title: liver metastasis of RJPDAC15

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC15HM


title: tumor adjacent control tissue of RJPDAC01

status: Public on Jun 02 2020

type: SRA

city: Shanghai

first: Ping

last: Lin

address: No.320 Yueyang Road, Xuhui District

country: China

institute: Shanghai Institute of Nutrition and Health

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC01N

library_source: transcriptomic

data_processing:
TrimGalore (v0.5.0) were used to trim bad-quality bases or reads of raw sequencing data.
The resulting clean reads were then mapped to human genome reference (hg19) by using STAR (v2.5.2b) algorithm.
Htseq-count (v0.6.0) were used to count the total number of uniquely mapped reads mapped to each gene.
Genome_build: hg19
Supplementary_files_format_and_content: expression count table (txt file)

molecule: total RNA

organism: Homo sapiens

source_name: pancreatic ductal adenocarcinoma

extract_protocol:
Total RNA was prepared with QIAzol Lysis Reagent and RNeasy MinElute Cleanup Kit (Qiagen, Germany). The RNA quality and integrity were analyzed by Qubit 2.0(Life Technologies, USA) and Bioanalyzer 2100 (Agilent, Germany).
For library preparation, 3 ug total RNA were captured by NEBNext Oligo d(T) 25 beads (NEB, USA), sheared to fragements of ~250bp, and reverse transcripted by NEBNext RNA first and second Strand Synthesis Module (NEB, USA). The products were end-repaired, A-tailed and ligated to Illumina sequencing adapters and amplified by PCR. The sequencing library were qualified by Qubit 2.0 (Life technologies, USA) and Bioanalyzer 2100 (Agilent, Germany), then sequenced on Illumina Hiseq X-Ten with 2×150 bp paired-end sequencing, which were controlled by Hiseq Control Software (HCS).

treatment_protocol: All assessed samples were treatment-naive tissues (No chemo- or targeted- therapy history before sample collection)

tag: tissue

value: Normal tissue

tag: treatment

value: untreatment

tag: tumor stage

value: stage IV


title: liver metastasis of RJPDAC18

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC18HM

value: Hepatic metastasis


title: primary tumor of RJPDAC17

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC17PT

value: Primary tumor


title: liver metastasis of RJPDAC17

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC17HM


title: Living donor 6

type: RNA

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using log2 normalisation with Illumina Genomestudio

label: biotin

source_name: Living donor_renal biopsy

label_protocol: Biotinylated cDNA was prepared with the Illumina WG-DASL asay

extract_protocol: RNA was extracted with QIAGEN miRNeasy FFPE kit in accordance with the prescribed protocol provided with the kit.

tag: subject status

value: Living donor

tag: classification

value: Living donors

value: renal biopsy


title: primary tumor of RJPDAC15

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC15PT


title: Living donor 5


title: Living donor 1


title: Membranous glomerulonephritis 2

source_name: Membranous glomerulonephritis _renal biopsy

value: Membranous glomerulonephritis


title: Living donor 4


title: Membranous glomerulonephritis 3


title: Living donor 3


title: Membranous glomerulonephritis 1


title: IgAN 54

source_name: IgAN patient_renal biopsy

value: IgAN patient


title: primary tumor of RJPDAC13

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC13PT


title: Living donor 2


title: liver metastasis of RJPDAC13

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC13HM


title: primary tumor of RJPDAC12

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC12PT


title: primary tumor of RJPDAC14

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC14PT


title: liver metastasis of RJPDAC14

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC14HM


title: tumor adjacent control tissue of RJPDAC12

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC12N


title: primary tumor of RJPDAC10

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC10PT


title: IgAN 51


title: Living donor 7


title: IgAN 55


title: tumor adjacent control tissue of RJPDAC13

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC13N


title: tumor adjacent control tissue of RJPDAC10

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC10N


title: IgAN 53


title: IgAN 48


title: IgAN 52


title: liver metastasis of RJPDAC10

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC10HM


title: IgAN 45


title: IgAN 50


title: IgAN 47


title: GBE HCC Replicate 2

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

country: USA

institute: NIEHS

description: miRNA Expression Profile

hyb_protocol: Each labeled sample was hybridized for 16 hours at 48°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls (Affymetrix, Santa Clara, CA) and protocol.  Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 3.2) and Expression Console (Version 1.2).

data_processing: The raw miRNA data were normalized using the Robust Multichip Analysis (RMA) approach

organism: Mus musculus

source_name: GBE-exposed HCC

label_protocol: miRNA expression analysis was conducted using Affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, CA) following the Affymetrix hybridization protocols.  According to the manufacturer’s protocol, the Affymetrix FlashTagTM Biotin HSR labeling (Affymetrix, Santa Clara, CA) was used to label 200 ng of total RNA.

extract_protocol: miRNA extraction was performed using MirVANA miRNA Isolation Kit (Life technologies, Carlsbad, CA) and RNA integrity was measured with Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male and female B6C3F1/N mice were exposed to 0, 200, 600, and 2,000 mg/kg GBE by corn-oil gavage, 5 days a week for 2 years.

tag: strain

value: liver

value: GBE-exposed

tag: cell type

value: Hepatocellular Carcinomas (HCC)


title: IgAN 44


title: IgAN 41


title: IgAN 36


title: IgAN 35


title: GBE HCC Replicate 5

description: miRNA Expression Profile


title: IgAN 38


title: IgAN 43


title: GBE HCC Replicate 4

description: miRNA Expression Profile


title: IgAN 49


title: Spont HCC Replicate 3

description: miRNA Expression Profile

source_name: spontaneous HCC

value: NA; no treatment was performed.


title: GBE HCC Replicate 1

description: miRNA Expression Profile


title: GBE HCC Replicate 3

description: miRNA Expression Profile


title: IgAN 42


title: IgAN 40


title: liver metastasis of RJPDAC12

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC12HM


title: Spont HCC Replicate 5

description: miRNA Expression Profile


title: IgAN 39


title: IgAN 46


title: Spont HCC Replicate 1

description: miRNA Expression Profile


title: IgAN 37


title: IgAN 32


title: Spont HCC Replicate 4

description: miRNA Expression Profile


title: IgAN 34


title: IgAN 28


title: normal liver Replicate 4

description: miRNA Expression Profile

source_name: age-matched normal livers

value: Normal


title: normal liver Replicate 5

description: miRNA Expression Profile


title: normal liver Replicate 2

description: miRNA Expression Profile


title: H_4E_R3_M: moderate polysome fraction sh eIF4E replicate 2

city: Laurel

first: Amanda

last: Ernlund

address: 11100 Johns Hopkins Rd

department: REDD

institute: Johns Hopkins APL

data_processing:
Reads were aligned to hg19 using Star (v2.5.0c)
Read counts were quantified using  Star (v2.5.0c)
Differential Expression was performed using RIVET software (based on voom normalization and Limma statistical tests)
Genome_build: hg19
Supplementary_files_format_and_content: read counts

molecule: polyA RNA

source_name: HME cells

growth_protocol: HMEC cells and MD-231 cells were cultured in DMEM + 10% FBS

extract_protocol:
RNA was extracted using Qiagen RNAeasy extraction kit
Paired-end libraries were constructed

treatment_protocol: All cell lines were treated with doxcycline for 6 days to induce eIF4E silencing

value: mammary epithelial cells

tag: cell line

value: HME


title: IgAN 33


title: Spont HCC Replicate 2

description: miRNA Expression Profile


title: H_4E_R3_L: light polysome fraction sh eIF4E replicate 2


title: IgAN 22


title: IgAN 29


title: IgAN 25


title: IgAN 31


title: H_NS_R5_L: light polysome fraction non-silencing control replicate 2


title: H_NS_R5_T: total RNA non-silencing control replicate 2


title: H_4E_R3_H: heavy polysome fraction sh eIF4E replicate 2


title: H_NS_R5_M: moderate polysome fraction non-silencing control replicate 2


title: IgAN 26


title: H_4E_R4_T: total RNA sh eIF4E replicate 1


title: H_NS_R5_H: heavy polysome fraction non-silencing control replicate 2


title: normal liver Replicate 3

description: miRNA Expression Profile


title: IgAN 20


title: IgAN 24


title: normal liver Replicate 1

description: miRNA Expression Profile


title: H_4E_R4_L: light polysome fraction sh eIF4E replicate 1


title: IgAN 21


title: IgAN 23


title: H_NS_R4_H: heavy polysome fraction non-silencing control replicate 1


title: IgAN 27


title: H_4E_R4_M: moderate polysome fraction sh eIF4E replicate 1


title: H_NS_R4_L: light polysome fraction non-silencing control replicate 1


title: IgAN 18


title: MD_NS_R5_T: total RNA non-silencing control replicate 2

source_name: MDA-MB-231 cells

value: breast cancer


title: MD_NS_R5_L: moderate polysome fraction non-silencing control replicate 2


title: MD_NS_R5_M: light polysome fraction non-silencing control replicate 2


title: MD_NS_R5_H: heavy polysome fraction non-silencing control replicate 2


title: IgAN 19


title: IgAN 14


title: IgAN 15


title: IgAN 13


title: IgAN 17


title: MD_4E_R5_T: total RNA sh eIF4E replicate 2


title: H_NS_R4_M: moderate polysome fraction non-silencing control replicate 1


title: IgAN 12


title: H_NS_R4_T: total RNA non-silencing control replicate 1


title: IgAN 11


title: Eomes input_rep 2

city: St Louis

first: Todd

middle: A

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

library_source: genomic

data_processing:
The raw data was demultiplexed and aligned to the reference genome using Novoalign
MACS was used to call peaks
The Bioconductor library ChIPseeker was used to annotate the peaks by identifying nearby genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimitted text file containing annotated eomes IP peaks minus non-immunoprecipitated DNA input control

molecule: genomic DNA

source_name: NK cell

growth_protocol: In 3 separate experiments, 8-12 week old mice were scarificed and splenocytes were harvested.

extract_protocol:
Chromatin immunoprecipiation was performed using the MAGnify Chromatin Immunoprecipitation System (Thermo Fisher) as per manufacturer’s instructions with a ChIP-grade anti-Eomes antibody from Abcam (ab23345). Non - immunoprecipitated DNA was used as an input control.
ChIP DNA was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs, and underwent amplification for 15 cycles with primers incorporating p5 and p7 sequences and a unique index tag for multiplexing.

treatment_protocol: NK cells purified from pooled splenocytes from WT mice were expanded in vitro for 4 days with 100ng/mL IL-15. Cells were then harvested and approximately 10e6 cells were used per ChIP experiment.

value: spleen


title: H_4E_R4_H: heavy polysome fraction sh eIF4E replicate 1


title: IgAN 8


title: Eomes input_rep 1


title: IgAN 16


title: MD_4E_R5_M: moderate polysome fraction sh eIF4E replicate 2


title: Eomes ChIPseq_rep 2

tag: chip-antibody

value: anti-Eomes (abcam;ab23345)


title: MD_4E_R5_L: light polysome fraction sh eIF4E replicate 2


title: Eomes input_rep 3


title: Eomes ChIPseq_rep 1


title: IgAN 9


title: Eomes ChIPseq_rep 3


title: IR_6_1w

city: Stockholm

first: Ahmed

last: Osman

address: Solnavägen 30

country: Sweden

institute: Karolinska Institute

data_processing:
Illumina bcl2fastq (v2.20.0) was used for basecalling and demultiplexing.
Read quality was checked for each sample using FastQC (v0.11.8).
Reads were aligned to Ensemble GRCm38 reference genome using STAR (v2.6.1d).
Read summarization to gene counts was performed using featureCounts (v1.5.1).
Reads Per Kilobase Million (RPKM) values were calculated from gene counts.
Genome_build: GRCm38/mm10.
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each sample.

source_name: Microglia

extract_protocol:
Single cell suspension was genereated after mild enzymatic digestion.
QIAseq FX single cell RNA library kit (Qiagen).

treatment_protocol: Whole brain irradiation with 8Gy delivered as a single dose using X-RAD320 radiation mechine.

value: Hippocampus

tag: time point


title: IR_5_1w


title: MD_NS_R2_T: total RNA non-silencing control replicate 1


title: IgAN 7


title: IgAN 10


title: MD_4E_R5_H: heavy polysome fraction sh eIF4E replicate 2


title: IR_2_1w


title: IR_3_1w


title: MD_NS_R2_L: light polysome fraction non-silencing control replicate 1


title: IR_4_1w


title: IR_1_1w


title: SH_6_1w


title: MD_NS_R2_M: moderate polysome fraction non-silencing control replicate 1


title: SH_5_1w


title: SH_4_1w


title: SH_3_1w


title: SH_2_1w


title: IgAN 6


title: MD_4E_R2_T: total RNA sh eIF4E replicate 1


title: SH_1_1w


title: MD_NS_R2_H: heavy polysome fraction non-silencing control replicate 1


title: IR_6_1d


title: IgAN 5


title: IgAN 4


title: IgAN 2


title: MD_4E_R2_M: moderate polysome fraction sh eIF4E replicate 1


title: IgAN 1


title: IgAN 3


title: MD_4E_R2_L: light polysome fraction sh eIF4E replicate 1


title: MD_4E_R2_H: heavy polysome fraction sh eIF4E replicate 1


title: IR_3_1d


title: IR_1_1d


title: Focal Segmental Glomerulosclerosis

source_name: Focal Segmental Glomerulosclerosis_renal biopsy

value: Focal Segmental Glomerulosclerosis


title: IR_2_1d


title: SH_5_1d


title: IR_4_1d


title: SH_4_1d


title: SH_2_1d


title: Spata7_KO_6M

city: Houston

first: sangbae

last: Kim

address: 1 baylor plaza

institute: Baylor College of Medicine

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome mm10 (GRCm38) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflelink
Read count profile were analyzed for the differential expression analysis using Seurat package (https://satijalab.org/seurat/, version 2.3.4) for data analysis including quality control, normalization, dimensional reduction, clustering, and visualization. Cells with less than 15% of total expressed genes, and genes that were detected in less than 3% of total cells in each dataset were discarded forom all further analyses. In addition, cells with over 20% mitochondrial gene percentage were excluded for filtering of dead or poor-quality cells
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample condition.

growth_protocol: For all experiments, male Spata7 (Eblimit et al., 2015) mutant mice were compared with age-matched male C57BL6/J mice, to avoid sex as a biological variable.

extract_protocol:
Using ICELL8 multisample nanodispenser (Wafergen Biosystems), 50nl (3E4/ml) of the live cell or nuclear suspension was precisely dispensed into an ICELL8 nanowell microchip containing 5184 wells (150nl capacity) as described previously (Goldstein et al., 2017). Assuming a Poisson distribution frequency for the number of cells per well, about 30% of the nanowells were expected to contain a single nucleus under optimal conditions. Automated scanning fluorescent microscopy (using Olympus BX43 fluorescent microscope with a robotic stage) of the microchip was used to select ~1400 wells containing a single live cell or a single nucleus (CellSelect software, Wafergen Biosystems).  The candidate wells were manually evaluated for debris or clumps as an additional QC.
The chip was subjected to freeze-thaw in order to lyse the cells and 50 nl of reverse transcription and amplification solution (following ICELL8 protocol) was dispensed using the multisample nanodispenser to candidate wells. SCRB-seq was then performed on the candidate wells using pre-printed primer that adds a well-specific barcode to the (A)n mRNA tail of the cellular transcript. The cDNA libraries were pooled, concentrated (Zymo Clean and Concentrator kit, Zymogen) and purified (using 0.6x AMPure XP beads). 3’ transcriptome enriched library was made by Nextera XT Kit and 3’-specific P5 primer, and sequenced on Illumina Hiseq2500.

treatment_protocol: Mice for all the time points were housed on a standard diet and in a 12 -hr light to 12 -hr dark cycle.

tag: background strain

tag: Sex

value: Male

tag: genotype/variation

value: Spata7 mutant (Eblimit et al., 2015, PMID:25398945)

value: Retina

tag: age

value: 6 month


title: Spata7_KO_3M

value: 3 month


title: SH_1_1d


title: Spata7_KO_1M

value: 1 month


title: IR_6_6h


title: Spata7_WT_6M

value: Wildtype


title: SH_3_1d


title: IR_5_6h


title: Spata7_WT_3M


title: IR_4_6h


title: IR_2_6h


title: IR_1_6h


title: Spata7_WT_1M


title: IR_3_6h


title: SH_6_6h


title: IR_5_1d


title: SH_6_1d


title: SH_5_6h


title: sample.eomes_ko_st_ii_rep_1

description: Gene expression data

data_processing:
Low-base-quality reads and adaptors were trimmed and reads were aligned to m_musculus reference build Ensembl_R76 with STAR version 2.0.4
Gene counts were derived from the numberof uniquelyaligned unambiguous reads by Subread:featureCount version 1.4.5
Genome_build: m_musculus reference build Ensembl_R76
Supplementary_files_format_and_content: tab-delimitted text file containing counts of uniquely aligned unambiguous reads per gene

source_name: NK cells

growth_protocol: In 3 separate experiments, 8-12 week old mice were treated with Tamixifen for 3 days and their spleens were harvested.

extract_protocol:
RNA was isolated using the Direct-zol RNA MicroPrep kit (zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NK cells were purified from pooled ILC-EomesΔ/Δ (Ncr1-iCreERT2 KI/WT x Rosa26YFPLSL x Eomesfl/fl mice treated with Tamoxifen) or WT splenocytes and sorted to Stage II (CD27+CD11b-), Stage III (CD27+CD11b+), or Stage IV (CD27-CD11b+).  Cells were stored in Trizol at -80C until RNA isolation.

tag: genotype


title: SH_4_6h


title: sample.eomes_ko_st_iii_rep_1

description: Gene expression data

value: Ncr1-iCreERT2 KI/WT x Rosa26YFPLSL x Eomesfl/fl


title: SH_2_6h


title: sample.eomes_ko_st_iv_rep_1

description: Gene expression data


title: IR_6_2h


title: SH_1_6h


title: sample.wt_st_ii_rep_1

description: Gene expression data

value: WT


title: IR_5_2h


title: IR_4_2h


title: SH_3_6h


title: sample.wt_st_iii_rep_1

description: Gene expression data


title: IR_2_2h


title: IR_1_2h


title: SH_6_2h


title: sample.wt_stage_ii_rep_2

description: Gene expression data


title: SH_5_2h


title: SH_4_2h


title: IR_3_2h


title: SH_2_2h


title: sample.wt_stage_iii_rep_2

description: Gene expression data


title: sample.wt_stage_iv_rep_2

description: Gene expression data


title: sample.ko_stage_ii_rep_2

description: Gene expression data


title: sample.ko_stage_iii_rep_2

description: Gene expression data


title: sample.ko_stage_iv_rep_2

description: Gene expression data


title: siDF123_ActD_2h_2

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: RNAseq

data_processing:
For Riboseq,  adapters and low-quality based reads were trimmed using flexbar v2.5: flexbar -n 20 -a AGATCGGAAGAGCGGTTCAG -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1
The Ribo-seq reads were then demultiplexed using pyBarcodeFilter.py and de-deduplicted using pyFastqDuplicateRemover.py from the pyCRAC software suite.
The processed reads were aligned first to the ribosomal DNA, then to the following siRNA sequences: siDF1 CATCAGGCTGGAGAATAACGACAACAA, TTTTTAGCAAACATAAGAAACCATGAGTC, CAATCAGACTGATCTAATGTGAAATGTA; siDF2 TTGCAGTTTAAGTATTGGAATTTCACAA; siDF3 AAATAGCAATACAGTAGATTTGAATACC. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner using the following parameters -outFilterMultimapNmax 8  --alignEndsType EndToEnd
Mapped reads were then analyzed for different criteria (length, mappability to coding sequence region, P site offset) to select only high quality reads that represent ribosome protected fragments.
For RNAseq, low-quality based reads and short reads were trimmed using flexbar v2.5: flexbar -n 20 -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1. Reads were then mapped to the ribosomal DNA and the siRNA sequences as described for the Riboseq samples. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data are in txt files: Ribo_RNA_TE_siDF1_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1 silencing, Ribo_RNA_TE_siDF2_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF2 silencing,  Ribo_RNA_TE_siDF3_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF3 silencing, Ribo_RNA_TE_siDF123_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1, DF2 and DF3 silencing, RNA_siDF12_HeLa.txt file contains the RNAseq changes upon DF1 and DF2 silencing, RNA_siDF13_HeLa.txt file contains the RNAseq changes upon DF1 and DF3 silencing , RNA_siDF23_HeLa.txt file contains the RNAseq changes upon DF2 and DF3 silencing

source_name: HeLa

extract_protocol:
Total RNA was harvested using either Trizol (RNAseq), or using the cell lysis Ribosome profiling conditions (Riboseq input/Ribosome protected fragments)
Libraries were constructed using either NEBNext Ultra II Directional RNA library prep kit (Ribosome protected fragments inputs/RNAseq), or using the miCLIP cloning protocol (Ribosome protected fragments)

tag: sirna

value: DF1,DF2 and DF3 siRNAs

tag: rna processing

value: rRNA depleted RNA

value: Actinomycin D for 2 hours

tag: spike-in

value: ERCC-1 spike in


title: sample.wt_stage_ii_rep_3

description: Gene expression data

tag: tissue

value: spleen


title: siDF123_ActD_2h_1

description: RNAseq

tag: treatment


title: sample.wt_st_iv_rep_1

description: Gene expression data


title: sample.wt_stage_iii_rep_3

description: Gene expression data


title: SH_3_2h


title: siDF12_2

description: RNAseq

value: DF1 and DF2 siRNAs


title: sample.wt_stage_iv_rep_3

description: Gene expression data


title: SH_1_2h

value: Hippocampus


title: siDF12_1

description:
RNAseq
RNA_siDF12_HeLa.txt


title: LR_46

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

hyb_protocol: One aliquot from each sample was transcriptionally profiled using Illumina (RatRef-12v1 Beadchip) microarray according to standard manufacturer’s procedures.

scan_protocol: not provided

data_processing: To extract the AVG_Signal for all probes for each of the samples, we used the read.idat() function (R package limma version 3.28.21; Ritchie et al. 2015, Nucleic Acids Res. 43: e47). We performed a log2 transformation and then quantile normalized the data using the normalize.quantiles() function in the R package preprocessCore (version 1.34.0; Bolstad 2016 https://github.com/bmbolstad/preprocessCore). During quality control, a potential outlier was noted during principal components analysis (PCA). However, due to the strong sample-sample correlations among all samples (>0.98), removing the outlier was deemed unnecessary. The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.

organism: Rattus norvegicus

source_name: Whole Hippocampus

extract_protocol: The rats were sacrificed at postnatal day 14 (P14) via rapid decapitation followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The RNA was divided into two aliquots earmarked for transcriptional profiling using different microarray platforms. The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.

tag: bred line

value: bred Low Responder (bLR)

value: hippocampus


title: LR_38

label_protocol: One aliquot from each sample was transcriptionally profiled using Illumina (RatRef-12v1 Beadchip) microarray according to standard manufacturer’s procedures.

value: Male


title: HR_29

value: bred High Responder (bHR)


title: HR_27


title: LR_28


title: sample.ko_stage_ii_rep_3

description: Gene expression data


title: LR_26


title: HR_47


title: LR_42


title: HR_39


title: riboseq_siDF123_3

description: Ribosome protected fragments

data_processing:
Library strategy: Ribo-seq
For Riboseq,  adapters and low-quality based reads were trimmed using flexbar v2.5: flexbar -n 20 -a AGATCGGAAGAGCGGTTCAG -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1
The Ribo-seq reads were then demultiplexed using pyBarcodeFilter.py and de-deduplicted using pyFastqDuplicateRemover.py from the pyCRAC software suite.
The processed reads were aligned first to the ribosomal DNA, then to the following siRNA sequences: siDF1 CATCAGGCTGGAGAATAACGACAACAA, TTTTTAGCAAACATAAGAAACCATGAGTC, CAATCAGACTGATCTAATGTGAAATGTA; siDF2 TTGCAGTTTAAGTATTGGAATTTCACAA; siDF3 AAATAGCAATACAGTAGATTTGAATACC. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner using the following parameters -outFilterMultimapNmax 8  --alignEndsType EndToEnd
Mapped reads were then analyzed for different criteria (length, mappability to coding sequence region, P site offset) to select only high quality reads that represent ribosome protected fragments.
For RNAseq, low-quality based reads and short reads were trimmed using flexbar v2.5: flexbar -n 20 -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1. Reads were then mapped to the ribosomal DNA and the siRNA sequences as described for the Riboseq samples. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data are in txt files: Ribo_RNA_TE_siDF1_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1 silencing, Ribo_RNA_TE_siDF2_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF2 silencing,  Ribo_RNA_TE_siDF3_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF3 silencing, Ribo_RNA_TE_siDF123_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1, DF2 and DF3 silencing, RNA_siDF12_HeLa.txt file contains the RNAseq changes upon DF1 and DF2 silencing, RNA_siDF13_HeLa.txt file contains the RNAseq changes upon DF1 and DF3 silencing , RNA_siDF23_HeLa.txt file contains the RNAseq changes upon DF2 and DF3 silencing

molecule: cytoplasmic RNA

value: RNase digested and rRNA depleted RNA


title: HR_33


title: LR_30


title: riboseq_siDF123_2

description: Ribosome protected fragments


title: sample.ko_stage_iii_rep_3

description: Gene expression data


title: riboseq_siDF123_1

description:
Ribosome protected fragments
Ribo_RNA_TE_siDF123_HeLa.txt


title: riboseq_siDF3_3

description: Ribosome protected fragments

value: DF3 siRNA


title: HR_41


title: sample.ko_stage_iv_rep_3

description: Gene expression data


title: Input CTGF-pos tdTomato-pos cells after Bleomycin treatment Replication 2

first: Yoshihiko

last: Kobayashi

address: 307 Research Dr

department: Cell Biology

institute: Duke University

description: CTGFpos_tdTomatopos_Bleomycin_Input.bedgraph

data_processing:
A pipeline called MintChIP was used (https://github.com/jianhong/MintChIP)
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph

source_name: alveolar epithelial cells induced by Bleomycin treatment

extract_protocol:
For sorting AEC2 cells from Mki67-tagRFP mice, cells were stained with CD31, CD45, CD326 and lysotracker then CD31-neg/CD45-neg/CD326-pos/Lysotracker-pos/tagRFP-neg cells were sorted. For sorting CTGFpos cells from CTGF-GFP mice, cells were stained with CD31, CD45, Lgals3, CD326 then CD31-neg/CD45-neg/Lgals3-neg/CD326-pos/GFP-pos cells were sorted.
Extraction of DNA, ChIP reactions and library constractions were performed uisng Mint-ChIP3 protocol (https://www.protocols.io/view/mint-chip3-a-low-input-chip-seq-protocol-using-mul-wbefaje)

treatment_protocol: 2.5 U/Kg bleomycin was administered intranasally and mice were monitored daily. Mice were sacrificed at day 12 after bleomycin injury.

value: CTGF-pos tdTomato+ cells

value: 3 months


title: T12

city: Strabourg

first: Marie-Edith

last: Chabouté

address: 12, rue du Général Zimmer

country: France

institute: CNRS

description: JBB1, JBB2, JBB3

data_processing:
Reads were cleaned using cutadapt v.1.8.1, with options : -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a ATCTCGTATGCCGTCTTCTGCTTG -a "A{50}" -q 30 -m 10
Mapping against the Arabidopsis thaliana reference genome (TAIR10) vith Hisat2 v.2.1.0
Reads were counted using FeatureCounts v.1.6.2, with options : -t "gene" -g "ID" --extraAttributes "Name" -M --fraction
Differential Expression analysis was performed with DEseq2 v.1.22.2
Genome_build: TAIR10
Supplementary_files_format_and_content: 2 files Ctrl_vs_T12 and Ctrl_vs_T34 showing Gene accession numbers and log fold change in the control versus mutant

organism: Arabidopsis thaliana

source_name: 9-day-old seedlings

extract_protocol:
Total RNA was extracted from 9-day-old seedlings using Nucleospin RNA Plant kit. Quantity and quality of the extracted RNAs were determined using QuBit RNA HS assay kit (Thermo Fisher Scientific, Waltham, USA) and a Bioanalyser 2100 (Agilent Technologies, Santa Clara, USA), respectively. RNA Seq was done by Fasteris SA
Libraries were constructed by Fasteris with RiboZero_Stranded_RNA kit.

value: Cross between gip1 (GABI_213D01) and gip2 (FLAG_36406)


title: riboseq_siDF3_2

description: Ribosome protected fragments


title: WT

description: JBB7, JBB8, JBB9

value: wild type


title: riboseq_siDF3_1

description:
Ribosome protected fragments
Ribo_RNA_TE_siDF3_HeLa.txt


title: T34

description: JBB4, JBB5, JBB7


title: riboseq_siDF2_3

description: Ribosome protected fragments

value: DF2 siRNA


title: RARdnfl/fl; Neurog3:Cre_2

city: Aurora

first: David

last: Lorberbaum

state: CO

address: 1775 Aurora Court

department: Barbara Davis Center for Diabetes

institute: University of Colorado Denver

data_processing:
FastQC for quality check
Cutadapt to trim adapters
HiSAT2 to align to Mm10 ( using Ensembl Mus_musculus.GRCm38.95.gtf)
HT-Seq to generate counts (.txt files)
Bedtools to Align and Sort to create .sam and .bam files
DESeq2 for differential expression analysis
Genome_build: Mm10 (Mus_musculus.GRCm38.95.gtf)
Supplementary_files_format_and_content: .txt file with column 1 (gene) and column 2 (read counts)

source_name: RARdnfl/fl; Neurog3:Cre_e16.5 whole pancreas

extract_protocol:
Whole pancreas was dissected from e16.5 mouse embryos, pulverized in buffer RLT +beta mercaptoethanol (RNAeasy Mini Kit Qiagen, Cat# 74134), frozen on dry ice. RNA was extracted using Qiagen RNAeasy Mini kit, eluted in 30ul RNAse free H20.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mixed, C57Bl6/129SV

tag: Stage

value: pancreas


title: riboseq_siDF2_2

description: Ribosome protected fragments


title: RARdnfl/fl; Neurog3:Cre_3


title: 14251X21: WT_0hr

city: Salt Lake City

first: Jordan

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description: Timecourse

data_processing:
Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001).
50 cycle single-read sequence run performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002)
Read pre-processing (Fastp, v0.20.0)
Read alignment (STAR, v2.7.3a)
Read quantification (htseq, v0.11.3)
Read QC (fastqc, v0.11.9)
Total QC (multiqc, v1.8)
Library complexity QC (dupradar, v1.10.0)
Genome_build: Ensembl R64-1-1 (GCA_000146045.2), version 100
Supplementary_files_format_and_content: Tab-delimited files with raw sequencing counts after identical, within sample read de-duplication

organism: Saccharomyces cerevisiae

source_name: Yeast cell culture

growth_protocol: Yeast cultures were grown in synthetic media supplemented with 2% glucose

extract_protocol:
Cultures were flash frozen and later total RNA was isolated using the Direct-zol kit (Zymo Research) with on-column DNase digestion and water elution.
Sequencing libraries were prepared by purifying intact poly(A) RNA from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).

treatment_protocol: Yeast cultures were removed from original media and transferred to synthetic media with 2% raffinose

tag: strain

tag: media

value: Glucose

tag: timepoint

value: WT


title: 14251X22: WT_3hr

description: Timecourse

value: Raffinose


title: Input CTGF-pos tdTomato-pos cells after Bleomycin treatment Replication 1

tag: cell type


title: 14251X23: mct1del_0hr

description: Timecourse


title: riboseq_siDF2_1

description:
Ribosome protected fragments
Ribo_RNA_TE_siDF2_HeLa.txt


title: RARdnfl/fl; Neurog3:Cre_1


title: 14251X20: mct1del_12hr

description: Timecourse


title: 14251X24: mct1del_3hr

description: Timecourse


title: Neurog3:Cre_3

source_name: Neurog3:Cre_e16.5 whole pancreas


title: hu06_120518

city: Ithaca

first: Andrea

middle: J

last: De Micheli

state: NY

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to GRCh38 using Cell Ranger v3 pipeline (10X Genomics)
Gene expression data was processed with Seurat v3.1.2 (Satija lab) using R v3.6.2 (2019-12-12)
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 200)
Filtering by percent mitochondiral genes in included cells (maximum 0.2), number of UMIs in included cells (minimum 1000, maximum 60000), and number of mapped genes in included cells (maximum 8000)
Dataset integration with Scanorama (Hie B. et al., 2019).
Cell annotations in metadata derived from Scanorama-integrated values and SNN clustering performed by Seurat in PCA reduced space (Satija Lab).
Genome_build: GRCh38
Supplementary_files_format_and_content: .txt tabulated files of metadata information, normalized gene expression matrix, and raw gene expression matrix

source_name: Right external oblique

extract_protocol:
Human muscle samples from donors were digested into a single-cell suspension in Collagenase D and Dispase II for about 1h, then filtered to remove debris. Red blood cells were lyzed.
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics) following the directions of the manufacturer. Kit version information in metadata.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: F

value: Right external oblique


title: hu10_101018

source_name: Left rectus abdominus

value: M

value: Left rectus abdominus


title: hu05_111418

source_name: Trapezius

value: Trapezius


title: 14251X19: WT_12hr

description: Timecourse


title: hu09_092718

source_name: Left external oblique

value: Left external oblique


title: riboseq_siDF1_3

description: Ribosome protected fragments

value: DF1 siRNA

value: RNase digested and rRNA depleted RNA


title: hu08_092618

source_name: Left vastus lateralis

value: Left vastus lateralis


title: Neurog3:Cre_2


title: riboseq_siNC1_3

description: Ribosome protected fragments

value: control siRNA


title: hu04_080619

source_name: Eye lid

value: Eye lid


title: riboseq_siNC1_2

description: Ribosome protected fragments


title: H3 ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 2

data_processing:
A pipeline called MintChIP was used (https://github.com/jianhong/MintChIP)
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph, bed

value: GFP-pos epithelial cells

tag: group

value: Ctgf-GFP

value: 3 months


title: hu03_062719

source_name: Orbicularis oris

tag: Sex

value: Orbicularis oris


title: riboseq_siNC1_1

description: Ribosome protected fragments


title: 14251X16: WT_3hr

description: Timecourse

value: WT


title: H3 ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 1


title: hu02_062419

source_name: Flexor hallucis longus

value: Flexor hallucis longus


title: H3K36me3 ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 2


title: siDF123_4

description: RNAseq

value: DF1,DF2 and DF3 siRNAs

value: rRNA depleted RNA

value: ERCC-1 spike in


title: 14251X14: mct1del_12hr

description: Timecourse

value: Raffinose


title: 14251X18: mct1del_3hr

description: Timecourse


title: riboseq_input_siDF123_2

description: Ribosome protected fragments input


title: Neurog3:Cre_1

value: mixed, C57Bl6/129SV

tag: genotype/variation

value: pancreas


title: 14251X17: mct1del_0hr

description: Timecourse

value: Glucose


title: 14251X15: WT_0hr

description: Timecourse


title: hu07_021219

tag: age

value: M


title: H3K36me3 ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 1


title: riboseq_input_siDF123_1

description:
Ribosome protected fragments input
Ribo_RNA_TE_siDF123_HeLa.txt


title: H3K27ac ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 2


title: 14251X13: WT_12hr

description: Timecourse

tag: genotype


title: IRI 28days GFP positive

city: Los Angeles

first: Kari

middle: Ann

last: Koppitch

state: CA

address: 1425 San Pablo Street, BCC 312

department: Stem Cell

institute: USC

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed; unused barcodes deleted
Reads were mapped using STAR 2.5.1b
Count tables were generated from the FASTQ files using the Cell Ranger software version 2.1 with default parameters.
Read 1 is the Cell Barcode + UMI and read 2 is the actual RNA sequence
Genome_build: mm10-1.2.0_premrna
Supplementary_files_format_and_content: filtered gene bc matrix CellRanger output, contains only detected cellular barcodes. Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. It also contains gzipped TSV files with gene and barcode sequences corresponding to row and column indices respectively.

source_name: Kidney Tissue

extract_protocol:
For a single-cell transcriptional profile, at time of harvesting animals were perfused with ice cold HPBS till kidneys cleared of blood. Kidney halves were immediately placed in cold HPBS with RNasin Plus RNase Inhibitor (0.4U/µl, purchased from Promega N2615 and cut into small pieces (>25). These pieces were immediately transferred into a 2 ml dounce (D8938 SIGMA) loaded with 1ml of NEZ Lysis Buffer (+ Rnase Inh) on ice. Samples were then dounced on ice with 5 strokes of the looser pestle (A) every 2 minutes for 8 mins (25 strokes total). Samples were then dounced 25 times slowly with the tighter pestle (B) on ice. The dounced sample was then filtered through a 40-µm Falcon Nylon Cell Strainer. The filter was then washed with 8 ml of 1% BSA PBS (diluted from SRE0036 SIGMA in CaCl/MgCl free HPBS + Rnase Inh) and nuclei suspension spun in a precooled (4°C) centrifuge at 650g for 8 min. Supernatant was removed and pellet was re-suspended in 1%BSA PBS (+Rnase Inh) and moved to a low bind Eppendorf tube. Nuclei quality and number were assessed with Tryptan Blue staining and a hemocytometer. An appropriate number of nuclei was then pipetted out and spun down again (700g/8min). Supernatant was removed and pellet was resuspended in 2%BSA (+RNase inh) by excessive pipetting to avoid clumping and kept on ice until FACS sorting. Nuclei were sorted on a BD Aria 1 into same 2% BSA solution. Nuclei were first sorted as DAPI positive and then for GFP expression. 10X Genomics Chromium v2 Single Cell 3’ protocol:  4,000 singlet nuclei loaded/lane, nuclei capture, lysis and mRNA reverse transcription occurred in-droplets.  cDNA recovered from the emulsion was cleaned-up, amplified by PCR, checked for size and yield on a 4200 Tape station (Agilent), processed into barcoded Illumina ready sequencing libraries and again assayed for size and yield.
10X Genomics Chromium v2 Single Cell 3’ protocol

treatment_protocol: Six2-TGC; Rosa26rtTA ; pTRE-H2BeGFP mice were genotyped and kept on doxycycline food (purchased from Envigo TD.08541) starting a few days after birth. 10- to 12-week-old, 25- 28g, male mice, were anesthetized with an intraperitoneal injection of a ketamine/xylazine (105 mg ketamine/kg; 10 mg xylazine/kg). Body temperature was maintained at 36.5-37°C throughout the procedure. The kidneys were exposed by a midline abdominal incision and both renal pedicles were clamped using non-traumatic microaneurysm clips (Roboz Surgical Instrument Co.). Restoration of blood flow was monitored by the return of normal color after removal of the clamps. All the mice received intraperitoneal (i.p) 1 ml of normal saline at the end of the procedure. Sham-operated mice underwent the same procedure except for clamping of the pedicles

tag: cell/nuclei type

value: adult nephron

value: Six2-TGC; Rosa26rtTA ; pTRE-H2BeGFP

value: Doxycyline Food (625 mg/kg)

tag: injury level

value: Serum Creatinine at Harvest 0.144 (mg/dL)  , BUN at Harvest 31.7 (mg/dL)

tag: molecule subtype

value: nuclear polyA RNA


title: H3K27ac ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 1

value: GFP-pos epithelial cells

value: Ctgf-GFP

value: 3 months


title: riboseq_input_siDF3_2

description: Ribosome protected fragments input

tag: sirna

value: DF3 siRNA

tag: rna processing


title: H3K4me3 ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 2

description:
CTGFpos_Bleomycin_H3K4me3.bedgraph
CTGFpos_Bleomycin_H3K4me3.calledpeaks.bed


title: IRI 96hours GFP positive

tag: treatment

value: Serum Creatinine at Harvest 0.312 (mg/dL)  , BUN at Harvest 91.8 (mg/dL)


title: riboseq_input_siDF3_1

description:
Ribosome protected fragments input
Ribo_RNA_TE_siDF3_HeLa.txt

value: rRNA depleted RNA


title: 14251X10: WT_3hr

description: Timecourse

value: WT


title: riboseq_input_siDF2_3

description: Ribosome protected fragments input

value: DF2 siRNA


title: p53 ChIP-seq CTGF-pos tdTomato-pos cells after Bleomycin treatment Replication 2

description: CTGFpos_tdTomatopos_Bleomycin_p53.bedgraph

data_processing:
A pipeline called MintChIP was used (https://github.com/jianhong/MintChIP)
Genome_build: mm10

value: CTGF-pos tdTomato+ cells


title: 14251X9: WT_0hr

description: Timecourse


title: 14251X12: mct1del_3hr

description: Timecourse

value: Raffinose


title: riboseq_input_siDF2_2

description: Ribosome protected fragments input


title: H3K4me3 ChIP-seq CTGF-pos epithelial cells after Bleomycin treatment Replication 1


title: IRI 64hours GFP positive

value: Serum Creatinine at Harvest 0.375 (mg/dL)  , BUN at Harvest 37.0 (mg/dL)


title: No Injury GFP positive

value: Serum Creatinine at Harvest 0.122 (mg/dL)  , BUN at Harvest 26.1 (mg/dL)


title: 14251X11: mct1del_0hr

description: Timecourse

value: Glucose


title: riboseq_input_siDF2_1

description:
Ribosome protected fragments input
Ribo_RNA_TE_siDF2_HeLa.txt


title: 14251X8: mct1del_12hr

description: Timecourse


title: p53 ChIP-seq CTGF-pos tdTomato-pos cells after Bleomycin treatment Replication 1


title: riboseq_input_siDF1_3

description: Ribosome protected fragments input

value: DF1 siRNA


title: 14251X6: mct1del_3hr

description: Timecourse


title: H3 RFP-neg AEC2s in homeostasis Replication 1

source_name: Alveolar epithelial type 2 cells in homeostasis

value: RFP-neg alveolar epithelial type 2 cells


title: H3 RFP-neg AEC2s in homeostasis Replication 2


title: 14251X5: mct1del_0hr

description: Timecourse


title: riboseq_input_siDF1_1

description:
Ribosome protected fragments input
Ribo_RNA_TE_siDF1_HeLa.txt

source_name: HeLa


title: H3K36me3 RFP-neg AEC2s in homeostasis Replication 2


title: PBS Control 2weeks

first: Margo

middle: Patricia

last: Cain

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

description: animal at 8 weeks of age underwent oropharyngeal instillation of PBS and was sacrificed 2 weeks later

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files can be opened with Seurat (R package) and analyzed. Cloupe file can be opened with Loupe cell browser to visualize the data.

source_name: lung

extract_protocol:
FACS-purified whole lung cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index (Read1).

tag: tissue

value: lung

value: 10 weeks

value: wild type

value: PBS


title: Sendai virus-infected 2weeks

description: animal at 8 weeks of age underwent oropharyngeal instillation of pfu Sendai virus and was sacrificed 2 weeks later

value: Sendai virus


title: riboseq_input_siNC1_3

description: Ribosome protected fragments input

value: control siRNA


title: 14251X4: WT_3hr

description: Timecourse


title: E16.5_TN3

city: Cambridge

first: Clare

last: Baker

state: Cambridgeshire

address: Downing Street

department: Dept. Physiology, Development & Neuroscience (PDN)

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality of sequenced reads was assessed with FastQC and mapped to mm10 mouse genome using Tophat2 version 2.1.0.
Alignment files were sorted by name and a count matrix was produced using HTSeq. The FPKM and differential expression analysis were generated using DESeq2 version 3.7.
Deseq outputs were combined into one file using a custom perl script.  Genes where FPKM was less than 1 in all samples were removed using a custom perl script.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx and DESeq outputs (differential expression analysis, FPKM based on counts table)

source_name: E16.5 Trigeminal Nerve

extract_protocol:
Olfactory and trigeminal nerve regions were isolated in situ by laser microdissection and RNA was extracted using the PicoPure RNA isolation kit (Arcturus). The SMART-seq V4 ultra low-input RNA kit for sequencing was used for cDNA synthesis and amplification using ~2000 pg of RNA.
1 ng of amplified cDNA was used for paired-end library preparation using the Nextera XT DNA library prep kit. Libraries were pooled to a final concentration of 4 nM and quantified using the KAPA Library Quantification Kit (ABI Prism) from Kapa Biosystems.

tag: embryonic stage

value: Trigeminal Nerve


title: Wild Type P7

first: Odemaris

middle: Narvaez

last: del Pilar

department: Pulmonary

description: animal at 7 days of age proccessed for single cell RNA-sequencing

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
Genome_build: mm10
Supplementary_files_format_and_content: Cloupe file can be opened with Loupe cell browser to visualize the data.

tag: strain

value: postnatal day 7


title: riboseq_input_siNC1_2

description: Ribosome protected fragments input

value: rRNA depleted RNA


title: 14251X3: WT_0hr

description: Timecourse

tag: media

value: WT


title: riboseq_input_siDF1_2

description: Ribosome protected fragments input


title: E16.5_TN2


title: riboseq_input_siNC1_1

description: Ribosome protected fragments input


title: H3K27ac RFP-neg AEC2s in homeostasis Replication 2

value: 3 months


title: E16.5_TN1


title: H3K27ac RFP-neg AEC2s in homeostasis Replication 1


title: E16.5_iONL4

source_name: E16.5 Inner Olfactory Nerve Layer

value: Inner Olfactory Nerve Layer


title: AD30R3

city: Beijing

first: Xianda

last: Hu

address: 218 Anwaixiaoguanbeili St

institute: Beijing Tibetan Hospital, CTRC

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Drosophila melanogaster whole genome dmel_r6.11   using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
The clean data were mapped to reference using Bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200, and fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using RSEM software.

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Massive of fly heads of each group were collected and total RNAs were extracted with Trizol reagent, from which mRNAs were purified by poly-T oligo-attached magnetic beads.
Libraries were constructed for sequencing using a Superscript Double-Stranded cDNA Synthesis kit according to manufacturer's specifications.

value: day 30 after eclosion

value: hAPP transgenic

value: male


title: 14251X1: WT_12hr

description: Timecourse

source_name: Yeast cell culture

value: Raffinose

tag: timepoint


title: H3K4me3 RFP-neg AEC2s in homeostasis Replication 2

description:
AEC2_Homeostasis_H3K4me3.bedgraph
AEC2_Homeostasis_H3K4me3.calledpeaks.bed

tag: cell type

value: RFP-neg alveolar epithelial type 2 cells


title: E16.5_iONL3


title: hu01_061419

source_name: Right serratus

value: M

value: Right serratus


title: H3K4me3 RFP-neg AEC2s in homeostasis Replication 1

tag: group


title: AD20R3

value: day 20 after eclosion

tag: Sex


title: AD10R3

value: day 10 after eclosion


title: E16.5_iONL2


title: 185RS27__seedlings_pif7_ZT16.0_27.0C

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

institute: Cambridge University

data_processing:
Raw reads were aligned with Hisat2 with arguments ""--no-mixed --rna-strandness RF --dta --fr"" to produce a SAM file.
Alignments in SAM file were assembled into transcripts abundances with stringtie with argument ""--rf"".
Genome_build: TAIR10
Supplementary_files_format_and_content: Sample_processed_data_files_format_and_content

source_name: pif7 seedlings

growth_protocol: Seedlings were grown on 1/2 MS plates in long photoperiods (16 h light, 8 h dark) at a light intensity of 35-40 umol m-2 s-1 for 7 d. Temperature was either kept at constant 17°C or oscillated daily between 17°C and a warm 27°C midday from ZT4 to ZT12. Samples were collected at ZT0, 4, 5, 8, 12, 16 and 20 by snap-freezing in liquid nitrogen.

extract_protocol:
Total RNA was extracted from 30-40 mg of ground seedling tissue using the MagMAX™-96 Total RNA Isolation Kit (Thermo Fisher Scientific)  according to the manufacturer's instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed with 1 ug of high integrity total RNA using the Next Ultra Directional RNA library preparation kit (NEB) according to the manufacturer's instructions. The libraries were sequenced on a NextSeq 500 (Illumina) using paired-end sequencing with a NextSeq 500/550 High Output v2 kit (150 cycles).

value: seedlings

value: 7 d

tag: temperature

tag: time of subjective day


title: Retinoblastoma_1_Hta2_0_exon_level

city: Mexico City

first: Diana

middle: Emilce

last: Alvarez Suarez

state: Mexico

address: Av cuautemoc 330

department: Unidad de Investigacion Medica Enf. Infecciosas

country: Mexico

institute: hospital de pediatria CMNSXXI

description: RMA and DABG value derived from Expression Console software; exon analysis

hyb_protocol: Standard Affymetrix protocols

scan_protocol: Standard Affymetrix protocols

data_processing: Raw data from .CEL files were preprocessed using Affymetrix® Expression ConsoleTM software to exon-level normalization signals and to obtain the quality control data. The presence and absence score of probe-sets and junctions was calculated by Detection Above Background (DABG).

label: Biotin

source_name: Retinoblastoma

label_protocol: Standard Affymetrix protocols

growth_protocol: Samples from enucleated patients with no chemotherapy history. The samples were maintained in BSF 12% complemented RPMI medium for a week and collected in lysis buffered reagent.

extract_protocol: Total RNA was extracted from each sample using TRIzol reagent and was suspended in nuclease free water and stored at -70°C.

treatment_protocol: without treatment

tag: disease

value: Retinoblastoma

tag: laterality

value: Bilateral


title: MTECplus Drop-seq

data_processing:
scRNA-seq analysis of alveolar organoids was performed by processing FASTQ files using dropSeqPipe v0.3 (https://hoohm.github.io/dropSeqPipe) and mapped on the GRCm38 genome reference with annotation version 91.
Genome_build: GRCm38.91
Supplementary_files_format_and_content: MTECplus.tsv.gz: raw counts

source_name: Alveolar organoids

growth_protocol: lineage labeled AEC2s from Sftpc-CreER;R26R-tdTomato mice treated with Tmx were FACS-sorted and PDGFRα+ fibroblasts were resuspended in MTEC/Plus and mixed with equal amount of growth factor-reduced Matrigel (Corning #354230). Medium was changed every other day.

extract_protocol:
Organoids were dissociated using Accutase and Trypsin-EDTA. mRNA was captured using original Drop-seq methods
DNA polymerase for pre-amplification step (1 cycle of 95°C for 3 min, 15-17 cycles of 98°C for 15 sec, 65°C for 30 sec, 68°C for 4 min and 1 cycle of 72°C for 10 min) was replaced by Terra PCR Direct Polymerase (#639271, Takara). The other processes were performed as described in the original Drop-seq protocol.
single-cell RNA-seq (3' enrichment)

value: alveolar cells

tag: age


title: 185RS28__seedlings_pif7_ZT20.0_27.0C

tag: genotype


title: AD03R3

value: day 3 after eclosion


title: 185RS26__seedlings_pif7_ZT12.0_27.0C


title: E16.5_iONL1


title: 14251X2: mct1del_12hr

description: Timecourse


title: No Injury GFP negative

tag: cell/nuclei type

value: adult non-nephron

value: Six2-TGC; Rosa26rtTA ; pTRE-H2BeGFP

value: Doxycyline Food (625 mg/kg)

tag: injury level

value: Serum Creatinine at Harvest 0.122 (mg/dL)  , BUN at Harvest 26.1 (mg/dL)

tag: molecule subtype

value: nuclear polyA RNA


title: E16.5_oONL3

source_name: E16.5 Outer Olfactory Nerve Layer

tag: tissue

value: Outer Olfactory Nerve Layer


title: E16.5_oONL4

tag: embryonic stage


title: 185RS25__seedlings_pif7_ZT8.0_27.0C


title: Retinoblastoma_7_Hta2_0_exon_level

value: Unilateral


title: 185RS24__seedlings_pif7_ZT5.0_27.0C


title: Retinoblastoma_5_Hta2_0_exon_level


title: AD30R2

value: day 30 after eclosion

value: hAPP transgenic

value: male


title: AD20R2

value: day 20 after eclosion


title: E16.5_oONL2


title: Retinoblastoma_8_Hta2_0_exon_level


title: AD10R2

value: day 10 after eclosion


title: 185RS23__seedlings_pif7_ZT4.0_27.0C

value: seedlings

value: 7 d


title: Retinoblastoma_6_Hta2_0_exon_level

value: Retinoblastoma


title: Retinoblastoma_4_Hta2_0_exon_level

value: Bilateral


title: E16.5_oONL1


title: TRAC10: Field_sample10

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 10

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Only uniquely mapped reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
standard normalized count Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and Transcript Per Million (TPM) were calculated, except gene length in the formula is replaced with mapped length
Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: tpm_matrix.txt' contains matrix table with normalized count in Transcript Per Million for every gene and every sample

organism: Plasmodium falciparum

source_name: In vivo P. falciparum parasites obtained from venous blood in Southeast Asia Greater Mekong Subregion

growth_protocol: P. falciparum strain 3D7 was obtained from BEI Resources (MRA-102) and cultured under standard conditions described before (William Trager, James B. Jensen, Human malaria parasites in continuous culture, Science, 193, 4254, 1976). Prior to time-point experiment, parasites were double-synchronized with 5% sorbitol solution to achieve a synchrony of +/- 6 hours and cultured under constant agitation.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) with chloroform supplemantaiton (Merck) and Direct-Zol-96 kit (Zymo) following manufacturers' instructions. All RNA samples were analyzed for integrity using Agilent Bioanalyzer 2100 platform. RNA 6000 Nano Chip (Cat. No.: 5067-1511, Agilent) was used for RNA samples according to manufacturer instructions.
Reverse transcription and cDNA synthesis were done following modifed Smart-Seq2 protocol using only oligo(d)T primers to enrich for mRNA transcripts (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014)). Purified amplicon (cDNA) was used to generate sequencing libraries using Illumina Nextera XT kit as described in manufacturer’s protocol. Libraries were analyzed on the Bioanalyser High-Sensitivity DNA chips (Agilent, Cat. No.: 5067-4626), subsequently pooled (24 samples per lane) and sequenced on Illumina HiSeq4000 platform generating 150 bp paired end reads with 110 Gb data output generated per lane. For CRISPR treatment the reverse transcription product was first ampified for 5 cycles, then treated with CRISPR-Cas9 in vitro and subsequently amplified for another 14 cycles.

value: intraerythorcytic P.falciparum


title: TRAC8: Field_sample8

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 8


title: TRAC9: Field_sample9

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 9


title: AD03R2

value: day 3 after eclosion


title: 185RS21__seedlings_pif7_ZT20.0_17.0C


title: Retinoblastoma_3_Hta2_0_exon_level


title: TRAC7: Field_sample7

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 7


title: E16.5_ON4

source_name: E16.5 Olfactory Nerve

value: Olfactory Nerve


title: Retinoblastoma_2_Hta2_0_exon_level


title: AD30R1


title: TRAC5: Field_sample5

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 5


title: AD20R1


title: 185RS20__seedlings_pif7_ZT16.0_17.0C


title: TRAC4: Field_sample4

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 4


title: E16.5_ON2


title: AD10R1


title: 185RS22__seedlings_pif7_ZT0.0_27.0C


title: 185RS19__seedlings_pif7_ZT12.0_17.0C


title: AD03R1


title: E13.5_ONL5

source_name: E13.5 Olfactory Nerve Layer

value: Olfactory Nerve Layer


title: TRAC3: Field_sample3

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 3


title: TRAC6: Field_sample6

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 6


title: WT30R3

value: wild type


title: TRAC1: Field_sample1

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 1


title: TRAC2: Field_sample2

description:
cDNA amplified from total RNA using oligo(d)T primer
TRAC2 Clinical sample number 2


title: 5C14_p0.1_rep3: Crispr-depleted_pmia-0.1per_Rep3

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 0.1% parasitemia CRISPR treated 3

source_name: In vitro culture, asexual stage, laboratory strain 3D7

tag: strain


title: 185RS17__seedlings_pif7_ZT5.0_17.0C


title: E16.5_ON3


title: E13.5_ONL3


title: E13.5_ONL4


title: E16.5_ON1


title: 185RS15__seedlings_pif7_ZT0.0_17.0C


title: WT20R3


title: E13.5_ONL2


title: WT10R3


title: WT03R3


title: 185RS14__seedlings_Col-0_ZT20.0_27.0C

source_name: Col-0 seedlings


title: 185RS16__seedlings_pif7_ZT4.0_17.0C


title: 5C14_p0.1_rep1: Crispr-depleted_pmia-0.1per_Rep1

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 0.1% parasitemia CRISPR treated 1


title: 185RS13__seedlings_Col-0_ZT16.0_27.0C


title: WT30R2


title: 19amp_p0.1_rep3: Crispr-non-depleted_pmia-0.1per_Rep3

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 0.1% parasitemia CRISPR untreated 3


title: 185RS18__seedlings_pif7_ZT8.0_17.0C


title: 185RS12__seedlings_Col-0_ZT12.0_27.0C


title: E13.5_ON7

source_name: E13.5 Olfactory Nerve


title: WT20R2


title: 14251X7: WT_12hr

description: Timecourse

tag: media

value: Raffinose

value: WT


title: WT10R2


title: 19amp_p0.1_rep2: Crispr-non-depleted_pmia-0.1per_Rep2

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 0.1% parasitemia CRISPR untreated 2


title: 5C14_p0.1_rep2: Crispr-depleted_pmia-0.1per_Rep2

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 0.1% parasitemia CRISPR treated 2


title: 185RS11__seedlings_Col-0_ZT8.0_27.0C


title: WT03R2


title: 185RS10__seedlings_Col-0_ZT5.0_27.0C


title: H3K36me3 RFP-neg AEC2s in homeostasis Replication 1

source_name: Alveolar epithelial type 2 cells in homeostasis

value: RFP-neg alveolar epithelial type 2 cells

value: 3 months


title: 19amp_p0.1_rep1: Crispr-non-depleted_pmia-0.1per_Rep1

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 0.1% parasitemia CRISPR untreated 1


title: 5C14_p1_rep3: Crispr-depleted_pmia-1per_Rep3

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 1% parasitemia CRISPR treated 3


title: 5C14_p1_rep2: Crispr-depleted_pmia-1per_Rep2

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 1% parasitemia CRISPR treated 2


title: WT30R1

value: day 30 after eclosion


title: E13.5_ON4


title: E13.5_ON6


title: WT20R1

value: male


title: E13.5_ONL1


title: 185RS9__seedlings_Col-0_ZT4.0_27.0C


title: E13.5_ON3


title: 185RS8__seedlings_Col-0_ZT0.0_27.0C


title: E13.5_ON5


title: 5C14_p1_rep1: Crispr-depleted_pmia-1per_Rep1

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 1% parasitemia CRISPR treated 1


title: E13.5_ON2


title: 185RS7__seedlings_Col-0_ZT20.0_17.0C


title: WT10R1


title: E13.5_ON1


title: 19amp_p1_rep3: Crispr-non-depleted_pmia-1per_Rep3

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 1% parasitemia CRISPR untreated 3


title: 185RS6__seedlings_Col-0_ZT16.0_17.0C


title: WT03R1


title: 19amp_p1_rep2: Crispr-non-depleted_pmia-1per_Rep2

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 1% parasitemia CRISPR untreated 2


title: 185RS5__seedlings_Col-0_ZT12.0_17.0C


title: E11.5_ON4

source_name: E11.5 Olfactory Nerve


title: 19amp_p1_rep1: Crispr-non-depleted_pmia-1per_Rep1

description:
cDNA amplified from total RNA using oligo(d)T primer
samples of 1% parasitemia CRISPR untreated 1


title: 185RS4__seedlings_Col-0_ZT8.0_17.0C


title: E11.5_ON2


title: 185RS2__seedlings_Col-0_ZT4.0_17.0C


title: E11.5_ON1


title: 185RS3__seedlings_Col-0_ZT5.0_17.0C


title: BMDC_injected_mo_DCs_II

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling was done by the internal software of the NextSeq 500 sequencer "NextSeq Control/RTA v2” and bcl2fastq2 Conversion Software v.2 was used to demultiplex the pooled libraries and to convert the bcl files generated by the sequencer to standard fastq files for downstream analysis. The generated raw reads were processed using FastQC 0.11.61 for assessing read quality, number of duplicates and presence of adapter sequences. After this, the Illumina Nextera adaptors were cleaved using cutadapt (version 1.16) and resulting reads were further trimmed keeping a quality drop value below a mean of Q20. Further, the processed sequences were mapped to the mouse genome using the short-read aligner STAR (version-2.5.2b) with genome and annotation files retrieved from GENCODE (July 2017, GRCm38.p5, M16). For all the studied samples, the proportion of reads uniquely mapped to the mouse reference genome ranged between 83% and 87% in total. The sequences aligning to specific genes were quantified using bedtools subcommand intersect (version 2.15.0).
Genome_build: GRCm38.p5, M16
Supplementary_files_format_and_content: csv;Read count table for each gene per sample

source_name: Dentric cells

extract_protocol:
Mice were injected with LPS/BM-DCs into the footpad and the popliteal and inguinal LNs were collected after 48h. T and B cells were depleted by Dynabeads™ Biotin Binder (Invitrogen™) using Biotin-B220, CD3e, and CD4. The negatively selected cells were sorted for different migratory DC subsets using a BD FACS Aria III (precision: single-cell; nozzle: 100 μm). 100 cells for every population for in total 3 replicates were sorted into individual wells of a 48-well plate (Brand) ﬁlled with 4 µl lysis buffer (Takara). Cells were spun down, immediately chilled to 4°C and stored at −80 °C.
All the following experimental steps were performed using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) with a quarter of the recommended reagent volumes. The PCR amplification was performed according to the manual using 21 cycles. Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). 0.5 ng of each library was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using a quarter of the recommended reagent volumes, 10 min for tagmentation at 55 °C and 1 min extension time during PCR for multiplexing. After PCR, the libraries were purified using AMPure XP beads and eluted in 15 µl of resuspension buffer.
SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) + Nextera XT (Illumina)

value: Dentric cells

tag: subsets

value: mo

tag: condition

tag: replicates

value: II


title: 185RS1__seedlings_Col-0_ZT0.0_17.0C

value: seedlings

value: 7 d


title: WD7-3

city: Saint Paul

first: Kristin

middle: L

last: Sikkink

state: MN

address: 1987 Upper Buford Circle

department: Ecology, Evolution, and Behavior

institute: University of Minnesota

data_processing:
Base-calling and demultiplexing was performed by the University of Minnesota Genomics Center using Illumina software.
Raw reads were filtered and trimmed using Trimmomatic v 0.33. We trimmed low quality sequences when the average score within a sliding window of 4 bp reached Q < 5, as well as removing any Illumina Tru-seq adapter sequences. Reads shorter than 25 bp in length after trimming were discarded. Only sequences for which both reads of a pair passed quality filters were used.
Trimmed reads were aligned to the genome using STAR v 2.5.3a using two-pass alignment. The first mapping pass used default parameters and a reference set of splice junctions. For the second mapping pass, novel splice junctions inferred from all samples were merged using StringTie v 1.3.4d were used.
Read counts by gene were quantified using STAR --quantMode GeneCounts during the second mapping pass.
Genome_build: Teleogryllus oceanicus genome (Pascoal et al 2019 Evol Let)
Supplementary_files_format_and_content: tab-delimited text files with read counts per gene, output from STAR --quantMode GeneCounts

organism: Teleogryllus oceanicus

source_name: abdomenal tissue from pool of 1 flatwing and 1 normal-wing individual

growth_protocol: Cricket lab colonies were housed in groups of 25-40 adults in 15L containers in temperature, humidity, and light controlled incubators set at 26°C and 75% humidity with a 12:12 photoreversed light:dark schedule. Juvenile males were removed from their colony prior to their penultimate molt, and transferred to individual 118mL containers containing Teklad high-fiber rabbit chow, a small piece of water-soaked cotton, and egg carton material for shelter. Female flies were captured in the Santa Monica Mountains, Los Angeles County, California using acoustic traps and shipped overnight to the University of Minnesota. Flies were maintained separately from crickets in an incubator at 26°C and 75% humidity with a 12:12 photoreversed light:dark schedule until infestation.

extract_protocol:
Head and body tissues were separated and the digestive tract discarded. Samples were immediately stored in RNAlater Solution (Ambion) at 4°C for 24 hours. Immediately prior to extraction, pronotum, wings and legs were removed from the bodies; larvae were then dissected from the abdomen. Total RNA was extracted from remaining body tissue using RNeasy Plus kits with gDNA eliminator spin columns (Qiagen) according to the manufacturer’s directions.
Sequencing libraries enriched for mRNA were prepared using the TruSeq RNA Library Preparation Kit v2 (Illumina) at the University of Minnesota Genomics Center (UMGC; Minneapolis, MN).

treatment_protocol: Within 48 hours of arrival at UMN, first instar O. ochracea planidia were dissected from gravid female flies. Sexually mature adult male crickets were manually infested with two planidia by transferring them on the tip of a dissecting probe onto the body of the cricket under the junction between the thorax and the abdomen. Crickets were then returned to the incubator in their individual containers and left undisturbed for 24 hours. Crickets in the uninfested control group were handled in an identical manner and for the same amount of time, except that no larvae were transferred on the probe.

tag: population

value: Kauai

tag: time since infestation

value: 7 days


title: WD4-3

value: abdomenal tissue from pool of 1 flatwing and 1 normal-wing individual

value: 4 days


title: WD7-1


title: WD7-2


title: Ent. faecalis 14 delta bac rep. 3

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

description: Gene expression after 6h of culture

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mus musculus Sure Print GE 4x44 v2 microarrays with oligonucleotide 45,220 probes (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides 8x15K were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing:
The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Slides were 8-plex and only 1 or 2 blocks by slide concerned this project. In the title of the gpr file, the block of interest is indicated. Raw data .xls files include raw data in the block used in this study.

organism: Enterococcus faecalis

source_name: Ent. faecalis 14 delta bac rep. 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures of Ent. faecalis 14 and Ent. faecalis 14 ∆Bac  mutant and Ent. faecalis 14∆Bac-Comp complemented strains  were performed on the M17 medium supplemented with 0.5% (w/v) of glucose (GM17) at 37 °C under semi-aerobic conditions. Data related to genetic approach for mutants engineering as well as their antibacterial potency will be described elsewhere. Growth kinetics were performed on a 96-well microplate by measuring the optical density at a wavelength of 600 nm (OD600) using the SpectraMax i3 spectrophotometer (Molecular Devices, CA, USA). The cultures were inoculated with the same bacterial charge and a measurement points were taken every 30 minutes for 12 h. Bacterial stocks were stored at - 80°C in GM17 broth supplemented with 50% (v/v) glycerol.

extract_protocol: For microarray analysis, three distinct cultures of Ent. faecalis 14 ∆Bac were used (ΔBac1, ΔBac2 and ΔBac3) in order to carry comparisons with Ent. faecalis 14 (WT1, WT2 and WT3), after 6 h of growth in GM17 medium respectively. Analyses were performed with total RNA isolated using NucleoSpinTM RNA Plus columns (Macherey-Nagel, Hoerdt, France). RNA quality was observed with Nanodrop and absorbance ratios A260/280 and A260/230 were found between 2.0 and 2.2. RNA quality was also examined with Bioanalyzer 2100 (Agilent, Les Ulis, France) and a minimal RNA integrity number (RIN) of 0.8 was required for all samples.

value: delta bac

value: 6 hours of growth


title: Ent. faecalis 14 delta bac rep. 2

description: Gene expression after 6h of culture

source_name: Ent. faecalis 14 delta bac rep. 2


title: Ent. faecalis 14 delta bac rep.1

description: Gene expression after 6h of culture

source_name: Ent. faecalis 14 delta bac rep.1


title: WD4-2


title: BMDC_injected_mo_DCs_I

tag: cell type

value: I


title: L05M2.1

first: Megan

last: Hagenauer

hyb_protocol: The samples were transcriptionally profiled using Affymetrix Rat Expression Set 230 A (RAE230A) microarray according to standard manufacturer’s procedures. The samples were run in two batches: the first included the hippocampus and cortex samples and the second included the hypothalamus samples. Each brain region was run on a separate chip. Only data from the hippocampal samples are included in this data release.

data_processing: For our current analyses, the ReadAffy() function (from R package affy version 1.54.0; Gautier et al. 2004, Bioinformatics. 20: 307–315) was used to read the data from the hippocampal Affymetrix .CEL files into R studio (version 3.4.0). An expression set was generated using the Robust Multi-Array Average method (RMA: Irizarry et al. 2003, Biostatistics. 4: 249–264). Using a custom .cdf (Dai et al. 2005, Nucleic Acids Res. 33: e175) we summarized the probe signals into probesets for the RAE230A chip (“rae230arnentrezgcdf_19.0.0”) which mapped the probe sequences to Entrez Gene IDs (downloaded from http://nmg-r.bioinformatics.nl/NuGO_R.html on Jan 2017, release date Nov 2015). We re-annotated the data according to Official Gene Symbol using the function org.Rn.egSYMBOL() from the R package org.Rn.eg.db (version 3.4.1; Carlson 2017, http://bioconductor.org/packages/org.Rn.eg.db/), and then removed rows lacking annotation (leaving 9,959 gene symbols). Quality control identified two samples with low sample-sample correlation values (around 0.66: 13F4-H07M1.1-HPC-HR-1 and 22F4-L08M2.0-HPC-LR-5), leaving a final sample size of n=5 per group. The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.

source_name: Whole Hippocampus

extract_protocol: The rats were sacrificed in adulthood (between P102-P108) via rapid decapitation followed by immediate brain extraction. The whole hippocampus, frontal cortex, and hypothalamus samples were rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.

tag: bred line

value: bred Low Responder (bLR)

value: hippocampus

tag: locomotor activity in a novel field (beam breaks)

tag: Sex

value: Male


title: BMDC_injected_XCR1_DCs_III

value: DN

value: III


title: E11.5_ON3

value: Olfactory Nerve


title: WD4-1


title: H03M1.1

label_protocol: The samples were transcriptionally profiled using Affymetrix Rat Expression Set 230 A (RAE230A) microarray according to standard manufacturer’s procedures. The samples were run in two batches: the first included the hippocampus and cortex samples and the second included the hypothalamus samples. Each brain region was run on a separate chip. Only data from the hippocampal samples are included in this data release.

value: bred High Responder (bHR)

tag: age


title: Ent. faecalis 14 wild type rep.2

description: Gene expression after 6h of culture

source_name: Ent. faecalis 14 wild type rep.2

tag: genotype

value: wild type


title: WC-3

value: uninfested


title: IgAN 30

city: Bari

first: Fabio

last: Sallustio

address: Piazza G. Cesare N°11

institute: University of Bari

data_processing: The data were normalised using log2 normalisation with Illumina Genomestudio

source_name: IgAN patient_renal biopsy

extract_protocol: RNA was extracted with QIAGEN miRNeasy FFPE kit in accordance with the prescribed protocol provided with the kit.

tag: subject status

value: IgAN patient

tag: classification

value: renal biopsy


title: Ent. faecalis 14 wild type rep.1

description: Gene expression after 6h of culture

source_name: Ent. faecalis 14 wild type rep.1


title: BMDC_injected_mo_DCs_III

value: Dentric cells

value: mo


title: L08M2.0

address: 205 Zina Pitcher Pl.

institute: University of Michigan

description: Failed Quality Control

tag: tissue


title: WC-2

value: Kauai

value: abdomenal tissue from pool of 1 flatwing and 1 normal-wing individual


title: Ent. faecalis 14 wild type rep.3

description: Gene expression after 6h of culture

source_name: Ent. faecalis 14 wild type rep.3

value: 6 hours of growth


title: BMDC_injected_CD11b_DCs_III


title: BMDC_injected_XCR1_DCs_II

value: II


title: H01M2.0


title: oropharyngeal endoderm explant stage 41 rep4 [41_Q]

city: New London

first: Deborah

last: Eastman

state: CT

address: 270 Mohegan Ave

institute: Connecticut College

data_processing:
Illumina platform NextSeq 500 System used for base calling
adapter sequences, sequences with length <25 bp and sequences with PHRED score <15 were removed using Trimmomatic software
De novo transcriptome assembly was performed using Trinity (version 2.4.0) under the standard settings (read normalization to 50). Bowtie2 was used to map raw reads back to the de novo assembly and RSEM estimated transcript abundance in the assembly across the samples.
Gene isoform counts were collapsed to trinity gene counts for quantification across the samples
Genome_build: de novo assembly
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ambystoma mexicanum

source_name: oropharyngeal endoderm explant stage 41

growth_protocol: Axolotl embryos were obtained from the Ambystoma Genetic Stock Center at the University of Kentucky and incubated in 20% Holtfreter’s solution at 22°C

extract_protocol:
Replicates of oropharyngeal explants at different stages of development (37/38, 39, 41) were immersed in RNALater.  Samples were homogenized with a Dounce homogenizer in RLT buffer containing ß-mercaptoethanol (Qiagen).  The homogenate was then processed using an RNAEasy kit (Qiagen, Hilden, Germany). Replicate samples for each stage were analyzed for RNA quantity and quality on a Nanodrop 8000 spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos were staged and oropharyngeal endodermal explants were isolated at  developmental stage 15. Explants were cultured in L-15 medium (60% L15 +0.1% BSA, 400 mg/ml of penicillin and streptomycin, and 25 mg/ml gentamicin).  Whole embryo sibling timing controls were raised in 20% Holtfreter’s solution, and explants were harvested at stages 37/38, 39 and 41.

value: oropharyngeal endoderm explant

tag: developmental stage


title: oropharyngeal endoderm explant stage 39 rep6 [39_O]

source_name: oropharyngeal endoderm explant stage 39


title: oropharyngeal endoderm explant stage 41 rep3 [41_P]


title: oropharyngeal endoderm explant stage 39 rep5 [39_N]


title: L11M2.0

value: bred Low Responder (bLR)

value: hippocampus


title: BMDC_injected_DN_DCs_II


title: MD7-3

source_name: abdomenal tissue from pool of 2 normal-wing individuals

value: Mangaia

value: 7 days


title: WC-1


title: oropharyngeal endoderm explant stage 41 rep5 [41_R]


title: MD7-2

value: abdomenal tissue from pool of 2 normal-wing individuals


title: H11M1.1

value: bred High Responder (bHR)

value: Male


title: oropharyngeal endoderm explant stage 37_38 rep6 [37/38_M]


title: BMDC_injected_CD11b_DCs_II


title: oropharyngeal endoderm explant stage 37_38 rep5 [37/38_L]


title: L10M2.2


title: MD7-1


title: BMDC_injected_DN_DCs_III

value: III


title: BMDC_injected_XCR1_DCs_I

value: DN

value: I


title: oropharyngeal endoderm explant stage 37_38 rep4 [37/38_K]


title: oropharyngeal endoderm explant stage 41 rep2 [41_J]


title: MD4-3

value: 4 days


title: H10M2.2


title: BMDC_injected_DN_DCs_I

value: Dentric cells


title: MD4-2


title: BMDC_injected_CD11b_DCs_I


title: oropharyngeal endoderm explant stage 39 rep4 [39_G]


title: Non_injected_DN_DCs_III


title: MD4-1


title: oropharyngeal endoderm explant stage 39 rep3 [39_F]


title: Non_injected_XCR1_DCs_III


title: MC-3

value: uninfested


title: H09M1.0


title: L07M3.1


title: oropharyngeal endoderm explant stage 41 rep1 [41_H]


title: MC-2


title: H05

hyb_protocol: One aliquot from each sample was transcriptionally profiled using Affymetrix Rat Expression Set 230 (RAE230A) microarray according to standard manufacturer’s procedures.

data_processing: For our current analyses, the ReadAffy() function (from R package affy version 1.54.0; Gautier et al. 2004, Bioinformatics. 20: 307–315) was used to read the data from the hippocampal Affymetrix .CEL files into R studio (version 3.4.0). An expression set was generated using the Robust Multi-Array Average method (RMA: Irizarry et al. 2003, Biostatistics. 4: 249–264). Using a custom .cdf (Dai et al. 2005, Nucleic Acids Res. 33: e175) we summarized the probe signals into probesets for the RAE230A chip (“rae230arnentrezgcdf_19.0.0”) which mapped the probe sequences to Entrez Gene IDs (downloaded from http://nmg-r.bioinformatics.nl/NuGO_R.html on Jan 2017, release date Nov 2015). We re-annotated the data according to Official Gene Symbol using the function org.Rn.egSYMBOL() from the R package org.Rn.eg.db (version 3.4.1; Carlson 2017, http://bioconductor.org/packages/org.Rn.eg.db/), and then removed rows lacking annotation. During quality control, we found consistent irregularity associated with one subject (bLR subject X6_RN230_HC_P14_F15_L03.CEL) and it was removed prior to further analyses. The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.

extract_protocol: The rats were sacrificed at postnatal day 14 (P14) via rapid decapitation followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The RNA was divided into two aliquots earmarked for transcriptional profiling using different microarray platforms. The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.


title: MC-1


title: H07M1.1

description: Failed Quality Control


title: Non_injected_DN_DCs_II


title: Non_injected_CD11b_DCs_II


title: L37d-1C

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
The raw sequencing data are called raw tags. The raw tags were processed using the  following steps: remove low quality tags; remove tags with 5 primer contaminants;  remove tags without 3 primer; remove tags without insertion; remove tags with poly A;  remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the  reference genome and other sRNA database including miRbase, siRNA and snoRNA  with Bowtie2. Particularly, cmsearch was performed for Rfam mapping. The  software miRA was used to predict novel miRNA by exploring the secondary  structure. The softwares including psRobot, TAPIR   and TargetFinder were used  to predict target genes of miRNAs. The small RNA expression level was calculated by  counting absolute numbers of molecules using unique molecular identifiers   .  Differential expression analysis was performed using the DEGseq   , Q value ≤ 0.001  and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the  significance of expression difference. To annotate gene functions, all target genes were  aligned against the Kyoto Encyclopedia of Genes (KEGG)and Gene Ontology (GO)  database. GO enrichment analysis and KEGG enrichment analysis of target genes were  performed using phyper, a function of R. The P-value was corrected using the  Bonferroni method   , and a corrected P-value ≤ 0.05 was taken as a threshold. GO  terms or KEGG terms fulfilling this condition were defined as significantly enriched  terms.
Genome_build:  Helianthus annuus (assembly HanXRQr1.0)(https://www.ncbi.nlm.nih.gov/genome/?term=Helianthus+annuus)
Supplementary_files_format_and_content: EXCEL files include count and TPM values for each Sample

organism: Helianthus annuus

growth_protocol: L-1-OL-1 were planted in the experimental field under natural conditions at the industrial crops institute, Heilongjiang Academy of Agricultural Sciences (Harbin, China).Seed samples were collected at 7-, 22- and 37 day.

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent was used for the purification of total RNA from the plant tissue according to the manual instructions. Grind tissue samples about 80mg with liquid nitrogen into powder and transfer the powder samples in 1.5ml of preheated 65°C CTAB-pBIOZOL reagents. The samples were incubated by Thermo mixer for 15min at 65°C to permit the complete dissociation of nucleoprotein complexes. After centrifuge at 12000×g for 5min at 4°C, the supernatant was added 400ul of chloroform per 1.5ml of CTAB-pBIOZOL reagent and was centrifuged at 12000×g for 10min at 4°C. The supernatant was transferred to a new 2.0ml tube that added 700ul acidic phenol and 200ul chloroform followed by centrifuging 12000×g for 10 min at 4°C. The aqueous phase was added equal volume of aqueous phase of chloroform and centrifuged at 12000×g for 10 min at 4°C. The supernatant was added equal volume of supernatant of isopropyl alcohol and placed at -20°C for 2 hours for precipitation. After that, the mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml of 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and was dissolved by adding 50µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
RNA libraries were prepared for sequencing using standard BGI500 protocols
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by  electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis  (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker  lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the  18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique  molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated  small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse  Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with  PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The  PCR products were selected by agarose gel electrophoresis with target fragments  110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia,  CA). The library was quality and quantitated in two methods: check the distribution of  the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using  real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products  were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

tag: time point

value: 37 days


title: L04

label_protocol: One aliquot from each sample was transcriptionally profiled using Affymetrix Rat Expression Set 230 (RAE230A) microarray according to standard manufacturer’s procedures.


title: oropharyngeal endoderm explant stage 39 rep1 [39_D]


title: L09M1.0


title: L03

description: Failed Quality Control


title: Non_injected_XCR1_DCs_II


title: oropharyngeal endoderm explant stage 39 rep2 [39_E]


title: oropharyngeal endoderm explant stage 37_38 rep3 [37/38_C]


title: H03


title: oropharyngeal endoderm explant stage 37_38 rep2 [37/38_B]


title: Non_injected_DN_DCs_I


title: L37d-1A


title: Non_injected_CD11b_DCs_III


title: L37d-1B


title: H04


title: Non_injected_XCR1_DCs_I


title: L22d-1C

value: 22 days


title: Non_injected_CD11b_DCs_I


title: oropharyngeal endoderm explant stage 37_38 rep1 [37/38_A]


title: L22d-1B


title: L7d-1C


title: L22d-1A


title: L01


title: hiPSCs_THz_rep2

city: Kyoto

first: Ken-ichiro

last: Kamei

state: Kyoto

address: Yoshida-Ushinomiya-cho, Sakyo-ku

department: iCeMS

country: Japan

institute: Kyoto University

description:
THz_rep2
RNA obtained from 585A1 hiPSCs under mTeSR-1 self-renewal condition treated with THz light, replicate 2

data_processing:
Base-calling and demultiplexing were performed with EPI2ME software (Oxford NANOPORE Technologies).
Failed reads were discarded and Fast5 files were converted into FASTQ and FASTA files using EPI2ME software.
Generated FASTQ files were loaded to BioJupies for alignment with human genomes and annotation.
the counts were analysed using TCC in R Bioconducter. Briefly, the counted data set was introduced into the TCC-GUI package.
Genome_build: human_matrix.h5 v2
Supplementary_files_format_and_content: Gene counts were normalized using TMM (Trimmed mean of M values) methods in the edgeR package with the parameters: Number of Iterations = 3; FDR < 0.1; Elimination of Potential DEGs = 0.05.

source_name: 585A1 hiPSCs

growth_protocol: 585A1 hiPSCs were maintained in mTeSR-1-defined medium (Stem Cell Technologies).

extract_protocol:
Total RNA was extracted from differentiated primary myoblasts using the RNeasy mini kit (QIAGEN).
To prepare the cDNA library, 10 ng of total RNA was diluted with 9 µL of RNase free water, then mixed with VN primer (Oxford NANOPORE Technologies, UK), 1 µL of 10 mM dNTPs (New England Biolabs Inc. Ipswich, Massachusetts, USA), and incubated at 65˚C for 5 min as the RNA solution. Separately, 4 µL of 5x RT Buffer (Thermo Fisher Scientific), 1 µL of RNaseOUT (Thermo Fisher Scientific), 1 µL of Nuclease-free water and 2 µL of Strand-Switching Primer (Oxford NANOPORE Technologies) was mixed as the strand-switching buffer. The two solutions were mixed at 42˚C for 2 min; then, 1 µL of Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) was added, incubated at 42˚C for 90 min, 85˚C for 5 min, and stored at 4˚C until use as the cDNA library.

treatment_protocol: 0.5 MV/cm of THz light was irradiated to hiPSCs.

tag: conditions

value: self-renewal condition

tag: treatment

value: THz


title: L02

city: Ann Arbor

value: bred Low Responder (bLR)


title: H02

value: hippocampus


title: L7d-1B


title: hiPSCs_ctrl_rep2

description:
none_rep2
RNA obtained from 585A1 hiPSCs under mTeSR-1 self-renewal condition, replicate 2


title: H06


title: L7d-1A


title: L06


title: hiPSCs_ctrl_rep1

description:
none_rep1
RNA obtained from 585A1 hiPSCs under mTeSR-1 self-renewal condition, replicate 1


title: TL-panx1a knock-out#3

status: Public on Jun 01 2020

city: Toronto

first: Georg

last: Zoidl

state: Ontario

address: 4700 Keele Street

country: Canada

institute: York University

data_processing:
The sequencing data is in FASTQ format generated using bcl2fastq2 v2.17
The quality of the data is assessed using FastQC v.0.11.2
Adaptors are trimmed using Trim Galore v. 0.4.4.
The raw trimmed reads are aligned to the reference genome using Tophat v. 2.0.11
Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Genome_build: UCSC danRer11 , downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/.

organism: Danio rerio

source_name: whole larvae

growth_protocol: 6 day old larvae (6dpf)

extract_protocol:
Total RNAs were extracted from 6dpf larvae using RNeasy Plus Mini Kit and automated Qiacube platform (Qiagen).
The RNA library preparation was performed following the NEB NEBNext Ultra II Directional RNA Library Preparation protocol (New England Biolabs Inc., Ipswich, MA, USA). RNA libraries were loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size, quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: No treatment

value: TALEN mediate knock-out


title: TL-panx1a knock-out#2


title: TL-control#3

value: wild-type


title: TL-panx1a knock-out#1


title: TL-control#2


title: L05


title: H01


title: TL-control#1