title: 142_016

source_name: Normo4 Pancreatic islet MVEC(Microvascular Endothelial Cells)


title: TP0001651E05_7_30.000000uM_DMEM_6h_TC00283151_B02

status: Public on Jan 25 2021

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description:
TP0001651E05_7_30.000000uM_DMEM_6h
TC00283151_B02

library_source: transcriptomic

data_processing:
[Read alignment]  Each FASTQ file was aligned to the probe sequences in the hWTv1 assay using HISAT2 v2.1.0 with spliced alignment disabled.
[Probe counts]  Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Genome_build: hWTv1
Supplementary_files_format_and_content: httr_mcf7_pilot_count_data.csv - processed data provided as a single table of counts for all probes x all samples
hWTv1_mcf7_probes.csv - contains the targeted probes for the TempO-seq assay

molecule: total RNA

organism: Homo sapiens

source_name: MCF7 Cells

growth_protocol: Five vials of cryopreserved MCF7 (HTB-22TM) cells were purchased from American Tissue Culture Collection, designated as passage 0 (P0) and stored in vapor phase liquid nitrogen prior to initial thawing and expansion. A passage 3 (P3) MCF7 cryostock was generated by thawing and pooling all five original source vials and culturing through three consecutive passages in complete growth medium (DMEM + 10% FBS + 1% PSG). At each passage, cells from different culture vessels were pooled prior to re-seeding for subsequent expansion. At P3, cells were cryopreserved at 4 million cells per mL in complete growth medium + 5% DMSO according to manufacturer’s protocol. MCF7 cultures used in all phases of this study were maintained in humidified incubators with 5% CO2 atmosphere and internal temperature of 37°C. For chemical screening, MCF7 cells were thawed and subjected to a uniform expansion protocol from P3 to P6 through increasingly larger sizes of tissue culture vessels (T25 to T75 to T225) prior to plating in 384-well format. The three cultures were initiated on consecutive days and subject to uniform handling procedures to ensure that dosing and sample collection also occurred on consecutive days. All chemical screening experiments were performed on P7 cells.

extract_protocol:
Six hours after chemical treatment, HTTr assay plates were removed from the incubator and media in each assay well was drained to a residual volume of 10 µL using MultiFlo FX microdispenser equipped with a vacuum-driven aspiration manifold. To create cell lysates, 10 µL volumes of 2X BioSpyder lysis buffer were dispensed into each assay well using the same MultiFlo FX instrument equipped with 1 µL peristaltic pump dispensing cassette. Then, 20 µL volumes of UHRR, HBRR, BLDSMO, BLTSA and Lysis Buffer reference material were manually dispensed into duplicate wells of column 1 of each assay plate. The plates were sealed with an adhesive aluminum plate cover and incubated at room temperature, protected from light, for 30 minutes. The plates were then stored at -80°C prior to shipment to BioSpyder, Inc.
Samples were analyzed by BioSpyder using a custom-attenuated version of the TempO-Seq human whole transcriptome version 1 (hWTv1) assay, which includes 21,111 probes covering 19,287 genes. Lysates were processed as described in (House et al. 2017). In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv1 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 hours. Excess oligos were then removed via nuclease digestion (90 min at 37°C) and hybridized detector oligos were ligated (60 min at 37°) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured and 10 µL of each ligation product was transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification (10 min at 37°C, 2 min at 95°C, 6 cycles of 95°C for 30 s, 54°C for 30 s, 72°C for 120 s, 16 cycles of 95°C for 30s and 72°C for 120s, followed by 72°C for 60 s) with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were then pooled into a series of three sequencing libraries (1 for each plate). Pooled sequencing libraries were then distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

treatment_protocol: DMSO-solubilized chemical stock solutions were received frozen from the US EPA ToxCast chemical inventory management contractor (EvoTec, Princeton, NJ) and stored at -80°C prior to dose plate preparation. An eight-point dilution series (1/2 log10 spacing) of test chemicals was prepared in a LabCyte Echo-qualified 384-well polypropylene (384PP) plate at 200x the desired nominal test concentration for screening (0.03 – 100 µM). Singleton wells of dosing solutions for each test chemical concentration were arrayed in columns 2 through 23 of the dose plate (Figure 1A). Transcriptomics reference chemicals (genistein, trichostatin A, sirolimus) were solubilized as 200x dosing solutions corresponding to nominal test concentrations of 10, 1 and 0.1 µM, respectively. Triplicate wells of dosing solutions for each of the transcriptomic reference chemicals were added to the dose plate (column 24) along with quadruplicate wells of pure DMSO as a vehicle control. At 24 h post-plating, 200 nL of 200x dosing solutions were transferred to the assay plates using a LabCyte Echo 550 acoustic dispenser. The final concentration of DMSO in all treatment, reference treatment and vehicle control wells was 0.5%.  Well coordinates on each assay plate were uniquely randomized with respect to treatment so that any potential edge-well effects were distributed in an unbiased manner across all possible treatment conditions.

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 6h exposure of 30 uM of Atrazine

tag: chemical name

value: Atrazine

tag: chemical sample id

tag: chemical concentration

value: 30 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: col_r1_ATACseq

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
ATAC-seq read adaptors were removed with trim_galore and then mapped to the Arabidopsis thaliana reference genome TAIR10 using Bowtie (-X 2000 -m 1).
Reads aligned to chloroplast and mitochondrial DNA were filtered out and duplicated reads were removed using SAMtools.
ATAC-seq peaks were called by HMMRATAC with minlength 50 bp.
Paired-end Hi-C reads were aligned to tair10 with HiC-Pro (v2.11.1). Whole genome Hi-C heatmap was converted with juicer_tools (v1.13.02) and visualized with Juicebox (v1.11.08). Hi-C loops were called with analyzeHiC in Homer2 with 200 bp resolution and pvalue < 1e-10. The WashU EpiGenome Browser v46.2 (https://epgg-test.wustl.edu/browser/) was used to visualize Hi-C loops and ATAC-seq data. PC1 value of Hi-C data was calculated with Homer2. Regional Hi-C visualization was performed by hicexplorer (v3.4.3).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: ATAC-seq mapping file hic: Hi-C interaction file

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown at 22 °C in a long day (16 hour light, 8 hour dark) growth room. Flowers and leaves were collected from 4-5 week-old plants. For Hi-C, plants grown on agar plates at 21◦C under constant light for 14 days before seedling tissues (without roots) were harvested. Then, nuclei were isolated and flow–sorted from seedlings after formaldehyde fixation using a FACS Aria (BD Biosciences) according to their 2C and 4C ploidy level.

extract_protocol:
Inflorescence tissues were collected for nuclei extraction as follows. About 5 g of inflorescence tissue was collected and immediately transferred into ice-cold grinding buffer (300 mM sucrose, 20 mM Tris pH 8, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, 35% glycerol). The samples were ground with Omni International General Laboratory Homogenizer at 4 °C and then filtered through a two-layer Miracloth and a 40-µm nylon mesh Cell Strainer (Fisher). Samples were spin filtered for 10 min at 3,000 g, the supernatant was discarded, and the pellet was resuspended with 25 ml of grinding buffer using a Dounce homogenizer. The wash step was repeated once and the nuclei were resuspended in 0.5 ml of freezing buffer (50 mM Tris pH 8, 5 mM MgCl2, 20% glycerol, 5 mM β-mercaptoethanol).  Hi-C libraries for Illumina sequencing were generated53. The libraries were sequenced on HiSeq 2000 DNA sequencers obtaining paired-end 50- or 51-nucleotide reads following manufacturer instructions (Illumina).
Nuclei were subjected to transposition reaction with Tn5 (Illumina, cat. no. FC-121-1030). For transposition reaction, 25 µl of 2x DMF (66mM Tris-acetate (pH=7.8), 132 mM K-Acetate, 20mM Mg-Acetate, 32 % DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37 °C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo, cat. no. D5205). Libraries were preparated with Phusion High-Fidelity DNA Polymerase (NEB, cat. no. M0530S) (12.5µl 2x Phusion, 1.25µl 10 mM Ad1 primer, 1.25µl 10 mM Ad2 primer, 4 µl ddH2O and 6µl purified transposed DNA fragments).

tag: ecotype background

tag: genotype/variation

value: wild type

tag: developmental stage

value: 4 weeks

tag: tissue

value: flowers


title: 142_015

city: Uppsala

first: Anders

middle: Roger

last: Hedin

state: Uppland

address: Dag Hammarskjölds väg 20.

department: Clinical immunology

country: Sweden

institute: Uppsala University

description: NOTE: Raw data is not included because the files were deleted by the sequencing center.

data_processing:
The raw counts were generated at a separate facility using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip in 3 separate runs. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.  The produced reads were aligned to hg19 AmpliSeq Transcriptome ERCC v1. All further analysis was done using the raw counts estimated after mapping.
Two samples(142_021, 142_037, ) produced low quality reads and were excluded from further analysis
The counts from the arterial samples were excluded from further analysis, as they were produced with a different protocol
The transcripts were filtered using the edgeR function "filterbyexpr" with default options and the remaining counts
TMM normalization factors were calculated using "calcnormfactors" in edgeR
TMM- CPM- log2 normalized reads were producted using "cpm(method="TMM, log=TRUE)" in edgeR
Genome_build: Tab- delimited text file with raw counts for each sample that were sequenced
Supplementary_files_format_and_content: comma separated value(CSV) text file with TMM- CPM- log2 normalized counts for each included sample and each transcript that passed

source_name: IGM2 Pancreatic arterial luminal cells

extract_protocol:
Pancreatic islet tissue and pancreatic exocrine tissue was was digested to single cells and endothelial cells were then isolated using FACS. Luminal arterial cells were digested to single cells but not sorted. RNA was extracted.
Libraries were constructed using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit. RNA seq was then done using the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip in 3 separate runs. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.

value: Cells from luminal arteries in the pancreas

tag: condition

value: IGM(Impaired glucose metabolism)


title: UHRR_TC00283151_B01

description:
UHRR
TC00283151_B01

source_name: Universal Human Reference RNA

tag: sample type

value: UHRR

value: untreated


title: 49_M_WT_10_RRBS

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
reads were preprocessed with Trim Galore v. 0.4.0, a wrapper for cutadapt v. 1.9.1, with the --rrbs flag set
trimmed reads were aligned to the mm10 genome assembly using Bismark v. 0.18.1 with default parameters
CpG methylation calls were summarized using the bismark2bedgraph script which is part of the Bismark software suite
For each CpG, observations from both strands were added together to form an overall methylation level per CpG, and only CpGs covered by eight or more reads in every sample was retained
Genome_build: mm10
Supplementary_files_format_and_content: csv file with CpGs in rows and genomic annotation along with number of methylated and unmethylated observations for each sample in columns.

organism: Mus musculus

source_name: Male_WT_10_soleus muscle

extract_protocol:
A single soleus muscle or ~30 mg of powdered quadriceps was homogenized in 400 µl of RLT buffer (Qiagen) with β-mercaptoethanol using steal beads and subjected to 2 x 30 sec at 30 Hz of disruption using the TissueLyser II (Qiagen). RNA and DNA were simultaneously isolated from 350 µl of lysate using the RNA/DNA/miRNA AllPrep kit (Qiagen) as per instructions. Primary muscle cells were lysed directly in RLT buffer and RNA extracted using the RNeasy kit (Qiagen). RNA was eluted in 45 µl of RNAse free water and DNA in 60 µl of elution buffer (Qiagen).
Reduced Representation Bisulfite Sequencing (RRBS) was performed as described (Laker et al., 2017). Briefly, DNA samples were incubated with MpsI enzyme (NEB) in order to fragment DNA at CCGG positions to enrich for CpG regions. Bisulfite conversion was performed using the EZ DNA methylation Kit (Zymo Research) according to the manufacturer’s instructions. The DNA was then PCR amplified and ligated to TruSeq (Illumina) sequencing adapters. Libraries were subjected to 75-bp single-end sequencing on the NextSeq 550 (Illumina). On average 18.3 million reads/sample were aligned

tag: strain background

tag: Sex

value: Male

tag: genotype

value: WT

tag: timepoint

value: soleus muscle


title: 45_M_KO_10_RRBS

source_name: Male_KO_10_soleus muscle

value: KO


title: 47_F_WT_10_RRBS

source_name: Female_WT_10_soleus muscle

value: Female


title: 44_F_WT_30_RRBS

source_name: Female_WT_30_soleus muscle


title: cmt3_r2_ATACseq


title: 43_F_KO_30_RRBS

source_name: Female_KO_30_soleus muscle


title: TP0001651D06_7_30.000000uM_DMEM_6h_TC00283151_A24

description:
TP0001651D06_7_30.000000uM_DMEM_6h
TC00283151_A24

tag: cell line

tag: media

tag: treatment

value: 6h exposure of 30 uM of PFOS

tag: chemical name

value: PFOS


title: TP0001651C06_7_30.000000uM_DMEM_6h_TC00283151_A23

description:
TP0001651C06_7_30.000000uM_DMEM_6h
TC00283151_A23

value: DMEM + 10% HI-FBS

value: 6h exposure of 30 uM of Cycloheximide

value: Cycloheximide

tag: chemical sample id

tag: chemical concentration

tag: dose level

tag: exposure time


title: cmt2_r2_ATACseq

tag: ecotype background

tag: genotype/variation


title: TP0001651D06_3_0.300000uM_DMEM_6h_TC00283151_A22

description:
TP0001651D06_3_0.300000uM_DMEM_6h
TC00283151_A22

value: 6h exposure of 0.3 uM of PFOS

tag: assay plate

tag: assay plate well


title: 41_M_KO_30_RRBS

source_name: Male_KO_30_soleus muscle

tag: tissue


title: TP0001651C06_5_3.000000uM_DMEM_6h_TC00283151_B03

description:
TP0001651C06_5_3.000000uM_DMEM_6h
TC00283151_B03

value: 6h exposure of 3 uM of Cycloheximide

value: 3 uM


title: 42_M_WT_10_RRBS

tag: strain background


title: 142_014

source_name: IGM2 Pancreatic exocrine MVEC(Microvascular Endothelial Cells)

value: FACS sorted endothelial cells from exocrine pancretic tissue

tag: condition


title: cmt3_r1_ATACseq

tag: developmental stage

value: 4 weeks

value: flowers


title: 142_017

source_name: Normo4 Pancreatic exocrine MVEC(Microvascular Endothelial Cells)

value: Normoglycemic


title: cmt2_r1_ATACseq


title: col_r2_ATACseq

value: wild type


title: 48_M_KO_30_RRBS

tag: Sex

value: Male

tag: genotype

tag: timepoint


title: 142_011

source_name: Normo3 Pancreatic exocrine MVEC(Microvascular Endothelial Cells)


title: TP0001651E03_8_100.000000uM_DMEM_6h_TC00283151_A21

description:
TP0001651E03_8_100.000000uM_DMEM_6h
TC00283151_A21

tag: cell line

tag: media

tag: treatment

value: 6h exposure of 100 uM of Prochloraz

value: Prochloraz


title: cmt23_r2_ATACseq


title: TP0001651D03_4_1.000000uM_DMEM_6h_TC00283151_A20

description:
TP0001651D03_4_1.000000uM_DMEM_6h
TC00283151_A20

value: 6h exposure of 1 uM of Cypermethrin

tag: chemical name

value: Cypermethrin

tag: chemical sample id

tag: chemical concentration

value: 1 uM


title: 142_009

source_name: Normo2 Pancreatic arterial luminal cells

value: Cells from luminal arteries in the pancreas


title: TP0001651A03_8_100.000000uM_DMEM_6h_TC00283151_A19

description:
TP0001651A03_8_100.000000uM_DMEM_6h
TC00283151_A19

value: DMEM + 10% HI-FBS

value: 6h exposure of 100 uM of Butafenacil

value: Butafenacil

tag: dose level

tag: exposure time


title: 39_F_KO_10_RRBS

source_name: Female_KO_10_soleus muscle

value: Female

value: KO

value: soleus muscle


title: 142_010

source_name: Normo3 Pancreatic islet MVEC(Microvascular Endothelial Cells)

value: FACS sorted endothelial cells from pancreatic Islet


title: 38_M_WT_30_RRBS

source_name: Male_WT_30_soleus muscle

value: WT


title: cmt23_r1_ATACseq

tag: ecotype background

tag: genotype/variation

value: 4 weeks

value: flowers


title: 142_012

source_name: Normo3 Pancreatic arterial luminal cells

tag: tissue

value: Normoglycemic


title: ago4_r2_ATACseq


title: 36_M_KO_30_RRBS

tag: strain background

value: Male


title: TP0001651B02_2_0.100000uM_DMEM_6h_TC00283151_A18

description:
TP0001651B02_2_0.100000uM_DMEM_6h
TC00283151_A18

source_name: MCF7 Cells

value: 6h exposure of 0.1 uM of 3,5,3'-Triiodothyronine

tag: assay plate

tag: assay plate well


title: 37_M_WT_30_RRBS

tag: Sex


title: TP0001651H03_3_0.300000uM_DMEM_6h_TC00283151_A15

description:
TP0001651H03_3_0.300000uM_DMEM_6h
TC00283151_A15

value: 6h exposure of 0.3 uM of Fomesafen

value: Fomesafen


title: TP0001651D06_5_3.000000uM_DMEM_6h_TC00283151_A17

description:
TP0001651D06_5_3.000000uM_DMEM_6h
TC00283151_A17

value: 6h exposure of 3 uM of PFOS

value: PFOS

value: 3 uM


title: CL1

city: St Louis

first: Carolina

middle: B

last: Lopez

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
fastq files were aligned to human reference genome Homo_Sapiens.GRCh38 using Kallisto
Abundance resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (>1-fold and <1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample .

source_name: cbDVG-_nasal washes

extract_protocol:
Total RNA was extracted using Trizol
SMARTer Stranded Total RNA-seq kit v2-Pico Input Mammalian (Takara) was used to prepare the cDNA libraries according to the manufacturer’s instruction

tag: subject status

value: hospitalized pediatric patient

tag: cbdvg status

value: cbDVG-

tag: virus

value: RSV A

tag: sample type

value: nasal washes


title: 35_M_WT_10_RRBS

tag: genotype

tag: timepoint

value: soleus muscle


title: ago4_r1_ATACseq

tag: developmental stage


title: 34_M_KO_10_RRBS

value: KO


title: 142_006

source_name: Normo1 Pancreatic arterial luminal cells

value: Cells from luminal arteries in the pancreas

tag: condition


title: TP0001651A01_6_10.000000uM_DMEM_6h_TC00283151_A16

description:
TP0001651A01_6_10.000000uM_DMEM_6h
TC00283151_A16

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 6h exposure of 10 uM of Pyraclostrobin

tag: chemical name

value: Pyraclostrobin

tag: chemical sample id

tag: chemical concentration

value: 10 uM

tag: dose level


title: 142_005

source_name: Normo1 Pancreatic exocrine MVEC(Microvascular Endothelial Cells)

tag: tissue

value: FACS sorted endothelial cells from exocrine pancretic tissue

value: Normoglycemic


title: 33_F_KO_30_RRBS

tag: strain background

tag: Sex

value: Female


title: ZFDMS3_r1_ATACseq

tag: ecotype background

tag: genotype/variation

value: 4 weeks

value: flowers


title: 32_F_WT_30_RRBS

value: WT


title: 142_004

source_name: Normo1 Pancreatic islet MVEC(Microvascular Endothelial Cells)

value: FACS sorted endothelial cells from pancreatic Islet


title: 31_F_WT_30_RRBS


title: 142_008

source_name: Normo2 Pancreatic exocrine MVEC(Microvascular Endothelial Cells)


title: CL71

tag: subject status

value: hospitalized pediatric patient

tag: cbdvg status

value: cbDVG-

tag: virus

tag: sample type


title: 142_002

source_name: IGM1 Pancreatic exocrine MVEC(Microvascular Endothelial Cells)

tag: condition

value: IGM(Impaired glucose metabolism)


title: 142_007

source_name: Normo2 Pancreatic islet MVEC(Microvascular Endothelial Cells)


title: TP0001651A06_3_0.300000uM_DMEM_6h_TC00283151_A13

description:
TP0001651A06_3_0.300000uM_DMEM_6h
TC00283151_A13

tag: cell line

value: 6h exposure of 0.3 uM of Cyproconazole

value: Cyproconazole

tag: exposure time

tag: assay plate

tag: assay plate well


title: CL38

value: RSV A

value: nasal washes


title: ZFDMS3_r2_ATACseq

tag: developmental stage


title: TP0001651C03_3_0.300000uM_DMEM_6h_TC00283151_A12

description:
TP0001651C03_3_0.300000uM_DMEM_6h
TC00283151_A12

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 6h exposure of 0.3 uM of Simazine

tag: chemical name

value: Simazine

tag: chemical sample id

tag: chemical concentration


title: TP0001651C04_1_0.030000uM_DMEM_6h_TC00283151_A14

description:
TP0001651C04_1_0.030000uM_DMEM_6h
TC00283151_A14

value: 6h exposure of 0.03 uM of Simvastatin

value: Simvastatin

tag: dose level


title: TP0001651G04_3_0.300000uM_DMEM_6h_TC00283151_A11

description:
TP0001651G04_3_0.300000uM_DMEM_6h
TC00283151_A11

value: 6h exposure of 0.3 uM of Cladribine

value: Cladribine


title: CL136


title: 142_003

source_name: IGM1 Pancreatic arterial luminal cells

tag: tissue

value: Cells from luminal arteries in the pancreas


title: 142_001

source_name: IGM1 Pancreatic islet MVEC(Microvascular Endothelial Cells)


title: 142_013

source_name: IGM2 Pancreatic islet MVEC(Microvascular Endothelial Cells)


title: TP0001651C06_4_1.000000uM_DMEM_6h_TC00283151_A10

description:
TP0001651C06_4_1.000000uM_DMEM_6h
TC00283151_A10

value: 6h exposure of 1 uM of Cycloheximide

value: Cycloheximide

value: 1 uM


title: 29_F_KO_30_RRBS

source_name: Female_KO_30_soleus muscle

tag: strain background

tag: Sex

value: Female

tag: genotype

value: KO

tag: timepoint

value: soleus muscle


title: CL55

source_name: cbDVG+_nasal washes

tag: subject status

value: hospitalized pediatric patient

tag: cbdvg status

value: cbDVG+

tag: virus

tag: sample type


title: 27_M_KO_30_RRBS

source_name: Male_KO_30_soleus muscle

value: Male


title: CL43

value: cbDVG-

value: RSV A

value: nasal washes


title: 28_F_KO_10_RRBS

source_name: Female_KO_10_soleus muscle


title: CL48


title: CL72


title: TP0001651D02_6_10.000000uM_DMEM_6h_TC00283151_A09

description:
TP0001651D02_6_10.000000uM_DMEM_6h
TC00283151_A09

tag: cell line

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of PFOA

value: PFOA

value: 10 uM

tag: exposure time

tag: assay plate

tag: assay plate well


title: 26_M_KO_10_RRBS

source_name: Male_KO_10_soleus muscle


title: 30_F_WT_10_RRBS

source_name: Female_WT_10_soleus muscle

value: WT


title: CL111


title: TP0001651G05_5_3.000000uM_DMEM_6h_TC00283151_A06

description:
TP0001651G05_5_3.000000uM_DMEM_6h
TC00283151_A06

source_name: MCF7 Cells

tag: media

tag: treatment

value: 6h exposure of 3 uM of Cyproterone acetate

tag: chemical name

value: Cyproterone acetate

value: 3 uM


title: TP0001651E01_5_3.000000uM_DMEM_6h_TC00283151_A07

description:
TP0001651E01_5_3.000000uM_DMEM_6h
TC00283151_A07

value: 6h exposure of 3 uM of Bifenthrin

value: Bifenthrin

tag: chemical sample id

tag: chemical concentration

tag: dose level


title: 25_F_WT_60_RRBS

source_name: Female_WT_60_soleus muscle

tag: strain background

tag: Sex

value: Female

tag: tissue

value: soleus muscle


title: 24_F_KO_Bas_RRBS

source_name: Female_KO_Bas_soleus muscle

tag: genotype

value: KO

tag: timepoint

value: Bas


title: CL98

tag: subject status

value: hospitalized pediatric patient

tag: cbdvg status

value: cbDVG+

tag: virus


title: TP0001651B04_8_100.000000uM_DMEM_6h_TC00283151_A05

description:
TP0001651B04_8_100.000000uM_DMEM_6h
TC00283151_A05

tag: cell line

value: 6h exposure of 100 uM of Propiconazole

value: Propiconazole

tag: exposure time


title: CL44

value: RSV A

tag: sample type

value: nasal washes


title: TP0001651D05_2_0.100000uM_DMEM_6h_TC00283151_A04

description:
TP0001651D05_2_0.100000uM_DMEM_6h
TC00283151_A04

tag: media

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of Thiram

value: Thiram

tag: assay plate

tag: assay plate well


title: 23_F_KO_60_RRBS

source_name: Female_KO_60_soleus muscle


title: DMSO_DMEM_6h_TC00283151_A03

description:
DMSO_DMEM_6h
TC00283151_A03

tag: treatment

value: 0.5% DMSO vehicle control

tag: chemical name

value: DMSO

tag: chemical sample id

value: 0 uM


title: CL37


title: 22_F_WT_60_RRBS

tag: strain background

value: WT


title: TP0001651B03_4_1.000000uM_DMEM_6h_TC00283151_A02

description:
TP0001651B03_4_1.000000uM_DMEM_6h
TC00283151_A02

value: 6h exposure of 1 uM of Reserpine

value: Reserpine

tag: chemical concentration

value: 1 uM

tag: dose level


title: 21_F_KO_Bas_RRBS

tag: Sex

value: Female

tag: genotype

value: KO

value: Bas

tag: tissue

value: soleus muscle


title: TP0001651H05_1_0.030000uM_DMEM_6h_TC00283151_A08

description:
TP0001651H05_1_0.030000uM_DMEM_6h
TC00283151_A08

value: 6h exposure of 0.03 uM of Trifloxystrobin

value: Trifloxystrobin


title: 20_F_WT_Bas_RRBS

source_name: Female_WT_Bas_soleus muscle

tag: timepoint


title: CL39

tag: subject status

value: hospitalized pediatric patient

tag: cbdvg status

value: cbDVG+

tag: virus

value: RSV A

value: nasal washes


title: UHRR_TC00283151_A01

description:
UHRR
TC00283151_A01

source_name: Universal Human Reference RNA

tag: sample type

value: UHRR

value: untreated

tag: exposure time


title: wild type - control - animal 405 [re-analysis]

type: RNA

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Hybridization to Affymetrix HT MG-430 PM Array Plates was performed at the Microarray Department of the University of Amsterdam, the Netherlands according to Affymetrix protocols.

scan_protocol: Scanning was performed according to Affymetrix protocols.

data_processing: Quality control and RMA normalization were performed using the pipeline at the www.arrayanalysis.org website maintained by Maastricht University.

label: biotin

source_name: wild type - control

label_protocol: Labeling was performed at the Microarray Department of the University of Amsterdam, the Netherlands according to Affymetrix protocols.

growth_protocol: Ercc1Δ/- mice were obtained by crossing Ercc1Δ/+ (in a pure C57BL6J or FVB background) with Ercc1+/- mice (in a pure FVB or C57BL6J background respectively) to yield Ercc1Δ/- with an F1 C57BL6J/FVB hybrid background. Wild-type F1 littermates were used as controls.All animals used in the studies described in this paper were of the same F1 C57BL6J/FVB hybrid background. Typical unfavorable characteristics, like blindness in an FVB background or deafness in a C57BL6J background, do not occur in this hybrid background. Mice were weighed, visually inspected weekly, and scored for gross morphological and motor abnormalities. Experiments were performed in accordance with the Principles of Laboratory Animal Care and with the guidelines approved by the Dutch Ethical Committee in full accordance with European legislation.

extract_protocol: Total RNA was extracted from liver of 11 week old wild type and Ercc1Δ/- mice on AL and DR feeding regimen (n=5). Total RNA was extracted using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN, Hilden, Germany), following Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Fisher Scientific) and quality assessment of the RNA using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) following manufacturer’s instructions.

treatment_protocol: Animals were maintained in a controlled environment (20–22 °C, 12 h light:12 h dark cycle) and were housed in individual ventilated cages under Specific Pathogen Free conditions.  Food and water were offered ad libitum unless otherwise stated. All animals were bred and maintained on AIN93G synthetic pellets (Research Diet Services B.V., Wijk bij Duurstede, The Netherlands). For the rapamycin-containing diet, Microencapsulated rapamycin (eRapa) microcapsules were obtained from Southwestern Research Institute (San Antonio, TX, USA).140 mg eRapa, containg 10% Rapamycin, was added per kg AIN93G food mix, resulting in a 14 ppm rapamycin supplemented diet. Supplemented eRapa and control diets were supplied ad libitum to the mice at either 4 or 8 weeks of age for the remainder of their life. Dietary restriction was initiated at 7 weeks of age with 10% food reduction (2.1 g/day), when animals reached almost-maximum bodyweight and development was completed. Dietary restriction was increased weekly by 10%, until it reached 30% dietary restriction (1.6 g/day) from 9 weeks of age onward. Food was given to the animals just before the start of the dark (active) period to avoid alteration of the biological clock.

tag: strain

value: F1 C57BL6J/FVB

value: wild type

tag: protocol

value: control diet

value: liver


title: wild type - restricted - animal 423 [re-analysis]

source_name: wild type - restricted

value: dietary restriction


title: wild type - restricted - animal 425 [re-analysis]


title: wild type - control - animal 403 [re-analysis]


title: wild type - restricted - animal 421 [re-analysis]


title: SC_ADMi_1

city: Lund

first: Alexander

last: Pietras

address: Medicon Village 404:C3, Scheelevägen 2

department: Division of Translational Cancer Research

institute: Lund University

data_processing:
Demultiplexing: Demultiplexing step (bcl2fastq2) involves in reorganizing the FASTQ files based on the sample index information, and generating the statistics and reporting files.
Raw Quality Control (QC): FastQC provided quality control analyses and checked on raw sequence data coming from the above Demultiplexing step of the pipeline.
Read Mapping: This task was performed using the HISAT2 software, and the reference genome sequence was from the Ensembl database, and the human assembly was GRCh38.
Mapping QC: mapping quality control checked such as evaluating the distribution of reads mapped by the above mapping step.
Expression counts: assembled the alignments into full transcripts and quantified  the expression levels of each gene and transcript. This task was performed using the StringTie software package.
DE analysis: Differentially expressed genes (DEG) analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited files containing gene level FPKM and TPM values as obtained from the StringTie software package

source_name: U3082 HGCC human glioma cells

growth_protocol: U3082 cells were cultured in DMEM/F12 with Glutamax supplemented with 1% PenStrep, N2, B27, EGF, and FGF (HGC Medium) on  laminin-coated (BioLamina, Cat #LN521) plastic.

extract_protocol:
RNA Easy (qiagen)
Library was prepared according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.
TruSeq® Stranded mRNA Library Prep

treatment_protocol: U3082 cells were dissociated with Accutase and replated on matrix from primary human astrocytes obtained from either Lonza or 3H Biomedical.

tag: matrix source

value: 3H Biomedical astrocytes

tag: astrocyte treatment

value: 10 Gy Irradiated


title: P5251_508_4b-

data_processing:
Transcriptome libraries were generated using Illuminat TruSeq standard mRNA with Poly-A selection
Transcriptome libraries were seqenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2x126 setup using 'HiSeq SBS Kit v4' chemistry.
Reads were mapped with Tophat/2.0.4 to hg19
Merged bam files were sorted and duplicates removed using picard-tools/1.29.
Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
Counts were rlog normalized using DESeq2 combined with combat batch correction
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 rlog-ed and combat corrected gene based count matrix

source_name: human astrocytes_0 Gy

growth_protocol: Primary human astrocytes (3H Biomedical, Cat. #1800-10) were cultured in Human Astrocyte Medium (3H Biomedical, Cat. #SC1801) and were used below 15 passages.

extract_protocol:
RNeasy Mini Kit (Qiagen)
Illumina TruSeq standard mRNA with Ploy-A selection

treatment_protocol: Cells were treated with 0 Gy or 10 Gy gamma irradiation

tag: cell type

value: primary human astrocytes

tag: treatment

value: 0 Gy


title: wild type - restricted - animal 424 [re-analysis]


title: 19_M_KO_60_RRBS

source_name: Male_KO_60_soleus muscle

tag: strain background

value: Male

value: KO

value: soleus muscle


title: SC_ADMc_1

value: 0 Gy Control


title: SC_ADMi_2


title: LonAdmi

value: Lonza astrocytes


title: P5251_506_3a-


title: 17_M_KO_60_RRBS


title: 16_M_WT_60_RRBS

source_name: Male_WT_60_soleus muscle

value: WT


title: P5251_505_3a+

source_name: human astrocytes_10 Gy Irradiated


title: SC_ADMc_2


title: wild type - restricted - animal 422 [re-analysis]


title: 18_M_WT_60_RRBS


title: P5251_507_4a+


title: P5251_504_2a-


title: 14_M_WT_Bas_RRBS

source_name: Male_WT_Bas_soleus muscle

value: Bas


title: 3082_Nov17_1IR


title: 3082_Nov17_1C


title: 12_M_KO_Bas_RRBS

source_name: Male_KO_Bas_soleus muscle


title: P5251_503_2a+


title: P5251_502_1a-


title: wild type - control - animal 404 [re-analysis]


title: wild type - control - animal 402 [re-analysis]


title: Uveal melanoma biopsy, LH18.277

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Tumor tissues from patient diagnosed with uveal melanoma

data_processing:
The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Cell Ranger command used to produce output directory for each sample was executed using transcriptome based on human genome release hg38.
Samples were then merged after read depth correction using Cell Ranger aggregate function with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: HDF5: Cell Ranger raw gene / barcode hdf5 matrix file

source_name: Human uveal melanoma biopsy

extract_protocol:
Tumor tissues were obtained from patients diagnosed with ocular melanoma from the Nice CHU hospital. Surgically removed, primary tumor was kept in sterile and RPMI medium. To isolate viable single cells that are suitable for high-quality single-cell RNA-seq, tumor tissues were processed immediately after surgical resection to prepare individual cells suspension. Briefly, samples were minced on a plate and enzymatically digested with collagenase A (Roche), dispase II (Roche) and DNase I (Sigma) for 10 min at 37 °C, under agitation. The reaction is stop by adding fresh medium with 7% serum. To generate a single cell suspension, digested tumor tissue was subsequently filtered through 40-μm cell strainers to remove large clumps and debris. This step was repeated using a 15-μm cell strainer.   Pelleted cells were then resuspended in 2 mM EDTA in PBS, counted with the Scepter™ cell counter (MerckMillipore). Cell density was adjusted to 300 cells/µl. Dissociated single cells were stained for viability using the LIVE/DEAD® Viability/Cytotoxicity Kit for mammalian cells (Life Technologies).
Samples were run on the Chromium machine from 10x Genomics following the User Guide for v2 Chemistry. Single-cell RNA-Seq libraries were made following the User Guide for v2 Chemistry

tag: donor

tag: disease state

value: Uveal melanoma

value: Eye


title: 11_M_WT_Bas_RRBS

tag: Sex

tag: genotype


title: P5251_501_1a+


title: progeroid - rapamycin - animal 536

source_name: progeroid - rapamycin

value: F1 C57BL6J/FVB

value: rapamycin-containing diet

tag: tissue


title: LonAdmc


title: Uveal melanoma biopsy, LH17.3554


title: 10_M_KO_60_RRBS

tag: timepoint


title: progeroid - rapamycin - animal 537

value: liver


title: 13_M_WT_Bas_RRBS


title: progeroid - rapamycin - animal 535


title: wild type - control - animal 401 [re-analysis]

value: wild type

value: control diet


title: Uveal melanoma biopsy, LH17.3222


title: 9_M_WT_60_RRBS


title: Uveal melanoma biopsy, LH17.530


title: 8_M_KO_Bas_RRBS


title: 6_F_KO_60_RRBS

value: Female


title: progeroid - restricted - animal 366 [re-analysis]

source_name: progeroid - restricted

value: dietary restriction


title: Uveal melanoma biopsy, LH16.3814


title: 4_F_WT_60_RRBS

source_name: Female_WT_60_soleus muscle


title: progeroid - rapamycin - animal 538


title: progeroid - restricted - animal 365 [re-analysis]


title: Uveal melanoma biopsy, LH17.364


title: progeroid - restricted - animal 362 [re-analysis]


title: LH18.277

type: genomic

hyb_protocol: Standard Agilent protocols

scan_protocol: The microarray slide was scanned using a SureScan scanner (Agilent). Images were analyzed using Cytogenomics software v2.9.2.4 (Agilent)

data_processing: Data were analyzed using the rCGH R package.

source_name: Human uveal melanoma

label_protocol: DNA (500ng) was labeled using the Genomic DNA ULS Labeling Kit (Agilent) and hybridized onto a Sureprint G3 Human CGH microarray 4x180K, according to the manufacturer’s instructions (Agilent). Tumor DNA was labeled with Cy5 and gender-matched reference DNA (Promega) was labeled with Cy3.

extract_protocol: Genomic DNA was extracted from fresh tissue (case LH16.3814) using the Maxwell 16 LEV BLOOD DNA Purification kit (Promega, Madison, WI) or from FFPE tissue (cases (LH17.364, LH17.530, LH17.3554, LH17.3222, LH18.277)  using the Maxwell 16 FFPE Plus LEV DNA Purification kit (Promega). The human reference DNA was from Promega.

tag: gender

tag: disease

value: Uveal Melanoma

source_name: Human genomic DNA male (Promega ref G1471)

value: Human genomic DNA male (Promega)


title: progeroid - restricted - animal 368 [re-analysis]


title: LH17.3554

value: Male

tag: sample type


title: LH17.3222


title: progeroid - control - animal 326 [re-analysis]

source_name: progeroid - control


title: progeroid - control - animal 325 [re-analysis]


title: 2_F_KO_Bas_RRBS

source_name: Female_KO_Bas_soleus muscle

value: KO

value: soleus muscle


title: 3_F_KO_60_RRBS

source_name: Female_KO_60_soleus muscle


title: OSC si_gfp rep4

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Illumina TruSeq adapters and low-quality bases were removed using Trim galore! v0.6.4 with "--stringency 6 -q 20".
Reads matching known Drosophila viruses (https://obbard.bio.ed.ac.uk/data/Updated_Drosophila_Viruses.fas.gz) were identified using Bowtie v1.2.1.1 with "-S -n 2 -M 1 --best --strata --nomaqround --no-unal".
Remaining reads were aligned to a set of 122 transposon consensus sequences using Bowtie v1.1.2.1 and to dm6 using STAR v2.7.3a "--outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outSAMmultNmax 1 --outFilterMultimapNmax 1000 --winAnchorMultimapNmax 2000 --alignSJDBoverhangMin 1 --sjdbScore 3".
Aligned reads were counted using featureCounts with "-s 2 -O –largestOverlap -Q 50" and Ensembl (r97) gene annotations.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-separated values (tsv) files with raw counts per sample for each consensus transposon or gene.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ovarian somatic cells (OSC)

growth_protocol: OSCs were grown at 26°C. For ovary knockdowns, flies were grown at 27°C. Ovaries were dissected from 3-5 day old flies.

extract_protocol:
OSC pellets were lysed in Trizol. Ovaries were homogenized in Trizol. RNA was isolated using phenol/chloroform extraction.
NEBNext Poly(A) mRNA magnetic Isolation Module (NEB), followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)

treatment_protocol: OSCs were treated with siRNAs.

value: GFP knockdown (Control)

tag: cell line

value: Ovarian somatic cells (OSC)


title: progeroid - control - animal 323 [re-analysis]

tag: strain


title: TP0001651D05_8_100.000000uM_DMEM_6h_TC00283151_I09

description:
TP0001651D05_8_100.000000uM_DMEM_6h
TC00283151_I09

source_name: MCF7 Cells

tag: media

value: DMEM + 10% HI-FBS

value: 6h exposure of 100 uM of Thiram

tag: chemical name

value: Thiram

tag: chemical sample id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: SsE1-GFP-8-2 (replicate 2)

city: Pullman

first: Hao

last: Peng

state: WA

department: Crop and Soil Sciences

institute: Washington State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Hisat2/2.1.0 was used to build reference from Arabdopsis genome Athaliana_167_TAIR9.fa and map the RNASeq reads with parameters --dta -x -q
The sam files generated were conveted to bam files by Samtools/1.9.
Athaliana_447_Araport11.gene.gtf was used for transcript assembly and quantification with StringTie/2.1.4.
Differential expression analysis was performed using Ballgown.
Genome_build: Athaliana_167_TAIR9.fa
Supplementary_files_format_and_content: gtf files with transcript assembly and quantification information.

source_name: Ten-day old seedlings

growth_protocol: Arabidopsis seeds were plated on half-strength MS media, put in the dark cold room for three days (stratification), and grew on white light for ten days.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Kit (Qiagen). The DNase I Digestion Set (Sigma) was used for on-column elimination of genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: Stage

value: Seedling

tag: age

value: Ten days

tag: organs/parts

value: Whole plant

value: Overexpressing SsE1-GFP


title: SsE1-GFP-8-3 (replicate 3)

tag: genotype


title: 1_F_WT_Bas_RRBS

source_name: Female_WT_Bas_soleus muscle

tag: strain background

tag: Sex

value: WT

tag: timepoint

value: Bas

tag: tissue


title: 9_M_WT_60_RNA-seq

data_processing:
fastQC v. 0.11.5 was used to measure sample quality
STAR v 2.5.3a with standard parameters and removing non-canonical unannotated junctions (--outFilterIntronMotifs RemoveNoncanonicalUnannotated) was used to align reads to mm10
The GENCODE vM15 gene model was used
featureCounts v. 1.5.3 was used for summarizing fragments with both ends mapped using the the same GENCODE gene model as when mapping (parameters -p -B -C).
Genome_build: mm10
Supplementary_files_format_and_content: csv file with genes in row and gene info and samples in columns. Values are observed fragments.

source_name: Male_WT_60_soleus muscle

extract_protocol:
A single soleus muscle or ~30 mg of powdered quadriceps was homogenized in 400 µl of RLT buffer (Qiagen) with β-mercaptoethanol using steal beads and subjected to 2 x 30 sec at 30 Hz of disruption using the TissueLyser II (Qiagen). RNA and DNA were simultaneously isolated from 350 µl of lysate using the RNA/DNA/miRNA AllPrep kit (Qiagen) as per instructions. Primary muscle cells were lysed directly in RLT buffer and RNA extracted using the RNeasy kit (Qiagen). RNA was eluted in 45 µl of RNAse free water and DNA in 60 µl of elution buffer (Qiagen).
RNA was checked for quality using the Bioanalyser instrument (Agilent Technologies) and subject to the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina) and performed as described. Libraries were subjected to 75-bp paired-end sequencing on NextSeq 550 (Illumina). Approximately 32 million reads/sample were assigned to genes


title: MBC_IgG_2 [RNA-Seq]

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to fragments per kilobase per million (FPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 3 reads per million in all samples for at least one group.
Genome_build: mm10
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes.

source_name: IgG Memory B cell

extract_protocol:
Cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Total cells were harvested from the indicated organ from either naïve. Memory samples contained a pool of 4 spleens and LNs from 4 infected mice at 34-days post Influenza and were enriched on NP-PE prior to sorting  PR8 infection.

value: Female

tag: sorting markers

tag: strain

value: Spleen and mediastinal Lymph node

tag: bcr isotype

value: IgG

tag: time point

tag: agent

value: Influenza PR8


title: MBC_IgM_2 [RNA-Seq]

source_name: IgM Memory B cell

value: IgM


title: MBC_IgG_3 [RNA-Seq]


title: 8_M_KO_Bas_RNA-seq

source_name: Male_KO_Bas_soleus muscle

value: Male

value: KO

value: soleus muscle


title: MBC_IgM_3 [RNA-Seq]


title: OSC si_gfp rep2

tag: treatment

value: GFP knockdown (Control)

tag: cell line

value: Ovarian somatic cells (OSC)


title: OSC si_gfp rep3


title: OSC si_gfp rep1


title: SsE1-GFP-5-3 (replicate 3)


title: progeroid - control - animal 321 [re-analysis]

value: F1 C57BL6J/FVB

tag: protocol

value: control diet

value: liver


title: SsE1-GFP-8-1 (replicate 1)

value: Seedling

value: Ten days

value: Whole plant


title: MBC_IgM_1 [RNA-Seq]


title: 7_M_KO_Bas_RNA-seq

value: Bas


title: SsE1-GFP-5-2 (replicate 2)

value: Overexpressing SsE1-GFP


title: LH16.3814

tag: gender

value: Female

tag: donor

tag: disease

value: Uveal Melanoma

value: Eye

source_name: Human genomic DNA female (Promega Ref G1521)

tag: sample type

value: Human genomic DNA female (Promega)


title: LH17.364

value: Male

value: Human genomic DNA male (Promega)


title: LH17.530


title: OSC si_ctp rep4

value: Ctp knockdown


title: 6_F_KO_60_RNA-seq

tag: genotype

value: KO

value: soleus muscle


title: nB_IgM_2 [RNA-Seq]

source_name: naïve Follicular B cell

value: mediastinal Lymph node

value: IgM

value: uninfected


title: progeroid - restricted - animal 369 [re-analysis]

source_name: progeroid - restricted

value: F1 C57BL6J/FVB

value: dietary restriction

value: liver


title: OSC si_ctp rep3

value: Ovarian somatic cells (OSC)


title: nB_IgM_1 [RNA-Seq]


title: 4_F_WT_60_RNA-seq

source_name: Female_WT_60_soleus muscle

tag: strain background

value: WT


title: nB_IgM_3 [RNA-Seq]

tag: Sex

value: Female


title: MBC_IgG_1

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie2 with the default parameters  For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings  Read counts for each peak were summarized using GenomicRanges, normalized to reads per peak per million, and peaks annotated to the nearest gene TSS using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Annotation file containing reads per peak per million (rppm) normalized read counts for all peaks with at least 1 read per million in all samples of at least 1 group.

extract_protocol:
Cells were FACS sorted into FACS buffer using the indicated markers
Cells were centrifuged for 10 minutes at 500xg and resuspended in 25 ul of Tagmentation Reaction mix (1x TD Buffer, 2.5 ul Tn5 Transpoase, 0.2% Digitonin) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: Spleen and mediastinal Lymph node

value: IgG

value: 38 days

value: Influenza PR8


title: OSC si_ctp rep1


title: 5_F_WT_60_RNA-seq

tag: timepoint


title: SsE1-GFP-5-1 (replicate 1)

tag: Stage

value: Seedling

tag: age

value: Ten days

tag: organs/parts

value: Whole plant

value: Overexpressing SsE1-GFP


title: 3_F_KO_60_RNA-seq

value: KO

tag: tissue

value: soleus muscle


title: OSC si_ctp rep2

value: Ctp knockdown

tag: strain


title: Col-0-3 (replicate 3)

value: Wild-type


title: MBC_IgG_2

tag: sorting markers

tag: bcr isotype

tag: time point

value: 39 days

tag: agent


title: Col-0-2 (replicate 2)


title: Col-0-1 (replicate 1)


title: ovary sh_w rep2

source_name: Ovary

tag: treatment

value: w knockdown (Control)

value: Stock carrying UAS driven shRNA against the indicated gene crossed to hsD2G4 (Czech et al., 2013)

value: Ovary

tag: cell line


title: ovary sh_w rep4


title: 2_F_KO_Bas_RNA-seq

value: Female

value: Bas


title: MBC_IgM_3

value: Spleen and mediastinal Lymph node

value: IgM

value: 37 days


title: B. subtilis_DS313_recovery.phase_rep2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

hyb_protocol: 100 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 11.5.1.1, Agilent Technologies).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: 168 DS313_recovery.phase

label_protocol:
For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix,
Actinomycin D (final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling
(CyDye Mono-Reactive Dye,GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: B. subtilis 168 wild-type, Dtat and DS313 mutants were grown aerobically at 37 °C in Lysogeny Broth (1 % tryptone, 0.5 % yeast extract, without NaCl). The samples were collected at OD600 of ~2 (recovery phase).

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

value: Bacillus subtilis 168


title: MBC_IgM_2

value: 36 days

value: Influenza PR8


title: nB_IgM_3

value: Male

value: mediastinal Lymph node

value: uninfected


title: 25_F_WT_60_RNA-seq

value: WT

value: soleus muscle


title: 23_F_KO_60_RNA-seq

value: KO


title: ovary sh_w rep3

value: w knockdown (Control)


title: ovary sh_w rep1

value: Stock carrying UAS driven shRNA against the indicated gene crossed to hsD2G4 (Czech et al., 2013)


title: MBC_IgM_1

value: 35 days


title: 22_F_WT_60_RNA-seq

value: Female


title: ovary sh_panx rep4

value: Panx knockdown

value: Ovary


title: nB_IgM_2

value: IgM


title: progeroid - control - animal 327 [re-analysis]

source_name: progeroid - control

value: F1 C57BL6J/FVB

tag: protocol

value: control diet

value: liver


title: ovary sh_panx rep3


title: 20_F_WT_Bas_RNA-seq

value: Bas


title: 21_F_KO_Bas_RNA-seq

source_name: Female_KO_Bas_soleus muscle


title: nB_IgM_1

value: Male


title: ovary sh_panx rep2


title: B. subtilis_DS313_recovery.phase_rep1

value: Bacillus subtilis 168


title: ovary sh_panx rep1


title: mut6_RNAseq

city: Toronto

first: Miguel

last: Ramalho-Santos

state: ON

address: 25 Orde Street

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description: RNA-seq in E8.5 embryos

data_processing:
Raw sequence fastq files were trimmed using trim_galore v0.4.0 to remove residual Illumina adapter sequences and check library quality.
For RNA-seq, trimmed fq files were aligned to the mm10 transcriptome using tophat v2.1.1 (options -p 8 -g 20 --no-coverage-search --library-type fr-firststrand --no-novel-indels).     For ChIP-seq, trimmed fq files were aligned to the mm10 genome using bowtie2 v2.2.5 for genomic alignment (-p 8 --local --very-sensitive-local --no-unal).
Aligned files were sorted using samtools sort.
ChIP-seq bam files were deduplicated using picard MarkDuplicates (REMOVE_DUPLICATES=true) and indexed using samtools.
Reads were imported into R/Bioconductor for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq read counts over genes were obtained using featureCounts (-t exon -T 8 -s 2 -g gene_id) and a .gtf file for the mm10 transcriptome. Processed ChIP-seq files were converted to normalized bigwig (bw) files using the bamCoverage (--scaleFactor <> --binSize 10 -p max) and replicates merged by bigwigCompare (-of --operation add --binSize 10 -p max), both in the deepTools package. Peaks were called in ChIPseq replicates using epic2 (-gn mm10 -d chrM) and shared peaks determined by bedtools intersect. Peaks within 3kb were merged using bedtools (merge -d 3000).

source_name: E8.5 embryo

growth_protocol: E14 ES cells were cultured in DMEM GlutaMAX with Na Pyruvate, 15% FBS, 0.1 mM Non-essential amino acids, 50 U/ml Penicillin/Streptomycin, 0.1 mM EmbryoMax 2-Mercaptoethanol, and 1000 U/ml ESGRO supplement (LIF).   Animal experiments were performed with 5-8-week-old female and 2-6-month-old male C57BL/6J mice.

extract_protocol:
For ES cells, RNA was extracted from the same number of cells using Qiagen RNeasy mini columns. Synthetic RNAs from the Exteral RNAs Control Consortium (ERCC) were spiked in at known concentrations to the same volume of RNA.    For ChIP in ES cells, 1 million cells were sorted and cross-linked for 10 min a room temperature in 1% formaldehyde/PBS. Cross-links were quenched with glycine (final 125 mM) for 5 min at room temperature. Cell pellets were washed in cold PBS, snap frozen, and stored at -80˚C. All subsequent steps were performed on ice or at 4˚C. Fixed cell pellets were thawed and lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8 with protease inhibitors (1x Protease inhibitor cocktail, 1 mM PMSF, 1 mM NaF) for for 30 min. Chromatin was sheared to 200-500 bp fragments on a Covaris S220 with settings PIP 105, duty 2, cpb 200 for 9 min. Chromatin lysates were clarified by centrifugation and diluted 1:10 in dilution buffer (1% Triton X-100, 2 mM EDTA, 167 mM NaCl, 20 mM Tris-HCl pH 8) with protease inhibitors. Inputs were collected at the same time. IPs were performed overnight using 2.5 ug of antibody (CST #9733 H3K27me3) per equivalent of 500,000 cells, rotating at 4˚C. The next day, immunocomplexes were precipitated by incubation with pre-washed Protein A Dynabeads for 2h. Beads were washed 4x10 min in low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl pH 8), 1x10 min in high-salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500 mM NaCl, 20 mM Tris-HCl pH 8), 1x10 min in LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% Na deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8), and 1x fast in TE. ChIP and input samples were eluted in fresh ChIP elution buffer (1% SDS, 50 mM NaHCO3, 50 mM Tris-HCl pH 8, 1 mM EDTA) and treated with RNase A for 1h at 37˚C. Cross-links were reversed by shaking overnight at 65˚C with Proteinase K.    For embryos, RNA was extracted from whole E8.5 embryos cleaned of extraembryonic tissues using Qiagen RNeasy mini columns.
For ES cells, RNA-seq libraries were constructed starting from 1 ug of total RNA using the NEBNext Directional II Directional RNA Library Kit for Illumina (NEB #E7760S) and Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S). Libraries were indexed with NEBNext Multiplex Oligos for Illumina and sequenced as a pool.     ChIP-seq libraries were constructed using the NEBNext Ultra II DNA Library Kit for Illumina (NEB #E7645S). Libraries were indexed with NEBNext Multiplex Oligos for Illumina and sequenced as a pool.     For embryos, RNA-seq libraries were constructed starting from 300 ng of total RNA using the NEBNext Directional II Directional RNA Library Kit for Illumina (NEB #E7760S) and Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S). Libraries were indexed with NEBNext Multiplex Oligos for Illumina and sequenced as a pool.

treatment_protocol: Auxin was added to ES cells at a final concentration of 500 uM for 8h or 48h, as indicated. Water was used as vehicle control. ES cells were sorted prior to RNA or chromatin extraction.

tag: cell type

value: whole embryo

value: Usp9x del/Y (Sox2-Cre+ mutant)

tag: developmental stage

value: embryonic day 8.5


title: mut5_RNAseq

description: RNA-seq in E8.5 embryos

tag: genotype


title: 24_F_KO_Bas_RNA-seq

tag: strain background

tag: Sex

value: KO

value: soleus muscle


title: 1_F_WT_Bas_RNA-seq

value: WT

tag: timepoint


title: B. subtilis_Δtat_recovery.phase_rep1

description: Bacillus subtilis 168 Dtat (trpC2; tatAc::Em; tatAy-tatCy::Sp; tatAd-tatCd::Cm)

source_name: 168 Δtat_recovery.phase

label_protocol:
For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D
(final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye,
GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: B. subtilis 168 wild-type and Δtat mutant were grown aerobically at 37 °C in Lysogeny Broth (1 % tryptone, 0.5 % yeast extract, without NaCl). The samples were collected at two time points: OD600 of ~0.9 (when the lysis of the Δtat mutant started) and OD600 of ~2 (recovery phase).

value: deltatat (trpC2; tatAc::Em; tatAy-tatCy::Sp; tatAd-tatCd::Cm)


title: B. subtilis_Δtat_recovery.phase_rep2


title: B. subtilis_Δtat_recovery.phase_rep3


title: ovary sh_ctp rep4

value: Ctp knockdown

value: Stock carrying UAS driven shRNA against the indicated gene crossed to hsD2G4 (Czech et al., 2013)


title: B. subtilis_wild type_recovery.phase_rep2

description: Bacillus subtilis 168 (trpC2)

growth_protocol: B. subtilis 168 wild-type and Dtat mutant were grown aerobically at 37 °C in Lysogeny Broth (1 % tryptone, 0.5 % yeast extract, without NaCl). The samples were collected at two time points: OD600 of ~0.9 (when the lysis of the Δtat mutant started) and OD600 of ~2 (recovery phase).

value: wild-type


title: B. subtilis_wild type_recovery.phase_rep3

description: Bacillus subtilis 168 (trpC2)


title: 18_M_WT_60_RNA-seq


title: 17_M_KO_60_RNA-seq

source_name: Male_KO_60_soleus muscle


title: mut4_RNAseq

description: RNA-seq in E8.5 embryos


title: ovary sh_ctp rep3

value: Ovary


title: mut3_RNAseq

description: RNA-seq in E8.5 embryos


title: 19_M_KO_60_RNA-seq


title: 16_M_WT_60_RNA-seq


title: mut2_RNAseq

description: RNA-seq in E8.5 embryos


title: mut1_RNAseq

description: RNA-seq in E8.5 embryos


title: ovary sh_ctp rep1


title: OSC siGFP rep2

data_processing:
Illumina small RNA adapters and an rRNA sequence were removed using Trim galore! v0.6.4 with "--stringency 6 -q 0 --length 18" followed by "--stringency 30 -q 0 --length 18 -a TGCTTGGACTACATATGGTTGAGGGTTGTA".
Reads matching known Drosophila viruses (https://obbard.bio.ed.ac.uk/data/Updated_Drosophila_Viruses.fas.gz) were identified using Bowtie v1.2.3 with "-S -n 2 -M 1 --best --strata --nomaqround --no-unal".
Remaining reads were aligned to a set of 122 transposon consensus sequences using Bowtie v1.2.3 and to dm6 using TopHat2 with "-g 2 --segment-length 13". Secondary alignments were removed and excluded from the subsequent analyses.
Aligned reads were counted using featureCounts with "-O –largestOverlap -Q 50" and Ensembl (r97) gene annotations.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-separated values (tsv) files with raw counts per sample for each consensus transposon.

source_name: Ovarian somatic cells (OSC)

growth_protocol: OSCs were grown at 26°C.

extract_protocol:
OSC pellets were lysed in Trizol. RNA was isolated using phenol/chloroform extraction and small RNAs were size selected by PAGE from 15 ug total RNA.
CleanTag Small RNA Library Preparation Kit (TriLink, L-3206)

value: GFP knockodown (Control)

value: Ovarian somatic cells (OSC)


title: 15_M_KO_Bas_RNA-seq


title: ctrl6_RNAseq

description: RNA-seq in E8.5 embryos

value: Usp9x flox/Y (control)


title: B. subtilis_wild type_recovery.phase_rep1

description: Bacillus subtilis 168 (trpC2)


title: OSC siGFP rep1


title: 14_M_WT_Bas_RNA-seq

source_name: Male_WT_Bas_soleus muscle

value: Bas


title: ctrl5_RNAseq

description: RNA-seq in E8.5 embryos


title: B. subtilis_Δtat_lysis.phase_rep3

description: Bacillus subtilis 168 Δtat (trpC2; tatAc::Em; tatAy-tatCy::Sp; tatAd-tatCd::Cm)

source_name: 168 Δtat_lysis.phase


title: ovary sh_ctp rep2


title: B. subtilis_Δtat_lysis.phase_rep1


title: B. subtilis_Δtat_lysis.phase_rep2


title: ctrl3_RNAseq

description: RNA-seq in E8.5 embryos


title: ctrl4_RNAseq

description: RNA-seq in E8.5 embryos


title: IgG 2

city: Rehovot

first: Idit

last: Shachar

address: Herzl 234

department: immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
library strategy: MARS-seq
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome mm10 (UCSC)
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Fdr correction: - The pipeline computes the fractions of the p-values between 0.25 and 1, and uses them to recompute the fractions for the following bins: (0.25,0.5], (0.5,0.75], and (0.75,1). If the result is not between 0.28 and 0.38 for at least one of these bins, we apply the fdrtool (R package, DOI: 10.1186/1471-2105-9-303) correction, to compensate for the uneven distribution of p values between 0.25 and 1. - The fdrtool correction is also applied if the fraction of the p-values between 0 and 0.25 is less than 0.2, since that could indicate an over-estimation of the negative binomial dispersion.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: [Deseq_all_results.txt]  normalized abundance measurements and DESeq2 analysis

source_name: Sorted Bregs

extract_protocol:
Spleens were harvested; B cells were enriched using B220 magentic beads (Bd Biosciences) and then sorted for CD19+GFP+ (IL10+).
Libraries were prepared with the MARS-seq protocol (Diego Adhemar Jaitin, 2017) and sequenced using Illumina NextSeq 550 High Output v2 Kit (75 cycles).

treatment_protocol: Cells were isolated of Vert-X mice in EAE remission, and incubated at a concentration  of  2.5x10e6/ml  for  24 hrs in  the  presence  of  5ug/ml  LPS  (Sigma)  and 30 μg/ml SLAMF5 blocking Ab or isotype control IgG2a (MG2a-53, BioLegend)

value: C57BL/6 Vert-X

value: spleen

tag: condition

value: State of EAE remission

value: IgG


title: 13_M_WT_Bas_RNA-seq

value: Male


title: OSC siCtp rep2


title: B. subtilis_wild type_lysis.phase_rep3

description: Bacillus subtilis 168 (trpC2)

value: Bacillus subtilis 168


title: IgG 1


title: 11_M_WT_Bas_RNA-seq

value: soleus muscle


title: 12_M_KO_Bas_RNA-seq

value: KO


title: B4 Blocking 2

value: B4 blocking


title: B. subtilis_wild type_lysis.phase_rep2

description: Bacillus subtilis 168 (trpC2)


title: ctrl2_RNAseq

description: RNA-seq in E8.5 embryos

value: whole embryo

value: embryonic day 8.5


title: B4 blocking 1


title: OSC H3K9me3 si-gfp rep2

data_processing:
Illumina TruSeq adapters and low-quality bases were removed using Trim galore! v0.6.4 with "--stringency 6 -q 20".
The single-end OSC reads were aligned to a set of 122 transposon consensus sequences and to the dm6 genome using Bowtie v1.2.1.1 with "-S -n 2 -M 1 --best --strata --nomaqround --no-unal". For the paired-end reads from S2 cells, Bowtie v1.2.3 was used with the additinal options "-y --maxins 500 --fr --allow-contain".
PCR duplicates were removed using MarkDuplicates from Picard tools v2.21.2.
BigWig files were constructed using bamCoverage from deepTools with "--binSize 1 --ignoreForNormalization chrM --normalizeUsing CPM --centerReads --exactScaling" and either "--extendReads 260" for single-end or "--extendReads" for paired-end data.
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files with either all mapped reads or uniquely mapped reads only.

growth_protocol: OSC and S2 cells were grown at 26°C

extract_protocol:
Samples were crosslinked in formaldehyde and lysed, followed by sonication.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB)

treatment_protocol: OSCs were treated with siRNAs and S2 cells were transfected with indicated plasmids

value: GFP knockdown (Control)

tag: chip antibody

value: anti-H3K9me3 (Active Motif #39161; LOT:14418003)


title: 10_M_KO_60_RNA-seq

tag: tissue


title: ctrl1_RNAseq

description: RNA-seq in E8.5 embryos


title: OSC H3K9me3 si-ctp rep2

value: Ctp knockdown


title: OSC siCtp rep1

value: Ovarian somatic cells (OSC)


title: s7_pbmc_10x_esat

city: Ithaca

first: Gerlinde

last: Van de Walle

state: NY

address: 235 Hungerford Hill Road

institute: Cornell University

data_processing:
fastq files were aligned to version 95 of the horse genome reference (with manually annotated immunoglobulins (adapted from Wagner B. Immunoglobulins and immunoglobulin genes of the horse. Developmental & Comparative Immunology. 2006;30: 155–164. doi:10.1016/j.dci.2005.06.008)) from ensembl using the count function in the cellranger suite (10X Genomics, v3.0.1)
Intermediate BAM files were extracted and modified by appending cell barcode and unique molecular identifiers to their read names
The End Sequence Analysis Toolkit(v0.1.1) was applied on the resulting BAM files to obtain gene-cell barcode expression matrices (Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016;26: 1397–1410. doi:10.1101/gr.207902.116)
Custom script was applied to identify duplicated genes and scale their expression proportionally
Genome_build: EquCab3.0
Supplementary_files_format_and_content: ESAT processed gene-cell barcode matrix

organism: Equus caballus

source_name: Peripheral blood mononuclear cells

extract_protocol:
Periperal blood mononuclear cells were isolated from healthy horses by Ficoll gradient separation
Libraries were prepared in accordance to the 10X Genomics 3' end single cell RNA sequencing library prepration protocol, version 2

value: Peripheral blood mononuclear cells

tag: age

value: Female

tag: breed

value: Warmblood


title: s6_pbmc_10x_esat

value: Quarter horse


title: OSC H3K4me2 si-gfp rep2


title: OSC H3K9me3 si-ctp rep1


title: testis transcriptome experimental mouse 3

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

description:
gene_exp.diff: E_2
genes.read_group_tracking: E_2

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The 'gene_exp.diff' file contains average FPKM values for each pair of replicates as well as results for statistical testing for differential expression. The 'genes.read_group_tracking' file contains raw mapped read counts and FPKM values for individual samples.

source_name: testis

growth_protocol: standard mouse facility

extract_protocol:
Total RNA was extracted with the Qiagen RNAeasy Mini kit.
Diretional RNA-seq libraries were prepared from 500ng total RNA using the NEBNext Directional Ultra RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Control mice were injected with 10 microliters per gram body weight with saline:cremophor:ethanol (7:2:0.9). Experimental mice were injected with vehicle in which was dissolved 1NaPP1-HCl at 4/465 mg/ml vehicle. Injections continued daily for 9 days total. Mice were allowed to recover for 5 days prior to testis dissection (experiment day 14).

tag: strain

tag: mutation

value: Homozygous Ret (V805A)

value: injected for 9 days with vehicle [saline:cremophor:ethanol (7:2:0.9)] containing 1NaPP1-HCl at 4/465 mg/ml, 10 microliters per gram body weight

value: ~120 days


title: OSC H3K4me2 si-gfp rep1


title: wild type - restricted - animal 425 [re-analysis 2]

data_processing: Quality control and RMA normalization were performed using the pipeline at the www.arrayanalysis.org website maintained by Maastricht University.

source_name: wild type - restricted

extract_protocol: Total RNA was extracted from liver of 11 week old wild type and Ercc1Δ/- mice on AL and DR feeding regimen (n=5). Total RNA was extracted using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN, Hilden, Germany), following Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Fisher Scientific) and quality assessment of the RNA using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) following manufacturer’s instructions.

value: F1 C57BL6J/FVB

value: wild type

value: dietary restriction

value: liver


title: testis transcriptome experimental mouse 2

description:
gene_exp.diff: E_1
genes.read_group_tracking: E_1


title: testis transcriptome control mouse 3

description:
gene_exp.diff: C_2
genes.read_group_tracking: C_2

value: injected for 9 days with vehicle [saline:cremophor:ethanol (7:2:0.9)], 10 microliters per gram body weight


title: B. subtilis_wild type_lysis.phase_rep1

description: Bacillus subtilis 168 (trpC2)

value: Bacillus subtilis 168

tag: time point

value: wild-type


title: wild type - restricted - animal 424 [re-analysis 2]


title: OSC H3K9me3 si-gfp rep1

tag: treatment

value: GFP knockdown (Control)

value: anti-H3K9me3 (Active Motif #39161; LOT:14418003)


title: wild type - restricted - animal 423 [re-analysis 2]


title: s5_pbmc_10x_esat

value: Male

value: Thoroughbred


title: OSC H3K4me2 si-ctp rep2

value: Ctp knockdown

tag: cell line

value: Ovarian somatic cells (OSC)


title: testis transcriptome control mouse 2

description:
gene_exp.diff: C_1
genes.read_group_tracking: C_1


title: s3_pbmc_10x_esat

value: Peripheral blood mononuclear cells

value: Warmblood


title: OSC H3K4me2 si-ctp rep1


title: OSC input si-gfp rep2


title: s2_pbmc_10x_esat

value: Female


title: testis transcriptome control mouse 1

description:
gene_exp.diff: C_0
genes.read_group_tracking: C_0

value: Homozygous Ret (V805A)

value: ~120 days


title: wild type - restricted - animal 421 [re-analysis 2]

value: F1 C57BL6J/FVB

value: wild type

tag: protocol


title: testis transcriptome experimental mouse 1

description:
gene_exp.diff: E_0
genes.read_group_tracking: E_0

value: injected for 9 days with vehicle [saline:cremophor:ethanol (7:2:0.9)] containing 1NaPP1-HCl at 4/465 mg/ml, 10 microliters per gram body weight


title: wild type - restricted - animal 422 [re-analysis 2]

value: dietary restriction

value: liver


title: S2 H3K9me3 ren rep1

source_name: Schneider 2 (S2) cells

value: stable cell line transfected with LacI-Renilla

value: anti-H3K9me3 (Active Motif #39161; LOT:21518003)

value: Schneider 2 (S2) cells


title: wild type - control - animal 404 [re-analysis 2]

source_name: wild type - control

value: control diet


title: OSC input si-ctp rep2


title: OSC input si-ctp rep1


title: S2 H3K9me3 panx rep2

value: stable cell line transfected with LacI-Panx


title: PBS-2

type: protein

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: Negative control

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing:
Genepix 4000B scanner (Molecular Device) with laser wavelengths of 532 and 635 nm. The resulting images were analyzed using Genepix Pro 6.0 software (Molecular devices)
The medium of the signal intensity from each spot was calculated and subtracted from local background, and data obtained from duplicated spots were averaged.
The net fluorescence intensity for each antigen was calculated by subtracting a PBS control that was included for each experimental as a negative control.
Finally, the background subtracted signal intensity of each antigen was normalized by robust linear model (RLM) using internal positive controls.

label: IgM and IgG Autoantibodies

molecule: protein

organism: blank sample

source_name: blank sample

label_protocol: Not provided

extract_protocol: Blood was collected immediately following euthanasia be cardiac puncture. After 2 hours at room temperature, blood was centrifuged for 20 minutes at 0.7 g and the sera collected. Sera were stored at -20C until use.

tag: slide

value: blank sample


title: S2 H3K9me3 panx rep1


title: LSL-Vav-4

source_name: Serum

value: Serum

value: 6 - 7 months


title: LSL-Vav-5


title: S2 H3K9me3 egg rep2

value: stable cell line transfected with LacI-Egg


title: wild type - control - animal 403 [re-analysis 2]


title: S2 H3K9me3 ren rep2


title: s4_pbmc_10x_esat

tag: cell type

value: Peripheral blood mononuclear cells

value: Male

value: Thoroughbred


title: S2 H3K9me3 egg rep1


title: B. subtilis_DS313_recovery.phase_rep3

source_name: 168 DS313_recovery.phase

value: Bacillus subtilis 168

tag: genotype


title: LSL-Vav-3

value: Female


title: wild type - control - animal 405 [re-analysis 2]

value: F1 C57BL6J/FVB

value: wild type


title: S2 H3K4me2 ren rep2


title: CD45+ Jak2V617F rep2, scRNA-seq

city: New York

first: Chenyi

last: Xue

institute: Columbia University

data_processing:
Fastq files were processed by 10X Cell Ranger v.3.1.0. Reads were aligned to mouse reference genome build mm10 and transcriptome based on Ensembl 93 annotation.
Unique molecular identifier (UMI) count matrices were generated by Cell Ranger.
Genome_build: mm10
Supplementary_files_format_and_content: Gene-cell UMI count matrix

source_name: CD45+ cells harvested from aortas

growth_protocol: Ldlr-/- recipients were irradiated with 9.5gly, then transplanted with bone marrow from mice with Mx1-Cre driving Jak2V617F +/- Gsdmd-/- or littermate control, 4 weeks later ldlr-/- mice were subjected to western type diet (Teklad TD88137) for 12 weeks

extract_protocol:
Aortas were mechanically cleaned, then diced and digested with Liberase, hyaluronidase, and Dnase in media for 45 minutes at 37C. Cells were then washed, blocked with FC block, and stained for DAPI and CD45. Samples were then sorted using flow cytometry (DAPI negative, CD45 postive) and subjected to scRNA-Seq pipeline
Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s instructions. 5000 cells and 200M reads per sample were targeted. 12 cycles for cDNA amplification and 12 cycles for sample index PCR were used.

treatment_protocol: After 4 weeks recover at bone marrow transplantation, mice were subjected to a 12 week western type diet (Teklad TD88137)

value: Ldlr-/-

tag: transplantation

value: bone marrow from mice with MX1-Cre driving Jak2V617F mutations

value: Western type diet 12 weeks (Teklad TD 88137)

value: DAPI negative, CD45+ cells from aortas


title: CD45+ Jak2V617F rep1, scRNA-seq

tag: Sex


title: LSL-Vav-2


title: progeroid - rapamycin - animal 537 [re-analysis]

source_name: progeroid - rapamycin

value: rapamycin-containing diet

value: liver


title: wild type - control - animal 401 [re-analysis 2]

value: control diet


title: S2 H3K4me2 ren rep1

value: stable cell line transfected with LacI-Renilla

value: Schneider 2 (S2) cells


title: CD45+ Control, scRNA-seq

value: bone marrow from littermate control


title: LSL-Vav-1

value: Serum

value: 6 - 7 months


title: progeroid - rapamycin - animal 538 [re-analysis]


title: Calvaria Tmem53-/- rep3

city: Tokyo

first: Long

last: Guo

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: RIKEN

data_processing:
Illumina Casava1.8.2 used for basecalling.
Adaptors were trimmed from the reads using FASTX-toolkit 0.0.14_1
The reads were aligned to the mouse genome (NCBI build37.2) using Tophat 2.1.1_6.
The aligned reads were quantified using Cufflinks (v2.1.1). Differential gene expression analysis was performed with Cuffdiff (v2.1.1).
Genome_build: NCBI build37.2
Supplementary_files_format_and_content: Text file including FPKM values of each gene for each sample

source_name: Calvaria

extract_protocol:
The dissected calvaria were frozen in liquid nitrogen and crashed by a cryopress (Microtec). The homogenized tissue powders were dissolved in ISOGEN solution (Nippon Gene) followed by total RNA extraction using Qiagen RNeasy kit (Qiagen).
rRNA was removed by Ribo-ZeroTM Magnetic Gold Kit (Illumina). The cDNA was synthesized by NEBNext Ultra Directional RNA Library Prep Kit for Illumina R (New England biolabs).

value: Calvaria

value: Post natal day 3


title: CD45+ Jak2V617F Gsdmd-/-, scRNA-seq

value: Female

value: bone marrow from mice with  Mx1-Jak2V617F mutations lacking Gsdmd


title: wild type - control - animal 402 [re-analysis 2]

value: F1 C57BL6J/FVB

value: wild type


title: progeroid - rapamycin - animal 535 [re-analysis]


title: Calvaria Tmem53-/- rep2


title: LSL-KO-5


title: Calvaria Tmem53-/- rep1


title: LSL-KO-4


title: S2 H3K4me2 egg rep2

value: stable cell line transfected with LacI-Egg


title: progeroid - restricted - animal 369 [re-analysis 2]

source_name: progeroid - restricted

value: dietary restriction


title: LSL-KO-3


title: Calvaria Tmem53+/- rep3


title: LSL-KO-2


title: LSL-KO-1


title: progeroid - restricted - animal 368 [re-analysis 2]


title: progeroid - rapamycin - animal 536 [re-analysis]


title: S2 input ren rep2


title: Calvaria Tmem53+/- rep2


title: progeroid - restricted - animal 366 [re-analysis 2]


title: LSL-Het-5


title: progeroid - restricted - animal 362 [re-analysis 2]


title: S2 input ren rep1


title: progeroid - restricted - animal 365 [re-analysis 2]


title: S2 H3K4me2 panx rep1

value: stable cell line transfected with LacI-Panx


title: OSC input si-gfp rep1

value: GFP knockdown (Control)

value: Ovarian somatic cells (OSC)


title: S2 H3K4me2 panx rep2


title: LSL-Het-4


title: progeroid - control - animal 327 [re-analysis 2]

source_name: progeroid - control

value: control diet

value: liver


title: RNA-Seq Ush-B repl4

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse genome dm3 or dm6 using Bowtie 2.0 (Galaxy Version 2.3.4.3), using standard settings.
Bigwig files were optained using deepTools/bamCoverage (Galaxy Version 3.0.2.0), using standard settings.
RNA-Seq data were aligned to Drosophila transcriptome dm6 using RNA Star (Galaxy Version 2.6.0b-1). Counts per gene were determined using FeatureCounts (Galaxy Version 1.6.2). Differentially expressed genes and normalized reads were determined using DeSeq2 (Galaxy Version 2.11.40.2).
Genome_build: dm3, dm6
Supplementary_files_format_and_content: bw

source_name: S2 Schneider cells

growth_protocol: Drosophila S2 cells were cultured in Schneider’s Drosophila Medium (2172001, Gibco) supplemented with 10% (v/v) fetal bovine serum (F7524, Sigma) and 1% (v/v) Penicillin-Streptomycin (15140122, Gibco). Cells were grown at 26 °C and passaged at confluency.

extract_protocol:
For ChIP-seq chromatin was prepared by crosslinking cells with 1% Formaldehyde followed by lysis in TE buffer containing 1% SDS and sonication. GFP-Trap Agarose (gta, ChromoTek) was used for immunoprecipitation. Precipitated DNA was purified using the QIAquick PCR purification kit (28106, Qiagen). RNA for RNA-seq was isolated using the peqGOLD Total RNA Kit (12-6834-02, Peqlab).
ChIP-seq libraries were generated from 1 ng of DNA using the MicroPlex Library Preparation Kit v2 (C05010012, Diagenode). RNA-seq libraries were generated using a TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: For ChIP-seq a GFP-tag sequence was inserted in the genome of S2 cells at the 3’ end of the dMi-2 or Ush coding region using a CRISPR/Cas9-based approach. For RNA-seq after knockdown dsRNA targeting dMi-2, Ush or the Ush-B isoform was transfected and S2 cells were harvested 4 days post transfection. A non-targeting dsRNA against GFP (dsEGFP) was used as control.

value: dsRNA Ush-B


title: S2 input panx rep2

value: Schneider 2 (S2) cells


title: progeroid - control - animal 326 [re-analysis 2]


title: S2 H3K4me2 egg rep1


title: LSL-Het-3

value: Serum


title: RNA-Seq Ush-B repl2


title: RNA-Seq Ush-B repl3


title: S2 input egg rep2


title: LSL-Het-2

value: 6 - 7 months


title: LSL-Het-1


title: S2 input egg rep1


title: S2 input panx rep1


title: Calvaria Tmem53+/- rep1

value: Calvaria


title: progeroid - control - animal 325 [re-analysis 2]


title: RNA-Seq Ush-B repl1


title: RNA-Seq EGFP (for Ush-B) repl4

value: dsRNA EGFP


title: Patient 9, biological replicate 1, single cells, part 4

city: Shanghai

first: Xianbin

last: Su

address: Dongchuan Road 800

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
The C1 mRNA Sequencing High Throughput Demultiplexer Script (Fluidigm) was used for sequencing data de-multiplexing and generation of FASTQ files for each single cell.
The raw reads in FASTQ format were mapped to the human reference genome GRCh37/hg19 via Tophat 2.1.0.
The transcript levels were quantified as count per gene with HTSeq-count.
The count of ERCC spike-ins are obtained in the same way with ERCC92 reference sequence.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression matrix table: count values for each gene in each single cell

source_name: liver tumor

extract_protocol:
Single cells were captured on a Fluidigm C1 mRNA Seq HT IFC (10-17 μm). Cell lysis, reverse transcription, and cDNA amplification were done according to the vendor’s protocol. ERCC Spike-in Mix (Ambion) were used as technical control.
Sequencing libraries were prepared using Fluidigm C1 HT protocol.

treatment_protocol: The liver tumor tissues were minced and digested in 0.05% collagenase IV at 37°C for 30 min. Repeated 50× g centrifugations for 2 min were used to enrich tumor cells, and a 40-μm cell strainer was used to remove undigested tissues.

tag: subject id

value: Patient 9

tag: subject status

value: HCC patient

tag: gender

value: male

tag: hcc grade

value: II

tag: sample type

value: 200 single cells

value: human hepatocellular carcinoma (HCC)


title: RNA-Seq EGFP (for Ush-B) repl3


title: PBS-1

description: Negative control

tag: tissue

value: blank sample

tag: age


title: progeroid - control - animal 323 [re-analysis 2]

tag: strain

value: F1 C57BL6J/FVB


title: UPC-Normal

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices.
Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each single cell

source_name: urine-derived cell

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
Sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: 12 Chinese healthy adults

tag: sample source

value: urine

value: urine-derived cell


title: Lung_Neutro_LF3

city: Montreal

first: Logan

middle: A.

last: Walsh

state: QUEBEC

address: 1160 Pine Avenue, Box 532

institute: MCGILL UNIVERSITY

description: RNA-Seq of mus musculus: Female C57BL6 lung neutrophils_LF3

data_processing: Fastp (version 0.19.4) was used to collect QC metrics of the raw reads. RNA sequences were aligned and sorted by coordinates, to the NCBI mouse genome build 38 version 94, using STAR aligner (STAR-2.6.1b). The removal of alignment duplicates was done with Sambamba (version 0.6.8). Quantification of genes was performed using featureCounts (v1.6.3). DESeq2 (v 1.20.0) was used to normalize feature counts and to test find the differentially expressed genes. The HGNC symbols were extracted and added to the DESeq2 results data frame using biomaRt (version 2.36.1) using the "mmusculus_gene_ensembl" dataset and the "Ensembl Release 94

source_name: Neutrophils (CD45+ CD11b+ Ly6Clo Ly6G+) were FACS-purified from lungs of LF mice

extract_protocol:
RNA was isolated with TRIzol LS (Invitrogen) and integrity was assessed via Agilent Bioanalyzer 2100.
SMART-Seq library preparation kit

value: Female

value: lung

value: neutrophils


title: Delta-5

value: Serum

value: 6 - 7 months


title: Patient 9, biological replicate 1, single cells, part 3


title: RNA-Seq EGFP (for Ush-B) repl2

value: dsRNA EGFP


title: Lung_Neutro_LF2

description: RNA-Seq of mus musculus: Female C57BL6 lung neutrophils_LF2


title: Patient 9, biological replicate 1, single cells, part 2

value: Patient 9


title: Lung_Neutro_LF1

description: RNA-Seq of mus musculus: Female C57BL6 lung neutrophils_LF1


title: Delta-3


title: progeroid - control - animal 321 [re-analysis 2]

first: Jeroen

last: Pennings

institute: Natl. Inst. Public Health & Environment

value: control diet

value: liver


title: RNA-Seq EGFP (for Ush-B) repl1


title: Patient 5, biological replicate 1, single cells, part 4

value: Patient 5

value: HCC patient

value: female

value: II


title: Delta-4


title: Lung_Neutro_HF4

description: RNA-Seq of mus musculus: Female C57BL6 lung neutrophils_HF4

source_name: Neutrophils (CD45+ CD11b+ Ly6Clo Ly6G+) were FACS-purified from lungs of HF mice


title: Delta-2


title: RNA-Seq Mi-2 repl3

value: dsRNA Mi-2


title: Patient 9, biological replicate 1, single cells, part 1

value: male

value: 200 single cells

value: human hepatocellular carcinoma (HCC)


title: Delta-1

value: Female


title: Lung_Neutro_HF3

description: RNA-Seq of mus musculus: Female C57BL6 lung neutrophils_HF3

value: lung


title: Patient 5, biological replicate 1, single cells, part 3


title: RNA-Seq Mi-2 repl2


title: Patient 5, biological replicate 1, single cells, part 2


title: Patient 5, biological replicate 1, single cells, part 1


title: Lung_Neutro_HF2

description: RNA-Seq of mus musculus: Female C57BL6 lung neutrophils_HF2

value: neutrophils


title: RNA-Seq Ush repl3

value: dsRNA Ush


title: RNA-Seq Mi-2 repl1


title: Lung_Neutro_HF1

description: RNA-Seq of mus musculus: Female C57BL6 lung neutrophils_HF1


title: Floxed-4

value: Serum

value: 6 - 7 months


title: RNA-Seq Ush repl2


title: Lung_Endothelial_LF4

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_LF4

data_processing: Fastp (v0.20.0) was used to collect QC metrics of the raw reads. RNA sequences were aligned and sorted by coordinates, to the NCBI mouse genome build 38 version 96, using STAR aligner (STAR-2.6.1b). The removal of alignment duplicates was done with Sambamba (v0.7.0). Quantification of genes was performed using featureCounts (v2.0.0). DESeq2 (v1.24.0) was used to normalize feature counts and to test for differentially expressed genes. The HGNC symbols were extracted and added to the DESeq2 results data frame using biomaRt (v2.40.4) using the "mmusculus_gene_ensembl" dataset and the Ensembl Release 96.

source_name: Endothelial cell (CD45- CD31+) were FACS-purified from lungs of LF mice

value: endothelial cells


title: Floxed-3


title: Patient 2, biological replicate 1, single cells, part 4

value: Patient 2


title: Floxed-2


title: Patient 2, biological replicate 1, single cells, part 3


title: RNA-Seq Ush repl1


title: Lung_Endothelial_LF3

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_LF3


title: Floxed-1


title: Patient 2, biological replicate 1, single cells, part 2


title: RNA-Seq EGFP repl3

value: dsRNA EGFP


title: Lung_Endothelial_LF2

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_LF2


title: RNA-Seq EGFP repl2


title: NOD.B10-5


title: Lung_Endothelial_LF1

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_LF1


title: Patient 2, biological replicate 1, single cells, part 1


title: NOD.B10-4


title: Floxed-5


title: ChIP-Seq Ush

description:
Ush_dm3.bigwig
Ush_dm6.bigwig

tag: antibody

value: GFP-Trap Agarose (gta, ChromoTek)

value: Ush-GFP

tag: tag

value: C-terminal GFP (endogenously tagged)


title: RNA-Seq EGFP repl1


title: Patient 1, biological replicate 1, single cells, part 3

value: Patient 1

value: HCC patient

value: II~III


title: Lung_Endothelial_HF3

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_HF3

source_name: Endothelial cell (CD45- CD31+) were FACS-purified from lungs of HF mice


title: ChIP-Seq Ush Input

description:
Ush Input_dm3.bigwig
Ush Input_dm6.bigwig


title: Lung_Endothelial_HF2

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_HF2


title: NOD.B10-2


title: ChIP-Seq Mi-2

description:
Mi-2_dm3.bigwig
Mi-2_dm6.bigwig


title: Patient 1, biological replicate 1, single cells, part 2

value: male

value: 200 single cells


title: NOD.B10-1

value: Female


title: ChIP-Seq Mi-2 Input

description:
Mi-2 Input_dm3.bigwig
Mi-2 Input_dm6.bigwig


title: RM6/66-3

status: Public on Jan 24 2021

city: Beijing

last: Dong

address: Huatuo road NO.31

institute: National Institutes for Food and Drug Control

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: ASM74033v1
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Brucella canis

source_name: Gram-negative bacteria

growth_protocol: Brucella canis RM6/66 and ΔmucR strains were grown in TSB at 37℃ until the log phase was reached

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Brucella canis RM6/66 was obatined from IVDC, and the ΔmucR strains was constructed from its parent strain RM6/66

value: RM6/66 (parental)


title: RM6/66-1


title: RM6/66-2


title: ΔmucR-3

value: {delta}mucR


title: Patient 1, biological replicate 1, single cells, part 4

value: human hepatocellular carcinoma (HCC)


title: ΔmucR-2


title: ΔmucR-1


title: Lung_Endothelial_HF4

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_HF4

value: lung


title: NOD.B10-3

value: Serum

value: 6 - 7 months


title: extended_1-W532_LTRI-946_R1

first: Jeff

last: Wrana

address: 600 Unv Ave

institute: Lunenfeld Tanenbaum Research Institute

description:
SparSeq multiplexed PCR library
Extended_ReadCount_Table.csv

data_processing:
Single-end reads mapped to amplicon sequences using Bowtie and allowing 3 mismatch for mapped read count / amplicon quantification.
Genome_build: Custom genome consists of amplicons targeted in GRCh38 and Sars-CoV-2 (Wuhan-Hu-1).
Supplementary_files_format_and_content: Sample name/ read count mapped to each targeted amplicon.

source_name: Human Sample

extract_protocol:
Total RNA extraction by Norgen total RNA Kit or RNA-XP beads.
C19-SparSeq-Barcoded multiplexed PCR reactions were pooled and cleaned with SPRIselect beads.


title: extended_1-W532_LTRI-946_R2


title: extended_1-W531_LTRI-945_R1


title: extended_1-W535_LTRI-949_R1


title: extended_1-W535_LTRI-949_R2


title: extended_1-W533_LTRI-947_R1


title: extended_1-W531_LTRI-945_R2


title: extended_1-W530_LTRI-944_R1


title: extended_1-W546_LTRI-937_R2


title: Lung_Endothelial_HF1

description: RNA-Seq of mus musculus: Female C57BL6 lung endothelial cells_HF1

value: endothelial cells


title: extended_1-W484_LTRI-923_R2


title: extended_1-W484_LTRI-923_R1


title: extended_1-W483_LTRI-922_R2


title: extended_1-W545_LTRI-936_R1


title: extended_1-W546_LTRI-937_R1


title: extended_1-W483_LTRI-922_R1


title: Patient 1, biological replicate 1, single cells, part 1


title: extended_1-W257_LTRI-912_R1


title: extended_1-W533_LTRI-947_R2


title: extended_1-W256_LTRI-911_R2


title: extended_1-W257_LTRI-912_R2


title: extended_1-W530_LTRI-944_R2


title: extended_1-W255_LTRI-910_R1


title: extended_1-W255_LTRI-910_R2


title: extended_1-W253_LTRI-908_R2


title: extended_1-W253_LTRI-908_R1


title: extended_1-W243_LTRI-898_R2


title: extended_1-W256_LTRI-911_R1


title: extended_1-W243_LTRI-898_R1


title: extended_1-W242_LTRI-897_R2


title: extended_1-W242_LTRI-897_R1


title: extended_1-W234_LTRI-889_R2


title: extended_1-W231_LTRI-886_R1


title: extended_1-W231_LTRI-886_R2


title: extended_1-W233_LTRI-888_R2


title: extended_1-W233_LTRI-888_R1


title: extended_1-W545_LTRI-936_R2


title: extended_1-W234_LTRI-889_R1


title: extended_1-W258_LTRI-913_R2


title: extended_1-W222_LTRI-877_R2


title: extended_1-W230_LTRI-885_R1


title: extended_1-W221_LTRI-876_R2


title: extended_1-W258_LTRI-913_R1


title: extended_1-W220_LTRI-875_R2


title: extended_1-W222_LTRI-877_R1


title: extended_1-W220_LTRI-875_R1


title: extended_1-W221_LTRI-876_R1


title: extended_1-W219_LTRI-874_R2


title: extended_1-W219_LTRI-874_R1


title: extended_1-W217_LTRI-872_R1


title: extended_1-W217_LTRI-872_R2


title: extended_1-W218_LTRI-873_R1


title: extended_1-W210_LTRI-865_R2


title: extended_1-W210_LTRI-865_R1


title: extended_1-W230_LTRI-885_R2


title: extended_1-W207_LTRI-862_R1


title: extended_1-W616_LTRI-850_R1


title: extended_1-W352_LTRI-839_R1


title: extended_1-W207_LTRI-862_R2


title: extended_1-W205_LTRI-860_R2


title: extended_1-W352_LTRI-839_R2


title: extended_1-W341_LTRI-828_R2


title: extended_1-W339_LTRI-826_R2


title: extended_1-W205_LTRI-860_R1


title: extended_1-W349_LTRI-836_R2


title: extended_1-W337_LTRI-824_R2