiagen, www.qiagen.com). RNA was isolated using a combination of the maxi RNeasy kit (Qiagen RNeasy; www.qiagen.com), the Master Pure Yeast RNA purification kit (Epicentre, www.epibio.com) and the mini RNeasy kit (Qiagen RNeasy; www.qiagen.com) (van Leeuwen et al., 2012).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Conidia were harvested in 0.8 % NaCl, 0.005 %  Tween-80. Pelleted conidia were frozen in liquid N2

tag: developmental stage

value: 8 day maturation on the conidiophore


title: 5dC(T2)

value: 5 day maturation on the conidiophore


title: 2dC(T1)

value: 2 day maturation on the conidiophore


title: Myb knockout activated Tregs rep2

value: Myb-/- activated


title: Myb knockout activated Tregs rep1


title: MBA4_Glc

value: log phase


title: 2dA(T1)


title: WtSt3

city: Kgs. Lyngby

first: Klara

last: Bojanovic

address: Building 220, Kemitorvet

department: Novo Nordisk Foundation Center for Biosustainability

country: Denmark

institute: Technical University of Denmark

description: 9 C

data_processing:
The RNA-seq data was trimmed by Beckman
RNA-seq data was analysed with open source software Rockhopper (version 2.0.3) (McClure et al., 2013)
Differential gene and sRNA expression analysis were carried out with the webserver T-REx (de Jong et al., 2015) using the RPKM values generated in the Rockhopper analysis. Differential expression of genes was considered significant with a fold change ≥ 2 and adjusted p-value ≤ 0.05
Genome_build: GenBank accession no. NC_002947.3
Supplementary_files_format_and_content: One file with all the processed results in excel: Raw counts, Normalized counts, RPKM, Expression values, q-values

organism: Pseudomonas putida

source_name: Bacteria

growth_protocol: P. putida KT2440 was grown at 30 °C, 250 rpm and routinely cultured in LB medium according to standard protocols

extract_protocol:
RNA extraction for cDNA library KB1 preparations was performed as previously described (Gómez-Lozano et al., 2012). Briefly, 10 ml of harvested culture was mixed with 0.2 volumes of STOP solution (95% [v/v] ethanol, 5% [v/v] phenol). Cells were centrifuged, 1 mL of Trizol (Invitrogen) was added and the samples were snap frozen. Total RNA was extracted and treated with DNase I (Fermentas). Total RNA integrity and quality were validated by Bioanalyzer (Agilent).
For KB1 cDNA library, RNA was size-selected (up to 500 nt) as described previously (Gómez-Lozano et al., 2012) using 10% polyacrylamide-urea gels containing urea (Bio-Rad) with some changes. Sample was depleted of rRNA using MICROBExpress Kit (Ambion) and treated with Tobacco Acid Pyrophosphatase TAP (Epicentre). Following the fragmentation with RNaseIII, libraries were prepared using TruSeq Small RNA Sample Preparation Kit (Illumina).

treatment_protocol: For all experiments the overnight culture of P. putida was diluted to starting OD600 0.1 in 100 ml of LB. Cells were harvested at three time points on the growth curve: mid-exponential (OD600~0.5), transition (OD600~2.5), and stationary phase (twice doubling time after the transition phase). For size-selected library KB1 three biological replicates of wt and Δhfq strains were grown.

tag: strain/genotype

value: stationary


title: WtTran3

description: 9 B

value: transition


title: bd1bd2mut_8h_3

city: Grenoble

first: Encar

middle: García

last: Oliver

address: 17, avenue des Martyrs

institute: INSERM

data_processing:
Reads were quality-checked using FastQC before and after cleaning by Trimmomatic applying default parameters (Bolger et al., 2014).
Reads were then aligned to S. cerevisiae S288c genome (Ensembl R64.1.1) using Bowtie2 (Langmead and Salzberg, 2012).
Raw read counts for each gene were calculated using HTSeqCount (Anders et al., 2015).
Read count data were analyzed using standard differential analysis pipeline proposed by the DESeq2 R-package.
Genome_build: Saccharomyces_cerevisiae.R64-1-1.82.gtf
Supplementary_files_format_and_content: Tab-delimited text files. Include raw read counts for each gene calculated using HTSeqCount

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Diploid yeast strains with the SK1 genetic background (wild-type and bdf1-Y187F-Y354F) were grown to an OD600of 0.5 in YPD. Cells were washed and resuspended in YPA at an OD600of 0.03. After 12 h cells were collected (time-point 0) or washed and transferred into sporulation media (K acetate 2%) supplemented with auxotrophic amino acids at OD600 reached 2. The second and third sporulation time-points were collected after 4 and 8 hours respectively. Sporulation efficiency was generally assessed after 24 h of induction and is defined by the number of original cells that formed tetrads, and is usually >98% in a wild-type SK1 background.

extract_protocol:
Samples were collected from sporulating cells (wild-type andbdf1-Y187F-Y354F mutant) at 0 (YPA), 4 and 8 h. Cell pellets were washed and stored at -80 ºC. Total RNA was extracted from three independent biological replicates by phenol:chloroform extraction (Ref. 2190191). RNA integrity and purity were determined using the Agilent 2100 Bioanalyzer (2100, Agilent Technologies, CA). DNaseI treatment (Thermo, ref. AM2222) was performed using 1 µg of total RNA and RNAs were purified by phenol:chloroform extraction. Afther this, the intact poly(A)+ RNA was isolated by using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S).
cDNA libraries were constructed from 10 ng of total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, ref. E7530S). Fragments were enriched by 15 cycles of PCR amplification. During the quality-control step, the Agilent 2100 Bioanalyzer (2100, Agilent Technologies, CA) was used to qualify and quantify the sample library. Eighteen barcoded cDNA libraries were pooled and sequenced on an Illumina HiSeqTM 2000, generating 5-8 million single reads for each sample.

value: bdf1-Y187F-Y354F mutant

tag: time-point after sporulation induction (h)

tag: replicate


title: Wild type activated Tregs rep2

tag: strain

tag: tissue


title: WTA

value: Wildtype

value: TSB

tag: chip antibody

value: monoclonal anti-FLAG M2 antibody (Sigma-Aldrich, catalog# F1804, lot# 080M6035)


title: 8dC(T3)


title: bd1bd2mut_4h_3


title: WtEx3

description: 9 A

value: exponential


title: bd1bd2mut_0h_3


title: Sc_WT_8h_3

value: Wild-type


title: WtTran2

description: 8 B


title: WtSt2

description: 8 C


title: WtEx2

description: 8 A


title: 5dA(T2)


title: Sc_WT_0h_3


title: bd1bd2mut_8h_2


title: WtSt1

description: 7 C


title: WtEx1

description: 7 A


title: bd1bd2mut_4h_2


title: WtTran1

description: 7 B


title: bd1bd2mut_0h_2


title: HfqSt3

description: 6 C

value: KT2440 Δhfq


title: Sc_WT_8h_2


title: HfqEx3

description: 6 A


title: Sc_WT_4h_2


title: bd1bd2mut_8h_1


title: Sc_WT_0h_2


title: bd1bd2mut_0h_1


title: HfqSt1

description: 4 C


title: HfqSt2

description: 5 C


title: HfqTran3

description: 6 B


title: bd1bd2mut_4h_1


title: Sc_WT_8h_1


title: HfqEx2

description: 5 A


title: HfqEx1

description: 4 A


title: Sc_WT_0h_1


title: HfqTran1

description: 4 B


title: Sc_WT_4h_3


title: Sc_WT_4h_1


title: HfqTran2

description: 5 B


title: total_RNA_0

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

data_processing:
Data was preprocessed using the fastx package
Fastq files were split by barcode using pyBarcodeFilter.py in the pyCRAC package (Webb, et al, 2014). -m 0
Reads were aligned to the genome using Novoalign. -r Random
Reads were counted using pyReadCounter. --sense
Sequences were plotted along the genome using pyGTF2bedgraph
Genome_build: EF4.68
Supplementary_files_format_and_content: bedgraph or bigwig files showing the distribution of reads across the yeast genome

source_name: total RNA 0

growth_protocol: Yeast cells were grown in SD -TRP media containing 2% glucose overnight and inoculated into fresh media at a starting OD600 of 0.05. Cells were grown for about 7 hours (until OD600=0.5) and either UV crosslinked (0 timepoint) or filtered and transferred to SD -TRP containing 2% glycerol and ethanol instead of glucose. Cells were UV crosslinked 4 or 8 minutes later.

extract_protocol:
Hot phenol RNA extraction followed by rRNA depletion using the RiboZero kit (Epicentre)
RNA libraries were prepared using standard Illumina protocols

tag: sample type

value: poly(A) RNA


title: Mtr4_8_replicate1

description: Barcode: NNNCGCTTAGC

data_processing:
Data was preprocessed using the fastx package. All sequences are of the form:
5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNXXXXXX==INSERT==TGGAATTCTCGGGTGCCAAGGCCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG-3’
where NNN are random nucleotides to assess for duplicates in PCR amplification and XXXXXX is a barcode to allow for multiplexing of different libraries. The barcode used for each sample is listed in the 'description' field.
Fastq files were split by barcode using pyBarcodeFilter.py in the pyCRAC package (Webb, et al, 2014). -m 0
Reads were aligned to the genome using Novoalign. -r Random
Reads were counted using pyReadCounter. --sense
Sequences were plotted along the genome using pyGTF2bedgraph
Genome_build: EF4.68
Supplementary_files_format_and_content: bedgraph or bigwig files showing the distribution of reads across the yeast genome

source_name: Mtr4 8

extract_protocol:
Cells were lysed, followed by stringent, denaturing, two-step affinity purification of the tagged protein. Bound RNA was partially degraded with RNase, radiolabeled, and 5’ and 3’ linkers were added. Finally, covalent RNA-protein complexes were isolated by SDS-PAGE. Following Proteinase K digestion of the bound proteins, RNA fragments were amplified by RT-PCR.
RNA libraries were prepared using the standard CRAC protocol (Tuck and Tollervey, 2013)

value: crosslinked RNA


title: Mtr4_8_replicate2

description: Barcode: NNNCACTAGC


title: Mtr4_4_replicate2

description: Barcode: NNNTCTCTAGC

source_name: Mtr4 4


title: total_RNA_8

source_name: total RNA 8


title: Mtr4_0_replicate1

description: Barcode: NNNATTAGC

source_name: Mtr4 0


title: Mtr4_4_replicate1

description: Barcode: NNNGCGCAGC


title: Nab3_8_replicate1

description: Barcode: NNNTGGAGC

source_name: Nab3 8


title: Nab3_0_replicate2

description: Barcode: NNNTAAGC

source_name: Nab3 0


title: Nab3_0_replicate1

description: Barcode: NNNCTAGC


title: Rpo21_0_replicate2

description: Barcode: NNNATTAGC

source_name: Rpo21 0


title: Rpo21_0_replicate1

description: Barcode: NNNCACTAGC


title: Rpo21_8_replicate1

description: Barcode: NNNTCTCTAGC

source_name: Rpo21 8


title: Rpo21_8_replicate2

description: Barcode: NNNGCGCAGC


title: chow-fed_rat_rep3

city: Solna

first: Wenjing

last: Kang

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

data_processing:
Base calling and quality score calculation was performed from raw intensities using Illumina’s pipeline version 1.8.1.
The low-quality reads were removed by fastx_artifacts_filter. Adapters were clipped using the AdRec.jar program from the Seqbuster suite with following options: java -jar AdRec.jar 1 8 0.3. Reads shorter than 18 nucleotides were discarded.
The clade-specific miRNA reference sequences were extracted from miRBase v21 based on a previous curated clade-specific miRNA family list (Sempere et al. 2006; Wheeler et al. 2009; Taylor et al. 2014). The read was identified as clade-specific miRNA if its first 20 nt are matched to the first 20 nt of the reference sequences.
Supplementary_files_format_and_content: tab-delimited text file includes clade-specific miRNA family counts for each sample

organism: Rattus norvegicus

source_name: Serum

extract_protocol:
The total RNA were extracted using the Qiagen miRNeasy® Mini Kit (Qiagen, Hilden, Germany)
Extracted total serum RNA from the two different animal models was concentrated in a speedvac to a final volume of 10 µl. From this 5µl was used as input in the libraries, which were prepared accordingly with TruSeq Small RNA Sample Preparation kit (Illumina). There was made one modification to the Illumina protocol, since we increased the number of PCR cycles from 11 to 16 for total RNA with a 1 µg as starting material. Additionally, we applied TruSeq SR Cluster Kit v3 for cluster generation and furthermore for sequencing TruSeq SBS Kit v3 was applied.

value: Serum

tag: diet

value: chow


title: chow-fed_rat_rep1


title: Mtr4_0_replicate2

description: Barcode: NNNCACTAGC


title: total_RNA_16

source_name: total RNA 16


title: rice-fed_rat_rep3

value: rice


title: chow-fed_rat_rep2


title: rice-fed_rat_rep2


title: Input DNA

city: Moscow

first: Evgeny

middle: Sergeevich

last: Gerasimov

address: Leninskie gori, 1, 12

department: Biological

country: Russia

institute: Lomonosov Moscow State University

data_processing:
Reads were trimmed with Trimmomatic for quality and adapter sequences
Trimmed reads were mapped on reference genome (danRer10) with bowtie2 (v10) with --end-to-end --very-sensitive options, produced alignments were converted into bam files using samtools (v0.18)
Regions of acetylation were determined using paek calling with MACS2 (--broad, -B -q 0.05) and with our domain calling algorithm implemented as python script
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: .gff with called acetylation domain boundaries

organism: Danio rerio

source_name: erythrocyte

growth_protocol: The blood from adult fishes and larvaes was collected into red cell isolation buffer (0.14 M NaCl, 20 mM HEPES pH 8.0, 5 % fetal bovine serum, and 100 U heparin/mL). For each ChIP, a minimum of 107 cells were used.

extract_protocol:
Lysates were clarified from micrococcal nuclease treated erythrocytes nuclei and histone-DNA complexes were isolated with antibody.
The ChIP-seq libraries were prepared with the Hyper Library Construction Kit (Kapa Biosystems) according to the manufacturer's protocol. The libraries were pooled in equimolar concentration, quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq2500 using a HiSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina). As a result 210705238 reads were obtained and used in the downstream analysis.

value: blood


title: potato-fed_rat_rep2

value: potatoes


title: rice-fed_rat_rep1


title: potato-fed_rat_rep1


title: potato-fed_rat_rep3


title: H3PanAc_Embr_ChIP

tag: age

value: 18 days


title: Nab3_8_replicate2

description: Barcode: NNNCTAGC


title: Ncrassa_CHAP-Dam_DamID-seq

city: Portland

first: Michael

last: Rountree

state: OR

address: 3429 NE Sandy Blvd. #330

institute: Nzumbe, Inc.

description: genomic DNA purified from a CHAP-Dam expressing strain

data_processing:
Library strategy: DamID-Seq
raw data .fastq files were mapped to the Ncrassa12 genome using Bowtie2, generating .sam files
using samtools, .sam files were converted to .bam files, duplicates were removed (rmdup), and the .bam file was sorted
the sorted .bam file was indexed, and then used for building the .tdf file on igvtools
Genome_build: Neurospora crassa version12
Supplementary_files_format_and_content: tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011)

organism: Neurospora crassa

source_name: mycelium

extract_protocol:
Whole-genome DamID-seq was performed using a procedure adapted from (Zhou, V.W., 2012)(48). Briefly, genomic DNA from the Dam-tagged CHAP strain was digested with DpnI. Digested DNA was ligated to adapters and amplified using a biotin-tagged primer. The amplified DNA was fragmented by sonication to 100-500 bp products and purified using streptavidin conjugated beads (Sigma). Bound DNA was eluted using a DpnII digestion.
Purified DNA was prepared for sequencing using Illumina TruSeq ChIP-Seq Sample Prep Kit.

tag: growth medium

value: 1xVogels, 1.5% sucrose

tag: growth time

value: 48 hrs.

tag: experiment


title: Ncrassa_N’CHAP_DNAaffinity

description: affinity purified DNA

data_processing:
raw data .fastq files were mapped to the Ncrassa12 genome using Bowtie2, generating .sam files
using samtools, .sam files were converted to .bam files, duplicates were removed (rmdup), and the .bam file was sorted
the sorted .bam file was indexed, and then used for building the .tdf file on igvtools
Genome_build: Neurospora crassa version12
Supplementary_files_format_and_content: tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011)

source_name: in vitro recombinant MBP-N’CHAP

extract_protocol:
Amylose resin (NEB) containing immobilized MBP-CHAP was incubated with sonicated wild-type genomic DNA (~250 bp fragments) in binding buffer [20 mM HEPES (pH 7.5), 80 mM NaCl, 37.5 mM Imadazole, 0.7 mM MgCl2, 0.35 mM EDTA, 0.7 mM DTT and 17.8% glycerol] for 2 h at 4 degrees. Beads were washed 6 times with 1 ml of wash buffer [10 mM Tris (pH 7.5), 50 mM NaCl, 1 mM MgCl2, 0.5 mM EDTA and 4% glycerol]. Following washes, DNA was eluted with TES [20 mM Tris (pH 8.0), 10 mM EDTA and 1% SDS] by heating for 10 min at 65 degrees. Eluted samples were treated with proteinase K and DNA was purified with MinElute columns (Qiagen).
Purified DNA was prepared for sequencing using Illumina TruSeq ChIP-Seq Sample Prep Kit.


title: Ncrassa_cdp-2_BSseq

data_processing:
The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping.
BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged.
The average 5mC level was determined for 500bp step-wise window size across the genome using the Methpipe program (http://smithlabresearch.org/software/methpipe/).
The resulting file was renamed with a “.igv” file extension to allow display on the Integrated Genome Viewer (IGV; www.broadinstitute.org/igv/)
Genome_build: NC12
Supplementary_files_format_and_content: .igv files displaying the % methylation over 500bp windows where a score of 0 is a DNA region that has no cytosine methylation and a score of 1.0 is DNA where all of the cytosines are methylated in the region.  Values in between 0 and 1.0 represent partial methylation of a region.

growth_protocol: grown in 1xVogels medium + 1.5% sucrose for 48 hours on a rocking shaker at 32oC

extract_protocol:
Genomic DNA was isolated using a protocol modified from (Oakley et al, 1987).  Genomic DNA (50ng) was treated with bisulfite using the EZ DNA Methylation LightningTM kit (ZYMO Research) per the manufacturer's protocol.
Bisulfite-Seq Libraries were prepared for sequencing using the EpiGnomeTM Methyl-Seq Kit (Epicentre cat #EGMK91324) and EpiGnomeTM Index PCR Primers (Epicentre cat#  EGIDX81312), the library was purified with Agencourt AMPure XP beads (Beckman Coulter), quantified using a Qubit HS Assay (Life Technologies), visualized on the Fragment AnalyzerTM (Advanced Analytical), and sequenced on a Illumina HiSeq 2000

tag: genotype/variation


title: Ncrassa_hpo_BSseq

value: hpo


title: Ncrassa_chap_BSseq

value: chap


title: Ncrassa_hda-1_BSseq


title: Ncrassa_WT_BSseq

value: WT


title: Tick19

city: Addlestone

first: Richard

last: Ellis

address: APHA Weybridge

institute: Animal and Plant Health Agency

data_processing:
Basecalling with CASAVA v1.8
Alignment using BowTie2
Identification of splice junctions using TopHat2
Estimation of gene abundance and differential gene expression using Cufflinks.
Normalization of biological replicates using Cuffmerge
Estimation of abundance across normalized samples using Cuffquant.
Identification of differentially expressed genes using Cuffdiff.
Genome_build: JCVI_ISG_i3_1.0
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for all Samples

organism: Ixodes ricinus

source_name: cultured cells

growth_protocol: IRE/CTVM20 cells were maintained in a 1:1 mixture of L-15 (Leibovitz) medium and L-15B medium.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen), according to the manufacturer's protocol, and further purified using the Rneasy Mini kit (Qiagen). Ribosomal RNA was depleted using Terminator Exonuclease (Epicentre).
Double stranded cDNA synthesis using Roche cDNA Synthesis System.  Illumina library construction using NexteraXT kit

treatment_protocol: Tick cells were infected with Louping ill virus (LI3/1 strain) or tick-borne encephalitis virus (Neudorfl H2J strain), and cells/supernatant sampled at 7 post-infection. Mock infected (uninfected) cells/supernatant were sampled at day 0.

tag: time point

tag: agent

value: Tick-borne encephalitis virus infected


title: Tick20


title: RPMI8226_MCL1_CD28

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
mRNA-seq
Processed data file: diff.geneFpkm.exon.glm.LogFc.0.exc.Gapdh.RPMI8226_MCL1.txt

data_processing:
RNA-seq data was mapped back to the UCSC human genome hg19 using Tophat2 (v.2.0.13) with the following parameters "-p 8 -N2 -max-multihits 1 -read-gap-length 1" and the UCSC Known Genes hg19 transcript file as a guide.
PCR duplicates were determined using Picard (http://broadinstitute.github.io/picard/) and removed from subsequent analyses.
Reads that uniquely overlapped hg19 exons were determined in R (v.3.2.2) using the 'summarizeOverlaps' function in mode 'IntersectionNotEmpty' of the 'GenomicAlignments' package (v.1.6.3).
Reads per million (RPM) were calculated for each gene based on the number reads in all potential exons for a given gene and the total number of uniquely mappable reads per sample.
Fragments per kilobase per million (FPKM) were calculated based on RPM and the total size of non-overlapping exons for a gene.
Differentially expressed genes were determined with EdgeR (v.3.12.1) where an FDR less than 0.01 was considered significant.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: diff.geneFpkm.exon.glm.LogFc.0.exc.Gapdh.RPMI8226_MCL1.txt: Tab-delimited text file includes normalized read counts (that map to exons) expressed in fragments per kilobase per million (FPKM) for UCSC mm9 KnownGenes, and a summary of differential statistics, not including the RPMI8226 overexpressing Mcl1.

source_name: RPMI8226 cells overexpressing Mcl1, CD28 shRNA

extract_protocol:
RNA was isolated using the Qiagen RNeasy kit following the manufacturer's instructions.
1 mg of RNA was sent to Hudson Alpha for RNA-seq library construction using the Illumina TruSeq mRNA protocol.

treatment_protocol: The myeloma cell lines were transfected with short hairpin RNAs targeting CD28, CD86, Gapdh (control), or empty vector (pLK0.1)

tag: cell line

tag: cell type

value: myeloma cell line

tag: shRNA

tag: overexpression


title: RPMI8226_MCL1_CD86

source_name: RPMI8226 cells overexpressing Mcl1, CD86 shRNA


title: Tick04

value: Uninfected


title: RPMI8226_MCL1_Vec

source_name: RPMI8226 cells overexpressing Mcl1, Vec shRNA

value: Vec


title: Tick17

value: Louping ill virus infected


title: KMS18_CD28

source_name: KMS18 cells, CD28 shRNA


title: KMS18_CD86

source_name: KMS18 cells, CD86 shRNA


title: Tick03


title: RPMI8226_MCL1_Gapdh

source_name: RPMI8226 cells overexpressing Mcl1, Gapdh shRNA

value: Gapdh


title: Tick02

data_processing:
Basecalling with CASAVA v1.8
Alignment using BowTie2
Identification of splice junctions using TopHat2
Estimation of gene abundance and differential gene expression using Cufflinks.
Normalization of biological replicates using Cuffmerge
Estimation of abundance across normalized samples using Cuffquant.
Identification of differentially expressed genes using Cuffdiff.
Genome_build: Ixodes scapularis 1.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cell culture

growth_protocol: IRE/CTVM20 cells were maintained in a 1:1 mixture of L-15 (Leibovitz) medium and L-15B medium, and ISE6 cells were maintained in L-15B300 medium.

treatment_protocol: Tick cells were infected with Anaplasma phagocytophilum (NY18 human strain), and cells/supernatant sampled at 7 post-infection. Mock infected (uninfected) cells/supernatant were sampled at day 0.

tag: time

tag: infection status


title: Tick15

value: Anaplasma phagocytophilum infected


title: KMS18_Vec

source_name: KMS18 cells, Vec shRNA


title: RPMI8226_CD86

source_name: RPMI8226 cells, CD86 shRNA


title: H3PanAc_Adult_ChIP

value: >20 days

tag: tissue


title: KMS18_Gapdh

source_name: KMS18 cells, Gapdh shRNA


title: RPMI8226_CD28

source_name: RPMI8226 cells, CD28 shRNA


title: cow-milk-fed_pig_rep3

organism: Sus scrofa

source_name: Serum

value: Serum

value: cow milk


title: cow-milk-fed_pig_rep1


title: RPMI8226_Vec

source_name: RPMI8226 cells, Vec shRNA


title: MM1S_CD86

source_name: MM.1s cells, CD86 shRNA


title: maize-fed_pig_rep3

value: maize


title: Tick18


title: maize-fed_pig_rep2


title: MM1S_CD28

source_name: MM.1s cells, CD28 shRNA


title: Tick16


title: MM1S_Gapdh

source_name: MM.1s cells, Gapdh shRNA


title: maize-fed_pig_rep1


title: Anti-TERT_VA13_Replicate 2

city: Singapore

first: Vinay

last: Tergaonkar

address: 61, Biopolis Drive

department: IMCB

country: Singapore

institute: A*STAR

description:
antibody: TERT (abcam, ab32020, Lot YI021602CR)
Chipped DNA

data_processing:
Reads from cell lines were mapped to the hg19 genome using bowtie (version. 2.2.3) keeping uniquely aligned reads
Replicate bam files were merged using Samtools
PCR duplicates were removed from merged file and sorted indexed files were used for peak calling using MACS (version 2.1.10) with default parameters using q value of 0.05 to identified significantly enriched region/ peaks compared to input control sample
Coverage file for read density visualization is created using deepTools software and normalize to 1x options for normalization of read coverage across the sequencing libraries
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig (.bw) for read density visualization is created using deepTools software and normalize to 1x options for normalization of read coverage across the sequencing libraries.

source_name: transformed lung fibroblasts, TERT negative

growth_protocol: VA13  cells were grown in DMEM medium.  All cells were cultured at 37 degree celcius with 5% Carbon dioxide.

extract_protocol:
Lysates were clarified from sonicated nuclei and TERT-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the NEB NEXT ULTRA ILLUMINA Library preparation kit (E7370L).

treatment_protocol: All the cells were fixed in medium  Cells were fixed directly in growth medium with 1% formaldehyde for 10 minutes at room temprature with shaking.


title: Tick01


title: gastrulating epiblast day 12-13 embryos rep3

city: Frederiksberg

first: Kristine

middle: Karla

last: Freude

address: Groennegardsvej

institute: University Copenhagen

data_processing:
Sequenced reads were trimmed for adaptor sequence, poly A/T tails and low-quality then filtered for low-complexity and for minimum read length (50 bp).
Pre-processed reads were mapped to Sscrofa10.2 with STAR (setting default parameters and allowing for maximum 5 mismatches).
Reads mapped to each gene (Ensembl Sus Scrofa 10.2.75) were counted with HTSeq-count
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files includes read counts for each Ensembl gene ID

source_name: Gastrulating epiblast from day 12-13 embryos

growth_protocol: piPSC were grown in DMEMF12, 20% KOSR, 2i with either LIF or FGF (Secher et al., 2016)

extract_protocol:
iPSC RNA was isolated with RNAeasy micro kits from Qiagen and
embryonic RNA was isolated using TriZol and the PureLink™ RNA Micro Kit (Invitrogen)
iPSC: After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes).  Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates.
embryonic material: RiboZero kit (EpiBio, Medison USA) was used to deplete for ribosomal RNA, and hexamers for priming the reverse transcription, followed by regular sample preparation for sequencing.

treatment_protocol: ICM for porcine embryos 7-8 were isolated by immunosurgery. Porcine embryo day 10-11 epiblast and day 12-13 embryonic disc were manually isolated.


title: VA13 INPUT

description:
antibody: none
genomic DNA


title: porcine epiblast day 10-11 embryos rep3

source_name: Epiblast from day 10-11 embryos

value: Epiblast from day 10-11 embryos


title: MM1S_Vec

source_name: MM.1s cells, Vec shRNA


title: gastrulating epiblast day 12-13 embryos rep2

value: Gastrulating epiblast from day 12-13 embryos


title: porcine epiblast day 10-11 embryos rep2


title: RNA Pol II ChIP on A771726-treated cells.

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph pileup from MACS 2.0 output

source_name: A375 melanoma cell line

growth_protocol: Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).

extract_protocol:
DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp.  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: One hundred million A375 cells per condition were treated with DMSO or 25 μM A771726.  Drugs used were DMSO (Sigma) and A771726 (Enzo Life Sciences) After a 48 hr treatment, cells were washed, proteins and DNA were cross-linked with 11% formaldehyde and cell pellets were frozen down at -80C.

tag: treatment


title: RNA Pol II ChIP on DMSO-treated cells.

value: DMSO


title: HEXIM1 ChIP on A771726-treated cells.


title: cow-milk-fed_pig_rep2