title: Gravity

city: Madras Institute of Technology, Chrompet

first: Suvro

last: Chatterjee

state: Tamil Nadu

address: Vascular Biology Laboratory

country: India

institute: AU-KBC Research Centre, Anna University

data_processing:
Raw reads were trimmed to remove the clipped NEBNext adapter sequences at 5'(GTTCAGAGTTCTACAGTCCGACGATC) and 3' (AGATCGGAAGAGCACACGTCT) using cutadapt program v1.8.1
The other non-coding RNAs like siRNA, piRNA, snoRNA, snRNA, tRNA, rRNA were filtered from adapter trimmed reads using bowtie2 version 2.1.0
The conservered miRNAs were identified by mapping the  filtered reads against miRBase release 21 database using bowtie version 0.12.9
The novel miRNA identification was performed using miRDeep2 version 2.0.0.7 by mapping the unaligned reads from previous steps against human genome hg19
Differential expression analysis of samples was done using R version 3.0.2 software DESeq package
Genome_build: Human genome hg19 reference fasta files were indexed using bowtie tool version 0.12.9
Supplementary_files_format_and_content: Gene expression of the samples in comma seperated format

source_name: HUVECs

growth_protocol: Cells were grown in simulated microgravity condition(experimental group)for 2 hours and gravity(control) cells were grown in static condition. All experiments were done at 37°C.

extract_protocol:
Total RNA was isolated using Trizol reagent, Invitrogen Life Technologies. The total RNA samples was checked for quality using Nanodrop and 1% agarose gel. RNA  samples, free of DNA and protein contamination was resuspended in in nuclease free water. 1ug of RNA sample for each stage was given for Next Generation Sequencing.
Small RNA library was prepared using NEBNext Multiplex small RNA Library prep kit in which 3’(AGATCGGAAGAGCACACGTCT) adaptors and 5’ (GTTCAGAGTTCTACAGTCCGACGATC) adaptors ligated to the total RNA, later performed with reverse transcription reaction. The library was enriched by PCR amplification of 15 cycles and size selected using 4% E-gel (Invitrogen). The product at ~147bp was purified using PureLink Gel Extraction and PCR purification Combo kit, Invitrogen and eluted in 25ul Nuclease Free water. The quality of library was checked using TapeStation (Agilent Technologies) to confirm the average library size. The final library product was sequenced with 1x50bp single end cycles to obtain 20-30 million reads per sample using Illumina HiSeq2500 platform (Illumina Inc, USA).

tag: envirnoment

value: clinostat


title: Microgravity

status: Public on Aug 24 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: static


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E8_AD010_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOs

tag: Sex

value: male

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E8_AD008_indexed


title: 323_colon1 [re-analysis]

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
323-AS-1_S1
reanalysis of GSM3131535

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
Human and mouse genes were separated and then human and mouse cells were deconvolved to observe doublet rate.
Mouse cells were selected for further analysis.
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

organism:
Homo sapiens
Mus musculus

growth_protocol: primary cells/cell line mix

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA extraction and Collagenase/DNAse dissociation. Viable cells were enriched with MACS. K562 cells were spiked in. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

tag: mouse strain

tag: human cell line


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E8_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E8_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E9_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD007_indexed


title: Plus Whisker 2

first: Robert

last: Pulido

address: 9500 Gilman Ave, BSB 3095

institute: UC San Diego

data_processing:
Sequenced reads were mapped to Ensembl mm9 v67 whole genome using tophat v 2.0.11 and bowtie2 v2.2.1 with parameters no-coverage-search -m 2 -a 5 -p 7
Alignment files were sorted using SAMtools v.0.1.19
Count tables were generated using HTSeq-0.6.1
Differential expression was analyzed using DESeq2
Genome_build: Ensembl mm9 v67
Supplementary_files_format_and_content: .xlsx files with the output of DESeq2 from the 3 experiments and what was considered gene expression changes. The master file has the counts per million (CPM) for each replicate

source_name: Brain: Barrel Cortex

extract_protocol:
Neural Activity was manipulated, brain regions were dissociated using both chemical and mechanical dissociation methods and CD31-Alexa 647+ cells were enriched using FACS sorting
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were sequenced using the HiSeq4000 using paired-end 100 base pair reads

tag: tissue

value: Brain:Barrel Cortex

tag: strain/genotype

tag: condition

value: Whisker/barrel stimulation


title: Plus Whisker 3


title: Minus Whisker 3

value: No whisker/barrel stimulation


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD008_indexed


title: Silencing 4

source_name: Brain: Cortex and Hippocampus

value: Brain:Cortex and Hippocampus

value: C57BL/6 CamKIIa-tTA; TRE-hM4Di

value: Glutamatergic Silencing


title: Minus Whisker 1


title: Plus Whisker 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD010_indexed


title: Silencing 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD001_indexed


title: Silencing 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD012_indexed


title: Silencing Control 4

value: Control


title: Silencing Control 2


title: Silencing Control 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E8_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD008_indexed


title: Silencing Control 1


title: Minus Whisker 2


title: Activating 4

value: C57BL/6 CamKIIa-tTA; TRE-hM3Dq

value: Glutamatergic Activation


title: Activating 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD007_indexed


title: Activating 2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD012_indexed


title: Silencing 2


title: Activating Control 4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD008_indexed


title: Activating 1


title: Activating Control 2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_F10_AD001_indexed


title: Activating Control 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD002_indexed


title: Activating Control 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E4_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E7_AD006_indexed


title: KD2

city: Gangzhou

first: jin

last: wang

address: Xinzao Panyu District

country: China

institute: Guangzhou Medical University

data_processing:
The library preparations were sequenced on an Illumina Hiseq 4000 and 150bp paired-end reads were generated.
Image analysis and base calling were performed with Illumina CASAVA pipeline
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis was performed using the DESeq2 R package (1.10.1).
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include count or FPKM values for each gene in each sample

source_name: hippocampus

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

treatment_protocol: 6 adult (2-3 month-old) C57BL/6J mice were divided into two groups, one fed with control diet and the other fed with the ketogenic diet. After 3 weeks of feeding, hippocampi were collected and subjected to RNA extraction.

value: hippocampus

tag: treatment

value: ketogenic diet

value: adult (2-3 month-old)


title: KD1


title: KD3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD007_indexed


title: CD2

value: control


title: CD3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E4_AD007_indexed


title: CD1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E4_AD006_indexed


title: GI_2043: FMTg Small Intestine_Rep 5

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.5.1) using Bioconductor package DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-deliminated data matrix of normalized gene counts

source_name: Small Intestine

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent following manufacturers protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small Intestine

value: 60 days post-natal

tag: genotype

value: Mdm2FM/- Cag-CreERTg


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E6_AD006_indexed

value: MOs

value: male


title: GI_2235: FMTg Small Intestine_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E4_AD010_indexed


title: GI_2806: FMTg Small Intestine_Rep 2


title: GI_2972: FMTg Small Intestine_Rep 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E4_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E4_AD001_indexed


title: GI_2933: Tg Small Intestine_Rep 3

value: Mdm2+/- Cag-CreERTg


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E5_AD001_indexed


title: GI_2598: Tg Small Intestine_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD012_indexed


title: GI_2808: Tg Small Intestine_Rep 2


title: Heart_1977: FMTg Heart_Rep 4

source_name: Heart

value: Heart


title: Heart_2972: FMTg Heart_Rep 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD006_indexed


title: Heart_1964: FMTg Heart_Rep 5


title: Heart_2806: FMTg Heart_Rep 2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD007_indexed


title: GI_2039: FMTg Small Intestine_Rep 4


title: Heart_2235: FMTg Heart_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD006_indexed


title: Heart_2933: Tg Heart_Rep 3


title: hESC_drived_organoid_TES

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: applying single cell method to hESC-derived 3D retinal organoids

data_processing:
Illumina Casava1.7 software used for basecalling.
5' and 3' sequences were extracted from paired-end sequences using Perl, Python and shell script
5' and 3' sequences were aligned  to mm10, using STAR (2.6.1a), with with parameters (--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6).
Peaks were called with CAGEr (v 1.24.0) .
For smart-seq2 data, sequenced reads were trimmed for adaptor sequence using cutapapt (v 1.18) and aligned to mm10 using STAR  with with parameters as described above.
For Iso-seq data, sequence data were processed using the SMRTlink5.0 software. Circular consensus sequence (CCS) was generated from subread BAM files, parameters: min_length 200, max_drop_fraction 0.8, no_polish TRUE, min_zscore -9999, min_passes 1, min_predicted_accuracy 0.8, max_length 18000. CCS.BAM files were  classified into full length and non-full length reads using pbclassify.py script, ignore polyA false, minSeq Length 200. Non-full length and full-length fasta files produced were then fed into the cluster step, which does isoform-level clustering(ICE), followed by final Arrow polishing, hq_quiver_min_accuracy 0.99, bin_by_primer false, bin_size_kb 1, qv_trim_5p 100, qv_trim_3p 30.
Additional nucleotide errors in consensus reads were corrected using the Illumina RNA seq data with the software LoRDEC.
consensus reads were aligned to reference Genome using GMAP with parameters --no-chimeras --cross-species --expand-offsets 1 –B 5 –K 50000 –f samse –n 1 against reference genome.
Gene structure analysis was performed using TAPIS pipeline.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: [scRCAT-seq] *bed file reports the TSS/TES position
Supplementary_files_format_and_content: [Iso-seq] *gtf reports the isoform information which were detected by Iso-seq.

molecule: polyA RNA

extract_protocol:
DRG, oocytes, hESC, HEK293T, ARPE, mESC, hESC_drived_organoid were dissected and dissociated into single cells. hESC, HEK293T, ARPE, mESC, hESC_drived_organoid were dissected respectively and mixed together.
The scRCAT-seq library was prepared according to the scRCAT-seq protocol
The smart-seq2 library was prepared according to the smart-seq2 protocol
The Iso-Seq library was prepared according to the Isoform Sequencing protocol

value: hESC-derived 3D retinal organoids


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD012_indexed


title: scRCAT-seq_single_hESC_23

description:
applying single cell method to hESC
hESCsccatUMI_5.bed.gz, hESCsccatUMI_3.bed.gz

source_name: hESC

value: hESC


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E3_AD002_indexed


title: scRCAT-seq_single_hESC_22


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD010_indexed


title: scRCAT-seq_single_hESC_21


title: Heart_2808: Tg Heart_Rep 2


title: scRCAT-seq_single_hESC_20


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD002_indexed


title: Ovary_2119: FMTg Ovary_Rep 5

source_name: Ovary

value: Ovary


title: Heart_2598: Tg Heart_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD012_indexed


title: Ovary_2041: FMTg Ovary_Rep 4


title: scRCAT-seq_single_hESC_19


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD008_indexed


title: scRCAT-seq_single_hESC_18


title: Ovary_2972: FMTg Ovary_Rep 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD007_indexed


title: Ovary_2806: FMTg Ovary_Rep 2


title: scRCAT-seq_single_hESC_17


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E2_AD007_indexed


title: scRCAT-seq_single_hESC_16


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E12_AD012_indexed


title: Ovary_2235: FMTg Ovary_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E4_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E12_AD008_indexed


title: scRCAT-seq_single_hESC_15


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD010_indexed


title: Ovary_2933: Tg Ovary_Rep 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD001_indexed


title: Ovary_2808: Tg Ovary_Rep 2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD010_indexed


title: scRCAT-seq_single_hESC_13


title: scRCAT-seq_single_hESC_14


title: Ovary_2598: Tg Ovary_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E12_AD004_indexed


title: Kidney_1964: FMTg Kidney_Rep 5

source_name: Kidney

value: Kidney


title: scRCAT-seq_single_hESC_12


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E12_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD008_indexed


title: scRCAT-seq_single_hESC_11


title: Kidney_1977: FMTg Kidney_Rep 4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD002_indexed


title: scRCAT-seq_single_hESC_10


title: scRCAT-seq_single_hESC_9


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD007_indexed


title: Kidney_2972: FMTg Kidney_Rep 3


title: Kidney_2806: FMTg Kidney_Rep 2


title: scRCAT-seq_single_hESC_8


title: Kidney_2235: FMTg Kidney_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD006_indexed


title: Kidney_2933: Tg Kidney_Rep 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E12_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD004_indexed


title: Kidney_2808: Tg Kidney_Rep 2


title: scRCAT-seq_single_hESC_6


title: Kidney_2598: Tg Kidney_Rep 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E11_AD002_indexed


title: scRCAT-seq_single_hESC_7


title: scRCAT-seq_single_hESC_5


title: scRCAT-seq_single_hESC_4


title: total B Day6 G9A-Inhibition donor3

type: RNA

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data were quantile normalised using Lumi for R.

label: Biotin

source_name: Peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol:
Peripheral blood was obtained from healthy donors after informed consent. Mononuclear cells were isolated by Lymphoprep (Axis Shield) density gradient centrifugation. Total B-cells were isolated by negative selection with the Memory B-cell Isolation Kit (Miltenyi Biotec). Memory-enriched B cells fractions were isolated by negative selection following incubation of total, negatively selected B cell fractions with CD23 Biotin and anti-Biotin Microbeads (Miltenyi Biotec)
Cells were grown in 24 well plates in Iscove Modified Dulbecco Medium (IMDM) supplemented with Glutamax and 10% heat-inactivated fetal bovine serum (HIFBS, Invitrogen). This was supplementetd from Day 3 onwards with Hybridomax hybridoma growth supplement (11 µl/ml), Lipid Mixture 1, chemically defined and MEM Amino Acids solution (both at 1x).
B cells were cultured at 2.5 X 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (10 µg/ml) on γ-irradiated CD40L expressing L cells (6.25 X 10^4/well).
At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).
For the G9Ai (small molecule inhibitor UNC0638) experiments, ABCs were treated at day-3 with UNC0638 inhibitor (2 µM). Cells were sampled at the indicated time points without further addition of inhibitor
RNA was extracted with Trizol and amplified using Illumina® TotalPrepTM-96 RNA Amplification Kit

tag: cell type

value: total B cells

tag: differentiation

tag: culture-conditions

value: At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml) + 2 µM UNC0638 G9A inhibitor


title: Pancreas_2043: FMTg Pancreas_Rep 5

source_name: Pancreas

value: Pancreas


title: scRCAT-seq_single_hESC_3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD007_indexed


title: Pancreas_2039: FMTg Pancreas_Rep 4


title: total B Day6 G9A-Inhibition donor2


title: total B Day6 G9A-Inhibition donor1


title: total B Day5 G9A-Inhibition donor3


title: total B Day5 G9A-Inhibition donor2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD006_indexed


title: Pancreas_2972: FMTg Pancreas_Rep 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD004_indexed


title: scRCAT-seq_single_hESC_1


title: total B Day5 G9A-Inhibition donor1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E1_AD004_indexed


title: total B Day4 G9A-Inhibition donor2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD010_indexed


title: scRCAT-seq_single_HEK293T_24

description: applying single cell method to HEK293T


title: scRCAT-seq_single_HEK293T_23

description: applying single cell method to HEK293T


title: Pancreas_2806: FMTg Pancreas_Rep 2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD012_indexed


title: Pancreas_2933: Tg Pancreas_Rep 3


title: scRCAT-seq_single_hESC_2


title: Pancreas_2808: Tg Pancreas_Rep 2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD012_indexed


title: Pancreas_2598: Tg Pancreas_Rep 1


title: Pancreas_2971: FMTg Pancreas_Rep 1


title: scRCAT-seq_single_HEK293T_20

description: applying single cell method to HEK293T


title: scRCAT-seq_single_HEK293T_19

description: applying single cell method to HEK293T


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD010_indexed


title: scRCAT-seq_single_HEK293T_21

description: applying single cell method to HEK293T


title: Ctl_WT_6

city: Memphis

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: whole testes from male mice

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, and mapped to the moouse mm10 whole genome with the STAR aligner. TPM for transcripts were reported.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all samples

source_name: wild type without heat shock replicate 6

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase.
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 4000 platform.

value: testis

value: wild type


title: Ctl_WT_4

description: whole testes from male mice

source_name: wild type without heat shock replicate 4


title: Ctl_WT_5

description: whole testes from male mice

source_name: wild type without heat shock replicate 5


title: scRCAT-seq_single_HEK293T_22

description: applying single cell method to HEK293T


title: total B Day4 G9A-Inhibition donor1


title: total B Day3 +12hr G9A-Inhibition donor3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD007_indexed


title: total B Day3 +12hr G9A-Inhibition donor2


title: total B Day3 +12hr G9A-Inhibition donor1


title: total B Day3 +6hr G9A-Inhibition donor3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD006_indexed


title: total B Day3 +6hr G9A-Inhibition donor2


title: total B Day4 G9A-Inhibition donor3


title: scRCAT-seq_single_HEK293T_17

description: applying single cell method to HEK293T


title: scRCAT-seq_single_HEK293T_18

description: applying single cell method to HEK293T


title: total B Day3 +3hr G9A-Inhibition donor3


title: Ctl_WT_3

description: whole testes from male mice

source_name: wild type without heat shock replicate 3


title: total B Day3 +3hr G9A-Inhibition donor2


title: total B Day3 +3hr G9A-Inhibition donor1


title: scRCAT-seq_single_HEK293T_16

description: applying single cell method to HEK293T


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD008_indexed


title: Ctl_WT_2

description: whole testes from male mice

source_name: wild type without heat shock replicate 2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD002_indexed


title: Ctl_WT_1

description: whole testes from male mice

source_name: wild type without heat shock replicate 1


title: scRCAT-seq_single_HEK293T_15

description: applying single cell method to HEK293T


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD001_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD007_indexed


title: Ctl_KO_6

description: whole testes from male mice

source_name: Mageb4 KO without heat shock replicate 6

value: Mageb4 knockout


title: scRCAT-seq_single_HEK293T_13

description: applying single cell method to HEK293T


title: total B Day6 Standard donor3

value: At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).


title: Ctl_KO_5

description: whole testes from male mice

source_name: Mageb4 KO without heat shock replicate 5


title: total B Day3 +6hr G9A-Inhibition donor1


title: scRCAT-seq_single_HEK293T_12

description: applying single cell method to HEK293T


title: Ctl_KO_4

description: whole testes from male mice

source_name: Mageb4 KO without heat shock replicate 4


title: Ctl_KO_3

description: whole testes from male mice

source_name: Mageb4 KO without heat shock replicate 3


title: scRCAT-seq_single_HEK293T_11

description: applying single cell method to HEK293T


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D9_AD004_indexed


title: Ctl_KO_2

description: whole testes from male mice

source_name: Mageb4 KO without heat shock replicate 2


title: scRCAT-seq_single_HEK293T_14

description: applying single cell method to HEK293T


title: scRCAT-seq_single_HEK293T_10

description: applying single cell method to HEK293T


title: Ctl_KO_1

description: whole testes from male mice

source_name: Mageb4 KO without heat shock replicate 1


title: scRCAT-seq_single_HEK293T_9

description: applying single cell method to HEK293T


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD002_indexed


title: scRCAT-seq_single_HEK293T_8

description: applying single cell method to HEK293T


title: 72h_WT_4

description: whole testes from male mice

source_name: wild type 72h after heat shock replicate 4


title: total B Day6 Standard donor2


title: 72h_WT_3

description: whole testes from male mice

source_name: wild type 72h after heat shock replicate 3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E12_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD010_indexed


title: total B Day6 Standard donor1

source_name: Peripheral blood


title: scRCAT-seq_single_HEK293T_6

description: applying single cell method to HEK293T


title: 72h_WT_2

description: whole testes from male mice

source_name: wild type 72h after heat shock replicate 2


title: scRCAT-seq_single_HEK293T_5

description: applying single cell method to HEK293T


title: total B Day5 Standard donor2


title: 72h_WT_1

description: whole testes from male mice

source_name: wild type 72h after heat shock replicate 1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD012_indexed


title: total B Day3 +12hr Standard donor2


title: total B Day5 Standard donor3


title: total B Day4 Standard donor3


title: total B Day3 +12hr Standard donor3


title: total B Day5 Standard donor1


title: scRCAT-seq_single_HEK293T_7

description: applying single cell method to HEK293T


title: scRCAT-seq_single_HEK293T_4

description: applying single cell method to HEK293T


title: 72h_KO_4

description: whole testes from male mice

source_name: Mageb4 KO 72h after heat shock replicate 4


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD008_indexed


title: scRCAT-seq_single_HEK293T_3

description: applying single cell method to HEK293T


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD006_indexed


title: total B Day4 Standard donor1


title: total B Day4 Standard donor2


title: 72h_KO_5

description: whole testes from male mice

source_name: Mageb4 KO 72h after heat shock replicate 5


title: scRCAT-seq_single_HEK293T_2

description: applying single cell method to HEK293T


title: scRCAT-seq_single_HEK293T_1

description: applying single cell method to HEK293T


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD006_indexed


title: 72h_KO_2

description: whole testes from male mice

source_name: Mageb4 KO 72h after heat shock replicate 2


title: total B Day3 +6hr Standard donor1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD004_indexed


title: total B Day3 +6hr Standard donor3


title: total B Day3 +12hr Standard donor1


title: total B Day3 +3hr Standard donor2


title: total B Day3 +6hr Standard donor2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD007_indexed


title: 72h_KO_3

description: whole testes from male mice

source_name: Mageb4 KO 72h after heat shock replicate 3


title: total B Day3 +3hr Standard donor3


title: MCF7_tgfb_treated_2

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

institute: Indian Institute of Science Education and Research Bhopal

description: Transcriptome data after treating MCF7 cells with 10 ng/ml TGF-β ligand (Biological Rep 2)

hyb_protocol: Hybridization was done on Affymetrix GeneChipTM Human Transcriptome Array 2.0 (HTA 2.0) chips at 45 ⁰C for 16 hrs.

scan_protocol: Chips were scanned using Affymetrix Scanner 7G

data_processing:
Transcriptome Analysis Console 4.0 was used to analyze files generated after scanning
HTA-2_0.r1.pgf
HTA-2_0.na33.1.hg19

source_name: Breast cancer cell line MCF7

label_protocol: 100 ng of total RNA was used to prepare biotinylated cDNA using GeneChipTM WT Plus Reagent Kit (Applied Biosystems) as per the instructions given by the manufacturer.

growth_protocol: MCF7 and HCC1806 cells were cultured in media recommended by American Type Cell Culture in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol: Samples were lysed using TRIzol reagent (Invitrogen), and total RNA was isolated using the PureLink RNA Mini Kit (Invitrogen)

treatment_protocol: For analyzing alternative splicing under hypoxia, cell were either cultured at 21% O2 (normoxia) or at 1% O2 (hypoxia). For TGF-β treatment, cells were treated with 10 ng/ml of TGF-β ligand.

tag: cell line

value: Breast cancer cell line (luminal)

tag: gender

value: Female


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D7_AD002_indexed

source_name: C57BL/6J Male P56 Mouse Brain

value: MOs


title: ko2 12h

city: Montreal

first: Nathalie

last: Labrecque

state: QC

address: 5415, boul. de l’Assomption Montréal (Québec)

department: Microbiology and Immunology

country: Canada

institute: Université de Montréal

data_processing:
NexteraPE-PE adapters were removed using Trimmomatic 0.36
Reads were aligned to mm10 reference genome using Bowtie2.2.6. Obtained bam files were converted to bigwig files for visualization.
PCR duplicates were removed with Picard MarkDuplicates 2.4.1 and reads mapping to mitochondiral DNA were removed.
Deeptools was used to shift reads coordinates to represent the real Tn5 binding site and to remove ENCODE's blacklisted regions (signal artefact regions).
MACS 2.0.10 was used for peak calling using q-value < 0.001 to define peaks
DESeq2 was used to identify DARs (differentially accessible regions) between WT and KO.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for each sample

source_name: CD8+ T cells (OT-I)

growth_protocol: Nr4a3 deficient or sufficient naive OT-I CD8+ T cells were isolated from lymph nodes and purified with EasySep kit (ref #: 19858) to isolate naive OT-I CD8+ T cells

extract_protocol:
DNA was purified by Mini-Elute PCR Purification columns (Qiagen) and enriched by 12 cycles of PCR. The library was recovered from PCR reaction by GeneRead Purification columns (Qiagen) and then it was double strand sequenced on Illumina (HiSeq4000 PE50)
Prified DNA was enriched by 12 cycles of PCR. The library was recovered from PCR reaction by GeneRead Purification columns (Qiagen) and then it was double strand sequenced on Illumina (HiSeq4000 PE100)

treatment_protocol: Naive Nr4a3 deficient or sufficient OT-I CD8+ T cells were stimulated with plate bound anti-CD3 and soluble anti-CD28 antibodies for 12h; nuclei of  stimulated OT-I CD8 T cells were then immediately isolated and used for tagmentation reaction and DNA purification

tag: activating condition

tag: activation details

value: In vitro activation of naive OT-I CD8 T cells

value: Nr4a3 KO OT-I


title: wt2 12h

value: Nr4a3 WT OT-I


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD010_indexed

tag: brain region

tag: Sex

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD012_indexed

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD008_indexed


title: ko1 12h


title: total B Day3 +3hr Standard donor1


title: wt1 12h


title: 72h_KO_1

description: whole testes from male mice

source_name: Mageb4 KO 72h after heat shock replicate 1


title: 9: Nutlin 3b D2211B

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling was performed using Illumina’s RTA version 2.7.3.
Data were analyzed by the MAP-RSeq 3.0.1 pipeline developed by the Mayo Clinic Bioinformatics Core (Kalari et al., BMC Bioinformatics 2014;15:224)
Reads aligned to the mouse reference genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR) software package (PMID: 23104886)
RSeQC software was used for estimating the distance between paired end reads, evaluating the sequencing depth for alternate splicing analysis, determining the rate of duplicate reads, and evaluating coverage of reads across genes
Gene and exon counts were estimated using the featureCounts program in the Subread package (PMID: 24227677)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene counts with corresponding RPKM values

source_name: D2211B cells

growth_protocol: Cell line was cultured in Lonza® SmGM-2 at at 39.5°C without interferon-gamma. The SV40 tsA58 large T antigen was undetectable by western blot and immunofluorescence.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit.
RNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the TruSeq® Stranded Total RNA LT - (with Ribo-Zero™ Human/Mouse/Rat) - Set A (Cat# RS-122-2201, Illumina, San Diego, CA).

treatment_protocol: Nutlin 3a or nutlin 3b applied at 30 µM for 72 hours

value: gastric tunica muscularis

value: ICC stem cell


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD004_indexed


title: 7: Nutlin 3a D2211B


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD007_indexed


title: total B Day3 donor3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD001_indexed


title: MCF7_tgfb_treated_1

description: Transcriptome data after treating MCF7 cells with 10 ng/ml TGF-β ligand (Biological Rep 1)


title: MCF7_tgfb_control_2

description: Transcriptome data for MCF7 cells without TGF-β treatment  (control) (Biological Rep 2)


title: total B Day3 donor1


title: HCC1806_tgfb_treated_2

description: Transcriptome data after treating HCC1806 cells with 10 ng/ml TGF-β ligand (Biological Rep 2)

source_name: Breast cancer cell line HCC1806

value: Breast cancer cell line (triple negative)


title: 5: Nutlin 3b D2211B


title: total B Day3 donor2

value: total B cells


title: MCF7_tgfb_control_1

description: Transcriptome data for MCF7 cells without TGF-β treatment  (control) (Biological Rep 1)


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD006_indexed


title: 1: Nutlin 3b D2211B


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD012_indexed


title: total B Day0 donor2

value: B cells were cultured at 2.5 X 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (10 µg/ml) on γ-irradiated CD40L expressing L cells (6.25 X 10^4/well).


title: total B Day0 donor3


title: HCC1806_tgfb_control_2

description: Transcriptome data for HCC1806 cells without TGF-β treatment  (control) (Biological Rep 2)


title: total B Day0 donor1


title: HCC1806_tgfb_control_1

description: Transcriptome data for HCC1806 cells without TGF-β treatment  (control) (Biological Rep 1)


title: 11: Nutlin 3a D2211B


title: HCC1806_tgfb_treated_1

description: Transcriptome data after treating HCC1806 cells with 10 ng/ml TGF-β ligand (Biological Rep 1)


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD001_indexed


title: 3: Nutlin 3a D2211B


title: MCF7_hypoxia_2

description: Transcriptome data after culturing MCF7 cells in 1% O2 (Biological Rep 2)


title: memory B Day6 donor3

value: memory B cells


title: memory B Day6 donor1


title: memory B Day6 donor2


title: MCF7_hypoxia_1

description: Transcriptome data after culturing MCF7 cells in 1% O2 (Biological Rep 1)


title: PCMO cells isolated from donor D

city: Kuopio

first: Tuija

last: Kekarainen

state: Northern Savonia

address: Microkatu 1

department: Cell Therapy Unit

country: Finland

institute: Kuopio Center for Gene and Cell Therapy

data_processing:
STAR_2.5.2b;   runMode alignReads;  outSAMtype BAM Unsorted
R GenomicAlignments::summarizeOverlaps  mode = "Union"  fragments = FALSE  singleEnd = FALSE  ignore.strand = FALSE  preprocess.reads = invertStrand
DESeq2
Genome_build: Ensembl GRCh38 patch 12 release 95
Supplementary_files_format_and_content: raw counts

source_name: peripheral blood

growth_protocol: All cells were harvested from a separately designated culture vessel (bag or flask) directly in RNAprotect Cell reagent (Qiagen). Isolated cells were allocated 5x106 cells per tube and frozen at -20°C. Aliquots of CD14+ monocytes were resuspended in RNAprotect Cell reagent immediately after LP14 purification and frozen at -20°C. For prolonged storage cells were transferred to -80°C freezer.

extract_protocol:
Two aliquots of frozen cells (5x106 cells each) were sent off to GATC (Eurofins) Biotech where RNA purification and next generation sequencing (NGS) were completed. An extraction kit was used (Eurofins won't say which one), that has stranded templating, and uses the second directional strand for templating (fr-secondstrand)
A commercially available kit that Eurofins refuses to specify, citing "property rights"  - Purification of poly-A containing mRNA molecules  - mRNA fragmentation  - Random primed cDNA synthesis (strand specific)  - Adapter ligation and Adapter specific PCR amplification

treatment_protocol: Variations of LPS, Interferon-gamma, Human AB serum, IL-3, IL-4, Human mCSF, media changes, and plastic container

tag: leukapheresis donor

value: D

value: PCMO

tag: polarization stimulant

tag: culture vessel

value: flask


title: PCMO cells isolated from donor C

value: C


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D6_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D8_AD010_indexed


title: memory B Day5 donor3

value: At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD008_indexed


title: MCF7_normoxia_2

description: Transcriptome data after culturing MCF7 cells in 21% O2 (Biological Rep 2)

tag: tissue

value: Breast cancer cell line (luminal)

value: Female


title: memory B Day5 donor1


title: memory B Day4 donor3


title: MCF7_normoxia_1

description: Transcriptome data after culturing MCF7 cells in 21% O2 (Biological Rep 1)


title: memory B Day5 donor2


title: HCC1806_hypoxia_1

description: Transcriptome data after culturing HCC1806 cells in 1% O2 (Biological Rep 1)


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD006_indexed

value: MOs


title: PCMO cells isolated from donor B

value: B


title: HCC1806_hypoxia_2

description: Transcriptome data after culturing HCC1806 cells in 1% O2 (Biological Rep 2)


title: HCC1806_normoxia_2

description: Transcriptome data after culturing HCC1806 cells in 21% O2 (Biological Rep 2)


title: memory B Day4 donor2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD010_indexed


title: Mreg_UKR cells isolated from donor H

value: H

value: IFNg

value: bag


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD007_indexed

value: male


title: HCC1806_normoxia_1

description: Transcriptome data after culturing HCC1806 cells in 21% O2 (Biological Rep 1)

value: Breast cancer cell line (triple negative)


title: Mreg_UKR cells isolated from donor I

value: I


title: PCMO cells isolated from donor A

value: A


title: memory B Day4 donor1

value: memory B cells


title: GII-III.5

city: Sydney

first: Susannah

last: Hallal

state: NSW

address: 119-143 Missenden Road

department: Neurosurgery

country: Australia

institute: Chris O'Brien Lifehouse

description: sncRNA data

data_processing:
The fastq files were uploaded to the Qiagen GeneGlobe® Data Analysis Centre for analysis by the QiaSeq® miRNA primary quantification pipeline (Qiagen, Venlo, Netherlands)
3’ adapter and low-quality bases were trimmed from the reads using Cutadapt
Insert sequences and unique molecular index (UMI) sequences were identified and annotated and Bowtie was used to remove known contaminants by sequentially aligning the reads
Reads were mapped by perfect match to miRBase mature, miRBase hairpin, noncoding RNA, mRNA and other RNA. At each step, only unmapped sequences passed to the next step and remaining unmapped sequences were mapped to the human miRBase mature database (human: Genome Reference Consortium GRCh38) where up to two mismatches were tolerated
Genome_build: Genome Reference Consortium GRCh38
Supplementary_files_format_and_content: .xlsx normalized read and UMI counts and differential expression data

source_name: Brain, Neurosurgical fluid, Extracellular Vesicles

extract_protocol:
Total RNA extraction by plasma/serum circulating and exosomal RNA purification kit (Slurry Format; Norgen Biotek Corp, ON, Canada; Cat No. 42800)
Starting total template CUSA-EV RNA (4 ng) was used to prepare the small RNA (sRNA) libraries using a QIASeqTM miRNA Library Kit (Qiagen, Venlo, Netherlands)
NGS was performed on an Illumina® NextSeqTM 500 NGS System (Illumina, San Diego, CA, USA). The libraries were sequenced in a single-end 75 bp, high-output protocol to generate an output of up to 400 million reads at a Q30 > 85 %

treatment_protocol: No treatment

tag: disease state

value: Glioma, Grade II-III astrocytoma


title: GII-III.2

description: sncRNA data


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D5_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD006_indexed


title: GII-III.4

description: sncRNA data


title: Mreg_UKR cells isolated from donor E

value: E


title: Mreg_UKR cells isolated from donor G

value: G


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD012_indexed


title: GBM.12

description: sncRNA data

value: Glioblastoma, Grade IV astrocytoma


title: Mreg_UKR cells isolated from donor F

value: F


title: GII-III.3

description: sncRNA data


title: Mreg_UKR cells isolated from donor D

value: D


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD008_indexed


title: Mreg_UKR cells isolated from donor C

value: C


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD010_indexed

value: MOs


title: Mreg_UKR cells isolated from donor B

value: B


title: GBM.11

description: sncRNA data


title: GBM.10

description: sncRNA data


title: Mreg_UKR cells isolated from donor A


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD012_indexed


title: GII-III.1

description: sncRNA data


title: GBM.9

description: sncRNA data


title: memory B Day3 +12hr donor3

value: At day-3 cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).


title: memory B Day3 +12hr donor2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD004_indexed


title: memory B Day3 +6hr donor2


title: Mreg cells isolated from donor D

value: Mreg

value: IFNg

value: flask


title: memory B Day3 +6hr donor3


title: memory B Day3 +6hr donor1


title: memory B Day3 +12hr donor1


title: GBM.7

description: sncRNA data


title: Mreg cells isolated from donor C


title: memory B Day3 +3hr donor3


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD002_indexed

value: male


title: GBM.8

description: sncRNA data


title: Mreg cells isolated from donor B


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D4_AD001_indexed


title: GBM.6

description: sncRNA data


title: memory B Day3 +3hr donor1


title: memory B Day3 +3hr donor2


title: Mreg cells isolated from donor A


title: GBM.5

description: sncRNA data


title: M2a cells isolated from donor I

value: I

value: bag


title: memory B Day3 donor2

value: memory B cells


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD010_indexed


title: GBM.4

description: sncRNA data


title: memory B Day3 donor3


title: AS601

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Alignment of sequenced reads was done with STAR 2.4.2a. STAR index was created using splice junction annotation database for guidance and both genome sequence and annotation files of Ensembl Rnor 6.0
Quantification of gene expression was achieved through featureCounts 1.4.3-p1 with Ensembl Rnor 6.0 annotation
Genome_build: Ensembl rnor 6.0
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

organism: Rattus norvegicus

source_name: Brain

growth_protocol: Male Long Evans rats weighing between 250-300 grams and approximately 10-12 weeks of age were utilized.

extract_protocol:
Whole brains were extracted and flash frozen in methylbutane chilled with dry ice. Frozen brains were subsequently coronally sectioned using a 1mm brain matrix. Sections were gently brushed onto slides and stored in -80°C.  . Bihemispheric tissue samples of the central nucleus/ basolateral (CeA/BLA) amygdala were collected for each subject using 1.50-mm tissue punches and stored for downstream processing. Punches were taken between approximately -2.6mm and -3.2mm from Bregma (28)
RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (Kapa Biosystems) in accordance with the manufacturer’s instructions and sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 2 x 50bp cycles.

treatment_protocol: Rats were exposed to multiple BOP (blast overpressure) events using the Walter Reed Army Institute of Research (WRAIR) shock tube. The Subjects assigned to blast-exposed groups received a single 74.5 kPa (≈10.8 psi) BOP event every 24 hours for 72 hours.  Control (i.e., sham blast) subjects were treated in an identical manner to blast-exposed subjects barring the BOP exposures.

value: CeA/BLA amygdala

tag: timepoint

value: Acute

tag: treatment

value: Sham


title: AS238


title: M2a cells isolated from donor H

value: H

tag: cell type


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD004_indexed


title: GBM.2

description: sncRNA data

value: Glioblastoma, Grade IV astrocytoma


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD007_indexed


title: AB226

value: Blast


title: GBM.3

description: sncRNA data


title: memory B Day3 donor1

tag: differentiation

tag: culture-conditions


title: M2a cells isolated from donor F

value: F


title: AS232


title: M2a cells isolated from donor G

value: G


title: AS224


title: M2a cells isolated from donor E

value: E


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD010_indexed

value: MOs


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD012_indexed


title: GBM.1

description: sncRNA data


title: AS221


title: AS204


title: M1 cells isolated from donor D

value: D

value: IFNg+LPS


title: M1 cells isolated from donor C

value: C


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD004_indexed

value: male


title: wi_38_p40_1_wgbs

city: Basel

first: Alejandro

last: Reyes

address: Fabrikstrasse 22

department: Data Sciences

country: Switzerland

institute: Novartis Institutes For BioMedical Research

data_processing:
BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
Methylation data processing. BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
HiC Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
HiChip Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Supplementary_files_format_and_content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary_files_format_and_content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.

source_name: Cell line

extract_protocol: Total genomic DNA was isolated using the DNAeasy Blood & Tissue Kit (Qiagen) and for each sample, one microgram of DNA was sheared using the Covaris LE220. Libraries were prepared according to manufacturer’s instructions using the NEXTFLEX bisulfite library prep kit (NOVA-5119-01). Libraries were sequenced on the Illumina NextSeq500 instrument.

tag: sample type

value: Cell line

tag: biological sample


title: AB109


title: AS105


title: M1 cells isolated from donor B

value: B

value: bag


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD008_indexed


title: wi_38_p30_1_wgbs


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD001_indexed


title: M0 cells isolated from donor D


title: AB234

value: CeA/BLA amygdala


title: wi_38_p16_2_wgbs


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD002_indexed


title: M0 cells isolated from donor C


title: AB108

value: Acute


title: CD14 cells isolated from donor I

value: I


title: SW480-2_RNA-seq

data_processing:
RNA-seq data was mapped to the reference transcriptome (hg19) using salmon (Patro et al, 2017) and differential expression analyses were done as described in Bioconductor’s RNA-seq workflow by Love et al., 2015.
Methylation data processing. BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
HiC Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
HiChip Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Supplementary_files_format_and_content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary_files_format_and_content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.

extract_protocol: Whole RNA was extracted using the QIAGEN RNeasy kit according to the manufacturer’s protocol. For RNA-seq library preparation, Poly(A) RNA was enriched using magnetic oligo(dT)-beads (Life Technologies) and then ligated to RNA adaptors for sequencing. RNA-seq was performed with two biological replicates per colon cancer line and in singlicate for tumor samples. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.


title: M0 cells isolated from donor B


title: wi_38_p16_1_wgbs


title: CD14 cells isolated from donor H

value: H


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD006_indexed


title: CS119

value: Chronic

value: Sham


title: CB135

value: Blast


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D3_AD006_indexed


title: wi_38_p30_2_wgbs


title: CS150


title: RKO-2_RNA-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD001_indexed


title: RKO-1_RNA-seq


title: CD14 cells isolated from donor G

value: G


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD007_indexed


title: CS140


title: CD14 cells isolated from donor F

value: F


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD006_indexed

value: MOs


title: SW480-1_RNA-seq


title: MGH8416_RNA-seq

source_name: Colon tumor

value: Colon tumor


title: CS125


title: MGH5328_RNA-seq


title: CD14 cells isolated from donor E

value: E


title: wi_38_p40_2_wgbs


title: CS112


title: CD14 cells isolated from donor D

value: D


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD012_indexed

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D2_AD002_indexed


title: CB143


title: MGH3535-WCE_ChIP-seq

data_processing:
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Methylation data processing. BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
HiC Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
HiChip Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Supplementary_files_format_and_content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary_files_format_and_content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.

extract_protocol: ChIP-seq was performed as described previously (Liau et al., 2016).  In brief, crosslinked cells were lysed and DNA was sheared to between 400 and 2,000 base pair fragments.  Antibodies were as follows: CTCF (Cell signaling #3418), H3K27ac (Active Motif #39133), H3K9me3 (Abcam #8898), H3K27me3 (Cell Signaling #97335).  ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3′ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters. Barcoded fragments were amplified via PCR. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD007_indexed

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: CS146


title: CD14 cells isolated from donor B


title: CS148


title: MGH28891-WCE_ChIP-seq


title: MGH29208-K27me3_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D12_AD010_indexed


title: CB128


title: MGH29208-WCE_ChIP-seq


title: CS118


title: NEG005-Input

city: Jinan

first: Jin

state: China

address: No.2,  Jianguo xiaojing road, Jinan City, Shandong Province, PR China

institute: Jinan Maternal and Child Health Care Hospital

data_processing:
library strategy: meRIP-seq
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter,trimmed adaptor bases by cutadapt) were aligned to genome sequences from Ensembl using HISAT2 software (v2.1.0).
Aligned reads were used for peak calling by exomePeak, statistically significant MeRIP enriched regions (peaks) were also identified for each compare by exomePeak.
The MeRIP enriched regions (peaks)were annotated by the overlapped gene using the newest Ensembl database.
Then the statistic of peak in each transcript region was done.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The read Numbers at each position of chromosomes in the comparison results were calculated, and the results were saved as UCSCbedGraph format after being standardized (RPM)

extract_protocol:
Total RNA samples are qualified by agarose gel electrophoresis and quantified using Nanodrop.
mRNA was isolated and then fragmented to 100-nucleotide-long fragments. m6A methylated mRNAs were enriched with anti-N6-methyadenosine (m6A) antibody. We use commercial kit for RNA-seq library preparation of m6A mRNA and input samples. Completed libraries were qualified and then sequenced on Hiseq 4000 platform.

tag: subject status

value: control patient

tag: gestational age

value: placenta


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D12_AD007_indexed

tag: brain region

tag: Sex


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD010_indexed

tag: age

tag: strain


title: AS219


title: AB216


title: NEG004-Input


title: NEG004-IP

tag: antibody

value: anti-N6-methyadenosine(m6A) antibody


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_E10_AD002_indexed


title: CD14 cells isolated from donor C

tag: leukapheresis donor

value: C

tag: polarization stimulant

tag: culture vessel


title: MGH2834-K36me3_ChIP-seq


title: AB222

tag: tissue

value: CeA/BLA amygdala

tag: timepoint

value: Acute


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D12_AD008_indexed


title: NEG003-IP


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D12_AD012_indexed


title: AB227

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD004_indexed


title: NEG003-Input


title: NEG005-IP


title: AS237


title: LS174T-2_RNA-seq

value: Cell line


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD002_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C9_AD012_indexed


title: NEG002-IP


title: LS174T-1_RNA-seq


title: MGH28891-K36me3_ChIP-seq


title: MGH2834-WCE_REP4_ChIP-seq


title: AB236


title: NEG002-Input


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D10_AD004_indexed


title: CD14 cells isolated from donor A

value: A

tag: cell type


title: HCT116-DMSO-24h-2_RNA-seq

value: 5-azacytidine was obtained from SelleckChem (S1782) and HCT116 cells were cultured in the presence of 5 uM or 1:2000 DMSO control.  Cells were plated in media containing 5-aza or DMSO and harvested at 24 h and 7 days.  Media was refreshed with fresh 5-aza every 2nd day for the 7 day culture.


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D1_AD001_indexed


title: ECL005-IP

value: preeclampsia patient


title: HCT116-DMSO-24h-1_RNA-seq


title: ECL005-Input


title: AB239

value: Blast


title: MGH2834_RNA-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D10_AD012_indexed


title: AS212

value: Sham


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D10_AD010_indexed

value: MOs


title: HCT116-5AZA-24h-1_RNA-seq


title: HCT116-5AZA-24h-2_RNA-seq


title: AS211


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D10_AD008_indexed


title: ECL004-Input


title: ECL003-IP


title: AS209


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C9_AD004_indexed


title: HCT116-2_RNA-seq


title: HCT116-1_RNA-seq


title: ECL003-Input


title: AS104


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C9_AD010_indexed


title: CB147

value: Chronic


title: ECL001-IP


title: CB124


title: CB126


title: ECL001-Input


title: ECL004-IP


title: FHC-1_RNA-seq


title: BRD3409N-K36me3_ChIP-seq

value: Colon tumor


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C9_AD007_indexed


title: FHC-2_RNA-seq


title: BRD3187N_RNA-seq

source_name: Normal colon

value: Normal colon


title: NEG005

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: placenta

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

tag: disease

value: control


title: CB121

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D10_AD002_indexed


title: CS115


title: NEG004


title: BRD3187_RNA-seq

tag: sample type


title: CB136


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD004_indexed


title: CS129


title: BRD3179_RNA-seq

tag: biological sample


title: NEG002


title: BRD3174_RNA-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD001_indexed


title: MGH3535-K36me3_ChIP-seq


title: CS137


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD006_indexed


title: ECL005

value: preeclampsia


title: CS127


title: ECL004


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C9_AD008_indexed


title: BRD3162N-K36me3_ChIP-seq


title: CS141


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD012_indexed


title: BRD3162_RNA-seq


title: ECL003


title: ECL001


title: NEG003


title: right colon CD

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: colon

growth_protocol: primary cells

extract_protocol:
Human epithelial cell suspensions were obtained by EDTA extraction and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

tag: disease state

value: Crohn's Disease (remission with mild disease index)

value: colon

tag: biopsy

value: right colonic biopsy


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD002_indexed

tag: brain region


title: CB149

value: CeA/BLA amygdala

tag: Sex


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD008_indexed

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD007_indexed

tag: strain


title: left colon CD

value: left colonic biopsy


title: MGH8416-WCE_REP2_ChIP-seq

data_processing:
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
processed data files format and content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.
Genome_build: hg19

extract_protocol: ChIP-seq was performed as described previously (Liau et al., 2016).  In brief, crosslinked cells were lysed and DNA was sheared to between 400 and 2,000 base pair fragments.  Antibodies were as follows: CTCF (Cell signaling #3418), H3K27ac (Active Motif #39133), H3K9me3 (Abcam #8898), H3K27me3 (Cell Signaling #97335).  ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3‚Ä≤ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters. Barcoded fragments were amplified via PCR. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.


title: CD4_A_g_80

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

description:
rawReadsData.csv
Counts_Normalization_cd4.csv

data_processing:
Reads were mapped, using STAR software (version 2.6.0a), to human reference genome GrCh38 (v83), obtaining 60,675 annotated genes.
The number of reads (counts) for each gene was determined using HTSeq python package (version 0.9.0)
Between-lane normalization from EDASeq R package (version 2.18.0) was performed to force the upper quartile of reads in each lane to be the same.
Normalized data not available for five samples that did not not pass QC (PBMC_A_g_09, CD14_E_g_32, CD14_E_g_39, CD4_A_m_63, CD4_E_g_32).
Genome_build: GrCh38 (v83)
Supplementary_files_format_and_content: Raw read counts; normalized counts

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll-Paque™ (GE healthcare life Sciences, Little Chalfont, United Kingdom). The PBMCs were subsequently sorted using Magnetic Cell Isolation and Cell Separation (AutoMACS Pro 360; Miltenyi Biotec, Bergisch Gladbach, Germany), positively selected for monocytes using CD14 MicroBeads, human, and negatively selected for CD4+ T cells using the CD4+ T Cell Isolation Kit, human (both from Miltenyi Biotec), according to the manufacturer’s protocol. RNA was extracted using the RNeasy Mini Kit (Qiagen) and tested for quantity and purity by Nanodrop (Thermo Scientific) and quality by RIN-value with Agilent 2100 Bioanalyzer (Agilent technologies, Inc., Santa Clara, Ca, USA). All Samples were aliquoted and stored per 1.5-2.0 µg at -80°C until use.
Total RNA was sent to GenomeScan B.V. (Leiden, Netherlands) for library preparation and sequencing. Before sequencing, the RNA sample preparation was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s protocol. Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed.

tag: sequencingid

value: CD4+ T cells

value: m

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: good

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf

value: Positive

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CB111

tag: tissue

tag: timepoint

value: Chronic

tag: treatment

value: Blast


title: CD4_E_m_79

tag: cell type

tag: Sex

tag: disease state

tag: age

value: Etanercept

value: moderate

value: yes


title: MGH8416-WCE_ChIP-seq

value: Colon tumor

tag: biological sample


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD012_indexed

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: brain region

value: MOs

value: male

tag: strain


title: BRD3162N-WCE_ChIP-seq

tag: sample type


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD010_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD001_indexed


title: CB134

value: CeA/BLA amygdala


title: CD4_E_n_76

tag: sequencingid

value: f

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

value: never

tag: weight


title: MGH8416-K27me3_ChIP-seq

tag: tissue


title: CD4_E_n_77

value: CD4+ T cells

value: rheumatoid arthritis (RA)

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CB132

tag: Sex

tag: timepoint

tag: treatment


title: CS144

value: Sham


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD004_indexed

tag: brain region

tag: age

tag: strain


title: AB206

value: Acute


title: CD4_E_n_75

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

value: Positive


title: CD4_A_n_74

value: Adalimumab

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight

value: Negative


title: AS233

tag: tissue


title: MGH5328-K27Ac_ChIP-seq

tag: biological sample


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD008_indexed

tag: Sex


title: CD4_A_m_73

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C8_AD010_indexed

tag: brain region

tag: age

tag: strain


title: MGH5328-CTCF_ChIP-seq

tag: treatment


title: AB229

tag: timepoint

value: Blast


title: CB139

value: Chronic


title: CD4_E_m_72

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: moderate

value: stopped


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD002_indexed

value: MOs

tag: Sex

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD012_indexed


title: MGH8416-K27Ac_ChIP-seq

tag: tissue

value: Colon tumor

tag: biological sample


title: MGH5238-WCE_ChIP-seq


title: AB218

value: CeA/BLA amygdala


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C9_AD002_indexed


title: MGH2834-WCE_REP2_ChIP-seq


title: CD4_A_m_70

value: m

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount


title: AB110

tag: treatment


title: AB101

tag: timepoint


title: CD4_E_g_69

tag: sequencingid

value: CD4+ T cells

tag: age

value: good

tag: leucocytencount

tag: trombocytencount


title: MGH2834-WCE_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD010_indexed

tag: brain region

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C7_AD007_indexed

tag: Sex


title: MGH2834-K9me3_ChIP-seq

tag: tissue


title: CD4_E_n_68

tag: cell type

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

value: no


title: CB122


title: AB207

value: Acute


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD007_indexed


title: MGH2834-K27Ac_ChIP-seq

tag: biological sample


title: MGH2834-CTCF_ChIP-seq


title: CD4_E_n_67

tag: height

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

value: Positive

tag: anti-ccp

tag: hemoglobinecount


title: AB205

tag: timepoint

tag: treatment

value: Blast


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD004_indexed

tag: brain region

tag: age

tag: strain


title: CD4_E_n_71

tag: sequencingid

tag: cell type

tag: Sex

value: Etanercept

tag: leucocytencount

tag: trombocytencount


title: MGH1904-WCE_ChIP-seq

tag: tissue

tag: biological sample


title: AS215

value: Sham


title: AS223


title: CD4_A_n_64

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

tag: height

tag: alcoholuseunitsweek

value: stopped

value: Negative


title: HCT116-DMSO-24h-WCE-2_ChIP-seq

value: HCT116 Cell line

tag: treatment

value: 5-azacytidine was obtained from SelleckChem (S1782) and HCT116 cells were cultured in the presence of 5 uM or 1:2000 DMSO control.  Cells were plated in media containing 5-aza or DMSO and harvested at 24 h and 7 days.  Media was refreshed with fresh 5-aza every 2nd day for the 7 day culture.


title: AB103

value: CeA/BLA amygdala

value: male

tag: timepoint


title: 2304B-08-37B

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchips using standard Illumina protocol

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

data_processing:
R 3.4.2, minfi 1.24
Unmethylated and methylated signal intensities and detection p-value
normalized Average Beta by minfi stratified quantile normalization, cross-reactionary probes and probes with bad quality were removed

label: Cy3, Cy5

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Whole blood was collected for session 1 (28 subjects) at pre exposure, session 2 (31 subjects) at both pre- and post- exposure, using PAXgene blood DNA tubes and stored at -80˚C. Genomic DNA was isolated using PAXgene Blood DNA kit

treatment_protocol: Subjects went throught a 3-day explosive breaching training course where they were exposed to controlled, low-level blast

value: Whole blood

tag: session

value: Session 1 (site 8)

tag: time

value: post

tag: age

tag: tbi

tag: breaching history


title: CD4_A_m_63

tag: sequencingid

tag: cell type

value: CD4+ T cells

tag: Sex

value: f

value: rheumatoid arthritis (RA)

value: moderate

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD012_indexed

tag: brain region

value: MOs

tag: strain


title: HCT116-DMSO-24h-K27me3_ChIP-seq

tag: tissue

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD010_indexed


title: BRD3328N-WCE_ChIP-seq

value: Normal colon


title: MGH8416-K9me3_ChIP-seq

value: Colon tumor


title: CD4_E_n_66

tag: disease state

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

value: Positive

tag: trombocytencount


title: 2304B-08-35B

tag: session

tag: time

tag: age

tag: Sex

tag: tbi

tag: breaching history


title: BRD3328N-CTCF_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD006_indexed

tag: brain region

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD002_indexed


title: CD4_E_m_61

tag: sequencingid

tag: cell type

value: never

tag: weight

tag: rf

value: Negative

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount


title: CD4_E_n_65

tag: disease state

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

value: stopped


title: CD4_A_n_60

tag: Sex

value: m

tag: age

value: Adalimumab

value: yes

tag: trombocytencount


title: 2304B-08-32B

tag: tissue

value: Whole blood

tag: session

value: Session 1 (site 8)

tag: time

value: post

value: male

tag: tbi

tag: breaching history


title: CD4_E_n_62

tag: sequencingid

tag: cell type

value: CD4+ T cells

value: rheumatoid arthritis (RA)

tag: weight

tag: rf

tag: anti-ccp


title: AS208

value: CeA/BLA amygdala

tag: timepoint

value: Acute

tag: treatment

value: Sham


title: BRD3187-WCE_REP2_ChIP-seq

value: Colon tumor

tag: biological sample


title: CD4_A_g_59

value: f

tag: disease state

tag: studysubjectid

tag: drug

tag: response

value: good

tag: height

tag: alcoholuseunitsweek

value: Positive

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD007_indexed

tag: brain region

value: MOs

tag: Sex

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD006_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C6_AD001_indexed


title: BRD3187-WCE_ChIP-seq

tag: tissue


title: BRD3187N-WCE_ChIP-seq

value: Normal colon


title: 2304B-08-29B

tag: session

tag: time

tag: tbi

tag: breaching history


title: CD4_A_n_58

tag: sequencingid

tag: cell type

tag: disease state

value: Adalimumab

value: no

tag: weight

tag: rf

tag: anti-ccp

tag: trombocytencount


title: CD4_E_m_57

value: m

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

value: yes

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD004_indexed

tag: brain region

tag: Sex

value: male

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD002_indexed


title: BRD3187N-K27me3_ChIP-seq

tag: tissue

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD008_indexed


title: MGH1904-CTCF_ChIP-seq


title: 2304B-08-28B

value: Whole blood

tag: session

value: Session 1 (site 8)

tag: time

value: post

tag: tbi

tag: breaching history


title: CD4_E_n_56

tag: sequencingid

tag: cell type

value: CD4+ T cells

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: stopped

tag: weight

tag: rf

tag: anti-ccp

tag: trombocytencount


title: BRD3187-K9me3_ChIP-seq

value: Colon tumor


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C5_AD001_indexed

tag: brain region

tag: Sex

tag: age

tag: strain


title: 2304B-08-27B

tag: tissue

tag: session


title: CD4_E_g_55

value: f

tag: response

value: good

tag: height

tag: alcoholuseunitsweek

value: never

value: Negative

value: Positive

tag: hemoglobinecount

tag: leucocytencount


title: BRD3187-K27me3_ChIP-seq

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C4_AD012_indexed

value: MOs


title: CD4_E_n_54

tag: sequencingid

tag: cell type

value: m

tag: disease state

tag: studysubjectid

tag: drug

value: Etanercept

value: no

tag: weight


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C4_AD010_indexed

tag: brain region

tag: Sex

value: male

tag: age


title: BRD3187-K27Ac_ChIP-seq

tag: tissue


title: 2304B-08-25B

value: Whole blood

tag: session

tag: time

tag: tbi

tag: breaching history


title: 2304B-08-26B

value: Session 1 (site 8)


title: CD4_E_m_53

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 2304B-08-24B

value: post


title: 2304B-08-30B


title: BRD3187-CTCF_ChIP-seq

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C4_AD006_indexed

tag: brain region

tag: Sex

tag: strain


title: BRD3179-WCE_ChIP-seq

tag: tissue


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C4_AD004_indexed

tag: age


title: BRD3179N-WCE_REP3_ChIP-seq

value: Normal colon


title: 2304B-08-23B

tag: session

tag: time

tag: tbi


title: CD4_E_g_51

tag: sequencingid

tag: cell type

value: CD4+ T cells

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: weight


title: 2304B-08-22B

tag: breaching history


title: BRD3179N-WCE_REP2_ChIP-seq

tag: biological sample

tag: treatment


title: CD4_E_g_50

tag: Sex

value: f

tag: alcoholuseunitsweek

value: stopped

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C4_AD001_indexed

tag: brain region

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD012_indexed


title: CD4_A_g_78

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

value: good


title: 2304B-08-20B

tag: tissue

tag: session

tag: time

tag: tbi

tag: breaching history


title: 2304B-08-21B

tag: Sex


title: CD4_E_g_48

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Positive

tag: anti-ccp

tag: hemoglobinecount


title: BRD3179N-WCE_ChIP-seq

tag: biological sample

tag: treatment


title: BRD3179N-K27me3_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD010_indexed

tag: brain region

value: MOs

tag: age

tag: strain


title: 2304B-08-19B

tag: tissue

tag: session


title: BRD3179N-K27Ac_ChIP-seq


title: CD4_E_g_47

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

tag: leucocytencount

tag: trombocytencount


title: 2304B-08-17B

tag: time

tag: Sex

tag: tbi

tag: breaching history


title: CD4_E_n_52

value: m

tag: response

tag: height

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD008_indexed

tag: brain region

tag: age

tag: strain


title: CD4_A_g_46

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

value: never

value: Negative


title: BRD3179N-CTCF_REP2_ChIP-seq

tag: tissue

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD007_indexed

tag: Sex

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C4_AD002_indexed


title: CD4_A_n_45

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: leucocytencount

tag: trombocytencount


title: BRD3179N-CTCF_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD006_indexed

tag: brain region


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD004_indexed

tag: age


title: CD4_E_g_44

value: Etanercept

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount


title: 2304B-08-11B

value: Whole blood

tag: session

value: Session 1 (site 8)

tag: time

value: post

tag: tbi

tag: breaching history


title: BRD3179-K27Ac_ChIP-seq

tag: tissue

value: Colon tumor

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD002_indexed

tag: Sex

tag: strain


title: BRD3179-CTCF_ChIP-seq


title: 2304B-08-12B


title: CD4_E_n_43

tag: sequencingid

tag: cell type

value: CD4+ T cells

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

tag: leucocytencount


title: CD4_A_n_42

tag: age

value: Adalimumab

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: 2304B-08-10B

tag: tissue

tag: session

tag: time

tag: Sex

tag: tbi

tag: breaching history


title: 2304B-08-33B


title: BRD3170N-WCE_ChIP-seq

value: Normal colon

tag: biological sample

tag: treatment


title: 2304B-08-9B


title: 2304B-08-8B


title: CD4_E_n_40

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

tag: response

tag: height

value: stopped

value: Positive


title: BRD3170N-K9me3_ChIP-seq


title: 2304B-08-16B

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C2_AD012_indexed

tag: brain region

value: MOs

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C2_AD008_indexed