title: CD3eKO_2_79

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.21.0 with the parameters “--cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 30 --length_required 30”
The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.5c)
The reads aligned to exon were counted using featureCounts
Genome_build: For single-cardiomyocyte RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from GENCODE (release 25, https://www.gencodegenes.org/)
Supplementary_files_format_and_content: ReadCounts file generated using featureCounts.

source_name: Cardiomyocyte

growth_protocol: All mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2500 (Illumina) in rapid mode

treatment_protocol: The transverse aorta was constricted with a 7-0 nylon suture across a 27-gauge blunt needle, which was removed after constriction

tag: operation

value: TAC

value: single-cardiomyocyte

tag: name in supplementary file


title: CD3eKO_2_80

status: Public on Oct 04 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: condition

tag: tissue


title: CD3eKO_2_77


title: CD3eKO_2_78


title: CD3eKO_2_76


title: CD3eKO_2_75


title: CD3eKO_2_74


title: sh15-LOX-2.2865-9

city: Nanchong

first: zhengmin

last: xu

address: Fujiang

department: Department of Pharmacy

country: China

institute: North Sichuan Medical College

data_processing:
Illumina sequencing workflow
Sequenced reads were mapped to GRCm38 whole genome using STAR v2.6.0 .
Transcripts Per Kilobase Million of library size (TPM) were calculated .
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx  files include TPM values for each Sample ...

growth_protocol: Ana-1-sh15-LOX-2 cells were generated by re-plating 6-well plate with complete RIPM 1640 medium

extract_protocol:
Ana-1-sh15-LOX-2 cells were harvested and transduced with shRNAs targeting either shAlox15b, fluorescence activated cell sorting of transduced cells were conducted 48h post-infection and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type


title: Whole brain_Female_Prenatal titanium dioxide nanoparticle exposure_1d

type: genomic

city: Sanyo-onoda

first: Ken

last: Tachibana

state: Yamaguchi

address: 1-1-1 Daigaku-Dori

institute: Sanyo-Onoda City University

description: DNA methylation analysis in 1-day-old brain of male mice prenatally exposed (GD14) to vehicle (Input DNA: Cy3-labeled, MeDIP DNA: Cy5-labeled)

hyb_protocol: Cy3-labeled input samples or Cy5-labeled methylated samples were mixed and then competitively hybridized to a Mouse CpG Island 2× 105 K Microarray (Agilent Technologies), consisting of 88737 probes, using Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent Technologies), washed with Oligo aCGH/ChIP-on-chip Wash Buffer (Agilent Technologies), according to the manufacturer’s instructions.

scan_protocol: Slides were scanned scanned by SureScan G2600D (Agilent Technologies).

data_processing: Scanner output images were normalized and digitalized using Agilent Genomic Workbench (Agilent Technologies), and probes with a p-value less than 0.05 were extracted.

molecule: genomic DNA

source_name: Pooled whole mouse brain, Female, 1d, TiO2-NP, Prenatal exposure (GD14)

label_protocol: Input DNA and methylated DNA fragments (500 ng for each group) were labeled with Cy3 or Cy5 and purified using the SureTag DNA Labeling Kit (Agilent Technologies Inc., Santa Clara, CA, USA), respectively.

growth_protocol: Pregnant C57BL/6J mice at GD 6.5, 7.5, or 8.5 were purchased from Japan SLC, Inc. (Shizuoka, Japan). All animals were housed under controlled conditions (temperature: 22±1°C, humidity: 50±5%) with a 12-h light/12-h dark cycle and ad libitum access to food and water.

extract_protocol: Whole-brain tissues were homogenized in 300 uL of phosphate-buffered saline (PBS) and 200 uL of aliquot was used for extracting genomic DNA. 150 uL of PBS and 350 uL of 2× extraction buffer (20 mM Tris-HCl [pH8.0], 0.2 M EDTA, 1% SDS, and 0.6 mg/mL Proteinase K) were added and incubated overnight at 55ºC. After RNase A treatment, genomic DNA was extracted by phenol/chloroform extraction and ethanol precipitation, followed by purification using NucleoSpin gDNA Clean-up (Macherey-Nagel, KG, Germany), according to the manufacturer’s instructions. Genomic DNA obtained from the brain of offspring was pooled for each of the following four groups (two offspring were randomly selected from each dam [Sham: n=5, TiO2-H: n=6]): Sham male, Sham female, TiO2-H male, TiO2-H female; the pooled DNA was then sonicated with Bioruptor (Cosmo Bio. Co., Ltd., Tokyo, Japan) to produce a random fragment, mainly ranging from 200 to 800 bp. The fragmented DNA (1.5 ug/100 uL) was denatured for 10 min at 95ºC and incubated in a mixture of anti-5-methyl cytosine antibody [33D3] (ab10805; Abcam Inc., Cambridge, MA, USA) and Dynabeads M-280 sheep anti-mouse IgG (Life Technologies Inc., Gaithersburg, MD, USA) in 300 uL of immunoprecipitation (IP) buffer (20 mM Tris-HCl [pH8.0], 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) overnight at 4ºC. The beads combined with methylated DNA fragments were collected using a magnetic separator, washed with IP buffer, and then incubated with elution buffer (25 mM Tris-HCl [pH8.0], 10 mM EDTA, 0.5% SDS, 0.25 mM DTT) for 15 min at 65ºC. Finally, DNA fragments were removed from beads using a magnetic separator and purified by phenol/chloroform extraction and ethanol precipitation.

treatment_protocol: 11 pregnant mice were divided into two groups: sham exposure group: Sham (dams: n=5); titanium dioxide nanoparticle (4 ug/L) exposure group: TiO2-H (dams: n=6). On GD 10.5, 25 uL of the vehicle or TiO2-NP suspension was intratracheally administered to pregnant mice of Sham and TiO2-NP exposure groups using MicroSprayer (MicroSprayer/Syringe Assembly–MSA-250-M for Mouse, Penn-Century Inc., PA, USA). The brains of offspring mice were collected on postnatal day 1.

tag: age

value: 1 d

value: Whole brain

tag: treatment

value: TiO2-NP, Prenatal exposure

tag: fraction

value: Input DNA

value: MeDIP DNA


title: sh15-LOX-2.1252-6


title: Whole brain_Female_Prenatal vehicle exposure_1d

source_name: Pooled whole mouse brain, Female, 1d, Vehicle, Prenatal exposure (GD14)

value: Vehicle, Prenatal exposure


title: Whole brain_Male_Prenatal vehicle exposure_1d

source_name: Pooled whole mouse brain, Male, 1d, Vehicle, Prenatal exposure (GD14)


title: Whole brain_Male_Prenatal titanium dioxide nanoparticle exposure_1d

source_name: Pooled whole mouse brain, Male, 1d, TiO2-NP, Prenatal exposure (GD14)


title: CD3eKO_2_70


title: CD3eKO_2_72


title: CD3eKO_2_68


title: CD3eKO_2_66


title: CD3eKO_2_58


title: CD3eKO_2_64


title: CD3eKO_2_67


title: CD3eKO_2_62


title: CD3eKO_2_69


title: CD3eKO_2_73


title: CD3eKO_2_65


title: CD3eKO_2_60


title: CD3eKO_2_63


title: CD3eKO_2_57


title: CD3eKO_2_71


title: CD3eKO_2_59


title: CD3eKO_2_55


title: CD3eKO_2_56


title: CD3eKO_2_51


title: CD3eKO_2_53


title: CD3eKO_2_52


title: CD3eKO_2_54


title: CD3eKO_2_48


title: CD3eKO_2_49


title: CD3eKO_2_47


title: CD3eKO_2_61


title: CD3eKO_2_46


title: CD3eKO_2_45


title: CD3eKO_2_42


title: CD3eKO_2_44


title: CD3eKO_2_43


title: CD3eKO_2_41


title: CD3eKO_2_40


title: CD3eKO_2_37


title: CD3eKO_2_39


title: CD3eKO_2_38


title: CD3eKO_2_36


title: CD3eKO_2_34


title: CD3eKO_2_33


title: CD3eKO_2_35


title: CD3eKO_2_31


title: CD3eKO_2_28


title: CD3eKO_2_50


title: CD3eKO_2_26


title: CD3eKO_2_30


title: CD3eKO_2_32


title: CD3eKO_2_25


title: CD3eKO_2_23


title: CD3eKO_2_22


title: CD3eKO_2_27


title: CD3eKO_2_19


title: CD3eKO_2_20


title: CD3eKO_2_18


title: CD3eKO_2_21


title: CD3eKO_2_16


title: CD3eKO_2_17


title: CD3eKO_2_29


title: CD3eKO_2_13


title: CD3eKO_2_12


title: CD3eKO_2_15


title: CD3eKO_2_14


title: CD3eKO_2_11


title: CD3eKO_2_10


title: CD3eKO_2_5


title: CD3eKO_2_24


title: CD3eKO_2_6


title: CD3eKO_2_8


title: CD3eKO_2_3


title: CD3eKO_2_9


title: CD3eKO_1_31


title: CD3eKO_2_4


title: CD3eKO_2_1


title: CD3eKO_2_7


title: CD3eKO_1_30


title: CD3eKO_2_2


title: CD3eKO_1_27


title: CD3eKO_1_26


title: CD3eKO_1_28


title: CD3eKO_1_22


title: CD3eKO_1_21


title: CD3eKO_1_24


title: CD3eKO_1_23


title: CD3eKO_1_25


title: CD3eKO_1_19


title: CD3eKO_1_20


title: CD3eKO_1_15


title: CD3eKO_1_14


title: CD3eKO_1_18


title: CD3eKO_1_17


title: CD3eKO_1_29


title: CD3eKO_1_13


title: CD3eKO_1_16


title: CD3eKO_1_12


title: CD3eKO_1_8


title: CD3eKO_1_10


title: CD3eKO_1_7


title: aCD8_2_62

value: CD8 T cell depletion


title: CD3eKO_1_9


title: CD3eKO_1_5


title: CD3eKO_1_2


title: CD3eKO_1_4


title: CD3eKO_1_1


title: CD3eKO_1_3


title: aCD8_2_60


title: aCD8_2_58


title: aCD8_2_56


title: aCD8_2_57


title: aCD8_2_59


title: aCD8_2_55


title: aCD8_2_53


title: aCD8_2_52


title: aCD8_2_49


title: CD3eKO_1_11


title: CD3eKO_1_6


title: aCD8_2_51


title: aCD8_2_50


title: aCD8_2_46


title: aCD8_2_47


title: aCD8_2_45


title: aCD8_2_41


title: aCD8_2_44


title: aCD8_2_61


title: aCD8_2_40


title: aCD8_2_37


title: aCD8_2_42


title: aCD8_2_33


title: aCD8_2_34


title: aCD8_2_38


title: aCD8_2_39


title: aCD8_2_35


title: aCD8_2_36


title: aCD8_2_54


title: aCD8_2_31


title: aCD8_2_29


title: aCD8_2_28


title: aCD8_2_30


title: aCD8_2_32


title: aCD8_2_48


title: aCD8_2_27


title: aCD8_2_26


title: aCD8_2_43


title: aCD8_2_24


title: aCD8_2_22


title: aCD8_2_25


title: aCD8_2_23


title: aCD8_2_21


title: aCD8_2_19


title: aCD8_2_20


title: aCD8_2_11


title: aCD8_2_12


title: aCD8_2_16


title: aCD8_2_9


title: aCD8_2_17


title: aCD8_2_8


title: aCD8_2_5


title: aCD8_2_4


title: aCD8_2_10


title: aCD8_2_7


title: aCD8_2_15


title: aCD8_2_6


title: aCD8_2_3


title: aCD8_2_1


title: aCD8_2_2


title: aCD8_1_74


title: aCD8_1_73


title: aCD8_1_72


title: aCD8_1_71


title: aCD8_2_18


title: aCD8_1_69


title: aCD8_1_70


title: aCD8_2_14


title: aCD8_2_13


title: aCD8_1_65


title: aCD8_1_67


title: aCD8_1_64


title: aCD8_1_66


title: aCD8_1_63


title: aCD8_1_62


title: aCD8_1_59


title: aCD8_1_56


title: aCD8_1_58


title: aCD8_1_60


title: aCD8_1_57


title: aCD8_1_53


title: aCD8_1_55


title: aCD8_1_61


title: aCD8_1_47


title: aCD8_1_50


title: aCD8_1_49


title: aCD8_1_46


title: aCD8_1_52


title: aCD8_1_48


title: aCD8_1_68


title: aCD8_1_54


title: aCD8_1_44


title: aCD8_1_43


title: aCD8_1_41


title: aCD8_1_38


title: aCD8_1_42


title: aCD8_1_40


title: aCD8_1_39


title: aCD8_1_37


title: aCD8_1_36


title: aCD8_1_35


title: aCD8_1_34


title: aCD8_1_51


title: aCD8_1_33


title: aCD8_1_30


title: aCD8_1_28


title: aCD8_1_31


title: aCD8_1_25


title: aCD8_1_26


title: aCD8_1_21


title: aCD8_1_17


title: aCD8_1_18


title: aCD8_1_19


title: aCD8_1_22


title: aCD8_1_45


title: aCD8_1_20


title: aCD8_1_14


title: aCD8_1_24


title: aCD8_1_15


title: aCD8_1_11


title: aCD8_1_13


title: aCD8_1_12


title: aCD8_1_10


title: aCD8_1_9


title: aCD8_1_32


title: aCD8_1_8


title: aCD8_1_16


title: aCD8_1_7


title: aCD8_1_29


title: aCD8_1_5


title: aCD8_1_23


title: aCD8_1_4


title: aCD8_1_27


title: aCD8_1_3


title: aCD8_1_2


title: WT_2_62

value: Wild Type


title: WT_2_63


title: aCD8_1_1


title: WT_2_59


title: WT_2_60


title: WT_2_58


title: WT_2_55


title: WT_2_54


title: WT_2_56


title: WT_2_53


title: WT_2_57


title: aCD8_1_6


title: WT_2_52


title: WT_2_50


title: WT_2_51


title: WT_2_48


title: WT_2_49


title: WT_2_43


title: WT_2_45


title: WT_2_42


title: WT_2_46


title: WT_2_47


title: WT_2_40


title: WT_2_38


title: WT_2_41


title: WT_2_61


title: WT_2_34


title: WT_2_35


title: WT_2_32


title: WT_2_33


title: WT_2_26


title: WT_2_30


title: WT_2_29


title: WT_2_27


title: WT_2_25


title: WT_2_28


title: WT_2_31


title: WT_2_44


title: Unpaired control RNAi males repeat1

city: Dallas

first: James

middle: J.

last: Collins

state: TX

address: 5323 Harry Hines Blvd.

department: Pharmacology

country: USA

institute: UT Southwestern

description: Con_MUP_v_Con_MP.csv, Con_MUP_v_gli1_MP.csv, Con_MUP_v_gli1_MUP.csv

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Schistosoma mansoni genome (v7) using STAR.
Pairwise comparisons of differential gene expression were performed with DESeq2.
Genome_build: Schistosoma mansoni v7
Supplementary_files_format_and_content: .csv file containing analysis of data generated from one-to-one comparison of three replicates of each group within the same sex by the Wald test in DESeq2

molecule: polyA RNA

organism: Schistosoma mansoni

source_name: single sex adult male parasites

growth_protocol: Virgin males were pretreated with dsRNA for a week in BM169 and then paired up/separate with virgin females for three days in no dsRNA media in BM169.

extract_protocol:
Sexes were separated and flash frozen in liquid N2 and stored in 200 𝜇L Trziol at -80℃ until all three biological replicates were collected for the sequencing. Total RNA was extracted and purified using a Zymo Direct-zol RNA miniprep kit before Illumina sequencing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA library preparation kit. The total RNA input amount per each sample was 500ng -1 ug; 94C for 6 minutes was used for mRNA fragmentation; the UMI adapters synthesized by IDT were used in the ligation step; and PCR amplification using 11-13 cycles to generate the final cDNA libraries.

treatment_protocol: 30ug/ml of either gli1 or control dsRNA on virgin males for one week before  co-culture.

value: NMRI (Puerto Rico)

value: whole worm extract

value: 6 weeks intra-mammalian


title: Unpaired control RNAi males repeat2


title: WT_2_23


title: Paired control RNAi males repeat2

description: Con_MP_v_gli1_MP.csv, Con_MP_v_gli1_MUP.csv, Con_MUP_v_Con_MP.csv,


title: WT_2_24


title: Paired control RNAi males repeat3


title: WT_2_22


title: WT_2_39


title: WT_2_20


title: WT_2_37


title: WT_2_18


title: WT_2_36


title: WT_2_16


title: WT_2_21


title: Females separated with control RNAi males repeat3

description: Con_FUP_v_Con_FP.csv, Con_FUP_v_gli1_FP.csv, Con_FUP_v_gli1_FUP.csv

source_name: single sex adult female parasites


title: WT_2_19


title: Females separated with control RNAi males repeat2


title: Females paired up with control RNAi males repeat2

description: Con_FP_v_gli1_FP.csv, Con_FP_v_gli1_FUP.csv, Con_FUP_v_Con_FP.csv,


title: Females separated with control RNAi males repeat1


title: Unpaired control RNAi males repeat3


title: Females paired up with control RNAi males repeat3


title: WT_2_13


title: Unpaired gli1 RNAi males repeat2

description: Con_MP_v_gli1_MUP.csv,  Con_MUP_v_gli1_MUP.csv, gli1_MUP_v_gli1_MP.csv


title: WT_2_14


title: Unpaired gli1 RNAi males repeat3


title: Paired gli1 RNAi males repeat3

description: Con_MP_v_gli1_MP.csv,   Con_MUP_v_gli1_MP.csv, gli1_MUP_v_gli1_MP.csv


title: Unpaired gli1 RNAi males repeat1


title: WT_2_8


title: WT_2_17


title: Paired control RNAi males repeat1


title: WT_2_10


title: Females paired up with control RNAi males repeat1


title: Paired gli1 RNAi males repeat1


title: WT_2_12


title: Females separated with gli1 RNAi males repeat2

description: Con_FP_v_gli1_FUP.csv,   Con_FUP_v_gli1_FUP.csv, gli1_FUP_v_gli1_FP.csv


title: WT_2_7


title: Females separated with gli1 RNAi males repeat1


title: WT_2_9


title: Females separated with gli1 RNAi males repeat3


title: WT_2_11


title: WT_2_6


title: WT_2_15


title: Females paired up with gli1 RNAi males repeat3

description: Con_FP_v_gli1_FP.csv,  Con_FUP_v_gli1_FP.csv, gli1_FUP_v_gli1_FP.csv


title: WT_2_4


title: WT_2_5


title: Females paired up with gli1 RNAi males repeat1


title: Females paired up with gli1 RNAi males repeat2


title: Paired gli1 RNAi males repeat2


title: WT_2_1


title: WT_2_2


title: WT_1_66


title: Kryptolebias marmoratus embryos St.17 balltail mutant

city: Exeter

first: Paul

middle: Andrew

last: O'Neill

state: --- Select a state ---

address: Stocker Road

department: Sequencing Service

country: United Kingdom

institute: University of Exeter

data_processing:
remove sequencing adaptors and low quality terminal ends (<Q20) and then remove short sequences using fastq-mcf v1.1.2-537
Variants between the groups were identified and quantified using KisSplice v2.4.0-p1 (Lopez-Maestre et al., 2016) with a k-mer size of 53
De-novo transcriptome assembly was performed for each of the groups using Trinity v v2.2.0 (Haas et al., 2013)
Quantification of gene expression was performed using Salmon (1.5.0) against the coding sequences in the reference assembly
Differential expression, without replicates, was performed using NOISeq (2.28.0)
Genome_build: ASM164957v2
Supplementary_files_format_and_content: quant.sf (salmon quantification)
Supplementary_files_format_and_content: fa - standard fasta file with variant counts encoded in header line - kissplice bespoke format.
Supplementary_files_format_and_content: deg.csv - output from noiseq differential expression evaluation
Supplementary_files_format_and_content: counts.csv - expression raw expression counts matrix
Supplementary_files_format_and_content: rpkm.csv - matrix of normalised expression counts

organism: Kryptolebias marmoratus

source_name: embryos

growth_protocol: Embryos were cultured in brackish water at 26C until Stage 17 (may contain St. 16 and 18). 20 to 25 embryos were pooled for RNA extraction.

extract_protocol:
20 to 25 embryos were frozen for each library. Total RNAs were purified by TRI reagent.
TruSeq RNA Library Prep

tag: Stage

value: St 17 (may contain St. 16 and 18)

value: all embryonic cells

value: balltail (-/-) mutant


title: Kryptolebias marmoratus embryos St.17 balltail sibling

value: balltail sibling


title: Kryptolebias marmoratus embryos St.17 shorttail mutant

value: shorttail (-/-) mutant


title: WT_1_61

value: TAC

value: single-cardiomyocyte


title: WT_1_64


title: WT_1_65


title: Kryptolebias marmoratus embryos St.17 shorttail sibling

value: shorttail sibling


title: Kryptolebias marmoratus embryos St.17 WT

value: WT


title: WT_2_3


title: WT_1_63


title: WT_1_60


title: WT_1_55


title: WT_1_58


title: WT_1_59


title: MIT/PCC1 3

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38/hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

organism: Homo sapiens

source_name: Prostate stromal cell

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS. For mouse in vivo implantation, a total number of approximately 250,000 was reached and subject to in vitro combination with human prostate cancer cells (PC3, in a number of 1,000,000). After xenografting of cell mixtures to the hind flank of animals, the chemotherapeutic agent mitoxantrone (MIT) and/or PCC1 was administered biweekly from the 3rd week post implantation.

extract_protocol:
Stromal cells were specifically isolated via laser capture microdissection (LCM) of histologically stained (hematoxylin) mouse tumor sections before lysed for RNA preparation. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total amplified RNA for the construction of sequencing libraries per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols. Three independent libraries were generated from 3 individual samples per treatment group.

treatment_protocol: Animals were treated by MIT (0.2 mg/kg) alone or MIT plus PCC1 (20 mg/kg) (dissolved in ethanol: polyethylene glycol 400: Phosal 50 PG at 10:30:60). Agents were delivered intraperitoneally (i.p.) once every 2 weeks starting from the beginning of the 3rd week, with a total number of 3 biweek cycles throughout the whole regimen (8-weeks).

value: Normal human prostate derived primary stromal cells

tag: passage

tag: name


title: MIT/PCC1 1


title: WT_1_54


title: WT_1_57


title: WT_1_56


title: MIT/PCC1 2


title: MIT 3

value: mitoxantrone (MIT)


title: MIT 1


title: Whole brain_Female_Prenatal titanium dioxide nanoparticle exposure_1d

type: RNA

description: Gene expression in 1-day-old brain of female mice prenatally exposed (GD14) to titanium dioxide nanoparticle

hyb_protocol: Cy3-labeled cRNA was hybridized to the SurePrint G3 Mouse GE 8× 60 K Microarray (Agilent Technologies Inc., Santa Clara, CA, USA), using the Gene Expression Hybridization Kit (Agilent Technologies). The microarray was then washed using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: The microarray was scanned using a DNA microarray scanner (G2565CA; Agilent Technologies).

data_processing: Scanner output images were normalized and digitalized using Feature Extraction software (Agilent Technologies).

label_protocol: Each of the pooled RNA samples was labeled with Cy3 using Low Input Quick Amp Labeling Kit, One-color (Agilent Technologies Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.

extract_protocol: Whole-brain tissues were homogenized in 300 L of phosphate-buffered saline (PBS) and 100 uL of aliquot was used for extracting total RNA. Total RNA was extracted and purified using ISOGEN-LS (Nippon Gene Co., Tokyo, Japan) according to the manufacturer’s instructions. Total RNA was equally pooled from each sample (two offspring were randomly selected from each dam [Sham: n=5, TiO2-H: n=6]) to obtain 45 ug for each of the four groups (Sham male, Sham female, TiO2-H male and TiO2-H female), and then purified using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA integrity was evaluated using a Bioanalyzer 2100 (Agilent Technologies).

value: Whole brain

tag: gender

value: Female

value: TiO2-NP, Prenatal exposure


title: Whole brain_Male_Prenatal titanium dioxide nanoparticle exposure_1d

description: Gene expression in 1-day-old brain of male mice prenatally exposed (GD14) to  titanium dioxide nanoparticle

value: Male


title: WT_1_49

value: Wild Type


title: WT_1_53


title: WT_1_47


title: WT_1_46


title: WT_1_52


title: NTERT GCN2 KO cells- RNASeq_wounded_3

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: Indiana

address: 635 Barnhill Drive, MS4067

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Barcodes and sequencing adapters were trimmed using Trimmomatic
Reads were aligned to human reference genome GRCh38 (ENSEMBL) using STAR aligner
Mapped reads were assigned to annotated genomic features of GRCh38 using featureCounts
Differential expression analysis was carried out using DESeq2 package
Genome_build: GRCh38 ENSEMBL
Supplementary_files_format_and_content: comma-separated values (csv) files showes the number of reads mapping to each gene (unnormalized counts)

source_name: NTERT GCN2 KO cells- RNASeq_wounded

growth_protocol: NTERT WT and GCN2 KO cells grown in low calcium EpiLife Complete media supplemented with human keratinocyte growth supplement and 1x Penicilin/Streptomycin

extract_protocol:
For Total RNASeq, RNA was extracted with RNA easy plus kit (Qiagen) according to manufacturer's protocol.
Total RNA was submitted to Genewiz (South Plainfield, NJ) where they performed library preparation and sequencing.

treatment_protocol: WT and GCN2KO NTERT cells were plated and left unwounded or subjected to high density wound in replicates of five

tag: cell line

value: NTERT

value: Human Kerationcytes

tag: genotype/variation

value: GCN2 KO

value: Wounded


title: NTERT GCN2 KO cells- RNASeq_wounded_5


title: MIT 2


title: Vehicle 3

value: vehicle


title: WT_1_51


title: Whole brain_Female_Prenatal vehicle exposure_1d

description: Gene expression in 1-day-old brain of female mice prenatally exposed (GD14) to vehicle

value: Vehicle, Prenatal exposure


title: Vehicle 1


title: WT_1_50

value: TAC


title: NTERT GCN2 KO cells- RNASeq_wounded_4


title: WT_1_48

value: single-cardiomyocyte


title: Vehicle 2


title: NTERT GCN2 KO cells- RNASeq_unwounded_4

source_name: NTERT GCN2 KO cells- RNASeq_unwounded

value: Unwounded


title: NTERT GCN2 KO cells- RNASeq_wounded_1


title: NTERT GCN2 KO cells- RNASeq_unwounded_1


title: WT_1_42


title: NTERT GCN2 KO cells- RNASeq_wounded_2


title: WT_1_45


title: WT_1_41


title: NTERT GCN2 KO cells- RNASeq_unwounded_5


title: NTERT GCN2 KO cells- RNASeq_unwounded_3


title: NTERT GCN2 KO cells- RNASeq_unwounded_2


title: WT_1_40


title: NTERT WT cells- RNASeq_wounded_5

source_name: NTERT WT cells- RNASeq_wounded

value: wild type


title: Whole brain_Male_Prenatal vehicle exposure_1d

description: Gene expression in 1-day-old brain of male mice prenatally exposed (GD14) to vehicle


title: WT_1_37


title: NTERT WT cells- RNASeq_wounded_4


title: WT_1_39


title: WT_1_38


title: NTERT WT cells- RNASeq_wounded_2


title: WT_1_34


title: WT_1_36


title: NTERT WT cells- RNASeq_wounded_3


title: WT_1_33


title: WT_1_43


title: NTERT WT cells- RNASeq_wounded_1


title: WT_1_32


title: WT_1_44


title: NTERT WT cells- RNASeq_unwounded_4

source_name: NTERT WT cells- RNASeq_unwounded


title: NTERT WT cells- RNASeq_unwounded_5


title: WT_1_31


title: WT_1_29


title: WT_1_35


title: WT_1_30


title: NTERT WT cells- RNASeq_unwounded_1


title: NTERT WT cells- RNASeq_unwounded_2


title: NTERT WT cells- RNASeq_unwounded_3


title: BLEO/PCC1 - 02

description: Sample 8 (XF02)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or senolytics (PCC1).

extract_protocol:
Cells were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To induce apoptosis of senescent cells, the phytochemical compound PCC1 was applied to the media at 50 µM, individually.

value: Normal human prostate derived primary stromal cells


title: BLEO/PCC1 - 01

description: Sample 7 (XF01)


title: WT_1_28


title: BLEO - 03

description: Sample 6 (XB03)

value: bleomycin


title: WT_1_27


title: BLEO - 02

description: Sample 5 (XB02)


title: CTRL - 02

description: Sample 2 (XA02)

value: control


title: WT_1_25


title: BLEO/PCC1 - 03

description: Sample 9 (XF03)


title: CTRL - 03

description: Sample 3 (XA03)


title: WT_1_21


title: WT_1_24


title: WT_1_23


title: WT_1_18


title: BLEO - 01

description: Sample 4 (XB01)


title: WT_1_22


title: Control_Replicate 3

city: Atlanta

first: Parvin

last: Forghani

state: GA

address: 2015 uppergate drive

department: Pediatric department

institute: Emory University

data_processing:
Illumina CASAVA base recognition software used for basecalling.
Indexes of the reference genome (GRCh38) was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
Data were filtered using the following specifications: remove reads with adaptor contamination; (2) remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%); (3) remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene, and then Fragments Per Kilobase Million (FPKM) was calculated to estimate gene abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows)

source_name: hiPSC-CMs

growth_protocol: The hiPSC line SCVI-273 (Stanford Cardiovascular Institute) was fed daily on Matrigel-coated plates with mTeSR™1-defined medium and passaged using Versene when confluency reached  to 90%. hiPSCs were induced using a small molecule-guided differentiation protocol. At the day of induction (day 0), medium was replaced with RPMI 1640 medium supplemented with 2% B27 minus insulin and 6 µM CHIR99021. After 48 h (day 2), RPMI supplemented with 2% B27 minus insulin was used for 24 h. At day 3, 5 µM IWR1 was added to RPMI supplemented with 2% B27 minus insulin for another 48 h. From day 5, the small molecule-containing medium was replaced with RPMI supplemented with 2% regular B27 and the medium was changed every other day. Treatment with Cfz  started at week 5th post differentiation.

extract_protocol:
RNA was isolated from 1-1.5×10e6 hiPSC-CMs per sample using AurumTM total RNA mini kit per the manufacturer’s instructions. RNA quality and concentration were measured by Nanodrop Spectrophotometer. Total RNA quality was tested by Agarose Gel Electrophoresis and Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina TruSeq technology protocols.

treatment_protocol: At differentiation day 30, hiPSC-CMs were treated with DMSO, 1 µM Cfz, for one days.

value: SCVI273 hiPSC derived cardiomyocytes

tag: developmental stage

value: Day 30 post differentiation

value: standard medium with DMSO


title: WT_1_20

value: Wild Type


title: CTRL - 01

description: Sample 1 (XA01)


title: Control_Replicate 1


title: Cfz_Replicate 3

value: standard medium with CFZ treatment


title: Cfz_Replicate 1


title: Cfz_Replicate 2


title: WT_1_17


title: WT_1_26


title: WT_1_16


title: WT_1_12


title: bleomycin/grape seed extract 01

description: Sample 7 (G01)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BLEO/GSE 01

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or grape seed extract (GSE).

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, the medicinal product GSE was applied to the media at 10 µM.

value: bleomycin/grape seed extract


title: bleomycin 03

description: Sample 6 (B03)

source_name: BLEO 03


title: bleomycin 01

description: Sample 4 (B01)

source_name: BLEO 01


title: Control_Replicate 2


title: WT_1_15

source_name: Cardiomyocyte


title: WT_1_14


title: control 02

description: Sample 2 (A02)

source_name: CTRL 02


title: WT_1_7


title: control 01

description: Sample 1 (A01)

source_name: CTRL 01


title: WT_1_5


title: H151_GC_astrocyte_10weeks

city: Frederiksberg

first: Kristine

middle: Karla

last: Freude

address: Groennegardsvej

country: Denmark

institute: University Copenhagen

data_processing:
Quality of reads were checked using Fastqc
Adapters and low quality reads were trimmed using Cutadapt
Reads were mapped to Human reference GRCh38 using Hisat2
The aligned files (sam) generated were converted into bam and sorted bam using samtools
Featurecounts software was used to generate the read counts mapping to all the genes
Differential gene expression were analysed using Cuffdiff option of cufflinks softwares
Pathway analysis using Reactome, GSEA etc
Genome_build: GRCh38
Supplementary_files_format_and_content: Differential gene expression files in excel

source_name: Induced Pluripotent Stem cells (iPSCs)

growth_protocol: Astrocyte maturation was achieved by plating astrocyte progenitor cells at a seeding density of 50.000 cells/cm2 in AMM medium supplemented with 10 ng/ml of Activin A (Thermofisher, PHG9014) HRGβ1 (Peprotech, 100-03), 200 ng/ml of IGFI (Peprotech, 100-11), 10% FBS and 200 μM L-Ascorbic acid 2-phosphate (Sigma, A8960).

extract_protocol:
Total RNA was isolated from iPSCs, APCs and differentiated astrocytes using the RNeasy mini extraction kit (Qiagen). The quality of extracted RNA was checked on Agilent 2100 Bioanalyzer system. All the RNA samples were having RIN value > 6. QC passed RNA samples  to construct the RNA libraries with TruSeq RNA Library Prep Kit.
TruSeq RNA Library Prep Kit v2

tag: development stage

value: Differentiated cell lines 10 weeks

value: iPSC-derived astrocytes

tag: cell source

value: H151_Gene corrected CHMP2B_Control cells


title: H151_astrocyte_10weeks

value: H151_CHMP2B mutation_Patient cells


title: WT_1_4

tag: operation

value: TAC

tag: name in supplementary file


title: bleomycin/grape seed extract 02

description: Sample 8 (G02)

source_name: BLEO/GSE 02


title: bleomycin/grape seed extract 03

description: Sample 9 (G03)

source_name: BLEO/GSE 03


title: WT_1_11

tag: strain

tag: condition

value: single-cardiomyocyte


title: H150_GC_astrocyte_10weeks

tag: tissue

value: H150_Gene corrected CHMP2B_Control cells


title: WT_1_10


title: WT_1_9


title: WT_1_8


title: WT_1_2


title: bleomycin 02

description: Sample 5 (B02)

source_name: BLEO 02

tag: cell type


title: WT_1_1


title: control 03

description: Sample 3 (A03)

source_name: CTRL 03

tag: treatment


title: WT_1_6


title: H150_astrocyte_10weeks

value: H150_CHMP2B mutation_Patient cells


title: H151_astrocyte_5weeks

value: Differentiated cell lines 5 weeks


title: EO771 BML-210 rep2

first: Xiongbin

last: Lu

address: 980 W. Walnut Street, R3-C218D	MMGE

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 2 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: raw count

growth_protocol: EO771 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from EO771 cells using TRIzol (Ambion) and the miRNeasy Mini kit (Qiagen).
The cDNA library was constructed using the KAPA RNA Hyper Prep Kit (Roche Corporate) and the quality was accessed by the Qubit and Agilent Bioanalyzer. The library pool was sequenced in 100b paired-end read format on NovaSeq 6000 (Illumina)

treatment_protocol: EO771 cells treated with vehicle control or BML-210 (1.0 μM) for 48 h .

value: Breast; Mammary gland

value: BML-210 treated for 48 h


title: WT_1_13


title: WT_1_19


title: H150_GC_astrocyte_5weeks


title: EO771 WT rep2

value: untreated


title: H150_astrocyte_5weeks


title: EO771 WT rep1


title: EO771 BML-210 rep1


title: K3_astrocyte_5weeks

value: K3_Wild type


title: WT_1_3


title: circSry KO 2

city: Beijing

first: Yanze

last: Song

state: Beijing

address: 1 Beichen West Road

institute: Chinese Academy of Sciences,Institute of Zoology

data_processing:
Clean data of RNA sequencing reads were aligned to mouse reference sequence GRCm39 using STAR (2.7.0f)
. Read counts and TPM (Transcripts Per Kilobase Million) were counted using RSEM (1.3.2).
Differential expression genes (DEG) (FDR < 0.05, log2 (fold change) (log2 FC) ≥ 1 or ≤ −1) were calculated by edgeR (3.28.1) package. The DEG genes were carried out Gene Ontology Pathway analysis and Kyoto Encyclopedia of Genes and Genomes analysis by clusterProfiler (3.14.3) and org.Hs.eg.db (3.10.0) packages.
Heatmap (1.0.12) was used for the heatmap visualization; colors represent the Z-score derived from the log2 transformed FPKM data. Principal Component Analysis (PCA) was performed by R packages, including tidyr(1.1.2), dplyr (1.0.2) and ggplot2 (3.3.2).
Genome_build: mm9

source_name: Primary spermatocyte

extract_protocol:
Primary spermatocytes were collected using flow cytometry via Hoechst staining of single cell suspension of testes and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spermatocyte

value: adult 8 weeks

tag: genotype

value: circSry KO


title: circSry KO 3


title: H151_GC_astrocyte_5weeks


title: WT 3

value: Wild type


title: NA-PXD-7-17 (bulk RNA-seq)

city: Hong Kong

first: Ken Hung-On

last: Yu

address: 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
For scRNA-seq, sequencing reads were aligned to the mm10 (Ensembl 84) reference genome and processed using Cell Ranger 3.0.2 (10X Genomics). For bulk RNA-seq, sequencing reads were aligned to the mm10 (Ensembl 84) reference genome using STAR (version 2.7.3) and raw count was calculated using RSEM (version 1.3.1).
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq, filtered UMI counts matrices generated by Cell Ranger. In total, we received 36,006 cells, comprising 4,732 cells for Day3_tdTomato+, 5,962 cells for Day3_tdTomato-, 8,965 cells for Day10_tdTomato+, 5,067 cells for Day10_tdTomato-, 6,843 cells for Day30_tdTomato+, and 4,437 cells for Day30_tdTomato-. For bulk RNA-seq, raw count were generated by RSEM.

source_name: hepatocellular carcinoma

extract_protocol:
scRNA-seq: HCC tumor resident cells are isolated by a modified two-step collagenase perfusion method. Tumors from three to five mice at the indicated time points were pooled. Viable tdTomato+ and tdTomato- cells were FACS sorted. Single cells were resuspended in PBS with 0.04% BSA, fixed and rehydrated for scRNA-seq.  Bulk RNA-seq: Tissues were snap frozen and RNAiso Plus (TaKaRa) was used to isolate mRNA from frozen tissues.
scRNA-seq: Samples were processed using Single Cell 5’ Reagent Kits and Single Cell A Chip Kit (Chromium™, 10X Genomics) following the manufacturer’s instructions. A total of 5,000 cells of each sample were loaded into each lane of the 10X chip. Libraries were sequenced on a NovaSeq 6000.  Bulk RNA-seq: 1µg total RNA was used for poly-A mRNA library preparation using KAPA mRNA HyperPrep Kit (KR1352-v3.16) following manufacturer's instruction. Libraries were sequenced on a NovaSeq 6000.

tag: model


title: NA-PXD-7-11 (bulk RNA-seq)


title: circSry KO 1


title: NA-CTRL-7-15 (bulk RNA-seq)

value: CTRL


title: NA-CTRL-7-10 (bulk RNA-seq)


title: NA-PXD-7-6 (bulk RNA-seq)


title: WT 1


title: Control_sperm_2

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Raw sequencing reads were trimmed for adaptor sequences, low-quality (Phred < 20) and too small (length < 17 bases)sequenced reads were removed using CutAdatp and FastQC.
against the Mus musculus reference genome 9 (NCBI37/mm9) (June 2007, NCBI) using Bowtie  and Bowtie 2. Bowtie was used with -n alignment default mode selected coupled with -best mode to align the short reads to the reference databases, reads producing unique alignments were considered successfully mapped. The remaining unaliged reads were re-processed again using Bowtie 2 with default settings. Unaligned reads left after processing were excluded from further analyses.
Annotation of aligned reads was performed using an in-house script querying the RNAcentral database to retrieve the relevant information using the individual accession numbers.
The number of each unique miRNA molecules identified in both sample groups were compiled and calculated using another in-house script. Long non-coding RNAs, ribozyme RNAs and Rnase P were excluded from further analysis due to technical considerations and experimental design.
R Statistical Software and edgeR package was used to calculate differential accumulation of sncRNA between samples groups and perform statistical testing.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files for ncRNA-seq contain ncRNA type, accession number and read counts for each sample
Supplementary_files_format_and_content: Sperm sncRNA analysis file contains ncRNA type, accession number, name, read counts for each samples, fold change and p-value

source_name: mature cauda spermatozoa

extract_protocol:
Total RNA was extracted from purified mature cauda spermatozoa using a Direct-zol™ RNA MiniPrep Kit (Zymo Research Corporation, Irvine, CA, USA) according to manufacturer’s instructions. Total RNA was extracted from groups of 2-cell embryos using a Direct-zol RNA MicroPrep Kit (Zymo Research Corporation) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Ilumina protocols (sncRNA-seq) or Nugen trio kit RNA sample kit (RNA-seq).

treatment_protocol: Treatment involved the administration of 25mg/kg/bw/day of acrylamide or vehicle alone (PBS; control) for five conseuctive days via intraperitoneal injection. Sperm from acrylamide treated males was collected at two time points, either three (epididymal exposure, AAE) or twenty four (spermatocyte exposure, AAS) days following the final injection.

value: Swiss

value: control, PBS

value: cauda epididymis

value: sperm


title: AAE_sperm_2

value: acrylamide


title: NA-CTRL-7-3 (bulk RNA-seq)


title: AAE_sperm_1


title: Control_sperm_1


title: WT rep1 [WD1_S49]

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description:
Expression profiling of WT differentiated mesendodermal cells
Genecounts.csv
ERCCcounts.csv

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat2 (2.0.11) with parameters -r 100 --library-type fr-firststrand -N 2 --b2-very-sensitive --b2-L 25 -p 8
Gene annotations were obtained from Ensembl Mouse genome (NCBIM37). Gene-based read count and ERCC count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes raw Gene counts for each Sample
Supplementary_files_format_and_content: csv file includes raw ERCC counts for each Sample

source_name: WT differentiated mesendodermal cells

growth_protocol: Cells were differentiated from wild-type and Cnot3-T292A/S294A mouse ES cells for 4 days into mesendoderm using BMP4 and FGF2 in serum free media

extract_protocol:
Cells were collected and counted. RNA was extracted from 2 million cells using Trizol (ThermoFisher), 2 ul of a 1:10 dilution of ERCC Spike-in Mix (ThermoFisher) were added to each sample.
500 ng of RNA were used to prepare a polyA RNA library using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: wild type

value: 4-day differentiated mesendodermal cells

tag: derived from

value: wild type E14 mouse embryonic stem (ES) cells


title: Cnot3-T292A/S294A rep3 [CD3_S54]

description:
Expression profiling of Cnot3-T292A/S294A differentiated mesendodermal cells
Genecounts.csv
ERCCcounts.csv

value: Cnot3-T292A/S294A, Cnot3 Thr and Ser to Ala

value: Cnot3-T292A/S294A E14 mouse ES cells


title: BxPC3_NT_rep2

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

data_processing:
Raw fastq files were passed to Salmon with Refseq transcript index for MM10 or HG19
reads across isoforms were summed to give single value for each gene
Genome_build: MM10, HG19
Supplementary_files_format_and_content: TPM per gene

growth_protocol: Cells were grown in DMEM

extract_protocol:
PureLink RNA mini kit (Thermo, as recommended by manufacturer)
PolyA selection, fragmentation and ligation of adapters followed by PCR amplification
random fragmentation of mRNA and sequencing

treatment_protocol: As noted per sample, cells were typically treated for 1-3hrs with BB (dimerizer), 4OHT, or Digitonin

tag: construct

tag: media

value: DMEM

value: NT


title: DC-PXD-2-10 (bulk RNA-seq)


title: DC-CTRL-2-13 (bulk RNA-seq)


title: Cnot3-T292A/S294A rep2 [CD2_S53]

source_name: Cnot3-T292A/S294A differentiated mesendodermal cells


title: DC-PXD-2-9 (bulk RNA-seq)


title: Cnot3-T292A/S294A rep1 [CD1_S52]


title: WT 2

value: spermatocyte


title: WT rep3 [WD3_S51]


title: DC-PXD-2-6 (bulk RNA-seq)


title: BxPC3_NT_rep1

tag: cell line


title: BxPC3_Digitonin_40ug/mL_rep2


title: BxPC3_Digitonin_40ug/mL_rep1


title: DC-CTRL-2-8 (bulk RNA-seq)


title: HT29_NT_rep2


title: HT29_Digitonin_40ug/mL_rep2


title: DC-CTRL-2-7 (bulk RNA-seq)


title: TS35_11_11_494_1M_S2

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

data_processing:
Reads were aligned to the human genome (GRCh38 and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: TS35_RNA_Seq_read_counts.csv

source_name: Primary AML

growth_protocol: Cryopreserved primary AML cells were defrosted then immediately FACS sorted and subjected to RNA extraction and sequencing.

extract_protocol:
Total RNA was extracted from 10^3-10^5 sorted blasts using QIAshredder spin columns and an RNeasy® Plus Micro kit (Qiagen). Prior to sequencing RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual id

value: primary refractory AML

tag: immunophenotype

tag: treatment protocol

value: Pre-chemotherapy


title: WT rep2 [WD2_S50]


title: HT29_NT_rep1


title: TS35_10_10_349_3M_S1

value: Post-chemotherapy


title: tdTpos-day10 (scRNA-seq)

description: tdT+ day 10

value: tdTomato+


title: TS35_12_12_494_3M_S3


title: TS35_9_9_349_1M_S12


title: tdTneg-day30 (scRNA-seq)

description: tdT- day 30

value: tdTomato-


title: tdTpos-day30 (scRNA-seq)

description: tdT+ day 30


title: HT29_Digitonin_40ug/mL_rep1


title: TS35_7_7_285_1B_P5_S10


title: TS35_8_8_285_2M_P3_S11


title: TS35_2_2_64_2M_S5


title: tdTpos-day3 (scRNA-seq)

description: tdT+ day 3


title: TS35_5_5_205_1B_S8


title: TS35_4_4_121_3M_S7


title: Genomic DNA from Airway Macrophages [IPF_AM_25]

first: Adam

last: Byrne

state: London

address: South Kensingtion Campus

department: National Heart and Lung Institute

institute: Imperial College London

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina EPIC Human Methylation array using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using QIAGEN All Prep kit.

treatment_protocol: Airway macrophages were enriched from bronchioalveolar lavage using marker CD206 and either FACS or MACS-based methods.

tag: disease

value: Idiopathic pulmonary fibrosis (IPF)

value: Airway macrophages

tag: gender

value: Male

tag: isolation

value: FACS

tag: age

tag: smoking history

value: Ex


title: Genomic DNA from Airway Macrophages [IPF_AM_24]


title: TS35_3_3_121_1M_S6


title: Genomic DNA from Airway Macrophages [IPF_AM_30]

value: Female


title: TS35_1_1_64_1B_S4


title: Genomic DNA from Airway Macrophages [IPF_AM_29]

value: Never


title: tdTneg-day3 (scRNA-seq)

description: tdT- day 3

tag: strain


title: 223 PC-6500

city: New York

first: Natalia

last: Teleshova

state: NY

address: 1230 York Avenue

institute: Population Council

description:
column "223Post" of counts.matrix
column "223Post_copy1" column of counts.matri
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.

data_processing:
Input adapter trimming using Cutadapt version 1.9.1 with -a AAAAAAAAAAAAA -a TTTTTTTTTTTTT -a AGATCGGAAGAG -a CTCTTCCGATCT
Aligning the input reads to reference genome using STAR_2.4.2a
Quality assesment on aligned data using FastQC v0.11.5
Quality assesment on aligned data using QualiMap  v.2.2
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genome_build: Hsapiens/GRCh37
Supplementary_files_format_and_content: .counts summarizing count information of gene presented after aligning samples to the reference genome

source_name: ectocervix

extract_protocol:
Tissue RNA was extracted using total RNAase Fibrous Tissue Mini Kit (Qiagen, Valencia, CA). The concentration and purity of the extracted RNA were assessed by the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
100 ng of total RNA was used to generate RNA-Seq libraries using Illumina TruSeq stranded mRNA LT kit (Cat# RS-122-2101).
Libraries prepared with unique barcodes were pooled at equal molar ratios.  The pool was denatured and sequenced on Illumina NextSeq 500 sequencer using high output V2 reagents and NextSeq Control Software v1.4 to generate 75 bp single reads, following manufactures protocol (Cat# 15048776 Rev.E)

treatment_protocol: Ectocervical biopsies from subjects in the clinical trial were stored in RNAlater at -20°C before RNA extraction

tag: subject id

tag: organ

value: ectocervix

tag: tissue

value: mucosa

tag: time point

value: after use of PC-6500


title: Genomic DNA from Airway Macrophages [IPF_AM_26]

tag: cell type


title: 221 PC-6500

description:
column "221Post" of counts.matrix
column "221Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Genomic DNA from Airway Macrophages [IPF_AM_23]


title: 220 PC-6500

description:
column "220Post" of counts.matrix
column "220Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 220 BL

description:
column "220BL" of counts.matrix
column "220BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.

value: baseline


title: 221 BL

description:
column "221BL" of counts.matrix
column "221BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: TS35_6_6_205_2M_S9


title: 219 BL

description:
column "219BL" of counts.matrix
column "219BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Genomic DNA from Airway Macrophages [IPF_AM_18]


title: 216 PC-6500

description:
column "216Post" of counts.matrix
column "216Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Genomic DNA from Airway Macrophages [IPF_AM_22]


title: 219 Placebo

description:
column "219Post" of counts.matrix
column "219Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 215 PC-6500

description:
column "215Post" of counts.matrix
column "215Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Infected mouse 3

city: Houston

first: Mary

last: Estes

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description:
10x-Estes-06
Chromium Single Cell 3′ Kit v3

data_processing:
To compensate for mixed Chromium Single Cell 3′ Kit v2 and v3 chemistry, sequencing cycling conditions were as follows: Read 1: 28 Index 1: 8  Read 2: 91.
Sequencing reads were aligned to the GRCm38 murine genome and RV genome ASM325908v1 using the default parameters of the10x Genomics Cell Ranger pipeline.
Genome_build: GRCm38 and ASM325908v1
Supplementary_files_format_and_content: barcodes.tsv: Cell barcode tab-separated file.
Supplementary_files_format_and_content: matrix.mtx: Feature barcode matrix mtx file.
Supplementary_files_format_and_content: features.tsv: Feature tab-separated file.

source_name: Small intestine epithelium

growth_protocol: C57Bl6J wild-type mice were orally gavaged with murine rotavirus strain EC (1e3 infectious dose 50) or PBS gut homogenate 4 days prior to cell isolation.

extract_protocol: 10x Genomics Chromium Single Cell 3′ Kit.

treatment_protocol: The small intestine was flushed with cold Dulbecco’s PBS (DPBS), opened lengthwise, and dissected into 1 cm pieces. The tissue was rocked in 2mM EDTA/DPBS on ice for 30 min then transferred to a 1% sucrose 1% sorbitol/DPBS solution and manually shaken for 2 min to dissociate crypts. After three rounds of shaking, the isolated crypts were combined with fragmented villi from the previous rounds of shaking and filtered through a 70 µm strainer. The cells were resuspended in TrypLE supplemented with 100 µg/ml DNaseI and 10 nM Y27632 in a 37 degree water bath for 30 min and gently pipetted every 10 min to obtain single cells. Single cells were filtered through a 40 µm strainer and washed with 1% BSA/DPBS prior to staining. EpCAM+CD31-CD45-TER119- intestinal tuft cells were collected via FACS.

tag: genotype

value: Wild-type

value: Small intestine epithelium

tag: treatment

value: infected with rotavirus


title: 215 BL

description:
column "215BL" of counts.matrix
column "215BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 223 BL

description:
column "223BL" of counts.matrix
column "223BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 216 BL

description:
column "216BL" of counts.matrix
column "216BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Genomic DNA from Airway Macrophages [IPF_AM_21]


title: Genomic DNA from Airway Macrophages [IPF_AM_20]


title: 213 PC-6500

description:
column "213Post" of counts.matrix
column "213Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Uninfected mouse 3

description:
10x-Estes-05
Chromium Single Cell 3′ Kit v3

value: uninfected


title: 213 BL

description:
column "213BL" of counts.matrix
column "213BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 210 PC-6500

description:
column "210Post" of counts.matrix
column "210Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Genomic DNA from Airway Macrophages [IPF_AM_27]


title: Infected mouse 2

description:
10x-Estes-04
Chromium Single Cell 3′ Kit v3


title: Genomic DNA from Airway Macrophages [IPF_AM_28]


title: Genomic DNA from Airway Macrophages [IPF_AM_16]


title: 206 Placebo

description:
column "206Post" of counts.matrix
column "206Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 206 BL

description:
column "206BL" of counts.matrix
column "206BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 210 BL

description:
column "210BL" of counts.matrix
column "210BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Uninfected mouse 2

description:
10x-Estes-03
Chromium Single Cell 3′ Kit v3


title: Genomic DNA from Airway Macrophages [IPF_AM_19]


title: Uninfected mouse 1

description:
10x-Estes-02
Chromium Single Cell 3′ Kit v2


title: 203 Placebo

description:
column "203Post" of counts.matrix
column "203Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 203 BL

description:
column "203BL" of counts.matrix
column "203BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: 202 PC-6500

description:
column "202Post" of counts.matrix
column "202Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Infected mouse 1

description:
10x-Estes-01
Chromium Single Cell 3′ Kit v2


title: 201 PC-6500

description:
column "201Post" of counts.matrix
column "201Post_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Genomic DNA from Airway Macrophages [IPF_AM_17]


title: 201 BL

description:
column "201BL" of counts.matrix
column "201BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: Genomic DNA from Airway Macrophages [IPF_AM_13]

value: MACS


title: Infected mouse rv3 [RV3_S133]

data_processing:
Sequencing reads were pseudo-aligned to the GRCm38 murine genome and RV genome ASM325908v1 using kallisto -b 100
kallisto output was processed with R tximport and edgeR
Genome_build: GRCm38 and ASM325908v1
Supplementary_files_format_and_content: raw count comma separated file

source_name: Infected_Small intestine tuft cells

extract_protocol:
RNA was isolated with the Qiagen RNeasy Micro kit according to the manufacturer's protocol.
Libraries were synthesized with Takara's SMARTer Stranded Total RNA-Seq Kit v2 Pico Input kit according to the manufacturer’s protocol.

treatment_protocol: The small intestine was flushed with cold Dulbecco’s PBS (DPBS), opened lengthwise, and dissected into 1 cm pieces. The tissue was rocked in 2mM EDTA/DPBS on ice for 30 min then transferred to a 1% sucrose 1% sorbitol/DPBS solution and manually shaken for 2 min to dissociate crypts. After three rounds of shaking, the isolated crypts were combined with fragmented villi from the previous rounds of shaking and filtered through a 70 µm strainer. The cells were resuspended in TrypLE supplemented with 100 µg/ml DNaseI and 10 nM Y27632 in a 37 degree water bath for 30 min and gently pipetted every 10 min to obtain single cells. Single cells were filtered through a 40 µm strainer and washed with 1% BSA/DPBS prior to staining. EpCAM+Siglecf+ intestinal tuft cells were collected via FACS.

value: infected

tag: tissue/cell type

value: Small intestine tuft cells


title: PBMA-4

city: Boston

first: Lynn

last: Bry

state: MA

address: 75 Francis St.

department: Pathology

institute: Brigham and Women's Hospital

description: P. bifermentans mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 4

data_processing:
Bowtie2 was used to align filtered and trimmed reads to a library consisting of C. diffcile, P. bifermentans, C. saridiniense, and Mus musculus DNA sequences for all reactions to ensure specific alignments to C. difficile gene features.
Reads were assigned to features in alignments using HTSeq. Reads overlapping multiple features were assigned to both to account for polycistronic RNAs.
Unaligned reads were also analyzed with Kraken to check for contaminants. Note - mouse chow contains RNAs which are present in caecal contents.
A 10 read average cutoff was applied. C. difficile genomic features were analyzed.
DESeq2 was used to normalize read counts and for subsequent differential expression analyses.
Supplementary_files_format_and_content: Normalized_counts_PBI.csv
Supplementary_files_format_and_content: Raw_counts_10_read_cutoff_PBI.csv

source_name: Mouse caecal contents

growth_protocol: 6-7 week-old male and female gnotobiotic (germ-free) mice were pre-colonized by gavage (P. bifermentans and C. sardiniense) with 10^8 cfu 1 week before inoculation by gavage with10^3 C. difficile ATCC43255 spores. Mono-associated mice were gavaged with sterile water instead of the corresponding bacterial dose.

extract_protocol:
Mice were sacfiriced at the indicated timepoint and dissected. Cecal contents were cryogenically stored for extraction.
Purified RNAs were rRNA depleted and eukaryotic (mouse) poly-A mrRNA depleted. Illumina Nextseq500 with paired-end 150 nucleotide runs were performed. Additional runs were done with the same library when additional reads were needed.

tag: pre-colonization

value: Paraclostridium bifermentans

tag: sample type

value: Mouse caecal contents


title: 202 BL

description:
column "202BL" of counts.matrix
column "202BL_copy1" column of counts.matrix
Each library was run in two lanes.  "Copy" refers to the second lane of sequencing.


title: PBMA-5

description: P. bifermentans mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 5


title: Infected mouse rv2 [RV2_S132]


title: tdTneg-day10 (scRNA-seq)

description: tdT- day 10

tag: model

value: tdTomato-


title: PBMA-3

description: P. bifermentans mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 3


title: Genomic DNA from Airway Macrophages [IPF_AM_15]

tag: disease

value: Idiopathic pulmonary fibrosis (IPF)

value: Airway macrophages

value: Male

value: Ex


title: PBMA-2

description: P. bifermentans mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 2


title: Genomic DNA from Airway Macrophages [IPF_AM_12]

tag: gender

value: Female

value: Never


title: PBMA-1

description: P. bifermentans mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 1


title: Genomic DNA from Airway Macrophages [IPF_AM_14]

tag: isolation


title: Infected mouse rv1 [RV_S8]


title: CSMA-5

description: C. sardiniense mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 5

data_processing:
Bowtie2 was used to align filtered and trimmed reads to a library consisting of C. diffcile, P. bifermentans, C. saridiniense, and Mus musculus DNA sequences for all reactions to ensure specific alignments to C. difficile gene features.
Reads were assigned to features in alignments using HTSeq. Reads overlapping multiple features were assigned to both to account for polycistronic RNAs.
Unaligned reads were also analyzed with Kraken to check for contaminants. Note - mouse chow contains RNAs which are present in caecal contents.
A 10 read average cutoff was applied. C. difficile genomic features were analyzed.
DESeq2 was used to normalize read counts and for subsequent differential expression analyses.
Supplementary_files_format_and_content: Normalized_counts_CSAR.csv
Supplementary_files_format_and_content: Raw_counts_10_read_cutoff_CSAR.csv

value: Clostridium sardiniense


title: CSMA-6

description: C. sardiniense mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 6


title: Uninfected mouse pbs 2 [Mock2_S130]

source_name: Uninfected_Small intestine tuft cells


title: Uninfected mouse pbs 1 [Mock_S7]


title: CSCD-24hr-6

description: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 6

data_processing:
Bowtie2 was used to align filtered and trimmed reads to a library consisting of C. diffcile, P. bifermentans, C. saridiniense, and Mus musculus DNA sequences for all reactions to ensure specific alignments to C. difficile gene features.
Reads were assigned to features in alignments using HTSeq. Reads overlapping multiple features were assigned to both to account for polycistronic RNAs.
Unaligned reads were also analyzed with Kraken to check for contaminants. Note - mouse chow contains RNAs which are present in caecal contents.
A 10 read average cutoff was applied. C. difficile genomic features were analyzed.
DESeq2 was used to normalize read counts and for subsequent differential expression analyses.
Supplementary_files_format_and_content: Normalized_counts.xlsx
Supplementary_files_format_and_content: Raw_counts_10_read_cutoff.csv

tag: agent

value: Clostridium sardiniense, Clostridioides difficile


title: CSMA-4

description: C. sardiniense mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 4


title: CSCD-24hr-5

description: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 5


title: CSMA-2

description: C. sardiniense mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 2


title: Genomic DNA from Airway Macrophages [IPF_AM_10]

tag: age

tag: smoking history


title: APCmin/-;BMAL1-/- CT46 (S47)

city: Windsor

first: Phillip

last: Karpowicz

state: Ontario

address: 401 Sunset Ave

department: Biomedical Sciences

country: Canada

institute: University of Windsor

description:
Karpowicz_Windsor_71_047_S47
collected 46h post synchronization

data_processing:
Raw transcriptome sequencing reads were aligned against GRCm38 and Ensembl release 96 transcript annotations using STAR v2.5 (Dobin et al., 2013)
RSEM v1.3.0 (Li and Dewey, 2011, BMC Bioinformatics) was used for transcript quantification.
low quality samples were removed and Transrcipts Per Million (TPM) for remaining samples were merged into one file
Quantile normalization was performed for each expression table using preprocessCore package. Genes with null expression in at least one sample within an expression table were removed from that table
rhythmic analysis was performed using MetaCycle2d, base expression >0.5, relative amplitude >0.05, BH q-value <0.1
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-separated values tables, identified with 'star_rsem_allgenes', report the TPM values for all genes in each genotype, obtained after STAR alignment and RSEM quantification.
Supplementary_files_format_and_content: comma-separated values tables, identified with 'quant-norm_filtered_CT-header', contain the data after quantile normalization and removal of null-expressing genes in each genotype. Sample (column) names were replaced by the corresponding time post synchronization (CT)
Supplementary_files_format_and_content: STAR alignment stats

source_name: Primary Derived

growth_protocol: 2 organoids lines (biological replicates) per genotype  were grown in ENR or EN media (the second for APCmin genotypes).

extract_protocol:
RNA was extracted using the Qiagen Rneasy mini Purification Kit (Cat# 74105)
Libraries were prepared using 96 NEB - NEBNext Ultra II Directional RNA Library Prep Kit including quality control and DNase treatment (#E7765, New England Biolabs Inc). Sequencing was done on a 1 Flowcell, Illumina NovaSeq6000 (Illumina), S2, 100 Cycles, v1 chemistry Read 1: 101bp, Index Read 1: 8bp, Index Read 2: 8bp
Each library was sequenced in two separate lanes, which generated 2 fastq files for each sample

treatment_protocol: each organoid line (n=8) were treated with 0.1µm dexamethasone for 1h. Dexamethasone replaced with  fresh media. Samples were collected every 2h from 24-48h post synchroniztion

value: Intestinal Adenoma Organoids

tag: clock function

value: Circadian Clock Mutant

tag: strain

tag: time

tag: synchronization

value: 1h 0.1µm Dexamethasone


title: CSCD-24hr-4

description: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 4

tag: time point


title: APCmin/-;BMAL1-/- CT46 (S46)

description:
Karpowicz_Windsor_70_046_S46
collected 46h post synchronization

tag: cell type

tag: genotype


title: CSCD-24hr-3

description: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 3


title: CSMA-1

description: C. sardiniense mono-associated (not infected with C. difficile), 7 days after colonization. Mouse 1


title: CSCD-24hr-2

description: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 2


title: APCmin/-;BMAL1-/- CT44 (S43)

description:
Karpowicz_Windsor_65_043_S43
collected 44h post synchronization


title: CSCD-24hr-1

description: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 1


title: Genomic DNA from Airway Macrophages [IPF_AM_11]

value: FACS


title: PBCD-24hr-6

description: P. bifermentans with subsequent C. difficile 24 hours post infection Mouse 6

value: Paraclostridium bifermentans, Clostridioides difficile


title: Genomic DNA from Airway Macrophages [IPF_AM_9]


title: PBCD-24hr-5

description: P. bifermentans with subsequent C. difficile 24 hours post infection Mouse 5


title: Genomic DNA from Airway Macrophages [IPF_AM_8]


title: Genomic DNA from Airway Macrophages [IPF_AM_7]


title: APCmin/-;BMAL1-/- CT44 (S42)

description:
Karpowicz_Windsor_64_042_S42
collected 44h post synchronization


title: Uninfected mouse pbs 3 [Mock3_S131]

tag: treatment

value: uninfected

tag: tissue/cell type

value: Small intestine tuft cells


title: PBCD-24hr-4

description: P. bifermentans with subsequent C. difficile 24 hours post infection Mouse 4


title: APCmin/-;BMAL1-/- CT42 (S39)

description:
Karpowicz_Windsor_59_039_S39
collected 42h post synchronization


title: PBCD-24hr-3

description: P. bifermentans with subsequent C. difficile 24 hours post infection Mouse 3


title: PBCD-24hr-2

description: P. bifermentans with subsequent C. difficile 24 hours post infection Mouse 2


title: Genomic DNA from Airway Macrophages [IPF_AM_6]


title: APCmin/-;BMAL1-/- CT42 (S38)

description:
Karpowicz_Windsor_58_038_S38
collected 42h post synchronization


title: Genomic DNA from Airway Macrophages [IPF_AM_4]


title: PBCD-24hr-1

description: P. bifermentans with subsequent C. difficile 24 hours post infection Mouse 1


title: CDMA-24hr-6

description: C. difficile 24 hours post infection Mouse 6

value: Clostridioides difficile


title: APCmin/-;BMAL1-/- CT40 (S35)

description:
Karpowicz_Windsor_53_035_S35
collected 40h post synchronization


title: CDMA-24hr-5

description: C. difficile 24 hours post infection Mouse 5


title: Genomic DNA from Airway Macrophages [Healthy_AM_14]

value: Healthy


title: APCmin/-;BMAL1-/- CT40 (S34)

description:
Karpowicz_Windsor_52_034_S34
collected 40h post synchronization


title: CDMA-24hr-4

description: C. difficile 24 hours post infection Mouse 4


title: Genomic DNA from Airway Macrophages [IPF_AM_5]

value: Idiopathic pulmonary fibrosis (IPF)

value: MACS


title: CDMA-24hr-2

description: C. difficile 24 hours post infection Mouse 2


title: APCmin/-;BMAL1-/- CT38 (S31)

description:
Karpowicz_Windsor_47_031_S31
collected 38h post synchronization


title: CDMA-24hr-3

description: C. difficile 24 hours post infection Mouse 3


title: CDMA-24hr-1

description: C. difficile 24 hours post infection Mouse 1


title: CSCD-20hr-6

description: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 6


title: APCmin/-;BMAL1-/- CT38 (S30)

description:
Karpowicz_Windsor_46_030_S30
collected 38h post synchronization


title: Genomic DNA from Airway Macrophages [IPF_AM_3]

value: Airway macrophages


title: AH2-23

city: Madrid

first: Alejandro

last: Higuera-Matas

state: Madrid

address: Calle Juan del Rosal 10

department: Psychobiology

country: Spain

institute: Universidad Nacional de Educación a Distancia (UNED)

data_processing:
We used the Illumina Basespace workflow version. 2.1.0.  The BAM summary method was BamStats. The alligner software used was STAR (version 2.6.25.17) and the software for the analysis was Isis (2.6.25.17 version).
Differential expression analysis was carried out using the CUFFDIFF tool (2.2.1 version).
Genome_build: UCSC Rn5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Nucleus Accumbens (bulk tissue)

extract_protocol:
Samples were homogenized, and RNA extracted according to the protocol, tools and reagents provided by RNeasy Mini Kit (Qiagen).
Libraries were prepared according to the instructions of the NEBNext Ultra Directional RNA Library Prep kit for Illumina kit (New England Biolabs), as detailed in “Chapter 1: Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module”. The input yield of total RNA to start the protocol was 1 µg quantified by an Agilent 2100 Bioanalyzer using an RNA 6000 nano LabChip kit. We performed the library amplification included in the cited protocol using a PCR of 14 cycles. The obtained libraries were validated and quantified by an Agilent 2100 Bioanalyzer using a DNA7500 LabChip kit and an equimolecular pool of libraries were titrated by quantitative PCR using the “Kapa-SYBR FAST qPCR kit forLightCycler480” (Kapa BioSystems) and a reference standard for quantification.

treatment_protocol: We injected lipopolysaccharide (LPS) or saline on gestational days 15 and 16 to pregnant rats. Their male offspring were then subjected to unpredictable stress or handling during adolescence. At PND 90, animals were deeply anaesthetised with isoflurane and sacrificed by decapitation. Brains were extracted and, with the help of a brain matrix, 1 mm thick coronal slices were obtained between 2.28 mm and 1.08 mm, approximately, anterior from bregma. With the help of two dissecting lancet-shaped needles, the dorsolateral striatum and the nucleus accumbens were dissected according to the Paxinos and Watson atlas. The tissue samples were snap-frozen with dry ice and stored at -70º C.

tag: tissue

value: Nucleus Accumbens (bulk tissue)

value: Sprague-Dawley

tag: Sex

value: Male

tag: maternal immune activation

value: LPS

tag: stress

value: Stress


title: CSCD-20hr-3

description: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 3

value: Clostridium sardiniense, Clostridioides difficile


title: AH2-22


title: Genomic DNA from Airway Macrophages [IPF_AM_2]

tag: disease

tag: gender

tag: isolation

value: Never


title: CSCD-20hr-4

description: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 4

tag: agent


title: CSCD-20hr-1

description: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 1


title: AH2-24


title: PBCD-20hr-6

description: P. bifermentans with subsequent C. difficile 20 hours post infection Mouse 6


title: PBCD-20hr-5

description: P. bifermentans with subsequent C. difficile 20 hours post infection Mouse 5


title: APCmin/-;BMAL1-/- CT34 (S23)

description:
Karpowicz_Windsor_35_023_S23
collected 34h post synchronization

value: Intestinal Adenoma Organoids

tag: clock function

value: Circadian Clock Mutant

value: 1h 0.1µm Dexamethasone


title: AH2-21

tag: strain

value: No Stress


title: CSCD-20hr-2

description: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 2


title: Genomic DNA from Airway Macrophages [Healthy_AM_13]

value: Female

tag: age

tag: smoking history


title: APCmin/-;BMAL1-/- CT34 (S22)

description:
Karpowicz_Windsor_34_022_S22
collected 34h post synchronization

tag: time

tag: synchronization


title: CSCD-20hr-5

description: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 5

tag: time point


title: PBCD-20hr-4

description: P. bifermentans with subsequent C. difficile 20 hours post infection Mouse 4

value: Paraclostridium bifermentans, Clostridioides difficile


title: AH2-19


title: PBCD-20hr-3

description: P. bifermentans with subsequent C. difficile 20 hours post infection Mouse 3


title: PBCD-20hr-2

description: P. bifermentans with subsequent C. difficile 20 hours post infection Mouse 2


title: APCmin/-;BMAL1-/- CT32 (S19)

description:
Karpowicz_Windsor_29_019_S19
collected 32h post synchronization

tag: cell type

tag: genotype


title: CDMA-20hr-6

description: C. difficile 20 hours post infection Mouse 6

value: Clostridioides difficile


title: AH2-20

tag: tissue


title: PBCD-20hr-1

description: P. bifermentans with subsequent C. difficile 20 hours post infection Mouse 1


title: CDMA-20hr-3

description: C. difficile 20 hours post infection Mouse 3


title: AH2-17

tag: Sex

value: Saline


title: Genomic DNA from Airway Macrophages [Healthy_AM_10]

value: Healthy

value: MACS

value: Ex


title: CDMA-20hr-5

description: C. difficile 20 hours post infection Mouse 5


title: CDMA-20hr-2

description: C. difficile 20 hours post infection Mouse 2


title: AH2-16

value: Nucleus Accumbens (bulk tissue)

value: Sprague-Dawley

tag: maternal immune activation


title: Genomic DNA from Airway Macrophages [Healthy_AM_11]

value: Airway macrophages

value: FACS


title: APCmin/-;BMAL1-/- CT30 (S14)

description:
Karpowicz_Windsor_22_014_S14
collected 30h post synchronization


title: CDMA-20hr-1

description: C. difficile 20 hours post infection Mouse 1


title: AH2-18

value: Male

tag: stress

value: Stress


title: APCmin/-;BMAL1-/- CT36 (S26)

description:
Karpowicz_Windsor_40_026_S26
collected 36h post synchronization

value: Intestinal Adenoma Organoids


title: Genomic DNA from Airway Macrophages [Healthy_AM_7]

tag: disease

value: Never


title: LLC_Digitonin_55ug/mL_rep1

tag: cell line

value: LLC

tag: construct

tag: media

value: DMEM

tag: treatment


title: Genomic DNA from Airway Macrophages [Healthy_AM_12]

tag: gender

tag: isolation


title: Genomic DNA from Airway Macrophages [Healthy_AM_8]

value: Female

tag: age

tag: smoking history


title: Genomic DNA from Airway Macrophages [Healthy_AM_9]


title: Genomic DNA from Airway Macrophages [IPF_AM_1]

value: Idiopathic pulmonary fibrosis (IPF)


title: APCmin/-;BMAL1-/- CT36 (S27)

description:
Karpowicz_Windsor_41_027_S27
collected 36h post synchronization

tag: clock function

value: Circadian Clock Mutant

tag: strain

tag: time

tag: synchronization

value: 1h 0.1µm Dexamethasone


title: Genomic DNA from Airway Macrophages [Healthy_AM_3]

value: Healthy

tag: cell type


title: LLC_noDig_rep2

value: NT


title: AH2-15

tag: tissue

tag: Sex

value: Saline

value: No Stress


title: LLC_noDig_rep1


title: NIH3T3_Digitonin_55ug/mL_rep2


title: AH2-13

value: Nucleus Accumbens (bulk tissue)

value: Sprague-Dawley

tag: maternal immune activation

tag: stress


title: AH2-14


title: APCmin/-;BMAL1-/- CT28 (S10)

description:
Karpowicz_Windsor_16_010_S10
collected 28h post synchronization

tag: genotype


title: NIH3T3_noDig_rep2

tag: cell line

tag: construct


title: APCmin/-;BMAL1-/- CT26 (S7)

description:
Karpowicz_Windsor_11_007_S7
collected 26h post synchronization


title: NIH3T3_Digitonin_55ug/mL_rep1

tag: media

tag: treatment


title: Genomic DNA from Airway Macrophages [Healthy_AM_6]

tag: disease

value: Airway macrophages

tag: gender

tag: isolation

value: FACS


title: NIH3T3_p65ko_BB_rep2


title: APCmin/-;BMAL1-/- CT26 (S6)

description:
Karpowicz_Windsor_10_006_S6
collected 26h post synchronization

tag: clock function


title: APCmin/-;BMAL1-/- CT24 (S3)

description:
Karpowicz_Windsor_5_003_S3
collected 24h post synchronization

tag: strain


title: Genomic DNA from Airway Macrophages [Healthy_AM_1]

value: Male

value: MACS

tag: age

tag: smoking history


title: Genomic DNA from Airway Macrophages [Healthy_AM_5]

tag: cell type

value: Never


title: AH2-10

source_name: Dorsolateral striatum (bulk tissue)

tag: tissue

value: Dorsolateral striatum (bulk tissue)

value: LPS

value: Stress


title: NIH3T3_noDig_rep1

value: DMEM


title: APCmin/-;BMAL1-/- CT28 (S11)

description:
Karpowicz_Windsor_17_011_S11
collected 28h post synchronization

value: Intestinal Adenoma Organoids

value: Circadian Clock Mutant

tag: time

tag: synchronization


title: Genomic DNA from Airway Macrophages [Healthy_AM_4]

value: Healthy


title: Genomic DNA from Airway Macrophages [Healthy_AM_2]

value: Current


title: NIH3T3_p65ko_BB_rep1


title: NIH3T3_p65ko_NT_rep1

value: NT


title: APC+/+;BMAL1-/- CT46 (S96)

description:
Karpowicz_Windsor_126_096_S96
collected 46h post synchronization

value: Intestinal Organoids

value: 1h 0.1µm Dexamethasone


title: AH2-12

value: Sprague-Dawley

tag: Sex

tag: maternal immune activation

tag: stress


title: APCmin/-;BMAL1-/- CT30 (S15)

description:
Karpowicz_Windsor_23_015_S15
collected 30h post synchronization

tag: genotype


title: APCmin/-;BMAL1-/- CT24 (S2)

description:
Karpowicz_Windsor_4_002_S2
collected 24h post synchronization


title: NIH3T3_noko_BB_rep1

tag: cell line

tag: construct

tag: media


title: AH2-11


title: AH2-7

value: No Stress


title: NIH3T3_noko_NT_rep2

tag: treatment


title: NIH3T3_noko_BB_rep2


title: NIH3T3_p65ko_NT_rep2


title: CDMA-20hr-4

description: C. difficile 20 hours post infection Mouse 4

tag: time point

tag: agent

value: Clostridioides difficile


title: AH2-9

tag: strain

value: Male


title: APC+/+;BMAL1-/- CT46 (S95)

description:
Karpowicz_Windsor_125_095_S95
collected 46h post synchronization

tag: clock function


title: NIH3T3_BB_siPKC_rep1


title: APC+/+;BMAL1-/- CT44 (S92)

description:
Karpowicz_Windsor_122_092_S92
collected 44h post synchronization


title: NIH3T3_NT_siPKC_rep2


title: NIH3T3_BB_siCTR_rep1


title: NIH3T3_BB_siCTR_rep2


title: NIH3T3_NT_siPKC_rep1


title: AH2-8


title: AH2-4

value: Saline


title: AH2-6


title: APC+/+;BMAL1-/- CT42 (S88)

description:
Karpowicz_Windsor_118_088_S88
collected 42h post synchronization


title: NIH3T3_NT_siCTR_rep1


title: NIH3T3_NT_siCTR_rep2


title: APC+/+;BMAL1-/- CT42 (S87)

description:
Karpowicz_Windsor_117_087_S87
collected 42h post synchronization
Removed from processing due to poor RNA quality.


title: NIH3T3_GD_4OHT_rep1


title: NIH3T3_GD_4OHT_rep2


title: AH2-5


title: NIH3T3_GD_NT_rep2


title: APC+/+;BMAL1-/- CT40 (S83)

description:
Karpowicz_Windsor_113_083_S83
collected 40h post synchronization


title: NIH3T3_noko_NT_rep1


title: APC+/+;BMAL1-/- CT40 (S84)

description:
Karpowicz_Windsor_114_084_S84
collected 40h post synchronization


title: AH2-3


title: AH2-2


title: NIH3T3_GD_NT_rep1


title: LLC_181_BB_r2

value: LLC


title: APCmin/-;BMAL1-/- CT32 (S18)

description:
Karpowicz_Windsor_28_018_S18
collected 32h post synchronization


title: APC+/+;BMAL1-/- CT44 (S91)

description:
Karpowicz_Windsor_121_091_S91
collected 44h post synchronization


title: LLC_18_BB_r2


title: APC+/+;BMAL1-/- CT38 (S80)

description:
Karpowicz_Windsor_110_080_S80
collected 38h post synchronization


title: LLC_181_noBB_r2


title: LLC_GD_4OHT_rep1


title: LLC_181_noBB_r1


title: LLC_GD_4OHT_rep2


title: Ifnar1-KO spleen, day 7, Seq-Well plate 5

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description:
sIFNR7-5
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz

data_processing:
Convert paired-end reads to single-ended, extracting the 12-base cell barcode and 8-base unique molecule identifier (UMI) from R1 read and appending them to the R2 read name as a colon-separated pair. Reads with Ns in either the cell barcode or UMI are discarded. (custom Python script)
Align reads to rat rn6 genome, with RefSeq gene annotations. (tophat2 v2.0.12)
Quantify transcript counts using RefSeq rn6 gene annotations. (ESAT v1.0, https://github.com/garber-lab/ESAT)
Build t-SNE map of all cells (custom R script, using the dim_reduce() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Density-based clustering (custom R script, using the cluster_sc() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Cell type identification (custom R script based on density-based cluster boundaries and known marker genes to identify major cell types)
Viral transcript counting - NCBI magic-blast (https://ncbi.github.io/magicblast/) of all transcript sequence reads against the KRV virus genome (U79033.1), followed by a custom Python script to quantify the number of unique viral transcripts in each cell, using UMIs to remove PCR duplicates.
Genome_build: rn6
Supplementary_files_format_and_content: Ifnar_KO_exp_rawCounts.txt.gz: raw transcript counts from ESAT, 12889 genes x 4765 cell transcript counts matrix
Supplementary_files_format_and_content: Ifnar_KO_exp_phenotype.txt.gz: per-cell phenotype information, 4765 cell x 6 column cell phenotype information. Columns: sample (sample ID), plate (Seq-Well plate ID, 5 for each sample), tSNE1, tSNE2 (t-SNE mapping coordinates), cellType (assigned cell type), KRV (KRV virus transcript count)

source_name: spleen

extract_protocol: Seq-Well S^3 Master Protocol (June 2019) (http://shaleklab.com/wp-content/uploads/2019/07/SeqWell-S3-Protocol.pdf)

tag: days post infection


title: AH2-1

value: Dorsolateral striatum (bulk tissue)


title: APC+/+;BMAL1-/- CT36 (S76)

description:
Karpowicz_Windsor_106_076_S76
collected 36h post synchronization
Removed from processing due to poor RNA quality.

tag: cell type


title: LLC_GD_NT_rep2


title: LLC_WT_4OHT_rep2


title: Ifnar1-KO spleen, day 7, Seq-Well plate 4

description:
sIFNR7-4
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: LLC_GD_NT_rep1


title: APC+/+;BMAL1-/- CT36 (S75)

description:
Karpowicz_Windsor_105_075_S75
collected 36h post synchronization


title: Ifnar1-KO spleen, day 7, Seq-Well plate 3

description:
sIFNR7-3
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: Ifnar1-KO spleen, day 7, Seq-Well plate 2

description:
sIFNR7-2
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: LLC_WT_NT_rep1


title: Ifnar1-KO spleen, day 7, Seq-Well plate 1

description:
sIFNR7-1
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: APC+/+;BMAL1-/- CT34 (S72)

description:
Karpowicz_Windsor_102_072_S72
collected 34h post synchronization


title: APC+/+;BMAL1-/- CT34 (S71)

description:
Karpowicz_Windsor_101_071_S71
collected 34h post synchronization


title: NIH3t3_181_noCa_BB_rep2


title: Ifnar1-KO spleen, day 3, Seq-Well plate 5

description:
sIFNR3-5
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: NIH3t3_181_noCa_BB_rep1


title: NIH3t3_181_noCa_NT_rep2


title: NIH3t3_181_BB_rep2


title: APC+/+;BMAL1-/- CT38 (S79)

description:
Karpowicz_Windsor_109_079_S79
collected 38h post synchronization


title: APC+/+;BMAL1-/- CT32 (S67)

description:
Karpowicz_Windsor_97_067_S67
collected 32h post synchronization


title: APC+/+;BMAL1-/- CT30 (S64)

description:
Karpowicz_Windsor_94_064_S64
collected 30h post synchronization


title: NIH3t3_181_noCa_NT_rep1


title: Ifnar1-KO spleen, day 3, Seq-Well plate 4

description:
sIFNR3-4
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: NIH3t3_181_BB_rep1


title: Ifnar1-KO spleen, day 3, Seq-Well plate 3

description:
sIFNR3-3
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: Ifnar1-KO spleen, day 3, Seq-Well plate 2

description:
sIFNR3-2
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: NIH3t3_WT_BB_rep1


title: NIH3t3_181_NT_rep2


title: LLC_Digitonin_55ug/mL_rep2


title: NIH3t3_181_NT_rep1


title: APC+/+;BMAL1-/- CT30 (S63)

description:
Karpowicz_Windsor_93_063_S63
collected 30h post synchronization


title: LLC_WT_NT_rep2


title: LLC_WT_4OHT_rep1


title: Ifnar1-KO spleen, day 3, Seq-Well plate 1

description:
sIFNR3-1
Ifnar_KO_exp_rawCounts.txt.gz
Ifnar_KO_exp_phenotype.txt.gz


title: NIH3t3_WT_NT_rep2


title: NIH3t3_WT_NT_rep1


title: APC+/+;BMAL1-/- CT28 (S60)

description:
Karpowicz_Windsor_90_060_S60
collected 28h post synchronization


title: APC+/+;BMAL1-/- CT32 (S68)

description:
Karpowicz_Windsor_98_068_S68
collected 32h post synchronization


title: NIH3t3_WT_BB_rep2


title: APC+/+;BMAL1-/- CT26 (S55)

description:
Karpowicz_Windsor_85_055_S55
collected 26h post synchronization


title: Control cytoDNA rep2

first: Danny

last: Leung

address: Clear Water Bay

institute: Hong Kong University of Science and Technology

library_source: genomic

data_processing:
library strategy: CytoDNA-seq
Reads quality trimmed using Trim Galore
Bowtie alignment to mm10
CytoDNA regions were defined by 100bp bins with RPKM over 10x that of the genome average
Bins in blacklist regions or chromatin immunoprecipitation input peaks were removed
Bins that were within 100 base pairs were merged
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: Control cytoDNA

growth_protocol: A mixed glial cell population was obtained from P5 pups and was cultured for two weeks in T75 flasks with DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (10,000 U/mL; Thermo Fisher Scientific). An enriched microglial cell preparation was obtained by shaking the flasks at 37 °C for 2 hours. Microglia were plated on poly-L-lysine-coated glass coverslips at a final density of 50,000 cells per well in a 24-well plate or 200,000 cells per well in poly-L-lysine coated 6-well plates and grown for 24 hours. The purity of the microglial cultures was assessed using immunostaining for the microglia specific marker, Iba1. Cultures with over 90% Iba1 positive cells were used for further experiments. For all experiments, the medium was changed to serum free media 12 hours before any treatment.

extract_protocol:
Primary cultured microglia were lysed in a lysis buffer containing 10 mM HEPES (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% (v/v) glycerol, 0.1% (v/v) Triton X-100 plus protease inhibitors for 5 min on ice. Cell nuclei were removed by low-speed centrifugation (1500 g, 10 minutes). Cytoplasmic extracts were treated with 1 mg/ml Proteinase K at 56 °C for 2 hours. The aqueous supernatant was incubated with 500 mg/ml DNase-free RNase A (QIAGEN) for 30 minutes at 37 °C and followed by phenol/chloroform extraction. The DNA-containing aqueous phase was precipitated and resuspended in TE buffer. DNA concentrations were adjusted according to the protein concentration of cytoplasmic fractions and analyzed on a 2% agarose gel infused with ethidium bromide. The DNA concentrations were determined by Qubit Assays on a Qubit 4 Fluorometer.
CytoDNA sequencing was performed on two biological replicates. Library preparation for cytoplasmic DNA was performed according to the KAPA Hyper Prep Kit (KR0961 – v6.17, KAPA biosystems) protocol, omitting the library amplification step to avoid sequence enrichment bias. The cytoplasmic DNA library was then analyzed on the Advanced Analytical Technologies Fragment Analyzer Automated CE System using an Agilent HS NGS Fragment Kit (Part # DNF- 474-0500), and size selected using AMPure XP beads (Beckman Coulter) for fragment sizes between 200-700 base pairs.

treatment_protocol: Cultured microglia cells were incubate in DMEM containing 1 µM KU-60019  for 48 hours

value: Cultured microglia from postnatal day 5 mice

value: Untreated

tag: molecule subtype

value: cytoplasmic DNA


title: Control cytoDNA rep1