title: WT2_F

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
RNAseq data were first processed using Trimmomatic (Bolger et al., 2014) to trim Illumina adapters and remove low‐quality or short‐length reads (quality score <15 or length <30 bp). Paired‐end reads were then aligned to the Genome Reference Consortium mouse genome assembly GRCm38 using STAR (Dobin et al., 2013) and quantified by HTseq (Anders et al., 2015) on the Gekko high‐performance computing cluster at Nanyang Technological University.
Counts were filtered to retain genes with at least one log2‐transformed count per million mapped reads (log‐CPMs) in a minimum of three samples (N = 15,521), and upper‐quartile normalization was applied. Differential expression (DE) analysis was conducted using edgeR (likelihood ratio test with robust dispersion estimation; Robinson et al., 2010).
To reduce the impact of unwanted variation, we used RUVseq (Risso et al., 2014) to identify factors of variation in the expression of empirically defined negative control genes (all genes except the top‐ranked 5000 in a first‐pass differential expression analysis) and we incorporated the top two factors into the model for DE analysis.
We analyzed differential expression between AD and WT conditions for each sex and both combined, as well as the interaction effect defined as [(AD.F ‐ WT.F) ‐ (AD.M ‐ WT.M)]. We identified DE genes using a false discovery rate (FDR) threshold of 10%.
To analyze enriched biological functions, we conducted Kolmogorov–Smirnov tests for GO Biological Process terms on genes ranked by FDR from DE tests using the topGO package (Alexa & Rahnenfuhrer, 2020), using the weight01 algorithm to reduce redundancy between terms (Alexa et al., 2006). To determine whether gene sets were predominantly upregulated or downregulated compared with the control groups, we then calculated direction scores for each term (formula: (ΣNup ‐ ΣNdown)/√(ΣNup + ΣNdown), where Nup and Ndown represent the number of genes in each term with LFCs above and below 0 [up‐ and downregulated, respectively]).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw count matrix for every gene and sample

source_name: Hippocampus

extract_protocol:
Whole right hippocampi were dissected, snap‐frozen and stored at −80°C. Hippocampi were homogenized in TRIzol Reagent (Invitrogen). Total RNA was then extracted and column‐purified using the RNeasy kit (Qiagen) according to the user manual.
Directional libraries of 250-300bp poly-A-enriched mRNA were prepared and sequenced by NovogeneAIT Genomics on the Illumina NovaSeq 6000 platform (45 M 150‐bp paired‐end reads per sample). Prior to sequencing, RNA quality was assessed by electrophoresis and Agilent 2100 Bioanalyser analysis. All input RNA samples had RIN >8.0.

value: Hippocampus

tag: strain

value: Wild-type

tag: Sex

value: Female

value: 4.5 months


title: WT2_M

status: Public on Oct 30 2021

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: Male

tag: age


title: Colonoid treated with aafA mutant (C9_aafA)

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

country: USA

institute: Baylor College of Medicine

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Intestine

growth_protocol: The undifferentiated enteroids/colonoids monolayers were grown in CMGF(+) for 3 days and in differentiation media from days 3-5.

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The differentiated monolayers were then infected with bacterial cultures at a multiplicity of infection of 10 for 3 hours

value: Intestine

tag: segment

value: Colon

tag: sample type

value: Colonoid

tag: format

value: Monolayer

tag: substrate

value: Collagen IV

tag: treatment

value: aafA mutant

tag: individual


title: IMR90 shLARP7 rep1

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using hisat2.
Count  per Million mapped reads (CPM) were calculated using HTseq
Genome_build: mm10

source_name: IMR90 human fibroblasts

growth_protocol: IMR90 human diploid fibroblast line was grown in MEM medium supplemented with 10% fetal bovine serum (FBS), L-glutamine, sodium pyruvate, nonessential amino and sodium bicarbonate. Mouse embryonic fibroblasts (MEFs) were isolated from E13.5 embryos of LARP7+/+ or LARP7-/- and grown in DMEM medium (Gibco) supplemented with 10% FBS.

extract_protocol:
Total RNA obtained from IMR90 cells and MEFs were extracted using a RNeasy RNA isolation Kit (Qiagen) coupled with an on-column DNase I digestion to eliminate residual DNA and 1ug total RNA was used for sequencing library  construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IMR90 fibroblasts were infected with lentivirus expressing control shRNA or LARP7 shRNA, and then selected with puromycin (1μg/ml) for 7 days. The stable cell lines were maintained and passaged in the culture medium supplemented with 0.2 μg/ml puromycin.

tag: cell line

tag: cell type

value: fibroblasts


title: HeLa, 24 h, selected, replicate 1

city: Kyoto

first: Hirohide

last: Saito

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Life Science Frontiers

country: Japan

institute: Kyoto University

data_processing:
Sequenced reads were filtered by fastp 0.12.4 with parameters -i $rawpath -h $html -j $json -o $outpath -q 15 -n 5 -l 15 -w $core --adapter_sequence=GATCGGAAGAGCACACGTCTGAACTCCAGTCA.
The reads were mapped to custom human genome including EGFP and Bsd gene by STAR 2.7.9a with parameters --runThreadN $core --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --genomeDir $star_index --readFilesCommand zcat --readFilesIn $fastq_path
The uniquely mapped reads were counted using htseq-count 0.13.5 with parameters --format bam --stranded reverse --idattr gene_name $star_path $GTF
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include read counts.

source_name: HeLa

extract_protocol:
RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
The RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina) with IDT for Illumina TruSeq RNA UD Indexes (Illumina), quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

value: HeLa

tag: replicate

value: selected

tag: time point

value: 24 hr


title: Crohn's_Colonoid_6

growth_protocol: Colonoids were grown and maintained in CMGF(+)

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared for sequencing using an Illumina TruSeq kit

value: Crohn's patient

value: Matrigel

value: Undifferentiated Colonoid


title: HALO-GST_500_berry

city: Paterna

first: José Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: Institute for Integrative Systems Biology

library_source: genomic

data_processing:
library strategy: DAP-seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Raw reads were trimmed using fastp version 0.21.0 with the following parameters: " -w 16 --n_base_limit 5 cut_front_window_size 1 cut_front_mean_quality 30 --cut_front cut_tail_window_size 1 cut_tail_mean_quality 30 --cut_tail -l 20 -i "
Trimmed reads were aligned by bowtie2 version 2.0-beta7  against the Vitis vinifera genome assembly PN40024_12X.2 with default parameters, and additionally filter for alignments with MAPQ score of at least 30.
Peaks were called using GEM peak caller version 3.4 with the default version 3.4 read distribution, PN40024_12X.2 genome sequences, in multi-replicate mode when it was possible and with the GST samples as control, and parameters “–q 1 –t 1 –k_min 6 –kmax 20 –k seqs 600 –k_neg_dinu_shuffle”, limited to nuclear chromosomes.
Peak summits called by GEM were associated with the closest gene model in the custom annotation file using the BioConductor package ChIPpeakAnno (16) with default parameters (i.e., NearestLocation).
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.

molecule: genomic DNA

organism: Vitis vinifera

source_name: berry

growth_protocol: Leaf material was collected and pooled from fruiting cuttings of cv. ‘Syrah’.

extract_protocol:
Genomic DNA was extracted following procedure described in Thomas et al., 1993 (Thomas MR, Scott NS. 1993. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theoretical and Applied Genetics. 86(8):985-90. doi: 10.1007/BF00211051. PMID: 24194007). DAP-seq experiment was performed as described in Bartlett et al., 2017 (Bartlett, A., O'Malley, RC., Huang, SC. et al. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc 12:1659-1672 (2017). https://doi.org/10.1038/nprot.2017.055).  The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  Separately, a construct containing a HALO-tagged transcription factor is translated by in vitro (rabbit reticulocyte) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina NextSeq 500.

treatment_protocol: Leaf material was collected and flash frozen with liquid nitrogen prior gDNA isolation.

tag: cultivar

value: Syrah

tag: protein

value: HALO-GST

tag: protein affinity tag

value: HALO

tag: expression system

value: rabbit reticulocyte lysate

tag: dna source


title: WT1_M

tag: tissue

value: Hippocampus

tag: strain

tag: genotype

value: Wild-type

tag: Sex

value: Male

value: 4.5 months


title: HALO-GST_1000_leaf

source_name: young leaf


title: Colonoid treated with non-pathogenic control E. Coli strain (C4_HS)

value: Intestine

tag: segment

value: Colon

tag: sample type

value: Colonoid

tag: format

value: Monolayer

value: Collagen IV

value: non-pathogenic control E. Coli strain


title: WT1_F

value: Female

tag: age


title: Crohn's_Colonoid_5

tag: individual

value: Crohn's patient

tag: substrate

value: Matrigel


title: AP4_M


title: HALO-GST_500_leaf

value: Syrah

tag: replicate


type: RNA

city: shanghai

first: Mingliang

last: Bai

state: shanghai

address: siping road

institute: tongji university

description: mRNA profiles of KO-Linc1548 46C cells at day 5 of neural differentiation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version13.1,Agilent Technologies)were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs.

source_name: mESCs line 46C

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 46C mES cells were dissociated to single cells in 0.25% trypsin-EDTA (Invitrogen) and quickly re-aggregated in the differentiation medium ((5 ± 1) ×103 cells/mL) using low-cell-adhesion 6cm dishes and cultured in G-MEM (Gibco) supplemented with 8% knockout serum replacement (KOSR, Gibco), 0.1mmol/L β-mercaptoethanol, 2 mmol/L glutamine, 2 mmol/L nonessential amino acids, 1 mmol/L sodium pyruvate.

extract_protocol: Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).

treatment_protocol: Change the medium every other day.

tag: cell line


title: VvCARPO_500_berry

tag: cultivar

value: CARPO (NAC60)

tag: gene id vcost

tag: gene id v1

tag: protein family

value: NAC

tag: protein source

value: Vitis vinifera


title: Crohn's_Colonoid_2

tag: tissue

value: Undifferentiated Colonoid


title: AP4_F

value: Hippocampus

tag: strain


title: Crohn's_Colonoid_4


title: Colonoid treated with extra-intestinal pathogenic E. coli (C4_expec)

tag: treatment

value: extra-intestinal pathogenic E. coli


title: Crohn's_Colonoid_3


description: mRNA profiles of wild type (WT) 46C cells at day 5 of neural differentiation

tag: genotype

value: WT


title: VvCARPO_1000_leaf

tag: protein

tag: protein affinity tag

value: HALO

tag: expression system

value: rabbit reticulocyte lysate

tag: dna source


title: Colonoid treated with enterohemorrhagic E. coli strain 8624 (C4_ehec)

value: Intestine

tag: segment

value: Colon

tag: sample type

value: Colonoid

tag: format

value: enterohemorrhagic E. coli strain 8624

tag: individual


title: AP3_F

tag: Sex

value: Female

tag: age

value: 4.5 months


title: AP2_M

value: Male


title: AP3_M


title: Healthy Colonoid_6

value: healthy

tag: substrate

value: Matrigel


title: Crohn's_Colonoid_1

value: Crohn's patient


title: VvCARPO_500_leaf_r1

tag: cultivar

value: Syrah

value: CARPO (NAC60)

tag: gene id vcost

tag: gene id v1

tag: protein family

value: NAC

value: Vitis vinifera

tag: replicate


title: Colonoid treated with aafA mutant (C4_aafA)

tag: tissue

value: Monolayer

value: Collagen IV

tag: treatment

value: aafA mutant


title: VvCARPO_500_leaf_r2

tag: protein

tag: protein source

tag: protein affinity tag

value: HALO

value: rabbit reticulocyte lysate


title: Colonoid Mock treated (C4_Mock)

value: Intestine

tag: segment

value: Colon

value: Colonoid

value: Mock treated


title: Colonoid Mock treated (C3_Mock)

tag: sample type


title: AP2_F

value: Hippocampus

tag: strain

tag: genotype

value: Female

value: 4.5 months


title: VvNAC33_500_berry

tag: expression system

tag: dna source


title: Colonoid treated with non-pathogenic control E. Coli strain (C3_HS)

tag: format

tag: substrate

value: non-pathogenic control E. Coli strain

tag: individual


title: Healthy Colonoid_4

value: healthy

value: Matrigel

value: Undifferentiated Colonoid


title: VvNAC33_1000_leaf

tag: cultivar

value: Syrah

tag: gene id vcost

tag: gene id v1

value: NAC

value: Vitis vinifera


title: AP1_M

tag: tissue

tag: Sex

value: Male

tag: age


title: Colonoid treated with extra-intestinal pathogenic E. coli (C3_expec)

value: Monolayer

value: Collagen IV

tag: treatment

value: extra-intestinal pathogenic E. coli


title: Healthy Colonoid_3

value: Intestine

value: Colon


title: VvNAC33_500_leaf_r2

tag: protein

tag: protein family

tag: protein source

tag: protein affinity tag

value: HALO

value: rabbit reticulocyte lysate

tag: replicate


title: Healthy Colonoid_2

tag: segment

tag: sample type


title: Colonoid treated with enterohemorrhagic E. coli strain 8624 (C3_ehec)

value: Colonoid

tag: format

value: enterohemorrhagic E. coli strain 8624


title: Colonoid treated with enteroaggregative E. coli strain 042 (c4_eaec)

tag: substrate

value: enteroaggregative E. coli strain 042


title: AP1_F

value: Hippocampus

tag: strain

tag: genotype

value: Female

value: 4.5 months


title: VvNAC33_500_leaf_r1

tag: cultivar

value: Syrah

tag: gene id vcost

tag: expression system

tag: dna source


title: Colonoid treated with enteroaggregative E. coli strain 042 (C3_eaec)

tag: tissue

tag: individual


title: Healthy Colonoid_1

value: healthy

value: Matrigel

value: Undifferentiated Colonoid


title: Colonoid treated with aafA mutant (C3_aafA)

value: Monolayer

tag: treatment

value: aafA mutant


title: Healthy Colonoid_5


title: LPC-Hras cells, shETV4

city: Shanghai

first: Xiaoli

last: Xu

address: Shanghai Jiaotong University

institute: Shanghai Jiaotong University

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using SeqPrep (https://github.com/jstjohn/SeqPrep)
Clean reads were mapped to mouse genome (GRCm38.p4) with HiSat2 (http://ccb.jhu.edu/software/hisat2/index.shtml)
The uniquely mapped fragments of genes were counted by RSEM（http://deweylab.github.io/RSEM/）
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files include TPM for each gene in each sample

source_name: liver

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies,  Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using the TruSeqTM RNA sample preparation kit for Illumina

tag: cell line

value: LPC-HRas

value: liver

tag: cell type

value: Mouse hepatocellular carcinoma cells

value: ETV4 knockdown by shETV4


title: LPC-Hras cells, shRFP

value: RFP knockdown by shRFP


title: Mouse PFC male RES 5

status: Public on Oct 29 2021

city: Quebec City

first: Caroline

last: Menard

state: QC

address: CERVO Brain Research Center, 2601 de la Canardiere

department: Psychiatry and Neuroscience

country: Canada

institute: Université Laval

description: Endothelial cell transcriptome in the male mouse PFC phenotyped as resilient after 10 days of chronic social stress exposure

hyb_protocol: Samples were hybridized by Genome Quebec using the Affymetrix Clariom S mouse array Pico according to the manufacturer's instructions.

scan_protocol: Array scanning was performed by Genome Quebec using the Affymetrix Clariom S mouse array Pico according to the manufacturer's instructions.

data_processing: Raw data were processed with the Thermofisher Transcriptomic Analysis Console 4.0 for background correction and normalization. Data analysis and statistical evaluations were performed with expression analysis settings at gene-level fold change < -2 or > 2; gene-level p-value < 0.05, anova method: ebayes; a probeset is considered expressed if > 50%  samples have DABG values below DABG threshold; DABG p-value < 0.05. The genome version is mm10 (mus musculus) and summarization method: gene level - SST-RMA.

label: Affymetric Clariom S array

source_name: Resilient

label_protocol: Labeling was performed by Genome Quebec using the Affymetrix Clariom S mouse array Pico according to the manufacturer's instructions.

extract_protocol: RNA was shipped to Genome Quebec and extracted according to the manufacturer’s instructions.

tag: sample group

value: Resilient

tag: Sex

value: Male

value: Brain PFC

value: endothelial


title: Mouse PFC male SS 5

description: Endothelial cell transcriptome in the male mouse PFC phenotyped as stress-susceptible after 10 days of chronic social stress exposure

source_name: Stress-susceptible

value: Stress-susceptible


title: Mouse PFC male SS 2


title: Mouse PFC male RES 4


title: Mouse PFC male SS 3


title: Mouse PFC male SS 4


title: Mouse PFC male CTRL 5

description: Endothelial cell transcriptome in the male mouse PFC under control conditions

source_name: Control

value: Control


title: Mouse PFC male RES 1


title: Mouse PFC male CTRL 9


title: Mouse PFC male RES 3


title: Mouse PFC male CTRL 8


title: Mouse PFC male SS 6


title: Mouse PFC male RES 2


title: Mouse PFC male SS 1


title: Mouse PFC male CTRL 3


title: Mouse PFC male RES 6


title: Mouse PFC male CTRL 6


title: Mouse PFC male CTRL 7


title: VvNAC03_500_leaf

value: Syrah

tag: protein

tag: gene id v1

tag: protein family

value: NAC

tag: protein source

value: Vitis vinifera

tag: protein affinity tag

value: HALO

value: rabbit reticulocyte lysate

tag: replicate


title: Mouse NAc male SS 4 [CSDS_M_SS4]

label: biotin

source_name: Endothelial cell transcriptome in the male mouse NAc phenotyped as stress-susceptible after 10 days of chronic social stress exposure

value: Brain NAc

value: Endothelial cell


title: Mouse NAc male SS 3 [CSDS_M_SS3]


title: Mouse NAc male SS 5 [CSDS_M_SS5]


title: Mouse NAc male SS 1 [CSDS_M_SS1]


title: Mouse PFC female Stressed 17 [SCVS_F_CVS17]

source_name: Endothelial cell transcriptome in the female mouse PFC following 6 days of variable stress exposure

value: Stressed

value: Female


title: Mouse PFC male CTRL 2


title: Mouse NAc male SS 2 [CSDS_M_SS2]


title: Mouse PFC male CTRL 1


title: Mouse PFC female Stressed 15 [SCVS_F_CVS15]


title: Mouse PFC female Stressed 16 [SCVS_F_CVS16]


title: Mouse PFC male CTRL 4


title: Mouse PFC female Stressed 13 [SCVS_F_CVS13]


title: Mouse PFC female Stressed 6 [SCVS_F_CVS6]


title: Mouse PFC female Stressed 10 [SCVS_F_CVS10]


title: Mouse PFC female Stressed 2 [SCVS_F_CVS2]


title: Mouse PFC female Stressed 14 [SCVS_F_CVS14]


title: Mouse PFC female Stressed 9 [SCVS_F_CVS9]


title: Mouse PFC female Stressed 11 [SCVS_F_CVS11]


title: Mouse PFC female Stressed 7 [SCVS_F_CVS7]


title: Mouse PFC female Stressed 5 [SCVS_F_CVS5]


title: Mouse PFC female Stressed 8 [SCVS_F_CVS8]


title: Mouse PFC female Stressed 4 [SCVS_F_CVS4]


title: Mouse PFC female CTRL 6 [SCVS_F_C6]

source_name: Endothelial cell transcriptome in the female mouse PFC under control conditions


title: Mouse PFC female CTRL 5 [SCVS_F_C5]


title: Mouse PFC female CTRL 4 [SCVS_F_C4]


title: Mouse PFC female Stressed 3 [SCVS_F_CVS3]


title: Mouse PFC female Stressed 12 [SCVS_F_CVS12]


title: Mouse PFC female CTRL 2 [SCVS_F_C2]


title: Mouse PFC female Stressed 1 [SCVS_F_CVS1]


title: Mouse PFC female CTRL 3 [SCVS_F_C3]


title: Mouse PFC female CTRL 1 [SCVS_F_C1]


title: Mouse PFC female RES 4 [CSDS_F_RES4]

source_name: Endothelial cell transcriptome in the female mouse PFC phenotyped as resilient after 10 days of chronic social stress exposure


title: Mouse PFC female RES 5 [CSDS_F_RES5]


title: Mouse PFC female SS 5 [CSDS_F_SS5]

source_name: Endothelial cell transcriptome in the female mouse PFC phenotyped as stress-susceptible after 10 days of chronic social stress exposure


title: Mouse PFC female RES 2 [CSDS_F_RES2]


title: Mouse PFC female SS 6 [CSDS_F_SS6]


title: Mouse PFC female SS 7 [CSDS_F_SS7]


title: Mouse PFC female RES 1 [CSDS_F_RES1]


title: Mouse PFC female SS 1 [CSDS_F_SS1]


title: Mouse PFC female RES 3 [CSDS_F_RES3]


title: CD14p.TW.coculture.HEK.orf10#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: ~ 25K HEK 293 cells were transfected with lipofectamine and a plasmid encoding a SARS-CoV2 viral protein - replated in Transwell setting. 24 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.

data_processing:
Reads were mapped to the human reference genome (GRCh38) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (v34)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts

source_name: Monocyte

extract_protocol:
We established a co-culture model in which ex vivo blood immunocytes were placed in direct contact with virus-infected epithelial cells or SARS-CoV2 single protein transfected epithelial cells. We used as a virus SARS-CoV2 and two other relevant viruses for comparison : influenza A virus and Ebola virus. Thirty-five hours after viral infection of the Caco-2 monolayer, unbound virus was removed and peripheral blood mononuclear cells (PBMC) from healthy donors (HD) were added to the cultures. These were harvested 14 h later, and subpopulations (epithelial cells, CD45+CD19+ and CD45+CD14+) were magnetically purified for transcriptome profiling by RNAseq. We used the same coculture model to assess the role of individual SARS-CoV2 proteins : Caco-2 cells were transfected, in biological duplicates, with a panel of 27 plasmids encoding single viral proteins or GFP as a control; Forty-eight hour later, these transfectants were co-cultured with HD PBMCs, and the monocytes as well as the transfected epithelial cells were profiled by RNAseq after 14 h.
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

tag: genotype

value: HD

value: Blood

tag: experiment


title: CD14p.TW.coculture.HEK.GFP#1


title: CD14p.TW.coculture.HEK.orf6#2


title: CD14p.TW.coculture.HEK.GFP#2


title: CD14p.TW.coculture.HEK.orf10#2


title: Mouse PFC female SS 2 [CSDS_F_SS2]


title: Mouse PFC female SS 4 [CSDS_F_SS4]


title: Mouse PFC female CTRL 5 [CSDS_F_C5]


title: Mouse PFC female SS 3 [CSDS_F_SS3]


title: CD14p.TW.coculture.HEK.orf6#1


title: CD14p.TW.coculture.HEK.S#1


title: CD14p.TW.coculture.HEK.S#2


title: CD14p.TW.coculture.HEK.nsp14#2


title: Mouse PFC female CTRL 1 [CSDS_F_C1]


title: Mouse PFC female CTRL 6 [CSDS_F_C6]


title: Mouse PFC female CTRL 3 [CSDS_F_C3]


title: CD14p.TW.coculture.HEK.nsp14#1


title: Mouse PFC female CTRL 4 [CSDS_F_C4]


title: CD14p.TW.coculture.HEK.nsp5#1


title: CD14p.TW.coculture.HEK.nsp5#2


title: Mouse PFC female CTRL 2 [CSDS_F_C2]


title: CD14p.coculture.FLU.MOI.0.5.CACO_adult#3

description: ~ 125K CACO cells were insfected with  FLU  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.MOCK.Flu.CACO_kid#2

description: ~ 125K CACO cells were insfected with mock  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.MOCK.Flu.CACO_adult#3

description: ~ 125K CACO cells were insfected with  MOCK.Flu  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.FLU.MOI.0.01.CACO_adult#3


title: CD14p.coculture.FLU.MOI.0.1.CACO_adult#3


title: CD14p.coculture.FLU.MOI.0.2.CACO_kid#3


title: CD14p.coculture.FLU.MOI.0.2.CACO_adult#3


title: CD14p.coculture.FLU.MOI.0.2.CACO_adult#2


title: CD14p.coculture.FLU.MOI.0.2.CACO_kid#2


title: CD14p.coculture.MOCK.Flu.CACO_kid#3


title: CD14p.coculture.MOCK.Flu.CACO_kid#1


title: CD14p.coculture.MOCK.Flu.CACO_adult#1


title: CD14p.coculture.MOCK.Flu.CACO_adult#2


title: MOCK.EBOV.CACO#1

description: ~ 25K CACO cells were transfected with Mock - 33 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.

source_name: Epithelial Cell

value: Colon


title: CD14p.cult.alone#4

description: ~ 25K HEK 293 cells were transfected with lipofectamine and a plasmid encoding a SARS-CoV2 viral protein.They were selected with Puromycine for 5 days and then doing a long term culture. Cells  were then washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.


title: CD14p.cult.alone#3


title: CD14p.coculture.FLU.MOI.0.2.CACO_adult#1


title: CD14p.cult.alone#2


title: EBOV.CACO#3

description: ~ 25K CACO cells were transfected with S EBOV protein - 33 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.


title: MOCK.EBOV.CACO#2


title: EBOV.CACO#2


title: EBOV.CACO#1


title: MOCK.EBOV.CACO#3


title: CD14p.coculture.MOCK.Ebov.CACO_adult#2

description: ~ 125K CACO cells were insfected with  MOCK.Ebov  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.EBOV.CACO_adult#4

description: ~ 125K CACO cells were insfected with  EBOV  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.FLU.MOI.0.2.CACO_kid#1


title: MOCK.SARS.CACO#3


title: CD14p.coculture.MOCK.Ebov.CACO_adult#3


title: CD14p.coculture.EBOV.CACO_adult#3


title: MOCK.SARS.CACO#2


title: MOCK.SARS.CACO#1


title: CD14p.cult.alone#1


title: SARSCOV2.CACO#5

description: ~ 25K CACO cells were transfected with S SARSCOV2 protein - 33 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.


title: SARSCOV2.CACO#4


title: SARSCOV2.CACO#6


title: CD14p.coculture.MOCK.sars.CACO_adult#5

description: ~ 125K CACO cells were insfected with  MOCK.sars  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.MOCK.sars.CACO_kid#2


title: CD14p.coculture.MOCK.sars.CACO_kid#4


title: CD14p.coculture.MOCK.sars.CACO_adult#4


title: CD14p.coculture.MOCK.sars.CACO_adult#2


title: CD14p.coculture.SARSCOV2.CACO_kid#2


title: CD14p.coculture.EBOV.CACO_adult#1


title: CD14p.coculture.EBOV.CACO_adult#2


title: CD14p.coculture.SARSCOV2.CACO_kid#1

description: ~ 125K CACO cells were insfected with  SARSCOV2  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.SARSCOV2.CACO_adult#2


title: CD14p.coculture.SARSCOV2.CACO_adult#1


title: MOCK.FLU.CACO#3


title: MOCK.FLU.CACO#1


title: MOCK.FLU.CACO#2


title: FLU.CACO#1

description: ~ 25K CACO cells were transfected with S FLU protein - 33 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.


title: FLU.CACO#3


title: CD19p.coculture.FLUMOCK.CACO#3

description: ~ 125K CACO cells were insfected with FLUMOCK  - 33 hours later cells were washed once with PBS and 600K PBMCs from healthy donor were added, cocultured for 14h then stained and sorted then lysed for RNA extraction.

source_name: B Cell


title: CD19p.coculture.FLUMOCK.CACO#1


title: CD19p.coculture.FLUMOCK.CACO#2


title: CD19p.coculture.FLU.CACO#4


title: CD19p.coculture.FLU.CACO#2


title: CD14p.coculture.SARSCOV2.CACO_adult#5


title: CD19p.coculture.FLU.CACO#3


title: CD19p.coculture.FLU.CACO#1


title: CD14p.coculture.FLUMOCK.CACO#1


title: CD14p.coculture.FLUMOCK.CACO#3


title: CD14p.coculture.FLUMOCK.CACO#4


title: CD14p.coculture.FLU.CACO#4


title: FLU.CACO#2


title: CD14p.coculture.FLUMOCK.CACO#2


title: CD19p.coculture.FLUMOCK.CACO#4


title: CD14p.coculture.FLU.CACO#1


title: CD14p.coculture.FLU.CACO#2


title: CD14p.coculture.FLU.CACO#3


title: MOCK.NEILD.CACO#2


title: CD19p.coculture.MOCK.NEILD.CACO#5


title: CD19p.coculture.MOCK.NEILD.CACO#2


title: SARSCOV2.CACO#3


title: CD19p.coculture.MOCK.NEILD.CACO#4


title: CD19p.coculture.SARSCOV2.CACO#4


title: CD19p.coculture.MOCK.NEILD.CACO#6


title: CD19p.coculture.MOCK.NEILD.CACO#1


title: SARSCOV2.CACO#1


title: MOCK.NEILD.CACO#1


title: CD19p.coculture.MOCK.NEILD.CACO#3


title: SARSCOV2.CACO#2


title: CD19p.coculture.SARSCOV2.CACO#6


title: CD19p.coculture.SARSCOV2.CACO#5


title: CD14p.coculture.MOCK.NEILD.CACO#3


title: CD14p.coculture.MOCK.NEILD.CACO#2


title: MOCK.NEILD.CACO#3


title: CD14p.coculture.MOCK.NEILD.CACO#5


title: CD19p.coculture.SARSCOV2.CACO#3


title: CD14p.coculture.MOCK.NEILD.CACO#4


title: CD14p.coculture.MOCK.NEILD.CACO#6


title: CD19p.coculture.SARSCOV2.CACO#2


title: CD19p.coculture.SARSCOV2.CACO#1


title: CD14p.coculture.SARSCOV2.CACO#3


title: CD14p.coculture.SARSCOV2.CACO#5


title: CD14p.coculture.SARSCOV2.CACO#6


title: CD14p.coculture.SARSCOV2.CACO#1


title: CD14p.coculture.MOCK.NEILD.CACO#1


title: CD14p.coculture.GFP.transfected.CACO#2

description: ~ 25K CACO cells were transfected with S SARSCOV2 protein - 48 hours later cells were washed once with PBS then lysed for RNA extraction.


title: CD14p.coculture.SARSCOV2.CACO#4


title: CD14p.coculture.GFP.transfected.CACO#3


title: CD14p.coculture.ORF9C.transfected.CACO#2


title: CD14p.coculture.GFP.transfected.CACO#1


title: CD14p.coculture.ORF9B.transfected.CACO#2


title: CD14p.coculture.ORF9C.transfected.CACO#1


title: CD14p.coculture.ORF9B.transfected.CACO#1


title: CD14p.coculture.M.transfected.CACO#2


title: CD14p.coculture.M.transfected.CACO#1


title: GON1_RNASeq

city: Ste-Anne-de-Bellevue

first: Martina

last: Stromvik

state: Quebec

address: 21,111 Lakeshore Rd

department: Department of Plant Science

institute: McGill University

data_processing:
Raw reads were trimmed and cleaned using trimmomatic with the following parameters: TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50
RNA-Seq reads were aligned to the potato DM v4.04 genome using STAR aligner.
Regions with read depth less than 10 were removed. Bases with quality less than 20 were removed.
Variant calling was performed with Freebayes.
The RNA-Seq data were de novo assembles using Trans-ABySS software.
Genome_build: DM v4.04
Supplementary_files_format_and_content: gene-level expression, Cufflinks output
Supplementary_files_format_and_content: transcript-level expression, Cufflinks output

organism: Solanum stenotomum subsp. goniocalyx

source_name: Young Leaf

growth_protocol: In vitro plants.

extract_protocol:
Leaves from young plants were collected, put on dry ice, and RNA was harvested using TIANGEN RNAprep Pure Plant Kit(Polysaccharides& Polyphenolies-rich). The RNA extraction was performed by Novogene.
RNA libraries were prepared by Novogene for sequencing standard Illumina protocols.

treatment_protocol: No special treatment. The leaves of young plant material were used for the extraction of RNA.

tag: potato landraces


title: GON2_RNASeq


title: CD14p.coculture.NSP14.transfected.CACO#2


title: CD14p.coculture.NSP14.transfected.CACO#1


title: CD14p.coculture.S.transfected.CACO#2


title: CD14p.coculture.NSP5.transfected.CACO#1


title: CD14p.coculture.NSP5.transfected.CACO#2


title: CD14p.LPS.lowdose#2

description: ~ 25K HEK 293 cells were plated - 24 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, associated with 1ng/mL of LPS, cocultured for 13h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.S.transfected.CACO#1


title: CD14p.coculture.HEK.GFP#4

description: ~ 25K HEK 293 cells were transfected with lipofectamine and a plasmid encoding a SARS-CoV2 viral protein. 24 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.


title: 6 month Cd treated cells (CR6M 2)_progression

city: RTP

first: Rick

middle: David

last: Fannin

state: NC

address: 111 Tw Alexander Dr, MD D204

department: NIEHS/NIH

institute: Mr.

description: Uterine Fibroid Cells, Uterine Fibroid Tumor

hyb_protocol: Reporter and Capture probes were added according to the manufacturer’s directions (nanostring.com) to 100 ng of total RNA in a final volume of 10 ul followed by hybridization for at least 14 hours at 65oC

scan_protocol: After sample processing according to manufacturer’s instructions on the nCounter Prep Station Model 5S, sample cartridges were scanned on an nCounter Digital Analyzer Model 5S, using 555 Fields of Vision (FOV) and the .rlf file ‘NS_CancerProg_C4972’.

data_processing:
Raw data were normalized to the geometric mean of the positive control probes and to the geometric mean of 3 housekeeping genes (HDAC, MTMR14, and EIF2B4) using nSolver Analysis Software 3.0. Data were then imported into Partek Genomics Suite®, release 7.19.1225, log2 transformed and quantile normalized.
Values are direct ‘counts’ of the number of gene specific epifluorescent dye barcodes in the scanned image.

source_name: 6 month Cd treated cells

growth_protocol: ht-UtLM cultures were maintained continuously in ht-UtLM culture medium supplemented with 10 uM CdCl2 for 16 weeks. The culture medium was replaced with fresh medium with or without 10 uM CdCl2 every 3 days. Passage-matched control ht-UtLM cultures were run concurrently with Cd exposed cells. All cultures were kept in a standard tissue culture incubator at 37°C with 5% CO2

extract_protocol: Total RNA was extracted from the cells using the Qiagen®  Rneasy kit, followed by Dnase treatment.

value: ht-UtLM

value: female

value: Cd

tag: time

value: 6 months


title: CHA_RNASeq

organism: Solanum chaucha

value: CHA


title: 6 month control cells (LM6M 1)_progression

source_name: 6 month control cells

treatment_protocol: The culture medium was replaced with fresh medium with or without 10 uM CdCl2 every 3 days

value: control


title: 6 month control cells (LM6M 2)_progression


title: 6 month Cd treated cells (CR6M 1)_progression


title: CD14p.coculture.HEK.orf10#3

tag: tissue


title: 6 month control cells (LM6M 3)_progression


title: 2 month Cd treated cells (CR2M 1)_progression

source_name: 2 month Cd treated cells

value: 2 months


title: CD14p.LPS.lowdose#1


title: 2 month Cd treated cells (CR2M 3)_progression


title: 2 month Cd treated cells (CR2M 2)_progression


title: 6 month Cd treated cells (CR6M 3)_progression


title: 2 month control cells (LM2M 2)_progression

source_name: 2 month control cells


title: CD14p.coculture.HEK.orf10#4


title: 2 month control cells (LM2M 1)_progression


title: CD14p.coculture.HEK.S#4


title: CD14p.coculture.HEK.orf6#3


title: CD14p.coculture.HEK.S#3


title: CD14p.coculture.HEK.nsp14#3


title: CD14p.coculture.HEK.nsp14#4


title: CD14p.coculture.HEK.nsp5#2


title: CD14p.coculture.HEK.GFP#3


title: 2 month control cells (LM2M 3)_progression


title: 786-O WT_HIF1b_IP

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description:
WT_HIF1b_IP
Wild type 786-O ccRCC line

data_processing:
ChIP-Seq quality check: FastQC
ChIP-Seq read alignment: Bowtie (-n 2, -m 1)
ChIP-Seq peak calling: MACS2 (--nomodel --extsize 300); inputs used as controls
ChIP-Seq heatmaps: deepTools (version 2.4.1) bamCoverage (--binSize 50 --normalizeTo1x 2913022398 --extendReads 300 --ignoreDuplicates -of bigwig) to normalize read numbers to 1x sequencing depth, obtaining read coverage per 50-bp bins across the whole genome (bigWig files). We then used the bigWig files to compute read numbers across 6 kb centered on HIF2-2a peaks called by MACS2 across all 786O cell lines, subtracted of V5 peaks called by MACS2 in WT 786O cells (computeMatrix reference-point --referencePoint=TSS --upstream 3000 --downstream 3000 --missingDataAsZero --sortRegions=no). We sorted the output matrices by decreasing WT 786O enrichment, calculated as the total number of reads within a MACS2 called ChIP-seq peak. Finally, heatmaps were created with the plotHeatmap tool (--averageTypeSummaryPlot=mean --colorMap='Blues' --sortRegions=no).
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-Seq bigWig files: read coverage per 50-bp bins across the whole genome (read numbers normalized to 1x sequencing depth; merged duplicates)

source_name: Clear cell renal cell carcinoma

growth_protocol: Human 786-O ccRCC cells were cultured at 37°C with 5% CO2 in 4.5 g/L glucose DMEM (ThermoFisher, Waltham, MA, #10566016) supplemented with 10% Fetal Bovine Serum (HyClone, Logan, UT, Cat. #SH30396.03, lot #AE28209315), 1 mM Sodium Pyruvate (ThermoFisher #11360070) and 100 U/mL Penicillin-Streptomycin (ThermoFisher #15140122). Cells were subcultured at a ratio of 1:4 to 1:12 every 2 to 4 days for no longer than 30 days.

extract_protocol:
Cell pellets were thawed and resuspended in 2 ml of cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) w/ protease inhibitors and incubated for 10’ on ice. Lysates were centrifuged for 10’ at 4000 rpm and nuclear pellets resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS) w/ protease inhibitors, incubated on ice for 10’, and sonicated to obtain DNA fragments around 500 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 150 peak incident power, 10 cycles 30” on and 30" off). Sonicated lysates were cleared by centrifugation and chromatin (400 ug per antibody) was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) w/ protease inhibitors to a final concentration of 0.8 ug/ul.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645) according to manufacturer instructions with a few modifications. 20 ng of ChIP input DNA (as measured by Nanodrop) and 25 ul of the immunoprecipitated DNA were used as a starting material and the recommended reagents’ volumes were cut in half. The NEBNext Adaptor for Illumina was diluted 1:10 in Tris/NaCl, pH 8.0 (10 mM Tris-HCl pH 8.0, 10 mM NaCl) and the ligation step extended to 30’. After ligation, a single purification step with 0.9X volumes of Agencourt AMPure XP PCR purification beads (Beckman Coulter A63880) was performed, eluting DNA in 22 ul of 10 mM Tris-HCl pH 8.0. 20 ul of the eluted DNA were used for the library enrichment step, performed with the KAPA HotStart PCR kit (Roche Diagnostics KK2502) in 50 ul of total reaction volume (10 ul 5X KAPA buffer, 1.5 ul 10 mM dNTPs, 0.5 ul 10 uM NEB Universal PCR primer, 0.5 ul 10 uM NEB index primer, 1 ul KAPA polymerase, 16.5 ul nuclease-free water and 20 ul sample). Samples were enriched with 9 PCR cycles (98 'C, 45”; [98 'C, 15”; 60 'C, 10”] x 9; 72 'C, 1’; 4 'C, hold), purified with 0.9 volumes of AMPure XP PCR purification beads and eluted with 33 ul of 10 mM Tris-HCl pH 8.0. Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. Libraries were pooled and sequenced in one lane on the Illumina HiSeq4000 sequencing platform (50-bp, single end-reads).

treatment_protocol: Cells were expanded to two 15-cm dishes and cross-linked 5’ at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10’ and pellets were flash-frozen.

value: Wild type

tag: chip antibody

value: HIF-1b (Novus Biologicals NB100-124)


title: CD14p.coculture.CACO-2.GFP#3

description: ~ 25K CACO-2 293 cells were transfected with lipofectamine and a plasmid encoding a SARS-CoV2 viral protein. 24 hours later cells were washed once with PBS and 200K PBMCs from healthy donor were added, cocultured for 13h then stained and sorted then lysed for RNA extraction.


title: CD14p.coculture.HEK.nsp5#1


title: CD14p.coculture.HEK.orf6#4


title: 786-O WT_rV5_IP

description:
WT_rV5_IP
Wild type 786-O ccRCC line

value: V5 (Abcam ab9116)


title: 786-O A31_input

description:
A31_input
Homozygous clonal cell line with endogenous HIF-2a loci tagged with V5 and Halo moieties

value: V5-Halo-HIF-2a endogenous knock-in, clone A31


title: 786-O WT_HIF2a_IP

description:
WT_HIF2a_IP
Wild type 786-O ccRCC line

value: HIF-2a (Novus Biologicals NB100-122)


title: 786-O WT_input

description:
WT_input
Wild type 786-O ccRCC line


title: CD14p.coculture.CACO-2.orf9c#1


title: ATAC-GSKJ4BE2C-ATAC-control-1

city: Memphis

first: Beisi

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Basecalls performed using CASAVA
2x100bp paired-end reads obtained from all samples were trimming for Nextera adapter by cutadapt(version 1.9, paired-end mode, default parameter with “-m 6 -O 20”) and aligned to human genome hg19(GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter). Duplicated reads were then marked with Picard(version 2.6.0-SNAPSHOT) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). After adjustment of Tn5 shift (reads were offset were offset by +4 bp for the sense strand and -5 bp for the antisense strand), we separated reads into nucleosome free, mononucleosome, dinucleosome, trinucleosome as described in Buenrostro et.al by fragment size and generated bigwig files by using the center 80bp of fragments and scale to 20M nucleosome free reads. We observed reasonable nucleosome free peaks and pattern of mono-, di-, tri-nucleosome on IGV (version 2.4.13) and all samples have about 10M nucleosome free reads so we conclude the data qualities are good and have enough depth.
Next we merged each 2 replicates to enhance peak calling on nucleosome free reads by MACS2(version 2.1.1.20160309 default parameters with “--extsize 200 --nomodel "). To assure the replicability, merged peaks from three groups to create a reference peak set and counted nucleosome free reads at these peaks to make sure the correlation between replicates were higher than between two different group.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig

source_name: cell line

growth_protocol: BE2C cells were cultured in RPMI medium, supplemented with 100 U/mL penicillin/streptomycin, and 10% FBS.

extract_protocol:
Fresh cultured BE2C cells (100,000 per sample) with or without GSK-J4 2.5mM treatment were harvested and washed with 150ml cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing protease inhibitor (PI). Nuclei were collected by centrifuging at 500g for 10 minutes at 4°C after cell pellets were resuspended in lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 containing 0.1% NP-40 and PI. Nuclei were incubated with Tn5 transposon enzyme in transposase reaction mix buffer (Illumina) for 30 min at 37°C. DNAs were purified from transposition sample by using Min-Elute PCR purification kit (Qiagen, Valencia, CA) and measured by Qubit.
Polymerase chain reaction (PCR) was performed to amplify with High-Fidelity 2X PCR Master Mix [72°C/5mins+ 98 °C /30 s +12 × (98 °C /10 s + 63 °C /30 s + 72 °C /60 s) + 72 °C /5 min]. The libraries were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA). ATAC-seq libraries followed by pair-end sequencing on HiSeq4000 (Illumina) in the Hartwell Center at St Jude Children's Research Hospital.

treatment_protocol: BE2C cells were treated with GSK-J4 for 24h or 48h.

tag: treatment

value: BE2C GSKJ4 control


title: ATAC-GSKJ4BE2C-ATAC-48h-1

tag: cell line

value: BE2C GSKJ4 treat 48 hours


title: CD14p.coculture.CACO-2.orf9b#1

value: HD


title: CD14p.coculture.CACO-2.orf9b#2

value: Blood


title: CD14p.coculture.CACO-2.orf8#2


title: ATAC-GSKJ4BE2C-ATAC-24h-2

value: BE2C GSKJ4 treat 24 hours


title: ATAC-GSKJ4BE2C-ATAC-24h-1


title: CD14p.coculture.CACO-2.N#1


title: IMR-90_IR-senescent_shRB_2

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC hg19 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: IMR-90 cells

extract_protocol:
RNA was column-extracted using Rneasy Micro kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: For IR-senescent IMR-90cells were generated by exposing proliferating cells to 10 Gy gamma-radiation (137Caesium source) and cultured for 10 days. Cells were replated and infected with lentivirus containing shRNAs against P21 or RB, or scrambled control shRNA (shScr). 72 hrs after the first infection cells were harvest and RNA was extracted.

value: embryonic lung

tag: lentivirus

value: shRNAs against RB


title: IMR-90_IR-senescent_shRB_3


title: CD14p.coculture.CACO-2.orf8#1


title: IMR-90_IR-senescent_shRB_1


title: IMR-90_IR-senescent_shP21_3

value: shRNAs against p21


title: ATAC-GSKJ4BE2C-ATAC-48h-2


title: CD14p.coculture.CACO-2.orf10#2


title: CD14p.coculture.CACO-2.orf7b#2


title: ATAC-GSKJ4BE2C-ATAC-control-2


title: CD14p.coculture.CACO-2.orf10#1


title: IMR-90_IR-senescent_shP21_2


title: CD14p.coculture.CACO-2.orf9c#2


title: IMR-90_IR-senescent_shP21_1


title: CD14p.coculture.CACO-2.N#2


title: CD14p.coculture.CACO-2.orf6#1


title: CD14p.coculture.CACO-2.orf7b#1


title: CD14p.coculture.CACO-2.orf6#2


title: CD14p.coculture.CACO-2.orf7a#1


title: CD14p.coculture.CACO-2.orf7a#2


title: IMR-90_IR-senescent_shScr_2

value: scrambled control shRNA


title: IMR-90_IR-senescent_shScr_1


title: CD14p.coculture.CACO-2.E#1


title: CD14p.coculture.CACO-2.M#2


title: CD14p.coculture.CACO-2.orf3b#2


title: CD14p.coculture.CACO-2.orf3a#2


title: IMR-90_IR_senescent_2

treatment_protocol: For IR-experiments, we established the following cultures from technical replicates of IMR-90 cells: proliferating cells (to derive Control1) and cells exposed to 10 Gy gamma-radiation (137Caesium source) and cultured for 10 days to derive IR-senescent IMR-90 cells.

tag: cell state

value: senescent


title: IMR-90_IR-senescent_shScr_3


title: IMR-90_IR_senescent_1


title: IMR-90_IR_senescent_3


title: IMR-90_IR_control1_1

value: control


title: IMR-90_IR_control1_3


title: CD14p.coculture.CACO-2.S#2


title: CD14p.coculture.CACO-2.S#1


title: CD14p.coculture.CACO-2.nsp15#2


title: IMR-90_H3K27Ac_IR_senescent_1

data_processing:
Fastq files of pair-end reads were mapped with Bowtie 1.1.2 50 using parameters -k 1 -m 1 -e 70 -l 51 --best to the human reference genome hg19.
MACS 1.4.2 was used to identify peaks for each sample against the background using a p-value cutoff of 10e-5. All the other parameters were left as default.
Super enhancers were identified using ROSE by stitch neighboring peaks within 12.5kb from each other were stitched together while excluding regions ± 2000 bps from any transcription start site.
BigWig files of H3K27Ac occupancy profiles were generated using deepTools 3.1.0 by first normalizing each ChIP sample and its matching input to CPM and then subtracting the input signal from each ChIP sample.
Genome_build: hg19
Supplementary_files_format_and_content: peak calls in bed format; super enhancers in bed format; bigwig files for occupancy profile.

source_name: IMR-90 cells, senescent

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 1-5 ng precipitated chromatin or input DNA using the Ovation ultralow DR Multiplex kit (NuGEN) or the ThruPLEX DNA-seq Kit V2 (Rubicon Genomics).

treatment_protocol: We established the following three cultures from three technical replicates: proliferating IMR-90 ells (to derive Control1); cells exposed to 10 Gy gamma-radiation (137Caesium source) and cultured for two days (to derive Control2); and IMR-90 cells exposed to 10 Gy gamma-radiation and cultured for 10 days (to derive IR-senescent cells).

tag: chip-antibody


title: IMR-90_H3K27Ac_IR_senescent_2


title: CD14p.coculture.CACO-2.M#1


title: IMR-90_H3K27Ac_IR_control2_3

source_name: IMR-90 cells, induced


title: IMR-90_H3K27Ac_IR_senescent_3


title: CD14p.coculture.CACO-2.nsp15#1


title: CD14p.coculture.CACO-2.nsp14#2


title: IMR-90_H3K27Ac_IR_control2_2


title: IMR-90_H3K27Ac_IR_control2_1


title: CD14p.coculture.CACO-2.nsp13#2


title: CD14p.coculture.CACO-2.GFP#2


title: CD14p.coculture.CACO-2.nsp12#2


title: CD14p.coculture.CACO-2.nsp14#1


title: CD14p.coculture.CACO-2.orf3b#1


title: IMR-90_H3K27Ac_IR_input_3

source_name: IMR-90 cells, proliferating


title: IMR-90_H3K27Ac_IR_control1_3


title: IMR-90_H3K27Ac_IR_control1_2


title: IMR-90_H3K27Ac_IR_input_2


title: CD14p.coculture.CACO-2.nsp11#2


title: IMR-90_H3K27Ac_IR_control1_1


title: CD14p.coculture.CACO-2.nsp10#1


title: CD14p.coculture.CACO-2.nsp9#2


title: IMR-90_IR_control1_2


title: IMR-90_H3K27Ac_IR_input_1


title: CD14p.coculture.CACO-2.nsp10#2


title: CD14p.coculture.CACO-2.nsp9#1


title: chipnexus_Ada2b_rep_1

city: Kansas City

first: Hua

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description: ChIP-nexus

data_processing:
bcl2fastq2-v2.20.0.422 was used to generate fastq files.
Reads were aligned to dm6 genome using bowtie2-2.3.4.1 with the default parameters.
Genome_build: dm6

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: Kc167 cells were maintained at 1-2 e6 cells/mL in SFX medium (HyQ SFX-Insect;HyClone Laboratories, Inc) at 27 dC. Drosophila melanogaster were grown on standardsyrup  medium at 25 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

value: wild type


title: chipnexus_SAF6_rep_1

description: ChIP-nexus


title: ChIP-seq on KAP1 with estradiol treatment of MCF-7 cells [KAP1_plusE2_Fan398]

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) was used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012) was employed to align ChIP-seq and ChIRC-seq samples to hg38 genome and we have kept 1 copy/read per genome position.
Peak finding: we have called the ChIP-seq and ChiRC-seq peaks by using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/). For the CHIP-seq analysis, we have used the default settings. in HOMER. For the ChIRC-seq analysis, we have used the input samples in order to estimate the background, and the default settings were adjusted to order to capture the biology of ncRNA binding to the genome.
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser. For the CHIP-seq analysis, we have used the default settings in HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph and peak file

growth_protocol: MCF-7 cells were cultured in DMEM, 10% FBS and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
ChIP was performed as previously described, with minor modifications. Briefly, approximately 5 x 10^7 cells were crosslinked with 1% formaldehyde at room temperature for 15 min and quenched with 0.125M glycine for 5 min. Cells were then harvested and incubated with nuclei preparation buffer (50 mM Tris pH 7.5, 150 mM NaCl , 5 mM EDTA, 0.5% NP-40, 1% TX-100), with protease inhibitor (Sigma, Cat#P2714-1BTL) included, for 10 min. After centrifugation, the pellet was suspended in sonication buffer (10 mM Tris, pH8.0, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine, with protease inhibitor included) for sonication. After sonication, 1/10 volume of 10% Triton X-100 was added to sonicated lysate. The supernatant, after centrifugation, was then incubated with 5μg of antibody at 4°C overnight. Immunoprecipitated complexes were collected using Protein G magnetic beads (Invitrogen, Cat#10004D). Immuno-complexes were washed with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholate, with protease inhibitor included) for at least 5 times and TE buffer containing 50 mM Nacl once. After de-crosslinking, DNA was then purified by QIAquick Spin columns (Qiagen).
For Bio-ChIP, 5x10^7 MCF-7 cells stably expressing BirA and biotin acceptor peptide (BAP)-HP1α (4A) or BAP- HP1α (4E) were crosslinked with 1% formaldehyde at room temperature for 15 min, and then incubated with 0.125M glycine for 5 min. To isolate nuclei, cells were incubated with nuclei preparation buffer (50 mM Tris pH 7.5, 150 mM NaCl , 5 mM EDTA, 0.5% NP-40, 1% TX-100), with protease inhibitor (Sigma, Cat#P2714-1BTL) included, for 10 min. The obtained nuclei were suspended in immunoprecipitation buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and 1% Triton X-100, with protease inhibitor included) for sonication. The sonicated chromatin in immunoprecipitation buffer was then incubated with 50 ul of pre-blocked Pierce™ Streptavidin Magnetic Beads (Thermo Fisher, Cat#88816) overnight at 4°C on a rotating wheel. Beads were extensively washed with SDS buffer (10 mM Tris, pH 8, 1 mM EDTA, 2% SDS, protease inhibitor included) twice, high salt buffer (50 mM HEPES pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and 500 mM NaCl) twice, DOC buffer (250 mM LiCl, 0.5%, NP-40, 0.5% deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) once and TE buffer containing 50 mM Nacl once. Beads were then treated with RNase A (Thermo Fisher Scientific, Cat# AM2270) and Proteinase K (Thermo Fisher Scientific, Cat# AM2548) before de-crosslinking overnight at 65°C. DNA was finally purified by QIAquick Spin columns (Qiagen, Cat#28106).
The library construction protocol followed the manufacturer’s instructions.

treatment_protocol: For estrogen stimulation, these cells were cultured in phenol-red free DMEM with 5% charcoal stripped FBS for at least 3 days and then treated with 100nM 17β-estradiol (E2) for 40 minutes. Control samples were treated with ethanol.


title: CD14p.coculture.CACO-2.nsp8#2


title: CD14p.coculture.CACO-2.nsp7#2


title: chipnexus_Spt3_rep_1

description: ChIP-nexus


title: CD14p.coculture.CACO-2.nsp8#1


title: chipnexus_Sgf11_rep_1

description: ChIP-nexus


title: ChIP-seq on KAP1 no estradiol treatment of MCF-7 cells [KAP1_minusE2_Fan397]


title: CD14p.coculture.CACO-2.nsp5#1


title: CD14p.coculture.CACO-2.nsp4#2


title: CD14p.coculture.CACO-2.GFP#1


title: ChIP-seq on HEXIM1 with estradiol treatment of MCF-7 cells [HEXIM1_plusE2_Fan394]


title: ChIRC-seq on 7SK with estradiol treatment of MCF-7 cells Fan396

data_processing:
Library strategy: ChIRC-seq
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) was used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012) was employed to align ChIP-seq and ChIRC-seq samples to hg38 genome and we have kept 1 copy/read per genome position.
Peak finding: we have called the ChIP-seq and ChiRC-seq peaks by using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/). For the CHIP-seq analysis, we have used the default settings. in HOMER. For the ChIRC-seq analysis, we have used the input samples in order to estimate the background, and the default settings were adjusted to order to capture the biology of ncRNA binding to the genome.
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser. For the CHIP-seq analysis, we have used the default settings in HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

extract_protocol:
All the experiments were performed in RNase-free environment and every buffer used in the experiment was supplemented with SUPERase• In™ RNase Inhibitor (Thermo Fisher Scientific, Cat#AM2696). Briefly, 5x10^7 cells stably expressing biotin acceptor peptide (BAP)-dCas13a, BirA and corresponding gRNA were crosslinked with 1% formaldehyde at room temperature for 15 min before being quenched with 0.125M glycine for 5 min. Cells were first incubated in Lysis buffer 1 (10 mM Tris pH 8, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, protease inhibitor included) for 10 min on ice and then were incubated in Lysis buffer 2 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA and 200 mM NaCl, protease inhibitor included) for 5 min on ice for nuclei isolation. After centrifugation, the pellet was suspended in immunoprecipitation buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and 1% Triton X-100, with protease inhibitor included) for sonication. The supernatant, after centrifugation, was then incubated with 50 ul of pre-blocked Pierce™ Streptavidin Magnetic Beads (Thermo Fisher, Cat#88816) at 4°C overnight. Beads were then washed with SDS buffer (10 mM Tris, pH 8, 1 mM EDTA, 2% SDS, protease inhibitor included) twice, high salt buffer (50 mM HEPES pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and 500 mM NaCl) twice, DOC buffer (250 mM LiCl, 0.5%, NP-40, 0.5% deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) once and TE buffer containing 50 mM Nacl once. After RNase A, Proteinase K treatment and de-crosslinking, DNA was then purified by QIAquick Spin columns (Qiagen)
For ChIRC-seq, the extracted DNA was ligated to specific adaptors followed by deep sequencing with the Illumina's HiSeq 2500 system according to the manufacturer's instructions.

tag: complex


title: ChIP-seq on HEXIM1 no estradiol treatment of MCF-7 cells [HEXIM1_minusE2_Fan393]


title: CD14p.coculture.CACO-2.nsp4#1


title: ChiRC-seq on 7SK no estradiol treatment of MCF-7 cells Fan395


title: CD14p.coculture.CACO-2.nsp2#2


title: chipnexus_WDA_rep_1

description: ChIP-nexus

value: WDA


title: CD14p.coculture.CACO-2.nsp11#1


title: CD14p.coculture.CACO-2.nsp2#1


title: CD14p.coculture.CACO-2.nsp1#1


title: CD14p.coculture.CACO-2.nsp5#2


title: CD14p.coculture.CACO-2.nsp1#2


title: CACO.orf9c#2

description: CACO-2 cells were transfected with lipofectamine and a plasmid encoding a SARS-CoV2 viral protein. 24 hours later cells were treated with puromycin for 72h then washed once with PBS and lysed for RNA extraction.

value: Colon


title: CACO.orf9c#1


title: CACO.orf10#1


title: ANKLE1_3day_rep4

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: rRNA depeleted RNA

data_processing:
HISAT2
HTSeq
DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: .csv: table with fpm for all samples and DESeq results for comparission ANKLE1 versus GFP for each day

growth_protocol: HEK293T cells were maintained in Dulbecco’s High Glucose Modified Eagles Medium with 10% FBS.

extract_protocol:
Total RNA from sorted cells was extracted by Trizol reagent (Invitrogen) and purified with column-based Direct-zol RNA Microprep kit (Zymo Research).
rRNA depletion was done using NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) and RNA was purified using Agencourt RNAClean XP Beads (New England Biolabs). Library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were measured by Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific) and quality control was done using TapeStation (Agilent). Libraries were pooled together and sequenced in University of Virginia Genome Analysis and Technology Core using the Illumina HiSeq 2500 instrument.

treatment_protocol: Live, nonapoptotic, GFP-positive HEK293T cells were sorted 1, 3 and 7 days after transfection with pEGFP-C1-ANKLE1 or pEGFP-C1 plasmids.

tag: transgene

value: ANKLE1 overexpressing

value: Day 3


title: ANKLE1_7day_rep1

description: rRNA depeleted RNA

value: Day 7


title: CACO.orf9b#2


title: ANKLE1_3day_rep3

description: rRNA depeleted RNA


title: CACO.orf9b#1


title: GFP_7day_rep3

description: rRNA depeleted RNA

value: GFP

value: Control


title: GFP_7day_rep2

description: rRNA depeleted RNA


title: ANKLE1_7day_rep3

description: rRNA depeleted RNA


title: CACO.N#1


title: CACO.GFP#5


title: GFP_7day_rep1

description: rRNA depeleted RNA


title: GFP_3day_rep4

description: rRNA depeleted RNA


title: GFP_3day_rep2

description: rRNA depeleted RNA


title: CACO.orf8#1


title: GFP_3day_rep3

description: rRNA depeleted RNA


title: ANKLE1_7day_rep2

description: rRNA depeleted RNA


title: CACO.orf7b#2


title: GFP_3day_rep1

description: rRNA depeleted RNA


title: CACO.orf7b#1


title: ANKLE1_3day_rep1

description: rRNA depeleted RNA


title: ANKLE1_1day_rep3

description: rRNA depeleted RNA

value: Day 1


title: CACO.orf7a#1


title: CACO.orf7a#2


title: ANKLE1_3day_rep2

description: rRNA depeleted RNA


title: ANKLE1_1day_rep2

description: rRNA depeleted RNA


title: ANKLE1_1day_rep4

description: rRNA depeleted RNA


title: CACO.orf6#2


title: ANKLE1_1day_rep1

description: rRNA depeleted RNA


title: GFP_1day_rep3

description: rRNA depeleted RNA


title: CACO.orf8#2


title: GFP_1day_rep4

description: rRNA depeleted RNA


title: CACO.GFP#4


title: CACO.M#2


title: SilkDay30-12silkLam

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

data_processing:
Basecalling using bcl2fastq 2.19
Cell Ranger pipeline (10x Genomics, Cellranger count v2) with default parameters  and GrCh38 as the reference genome
Seurat (v 3.1 and R version 3.6.1) was applied to the scRNA-data for downstream analysis of matrix files.
Genome_build: GrCH38

source_name: Organoid silk+laminin culture day 30

growth_protocol: Undifferentiated RC17 (Roslin Cells, #hPSCreg RCe021-A), H9 (WiCell, #hPSCreg WAe009-A), HS999 and HS1001 (kindly provided by the Karolinska Institute), and TH-Cre hPSC cells were maintained on 0.5 μg/cm2 Lam-521 (BioLamina, #LN-521)-coated plates in iPS Brew medium (Miltenyi, #130-104-368) and were differentiated into 2D VM-patterned progenitors

extract_protocol:
For 10x Genomics single cell RNA sequencing,  single cell suspensions were loaded onto 10x Genomics Single Cell 3′ Chips along with the mastermix as per the manufacturer’s protocol
According to 10X protocols.

treatment_protocol: After three days in culture, embryoid bodies were transferred to differentiation medium consisting of 1:1 DMEM/F12:Neurobasal medium (Thermo Fisher Scientific, #21331020 and #A1371201), 1:100 N2 supplement (Thermo Fisher Scientific, #A1370701), 10 μM SB431542 (Miltenyi, #130-106-543), 150 ng/ml rhNoggin (Miltenyi, #130-103-456), 400 ng/ml SHH-C24II (Miltenyi, #130-095-727), and 1.5 μM CHIR99021 (Miltenyi, #130-106-539), and in presence of 200 mM L-glutamine (Thermo Fisher Scientific, #25030081) and 10,000 U/mL penicillin-streptomycin (Thermo Fisher Scientific, #15140122).

tag: culture condition

value: silk+laminin

tag: days in culture


title: CACO.E#1


title: GFP_1day_rep1

description: rRNA depeleted RNA


title: GFP_1day_rep2

description: rRNA depeleted RNA


title: CACO.E#2


title: SilkDay30-11silkLam


title: SilkDay30-09silk

source_name: Organoid silk culture day 30

value: silk


title: CACO.M#1


title: SilkDay30-10silkLam


title: SilkDay30-07silk


title: CACO.orf3b#1


title: CACO.GFP#3


title: SilkDay30-06silk


title: CACO.orf3a#1


title: CACO.orf3b#2


title: CACO.S#2


title: 2standardorgday90

source_name: Organoid standard culture day 90

value: standard


title: CACO.S#1

source_name: Epithelial Cell


title: 1standardorgday90


title: CACO.orf6#1


title: SilkDay30-08silk


title: CACO.orf3a#2


title: 6standardorgday120

source_name: Organoid standard culture day 120


title: CACO.nsp15#1


title: CACO.nsp15#2


title: 5standardorgday120


title: CACO.nsp14#2


title: 3standardorgday120


title: CACO.nsp14#1


title: 4standardorgday120


title: 2standardorgday120


title: CACO.nsp13#2


title: 1standardorgday120


title: CACO.nsp12#2


title: CACO.nsp13#1


title: CACO.nsp12#1


title: 2standardorgday30

source_name: Organoid standard culture day 30


title: 12standardorgday60

source_name: Organoid standard culture day 60


title: CACO.nsp11#2


title: CACO.nsp11#1


title: 3standardorgday30


title: 13standardorgday60


title: CACO.nsp10#2


title: CACO.nsp10#1


title: 4standardorgday30


title: CACO.nsp9#2


title: 15standardorgday60


title: 1standardorgday30


title: CACO.nsp9#1


title: CACO.nsp8#2


title: 14standardorgday60


title: 16standardorgday60


title: CACO.nsp8#1


title: 5standardorgday30


title: CACO.GFP#2


title: 2standardorgday15

source_name: Organoid standard culture day 15


title: CACO.nsp7#2


title: 1standardorgday15


title: CACO.nsp7#1


title: RNA-TM.18R048_KCtrl2

description: RNA-seq in MDA-MB-231 control, Replicate2

data_processing:
Paired-end 150-cycle sequencing was performed on HiSeq X or HiSeq 2500, per the manufacturer’s directions (Illumina).
After adapter trimming by cutadapt RNA-Seq was mapped to human genome hg19(GRCh37) by STAR(version 2.5.2b, parameters “--outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --twopassMode Basic”) and HTSeq(version 0.6.1 p1) were used to count the gene-based reads using gene annotation from GENCODE(v24lift37).
For differential expression analysis, we performed trimmed mean normalization then Voom was used to identify differential expressed genes. Gene ontology analysis were performed on PANTHER that level 1 terms from Biological Process were used for presentation.
For GSEA analysis, gene sets downloaded from MSigDB database(v6.0) were analyzed against the log2 fold change from differential analysis using GSEA prerank mode (version 3.0).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: txt file with abuabundance measurements

source_name: Cell Line

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: hTrmt13 siControl


title: RNA-TM.18R049_KD2

description: RNA-seq in MDA-MB-231 with siRNA knockdown hTrmt13, Replicate2

value: hTrmt13 siKnockdown


title: CACO.nsp6#1


title: CACO.nsp6#2


title: VCAP_H3K27ac_HiChIP_DHT_2hr

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

description: H3K27ac HiChIP in VCaP cells

data_processing:
Pair-end HiChIP reads were aligned to hg19 human reference genome by HiCUP pipeline. The default settings were used to filter experimental Hi-C artefacts and other uninformative di-tags. The resultant bam file was used to generate valid pairs for downstream loop calling. HiChIP loops were identified by hichipper pipeline. The corresponding ChIP-Seq peaks were used to locate HiChIP loop anchors during loop calling.
Genome_build: hg19
Supplementary_files_format_and_content: Txt files containing H3K27ac-mediated chromatin loops

source_name: VCaP cells

growth_protocol: VCaP cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) medium containing 10% FBS.

extract_protocol:
10 million cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature and then quenched by 125mM glycine. After washing in PBS, the crosslinked cells were lysed in Hi-C lysis buffer (10 mM NaCl, 10 mM Tris-HCl, 0.2% NP-40 and 1×protease inhibitor) and digested by MboI restriction enzyme (NEB-R0147). The biotin-dATP (Thermo 19524016) was incorporated to DNA in a fill-in master mix containing DNA polymerase I (NEB-M0210). After ligation and sonication, the sheared chromatin was incubated together with Protein A beads and anti-H3K27ac antibody (Abcam, ab4729) for overnight at 4°C with rotation. ChIPed DNA was purified from the eluted chromatin using Zymo DNA Clean & Concentrator kit. Biotin-labeled DNA was captured by Streptavidin C-1 bead (Thermo Fisher, Cat#65002) and fragmented by Tn5 enzyme to generate library for high throughput sequencing. Next generation sequencing was conducted on a HiSeq4000 machine with 150 bp pair-end reads.
Libraries were prepared using the Tn5 transposase.
HiChIP

treatment_protocol: For androgen-starving conditions, cells were grown in medium containing CDS (charcoaldextran stripped serum, from Hyclone)

value: DHT for 2 h


title: CACO.nsp5#2


title: CACO.nsp5#1


title: CACO.GFP#1


title: VCAP_H3K27ac_HiChIP_Veh

description: H3K27ac HiChIP in VCaP cells

value: vehicle


title: CACO.nsp4#2


title: VCAP_4C_Veh

description: 4C-Seq in VCaP cells

data_processing:
Library strategy: 4C-Seq
The PE reads were first aligned to hg19 human reference genome using Bowtie2 (version 2.2.1). The resultant bam files were then used for downstream analyses by R package ‘Basic4Cseq’. A fragment library was created by the function ‘createVirtualFragmentLibrary’ using the parameter firstCutter = " ctgcag", secondCutter = "gtac". 4C bam files were then loaded to initiate a Data4Cseq object and the view point was set at MYC promoter region. The raw read count was RPM-normalized for the comparability between different samples. A near-cis plot was finally generated to cover the MYC promoter and PCAT1 super-enhancer regions.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files containing normalized frequency of 4C interaction to MYC promoter

extract_protocol:
Each 3C library DNA sample was added 100 μl of 10×REB, 500U of DpnII restriction enzyme (NEB, R0543S), and Milli-Q to final volume 1ml. Incubate O/N at 37 °C with rotation and then inactivate the reaction by incubating at 80 °C for 45 min. Perform 4C ligation by adding the following to a 15ml tissue culture tube containing digested DNA: 1ml of 10 × T4 ligation buffer, 50 μl T4 DNA ligase (400U/μl, NEB), and add H2O to 10 ml. Ligation was performed at room temperature for overnight with rotation. For precipitation, divide the ligation product into 4x 15ml tubes (2.5ml each), and then in each tube add: 2.5 μl glycogen (20 μg/μL); 0.25 ml of 3M NaAc (sodium acetate, pH 5.2); and 7ml of 100% ethanol. Store at − 80 °C for 2-3hrs until completely frozen and then spin for 45 m at 3200 × g at 4 °C. Add 10 ml of cold 75% ethanol to wash the samples, and spin for 15 m at 3200 × g at 4 °C. Remove the ethanol, air-dry for 30min and then dissolve pellet in each tube in 250 μl of 10 mM Tris pH 7.5 at 37 °C for 30min.
Purify the samples with the QIAquick PCR purification kit (Qiagen, 28106) and use 6 columns per sample. dsDNA product was pooled and quantified using Qubit. The 4C-DpnII library (ng) was then amplified on the Veriti 96-Well Thermo Cycler (Applied Biosystems). Limited PCR (round-1) was conducted with the MYC-promoter region as the bait. PCR was performed using the following conditions: 5 min at 94C, 35 cycles of (20 s at 94C, 20 s at 61C, and 30 s at 72C), and 10 min at 72C. The PCR products (ng) were purified using PCR purification kit and re-amplified by limited PCR (round-2) with primers containing Illumina sequencing adaptors. PCR was performed using the following conditions: 5 min at 94C, 35 cycles of (20 s at 94C, 20 s at 61C, and 30 s at 72C), and 10 min at 72C. 4C library purification was performed using Ampure beads and  then submitted to deep-seq at PE150 (85M reads per sample) using the Illumine platform.

value: VCaP cells

value: prostate cancer


title: CACO.nsp4#1


title: CACO.nsp2#2


title: CACO.nsp2#1


title: CACO.nsp1#2


title: VCAP_4C_DHT

description: 4C-Seq in VCaP cells


title: CD14p.coculture.HEK.S#2

source_name: Monocyte

value: HD

value: Blood


title: VCAP_H3K27AC_FBS_REP1

description: H3K27ac ChIP-Seq in VCaP cells

data_processing:
ChIP-Seq reads were aligned to hg19 human genome by Bowtie2 (version 2.2.1). The bam files were then subjected to MACS2 for peak calling with the parameter “--SPMR” on and --keep-dup=1. Significant peaks were identified by q-value < 0.05. UCSC bedGraphToBigWig tool was used to convert Resultant bedgraph files to bigWig files, which were then used for peak shape visualization in IGV (version 2.8.2) and heatmap analysis by deeptools (version 3.3.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated txt files containing ChIP-Seq peak regions.

extract_protocol:
ChIP experiment was performed as previously described. Briefly, cell crosslinking was conducted in 1% formaldehyde for 10 minutes and quenched by glycine. Cell nuclear fraction was extracted by LB1 buffer (50 mM Hepes–KOH, pH 7.5; 1 mM EDTA; 140 mM NaCl; 10% Glycerol; Igepal CA-630; 0.25% Triton X-100) followed by washing in LB2 (10 mM Tris–HCL,pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA) and LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin was sheared to 300-500 bp by Diagenode’s bioruptor sonicator and then incubated with antibody-conjugated protein A and G beads for overnight at 4°C with rotation. After washing in RIPA buffer (50 mM Tris, pH 7.6, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Igepal CA630, 0.5% sodium deoxycholate, Protease inhibitor and RNase inhibitor), the beads were eluted in elution buffer (0.1M NaHCO3, 1% SDS and Proteinase K) for 8~16 hours at 65°C. ChIPed DNA was purified by phenol–chloroform extraction and then used for ChIP-qPCR or ChIP-Seq library preparation.
ThruPLEX DNA-Seq kit

treatment_protocol: For androgen-starving conditions, cells were grown in medium containing CDS (charcoaldextran stripped serum, from Hyclone). Plasmids and siRNA transfections were carried out using the Lipofectamine 2000 (Invitrogen), following the manufacturer’s directions.


title: VCAP_H3K27AC_DHT_REP3

description: H3K27ac ChIP-Seq in VCaP cells


title: VCAP_H3K27AC_DHT_REP2

description: H3K27ac ChIP-Seq in VCaP cells


title: CD14p.coculture.HEK.orf9c#2


title: CD14p.coculture.HEK.S#1


title: VCAP_H3K27ac_HiChIP_DHT_24hr

description: H3K27ac HiChIP in VCaP cells

value: DHT for 24 h


title: CD14p.coculture.HEK.orf8#2


title: VCAP_H3K27AC_DHT_ENZ_REP2

description: H3K27ac ChIP-Seq in VCaP cells


title: VCAP_H3K27AC_DHT_ENZ_REP1

description: H3K27ac ChIP-Seq in VCaP cells


title: VCAP_H3K27AC_DHT_ENZ_REP3

description: H3K27ac ChIP-Seq in VCaP cells


title: CD14p.coculture.HEK.orf9c#1


title: H3K27ac-VCAP-2hr

description: H3K27ac ChIP-Seq in VCaP cells


title: H3K27ac-VCAP-Veh

description: H3K27ac ChIP-Seq in VCaP cells


title: CD14p.coculture.HEK.orf8#1


title: VCAP_H3K27AC_FBS_REP3

description: H3K27ac ChIP-Seq in VCaP cells


title: CD14p.coculture.HEK.orf7b#2


title: VCAP_H3K27AC_FBS_REP2

description: H3K27ac ChIP-Seq in VCaP cells


title: VCAP_RNASeq_Veh_24hr_REP2

data_processing:
Sequencing reads were aligned to hg19 human genome using STAR (version 2.4.2a). Reads per kilobase per million mapped reads (RPKM) was then calculated based on gene read count and GENCODE v24 GRCh37 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain the gene expression matrices

growth_protocol: LNCaP were grown in RPMI-1640 containing 10% FBS (GIBCO, 10437-028); LNCaP cell line overexpression of Flag-tagged AR (LNCaP-AR, or LA) was based on LNCaP cells infection with lenti-viral AR expression vector and selected on hygromycin B (200ug/ml); VCaP cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) medium containing 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy MiniKit (74106, Qiagen) following manufacturer’s procedure.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.


title: H3K27ac-VCAP-24hr

description: H3K27ac ChIP-Seq in VCaP cells


title: VCAP_RNASeq_Veh_24hr_REP1


title: CD14p.coculture.HEK.orf7a#2

data_processing:
Reads were mapped to the human reference genome (GRCh38) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (v34)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts

extract_protocol:
We established a co-culture model in which ex vivo blood immunocytes were placed in direct contact with virus-infected epithelial cells or SARS-CoV2 single protein transfected epithelial cells. We used as a virus SARS-CoV2 and two other relevant viruses for comparison : influenza A virus and Ebola virus. Thirty-five hours after viral infection of the Caco-2 monolayer, unbound virus was removed and peripheral blood mononuclear cells (PBMC) from healthy donors (HD) were added to the cultures. These were harvested 14 h later, and subpopulations (epithelial cells, CD45+CD19+ and CD45+CD14+) were magnetically purified for transcriptome profiling by RNAseq. We used the same coculture model to assess the role of individual SARS-CoV2 proteins : Caco-2 cells were transfected, in biological duplicates, with a panel of 27 plasmids encoding single viral proteins or GFP as a control; Forty-eight hour later, these transfectants were co-cultured with HD PBMCs, and the monocytes as well as the transfected epithelial cells were profiled by RNAseq after 14 h.
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.


title: VCAP_RNASeq_DHT_24hr_REP2


title: CACO.nsp1#1

value: Colon


title: VCAP_H3K27AC_DHT_REP1

description: H3K27ac ChIP-Seq in VCaP cells


title: RNASeq_VCaP_Veh_siMYC_REP2


title: CD14p.coculture.HEK.orf7a#1


title: RNASeq_VCaP_Veh_siMYC_REP1


title: CD14p.coculture.HEK.orf6#2


title: CD14p.coculture.HEK.orf3b#2


title: CD14p.coculture.HEK.orf3a#2


title: RNASeq_VCaP_Veh_siCtrl_REP1


title: CD14p.coculture.HEK.orf6#1


title: CD14p.coculture.HEK.orf7b#1


title: RNASeq_VCaP_Veh_REP2


title: CD14p.coculture.HEK.orf3a#1


title: CD14p.coculture.HEK.orf3b#1


title: RNASeq_VCaP_Veh_REP1


title: VCAP_RNASeq_DHT_24hr_REP1


title: CD14p.coculture.HEK.orf10#1


title: RNASeq_VCaP_Veh_siCtrl_REP2


title: CD14p.coculture.HEK.nsp9#1


title: RNASeq_VCaP_DHT_10hr_REP1


title: RNASeq_VCaP_DHT_2hr_REP1


title: RNASeq_LNCAP.AR_Veh_REP1

source_name: LNCaP cells with AR overexpression

value: LNCaP cells with AR overexpression


title: RNASeq_LNCAP.AR_DHT_REP2


title: CD14p.coculture.HEK.nsp15#2


title: RNASeq_VCaP_DHT_10hr_REP2


title: RNASeq_LNCAP.AR_DHT_REP1


title: CD14p.coculture.HEK.nsp12#2


title: CD14p.coculture.HEK.nsp8#2


title: CD14p.coculture.HEK.nsp8#1


title: CD14p.coculture.HEK.orf10#2


title: 6 month Cd treated cells (CR6M 2)

scan_protocol: After sample processing according to manufacturer’s instructions on the nCounter Prep Station Model 5S, sample cartridges were scanned on an nCounter Digital Analyzer Model 5S, using 555 Fields of Vision (FOV) and the .rlf file ‘NS_CancerPath_C2535’.

data_processing:
Raw data were normalized to the geometric mean of the positive control probes and to the geometric mean of 3 housekeeping genes (NOL7, MTMP14, and COG7) using nSolver Analysis Software 3.0. Data were then imported into Partek Genomics Suite®, release 7.19.1225, log2 transformed and quantile normalized.
Values are direct ‘counts’ of the number of gene specific epifluorescent dye barcodes in the scanned image.

source_name: 6 month Cd treated cells

value: ht-UtLM

tag: Sex

value: female

value: Cd

value: 6 months


title: 6 month Cd treated cells (CR6M 3)


title: CD14p.coculture.HEK.nsp9#2

tag: genotype


title: RNASeq_LNCAP.AR_Veh_REP2


title: 6 month Cd treated cells (CR6M 1)


title: CD14p.coculture.HEK.nsp14#1

tag: experiment


title: RNASeq_VCaP_DHT_2hr_REP2


title: CD14p.coculture.HEK.nsp10#2


title: CD14p.coculture.HEK.N#1


title: 2 month Cd treated cells (CR2M 3)

source_name: 2 month Cd treated cells

value: 2 months


title: CD14p.coculture.HEK.nsp14#2


title: CD14p.coculture.HEK.nsp11#2


title: CD14p.coculture.HEK.GFP#2


title: siYAPsiTAZ_SMARCC1_Rep2

city: Stanford

first: Zohar

last: Shipony

address: Beckman Center B-279A  279 Campus Drive West

institute: Stanford University

description: CnR FaDu siYAP siTAZ SMARCC!

data_processing:
Library strategy: Cut&Run
sequencing was performed on the NextSeq 500 sequencing system (Illumina) with 75-cycle, paired-end sequencing setup. Reads were first trimmed from Illumina adapters using SeqPurge. Demultiplexed fastq files were mapped to the hg19 assembly of the human genome as 2×36 mers using Bowtie2 , and generated BAM files were then filtered for low-quality reads and duplicated reads. Coverage bigwigs were generated using bamCoverage with CPM normalization. Peaks were called using macs2 with the nomodel option
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: pharynx, cell line

growth_protocol: FaDu, a pharyngeal squamous cell carcinoma cell line, was cultured in ATCC-formulated Eagle's Minimum Essential Medium supplemented with 10% fetal bovine serum (FBS; Omega Scientific) and antibiotics (100 units/mL Penicillin and 100 µg/mL Streptomycin; Gibco).  Adult (HEKa) were purchased from Gibco (C0055C) and cultured on Geltrex (Gibco) coated plates with EpiLife basal medium with 60 µM calcium (Gibco) plus 100 µg/mL insulin, 15 µg/mL transferrin, 10ng/mL epidermal growth factor, 15 µM forskolin, 500nM VX-745, 250nM RO4929097, 100nM dexamethasone and antibiotics.  Cells were maintained in a humidified incubator at 37 °C in the presence of 5% CO2 and passaged every 2–3 days. Cell lines were routinely tested for mycoplasma and immediately tested upon suspicion. None of the cell lines used in the reported experiments tested positive.

extract_protocol:
See Skene PJ et al 2018 (PMID: 29651053)
250,000 cells were bound to 10 µl concanavalin-A beads and collected into a 0.2 ml PCR tube. Antibody binding was conducted in the volume of 50 µl on thermomixer for 96-well PCR plates (Eppendorf) in 4 °C cold room for 2 hours, and Protein A-MNase binding for 1 hour. Wash buffer volume was adjusted to 150 µl. The digestion was performed under high Ca2+/low salt condition on ice for 15 minutes, followed by incubation at 37 °C for 30 min to release CUT&RUN fragments. Antibodies were diluted 1/100 . For histone marks profiling, CUT&RUN fragments were purified by spin column-based methods (Zymo DNA clean & concentrator-5 kit). For transcription factors and BAF complex profiling, CUT&RUN fragments were extracted by phenol-chloroform to recover small fragments. The libraries were generated by using the NEBNext ultraII DNA library prep kit for Illumina coupled with NEBNext multiplex oligos for Illumina (New England Biolabs) with few modifications optimized for small fragments (detailed in dx.doi.org/10.17504/protocols.io.wvgfe3w.)

treatment_protocol: siRNA transfections were performed with DharmaFECT 1 transfection reagents (Horizon Discovery) in the antibiotics-free medium according to the manufacturer’s instructions. Lentiviral transduction was used for overexpression experiments.

value: pharynx

value: siRNA YAP/TAZ

tag: antibody

value: BAF155 (Crabtree laboratory),

value: FaDu


title: CD14p.coculture.HEK.nsp12#1


title: 2 month control cells (LM2M 2)

source_name: 2 month control cells

extract_protocol: Total RNA was extracted from the cells using the Qiagen®  Rneasy kit, followed by Dnase treatment.

value: control

tag: time


title: siYAPsiTAZ_SMARCC1_Rep1

description: CnR FaDu siYAP siTAZ SMARCC!

tag: tissue


title: 6 month control cells (LM6M 3)

source_name: 6 month control cells


title: CD14p.coculture.HEK.nsp15#1


title: siYAPsiTAZ_TEAD1_Rep1

description: CnR FaDu siYAP siTAZ TEAD1

value: TEAD1 (cell signaling, 12292S)


title: CD14p.coculture.HEK.N#2


title: 2 month Cd treated cells (CR2M 2)


title: siControl_TEAD1_Rep2

description: CnR FaDu Control TEAD1

value: siRNA Control


title: 2 month Cd treated cells (CR2M 1)


title: CD14p.coculture.HEK.nsp11#1

value: HD


title: 6 month control cells (LM6M 2)


title: 2 month control cells (LM2M 3)


title: CD14p.coculture.HEK.nsp10#1

value: Blood


title: 6 month control cells (LM6M 1)


title: MEF_p16OE_senescent_D10_3

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: Mouse embryonic fibroblasts

treatment_protocol: RNA-sequencing analyses on cells overexpressing p16 via lentivirus. Cells were harvested and RNA was isolated 10 days after p16 overexpression, at this timepoint cells have entered cellular senescence.

value: embryo

tag: strain


title: MEF_p16OE_senescent_D10_2


title: siYAPsiTAZ_YAP_Rep1

description: CnR FaDu siYAP siTAZ YAP

tag: treatment

value: YAP (cell signaling, 14074T)


title: CD14p.coculture.HEK.GFP#1


title: MEF_p16OE_senescent_D10_1


title: AR3085_02

city: Sinjuku-ku

first: Hidekazu

last: Sugiura

state: Tokyo

address: Kawada-cho 8-1

institute: Tokyo Women’s Medical University

description: Agilent Human 1 cDNA Microarray (G4100A) [layout A]

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: HEK293T, 1064 µg/cm2 calcium oxalate monohydrate (COM), 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell lines of human embryonic kidney cells 293T (HEK293T) were grown to confluence in DMEM/F-12,Hepes (Thermo Fisher Scientific), respectively, on plastic dishes (Falcon). The medium was supplemented with 10% fetal bovine serum (Invitrogen), 100 units/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol: Total RNA was isolated from cells using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: 80% confluence 293T (HEK293T) were incubated in DMEM/F-12,Hepes without 10% fetal bovine serum (Invitrogen), 100 units/mL penicillin, and 100 μg/mL streptomycin for 24 hr. Then HEK293T  were challenged with 1064 µg/cm2 calcium oxalate monohydrate (COM)  or sodium oxalate (NaOx) 4mM or vehicle for 24 hours.

tag: cell line

value: 1064 ug/cm2 calcium oxalate monohydrate (COM), 24 hours


title: siControl_SMARCC1_Rep2

description: CnR FaDu Control SMARCC!


title: siControl_SMARCC1_Rep1

description: CnR FaDu Control SMARCC!


title: MEF_p16OE_non-senescent_D4_2

treatment_protocol: RNA-sequencing analyses on cells overexpressing p16 via lentivirus. Cells were harvested and RNA was isolated 4 days after p16 overexpression.

value: mouse embryonic fibroblasts (MEF)

tag: cell status

value: non-senescent

tag: lentivirus

value: p16 overexpression


title: siYAPsiTAZ_TEAD1_Rep2

description: CnR FaDu siYAP siTAZ TEAD1


title: AR3085_03

source_name: HEK293T, sodium oxalate (NaOx) 4mM, 24 hours

value: sodium oxalate (NaOx) 4mM, 24 hours


title: MEF_p16OE_non-senescent_D4_1


title: MEF_p16OE_non-senescent_D4_3


title: 2 month control cells (LM2M 1)

value: ht-UtLM

value: female

value: 2 months


title: siYAPsiTAZ_YAP_Rep2

description: CnR FaDu siYAP siTAZ YAP

value: pharynx

value: siRNA YAP/TAZ