title: SLE_GM12878_3

city: Cincinnati

first: Xiaoming

last: Lu

state: Ohio

address: 3333 Burnet Ave

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Library strategy: Massively parallel reporter assay (MPRA)
Paired-end, 125 bp reads were first quality filtered through Trimmomatic-0.3864 (flags: PE -phred33, LEADING:25, TRAILING:25, MINLEN:80). Read 1 was then separated into the 20bp barcode region and the oligo-matching region. The trimmed oligo-matching region of Read 1 and Read 2 were mapped back to the synthesized oligo sequences using Bowtie265 (flags: -X 250, --very-sensitive, -p 16). Barcodes were then associated with the oligo sequences using the read ID. Only uniquely mapped barcodes were used for downstream analysis.
Single end reads were first quality filtered using Trimmomatic-0.3864 (flags: PE -phred33, LEADING:3, TRAILING:3, MINLEN:70). Each read was then separated into the 20bp barcode region and the constant region. The trimmed constant regions of the reads were mapped back to the constant regions within the GFP 3’ UTR using Bowtie265 (flags: --very-sensitive, -p 16). Only reads with Levenshtein distance of 4 or less within the constant region and perfect matches to the two bases directly adjacent to the barcode were kept. Barcodes were then associated with the retained reads using the read ID. Only barcodes that met our quality threshold requirements were used for downstream analysis.
We followed the procedures described in the “Identification of Regulatory Oligos” section of Tewhey et al (PMID: 27259153) with minor modifications. In brief, oligos (alleles) with 30 or more unique barcodes from the plasmid control were included for analysis. Barcode count totals for each oligo, including SLE variants and the 20 control variants, were passed into DESeq2 (R version 3.5.367) to estimate the fold change and significance between plasmid controls and the triplicate experiments. An adjusted p-value of less than 0.05 was required for significance. Only significant alleles with greater than or equal to a 1.5x fold change were identified as enhancer alleles (enAlleles). A variant was identified as an enhancer variant (enVar) if any allele of this variant was an enAllele. Results for the 20 control variants were compared to data from Tewhey et al (PMID: 27259153) to estimate accuracy, sensitivity, and specificity.
Only enVars were considered for allelic analysis. The barcode counts from every allele of enVars were used for calculating p-values by comparing the log2 ratios of the non-reference allele vs the reference allele, normalized by plasmid controls, using Student’s t-test (PMID: 27259153). P-values were adjusted with the Benjamini-Hochberg FDR-based procedure. A corrected p-value of less than 0.05 was required for significance. Only significant alleles with 25%-fold changes or greater were identified as allelic enVars. We have created an R package (mpraprofiler) for performing this analysis, which is available on the Weirauch lab GitHub page (https://github.com/WeirauchLab/).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file: barcodes and count for each element, enhancer sequences. xlsx: summarized counts from all data

source_name: EBV transformed B cell line

growth_protocol: GM12878 cell line was grown in RPMI medium supplemented with 10% FBS, 100 units/mL of penicillin, and 100 µg/mL of streptomycin. Cells were seeded at a density of 5 x 10E5 cells/mL the day before transfection

extract_protocol:
Total RNA of transfected cells was extracted by the RNeasy Midi Kit following the manufacturer’s instructions.
Extracted RNA was subjected to DNase treatment in a 375 uL system with 2.5 uL Turbo DNase, and 37.5 uL Turbo DNase Buffer at 37°C for 1 hr.  3.75 uL 10% SDS and 37.5 uL 0.5M EDTA was added to stop DNase with 5 mins of incubation at 75°C. The whole volume was used for eGFP probe hybridization in an 1800 uL system, with 450 ul 20X SSC Buffer, 900 uL Formamide, and 1 uL of each 100 uM Biotin-labeled GFP probe One to Three. The probe hybridization was performed through incubation at 65°C for 2.5 hrs. 200 ul Dynabeads™ MyOne™ Streptavidin C1 was prepared according to the manufacturer’s instructions. The beads were suspended in 250 uL 20X SSC Buffer and incubated with the above probe hybridization reaction at room temperature for 15 mins. Beads were then collected on a magnet and washed with 1X SSC Buffer once, and 0.1X SSC Buffer twice. eGFP mRNA was eluted first through adding 12.5 uL ddH2O, heating at 70°C for 2 mins and collecting on a magnet, then adding another 12.5 uL ddH2O, heating at 80°C for 2 mins and collecting on a magnet. All collected elution was performed with another DNase treatment in a 30 uL system containing 0.5 uL Turbo DNase, and 3 uL Turbo DNase Buffer at 37°C for 1 hr.  0.5 uL 10% SDS was added to halt DNase reactions. Eluted mRNA was purified through RNA Clean SPRI Beads. mRNA was reverse transcribed to cDNA using SuperScript™ IV First-Strand Synthesis System with specific primer MPRA_v3_Amp2Sc_R, following the manufacturer’s instructions. cDNA and plasmid control were then used for building sequencing libraries following Tag-seq Library Construction section in the paper of Tewhey et al (PMID: 27259153). A total of two PCR rounds were needed for building the sequencing library. The first PCR was performed with TruSeq_TruSeq_Universal_Adapter_P5 and MPRA_V3_Illumina_GFP_F. The second PCR was performed with TruSeq_TruSeq_Universal_Adapter_P5 and index primer. Samples were purified, molar pooled and sequenced using Illumina 1x50/75bp on NextSeq 500.

treatment_protocol: For triplicate transfections, we collected a total of 5 x 10E7 cells per replicate. Cells were then suspended with 50 ug transfection library plasmid in 400 uL Buffer R. Electroporation was performed with the Neon transfection system in 100ul needles with 3 pulses of 1200V, 20 ms each. After transfection, cells were recovered in 50 mL pre-warmed RPMI medium supplemented only with 10% FBS for 24 hrs. Cells were then collected for preparation of the sequencing library for barcode counting.

tag: replicate

tag: disease state

value: Systemic Lupus Erythematosus (SLE)


title: SLE_GM12878_1

status: Public on Jan 31 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: SLE_GM12878_2


title: ES-KO

city: Brussels

first: Maud

last: de Dieuleveult

address: Route de Lennik 808

country: Belgium

institute: Free University of Brussels

description: 5hmC level in mouse embryonic stem cells knocked out for LSH

library_source: genomic

data_processing:
Library strategy: hMeDIP-Seq
The BWA software was used to map reads on mouse genome (NCBI 37; UCSC mm9). Reads not uniquely mapped to the reference genome were discarded.
sam files were converted into bam and sorted using samtools (version 1.3.1)
Duplicates reads (i.e. mapping to the same location) were removed using Picardtool MarkDuplicates (version 1.64)
For visualisation, bam were converted into bedgraph using bamTobw tool (https://github.com/YangLab/bamTobw)
Genome_build: NCBI 37; mm9
Supplementary_files_format_and_content: bedGraph file containing hmC enrichment profile across mm9 genome

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Embryonic Stem cell

growth_protocol: MEF (DMEM, 10%FBS, penicillin/streptomicin), ES (DMEM, 15%FBS, NEAA, 2mM L-Glu, penicillin/streptomicin, LIF, 100nM of β-mercaptoethanol)

extract_protocol:
Genomic DNA using the Qiagen-DNeasy Blood &Tissue Kit according to the supplier's instructions (Qiagen, Hilden, Germany). This included a proteinase K digestion at 55C overnight. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina)

tag: genotype

value: LSH Knock out

tag: cell type

value: Stem cell

tag: ip

value: hydroxymethylcytosine (5hmC)


title: ES-WT

description: 5hmC level in wild-type mouse embryonic stem cells

value: Wild type


title: MEF-WT

description: 5hmC level in wild-type mouse embryonic fibroblasts

source_name: Mouse Embryonic Fibroblasts

value: Fibroblast


title: MEF-KO

description: 5hmC level in mouse embryonic  fibroblasts knocked out for LSH


title: HB3clone2.7F-2_0714

type: RNA

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

hyb_protocol: Cy3 labeled cDNA was allowed to hybridize for 17 h to a custom Agilent microarray (GPL22280)  at 65°C at 10 rpm

scan_protocol: The microarray image was taken using a 2 μM scanner and probe intensity values were obtained using Agilent Feature Extraction software.

data_processing: Probe intensities for all samples were quantile normalized. Samples were visualized using Principle Component Analysis. Transcript expression levels were summarized for each gene by averaging the processed signal intensity of all the probes across its exons.

organism: Plasmodium falciparum

label_protocol: 1µg of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.

growth_protocol: The parasite strains HB3 and Dd2 were maintained in identical standard culture conditions in human red blood cells (Indiana Regional Blood Center, Indianapolis, Indiana) suspended in complete medium (CM) containing RPMI 1640 with L-glutamine (Invitrogen Corp.), 50 mg/L hypoxanthine (Sigma-Aldrich), 25 mM HEPES (Cal Biochem), 0.5% Albumax II (Invitrogen Corp.), 10 mg/L gentamicin (Invitrogen Corp.) and 0.225% NaHCO3 (Biosource) at 5% hematocrit. Cultures were grown separately in sealed flasks at 37˚C under an atmosphere of 5% CO2, 5% O2, and 90% N2. Replicated cultures were thawed and triple sorbitol synchronized. Total RNA was  collected at 24 hours post invasion (hpi).

extract_protocol: RNA was extracted using TriZol reagent (Invitrogen, Carlsbad, CA) and the quality and quantity determined by NanoDrop (NanoDrop Technologies). 300ng of RNA was used as starting material for cDNA synthesis using the Sigma WTA2 whole transcriptome amplification kit (Sigma Aldrich, St Louis, MO).

treatment_protocol: Culture were maintained under standard culture conditions.

tag: strain

tag: time point (hours post invasion)

tag: clone

tag: sub-clone

tag: culture date

tag: feplicate


title: HB3clone2.7F-1_0714


title: HB3clone2.7F_2.8B_0714


title: HB3clone2.7F_1.3F_0714


title: HB3clone2.7F_2.2E-1_0714


title: HB3clone2.7F_2.2E-2_0714


title: HB3clone2.7F_2.2E-3_0714


title: HB3clone2.7F_0313


title: HB3clone1.6A_0313


title: HB3clone2.1C-1_0714


title: HB3clone2.1C_061913


title: HB3clone2.1C_060513


title: HB3clone1.7F_0714


title: HB3clone2.1C-2_0714


title: HB3clone2.1C-3_0714


title: HB3clone1.6A_0714


title: HB3clone2.7F-3_0714


title: HB3clone1.7F_0313


title: Dd2clone1.2A_0714


title: HB3clone2.1C_0313


title: Dd2clone1.1F-0714


title: Dd2clone1.1F_0313


title: Dd2clone2.8E_0313


title: Dd2clone2.8E_0714


title: Dd2clone1.2A_0313


title: HB3_0313


title: Dd2clone1.10H-3_0714


title: HB3_0714


title: HB3clone2.7F_2.10D_0714


title: Dd2clone1.10H-2_0714


title: Dd2clone1.10H-1_0714


title: Dd2clone1.10H_2.9H-3_0714


title: Dd2clone1.10H_2.10E_0714


title: Dd2clone1.10H_1.1B_0714


title: 12W_C_04

city: Zuerich

first: Natalie

last: Russi

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich and ETH Zurich

data_processing:
Fastq files were generated with the illumina software bcl2fastq v2.19.05. All subsequent analyses were run through the Sushi web framework (Hatakeyama, M., Opitz, L., Russo, G., Qi, W., Schlapbach, R., & Rehrauer, H. (2016). SUSHI: An exquisite recipe for fully documented, reproducible and reusable NGS data analysis. BMC Bioinformatics, 17(1), 1–9.)
Reads were trimmed with trimmomatic (Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120.) to remove 3'-adapters
Reads were aligned with the STAR aligner v2.5.3a with the options '--twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes'
Strand-specific (reversely stranded) read counting was performed using featureCount (subread, version 1.2.6) (Liao, Y., Smyth, G. K., & Shi, W. (2013). The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10)).
Genome_build: Ensembl/Rnor_6.0
Supplementary_files_format_and_content: text files holding read counts per gene

organism: Rattus norvegicus

source_name: sham surgery_12wk_gray matter of spinal cord

extract_protocol:
RNA was extracted using the Nucleospin RNA XS kit (Macherey-Nagel, Germany). Briefly, tissue samples were lysed in 1 ml TRIzol reagent (Thermo Fisher Scientific, USA) and mechanically disrupted using a homogenizer. Chloroform was added and the aqueous  phase containing the RNA was added onto the Nucleospin column. From there the manufacturer’s protocol was followed including the DNAse treatment. The quality and quantity of the isolated total RNA was determined with a Qubit 2.0 Fluorometer (Life Technologies,  USA) and a Tapestation 2200 (Agilent, Germany)
cDNA libraries were prepared by the Functional Genomics Center Zürich (University and ETH Zürich) according to the procedure described as follows: TruSeq Stranded Total RNA Library Prep Kit (Illumina Inc, USA) was used in the following steps. Briefly, the 200 ng total RNA samples were ribo-depleted using Ribo Zero Gold (Illumina Inc, USA) and fragmented with divalent cations and an elevated temperature. The fragmented RNA was then reverse-transcribed into cDNA with Actinomycin, which prevents DNA-dependent synthesis but allows RNA-dependent synthesis. Actinomycin is added during first strand synthesis. To achieve strand specificity, dUTP was incorporated instead of dTTP in the course of the second strand synthesis. The polymerase used for the subsequent PCR amplification will not incorporate past dUTP and so the second strand will be suppressed. A single ‘A’ nucleotide is added to the 3’ ends of the cDNA fragments before ligation of the TruSeq adapters. The adapters contain the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using qPCR (LightCycler 96, Roche, Switzerland) and Tapestation 2200 (Agilent, Germany). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.    Cluster Generation and sequencing were performed by the Functional Genomics Center Zürich (University and ETH Zürich) according to the procedure described as follows: The TruSeq SR Cluster Kit v4-cBot-HS (Illumina Inc, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 4000 single end 125 bp using the TruSeq SBS Kit v4-HS (Illumina Inc, USA).

treatment_protocol: At 1, 3, 6 or 12 weeks after surgery, animals were deeply anaesthetized with 5% isoflurane followed by an intraperitoneal injection of Esconarkon (600 mg/kg body weight, Streuli Pharma AG, Switzerland) and transcardially perfused with ice cold Ringer solution (Braun, Germany) supplemented with Heparin (100 000 IU/l, Roche Pharmaceuticals, Switzerland), 0.017% NaHCO3 and 0.25% NaNO2. Immediately afterwards, a 1 mm thick transverse slice of the spinal cord at vertebral level C3 was prepared, and the bilateral intermediate laminae (laminae IV-VII) were dissected. The tissue was immediately frozen in liquid nitrogen. Samples were stored in -80°C until RNA extraction. For the histological assessment of the lesion site, spinal cord tissue containing the lesion site was dissected and incubated in 4% paraformaldehyde (PFA) supplemented with 5% sucrose for 24 hours. Tissue was then transferred into a 0.1M phosphate-buffered solution containing 30% sucrose for cryoprotection and stored until histological processing.

value: Long Evans Crl:LE

tag: age

value: adult (>10 weeks)

tag: surgery

value: sham surgery

tag: time point of tissue dissection in weeks

tag: tissue

value: gray matter of spinal cord


title: Dd2clone1.10H_2.9H-2_0714


title: 12W_C_01


title: 12W_C_05


title: Dd2_0313


title: Dd2clone1.10H_2.9H-1_0714


title: Dd2_0714


title: 01W_C_05

source_name: sham surgery_1wk_gray matter of spinal cord


title: 12W_C_03


title: 01W_C_04


title: 01W_C_02


title: 01W_C_03


title: 01W_C_01

source_name: spinal cord injury_1wk_gray matter of spinal cord

value: spinal cord injury


title: 12W_C_02


title: Dd2clone1.10H_2.11A_0714


title: Dd2clone1.10H_0313


title: 12W_S_01

source_name: spinal cord injury_12wk_gray matter of spinal cord


title: 12W_S_03


title: 12W_S_05


title: 06W_S_05

source_name: spinal cord injury_6wk_gray matter of spinal cord


title: 12W_S_02


title: 06W_S_04


title: 06W_S_03


title: 06W_S_02


title: 03W_S_05

source_name: spinal cord injury_3wk_gray matter of spinal cord


title: 06W_S_01


title: 03W_S_03


title: KPTR2-T30

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
Raw sequence reads were mapped against the Klebsiella pneumoniae MGH78578 (NCBI Refence Sequence NC_009648.1) using Segemehl with mapping with default mapping parameters.
Number of reads mapped to each genes was calculated using custom Perl script.
Reads were normalized using VOOM transformation (Log2 normalized read counts) from Limma R package
Differential gene expression was calculated using Limma package
Genome_build: NC_009648.1
Supplementary_files_format_and_content: Tab-delimited text file includes VOOM transformaed log2 normalized read counts for each samples.

organism: Klebsiella pneumoniae MGH 78578

source_name: Bacterial cell

extract_protocol:
RNeasy Mini Kit (Qiagen, USA)
Illumina RNA-seq library preparation protocol

tag: growth stage

value: Mid-log phase

tag: treatment

value: L-Ag NPs treatment- 30 min. at 37 °C


title: 03W_S_04


title: 01W_S_02


title: 01W_S_04


title: 01W_S_05


title: 01W_S_01


title: KPCR2-T30

value: No treatment- 30 min. at 37 °C


title: 01W_S_03


title: 03W_S_02


title: 03W_S_01


title: KPTR1-T30


title: 12W_S_04


title: KPCR2-T05

value: No treatment- 5 min. at 37 °C


title: KPCR1-T05


title: SLE_Tag_Library

molecule: other

organism: unidentified plasmid

source_name: plasmid control

extract_protocol:
Extracted RNA was subjected to DNase treatment in a 375 uL system with 2.5 uL Turbo DNase, and 37.5 uL Turbo DNase Buffer at 37°C for 1 hr.  3.75 uL 10% SDS and 37.5 uL 0.5M EDTA was added to stop DNase with 5 mins of incubation at 75°C. The whole volume was used for eGFP probe hybridization in an 1800 uL system, with 450 ul 20X SSC Buffer, 900 uL Formamide, and 1 uL of each 100 uM Biotin-labeled GFP probe One to Three. The probe hybridization was performed through incubation at 65°C for 2.5 hrs. 200 ul Dynabeads™ MyOne™ Streptavidin C1 was prepared according to the manufacturer’s instructions. The beads were suspended in 250 uL 20X SSC Buffer and incubated with the above probe hybridization reaction at room temperature for 15 mins. Beads were then collected on a magnet and washed with 1X SSC Buffer once, and 0.1X SSC Buffer twice. eGFP mRNA was eluted first through adding 12.5 uL ddH2O, heating at 70°C for 2 mins and collecting on a magnet, then adding another 12.5 uL ddH2O, heating at 80°C for 2 mins and collecting on a magnet. All collected elution was performed with another DNase treatment in a 30 uL system containing 0.5 uL Turbo DNase, and 3 uL Turbo DNase Buffer at 37°C for 1 hr.  0.5 uL 10% SDS was added to halt DNase reactions. Eluted mRNA was purified through RNA Clean SPRI Beads. mRNA was reverse transcribed to cDNA using SuperScript™ IV First-Strand Synthesis System with specific primer MPRA_v3_Amp2Sc_R, following the manufacturer’s instructions. cDNA and plasmid control were then used for building sequencing libraries following Tag-seq Library Construction section in the paper of Tewhey et al (PMID: 27259153). A total of two PCR rounds were needed for building the sequencing library. The first PCR was performed with TruSeq_TruSeq_Universal_Adapter_P5 and MPRA_V3_Illumina_GFP_F. The second PCR was performed with TruSeq_TruSeq_Universal_Adapter_P5 and index primer. Samples were purified, molar pooled and sequenced using Illumina 1x50/75bp on NextSeq 500.
Extracted RNA was subjected to DNase treatment in a 375 uL system with 2.5 uL Turbo DNase, and 37.5 uL Turbo DNase Buffer at 37°C for 1 hr.  3.75 uL 10% SDS and 37.5 uL 0.5M EDTA was added to stop DNase with 5 mins of incubation at 75°C. The whole volume was used for eGFP probe hybridization in an 1800 uL system, with 450 ul 20X SSC Buffer, 900 uL Formamide, and 1 uL of each 100 uM Biotin-labeled GFP probe One to Three. The probe hybridization was performed through incubation at 65°C for 2.5 hrs. 200 ul Dynabeads™ MyOne™ Streptavidin C1 was prepared according to the manufacturer’s instructions. The beads were suspended in 250 uL 20X SSC Buffer and incubated with the above probe hybridization reaction at room temperature for 15 mins. Beads were then collected on a magnet and washed with 1X SSC Buffer once, and 0.1X SSC Buffer twice. eGFP mRNA was eluted first through adding 12.5 uL ddH2O, heating at 70°C for 2 mins and collecting on a magnet, then adding another 12.5 uL ddH2O, heating at 80°C for 2 mins and collecting on a magnet. All collected elution was performed with another DNase treatment in a 30 uL system containing 0.5 uL Turbo DNase, and 3 uL Turbo DNase Buffer at 37°C for 1 hr.  0.5 uL 10% SDS was added to halt DNase reactions. Eluted mRNA was purified through RNA Clean SPRI Beads. mRNA was reverse transcribed to cDNA using SuperScript™ IV First-Strand Synthesis System with specific primer MPRA_v3_Amp2Sc_R, following the manufacturer’s instructions. cDNA and plasmid control were then used for building sequencing libraries following Tag-seq Library Construction section in the paper of Tewhey et al19. A total of two PCR rounds were needed for building the sequencing library. The first PCR was performed with TruSeq_Universal_Adapter_P5 and MPRA_V3_Illumina_GFP_F. The second PCR was performed with TruSeq_Universal_Adapter_P5 and index primer. Samples were purified, molar pooled and sequenced using Illumina 1x75bp on NextSeq 500.

tag: source

value: plasmid control


title: KPCR1-T30


title: SLE_BC_Library

extract_protocol:
The oligo and barcode regions were amplified from the backbone library through 4X PCR with a 100 uL system containing 200 ng plasmid, 50 uL NEBNext® Ultra™ II Q5® Master Mix, 0.5 uM TruSeq_Universal_Adapter_P5 and MPRA_v3_TruSeq_Amp2Sa_F_P7. PCR was performed under the following conditions: 95°C for 20 sec, 6 cycles of (95°C for 20 sec, 62°C for 15 sec, 72°C for 30 sec), 72°C for 2 mins. The product was then purified, and indices were added through a 100ul system containing all purified product, 50ul NEBNext® Ultra™ II Q5® Master Mix, 0.5 uM TruSeq_Universal_Adapter_P5 and index primer. PCR was performed as above, except for only 5 cycles. Samples were purified, molar pooled, and sequenced using 2x125bp on Illumina NextSeq 500.
Extracted RNA was subjected to DNase treatment in a 375 uL system with 2.5 uL Turbo DNase, and 37.5 uL Turbo DNase Buffer at 37°C for 1 hr.  3.75 uL 10% SDS and 37.5 uL 0.5M EDTA was added to stop DNase with 5 mins of incubation at 75°C. The whole volume was used for eGFP probe hybridization in an 1800 uL system, with 450 ul 20X SSC Buffer, 900 uL Formamide, and 1 uL of each 100 uM Biotin-labeled GFP probe One to Three. The probe hybridization was performed through incubation at 65°C for 2.5 hrs. 200 ul Dynabeads™ MyOne™ Streptavidin C1 was prepared according to the manufacturer’s instructions. The beads were suspended in 250 uL 20X SSC Buffer and incubated with the above probe hybridization reaction at room temperature for 15 mins. Beads were then collected on a magnet and washed with 1X SSC Buffer once, and 0.1X SSC Buffer twice. eGFP mRNA was eluted first through adding 12.5 uL ddH2O, heating at 70°C for 2 mins and collecting on a magnet, then adding another 12.5 uL ddH2O, heating at 80°C for 2 mins and collecting on a magnet. All collected elution was performed with another DNase treatment in a 30 uL system containing 0.5 uL Turbo DNase, and 3 uL Turbo DNase Buffer at 37°C for 1 hr.  0.5 uL 10% SDS was added to halt DNase reactions. Eluted mRNA was purified through RNA Clean SPRI Beads. mRNA was reverse transcribed to cDNA using SuperScript™ IV First-Strand Synthesis System with specific primer MPRA_v3_Amp2Sc_R, following the manufacturer’s instructions. cDNA and plasmid control were then used for building sequencing libraries following Tag-seq Library Construction section in the paper of Tewhey et al19. A total of two PCR rounds were needed for building the sequencing library. The first PCR was performed with TruSeq_Universal_Adapter_P5 and MPRA_V3_Illumina_GFP_F. The second PCR was performed with TruSeq_Universal_Adapter_P5 and index primer. Samples were purified, molar pooled and sequenced using Illumina 1x75bp on NextSeq 500.

value: Plasmid for Barcode and Oligo association


title: KPTR1-T05

value: L-Ag NPs treatment- 5 min. at 37 °C


title: Endurant [SampleG]

city: Paris

first: Valerie

last: Ducret

address: 55 rue buffon

country: France

institute: MNHN

description: SampleG

data_processing:
Paired-end sequence reads were pooled together to generate a de novo transcriptome assembly
The raw sequence reads were trimmed and Illumina adapters removed using Trimmomatic with the following parameters: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36.
Transcriptome assembly was then performed de novo with the program Trinity
Transcript-level abundance was estimated using Kallisto in addition to a normalized measure of transcript expression (TPM)
Supplementary_files_format_and_content: tab-delimited text files include abundance estimates and TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Xenopus allofraseri

source_name: limb muscle

extract_protocol:
the knee extensor muscles of the right leg were extracted, tissues conserved at -80C, and RNA was harvested using Trizol reagent. PolyA-RNA was isolated.
Sequencing RNA libraries were prepared using ScriptSeq (Illumina)

tag: locomotory performance

value: Endurant


title: KPTR2-T05


title: Endurant [SampleE]

description: SampleE


title: Burst-performant [SampleF]

description: SampleF

value: Burst-performant


title: Burst-performant [SampleH]

description: SampleH


title: Burst-performant [SampleC]

description: SampleC


title: Endurant [SampleD]

description: SampleD


title: Endurant [SampleA]

description: SampleA


title: Burst-performant [SampleB]

description: SampleB


title: TetON_CDCP1CG_mutant_MDCK_cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
B4
MDCK cell lines with a doxycycline-inducible (TetON) form of the CDCP1CG-EGFP gene.

hyb_protocol: Before hybridization, 600 ng labeled cRNA was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65˚C. The slides were washed according to the manufacturer's manual.

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1).

organism: Canis lupus familiaris

label_protocol: 38.5 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: MDCK type I cells harboring TRE-CDCP1-EGFP or its mutant were incubated in collagen matrix in DMEM supplemented with 5% FBS for 9 days.

extract_protocol: Total RNA was extracted using Sepasol-G (Nacalai). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

treatment_protocol: After cystogenesis in collagen matrix, MDCK cysts were incubated with doxycycline, and then total RNA samples were extracted for microarray analysis.

tag: cell line

value: MDCK type I

tag: transgene

tag: expression system

value: Tet-On


title: KD seedling Rep1

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

data_processing:
3’ adapter (5’-TGGAATTCTCGGGTGCCAAGG-3’) was removed from sequenced reads using UEA small RNA workbench.
The small RNA reads of length 19nt-25nt filtered and were analyzed.
Supplementary_files_format_and_content: Text file containing 19nt-25nt long unique reads and their raw abundance after removal of adapter.

organism: Oryza sativa

source_name: Five weeks old seedlings

extract_protocol:
Total RNA from 5 week old seedlings of both wild-type and transgenic lines were extracted using Trizol (Invitrogen) reagent.
Size fractionation

tag: subspecies, cultivar

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB1)

tag: genotype/variation

value: KD


title: WT seedling Rep2

value: WT


title: OE seedling Rep1

value: OE


title: OE seedling Rep2


title: WT seedling Rep1


title: KD seedling Rep2


title: TetOFF_CDCP1CG_mutant_MDCK_cells

description:
B3
MDCK cell lines with a doxycycline-inducible (TetOFF) form of the CDCP1CG-EGFP gene.

value: Tet-Off


title: Season_Jun-14_G8

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

institute: Forest Tree Breeding Center

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Gene Expression Custom 8×60K Array (G4102A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on SureScan Microarray Scanner G4900DA using one color scan setting for 8x60k array slides (AgilentG3_HiSen_GX_1Color).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (Protocol: GE1_1105_Oct12 and Grid: 056873_D_F_20130730) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Cryptomeria japonica

source_name: season, Jun-14,  replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from  200 ng total RNA using the One-Color Low Input Quick Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA of seasonal samples was extracted from 500 mg samples as Gehrig et al. (2000) reported using an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), and a DNase digestion was performed on-column using an RNase-free DNase Set (Qiagen).The total RNA of cuttings placed at the controlled-environmental chamber was extracted by LiCl precipitation as described in le Provost et al. (2007), and subsequently extracted using RNeasy Plant Mini Kit as described above.

value: shoot

tag: condition

value: Natural condition

tag: day of sampling


title: 46_M_WT_30_RRBS

status: Public on Jan 29 2021

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description: This sample was used to estimate global DNA methylation levels and mitochondrial DNA copy numbers, but was excluded from all differential methylation analyses.

data_processing:
reads were preprocessed with Trim Galore v. 0.4.0, a wrapper for cutadapt v. 1.9.1, with the --rrbs flag set
trimmed reads were aligned to the mm10 genome assembly using Bismark v. 0.18.1 with default parameters
CpG methylation calls were summarized using the bismark2bedgraph script which is part of the Bismark software suite
For each CpG, observations from both strands were added together to form an overall methylation level per CpG, and only CpGs covered by eight or more reads in every sample was retained
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: csv file with CpGs in rows and genomic annotation along with number of methylated and unmethylated observations for each sample in columns.

source_name: Male_WT_30_soleus muscle

extract_protocol:
A single soleus muscle or ~30 mg of powdered quadriceps was homogenized in 400 µl of RLT buffer (Qiagen) with β-mercaptoethanol using steal beads and subjected to 2 x 30 sec at 30 Hz of disruption using the TissueLyser II (Qiagen). RNA and DNA were simultaneously isolated from 350 µl of lysate using the RNA/DNA/miRNA AllPrep kit (Qiagen) as per instructions. Primary muscle cells were lysed directly in RLT buffer and RNA extracted using the RNeasy kit (Qiagen). RNA was eluted in 45 µl of RNAse free water and DNA in 60 µl of elution buffer (Qiagen).
Reduced Representation Bisulfite Sequencing (RRBS) was performed as described (Laker et al., 2017). Briefly, DNA samples were incubated with MpsI enzyme (NEB) in order to fragment DNA at CCGG positions to enrich for CpG regions. Bisulfite conversion was performed using the EZ DNA methylation Kit (Zymo Research) according to the manufacturer’s instructions. The DNA was then PCR amplified and ligated to TruSeq (Illumina) sequencing adapters. Libraries were subjected to 75-bp single-end sequencing on the NextSeq 550 (Illumina). On average 18.3 million reads/sample were aligned

tag: strain background

tag: Sex

value: Male

tag: genotype

tag: timepoint

value: soleus muscle


title: 50_F_KO_10_RRBS

source_name: Female_KO_10_soleus muscle

value: Female

value: KO


title: Season_Jun-13_G3

source_name: season, Jun-13,  replicate 3


title: 40_F_WT_10_RRBS

source_name: Female_WT_10_soleus muscle


title: 15_M_KO_Bas_RRBS

source_name: Male_KO_Bas_soleus muscle

value: Bas


title: Season_May-14_G8

source_name: season, May-14,  replicate 3


title: 7_M_KO_Bas_RRBS


title: Season_Apr-14_G1

source_name: season, Apr-14,  replicate 3


title: TetON_CDCP1_MDCK_cells

description:
B2
MDCK cell lines with a doxycycline-inducible (TetON) form of the CDCP1-EGFP gene.


title: Season_Jan-14_G5

source_name: season, Jan-14,  replicate 3


title: Season_Feb-14_G6

source_name: season, Feb-14,  replicate 3


title: Season_Oct-13_G3

source_name: season, Oct-13,  replicate 3


title: Season_Dec-13_G1

source_name: season, Dec-13,  replicate 3


title: Season_Mar-14_G2

source_name: season, Mar-14,  replicate 3


title: Season_Aug-13_G1

source_name: season, Aug-13,  replicate 3


title: Season_Nov-13_G4

source_name: season, Nov-13,  replicate 3


title: Season_Sep-13_G2

source_name: season, Sep-13,  replicate 3


title: TetOFF_CDCP1_MDCK_cells

description:
B1
MDCK cell lines with a doxycycline-inducible (TetOFF) form of the CDCP1-EGFP gene.


title: Replicate #7 of the Houhe (HH) forest

type: genomic

city: Biejing

first: Jingmin

last: Cheng

address: NO. 30 Shuangqing Road, Haidian District

department: School of Environment

country: China

institute: Tsinghua University

hyb_protocol: For each sample, 1 ug of DNA was labeled with Cy5 fluorescent dye (GE Healthcare, Madison, WI, USA) and hybridized with GeoChip microarrays at 45 C for 10 hours. Unbounded DNA was washed away.

scan_protocol: Then the arrays were washed and dried, and scanned by an MS 200 Microarray Scanner (NimbleGen) at 635 nm.

data_processing: Signal intensities were measured using ImaGene 6.0 (Biodiscovery, El Segundo, CA), and only those with a signal-to-noise ratio (SNR) > 2.0 [SNR = (signal intensity - background intensity)/standard deviation of the background] were used for further analyses. The following data transformation included: (1) removing genes detected in less than 3 of 9 samples in each forest; (2) dividing the signal intensity of each gene by the sum of each sample, and then multiplying it by the average of all samples; and (3) performing natural log-transformation.

organism: soil metagenome

source_name: Soil microbial communities

label_protocol: One microgram of DNA from each sample was mixed with random primers and denatured before dNTP, fluorescent dye Cy-5 dUTP and DNA polymerase were added for labelling at 37  C for 6 h, followed by heating at 95  C for 3 min.

extract_protocol: Soil DNA was extracted following the instructions of the PowerMax Soil DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA). DNA quality was assessed via NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA).

tag: location

value: Houhe (HH) forest


title: Replicate #6 of the Houhe (HH) forest


title: Replicate #5 of the Houhe (HH) forest


title: Replicate #2 of the Houhe (HH) forest


title: Replicate #4 of the Houhe (HH) forest


title: Replicate #8 of the Badagongshan (BDGS) forest

value: Badagongshan (BDGS) forest


title: genomic DNA from MCF10CA1h cells treated with vehicle control (ethanol), biological replicate 2

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

description: human lowly invasive breast cancer cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from human breast cancer cell lines using standard phenol:chloroform extraction protocol

value: Ethanol vehicle control

tag: sample type

value: breast cancer cells

tag: disease state

value: cancer


title: Replicate #8 of the Houhe (HH) forest


title: Replicate #9 of the Badagongshan (BDGS) forest


title: Replicate #5 of the Badagongshan (BDGS) forest


title: genomic DNA from MCF10CA1h cells treated with 15 µM  RSV (resveratrol) for 4 days , biological replicate 2

source_name: MCF10CA1h cells treated with RSV

tag: treatment

value: RSV tested sample


title: Replicate #4 of the Badagongshan (BDGS) forest


title: Replicate #9 of the Houhe (HH) forest


title: Replicate #1 of the Houhe (HH) forest


title: Replicate #3 of the Houhe (HH) forest


title: Replicate #6 of the Badagongshan (BDGS) forest


title: Replicate #3 of the Badagongshan (BDGS) forest


title: Replicate #9 of the Saiwudang (SWD) forest

value: Saiwudang (SWD) forest


title: Replicate #2 of the Badagongshan (BDGS) forest


title: Replicate #7 of the Saiwudang (SWD) forest


title: Replicate #5 of the Saiwudang (SWD) forest


title: Replicate #6 of the Saiwudang (SWD) forest


title: genomic DNA from MCF10CA1h cells treated with vehicle control (ethanol), biological replicate 3


title: Replicate #8 of the Saiwudang (SWD) forest


title: genomic DNA from MCF10CA1h cells treated with vehicle control (ethanol), biological replicate 1


title: Replicate #1 of the Badagongshan (BDGS) forest


title: genomic DNA from MCF10CA1h cells treated with 15 µM  RSV (resveratrol) for 4 days , biological replicate 3


title: genomic DNA from MCF10CA1h cells treated with 15 µM  RSV (resveratrol) for 4 days , biological replicate 1


title: mESCs, MapR_GST-MNase

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
Alignment (MapR, BisMapR): Bowtie2
Reads from .bam files were strand-separated using the calls "samtools view | awk '$1~"@" || $2 ~/^(99|147)$/{print}'" for forward strand and "samtools view | awk '$1~"@" || $2 ~/^(83|163)$/{print}'" for reverse strand.
Alignment (RNA-Seq): STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from composite and strand-separated .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and a scale factor based on the total number of paired reads in the composite.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C.

extract_protocol:
R-loops were collected from supernatant after treatment with MapR protocol (Yan et al. Cell Reports 2019).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
BisMapR converted R-loops was converted to dsDNA using the Second Synthesis buffer and enzyme mix from Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

treatment_protocol: For BisMapR treatment, R-loops were incubated with 130µL CT Conversion Reagent from the EZ DNA Methylation-Gold Kit (Zymo) at 25 ˚C for 3 hours, then column purified with EZ DNA Methylation-Gold Kit.

value: ES cell line E14

tag: protocol

value: MapR

tag: fusion protein

value: GST-MNase


title: P39

status: Public on Jan 24 2021

city: Suzhou

first: Yixin

last: Li

address: No.218,Xinghu Street

institute: singleron

data_processing:
Quality control
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 020201
aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Genome_build: GRCh38
Supplementary_files_format_and_content: expression matrix file using RNA raw count

source_name: lung

extract_protocol: The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS. Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

treatment_protocol: Prior to tissue dissociation, the specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times and minced into 1–2 mm pieces. The tissue pieces were digested in 2ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) at 37°C for 15min in a 15ml centrifuge tube with continuous agitation

tag: age

tag: gender

value: male


title: P42


title: P41


title: mESCs, MapR_NBSS

data_processing:
Library strategy: DNA-Seq
Alignment (MapR, BisMapR)
Bowtie2
Reads from .bam files were strand-separated using the calls "samtools view | awk '$1~"@" || $2 ~/^(99|147)$/{print}'" for forward strand and "samtools view | awk '$1~"@" || $2 ~/^(83|163)$/{print}'" for reverse strand.
Alignment (RNA-Seq)
STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from composite and strand-separated .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and a scale factor based on the total number of paired reads in the composite.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment

value: GST-RHdelta-Mnase


title: s1_pbmc_10x_esat

status: Public on Jan 25 2021

city: Ithaca

first: Gerlinde

last: Van de Walle

state: NY

address: 235 Hungerford Hill Road

department: Microbiology and Immunology

institute: Cornell University

data_processing:
fastq files were aligned to version 95 of the horse genome reference (with manually annotated immunoglobulins (adapted from Wagner B. Immunoglobulins and immunoglobulin genes of the horse. Developmental & Comparative Immunology. 2006;30: 155–164. doi:10.1016/j.dci.2005.06.008)) from ensembl using the count function in the cellranger suite (10X Genomics, v3.0.1)
Intermediate BAM files were extracted and modified by appending cell barcode and unique molecular identifiers to their read names
The End Sequence Analysis Toolkit(v0.1.1) was applied on the resulting BAM files to obtain gene-cell barcode expression matrices (Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016;26: 1397–1410. doi:10.1101/gr.207902.116)
Custom script was applied to identify duplicated genes and scale their expression proportionally
Genome_build: EquCab3.0
Supplementary_files_format_and_content: ESAT processed gene-cell barcode matrix

organism: Equus caballus

source_name: Peripheral blood mononuclear cells

extract_protocol:
Periperal blood mononuclear cells were isolated from healthy horses by Ficoll gradient separation
Libraries were prepared in accordance to the 10X Genomics 3' end single cell RNA sequencing library prepration protocol, version 2

tag: cell type

value: Peripheral blood mononuclear cells

value: Male

tag: breed

value: Warmblood


title: P40


title: P37

value: female


title: P38


title: P35


title: P36


title: P34


title: P32


title: Replicate #2 of the Saiwudang (SWD) forest


title: P31


title: P30


title: Replicate #1 of the Saiwudang (SWD) forest


title: P28


title: P26


title: Replicate #3 of the Saiwudang (SWD) forest


title: P27


title: Mouse No.2 treated with PhIP

city: Guangzhou

first: xu

last: yang

address: jinsui road 9

institute: Guangzhou Women and Children's Medical Center

description: Total RNA was labelled and hybridized to the microarray chip

hyb_protocol: Biotinylated cRNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the surface of MEEBO microarray slides enclosed in custom hybridization chambers.  The slides were hybridized for 16-18 hours under constant rotation in a Model 400 hybridization oven (Scigene, Sunnyvale, CA). After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen).

scan_protocol: After hybridization and washing, the microarray slides scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. Spot intensities were transformed by taking the base 2 logarithm of each value. The spot intensities were then normalized by subtracting the 70th percentile of the spot intensities of probes against mouse constitutive exons and adding back a scaling factor (grand mean of 70th percentile). After removing data for low quality spots, control sequences, and non-mouse probes, 34,279 mouse probe intensities remained. The mouse probes intensities were filtered to identify all probes with intensity above a normalized threshold (log2 (5* standard deviation of raw local background) + mean of log2-transformed negative controls) in at least 20% of sample, to arrive at 19,327 probes complementary to coding mRNA above threshold in all samples from at least one treatment group.

source_name: PhIP_Colon epithelium

label_protocol: Biotin-labeled complementary RNA (cRNA) was prepared from DNase treated total RNA. In briefly, an oligonucleotide containing a 5'-T7-promoter sequence and a 3' T24VN sequence was used to prime reverse transcription of RNA catalyzed by Superscript II (Invitrogen, Carlsbad, CA). Double-stranded cDNA was prepared from the 1st strand product and purified on a PCR purification column (Qiagen, Valencia, CA). The double-stranded cDNA was then used as a template for in vitro transcription with T7 RNA polymerase using a high yield transcription kit (Ambion, Austin, TX) and including biotin-16-UTP (Ambion) in the reaction mixture.

extract_protocol: Mouse colon epitlelium tissues were scapped by a glass slide under the dissection microscope and then used for extracting RNA using the Qiagen Rneasy Mini kit.

treatment_protocol: The hCYP1A mice on AIN93M diet were treated with one doses of PhIP (200 mg/kg body weight) or PBS by govoge at the age of 8 weeks.  Then the mice were maintained for 24 hours without any other treatment; then, mice were sacrificed for collecting colon and colon cryptic epithelia scraped for RNA extracting.

value: 8 weeks

tag: genetics

value: hCYP1A humanized mice

value: PhIP-treated

tag: histology/tissue

value: Normal colon epithelium


title: Mouse No.1 treated with PBS

source_name: PBS_Colon epithelium

value: PBS (control)


title: Mouse No.3 treated with PhIP


title: Mouse No.5 treated with PhIP


title: P29


title: Mouse No.3 treated with PBS


title: P23


title: P24


title: Mouse No.2 treated with PBS


title: Mouse No.1 treated with PhIP


title: P25


title: P22


title: P33


title: P19


title: P18


title: Mouse No.4 treated with PhIP


title: P21


title: P15


title: P16


title: P17


title: P14


title: P13


title: P12


title: P11


title: P20


title: P9


title: P5


title: P10


title: P6


title: P8


title: P7


title: P3


title: 13474_Nog2_rep1_ChIP-exo

status: Public on Jan 13 2021

first: B. Franklin

last: Pugh

state: New York

address: 465 Biotechnology Building

department: Molecular Biology and Genetics

data_processing:
Library strategy: ChIP-exo
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using ChExMix version: 0.3 with the following setting: q-value (0.01) and the rest of the options as recommended defaults.
Genome_build: sacCer3
Supplementary_files_format_and_content: bw, bed format, ChExMix peak calls

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: antibody

value: TAP-tag:Sigma i5006

tag: growthmedia

value: YPD

tag: assaytype

value: ChIP-exo


title: 5_F_WT_60_RRBS

source_name: Female_WT_60_soleus muscle

tag: strain background

tag: Sex

value: Female

tag: genotype

value: WT

tag: tissue

value: soleus muscle


title: 13804_Nop58_rep1_ChIP-exo


title: P2

value: male


title: P1


title: 14532_Nmd5_rep1_ChIP-exo


title: 12947_Not3_rep1_ChIP-exo


title: 20442_Nnf2_rep1_ChIP-exo


title: 14401_Nma2_rep1_ChIP-exo


title: 14764_Nma1_rep1_ChIP-exo


title: 14620_Nkp2_rep2_ChIP-exo


title: 12455_Nkp2_rep1_ChIP-exo


title: 17055_Nkp1_rep2_ChIP-exo

value: HA-tag:Santa Cruz sc-7392


title: 14861_Nkp1_rep1_ChIP-exo


title: 14468_Nic96_rep1_ChIP-exo


title: P4


title: 14606_Nhp6a_rep2_ChIP-exo


title: 17767_Ngg1_rep2_ChIP-exo


title: 12052_Nhp6a_rep1_ChIP-exo


title: 14590_Ndd1_rep1_ChIP-exo


title: 20440_Ncl1_rep1_ChIP-exo


title: 20439_Ncb2_rep2_ChIP-exo


title: 12861_Ncb2_rep1_ChIP-exo


title: 12092_Ngg1_rep1_ChIP-exo


title: 14526_Nan1_rep1_ChIP-exo


title: 17949_Ndd1_rep2_ChIP-exo


title: 17868_Nap1_rep1_ChIP-exo


title: 15000_Nab2_rep1_ChIP-exo


title: 14384_Mxr1_rep1_ChIP-exo


title: 24336_Nhp10_rep2_ChIP-exo


title: 17788_Nhp10_rep1_ChIP-exo


title: 17118_Nab2_rep2_ChIP-exo


title: 13449_Mus81_rep1_ChIP-exo


title: 14379_Naf1_rep1_ChIP-exo


title: 17953_Nfi1_rep1_ChIP-exo


title: 17796_Mud1_rep1_ChIP-exo


title: Replicate #7 of the Badagongshan (BDGS) forest

tag: location

value: Badagongshan (BDGS) forest


title: 17038_Mth1_rep1_ChIP-exo


title: 15218_Mss11_rep1_ChIP-exo


title: 14839_Msn4_rep1_ChIP-exo


title: 8584_Msn2_rep1_ChIP-exo

value: Abcam 18181


title: 12066_Net1_rep1_ChIP-exo


title: 17125_Msn1_rep1_ChIP-exo


title: 17960_Msi1_rep1_ChIP-exo


title: 14525_Msc6_rep1_ChIP-exo


title: 15004_Naf1_rep2_ChIP-exo


title: 14292_Mot3_rep2_ChIP-exo


title: 11807_Mot3_rep1_ChIP-exo


title: 19997_Abf1_rep3_ChIP-exo

value: Weil Lab


title: 17196_Mlp1_rep2_ChIP-exo


title: 19309_Mud1_rep2_ChIP-exo


title: 17039_Mot1_rep1_ChIP-exo


title: 14382_Mor1_rep1_ChIP-exo


title: 12425_Mlp1_rep1_ChIP-exo


title: 19327_Mig1_rep2_ChIP-exo


title: 15661_Mss11_rep2_ChIP-exo


title: 17869_Mig1_rep1_ChIP-exo


title: 12946_Mig2_rep1_ChIP-exo


title: 18474_Mif2_rep2_ChIP-exo


title: 16540_Mif2_rep1_ChIP-exo


title: 11908_Mga2_rep1_ChIP-exo


title: 12130_Mft1_rep1_ChIP-exo


title: 13813_Mft1_rep2_ChIP-exo


title: 11990_Met4_rep1_ChIP-exo


title: 20438_Met4_rep2_ChIP-exo


title: 15791_Met32_rep2_ChIP-exo


title: 12464_Met32_rep1_ChIP-exo


title: 14772_Mre11_rep1_ChIP-exo


title: 11806_Met31_rep1_ChIP-exo


title: 13211_Met30_rep1_ChIP-exo


title: 28348_Met28_rep3_ChIP-exo


title: Replicate #4 of the Saiwudang (SWD) forest

value: Saiwudang (SWD) forest


title: 18493_Mig2_rep2_ChIP-exo


title: 19657_Met28_rep2_ChIP-exo

tag: treatment

value: 6 min heat shock


title: 14854_Mig3_rep1_ChIP-exo


title: 11797_Met28_rep1_ChIP-exo


title: 17969_Med20_rep1_ChIP-exo


title: 15187_Med2_rep2_ChIP-exo


title: 15800_Med6_rep2_ChIP-exo


title: 16043_Med11_rep1_ChIP-exo


title: 12470_Med6_rep1_ChIP-exo


title: 14611_Med4_rep2_ChIP-exo


title: 12084_Med2_rep1_ChIP-exo


title: 12083_Med4_rep1_ChIP-exo


title: 17597_Med8_rep1_ChIP-exo


title: 14983_Med1_rep1_ChIP-exo


title: 18486_Med11_rep2_ChIP-exo


title: 14618_Mcm1_rep2_ChIP-exo


title: 14480_Mcm16_rep1_ChIP-exo


title: 14997_Mcm16_rep2_ChIP-exo


title: 13441_Mck1_rep1_ChIP-exo


title: 12441_Mcm1_rep1_ChIP-exo


title: 15634_Met31_rep2_ChIP-exo


title: 14797_Mcd1_rep1_ChIP-exo


title: 15655_Mbp1_rep2_ChIP-exo


title: 12937_Mbp1_rep1_ChIP-exo


title: 14191_Met18_rep1_ChIP-exo


title: 14362_Mca1_rep1_ChIP-exo


title: 17115_Mbf1_rep1_ChIP-exo


title: 11824_Maf1_rep1_ChIP-exo


title: 17985_Mot2_rep1_ChIP-exo


title: 14847_Mal33_rep1_ChIP-exo


title: 14973_Matalpha2_rep2_ChIP-exo


title: 13808_Mac1_rep2_ChIP-exo


title: 12869_Mas6_rep1_ChIP-exo


title: 17010_Maf1_rep2_ChIP-exo


title: 12006_Mac1_rep1_ChIP-exo


title: 12114_Lys20_rep1_ChIP-exo


title: 15656_Lys21_rep2_ChIP-exo


title: 14817_Lys14_rep2_ChIP-exo


title: 12089_Lys21_rep1_ChIP-exo


title: 13464_Lot5_rep1_ChIP-exo


title: 15669_Leu3_rep2_ChIP-exo


title: 13793_Leo1_rep2_ChIP-exo


title: 14417_Lge1_rep1_ChIP-exo


title: 14199_Leu3_rep1_ChIP-exo


title: 18473_Lea1_rep1_ChIP-exo


title: 20437_Lea1_rep2_ChIP-exo


title: 11773_Leo1_rep1_ChIP-exo


title: 14496_Matalpha2_rep1_ChIP-exo


title: 17935_Kti12_rep1_ChIP-exo


title: 14180_Kss1_rep1_ChIP-exo


title: 19392_Kin28_rep2_ChIP-exo


title: 17983_Kin28_rep1_ChIP-exo


title: 14972_Kar4_rep2_ChIP-exo


title: 14492_Kar4_rep1_ChIP-exo


title: 17012_Lys20_rep2_ChIP-exo


title: 13465_Kap95_rep1_ChIP-exo


title: 18002_Jhd2_rep1_ChIP-exo


title: 14428_Lys14_rep1_ChIP-exo


title: 17792_Jhd1_rep1_ChIP-exo


title: 12140_Lrg1_rep1_ChIP-exo


title: 13443_Kar2_rep1_ChIP-exo


title: 17146_Iwr1_rep1_ChIP-exo


title: 12107_Iws1_rep1_ChIP-exo


title: 14601_Iws1_rep2_ChIP-exo


title: 17850_Ixr1_rep1_ChIP-exo


title: 17954_Irr1_rep2_ChIP-exo


title: 16344_Irc20_rep1_ChIP-exo


title: 18013_Isw1_rep1_ChIP-exo


title: 14992_Irr1_rep1_ChIP-exo


title: 17032_Ioc4_rep1_ChIP-exo


title: 17152_Itc1_rep1_ChIP-exo


title: 17998_Ioc2_rep1_ChIP-exo


title: 17581_Ino80_rep1_ChIP-exo


title: 12012_Ino2_rep1_ChIP-exo


title: 14597_Ino4_rep1_ChIP-exo


title: 15653_Ino4_rep2_ChIP-exo


title: 17971_Ino2_rep2_ChIP-exo


title: 12853_Iml2_rep1_ChIP-exo


title: 12033_Imd2_rep1_ChIP-exo


title: 16542_Kae1_rep1_ChIP-exo


title: 11925_Ilv5_rep1_ChIP-exo


title: 12077_Iki3_rep1_ChIP-exo


title: 8936_Ifh1_rep2_ChIP-exo

value: Abcam ab56


title: 14439_Iki1_rep1_ChIP-exo


title: 14811_Ies5_rep1_ChIP-exo


title: 17042_Ies6_rep2_ChIP-exo


title: 14984_Ies6_rep1_ChIP-exo


title: 8934_Ifh1_rep1_ChIP-exo


title: 11994_Ies4_rep1_ChIP-exo


title: 14762_Isw2_rep1_ChIP-exo


title: 17136_Ies2_rep1_ChIP-exo


title: 20436_Ies3_rep2_ChIP-exo


title: 17891_Ies3_rep1_ChIP-exo


title: 18004_Ioc3_rep1_ChIP-exo


title: 17984_Ies1_rep1_ChIP-exo


title: 14399_Ids2_rep1_ChIP-exo


title: 12842_Hxk2_rep1_ChIP-exo


title: 14476_Idi1_rep1_ChIP-exo


title: 20435_Htl1_rep2_ChIP-exo


title: 17028_Htl1_rep1_ChIP-exo


title: 14255_Htb2_rep2_ChIP-exo


title: 11819_Hst4_rep1_ChIP-exo


title: 11844_Hta2_rep1_ChIP-exo


title: 11772_Htb2_rep1_ChIP-exo


title: 15784_Hta2_rep2_ChIP-exo


title: 15796_Hst3_rep2_ChIP-exo


title: 13143_Hst3_rep1_ChIP-exo


title: 14467_Hst2_rep1_ChIP-exo


title: 15798_Hst1_rep2_ChIP-exo


title: 13140_Hst1_rep1_ChIP-exo


title: 23750_Hsf1_rep4_ChIP-exo

value: Gross Lab


title: 10406_Hsf1_rep3_ChIP-exo


title: 10401_Hsf1_rep2_ChIP-exo


title: 23755_Hsf1_rep5_ChIP-exo


title: 8581_Hsf1_rep1_ChIP-exo


title: 12868_Hsl7_rep1_ChIP-exo


title: 17929_Hrb1_rep1_ChIP-exo


title: 14487_Hpt1_rep1_ChIP-exo


title: 15193_Htz1_rep2_ChIP-exo


title: 14993_Hrr25_rep1_ChIP-exo


title: 11759_Htz1_rep1_ChIP-exo


title: 20434_Hpc2_rep2_ChIP-exo


title: 28336_Hrb1_rep2_ChIP-exo


title: 14810_Hpr1_rep1_ChIP-exo


title: 17936_Hpr1_rep2_ChIP-exo


title: 13141_Hot1_rep1_ChIP-exo


title: 12941_Hpa3_rep1_ChIP-exo


title: 17797_Hos4_rep2_ChIP-exo


title: 15491_Hot1_rep2_ChIP-exo


title: 16044_Hos4_rep1_ChIP-exo


title: 13157_Hos2_rep1_ChIP-exo


title: 20433_Hos2_rep2_ChIP-exo


title: 17564_Hos3_rep1_ChIP-exo


title: 17593_Hos1_rep1_ChIP-exo


title: 12432_Hom6_rep1_ChIP-exo


title: 17213_Hmt1_rep1_ChIP-exo


title: 14781_Hor2_rep1_ChIP-exo


title: 16033_Hog1_rep1_ChIP-exo


title: 17849_Hms2_rep2_ChIP-exo


title: 16018_Hms2_rep1_ChIP-exo


title: 14842_Hms1_rep1_ChIP-exo


title: 14622_Hmo1_rep2_ChIP-exo


title: 14865_Hmlalpha2_rep1_ChIP-exo


title: 12836_Hmo1_rep1_ChIP-exo


title: 17987_Hir3_rep2_ChIP-exo


title: 15197_Hir2_rep2_ChIP-exo


title: 15789_Hir3_rep1_ChIP-exo


title: 17575_Hir1_rep1_ChIP-exo


title: 11847_Hir2_rep1_ChIP-exo


title: 15662_Hht2_rep2_ChIP-exo


title: 14465_Hif1_rep1_ChIP-exo


title: 19308_Hht1_rep2_ChIP-exo


title: 14989_Hpc2_rep1_ChIP-exo


title: 11758_Hht2_rep1_ChIP-exo


title: 17783_Hht1_rep1_ChIP-exo


title: 18495_Hhf2_rep2_ChIP-exo


title: 11771_Hho1_rep1_ChIP-exo


title: 15663_Hhf1_rep2_ChIP-exo


title: 17043_Hem2_rep2_ChIP-exo


title: 14431_Hem2_rep1_ChIP-exo


title: 20432_Hda1_rep2_ChIP-exo


title: 12858_Hda1_rep1_ChIP-exo


title: 13460_Hch1_rep1_ChIP-exo


title: 10706_Hap5_rep2_ChIP-exo


title: 17865_Hir1_rep2_ChIP-exo


title: 18494_Hap3_rep2_ChIP-exo


title: 12039_Hcm1_rep1_ChIP-exo


title: 10535_Hap5_rep1_ChIP-exo


title: 14830_Hat2_rep1_ChIP-exo


title: 12034_Hac1_rep1_ChIP-exo


title: 16025_Hho1_rep2_ChIP-exo


title: 12438_Ham1_rep1_ChIP-exo


title: 12013_Hap3_rep1_ChIP-exo


title: 13899_H4K12ac_rep2_MNase-ChIP-seq

value: Abcam ab46983

value: MNase-ChIP-seq


title: 14855_Hap1_rep1_ChIP-exo


title: 13890_H4K12ac_rep1_MNase-ChIP-seq


title: 11804_Hal9_rep1_ChIP-exo

value: TAP-tag:Sigma i5006


title: 18014_Haa1_rep1_ChIP-exo

value: YPD


title: 13794_Hal9_rep2_ChIP-exo

value: ChIP-exo


title: 13894_H3K9ac_rep2_MNase-ChIP-seq

value: Milliporte 07-352


title: 11805_Hap2_rep1_ChIP-exo


title: 13885_H3K9ac_rep1_MNase-ChIP-seq


title: 15633_Hap2_rep2_ChIP-exo


title: 14818_Hhf2_rep1_ChIP-exo


title: 11757_Hhf1_rep1_ChIP-exo


title: 13897_H3K79me3_rep2_MNase-ChIP-seq

value: Abcam ab2621


title: 13888_H3K79me3_rep1_MNase-ChIP-seq


title: 13893_H3K4me3_rep2_MNase-ChIP-seq

value: Abcam ab8580


title: 13884_H3K4me3_rep1_MNase-ChIP-seq


title: 13887_H3K36me3_rep1_MNase-ChIP-seq

value: Abcam ab9050


title: 13896_H3K36me3_rep2_MNase-ChIP-seq


title: 17050_Hap1_rep2_ChIP-exo

value: HA-tag:Santa Cruz sc-7392


title: 13886_H3K27ac_rep1_MNase-ChIP-seq

value: Abcam ab4729


title: 13895_H3K27ac_rep2_MNase-ChIP-seq


title: 10947_H3_rep1_MNase-ChIP-seq

value: Abcam ab1791


title: 10966_H3_rep3_MNase-ChIP-seq


title: 13898_H2BK123ub_rep2_MNase-ChIP-seq

value: Cell signaling 5546S


title: 10951_H2B_rep1_MNase-ChIP-seq

value: Active Motif 39237


title: 10952_H2B_rep2_MNase-ChIP-seq


title: 10967_H2B_rep3_MNase-ChIP-seq


title: 14363_Gzf3_rep1_ChIP-exo


title: 20431_Gzf3_rep2_ChIP-exo


title: 17881_Gts1_rep1_ChIP-exo


title: 20430_Gts1_rep2_ChIP-exo


title: 14352_Grx3_rep1_ChIP-exo


title: 14445_Gtr1_rep1_ChIP-exo


title: 13466_Grx4_rep1_ChIP-exo


title: 14482_Gtr2_rep1_ChIP-exo


title: 12437_Gpb2_rep1_ChIP-exo


title: 20429_Gln3_rep2_ChIP-exo


title: 14786_Gre2_rep1_ChIP-exo


title: 13458_Gpx2_rep1_ChIP-exo


title: 10948_H3_rep2_MNase-ChIP-seq


title: 17877_Gln3_rep1_ChIP-exo


title: 19310_Gpn2_rep1_ChIP-exo


title: 17932_God1_rep2_ChIP-exo


title: 13478_Gis2_rep1_ChIP-exo


title: 11940_God1_rep1_ChIP-exo


title: 13889_H2BK123ub_rep1_MNase-ChIP-seq


title: 14460_Glc7_rep1_ChIP-exo


title: 17040_Gis1_rep2_ChIP-exo


title: 14479_Gre3_rep1_ChIP-exo


title: 15794_Gis1_rep1_ChIP-exo


title: 14815_Grs1_rep1_ChIP-exo


title: 16050_Gcr1_rep2_ChIP-exo


title: 19996_Gcn5_rep3_ChIP-exo

value: Weil Lab


title: 15202_Gcn5_rep2_ChIP-exo


title: 12449_Gcr1_rep1_ChIP-exo


title: 11826_Gcn5_rep1_ChIP-exo


title: 18488_Gcn4_rep2_ChIP-exo


title: 16046_Gcn4_rep1_ChIP-exo


title: 14495_Gal11_rep1_ChIP-exo


title: 15788_Fzf1_rep2_ChIP-exo


title: 11796_Gal4_rep1_ChIP-exo


title: 17127_Gal11_rep2_ChIP-exo


title: 17980_Gat1_rep1_ChIP-exo


title: 14366_Gal83_rep1_ChIP-exo


title: 15659_Gal4_rep2_ChIP-exo


title: 14187_Gal3_rep1_ChIP-exo


title: 13138_Fzf1_rep1_ChIP-exo


title: 13457_Fus3_rep1_ChIP-exo


title: 11911_Fun30_rep1_ChIP-exo


title: 14269_Fun30_rep2_ChIP-exo


title: 13452_Fsh1_rep1_ChIP-exo


title: 17142_Fra1_rep1_ChIP-exo


title: 14190_Fpr4_rep1_ChIP-exo


title: 12843_Gdh1_rep1_ChIP-exo


title: 11289_Fkh1_rep2_ChIP-exo


title: 13471_Fap7_rep1_ChIP-exo


title: 11009_Fkh1_rep1_ChIP-exo


title: 8938_Fhl1_rep1_ChIP-exo

value: Abcam ab56


title: 17157_Fcp1_rep1_ChIP-exo


title: 10542_Fkh2_rep1_ChIP-exo


title: 8944_Fhl1_rep2_ChIP-exo


title: 17968_Fkh2_rep2_ChIP-exo


title: 14462_Ess1_rep1_ChIP-exo


title: 14383_Fap1_rep1_ChIP-exo


title: 28366_Ess1_rep2_ChIP-exo


title: 14392_Esc8_rep1_ChIP-exo


title: 18480_Esc2_rep2_ChIP-exo


title: 17577_Esa1_rep1_ChIP-exo


title: 14434_Elp4_rep1_ChIP-exo


title: 12082_Esc2_rep1_ChIP-exo


title: 14836_Elp6_rep1_ChIP-exo


title: 15479_Elp3_rep1_ChIP-exo


title: 14426_Emi2_rep1_ChIP-exo


title: 14385_Erg8_rep1_ChIP-exo


title: 18477_Esa1_rep2_ChIP-exo


title: 17209_Elc1_rep1_ChIP-exo


title: 17781_Elp2_rep1_ChIP-exo


title: 13448_Ela1_rep1_ChIP-exo


title: 14982_Elf1_rep2_ChIP-exo


title: 14856_Eds1_rep1_ChIP-exo


title: 14188_Fpr3_rep1_ChIP-exo


title: 17159_Ecm5_rep2_ChIP-exo


title: 20427_Ecm22_rep2_ChIP-exo


title: 12461_Eaf7_rep1_ChIP-exo


title: 17940_Eaf6_rep2_ChIP-exo


title: 17131_Edc3_rep1_ChIP-exo


title: 14793_Ecm5_rep1_ChIP-exo


title: 18487_Ecm22_rep1_ChIP-exo


title: 11760_Eaf3_rep1_ChIP-exo


title: 14368_Ecm15_rep1_ChIP-exo


title: 14792_Eaf6_rep1_ChIP-exo


title: 17025_Eaf5_rep2_ChIP-exo


title: 13470_Doa1_rep1_ChIP-exo


title: 14481_Elf1_rep1_ChIP-exo


title: 17599_Dig1_rep1_ChIP-exo


title: 14828_Dep1_rep1_ChIP-exo


title: 13142_Eaf5_rep1_ChIP-exo


title: 13147_Dot1_rep1_ChIP-exo


title: 17867_Dst1_rep2_ChIP-exo


title: 17870_Dig1_rep2_ChIP-exo


title: 14770_Dhh1_rep1_ChIP-exo


title: 12423_Ddp1_rep1_ChIP-exo


title: 14391_Dus1_rep1_ChIP-exo


title: 14184_Dcp2_rep1_ChIP-exo


title: 14527_Dbp2_rep1_ChIP-exo


title: 14484_Dcc1_rep1_ChIP-exo


title: 17128_Dbf4_rep2_ChIP-exo


title: 20426_Dat1_rep2_ChIP-exo


title: 17026_Dbf4_rep1_ChIP-exo


title: 14175_Dat1_rep1_ChIP-exo


title: 17847_Dbp2_rep2_ChIP-exo


title: 11778_Dal81_rep1_ChIP-exo


title: 13210_Cyc8_rep2_ChIP-exo


title: 18501_Cup9_rep2_ChIP-exo


title: 12132_Dst1_rep1_ChIP-exo


title: 14387_DOT5_rep1_ChIP-exo


title: 11777_Cup9_rep1_ChIP-exo


title: 14409_Dcp1_rep1_ChIP-exo


title: 17866_Dot6_rep1_ChIP-exo


title: 12949_Cyc8_rep1_ChIP-exo


title: 17208_Cup2_rep1_ChIP-exo


title: 13445_Dbp3_rep1_ChIP-exo


title: 11749_Ctr9_rep1_ChIP-exo


title: 15196_Ctr9_rep2_ChIP-exo


title: 14975_Ctk3_rep1_ChIP-exo


title: 16047_Ctk1_rep2_ChIP-exo


title: 20082_CTDSer5_rep2_ChIP-exo

value: Millipore 04-1572-I


title: 12134_Ctk1_rep1_ChIP-exo


title: 20083_CTDSer7_rep2_ChIP-exo

value: Millipore 04-1570-I


title: 20079_CTDSer7_rep1_ChIP-exo


title: 20078_CTDSer5_rep1_ChIP-exo


title: 20081_CTDSer2_rep2_ChIP-exo

value: Millipore 04-1571-I


title: 20077_CTDSer2_rep1_ChIP-exo


title: 14866_Csr2_rep1_ChIP-exo


title: 14536_Csl4_rep1_ChIP-exo

value: TAP-tag:Sigma i5006


title: 12051_Csn12_rep1_ChIP-exo

value: YPD


title: 13817_Cse2_rep2_ChIP-exo

value: ChIP-exo


title: 26215_Cse4_rep1_ChIP-exo

value: Wu Lab


title: 12053_Cse2_rep1_ChIP-exo


title: 12876_Crz1_rep1_ChIP-exo


title: 12081_Cts1_rep1_ChIP-exo


title: 17034_Crz1_rep2_ChIP-exo


title: 13805_Cpr1_rep1_ChIP-exo


title: 17927_Crm1_rep1_ChIP-exo


title: 16598_Ctk2_rep2_ChIP-exo


title: 17956_Cln1_rep2_ChIP-exo


title: 15001_Cln1_rep1_ChIP-exo


title: 14451_Cks1_rep1_ChIP-exo


title: 28330_Cmr3_rep1_ChIP-exo


title: 18481_Ckb2_rep2_ChIP-exo


title: 12879_Ctk2_rep1_ChIP-exo


title: 14396_Ckb1_rep1_ChIP-exo


title: 20424_Cka2_rep1_ChIP-exo


title: 12875_Ckb2_rep1_ChIP-exo


title: 20423_Cka1_rep2_ChIP-exo


title: 17890_Cin5_rep2_ChIP-exo


title: 12011_Cin5_rep1_ChIP-exo


title: 17589_Csn12_rep2_ChIP-exo


title: 12056_Chd1_rep1_ChIP-exo


title: 18006_Chz1_rep1_ChIP-exo


title: 18003_Chd1_rep2_ChIP-exo


title: 20422_Cha4_rep2_ChIP-exo


title: 12003_Cha4_rep1_ChIP-exo


title: 12841_Cka1_rep1_ChIP-exo


title: 23472_Cet1_rep1_ChIP-exo


title: 17809_Cft1_rep2_ChIP-exo


title: 13456_Cdc48_rep1_ChIP-exo


title: 13450_Cdc55_rep1_ChIP-exo


title: 12010_Cdc53_rep1_ChIP-exo


title: 14403_Cdd1_rep1_ChIP-exo


title: 12029_Cdc47_rep1_ChIP-exo


title: 18483_Cdc46_rep2_ChIP-exo


title: 12934_Cdc36_rep1_ChIP-exo


title: 20994_Cka2_rep2_ChIP-exo


title: 13480_Cdc33_rep1_ChIP-exo


title: 12940_Cdc39_rep1_ChIP-exo


title: 12095_Cdc26_rep1_ChIP-exo


title: 12087_Cdc28_rep1_ChIP-exo


title: 17942_Cdc46_rep1_ChIP-exo


title: 12091_Ccr4_rep1_ChIP-exo


title: 10352_Cbf1_rep1_ChIP-exo


title: 17016_Cca1_rep2_ChIP-exo


title: 14529_Ccl1_rep1_ChIP-exo


title: 16571_Ccl1_rep2_ChIP-exo


title: 24636_Cbf1_rep2_ChIP-exo


title: 14988_Cbc2_rep2_ChIP-exo


title: 14357_Cbc2_rep1_ChIP-exo


title: 14757_Car1_rep1_ChIP-exo


title: 11922_Cam1_rep1_ChIP-exo


title: 12427_Cft1_rep1_ChIP-exo


title: 13158_Caf40_rep1_ChIP-exo


title: 17030_Caf4_rep1_ChIP-exo


title: 16544_Caf16_rep1_ChIP-exo


title: 12457_Caf130_rep1_ChIP-exo


title: 14777_Cad1_rep1_ChIP-exo


title: 17598_Caf120_rep1_ChIP-exo


title: 16029_Cac2_rep1_ChIP-exo


title: 20421_Cad1_rep2_ChIP-exo


title: 13149_Bye1_rep1_ChIP-exo


title: 20420_Bur6_rep3_ChIP-exo


title: 12435_Cca1_rep1_ChIP-exo


title: 11903_Bud6_rep1_ChIP-exo


title: 17145_Bud22_rep1_ChIP-exo


title: 17876_Bur6_rep1_ChIP-exo


title: 14493_Bud32_rep1_ChIP-exo


title: 14631_Bur2_rep2_ChIP-exo


title: 12877_Bur2_rep1_ChIP-exo


title: 19995_Bur6_rep2_ChIP-exo


title: 12844_Car2_rep1_ChIP-exo


title: 13462_Bud20_rep1_ChIP-exo


title: 17986_Brn1_rep2_ChIP-exo


title: 12943_Brn1_rep1_ChIP-exo


title: 13145_Brf1_rep1_ChIP-exo


title: 17951_Bre2_rep2_ChIP-exo


title: 14798_Bre2_rep1_ChIP-exo


title: 13446_Bmh2_rep1_ChIP-exo


title: 11752_Bre1_rep1_ChIP-exo


title: 14769_Bmh1_rep1_ChIP-exo


title: 17799_Bye1_rep2_ChIP-exo


title: 14765_Bim1_rep1_ChIP-exo


title: 12139_Bdf1_rep1_ChIP-exo


title: 15630_Bdf1_rep2_ChIP-exo


title: 12854_Bem4_rep1_ChIP-exo


title: 14278_Bdp1_rep2_ChIP-exo


title: 12113_Bdp1_rep1_ChIP-exo


title: 18464_Bcy1_rep2_ChIP-exo


title: 17013_Bdf2_rep2_ChIP-exo


title: 12116_Bdf2_rep1_ChIP-exo


title: 12870_Bud17_rep1_ChIP-exo


title: 17139_Bcy1_rep1_ChIP-exo


title: 13440_Bat2_rep1_ChIP-exo


title: 15488_Brf1_rep2_ChIP-exo


title: 19305_Azf1_rep2_ChIP-exo


title: 17773_Azf1_rep1_ChIP-exo


title: 15649_Bas1_rep2_ChIP-exo


title: 12018_Bas1_rep1_ChIP-exo


title: 20419_Asf2_rep2_ChIP-exo


title: 13789_Bre1_rep2_ChIP-exo


title: 12845_Arx1_rep1_ChIP-exo


title: 17557_Asf1_rep1_ChIP-exo


title: 17802_Asf2_rep1_ChIP-exo


title: 14860_Arr1_rep1_ChIP-exo


title: 12111_Ask10_rep1_ChIP-exo


title: 12024_Ash1_rep1_ChIP-exo


title: 28363_Asg1_rep2_ChIP-exo


title: 14374_ARP9_rep1_ChIP-exo


title: 12453_Asg1_rep1_ChIP-exo


title: 17800_Arp7_rep2_ChIP-exo


title: 12434_Arp7_rep1_ChIP-exo


title: 17582_Arp6_rep2_ChIP-exo


title: 14377_Arp4_rep1_ChIP-exo


title: 12865_Aro9_rep1_ChIP-exo


title: 17158_Arp6_rep1_ChIP-exo


title: 17950_Arp5_rep1_ChIP-exo


title: 14469_Aro80_rep1_ChIP-exo


title: 13467_Aro3_rep1_ChIP-exo


title: 12032_Arg82_rep1_ChIP-exo


title: 14970_Aro80_rep2_ChIP-exo


title: 14478_Apt1_rep1_ChIP-exo


title: 14851_Arg80_rep1_ChIP-exo


title: 14850_Arg81_rep1_ChIP-exo


title: 12090_Arp8_rep1_ChIP-exo


title: 12040_Apc9_rep1_ChIP-exo


title: 12021_Apc5_rep1_ChIP-exo


title: 17794_Aor1_rep2_ChIP-exo


title: 12950_Aor1_rep1_ChIP-exo


title: 11942_Aft2_rep1_ChIP-exo


title: 17594_Ahc1_rep1_ChIP-exo


title: 14183_Ade12_rep1_ChIP-exo


title: 13439_Aro4_rep1_ChIP-exo


title: 17768_Adr1_rep1_ChIP-exo


title: 14405_Ado1_rep1_ChIP-exo


title: 15627_Aft2_rep2_ChIP-exo


title: 19994_Ada2_rep3_ChIP-exo


title: 14778_Adk1_rep1_ChIP-exo


title: 14822_Ahc2_rep1_ChIP-exo


title: 19993_Ada1_rep1_ChIP-exo


title: 12860_Ada2_rep1_ChIP-exo


title: 11926_Acs2_rep1_ChIP-exo


title: 14640_Acs1_rep1_ChIP-exo


title: 11920_Aco1_rep1_ChIP-exo


title: 16021_Ace2_rep1_ChIP-exo


title: 19442_Abf1_rep2_ChIP-exo


title: 15254_Abf1_rep1_ChIP-exo


title: 17031_Aap1_rep2_ChIP-exo


title: 14449_Aap1_rep1_ChIP-exo


title: 14859_Abd1_rep1_ChIP-exo


title: 8 months after first infusion

status: Public on Jan 11 2021

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: scRNA sequencing with 10X 3' v2 kit

data_processing:
The Cell Ranger Suite (v3.1.0) from 10X genomics with GRCh38 reference genome was used to perform sample de-multiplexing, barcode processing and unique molecular identifier (UMI) counting. Cellranger mkfastq and count funtions were used to quantify the expression values for captured single cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: Hierarchical Data Format (HDF5 or H5) files from 10X Cell Ranger pipeline have been provided.

source_name: BM cells from a patient with MM

extract_protocol:
Bone marrow cells from a patinet with Multiple myeloma collected at various time points during the CAR T cell treatment based on the study protocol.
For all eight samples single-cell library constructions were performed using Chromium Single Cell 3` Reagent kits v2. Each sample was processed individually according to 10X genomics protocols. Poly-A selected transcripts were reverse-transcribed and full-length cDNA along with cell barcode identifiers were PCR-amplified. The constructed libraries then sequenced with Illumina platform using paired end sequencing.

tag: disease state

value: Multiple Myeloma

value: Bone Marrow


title: Relapse after first infusion

description: scRNA sequencing with 10X 3' v2 kit


title: CLL45NP

status: Public on Jan 09 2021

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

description:
AE5971
COUNTS_genes_uniquely_CLLPR_02

data_processing:
Reads were mapped against the human reference genome (GENCODE release 28) using STAR version 2.5.3a17 with the parameter outFilterMultimapNmax=1.
Genes were quantified with RSEM version 1.3.018 using the GENCODE release 28 human annotation.
Differential expression analysis was performed adjusting for patient with DESeq2 version 1.18.1.19
Genome_build: hg38
Supplementary_files_format_and_content: COUNTS_genes_uniquely_CLLPR_02

source_name: CD3+ T lymphocytes

extract_protocol:
T cells from PBMCs samples were immunomagnetically isolated using the EasySepTM Human T cell Isolation Kit (StemCell). The purity of isolated cells was >85% CD3+ as assessed by flow cytometry. Then, RNA was extracted from isolated T cells using the AllPrep DNA/RNA (Qiagen). 10ng of full-length T-cell-RNA were used to prepare sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara).
Libraries for RNA-Seq were sequenced on HiSeq2500 (Illumina) with a read length of 100bp paired-end using TruSeq SBS Kit v4 (Illumina). On average, 50 M paired-end reads were obtained per sample and 90% mapped to the reference genome.

tag: Stage

value: Non-progression


title: 17019_Ada2_rep2_ChIP-exo


title: CLL46NP

description:
AE5972
COUNTS_genes_uniquely_CLLPR_02


title: CLL47NP

description:
AE5973
COUNTS_genes_uniquely_CLLPR_02


title: CLL44NP

description:
AE5970
COUNTS_genes_uniquely_CLLPR_02


title: CLL42NP

description:
AE5969
COUNTS_genes_uniquely_CLLPR_02


title: CLL23NP

description:
AE5968
COUNTS_genes_uniquely_CLLPR_02


title: CLL18P

description:
AE5961
COUNTS_genes_uniquely_CLLPR_02

value: Progression


title: CLL51P

description:
AE5967
COUNTS_genes_uniquely_CLLPR_02


title: CLL32P

description:
AE5966
COUNTS_genes_uniquely_CLLPR_02


title: CLL17P

description:
AE5960
COUNTS_genes_uniquely_CLLPR_02


title: CLL29P

description:
AE5964
COUNTS_genes_uniquely_CLLPR_02


title: CLL19P

description:
AE5962
COUNTS_genes_uniquely_CLLPR_02


title: 17958_Ace2_rep2_ChIP-exo


title: 17945_Acs2_rep2_ChIP-exo


title: CLL7P

description:
AE5959
COUNTS_genes_uniquely_CLLPR_02


title: CLL6P

description:
AE5958
COUNTS_genes_uniquely_CLLPR_02


title: CLL2P

description:
AE5955
COUNTS_genes_uniquely_CLLPR_02


title: CLL46

description:
AE5953
COUNTS_genes_uniquely_CLLPR_02

value: Diagnosis


title: CLL3P

description:
AE5956
COUNTS_genes_uniquely_CLLPR_02


title: CLL5P

description:
AE5957
COUNTS_genes_uniquely_CLLPR_02


title: CLL47

description:
AE5954
COUNTS_genes_uniquely_CLLPR_02


title: CLL42

description:
AE5950
COUNTS_genes_uniquely_CLLPR_02


title: CLL31P

description:
AE5965
COUNTS_genes_uniquely_CLLPR_02


title: CLL24P

description:
AE5963
COUNTS_genes_uniquely_CLLPR_02


title: CLL23

description:
AE5949
COUNTS_genes_uniquely_CLLPR_02


title: CLL44

description:
AE5951
COUNTS_genes_uniquely_CLLPR_02


title: CLL32

description:
AE5947
COUNTS_genes_uniquely_CLLPR_02


title: CLL31

description:
AE5946
COUNTS_genes_uniquely_CLLPR_02


title: CLL24

description:
AE5944
COUNTS_genes_uniquely_CLLPR_02


title: CLL29

description:
AE5945
COUNTS_genes_uniquely_CLLPR_02


title: CLL17

description:
AE5941
COUNTS_genes_uniquely_CLLPR_02


title: CLL18

description:
AE5942
COUNTS_genes_uniquely_CLLPR_02


title: CLL7

description:
AE5940
COUNTS_genes_uniquely_CLLPR_02


title: CLL2

description:
AE5936
COUNTS_genes_uniquely_CLLPR_02


title: CLL19

description:
AE5943
COUNTS_genes_uniquely_CLLPR_02


title: CLL6

description:
AE5939
COUNTS_genes_uniquely_CLLPR_02


title: Packaged full-length RNA IP m6A Rep 2

status: Public on Jan 02 2021

city: Santiago

first: Daniela

last: Toro Ascuy

state: Region Metropolitana

address: Av. Independencia 1027

department: Virology

country: Chile

institute: University of Chile

description:
IP m6A RNA
MAPPED_particle_peaks.xls

data_processing:
Read quality was evaluated with FastQC v0.11.8
Burrows-Wheeler Alignment Tool v0.7.17-r1188  (BWA -Mem) were used for mapping reads to the HIV-1 genome with default parameters.
The Aligment data were analazed by MACS2 v2.1.1.20160309 to call peaks  with -f BAMPE  --nomodel --SPMR -q 0.05 options to generated viral peaks data, and to generated FPKM (Fragments Per Kilobase per Million mapped reads). Predicted peaks were sorted by average coverage.
For the adenosine conservation analysis, all the HIV-1 sequences present in HIV database were aligned with HIV Premade Aligments,ALL GENOME options, processed and classified with a inhouse script. Motif was analyzed by WebLogo v2.8.2
Genome_build: HIV-1 fasta sequence AF324493.2 vector pNL4-3
Supplementary_files_format_and_content: tab-delimited text files

organism:
Homo sapiens
HIV-1 vector pNL4-3

source_name: embryonic kidney cells

growth_protocol: HEK293T and HeLa cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Hyclone) and antibiotics (Hyclone) at 37ºC and 5% CO2 atmosphere.

extract_protocol:
Poly(A) RNA was purified from 100 mg of total RNA extracted from HEK293T cells previously transfected with pNL4.3 and pCMV-VSVg. Briefly, total RNA in 500 ml of water was incubated at 65ºC for 10 minutes and incubated with 3 ml of oligo dT-Biotin (dT-B) (50 pmol/ml) and 13 ml of SSC Buffer 20X (Santa Cruz Biotechnology) and allowed to cool at room temperature. 600 mg of Dynabeads-Streptavidin (60 ml; Thermo Fisher) were washed three times with Buffer SSC 0.5X and resuspended in 100 ml of Buffer SSC 0.5X. Then, the RNA/oligo dT-B was incubated with the streptavidin beads at room temperature for 10 minutes in head-over-tail rotation. RNA-beads were washed four times with 300 ml Buffer SSC 0.1X and bound RNA was eluted with 100 ml of water two times. The RNA was precipitated with 10 mM MgCl2, 20 mg glycogen (Thermo Fisher) and 2.5 volume of ETOH 100% overnight at -20ºC and then washed with ETOH 70%. Poly(A) RNA as well as RNA obtained from purified viral particle were fragmented using Fragmentation Reagent (Thermo Fisher). For this, 2 mg of RNA in 9 ml of water was incubated with 1 ml of Fragmentation Buffer 10X for 15 minutes at 70ºC, then 1 ml of Stop solution was added and incubated on ice. The RNA fragmented was precipitated overnight as described above. Fragmented RNA diluted in 380 ml was heated at 70ºC for 5 minutes, placed on ice for 3 minutes and incubated with 10 mL of an anti-m6A antibody (0,5 mg/mL; Synaptic System #202003). cDNA libraries preparations and RNAseq was performed at Genoma Mayor. All the samples were sequenced in an Illumina HiSeq200 platform with paired-end 100 bp read length
This was obtained as a service from Genoma Mayor, Chile.  RNA Seq/TruSeq Stranded RNA + RiboMinus.

treatment_protocol: No treatments were performed

tag: sample type

value: supernatant HEK293T, embryonic kidney cells


title: CLL3

description:
AE5937
COUNTS_genes_uniquely_CLLPR_02


title: Packaged full-length RNA Input Rep 2

description:
total RNA
MAPPED_particle_peaks.xls


title: intracellular full-length RNA IP m6A Rep 1

description:
IP m6A RNA
MAPPED_intracell_peaks.xls

value: HEK293T, embryonic kidney cells

value: m6A antibody (0,5 mg/mL; Synaptic System #202003)


title: intracellular full-length RNA IP m6A Rep 2

description:
IP m6A RNA
MAPPED_intracell_peaks.xls


title: Packaged full-length RNA IP m6A Rep 1

description:
IP m6A RNA
MAPPED_particle_peaks.xls


title: intracellular full-length RNA Input Rep 2

description:
total RNA
MAPPED_intracell_peaks.xls


title: Packaged full-length RNA Input Rep 1

description:
total RNA
MAPPED_particle_peaks.xls


title: intracellular full-length RNA Input Rep 1

description:
total RNA
MAPPED_intracell_peaks.xls


title: DIE_0h.2

status: Public on Jan 01 2021

city: Utrecht

first: Niels

last: Geijsen

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Hubrecht institute

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Cells with a minimum of 6000 transcripts were considered, and data normalization was performed by downsampling transcript counts to 6000 for all cells. Initial analysis revealed a batch effect between the two uninduced biological replicates. One sample showed signs of additional metabolic stress. The top 187 diverging genes (padj < 10**-7) between the two uninduced biological replicates were removed from all data to account for any source of metabolic stress. Dimensionality reduction of cells was done using RaceID, after which the clusters were manually determined by dividing the y-axis of the tSNE map in 10 clusters of equal size. Differential expression of genes between cell clusters were identified as described by Muraro et al. (2016), based on a previous publication of Anders and Huber (2010).
Genome_build: hg19
Supplementary_files_format_and_content: Mapped data files in tekst format containing UMI normalized barcode count, read counts and transcript counts, per cell.
Supplementary_files_format_and_content: Differential gene expression

source_name: Chronic myeloid leukemia cells

growth_protocol: IMDM basal media with 10% Tet approved FBS, and 100μM 2-ME.

extract_protocol: The library prep was performed using CEL-seq1 primers, and were processed using CEL-seq2 protocol.

treatment_protocol: 1000ng/ml doxycyline was added to growth media. DIE cells were treated with docycyline for 2, 3, 4 or 6 hours before sample collection.

tag: parental line

tag: cell line

value: DIE

value: no treattment


title: DIE_2h

value: 2h doxycline induction


title: DIE_6h

value: 6h doxycline induction


title: DIE_4h

value: 4h doxycline induction


title: DIE_2h.2


title: CLL5

description:
AE5938
COUNTS_genes_uniquely_CLLPR_02


title: DIE_3h

value: 3h doxycline induction


title: DIE_3h.2


title: CLL45

description:
AE5952
COUNTS_genes_uniquely_CLLPR_02


title: DIE_0h

value: no treatment


title: WT-0-replicate 2

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

description: Wild type small airway epithelial cells

data_processing:
bar codes were removed by skewer
alignment and quantification were performed using Salmon
differential analysis was using DESeq2

source_name: hSAEC wild type

growth_protocol: hSAECs were grown in SAGM small airway epithelial cell growth medium (Lonza, cc-3118).

extract_protocol: Cells were harvested for RNA isolation using RNeasy kit with on-column DNase digestion (Qiagen). Synthesis of complementary DNAs (cDNAs) was done with First Strand cDNA Synthesis Kit (Thermo Scientific).

treatment_protocol: SMARCA4 KD cells (“723”) with short hairpin RNA (shRNA) were generated using lentiviral particles (Sigma, TRCN0000380723 for SMARCA4 KD and SHC001V for control).  The human RSV Long strain was grown in Hep-2 cells and prepared by sucrose cushion

tag: cell type

value: human small airway epithelial cells (hSAEC)

value: Wild type

value: uninfected (0h)


title: WT-24 h-replicate 2

description: Wild type small airway epithelial cells

value: RSV infected 24 h


title: WT-0-replicate 3

description: Wild type small airway epithelial cells


title: WT-0-replicate 1

description: Wild type small airway epithelial cells


title: WT-24 h-replicate 3

description: Wild type small airway epithelial cells


title: WT-24 h-replicate 1

description: Wild type small airway epithelial cells


title: WIMR_091

status: Public on Dec 17 2020

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

country: Germany

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4, reference see link below), then trimmed using Trimgalore (version 0.4.4, reference see link below) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Sex was validated by gene expression for Y-specific genes and corrected if different from recorded sex. Two strong outliers (assigned as infected but grouping with controls and vice versa) were removed from the dataset after principle component analy
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: blood

extract_protocol:
Whole blood RNA was extracted from PAXgene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 40 million reads per RNA sample

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes.

tag: status

value: M


title: WIMR_087


title: WIMR_090


title: WIMR_088


title: WIMR_089


title: WIMR_085

value: F


title: WIMR_084


title: DIE_4h.2


title: WIMR_086


title: DIE_6h.2


title: WIMR_083


title: WIMR_080


title: WIMR_081


title: WIMR_079


title: WIMR_076


title: WIMR_082


title: WT-24 h-replicate 4

description: Wild type small airway epithelial cells


title: WIMR_075


title: WIMR_074


title: WIMR_078


title: WT-0-replicate 4

description: Wild type small airway epithelial cells


title: WIMR_072


title: WIMR_077


title: WIMR_068


title: WIMR_067


title: WIMR_065


title: WIMR_066


title: WIMR_071


title: WIMR_069


title: WIMR_063


title: WIMR_059


title: WIMR_062


title: WIMR_058


title: CLL51

description:
AE5948
COUNTS_genes_uniquely_CLLPR_02

value: Diagnosis


title: WIMR_054


title: WIMR_057


title: WIMR_061


title: WIMR_056


title: WIMR_053


title: WIMR_052


title: WIMR_051

value: Hlty


title: WIMR_050


title: WIMR_046


title: WIMR_048


title: WIMR_049


title: WIMR_047


title: WIMR_045


title: WIMR_043


title: WIMR_039


title: WIMR_042


title: WIMR_041


title: WIMR_040


title: WIMR_038


title: WIMR_060


title: WIMR_035


title: WIMR_037


title: WIMR_034


title: WIMR_032


title: WIMR_029


title: WIMR_028


title: WIMR_031


title: WIMR_027


title: WIMR_026


title: WIMR_025


title: WIMR_024


title: WIMR_022


title: WIMR_023


title: WIMR_021


title: WIMR_018


title: WIMR_015


title: WIMR_016


title: WIMR_014


title: WIMR_008


title: WIMR_009


title: WIMR_007


title: WIMR_036


title: WIMR_005


title: WIMR_003


title: WIMR_002


title: WIMR_004


title: WIMR_006


title: INFG_168


title: INFG_169


title: WIMR_001


title: INFG_165


title: INFG_162


title: INFG_161


title: INFG_166


title: INFG_163


title: INFG_164


title: INFG_159


title: INFG_160


title: INFG_157


title: WIMR_020


title: INFG_154


title: WIMR_017


title: INFG_152


title: INFG_151


title: INFG_149


title: INFG_148


title: INFG_145


title: INFG_146


title: INFG_167


title: INFG_144


title: INFG_140


title: GB941996_S247

status: Public on Dec 14 2020

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

description: iscChIC-seq

data_processing:
Library strategy: iChiC-seq
Basecalls performed
Each raw fastq file are reads corresponding to 96 cell barcodes . The 96 pairs are shown in barcode_96.txt. Read 1 is considered  to belong to one of the barcodes if  it corresponding read 2 contains  that barcode.  After separting each set of fastq files into 96 files, read 1 is mapped to the human genome hg18 using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910?914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 3000 (4000)reads for H3K4me3 (H3K27me3)  With these requirements, 7798 (9207) cells were obtained . From the bulk-cell ENCODE data, we obtaind a set of H3K4me3 peaks  (52798 peaks) that are shown in peakname3.txt and a set of H3K27me3 peaks (79100 peaks ) that are shown in combined_sicer_E100_peaks.sort.merge.txt. Using  BedTools and the H3K4me3 and H3K27me3 peak files, we obtained a set of bivalent domains (25951 bivalent domains) that are shown in K4_K27_bivalent_domain.txt.   For each H3K4me3 cell, we calculated the reads that were located within the H3K4me3 peaks and stored the results in a matrix, which can be found from the file 'scH3K4me3_7798_cell_counts_at_WBCpeaks.txt.gz' . We also calculated the reads that were located within the bivalent domains and stored the results in a matrix, which can be found from the file 'scK4_rc_at_25951_bipeaks.txt.gz' .   For each H3K27me3 cell, we calculated the reads that were located within the H3K27me3 peaks and stored the results in a matrix, which can be found from the file 'scK27_4lanes_rc_at_79100peaks_width10k.txt.gz' . We also calculated the reads that were located within the bivalent domains and stored the results in a matrix, which can be found from the file 'scK27_4lanes_rc_at_25951_bipeaks.txt.gz' .
Genome_build: hg18
Supplementary_files_format_and_content:
barcode_96.txt: one column  refers to a DNA barcode starting from the 3'
combined_sicer_E100_peaks.sort.merge.txt:first column is for chromsome, second column is for H3K27me3 peak start site, and third column is for H3K27me3 peak end site
K4_K27_bivalent_domain.txt: first column is for chromsome, second column is for bivalent domain start site, and third column is for bivalent domain end site
peakname3.txt: first column is for chromsome, second column is for H3K4me3 peak start site, and third column is for H3K4me3 peak end site
scH3K4me3_7798_cell_counts_at_WBCpeaks.txt.gz: This file contains read count data for single cells in text format. The rows refer to H3K4me3 peaks while the column refer to single cells. Reading the matrix results in a 52798 x 7798 matrix.
scK27_4lanes_rc_at_25951_bipeaks.txt.gz: This file contains read count data for single cells in text format. The rows refer to bivalent domains while the column refer to single cells. Reading the matrix results in a 25951 x 9207 matrix.
scK27_4lanes_rc_at_79100peaks_width10k.txt.gz:This file contains read count data for single cells in text format. The rows refer to H3K27me3 peaks while the column refer to single cells. Reading the matrix results in a 79100 x 9207matrix
scK4_rc_at_25951_bipeaks.txt.gz: This file contains read count data for single cells in text format. The rows refer to bivalent domains while the column refer to single cells. Reading the matrix results in a 25951 x 7798 matrix.

source_name: human WBC H3K27me3

extract_protocol:
iscChIC-seq human 1.25M 2-step crosslink human healthy WBC, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 30 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of WBCsuspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 106 cells per tube) at −80°C until use.

value: WBC


title: GB941992_S243

description: iscChIC-seq


title: INFG_156


title: GB941994_S245

description: iscChIC-seq


title: GB941990_S241

description: iscChIC-seq


title: GB941987_S238

description: iscChIC-seq


title: GB941993_S244

description: iscChIC-seq


title: GB941995_S246

description: iscChIC-seq


title: GB941985_S236

description: iscChIC-seq


title: GB941984_S235

description: iscChIC-seq


title: GB941988_S239

description: iscChIC-seq


title: GB941986_S237

description: iscChIC-seq


title: GB941982_S233

description: iscChIC-seq


title: GB941983_S234

description: iscChIC-seq


title: INFG_153


title: GB941981_S232

description: iscChIC-seq


title: INFG_139


title: GB941991_S242

description: iscChIC-seq


title: INFG_147


title: GB941979_S230

description: iscChIC-seq


title: GB941980_S231

description: iscChIC-seq


title: GB941977_S228

description: iscChIC-seq


title: GB941978_S229

description: iscChIC-seq


title: INFG_141


title: GB941975_S226

description: iscChIC-seq


title: GB941976_S227

description: iscChIC-seq


title: GB941974_S225

description: iscChIC-seq


title: GB941989_S240

description: iscChIC-seq


title: GB941973_S224

description: iscChIC-seq


title: GB941971_S222

description: iscChIC-seq


title: GB941970_S221

description: iscChIC-seq


title: GB941969_S220

description: iscChIC-seq


title: GB941968_S219

description: iscChIC-seq


title: GB941972_S223

description: iscChIC-seq


title: GB941959_S210

description: iscChIC-seq


title: GB941960_S211

description: iscChIC-seq


title: GB941965_S216

description: iscChIC-seq


title: GB941962_S213

description: iscChIC-seq


title: GB941964_S215

description: iscChIC-seq


title: GB941958_S209

description: iscChIC-seq


title: GB941957_S208

description: iscChIC-seq


title: GB941963_S214

description: iscChIC-seq


title: GB941967_S218

description: iscChIC-seq


title: GB941956_S207

description: iscChIC-seq


title: GB941953_S204

description: iscChIC-seq


title: GB941955_S206

description: iscChIC-seq


title: GB941952_S203

description: iscChIC-seq


title: GB941954_S205

description: iscChIC-seq


title: GB941951_S202

description: iscChIC-seq


title: GB941949_S200

description: iscChIC-seq


title: GB941946_S197

description: iscChIC-seq


title: GB941948_S199

description: iscChIC-seq


title: GB941950_S201

description: iscChIC-seq


title: GB941945_S196

description: iscChIC-seq


title: GB941947_S198

description: iscChIC-seq


title: GB941966_S217

description: iscChIC-seq


title: GB941942_S193

description: iscChIC-seq


title: GB941944_S195

description: iscChIC-seq


title: GB941941_S192

description: iscChIC-seq


title: GB941961_S212

description: iscChIC-seq


title: GB941940_S191

description: iscChIC-seq


title: GB941938_S189

description: iscChIC-seq


title: GB941939_S190

description: iscChIC-seq


title: GB941937_S188

description: iscChIC-seq


title: GB941934_S185

description: iscChIC-seq


title: GB941935_S186

description: iscChIC-seq


title: GB941929_S180

description: iscChIC-seq


title: GB941932_S183

description: iscChIC-seq


title: GB941931_S182

description: iscChIC-seq


title: GB941928_S179

description: iscChIC-seq


title: GB941920_S171

description: iscChIC-seq


title: GB941924_S175

description: iscChIC-seq


title: GB941921_S172

description: iscChIC-seq


title: GB941925_S176

description: iscChIC-seq


title: GB941926_S177

description: iscChIC-seq


title: GB941927_S178

description: iscChIC-seq


title: GB941943_S194

description: iscChIC-seq


title: GB941917_S168

description: iscChIC-seq


title: GB941918_S169

description: iscChIC-seq


title: GB941916_S167

description: iscChIC-seq