title: AdultHuman-Spermatocytes_17-11

city: San Antonio

first: Brian

last: Hermann

address: 1 UTSA Circle

institute: University of Texas at San Antonio

description:
single-cell
AdultHuman-Spermatocytes_17-11_barcodes.tsv
AdultHuman-Spermatocytes_17-11_genes.tsv
AdultHuman-Spermatocytes_17-11_matrix.mtx

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq. Trimmed FASTQ files (26bp Cell barcode and UMI Read1, 8bp i7 index, and 100bp Read2), were generated using the CellRanger mkfastq command (a 10X Genomics wrapper around BCL2Fastq).
Primary data analysis (alignment, filtering, and UMI counting) to determine gene transcript counts per cell (producing a gene-barcode matrix), quality control, clustering and statistical analysis were performed using CellRanger count (10X Genomics) and the hg19 (human), mm10 (mouse) or hg19+mm10 (human and mouse, for multiplet tests) genome assembly/annotation references
Outputs from multiple independent samples of single-cells were combined using CellRanger aggr (10X Genomics) based on mapped read counts to normalize sequencing depth and produce aggregated gene-barcode matrices and clustering models.
Genome_build: Human reference genome NCBI build 38 (GRCh38) or a combined hg19 (hGRC37) + Mouse reference genome NCBI build 38, GRCm38 (mm10) for multiplet tests
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

source_name: Adult testis

extract_protocol:
Suspensions of human seminiferous tubule cells were prepared from adult testicular tissue parenchyma by a two-step enzymatic digestion was as described previously (Hermann et al., 2007b; Hermann et al., 2009; Dovey et al., 2013). Briefly, testis tissue was digested with 2mg/ml collagenase type IV at 37oC with vigorous agitation, washed with HBSS to remove interstitial cells, followed by digestion with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I for 15 minutes at 37oC with trituration every 5 minutes, and quenched with 10% FBS. In all cases, cell suspensions were strained (40um pore size for mouse, 70um pore size for humans) and suspended in MEMα containing 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 106 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S), labeled with antibodies (see Key Resources Table), and subjected to FACS using  a FACS Aria (BD). Positive antibody labeling was determined by comparison to staining with isotype control antibodies. Human spermatogonia were isolated by sorting cells with the phenotype HLA-ABCnegative / CD49enegative / THY1dim / ITGA6+ / EpCAMdim dim. These markers were chosen because previous results indicate they specifically label undifferentiated spermatogonia, including some with colonization potential based on xenotransplantation (Dovey et al., 2013; Altman et al., 2014; Smith et al., 2014; Valli et al., 2014). Adult Human testis cells were also enriched for spermatocytes and spermatids based on sedimentation velocity at unit gravity (Romrell et al., 1976; Bellve et al., 1977). Briefly, testis cells (10^6-10^7) suspended in 2 ml of buffer plus 0.5% BSA were loaded onto a 50 ml gradient of 2-4% BSA (McCarrey et al., 1992) and allowed to sediment for 2.5 hr at 4°C. Approximately one hundred 0.5 ml fractions were then collected in microcentrifuge tubes and analyzed for content of spermatocytes or spermatids on the basis of morphology under phase contrast optics (which typically yields ≥85% purity). Fractions containing spermatocytes or spermatids were pooled separately, concentrated (to ~2 x106 cells/ml) and stored in buffer containing FBS on ice until use. Ultimately, sorted spermatoginia,Sta-Put-enriched spermatocytes and spermatids, or unselected spermatogenic cells from adult human testicular tissue were used for single-cell RNA-seq facilitated by the 10X Genomics Chromium Drop-Seq approach. Briefly, Cell suspensions were loaded into Chromium microfluidic chips with 3’ v2 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10X Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~8700 cells were loaded on the instrument with the expectation of collecting up to 5,000 GEMs containing single cells. For the multiplet test, equal numbers of mouse and human cells were loaded. GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
Single-cell 3' libraries were prepared according to manufacturer recommendations (v2 chemistry).

treatment_protocol: De-identified, surgical excess normal adult human testicular tissue was obtained through the Infertility Center of St. Louis from patients undergoing a diagnostic testicular biopsy (n=28) in preparation for microscopic vasectomy reversal (MVR) or testicular sperm extraction (TESE) for obstructive azoospermia with the informed consent of patients. Testicular tissue was also recovered from male organ donors (n=2) through the Texas Organ Sharing Alliance and the University of Texas Transplant Center with informed consent of the next of kin. The University of Texas at San Antonio IRB determined that research on these tissues did not constitute human subjects research (IRB #12-098N and #17-074N). The age of the individuals was recorded (median = 42yr, mean = 41.6 ± 1.3yr), and while organ donors tended to be younger (34.3 ± 7.2yr) than biopsy patients (42.4 ± 1.2yr), the difference was not significant (p=0.32). Procured tissue was transported to the laboratory on ice in either Lactated Ringer’s solution or minimal essential medium alpha (MEMα) containing 10% fetal bovine serum. The amount of time tissues were exposed to cold ischemia prior to processing was recorded (median = 18.7hr; mean = 24.7 ± 3.8 hr).

tag: number of cells

value: Sta-Put enriched Spermatocytes


title: AdultHuman-Spermatids_17-11

status: Public on Nov 06 2018

type: SRA

middle: P.

state: TX

department: Department of Biology

country: USA

description:
single-cell
AdultHuman-Spermatids_17-11_barcodes.tsv
AdultHuman-Spermatids_17-11_genes.tsv
AdultHuman-Spermatids_17-11_matrix.mtx

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

value: Sta-Put enriched Spermatids


title: UMI-4C p63KO Day 7 - Replicate 1

city: Stanford

first: Anthony

middle: E

last: Oro

state: CA

address: 269 Campus Dr, CCSR 2140

institute: Stanford University

library_source: genomic

data_processing:
Library strategy: UMI-4C
Reads were processed using HiC-Pro, which performed Bowtie alignment, removal of PCR duplicates, assignment to MboI restriction fragments, and filtering for valid long-range contacts.
Binned 5 kb resolution interaction matrix files were converted to tab-delimited bed files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *matrix.bed: Tab-delimited bed files of HiC-Pro filtered read counts from 5 kb contact matrix file.

molecule: genomic DNA

source_name: Surface Ectoderm Cells

growth_protocol: hESCs were cultured on Vitronectin Recombinant Human Protein in Essential 8 medium.

extract_protocol:
After treatment with Accutase, cells were fixed in 1% formaldehyde. After crosslinking, 1x10^7 cells were pelleted for isolating nuclei and digesting with DpnII overnight. Proximity ligations were generated and DNA was purified through a phenol/chloroform extraction and ethanol precipitation.
After Qubit quantification, 10 ug of 4C library was sonicated and used for library preparation using NEBNext kit (New England Biolabs) and Agencourt AMPure XP beads (Beckman) according to the manufacturer’s protocol. Two rounds of PCR were performed using custom bait primers at the TFAP2C locus along with the UMI-4C universal adapter. Library concentration was determined via Bioanalyzer (Agilent) and duplicates were sequenced paired-end on Illumina NextSeq sequencer.

treatment_protocol: For surface ectoderm differentiation, 6.2x10^3 cells/cm2 were plated as colonies on Vitronectin coated plates. Next day, media was changed to Essential 6 media supplemented with 1 uM RA and 5 ng/ml Recombinant Human BMP4, and replaced every two days for seven days.

tag: cell line

tag: genotype/variation

tag: treatment

value: Day 7 of differentiation with RA/BMP4

value: Surface Ectoderm Cells


title: WBS_097_13_08

type: RNA

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented and hybridized at 65 °C for 17 hours according to the manufacturer's instructions.

scan_protocol: Slides were scanned on the Agilent Microarray scanner (G2565CA).

data_processing: Data were extracted with Agilent Feature Extraction software version 11.0.1.1 (Agilent Technologies). Raw gene expression data were background corrected using the normexp method and normalized by the quantile method in Limma R package (Smyth et al.).

molecule: total RNA

source_name: Peripheral blood from WBS patient

label_protocol: Total RNA (100 ng) was labeled with Cy3 using Low Input Quick Amp RNA Labeling kit, One-Color (Agilent Technologies) according to the manufacturer's instructions. Labelled cRNA were purified using an RNeasy mini kit (QIAGEN)..  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from peripheral blood of participants by using the Paxgene Blood RNA System (QIAGEN, Tokyo, Japan) following the manufacture’s protocol with on-column DNase digestion.RNA quantity was measured using a Nano-drop ND-2000 spectrophotometer (Thermo Fisher Scientific, Yokohama, Japan). Qualities of RNA was determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, Tokyo, Japan). RNA integrity number (RIN) values greater than 8 were used for subsequent analyses.

tag: diagnosis

value: Williams Syndrome (WS)

tag: tissue

value: whole blood

tag: age

tag: gender

value: female


title: Neurons_WT_WNV_24h_rep1

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: gene expression after 24h in cultured neurons

hyb_protocol: For each sample, 3 ug of Cy3 labeled cDNA was hybridized for 17 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: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using OmicSoft Array Studio (Version 9.0) software. Raw feature extraction (FA) files were loaded in R (3.5.1) using limma (3.36.1). FA files were background corrected, control probes removed , and quantile normalized using limma.

organism: Mus musculus

source_name: Neurons, WT, WNV, 24 hours, replicate 1

label_protocol: Fifty nanograms (50 ng) of total RNA was amplified as directed in the NuGEN Ovation Pico WTA System and 5 ug of amplified cDNA was enzymatically labeled using the Agilent SureTag DNA Labeling Kit.

growth_protocol: Cortical neurons were isolated from E14.5 mouse embryos and cultured for

extract_protocol: RNA was extracted using a Qiagen Rneasy Kit according to manufacturer's instructions.

value: cortical neurons

value: wild type

tag: infection

value: West Nile virus (WNV) strain TX 2002-HC at an MOI of 0.001


title: Neurons_WT_WNV_24h_rep2

source_name: Neurons, WT, WNV, 24 hours, replicate 2


title: control low density, 57 dpw, fish 3, replicate

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

source_name: low density_57 dpw_skin

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

tag: FISH id

value: fish 3

tag: stocking density

value: control low fish density (20 kg/m3)

tag: time point

value: 57 dpw

value: skin


title: Neurons_WT_PBS_24h_rep1

source_name: Neurons, WT, PBS, 24 hours, replicate 1

value: PBS


title: WBS_094_27_04


title: WBS_093_27_03

value: male


title: control low density, 57 dpw, fish 3


title: CD56 bright 1

city: Genova

first: annalisa

last: barla

state: GE

address: via Dodecaneso 35

department: DIBRIS

country: Italy

institute: Università degli Studi di Genova

hyb_protocol: The hybridization procedure was performed according to the “miRNA Complete Labeling and Hyb Kit” protocol (version 2.4, part number G4170-90011) using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies). Briefly, Cy3-labeled RNA in hybridization buffer was hybridized overnight (20 hours, 55 °C) to Agilent Human microRNA Microarrays 8x60K v19 (Design ID 046064) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 5 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 5 min

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: CD56bright (CD16-) NK cells

label_protocol: Sample labeling was performed as detailed in the “miRNA Microarray System with miRNA Complete Labeling and Hyb Kit” protocol (version 2.4, part number G4170-90011). Briefly, 100 ng of each total RNA sample was used for the labeling step using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies).

growth_protocol: Pure populations of NK cells were obtained from peripheral blood mononuclear cells (PBMC) using the NK cell isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instruction. Freshly purified NK cells were then sorted based on the expression of CD56 and CD16 molecules to collect the different NK cell subsets

extract_protocol: RNA was extracted using the miRNeasy mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Sorted NK cells were washed in PBS and the pellet freeze-dried (20 sec in liquid nitrogen and then stored at -80°C)

tag: subject status/id

value: healthy donor 1

tag: cell subtype

value: CD56bright (CD16-) NK cells


title: WBS_089_13_05


title: control low density, 57 dpw, fish 2

value: fish 2


title: UMI-4C WT Day 7 - Replicate 2

value: wild-type

value: Day 7 of differentiation with RA/BMP4


title: Neurons_WT_PBS_24h_rep3

source_name: Neurons, WT, PBS, 24 hours, replicate 3


title: Neurons_RIPK3 KO_ZIKV_24h_rep2

source_name: Neurons, RIPK3 KO, ZIKV, 24 hours, replicate 2

value: Zika virus (ZIKV) strain MR766 at an MOI of 0.1


title: UMI-4C WT Day 7 - Replicate 1

value: Surface Ectoderm Cells


title: WBS_079_19re_01

value: Williams Syndrome (WS)

value: whole blood


title: WBS_081_27_02

value: female


title: WBS_076_08_07


title: Neurons_WT_PBS_24h_rep2

source_name: Neurons, WT, PBS, 24 hours, replicate 2

value: cortical neurons

value: wild type


title: Neurons_RIPK3 KO_ZIKV_24h_rep3

source_name: Neurons, RIPK3 KO, ZIKV, 24 hours, replicate 3


title: Neurons_RIPK3 KO_ZIKV_24h_rep1

source_name: Neurons, RIPK3 KO, ZIKV, 24 hours, replicate 1


title: AdultHuman-Spermatocytes_17-6

description: single-cell

extract_protocol:
Suspensions of human seminiferous tubule cells were prepared from adult testicular tissue parenchyma by a two-step enzymatic digestion was as described previously (Hermann et al., 2007b; Hermann et al., 2009; Dovey et al., 2013). Briefly, testis tissue was digested with 2mg/ml collagenase type IV at 37oC with vigorous agitation, washed with HBSS to remove interstitial cells, followed by digestion with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I for 15 minutes at 37oC with trituration every 5 minutes, and quenched with 10% FBS. In all cases, cell suspensions were strained (40um pore size for mouse, 70um pore size for humans) and suspended in MEMα containing 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 106 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S), labeled with antibodies (see Key Resources Table), and subjected to FACS using  a FACS Aria (BD). Positive antibody labeling was determined by comparison to staining with isotype control antibodies. Human spermatogonia were isolated by sorting cells with the phenotype HLA-ABCnegative / CD49enegative / THY1dim / ITGA6+ / EpCAMdim dim (see Fig. 2C). These markers were chosen because previous results indicate they specifically label undifferentiated spermatogonia, including some with colonization potential based on xenotransplantation (Dovey et al., 2013; Altman et al., 2014; Smith et al., 2014; Valli et al., 2014). Adult Human testis cells were also enriched for spermatocytes and spermatids based on sedimentation velocity at unit gravity (Romrell et al., 1976; Bellve et al., 1977). Briefly, testis cells (10^6-10^7) suspended in 2 ml of buffer plus 0.5% BSA were loaded onto a 50 ml gradient of 2-4% BSA (McCarrey et al., 1992) and allowed to sediment for 2.5 hr at 4°C. Approximately one hundred 0.5 ml fractions were then collected in microcentrifuge tubes and analyzed for content of spermatocytes or spermatids on the basis of morphology under phase contrast optics (which typically yields ≥85% purity). Fractions containing spermatocytes or spermatids were pooled separately, concentrated (to ~2 x106 cells/ml) and stored in buffer containing FBS on ice until use. Ultimately, sorted spermatoginia,Sta-Put-enriched spermatocytes and spermatids, or unselected spermatogenic cells from adult human testicular tissue were used for single-cell RNA-seq facilitated by the 10X Genomics Chromium Drop-Seq approach. Briefly, Cell suspensions were loaded into Chromium microfluidic chips with 3’ v2 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10X Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~8700 cells were loaded on the instrument with the expectation of collecting up to 5,000 GEMs containing single cells. For the multiplet test (Fig. S1), equal numbers of mouse and human cells were loaded. GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
Single-cell 3' libraries were prepared according to manufacturer recommendations (v2 chemistry).

treatment_protocol: De-identified, surgical excess normal adult human testicular tissue was obtained through the Infertility Center of St. Louis from patients undergoing a diagnostic testicular biopsy (n=28) in preparation for microscopic vasectomy reversal (MVR) or testicular sperm extraction (TESE) for obstructive azoospermia with the informed consent of patients (see Supplemental Table 2). Testicular tissue was also recovered from male organ donors (n=2) through the Texas Organ Sharing Alliance and the University of Texas Transplant Center with informed consent of the next of kin. The University of Texas at San Antonio IRB determined that research on these tissues did not constitute human subjects research (IRB #12-098N and #17-074N). The age of the individuals was recorded (median = 42yr, mean = 41.6 ± 1.3yr), and while organ donors tended to be younger (34.3 ± 7.2yr) than biopsy patients (42.4 ± 1.2yr), the difference was not significant (p=0.32). Procured tissue was transported to the laboratory on ice in either Lactated Ringer’s solution or minimal essential medium alpha (MEMα) containing 10% fetal bovine serum. The amount of time tissues were exposed to cold ischemia prior to processing was recorded (median = 18.7hr; mean = 24.7 ± 3.8 hr).

value: Sta-Put enriched Spermatocytes


title: AdultHuman-Spermatids_17-6

description: single-cell

value: Sta-Put enriched Spermatids


title: WBS_077_27_01


title: control low density, 57 dpw, fish 1

value: fish 1

value: control low fish density (20 kg/m3)

value: 57 dpw

value: skin


title: WBS_074_08_06

value: male


title: control low density, 43 dpw, fish 5

source_name: low density_43 dpw_skin

value: fish 5

value: 43 dpw


title: control low density, 43 dpw, fish 3

value: fish 3


title: Neurons_RIPK3 KO_WNV_24h_rep2

source_name: Neurons, RIPK3 KO, WNV, 24 hours, replicate 2

value: West Nile virus (WNV) strain TX 2002-HC at an MOI of 0.001


title: Neurons_RIPK3 KO_WNV_24h_rep3

source_name: Neurons, RIPK3 KO, WNV, 24 hours, replicate 3


title: control low density, 43 dpw, fish 2

value: fish 2


title: Neurons_RIPK3 KO_WNV_24h_rep1

source_name: Neurons, RIPK3 KO, WNV, 24 hours, replicate 1


title: Neurons_RIPK3 KO_PBS_24h_rep2

source_name: Neurons, RIPK3 KO, PBS, 24 hours, replicate 2

value: PBS


title: Neurons_RIPK3 KO_PBS_24h_rep3

source_name: Neurons, RIPK3 KO, PBS, 24 hours, replicate 3


title: control low density, 43 dpw, fish 4

value: fish 4


title: WBS_041_01_08

source_name: Peripheral blood from WBS patient

value: Williams Syndrome (WS)

value: whole blood

value: female


title: control low density, 43 dpw, fish 1


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep4

city: chongqing

first: bin

last: tang

state: chongqing

address: Southwest Hospital &College of Medical Laboratory Science; Third Military Medical University

department: Department of Clinical Microbiology and Immunology

country: China

description:
adjacent normal tissues
expression data from the adjacent normal tissues (Control) with F. nucleatum infection

hyb_protocol: The Fluidics Station 450/250 is used to wash and stain the probe arrays. It is operated using Affymetrix GeneChip Command Console (GeneChip® Expression Wash, Stain and Scan User Manual, Affymetrix).

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

data_processing: Affymetrix GeneChip® Command Console® Software (AGCC)

label: biotin

label_protocol: cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit from 6 ug total RNA (GeneChip® Expression Wash, Stain and Scan User Manual, Affymetrix).

extract_protocol: Total RNA of cells was extracted using the TRIzol® Reagent (Life Technologies) and cRNA was generated using the PimeScript TMRT Reagent Kit (Takara).

treatment_protocol: Tissue is stored in liquid nitrogen.

value: colorectal normal tissues


title: Neurons_RIPK3 KO_PBS_24h_rep1

source_name: Neurons, RIPK3 KO, PBS, 24 hours, replicate 1

value: cortical neurons


title: WBS_072_21_06


title: WBS_070_02_06


title: WBS_040_01_07


title: control low density, 36 dpw, fish 4

source_name: low density_36 dpw_skin

value: 36 dpw


title: ASD_193_30_05

source_name: Peripheral blood from ASD patient

value: autism spectrum disorder (ASD)


title: control low density, 36 dpw, fish 3

value: control low fish density (20 kg/m3)


title: control low density, 36 dpw, fish 5

value: skin


title: WBS_039_21_05

value: male


title: ASD_190_30_03


title: control low density, 36 dpw, fish 2


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep2

institute: Southwest Hospital &College of Medical Laboratory Science; Third Military Medical University


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep1


title: Con_232

hyb_protocol: Following manufacturer's instructions, labelled RNA was hybridized to the SurePrint G3 Human miRNA 8x60K Microarray (G4870C) (Agilent Technologies) using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies). Hybridization step was performed for 20 hours at 55°C at a constant speed rotation of 20rpm. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 5 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner(p/n G2565BA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent Technologies) using default parameters (protocol: miRNA_1100_Jul11 and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral blood from control subject

label_protocol: Following manufacturer's instructions, total RNA (100ng) was labeled with Cy3 using the miRNA Complete Labeling and Hyb Kit(Agilent Technologies, Tokyo, Japan).

extract_protocol: miRNA was extracted from peripheral blood of participants by using the PAXgene Blood miRNA System (QIAGEN, Tokyo, Japan) following the manufacturer's protocol with DNase treatment step. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific, Yokohama, Japan), and quality was determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, Tokyo, Japan).

value: control


title: Con_233


title: the adjacent normal tissues (Control) without F. nucleatum infection rep5

description:
Colorectal normal tissues
expression data from the adjacent normal tissues (Control) without F. nucleatum infection

value: Human colorectal tissues


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep3


title: Con_231


title: control low density, 36 dpw, fish 1

value: fish 1


title: control low density, 14 dpw, fish 5

source_name: low density_14 dpw_skin

value: fish 5

value: 14 dpw


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep5


title: control low density, 14 dpw, fish 4


title: Con_226


title: ASD_176_26_08


title: ASD_175_25_08


title: Con_225


title: ASD_170_26_07


title: Con_222


title: the adjacent normal tissues (Control) without F. nucleatum infection rep2


title: ASD_165_24_08


title: the adjacent normal tissues (Control) without F. nucleatum infection rep3


title: ASD_177_19re_08


title: Con_220


title: the adjacent normal tissues (Control) without F. nucleatum infection rep4


title: ASD_189_30_02


title: the adjacent normal tissues (Control) without F. nucleatum infection rep1


title: Con_171


title: control low density, 14 dpw, fish 1


title: control low density, 7 dpw, fish 5

source_name: low density_7 dpw_skin

value: 7 dpw


title: Colorectal cancer tissues without F. nucleatum infection rep4

description:
Colorectal cancer tissues
expression data from Colorectal cancer tissues without F. nucleatum infection

value: Human colorectal adenocarcinoma


title: Colorectal cancer tissues without F. nucleatum infection rep5


title: ASD_151_19re_07


title: control low density, 14 dpw, fish 2

value: fish 2


title: Con_169

value: whole blood


title: Con_163


title: ASD_147_23_08


title: Colorectal cancer tissues without F. nucleatum infection rep3


title: ASD_145_23_07


title: control low density, 7 dpw, fish 4

value: fish 4


title: control low density, 14 dpw, fish 3

value: fish 3


title: ASD_191_30_04


title: control low density, 7 dpw, fish 3


title: Con_161

value: female


title: Colorectal cancer tissues without F. nucleatum infection rep2


title: Con_160


title: Con_162


title: ASD_131_25_05


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep5

description:
Colorectal cancer tissues
expression data from Advanced stage of colorectal cancer tissues without F. nucleatum infection

source_name: Colorectal cancer tissues with F. nucleatum infection


title: control low density, 7 dpw, fish 1


title: control low density, 3 dpw, fish 5

source_name: low density_3 dpw_skin

value: 3 dpw


title: control low density, 3 dpw, fish 3


title: Con_159


title: control low density, 3 dpw, fish 4


title: Con_157


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep3


title: Con_156


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep4


title: ASD_140_19re_06

value: autism spectrum disorder (ASD)


title: Colorectal cancer tissues without F. nucleatum infection rep1


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep1


title: control low density, 3 dpw, fish 2

value: control low fish density (20 kg/m3)


title: Con_155


title: ASD_067_16_07


title: ASD_114_22_05


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep5

description:
Colorectal cancer tissues
expression data from Early stage of colorectal cancer tissues without F. nucleatum infection


title: ASD_068_16_08


title: Con_158


title: control low density, 3 dpw, fish 1

value: skin


title: ASD_115_22_06


title: Con_168

value: male


title: ASD_059_16_05


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep2


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep4


title: control low density, 1 dpw, fish 5

source_name: low density_1 dpw_skin

value: 1 dpw


title: Transgenic rep 3

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

data_processing:
The reads for Experiment 2 were mapped to the Ensembl Mus musculus genome (GRCm38). Mapping was performed with Tophat2 (v 2.0.12) [14] calling Bowtie2 (v 2.1.0). 50 bp used in Tophat mapping.
HTSeq-count (Python package HTSeq, python v 2.7.3) (47) was used to generate counts of reads uniquely mapped to annotated genes using the GRCm38 annotation gtf file.
The table of read counts was used as input to assess differential expression using the Bioconductor packages, edgeR and limma (voom).
Genome_build: Ensembl Mus musculus genome (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.

source_name: Skin tissue

extract_protocol:
RNA was extracted from the dissected mouse tissues using TRI-reagent (Sigma), following the manufacturer’s instructions, which included a chloroform phase separation and ethanol precipitation. RNA was resuspended in 70 μL of RNase-free water. RNA samples were assessed for quantity and quality using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), conventional RNA electrophoresis and using a Bioanalyser (Agilent Technology Inc). All RNA integrity numbers (RIN) for the analysed samples ranged from 9 to 9.5
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded Total RNA Prep Kit was used  .The six RNA-Seq libraries in Experiments 2 were sequenced using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.

tag: strain

value: P33 YAP2-5SA-deltaC mice

tag: Sex

tag: condition

value: YAP2-5SA-DC transgenic mouse


title: Con_062

value: control


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep3


title: ASD_058_16_04


title: Con_118


title: control low density, 1 dpw, fish 4


title: control low density, 1 dpw, fish 2


title: control low density, 1 dpw, fish 1

value: fish 1


title: Transgenic rep 2


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep1


title: control low density, 1 dpw, fish 3


title: ASD_055_16_03


title: Con_045


title: Con_047


title: Con_044


title: ASD_034_17_03


title: Con_056


title: Con_042


title: Transgenic rep 1


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep2


title: Wildtype rep 3

value: Control


title: ASD_033_17_02


title: High density, 57 dpw, fish 5

source_name: High density_57 dpw_skin

value: fish 5

value: high fish density (100 kg/m3)

value: 57 dpw


title: ASD_130_23_05

value: whole blood


title: Wildtype rep 1


title: Con_028


title: ASD_030_15_04


title: ASD_054_16_02


title: AdultMouse_Std

description: single-cell

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq. Trimmed FASTQ files (26bp Cell barcode and UMI Read1, 8bp i7 index, and 100bp Read2), were generated using the CellRanger mkfastq command (a 10X Genomics wrapper around BCL2Fastq).
Paired FASTQ files from each sample trimmed and the quality confirmed using FASTQC
Primary data analysis (alignment, filtering, and UMI counting) to determine gene transcript counts per cell (producing a gene-barcode matrix), quality control, clustering and statistical analysis were performed using CellRanger count (10X Genomics) and the mm10 (mouse) genome assembly/annotation references
Outputs from multiple independent samples of single-cells were combined using CellRanger aggr (10X Genomics) based on mapped read counts to normalize sequencing depth and produce aggregated gene-barcode matrices and clustering models.
Genome_build: Mouse reference genome NCBI build 38, GRCm38 (mm10)
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

source_name: Adult testis

growth_protocol: Normal mouse husbandry with ad libitum food and water.

extract_protocol:
Single-cell suspensions of seminiferous tubules were generated from adult mouse testes using a two-step enzymatic digestion approach. Briefly, testicular parenchyma from 2 or more adult mice were digested with 1mg/ml Collagenase Type IV (Worthington Biochemicals) for 2-3 minutes at 37oC, washed with Hank’s Buffered Salt Solution (HBSS) to remove interstitial cells, digested with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I (Sigma) for 7-9 minutes at 37oC, and quenched with 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 10^6 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S). Cells were pre-enriched for spermatogonia by density centrifugation in DPBS+S over a 30% Percoll cushion (Sigma) for 8 minutes at 600xg without braking. Pelleted cells were subjected to FACS and spermatogonia isolated based on gating CD9-bright and ID4-EGFP double-positive cells using  a FACS Aria (BD). Cells from adult Adult Id4-eGfp+ mouse were also enriched for spermatocytes and spermatids based on sedimentation velocity at unit gravity (Romrell et al., 1976; Bellve et al., 1977). Briefly, testis cells (10^6-10^7) suspended in 2 ml of buffer plus 0.5% BSA were loaded onto a 50 ml gradient of 2-4% BSA (McCarrey et al., 1992) and allowed to sediment for 2.5 hr at 4°C. Approximately one hundred 0.5 ml fractions were then collected in microcentrifuge tubes and analyzed for content of spermatocytes or spermatids on the basis of morphology under phase contrast optics (which typically yields ≥85% purity). Fractions containing spermatocytes or spermatids were pooled separately, concentrated (to ~2 x106 cells/ml) and stored in buffer containing FBS on ice until use. Ultimately, CD9bright/ID4-EGFP-birght,CD9bright/ID4-EGFP-dim spermatogonia, Sta-Put-enrichedspermatocytes and spermatids, or CD9-bright testis cells fromadult mice were used for single-cell RNA-seq facilitated by the 10X Genomics Chromium Drop-Seq approach. Briefly, Cell suspensions were loaded into Chromium microfluidic chips with 3’ v2 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10X Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~8700 cells were loaded on the instrument with the expectation of collecting up to 5,000 GEMs containing single cells. For the multiplet test (Fig. S1), equal numbers of mouse and human cells were loaded. GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
Single-cell 3' libraries were prepared according to manufacturer recommendations (v2 chemistry).

treatment_protocol: Animal were untreated.

tag: number of cells

tag: cell type

value: Sta-Put enriched Spermatids


title: ASD_037_17_04


title: AdultMouse_Sct

description: single-cell

value: Sta-Put enriched Spermatocytes


title: Con_015

value: female


title: Wildtype rep 2


title: High density, 57 dpw, fish 1


title: Con_014


title: High density, 43 dpw, fish 5

source_name: High density_43 dpw_skin

value: 43 dpw


title: High density, 43 dpw, fish 4

value: fish 4


title: ASD_009_02_01

value: autism spectrum disorder (ASD)


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep5

description:
adjacent normal tissues
miRNA data from the adjacent normal tissues (Control) with F. nucleatum infection

hyb_protocol: The GeneChip2 Hybridization Oven 640 is used to Hybridization.   1. Bring the reagents listed in step 3, below, to room temperature.  2. Completely thaw and then heat the 20X Eukaryotic Hybridization Controls (bioB, bioC, bioD, cre from  GeneChip Eukaryotic Hybridization Control Kit) for 5 minutes at 65°C.  3. Add the following components to the 21.5μl biotin-labeled sample in the order listed, to prepare the array  hybridization cocktail:  50μl 2X Hybridization Mix (from GeneChip Hyb, Wash and Stain Kit)  15μl 27.5% Formamide (Vial 12)  10μl DMSO (from GeneChip Hyb, Wash and Stain Kit)  5μl 20X Eukaryotic Hybridization Controls (from GeneChip Eukaryotic Hyb Control Kit)  1.7μl Control Oligonucleotide B2, 3nM (from GeneChip Eukaryotic Hyb Control Kit)  4. The volume will be 103.2μl. Incubate at 99oC for 5 minutes, then 45oC for 5 minutes.  5. Aspirate 100μl and inject into an array.  6. Remove the pipet tip from the upper right septum of the array.  7. Cover both septa with 1/2 Tough-Spots to minimize evaporation and/or prevent leaks.  8. Place the arrays into hybridization oven trays.  9. Load the trays into the hybridization oven.  10. Incubate the arrays at 48°C and 60 rpm for 16 hours.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G.

data_processing: Affymetrix GeneChip® miRNA QC Tool version 1.0.33.0

label_protocol: RNA input for FlashTag Biotin HSR labeling. 1,Poly (A) Tailing; 2, FlashTag Biotin HSR Ligation

extract_protocol: Total RNA of cells was extracted using the QIAGEN miRNeasy Mini Kit（Germany).

value: colorectal normal tissues


title: High density, 57 dpw, fish 3

value: fish 3

value: skin


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep4


title: High density, 43 dpw, fish 3


title: Con_013


title: High density, 57 dpw, fish 2

value: fish 2


title: Con_171_20_05

value: control


title: ASD_010_15_01

value: male


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep3


title: WBS_218

value: Williams Syndrome (WS)


title: High density, 43 dpw, fish 2


title: WBS_187


title: Con_168_26_05


title: ASD_011_15_02


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep2


title: the adjacent normal tissues (Control) with F. nucleatum infection,rep1


title: High density, 43 dpw, fish 1

value: fish 1


title: WBS_186


title: Con_162_26_02


title: WBS_224


title: High density, 36 dpw, fish 5

source_name: High density_36 dpw_skin

value: fish 5

value: high fish density (100 kg/m3)

value: 36 dpw


title: the adjacent normal tissues (Control) without F. nucleatum infection rep4

description:
Colorectal normal tissues
miRNA data from the adjacent normal tissues (Control) without F. nucleatum infection

value: Human colorectal tissues


title: High density, 36 dpw, fish 4


title: WBS_183

value: whole blood


title: the adjacent normal tissues (Control) without F. nucleatum infection rep5


title: the adjacent normal tissues (Control) without F. nucleatum infection rep3


title: the adjacent normal tissues (Control) without F. nucleatum infection rep2


title: WBS_180


title: High density, 36 dpw, fish 2


title: High density, 36 dpw, fish 1


title: the adjacent normal tissues (Control) without F. nucleatum infection rep1


title: High density, 36 dpw, fish 3


title: Colorectal cancer tissues without F. nucleatum infection rep5

description:
Colorectal cancer tissues
miRNA data from Colorectal cancer tissues without F. nucleatum infection

value: Human colorectal adenocarcinoma


title: WBS_181


title: Con_161_26_01

value: female


title: Con_158_25_02


title: control low density, 7 dpw, fish 2

value: control low fish density (20 kg/m3)

value: 7 dpw


title: High density, 14 dpw, fish 5

source_name: High density_14 dpw_skin

value: 14 dpw


title: WBS_178


title: WBS_173


title: WBS_150


title: Con_160_25_04


title: Con_159_25_03


title: ASD_003_17_01

value: autism spectrum disorder (ASD)


title: Con_156_24_03


title: WBS_139


title: Con_157_25_01


title: High density, 14 dpw, fish 4

value: fish 4

value: skin


title: Con_148_24_01

value: control


title: Colorectal cancer tissues without F. nucleatum infection rep3


title: High density, 14 dpw, fish 3

value: fish 3


title: High density, 14 dpw, fish 2

value: fish 2


title: Colorectal cancer tissues without F. nucleatum infection rep2


title: Con_065_13_02

value: male


title: Colorectal cancer tissues without F. nucleatum infection rep4


title: Colorectal cancer tissues without F. nucleatum infection rep1


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep5

description:
Colorectal cancer tissues
miRNA data from Advanced stage of colorectal cancer tissues without F. nucleatum infection


title: High density, 7 dpw, fish 5

source_name: High density_7 dpw_skin

value: fish 5


title: WBS_136

source_name: Peripheral blood from WBS patient

value: Williams Syndrome (WS)


title: High density, 7 dpw, fish 4

value: high fish density (100 kg/m3)


title: WBS_134


title: High density, 57 dpw, fish 4

value: 57 dpw


title: Con_063_14_03

value: whole blood


title: ASD_032_01_02


title: Con_061_13_01


title: WBS_127


title: Con_064_14_04


title: WBS_126


title: High density, 7 dpw, fish 3


title: Con_062_21_04


title: WBS_138


title: Con_060_10_08


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep3

value: Human colorectal adenocarcinoma


title: WBS_135


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep4


title: High density, 14 dpw, fish 1

value: fish 1


title: WBS_122


title: High density, 7 dpw, fish 2


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep2


title: High density, 7 dpw, fish 1


title: WBS_106


title: Advanced stage of colorectal cancer tissues without F. nucleatum infection,rep1


title: High density, 3 dpw, fish 5

source_name: High density_3 dpw_skin

value: 3 dpw


title: Con_051_10_04


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep5

description:
Colorectal cancer tissues
miRNA data from Early stage of colorectal cancer tissues without F. nucleatum infection


title: Con_052_10_05

value: female


title: WBS_099


title: WBS_101


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep4


title: Con_047_10_03


title: Con_056_10_06


title: WBS_097


title: Con_046_10_02


title: High density, 3 dpw, fish 1


title: High density, 3 dpw, fish 3


title: High density, 3 dpw, fish 2


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep2


title: High density, 3 dpw, fish 4


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep3


title: WBS_094


title: WBS_093


title: Con_044_02_05


title: Early stage of colorectal cancer tissues without F. nucleatum infection,rep1


title: High density, 1 dpw, fish 5

source_name: High density_1 dpw_skin

value: 1 dpw


title: High density, 1 dpw, fish 3


title: WBS_095


title: High density, 1 dpw, fish 4


title: Con_038_08_03


title: High density, 1 dpw, fish 2


title: WBS_092


title: WBS_081


title: Alveolar macrophages unimmunized rep3

city: Hamilton

first: Zhou

last: Xing

state: Ontario

address: 1280 Main Street West

department: Pathology and Molecular Medicine

country: Canada

institute: McMaster University

hyb_protocol: 16hr at 45C washing FS450_0002

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Preprocessing was done by using Affymetrix Expression Console Software 1.4: with RMA-Gene procedure; the values were Log2-transformed.

label: Biotin-allonamide Triphosphate

source_name: Alveolar macrophages unimmunized rep3

label_protocol: Biotin Allonamide Triphosphate

growth_protocol: mice were housed in a specific pathogen free level B facility at McMaster University.

extract_protocol: RNA from purified alveolar macrophages was isolated using RNeasy® Mini Kit (Qiagen, Germantown, MD, USA) Sample preparation-Affymetrix WT PLUS kit

treatment_protocol: Naïve Balb/c mice were intranasally inoculated with a recombinant human serotype 5 adenovirus expressing an Mtb protein Ag85A at 5×107 PFU per mouse. PBS inoculated mice were used as control. At 4 weeks post infection alveolar macrophages were purified from bronchoalveolar lavage fluid.

value: BALB/C

value: Female


title: Con_035_02_04

source_name: Peripheral blood from control subject


title: Alveolar macrophages unimmunized rep2

source_name: Alveolar macrophages unimmunized rep2


title: WBS_079


title: Alveolar macrophages unimmunized rep1

source_name: Alveolar macrophages unimmunized rep1


title: Con_045_01_05


title: Con_029_01_04


title: High density, 1 dpw, fish 1

value: skin


title: WBS_077


title: Con_042_08_04

value: control


title: Con_029


title: Con_028_01_03


title: Alveolar macrophages d28 post Ad infection rep3


title: Before wounding, low density, fish 8

source_name: Before wounding_low density_skin

value: fish 8

value: control low fish density (20 kg/m3)

value: Before wounding


title: PL31_chc

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

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:
Using R version 3.4.1. One amnion sample was removed from the analysis as it was a poor quality sample (sample not included in these GEO records). Array probes targeting sex chromosomes, with evidence of cross-hybridization, 59 rs probes, polymorphic probes, poor quality probes (detection p value >0.01 in >20 % of samples or <3 bead replicates in >20 % of samples) were eliminated.
Processed data matrices include: average beta (normalized by functional normalization and combat corrected for batch variables)
Signal intensities file includes: Methylated (signal A) and unmethylated (signal B) signal intensities

label: Cy5 and Cy3

source_name: genomic DNA from PL31 aCA placenta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: patient id

value: Chorion

tag: pathology group

value: chorioamnionitis

tag: fetal sex

value: F

tag: gestational age

tag: 850k plate

tag: 850k sentrix_id

tag: 850k sentrix_position


title: PL57_chc

source_name: genomic DNA from PL57 aCA placenta

tag: tissue

value: M


title: PL34_chc

source_name: genomic DNA from PL34 aCA placenta


title: Before wounding, low density, fish 5

tag: FISH id

value: fish 5

tag: stocking density


title: Before wounding, low density, fish 7

value: fish 7

tag: time point


title: PL73_chc

source_name: genomic DNA from PL73 aCA placenta


title: WBS_070

tag: diagnosis

value: Williams Syndrome (WS)

value: whole blood

tag: age

tag: gender


title: WBS_041

value: female


title: Before wounding, low density, fish 6

value: fish 6


title: PL25_chc

source_name: genomic DNA from PL25 aCA placenta


title: PL29_amc

source_name: genomic DNA from PL29 aCA placenta

value: Amnion


title: Alveolar macrophages d28 post Ad infection rep2

tag: strain

value: BALB/C

tag: Sex

value: Female


title: WBS_040


title: PL20_chc

source_name: genomic DNA from PL20 aCA placenta


title: Con_015_22_01

value: control


title: PL56_chc

source_name: genomic DNA from PL56 aCA placenta


title: Before wounding, high density, fish 4

source_name: Before wounding_high density_skin

value: fish 4

value: high fish density (100 kg/m3)

value: skin


title: Before wounding, high density, fish 2

value: fish 2

value: Before wounding


title: 15010_whole_skin

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: gene_counts_keratinocytesLN.txt and TPM_keratinocytesLN.txt

data_processing:
All reads were assessed for quality and (when necessary) adaptors were removed using Cutadapt.
RNA-Seq reads were aligned to hg38 (Ensembl Gene annotation build 79) using STAR 2.5.2b
Reads were quantified using RSEM 1.2.31
Genome_build: hg38 (Ensembl Gene annotation build 79)
Supplementary_files_format_and_content: TPM_keratinocytes.txt: tab separated file with TPM values for each gene and sample; gene_counts_keratinocytes.txt: tab separated file with raw gene expression counts for each gene and sample

source_name: normal epidermal skin

growth_protocol: freshly isolated adult normal skin keratinocytes were either co-cultured with lethally irradiated 3T3-J2 fibroblasts or in wells coated with LN-511 or LN-421. Confluent wells of cells at P0 were collected for RNA extraction. For whole skin RNA extraction, skin was either freshly processed for RNA extraction or kept at 4degC in RNA later no longer than 3 days before RNA extraction was performed.

extract_protocol:
Libraries were constructed with TruSeq stranded total RNA library Prep Kit (Illumina).
illumina TruSeq stranded total RNA kit with RiboZero Gold
Samples were sequenced in Illumina HiSeq 3000 RNA sequencing platform (100bp pair-end reads)

treatment_protocol: RNA was isolated with Norgen Biotek's Single-cell RNA-isolation kit according to manufacturer's protocol. 700 ng of total RNA was used for library construction.

tag: cell line

value: breast

tag: technical replicate

tag: culture conditions

tag: source patient id

tag: cell type

value: keratinocyte

tag: protocol

value: dermatome collected sample


title: Con_013_21_01


title: 15002_whole_skin

value: skin from left groin


title: Alveolar macrophages d28 post Ad infection rep1


title: WBS_076

source_name: Peripheral blood from WBS patient

value: Williams Syndrome (WS)


title: 1605_511_TR2

value: Cells cultured on LN-511


title: WBS_039

value: whole blood

value: male


title: WBS_072

value: female


title: Before wounding, high density, fish 1

value: fish 1


title: PL122_chc

source_name: genomic DNA from PL122 aCA placenta

tag: patient id

value: Chorion

tag: pathology group

value: chorioamnionitis

tag: fetal sex

value: F

tag: gestational age

tag: 850k plate

tag: 850k sentrix_id


title: Cohesin HiChIP p63KO Day 7 - Replicate 3

description:
Cohesin HiChIP
processed data file: H9D7KO_10000.matrix
processed data file: H9D7KO_merge_10kb.FitHiC_c10_fdr0.001_ID.bed

data_processing:
Library strategy: HiChIP
Reads were processed using HiC-Pro, which performed Bowtie alignment, removal of PCR duplicates, and filtering for valid long-range contacts.
Raw matrix files were run through FitHiC to call chromosome contacts.
High confidence FitHiC loops were filtered with the following parameters: counts greater than or equal to 10, FDR < 0.001.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.matrix: Final binned 10 kb resolution matrix files, containing connected portions of the genome and processed HiC-Pro read counts.
Supplementary_files_format_and_content: *.bed, *.txt: Final FitHiC tab-delimited bed/txt files containing high confidence loop calls.

source_name: Surface Ectoderm Cells

extract_protocol:
After treatment with Accutase, cells were crosslinked in 1% formaldehyde for 10 min before lysis in Hi-C Lysis Buffer. 25x10^6 nuclei were digested with MboI and restriction fragment overhangs were marked with biotin. Proximity ligations were formed before purifying cohesin-bound DNA fragments with an SMC1-antibody, and DNA was further enriched by a biotin pull-down.
Libraries were amplified by PCR for 5 cycles and then purified on a PAGE gel selecting for 225 - 500 bp fragments. Libraries were quantified on a Bioanalyzer prior to deep sequencing on Illumina HiSeq 4000 sequencer.

treatment_protocol: For surface ectoderm differentiation, 6.2x10^3 cells/cm2 were plated as colonies on Vitronectin coated plates. Next day, media was changed to Essential 6 media supplemented with 1 uM RA and 5 ng/ml Recombinant Human BMP4, and replaced every two days for seven days. For p63GOF line, cells were treated with 2 ug/ml Doxycycline for two days to induce p63 expression.

tag: genotype/variation

tag: treatment

value: Day 7 of differentiation with RA/BMP4

value: Surface Ectoderm Cells

tag: chip antibody

value: SMC1 (Bethyl, A300-055A)


title: Before wounding, high density, fish 3

tag: FISH id

value: fish 3

tag: stocking density

value: high fish density (100 kg/m3)

tag: time point

value: Before wounding

tag: tissue

value: skin


title: 1605_511_TR1

tag: cell line

value: breast

tag: technical replicate

tag: culture conditions

value: keratinocyte


title: Cohesin HiChIP p63KO Day 7 - Replicate 1

tag: cell type


title: PL78_chc

source_name: genomic DNA from PL78 aCA placenta

tag: patient id

value: M

tag: 850k sentrix_position


title: 15006_whole_skin

value: abdomen

tag: source patient id

tag: protocol

value: dermatome collected sample


title: 1605_421_TR2

value: Cells cultured on LN-421


title: PL32_chc

source_name: genomic DNA from PL32 aCA placenta

tag: pathology group

tag: fetal sex

tag: gestational age

tag: 850k plate


title: PL30_chc

source_name: genomic DNA from PL30 aCA placenta

tag: 850k sentrix_id


title: 1605_421_TR1


title: 1605_3T3_TR2

value: Cells co cultured with 3T3


title: Cohesin HiChIP p63GOF Day 0 - Replicate 3

description:
Cohesin HiChIP
processed data file: p63ect_cohesin_merge_10000.matrix
processed data file: p63ect_merge_10kb.FitHiC_c10_fdr0.001.txt

source_name: human Embryonic Stem Cells

tag: genotype/variation

tag: treatment

value: Doxycycline for 2 days

value: Embryonic Stem Cells

tag: chip antibody


title: Cohesin HiChIP WT Day 7 - Replicate 1

description:
Cohesin HiChIP
processed data file: H9D7_10000.matrix
processed data file: H9D7_merge_10kb.FitHiC_c10_fdr0.001_ID.bed

value: wild-type


title: PL11_chc

source_name: genomic DNA from PL11 aCA placenta

tag: tissue

value: Chorion


title: PL104_chc

source_name: genomic DNA from PL104 aCA placenta

value: F


title: 1605_3T3_TR1

tag: cell line


title: Cohesin HiChIP p63KO Day 7 - Replicate 2

value: Day 7 of differentiation with RA/BMP4

value: Surface Ectoderm Cells

value: SMC1 (Bethyl, A300-055A)


title: Cohesin HiChIP p63GOF Day 0 - Replicate 2


title: sort iMSC-1

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: Gene expression induced myogenic stem cell sorted with CD106(-) / α7-Integrin(+)

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-028279 SurePrint G3 Rat GE Microarray 8x60K for 17 hours at 65°C in a rotating SureHyb chamber.  After hybridization, microarrays were washed 1minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: FACS sorting with CD106(-)/ α7-Integrin(+), induced myogenic stem cell, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling 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: The cells were maintained in the high glucose-DMEM supplemented with 10% fetal bovine serum, 10% horse serum, 5 ng/ml murine basic fibroblast growth factor, and 1% penicillin/streptomycin.

extract_protocol: Samples were lysed and RNA isolation was carried out using the RNA-spin total RNA extraction kit (iNtRON Biotechnology, Sungnam, Kyungki-Do, South Korea) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The cultures were incubated at 37ºC in a humidified incubator with 5% CO2.

tag: strain

tag: developmental stage

value: adult


title: PL15_chc

source_name: genomic DNA from PL15 aCA placenta

value: chorioamnionitis


title: sort iMSC-2

source_name: FACS sorting with CD106(-)/ α7-Integrin(+), induced myogenic stem cell, replicate 2


title: 1602_511_TR1

value: breast

tag: technical replicate

tag: culture conditions

tag: cell type

value: Cells cultured on LN-511


title: iMSC-1

description: Gene expression induced myogenic stem cell

source_name: induced myogenic stem cell, replicate 1


title: 1602_511_TR2

tag: source patient id

value: keratinocyte


title: Cohesin HiChIP p63GOF Day 0 - Replicate 1


title: iMSC-2

source_name: induced myogenic stem cell, replicate 2


title: Cohesin HiChIP WT Day 0 - Replicate 3

description:
Cohesin HiChIP
processed data file: H9D0_merge_10000.matrix
processed data file: H9D0_merge_10kb.FitHiC_c10_fdr0.001_ID.bed

value: Day 0 of differentiation


title: MDSC-2

description: Gene expression MDSC

source_name: Muscle derived stem cell, replicate 2


title: PL57_amc

source_name: genomic DNA from PL57 aCA placenta

tag: patient id

value: Amnion

value: M

tag: 850k sentrix_position


title: Cohesin HiChIP WT Day 7 - Replicate 3


title: Cohesin HiChIP WT Day 7 - Replicate 2


title: Cohesin HiChIP WT Day 0 - Replicate 2


title: 1602_421_TR1

source_name: normal epidermal skin

tag: protocol

value: Cells cultured on LN-421


title: MDSC-1

description: Gene expression MDSC

source_name: Muscle derived stem cell, replicate 1


title: 1601_421_TR2

value: abdomen


title: PL91_chc

source_name: genomic DNA from PL91 aCA placenta

tag: pathology group

tag: fetal sex

tag: gestational age


title: 1601_421_TR1


title: PL34_amc

source_name: genomic DNA from PL34 aCA placenta

tag: 850k plate

tag: 850k sentrix_id


title: Cohesin HiChIP WT Day 0 - Replicate 1

tag: genotype/variation

tag: treatment

value: Embryonic Stem Cells

tag: chip antibody


title: MEF-2

description: Gene expression of MEF

source_name: Mouse embryonic fibroblast, replicate 2

tag: strain

value: embryo


title: GM12878.starr_seq_input_12

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description: GM12878 STARR-seq input libraries were generated by PCR enrichment of the reporter sequences from the GM12878 Whole Genome STARR-seq plasmid library

data_processing:
Library strategy: STARR-seq
STARR-seq input and output libraries were aligned to the human genome assembly hg38 with Bowtie2 (version 2.2.4)32, using the following parameters: bowtie2 -X 2000 --sensitive
Samtools was used to process alignments. Only properly-paired alignments with a MAPQ score ≥ 30 outside hg38 centromeres, gap and blacklist regions were were retained in downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: hg38 genomic coordinates for putative enhancers identified by WGSS (bed files)
Supplementary_files_format_and_content: hg38 signal files for WGSS samples (bigwig)

source_name: GM12878 Whole Genome STARR-seq Plasmid Library

growth_protocol: A549 cells were grown in Ham's F-12K (Kaighn's) Medium, 10% FBS, 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
Each washed cell pellet harvested from a 500 cm2 plate was lysed in a 50 mL conical tube with 5 mL of a 1:10 mixture of β-mercaptoethanol and Qiagen Buffer RLT. The lysates were vortexed, snap frozen, and stored at -80°C. Lysates were thawed on ice and passed through a 20-guage needle 10x. Total RNAs were purified with the Qiagen RNeasy midi-columns performing the on-column DNase step. The amount of purified RNA was quantified using a Nanodrop instrument, and RNA quality was assessed using an Agilent TapeStation 2200 with RNA ScreenTape. After adding 1 ul RNase Block (Agilent) samples were stored at -80
Total RNAs harvested from A549 cells transfected with the GM12878 Whole Genome STARR-seq plasmid library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment.

treatment_protocol: The GM12878 Whole Genome STARR-seq Reporter Library was transfected into A549 cells with Lipofectamine 3000 according to the manufacturer’s protocol. The following day the media was changed. At 36 hours post-transfection the media was changed again and the cells were treated with 100 nM dex or an equal volume of EtOH vehicle (0.1% volume) for 0, 1, 4, 8, or 12 hours. Treatments were started such that all time points were harvested at 48 hours post-transfection. Following treatment, the media was removed and cells were washed with 1x warm PBS prior to performing an extracellular DNase digestion. After removing the digestion buffer cells were trypsinized, washed with PBS, and total RNAs harvested using the Qiagen RNeasy system

tag: starr-seq reporter library

tag: cell line


title: PL25_amc

source_name: genomic DNA from PL25 aCA placenta

tag: tissue


title: 15006_511

tag: technical replicate

tag: culture conditions

tag: cell type


title: PL56_amc

source_name: genomic DNA from PL56 aCA placenta

tag: patient id

tag: 850k sentrix_position


title: GM12878.starr_seq_input_11

value: GM12878 Whole Genome STARR-seq Reporter Library


title: Sample taken 23h after transition T8

city: Groningen

first: Jasper

last: Bosman

state: Groningen

address: Zernikeplein 11

department: Bioinformatics

country: Netherlands

institute: Hanzehogeschool

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 23h after release to 28°C (freerun)

hyb_protocol: Hybridization is performed by Service XS (Leiden The Netherland): The affymetrix protocols are strickly followed for the hybridization, washing staining and scanning of the chips. To the 270ul hydridization cocktail, 30ul labeled material is added according the manual of the affymetrix One Cycle Target Labeling Kit

scan_protocol: Scanning is performed by Service XS (Leiden The Netherland): The affymetrix protocols are strickly followed scanning

data_processing: CEL files were inported into the R-studio enviroment and normalized using RMA normaliation from the affy package and further analysed using Circwave

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Sample taken 23h after transition T8

label_protocol: Labeling is performed by Service XS (Leiden The Netherland): The affymetrix One-Cycle Target Labeling Kit abd Control Reagens (#900493) are used to synthesize Biotin-labeled cRNA. For each RNA sample 2ul is used for the labeling experiment

growth_protocol: The strain used throughout this study was S. cerevisiae FY1679-2B (MATα ura3-52 leu2Δ1 TRP1 his3Δ200 GAL2; EUROSCARF, Frankfurt am Main, Germany). All experiments were performed in fermentors (APPLIKON) to facilitate control and monitoring of the cultures. The 1-L culture vessels were inoculated with overnight cultures grown from single colonies in YPD (1% yeast extract, 2% peptone, 2% dextrose). The remainder of the experiment was then performed using YPD plus 10 mL l−1 Sigma Antifoam A. A batch culture at 30 °C lasted ≈36 h. When a rapid decrease in dO2 was observed, the culture was starved for an additional 4 h. Cultures were then operated in continuous mode (a constant rate of media inflow and outflow) with agitation at 750 rpm, aeration at 150 mL min−1, and dilution at 0.09–0.1 h−1 (unless otherwise specified). The dO2 and the pH were monitored online; the dilution rate was monitored offline. The cell number was stable at around 2–3 × 109 cells/mL. It usually took about 2 weeks for the culture to become stable, such that it showed the same phase angle each day for weeks or months. Transitions from one cycle condition to another (i.e., from 24 to 23.5 h in length) would take up to a week to stabilize at a new entrained phase.

extract_protocol: Total  RNA was obtained using a modiﬁed version of the hot phenol method81. The flash-frozen yeast pellets were suspended in 400 μL AE buffer (50 mM NaOAc pH 5.3 and 10 mM EDTA) to which 40 μL SDS (10%) and 400 μL acidic phenol were added. Next, cells were disrupted by vortexing, followed by heating the sample to 65 °C for 30 min. The disrupted cells were quickly chilled on ice, centrifuged, and the aqueous phase was re-extracted using 400 μL acidic phenol followed by the addition of 400 μL chloroform, mixing, centrifuging and re-extraction of the liquid phase. The final step was puriﬁcation and concentration of the RNA samples using the NucleoSpin RNA II kit (Macherey-Nagel).

treatment_protocol: Cells were centrifuged for 1 minute at 4°C and 14000 rpm. Pellets were flash-frozen in liquid nitrogen and stored at -80°C until processing.

tag: time

value: 23h after transition from 21°C to 28°C

value: FY1679-2B (MAT-alpha ura3-52 leu2delta1 TRP1 his3delta200; EUROSCARF, Frankfurt am Main, Germany).


title: Sample taken 20h after transition T7

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 20h after release to 28°C (freerun)

source_name: Sample taken 20h after transition T7

value: 20h after transition from 21°C to 28°C


title: Sample taken 17h after transition T6

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 17h after release to 28°C (freerun)

source_name: Sample taken 17h after transition T6

value: 17h after transition from 21°C to 28°C


title: 15006_421

tag: source patient id

tag: protocol


title: 1602_421_TR2


title: Sample taken 14h after transition T5

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 14h after release to 28°C (freerun)

source_name: Sample taken 14h after transition T5

value: 14h after transition from 21°C to 28°C


title: MEF-1

description: Gene expression of MEF

source_name: Mouse embryonic fibroblast, replicate 1

tag: developmental stage


title: PL29_chc

source_name: genomic DNA from PL29 aCA placenta

value: Chorion

tag: pathology group

tag: fetal sex

value: F

tag: gestational age

tag: 850k plate

tag: 850k sentrix_id


title: GM12878.starr_seq_input_10

tag: starr-seq reporter library


title: Sample taken 11h after transition T4

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 11h after release to 28°C (freerun)

source_name: Sample taken 11h after transition T4

value: 11h after transition from 21°C to 28°C

tag: strain


title: 15006_3T3

tag: cell line

value: keratinocyte

value: Cells co cultured with 3T3


title: PL73_amc

source_name: genomic DNA from PL73 aCA placenta

tag: tissue

value: Amnion


title: GM12878.starr_seq_input_9


title: PL20_amc

source_name: genomic DNA from PL20 aCA placenta

value: M


title: PL122_amc

source_name: genomic DNA from PL122 aCA placenta

value: chorioamnionitis


title: AdultHuman_17-5

description: single-cell

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq. Trimmed FASTQ files (26bp Cell barcode and UMI Read1, 8bp i7 index, and 100bp Read2), were generated using the CellRanger mkfastq command (a 10X Genomics wrapper around BCL2Fastq).
Primary data analysis (alignment, filtering, and UMI counting) to determine gene transcript counts per cell (producing a gene-barcode matrix), quality control, clustering and statistical analysis were performed using CellRanger count (10X Genomics) and the hg19 (human), mm10 (mouse) or hg19+mm10 (human and mouse, for multiplet tests) genome assembly/annotation references
Outputs from multiple independent samples of single-cells were combined using CellRanger aggr (10X Genomics) based on mapped read counts to normalize sequencing depth and produce aggregated gene-barcode matrices and clustering models.
Genome_build: Human reference genome NCBI build 38 (GRCh38) or a combined hg19 (hGRC37) + Mouse reference genome NCBI build 38, GRCm38 (mm10) for multiplet tests
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

source_name: Adult testis

tag: number of cells

value: Steady-state Spermatogenic cells


title: PL78_amc

source_name: genomic DNA from PL78 aCA placenta


title: AdultHuman_17-4

description: single-cell

tag: cell type


title: GM12878.starr_seq_input_7


title: HeLa mock CHART-seq

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
library strategy: Capture Hybridisation Analysis of RNA Targets (CHART)-Seq
High-throughput sequencing reads were trimmed using Trimmomatic (v.0.36) to remove adapters and low quality reads
Trimmed reads were aligned against GRCh38/hg38 using HISAT2 (v2.0.5), two mismatches were allowed for each read.
Mapped reads in SAM format for each sample were transferred into bigWig format using utilities supported by UCSC for data visualization.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bigWig

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
For RNA, Cells were homogenized with dounce and pellet the nucleus suspended in WB100 buffer (10 mM HEPES pH7.5, 100 mM NaCl, 1 mM PMSF, 0.1% N-lauroylsarcosine, 40 U/mL RNasin) followed by sonication with S220 Focused-ultrasonicators (Covaris) (100 PW, 20% duty cycle, 200 burst, 1.5 min, 4℃). The lysate was digested with DNase at 37℃ for 15 min and stoped by adding 10 mM EDTA and 5 mM EGTA. Then, the lysate was pre-cleared with 50 μL Strepavidin C-1 magnetic beads with at 4℃ for 20 min. Then the pre-cleared lysates were hybridized with 350 nM probes at room temperature for 6 hours followed by adding 150 μL Strepavidin C-1 magnetic beads and incubating overnight at room temperature. The beads were washed with WB250 buffer (10 mM HEPES pH7.5, 250 mM NaCl, 0.2% SDS, 1 mM EGTA, 2mM EDTA, 1 mM PMSF, 0.1% N-lauroylsarcosine,) four times for 5 min each, and then were digested by Proteinase K at 50℃ for 1 hour followed by boiling at 100℃ for 10 min. Finally, 500 µL Trizol was added for RNA isolation.
RNA-seq libraries were prepared with Illumina TruSeq Stranded mRNA Sample Preparation Kit and CHART-seq libraries were prepared with Illumina TruSeq RNA Sample Preparation v2. Deep sequencing was performed on Illumina Hiseq X ten and Hiseq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: Plasmid transfection was carried out with X-tremeGENE 9 (Roche) for HeLa (60%–70% confluence) according to the manufacturer’s protocol, with 80%~90% transfection efficiency in general.

value: HeLa

tag: genotype/variation

value: Mock


title: Sample taken 5h after transition T2

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 5h after release to 28°C (freerun)

source_name: Sample taken 5h after transition T2

value: 5h after transition from 21°C to 28°C


title: Sample taken 2h after transition T1

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 2h after release to 28°C (freerun)

source_name: Sample taken 2h after transition T1

value: 2h after transition from 21°C to 28°C


title: AdultHuman_17-3

description: single-cell


title: GM12878.starr_seq_input_6

source_name: GM12878 Whole Genome STARR-seq Plasmid Library

value: GM12878 Whole Genome STARR-seq Reporter Library


title: PL30_amc

source_name: genomic DNA from PL30 aCA placenta

tag: patient id

tag: 850k sentrix_position


title: HeLa NEAT1 CHART-seq

value: NEAT1 CHART


title: HumanSpermatogonia_17-5

description: single-cell

value: Spermatogonia


title: PL32_amc

source_name: genomic DNA from PL32 aCA placenta


title: GM12878.starr_seq_input_5


title: HumanSpermatogonia_17-2

description: single-cell


title: GM12878.starr_seq_input_4


title: PL11_amc

source_name: genomic DNA from PL11 aCA placenta


title: HumanSpermatogonia_17-1

description: single-cell


title: PL104_amc

source_name: genomic DNA from PL104 aCA placenta


title: GM12878.starr_seq_input_3


title: Sample taken 8h after transition T3

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 8h after release to 28°C (freerun)

source_name: Sample taken 8h after transition T3

tag: time

value: 8h after transition from 21°C to 28°C

value: FY1679-2B (MAT-alpha ura3-52 leu2delta1 TRP1 his3delta200; EUROSCARF, Frankfurt am Main, Germany).


title: GM12878.starr_seq_input_8


title: PL91_amc

source_name: genomic DNA from PL91 aCA placenta

value: F


title: GM12878.starr_seq_input_2


title: PL15_amc

source_name: genomic DNA from PL15 aCA placenta


title: GM12878.starr_seq_input_1


title: PL111_vc

source_name: genomic DNA from PL111 aCA placenta

value: Chorionic villi


title: A549.starr_seq.dex.12hr.rep5

description: Total RNAs harvested from A549 cells transfected with the GM12878 Whole Genome STARR-seq plasmid library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment.

source_name: A549 Cells

growth_protocol:
A549 cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cel Culture Facilities and were maintained in Ham's F-12K (Kaighn's) Medium, 10% FBS, 1% penicillin-streptomycin at 37°C with 5% CO2
A549 cells were grown in Ham's F-12K (Kaighn's) Medium, 10% FBS, 1% penicillin-streptomycin at 37°C with 5% CO2.

tag: time point (hour)

tag: agent

value: dexamethasone


title: AAA0500991  [miRNA-Seq]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: G5_Intestinal samples from Non-Responders (NR) patients collected on the 3rd day

data_processing:
Quality Control: performed  by an in-house written quality control function, axShortReadQCAnax. This function formats and filters the reads based of their per-base reported quality
Adapters removing: using Trimmomatic v 0.32.
Alignment: aligned to miRBase v21 mature miRNA sequences using Bowtie 2 with parameters '--local','-L 16'
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
Feature Count
Expression normalization and Differential expression analysis using R bioconductor packages EdgeR and Limma
Genome_build: mature miRNAs (miRBase version 21)
Supplementary_files_format_and_content: tab-delimited text file of raw counts for mature miRNAs (miRBase version 21) across samples.  Tab delimited text files of edger , limma (voom) normalized counts

extract_protocol:
miRNeasy Mini Kit (QIAGEN)
TruSeq Small RNA Sample Prep Kit (Illumina Inc.)
Isolation of mature microRNA fraction

value: intestinal tissue

tag: disease state

value: ulcerative colitis

tag: group


title: Sample taken 1 h before transition T0

description:
1 × 10^9 yeast cells
Gene expression of yeast cells 1h before release to 28°C (freerun)

source_name: Sample taken 1 h before transition T0

value: 1 h before transition from 21°C to 28°C


title: A549.starr_seq.dex.12hr.rep4


title: AAA0500990  [miRNA-Seq]

description: G4_intestinal samples collected on the third day of treatment in treatment-responders (R) patients


title: PL11_vc

tag: pathology group

tag: fetal sex

value: M

tag: gestational age


title: PL76_vc

source_name: genomic DNA from PL76 aCA placenta

value: chorioamnionitis

tag: 850k plate

tag: 850k sentrix_id


title: A549.starr_seq.dex.12hr.rep3

tag: starr-seq reporter library

tag: cell line


title: Podocyte_LMB2day7_03

city: Isehara

first: Masahiro

last: Okabe

address: 143 Shimokasuya

institute: Tokai University School of Medicine

description: Gene expression in murine podocytes 7 days after LMB2 injection

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized using Gene Expression Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner ( G2600D SG13164306) using one color scan setting for 8x60k array slides using scan protocol AgilentG3_HiSen_GX_1Color.

data_processing: The scanned images were analyzed with Feature Extraction Software11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Podocytes, LMB2, day7, 03

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop.

extract_protocol: Podocyte RNA was isolated from podocyte specific polysomes which were immunoprecipitated with HA antibody. Glomerular RNA was isolated from unprecipitated polysomes. Total RNA was prepared using RNeasy Micro kit (QIAGEN, Tokyo, Japan)

treatment_protocol: To induce podocyte injury, 0.625 ng/gBW LMB2 was injected into tail vein of Nphs1-RiboTag-NEP25 mice once.

value: Kidey podocytes

tag: genetic background


title: PL18_vc

source_name: genomic DNA from PL18 aCA placenta

tag: tissue


title: A549.starr_seq.dex.12hr.rep2


title: AAA0500989  [miRNA-Seq]

value: Non-Responders (NR) patients collected on the 3rd day


title: PM20r_vc

source_name: genomic DNA from PM20 aCA technical replicate placenta


title: AAA0500988  [miRNA-Seq]


title: A549.starr_seq.dex.12hr.rep1


title: Podocyte_LMB2day4_04

description: Gene expression in murine podocytes 4 days after LMB2 injection

source_name: Podocytes, LMB2, day4, 04

tag: cell type


title: AAA0500987  [miRNA-Seq]


title: PL122_vc

source_name: genomic DNA from PL122 aCA placenta

tag: patient id


title: PL57_vc

source_name: genomic DNA from PL57 aCA placenta

tag: 850k sentrix_position


title: AAA0500985  [miRNA-Seq]

description: G1_healthy controls

value: healthy controls


title: Podocyte_LMB2day7_01

source_name: Podocytes, LMB2, day7, 01


title: A549.starr_seq.dex.8hr.rep4


title: AAA0500978  [miRNA-Seq]

description: G2_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids  tand who have a good response to treatment (responders, R)


title: Podocyte_LMB2day7_02

source_name: Podocytes, LMB2, day7, 02


title: Podocyte_LMB2day7_04

source_name: Podocytes, LMB2, day7, 04


title: PL77_vc

source_name: genomic DNA from PL77 aCA placenta


title: HepG2 cells_AP treated_24hrs

city: Pune

first: Saroj

last: Ghaskadbi

email: ssg@unipune.ac.in, sghaskadbi@gmail.com

state: Maharashatra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: SPPU

hyb_protocol: Hybridization was carried out according to standard protocols of Agilent

scan_protocol: Hybridized array was scanned using G2600D Agilent microarray scanner

data_processing: Normalization of the data was done in GeneSpring GX using the 75th percentile.

source_name: HepG2 cells_AP treated_24hrs

label_protocol: Labeled cRNA were prepared from 500 ng of total RNA by incorporating the dye cyanine 3-CTP according to standard Agilent  protocol.

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% FBS and seeded  in 25cm cell culture flasks.

extract_protocol: Cells were washed with chilled 1X PBS and harvested in 2ml of 1X PBS. Total RNA was extracted using Rneasy Mini kit from Qiagen according to manufacturers protocol.

treatment_protocol: 24 hrs after seeding , cells were treated with DMEM containing AP or AP20 extract (0.01%) for 24hrs.

tag: treatment

value: AP treated


title: HepG2 cells_AP20 treated_24hrs

source_name: HepG2 cells_AP20 treated_24hrs

value: AP20 treated


title: A549.starr_seq.dex.8hr.rep2

value: GM12878 Whole Genome STARR-seq Reporter Library

tag: time point (hour)


title: Podocyte_LMB2day4_02

source_name: Podocytes, LMB2, day4, 02


title: PL94_vc

source_name: genomic DNA from PL94 aCA placenta


title: A549.starr_seq.dex.8hr.rep5

source_name: A549 Cells

tag: agent


title: HepG2 cells_untreated_24hrs

source_name: HepG2 cells_untreated_24hrs

value: untreated


title: Podocyte_LMB2day4_01

source_name: Podocytes, LMB2, day4, 01


title: AAA0500976  [miRNA-Seq]

tag: disease state

value: third day of treatment in treatment-responders (R) patients


title: AAA0500977  [miRNA-Seq]

description: G3_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids  and who will have a poor response to treatment (non-responders, NR)

tag: group


title: Podocyte_LMB2day4_03

source_name: Podocytes, LMB2, day4, 03


title: GlomerularCells_normal_03

description: Gene expression in normal murine glomerular cells

source_name: Glomerular cells, normal, 03

value: Kidey glomerular cells


title: GlomerularCells_normal_02

source_name: Glomerular cells, normal, 02


title: A549.starr_seq.dex.8hr.rep1


title: Podocyte_normal_04

description: Gene expression in normal murine podocytes

source_name: Podocytes, normal, 04


title: Podocyte_normal_03

source_name: Podocytes, normal, 03


title: A549.starr_seq.dex.4hr.rep5


title: A549.starr_seq.dex.8hr.rep3


title: GlomerularCells_normal_04

source_name: Glomerular cells, normal, 04


title: AAA0500973  [miRNA-Seq]

description: G1_healthy controls


title: GlomerularCells_normal_01

source_name: Glomerular cells, normal, 01


title: A549.starr_seq.dex.4hr.rep4


title: Podocyte_normal_02

source_name: Podocytes, normal, 02


title: A549.starr_seq.dex.4hr.rep3


title: PL112_vc

source_name: genomic DNA from PL112 aCA placenta

tag: pathology group


title: PL30_vc

source_name: genomic DNA from PL30 aCA placenta

tag: fetal sex


title: PL34_vc

source_name: genomic DNA from PL34 aCA placenta

value: F

tag: gestational age


title: AAA0500966  [miRNA-Seq]


title: Podocyte_normal_01

source_name: Podocytes, normal, 01


title: PL26_vc

source_name: genomic DNA from PL26 aCA placenta

value: Chorionic villi

tag: 850k plate


title: A549.starr_seq.dex.4hr.rep2

value: dexamethasone


title: PL16_vc

source_name: genomic DNA from PL16 aCA placenta

tag: 850k sentrix_id


title: AAA0500964  [miRNA-Seq]

value: intestinal tissue


title: A549.starr_seq.dex.4hr.rep1

source_name: A549 Cells

tag: starr-seq reporter library


title: PL79_vc

source_name: genomic DNA from PL79 aCA placenta


title: PL107_vc

source_name: genomic DNA from PL107 aCA placenta


title: A549.starr_seq.dex.1hr.rep5

tag: cell line


title: AAA0500975  [miRNA-Seq]

value: ulcerative colitis

value: patients with active ulcerative colitis before receiving glucocorticoids  and who will have a poor response to treatment (non-responders, NR)


title: AAA0500965  [miRNA-Seq]


title: A549.starr_seq.dex.1hr.rep4


title: PM77_vc

source_name: genomic DNA from PM77 aCA placenta

value: M


title: A549.starr_seq.dex.1hr.rep3


title: AAA0500955  [miRNA-Seq]

description: G2_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)


title: PL115_vc

source_name: genomic DNA from PL115 aCA placenta

value: chorioamnionitis


title: MIF_161208_8h Rep. 3

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix haybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0007

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: cardiac fibroblasts treated for 8 hrs with 8 nM MIF

label_protocol: Fragmented, biotinylated cDNAs were prepared from 150 ng total RNA using  the Affymetrix WT plus reagent kit according to the manufacturers instructions.

growth_protocol: Cardiac fibroblasts were isolated from hearts of neonatal wildtype mice (C57BL/6J) and maintained for 10 to 14 days in culture, where they fully differentiated into myofibroblasts.

extract_protocol: After 8 hours of stimulation, supernatant was removed and total RNA was isolated using the Nucleo Spin RNA/Protein kit (Machery-Nagel, Düren, Germany).

treatment_protocol: Myofibroblasts were solitarily as well as co-treated with either 8nM MIF or 40nM sCD74 for 8 hours.

value: heart

tag: age

value: 1-7 days post natal

tag: genetic background

tag: genotype

value: wildtype

value: cardiac fibroblasts


title: sCD74_161208_8h Rep. 3

source_name: cardiac fibroblasts treated for 8 hrs with 40 nM sCD74

tag: tissue

tag: cell type


title: AAA0500961  [miRNA-Seq]

description: G1_healthy controls

value: healthy controls


title: AAA0500954  [miRNA-Seq]

value: patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)


title: AAA0500967  [miRNA-Seq]


title: PL43_vc

source_name: genomic DNA from PL43 aCA placenta

tag: patient id

tag: 850k sentrix_position


title: AAA0500953  [miRNA-Seq]


title: sCD74_161118_8h Rep. 2


title: A549.starr_seq.dex.1hr.rep2

value: GM12878 Whole Genome STARR-seq Reporter Library

tag: time point (hour)

tag: agent


title: A549.starr_seq.dex.1hr.rep1


title: PL31_vc

source_name: genomic DNA from PL31 aCA placenta


title: MIF_161027_8h Rep. 1


title: MIF_161118_8h Rep. 2


title: AAA0500952  [miRNA-Seq]

tag: disease state

tag: group


title: A549.starr_seq.dex.0hr.rep5

value: Vehicle treatment (Ethanol)


title: PL20_vc

source_name: genomic DNA from PL20 aCA placenta

tag: pathology group

tag: fetal sex


title: AAA0500949  [miRNA-Seq]

description: G1_healthy controls


title: AAA0500943  [miRNA-Seq]

value: third day of treatment in treatment-responders (R) patients


title: PL108_vc

source_name: genomic DNA from PL108 aCA placenta

value: F

tag: gestational age

tag: 850k plate


title: PL58_vc

source_name: genomic DNA from PL58 aCA placenta

value: Chorionic villi

tag: 850k sentrix_id


title: con_161208_8h Rep. 3

source_name: cardiac fibroblasts treated for 8 hrs with carrier solution


title: A549.starr_seq.dex.0hr.rep3

tag: starr-seq reporter library

tag: cell line


title: sCD74_161027_8h Rep. 1

tag: age

tag: genetic background


title: A549.starr_seq.dex.0hr.rep4


title: PL14_vc

source_name: genomic DNA from PL14 aCA placenta

tag: tissue


title: A549.starr_seq.dex.0hr.rep2


title: BH500(pSW4)_OD=16_Run3

city: Bethesda

first: Ashish

middle: K

last: Sharma

state: MD

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institute of Health

data_processing:
Bcl2fastq2 software was used for base-calling.
The sequenced reads were trimmed to remove the low quality bases with the following parameters Trim based on : Quality score; Min read length : 25; Max N : FALSE ; End min quality level (Phred) : 20 ; Trim from end : 3-prime (right end).
Bowtie2 method was used to align the RNA-seq reads with the reference organism Bacillus anthracis str ames AE017334.2.
The quantification of transcriptome abundance was performed using Partek E/M algorithm in PartekFlow software.
Data was normalized using TPM method and differential gene expression were predicted across comparisions using ANOVA.
Genome_build: ASM844v1
Supplementary_files_format_and_content: tab-delimited text file contains normalized values obtained after TPM normalization, addition +1 and log2 transformation.
tab-delimited text file contains results from ANOVA and includes fold change calculations among pYS5 LagPhase vs pSW4 LagPhase, pYS5 LogPhase vs pSW4 LogPhase, pYS5 LateLogPhase vs pSW4 LateLogPhase, along with p-value, FDR stepup etc.

organism: Bacillus anthracis str. Ames

extract_protocol:
Culture samples were immediately treated with RNA protect and preserved in Trizol at -80 degree celcius and total RNA was extracted using hot phenol method.
The NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used to prepare the complete RNA-seq library preparation. First strand cDNA synthesis was performed using NEBNext first strand synthesis reaction buffer, random primers, Protoscript II reverse. To the same reaction mix, second strand synthesis enzyme mix was added and second strand synthesis was. The synthesized cDNA strands were purified using a 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Later steps involved end repair of extracted cDNA, adapter ligation using blunt/TA ligase and cleavage by USER enzyme, purification with AMPure XP beads and PCR enrichment of cDNA library using different sets of Multilex oligos for Illumina. The enriched library was again purified with Agencourt AMPure XP beads, and its quality was checked on a Bioanalyzer using Agilent DNA high sensitivity chips according to the manufacturer’s instructions.

tag: strain

tag: growth phase

value: Late log phase

tag: protocol

value: control

tag: expression

value: Non-Producer

tag: od at harvest


title: PL103_vc

source_name: genomic DNA from PL103 aCA placenta

tag: patient id

tag: 850k sentrix_position


title: AAA0500941  [miRNA-Seq]

value: intestinal tissue

tag: disease state

value: ulcerative colitis

tag: group

value: Non-Responders (NR) patients collected on the 3rd day


title: A549.starr_seq.dex.0hr.rep1

tag: agent


title: BH500(pSW4)_OD=10_Run3

value: log phase


title: AAA0500940  [miRNA-Seq]


title: con_161118_8h Rep. 2

value: heart

value: 1-7 days post natal

tag: genotype

tag: cell type


title: BH500(pSW4)_OD=3_Run3

value: lag phase


title: CD74_MIF_161208_8h Rep. 3

source_name: cardiac fibroblasts treated for 8 hrs with 8 nM MIF & 40 nM sCD74

value: wildtype

value: cardiac fibroblasts


title: PL106_vc

source_name: genomic DNA from PL106 aCA placenta

tag: pathology group

value: chorioamnionitis

tag: fetal sex

tag: gestational age

tag: 850k plate

tag: 850k sentrix_id


title: PL28_vc

source_name: genomic DNA from PL28 aCA placenta

tag: tissue


title: CD74_MIF_161118_8h Rep. 2

tag: age

tag: genetic background


title: BH500(pSW4)_OD=16_Run2

tag: strain

tag: growth phase

tag: protocol

tag: expression


title: flower-day8, rep2

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

data_processing:
miRNA-seq reads were subjected to quality and adapter trimming using the Trim Galore tool (https://github.com/FelixKrueger/TrimGalore) with parameters ‘--length 17 --phred33’.
Clean reads were mapped to A. thaliana genome using the STAR algorithm with the following parameters: ‘--outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.03 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1 --genomeLoad NoSharedMemory’.
miRNAs were quantified in RPM (reads per million mapped reads) values based on the count number from STAR output. Annotation of miRNA genes were obtained from the miRBase database (release 21) (Griffiths-Jones et al. 2008).
Genome_build: TAIR10
Supplementary_files_format_and_content: xlsx

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: Plants were grown in a climatized greenhouse under long day conditions(16 h light, 8 h dark).

extract_protocol:
RNAs were isolated by the Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen, Germany) according to manufacturer.
2 μg total RNA was used to produce libraries using TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina, USA). Pooled libraries were submitted to a NextSeq®550 sequencing platform (Illumina, USA) for sequencing.

treatment_protocol: pAP1:AP1-GR ap1-1 cal-1 plants were induced daily with DEX- induction solution (2 mM Dexamethasone, 0.01% (v/v) ethanol, and 0.01% Silwet L-77). Inflorescences were harvested before treatment and 2, 4 and 8 days after induction.

tag: ecotype

value: Landsberg

tag: genotype/variation

value: pAP1:AP1:GR ap1 cal

value: DEX

value: inflorescences

tag: time

value: 8 days after treatment


title: AAA0500930  [miRNA-Seq]

tag: disease state

tag: group

value: patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)


title: CD74_MIF_161027_8h Rep. 1

tag: genotype

tag: cell type


title: flower-day8, rep1

tag: agent


title: flower-day8, rep3


title: AAA0500942  [miRNA-Seq]

value: third day of treatment in treatment-responders (R) patients


title: con_161027_8h Rep. 1


title: PL56_vc

source_name: genomic DNA from PL56 aCA placenta

tag: patient id

value: Chorionic villi

tag: pathology group

tag: fetal sex

value: F

tag: gestational age

tag: 850k plate

tag: 850k sentrix_position


title: AAA0500929  [miRNA-Seq]

tag: tissue

value: intestinal tissue

value: ulcerative colitis

value: patients with active ulcerative colitis before receiving glucocorticoids  and who will have a poor response to treatment (non-responders, NR)


title: BH500(pSW4)_OD=10_Run2

tag: strain

tag: growth phase

value: log phase

tag: protocol

value: control

value: Non-Producer

tag: od at harvest


title: flower-day4, rep1

tag: ecotype

tag: genotype/variation

tag: time

value: 4 days after treatment


title: flower-day4, rep2


title: PL104_vc

source_name: genomic DNA from PL104 aCA placenta

tag: 850k sentrix_id


title: AAA0500931  [miRNA-Seq]

tag: disease state

tag: group


title: BH500(pSW4)_OD=16_Run1

value: Late log phase

tag: expression


title: flower-day2, rep3

value: Landsberg

tag: agent

value: 2 days after treatment


title: AAA0500919  [miRNA-Seq]


title: BH500(pSW4)_OD=10_Run1


title: PM161_vc

source_name: genomic DNA from PM161 aCA placenta

tag: patient id

tag: pathology group

tag: fetal sex


title: BH500(pSW4)_OD=3_Run1

value: lag phase


title: PM116r_vc

source_name: genomic DNA from PM116 aCA technical replicate placenta

value: M

tag: gestational age

tag: 850k plate

tag: 850k sentrix_position


title: PL42_vc

source_name: genomic DNA from PL42 aCA placenta

tag: tissue

value: chorioamnionitis


title: AAA0500916  [miRNA-Seq]

value: Non-Responders (NR) patients collected on the 3rd day


title: BH500(pYS5)_OD=16_Run3

tag: strain

tag: growth phase

tag: protocol

value: transformed with pYS5

value: PA producer


title: flower-day2, rep2

tag: ecotype

tag: genotype/variation

value: pAP1:AP1:GR ap1 cal

value: DEX

value: inflorescences


title: flower-day2, rep1

tag: time

value: 0 days after treatment


title: AAA0500914  [miRNA-Seq]

value: intestinal tissue

tag: disease state

value: ulcerative colitis


title: flower-day0, rep2

value: not treated