title: serum 9 SH87Z31_Cell3

source_name: IgG4 related ophthalmic disease

value: IgG4 related ophthalmic disease


title: Ly6C-Hi+CF+Il17A_Rep2

status: Public on Aug 01 2021

type: RNA

city: Baltimore

first: Daniela

last: Cihakova M.D. Ph.D. D(ABMLI)

state: MD

address: 720 Rutland Avenue

department: Pathology-Immunopathology

country: USA

institute: The Johns Hopkins University School of Medicine

hyb_protocol: Hybridization was 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using the Affymetrix GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values that were used in subsequent two-tailed one-way ANOVA analysis.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Ly6Chi + CF + IL-17

label_protocol: The Affymetrix3' IVT Pico Kit kit was used with the Affymetrix protocol.

growth_protocol: Cells were plated in DMEM (Gibco)  with 20% FBS (GE Healthcare Life Sciences), nonessential amino acids (Sigma), Penicillin/Streptomycin, 2mM L-Glutamine, and 25mM HEPES (all Quality Biological). Non-adherent cells were washed away after 1h. Fibroblasts from second passage were used in experiments.

extract_protocol: Total RNA was extracted using QIAGEN miRNeasy kit mini columns and QIAGEN protocol.

treatment_protocol: Recombinant mouse IL-17A cytokines at 50 ng/mL (Peprotech) were used after second passage of the fibroblasts.

tag: tissue

value: spleen

tag: cell type

value: Ly6Chi monocytes

tag: culture protocol

value: splenic monocytes co-cultured with cardiac fibroblasts

tag: treatment

value: IL-17A stimulation


title: serum 7 SH87Z29_Cell1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Homo sapiens

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: All samples have not been used steroid for over three months.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: A sample of venous blood (~5.0 mL) was collected from each patient enrolled in this study. The samples were placed in tubes and centrifuged (8000 rpm, 4 °C, 15 min) to collect the serum, which was stored at −80 °C until further analysis. Surgically biopsied specimens of IgG4-ROD and orbital MALT lymphoma were delivered immediately to the laboratory and stored at −80 °C until the assay.

tag: diagnosis

value: serum

tag: age

tag: Sex

value: F

tag: swollen eyelid

value: P

tag: diplopia

tag: decrease of vision

value: N

tag: other organ lesion

value: submandibular lymph nodes


title: serum 10 SH87Z31_Cell4

value: submandibular lymph nodes, bile duct dilation


title: serum 11 SH8XB58_Cell2


title: Ly6C-Hi+CF+Il17A_Rep1


title: serum 8 SH87Z29_Cell2

value: parotid gland


title: serum 6 SH87Z25_Cell4


title: serum 4 SH87Z23_Cell2

value: M


title: serum 3 SH87Z16_Cell3


title: biopsied specimen 14 SH88801_Cell4

source_name: orbital MALT lymphoma

value: orbital MALT lymphoma

value: biopsied specimen


title: serum 1 SH87Z04_Cell2


title: biopsied specimen 11 SH88261_Cell3


title: biopsied specimen 12 SH88801_Cell2


title: biopsied specimen 6 SH88261_Cell4


title: biopsied specimen 7 SH88259_Cell1


title: biopsied specimen 10 SH88261_Cell1


title: serum 5 SH87Z23_Cell4


title: Adjacent 3 [B633270_NC_miRNA]

city: Dongguan

first: Guangxian

last: Xu

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: College of Medical Technology

country: China

institute: Guangdong Medical University

description: miRNA expression in CRC

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase. The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (Agilent p/n G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v14.9 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 1 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

label: Cyanine 3-pCp

source_name: human colorectal cancer

extract_protocol: The three pairs of prefrozen tissues were homogenized with TRIzol reagent (Invitrogen, USA) using the Mini-Bead-Beater-16 (Biospec, USA). Then, total RNA was extracted from the mixture using a RNeasy Mini Kit (Qiagen, German) with synchronous digestion using DNase (Baseline-ZERO DNase, Epicentre, USA). Subsequently, RNA quantity and quality were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was assessed by denaturing agarose gel electrophoresis.

tag: disease state

value: colorectal cancer

value: adjacent normal tissue


title: biopsied specimen 3 SH88257_Cell3

value: IgG4 related ophthalmic disease


title: Cancer 3 [B633270_CA_miRNA]

description: miRNA expression in CRC

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

value: cancer


title: Cancer 1 [B541155_CA_miRNA]

description: miRNA expression in CRC


title: Adjacent 1 [B541155_NC_miRNA]

description: miRNA expression in CRC


title: Adjacent 2 [B629380_NC_miRNA]

description: miRNA expression in CRC


title: Donor2

type: SRA

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

library_source: genomic

data_processing:
Amplicon-seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore v0.3.7, then aligned to the hg19 genome assembly using bismark v0.14.1.
Genome_build: hg19
Supplementary_files_format_and_content: text format and files contain position of CpG site, the number of methylated or unmethyated reads and methylation levels

molecule: genomic DNA

source_name: Sperm

growth_protocol: Ejaculates were provided by the patients who visited the Reproduction Center in the Ichikawa General Hospital, Tokyo Dental College. Human semen was diluted twice with saline, and was layered on 5.0 mL of 20 mM HEPES buffered 90% isotonic Percoll (Cytiba, Uppsala, Sweden) and centrifuged at 400× g for 22 min. The sperm in the sediment was recovered to yield 0.2 mL, and then introduced to the bottom of 2.0 mL of Hanks’ solution to facilitate swim-up. The motile sperm in the upper layer was then recovered.

extract_protocol:
Genomic DNA was extracted by Phenol chloroform method
Genomic DNA was subjected to bisulphite-meidated C to U conversion using MethylCode Bisulfite Convrsion Kit (ThermoFisher Scientific), and then used as a template for PCR for 35 cycles with EpiTaq (TAKARA) using the following primer: SVA_1_Fw TTATTGTAATTTTTTTGTTTGATTTTTTTGTTTTAG. SVA_1_Rv  AAAAAAACTCCTCACATCCCAAAC. SVA_2_Fw TTAATGTTGTTTAGGTTGGAGTGTAGTG. SVA_2_Rv CAAAAAAACTCCTCACTTCCCAATA. SVA_3_Fw TTTGGGAGGTGTATTTAATAGTTTATTGAGAA. SVA_3_Rv TAAACAAAAATCTCTAATTTTCCTAAACAAAAAACC). The PCR products from 3 set of perimers were combined, were purified by MinElute PCR Purification Kit (QIAGEN), and were fragmented by Picoruptor (Diagenode) for 10 cycles of 30 seconds on, 30 seconds off. Then, amplicon-seq library was constracted by KAPA LTP Library Preparation Kits (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche). The amplicon-seq libraries were sequenced on a HiSeq X platform (Illumina).

value: sperm


title: biopsied specimen 2 SH88257_Cell2


title: biopsied specimen 8 SH88259_Cell2


title: biopsied specimen 5 SH88259_Cell4


title: biopsied specimen 4 SH88257_Cell4


title: biopsied specimen 13 SH88801_Cell3

value: abdomen lymph node


title: Donor4


title: Cancer 2 [B629380_CA_miRNA]

description: miRNA expression in CRC


title: Donor3


title: Donor5


title: biopsied specimen 9 SH88259_Cell3


title: indrops-drop-8mWt_2

city: Boston

first: Jeong

middle: H

last: Yun

state: MA

address: 181 Longwood Ave

institute: BRIGHAM AND WOMEN'S HOSPITAL

library_source: transcriptomic

data_processing:
For 10X Chromium libraries, sequencing output was demultiplexed by Cell Ranger (version 2.0.0), for inDrops libraries, sequencing output was demultiplexed by dropTag-dropEst pipeline
Cells were filtered if UMI counts were over 3000 or less than 200, as well as mitochondrial percent over 15%
Each library count matrices was processed with variance stabilizing transformation (SCTransform workflow) in Seurat v3.1.4. All library count matrices were integrated using a reference library (4m Het-2) that had the highest sequencing depth per cell using 30 dimensions.
Cell clusters were identified by inputing 40 principal components for UMAP embedding and cluster identification using Leiden algorithm with resolution 1.5 in Seurat v3.1.4.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object with meta data  (Seurat R object retrieve by readRDS)

source_name: lung

extract_protocol:
For harvesting, mice were euthanized by CO2 asphyxiation followed by exsanguination.  Lungs were perfused with chilled PBS via the right heart.  For lung cells isolation without enrichment (15 out of 18 samples), dispase (50 U-mL) was instilled into lungs, which were dissected and minced on ice into approximately 1 mm3 cubes.  Lungs were digested using collagenase-dispase for 30 mins at 37°C, then passed through a 40 um cell strainer.  Cells were centrifuged at 300 RCF for 5 mins, then incubated with RBC lysis buffer.  Cells were stained with trypan blue for viability assessment which showed greater than 85% viability with this method. The single cell suspension was sorted by FACS for DAPI-negative viable cells using MoFlo Astrios EQ.
For enriched CD45- lung cells (4mHet-3, 4mWt-2, 8mHet-3), lungs were digested using a mouse lung isolation kit with gentleMACS dissociator (Miltenyi), then were passed through a 40 um cell strainer. After centrifugation at 300 RCF for 5 mins, cells were incubated with RBC lysis buffer. Cells were then stained with DAPI, DRAQ5 (abcam) and CD45-PE Ab (BioLegend), and selected for DAPI negative, DRAQ5 positive and CD45 negative cells using On-chip Sort cell sorter (On-chip Biotechnologies)(Watanabe et al., 2014).
single cell RNA libraries were prepared for sequencing using 10X Genomics Chromium V2 protocols and inDrops

tag: strain

value: lung

value: postnatal day 15

tag: genotype

value: Hhip+-+

tag: cell type enrichement


title: serum 2 SH87Z06_Cell2

value: serum

value: P


title: p15-p15Het_1

value: Hhip+--


title: p15-p15Wt_1


title: p15-p15Het_2


title: p15-p15Wt_2


title: biopsied specimen 1 SH88257_Cell1

value: F

value: N

value: submandibular lymph nodes


title: indrops-drop-8mWt_1

value: 8 months


title: indrops-drop-8mHet_1


title: G7_plate6

city: Medford

first: Eric

middle: R

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

data_processing:
All reads containing bases with quality lower than Q10 are filtered out.
Reads that pass filter are assigned to a well and aligned to the transcriptome (GRCm38) which includes mitochondrial genes using BWA aln version 0.7.10. Reads that only align to multiple isoforms of the same gene are considered uniquely mapped.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: (1) HGNC symbols (2)Read Counts.

source_name: NIH 3T3-L1

growth_protocol: NIH 3T3-L1 (ATCC: CL-173, RRID:CVCL_0123) cells were maintained in high-glucose DMEM with 10% calf serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.25 μg/ml amphotericin B. Cells were plated in 24 well plates at 50,000 cells per well in 0.5 ml maintenance medium and incubated for 4 days. “Naïve” cells were cultured in maintenance medium for the duration of the experiment. To induce adipogenesis, the medium was replaced with DMEM containing 10% fetal bovine serum (FBS, Sigma-Aldrich), 250 nM dexamethasone, 167 nM of 1 µg/ml human insulin, 0.5 mM IBMX, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Cells were thawed on ice and each sample was lysed using 1uL of 1mg/mL Proteinase K (ThermoFisher Scientific) followed by incubation at 50oC for 15 min, then 95oC for 10 min uncovered to evaporate all liquid.
Single Cell RNA Barcoding and Sequencing (SCRB-seq) was performed as described in Soumillon M., Cacchiarelli D., Semrau S., van Oudenaarden A. and Mikkelsen T.S. (2014). Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv. 10.1101/003236. Sequencing generates two files: read1 and read2.  Read1 contains 17 base reads (6 base barcode + 10 base UMI + an N in the 17th position).  Read2 contains the 46 bp cDNA sequence.

treatment_protocol: Experimental wells received induction medium and were treated with Vh (DMSO, 0.2% final concentration), or test chemicals. On days 3 and 5 of differentiation, medium was replaced with adipocyte maintenance medium (DMEM, 10% FBS, 167 nM human insulin, 100 U/ml penicillin, 100 μg/ml streptomycin), and the cultures were re-dosed. On Day 7 of differentiation, medium was replaced with adipocyte medium (DMEM, 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin) and the cultures re-dosed.

tag: cell line

value: NIH 3T3-L1

tag: chemical

value: DMSO

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: H7_plate6


title: Donor1

tag: tissue


title: G6_plate6

value: TROG

value: Troglitazone


title: indrops-drop-8mHet_2

tag: age


title: G11_plate6

value: TESA

value: Tesaglitazar


title: H11_plate6


title: H1_plate6

value: NAIVE


title: H10_plate6


title: H9_plate6

value: DPP

value: Diphenyl phosphate


title: serum 31 SH88139_Cell1

source_name: healthy individual

tag: diagnosis

value: healthy individual

tag: Sex

tag: swollen eyelid


title: G10_plate6


title: G9_plate6


title: H3_plate6


title: G3_plate6


title: G12_plate6


title: H8_plate6

value: CL


title: H2_plate6


title: H9_plate5


title: G8_plate6


title: H8_plate5

value: ROSCO

value: Roscovitine


title: G2_plate6


title: H11_plate5

value: TELMISARTAN

value: Telmisartan


title: H10_plate5

value: TEBUCON

value: Tebuconazole


title: H2_plate5

value: NIH 3T3-L1

value: TBUP

value: Tributyl phosphate


title: H7_plate5

value: RESOLVIN


title: H1_plate5

value: MAGNOLOL

value: Magnolol


title: G10_plate5

value: FENTHION

value: Fenthion


title: G11_plate5

value: FLUDIOX

value: Fludioxonil


title: H3_plate5

value: TPHP

value: Triphenyl phosphate


title: G9_plate5

value: Dexamethasone sodium phosphate


title: G5_plate5

value: ALLETHRIN

value: d-cis,trans-Allethrin


title: G3_plate5


title: G4_plate5

value: DMSO


title: G7_plate5

value: CORT

value: Corticosterone


title: G2_plate5

value: NIH 3T3-L1

value: TONALID

value: Tonalid


title: F10_plate5

value: TEBUCON

value: Tebuconazole


title: H5_plate5

value: PIOG

value: Pioglitazone hydrochloride


title: F8_plate5

value: ROSCO

value: Roscovitine


title: F7_plate5

value: RESOLVIN


title: F6_plate5

value: PROTECTIN

value: Protectin D1


title: F3_plate5

value: 9-cis-retinoic acid


title: E10_plate5

value: FENTHION

value: Fenthion


title: E6_plate5

value: CANDESARTAN

value: Candesartan


title: E9_plate5

value: NIH 3T3-L1

value: Dexamethasone sodium phosphate


title: F9_plate5


title: E12_plate5

value: HONOKIOL

value: Honokiol


title: E8_plate5

value: CYAZOFAMID

value: Cyazofamid


title: F4_plate5


title: E5_plate5

value: ALLETHRIN

value: d-cis,trans-Allethrin


title: G12_plate5


title: D9_plate5


title: D11_plate5

value: TELMISARTAN

value: Telmisartan


title: E7_plate5

value: CORT

value: Corticosterone


title: D8_plate5

value: ROSCO

value: Roscovitine


title: E4_plate5

value: DMSO


title: F11_plate5


title: D12_plate5

value: TTBP


title: D4_plate5


title: D7_plate5

value: RESOLVIN


title: C11_plate5

value: NIH 3T3-L1

value: FLUDIOX

value: Fludioxonil


title: F5_plate5

value: PIOG

value: Pioglitazone hydrochloride


title: F1_plate5

value: DBT

value: Dibutyltin


title: D6_plate5

value: PROTECTIN

value: Protectin D1


title: C9_plate5

value: Dexamethasone sodium phosphate


title: C7_plate5

value: CORT


title: C5_plate5

value: ALLETHRIN

value: d-cis,trans-Allethrin


title: D1_plate5

value: ARSENITE

value: Sodium arsenite


title: C6_plate5

value: CANDESARTAN

value: Candesartan


title: C8_plate5

value: NIH 3T3-L1

value: CYAZOFAMID

value: Cyazofamid


title: C4_plate5

value: DMSO


title: C3_plate5

value: NAIVE


title: Long trained 24h, Rep 2

city: Ottawa

first: Vern

last: Lewis

state: Ontario

address: 1125 Colonel By Drive

department: Neuroscience

country: Canada

institute: Carleton University

description:
Long-trained_VS_Short_trained_Analysis
Annotation_File_Trinotate
Assembled_Transctiptome
Long_vs_Short_24h_DESeq2.csv

data_processing:
RNA-seq was performed on RNA extracted from Brain tissue.
Quality trimming and de novo transcriptome assembly was performed using the Trinity assembly suite. Current samples were combined with 2h & 24h samples from previous GEO submission: GSE135054.
Read alignment was performed using Bowtie2 integrated in to the Trinity suite.
Differential expression analysis was performed using RSEM and DESeq2
Annotation was done using the Trinotate annotation platform which uses the ref-seq NCBI, and Uniprot databases to run homology searches.
Gene ontology and pathway enrichment analysis  was performed using the David Bioinformatics Resources website, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
Supplementary_files_format_and_content: Differential expression measure: DESeq2 files for each treatment comparison (Extinction 2h vs. Acquisition 2h, Extinction 24h vs. Acquisition 24h, Long-trained 2h vs. Short-trained 2h, Long-trained 24h vs. Short-trained 24h). Files are comma delimited and the output consists of log2 fold changes, p-values, and p-adjusted values (FDR).
Supplementary_files_format_and_content: Filtered processed data file for each analysis (Extinction vs. Acquisition & Long-trained vs. Short-Trained). Each file includes the log2 fold change, FDR, and annotation information for all DEG in each analysis. These files contain the final processed datasets used in the publication.
Supplementary_files_format_and_content: Full processed dataset is a tab delimited file which includes the unfiltered output from the Trinotate annotation tool, abundance measure from the RSEM tool, and differential expression output from DSeq2. Trinotate output consists of homology search results from both NCBI's refseq database and Uniprots protein database. Also included are pfam, signalP, eggnog, KEGG, and gene ontology annotations, as well as the associated nucleotide and protein sequences. The log2 Fold-change and FDR for all differentially expressed transcripts are included.
Supplementary_files_format_and_content: Assembled Transcriptome file contains all de novo assembled transcripts from the Trinity tool.

molecule: polyA RNA

organism: Bombina orientalis

source_name: Whole brain

extract_protocol:
Trizol extraction + isolation with a Qiagen RNease kit
RNA libraries were prepared for sequencing using standard Illumina protocols by The Center for Advanced Genomic (TCAG) at The Hospital for Sick Children's.

value: Brain

tag: post-training sacrifice timings

value: 24 hours post

tag: acquisition training

value: Long (36 trials)


title: Long trained 24h, Rep 3


title: A11_plate5

value: FLUDIOX

value: Fludioxonil


title: B11_plate5

value: TELMISARTAN

value: Telmisartan


title: A6_plate5


title: B4_plate5


title: B8_plate5

value: ROSCO

value: Roscovitine


title: C1_plate5

value: 9-cis-retinoic acid


title: B2_plate5

value: PFOA

value: Perfluorooctanoic acid


title: B1_plate5

value: NIH 3T3-L1


title: B7_plate5

value: RESOLVIN


title: B6_plate5

value: PROTECTIN

value: Protectin D1


title: B9_plate5


title: B12_plate5

value: TTBP


title: A8_plate5

value: CYAZOFAMID

value: Cyazofamid


title: Long trained 24h, Rep 1

value: Brain

value: 24 hours post

value: Long (36 trials)


title: Short trained 24h, Rep 3

description:
Long-trained_VS_Short_trained_Analysis
Extinction_VS_Acquisition_Analysis
Annotation_File_Trinotate
Assembled_Transctiptome
Ext_vs_Acq_24h_DESeq2.csv
Long_vs_Short_24h_DESeq2.csv

value: Short (12 trials)


title: A3_plate5

value: TRIFLUMIZOLE

value: Triflumizole


title: A2_plate5

value: MBUP

value: Mono-n-butyl phthalate


title: A1_plate5

value: NAIVE


title: Long trained 2h, Rep 3

description:
Long-trained_VS_Short_trained_Analysis
Annotation_File_Trinotate
Assembled_Transctiptome
Long_vs_Short_2h_DESeq2.csv

value: 2 hours post


title: Short trained 24h, Rep 2


title: A4_plate5

value: NIH 3T3-L1

value: DMSO


title: F2_plate4


title: Long trained 2h, Rep 2


title: Short trained 2h, Rep 3

description:
Long-trained_VS_Short_trained_Analysis
Extinction_VS_Acquisition_Analysis
Annotation_File_Trinotate
Assembled_Transctiptome
Ext_vs_Acq_2h_DESeq2.csv
Long_vs_Short_2h_DESeq2.csv


title: A9_plate5

value: Dexamethasone sodium phosphate


title: Short trained 2h, Rep 1


title: Short trained 2h, Rep 2


title: E5_plate4


title: Long trained 2h, Rep 1


title: 24 hour rep 3

description:
Extinction_VS_Acquisition_Analysis
Ext_vs_Acq_24h_DESeq2.csv


title: 24 hour rep 2


title: F1_plate4


title: 24 hour rep 1


title: E2_plate4


title: E3_plate4


title: E6_plate4


title: A5_plate5

value: ALLETHRIN

value: d-cis,trans-Allethrin


title: Short trained 24h, Rep 1


title: 2 hour rep 1

description:
Extinction_VS_Acquisition_Analysis
Ext_vs_Acq_2h_DESeq2.csv


title: E1_plate4


title: A7_plate5

value: CORT

value: Corticosterone


title: f5C_spikein_70C_DMSO

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

description: 5fC_calibration_curve.xlsx, 5fC_SpikeIn_context.xlsx

data_processing:
Basecalls performed using CASAVA version 1.4
Low-quality and adapter-containing reads were trimmed from Spike-In oligos raw sequencing data using trim-galore package in single-end mode. Reads shorter than 50 bp were removed.
We used fastx_collapser in FASTX-toolkit to collapse identical sequences in a fastq file into a single sequence, which was used to remove duplicated  reads from PCR amplification.
For the reason of In-line barcode design in the Spike-In libraries, First 5bp bases and last 11bp bases were cut from the collapsed reads.
The modified reads were finally used to calculate mutation rates based on different sequence context and generate the calibration curve.
Genome_build: Spike-In sequence
Supplementary_files_format_and_content: xlsx/calibration curve&Spike-In context
Library strategy: f5C-seq

organism: synthetic construct

source_name: Spike-In RNA oligos

extract_protocol: Libraries were prepared according to Illumina's instructions

tag: cell type

tag: rna population

value: Spike-In RNA oligo


title: 2 hour rep 3

value: Brain


title: f5C_spikein_70C_ACN

tag: genotype


title: E4_plate4

tag: cell line


title: f5C_spikein_65C_DMSO


title: D3_plate4

tag: chemical

value: NTZDPA

value: nTZDpa


title: 2 hour rep 2


title: D1_plate4

value: BPS

tag: chemical full

value: Bisphenol S


title: D5_plate4

value: TBUP

value: Tributyl phosphate

tag: volume mol


title: C6_plate4

value: TCCP

value: Tris(1-chloro-2-propyl) phosphate

tag: concentration


title: E9.5 KO: Mekk3 fl/-; Tie2Cre+

city: San Francisco

first: Qin

last: Zhu

state: CA

address: 600 Minnesota Street

institute: UCSF

description: 10X sc-RNA-seq with cells from dissociated mouse embryos

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Filtering was performed on the raw gene-barcode matrix output by the Cell Ranger cellranger count function, removing barcodes that have fewer than 500 transcripts
Genome_build: mm10
Supplementary_files_format_and_content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, genotype, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.

source_name: dorsal aorta plus umbilical and vitelline arteries

extract_protocol:
Cells were sorted into IMDM with 20% FBS. Using the Chromium controller (10x Genomics) and reagents from the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics), cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) where each cell's trascriptome was indexed with a specific 10x BarCode. cDNA were amplified and purified for library preparation.
cDNA were used for library preparation using the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics) according to manufacturer’s protocol.

treatment_protocol: Embryos were harvested at the appropriate embryonic day and cells were sorted on the same day as harvest.

tag: strain

tag: developmental stage

value: Embryonic day 9.7

value: Mekk3 fl/-; Tie2Cre+

tag: marker


title: D4_plate4

value: NIH 3T3-L1

value: QUINOXYFEN

value: Quinoxyfen

tag: plate

tag: well


title: D6_plate4

value: TDCPP

value: Tris(1,3-dichloro-2-propyl) phosphate


title: D2_plate4

value: Ethylene brassylate


title: f5C_spikein_65C_ACN

value: Spike-In RNA oligo


title: C5_plate4

value: TONALID

value: Tonalid


title: Lung CD4 cells form OmpX_LTA1 [VDJ_GEX]

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description: VDJ_GEX #2

data_processing:
10x Cellranger V.3.1.0 and V.2.1.0 were used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.2.3.1 and V.3.0.0 for scRNA QC and further analysis
Supplementary_files_format_and_content: filtered_contig_annotations.csv
Supplementary_files_format_and_content: clonotypes.csv
Supplementary_files_format_and_content: H5

source_name: Lung

growth_protocol: All mice were obtained from Jax farm and maintained in specific pathogen-free rooms at Tulane University. Experiment were preformed when mice were at age of six to ten weeks

extract_protocol:
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit
Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v2 protocol or by 10x Single Cell 5' VDJ v1 enrichment and gene expression

treatment_protocol:
I. immunization with OmpX with LTA1 or heat killed Klebsiella pneumoniae (ATCC 43816) twice 3 weeks apart
II. immunization with OmpX or OmpC with LTA1 twice 3 weeks apart

value: IL-17F-Thy1.1 reporter mice

tag: infection

value: without infection


title: Lung CD4 cells form OmpX_LTA1 [VDJ_mTCR]

description: VDJ_mTCR #2


title: Naïve spleen CD4 cells [VDJ_GEX]

description: VDJ_GEX #1

source_name: Spleen


title: B4_plate4

value: PREGNEN

value: Pregnenolone 16Î±-carbonitrile


title: C4_plate4

value: PROPARA

value: Propylparaben


title: C2_plate4

value: DOSS

value: Dioctyl sulfosuccinate sodium


title: Naïve spleen CD4 cells [VDJ_mTCR]

description: VDJ_mTCR #1


title: C3_plate4

value: NIH 3T3-L1

value: MBUP

value: Mono-n-butyl phthalate


title: B6_OmpXvac_Lung_CD4+_2


title: B3_plate4

value: MBZP

value: Monobenzyl phthalate


title: B6_HKdKPvac_Lung_CD4+_2


title: C1_plate4

value: BADGE

value: Bisphenol A diglycidyl ether


title: B6_HKdKPvac_Lung_CD4+_1


title: B1_plate4

value: BPA

value: Bisphenol A


title: A6_plate4

value: TPHT

value: Triphenyltin


title: B6_Naive_Spleen_CD4+_2

value: without infection


title: A5_plate4

value: TBB


title: MDA231-miR-122 KO EV rep1

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Sequenced reads were processed to remove 3-bp at 5'-end and any adapters at 3'-end using cutadapt
Trimmed reads were aligned to hg19 genome using Bowtie with default settings
miRNAs in miRBase v21 were counted using customized R scripts
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files containing raw expression count

source_name: Extracellular vesicles

growth_protocol: MDA-MB-231 cells were grown in DMEM plus 10% fetal bovine serum (FBS). Stable knockdown of RAB27A (Rab27a KD) was achieved by lentiviral transduction using the MISSION® shRNA system (Clone ID: NM_004580.3-735s1c1; MilliporeSigma), whereas the empty vector control (Cat# SHC001) was used to construct the control line. To generate miR-122 KO by knocking out hsa-miR-122 gene using CRISPR-Cas9 genomic editing system, two single guide RNAs (sequences CACACTAAATAGCTACTGCT and CACACTCCACAGCTCTGCTA) were used. Gene knockout was confirmed by Sanger sequencing.

extract_protocol:
TRIZOL reagent (Thermo Fisher Scientific) was used to extract total RNA from cells, whereas TRIZOL LS reagent (Thermo Fisher Scientific) was used to extract total RNA from EVs following the manufacturer’s protocol. RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
Each sample was independently subjected to library preparation and deep sequencing.  All small RNAs of 15–52 nts were selected and sequenced using the Illumina system, following the manufacturer’s protocol (Illumina Inc., San Diego, CA).  Library preparation, as well as cluster generation and deep sequencing, was performed according to the 5' ligation-dependent (5′ monophosphate-dependent) manufacturer’s protocol (Digital Gene Expression for small RNA; Illumina).  Small RNAs were size-selected between 17 and 52 nt according to the single-stranded DNA marker in the small RNA sequencing kit (Illumina).  The library was quantified using picoGreen and qPCR.  Sequencing was performed on a Genome Analyzer IIx (Illumina), and image processing and base calling were conducted using Illumina’s pipeline.

treatment_protocol: For EV preparation, conditioned medium (CM) was collected from cultured cells grown in serum-free medium containing 1% BSA for 24 h, and pre-cleared by centrifugation at 500 g for 15 min and then at 10,000 g for 20 min. EVs were pelleted by ultracentrifugation at 110,000 g for 70 min, and washed in PBS using the same ultracentrifugation conditions. The EV-producing cells were collected simultaneously for small RNA-seq.

tag: treatment/genotype

value: miR-122 KO


title: A4_plate4

value: PRALLETHRIN

value: Prallethrin


title: MDA231-miR-122 KO EV rep2


title: A3_plate4

value: MEHP

value: Mono(2-ethylhexyl) phthalate


title: E9.5 WT: Mekk3 fl/fl, Mekk3 fl/+

value: Embryonic day 9.5

value: Mekk3 fl/fl, Mekk3 fl/+

tag: tissue

value: dorsal aorta plus umbilical and vitelline arteries


title: A1_plate4

value: NIH 3T3-L1

value: METBP

value: Mono-(2-ethyhexyl) tetrabromophthalate


title: MDA231-Rab27a KD EV rep1

value: Rab27a KD


title: MDA231-Rab27a KD EV rep2


title: MDA231-CTRL EV rep2

value: control


title: A2_plate4

value: DDT


title: B6_OmpXvac_Lung_CD4+_1


title: H11_plate3


title: H10_plate3

value: PFOS

value: Perfluorooctanesulfonic acid


title: MDA231-CTRL EV rep1


title: MDA231-miR-122 KO Cell rep1

source_name: Breast cancer cell line


title: MDA231-miR-122 KO Cell rep2


title: H7_plate3

value: ATRA

value: All-trans retinoic acid


title: B2_plate4

value: DINP

value: Diisononyl phthalate


title: MDA231-Rab27a KD Cell rep1


title: B6_Naive_Spleen_CD4+_1

value: without infection


title: H8_plate3

value: DDE


title: MDA231-Rab27a KD Cell rep2


title: input_ShNC_H3K79me3

city: Guangzhou

first: Wen-Tao

last: Wang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

data_processing:
The raw sequencing reads from ChIP-seq were aligned to human reference genome (Ensembl GRCh38, hg38) using Bowtie 2.
Peak calling was performed using MACS2 (version 2.1.1) using the following settings: B --nomodel --SPMR -g hs --extsize 147. The resulting normalized (per million reads) bedgraph files were converted to bigWig files using bdg2bw.
Normalized read density was calculated from pooled replicates using bedtools multicov and DEseq2 tools
Genome_build: hg19
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.

source_name: Leukemia cell line

growth_protocol: The  Leukemia cell  was established by dissociating patient-derived xenograft and further cultured in DMEM supplemented with 10% fetal bovine serum and 1% NEAA for over 20 culture passages.

extract_protocol:
Cross-linked chromatin was sheared by sonication and immunoprecipitated with indiacted antibodies. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Leukemia cells were transfected with KLF11 or control siRNA and cultured for 48h. Leukemia cells were transfected with YAP or control siRNA and cultured for 48h.

tag: antibody

tag: transfection

value: control siRNA


title: G11_plate3

value: TUNGSTEN

value: Sodium tungstate


title: H9_plate3

value: NIH 3T3-L1

value: MELENG

value: Melengestrol acetate


title: MDA231-CTRL Cell rep2


title: G9_plate3

value: MAGNOLOL

value: Magnolol


title: G10_plate3

value: PFOA

value: Perfluorooctanoic acid


title: input_ShLAMP5-AS1_H3K79me3

tag: cell type


title: G7_plate3

value: 9-cis-retinoic acid


title: ChIP_ShNC_H3K79me3

description: ShNC-vs-ShLAMP5-AS1_H3K79me3.diffpeak.annotation.xls


title: F11_plate3

value: ARSENITE

value: Sodium arsenite


title: ChIP_ShLAMP5-AS1_H3K79me3


title: F8_plate3

value: DEHP

value: Di(2-ethylhexyl) phthalate


title: input_ShLAMP5-AS1_H3K79me2


title: F9_plate3


title: input_ShNC_H3K79me2


title: F10_plate3


title: ChIP_ShLAMP5-AS1_H3K79me2

description: ShNC-vs-ShLAMP5-AS1_H3K79me2.diffpeak.annotation.xls


title: G8_plate3

value: DBT

value: Dibutyltin


title: F7_plate3

value: TBBPA

value: Tetrabromobisphenol A


title: MDA231-CTRL Cell rep1

value: control


title: ChIP_ShNC_H3K79me2

value: control siRNA


title: EB4_Kcnh2_KO rep2

city: Shanghai

first: Luying

last: Peng

state: Shanghai

address: 1239 Siping Road

department: School of Medicine

institute: Tongji University

data_processing:
Basecalls performed using CASAVA1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using tophat v2.0.13  with parameters -p 2 -G -o
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1 with parameters -u -p 4 -G -o.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Rattus norvegicus

source_name: embryonic stem cells

growth_protocol: WT and Kcnh2-/- rESCs were trypsinized into single cells in the CM with 0.75 μM CHIR9902, 0.1 μM PD0325901, and 10 μM Y27632 (Selleckchem), then diluted to 2.0×10^5 cells/ml. The cell drops (20ul each drop) were hung for 2 days to form the rEB, which were then harvested and transferred onto 50X laminin (Gibco)-coated 6 well plates and cultured in the CM medium with 0.75 μM CHIR9902 and 0.1 μM PD0325901 for 24 hours. Then the attached rEBs were grown in the fresh DM medium for 1 day.

extract_protocol:
When rat embryonic stem cells (WT, Kcnh2-/-) form embryoid body and differentiate to day 4, total RNA was extracted through RNAiso Plus (Takara).  In order to obtain high-quality sequencing data, ribosomal RNA was removed using a biotin-labeled specific probe (Ribo-ZeroTMrRNA Removal Kit). After purification, the RNA was fragmented under a certain temperature and ionic environment. Subsequently, using the random primers and reverse transcriptase in the TruSeq® Stranded kit synthesizes cDNA strands. And then double-stranded cDNA was synthesized using DNA polymeraseⅠ and RNase H. During this progress, the RNA template was removed and dTTP was replaced by dUTP. The double-stranded cDNA was treated with the addition of “A” bases and adaptors. After amplification and purification, the cDNA library was obtained. Finally, the constructed cDNA library was sequenced using Illumina Hiseq platform with the 100-bp pair-end sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The samples are the cells at differentiation day4 derived from WT and Kcnh2-/- rESCs

value: DASD

tag: differentiation days

value: day 4

tag: genotype


title: E10_plate3

tag: cell line

value: NIH 3T3-L1

tag: chemical


title: EB4_Kcnh2_KO rep1


title: E8_plate3

value: BBZP

tag: chemical full

value: Benzyl butyl phthalate

tag: volume mol


title: met2cd_eemb_20°C_rep3

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (WormbaseID), following columns contain raw counts of reads overlapping each gene for each sample.

organism: Caenorhabditis elegans

growth_protocol: RNA was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in three independent biological replicates.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using Trizol and further purified using the RNA Clean & Concentrator kit (Zymo Research R1015) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.
Libraries were prepared using the TruSeq Total RNA-seq (stranded-high input) Library Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: as indicated worm cultures were either maintained at 20°C, or exposed to a 1hr heatstress at 37°C prior to RNA extraction.

tag: strain

value: met-2(gw1660) III

value: early embryo


title: met2cd_eemb_20°C_rep2


title: E7_plate3

tag: concentration


title: E9_plate3

value: IMIDACLOPRID


title: EB4_Kcnh2_WT rep1

value: wild type


title: D11_plate3

value: ROSI

value: Rosiglitazone


title: D10_plate3


title: D8_plate3

value: BUPARA

value: n-Butylparaben


title: met2cd_eemb_20°C_rep1


title: C12_plate3

value: DMSO


title: D7_plate3


title: met2_eemb_37°C_rep3


title: met2_eemb_37°C_rep2


title: H12_plate2

value: TDCPP

value: Tris(1,3-dichloro-2-propyl) phosphate


title: met2_eemb_37°C_rep1


title: met2_eemb_20°C_rep2


title: C11_plate3


title: N2_eemb_37°C_rep3

value: N2 (Bristol)


title: EB4_Kcnh2_WT rep2

value: DASD


title: H10_plate2

value: QUINOXYFEN

value: Quinoxyfen


title: H9_plate2

value: NIH 3T3-L1

value: NTZDPA

value: nTZDpa


title: N2_eemb_20°C_rep3

value: early embryo


title: D9_plate3

value: Firemaster 550


title: N2_eemb_20°C_rep1


title: H11_plate2

value: TBUP

value: Tributyl phosphate


title: H7_plate2

value: BPS

value: Bisphenol S


title: H4_plate2


title: N2_eemb_20°C_rep2


title: N2_eemb_37°C_rep1


title: H5_plate2


title: H6_plate2

value: TRIFLUMIZOLE

value: Triflumizole


title: N2_eemb_37°C_rep2


title: H3_plate2

value: IMIDACLOPRID


title: met2_eemb_20°C_rep1


title: H1_plate2


title: ChIP_H3K27ac_met2cd_3

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
The qCount function in the QuasR package was used to count reads overlapping the ce6 genome assembly split into fragments of 500bp.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains seqnames, followed by start and end position and columns contain raw counts of reads overlapping each fragment for each sample.

source_name: early embryo

growth_protocol: chromatin was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in two independent biological replicates.

extract_protocol:
ChIP experiments were performed as previously described (Zeller et al., 2016). In brief: Embryos were harvested from synchronized animals in three replicates. 40 μg of chromatin was incubated overnight with primary antibody (H3K27ac (Abcam, ab177178) and H3K9me2 (MBL, #MABI0317) ) coupled to Dynabeads Sheep Anti-Rabbit IgG (Invitrogen), in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl)) containing 1% SDS. Antibody bound chromatin was washed 3 × 5 min FA buffer; 5 min FA buffer with 1 M NaCl; 10 min FA buffer with 500 mM NaCl; 5 min with TEL buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0) and 2 × 5 min with TE. Complexes were eluted in 1% SDS in TE with 250 mM NaCl at 65°C for 15 min. Samples and inputs were treated with 20 μg of RNAse A for 30 min at 37°C and 20 μg of proteinase K for 1 hr at 55°C. Crosslinks were reversed by overnight incubation at 65°C. DNA was subsequently purified using Zymo DNA purification columns (Zymo Research).
Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335), according to the manufacturers recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 12 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).

treatment_protocol: as indicated worm cultures were either maintained at 20°C, or exposed to a 1hr heatstress at 37°C prior to chromatin extraction.

value: met-2(gw1660) III

tag: chip antibody

tag: name in processed data


title: H2_plate2

value: BBZP

value: Benzyl butyl phthalate

tag: plate

tag: well


title: G12_plate2

value: NAIVE


title: G11_plate2


title: G10_plate2


title: G9_plate2


title: ChIP_H3K27ac_met2cd_1


title: ChIP_H3K27ac_met2cd_2


title: ChIP_H3K27ac_met2_1


title: ChIP_H3K27ac_met2_2


title: ChIP_H3K27ac_met2_3


title: G8_plate2

value: DMSO


title: ChIP_H3K27ac_wt_37°C_3

value: N2 (Bristol)


title: ChIP_H3K27ac_wt_37°C_2


title: ChIP_H3K27ac_wt_37°C_1


title: G6_plate2

value: NIH 3T3-L1

value: TBT

value: Tributyltin hydride (6CI)


title: met2_eemb_20°C_rep3

value: early embryo


title: ChIP_H3K27ac_wt_3


title: G5_plate2

value: ROSI

value: Rosiglitazone


title: ChIP_H3K27ac_wt_2


title: TN_1004719_G05

type: genomic

first: Wansheng

last: Chen

address: 415 Fengyang Road

department: Department of Pharmacy

institute: Changzheng Hospital, Second Military Medical University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan System using standard recommended Illumina scanner setting

data_processing: ChAMP v3.6 pipeline

label: Cy5 and Cy3

source_name: frozen tissue collected during operation

label_protocol: Cy5 and Cy3 Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAGEN AllPrep DNA/RNA/miRNA universal kit according to standard instructions

tag: gender

value: male

tag: age

tag: tissue type

value: normal colorectal tissue

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: G7_plate2

tag: cell line

tag: chemical

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: TT_14794_H02

tag: gender

tag: age

tag: tissue type

value: colorectal cancer tissue

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms


title: TN_1004719_H05

value: female

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea

tag: neutropenia

tag: tcp

tag: vomiting


title: TN_1004719_C05

tag: overall


title: G4_plate2

tag: cell line

tag: chemical

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: TN_1004719_D04

tag: gender

tag: age

tag: tissue type

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms


title: ChIP_H3K27ac_wt_1

tag: strain

tag: tissue

tag: chip antibody

tag: name in processed data


title: TT_1004719_F05

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: TN_1004719_E05

tag: gender

tag: age

tag: tissue type

tag: height

tag: weight


title: TT_14794_E03

tag: bmi

tag: anemia

tag: bms


title: TT_14794_A03

tag: diarrhea


title: input_met2cd_H3K27ac_3

tag: strain

tag: tissue

tag: chip antibody

value: none (input)

tag: name in processed data


title: TT_14794_E02

tag: fever

tag: headache

tag: hfs

tag: nausea

tag: neutropenia


title: TN_1004719_F04

tag: gender

tag: age

tag: tcp

tag: vomiting

tag: overall


title: TT_14794_H01

tag: tissue type

tag: height

tag: weight

tag: bmi

tag: anemia


title: input_met2cd_H3K27ac_2

tag: strain

value: met-2(gw1660) III

tag: tissue

tag: chip antibody


title: G2_plate2

tag: cell line

tag: chemical

value: BUPARA

tag: chemical full

value: n-Butylparaben

tag: volume mol

tag: concentration

tag: plate

tag: well


title: TN_1004719_B05

tag: gender

tag: age

tag: bms

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea

tag: neutropenia

tag: tcp

tag: vomiting


title: TT_14794_H03

tag: tissue type

tag: height

tag: weight

tag: bmi

tag: anemia

tag: overall


title: TN_1004719_D05

tag: gender


title: TT_14794_D03

tag: age


title: TN_1004719_A05

tag: bms


title: input_met2cd_H3K27ac_1

tag: strain

tag: tissue

tag: chip antibody

tag: name in processed data


title: TT_14794_B03

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea


title: TT_1004719_G04

tag: tissue type

tag: height

tag: neutropenia

tag: tcp

tag: vomiting


title: TN_1004719_H04

tag: gender

tag: weight

tag: bmi

tag: anemia

tag: overall


title: F11_plate2

tag: cell line

tag: chemical

value: TONALID

tag: chemical full

value: Tonalid

tag: volume mol

tag: concentration

tag: plate

tag: well


title: TT_14794_A02

tag: age

tag: tissue type

tag: bms

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea


title: input_met2_H3K27ac_3

tag: strain

tag: tissue

tag: chip antibody

tag: name in processed data


title: TT_14794_B01

tag: gender

tag: height

tag: weight

tag: bmi

tag: anemia

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: TT_14794_E01

tag: age

tag: tissue type

tag: bms

tag: diarrhea

tag: fever


title: G1_plate2

tag: cell line

tag: chemical

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: TT_14794_B02

tag: gender

tag: height

tag: weight

tag: bmi

tag: anemia

tag: headache

tag: hfs

tag: nausea


title: input_met2_H3K27ac_1

tag: strain

tag: tissue

tag: chip antibody

tag: name in processed data


title: TN_1004719_C04

tag: age

tag: tissue type

tag: bms

tag: diarrhea

tag: fever

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: input_met2_H3K27ac_2


title: F6_plate2

tag: cell line

tag: chemical

value: DMSO

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: input_wt_37°C_H3K27ac_3

tag: strain

value: N2 (Bristol)

tag: tissue

tag: chip antibody

tag: name in processed data


title: F7_plate2

value: NIH 3T3-L1

value: BADGE

value: Bisphenol A diglycidyl ether


title: TN_1004719_E04

tag: gender

tag: age

tag: tissue type

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: headache

tag: hfs

tag: nausea


title: TT_1004719_G03

tag: fever

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: Cloning ppm2 small RNA rep2

city: Riverside

first: Weifeng

last: Gu

state: California

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

description:
Small RNA analysis
ppm2rep2

data_processing:
The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
Genome_build: C. elegans WS215
Supplementary_files_format_and_content: tabbed txt file containing sequence and read number for the analysis

source_name: Cloning ppm2 small RNA

growth_protocol: Worms were grown on NGM plates with OP50 at 20 °C.

extract_protocol:
RNAs were extracted with TRIzol
RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with ~20 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker.
5' RNA ligation and 3' RNA ligation

treatment_protocol: For cloning 22G-RNA, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours in the ligation condition

tag: genotype

value: ppm2 mutant

tag: developmental stage

value: adult worms

tag: treatment

value: PIR-1 treatment


title: F4_plate2

tag: cell line

tag: chemical

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: Cloning ppm2 small RNA rep1

description:
Small RNA analysis
ppm2rep1


title: TN_1004719_B04

tag: gender

tag: age

tag: tissue type

value: normal colorectal tissue

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: headache

tag: hfs


title: F3_plate2

tag: cell line

tag: chemical


title: input_wt_37°C_H3K27ac_2

tag: strain

tag: tissue

value: early embryo

tag: chip antibody

tag: name in processed data


title: input_wt_37°C_H3K27ac_1


title: G3_plate2

tag: chemical full

value: Firemaster 550

tag: volume mol

tag: concentration

tag: plate

tag: well


title: Cloning N2 small RNA rep2

description:
Small RNA analysis
N2rep2

source_name: Cloning N2 small RNA

tag: genotype

value: wild type

tag: developmental stage

tag: treatment


title: E12_plate2


title: input_wt_H3K27ac_3

value: none (input)


title: S2-RNAPII-ChIA-PET_Rep1

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description:
nuclear chromatin
Replicate 1

data_processing:
Library strategy: ChIA-PET
RICh-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: RICh-PET:Tab-delimited file documenting the genomic coodinates of DNA and RNA of each interaction PET with RNA strand information; ChIA-PET: Tab-delimited file documenting the genomic coodinates and frequency of each interaction PET clusters.

organism: Drosophila melanogaster

growth_protocol: S2 was cultured following manufacture’s instruction.

extract_protocol:
Chromatin was obtained and subjected to fragmentation with an average length of 500 bp by sonication. The anti-RNAPII monoclonal antibody 8WG16 (Biolegend, 920102) was used to enrich RNAPII-bound chromatin fragments, respectively.
The DNA fragments in the streptavidin beads-bound chromatin for Standard RICh-PET  or antibody beads-bound chromatin for RNAPII RICh-PET were end-repaired using T4 polymerase (Promega) in mixture (70 µl 10× T4 polymerase buffer, 7 µl 10mM dNTP, 3.5 µl RI, 612.3 µl Nuclease-free water, with 7.2 µl of T4 polymerase), washed with RICh-PET Wash Buffer (10 mM Tris.HCl pH 7.0, 10 mM Tris.HCl pH 8.0, 10 mM EDTA, 50 mM NaCl) three times. The RNA fragments were linked to RNA linker for first-strand cDNA synthesis using the Superscript III First Strand Synthesis System (Thermo Fisher Scientific). In more details, 1 µg of biotinylated and barcoded RNA linker R1 (tube 1) and R2 (tube 2) containing a flanking MmeI site were added to two tubes containing cDNA synthesis mixture (20 µl RNA liker, 20 µl dNTP, 80 µl 5× RT buffer, 20 µl 0.1 M DTT, 20 µl RI, 220 µl Nuclease-free water) and incubated at 65 °C for 5 min (Alternative, incubated at 42 °C for 5 min when performing RNAPII RICh-PET), then placed on ice for at least 1 min, and added 20 µl superScriptIII RT, and incubated for 10 min at 25 °C on Intelli-Mixer (Program F1, 10rpm), followed by 30 min at 50 °C (Alternative, 1 hour at 37 °C when performing RNAPII RICh-PET). The RNA linker ligated chromatin was washed with Wash Buffer three times, then incubated with 1 µg of DNA linker D1 (tube 1) and D2 (tube 2) respectively in the ligation mixture (15 µl DNA linker, 140 µl 5× T4 DNA ligase buffer with PEG, 3.5 µl RI, 536.5 µl Nuclease free water) by using 5 µl of T4 DNA ligase at 16 °C for overnight. The linker-added DNA fragments were washed with Wash Buffer three times and then phosphorylated with 14 µl of T4 polynucleotide kinase (NEB) in PNK master mix buffers (70 µl 10× T4 DNA ligase buffer, 3.5 µl RI in 612.5 µl Nuclease-free water). The samples from two tubes were washed with Wash Buffer three times and then were mixed and followed by proximity ligation with 34 µl of T4 DNA ligase in reaction buffer (1,000 µl 10× T4 DNA ligase buffer, 50 µl RI, 8,916 µl Nuclease-free water) overnight at 16 °C. After washing with Wash Buffer three times, the chromatin DNA fragments with linkers were subjected to second-strand cDNA synthesis with a Superscript Double-stranded cDNA Synthesis Kit (Thermo Fisher Scientific) and chromatin mixing with second-strand cDNA mixture (333 µl Nuclease-free water, 90 µl 5× second-strand reaction buffer, 9 µl 10 mM dNTP mix, 3 µl E.coli DNA ligase, 12 µl E.coli DNA Polymerase I, 3 µl E.coli RNase H) were incubated at 16 °C for 2 hours; then 6 µl of T4 DNA polymerase were added and continued to be incubated at 16 °C for 5 min. Crosslinks in the DNA/RNA/protein complexes were then reversed by incubation at 65 °C overnight with 0.5% SDS (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific), and the cDNA-DNA fragments were purified by phenol/chloroform isopropanol precipitation. The purified cDNA-DNA was then digested by 1 µl of MmeI (NEB) in buffer (5 µl 10× NE Buffer 4, 5 µl Half linker non-Biotinylated to quench excess MmeI, 5 µl 10× SAM) for 2 hours at 37 °C to release the [cDNA tag]-[RNA linker]-[DNA linker]-[DNA tag] Paired-End-Tag structure. The biotinylated PETs were then immobilized on streptavidin-conjugated magnetic Dynabeads (Thermo Fisher Scientific, 11206D-10ml) in 50 µl of 2× B&W buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 1 M NaCl), and rotated at room temperature for 45 min. The ends of each PET structure were then ligated to a sequencing adaptor by 1 µl of T4 DNA ligase (Thermo Fisher Scientific, EL0013) in Adaptor ligation buffer (4 µl Adaptor A, 4 µl Adaptor B, 5 µl 10× T4 DNA ligase buffer, 36 µl Nuclease-free water) at 16 °C for overnight with rotation. Then the beads were washed three times with 1× B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl). Nick translation was performed by adding 4 µl of E.coli DNA polymerase I solution mixture (38.5 µl Nuclease free water, 10× NEBuffer 2, 2.5 µl 10 mM dNTP) and incubated at room temperature for 2 hours with rotation on the Intelli-Mixer (F8, 30rpm, U = 50, u = 60). Then 10-16 rounds of PCR reactions were performed to amplify the PETs, and the resultant RICh-PET libraries were subjected for sequencing by HiSeq2500 with paired-end reads of 36 bp.

treatment_protocol: Drosophila S2 cells were permeabilized with DPBS containing 0.015% Triton X-100 for 5 min at room temperature, then treated with or without RNaseA at a series of concentration at 100 μg/ml, 200 μg/ml, 400 μg/ml and 800 μg/ml respectively for 10min, then washing with DPBS.

tag: cell type

tag: factor

value: RNAPII


title: S2-RNAPII-ChIA-PET_Rep2

description:
nuclear chromatin
Replicate 2


title: ATAC-Seq (RNaseA + 800μg/ml)_Rep2

description:
Open chromatin
Replicate 2

data_processing:
Library strategy: ATAC-Seq
RICh-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: RICh-PET:Tab-delimited file documenting the genomic coodinates of DNA and RNA of each interaction PET with RNA strand information; ChIA-PET: Tab-delimited file documenting the genomic coodinates and frequency of each interaction PET clusters.


title: F5_plate2


title: input_wt_H3K27ac_2


title: ATAC-Seq (RNaseA + 400μg/ml)_Rep2

description:
Open chromatin
Replicate 2


title: E7_plate2

value: BPA

value: Bisphenol A


title: ATAC-Seq (RNaseA + 200μg/ml)_Rep2

description:
Open chromatin
Replicate 2


title: ATAC-Seq (RNaseA + 800μg/ml)_Rep1

description:
Open chromatin
Replicate 1


title: E11_plate2

value: TOLYLFLUANID

value: Tolylfluanid


title: TT_14794_F03

tag: gender

value: female

tag: age

tag: tissue type

value: colorectal cancer tissue

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: input_wt_H3K27ac_1

tag: strain

value: N2 (Bristol)

tag: tissue

tag: chip antibody

tag: name in processed data


title: E8_plate2

tag: cell line

value: NIH 3T3-L1

tag: chemical

value: DINP

tag: chemical full

value: Diisononyl phthalate

tag: volume mol

tag: concentration

tag: plate

tag: well


title: TN_1004719_F03

tag: gender

tag: age

tag: tissue type

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: fever

tag: headache

tag: hfs


title: ATAC-Seq (RNaseA - control)_Rep2

description:
Open chromatin
Replicate 2

tag: cell type

tag: factor


title: Cloning N2 small RNA rep1

description:
Small RNA analysis
N2rep1

tag: genotype

tag: developmental stage

value: adult worms

tag: treatment

value: PIR-1 treatment


title: ChIP_wt_H3K9me2_20°C_2

tag: strain

tag: tissue

value: early embryo

tag: chip antibody

tag: name in processed data


title: ChIP_wt_H3K9me2_37°C_2


title: ATAC-Seq (RNaseA + 400μg/ml)_Rep1

description:
Open chromatin
Replicate 1


title: TN_1004719_A04

tag: gender

value: male

tag: age

tag: tissue type

value: normal colorectal tissue

tag: height

tag: weight

tag: nausea

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: ChIP_wt_H3K9me2_20°C_1


title: ChIP_wt_H3K9me2_37°C_1


title: TN_1004719_H03

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: fever

tag: headache

tag: hfs


title: D11_plate2

tag: cell line

tag: chemical

value: TBB

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: ATAC-Seq (RNaseA + 200μg/ml)_Rep1

description:
Open chromatin
Replicate 1

tag: cell type

tag: factor


title: ATAC-Seq (RNaseA - control)_Rep1

description:
Open chromatin
Replicate 1


title: Input-ChIRP-Seq

description: nuclear chromatin

data_processing:
Library strategy: ChIRP-Seq
RICh-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: RICh-PET:Tab-delimited file documenting the genomic coodinates of DNA and RNA of each interaction PET with RNA strand information; ChIA-PET: Tab-delimited file documenting the genomic coodinates and frequency of each interaction PET clusters.


title: D12_plate2

value: TPHT

value: Triphenyltin


title: input_wt_H3K9me2_37°C_1

tag: strain

tag: tissue

tag: chip antibody

value: none (input)

tag: name in processed data


title: RNAPII-RICh-PET_Rep2

description:
nuclear chromatin associated RNA
Replicate 2

data_processing:
Library strategy: RICh-PET
RICh-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: RICh-PET:Tab-delimited file documenting the genomic coodinates of DNA and RNA of each interaction PET with RNA strand information; ChIA-PET: Tab-delimited file documenting the genomic coodinates and frequency of each interaction PET clusters.

value: RNAPII


title: roX2-ChIRP-Seq__Rep2

description:
nuclear chromatin
Replicate 2


title: input_wt_H3K9me2_37°C_2


title: D9_plate2

value: MEHP

value: Mono(2-ethylhexyl) phthalate


title: D7_plate2

value: METBP

value: Mono-(2-ethyhexyl) tetrabromophthalate


title: input_wt_H3K9me2_20°C_2

value: N2 (Bristol)


title: RNAPII-RICh-PET_Rep1

description:
nuclear chromatin associated RNA
Replicate 1


title: TN_1004719_D03

tag: gender

tag: age

tag: tissue type

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: nausea

tag: neutropenia

tag: tcp

tag: vomiting

tag: overall


title: TT_14794_G01

value: colorectal cancer tissue

tag: fever

tag: headache

tag: hfs


title: TT_14794_G03

tag: gender


title: TT_14794_G02

tag: age


title: TN_1004719_E03

tag: tissue type


title: D10_plate2

tag: cell line

value: NIH 3T3-L1

tag: chemical

value: PRALLETHRIN

tag: chemical full

value: Prallethrin

tag: volume mol

tag: concentration

tag: plate

tag: well


title: TT_14794_D02

tag: height

tag: weight

tag: bmi

tag: anemia

tag: bms

tag: diarrhea

tag: nausea

tag: neutropenia


title: C12_plate2

value: Triphenyl phosphite


title: Left Atrial Appendage_AF#12

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

institute: Osaka Prefecture University

description:
AF180225#12
RNA from FFPE specimens.

hyb_protocol: Fifteen ug of cRNA were subjected to fragmentation using the 3' fragmentation buffer hybridized for 16 hr at 45C on Affymetrix Human Clariom D Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis Console® using RMA as a summarization algorithm.

source_name: Atrial fibrillation recurrence

label_protocol: Biotinylated cRNA were prepared using the GeneChip® WT Pico Reagent Kit from 100 ng total RNA (GeneChip® WT Pico Reagent Kit User Manual, Affymetrix).

extract_protocol: Total RNA was isolated using the NucleoSpin® total RNA FFPE XS Kit (MACHEREY-NAGEL, Düren, Germany) according to the manufacturer's instructions. On-column DNaseI digestion was performed to avoid genomic DNA contamination.

tag: tissue

value: heart (left atrial appendage)

tag: gender

value: male

tag: age

tag: treatment

value: Maze surgery

tag: diagnosis

value: Atrial fibrillation recurrence


title: TN_1004719_B03

tag: tissue type

value: normal colorectal tissue

tag: fever

tag: headache

tag: hfs

tag: tcp

tag: vomiting

tag: overall


title: Left Atrial Appendage_SR#16

description:
SR180225#16
RNA from FFPE specimens.

source_name: Sinus rhythm maintenance

value: Sinus rhythm maintenance


title: Left Atrial Appendage_SR#7

description:
SR180225#7
RNA from FFPE specimens.


title: TN_1004719_C03

tag: height

tag: weight

tag: bmi

tag: anemia


title: input_wt_H3K9me2_20°C_1

tag: strain

value: early embryo

tag: chip antibody

value: none (input)

tag: name in processed data


title: TT_14794_A01

tag: gender

value: female

tag: age

tag: bms

tag: diarrhea

tag: nausea

tag: neutropenia


title: TT_14794_C02

tag: tissue type

tag: fever

tag: headache

tag: hfs


title: Left Atrial Appendage_SR#9

description:
SR180225#9
RNA from FFPE specimens.

tag: tissue

tag: treatment

tag: diagnosis


title: RICh-PET_Rep2

tag: cell type

tag: factor

value: All chromatin assocatied proteins


title: RNA_degron-auxin_muscle_rep2 [auxin_2]

description:
rnaseq_2183F6-1_muscle_aux_3
processed data file: expression_genes_muscle_degron.txt

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (Sanger identifiers) and width of genes, following columns contain raw counts of reads overlapping each gene for each sample.

growth_protocol: RNA was isolated from purified tissues from L3 larvae grown after L1 synchronization  in two independent biological replicates.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). For isolated tissues, RNA was purified from lysed muscle or seam cells following the instructions of the Norgen Single Cell RNA Purification Kit (51800, Norgen Biotek).
Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).

tag: strain/genotype

value: L3 body wall muscle


title: Left Atrial Appendage_AF#6

description:
AF180225#6
RNA from FFPE specimens.


title: Left Atrial Appendage_SR#5

description:
SR180225#5
RNA from FFPE specimens.


title: roX2-ChIRP-Seq_Rep1

description:
nuclear chromatin
Replicate 1


title: TN_1004719_A03

tag: height

tag: weight

tag: bmi

tag: anemia

tag: tcp

tag: vomiting

tag: overall


title: C10_plate2

data_processing:
All reads containing bases with quality lower than Q10 are filtered out.
Reads that pass filter are assigned to a well and aligned to the transcriptome (GRCm38) which includes mitochondrial genes using BWA aln version 0.7.10. Reads that only align to multiple isoforms of the same gene are considered uniquely mapped.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: (1) HGNC symbols (2)Read Counts.

source_name: NIH 3T3-L1

tag: cell line

tag: chemical

value: PFOS

tag: chemical full

value: Perfluorooctanesulfonic acid

tag: volume mol

tag: concentration

tag: plate

tag: well


title: RNA_degron-auxin_muscle_rep1 [auxin_1]

description:
rnaseq_2183F5-1_muscle_aux_2
processed data file: expression_genes_muscle_degron.txt

treatment_protocol: For isolated tissues, RNA was purified from lysed muscle or seam cells following the instructions of the Norgen Single Cell RNA Purification Kit (51800, Norgen Biotek). Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).

tag: tissue


title: TT_14794_C03

tag: gender

tag: age

tag: tissue type

value: colorectal cancer tissue

tag: bms

tag: diarrhea

tag: fever

tag: headache

tag: hfs

tag: nausea

tag: neutropenia


title: RNA_degron-nonauxin_muscle_rep2 [no_auxin_2]

description:
rnaseq_2183F3-1_muscle_noaux_3
processed data file: expression_genes_muscle_degron.txt

tag: strain/genotype


title: C7_plate2

tag: cell line

value: NIH 3T3-L1

tag: chemical

value: ATRA

tag: chemical full

value: All-trans retinoic acid


title: RICh-PET_Rep1

tag: cell type

tag: factor


title: WT Monosome Rep2

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
Adapter trimming and quality filtering: reads were trimmed and filtered using cutadapt v.1.4, using paired-end mode
Reads were pre-mapped to rRNA to assess the amount of rRNA contamination
Reads were mapped to the sacCer3 genome in paired end mode using StaR version 2.4
Duplicates were removed using samtools v 0.1.19
Reads were converted into counts using RSEM version 1.2.18
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts table per gene and condition (tsv)

organism: Saccharomyces cerevisiae

source_name: WT Monosome

growth_protocol: Yeast was grown to log phase (OD = 0.6-0.8)

extract_protocol:
Polysome-bound RNAs were fractionated using sucrose gradients.
RNA libraries were prepared for sequencing using standard Illumina protocols
Frac-Seq / PolysomeSeq

treatment_protocol: Cycloheximide

tag: growth phase

value: Log phase (OD 0.6-0.8)

tag: strain

value: WT

tag: rna pool

value: Monosome fraction


title: WT Input Rep2

source_name: WT Input

value: Input fraction


title: RNA_degron-nonauxin_muscle_rep1 [no_auxin_1]

description:
rnaseq_2183F2-1_muscle_noaux_2
processed data file: expression_genes_muscle_degron.txt

tag: tissue


title: C9_plate2

value: MELENG

value: Melengestrol acetate

tag: volume mol

tag: concentration

tag: plate

tag: well


title: RNA_met2set25_seamcell_rep2 [met2set25_b]

description:
rnaseq_2093F11-1_seamcell_met2set25_2
processed data file: expression_genes_seamcell_mutants.txt

value: L3 seamcell


title: WT Monosome Rep1


title: C8_plate2

value: DDE


title: C11_plate2


title: WT  PolysomeLow Rep2

source_name: WT  PolysomeLow

value: PolysomeLow fraction


title: D8_plate2

value: DDT


title: WT Input Rep1


title: RNA_set25_seamcell_rep2 [set25_b]

description:
rnaseq_2093F8-1_seamcell_set25_2
processed data file: expression_genes_seamcell_mutants.txt


title: Dermal pericyte 1

city: Baltimore

first: Aaron

middle: W

last: James

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

hyb_protocol: 17 hours at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted with the Partek GS 7.0 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis.
Clariom_D_Human.r1.pgf
Clariom_D_Human.na36.hg38.probeset.csv

source_name: human dermis biopsy

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.

growth_protocol: Cells were trypsinized and passaged at subconfluency, medium was changed every three days

treatment_protocol: Standard growth medium only (DMEM, 10% fetal bovine serum, 1% pen/strep)

value: Dermal pericyte


title: Dermal pericyte 3

extract_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.


title: WT PolysomeLow Rep1

source_name: WT PolysomeLow


title: Left Atrial Appendage_AF#2

description:
AF180225#2
RNA from FFPE specimens.

value: heart (left atrial appendage)

tag: gender

value: male

tag: age

tag: treatment

value: Maze surgery

tag: diagnosis

value: Atrial fibrillation recurrence


title: Dermal pericyte 2


title: RNA_met2set25_seamcell_rep1 [met2set25_a]

description:
rnaseq_2093F10-1_seamcell_met2set25_1
processed data file: expression_genes_seamcell_mutants.txt

tag: strain/genotype


title: B8_plate2

extract_protocol:
Cells were thawed on ice and each sample was lysed using 1uL of 1mg/mL Proteinase K (ThermoFisher Scientific) followed by incubation at 50oC for 15 min, then 95oC for 10 min uncovered to evaporate all liquid.
Single Cell RNA Barcoding and Sequencing (SCRB-seq) was performed as described in Soumillon M., Cacchiarelli D., Semrau S., van Oudenaarden A. and Mikkelsen T.S. (2014). Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv. 10.1101/003236. Sequencing generates two files: read1 and read2.  Read1 contains 17 base reads (6 base barcode + 10 base UMI + an N in the 17th position).  Read2 contains the 46 bp cDNA sequence.

tag: cell line

value: NIH 3T3-L1

tag: chemical

value: DBT

value: Dibutyltin


title: B12_plate2

tag: chemical full

value: Triphenylphosphine oxide


title: B11_plate2

value: TUNGSTEN

value: Sodium tungstate


title: RNA_set25_seamcell_rep1 [set25_a]

description:
rnaseq_2093F7-1_seamcell_set25_1
processed data file: expression_genes_seamcell_mutants.txt


title: A12_plate2

value: TPHP

value: Triphenyl phosphate


title: RNA_met2_seamcell_rep2 [met2_b]

description:
rnaseq_2093F6-1_seamcell_met2_2
processed data file: expression_genes_seamcell_mutants.txt

value: L3 seamcell


title: WT PolysomeHigh Rep1

source_name: WT PolysomeHigh

value: Log phase (OD 0.6-0.8)

value: WT

value: PolysomeHigh fraction


title: WT  PolysomeHigh Rep2

source_name: WT  PolysomeHigh


title: RNA_N2_seamcell_rep2 [wt_b]

description:
rnaseq_2093F2-1_seamcell_wt_2
processed data file: expression_genes_seamcell_mutants.txt

value: N2 (Bristol)


title: Adipose pericyte 1

source_name: human adipose biopsy

tag: cell type

value: Adipose pericyte


title: ∆RPL22B Input Rep1

source_name: ∆RPL22B Input

tag: growth phase

value: Input fraction


title: Adipose pericyte 2


title: RNA_met2_seamcell_rep1 [met2_a]

description:
rnaseq_2093F5-1_seamcell_met2_1
processed data file: expression_genes_seamcell_mutants.txt


title: CONT-S2

city: Wenzhou

first: RI

last: CUI

address: University Town, Chashan

institute: Wenzhou Medical University

description: Assay includes probes for the following: 800 Human miRNAs, 5 Housekeeping gene, 6 positive miRNA assay, 6 Negative miRNA assay, 5 spikein assay

hyb_protocol: See manufacturer's website: http://www.nanostring.com

scan_protocol: Cartrige were placed into the nCounter Digital Analyzer for direct digital counting

data_processing: The raw data in RCC file were uploaded to nSolver Nanostring software 3.0 and processed with default quality control settings, and then for data normalization and expression analysis.

label: digital molecular barcode

source_name: cell line

label_protocol: digital molecular barcode

extract_protocol: Total RNAs were extracted from QKI5 knockdown H1299 cells or control cells with Tryzol Regent.

value: Lung cancer cell line


title: ∆RPL22B Input Rep2

tag: strain


title: Adipose pericyte 3


title: CONT-S3


title: RNA_N2_seamcell_rep1 [wt_a]

description:
rnaseq_2093F1-1_seamcell_wt_1
processed data file: expression_genes_seamcell_mutants.txt


title: A9_plate2


title: A10_plate2


title: ∆RPL22B Monosome Rep2

source_name: ∆RPL22B Monosome

tag: rna pool

value: Monosome fraction


title: Periosteal pericyte 3

source_name: human periosteum biopsy

value: Periosteal pericyte


title: Periosteal pericyte 1


title: Periosteal pericyte 2


title: ∆RPL22B Monosome Rep1


title: QKI5-KO-S3


title: H5_plate1

value: NIH 3T3-L1

value: TOLYLFLUANID

value: Tolylfluanid


title: CONT-S1


title: H4_plate1

value: PREGNEN

value: Pregnenolone 16Î±-carbonitrile


title: H3_plate1

value: MBZP

value: Monobenzyl phthalate


title: QKI5-KO-S1


title: A8_plate2

value: DEHP

value: Di(2-ethylhexyl) phthalate


title: ∆RPL22B  PolysomeLow Rep2

source_name: ∆RPL22B  PolysomeLow

value: Log phase (OD 0.6-0.8)

value: PolysomeLow fraction


title: H2_plate1

value: DINP

value: Diisononyl phthalate


title: RNA_met2_muscle_rep2 [muscle_met2_2]

description:
rnaseq_1131F20-1_muscle_met2_2
processed data file: expression_genes_muscle_mutants.txt

tag: tissue

value: L3 body wall muscle


title: RNA_set25_muscle_rep2 [muscle_set25_2]

description:
rnaseq_1131F23-1_muscle_set25_2
processed data file: expression_genes_muscle_mutants.txt


title: ∆RPL22B  PolysomeHigh Rep2

source_name: ∆RPL22B  PolysomeHigh

value: PolysomeHigh fraction


title: RNA_set25_muscle_rep1 [muscle_set25_1]

description:
rnaseq_1131F11-1_muscle_set25_1
processed data file: expression_genes_muscle_mutants.txt


title: RNA_met2set25_muscle_rep2 [muscle_met2set25_2]

description:
rnaseq_1131F17-1_muscle_met2set25_2
processed data file: expression_genes_muscle_mutants.txt


title: NCCIT-dCD24 5

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing. Data analyses on fastq files were conducted with CLC Genomics Workbench (version 12.0.2, QIAGEN, Venlo. NL). The reads of all probes were adapter (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides max. 2).
Genome_build: Mapping was done against the Homo sapiens (hg38) (May 25, 2017) genome sequence.
Supplementary_files_format_and_content: Statistical differential expression tests were determined using the ‘Differential Expression in Two Groups’ tool (version 1.02). The resulting p-values were corrected for multiple testing by false discovery rate- (FDR) and Bonferroni-correction. A p-value of ≤0.05 was considered significant.

source_name: non-seminoma germ cell tumor, embryonal carcinoma

growth_protocol: NCCIT cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin)

extract_protocol:
RNA was isolated (including DNase I digestion) using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manual
RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific, Meerbusch, Germany) and quality was measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ (Agilent Technologies Inc., Santa Clara, USA). The library preparation was performed according to the manufacturer’s protocol (‘VAHTS Stranded mRNA-Seq Library Prep Kit’). 300 ng total RNA were used for mRNA capturing, fragmentation, synthesis of cDNA, adapter ligation, and library amplification. Bead purified libraries were normalized.
RNA sequencing performed on the HiSeq 3000/4000 system (Illumina Inc., San Diego, USA) with a read setup of 1x150 basepairs (bp).

treatment_protocol: CD24 deficiency was generated by CRISPR/Cas9 method

tag: genotype

value: CD24 deficient clone


title: NCCIT-dCD24 4


title: ∆RPL22B PolysomeHigh Rep1

source_name: ∆RPL22B PolysomeHigh


title: ∆RPL22A Input Rep2

source_name: ∆RPL22A Input

value: Input fraction


title: RNA_met2_muscle_rep1 [muscle_GWmet2_1]

description:
rnaseq_1131F8-1_muscle_met2_1
processed data file: expression_genes_muscle_mutants.txt


title: QKI5-KO-S2

value: Lung cancer cell line


title: RNA_N2_non-muscle_rep2 [negative_wt_2]

description:
rnaseq_1131F15-1_muscle_negative_2
processed data file: expression_genes_muscle_mutants.txt

value: N2 (Bristol)


title: ∆RPL22A Monosome Rep2

source_name: ∆RPL22A Monosome

value: Monosome fraction


title: NCCIT-dCD24 2


title: RNA_met2set25_muscle_rep1 [muscle_met2set25_1]

description:
rnaseq_1131F5-1_muscle_met2set25_1
processed data file: expression_genes_muscle_mutants.txt


title: G6_plate1

first: Eric

last: Reed

address: 419 Boston Ave.

institute: Tufts University

source_name: NIH 3T3-L1

value: NIH 3T3-L1

value: TPHT

value: Triphenyltin

tag: volume mol

tag: concentration


title: G4_plate1

value: PRALLETHRIN

value: Prallethrin

tag: plate

tag: well


title: NCCIT-dCD24 3


title: RNA_N2_muscle_rep1 [muscle_wt_1]

description:
rnaseq_1131F2-1_muscle_wt_1
processed data file: expression_genes_muscle_mutants.txt


title: ∆RPL22A  PolysomeLow Rep2

source_name: ∆RPL22A  PolysomeLow


title: G5_plate1

value: TBB


title: NCCIT-CD24 wt 1

value: parental control, CD24 'wildtype'


title: ∆RPL22A Input Rep1

value: Log phase (OD 0.6-0.8)


title: NCCIT-dCD24 1


title: H1_plate1

value: BPA

value: Bisphenol A


title: RNA_N2_non-muscle_rep1 [negative_wt_1]

description:
rnaseq_1131F3-1_muscle_negative_1
processed data file: expression_genes_muscle_mutants.txt

value: L3 body wall muscle


title: ∆RPL22A Monosome Rep1


title: NCCIT-CD24 wt 2


title: G3_plate1

value: MEHP

value: Mono(2-ethylhexyl) phthalate


title: SCV107_2

city: Bethesda

first: Subhash

middle: (Optional)

last: Verma

address: 37 Convent Drive, BLDG 37 Room 5138

institute: National Institutes of Health

description:
Biological replicate 2
SCV107_2_S18

data_processing:
The reads were trimmed for adapters and low-quality bases using Cutadapt 1.18
Alignment of the reads to the E. coli K12 MG1655 reference genome and the annotated transcriptome was done using STAR 2.6.1
Transcript abundances were calculated by RSEM 1.2.31
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified using the glmTreat function in edgeR by following the steps outlined in (Chen Y et al  F1000Res. 2016 Jun 20 [revised 2016 Aug 2];5:1438).
Genome_build: ASM584v2 Escherichia coli K12 MG1655
Supplementary_files_format_and_content: tab-delimited output files of rsem_calculate_expression with expected_count, transcript per million (TPM), Fragments Per Kilobase of transcript per Million mapped reads (FPKM)

organism: Escherichia coli

source_name: hupAmVenus P63A ∆hupB

growth_protocol: cells were grown in M63 minimal media supplemented with 0.1% glycerol (v/v), 10 µg ml-1 thiamine, and 0.5 mg ml-1 casamino acids

extract_protocol:
For total RNA isolation, a frozen pellet of cells was resuspended in 1 ml TRIzol reagent (Life Technologies) to homogenization and incubated at room temperature for 5 min. To the resuspension, 0.2 ml chloroform was added and mixed by inverting the tube for 15 seconds. The mixture was incubated at room temperature for 10 min and then centrifuged at 20,000 × g for 10 min at 4 °C. After centrifugation, ~0.6 ml of the upper phase was transferred to a new centrifuge tube containing 0.5 ml isopropanol. The mixture was incubated at room temperature for 10 min and then centrifuged at 20,000 × g for 15 min at 4 °C. After centrifugation, the supernatant was discarded and the pellet was washed twice with 1 ml 75% ethanol, made with Diethyl pyrocarbonate (DEPC)-treated water, by centrifugation at 13,544 × g, for 5 min at 4 °C. After the second wash, the tube was left open for 10–15 min at room temperature to dry the pellet. To the pellet, 50 µl DEPC treated water was added and the tube was left at 37 °C for 10–15 min and then the pellet was fully resuspended using a pipette. DNA was removed using TURBO DNA-free Kit (Invitrogen).
Paired-end sequencing libraries were prepared with 2.5 µg of total RNA using Illumina® TruSeq® Stranded Total RNA library prep workflow with Ribo-Zero according to the manufacturer’s instructions.

tag: background strain

value: Escherichia coli K12  MG1655

value: hupAmVenus P63A {delta}hupB

value: Growth in M63 minimal media pH 7.0

value: Cells harvested at OD 600 between 0.4-0.6


title: RNA_N2_muscle_rep2 [muscle_wt_2]

description:
rnaseq_1131F4-1_muscle_wt_2
processed data file: expression_genes_muscle_mutants.txt

value: N2 (Bristol)


title: G1_plate1

city: Medford

value: NIH 3T3-L1

value: METBP

value: Mono-(2-ethyhexyl) tetrabromophthalate


title: F6_plate1

value: Triphenyl phosphite


title: ∆RPL22A PolysomeLow Rep1

source_name: ∆RPL22A PolysomeLow

value: PolysomeLow fraction


title: ∆RPL22B PolysomeLow Rep1

source_name: ∆RPL22B PolysomeLow


title: SCV107_3

description:
Biological replicate 3
SCV107_3_S30

treatment_protocol: M63 minimal media supplemented with 0.1% glycerol (v/v), 10 µg ml-1 thiamine, and 0.5 mg ml-1 casamino acids

value: Escherichia coli K12  MG1656

tag: treatment