title: OKS_D1_shTead2_re2

city: Guangzhou

first: Jiadong

last: Liu

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: GIBH

data_processing:
ATAC-seq and ChIP-seq data were aligned to the mm10 genome using bowtie2 (with the options ‘-p 20–very-sensitive–end-to-end–nounal–no-mixed -X 2000’).
SAMtools (view –q 30) was used for removing the low-quality mapped reads, and uniquely mapped reads were only retained after removed PCR duplicates.
Peaks were called using MACS2 (-g mm -f BAMPE)
The reference transcriptome index was produced with RSEM using the reference genome mm10 (ensemble gene annotation track v79) and ERCC RNA spike-in sequence.
The reads were mapped to the reference transcriptome using RSEM and bowtie 2 (with options ‘rsem-calculate-expression -p 12–bowtie2–no-bamout’).
Expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq.
Genome_build: mm10
Supplementary_files_format_and_content: Alignment bam files were transformed into bigwig files using deepTools with the RPKM normalization method. Scores represent the number of fragments overlapping each genomic position.
Supplementary_files_format_and_content: Excel file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: reprogramming cells

growth_protocol: Reprogramming cells were cultured in iCD1 medium. ESCs cells and iPSCs cells were cultured in N2B27+2i+LIF medium, MEF cells were cultured in 10% FBS medium

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015; Li et al., 2017b). In brief, 50,000 cells were washed in PBS and lysed using 50 μl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were centrifuged at 500 ×g for 5 min and resuspended with 50 μl transposition reaction mix from a TruePrep DNA Library Prep Kit V2 for Illumina. The samples were incubated at 37°C for 30 min, and DNA was purified using a MinElute kit. Libraries were first preamplified for 5 cycles, and then assessed by quantitative PCR as described (Buenrostro et al., 2015) to determine the suitable PCR cycles. After appropriate amplification, libraries were purified with the MinElute kit and quantified using a VAHTS Library Quantification Kit for Illumina. Gel electrophoresis was used for examining the library integrity. Finally, the sequencing was carried out on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles).
ChIP was performed as described previously with some modifications (Li et al., 2017b). Briefly, reprogramming cells were harvested by trypsinisation at day 1 and chemically crosslinked with 1% formaldehyde for 10 min at room temperature with gentle rotation. The reaction was quenched by 0.125M glycine for 5 min at room temperature and cells were washed twice with cold PBS. 1× 107 cells were lysed in ChIP lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitor cocktail) for 10 min at 4°C. The DNA was fragmented to 150-500 bp by sonication, and then centrifuged at 14,000 g for 10 min at 4°C. The supernatant was diluted with ChIP IP buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 50mM Tris-HCl, pH 8.0, 150 mM NaCl and protease inhibitor cocktail). Immunoprecipitation was performed with 5 μg rabbit anti-TEAD2 antibody coupled to 50 μl protein A/G mix overnight at 4°C with gently rotation. Beads were washed at 4°C for 5 min in the following order: twice low salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% TritonX-100, 2 mM EDTA, 150 mM NaCl), twice high salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% TritonX-100, 2 mM EDTA, 500 mM NaCl), twice LiCl buffer (500mM LiCl, 50 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% NP-40, 0.5% Sodium Deoxycholate), once TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA) with final elution in 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS buffer. The eluted chromatin and input samples were reverse crosslinked by overnight incubation at 65°C. After treated with proteinase K at 56°C for 30 min, the DNA was purified using the MinElute PCR Purification Kit. The libraries were constructed by a VAHTS Universal DNA Library Prep Kit for Illumina V3 according to the manufacturer’s instructions.
Cells were lysed by TRIzol reagent, following which total RNAs were extracted by the chloroform-isopropanol method. The VAHTS mRNA-seq V3 Library Prep Kit for Illumina was used for RNA library preparation. In brief, mRNA was enriched from 1 μg of total RNA using oligo-dT Dynabeads, followed by fragmentation at 94°C 8min. Secondly, First-strand and second-strand cDNA were synthesis successively using corresponding reagents. After purified by VAHTS DNA Clean Beads, the cDNA was end repaired and added with a dA base, followed by adapter ligation, two-round purification, PCR amplification and purification.
Libraries were prepared for sequencing using standard Illumina protocols
ATAC-seq, ChIP-seq and RNA-seq

treatment_protocol: iPSCs were generated as previously described (Chen et al., 2011; Guo et al., 2019). In brief, 8 × 106 Plat-E cells were plated onto 10 cm dish and cultured overnight, and then  retrovirus were made by transfection of 25 μg of pMXs vector DNA containing Oct4, Sox2, and Klf4 or pSuper-puro vector DNA containing shRNAs into Plat-E cells using the calcium phosphate method. The medium was changed after 12 hours. The viral supernatants were collected 48 hours and 72 hours posttransfection and filtered through a 0.45 μm filter (Millipore). MEFs were plated at density of 1×104 per well (24-well plate) 12 hours before infection with retrovirus and a final concentration of 4 μg/ml polybrene was added during the infection. The infection was performed repeatedly the following day and the shRNA retrovirus infected cells were selected with 1 μg/ml puromycin for two days (from reprogramming D -1 to D1). Day 0 was defined as the day that viral supernatants were removed and the specific reprogramming medium were added. Cells were treated with 10 μg/ml actinomycin D or DMSO for 4 hours and 8 hours for mRNA profiling, respectively

value: reprogramming cells

tag: day of reprogramming

value: day 1


title: 3165_PBMC

status: Public on Aug 19 2020

type: SRA

city: San Diego

first: Rekha

last: Dhanwani

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institure for Immunology

description: processed data file: all_counts.tsv

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the human GRCh38 reference using STAR (v 2.6.1c).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5) and features with 0 counts across all samples were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: all_counts.tsv: Tab-separated count matrix with rows as genes and columns as samples.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC AD

growth_protocol: Frozen PBMCs were thawed, stained for T cell surface and memory markers, and sorted in Trizol.

extract_protocol:
100,000 PBMCs, CD4 and CD8 memory T cells were sorted and collected in Trizol in a 1.5 ml tube. Tubes were vortexed, spun and stored at -80C until processed. RNA was extracted using RNA microRNA kit (Qiagen) on a Qiacube.
Purified total RNA was amplified following the Smart-Seq2 protocol. cDNA was purified using AMPure XP beads, and barcoded Illumina sequencing libraries were generated, loaded and sequenced on the Illumina sequencing platform HiSeq 2500.

treatment_protocol: No treatment

tag: disease state

value: Alzheimer's disease

tag: cell type

value: PBMC

tag: gender

value: Female


title: ChIPseq_CUTLL1_CTCF_DMSO

city: Charlottesville

first: Zhenjia

last: Wang

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

library_source: genomic

data_processing:
ChIP-seq sequence reads were aligned to the hg38 genome using bwa, MACS2 was used to call peaks.
ATAC-seq sequence reads were aligned to the hg38 genome using bowtie.
RNA-seq datasets were processed using Salmon.
Hi-C data were processed using HiC-Pro.
Methylation calls were performed with Bismark.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: ChIP-seq: peak file in BED, RNA-seq: transcript level quantification from salmon, Hi-C: raw matrix, DNA methylation: bigwig or bismark.cov

molecule: genomic DNA

extract_protocol:
Phenol/chloroform DNA extraction
Libraries were prepped with a KAPA high throughput library prep kit using a Sciclone® G3 NGS and NGSx Workstation

tag: chip antibody

value: CTCF


title: ChIPseq_CUTLL1_CTCF_DMSO_input


title: OKS_D1_shTead2_re1

country: China

molecule: polyA RNA

organism: Mus musculus


title: ChIPseq_CUTLL1_CTCF_rep2_input


title: 3152_PBMC

description: processed data file: all_counts.tsv

value: Male


title: ATACseq-EryP-Rep2

city: Boston

first: Jialiang

last: Huang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
ATAC-seq reads were trimmed for adapter sequences and low alignment quality using Cutadapt (Martin, 2011), with the parameters -q 30 --minimum-length 36. Paired-end reads were aligned to the mm10 reference genome by using Bowtie2 (Langmead et al., 2009), with the parameter -X 2000 allowing fragments of up to 2 kb to be aligned (Buenrostro et al., 2015). ATAC-seq peaks were called using MACS2 (Zhang et al., 2008) with following parameters (--nomodel --nolambda --keep-dup all --call-summits) (Buenrostro et al., 2015). Peak calling was done in two biological replicates respectively with the same parameter settings. One replicate of each cell type was used for subsequent analysis. We then extended the summits to 500-bp window (±250 bp) as peaks and filtered using the consensus excludable ENCODE blacklist (Consortium, 2012).
HiChIP datasets were processed using HiC-Pro (Mumbach et al., 2016; Mumbach et al., 2017; Servant et al., 2015) with default settings. Specifically, HiChIP paired-end reads were aligned using Bowtie2 with –very-sensitive -L 30 –score-min L, -0.6, -0.2 --end-to-end –reorder. The restriction sites were obtained by scanning MboI restriction fragments across mouse genome (mm10). Specific configuration file (config-hicpro.txt) can be found at https://bitbucket.org/qzhu/wenqing-hichip/src/default/hicpro/config-hicpro.txt. Valid interactions pairs (named valid Pairs) were converted to a .hic file using hicpro2juicebox.sh script (utility tool of HiC-Pro). The generated .hic file contains interaction matrices at fragment and base pair resolutions. Interaction maps were visualized with Juicebox (Durand et al., 2016a). The HiCCUPS function of Juicer-tools 1.7.6 was used to call high-confidence loops based on a .hic file (Rao et al., 2014). We set -m 512 -r 5000,10000,25000 -f 0.2,0.2,0.2 -p 4,2,1 -k VC_SQRT -i 7,5,3 -d 20000,20000,50000 --ignore_sparsity -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y -t 0.02,1.5,1.75,2. This combination of settings finds loops at the 5-kb, 10-kb, and 25-kb resolutions using the interaction matrices at matched resolutions, and also applied the appropriate normalization step for interaction matrix (vanilla coverage square-root, VC SQRT). Loops at these resolutions were subsequently merged.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig  generated using macs2 pileup, following by bedGraphToBigWig; Peak  were called using MACS2

source_name: Primitive erythroblast

growth_protocol: EryP was collected from peripheral blood of E10.5 mouse embryos in HBSS supplemented with 10% FBS and 0.25% EDTA. EryD was collected by mechanically dissociation of E13.5 whole fetal liver. All mouse embryos were obtained from C57BL/6 mouse. MEL cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2mM L-glutamine and Penicillin and Streptomycin. 2% DMSO in culture medium was used to induce MEL cells differentiation. Medium was changed on differentiation day 3.

extract_protocol:
HiChIP was performed as previously described (Mumbach et al 2016) using the Gata1 antibody (ab11852, Abcam). In brief, 15 million of either peripheral blood cells of E10.5 mouse embryos or single cells of E14.5 fetal liver were cross-linked with 1% v/v formaldehyde at room temperature for 10 minutes, and were quenched with 0.125 M Glycine for 5minutes. Crosslinked cells were lysed in cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40, 1x Roche protease inhibitors) and followed by 1 U/ul MboI (NEB) digestion at 37oC for 6 h, fill-in of overhangs with biotin-dATP (Thermo Fisher) at 37oC for 1.5 h, and ligation with 4 U/ul T4 DNA Ligase (NEB) at room temperature for 6 h. The nuclear pellet was sheared using a Covaris E220 with following parameters: Duty Factor = 5.0, Peak Power = 140, Cycle/Burst = 200, Time = 240 seconds. Chromatin extracts were immunoprecipitated with Gata1 antibodies overnight at 4oC, and then incubated with protein A Dynabeads (Invitrogen) for another 4 hours. ChIP complexes were eluted and cross-linking reversed by heating at 65oC overnight. DNA was extracted with DNA Clean and Concentrator columns (Zymo Research).
ATAC-seq was performed as described (Buenrostro et al., 2013) on FACS isolated EryP and EryD cells. 2.5 x 104 cells were used per sample. 2.5 l Tn5 Transposases (Illuminar) was used to make the transposition reaction. Libraries were generated using Ad1_noMX and Ad2.1-2.4 barcoded primers (Buenrostro et al., 2013) and were amplified for 6-9 total cycles. All libraries were sequenced on Illumina HiSeq2000 with 100 bp paired-end reads. HiChIP was performed as previously described (Mumbach et al., 2016) using the Gata1 antibody (ab11852, Abcam). In brief, 15 million of either peripheral blood cells of E10.5 mouse embryos or single cells of E14.5 fetal liver were cross-linked with 1% v/v formaldehyde at room temperature for 10 minutes, and were quenched with 0.125 M Glycine for 5minutes. Crosslinked cells were lysed in cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40, 1x Roche protease inhibitors) and followed by 1 U/l MboI (NEB) digestion at 37oC for 6 h, fill-in of overhangs with biotin-dATP (Thermo Fisher) at 37oC for 1.5 h, and ligation with 4 U/l T4 DNA Ligase (NEB) at room temperature for 6 h. The nuclear pellet was sheared using a Covaris E220 with following parameters: Duty Factor = 5.0, Peak Power = 140, Cycle/Burst = 200, Time = 240 seconds. Chromatin extracts were immunoprecipitated with Gata1 antibodies overnight at 4oC, and then incubated with protein A Dynabeads (Invitrogen) for another 4 hours. ChIP complexes were eluted and cross-linking reversed by heating at 65oC overnight. DNA was extracted with DNA Clean and Concentrator columns (Zymo Research).   For library preparation, Biotin labeled post-ChIP DNA was captured by 5 l Streptavidin C-1 beads (Thermo Fisher), and followed by Tn5 treatment. The amount of Tn5 used and the number of PCR cycles performed was based on the post-ChIP Qubit amounts, as previously described (Mumbach et al., 2016). HiChIP libraries were size-selected for 300-800bp fragments. All libraries were sequenced on the Illumina Nextseq 500 to an average depth of 200 million total reads.

value: erythroblast

tag: developmental stage


title: ChIPseq_CUTLL1_CTCF_rep2


title: 3322_PBMC

description: processed data file: all_counts.tsv


title: 3118_PBMC

description: processed data file: all_counts.tsv


title: 3831_PBMC

description: processed data file: all_counts.tsv

source_name: PBMC HC

value: Healthy control


title: ChIPseq_CUTLL1_CTCF_rep1_input


title: OKS_D1_shLuc_re1


title: OKS_D1_shLuc_re2


title: Peripheral blood, Subject 95

type: RNA

city: Atlanta

first: Mandakh

last: Bekhbat

state: GA

address: 1365 Clifton Rd NE, Room 5204

department: Psychiatry and Behavioral Sciences

institute: Emory University

description:
replicate 1
95.AVG_Signal

hyb_protocol: Hybridization to Illumina Human HT-12 Expression BeadChips (Illumina) was performed using the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina) and standard Illumina hybridization protocol.

scan_protocol: BeadChips were scanned on the Illumina HiScan (Illumina) using standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in GenomeStudio version 1.9.0.

label: biotin

source_name: Human peripheral blood

label_protocol: Each sample was linearly amplified by TotalPrep-96 RNA Amplification Kit for Array Analysis (Illumina, San Diego CA, USA).

extract_protocol: RNA was extracted using Ambion Tempus RNA Spin kit (Thermo Fisher, Asheville, NC, USA) according to manufacturer instructions. Quality control was performed using Tecan iControl (Life Sciences, Switzerland) and with the Agilent Bioanalyzer 2100 RNA Nano assay (Agilent, Santa Clara, CA, USA).

tag: individual

value: Subject 95

tag: age

tag: Sex

tag: bmi

tag: race

value: Black

tag: hamd score excluding item 8

tag: college (yes/no)

tag: psychomotor composite score

tag: tissue

value: peripheral blood


title: peripheral blood mononuclear cells at secondary syphilis patient, biological rep1

city: Beijing

first: sheng

middle: zhu

last: yang

address: No. 1 Dongjiaomin Lane, Dong Cheng District

institute: Beijing Tongren Hospital

description:
Gene expression data from peripheral blood mononuclear cells in untreated secondary syphilis patients. Lesion; TPHA (+); TRUST (+),1:16; HIV (-); Hepatitis B (-); Hepatitis C (-)
whole blood

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on Affymetrix® GeneChip® miRNA Array. Washing, staining, and scanning, refer to the Genechip® Expression  Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G.The instructions for using the scanner and scanning arrays can be found in the Affymetrix® Command  Console® User Manual (P/N 702569).

data_processing:
The data were analyzed with Partek Genomics Suite 6.6. Use Expression Console software for data summarization, normalization, and quality control (v. 1.2 and  higher). Please refer to the website for Expression Console for instructions on miRNA Array analysis.  Affymetrix recommends using RMA + DABG for analysis.
Affymetrix GeneChip Command Console (AGCC) software

source_name: Peripheral blood mononuclear cells from secondary syphilis patient

label_protocol: FlashTag Biotin HSR RNA Labeling Procedure

growth_protocol: Blood samples (8–10 ml in EDTA) were obtained by venipuncture from secondary syphilis patients and healthy subjects.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The miRNAs expression profiles in peripheral blood mononuclear cells(PBMCs) of 6 untreated syphilis patients and 6 healthy controls were detected by miRNAs expression microarray (Gene Tech (Shanghai) Company Limited ).

treatment_protocol: PBMCs were extracted immediately after the collection of whole blood using a standard procedure of Ficoll gradient centrifugation, performed in accordance with the manufacturer’s instructions.

value: peripheral blood mononuclear cells


title: MEF_shYthdf3_re2

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

tag: passages


title: Peripheral blood, Subject 11

description:
replicate 1
11.AVG_Signal

value: Subject 11

value: White


title: 3183_PBMC

description: processed data file: all_counts.tsv


title: ChIPseq_Jurkat_CTCF_rep2_input

source_name: Jurkat

value: Jurkat


title: Peripheral blood, Subject 74

description:
replicate 1
74.AVG_Signal

value: Subject 74


title: MEF_shYthdf2_re2


title: peripheral blood mononuclear cells at secondary syphilis patient, biological rep2

description:
Gene expression data from peripheral blood mononuclear cells in untreated secondary syphilis patients. Lesion; TPHA (+); TRUST (+),1:64; HIV (-); Hepatitis B (-); Hepatitis C (-)
whole blood


title: 18_Mixed-Infected

city: Belo Horizonte

first: Gloria Regina

last: Franco

state: Minas Gerais

address: Av. Pres. Antônio Carlos, 6627

department: Bioquimica e Imunologia

country: Brazil

institute: Universidade Federal de Minas Gerais

data_processing:
Fastq files were pseudoalign and quantified through Kallisto version 0.43.
Processed files were analysed with Sleuth version 0.30
Genome_build: mm10
Supplementary_files_format_and_content: Processed files generated using Kallisto version 0.43.0.

source_name: Whole Heart

extract_protocol:
Frozen hearts were kept in liquid nitrogen and thoroughly pulverized into a powder using a sterile porcelain crucible. The total RNA for sequencing was extracted using the Trizol reagent (Life Technologies) following the manufacturer’s protocol and precipitated with isopropanol. The quality and integrity of the samples were verified by electrophoresis on a Bioanalyser 2100 (Agilent Technologies), and only samples with an RNA integrity number (RIN) greater than seven were selected for library construction.
The cDNA libraries were prepared and sequenced at the Beijing Genomics Institute (Shenzhen, China). In short, polyadenylated RNA was purified from total RNA, converted to cDNA using random hexamer primers, sheared, and size-selected for fragments ~200 bp in length using the Illumina TruSeq RNA Sample Preparation Kit v2. Sequencing was performed on the Illumina Hiseq 2000 (Illumina, CA) platform and generated approximately 12 million paired-end reads, which were 90 nucleotides in length for each sample. Each group was sequenced in triplicate.

value: Heart

tag: strain

value: Balb/c

tag: parasite strain


title: 14_JG-Infected

value: JG


title: 17_Mixed-Infected


title: peripheral blood mononuclear cells at secondary syphilis patient, biological rep3

description:
Gene expression data from peripheral blood mononuclear cells in untreated secondary syphilis patients. Lesion; TPHA (+); TRUST (+),1:128; HIV (-); Hepatitis B (-); Hepatitis C (-)
whole blood


title: ChIPseq_Jurkat_CTCF_rep1_input


title: Peripheral blood, Subject 71

description:
replicate 1
71.AVG_Signal

value: Subject 71


title: MEF_shYthdf2_re1


title: 3157_PBMC

description: processed data file: all_counts.tsv

tag: disease state

value: Alzheimer's disease

value: PBMC


title: Peripheral blood, Subject 73

description:
replicate 1
73.AVG_Signal

value: Subject 73

value: Female


title: ChIPseq_Jurkat_CTCF_rep2

tag: cell type

value: CTCF


title: 11_JG-Infected


title: ChIPseq_CUTLL1_CTCF_rep1


title: 16_Mixed-Infected


title: MEF_shLuc_re1


title: RNAseq_CUTLL1_GSI3d_w6hr_rep2

extract_protocol:
Cells were spun down and lysed with RLT buffer; RNA extraction was conducted using the Aurum BioRad RNA isolation kit
rRNA depletion with TruSeq® Stranded Total RNA Library Prep kit

tag: treatment

value: Compound E (CAS 209986-17-4), was applied at a 1 uM concentration every 24 hours for 72 hours


title: MEF_shYthdf3_re1


title: 13_JG-Infected


title: 6_Col1.7G2-Infected


title: iPS_shYthdf2_re2

source_name: Mouse iPSCs

value: Mouse iPSCs


title: 3677_PBMC

description: processed data file: all_counts.tsv

value: Healthy control

tag: gender

value: Male


title: ChIPseq_Jurkat_CTCF_GSI3d_w4hr_rep2

tag: chip antibody


title: iPS_shYthdf2_re1


title: MEF_shLuc_re2

value: Mouse embryonic fibroblasts


title: 2983_PBMC

description: processed data file: all_counts.tsv


title: 2978_PBMC

description: processed data file: all_counts.tsv


title: ChIPseq_Jurkat_CTCF_rep1


title: 8_Col1.7G2-Infected


title: 7_Col1.7G2-Infected

description: Mouse Infection Probably Failed


title: iPS_shYthdf3_re2


title: 3_Control-NonInfected


title: 3635_PBMC

description: processed data file: all_counts.tsv


title: RNAseq_CUTLL1_GSI3d_w6hr_rep1


title: 5_Control-NonInfected


title: iPS_shLuc_re1


title: 3417_PBMC

description: processed data file: all_counts.tsv


title: 3420_PBMC

description: processed data file: all_counts.tsv


title: 3454_PBMC

description: processed data file: all_counts.tsv


title: 2930_PBMC

description: processed data file: all_counts.tsv


title: RNAseq_CUTLL1_GSI3d_rep1


title: RNAseq_CUTLL1_DMSO_rep2


title: 2948_PBMC

description: processed data file: all_counts.tsv


title: 4_Control-NonInfected


title: RNAseq_CUTLL1_GSI3d_rep2


title: RNAseq_CUTLL1_DMSO_rep1


title: 3434_PBMC

description: processed data file: all_counts.tsv


title: iPS_shLuc_re2


title: ES_shYthdf3_re1

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells

value: CBA/CaJ X C57BL/6J


title: iPS_shYthdf3_re1


title: 3407_PBMC

description: processed data file: all_counts.tsv


title: RNAseq_Jurkat_GSI3d_w4hr_rep1

value: Jurkat


title: 3344_PBMC

description: processed data file: all_counts.tsv


title: RNAseq_Jurkat_GSI3d_rep2


title: ES_shYthdf3_re2


title: RNAseq_Jurkat_GSI3d_rep1


title: 3292_PBMC

description: processed data file: all_counts.tsv


title: 3279_PBMC

description: processed data file: all_counts.tsv


title: RNAseq_Jurkat_DMSO_rep1


title: ES_shLuc_re2


title: 3189_PBMC

description: processed data file: all_counts.tsv


title: UC MSC, IFN-γ primed, biological rep2

city: Medicine Hat

first: Lorena

last: Braid

state: Alberta

address: PO Box 21053, Crescent Heights PO

country: Canada

institute: Aurora BioSolutions Inc.

description: Gene expression data from umbilical cord-derived mesenchymal stromal cells exposed to IFN-γ.

hyb_protocol: The total amount of cRNA for the hybridization reaction was 20 µg. Arrays were hybridized for 16 hours at 45°C, 60 RPM in a GeneChip™ Hybridization Oven 640 (Affymetrix, Waltham, MA).

scan_protocol: Program FS450_0002 was used with GeneChip™ Fluidics Station 450 (Affymetrix, Waltham, MA). Chips were scanned using a GeneChip™ 3000 7G Scanner (Affymetrix, Waltham, MA) and the resulting probe array images subjected to grid alignment and fluorescence intensity review in AGCC Viewer.

data_processing: The data were analyzed using R/Bioconductor packages, including simpleaffy for .CEL file upload and Affymetrix-recommended quality assessment, and gcrma for GCRMA pre-processing.

label: 3' IVT Biotin

source_name: umbilical cord-derived mesenchymal stromal cells, passage 5

label_protocol: RNA was amplified and labeled using GeneChip™ 3’ IVT Plus kits (Affymetrix, Waltham, MA) following the manufacturer’s instructions with the following modification: 200 ng of RNA was used for the cDNA synthesis.

growth_protocol: For cell expansion, MSCs were seeded at a density of 1333 cells/cm2 in RoosterNourish™-MSC-XF (RoosterBio Inc.). Cells were incubated at 37o C, 5% CO2 with media changes every 3-4 days and passaged once the monolayer reached 70-80% confluence. Culture media was aspirated and cells washed with DPBS-/- (ThermoFisher Scientific, Waltham, MA), then enzymatically detached using TrypLE™ Select (ThermoFisher Scientific, Waltham, MA). Once cells were dissociated, an equal volume of media was added to the suspension and cells were counted with a Millipore Scepter cell counter using 60 µm probes (Millipore, Billerica, MA). Cells were centrifuged at 149 x g for 5 minutes, and the cell pellet re-suspended in fresh media and seeded in new culture vessels at a density of 1333 cells/cm2.

extract_protocol:
To collect mRNA, cells were enzymatically detached from the culture vessel as described earlier. Suspended cells were pelleted by centrifugation as described above and re-suspended in 0.5 ml of RNAprotect® Cell Reagent (Qiagen, Germantown, MD) for short-term storage at -80C.
Cell pellets from technical replicates (n = 3 for each donor population) were combined to produce a single RNA sample. RNA was extracted using Qiagen RNeasy® Plus Mini Kits (Qiagen, Germantown, MD) according to manufacturer’s recommendations. 20 µl of 2 M dithiothreitol (DTT) was added per ml of kit buffer (RLT buffer) and 600 µl RLT buffer was used for each sample.  RNA concentration and quality were assessed in 96 well plates using a BioTek Synergy HT microplate reader (BioTek Instruments Inc., Winooski, VT) and Gen5 2.05 software accounting for path length correction.

treatment_protocol: MSCs at P4 or P5 (mPDL 14.6-16.5) were seeded in 25 cm2 flasks at a density of 13,333 cells/cm2 in 3ml RoosterNourish™-MSC-XF and allowed to adhere overnight. Purified recombinant human cytokines (PeproTech, Inc., Rocky Hill, NJ) were diluted in protein-free (PF) RoosterBasal™-PF media (RoosterBio Inc.) at the following concentrations: TNF-α (50 ng/ml), IL-1β (80 pg/ml) and IFN-γ (50 ng/ml). Complete media was removed from the monolayers and replaced with 2 ml of cytokine solution for 24 hours. Unstimulated cultures received 2 ml of RoosterBasal™-PF without cytokine supplements.

tag: mean population doubling level

tag: cytokine priming condition

value: IFNg

tag: donor sex

value: F

tag: culture start date batch

tag: chip run batch

tag: overall batch


title: RNAseq_Patient2

source_name: Patient xenograft

extract_protocol:
Cells were spun down and lysed with RLT buffer; RNA extraction was conducted using the Aurum BioRad RNA isolation kit
Poly-A selection with Illumina TruSeq RNA Library Prep Kit v2

value: T-ALL from patient xenograft


title: RNAseq_Jurkat_DMSO_rep2


title: RNAseq_Jurkat_GSI3d_w4hr_rep2


title: ES_shYthdf2_re2


title: 3175_PBMC

description: processed data file: all_counts.tsv


title: 4.5 smRNA

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Raw reads were trimmed using Cutadapt v1.6 to remove adapters and only keep reads that were 18 - 30 bp in length.
Remaining reads were mapped to the Stettler14 genome using Bowtie2 v2.2.3 with the very-sensitive-local parameter.
Genome_build: Populus trichocarpa Stettler 14 v1.1
Supplementary_files_format_and_content: <chromosome> <position, 1-indexed> <strand> <Count> <sequence; reverse complemented if minus strand> <sequence length>

organism: Populus trichocarpa

source_name: leaf tissue

growth_protocol: All samples are from a wild P. trichocarpa tree growing in Oregon

extract_protocol: Total RNA was used as input for the TruSeq Small RNA Sample Prep Kit (Illumina) following manufacturer's instructions.

value: leaf


title: UC MSC, IL-1β primed, biological rep2

description: Gene expression data from umbilical cord-derived mesenchymal stromal cells exposed to IL-1β.


title: OKS_D1_Input

value: reprogramming cells

tag: day of reprogramming

value: day 1


title: ES_shLuc_re1


title: ES_shYthdf2_re1


title: UC MSC, TNF-α primed, biological rep2

description: Gene expression data from umbilical cord-derived mesenchymal stromal cells exposed to TNF-α.

value: TNFa


title: BM MSC, IL-1β primed, biological rep2

description: Gene expression data from bone marrow mesenchymal stromal cells exposed to IL-1β.

source_name: bone marrow mesenchymal stromal cells, passage 4

value: M


title: UC MSC, resting, biological rep2

description: Gene expression data from resting (unprimed) umbilical cord-derived mesenchymal stromal cells.


title: BM MSC, IFN-γ primed, biological rep2

description: Gene expression data from bone marrow mesenchymal stromal cells exposed to IFN-γ.


title: 4.4 smRNA


title: RNAseq_Patient1_rep2


title: RNAseq_Patient1_rep1


title: 3182_PBMC

description: processed data file: all_counts.tsv

value: Alzheimer's disease

value: PBMC


title: 3170_PBMC

description: processed data file: all_counts.tsv

value: Female


title: RNAseq_Jurkat_rep2


title: RNAseq_Jurkat_rep3


title: BM MSC, IL-1β primed, biological rep3


title: 3169_PBMC

description: processed data file: all_counts.tsv

value: Healthy control


title: OKS_D1_TEAD2_ChIP_seq

value: anti-TEAD2 (Proteintech, Cat# 21159-1-AP)


title: 4.3 smRNA


title: BM MSC, TNF-α primed, biological rep2

description: Gene expression data from bone marrow mesenchymal stromal cells exposed to TNF-α.


title: 3153_PBMC

description: processed data file: all_counts.tsv

value: Male


title: 3155_PBMC

description: processed data file: all_counts.tsv


title: BM MSC, IFN-γ primed, biological rep3


title: BM MSC, resting, biological rep2

description: Gene expression data from resting (unprimed) bone marrow mesenchymal stromal cells.


title: 4.2 smRNA


title: RNAseq_Jurkat_rep1


title: 3139_PBMC

description: processed data file: all_counts.tsv


title: 14.5 smRNA


title: RNAseq_Tcell_rep3

source_name: T-cell

value: T-cell


title: 14.4 smRNA


title: RNAseq_Tcell_rep2


title: BM MSC, TNF-α primed, biological rep3


title: BM MSC, resting, biological rep3


title: 3125_PBMC

description: processed data file: all_counts.tsv


title: 3115_PBMC

description: processed data file: all_counts.tsv


title: RNAseq_Tcell_rep1


title: 3114_PBMC

description: processed data file: all_counts.tsv


title: 14.3 smRNA


title: 14.2 smRNA


title: UC MSC, TNF-α primed, biological rep1


title: UC MSC, IL-1β primed, biological rep1


title: UC MSC, IFN-γ primed, biological rep1


title: 3022_PBMC

description: processed data file: all_counts.tsv


title: Hy-48h

city: Seoul

first: KeunOh

last: Choi

address: Chungmugwan 602, 209, Neungdong-ro, Gwangjin-gu, Seoul

country: South Korea

institute: Sejong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Sebaceous gland

growth_protocol: The immortalized human sebaceous gland cell line SZ95 was maintained in DMEM/Ham’s F12 medium (1:1) containing 10% FBS and penicillin/streptomycin, and 5 ng/ml human epidermal growth factor.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Cells were incubated at a CO2 level of 5% with 1% O2 balanced with N2 using a hypoxic chamber.

value: hypoxia 48hr


title: RNAseq_Tcell_rep4


title: 4.1 smRNA


title: Hy-24h

value: hypoxia 24hr


title: 13.5 smRNA


title: 14.1 smRNA


title: 3019_PBMC

description: processed data file: all_counts.tsv


title: 2972_PBMC

description: processed data file: all_counts.tsv


title: BM MSC, IFN-γ primed, biological rep1

value: IFNg


title: NOR


title: 13.4 smRNA


title: 4.5 r3 mRNA

data_processing:
Paired-end reads were trimmed using Trimmomatic v0.36 to remove TruSeq3 adapters, bases with quality score less than 10, and any reads less than 50 bp long.
Remaining reads were mapped to the Stettler14 genome using HiSAT2 v2.1.0 with default parameters except to report alignments for transcript assemblers (--dta)
Transcript abundances were estimated using StringTie v1.3.4d using default parameters except to limit estimates to reference transcripts only (-e) and to specificy tab-delimited output (-A).
Genome_build: Populus trichocarpa Stettler 14 v1.1
Supplementary_files_format_and_content: <gene name> <chromosome>  <strand> <start, 1-index> <end, 1-index> <FPKM, fragments per kilobase of transcript per million read pairs> <TPM, transcripts per million>

growth_protocol: All samples  in this study are from a wild P. trichocarpa tree growing in Oregon

extract_protocol: Total RNA was extracted from leaf tissue in each branch using the Direct-zol RNA MiniPrep Plus kit (Zymo Research) with Invitrogen’s Plant RNA Reagent. Strand-specific RNA-seq libraries were constructed using the TruSeq Stranded mRNA LT kit (Illumina) following the manufacturer’s instructions.


title: 3015_PBMC

description: processed data file: all_counts.tsv


title: BM MSC, IL-1β primed, biological rep1

value: F


title: 2964_PBMC

description: processed data file: all_counts.tsv


title: hP-MSCs-2: Human placenta-derived MSCs

city: Zhunan, Miaoli County

first: Li-Tzu

address: 35 Keyan Road

department: Institute of Cellular and System Medicine

country: Taiwan

institute: National Health Research Institutes (NHRI)

hyb_protocol: Samples were hybridized with Affymetrix Human Transcriptome Array 2.0 and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

source_name: P-MSC culture at passage 9

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: P-MSCs were cultured in DMEM with 10% FBS,  2mM L-glutamine and 100 U/ml antibiotics. Cells were sub-cultured in a dilution of 1:3 at 80-90% conﬂuence.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Inclusion of 1 U/ µL of the RiboLock RNase Inhibitor (Thermo) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with RQ1 RNase-Free DNasee (Peomega) to remove trace amounts of genomic DNA.

value: MSC

tag: original derivation

value: Placenta

tag: treatment protocol

value: Seeded 20000 cells in 24 well culture plate and culture for 3 days.


title: BM MSC, TNF-α primed, biological rep1


title: hP-MSCs-1: Human placenta-derived MSCs


title: UC MSC, resting, biological rep1


title: 2965_PBMC

description: processed data file: all_counts.tsv


title: BM MSC, resting, biological rep1


title: 4.5 r1 mRNA

tag: tissue

value: leaf


title: 2951_PBMC

description: processed data file: all_counts.tsv


title: 4.5 r2 mRNA


title: UC MSC, IFN-γ primed, biological rep3


title: UC MSC, IL-1β primed, biological rep3


title: 4.4 r3 mRNA


title: Hy-8h

value: hypoxia 8hr


title: hESCs: Human ESC cells

source_name: ESC culture (feeder-free conditions) at passage 40

growth_protocol: hESCs were maintained in feeder-free conditions and cultured in mTeSR medium. Cells were sub-cultured in a dilution of 1:3 at 70-80% conﬂuence.

value: PSC

value: H1 hESC line

value: Undifferentiated  hESCs were maintained in feeder-free conditions and cultured in mTeSR medium at passage 40


title: hiPSCs: Human iPSCs generated from CD34+ blood cells

source_name: ESC culture (feeder-free conditions) at passage 26

growth_protocol: hiPSCs were maintained in feeder-free conditions and cultured in mTeSR medium. Cells were sub-cultured in a dilution of 1:3 at 70-80% conﬂuence.

value: CD34+ cells using Sendai viral transduction of Oct-4, Sox-2, Klf-4, and c-Myc

value: Undifferentiated  hiPSCs were maintained in feeder-free conditions and cultured in mTeSR medium at passage 26


title: 2950_PBMC

description: processed data file: all_counts.tsv

source_name: PBMC HC

value: Healthy control

value: PBMC


title: hiPSC-MSCs: MSCs derived from iPSCs generated from human CD34+ blood cells

source_name: iPSC-MSC culture at passage 5

growth_protocol: ESC-MSC were derived from H1 hESC by replacing the medium of hESCs with BMMSC medium which is DMEM with 10% FBS,  2mM L-glutamine and 100 U/ml antibiotics. Cells were sub-cultured in a dilution of 1:3 at 80-90% conﬂuence.

value: Male

value: MSC differentiated from iPSCs generated by CD34+ cells using Sendai viral transduction of Oct-4, Sox-2, Klf-4, and c-Myc


title: 4.4 r2 mRNA


title: GST-sample09

city: Ann Arbor

first: P. Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

description: Total RNA (5 µg) was combined with ERCC Spike-In Standards (5 µl of 1:50 diluted stock solution; Invitrogen). RNA TruSeq strand-specific 50 bp dual indexed RNA libraries were prepared using RiboZero rRNA depletion (Illumina) and sequenced on a HiSeq 2500 in High-output mode.

data_processing:
quality control, FastQC (version 0.10.1) and MultiQC (v1.0.dev0)
fixed-length trimming, Cutadapt (version 1.8.1), parameters: -u 10
quality trimming, Trimmomatic (version 0.33), parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:26
alignment, STAR (version 2.5.2b). The STAR index was built from the customized combined genome with the above sequences as a FASTA file, annotations as a GTF file, and an overhang length of 100. STAR alignment was performed using trimmed reads 1 and 2 in paired-end mode for each sample and written as BAM (Li et al. 2009) files sorted by alignment coordinates.
quantification, HTSeq (version 0.6.1p1), parameter: stranded set to reverse and requirement of minimum alignment quality score set to 10, supplied with customized annotations as used in alignment. The overlap resolution of feature quantification in HTSeq was set as --mode=union with --nonunique=none
differential expression analysis, DESeq2 (version 1.16.1)
Genome_build: custom genome containing GRCh38 (release 92, accessed 2018-06-18), NOCT ∆(2-15)-3F pFC3F plasmid sequence, GST-3F pFC3F plasmid sequence, and the ERCC spike-ins
Supplementary_files_format_and_content: .htseq.count.txt files contains raw output of HTSeq quantification as text files with two columns separated by a tab and summary statistics in the last 5 rows; .csv files are comma-separated values files, column names in TPM.csv stands for gene Ensembl ID, indiviual TPM values in 6 samples respectively, gene HGNC symbol, and gene description; column names in deseq.shrinkage.patched.csv stand for gene Ensembl ID, gene expression base mean as in DESeq2 output, shrunken log2 fold change as in DESeq2 output, standard error of log2 fold changes as calculated by DESeq2 and written by a homemade patch for DESeq2 1.16.1, Wald statistics as in DESeq2 output, p-values as in DESeq2 output, and adjusted p-values as in DESeq2 output

source_name: HEK293 cells overexpressing GST-3F, biological replicate sample 09

growth_protocol: For each clonal cell line (3 lines expressing GST-3F and 3 lines expressing NOCT ∆(2-15)-3F), two 10 cm dishes were plated with 3x106 cells in DMEM + 10% FBS and incubated for three days at 37 °C and 5% CO2.

extract_protocol:
Cells were harvested by dissociation with TrypLE (Thermo), washed twice with cold 1x PBS, pH 7.4 (Gibco), and rapidly frozen at -80 °C.
Total RNA was isolated from frozen cell pellets using a Maxwell RSC SimplyRNA Cells kit (Promega) using a 2x concentration of DNAse I.  RNA was eluted in 50 µL nuclease-free water and was analyzed using a bioanalyzer tapestation (Agilent), with RIN values between 9.6 and 10.0. Total RNA (5 µg) was combined with ERCC Spike-In Standards (5 µl of 1:50 diluted stock solution; Invitrogen) and submitted to the University of Minnesota Genomics Center for library generation and sequencing. RNA TruSeq strand-specific 50 bp dual indexed RNA libraries were prepared using RiboZero rRNA depletion (Illumina) and sequenced on a HiSeq 2500 in High-output mode. Library generation and sequencing was performed by the University of Minnesota Genomics Center.

tag: cell line

tag: overexpression


title: hESC-MSCs: Human ESC-derived MSCs

source_name: ESC-MSC culture at passage 10

value: MSC differentiated from H1 hESC line


title: 4.4 r1 mRNA


title: homozygous Lrap-/- rat 1

city: Aurora

first: Laura

middle: Maren

last: Saba

state: CO

address: 12850 East Montview Blvd.

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

data_processing:
Reads were trimmed to remove adapters and low-quality base calls using cutadapt
Trimmed reads were aligned to the rn6 version of the rat genome using HISAT2
A genome and transcriptome–guided reconstruction was executed using the StringTie software for each genotype independently using the Ensembl rat transcriptome (rn6), and then genotype-specific transcriptomes were merged into a single transcriptome using the merge function within StringTie. Transcripts were annotated by comparing the merged transcriptome back to the Ensembl rat transcriptome (rn6) using ‘gffcompare’
Individual isoforms and genes from the merged transcriptome were quantitated using RSEM.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include estamated read counts, TPM, and FPKM values for each Sample (standard RSEM output)
Supplementary_files_format_and_content: estimated count matrices with genes or isoforms as rows and Samples as columns
Supplementary_files_format_and_content: GTF file for reconstructed transcriptome

organism: Rattus norvegicus

source_name: whole brain

extract_protocol:
Total RNA was extracted from whole brain of three alcohol-naïve male rats using the RNeasy Midi Kit with additional cleanup performed using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Sequencing libraries were constructed using the Illumina TruSeq Stranded RNA Library Prep Kit with Ribo-Zero (Illumina, San Diego, CA, USA), in accordance with the manufacturers protocol.
Library quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Samples were sequenced (2x100 paired-end reads) on the Illumina HiSeq2500 (Illumina, San Diego, CA, USA) with 4 libraries multiplexed per lane.

value: brain

tag: genotype

value: homozygous Lrap knockout


title: homozygous Lrap-/- rat 3


title: GST-sample08

source_name: HEK293 cells overexpressing GST-3F, biological replicate sample 08


title: hBM-MSCs-2: Human BM-derived MSCs

source_name: BM-MSC culture at passage 7

growth_protocol: BM-MSCs were cultured in DMEM with 10% FBS,  2mM L-glutamine and 100 U/ml antibiotics. Cells were sub-cultured in a dilution of 1:3 at 80-90% conﬂuence.

tag: cell type

value: MSC

value: BM


title: UC MSC, resting, biological rep3

value: M


title: 4.3 r3 mRNA

value: leaf


title: heterozygous Lrap-/+ rat 3

value: heterozygous Lrap knockout

tag: treatment


title: hBM-MSCs-1: Human BM-derived MSCs

tag: gender

value: Female

value: Seeded 20000 cells in 24 well culture plate and culture for 3 days.


title: homozygous Lrap-/- rat 2


title: UC MSC, TNF-α primed, biological rep3

value: TNFa


title: heterozygous Lrap-/+ rat 2


title: 4.3 r2 mRNA


title: 4.3 r1 mRNA


title: GST-sample02

source_name: HEK293 cells overexpressing GST-3F, biological replicate sample 02


title: 4.2 r3 mRNA


title: heterozygous Lrap-/+ rat 1


title: wild type rat 3

value: wild type


title: YapOffD33

city: Worcester

first: Tomas

middle: Christopher

last: Rodriguez

address: 55 N Lake Ave, AS5-2005

department: RNA Therapeutic Institute

institute: University of Massachusetts Medical School

data_processing:
Demultiplexed using Illumina bcl2fastq software
trimmed using cutadapt  (-b CTGTCTCTTATACACATCT -B AGATGTGTATAAGAGACAG -q 20 -m 20)
aligned to mm10 using BWA mem, marking duplicates (bwa mem -M)
SAM converted to BAM, sorted, merged (lanes L001-4) and indexed with samtools
duplictes removed using picard (MarkDuplicates REMOVE_DUPLICATES=true)
peakcalling using zpeaks (-forwardShift 4 -reverseShift -5 -signalResolution 12 -smoothingFactor 30 -peaksOut) (github.com/krews-community/zpeaks)
Genome_build: mm10
Supplementary_files_format_and_content: BED

source_name: Liver

extract_protocol:
nuclear isolation and tagmentation according to Omni ATAC (Corces et al. Nature Methods 2017)
Custom Nextera library preparation according to Omni ATAC (Corces et al. Nature Methods 2017)

value: Yap Off D33


title: 4.2 r2 mRNA


title: Liver

value: WT


title: YapOffD64

value: Yap Off D64


title: wild type rat 2


title: Noct_del2-15-sample11

source_name: HEK293 cells overexpressing NOCT ∆(2-15)-3F, biological replicate sample 11

value: NOCT delta(2-15)-3F


title: MCF10AT1 CD24low FACS replicate 3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

data_processing:
Sequences were aligned with STAR (v2.5.2) to hg38 using Gencode (v28) reference annotation
Aligned reads were counted using GenomicRanges, GenomicAlignments and GenomicFeatures packages in R (v3.5.0)
Differential expression was evaluated by the DEseq2 package in R (v3.5.0)
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2_normalized_counts.csv

growth_protocol: MCF10AT1 were grown in DMEM: F12 (Hyclone: SH30271, Thermo Fisher Scientific, Waltham, MA) with 5% (v/v) horse serum (Gibco: 16050, Thermo Fisher Scientific, Waltham, MA, USA) + 10 μg/ml human insulin (Sigma Aldrich, St. Louis, MO: I-1882) + 20 ng/ml recombinant hEGF (Peprotech, Rocky Hill, NJ, USA: AF-100-15) + 100 ng/ml cholera toxin (Sigma Aldrich: C-8052) + 0.5 μg/ml hydrocortisone (Sigma Aldrich: H-0888) 50 IU/ml penicillin/50 μg/ml streptomycin and 2 mM glutamine (Life Technologies, Carlsbad, CA, USA: 15140-122 and 25030-081, respectively).

extract_protocol:
Trizol
Total RNA was depleted of ribosomal RNA, reverse transcribed using a random hexamer strategy, and strand-specific adapters were added following manufacturer’s protocol (TruSeq Stranded Total RNA Library Prep kit with Ribo-Zero Gold, Illumina, San Diego, CA) with the exception that the final cDNA libraries were amplified using the Real-time Library Amplification Kit (Kapa Biosystems, Wilmington, MA) to reduce over-amplification of libraries.

treatment_protocol: Cells were incubated with antibodies against CD24 ( Biolegend Cat: 311120, Cy7-conjugated) and CD44 (BD Pharmingen Cat: 55942, APC conjugated) and then sorted for high/low expression of respective cell surface markers.

value: breast


title: YapOffD14

value: Yap Off D14


title: wild type rat 1

value: brain


title: 4.1 r3 mRNA

source_name: leaf tissue


title: MCF10AT1 CD24low FACS replicate 2


title: YapOn

value: Yap On


title: MCF10AT1 CD24low FACS replicate 1


title: OWOP6

city: Shanghai

first: Lincai

last: Ye

state: China

address: Heart Center 7003, 1678 Dongfang Road

department: Shanghai Institute For Pediatric Congenital Heart Disease

institute: Shanghai Children's Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: right ventricular cardiomyocyte

extract_protocol:
Cardiomyocytes were isolated and purified , flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: right ventricular cardiomyocyte

tag: treatment group

value: PAB


title: OKS_shYthdf3_DMSO_8h_lifetime_re2

data_processing:
ATAC-seq and ChIP-seq data were aligned to the mm10 genome using bowtie2 (with the options ‘-p 20–very-sensitive–end-to-end–nounal–no-mixed -X 2000’).
SAMtools (view –q 30) was used for removing the low-quality mapped reads, and uniquely mapped reads were only retained after removed PCR duplicates.
Peaks were called using MACS2 (-g mm -f BAMPE)
The reference transcriptome index was produced with RSEM using the reference genome mm10 (ensemble gene annotation track v79) and ERCC RNA spike-in sequence.
The reads were mapped to the reference transcriptome using RSEM and bowtie 2 (with options ‘rsem-calculate-expression -p 12–bowtie2–no-bamout’).
Expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq.
Genome_build: mm10
Supplementary_files_format_and_content: Alignment bam files were transformed into bigwig files using deepTools with the RPKM normalization method. Scores represent the number of fragments overlapping each genomic position.
Supplementary_files_format_and_content: Excel file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: reprogramming cells

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015; Li et al., 2017b). In brief, 50,000 cells were washed in PBS and lysed using 50 μl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were centrifuged at 500 ×g for 5 min and resuspended with 50 μl transposition reaction mix from a TruePrep DNA Library Prep Kit V2 for Illumina. The samples were incubated at 37°C for 30 min, and DNA was purified using a MinElute kit. Libraries were first preamplified for 5 cycles, and then assessed by quantitative PCR as described (Buenrostro et al., 2015) to determine the suitable PCR cycles. After appropriate amplification, libraries were purified with the MinElute kit and quantified using a VAHTS Library Quantification Kit for Illumina. Gel electrophoresis was used for examining the library integrity. Finally, the sequencing was carried out on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles).
ChIP was performed as described previously with some modifications (Li et al., 2017b). Briefly, reprogramming cells were harvested by trypsinisation at day 1 and chemically crosslinked with 1% formaldehyde for 10 min at room temperature with gentle rotation. The reaction was quenched by 0.125M glycine for 5 min at room temperature and cells were washed twice with cold PBS. 1× 107 cells were lysed in ChIP lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitor cocktail) for 10 min at 4°C. The DNA was fragmented to 150-500 bp by sonication, and then centrifuged at 14,000 g for 10 min at 4°C. The supernatant was diluted with ChIP IP buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 50mM Tris-HCl, pH 8.0, 150 mM NaCl and protease inhibitor cocktail). Immunoprecipitation was performed with 5 μg rabbit anti-TEAD2 antibody coupled to 50 μl protein A/G mix overnight at 4°C with gently rotation. Beads were washed at 4°C for 5 min in the following order: twice low salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% TritonX-100, 2 mM EDTA, 150 mM NaCl), twice high salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% TritonX-100, 2 mM EDTA, 500 mM NaCl), twice LiCl buffer (500mM LiCl, 50 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% NP-40, 0.5% Sodium Deoxycholate), once TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA) with final elution in 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS buffer. The eluted chromatin and input samples were reverse crosslinked by overnight incubation at 65°C. After treated with proteinase K at 56°C for 30 min, the DNA was purified using the MinElute PCR Purification Kit. The libraries were constructed by a VAHTS Universal DNA Library Prep Kit for Illumina V3 according to the manufacturer’s instructions.
Cells were lysed by TRIzol reagent, following which total RNAs were extracted by the chloroform-isopropanol method. The VAHTS mRNA-seq V3 Library Prep Kit for Illumina was used for RNA library preparation. In brief, mRNA was enriched from 1 μg of total RNA using oligo-dT Dynabeads, followed by fragmentation at 94°C 8min. Secondly, First-strand and second-strand cDNA were synthesis successively using corresponding reagents. After purified by VAHTS DNA Clean Beads, the cDNA was end repaired and added with a dA base, followed by adapter ligation, two-round purification, PCR amplification and purification.
Libraries were prepared for sequencing using standard Illumina protocols
ATAC-seq, ChIP-seq and RNA-seq

value: reprogramming cells

value: day 1

value: DMSO for 8 hours


title: Noct_del2-15-sample04

source_name: HEK293 cells overexpressing NOCT ∆(2-15)-3F, biological replicate sample 04


title: OWOP5


title: MCF10AT1 CD24high FACS replicate 3


title: 4.1 r1 mRNA

value: leaf


title: 4.1 r2 mRNA


title: MCF10AT1 CD24high FACS replicate 2


title: Noct_del2-15-sample12

source_name: HEK293 cells overexpressing NOCT ∆(2-15)-3F, biological replicate sample 12


title: OKS_shYthdf3_DMSO_8h_lifetime_re1


title: 14.5 r3 mRNA


title: OWOP4


title: OWOP3


title: OKS_shYthdf3_DMSO_4h_lifetime_re2

value: DMSO for 4 hours


title: 4.2 r1 mRNA


title: OWOP2


title: 14.5 r2 mRNA


title: OKS_shYthdf3_DMSO_4h_lifetime_re1


title: OKS_shYthdf3_Dact_8h_lifetime_re1

value: Actinomycin D for 8 hours


title: OWOP1


title: 14.4 r3 mRNA


title: OWCON6

value: Sham


title: 14.4 r2 mRNA


title: OKS_shYthdf3_Dact_4h_lifetime_re2

value: Actinomycin D for 4 hours


title: OWCON5


title: 14.4 r1 mRNA


title: OKS_shYthdf3_Dact_4h_lifetime_re1


title: OWCON4


title: 14.3 r3 mRNA


title: HiC_Tcell

source_name: T-cell

extract_protocol:
Biotinylated DNA was extracted with Dynabeads MyOne Streptavidin C1 beads
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: T-cell


title: OWCON3


title: OKS_shYthdf2_DMSO_8h_lifetime_re2


title: MCF10AT1 CD24high FACS replicate 1


title: Δflo8_0.05_rep3

city: Vienna

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

data_processing:
Conversion BAM → FASTQ with picard tools (v2.17.3-3g3bf7fdc-SNAPSHOT) SamToFastq
Quality Control with FastQC 0.11.5
Read trimming with TrimGalore 0.4.2
Read quantification with kallisto (v0.43.1) and samtools (v1.5) (kallisto index based on K. phaffii CBS7435 genomic sequence as reference)
Differential expression analysis with R (DESeq2 (v1.14.1))
Genome_build: PicPas_Mar2011
Supplementary_files_format_and_content: raw counts (tsv) and DESeq2 abundance (csv)

organism: Komagataella phaffii

source_name: Cells from chemostat fixed with 5% (vol/vol) phenol in absolute ethanol

growth_protocol: Samples were collected from glucose-limited chemostat and fixed immediately by adding in 2:1 ratio to precooled fixing solution containing 5% (vol/vol) phenol in absolute ethanol. These were then centrifuged for 1 min at 10,000 x g and 4°C, afterwards the supernatant was removed and the pellet was stored at -80°C until further processing.

extract_protocol:
The ethanol/phenol fixed cells were resuspended in 1 mL TRI reagent (Sigma Aldrich), lysed using glass beads as described in the previous section and RNA was extracted according to the TRI reagent protocol. DNase treatment was carried out using the Ambion DNA-free kit (Invitrogen). RNA concentration and integrity was analysed using the Nanodrop spectrophotometer and Bioanalyzer (Agilent).
mRNA library preparation, polyA enrichment

tag: strain

tag: medium

value: Chemostat medium


title: HiC_Patient2

data_processing:
ChIP-seq sequence reads were aligned to the hg38 genome using bwa, MACS2 was used to call peaks.
ATAC-seq sequence reads were aligned to the hg38 genome using bowtie.
RNA-seq datasets were processed using Salmon.
Hi-C data were processed using HiC-Pro.
Methylation calls were performed with Bismark.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: ChIP-seq: peak file in BED, RNA-seq: transcript level quantification from salmon, Hi-C: raw matrix, DNA methylation: bigwig or bismark.cov

source_name: Patient xenograft

value: T-ALL from patient xenograft


title: 14.3 r2 mRNA


title: OWCON2


title: Δflo8_0.05_rep2


title: 14.3 r1 mRNA


title: OKS_shYthdf2_DMSO_8h_lifetime_re1

city: Guangzhou

first: Jiadong

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH


title: OKS_shYthdf2_DMSO_4h_lifetime_re2


title: OKS_shYthdf3_Dact_8h_lifetime_re2


title: HiC_Patient1


title: Δflo8_0.05_rep1


title: OWCON1


title: OKS_shYthdf2_DMSO_4h_lifetime_re1


title: HiC_CUTLL1


title: HiC_Jurkat

source_name: Jurkat

value: Jurkat


title: 14.2 r3 mRNA


title: Δflo8_0.1_rep3


title: Δflo8_0.1_rep2


title: Δflo8_0.1_rep1


title: 14.1 r3 mRNA


title: 14.2 r1 mRNA


title: OKS_shYthdf2_Dact_8h_lifetime_re1


title: WT_0.1_switchback_rep3

value: Wild-type


title: OKS_shYthdf2_Dact_4h_lifetime_re1


title: 14.1 r2 mRNA


title: 14.1 r1 mRNA


title: OKS_shLuc_DMSO_8h_lifetime_re2


title: WT_0.1_switchback_rep2


title: WT_0.1_switchback_rep1


title: OKS_shLuc_DMSO_8h_lifetime_re1


title: 14.2 r2 mRNA


title: OKS_shYthdf2_Dact_8h_lifetime_re2


title: 13.5 r3 mRNA


title: OKS_shLuc_DMSO_4h_lifetime_re2


title: WT_0.05_rep3


title: 13.5 r2 mRNA


title: WT_0.05_rep2


title: 13.5 r1 mRNA


title: OKS_shYthdf2_Dact_4h_lifetime_re2


title: OKS_shLuc_DMSO_4h_lifetime_re1


title: WT_0.05_rep1


title: OKS_shLuc_Dact_8h_lifetime_re2


title: 13.4 r3 mRNA


title: WT_0.1_rep3


title: 13.4 r2 mRNA


title: OKS_shLuc_Dact_8h_lifetime_re1


title: WT_0.1_rep2


title: 13.4 r1 mRNA


title: WT_0.1_rep1


title: OKS_shLuc_Dact_4h_lifetime_re2


title: OKS_shLuc_Dact_4h_lifetime_re1


title: 14.5 WGBS

data_processing:
MethylC-seq analysis were performed as described in (Schultz et al. 2015). This uses methylpy v1.3.2 with default parameters.
Genome_build: Populus trichocarpa Stettler 14 v1.1
Supplementary_files_format_and_content: <chromosome> <cytosine position, 1-index> <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>

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).


title: 14.4 WGBS


title: Rp_H_6M_05

city: Dunedin

first: Eddy

last: Dowle

address: 270 Gt King St

department: Department of Anatomy

country: New Zealand

institute: University of Otago

description: Pool of 10 CNS

data_processing:
Reads were mapped to the Rhagoletis zephyria genome using STAR
Read counts were estimated in RSEM
Genome_build: NCBI Assembly: GCA_001687245.1, Rhagoletis_zephyria_1.0
Supplementary_files_format_and_content: RSEM output file - counts per gene

organism: Rhagoletis pomonella

source_name: Central Nervous System CNS

growth_protocol: Infested apple and hawthorn fruits were collected from Urbana, IL in the late summer and fall of 2014. Infested fruit were returned to the laboratory at the University of Florida, emerging larvae were collected and held at ~24C 14:10 LD for 10 days to complete pupation and enter diapause, then pupae were transferred to 3.5C at 95% Relative Humidity (RH). At monthly intervals from 2 to 6 months we dissected out the Central Nervous System (CNS), homogenized pools of 10 CNS, and extracted RNA (5 samples per time point per host). RNA sequencing libraries were prepared using Illumina’s tru-seq stranded mRNA kit and sequenced using 100bp single end Illumina HiSeq 2500. Cleaned reads were mapped to the R. zephyria genome using STAR, and read counts were generated using RSEM.

extract_protocol:
Flies were disected and CNS removed, extractions consisted of pools of 10 fly CNS, RNA extraction
Illumina mRNA tru-seq stranded

tag: host

value: Hawthorn Tree

tag: diapause age

value: 6 Months diapause

tag: location

value: USA:Urbana Illinois

tag: lifestage

value: Pupa

tag: collection year


title: OKS_shYthdf3_D7_re2

last: Liu

growth_protocol: Reprogramming cells were cultured in iCD1 medium. ESCs cells and iPSCs cells were cultured in N2B27+2i+LIF medium, MEF cells were cultured in 10% FBS medium

value: reprogramming cells

tag: day of reprogramming

value: day 7


title: 14.3 WGBS


title: Rp_H_6M_04

description: Pool of 10 CNS


title: Rp_H_6M_03B

description: Pool of 10 CNS


title: 14.2 WGBS


title: OKS_shYthdf3_D5_re2

value: day 5


title: 14.1 WGBS

value: leaf


title: OKS_shYthdf3_D5_re1


title: OKS_shYthdf3_D3_re2

value: day 3


title: Rp_H_6M_02

description: Pool of 10 CNS


title: Rp_H_6M_01

description: Pool of 10 CNS


title: OKS_shYthdf3_D3_re1


title: 13.5 WGBS


title: 13.4 WGBS


title: Rp_H_5M_05

description: Pool of 10 CNS

value: 5 Months diapause


title: Rp_H_5M_04

description: Pool of 10 CNS


title: OKS_shYthdf3_D7_re1


title: OKS_shYthdf3_D1_re2

value: day 1


title: Rp_H_5M_03

description: Pool of 10 CNS


title: OKS_shYthdf3_D1_re1


title: 4.4 ATAC

data_processing:
Paired-end reads were trimmed using Trimmomatic v0.36 to remove NexteraPE adapters, low quality bases using a slidding 3-basepair window cutting when average basepair quality was less than 20, and removing reads less the 30 bp.
Remaining reads were mapped to the Stettler14 genome using bowtie v1.1.1 using default parameters.
Peaks were called using Macs2 v2.1.2 without an input control sample; parameters used were calling broad peaks, q-value cutoff 0.01, broad cutoff 0.01, and effective genome size of 392e6.
Genome_build: Populus trichocarpa Stettler 14 v1.1
Supplementary_files_format_and_content: <chromosome> <start; 1-index> <end; 1-index> <peak name> <score; -10 * log10(qvalue)> <strand> <-log10(pvalue)> <-log10(qvalue)>

growth_protocol: Leaves were collected from wild Populus trichocarpa tree in Orgegon.

extract_protocol: After collection, leaves were and immediately flash-frozen with liquid N2. ATAC-seq libraries were prepared following the ATAC-seq protocol as previously described in (Lu et al. 2016).


title: 4.3 ATAC


title: Rp_H_5M_02

description: Pool of 10 CNS


title: Rp_H_5M_01

description: Pool of 10 CNS


title: OKS_shYthdf2_D7_re2


title: uLGNET #5

type: genomic

city: Stanford

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.28.4) in R. The detection p-value for each sample was computed. All samples had detection p values less than 0.002. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: low-grade neuroepithelial tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25).  Genomic DNA was extracted from these punches using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered.  No ex vivo culture or xenografting was performed.

value: male

value: low-grade neuroepithelial tumor tissue


title: 14.5 r1 mRNA


title: OKS_shYthdf2_D7_re1


title: Rp_H_4M_05

description: Pool of 10 CNS

value: 4 Months diapause


title: 1.1 ATAC


title: 4.2 ATAC


title: 4.5 ATAC


title: OKS_shYthdf2_D5_re2


title: EVN #2


title: uLGNET #2

value: female


title: Rp_H_4M_04

description: Pool of 10 CNS


title: EVN #1


title: 14.5 ATAC


title: 14.4 ATAC


title: OKS_shYthdf2_D3_re2


title: Rp_H_4M_03

description: Pool of 10 CNS


title: Rp_H_4M_02

description: Pool of 10 CNS


title: 14.3 ATAC


title: OKS_shYthdf2_D3_re1


title: PA #8


title: uLGNET #4


title: uLGNET #1


title: PA #3


title: DNT #2


title: Rp_H_4M_01

description: Pool of 10 CNS


title: uLGNET #3


title: 14.2 ATAC


title: DNT #1


title: DNT #5


title: OKS_shYthdf2_D1_re2


title: OKS_shYthdf2_D5_re1


title: PA #6


title: 13.5 ATAC


title: Rp_H_3M_04

description: Pool of 10 CNS

value: 3 Months diapause


title: OKS_shLuc_D7_re2


title: PA #5


title: DNT #3


title: PA #7


title: PA #4


title: Rp_H_3M_05

description: Pool of 10 CNS


title: YT30: fused cell_rep9

first: YONAS

last: TEKLE

address: 350 Spelman Ln SW

institute: Spelman College

data_processing:
HiSeq 2500 for sequencing
Sequenced reads were quality checked and trimmed for adaptor sequence, and masked for low-quality sequence using FastQC and Bbduk
Program Kallisto was used to map the reads to the transcriptome for transcript quantification
Genome_build: Transcriptome was assembled de novo using rnaSPAdes
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Cochliopodium minus

source_name: Cell

growth_protocol: Cultures were maintained until they reached maximum-growth density that we have consistently achieved in our laboratory cultures

extract_protocol:
RNA was isolated from cells using NucleoSpin® RNA kit
libraries were prepared for sequencing using the Nextera® XT DNA Library Preparation Kit

treatment_protocol: Individual cells (unfused or fused) were picked using a platinum wire loop (tip) or mouth pipetting techniques and transferred to a clean glass slide or sterile agar medium to wash off bacteria from the amoeba

value: fused


title: Rp_H_3M_02

description: Pool of 10 CNS

value: Hawthorn Tree


title: 13.4 ATAC


title: 14.1 ATAC


title: OKS_shYthdf2_D1_re1


title: DNT #4


title: OKS_shLuc_D7_re1


title: 13.3 smRNA

data_processing:
Raw reads were trimmed using Cutadapt v1.6 to remove adapters and only keep reads that were 18 - 30 bp in length.
Remaining reads were mapped to the Stettler14 genome using Bowtie2 v2.2.3 with the very-sensitive-local parameter.
Genome_build: Populus trichocarpa Stettler 14 v1.1
Supplementary_files_format_and_content: <chromosome> <position, 1-indexed> <strand> <Count> <sequence; reverse complemented if minus strand> <sequence length>

extract_protocol: Total RNA was used as input for the TruSeq Small RNA Sample Prep Kit (Illumina) following manufacturer's instructions.


title: YT29: fused cell_rep8


title: Rp_H_3M_01

description: Pool of 10 CNS


title: RGNT #10


title: OKS_shLuc_D5_re2


title: YT28: fused cell_rep7


title: OKS_shLuc_D5_re1


title: Rp_H_2M_05

description: Pool of 10 CNS

value: 2 Months diapause


title: 13.1 smRNA


title: OKS_shLuc_D3_re2


title: 13.2 smRNA


title: Rp_H_3M_03

description: Pool of 10 CNS

value: USA:Urbana Illinois


title: YT27: fused cell_rep6


title: YT26: fused cell_rep5


title: PA #2


title: Rp_H_2M_04

description: Pool of 10 CNS

value: Pupa


title: 13.3 r3 mRNA


title: Rp_H_2M_03

description: Pool of 10 CNS


title: 13.3 r2 mRNA


title: RGNT #7


title: RGNT #5


title: OKS_shLuc_D1_re2

value: reprogramming cells


title: YT24: unfused cell_rep10

value: unfused


title: OKS_shLuc_D3_re1


title: OKS_shLuc_D1_re1


title: Rp_H_2M_02

description: Pool of 10 CNS


title: Rp_A_6M_05

description: Pool of 10 CNS

value: Apple Tree

value: 6 Months diapause


title: RGNT #9


title: 13.3 r1 mRNA

value: leaf


title: 13.2 r3 mRNA


title: YT22: unfused cell_rep8


title: YT23: unfused cell_rep9


title: Rp_H_2M_01

description: Pool of 10 CNS


title: PA #1


title: 13.2 r2 mRNA


title: OKS_shYthdf3_D7_ATAC_seq

value: day 7


title: YT25: unfused cell_rep11


title: RGNT #6


title: RGNT #8


title: Rp_A_6M_03

description: Pool of 10 CNS


title: Rp_A_6M_04

description: Pool of 10 CNS


title: 13.2 r1 mRNA


title: 13.1 r3 mRNA


title: OKS_shYthdf3_D3_ATAC_seq

value: day 3


title: YT20: fused cell_rep4


title: OKS_shYthdf3_D5_ATAC_seq

value: day 5


title: OKS_shYthdf3_D1_ATAC_seq

value: day 1


title: Rp_A_6M_02

description: Pool of 10 CNS


title: YT19: fused cell_rep3


title: 13.1 r1 mRNA


title: OKS_shYthdf2_D7_ATAC_seq


title: 13.1 r2 mRNA


title: Rp_A_6M_01

description: Pool of 10 CNS


title: 13.3 WGBS


title: Rp_A_5M_05

description: Pool of 10 CNS

value: 5 Months diapause


title: YT17: unfused cell_rep7


title: OKS_shYthdf2_D3_ATAC_seq


title: Rp_A_5M_04

description: Pool of 10 CNS


title: OKS_shYthdf2_D5_ATAC_seq


title: 13.2 WGBS


title: YT16: unfused cell_rep6


title: YT15: unfused cell_rep5


title: Rp_A_5M_03

description: Pool of 10 CNS


title: OKS_shYthdf2_D1_ATAC_seq


title: 13.1 WGBS


title: YT18: fused cell_rep2


title: YT14: unfused cell_rep4


title: OKS_shLuc_D7_ATAC_seq


title: Rp_A_5M_02

description: Pool of 10 CNS


title: OKS_shLuc_D5_ATAC_seq


title: 13.3 ATAC


title: YT13: fused cell_rep1


title: RGNT #2

value: female

value: low-grade neuroepithelial tumor tissue


title: Rp_A_5M_01

description: Pool of 10 CNS


title: OKS_shLuc_D3_ATAC_seq


title: YT12: unfused cell_rep3


title: Rp_A_4M_05

description: Pool of 10 CNS

value: 4 Months diapause


title: RGNT #1

value: male


title: 13.1 ATAC


title: OKS_shLuc_D1_ATAC_seq


title: YT07: unfused cell_rep2


title: BD_ICM_Dnmt3aMatKO_RNA_rep2

city: Vancouver

first: Matthew

last: Lorincz

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

institute: University of British Columbia

description: strand-specific RNAseq

data_processing:
Reads were trimmed using Trimmomatic v0.32
Trimmed reads were aligned to the mm10 reference genome and a diploid pseudogenome using MEA and default parameters (Richard Albert et al. 2018)
RNA-seq: PCR duplicates and multi-aligned reads (q<255) were filtered out using Picard tools v1.92 and samtools v1.1
WGBS: PCR duplicates were filtered out using Picard tools v1.92 and samtools v1.1
Aligned read maps were converted to Wiggle format using bedtools v2.22.1 and bedGraphToBigWig (UCSC).
RNA-seq: total and allele-specific tracks were normalized by the number of uniquely aligned total reads
Genome_build: mm10
Supplementary_files_format_and_content: 3x bigWigs (total, maternal, paternal)

extract_protocol:
Cumulus cells were removed using hyaluronidase after insemination and embryos were cultured in KSOM at 37oC and 5% CO2. Total RNA was extracted from 2-7 pooled blastocysts using Trizol reagent. ICM cells were purified by immunodissection using anti-mouse IgG (Cedarlane) and guinea pig complement (Rockland).
Strand-specific RNA-seq libraries were generated using NEBNext: rRNA Depletion Kit, RNA First Strand Synthesis Module, Ultra Directional RNA Second Strand Synthesis Module, and Ultra II DNA Library Prep Kit. Libraries were sequenced on HiSeq 1500 or HiSeq 2500

tag: strain background

value: C57BL/6J x DBA/2J F1 hybrid

tag: developmental stage

value: inner cell mass of the blastocyst

tag: genotype/variation

value: Dnmt3a2lox;Zp3-cre x WT


title: YT06: unfused cell_rep1

city: Atlanta


title: Rp_A_4M_04

description: Pool of 10 CNS

value: USA:Urbana Illinois

value: Pupa


title: Con_3

city: Lebanon

first: Britton

middle: C

last: Goodale

state: NH

address: 1 Medical Center Drive

department: Dartmouth Cancer Center

institute: Geisel School of Medicine at Dartmouth

data_processing:
Demultiplexing and barcode processing of raw sequencing data was conducted by the Dartmouth Genomics Shared Resource Core using Cell Ranger v. 3.0.1 (10X Genomics). Reads were aligned to mouse (GRCm38) and influenza A virus (A/PR8/34, genome build GCF_000865725.1) genomes to generate unique molecular index (UMI) count matrices.
Filtered count matrices were further analyzed in the R statistical working environment (version 3.6.1) with Seurat (v. 3.1.1) and the percentage of mitochondrial, hemoglobin, and influenza A transcripts calculated per cell. Cells were filtered from analysis if they had < 1000 or > 20,000 UMIs, expressed fewer than 300 features, greater than 10% of reads mapped to mitochondrial genes, or if greater than 1% of reads mapped to hemoglobin genes.
Data were then normalized using SCTransform (Hafemeister et al., 2019) and variable features identified for each sample. Integration anchors between samples were identified using canonical correlation analysis (CCA) and mutual nearest neighbors (MNNs), as implemented in Seurat V3 and used to integrate samples into a shared space for further comparison.
Principal components were identified from the integrated dataset and were used for Uniform Manifold Approximation and Projection (UMAP) visualization of the data in two-dimensional space. A shared-nearest-neighbor (SNN) graph was constructed using default parameters, and clusters identified using the SLM algorithm in Seurat at a range of resolutions (0.2-2).
Genome_build: GRCm38,  GCF_000865725.1
Supplementary_files_format_and_content: matrix.mtx files contain filtered matrices of UMI counts produced by CellRanger pipeline in sparse matrix format. Barcodes.tsv files contain column (cell) metadata, features.tsv files contain row (gene) metadata.

source_name: lung

growth_protocol: Mice were housed on Carefresh bedding (International Absorbents, Inc., Ferndale, WA) in autoclaved cages and fed TEK-LAD AIN-76A diet (Envigo, Madison, WI) ad libitum.

extract_protocol:
Lungs were perfused with PBS, collected, and whole lung strained through 70- and 30-µm filters to obtain a single-cell suspension. Dead cells were removed (annexin V EasySep kit, StemCell Technologies), and samples were enriched for CD45+ cells by magnetic separation with CD45 microbeads (Miltenyi). Single-cell suspensions of 6 samples were loaded on a Chromium Single Cell system (10X Genomics) to generate single cell libraries.
Libraries were constructed using Single Cell 3’ Version 2 chemistry (10X Genomics). Libraries were multiplexed and sequenced on 4 lanes of a Nextseq 500 sequencer (Illumina).

treatment_protocol: Mice were placed into breeding pairs and when female mice showed cervical plug formation, mice in the arsenic treatment group were given drinking water with 100ppb sodium arsenite ad libitum. Arsenic was removed from drinking water when pups were born, and F1 pups were allowed to mature to adulthood (7-8 weeks). Adult female mice were matched for body weight, anesthetized with ketamine/xylazine and inoculated intranasally with 0.5 LD50 of influenza A/PR8/34. Morbidity was monitored until sacrifice at day 3 of infection by daily measurement of weight loss.

value: CD45+ lung cells

tag: virus strain

value: influenza A/PR8/34

tag: age

value: 7-8 weeks

value: control


title: Rp_A_4M_03

description: Pool of 10 CNS

value: Apple Tree


title: As_3

tag: cell type

value: 100ppb sodium arsenite


title: BD_ICM_Dnmt3aMatWT_RNA_rep2

description: strand-specific RNAseq

value: Dnmt3a2lox x WT


title: 13.2 ATAC

tag: tissue

value: leaf


title: BD_ICM_Dnmt3aMatKO_RNA_rep1

description: strand-specific RNAseq


title: Rp_A_3M_05

description: Pool of 10 CNS

value: 3 Months diapause


title: BD_4C_Dnmt3aMatKO_RNA_rep2

description: strand-specific RNAseq

extract_protocol:
Cumulus cells were removed using hyaluronidase after insemination and embryos were cultured in KSOM at 37oC and 5% CO2. Total RNA was extracted from 5-10 pooled 4 cell embryos using Trizol reagent.
Strand-specific RNA-seq libraries were generated using NEBNext: rRNA Depletion Kit, RNA First Strand Synthesis Module, Ultra Directional RNA Second Strand Synthesis Module, and Ultra II DNA Library Prep Kit. Libraries were sequenced on HiSeq 1500 or HiSeq 2500

value: 4 cell embryo


title: Rp_A_4M_01

description: Pool of 10 CNS

value: 4 Months diapause


title: Δflo8_0.1_switchback_rep1

data_processing:
BAM Quality Assesment with QualiMap (v2.2.1)
Alignment to reference with BWA_MEM (v0.7.13)
Conversion, Sorting of resulting SAM-Files with samtools (v1.3)
Peak calling with zinba (v2.02.03)
Genome_build: K.phaffii CBS7435 (FR839628.1, FR839629.1, FR839630.1, FR839631.1, FR839632.1)
Supplementary_files_format_and_content: BED, called peaks

source_name: delta-flo8; Steady state sample at µ=0.1 h-1

growth_protocol: For formaldehyde fixation of samples for FAIRE-Seq, first the OD600 of the culture was measured. Then fixation solution was prepared in a 500 mL shake flask which contained 100 mL PBS with 1% formaldehyde per 50 OD600 units of cells to be fixed. The required amount of bioreactor culture was drawn and directly added to the fixation solution. The flask was shaken at room temperature for about 30 mins, after which the formaldehyde was quenched by addition of 500 mM Tris-Cl (pH 8.0) and shaking for 5 mins. Finally, cells were harvested, washed with PBS and stored at -80°C.

extract_protocol:
The formaldehyde-fixed cells were thawed and resuspended in 1 mL lysis buffer and transferred to 2 mL screwcap tubes containing 500 µL of acid-washed 500 µm glass beads. Cells were lyzed in a FastPrep®-24 equipment (MP Biomedicals) for 5X 40 sec cycles, with 2 min rest in between. The lysate was transferred to a 15 mL conical tube. The glass beads were washed with an additional 600 µL lysis buffer which was then added to the same conical tube. The lysate was sonicated in a Bioruptor® Plus (Diagenode) for 10 cycles (30 sec on/ 30 sec off) at high power setting. The sonicated lysate was clarified by centrifugation at 10,000X g for 5 mins and around 150 µL of this clarified lysate was removed for preparation of input control DNA. The remaining lysate was aliquoted into fresh 1.5 mL tubes. 1 volume of Phenol/Chloroform/Isoamyl alcohol was added to them, vortexed vigorously and centrifuged at full speed for 10 mins and the top layer was transferred to a fresh tube. This was repeated one more time after which 200 µL of Chloroform/isoamyl alcohol was added to each tube to remove any remnant phenol. The tubes were vortexed, centrifuged and the aqueous layer transferred to a fresh tube. 1/10 volume 3M sodium acetate (pH 5.2), 2 volumes 95% ethanol and 1 µL 20 mg/mL glycogen was added to each tube and the tubes were incubated at -80°C overnight. The tubes were centrifuged at full speed for 20 mins to precipitate the DNA, after which the pellets were washed with 75% ice-cold ethanol and centrifuged again for another 10 mins. Finally, the ethanol was removed and the pellets dried and resuspended in 50 µL 10 mM Tris-HCl (pH 7.4). These FAIRE samples were treated with DNase-free RNase A (30 mins, 37°C), Proteinase K (1 h, 55°C) and finally incubated overnight at 65°C for decrosslinking. For preparation of input control DNA, the 150 µL clarified lysate removed after sonication was first treated with DNase-free RNase A, Proteinase K and decrosslinked overnight at 65°C before proceeding with Phenol/Chloroform/Isoamyl alcohol extraction as described for the FAIRE samples. Both the FAIRE DNA and input control DNA were further purified using MinElute PCR purification kit (Qiagen) and quantified.
NEB DNA library preparation kit

tag: genotype


title: Input control 1

source_name: WT;Input Control

value: Wild type


title: BD_ICM_Dnmt3aMatWT_RNA_rep1

description: strand-specific RNAseq

value: C57BL/6J x DBA/2J F1 hybrid


title: RGNT #3

tag: gender

value: female

value: low-grade neuroepithelial tumor tissue


title: RGNT #4

value: male


title: Input control 2

source_name: delta-flo8;Input Control

tag: strain


title: Rp_A_4M_02

description: Pool of 10 CNS

value: USA:Urbana Illinois

value: Pupa


title: WT_0.1_switchback_rep2

source_name: WT; Steady state sample at µ=0.1 h-1


title: Con_2

value: CD45+ lung cells

value: influenza A/PR8/34

tag: treatment


title: As_1

value: 7-8 weeks


title: BD_4C_Dnmt3aMatKO_RNA_rep1

description: strand-specific RNAseq

value: Dnmt3a2lox;Zp3-cre x WT


title: As_2

value: 100ppb sodium arsenite


title: BD_4C_Dnmt3aMatWT_RNA_rep2

description: strand-specific RNAseq

value: Dnmt3a2lox x WT


title: Δflo8_0.05_rep1

source_name: delta-flo8; Steady state sample at µ=0.05 h-1


title: Rp_A_3M_03

description: Pool of 10 CNS

tag: host

value: Apple Tree


title: Rp_A_3M_04

description: Pool of 10 CNS

tag: diapause age

value: 3 Months diapause


title: P8 MG ATAC

city: Seattle

first: Thomas

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structure

institute: University of Washington

description: transposase-digested DNA

data_processing:
ATAC filtration:  Adapter and barcode sequence were removed from the reads and low-quality sequences (Phred score <33) were removed using Trim Galore (Krueger 2015)
ATAC mappting: Remaining reads were mapped using Bowtie2 (Langmead and Salzberg 2012), marking duplicate reads with Picard (http://broadinstitute.github.io/picard/), and removing reads using Samtools (Li et al. 2009).
ATAC-seq peak calling: Peaks were called using HOMER (Heinz et al. 2010) findPeaks dnase style with a minimum distance of 415 and size of 150.
ATAC peak overlaps: Bedops -e 1 function was used to compare peak files for overlaps between samples(Neph et al. 2012)
RNA-seq mapping: Reads that passed Illumina’s base call quality filter were mapped to mm10 using TopHat v2.0.12
RNA-seq counts: To generate counts for each gene using htSeq-count v0.6.1p1, in “intersection-strict” overlap mode, genes with zero counts across all samples were removed, and data normalized using edgeR v3.12.0.
RNA-seq thin counts:  Further analysis was done using Bioconductor and R (version 3.2.3).  Prior to testing, samples with higher reads were thinned to the level of other samples using thinCounts.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files in bed or xlsx file format

source_name: Retinal Müller glia

extract_protocol:
Retinas were isolated via dissection away from surrounding tissues and then washed in PBS. Fluorescence was confirmed via live imaging under an inverted fluorescent microscope (Zeiss). Retinas were then incubated on a nutator in Papain and DNase I for 10 min at 37 °C. Retinas were then triturated to generate a single-cell suspension and transferred to a tube containing an equal volume of Ovomucoid. The suspension was then spun down at 300g for 10 min at 4 °C. Cells were resuspended in a solution of 100:1:1 Neurobasal:DNase:Ovomucoid, and passed through a 35 μm filter before sorting using a BD FACSAria III Cell Sorter (BD Biosciences). Gating was performed to isolate intact cells from debris and to isolate positive fluorescent glial or progenitor cells. Progenitor cells were isolated from Sox2+ Amacrine cells by removing the higher fluorescent neuronal population. Positive fractions containing fluorescently labelled MG were then spun down at 300g and resuspended for the appropriate assay.
Purified cells from live-cell FACS were input into a 15 μl transposase reaction with an input of 100k cells in a protocol modified from the Greenleaf lab (Buenrostro et al. 2015).  Transposition was carried out with reagents from the Nextera DNA Sample prep kit: 7.5 μl 2X TD Buffer, 0.75 μl Tn5 Transposases, and nuclease-free water to 15 μl. The reaction was mixed and incubated at 37 °C for one hour before being purified with the Qiagen Reaction Cleanup Minelute kit and eluted into 10 μl.
ATAC libraries were prepared through subsequent PCR using Illumina Nextera kit (Cat. No. FC-121-1030) using a test qPCR output to estimate the number of cycles necessary to properly amplify the library. Amplified libraries were purified with the Qiagen PCR cleanup minelute kit and eluted into 20 μl. Library QC was performed using gel electrophoresis, and quantitated on a Qubit 3.0 Fluorometer with the dsDNA HS Assay kit and A260/280 and A260/230 checked by nanodrop before sending for Illumina NextGen sequencing on a Next Seq 500 in rapid mode employing a paired-end 50 base read length sequencing strategy (Seattle Genomics). RNA-seq libraries were prepared for sequencing using standard Illumina protocols

value: rlbp-creER;flox-stop-tdtomato


title: Rp_A_3M_02

description: Pool of 10 CNS

tag: location


title: Con_1

value: control


title: P2 Progenitor ATAC rep 2

description: transposase-digested DNA

source_name: Retinal Progenitor cells


title: BD_2C_Dnmt3aMatKO_RNA_rep2

description: strand-specific RNAseq

extract_protocol:
Cumulus cells were removed using hyaluronidase after insemination and embryos were cultured in KSOM at 37oC and 5% CO2. Total RNA was extracted from 20-40 pooled 2 cell embryos using Trizol reagent.
Strand-specific RNA-seq libraries were generated using NEBNext: rRNA Depletion Kit, RNA First Strand Synthesis Module, Ultra Directional RNA Second Strand Synthesis Module, and Ultra II DNA Library Prep Kit. Libraries were sequenced on HiSeq 1500 or HiSeq 2500

value: early-mid 2 cell embryo


title: P2 Progenitor ATAC rep 1

description: transposase-digested DNA


title: WT_0.05_rep2

source_name: WT; Steady state sample at µ=0.05 h-1

value: Wild type


title: BD_4C_Dnmt3aMatWT_RNA_rep1

description: strand-specific RNAseq

value: C57BL/6J x DBA/2J F1 hybrid

value: 4 cell embryo


title: Rp_A_3M_01

description: Pool of 10 CNS

tag: lifestage


title: Rp_A_2M_05

description: Pool of 10 CNS

value: 2 Months diapause

tag: collection year


title: WT_0.05_rep1


title: BD_2C_Dnmt3aMatWT_RNA_rep2

description: strand-specific RNAseq


title: Δflo8_0.1_rep1


title: Rp_A_2M_04

description: Pool of 10 CNS

value: USA:Urbana Illinois


title: HiChIP-Gata1-EryD-Rep2

city: Boston

first: Jialiang

last: Huang

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
Library strategy: HiChIP
ATAC-seq reads were trimmed for adapter sequences and low alignment quality using Cutadapt (Martin, 2011), with the parameters -q 30 --minimum-length 36. Paired-end reads were aligned to the mm10 reference genome by using Bowtie2 (Langmead et al., 2009), with the parameter -X 2000 allowing fragments of up to 2 kb to be aligned (Buenrostro et al., 2015). ATAC-seq peaks were called using MACS2 (Zhang et al., 2008) with following parameters (--nomodel --nolambda --keep-dup all --call-summits) (Buenrostro et al., 2015). Peak calling was done in two biological replicates respectively with the same parameter settings. One replicate of each cell type was used for subsequent analysis. We then extended the summits to 500-bp window (±250 bp) as peaks and filtered using the consensus excludable ENCODE blacklist (Consortium, 2012).
HiChIP datasets were processed using HiC-Pro (Mumbach et al., 2016; Mumbach et al., 2017; Servant et al., 2015) with default settings. Specifically, HiChIP paired-end reads were aligned using Bowtie2 with –very-sensitive -L 30 –score-min L, -0.6, -0.2 --end-to-end –reorder. The restriction sites were obtained by scanning MboI restriction fragments across mouse genome (mm10). Specific configuration file (config-hicpro.txt) can be found at https://bitbucket.org/qzhu/wenqing-hichip/src/default/hicpro/config-hicpro.txt. Valid interactions pairs (named valid Pairs) were converted to a .hic file using hicpro2juicebox.sh script (utility tool of HiC-Pro). The generated .hic file contains interaction matrices at fragment and base pair resolutions. Interaction maps were visualized with Juicebox (Durand et al., 2016a). The HiCCUPS function of Juicer-tools 1.7.6 was used to call high-confidence loops based on a .hic file (Rao et al., 2014). We set -m 512 -r 5000,10000,25000 -f 0.2,0.2,0.2 -p 4,2,1 -k VC_SQRT -i 7,5,3 -d 20000,20000,50000 --ignore_sparsity -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y -t 0.02,1.5,1.75,2. This combination of settings finds loops at the 5-kb, 10-kb, and 25-kb resolutions using the interaction matrices at matched resolutions, and also applied the appropriate normalization step for interaction matrix (vanilla coverage square-root, VC SQRT). Loops at these resolutions were subsequently merged.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig  generated using macs2 pileup, following by bedGraphToBigWig; Peak  were called using MACS2

source_name: Definitive erythroblast

growth_protocol: EryP was collected from peripheral blood of E10.5 mouse embryos in HBSS supplemented with 10% FBS and 0.25% EDTA. EryD was collected by mechanically dissociation of E13.5 whole fetal liver. All mouse embryos were obtained from C57BL/6 mouse. MEL cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2mM L-glutamine and Penicillin and Streptomycin. 2% DMSO in culture medium was used to induce MEL cells differentiation. Medium was changed on differentiation day 3.

extract_protocol:
HiChIP was performed as previously described (Mumbach et al 2016) using the Gata1 antibody (ab11852, Abcam). In brief, 15 million of either peripheral blood cells of E10.5 mouse embryos or single cells of E14.5 fetal liver were cross-linked with 1% v/v formaldehyde at room temperature for 10 minutes, and were quenched with 0.125 M Glycine for 5minutes. Crosslinked cells were lysed in cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40, 1x Roche protease inhibitors) and followed by 1 U/ul MboI (NEB) digestion at 37oC for 6 h, fill-in of overhangs with biotin-dATP (Thermo Fisher) at 37oC for 1.5 h, and ligation with 4 U/ul T4 DNA Ligase (NEB) at room temperature for 6 h. The nuclear pellet was sheared using a Covaris E220 with following parameters: Duty Factor = 5.0, Peak Power = 140, Cycle/Burst = 200, Time = 240 seconds. Chromatin extracts were immunoprecipitated with Gata1 antibodies overnight at 4oC, and then incubated with protein A Dynabeads (Invitrogen) for another 4 hours. ChIP complexes were eluted and cross-linking reversed by heating at 65oC overnight. DNA was extracted with DNA Clean and Concentrator columns (Zymo Research).
ATAC-seq was performed as described (Buenrostro et al., 2013) on FACS isolated EryP and EryD cells. 2.5 x 104 cells were used per sample. 2.5 l Tn5 Transposases (Illuminar) was used to make the transposition reaction. Libraries were generated using Ad1_noMX and Ad2.1-2.4 barcoded primers (Buenrostro et al., 2013) and were amplified for 6-9 total cycles. All libraries were sequenced on Illumina HiSeq2000 with 100 bp paired-end reads. HiChIP was performed as previously described (Mumbach et al., 2016) using the Gata1 antibody (ab11852, Abcam). In brief, 15 million of either peripheral blood cells of E10.5 mouse embryos or single cells of E14.5 fetal liver were cross-linked with 1% v/v formaldehyde at room temperature for 10 minutes, and were quenched with 0.125 M Glycine for 5minutes. Crosslinked cells were lysed in cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40, 1x Roche protease inhibitors) and followed by 1 U/l MboI (NEB) digestion at 37oC for 6 h, fill-in of overhangs with biotin-dATP (Thermo Fisher) at 37oC for 1.5 h, and ligation with 4 U/l T4 DNA Ligase (NEB) at room temperature for 6 h. The nuclear pellet was sheared using a Covaris E220 with following parameters: Duty Factor = 5.0, Peak Power = 140, Cycle/Burst = 200, Time = 240 seconds. Chromatin extracts were immunoprecipitated with Gata1 antibodies overnight at 4oC, and then incubated with protein A Dynabeads (Invitrogen) for another 4 hours. ChIP complexes were eluted and cross-linking reversed by heating at 65oC overnight. DNA was extracted with DNA Clean and Concentrator columns (Zymo Research).   For library preparation, Biotin labeled post-ChIP DNA was captured by 5 l Streptavidin C-1 beads (Thermo Fisher), and followed by Tn5 treatment. The amount of Tn5 used and the number of PCR cycles performed was based on the post-ChIP Qubit amounts, as previously described (Mumbach et al., 2016). HiChIP libraries were size-selected for 300-800bp fragments. All libraries were sequenced on the Illumina Nextseq 500 to an average depth of 200 million total reads.

value: erythroblast

tag: chip antibody


title: Δflo8_0.1_rep2


title: HiChIP-Gata1-EryD-Rep1


title: BD_2C_Dnmt3aMatKO_RNA_rep1

description: strand-specific RNAseq

tag: strain background


title: Rp_A_2M_03

description: Pool of 10 CNS

value: Pupa


title: WT_0.1_switchback_rep1


title: BD_2C_Dnmt3aMatWT_RNA_rep1

description: strand-specific RNAseq

tag: developmental stage


title: Rp_A_2M_02

description: Pool of 10 CNS


title: HiChIP-Gata1-EryP-Rep2

source_name: Primitive erythroblast


title: WT_0.1_rep2

source_name: WT ; Steady state sample at µ=0.1 h-1


title: BD_2C_Dnmt3aMatKO_DNAme_rep2

description: Post-Bisulfite Adaptor Tagging (PBAT)

extract_protocol:
Cumulus cells were removed using hyaluronidase after insemination and embryos were cultured in KSOM at 37oC and 5% CO2. Zona pellucida and polar bodies of 2C embryos were removed.
DNA from 20-30 pooled 2C embryos per replicate was purified and spiked with 1% unmethylated lambda phage DNA, and WGBS libraries were generated by PBAT with 4 cycles of library amplification (Au Yeung et al. 2019, Miura et al. 2012).

tag: genotype/variation

tag: molecule subtype

value: bisulphite converted genomic DNA


title: HiChIP-Gata1-EryP-Rep1


title: WT_0.1_rep1


title: BD_2C_Dnmt3aMatWT_DNAme_rep2

description: Post-Bisulfite Adaptor Tagging (PBAT)