title: Four cycles BAY cancer cell Rep2

description: processed data file: CancerCell.txt


title: Four cycles Vehicle cancer cell Rep4

status: Public on Nov 23 2021

type: SRA

city: Beijing

first: Zihan

last: Xu

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description: processed data file: CancerCell.txt

library_source: transcriptomic

data_processing:
Quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore with parameters ‘-q 30 --length 30 --stringency 5’.
The clean paired-end reads were aligned to the mm10 reference genome by Tophat with the parameter --no-novel-juncs. Gene expression levels and differentially expressed genes between samples were calculated with Cuffdiff and visualized with the R package cummeRbund.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: cancer cell isolated in prostate tumor

growth_protocol: Lncap/CAP2/CAP8/PC3 was cultured as ATCC described, Pb-Cre;pten loxp mice was maintained as described (Wang et al. 2003 cancer cell).

extract_protocol:
RNA was extracted using RNA extraction kit from Qiagen.
Tumor tissue or cell line library was constructed using kits from NEB(E7530),  CD8T cell and cancer cell library was constructed using smart-seq 2 protocol.

treatment_protocol: Cell lined was treated with vehicle or 5umol BAY1082439 for 48h then harvasted, castrated CP mice was treated with vehicle, BAY1082439 for 2 days, daily or intermittent for 4 weeks, intermittent 4 weeks then release 4 weeks or intermittent follow PD-1 therapy for 4 weeks, tumor tissue, tumor CD8T cell and cancer cell was harvasted

tag: cell type

value: cancer cell isolated in prostate tumor

tag: treatment

value: castration + vehicle


title: stubl2-3_R1_SxaQSEQsYA067L2_index_13

city: Los Angeles

first: magdalena

middle: ewelina

last: potok

state: CA

address: 4045 Terasaki Life Sciences Building

department: MCDB

country: USA

institute: UCLA

data_processing:
Reads were aligned using Tophat by allowing up to two mismatches and mapping only to one location. Chromosome mitochondria and chloroplast were exluded from alignments.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each genes generated by Cufflinks

organism: Arabidopsis thaliana

source_name: cotyledons

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .

tag: developmental stage

value: two-week-old

tag: tissue

value: cotyledons

tag: genotype


title: stubl2-3_R2_SxaQSEQsYA067L2_index_14


title: Four cycles Vehicle cancer cell Rep2

description: processed data file: CancerCell.txt


title: sid_1757_dis_BC_age_43

type: RNA

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

hyb_protocol: Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression v2 8x60K microarray kit, according to the manufacture’s instruction (Agilent Technologies).

scan_protocol: Standard Agilent protocol.

data_processing: All gene expression microarrays were processed using the LIMMA [R] package: background correction and between array normalization. All probes not higher expressed than 1.2 times the background signal were removed. In the publication, all probes representative of the same Entrez Gene ID were averaged.

molecule: total RNA

organism: Homo sapiens

source_name: CD4+ T cells

label_protocol: The cRNA was prepared using a Low Input QuickAmp Labeling Kit.

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA Micro kit (Qiagen, Hilden, Germany; cat. no. 80284) according to the manufacturer’s instructions.

value: CD4+ T cells

tag: primary diagnosis

value: Breast cancer

tag: Sex

value: Female

tag: age


title: mbd9-3_R3_SxaQSEQsYA067L2_index_11


title: mbd9-3_R4_SxaQSEQsYA067L2_index_12


title: Four cycles Vehicle cancer cell Rep3

description: processed data file: CancerCell.txt


title: sid_1753_dis_BC_age_70


title: 178-A031887

city: Basel

first: Jasmin

last: Haslbauer

address: Schönbeinstrasse 40

department: Institute of Medical Genetics and Pathology

country: Switzerland

institute: University of Basel

data_processing:
Alignment: four demultiplexed FASTQ files per well in the assay sequenced with the HTG EdgeSeq Parser (version 5.0.535.3181) see HTG EdgeSeq System User Manual (RUO).
Post sequencing quality control: POS% ≥ 28% as failure; Read depth ≤ 750,000 as failure; RSD ≤ 0.094 as failure .
Normalization: No pre-filtering is applied to the data prior to analysis. The DESeq2 (package version 1.14.1)model corrects for library size using the median ratio method from Anders and Huber (2010).
Dispersions are estimated with the Cox Reid-adjusted profile likelihood method developed by McCarthy et al. (2012).  Log2 fold change is estimated via Tikhonov/ridge regularization with a zero-centered normal prior distribution with variance calculated using the observed distribution of maximum likelihood coefficients (see DESeq2 documentation for details).
Supplementary_files_format_and_content: Excel file containing tables of raw, QC raw, log2 CPM (counts per million), and median normalized data.

source_name: Control_lymph node

extract_protocol:
HTG uses an extraction free technology that involves resuspending crude sample in Lysis Buffer.  The sample is then treated with Proteinase K and stored or used.
HTG EdgeSeq library construction is defined in the HTG EdgeSeq System User Manual (RUO)

tag: group

value: Control

value: lymph node


title: Four cycles BAY tissue Rep6

description: processed data file: FourCycleTissue.txt

source_name: prostate tumor tissue

value: prostate tumor tissue

value: castration + BAY-I


title: 178-A031890


title: Four cycles BAY tissue Rep7


title: 178-A031884


title: 178-A031885


title: mbd9-3_R2_SxaQSEQsYA067L2_index_10


title: Four cycles Vehicle cancer cell Rep1

description: processed data file: CancerCell.txt


title: mbd9-3_R1_SxaQSEQsYA067L2_index_9


title: sid_6001_dis_HC_age_47


title: 178-A031897

source_name: COVID-19_lymph node


title: sid_6000_dis_HC_age_57


title: sid_1785_dis_BC_age_62


title: sac3b-3_R4_SxaQSEQsYA067L2_index_8


title: sid_1771_dis_BC_age_74


title: sid_UC8_dis_UC_age_22_gender_M

hyb_protocol: Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression v2 8x60K microarray kit, according to the manufacturer’s instruction (Agilent Technologies).

data_processing: All gene expression microarrays were processed using the LIMMA [R] package: background correction and between array normalization. Technical replicates were averaged. All probes not higher expressed than 1.2 times the background signal were removed. In the publication, all probes representative of the same Entrez Gene ID were averaged.

value: Male


title: sac3b-3_R3_SxaQSEQsYA067L2_index_7


title: 178-A031889


title: Four cycles BAY tissue Rep5


title: 178-A031882


title: sid_UC7_dis_UC_age_50_gender_F


title: sac3b-3_R2_SxaQSEQsYA067L2_index_6


title: 178-A031880


title: Four cycles BAY tissue Rep2


title: Four cycles BAY tissue Rep3


title: sid_UC6_dis_UC_age_53_gender_F


title: 178-A031881


title: Four cycles BAY tissue Rep4


title: WT_R4_SxaQSEQsYA067L2_index_4

value: WT


title: 178-A031878


title: sac3b-3_R1_SxaQSEQsYA067L2_index_5


title: Four cycles Vehicle tissue Rep6


title: 178-A031874


title: 178-A031872


title: 178-A031873


title: sid_UC4_dis_UC_age_56_gender_F


title: sid_UC3_dis_UC_age_47_gender_M


title: Four cycles BAY tissue Rep1


title: sid_UC5_dis_UC_age_54_gender_F


title: WT_R3_SxaQSEQsYA067L2_index_3


title: sid_UC2_dis_UC_age_47_gender_M


title: WT_R2_SxaQSEQsYA067L2_index_2


title: WT_R1_SxaQSEQsYA067L2_index_1


title: sid_UC1_dis_UC_age_69_gender_F


title: Four cycles Vehicle tissue Rep5


title: sid_417_dis_UC_age_69_gender_M


title: 178-A031871


title: Four cycles Vehicle tissue Rep4


title: Four cycles Vehicle tissue Rep3


title: mbd9-3_R1_SxaQSEQsYA067L1_index_27

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. A single replicate was collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .


title: Four cycles Vehicle tissue Rep2


title: T2:MBD9:MBD9-9xMYC in mbd9-3 atxr5/6 (W)_R1_SxaQSEQsYA067L1_index_23


title: 178-A031868


title: T2:MBD9:MBD9-3xFlag in mbd9-3 atxr5/6 (W)_R1_SxaQSEQsYA067L1_index_22


title: 178-A031869


title: sid_415_dis_UC_age_20_gender_M


title: Four cycles Vehicle tissue Rep1


title: 178-A031866


title: mbd9-3 atxr5/6 (W)_R1_SxaQSEQsYA067L1_index_20

value: mbd9-3 atxr5/6 (W)


title: 178-A031862


title: Bully dose BAY tissue Rep6

description: processed data file: BullyDoseTissue.txt

value: bullet dose BAY1082439


title: 178-A031858


title: Bully dose BAY tissue Rep5


title: 178-A031861


title: atxr5/6 (W)_R1_SxaQSEQsYA067L1_index_19

value: atxr5/6 (W)


title: Bully dose BAY tissue Rep4


title: atxr5/6 (W)_R4_SxaQSEQsYB053L6_index_4

source_name: roots

extract_protocol:
Total RNA was extracted from two-week-old roots grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 10 roots from individual plants. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .

value: roots


title: sid_2003_dis_TONS_age_39_gender_F


title: sid_2005_dis_TONS_age_42_gender_F


title: sid_2004_dis_TONS_age_46_gender_F


title: 178-A031855


title: Bully dose BAY tissue Rep2


title: atxr5/6 (W)_R3_SxaQSEQsYB053L6_index_3


title: 178-A031856


title: sid_2001_dis_TONS_age_35_gender_F


title: sid_2002_dis_TONS_age_26_gender_F


title: atxr5/6 (W)_R2_SxaQSEQsYB053L6_index_2


title: sid_910_dis_T1D_age_11_gender_M


title: sid_2000_dis_TONS_age_27_gender_F_dis2_ASTHMA

value: ASTHMA


title: Bully dose BAY tissue Rep1


title: WT_R1_SxaQSEQsYA067L1_index_18


title: Bully dose Vehicle tissue Rep6

value: bullet dose vehicle


title: 178-A031853


title: sid_909_dis_T1D_age_16_gender_M


title: atxr5/6 (W)_R1_SxaQSEQsYB053L6_index_1

value: two-week-old


title: sid_908_dis_T1D_age_12_gender_M_dis2_ECZ


title: 178-A031852


title: 178-A031851


title: WT_R3_SxaQSEQsYB052L8_index_25


title: Bully dose Vehicle tissue Rep5


title: Bully dose BAY tissue Rep3


title: WT_R4_SxaQSEQsYB052L8_index_27


title: WT_R2_SxaQSEQsYB052L8_index_23


title: 178-A031850


title: Bully dose Vehicle tissue Rep3


title: Bully dose Vehicle tissue Rep4


title: 178-A031849


title: 178-A031847


title: sid_905_dis_T1D_age_16_gender_M_dis2_ASTHMA


title: Bully dose Vehicle tissue Rep2


title: 178-A031846


title: mbd9-3 atxr5/6 (W)_R3_SxaQSEQsYB052L2_index_25

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .

value: cotyledons


title: mbd9-3 atxr5/6 (W)_R4_SxaQSEQsYB052L2_index_27


title: sid_900_dis_T1D_age_15_gender_F

value: CD4+ T cells


title: sid_902_dis_T1D_age_12_gender_M


title: BAY daily CD8T Rep7

description: processed data file: CD8T.txt

source_name: CD8T cell isolated in prostate tumor

value: CD8+ T cell isolated in prostate tumor

value: BAY-D


title: sid_904_dis_T1D_age_13_gender_F

description: This Sample represents 2 technical replicates.

value: Female


title: BAY daily CD8T Rep6

description: processed data file: CD8T.txt


title: sid_906_dis_T1D_age_11_gender_M


title: mbd9-3 atxr5/6 (W)_R1_SxaQSEQsYB052L2_index_22


title: sid_215_dis_SAR_age_49_gender_M_dis2_ASTHMA


title: BAY daily CD8T Rep5

description: processed data file: CD8T.txt


title: mbd9-3 ddm1-2_R4_SxaQSEQsYB052L2_index_21

value: mbd9-3 ddm1-2


title: BAY daily CD8T Rep3

description: processed data file: CD8T.txt


title: WT_R1_SxaQSEQsYB052L8_index_22


title: sid_211_dis_SAR_age_41_gender_F


title: mbd9-3 ddm1-2_R3_SxaQSEQsYB052L2_index_20


title: Bully dose Vehicle tissue Rep1

value: prostate tumor tissue


title: pDCRNA7406

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

data_processing:
Illumina bcl2fastq via BaseSpace was used for basecalling and trimming adaptor sequences
FastQC was used to ensure no contamination and reads were of sufficient quality
Intron quantification was done with iREAD, (Li, HD., Funk, C.C. & Price, N.D. iREAD: a tool for intron retention detection from RNA-seq data. BMC Genomics 21, 128 (2020)
Transcript quantification was done with salmon (Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods.)
Genome_build: Gencode hg38
Supplementary_files_format_and_content: tab delimited files of FPKM of introns (iREAD) and TPM for transcripts (salmon)

source_name: peripheral blood

extract_protocol:
PBMCs were extracted over Ficoll-Paque using established methods. pDCs were isolated using Miltenyi Biotec Human Plasmacytoid Dendritic Cell Isolation Kit II (130-097-415) in accordance with the manufacturer’s protocol.
Libraries were prepared using the Illumina TruSeq stranded Library kit and sequenced on a NextSeq 500 following manufacturer’s instructions.

value: plasmacytoid dendritic cells

tag: gender


title: pDCRNA5444


title: pDCRNA8461

value: Male


title: mbd9-3 ddm1-2_R2_SxaQSEQsYB052L2_index_19


title: pDCRNA8640


title: pDCRNA8123


title: BAY daily CD8T Rep2

description: processed data file: CD8T.txt


title: sid_208_dis_SAR_age_19_gender_F


title: mbd9-3 ddm1-2_R1_SxaQSEQsYB052L2_index_18


title: BAY daily CD8T Rep1

description: processed data file: CD8T.txt


title: mbd9-3 atxr5/6 (W)_R2_SxaQSEQsYB052L2_index_23


title: pDCRNA5050


title: sid_214_dis_SAR_age_38_gender_F


title: sid_206_dis_SAR_age_48_gender_F


title: pDCRNA4855


title: mbd9-3_R4_SxaQSEQsYB052L2_index_16


title: sid_207_dis_SAR_age_38_gender_F_dis2_OB

value: OBESITY


title: sid_205_dis_SAR_age_24_gender_F


title: CAP8 BAY Rep3

description: processed data file: CAP2CAP8.txt

source_name: CAP8 prostate cancer cell line

value: CAP8 prostate cancer cell line


title: pDCRNA4317


title: BAY daily CD8T Rep4

description: processed data file: CD8T.txt


title: mbd9-3_R3_SxaQSEQsYB052L2_index_15


title: CAP8 BAY Rep1

description: processed data file: CAP2CAP8.txt


title: CAP8 BAY Rep2

description: processed data file: CAP2CAP8.txt


title: PRO-seq in Human K562 cells, rep2

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH Royal Institute of Technology

description: Nascent RNA

data_processing:
Library strategy: PRO-seq
Reanalyses of GSM3639850 (replicate 1) and GSM3639851 (replicate 2). The replicates were merged.
Adapters (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) were removed using cutadapt (Marcel, 2011).
The reads were trimmed and filtered, and complements of reads were generated using fastx (http://hannonlab.cshl.edu/fastx_toolkit/).
The reads were aligned to hg38 genome using Bowtie2 (Langmead et al., 2009).
Reads that uniquely mapped to hg38 were processed to bed, bedgraph and bigWig files.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Bed file reporting coordinates of aligned reads.
Supplementary_files_format_and_content: Unnormalized bigWig file of nascent transcripts coded by the plus strand.
Supplementary_files_format_and_content: Unnormalized bigWig file of nascent transcripts coded by the minus strand.

source_name: K562 cells

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were grown below 5x10^5 cells/ml confluency.

extract_protocol:
The cells were harvested by centrifugation and washed twice with PBS. Nuclei were isolated and run-on reactions were performed with biotinylated nucleotides as described by Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. The run-on reaction was conducted in the presence of nuclei from S2 cells, which provides an invariant whole-genome spike-in control between samples.
The libraries were generated using TruSeq small-RNA adaptors, amplified 11 cycles, gel-purified and size-selected to 125-400 bp fragments. The libraries were sequenced using NextSeq 500 (Illumina).

treatment_protocol: The cells were untreated.

tag: cell line

tag: condition

value: Unstressed (no heat shock)

tag: transfection

value: No transfection


title: sid_203_dis_SAR_age_28_gender_F


title: CAP8 Vehicle Rep3

description: processed data file: CAP2CAP8.txt

value: vehicle


title: sid_204_dis_SAR_age_47_gender_F


title: mbd9-3_R2_SxaQSEQsYB052L2_index_14


title: ddm1-2_R3_SxaQSEQsYB052L2_index_11


title: ddm1-2_R4_SxaQSEQsYB052L2_index_12


title: mbd9-3_R1_SxaQSEQsYB052L2_index_13


title: PRO-seq in Human K562 cells, rep1

description: Nascent RNA


title: 24hpi interferon-gamma [C9]

city: Omaha

first: Scot

middle: P

last: Ouellette

state: NE

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C9

data_processing:
original fastq format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns), and low quality 3’ regions (Phred score < 30)
trimmed fastq files were processed by FastQC
fastq files were mapped to Chlamydia trachomatis 434/Bu or Streptococcus pyogenes NZ131 by CLC Genomics Workbench 12 for RNAseq analyses
read counts were modeled using Generalized Linear Model (GLM), assuming a negative binomial distribution, and reported as transcripts per million (TPM)
Wald test was used for statistical analysis of two-group comparisons
Genome_build: http://bacteria.ensembl.org/Chlamydia_trachomatis_434_bu_gca_000068585/Info/Index or http://bacteria.ensembl.org/Streptococcus_pyogenes_nz131_gca_000018125/Info/Index
Supplementary_files_format_and_content: excel file showing fold changes and statistical significance between timepoints and treatment conditions

source_name: Infected human HEp2 cell line

growth_protocol: HEp2 cells were infected with C. trachomatis L2 and treated or not at 10hpi with inducers of amino acid starvation. Samples were collected at 10, 14, and 24hpi. S. pyogenes strains were cultured for 1h in the presence or absence of tryptophan.

extract_protocol:
Total RNA was collected from C. trachomatis infected cell cultures using Trizol. Total RNA was DNased then further purified to remove eukaryotic mRNA and both prokaryotic and eukaryotic rRNA using Oligotex, MicrobEnrich, MicrobExpress, and Ribozero. For S. pyogenes, total RNA was collected, DNased, and purified with Ribozero to remove rRNA.
TruSeq® Stranded Total RNA Library Prep

treatment_protocol: Indicated above in the the first characteristics column.

tag: agent

value: Chlamydia trachomatis L2 434/Bu

tag: protocol

value: 0.5ng/mL IFN-gamma pre-treatment 11h before infection

tag: genotype/variation

value: Persistent Sample


title: sid_200_dis_SAR_age_53_gender_F


title: CAP8 Vehicle Rep1

description: processed data file: CAP2CAP8.txt


title: CAP8 Vehicle Rep2

description: processed data file: CAP2CAP8.txt


title: CAP2 BAY Rep3

description: processed data file: CAP2CAP8.txt

source_name: CAP2 prostate cancer cell line

value: CAP2 prostate cancer cell line


title: sid_202_dis_SAR_age_26_gender_F

value: CD4+ T cells


title: 24hpi interferon-gamma [B9]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B9


title: CAP2 BAY Rep2

description: processed data file: CAP2CAP8.txt


title: ddm1-2_R1_SxaQSEQsYB052L8_index_12

value: two-week-old

value: cotyledons


title: 24hpi interferon-gamma [A9]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A9


title: pDCRNA2727

value: Female


title: sid_154_dis_PSO_age_20_gender_M

value: PSORIASIS


title: atxr5/6 (W)_R4_SxaQSEQsYB052L2_index_8

value: atxr5/6 (W)


title: sid_110_dis_PSO_age_48_gender_F


title: sid_109_dis_PSO_age_71_gender_F


title: atxr5/6 (W)_R3_SxaQSEQsYB052L2_index_7


title: 14h AN3365 treatment, 14hpi [C7]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C7

value: 1ug/mL AN3365 in DMEM


title: 14hpi interferon-gamma [A5]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A5


title: CAP2 Vehicle Rep3

description: processed data file: CAP2CAP8.txt


title: atxr5/6 (W)_R2_SxaQSEQsYB052L2_index_6


title: CAP2 Vehicle Rep2

description: processed data file: CAP2CAP8.txt


title: ddm1-2_R2_SxaQSEQsYB052L2_index_10


title: 14h AN3365 treatment, 14hpi [B7]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B7


title: CAP2 Vehicle Rep1

description: processed data file: CAP2CAP8.txt


title: 14h AN3365 treatment, 14hpi [A7]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A7


title: atxr5/6 (W)_R1_SxaQSEQsYB052L2_index_5


title: sid_108_dis_PSO_age_64_gender_F


title: sid_201_dis_SAR_age_32_gender_F


title: sid_106_dis_PSO_age_45_gender_F


title: 4h AN3365 treatment, 14hpi [C3]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C3


title: sid_107_dis_PSO_age_56_gender_M

value: Male


title: PC3 BAY Rep3

description: processed data file: LNCAPPC3.txt

source_name: PC3 prostate cancer cell line

value: PC3 prostate cancer cell line


title: sid_105_dis_PSO_age_49_gender_M


title: 14hpi interferon-gamma [C5]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C5


title: WT_R4_SxaQSEQsYB052L2_index_4

value: WT


title: PC3 BAY Rep2

description: processed data file: LNCAPPC3.txt


title: sid_102_dis_PSO_age_54_gender_M


title: WT_R3_SxaQSEQsYB052L2_index_3


title: 4h AN3365 treatment, 14hpi [A3]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A3


title: 4h AN3365 treatment, 14hpi [B3]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B3


title: PC3 BAY Rep1

description: processed data file: LNCAPPC3.txt


title: sid_103_dis_PSO_age_42_gender_M


title: PC3 Vehicle Rep3

description: processed data file: LNCAPPC3.txt


title: CAP2 BAY Rep1

description: processed data file: CAP2CAP8.txt


title: ddm1-2_R4_SxaQSEQsYB052L8_index_21

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the NeoPrep Library Prep System (Illumina) or the TrueSeq Stranded mRNA-Seq kit (Illumina) .


title: 14h Indolmycin treatment, 14hpi [B8]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B8

value: 120uM Indolmycin in trp-free DMEM


title: PC3 Vehicle Rep2

description: processed data file: LNCAPPC3.txt


title: WT_R1_SxaQSEQsYB052L2_index_1


title: PC3 Vehicle Rep1

description: processed data file: LNCAPPC3.txt


title: LNCAP BAY Rep3

description: processed data file: LNCAPPC3.txt

source_name: LNCAP prostate cancer cell line

value: LNCAP prostate cancer cell line


title: sid_100_dis_PSO_age_43_gender_F


title: sid_3014_dis_OB_age_29_gender_F

value: OBESITY


title: LNCAP BAY Rep2

description: processed data file: LNCAPPC3.txt


title: 14h Indolmycin treatment, 14hpi [A8]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A8

value: Chlamydia trachomatis L2 434/Bu


title: ddm1-2_R3_SxaQSEQsYB035L3_index_23


title: 4h Indolmycin treatment, 14hpi [C4]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C4


title: 4h Indolmycin treatment, 14hpi [B4]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B4


title: ddm1-2_R2_SxaQSEQsYB035L3_index_18


title: sac3b-3 ddm1-2_R4_SxaQSEQsYB052L8_index_20

value: sac3b-3 ddm1-2


title: sid_3007_dis_OB_age_52_gender_F


title: WT_R2_SxaQSEQsYB052L2_index_2


title: sid_101_dis_PSO_age_41_gender_F


title: 14h Indolmycin treatment, 14hpi [C8]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C8

value: Persistent Sample


title: sid_3013_dis_OB_age_42_gender_F


title: sac3b-3 ddm1-2_R3_SxaQSEQsYB035L3_index_25


title: LNCAP Vehicle Rep3

description: processed data file: LNCAPPC3.txt

value: vehicle


title: sid_3000_dis_OB_age_40_gender_F

value: CD4+ T cells


title: sid_964_dis_OB_age_14_gender_M


title: 24h post-infection (hpi) untreated [B6]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B6

value: Untreated condition (in DMEM)

value: Normal Developmental Cycle


title: sid_962_dis_OB_age_10_gender_M


title: sac3b-3 ddm1-2_R1_SxaQSEQsYB035L3_index_20

value: two-week-old

value: cotyledons


title: ddm1-2_R1_SxaQSEQsYB035L3_index_11


title: 24h post-infection (hpi) untreated [A6]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A6


title: 14h post-infection (hpi) untreated [C2]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C2


title: sid_961_dis_OB_age_8_gender_F

value: Female


title: sac3b-3 atxr5/6 (W)_R3_SxaQSEQsYB035L3_index_10

value: sac3b-3 atxr5/6 (W)


title: 24h post-infection (hpi) untreated [C6]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C6


title: LNCAP Vehicle Rep1

description: processed data file: LNCAPPC3.txt


title: sac3b-3 atxr5/6 (W)_R4_SxaQSEQsYB052L8_index_19


title: 14h post-infection (hpi) untreated [B2]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B2


title: 14h post-infection (hpi) untreated [A2]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A2


title: sac3b-3 ddm1-2_R2_SxaQSEQsYB035L3_index_8


title: LNCAP BAY Rep1

description: processed data file: LNCAPPC3.txt


title: sid_966_dis_OB_age_13_gender_M

value: Male


title: sac3b-3 atxr5/6 (W)_R2_SxaQSEQsYB035L3_index_1


title: 10h post-infection (hpi) untreated [C1]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
C1


title: LNCAP Vehicle Rep2

description: processed data file: LNCAPPC3.txt


title: sac3b-3 atxr5/6 (W)_R1_SxaQSEQsYB035L3_index_21


title: sid_960_dis_OB_age_14_gender_M


title: sid_956_dis_OB_age_8_gender_F


title: sid_953_dis_OB_age_12_gender_M


title: MC3T3-E1_Isolated_Nano_R3

city: Ribeirão Preto

first: Rayana

middle: Longo

last: Bighetti-Trevisan

state: São Paulo

address: Avenida do Café s/n.

department: Basic and Oral Biology

country: Brazil

institute: University of São Paulo

data_processing:
The dataset analysis was performed using the Galaxy Platform and RStudio (version 3.6.0).
The trimming was done using Cutadapt (Galaxy Version 1.6dev)
The quality control of raw reads was done using FastQC (Galaxy Version 0.63)
The alignment to reference genome mm10 was done using STAR (Galaxy Version 2.4).
The process data from high-throughput sequencing assays (expression counts) was performed using HTSeq (Galaxy Version 0.6.1galaxy3) with gene annotations (Gencode v23)
Differential expression was analyzed by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts text file

source_name: MC3T3-E1 cell line

growth_protocol: MC3T3-E1 osteoblastic cells were plated at the density of 1x104 cells/well on the Ti discs with nanotopography and Ti control, in 24-well plates in osteogenic medium and kept isolated for 5 days to allow cell adhesion. Osteoclast cells from the RAW 264.7 lineage were cultured on osteoclastogenic medium on ThinCert™ cell culture inserts (Greiner Bio-One), with 0.4 μm pore, at the density of 1x104 cells/membrane, and was also be kept isolated for 5 days to allow cell adhesion. At the end of this period theThinCert™ cell culture inserts (Greiner Bio-One), containing the osteoclast cells were positioned on the osteoblastic cell cultures, thereby establishing indirect co-culture. The controls were osteoblastic cells of the MC3T3-E1 lineage grown on the Ti discs in the absence of osteoclast cells of the RAW 264.7 lineage, i.e., not maintained in co-culture.

extract_protocol:
On day 7, the total RNA was isolated from the osteoblasts using TRizol reagent (Thermo Fisher Scientific), according to the manufacturer’s specifications.
RNA-Seq libraries were built with the SMARTer® (Takara) according to the manufacturer’s protocol.

treatment_protocol: MC3T3-E1 osteoblastic cells were plated and kept in osteogenic medium with 7 mM β-glycerophosphate (Sigma-Aldrich) and 5 μg/mL L-ascorbic acid (Sigma-Aldrich) and RAW 264.7 cells were cultured under osteoclastogenic conditions (osteoclasts), with 50 ng/mL of RANKL (Peprotech) and kept separated for 5 days. On day 5, the inserts containing the osteoclasts were positioned above osteoblast cultures, thereby establishing an indirect coculture system, which was kept under osteogenic and osteoclastogenic conditions for another 2 days, completing 7 days of culture in differentiation media. The controls were non-cocultured osteoblasts grown on both Ti surfaces.

tag: tissue source

value: Bone; Calvaria

value: preosteoblast

value: MC3T3-E1 Subclone 14

tag: sample group


title: MC3T3-E1_Isolated_Control_R3

tag: cell type


title: MC3T3-E1_Isolated_Nano_R1


title: MC3T3-E1_Isolated_Nano_R2


title: MC3T3-E1_Isolated_Control_R2


title: 10h post-infection (hpi) untreated [B1]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
B1


title: sac3b-3 _R3_SxaQSEQsYB035L3_index_19

tag: developmental stage


title: 10h post-infection (hpi) untreated [A1]

description:
PolyA and rRNA depleted for both human and bacteria
Processed RNAseq data for Ctr
A1


title: sid_951_dis_OB_age_8_gender_M


title: MC3T3-E1_Isolated_Control_R1


title: Leukemic

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

data_processing:
Counts were generated from raw_fastq using 10x Genomics Cellranger v-2.1.0 (count)
Genome_build: GRCh38
Supplementary_files_format_and_content: A comma seperated file with counts for every gene in cells in all samples

source_name: CD10+CD19+ cells

growth_protocol: transduced human cord blood / BM from transplanted mice were ransplanted in NSG mice. Human cells from mouse BM/spleen were sorted, counted and processed for 10X sequencing

extract_protocol:
Nucleic acids were extracted according to 10X protocols
Libraries were prepared according to the 10X Chromium Single Cell 3' Reagent Kit User Guide

tag: tissue

value: Blood

tag: strain


title: MC3T3-E1_Co-culture_Nano_R3


title: mouse engrafted with matching CB transduced with control BackBone virus


title: sac3b-3 _R2_SxaQSEQsYB035L3_index_15

tag: genotype


title: sid_950_dis_OB_age_15_gender_M

tag: primary diagnosis

value: OBESITY

tag: Sex


title: MC3T3-E1_Co-culture_Nano_R2


title: sid_952_dis_OB_age_11_gender_M

tag: age


title: atxr5/6 (W)_R4_SxaQSEQsYB035L3_index_14

value: atxr5/6 (W)


title: sid_700_dis_OB_age_54_gender_M


title: sac3b-3 _R1_SxaQSEQsYB035L3_index_5


title: Preleukemic2

source_name: CD10highCD19low sub-population


title: Preleukemic1


title: MC3T3-E1_Co-culture_Nano_R1


title: sac3b-3 _R4_SxaQSEQsYB052L8_index_18

source_name: cotyledons


title: MC3T3-E1_Co-culture_Control_R3


title: sid_1009_dis_INFLU_age_28_gender_F

source_name: CD4+ T cells

value: INFLUENZA


title: sid_1008_dis_INFLU_age_58_gender_M


title: atxr5/6 (W)_R2_SxaQSEQsYB035L3_index_13


title: Lung_AR_rep3

city: Milano

first: Chiara

last: Laura

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Reads were trimmed using the JAVA tool trimmomatic (V 0.32)
Raw reads were aligned using STAR aligner V 2.5.3a
Read counts per gene calculated using the featureCounts function from the Rsubread package (V 1.32.4), based on GENCODE gene annotation M22
Genome_build: GRCm38 (GENCODE)
Supplementary_files_format_and_content: Raw reads

source_name: Lung homogenates 6 days after AR infection

extract_protocol:
100 ml of Chloroform were added in 500 ml of homogenized sample and total RNA was extracted using ReliaPrep™ RNA Tissue Miniprep column (Promega, Cat #Z6111). Total RNA was isolated according to the manufacturer’s instructions. qPCR was performed using TaqMan Fast virus 1 Step PCR Master Mix (Lifetechnologies #4444434), standard curve was drawn with 2019_nCOV_N Positive control (IDT#10006625), primer used are: 2019-nCoV_N1- Forward Primer (5’-GAC CCC AAA ATC AGC GAA AT-3’), 2019-nCoV_N1- Reverse Primer (5’-TCT GGT TAC TGC CAG TTG AAT CTG-3’) 2019-nCoV_N1-Probe (5’-FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1-3’) (Centers for Disease Control and Prevention (CDC) Atlanta, GA 30333)
Smart-seq2 protocol
Libraries were purified with AMPure XP beads, quantified using Qubit 3.0 and single-end sequenced (75 bp) on an Illumina NextSeq 500.

value: Lung

tag: treatment

value: SARS-CoV-2_AR route

tag: timepoint

value: Day 6


title: Lung_AR_rep4


title: MC3T3-E1_Co-culture_Control_R2

tag: cell line


title: atxr5/6 (W)_R1_SxaQSEQsYB052L8_index_16


title: MC3T3-E1_Co-culture_Control_R1


title: sid_1006_dis_INFLU_age_23_gender_M

value: CD4+ T cells


title: sid_1007_dis_INFLU_age_93_gender_F


title: Lung_AR_rep2


title: N8

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Unstranded single-end reads with 51 bp in length were trimmed for adaptor and low quality sequences using Cutadapt (v 1.18) with parameters -q 20 -O 7 -m 16 –trim-n
Trimmed reads were mapped to the human genome (hg38 UCSC) using Bowtie2 (v 2.2.6) with parameters -p 6 -N 1 –un-gz
Mapped reads were summarized using featureCounts (v 1.6.3) with parameters -s 0 -T 6 -t miRNA -g ID and MirBase (v 22) annotations
Normalized gene expression was achieved using R/edgeR (v 3.28) by applying TMM normalization of read counts
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including TMM normalized abundance measurements (CPM, counts per million mapped reads) for each sample and differential expression information between tumor subtypes (log fold changes, p-values, FDR-values)

source_name: primary thyroid tumor

extract_protocol:
Total RNA was extracted from 30 micrograms of primary tumor tissue using the Qiagen ALLprep tumour protocol with miRNeasy kits. 500 ng of total RNA was used in the small RNA protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) according to the instructions of the manufacturer.
The barcoded libraries were size restricted between 140 and 165bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 50 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer. Demultiplexing of raw reads, adapter trimming and quality filtering was done according to Stokowy et al. (PMID: 24625073).

tag: tumor subtype

value: NT

tag: subtype info

value: non-malignant human thyroid


title: N7


title: sid_1005_dis_INFLU_age_97_gender_M


title: WT_R3_SxaQSEQsYB052L8_index_14

value: two-week-old

value: cotyledons

value: WT


title: sid_1004_dis_INFLU_age_68_gender_M_dis2_ATHERO

value: ATHEROSCLEROSIS

value: Male


title: Lung_IN_rep3

source_name: Lung homogenates 6 days after IN infection

value: SARS-CoV-2_IN route


title: atxr5/6 (W)_R3_SxaQSEQsYB035L3_index_12


title: Lung_IN_rep2


title: N5


title: WT_R2_SxaQSEQsYB052L8_index_13


title: sid_1003_dis_INFLU_age_40_gender_M


title: WT_R1_SxaQSEQsYB035L3_index_6


title: Lung_IN_rep1


title: N4


title: T2: SAC3b:SAC3B-Flag in sac3b-3 atxr5/6 (W)_SxaQSEQsYA038L4_index_25

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. A single replicate was collected for each genotype.Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the NeoPrep Library Prep System (Illumina).

value: T2:SAC3b:SAC3B-Flag in sac3b-3 atxr5/6 (W)


title: sid_1002_dis_INFLU_age_51_gender_M


title: N3


title: WT_R4_SxaQSEQsYB052L8_index_15


title: N2


title: Lung_AR_rep1


title: atxr5/6 (W)_R1_SxaQSEQsYA038L4_index_12


title: Lung_ctrl_rep2

source_name: Lung homogenates of PBS treated control

value: PBS

value: Day 0


title: Lung_ctrl_rep1


title: WT_R1_SxaQSEQsYA038L4_index_6


title: sid_1000_dis_INFLU_age_81_gender_F

value: Female


title: FASTED-Input-Hmgcs2-IKO_R1_ChIP-seq

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the mm9 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Genome_build: mm9
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K9bhb, H4K12bhb and H3K27ac enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

molecule: genomic DNA

source_name: Small Intestine

growth_protocol: Male and female mice (strains: Lgr5EGFP-IRES-CreERT2/+ Strain name: B6.129P2-Lgr5tm1(cre/ERT2)Cle/J, JAX, 008875) and C57BL/6J (JAX, 000664)) were purchased, bred in house, and maintained at 72°F +/- 2 °F on a 12h light/dark cycle. Six- to twelve-week-old aged matched males and females were randomly assigned to either fed or fasted groups. Fed animals were provided ad libitium access to food (PicoLab 5053, #0007688) and water for 24h, fasted animals were completely food deprived for 24h with ad libitium access to water. Experimental mice were singly housed on aspen bedding for the duration of experiments. Intestinal-specific Hmgcs2 knockout was achieved as previously described in Cheng et al., 2019 (https://doi.org/10.1016/j.cell.2019.07.048) . Briefly, adult Hmgcs2loxp/loxp;Villin-CreERT2 mice received tamoxifen injections (10 mg/ml, 250ul per 25 g of body weight) every other day, for up to ten days for a total of five doses. Two weeks after the last tamoxifen injection, mice were assigned to ad libitum and fasting groups for 24hrs.

extract_protocol:
Chromatin immunoprecipitations were performed using a previously published protocol with modifications for SI crypts. Briefly, whole isolated crypts from 4 animals were pooled per treatment per replicate and cross linked for 10 min at 37°C with 1% formaldehyde in supplemented media and quenched with 0.125M glycine for 5 min at 37°C. Crypts were washed with PBS with 1× protease inhibitor cocktail (Sigma-Aldrich) and stored at -80°C. Pellets were thawed and then lysed for 30 min on ice with I-ChIP buffer (12mM Tris–HCl pH 8.0, 6mM EDTA pH 8.0, 0.1x PBS, 0.5% SDS) plus cOmplete mini protease inhibitors. Sonication conditions were optimized for SI crypt cells using a Bioruptor (Diagnode) to achieve shear length of 250-500bp. 10% total chromatin was reserved as an input control. Chromatin was diluted 5 fold and immunoprecipitation was performed overnight by incubation of the sonicated cell lysate with 30ul of protein G magnetic dynabeads (Invitrogen) previously coupled to target antibody for a minimum of 1h at 4°C. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). Elution and reverse cross linking was performed in 50ul direct elution buffer (10mM Tris–HCl, pH 8.0, 5mM EDTA, pH 8.0, 300mM NaCl and 0.5% SDS) with Proteinase K and RNaseA at 65°C overnight. Eluted DNA was cleaned up with solid-phase reversible immobilization (SPRI) beads (Beckman-Coulter).
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

treatment_protocol:
Crypt isolation followed previously published protocols with minor modifications [Guo, 2009 #5169;Tinkum, 2015 #4005]. Briefly fed or fasted mice were euthanized by CO2, the whole SI was collected, flushed with PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) to remove feces, and the mesentery was removed. The SI sample was cut longitudinally then cut transversely into 4 equal pieces. Each sample was placed on ice in PBS (Ca2+- and Mg2+-free, 100nM TSA) while the remaining samples were collected. After collection of all samples, SI were incubated in PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) for 10 min then transferred to HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA). Crypts were released through a series of vortex washes at 1,600rpm in HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) at 4°C. Supernatants from all vortex washes were filtered through 70-μm mesh and pooled into 50ml conical tubes to remove villus material and tissue fragments. Isolated crypts were pelleted at 1000rpm at 4°C. After this step, whole crypts were utilized for flow cytometry (detailed below), spheroid cell line establishment [de la Cruz Bonilla, 2018 #5161] and treatment (detailed below), or ChIP-seq (detailed below). For ChIP-seq, crypts were first suspended in ADMEM/F12 (D6421, Sigma) supplemented with 10 U/mL penicillin, 10μg/mL streptomycin, 2mM L-glutamine, 10mM HEPES, 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem), 10µM Y-27632 dihydrochloride (Sigma), 0.5mM N-acetylcysteine amide (Sigma), and 100nM TSA.
Whole crypt isolates were suspended in Matrigel™ and plated in a 24-well tissue culture dish (30 μl per well) as described [de la Cruz Bonilla, 2018 #5161]. Cultures were grown in 50% L-WRN conditioned media supplemented with 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem) and 10µM Y-27632 dihydrochloride (Sigma) added to each culture well. Media was changed every second day and spheroids were subcultured every third day. For experimental treatments of spheroid cultures, 50% L-WRN conditioned media was supplemented with either 5 or 10mM (R)-(–)-3-Hydroxybutyric acid (298360, Sigma) with 10µM TGF-β RI Kinase Inhibitor VI and 10µM Y-27632 dihydrochloride added to each treatment culture well. Standard media changes occurred for untreated control culture wells. All treatments were 24h prior to spheroid isolation from Matrigel™ for ChIP-qPCR or immunoblotting analyses.

value: crypt

value: male


title: sid_1001_dis_INFLU_age_94_gender_F

value: INFLUENZA


title: Aza1-1

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

data_processing:
Pre-processed high quality reads were mapped to the TAIR10 genome using bismark (Krueger and Andrews 2011, Bioinformatics) with default settings for paired-end libraries, and all downstream analysis were performed using custom R scripts
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with cytosine methylation values (CG,CHG,CHH)

source_name: Seedlings

growth_protocol: Seeds were germinated on MS plates for 2 weeks.

extract_protocol:
Genomic DNA was isolated from ten pooled seedlings using the Quick DNA purification kit (Zymo)
Whole genome bisulfite sequencing was performed by BGI Genomics (Hong Kong). Briefly, genomic DNA was fragmented by sonication, end-repaired and ligated to methylated adaptors. After bisulfite treatment, bisulfite-treated fragments were PCR amplified and sequenced as paired-end 100bp reads (PE100) with DNBSEQ technology (BGI).

tag: ecotype

tag: mutant allele


title: Aza1-2


title: P5

value: PTC

value: papillary thyroid carcinoma


title: WT_R3_SxaQSEQsYA032L2_index_6

source_name: rosette leaves

extract_protocol:
Total RNA was extracted from four-week-old rosette leaves grown on soil under long day conditions.  Three replicates from seperate plants were collected for each genotype. Each replicate conisted of 1 rosette leaf. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the NeoPrep Library Prep System (Illumina).

value: four-week-old

value: rosette leaves


title: FASTED-H3K9bhb-Hmgcs2-IKO_R1_ChIP-seq

tag: chip-antibody

value: H3K9bhb PTM-biolabs PTM-1250


title: P6


title: WT_R2_SxaQSEQsYA032L2_index_11


title: P4


title: Aza25


title: FED-Input-Hmgcs2-IKO_R1_ChIP-seq


title: Aza26


title: WT_R1_SxaQSEQsYA032L2_index_25


title: Aza16


title: P3


title: atxr5/6 (W)_R3_SxaQSEQsYB015L3_index_11

value: atxr5/6 (W)


title: atxr5/6 (W)_R2_SxaQSEQsYB015L3_index_25


title: sid_4013_dis_HC_age_13_gender_M

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA Micro kit (Qiagen, Hilden, Germany; cat. no. 80284) according to the manufacturer’s instructions.

value: CD4+ T cells


title: FED-H3K9bhb-Hmgcs2-IKO_R1_ChIP-seq


title: Aza18


title: P2


title: F6

value: FTC

value: follicular thyroid carcinoma


title: FASTED-Input_R2_ChIP-seq

value: wildtype

value: pooled male and female


title: Aza14


title: DNA-seq_med12 atxr5/6 (W)

data_processing:
Library strategy: DNA-seq
DNA-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie using default settings and allowing only uniquely mapping reads.
Duplicated reads were removed using Samtools.
Normalized (RPM) 100kb binned windows were generated with biotoolbox application get_datasets.pl (https://github.com/tjparnell/biotoolbox).
Genome_build: TAIR10
Supplementary_files_format_and_content: Normalized (RPM) 100kb binned windows (txt).

source_name: Rosette leaves

growth_protocol: About three 5-week-old rosette leaves grown on soil were pooled from each genotype.

extract_protocol:
Nuclei were released by fine chopping in Galbraith's buffer and stained with PI followed by fluorescent activated nuclei sorting. DNA from 10,000 FACS sorted 16C nuclei was isolated using Pico Pure DNA Extraction Kit (KIT0103, Arcturus). Genomic DNA was sonicated to 200 bp with a Covaris S.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

value: Rosette leaves

value: med12 atxr5/6 (W)


title: FASTED-Input_R1_ChIP-seq


title: F5


title: F4


title: FASTED-H3K9ac_R2_ChIP-seq

value: H3K9ac Abcam ab4441


title: Aza10


title: FED-Input_R2_ChIP-seq

value: crypt


title: Aza5


title: DNA-seq_WT

value: WT


title: DNA-seq_atxr5/6 (W)


title: Aza1


title: input_SxaQSEQsYA110L6_index_12

data_processing:
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie using default settings and allowing only uniquely mapping reads.
Duplicated reads were removed using Samtools.
Normalized read coverage tracks were generated using the bioloobox bam2wig.pl application.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig

growth_protocol: About 0.5g of 4-week-old rosette leaves grown on soil were collected and frozen in -80 °C.

extract_protocol:
Following tissue grining and in-vitro fixation, isolated nuclei were sonicate, cell lysates were cleared and  histone-DNA complexes were isolated with  antibody.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

tag: chip antibody

value: input

value: sac3b-3 atxr5/6 (W)


title: DMSO#2

value: DMSO


title: F3


title: FED-Input_R1_ChIP-seq


title: F2


title: P1

value: PTC

value: papillary thyroid carcinoma


title: DMSO#1


title: FED-H3K9ac_R2_ChIP-seq


title: F1


title: A12

value: ATC

value: anaplastic thyroid carcinoma


title: input_SxaQSEQsYA110L6_index_10

value: subl2-3 atxr5/6 (W)


title: input_SxaQSEQsYA110L6_index_11

value: mbd9-3 atxr5/6 (W)


title: atxr5/6 (W)_R1_SxaQSEQsYA032L2_index_14

value: four-week-old

value: rosette leaves

value: atxr5/6 (W)


title: FED-H3K9ac_R1_ChIP-seq

value: wildtype

value: pooled male and female


title: untreated jas-3#2

value: untreated


title: untreated jas-3#1


title: FASTED-H3K9ac_R1_ChIP-seq

value: crypt

value: H3K9ac Abcam ab4441


title: A10


title: A7


title: input_SxaQSEQsYA110L6_index_9

value: Rosette leaves

value: input


title: input_SxaQSEQsYA110L6_index_8

value: WT


title: Aza1 eM2 rep3

data_processing:
Sequencing of messenger RNA was performed by BGI Genomics (Hong Kong) using DNBSEQ technology.
High quality raw reads were aligned to the Arabidopsis TAIR10 genome using STAR (Dobin et al., 2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files showing the number of reads mapped to TAIR10 features

source_name: Siliques

growth_protocol: Plants were grown in greenhouse long-day conditions (16h photoperiod).

extract_protocol:
Total RNA was extracted from three siliques 6-9 days after anthesis
Library construction and sequencing was performed at BGI genomics (Hong Kong)


title: A9


title: Aza1 eM2 rep2


title: Aza1 eM2 rep4


title: A6


title: H3K27me1_SxaQSEQsYA110L6_index_5

value: H3K27me1 (Millipore Sigma 07-448)

value: sac3b-3 atxr5/6 (W)


title: H3K27me1_SxaQSEQsYA110L6_index_4


title: A5

value: ATC


title: day42-TP+saline rep2

city: Shinjuku Tokyo

first: Momotaro

last: Kawai

address: 35 Shinanomachi

department: Department of Orthopaedic Surgery

country: Japan

institute: Keio University School of Medicine

description: Library was sequenced further to obtain sufficient amount of human transcripts. Similarly processed to the main data and processed human transcripts were combined for further analyses.

data_processing:
Raw reads were trimmed based on the read quality and read length using Trim Galore version 0.6.6.
Mouse and human mRNA sequences were separated using Xenome version 1.0.0.
Separated RNA-seq data were mapped to the corresponding genomic DNA sequence (human GENCODE v34 and mouse GENCODE vM25) using Salmon version 1.4.0 with the default setting.
To obtain sufficient volume of human transcripts, the 42-days spinal cord RNAs were additionally sequenced to gain < 500 M reads of human transcripts. Human data were combined for further analyses.
Genome_build: human GENCODE v34 and mouse GENCODE vM25
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism:
Homo sapiens
Mus musculus

source_name: transplanted human neural cells in the injured mouse spinal cord

extract_protocol:
The epicenter segmentsspinal cords were dissected in 4 mm-length and were rapidly frozen, and total RNA were isolated using NucleoSpin RNA/Protein (740933.50; Macherey-Nagel)
Total RNA from each sample was purified and mRNA libraries were prepared according to the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, United States) protocol and sequenced using NovaSeq 6000 (Illumina) to obtain 150-bp paired-end reads.

tag: cell type

value: neural cells differentiated from 414C2-iPS cell-derived neural stem/progenitor cells in the injured NOD-SCID mouse spinal cord, 42-days after the spinal cord injury.

tag: treatment 1

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 20-days after the injury.

tag: treatment 2

value: intraperitoneal injection of 5 mg/kg of equal volume of vehicle


title: Aza1 eM2 rep1


title: day42-TP+saline rep3

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 21-days after the injury.


title: H3K27me1_SxaQSEQsYA110L6_index_3

tag: tissue

value: subl2-3 atxr5/6 (W)


title: Aza1 eM1 rep2


title: H3K27me1_SxaQSEQsYA110L6_index_2

tag: genotype

value: atxr5/6 (W)


title: H3K27me1_SxaQSEQsYA110L6_index_1


title: ChIPseq_H3_atxr5/6 (W)_cotyledons

data_processing:
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie using default settings and allowing only uniquely mapping reads.
Duplicated reads were removed using Samtools.
Normalized read coverage tracks and data metaplots were generated using deepTools.
Genome_build: TAIR10
Supplementary_files_format_and_content: bw

growth_protocol: Roughly 3X 1.5ml eppendorf tubes of two-week old cotyledons were collected and frozen in -80 °C.

extract_protocol:
Tissue was grounded to fine powder by mortar and pestle. Following in-vitro fixation, isolated nuclei were sonicate, cell lysates were cleared and  histone-DNA complexes were isolated with antibody.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

value: cotyledons

tag: background


title: A3

value: anaplastic thyroid carcinoma


title: Aza1 eM1 rep1


title: day42-TP+CNO rep3

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 18-days after the injury.

value: intraperitoneal injection of 5 mg/kg of CNO


title: A4


title: day42-TP+saline rep1

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 19-days after the injury.


title: ChIPseq_input_atxr5/6 (W)_cotyledons


title: A2


title: ChIPseq_H3_WT_cotyledons


title: DMSO bio rep3

value: DMSO


title: day42-TP+CNO rep2

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 17-days after the injury.


title: A1


title: Aza1 eM1 rep3


title: jas-3 bio rep2


title: DMSO bio rep1


title: DMSO bio rep2


title: day42-TP+CNO rep1

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 16-days after the injury.


title: day14-TP+saline rep2

value: neural cells differentiated from 414C2-iPS cell-derived neural stem/progenitor cells in the injured NOD-SCID mouse spinal cord, 14-days after the spinal cord injury.

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 14-days after the injury.


title: day14-TP+saline rep3

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 15-days after the injury.


title: day14-TP+saline rep1

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 13-days after the injury.


title: jas-3 bio rep1


title: day14-TP+CNO rep3

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 11-days after the injury.


title: ChIPseq_H3K9me2_atxr5/6 (W)_cotyledons

value: H3K9me2 (Abcam 1220)


title: ChIPseq_H3K9me2_WT_cotyledons

value: WT


title: day14-TP+CNO rep4

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 12-days after the injury.


title: day14-TP+CNO rep2

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 10-days after the injury.


title: WT bio rep2


title: WT bio rep1


title: E90-2019_V1

city: San Francisco

first: Alex

middle: A

last: Pollen

address: 35 Medical Center Way

department: Neurology

institute: UCSF

data_processing:
kallisto quantification RheMac10
cellbender ambient RNA removal
normalization, +1 log transform and scaling applied to h5ad X
Genome_build: RheMac10
Supplementary_files_format_and_content: MacaqueDevInhibitoryNeurons.h5ad contains normalized, log1p, and scaled data along with PCA and UMAP projections, obs.csv contains cell metadata, var.csv contains gene metadata, X.csv is the raw cells by genes kallisto + cellbender matrix

organism: Macaca mulatta

source_name: primary brain tissue

extract_protocol:
whole cells, dissociated using papain
10X chromium 3’ RNAseq V2/3

value: brain

tag: region


title: ChIPseq_H2AZ_atxr5/6 (W)_cotyledons

value: cotyledons

tag: age

value: H2AZ (Polyclonal antibodies specific to Arabidopsis H2A.Zs HTA11 and HTA9, described in Potok, M.E, et al, 2019).

value: atxr5/6 (W)


title: ChIPseq_H2AZ_WT_cotyledons


title: E90-2019_Parietal

value: Parietal


title: ChIPseq_input_WT_cotyledons

value: input


title: Spinal-cord-2 scRNA-seq

city: La Jolla

first: Richard

last: Daneman

state: California

address: 9500 Gilman Dr

institute: UCSD

data_processing:
FASTQ files were run through the 10X Genomics CellRanger pipeline to generate gene counts data using CellRanger version 6.0.1
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, a folder containing the filtered counts matrix, cell barcodes, and feature (gene) names is provided

source_name: Brain

extract_protocol:
Dissectied brain regions were dissociated using both chemical and mechanical dissociation methods and single, tdTomato+ cells were sorted using FACS sorting
RNA libraries were prepared for sequencing using the 10x Genomics v3.1 Dual Index standard protocols

treatment_protocol: 1 week before endothelial cells purification, mice were injected I.P. with 20mg/mL Tamoxifen for 3 consecutive days (100 µL/day) to induce tdTomato expression in endothelial cells

tag: strain

value: tdTomato VeCreERT2; C57/BL6 background

value: Spinal-cord


title: Spinal-cord-3 scRNA-seq


title: day14-TP+CNO rep1

value: neural cells differentiated from 414C2-iPS cell-derived neural stem/progenitor cells in the injured NOD-SCID mouse spinal cord, 14-days after the spinal cord injury.

value: transplantation of 5 X 10e5 human iPS cell-derived neural stem/progenitor cells in the injured spinal cord 9-days after the injury.

value: intraperitoneal injection of 5 mg/kg of CNO


title: Midbrain-3 scRNA-seq

value: Midbrain


title: ChIPseq_H4Ac_atxr5/6 (W)_cotyledons

value: H4Ac (Active Motif, 39244)


title: Midbrain-2 scRNA-seq


title: Thalamus-3 scRNA-seq

value: Thalamus


title: Striatum-3 scRNA-seq

value: Striatum


title: Medulla-pons-3 scRNA-seq

value: Medulla-pons


title: E80-2019_MGE

value: MGE


title: ChIPseq_H3K27me3_WT_cotyledons

value: H3K27me3 (Millipore 07-449)

value: WT


title: ChIPseq_H4Ac_WT_cotyledons

value: cotyledons


title: Hippocampus-2 scRNA-seq

value: Hippocampus


title: Hippocampus-3 scRNA-seq


title: Hypothalamus-3 scRNA-seq

value: Hypothalamus


title: ChIPseq_H3Ac_WT_cotyledons

value: H3Ac (Active Motif, 39140)


title: ChIPseq_H3Ac_atxr5/6 (W)_cotyledons

value: atxr5/6 (W)


title: Day 36

city: Boston

first: Karl

last: Koehler

address: 3 Blackfan Cir

institute: Boston Children's Hospital

data_processing:
The 10x Genomics CellRanger 4.0.0 pipeline (http://support.10xgenomics.com/) was used to prepare data for analysis. Briefly, the CellRanger mkfastq command was used to demultiplex raw base sequenced calls into FASTQ files. The mkfastq command is a wrapper for bcl2fastq (http://support.illumina.com/) designed for multiplexed 10x libraries. The FASTQ files were then aligned to a reference GRCh38 genome using STAR aligner, an aligner designed to process mRNA transcripts. Once the reads were aligned, they were traced back to the individual encapsulated cell droplets of origin. Gene expression level was analyzed based on the number of UMIs (unique molecular indices) detected in each cell. Filtered gene expression matrices were generated using CellRanger’s count command. Cells which contained a UMI number that was very high or very low were excluded from further analysis. Also, cells that contained exceptionally high percentages of transcripts aligning to the mitochondrial genome were excluded. After removing these cells by filtering, gene expression levels were normalized for each cell by the total number of UMIs in the cell and multiplied by a scaling factor of 10,000. After log-transformation, Seurat 3 was used for cell clustering and principal component analysis (PCA) to determine the most highly variable genes (Butler et al., 2018). Clusters of cells were visualized using Uniform Manifold Approximation and Projection (UMAP) plotting techniques. Specific gene markers to identify cell clusters were determined through differential expression analysis, comparing the expression of a specific cell cluster to the other cells in the dataset. To accomplish the integration of two or more datasets, we made use of the Harmony Package for R (Korsunsky et al., 2019). Briefly, gene expression matrices were loaded as count matrices, and a pooled Seurat object was generated using the cbind command on the specified count matrices. Filtering, normalization, and scaling were performed on this large Seurat object; however, the RunHarmony command was used to iteratively integrate cells to the point of convergence. For integrated datasets, harmony embeddings were used for all downstream analyses. Cell cluster identification was manually performed using cell type-specific marker genes. R packages ggplot2 and ggrepel (https://github.com/slowkow/ggrepel) were used to plot quantitative gene expression analysis. Violin plots (VlnPlot) and Feature plots (FeaturePlot) were used to analyze the specific gene expression patterns across different clusters. Raw sequencing files, and output files from the 10x CellRanger pipeline, have been provided on the Gene Expression Omnibus.
Genome_build: GRCh38

source_name: Human pluripotent stem cell-derived inner ear organoids

growth_protocol: Stem cell differentiation experiments were performed primarily with the WTC (wild type C) hiPSC line (passage 35-51) obtained from the Allen Institute for Cell Science and the Coriell Institute (Miyaoka et al., 2014). Within the Allen Institute’s catalog of fluorescent reporter cell lines, the Desmoplakin-mEGFP (DSP-GFP) is particularly helpful for real time culture monitoring of otic vesicle development (Roberts et al., 2017). In order to maintain a source of stem cells for differentiation, pluripotent stem cells were cultured on 6-well plates with a coating of Vitronectin Recombinant Human Protein (Invitrogen) at a concentration of 0.5 µg/cm2. Cells were grown in Essential 8 Flex medium (Gibco) supplemented with 100 µg/ml Normocin (hereafter, E8; Invivogen). Culture media was replenished every other day. Around every 4 to 5 days of culture, cells reached 80% confluency and required passaging. Passaging procedures include removing adherent cell colonies using StemPro Accutase Cell Dissociation Reagent (hereafter, Accutase; Gibco). Cells were passaged in a medium containing 10 µM Y27632 (hereafter, Y; Stemgent) to inhibit excessive apoptosis. Newly plated colonies received new E8 media within 24 hours of passaging. Further information concerning the cell line used is available: https://www.allencell.org/cell-catalog.html.

extract_protocol:
In order to prepare for single-cell transcriptomic analysis, cell aggregates were dissociated into single cells. Randomly selected cell aggregates were pooled at specified time points. Pooled cell aggregates were incubated in warm TrypLE in an incubator at 37°C on a shaker set to 65 rpm. During the TrypLE incubation, the cell aggregate mixture was triturated with a pipette using wide bore p1000 or p200 tips every 10 minutes, depending on aggregate size. By the end of incubation of 10-60 minutes, tissues were dissociated into single cells, leaving a single cell suspension containing a heterogeneous mix of cell types. Dissociation was confirmed by bright-field visualization at 10x using a Nikon TS2R to ensure no residual cell aggregation. Once dissociation was complete, cold 3% BSA solution (Sigma-Aldrich) was added to the single-cell suspension to halt enzymatic TrypLE activity. The suspension was then filtered with a 40 µm Flowmi™ cell strainer (Bel-Art™). Filtering ensured that any residual cell aggregation or debris was removed. Three washes with cold 3% BSA were performed to ensure ambient RNA in the solution was minimized. After washing, cells were resuspended in cold 3% BSA and filtered once more with a 40 µm Flowmi™ cell strainer. The cell suspension was analyzed for cell viability (live cell percentage) and cell count using Trypan Blue and a Countess II Automated Cell Counter (Thermo-Fisher). Cell suspensions were diluted with cold 3% BSA as necessary to reach a final concentration of 1,000 cells/µl. Cell viability was consistently 90% or higher.
Single cell 3’ RNA-seq was performed using the Chromium platform (10x Genomics, Inc) and the NovaSeq 6000 sequencer (Illumina, Inc). Briefly, about 17,000 cells (targeting 10,000 cells captured) per sample were added to a separately prepared single-cell master mix according to the Chromium Single Cell 3’ Reagent Kit v3 User Guide, CG000183 Rev C (10x Genomics, Inc). The master mix with added cells was pipetted into a well of a Single Cell Chip B, while gel beads and partitioning oil were loaded into their respective wells according to the Chromium User Guide. Once single-cell encapsulation was complete, cDNA was synthesized with reverse transcription, and Illumina libraries were prepared. At specific steps in the library preparation process, cDNA length and quality were analyzed with a Bioanalyzer. The final libraries were sequenced on an Illumina NextSeq 500 or NovaSeq 6000 using 28b plus 91b paired-end sequencing to a final read depth of >30,000 reads per cell.

treatment_protocol: Pluripotent hPSC colonies were detached in a similar manner as in passaging. Accutase was used for detachment and dissociation while Y was used for apoptosis inhibition. An accurate measure of cell concentration was obtained using an automated cell counter (Countess™ II Automated Cell Counter; Countess II, Life Technologies); Trypan blue (Gibco) was used at a ratio of 1:1 (Trypan blue:cell suspension) to determine cell viability. Using the cell concentration measurement, the volume of cell suspension needed was calculated based on the target count of 3,500 cells in 100 µl of media per well of a 96-well U-bottom plate (Thermo Scientific). Once the appropriate volume of cell suspension was added to each well, plates were centrifuged at 110 rcf for 6 min to properly form cell aggregates. Plates containing cell aggregates were placed in an incubator at 37°C and 5% CO2 for 48 hrs. This 48 hour incubation period was performed in E8 media, thus maintaining pluripotency. Therefore, our aggregation day is termed day -2. Halfway through the initial 48 hour incubation period, 100 µl of fresh E8 medium was added to dilute Y and aid in cell maintenance. After the 48 hour incubation period in E8 medium, all individual aggregates were collected and plated into a new 96-well U-bottom plate with 100 µl of differentiation media per well. This time point is termed day 0. Differentiation media consisted of 100 µl of Essential 6 (supplemented with 100 µg/ml of normocin, hereafter, E6) medium containing 2% Matrigel (Corning), 10 µM SB (Stemgent), 4 ng/ml basic-FGF (hereafter, FGF2; PeproTech), and 2.5 ng/ml BMP-4 (PeproTech). After three days of incubation (day 3), 1 µM LDN (BMP inhibitor, Stemgent), and 250 ng/ml of FGF2 were added in a volume of 25 µl per well, thus increasing the volume of each well to 125 µl (final concentrations of 200 nM and 50 µg/ml of LDN and FGF2, respectively in 125 µl of media per well). After another three days of incubation (day 6), 75 µl of fresh E6 medium was added to each well, increasing the volume of each well to 200 µl. On days 8 and 10 of culture, 100 µl of the culture media from each well was removed and replaced with 100 µl of fresh E6 media containing 6 µM CHIR 99021 (CHIR), making a final concentration of 3 µM in the final volume of 200 µl per well. On day 12, cell aggregates were transferred to floating culture in 24-well low-attachment plates (Thermo Scientific) in 500 µl organoid maturation medium (OMM) with 1% Matrigel. In order to ensure aggregates did not adhere to the bottom of the well, plates were incubated on an orbital shaker at a speed of 65 rpm. The plates and orbital shaker were housed in an incubator maintained at 37°C and 5% CO2. The composition of OMM includes Advanced DMEM/F12 (Gibco) and Neurobasal (Gibco) media at a ratio of 1:1, 1X GlutaMax™ (Gibco), 0.5X B-27 Without Vitamin A (Gibco), and 0.5X N2 (Gibco) supplements, 0.1 mM 2-Mercaptoethanol (Gibco), and 100 µg/ml Normocin. CHIR was added to OMM to maintain a consistent concentration of 3 µM. On day 15, half of the spent media from each well was removed and replaced with new OMM media containing 1% Matrigel and 3 µM CHIR. On day 18 and onward, the media was replenished with fresh OMM every three days (day 18 to day 30) or every other day (day 30 onward). However, Matrigel was not added to the media beyond day 15. As aggregates enlarged and increased in cell number, it was necessary at times to increase the media volume to 1 mL per well.

tag: tissue type

value: hiPSC-derived inner ear organoids

value: WTC DSP-GFP

tag: days of differentiation

value: Day 36


title: Day 30

tag: cell line

value: Day 30


title: ChIPseq_H3K4me3_atxr5/6 (W)_cotyledons

value: H3K4me3 (millipore 04-745)


title: Day 24

value: Day 24


title: Cerebellum-2 scRNA-seq

value: tdTomato VeCreERT2; C57/BL6 background

value: Cerebellum


title: ChIPseq_H3K4me3_WT_cotyledons


title: PC3 BAY Release Rep3

city: Beijing

first: Zihan

last: Xu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

description: processed data file: PC3BR.txt

data_processing:
Quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore with parameters ‘-q 30 --length 30 --stringency 5’.
The clean paired-end reads were aligned to the mm10 reference genome by Tophat with the parameter --no-novel-juncs. Gene expression levels and differentially expressed genes between samples were calculated with Cuffdiff and visualized with the R package cummeRbund.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each sample

source_name: PC3 prostate cancer cell line

extract_protocol:
RNA was extracted using RNA extraction kit from Qiagen.
Tumor tissue or cell line library was constructed using kits from NEB(E7530),  CD8T cell and cancer cell library was constructed using smart-seq 2 protocol.

value: PC3 prostate cancer cell line

tag: treatment

value: BAY1082439 treatment 48hr withdraw 72h


title: Cortex-2 scRNA-seq

value: Cortex


title: Cerebellum-3 scRNA-seq


title: ChIPseq_H3K4me1_WT_cotyledons

city: Los Angeles

first: magdalena

last: potok

address: 4045 Terasaki Life Sciences Building

institute: UCLA

value: WT


title: PC3 BAY Release Rep2

description: processed data file: PC3BR.txt


title: PC3 BAY Release Rep1

description: processed data file: PC3BR.txt


title: Eosinophils_anti_Siglec_F_plus_IL_33_rep2

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

institute: University Clinic Erlangen

data_processing:
Raw reads of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) used in downstream analysis were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Reference genome mm10 and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using STAR (v2.6.1d) software.
Determined read quality (fastqc v0.11.8)
FeatureCounts (v1.5.0-p3) was used to count the read numbers mapped of each gene used for downstream analysis in the lab (29).
Genome_build: mm10
Supplementary_files_format_and_content: Westermann_et_al_raw_counts.txt
Supplementary_files_format_and_content: Westermann_et_al_Deseq2_normalized_counts.txt

source_name: primary eosinophils (IL-5tg_4get/C57BL/6 mice)

growth_protocol: Sorted eosinophils (3x10^6/mL) were cultured in medium (RPMI complemented with 20% (v/v) FBS, 25mM Hepes, 50µl β-Mercaptoethanol, 2mM L-Glutamine, 10mM Non-essential amino acids, 1mM Sodium Pyruvat, 10µg/mL Streptomycin, 100 U/mL Penicillin) for 4 hrs and treated as indicated for single samples.

extract_protocol:
RNA was isolated by phenol/chloroform extraction using a commercial RNA Isolation kit (SIGMA-ALDRICH 83913) according to manufacturer’s instructions except that volumes were downscaled to 1/6 of recommended volume, samples were sheared through 27G cannulas during initial lysis and precipitation was performed at -80°C instead of -20°C. Then RNA was dissolved in DEPC H2O.
RNA was sent to Novogene Europe (Cambridge, UK) for sequencing as a service. There, library preparation was performed with NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to mark sequences of individual samples.

treatment_protocol: Cells were stimulated with 5µg/mL Purified Rat Anti-Mouse Siglec-F antibody (clone E50-2440, BD Heidelberg, Germany) or Purified Rat IgG2a isotype control (BD Pharmingen, Heidelberg, Germany or Invitrogen, Carlsbad, CA) and/or 10ng/mL recombinant murine IL-33 (R&D Systems, Minneapolis, MN) for 4hrs.

value: SSChigh4get+ splenic eosinophils


title: Day 13 (NO CHIR)

value: Day 13


title: H3K14Ac_SxaQSEQsYB054L8_index_18

source_name: cotyledons

value: cotyledons


title: Day 10

value: Day 10


title: Day 13


title: Day 10 (NO CHIR)


title: Eosinophils_anti_Siglec_F_plus_IL_33_rep1


title: ChIPseq_H3K4me1_atxr5/6 (W)_cotyledons

value: atxr5/6 (W)


title: H3K27Ac_SxaQSEQsYAP029L8_index_11_combined

value: H3K27Ac (Abcam 4729)


title: Cortex-3 scRNA-seq


title: Day 8

value: hiPSC-derived inner ear organoids

value: WTC DSP-GFP

value: Day 8


title: Eosinophils_anti_Siglec_F_rep2


title: Eosinophils_anti_Siglec_F_plus_IL_33_rep3


title: H3K27Ac_SxaQSEQsYAP029L8_index_10_combined


title: LNCAP BAY Release Rep1

description: processed data file: LNCAPBR.txt

source_name: LNCAP prostate cancer cell line

value: LNCAP prostate cancer cell line


title: Eosinophils_anti_Siglec_F_rep3


title: LNCAP BAY Release Rep2

description: processed data file: LNCAPBR.txt


title: ChIPseq_H3K14Ac_atxr5/6 (W)_cotyledons


title: S437E 2

city: Shanghai

first: Jian

last: Huang

address: No. 150 Jimo Road

department: Department of Cardiology

institute: Shanghai East Hospital, Tongji University School of Medicine

description: total RNA

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm.
The probes detected with at least 75.0 percent in any group were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

source_name: Clk4-cKO myocardium treated by AAV NEXN-S437E

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was isolated from cells or tissue samples using TRIzol Reagent (Ambion) according to the manufacturer’s protocol.

treatment_protocol: Clk4-cKO myocardium treated with AAV NEXN-S437E, wherein AAV NEXN-WT served as a control.

tag: Sex

value: male

tag: agent

value: AAV NEXN-S437E


title: NEXN-WT 3

description: total RNA

source_name: Clk4-cKO myocardium treated by AAV NEXN-WT

value: AAV NEXN-WT


title: Day 6

value: Day 6


title: S437E 1

description: total RNA


title: S437E 3

description: total RNA


title: NEXN-WT 2

description: total RNA


title: Day 3

value: Day 3


title: H3K27me1_SxaQSEQsYB054L8_index_21

value: H3K27me1 (Millipore Sigma 07-448)


title: H3K27me1_SxaQSEQsYB054L8_index_13


title: Day 0

value: Day 0


title: LNCAP BAY Release Rep3

description: processed data file: LNCAPBR.txt

value: BAY1082439 treatment 48hr withdraw 72h


title: tRNA_Seq input

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

description: tRNA-seq

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with bowtie2 v2.1.0
Read quantitation using custom scripts
Genome_build: NC_000913.2
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Escherichia coli

extract_protocol: MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification  (for ribosome profiling) or deacylation reaction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification  (for tRNA-seq)


title: vehicle control rep3

data_processing:
Raw reads were trimmed based on the read quality and read length using Trim Galore version 0.6.6.
The RNA-seq data were mapped to the corresponding genomic DNA sequence (human GENCODE v34) and the TPM counts were generated using Salmon version 1.4.0 with the default setting.
Genome_build: human GENCODE v34
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: neural cells

extract_protocol:
Total RNA from hM3Dq neural cells was isolated using NucleoSpin RNA/Protein (740933.50; Macherey-Nagel, Duren, Germany).
Total RNA from each sample was purified and mRNA libraries were prepared according to the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, United States) protocol and sequenced using NovaSeq 6000 (Illumina) to obtain 150-bp paired-end reads.

value: neural cells differentiated from 414C7-iPS cell-derived neural stem/progenitor cells

value: untreated (vehicle for two hours)


title: NEXN-WT 1

description: total RNA


title: tRNA_Seq RNC2

description: tRNA-seq


title: Eosinophils_IL_33_rep2

value: SSChigh4get+ splenic eosinophils


title: tRNA_Seq RNC1

description: tRNA-seq


title: Eosinophils_anti_Siglec_F_rep1


title: Eosinophils_isotype_rep3

value: isotype


title: Eosinophils_IL_33_rep1


title: cm_hs2

description: Ribosome Profiling

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with bowtie2 v2.1.0
Read quantitation using custom scripts
Genome_build: NC_000913.2
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

value: chloramphenicol and High-salt-wash


title: vehicle control rep2

value: neural cells differentiated from 414C6-iPS cell-derived neural stem/progenitor cells


title: CNO stimulation rep3

value: neural cells differentiated from 414C4-iPS cell-derived neural stem/progenitor cells

value: 5 uM of CNO for two hours


title: cm_hs1

description: Ribosome Profiling


title: Eosinophils_IL_33_rep3


title: cm2

description: Ribosome Profiling

value: chloramphenicol


title: Day 18

value: hiPSC-derived inner ear organoids

value: WTC DSP-GFP

value: Day 18


title: Eosinophils_isotype_rep2


title: CNO stimulation rep2

value: neural cells differentiated from 414C3-iPS cell-derived neural stem/progenitor cells


title: Eosinophils_isotype_rep1


title: cm1

description: Ribosome Profiling


title: complement-48 rep3

status: Public on Nov 22 2021

first: Chen

last: Lin

address: NO.2005 Songhu road

institute: Fudan university

data_processing:
High-throughput sequencing was carried out on an Illumina HiSeq 2500 system according to the  manufacturer’s instructions (Illumina HiSeq 2500 User Guide)
The raw reads were fltered by Seqtk and then mapped to the M. marinum M strain reference sequence (GenBank  GCA_000018345.1) using Bowtie2 (version: 2–2.0.5)
Counting of reads per gene was performed using HTSeq followed by TMM (trimmed mean of M-values) normalization
Genome_build: M. marinum M strain reference sequence (GenBank  GCA_000018345.1)
Supplementary_files_format_and_content: tab-delimited excel file include FPKM values for all defferential expression genes during reaeration between wild type and whiB4 mutant strain

organism: Mycobacterium marinum

source_name: mycobacteria marinum

growth_protocol: Cultures of M. marinum were grown to mid-log phase (OD600 0.4–0.45), and then transferred to a hypoxia culture based on the Wayne model with a headspace ratio of 0.5.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and purifed using the RNAClean XP Kit (Beckman Coulter) and  RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions.
Purifed RNA was used to construct cDNA library according to the TruSeq Stranded RNA LT Guide from Illumina.

treatment_protocol: cultures were sealed and incubated with slow stirring in the dark at 30°C in a conical flask for 7 days. Samples were taken 0, 0.5, 4, 24, and 48 h after reaeration

value: 7 days' hypoxia, 48 hours' reaeration

value: whiB4 complement


title: complement-48 rep2


title: complement-24 rep3

value: 7 days' hypoxia, 24 hours' reaeration


title: vehicle control rep1

value: neural cells differentiated from 414C5-iPS cell-derived neural stem/progenitor cells


title: complement-4 rep3

value: 7 days' hypoxia, 4 hours' reaeration


title: complement-24 rep2


title: complement-24 rep1


title: complement-0.5 rep1

value: 7 days' hypoxia, 0.5 hours' reaeration


title: complement-0 rep1

value: 7 days' hypoxia


title: complement-0 rep2


title: complement-0.5 rep3


title: CNO stimulation rep1

value: neural cells differentiated from 414C2-iPS cell-derived neural stem/progenitor cells


title: WT-1218R-48 rep1

value: wild type


title: complement-0 rep3


title: complement-0.5 rep2


title: complement-4 rep2


title: complement-4 rep1


title: complement-48 rep1


title: WT-1218R-48 rep2


title: WT-1218R-4 rep2


title: WT-1218R-24 rep1


title: WT-1218R-24 rep2


title: WT-1218R-4 rep1


title: WT-1218R-0 rep1


title: WT-1218R-0.5 rep2


title: WT-1218R-0.5 rep1


title: WT-1218R-0 rep2


title: Neuron_PHIP_KO_RNA_Clone2

city: Chicago

first: Marc

last: Morgan

state: IL

address: 303 East Superior St, SQI 7-511

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: v6.5 ESCs

growth_protocol: HCT116 cells were grown in DMEM supplemented with 15% fetal bovine serum. Mouse ESCs were grown in N2/B27 medium supplemented with 2i and leukemia inhibitory factor (LIF)

extract_protocol:
RNA was prepared usng a Qiagen Rneasy Miniprep kit. ChIP DNA was purified using phenol:chloroform
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were subjected to neuronal differentiation by culture in N2/B27 medium on lamnin coated plates.

value: v6.5 ESCs

value: Embryonic stem cell


title: ASPC1-GFP Fluvastatin rep3

city: Essen

first: Barbara

last: Grüner

address: Hufelandstr. 55

institute: University Hospital Essen

description: ASPC1-GFP treated for 48 hours with fluvastatin rep3

hyb_protocol: (according to user manual Affymetrix WT PLUS Reagent Kit)  5,5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Applied Biosystems™ human Clariom™ S Assay.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: biotin

source_name: commercial cell line

label_protocol: The Applied Biosystems™ WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100ng total RNA

growth_protocol: Cells were seeded in cell culture dishes in triplicates.

extract_protocol: After treatment cells were harvested and cell pellets were stored at -80 °C. RNA isolation was performed using the Rneasy Mini Kit (Qiagen) according to the manufacturer’s manual and stored at -80 °C.

treatment_protocol: 24 hours after seeding, cells were treated either with DMSO control or with fluvastatin [5 µM] for 48 hours.

value: pancreas; derived from metastatic site:ascites

value: fluvastatin


title: Neuron_PHIP_KO_RNA_Clone1


title: Neuron_PHIP_KO_RNA_Clone4


title: Neuron_WT_RNA_Clone5

value: wild-type


title: Neuron_PHIP_KO_RNA_Clone3


title: ASPC1-GFP Fluvastatin rep2

description: ASPC1-GFP treated for 48 hours with fluvastatin rep2


title: Neuron_WT_RNA_Clone4


title: Neuron_WT_RNA_Clone1


title: ESC_PHIP_KO_RNA_Clone2


title: ESC_PHIP_KO_RNA_Clone1


title: ESC_PHIP_KO_RNA_Clone3


title: Neuron_WT_RNA_Clone3


title: ESC_PHIP_KO_RNA_Clone4


title: Neuron_WT_RNA_Clone2


title: ESC_WT_RNA_Clone5


title: ESC_WT_RNA_Clone3


title: ESC_WT_RNA_Clone2


title: ESC_WT_RNA_Clone4


title: ESC_WT_RNA_Clone1


title: ASPC1-GFP DMSO rep1

description: ASPC1-GFP treated for 48 hours with DMSO rep1

value: DMSO


title: ASPC1-GFP DMSO rep3

description: ASPC1-GFP treated for 48 hours with DMSO rep3


title: ASPC1-GFP Fluvastatin rep1

description: ASPC1-GFP treated for 48 hours with fluvastatin rep1


title: SINVNoV B2：tick microinjection 14dpi repeat

first: Yang

last: Li

address: 2005 Songhu Road

institute: Fudan University

description: tick infection with SINVNoV B2 by microinjection

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Genome_build: AF174533.1,AF174534.1;KX641909.1,KX641913.1,KX641917.1;J02363.1;NC_001560.1
Supplementary_files_format_and_content: mapping results files generated by bowtie1.1.2

organism: Haemaphysalis longicornis

source_name: tick whole body

extract_protocol:
Total RNA was extracted from ticks using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

tag: infection

tag: injection way

value: microinjection


title: SFTSV: tick replete on A6 6dpi

description: tick infection with SFTSV by blood-feeding on A6

value: SFTSV

value: blood-feeding

tag: mice strains


title: ASPC1-GFP DMSO rep2

description: ASPC1-GFP treated for 48 hours with DMSO rep2


title: NoV: tick replete on C57BL/6 8dpi

description: tick infection with NoV by blood-feeding on C57BL/6

value: NoV


title: SINV: tick microinjection 5dpi

description: tick infection with SINV by microinjection

value: SINV


title: IFITM3_46

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Sequencing reads were aligned to the mouse genome using STAR 2.7.0f.
Gene-level read counts were generated using STAR 2.7.0f.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts

source_name: lung

growth_protocol: Mice were housed in SPF facility

extract_protocol:
lung lobes were harvested aseptically at the indicated time points and homogenized in Trizol for RNA extraction. RNA was extracted using the DirectZol kit (Zymo Research)
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: intranasal challenge with influenza virus in 50 microliter of PBS

value: lung

tag: ifitm3 genotype

value: WT

value: F

tag: first challenge strain

tag: second challenge strain

tag: second challenge days post infection


title: SINVNoV mB2：tick microinjection 14dpi repeat

description: tick infection with SINVNoV mB2 by microinjection


title: Thin Tail replicate 3

city: Tabriz

first: Sana

last: Farhadi

address: Golgasht street

country: Iran

institute: Tabriz University

data_processing:
Fastqc-Trimmomatics-Tophat-Cufflink-Cuffmerge-cuffdiff-rstudio-Enrichment analysis-Network analysis
Sequenced reads were trimmed for adaptor and low-quality sequence
Clean reads mapped to Ovis-aries whole genome using Tophat software
Assembled reads
individual transcripts were merged to form a single transcript assembly
merged transcript was used for quantification of the transcripts
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Ovis aries

source_name: Iranian native Sheep breed

growth_protocol: All lambs were weaned at 90 days of age and then fostered under similar conditions at the research station of the Faculty of Agriculture, University of Tabriz, Tabriz, Iran (Khalatpoushan). The lambs were housed in individual pens and provided the same diet ad libitum for 120 days. Animals were slaughtered after 7 months.

extract_protocol:
Total RNA was extracted using TRIzol reagent using manufacturer instractions
PolyA enriched RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: tissue

value: Fat Tail

tag: breed

value: thin tail breed 'Zel'

value: 7 months


title: Thin Tail replicate 2

tag: age


title: Thin Tail replicate 1


title: IFITM3_38

value: mock


title: IFITM3_39

value: KO


title: IFITM3_43


title: IFITM3_45


title: IFITM3_44


title: IFITM3_41


title: SFTSV: tick replete on A6 2dpi


title: IFITM3_37


title: IFITM3_42


title: Thin Tail replicate 4


title: Fat Tail replicate 1

value: fat tail breed 'Ghezel'


title: 5hmc data of wild type hippocampus replicate 3

city: Atlanta

first: Yuwen

last: Zhao

state: GA

address: 615 Michael ST NE, Suite 305

institute: Emory University

description: genome-wide 5hmC profiles

data_processing:
Library strategy: 5hmC- seq
The raw fastq files generated from the high-throughput sequencing machine were aligned to the mouse genome (mm9) using Bowtie2
The whole mouse genome (mm9) was cut into 500bp bins, and all bins with genomic features and nearby gene were annotated by Homer
The DhMRs detection was performed by comparing the bin-level read counts between cases and controls using DESeq2
After accounting for multiple testing, the bins with an adjusted p value smaller than 0.20 was deemed as DhMRs
Gene ontology and pathway enrichment analysis was performed with EnrichR
Genome_build: mm9
Supplementary_files_format_and_content: KO_WT_raw_readcounts

source_name: hippocampus

extract_protocol:
5hmC enrichment was performed following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A), 20 ng of input genomic DNA or 5hmC-captured DNA were used for DNA libraries preparation (Antibody：5hmC，Active Motif，Cat# 39769, RRID:AB_10013602). Illumina Hi-seq 2000 machines were used for running sequencing libraries.
5hmC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: unstressed

tag: strain

tag: condition

value: unstressed

value: hippocampus

tag: genotype


title: IFITM3_40


title: SINV: tick replete on C57BL/6 6dpi

description: tick infection with SINV by blood-feeding on C57BL/6


title: 5hmc data of wild type hippocampus replicate 2

description: genome-wide 5hmC profiles


title: 5hmc data of TET2 knockout hippocampus replicate 1

description: genome-wide 5hmC profiles

value: Tet2 CKO


title: IFITM3_36


title: 5hmc data of wild type hippocampus replicate 1

description: genome-wide 5hmC profiles


title: Fat Tail replicate 2


title: Fat Tail replicate 3


title: IFITM3_35


title: IFITM3_32


title: Prdm16-Mx1-Cko/Cko; Tg/+ (Cko rep 1)

city: Frederick

first: Kristbjorn

middle: Orri

last: Gudmundsson

state: MD

address: 1050 Boyles St.

department: MCGP

institute: NCI

data_processing:
Processed and trimmed FASTQ sequencing files were uploaded and analyzed using the Galaxy platform (usegalaxy.org).
FASTQ files were analyzed by FastQC to ensure sequence quality and then aligned to the mouse genome (mm10) using HISAT2.
Read counts were determined from aligned BAM files with FeatureCounts.
Differential gene expression performed using the Limma Bioconductor package with a cut off of p<0.05 and 1.5 fold change.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene counts for each sample

source_name: Bone marrow LT-HSC

extract_protocol:
LT-HSC were sorted directly into RNA lysis buffer and stored at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control animals (Prdm16-Mx1-Cko/Cko; +/+) and test animals (Prdm16-Mx1-Cko/Cko; Tg/+) were injected 5 times with pIpC every other day to induce Cre expression. At 5 weeks post pIpC LT-HSCs were sorted from bone marrow for RNA-Sequencing.

value: adult

value: Bone marrow LT-HSC

value: Prdm16-Mx1-Cko/Cko; Tg/+


title: Prdm16-Mx1-Cko/Cko; +/+ (WT rep 3)

value: Prdm16-Mx1-Cko/Cko; +/+


title: IFITM3_34


title: Prdm16-Mx1-Cko/Cko; Tg/+ (Cko rep 3)


title: IFITM3_33


title: 5hmc data of TET2 knockout hippocampus replicate 4

description: genome-wide 5hmC profiles


title: IFITM3_27


title: Prdm16-Mx1-Cko/Cko; +/+ (WT rep 1)


title: IFITM3_26


title: Prdm16-Mx1-Cko/Cko; Tg/+ (Cko rep 2)


title: 5hmc data of TET2 knockout hippocampus replicate 3

description: genome-wide 5hmC profiles


title: IFITM3_28


title: IFITM3_31


title: Prdm16-Mx1-Cko/Cko; +/+ (WT rep 2)