title: HCT-15_vorinostat_5000nM_6h

description: gene expression data from HCT-15 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line HCT-15


title: C2C12 ChILT-DNA at 100 cells (0.5ul of Tn5 added) replicate 1

status: Public on Oct 09 2018

type: SRA

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description:
countMatrix10k_C2C12_conditions.csv.gz
countMatrix4k_C2C12_conditions.csv.gz

library_source: genomic

data_processing:
The raw sequence reads were aligned to the mouse and human reference genomes (GRCm38 and GRCh38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained.
The bigWig files were generated using bamCoverage command of deepTools (ver. 2.4.2) with the option: --smoothLength x --binSize y, where x and y are specified in the file names.
The csv countmatrix files were generated with multiBamSummary with the option bins -bs 4000 (or 10000).
ChILT peaks were generated with Homer findPeaks with the options -style histone -style histone -gsize 3e9 -size 4000 -regionRes 1 -minDist 1 -fdr 0.2.
ChIP peaks were generated with MACS2 (ver. 2.1.1) with the options -g hs -q 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all.
Genome_build: GRCm38/mm10 and GRCh38/hg38
Supplementary_files_format_and_content: bigWig files contain signal data for visualization via tools such as the Integrative Genomics Viewer, csv files include comma-delimited matrices, the bed file contains the peak data for C2C12, MCF-7 and MDA-MB-231 data.

molecule: genomic DNA

organism: Mus musculus

source_name: Immortal cell line

extract_protocol:
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.

tag: cell line

tag: antibody target

value: ChILT-DNA

tag: primary antibody


title: C2C12 ChILT-DNA at 100 cells (0.1ul of Tn5 added) replicate 2


title: ΔH3.V/ΔH4.V 1 cell N707/S504

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
processed data column: D7
ERCC spike-in control added

library_source: transcriptomic

data_processing:
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15
Read alignment: BWA-mem v0.7.16
scRNAseq analysis: python  3.6
samtools v1.8
bedtools v2.26.0
picard v2.9.0
Genome_build: Tb427v9
Supplementary_files_format_and_content: txt; scRNA-seq normalization and quantification from scRNA-seq I

molecule: total RNA

organism: Trypanosoma brucei brucei

source_name: single cell

extract_protocol:
Cells were sorted and lysed in lysis buffer ((0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water) and RNA was extracted from 1 and 50 cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) with a fourth of the recommended volumes of reagents. PCR amplification was performed for 26 cycles.
Libraries were constructed using a Nextera XT kit (Illumina) according to the manufacturer's instructions, but using only one fourth of the recommended voulmens and 1 ng of cDNA.

tag: strain

value: Lister 427 MITat 1.2

tag: genotyope

tag: life cycle stage

value: bloodstream form


title: C2C12 H3K27me3 at 100 cells (with probes with excessive DNA oligos) replicate 1

value: mouse monoclonal anti-H3K27me3 (Hayashi-Takanaka et al., Nucleic Acids Res. 2011 Aug;39(15):6475-88., CMA323)


title: C2C12 H3K27me3 at 100 cells (with probes with excessive DNA oligos) replicate 2


title: C2C12 ChILT-DNA at 100 cells (0.1ul of Tn5 added) replicate 1


title: HCT-15_vorinostat_5000nM_2h

type: RNA

city: Rockville

first: Anne

last: Monks

state: MD

address: 9609 Medical Center Dr

department: Developmental Therapeutics Program

country: USA

institute: National Cancer Institute

description: gene expression data from HCT-15 treated with 5000nM vorinostat for 2h

hyb_protocol: Biotin labeled antisense cRNA (4 µg per sample) was hybridized to Affymetrix GeneChip HT Human Genome U133A 96-Array plates overnight

scan_protocol: Plates were washed, stained, then scanned on an Affymetrix GeneTitan HT array plate scanner

data_processing: Data were collected using Affymetrix AGCC software.  Initial data quality control was performed using percent present calls generated by Affymetrix Quality Reporter software. Samples failing QC were repeated (R2)

label: biotin

organism: Homo sapiens

label_protocol: Samples (96-well format, 1 µg each) were labeled using Affymetrix (Cleveland OH) HT One-Cycle Eukaryotic Labeling Kit on Biomek FX Target Prep Express system following manufacturer’s suggested protocols

growth_protocol: All cell lines were cultured in RPMI-1640 media with 10% FBS and L-Glutamine and incubated at 37oC, 5%CO2.

extract_protocol: Total RNA was isolated using the Qiagen Rneasy mini kit, quantitated by measuring absorbance at A260, quality of RNA was determined on a Caliper LabChip GX all samples used had an RQS>7.5

treatment_protocol: All drugs were dissolved in DMSO, diluted to their appropriate concentrations in culture media and added to the cells pre-plated for 24h (DMSO final concentration of 0.25%) , and incubated for the indicated times

tag: group

value: member of the NCI-60 cell line panel

tag: tissue

value: Colon


title: C2C12 ChILT-DNA at 100 cells (0.02ul of Tn5 added) replicate 2


title: HCT-15_vorinostat_1000nM_6h

description: gene expression data from HCT-15 treated with 1000nM vorinostat for 6h


title: HCT-15_vorinostat_5000nM_24h

description: gene expression data from HCT-15 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V 50 cells N7012/S503

description:
processed data column: C12
ERCC spike-in control added

source_name: 50 cells


title: HCT-15_vorinostat_1000nM_2h

description: gene expression data from HCT-15 treated with 1000nM vorinostat for 2h


title: C2C12 ChILT-DNA at 100 cells (0.02ul of Tn5 added) replicate 1


title: C2C12 H3K27me3 at 100 cells (with probes without PEG linkers) replicate 1


title: C2C12 ChILT-DNA at 100 cells (Tn5 integration at RT) replicate 1


title: C2C12 ChILT-DNA at 100 cells (Tn5 integration at RT) replicate 2


title: ΔH3.V/ΔH4.V 1 cell N711/S503

description:
processed data column: C11
ERCC spike-in control added


title: HCT-15_vorinostat_1000nM_24h

description: gene expression data from HCT-15 treated with 1000nM vorinostat for 24h


title: C2C12 ChILT-DNA at 100 cells (Tn5 integration at 4 degrees) replicate 2


title: C2C12 ChILT-DNA at 100 cells (Tn5 integration at 4 degrees) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N710/S503

description:
processed data column: C10
ERCC spike-in control added


title: C2C12 H3K27me3 at 1 cell replicate 4


title: ΔH3.V/ΔH4.V 1 cell N709/S503

description:
processed data column: C9
ERCC spike-in control added


title: C2C12 H3K27me3 at 1 cell replicate 5


title: HCT-15_vorinostat_0nM_6h

description: gene expression data from HCT-15 treated with 0nM vorinostat for 6h


title: C2C12 H3K27me3 at 1 cell replicate 3


title: ΔH3.V/ΔH4.V 1 cell N708/S503

description:
processed data column: C8
ERCC spike-in control added


title: HCT-15_vorinostat_0nM_2h

description: gene expression data from HCT-15 treated with 0nM vorinostat for 2h


title: C2C12 H3K27me3 at 1 cell replicate 2


title: ΔH3.V/ΔH4.V 1 cell N707/S503

description:
processed data column: C7
ERCC spike-in control added


title: C2C12 H3K27me3 at 1 cell replicate 1


title: HCT-116_vorinostat_5000nM_6h

description: gene expression data from HCT-116 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line HCT-116


title: HCT-116_vorinostat_5000nM_2h

description: gene expression data from HCT-116 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V 50 cells N7012/S502

description:
processed data column: B12
ERCC spike-in control added


title: HCT-15_vorinostat_0nM_24h

description: gene expression data from HCT-15 treated with 0nM vorinostat for 24h


title: C2C12 H3K27ac at 1 cell replicate 3

value: mouse monoclonal anti-H3K27ac (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA309)


title: C2C12 H3K27ac at 1 cell replicate 4


title: ΔH3.V/ΔH4.V 1 cell N711/S502

description:
processed data column: B11
ERCC spike-in control added


title: C2C12 H3K4me3 at 1 cell replicate 5

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: C2C12 H3K4me3 at 1 cell replicate 3


title: HCT-116_vorinostat_5000nM_24h

description: gene expression data from HCT-116 treated with 5000nM vorinostat for 24h


title: C2C12 H3K4me3 at 1 cell replicate 4


title: C2C12 H3K9me3 at 100 cells replicate 2

description:
countMatrix4k_C2C12_cellnumbers.csv.gz
countMatrix10k_C2C12_cellnumbers.csv.gz

value: mouse monoclonal anti-H3K9me3 (Hayashi-Takanaka et al., Nucleic Acids Res. 2011 Aug;39(15):6475-88., CMA318)


title: HCT-116_vorinostat_1000nM_6h

description: gene expression data from HCT-116 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V 1 cell N710/S502

description:
processed data column: B10
ERCC spike-in control added


title: C2C12 H3K9me3 at 100 cells replicate 1


title: ΔH3.V/ΔH4.V 1 cell N709/S502

description:
processed data column: B9
ERCC spike-in control added


title: C2C12 H3K9me3 at 1k cells replicate 2


title: HCT-116_vorinostat_1000nM_2h

description: gene expression data from HCT-116 treated with 1000nM vorinostat for 2h


title: C2C12 H3K9me3 at 1k cells replicate 1


title: C2C12 H3K27ac at 1 cell replicate 5


title: C2C12 H3K9me3 at 10k cells replicate 2


title: C2C12 H3K9me3 at 10k cells replicate 1


title: HCT-116_vorinostat_1000nM_24h

description: gene expression data from HCT-116 treated with 1000nM vorinostat for 24h


title: C2C12 H3K9me3 at 100k cells replicate 2


title: ΔH3.V/ΔH4.V 1 cell N711/S501

description:
processed data column: A11
ERCC spike-in control added


title: HCT-116_vorinostat_0nM_6h

description: gene expression data from HCT-116 treated with 0nM vorinostat for 6h


title: C2C12 H3K9me3 at 100k cells replicate 1


title: C2C12 H3K27me3 at 1k cells replicate 2


title: C2C12 H3K27me3 at 1k cells replicate 1


title: ΔH3.V/ΔH4.V 1 cell N710/S501

description:
processed data column: A10
ERCC spike-in control added


title: C2C12 H3K27me3 at 10k cells replicate 2


title: ΔH3.V/ΔH4.V 1 cell N709/S501

description:
processed data column: A9
ERCC spike-in control added


title: HCT-116_vorinostat_0nM_2h

description: gene expression data from HCT-116 treated with 0nM vorinostat for 2h


title: C2C12 H3K27me3 at 10k cells replicate 1


title: C2C12 H3K27me3 at 100k cells replicate 2


title: C2C12 H3K27me3 at 100k cells replicate 1


title: ΔH3.V/ΔH4.V 1 cell N708/S502

description:
processed data column: B8
ERCC spike-in control added


title: ΔH3.V/ΔH4.V 1 cell N708/S501

description:
processed data column: A8
ERCC spike-in control added


title: HCC-2998_vorinostat_5000nM_2h

description: gene expression data from HCC-2998 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line HCC-2998


title: HCC-2998_vorinostat_5000nM_6h

description: gene expression data from HCC-2998 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V 1 cell N707/S501

description:
processed data column: A7
ERCC spike-in control added


title: C2C12 H3K27ac at 10k cells replicate 1


title: ΔH3.V/ΔH4.V 1 cell N707/S502

description:
processed data column: B7
ERCC spike-in control added


title: C2C12 H3K27ac at 10k cells replicate 2

description:
countMatrix4k_C2C12_cellnumbers.csv.gz
countMatrix10k_C2C12_cellnumbers.csv.gz


title: C2C12 H3K27ac at 100k cells replicate 1


title: wild-type 1 cell N706/S508

description:
processed data column: H6
ERCC spike-in control added

value: wild-type


title: C2C12 H3K27ac at 100k cells replicate 2


title: HCC-2998_vorinostat_5000nM_24h

description: gene expression data from HCC-2998 treated with 5000nM vorinostat for 24h


title: wild-type 1 cell N705/S508

description:
processed data column: H5
ERCC spike-in control added


title: HCC-2998_vorinostat_1000nM_2h

description: gene expression data from HCC-2998 treated with 1000nM vorinostat for 2h


title: wild-type 1 cell N704/S508

description:
processed data column: H4
ERCC spike-in control added


title: wild-type 1 cell N703/S508

description:
processed data column: H3
ERCC spike-in control added


title: HCT-116_vorinostat_0nM_24h

description: gene expression data from HCT-116 treated with 0nM vorinostat for 24h


title: HCC-2998_vorinostat_1000nM_24h

description: gene expression data from HCC-2998 treated with 1000nM vorinostat for 24h


title: wild-type 1 cell N702/S508

description:
processed data column: H2
ERCC spike-in control added


title: wild-type 1 cell N701/S508

description:
processed data column: H1
ERCC spike-in control added


title: HCC-2998_vorinostat_1000nM_6h

description: gene expression data from HCC-2998 treated with 1000nM vorinostat for 6h


title: wild-type 1 cell N705/S507

description:
processed data column: G5
ERCC spike-in control added


title: HOP-62_vorinostat_1000nM_6h

description: gene expression data from HOP-62 treated with 1000nM vorinostat for 6h

source_name: human tumor cell line HOP-62

value: Lung


title: wild-type 1 cell N706/S507

description:
processed data column: G6
ERCC spike-in control added


title: C2C12 H3K4me3 at 100 cells (Tn5 integration at RT) replicate 1

description:
countMatrix10k_C2C12_conditions.csv.gz
countMatrix4k_C2C12_conditions.csv.gz


title: HCC-2998_vorinostat_0nM_24h

description: gene expression data from HCC-2998 treated with 0nM vorinostat for 24h


title: HCC-2998_vorinostat_0nM_2h

description: gene expression data from HCC-2998 treated with 0nM vorinostat for 2h


title: C2C12 H3K4me3 at 100k cells replicate 2

description:
countMatrix4k_C2C12_cellnumbers.csv.gz
countMatrix10k_C2C12_cellnumbers.csv.gz


title: C2C12 H3K4me3 at 100k cells replicate 1


title: wild-type 1 cell N704/S507

description:
processed data column: G4
ERCC spike-in control added


title: EKVX_vorinostat_5000nM_24h

description: gene expression data from EKVX treated with 5000nM vorinostat for 24h

source_name: human tumor cell line EKVX


title: EKVX_vorinostat_5000nM_2h

description: gene expression data from EKVX treated with 5000nM vorinostat for 2h


title: C2C12 H3K4me3 at 1k cells replicate 1


title: Single-cell Pituitary cells in RNA-Best H10

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

description:
featureCounts.txt
cell 54

data_processing:
The RNA-seq fastq files were aligned with STAR v2.5.1b with the mouse GENCODE annotation.
featureCounts v1.5.0-p1 is used to summarize the reads for all genes and samples
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all genes and for each cell

molecule: polyA RNA

source_name: Single-cell Pituitary cells in RNA-Best

growth_protocol: Whole pituitaries were collected from randomly cycling pure C57BL/6 female mice aged 10-12 weeks, and acutely dissociated into single-cell suspensions. Upon collection, pituitaries were acutely dissociated, i.e. digested with collagenase and dispersed with pancreatine. Cells were washed and plated into M199 medium supplemented with HEPES, 10% FBS, and antibiotics. About 500,000-700,000 cells were collected from 5 pituitaries, making up a sample.

extract_protocol:
Primary pituitary cell samples were stored in RNA-Best at 400,000 cells/ml. RNA-Best-stabilized cells were filtered through a 10-μm filter and prepared for assay on the C1 according to the standard Fluidigm protocol for the SMART-Seq V4 Ultra low Input RNA Kit (Clontech, 032416), using a small 5-10 μm primed chip.
SC libraries were prepared using the Nextera RT DNA library kits (Illumina).

treatment_protocol: Non applicable

tag: cell type

value: Dissociated primary cells

tag: gender

value: female

tag: cycling

value: randomly cycling 3 weeks

tag: cell culture

value: pituitary, primary cells, untreated

tag: stabilized with

value: Grown as pituitary cells for 4 days, then trypsinized and resuspended in RNA-Best


title: Single-cell Pituitary cells in RNA-Best H11

description:
featureCounts.txt
cell 55


title: Single-cell Pituitary cells in RNA-Best H12

description:
featureCounts.txt
cell 56


title: Single-cell Pituitary cells in RNA-Best H7

description:
featureCounts.txt
cell 52


title: Single-cell Pituitary cells in RNA-Best H6

description:
featureCounts.txt
cell 51


title: wild-type 1 cell N702/S507

description:
processed data column: G2
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best H5

description:
featureCounts.txt
cell 50


title: EKVX_vorinostat_1000nM_2h

description: gene expression data from EKVX treated with 1000nM vorinostat for 2h


title: HCC-2998_vorinostat_0nM_6h

description: gene expression data from HCC-2998 treated with 0nM vorinostat for 6h


title: C2C12 H3K4me3 at 1k cells replicate 2


title: Single-cell Pituitary cells in RNA-Best H4

description:
featureCounts.txt
cell 49


title: wild-type 1 cell N701/S507

description:
processed data column: G1
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best H3

description:
featureCounts.txt
cell 48


title: Single-cell Pituitary cells in RNA-Best H2

description:
featureCounts.txt
cell 47


title: EKVX_vorinostat_1000nM_6h

description: gene expression data from EKVX treated with 1000nM vorinostat for 6h


title: EKVX_vorinostat_5000nM_6h

description: gene expression data from EKVX treated with 5000nM vorinostat for 6h


title: wild-type 1 cell N705/S506

description:
processed data column: F5
ERCC spike-in control added


title: wild-type 1 cell N706/S506

description:
processed data column: F6
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best G2

description:
featureCounts.txt
cell 44


title: Single-cell Pituitary cells in RNA-Best H9

description:
featureCounts.txt
cell 53


title: EKVX_vorinostat_0nM_2h

description: gene expression data from EKVX treated with 0nM vorinostat for 2h


title: wild-type 1 cell N703/S507

description:
processed data column: G3
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best G1

description:
featureCounts.txt
cell 43


title: EKVX_vorinostat_0nM_6h

description: gene expression data from EKVX treated with 0nM vorinostat for 6h


title: Single-cell Pituitary cells in RNA-Best F12

description:
featureCounts.txt
cell 42


title: EKVX_vorinostat_0nM_24h

description: gene expression data from EKVX treated with 0nM vorinostat for 24h


title: Single-cell Pituitary cells in RNA-Best F11

description:
featureCounts.txt
cell 41


title: wild-type 1 cell N704/S506

description:
processed data column: F4
ERCC spike-in control added


title: EKVX_vorinostat_1000nM_24h

description: gene expression data from EKVX treated with 1000nM vorinostat for 24h


title: DU-145_vorinostat_5000nM_6h

description: gene expression data from DU-145 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line DU-145

value: Prostate


title: wild-type 1 cell N702/S506

description:
processed data column: F2
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best F6

description:
featureCounts.txt
cell 40


title: Single-cell Pituitary cells in RNA-Best F4

description:
featureCounts.txt
cell 39


title: Single-cell Pituitary cells in RNA-Best F3

description:
featureCounts.txt
cell 38


title: Single-cell Pituitary cells in RNA-Best E9

description:
featureCounts.txt
cell 37


title: wild-type 1 cell N701/S506

description:
processed data column: F1
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best G10

description:
featureCounts.txt
cell 46


title: Single-cell Pituitary cells in RNA-Best E8

description:
featureCounts.txt
cell 36


title: DU-145_vorinostat_5000nM_2h

description: gene expression data from DU-145 treated with 5000nM vorinostat for 2h


title: Single-cell Pituitary cells in RNA-Best G7

description:
featureCounts.txt
cell 45


title: DU-145_vorinostat_1000nM_6h

description: gene expression data from DU-145 treated with 1000nM vorinostat for 6h


title: DU-145_vorinostat_5000nM_24h

description: gene expression data from DU-145 treated with 5000nM vorinostat for 24h


title: Single-cell Pituitary cells in RNA-Best E7

description:
featureCounts.txt
cell 35


title: wild-type 1 cell N706/S505

description:
processed data column: E6
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best E3

description:
featureCounts.txt
cell 33


title: Single-cell Pituitary cells in RNA-Best E6

description:
featureCounts.txt
cell 34


title: wild-type 1 cell N705/S505

description:
processed data column: E5
ERCC spike-in control added


title: wild-type 1 cell N703/S506

description:
processed data column: F3
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best E1

description:
featureCounts.txt
cell 32


title: wild-type 1 cell N704/S505

description:
processed data column: E4
ERCC spike-in control added


title: wild-type 1 cell N703/S505

description:
processed data column: E3
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best D11

description:
featureCounts.txt
cell 30


title: Single-cell Pituitary cells in RNA-Best D12

description:
featureCounts.txt
cell 31


title: MAT1_2_OE1

city: Erlangen

first: Sven

last: Krappmann

address: Wasserturmstr. 3/5

department: Institute for Microbiology

institute: FAU Erlangen-Nuernberg

data_processing: Sequencing in 50 bp single reads was performed on the Genome Sequencer Illumina HiSeq2000, and trimming to eliminate contaminating adapter sequences was carried out using Trimmomatic, version 0.36. The number of total raw and trimmed reads per sample ranged from 19.1 to 29.5 Mio and 18.0 to 28.1 Mio, respectively, with mapping percentages reaching at least 96% throughout all samples (minimum 96.0%, maximum 97.6%) upon alignment to the annotated reference genome sequences of the A. fumigatus A1163 [MAT1-1] and Af293 [MAT1-2] isolates using the most recent version 2.1.0 of HISAT2. The resulting read count data were then analysed for differential expression by comparison between sample and control (AfS146 and AfS147 compared to D141 and Af293, respectively) by means of the DESeq2 software package (v1.20.0).

organism: Aspergillus fumigatus

source_name: case mating-type MAT1-2

growth_protocol: liquid cultures were inoculated with fungal conidia and allowed to grow overnight before shifting the formed mycelia to inducing, xylose-containing culture media

extract_protocol:
nucleic acids from frozen and ground mycelia were extraced with the TRIzole reagent, cleaned, and DNase I digested to be followed by RNA purification
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mycelia were separated from culture broth by filtration, washed, and snap frozen in liquid nitrogen

tag: mating-type

tag: genotype

value: mycelium


title: DU-145_vorinostat_0nM_6h

description: gene expression data from DU-145 treated with 0nM vorinostat for 6h


title: MAT1_2_WT2

source_name: control mating-type MAT1-2


title: DU-145_vorinostat_0nM_2h

description: gene expression data from DU-145 treated with 0nM vorinostat for 2h


title: Single-cell Pituitary cells in RNA-Best D10

description:
featureCounts.txt
cell 29


title: MAT1_2_WT1


title: DU-145_vorinostat_0nM_24h

description: gene expression data from DU-145 treated with 0nM vorinostat for 24h


title: wild-type 1 cell N701/S505

description:
processed data column: E1
ERCC spike-in control added

value: Lister 427 MITat 1.2


title: Single-cell Pituitary cells in RNA-Best D7

description:
featureCounts.txt
cell 28


title: COLO-205_vorinostat_5000nM_6h

description: gene expression data from COLO-205 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line COLO-205


title: DU-145_vorinostat_1000nM_2h

description: gene expression data from DU-145 treated with 1000nM vorinostat for 2h


title: wild-type 50 cells N706/S504

description:
processed data column: D6
ERCC spike-in control added

value: bloodstream form


title: MAT1_1_OE1

source_name: case mating-type MAT1-1


title: MAT1_2_OE2


title: DU-145_vorinostat_1000nM_24h

description: gene expression data from DU-145 treated with 1000nM vorinostat for 24h


title: Single-cell Pituitary cells in RNA-Best D5

description:
featureCounts.txt
cell 27


title: Single-cell Pituitary cells in RNA-Best D4

description:
featureCounts.txt
cell 26


title: COLO-205_vorinostat_5000nM_2h

description: gene expression data from COLO-205 treated with 5000nM vorinostat for 2h


title: Single-cell Pituitary cells in RNA-Best D3

description:
featureCounts.txt
cell 25


title: wild-type 1 cell N705/S504

description:
processed data column: D5
ERCC spike-in control added


title: COLO-205_vorinostat_5000nM_24h

description: gene expression data from COLO-205 treated with 5000nM vorinostat for 24h


title: MAT1_1_WT2

source_name: control mating-type MAT1-1


title: MAT1_1_WT1


title: wild-type 1 cell N704/S504

description:
processed data column: D4
ERCC spike-in control added


title: wild-type 1 cell N702/S505

description:
processed data column: E2
ERCC spike-in control added


title: wild-type 1 cell N703/S504

description:
processed data column: D3
ERCC spike-in control added


title: COLO-205_vorinostat_1000nM_6h

description: gene expression data from COLO-205 treated with 1000nM vorinostat for 6h


title: Single-cell Pituitary cells in RNA-Best C11

description:
featureCounts.txt
cell 23


title: COLO-205_vorinostat_1000nM_2h

description: gene expression data from COLO-205 treated with 1000nM vorinostat for 2h


title: wild-type 1 cell N702/S504

description:
processed data column: D2
ERCC spike-in control added


title: COLO-205_vorinostat_1000nM_24h

description: gene expression data from COLO-205 treated with 1000nM vorinostat for 24h


title: MAT1_1_OE2


title: wild-type 50 cells N706/S503

description:
processed data column: C6
ERCC spike-in control added


title: COLO-205_vorinostat_0nM_6h

description: gene expression data from COLO-205 treated with 0nM vorinostat for 6h


title: wild-type 1 cell N705/S503

description:
processed data column: C5
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best C9

description:
featureCounts.txt
cell 21


title: wild-type 1 cell N704/S503

description:
processed data column: C4
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best D2

description:
featureCounts.txt
cell 24


title: Single-cell Pituitary cells in RNA-Best C7

description:
featureCounts.txt
cell 19


title: wild-type 1 cell N703/S503

description:
processed data column: C3
ERCC spike-in control added


title: wild-type 1 cell N701/S504

description:
processed data column: D1
ERCC spike-in control added


title: MDA-MB-231 input at 100 cells replicate 2

extract_protocol:
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.


title: Single-cell Pituitary cells in RNA-Best C2

description:
featureCounts.txt
cell 18


title: Single-cell Pituitary cells in RNA-Best C1

description:
featureCounts.txt
cell 17


title: Single-cell Pituitary cells in RNA-Best C10

description:
featureCounts.txt
cell 22


title: COLO-205_vorinostat_0nM_24h

description: gene expression data from COLO-205 treated with 0nM vorinostat for 24h


title: Single-cell Pituitary cells in RNA-Best B12

description:
featureCounts.txt
cell 16


title: COLO-205_vorinostat_0nM_2h

description: gene expression data from COLO-205 treated with 0nM vorinostat for 2h


title: wild-type 1 cell N701/S503

description:
processed data column: C1
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best C8

description:
featureCounts.txt
cell 20


title: CCRF-CEM_vorinostat_5000nM_6h

description: gene expression data from CCRF-CEM treated with 5000nM vorinostat for 6h

source_name: human tumor cell line CCRF-CEM

value: Leukemia


title: CCRF-CEM_vorinostat_5000nM_24h

description: gene expression data from CCRF-CEM treated with 5000nM vorinostat for 24h

value: member of the NCI-60 cell line panel


title: Axl-2+Dox_2

city: Baltimore

first: Haley

middle: Dara

last: Axelrod

address: 600 N. Wolfe St.

department: Urology

institute: Johns Hopkins SOM

description:
High agg rep 2
Gene expression in C42B Tet-Axl 2 cells treated with doxycycline.
Replicate 2

hyb_protocol: Agilent human GE 4x 44K v2 microarrays (G4845A) were used, which contain 41,000 unique probes targeting 27,958 Entrez gene RNAs. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

scan_protocol: Microarrays were scanned using an Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

data_processing: Control probesets were removed from the raw gene expression data. Next, the samples were background corrected and quantile normalized. Probesets were then mapped to gene names using Agilent annotations from the microarray data. Multiple probesets mapping to single gene were summarized by median. Probesets that did not map to a gene were excluded from the analysis.

source_name: Tet-Axl 2 cells, dox

label_protocol: Sample amplification and labeling procedures were carried out by using Quick RNA Amplification and Labeling Kit (Cat# 5190-0447, Agilent Technologies) with minor modifications. Briefly, 400 ng total RNA was reverse-transcribed into cDNA by MMLV-RT using oligo dT primers (Cat# RA300A-2, System Bioscience) that incorporate T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: C42B Tet-Axl 1 and Tet-Axl 2 cells were serum starved in 0.1% FBS overnight prior to seeding. Cells were seeded at 0.3e6 cells per 6cm2 plate in Tet-approved FBS.

extract_protocol: Total RNA was isolated from cell pellets using RLT buffer (Qiagen) and a QIAshredder, followed by RNeasy Mini Kit with DNase on-column digestion (Qiagen). RNA was quantified using NanoDrop.

treatment_protocol: Doxycycline (100 ng/mL) was added to the samples at the time of seeding.

value: C42B Tet-Axl 2

tag: treatment

value: dox


title: CCRF-CEM_vorinostat_5000nM_2h

description: gene expression data from CCRF-CEM treated with 5000nM vorinostat for 2h


title: CCRF-CEM_vorinostat_1000nM_6h

description: gene expression data from CCRF-CEM treated with 1000nM vorinostat for 6h


title: Axl-1+Dox_2

description:
Low agg rep 2
Gene expression in C42B Tet-Axl 1 cells treated with doxycycline.
Replicate 2

source_name: Tet-Axl 1 cells, dox

value: C42B Tet-Axl 1


title: Axl-2+Dox_3

description:
High agg rep 3
Gene expression in C42B Tet-Axl 2 cells treated with doxycycline.
Replicate 3


title: Axl-1+Dox_3

description:
Low agg rep 3
Gene expression in C42B Tet-Axl 1 cells treated with doxycycline.
Replicate 3


title: Axl-2+Dox_1

description:
High agg rep 1
Gene expression in C42B Tet-Axl 2 cells treated with doxycycline.
Replicate 1


title: Axl-1+Dox_1

description:
Low agg rep 1
Gene expression in C42B Tet-Axl 1 cells treated with doxycycline.
Replicate 1


title: MDA-MB-231 H3K4me3 ChIP at 100k cells replicate 2

source_name: Immortal cell line

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: CCRF-CEM_vorinostat_1000nM_2h

description: gene expression data from CCRF-CEM treated with 1000nM vorinostat for 2h


title: wild-type 50 cells N706/S502

description:
processed data column: B6
ERCC spike-in control added

value: wild-type


title: Single-cell Pituitary cells in RNA-Best B11

description:
featureCounts.txt
cell 15


title: MDA-MB-231 H3K4me3 ChIP at 100k cells replicate 1


title: wild-type 1 cell N705/S502

description:
processed data column: B5
ERCC spike-in control added

source_name: single cell


title: Single-cell Pituitary cells in RNA-Best B6

description:
featureCounts.txt
cell 14


title: wild-type 1 cell N702/S503

description:
processed data column: C2
ERCC spike-in control added


title: MDA-MB-231 input at 100 cells replicate 1


title: wild-type 1 cell N704/S502

description:
processed data column: B4
ERCC spike-in control added


title: MCF-7 input at 100 cells replicate 2


title: Single-cell Pituitary cells in RNA-Best B5

description:
featureCounts.txt
cell 13


title: MCF-7 input at 100 cells replicate 1


title: wild-type 1 cell N703/S502

description:
processed data column: B3
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best B4

description:
featureCounts.txt
cell 12


title: CCRF-CEM_vorinostat_0nM_6h

description: gene expression data from CCRF-CEM treated with 0nM vorinostat for 6h


title: CCRF-CEM_vorinostat_0nM_2h

description: gene expression data from CCRF-CEM treated with 0nM vorinostat for 2h


title: MCF-7 H3K4me3 ChIP at 100k cells replicate 1


title: wild-type 1 cell N702/S502

description:
processed data column: B2
ERCC spike-in control added


title: MDA-MB-231 H3K4me3 at 1k cells replicate 2


title: CCRF-CEM_vorinostat_0nM_24h

description: gene expression data from CCRF-CEM treated with 0nM vorinostat for 24h


title: wild-type 1 cell N701/S502

description:
processed data column: B1
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best B3

description:
featureCounts.txt
cell 11


title: CCRF-CEM_vorinostat_1000nM_24h

description: gene expression data from CCRF-CEM treated with 1000nM vorinostat for 24h


title: wild-type 1 cell N705/S501

description:
processed data column: A5
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best B2

description:
featureCounts.txt
cell 10


title: Single-cell Pituitary cells in RNA-Best A11

description:
featureCounts.txt
cell 9


title: MDA-MB-231 H3K4me3 at 10k cells replicate 2


title: CAKI-1_vorinostat_5000nM_2h

description: gene expression data from CAKI-1 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line CAKI-1

value: Renal


title: MDA-MB-231 H3K4me3 at 1k cells replicate 1


title: wild-type 1 cell N704/S501

description:
processed data column: A4
ERCC spike-in control added


title: Single-cell Pituitary cells in RNA-Best A10

description:
featureCounts.txt
cell 8

value: Dissociated primary cells


title: CAKI-1_vorinostat_5000nM_6h

description: gene expression data from CAKI-1 treated with 5000nM vorinostat for 6h


title: MDA-MB-231 H3K4me3 at 10k cells replicate 1


title: wild-type 1 cell N703/S501

description:
processed data column: A3
ERCC spike-in control added


title: MDA-MB-231 H3K4me3 at 100 cells replicate 2


title: Single-cell Pituitary cells in RNA-Best A8

description:
featureCounts.txt
cell 6

value: female


title: CAKI-1_vorinostat_5000nM_24h

description: gene expression data from CAKI-1 treated with 5000nM vorinostat for 24h


title: Single-cell Pituitary cells in RNA-Best A9

description:
featureCounts.txt
cell 7

value: randomly cycling 3 weeks


title: CAKI-1_vorinostat_1000nM_6h

description: gene expression data from CAKI-1 treated with 1000nM vorinostat for 6h


title: wild-type 1 cell N702/S501

description:
processed data column: A2
ERCC spike-in control added


title: wild-type 1 cell N701/S501

description:
processed data column: A1
ERCC spike-in control added


title: MDA-MB-231 H3K4me3 at 100 cells replicate 1


title: CAKI-1_vorinostat_1000nM_2h

description: gene expression data from CAKI-1 treated with 1000nM vorinostat for 2h


title: Single-cell Pituitary cells in RNA-Best A7

description:
featureCounts.txt
cell 5

value: pituitary, primary cells, untreated


title: CAKI-1_vorinostat_1000nM_24h

description: gene expression data from CAKI-1 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3H12

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv

data_processing:
NextSeq 500
bcl2fastq v.20.0.422
cutadapt v.1.15
BWA-mem v0.7.16
python  3.6
samtools v1.8
bedtools v2.26.0
picard v2.9.0
Genome_build: Tb427v9
Supplementary_files_format_and_content: Feature counts of all RNA seq data from 1, 10 and 50 cells can be found in Feature_counts_scRNAseq_set_two.tsv. Single-cell samples with appropriate coverage (more than 500 genes captured with at least 10 read counts per gene) were considered for VSG expression analysis and are listed in VSG_raw_counts_scRNAseq_set_two.tsv.
Supplementary_files_format_and_content: txt; scRNA-seq normalization and quantification from scRNA-seq II

extract_protocol:
Cells were sorted and lysed in lysis buffer ((0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water) and RNA was extracted from 1, 10 and 50 cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) with a fourth of the recommended volumes of reagents. PCR amplification was performed for 26 cycles.
Libraries were constructed using a Nextera XT kit (Illumina) according to the manufacturer's instructions, but using only one fourth of the recommended voulmens and 1 ng of cDNA.


title: MDA-MB-231 ChILT-DNA at 100 cells replicate 2

value: ChILT-DNA


title: Single-cell Pituitary cells in RNA-Best A6

description:
featureCounts.txt
cell 4

value: Grown as pituitary cells for 4 days, then trypsinized and resuspended in RNA-Best


title: CAKI-1_vorinostat_0nM_2h

description: gene expression data from CAKI-1 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3H11

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: Single-cell Pituitary cells in RNA-Best A3

description:
featureCounts.txt
cell 3


title: CAKI-1_vorinostat_0nM_6h

description: gene expression data from CAKI-1 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T3H9


title: Single-cell Pituitary cells in RNA-Best A1

description:
featureCounts.txt
cell 1


title: Pituitary_RNAlater

description:
featureCounts.txt
pituitaries were acutely dissociated

data_processing:
The RNA-seq fastq files were aligned with STAR v2.5.1b with the mouse GENCODE annotation.
featureCounts v1.5.0-p1 is used to summarize the reads for all genes and samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all genes and for all samples

source_name: pituitary

extract_protocol:
RNA was extracted using an Agilent Absolutely RNA 96 kit.
RNA-seq libraries were prepared using the Illumina Truseq LT mRNA kit (Illumina, #RS-122-2101).

treatment_protocol: Primary pituitary cell samples were immediately stored in either RNA-Best or RNAlater.

value: pituitary

value: RNAlater


title: CAKI-1_vorinostat_0nM_24h

description: gene expression data from CAKI-1 treated with 0nM vorinostat for 24h


title: MDA-MB-231 ChILT-DNA at 100 cells replicate 1


title: MCF-7 H3K4me3 at 1k cells replicate 1


title: BT-549_vorinostat_5000nM_2h

description: gene expression data from BT-549 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line BT-549

value: Breast


title: MCF-7 ChILT-DNA at 100 cells replicate 2


title: Single-cell Pituitary cells in RNA-Best A2

description:
featureCounts.txt
cell 2


title: MCF-7 H3K4me3 at 1k cells replicate 2


title: ΔH3.V/ΔH4.V_T3H10

value: Lister 427 MITat 1.2

value: bloodstream form


title: MCF-7 H3K4me3 at 10k cells replicate 2


title: ΔH3.V/ΔH4.V_T3H8


title: RNA-Best3

description: featureCounts.txt

source_name: pituitary gonadotrope-derived cells

growth_protocol: LβT2 cells were cultured at 37°C in DMEM (Mediatech, Herndon, VA) supplemented with 10% fetal bovine serum (FBS; Gemini, Calabasas, CA) in a humidified air atmosphere of 5% CO2.

extract_protocol:
Cells were then trypsinized, pelleted at 2,200 rpm for 5 min, and either directly lysed in a guanidium thiocyanate RNA lysis buffer (4 M guanidium thiocyanate, 25 mM sodium citrate pH 7, 0.5% sarcosyl [N-lauroyl sarcosine], and 0.1 M 2-mercaptoethanol), or resuspended in 400 μl RNA-Best (proprietary reagent, but available upon request). RNA-Best-preserved cells were stored at 4°C for at least 4 days, then spun down at 2,200 rpm for 5 min; pelleted cells were then lysed in 360 μl guanidium thiocyanate RNA lysis buffer. RNA was extracted using the “Absolutely RNA 96 microprep” kit (Agilent, Santa Clara, CA) according to the manufacturer's protocol, and resuspended in elution buffer (Agilent, Santa Clara, CA).
RNA-seq libraries were prepared with 2 μg of RNA using the Illumina Truseq LT mRNA kit (Illumina, #RS-122-2101).

treatment_protocol: LβT2 cells were seeded at 350,000 cells per well in 12-well plates in DMEM/10% FBS. After 2 days of culture at 37°C/5% CO2, cells were treated with 2 nM GnRH for 40 min.

value: immortalized gonadotrope cells

tag: passages

value: anterior pituitary

value: GnRH

value: RNA-Best


title: ΔH3.V/ΔH4.V_T3H7


title: BT-549_vorinostat_1000nM_2h

description: gene expression data from BT-549 treated with 1000nM vorinostat for 2h

value: member of the NCI-60 cell line panel


title: BT-549_vorinostat_5000nM_6h

description: gene expression data from BT-549 treated with 5000nM vorinostat for 6h


title: Pituitary_RNA-Best


title: RNA-Best2

description: featureCounts.txt


title: BT-549_vorinostat_5000nM_24h

description: gene expression data from BT-549 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3H6


title: MCF-7 H3K4me3 at 10k cells replicate 1

tag: cell line

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: MCF-7 ChILT-DNA at 100 cells replicate 1

tag: antibody target


title: ΔH3.V/ΔH4.V_T3H3


title: BT-549_vorinostat_1000nM_24h

description: gene expression data from BT-549 treated with 1000nM vorinostat for 24h


title: RNA-Best1

description: featureCounts.txt


title: Fresh3

description: featureCounts.txt

value: fresh


title: Fresh2

description: featureCounts.txt


title: ΔH3.V/ΔH4.V_T3H2


title: HEK-293 cells, standard RIBOseq, rep 1

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description:
standard ribosome profiling from HEK-293 cells
HEK_count_table.txt

data_processing:
Raw reads were processed by removing 5’ adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide (using Trimmomatic v0.36). Reads mapping on rRNAs and tRNAs (downloaded from the SILVA rRNA and the Genomic tRNA databases respectively) were removed. The remaining reads were aligned to the human transcriptome (Ensembl v85, corresponding to GENCODE 25) with Bowtie2 (v2.2.6) employing the default settings. All reads aligning to the very same region were collapsed to avoid potential PCR duplicates, and only strand-specific reads were kept.  The number of ribosome protected fragments was determined with samtools idxstats.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: HEK_count_table.txt: tab-delimited text file including transcript annotation (columns 1-8) and sample-specific counts of aligned reads

molecule: cytoplasmic RNA

source_name: HEK-293 cells, standard ribosome profiling, biological replicate 1

growth_protocol: HEK-293 were seeded at 1.5 × 106 cells/dish  on adherent plates and maintained at 37 °C, 5% CO2 in DMEM with red phenol supplemented with 10% Fetal Bovine Serum (FBS), 2 mM L-glutamine, 100 units/mL penicillin and 100 mg/mL of streptomycin. Cells were grown until 80% of confluence before lysis.

extract_protocol:
Cells were washed at 4°C with PBS complemented with cycloheximide 10 μg/mL and scraped on the plate with 300 μL of lysis buffer (10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 5 U/mL DNAseI, 200 U/mL RNase inhibitor and 10 μg/mL cycloheximide) for each dish. Nuclei and cellular debris were removed by two centrifugations at 18000g, 4°C, 5 min. The lysate was aliquoted and stored at -80°C for not more than a month, avoiding more than one freeze/thaw cycle.
For RiboLace Ribo-Seq, the RNA absorbance of the lysate (at 260 nm) was measured by Nanodrop ND-1000 UV-VIS Spectrophotometer and the lysate diluted to 1.7 a.u. A260/µL with W-buffer (10 mM NaCl, 10 mM MgCl2, 20 µg/mL cycloheximide, 10 mM Hepes, pH 7 in DEPC water). RNase I nuclease (catalog no AM2295, diluted 1:100, µL used for each sample = 1.7 x 0,75) was used to footprint ribosomes for 45 min at 20°C. The reaction was then quenced  with SUPERase●In RNase Inhibitor on ice for 15 min. Then, the reaction was added directly to the RiboLace beads and the suspension incubated on a wheel for at least 1 hour in orbital rotation, 3 rpm at 4°C. After incubation, the tubes were kept on ice on a magnetic stand for 5 min to capture the beads–bounded-ribosomes. The supernatant was discarded (unbound fraction) and beads washed two times with 500 µL of W-buffer. Beads were resuspended in 200 µL of W-buffer containing 20 U SUPERase●In, 1% SDS and treated with 0.1 mg of proteinase K (Euroclone, catalog no. EMR022001) at 37°C for 75 min. Ribosome Protected Fragments (RPFs) were extracted with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and size selected (25-35 nt) by urea-page. RPFs were treated to remove 3’ phosphate, ligated to the 3’ adaptor and purified by UREA page. Ligated RPFs were retrotranscribed and the cDNA circularized. Libraries were finally amplified by PCR using Illumina PCR Primer Index.   Standard ribosome Ribosome profiling was performed as RboLace Ribo-Seq buth without incubation with RiboLace beads. Briefly, CHX-treated cells were lysed with 300 μL of lysis buffer and the cell lysate diluted to 1.7 a.u. A260/µL with W-buffer (10 mM NaCl, 10 mM MgCl2, 20 µg/mL cycloheximide, 10 mM Hepes, pH 7 in DEPC water) to a final volume of 150 µL. RNase I nuclease (catalog no AM2295, diluted 1:100, µL used for each sample = 1.7 x 0,75) was used to footprint ribosomes for 45 min at 20°C. The reaction was then quenced with  SUPERase●In RNase Inhibitor on ice for 15 min. Samples were then incubated with 1% SDS and treated with 0.1 mg of proteinase K (Euroclone, catalog no. EMR022001) at 37°C for 75 min. Ribosome Protected Fragments (RPFs) were extracted with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and size selected (25-35 nt) by urea-page. RPFs were treated to remove 3’ phosphate, ligated to the 3’ adaptor and purified by UREA page. Ligated RPFs were retrotranscribed and the cDNA circularized. Libraries were finally amplified by PCR using Illumina PCR Primer Index.

treatment_protocol: Cells were then treated with 10 µg/mL of cycloheximide (CHX) for 5 min at 37°C before lysis in order to inhibit translation elongation.

tag: cells

tag: rna fraction

value: standard-RIBOseq

tag: replicate


title: ΔH3.V/ΔH4.V_T3H4

tag: strain

tag: genotyope

tag: life cycle stage


title: BT-549_vorinostat_0nM_2h

description: gene expression data from BT-549 treated with 0nM vorinostat for 2h

tag: group

tag: tissue


title: BT-549_vorinostat_0nM_6h

description: gene expression data from BT-549 treated with 0nM vorinostat for 6h


title: BT-549_vorinostat_1000nM_6h

description: gene expression data from BT-549 treated with 1000nM vorinostat for 6h


title: BT-549_vorinostat_0nM_24h

description: gene expression data from BT-549 treated with 0nM vorinostat for 24h


title: Fresh1

description: featureCounts.txt

tag: cell type


title: ΔH3.V/ΔH4.V_T3H5


title: ΔH3.V/ΔH4.V_T3G12


title: HEK-293 cells, RiboLace RIBOseq, rep 1

description:
active ribosome profiling with RiboLace from HEK-293 cells
HEK_count_table.txt

source_name: HEK-293 cells, active ribosome profiling with RiboLace, biological replicate 1

value: RiboLace-RIBOseq


title: cfDNA_HCC_3

city: Beijing

first: Bo

last: He

state: Beijing

address: Yiheyuan Road 5th.

department: School of Life Science

country: China

institute: Peking University

description:
gene_list.txt
This gene list was derived from  all cfDNA samples.

data_processing:
Library strategy: CATCH-Seq
Low-quality bases to be removed and then PCR duplicates were removed. Unique reads were trimmed for the poly-C sequence in the end of reads.
Reads with minimum length of 40 bp were were mapped to the human (hg19) reference genome by bismark(v0.15.0) using options –bowtie2 -N 1 -L 30.
We use deeptools software to generate bigwig file.
The identification of 5hmC-enriched regions (peaks) in each sample was performed using MACS(1.4.2), with the corresponding input sample.
Samtools mpileup (1.2) was used to extract the reads mapping of every nucleotide
5hmC sites with known SNPs (UCSC, Common SNPs (142)) were discarded.
5hmC sites were calculated using scripts.
Differentially modified genes in autosomes between healthy control samples and cancer patients were analysed using DESeq2 package (|FC| >= 1.41 and p.adj =< 0.05).
Genome_build: hg19
Supplementary_files_format_and_content: 5hmC sites in tab-delimited format; peak file in bed format.

source_name: cell-free DNA

growth_protocol: H1 hESCs were maintained on Mitomycin C-treated MEFs in hES Cell culture medium consisting of 80% DMEM/F12 (Invitrogen), 20% Knockout serum replacement (KSR) (Invitrogen), 1% non-essential amino acids,1 mM L-glutamine, 0.1 mM beta-mercaptoethanol (all from Invitrogen) and 4 ng/ml basic fibroblast growth factor bFGF (P&A Biotech).

extract_protocol:
using Universal Genomic DNA Kit (CWBIO) to extract DNA from hESCs.
The AI-labeled DNA were used directly for library preparation with the TELP protocol except PCR amplification.
single strand DNA library construction.

treatment_protocol: 1,DNA was denatured in 0.05 M NaOH (total volume 48.5 μL) for 30 min at 37°C. The reaction was snap cooled on ice-water bath (0 °C) for 5 min. Add 1.5ul 1x oxidant to the denatured DNA sample and briefly mix the reaction. Leave the oxidation reaction on ice for 1 h. The oxidized sample was purified by a Bio-Rad Micro Bio-Spin P-6 SSC column.2,The reaction was performed in a suspension of AI (self-synthesized) in 50 mM ammonium acetate buffer (pH 6.5). The 100ul reaction mixture in 1.5ml Eppendorf tube was incubated in the thermomixer (Eppendorf) for 18 h at 37°C (850 rpm).

value: oxidation, AI labeling

tag: enrichment

value: chemical assisted pulldown with biotin


title: HEK-293 cells, standard RIBOseq, rep 2

source_name: HEK-293 cells, standard ribosome profiling, biological replicate 2


title: LβT2 cells_GnRH

description: RNA-Best

data_processing:
Single-cell RNA-seq data were processed using the Cell Ranger pipeline v1.3, which provides a data matrix of expression for all genes and all cells.
Genome_build: mm10
Supplementary_files_format_and_content: hdf5 matrix file that contains the UMIs of all genes and all cells

extract_protocol:
Cells were then trypsinized, pelleted, resuspended in 1ml RNA-Best, and stored at 4°C for 3 weeks. Next, cells were filtered, counted on a Countess instrument, and the final concentration was set at 1,000 cells/μl in RNA-Best. As a starting point, ~8,000 cells from each sample were loaded into the fluidics chip.
Reverse-transcription was performed in the emulsion and cDNA was amplified for 12 cycles before library construction (Chromium Single Cell 3’ Library and Gel Bead Kit V2 PN-120237). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Library quality control and quantification were assessed by spectrophotometry (Nanodrop), fluorometry (Qubit dsDNA High sensitivity Assay Kit), qPCR (Kapa Library Quantification Kit Illumina Platforms, Kapa Biosystems, #KK4835), and on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit, Agilent). Additionally, the quality of each library was assessed by qPCR of selected genes.
GEM Drop-Seq, Chromium™ Single Cell 3’ Library & Gel Bead Kit v2

treatment_protocol: LβT2 cells were seeded at 350,000 cells per well in 12-well plates in DMEM/10% FBS. After 2 days of culture at 37°C/5% CO2, cells were treated with either vehicle or 2 nM GnRH for 40 min.


title: ΔH3.V/ΔH4.V_T3G11


title: cfDNA_HCC_2


title: ACHN_vorinostat_5000nM_6h

description: gene expression data from ACHN treated with 5000nM vorinostat for 6h

source_name: human tumor cell line ACHN

value: Renal


title: HEK-293 cells, RiboLace RIBOseq, rep 2

source_name: HEK-293 cells, active ribosome profiling with RiboLace, biological replicate 2


title: LβT2 cells_Vehicle

description: RNA-Best

value: Vehicle


title: cfDNA_HCC_1


title: ΔH3.V/ΔH4.V_T3G10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T3G9


title: cfDNA_healthy_3


title: ACHN_vorinostat_5000nM_2h

description: gene expression data from ACHN treated with 5000nM vorinostat for 2h


title: cfDNA_healthy_2


title: ACHN_vorinostat_1000nM_6h

description: gene expression data from ACHN treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T3G8


title: cfDNA_healthy_1


title: ΔH3.V/ΔH4.V_T3H1


title: cpr1 aba1_Rep2

city: Shenzhen

first: Xuemei

last: Chen

state: Guangdong

address: Nanhai Road 3688

institute: Shenzhen University

data_processing:
The clean reads were mapped to the Arabidopsis thaliana genome TAIR10 using the Bowtie program
The small RNA reads were calculated and normalized in RPM (reads per million mapped reads).
Genome_build: Arabidopsis thaliana (assembly TAIR10)
Supplementary_files_format_and_content: wig files with raw coverage without normalization

organism: Arabidopsis thaliana

source_name: 15-day-old seedlings

growth_protocol: All seeds were grown on petri dishes containing 1/2 Murashige and Skoog Basal Medium (Sigma-Aldrich, M5519) plus 2% Sucrose and 0.8% Agar. All plants were grown in growth chambers at 22°C for 16 hrs light and 8 hrs dark cycles.

extract_protocol:
Total RNAs were isolated from 15-day-old seedlings with TRI reagent (Molecular Research Center, TR118).
Total RNA extracted from 15-day-old seedlings of both wild type and mutants. For library construction, 30μg total RNA were resolved on a 15% polyacrylamide gel with 8M urea. Small RNAs in the 15-40 nt size range were recovered as described (Liu et al., 2012). Small RNA libraries were prepared using the library preparation kit (NEB, E7100), and sequenced with an Illumina HiSeq2500 platform at BerryGenomics, China.

value: seedlings

tag: age

tag: genetic background ecotype

value: Col

value: cpr1 aba1


title: ACHN_vorinostat_1000nM_2h

description: gene expression data from ACHN treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3G7

value: Lister 427 MITat 1.2

value: bloodstream form


title: ΔH3.V/ΔH4.V_T3G6


title: cpr1 aba1_Rep1

tag: genotype


title: Col_Rep2

value: wildtype Col


title: hESC_10ng_rep2_input

description: 10ng.rep2.peaks.bed: derived from hESC_10ng_rep2_input.fastq.gz and hESC_10ng_rep2_output.fastq.gz.

value: human embryonic stem cell

tag: treatment


title: Col_Rep1


title: ΔH3.V/ΔH4.V_T3G5


title: ΔH3.V/ΔH4.V_T3G4


title: hESC_10ng_rep2_output


title: ACHN_vorinostat_1000nM_24h

description: gene expression data from ACHN treated with 1000nM vorinostat for 24h


title: ACHN_vorinostat_0nM_6h

description: gene expression data from ACHN treated with 0nM vorinostat for 6h


title: ACHN_vorinostat_0nM_2h

description: gene expression data from ACHN treated with 0nM vorinostat for 2h


title: amiR-SUL snc1-1_Rep3

value: amiR-SUL snc1-1


title: hESC_10ng_rep1_output

description:
10ng.rep1.peaks.bed: derived from hESC_10ng_rep1_input.fastq.gz and hESC_10ng_rep1_output.fastq.gz.
hESC_10ng.bw' was derived from hESC_10ng_rep1_output.fastq.gz.


title: ACHN_vorinostat_5000nM_24h

description: gene expression data from ACHN treated with 5000nM vorinostat for 24h

value: member of the NCI-60 cell line panel


title: ACHN_vorinostat_0nM_24h

description: gene expression data from ACHN treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3G3


title: ΔH3.V/ΔH4.V_T3G2


title: amiR-SUL snc1-1_Rep2


title: ΔH3.V/ΔH4.V_T3G1


title: amiR-SUL#_Rep3

description: Control for amiR-SUL snc1-1

value: amiR-SUL


title: A549_vorinostat_5000nM_6h

description: gene expression data from A549 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line A549

value: Lung


title: amiR-SUL snc1-1_Rep1


title: hESC_50ng_rep2_output

description: 50ng.rep2.peaks.bed: derived from hESC_50ng_rep2_input.fastq.gz and hESC_50ng_rep2_output.fastq.gz.


title: hESC_10ng_rep1_input

description: 10ng.rep1.peaks.bed: derived from hESC_10ng_rep1_input.fastq.gz and hESC_10ng_rep1_output.fastq.gz.


title: hESC_50ng_rep1_output

description:
50ng.rep1.peaks.bed: derived from hESC_50ng_rep1_input.fastq.gz and hESC_50ng_rep1_output.fastq.gz.
hESC_50ng.bw' was derived from hESC_50ng_rep1_output.fastq.gz.


title: hESC_50ng_rep2_input


title: amiR-SUL#_Rep2

description: Control for amiR-SUL snc1-1


title: hESC_100ng_rep2_output

description:
100ng.rep2.peaks.bed: derived from hESC_100ng_rep2_input.fastq.gz and hESC_100ng_rep2_output.fastq.gz.
5hmC sites was derived from  hESC_100ng_rep1_output.fastq.gz and hESC_100ng_rep2_output.fastq.gz.


title: hESC_50ng_rep1_input

description: 50ng.rep1.peaks.bed: derived from hESC_50ng_rep1_input.fastq.gz and hESC_50ng_rep1_output.fastq.gz.


title: A549_vorinostat_1000nM_6h

description: gene expression data from A549 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T3F10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: amiR-SUL sup-B65_Rep3

value: amiR-SUL sup-B65


title: A549_vorinostat_5000nM_24h

description: gene expression data from A549 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3F9


title: hESC_100ng_rep2_input

description: 100ng.rep2.peaks.bed: derived from hESC_100ng_rep2_input.fastq.gz and hESC_100ng_rep2_output.fastq.gz.


title: A549_vorinostat_5000nM_2h

description: gene expression data from A549 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3F11


title: A549_vorinostat_1000nM_24h

description: gene expression data from A549 treated with 1000nM vorinostat for 24h


title: A549_vorinostat_1000nM_2h

description: gene expression data from A549 treated with 1000nM vorinostat for 2h


title: amiR-SUL sup-B65_Rep2


title: A549_vorinostat_0nM_6h

description: gene expression data from A549 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T3F12


title: ΔH3.V/ΔH4.V_T3F8


title: hESC_100ng_rep1_output

description:
100ng.rep1.peaks.bed: derived from hESC_100ng_rep1_input.fastq.gz and hESC_100ng_rep1_output.fastq.gz.
hESC_100ng.bw' was derived from hESC_100ng_rep1_output.fastq.gz
5hmC sites was derived from  hESC_100ng_rep1_output.fastq.gz and hESC_100ng_rep2_output.fastq.gz.


title: A549_vorinostat_0nM_2h

description: gene expression data from A549 treated with 0nM vorinostat for 2h


title: amiR-SUL sup-B65_Rep1


title: amiR-SUL#_Rep1

description: Control for amiR-SUL snc1-1


title: amiR-SUL_Rep3

description: Control for amiR-SUL sup-B65


title: GBM cells

data_processing:
Single-cell RNA-seq data were processed using the dropseqtools 1.13 (http://mccarrolllab.com/dropseq/), which provides a data matrix of expression for all genes and all cells.
See mini_dropseq.README
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all cells and genes that has at least one read in one of the cells

source_name: Brain

growth_protocol: Human cortical tissue was obtained from epilepsy or glioblastoma surgical resections.

extract_protocol:
The tissue was divided into several pieces, one of which was used for fresh dissociation and RNA-Best stabilization. The fresh tissue was first dissociated into SC suspension by mechanical and enzymatic papain dissociation as previously described (Tome-Garcia 2017 PMID 28434940 and https://bio-protocol.org/e2659) and then stabilized in RNA-Best at 100,000 cells per ml. SC Mini Drop-seq experiments were performed similarly as described in Macosko et al. (2015 PMID 26000488). Ficoll PM-400 was added to the cell buffer to match fluid viscosity of the aqueous flows.
Nextera library preparation was performed as in the original manuscript by Macosko et al. (2015 PMID 26000488).

value: brain, cortex

tag: tissue status

value: Tumor

value: Dissociated  cells from biopsy

tag: stabilized with

value: Dissociated and stabilized in RNA-Best, stored in the fridge for 14 days


title: ΔH3.V/ΔH4.V_T3F7


title: hESC_100ng_rep1_input

description:
100ng.rep1.peaks.bed: derived from hESC_100ng_rep1_input.fastq.gz and hESC_100ng_rep1_output.fastq.gz.
hESC_100ng_input.bw' was derived from hESC_100ng_rep1_input.fastq.gz

value: oxidation, AI labeling


title: PAP + ATP + LiCl rep 3

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

data_processing:
Base calling was performed using standard Illumina settings by the ACRF Biomolecular Resource Facility at the Australian National University
Raw sequenced reads were trimmed for adaptor sequences and low-quality base-calls using sickle and scythe.
Adapter and quality trimmed reads were aligned to the TAIR10 genome using Subjunc
Transcript abundance (CPM) was assigned to genic features based on the TAIR10 annotation using featureCounts
Transcripts were filtered based on abundance (CPM > 0) as well as those derived from rRNA and plastids.
Genome_build: TAIR10
Supplementary_files_format_and_content: CSV file containing CPM values for each sample

source_name: 35 day old Col-0 Ler leaf tissue

growth_protocol: Plants were grown as per Pornsiriwong W et al (2017) A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination. eLife 6, 1–34. Seeds were germinated in soil and kept at 4 ̊C for three days to synchronize germination. Seedlings were grown at 100–150 mmol photons m-2 s-1, 12 hr photoperiod, 21–23 ̊C and 50–55% humidity.

extract_protocol:
RNA was extracted from petiole-fed leaves using Trizol reagent (Life Technologies) using a procedure adapted from Allen et al. (2010). Briefly, up to100mg of snap-frozen tissue wa sground then lysed in 1mL of Trizol with gentle agitation. Following 5 min incubation at room temperature, the organic phase was extracted twice with 200 mL of chloroform. The RNA was precipitated by addition of an equal volume of 100% isopropanol and incubated overnight at –20°C. RNA was recovered by centrifugation (20,000 relative centrifugal force) at 4°C for 20min and washed with 70% ethanol, air-dried at room temperature, resuspended in water or Tris buffer, and stored at –80°C
The Illumina TruSeq V2 Kit was used for mRNA-seq library preparation as per the manufacturer’s instructions (TruSeq User Guide Revision D) using 1/3 reaction volume as documented here (https://goo.gl/iwAE9R).

treatment_protocol: Petiole feeding of pharmacological treatments were performed as per Pornsiriwong W et al (2017) A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination. eLife 6, 1–34. 100 mM LiCl, or 1 mM ATP, 1 mM or 100 mM PAP (Sigma-Aldrich) alone or in differ- ent combinations were prepared in infiltration buffer (1 mM PIPES KOH pH 6.0, 1 mM Sodium cit- rate, 1 mM KCl, 15 mM Sucrose) modified from a cordycepin infiltration buffer (Seeley et al., 1992). Solutions were administered through the petioles of excised leaves.

value: Col-0 Ler F1 hybrid

value: Excised leaf tissue

value: 35 days

value: 100 μM PAP + 100 mM LiCl + 1 mM ATP


title: ΔH3.V/ΔH4.V_T3F6

value: Lister 427 MITat 1.2

value: bloodstream form


title: amiR-SUL_Rep2

description: Control for amiR-SUL sup-B65

value: seedlings

value: Col


title: ΔH3.V/ΔH4.V_T3F5


title: Cortex cells

value: Healthy tissue

value: Dissociated and stabilized in RNA-Best, stored in the fridge for 6 days


title: A549_vorinostat_0nM_24h

description: gene expression data from A549 treated with 0nM vorinostat for 24h

value: member of the NCI-60 cell line panel

value: Lung


title: ΔH3.V/ΔH4.V_T3F3

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: amiR-SUL_Rep1

description: Control for amiR-SUL sup-B65

value: amiR-SUL


title: ΔH3.V/ΔH4.V_T3F4


title: PAP + ATP + LiCl rep 1


title: ΔH3.V/ΔH4.V_T3F2


title: HA

city: East Geelong

first: Siying

last: Ye

state: VIC

address: AAHL CSIRO, 5 Portarlington Road

country: Australia

institute: Deakin University

data_processing:
After confirming checksums and assessing raw data quality of the FASTQ files with FASTQC, RNA-Seq reads were processed according to standard Tuxedo pipeline protocols, using the annotated human genome (GRCh37, downloaded from Illumina iGenomes) as a reference. Briefly, raw reads for each sample were mapped to the human genome using TopHat2, sorted and converted to SAM format using Samtools and then assembled into transcriptomes using Cufflinks. Cuffmerge was used to combine transcript annotations from individual samples into a single reference transcriptome, and Cuffquant was used to obtain per-sample read counts. Cuffdiff was then used to conduct differential expression analysis. All programs were run using recommended parameters, however the reference gtf file provided to cuffmerge was first edited using a custom python script to exclude lines containing features other than exon/cds, and contigs other than chromosomes 1-22, X, Y.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: H5N1-infected human ATII cells treated with 1mM apocynin dissolved in DMSO

growth_protocol: Lung tissue with visible bronchi was removed and perfused with abundant PBS and submerged in 0.5% Trypsin-EDTA (Gibco) twice for 15 min at 37°C. The partially digested tissue was sliced into sections and further digested in Hank's Balanced Salt Solution (HBSS) containing elastase (12.9 units/mL; Roche Diagnostics) and DNase I (0.5 mg/mL; Roche Diagnostics) for 60 min at 37°C. Single cell suspensions were obtained by filtration through a 40 μm cell strainer and cells (including macrophages and fibroblasts) were allowed to attach to a tissue-culture treated Petri dishes in a 1:1 mixture of DMEM/F12 medium (Gibco) and small airway growth medium (SAGM) medium (Lonza) containing 5% fetal calf serum (FCS) and 0.5 mg/mL DNase I for 2 hours at 37°C. The non-adherent cells, including ATII cells, were collected and subjected to centrifugation at 300 g for 20 min on a discontinuous Percoll density gradient (1.089 and 1.040 g/mL). Purified ATII cells from the interface of two density gradients was collected, washed in HBSS, and re-suspended in SAGM medium supplemented with 1% charcoal-filtered FCS (Gibco) and 100 units/mL penicillin and 100 µg/mL streptomycin (Gibco), prior to plating on polyester Transwell inserts (0.4 μm pore; Corning) coated with type IV human placenta collagen (0.05 mg/mL; Sigma) at 300,000 cells/cm2. Cells were then cultured under liquid-covered conditions in a humidified incubator (5% CO2, 37°C) and growth medium was changed every 48 hours.

extract_protocol:
Total RNA was extracted from cells using a RNeasy Mini kit (Qiagen). Influenza-infected cells were washed with PBS three times and cells lysed with RLT buffer supplemented with β-mercaptoethanol (10 μL/mL; Gibco). Cell lysates were homogenized with QIAshredder columns followed by on-column DNA digestion with the RNase-Free DNase Set (Qiagen), and RNA extracted according to manufacturer’s instructions. Initial QC was conducted to ensure that the quantity and quality of RNA samples for HiSeq analysis met the following criteria; 1) RNA samples had OD260/280 ratios between 1.8 and 2.0 as measured with NanoDropTM Spectrophotometer (Thermo Scientific); 2) Sample concentrations were at a minimum of 100 ng/μl; 3) RNA was analyzed by agarose gel electrophoresis. RNA integrity and quality were validated by the presence of the sharp clear bands of 28S and 18S ribosomal RNA, with a 28S:18S ratio of 2:1, along with the absence of genomic DNA and degraded RNA.
TruSeq RNA libraries (designated insert size) were prepared for sequencing by Macrogen Korea.
Illumina HiSeq 2000 Sequencing System, 100bp paired-end sequencing with designated insert size (100 bp)

treatment_protocol: For influenza virus infection, ATII cells from three donors were infected on the apical side with H5N1 at a MOI of 2 for 24 hours in serum-free SAGM medium supplemented with 0.3% bovine serum albumin (BSA) containing 1 mM apocynin dissolved in DMSO or 1% DMSO vehicle control. Uninfected ATII cells incubated in media containing 1% DMSO were used as a negative control. Briefly, culture media was removed and cells were washed with warm PBS three times followed by inoculation with virus for 1 hour. Virus was then removed and cells were washed with warm PBS three times, and incubated in the appropriate fresh serum-free culture media containing 0.3% BSA at 37℃. Uninfected and infected cells were processed identically. RNA were extracted from cells using a RNeasy Mini kit (Qiagen) and submitted for HiSeq analysis (Illumina HiSeq 2000 Sequencing System, 100bp paired-end sequencing).

value: ATII cells isolated from normal human lung tissue

tag: avian influenza h5n1 infection

value: Infected

tag: apocynin treatment

value: Treated


title: PAP + ATP rep 2

value: 100 μM PAP + 1 mM ATP


title: PAP + ATP rep 3

value: Col-0 Ler F1 hybrid


title: PAP + ATP rep 1

value: Excised leaf tissue


title: HD

source_name: H5N1-infected human ATII cells treated with 1% DMSO

value: Untreated


title: ΔH3.V/ΔH4.V_T3F1

source_name: single cell


title: PAP + LiCl rep 3

value: 35 days

value: 100 μM PAP + 100 mM LiCl


title: pTPR1-TPR1-HA_Rep3

data_processing:
The data analysis was performed the PIHSDA pipeline (https://github.com/grubbybio/PIHSDA).
Clean reads were trimmed to remove adapter sequences and mapped to Arabidopsis genome TAIR 10 using HISAT2 with default settings.
Transcript levels were calculated in RPM (reads per million total read counts) by uniquely mapping.
Gene expression levels were normalized and differentially expressed genes (DEGs) were calculated with the cut off of P < 0.01 and fold change of 1.5 using DEseq2.
Genome_build: Arabidopsis thaliana (assembly TAIR10)
Supplementary_files_format_and_content: Text files include raw read count from exon or intron of the gene. The length = gene length.

extract_protocol:
Total RNAs were isolated from 15-day-old seedlings with TRI reagent (Molecular Research Center, TR118).
Total RNA extracted from 15-day-old seedlings of both wild type and mutants were sent to Novogene, China, for mRNA-seq library construction and the libraries were sequenced on an Illumina Hiseq X10 platform to generate single-end reads of 150bp in length.

value: seedling

value: 15 days


title: PAP + ATP + LiCl rep 2

value: 100 μM PAP + 100 mM LiCl + 1 mM ATP


title: total RNA, serum starved MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved, total RNA
MCF7_fpkm_table.txt
total_STARV_2

data_processing:
Fastq files were checked for quality control with FastQC. Reads generated from each sample were aligned to the human genome with Tophat (version 2.0.14), using the Gencode 22 transcript annotation as transcriptome guide. All programs were used with default settings. Mapped reads were assembled into transcripts guided by reference annotation (Gencode 22) with Cufflinks (version 2.2.1). Expression levels were quantified by Cufflinks with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: a tab-delimited text file including including gene annotations (columns 1-3) and sample-specific FPKM values

source_name: MCF7 cells, serum starved, total RNA, biological replicate 2

growth_protocol: MCF7 cells were seeded at 1.5 × 10^6 cells/dish and left until they reached 80% of confluence. After treatments, cells were then treated with 10 µg/mL of cycloheximide (CHX) for 5 min at 37°C before lysis in order to inhibit translation elongation. Cells were washed at 4°C with PBS complemented with cycloheximide 10 μg/mL and scraped on the plate with 300 μL of lysis buffer (10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 5 U/mL DNAseI, 200 U/mL RNase inhibitor, 1 mM dithiothreitol and 10 μg/mL cycloheximide) for each dish. Nuclei and cellular debris were removed by two centrifugations at 18000g, 4°C, 5 min. RNA absorbance was measured (260 nm) by Nanodrop ND-1000 UV-VIS Spectrophotometer before use or storage. The lysate was aliquoted and stored at -80°C for not more than a month, avoiding more than one freeze/thaw cycle.

extract_protocol:
RNA was extracted by acidic-phenol chloroform separation. The quality of the RNA samples was assessed using Agilent Bioanalyzer 2100 and Nanodrop ND-1000 Spectrophotometer (Thermo Scientific).
Whole transcriptome library preparation was performed starting from 1 µg of total RNA with RIN ≥ 8. Following enrichment of poly-A containing mRNA molecules using poly-dT oligo-attached magnetic beads, all recovered RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit (Illumina #FC-122-1001 #FC-122-1002) and the protocol v2 Rev. C. Completed libraries were evaluated by DNA quantification and Bioanalyzer analysis (mean fragment length = 274 bp), and then submitted for sequencing. RNA-seq was constructed with barcodes to allow multiplexing of 12 samples per lane. Sequencing was carried out by the NGS UniTrento Facility on Illumina HiSeq 2000 using the protocol HCS 1.5.15.1 in single reads.

treatment_protocol: For EGF treatment, after seeding, MCF7 cells were maintained in culture until 80% of confluence before replacing the media with DMEM-red phenol supplemented with 0.5% FBS, 2 mM L-glutamine, 100 units/mL penicillin and 100 mg/mL of streptomycin (starvation condition). Cells were kept in starvation for 12 hours at 37 °C, 5% CO2 before adding EGF (1 µg/µL) for 4 hours. For the starvation condition, cells were kept in starvation for 12 hours at 37 °C, 5% CO2 before lysis.

tag: cell line

value: serum starvation

tag: rna fraction

value: total RNA


title: ΔH3.V/ΔH4.V_T3E12

tag: strain

value: Lister 427 MITat 1.2

value: bloodstream form


title: total RNA, serum starved MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved, total RNA
MCF7_fpkm_table.txt
total_STARV_1

source_name: MCF7 cells, serum starved, total RNA, biological replicate 1

tag: replicate


title: pTPR1-TPR1-HA_Rep2

value: Col


title: PAP + LiCl rep 2


title: ΔH3.V/ΔH4.V_T3E11

tag: genotyope

tag: life cycle stage


title: pTPR1-TPR1-HA_Rep1

tag: tissue


title: ΔH3.V/ΔH4.V_T3E9


title: total RNA, EGF treated MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated, total RNA
MCF7_fpkm_table.txt
total_EGF_1

source_name: MCF7 cells, serum starved and EGF treated, total RNA, biological replicate 1

value: serum starvation + EGF treatment


title: total RNA, EGF treated MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated, total RNA
MCF7_fpkm_table.txt
total_EGF_2

source_name: MCF7 cells, serum starved and EGF treated, total RNA, biological replicate 2


title: LiCl rep 1

value: 100 mM LiCl


title: LiCl rep 3


title: PAP rep 3

value: 100 μM PAP


title: total RNA, control MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, control, total RNA
MCF7_fpkm_table.txt
total_CTRL_1

source_name: MCF7 cells, control, total RNA, biological replicate 1

value: control


title: PAP + LiCl rep 1

value: Col-0 Ler F1 hybrid


title: ΔH3.V/ΔH4.V_T3E10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: total RNA, control MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, control, total RNA
MCF7_fpkm_table.txt
total_CTRL_2

source_name: MCF7 cells, control, total RNA, biological replicate 2


title: Col__Rep3

value: wildtype


title: Col__Rep


title: ΔH3.V/ΔH4.V_T3E8


title: cpr1 aba1_Rep3

value: cpr1 aba1


title: Col__Rep1


title: ND

source_name: uninfected human ATII cells treated with 1% DMSO (vehicle control)

tag: cell type

value: ATII cells isolated from normal human lung tissue

value: Uninfected

value: Untreated


title: ΔH3.V/ΔH4.V_T3E6


title: cpr1 aba1_Rep2

value: seedling

value: 15 days


title: riboLace, serum starved MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved, riboLace
MCF7_fpkm_table.txt
ribolace_STARV_1

data_processing:
Library strategy: RiboLace Ribo-Seq
Fastq files were checked for quality control with FastQC. Reads generated from each sample were aligned to the human genome with Tophat (version 2.0.14), using the Gencode 22 transcript annotation as transcriptome guide. All programs were used with default settings. Mapped reads were assembled into transcripts guided by reference annotation (Gencode 22) with Cufflinks (version 2.2.1). Expression levels were quantified by Cufflinks with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: a tab-delimited text file including including gene annotations (columns 1-3) and sample-specific FPKM values

source_name: MCF7 cells, serum starved, riboLace, biological replicate 1

value: serum starvation

value: riboLace


title: PAP rep 2

value: Excised leaf tissue

value: 35 days


title: riboLace, EGF treated MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated, riboLace
MCF7_fpkm_table.txt
ribolace_EGF_2

source_name: MCF7 cells, serum starved and EGF treated, riboLace, biological replicate 2


title: cpr1 aba1_Rep1

value: Col


title: LiCl rep 2


title: ΔH3.V/ΔH4.V_T3E5

value: Lister 427 MITat 1.2

value: bloodstream form


title: ATP rep 3

value: 1 mM ATP


title: PAP rep 1

value: 100 μM PAP


title: ΔH3.V/ΔH4.V_T3E3


title: ΔH3.V/ΔH4.V_T3E4


title: riboLace, EGF treated MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated, riboLace
MCF7_fpkm_table.txt
ribolace_EGF_1

source_name: MCF7 cells, serum starved and EGF treated, riboLace, biological replicate 1

value: serum starvation + EGF treatment


title: Col_Rep2

source_name: 15-day-old seedlings

value: wildtype


title: ΔH3.V/ΔH4.V_T3E7


title: ATP rep 2

value: Col-0 Ler F1 hybrid


title: ΔH3.V/ΔH4.V_T3E2


title: riboLace, control MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, control, riboLace
MCF7_fpkm_table.txt
ribolace_CTRL_1

source_name: MCF7 cells, control, riboLace, biological replicate 1

value: control


title: ATP rep 1


title: ΔH3.V/ΔH4.V_T3E1


title: riboLace, serum starved MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved, riboLace
MCF7_fpkm_table.txt
ribolace_STARV_2

source_name: MCF7 cells, serum starved, riboLace, biological replicate 2


title: polysomal RNA, serum starved MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved, polysomal RNA
MCF7_fpkm_table.txt
polysomal_STARV_2

source_name: MCF7 cells, serum starved, polysomal RNA, biological replicate 2

value: polysomal RNA


title: control rep 2

source_name: 35 day old Col-0 Ler leaf tissue

value: buffer only


title: polysomal RNA, serum starved MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved, polysomal RNA
MCF7_fpkm_table.txt
polysomal_STARV_1

source_name: MCF7 cells, serum starved, polysomal RNA, biological replicate 1


title: ΔH3.V/ΔH4.V_T3D12

source_name: 50 cells


title: control rep 3


title: ΔH3.V/ΔH4.V_T3D11

source_name: single cell


title: control rep 1


title: polysomal RNA, EGF treated MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated, polysomal RNA
MCF7_fpkm_table.txt
polysomal_EGF_2

source_name: MCF7 cells, serum starved and EGF treated, polysomal RNA, biological replicate 2


title: ΔH3.V/ΔH4.V_T3D10


title: Col_Rep3

value: seedling


title: MCF-7 H3K4me3 ChIP at 100k cells replicate 2

data_processing:
The raw sequence reads were aligned to the mouse and human reference genomes (GRCm38 and GRCh38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained.
The bigWig files were generated using bamCoverage command of deepTools (ver. 2.4.2) with the option: --smoothLength x --binSize y, where x and y are specified in the file names.
The csv countmatrix files were generated with multiBamSummary with the option bins -bs 4000 (or 10000).
ChILT peaks were generated with Homer findPeaks with the options -style histone -style histone -gsize 3e9 -size 4000 -regionRes 1 -minDist 1 -fdr 0.2.
ChIP peaks were generated with MACS2 (ver. 2.1.1) with the options -g hs -q 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all.
Genome_build: GRCm38/mm10 and GRCh38/hg38
Supplementary_files_format_and_content: bigWig files contain signal data for visualization via tools such as the Integrative Genomics Viewer, csv files include comma-delimited matrices, the bed file contains the peak data for C2C12, MCF-7 and MDA-MB-231 data.

source_name: Immortal cell line

tag: antibody target

tag: primary antibody

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: riboLace, control MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, control, riboLace
MCF7_fpkm_table.txt
ribolace_CTRL_2

source_name: MCF7 cells, control, riboLace, biological replicate 2


title: K562 H3K4me3 at 1k cells replicate 2

extract_protocol:
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.


title: ΔH3.V/ΔH4.V_T3D9

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: DK3_2

city: Fuzhou

first: Qihua

last: Lin

state: Fujian

address: No.102, Xiyuan Road,  Xindian Town, Jinan District

department: Tropical and subtropical fruit tree Research Laboratory

institute: Fruit Research Institute of Fujian Academy of Agricultural Sciences

data_processing: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality

organism: Morella rubra

source_name: fruits

extract_protocol:
flash frozen on dry ice, and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fruits

tag: colour

value: black

tag: age


title: BDK3_2

value: pink


title: BDK3_3


title: polysomal RNA, control MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, control, polysomal RNA
MCF7_fpkm_table.txt
polysomal_CTRL_2

source_name: MCF7 cells, control, polysomal RNA, biological replicate 2

tag: treatment


title: DK3_1


title: polysomal RNA, EGF treated MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated, polysomal RNA,
MCF7_fpkm_table.txt
polysomal_EGF_1

source_name: MCF7 cells, serum starved and EGF treated, polysomal RNA, biological replicate 1


title: Col_Rep1

value: 15 days

tag: genetic background ecotype

tag: genotype


title: ΔH3.V/ΔH4.V_T3D8


title: polysomal RNA, control MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, control, polysomal RNA
MCF7_fpkm_table.txt
polysomal_CTRL_1

source_name: MCF7 cells, control, polysomal RNA, biological replicate 1


title: BDK3_1


title: K562 H3K4me3 at 100 cells replicate 2


title: ΔH3.V/ΔH4.V_T3D7


title: BDK2_3


title: mP beads, serum starved MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved, mP beads
MCF7_fpkm_table.txt
mP_STARV_2

source_name: MCF7 cells, serum starved, mP beads, biological replicate 2

value: serum starvation

value: mP beads


title: DK3_3


title: mP beads, serum starved MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved, mP beads
MCF7_fpkm_table.txt
mP_STARV_1

source_name: MCF7 cells, serum starved, mP beads, biological replicate 1


title: BDK2_2


title: mP beads, EGF treated MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated
MCF7_fpkm_table.txt
mP_EGF_2

source_name: MCF7 cells, serum starved and EGF treated, mP beads, biological replicate 2


title: BDK2_1


title: ΔH3.V/ΔH4.V_T3D5

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv

value: Lister 427 MITat 1.2

value: bloodstream form


title: mP beads, EGF treated MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, serum starved and EGF treated, mP beads
MCF7_fpkm_table.txt
mP_EGF_1

source_name: MCF7 cells, serum starved and EGF treated, mP beads, biological replicate 1


title: ΔH3.V/ΔH4.V_T3D3


title: ΔH3.V/ΔH4.V_T3D4


title: BDK1_3


title: ΔH3.V/ΔH4.V 0 cells N7012/S501

description:
processed data column: A12
no ERCC spike-in control added

data_processing:
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15
Read alignment: BWA-mem v0.7.16
scRNAseq analysis: python  3.6
samtools v1.8
bedtools v2.26.0
picard v2.9.0
Genome_build: Tb427v9
Supplementary_files_format_and_content: txt; scRNA-seq normalization and quantification from scRNA-seq I

organism: other sequences

source_name: negative contol

extract_protocol:
Cells were sorted and lysed in lysis buffer ((0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water) and RNA was extracted from 1 and 50 cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) with a fourth of the recommended volumes of reagents. PCR amplification was performed for 26 cycles.
Libraries were constructed using a Nextera XT kit (Illumina) according to the manufacturer's instructions, but using only one fourth of the recommended voulmens and 1 ng of cDNA.

tag: strain:

tag: genotyope:

tag: life cycle stage:


title: BDK1_1


title: MCF-7 H3K4me3 at 100 cells replicate 1

extract_protocol:
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.

tag: cell line


title: K562 H3K4me3 at 1k cells replicate 1


title: ΔH3.V/ΔH4.V_T3D1

tag: strain


title: wild-type 0 cell N706/S501

description:
processed data column: A6
no ERCC spike-in control added


title: mP beads, control MCF7 cells, rep 1

description:
cytoplasmic RNA
MCF7 cells, control, mP beads
MCF7_fpkm_table.txt
mP_CTRL_1

source_name: MCF7 cells, control, mP beads, biological replicate 1

tag: rna fraction

tag: replicate


title: BDK1_2


title: mP beads, control MCF7 cells, rep 2

description:
cytoplasmic RNA
MCF7 cells, control, mP beads
MCF7_fpkm_table.txt
mP_CTRL_2

source_name: MCF7 cells, control, mP beads, biological replicate 2


title: K562 H3K4me3 at 100 cells replicate 1


title: Cingulate gyrus tissue from tissue donor PD 1 [small RNA-seq]

status: Public on Oct 08 2018

city: Regensburg

first: Markus

last: Schulze

address: Franz-Josef-Strauss Allee 11

department: Neuropathology

institute: University Hospital Regensburg

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into .fastq files by the CASAVA1.8.2 software
Fastq files were imported to the commercially available Genomatix mining station with the data import and validation tool ver. 2.2.2
Fastq files were mapped against small RNA libraries (mature miRNAs and piRNAs, annotation based on ElDorado 6-2015) allowing one mismatch with the commercially available Genomatix mapper ver. 3.7.6.3
Count tables were created for each small RNA type (piRNA, mature miRNA) with the small RNA workflow available in the Genomatix Genome Analyzer v3.51106 based on the annotation ElDorado 6-2015. Normalized expression values were calculated by dividing the counts per small RNA by the sum of all small RNA counts in a sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited file with counts and normalized expression values, columns are column1: miRNA_Genomatix_ID column2: miRNA_Name column3: miRNA_Count column4:  miRNA_NE column5: empty column6: piRNA_Genomatix_ID column 7: piRNA_Name column8:piRNA_Count  column9: piRNA_NE

extract_protocol:
Small RNA libraries were prepared from 1 µg total RNA containing small RNAs with the TrueSeq Small RNA kit (Illumina) according to the manufacturer´s instructions. Briefly, a 3´adapter was added to the RNA, denaturation was performed for two minutes at 70°C and afterwards the mixture was put on ice immediately. Then, the adapter was ligated with a T4 RNA Ligase2 deletion mutant (epicentre) for 1h at 28°C. Then the reaction was stopped with stop solution for 15 minutes at 28°C, the previously denatured 5´ adapter was added together with ATP and T4 DNA Ligase and ligated to the RNA for 1h at 28°C. After that, cDNA synthesis was performed with super script II and Illumina supplied dNTPs for 1h at 50°C. Afterwards, the cDNA was amplified and indexed with the primers and PCR mix supplied in the kit (eleven cycles of denaturation at 98°C for 10 seconds,annealing 60°C for 30 seconds and extension at 72°C for 15 seconds with a final extension at 72 for 10 minutes) and size selection was performed on 5% TBE acrylamide gels (Bio-Rad, munich, Germany). Here, the region marked by Illumina´s custom ladder between 145 bp and 160 bp were cut out and pooled for sequencing. The gel was homogenized by centrifugation at 20000 xg through a gel breaker tube (Bio-Cat) and 300 µl ultrapure H2O were added to elute the DNA O/N in a DNA LoBind tube (Eppendorf). The following day, the gel debris was separated from the water by centrifugation for 10 seconds at 600 xg through a 5µm filter tube (Bio-Cat). Then, 2 µl glycogen (CALBIOCHEM), 30 µl sodium acetate (Thermo-Fisher Scientific), 2 µl 0.1x pellet paint and 975 µl prechilled 100% ethanol were added and the mixture was incubated for 20 minutes at -80°C. Then, the library was pelleted by centrifugation for 20 minutes at 4°C and 20000 xg, washed with 70% ethanol and recentrifuged for 5 minutes. Finally, the ethanol was removed, the pellet dried for five minutes at 37°C and resuspended in 15 µl ultrapure water.
High throughput sequencing of small RNA

tag: patient status/id

value: tissue donor PD 1

tag: type

value: brain tissue

tag: molecule subtype

value: total RNA containing small RNA


title: Cingulate gyrus tissue from tissue donor PD 7 [small RNA-seq]

value: tissue donor PD 7


title: Cingulate gyrus tissue from tissue donor PD 5 [small RNA-seq]

value: tissue donor PD 5


title: Cingulate gyrus tissue from tissue donor PD 8 [small RNA-seq]

value: tissue donor PD 8


title: Cingulate gyrus tissue from tissue donor control 8 [small RNA-seq]

value: tissue donor control 8


title: Cingulate gyrus tissue from tissue donor PD 2 [small RNA-seq]

value: tissue donor PD 2


title: Cingulate gyrus tissue from tissue donor PD 3 [small RNA-seq]

value: tissue donor PD 3


title: MCF-7 H3K4me3 at 100 cells replicate 2

tag: antibody target

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: Cingulate gyrus tissue from tissue donor control 6 [small RNA-seq]

value: tissue donor control 6


title: Cingulate gyrus tissue from tissue donor control 4 [small RNA-seq]

value: tissue donor control 4


title: Cingulate gyrus tissue from tissue donor control 5 [small RNA-seq]

value: tissue donor control 5


title: ΔH3.V/ΔH4.V_T3D6

extract_protocol:
Cells were sorted and lysed in lysis buffer ((0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water) and RNA was extracted from 1, 10 and 50 cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) with a fourth of the recommended volumes of reagents. PCR amplification was performed for 26 cycles.
Libraries were constructed using a Nextera XT kit (Illumina) according to the manufacturer's instructions, but using only one fourth of the recommended voulmens and 1 ng of cDNA.

tag: genotyope

tag: life cycle stage


title: ΔH3.V/ΔH4.V_T3D2


title: Cingulate gyrus tissue from tissue donor control 3 [small RNA-seq]

value: tissue donor control 3


title: Differentiated neurons established from PD patient 5 clone 1 [small RNA-seq]

value: PD patient 5

value: differentiated midbrain neuron


title: Differentiated neurons established from PD patient 3 clone 1 [small RNA-seq]

value: PD patient 3


title: Cingulate gyrus tissue from tissue donor control 1 [small RNA-seq]

value: tissue donor control 1


title: Differentiated neurons established from PD patient 1 clone 1 [small RNA-seq]

value: PD patient 1


title: Cingulate gyrus tissue from tissue donor PD 6 [small RNA-seq]

value: tissue donor PD 6

value: brain tissue

value: total RNA containing small RNA


title: Cingulate gyrus tissue from tissue donor control 7 [small RNA-seq]

value: tissue donor control 7


title: Cingulate gyrus tissue from tissue donor PD 4 [small RNA-seq]

value: tissue donor PD 4


title: Differentiated neurons established from PD patient 2 clone 2 [small RNA-seq]

value: PD patient 2


title: Differentiated neurons established from control patient 5 clone 1 [small RNA-seq]

value: control patient 5


title: Differentiated neurons established from control patient 3 clone 1 [small RNA-seq]

value: control patient 3


title: Differentiated neurons established from control patient 2 clone 2 [small RNA-seq]

value: control patient 2


title: Differentiated neurons established from control patient 4 clone 1 [small RNA-seq]

value: control patient 4


title: Embryonic stem cell line HUES6 [small RNA-seq]

source_name: Embryonic stem cell line HUES6

value: embryonic stem cell


title: Human induced pluripotent stem cell line established from PD patient 8 clone 2 [small RNA-seq]

value: PD patient 8

value: induced pluripotent stem cell


title: Cingulate gyrus tissue from tissue donor control 2 [small RNA-seq]

value: tissue donor control 2


title: Embryonic stem cell line H9 [small RNA-seq]

source_name: Embryonic stem cell line H9


title: Human induced pluripotent stem cell line established from PD patient 4 clone 2 [small RNA-seq]

value: PD patient 4


title: Human induced pluripotent stem cell line established from PD patient 4 clone 3 [small RNA-seq]


title: Human induced pluripotent stem cell line established from PD patient 5 clone 3 [small RNA-seq]

value: PD patient 5


title: Human induced pluripotent stem cell line established from PD patient 5 clone 1 [small RNA-seq]


title: Human induced pluripotent stem cell line established from control patient 6 clone 1 [small RNA-seq]

value: control patient 6


title: Human induced pluripotent stem cell line established from control patient 6 clone 2 [small RNA-seq]


title: Human induced pluripotent stem cell line established from control patient 5 clone 1 [small RNA-seq]


title: Human induced pluripotent stem cell line established from PD patient 1 clone 1 [small RNA-seq]

value: PD patient 1


title: Human induced pluripotent stem cell line established from PD patient 4 clone 1 [small RNA-seq]