title: H3K4me1 granule cells r1 IP

description:
GC_E1_Promoters.txt
GC_E2_Non_regulatory.txt
GC_E3_Primed_Enhancers.txt
GC_E4_Active_Enhancers.txt
Barcode: ATGTCA


title: YL-C-8

status: Public on Aug 29 2017

type: SRA

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

country: USA

institute: USC

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and  low-quality sequence, then mapped to mm 10 whole genome using TopHat 2
Read density as Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following a method of Mortazavi et al 2008, Nature Methods 2008 using an exon model.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include RPKM values for each wt and mutant mouse is attached as File 1 Normlaized RPKM values

molecule: total RNA

organism: Mus musculus

source_name: tooth germ

extract_protocol:
First mandibular molars at PN4 from Nfic-/- and littermate Nfic+/- control mice were dissected out, and the apical half was cut with a fine blade and transferred to RNA stabilization reagent (Qiagen, 76104). Total RNA was extracted with an RNeasy Mini Kit (Qiagen, 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: apical half of tooth germ

tag: age

value: post natal day 4

tag: genotype

value: Control Nfic+/-


title: YL-M-7

value: Nfic-/-


title: ORGANIC MeCP2 granule cells r1 IN

city: NYC

first: Marian

last: Mellen

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
native ChIP-Seq
Barcode: ACAGTG

library_source: genomic

data_processing:
100 bp paired-end reads were aligned using Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012) with default parameters in a sensitive-local configuration with a minimum alignment score of G,20,8.
Duplicates removed using  SAMtools (Li et al., 2009)
HOMER (v4.8) (Heinz et al., 2010) scripts were used for tag quantification in RefSeq annotated TSS, TTS and transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: List of autosomal genes analyzed in Mellen et al.,  2017, where the MeCP2 enrichment value is indicated. Enrichment measurements for  ORGANIC MeCP2 ChIP were calculated per transcript length as the fraction of normalized values in Fragments per Kilobase per Million (FPKM) to the mean value of the genome of IP and input (MeCP2 Enrichment=((MeCP2 IP/mean [MeCP2  IP]))/((input/mean [input])). Enrichment of each pair was calculated individually. Final MeCP2 enrichment value is the average of individual replicas.

molecule: genomic DNA

source_name: Cerebellar Granule Cells

extract_protocol:
Nuclei isolation and sorting were performed as described in (Kriaucionis and Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine [pH 7.8]), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor cocktail using loose (A) and tight (B) glass-glass dounce. The homogenate was supplemented with 50% iodixanol (OptiPrep), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine (pH 7.8); and laid on a 29% iodixanol cushion. Nuclei were pelleted by centrifugation for 30 min at 10,000 g and at 4 °C in swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in homogenization buffer and co-stained with DyeCycle Ruby to 20 μM final concentration. A total of 4 cerebella (2 males and 2 females) were pooled before sorting. Nuclei were sorted in a BD FASCAria cell sorter using 635 nm and 488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice) indicating bacTRAP positive cells and lowest signal for DyeCycle Ruby indicating singlets.
After sorting, 3x10e6 nuclei were centrifuged (1200 g 15 min at 4 °C), and resuspended in 500 μL of pre-warmed MNase digestion buffer: 15mM Tris-HCL pH 8, 1 mM CaCl2, 15 mM NaCl, 60 mM KCl, 0.5 mM spermidine. Nuclei were digested with 2.5 U of micrococcal nuclease at 37 °C for 6 minutes. Digestion was stopped on ice by adding 5 mM of EDTA. After spinning (as described in ChIP-Seq) pellet was resuspended in 500 μL of extraction buffer: 10 mM Tris-HCL pH 8, 150 mM of NaCL 0.1% Triton-X 1.5 mM EDTA pH 8 and 0.5 spermidine.  Supernatant (S1) was kept at 4 °C after NaCl and Triton-X were adjusted to 150 mM and 0.1% respectively. DNA was mechanically extracted using a 26-ga needle ten times on ice prior to 4 °C end-over-end incubation for 2h. The extract was then centrifuged at 10,000 rpm and 4 °C for 10 min and supernatant was kept as fraction S2. S1 and S2 were combined and 25 μL was reserved as Input. Immunoprecipitation was performed at 4 °C overnight in an end-to-end rotator by combining the extract (S1+S2) with anti MeCP2 antibody (AB1) coated beads (50 μL of protein G and 50 μL of protein A Dynabeads per sample). After incubation, beads were washed in extraction buffer, DNA extracted and library prepared for Illumina sequencing .

tag: facs condition

value: GFP+

tag: chip antibody


title: YL-C-7


title: ORGANIC MeCP2 granule cells r2 IN

description:
native ChIP-Seq
Barcode: GCCAAT


title: ORGANIC MeCP2 granule cells r1 IP

description:
native ChIP-Seq
Barcode: CTTGTA

value: MeCP2; Cell Signaling; D4F3; lot # 2


title: ORGANIC MeCP2 granule cells r2 IP

description:
native ChIP-Seq
Barcode: GTGAAA


title: YL-C-6


title: YL-C-5


title: H3K27ac granule cells r1 IP

description:
GC_E1_Promoters.txt
GC_E2_Non_regulatory.txt
GC_E3_Primed_Enhancers.txt
GC_E4_Active_Enhancers.txt
Chromatin_ratio_GC_MellenM_genes.bed.txt
Barcode: GCCAAT

data_processing:
50 bp single-end reads were aligned using Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012) with default parameters in a sensitive-local configuration with a minimum alignment score of G,20,8
Duplicates removed using  SAMtools (Li et al., 2009)
HOMER (v4.8) (Heinz et al., 2010) scripts were used for tag quantification in RefSeq annotated TSS, TTS and transcripts.
We used ChromHMM for the analysis of chromatin states using a combination of marks. We used H3K4me3, H3K4me1 and H3K27Ac bam files and defined a learning model of four chromatin states with a resolution of 200 bp bins.
Genome_build: mm10
Supplementary_files_format_and_content: Chromatin accessibility ratio (EC/HC). To obtain this ratio, we first calculated the normalized (RPM) enrichment as follows:EC=((H3K27Ac ChIP /mean [H3K27Ac ChIP]))/(( input /mean [input])) HC=((H3K9me3 ChIP /mean [H3K9me3 ChIP]))/(( input /mean [input])). These values were then used to obtain the ratio EC/HC and an estimation of euchromatic and heterochromatic DNA. ChromHMM released four chromatin states. After confirmation of genomic localization and ATAC-Seq peak correlation in the genome browser, we defined emitted state 1 as active promoters, state 2 as non-regulatory DNA, state 3 as primed enhancers and state 4 as active enhancers. Genomic coordinates of each state are shown.

extract_protocol:
Nuclei isolation and sorting were performed as described in (Kriaucionis and Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine [pH 7.8]), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor cocktail using loose (A) and tight (B) glass-glass dounce. The homogenate was supplemented with 50% iodixanol (OptiPrep), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine (pH 7.8); and laid on a 29% iodixanol cushion. Nuclei were pelleted by centrifugation for 30 min at 10,000 g and at 4 °C in swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in homogenization buffer and co-stained with DyeCycle Ruby to 20 μM final concentration. A total of 4 cerebella (2 males and 2 females) were pooled before sorting. Throughout the protocol buffers were supplemented with EDTA-free protease inhibitor cocktail and 10 mM of sodium butyrate. For ChIP-Seq homogenates were fixed prior to the addition of 50% iodixanol by adding 1% paraformaldehyde (PFA) for 8 minutes end-to-end rotation.  PFA was then quenched by adding 125 μL of glycine for 5 min. Nuclei were sorted in a BD FASCAria cell sorter using 635 nm and 488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice) indicating bacTRAP positive cells and lowest signal for DyeCycle Ruby indicating singlets. Alternatively, for H3K27Ac and H3K4me1 ChIP-Seq, granule cell nuclei from C57BL/6J were sorted by selecting a specific FSC/SSC population identified from GC EGFP+ mice. We observed that this FSC/SSC gated population in granule cell EGFP+ animals resulted > 92% of the sorted nuclei being EGFP positive. Thus, the gate selected allows us to enrich the sample from 65%–70% to 92%–96% on granule cells, as described in (Mellen et al., 2012).
After sorting, nuclei were processed using LowCell# ChIP kit. 105 Nuclei were sonicated in a Bioruptor water bath sonicator for 15 min at intervals of 30s on and 30 s off to obtain ~350 bp fragments and chromatin frozen in liquid nitrogen and kept at -80 °C. Each immunoprecipitation (IP) was performed in chromatin aliquots of 5x10e5 nuclei. Immunoprecipitation was performed following LowCell# ChIP kit manufacturer’s instructions, mixing 50:50 IgA and IgG coated beads to 3 μg of antibodies. 1:10 of resuspended chromatin per sonicated nuclei was saved as input sample of the procedure. Immunoprecipitation was performed at 4 °C overnight in an end-to-end rotator. After washing beads with IP DNA, both input and IP samples were digested with Proteinase K 100 μg/ml in the presence of SDS 1% for 2 hr at 50 °C. Then, the lysate was treated with RNase A/T1 mix for 1h at 37 °C to and DNA was extracted with phenol: chloroform: isoamyl alcohol (25:24:1), precipitated in 70% ethanol and dissolved in TruSeq DNA Sample kit resuspension buffer.

value: GC size


title: MethylC granule cells replica2

data_processing:
Sequencing data were aligned to UCSC mm10 Mus musculus genome using bsmap aligner (v2.87) (Xi and Li, 2009) with default parameters and un-stranded configuration, allowing read length * 8% number of mismaches.
MOABS (Sun et al., 2014) methylation ratio calling module (mcall) was used to summarize the methylation levels of individual cytosines.
Files were further processed using SAMtools (Li et al., 2009) and BEDtools (Quinlan and Hall, 2010).
Only good-quality base calls (Phred score of 20 or greater) and total read count greater than 5 per site were considered.  Each base call was paired between MethylC-Seq and oxBS-Seq per replica and 5hmC estimated by the difference between the two fractions of modification. Negative values were then removed from the analysis. DNA methylation analysis is based on the level (5(h)mCG/CG, or 5(h)mCA/CA, which are estimates of the fraction of cytosines in the sequenced population that are methylated.
HOMER (v4.8) (Heinz et al., 2010) scripts were used for tag quantification in RefSeq annotated TSS, TTS and transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: List of autosomal genes analyzed in Mellen et al.,  2017, where average percentage of cytosine modifications per CG and CA context are indicated. Technical and biological MethylC-Seq and oxBS-Seq replicas were merged in a single biological replicas before processing. Base calls with less than 5 total reads or more than 100 total reads were eliminated from the analysis. HOMER (v4.8)scripts were used for quantification of percentage of modification in autosomal transcripts.

extract_protocol:
Nuclei isolation and sorting were performed as described in (Kriaucionis and Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine [pH 7.8]), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor cocktail using loose (A) and tight (B) glass-glass dounce. The homogenate was supplemented with 50% iodixanol (OptiPrep), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine (pH 7.8); and laid on a 29% iodixanol cushion. Nuclei were pelleted by centrifugation for 30 min at 10,000 g and at 4 °C in swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in homogenization buffer and co-stained with DyeCycle Ruby to 20 μM final concentration. A total of 4 cerebella (2 males and 2 females) were pooled before sorting. Nuclei were sorted in a BD FASCAria cell sorter using 635 nm and 488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice) indicating bacTRAP positive cells and lowest signal for DyeCycle Ruby indicating singlets.
Ox-BS-Seq and MethylC-Seq experiments were performed using TrueMethyl-Seq reagents and workflow, following manufacturer’s instructions. A total of 4 cerebella (2 males and 2 females) were pooled before sorting. For oxbS-Seq and MethylC-Seq nuclei were fast frozen in liquid nitrogen after sorting and kept at −80 °C until analysis was performed.  The day of the experiment, nuclei were digested with Proteinase K 100 μg/ml in the presence of SDS 1% for 2 hr at 50 °C. Then, the lysate was treated with RNase A/T1 mix for 1h at 37 °C to and DNA was extracted with phenol: chloroform: isoamyl alcohol (25:24:1), precipitated in 70% ethanol and dissolved in Tris-EDTA buffer. At least 1 μg  of DNA per sample was sonicated using Covaris-S2 system, DNA fragments of ~ 200 bp were end-repaired using TruSeq DNA Sample kit as per manufacturer‘s instructions. 4 ng of TrueMethyl sequencing spike-in controls were added to the DNA sample prior to adapter ligation. After TruSeq DNA adapters ligation, libraries were re-purified to eliminate potential contaminating compounds using 80% Acetonitrile and TrueMethyl-Seq magnetic beads. DNA libraries in bead pellets were then incubated 5 minutes at 37 °C in 20 µL of denaturing solution. ssDNA libraries were then transferred into two independent tubes: 1 μL of oxidation solution was added to the oxBS sample and 1 μL of ultra-pure water added to MethylC sample. After the oxidation step, bisulfite conversion, desulfonation and purification were performed in both oxBS library and MethylC library as per manufacturer’s instructions. PCR amplification suitable for HiSeq2000 sequencing was performed using TruSeq DNA primers and TrueMethyl-Seq reagents. Quality of libraries was assessed using High Sensitivity D1000 ScreenTape for the 2200 TapeStation system.

tag: dna oxidation

value: NO


title: HSVd-HPM rep 2

city: Pullman

first: Madhu

last: Kappagantu

state: WA

address: 345 Johnson Hall

department: Plant Pathology

institute: Washington State University

data_processing:
Quality control for raw reads was conducted using CLC Genomics Workbench 9.0.1. Low quality reads and reads with ambiquous nucleotides were removed
Adopter sequences were trimmed
Trimmed raw reads were used in RNA sequence expression analysis.
Expression analysis was performed using the hop transcriptome available in National Centre for Biotechnology Information (NCBI) data base (GenBank Transcript BioProject 270039 (387,929 transcript contigs) as the reference genome
Expression values for each contig were calculated as reads per kilobase per million mapped reads (RPKM) [Mortazavi et al., 2008 Nature methods. 5(7): 621-628]
Genome_build: BioProject 270039 (387,929 transcript contigs)     PRJDB3233
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for all the samples

organism: Humulus lupulus

source_name: leaf

growth_protocol: Hop cultivar Willamette was used in this study,  all plants were grown at 25°C to 28°C with a 14 h light and 10 h dark cycle

extract_protocol:
Total RNA was isolated from leaf tissues with the RNeasy Plant Mini Kit (Qiagen, Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Plants were inoculated with an extract from a single hop plant infected with Hop stunt viroid
Healthy and Hop stunt viroid infected hop leaves were later collected and inoculated with Podospheara macularis (inouculum concentration : 20,000 spores/mL)

tag: treatment

value: hop leaf inoculated with HSVd and Podospheara macularis

value: Fully expanded mature leaf


title: oxBS granule cells replica2

data_processing:
Library strategy: oxBS-Seq
Sequencing data were aligned to UCSC mm10 Mus musculus genome using bsmap aligner (v2.87) (Xi and Li, 2009) with default parameters and un-stranded configuration, allowing read length * 8% number of mismaches.
MOABS (Sun et al., 2014) methylation ratio calling module (mcall) was used to summarize the methylation levels of individual cytosines.
Files were further processed using SAMtools (Li et al., 2009) and BEDtools (Quinlan and Hall, 2010).
Only good-quality base calls (Phred score of 20 or greater) and total read count greater than 5 per site were considered.  Each base call was paired between MethylC-Seq and oxBS-Seq per replica and 5hmC estimated by the difference between the two fractions of modification. Negative values were then removed from the analysis. DNA methylation analysis is based on the level (5(h)mCG/CG, or 5(h)mCA/CA, which are estimates of the fraction of cytosines in the sequenced population that are methylated.
HOMER (v4.8) (Heinz et al., 2010) scripts were used for tag quantification in RefSeq annotated TSS, TTS and transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: List of autosomal genes analyzed in Mellen et al.,  2017, where average percentage of cytosine modifications per CG and CA context are indicated. Technical and biological MethylC-Seq and oxBS-Seq replicas were merged in a single biological replicas before processing. Base calls with less than 5 total reads or more than 100 total reads were eliminated from the analysis. HOMER (v4.8)scripts were used for quantification of percentage of modification in autosomal transcripts.

value: YES


title: oxBS granule cells replica3


title: YL-M-5


title: MethylC granule cells replica1


title: oxBS granule cells replica1


title: HSVd-HPM rep 1


title: HSVd-HPM rep 3


title: nuclear RNA granule cells r3

description:
Nuclear_RNA_GC_MellenM_genes.bed.txt
Barcode: GTGAAA

data_processing:
50 bp single end sequencing data were aligned to mm10 Mus musculus genome using STAR (v2.4.2a) (Dobin et al., 2013) and processed with SAMtools (Li et al., 2009).
HOMER (v4.8) (Heinz et al., 2010) scripts were used for quality control and to quantify gene expression in gene bodies allowing multiple isoforms per gene.
Genome_build: mm10
Supplementary_files_format_and_content: List of autosomal genes analyzed in Mellen et al.,  2017, where the mean RPKM values per transcript are indicated, calculated with HOMER. The magnitude and direction of gene expression dysregulation in  Dnmt3acko compared to the wt IS defined  as the effect size   Z=(M(ko)-M(wt))/√([SD(ko)+SD(wt)]/2). This metric compares the extent of difference between mean Dnmt3acko expression and wt expression (in Reads per Kilobase per Million- RPKM) per each gene, scaled by the degree of variation of both phenotypes.

molecule: nuclear RNA

extract_protocol:
Nuclei isolation and sorting were performed as described in (Kriaucionis and Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in the presence of 0.5 mM dithiothreitol and RNasin RNase inhibitors.  in homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine [pH 7.8]), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor cocktail using loose (A) and tight (B) glass-glass dounce. The homogenate was supplemented with 50% iodixanol (OptiPrep), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine (pH 7.8); and laid on a 29% iodixanol cushion. Nuclei were pelleted by centrifugation for 30 min at 10,000 g and at 4 °C in swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in homogenization buffer and co-stained with DyeCycle Ruby to 20 μM final concentration.  Nuclei were sorted in a BD FASCAria cell sorter using 635 nm and 488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice) indicating bacTRAP positive cells and lowest signal for DyeCycle Ruby indicating singlets.
After sorting, RNeasy Micro kit with in-column DNase digestion was used to extract RNA from nuclei. 10 ng of total RNA per sample were converted to cDNA using the NuGEN Ovation RNA-Seq kit following manufacturers’ instructions. cDNA obtained was quality scored by RNA 6000 PicoChip for Agilent 2100 Bioanalyzer. 1 mg of cDNA per sample was sonicated using Covaris-S2, cDNA fragments of 200 bp were end-repaired and adapters were ligated for HiSeq 2000 technology using TruSeq DNA Sample kit and following manufacturer ‘s instructions.


title: HPM rep 2

value: hop leaf inoculated with Podospheara macularis


title: HPM rep 3


title: HSVd rep 3

value: hop leaf inoculated with HSVd


title: nuclear RNA granule cells r2

description:
Nuclear_RNA_GC_MellenM_genes.bed.txt
Barcode: CAGATC


title: HPM rep 1


title: nuclear RNA granule cells r1

description:
Nuclear_RNA_GC_MellenM_genes.bed.txt
Barcode: CGATGT


title: HSVd rep 2


title: Mito_ChiP_A16

data_processing:
Basecalls, demultiplexing and fastq generation was carried out using CASAVA v 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using BWA (Burrough Wheel Aligner).
Data were filtered and
Peaks were called using MACS using mfold 32 p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: wig and bedgraph files were generated.

source_name: Raw 264.7_mtDNA

growth_protocol: The cells were cultured in DMEM medium containing 4.5 g/L glucose supplemented with 10% FBS, 4mM L-glutamine, and 1mM sodium pyruvate.

extract_protocol:
LPS-treaetd M1 cells are firstly fixed in 1% final concentration of formaldehyde for 10 minutes. For mtDNA ChIP-seq, mitochondria are purified from the formaldehyde fixed cells. In both case, ChIP-isolated DNA fragments are carried out using the ChIP Assay Kit (Millipore # 17-295).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired and blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters.  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 Illumina Hi-Seq  following the manufacturer's protocols.sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells are treated with 100 ng/ml of lipopolysaccharide (LPS) for 4 hours to induce M1 phenotype.

tag: cell line

value: RAW 264.7 (ATCC TIB-71)

tag: cell type

value: macrophage-like; Abelson leukemia virus transformed

tag: molecule subtype

value: mitochondrial DNA (mtDNA)

value: Anti-Notch1 antibody - ChIP Grade

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Mito_Input_A14


title: HSVd rep 1


title: Cell_ChIP_A12

source_name: Raw 264.7_nuclear DNA

value: nuclear genomic DNA


title: Control rep 3

value: leaf, untreated


title: Cell_Input_A11


title: YL-M-6

value: apical half of tooth germ

value: post natal day 4

value: Nfic-/-


title: MethylC granule cells replica3

value: GFP+


title: 26h-2

city: Wuhan

first: Xinfeng

last: Li

address: Shi zi shan street

country: China

institute: Huazhong Agricultural University

data_processing:
The quality of the raw sequence data were first assessed by FastQC and the sequences were then filtered and trimmed by Trimmomatic
The remaining reads were used to map to the reference genome of M. smegmatis (NC_008596.1) by Bowtie2
Alignments reported from Bowtie2 were further processed by the BEDTools software
Differential expression of all of transcripts was quantified through DEGseq software
Differential expressed genes were simply defined as at least 2-fold change with FDR (false discovery rate) less than 0.001.
Genome_build: M. smegmatis mc2155 (NC_008596.1; ASM1500v1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Mycolicibacterium smegmatis MC2 155

source_name: 26h, Mycobacteriun smegmatis mc2155

growth_protocol: Bacteria were growth in 7H9 broth medium with initial OD600=0.02

extract_protocol:
Bacteria were lysed by constantly grinding in the presence of liquid nitrogen with the total RNA extracted using TRIzol reagent (Invitrogen), and finally dissolved in 50 μL RNase-free water.
The total RNA quality was evaluated after ribosomal RNAs were removed. The RNA was then fragmented and used as a template for a randomly primed PCR. Strand-specific cDNA libraries were prepared by standard techniques for subsequent Illumina sequencing (Illumina HiSeq 2000)

tag: time


title: 39h-2

source_name: 39h, Mycobacteriun smegmatis mc2155


title: 26h-1


title: 39h-1


title: Control rep 2


title: GRIDseq.S2_rep2

city: San Diego

first: Bing

last: Zhou

state: CALIFORNIA

address: 9500 Gilman Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
library strategy: GRID-seq
total RNA and genomic DNA
Processed data for merged replicates is available on GSM2188870.

data_processing:
Upon sequencing, individual libraries were segregated according to multiplexing barcodes and then both barcode and residual adapter sequences were removed from each tag to produce tags with non-uniform length, the majority of which ranged from 84 bp to 87 bp in each library. To precisely remove linker sequence from the DNA and cDNA tags, MmeI motifs were used for defining linker boundaries. Linker orientation also dictated whether the tags at each side were originated from genomic DNA or RNA. To minimize the loss of tags due to sequencing errors, tags were first filtered based on the presence of two opposite-orientated MmeI motifs, then aligned to the linker sequence from both directions to determine its orientation. DNA and corresponding RNA tags, most of which ranged from 18 bp to 23 bp, were extracted for alignment.
All processed tags were aligned to their indicated genome build using Bowtie2 with parameter of --local. Human samples were aligned to genome build hg38, mouse samples to genome build mm9 and Drosophila samples to genome build dm3 with parameters -q 2. To estimate the numbers of cross-species-ligated RNA and DNA tags in the mix of MDA-MB-231 and S2 cell nuclei, RNA tags were first aligned independently to the transcriptome builds of hg38 and dm3, with the most stringent parameter of -q 44. Linked DNA tags of those RNA tags that were unambiguously aligned to human transcriptome were then aligned to human genome with the parameter of -q 2. These DNA tags failed to align to the human genome were then aligned to the Drosophila genome, with the parameter of -q 2. Conversely, DNA tags linked to the RNA tags that were unambiguously aligned (-q 44) to the Drosophila transcriptome were first aligned to the Drosophila genome (-q 2), and those unaligned DNA tags were then aligned to the human genome (-q 2)
Genomic regions with enriched GRID-seq RNA reads were detected by MACS2 using the model for broad-peak detection. These mapped regions with significant enrichment (p < 0.001) and overlapping with known-gene annotation (Ensemble genes GRCh38.83 for human, NCBI m37 for mouse and BDGP5.78 for Drosophila) were assigned to their respective largest annotated genes. Enriched regions that did not overlap with any known gene were assigned as “unannotated transcripts”. The RNA read-coverage of genomic regions was calculated by BEDtools and SAMtools. The genes with the tag-coverage above the sliding-window threshold [(Ni+n - Ni) ≥ n, where i was the rank of given RNA, N was the read-counts of this RNA and n was the 1/100 of the total number of ranked RNAs] were selected as abundant chromatin-interacting RNAs. A subset of abundant RNAs with sufficient RNA read-density [RPK (reads per Kb) ≥ 100] or with significant DNA read-densities (RPK ≥ 10) associated at any genomic region was identified as hit RNAs for further analysis (Supplementary Table 1).
To determine the specific RNA-chromatin interaction pattern of each hit RNA, we developed a genome-wide background for non-specific interactions. Ideally, for each library, we could setup mixed nuclei from different species in order to evaluate cross-species RNA-chromatin interactions, which would represent the true background. In practice, it is feasible to generate such background with sufficient density on the Drosophila genome by using RNA reads from human cells because of the much smaller Drosophila genome, but the RNA density on the human genome based on the RNA reads from Drosophila is often too scattered to provide a reliable background. We thus sought to deduce the background in the Drosophila genome based on endogenous RNA reads in comparison with the true background based on cross-species RNA-chromatin interactions. Toward this goal, we selected RNAs from protein-coding genes engaged in trans-chromosomal interactions, and calculated their density on the 1 Kb-binned genome. Such deduced background read-density at each 1 Kb bin was then smoothed by a moving widow of 100 Kb and normalized by the total read number and chromosome size.  The resulting background in the Drosophila genome was highly correlated with the cross-species background. This strategy enabled us to deduce the background on any human cells by using endogenous RNA reads.
To evaluate specific RNA-chromatin interactions of each hit RNA at each genomic bin, we first summarized the DNA reads for each gene at each genomic bin, and then normalized them to 1 million reads followed by further normalization of total number of bins of each chromosome. A ratio was next calculated by dividing the normalized DNA read density with background read density, which represents specific binding of this RNA at the genomic bin.   To construct a robust global binding matrix for all hit RNAs, genomic bins with significant binding level (at least 3 bins with binding level ≥ 2 in every 10 bin-window) were preserved and further smoothed by a moving-widow of 10 bins. All subsequent analyses involving binding levels and patterns were based on such genomic binding matrix.
In the processing of GRO-seq data, multiplexing barcode sequences were removed from each tag after sequecing. All tags were aligned to hg38 genome build using Bowtie2 --local -q2. Due to high variability of small transcripts, only transcripts with lengths larger than 4 Kb were included in the analysis. First, coverages on promoter regions (2 Kb upstream of TSS to 2 Kb downstream of TSS) were compared among transcript isoforms of each gene, and the transcript with highest promoter coverage was selected to represent the gene. To finally estimate the transcription activity for each gene’s representative transcript, normalized read densities (read per Kb per million total reads, RPKM) were calculated within a 2 Kb region that started at 2 Kb downstream of TSS and ended at 4 Kb downstream of TSS. Analysis were applied in all samples, and JQ1/DMSO log-ratio for each gene was calculated as [log2(JQ1_RPKM+1)- log2(DMSO_RPKM+1)].
Genome_build: human genome hg38, mouse mm9 and Drosophila genome dm3
Supplementary_files_format_and_content: The processed GRID-seq data are recorded as tab-delimited text files with 9 columns for each sample , representing RNA_Chrom, RNA_Start, RNA_End, GeneID, RNA_Total_Reads, RNA_Strand, DNA_Chrom, DNA_Bin and Value. The GRID-seq value is normalized interaction density between RNA and DNA. And the processed GRO-seq data are recorded in one tab-delimited text file with 8 columns representing GeneID, DMSO_rep1, DMSO_rep2, JQ1_rep1, JQ1_rep2, DMSO_sum, JQ1_sum, LogRatio_JQ1_vs_DMSO. GRO-seq values represent the densities of genes (RPKM) in each samples, where the DMSO_sum and JQ1_sum are the summarized densities in the two repeats and the LogRatio_JQ1_vs_DMSO is based on the summarized values.

organism: Drosophila melanogaster

growth_protocol: MDA-MB-231 breast cancer cells (HTB-26 ATCC) and MM.1S multiple myeloma cells were grown at 37°C and 5% CO2. MDA-MB-231 cells were cultured in Dulbecco's Modified Eagle Medium (Thermo Fisher Sci.) supplemented with 10% fetal bovine serum. MM.1S cells were cultured in RPMI-1640 supplemented with 1% GlutaMAX (Thermo Fisher Sci.) and 10% fetal bovine serum. Mouse ES Cells were maintained in KnockoutTM DMEM supplemented with 15% KnockoutTM Serum Replacement, 2 mM L-glutamine, 1X Non-essential amino acids, 1X Penicillin-Streptomycin, 0.1 mM 2-Mercaptoethanol, 1000 U/ml LIF, 3 µM CHIR99021 and 1 µM PD0325901. Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Thermo Fisher Sci.) supplemented with 10% fetal bovine serum and 2 mM L-glutamine (Thermo Fisher Sci.), at room temperature in ambient CO2.

extract_protocol:
Approximately 2 million mammalian cells or 10 million Drosophila cells were sequentially crosslinked with 2 mM DSG and 3% formaldehyde. Nuclei were isolated, washed and digested in situ by AluI restriction enzyme. All DNA and RNAs in the nuclei were then treated by T4 PNK. After washing, nuclei were mixed with GRID-seq linkers and T4 RNA Ligase 2-truncated KQ for ssRNA ligation. Shorter strand of the linker was extended by SuperScript III Reverse Transcriptase to generate cDNA. Nuclei were washed again and resuspended in T4 DNA ligase solution for ligation of genomic DNA. By Proteinase K digestion at 65°C, linker-ligated DNA were reverse-crosslinked and extracted, followed by affinity purification by Streptavidin-conjugated beads. By denaturation with 150 mM NaOH solution, the non-biotinylated strand of the linker-ligated-DNA were released, and subjected to second strand synthesis by Klenow Fragment (3' to 5' exo-) enzyme. Newly synthesized dsDNA were then digested by MmeI for paired-end-tag generation, followed by size-selection in 12% native polyacrylamide gel. Recovered dsDNA was further ligated with adapters, PCR amplified to generate libraries for illumina sequencing. GRO-seq protocol was adapted from (Core, L. J. et al, Science, 2008).
Adapters were prepared by annealing the following two oligonucleotides in 1× NEB Buffer 2 to a final concentration of 25 mM: 5’-/5Phos/AGATCGGAAGAGCACACGTCT-3’ and 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNN-3’. Purified DNA was dissolved in 10 µl of 1× NEB Buffer CutSmart and 0.5 U Shrimp Alkaline Phosphatase, incubated at 37 °C for 30 min and heat inactivated at 65°C for 5 min. The reaction was diluted with 36 µl H2O, mixed with 10 µl of 10× T4 DNA Ligase Buffer, 32 µl of PEG-6000, 200 pmol of Adapters and 1,600 U T4 DNA Ligase, and incubated at room temperature for 1 h. Unligated nick was phosphorylated by 20 U T4 Polynucleotide Kinase supplemented by 100 pmol ATP and incubated at 37°C for 30 min. Nick was then ligated by addition of 1 µl of 10× T4 DNA Ligase Buffer, 100 pmol ATP and 1,600 U T4 DNA Ligase, and incubation at room temperature for 30 min. DNA along with excessive Adapters were extracted and purified before loading to 10% native PAGE gel for size-selection. The desired band at approximately 185 bp was excised. DNA was extracted and dissolved in 20 µl of H2O. To amplify each library, 20 µl of PCR amplification mix (9.4 µl of H2O, 5 µl of DNA sample, 4 µl of 5× Phusion HF Buffer, 40 pmol dNTP, 5 pmol Primer#1, 5 pmol Primer#2, 0.4 U Phusion High-Fidelity DNA Polymerase was prepared. PCR primers consist of Primer#1 (5’- AATGATACGGCGACCACCGAGATCTACACBBBBBACACTCTTTCCCTACACGACGCTCTTCCGATCT -3’ (BBBBB: 5 nt barcode for multiplexing libraries)) and Primer#2 (5’- CAAGCAGAAGACGGCATACGAGACGTGTGCTCTTCCGATCT -3’).  PCR was performed with an initial 30 sec denaturation at 98°C, followed by 16 cycles of 10 sec denaturation at 98°C, 30 sec annealing at 65°C and 15 sec extension at 72°C. The PCR product was separated on a native 10% PAGE gel and the band at 188 bp was recovered. DNA was subsequently subjected to Illumina HiSeq 2500 for single-end 100 bp sequencing, with the sequencing primer (5’- ACACTCTTTCCCTACACGACGCTCTTCCGATCT -3’).

treatment_protocol: For JQ1 treatment, MDA-MB-231 cells were resuspended in fresh media containing 500 nM JQ1 or 0.05% DMSO as vehicle for a duration of 6 h.

value: S2 cells


title: 16h-2

source_name: 16h, Mycobacteriun smegmatis mc2155


title: pressureQF

city: Shanghai

first: feng

last: qi

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

description: miRNA

data_processing:
FastQC
Data Filtering by quality
miRNA Mapping to miRBase Database of Rat
miRNA Mapping to rnor5 Genome
novel miRNA Prediction
miRNA Mapping to miRBase Database of mouse and human
miRNA Counts Analysis
Genome_build: miRBase20.0 rnor5
Supplementary_files_format_and_content: counts

organism: Rattus norvegicus

source_name: Hepatic stellate cell

growth_protocol: Primary HSCs were extracted from male Sprague-Dawley rats (weighted about 400-600g). The isolated HSCs were cultured in DMEM (Dulbecco’s modified Eagle’s medium) , containing 20% FBS, 100 U/ml penicillin and 100 mg/ml streptomycin

extract_protocol:
miRNeasy Mini Kit (Qiagen)
Ion  Proton Sequencing Protocol

treatment_protocol: Taking 14 days cultured primary HSCs in the pressure device, respectively connected the nitrogen and hematomanometer, opened the hematomanometer, slowly injected nitrogen, when the pressure rose to 10 mmHg, closed the valve and sealed the container, it could be used in subsequent experiments after loading 1 hour

value: Hepatic stellate cell

value: activated pressure

value: Sprague-Dawley


title: controlQF

description: miRNA

value: control


title: GRIDseq.S2_rep1

description:
library strategy: GRID-seq
total RNA and genomic DNA


title: YJ171_2

status: Public on Aug 28 2017

city: Boston

first: L.

middle: Stirling

last: Churchman

state: Massachusetts

address: 77 Avenue Lois Pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

description: Nascent RNA attached to RNAPII

data_processing:
Library strategy: NET-Seq
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
Only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python .
Negative values in the bedgraph file indicates the Crick strand mappings.
Genome_build: sacCer3 (Saccharomyces Cerevisiae)
Supplementary_files_format_and_content: bedgraph

organism: Saccharomyces cerevisiae

source_name: Whole cell lysate

growth_protocol: K. lactis and D. hansenii were grown in custom medium containing: SC Amino Acid mix (Sunrise Science) (0.2%), Yeast extract (1.5%), Peptone (1%), Dextrose (2%), Adenine (0.01%), Uracil (0.01%), and Tryptophan (0.01%), as previously described (Tsankov et al., 2010). All YAC containing culture was grown in slightly modified medium containing: SC –Tryptophan –Uracil mix (Sunrise Sciences) (0.2%), Yeast extract (1.5%), Peptone (1%), Dextrose (2%), and Adenine (0.01%) (Hughes et al., 2012). All yeast culture was grown at 30°C, except that D. hansenii was cultured at 28°C.

extract_protocol:
Frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.
NET-Seq libraries were constructed and sequenced as previously described with minor modifications (Churchman and Weissman 2012). An improved version of NET-seq DNA linker featured 6 random nucleotides at 5’ terminus was used to further increase ligation efficiency, as well as minimizing ligation bias and library amplification artifacts.

treatment_protocol: Rpb3 was epitope-tagged at C-terminus with 3X-Flag tag and expressed from its endogenous locus. In order to accommodate alternative codon usage in D. hansenii (i.e., CUG translated as serine, instead of leucine) (Moura et al., 2007), codons of the epitope tag and selection marker were modified accordingly. To promote higher efficiency of gene targeting through homologous recombination in K. lactis and D. hansenii, extra long homologous regions adjacent to the target site (up to 1000 bp) were used to flank the epitope tag and selection marker. Electroporation based transformation method were also optimized to achieve high-efficiency transformation in K. lactis and D. hansenii. Further details of strain construction are available upon request.

value: AB1380 + 216 kb YAC (D. hansenii Chromosome D 1148162~1364529)

value: Whole cell lysate


title: 16h-1


title: YJ169_2

description: Nascent RNA attached to RNAPII

value: AB1380 + 136 kb YAC (K. lactis Chromosome C 443175~578764)


title: YJ171_1

description: Nascent RNA attached to RNAPII


title: Treg ATAC matched biological replicate 3 technical replicate 1

city: Stanford

first: Howard

middle: Y

last: Chang

address: 269 Campus Drive

institute: Stanford University

description: Open chromatin

data_processing:
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm9
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.

organism: Homo sapiens

source_name: Treg primary cell

growth_protocol: Sorted from PBMCs

extract_protocol:
Tn5 transposition
Nextera

value: Sorted primary Treg cells

tag: Sex

value: male


title: Treg ATAC matched biological replicate 2 technical replicate 2

description: Open chromatin


title: Treg ATAC matched biological replicate 2 technical replicate 1

description: Open chromatin


title: YJ167_1

description: Nascent RNA attached to RNAPII

value: AB1380 + 128 kb YAC (K. lactis Chromosome F 872404~1000550)


title: YJ167_2

description: Nascent RNA attached to RNAPII


title: YJ168_2

description: Nascent RNA attached to RNAPII

value: AB1380 + 143 kb YAC (K. lactis Chromosome C 339713~482935)


title: YJ169_1

description: Nascent RNA attached to RNAPII


title: Th17 ATAC matched biological replicate 3 technical replicate 2

description: Open chromatin

source_name: Th17 primary cell

value: Sorted primary Th17 cells


title: YJ168_1

description: Nascent RNA attached to RNAPII


title: Treg ATAC matched biological replicate 1 technical replicate 1

description: Open chromatin


title: Th17 ATAC matched biological replicate 3 technical replicate 1

description: Open chromatin


title: Th17 ATAC matched biological replicate 1 technical replicate 2

description: Open chromatin


title: Naïve ATAC matched biological replicate 3 technical replicate 1

description: Open chromatin

source_name: Naïve T primary cell

value: Sorted primary Naive T cells


title: Naïve ATAC matched biological replicate 2 technical replicate 2

description: Open chromatin


title: YJ170_1

description: Nascent RNA attached to RNAPII

value: AB1380 + 115 kb YAC (D. hansenii Chromosome C 1165392~1280355)


title: Naïve ATAC matched biological replicate 3 technical replicate 2

description: Open chromatin


title: Naïve ATAC matched biological replicate 1 technical replicate 1

description: Open chromatin


title: Th17 ATAC matched biological replicate 2 technical replicate 1

description: Open chromatin


title: Treg ATAC matched biological replicate 1 technical replicate 2

description: Open chromatin


title: HCASMC HiChIP H3K27ac biological replicate 1 technical replicate 3

description:
Protein-enriched long-range contact
HCASMC_HiChIP_H3K27ac.hic
HCASMC_HiChIP_H3K27ac_G2.hic

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm9
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.

source_name: HCASMC cell line

growth_protocol: Grown in smooth muscle growth medium supplemented with hEGF, insulin, hFGF-b, and 5% FBS

extract_protocol:
Protein enrichment of 3C library
Nextera

treatment_protocol: Crosslinked with 1% formaldehyde

value: HCASMC

value: Coronary Artery Smooth Muscle


title: HCASMC HiChIP H3K27ac biological replicate 1 technical replicate 2


title: Treg ATAC matched biological replicate 3 technical replicate 2

description: Open chromatin


title: Th17 ATAC matched biological replicate 2 technical replicate 2

description: Open chromatin


title: Control rep 1

value: leaf, untreated

value: Fully expanded mature leaf


title: Th17 ATAC matched biological replicate 1 technical replicate 1

description: Open chromatin


title: HCASMC HiChIP H3K27ac biological replicate 1 technical replicate 1


title: Naïve HiChIP CTCF biological replicate 2

description:
Protein-enriched long-range contact
Naive_HiChIP_CTCF.hic
Naive_HiChIP_CTCF_B2.hic


title: Th17 HiChIP H3K27ac biological replicate 1 technical replicate 2

description:
Protein-enriched long-range contact
Th17_HiChIP_H3K27ac.hic
Th17_HiChIP_H3K27ac.hic


title: YJ170_2

description: Nascent RNA attached to RNAPII


title: Th17 HiChIP H3K27ac biological replicate 3 technical replicate 1

description:
Protein-enriched long-range contact
Th17_HiChIP_H3K27ac.hic
Th17_HiChIP_H3K27ac_B3.hic


title: Naïve HiChIP H3K27ac biological replicate 3 technical replicate 2

description:
Protein-enriched long-range contact
Naive_HiChIP_H3K27ac.hic
Naive_HiChIP_H3K27ac_B3.hic


title: Naïve ATAC matched biological replicate 2 technical replicate 1

description: Open chromatin


title: Naïve HiChIP H3K27ac biological replicate 3 technical replicate 1


title: Naïve ATAC matched biological replicate 1 technical replicate 2

description: Open chromatin


title: Naïve HiChIP CTCF biological replicate 1

description:
Protein-enriched long-range contact
Naive_HiChIP_CTCF.hic
Naive_HiChIP_CTCF_B1.hic


title: Naïve HiChIP H3K27ac biological replicate 1 technical replicate 1

description:
Protein-enriched long-range contact
Naive_HiChIP_H3K27ac.hic
Naive_HiChIP_H3K27ac.hic


title: Naïve HiChIP H3K27ac biological replicate 2 technical replicate 2

description:
Protein-enriched long-range contact
Naive_HiChIP_H3K27ac.hic
Naive_HiChIP_H3K27ac_B2.hic


title: Naïve HiChIP H3K27ac biological replicate 2 technical replicate 1


title: Treg HiChIP H3K27ac biological replicate 2 technical replicate 1

description:
Protein-enriched long-range contact
Treg_HiChIP_H3K27ac.hic
Treg_HiChIP_H3K27ac_B2.hic


title: K562 HiChIP H3K27ac biological replicate 3

description:
Protein-enriched long-range contact
K562_HiChIP_H3K27ac.hic
K562_HiChIP_H3K27ac_B3.hic

source_name: K562 cell line

growth_protocol: Grown in RPMI-1640 with 15% FBS

value: Chronic Myelogenous Leukemia

value: female


title: Th17 HiChIP H3K27ac biological replicate 2 technical replicate 1

description:
Protein-enriched long-range contact
Th17_HiChIP_H3K27ac.hic
Th17_HiChIP_H3K27ac_B2.hic


title: K562 HiChIP H3K27ac biological replicate 1

description:
Protein-enriched long-range contact
K562_HiChIP_H3K27ac.hic
K562_HiChIP_H3K27ac_B1.hic


title: K562 HiChIP H3K27ac biological replicate 2

description:
Protein-enriched long-range contact
K562_HiChIP_H3K27ac.hic
K562_HiChIP_H3K27ac_B2.hic


title: GM HiChIP H3K27ac biological replicate 2

description:
Protein-enriched long-range contact
GM_HiChIP_H3K27ac.hic
GM_HiChIP_H3K27ac_B2.hic

source_name: GM12878 cell line

value: Lymphoblastoid


title: Treg HiChIP H3K27ac biological replicate 3 technical replicate 1


title: MyLa HiChIP H3K27ac biological replicate 2

description:
Protein-enriched long-range contact
MyLa_HiChIP_H3K27ac.hic
MyLa_HiChIP_H3K27ac_B2.hic

source_name: My-La cell line

value: My-La

value: CD4+ T Lymphocyte


title: Th17 HiChIP H3K27ac biological replicate 1 technical replicate 1


title: MyLa HiChIP H3K27ac biological replicate 1

description:
Protein-enriched long-range contact
MyLa_HiChIP_H3K27ac.hic
MyLa_HiChIP_H3K27ac_B1.hic


title: D30IMQEpdSC_R1_ATAC-seq

city: New York

first: Nicholas

last: Gomez

address: 1230 York Ave

institute: Rockefeller University

description:
Sample 23
PCR amplified library from genomic DNA

data_processing:
Reads were aligned to the reference mouse genome (mm10) with bowtie as previously described (Buenrostro 2013).
Genome_build: mm10
Supplementary_files_format_and_content: .bw

source_name: Skin

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2694
Nextera DNA Library Preparation Kit

treatment_protocol: postnatal day 60 mice were treated with topical imiquimod for 6 days and harvested 30 days after treatment

value: adult skin epithelia

tag: sort markers

value: Integrin A6+, B1+ SCa1+ CD34-


title: D30CtrlEpdSC_R2_ATAC-seq

description:
Sample 22
PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2693
Nextera DNA Library Preparation Kit

treatment_protocol: postnatal day 60 mice were treated with vanicream for 6 days and harvested 30 days after treatment


title: D30CtrlEpdSC_R1_ATAC-seq

description:
Sample 21
PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2692
Nextera DNA Library Preparation Kit

value: vanicream for 6 days and harvested 30 days after treatment


title: D30IMQEpdSC_R2_ATAC-seq

description:
Sample 24
PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2695
Nextera DNA Library Preparation Kit

value: topical imiquimod for 6 days and harvested 30 days after treatment


title: D6CtrlEpdSC_R2_ATAC-seq

description:
Sample 18
PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2689
Nextera DNA Library Preparation Kit

treatment_protocol: postnatal day 60 mice were treated with control vanicream for 6 days

value: control vanicream for 6 days


title: D6CtrlEpdSC_R1_ATAC-seq

description:
Sample 17
PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2688
Nextera DNA Library Preparation Kit


title: D6IMQlEpdSC_R2_ATAC-seq

description:
Sample 20
PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2691
Nextera DNA Library Preparation Kit

treatment_protocol: postnatal day 60 mice were treated with topical imiquimod for 6 days

value: topical imiquimod for 6 days


title: Treg HiChIP H3K27ac biological replicate 1 technical replicate 1

description:
Protein-enriched long-range contact
Treg_HiChIP_H3K27ac.hic
Treg_HiChIP_H3K27ac.hic

value: Sorted primary Treg cells

value: male


title: D6CtrlEpdSC_R2_RNA-seq

description:
Sample 2
mRNA library made from total RNA

data_processing:
50-bp sequences were aligned to mm10 using STAR and Gencode release M9 and counts generated from STAR output --quantMode GeneCounts.
Genome_build: mm10
Supplementary_files_format_and_content: GENE_ID, Counts

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers directly into Trizol. Total RNA extracted via Trizol/Zymo RNA extraction kit.
Illumina TruSeq RNA Sample Preparation


title: H3K4me3 granule cells r1 IP

description:
GC_E1_Promoters.txt
GC_E2_Non_regulatory.txt
GC_E3_Primed_Enhancers.txt
GC_E4_Active_Enhancers.txt
Barcode: CTTGTA

source_name: Cerebellar Granule Cells

extract_protocol:
Nuclei isolation and sorting were performed as described in (Kriaucionis and Heintz, 2009). Briefly, cerebella were dissected as described above and homogenized in homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine [pH 7.8]), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor cocktail using loose (A) and tight (B) glass-glass dounce. The homogenate was supplemented with 50% iodixanol (OptiPrep), 150 mM KCl, 5 mM MgCl2, 20 mM Tricine (pH 7.8); and laid on a 29% iodixanol cushion. Nuclei were pelleted by centrifugation for 30 min at 10,000 g and at 4 °C in swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge. The nuclear pellet was resuspended in homogenization buffer and co-stained with DyeCycle Ruby to 20 μM final concentration. A total of 4 cerebella (2 males and 2 females) were pooled before sorting. Throughout the protocol buffers were supplemented with EDTA-free protease inhibitor cocktail and 10 mM of sodium butyrate. For ChIP-Seq homogenates were fixed prior to the addition of 50% iodixanol by adding 1% paraformaldehyde (PFA) for 8 minutes end-to-end rotation.  PFA was then quenched by adding 125 μL of glycine for 5 min. Nuclei were sorted in a BD FASCAria cell sorter using 635 nm and 488 nm excitation lasers and by gating with two parameters: high GFP signal (compared to wt mice) indicating bacTRAP positive cells and lowest signal for DyeCycle Ruby indicating singlets. Alternatively, for H3K27Ac and H3K4me1 ChIP-Seq, granule cell nuclei from C57BL/6J were sorted by selecting a specific FSC/SSC population identified from GC EGFP+ mice. We observed that this FSC/SSC gated population in granule cell EGFP+ animals resulted > 92% of the sorted nuclei being EGFP positive. Thus, the gate selected allows us to enrich the sample from 65%–70% to 92%–96% on granule cells, as described in (Mellen et al., 2012).
After sorting, nuclei were processed using LowCell# ChIP kit. 105 Nuclei were sonicated in a Bioruptor water bath sonicator for 15 min at intervals of 30s on and 30 s off to obtain ~350 bp fragments and chromatin frozen in liquid nitrogen and kept at -80 °C. Each immunoprecipitation (IP) was performed in chromatin aliquots of 5x10e5 nuclei. Immunoprecipitation was performed following LowCell# ChIP kit manufacturer’s instructions, mixing 50:50 IgA and IgG coated beads to 3 μg of antibodies. 1:10 of resuspended chromatin per sonicated nuclei was saved as input sample of the procedure. Immunoprecipitation was performed at 4 °C overnight in an end-to-end rotator. After washing beads with IP DNA, both input and IP samples were digested with Proteinase K 100 μg/ml in the presence of SDS 1% for 2 hr at 50 °C. Then, the lysate was treated with RNase A/T1 mix for 1h at 37 °C to and DNA was extracted with phenol: chloroform: isoamyl alcohol (25:24:1), precipitated in 70% ethanol and dissolved in TruSeq DNA Sample kit resuspension buffer.

value: GFP+


title: D6IMQlEpdSC_R2_RNA-seq

description:
Sample 4
mRNA library made from total RNA


title: protein_10_Donor_3_with_aCD27

city: Cambridge

first: Kelvin

last: Zhang

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

data_processing:
library strategy: scRNA-seq
Single-cell RNA sequencing computational analyses: Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 1.3). First, cellranger mkfastq demultiplexed libraries based on sample indices and converted the barcode and read data to FASTQ files. Second, cellranger count took FASTQ files and performed alignment (UCSC hg19, STAR), filtering, and unique molecular identifier (UMI) counting.  Lastly, cellranger aggr took outputs from multiple runs of cellranger count, and normalized these runs to the same sequencing depth and recomputed the gene-barcode matrices and analysis on the combined data. Then we selected cells that had a mitochondrial read rate < 20% and expressed > 250 genes (PBMCs) or >500 genes (aCD27 assay) to filter out low-quality cells from our data set. Count data of each cell was first scaled to a total of 1x10000 molecules and then log transformed using the R package Seurat (v1.4).
Single-cell protein sequencing computational analyses: BCL files were converted to FASTQ files using Illumina bcl2fastq (version 2.17.14).  In the proteomic assay read 1 and read 2 are switched relative to 10x Genomics standard single cell RNA-seq pipeline (v1 chemistry), so the “R1” and “R2” names in FASTQ files were switched to “R2” and “R1” respectively in order to be compatible with  the cellranger count pipeline (version 1.3).  A post sorted genome BAM file containing the cell barcode (14 bp), UMI (10 bp), and Ab barcode (8 bp) was generated using the cellranger count pipeline. The BAM file was converted to a SAM file using SAMtools (version 1.2).
We developed an aligner called REAP-seq (RS) Aligner to process the SAM files containing the antibody barcode (8 bp) sequences. First, an antibody barcode (AbB) dictionary file was created that associates antibody names to the unique 8 bp DNA sequences that were conjugated to each antibody. Second, a hash table of cell barcodes was generated to parse the cell barcode information. Reads were grouped by their cell barcodes and UMIs were used to avoid double counting sequence reads that arose from the same AbB molecule. Third, the reads were aligned to the antibody dictionary using a Hamming distance <1. Finally, a protein digital expression matrix was generated that contained UMI-corrected read counts for each antibody and cell barcode. In order to filter out the cells representing background noise, we utilized the inflection point of detected cell numbers as a function of cumulative read counts as a cutoff.  In addition, for each sample, we generated a protein expression matrix for cells also identified in the single cell RNA-seq data. The protein expression matrices were log normalized, first scaling each cell to a total of 1x104 molecules using Seurat and then PCA was performed on the normalized data.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include matrices that contain UMI corrected read counts for each sample.

source_name: CD8+ naïve T cells

extract_protocol:
Frozen PBMCs or aCD27 treated and untreated CD8+ naïve T cells were thawed and labeled with AbBs, then single cells were lysed in droplets on the 10x Chromium Controller instrument (10x Genomics).
For mRNA data the standard 10x Genomics scRNA-seq library construction protocol (v1) was used and for protein data the REAP-seq protocol as described in detail in the methods section was used.  Briefly, cells are initially labeled with Ab-Barcodes (AbBs) before compartmentalization into discrete droplets containing a bead with cell-barcode primers.  Upon droplet formation the cell is lysed and the polyadenylated mRNA and AbBs hybridize to the poly(dT) cell barcoded primer. REAP-seq leverages the DNA polymerase activity of reverse transcriptase to simultaneously extend the hybridized AbB and synthesize complementary DNA from mRNA in the same reaction. The droplet emulsion is then broken and the cell barcoded AbB sequences (~155 bp) are size fractionated from the cell barcoded cDNA derived from mRNA (>~500 bp). Exonuclease I is used to degrade any excess unbound single-stranded oligonucleotides from the protein dsDNA (~155 bp) products to prevent crosstalk between AbBs and cell barcodes from different cells. The dsDNA product is then amplified using primers containing a sample index and an Illumina adapter sequence to create a final library product that can be sequenced in a multiplexed fashion with other samples.

treatment_protocol: Untreated PBMCs or CD8+ naïve T cells treated with either 1) aCD3 and aCD28 or 2) aCD3, aCD28, and aCD27

value: CD8+ naive T cells

tag: treated with

value: aCD3, aCD28, and aCD27

tag: condition

value: AbBs and Blocking buffer

tag: mrna or protein

value: protein

tag: supplemental table sample number

tag: donor

value: Donor 3

value: AbBs from single cell


title: GM HiChIP H3K27ac biological replicate 1

description:
Protein-enriched long-range contact
GM_HiChIP_H3K27ac.hic
GM_HiChIP_H3K27ac_B1.hic

value: Lymphoblastoid

value: female


title: D6IMQlEpdSC_R1_RNA-seq

description:
Sample 3
mRNA library made from total RNA

tag: strain

value: adult skin epithelia


title: protein_5_Donor_2_no_aCD27

value: aCD3 and aCD28

value: no aCD27

value: Donor 2


title: protein_3_Donor_1_with_aCD27

value: Donor 1


title: protein_4_Donor_1_with_aCD27


title: protein_6_Donor_2_with_aCD27


title: protein_2_Donor_1_no_aCD27


title: protein_1_Donor_1_no_aCD27


title: mRNA_10_Donor_3_with_aCD27

value: mRNA

value: total RNA from single cell


title: mRNA_8_Donor_3_no_aCD27


title: mRNA_9_Donor_3_with_aCD27


title: D6IMQlEpdSC_R1_ATAC-seq

description:
Sample 19
PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: sort markers, and Nuclei were extracted and genomic DNA was transposed per protocl outlined in doi:10.1038/nmeth.2690
Nextera DNA Library Preparation Kit

value: Integrin A6+, B1+ SCa1+ CD34-

value: topical imiquimod for 6 days


title: mRNA_7_Donor_2_with_aCD27

value: CD8+ naive T cells


title: mRNA_6_Donor_2_with_aCD27

value: aCD3, aCD28, and aCD27


title: mRNA_5_Donor_2_no_aCD27

value: AbBs and Blocking buffer


title: mRNA_4_Donor_1_with_aCD27


title: protein_5_CD11b_enriched

source_name: CD11b enriched PBMCs

value: CD11b enriched PBMCs

value: none; untreated

value: protein


title: mRNA_2_Donor_1_no_aCD27


title: mRNA_1_Donor_1_no_aCD27


title: mRNA_3_Donor_1_with_aCD27


title: protein_4_CD3_enriched

source_name: CD3 enriched PBMCs

value: CD3 enriched PBMCs

value: AbBs from single cell


title: D6CtrlEpdSC_R1_RNA-seq

description:
Sample 1
mRNA library made from total RNA

value: female

value: adult skin epithelia

value: control vanicream for 6 days


title: protein_9_Donor_3_with_aCD27

value: Donor 3


title: protein_3_PBMCs

source_name: PBMCs

value: PBMCs


title: protein_7_Donor_2_with_aCD27

value: Donor 2


title: protein_6_CD19_enriched

source_name: CD19 enriched PBMCs

value: CD19 enriched PBMCs


title: protein_2_PBMCs

value: AbBs and No Blocking buffer


title: mRNA_6_CD19_enriched

value: mRNA

value: total RNA from single cell


title: mRNA_5_CD11b_enriched


title: BY4741_Unstressed_1784042189_BY92

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

institute: University of Wisconsin

data_processing:
Sequenced reads were mapped to S288c reference R64-2-1 using BWA mem
FeatureCounts was used to sum read counts per gene
Identical fragments were collapsed to a single count using XXXXX
Data were normalized by SCNorm method (Bacher et al. 2017)
Picard-tools MarkDuplicates.jar  REMOVE_DUPLICATES=true
Genome_build: S288C R64-2-1

organism: Saccharomyces cerevisiae BY4741

source_name: S. cerevisiae BY4741, unstressed

growth_protocol: Cells were grown in rich YPD medium in shake flasks to early log phase in batch cultures in shaker flasks at 30C.

extract_protocol:
Cells were sorted on the C1 fluidim and lysed in the system according to manufaturer protocol.
Libraries were generated by SMART-seq method.

treatment_protocol: Sodium chloride was added to 0.7M final concentration and cells were collected at 30 min after treatment.

tag: tissue

value: individual cell


title: BY4741_Unstressed_1784042189_BY94


title: mRNA_3_PBMCs

value: AbBs and Blocking buffer


title: BY4741_Unstressed_1784042189_BY93


title: mRNA_4_CD3_enriched


title: BY4741_Unstressed_1784042189_BY91


title: BY4741_Unstressed_1784042189_BY86


title: mRNA_1_PBMCs

value: No AbBs and No Blocking buffer


title: BY4741_Unstressed_1784042189_BY89


title: BY4741_Unstressed_1784042189_BY9


title: BY4741_Unstressed_1784042189_BY81


title: BY4741_Unstressed_1784042189_BY88


title: BY4741_Unstressed_1784042189_BY87


title: BY4741_Unstressed_1784042189_BY82


title: BY4741_Unstressed_1784042189_BY85


title: BY4741_Unstressed_1784042189_BY75


title: BY4741_Unstressed_1784042189_BY8


title: BY4741_Unstressed_1784042189_BY77


title: BY4741_Unstressed_1784042189_BY79


title: BY4741_Unstressed_1784042189_BY84


title: BY4741_Unstressed_1784042189_BY78


title: BY4741_Unstressed_1784042189_BY76


title: mRNA_2_PBMCs

value: none; untreated


title: BY4741_Unstressed_1784042189_BY74


title: BY4741_Unstressed_1784042189_BY73


title: BY4741_Unstressed_1784042189_BY80


title: BY4741_Unstressed_1784042189_BY71


title: BY4741_Unstressed_1784042189_BY72


title: BY4741_Unstressed_1784042189_BY7


title: BY4741_Unstressed_1784042189_BY67


title: BY4741_Unstressed_1784042189_BY70


title: BY4741_Unstressed_1784042189_BY83


title: BY4741_Unstressed_1784042189_BY65


title: BY4741_Unstressed_1784042189_BY63


title: BY4741_Unstressed_1784042189_BY64


title: BY4741_Unstressed_1784042189_BY62


title: BY4741_Unstressed_1784042189_BY61


title: BY4741_Unstressed_1784042189_BY60


title: BY4741_Unstressed_1784042189_BY6


title: BY4741_Unstressed_1784042189_BY53


title: BY4741_Unstressed_1784042189_BY54


title: BY4741_Unstressed_1784042189_BY57


title: BY4741_Unstressed_1784042189_BY55


title: BY4741_Unstressed_1784042189_BY52


title: BY4741_Unstressed_1784042189_BY59


title: BY4741_Unstressed_1784042189_BY56


title: BY4741_Unstressed_1784042189_BY50


title: BY4741_Unstressed_1784042189_BY4


title: BY4741_Unstressed_1784042189_BY5


title: BY4741_Unstressed_1784042189_BY45


title: BY4741_Unstressed_1784042189_BY39


title: BY4741_Unstressed_1784042189_BY38


title: BY4741_Unstressed_1784042189_BY37


title: BY4741_Unstressed_1784042189_BY66


title: BY4741_Unstressed_1784042189_BY35


title: BY4741_Unstressed_1784042189_BY33


title: BY4741_Unstressed_1784042189_BY34


title: BY4741_Unstressed_1784042189_BY58


title: BY4741_Unstressed_1784042189_BY31


title: BY4741_Unstressed_1784042189_BY51


title: BY4741_Unstressed_1784042189_BY3


title: BY4741_Unstressed_1784042189_BY29


title: BY4741_Unstressed_1784042189_BY90


title: BY4741_Unstressed_1784042189_BY49


title: BY4741_Unstressed_1784042189_BY28


title: BY4741_Unstressed_1784042189_BY23


title: BY4741_Unstressed_1784042189_BY26


title: BY4741_Unstressed_1784042189_BY68


title: BY4741_Unstressed_1784042189_BY22


title: BY4741_Unstressed_1784042189_BY24


title: BY4741_Unstressed_1784042189_BY43


title: BY4741_Unstressed_1784042189_BY25


title: BY4741_Unstressed_1784042189_BY21


title: BY4741_Unstressed_1784042189_BY20


title: BY4741_Unstressed_1784042189_BY19


title: BY4741_Unstressed_1784042189_BY18


title: BY4741_Unstressed_1784042189_BY32


title: BY4741_Unstressed_1784042189_BY14


title: BY4741_Unstressed_1784042189_BY2


title: BY4741_Unstressed_1784042189_BY16


title: BY4741_Unstressed_1784042189_BY12


title: BY4741_Unstressed_1784042189_BY13


title: BY4741_Stressed_1784042160_C50_BY89

source_name: S. cerevisiae BY4741, salt stressed


title: BY4741_Unstressed_1784042189_BY1


title: protein_8_Donor_3_no_aCD27

value: CD8+ naive T cells

value: aCD3 and aCD28

value: no aCD27

value: protein


title: BY4741_Unstressed_1784042189_BY11


title: BY4741_Stressed_1784042160_C50_BY9


title: BY4741_Stressed_1784042160_C50_BY88


title: BY4741_Stressed_1784042160_C50_BY87


title: BY4741_Stressed_1784042160_C50_BY86


title: BY4741_Stressed_1784042160_C50_BY82


title: BY4741_Stressed_1784042160_C50_BY83


title: BY4741_Stressed_1784042160_C50_BY85


title: BY4741_Unstressed_1784042189_BY17


title: BY4741_Stressed_1784042160_C50_BY84


title: BY4741_Stressed_1784042160_C50_BY79


title: BY4741_Stressed_1784042160_C50_BY81


title: BY4741_Stressed_1784042160_C50_BY78


title: BY4741_Stressed_1784042160_C50_BY77


title: BY4741_Stressed_1784042160_C50_BY80


title: BY4741_Stressed_1784042160_C50_BY75


title: BY4741_Unstressed_1784042189_BY10


title: BY4741_Stressed_1784042160_C50_BY8


title: BY4741_Stressed_1784042160_C50_BY76


title: BY4741_Stressed_1784042160_C50_BY7


title: BY4741_Stressed_1784042160_C50_BY67


title: p65ChIP on WT sample, rep 2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description:
WT-Treg2_S18
Processed data file: p65ChIP-WT-FDR0.05_summits.bed

data_processing:
Sequence reads were mapped to mm9 build (NCBI Build 37) of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
The binding peaks of the Irf4 and p65 transcription factors were called on wild-type samples and/or p65KO samples by using the Macs2 v2.1.0 program. The binding peaks of the Irf4 transcription factor on the p65KO samples were called from the p65KO-Treg-Irf4ChIP_S12 and Irf4ChIP-p65KO_S8 samples (as technical replicates) at an FDR cutoff of 1e-6; the binding peaks of the Irf4 transcription factor on the wild-type samples were called from the WT-Treg-Irf4ChIP_S11, Irf4ChIP-WT_S7 and Irf4_C5N5JANXX_CAGATC_L007 samples (as technical replicates) at an FDR cutoff of 1e-6; the binding peaks of the p65 transcription factor on the wild-type samples were called from the WT-Treg2_S18 and p65ChIP-WT_S9 samples (as technical replicates) at an FDR cutoff of 0.05. Neither input control nor IgG samples were provided for calling the peaks.
Genes with binding peaks falling within 20 kilobases upstream and 5 kilobases downstream of the gene body were considered to be the binding targets. NCBI RefSeq mouse annotation build 37 was used to obtain chromosomal coordinates of genes. Binding peaks were assigned to genes using the featureCounts program.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bed: Peak calling output from Macs2 in BED format.

source_name: WT murine Treg cells, p65 ChIP

extract_protocol:
5 million Treg cells were stimulated with anti-CD3 and anti-CD28 for 48 h before fixing and immunoprecipitating IRF4-bound chromatin. For RelA IP, 5 million Treg cells were PMA/Ionomycin stimulated for 30 min.
DNA fragments were blunt-end ligated to the Illumina adaptors, amplified, and sequenced with an Illumina HiSeq Sequencer.

tag: strain/background

tag: genotype/variation

value: WT

value: Spleen

value: Treg

tag: chip antibody

value: Anti-NFkB/p65 (C-20) (Santa Cruz Biotechnology, sc-372)


title: BY4741_Stressed_1784042160_C50_BY71


title: BY4741_Stressed_1784042160_C50_BY70


title: BY4741_Stressed_1784042160_C50_BY72


title: BY4741_Stressed_1784042160_C50_BY69


title: p65ChIP on WT sample, rep 1

description:
p65ChIP-WT_S9
Processed data file: p65ChIP-WT-FDR0.05_summits.bed

tag: cell type


title: BY4741_Stressed_1784042160_C50_BY66


title: Irf4ChIP on p65KO sample, rep 2

description:
p65KO-Treg-Irf4ChIP_S12
Processed data file: Irf4ChIP-p65KO-FDR1e-6_summits.bed

source_name: RelA-deficient murine Treg cells, Irf4 ChIP

value: Anti-IRF4 (M-17) (Santa Cruz Biotechnology, sc-6059x)


title: Irf4ChIP on p65KO sample, rep 1

description:
Irf4ChIP-p65KO_S8
Processed data file: Irf4ChIP-p65KO-FDR1e-6_summits.bed


title: BY4741_Stressed_1784042160_C50_BY64


title: BY4741_Stressed_1784042160_C50_BY65


title: BY4741_Unstressed_1784042189_BY15


title: Irf4ChIP on WT sample, rep 3

description:
WT-Treg-Irf4ChIP_S11
Processed data file: Irf4ChIP-WT-FDR1e-6_summits.bed

source_name: WT murine Treg cells, Irf4 ChIP


title: BY4741_Stressed_1784042160_C50_BY63


title: Th17 ATAC nonmatched biological replicate 2

description: Open chromatin

source_name: Th17 primary cell

tag: cell line

value: Sorted primary Th17 cells

value: male


title: Treg ATAC nonmatched biological replicate 2

description: Open chromatin

source_name: Treg primary cell

value: Sorted primary Treg cells


title: BY4741_Stressed_1784042160_C50_BY60


title: Treg ATAC nonmatched biological replicate 1

description: Open chromatin


title: BY4741_Stressed_1784042160_C50_BY6


title: Irf4ChIP on WT sample, rep 2

description:
Irf4ChIP-WT_S7
Processed data file: Irf4ChIP-WT-FDR1e-6_summits.bed


title: BY4741_Stressed_1784042160_C50_BY61


title: BY4741_Stressed_1784042160_C50_BY58


title: BY4741_Stressed_1784042160_C50_BY59


title: Th17 ATAC nonmatched biological replicate 1

description: Open chromatin


title: UNC-30_Input

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
peakcalls performed with cisGenome
ChIP-seq reads were aligned to the ce6 genome allowing 1 mismatch.
Data were filtered using the following specifications…
peaks were called using cisGenome with the following setting:  Enrichment Fold (3), P value (10^-5).
Genome_build: ce6

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were grown on NGM (Nematode Growth Medium) plates seeded with OP50 at 22 °C or 25 °C

extract_protocol: ChIP DNAs were isolated with antibody from whole worm lystaes.

tag: developmental stage

value: whole worms

tag: antibody


title: BY4741_Stressed_1784042160_C50_BY57

value: individual cell


title: Naïve ATAC nonmatched biological replicate 1

description: Open chromatin

source_name: Naïve T primary cell

value: Sorted primary Naive T cells


title: UNC-55_ChIPSeq

value: GFP beads(ChromoTek, Gat-20)


title: UNC-30_ChIPSeq


title: UNC-55_Input


title: D180CtrlEpdSC_R2_ATAC-seq

description: PCR amplified library from genomic DNA

data_processing:
Reads were aligned to the reference mouse genome (mm10) with bowtie as previously described (Buenrostro 2013).
Genome_build: mm10

treatment_protocol: starting at postnatal day 60 mice were treated with topical imiquimod (IMQ) on control vanicream and harvested at inticated timepoints; samples 9-16 30days post IMQ/vanicream mice were subject to full thickness wounds in dorsal skin

value: female

tag: cell types

value: adult skin epithelia

value: Integrin A6+, B1+ SCa1+ CD34-


title: Naïve ATAC nonmatched biological replicate 2

description: Open chromatin

tag: Sex


title: BY4741_Stressed_1784042160_C50_BY56


title: D180CtrlEpdSC_R1_ATAC-seq

description: PCR amplified library from genomic DNA

tag: sort markers


title: BY4741_Stressed_1784042160_C50_BY55


title: D180IMQEpdSC_R2_ATAC-seq

description: PCR amplified library from genomic DNA


title: anti-CD24 stimulated rep 1

city: Moncton

first: D. Craig

last: Ayre

state: New Brunswick

address: 35 rue Providence Street

country: Canada

institute: Atlantic Cancer Research Institute

data_processing:
Our workflow follows the protocol described by Anders et al, Nat Protoc. 2013 Sep;8(9):1765-86.
Sequence reads were trimmed using fastq_quality trimmer (FASTX-Toolkit  0.0.13.2) with parameters  -Q 33 -t 22 -l 28 then mapped to mouse whole genome (GRCm38.p4) using tmap (Ion Torrent Mapper) version 3.0.1 with parameters -B 18 -a 2 -v stage1 map1 map2 map3.
Read counts were obtained using HTSeq (version 0.5.4p5) and mouse genome annotation Ensembl release 84 with parameters --mode=union --stranded=yes --type=exon --idattr=gene_id -a 0
Genome_build: Mus musculus GRCm38.p4
Supplementary_files_format_and_content: tab delimited text files with read counts per feature

source_name: WEHI-231 B cells

growth_protocol: WEHI-231 cells were grown in RPMI-1640 media supplemented with 10% heat inactivated, vesicle depleted media, 1% sodium pyruvate, 1% penicillin/streptomycin, 0.1% beta-mercaptoethanol

extract_protocol:
Trizol extraction protocol from Life Technologies
Libraries were prepared following the Ion Total RNA-Seq Kit v2 protocol

treatment_protocol: 500,000 cells in 1mL were stimulated for 1h with either 10 ug/mL rat-anti-mouse M1/69 anti-CD24 antibody pre-incubated with 5 ug/mL donkey-anti-rat secondary antibody, or a matched isotype control and secondary antibody

value: Splenic B cell lymphoma

tag: treatment

value: 10 ug/mL anti-CD24 Ab + 5ug/mL secondary Ab


title: Isotype-treated rep 3

value: 10 ug/mL Isotype + 5 ug/mL secondary Ab


title: anti-CD24 stimulated rep 2


title: Isotype-treated rep 1


title: Isotype-treated rep 2


title: BY4741_Stressed_1784042160_C50_BY62


title: BY4741_Stressed_1784042160_C50_BY53


title: D180IMQEpdSC_R1_ATAC-seq

description: PCR amplified library from genomic DNA

source_name: Skin


title: BY4741_Stressed_1784042160_C50_BY52


title: anti-CD24 stimulated rep 3


title: 12hrwounding_PIEpdSC__R1_RNA-seq

description:
Sample 15
mRNA library made from total RNA

treatment_protocol: postnatal day 60 mice were treated with topical imiquimod for 6 days and wounded at 30 days. 12hr wounds were harvested


title: 12hrwounding_PIEpdSC__R2_RNA-seq

description:
Sample 16
mRNA library made from total RNA

value: topical imiquimod for 6 days and wounded at 30 days. 12hr wounds were harvested


title: 6hrwounding_PIEpdSC__R2_RNA-seq

description:
Sample 12
mRNA library made from total RNA

treatment_protocol: postnatal day 60 mice were treated with topical imiquimod for 6 days and wounded at 30 days. 6hr wounds were harvested


title: BY4741_Stressed_1784042160_C50_BY50


title: 12hrwounding_CtrlEpdSC__R2_RNA-seq

description:
Sample 14
mRNA library made from total RNA

treatment_protocol: postnatal day 60 mice were treated with vanicream for 6 days and wounded at 30 days. 12hr wounds were harvested


title: BY4741_Stressed_1784042160_C50_BY5


title: 6hrwounding_PIEpdSC__R1_RNA-seq

description:
Sample 11
mRNA library made from total RNA

value: topical imiquimod for 6 days and wounded at 30 days. 6hr wounds were harvested


title: BY4741_Stressed_1784042160_C50_BY44


title: 6hrwounding_CtrlEpdSC__R2_RNA-seq

description:
Sample 10
mRNA library made from total RNA

treatment_protocol: postnatal day 60 mice were treated with vanicream for 6 days and wounded at 30 days. 6hr wounds were harvested


title: 12hrwounding_CtrlEpdSC__R1_RNA-seq

description:
Sample 13
mRNA library made from total RNA

value: vanicream for 6 days and wounded at 30 days. 12hr wounds were harvested


title: BY4741_Stressed_1784042160_C50_BY51


title: D30IMQEpdSC_R2_RNA-seq

description:
Sample 8
mRNA library made from total RNA

value: topical imiquimod for 6 days and harvested 30 days after treatment


title: BY4741_Stressed_1784042160_C50_BY4


title: 6hrwounding_CtrlEpdSC__R1_RNA-seq

description:
Sample 9
mRNA library made from total RNA

value: vanicream for 6 days and wounded at 30 days. 6hr wounds were harvested


title: BY4741_Stressed_1784042160_C50_BY40


title: BY4741_Stressed_1784042160_C50_BY39


title: BY4741_Stressed_1784042160_C50_BY49


title: D30CtrlEpdSC_R2_RNA-seq

description:
Sample 6
mRNA library made from total RNA

value: vanicream for 6 days and harvested 30 days after treatment


title: BY4741_Stressed_1784042160_C50_BY36


title: BY4741_Stressed_1784042160_C50_BY37


title: BY4741_Stressed_1784042160_C50_BY54


title: D30CtrlEpdSC_R1_RNA-seq

description:
Sample 5
mRNA library made from total RNA


title: BY4741_Stressed_1784042160_C50_BY38


title: 4762_restingBcells_MLL4wt_RNAseq

first: Yanwen

last: Jiang

institute: Weill Cornell Medical College

description: RNA-seq

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Read counts were derived from HTSeq.scripts.count module in HTSeq-0.6.0 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: reads counts in .txt format

growth_protocol: Isolated primary B cells were cultured in RPMI supplemented with 10%FBS.

extract_protocol:
RNA extraction was performed using TRIzol (Ambion) following the manufacturer’s protocol. RNA was washed, purified with an RNeasy kit (QIAGEN) and measured for quality using Agilent Bioanalyzer.
RNA-seq libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v2. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT dsDNA HS Assay (Life Technologies).
RNA-seq was run using 50bp single or paired-end reads

treatment_protocol: B220+ cells were purified from mouse spleeens by immunomagnetic depletion with anti-CD43 microbeads (Miltenyi Biotech).  Stimulated B cells were treated with LPS (25ug/ml; Sigma), IL4 (5 ng/ml; Sigma), Anti-Mouse CD180 (0.5 ug/ml; BD Pharmingen) for 3 days.

tag: genotype

value: MLL4F/F CD19+ CRE- (WT)

value: resting B cell


title: 4746_restingBcells_MLL4ff_RNAseq

description: RNA-seq

value: MLL4F/F CD19+ CRE+ (KO)


title: 4885_restingBcells_MLL4wt_RNAseq

description: RNA-seq


title: BY4741_Stressed_1784042160_C50_BY34

value: individual cell


title: 4745_restingBcells_MLL4ff_RNAseq

description: RNA-seq


title: BY4741_Stressed_1784042160_C50_BY33


title: BY4741_Stressed_1784042160_C50_BY42


title: BY4741_Stressed_1784042160_C50_BY32


title: s5_131218_B_MLL4_4330_MLL4wt_MLL3wt

description: RNA-seq

value: stimulated B cell


title: s3_131218_B_MLL4_4328_MLL4wt_MLL3wt

description: RNA-seq


title: BY4741_Stressed_1784042160_C50_BY31


title: s2_131218_B_MLL4_4313_MLL4mm_MLL3wt

description: RNA-seq


title: BY4741_Stressed_1784042160_C50_BY30


title: s1_131218_B_MLL4_4312_MLL4mm_MLL3wt

description: RNA-seq


title: BY4741_Stressed_1784042160_C50_BY3


title: BY4741_Stressed_1784042160_C50_BY29


title: D30IMQEpdSC_R1_RNA-seq

description:
Sample 7
mRNA library made from total RNA

value: female


title: BY4741_Stressed_1784042160_C50_BY28


title: LT2 ridA Rep 3

city: Athens

first: Diana

middle: M

last: Downs

state: GA

address: 527 Biological Sciences Building

department: Microbiology

institute: University of Georgia

description: rRNA was removed from 5 μg total RNA using the Ribo-Zero rRNA removal kit (Bacteria, Illumina)

data_processing:
Real-Time Analysis v2 software used for basecalling.
Data Processing steps were performed by Walter Lorenz of the Quantitative Biology Consulting Group at the University of Georgia after data was downloaded from the Georgia Genomics Facility BaseSpace link.
Sequenced reads were trimmed by Trimmomatic for adaptor sequence, and masked for low-complexity or low-quality sequence, and only trimmed data that was maintained as paired data was used to map to the S. enterica LT2 genome using EdgePro version 1.3.1
The matrix files generated by EdgePro were imported into Deseq in order to perform statistical analysis for determination of differentially expressed genes (FDR > 0.05).
Genome_build: ASM694v1
Supplementary_files_format_and_content: SE_Deseq_Processed.xlsx is an excel file format file generated by the Quantitative Biology Consulting Group at the University of Georgia and provided to the researchers in this study. It contains raw and normalized reads generated by Deseq as well as FDR values for all LT2 ORFs given as well as a calculated fold-change number for each gene between the wild-type and ridA strains

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: cell lysate

growth_protocol: S. enterica LT2 WT and ridA strains were subcultured from overnight cultures grown in nutrient broth medium and subcultured 1:100 in 5 mL no-carbon E medium supplemented with 1 mM MgSO4, trace minerals, and 11mM D-glucose and grown at 37C shaking until to mid-log (OD650 = 0.6)

extract_protocol:
Each 5 mL sample was quickly  centrifuged at 16,000 x g in 1.5 mL Eppendorf tubes, supernatant removed and pellets flash-frozen in liquid nitrogen and kept on dry ice.  Total RNA was extracted using the RNAsnapTM method (Stead, et al., 2012).  RNA was subjected to an ethanol precipitation and DNA/RNA pellets were resuspended in 90 μl UltraPureTM water at 4°C overnight prior to treatment with RNase-free Turbo DNase (Ambion), and being precipitated once more by sodium acetate-ethanol treatment. Resulting RNA was resuspended at 4°C for 3 h and stored at -80°C until use. The total RNA was extracted from four independent replicates of S. enterica wild-type and ridA mutant strains. In each of the resulting eight samples, rRNA was removed from 5 μg total RNA using the Ribo-Zero rRNA removal kit (Bacteria; Illumina) following manufacturer’s recommendations.
A cDNA library was created from samples containing <10% rRNA contamination, as measured by the RNA 6000 pico kit for the Agilent 2100 bioanalyzer, and sequenced by the University of Georgia Genomics Facility (GGF) from these RNA samples. Specifically, one hundred nanograms of the rRNA-free RNA was used to create each sequencing library using the KAPA stranded RNA-seq kit (KAPA Biosystems).

treatment_protocol: Growth in minimal medium was the only treatment condition

value: ridA


title: LT2 ridA Rep 2


title: LT2 ridA Rep 4


title: BY4741_Stressed_1784042160_C50_BY27


title: LT2 ridA Rep 1


title: BY4741_Stressed_1784042160_C50_BY26


title: BY4741_Stressed_1784042160_C50_BY25


title: GF_BDE99_3

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with parameters -q --pen-noncansplice1000000 -p 15 -x
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from cufflinks. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: sorted bam files; Cufflinks output in tab-delimited text format include FPKM values for each Sample

source_name: liver

extract_protocol:
Liver were removed, flash frozen in the liquid nitrogen, and RNA was extracted using RNA Bee reagent.TruSeq Stranded mRNA kit (Illumina, San Diego, CA)  was used with 1.25 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
multiplexed (n=5 per lane)

treatment_protocol: At 9-weeks of age, CV mice (n=5 per group) were randomly allocated for the treatment of vehicle (corn oil, 10ml/kg), BDE-47 (100 μmol/kg), or BDE-99 (100 μmol/kg) via oral gavage once daily for 4 days.

tag: enterotype

value: liver

tag: age

value: 9-weeks old at the beginning of treatment

tag: gender

value: male


title: LT2 WT Rep 4

tag: strain

value: wild-type


title: GF_BDE99_2


title: BY4741_Stressed_1784042160_C50_BY35

tag: tissue


title: BY4741_Stressed_1784042160_C50_BY24


title: GF_BDE47_3


title: LT2 WT Rep 3


title: GF_BDE47_2


title: GF_CO3


title: LT2 WT Rep 2


title: LT2 WT Rep 1


title: BY4741_Stressed_1784042160_C50_BY23


title: BY4741_Stressed_1784042160_C50_BY22


title: GF_CO2


title: GF_BDE47_1


title: CV_BDE99_1


title: CV_BDE99_2


title: mES HiChIP H3K27ac 50k biological replicate 2

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_50k.hic
mES_HiChIP_H3K27ac_50k_B2.hic

organism: Mus

source_name: v6.5 embryonic stem cell line

growth_protocol: Grown on gelatin-coated plates with KO DMEM supplemented with LIF

extract_protocol:
Protein enrichment of 3C library
Nextera

value: ES cell


title: BY4741_Stressed_1784042160_C50_BY21


title: GF_CO1


title: mES HiChIP H3K27ac 50k biological replicate 1

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_50k.hic
mES_HiChIP_H3K27ac_50k_B1.hic


title: BY4741_Stressed_1784042160_C50_BY20


title: GF_BDE99_1


title: mES HiChIP H3K27ac 100k biological replicate 2

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_100k.hic
mES_HiChIP_H3K27ac_100k_B2.hic


title: CV_BDE47_3


title: CV_BDE47_4


title: CV_BDE47_1


title: mES HiChIP H3K27ac 100k biological replicate 1

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_100k.hic
mES_HiChIP_H3K27ac_100k_B1.hic


title: mES HiChIP H3K27ac 500k biological replicate 2

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_500k.hic
mES_HiChIP_H3K27ac_500k_B2.hic


title: BY4741_Stressed_1784042160_C50_BY19


title: BY4741_Stressed_1784042160_C50_BY2


title: CV_BDE47_2


title: CV_CO3


title: BY4741_Stressed_1784042160_C50_BY18


title: BY4741_Stressed_1784042160_C50_BY17


title: CV_CO2


title: mES HiChIP H3K27ac 25m biological replicate 2 technical replicate 2

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_25m.hic
mES_HiChIP_H3K27ac_25m_B2.hic


title: BY4741_Stressed_1784042160_C50_BY16


title: CV_CO1


title: mES HiChIP H3K27ac 25m biological replicate 1 technical replicate 2

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_25m.hic
mES_HiChIP_H3K27ac_25m_B1.hic


title: DDX46 +/-

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

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, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: peritoneal macrophages

extract_protocol:
Peritoneal macrophages RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peritoneal macrophages


title: BY4741_Stressed_1784042160_C50_BY13


title: WT 8 h


title: BY4741_Stressed_1784042160_C50_BY14


title: Irf4ChIP on WT sample, rep 1

description:
Irf4_C5N5JANXX_CAGATC_L007
Processed data file: Irf4ChIP-WT-FDR1e-6_summits.bed

tag: strain/background

value: WT

value: Spleen

value: Treg

value: Anti-IRF4 (M-17) (Santa Cruz Biotechnology, sc-6059x)


title: mES HiChIP H3K27ac 25m biological replicate 1 technical replicate 1


title: BY4741_Stressed_1784042160_C50_BY12


title: YJ177_1

description: Nascent RNA attached to RNAPII

organism: Debaryomyces hansenii

source_name: Whole cell lysate

extract_protocol:
Frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.
NET-Seq libraries were constructed and sequenced as previously described with minor modifications (Churchman and Weissman 2012). An improved version of NET-seq DNA linker featured 6 random nucleotides at 5’ terminus was used to further increase ligation efficiency, as well as minimizing ligation bias and library amplification artifacts.

treatment_protocol: Rpb3 was epitope-tagged at C-terminus with 3X-Flag tag and expressed from its endogenous locus. In order to accommodate alternative codon usage in D. hansenii (i.e., CUG translated as serine, instead of leucine) (Moura et al., 2007), codons of the epitope tag and selection marker were modified accordingly. To promote higher efficiency of gene targeting through homologous recombination in K. lactis and D. hansenii, extra long homologous regions adjacent to the target site (up to 1000 bp) were used to flank the epitope tag and selection marker. Electroporation based transformation method were also optimized to achieve high-efficiency transformation in K. lactis and D. hansenii. Further details of strain construction are available upon request.

value: NCYC 2572

value: Whole cell lysate


title: P65KO-rep2

description:
MM10.AB4_l1
Processed data file: Supp_Raw_Counts.txt

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and had an expression change of two folds or greater. The called differentially expressed genes must also have at least 2 FPKMs (fragments per kilobase of exon length per million mapped fragments) in one or both of the two cell types being compared. A minimum fold change of 1.5 was also required to call the DE genes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include normalized log2-RPKM values for each library.
Supplementary_files_format_and_content: The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.

source_name: Spleen+peripheral LNs, Treg cells, P65KO

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: genotype/variation

value: Spleen + peripheral lymph nodes

value: CD4+Foxp3+ Treg


title: YJ177_2

description: Nascent RNA attached to RNAPII


title: BY4741_Stressed_1784042160_C50_BY11

value: individual cell


title: WT-rep2

description:
MM10.AB2_l1
Processed data file: Supp_Raw_Counts.txt

source_name: Spleen+peripheral LNs, Treg cells, WT


title: BY4741_Stressed_1784042160_C50_BY1

source_name: S. cerevisiae BY4741, salt stressed


title: WT-rep1

description:
MM10.AB1_l1
Processed data file: Supp_Raw_Counts.txt


title: mES HiChIP H3K27ac 500k biological replicate 1

description:
Protein-enriched long-range contact
mES_HiChIP_H3K27ac_500k.hic
mES_HiChIP_H3K27ac_500k_B1.hic

treatment_protocol: Crosslinked with 1% formaldehyde


title: YJ160_1

description: Nascent RNA attached to RNAPII

organism: Kluyveromyces lactis

value: CLIB 209