title: RNA-Seq_MCF7_siCTL_CTL_rep2

value: ethanol+siCTL


title: H2BK123ub ChIP-exo 5.0 LGE1-WT Replicate 1

status: Public on Jan 17 2020

type: SRA

city: State College

first: Chitvan

last: Mittal

state: PA

address: 453 North Frear, University Park

department: BMB

country: USA

institute: Pennsylvania State University

description: LGE1-WT_H2BK123ub ChIP-exo 5.0 rep1

library_source: genomic

data_processing:
High-throughput DNA sequencing in paired end mode was performed with Illumina NextSeq 500.
Sequence reads were aligned to the yeast genome (sacCer3) using bwa-mem (v0.7.9a). Reference : https://arxiv.org/pdf/1303.3997.pdf
Aligned reads obtained were filtered to remove PCR duplicates and non-unique alignments.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph, deduplicated BAM files aligned to sacCer3

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: yeast strains were grown to an O.D600 of ~0.8 at 30°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were purified using appropriate antibody.
Libraries were prepared as described in PMID: 30030442

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: antibody

value: H2BK123ub (Cell Signaling, Catalogt# 5546s, Lot#5)

tag: strain

tag: cell description


title: K562_vector_control [K562Vec-0]

city: Tsuruoka

first: Junko

last: Murai

state: Yamagata

address: 246-2 Kakuganji Mizugami

country: Japan

institute: Keio University

data_processing:
Raw reads were trimmed using trimmomatic (v0.39).
Trimmed reads were aligned to the hg19 genome version using the bowtie2 (v2.2.6) aligner.
Aligned reads were sorted using samtools (v1.8), duplicate reads were marked with picard-tools (v2.9.2).
ATAC-seq peaks were called using MACS (v2.1.2) with the "--nomodel", "--shift -37" and "--extsize 73" settings, filtering out peaks with >0.01 FDR p--value.
Alignment files were converted to bigwig format using the BAMscale cov (v0.1) program with default settings (genome scaling).
Genome_build: Human - hg19
Supplementary_files_format_and_content: Bigwig coverage track files for visualization were created with BAMscale
Supplementary_files_format_and_content: Narrow peaks were called using MACS peak caller

organism: Homo sapiens

growth_protocol: All cells were cultured in RPMI1640 medium supplied with 10% FBS

extract_protocol:
Fifty thousand cells were treated with DMSO or camptothecin for the indicated time. To prepare nuclei, cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately following the nuclei preparation, the pellet was re-suspended in the transposase reaction mix [25 μl 2x TD buffer, 2.5 μl Transposase (Illumina) and 22.5 μl of nuclease free water], and incubated for 30 minutes at 37 °C. Directly following transposition, the sample was purified using a DNA Clean and Concentrator-5 (ZYMO RESEARCH) and eluted with 25 μl of DNA elution buffer. Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermo-cycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. We amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Syber Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. Libraries were amplified for a total of 10–12 cycles and purified using a PCRClean DX yielding a final library concentration of ~30 nM in 20 μl.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).

treatment_protocol: Camptothecin or DMSO was added to the medium and cells were incubated for different time

tag: cell line

tag: cell type

value: Lymphoblast

tag: genotype/variation

value: vector control

tag: treatment

value: DMSO treatment

tag: molecule subtype

value: PCR amplified DNA


title: RNA-Seq_MCF7_siMED12-2_E2_rep1

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

library_source: transcriptomic

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19

molecule: total RNA

source_name: breast cancer

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality. RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: MCF7 cells were maintained in stripping medium (phenol red free) for three days before treating with or without estrogen (E2, 10-7 M) for 6h.

value: estrogen+siRNA


title: H2B ChIP-exo 5.0 BY4741 Replicate 2

description: BY4741_H2B ChIP-exo 5.0 rep2

value: H2B (Abcam, Catalog# ab1790, Lot# GR310932-1)

value: GRF88, MATa his4-38, S288C background


title: LoVo ChIP-seq IgG rep2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description: LoVo (male) cells were cultured in DMEM media supplemented with 10% FBS, 1% L-glutamine, and 1% Nonessential amino acids.

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 or mm10 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
SLAM-seq was processed using SLAMdunk.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: SLAM-seq: tab-delimited text file include raw counts for each Sample

source_name: LoVo

growth_protocol: Media for all cell lines was supplemented with 100 IU/ml Penicillin and 100 μg/ml streptomycin.

extract_protocol:
ChIP-seq assays (performed as described in Weissmiller, et. al. Nat Commun,10, Article number: 2014 (2019)): Briefly, cross-linking was carried out with 0.75% formaldehyde (Sigma-Aldrich; in PBS pH 7.4) at room temperature for 10 minutes. The reaction was quenched with 125 mM glycine for 10 minutes at room temperature, after which cells were washed twice with ice-cold PBS. Nuclei were prepared by incubating cells in Nuclear Lysis Buffer A (1 M HEPES pH 7.9, 1 M KCl, 0.5 M EDTA, 0.4% NP-40, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 5 minutes on ice, after which they were collected by centrifugation. Nuclei were then lysed in Formaldehyde Lysis Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1% SDS, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 15 minutes on ice. Chromatin was sheared by 17–24 minute sonication (BioRuptor UCD-200, Diagenode; on highest setting, alternating between 30 seconds on and 30 seconds off) to yield a mean chromatin size of ~250 bp. After sonication, debris was cleared by centrifugation, and sheared chromatin diluted 10-fold in Formaldehyde Lysis Buffer without SDS. Chromatin from 107 cells was used per immunoprecipitation reaction. Immunoprecipitation reactions were performed with either 0.8 µL of IgG or 4.0 µL of α-WDR5 antibody as indicated. Immune complexes were recovered on Protein A agarose beads (Roche) and washed sequentially with Low Salt Wash buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), High Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), LiCl Wash buffer (10 mM Tris pH 8.9, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail) and TE (10 mM Tris pH 8.0, 1 mM EDTA, supplemented with PMSF and Complete Protease Inhibitor Cocktail). Protein–DNA complexes were de-crosslinked overnight at 65°C in 50 µL Elution Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.1% SDS, and 20 µg Proteinase K (740506, Clontech).  ---   RNA-seq assays: CHP134 cells were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ.   ---   SLAM-seq assays: Nascent RNA was labeled using the SLAMseq Kinetics Kit–Anabolic Kinetics Module (061, Lexogen).  LoVo cells were pretreated with 25 uM C6, C6nc, or 0.1% DMSO prior to a three hour labeling with 1 mM 4-Thiouridine (S4U). Following the manufacturer's instructions, total RNA was isolated, alkylated with iodoacetamide, flash frozen, and shipped to Lexogen for analysis.
For analysis of ChIP-Seq, de-crosslinked DNA samples from three ChIP reactions were pooled (a total of 3 x 107 cellular equivalents per sample), and DNA purified by phenol-chloroform extraction and recovered by ethanol precipitation. Indexed libraries were then made using the DNA Ultra II Library Prep Kit for Illumina (E7645, New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subject to 75 bp single sequencing according to the manufacturer’s protocol (Illumina NextSeq500). Sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Shared Resource. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.   ---   RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. RNA-Seq for CHP-134 cells was completed with three biological replicates.   ---    For analysis of SLAM-seq: After quality control analyses, libraries were prepared (250 ng RNA per sample) using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the User Guide (015UG009V0251) recommendations. Sequencing was performed by Lexogen on an Illumina NextSeq 500 system, using the SR75 High Output Kit. The SLAMdunk analysis pipeline (34) was used to analyze SLAMseq sequencing data. SLAM-Seq completed with three biological replicates.

value: LoVo

tag: chip antibody

value: Cell Signaling IgG (2729S)


title: LoVo ChIP-seq WDR5 rep1

value: Cell Signaling WDR5 (D9E1I)


title: SLFN11KO_CPT4h [CB45_KO_4]

data_processing:
Raw reads were trimmed using trimgalore (v0.6.2) and trimmomatic (v0.39).
Trimmed reads were aligned to the hg19 genome version using bwa mem (v0.7.17) aligner.
Aligned reads were sorted using samtools (v1.8), duplicate reads were marked with picard-tools (v2.9.2).
ATAC-seq peaks were called using MACS (v2.1.2) with the "--nomodel", "--shift -37" and "--extsize 73" settings, filtering out peaks with >0.01 FDR p--value.
Alignment files were converted to bigwig format using the BAMscale cov (v0.1) program with default settings (genome scaling).
Genome_build: Human - hg19
Supplementary_files_format_and_content: Bigwig coverage track files for visualization were created with BAMscale
Supplementary_files_format_and_content: Narrow peaks were called using MACS peak caller

value: CCRF-CEM

value: T lymphoblast

value: SLFN11 gene knockout

value: Camtothecin 100 nM treatment for 4h


title: LoVo ChIP-seq IgG rep1


title: H2B ChIP-exo 5.0 BY4741 Replicate 1

description: BY4741_H2B ChIP-exo 5.0 rep1


title: SLFN11KO_CPT2h [CB45_KO_2]

value: Camtothecin 100 nM treatment for 2h


title: RNA-Seq_MCF7_siMED12-2_CTL_rep1

value: ethanol+siRNA


title: H2B ChIP-exo 5.0 WAC-Lge1CC Replicate 2

description: WAC-lge-CC_H2B ChIP-exo 5.0 rep2


title: H2B ChIP-exo 5.0 WAC-Lge1CC Replicate 1

description: WAC-lge-CC_H2B ChIP-exo 5.0 rep1


title: LoVo ChIP-seq WDR5 rep2


title: RNA-Seq_MCF7_siCARM1-2_E2_rep1


title: H2B ChIP-exo 5.0 LAF1-Lge1CC Replicate 2

description: Laf1-IDR-lge1-CC_H2B ChIP-exo 5.0 rep2


title: SLFN11KO_control [CB45_KO]


title: Parent_CPT4h [CCRF_WT4]

value: wild-type


title: Parent_CPT2h [CCRF_WT2]


title: DU145 CPT 6h 3

type: RNA

description: SLFN11-proficient parent

hyb_protocol: Four replicates of each group were hybridized to Affymetrix human Gene ST 2.0 GeneChip (Platform GPL19251) in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.

scan_protocol: Wash and stain were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000 with AutoLoader.

data_processing: Data were collected using Affymetrix AGCC software. Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.  Genes that are up- or down-regulated more than 2 fold and with a p<0.001 were considered significant.

label: biotin

source_name: DU145 CPT treatment for 6h

label_protocol: 100 ng of RNA was reverse transcribed, amplified and sense strand cDNA was fragmented and labeled using Affymetrix’s GeneChip WT Plus Reagent Kit following manufacturer’s suggested protocol.

extract_protocol: Total RNA were extracted using TRIzol reagent (Invitrogen), followed by further purification using PureLink RNA Mini Kit (Life Technology) with DNase treatment (Qiagen).

treatment_protocol: Camptothecin (250 nM) or DMSO was added to the medium and cells were incubated for 6 hours or 12 hours

value: prostate DU145

value: camptothecin for 6 hrs

tag: sample type

value: SLFN11-proficient parent


title: RNA-Seq_MCF7_siCARM1-2_CTL_rep1


title: RNA-Seq_MCF7_siMED12-1_CTL_rep1


title: RNA-Seq_MCF7_siCARM1-1_E2_rep1


title: Scc9 Control 3

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with NextSeq Control/RTA v2 and FASTQ file generation with bcl2fastq v2.20.0.422
Quality and adapter trimming with Cutadapt 1.16/1.17 (command line parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Read alignment to GENCODE GRCh38.p12 Human genome using STAR version 2.5.2b with default parameters and including GENCODE Human Release 28 transcript annotations to support the mapping
Reads aligning to protein coding gene annotations from GENCODE Human Release 28 were quantified using BEDTools (bedtools intersect -S -wa –c –a GENE_ANNOTATION_FILE –b BAM_FILE)
Differentially expressed genes between HGF-treated and untreated libraries for each cell line were identified using DESeq2 version 1.22.1
Genome_build: GENCODE GRCh38.p12
Supplementary_files_format_and_content: Character (TAB) seperated value file containing mRNA abundance measurements

source_name: HNSCC cell line SCC-9

growth_protocol: HNSCC cell lines were obtained from ATCC. Detroit 562 and FaDu were cultured in MEM-α, and SCC-9 in DMEM F12 (+HEPES) containing 400ng/ml Hydrocortison (Thermo Fisher Scientific).

extract_protocol:
Cells were centrifuged for 5 min at 2000 rpm and 4°C. Total RNA was isolated using a commercially available kit (RNeasy Mini Kit, Qiagen). Cells were lysed using 350 µl RLT lysis buffer, and syringe and needle were used for homogenization. Further processing was performed as described in instructions provided by the manufacturer.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA kit (Illumina) with 600 ng total RNA as input for mRNA capture with oligo-dT beads.

treatment_protocol: Cells were seeded in 6-well plates (750000 cells/well) and on the next day were treated with 50 ng/ml HGF or were left untreated. After 16h treatment, cells were washed with 2 ml cold PBS and detached from the plate using 1 ml of 10% Trypsin-EDTA (Merck).

value: HNSCC cell line SCC-9


title: FaDu HGF 3

source_name: HNSCC cell line FaDu

value: 50 ng/ml HGF

value: HNSCC cell line FaDu


title: Parent_control [CCRF_WT]

value: DMSO treatment

value: PCR amplified DNA


title: Detroit HGF 3

source_name: HNSCC cell line Detroit 562

value: HNSCC cell line Detroit 562


title: Scc9 HGF 3


title: SLFN11KO_CHK1i6h [9_CB45_CHK1i_6h_S79]

extract_protocol:
Fifty thousand cells were treated with DMSO, prexasertib or camptothecin for the indicated time. To prepare nuclei, cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately following the nuclei preparation, the pellet was re-suspended in the transposase reaction mix [25 μl 2x TD buffer, 2.5 μl Transposase (Illumina) and 22.5 μl of nuclease free water], and incubated for 30 minutes at 37 °C. Directly following transposition, the sample was purified using a DNA Clean and Concentrator-5 (ZYMO RESEARCH) and eluted with 25 μl of DNA elution buffer. Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermo-cycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. We amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Syber Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. Libraries were amplified for a total of 10–12 cycles and purified using a PCRClean DX yielding a final library concentration of ~30 nM in 20 μl.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).

treatment_protocol: Prexasertib, camptothecin or DMSO was added to the medium and cells were incubated for different time

value: Prexasertib 100 nM for 6h


title: RNA-Seq_MCF7_siCARM1-1_CTL_rep1


title: SLFN11KO_CHK1i4h [8_CB45_CHK1i_4h_S78]

value: CCRF-CEM

value: Prexasertib 100 nM for 4h


title: H2B ChIP-exo 5.0 Lge1Δ1-80 Replicate 2

description: lge1D1-80_H2B ChIP-exo 5.0 rep2

value: H2B (Abcam, Catalog# ab1790, Lot# GR310932-1)


title: SLFN11KO_CPT4h [10_CB45_CPT_4h_S80]

value: T lymphoblast

value: SLFN11 gene knockout

value: Camtothecin 100 nM for 4h


title: H2B ChIP-exo 5.0 LGE1-CC Replicate 1

description: lge1-CC_H2B ChIP-exo 5.0 rep1


title: RNA-Seq_MCF7_siMED12-1_E2_rep1

value: estrogen+siRNA


title: RNA-Seq_MCF7_siCTL_E2_rep1

value: estrogen+siCTL


title: Scc9 HGF 2


title: SLFN11KO_CHK1i2h [7_CB45_CHK1i_2h_S77]

value: Prexasertib 100 nM for 2h


title: H2B ChIP-exo 5.0 LAF1-Lge1CC Replicate 1

description: Laf1-IDR-lge1-CC_H2B ChIP-exo 5.0 rep1


title: H2B ChIP-exo 5.0 Lge1Δ1-80 Replicate 1

description: lge1D1-80_H2B ChIP-exo 5.0 rep1


title: RNA-Seq_MCF7_siCTL_CTL_rep1

value: ethanol+siCTL


title: H2B ChIP-exo 5.0 LGE1-CC Replicate 2

description: lge1-CC_H2B ChIP-exo 5.0 rep2


title: Scc9 Control 2

value: HNSCC cell line SCC-9


title: FaDu Control 3


title: SLFN11KO_control [6_CB45_con_S76]

value: DMSO


title: H2B ChIP-exo 5.0 NLS-Lge1 IDR Replicate 2

description: NLS-lge1-IDR_H2B ChIP-exo 5.0 rep2


title: Parent_CPT4h [5_CEM_CPT_4h_S75]

value: wild-type


title: FaDu Control 2

value: HNSCC cell line FaDu


title: H2B ChIP-exo 5.0 NLS-Lge1 IDR Replicate 1

description: NLS-lge1-IDR_H2B ChIP-exo 5.0 rep1


title: Parent_CHK1i6h [4_CEM_CHK1i_6h_S74]

value: PCR amplified DNA


title: Detroit HGF 2

value: 50 ng/ml HGF

value: HNSCC cell line Detroit 562


title: H2B ChIP-exo 5.0 lge1Δ Replicate 2

description: lge1D_H2B ChIP-exo 5.0 rep2


title: Parent_CHK1i4h [3_CEM_CHK1i_4h_S73]

value: CCRF-CEM


title: FaDu HGF 2


title: H2B ChIP-exo 5.0 lge1Δ Replicate 1

description: lge1D_H2B ChIP-exo 5.0 rep1


title: Detroit Control 3


title: Scc9 HGF 1


title: Parent_control [1_CEM_con_S71]


title: Parent_CHK1i2h [2_CEM_CHK1i_2h_S72]


title: H2B ChIP-exo 5.0 lge1Δbre1Δ Replicate 1

description: lge1D-bre1D_H2B ChIP-exo 5.0 rep1


title: EV, sheep milk rep3

city: Beijing

first: suyu

last: quan

address: Yuanmingyuan West Road No.2, Haidian Distric

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

description:
1_all_miRNA_counts_Sheep.txt
2_all_miRNA_TPM_Sheep.txt
E3

data_processing:
Cutadapt (version 1.14), fastx_toolkit (version 0.0.13) and NGSQCToolkit (version 2.3.3) were used to get clean reads.
Clean reads were matched with Rfam (version 10.0), and rRNA, snRNA, cis-reg, tRNA and other specific sequences were annotated.
The transcripts were filtered using bowtie.
MiRBase (version 22.0) was used for miRNA alignment to annotate known miRNAs.
Novel miRNA prediction of unannotated sequences was performed with miRDeep2. Novel miRNA secondary structure prediction was performed using RNAfold.
Genome_build: GCF_002742125.1
Supplementary_files_format_and_content: The TPM (transcript per million) metric represented the miRNA expression level.

organism: Ovis aries

source_name: milk  EV

growth_protocol: The milk  EV-miRNAs of 3 Ordos fine wool sheep were analyzed in this study and compared with that of Holstein cows in our prior study.

extract_protocol:
Total Exosome Isolation kit (from other body fluids) (Invitrogen, Catalog Number: 4484453) was used for the isolation of milk EVs. The miRNeasy Mini Kit (QIAGEN, Catalog Number: 217004) was used to extract EV-miRNAs.
TruSeq Small RNA Sample Prep Kits (no. RS-200-0012, Illumina), Qubit dsDNA Assay Kit (no. Q328520, Life Technologies), Qubit RNA Assay Kit (no. Q32852, Life Technologies), SuperScript II Reverse Transcriptase (no.18064-014, Invitrogen) and DNA loading dye (no.LC6678, Invitrogen) were utilized in this step, following the manufacturer’s instructions. Briefly, 3' adapter and 5' adapter were ligated to the end of the RNA molecules. Then the libraries were reverse transcribed and PCR amplified subsequently. The cDNA constructs were purified and recovered, and the libraries was checked and normalized eventually.

treatment_protocol: The milk  came form Ordos fine wool sheep.

tag: breed

value: Ordos fine wool sheep

tag: tissue

value: milk

tag: developmental stage

value: female, mid lactation

value: EV


title: H2B ChIP-exo 5.0 LGE1-WT Replicate 2

description: LGE1-WT_H2B ChIP-exo 5.0 rep2

value: H2B (Abcam, Catalog# ab1790, Lot# GR310932-1)


title: Scc9 Control 1


title: EV, sheep milk rep2

description:
1_all_miRNA_counts_Sheep.txt
2_all_miRNA_TPM_Sheep.txt
E2


title: FaDu HGF 1


title: H2B ChIP-exo 5.0 LGE1-WT Replicate 1

description: LGE1-WT_H2B ChIP-exo 5.0 rep1


title: SLFN11KO_CPT4h_3 [CB45_CPT4h_18_S55]

data_processing:
Raw reads were trimmed using trimgalore (v0.6.2) and trimmomatic (v0.39).
Reads were aligned using the STAR aligner (v2.5.4a) in 2-pass mode using the hg19 genome and gencode v19 gene annotation.
Duplicate reads were marked using picard-tools (v2.9.2).
Gene expression raw read counts were quantified using TPMcalculator (v0.0.1).
Genome_build: Human - hg19
Supplementary_files_format_and_content: Quantified gene expression quantified by TPMcalculator.

extract_protocol:
Total RNA were extracted using TRIzol reagent (Invitrogen), followed by further purification using PureLink RNA Mini Kit (Life Technology) with DNase treatment (Qiagen).
RNA quality and quantity were analyzed with 2100 Expert (Agilent). RIN (the RNA Integrity Number) of all samples were above 8.0. RNA-Seq samples were pooled and sequenced on one paired-end run, which was conducted on HiSeq4000 with HiSeq3000/4000 chemistry.

treatment_protocol: Camptothecin (100 nM) or DMSO was added to the medium and cells were incubated for different time

value: T lymphoblast

value: SLFN11 gene knockout

value: Camptothecin 100 nM treatment for 4h


title: PAOLB2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

data_processing:
We use Rockhopper for alignment and the complete analysis of data
Genome_build: NC_002516.2

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 untreated

extract_protocol:
Single colonies of P. aeruginosa were grown overnight in Luria-Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), Inulin and FOS were added at sub-lethal concentrations to the culture medium. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pseudomonas aeruginosa PAO1 culture


title: Detroit HGF 1


title: Detroit Control 2


title: FaDu Control 1


city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 8

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: SARA group, 6 weeks after parturition Cattle No. 8_Liver tissue

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 500 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the rumen epithelium using Trizo (Invitrogen) according to the manufacturer's instructions.

value: Liver tissue


title: PAOLB1


title: H2B ChIP-exo 5.0 lge1Δbre1Δ Replicate 2

description: lge1D-bre1D_H2B ChIP-exo 5.0 rep2


title: SLFN11KO_CPT4h_2 [CB45_CPT4h_17_S54]


description: Gene expression in the liver tissue of the Non group, 6 weeks after parturition Cattle No. 4

source_name: Non group, 6 weeks after parturition Cattle No. 4_Liver tissue


title: Detroit Control 1


title: SLFN11KO_CPT4h_1 [CB45_CPT4h_16_S53]


description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 7

source_name: SARA group, 6 weeks after parturition Cattle No. 7_Liver tissue


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 6

source_name: Control group, 6 weeks after parturition Cattle No. 6_Liver tissue


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 8

source_name: Control group, 6 weeks after parturition Cattle No. 8_Liver tissue


title: PAOINU2

source_name: PAO1 treated with Inulin


title: hESCs_Scr_H2

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

description:
processed data file:
Boskovic_Table_S2.xlsx

data_processing:
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcodes were separated using Novobarcode
Sequences were aligned to mm10 genome using Tophat/Bowtie2 with default settings
Normalized abundance was generated by RSEM
Genome_build: mm10, hg19 for hESCs
Supplementary_files_format_and_content: Excell sheet with FPKM for all genes

source_name: hESCs_scrambled LNA

growth_protocol: E14 mESCs were maintained on standard mESC protocol from Jaenisch lab. H9 hESCs were maintained feeder free using recommended protocol from StemCell Technologies using mTESR1.

extract_protocol:
RNAs were extracted using Trizol. ATACseq follows standard protocol.
RNAseq libraries were prepared using protocol described in Heyer et a. 2015 NAR. ATAC-seq uses standard tagmentation protocol. Ribomethseq used NEB small-RNA library construction kit.

treatment_protocol: E14 cells were transfected with LNA or siRNAs or small RNAs. hESCs were treated with LNAs using nucleofection

value: Human embryonic stem cells H9

tag: transfected with

value: scrambled LNA


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 5

source_name: Control group, 6 weeks after parturition Cattle No. 5_Liver tissue


description: Gene expression in the liver tissue of the Non group, 6 weeks after parturition Cattle No. 3

source_name: Non group, 6 weeks after parturition Cattle No. 3_Liver tissue


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 7

source_name: Control group, 6 weeks after parturition Cattle No. 7_Liver tissue


title: SLFN11KO_control_3 [CB45_con_15_S52]

value: DMSO treatment


title: PAOINU1


title: EV, sheep milk rep1

description:
1_all_miRNA_counts_Sheep.txt
2_all_miRNA_TPM_Sheep.txt
E1


title: hESCs_Scr_H1


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 8

source_name: SARA group, 2 weeks after parturition Cattle No. 8_Liver tissue


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 7

source_name: SARA group, 2 weeks after parturition Cattle No. 7_Liver tissue


title: SLFN11KO_control_2 [CB45_con_14_S51]


description: Gene expression in the liver tissue of the Control group, 2 weeks after parturition Cattle No. 8

source_name: Control group, 2 weeks after parturition Cattle No. 8_Liver tissue


title: PAOFOS2

source_name: PAO1 treated with FOS


title: Parent_CPT4h_3 [CEM_CPT4h_6_S43]

value: wild-type


title: hESCs_GFP_H1

source_name: hESCs_esiRNA against GFP

value: esiRNA against GFP


title: Mouse 5 infantum infected spleen

city: York

first: Paul

last: Kaye

address: Wentworth way

country: United Kingdom

institute: University of York

description:
Mouse infected with Leishmania
M5IS

data_processing:
Adaptors removed using cutadapt, reads trimmed for quality using sickle, reads aligned using STAR, and mapped to mouse and leishmania infantum and donovani references
HTseq count was used to generate gene expression counts, and differential gene expression calculated using the R package edgeR
Supplementary_files_format_and_content: Data files show the counts and differential expression, and have additional tabs for annotation, parasite and gene calls are given seperately

organism:
Leishmania infantum
Mus musculus

source_name: Spleen

growth_protocol: L. donovani LV9 (MHOM/ET/67/HU3) and L. infantum NCL  were grown as promastigotes in modified Eagle’s medium, designated HOMEM (Thermo Fisher Scientific, Waltham, MA, USA), that was supplemented with 10% heat-inactivated fetal bovine serum (FBS, Thermo Fisher Scientific) and incubated at 25°C. 6-8 week old female BALB/c were used, uninfected mice were used as controls.

extract_protocol:
Tissues were kept in RNAlater, thawed on ice and transferred to 0.6ml lysis buffer. Homogenised for 5 mins, and RNA extracted using the PureLink RNA Mini kit
cDNA was generated using Superscript VILO master mix and made into libraries using the NEB next II ultra kit

value: BALB/C


title: PAOFOS1


title: hESCs_tGG_H1

source_name: hESCs_LNA against tRF-GG

value: LNA against tRF-GG


description: Gene expression in the liver tissue of the Non group, 2 weeks after parturition Cattle No. 4

source_name: Non group, 2 weeks after parturition Cattle No. 4_Liver tissue


title: hESCs_tGG_H2


title: Parent_CPT4h_2 [CEM_CPT4h_5_S42]

value: CCRF-CEM


title: hESCs_tGG_H3

value: Human embryonic stem cells H10


title: Parent_CPT4h_1 [CEM_CPT4h_4_S41]


title: Mouse 4 infantum infected spleen

description:
Mouse infected with Leishmania
M4IS


title: EV, bovine milk rep3

description:
1_all_miRNA_counts_Cow.txt
2_all_miRNA_TPM_Cow.txt
Con3

source_name: milk  EV

value: Holstein cow

value: milk

value: female, mid lactation


title: Mouse 3 infantum infected spleen

description:
Mouse infected with Leishmania
M3IS


title: Parent_control_3 [CEM_con_3_S40]

value: T lymphoblast


description: Gene expression in the liver tissue of the Control group, 2 weeks after parturition Cattle No. 6

source_name: Control group, 2 weeks after parturition Cattle No. 6_Liver tissue


description: Gene expression in the liver tissue of the Control group, 2 weeks after parturition Cattle No. 7

source_name: Control group, 2 weeks after parturition Cattle No. 7_Liver tissue


description: Gene expression in the liver tissue of the Control group, 2 weeks after parturition Cattle No. 5

source_name: Control group, 2 weeks after parturition Cattle No. 5_Liver tissue


title: Parent_control_2 [CEM_con_2_S39]


title: Mouse 2 infantum infected spleen

description:
Mouse infected with Leishmania
M2IS


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 8

source_name: Control group, -3 weeks after parturition Cattle No. 8_Liver tissue


title: Mouse 1 infantum infected speen

description:
Mouse infected with Leishmania
M1IS


title: EV, bovine milk rep1

description:
1_all_miRNA_counts_Cow.txt
2_all_miRNA_TPM_Cow.txt
Con1

value: EV


title: Parent_control_1 [CEM_con_1_2_S6]


title: SLFN11KO_control_1 [CB45_con_13_S50]

value: SLFN11 gene knockout


title: Mouse 5 infantum infected liver

description:
Mouse infected with Leishmania
M5IL

source_name: Liver


title: SLFN11KO_CHK1i6h_3 [CB45_CHK1i6_15_S15]

treatment_protocol: Prexasertib (100 nM) or DMSO was added to the medium and cells were incubated for different time

value: Prexasertib 100 nM treatment for 6h


title: Mouse 5 uninfected spleen

description:
Mouse infected with Leishmania
M5US

organism: Mus musculus


title: Mouse 4 infantum infected liver

description:
Mouse infected with Leishmania
M4IL


title: Mouse 4 uninfected spleen

description:
Mouse infected with Leishmania
M4US


title: Mouse 3 uninfected spleen

description:
Mouse infected with Leishmania
M3US


title: SLFN11KO_CHK1i6h_2 [CB45_CHK1i6_14_S14]


title: SLFN11KO_CHK1i6h_1 [CB45_CHK1i6_13_S13]


description: Gene expression in the liver tissue of the SARA group, -3 weeks after parturition Cattle No. 7

source_name: SARA group, -3 weeks after parturition Cattle No. 7_Liver tissue

value: Liver tissue


title: Mouse 2 uninfected spleen

description:
Mouse infected with Leishmania
M2US


title: EV, bovine milk rep2

description:
1_all_miRNA_counts_Cow.txt
2_all_miRNA_TPM_Cow.txt
Con2


title: Mouse 3 infantum infected liver

description:
Mouse infected with Leishmania
M3IL


title: SLFN11KO_control_3 [CB45_con_12_S12]


description: Gene expression in the liver tissue of the SARA group, -3 weeks after parturition Cattle No. 8

source_name: SARA group, -3 weeks after parturition Cattle No. 8_Liver tissue


title: SLFN11KO_control_2 [CB45_con_11_S11]


title: Mouse 1 uninfected spleen

description:
Mouse infected with Leishmania
M1US


title: Mouse 2 infantum infected liver

description:
Mouse infected with Leishmania
M2IL


title: Mouse 5 uninfected liver

description:
Mouse infected with Leishmania
M5UL


title: Mouse 1 infantum infected liver

description:
Mouse infected with Leishmania
M1IL


title: SLFN11KO_control_1 [CB45_con_10_S10]


description: Gene expression in the liver tissue of the Non group, -3 weeks after parturition Cattle No. 4

source_name: Non group, -3 weeks after parturition Cattle No. 4_Liver tissue


title: Mouse 4 uninfected liver

description:
Mouse infected with Leishmania
M4UL


description: Gene expression in the liver tissue of the Non group, 2 weeks after parturition Cattle No. 3

source_name: Non group, 2 weeks after parturition Cattle No. 3_Liver tissue


title: Parent_CHK1i6h_3 [CEM_CHK1i6_6_S6]


title: Mouse 3 uninfected liver

description:
Mouse infected with Leishmania
M3UL


title: F2 [miRNA]

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts. Then, clean reads were aligned to the reference genome using TopHat v2.0.12.
The read counts for each gene was calculated by HTSeq v0.6.1, and then gene expression levels were estimated using FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values.
sRNA libraries were sequenced using the Illumina Hiseq2500. Raw data of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze the expression and distribution on the reference.miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts.The mapped sRNA tags were also mapped to Rfam, RepeatMasker, to annotate the tags and remove those originating from proteincoding genes, repeat sequences, ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). The remaining unannotated tags were used to predict novel miRNAs by exploring secondary structures, Dicer cleavage sites, and minimum free energies using the miREvo and miRDeep2 software packages.
Genome_build: GigaScience GigaDB   (http://gigadb.org/dataset/100209, Guan et al. 2016).
Supplementary_files_format_and_content: Text file miRNA.readcount (miRNA_name, S1_readcount, S2_readcount, S3_readcount, N1_readcount, N2_readcount, N3_readcount, F1_readcount, F2_readcount, F3_readcount).

organism: Ginkgo biloba

source_name: February of embryo

growth_protocol: Embryo were obtained from healthy G. biloba trees of different development stages growing under natural conditions in Yangzhou University (32°39′N ,119°43′E; Yangzhou, China)

extract_protocol:
Samples were collected in September 2015, November 2015 and February 2016. Total RNAs of embryo were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: embryo


title: F3 [miRNA]


title: F1 [miRNA]


title: Mouse 2 uninfected liver

description:
Mouse infected with Leishmania
M2UL


title: N3 [miRNA]

source_name: November of embryo


title: Parent_CHK1i6h_1 [CEM_CHK1i6_4_S4]


title: Mouse 1 uninfected liver

description:
Mouse infected with Leishmania
M1UL


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 6

source_name: Control group, -3 weeks after parturition Cattle No. 6_Liver tissue


title: Parent_control_3 [CEM_con_3_S3]


description: Gene expression in the liver tissue of the Non group, -3 weeks after parturition Cattle No. 3

source_name: Non group, -3 weeks after parturition Cattle No. 3_Liver tissue


description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 5

source_name: SARA group, 6 weeks after parturition Cattle No. 5_Liver tissue


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 7

source_name: Control group, -3 weeks after parturition Cattle No. 7_Liver tissue


description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 6

source_name: SARA group, 6 weeks after parturition Cattle No. 6_Liver tissue


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 4

source_name: Control group, 6 weeks after parturition Cattle No. 4_Liver tissue


title: Parent_control_2 [CEM_con_2_S2]


description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 3

source_name: SARA group, 6 weeks after parturition Cattle No. 3_Liver tissue


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 5

source_name: Control group, -3 weeks after parturition Cattle No. 5_Liver tissue


title: N1 [miRNA]


title: S3 [miRNA]

source_name: September of embryo


title: Hoxa11-/- WT BMT 385

city: New Haven

first: Myles

middle: H

last: Alderman III

state: Ct

address: 10 Amistad St

department: Cell Biology

institute: Yale University School of Medicine

description: gene_exp.diff,genes.fpkm_tracking, genes.count_tracking

data_processing:
Basecalling was performed by the HiSeq Control Software (2.0), and exported unaligned.
Data was uploaded to PartekFlow, and trimmed by phred score to >19 using the Partek Quality Trim Program.
Trimmed reads were aligned by the STAR aligner v. 2.4.1.
aligned reads were normalized by FPKM and quantified utiilizing Cufflinks 2.2.1 with default settings
Differential transcriptome analysis was performed using Cuffdiff version 2.2.1 with default settings.
Genome_build: Partek mm10_refseq_16_05_02_v2
Supplementary_files_format_and_content: CuffDiff output files (.data,* _tracking) files.

extract_protocol:
Total RNA was extracted using the TRIZOL-chloroform extraction method. RNA was cleaned using the QIAGEN Rneasy Cleanup kit.
Poly-A RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications.

treatment_protocol: B6.129-Hoxa11tm1Dmwe/J knockout, heterozygote, and wildtype animals were given a bone marrow transplant from either wild type or knockout animals. After mating, implantation/decidualization sites were removed on ED 5.5 for RNA-seq analysis.

tag: host hoxa11 genotype

tag: donor hoxa11 genotype

tag: mouse strain


title: Hoxa11-/- WT BMT 99


title: Parent_control_1 [CEM_con_1_S1]


title: Parent_CHK1i6h_2 [CEM_CHK1i6_5_S5]


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 6

source_name: SARA group, 2 weeks after parturition Cattle No. 6_Liver tissue


title: SLFN11KO_CPT4h [CB45_4_H3K27Ac_S3]

data_processing:
Raw reads were trimmed using trimgalore (v0.6.2) and trimmomatic (v0.39).
Trimmed reads were aligned to the hg19 genome version using bwa mem (v0.7.17) aligner.
Aligned reads were sorted using samtools (v1.8), duplicate reads were marked with picard-tools (v2.9.2).
ATAC-seq peaks were called using MACS (v2.1.2) with the brow peak setting, filtering out peaks with >0.1 FDR p--value.
Alignment files were converted to bigwig format using the BAMscale cov (v0.1) program with default settings (genome scaling).
Genome_build: Human - hg19
Supplementary_files_format_and_content: Bigwig coverage track files for visualization were created with BAMscale
Supplementary_files_format_and_content: Broad peaks were called using MACS peak caller

extract_protocol: Twenty-five million CCRF-CEM parental and SLFN11-KO cells were treated or untreated with CPT (100 nM) for 4 hours. ChIP assay was done by following the instruction manual of ChIP-IT Express (Active Motif). Briefly, cells were fixed with 1% formaldehyde in medium for 10 min at room temperature. Fixation was stopped with x1 glycine/PBS. Cells were lysed with lysis buffer with proteinase inhibitor cocktail and PMSF, and homogenized 60 times by small tight homogenizer. Cell pellets were re-suspended with sharing buffer, and sonicated 30 minutes by the following settings: 30 s on, 30 s off, level at H,  (Bioruptor XL). Five %/volume of each sample was saved as input. The left of the supernatant was incubated with 2 g antibody (H3K27ac or normal rabbit IgG) and protein G beads for overnight at 4°C. After reversing cross-link and proteinase K treatment, immunoprecipitated DNA was purified with ChIP DNA Clean & concentrator-5 (ZYMO Research) according to the manual.

treatment_protocol: Camptothecin (100 nM) or DMSO was added to the medium and cells were incubated for the indicated time

value: Camptothecin 100 nM treatment for 4h

value: H3K27ac (abcam ab4729)


title: N2 [miRNA]


title: S2 [miRNA]


title: Hoxa11-/- KO BMT 361


title: S1 [miRNA]


title: SLFN11KO_CPT2h [CB45_2_H3K27Ac_S2]

value: Camptothecin 100 nM treatment for 2h


title: Hoxa11-/- WT BMT 546


description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 4

source_name: SARA group, 6 weeks after parturition Cattle No. 4_Liver tissue


title: SLFN11KO_control [CB45_0_H3K27Ac_S1]

value: DMSO treatment


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 5

source_name: SARA group, 2 weeks after parturition Cattle No. 5_Liver tissue


title: Parent_CPT4h [CEM_4_H3K27Ac_S6]

value: wild-type


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 4

source_name: SARA group, 2 weeks after parturition Cattle No. 4_Liver tissue


title: Parent_CPT2h [CEM_2_H3K27Ac_S5]


title: Hoxa11+/- WT BMT 98


title: DCIS.COM-BCL9 KD -Replicate 2

city: Kansas City

first: Hanan

last: Elsarraj

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

data_processing:
Original image data file from high-throughput sequencing (like Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
STAR software is used to accomplish the mapping.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: DCIS-breast cancer cell line

growth_protocol: Control (NS) and BCL9 KD DCIS.com cells were cultured in T75 flasks as 3 biological replicates . Culture media is DMEM/F12 supplemented with 5% horse serum and 1% antibiotic

extract_protocol:
Lysates were extracted using Qiagen miRNeasy minikit (Qiagen, Cat # 217004) following the manufacturer's protocol.
RNA libraries were prepared for sequencing using NEB Next® Ultra™ RNA Library Prep Kit

treatment_protocol: Cells were transduced with control and BCL9 shRNA lentiviral vectors

value: PLKO.1 BCL9-Knockdown

tag: replicate


title: DCIS.COM-BCL9 KD -Replicate 3


title: DCIS.COM-BCL9 KD -Replicate 1


description: Gene expression in the liver tissue of the Control group, 2 weeks after parturition Cattle No. 4

source_name: Control group, 2 weeks after parturition Cattle No. 4_Liver tissue


title: Parent_control [CEM_0_H3K27Ac_S4]

value: CCRF-CEM


title: Hoxa11+/- KO BMT 272


title: Hoxa11-/- KO BMT 82


description: Gene expression in the liver tissue of the SARA group, -3 weeks after parturition Cattle No. 4

source_name: SARA group, -3 weeks after parturition Cattle No. 4_Liver tissue


description: Gene expression in the liver tissue of the SARA group, -3 weeks after parturition Cattle No. 6

source_name: SARA group, -3 weeks after parturition Cattle No. 6_Liver tissue


title: DCIS.COM-Control-Replicate 2

value: PLKO.1 Non-silencing control


title: Hoxa11+/- KO BMT 271


title: 3mb3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
FastQ files generating by demultiplexing using bcl2fastq v2.17.1.14
Quality control of sequences calculated using FastQC 0.11.5
Read alignment using STAR 2.5 using no more than 2 mismatches
Count reads within genes in Rattus norvegicus v87 using FeatureCounts v1.5.0-p1
Differential expression analysis run using DESeq2 v1.14.1 in R v3.4.2
Genome_build: rn6

organism: Rattus norvegicus

source_name: CD4+ Beta-synuclein reactive T cell

extract_protocol:
Blood and brain were were removed, beta-synuclein T cells were sorted out and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina

tag: strain

value: LEW/Crl

tag: genotype

value: b-syn TCR Tg

value: Meninges Brain


title: Hoxa11+/- WT BMT 589


title: 2mb3


title: DCIS.COM-Control-Replicate 1

tag: cell line


title: 1mb3


title: Hoxa11+/- WT BMT 582


title: Hoxa11+/- KO BMT 86


title: Control 3

city: Shijiazhuang

first: Zhirong

last: Li

state: Hebei

address: 12# Jiankang road, Shijiazhuang, China

department: Research Center

institute: The Fourth Hospital of Hebei Medical University

data_processing:
Illumina NovaSeq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by software FastQC, then mapped to GRCh38.91 whole genome using software Hisat2.
Supplementary_files_format_and_content: gene_expression_processed data.xls

source_name: lung caner cell

growth_protocol: Cell lines were maintained at 37℃ with 5% CO2 with RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Three biological replicates for each pair of SNHG5 or Vector transfected cell were performed. Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeqTM RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide.
The library construction and sequencing was performed at Shanghai Sinomics Corporation.

tag: cell type

value: lung adenocarcinoma

tag: passages


title: Control 2


description: Gene expression in the liver tissue of the Non group, -3 weeks after parturition Cattle No. 2

source_name: Non group, -3 weeks after parturition Cattle No. 2_Liver tissue


title: Hoxa11+/+ WT BMT 376


title: DCIS.COM-Control-Replicate 3

tag: treatment


title: 3br4

value: Brain parenchyma


title: Control 1


title: Hoxa11+/+ WT BMT 218


description: Gene expression in the liver tissue of the SARA group, -3 weeks after parturition Cattle No. 3

source_name: SARA group, -3 weeks after parturition Cattle No. 3_Liver tissue


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 4

source_name: Control group, -3 weeks after parturition Cattle No. 4_Liver tissue


title: 2br4


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 3

source_name: Control group, 6 weeks after parturition Cattle No. 3_Liver tissue


title: Hoxa11+/+ WT BMT 76


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 3

source_name: SARA group, 2 weeks after parturition Cattle No. 3_Liver tissue


title: SNHG5-overexpressed sample3


title: SNHG5-overexpressed sample2


title: 1br4


title: SNHG5-overexpressed sample1


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 2

source_name: Control group, 6 weeks after parturition Cattle No. 2_Liver tissue


title: 2bl3

value: Blood


description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 2

source_name: SARA group, 6 weeks after parturition Cattle No. 2_Liver tissue


title: 1bl3


title: B-bl3-3

value: wt


title: CHP134 RNA-seq dTAG47 rep2

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-dTAG47-count.txt

extract_protocol:
ChIP-seq assays (performed as described in Weissmiller, et. al. Nat Commun,10, Article number: 2014 (2019)): Briefly, cross-linking was carried out with 0.75% formaldehyde (Sigma-Aldrich; in PBS pH 7.4) at room temperature for 10 minutes. The reaction was quenched with 125 mM glycine for 10 minutes at room temperature, after which cells were washed twice with ice-cold PBS. Nuclei were prepared by incubating cells in Nuclear Lysis Buffer A (1 M HEPES pH 7.9, 1 M KCl, 0.5 M EDTA, 0.4% NP-40, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 5 minutes on ice, after which they were collected by centrifugation. Nuclei were then lysed in Formaldehyde Lysis Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1% SDS, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 15 minutes on ice. Chromatin was sheared by 17–24 minute sonication (BioRuptor UCD-200, Diagenode; on highest setting, alternating between 30 seconds on and 30 seconds off) to yield a mean chromatin size of ~250 bp. After sonication, debris was cleared by centrifugation, and sheared chromatin diluted 10-fold in Formaldehyde Lysis Buffer without SDS. Chromatin from 107 cells was used per immunoprecipitation reaction. Immunoprecipitation reactions were performed with either 0.8 µL of IgG or 4.0 µL of α-WDR5 antibody as indicated. Immune complexes were recovered on Protein A agarose beads (Roche) and washed sequentially with Low Salt Wash buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), High Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), LiCl Wash buffer (10 mM Tris pH 8.9, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail) and TE (10 mM Tris pH 8.0, 1 mM EDTA, supplemented with PMSF and Complete Protease Inhibitor Cocktail). Protein–DNA complexes were de-crosslinked overnight at 65°C in 50 µL Elution Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.1% SDS, and 20 µg Proteinase K (740506, Clontech).  ---   RNA-seq assays: CHP134 cells treated with C6 were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ.   ---   SLAM-seq assays: Nascent RNA was labeled using the SLAMseq Kinetics Kit–Anabolic Kinetics Module (061, Lexogen).  LoVo cells were pretreated with 25 uM C6, C6nc, or 0.1% DMSO prior to a three hour labeling with 1 mM 4-Thiouridine (S4U). Following the manufacturer's instructions, total RNA was isolated, alkylated with iodoacetamide, flash frozen, and shipped to Lexogen for analysis.  ---   RNA-seq assays: CHP134 + dTAG-WDR5 cells were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at VANTAGE. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on a NovaSeq6000 (S4) was performed by VANTAGE.
For analysis of ChIP-Seq, de-crosslinked DNA samples from three ChIP reactions were pooled (a total of 3 x 107 cellular equivalents per sample), and DNA purified by phenol-chloroform extraction and recovered by ethanol precipitation. Indexed libraries were then made using the DNA Ultra II Library Prep Kit for Illumina (E7645, New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subject to 75 bp single-end sequencing according to the manufacturer’s protocol (Illumina NextSeq500). Sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Shared Resource. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.   ---   RNA-Seq analysis (with rRNA reduction) on CHP134 cells treated with C6 was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. RNA-Seq for CHP-134 cells treated with C6 was completed with three biological replicates.   ---    For analysis of SLAM-seq: After quality control analyses, libraries were prepared (250 ng RNA per sample) using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the User Guide (015UG009V0251) recommendations. Sequencing was performed by Lexogen on an Illumina NextSeq 500 system, using the SR75 High Output Kit. The SLAMdunk analysis pipeline (34) was used to analyze SLAMseq sequencing data. SLAM-Seq completed with three biological replicates.   ---   RNA-Seq analysis (with rRNA reduction) on CHP134 + dTAG-WDR5 cells was performed at VANTAGE. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina NovaSeq6000 (S4) was performed by VANTAGE. RNA-Seq for CHP-134 + dTAG-WDR5 cells was completed with three biological replicates.

treatment_protocol: Treatment that occurred is noted in SAMPLES section.

value: 500 nM dTAG47


title: CHP134 RNA-seq dTAG47 rep3


title: B-bl3-2


title: CHP134 RNA-seq dTAG47 rep1


description: Gene expression in the liver tissue of the SARA group, 6 weeks after parturition Cattle No. 1

source_name: SARA group, 6 weeks after parturition Cattle No. 1_Liver tissue

value: Liver tissue


title: CHP134 RNA-seq dTAG47-DMSO rep3

value: DMSO


description: Gene expression in the liver tissue of the Non group, 2 weeks after parturition Cattle No. 1

source_name: Non group, 2 weeks after parturition Cattle No. 1_Liver tissue


title: 3bl3


title: Mouse 5 donovani infected spleen

description:
Mouse infected with Leishmania
M5DS

organism:
Leishmania donovani
Mus musculus

source_name: Spleen

value: BALB/C


title: CHP134 RNA-seq dTAG47-DMSO rep2


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 2

source_name: SARA group, 2 weeks after parturition Cattle No. 2_Liver tissue


title: CHP134 RNA-seq dTAG47-DMSO rep1


title: Mouse 4 donovani infected spleen

description:
Mouse infected with Leishmania
M4DS


description: Gene expression in the liver tissue of the Control group, 2 weeks after parturition Cattle No. 1

source_name: Control group, 2 weeks after parturition Cattle No. 1_Liver tissue


title: THP1; EPI 0.25 ug/ml; LPS 100 ng/ml; dup2

city: Jena

first: Sven

last: Stengel

address: Am Klinikum 1

department: Clinic for Internal Medicine IV

institute: Jena University Hospital

description: Gene expression data from THP1 macrophages treated with 0.25 ug/ml Epirubicin and 100 ng/ml LPS, duplicate 2

hyb_protocol: According to manufacture protocol (GeneChip® WT PLUS Reagent Kit, ThermoFisher Scientific).

scan_protocol: Clariom S HT 24 array plate was scanned using an Affymetrix GeneTitan Scanner.

data_processing: CHP files were created using Transcriptome analysis concole (TAC, ThermoFisher Scientific). GC Correction, SST (Signal Space Transformation), RMA background and quantile normalization were applied. Differential gene expression between Epirubicin treated and untreated cells was analyzed in steady state or following LPS stimulation using the TAC software package.

source_name: THP1, medium 0.25 ug/ml Epirubicin, 100 ng/ml LPS for 3h, Sample 2

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent Kit).

growth_protocol: THP-1 cells (500,000 cells per well) were seeded in RPMI supplemented with 10% FCS and 1% L-glutamine-penicillin-streptomycin in 24 well cell culture plates and differentiated to macrophages using Phorbol 12-myristate 13-acetate (PMA) (100 ng/ml) over-night.

extract_protocol: Total RNA was isolated by using NucleoSpin® RNA Plus kit by manufacturer´s instructions. The RNA concentration and purity were determined spectrophotometrically (DS-11 FX, DeNovix, USA) and confirmed by RNA ScreenTape system (Tapestation 2200, Agilent, US).

treatment_protocol: Following, cells were treated with or without epirubicin (0.25 μg/ml) for 24h, and TLR4 activation was performed by treating the cells with LPS (100 ng/ml) for three hours. LPS untreated cells were used as control, resulting in four treatment conditions (1. -EPI/- LPS; 2. –EPI/+LPS;  3. +EPI/-LPS; 4. +EPI/+LPS)

tag: duplicate

tag: epirubicin treatment

value: EPI

tag: lps treatment

value: LPS

value: THP-1 cells


title: THP1; EPI 0.25 ug/ml; LPS 100 ng/ml; dup1

description: Gene expression data from THP1 macrophages treated with 0.25 ug/ml Epirubicin and 100 ng/ml LPS, duplicate 1

source_name: THP1, medium 0.25 ug/ml Epirubicin, 100 ng/ml LPS for 3h, Sample 1


title: THP1; EPI 0.25 ug/ml; LPS 0 ng/ml; dup1

description: Gene expression data from THP1 macrophages treated with 0.25 ug/ml Epirubicin, no LPS treatment, duplicate 1

source_name: THP1, medium 0.25 ug/ml Epirubicin, without LPS for 3h, Sample 1

value: NoLPS


description: Gene expression in the liver tissue of the SARA group, 2 weeks after parturition Cattle No. 1

source_name: SARA group, 2 weeks after parturition Cattle No. 1_Liver tissue

tag: tissue


title: Mouse 3 donovani infected spleen

description:
Mouse infected with Leishmania
M3DS


title: THP1; EPI 0 ug/ml; LPS 100 ng/ml; dup2

description: Gene expression data from THP1 macrophages treated without Epirubicin and 100 ng/ml LPS, duplicate 2

source_name: THP1, medium without Epirubicin, 100ng/ml LPS  for 3h, Sample 2

value: NoEPI


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 3

source_name: Control group, -3 weeks after parturition Cattle No. 3_Liver tissue


title: B-bl3-1

source_name: CD4+ Beta-synuclein reactive T cell


description: Gene expression in the liver tissue of the Control group, 2 weeks after parturition Cattle No. 2

source_name: Control group, 2 weeks after parturition Cattle No. 2_Liver tissue


description: Gene expression in the liver tissue of the Control group, 6 weeks after parturition Cattle No. 1

source_name: Control group, 6 weeks after parturition Cattle No. 1_Liver tissue


title: THP1; EPI 0.25 ug/ml; LPS 0 ng/ml; dup2

description: Gene expression data from THP1 macrophages treated with 0.25 ug/ml Epirubicin, no LPS treatment, duplicate 2

source_name: THP1, medium 0.25 ug/ml Epirubicin, without LPS for 3h, Sample 2


title: Mouse 5 donovani infected liver

description:
Mouse infected with Leishmania
M5DL

source_name: Liver


title: Mouse 1 donovani infected spleen

description:
Mouse infected with Leishmania
M1DS


title: THP1; EPI 0 ug/ml; LPS 100 ng/ml; dup1

description: Gene expression data from THP1 macrophages treated without Epirubicin and 100 ng/ml LPS, duplicate 1

source_name: THP1, medium without Epirubicin, 100ng/ml LPS  for 3h, Sample 1


description: Gene expression in the liver tissue of the Non group, -3 weeks after parturition Cattle No. 1

source_name: Non group, -3 weeks after parturition Cattle No. 1_Liver tissue


title: F2

description: gene.description.txt

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts. Then, clean reads were aligned to the reference genome using TopHat v2.0.12.
The read counts for each gene was calculated by HTSeq v0.6.1, and then gene expression levels were estimated using FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values.
sRNA libraries were sequenced using the Illumina Hiseq2500. Raw data of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze the expression and distribution on the reference.miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts.The mapped sRNA tags were also mapped to Rfam, RepeatMasker, to annotate the tags and remove those originating from proteincoding genes, repeat sequences, ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). The remaining unannotated tags were used to predict novel miRNAs by exploring secondary structures, Dicer cleavage sites, and minimum free energies using the miREvo and miRDeep2 software packages.
Genome_build: GigaScience GigaDB   (http://gigadb.org/dataset/100209, Guan et al. 2016).
Supplementary_files_format_and_content: Text files include gene.description (Gene_id, chromosome, strand, start, end, length, S1_fpkm, S2_fpkm, N1_fpkm, N2_fpkm, F1_fpkm, F2_fpkm) and miRNA.readcount (miRNA_name, S_readcount N_readcount, F_readcount).

source_name: February of embryo

value: embryo


title: Mouse 4 donovani infected liver

description:
Mouse infected with Leishmania
M4DL


title: THP1; EPI 0 ug/ml; LPS 0 ng/ml; dup 1

description: Gene expression data from untreated THP1 macrophages, duplicate 1

source_name: THP1, medium without Epirubicin and without LPS for 3h, Sample 1


description: Gene expression in the liver tissue of the SARA group, -3 weeks after parturition Cattle No. 1

source_name: SARA group, -3 weeks after parturition Cattle No. 1_Liver tissue


title: N2

description: gene.description.txt

source_name: November of embryo


title: N1

description: gene.description.txt


title: Mouse 3 donovani infected liver

description:
Mouse infected with Leishmania
M3DL


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 1

source_name: Control group, -3 weeks after parturition Cattle No. 1_Liver tissue


title: THP1; EPI 0 ug/ml; LPS 0 ng/ml; dup 2

description: Gene expression data from untreated THP1 macrophages, duplicate 2

source_name: THP1, medium without Epirubicin and without LPS for 3h, Sample 2


title: Mouse 2 donovani infected spleen

description:
Mouse infected with Leishmania
M2DS

source_name: Spleen


title: PCC6803_F-WT_1

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 0.6 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: WT in the presence of formate

label_protocol: DNAse treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol and as detailed by Voss and Hess (2014).

growth_protocol: Axenic cultures of glucose-tolerant Synechocystis sp. PCC 6803 strains used in this study were propagated in liquid batch cultures in BG11 medium (Rippka et al., 1979) at 30 °C under continuous illumination and bubbling with air. Cells for RNA isolation were cultured with or without addition of 10 mM sodium formate for 3 days.

extract_protocol: RNA for microarray hybridization was extracted via the PGTX method adapted from Pinto et al (Pinto et al., 2009). Therefore, 15 ml cyanobacterial cultures (OD750 ~1.0) were harvested through centrifugation (6000 x g, 20°C, 8 min). The pellets were resuspended in 1 ml PGTX, vortexed shortly, snap frozen in liquid nitrogen and stored at -80°C until continuing with the extraction. Samples were then incubated for 5 min at 95°C and put on ice for 5 min. After addition of 1 ml of chloroform/isoamylalcohol (24:1) and thorough agitation, samples were incubated at room temperature for 10 min. Samples were centrifuged with a swing out rotor at 4000 x g, 15°C for 15 min. The supernatant was transferred into sterile RNase-free 2 ml cups and mixed with an equal amount of the chloroform:isoamyl alcohol mixture (24:1) before another centrifugation step for 15 min at 4000 x g was performed and the extraction was repeated. An equal amount volume of isopropanol was added to the supernatant before incubation at -80°C overnight. Finally, the samples were centrifugated for 30 min at 25000 x g and 4°C before washing the resulting pellet with 1 ml of 70 % (v/v) cold ethanol. After removing the supernatant, the pellet was air dried on ice. The resulting RNA was then diluted in the desired amount of RNase-free water for further use.

treatment_protocol: For the overexpression of the ftl gene from M. extorquens AM1 in the cyanobacterium Synechocystis sp. PCC 6803, a codon-optimized version of ftl was kindly provided by Oren Yishai and Arren Bar-Even (Yishai et al., 2017). Gene ftl was amplified with primers adding BglII and MunI restriction sites at its 5’ and 3’ terminus, and inserting it under control of the strong light-induced PpsbAII promoter into plasmid pAII carrying an erythromycin resistance cassette (Lagarde et al., 2000). Batches of wild-type (WT) amd ftl-expressing strains (exFTL) were grown in the absence or in the presence of 10 mM sodium formate for 3 consecutive days.

value: WT

value: sodium formate


title: PCC6803_WT_2

source_name: WT in the absence of formate

value: control


title: F1

description: gene.description.txt


title: PCC6803_F-exFTL_2

source_name: exFTL in the presence of formate

value: exFTL


title: PCC6803_F-WT_2


description: Gene expression in the liver tissue of the Control group, -3 weeks after parturition Cattle No. 2

source_name: Control group, -3 weeks after parturition Cattle No. 2_Liver tissue


title: S2

description: gene.description.txt

source_name: September of embryo


title: PCC6803_WT_1


title: Mouse 2 donovani infected liver

description:
Mouse infected with Leishmania
M2DL


title: Mouse 1 donovani infected liver

description:
Mouse infected with Leishmania
M1DL


title: PCC6803_exFTL_2

source_name: exFTL in the absence of formate


title: PCC6803_F-exFTL_1


title: 5-ITU_1uM_rep2

status: Public on Jan 16 2020

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

description: E14 cells treated with 1uM 5-ITU

hyb_protocol: Affymetrix protocols and procedures were followed

scan_protocol: Chips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: Data were processed using GeneSpring 13.0 software (Agilent). RMA normalization was performed and only probes above the background threshold (=353) were considered for further evaluation.   We used the background cutoff on the raw values.  The actual number (353) is based on values  obtained for background from the Affymetrix Expression Console.

source_name: 5-ITU_1uM, E14 stem cells

growth_protocol: E14 stem cells were cultured under standard undifferentiated conditions (serum&LIF).

extract_protocol: Total RNA was extracted using RNeasy protect mini kit (Qiagen) with on-column DNAse digestion.

treatment_protocol: Cells were treated for 26 hours either with DMSO only, 0.1uM 5-ITU or 1 uM 5-ITU

tag: developmental stage

value: E14 stem cells

tag: dose


title: 5-ITU_1uM_rep3

description: E14 cells treated with 1uM 5-ITU

label_protocol: Affymetrix protocols and procedures were followed


title: PCC6803_exFTL_1


title: 5-ITU_1uM_rep1

description: E14 cells treated with 1uM 5-ITU


title: Pancreatitis tuft cells-5

first: Kathleen

middle: E

last: DelGiorno

address: 465 21st Ave S

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Sequencing reads were quality checked with FastQC and mapped to the mouse genome (mm9) using Hisat2. Transcript assembly and quantification were performed by Stringtie and Ballgown. Gene expression distribution between samples was checked to ensure similar transcriptome quality. Genes that have RPKM variance across samples < 1 were first removed to exclude non-expressed genes. The RPKM values were then log2 transformed and quantile normalized with the R package preprocessCore. Differential expression analysis between tuft and non-tuft epithelial cells was performed with empirical Bayes shrinkage and moderated t-test using the Limma package and p values were converted into false discovery rates (FDR) using the Benjamini-Hochberg procedure.
Genome_build: mm9
Supplementary_files_format_and_content: Quantile normalized log2(RPKM+1) value for each sample

molecule: polyA RNA

source_name: WT mouse with pancreatitis

extract_protocol:
Pancreatic tuft cells were isolated from 5 CD1 male mice with caerulein-induced pancreatitis.  The pancreas was quickly dissected, minced in 5 ml of DMEM with FBS and allowed to incubate at room temperature for 2 min.  Supernatant and fat were removed and pancreatic tissue was then incubated in 10 ml DMEM supplemented with 1 mg/ml collagenase I (Sigma), 1 mg/ml soybean trypsin inhibitor (Gibco), 1.5 mg/ml hyaluronidase (Sigma), and 250 μl of DNAse I, shaking gently at 37°C for a maximum of 30 min.  Digestion was monitored and tissue was further digested mechanically by pipetting.  Digested tissue was passed through a 100 μm filter, washed with FACS buffer (PBS, 1 mM EDTA, 0.5% BSA) containing DNase I, and incubated with ACK lysing buffer (Gibco) to remove red blood cells before staining for FACS.
Single cell suspensions were incubated on ice with mouse Fc receptor block (BD Biosciences, 1:200) followed by antigen-specific antibodies in FACS buffer.  DAPI (molecular probes, 1:1000) and Annexin V (Biolegend, Pacific Blue conjugate at 1:200) were used to exclude dead and dying cells.  Cells were labeled with Cd45 (Alexa Fluor 488), EpCAM (Alexa Fluor 647), and Siglec F (PE) (Biolegend, 1:200).  Fluorescence Minus One (FMO) staining controls were included for gating populations of interest. Cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy; these were deposited directly into lysis buffer composed of DNase/RNase-free water, Triton X-100, and Ribolock (Thermo Fischer) in a 96 well plate.
Low input bulk RNA sequencing (RNA-seq) on pancreatic tuft cells was performed using the Smart-Seq2 protocol as previously described. In brief, five biological replicates, each with 100 tuft cells from an individual mouse, were sorted directly into 2 μl of Smart-Seq2 lysis buffer. Full-length cDNA was generated, and size distribution was checked with Agilent TapeStation 4200 to ensure RNA quality. cDNA were then amplified with 18-24 PCR cycles, tagmentated, and amplified again with 10 PCR cycles using a Nextera XT kit (Illumina FC-131-1096). The sequencing library was purified with AMPure XP beads.
SmartSeq2 (Picelli et al., 2014) or TruSeq stranded mRNA Sample Preparation Kit v2.

value: Mixed

value: Pancreas

value: Pancreatitis tuft cells


title: Pancreatitis non-tuft epithelial cells-1

value: Pancreatitis non-tuft epithelial cells


title: Pancreatitis tuft cells-4


title: Pancreatitis non-tuft epithelial cells-2


title: Pancreatitis non-tuft epithelial cells-5


title: Pancreatitis tuft cells-3


title: Pancreatitis non-tuft epithelial cells-4


title: Pancreatitis non-tuft epithelial cells-3


title: Pancreatitis tuft cells-2


title: Pancreatitis tuft cells-1


title: DMSO_control_rep3

description: E14 cells treated with DMSO only

source_name: DMSO_control, E14 stem cells

value: DMSO only


title: TT05_01: Triparental triploid bio rep5 tech rep1

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Sequencing performed by: Bielefeld University, CeBiTec & Faculty of Biology
Sequenced reads were trimmed for adaptor sequences with trimmomatic version 0.38 using the paramters SE -phred33 ILLUMINACLIP:adapter_sequences.fasta:2:30:10
Low quality regions were removed using trimmomatic version 0.38 with parameters: SE -phred33 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to protein coding sequences using STAR version 2.6.0c with parameters: --alignIntronMin 20 --alignIntronMax 50000 --outFilterMismatchNmax 2 --outFilterMultimapNmax 50 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --quantMode TranscriptomeSAM
Read assignment was done by salmon version 0.11.3 with the parameters: quant –libType U –gcBias –seqBias –useErrorModel
Normalization of counts was performed with DESeq2 version 1.22
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: semicolon separated files contain DESeq2 library size normalized counts (deseq2_norm), regularized log transformed counts (deseq2_rlog), and TPM normalized expression values for each biological replicate

organism: Arabidopsis thaliana

source_name: aerial tissues of 18 DAS plants

growth_protocol: The plant materials were grown in a Conviron MTPS growth chamber under long-day conditions (16 hours light/8 hours dark) at 23 ̊C.

extract_protocol:
The aerial tissues of 18 DAS plants were frozen and grinded in pre-cooled EP tubes with metal beads and total RNA was isolated following the procedure of GeneMATRIX Universal RNA purification kit.
750 ng total RNA per sample was used to prepare sequencing libraries according to the Illumina TruSeq RNA Sample Preparation v2 Guide. Purification of the poly-A containing mRNA was performed using two rounds of poly-T Oligos attached to magnetic beads. During the second elution of the poly-A RNA, the RNA was fragmented and primed for cDNA synthesis. After cDNA synthesis the fragments were end-repaired and A-tailing was performed. Multiple indexing adapters were ligated to the ends of the cDNA fragments and the adapter ligated fragments were enriched by 10 cycles of PCR. After quali- and quantification the resulting sequencing libraries were pooled equimolar and sequenced 75 bp single-read on an Illumina NextSeq500.

treatment_protocol:
For all the crosses, ein3-1 mutants were used as female plant. Triparental triploids (TT) were obtained from double pollination as previously described (Nakel et al. Nat Comm. 2017), while biparental triploids (BT) were recovered from a cross of 2n female with 4n male pollen donor pRPS5a::mGAL4-VP16/-; pUAS::BAR-YFP/-. Biparental diploids (BD) were generated from a cross of 2n female with 2n pollen donor pRPS5a::mGAL4-VP16/-; pUAS::BAR-YFP/-.
Seeds that contain TT, BT and BD were selected on 0.5 MS medium containing 25 mg/l Glufosinate-ammonium (PPT, Sigma), and the seedlings were transferred to soil 9 days after sowing (DAS). YFP and ploidy analysis was carried out 17 DAS to confirm TT, BT and BD profile.

value: aerial tissues of 18 DAS plants

tag: genotype/variation

value: Triparental triploid


title: TT05_03: Triparental triploid bio rep5 tech rep3


title: TT05_04: Triparental triploid bio rep5 tech rep4


title: TT05_02: Triparental triploid bio rep5 tech rep2


title: TT04_04: Triparental triploid bio rep4 tech rep4


title: S16_DM2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Circular RNA

data_processing:
The reads were cleaned using cutadapt program.
The tags were aligned using Tophat and Tophat fusion (v2.1.0) with --GTF option using mm9 Ensembl v67 annotation database and segment length of 20 (all other parameters were at their default values).
Cufflinks (v2.2.1) was used to assemble the transcripts.
CIRCexplorer (v1.1.7) was used to find circRNAs.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_fromRNAassembly_circRNA.txt: The processed data files contain information about the circRNA and the junctional read counts in a tab-delimited TXT format.

source_name: Myoblast

growth_protocol: Proliferating C2C12 myoblasts were cultured in growth medium (GM), DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), and antibiotics penicillin and streptomycin (Life Technologies). Proliferating, subconfluent C2C12 myoblasts were induced to differentiate by culturing them to high density and switching to differentiation medium [(DM), DMEM with 2% horse serum] for 3-4 days.

extract_protocol:
Total RNA from cultured cells was isolated using the miRNeasy Mini Kit (#217004, Qiagen Inc.) following the manufacturer’s protocol. For the RPAD samples, a 20-µl reaction was set with 2 µg of Hela RNA, 20 units of RiboLock RNase inhibitor (Thermo Fisher Scientific), 1× RNase R buffer and 20 units of RNase R (RNR07250, Epicentre), and incubated for 30 min at 37°C. The RNA from control and RNase R-treated samples were isolated using miRNeasy Mini Kit following the manufacturer’s instructions. The RNase R treated sample was treated with PolyA polymerase to add polyA tail to linear RNAs followed by incubation with Oligo-dT Dynabeads from Poly(A)Purist™ MAG Kit (AM1922) and the supernatant was collected for RNA isolation. The miRNeasy Mini Kit was used to prepare RNA from the control and RNase R-polyadenylation and poly(A)+ RNA depletion (RPAD) samples.
After isolation of total RNA and RPAD-prepared RNA using miRNeasy Mini Kit, ribosomal (r)RNA was removed by rRNA Depletion Nano kit (Qiagen), whereupon cDNA was prepared and amplified using the Ovation RNA-Seq System V2 (NuGEN) kit following the manufacturer’s instructions. The amplified cDNA was fragmented using a Bioruptor (Diagenode) followed by ligation of adaptors using TruSeq ChiP Sample Preparation kit (Illumina, San Diego, CA) and DNA fragments ranging 300-350 bp were isolated from a 2.5% agarose gel and subjected to 17 cycles of PCR amplification. A Bioanalyzer 2100 instrument was used to analyze the quality of the cDNA libraries, which were sequenced using an Illumina HiSeq2500 instrument.

treatment_protocol: RPAD (RNase R digestion, polyadenylation, and poly(A)+ RNA depletion) yields almost-pure circRNAs.

value: Myoblast cell line

value: Control


title: S15_DM1

description: Circular RNA


title: S17_DM_RPAD1

description: Circular RNA

value: RPAD


title: 5-ITU_0.1uM_rep3

description: E14 cells treated with 0.1uM 5-ITU

source_name: 5-ITU_0.1uM, E14 stem cells


title: 5-ITU_0.1uM_rep2

description: E14 cells treated with 0.1uM 5-ITU


title: TT04_02: Triparental triploid bio rep4 tech rep2


title: 5-ITU_0.1uM_rep1

description: E14 cells treated with 0.1uM 5-ITU


title: S18_DM_RPAD2

description: Circular RNA


title: TT03_04: Triparental triploid bio rep3 tech rep4


title: DMSO_control_rep2

description: E14 cells treated with DMSO only


title: DMSO_control_rep1

description: E14 cells treated with DMSO only


title: Motor neurons - mut replicate 1

city: Cleveland

first: Polyxeni

last: Philippidou

state: OH

address: 2109 Adelbert Rd

department: Neurosciences

institute: Case Western Reserve University

data_processing:
Read quality was assessed using FASTQC and adapters were trimmed using Trim Galore.
Filtered and trimmed reads were aligned to the mouse genome (GRCm38.p5) using TopHat v2.1.0
Gene counts were obtained using htseq-count.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: excel tables of raw gene counts for each sample

source_name: Cervical motor neurons

extract_protocol:
e12.5 C3-C6 spinal cord segments were dissociated with papain/DNase. Hb9::GFP+ MNs were isolated by flow sorting directly into Arcturus Picopure Extraction buffer, and total RNA was isolated using the Arcturus Picopure RNA isolation kit.
rRNA depleted libraries were prepared from 10-20ng of total RNA using the KAPA stranded RNA-seq kit with Riboerase (KAPA, #KK8483)

value: Cervical spinal cord

tag: age

value: Hox5MNdelta Bax -/-


title: Motor neurons - control replicate 1

value: Control Bax-/-


title: Motor neurons - mut replicate 2


title: Motor neurons - control replicate 3


title: Motor neurons - mut replicate 3


title: Motor neurons - control replicate 2


title: TT04_03: Triparental triploid bio rep4 tech rep3


title: TT03_03: Triparental triploid bio rep3 tech rep3


title: TT04_01: Triparental triploid bio rep4 tech rep1


title: TT03_01: Triparental triploid bio rep3 tech rep1


title: Delta-N-RNMT study induced replicate 2 3'end tag-Seq

city: Columbus

first: Ralf

last: Bundschuh

address: 191 West Woodruff Avenue

department: Department of Physics

institute: The Ohio State University

description:
cytoplasmic RNA isolates
Induced 2

data_processing:
REV Human Lexogen QuantSeq pipeline 2.2.3
Genome_build: hGRC38
Supplementary_files_format_and_content: space delimited text files with read counts for each gene

source_name: U2OS-TR/ΔN-RNMT cell line

growth_protocol: 3x10^6 cells were split into a 10 cm dish.

extract_protocol:
Twenty-four hours later cells were rinsed once with ice cold phosphate buffered saline (PBS) and suspended in 1 ml of PBS with a cell scraper. The recovered cells were centrifuged at 2,500 xg for 5 minutes at 4°C, washed once with 1 ml PBS and centrifuged again at 2,500 xg for 5 minutes at 4°C. The pelleted cells were resuspended in 5 volumes of lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 0.2% NP-40, 80 U/ml RNaseOUT (Invitrogen)) and incubated on ice for 10 minutes. Nuclei were removed by centrifugation at 12,000 xg for 10 minutes at 4°C. The supernatant fraction was used for western blot analysis and for RNA isolation using Direct-zol RNA MiniPrep Kit (Zymo Research R2053) including an in-column DNAse I digestion. Purified RNA was eluted in RNAse free water.
Sequencing libraries were prepared from 2 μg of cytoplasmic RNA from uninduced or 24 hr doxycycline-treated (induced) cells carrying the ΔN-RNMT transgene (n=5 for each) or parental U2OS-TR cells (n=3 for each) using the QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina (Lexogen) according to manufacturer’s protocol. The final concentration of each library was determined using Qubit 2.0 Fluorometer (Invitrogen).

treatment_protocol: After 48 hr, 1 μg/ml of doxycycline was added.

value: bone

tag: disease

value: osteosarcoma


title: Delta-N-RNMT study induced replicate 5 3'end tag-Seq

description:
cytoplasmic RNA isolates
Induced 5


title: Delta-N-RNMT study induced replicate 3 3'end tag-Seq

description:
cytoplasmic RNA isolates
Induced 3


title: Delta-N-RNMT study induced replicate 1 3'end tag-Seq

description:
cytoplasmic RNA isolates
Induced 1


title: Delta-N-RNMT study induced replicate 4 3'end tag-Seq

description:
cytoplasmic RNA isolates
Induced 4


title: Delta-N-RNMT study control replicate 5 3'end tag-Seq

description:
cytoplasmic RNA isolates
Control 5


title: TT03_02: Triparental triploid bio rep3 tech rep2

city: Würzburg


title: Delta-N-RNMT study control replicate 4 3'end tag-Seq

description:
cytoplasmic RNA isolates
Control 4


title: TT02_04: Triparental triploid bio rep2 tech rep4


title: TT02_02: Triparental triploid bio rep2 tech rep2


title: TT02_03: Triparental triploid bio rep2 tech rep3


title: Delta-N-RNMT study control replicate 1 3'end tag-Seq

description:
cytoplasmic RNA isolates
Control 1


title: LN_shUSP22_2

city: Philadelphia

first: Christopher

last: McNair

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
alignment to hg19 with STAR v2.5.2a
Generate count table using featureCounts Version 1.5.0-p3
Differential expression using DESeq2_1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: Raw Count Matrix

growth_protocol: LNCaP-derived cells were grown in hormone proficient media

extract_protocol:
RNA Seq was prepared according to manufacturesrs instructions ( RNAeasy Mini kit, Qiagen)
RNA-Seq libraries were constructed using TruSeq Stranded Total RNA Library Prep Gold kit (protocol# 15031048 Rev E)

treatment_protocol: shRNA cells were treated with 1ug/mL doxycycline every 48 hours (both shControl and shUSP22-4693 cells)

value: LNCaP

value: prostate cancer cells

value: shRNA-mediated USP22 depletion

value: 5 days, 1 ug/mL doxycycline (every 48 hours)


title: LN_shUSP22_1


title: TT02_01: Triparental triploid bio rep2 tech rep1


title: TT01_03: Triparental triploid bio rep1 tech rep3


title: LN_shCON_3

source_name: LN-shCtrl

value: shRNA-control


title: LN_shCON_1


title: LN_shCON_2


title: BT05_04: Biparental triploid bio rep5 tech rep4

value: Biparental triploid


title: LN_USP22hi_3

value: USP22 overexpression


title: BT05_03: Biparental triploid bio rep5 tech rep3

value: aerial tissues of 18 DAS plants


title: TT01_01: Triparental triploid bio rep1 tech rep1

value: Triparental triploid


title: LN_USP22hi_2


title: LN_pLPLUC_3

source_name: LN-pLPLUC

value: pLPLUC vector control


title: TT01_04: Triparental triploid bio rep1 tech rep4


title: Surgical specimen 33

type: genomic

city: Brussels

first: Sandra

last: Schmitz

address: Avenue Hippocrate, 54

country: Belgium

institute: Universite catholique de louvain

hyb_protocol: Samples were loaded to the Beadchip and incubated in the Illumina Hybridization Oven, according to manufacturer's protocol

scan_protocol: Beadchips were scanned using the Methylation Module of GenomeStudio 1.0 of the Illumina HiScan equiptment.

data_processing: iDat files were loaded with minfi version 1.22.1 and normalized with NOOB to compute beta values for each probe.

label: Cy5 and Cy3

source_name: Surgical specimen

label_protocol: Infinium Human MethylationEPIC Beadchip Kit (Illumina), following manufacturer's instructions.

extract_protocol: DNA extraction from FFPE slides (surgical specimen)

treatment_protocol: Cetuximab two weeks before surgery

tag: disease state

value: HNSCC

value: cetuximab

tag: sample id

tag: code

tag: gender

value: male

tag: tumor site

value: oral cavity

tag: pathology

value: squamous cell carcinoma

tag: clinical staging


title: BT04_04: Biparental triploid bio rep4 tech rep4


title: BT04_02: Biparental triploid bio rep4 tech rep2


title: MV411 Resistant Entospletinib 24h replicate3

city: Cambridge

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Quality control tests for the sequenced reads  were performed using the FASTQC v0.11.5 software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Tophat2 v2.1.1. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2.1 and the SARTools  pipelines.
Gene level reads and gene level expression estimated as log2(1+FPKM) (Fragments Per Kilobase of transcript per Million mapped reads) scores were computed using the Feature Counts method implemented in the Bioconductor v3.5  RSubread v1.5.3 package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene level counts values for each sample.

source_name: MV4-11 acute myeloid leukemia cell line

extract_protocol: RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen). For RNA-sequencing of MV4-11 cells, polyA mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol.  All samples were sequenced on a NextSeq500 instrument with single-end 75bp reads to a depth of 30-50M reads/sample.

tag: cell line

tag: entospletinb resistance status

value: Resistant

tag: agent

value: Entospletinib

tag: time point (hours)

tag: replicate

value: Replicate 3


title: LN_pLPLUC_2

value: LNCaP

tag: cell type

value: prostate cancer cells


title: LN_USP22hi_1


title: BT04_01: Biparental triploid bio rep4 tech rep1

tag: tissue


title: BT05_02: Biparental triploid bio rep5 tech rep2

tag: genotype/variation


title: BT05_01: Biparental triploid bio rep5 tech rep1


title: MV411 Resistant Entospletinib 24h replicate1

value: Replicate 1


title: BT03_04: Biparental triploid bio rep3 tech rep4


title: LN_pLPLUC_1


title: BT04_03: Biparental triploid bio rep4 tech rep3


title: BT03_03: Biparental triploid bio rep3 tech rep3


title: MV411 Resistant DMSO 24h replicate3

value: DMSO


title: MV411 Resistant Entospletinib 24h replicate2

value: Replicate 2


title: Surgical specimen 26

tag: treatment


title: Surgical specimen 31


title: Surgical specimen 21


title: BT03_02: Biparental triploid bio rep3 tech rep2

value: Biparental triploid


title: MV411 Resistant DMSO 24h replicate2


title: BT03_01: Biparental triploid bio rep3 tech rep1

value: aerial tissues of 18 DAS plants


title: MV411 Resistant DMSO 24h replicate1


title: BT02_02: Biparental triploid bio rep2 tech rep2


title: BT02_01: Biparental triploid bio rep2 tech rep1


title: MV411 Resistant Entospletinib 8h replicate1


title: BT01_02: Biparental triploid bio rep1 tech rep2


title: MV411 Resistant Entospletinib 8h replicate2


title: BT02_04: Biparental triploid bio rep2 tech rep4


title: BT01_04: Biparental triploid bio rep1 tech rep4


title: BT01_01: Biparental triploid bio rep1 tech rep1


title: BT01_03: Biparental triploid bio rep1 tech rep3


title: MV411 Resistant DMSO 8h replicate2


title: MV411 Naive Entospletinib 24h replicate2

value: Naïve


title: MV411 Resistant DMSO 8h replicate3


title: BD05_04: Biparental diploid bio rep5 tech rep4

value: Biparental diploid


title: MV411 Resistant DMSO 8h replicate1


title: LN_shUSP22_3

value: shRNA-mediated USP22 depletion

value: 5 days, 1 ug/mL doxycycline (every 48 hours)


title: Surgical specimen 27

value: HNSCC

value: cetuximab

value: female

value: larynx


title: BD05_03: Biparental diploid bio rep5 tech rep3


title: Surgical specimen 34

value: male

value: oral cavity

value: squamous cell carcinoma


title: MV411 Resistant Entospletinib 8h replicate3

value: Resistant

value: Entospletinib

value: Replicate 3


title: S1

description: gene.description.txt

extract_protocol:
Samples were collected in September 2015, November 2015 and February 2016. Total RNAs of embryo were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: embryo


title: MV411 Naive DMSO 24h replicate3

value: DMSO


title: BT02_03: Biparental triploid bio rep2 tech rep3

value: aerial tissues of 18 DAS plants

value: Biparental triploid


title: BD05_02: Biparental diploid bio rep5 tech rep2

value: Biparental diploid


title: MV411 Naive Entospletinib 24h replicate3

value: Naïve


title: BD05_01: Biparental diploid bio rep5 tech rep1


title: MV411 Naive DMSO 24h replicate2

value: Replicate 2


title: MV411 Naive Entospletinib 24h replicate1

value: Replicate 1


title: Delta-N-RNMT study control replicate 3 3'end tag-Seq

description:
cytoplasmic RNA isolates
Control 3

value: bone

tag: disease

value: osteosarcoma


title: Surgical specimen 24

tag: disease state

value: HNSCC

value: cetuximab

tag: sample id

value: female

value: larynx


title: Surgical specimen 22

tag: code

tag: gender

value: male

value: oral cavity

value: squamous cell carcinoma


title: MV411 Naive Entospletinib 8h replicate3

value: Entospletinib

value: Replicate 3


title: MV411 Naive DMSO 24h replicate1

value: DMSO


title: BD04_02: Biparental diploid bio rep4 tech rep2

value: aerial tissues of 18 DAS plants


title: MV411 Naive Entospletinib 8h replicate1


title: BD04_03: Biparental diploid bio rep4 tech rep3

value: Biparental diploid


title: BD04_01: Biparental diploid bio rep4 tech rep1


title: MV411 Naive Entospletinib 8h replicate2

value: Naïve


title: Delta-N-RNMT study control replicate 2 3'end tag-Seq

description:
cytoplasmic RNA isolates
Control 2


title: BD03_04: Biparental diploid bio rep3 tech rep4


title: MV411 Naive DMSO 8h replicate3


title: MV411 Naive DMSO 8h replicate2

value: Replicate 2


title: BD03_03: Biparental diploid bio rep3 tech rep3


title: BD03_02: Biparental diploid bio rep3 tech rep2


title: BD03_01: Biparental diploid bio rep3 tech rep1


title: MV411 Naive DMSO 8h replicate1

value: Replicate 1


title: BD02_04: Biparental diploid bio rep2 tech rep4


title: BD02_03: Biparental diploid bio rep2 tech rep3