title: reactivated_mTr_rep1 (Sample 61)

description: YFP+ Treg cells were isolated from bone marrow chimeric mice 60 days post-diphtheria toxin treatment and transferred into lymphopenic recipients together with activated effector CD4 T cells and GFP+YFP- resting Treg cells. YFP+ Reactivated Treg cells were isolated 14 days later for RNA-seq

value: Reactivated mTr cells

value: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow

value: Transfer into lymphopenic mice in presence of activated effector T cells

value: 14 days


title: aTr_primary_activation_rep1 (Sample 58)

status: Public on Aug 04 2016

type: SRA

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: GFP+ Treg cells were isolated from untreated bone marrow chimeric mice and transferred into lymphopenic recipients together with activated effector CD4 T cells and YFP+ inflammation-experienced Treg cells. GFP+ YFP- Activated Treg cells were isolated 14 days later for RNA-seq

library_source: transcriptomic

data_processing:
Sequences mapped using STAR 2.5.0
Expression level was quantified with refGene annotation
DESeq2 analysis was run with q-value cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples

molecule: total RNA

organism: Mus musculus

extract_protocol: Sorted cells were lysed with TRIzol and stored at -80 degree. RNA was extracted according to the manufacturer’s manual (Life Technologies). cDNA libraries were generated using SMARTer amplification (Clontech) and individually indexed. Libraries were sequenced on HiSeq 2000 platform (Illumina).

tag: tissue

value: Spleen and peripheral lymph nodes

tag: cell type

value: Activated Treg cells

tag: source

tag: activating stimulus

tag: days post-stimulus


title: reactivated_mTr_rep2 (Sample 62)


title: aTr_primary_activation_rep2 (Sample 59)


title: rTr_rep2 (Sample 56)

description: GFP+ Treg cells were isolated from untreated control animals

source_name: rTr

value: Resting Treg cells


title: aTr_primary_activation_rep3 (Sample 60)


title: rTr_rep3 (Sample 57)


title: rTr_rep1 (Sample 64)

description: Treg cells were isolated from untreated animals based on GFP expression


title: aTr_H3K27Ac_rep2 (Sample 52)

description: YFP+ GFP+ Treg cells were isolated from animals treated with tamoxifen and diphtheria toxin

library_source: genomic

data_processing:
Sequences mapped using bowtie2 2.2.0
Peak was called with macs2 with p-value cutoff of 0.01
Peaks below the IDR cutoff of 0.05 were selected
The union of ATAC-seq peaks were found, and reads overlapping this peak atlas were counted.
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples

molecule: genomic DNA

extract_protocol: FACS-sorted cell populations (1x105 cells) were crosslinked in 1% paraformaldehyde for 5 minutes at RT. The reaction was quenched by addition of 125mM glycine. Crosslinked cells were lysed and partially digested with micrococcal nuclease (12,000 units/ml) for 1 minute at 37 degrees. Digestion was stopped by addition of EDTA and digested nuclei were resuspended in nuclear lysis buffer containing 1% SDS. Following sonication, chromatin was incubated overnight with antibodies against H3K27me3, H3K27Ac, or H3K4me1 and immunocomplexes were precipitated with protein A Dynabeads. After washing, precipitated chromatin was decrosslinked overnight at 65 degrees in the presence of proteinase K and DNA fragments were isolated using Qiagen PCR-purification kit. Purified DNA was processed for sequencing on Illumina Hiseq.

value: Transient Treg cell depletion

value: 11 days

tag: chip antibody

value: anti-H3K27Ac (Abcam; Cat #:ab4729; Lot:GR117011-1)


title: aTr_H3K27Ac_rep1 (Sample 51)


title: mTr_H3K27Ac_rep2 (Sample 54)

value: Inflammation-experienced Treg cells

value: 60 days


title: mTr_H3K27me3_rep2 (Sample 49)


title: mTr_H3K27Ac_rep1 (Sample 53)


title: BDCA1+CD14+_donor III

city: Nijmegen

first: Ghaith

last: Bakdash

address: Geert Grooteplein 26

country: Netherlands

institute: Radboudumc

data_processing:
Illumina RTA 1.13.48 and OLB-1.9.4 software used for basecalling.
As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean  data). The procedure include following steps:1. Remove reads with adaptor sequences.2. Remove reads in which the percentage of unknown bases (N) is greater than 10%.3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality,
Allignment (SOAPaligner/SOAP2): Sequencing data produced by Illumina HiSeqTM 2000 was aligned to HG19 using SOAPaligner/soap2 Version2.21t with parameter -m 0 -x 1000 -s 40 -l 32 -v 5 -r 2 -p 3
The gene expression level is calculated by using RPKM( Mortazavi, A., B. A. Williams, et al . (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5(7): 621-8.) method (Reads Per kb per Million reads)
gene structures analysis(includes Refinement of gene structures,Identification of alternative spliced transcripts and Prediction and annotation of novel transcripts  ) were performed with the below software and parameters:1, tophat-2.0.8.Linux_x86_64 with parameters ：-p 6 --b2-very-sensitive  --solexa1.3-quals  --segment-length 30 --segment-mismatches 2 -r 20 --mate-std-dev 20 --library-type  fr-unstranded; 2,cufflinks-2.0.2.Linux_x86_64 with parameters  -u -p 6  3, blat with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing 1) the number of samples for each cell type for which the normalized RPKM value was above, 2) the filtered normalized RPKM values and 3) the log transformed mean centred RPKM values

organism: Homo sapiens

source_name: Blood

extract_protocol:
BDCA1+ DCs, BDCA1+CD14+ cells and monocytes were isolated from blood by fluorescence activated cell sorting (FACS). Total RNA was isolate using Trizol. The quality of the isolated RNA (concentration, RIN, 28S/18S and size) was determined by Agilent 2100 Bioanalyzer.
RNA libraries were prepared according to the TruSeq RNA Sample Prep Kit v2 (Illumina)

tag: health condition

value: Healthy Volunteer

value: Blood

tag: isolation method

value: FACS


title: Monocyte_donor II

value: Monocyte


title: aTr_H3K27me3_rep2 (Sample 47)


title: Monocyte_donor III


title: BDCA1+CD14+_donor I


title: rTr_rep1 (Sample 55)


title: BDCA1+ DC_donor III

value: BDCA1+ DC


title: aTr_H3K27me3_rep1 (Sample 46)


title: BDCA1+ DC_donor II


title: mTr_H3K27me3_rep1 (Sample 48)


title: reactivated_mTr_rep3 (Sample 63)

value: Reactivated mTr cells


title: BDCA1+ DC_donor I


title: rTr_H3K27Ac_rep1 (Sample 50)

description: Bulk GFP+ Treg cells were isolated from animals treated with tamoxifen only

value: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow


title: Monocyte_donor I


title: mTr_H3K4me1_rep2 (Sample 43)

value: anti-H3K4me1 (Abcam; Cat #:ab8895; Lot:GR61306-1)


title: rTr_H3K27me3_rep2 (Sample 45)


title: mTr_H3K4me1_rep1 (Sample 42)


title: rTr_H3K27me3_rep1 (Sample 44)


title: aTr_H3K4me1_rep2 (Sample 41)


title: Trdj1_3P_WT_rep1

city: Boston

first: Lijuan

last: Zhao

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: LAM-HTGTS

data_processing:
Library strategy: LAM-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils
Genome_build: Modified-mm9 genome, in which Tcra-Tcrd locus at positions chr14: 52971974-54848751 was replaced with a 1666365nt-long segment from the 129S1/SvImJ strain (NT_039614.1).
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of aligned prey junction, bait chromosome (B_Rname), beginning (B_Rstart) and end (B_Rend) nucleotide position of aligned bait junction, chromosome orientation of the bait junction (B_Strand), start (B_Qstart) and end (B_Qend) positions on the sequence read for the bait junction, start (Qstart) and end (Qend) position on the sequence read for the prey junction, the length of the sequence read (Qlen), the entire sequence read (Seq), sequence at the junction (J_Seq), and the experiment assocaited with the read (Library).

source_name: DN2/DN3 T cell precursors

growth_protocol: OP9-DL1 stromal cell lines were maintained in α-MEM (Invitrogen, 12571-071), supplemented with 20% FBS (Gibco, 10438-026). Flt3-L (R&D, 427FL), IL-7 (R&D, 407-ML) were purchased from R&D and used at concentration of 5ng/ml each in co-culture. After 14 days of monitoring of differentiation, stromal cells were excluded by staining with CD140a MicroBeads (Miltenyi Biotec, 130-101-547) and B cells were excluded by staining with an antibody to B220 (Miltenyi Biotec, 130-049-501). Genomic DNA was collected for LAM-HTGTS library preparation.

extract_protocol:
DNA was extracted overnight at 55degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using linear amplification-mediated HTGTS (LAM-HTGTS).

treatment_protocol: Genomic DNA was collected after 14 days of differentiation

tag: genotype

value: WT

tag: stromal cell line

tag: culture condition

value: 5ng/ml IL-7; 5ng/ml Flt3-L

tag: fragmentation

value: sonication


title: Trdj1_5P_WT_rep2

description: LAM-HTGTS


title: Trdj1_3P_WT_rep3

description: LAM-HTGTS


title: Trdj1_3P_WT_rep2

description: LAM-HTGTS


title: Trdd1_3P_INT1-2KO_rep3

description: LAM-HTGTS

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils
Genome_build: Modified-mm9 genome, in which Tcra-Tcrd locus at positions chr14: 52971974-54848751 was replaced with a 1666365nt-long segment from the 129S1/SvImJ strain (NT_039614.1).
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of aligned prey junction, bait chromosome (B_Rname), beginning (B_Rstart) and end (B_Rend) nucleotide position of aligned bait junction, chromosome orientation of the bait junction (B_Strand), start (B_Qstart) and end (B_Qend) positions on the sequence read for the bait junction, start (Qstart) and end (Qend) position on the sequence read for the prey junction, the length of the sequence read (Qlen), the entire sequence read (Seq), sequence at the junction (J_Seq), and the experiment assocaited with the read (Library).


title: Trdj1_5P_WT_rep3

description: LAM-HTGTS


title: Trdj1_5P_WT_rep1

description: LAM-HTGTS


title: BDCA1+CD14+_donor II


title: Trdd1_3P_INT1-2KO_rep2

description: LAM-HTGTS


title: rTr_H3K4me1_rep2 (Sample 39)

value: Spleen and peripheral lymph nodes

value: Resting Treg cells


title: Trdd1_3P_INT1-2KO_rep1

description: LAM-HTGTS


title: Trdd1_3P_WT_rep3

description: LAM-HTGTS


title: rTr_H3K4me1_rep1 (Sample 38)


title: Trdd1_3P_WT_rep2

description: LAM-HTGTS


title: mTr_ATAC_rep2 (Sample 37)

data_processing:
Library strategy: ATAC-seq
Sequences mapped using bowtie2 2.2.0
Peak was called with macs2 with p-value cutoff of 0.01
Peaks below the IDR cutoff of 0.005 were selected
The union of ATAC-seq peaks were found, and reads overlapping this peak atlas were counted.
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples

extract_protocol: FACS-sorted cell populations (5x104 cells) were lysed and accessible chromatin was transposed using Nextera Tn5 transposase. Transposed DNA fragments were isolated using Qiagen MinElute kit and amplified 5-10 cycles using Nextera PCR primers. ATAC-seq libraries were sequenced on Illumina Hiseq.

value: Transient Treg cell depletion


title: mTr_ATAC_rep1 (Sample 36)


title: Trdd1_5P_INT1-2KO_rep3

description: LAM-HTGTS


title: Trdd1_5P_WT_rep3

description: LAM-HTGTS


title: Trdd1_5P_INT1-2KO_rep2

description: LAM-HTGTS


title: Trdd1_5P_WT_rep2

description: LAM-HTGTS


title: Trdd1_5P_INT1-2KO_rep1

description: LAM-HTGTS


title: aTr_ATAC_rep1 (Sample 34)

value: Activated Treg cells

value: 11 days


title: Trdd1_5P_WT_rep1

description: LAM-HTGTS


title: rTr_ATAC_rep2 (Sample 33)


title: aTr_H3K4me1_rep1 (Sample 40)


title: Trdd2_3P_INT1-2KO_rep3

description: LAM-HTGTS


title: Trdd2_3P_INT1-2KO_rep2

description: LAM-HTGTS


title: Trdd2_3P_INT1-2KO_rep1

description: LAM-HTGTS


title: Trdd2_3P_WT_rep3

description: LAM-HTGTS


title: mTr_LCMV_rep3 (Sample 31)

description: tdTomato+ Foxp3+ CD4 T cells were isolated from animals treated with tamoxifen and infected with LCMV

value: Spleen

value: Inflammation-experienced Treg cells

value: LCMV-infection

value: 60 days


title: Trdd2_3P_WT_rep2

description: LAM-HTGTS


title: Trdd2_5P_INT1-2KO_rep2

description: LAM-HTGTS


title: Trdd2_5P_INT1-2KO_rep1

description: LAM-HTGTS


title: mTr_LCMV_rep1 (Sample 29)


title: rTr_ATAC_rep1 (Sample 32)


title: Trdd2_5P_WT_rep3

description: LAM-HTGTS


title: mTr_LCMV_rep2 (Sample 30)


title: Trdd2_3P_WT_rep1

description: LAM-HTGTS


title: Trdd2_5P_INT1-2KO_rep3

description: LAM-HTGTS


title: aTr_LCMV_rep3 (Sample 28)


title: Trdd1_3P_WT_rep1

description: LAM-HTGTS


title: Trdd2_5P_WT_rep1

description: LAM-HTGTS


title: aTr_ATAC_rep2 (Sample 35)


title: Trdd2_5P_WT_rep4

description: LAM-HTGTS


title: KO-77

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description: Mitochondria were isolated from homogenized hearts and isolated by differential centrifugation as described previously (Lagouge et al., 2015; Mourier et al., 2014), with some modifications. Hearts were cut and washed three times with ice cold PBS, and once with mitochondrial isolation buffer (MIB) containing 310 mM sucrose, 10 mM Tris-HCl and 0.05 % BSA (w/v) by centrifugation at 4,500 g for 1 min at 4°C. Heart pieces were homogenized in 5 ml of fresh MIB using a Potter S pestle (Sartorius). The homogenate was centrifuged at 1,000 g for 10 min at 4°C and the supernatant was centrifuged at 4,500 g for 15 min at 4°C to isolate mitochondria. Crude mitochondrial pellets were suspended in MIB supplemented with 1x Complete EDTA-free protease inhibitor cocktail (Roche).

data_processing:
Library strategy: PARE
Basecalling was performed by NextSeq Control Software
The 5 bp adapter sequence was trimmed and paired-end reads were merged with CLC Genomics Workbench (Qiagen) if the read overlap exceeded 95% identity.
Merged reads were aligned to the mouse mitochondrial genome (chrM) with Bowtie2 using default parameters
Strand-specific depth of read coverage at the 5' terminal position of aligned reads was calculated with BEDTools (-d -5 -strand [+/-])
Read depth was normalised using the trimmed mean of M values (TMM) method from the edgeR package
genome build: mm10
Strand-specific 5' end coverage for each sample in bedGraph format, normalised by TMM (edgeR)

growth_protocol: Mice were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-h light/dark schedule (lights on 7 am to 7 pm) in controlled environmental conditions of 22 ± 2 °C and 50 + 10% relative humidity and fed a normal chow diet (Rat & Mouse Chow, Specialty Foods, Glen Forrest, Western Australia) and water were provided ad libitum.

extract_protocol:
RNA was isolated from total hearts or heart mitochondria using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Total RNA libraries were prepared according to the Illumina TruSeq protocol, using random hexamer primers for cDNA generation and the Ribo-Zero rRNA removal kit for cytoplasmic RNA deptetion. Mitochondrial RNA was prepared according to the PARE protocol as described by German et al. (Nature Protocols, Vol.4 No.3, 2009).

value: Heart

tag: age

value: 11 weeks

value: Mrpp3^loxP/loxP, +/Ckmm

tag: strain

tag: molecule

value: total mitochondrial RNA from heart


title: aTr_LCMV_rep1 (Sample 26)


title: KO-76


title: rTr_LCMV_rep2 (Sample 25)

description: tdTomato+ Foxp3+ CD4 T cells were isolated from animals treated with tamoxifen only

value: Uninfected Control


title: WT-114-5


title: WT-115


title: ccp1_ChIPSeq rep1

first: Fei

last: Li

address: 100 Washington Square East

department: Biology

institute: New York University

description: ChIPed DNA

data_processing:
Read alignments to the S. pombe genome were performed using Bowtie2.
Data were normalized to per base genome coverage using the BEDTools genomeCoverageBed function.
Log2-fold changes of ccp1Δ versus wild-type cnp1-GFP signal were computed using deepTools bamCompare.
All data were converted to bedgraph files for visualization in the integrative genome viewer (IGV).
Genome_build: Schizosaccharomyces_pombe.ASM294v2.28
Supplementary_files_format_and_content: Bedgraph file contains normalized reads of ChIP-Seq data. Bw files contain information of log2-fold changes of ccp1Δ versus wild-type in binary format.

organism: Schizosaccharomyces pombe

source_name: pombe

growth_protocol: Cells were grown to log phase in rich medium at 30°C

extract_protocol:
Log phase yeast cells were treated with 1% formaldehyde to generate DNA-protein crosslinking. Immunoprecipitation was performed using an anti-GFP antibody. Precipitated DNA was suspended TE buffer.
Libraries were prepared following the instructions of the Illumina TruSeq ChIP sample prep kit.

value: h?  ccp1{delta}::ura4+ ade6+::cnp1-GFP leu1-32 ura4-D18

tag: antibody

value: GFP (Abcam, ab290)


title: ccp1_ChIPSeq rep2

description: ChIPed DNA

value: h?  ccp1{delta}::kanMX6 ade6+::cnp1-GFP leu1-32 ura4-D18


title: KO-79


title: WT-114


title: wt_ChIPSeq

description: ChIPed DNA

value: h-  ade6+::cnp1-GFP leu1-32 ura4-D18


title: Sox2 KO stomach 3 [RNA-seq]

first: Abby

last: Sarkar

state: MA

address: 185 Cambridge Street

department: Cancer Center

institute: Harvard University

data_processing:
Basecalls performed using CASAVA version 1.7
Subsequent to demultiplexing and adapter trimming, fastqs were mapped to mm10 with splice-aware aligner STAR vers-2.3.0 using mm10 Ensembl gtf version 75
To calculate RPKM expression values, sequencing reads were counted over an assembly of all putative exons for each gene and normalized by the length of the exon assembly and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values for each sample are given in tab-delimited txt files.  A matrix of RPKM values for those samples is also available.

source_name: Sox2 KO stomach

extract_protocol:
Stomachs were laid out flat, cleaned, and pylorus was carefully excised. The pylorus was then placed in 5 mL of Corning Cell Recovery solution for 1 hour at 4 degrees. After this incubation, the muscle layer was gently separated from the epithelium/mesenchyme using fine tweezers. RNA was extracted from the epithelium/mesenchyme layer using the RNeasy kit from Qiagen according to their protocol. 1 ug of total RNA was used for the construction of the sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both Sox2 KO mice (Rosa26CreER; Sox2 fl/fl) and Sox2 WT mice (Rosa26WT; Sox2fl/fl) were treated with Tamoxifen at 8 weeks of age. Stomaches from these mice were isolated 2 weeks later.

value: C57BL/6 x 129 mixed

value: Stomach

value: 8 weeks

tag: genotype/variation

value: RosaCreER;; Sox2fl/fl


title: mTe_rep2 (Sample 23)

description: tdTomato+ Foxp3- CD4 T cells were isolated from animals treated with tamoxifen and diphtheria toxin

source_name: mTe

tag: tissue

value: Spleen and peripheral lymph nodes

value: Inflammation-experienced effector T cells

value: Transient Treg cell depletion


title: Trdd2_5P_WT_rep2

description: LAM-HTGTS

value: WT

value: 5ng/ml IL-7; 5ng/ml Flt3-L

value: sonication


title: Sox2 KO stomach 2 [RNA-seq]


title: Sox2 WT stomach 3 [RNA-seq]

source_name: Sox2 WT stomach

value: wild type


title: aTe_rep1 (Sample 20)

source_name: aTe

tag: cell type

value: Activated effector T cells

value: 11 days


title: Sox2 WT stomach 2 [RNA-seq]


title: Sox2 KO stomach 1 [RNA-seq]


title: rTe_rep2 (Sample 19)

description: tdTomato+ Foxp3- CD4 T cells were isolated from animals treated with tamoxifen only

source_name: rTe

value: Resting effector T cells

tag: source


title: rTe_rep1 (Sample 18)

tag: activating stimulus


title: Sox2 WT stomach 1 [RNA-seq]


title: GP66+_d75_LCMV_rep2 (Sample 16)

description: LCMV-specific CD4 T cells were isolated based on GP66-77/I-Ab tetramer staining

value: Spleen

value: GP66 tetramer+ CD4 T cells

value: LCMV-infection

tag: days post-stimulus

value: 75 days


title: GP66+_d75_LCMV_rep1 (Sample 15)


title: GP66+_d75_LCMV_rep3 (Sample 17)


title: aTe_rep2 (Sample 21)


title: GP66+_d7_LCMV_rep1 (Sample 13)

value: 7 days


title: GP66+_d7_LCMV_rep2 (Sample 14)


title: rTr_LCMV_rep1 (Sample 24)

value: Resting Treg cells

value: Uninfected Control


title: Naïve_CD4_rep1 (Sample 11)

description: Naïve CD4 T cells were isolated based on expression of activation markers CD44 and CD62L

value: naive CD4 T cells

value: Uninfected control


title: Naïve_CD4_rep2 (Sample 12)


title: GBE rep2

city: Santiago

first: Christian

middle: E

last: Hodar

state: Santiago

address: Av. El Libano 5524

department: INTA

country: Chile

institute: Universidad de Chile

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were received already filtered by quality and mapped using STAR alignment using M. domestica Aabys strain genomic scaffold sequences (VectorBase) as reference.
Counts were extracted from BAM files using htseq-count
Genome_build: MdomA1.1
Supplementary_files_format_and_content: tab-delimited text files include counts each Sample.

organism: Musca domestica

source_name: Whole embryo

extract_protocol:
100 embryos of each stage were flash frozen on liquid N2 and RNA was extracted using Tri-reagent. Remain DNA was digested with Ambion Turbo DNAse and purified using the RNA cleanup protocol from the RNAeasy Mini Kit (Quiagen)
Transcriptome sequencing was performed at the Duke Center for Genomic and Computational Biology in a Hiseq2000 platform (Illumina) with a 100 bp pair end library and 200 bp insert size

tag: developmental stage

value: Germ band extension


title: mTr_rep4 (Sample 10)

source_name: mTr

value: Spleen and peripheral lymph nodes

value: Inflammation-experienced Treg cells

value: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow

value: Transient Treg cell depletion

value: 60 days


title: DC rep1

value: Dorsal closure


title: DC rep2


title: GBE rep1


title: mTr_rep3 (Sample 9)


title: aTr_rep3 (Sample 6)

source_name: aTr

value: Activated Treg cells

value: 11 days


title: mTr_rep1 (Sample 7)


title: GLU_PK3

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Illumina reads were mapped to the Streptococcus pneumoniae 6A10 genome using Bowtie v. 1.4
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
RPKMs for each gene were calculated for each sample.
Genome_build: 6A10 [pending]
Supplementary_files_format_and_content: [.txt] RPKMs
Column 1: Chromosome.ID/Contig.ID
Column 2: Start
Column 3: Stop
Column 4: Gene.ID
Column 5: Score(unused)
Column 6: Strand
Column 7: Read.Count
Column 8: Number.of.bases.covered
Column 9: Total.Gene.Length
Column 10: Fraction.of.Gene.Covered
Column 11: RPKM.Value

organism: Streptococcus pneumoniae

growth_protocol: S. pneumoniae was grown planktonically or in polystyrene 6-well plates as 2-day-old biofilms in 50% THB supplemented with the designated sugar at 1%.

extract_protocol:
Total RNA was extracted from each replicate separately using enzymatic lysis of pneumococcal cells (10 µL mutanolysin, 20 µL proteinase K, 15 µL lysozyme, and 55 µL TE) followed by RNA extraction with the RNeasy Micro Kit (Qiagen) with DNase treatment on column and in solution. Samples were then depleted of rRNAs using the Ribo-Zero rRNA Removal Kit for Gram-positive bacteria (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

value: grown planktonically, THB supplemented with GLU


title: GLU_PK2


title: CB rep2

value: Cellular blastoderm


title: mTe_rep1 (Sample 22)

value: Inflammation-experienced effector T cells


title: G rep1

value: Gastrula


title: aTr_rep2 (Sample 5)


title: mTr_rep2 (Sample 8)


title: rTr_rep3 (Sample 3)

value: Resting Treg cells


title: GAL_BF3

value: grown as biofilm, THB supplemented with GAL


title: aTr_rep1 (Sample 4)


title: CB rep1


title: GAL_BF2


title: GAL_PK3

value: grown planktonically, THB supplemented with GAL


title: rTr_rep1 (Sample 1)


title: rTr_rep2 (Sample 2)


title: GLU_PK1


title: SB rep1

value: Synsytial blastoderm


title: GAL_PK1


title: EREB_plus_2

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

description: Library strategy: 4C-Seq

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 platform using the default RTA analysis software.
Reads were trimmed using trim galore v0.4 using default parameters to remove standard illumina adapters. Reads were mapped to the GRCh37 human genome assembly using bowtie2. Uniquely mapping reads were imported into SeqMonk v0.32.1 for analysis. Raw overlapping read counts were calculated for non-overlapping 10kb regions throughout the whole genome.
Genome_build: GRCh37
Supplementary_files_format_and_content: [.txt] Quantitated 4C-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4) (5-8) Read Count

source_name: EREB_plus, ER-EB 2.5 LCL

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 1 µM β-estradiol , 10% foetal bovine serum and antibiotics and passaged twice weekly.

extract_protocol:
MYC promoter interacting fragments were captured using a 2.7 kb NlaIII fragment encompassing the MYC promoter, prior to further digestion by DpnII. Cells were passed through a 70 µm filter to obtain a single cell preparation. 1×107 cells were then fixed in 2% formaldehyde in the presence of 10% FCS for 10 mins at room temperature. The reaction was quenched with 0.125M glycine, and cells collected by centrifugation at 400 g for 8 min at 4°C. The pellet was resuspended in 0.5 ml lysis buffer (50 mM Tris-HCl, pH 7.5; 150 mM NaCl, 0.5 mM EDTA, 0.5% NP-40, 1% Triton X-100) with freshly added complete protease inhibitors (Roche), and lysed on ice for 10 mins. The nuclei were collected by centrifugation at 750 g for 5 min at 4°C, then resuspended in 0.5 ml of 1.2X CutSmart Buffer (New England Biolabs) containing 0.3% SDS and incubated for 1 hr at 37°C, while shaking at 900 rpm. Triton X-100 was then added to the nuclei to give a final concentration of 3% and the samples incubated for 1 hr at 37°C, with shaking. 200 U NlaIII (New England Biolabs) were added to the nuclei and the samples incubated for 4 hrs at 37°C, while shaking at 900rpm. The reaction was supplemented with a further 200U NlaIII and incubated overnight at 37°C with shaking at 900rpm. A further 200U NlaIII was added, followed by an additional 4 hr incubation at 37°C while shaking at 900rpm. The digestion reaction was stopped by incubation at 65°C for 20 mins. The sample was then diluted 10-fold with 1.15X ligation buffer (Roche). 50 U DNA ligase (Roche) were added to the sample, and the reaction was incubated overnight at 16°C. 300 µg of Proteinase K (Roche) were added to the sample and the reaction incubated at 65°C overnight. RNA was removed by incubation with 300 µg of RNAse for 45 mins at 37°C. Following two rounds of phenol-chloroform extraction, DNA was ethanol precipitated prior to resuspension in 150µl of 10mM Tris-HCL pH7.5 at 37°C. The samples were then diluted 10-fold with 1X DpnII buffer (New England Biolabs). 50U DpnII (New England Biolabs) were added, followed by an overnight incubation at 37°C whilst shaking at 900rpm. The digestion reaction was stopped by incubation at 65°C for 20 mins. Samples were diluted 10-fold in 1.15X ligation buffer. 100 U DNA ligase were added and the reaction incubated overnight at 16°C. The samples were then ethanol precipitated in the presence of glycogen at -80°C, prior to purification over a QIAquick PCR purification Kit (Qiagen), and eluted in 150µl 10mM Tris-HCL pH7.5.
Fragments captured by the bait region were amplified by inverse PCR using primers designed to amplify outwards from the bait region (Table S3). Individual forward primers included a 5’ overhang of the Illumina sequence adapter P5 and a unique ‘barcode’ sequence and encompassed the primary NlaIII restriction site of the MYC promoter bait. Common reverse primers included a 5’ overhang of the Illumina sequence adapter P7 and were designed to bind less than 100 bps from the secondary restriction site (DpnII) in the MYC promoter bait. PCR was performed using Expand Long Template Polymerase (Roche), with 3.2 µg of template and 1.12 nmol of the P5 and P7 primers for 2 mins at 94°C, 10 secs at 94°C, 1 min at 55°C, 3 mins at 68°C for 29 cycles followed by 5 mins at 68°C. 16 individual PCR reactions were carried out for each sample. The reactions were pooled and purified to separate the unused adapter primers from the PCR product using the High Pure PCR Product Purification Kit (Roche). Replicate chromatin samples were generated from the same cell batch and processed separately through each stage. Samples were combined for multiplex 100bp single-end Illumina HiSeq sequencing. Four ER-EB 2.5 LCL samples were sequenced in a single lane.

treatment_protocol: The EBV-immortalised ER-EB 2.5 LCL, expressing a conditionally-active oestrogen receptor (ER)-EBNA2 fusion protein, was provided by Prof B. Kempkes, and was cultured in the presence of β-estradiol. To study MYC activation by EBNA2, ER-EB 2.5 cells were washed and incubated in the absence of β-estradiol for 4 days. 1 µM β-estradiol was then re-added for 17 hrs (ER-EB 2.5 plus). Control cells were incubated for a further 17 hrs in the absence of β-estradiol (ER-EB 2.5 minus).

tag: cell origin

value: B cell

tag: cell line type

value: Lymphoblastoid Cell Line

tag: cell line

value: ER-EB 2.5

tag: treatment

value: beta-estradiol


title: G rep2


title: EREB_minus_1

description: Library strategy: 4C-Seq

source_name: EREB_minus, ER-EB 2.5 LCL


title: EREB_minus_2

description: Library strategy: 4C-Seq


title: THB_BF2

value: grown as biofilm, THB


title: GAL_PK2


title: THB_PK3

value: grown planktonically, THB


title: THB_BF1


title: CD40L_2

description: Library strategy: 4C-Seq

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 platform using the default RTA analysis software.
Reads were trimmed using trim galore v0.4 using default parameters to remove standard illumina adapters. Reads were mapped to the GRCh37 human genome assembly using bowtie2. Uniquely mapping reads were imported into SeqMonk v0.32.1 for analysis. Raw overlapping read counts were calculated for non-overlapping 10kb regions throughout the whole genome.
Genome_build: GRCh37
Supplementary_files_format_and_content: [.txt] Quantitated 4C-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4) (5-10) Read Count

source_name: CD40L, CD19+ B cell

growth_protocol: Primary resting B cells were isolated from blood from fresh apheresis cones obtained from the NHSBT under the ethically approved study 14/WM/0001. The Peripheral blood mononuclear cells were isolated by density centrifugation on lymphoprep (Axis Shield) and the B cells were subsequently purified by positive isolation using pan-CD19 Dynabeads (Dynal). The Dynabeads were removed from the purified B cells by incubation with Detachabead (Dynal).

extract_protocol:
MYC promoter interacting fragments were captured using a 2.7 kb NlaIII fragment encompassing the MYC promoter, prior to further digestion by DpnII. Cells were passed through a 70 µm filter to obtain a single cell preparation. 1×107 cells were then fixed in 2% formaldehyde in the presence of 10% FCS for 10 mins at room temperature. The reaction was quenched with 0.125M glycine, and cells collected by centrifugation at 400 g for 8 min at 4°C. The pellet was resuspended in 0.5 ml lysis buffer (50 mM Tris-HCl, pH 7.5; 150 mM NaCl, 0.5 mM EDTA, 0.5% NP-40, 1% Triton X-100) with freshly added complete protease inhibitors (Roche), and lysed on ice for 10 mins. The nuclei were collected by centrifugation at 750 g for 5 min at 4°C, then resuspended in 0.5 ml of 1.2X CutSmart Buffer (New England Biolabs) containing 0.3% SDS and incubated for 1 hr at 37°C, while shaking at 900 rpm. Triton X-100 was then added to the nuclei to give a final concentration of 3% and the samples incubated for 1 hr at 37°C, with shaking. 200 U NlaIII (New England Biolabs) were added to the nuclei and the samples incubated for 4 hrs at 37°C, while shaking at 900rpm. The reaction was supplemented with a further 200U NlaIII and incubated overnight at 37°C with shaking at 900rpm. A further 200U NlaIII was added, followed by an additional 4 hr incubation at 37°C while shaking at 900rpm. The digestion reaction was stopped by incubation at 65°C for 20 mins. The sample was then diluted 10-fold with 1.15X ligation buffer (Roche). 50 U DNA ligase (Roche) were added to the sample, and the reaction was incubated overnight at 16°C. 300 µg of Proteinase K (Roche) were added to the sample and the reaction incubated at 65°C overnight. RNA was removed by incubation with 300 µg of RNAse for 45 mins at 37°C. Following two rounds of phenol-chloroform extraction, DNA was ethanol precipitated prior to resuspension in 150µl of 10mM Tris-HCL pH7.5 at 37°C. The samples were then diluted 10-fold with 1X DpnII buffer (New England Biolabs). 50U DpnII (New England Biolabs) were added, followed by an overnight incubation at 37°C whilst shaking at 900rpm. The digestion reaction was stopped by incubation at 65°C for 20 mins. Samples were diluted 10-fold in 1.15X ligation buffer. 100 U DNA ligase were added and the reaction incubated overnight at 16°C. The samples were then ethanol precipitated in the presence of glycogen at -80°C, prior to purification over a QIAquick PCR purification Kit (Qiagen), and eluted in 150µl 10mM Tris-HCL pH7.5.
Fragments captured by the bait region were amplified by inverse PCR using primers designed to amplify outwards from the bait region. Individual forward primers included a 5’ overhang of the Illumina sequence adapter P5 and a unique ‘barcode’ sequence and encompassed the primary NlaIII restriction site of the MYC promoter bait. Common reverse primers included a 5’ overhang of the Illumina sequence adapter P7 and were designed to bind less than 100 bps from the secondary restriction site (DpnII) in the MYC promoter bait. PCR was performed using Expand Long Template Polymerase (Roche), with 3.2 µg of template and 1.12 nmol of the P5 and P7 primers for 2 mins at 94°C, 10 secs at 94°C, 1 min at 55°C, 3 mins at 68°C for 29 cycles followed by 5 mins at 68°C. 16 individual PCR reactions were carried out for each sample. The reactions were pooled and purified to separate the unused adapter primers from the PCR product using the High Pure PCR Product Purification Kit (Roche). Replicate chromatin samples were generated from the same cell batch and processed separately through each stage. Samples were combined for multiplex 100bp single-end Illumina HiSeq sequencing. Six primary B cell samples were combined in a single lane.

treatment_protocol: Purified B cells were incubated with 2089 EBV at an MOI of 100 for 1 hour at 37°C and the unbound virus was washed off. One million uninfected purified B cells were cultured in 4ml of medium supplemented with 50ng/ml soluble mega CD40L (Enzo) and 50ng/ml IL4. The infected and CD40L-stimulated B cells were grown in RPMI, 10% FBS and supplemented with penicillin/streptomycin and glutamine.

value: CD19+ B cell

value: CD40 ligand and IL-4 treated


title: EBV_2

description: Library strategy: 4C-Seq

source_name: EBV, CD19+ B cell

value: EBV infected


title: SB rep2


title: THB_PK2


title: EBV_1

description: Library strategy: 4C-Seq


title: UI_2

description: Library strategy: 4C-Seq

source_name: UI, CD19+ B cell


title: THB_PK1


title: control

city: Hakodate

first: Shigeho

last: Ijiri

state: Hokkaido

address: Minato-cho 3-1-1

department: Division of Marine Life Sciences

country: Japan

institute: Graduate School of Fisheries Sciences, Hokkaido University

description: control

data_processing:
Basecalls performed using CASAVA.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the TSA contig dataset (97925 contigs: IABA01000001 to IABA01097925) using bowtie.
Reads Per Megabase of library size (RPM) were calculated.
Genome_build: TSA, 97925 contigs: IABA01000001 to IABA01097925
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

organism: Oncorhynchus masou masou

source_name: Granulosa layer

extract_protocol:
total RNAs were extracted from the granulosa layers using RNeasy Mini Kit (Qiagen)
cDNA libraries were prepared using mRNA-Seq-8 Sample Prep Kit (Illumina)

tag: agent


title: UI_1

description: Library strategy: 4C-Seq


title: VirR-1

status: Public on Aug 03 2016

city: Clayton

first: Julian

last: Rood

state: VIC

address: Wellington Rd

department: Microbiology

institute: Monash University

description:
Gram positive bacteria
virR regulatory mutant

data_processing:
Reads were clipped using the “clip” tool in the “nesoni” package. https://github.com/Victorian-Bioinformatics-Consortium/nesoni
Reads were aligned to the reference genome using Bowtie2.
Read-pairs aligning to annotated genes in the reference genome were counted using the “count” tool in the “nesoni” package. Where a read-pair had multiple best alignments, it was counted multiple times.
Genome_build: NC_003366.1 Clostridium perfringens str. 13
Supplementary_files_format_and_content: counts.csv contains counts of the number of read-pairs aligning to each gene.

organism: Clostridium perfringens

source_name: ∆revRΩerm

growth_protocol: C. perfringens broth cultures were grown overnight at 37°C in fluid thioglycolate (FTG) medium or in TPG broth medium (5% [wt/vol] tryptone, 0.5% [wt/vol] protease peptone and 0.1% [wt/vol] sodium thioglycolate) with glucose added to a final concentration of 0.38% (wt/vol) after sterilization.  Agar cultures of C. perfringens were grown on nutrient agar (NA) (Oxoid or Difco, BD) supplemented with rifampicin (10 μg/ml), nalidixic acid (10 μg/ml) or erythromycin (50 μg/ml) under anaerobic conditions (10% H2, 10% CO2 and 80% N2).

extract_protocol:
C. perfringens strains were grown in TPG broth at 37°C and cells were harvested by centrifugation at 8000 g for 10 min at room temperature when the culture had reached late logarithmic phase (5 h). The harvested cells were resuspended and incubated in lysis buffer (10mM Tris-HCI pH 7.5, 0.4 M sucrose, 5 mg/ml lysozyme) at 37°C for 30 min. Following centrifugation at 16, 060 g for 10 min, the supernatant was discarded and total RNA was isolated from the cells using TriZol reagent (Invitrogen) as previously described {Hiscox, 2011 #5652}.
Total RNA was first treated to retain the strand-specific information of the library. For first strand synthesis (FSS), a 100 μl reaction that contained 8 μg of RNA and 15 μg of random hexamers (Promega) were incubated at 65°C for 5 min and placed into ice for 5 min. The reaction was then added with 20 μl of 5X first strand buffer (Invitrogen), 10 μl of 100 mM of dithiothreitol (DTT) (Invitrogen), 5 μl of 10 mM of deoxynucleotide mix (Promega) and 2.5 μl of 40U/μl of RNasin (Promega) and incubated at 25°C for 2 min. Subsequently, 5 μl of 200U/μl SuperScript III was added to the reaction and incubated under the following conditions: 25°C for 10 min, 42°C for 50 min and 70°C for 15 min. Before proceeding to the second strand synthesis as previously described {Parkhomchuk, 2009 #5631}, the FSS reaction was treated with a G-50 gel filtration spin column (GE Healthcare) according to the manufacturer’s instructions to remove excess dNTPs.  The resulting cDNA samples were used to construct cDNA libraries using the Truseq RNA sample preparation kit version 1 (Illumina) as per the manufacturer’s instructions.


title: VirR-2


title: WT1

description:
Gram positive bacteria
wild type

source_name: wild type


title: Rev-1

description:
Gram positive bacteria
revR regulatory mutant

source_name: virRΩTTermB


title: THB_BF3


title: Rev-2


title: WT2

description:
Gram positive bacteria
wild type


title: GAL_BF1


title: CD40L_1

description: Library strategy: 4C-Seq


title: A549_shIno80_rep2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: Gene expression 4 days after transfection

data_processing:
Aligned with TopHat2 version 2.0.4 with the following parameters: -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)

source_name: human A549_shIno80

growth_protocol: A549 cells were obtained from ATCC, and cultured in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated from cells using the GeneJet RNA purification kit (Thermo Scientific)
For RNA-seq, One microgram total RNA was used for sequencing library generation using the Truseq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions.  Truseq RNA Library Prep Kit V2 (Illumina)

treatment_protocol: Human lung cancer cell line A549 cells were infected with shNT or shIno80, and total RNA was extracted 4 days after infection. The RNA was submitted to RNA-Seq subsequently.

value: lung cancer cell line


title: A549_shIno80_rep1


title: EREB_plus_1

description: Library strategy: 4C-Seq


title: A549_shIno80_Input

description: ChIP-Seq was performed 48 hours after infection

data_processing:
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -m 1 --best --strata
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: coverage normalized to reads per 10 million aligned reads

growth_protocol: A549 cell lines were obtained from ATCC, and cultured in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Ino80 ChIP were performed as described previously. Briefly, A549 cells were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop the fixation. Cells were harvested, and DNA was fragmented to 300–500 bp by sonication with a micro-tip attached to a Misonix 3000 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated.
For ChIP-seq, 1 ng ChIP DNA or input DNA was used to generate sequencing libraries using the Nextera XT DNA sample preparation Kit (Illumina).  Nextera XT DNA sample preparation kit (illumina)

treatment_protocol: A549 infected with shNT or shIno80, was used for ChIP-Seq for corresponding factors 2 days after infection.


title: A549_shNT_H3K56ac

source_name: human A549_shNT

tag: antibody vendor

value: Active motif

tag: antibody cat. #

tag: antibody lot #


title: A549_shNT_Input


title: A549_shNT_rep1


title: A549_Input

description: ChIP-Seq in wild type cells

source_name: human A549


title: A549_shNT_rep2


title: A549_Ino80

description: ChIP-Seq in wild type cells

value: proteintech


title: CONCR_KD_input_DNA

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using bedtools v2.17.0

source_name: A549 cells_input_CONCR_KD

growth_protocol: A549 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
For the ChIP, cells were cross-linked with 1% formaldehyde and chromatin prepared by sonication to obtain DNA fragments between 100 bp and 500 bp. DDX11 bound DNA was then immunoprecipitated using the anti-DDX11 antibody (ab66971, Abcam), decrosslinked and extracted for analysis by sequencing
Libraries were prepared using the NEBNext Ultra DNA Library Prep Kit (Illumina)

treatment_protocol: For RNAi, cells were transfected twice, 24 h apart, using 40 nM siRNA (final concentration) and Lipofectamine 2000 (Invitrogen). G1/S synchronized cells were obtained by double thymidine block procedure; cells were cultured for 16 hours in the presence of 2 mM thymidine, 9 hours in normal medium and then again 16 hours in the presence of 2 mM thymidine.

tag: knockdown

value: CONCR KD


title: Control_KD_input_DNA

source_name: A549 cells_input_control_KD

value: control KD


title: DDX11_ChIP-Seq_in_Control_KD_rep2

source_name: A549 cells_anti-DDX11_Control_KD


title: DDX11_ChIP-Seq_in_Control_KD_rep1


title: DDX11_ChIP-Seq_in_CONCR_KD_rep2

source_name: A549 cells_anti-DDX11_CONCR_KD


title: DDX11_ChIP-Seq_in_CONCR_KD_rep1


title: A549_shIno80_H2AZ


title: WT2 2 ng/mL TGF-b

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

description:
Sample 9
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt

data_processing:
Sample reads were trimmed of adapters and low-quality bases using Trimmomatic software.
Trimmed reads were aligned to the reference mouse genome mm9 using Tophat.
FPKM values were calculated using Cufflinks and compared between samples using Cuffdiff.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Processed data files are tab-delimited text files containing FPKM values for each replicate RNA-Seq measurement.

source_name: Splenic CD4+ T cells, Cd4Cre, 2ng/ml TGF-b

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kits according to manufacturer's instructions.
mRNA samples were processed using the Clontech SMARTer Ultra low input RNA-v3 kit and sequenced using either an Illumina HiSeq 2500 (Samples 1-12) or an Illumina HiSeq 2000 (Samples 13-18).

treatment_protocol: Naïve CD4+ T cells were isolated by FACS from spleens of mice of indicated genotypes and stimulated in vitro with anti-CD3 and anti-CD28 antibodies in the presence of indicated concentrations of TGF-b. Cells were harvested at day 4 post-stimulation for analysis.

tag: strain/background

tag: genotype/variation

value: CD4+ T cells

tag: tgf-b concentration (ng/ml)


title: tKO2 0.2 ng/mL TGF-b

description:
Sample 11
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt

source_name: Splenic CD4+ T cells, Egln1fl/fl Egln2fl/fl Egln3fl/fl Cd4Cre, 0.2ng/ml TGF-b

value: Egln1fl/fl Egln2fl/fl Egln3fl/fl Cd4Cre

tag: cell type


title: WT2 0.2 ng/mL TGF-b

description:
Sample 8
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt

source_name: Splenic CD4+ T cells, Cd4Cre, 0.2ng/ml TGF-b


title: A549_shIno80_H3K56ac


title: forskolin

description: incubated with forskolin

value: forskolin


title: tKO1 0 ng/mL TGF-b

description:
Sample 4
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt

source_name: Splenic CD4+ T cells, Egln1fl/fl Egln2fl/fl Egln3fl/fl Cd4Cre, 0ng/ml TGF-b


title: tKO1 0.2 ng/mL TGF-b

description:
Sample 5
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt


title: tKO1 2 ng/mL TGF-b

description:
Sample 6
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt

source_name: Splenic CD4+ T cells, Egln1fl/fl Egln2fl/fl Egln3fl/fl Cd4Cre, 2ng/ml TGF-b


title: WT1 0.2 ng/mL TGF-b

description:
Sample 2
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt


title: WT1 2 ng/mL TGF-b

description:
Sample 3
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt


title: WT1 0 ng/mL TGF-b

description:
Sample 1
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt

source_name: Splenic CD4+ T cells, Cd4Cre, 0ng/ml TGF-b


title: A549_shNT_H2AZ


title: AdV-GFP replicate 2

first: Benjamin

last: tenOever

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Libraries were run on an Illumina MiSeq.
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using the RNAExpress application on BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing gene symbol and raw read numbers for each gene in each sample

source_name: AdV-GFP replicate 2

extract_protocol:
Lung tissue was homogenized in Trizol and RNA was extracted according to manufactures protocols. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: 6-8 weeks

tag: tissue

value: lung


title: AdV-GFP replicate 1

source_name: AdV-GFP replicate 1


title: PBS replicate 1

source_name: PBS replicate 1


title: AdV-VP55 replicate 1

source_name: AdV-VP55 replicate 1


title: P24_32_044

city: Easter Bush

first: Jason

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

institute: The Roslin Institute

description: P = Pregnant

data_processing:
All data analysis steps were carried out using sRNAbench 1.0 (part of sRNAtoolbox), using default settings. Please refer to the sRNAbench manual for additional details.
Genome_build: Bos taurus UMD3.1
Supplementary_files_format_and_content: All processed data provided in a single spreadsheet (.xlsx) file, named processed_data.xlsx: read counts, reads per million

organism: Bos taurus

source_name: Plasma

extract_protocol:
All plasma samples were extracted using TRIzol LS, following the manufacturer's recommendations.
Sequencing libraries were prepared following the Illumina TruSeq small-RNA library preparation kit protocol.

tag: day

tag: subject

tag: group

value: Pregnant


title: P24_28_038

description: P = Pregnant


title: P24_26_050

description: P = Pregnant


title: P24_17_020

description: P = Pregnant


title: tKO2 0 ng/mL TGF-b

description:
Sample 10
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt


title: P24_14_026

description: P = Pregnant


title: WT2 0 ng/mL TGF-b

description:
Sample 7
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt


title: tKO2 2 ng/mL TGF-b

description:
Sample 12
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp1.txt


title: P24_29_015

description: P = Pregnant


title: P24_12_029

description: P = Pregnant


title: P16_32_053

description: P = Pregnant


title: P24_10_054

description: P = Pregnant


title: P24_11_056

description: P = Pregnant


title: aTr_LCMV_rep2 (Sample 27)

description: tdTomato+ Foxp3+ CD4 T cells were isolated from animals treated with tamoxifen and infected with LCMV

data_processing:
Sequences mapped using STAR 2.5.0
Expression level was quantified with refGene annotation
DESeq2 analysis was run with q-value cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples

extract_protocol: Sorted cells were lysed with TRIzol and stored at -80 degree. RNA was extracted according to the manufacturer’s manual (Life Technologies). cDNA libraries were generated using SMARTer amplification (Clontech) and individually indexed. Libraries were sequenced on HiSeq 2000 platform (Illumina).

value: Spleen

value: Activated Treg cells

tag: source

tag: activating stimulus

value: LCMV-infection

tag: days post-stimulus

value: 11 days


title: AdV-VP55 replicate 2

source_name: AdV-VP55 replicate 2


title: P16_26_043

description: P = Pregnant


title: P16_17_025

description: P = Pregnant


title: P16_29_049

description: P = Pregnant


title: P16_31_045

description: P = Pregnant


title: PBS replicate 2

source_name: PBS replicate 2


title: P16_24_013

description: P = Pregnant


title: Case12_T

city: Columbus

first: Albert

last: de la Chapelle

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

data_processing:
Pre-alignment data QC were assessed with FastQC. Post-alignment data quality was assessed with an in-house quality control pipeline/database for RNA-seq database.
RNA-seq data were trimmed for any adapter sequences using Adapter Removal software. Any residual rRNA and mitoRNA in RNA-seq reads were removed by aligning to a custom human contaminome containing theses high abundance sequences using Bowtie2.
Mapped RNA-Seq reads to the human genome using TopHat and quantified the reads using Cufflinks software. The relative abundance of transcripts was measured in fragments per kilobase of exons per million fragments mapped (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: TXT: FPKM values for each Sample (GENCODE annotation)
Supplementary_files_format_and_content: TXT: FPKM values for each Sample (UCSC annotation)
Supplementary_files_format_and_content: GTF: Denovo gene annotation file obtained by merging denovo gene annotation files for each sample

source_name: Thyroid tissue

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The purity of extracted RNA was measured using a NanoDrop ND- 1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE) and the concentration was assessed with Qubit 2.0 Fluorometer (Agilent Technologies, Santa Clara, CA) using an RNA HS Assay Kit. Samples with RNA Integrity Number (RIN) greater than 4 as assessed by a BioAnalyzer (Agilent) with no visible sign of genomic DNA contamination from the HS Nanochip tracings were used for total RNA library generation.
Used the Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (catalog #RS-122-2201), which transformed RNA into cDNA. This kit employed Ribo-Zero to remove rRNA and mitochondrial RNA prior to library preparation. The protocol consisted of random primer and stranded RNA extraction, RNA fragmentation, reverse transcription, and 100bp paired-125 end sequencing using the Illumina HiSeq 2500 system.

tag: disease type

value: Papilary Thyroid Carcinoma

tag: tissue type

value: Tumor tissue


title: P16_14_014

description: P = Pregnant


title: Case12_N

value: Noncancerous tissue


title: P16_11_035

description: P = Pregnant


title: P24_31_051

description: P = Pregnant


title: P16_12_019

description: P = Pregnant


title: Case11_N


title: NP8_35_011

description: NP = Non-Pregnant

value: Non-Pregnant


title: Case10_T


title: P24_24_055

description: P = Pregnant


title: NP8_34_027

description: NP = Non-Pregnant


title: Case9_T


title: Case9_N


title: P16_10_032

description: P = Pregnant


title: Case10_N


title: NP8_25_017

description: NP = Non-Pregnant


title: Case8_T


title: Case8_N


title: P16_28_039

description: P = Pregnant


title: NP8_20_037

description: NP = Non-Pregnant


title: NP8_18_041

description: NP = Non-Pregnant


title: NP8_21_023

description: NP = Non-Pregnant


title: Case7_T


title: Case6_N


title: NP16_34_012

description: NP = Non-Pregnant


title: Case5_N


title: Case11_T


title: NP8_22_028

description: NP = Non-Pregnant


title: NP16_35_018

description: NP = Non-Pregnant


title: Case5_T


title: NP16_25_036

description: NP = Non-Pregnant


title: NP16_22_052

description: NP = Non-Pregnant


title: Case4_T


title: Case4_N


title: Case6_T


title: NP16_18_031

description: NP = Non-Pregnant


title: NP16_21_048

description: NP = Non-Pregnant


title: Case2_T


title: NP16_20_042

description: NP = Non-Pregnant


title: Case3_T


title: Case3_N


title: Case1_T


title: SRP72-bound polysomes, CHX

city: Stanford

first: Justin

middle: William

last: Chartron

state: California

address: Clark Center E200, 318 Campus Drive

institute: Stanford University

description:
Ribosome protected mRNA
SRP72 copurifying polysomes with CHX during harvesting

data_processing:
Library strategy: ribosome profiling
Base calls performed by Illumina CASAVA.
3' adaptor sequence was trimmed using Cutadapt 1.3.
Ribosomal RNA reads were removed by alignment to reference sequences using Bowtie.
Reads were aligned to the yeast genome using TopHat.
Aligned reads were assigned to open reading frames using GenomicAlignments package in Bioconductor.
Genome_build: sacCer3
Supplementary_files_format_and_content: XLSX file containing open reading frame names, total mapped reads, enrichment scores, and other attributes resulting from the analysis.

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast were grown in YPD media to mid-log phase. Cultures were harvested by fast filtration and plunged in liquid nitrogen.

extract_protocol:
Cells were lysed using a cryogenic mixer mill. Soluble and membrane-bound ribosomal fractions were separated by centrifugation. SRP72-TAP was immunoprecipitated and copurifying ribosomes were recovered. Polysomes and monosomes were separated using sucrose gradient ultracentrifugation. Samples were then digested with RNase I, and ribosomes were isolated by ultracentrifugation through a sucrose cushion. RNA was extracted from the ribosomal pellet.
RNA fragments of approximately 30 nucleotides were extracted from a denaturing polyacrylamide gel. A DNA adapter (CTGTAGGCACCATCAAT) was ligated to the 3' of fragments and used to prime reverse transcription. cDNA were circularized and rRNA-originating fragments were removed using biotinylated subtraction oligonucleotides. Libraries were barcoded during PCR amplification.

treatment_protocol: Where indicated with CHX, cultures were supplemented with cycloheximide to 100 µg/mL and immediately harvested with fast filtration.

tag: genotype

tag: treatment

value: Cycloheximide (CHX)


title: Membrane ribosomes, CHX

description:
Ribosome protected mRNA
Membrane ribosomes with CHX during harvesting


title: Soluble monosomes, CHX

description:
Ribosome protected mRNA
Soluble monosomes with CHX during harvesting


title: Case2_N


title: Case7_N


title: NP8_16_047

description: NP = Non-Pregnant


title: NP0_35_016

description: NP = Non-Pregnant


title: NP0_22_040

description: NP = Non-Pregnant


title: NP0_25_033

description: NP = Non-Pregnant


title: Soluble polysomes, CHX

description:
Ribosome protected mRNA
Soluble polysomes with CHX during harvesting


title: Case1_N


title: SRP72-bound monosomes, replicate 2

description:
Ribosome protected mRNA
SRP72 copurifying monosomes


title: NP0_34_046

description: NP = Non-Pregnant


title: NP0_20_034

description: NP = Non-Pregnant


title: NP16_16_024

description: NP = Non-Pregnant


title: NP0_16_010

description: NP = Non-Pregnant


title: Membrane polysomes, replicate 2

description:
Ribosome protected mRNA
Membrane polysomes


title: SRP72-bound polysomes, replicate 2

description:
Ribosome protected mRNA
SRP72 copurifying polysomes


title: NP0_21_030

description: NP = Non-Pregnant


title: SRP72-bound monosomes, replicate 1


title: SRP72-bound polysomes, replicate 1


title: NP0_18_021

description: NP = Non-Pregnant


title: TP53 knockout RNA-Seq_12h

data_processing:
Illumina Casava1.7 software used for basecalling.
The processing of reads included elimination of contaminant adaptar substrings with Scythe and quality-based trimming using Sickle. The alignment of reads to the human genome (hg19) was performed using Tophat2 mapper.
The transcript assembly  and quantification using FPKM of transcripts was carried out using Cufflinks2.
Annotation of the gene locus obtained was performed using Cuffmerge with Gencode v19 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample using cufflinks and GENCODE v19

source_name: HCT116 colon cancer cell lines, p53 -/-

growth_protocol: HCT116 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
RNA was isolated with TRIzol and purified with a Qiagen column kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For DNA damage, cells were treated with 350 µM 5-fluorouracil (F6627; Sigma) for 4h and 12h.

tag: passages

value: 8-10 passages

tag: dna-damage

tag: cell line


title: TP53 knockout RNA-Seq_0h


title: TP53 knockout RNA-Seq_4h


title: AdV-VP55

data_processing:
Linker sequences were removed from raw reads, consolidated, and then aligned to human annotated miRNA sequences using Bowtie.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing the miRNA name, mature miRNA sequence, and raw reads for each condition

source_name: HEK 293T cells

extract_protocol:
Total RNA was extracted from cells using Trizol reagent.
10µg of total RNA was separated on a 12% denaturing Tris-Urea gel. The ~19-24nt size fraction was excised, purified, and ethanol precipitated. The 3’ linker was ligated using T4RNA ligase2, truncated (NEB). RNA was again fractioned and purified. The 5’ linker was then ligated using T4 RNA ligase (Ambion) followed by another round of size fractionation, purification, and precipitation. Both 3’ and 5’ linkers have randomized ends with four random nucleotides (N) at the insertion site to reduce ligase bias (Jayaprakash et al., 2011). RNA containing both the 3’ and 5’ linkers was then reverse transcribed using SuperScript III (Invitrogen). PCR amplification of cDNA was performed using OneTaq 2x PCR Master Mix (NEB) and barcoded reverse primer for multiplexed sequencing.

value: HEK 293T


title: Soluble monosomes, replicate 1

description:
Ribosome protected mRNA
Soluble monosomes


title: Soluble polysomes, replicate 1

description:
Ribosome protected mRNA
Soluble polysomes


title: Soluble ribosomes, CHX

description:
Ribosome protected mRNA
Soluble ribosomes with CHX during harvesting


title: Membrane polysomes, replicate 1


title: 2ng/ml TGF-b DMOG (1mM) Repl 3

description:
Sample 18
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp2.txt

source_name: Splenic CD4+ T cells, WT, 2ng/ml TGF-b, DMOG

treatment_protocol: Naïve CD4+ T cells were isolated by FACS from spleens of wildtype mice and stimulated in vitro with anti-CD3 and anti-CD28 antibodies in the presence of indicated concentrations of TGF-b and either DMOG (1mM) or vehicle control. Cells were harvested at day 4 post-stimulation.

tag: strain/background

tag: genotype/variation

value: Wildtype

tag: cell type

value: CD4+ T cells

tag: tgf-b concentration (ng/ml)

value: Dimethyloxaloylglycine (DMOG)


title: Mock

value: Mock


title: AdV-GFP

value: AdV-GFP


title: 2ng/ml TGF-b Veh Repl 3

description:
Sample 17
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp2.txt

source_name: Splenic CD4+ T cells, WT, 2ng/ml TGF-b, vehicle

value: Vehicle


title: 2ng/ml TGF-b DMOG (1mM) Repl 2

description:
Sample 16
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp2.txt


title: 2ng/ml TGF-b DMOG (1mM) Repl 1

description:
Sample 14
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp2.txt


title: WT rep2

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

institute: UNSW

description:
WT2
Processed data file: count_matrix.txt

data_processing:
RNA libraries were sequenced on the Illumina HiSeq 2000 platform.
Sequenced reads were mapped to GRCm38 whole genome using Tophat2 (v 2.0.8) calling Bowtie2 (v 2.1.0).
HTSeq-count (Python package HTSeq, python v 2.7.3) was used to generate counts of reads uniquely mapped to annotated genes using the GRCm38 annotation GTF file.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: count_matrix.txt: Tab-delimited text file with read counts for each sample.

source_name: Lip tissue, WT

extract_protocol:
RNA was extracted from the dissected mouse tissues using TRI-reagent (Sigma), following the manufacturer's instructions, which included a chloroform phase separation and ethanol precipitation. RNA was resuspended in 70 μL of RNase-free water. RNA samples were assessed for quantity and quality using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), conventional RNA electrophoresis and using a Bioanalyser (Agilent Technology Inc). All RNA integrity numbers (RIN) for the analysed samples ranged from 9 to 9.5.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Wild type

tag: tissue

value: Lip


title: Gtf2ird1-KO rep3

description:
KO3
Processed data file: count_matrix.txt

source_name: Lip tissue, Gtf2ird1-KO

value: Gtf2ird1 KO


title: Soluble monosomes, replicate 2

tag: strain


title: Gtf2ird1-KO rep2

description:
KO2
Processed data file: count_matrix.txt


title: Gtf2ird1-KO rep1

description:
KO1
Processed data file: count_matrix.txt


title: WT rep3

description:
WT3
Processed data file: count_matrix.txt


title: RNA-pDC

city: Aachen

first: Manuel

last: Allhoff

address: Schinkelstr. 2

country: Germany

institute: AICES

data_processing:
We use BWA version 0.6.1  with standard parameter for read mapping on either mouse genome (mm9)
Differential peaks were detected with THOR (default parameters)  by comparison of samples from MPP vs. CDP, CDP vs. cDC, CDP vs. pDC and cDC vs. pDC.
Next, we counted the number of RNA-Seq reads overlapping with the differential peaks. We provide relative expression estimates around the differential peaks in bedgraph format.
Genome_build: mm9
Supplementary_files_format_and_content: Differential peaks in bed format (for ChIP-seq) and relative expression in bed graph format (for RNA-seq)

source_name: Plasmacytoid dendritic cell (pDC)

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described before (Dahl and Collas, 2008; Chauvistré et al., Eur. J. Immunol. 44, 2478-2488, 2014) with minor modifications. Briefly, sorted cells were cross-linked at a concentration of 2 million cells/ml with 1% formaldehyde for 6 min at room temperature. Cross-linking was stopped with 0.125 M glycine. Chromatin sonification into fragments of 200-400 bp in size was done in Bioruptor with cooling device (Diagenode) at 4°C for 10 min with 30 s pulse/pause cycles. Sheared lysates were clarified by centrifugation at 12,000g (10 min, 4°C). 10 µl Dynabeads Protein A (Life Technologies) were preincubated with either 1 µg H3K27Ac or IgG control (both Santa Cruz Biotechnology). For immunoprecipitation sheared chromatin of 1 million cells was added to the preincubated beads over night at 4°C. Chromatin complexes were isolated by magnetic bead selection and washed with RIPA and TE buffer. Chromatin complexes were digested with 50 µg/ml RNase (Roche) at 37°C for 30 min. Immunoprecipitated DNA was purified using QIAquick PCR Purification Kit (Qiagen). DNA concentration of immunoprecipitated DNA was determined by using Qubit dsDNA HS Assay kit (Life Technologies).
RNA was isolated using RNeasy Mini Kit with DNaseI digestion (Qiagen) as before (Felker et al., J. Immunol. 185, 5326-5335, 2010)
ChIP-Seq Libraries were prepared and subjected to deep-sequencing on the Illunima platform according to then manufacturer's protocols.
RNA-Seq libraries were prepared and subjected to strand-specific RNA-seq on the Illumina platform according to the manufacturer's protocols.

value: Plasmacytoid dendritic cell (pDC)


title: prt1-1, 37C, soluble

description:
PolyA RNA
Soluble mRNA from CY2522 cells shifted to 37C for 1 hour.

data_processing:
Base calls performed by Illumina CASAVA.
3' adaptor sequence was trimmed using Cutadapt 1.3.
Ribosomal RNA reads were removed by alignment to reference sequences using Bowtie.
Reads were aligned to the yeast genome using TopHat.
Aligned reads were assigned to open reading frames using GenomicAlignments package in Bioconductor.
Genome_build: sacCer3
Supplementary_files_format_and_content: XLSX file containing open reading frame names, total mapped reads, enrichment scores, and other attributes resulting from the analysis.

extract_protocol:
Cells were lysed using a cryogenic mixer mill. Soluble and membrane-bound fractions were separated by centrifugation. SRP72-TAP was immunoprecipitated from the soluble fraction. PolyA RNA was recovered by each fraction using oligo-dT beads and fragemented by alkaline hydrolysis.
RNA fragments of approximately 40 nucleotides were extracted from a denaturing polyacrylamide gel. A DNA adapter (CTGTAGGCACCATCAAT) was ligated to the 3' of fragments and used to prime reverse transcription. cDNA were circularized and libraries were barcoded during PCR amplification.

value: 1 hr temperature shift to 37C


title: 2ng/ml TGF-b Veh Repl 2

description:
Sample 15
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp2.txt


title: WT rep1

description:
WT1
Processed data file: count_matrix.txt


title: wild-type_osteoclast_M-CSF_RANKL_24H_rep1

city: Gwangju

first: Nacksung

last: Kim

address: B218, 160, Baekseo-ro, Dong-gu

department: Pharmacology

country: South Korea

institute: Chonnam National University Medical School

description:
bone marrow derived macrophages differentiated to osteoclasts
2-WT-M-CSF-RANKL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using TopHat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.1 software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Cells were lysed in Qiazol (Qiagen) and total RNA was isolated according to the manufacturer instruction
RNA libraries were prepared for sequencing using TruSeq RNA kit

value: wildtype (Stat5fl/fl)

value: osteoclast

tag: age

value: 8 weeks

tag: gender

value: Male


title: RNA-MPP

source_name: Multipotent progenitor (MPP)

value: Multipotent progenitor (MPP)


title: W303, 37C, membrane

description:
PolyA RNA
Membrane mRNA from cells W303 shifted to 37C for 1 hour.


title: wild-type_osteoclast_M-CSF_RANKL_IL-3_24H_rep1

description:
bone marrow derived macrophages differentiated to osteoclasts
3-WT-M-CSF-RANKL-IL-3


title: prt1-1, 37C, membrane

description:
PolyA RNA
Membrane mRNA from CY2522 cells shifted to 37C for 1 hour.


title: SRP72-bound monosomes, CHX

description:
Ribosome protected mRNA
SRP72 copurifying monosomes with CHX during harvesting

value: Cycloheximide (CHX)


title: 2ng/ml TGF-b Veh Repl 1

description:
Sample 13
PolyA RNA
Processed data file: Clever_et_al_PHD_proteins_2016_FPKM_Exp2.txt

value: Wildtype


title: RNA-cDC

source_name: Classical dendritic cell (cDC)

value: Classical dendritic cell (cDC)


title: prt1-1, 25C, membrane

description:
PolyA RNA
Membrane mRNA from CY2522 cells grown at 25C.

value: Growth at 25C


title: wild-type_osteoclast precursor_M-CSF_24H_rep1

description:
bone marrow derived macrophages differentiated to osteoclasts
1-WT-M-CSF

source_name: mouse bone marrow,wild-type,osteoclast precursor,M-CSF,24H


title: Input_CDP

source_name: Common dendritic cell progenitor (CDP)

value: Common dendritic cell progenitor (CDP)

tag: chip antibody

value: Input


title: RNA-CDP


title: prt1-1, 25C, soluble

description:
PolyA RNA
Soluble mRNA from CY2522 cells grown at 25C.


title: Input_cDC


title: W303, 25C, membrane

description:
PolyA RNA
Membrane mRNA W303 from cells grown at 25C.


title: Soluble polysomes, replicate 2

description:
Ribosome protected mRNA
Soluble polysomes


title: W303, 25C, soluble

description:
PolyA RNA
Soluble mRNA from W303 cells grown at 25C.


title: cDC_H3K27ac_2

value: H3K27ac (abcam-ab4729)


title: Input_MPP


title: Input_pDC


title: Soluble mRNA, puromycin

description:
PolyA RNA
Soluble mRNA from lysates with puromycin.

value: Lysate incubated with puromycin


title: pDC_H3K27ac_2


title: ko_osteoclast_M-CSF_RANKL_IL-3_24H_rep1

description:
bone marrow derived macrophages differentiated to osteoclasts
4-KO-M-CSF-RANKL-IL-3

value: STAT5 cKO (STAT5;MX1-Cre)


title: pDC_H3K27ac_1


title: MPP_H3K27ac_2


title: CDP_H3K27ac_2


title: SRP72-bound mRNA, CHX

description:
PolyA RNA
SRP-bound mRNA from lysates with cycloheximide.

value: Lysate incubated with cycloheximide


title: cDC_H3K27ac_1


title: Pt 1 cl1 PAPD5 KD

status: Public on Aug 02 2016

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

data_processing:
Alignment to transcriptome with HISAT 0.1.6.
Transcript quantification using Salmon 0.3.2.
Gene-level summarization.
Natural log transform (plus one pseudocount)
Genome_build: GRCh38

source_name: induced pluripotent stem cells

growth_protocol: iPS cells were maintained in Essential 8 medium on hES-qualified matrigel matrix and were routinely passaged with accutase (typically 200,000 to 300,000 cells/well onto 6 well plate). HEK 293 cells were maintained in DMEM (10-15% FBS) and passaged with 0.05% trypsin.

extract_protocol:
From plates of cells at 90-100% confluence, 1ml of Trizol was added directly onto cells after a PBS wash and scraped into eppendorf tubes for extraction according to protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: induced pluripotent stem cells

value: PAPD5 KD


title: WT iPSC ctrl KD

value: ctrl LUC KD


title: Pt 1 cl1 ctrl KD


title: W303, 37C, soluble

description:
PolyA RNA
Soluble mRNA from cells W303 shifted to 37C for 1 hour.

value: 1 hr temperature shift to 37C


title: SRP72-bound mRNA, puromycin

description:
PolyA RNA
SRP-bound mRNA from lysates with puromycin.


title: Membrane mRNA, puromycin

description:
PolyA RNA
Membrane mRNA from lysates with puromycin.


title: CDP_H3K27ac_1


title: Membrane mRNA, CHX

description:
PolyA RNA
Membrane mRNA from lysates with cycloheximide.


title: WT iPSC PAPD5 KD


title: Soluble mRNA, CHX

description:
PolyA RNA
Soluble mRNA from lysates with cycloheximide.


title: Pt 1 cl2 PAPD5 KD


title: Pt 1 cl2 ctrl KD


title: Input 1

city: Cleveland

first: Michelle

middle: Suzanne

last: Longworth

address: 9500 Euclid Ave NE20

department: Molecular Genetics

institute: Cleveland Clinic Foundation

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were trimmed of adapters and low-quality bases with Trim Galore (v.0.3.7 with cutadapt v.1.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode using default parameters.
FastQC (v.0.11.3,  http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) was used to verify the quality of trimmed samples.
Reads were aligned with bowtie (v.1.0.0, -m 1 --best --strata) and filtered to retain only properly paired alignments
Shiftsize for MACS2 was estimated from 100,000 properly paired alignments
MACS2 (v.2.0.9 20111102) was run with default settings except for explicit --shiftsize=125 --nomodel
Genome_build: BDGPr6 (from Flybase FB2015_01 release, 24 February 2015)
Supplementary_files_format_and_content: peak

organism: Drosophila melanogaster

source_name: S2R+ cells

growth_protocol: S2R+ cells were grown in Shields and Sang M3 Insect Medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
See protocol using Mnase digestion published in Schuster et. al. PLOS Genetics (2013).  10 units of micrococcal nuclease were used to digest DNA in each sample.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: embryonic

value: Oregon R


title: MPP_H3K27ac_1

value: Multipotent progenitor (MPP)


title: dCAP-D3 ChIP 2

value: YZ384 (Longworth lab)


title: dCAP-D3 ChIP 1


title: HEK 293 ctrl KD

source_name: HEK 293

value: HEK 293


title: IgG ChIP 1

value: Normal Rabbit IgG (Millipore 12-370)


title: 2.set2-K79me3-K18ac

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

department: School of Engineering

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Pair-end reads were mapped to the yeast genome (sacCer3) using bowtie2 with maximal fragment size of 1000bp.
We treated duplicate fragments as potential PCR artifacts. We thus treated the set of unique fragments found as the read-set. We defined mononucleosome fragments as these shorter than 220bp.
We used the nucleosome location atlas defined by Weiner et al(Weiner et al., 2015). We measured nucleosome coverage by counting the number of fragments overlapping a window of size 50bp around the center of the nucleosome.
Genome_build: sacCer3
Supplementary_files_format_and_content: csv file containing read counts for each nucleosome location in each combinatorial ChIP sample

source_name: yeast cells

growth_protocol: Yeast cells were grown in YPD media at 30ºC with constant shaking to OD 0.6-0.8.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature with occasional shaking, quenched with 0.125 M glycine for 5 minutes at room temperature with occasional shaking, collected by centrifugation, (4000 g, 5 minutes), washed with cold ddH2O supplemented with EDTA-free protease inhibitors cocktail (Roche) and the pellet was resuspended in buffer Z (1 M sorbitol, 50 mM Tris 7.4, 10 mM β-mercaptoethanol) with zymolyase (Seikagaku) at 0.3 - 1 units per 1 ml of original cell volume. Cells were gently rotated at 30ºC for 25 minutes until > 95% of cells were spheroplasted. Spheroplasts were pelleted (6500 g, 10 minutes) and resuspended in NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail) at final concentration of 200 OD/ml. Chromatin was digested with 12.5 units/ml MNase (Worthington) for 20 minutes at 37ºC, and digestion was stopped by removing the tubes into ice and addition of 1 volume of ice cold MNase stop buffer ( 220 mM NaCl, 0.2% SDS, 0.2% DOX, 10 mM EDTA, 2%,Triton X-100, EDTA-free protease inhibitor cocktail). Tubes were kept on ice for 10 minutes, vortexed 3 x 10 seconds, centrifuged (16,000 g, 10 minutes, 4ºC), and the supernatant containing the nucleosomes was removed to a fresh tube.
See attached paper - http://biorxiv.org/content/early/2016/06/27/060962

tag: library

value: Yeast deletion library

tag: 1st ip

tag: 2nd ip / input


title: 2.set2-K79me3-K4me3


title: IgG ChIP 2


title: 2.set2-K79me3-Input


title: Input 2


title: 2.set2-K4me3-K18ac


title: 2.set2-K4me3-K36me3


title: 2.set2-K36me3-Input


title: HEK 293 PAPD5 KD


title: 2.set2-K79me3-K79me3


title: 2.set2-K4me3-K79me3


title: All_samples_single-cell_RNA-seq_TPM

last: Sinha

state: CA

address: 265 Campus Drive

department: ISCBRM

institute: Stanford University School of Medicine

description: These files are matrices containing TPM values, where each row is a gene and each column a sample.

data_processing:
Sequenced reads were trimmed for adaptor sequences using skewer 0.1.127 with parameters -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -t 16 -q 21 -l 21 -n -u -f sanger for bulk-population RNA-seq and parameters -x CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG -y CTGTCTCTTATACACATCTGACGCTGCCGACGANNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT -t 16 -q 21 -l 21 -n -u -f sanger for single-cell RNA-seq.
Trimmed reads were then mapped to hg38 using STAR 2.4 with parameters  --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD  --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000  --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1 --twopassMode Basic --twopass1readsN -1 --outWigStrand Stranded
Normalized expression values (TPM) and transcript counts were then calculated using RSEM 1.2.21 with parameters --bam --estimate-rspd --seed 12345 --paired-end --forward-prob 0
Genome_build: hg38

source_name: H7 ESC

extract_protocol:
Total RNA or chromatin was extracted as described below
Bulk RNA-seq: Total RNA from flow-sorted or differentiated cell populations was isolated using Trizol (ThermoFisher) as per manufacturer’s recommendation and was facilitated by addition of linear polyacrylamide (Sigma) as a carrier during RNA precipitation. Purified total RNA was treated with 4 units of RQ1 RNase-free DNase (Promega) at 37 dgrees Celsius for 1 hour to remove trace amounts of genomic DNA. The DNase-treated total RNA was cleaned-up using RNeasy micro kit (QIAGEN). Subsequently, the integrity of extracted RNA was assayed by on-chip electrophoresis (Agilent Bioanalyzer) and only samples with a high RNA integrity (RIN) value were used for subsequent cDNA preparation. Purified total RNA (10-50 ng) was reverse-transcribed into cDNA and amplified using the Ovation  RNA-seq System V2 (NuGEN). Amplified cDNA was sheared using the Covaris S2 (Covaris) using the following settings: total volume 120 l, duty cycle 10%, intensity 5, cycle/burst 100, total time 2 min. The sheared cDNA was cleaned up using Agencourt Ampure XP (Beckman Coulter) to obtain cDNA fragments >= 400 base pairs (bp). 500 ng of sheared and size-selected cDNA were used as input for library preparation using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s recommendations. Resulting libraries (fragment distribution: 300-700 bp; peak 500-550 bp) were pooled (multiplexing) and sequenced using HiSeq 4000 or NextSeq 500 (Illumina) at the Stanford Functional Genomics Facility to obtain 2x150 base pair paired-end reads. For each RNA-seq library, the effectiveness of adapter ligation and the effective library concentration was determined by qPCR and bioanalyzer (Agilent) prior to pooling and loading them onto the sequencers. The reads obtained were trimmed for base call quality (PHRED score >= 21) and the presence of adapter sequences at the 3' end using Skewer (version: 0.1.127; Jiang et al, BMC Bioinformatics, 2014). Single-cell RNA-seq: Cells were briefly washed (DMEM/F12), dissociated (TrypLE Express), strained (100 micron filter), pelleted and resuspended in DMEM/F12 for counting. Before single-cell capture, two quality control steps were implemented. Firstly, cell size was estimated in order to determine whether cells should be loaded onto C1 capture arrays of either 10-17 micron or 17-25 micron size. Arrays were chosen for each lineage by estimating the median cell size of each given population on a flow cytometer on the basis of the FSC-W signal and choosing an array with an appropriate pore size to accommodate such cells. Secondly, to ensure the high viability of in vitro-differentiated cells prior to commencing single-cell RNA-seq, for each population a separate aliquot of cells was stained with 1.1 micromolar DAPI and analyzed by flow cytometry; for all cell populations that were used for single-cell RNA-seq, 98% of cells were viable (i.e., DAPI negative). For single-cell capture, cells were diluted to a concentration of 1000 cells/microliter, diluted 3:2 in C1 Cell Suspension Reagent, and loaded onto a Fluidigm C1 single-cell capture array chip for automated capture on a Fluidigm C1 Machine (Stanford Stem Cell Institute single-cell Core). After loading, the efficiency of single-cell capture was verified using an automated microscope that imaged each catured cell on the chip. The subsequent cell lysis, cDNA synthesis, and aplification was carried on the array chip inside the microfuidic chamber in an automated fashion using C1 machine using the SMARTer Ultra Low RNA Kit (Clontech, 634833) reagents as per the manufacturers' instructions (Fluidigm, PN 100-7168 Rev. A2). The amplified cDNA from individual cells was harvested into a 96 well and diluted using the harvesting reagent (Fluidigm). The concentration and integrity of amplified cDNA were assessed using a Fragment Analyzer (Advanced Analytical) in a 96 well plate format. Amplified cDNAs form only thos wells that (1) were not degraded, and (2) originated from wells that were microscopically verified to contain a single cell, were carried forward for subsequent library construction. Using a single-channel liquid handeling robot, Mosquito (TTP Labtech), amplified cDNAs from single-cells from all the lineages were diluted to a concentration range of 0.05-0.16 ng/microliter using C1 Harvest Reagent (Fluidigm) as a diluent and consolidated into 384 well plates. The diluted single-cell cDNAs were tagmented and converted to sequencing libraries in the 384 well plates using the Nextera XT DNA Sample Prep Kit (Illumina, FC-131-1096) in an automated fashion using another 16-channel Moquito robot (TTP Labtech) and 384 distinct illumina compatiblr molecular barcodes. The resulting sequencing libraies from a single such 384 plate were then pooled and cleaned up using Agencourt AMPure XP beads (Beckman Coulter). The pooled libraries were then analyzed for quality and concentration using bioanalyzer (Agilent) and qPCR and loaded on a single lane of NextSeq 500 or two lanes of Hiseq 4000 to obtain 1-2 million 2x150 reads per cell. The reads obtained were trimmed for base call quality (PHRED score >= 21) and the presence of adapter sequences using Skewer (version: 0.1.127; Jiang et al, BMC Bioinformatics, 2014). ATAC-seq: For each replicate, 50,000 cells were lysed in lysis buffer containing 0.01% IGEPAL CA-630 (Sigma, I8896) to obtain nuclei, which were directly used in the Tn5 transposition reaction (reagents from Nextera DNA Sample Preparation Kit; Illumina, FC-121-1030). Immediately following transposition, DNA fragments were purified (MinElute Kit, Qiagen) and PCR amplified for a total of 12-13 cycles using previously-designed primer sequences that include illumina compatible adapters and barcodes. The resulting ATAC-seq libraries were purified (MinElute Kit, Qiagen), pooled and final library-pool concentrations were assessed (Bioanalyzer) prior to next-generation sequencing. The quality of ATAC-seq libraries was confirmed by a shallow sequencing run using a MiSeq v3 (Stanford Functional Genomics Facility, 2x75bp reads) before deep sequencing was performed on a NextSeq 500 (2x75bp reads).

treatment_protocol: H7 hESC  Design: H7 human embryonic stem cells (WiCell) were cultured feeder-free in mTeSR1 (StemCell Technologies; supplemented with 1% penicillin/streptomycin) on a Geltrex basement membrane (Gibco), with mTeSR1 media changed daily.  Anterior Primitive Streak (APS)  Design: Partially confluent cultures of mTeSR1-maintained H7 human embryonic stem cells (WiCell) were dissociated into very fine clumps using Accutase (Gibco) and sparsely passaged ~1:12-1:20 onto new Geltrex-coated cell culture plates in mTeSR1 supplemented with 1 μM thiazovivin (Tocris; a ROCK inhibitor to prevent cell death after dissociation) overnight. The following morning, H7 human embryonic stem cells were briefly washed (in DMEM/F12) before treatment for 24 hours with 30 ng/mL Activin A + 4 μM CHIR99021 + 20 ng/mL FGF2 + 100 nM PIK90 in CDM2 basal media to induce differentiation into anterior primitive streak.  Mid Primitive Streak (MPS)  Design: Partially confluent cultures of mTeSR1-maintained H7 human embryonic stem cells (WiCell) were dissociated into very fine clumps using Accutase (Gibco) and sparsely passaged ~1:12-1:20 onto new Geltrex-coated cell culture plates in mTeSR1 supplemented with 1 μM thiazovivin (Tocris; a ROCK inhibitor to prevent cell death after dissociation) overnight. The following morning, H7 human embryonic stem cells were briefly washed (in DMEM/F12) before treatment for 24 hours with 30 mg/mL Activin A + 40 ng/mL BMP4 + 6 μM CHIR99021 + 20 ng/mL FGF2 + 100 nM PIK90 in CDM2 basal media to induce differentiation into mid primitive streak.  Paraxial Mesoderm (DLL1+)  Design: H7-derived day 1 anterior primitive streak was briefly washed (DMEM/F12) and differentiated towards day 2 paraxial mesoderm for 24 hours (1 μM A-83-01 + 3 μM CHIR99021 + 250 nM LDN-193189 + 20 ng/mL FGF2) in CDM2 basal medium. Subsequently, day 2 paraxial mesoderm-containing cultures were dissociated into single cells (TrypLE Express) and stained with an anti-DLL1 PE antibody (Biolegend) and DAPI (Biolegend). Then, viable DLL1+ paraxial mesoderm cells were purified using a fluorescence-activated cell sorter (FACSAria II, BD Biosciences).     Non-Paraxial Mesoderm (DLL1-)  Design: H7-derived day 1 anterior primitive streak was briefly washed (DMEM/F12) and differentiated towards day 2 paraxial mesoderm for 24 hours (1 μM A-83-01 + 3 μM CHIR99021 + 250 nM LDN-193189 + 20 ng/mL FGF2) in CDM2 basal medium. Subsequently, day 2 paraxial mesoderm-containing cultures were dissociated into single cells (TrypLE Express) and stained with an anti-DLL1 PE antibody (Biolegend) and DAPI (Biolegend). Then, viable DLL1- non-paraxial mesoderm cells were purified using a fluorescence-activated cell sorter (FACSAria II, BD Biosciences).  Early Somites  Design: H7-derived day 2 paraxial mesoderm was briefly washed (DMEM/F12) and further differentiated into day 3 early somites for 24 hours (1 μM A-83-01 + 250 nM LDN-193189 + 1 μM C59 + 500 nM PD0325901; sometimes with the use of 1 μM XAV939 in lieu of C59) in CDM2 basal medium.  Sclerotome  Design: H7-derived day 3 early somites were briefly washed (DMEM/F12) and further differentiated into day 5-6 ventral sclerotome for 48-72 hours (5 nM 21K + 1 μM C59) in CDM2 basal media.  Dermomyotome  Design: H7-derived day 3 early somites were briefly washed (DMEM/F12) and further differentiated into day 5 dermomyotome (3 μM CHIR99021 + 150 nM Vismodegib) for 48 hours, optionally with the addition of 50 ng/mL BMP4.  Central Dermomyotome  Design: H7-derived day 3 early somites were briefly washed (DMEM/F12), treated with 3 μM CHIR99021 + 150 nM Vismodegib + 50 ng/mL BMP4 for 24 hours, and then washed again (DMEM/F12) and subsequently treated with CHIR99021 (3 μM) + 21K (5 nM) for 24 hours to yield day 5 central dermomyotome.  Lateral Mesoderm  Design: H7-derived day 1 mid primitive streak was briefly washed (DMEM/F12) and differentiated towards day 2 lateral mesoderm for 24 hours (1 μM A-83-01 + 30 ng/mL BMP4 + 1 μM C59) in CDM2 basal medium.  Cardiac Mesoderm (GARP+)  Design: H7-derived day 2 lateral mesoderm was differentiated into day 4 cardiac mesoderm by briefly washing (DMEM/F12), treatment with 1 μM A8301 + 30 ng/mL BMP4 + 20 ng/mL FGF2 for 24 hrs followed by brief washing (DMEM/F12) and then treatment with 25 ng/mL Activin + 30 ng/mL BMP4 + 1 μM C59 for the next 24 hrs. Subsequently, day 4 cardiac mesoderm-containing cultures were dissociated into single cells (TrypLE Express) and stained with an anti-GARP APC antibody (Biolegend) and DAPI (Biolegend). Then, viable GARP+ cardiac mesoderm cells were purified using a fluorescence-activated cell sorter (FACSAria II, BD Biosciences)  D2.25 Somitomeres (single-cell RNA-seq)  Design: H7-derived day 2 paraxial mesoderm was briefly washed (DMEM/F12) and further differentiated into day 2.25 somitomeres for 6 hours (1 μM A-83-01 + 250 nM LDN-193189 + 1 μM XAV939 + 500 nM PD0325901) in CDM2 basal medium.

tag: source

value: H7 ESC

tag: sample type

value: In vitro cultured H7 human embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors


title: 2.set2-K4me3-Input

value: Input


title: 2.set2-K79me3-K36me3


title: 2.eaf3-K79me3-K36me3


title: 2.set2-K36me3-K79me3


title: 2.eaf3-K79me3-K4me3


title: 2.set2-K36me3-K18ac


title: 2.set2-K36me3-K36me3


title: 2.set2-K4me3-K4me3


title: 2.eaf3-K79me3-Input


title: 2.set2-K18ac-K4me3


title: 2.set2-K36me3-K4me3


title: 2.eaf3-K4me3-Input


title: 2.eaf3-K36me3-K79me3


title: 2.eaf3-K79me3-K18ac


title: 2.eaf3-K79me3-K79me3


title: 2.set2-K18ac-Input


title: 2.eaf3-K36me3-K36me3


title: 2.eaf3-K4me3-K4me3


title: 2.eaf3-K4me3-K18ac


title: 2.eaf3-K4me3-K36me3


title: 2.set2-K18ac-K36me3


title: 2.eaf3-K36me3-Input


title: 2.set2-K18ac-K79me3


title: 2.eaf3-K36me3-K4me3


title: 2.eaf3-K18ac-K36me3


title: 2.eaf3-K18ac-K79me3


title: 2.set2-K18ac-K18ac


title: 2.eaf3-K36me3-K18ac


title: 2.eaf3-K18ac-K4me3


title: 2.eaf3-K18ac-K18ac


title: 2.WT-K79me3-K4me3


title: 2.WT-K79me3-K36me3


title: 2.WT-K79me3-K79me3


title: 2.eaf3-K18ac-Input


title: 2.eaf3-K4me3-K79me3


title: 2.WT-K79me3-Input


title: 2.WT-K79me3-K18ac


title: 2.WT-K4me3-K18ac


title: 2.WT-K4me3-Input


title: 2.WT-K36me3-K79me3


title: 2.WT-K36me3-K4me3


title: 2.WT-K36me3-K36me3


title: 2.WT-K18ac-K79me3


title: 2.WT-K4me3-K4me3


title: 2.WT-K36me3-Input


title: 2.WT-K18ac-K18ac


title: 2.WT-K18ac-K4me3


title: 2.WT-K18ac-Input


title: 2.WT-K18ac-K36me3


title: 2.WT-K36me3-K18ac


title: 1.WT-K79me3-K79me3

value: WT H3

value: Histone mutation library


title: 1.WT-K79me3-Input


title: 1.WT-K79me3-K36me3


title: 1.WT-K79me3-K4me3


title: 1.WT-K79me3-H3


title: 1.WT-K79me3-K18ac


title: 1.WT-K4me3-Input


title: 1.WT-K4me3-K79me3


title: 2.WT-K4me3-K36me3


title: 1.WT-K4me3-K4me3


title: 1.WT-K4me3-K18ac


title: 1.WT-K4me3-H3


title: 1.WT-K36me3-K4me3


title: 1.WT-K36me3-Input


title: 1.WT-K36me3-K79me3


title: 1.WT-K36me3-K18ac


title: 1.WT-K36me3-K36me3


title: 1.WT-K18ac-K79me3


title: 2.WT-K4me3-K79me3


title: 1.WT-K18ac-K18ac


title: 1.WT-K18ac-K36me3


title: 1.WT-K18ac-H3


title: 1.WT-K36me3-H3


title: 1.WT-K18ac-Input


title: 1.WT-H3-Input


title: 1.WT-H3-K36me3


title: 1.WT-H3-K79me3


title: 1.WT-K18ac-K4me3


title: 1.WT-H3-H3


title: 1.WT-H3-K18ac


title: 1.K4R-K79me3-Input


title: 1.WT-H3-K4me3


title: 1.WT-K4me3-K36me3


title: 1.K4R-K79me3-K79me3


title: 1.K4R-K79me3-H3


title: 1.K4R-K79me3-K36me3


title: 1.K4R-K4me3-Input


title: 1.K4R-K4me3-K79me3


title: 1.K4R-K4me3-K18ac


title: 1.K4R-K4me3-K4me3


title: 1.K4R-K4me3-K36me3


title: 1.K4R-K4me3-H3


title: 1.K4R-K36me3-K4me3


title: 1.K4R-K36me3-K36me3


title: 1.K4R-K36me3-K79me3


title: 1.K4R-K36me3-K18ac


title: 1.K4R-K79me3-K18ac


title: 1.K4R-K18ac-K79me3