title: MNasecontrol_met2_muscle [met2_MNAseControl_a]

description: chicseq_2544F19-1_muscle_met2_MNAseControl

data_processing:
library strategy: CUT&RUN; ChICseq
Adaptors were trimmed using Trimmomatic 0.39 (http://www.usadellab.org/cms/?page=trimmomatic) with parameters set to: CROP:75 HEADCROP:12.
reads were aligned to the ce10 genome assembly using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
reads were deduplicated using the deduplicate_bismark function in the Bismark program (https://github.com/FelixKrueger/Bismark)
Read density was calculated by tiling the genome into 500-bp non-overlapping windows and using the qCount function of the QuasR package to quantify the number of reads in each window (qCount(proj,GRange_object,orientation="any"))
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains chromosome identifier, start and end position of fragment, following columns contain raw counts of reads overlapping each fragment for each sample.

source_name: L3 body wall muscle

growth_protocol: DNA was isolated from purified tissues from L3 larvae grown after L1 synchronization.

extract_protocol:
For ChIC-seq, filtered cells were pelleted, resuspended in 1 ml of M9, then fixed by slowly adding 2.33 mL of -20oC EtOH (100%) while vortexing cells. Cells were left at -20oC for 1h, centrifuged, and washed with wash buffer 1 (WB1) (20 mM HEPES pH 7.5, 150 mM NaCl, 0.46 mM spermidine, 0.05% Tween-20, 1x cOmplete protease inhibitor, 2 mM EDTA). Washed cells were resuspended in WB1 + 10% DMSO and stored at -80oC until ready to process. Cells were thawed on ice (all subsequent steps on ice), and washed 1x with WB1. Cells were then counted and diluted in WB1 to ~500K cells/200 µL. For each antibody and mutant, 200 µL of cells were transferred to 0.5 mL low-bind tubes (Eppendorf). 200 µL of primary antibodies, diluted to 2x in WB1, were then added cells and incubated on rotator overnight at 4oC. (Antibodies used: H3K9me3 (1:2000, MABI0318 (MBL; Kimura et al., 2008), H3K9me2 (1:5000, MABI0317 (MBL; Kimura et al., 2008) and H3K27ac (1:5000, ab177178)). Cells were washed 1x with wash buffer 2 (WB2, WB1 no EDTA), then resuspended in 500 µL of WB2 containing ProteinA-MNase (1 ng/mL - recombinant) and 5 µg/mL Hoechst 33258, and incubated on rotator 1 hr at 4oC. Cells were then washed 2x with 500 µL of WB2, then filtered into sorting tubes with ~500 µL WB2 final volume. For each sample, ~5K cells were sorted into 5 µL of wash buffer 3 (WB3, WB1 no EDTA and no protease inhibitor). Note: Hoechst was used as a sorting marker for gating fixed/lysed cells. After sorting, MNase was activated, by adding 10 µL WB3 containing 4 mM CaCl2, for 30 min on ice. The reaction was then stopped with the addition of 20 µL Stop solution (40 mM EGTA, 1.5% NP40, 2 mg/mL Proteinase K), then proteins were digested (65oC for 6h, 80oC for 20 mins, hold at 4oC).
DNA fragments were blunt ended by adding 30 µL blunt end mix (2.5 U Klenow large fragment, 5 U T4-PNK, 0.4 mM dNTPs, 2.3 mM ATP, 1.7 mM MgCl2, 7 µL PNK buffer 10X, 0.24 ng/ml BSA, 2,5% PEG8000) and incubating for 30 min at 37oC followed by 20 min at 75oC for enzyme inactivation. Fragments were A-tailed by adding 30 µL tail mix (1 U AmpliTaq 360, 0.7 mM dATP, 167 mM KCL, 0.1 ng/ml BSA, 2.5% PEG8000) and incubation at 72oC for 15 min. fragments were further ligated to T-Tail containing adaptors with the sequence: forward strand: GGTGATGCCGGTAATACGACTCACTATAGG GAGTTCTACAGTCCGACGATCNNNACACACTAT, reverse strand: /5Phos/TAGTGTGTNNN GATCGTCGGACTGTAGAACTCCCTATAGTGAGTCGTATTACCGGCGAGCTT. The first 6 italic basepairs form a fork, the underlined basepairs afterwards a T7 promotor, the following underlined bases are the binding site (RA5) for the TruSeq Small RNA indexing primers (RPIx), the underlined 3 random base pairs represent the unique molecular identifier. Ligation was performed by adding 40 µL ligation mix (1.25 µM adaptor, 2000 U T4 ligase, 17.5 mM MgCl2, 52.5 mM Tris pH 7.5, 26.25 mM DTT, 1.75 mM ATP, 0.1 ng/ml BSA, 2.5% PEG8000) and incubating for 20 min at 4oC followed by 16 hrs at 16oC. Ligase was inactivated by incubation for 10 min at 65oC. Ligation reactions were cleaned with Ampure XP beads at a 0.8 beads to sample ratio and resuspended in 8 µL clean water. Cleaned fragments were amplified by adding 12 µL of MEGAscript™ T7 Transcription Kit and incubation for 12 hrs at 37oC. Template DNA is removed by addition of 2 µL TurboDNAse (IVT kit) and incubation for 15 min at 37oC. The produced RNA is further purified using RNA Clean XP beads at 0.8 beads to sample ratio, followed by RNA fragmentation for 2 min at 94oC. After another bead cleanup, 40% (5 µL) of the RNA is primed for reverse transcription by adding 1,5 µL of 3.3 mM dNTPs and 13.3 µM randomhexamer RT primer (GCCTTGGCACCCGAGAATTCCANNNNNN) and hybridizing it by incubation at 65oC for 5 min followed by direct cool down on ice. Reverse transcription is performed by further addition of 4 µL RT mix (2.5x first strand buffer, 25 mM DTT, 20 U RNAseOUT and 100 U SuperscriptII) and incubating at 25oC for 10 min followed by 1 hr at 42oC. Single stranded DNA is purified through incubation with 5 ug/25 U RNAseA for 30 min at 37oC and PCR amplification to add the Illumina smallRNA barcodes and handles. 40 µL of PCR mix (3.1x NEBNext Ultra II Q5 Master Mix (5x stock), 0.5 µM RP1 and 0.5 µM RPIx primers) was added. PCR cycles depended on the abundance of the histone modification assayed and PCR products were cleaned twice Ampure XP beads at a 0.8x bead to sample ratio. The final libraries were eluted in 7 µL Nuclease free water and abundance and quality were assessed by QUBIT and bioanalyzer.


title: ∆RPL22A  PolysomeHigh Rep2

status: Public on Aug 01 2021

type: SRA

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

library_source: transcriptomic

data_processing:
Adapter trimming and quality filtering: reads were trimmed and filtered using cutadapt v.1.4, using paired-end mode
Reads were pre-mapped to rRNA to assess the amount of rRNA contamination
Reads were mapped to the sacCer3 genome in paired end mode using StaR version 2.4
Duplicates were removed using samtools v 0.1.19
Reads were converted into counts using RSEM version 1.2.18
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts table per gene and condition (tsv)

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: ∆RPL22A  PolysomeHigh

growth_protocol: Yeast was grown to log phase (OD = 0.6-0.8)

extract_protocol:
Polysome-bound RNAs were fractionated using sucrose gradients.
RNA libraries were prepared for sequencing using standard Illumina protocols
Frac-Seq / PolysomeSeq

treatment_protocol: Cycloheximide

tag: growth phase

value: Log phase (OD 0.6-0.8)

tag: strain

tag: rna pool

value: PolysomeHigh fraction


title: MNasecontrol_N2_muscle [wt_MNAseControl_a]

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: chicseq_2544F17-1_muscle_wt_MNAseControl

library_source: genomic

molecule: genomic DNA

organism: Caenorhabditis elegans

tag: strain/genotype

value: N2 (Bristol)

tag: tissue

value: L3 body wall muscle


title: F5_plate1

city: Medford

first: Eric

middle: R

last: Reed

state: MA

address: 419 Boston Ave.

department: Data Intensive Studies Center

country: USA

institute: Tufts University

data_processing:
All reads containing bases with quality lower than Q10 are filtered out.
Reads that pass filter are assigned to a well and aligned to the transcriptome (GRCm38) which includes mitochondrial genes using BWA aln version 0.7.10. Reads that only align to multiple isoforms of the same gene are considered uniquely mapped.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: (1) HGNC symbols (2)Read Counts.

molecule: total RNA

organism: Mus musculus

source_name: NIH 3T3-L1

growth_protocol: NIH 3T3-L1 (ATCC: CL-173, RRID:CVCL_0123) cells were maintained in high-glucose DMEM with 10% calf serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.25 μg/ml amphotericin B. Cells were plated in 24 well plates at 50,000 cells per well in 0.5 ml maintenance medium and incubated for 4 days. “Naïve” cells were cultured in maintenance medium for the duration of the experiment. To induce adipogenesis, the medium was replaced with DMEM containing 10% fetal bovine serum (FBS, Sigma-Aldrich), 250 nM dexamethasone, 167 nM of 1 µg/ml human insulin, 0.5 mM IBMX, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Cells were thawed on ice and each sample was lysed using 1uL of 1mg/mL Proteinase K (ThermoFisher Scientific) followed by incubation at 50oC for 15 min, then 95oC for 10 min uncovered to evaporate all liquid.
Single Cell RNA Barcoding and Sequencing (SCRB-seq) was performed as described in Soumillon M., Cacchiarelli D., Semrau S., van Oudenaarden A. and Mikkelsen T.S. (2014). Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv. 10.1101/003236. Sequencing generates two files: read1 and read2.  Read1 contains 17 base reads (6 base barcode + 10 base UMI + an N in the 17th position).  Read2 contains the 46 bp cDNA sequence.

treatment_protocol: Experimental wells received induction medium and were treated with Vh (DMSO, 0.2% final concentration), or test chemicals. On days 3 and 5 of differentiation, medium was replaced with adipocyte maintenance medium (DMEM, 10% FBS, 167 nM human insulin, 100 U/ml penicillin, 100 μg/ml streptomycin), and the cultures were re-dosed. On Day 7 of differentiation, medium was replaced with adipocyte medium (DMEM, 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin) and the cultures re-dosed.

tag: cell line

value: NIH 3T3-L1

tag: chemical

tag: chemical full

tag: volume mol

tag: concentration

tag: plate

tag: well


title: MC38CEA cells, SL2 IL IFN3

city: Kraków

first: Joanna

last: Bereta

address: Gronostajowa 7

department: Cell Biochemistry

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

data_processing:
Basecalling, quality control, mapping and read counts on Ion Torrent Suite v. 5.12.1
Genome_build: mm10
Supplementary_files_format_and_content: shRNA RNAseq.xls file containing numbers of reads for all genes and differential gene expression analysis

growth_protocol: The cells were grown in DMEM + 5% FBS at standard conditions (37°C, 5% CO2, 95% humidity).

extract_protocol:
The cells were lysed in Fenozol; total RNA was isolated using Direct-Zol RNA Mini Kit. poly(A)+ RNA was isolated using Dynabead mRNA DIRECT Micro Purification Kit
libraries were prepared according to the manufacturer's protocol with the Ion Total RNA-Seq Kit v2 (ThermoFisher)

treatment_protocol: 6 h,  IL1b (10 ng/ml) and  IFNg (10 ng/ml) or left untreated

tag: cell type

value: colon adenocarcima

tag: treatment

value: hr IL1b (10 ng/ml) and mr IFNg (10 ng/ml)

tag: transduction

value: ADAM17-targeting shRNA

tag: biological replicate


title: H3K27ac_N2_muscle [wt_H3K27ac_a]

tag: antibody


title: F3_plate1

value: MELENG

value: Melengestrol acetate


title: F4_plate1

value: PFOS

value: Perfluorooctanesulfonic acid


title: H3K27ac_met2_muscle [met2_H3K27ac_a]


title: SCV130_3

city: Bethesda

first: Subhash

middle: (Optional)

last: Verma

state: MD

address: 37 Convent Drive, BLDG 37 Room 5138

institute: National Institutes of Health

description:
Biological replicate 3
SCV130_3_S26

data_processing:
The reads were trimmed for adapters and low-quality bases using Cutadapt 1.18
Alignment of the reads to the E. coli K12 MG1655 reference genome and the annotated transcriptome was done using STAR 2.6.1
Transcript abundances were calculated by RSEM 1.2.31
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified using the glmTreat function in edgeR by following the steps outlined in (Chen Y et al  F1000Res. 2016 Jun 20 [revised 2016 Aug 2];5:1438).
Genome_build: ASM584v2 Escherichia coli K12 MG1655
Supplementary_files_format_and_content: tab-delimited output files of rsem_calculate_expression with expected_count, transcript per million (TPM), Fragments Per Kilobase of transcript per Million mapped reads (FPKM)

organism: Escherichia coli

source_name: hupAmVenus ∆hupB

growth_protocol: cells were grown in M63 minimal media supplemented with 0.1% glycerol (v/v), 10 µg ml-1 thiamine, and 0.5 mg ml-1 casamino acids

extract_protocol:
For total RNA isolation, a frozen pellet of cells was resuspended in 1 ml TRIzol reagent (Life Technologies) to homogenization and incubated at room temperature for 5 min. To the resuspension, 0.2 ml chloroform was added and mixed by inverting the tube for 15 seconds. The mixture was incubated at room temperature for 10 min and then centrifuged at 20,000 × g for 10 min at 4 °C. After centrifugation, ~0.6 ml of the upper phase was transferred to a new centrifuge tube containing 0.5 ml isopropanol. The mixture was incubated at room temperature for 10 min and then centrifuged at 20,000 × g for 15 min at 4 °C. After centrifugation, the supernatant was discarded and the pellet was washed twice with 1 ml 75% ethanol, made with Diethyl pyrocarbonate (DEPC)-treated water, by centrifugation at 13,544 × g, for 5 min at 4 °C. After the second wash, the tube was left open for 10–15 min at room temperature to dry the pellet. To the pellet, 50 µl DEPC treated water was added and the tube was left at 37 °C for 10–15 min and then the pellet was fully resuspended using a pipette. DNA was removed using TURBO DNA-free Kit (Invitrogen).
Paired-end sequencing libraries were prepared with 2.5 µg of total RNA using Illumina® TruSeq® Stranded Total RNA library prep workflow with Ribo-Zero according to the manufacturer’s instructions.

tag: background strain

value: Escherichia coli K12  MG1656

tag: genotype

value: hupAmVenus {delta}hupB

value: Growth in M63 minimal media pH 7.0

tag: growth phase

value: Cells harvested at OD 600 between 0.4-0.6


title: SCV107_1

description:
Biological replicate 1
SCV107_1_S6

source_name: hupAmVenus P63A ∆hupB

treatment_protocol: M63 minimal media supplemented with 0.1% glycerol (v/v), 10 µg ml-1 thiamine, and 0.5 mg ml-1 casamino acids

value: Escherichia coli K12  MG1655

value: hupAmVenus P63A {delta}hupB


title: MC38CEA cells, SL2 IL IFN


title: A11_plate2

value: ARSENITE

value: Sodium arsenite


title: F2_plate1

value: DDE


title: MC38CEA cells, SL2 IL IFN2


title: H3K9me3_N2_muscle [wt_H3K9me3_a]

tag: strain/genotype

value: N2 (Bristol)

value: L3 body wall muscle


title: SCV130_1

description:
Biological replicate 1
SCV130_1_S2


title: SCV27_3

description:
Biological replicate 3
SCV27_3_S36

source_name: ∆hupA ∆hupB

value: {delta}hupA {delta}hupB


title: SCV130_2

description:
Biological replicate 2
SCV130_2_S14


title: G2_plate1

value: NIH 3T3-L1

value: DDT


title: ATAC_met2set25_muscle_rep2 [met2set25_b]

data_processing:
Adaptors were trimmed using cutadapt  (https://github.com/marcelm/cutadapt)
reads were aligned to the ce10 genome assembly using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with alignment parameters set to --sensitive
Mapped reads were marked and removed using the MarkDuplicates function of pickard tools 2.20.0 (https://broadinstitute.github.io/picard/)
Paired end reads were converted to single end reads using bedtools 2.26 (https://github.com/arq5x/bedtools2) and reads were shifted + 4 bp and − 5 bp for positive and negative strand respectively to account for characteristics of the Tn5 enzyme.
Peaks were called using MACS2 with the following parameters: -g 93260000 --nomodel --shift -100 --extsize 200, or reads were counted 1.5kb upstream and 200 bp downstream of the TSS using the qcount function in the QuasR R package (v. 3.2)
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (Sanger identifiers) and width of genes, following columns contain raw counts of reads overlapping each gene for each sample.

growth_protocol: DNA was isolated from purified tissues from L3 larvae grown after L1 synchronization  in two independent biological replicates.

extract_protocol:
ATAC-seq was performed on sorted muscle cells following the Omni-ATAC protocol (Corces et al., 2017)
Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).

tag: tissue


title: E6_plate1

tag: cell line

value: Triphenylphosphine oxide


title: SCV27_2

description:
Biological replicate 2
SCV27_2_S24


title: E5_plate1

tag: chemical

value: TUNGSTEN

value: Sodium tungstate


title: ∆RPL22A PolysomeHigh Rep1

source_name: ∆RPL22A PolysomeHigh

value: Log phase (OD 0.6-0.8)

tag: strain

tag: rna pool

value: PolysomeHigh fraction


title: H3K9me2_N2_muscle [wt_H3K9me2_a]


title: F1_plate1

value: ATRA

tag: chemical full

value: All-trans retinoic acid

tag: volume mol

tag: concentration


title: MC38CEA cells, ML IL IFN3

tag: cell type

value: colon adenocarcima

value: hr IL1b (10 ng/ml) and mr IFNg (10 ng/ml)

value: control shRNA


title: ATAC_set25_muscle_rep3 [set25_c]


title: MC38CEA cells, SL2 K3

tag: treatment

value: non treated

value: ADAM17-targeting shRNA


title: MC38CEA cells, SL2 K

tag: transduction


title: ATAC_met2set25_muscle_rep3 [met2set25_c]


title: MC38CEA cells, ML IL IFN2

tag: biological replicate


title: SCV96_2

description:
Biological replicate 2
SCV96_2_S23

source_name: wild-type

value: Escherichia coli K12  MG1655

value: wild-type

value: Growth in M63 minimal media pH 7.0

value: Cells harvested at OD 600 between 0.4-0.6


title: SCV96_3

description:
Biological replicate 3
SCV96_3_S35

value: Escherichia coli K12  MG1656


title: ATAC_set25_muscle_rep2 [set25_b]

value: L3 body wall muscle


title: SCV27_1

description:
Biological replicate 1
SCV27_1_S12

value: {delta}hupA {delta}hupB


title: ATAC_set25_muscle_rep1 [set25_a]


title: MC38CEA cells, ML IL IFN

description: raw file corrupted, gene counts included in shRNA RNAseq file


title: MC38CEA cells, SL2 K2


title: ATAC_met2_muscle_rep3 [met2_c]


title: MC38CEA cells, ML K3


title: D5_plate1

value: NIH 3T3-L1

value: ARSENITE

value: Sodium arsenite

tag: plate

tag: well


title: SCV96_1

description:
Biological replicate 1
SCV96_1_S11

tag: background strain

tag: genotype


title: D4_plate1


title: MC38CEA cells, ML K2


title: E1_plate1

value: 9-cis-retinoic acid


title: Oligo Precursor Cell_Female-No.4

city: Kobe

first: Yuichi

last: Ono

state: Hyogo

address: 6-8-2 Minatojima-minamimachi, Chuo-ku

department: Developmental Neurobiology

country: Japan

institute: KAN Research Institute Inc.

data_processing:
All raw sequencing reads were trimmed using Trimmomatic software.
Bases and QC were generated by FastQC.
The abundance of transcripts was then esdtimated using an Expectation-Maximization algotithm implicated in the software package Cufflink v2.2,1
Genome_build: Rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

organism: Rattus norvegicus

source_name: Cerebral cortex

growth_protocol: Mixed glial culture cells was prepared from 1-2 day old rat and maintained in DMEM conatining 20% FBS. Then oligodendrocyte precursor cells were collected as non-adherent cells and cultured in Neurobasal medium containing 2 mM glutamine, 1% penicillin/streptomycin, 10 ng/ml PDGF, 10 ng/ml FGF, and 2% B27 supplement on poly-DL-ornithine-coated plates for 4-5 days.

extract_protocol:
total RNA was harvested using RNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using Agilent SureSelect Strand Specific RNA prep kit (G9691A)

value: Sprague Dawley

value: Primary cultured oligodendrocyte precursor cells

tag: Sex

value: female

value: Cerebral cortex


title: ATAC_met2_muscle_rep2 [met2_b]

tag: strain/genotype

tag: tissue


title: D3_plate1

tag: cell line

tag: chemical


title: ATAC_met2set25_muscle_rep1 [met2set25_a]


title: MC38CEA cells, ML K

value: colon adenocarcima

value: non treated

value: control shRNA


title: Oligo Precursor Cell_Female-No.3

tag: strain


title: ATAC_met2_muscle_rep1 [met2_a]


title: D1_plate1

value: TBBPA

tag: chemical full

value: Tetrabromobisphenol A


title: Oligo Precursor Cell_Female-No.2


title: C10_plate1

value: NAIVE

tag: volume mol


title: ATAC_N2_muscle_rep2 [wt_b]

value: N2 (Bristol)


title: ATAC_N2_muscle_rep1 [wt_a]

value: L3 body wall muscle


title: Oligo Precursor Cell_Male-No.4

value: male


title: C9_plate1

value: NIH 3T3-L1

tag: concentration


title: ATAC_N2_muscle_rep3 [wt_c]


title: Oligo Precursor Cell_Female-No.1

tag: cell type


title: Oligo Precursor Cell_Male-No.3


title: C7_plate1


title: C8_plate1


title: adiposeTissue 17

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
processed data file:
adiposeTissue_consensusPeaks-from11samples_unionPeaksInAtLeast3samples.bed.gz
adiposeTissue_consensusPeaks-from17samples_unionPeaksInAtLeast3samples.bed.gz

data_processing:
We trimmed sequencing adapters and low quality base calls from the 3’ ends of reads using cutadapt with parameters -q 20 –minimum-length 36.
We aligned trimmed reads to the hg19 human genome using bowtie2 with parameters –minins 36 –maxins 1000 –no-mixed –no-discordant –no-unal
We selected nuclear chromosomal alignments with mapq>20 using samtools, removed alignments overlapping high-signal regions (Duke excluded and ENCODE/DAC exclusion list regions) using BEDTools pairToBed with the parameter -type notospan, and removed duplicate alignments using Picard MarkDuplicates.
We generated ATAC-seq quality metrics using ataqv. Ataqv is only designed for paired-end reads, so we wrote a customized script to calculate TSS enrichment for the single-end METSIM libraries.
Prior to peak calling, we trimmed alignments so their 5’ ends corresponded to the Tn5 binding site (+4 for + strand alignments and -5 for – strand alignments) and smoothed signal by extending alignments 100 bp on either side of the Tn5 binding sites using BEDTools slop. We called peaks (FDR<5%) with MACS2 with parameters -q 0.05 –nomodel –bdg.
For each analyzed day of SGBS differentiation, we generated a set of consensus ATAC peaks using the following method. First, we merged peak genomic coordinates across replicates for a given day using BEDTools merge. Second, we defined consensus peaks as merged peaks that overlapped individual replicate peaks in greater than 50% of replicates (at least 3 out of 5 replicates for D14 and 6 out of 10 replicates for D0 and D4). For each sample of METSIM adipose tissue, we generated a set of consensus ATAC peaks using the following method. First, we merged peak genomic coordinates across replicates for a given day using BEDTools merge. Second, we defined consensus peaks as merged peaks that overlapped individual replicate peaks in at least three individuals.
For SGBS, we generated a set of merged peaks to test for differential chromatin accessibility by merging the top 100,000 consensus peaks in each day (ranked by median peak p-value across replicates). We quantified the accessibility of these merged peaks in each library using featureCounts. We computed the GC percent of each peak using BEDTools nuc and generated within-library GC bias normalization factors using full quantile normalization with EDASeq. We then used EDASeq GC bias normalization factors within DESeq2 and used DESeq2 size factors to control for differences in sequencing depth between libraries. We tested for differential chromatin accessibility using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The files SGBS-day<day>_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz contain bed coordinates of the top 100,000 consensus ATAC peaks in each SGBS differentiation day ranked by median MACS2 p-value. The first three columns have peak genomic coordinates, the 4th column contains an arbitrary peak ID, columns 5-7 contain median MACS2 fold enrichment, p-value, and q-value across replicates that contributed to the peak, and column 8 lists the number of samples contributing to the peak.
Supplementary_files_format_and_content: The file mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz contains bed coordinates of the peaks used for differential chromatin accessibility testing. These are the union of the top 100,000 consensus peaks in each SGBS differentiation day. Columns 1-3 are peak bed coordinates, column 4 is an arbitrary peak ID, and column 5 contains the GC content of the peak calculated with BEDTools nuc.
Supplementary_files_format_and_content: The file DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.Rdata contains DESeq2 datasets of peak counts across samples in Rdata format and can be read directly into the R statistical software package. The file contains two DESeq2 datasets (1) peaks.gc.dds: raw peak counts by sample with EDASeq GC normalization and DESeq2 size factors and (2) peaks.gc.rlog: variance-stabilized peak counts using the DESeq2 rlog function. Sample information can be obtained using colData(peaks.gc.dds) or colData(peaks.gc.rlog).
Supplementary_files_format_and_content: The files "adiposeTissue<sampleNumber>_peaks.narrowPeak.gz" contain peaks called on individual adipose tissue samples using MACS2 and are in standard narrowPeak format.
Supplementary_files_format_and_content: The files "adiposeTissue_consensusPeaks-from11samples_unionPeaksInAtLeast3samples.bed.gz" and "adiposeTissue_consensusPeaks-from17samples_unionPeaksInAtLeast3samples.bed.gz" contain consensus peaks obtained using either all 17 adipose tissue samples or a subset of 11 samples after removing outliers. These files are in modified BED format with the first 3 columns representing peak genomic coordinates, column 4 containing an arbitrary peak ID, and column 5 listing the number of samples the peak was found in.

organism: Homo sapiens

source_name: adiposeTissue

growth_protocol: We cultured SGBS preadipocytes in serum-containing basal medium (DMEM:F12 + 33uM biotin + 17uM pantothenate) with 10% FBS.

extract_protocol:
All extraction steps were performed at 4C. For SGBS, nuclei were extracted by pelleting 50,000 cells at 500 RCF, resuspended and incubated on ice 3 minutes in 50 ul buffer containing 10 mM Tris-HCL, 10 mM NaCL, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. 1 mL buffer containing 10 mM Tris-HCL, 10 mM NaCL, 3 mM MgCl2, and 0.1% Tween-20 was added. Nuclei were pelleted at 500 RCF for 10 minutes. For adipose tissue, 50 mg of frozen tissue was crushed and then homogenized in a dounce with 1 mL buffer containing 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, and 40% Glycerol, pH 7.5. The homogenized sample was added to 9 mL of the same buffer and incubated on ice for 5 minutes and filtered through a Miracloth before pelleting at 1100xg for 10 minutes. The pellet was resuspended in 200 uL of the same buffer with an addition of 0.5% Triton X-100 and centrifuged at 500xg for 5 minutes. The pellet was resuspended in 250 uL of a wash buffer containing 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, pH 7.4.
For both SGBS and adipose tissue, nuclei were suspended in 25 μl transposase buffer from the Nextera kit, 5 μl TDE1 Transposase enzyme, and 20 μl water for 30 minutes at 37C. Transposition reaction was cleaned with a Zymo DNA Clean and Concentrator kit. Libraries were amplified with 10 μl transposed DNA, 10 μl nuclease-free H2O, 2.5 μl 25 μM PCR Primer 1, 2.5 μl 25 μM Barcoded PCR Primer 2, and 25 μl NEBNext High-Fidelity 2X PCR Master Mix. Final PCR product was cleaned again with Zymo DNA Clean and Concentrator kit.

treatment_protocol: We cultured SGBS preadipocytes using the growth protocol until confluent, then rinsed in phosphate-buffered-saline (PBS) and differentiated for four days in medium supplemented with 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine, 50 nM dexamethasone, 500 uM IBMX, and 2 uM rosiglitazone. After four days, we maintained differentiated SGBS cells in basal medium supplemented with 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine until harvested at the specified differentiation timepoint.

value: adiposeTissue


title: Oligo Precursor Cell_Male-No.2


title: C6_plate1

value: TRIFLUMIZOLE

value: Triflumizole


title: C5_plate1


title: adiposeTissue 16


title: miRNA-Seq si-circCpsf6-2

city: Shenzhen

first: Changrui

last: Tie

country: China

institute: Shenzhen Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs.
Comparative analysis of Rfam database and comparative analysis Repbase database
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include norm values for each Sample ...

source_name: N2A cells

growth_protocol: Neuro2A cells were cultured in DMEM supplemented with 10% fetal bovine serum, and 1% Penicillin/Streptomycin.

extract_protocol:
Different Total RNAs of N2A cells  were harvested using Trizol reagent. TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of small RNA sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For siRNA, si-NC and si-circCpsf6 were mixed with RNA iMAX Reagent and their final concentration was 100nM.

value: neuroblast

value: brain

tag: disease

value: neuroblastoma


title: C4_plate1


title: miRNA-Seq si-circCpsf6-3


title: Oligo Precursor Cell_Male-No.1

value: Sprague Dawley

value: Primary cultured oligodendrocyte precursor cells

value: Cerebral cortex


title: miRNA-Seq si-circCpsf6-1


title: adiposeTissue 14


title: 8763: RealSeq_MA_1_3

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2607

data_processing:
The sRNA sequencing libraries were trimmed for adaptors using Trimmomatic v0.32(15) with the following options -phred33; -threads 10; ILLUMINACLIP:4:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:10; MINLEN: 18.
Sequence quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Clean reads were aligned to the B73 Maize genome version 4(16) using the software Bowtie2 (Langmead and Salzberg, 2012).
Genome_build: B73 Maize genome version 4
Supplementary_files_format_and_content: Count format

organism: Zea mays

source_name: Maize anthers

growth_protocol: Anther samples were collected from 4- to 5-week-old W23 maize plants grown controlled conditions in greenhouses with temperatures of 28°C/22°C, relative humidity of 50%/60%, and a photoperiod of 16 h/8 h (day/night)

extract_protocol:
Total RNA was isolated using the Plant RNA Reagent (Thermo Fisher, cat #12322012). Briefly, samples were ground in a liquid nitrogen-frozen mortar and pestle. Then, the cold mortar with the powdered tissue was transferred to a chemical safe hood and 1 ml of Plant RNA Reagent was added directly in the mortar. The sample was ground with the reagent for another 20 sec and then collected with a 1ml micropipette and transferred to a 2 ml nuclease-free microcentrifuge tube. The remaining steps for the RNA extraction were followed as described previously (14).
All sRNA libraries were generated following the manufacturers’ instructions. A summarized workflow can be seen in Figure 1. Additionally, we performed a final step of size selection using 6% polyacrylamide gels as described in Mathioni et al., 2017

treatment_protocol: Two developmental stages were dissected, the premeiotic anther stage consisting of spikelets with 0.2 to 0.7 mm anthers, and the meiotic anther stage consisting of 1.5 mm anthers. Samples were flash frozen in liquid nitrogen and kept at -80°C until further processing.

value: Meiotic Anthers (MA)

tag: construction method

value: RealSeq

tag: molecule

value: Total RNA


title: B10_plate1

value: QUINOXYFEN

value: Quinoxyfen

tag: plate


title: adiposeTissue 15


title: Deox2-cy5_WT2-cy3

type: RNA

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 2 of 4.

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BY.

organism: Clostridioides difficile

source_name: 48H Biofilm with Deoxycholate

label_protocol: 5 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strain C630E Wt with and without deoxycholate Biofilm 48H

extract_protocol: Total RNA was extracted using QIAgen RNAeasy kit.

value: C630E Mullany

source_name: 48H Biofilm


title: adiposeTissue 12


title: adiposeTissue 11


title: Deox3-cy3_WT3-cy5

description: Biological replicate 3 of 4.


title: adiposeTissue 13


title: miRNA-Seq si-NC-3


title: Deox1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: miRNA-Seq si-NC-2


title: C3_plate1

value: IMIDACLOPRID

tag: well


title: Deox4-cy5_WT4-cy3

description: Biological replicate 4 of 4.


title: 8532: RealSeq_PMA_1_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 100ng of Total RNA as starting material. Library was sequenced using HiSeq 2602

value: Pre-meiotic Anthers (PMA)


title: 8761: RealSeq_MA_100_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 100ng of Total RNA as starting material. Library was sequenced using HiSeq 2601


title: miRNA-Seq si-NC-1


title: adiposeTissue 8

value: adiposeTissue


title: 8769: RealSeq_MA_1_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2606


title: 8768: RealSeq_PMA_1_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 100ng of Total RNA as starting material. Library was sequenced using HiSeq 2603


title: B8_plate1

value: NIH 3T3-L1

value: Ethylene brassylate


title: KP1-R7 resistant untreated rep2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-Seq reads were aligned to the mouse transcriptome prepared with an ensembl version 88 annotation using STAR version 2.5.3a and gene expression was summarized using RSEM version 1.3.0
Genome_build: mm10 with an Ensembl version 88 annotation
Supplementary_files_format_and_content: hmuller_intCt.txt.gz is a tab separated text file of integer count data
Supplementary_files_format_and_content: hmuller_l2tpm.txt.gz is a tab separated text file of log2 transcripts per million with a plus1 offset

source_name: KP393T5 cells - Kras G12D/P53 null Lung Adenocarcinoma cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Qiagen RNEasy Kit
Roche KAPA stranded RNA-Seq

tag: treatment

value: 0.1percent  DMSO for 72hrs

tag: selection

value: KP1 cell aliquots were treated for 12 days with 10µM EPZ015666 in 0.1% DMSO. Resistant lines are survivors of this treatment.


title: B6_plate1

value: TBT

value: Tributyltin hydride (6CI)


title: KP1-R7 resistant untreated rep3


title: 8762: RealSeq_PMA_1_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 100ng of Total RNA as starting material. Library was sequenced using HiSeq 2604


title: adiposeTissue 10


title: adiposeTissue 7


title: adiposeTissue 9


title: B7_plate1

value: BPS

value: Bisphenol S


title: 8533: RealSeq_MA_100_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 100ng of Total RNA as starting material. Library was sequenced using HiSeq 2599

value: Meiotic Anthers (MA)


title: 8767: RealSeq_MA_100_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 100ng of Total RNA as starting material. Library was sequenced using HiSeq 2600

value: RealSeq


title: KP1-R7 resistant untreated rep1


title: KP1-R6 resistant untreated rep3


title: B9_plate1

value: NTZDPA

value: nTZDpa


title: adiposeTissue 6


title: B1_plate1


title: 8534: RealSeq_MA_1_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2605

value: Total RNA


title: KP1-R6 resistant untreated rep2


title: KP1-R6 resistant untreated rep1


title: adiposeTissue 5


title: 8760: RealSeq_PMA_100_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2598


title: A12_plate1

value: TCCP

value: Tris(1-chloro-2-propyl) phosphate


title: KP1-R3 resistant untreated rep3


title: 8531: RealSeq_PMA_100_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2596

value: Pre-meiotic Anthers (PMA)


title: A10_plate1

value: PROPARA

value: Propylparaben


title: B4_plate1

value: NIH 3T3-L1


title: KP1-R3 resistant untreated rep2

value: 0.1percent  DMSO for 72hrs


title: B3_plate1

value: Firemaster 550


title: adiposeTissue 3

value: adiposeTissue


title: adiposeTissue 2


title: 8765: RealSeq_MA_10_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2595


title: A9_plate1

value: MBUP

value: Mono-n-butyl phthalate


title: KP1-R3 resistant untreated rep1

value: KP1 cell aliquots were treated for 12 days with 10µM EPZ015666 in 0.1% DMSO. Resistant lines are survivors of this treatment.


title: KP1 parental EPZ015666 treated rep3

value: 10 uM EPZ015666 in 0.1percent  DMSO for 72hrs

value: parental cells


title: 8536: RealSeq_MA_10_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2593

value: Meiotic Anthers (MA)

value: RealSeq


title: A8_plate1

value: DOSS

value: Dioctyl sulfosuccinate sodium


title: A7_plate1

value: BADGE

value: Bisphenol A diglycidyl ether


title: 8771: RealSeq_MA_10_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2594

value: Total RNA


title: 8766: RealSeq_PMA_100_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2597

value: Pre-meiotic Anthers (PMA)


title: 8764: RealSeq_PMA_10_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 1000cng of Total RNA as starting material. Library was sequenced using HiSeq 2592


title: adiposeTissue 4

description:
processed data file:
adiposeTissue_consensusPeaks-from11samples_unionPeaksInAtLeast3samples.bed.gz
adiposeTissue_consensusPeaks-from17samples_unionPeaksInAtLeast3samples.bed.gz


title: adiposeTissue 1


title: KP1 parental EPZ015666 treated rep2


title: SGBS_day14_batch1_rep3

description:
processed data file:
mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz
DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData
SGBS-day14_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz

value: adipocyte


title: SGBS_day14_batch1_rep2


title: A6_plate1

value: NIH 3T3-L1

value: DMSO


title: KP1 parental untreated rep3

value: 0.1percent  DMSO for 72hrs


title: 8770: RealSeq_PMA_10_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 1000cng of Total RNA as starting material. Library was sequenced using HiSeq 2591


title: A5_plate1


title: KP1 parental EPZ015666 treated rep1


title: SGBS_day14_batch1_rep1


title: A4_plate1


title: KP1 parental untreated rep2


title: 8535: RealSeq_PMA_10_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using RealSeq method with 1000cng of Total RNA as starting material. Library was sequenced using HiSeq 2590


title: SGBS_day0_batch1_rep2

description:
processed data file:
mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz
DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData
SGBS-day0_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz

value: preadipocyte


title: KP1 parental untreated rep1


title: 6232: SMARTer_MA_1000_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1cng of Total RNA as starting material. Library was sequenced using HiSeq 2589

value: SMARTer


title: A3_plate1


title: SGBS_day0_batch1_rep1


title: A2_plate1


title: 6231: SMARTer_MA_1000_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1cng of Total RNA as starting material. Library was sequenced using HiSeq 2588


title: RBD_ER_Input_2

city: Hangzhou

first: Yichen

last: Xu

address: Yuhangtang Road 866

institute: Zhejiang University

description: replicate: 2

data_processing:
Single-end reads were aligned against the Human Reference Genome (assembly hg19, NCBI GRCH37) using bowtie2
Peak-calling were performed using MACS version 2.2.6 with default settings
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Identified ChIP peaks

growth_protocol: cells were cultured in RPMI 1640 medium containing 10% FBS.

extract_protocol: Immunoprecipitated DNA was ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 50bp sequencing on an Illumina HiSeq 4000 according to the manufacturer’s recommendations

tag: genotype

tag: chip antibody

value: input


title: 6230: SMARTer_MA_1000_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1cng of Total RNA as starting material. Library was sequenced using HiSeq 2587

tag: tissue


title: WT_ER_Input_2

description: replicate: 2

tag: cell line


title: A1_plate1

tag: chemical


title: RBD_ER_Input_1

description: replicate: 1


title: Intestinal M-cell differentiation GRO-Seq mouse2 WENRC

city: Tampere

first: Mikko

last: Oittinen

address: Arvo Ylpön katu 34

department: Tampere Center for Child Health Research

country: Finland

institute: Tampere University

description:
GRO-Seq mouse2 WENRC
nuclear RNA
groseq_rankl_enri_wenrc_deseq2.txt

data_processing:
Sequence aligment was performed with Bowtie2 2.3.4.1.
Tag directories were created with HOMER toolset 4.11.1. Peak calling and differenctial DESeq2 analysis was conducted with Homer and R / Bioconductor / DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files containing either ChIP-Seq peaks or GRO-Seq nascent RNA RPKM values.

source_name: Small intestine; duodenum

extract_protocol: GRO-Seq, ChIP-Seq

value: intestinal stem cell

value: duodenum


title: Intestinal M-cell differentiation GRO-Seq mouse2 ENRI

description:
GRO-Seq mouse2 ENRI
nuclear RNA
groseq_rankl_enri_wenrc_deseq2.txt

value: enterocyte


title: 6229: SMARTer_MA_1_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1000bng of Total RNA as starting material. Library was sequenced using HiSeq 2586

value: Meiotic Anthers (MA)


title: Intestinal M-cell differentiation H3K27me3 WENRC

description:
H3K27me3 WENRC
genomic DNA
wenrc_diff_peaks_h3k27me3.txt


title: Intestinal M-cell differentiation GRO-Seq mouse1 ENRI

description:
GRO-Seq mouse1 ENRI
nuclear RNA
groseq_rankl_enri_wenrc_deseq2.txt


title: 6228: SMARTer_MA_1_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1000bng of Total RNA as starting material. Library was sequenced using HiSeq 2585


title: WT_ER_Input_1

description: replicate: 1


title: 6227: SMARTer_MA_1_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1000bng of Total RNA as starting material. Library was sequenced using HiSeq 2584


title: RBD_ER_ChIP_2

description: replicate: 2

value: Anti-FLAG (M2) (Sigma, F1084)


title: Intestinal M-cell differentiation GRO-Seq mouse1 WENRC

description:
GRO-Seq mouse1 WENRC
nuclear RNA
groseq_rankl_enri_wenrc_deseq2.txt


title: 6172: NEB_MA_1_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2571

value: NEB


title: RBD_ER_ChIP_1

description: replicate: 1


title: WT_ER_ChIP_2

description: replicate: 2


title: Intestinal M-cell differentiation H3K27me3 RANKL2

description:
H3K27me3 RANKL2
genomic DNA
rankl_diff_peaks_h3k27me3.txt

value: intestinal M-cell


title: 6171: NEB_MA_1_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2570


title: 6170: NEB_MA_1_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2569


title: Intestinal M-cell differentiation H3K27me3 RANKL1

description:
H3K27me3 RANKL1
genomic DNA
rankl_diff_peaks_h3k27me3.txt


title: Intestinal M-cell differentiation GRO-Seq RANKL2

description:
GRO-Seq RANKL2
nuclear RNA
groseq_rankl_enri_wenrc_deseq2.txt


title: 6169: NEB_PMA_1_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2568


title: Cancer 3 [B633270_CA]

city: Dongguan

first: Guangxian

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: College of Medical Technology

institute: Guangdong Medical University

description: mRNA and lncRNA expression in CRC

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (Agilent p/n G2565BA)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: human colorectal cancer

extract_protocol: The three pairs of prefrozen tissues were homogenized with TRIzol reagent (Invitrogen, USA) using the Mini-Bead-Beater-16 (Biospec, USA). Then, total RNA was extracted from the mixture using a RNeasy Mini Kit (Qiagen, German) with synchronous digestion using DNase (Baseline-ZERO DNase, Epicentre, USA). Subsequently, RNA quantity and quality were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was assessed by denaturing agarose gel electrophoresis.

tag: disease state

value: colorectal cancer

value: cancer


title: Intestinal M-cell differentiation GRO-Seq RANKL1

description:
GRO-Seq RANKL1
nuclear RNA
groseq_rankl_enri_wenrc_deseq2.txt


title: 6168: NEB_PMA_1_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2567

value: Pre-meiotic Anthers (PMA)

value: Total RNA


title: ESR1_CLIP

description: 3 replicates

data_processing:
After linker sequence removal and quality trimming (cutadapt; -u 5 -q 15 -m 20 -a GTGTCAGTCACTTCCAGCGG), sequence mapping was performed using BWA (v.0.7; -t 12 -n 0.06 -q 20) with default parameters (build hg19).  The binding sites were identified using the CTK package (Zhang and Darnell, Nature biotech, 2011).
Genome_build: hg19
Supplementary_files_format_and_content: Identified HITS-CLIP peaks

growth_protocol: cells were cultured in RPMI 1640 medium containing 10% FBS. Cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

extract_protocol: Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

tag: clip antibody

value: ERα (Santa Cruz, sc-542, Lot


title: Hippocampus_Male_Veh_Rep_3

city: Independencia

first: Wladimir

middle: Antonio

last: Corrales

address: Olivos 1007

department: Biochemistry and Molecular Biology

country: Chile

institute: Universidad de Chile

description: RNA < 200 nt

hyb_protocol: RNA samples were hybridized under standardized conditions (16 h at 48°C) in a hybridization oven (Affymetrix). Array slides were then stained with streptavidin/phycoerythrin and washed according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip® Operating Software (AGCC; Version 3.2).

data_processing: Microarray data analysis was performed using two bioinformatics tools: (i) Oligo v1.48.0 and Limma v3.40.0 R packages and (ii) Transcriptome Analysis Console (TAC, Affymetrix). For Oligo/Limma, background correction and normalization with the Robust Multichip Average method (RMA) were performed between all samples. Additionally, the Detection Above Background (DABG) algorithm was used for TAC. Log2 values of normalized probe intensities were then computed. To assess the quality of the microarray data and to identify abnormal arrays, several graphic representations (box plots, density plots, MA plots, and pseudo images) were generated for both raw and normalized data. The identification of differentially expressed miRNAs in each experimental group was achieved using an empirical Bayesian approach. Probes with an adjusted p-value < 0.05 and with a |fold change| ≥ 1.5 were considered as differentially expressed between experimental groups and controls.

label: Biotin

source_name: Whole hippocampus, male, adrenalectomized

label_protocol: RNAs < 200 nt were labeled using the Affymetrix FlashTag Biotin HSR kit, according to the manufacturer’s protocol.

extract_protocol: The whole hippocampi relative to bregma -3.10 to -4.44 mm coordinates (Paxinos, 1982) were dissected at 4°C and frozen under liquid nitrogen and kept at -80°C until processing for RNA isolation and protein extract. RNAs < 200 and > 200 nt from whole hippocampi were isolated as we have previously described (Castaneda et al., 2015) by using the RNeasy Mini Kit. RNA concentration and purity were determined at OD260/280 and samples with an absorbance ratio between 1.8 and 2.0 were chosen. RNA integrity was evaluated by nondenaturing agarose gel electrophoresis.

treatment_protocol: Two month-old Sprague Dawley male and female rats were given free access to water and pelleted food and were maintained at 22 ºC, with 55% of humidity and a photoperiod cycle of 12 h (lights on from 0700 to 1900h).

tag: gender

value: Male

tag: age

value: Two month-old

tag: strain

value: Sprague Dawley


title: Adjacent 3 [B633270_NC]

description: mRNA and lncRNA expression in CRC

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

value: adjacent normal tissue


title: Cancer 2 [B629380_CA]

description: mRNA and lncRNA expression in CRC


title: Adjacent 2 [B629380_NC]

description: mRNA and lncRNA expression in CRC


title: Hippocampus_Male_Veh_Rep_2

description: RNA < 200 nt


title: H1 Motor Neuron Puromycin Stress TIA1 IP Replicate 1 Read 1

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Fastq files were trimmed for adapters using cutadapt
Trimmed reads were aligned to the human genome build hg19 using STAR aligner
seCLIP : Binding region peaks were identified based on read pileup densities (Clipper)
seCLIP : Reproducible peaks were identified by comparing replicate read pileups along binding regions
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts text file
wiggle files
peak text files

source_name: motor neurons

growth_protocol: stem cells were grown in feeder-free conditions using mTeSR on matrigel-coated plates. Stem cell-derived motor neurons were generated using a widely published dual-smad inhibition-based protocol, including intermittent expansion of motor neuron progenitor (MNP) cells in DMEM/F12 medium supplemented with N2 and B27 supplements plus ascorbic acid, CHIR99021, DMH1, SB431542, retinoic acid, purmorphamine and valproic acid.

extract_protocol:
for ceFRA-seq samples, RNA was extracted using either Trizol (total, nuclear, insoluble) or Trizol LS (cytoplasm) following manufacturer's standard protocol
libraries for ceFRA-seq were generated using Illumina Truseq stranded mRNA library prep kits, eCLIP libraries using in-house seCLIP library prep protocol
RNAseq (polyA), seCLIP-seq

treatment_protocol: "stress" samples were treated with puromuycin at 10ug/ml for 24h. "recovery" samples were treated with puromycin at 10ug/ml for 24h, followed by a washout and allowed to recover in puromycin-free medium for 72h

tag: cell type

value: ESC-derived motor neurons

value: H1 ESC line

value: Puromycin

tag: fraction

value: Total


title: H1 Motor Neuron Puromycin Stress TIA1 INPUT Replicate 1 Read 1


title: 6127: SMARTer_PMA_1000_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2565

tag: construction method

value: SMARTer

tag: molecule


title: WT_ER_ChIP_1

description: replicate: 1

value: Anti-FLAG (M2) (Sigma, F1084)


title: Hippocampus_Male_Veh_Rep_1

description: RNA < 200 nt


title: R917_WN

city: San Francisco

first: Esther

last: Paulo

state: California

address: 555 Mission Blv South

institute: UCSF

data_processing:
Illumina Casava1.7 software used for basecalling.
In order to select cDNA fragments of 150~200bp in cDNA length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).
Libraries were sequenced in Illumina for 20 million reads with pair-end 150 bp (PE150).
In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length, and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions of base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments. (Mortazavi et al. 2008)
Genome_build: mm9
Supplementary_files_format_and_content: FPKMs

source_name: R917_WN, Brown adipocytes

extract_protocol:
Total RNA was extracted from tissues homogenized in TRIsure (Bioline) reagent. Isolated RNA was reverse transcribed using iScript cDNA Synthesis Kit (Biorad)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brown adipose

value: Brown adipocytes

value: LrpprcFF

tag: housing temperature

value: room temperature (22ºC)


title: 6125: SMARTer_PMA_1000_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2563

value: Pre-meiotic Anthers (PMA)


title: 6126: SMARTer_PMA_1000_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2564

value: Total RNA


title: Cancer 1 [B541155_CA]

description: mRNA and lncRNA expression in CRC

value: colorectal cancer

value: cancer


title: R916_WN

source_name: R916_WN, Brown adipocytes


title: E3830_KN

source_name: E3830_KN, Brown adipocytes

value: LrpprcFF Ucp1-Cre


title: H1 Motor Neuron Untreated TIA1 IP Replicate 2 Read 1

tag: treatment

value: Untreated


title: H1 Motor Neuron Untreated TIA1 INPUT Replicate 2 Read 1


title: Hippocampus_Male_Cort_Rep_3

description: RNA < 200 nt

source_name: Whole hippocampus, male, adrenalectomized+corticosterone

value: Male

value: Two month-old

value: Sprague Dawley


title: Hippocampus_Male_Cort_Rep_2

description: RNA < 200 nt


title: E3817_WN

source_name: E3817_WN, Brown adipocytes


title: 6124: SMARTer_PMA_1_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2562


title: 6167: NEB_PMA_1_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2566

value: NEB


title: H1 Motor Neuron Untreated TIA1 INPUT Replicate 1 Read 1

value: ESC-derived motor neurons

value: H1 ESC line

value: Total


title: CVC Motor Neuron Untreated G3BP IP Replicate 2

value: iPSC-derived motor neurons

value: CV-C hiPSC line


title: 6122: SMARTer_PMA_1_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2560

value: SMARTer


title: E3812_KN

source_name: E3812_KN, Brown adipocytes

value: Brown adipose

value: Brown adipocytes

value: room temperature (22ºC)


title: H1 Motor Neuron Untreated TIA1 IP Replicate 1 Read 1


title: E3834_KN

source_name: E3834_KN, Brown adipocytes


title: 6123: SMARTer_PMA_1_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using SMARTer method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2561

value: Pre-meiotic Anthers (PMA)

value: Total RNA


title: E3767_WN

source_name: E3767_WN, Brown adipocytes

value: LrpprcFF


title: 6074: NEB_MA_1000_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2559

value: Meiotic Anthers (MA)


title: CVC Motor Neuron Untreated G3BP INPUT Replicate 2

value: Untreated


title: E960_WNT

source_name: E960_WNT, Brown adipocytes

value: thermoneutrality (30ºC)


title: 6073: NEB_MA_1000_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2558

source_name: Maize anthers


title: Hippocampus_Female_Veh_Rep_3

description: RNA < 200 nt

source_name: Whole hippocampus, female, adrenalectomized

value: Female

value: Two month-old

value: Sprague Dawley


title: Hippocampus_Female_Veh_Rep_1

description: RNA < 200 nt


title: Hippocampus_Female_Veh_Rep_2

description: RNA < 200 nt


title: 6072: NEB_MA_1000_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2557

value: NEB


title: Hippocampus_Male_Cort_Rep_1

description: RNA < 200 nt

value: Male


title: E3813_KN

source_name: E3813_KN, Brown adipocytes

value: LrpprcFF Ucp1-Cre


title: CVC Motor Neuron Untreated G3BP INPUT Replicate 1

value: iPSC-derived motor neurons

value: CV-C hiPSC line

value: Total


title: CVC Motor Neuron Puromycin Stress G3BP IP Replicate 1

value: Puromycin


title: Hippocampus_Female_Cort_Rep_1

description: RNA < 200 nt

source_name: Whole hippocampus, female, adrenalectomized+corticosterone


title: Hippocampus_Female_Cort_Rep_3

description: RNA < 200 nt


title: Hippocampus_Female_Cort_Rep_2

description: RNA < 200 nt


title: CVC Motor Neuron Untreated G3BP IP Replicate 1


title: 6070: NEB_PMA_1000_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2555


title: CVC Motor Neuron Puromycin Stress G3BP INPUT Replicate 2


title: 6069: NEB_PMA_1000_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2554


title: CVC Motor Neuron Puromycin Stress G3BP IP Replicate 2


title: E957_WNT

source_name: E957_WNT, Brown adipocytes

value: Brown adipose

value: Brown adipocytes


title: CVC Motor Neuron Puromycin Stress G3BP INPUT Replicate 1


title: E017_KNT

source_name: E017_KNT, Brown adipocytes


title: E016_KNT

source_name: E016_KNT, Brown adipocytes


title: Adjacent 1 [B541155_NC]

description: mRNA and lncRNA expression in CRC

source_name: human colorectal cancer

value: colorectal cancer

value: adjacent normal tissue


title: E956_WNT

source_name: E956_WNT, Brown adipocytes

value: LrpprcFF


title: CVB Motor Neuron Untreated TDP43 IP Replicate 2

source_name: motor neurons

value: CV-B hiPSC line

value: Untreated


title: 6056: TriLink_MA_1000_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2553

value: Meiotic Anthers (MA)

value: TriLink

value: Total RNA


title: E015_KNT

source_name: E015_KNT, Brown adipocytes

value: thermoneutrality (30ºC)


title: 6071: NEB_PMA_1000_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using NEB method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2556

value: Pre-meiotic Anthers (PMA)

value: NEB


title: 2_2

city: Hohhot

first: Yuli

last: Guo

address: Zhaowuda Road

institute: Inner Mongolia Agricultural University

data_processing:
The cDNA library was sequenced on an Illumina HiSeq 4000 sequencing platform (Illumina, San Diego, USA ) by Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China).
The raw RNA-seq data was filtered to remove adaptor contamination, low-quality bases, and undetermined bases utilizing Cutadapt software (Maher CA, 2009)
Sequencing quality was verified using FASTQC software including the Q20, Q30, and GC content of the clean data. All downstream analysis was based on clean, high-quality data. The filtered reads were aligned and mapped to the reference genome using Hisat 2.0.
The aligned read files were processed by Cufflinks (Martin M, 2011.), which uses the normalized RNA-seq fragment counts to measure the relative abundances of the transcripts.
The unit of measurement is fragmented per kilobases of exon per million fragments mapped (FPKM). The DEGs were screened using R package edger (Trapnell C, 2009) with Fold change (FC)≥ 1.5 and P < 0.05 (50), which were considered significantly differentially expressed.
Genome_build: Felis_catus_9.0
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Felis catus

source_name: ovarian granulosa cells

extract_protocol:
Total RNA from untreated and AT-1 treated FOGCs was extracted using TRIzol® reagent (Invitrogen/Thermo Fisher Scientific, Carlsbad, CA, USA) following the manufacturer’s instructions.
To obtain mRNA, an approximately 5 µg sample of total RNA was used to isolate poly (A) mRNA with a poly-T oligo primer attached to magnetic beads (Invitrogen). Sequencing libraries were generated using an NEB Next Ultra™ RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following the manufacturer’s instructions. To synthesize the first-strand cDNA, purified mRNA was fragmented into small pieces then reverse transcriptase and random hexamer primers were utilized. Synthesis of second-strand cDNA was carried out using deoxynucleoside triphosphates containing DNA polymerase, dUTP, and RNase. End repair was achieved by adding dATP to all free 3’ ends and unique index sequences for the fragments were added with adaptor ligation. A sequencing library was obtained by PCR amplification of the products. The cDNA library was sequenced on an Illumina HiSeq 4000 sequencing platform (Illumina, San Diego, USA ) by Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China).

value: ovarian granulosa cell

tag: agent

value: Atractylenolide I


title: 6055: TriLink_MA_1000_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2552


title: 6053: TriLink_MA_10_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2550


title: 2_3


title: 6054: TriLink_MA_1000_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2551


title: 2_1


title: CVB Motor Neuron Untreated TDP43 IP Replicate 1

value: iPSC-derived motor neurons

value: Total


title: 1_3


title: 6052: TriLink_MA_10_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2549


title: CVB Motor Neuron Untreated TDP43 INPUT Replicate 1


title: CVB Motor Neuron Untreated TDP43 INPUT Replicate 2


title: 1_2


title: CVB Motor Neuron Puromycin Stress TDP43 IP Replicate 2

value: Puromycin


title: SHT-Uterus

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

description: Total RNAs were extracted from tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

hyb_protocol: Fluorescent targets were hybridized to Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that pass aforementioned criteria were normalized by R program in the limma package.

source_name: SHT treatment for 7 days

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

treatment_protocol: Mice were orally given with 200 mg/kg SHT for seven consecutive days.

value: BALB/c

value: Female

value: Uterus


title: 6051: TriLink_MA_10_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2548


title: Mock-Uterus

source_name: No treatment

extract_protocol: Total RNAs were extracted from tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).


title: SHT-Ovary

value: Ovary


title: 1_1


title: CVB Motor Neuron Puromycin Stress TDP43 IP Replicate 1

value: CV-B hiPSC line


title: Mock-Ovary


title: 6050: TriLink_MA_1_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2547


title: 6049: TriLink_MA_1_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2546


title: CVB Motor Neuron Puromycin Stress TDP43 INPUT Replicate 1


title: 6048: TriLink_MA_1_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2545


title: Mock-BC

value: Brain


title: SHT-BC


title: CR464 Line Untreated Total RNA Replicate 1

description:
total_CR464_ut_rep1
deseq2_normalized_counts.txt

value: CR464.2 hiPSC line

value: Untreated


title: 6046: TriLink_PMA_1000_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2543

value: TriLink

value: Total RNA


title: 6047: TriLink_PMA_1000_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2544

value: Pre-meiotic Anthers (PMA)


title: CR464 Line Recovery Total RNA Replicate 2

description:
total_CR464_rec_rep2
deseq2_normalized_counts.txt

value: Recovery


title: CR464 Line Recovery Total RNA Replicate 1

description:
total_CR464_rec_rep1
deseq2_normalized_counts.txt


title: 6044: TriLink_PMA_1_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2541


title: CVB Motor Neuron Puromycin Stress TDP43 INPUT Replicate 2


title: ELAVL1_depletion_repII

city: Rennes

first: Luc

last: Paillard

address: 2 Ave Leon Bernard

institute: Univ Rennes

description:
US82400123_252868010426_S01_GE2_107_Sep09_1_2.txt
Gene expression in ELAVL1 deprived cells

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanner Agilent G2565CA Feature extraction 10.7

data_processing: Feature extraction 10.7 with protocol GE_107_sep09 and grid 039494_G2_D_F_20120628. Both positive and negative control probes were excluded from data normalization and data was filtered by the average of the median of the samples. The probes with at least 1 value above the cut in at least one condition were included (resulting in 117,841 data rows in the sample data table).

source_name: HeLa cells, Depleted in ELAVL1, replicate#2

label_protocol: Labelling protocol was agilent protocol 'G4140-90050_GeneExpression_Two_Color_v6.5-mai 2010' and the labelling was pseudo mono color (1/2 of the sample with Cy3 and 1/2 of the sample with Cy5)

growth_protocol: We cultured HeLa Kyoto cells at 37 °C, 5% CO2 in DMEM (Gibco) with 10% FCS (PAA), 100 U / ml penicillin and 100 μg / ml streptomycin (Gibco).

extract_protocol: After 48 h, we recovered the cells for sampling in 500 μl of PBS by scraping after three washes with cold PBS and centrifuging them for 5 minutes at 3000 rpm at 4 ° C. Total RNA was extracted with TRIzol (Invitrogen) and treated with Turbo DNase (Ambion)

treatment_protocol: We transfected the cells (Jetprime, Polyplus) with the following siRNAs: 5 nM control siRNA (GUCUAGACGAGUGUGACAU) plus 5 nM siRNA against ELAVL1 (a pool of GAGGCAAUUACCAGUUUCA and UCUUAAGUUUCGUAAGUUA), 5 nM control siRNA plus 5 nM siRNA against CELF1 (a pool of GAGCCAACCUGUUCAUCUA, GCUCUUUAUUGGUAUGAUU, GCUGCAUUAGAAGCUCAGA), 5 nM siRNA against ELAVL1 plus 5 nM siRNA against CELF1, 10 nM control siRNA.

tag: sirna

value: HeLa


title: 6045: TriLink_PMA_1000_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2542


title: CR464 Line Untreated Total RNA Replicate 2

description:
total_CR464_ut_rep2
deseq2_normalized_counts.txt


title: Double_depletion_repIII

description:
US82400123_252868010426_S01_GE2_107_Sep09_1_1.txt
Gene expression in CELF1 + ELAVL1deprived cells

source_name: HeLa cells, Depleted in CELF1+ELAVL1, replicate#3


title: CELF1_depletion_repIII

description:
US82400123_252868010425_S01_GE2_107_Sep09_1_2.txt
Gene expression in CELF1 deprived cells

source_name: HeLa cells, Depleted in CELF1, replicate#3


title: Mammary carcinoma, #21

type: genomic

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 40 hours at 65°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

source_name: Mammary carcinoma induced by radiation

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Rats were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (CE-2; Clea Japan, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was isolated by proteinase K digestion, followed by phenol/chloroform extraction.

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (4 Gy, 0.5 Gy/min) at 7 weeks of age.

value: Carcinoma

value: F1 hybrid of Sprague-Dawley and Copenhagen rats

source_name: Normal ear

value: Ear skin


title: Double_depletion_repIV

description:
US82400123_252868010424_S01_GE2_107_Sep09_1_2.txt
Gene expression in CELF1 + ELAVL1deprived cells

source_name: HeLa cells, Depleted in CELF1+ELAVL1, replicate#4


title: CR464 Line Puromycin Treatment Total RNA Replicate 2

description:
total_CR464_puro_rep2
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons

value: Puromycin

value: Total


title: Mock_depletion_repII

description:
US82400123_252868010425_S01_GE2_107_Sep09_1_1.txt
Gene expression in control cells

source_name: HeLa cells, Mock depleted, replicate#2

value: Mock


title: CR464 Line Puromycin Treatment Total RNA Replicate 1

description:
total_CR464_puro_rep1
deseq2_normalized_counts.txt


title: Mammary carcinoma, #20

value: Female


title: CELF1_depletion_repIV

description:
US82400123_252868010424_S01_GE2_107_Sep09_1_1.txt
Gene expression in CELF1 deprived cells

source_name: HeLa cells, Depleted in CELF1, replicate#4


title: 6043: TriLink_PMA_1_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2540

source_name: Maize anthers


title: Mock_depletion_repIII

description:
US82400123_252868010426_S01_GE2_107_Sep09_1_1.txt
Gene expression in control cells

source_name: HeLa cells, Mock depleted, replicate#3


title: Mammary carcinoma, #18


title: 6042: TriLink_PMA_1_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2539


title: Mammary carcinoma, #16


title: ELAVL1_depletion_repIV

description:
US82400123_252868010425_S01_GE2_107_Sep09_1_2.txt
Gene expression in ELAVL1 deprived cells

source_name: HeLa cells, Depleted in ELAVL1, replicate#4


title: CR463 Line Untreated Total RNA Replicate 2

description:
total_CR463_ut_rep2
deseq2_normalized_counts.txt

value: CR463.4 hiPSC line


title: 6041: TriLink_PMA_10_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2538


title: Mock_depletion_repIV

description:
US82400123_252868010426_S01_GE2_107_Sep09_1_2.txt
Gene expression in control cells

source_name: HeLa cells, Mock depleted, replicate#4


title: Mammary carcinoma, #17


title: Mammary carcinoma, #19


title: 6039: TriLink_PMA_10_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2536


title: CR463 Line Recovery Total RNA Replicate 2

description:
total_CR463_rec_rep2
deseq2_normalized_counts.txt

source_name: motor neurons


title: CR463 Line Recovery Total RNA Replicate 1

description:
total_CR463_rec_rep1
deseq2_normalized_counts.txt


title: CR463 Line Untreated Total RNA Replicate 1

description:
total_CR463_ut_rep1
deseq2_normalized_counts.txt


title: CR463 Line Puromycin Treatment Total RNA Replicate 2

description:
total_CR463_puro_rep2
deseq2_normalized_counts.txt


title: SAMPLE 8: hippocampus_Ts1Cje_3-month-old_replicate4

city: Kyoto

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yamashina-ku

department: Department of Pathological Biochemistry

institute: Kyoto Pharmaceutical University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) was fragmented at 60ﾂｰC for 30 minutes. On completion of the fragmentation reaction, hybridized to SurePrint G3 Mouse GE 8x60 K microarray (G4851A) for 17 hours at 65ﾂｰC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ﾂｰC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting. (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with GeneSpring GX (ver 12.0.0) (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ts1Cje, hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the The Low Input Quick Amp Labeling kit, one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using RNAiso (Takara) according to the manufacturer's instructions, followed by treatment with DNase I.

tag: genotype

value: hippocampus


title: CELF1_depletion_repII

description:
US82400123_252868010424_S01_GE2_107_Sep09_1_2.txt
Gene expression in CELF1 deprived cells

source_name: HeLa cells, Depleted in CELF1, replicate#2


title: 6040: TriLink_PMA_10_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using TriLink method with 10ng of Total RNA as starting material. Library was sequenced using HiSeq 2537

tag: tissue


title: CR463 Line Puromycin Treatment Total RNA Replicate 1

description:
total_CR463_puro_rep1
deseq2_normalized_counts.txt

tag: cell line


title: ELAVL1_depletion_repIII

description:
US82400123_252868010425_S01_GE2_107_Sep09_1_1.txt
Gene expression in ELAVL1 deprived cells

source_name: HeLa cells, Depleted in ELAVL1, replicate#3


title: SAMPLE 6: hippocampus_Ts1Cje_3-month-old_replicate3


title: Mammary carcinoma, #14


title: SAMPLE 7: hippocampus_wild-type_3-month-old_replicate4

source_name: wild-type, hippocampus

value: wild-type


title: SAMPLE 5: hippocampus_wild-type_3-month-old_replicate3


title: 5992: Nextflex_v3_MA_1000_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2534

value: Meiotic Anthers (MA)


title: Mammary carcinoma, #13


title: SAMPLE 4: hippocampus_Ts1Cje_3-month-old_replicate2


title: CR464 Line Untreated Nuclear Fraction Replicate 1

description:
nuc_CR464_ut_rep1
deseq2_normalized_counts.txt

value: CR464.2 hiPSC line

value: Untreated

value: Nucleus


title: 5989: Nextflex_v3_MA_1_2

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2531

value: Total RNA


title: Mammary carcinoma, #11


title: 5991: Nextflex_v3_MA_1000_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2533


title: Double_depletion_repII

description:
US82400123_252868010424_S01_GE2_107_Sep09_1_1.txt
Gene expression in CELF1 + ELAVL1deprived cells

source_name: HeLa cells, Depleted in CELF1+ELAVL1, replicate#2

value: HeLa


title: Mammary carcinoma, #15

value: Carcinoma


title: Mammary carcinoma, #12

value: F1 hybrid of Sprague-Dawley and Copenhagen rats


title: CR464 Line Recovery Nuclear Fraction Replicate 2

description:
nuc_CR464_rec_rep2
deseq2_normalized_counts.txt

value: Recovery


title: RP11_3

city: Jinan

first: Jiajun

last: Du

address: 324 Jingwu Road

institute: Provincial Hospital Affiliated to Shandong University

description: experimental group 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In  this step, clean data (clean reads) were obtained by removing reads containing adapter, reads1  containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean  data with high quality.
Reference genome and gene model annotation files were downloaded from genome website  directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean  reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the  mapping tool for that Hisat2 can generate a database of splice junctions based on the gene  model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to 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, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, 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.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2  R package (1.20.0). DESeq2 provide statistical routines for determining differential expression  in digital gene expression data using a model based on the negative binomial distribution. The  resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling  the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were  assigned as differentially expressed
Prior to differential gene expression analysis, for  each sequenced library, the read counts were adjusted by edgeR program package through one  scaling normalized factor. Differential expression analysis of two conditions was performed  using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini &  Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the2  threshold for significantly differential expression.
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 cell

extract_protocol:
The total RNA of A549 was extracted via Trizol and samples were sent to Novogene Co., LTD beijing）for RNA-seq analysis. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer  2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: overexpressed AP001189.3


title: RP11_2

description: experimental group 2


title: 5988: Nextflex_v3_MA_1_1

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2530


title: Mammary carcinoma, #10

value: Ear skin


title: 5987: Nextflex_v3_PMA_1000_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2529

value: Pre-meiotic Anthers (PMA)


title: 5986: Nextflex_v3_PMA_1000_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2528


title: 5990: Nextflex_v3_MA_1_3

description: small RNA library from Maize Meiotic Anthers (MA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2532


title: SAMPLE 3: hippocampus_wild-type_3-month-old_replicate2


title: CR464 Line Untreated Nuclear Fraction Replicate 2

description:
nuc_CR464_ut_rep2
deseq2_normalized_counts.txt

value: iPSC-derived motor neurons


title: CR463 Line Untreated Nuclear Fraction Replicate 2

description:
nuc_CR463_ut_rep2
deseq2_normalized_counts.txt


title: Mammary carcinoma, #8

value: Female


title: L996_2

description: experimental group 1

value: overexpressed LINC00996


title: Mammary carcinoma, #7


title: Mammary carcinoma, #6


title: CR464 Line Puromycin Treatment Nuclear Fraction Replicate 1

description:
nuc_CR464_puro_rep1
deseq2_normalized_counts.txt

value: Puromycin


title: 5984: Nextflex_v3_PMA_1_3

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2526


title: Mammary carcinoma, #4


title: CR464 Line Recovery Nuclear Fraction Replicate 1

description:
nuc_CR464_rec_rep1
deseq2_normalized_counts.txt


title: Mammary carcinoma, #9


title: Mammary carcinoma, #2


title: Mammary carcinoma, #3


title: 5985: Nextflex_v3_PMA_1000_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1000ng of Total RNA as starting material. Library was sequenced using HiSeq 2527


title: Mammary carcinoma, #1


title: 5983: Nextflex_v3_PMA_1_2

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2525


title: SAMPLE 2: hippocampus_Ts1Cje_3-month-old_replicate1

value: hippocampus


title: CR463 Line Untreated Nuclear Fraction Replicate 1

description:
nuc_CR463_ut_rep1
deseq2_normalized_counts.txt

value: CR463.4 hiPSC line


title: L996_3

description: experimental group 1


title: F102C-3

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Infinium® MethylationEPIC Beadchip using standard Illumina protocol at the University of Minnesota Genomics Center.

scan_protocol: Arrays were imaged using BeadArray Reader Hi-Scan system.

data_processing:
Resultant IDAT files were processed and normalized using Illumina's GenomeStudio software (version 2011.1).
value definition: Average Beta

label: cy3, cy5

source_name: Prostate

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

extract_protocol: Genomic DNA were extracted using standard DNA extraction method

treatment_protocol: 22Rv1 cells were infected with lentivirus expressiong empty vector or SPOP F102C construct and cultured for 1 week to stably express SPOP F102C protein.

value: Pca cell line

tag: passage

tag: genotype/variation

value: SPOP F102C


title: CR463 Line Recovery Nuclear Fraction Replicate 2

description:
nuc_CR463_rec_rep2
deseq2_normalized_counts.txt

value: Nucleus


title: RP11_1

description: experimental group 2


title: F102C-2


title: 5982: Nextflex_v3_PMA_1_1

description: small RNA library from Maize Pre-meiotic Anthers (PMA)  in whole spikelets from W23. The small RNA library was constructed using Nextflex_v3 method with 1ng of Total RNA as starting material. Library was sequenced using HiSeq 2524

data_processing:
The sRNA sequencing libraries were trimmed for adaptors using Trimmomatic v0.32(15) with the following options -phred33; -threads 10; ILLUMINACLIP:4:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:10; MINLEN: 18.
Sequence quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Clean reads were aligned to the B73 Maize genome version 4(16) using the software Bowtie2 (Langmead and Salzberg, 2012).
Genome_build: B73 Maize genome version 4
Supplementary_files_format_and_content: Count format

extract_protocol:
Total RNA was isolated using the Plant RNA Reagent (Thermo Fisher, cat #12322012). Briefly, samples were ground in a liquid nitrogen-frozen mortar and pestle. Then, the cold mortar with the powdered tissue was transferred to a chemical safe hood and 1 ml of Plant RNA Reagent was added directly in the mortar. The sample was ground with the reagent for another 20 sec and then collected with a 1ml micropipette and transferred to a 2 ml nuclease-free microcentrifuge tube. The remaining steps for the RNA extraction were followed as described previously (14).
All sRNA libraries were generated following the manufacturers’ instructions. A summarized workflow can be seen in Figure 1. Additionally, we performed a final step of size selection using 6% polyacrylamide gels as described in Mathioni et al., 2017

value: Total RNA


title: PC3_3

description: control group

value: transfected PC3.3 plasmid


title: CR464 Line Puromycin Treatment Nuclear Fraction Replicate 2

description:
nuc_CR464_puro_rep2
deseq2_normalized_counts.txt

value: CR464.2 hiPSC line


title: L996_1

description: experimental group 1