title: atac_P56_rep3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

description:
cardiomycyte_atac_pk.mx
cardiomycyte_atac_tss.mx

data_processing:
Used HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data
FastX quality trimmer was used to trim bases with phred quality score less than 20. Reads with a length shorter than 20 bp after clipping were discarded.
Reads were mapped to the mouse genome primary assembly  (GRCm38) downloaded from Ensembl with BWA MEM (v0.7.10).
Duplicate reads were removed using Samtools v1.3.1
Aligned reads from each developmental stage were pooled. MACS v1.4.0 was then used to identify accessibility peaks in the P1, P14 and P56 datasets. MACS peak-calling was performed with a shift size of 75 bp and otherwise default parameters. The peak sets were merged using BedTools v2.26. FeatureCounts v1.4.2 was used to quantify reads mapping to peaks in each individual biological sample, with a minimum mapping quality of 10. FeatureCounts was also used to count reads mapping to regions immediately surrounding transcriptional start sites derived from Ensembl v85 annotations. Genes/peaks with fewer than 10 reads per sample on average were excluded.
Genome_build: GRCm38
Supplementary_files_format_and_content: Chromatin accessibility count matrix (peaks), Chromatin accessibility count matrix (TSSs)

growth_protocol: Neonatal CD-1 (ICR) mice were euthanized by decapitation 3 days after surgery and cardiac ventricles were dissected and washed in ADS buffer (116.3 mmol/l NaCl, 20 mmol/l HEPES, 1 mmol/l NaH2PO4, 5.5 mmol/l glucose, 5.36 mmol/l KCl, 0.83 mmol/l MgSO4,) and then cut into small pieces and pooled into groups of 6 ventricles per cell stirrer. Hearts were then digested at 37 ◦ C under constant agitation for 30-40 minutes (or until tissue was fully homogenized). The digestion buffer was made with 200 μg/ml Liberase DH (Roche) in ADS buffer. Myocytes and non-myocytes were then separated by on a Percoll gradient. Cell isolates were layered on Percoll gradients and centrifuged at 2100 xg for 30 minutes. The bottom layer (containing myocytes) and the top layer (containing enriched non-myocytes) were then collected separately and washed twice in ADS. The myocyte fraction was then lysed in Trizol. FACS was then performed on the non-myocyte fraction.  Adult CD-1 (ICR) mice were anesthetized with an i.p injection of ketamine (200 mg/kg) at day 3 post-surgery. Hearts were quickly dissected and washed in perfusion buffer (120.4 mmol/l NaCl, 14.7 mmol/l KCl, 0.6 mmol/l KH 2 PO 4 , 0.6 mmol/l Na 2 HPO 4 , 1.2 mmol/l MgSO 4 •7H2O, 4.6 mmol/l NaHCO 3 , 10 mmol/l Na-HEPES, 30 mmol/l taurine, 5.5 mmol/l glucose and 10 mM 2,3-Butanedione 2-monoxime). The aorta was then cannulated with a 21- gauge cannula, secured with 3-0 silk suture and perfused with 37 ◦ C, oxygenated perfusion buffer using a Langendorff apparatus (4ml/min). Once all blood was washed from the heart, digestion buffer (200 μg/ml Liberase DH (Roche) in perfusion buffer) was passed through the heart for ~8 minutes (until the hearts appeared waxy in color and flaccid to the touch). During perfusion, atria and excess tissue were removed. After enzymatic digestion, hearts were minced with fine scissors into small pieces and triturated to release cells. Cell isolates were passed through a 100 μm cell strainer and centrifuged at 30 xg for 3 minutes at room temperature. Supernatant (containing the non-myocyte cells) was collected and the myocyte pellet was washed with perfusion buffer and re-centrifuged. The supernatant was again collected and the purified myocyte pellet was lysed with 1 ml of Trizol (ThermoFisher). The non-myocyte supernatant was centrifuged at 500 xg for 5 minutes and FACS was performed.

extract_protocol:
Mouse hearts were pooled to obtain enough material for sequencing (P1: 12 hearts/sample, P14 and P56: 6-7 hearts/sample). The samples were homogenized in 15 mL lysis buffer (0.32 M sucrose, 10 mM Tris-HCl (pH = 8), 5 mM CaCl2, 5 mM magnesium acetate, 2 mM EDTA, 0.5 mM EGTA, 1 mM DTT and 1X complete protease inhibitor (all chemical reagents were acquired from Sigma-Aldrich). The heart lysate was combined with another 15 mL lysis buffer and subsequently homogenized for 10-15 strokes using a dounce tissue grinder (Wheaton, Millville, NJ, USA). The cell lysate was sequentially filtered through 70 μM and 40 μM cell strainers (Becton Dickinson, Franklin Lakes, NJ, USA) and centrifuged to pellet nuclei at 1000 x g for 5 mins. Nuclei pellets were then resuspended in 2-4mL sucrose buffer (1 M sucrose, 10 mM Tris-HCl (pH = 8), 5 mM magnesium acetate, 1 mM DTT and 1X complete protease inhibitor) and the suspension was cushioned on top of a 2x volume of the sucrose buffer, followed by centrifugation to pellet nuclei at 1000 xg for 5 mins. Nuclei pellets were then washed once in 1 mL of nuclei storage buffer (NSB, 0.44 M sucrose, 10 mM Tris-HCl (pH = 7.2), 70 mM KCl, 10 mM MgCl2, 1.5 mM spermine and 1x complete protease inhibitor). The washed nuclei pellets were then resuspended in NSB and stained for the cardiomyocyte nuclear specific marker, Pcm1 (1:200, HPA023374, Sigma-Aldrich) at 4oC for 45 minutes. Omitting the primary antibody served as a control for positive staining. Nuclei were washed twice in NSB and stained with secondary antibody conjugated with Alexa Fluor 633 (1:500, ThermoFisher Scientific (Molecular Probes)) or Brilliant Violet 421 (1:400, BioLegend, San Diego, CA, USA) at 4oC for 30 minutes. Nuclei were washed twice in NSB and resuspended in PBS before being processed for FACS. Pcm1 (-/+) nuclei were separated using the BD FACS ARIA cell sorter. Collected Pcm1 (-/+) nuclei were pelleted at 1500 x g for 15 minutes. The purity of nuclei isolations was checked by qPCR of cardiomyocyte enriched genes.
ATAC-seq library preparation. Nuclei pellets underwent the transposition reaction using Nextera DNA library preparation kit (FC-121-1030, Illumina) followed by purification using MinElute PCR purification kit (#28004, Qiagen) and PCR amplification. Size selection by agarose gel was performed after PCR to select for library fragment sizes of 200-400bp. Libraries were validated using the MultiNA bioanalyzer (Shimadzu). Libraries were sequenced with the HiSeq2500 using version 4 reagents (Illumina), yielding 100 bp single end reads. Base-calling was performed with RTA (version 1.8.66.3) and converted to fastq file using bcl2fastq (version 2.17.1.14).

tag: developmental stage

value: Isolated cardiomyocytes


title: H4K8ac_ring_hiseq

status: Public on Jul 24 2017

type: SRA

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

description: ChIP DNA

library_source: genomic

data_processing:
Raw sequencing reads were first processed by adapter trimming using skewer (version 0.1.125)
Trimmed reads were aligned to P.falciparum genome using BWA version 0.7.12
Uniquely aligned reads (mapping quality>20, the probability of incorrect mapping<0.01) were extracted out for further study.
For a genomic interval, read coverage was detected using BedTools version 2.18.
Peaks were called using MACS version 2.2 with the following setting: --broad --slocal 500 --nomodel
Genome_build: P. falciparum genome downloaded from GeneDB on July 2015
Supplementary_files_format_and_content: Tab-delimited txt files about peak information output from MACS peak calling algorithm

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: Asexual stages

growth_protocol: P. falciparum cells were cultured in RPMI media at 2% hematocrit and sorbitol synchronised

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-H4K8ac antibody
Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA library prep kit from Illumina

treatment_protocol: P. falciparum cells were formaldehyde cross linked and harvested at 10% parasetemia in 2% hematocrit  for immuno-precipitation

value: Ring

tag: strain

tag: chip antibody

value: H4K8ac(catalogue:Millipore 07-328, lot number:2488698)


title: atac_P14_rep3

organism: Mus musculus

tag: cell type


title: atac_P56_rep1


title: H4K8ac_troph_hiseq

description: ChIP DNA

value: Trophozoite


title: H4K8ac_schiz_hiseq

description: ChIP DNA

value: Schizont


title: atac_P56_rep2


title: atac_P14_rep2


title: Input_hiseq

description: Genomic DNA

value: none (input)


title: atac_P1_rep3


title: atac_P14_rep1


title: Zm_WL_rep_1

city: Cambridge

first: Steven

middle: James

last: Burgess

state: Cambridgeshire

address: Department of Plant Sciences, Downing College

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description:
Harvested between 4-6 hours after beginning of light cycle, Steven J. Burgess and Ivan Reyna-Llorens
DHS_Zm_WL.regionPeak.txt
DGF_Zm_WL.bed
DGF_DE_Zm_WL.bed

data_processing:
DNaseI digested reads were aligned to reference genomes using Bowtie2 using the following configuration: --local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75
DNaseI hypersensitive sites (DHS) were identified using MACS2 using the following configuration: -p 1e-1 --nomodel --extsize 150 --shift -75 --llocal 50000
The final set of DHS sequences was determined by selecting the optimal number of peaks called on the pooled replicates. This number is determined by the maximum number of consistent peaks between replicates, as determined spp with the following configuration: [peaks_1] [peaks] -1 0 F 0.02.
Digital genomic footprints (DGFs) were identified within DHS using wellington with the following parameters:  -fdr 0.05
Differential DGFs were identified with DHS using wellington bootstrap with the following parameters: -fdr 0.05
Genome_build: Bdistachyon_283_assembly_v2.0; Sbicolor_255_v2.0; Sitalica_164_v2; Zmays_284_AGPv3.
Supplementary_files_format_and_content: DHS are in MACS2 output BED6+4 format, DGF are Wellington output (BED), DGFs annotated with TF motifs BED3+2.

organism: Zea mays

source_name: Zea mays seedlings

growth_protocol: S. italica, S. bicolor and Z. mays were grown under controlled conditions at the University of Cambridge. A growth room was set on a 12h:12h day/night cycle; temperature, 28oC day/20oC night;  illumination, 400µm; humidity, 60%;  CO2, ambient air. Germination:  Sorghum bicolor and Zea mays seeds were imbibed in dH2O for 48h;  Setaria italica, seeds were germinated on wet filter paper at 30oC overnight in the dark. Growth medium: 3:1 M3 compost to medium vermiculite (v/v) mixture,  with a thin covering of soil. Seedlings were hand watered. For B. distachyon plants were grown under controlled conditions at the Sainsbury Lab Cambridge, first under SD condition 14h/10h, light/dark for 2 weeks and then shifted to LD 20h/4h, light/dark, for 1 week and harvested at ZT20. Temperature was set at 20oC, humidity 65% and light intensity 350µMols.

extract_protocol:
Small fragments of DNA (~50-600bp) were isolated using gel purification following phenol chloroform extraction of DNaseI treated nuclei.
Libraries were created using the Hyper Prep DNA Library preparation kit  according to the manufactures instructions and indexed for pooling using NextFlex DNA barcoded adapters (Bioo Scientific, Austin TX US). Libraries were quantified on a Tapestation DNA 1000 Screen tape and by qPCR using an NGS Library Quantification Kit (KAPA Biosystems) on an AriaMx qPCR system (Agilent). Libraries were then normalised, pooled, diluted and denatured for sequencing on the NextSeq 500 (Illumina, Chesterford UK) according to the manufacturer’s instructions. PhiX control library (Illumina) was spiked into the main library pool at 10% for quality control purposes and to improve library diversity.

treatment_protocol: Bundle Sheath tissues were isolated by filtering after shearing leaves in a Waring blender.

tag: tissue type

value: Whole Leaf

tag: tissue source

value: Third Leaf

value: 18 days


title: Zm_WL_rep_2


title: Zm_BS_rep_2

description:
Harvested between 4-6 hours after beginning of light cycle, Steven J. Burgess and Ivan Reyna-Llorens
DHS_Zm_BS.regionPeak.txt
DGF_Zm_BS.bed
DGF_DE_Zm_BS.bed

value: Bundle Sheath


title: MR-scRNAseq-40080044-cell-45

city: Stanford

first: Vittorio

last: Sebastiano

state: California

address: 265 Campus Drive

department: OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Fastq files were aligned against GRCm38.p5 reference mouse genome obtained from the Ensembl database using STAR RNA-seq aligner
Quantification of mapped reads for genomic features was calculated using Rsubread
Gene zero counts were excluded and QC matricies (paramaters set to exclude cells with ERCC >10%,  gene features < 2000 and total counts <40,000)  were calculated using the R package scater to create final feature counts file: MR-scRNAseq-40080044_35-cells_Feature_counts.csv
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: feature counts

molecule: polyA RNA

source_name: single MEF cell, 1 Gy irradiation, no micronuclei

growth_protocol: MEFs were grown in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 μg/ml streptomycin and 0.1 mM β-mercaptoethanol at 37°C in 5% CO2 and 3% O2

extract_protocol:
Individual cells were captured in 5 μl 0.2% (v/v) Triton-X100, 2 U/μl RNasin Ribonuclease Inhibitor (Promega) and cDNA obtained using the Smart-seq2 protocol
NextSeq550 with Nextera dual indexing
Single Cell RNA-Seq (NextSeq550)

treatment_protocol: Cells were irradiated (1 Gy) and re-seeded onto 50 mm PEN membrane dishes (Zeiss) 32 h later. Picogreen-containing medium (Quant-iT PicoGreen dsDNA reagent, 4 μl per ml) was added to the cells 48 h post-IR to stain DNA, and laser capture microdissection (LCM) performed

value: MEF

tag: treatment

value: 1 Gy irradiation, no micronuclei

tag: passed qc and used in paper

value: TRUE


title: MR-scRNAseq-40080044-cell-16

source_name: single MEF cell, 1 Gy irradiation, micronuclei

value: 1 Gy irradiation, micronuclei


title: MR-scRNAseq-40080044-cell-47


title: rna_P56_rep1

description:
rRNA depleted RNA
cardiomycyte_rna.mx

data_processing:
Used HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data
FastX quality trimmer was used to trim bases with phred quality score less than 20. Reads with a length shorter than 20 bp after clipping were discarded.
Reads were mapped to the mouse genome primary assembly  (GRCm38) downloaded from Ensembl with STAR (version2.4.0g1) and Ensembl v85 gene annotations.
FeatureCounts v1.4.2 was used to count reads that mapped to the entire gene body with a mapping quality score of 10 or greater. Genes with fewer than 10 reads per sample on average were excluded.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression count matrix

molecule: total RNA

extract_protocol:
Mouse hearts were pooled to obtain enough material for sequencing (P1: 12 hearts/sample, P14 and P56: 6-7 hearts/sample). The samples were homogenized in 15 mL lysis buffer (0.32 M sucrose, 10 mM Tris-HCl (pH = 8), 5 mM CaCl2, 5 mM magnesium acetate, 2 mM EDTA, 0.5 mM EGTA, 1 mM DTT and 1X complete protease inhibitor (all chemical reagents were acquired from Sigma-Aldrich). The heart lysate was combined with another 15 mL lysis buffer and subsequently homogenized for 10-15 strokes using a dounce tissue grinder (Wheaton, Millville, NJ, USA). The cell lysate was sequentially filtered through 70 μM and 40 μM cell strainers (Becton Dickinson, Franklin Lakes, NJ, USA) and centrifuged to pellet nuclei at 1000 x g for 5 mins. Nuclei pellets were then resuspended in 2-4mL sucrose buffer (1 M sucrose, 10 mM Tris-HCl (pH = 8), 5 mM magnesium acetate, 1 mM DTT and 1X complete protease inhibitor) and the suspension was cushioned on top of a 2x volume of the sucrose buffer, followed by centrifugation to pellet nuclei at 1000 xg for 5 mins. Nuclei pellets were then washed once in 1 mL of nuclei storage buffer (NSB, 0.44 M sucrose, 10 mM Tris-HCl (pH = 7.2), 70 mM KCl, 10 mM MgCl2, 1.5 mM spermine and 1x complete protease inhibitor). The washed nuclei pellets were then resuspended in NSB and stained for the cardiomyocyte nuclear specific marker, Pcm1 (1:200, HPA023374, Sigma-Aldrich) at 4oC for 45 minutes. Omitting the primary antibody served as a control for positive staining. Nuclei were washed twice in NSB and stained with secondary antibody conjugated with Alexa Fluor 633 (1:500, ThermoFisher Scientific (Molecular Probes)) or Brilliant Violet 421 (1:400, BioLegend, San Diego, CA, USA) at 4oC for 30 minutes. Nuclei were washed twice in NSB and resuspended in PBS before being processed for FACS. Pcm1 (-/+) nuclei were separated using the BD FACS ARIA cell sorter. Collected Pcm1 (-/+) nuclei were pelleted at 1500 x g for 15 minutes. The purity of nuclei isolations was checked by qPCR of cardiomyocyte enriched genes.   Isolated PCM1 nuclei were resuspended in 1mL TRIzol solution and followed by RNA extraction using Direct-zol RNA mini-prep kit (Zymo Research, Irvine, CA, USA), according to the manufacturer’s recommended protocol, with DNase I treatment in the column to remove genomic DNA contamination. RNA was eluted in 30μL 1xTE buffer. Quantity and quality of RNA were examined on MultiNA bioanalyzer (Shimadzu, Tokyo, Japan).
RNA-seq libraries were prepared using NEBNext rRNA Depletion Kit (#6310, NEB, USA) and NEBNext Ultra Directional RNA Library Prep Kit (#E7420, NEB, USA) according to the manufacturer’s recommended protocol. Libraries were validated on MultiNA bioanalyzer and sequenced at a concentration of 13 pM using HiSeq 2500 version 4 reagents (Illumina, SanDiego,CA, USA), generating 100 base pair reads.


title: rna_P56_rep2

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: atac_P1_rep2


title: atac_P1_rep1


title: Zm_BS_rep_1


title: MR-scRNAseq-40080044-cell-15


title: MR-scRNAseq-40080044-cell-18


title: rna_P14_rep2

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: rna_P14_rep1

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: rna_P14_rep3

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: rna_P1_rep3

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: rna_P1_rep2

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: rna_P1_rep1

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: MR-scRNAseq-40080044-cell-42


title: MR-scRNAseq-40080044-cell-31


title: rna_P56_rep3

description:
rRNA depleted RNA
cardiomycyte_rna.mx


title: MR-scRNAseq-40080044-cell-50


title: MR-scRNAseq-40080044-cell-55


title: MR-scRNAseq-40080044-cell-37


title: MR-scRNAseq-40080044-cell-26


title: MIP56_CD45_4

city: Brisbane

first: James

last: Hudson

state: QLD

address: 300 Herston Rd

institute: QIMR Berghofer Medical Research Institute

data_processing:
FASTQ files were quality trimmed with Trimmomatic (phred >20)
Reads were mapped to mm10 using RNA STAR
Count matrix was calculated with GRCm38.75/mm10 annotations using HTseq tools
EdgeR was used for all comparisons
Genome_build: GRCh38.75/mm10

source_name: Enzyme-dissociated cells

extract_protocol:
RNA was isolated with trizol according to manufacturer’s instructions with glycogen included as a carrier. Each sample was treated with DNase I (Roche) for 10 minutes and then RNA was further column purified with MinElute RNeasy kit (#28004, Qiagen).
Following cell extraction, the non-myocyte fraction was resuspended in 100ul 5 mg/ml bovine serum albumin in PBS solution. Cell isolates were then incubated at 4°C for 20 minutes with 3 ug of CD90-APC (A14727, ThermoFisher), CD45-FITC (130-102-778, Miltenyi Biotec), CD31-BV421 (102423, BioLegend) and Podoplanin-PE/Cy7 (127411, BioLegned). The stained cells were washed in PBS/BSA solution and sorted using a BD FACS ARIA cell sorter. Each purified cell population was centrifuged at 1000xg for 5 minutes, cell media was aspirated and 1 ml Trizol was added to isolate RNA.
Ribosomal RNA was depleted with Ribo Zero Gold (Illumina), RNA quality ascertained by Bioanalyser and cDNA generated with SuperScript II Reverse Transcriptase (ThermoFisher). Libraries were created with TruSeq Stranded Total RNA kits (Illumina) and read with HiSeq SR Cluster v4 kit (Illumina) on a HiSeq 2500 sequencer. Each sample contained ~45 million 50-bp single-end reads.

treatment_protocol:
For adult male surgeries, the animals were housed under standard conditions with 12h light/dark cycles and ad libitum access to food and water. At 8 weeks of age, male CD1 mice were anesthetized with 4% isoflurane (Bayer) and maintained with 2% isoflurane and 0.25 l/min oxygen during surgery. The animals were intubated and ventilated (Minivent, Harvard Apparatus) with a tidal volume of 250 µl and a respiration rate of 133 strokes/min. A thoracotomy at the 3rd and 4th intercostal space was performed and the pericardial sac removed. The left descending coronary artery was permanently ligated with 7-0 prolene suture (Ethicon). Following ligation, blanching of the myocardium was observed to determine if adequate ischaemia was achieved. The chest wall was then sutured closed, the mouse removed from anesthesia, supplied with s.c. injection of buprenorphine (0.05mg/kg) as required and allowed to recover from the surgery. Sham mice had the same procedure except MI was not performed.
Adult CD-1 (ICR) mice were anaesthetized with an i.p injection of ketamine (100 mg/kg) and Xylazil (12.5 mg/kg) 3 days post-surgery. Hearts were quickly dissected and washed in perfusion buffer (120.4 mmol/l NaCl, 14.7 mmol/l KCl, 0.6 mmol/l KH2PO4, 0.6 mmol/l Na2HPO4, 1.2 mmol/l MgSO4•7H2O, 4.6 mmol/l NaHCO3, 10 mmol/l Na-HEPES, 30 mmol/l taurine, 5.5 mmol/l glucose and 10 mM 2,3-Butanedione 2-monoxime). The aorta was then cannulated with a 21-gauge cannula, secured with 3-0 silk suture and perfused with 37◦C, oxygenated perfusion buffer using a Langendorff apparatus (4ml/min). Once all blood was washed from the heart, digestion buffer (200 µg/ml Liberase DH (Roche) in perfusion buffer) was passed through the heart for ~8 minutes (until the hearts appeared waxy in color and flaccid to the touch). During perfusion, atria and excess tissue was removed. After enzymatic digestion, hearts were minced with fine scissors into small pieces and triturated to release cells. Cell isolates were passed through a 100 µm cell strainer and centrifuged at 30xg for 3 minutes at room temperature. Supernatant (containing the non-myocyte cells) was collected and the myocyte pellet was washed with perfusion buffer and re-centrifuged. The supernatant was again collected and the purified myocyte pellet was lysed with 1 ml of Trizol (ThermoFisher). The non-myocyte supernatant was centrifuged at 500xg for 5 minutes and FACS was performed.

tag: background mouse strain

value: CD45+ Leukocyte

value: Myocardial Infarction


title: MIP56_Fibro_4

value: CD90+/CD45-/CD31- Fibroblast


title: MIP56_CD31_3

value: CD31+/CD45- Endothelial cell


title: MIP56_Myo_4

value: Cardiomyocyte


title: MR-scRNAseq-40080044-cell-33


title: MIP56_CD45_3


title: MR-scRNAseq-40080044-cell-20


title: MR-scRNAseq-40080044-cell-28


title: MR-scRNAseq-40080044-cell-44


title: MR-scRNAseq-40080044-cell-14


title: MIP56_Fibro_3


title: MIP56_Myo_3


title: MIP56_CD31_2


title: MR-scRNAseq-40080044-cell-23


title: MIP56_CD31_4


title: MIP56_CD45_2


title: MR-scRNAseq-40080044-cell-39


title: MIP56_CD31_1


title: MIP56_Fibro_2


title: MR-scRNAseq-40080044-cell-22


title: MIP56_Myo_2


title: MIP56_CD45_1


title: MR-scRNAseq-40080044-cell-17


title: MR-scRNAseq-40080044-cell-30


title: MR-scRNAseq-40080044-cell-41


title: MR-scRNAseq-40080044-cell-25


title: MR-scRNAseq-40080044-cell-36


title: MIP56_Myo_1


title: MIP56_Fibro_1


title: MR-scRNAseq-40080044-cell-49


title: MIP1_CD31_4

treatment_protocol:
For neonatal surgeries, timed pregnant CD1 female mice were housed under standard conditions with 12h light/dark cycles and ad libitum access to food and water. At postnatal day 1 mice (P1), neonatal MI surgeries were performed as previously described (Mahmoud, A.I., et al. (2014) Nat. Protocols 9, 305-311). Sham mice had the same procedure except MI was not performed.
Neonatal CD-1 (ICR) mice were decapitated 3 days after surgery and cardiac ventricles were dissected and washed in ADS buffer (116.3 mmol/l NaCl, 20mmol/l HEPES, 1mmol/l NaH2PO4, 5.5mmol/l glucose, 5.36 mmol/l KCl, 0.83 mmol/l MgSO4,) and then cut into small pieces and pooled into groups of 6 ventricles per cell stirrer. Hearts were then digested at 37◦C under constant agitation for 30-40 minutes (or until tissue was fully homogenized). The digestion buffer was made with 200 µg/ml Liberase DH (Roche) in ADS buffer. Myocytes and non-myocytes were then separated by percoll® as described above. Cell isolates were then layered on percoll gradients and centrifuged at 2100xg for 30 minutes. The bottom layer (containing myocytes) and the top layer (containing enriched non-myocytes) were then collected separately and washed twice in ADS. The myocyte fraction was then lysed in Trizol. FACS was then performed on the non-myocyte fraction.


title: MIP1_CD45_4


title: MIP1_CD31_3


title: MR-scRNAseq-40080044-cell-48


title: MR-scRNAseq-40080044-cell-32


title: MIP1_CD45_3


title: MR-scRNAseq-40080044-cell-19


title: MIP1_Fibro_3


title: MR-scRNAseq-40080044-cell-35


title: MR-scRNAseq-40080044-cell-24


title: MR-scRNAseq-40080044-cell-12


title: MIP1_Myo_3


title: MR-scRNAseq-40080044-cell-51


title: MIP1_CD31_2


title: MR-scRNAseq-40080044-cell-38


title: MIP1_CD45_2


title: MR-scRNAseq-40080044-cell-21


title: MR-scRNAseq-40080044-cell-34


title: MIP1_Fibro_2


title: 48 Hour - DES 56 AR81009 R3

city: St Louis

first: Rebecca

last: Bart

state: MO

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

data_processing:
Basecalling performed with Illumina's Real Time Analysis software version 1.18.64
RNASeq Reads were cleaned for adapter sequence and low quality reads using Trimmomatic v0.32 with parameters: PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
RNASeq Reads surviving trimming as pairs were mapped to the TM-1 NBI Gossypium Hirsutum with HISAT2 v2.0.6 using default parameters with the --dta-cufflinks flag for analysis with stringtie.
Read mapping data for each replicate was used to create gene models and merged into a single set of gene models using Stringtie v1.2.3 with default parameters.
Fragments Per Kilobase of transcript per Millions of mapped reads (FPKM) values were calculated using cuffdiff v2.2.1 with parameters: --max-bundle-frags 500000000
Genome_build: TM-1 NBI Gossypium Hirsutum Assembly Downloaded from CottonGen
Supplementary_files_format_and_content: Abundance measurement values were produced using cuffdiff v2.2.1. Tab deliimited files contain FPKM values, raw fragments, and scaled fragments per gene. These values come from the genes.read_group_tracking file produced by cuffdiff

organism: Gossypium hirsutum

source_name: Inoculated G. hirsutum leaf

growth_protocol: Disease assays were conducted in a growth chamber set at 30°C and 80% humidity. Xcm strains were grown on NYGA plates containing 100µg/ml rifampicin at 30°C for two days before inoculations were performed.

extract_protocol:
Infected and mock-treated tissue were collected and flash frozen at 24 and 48 hours post inoculation. RNA was extracted using the Sigma tRNA kit.
RNA quality was assessed on an Agilent Bioanalyzer. 5ug of total RNA was used as starting material for library construction. mRNA was isolated using the NEB magnetic mRNA isolation kit. Standard library prep protocol was followed for all samples. Library quality was assessed on an Agilent Bioanalyzer.

treatment_protocol: Inoculations were conducted by infiltrating a fully expanded leaf with an OD600: 0.5 bacterial solution in 10mM MgCl2 or a mock treatment of just 10mM MgCl2

tag: tissue

value: leaf

tag: hours after inoculation

tag: cotton cultivar

value: DES 56

tag: xcm strain


title: MIP1_CD45_1


title: MIP1_Fibro_1


title: MIP1_Fibro_4


title: BN4 PBS

city: Urbana

first: William

middle: Harold

last: Witola

state: Illinois

address: 2001 South Lincoln Avenue

department: Pathobiology

institute: University of Illinois at Urbana-Champaign

description: replicate 4

data_processing:
The compressed tgz tarball was transferred to the Biocluster (IGB’s high performance computing cluster) using Globus, and then was decompressed (using tar Linux command). Obtained the rat genome reference files for Rnor_6.0, and the T. gondii genome files for gt1.TGGT1 from Ensembl. Below are the commands one can use to download these same files. The rat annotation file was from Ensembl annotation release 84, and T. gondii’s was from release 31.
Then the rat and T. gondii FASTA files, also the GTF files were concatenated. A quality check was performed on the FASTQ files using FASTQC (version 0.11.4) software. The reads had already been adapter trimmed at the sequencing center.
The quality of reads was nearly perfect. The samples did not pass “sequence duplication”, “k-mer  content”, or “per sequence quality” metrics, however, upon manual inspection these looked fairly normal for an RNA-Seq project. L1Toxo and L2Toxo have 4 overrepresented sequences. I ran a BLAST alignment on these sequences and they matched rat mRNA, so these also appear to be normal. Trimmomatic (version 0.33) was used to trim any residual adapter content and low quality bases. Very few reads were lost to trimming.
A quality check was performed on the trimmed FASTQ files using FASTQC (version 0.11.4) software. Since few reads were removed, results do not look very different from the raw FASTQC/MultiQC reports. An index file has to be made from the reference genome for every aligner, which helps speed up the process of alignment. I used STAR (version 2.5.0a) to create an index of this genome using the command below. Ran alignments against the custom genome using STAR (version 2.5.0a) software.  The samples had fairly consistent results and ~89% of reads aligned uniquely to the reference genome.
All gene counts were generated using featureCounts in the subread (version 1.5.0) package. Only uniquely aligned reads are considered in featureCounts.
“MultiMapping” reads reported in the featureCounts section of the multiqc report is not an accurate count of the number of reads that mapped to multiple places. FeatureCounts instead returns one count for every position that a read maps to. Refer to the STAR section for a more accurate count of multiple mapped reads. STAR only gives one count per read that aligns to multiple places. For example, if a read aligns to 10 different places on the genome equally well, then featureCounts would count that as 10 under “MultiMapping”, while STAR would count that as 1 under “Mapped to multiple loci”. For all samples, approximately 60% of uniquely aligned reads were assigned to a gene.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: excel files with raw read counts or ANOVA results

organism: Rattus norvegicus

source_name: Brown Norway rat PBS control rep4

extract_protocol:
RNA was extracted with RNeazy mini kit (Qiagen) including DNase I treatment following the manufacturer’s instructions. Quality control was performed with Agilent 2100 Bioanalyzer (Agilent Technologies)
RNA sequencing libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina) following the manufacturer’s instructions. The libraries were quantitated by fluorometry (Qubit), run on a Bioanalyzer for fragment analysis and diluted to 10 nM. The libraries were quantitated by qPCR and sequenced on two lanes for 101 cycles from one end of the fragments on a HiSeq2500  using a HiSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion.

treatment_protocol: 3.5 x 10^6 freshly isolated T. gondii RH strain tachyzoites constitutively expressing cytosolic yellow fluorescent protein

value: Brown Norway

tag: age

value: Four weeks old

value: Peritoneal

tag: infected with

value: not infected (PBS control)


title: 24 Hour - DES 56 AR81009 R3


title: MIP1_Myo_1


title: BN3 PBS

description: replicate 3

source_name: Brown Norway rat PBS control rep3


title: MIP1_Myo_4


title: 24 Hour - Acala Maxxa AR81009 R3

value: Acala Maxxa


title: 48 Hour - Acala Maxxa AR81009 R3


title: 48 Hour DES 56 MS14003 R3


title: ShamP56_CD45_4

value: Sham-operation


title: BN2 PBS

description: replicate 2

source_name: Brown Norway rat PBS control rep2


title: ShamP56_Fibro_4


title: BN1 PBS

description: replicate 1

source_name: Brown Norway rat PBS control rep1


title: 24 Hour Acala Maxxa MS14003 R3


title: BN3Toxo

description: replicate 3

source_name: Brown Norway rat infected by T. gondii for 24 hours rep3

value: T. gondii


title: ShamP56_Myo_4


title: MIP1_Myo_2


title: ShamP56_CD31_3


title: MIP1_CD31_1


title: ShamP56_CD45_3


title: 48 Hour DES 56 Mock R3

value: Mock


title: BN1Toxo

description: replicate 1

source_name: Brown Norway rat infected by T. gondii for 24 hours rep1


title: 24 Hour DES 56 Mock R3


title: 48 Hour Acala Maxxa Mock R3


title: LEW3 PBS

description: replicate 3

source_name: Lewis rat PBS control rep3

value: Lewis


title: 24 Hour Acala Maxxa Mock R3


title: LEW4 PBS

description: replicate 4

source_name: Lewis rat PBS control rep4


title: 48 Hour DES 56 Mock R2


title: ShamP56_CD31_4


title: 24 Hour DES 56 MS14003 R3


title: ShamP56_Myo_3


title: 48 Hour Acala Maxxa Mock R2


title: ShamP56_CD31_2


title: 48 Hour Acala Maxxa MS14003 R3


title: ShamP56_CD45_2


title: L4Toxo

description: replicate 4

source_name: Lewis rat infected by T. gondii for 24 hours rep4


title: LEW1 PBS

description: replicate 1

source_name: Lewis rat PBS control rep1


title: BN4Toxo

description: replicate 4

source_name: Brown Norway rat infected by T. gondii for 24 hours rep4


title: 48 Hour DES 56 MS14003 R2


title: 48 Hour Acala Maxxa MS14003 R2


title: BN2Toxo

description: replicate 2

source_name: Brown Norway rat infected by T. gondii for 24 hours rep2


title: L3Toxo

description: replicate 3

source_name: Lewis rat infected by T. gondii for 24 hours rep3


title: ShamP56_Fibro_2


title: ShamP56_Myo_2


title: 48 Hour Acala Maxxa AR81009 R2


title: L2Toxo

description: replicate 2

source_name: Lewis rat infected by T. gondii for 24 hours rep2


title: ShamP56_CD31_1


title: ShamP56_Fibro_3


title: ShamP56_CD45_1


title: L1Toxo

description: replicate 1

source_name: Lewis rat infected by T. gondii for 24 hours rep1


title: 48 Hour DES 56 AR81009 R2


title: LEW2 PBS

description: replicate 2

source_name: Lewis rat PBS control rep2


title: ShamP56_Fibro_1

source_name: Enzyme-dissociated cells


title: 24 Hour Acala Maxxa AR81009 R2

source_name: Inoculated G. hirsutum leaf


title: 24 Hour DES 56 AR81009 R2


title: ShamP56_Myo_1


title: 24 Hour DES 56 MS14003 R2


title: 24 Hour Acala Maxxa MS14003 R2


title: ShamP1_Fibro_4


title: ShamP1_CD45_4


title: 48 Hour DES 56 Mock R1


title: 24 Hour Acala Maxxa Mock R2


title: ShamP1_CD31_3


title: 48 Hour DES 56 MS14003 R1


title: ShamP1_CD45_3


title: ShamP1_Myo_4


title: 24 Hour DES 56 Mock R2


title: 48 Hour Acala Maxxa  MS14003 R1


title: ShamP1_Fibro_3


title: ShamP1_CD31_2


title: 48 Hour Acala Maxxa AR81009 R1


title: ShamP1_Myo_3


title: 48 Hour DES 56 AR81009 R1


title: ShamP1_CD31_4


title: ShamP1_CD45_2


title: ShamP1_Fibro_2


title: 24 Hour DES 56 AR81009 R1


title: ShamP1_Myo_2


title: ShamP1_CD31_1


title: 24 Hour DES 56 MS14003 R1


title: Line 49x69 - F2-19

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Library strategy: MethylC–seq
Data were mapped to the TAIR10 reference genome
MethylC-seq analysis were performed as described in Schultz, M. D. et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523, 212-216 (2015).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text file; <chromosome> <cytosine position> <strand> <CNN (N = A, T, C, G)> <methylated cytosines at this site> <mapped cytosines at this site> <binomial test, 1 means methylated, 0 means unmethylated>

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: All samples  in this study are the Col-0 ecotype of Arabidopsis thaliana. Plants were grown in long-day (16 hour light) conditions at 24℃ and 3 week old leaf tissue was used for all experiments and sequencing.

extract_protocol: DNA was isolated using fractional precipitation followed by phenol-chloroform extraction and RNase A treatment. 1ug of DNA was used to prepare libraries as previously described (Urich et al. 2015).

tag: ecotype

value: ~3 weeks old


title: Line 49x69 - F2-20


title: Line 49x69 - F2-18


title: 24 Hour Acala Maxxa MS14003 R1


title: ShamP1_CD45_1

value: CD45+ Leukocyte


title: 48 Hour Acala Maxxa Mock R1


title: 24 Hour DES 56 Mock R1


title: Line 49x69 - F2-17


title: ShamP1_Fibro_1


title: Line 49x69 - F2-16


title: 24 Hour Acala Maxxa Mock R1


title: ShamP1_Myo_1


title: 24 Hour Acala Maxxa AR81009 R1


title: Line 49x69 - F2-12


title: Line 49x69 - F2-13


title: 977.Str.IP_P63_StrHip_RNAseq

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM and CPM) and differential expression analysis using limmavoom.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag

extract_protocol:
All samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip. RNA concentration determined by nanodrop.
Paired-end libraries for multiplexed sequencing were generated from 100ng of IP or input RNA using Nugen Ovation RNA-Seq System V2 kit with mRNA enrichment.

value: adult; P63

tag: strain background

value: FVB backcrossed with C57/Bl6N for 3 generations (~88% C57/Bl6N).

tag: genotype/variation

value: Aldh1l1-creERT2 hemi; Ribotag het

value: brain

tag: region

value: Striatum

tag: sample type

value: HA IP


title: 977.Str.input_P63_StrHip_RNAseq

source_name: cleared lysate as the input and control

value: input


title: 977.Hip.input_P63_StrHip_RNAseq

value: Hippocampus


title: 977.Hip.IP_P63_StrHip_RNAseq


title: 974.Str.IP_P63_StrHip_RNAseq


title: Line 49x69 - F2-11

value: leaf


title: WGBS of DNMT3b control rep3

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

institute: Washington University in St. Louis

data_processing:
Raw reads generated from the Illumina HiSeq 2500 sequencer were de-multiplexed using configurebcl2fastq.pl version 1.8.4.
Low-complexity reads and vector contamination were removed using sequence cleaner ("seqclean") and the NCBI UniVec database, respectively.
RNA-seq reads were mapped to mm9 using SHRiMP version 2.2.3.
WGBS reads were mapped to mm9 using Bismark version 0.9.0.
Methylation status was extracted using methylation extractor script from Bismark software.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA-seq bigWig files contain read density over exons.
Supplementary_files_format_and_content: WGBS .cov files are tab-delimited text files that contain methylated or un-methylated read counts on each C site.

source_name: Mouse cartilage tissue, control

extract_protocol:
Total RNA was collected using the AllPrep DNA/RNA Mini Kit (Qiagen, #80204). Total RNA concentration was determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality was assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next-generation sequencing library construction (as per the manufacturer's protocol) at the Genomics Research Center (GRC) at University of Rochester Medical School (URMC).

treatment_protocol: Primary articular chondrocytes were isolated from Dnmt3bf/f mice and treated with either Adeno-Cre or Adeno-GFP (MOI=100) for 72 h.

tag: strain/background

value: Adeno-GFP

tag: cell type

value: primary articular chondrocytes


title: WGBS of DNMT3b control rep2


title: WGBS of DNMT3b knockout rep3

source_name: Mouse cartilage tissue, DNMT3b knockout

value: Adeno-Cre


title: WGBS of DNMT3b control rep1


title: 974.Str.input_P63_StrHip_RNAseq


title: WGBS of DNMT3b knockout rep2


title: 974.Hip.IP_P63_StrHip_RNAseq


title: Line 49x69 - F2-10


title: Line 49x69 - F2-8


title: 974.Hip.input_P63_StrHip_RNAseq


title: Line 49x69 - F2-7


title: 971.Str.IP_P63_StrHip_RNAseq


title: WGBS of DNMT3b knockout rep1


title: RNA-seq of DNMT3b control rep2


title: RNA-seq of DNMT3b control rep3


title: Line 49x69 - F2-15


title: Line 49x69 - F2-14


title: Line 49x69 - F2-6


title: RNA-seq of DNMT3b knockout rep3


title: Line 49x69 - F2-5


title: Line 49x69 - F2-9


title: H4K8ac_schiz_miseq

description: ChIP DNA

source_name: Asexual stages

tag: developmental stage

value: Schizont

tag: strain

tag: chip antibody

value: H4K8ac(catalogue:Millipore 07-328, lot number:2488698)


title: 971.Hip.IP_P63_StrHip_RNAseq


title: RNA-seq of DNMT3b knockout rep2

tag: treatment


title: Line 49x69 - F2-4

tag: tissue


title: H4K8ac_troph_miseq

description: ChIP DNA

value: Trophozoite


title: Line 49x69 - F2-3

value: ~3 weeks old


title: H4K8ac_ring_miseq

description: ChIP DNA

value: Ring


title: RNA-seq of DNMT3b knockout rep1


title: Line 49x69 - F2-2


title: 970.Str.input_P63_StrHip_RNAseq

value: adult; P63


title: RNA-seq of DNMT3b control rep1


title: Line 69-G2


title: 971.Str.input_P63_StrHip_RNAseq

value: FVB backcrossed with C57/Bl6N for 3 generations (~88% C57/Bl6N).


title: Line 49x69 - F2-1


title: Input_miseq

description: Genomic DNA

value: none (input)


title: Sb_WL_rep_3

description:
Harvested between 4-6 hours after beginning of light cycle, Steven J. Burgess and Ivan Reyna-Llorens
DHS_Sb_WL.regionPeak.txt
DGF_Sb_WL.bed
DGF_DE_Sb_WL.bed

organism: Sorghum bicolor

source_name: Sorghum bicolor seedlings

tag: tissue type

value: Whole Leaf

tag: tissue source

value: Third Leaf

value: 18 days


title: Line 69-G1


title: Sb_WL_rep_2


title: Sb_WL_rep_1


title: 971.Hip.input_P63_StrHip_RNAseq

value: Aldh1l1-creERT2 hemi; Ribotag het

value: brain

value: input


title: Line 49-G2

value: leaf


title: Sb_BS_rep_2

description:
Harvested between 4-6 hours after beginning of light cycle, Steven J. Burgess and Ivan Reyna-Llorens
DHS_Sb_BS.regionPeak.txt
DGF_Sb_BS.bed
DGF_DE_Sb_BS.bed

value: Bundle Sheath


title: Line 49-G24 - mother


title: 970.Hip.input_P63_StrHip_RNAseq

value: Hippocampus


title: 970.Str.IP_P63_StrHip_RNAseq

value: Striatum

value: HA IP


title: Line 49-G1


title: Line 69-G28


title: Line 69-G20 - father


title: Bd_WL_rep_2

description:
Harvested ZT20, Katja Jaeger
DHS_Bd_WL.regionPeak.txt
DGF_Bd_WL.bed

organism: Brachypodium distachyon

source_name: Brachypodium distachyon seedlings

value: Seedling

value: 21 days


title: 970.Hip.IP_P63_StrHip_RNAseq


title: Sb_BS_rep_1


title: Line 69-G26

value: ~3 weeks old


title: Line 69-G22


title: Line 69-G31


title: Line 69-G30


title: Bd_WL_rep_1


title: Line 69-G23


title: Si_WL_rep_2

description:
Harvested between 4-6 hours after beginning of light cycle, Steven J. Burgess and Ivan Reyna-Llorens
DHS_Si_WL.regionPeak.txt
DGF_Si_WL.bed
DGF_DE_Si_WL.bed

organism: Setaria italica

source_name: Setaria italica seedlings

value: Third and Fourth Leaves


title: Si_WL_rep_3


title: Si_WL_rep_1


title: Si_BS_rep_2

description:
Harvested between 4-6 hours after beginning of light cycle, Steven J. Burgess and Ivan Reyna-Llorens
DHS_Si_BS.regionPeak.txt
DGF_Si_BS.bed
DGF_DE_Si_BS.bed


title: Line 69-G21


title: Si_BS_rep_1


title: Line 69-G18


title: Le_lab_CHIP_seq_F_TLS1620

status: Public on Jul 23 2017

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

data_processing:
For Hi-C, Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Caulobacter CB15N (NA1000) independently by Bowtie version 0.12.7 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, the same mapping procedure was used as for Hi-C but coverage was computed using BEDTools instead (Quinlan and Hall, 2010). Detailed protocols are listed in the Supplementary Materials and Methods.
The two resulting SAM files were then merged together. Unaligned reads were discarded.
The Caulobacter CB15N (NA1000) genome was then divided into restriction fragments (700 BglII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
The genome of Caulobacter CB15N was then divided into bins of 20 kb (for BglII Hi-C) and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID:    22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). Ten iterative normalization rounds were performed. Subsequent analysis and visualisation was done using Perl and R scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides

growth_protocol: Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290). After synchronization, swarmer cells were fixed formadehyde for chromosome conformation capture and Hi-C analysis. For antibiotic treatments, swarmer cells were incubated with 25 ug/mL rifampicin (final concentration) for 30 minutes before fixing with formadehyde.

extract_protocol:
Hi-C experiments were performed using BglII according to previous publications (Umbarger MA. 2012. Chromosome conformation capture assays in bacteria. PMID: 22776362 and Lieberman-Aiden, E. et al., 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. PMID: 19815776). Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2000/Hiseq 2500 sequencing platform

treatment_protocol:
Exponentially-growing cells were washed twice in 1x PBS before formadehyde was added to 1% final concentration.
None

value: mix population


title: Le_lab_CHIP_seq_F_TLS1613


title: Le_lab_CHIP_seq_F_TLS1622


title: Le_lab_CHIP_seq_F_ML2299


title: Le_lab_CHIP_seq_F_WT

value: wild type


title: Le_lab_CHIP_seq_FG_TLS1615

treatment_protocol:
Exponentially-growing cells were washed twice in 1x PBS before formadehyde and crosslinker Gold (Diagenode) was added to 1% final concentration.
None


title: Le_lab_CHIP_seq_FG_TLS1612


title: Le_lab_CHIP_seq_F_TLS1609


title: Line 69-G29


title: Le_lab_CHIP_seq_F_MT190.txt


title: Le_lab_CHIP_seq_FG_TLS1611


title: Le_lab_CHIP_seq_FG_TLS1599


title: LeLab_BglII_HiC_WT_swarmer_Rifampicin_25ugperml_30min_rep3

treatment_protocol:
Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE supplemented with 25ug per ml rifampicin for 30 min before fixing with 1% formadehyde.
None

value: swarmer cell, the adding rifampicin (25ug per ml) for 30min

tag: restriction enzyme

value: BglII


title: Le_lab_CHIP_seq_FG_TLS1608


title: Le_lab_CHIP_seq_FG_WT


title: LeLab_BglII_HiC_WT_swarmer_rep1

treatment_protocol:
Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE and fixed immediately by 1% formadehyde.
None

value: swarmer cells (0 min after synchronization)


title: LeLab_BglII_HiC_WT_swarmer_Rifampicin_25ugperml_30min_rep2


title: LeLab_BglII_HiC_TLS1617_swarmer_rifampicin_25ugperml_30min


title: LeLab_BglII_HiC_WT_swarmer_Rifampicin_25ugperml_30min_rep1


title: LeLab_BglII_HiC_TLS1618_swarmer_rifampicin_25ugperml_30min


title: LeLab_BglII_HiC_TLS1617_swarmer


title: LeLab_BglII_HiC_WT_swarmer_rep2


title: Line 69-G19

tag: age


title: LeLab_BglII_HiC_TLS1618_swarmer


title: LeLab_BglII_HiC_TLS1619_swarmer


title: LeLab_BglII_HiC_TLS1619_unsynchronized

treatment_protocol:
Caulobacter crescentus cells at exponential phase were fixed with 1% formadehyde
None

value: no synchronization, mixed population of cells


title: LeLab_BglII_HiC_TLS1616_swarmer


title: LeLab_BglII_HiC_TLS1614_swarmer


title: LeLab_BglII_HiC_WT_swarmer_rep3


title: LeLab_BglII_HiC_TLS1610_swarmer_rep1


title: LeLab_BglII_HiC_TLS1612_swarmer_rep1


title: LeLab_BglII_HiC_TLS1599_plus_xylose_60min

treatment_protocol:
Xylose was added to the exponentially growing culture for 60 min, then formadehyde was added to 1% final concentration
None

value: 60min after adding xylsoe


title: LeLab_BglII_HiC_TLS1601_swarmer


title: LeLab_BglII_HiC_TLS1608_swarmer_rep2


title: LeLab_BglII_HiC_TLS1600_swarmer_rep2


title: LeLab_BglII_HiC_TLS1612_swarmer_rifampicin_25ugperml_30min


title: LeLab_BglII_HiC_TLS1612_swarmer_rep2


title: LeLab_BglII_HiC_TLS1621_swarmer


title: LeLab_BglII_HiC_TLS1600_swarmer_rep1


title: LeLab_BglII_HiC_TLS1616_swarmer_rifampicin_25ugperml_30min


title: LeLab_BglII_HiC_TLS1608_swarmer_rep1


title: LeLab_BglII_HiC_TLS1599_plus_xylose_30min

treatment_protocol:
Xylose was added to the exponentially growing culture for 30 min, then formadehyde was added to 1% final concentration
None

value: 30min after adding xylsoe


title: LeLab_BglII_HiC_MT148_ParB_replenishment_plus_xylose_5min

treatment_protocol:
Exponentially-growing Caulobacter crescentus cells were washed off xylose twice in fresh PYE, then glucose is added to 0.2% final concentration. After 5 hr, cells were washed off glucose and xylose was added back (0.3% final concentration). After 5 min, formadehyde is added to 1% final concentration.
None

value: ParB depletion for 5 hr then adding back xylose (5min)


title: LeLab_BglII_HiC_TLS1599_plus_xylose_0min

treatment_protocol:
Xylose was added to the exponentially growing culture for 0 min, then formadehyde was added to 1% final concentration
None

value: 0min after adding xylsoe


title: LeLab_BglII_HiC_MT148_ParB_replenishment_plus_xylose_20min

treatment_protocol:
Exponentially-growing Caulobacter crescentus cells were washed off xylose twice in fresh PYE, then glucose is added to 0.2% final concentration. After 5 hr, cells were washed off glucose and xylose was added back (0.3% final concentration). After 20 min, formadehyde is added to 1% final concentration.
None

value: ParB depletion for 5 hr then adding back xylose (20min)


title: LeLab_BglII_HiC_MT148_ParB_replenishment_plus_xylose_0min

treatment_protocol:
Exponentially-growing Caulobacter crescentus cells were washed off xylose twice in fresh PYE, then glucose is added to 0.2% final concentration. After 5 hr, formadehyde is added to 1% final concentration
None

value: ParB depletion for 5 hr then adding back xylose (0min)


title: LeLab_BglII_HiC_MT148_ParB_replenishment_plus_xylose_15min

treatment_protocol:
Exponentially-growing Caulobacter crescentus cells were washed off xylose twice in fresh PYE, then glucose is added to 0.2% final concentration. After 5 hr, cells were washed off glucose and xylose was added back (0.3% final concentration). After 15 min, formadehyde is added to 1% final concentration.
None

value: ParB depletion for 5 hr then adding back xylose (15min)


title: LeLab_BglII_HiC_TLS1599_plus_xylose_15min

treatment_protocol:
Xylose was added to the exponentially growing culture for 15 min, then formadehyde was added to 1% final concentration
None

value: 15min after adding xylsoe


title: LeLab_BglII_HiC_MT148_ParB_replenishment_plus_xylose_10min

treatment_protocol:
Exponentially-growing Caulobacter crescentus cells were washed off xylose twice in fresh PYE, then glucose is added to 0.2% final concentration. After 5 hr, cells were washed off glucose and xylose was added back (0.3% final concentration). After 10 min, formadehyde is added to 1% final concentration.
None

value: ParB depletion for 5 hr then adding back xylose (10min)


title: LeLab_BglII_HiC_MT148_ParB_replenishment_plus_xylose_25min

treatment_protocol:
Exponentially-growing Caulobacter crescentus cells were washed off xylose twice in fresh PYE, then glucose is added to 0.2% final concentration. After 5 hr, cells were washed off glucose and xylose was added back (0.3% final concentration). After 25 min, formadehyde is added to 1% final concentration.
None

value: ParB depletion for 5 hr then adding back xylose (25min)


title: LeLab_BglII_HiC_ML2414_plus_xylose_1hr

treatment_protocol:
Xylose (final concentration of 0.3%) was added to an exponentially-growing Caulobacter crescentus culture for 1hr. After that, formadehyde is added to a final concentration of 1%.
None

value: 1hr after xylose addition


title: 0.2 ppm deoxynivalenol

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
The reads were processed using BWA software.
Mapped reads per annotated gene were counted by Bam2readcount.
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization.
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli

source_name: Bacterial culture with 0.2 ppm deoxynivalenol

growth_protocol: E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h.

extract_protocol:
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: K-12 substr. DH10B

tag: condition

value: myxotoxin

tag: toxin

value: deoxynivalenol

tag: concentration

value: 0.2 ppm


title: 2 ppm nivalenol

source_name: Bacterial culture with 2 ppm nivalenol

value: nivalenol

value: 2 ppm


title: 0.2 ppm nivalenol

source_name: Bacterial culture with 0.2 ppm nivalenol


title: LeLab_BglII_HiC_MT148_ParB_depletion_5hr_after_xylose_withdrawal

value: 5hr after withdrawal of xylose and addition of glucose

tag: genotype/variation

value: BglII


title: acetonitrile

source_name: Bacterial culture with acetonitrile

value: acetonitrile (control)


title: 2 ppm deoxynivalenol

source_name: Bacterial culture with 2 ppm deoxynivalenol


title: mef2c_KO mef2c_mouse_90

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

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

source_name: 3 mo-old Mef2C-KO mouse

extract_protocol:
10^4-10^5 cells from each macrophage subpopulation were sorted in 100-200 ul of Lysis/Binding Buffer (Life technologies), lysed for 5 min and frozen at -80°C. Cell lysates were thawed and mRNA was captured with 12 ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines. Purified messenger RNA was eluted at 70°C with 10 ul of 10 mM Tris-Cl pH 7.5 and stored at -80°C
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.
3' RNA-seq for digital gene expression quantitation

tag: organ

value: brain

tag: selection marker

value: CD11b+ CD45int


title: mef2c_WT mef2c_mouse_89

source_name: 3 mo-old Mef2C-CTRL mouse


title: mef2c_WT mef2c_mouse_107


title: mef2c_KO mef2c_mouse_119


title: HD4

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

description: Murine Longbone Osteocyte Y4

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter trimmed fastq files were generated.
Merged fastq files from lane 1 and lane 2. Fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using mm10 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used UCSC mm10 gtf file as guided annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: files for FPKM values for each sample and result of differential gene expression analysis

source_name: MLO-Y4 cells

growth_protocol: MLO-Y4 osteocyte-like cells (Kato et al., 1997), courtesy of Dr. Lynda Bonewald (University of Missouri-Kansas City) were maintained in normal growth medium (?-MEM [Invitrogen, Grand Island, NY] with 2.5% CS [Hyclone, Logan, UT], 2.5% FBS [Lonza, Walkersville, MD], 1% Penicillin/Streptomycin) throughout all portions of the experiment.  Cells were seeded 48 hours prior to fluid flow on 75 x 38 x 1 mm glass slides coated with 300 ?g/ml Type I Collagen (BD Biosciences, Bedford, MA) for 1 hour and washed.  Cell seeding density was 1.35 x 104 cells/cm2 so that upon flow exposure, cells were roughly 60% confluent and interconnected by dendritic processes.

extract_protocol:
When collecting samples, medium was aspirated and cells were lysed directly on glass slides using RLT buffer (Qiagen, Valencia, CA).  For each time point, triplicate samples were collected on separate days.  Total RNA was isolated using an Rneasy Mini Kit (Qiagen, Valencia, CA) per manufacturer instructions.
The cDNA libraries were prepared using the NEXTflex™ Rapid RNA Sequencing Kit and NEXTflex™ RNA-Seq Barcodes – 24 Kit (BioO Scientific) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Six libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).

treatment_protocol: Osteocyte-like MLO-Y4 cells were subjected to 2 hours of 10 dyn/cm^2 oscillating fluid flow in parallel-plate fluid flow chambers and harvested for analysis after an additional 2 hours post-flow incubation in fresh medium. Parallel control samples from sham treated cells were also collected. Triplicate samples of both flow and non-flow control conditions were collected to analyze flow vs. non-flow gene transcript regulation.

tag: experimental condition

value: Flow

tag: post-treatment incubation

value: 2 hours

tag: cell line


title: HD11

description: Murine Longbone Osteocyte Y4

value: Non-flow Control


title: HD19

description: Murine Longbone Osteocyte Y4


title: HD12

description: Murine Longbone Osteocyte Y4


title: HD3

description: Murine Longbone Osteocyte Y4


title: mef2c_WT mef2c_mouse_106

tag: strain


title: HD20

description: Murine Longbone Osteocyte Y4


title: mef2c_KO mef2c_mouse_105


title: mef2c_KO mef2c_mouse_101


title: mef2c_WT mef2c_mouse_102


title: mef2c_KO mef2c_mouse_103


title: mef2c_WT mef2c_mouse_115


title: WT-CONTROL 156

source_name: 10-mo-old CTRL mouse 14 days following AAV-CTRL administration

value: AAV-CTRL


title: KO-IFN 154

source_name: 10-mo-old IFNAR-KO 14 days following AAV-IFNb administration

value: mic-IFNAR-KO

value: AAV-IFNb


title: KO-CONTROL 155

source_name: 10-mo-old IFNAR-KO 14 days following AAV-CTRL administration


title: WT-IFN 157

source_name: 10-mo-old CTRL mouse 14 days following AAV-IFNb administration


title: KO-CONTROL 152


title: WT-IFN 153

value: mic-IFNAR-CTRL


title: KO-IFN 151


title: WT-CONTROL 150


title: WT-IFN 141


title: KO-CONTROL 149


title: KO-CONTROL 142


title: KO-IFN 143


title: KO-CONTROL 134


title: KO-IFN 139


title: WT-CONTROL 138


title: WT-IFN 132


title: KO-IFN 116


title: AAV-ctrl2

source_name: 3-mo-old mouse 14 days following AAV-CTLR administration


title: WT-IFN 115


title: AAV-ctrl1

source_name: 3-mo-old mouse 14 days following AAV-CTRL administration


title: KO-IFN 113


title: AAV-IFN3

source_name: 3-mo-old mouse 14 days following AAV-IFNb administration


title: young2

source_name: 3-mo-old mouse


title: KO-CONTROL 114


title: KO-IFN 127


title: AAV-IFN1


title: AAV-IFN2


title: H4K16ac_ChIPseq-chx2

city: San Francsico

first: Miguel

last: Ramalho-Santos

address: 35 Medical Center Way, RMB 912D

institute: UCSF

description: CHX replicate 2

data_processing:
Sequencing reads were trimmed for adaptor sequence.
ATAC-seq reads were aligned to the mouse genome build mm10 using bowtie2 v2.2.4.
ChIP-seq reads were aligned to the mouse genome build mm9 using bowtie2 v2.2.4.
Aligned reads were sorted and deduplicated using samtools.
Peak calling was performed using Macs14 version 1.4.2 20120305 (ATAC-seq).
Genome_build: ATAC-seq: mm10 (GRCm38)
Genome_build: ChIP-seq: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bed: Bed files include peaks (ATAC-seq).
Supplementary_files_format_and_content: bigWig (ATAC-seq, ChIP-seq).

source_name: E14 ES cells, CHX, H4K16ac ChIP

growth_protocol: E14 ES cells were cultured in DMEM GlutaMAX with Na Pyruvate (Thermo Fisher Scientific), 15% FBS (Atlanta Biologicals), 0.1 mM Non-essential amino acids, 50 U/ml Penicillin/Streptomycin (UCSF Cell Culture Facility), 0.1 mM EmbryoMax 2-Mercaptoethanol (Millipore) and 2000 U/ml ESGRO supplement (LIF, Millipore).

extract_protocol:
H4K16ac ChIPs were performed according to the recommendations of the Diagenode low-cell ChIP kit (C01010072).
ChIP-seq libraries were prepared using NEBNext ChIPseq library prep kit E6200L using NEB index primers 2, 4, 5, 6, 7, and 12.

treatment_protocol: Cells were treated with DMSO (Ctrl) or 1 ug/ml Cycloheximide (Amresco) for 3 hours.

tag: cell type

value: embryonic stem (ES) cells

value: cycloheximide


title: LeLab_BglII_HiC_ML2413_plus_xylose_1hr

tag: developmental stage

value: 1hr after xylose addition


title: H4K16ac_ChIPseq-chx_inp

description: CHX input

source_name: E14 ES cells, CHX, input

tag: treatment


title: KO-CONTROL 122


title: day14_ifnar2

source_name: 22-mo-old mouse 14 days following 10ug anti-IFNAR i.c.v.

value: 10ug anti-IFNAR i.c.v.


title: day7_ifnar1

source_name: 22-mo-old mouse 7 days following 10ug anti-IFNAR i.c.v.


title: young1


title: day14_igG2

source_name: 22-mo-old mouse 14 days following 10ug IgG i.c.v.

value: 10ug IgG i.c.v.


title: day7_igG2

source_name: 22-mo-old mouse 7 days following 10ug IgG i.c.v.


title: day7_ifnar2


title: day7_igG1


title: day14_ifnar1


title: day14_igG1


title: H4K16ac_ChIPseq-dmso2

description: DMSO (Ctrl) replicate 2

source_name: E14 ES cells, control, H4K16ac ChIP

value: DMSO


title: H4K16ac_ChIPseq-dmso1

description: DMSO (Ctrl) replicate 1


title: IgG_1

source_name: 22-mo-old mouse 2 days following 10ug IgG i.c.v.


title: IFNAR_3

source_name: 22-mo-old mouse 2 days following 10ug anti-IFNAR i.c.v.


title: H4K16ac_ChIPseq-dmso_inp

description: DMSO (Ctrl) input

source_name: E14 ES cells, control, input


title: CHX_ATACseq_rep3

description:
Processed data file: CHX-gained_ATAC-seq_peaks.bed
Processed data file: CHX-lost_ATAC-seq_peaks.bed

source_name: E14 ES cells, CHX

extract_protocol:
ATAC-seq samples were extracted as described in Buenrostro et al., Curr Protoc Mol Biol, 2016.
ATAC-seq libraries were prepared as described in Buenrostro et al., Curr Protoc Mol Biol, 2016.


title: IFNAR_1


title: CHX_ATACseq_rep2


title: CHX_ATACseq_rep4


title: young_mic_2


title: IFNAR_2


title: CHX_ATACseq_rep1


title: young_mic_3


title: Ctrl_ATACseq_rep4

source_name: E14 ES cells, control


title: H4K16ac_ChIPseq-chx1

description: CHX replicate 1


title: IgG_2


title: young_mic_1


title: Old_mic_3

source_name: 22-mo-old mouse


title: Old_mic_2


title: Ctrl_ATACseq_rep3


title: Ctrl_ATACseq_rep1


title: day8 RXR ChIP-seq in mES Rep2

status: Public on Jul 22 2017

city: Orlando

first: Laszlo

last: Nagy

state: Hungary

address: Sanger Road

institute: Sandford Burnham Prebys Institute

data_processing:
aligment was performed by BWA 0.6.0 using default parameters.
makeTagDirectory by HOMER v4.2 using default parameters.
peak calling was performed by MACS 2.0.10 using default parameters.
ENCODE blacklist (converted from mm9 to mm10 by liftOver) from the predicted peak sets.
Peak annotation was done with annotatePeaks.pl using default parameters.
Genome_build: mm10

source_name: embryonic stem cells

growth_protocol: Wild type E14 mouse ESCs were cultured on 0.1% gelatin coated plates in feeder-free condition in 5% CO2 at 37˚C. The ESC medium was prepared by supplementing DMEM Glutamax media with 15% FBS (Hyclone), 1000U of leukemia inhibitory factor (LIF), penicillin/streptomycin, non-essential amino acids and 2-mercaptoethanol. Cells were differentiated through embryoid body formation (Bibel et al., 2007). Briefly, for the induction of EB formation cells were aggregated in 100-mm bacteriological dishes (Greiner) at a specific density (4x106 cells/ 15 ml) in the absence of LIF. Over the span of four days, neural differentiation was induced by all-trans retinoic acid (RA) (Sigma) in 5 µM final concentration. After  four days of propagation trypsinized EBs were plated onto laminin (Sigma)/ poly-L-ornithine (Sigma) precoated plates at a density of 1 x 105 cells / cm2 in N2 medium (Bibel et al., 2007).

extract_protocol:
ChIP-seq experiments were carried out as previously described (Barish et al., 2012), with minor modifications. Briefly, cells were cultured in the presence or absence of RA for various time points and then cross-linked in two steps: (1) disuccinimidyl glutarate (DSG) for 30 min then (2) 1% methanol-free ultrapure formaldehyde for 10 min at room temperature. Glycine was added for 5 min in 125 mM final concentration. After fixation chromatin was sonicated with Diagenode Bioruptor to generate 200-1000bp fragments.
Chromatin was immunoprecipitated with antibodies against pre-immune IgG (Millipore,12-370), RXR (Santa Cruz, sc-774), and H3K27ac (Abcam, ab4729). The eluted DNA was purified (Qiagen, MinElute) and quantified with Qubit fluorometer (Invitrogen). ChIP-seq libraries were prepared by Illumina library preparation kit according to manufacturer instructions. A more detailed description is available upon request.

treatment_protocol: Cells were treated with vehicle (dimethylsulfoxide) or with the following ligands in 1µM final concentration: RA (Sigma), LG268 (Boehm et al., 1995) (a gift from R. Heyman; Ligand Pharmaceuticals, San Diego, CA), GW3965 (Sigma). For dose response analyses, ligands were used at the indicated concentrations.

value: Mouse embryonic stem cells

tag: chip antibody

value: RXR


title: Ctrl_ATACseq_rep2


title: day16 RXR ChIP-seq in mES Rep2


title: day16 RXR ChIP-seq in mES Rep1


title: day8 RXR ChIP-seq in mES Rep1


title: GW3965 24h treated H3K27ac ChIP-seq in mES


title: RA 24h treated RXR ChIP-seq in mES


title: RA 24h treated H3K27ac ChIP-seq in mES


title: LG268 24h treated H3K27ac ChIP-seq in mES


title: CTRL H3K27ac ChIP-seq in mES


title: GW3965 24h treated RXR ChIP-seq in mES


title: CTRL RXR ChIP-seq in mES


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [Mbd3del_LMPP_mouse10384]

first: Stephen

middle: John

last: Loughran

address: Wellcome Trust/MRC building, Addenbrooke's Hospital

department: Haematology

data_processing:
RNA-seq reads were aligned to GRCm38 using STAR (version 2.5.2b) using parameters --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1
Reads aligning to the features in the GENCODE comprehensive gene annotation (release M12) were counted using HTSeq (version 0.6.1p1) using parameter --mode=intersection-strict.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimted text file. Matrix of read counts per gene.

source_name: Bone marrow

extract_protocol:
Bone marrow cells were collected from the femurs and tibiae of 7 week old mice.
Cells were stained with antibodies and cells belonging to each population sorted using a FACS Influx5 (BD Biosciences)
Pools of 100 or 150 cells were sorted directly into individual wells of 96-well PCR plate containing lysis buffer.
RNA-sequencing was performed using the previously described smart-seq2 protocol  (Picelli et al (2014) Nat. protocols 9:171)
Pooled libraries were run on an Illumina HiSeq 2500 sequencer.
RNA libraries were prepared for sequencing using Illumina Nextera XT DNA preparation kit

value: Lymphoid-primed multipotent progenitor (LMPP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra- B220-)

value: 51 days

tag: Sex

value: male

tag: genotype

tag: cell number


title: LG268 24h treated RXR ChIP-seq in mES


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [Mbd3del_LMPP_mouse10376]

tag: age

value: 50 days

value: female


title: RNA-seq of Mus musculus : Mbd3-null haematopoietic stem cell [Mbd3del_HSC_mouse10376]

value: Haematopoietic stem cell (HSC, CD45+ CD150+ CD48- EPCR+)


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [Mbd3del_LMPP_mouse10365]

value: 48 days


title: RNA-seq of Mus musculus : Mbd3-null haematopoietic stem cell [Mbd3del_HSC_mouse10384]


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [Mbd3del_LMPP_mouse10361]

value: 47 days


title: RNA-seq of Mus musculus : Mbd3-null haematopoietic stem cell [Mbd3del_HSC_mouse10361]


title: RNA-seq of Mus musculus : Mbd3-null haematopoietic stem cell [Mbd3del_HSC_mouse10365]


title: RNA-seq of Mus musculus : Mbd3-null haematopoietic stem cell [Mbd3del_HSC_mouse10360]

value: 46 days


title: RNA-seq of Mus musculus : Mbd3-null B-biased progenitor cells (BLP) [Mbd3del_BLP_mouse10376]

value: B-biased lymphoid progenitor (BLP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D+ B220-)


title: RNA-seq of Mus musculus : Mbd3-null B-biased progenitor cells (BLP) [Mbd3del_BLP_mouse10384]


title: Old_mic_1

value: brain

value: CD11b+ CD45int


title: RNA-seq of Mus musculus : Mbd3-null B-biased progenitor cells (BLP) [Mbd3del_BLP_mouse10360]


title: RNA-seq of Mus musculus : Mbd3-null B-biased progenitor cells (BLP) [Mbd3del_BLP_mouse10361]


title: RNA-seq of Mus musculus : Mbd3-null B-biased progenitor cells (BLP) [Mbd3del_BLP_mouse10365]


title: RNA-seq of Mus musculus : Mbd3-null all-lymphoid progenitor cells (ALP) [Mbd3del_ALP_mouse10360]

value: All-lymphoid progenitor (ALP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D- B220-)


title: RNA-seq of Mus musculus : Mbd3-null all-lymphoid progenitor cells (ALP) [Mbd3del_ALP_mouse10365]


title: RNA-seq of Mus musculus : Mbd3-null all-lymphoid progenitor cells (ALP) [Mbd3del_ALP_mouse10361]


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [control_LMPP_mouse10381]


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [control_LMPP_mouse10380]


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [control_LMPP_mouse10358]


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [control_LMPP_mouse10357]


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [control_LMPP_mouse10372]


title: RNA-seq of Mus musculus : Mbd3-floxed haematopoietic stem cell [control_HSC_mouse10380]


title: RNA-seq of Mus musculus : Mbd3-floxed haematopoietic stem cell [control_HSC_mouse10381]


title: RNA-seq of Mus musculus : Mbd3-floxed haematopoietic stem cell [control_HSC_mouse10358]


title: RNA-seq of Mus musculus : Mbd3-floxed lymphoid primed multipotent progenitor cells (LMPP) [Mbd3del_LMPP_mouse10360]


title: RNA-seq of Mus musculus : Mbd3-floxed haematopoietic stem cell [control_HSC_mouse10357]


title: fl3-3

city: Shanghai

first: Jie-chen

last: Wang

address: 300 Fenglin Road

country: China

institute: SIPPE, CAS

data_processing:
FastQC combined with the NGS QC TOOLKIT v2.3.3 were used for quality control checks on raw sequencing data.
Clean reads were aligned to the B73 reference genome (RefGen_v3) and the reference gene model dataset (FGS 5b) using TopHat/Bowtie2 (ccb.jhu.edu/software/tophat/).
The gene expression value was normalized as fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: the B73 reference genome (RefGen_v3) and the reference gene model dataset (FGS 5b)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample， the clean reads aligned to reference genome were saved as BAM files

source_name: 10 DAF endosperm

growth_protocol: maize were grown during summer under natural environmental conditions in Songjiang experimental field

extract_protocol:
Total RNAs was extracted from 10-DAP old endosperms of WT and fl3 using TRIzol reagent (Invitrogen) and were then purified with the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared according to the Illumina Standard library preparation kit. Illumina HiSeqTM 2500 was used as a platform for RNA-seq at Shanghai OE Biotech Co, Ltd.

treatment_protocol: Developing endosperm that were harvested from both fl3 and WT at 10 DAF

tag: sample type

value: 10 DAF endosperm


title: fl3-1


title: RNA-seq of Mus musculus : Mbd3-floxed haematopoietic stem cell [control_HSC_mouse10372]


title: RNA-seq of Mus musculus : Mbd3-floxed B-biased progenitor cells (BLP) [control_BLP_mouse10380]


title: WT-3


title: WT-2


title: WT-1


title: 9L136_ST_3

city: Beijing

first: Ma

last: Xin

state: --- Select a state ---

address: 2 Yuanmingyuan West Road, Haidian District, Beijing, China, 2 Yuanmingyuan West Road, Haidian District, Beijing, China

institute: China Agricultural University

data_processing:
After removing adaptor sequences and low-quality reads, the high-quality paired-end reads were mapped to the Nipponbare reference genome (MSU Rice Genome Annotation Project Release 7) using the spliced read mapper TopHat version 2.0.12
Significant differentially expressed genes (DEGs) were determined based on a threshold of 2-fold expression change and false discovery rate (FDR) < 0.05 using Cuffdiff, one module of Cufflinks.
Genome_build: MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Oryza sativa

growth_protocol: Seedlings grown in Yoshida’s culture solution in greenhouse.

extract_protocol:
Roots of seedlings were collected and frozen in liqiud nitrogen, and RNA was extracted using TRizol  purified using a Qiagen RNeasy kit.
NEBNext Ultra RNA Library Prep kit was used for the cDNA library construction.

treatment_protocol: Two-half leaf seedlings were transferred to full-strength Yoshida’s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida’s  solution.

tag: cultivar

value: introgression line

tag: stress

value: Oryza sativa

tag: tissue

value: salt

value: two-half leaf


title: 9L136_ST_2


title: RNA-seq of Mus musculus : Mbd3-null all-lymphoid progenitor cells (ALP) [Mbd3del_ALP_mouse10384]

value: 51 days


title: RNA-seq of Mus musculus : Mbd3-floxed B-biased progenitor cells (BLP) [control_BLP_mouse10357]

value: male


title: 9L136_ST_1


title: RNA-seq of Mus musculus : Mbd3-null all-lymphoid progenitor cells (ALP) [Mbd3del_ALP_mouse10376]

value: 50 days


title: RNA-seq of Mus musculus : Mbd3-floxed B-biased progenitor cells (BLP) [control_BLP_mouse10358]


title: RNA-seq of Mus musculus : Mbd3-floxed all-lymphoid progenitor cells (ALP) [control_ALP_mouse10381]


title: 9L136_CK_2

value: control


title: RNA-seq of Mus musculus : Mbd3-floxed all-lymphoid progenitor cells (ALP) [control_ALP_mouse10380]

value: female


title: RNA-seq of Mus musculus : Mbd3-floxed all-lymphoid progenitor cells (ALP) [control_ALP_mouse10372]


title: RNA-seq of Mus musculus : Mbd3-floxed all-lymphoid progenitor cells (ALP) [control_ALP_mouse10358]


title: 9311_ST_3

value: indica


title: RNA-seq of Mus musculus : Mbd3-floxed B-biased progenitor cells (BLP) [control_BLP_mouse10381]


title: 9311_ST_2


title: RNA-seq of Mus musculus : Mbd3-floxed all-lymphoid progenitor cells (ALP) [control_ALP_mouse10357]


title: 9311_ST_1


title: 9311_CK_3


title: ATAC-seq of Mus musculus : Mbd3-null DN3b thymocytes

data_processing:
After checking quality control with FastQC v0.11.4, Nextera transposase sequence and adapter read-through were removed using Trimmomatic v0.33 in palindrome mode with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2 v2.2.3 with parameter –X 2000
Alignment files were converted to Bam format with SAMtools v1.2and deduplicated using Picard MarkDuplicates v1.119 with parameter REMOVE_DUPLICATES=true.
Reads mapping to the mitochondrial genome were discarded and alignment files were merged across replicates and indexed with BamTools v2.4.0
bigWig files were generated using Homer v4.9
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files describing ATAC-seq read density

source_name: Thymus

extract_protocol:
Bone marrow cells were collected from the femurs and tibiae of 7 week old mice.
Cells were stained with antibodies and cells belonging to each population sorted using a FACS Influx5 (BD Biosciences)
500 cells were sorted directly into individual wells of a PCR tube containing PBS.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed as previously described  (Buenrostro et al (2013) Nat. Methods 10:1213).
Pooled libraries were run on an Illumina HiSeq 2500 sequencer.
RNA libraries were prepared for sequencing using Illumina Nextera DNA preparation kit

value: DN3b thymocytes (Lin- CD4- CD8- CD44- CD25+ CD27+)


title: 9311_CK_2


title: fl3-2


title: RNA-seq of Mus musculus : Mbd3-floxed B-biased progenitor cells (BLP) [control_BLP_mouse10372]

value: 47 days


title: ATAC-seq of Mus musculus : Mbd3-floxed pro-B cells

value: Pro-B cells (c-Kit+ CD19+)


title: ATAC-seq of Mus musculus : Mbd3-floxed B-biased progenitor cells (BLP)

value: B-biased lymphoid progenitor (BLP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D+ B220-)


title: ATAC-seq of Mus musculus : Mbd3-null B-biased progenitor cells (BLP)


title: ATAC-seq of Mus musculus : Mbd3-floxed all-lymphoid progenitor cells (ALP)


title: 9L136_CK_3


title: MPRA_Distal_Vector

status: Public on Jul 21 2017

city: Kansas City

first: Scott

middle: T

last: Younger

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

data_processing:
Library strategy: MPRA
MPRA Read Alignment: First 10 bases of each read matched to MPRA oligonucleotide barcode
MPRA Differential Expression: DESeq2 with default options
processed data files format and content: TXT files are normalized read counts from amplicon sequencing for each sample (MPRA) and statistics comparing untreated and Doxorubicin-treated samples.

organism: synthetic construct

source_name: Plasmid

extract_protocol:
not provided
Amplicon sequencing


title: 9L136_CK_1


title: Ath_lncRNA

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality sequence and the percentage of unknown bases (N) is greater than 10%. At last, the obtained “clean bases” for further analysis.
Clean reads were mapped to the ribosomal RNA (rRNA) reference using SOAPaligner/SOAP2 (Li et al., 2009) in order to remove rRNA.
Then filtered reads were mapped to A. thaliana genome (TAIR 10) using TopHat2 (Kim et al., 2013), with three base mismatches allowed.
Subsequently, the mapped reads were used to assemble transcripts using Cufflinks (Trapnell et al., 2010). Expression levels of the assembled transcripts were calculated and normalized using reads per kilobases per million mapped reads (RPKM) by Cufflinks.
These transcripts that overlapped with known mRNAs and lncRNAs (Xie et al., 2014) were filtered through comparing with reference genes using Cuffcompare (Trapnell et al., 2010).
Any new transcripts with low mapping coverage (≤50%) and an optimum value (RPKM＜0.4) as well as transcript length ≤ 200 nucleotides were removed.
The coding potential of the remaining transcripts was evaluated using CPC (Kong et al., 2007), and transcripts with CPC scores >0 were discarded.
The remaining novel transcripts that encode any conserved protein domains were filtered against the Pfam database (Finn et al., 2014) using HMMER3.0 (E-value ≤ 1E-3).
The identified lncRNA transcripts that were mapped to the Arabidopsis known lncRNA transcripts identified from other public lncRNA databases [GreeNC (Gallart et al., 2016), CANTATAdb (Szcześniak et al., 2016), LncRNAdb (Quek et al., 2014), PLncDB (Jin et al., 2013)] were filtered out (BLASTN, coverage ≥ 55% and E-value < 1E-10). and 156
Finally, the filtered lncRNA transcripts were considered as candidate novel lncRNAs in A. thaliana for further analysis. The novel lncRNA were further categorized according to the overlap with genomic elements.
Genome_build: TAIR10
Supplementary_files_format_and_content: Text file includes lncRNA ID, length, chromosome, start, end, strand, expression (RPKM),  exon number, class code, category.

source_name: the whole plants across lifespan

growth_protocol: Wild-type (WT) A. thaliana Columbia ecotype (Col-0) was cultivated at 23/18℃ under 16/8 light/dark cycle.

extract_protocol: Strand-specific RNA library was prepared according to Illumina's instructions.  Briefly,  the mRNAs and non-coding RNAs are fragmented into short fragments(about 200~500nt).  Then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase). After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.

tag: ecotype

tag: developmental stages

value: whole plants from 7 developmental stages

value: whole plant


title: ATAC-seq of Mus musculus : Mbd3-floxed DN3b thymocytes

city: Cambridge

institute: University of Cambridge


title: ATAC-seq of Mus musculus : Mbd3-null pro-B cells


title: 9311_CK_1


title: MPRA_Proximal_Vector


title: Sh_G5_T1_C

first: Yoshie

last: Hanzawa

state: IL

address: 1201 West Gregory Drive

department: Cropsciences

institute: University of illinois at Urbana Chammpaign, USA

description: Read_counts: 15530248

data_processing:
The quality-scores line in fastq files processed with Casava1.8 using an ASCII offset of 33 (known as Sanger scores) instead of the previous 64 offset. (pools 1-2-3 run 160, HiSeq#1 with an error rate of 0.84 %, pools 4-5 run 162, HiSeq#1 with an error rate of 0.54% pools 6 through 12, run 226 HiSeq#2error rate: 0.88%).
Adapter Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
Reads were aligned onto soybean transcriptome (williams 82) obtained from Phytozome database (Schmutz et al, 2010) using Bowtie aligner (Langmead et al, 2009) with following parameters;  -S -q  -k 1 --best -p 4 --phred33-quals
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

organism: Glycine max

source_name: First trifoliate

growth_protocol: Plants were grown under long-day (16L:8D) or short-day (10L:14D) conditions for 26 days. For the shift experiment, plants were grown under long-day for three weeks were treated with short-day for 5 days. Sampling was carried out at three time points every 8 hours over a 24 hour period with 3 biological replicates.

extract_protocol:
Plant samples were ground and RNAs were extracted using the RNeasy® Plant Mini Kit (Qiagen®).
The RNAseq libraries were prepared with Illumina's 'TruSeq RNAseq Sample Prep kit. The libraries were pooled and quantitated by qPCR, and sequenced for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava-1.8 (pipeline 1.9), following the manufacturer's instructions (Illumina, San Diego, CA).

treatment_protocol: For LD treatment, plants were exposed to 16 hours of light from 6:45 until 22:45. For SD treatment, plants were exposed to 10 hours of light from 6:45 until 16:45.  For shift treatment, plants were grown under LD for 21 days and shifted to SD for 5 days. Sampling was carried out 26 DAP (days after planting) at three time points every 8 hours over a 24 hour period with 3 biological replicates.

value: Shift (LD 3 weeks -> SD 5 days)

tag: timepoint

value: morning 6:30 am

tag: age at rna extraction

value: 26 DAP


title: Sh_G5_T3_B

description: Read_counts: 7196747

value: afternoon 2:30 pm


title: Sh_G5_T5_B

description: Read_counts: 13680247

value: evening 10:30 pm


title: Sh_G5_T5_C

description: Read_counts: 14816175


title: Sh_G6_T3_C

description: Read_counts: 12839325


title: Sh_G6_T3_B

description: Read_counts: 14781571


title: Sh_G6_T3_A

description: Read_counts: 12082235


title: Sh_G5_T3_C

description: Read_counts: 8001110


title: Sh_G6_T1_C

description: Read_counts: 9696553


title: Sh_G5_T5_A

description: Read_counts: 13920497


title: Sh_G6_T1_B

description: Read_counts: 7566975


title: Sh_G5_T1_B

description: Read_counts: 10045532


title: Sh_G6_T1_A

description: Read_counts: 9602203


title: Sh_G6_T5_A

description: Read_counts: 9811518


title: Sh_G5_T3_A

description: Read_counts: 11879089


title: Sh_G6_T5_D

description: Read_counts: 8823368


title: Sh_G6_T5_C

description: Read_counts: 7057631


title: Sh_G4_T5_B

description: Read_counts: 9067236


title: Sh_G4_T5_C

description: Read_counts: 6131499


title: Sh_G4_T3_C

description: Read_counts: 12904313


title: Sh_G4_T3_B

description: Read_counts: 11855477


title: Sh_G4_T5_A

description: Read_counts: 10254159


title: Sh_G5_T1_A

description: Read_counts: 9056627


title: Sh_G4_T3_A

description: Read_counts: 12449952


title: Sh_G4_T1_C

description: Read_counts: 7324858


title: Sh_G3_T5_B

description: Read_counts: 12445522


title: Sh_G3_T3_B

description: Read_counts: 14876294


title: Sh_G4_T1_A

description: Read_counts: 7837068


title: Sh_G3_T5_A

description: Read_counts: 10362805


title: Sh_G3_T5_C

description: Read_counts: 10302044


title: Sh_G3_T3_C

description: Read_counts: 11488160


title: Sh_G2_T3_C

description: Read_counts: 10062702

value: Williams 82


title: Sh_G2_T5_C

description: Read_counts: 9623914


title: Sh_G2_T5_B

description: Read_counts: 14240416


title: Sh_G2_T1_B

description: Read_counts: 11046926


title: Sh_G2_T3_A

description: Read_counts: 17833272


title: Sh_G3_T1_A

description: Read_counts: 11779801


title: Sh_G2_T3_B

description: Read_counts: 9547726


title: Sh_G4_T1_B

description: Read_counts: 13922202


title: Sh_G3_T1_B

description: Read_counts: 9168216


title: Sh_G3_T1_C

description: Read_counts: 6099993


title: Sh_G2_T5_A

description: Read_counts: 17225210


title: Sh_G2_T1_A

description: Read_counts: 11895081


title: Sh_G1_T5_C

description: Read_counts: 11777308

value: Clark


title: Sh_G1_T3_C

description: Read_counts: 14963921


title: Sh_G2_T1_C

description: Read_counts: 9469404


title: Sh_G1_T5_B

description: Read_counts: 11157632


title: Sh_G1_T1_C

description: Read_counts: 8500860


title: Sh_G1_T3_A

description: Read_counts: 11950045


title: ATAC-seq of Mus musculus : Mbd3-null all-lymphoid progenitor cells (ALP)

value: All-lymphoid progenitor (ALP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D- B220-)

tag: strain


title: Sh_G3_T3_A

description: Read_counts: 10085900


title: Sh_G1_T1_B

description: Read_counts: 11596431


title: Sh_G1_T1_A

description: Read_counts: 9214958


title: Sh_G1_T5_A

description: Read_counts: 9740439


title: SD_G6_T3_C

description: Read_counts: 13668570

value: Short Day (10L:14D)


title: SD_G6_T5_A

description: Read_counts: 9977520


title: SD_G6_T3_B

description: Read_counts: 11337937


title: SD_G5_T5_C

description: Read_counts: 17321767


title: Sh_G1_T3_B

description: Read_counts: 10049022


title: SD_G5_T5_A

description: Read_counts: 15520545


title: SD_G6_T3_A

description: Read_counts: 10384275


title: SD_G5_T5_B

description: Read_counts: 9569562


title: SD_G6_T1_A

description: Read_counts: 7335067


title: SD_G5_T3_C

description: Read_counts: 6206309


title: SD_G6_T5_C

description: Read_counts: 17591295


title: SD_G5_T3_B

description: Read_counts: 12960840


title: SD_G4_T5_B

description: Read_counts: 10659372


title: SD_G6_T1_B

description: Read_counts: 7967494


title: SD_G4_T5_C

description: Read_counts: 16850611


title: SD_G4_T5_A

description: Read_counts: 8063375


title: SD_G5_T1_A

description: Read_counts: 10902808


title: SD_G4_T3_C

description: Read_counts: 7823815


title: SD_G4_T3_B

description: Read_counts: 9221203


title: SD_G5_T1_C

description: Read_counts: 12488057


title: SD_G4_T1_B

description: Read_counts: 14365009


title: SD_G4_T3_A

description: Read_counts: 14022582


title: SD_G6_T5_B

description: Read_counts: 9443336


title: SD_G4_T1_A

description: Read_counts: 10551002


title: SD_G6_T1_C

description: Read_counts: 9526236


title: SD_G3_T5_C

description: Read_counts: 10018379


title: SD_G3_T3_B

description: Read_counts: 12998431


title: SD_G5_T3_A

description: Read_counts: 11589817


title: SD_G3_T5_B

description: Read_counts: 14130110


title: SD_G3_T5_A

description: Read_counts: 11504828


title: SD_G3_T3_C

description: Read_counts: 8479165


title: SD_G5_T1_B

description: Read_counts: 10483986


title: SD_G3_T3_A

description: Read_counts: 12145007


title: SD_G3_T1_C

description: Read_counts: 10805344


title: SD_G2_T5_C

description: Read_counts: 9767413


title: SD_G2_T3_C

description: Read_counts: 11666543


title: SD_G3_T1_A

description: Read_counts: 13410781


title: SD_G2_T3_B

description: Read_counts: 11993073


title: SD_G2_T5_A

description: Read_counts: 8691505


title: SD_G1_T5_B

description: Read_counts: 14123734


title: SD_G2_T1_B

description: Read_counts: 10572811


title: SD_G2_T3_A

description: Read_counts: 13662179


title: SD_G2_T1_A

description: Read_counts: 10545171


title: SD_G2_T1_C

description: Read_counts: 8278017


title: SD_G1_T5_C

description: Read_counts: 13005518


title: SD_G3_T1_B

description: Read_counts: 10542281


title: SD_G1_T5_A

description: Read_counts: 8068037


title: SD_G2_T5_B

description: Read_counts: 10452151


title: SD_G1_T3_B

description: Read_counts: 15695151


title: SD_G1_T3_C

description: Read_counts: 8107437


title: LD_G6_T3_C

description: Read_counts: 13259142

value: Long Day (16L:8D)


title: SD_G1_T1_B

description: Read_counts: 8310321


title: LD_G6_T5_C

description: Read_counts: 11633014


title: SD_G1_T3_A

description: Read_counts: 13054389


title: LD_G6_T5_B

description: Read_counts: 10289020


title: LD_G6_T3_B

description: Read_counts: 11874515