title: Stage 22 - scRNA-seq library 10

first: James

middle: Alexander

last: Briggs

state: Massachusetts

address: 200 Longwood Avenue, Harvard Medical School

department: Department of Systems Biology

institute: Harvard Medical School

data_processing:
Overall, all 75 single cell libraries were sequenced on the Illumina NextSeq 500 platform, as 4 separate pools. 2 pools used Version 2 (v2) InDrops barcoding chemistry. The other 2 used an updated Version 3 (v3) barcoding structure discribed in the supplement of the published paper (Briggs et al, 2018). v2 InDrops scRNA-seq libraries were processed through the pipeline described in Zillionis et al., 2017 (doi:10.1038/nprot.2016.154). v3 InDrops scRNA-seq libraries were processed through an updated version of this pipeline (github.com/indrops). Both pipelines are publically available at these locations and have detailed implementation instructions. Both follow the same sequence of processing steps and generally used the same parameters, unless otherwise indicated. The updated pipeline can process both v2 and v3 data. Example .yaml files with all parameters used to run InDrops.py are included as supplementary files with the published paper (Briggs et al., 2018). The general steps and parameters are summarized below.
Basecalling and demultiplexing FASTQ files: BCL files were converted to FASTQ files using command "bcl2fastq --adapter-stringency 0.9 --barcode-mismatches 0 --fastq-compression-level 4 --min-log-level INFO --minimum-trimmed-read-length 0 --sample-sheet {path}/SampleSheet.csv --runfolder-dir {path} --output-dir {path} --processing-threads 8 --no-lane-splitting --mask-short-adapter-reads 0 --use-bases-mask y*,y*,y*,y*". FASTQ files were then demultiplexed using the library indexes indicated above for each sample (as a sample characteristic). For v2 libraries, this sequence is found on the index read (not provided), while for v3 libraries this index is found on read 3. For v2 libraries, read 1 contains cell barcode information and read 2 is the gene read. For v3 libraries, read 1 is the gene read, and cell barcode information is contained in reads 2 and 4. Raw FASTQ files supplied here are pre-dumultiplexed. They can be processed by InDrops.py as demultiplexed single libraries, or concatenated into the original pools as described above and then re-demultiplexed automatically.
Build reference transcriptome bowtie index: The FASTA format X. Tropicalis v9.0 transcript reference was downloaded from: http://www.xenbase.org/other/static/ftpDatafiles.jsp. 50bp polyA tails were added to all genes, and gene headers were adjusted to format "gene ID | gene ID" for compatibility with InDrops.py. A bowtie index was constructed from this file as described in the manual at github.com/indrops, using bowtie version 1.1.1. No .gtf file was used.
Filter reads: inDrops.py filters reads for presence of i) two cell barcode sequences, ii) unique molecular identifier (UMI), and iii) Illumina libray index (for non-demultiplexed FASTQ files). inDrops.py then trims the gene read using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:16).
Identify abundant barcodes: inDrops.py matches cell barcodes against a list of pre-determined barcodes. Gene reads are then split into barcode-specific files for mapping and UMI filtering. Cell barcodes with fewer than the minimum reads per cell (specified above as a sample characteristic) are excluded at this point.
Quantify expression: inDrops.py aligns the sorted reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 80 (v3) or 200 (v2) -m 200 -best -strata -a) to the X. Tr v9.0 reference transcriptome, which was built as described above. For each cell, all reads mapping to the same transcript are UMI corrected revealing a transcript count for each gene. Ambiguous reads that map to multiple genes are scored at each target by their proximity to the 3' end of a gene transcript to resolve conflicts, as true mappings should be 3' biased due to InDrops library capture. If conflicts are not clearly resolved, ambiguous reads are discarded. N.B. the InDrops.py pipeline used on v2 data from (Zillionis et al., 2017; doi:10.1038/nprot.2016.154) uses slightly different filtering criteria compared to the updated v3 pipeline (github.com/indrops) at this stage. Gene expression counts of UMI-filtered transcripts per gene (rows) per cell (columns) are ouput as .tsv files. These outputs are available as processed data files below (e.g. {stage}_{library_number}.annotated_counts.tsv.gz).
Filter, combine, and normalize data: InDrops.py output matrices were filtered for cells that were: i) > min UMIs per cell, ii) not background, and iii) not cell doublets as described in (Briggs et al., 2018). These filteres are provided as headers on each individual libraries processed data file in rows 3-5 respectively. Pass-filter cells were combined into a single counts matrix (Raw_combined.annotated_counts.tsv.gz). Combined counts were further batch corrected and total count normalized to yeild the final counts matrix (Corrected_combined.annotated_counts.tsv.gz) used for downstream analyses in the associated paper (more details in Briggs et al., 2018).
Genome_build: Xenopus Tropicalis v9.0 (available at: http://www.xenbase.org/other/static/ftpDatafiles.jsp)
Supplementary_files_format_and_content: Processed data files are genes (rows) versus cells (columns) scRNA-seq counts data, as used for analysis in the paper. They are supplied both for each individual sequencing library, and as a single combined file with all pass-filter cells. Both formats include relevant annotations for each cell as row headers.
Supplementary_files_format_and_content: In the single library counts files, rows 1-6 give cell annotations. Row 1 gives the barcode name for each cell. Row 2 gives the cell barcode sequence (used by InDrops.py during processing). Rows 3-5 are logical filtering masks (0 = false, 1 = true) describing whether each cell: was above the minimum UMI threshold (row 3), passed additional background filtering (row 4), or passed doublet filtering (row 5). Row 6 summarized which cells passed all filters. For rows > 6, column 1 gives the gene names, and columns 2:end give measured UMI counts for each gene in each cell. Cells passing all filters are included in the combined counts files.
Supplementary_files_format_and_content: Combined counts are supplied either as raw counts (Raw_combined.annotated_counts.tsv.gz), or as counts following batch correction and total count normalization (Corrected_combined.annotated_counts.tsv.gz). See supplemental materials and methods in the paper (Briggs et al., 2018) for details.
Supplementary_files_format_and_content: In the combined counts files, rows 1-9 give cell annotations. Row 1 gives the InDrops version used for each cell (either Version 2 or Version 3). Row 2 gives the experimental replicate name (either Timeseries 1, Timeseries 2, or NPB dissection). Row 3 gives the egg clutch ID. Row 4 gives the name of the individual sequencing library that the cell came from. Row 5 gives the barcode name for each cell. Row 6 gives the cell barcode sequence (used by InDrops.py during processing). Row 7 gives the developmental stage of the cell. Row 8 gives the cell state name assigned to each cell. Row 9 gives the name of the parent cell state for each cell, as defined in the cell state tree presented in Figure 2 of the associated paper (Briggs et al., 2018). For rows > 9, column 1 gives the gene names, and columns 2:end give measured UMI counts for each gene in each cell.

organism: Xenopus tropicalis

source_name: Whole embryo

extract_protocol:
5-15 healthy embryos at each desired developmental stage were collected, devitellinized using Pronase (1mg/mL in 1X MMR), dissociated to single cells (as described in Briggs et al., 2018), washed using a density gradient media replacement approach (on ice), and finally resuspended in cold PBS-/- with 0.5mg/mL BSA for scRNA-seq analysis by InDrops. Embryos were processed rapidly to minimize potential artifactual transcriptional changes in response to dissociation. Cells were generally ready for InDrops encapsulation within 1hr of starting Pronase treatment, and kept on ice from the washing steps onwards.
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with primer modifications for v3 libraries as summarized in supplement of the associated manuscript (Briggs et al., 2018)).

treatment_protocol: Xenopus tropicalis embryos were harvested via standard natural mating procedures (http://wiki.xenbase.org/xenwiki/index.php/Anesthesia,_in_vitro_fertilization,_and_natural_mating_of_Xenopus_tropicalis_(Conlon_lab)).

value: Whole embryo

tag: developmental stage (nieuwkoop faber)

value: Stage 22

tag: clutch (batch of eggs)

value: Clutch 5

tag: replicate / experiment

value: Timeseries 2

tag: sequencing pool

value: Pool 4

tag: indrops version

tag: library index sequence used to demultiplex

value: CTTAATAG

tag: library id

tag: minimum reads per cell during initial processing

tag: size of supplementary file (# cell barcodes > min reads)

tag: minimum counts per cell threshold used to remove background barcodes

tag: number pass filter cells (kept in combined data matrix)


title: Stage 22 - scRNA-seq library 19

status: Public on Apr 28 2018

type: SRA

city: Boston

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

value: Clutch 6

value: ACGCTCTT


title: Stage 22 - scRNA-seq library 14

value: TTACCTCC


title: Stage 22 - scRNA-seq library 20

value: CGCATTCT


title: Stage 22 - scRNA-seq library 16

value: CCTTTACT


title: Stage 22 - scRNA-seq library 11

value: ATAGCCTT


title: Stage 22 - scRNA-seq library 12

value: TAAGGCTC


title: Stage 22 - scRNA-seq library 13

value: TCGCATAA


title: yfp_2699c4_no4

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Alignment using STAR aligner with default settings
Raw counts calling using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: text file including raw counts of each gene for all samples

molecule: total RNA

organism: Mus musculus

source_name: sorted T cell low tumor cells

growth_protocol: T cell low or high pancreatic tumor cells were subcutaneously implanted into C57BL/6 mice. Sorted tumor cell samples were prepared from tumors 3 weeks following implantation.

extract_protocol:
RNA was extracted using Qiagen Rneasy Micro Kit.
500 ng of total RNA was used for the preparation of sequencing libraries using NEB RNA-seq library preparation kit with standard protocol. RNA-seq libraries were sequenced on an Illumina Nextseq 550 high-throughput sequencer.

treatment_protocol: no treatment administrated

tag: strain

tag: sample type

value: sorted tumor cells

tag: t cell phenotype

value: low


title: Stage 22 - scRNA-seq library 15

value: CAGTTATG


title: Stage 22 - scRNA-seq library 17

value: Whole embryo

value: GAGACGGA


title: yfp_2699c4_no3


title: Stage 22 - scRNA-seq library 9

value: Stage 22

value: Clutch 5

value: TCTTACGC


title: yfp_6419c5_no1


title: Stage 22 - scRNA-seq library 8

value: Timeseries 2

value: Pool 4

value: ACTCTAGG


title: Stage 22 - scRNA-seq library 18

value: Clutch 6

value: AGAAAGCT


title: yfp_2699c4_no2


title: Stage 22 - scRNA-seq library 7

value: AGCTAGAA


title: yfp_2699c4_no1


title: Stage 22 - scRNA-seq library 6

value: Clutch 1

value: Timeseries 1

value: Pool 2

value: AGTCAA


title: yfp_7160c5_no2

source_name: sorted T cell intermediate tumor cells

value: sorted tumor cells

value: intermediate


title: yfp_2838c3_no3

source_name: sorted T cell high tumor cells

value: high


title: Stage 22 - scRNA-seq library 5

value: Whole embryo

value: CTTGTA


title: yfp_7160c2_no2


title: yfp_7160c5_no1


title: miRNA expression of normal esophagus tissue

type: RNA

city: Shantou

first: Qian

last: Yang

state: Guangdong

address: Xinling 22 Road

country: China

institute: Medical College of Shantou University

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US). After the homogenization of the sample hybridization signal, the signal value after logarithmic transformation was performed on the base of 2.  The file "normalized_data.txt" contains the normalized signal.

organism: Homo sapiens

source_name: normal esophagus tissue

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: •Absolutely RNA miRNA Kit - Agilent p/n 400814  •miRNeasy Mini Kit - Qiagen p/n 217004  •mirVana RNA Isolation Kit - Applied Biosystem p/n AM1560  •TRIZOL Reagent (100 mL) - Invitrogen p/n 15596-026

tag: gender

value: female

value: esophagus

tag: disease state

value: normal


title: yfp_7160c2_no1


title: Stage 22 - scRNA-seq library 4

tag: developmental stage (nieuwkoop faber)

value: Stage 22

value: GGCTAC


title: miRNA expression of a esophageal NEC tissue

source_name: esophageal NEC tissue

value: esophageal NEC


title: yfp_7062c3_no1

source_name: not used


title: yfp_6883c4_no1


title: yfp_6694c2_no2

value: low


title: yfp_6694c2_no1


title: Stage 22 - scRNA-seq library 2

tag: clutch (batch of eggs)

value: Pool 1

value: ATGTCA


title: yfp_6620c1_no2


title: yfp_6883c1_no1


title: yfp_6620c1_no1


title: yfp_6556c4_no2


title: Stage 20 - scRNA-seq library 8

value: Stage 20

value: Clutch 6

tag: replicate / experiment

value: Timeseries 2

value: Pool 4

value: CTAGTCGA


title: yfp_6556c4_no1

value: sorted tumor cells

value: high


title: yfp_6556c3_no2


title: Stage 20 - scRNA-seq library 7

value: Whole embryo

tag: sequencing pool

value: CGGAGAGA


title: yfp_6556c3_no1


title: Stage 20 - scRNA-seq library 6

tag: indrops version

value: ATTAGACG


title: DNA methylation of normal esophagus

type: genomic

description: normal esophagus tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio Methylation Module v1.8

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to standard instructions in Illumina

value: female

value: esophagus

value: normal


title: yfp_6555c3_no2


title: yfp_6555c3_no1


title: Stage 20 - scRNA-seq library 5

value: Clutch 1

value: Timeseries 1

value: Pool 2

tag: library index sequence used to demultiplex

value: TAGCTT


title: I56

city: Guangzhou

first: li

middle: Xiao

last: Lu

address: Baiyun Road

department: Nanfang Hospital

institute: Southern Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 16 nt.
The clean reads were compared to the miRbase21 and Rfam database  to identify known miRNA and other non-coding RNAs.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Total clean reads were  also mapped to the Rat reference genome using the bwa aligner.The mapped reads were further annotated to the repeats and exon regions based on the genome annotation.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample…

organism: Rattus norvegicus

source_name: isograft cornea

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

value: isograft cornea

value: Wistar

tag: age

value: postal natal 6w


title: A12

source_name: allograft cornea

value: allograft cornea


title: I34


title: A56


title: I12


title: Stage 22 - scRNA-seq library 1

value: Stage 22

value: Pool 1

value: AGTTCC

tag: library id

tag: minimum reads per cell during initial processing


title: yfp_6499c4_no2

value: sorted tumor cells

value: high


title: yfp_6499c4_no1


title: Stage 22 - scRNA-seq library 3

value: Whole embryo

value: CCGTCC

tag: size of supplementary file (# cell barcodes > min reads)

tag: minimum counts per cell threshold used to remove background barcodes


title: N56

source_name: cornea

tag: tissue

value: normal cornea


title: yfp_6499c3_no2

tag: strain

value: low


title: Stage 20 - scRNA-seq library 3

value: Stage 20

value: Clutch 1

value: AGTCAA

tag: number pass filter cells (kept in combined data matrix)


title: DNA methylation of esophageal NEC

description: esophageal NEC tissue

source_name: esophagus NEC tissue

value: female

value: esophagus

value: tumor


title: Stage 20 - scRNA-seq library 2

value: Timeseries 1

value: CTTGTA


title: N34

value: Wistar

value: postal natal 6w


title: A34

value: allograft cornea


title: Stage 20 - scRNA-seq library 1

value: Pool 1

value: GGCTAC


title: N12


title: WAGO-4-associated small RNAs from F3 after oma-1 dsRNA P0

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

institute: University of Science & Technology of China

description: IPed small RNA

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 17 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
The data processing pipeline for 26S rRNA tail-seq was included as an additional column of the SAMPLES section.
Genome_build: WS243
Supplementary_files_format_and_content: .txt files. Basically, the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script.

organism: Caenorhabditis elegans

source_name: young adults

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm plates without food. Bleached embryos were exposed to 50 mJ/cm2 UV irradiation by Ultraviolet (HL-2000 HybriLinker) and recover for 2 hours.

extract_protocol: Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by the Beijing Genomics Institute (BGI Shenzhen). sRNAs ranging from 17 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

tag: genotype

tag: temperature

value: 20 C, F3 after oma-1 dsRNA on P0

tag: antibody

value: anti-FLAG M2 antibody (Sigma)


title: Stage 18 - scRNA-seq library 7

value: Whole embryo

tag: developmental stage (nieuwkoop faber)

value: Stage 18

value: Clutch 6

value: Timeseries 2

value: Pool 4

value: AGGCTTAG


title: WAGO-4-associated small RNAs from P0 after oma-1 dsRNA P0

description: IPed small RNA

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate). Synchronized embryos were incubated at 20°C, 15°C, or 4°C for 12 hours, then grown at 20°C for 2 hours before RNA extraction.

value: 20 C, P0 on oma-1 dsRNA on P0


title: WAGO-4-associated small RNAs from F1 after oma-1 dsRNA P0

description: IPed small RNA

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm plates without food.

value: 20 C, F1 after oma-1 dsRNA on P0


title: Stage 18 - scRNA-seq library 6

tag: clutch (batch of eggs)

value: TACTCCTT


title: Stage 18 - scRNA-seq library 5

tag: replicate / experiment

value: TATGCAGT


title: WAGO-4-associated small RNAs on HT115

description: IPed small RNA


title: Stage 18 - scRNA-seq library 4

value: Clutch 1

value: Timeseries 1

tag: sequencing pool

value: Pool 2

value: ACTTGA


title: WAGO-4-associated small RNAs after lin-15b RNAi

description: IPed small RNA

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).

value: 3xFLAG::GFP::WAGO-4; lin-15b(RNAi)


title: WAGO-4-associated small RNAs

description: IPed small RNA


title: Stage 18 - scRNA-seq library 2

value: Pool 1

tag: indrops version

value: TAGCTT


title: Stage 18 - scRNA-seq library 3

value: Whole embryo

tag: library index sequence used to demultiplex

value: GTCCGC


title: Stage 18 - scRNA-seq library 1

value: Stage 18

value: GATCAG


title: Stage 16 - scRNA-seq library 7

value: Stage 16

value: Clutch 5

value: Timeseries 2

value: Pool 4

value: CTCCTTAC


title: Vaginal swab, sample 8016

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomcis Suite using the RMA normalization method

label: biotin

source_name: human vaginal swab

label_protocol: Biotinylated cRNA were prepared according to the two-cycle Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).

extract_protocol: Swabs were incubated in the PAXGene tube for 24h at room temperature before RNA extraction with MasterPure Kit (Epicentre Cat#MCR85102) as per kit instructions.

treatment_protocol: Vaginal swabs were collected from 20 women (10 control, 10 HRT) and placed in PAXgene stabilizer media and vortexed for 4s.

tag: treatment

value: Control


title: Vaginal swab, sample 8014


title: Vaginal swab, sample 8019


title: Vaginal swab, sample 8013

value: ERT


title: Vaginal swab, sample 8002


title: MCF-7 ATP 100μM, biological rep2

city: Beijing

first: Ying

last: Liu

state: State...

address: Xueyuan Road 38, Haidian District, Beijing, China

department: Department of pathology

institute: Peking University Health Science Center

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

source_name: MCF-7 with 100μM ATP treatment for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: MCF-7 cells were cultured in 37℃, 5% CO2 atmosphere.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: C1, C2, C3 were cultured with normal culture media; T1, T2, T3 were cultured with corresponding media containing 100μM ATP for 24h.

tag: cell line

value: ATP treatment


title: Vaginal swab, sample 8008


title: Vaginal swab, sample 8003


title: Stage 16 - scRNA-seq library 6

value: AGAGGATA

tag: library id

tag: minimum reads per cell during initial processing


title: Vaginal swab, sample 8015


title: Vaginal swab, sample 8006


title: MCF-7 control, biological rep1

source_name: MCF-7 without ATP treatment

value: control


title: MCF-7 ATP 100μM, biological rep1


title: Stage 16 - scRNA-seq library 5

value: ATAGAGAG

tag: size of supplementary file (# cell barcodes > min reads)

tag: minimum counts per cell threshold used to remove background barcodes


title: Vaginal swab, sample 8004


title: Vaginal swab, sample 8001


title: MCF-7 ATP 100μM, biological rep3


title: MCF-7 control, biological rep2


title: MCF-7 control, biological rep3


title: Vaginal swab, sample 8012


title: Vaginal swab, sample 8017


title: Stage 16 - scRNA-seq library 4

tag: tissue

value: Clutch 1

value: Timeseries 1

value: Pool 2

value: CAGATC


title: Stage 16 - scRNA-seq library 3

value: Whole embryo

value: GCCAAT

tag: number pass filter cells (kept in combined data matrix)


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9032_NPS09_R3

city: Sophia Antipolis

first: CORINNE

last: MENIGOT

address: 2400 route des colles

country: France

institute: GALDERMA R & D

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Expression Console (Affymetrix) with RMA normalization.

source_name: Human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA).

extract_protocol: RNeasy Micro Kit_Qiagen RNA extraction was performed according to the manufacturer's instructions.

value: Whole skin


title: Stage 16 - scRNA-seq library 2

value: Stage 16

value: Pool 1

value: ACTTGA


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9026_NPS07_R3


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9028_NPS08_R3


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9021_NPS05_R3


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9019_NPS03_R3


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9020_NPS04_R3


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9017_NPS01_R3


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9028_NPS08_L3


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9032_NPS09_L3


title: non-inflammatory skin  after CD 5789 treatment (J27) (Back) 9016_NPS02_R3


title: Vaginal swab, sample 8011


title: RNA-seq_adult female esophagus_NEC

data_processing:
Tophat V2.0.6
easyRNAseq V1.6.0
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM values

source_name: adult female esophagus cancer tissue

extract_protocol: Total RNA was isolated using an RNeasy mini kit and analyzed on 1% formaldehyde-denatured agarose gels to ensure there was no degradation. Paired-end libraries were synthesized by using the TruSeq(tm) RNA Sample Preparation Kit following the TruSeq(tm) RNA Sample Preparation Guide. Briefly, poly-A containing mRNA was purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces by using divalent cations at 94oC for 8 min. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments then underwent an end repair process, the addition of a single 'A' base, and then ligation of the adapters. Products were then purified and enriched by PCR to create the final cDNA library. Purified libraries were quantified using a Qubit(r) 2.0 Fluorometer, and validated with a Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. A cluster was generated by cBot, with the library diluted to 10 pM, and then inserts were sequenced on the Illumina HiSeq 2500. Library construction and sequencing was performed at the Shanghai Biotechnology Corporation.

value: esophagus

tag: age

tag: disease state

value: esophageal NEC

tag: Sex

value: female


title: Stage 14 - scRNA-seq library 7

source_name: Whole embryo

tag: developmental stage (nieuwkoop faber)

value: Stage 14

value: Clutch 4

value: Timeseries 2

value: Pool 3

value: TCGCATAA


title: RNA-seq_adult female esophagus_normal

source_name: adult female normal esophagus tissue

value: normal esophageal tissue


title: Stage 14 - scRNA-seq library 6

tag: clutch (batch of eggs)

value: TAAGGCTC


title: Stage 16 - scRNA-seq library 1

value: Clutch 1

tag: replicate / experiment

value: Timeseries 1

value: CAGATC


title: Stage 14 - scRNA-seq library 5

value: Whole embryo

tag: sequencing pool

value: ATAGCCTT


title: DAOY N2KO Jagged1

city: Solna

first: Urban

last: Lendahl

address: Berzelius väg 35

department: CMB

country: Sweden

institute: Karolinska Institutet

data_processing:
Clustering was done by ‘cBot’ and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using ‘HiSeq SBS Kit v4’ chemistry.
he Bcl to FastQ conversion was performed using bcl2fastq_2.17 from the CASAVA software suite.
The quality scale used is Sanger / phred33 / Illumina 1.8+.
Genome_build: GRCh37

source_name: N2 KO Jagged1 treated (Notch on)

growth_protocol: DMEM+FBS+PEST

extract_protocol:
RNA extraction using RNA easy mini Kit
Type: Illumina TruSeq Stranded mRNA,  Poly-A selection
RNA-seq, Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_2.17 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.

treatment_protocol: DAOY/HTB186 cells were cultured on Jagged1-ligand coated plates to activate Notch signalling or Fc as a control, in combination  with the pan-Notch inhibitor DAPT for 12h to block Notch signalling.

tag: cell type

value: Medulloblastoma

value: DAOY

tag: culture condition

value: Jagged1-ligand coated plates

value: DMSO

tag: genotype


title: Stage 14 - scRNA-seq library 3

value: Pool 2

tag: indrops version

tag: library index sequence used to demultiplex

value: TGACCA


title: DAOY N1KO Jagged1+DAPT

source_name: DAPT supression of Jagged1  activation

tag: cell line

tag: treatment

value: DAPT


title: DAOY N2KO Fc

source_name: untreated (steady sate)

value: FC (control)


title: DAOY  N1KO + Jagged1

source_name: N1 KO Jagged1 treated (Notch on)


title: DAOY N2KO Jagged1+DAPT


title: Stage 14 - scRNA-seq library 2

value: Stage 14

value: Pool 1

value: GCCAAT

tag: library id

tag: minimum reads per cell during initial processing

tag: size of supplementary file (# cell barcodes > min reads)

tag: minimum counts per cell threshold used to remove background barcodes


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9026_NPS07_L3

tag: tissue

value: Whole skin


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9025_NPS06_L3


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9017_NPS01_L3


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9021_NPS05_L3


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9020_NPS04_L3


title: non-inflammatory skin  after vehicle treatment (J27) (Back) 9019_NPS03_L3


title: Stage 20 - scRNA-seq library 4

value: Stage 20

value: Clutch 1

value: GATCAG

tag: number pass filter cells (kept in combined data matrix)


title: Stage 14 - scRNA-seq library 4

value: Whole embryo

tag: developmental stage (nieuwkoop faber)

value: Timeseries 1

value: ACAGTG


title: DAOY  N1KO +Fc +DAPT

source_name: N1 KO DAPT treated (Notch off)

value: Medulloblastoma

value: DAOY


title: DAOY N1KO +Fc

source_name: N1 KO untreated (steady sate)

value: DMSO


title: DAOY+ Jagged1+DAPT

source_name: DAPT supression of Jagged1 activation

value: Jagged1-ligand coated plates

value: WT


title: DAOY+Fc+DAPT

source_name: DAPT treated (Notch off)

value: DAPT


title: DAOY N2KO Fc +DAPT

source_name: N2 KO DAPT treated (Notch off)

value: FC (control)


title: DAOY+ Jagged1

source_name: Jagged1 treated (Notch on)


title: DAOY+ Fc


title: Stage 14 - scRNA-seq library 1

value: Stage 14

tag: clutch (batch of eggs)


title: Stage 13 - scRNA-seq library 4

value: Stage 13

value: Clutch 4

tag: replicate / experiment

value: Timeseries 2

value: Pool 3

value: CTTAATAG


title: Stage 13 - scRNA-seq library 3

tag: sequencing pool

value: TCTTACGC


title: Stage 13 - scRNA-seq library 2

value: Whole embryo

value: ACTCTAGG


title: Stage 13 - scRNA-seq library 1

value: AGCTAGAA


title: Stage 12 - scRNA-seq library 6

value: Stage 12

value: CTAGTCGA


title: Stage 12 - scRNA-seq library 5

value: CGGAGAGA


title: Stage 12 - scRNA-seq library 4

value: ATTAGACG


title: Stage 12 - scRNA-seq library 3

value: Clutch 1

value: Timeseries 1

value: Pool 2

value: TTAGGC


title: Stage 12 - scRNA-seq library 2

value: Pool 1

value: TGACCA


title: VR13_PR

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Each primer had a gene-specific sequence and a universal PCR primer site; a prolonged annealing time of 16 h was used, with a temperature gradient from 70  to 30°C. PCR was performed using universal primers and a single colour (Cy3) assay. The amplified cDNA was then denatured with NaOH, precipitated, and washed with 75% alcohol. The cDNA was then re-suspended and hybridised to Illumina Human Reference 8 BeadArrays for 16 h at 65°C.

scan_protocol: The slides were washed and scanned using the Illumina BeadArray Reader (Illumina, San Diego, CA).

data_processing: Raw data intensities were loaded into R statistical environment and normalized using the quantile method. To remove batch effect between subsets of experiments, the combat function was applied to the dataset

source_name: Primary tumor

label_protocol: The biotinylated cDNA was then bound to streptavidin particles, and mis- and non-hybridised oligonucleotides were washed away.

extract_protocol: Total RNA extracted from FFPE and FF samples was converted to cDNA using oligo-dT18 and random nanomer primers. Pairs of query oligonucleotides, including three unique pairs for each of 24,000 genes, were annealed to complimentary sequences (~50 bp) flanking the specific cDNA target site.

value: primary intrahepatic cholangiocarcinoma

tag: gender


title: VR17_PR


title: Stage 12 - scRNA-seq library 1


title: TO10_PR

value: F


title: Stage 11 - scRNA-seq library 10 (NPB)

source_name: Dissected neural plate border (NPB) region

value: Stage 11

value: Clutch 3

value: NPB dissection

value: Pool 3

value: GAGACGGA


title: TO11_REC

source_name: Recurrent tumor of TO10_PR


title: VR15_REC

source_name: Recurrent tumor of VR13_PR


title: VR7_PR


title: VR21_REC

source_name: Recurrent tumor of VR17_PR


title: VR5_REC

source_name: Recurrent tumor of VR1_PR


title: VR1_PR


title: VR3_REC


title: VR11_REC

source_name: Recurrent tumor of VR5_PR


title: VR9_REC


title: Stage 11 - scRNA-seq library 9 (NPB)

value: Dissected neural plate border (NPB) region

value: CCTTTACT


title: TO13_REC

source_name: Recurrent tumor of TO12_PR


title: NA1_PR

value: M


title: TO8_REC

source_name: Recurrent tumor of TO7_PR


title: Stage 11 - scRNA-seq library 8 (NPB)

value: CAGTTATG


title: TO3_PR


title: TO12_PR


title: NA2_REC

source_name: Recurrent tumor of NA1_PR


title: TO4_REC

source_name: Recurrent tumor of TO3_PR


title: Stage 11 - scRNA-seq library 7 (NPB)

value: TTACCTCC


title: Stage 11 - scRNA-seq library 6

source_name: Whole embryo

value: Whole embryo

value: Timeseries 2

value: CGCATTCT


title: RO1_PR


title: RS_Setd2KO_H3K36me3

city: Shanghai

first: Fei

last: Lan

address: No131 Dongan Road, Xuhui District.

institute: Institute of Biochemical Science

library_source: genomic

data_processing:
Basecalls performed using CASAVA.
ChIP-seq datas were aligned to the mm9 genome assembly using bowtie with the following parameters:-p 5 -m 1 --sam
H3K36me3 peaks were called by MACS software under default parameters.
Mapped H3K36me3 ChIP-seq reads were transfer to bedgraph files for visualization using bedtools.
Genome_build: mm9
Supplementary_files_format_and_content: bed files include H3K36me3 peak lists identified by MASC;and bg files include normalized H3K36me3 ChIP-seq tag density.

source_name: round spermatids

growth_protocol: Testes from adults were collected in PBS and placed on ice. After removal of the tunica albuginea, the testes were first digested with PBS containing 120 U/ml of collagenase type I (Worthington), further digested with 0.25% trypsin (Gibco), and DNAse I (5mg/ml, Gibco), and then terminated by adding fetal bovine serum (FBS). The dissociated testicular cell suspension was collected and resuspended at a concentration of 1x106 cells/ml in DMEM (Hyclone). Spermatocytes and round spermatids were collected based on Ho33342/PI staining using fluorescence-activated cell sorting (FACS).

extract_protocol:
Chromatin samples were lysed with lysis buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% TritonX-100 and 0.1% SDS) and sonicated by Qsonica R2. A total of 2 ug of H3K36me3 antibody (CST 4909S) was incubated with each chromatin sample overnight at 4 ℃, together with 0.5 ug spike-in antibody (Active motif 61686) and 20 ng spike-in chromatin (Active motif 53083) for normalization purpose.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The sorted pachytene spermatocytes and round spermatids were crosslinked with 1% formaldehyde for 10 mins and then stopped by adding 125 mM Glycine.

tag: strain

tag: chip antibody

value: anti-H3K36me3 (Cell Signaling, catalog# 4909S, lot# 2)

tag: cell type

value: round spermatids


title: RS_WT_H3K36me3

tag: genotype

value: WT


title: RO6_PR

value: primary intrahepatic cholangiocarcinoma


title: PD_Setd2KO_H3K36me3

source_name: pachytene/diplotene spermatocytes

value: pachytene/diplotene spermatocytes


title: TO7_PR


title: RO2_REC

source_name: Recurrent tumor of RO1_PR


title: PD_WT_Input


title: RO3_REC

source_name: Recurrent tumor of RO6_PR


title: Stage 11 - scRNA-seq library 4

value: Stage 11

value: Clutch 3

tag: indrops version

tag: library index sequence used to demultiplex

value: AGAAAGCT


title: PD_WT_H3K36me3


title: S3

city: Yangling

first: Guan-jing

last: Ren

state: Shaanxi

address: NO.22 Xinong Road

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
The libraries were sequenced on an Illumina Hiseq 2500 platform
The raw reads were processed firstly by the in-house perl scripts. To obtain clean reads, low quality reads, containing adapter and ploy-N reads were removed from raw data in this step. Bowtie (v 2.0.6) was used to build index of the reference genome and TopHat (v 2.0.9) was used to align paired-end clean reads to the reference genome. In addition, the software find_circ was used to extend the anchor sequences. Four analytic tools, namely coding-non-coding-index (CNCI), coding potential calculator (CPC), phylogenetic codon substitution frequency (PhyloCSF) and Pfam-scan, were used to effectively distinguish protein-coding and non-coding sequences.The software phast (v 1.3) was usually used for phylogenetic analysis to evaluate the sequence conservation of transcripts. Fragments per kilobase for a million reads (FPKMs) of both lncRNAs and coding genes in each sample were calculated by the Cuffdiff (v 2.1.1). Besides, the transcript per million (TPM) was used to normalize the expression level of circRNAs. It was considered to be statistically significant when p-value < 0.05 or q-value < 0.05.
Genome_build: ftp://ftp.ensembl.org/pub/release-83/fasta/gallus_gallus/dna/
Supplementary_files_format_and_content: the information of dysregulated mRNAs, lncRNAs and circRNAs from RNA-seq experiment, xls

organism: Gallus gallus

source_name: Trachea

extract_protocol:
Total RNA was extracted from each trachea sample using TRIzol reagent. Then a total amount of 3 μg RNA per sample was used for the RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Chickens were firstly anesthetized with ether, and then the trachea from each chicken was rapidly sampled, washed with nuclease-free PBS. All instruments and reagents in the trial were treated with DEPC in advance and without RNase.

value: trachea

tag: age

value: 10 days post infection

tag: treatment

value: Cryptosporidium baileyi infection


title: Stage 10 - scRNA-seq library 2

value: Stage 10

value: Clutch 1

value: Timeseries 1

value: Pool 2

value: ATCACG

tag: library id

tag: minimum reads per cell during initial processing

tag: size of supplementary file (# cell barcodes > min reads)


title: Stage 11 - scRNA-seq library 3

tag: tissue

value: Whole embryo

value: Clutch 2

value: Timeseries 2

value: Pool 3

value: AGGCTTAG

tag: minimum counts per cell threshold used to remove background barcodes

tag: number pass filter cells (kept in combined data matrix)


title: Stage 10 - scRNA-seq library 3

tag: developmental stage (nieuwkoop faber)

tag: clutch (batch of eggs)

tag: replicate / experiment

value: CGATGT


title: Stage 11 - scRNA-seq library 2

value: Stage 11

tag: sequencing pool

value: TACTCCTT


title: S2


title: PD_Setd2KO_Input

tag: strain

tag: chip antibody

value: pachytene/diplotene spermatocytes


title: Stage 11 - scRNA-seq library 1

value: TATGCAGT


title: S1

value: trachea

value: 10 days post infection


title: Stage 11 - scRNA-seq library 5

value: Clutch 3

value: ACGCTCTT


title: Stage 10 - scRNA-seq library 1

value: Stage 10

value: Clutch 1

value: Timeseries 1

value: Pool 1


title: Stage 8 - scRNA-seq library 3

value: Whole embryo

value: Stage 8

value: Clutch 2

value: ATAGAGAG


title: C2

description: it was renamed as N2 in the manuscript

value: control


title: HaCaT-control-rep.3

city: Nanjing

first: Xuemin

last: Xiao

address: St. 12 Jiangwangmiao

department: Institute of Dermatology

institute: Chinese Academy of Medical Sciences

description:
Gene expression in 3 days after mismatch siRNA transfection
C3

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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

growth_protocol: HaCaT cells were cultured in dishes containing Dulbecco’s modiﬁed Eagle’s media (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/ml) and streptomycin (100 mg/ml). The cells were maintained in a humidiﬁed 5% carbon dioxide, 95% air incubator at 37℃. Cells were given fresh medium every 3 days and subcultured

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: HaCaT cells were placed into 6-well plates at 30-40% confluence.Each well was transfected with 100 pmol of either different NCSTN siRNA or m-siRNA control using lipofectamine 2000(Invitrogen) according to the manufacturer’s instructions.

tag: cell line

value: immortal keratinocyte cell line, HaCaT

tag: genotype/variation


title: HaCaT-sirna-rep.1

description:
Gene expression in 3 days after siRNA transfection
N1

value: NCSTN knock down


title: HaCaT-sirna-rep.2

description:
Gene expression in 3 days after siRNA transfection
N2


title: HaCaT-control-rep.2

description:
Gene expression in 3 days after mismatch siRNA transfection
C2


title: HaCaT-control-rep.1

description:
Gene expression in 3 days after mismatch siRNA transfection
C1


title: C1

description: it was renamed as N1 in the manuscript


title: HaCaT-sirna-rep.3

description:
Gene expression in 3 days after siRNA transfection
N3


title: Stage 8 - scRNA-seq library 1

tag: indrops version

tag: library index sequence used to demultiplex

value: ATCACG


title: C3

description: it was renamed as N3 in the manuscript

tag: age

tag: treatment


title: Stage 8 - scRNA-seq library 2

value: GTAGAG

tag: library id

tag: minimum reads per cell during initial processing


title: heart_Acsl1flox_10w_rep3

status: Public on Apr 27 2018

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description:
Acsl1flox_10w_03
Biological replicate 3 of 4

hyb_protocol: Cy-5 labeled cRNA was co-hybridized to Agilent 014868 Whole Mouse Genome Microarrays with equimolar amounts of Cy-3 labeled WMRR-derived cRNA. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner and processed using Agilent FeatureExtractor 9.5.3.1.

data_processing: Data files uploaded into Genespring 14.8 using a median value baseline transformation. Probes found in at least 70 percent of the samples that have flags in Present or Marginal were retained for analysis.

source_name: Whole Mouse Reference RNA (WMRR)

label_protocol: 500 ng of WMRR or heart RNA labeled with Cy-3 or Cy-5, respectively (Perkin Elmer) and amplified using the Low Input RNA Amplification Kit (Agilent) as described by the manufacturer.

growth_protocol: At 6 to 8 wk of age, Acsl1H-/- and littermate Acsl1flox/flox control male mice were injected i.p. with tamoxifen (Sigma, St. Louis MO) (75 mg/kg BW), dissolved in corn oil (20 mg/ml) for 4 consecutive days (3 mg/40 g body weight).

extract_protocol: Total RNA was isolated from heart ventricles using RNeasy Fibrous Tissues Kit (Qiagen) following manufacturer's instructions

treatment_protocol: At either two or ten weeks after tamoxifen induction, heart ventricles were removed and snap frozen in liquid nitrogen

tag: develolpmental stage

value: neonatal

tag: tissue type

value: whole animal

value: mixed 129Sv and C57BL/6

source_name: heart, 10 week post tamoxifen

tag: genotype

value: heart


title: heart_Acsl1H-/-_2w_rep2

description:
Acsl1HKO_2w_02
Biological replicate 2 of 3

source_name: heart, 2 week post tamoxifen


title: heart_Acsl1flox_2w_rep2

description:
Acsl1flox_2w_02
Biological replicate 2 of 4


title: heart_Acsl1H-/-_10w_rep3

description:
Acsl1HKO_10w_03
Biological replicate 3 of 4


title: heart_Acsl1H-/-_10w_rep4

description:
Acsl1HKO_10w_04
Biological replicate 4 of 4


title: heart_Acsl1flox_2w_rep4

description:
Acsl1flox_2w_04
Biological replicate 4 of 4


title: heart_Acsl1H-/-_10w_rep1

description:
Acsl1HKO_10w_01
Biological replicate 1 of 4


title: heart_Acsl1flox_2w_rep1

description:
Acsl1flox_2w_01
Biological replicate 1 of 4


title: heart_Acsl1flox_10w_rep2

description:
Acsl1flox_10w_02
Biological replicate 2 of 4


title: heart_Acsl1H-/-_2w_rep1

description:
Acsl1HKO_2w_01
Biological replicate 1 of 3


title: heart_Acsl1flox_2w_rep3

description:
Acsl1flox_2w_03
Biological replicate 3 of 4


title: heart_Acsl1flox_10w_rep4

description:
Acsl1flox_10w_04
Biological replicate 4 of 4


title: 5624867020_A

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

source_name: Cortical: WT ovx+E

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: 15-week old C57BL/6 female mice with deletion of ERα-AF1 or wild type were used.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were ovariectomized and injected subcutaneously one week later with either E2 (115 µg/kg body weight) or olive oil vehicle (Apoteksbolaget, Göteborg, Sweden).  Mice were scarified after 18 hours of treatment and RNA was isolated from either long bone shafts (flushed femora and tibiae) or vertebral bodies (L5+L6) using an RNAlater reagent (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

tag: tissue

value: cortical bone from femur

tag: Sex

value: female

value: 15 weeks

value: WT

tag: treated with


title: 5624867019_E

description: replicate 5


title: 5624867026_G

description: replicate 4

source_name: Cortical: KO ovx+E

value: Era-AF1 KO


title: heart_Acsl1flox_10w_rep1

description:
Acsl1flox_10w_01
Biological replicate 1 of 4


title: 5624867019_F

description: replicate 5


title: 5624867020_B

description: replicate 1


title: 5624867006_H

description: replicate 2


title: 5624867006_A

description: replicate 2


title: 5624867004_G

description: replicate 3


title: 5624867006_B

description: replicate 2

source_name: Cortical: KO ovx+P

value: vehicle


title: 5624867026_H

description: replicate 4


title: 5624867004_A

description: replicate 3


title: 5624867020_C

description: replicate 1


title: 5624867026_F

description: replicate 4


title: 5624867004_H

description: replicate 3


title: 5624867019_G

description: replicate 5


title: 5624867019_H

description: replicate 5

source_name: Cortical: WT ovx+P


title: 5624867019_D

description: replicate 5

source_name: Trabecular: WT ovx+P

value: trabecular bone from vertebrae L5 and L6


title: 5624867020_H

description: replicate 1


title: 5624867026_E

description: replicate 4


title: 5624867004_F

description: replicate 3


title: 5624867004_B

description: replicate 3


title: 5624867006_C

description: replicate 2


title: 5624867020_D

description: replicate 1


title: 5624867026_C

description: replicate 4

source_name: Trabecular: KO ovx+E


title: 5624867019_C

description: replicate 5

source_name: Trabecular: KO ovx+P


title: 5624867026_A

description: replicate 4


title: 5624867006_G

description: replicate 2


title: 5624867026_D

description: replicate 4


title: 5624867004_E

description: replicate 3


title: Lib4

first: Sarah

last: Tarr

address: Keppel Street

country: United Kingdom

institute: LSHTM

description:
Paired with Sample 2
Sample 79
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv

data_processing:
Bases were called and adaptor sequences were removed using the Illumina MiSeq software
Sequence reads were mapped the P. falciparum 3D7 May 2015 v3.1 reference genome using hisat2 version 2.0.4 with parameters -p 16 -t -q --dta-cufflinks --phred33 -x.  Duplicate reads were marked but not removed using Picard.
Resulting bam files were filtered  to exclude reads with MAPQ scores < 60.
Reads were counted against our GTF_VarRifStev_filtered out.gtf annotation file and summarized, using the genomicAligments package in R (with the following settings: mode="Union", singleEnd=FALSE,ignore.strand=TRUE,fragments=FALSE).  Read counts were extracted from the assays accessor of the summarized experiment.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the FPKM function of the DESeq2 package in R
Genome_build: P. falciparum 3D7 v3 reference genome
Supplementary_files_format_and_content: Comma-separated values files for raw counts and FPKM values.  Supplied as matricies with all samples in each file.
Supplementary_files_format_and_content: 'allData…' processed files contain data for all 81 samples included in the study.
Supplementary_files_format_and_content: 'E64_Untr…' processed files contain data relevant to the paired E64-treatment versus control comparison.
Supplementary_files_format_and_content: 'isolateComparison...' processed files contain data relevant to differential expression comparisons between isolates.
Supplementary_files_format_and_content: allDataCounts.csv: Count abundance measurements for all samples in the study
Supplementary_files_format_and_content: allDataFPKMs.csv: Fragments per kilobase per million measurements for all samples in the study
Supplementary_files_format_and_content: E64_Untr_Counts.csv: Count abundance measurements relevant to the paired E64-treatment versus control comparison.
Supplementary_files_format_and_content: E64_Untr_FPKMs.csv: Fragments per kilobase per million measurements relevant to the paired E64-treatment versus control comparison.
Supplementary_files_format_and_content: isolateComparisonCounts.csv: Count abundance measurements for 71 libraries relevant to differential expression comparisons between isolates.
Supplementary_files_format_and_content: isolateComparisonFPKMs.csv: Fragments per kilobase per million measurements for 71 libraries relevant to differential expression comparisons between isolates.

organism: Plasmodium falciparum

source_name: Schizonts

extract_protocol:
RNA was harvested from packed schizont pellets using Trizol reagent. Illumina TruSeq stranded RNA library Prep Kit was used with 0.3-1 ug of total RNA for the construction of sequencing libraries.
Stranded mRNA TruSeq libraries were prepared for sequencing using the standard Illumina protocol for this library type with a MiSeq sequencer

tag: purification

value: Percoll

value: Untreated

tag: isolate type

value: Laboratory-adapted


title: Lib62

description:
Unpaired
Sample 80
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv

value: MACS

tag: strain


title: 5624867019_A

description: replicate 5

source_name: Trabecular: WT ovx+E


title: 5624867020_G

description: replicate 1


title: 5624867006_E

description: replicate 2


title: 5624867004_C

description: replicate 3


title: 5624867019_B

description: replicate 5


title: 5624867006_D

description: replicate 2


title: 5624867020_E

description: replicate 1


title: 5624867006_F

description: replicate 2


title: 5624867020_F

description: replicate 1


title: 5624867026_B

description: replicate 4


title: INV296-7

description:
Unpaired
Sample 74
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv

value: Clinical


title: INV271-8

description:
Unpaired
Sample 75
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib29

description:
Paired with Sample 19
Sample 77
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv


title: INV296-8

description:
Unpaired
Sample 76
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib32

description:
Paired with Sample 21
Sample 78
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv


title: INV271-3

description:
Unpaired
Sample 72
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV293-14

description:
Unpaired
Sample 71
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV286-7

description:
Unpaired
Sample 66
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV280-10

description:
Unpaired
Sample 65
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV286-8

description:
Unpaired
Sample 67
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV286-9

description:
Unpaired
Sample 68
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV286-10

description:
Unpaired
Sample 69
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib7

description:
Paired with Sample 3
Sample 81
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv


title: INV293-12

description:
Unpaired
Sample 70
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: 5624867004_D

description: replicate 3


title: INV280-9

description:
Unpaired
Sample 63
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV280-1

description:
Unpaired
Sample 60
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV296-1

description:
Unpaired
Sample 61
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV271-7

description:
Unpaired
Sample 56
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV286-1

description:
Unpaired
Sample 58
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV286-4

description:
Unpaired
Sample 59
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV271-9

description:
Unpaired
Sample 57
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV293-8

description:
Unpaired
Sample 55
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV293-7

description:
Unpaired
Sample 54
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV271-5

description:
Unpaired
Sample 73
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV278-13

description:
Unpaired
Sample 53
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV280-5

description:
Unpaired
Sample 64
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV278-3

description:
Unpaired
Sample 45
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV280-3

description:
Unpaired
Sample 62
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV293-4

description:
Unpaired
Sample 44
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV293-2

description:
Unpaired
Sample 43
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV278-14

description:
Unpaired
Sample 49
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib74

description:
Unpaired
Sample 41
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV278-5&8

description:
Unpaired
Sample 46
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV278-12

description:
Unpaired
Sample 47
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib66

description:
Unpaired
Sample 38
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV296-5

description:
Unpaired
Sample 48
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib69

description:
Unpaired
Sample 39
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib73

description:
Unpaired
Sample 40
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib63

description:
Unpaired
Sample 42
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib71

description:
Unpaired
Sample 35
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib68

description:
Unpaired
Sample 34
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib59

description:
Unpaired
Sample 31
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib61

description:
Unpaired
Sample 32
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib65

description:
Unpaired
Sample 33
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV271-4

description:
Unpaired
Sample 52
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV280-4

description:
Unpaired
Sample 51
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib53

description:
Unpaired
Sample 28
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib55

description:
Unpaired
Sample 29
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib58

description:
Unpaired
Sample 30
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib43

description:
Unpaired
Sample 27
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: INV296-9

description:
Unpaired
Sample 50
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib39

description:
Unpaired
Sample 26
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib36

description:
Unpaired
Sample 24
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib35

description:
Unpaired
Sample 23
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib54

description:
Unpaired
Sample 37
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib34

description:
Unpaired
Sample 22
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib33

description:
Paired with Sample 78
Sample 21
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv


title: Lib72

description:
Unpaired
Sample 36
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib27

description:
Unpaired
Sample 17
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib31

description:
Unpaired
Sample 20
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: heart_Acsl1H-/-_10w_rep2

description:
Acsl1HKO_10w_02
Biological replicate 2 of 4


title: heart_Acsl1H-/-_2w_rep3

description:
Acsl1HKO_2w_03
Biological replicate 3 of 3


title: Lib26

description:
Unpaired
Sample 16
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib22

description:
Unpaired
Sample 12
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib24

description:
Unpaired
Sample 14
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib20

description:
Unpaired
Sample 10
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib21

description:
Unpaired
Sample 11
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib23

description:
Unpaired
Sample 13
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib19

description:
Unpaired
Sample 9
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib17

description:
Unpaired
Sample 8
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib16

description:
Unpaired
Sample 7
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib14

description:
Unpaired
Sample 6
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib1

description:
Unpaired
Sample 1
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib12

description:
Unpaired
Sample 4
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib5

description:
Paired with Sample 79
Sample 2
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv


title: Lib6

description:
Paired with Sample 81
Sample 3
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv


title: Lib13

description:
Unpaired
Sample 5
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib37

description:
Unpaired
Sample 25
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib30

description:
Paired with Sample 77
Sample 19
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv
E64_Untr_Counts.csv
E64_Untr_FPKMs.csv


title: Lib28

description:
Unpaired
Sample 18
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: Lib25

description:
Unpaired
Sample 15
allDataCounts.csv
allDataFPKMs.csv
isolateComparisonCounts.csv
isolateComparisonFPKMs.csv


title: DCB_WT_3d_3

city: Basel

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: cRNA synthesis, target hybridization, washing, staining and subsequent probe array scanning was done according to the manufacturer's instructions (3'IVT Express Kit User Manual Affymetrix)

scan_protocol: Scanner 3000 7G; Software AGCC (Affymetrix GeneChip Command Console) version 4.0

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

source_name: liver, 1,4-Dichlorobenzene, 600 mg/kg, 3 days

label_protocol: Labeling according to 3'IVT Express Kit User Manual Affymetrix

growth_protocol: Adult male mice (mus muculus), wild-type, or humanised or deleted for CAR and PXR on a C57BL/6J background were treated with 1,4-Dichlorobenzene for 3d (daily, 600mg/kg, oral gavage); cyproterone acetate for 3d (daily, 160mg/kg, oral gavage).

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany).

treatment_protocol: One day after 3 days treatment, mice were sacrificed by a rising concentration of carbon dioxide, and subject to necropsy to remove the liver, which was rinsed in sterile phosphate-buffered saline, snap-frozen in liquid nitrogen and stored at -80oC.

tag: gender

value: male

value: liver

tag: treatment short name

value: DCB

tag: treatment full name

tag: treatment duration [days]

tag: treatment dose

value: 600 mg/kg

tag: group

value: DCB WT 3d

tag: corresponding control

value: CO WT 3d


title: DCB_WT_3d_2


title: IRF8-/- BMDM infected with Salmonella typhimurium, rep 1

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

source_name: bone marrow derived macrophages infected for 4 hour with Salmonella typhimurium

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671)

growth_protocol: Primary BMDMs were grown for 6 days in DMEM (Gibco) supplemented with 1% non-essential amino acids (Gibco), 10% FBS (Atlanta Biologicals), 30% medium conditioned by L929 mouse fibroblasts, and 1% penicillin and streptomycin (Sigma).

extract_protocol: Total RNA was extracted using the Trizol according to the manufacturer's recommended methods

treatment_protocol: BMDMs in antibiotic–free medium were seeded onto 12-well plates at a density of 1 × 106 cells per well, followed by incubation overnight. Cells were then infected with Salmonella typhimurium (0.1 moi) and cultured for an additional 4 hours before extracting total RNA.

tag: genotype/variation


title: IRF8-/- BMDM infected with Salmonella typhimurium, rep 2


title: DCB_hCAR/hPXR_3d_3

value: DCB hCAR/hPXR 3d

value: CO hCAR/hPXR 3d


title: CPA_WT_6d_3

source_name: liver, Cyproterone acetate, 160 mg/kg, 6 days

value: CPA

value: Cyproterone acetate

value: 160 mg/kg

value: CPA WT 6d


title: Wild-type BMDM infected with Salmonella typhimurium, rep 1

value: Wild-type


title: DCB_CARko/PXRko_3d_3

value: DCB CARko/PXRko 3d

value: CO CARko/PXRko 3d


title: CPA_WT_6d_2


title: DCB_CARko/PXRko_3d_1


title: DCB_hCAR/hPXR_3d_1


title: Wild-type BMDM infected with Salmonella typhimurium, rep 2


title: KC_pre_3D_HLK_d3_rep3

city: Blacksburg

first: T. M.

last: Murali

state: VA

address: 225 Stanger St.

department: Department of Computer Science

institute: Virginia Tech

hyb_protocol: GeneChip Rat Genome Arrays are hybridized with 15 ug of fragmented aRNA. The hybridization, staining, and washing are carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit (P/N 900720) following the manufacturer’s protocols.  The arrays are hybridized for 16 hr at 45oC using Affymetrix Hybridization Oven 640 (P/N 800139).  FS450_0001 protocol is used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G using GCOS and software and Affymetrix preset settings.

data_processing: Samples were processed using RMA for background correction, quantile normalization and probe summarization. The quality of the samples was evaluated using the Simpleaffy package in R.

label_protocol: Samples of 500 pg-50 ng are amplified using NuGen Ovation Pico WTA system (#3300, 4200, NuGen Technologies, San Carlos, CA) following manufacturer’s protocols.

extract_protocol: Total RNA was extracted from each cell type using an RNeasy mini kit (Qiagen). Total RNA was converted into double-stranded complementary DNA using a T7-oligo (dT) primer (5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG–(dT)24–3′) and reverse transcription.

tag: culture system

value: 3D_HLK (pre)

tag: time

tag: cell type

value: Kupffer cell


title: DCB_WT_3d_1

value: male

tag: tissue


title: DCB_CARko/PXRko_3d_2

value: liver


title: DCB_hCAR/hPXR_3d_2

value: DCB


title: KC_pre_3D_HLK_d3_rep1


title: KC_3D_HLK_d12_rep1


title: CPA_CARko/PXRko_3d_1

source_name: liver, Cyproterone acetate, 160 mg/kg, 3 days

value: CPA CARko/PXRko 3d


title: CPA_CARko/PXRko_3d_2


title: CPA_CARko/PXRko_3d_3


title: KC_3D_HLK_d12_rep2


title: CPA_WT_6d_1


title: CPA_hCAR/hPXR_6d_3

value: CPA hCAR/hPXR 6d


title: KC_pre_3D_HLK_d3_rep2


title: CPA_hCAR/hPXR_6d_2


title: CPA_hCAR/hPXR_6d_1


title: LSEC_3D_HLK_d12_rep1

value: LSEC


title: LSEC_3D_HLK_d12_rep3


title: LSEC_3D_HLK_d12_rep2


title: CO_PXRko_3d_2

source_name: liver, Corn oil, 0 mg/kg, 3 days

value: CO

value: Corn oil

value: 0 mg/kg

value: CO PXRko 3d


title: CO_WT_3d_2

value: CO WT 3d


title: CO_WT_3d_3


title: CO_WT_3d_1


title: CO_PXRko_3d_1


title: LSEC_3D_HL_d12_rep2


title: LSEC_3D_HL_d12_rep3


title: Hep_3D_HLK_d12_rep3

value: Hepatocyte


title: CO_hCAR/hPXR_3d_3

value: CO hCAR/hPXR 3d


title: CO_PXRko_3d_3


title: CO_hCAR/hPXR_3d_1


title: LSEC_3D_HL_d12_rep1


title: Hep_3D_HL_d12_rep3


title: Hep_3D_HL_d12_rep2


title: CO_hCAR/hPXR_3d_2


title: PB_90d_4

source_name: liver, Phenobarbital, 80 mg/kg/day, 90 days

growth_protocol: CD-1 male mice were orally treated with 0,5% methylcellulose 15 (Dow Chemicals)  as vehicle control or 80 mg/kg/day Phenobarbital sodium (CAS 57-30-7)

treatment_protocol: The mice received a daily administration with 10 mL/kg of compound solution for 28 or 90 days. On the day after the last treatment, the animals were aneasthetized in isoflurane and exanguinated from the heart and subjected to necropsy. The left lateral liver lobe was isolated and snap frozen under -80°C conditions.

value: PB

value: Phenobarbital

tag: treatment dose [mg/kg/day]

value: PB 90d

value: CMC 90d


title: Hep_3D_HL_d12_rep1


title: CS_d12_rep2

value: collagen sandwich


title: CO_CARko/PXRko_3d_1

value: male

value: liver

value: CO CARko/PXRko 3d


title: CO_CARko/PXRko_3d_2


title: PB_90d_5


title: Hep_3D_HLK_d12_rep2


title: Hep_3D_HLK_d12_rep1


title: CO_CARko/PXRko_3d_3


title: CS_d12_rep1


title: EGF_CITCO_SiPXR_3 (PXR)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix® HG-U133+PM Array. StripChips were washed and stained on the fluidic station of the Affymetrix GeneAtlas system with HWS kit.

scan_protocol: GeneChips were washed stained and scanned using the Affymetrix GeneAtlas system.

data_processing: Raw data was RMA normalized using the limma package for R/Bioconductor.

source_name: liver, CITCO, EGF+, SiPXR

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneAtlas IVT PLUS protocol from 100 ng total RNA (GeneChip® 3'IVT PLUS Reagent Kit,P/N703210 Rev1 Affymetrix).

growth_protocol: Primary Human Hepatocytes were seeded in collagen-coated 24 well plates, maintained at confluence and cultured in a 5% CO2 humidified atmosphere at 37°C. Cells were maintained in Hepatocyte growth medium (HGM) (WME medium supplemented with 5µg/ml insulin, 0.1µM hydrocortisone, 10µg/ml transferrin, 250µg/ml ascorbic acid, 3.75mg/ml fatty acid free bovine serum albumin, penicillin, streptomycin, and glutamine). HGM was supplemented with EGF 10ng/ml in the +EGF condition

treatment_protocol: Primary Human Hepatocytes were transfected with targeting siRNA (si control (siCT) or siPXR) at D2 and D5 after plating. At D5, cells were treated with 1µM CITCO, 0.5mM PB or DMSO for 24h.

tag: donor id

value: primary hepatocyte

value: CITCO

tag: medium

value: EGF+

tag: sirna

value: SiPXR


title: HM_d12_rep1

value: hepatocyte monolayer


title: HM_d12_rep3


title: CS_d12_rep3


title: EGF_CITCO_SiPXR_4 (PXR)


title: EGF_CITCO_SiPXR_5 (PXR)


title: PB_90d_3

tag: strain


title: EGF_CITCO_SiPXR_2 (PXR)


title: EGF_CITCO_SiCT_5 (PXR)

source_name: liver, CITCO, EGF+, SiCT

value: SiCT


title: PB_90d_1

tag: gender


title: PB_90d_2

tag: treatment short name


title: EGF_CITCO_SiPXR_1 (PXR)


title: HM_d12_rep2


title: CMC_90d_3

source_name: liver, Methylcellulose 15, 0 mg/kg/day, 90 days

value: CMC

tag: treatment full name

value: Methylcellulose 15


title: CMC_90d_4

tag: treatment duration [days]


title: CMC_90d_2


title: PB_28d_5

source_name: liver, Phenobarbital, 80 mg/kg/day, 28 days

value: PB 28d

value: CMC 28d


title: CMC_90d_1


title: EGF_CITCO_SiCT_4 (PXR)


title: CMC_90d_5


title: EGF_CITCO_SiCT_2 (PXR)


title: EGF_CITCO_SiCT_1 (PXR)


title: co ass rep3

city: CAGLIARI

first: AMEDEO

last: COLUMBANO

address: VIA PORVELL 4

department: DIPARTIMENTO DI SCIENZE BIOMEDICHE

institute: UNIVERSITA' DEGLI STUDI DI CAGLIARI

description:
9700842112_A
Biological replicates 4

data_processing: The data were normalized using quantile normalization with Illumina BeadStudio 3.0.19.0 software (Illumina Inc) and BRB Array Tools (Version 4.6.0)

label: Biotin

source_name: Female, Liver

growth_protocol: Female C3H mice (25-30 g) were obtained from Charles River, Milano, Italy. Guidelines for Care and Use of Laboratory Animals were followed during the investigation. All animal procedures were approved by the Ethical Commission of the University of Cagliari and the Italian Ministry of Health.

extract_protocol: RNA was extracted from microdissected samples using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific)

treatment_protocol:
Experimental Protocol 1. Mice were injected intraperitoneally (i.p.) with DENA at a dose of 90 mg/kg body weight. After a 1-week recovery period, mice were treated intragastrically (i.g.) with TCPOBOP, (3 mg/kg body weight, Sigma) once/week for 28 weeks. Another group was given only TCPOBOP (once/week) for 28 and 42 weeks. Matched-aged mice treated with DMSO dissolved in corn oil were used as controls. The animals were euthanized at 28 and 42 weeks, respectively, time points when HCCs were observed in both the regimen protocols.
Experimental Protocol 2. Mice were treated with TCPOBOP, (3 mg/kg body weight) once/week for 1, 12, 16, and 21 weeks.

value: Liver

value: Female


title: EGF_CITCO_SiCT_3 (PXR)


title: co ass rep1

description:
9700842075_F
Biological replicates 4


title: co ass rep2

description:
9700842110_A
Biological replicates 4


title: Tcp 28 w rep2

description:
9700842075_E
Biological replicates 3


title: Tcp 28 w rep3

description:
9700842112_B
Biological replicates 3


title: EGF_PB_SiPXR_5 (PXR)

source_name: liver, Phenobarbital, EGF+, SiPXR

value: Phenobarbital


title: EGF_PB_SiPXR_3 (PXR)


title: Tcp 28 w rep1

description:
9700842074_F
Biological replicates 3


title: EGF_PB_SiPXR_2 (PXR)


title: EGF_PB_SiPXR_4 (PXR)


title: Dena +Tcp rep7

description:
9700842112_D
Biological replicates 2


title: EGF_PB_SiCT_4 (PXR)

source_name: liver, Phenobarbital, EGF+, SiCT


title: Dena +Tcp rep9

description:
9700842112_F
Biological replicates 2


title: H3K4me3 ChIP-seq, Spo11(-/-) adult

city: Bethesda

first: Galina

last: Petukhova

state: Maryland

address: 4301 Jones Bridge Rd

department: Biochemistry

institute: USUHS

description: NextSeq 500

data_processing:
Base-calls performed using CASAVA
All the reads sequenced at NextSeq500 is processed using bcl2fastq with default parameters
reads alligned with BWA(0.7.12), bigwigs made with deeptools(1.5.11)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig

source_name: Testis

extract_protocol:
DNA was extracted from whole testis after sonication
ChIP was performed on fixed tissue

value: Testis

tag: antibody

value: Millipore (#07-473)

tag: genotype

value: Spo11 KO


title: PB_28d_4

value: male

value: liver

value: PB

tag: group

tag: corresponding control


title: PB_28d_1


title: EGF_PB_SiPXR_1 (PXR)

value: primary hepatocyte

value: EGF+


title: CMC_28d_5

source_name: liver, Methylcellulose 15, 0 mg/kg/day, 28 days


title: Dena +Tcp rep8

description:
9700842112_E
Biological replicates 2


title: Dena +Tcp rep5

description:
9700842110_E
Biological replicates 2


title: EGF_PB_SiCT_2 (PXR)


title: EGF_UT_SiPXR_5 (PXR)

source_name: liver, none, EGF+, SiPXR

value: SiPXR


title: CMC_28d_1


title: CMC_28d_3


title: PB_28d_3


title: Dena +Tcp rep2

description:
9700842074_E
Biological replicates 2


title: CMC_28d_4


title: Dena +Tcp rep1

description:
9700842074_D
Biological replicates 2


title: Dena +Tcp rep3

description:
9700842110_C
Biological replicates 2


title: Dena +Tcp rep4

description:
9700842110_D
Biological replicates 2


title: Dena +Tcp rep6

description:
9700842110_F
Biological replicates 2


title: CMC_28d_2


title: EGF_PB_SiCT_1 (PXR)

value: SiCT


title: PB_28d_2


title: EGF_PB_SiCT_3 (PXR)


title: EGF_PB_SiCT_5 (PXR)


title: H3K4me3 ChIP-seq, Prdm9(K/K)

description: NextSeq 500

value: Prdm9 (K/K) (lacks KRAB domain)


title: H3K4me3 ChIP-seq, GC-1 ZincF #1

description: NextSeq 500

source_name: Spg GC-1 cell line

extract_protocol: ChIP was performed on fixed tissue

value: BALB/c

value: Spg GC-1 cell line

value: SPG GC-1 cells expressing GFP-PRDM9-ZincF


title: input, GC-1 WT

description: NextSeq 500

value: SPG GC-1 cells expressing GFP-PRDM9-WT


title: H3K4me3 ChIP-seq, GC-1 SSXRD #2

description: NextSeq 500

value: SPG GC-1 cells expressing GFP-PRDM9-SSXRD


title: H3K4me3 ChIP-seq, GC-1 SSXRD #1

description: NextSeq 500


title: H3K4me3 ChIP-seq, GC-1 ZincF #2

description: NextSeq 500


title: H3K4me3 ChIP-seq, GC-1 KRAB-2

description: NextSeq 500

value: SPG GC-1 cells expressing GFP-PRDM9-KR-SSX


title: H3K4me3 ChIP-seq, GC-1 KRAB-1 #3

description: NextSeq 500

value: SPG GC-1 cells expressing GFP-PRDM9-KRAB


title: H3K4me3 ChIP-seq, GC-1 KRAB-1 #2

description: NextSeq 500

value: Millipore (#07-473)


title: H3K4me3 ChIP-seq, GC-1 KRAB-1 #1

description: NextSeq 500


title: H3K4me3 ChIP-seq, GC-1 SET #2

description: NextSeq 500

value: SPG GC-1 cells expressing GFP-PRDM9-SET


title: EGF_UT_SiPXR_4 (PXR)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: Tcp 42 w rep6

description:
9700842075_C
Biological replicates 1

value: Liver

value: Female


title: EGF_UT_SiPXR_3 (PXR)

value: liver


title: EGF_UT_SiPXR_2 (PXR)

value: primary hepatocyte


title: Tcp 42 w rep5

description:
9700842075_B
Biological replicates 1


title: Mouse lung tumors harboring KrasLSL-G12D mutation rep 2

city: Worcester

first: George

last: Acquaah-Mensah

state: MA

address: 19 Foster Street

institute: MASS COLLEGE OF PHARM HEALTH SCIENCES

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the 'affy' Bioconductor R package.

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Tumor bearing lungs from 8-10 weeks old krasLSL-G12D_CC10 cre mice and control non-tumor (wild type)  lungs were collected from mice.

extract_protocol: Total RNA was isolated using TRIZOl reagent. RNA was further purified using RNeasy kit from Qiagen, quantified. Quality of RNA was evaluated using Bio-analyzer.

value: lung

value: Kras LSL-G12D CC10-Cre

tag: age

value: 8-10 weeks


title: Mouse lung tumors harboring KrasLSL-G12D mutation rep 4


title: Mouse lung tumors harboring KrasLSL-G12D mutation rep 5


title: Tcp 42 w rep3

description:
9700842074_C
Biological replicates 1


title: H3K4me3 ChIP-seq, GC-1 SET #1

description: NextSeq 500


title: Tcp 42 w rep7

description:
9700842075_D
Biological replicates 1


title: Mouse lung tumors harboring KrasLSL-G12D mutation rep 3


title: EGF_UT_SiCT_4 (PXR)

source_name: liver, none, EGF+, SiCT

value: EGF+

value: SiCT


title: EGF_UT_SiCT_1 (PXR)


title: Tcp 42 w rep2

description:
9700842074_B
Biological replicates 1


title: Tcp 42 w rep1

description:
9700842074_A
Biological replicates 1


title: NoEGF_CITCO_SiPXR_5 (PXR)

source_name: liver, CITCO, EGF-, SiPXR

value: CITCO

value: EGF-

value: SiPXR


title: EGF_UT_SiCT_5 (PXR)


title: EGF_UT_SiCT_3 (PXR)


title: EGF_UT_SiCT_2 (PXR)


title: Mouse lung tumors harboring KrasLSL-G12D mutation rep 1


title: EGF_UT_SiPXR_1 (PXR)


title: NoEGF_CITCO_SiPXR_4 (PXR)


title: Non-tumor-bearing mouse lung sample rep 3

source_name: Non-tumor-bearing mouse lung

value: wildtype


title: H3K4me3 ChIP-seq, GC-1 WT #3

description: NextSeq 500

value: BALB/c

value: Spg GC-1 cell line

value: SPG GC-1 cells expressing GFP-PRDM9-WT


title: NoEGF_CITCO_SiPXR_3 (PXR)


title: Tcp 42 w rep4

description:
9700842075_A
Biological replicates 1


title: H3K4me3 ChIP-seq, GC-1 WT #1

description: NextSeq 500

value: Millipore (#07-473)


title: AAV-TBG-Y67F FXR #3

city: Urbana

first: Young-Chae

last: Kim

state: IL

address: 394 Burrill Hall  407 S. Goodwin Ave

department: MIP

institute: University of Illinois at Urbana-Champaign

data_processing:
Using a HiSeq SBS sequencing kit version 4, Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Trimmomatic ver 0.36 was used to remove sequence adapters and low-quality bases and quality control was checked by FastQC ver 0.11.5
Sequencing alignment was performed by STAR ver 2.5.3a.
The differential expression profiles of RNA-seq were analyzed by the edgeR-based R (ver 3.4.1) pipeline
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include fold change, FDR between two conditions generated by edgeR

source_name: FXR floxed mice

extract_protocol:
RNA from the livers was isolated with the RNeasy Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols. The cDNA library was sequenced using an Illumina HiSeq2000 (Illumina, San Diego, CA) to produce paired-end 100 bp reads.

treatment_protocol: Eight week-old FXR floxed male mice were injected via the tail vein with 100 µl of a mixture of purified AAV serotype 8 (AAV8) containing a liver-specific TBG promoter driving Cre recombinase and either AAV8-TBG-FXR WT or AAV8-TBG-Y67F-FXR at 5 x1010 virus particles per mouse, and four weeks later, mice were fed 0.5% CA chow for 6 h to activate FXR signaling

value: male

tag: cells

tag: genotype/variation

value: AAV-TBG-Cre with AAV-TBG-Y67F FXR


title: AAV-TBG-Y67F FXR #1

value: liver


title: bulk1

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: bulk mRNAseq

data_processing:
Sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants.
The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices.
Bulk mRNA reads were mapped with STAR. Gene counts were computed with htseq-count.
Genome_build: Mus musculus 10
Supplementary_files_format_and_content: Digital Gene Expression matrices contain UMI counts per cell and per gene. Htseq-counts measure gene abundances in mRNA samples (read counts)

source_name: bulk mRNAseq of whole isolated glomeruli

extract_protocol: Stand-specific cDNA libraries were generated according to the Illumina TruSeq protocol (TruSeq Stranded mRNA LT Sample Prep Kit, Illumina) using 500 ng of total RNA extracted from glomeruli lysate.

tag: developmental stage

value: 8 week old males

tag: tissue type

value: whole isolated glomeruli

value: CD1 IGS outbred

tag: fixation

value: live samples; no fixation


title: bulk2

description: bulk mRNAseq

source_name: bulk mRNAseq of dissociated glomerular cells

extract_protocol: Stand-specific cDNA libraries were generated according to the Illumina TruSeq protocol (TruSeq Stranded mRNA LT Sample Prep Kit, Illumina) using 95 ng of total RNA from sorted, fixed single cells from dissociated glomeruli.

value: dissociated glomerular cells

value: 80% methanol/PBS


title: glom_rep4

description: single-cell transcriptomics

source_name: Drop-seq of whole isolated glomeruli

extract_protocol: Drop-seq (Alles et al BMC Biol 15; adapted from Macosko et al 2015 Cell 161)


title: glom_rep3

description: single-cell transcriptomics


title: H3K4me3 ChIP-seq, GC-1 WT #2

description: NextSeq 500

tag: tissue


title: AAV-TBG-WT FXR #3

value: AAV-TBG-Cre with AAV-TBG-WT FXR


title: AAV-TBG-WT FXR #2


title: AAV-TBG-WT FXR #1


title: Non-tumor-bearing mouse lung sample rep 1

value: lung

value: 8-10 weeks


title: glom_rep2

description: single-cell transcriptomics


title: AAV-TBG-Y67F FXR #2


title: Mouse wild type erythroid cells replicate 1

city: Oxford

first: Jelena

middle: M

last: Telenius

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington

department: Weatherall Institute of Molecular Medicine (WIMM)

institute: Oxford University

description:
Genes analysed: genome-wide
Nascent RNA

data_processing:
Mapping of reads in tophat (vs1.1.4b), with parameters -r 200 (inner-mate-distance).
Filtering of ribosomal regions (from RepeatMasker), and Blacklisted regions.
Counting genome-wide coverages of read pairs, in 4kb bins.
Transforming the coverages bedgraph to bigwig file (ucsctools bedGraphToBigWig).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: genomeWideCoverage_4kb_bins.bw: bigwig file of genome-wide read pair coverage, in 4kb bins.

source_name: Erythroid cells

growth_protocol: Fetal livers were dissected from E12.5 mouse embryos, and the dissociated cell suspension was expanded for 5-7 d in Stempro (Invitrogen) supplemented with Epo (1 U/ml), SCF (50 ng/ml) and dexamethasone (1 uM). After expansion of the cultures, mature red blood cells were removed by negative selection for Ter119 using anti-Ter119 magnetic beads (Miltenyi Biotec), to obtain a population of erythroid precursors. Cultures were then switched to medium containing a high Epo concentration (5 U/ml) to induce differentiation into mature erythroid cells.

extract_protocol:
Samples for nascent RNA were collected after 12 h of differentiation. Cells were lysed in TRI Reagent (Sigma), and RNA was extracted according to the manufacturer's instructions. Samples were treated with DNase I using Turbo DNA-free DNase (Ambion). To obtain nascent RNA, fetal liver cultures were pulsed with 50 uM 4-thiouridine (Sigma) for 1 h followed by immediate lysis in TRI Reagent. Nascent RNA was then extracted according to the method described by Dölken et al. (Dölken, L. et al. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14, 1959-1972 (2008)).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

tag: strain/background

value: Mixed

value: Wild type

tag: cell type

value: Erythroid

tag: tissue origination

value: Fetal liver


title: Non-tumor-bearing mouse lung sample rep 2

value: wildtype


title: NoEGF_CITCO_SiCT_4 (PXR)

source_name: liver, CITCO, EGF-, SiCT

tag: donor id

value: primary hepatocyte

value: CITCO

tag: medium

value: EGF-

tag: sirna

value: SiCT


title: NoEGF_CITCO_SiCT_3 (PXR)

value: liver


title: NoEGF_CITCO_SiPXR_1 (PXR)

value: SiPXR


title: NoEGF_CITCO_SiCT_5 (PXR)


title: NoEGF_CITCO_SiCT_2 (PXR)


title: NoEGF_CITCO_SiCT_1 (PXR)


title: NoEGF_PB_SiPXR_3 (PXR)

source_name: liver, Phenobarbital, EGF-, SiPXR

value: Phenobarbital


title: glom_rep1

description: single-cell transcriptomics

value: 8 week old males

value: dissociated glomerular cells

tag: strain

value: CD1 IGS outbred


title: NoEGF_PB_SiPXR_4 (PXR)


title: NoEGF_PB_SiPXR_1 (PXR)


title: KON_02

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Mus musculus GRCm38.p4 genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file.
Raw counts of mapped reads of each genes were derived using HTseq count.
DESeq2 was used for differential expression analysis.
Genome_build: Mus musculus GRCm38.p4 genome
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts for each Sample.

source_name: connective tissue

growth_protocol: MEFs are cultured in Dulbecco’s modified Eagle medium (DMEM) with high glucose (Sigma), 10% fetal bovine serum (Sigma) and 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma), in a humidified incubator with 5% CO2 at 37 Deg.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: MEFs were induced to neurons by the protocol described in the method for 20 days.

value: BALB/c

value: Actb -/-

value: 10.5 day old embryos

value: Chemically induced neurons from MEFs


title: HETN_03

value: Actb +/-


title: NoEGF_PB_SiCT_1 (PXR)

source_name: liver, Phenobarbital, EGF-, SiCT


title: NoEGF_PB_SiCT_2 (PXR)


title: KON_03


title: NoEGF_UT_SiPXR_5 (PXR)

source_name: liver, none, EGF-, SiPXR


title: NoEGF_CITCO_SiPXR_2 (PXR)


title: NoEGF_PB_SiCT_5 (PXR)


title: NoEGF_UT_SiPXR_4 (PXR)


title: HETN_02


title: HETN_01


title: NoEGF_UT_SiPXR_2 (PXR)


title: KON_01


title: WTN_03

value: Actb +/+


title: NoEGF_PB_SiCT_3 (PXR)


title: NoEGF_PB_SiPXR_2 (PXR)


title: NoEGF_UT_SiPXR_3 (PXR)


title: NoEGF_UT_SiCT_5 (PXR)

source_name: liver, none, EGF-, SiCT


title: NoEGF_PB_SiPXR_5 (PXR)


title: NoEGF_UT_SiPXR_1 (PXR)


title: WTN_01


title: WTN_02


title: NoEGF_UT_SiCT_4 (PXR)


title: NoEGF_PB_SiCT_4 (PXR)


title: H3K4me3 ChIP-seq, WT adult

data_processing:
Base-calls performed using CASAVA
reads alligned with BWA(0.7.12), bigwigs made with deeptools(1.5.11)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig

source_name: Testis

value: Testis

tag: antibody

value: Millipore (#07-473)

tag: genotype

value: Wild type


title: H3K4me3 ChIP-seq, GC-1 Pretransfection

description: NextSeq 500

value: Spg GC-1 cell line

value: pre-transfected SPG GC-1 cells


title: SSDS Prdm9(K/K)

data_processing:
Base-calls performed using CASAVA
Prdm9_krab_SSDS_type1.bed were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420). with the following parameters:--ratio [output from NCIS]  -g mm --bw 1000 --keep-dup all --slocal 5000
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: one bed file with aligned reads and one bed file with called peaks.

value: Prdm9 (K/K) (lacks KRAB domain)