title: Hippocampus P309 B6xCAST Cell 094


title: Hippocampus P309 B6xCAST Cell 096

status: Public on Jan 07 2021

type: SRA

city: Cambridge

first: Longzhi

last: Tan

state: MA

address: 12 Oxford St

department: Chemistry and Chemical Biology

country: USA

institute: Harvard University

library_source: genomic

data_processing:
Library strategy: Dip-C
Please see 00README.md
Genome_build: mm10
Supplementary_files_format_and_content: Please see 00README.md

molecule: genomic DNA

organism: Mus musculus

source_name: hippocampus

extract_protocol: [Isolation of cell nuclei] Cell nuclei were isolated based on protocols from (Krishnaswami et al., 2016; Lacar et al., 2016) with minor modifications. In particular, Tris buffer would react with formaldehyde, and was therefore substituted with equal molarity of HEPES buffer. See details below:  Cortex and hippocampus were dissected in ice-cold PBS, and placed in 2 mL nuclei isolation medium with Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT, 0.1% Triton X-100) in a 2 mL Dounce homogenizer (Sigma D8938). Note that DTT concentration was not specified in (Krishnaswami et al., 2016); here we used 1 uM from (Lacar et al., 2016).  Tissues were homogenized with 5 strokes of the loose (A) pestle, and 15 strokes of the tight (B) pestle. The homogenate was centrifuged for 8 min at 94 g, 4 C, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei isolation medium without Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT).  The tube was centrifuged for 8 min at 94 g, 4 C again, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei storage buffer (0.1665 M sucrose, 5 mM MgCl2, 10 mM HEPES pH 8.0), and filtered with 40 um. Note that sucrose concentration was not specified in (Krishnaswami et al., 2016); here we used 0.1665 M from (Lacar et al., 2016). Also note that the recipe in (Lacar et al., 2016) seems to have typos in some ingredient volumes; here we followed the final concentrations.  [Fixation of cell nuclei] Nuclei were fixed according to our Dip-C protocol (Tan et al., 2019) with minor modifications. In particular, nuclei were fixed directly in the 1 mL nuclei storage buffer (with HEPES instead of Tris buffer; see above) rather than switching to PBS; and centrifugation was performed at 1,000 g rather than 600 g. See detailed below:  Nuclei were directly in the nuclei storage buffer (1 mL) with the addition of 66.7 uL 32% PFA (EMS 15714) to a final concentration of 2%. The tube was rotated for 10 min at room temperature; and 200 uL 1% BSA in PBS was then added. The tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant removed. The pellet was resuspended in 1 mL ice-cold 1% BSA in PBS. Nuclei were counted and aliquoted to up to 0.5 million per tube. Each tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant was removed. The pellet was stored at -80 C.  [Diploid chromatin conformation Capture (Dip-C)] A pellet of fixed cell nuclei was thawed on ice. We then proceeded directly to the step where 50 uL 0.5% SDS was added in the Dip-C protocol (Tan et al., 2019) and followed through with no modifications. Cells were sorted on a Beckman Coulter MoFlo Astrios, and amplified with homemade Nextera.

tag: tissue

value: hippocampus

tag: age

tag: strain


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title: Cortex P7 CASTxB6 Cell 123


title: Cortex P7 CASTxB6 Cell 107


title: Cortex P7 CASTxB6 Cell 103


title: Cortex P7 CASTxB6 Cell 102


title: Cortex P7 CASTxB6 Cell 104


title: Cortex P7 CASTxB6 Cell 101


title: Cortex P7 CASTxB6 Cell 120


title: Cortex P7 CASTxB6 Cell 099


title: Cortex P7 CASTxB6 Cell 098


title: Cortex P7 CASTxB6 Cell 122


title: Cortex P7 CASTxB6 Cell 100


title: Cortex P7 CASTxB6 Cell 115


title: Cortex P7 CASTxB6 Cell 116


title: Cortex P7 CASTxB6 Cell 096


title: Cortex P7 CASTxB6 Cell 097


title: Cortex P7 CASTxB6 Cell 093


title: Cortex P7 CASTxB6 Cell 092


title: Cortex P7 CASTxB6 Cell 089


title: Cortex P7 CASTxB6 Cell 088


title: Cortex P7 CASTxB6 Cell 091


title: Cortex P7 CASTxB6 Cell 086


title: Cortex P7 CASTxB6 Cell 087


title: Cortex P7 CASTxB6 Cell 095


title: Cortex P7 CASTxB6 Cell 085


title: Cortex P7 CASTxB6 Cell 105


title: Cortex P7 CASTxB6 Cell 082


title: Cortex P7 CASTxB6 Cell 078


title: Cortex P7 CASTxB6 Cell 083


title: Cortex P7 CASTxB6 Cell 084


title: Cortex P7 CASTxB6 Cell 094


title: Cortex P7 CASTxB6 Cell 076


title: Cortex P7 CASTxB6 Cell 077


title: Cortex P7 CASTxB6 Cell 081


title: Cortex P7 CASTxB6 Cell 075


title: Cortex P7 CASTxB6 Cell 074


title: Cortex P7 CASTxB6 Cell 073


title: Cortex P7 CASTxB6 Cell 068


title: Cortex P7 CASTxB6 Cell 072


title: Cortex P7 CASTxB6 Cell 067


title: Cortex P7 CASTxB6 Cell 090


title: Cortex P7 CASTxB6 Cell 070


title: Cortex P7 CASTxB6 Cell 069


title: Cortex P7 CASTxB6 Cell 071


title: Cortex P7 CASTxB6 Cell 063


title: Cortex P7 CASTxB6 Cell 066


title: Cortex P7 CASTxB6 Cell 062


title: Cortex P7 CASTxB6 Cell 064


title: Cortex P7 CASTxB6 Cell 061


title: Cortex P7 CASTxB6 Cell 065


title: Cortex P7 CASTxB6 Cell 058


title: Cortex P7 CASTxB6 Cell 080


title: Cortex P7 CASTxB6 Cell 059


title: Cortex P7 CASTxB6 Cell 060


title: Cortex P7 CASTxB6 Cell 057


title: Cortex P7 CASTxB6 Cell 056


title: Cortex P7 CASTxB6 Cell 050


title: Cortex P7 CASTxB6 Cell 079


title: Cortex P7 CASTxB6 Cell 055


title: Cortex P7 CASTxB6 Cell 052


title: Cortex P7 CASTxB6 Cell 049


title: Cortex P7 CASTxB6 Cell 048


title: Cortex P7 CASTxB6 Cell 047


title: Cortex P7 CASTxB6 Cell 054


title: Cortex P7 CASTxB6 Cell 045


title: Cortex P7 CASTxB6 Cell 044


title: Cortex P7 CASTxB6 Cell 046


title: Cortex P7 CASTxB6 Cell 041


title: Cortex P7 CASTxB6 Cell 040


title: Cortex P7 CASTxB6 Cell 043


title: Cortex P7 CASTxB6 Cell 042


title: Cortex P7 CASTxB6 Cell 039


title: Cortex P7 CASTxB6 Cell 038


title: Cortex P7 CASTxB6 Cell 036


title: Cortex P7 CASTxB6 Cell 037


title: Cortex P7 CASTxB6 Cell 035


title: Cortex P7 CASTxB6 Cell 034


title: Cortex P7 CASTxB6 Cell 053


title: Cortex P7 CASTxB6 Cell 033


title: Cortex P7 CASTxB6 Cell 051


title: Cortex P7 CASTxB6 Cell 030


title: Cortex P7 CASTxB6 Cell 028


title: Cortex P7 CASTxB6 Cell 024


title: Cortex P7 CASTxB6 Cell 025


title: Cortex P7 CASTxB6 Cell 023


title: Cortex P7 CASTxB6 Cell 022


title: Cortex P7 CASTxB6 Cell 026


title: Cortex P7 CASTxB6 Cell 027


title: Cortex P7 CASTxB6 Cell 031


title: Cortex P7 CASTxB6 Cell 032


title: Cortex P7 CASTxB6 Cell 029


title: Cortex P7 CASTxB6 Cell 019


title: Cortex P7 CASTxB6 Cell 020


title: Cortex P7 CASTxB6 Cell 013


title: Cortex P7 CASTxB6 Cell 015


title: Cortex P7 CASTxB6 Cell 018


title: Cortex P7 CASTxB6 Cell 016


title: Cortex P7 CASTxB6 Cell 017


title: Cortex P7 CASTxB6 Cell 011


title: Cortex P7 CASTxB6 Cell 012


title: Cortex P7 CASTxB6 Cell 008


title: Cortex P7 CASTxB6 Cell 009


title: Cortex P7 CASTxB6 Cell 010


title: Cortex P7 CASTxB6 Cell 006


title: Cortex P7 CASTxB6 Cell 003


title: Cortex P7 CASTxB6 Cell 005


title: Cortex P7 CASTxB6 Cell 004


title: Cortex P7 CASTxB6 Cell 002


title: Cortex P7 CASTxB6 Cell 001


title: Cortex P7 CASTxB6 Cell 007


title: Cortex P1 CASTxB6 Cell 288


title: Cortex P1 CASTxB6 Cell 287


title: Cortex P1 CASTxB6 Cell 286


title: Cortex P1 CASTxB6 Cell 284


title: Cortex P1 CASTxB6 Cell 283


title: Cortex P1 CASTxB6 Cell 282


title: Cortex P1 CASTxB6 Cell 280


title: Cortex P1 CASTxB6 Cell 285


title: Cortex P7 CASTxB6 Cell 014


title: Cortex P1 CASTxB6 Cell 279


title: Cortex P1 CASTxB6 Cell 281


title: Hippocampus P56 CASTxB6 Cell 094


title: Hippocampus P56 CASTxB6 Cell 096


title: PCC7806

city: Seoul

first: Minkyung

last: Kim

address: Anam-ro 145, Seongbuk-gu

department: Laboratory of molecular environmental microbiology

country: South Korea

institute: Korea University

library_source: transcriptomic

data_processing:
RNA sequencing was performed on an Illumina HiSeq 2500 platform using single end 50-bp sequencing
The reference genome sequence was retrieved from the NCBI database.
Quality-filtered reads were aligned to the reference genome sequence using Bowtie2.
The relative abundance of transcripts is presented as RPKM, defined as the total exon reads/(mapped reads in millions × exon length in kilobases).
Supplementary_files_format_and_content: read counts, RPKM

molecule: total RNA

organism: Microcystis aeruginosa PCC 7806

source_name: Cyanobacteria cells

growth_protocol: Exponential phase on 140 µM H2O2 treated BG11 (cyanobacteria basal) media

extract_protocol:
Using an RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
Illumina sequencing library was constructed by the TruSeq Stranded mRNA Library Prep Lit (Illumina, San Diego, CA, USA) following the manufacturer's protocol

tag: growth phase

value: Mid-exponential phase

tag: agent


title: Cortex P7 CASTxB6 Cell 021


title: Hippocampus P56 CASTxB6 Cell 092


title: Hippocampus P56 CASTxB6 Cell 091


title: Cortex P1 CASTxB6 Cell 278


title: Hippocampus P56 CASTxB6 Cell 095


title: Hippocampus P56 CASTxB6 Cell 093


title: Cortex P1 CASTxB6 Cell 277


title: Cortex P1 CASTxB6 Cell 276


title: PCC7806 under H2O2 treatment


title: Cortex P1 CASTxB6 Cell 274


title: Hippocampus P56 CASTxB6 Cell 089


title: Hippocampus P56 CASTxB6 Cell 090


title: Cortex P1 CASTxB6 Cell 275


title: Cortex P1 CASTxB6 Cell 273


title: Hippocampus P56 CASTxB6 Cell 088


title: Hippocampus P56 CASTxB6 Cell 086


title: Hippocampus P56 CASTxB6 Cell 087


title: Cortex P1 CASTxB6 Cell 271


title: Cortex P1 CASTxB6 Cell 270


title: Hippocampus P56 CASTxB6 Cell 085


title: Cortex P1 CASTxB6 Cell 272


title: Hippocampus P56 CASTxB6 Cell 084


title: Cortex P1 CASTxB6 Cell 268


title: Hippocampus P56 CASTxB6 Cell 082


title: Cortex P1 CASTxB6 Cell 269


title: Hippocampus P56 CASTxB6 Cell 081


title: Cortex P1 CASTxB6 Cell 267


title: Hippocampus P56 CASTxB6 Cell 079


title: Hippocampus P56 CASTxB6 Cell 080


title: Hippocampus P56 CASTxB6 Cell 083


title: Cortex P1 CASTxB6 Cell 266


title: Hippocampus P56 CASTxB6 Cell 078


title: Hippocampus P56 CASTxB6 Cell 077


title: Cortex P1 CASTxB6 Cell 265


title: Cortex P1 CASTxB6 Cell 264


title: Cortex P1 CASTxB6 Cell 262


title: Cortex P1 CASTxB6 Cell 263


title: Cortex P1 CASTxB6 Cell 261


title: Hippocampus P56 CASTxB6 Cell 074


title: Cortex P1 CASTxB6 Cell 260


title: Cortex P1 CASTxB6 Cell 258


title: Cortex P1 CASTxB6 Cell 259


title: Hippocampus P56 CASTxB6 Cell 073


title: Cortex P1 CASTxB6 Cell 257


title: Hippocampus P56 CASTxB6 Cell 069


title: Hippocampus P56 CASTxB6 Cell 071


title: Cortex P1 CASTxB6 Cell 254


title: Cortex P1 CASTxB6 Cell 256


title: Hippocampus P56 CASTxB6 Cell 072


title: Cortex P1 CASTxB6 Cell 252


title: Cortex P1 CASTxB6 Cell 253


title: Hippocampus P56 CASTxB6 Cell 065


title: Hippocampus P56 CASTxB6 Cell 064


title: Hippocampus P56 CASTxB6 Cell 066


title: Hippocampus P56 CASTxB6 Cell 076


title: Cortex P1 CASTxB6 Cell 248


title: Cortex P1 CASTxB6 Cell 249


title: Hippocampus P56 CASTxB6 Cell 063


title: Hippocampus P56 CASTxB6 Cell 075


title: Hippocampus P56 CASTxB6 Cell 062


title: Cortex P1 CASTxB6 Cell 247


title: Cortex P1 CASTxB6 Cell 250


title: Hippocampus P56 CASTxB6 Cell 060


title: Cortex P1 CASTxB6 Cell 246


title: Hippocampus P56 CASTxB6 Cell 061


title: Cortex P1 CASTxB6 Cell 255


title: Hippocampus P56 CASTxB6 Cell 059


title: Hippocampus P56 CASTxB6 Cell 070


title: Cortex P1 CASTxB6 Cell 245


title: Hippocampus P56 CASTxB6 Cell 068


title: Cortex P1 CASTxB6 Cell 244


title: Hippocampus P56 CASTxB6 Cell 058


title: Hippocampus P56 CASTxB6 Cell 067


title: Cortex P1 CASTxB6 Cell 242


title: Hippocampus P56 CASTxB6 Cell 057


title: Hippocampus P56 CASTxB6 Cell 056


title: Cortex P1 CASTxB6 Cell 251


title: Cortex P1 CASTxB6 Cell 243


title: Cortex P1 CASTxB6 Cell 241


title: Hippocampus P56 CASTxB6 Cell 055


title: Hippocampus P56 CASTxB6 Cell 053


title: Cortex P1 CASTxB6 Cell 238


title: Cortex P1 CASTxB6 Cell 237


title: Hippocampus P56 CASTxB6 Cell 054


title: Cortex P1 CASTxB6 Cell 239


title: Cortex P1 CASTxB6 Cell 236


title: Hippocampus P56 CASTxB6 Cell 051


title: Cortex P1 CASTxB6 Cell 235


title: Hippocampus P56 CASTxB6 Cell 047


title: Hippocampus P56 CASTxB6 Cell 048


title: Cortex P1 CASTxB6 Cell 233


title: Cortex P1 CASTxB6 Cell 240


title: Cortex P1 CASTxB6 Cell 232


title: Hippocampus P56 CASTxB6 Cell 052


title: Hippocampus P56 CASTxB6 Cell 046


title: Cortex P1 CASTxB6 Cell 234


title: Cortex P1 CASTxB6 Cell 229


title: Cortex P1 CASTxB6 Cell 231


title: Hippocampus P56 CASTxB6 Cell 045


title: Hippocampus P56 CASTxB6 Cell 044


title: Hippocampus P56 CASTxB6 Cell 049


title: Hippocampus P56 CASTxB6 Cell 043


title: Cortex P1 CASTxB6 Cell 228


title: Cortex P1 CASTxB6 Cell 230


title: Cortex P1 CASTxB6 Cell 227


title: Hippocampus P56 CASTxB6 Cell 042


title: Hippocampus P56 CASTxB6 Cell 050


title: Cortex P1 CASTxB6 Cell 226


title: Hippocampus P56 CASTxB6 Cell 041


title: Hippocampus P56 CASTxB6 Cell 040


title: Cortex P1 CASTxB6 Cell 225


title: Hippocampus P56 CASTxB6 Cell 039


title: Hippocampus P56 CASTxB6 Cell 038


title: Hippocampus P56 CASTxB6 Cell 037


title: Cortex P1 CASTxB6 Cell 223


title: Cortex P1 CASTxB6 Cell 224


title: Cortex P1 CASTxB6 Cell 222


title: Hippocampus P56 CASTxB6 Cell 036


title: Cortex P1 CASTxB6 Cell 220


title: Hippocampus P56 CASTxB6 Cell 033


title: Hippocampus P56 CASTxB6 Cell 034


title: Cortex P1 CASTxB6 Cell 221


title: Cortex P1 CASTxB6 Cell 216


title: Hippocampus P56 CASTxB6 Cell 035


title: Cortex P1 CASTxB6 Cell 219


title: Hippocampus P56 CASTxB6 Cell 032


title: Cortex P1 CASTxB6 Cell 217


title: Cortex P1 CASTxB6 Cell 218


title: Hippocampus P56 CASTxB6 Cell 031


title: Hippocampus P56 CASTxB6 Cell 029


title: Cortex P1 CASTxB6 Cell 214


title: Hippocampus P56 CASTxB6 Cell 030


title: Cortex P1 CASTxB6 Cell 212


title: Hippocampus P56 CASTxB6 Cell 028


title: Hippocampus P56 CASTxB6 Cell 027


title: Cortex P1 CASTxB6 Cell 213


title: Hippocampus P56 CASTxB6 Cell 026


title: Cortex P1 CASTxB6 Cell 211


title: Cortex P1 CASTxB6 Cell 209


title: Hippocampus P56 CASTxB6 Cell 025


title: Hippocampus P56 CASTxB6 Cell 024


title: Cortex P1 CASTxB6 Cell 210


title: Cortex P1 CASTxB6 Cell 208


title: Hippocampus P56 CASTxB6 Cell 023


title: Cortex P1 CASTxB6 Cell 204


title: Dm_trigger_hair1

city: La Jolla

first: Carl

last: Procko

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2).
For each biological sample, the sequencing reads from the two sequencing runs were concatenated.
Concatenated reads were trimmed using Trimmomatic (v0.36.0).
Trimmed reads were aligned to our de novo Venus flytrap trap transcriptome (TSA accession GHJF00000000, generated using Trinity 2.5.1) using Bowtie.
RSEM (v1.2.12) was used to find expected gene counts (see file "expected.counts.RSEM.genes.results.csv").
edgeR (3.12.1) was used to find differentially-expressed genes using a paired experimental design for statistical testing.
For our analysis in edgeR, we first filtered our gene list to include only those Trinity components whose transcript(s) included an ORF coding for a peptide of at least 100 amino acids in length.
"Protein-coding" transcripts coding for peptides of 100 amino acids or greater were identified using TransDecoder (v1.0) (see file "Dm_proteome.pep")
For components with more than one such peptide assigned to them, the longest ORF was assumed to be the most relevant, and was used as the basis for assigning an Arabidopsis homolog to the gene/component.
To assign homologous sequences from Arabidopsis to our protein-coding transcripts, we blasted all complete and partial peptides against the Arabidopsis TAIR10 proteome using default settings in Blastp (v2.2.29), with an e-value threshold of < 0.01.
Genes that had counts per million (CPM) < 2 in over half the samples were excluded from our analysis in edgeR.
"Dm_DEGs.xlsx" shows genes passing these criteria and includes gene expression values, fold-change (trigger hair vs trap), FDR, and the Arabidopsis homolog for each Trinity component (gene).
Genome_build: TSA accession GHJF00000000 (de novo transcriptome)
Supplementary_files_format_and_content: expected.counts.RSEM.genes.results.csv, Dm_proteome.pep, Dm_proteome_blast_TAIR10_tophits.txt and Dm_DEGs.xlsx (see data processing for file descriptions)

molecule: polyA RNA

organism: Dionaea muscipula

source_name: Trigger hairs

growth_protocol: Clonal Venus flytraps (strain CP01) were prepared and grown under greenhouse conditions.

extract_protocol:
Plant tissue was isolated and RNA prepared using a modified LiCl-based method with DNase treatment.
Stranded mRNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit.

value: Trigger hairs


title: Dm_trap3

source_name: Whole trap

value: Whole trap


title: Cortex P1 CASTxB6 Cell 215


title: Cortex P1 CASTxB6 Cell 207


title: Dm_trap2


title: Cortex P1 CASTxB6 Cell 203


title: Cortex P1 CASTxB6 Cell 205


title: Hippocampus P56 CASTxB6 Cell 020


title: QO_1_1

first: Igojo

last: Kang

state: Seoul

address: Gwanak_1 Gwanak-ro, Gwanak-gu

department: Applied Biology and Chemistry

institute: Seoul National University

data_processing:
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
RNA-seq reads were aligned to the ACSNU 2.0 genome
Transcripts Per Million (TPM) were calculated using Kallisto program.
Genome_build: ACSNU 2.0
Supplementary_files_format_and_content: Text files include TPM values for each Sample.

organism: Apis cerana

source_name: Queen

extract_protocol:
Dissect organs from Apis cerana, flash frozen on dry ice, and RNA was isolated using Trizol reagent. Lexogen SENSE mRNA-seq Library Prep Kit (Cat. No. 001.96) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovary

tag: genotype

value: wild type


title: Dm_trap1


title: QO_2_1


title: WO_2_1

source_name: Worker


title: WO_1_1


title: Hippocampus P56 CASTxB6 Cell 019


title: Cortex P1 CASTxB6 Cell 202


title: Cortex P1 CASTxB6 Cell 206


title: Hippocampus P56 CASTxB6 Cell 018


title: Cortex P1 CASTxB6 Cell 201


title: Dm_trigger_hair3


title: Dm_trigger_hair2


title: Wvenom_2_1

value: Venom Gland


title: Cortex P1 CASTxB6 Cell 200


title: Hippocampus P56 CASTxB6 Cell 022


title: Hippocampus P56 CASTxB6 Cell 021


title: Wvenom_1_1


title: Brg1AID/AID_Vec_Tir1_D-3_MLL4

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3);
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilobase per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene.

source_name: Brown preadipocyte cell

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn Snf5f/f or Brg1AID/AID mice and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid.

extract_protocol:
Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x10e6 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

tag: cell type

value: BAT isolated brown preadipocytes

tag: stage of adipogenesis

value: Preadipocytes (D-3)

tag: chip antibody

value: anti-MLL4 (Homemade, Cho YK et al., Cell Metab, 2009)


title: WR_2_1

value: Rectum


title: Hippocampus P56 CASTxB6 Cell 016


title: Brg1AID/AID_Cebpb_Vec_D-3_MLL4


title: WR_1_1


title: Hippocampus P56 CASTxB6 Cell 015


title: Cortex P1 CASTxB6 Cell 198


title: Cortex P1 CASTxB6 Cell 197


title: WV_2_1

value: Ventriculus


title: Cortex P1 CASTxB6 Cell 195


title: Hippocampus P56 CASTxB6 Cell 014


title: Brg1AID/AID_Vec_Tir1_D-3_input


title: Brg1AID/AID_Vec_Vec_D-3_input


title: Brg1AID/AID_Cebpb_Tir1_D-3_input


title: WV_1_1


title: Brg1AID/AID_Vec_Vec_D-3_MLL4


title: Hippocampus P56 CASTxB6 Cell 017


title: Cortex P1 CASTxB6 Cell 194


title: WB_2_1

value: Brain


title: Cortex P1 CASTxB6 Cell 193


title: Hippocampus P56 CASTxB6 Cell 013


title: WB_1_1


title: Brg1AID/AID_Vec_Vec_D-3_H3K27ac

value: anti-H3K27ac (ab4729, Abcam)


title: Cortex P1 CASTxB6 Cell 196


title: DT_2_1

source_name: Drone

value: Testis


title: Cortex P1 CASTxB6 Cell 192


title: Brg1AID/AID_Cebpb_Vec_D-3_H3K27ac


title: Cortex P1 CASTxB6 Cell 199


title: Hippocampus P56 CASTxB6 Cell 009


title: DMGld_2_1

value: Mucus Gland


title: Hippocampus P56 CASTxB6 Cell 007

value: hippocampus


title: Cortex P1 CASTxB6 Cell 191

value: cortex


title: Brg1AID/AID_Cebpb_Tir1_D-3_H3K27ac


title: Hippocampus P56 CASTxB6 Cell 012


title: DMGld_1_1


title: Cortex P1 CASTxB6 Cell 189


title: DR_2_1


title: Cortex P1 CASTxB6 Cell 188


title: Cortex P1 CASTxB6 Cell 187


title: Hippocampus P56 CASTxB6 Cell 010


title: DR_1_1


title: Hippocampus P56 CASTxB6 Cell 006


title: Brg1AID/AID_Vec_Tir1_D-3_H3K27ac


title: Brg1AID/AID_Vec_Tir1_D-3_CEBPb

value: anti-C/EBPbeta (C-19, sc-150X, Santa Cruz)


title: Hippocampus P56 CASTxB6 Cell 005


title: Brg1AID/AID_Cebpb_Vec_D-3_CEBPb


title: Cortex P1 CASTxB6 Cell 186


title: Brg1AID/AID_Cebpb_Tir1_D-3_CEBPb


title: DV_2_1


title: Cortex P1 CASTxB6 Cell 190


title: Hippocampus P56 CASTxB6 Cell 008


title: Cortex P1 CASTxB6 Cell 184


title: Cortex P1 CASTxB6 Cell 185


title: DB_2_1


title: Brg1AID/AID_Vec_Vec_D-3_CEBPb


title: Hippocampus P56 CASTxB6 Cell 001


title: Brg1AID/AID_Vec_Tir1_D-3_ATAC

extract_protocol:
5 × 10e4 freshly collected cells were aliquoted into a new tube and spun down at 500 × g for 5 min at 4 °C. The cell pellet was incubated in 50 µl of ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega) on ice for 3 min and was washed out with 1 ml of ATAC-RSB buffer containing 0.1% Tween-20. Nuclei were collected by centrifugation at 500 × g for 10 min at 4 °C, then resuspended in 50 µl of transposition reaction buffer (25 µl 2x Tagment DNA buffer, 2.5 µl transposase (100 nM final; Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). The reaction was incubated at 37 °C for 30 min with mixing (1000 r.p.m.) and directly subjected to DNA purification using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer’s instructions.
DNA was amplified with PCR using Nextera i7- and i5-index primers for Illumina protocols.


title: Brg1AID/AID_Vec_Vec_D-3_ATAC


title: DB_1_1


title: Hippocampus P56 CASTxB6 Cell 004


title: Cortex P1 CASTxB6 Cell 183


title: Brg1AID/AID_Cebpb_Tir1_D-3_ATAC


title: Cortex P56 CASTxB6 Cell 192


title: Hippocampus P56 CASTxB6 Cell 002


title: Cortex P1 CASTxB6 Cell 182


title: Hippocampus P56 CASTxB6 Cell 003


title: Brg1AID/AID_Cebpb_Vec_D-3_ATAC


title: DV_1_1


title: Cortex P56 CASTxB6 Cell 190


title: Cortex P56 CASTxB6 Cell 191


title: BPbrm1_RNA_flox_D7

description: mRNA

extract_protocol:
Total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

value: Mature adipocytes (D7)


title: Cortex P1 CASTxB6 Cell 179


title: Cortex P56 CASTxB6 Cell 189


title: Mll3-/-Mll4f/f_Vec_GFP_ATAC_D-3


title: Cortex P56 CASTxB6 Cell 188


title: Cortex P56 CASTxB6 Cell 187


title: Cortex P1 CASTxB6 Cell 178


title: Cortex P56 CASTxB6 Cell 186


title: Mll3-/-Mll4f/f_CEBPb_GFP_ATAC_D-3


title: Cortex P1 CASTxB6 Cell 175


title: Mll3-/-Mll4f/f_CEBPb_Cre_ATAC_D-3


title: Cortex P1 CASTxB6 Cell 176


title: Cortex P1 CASTxB6 Cell 180


title: Cortex P56 CASTxB6 Cell 185


title: Cortex P56 CASTxB6 Cell 184


title: Mll3-/-Mll4f/f_Vec_GFP_Arid1a_D-3

value: anti-ARID1A (D2A8U, #12354, Cell Signaling)


title: HCT116, chronic hypoxia with P53 inhibition

type: RNA

city: Tokyo

first: Masatoshi

last: Wakui

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Laboratory Medicine

country: Japan

institute: Keio University School of Medicine

description: gene expression after culture

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Scan resolution 5um Feature Extraction Software: 10.5.1.1 Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

label_protocol: Agilent one-color Quick Amp Labeling Kit labeling protocol

growth_protocol: Acute culture was defined as the culture under normoxia or severe hypoxia for 2 days. Chronic culture was defined as the culture under normoxia or mild hypoxia for 7 days.

extract_protocol: Total RNAs were extracted from cultured HCT116 cells using the QIAzol reagent and the miRNeasy Mini Kit (QIAGEN) according to the manufacture’s instructions.

treatment_protocol: HCT116 cells were cultured normoxically or hypoxically with or without pharmacological inhibition of P53 signaling or fatty acid b oxidation (FAO) and then subjected to the transcriptomic analysis.

tag: cell line

tag: origin

value: colon cancer

tag: treatment

value: chronic hypoxia with P53 inhibition


title: HCT116, chronic normoxia with P53 inhibition

description: gene expression after culture

value: chronic normoxia with P53 inhibition


title: HCT116, chronic hypoxia without P53 inhibition

description: gene expression after culture

value: chronic hypoxia without P53 inhibition


title: Cortex P1 CASTxB6 Cell 181


title: HCT116, acute hypoxia without P53 inhibition

description: gene expression after culture

value: acute hypoxia without P53 inhibition


title: HCT116, acute hypoxia with P53 inhibition

description: gene expression after culture

value: acute hypoxia with P53 inhibition


title: Cortex P56 CASTxB6 Cell 183


title: Mll3-/-Mll4f/f_Vec_Cre_ATAC_D-3

value: BAT isolated brown preadipocytes

value: Preadipocytes (D-3)


title: HCT116, acute normoxia with P53 inhibition

description: gene expression after culture

value: acute normoxia with P53 inhibition


title: HCT116, chronic normoxia without P53 inhibition

description: gene expression after culture

value: chronic normoxia without P53 inhibition


title: DT_1_1

value: Testis

value: wild type


title: Cortex P56 CASTxB6 Cell 182


title: Mll3-/-Mll4f/f_Vec_Cre_Arid1a_D-3


title: Hippocampus P56 CASTxB6 Cell 011

value: hippocampus


title: Cortex P1 CASTxB6 Cell 174

value: cortex


title: Cortex P1 CASTxB6 Cell 173


title: Mll3-/-Mll4f/f_CEBPb_GFP_Arid1a_D-3


title: Cortex P1 CASTxB6 Cell 177


title: Mll3-/-Mll4f/f_CEBPb_Cre_Arid1a_D-3


title: HCT116, acute normoxia without P53 inhibition

description: gene expression after culture

value: acute normoxia without P53 inhibition


title: Mll3-/-Mll4f/f_Brg1_GFP_D-3

value: anti-SMARCA4/BRG1 (ab110641, Abcam)


title: Mll3-/-Mll4f/f_Brg1_GFP_D2

value: Differentiating preadipocytes (D2)


title: Cortex P56 CASTxB6 Cell 181


title: Cortex P1 CASTxB6 Cell 172


title: Cortex P1 CASTxB6 Cell 170


title: Mll3-/-Mll4f/f_Vec_GFP_input_D-3


title: Cortex P56 CASTxB6 Cell 180


title: Cortex P1 CASTxB6 Cell 171


title: Mll3-/-Mll4f/f_Vec_Cre_input_D-3


title: Mll3-/-Mll4f/f_Brg1_Cre_D2


title: Cortex P1 CASTxB6 Cell 169


title: Mll3-/-Mll4f/f_Brg1_Cre_D-3


title: Mll3-/-Mll4f/f_CEBPb_GFP_input_D-3


title: Cortex P56 CASTxB6 Cell 178


title: Mll3-/-Mll4f/f_CEBPb_Cre_input_D-3


title: Cortex P56 CASTxB6 Cell 177


title: Cortex P56 CASTxB6 Cell 179


title: Cortex P1 CASTxB6 Cell 167


title: Snf5f/f_RNA_Cre_D-3

description: mRNA


title: Cortex P1 CASTxB6 Cell 168


title: Mll3-/-Mll4f/f_Vec_GFP_Brg1_D-3


title: Mll3-/-Mll4f/f_CEBPb_GFP_Brg1_D-3


title: Cortex P56 CASTxB6 Cell 175


title: Cortex P56 CASTxB6 Cell 173


title: Cortex P56 CASTxB6 Cell 176


title: Mll3-/-Mll4f/f_Vec_Cre_Brg1_D-3


title: Cortex P1 CASTxB6 Cell 166


title: Cortex P56 CASTxB6 Cell 172


title: Cortex P1 CASTxB6 Cell 164


title: Cortex P56 CASTxB6 Cell 174


title: Cortex P1 CASTxB6 Cell 165


title: Cortex P1 CASTxB6 Cell 162


title: HCC11

city: Toronto

first: Marc

last: Angeli

state: Ontario

address: 101 College street

department: Multi Organ Transplant

country: Canada

institute: University Health Network

description: Gene Expression Data from Recurrent HCC, tumor explant.

hyb_protocol: strandard Affymetrix protocol

scan_protocol: strandard Affymetrix protocol

data_processing: NOT PROVIDED; REQUESTED

label: biotin

source_name: Recurrent HCC

label_protocol: strandard Affymetrix protocol

extract_protocol: Tumor take from removed livers or if reccrrent HCC from new tumor resection

tag: tumor

value: Recurrent HCC

tag: tissue type

value: tumor explant


title: Mll3-/-Mll4f/f_CEBPb_Cre_Brg1_D-3


title: Snf5f/f_ATAC_GFP_D-3


title: HCC6


title: Cortex P56 CASTxB6 Cell 171


title: HCC8


title: Brg1AID/AID_Cebpb_Vec_D-3_input


title: HCC9

description: Gene Expression Data from HCC, tumor explant from patients without a recurrence of HCC

source_name: Non Recurrent HCC

value: Non Recurrent HCC


title: HCC7


title: Snf5f/f_ATAC_GFP_D2


title: Cortex P1 CASTxB6 Cell 161


title: Cortex P56 CASTxB6 Cell 170


title: Cortex P1 CASTxB6 Cell 163


title: Snf5f/f_ATAC_Cre_D2


title: HCC5


title: Cortex P56 CASTxB6 Cell 169


title: Snf5f/f_ATAC_Cre_D-3


title: Snf5f/f_RNA_GFP_D2

description: mRNA


title: wh14

city: New York

first: Wellington

middle: V

last: Cardoso

state: New York

address: 650 West 168th Street

department: Department of Medicine

institute: Columbia University Medical Center

description: ALI day21

data_processing:
Base calling:  RTA-1.18.64.0
FASTQ generation:  bcl2fastq-1.8.4
Read trimming:  trimmomatic-0.35
Read QC:  fastQC-0.10.1
Alignment:  STAR-2.4.2
Mapping statistics:  bamtools-2.3.0
Differential expression: DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Nasopharyngeal

growth_protocol: The NP aspirates were resuspended in 5 mL sterile normal saline to dilute mucus, centrifuged (4°C, 400 rpm, 4 minutes) and the supernatant (including mucus) was discarded. The pellet was resuspended in 2 mL Bronchial Epithelium Growth Media (BEGM) containing penicillin-streptomycin, gentamicin, tobramycin, ceftazidime, vancomycin, and amphotericin B. Cells were seeded on 24-well collagen-coated plates ( 13.2 μL/mL PBS) and cultured under submerged conditions in BEGM at 37°C, 5% CO2. Media was changed 24 hours after and subsequently every 48 hours until cells reached approximately ~90% confluence (7-10 days). Cells were expanded to passage 3 prior to seeding 3.5 x 104 cells on 24 well collagen-coated transwell plates and cultured under submerged conditions in BEGM at 37°C, 5% CO2. Once cells reached 100% confluence (approximately 5-7 days), the upper chamber medium was aspirated to expose cells to air and the medium in the lower chamber was replaced with Air Liquid Interface (ALI) media and allowed to differentiate for 21-28 days, with media changed every 48 hours. Cultures were harvested for analysis at ALI day 0 (confluent pre-ALI) or at days 21.

extract_protocol:
Total RNA was extracted using RNeasymMini kit (#74104, Qiagen) according to the manufactories. RNA-seq libraries from preT and T NP basal cells were prepared with the TruSeq Stranded mRNA kit (Illumina) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nasopharyngeal

value: term

tag: other

value: ALI day21


title: Cortex P1 CASTxB6 Cell 158


title: HCC4


title: HCC3


title: HCC1


title: wh15

description: ALI day21


title: wh16

description: ALI day21


title: Cortex P56 CASTxB6 Cell 167


title: Cortex P1 CASTxB6 Cell 160


title: Cortex P56 CASTxB6 Cell 168


title: Snf5f/f_RNA_GFP_D-3

description: mRNA

value: BAT isolated brown preadipocytes


title: Cortex P1 CASTxB6 Cell 157


title: wh12

description: ALI day21


title: Cortex P56 CASTxB6 Cell 165


title: wh13

description: ALI day21

value: pre term


title: Snf5f/f_input_GFP_D2


title: Cortex P56 CASTxB6 Cell 166


title: wh11

description: ALI day21


title: Cortex P1 CASTxB6 Cell 155


title: wh10

description: ALI day21


title: Cortex P56 CASTxB6 Cell 164


title: Cortex P1 CASTxB6 Cell 156


title: Snf5f/f_input_GFP_D-3

value: Preadipocytes (D-3)


title: Cortex P1 CASTxB6 Cell 154


title: Snf5f/f_input_Cre_D2


title: Cortex P56 CASTxB6 Cell 163


title: Cortex P1 CASTxB6 Cell 159


title: Cortex P1 CASTxB6 Cell 153


title: Snf5f/f_RNA_Cre_D2

description: mRNA


title: Cortex P56 CASTxB6 Cell 162


title: wh09

description: ALI day21


title: Snf5f/f_input_Cre_D-3


title: Cortex P1 CASTxB6 Cell 152


title: Snf5f/f_SS18_GFP_D-3

value: anti-SS18 (D6I4Z, #21792, Cell Signaling)


title: wh08

description: ALI day0

value: ALI day0


title: Snf5f/f_SS18_GFP_D2


title: Cortex P56 CASTxB6 Cell 160


title: Cortex P1 CASTxB6 Cell 151


title: Cortex P1 CASTxB6 Cell 150


title: Cortex P56 CASTxB6 Cell 159


title: Snf5f/f_SS18_Cre_D2


title: wh06

description: ALI day0


title: Cortex P1 CASTxB6 Cell 149


title: wh05

description: ALI day0


title: Cortex P56 CASTxB6 Cell 158


title: Snf5f/f_SS18_Cre_D-3


title: wh04

description: ALI day0


title: Snf5f/f_Arid1a_GFP_D2

value: anti-ARID1A (D2A8U, #12354, Cell Signaling)


title: Cortex P56 CASTxB6 Cell 157


title: Snf5f/f_Arid1a_GFP_D-3


title: Cortex P1 CASTxB6 Cell 147


title: wh03

description: ALI day0


title: Cortex P56 CASTxB6 Cell 156


title: wh07

description: ALI day0


title: Cortex P56 CASTxB6 Cell 155


title: Cortex P56 CASTxB6 Cell 161


title: Snf5f/f_Arid1a_Cre_D2


title: wh02

description: ALI day0


title: wh01

description: ALI day0


title: Cortex P1 CASTxB6 Cell 146


title: Snf5f/f_Arid1a_Cre_D-3


title: Snf5f/f_Brd9_GFP_D2

value: anti-BRD9 (#61537, Active Motif)


title: Cortex P1 CASTxB6 Cell 145

value: cortex


title: Cortex P1 CASTxB6 Cell 148


title: Cortex P1 CASTxB6 Cell 143